A controlled vocabulary term defining axis direction in terms of anatomical direction.
+URI: ANATOMICALDIRECTION
+| Value | +Meaning | +Description | +
|---|---|---|
| left_to_right | +None | ++ |
| posterior_to_anterior | +None | ++ |
| inferior_to_superior | +None | ++ |
| superior_to_inferior | +None | ++ |
| anterior_to_posterior | +None | ++ |
| Name | +Description | +
|---|---|
| x_direction | +A controlled vocabulary attribute defining the x axis direction in terms of a... | +
| y_direction | +A controlled vocabulary attribute defining the y axis direction in terms of a... | +
| z_direction | +A controlled vocabulary attribute defining the z axis direction in terms of a... | +
name: ANATOMICAL_DIRECTION
+description: A controlled vocabulary term defining axis direction in terms of anatomical
+ direction.
+from_schema: https://w3id.org/my-org/anatomical-structure-schema
+rank: 1000
+permissible_values:
+ left_to_right:
+ text: left_to_right
+ title: left-to-right
+ posterior_to_anterior:
+ text: posterior_to_anterior
+ title: posterior-to-anterior
+ inferior_to_superior:
+ text: inferior_to_superior
+ title: inferior-to-superior
+ superior_to_inferior:
+ text: superior_to_inferior
+ title: superior-to-inferior
+ anterior_to_posterior:
+ text: anterior_to_posterior
+ title: anterior-to-posterior
+
+An activity is something that occurs over a period of time and acts upon or with entities; it may include consuming, processing, transforming, modifying, relocating, using, or generating entities.
+URI: biolink:Activity
+| Name | +Cardinality and Range | +Description | +Inheritance | +
|---|---|---|---|
| id | +1 String |
+A unique identifier for an entity | +direct | +
| iri | +0..1 IriType |
+An IRI for an entity | +direct | +
| category | +* Uriorcurie |
+Name of the high level ontology class in which this entity is categorized | +direct | +
| type | +* String |
++ | direct | +
| name | +0..1 LabelType |
+A human-readable name for an attribute or entity | +direct | +
| description | +0..1 NarrativeText |
+a human-readable description of an entity | +direct | +
| has_attribute | +* Attribute |
+connects any entity to an attribute | +direct | +
| deprecated | +0..1 Boolean |
+A boolean flag indicating that an entity is no longer considered current or v... | +direct | +
| provided_by | +* String |
+The value in this node property represents the knowledge provider that create... | +direct | +
| xref | +* Uriorcurie |
+A database cross reference or alternative identifier for a NamedThing or edge... | +direct | +
| full_name | +0..1 LabelType |
+a long-form human readable name for a thing | +direct | +
| synonym | +* LabelType |
+Alternate human-readable names for a thing | +direct | +
| Mapping Type | +Mapped Value | +
|---|---|
| self | +biolink:Activity | +
| native | +bican:Activity | +
| exact | +prov:Activity, NCIT:C43431, STY:T052 | +
| narrow | +STY:T056, STY:T057, STY:T064, STY:T066, STY:T062, STY:T065, STY:T058 | +
name: activity
+definition_uri: https://w3id.org/biolink/vocab/Activity
+description: An activity is something that occurs over a period of time and acts upon
+ or with entities; it may include consuming, processing, transforming, modifying,
+ relocating, using, or generating entities.
+from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
+exact_mappings:
+- prov:Activity
+- NCIT:C43431
+- STY:T052
+narrow_mappings:
+- STY:T056
+- STY:T057
+- STY:T064
+- STY:T066
+- STY:T062
+- STY:T065
+- STY:T058
+is_a: named thing
+mixins:
+- activity and behavior
+slots:
+- id
+- iri
+- category
+- type
+- name
+- description
+- has attribute
+- deprecated
+- provided by
+- xref
+- full name
+- synonym
+class_uri: biolink:Activity
+
+name: activity
+definition_uri: https://w3id.org/biolink/vocab/Activity
+description: An activity is something that occurs over a period of time and acts upon
+ or with entities; it may include consuming, processing, transforming, modifying,
+ relocating, using, or generating entities.
+from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
+exact_mappings:
+- prov:Activity
+- NCIT:C43431
+- STY:T052
+narrow_mappings:
+- STY:T056
+- STY:T057
+- STY:T064
+- STY:T066
+- STY:T062
+- STY:T065
+- STY:T058
+is_a: named thing
+mixins:
+- activity and behavior
+attributes:
+ id:
+ name: id
+ definition_uri: https://w3id.org/biolink/vocab/id
+ description: A unique identifier for an entity. Must be either a CURIE shorthand
+ for a URI or a complete URI
+ in_subset:
+ - translator_minimal
+ from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
+ exact_mappings:
+ - AGRKB:primaryId
+ - gff3:ID
+ - gpi:DB_Object_ID
+ rank: 1000
+ domain: entity
+ slot_uri: biolink:id
+ identifier: true
+ alias: id
+ owner: activity
+ domain_of:
+ - ontology class
+ - entity
+ - attribute
+ - named thing
+ - taxonomic rank
+ - organism taxon
+ - information content entity
+ - dataset
+ - physical entity
+ - activity
+ - procedure
+ - material sample
+ - biological entity
+ - gene
+ - genome
+ range: string
+ required: true
+ iri:
+ name: iri
+ definition_uri: https://w3id.org/biolink/vocab/iri
+ description: An IRI for an entity. This is determined by the id using expansion
+ rules.
+ in_subset:
+ - translator_minimal
+ - samples
+ from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
+ exact_mappings:
+ - WIKIDATA_PROPERTY:P854
+ rank: 1000
+ slot_uri: biolink:iri
+ alias: iri
+ owner: activity
+ domain_of:
+ - attribute
+ - entity
+ - named thing
+ - organism taxon
+ - information content entity
+ - dataset
+ - physical entity
+ - activity
+ - procedure
+ - material sample
+ - biological entity
+ - gene
+ - genome
+ range: iri type
+ category:
+ name: category
+ definition_uri: https://w3id.org/biolink/vocab/category
+ description: Name of the high level ontology class in which this entity is categorized.
+ Corresponds to the label for the biolink entity type class. In a neo4j database
+ this MAY correspond to the neo4j label tag. In an RDF database it should be
+ a biolink model class URI. This field is multi-valued. It should include values
+ for ancestors of the biolink class; for example, a protein such as Shh would
+ have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`.
+ In an RDF database, nodes will typically have an rdf:type triples. This can
+ be to the most specific biolink class, or potentially to a class more specific
+ than something in biolink. For example, a sequence feature `f` may have a rdf:type
+ assertion to a SO class such as TF_binding_site, which is more specific than
+ anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity,
+ biolink:NamedThing}
+ in_subset:
+ - translator_minimal
+ from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
+ rank: 1000
+ is_a: type
+ domain: entity
+ slot_uri: biolink:category
+ designates_type: true
+ alias: category
+ owner: activity
+ domain_of:
+ - entity
+ - attribute
+ - named thing
+ - organism taxon
+ - information content entity
+ - dataset
+ - physical entity
+ - activity
+ - procedure
+ - material sample
+ - biological entity
+ - gene
+ - genome
+ is_class_field: true
+ range: uriorcurie
+ multivalued: true
+ type:
+ name: type
+ definition_uri: https://w3id.org/biolink/vocab/type
+ from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
+ mappings:
+ - rdf:type
+ exact_mappings:
+ - gff3:type
+ - gpi:DB_Object_Type
+ rank: 1000
+ domain: entity
+ slot_uri: rdf:type
+ alias: type
+ owner: activity
+ domain_of:
+ - entity
+ - attribute
+ - named thing
+ - organism taxon
+ - information content entity
+ - dataset
+ - physical entity
+ - activity
+ - procedure
+ - material sample
+ - biological entity
+ - gene
+ - genome
+ range: string
+ multivalued: true
+ name:
+ name: name
+ definition_uri: https://w3id.org/biolink/vocab/name
+ description: A human-readable name for an attribute or entity.
+ in_subset:
+ - translator_minimal
+ - samples
+ from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
+ aliases:
+ - label
+ - display name
+ - title
+ mappings:
+ - rdfs:label
+ exact_mappings:
+ - gff3:Name
+ - gpi:DB_Object_Name
+ narrow_mappings:
+ - dct:title
+ - WIKIDATA_PROPERTY:P1476
+ rank: 1000
+ domain: entity
+ slot_uri: rdfs:label
+ alias: name
+ owner: activity
+ domain_of:
+ - attribute
+ - entity
+ - macromolecular machine mixin
+ - named thing
+ - organism taxon
+ - information content entity
+ - dataset
+ - physical entity
+ - activity
+ - procedure
+ - material sample
+ - biological entity
+ - gene or gene product
+ - gene
+ - genome
+ range: label type
+ description:
+ name: description
+ definition_uri: https://w3id.org/biolink/vocab/description
+ description: a human-readable description of an entity
+ in_subset:
+ - translator_minimal
+ from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
+ aliases:
+ - definition
+ mappings:
+ - dct:description
+ exact_mappings:
+ - IAO:0000115
+ - skos:definitions
+ narrow_mappings:
+ - gff3:Description
+ rank: 1000
+ slot_uri: dct:description
+ alias: description
+ owner: activity
+ domain_of:
+ - entity
+ - attribute
+ - named thing
+ - organism taxon
+ - information content entity
+ - dataset
+ - physical entity
+ - activity
+ - procedure
+ - material sample
+ - biological entity
+ - gene
+ - genome
+ range: narrative text
+ has attribute:
+ name: has attribute
+ definition_uri: https://w3id.org/biolink/vocab/has_attribute
+ description: connects any entity to an attribute
+ in_subset:
+ - samples
+ from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
+ exact_mappings:
+ - SIO:000008
+ close_mappings:
+ - OBI:0001927
+ narrow_mappings:
+ - OBAN:association_has_subject_property
+ - OBAN:association_has_object_property
+ - CPT:has_possibly_included_panel_element
+ - DRUGBANK:category
+ - EFO:is_executed_in
+ - HANCESTRO:0301
+ - LOINC:has_action_guidance
+ - LOINC:has_adjustment
+ - LOINC:has_aggregation_view
+ - LOINC:has_approach_guidance
+ - LOINC:has_divisor
+ - LOINC:has_exam
+ - LOINC:has_method
+ - LOINC:has_modality_subtype
+ - LOINC:has_object_guidance
+ - LOINC:has_scale
+ - LOINC:has_suffix
+ - LOINC:has_time_aspect
+ - LOINC:has_time_modifier
+ - LOINC:has_timing_of
+ - NCIT:R88
+ - NCIT:eo_disease_has_property_or_attribute
+ - NCIT:has_data_element
+ - NCIT:has_pharmaceutical_administration_method
+ - NCIT:has_pharmaceutical_basic_dose_form
+ - NCIT:has_pharmaceutical_intended_site
+ - NCIT:has_pharmaceutical_release_characteristics
+ - NCIT:has_pharmaceutical_state_of_matter
+ - NCIT:has_pharmaceutical_transformation
+ - NCIT:is_qualified_by
+ - NCIT:qualifier_applies_to
+ - NCIT:role_has_domain
+ - NCIT:role_has_range
+ - INO:0000154
+ - HANCESTRO:0308
+ - OMIM:has_inheritance_type
+ - orphanet:C016
+ - orphanet:C017
+ - RO:0000053
+ - RO:0000086
+ - RO:0000087
+ - SNOMED:has_access
+ - SNOMED:has_clinical_course
+ - SNOMED:has_count_of_base_of_active_ingredient
+ - SNOMED:has_dose_form_administration_method
+ - SNOMED:has_dose_form_release_characteristic
+ - SNOMED:has_dose_form_transformation
+ - SNOMED:has_finding_context
+ - SNOMED:has_finding_informer
+ - SNOMED:has_inherent_attribute
+ - SNOMED:has_intent
+ - SNOMED:has_interpretation
+ - SNOMED:has_laterality
+ - SNOMED:has_measurement_method
+ - SNOMED:has_method
+ - SNOMED:has_priority
+ - SNOMED:has_procedure_context
+ - SNOMED:has_process_duration
+ - SNOMED:has_property
+ - SNOMED:has_revision_status
+ - SNOMED:has_scale_type
+ - SNOMED:has_severity
+ - SNOMED:has_specimen
+ - SNOMED:has_state_of_matter
+ - SNOMED:has_subject_relationship_context
+ - SNOMED:has_surgical_approach
+ - SNOMED:has_technique
+ - SNOMED:has_temporal_context
+ - SNOMED:has_time_aspect
+ - SNOMED:has_units
+ - UMLS:has_structural_class
+ - UMLS:has_supported_concept_property
+ - UMLS:has_supported_concept_relationship
+ - UMLS:may_be_qualified_by
+ rank: 1000
+ domain: entity
+ slot_uri: biolink:has_attribute
+ alias: has_attribute
+ owner: activity
+ domain_of:
+ - entity
+ - attribute
+ - named thing
+ - organism taxon
+ - information content entity
+ - dataset
+ - physical entity
+ - activity
+ - procedure
+ - material sample
+ - biological entity
+ - gene
+ - genome
+ range: attribute
+ multivalued: true
+ deprecated:
+ name: deprecated
+ definition_uri: https://w3id.org/biolink/vocab/deprecated
+ description: A boolean flag indicating that an entity is no longer considered
+ current or valid.
+ from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
+ exact_mappings:
+ - oboInOwl:ObsoleteClass
+ rank: 1000
+ slot_uri: biolink:deprecated
+ alias: deprecated
+ owner: activity
+ domain_of:
+ - entity
+ - attribute
+ - named thing
+ - organism taxon
+ - information content entity
+ - dataset
+ - physical entity
+ - activity
+ - procedure
+ - material sample
+ - biological entity
+ - gene
+ - genome
+ range: boolean
+ provided by:
+ name: provided by
+ definition_uri: https://w3id.org/biolink/vocab/provided_by
+ description: The value in this node property represents the knowledge provider
+ that created or assembled the node and all of its attributes. Used internally
+ to represent how a particular node made its way into a knowledge provider or
+ graph.
+ from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
+ rank: 1000
+ is_a: node property
+ domain: named thing
+ slot_uri: biolink:provided_by
+ alias: provided_by
+ owner: activity
+ domain_of:
+ - named thing
+ - attribute
+ - organism taxon
+ - information content entity
+ - dataset
+ - physical entity
+ - activity
+ - procedure
+ - material sample
+ - biological entity
+ - gene
+ - genome
+ range: string
+ multivalued: true
+ xref:
+ name: xref
+ definition_uri: https://w3id.org/biolink/vocab/xref
+ description: A database cross reference or alternative identifier for a NamedThing
+ or edge between two NamedThings. This property should point to a database record
+ or webpage that supports the existence of the edge, or gives more detail about
+ the edge. This property can be used on a node or edge to provide multiple URIs
+ or CURIE cross references.
+ in_subset:
+ - translator_minimal
+ from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
+ aliases:
+ - dbxref
+ - Dbxref
+ - DbXref
+ - record_url
+ - source_record_urls
+ narrow_mappings:
+ - gff3:Dbxref
+ - gpi:DB_Xrefs
+ rank: 1000
+ domain: named thing
+ slot_uri: biolink:xref
+ alias: xref
+ owner: activity
+ domain_of:
+ - named thing
+ - gene
+ - attribute
+ - organism taxon
+ - information content entity
+ - dataset
+ - physical entity
+ - activity
+ - procedure
+ - material sample
+ - biological entity
+ - genome
+ range: uriorcurie
+ multivalued: true
+ full name:
+ name: full name
+ definition_uri: https://w3id.org/biolink/vocab/full_name
+ description: a long-form human readable name for a thing
+ from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
+ rank: 1000
+ is_a: node property
+ domain: named thing
+ slot_uri: biolink:full_name
+ alias: full_name
+ owner: activity
+ domain_of:
+ - named thing
+ - attribute
+ - organism taxon
+ - information content entity
+ - dataset
+ - physical entity
+ - activity
+ - procedure
+ - material sample
+ - biological entity
+ - gene
+ - genome
+ range: label type
+ synonym:
+ name: synonym
+ definition_uri: https://w3id.org/biolink/vocab/synonym
+ description: Alternate human-readable names for a thing
+ in_subset:
+ - translator_minimal
+ from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
+ aliases:
+ - alias
+ narrow_mappings:
+ - skos:altLabel
+ - gff3:Alias
+ - AGRKB:synonyms
+ - gpi:DB_Object_Synonyms
+ - HANCESTRO:0330
+ - IAO:0000136
+ - RXNORM:has_tradename
+ rank: 1000
+ is_a: node property
+ domain: named thing
+ slot_uri: biolink:synonym
+ alias: synonym
+ owner: activity
+ domain_of:
+ - named thing
+ - attribute
+ - organism taxon
+ - information content entity
+ - dataset
+ - physical entity
+ - activity
+ - procedure
+ - material sample
+ - biological entity
+ - gene
+ - genome
+ range: label type
+ multivalued: true
+class_uri: biolink:Activity
+
+Activity or behavior of any independent integral living, organization or mechanical actor in the world
+URI: biolink:ActivityAndBehavior
+| Name | +Cardinality and Range | +Description | +Inheritance | +
|---|---|---|---|
| + | + | + | + |
| mixed into | +description | +
|---|---|
| Activity | +An activity is something that occurs over a period of time and acts upon or w... | +
| Procedure | +A series of actions conducted in a certain order or manner | +
| Mapping Type | +Mapped Value | +
|---|---|
| self | +biolink:ActivityAndBehavior | +
| native | +bican:ActivityAndBehavior | +
| exact | +UMLSSG:ACTI | +
name: activity and behavior
+definition_uri: https://w3id.org/biolink/vocab/ActivityAndBehavior
+description: Activity or behavior of any independent integral living, organization
+ or mechanical actor in the world
+from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
+exact_mappings:
+- UMLSSG:ACTI
+is_a: occurrent
+mixin: true
+class_uri: biolink:ActivityAndBehavior
+
+name: activity and behavior
+definition_uri: https://w3id.org/biolink/vocab/ActivityAndBehavior
+description: Activity or behavior of any independent integral living, organization
+ or mechanical actor in the world
+from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
+exact_mappings:
+- UMLSSG:ACTI
+is_a: occurrent
+mixin: true
+class_uri: biolink:ActivityAndBehavior
+
+| Value | +Meaning | +Description | +
|---|---|---|
| birth | +NIMP:PD-RARAGG39 | +birth | +
| conception | +NIMP:PD-RARAGG39 | +conception | +
| Name | +Description | +
|---|---|
| age_at_death_reference_point | +The reference point for an age interval; for example, birth or conception | +
| Mapping Type | +Mapped Value | +
|---|---|
| self | +bican:3bed1f94-9d82-4ed7-afdf-79d896b24dbb | +
| native | +bican:age_at_death_reference_point | +
| exact | +NIMP:PD-RARAGG39 | +
name: age_at_death_reference_point
+from_schema: https://identifiers.org/brain-bican/library-generation-schema
+rank: 1000
+permissible_values:
+ birth:
+ text: birth
+ description: birth
+ meaning: NIMP:PD-RARAGG39
+ conception:
+ text: conception
+ description: conception
+ meaning: NIMP:PD-RARAGG39
+
+URI: AgeAtDeathUnit
+| Value | +Meaning | +Description | +
|---|---|---|
| days | +NIMP:PD-AVAVEV39 | +days | +
| months | +NIMP:PD-AVAVEV39 | +months | +
| years | +NIMP:PD-AVAVEV39 | +years | +
| Name | +Description | +
|---|---|
| age_at_death_unit | +The unit used for representing the donor age from the reference point | +
| Mapping Type | +Mapped Value | +
|---|---|
| self | +bican:b5436e99-f0a7-4c30-825d-56b88ee2ac1d | +
| native | +bican:age_at_death_unit | +
| exact | +NIMP:PD-AVAVEV39 | +
name: age_at_death_unit
+from_schema: https://identifiers.org/brain-bican/library-generation-schema
+rank: 1000
+permissible_values:
+ days:
+ text: days
+ description: days
+ meaning: NIMP:PD-AVAVEV39
+ months:
+ text: months
+ description: months
+ meaning: NIMP:PD-AVAVEV39
+ years:
+ text: years
+ description: years
+ meaning: NIMP:PD-AVAVEV39
+
+A subset of slots/attributes that are required for alignment.
+URI: Alignment
+A collection of cDNA molecules derived and amplified from an input barcoded cell sample. These cDNA molecules represent the gene expression of each cell, with all cDNA molecules from a given cell retaining that cell's unique barcode from the cell barcoding step. This is a necessary step for GEX methods but is not used for ATAC methods.
+URI: bican:AmplifiedCdna
+| Name | +Cardinality and Range | +Description | +Inheritance | +
|---|---|---|---|
| was_generated_by | +0..1 CdnaAmplification |
+The cDNA amplification process from which the amplified cDNA was generated by | +direct | +
| was_derived_from | +0..1 BarcodedCellSample |
+The input barcoded cell sample from which amplified cDNA was derived from | +direct | +
| name | +0..1 LabelType |
+Name of a collection of cDNA molecules derived and amplified from an input ba... | +direct | +
| quantity_ng | +0..1 Float |
+Amount of cDNA produced after cDNA amplification measured in nanograms | +direct | +
| pass_fail_result | +0..1 AmplifiedCdnaRnaAmplificationPassFail |
+Pass or Fail result based on qualitative assessment of cDNA yield and size | +direct | +
| percent_cdna_longer_than_400bp | +0..1 Float |
+QC metric to measure mRNA degradation of cDNA | +direct | +
| id | +1 String |
+A unique identifier for an entity | +NamedThing, PhysicalEntity, MaterialSample, Entity | +
| iri | +0..1 IriType |
+An IRI for an entity | +NamedThing, PhysicalEntity, MaterialSample, Entity | +
| category | +* Uriorcurie |
+Name of the high level ontology class in which this entity is categorized | +NamedThing, PhysicalEntity, MaterialSample, Entity | +
| type | +* String |
++ | NamedThing, PhysicalEntity, MaterialSample, Entity | +
| description | +0..1 NarrativeText |
+a human-readable description of an entity | +NamedThing, PhysicalEntity, MaterialSample, Entity | +
| has_attribute | +* Attribute |
+connects any entity to an attribute | +NamedThing, PhysicalEntity, MaterialSample, Entity | +
| deprecated | +0..1 Boolean |
+A boolean flag indicating that an entity is no longer considered current or v... | +NamedThing, PhysicalEntity, MaterialSample, Entity | +
| provided_by | +* String |
+The value in this node property represents the knowledge provider that create... | +NamedThing, PhysicalEntity, MaterialSample | +
| xref | +* Uriorcurie |
+A database cross reference or alternative identifier for a NamedThing or edge... | +NamedThing, PhysicalEntity, MaterialSample | +
| full_name | +0..1 LabelType |
+a long-form human readable name for a thing | +NamedThing, PhysicalEntity, MaterialSample | +
| synonym | +* LabelType |
+Alternate human-readable names for a thing | +NamedThing, PhysicalEntity, MaterialSample | +
| used by | +used in | +type | +used | +
|---|---|---|---|
| Library | +was_derived_from | +exactly_one_of[range] | +AmplifiedCdna | +
| LibraryConstruction | +used | +exactly_one_of[range] | +AmplifiedCdna | +
| Mapping Type | +Mapped Value | +
|---|---|
| self | +bican:AmplifiedCdna | +
| native | +bican:AmplifiedCdna | +
| exact | +NIMP:Amplified%20cDNA | +
name: AmplifiedCdna
+description: A collection of cDNA molecules derived and amplified from an input barcoded
+ cell sample. These cDNA molecules represent the gene expression of each cell, with
+ all cDNA molecules from a given cell retaining that cell's unique barcode from the
+ cell barcoding step. This is a necessary step for GEX methods but is not used for
+ ATAC methods.
+in_subset:
+- bican
+- library_generation
+from_schema: https://identifiers.org/brain-bican/library-generation-schema
+exact_mappings:
+- NIMP:Amplified%20cDNA
+is_a: material sample
+mixins:
+- ProvEntity
+slots:
+- was_generated_by
+- was_derived_from
+- name
+slot_usage:
+ was_generated_by:
+ name: was_generated_by
+ description: The cDNA amplification process from which the amplified cDNA was
+ generated by.
+ range: CdnaAmplification
+ was_derived_from:
+ name: was_derived_from
+ description: The input barcoded cell sample from which amplified cDNA was derived
+ from.
+ exact_mappings:
+ - NIMP:has_parent
+ range: BarcodedCellSample
+ name:
+ name: name
+ description: Name of a collection of cDNA molecules derived and amplified from
+ an input barcoded_cell_sample. These cDNA molecules represent the gene expression
+ of each cell, with all cDNA molecules from a given cell retaining that cell's
+ unique barcode from the cell barcoding step. This is a necessary step for GEX
+ methods but is not used for ATAC methods.
+ exact_mappings:
+ - NIMP:PD-YAAGGG39
+ slot_uri: bican:e2606a11-114e-472f-9e05-33f9b6fc3089
+ category:
+ name: category
+ pattern: ^bican:[A-Z][A-Za-z]+$
+attributes:
+ quantity_ng:
+ name: quantity_ng
+ local_names:
+ NIMP:
+ local_name_source: NIMP
+ local_name_value: amplified_cdna_amplified_quantity_ng
+ description: Amount of cDNA produced after cDNA amplification measured in nanograms.
+ in_subset:
+ - analysis
+ from_schema: https://identifiers.org/brain-bican/library-generation-schema
+ exact_mappings:
+ - NIMP:PD-TITIIC26
+ rank: 1000
+ slot_uri: bican:0db79d05-8612-4896-b9d3-eb1558841449
+ alias: amplified cDNA amplified quantity ng
+ domain_of:
+ - AmplifiedCdna
+ - Library
+ range: float
+ pass_fail_result:
+ name: pass_fail_result
+ local_names:
+ NIMP:
+ local_name_source: NIMP
+ local_name_value: amplified_cdna_rna_amplification_pass_fail
+ description: Pass or Fail result based on qualitative assessment of cDNA yield
+ and size.
+ in_subset:
+ - analysis
+ from_schema: https://identifiers.org/brain-bican/library-generation-schema
+ exact_mappings:
+ - NIMP:PD-XXXXFQ31
+ rank: 1000
+ slot_uri: bican:bc62bdb2-7dc8-4404-bb84-ce0bbcae59e5
+ alias: amplified cDNA RNA amplification pass-fail
+ domain_of:
+ - AmplifiedCdna
+ - Library
+ range: amplified_cdna_rna_amplification_pass_fail
+ percent_cdna_longer_than_400bp:
+ name: percent_cdna_longer_than_400bp
+ local_names:
+ NIMP:
+ local_name_source: NIMP
+ local_name_value: amplified_cdna_percent_cdna_longer_than_400bp
+ description: QC metric to measure mRNA degradation of cDNA. Higher % is higher
+ quality starting material. Over 400bp is used as a universal cutoff for intact
+ (full length) vs degraded cDNA and is a common output from Bioanalyzer and Fragment
+ Analyzer elecropheragrams.
+ in_subset:
+ - analysis
+ from_schema: https://identifiers.org/brain-bican/library-generation-schema
+ exact_mappings:
+ - NIMP:PD-JJJJWD35
+ rank: 1000
+ slot_uri: bican:8d150467-f69e-461c-b54c-bcfd22f581e5
+ alias: amplified cDNA percent cDNA longer than 400bp
+ domain_of:
+ - AmplifiedCdna
+ range: float
+
+name: AmplifiedCdna
+description: A collection of cDNA molecules derived and amplified from an input barcoded
+ cell sample. These cDNA molecules represent the gene expression of each cell, with
+ all cDNA molecules from a given cell retaining that cell's unique barcode from the
+ cell barcoding step. This is a necessary step for GEX methods but is not used for
+ ATAC methods.
+in_subset:
+- bican
+- library_generation
+from_schema: https://identifiers.org/brain-bican/library-generation-schema
+exact_mappings:
+- NIMP:Amplified%20cDNA
+is_a: material sample
+mixins:
+- ProvEntity
+slot_usage:
+ was_generated_by:
+ name: was_generated_by
+ description: The cDNA amplification process from which the amplified cDNA was
+ generated by.
+ range: CdnaAmplification
+ was_derived_from:
+ name: was_derived_from
+ description: The input barcoded cell sample from which amplified cDNA was derived
+ from.
+ exact_mappings:
+ - NIMP:has_parent
+ range: BarcodedCellSample
+ name:
+ name: name
+ description: Name of a collection of cDNA molecules derived and amplified from
+ an input barcoded_cell_sample. These cDNA molecules represent the gene expression
+ of each cell, with all cDNA molecules from a given cell retaining that cell's
+ unique barcode from the cell barcoding step. This is a necessary step for GEX
+ methods but is not used for ATAC methods.
+ exact_mappings:
+ - NIMP:PD-YAAGGG39
+ slot_uri: bican:e2606a11-114e-472f-9e05-33f9b6fc3089
+ category:
+ name: category
+ pattern: ^bican:[A-Z][A-Za-z]+$
+attributes:
+ quantity_ng:
+ name: quantity_ng
+ local_names:
+ NIMP:
+ local_name_source: NIMP
+ local_name_value: amplified_cdna_amplified_quantity_ng
+ description: Amount of cDNA produced after cDNA amplification measured in nanograms.
+ in_subset:
+ - analysis
+ from_schema: https://identifiers.org/brain-bican/library-generation-schema
+ exact_mappings:
+ - NIMP:PD-TITIIC26
+ rank: 1000
+ slot_uri: bican:0db79d05-8612-4896-b9d3-eb1558841449
+ alias: amplified cDNA amplified quantity ng
+ owner: AmplifiedCdna
+ domain_of:
+ - AmplifiedCdna
+ - Library
+ range: float
+ pass_fail_result:
+ name: pass_fail_result
+ local_names:
+ NIMP:
+ local_name_source: NIMP
+ local_name_value: amplified_cdna_rna_amplification_pass_fail
+ description: Pass or Fail result based on qualitative assessment of cDNA yield
+ and size.
+ in_subset:
+ - analysis
+ from_schema: https://identifiers.org/brain-bican/library-generation-schema
+ exact_mappings:
+ - NIMP:PD-XXXXFQ31
+ rank: 1000
+ slot_uri: bican:bc62bdb2-7dc8-4404-bb84-ce0bbcae59e5
+ alias: amplified cDNA RNA amplification pass-fail
+ owner: AmplifiedCdna
+ domain_of:
+ - AmplifiedCdna
+ - Library
+ range: amplified_cdna_rna_amplification_pass_fail
+ percent_cdna_longer_than_400bp:
+ name: percent_cdna_longer_than_400bp
+ local_names:
+ NIMP:
+ local_name_source: NIMP
+ local_name_value: amplified_cdna_percent_cdna_longer_than_400bp
+ description: QC metric to measure mRNA degradation of cDNA. Higher % is higher
+ quality starting material. Over 400bp is used as a universal cutoff for intact
+ (full length) vs degraded cDNA and is a common output from Bioanalyzer and Fragment
+ Analyzer elecropheragrams.
+ in_subset:
+ - analysis
+ from_schema: https://identifiers.org/brain-bican/library-generation-schema
+ exact_mappings:
+ - NIMP:PD-JJJJWD35
+ rank: 1000
+ slot_uri: bican:8d150467-f69e-461c-b54c-bcfd22f581e5
+ alias: amplified cDNA percent cDNA longer than 400bp
+ owner: AmplifiedCdna
+ domain_of:
+ - AmplifiedCdna
+ range: float
+ was_generated_by:
+ name: was_generated_by
+ description: The cDNA amplification process from which the amplified cDNA was
+ generated by.
+ from_schema: https://identifiers.org/brain-bican/library-generation-schema
+ rank: 1000
+ slot_uri: prov:wasGeneratedBy
+ alias: was_generated_by
+ owner: AmplifiedCdna
+ domain_of:
+ - TissueSample
+ - DissociatedCellSample
+ - EnrichedCellSample
+ - BarcodedCellSample
+ - AmplifiedCdna
+ - Library
+ - LibraryPool
+ - DissectionRoiPolygon
+ - ProvEntity
+ range: CdnaAmplification
+ was_derived_from:
+ name: was_derived_from
+ description: The input barcoded cell sample from which amplified cDNA was derived
+ from.
+ from_schema: https://identifiers.org/brain-bican/library-generation-schema
+ exact_mappings:
+ - NIMP:has_parent
+ rank: 1000
+ slot_uri: prov:wasDerivedFrom
+ alias: was_derived_from
+ owner: AmplifiedCdna
+ domain_of:
+ - BrainSlab
+ - TissueSample
+ - DissociatedCellSample
+ - EnrichedCellSample
+ - BarcodedCellSample
+ - AmplifiedCdna
+ - Library
+ - LibraryAliquot
+ - LibraryPool
+ - ProvEntity
+ range: BarcodedCellSample
+ name:
+ name: name
+ definition_uri: https://w3id.org/biolink/vocab/name
+ description: Name of a collection of cDNA molecules derived and amplified from
+ an input barcoded_cell_sample. These cDNA molecules represent the gene expression
+ of each cell, with all cDNA molecules from a given cell retaining that cell's
+ unique barcode from the cell barcoding step. This is a necessary step for GEX
+ methods but is not used for ATAC methods.
+ in_subset:
+ - translator_minimal
+ - samples
+ from_schema: https://identifiers.org/brain-bican/library-generation-schema
+ aliases:
+ - label
+ - display name
+ - title
+ mappings:
+ - rdfs:label
+ exact_mappings:
+ - NIMP:PD-YAAGGG39
+ narrow_mappings:
+ - dct:title
+ - WIKIDATA_PROPERTY:P1476
+ rank: 1000
+ domain: entity
+ slot_uri: bican:e2606a11-114e-472f-9e05-33f9b6fc3089
+ alias: name
+ owner: AmplifiedCdna
+ domain_of:
+ - attribute
+ - entity
+ - macromolecular machine mixin
+ - Donor
+ - BrainSlab
+ - TissueSample
+ - DissociatedCellSample
+ - EnrichedCellSample
+ - BarcodedCellSample
+ - AmplifiedCdna
+ - Library
+ - LibraryAliquot
+ - LibraryPool
+ - DissectionRoiPolygon
+ - named thing
+ - organism taxon
+ - information content entity
+ - dataset
+ - physical entity
+ - activity
+ - procedure
+ - material sample
+ - biological entity
+ - gene or gene product
+ - gene
+ - genome
+ range: label type
+ id:
+ name: id
+ definition_uri: https://w3id.org/biolink/vocab/id
+ description: A unique identifier for an entity. Must be either a CURIE shorthand
+ for a URI or a complete URI
+ in_subset:
+ - translator_minimal
+ from_schema: https://identifiers.org/brain-bican/library-generation-schema
+ exact_mappings:
+ - AGRKB:primaryId
+ - gff3:ID
+ - gpi:DB_Object_ID
+ rank: 1000
+ domain: entity
+ slot_uri: biolink:id
+ identifier: true
+ alias: id
+ owner: AmplifiedCdna
+ domain_of:
+ - ontology class
+ - entity
+ - attribute
+ - named thing
+ - taxonomic rank
+ - organism taxon
+ - information content entity
+ - dataset
+ - physical entity
+ - activity
+ - procedure
+ - material sample
+ - biological entity
+ - gene
+ - genome
+ range: string
+ required: true
+ iri:
+ name: iri
+ definition_uri: https://w3id.org/biolink/vocab/iri
+ description: An IRI for an entity. This is determined by the id using expansion
+ rules.
+ in_subset:
+ - translator_minimal
+ - samples
+ from_schema: https://identifiers.org/brain-bican/library-generation-schema
+ exact_mappings:
+ - WIKIDATA_PROPERTY:P854
+ rank: 1000
+ slot_uri: biolink:iri
+ alias: iri
+ owner: AmplifiedCdna
+ domain_of:
+ - attribute
+ - entity
+ - named thing
+ - organism taxon
+ - information content entity
+ - dataset
+ - physical entity
+ - activity
+ - procedure
+ - material sample
+ - biological entity
+ - gene
+ - genome
+ range: iri type
+ category:
+ name: category
+ definition_uri: https://w3id.org/biolink/vocab/category
+ description: Name of the high level ontology class in which this entity is categorized.
+ Corresponds to the label for the biolink entity type class. In a neo4j database
+ this MAY correspond to the neo4j label tag. In an RDF database it should be
+ a biolink model class URI. This field is multi-valued. It should include values
+ for ancestors of the biolink class; for example, a protein such as Shh would
+ have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`.
+ In an RDF database, nodes will typically have an rdf:type triples. This can
+ be to the most specific biolink class, or potentially to a class more specific
+ than something in biolink. For example, a sequence feature `f` may have a rdf:type
+ assertion to a SO class such as TF_binding_site, which is more specific than
+ anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity,
+ biolink:NamedThing}
+ in_subset:
+ - translator_minimal
+ from_schema: https://identifiers.org/brain-bican/library-generation-schema
+ rank: 1000
+ is_a: type
+ domain: entity
+ slot_uri: biolink:category
+ designates_type: true
+ alias: category
+ owner: AmplifiedCdna
+ domain_of:
+ - entity
+ - attribute
+ - named thing
+ - organism taxon
+ - information content entity
+ - dataset
+ - physical entity
+ - activity
+ - procedure
+ - material sample
+ - biological entity
+ - gene
+ - genome
+ is_class_field: true
+ range: uriorcurie
+ multivalued: true
+ pattern: ^bican:[A-Z][A-Za-z]+$
+ type:
+ name: type
+ definition_uri: https://w3id.org/biolink/vocab/type
+ from_schema: https://identifiers.org/brain-bican/library-generation-schema
+ mappings:
+ - rdf:type
+ exact_mappings:
+ - gff3:type
+ - gpi:DB_Object_Type
+ rank: 1000
+ domain: entity
+ slot_uri: rdf:type
+ alias: type
+ owner: AmplifiedCdna
+ domain_of:
+ - entity
+ - attribute
+ - named thing
+ - organism taxon
+ - information content entity
+ - dataset
+ - physical entity
+ - activity
+ - procedure
+ - material sample
+ - biological entity
+ - gene
+ - genome
+ range: string
+ multivalued: true
+ description:
+ name: description
+ definition_uri: https://w3id.org/biolink/vocab/description
+ description: a human-readable description of an entity
+ in_subset:
+ - translator_minimal
+ from_schema: https://identifiers.org/brain-bican/library-generation-schema
+ aliases:
+ - definition
+ mappings:
+ - dct:description
+ exact_mappings:
+ - IAO:0000115
+ - skos:definitions
+ narrow_mappings:
+ - gff3:Description
+ rank: 1000
+ slot_uri: dct:description
+ alias: description
+ owner: AmplifiedCdna
+ domain_of:
+ - entity
+ - attribute
+ - named thing
+ - organism taxon
+ - information content entity
+ - dataset
+ - physical entity
+ - activity
+ - procedure
+ - material sample
+ - biological entity
+ - gene
+ - genome
+ range: narrative text
+ has attribute:
+ name: has attribute
+ definition_uri: https://w3id.org/biolink/vocab/has_attribute
+ description: connects any entity to an attribute
+ in_subset:
+ - samples
+ from_schema: https://identifiers.org/brain-bican/library-generation-schema
+ exact_mappings:
+ - SIO:000008
+ close_mappings:
+ - OBI:0001927
+ narrow_mappings:
+ - OBAN:association_has_subject_property
+ - OBAN:association_has_object_property
+ - CPT:has_possibly_included_panel_element
+ - DRUGBANK:category
+ - EFO:is_executed_in
+ - HANCESTRO:0301
+ - LOINC:has_action_guidance
+ - LOINC:has_adjustment
+ - LOINC:has_aggregation_view
+ - LOINC:has_approach_guidance
+ - LOINC:has_divisor
+ - LOINC:has_exam
+ - LOINC:has_method
+ - LOINC:has_modality_subtype
+ - LOINC:has_object_guidance
+ - LOINC:has_scale
+ - LOINC:has_suffix
+ - LOINC:has_time_aspect
+ - LOINC:has_time_modifier
+ - LOINC:has_timing_of
+ - NCIT:R88
+ - NCIT:eo_disease_has_property_or_attribute
+ - NCIT:has_data_element
+ - NCIT:has_pharmaceutical_administration_method
+ - NCIT:has_pharmaceutical_basic_dose_form
+ - NCIT:has_pharmaceutical_intended_site
+ - NCIT:has_pharmaceutical_release_characteristics
+ - NCIT:has_pharmaceutical_state_of_matter
+ - NCIT:has_pharmaceutical_transformation
+ - NCIT:is_qualified_by
+ - NCIT:qualifier_applies_to
+ - NCIT:role_has_domain
+ - NCIT:role_has_range
+ - INO:0000154
+ - HANCESTRO:0308
+ - OMIM:has_inheritance_type
+ - orphanet:C016
+ - orphanet:C017
+ - RO:0000053
+ - RO:0000086
+ - RO:0000087
+ - SNOMED:has_access
+ - SNOMED:has_clinical_course
+ - SNOMED:has_count_of_base_of_active_ingredient
+ - SNOMED:has_dose_form_administration_method
+ - SNOMED:has_dose_form_release_characteristic
+ - SNOMED:has_dose_form_transformation
+ - SNOMED:has_finding_context
+ - SNOMED:has_finding_informer
+ - SNOMED:has_inherent_attribute
+ - SNOMED:has_intent
+ - SNOMED:has_interpretation
+ - SNOMED:has_laterality
+ - SNOMED:has_measurement_method
+ - SNOMED:has_method
+ - SNOMED:has_priority
+ - SNOMED:has_procedure_context
+ - SNOMED:has_process_duration
+ - SNOMED:has_property
+ - SNOMED:has_revision_status
+ - SNOMED:has_scale_type
+ - SNOMED:has_severity
+ - SNOMED:has_specimen
+ - SNOMED:has_state_of_matter
+ - SNOMED:has_subject_relationship_context
+ - SNOMED:has_surgical_approach
+ - SNOMED:has_technique
+ - SNOMED:has_temporal_context
+ - SNOMED:has_time_aspect
+ - SNOMED:has_units
+ - UMLS:has_structural_class
+ - UMLS:has_supported_concept_property
+ - UMLS:has_supported_concept_relationship
+ - UMLS:may_be_qualified_by
+ rank: 1000
+ domain: entity
+ slot_uri: biolink:has_attribute
+ alias: has_attribute
+ owner: AmplifiedCdna
+ domain_of:
+ - entity
+ - attribute
+ - named thing
+ - organism taxon
+ - information content entity
+ - dataset
+ - physical entity
+ - activity
+ - procedure
+ - material sample
+ - biological entity
+ - gene
+ - genome
+ range: attribute
+ multivalued: true
+ deprecated:
+ name: deprecated
+ definition_uri: https://w3id.org/biolink/vocab/deprecated
+ description: A boolean flag indicating that an entity is no longer considered
+ current or valid.
+ from_schema: https://identifiers.org/brain-bican/library-generation-schema
+ exact_mappings:
+ - oboInOwl:ObsoleteClass
+ rank: 1000
+ slot_uri: biolink:deprecated
+ alias: deprecated
+ owner: AmplifiedCdna
+ domain_of:
+ - entity
+ - attribute
+ - named thing
+ - organism taxon
+ - information content entity
+ - dataset
+ - physical entity
+ - activity
+ - procedure
+ - material sample
+ - biological entity
+ - gene
+ - genome
+ range: boolean
+ provided by:
+ name: provided by
+ definition_uri: https://w3id.org/biolink/vocab/provided_by
+ description: The value in this node property represents the knowledge provider
+ that created or assembled the node and all of its attributes. Used internally
+ to represent how a particular node made its way into a knowledge provider or
+ graph.
+ from_schema: https://identifiers.org/brain-bican/library-generation-schema
+ rank: 1000
+ is_a: node property
+ domain: named thing
+ slot_uri: biolink:provided_by
+ alias: provided_by
+ owner: AmplifiedCdna
+ domain_of:
+ - named thing
+ - attribute
+ - organism taxon
+ - information content entity
+ - dataset
+ - physical entity
+ - activity
+ - procedure
+ - material sample
+ - biological entity
+ - gene
+ - genome
+ range: string
+ multivalued: true
+ xref:
+ name: xref
+ definition_uri: https://w3id.org/biolink/vocab/xref
+ description: A database cross reference or alternative identifier for a NamedThing
+ or edge between two NamedThings. This property should point to a database record
+ or webpage that supports the existence of the edge, or gives more detail about
+ the edge. This property can be used on a node or edge to provide multiple URIs
+ or CURIE cross references.
+ in_subset:
+ - translator_minimal
+ from_schema: https://identifiers.org/brain-bican/library-generation-schema
+ aliases:
+ - dbxref
+ - Dbxref
+ - DbXref
+ - record_url
+ - source_record_urls
+ narrow_mappings:
+ - gff3:Dbxref
+ - gpi:DB_Xrefs
+ rank: 1000
+ domain: named thing
+ slot_uri: biolink:xref
+ alias: xref
+ owner: AmplifiedCdna
+ domain_of:
+ - named thing
+ - gene
+ - attribute
+ - organism taxon
+ - information content entity
+ - dataset
+ - physical entity
+ - activity
+ - procedure
+ - material sample
+ - biological entity
+ - genome
+ range: uriorcurie
+ multivalued: true
+ full name:
+ name: full name
+ definition_uri: https://w3id.org/biolink/vocab/full_name
+ description: a long-form human readable name for a thing
+ from_schema: https://identifiers.org/brain-bican/library-generation-schema
+ rank: 1000
+ is_a: node property
+ domain: named thing
+ slot_uri: biolink:full_name
+ alias: full_name
+ owner: AmplifiedCdna
+ domain_of:
+ - named thing
+ - attribute
+ - organism taxon
+ - information content entity
+ - dataset
+ - physical entity
+ - activity
+ - procedure
+ - material sample
+ - biological entity
+ - gene
+ - genome
+ range: label type
+ synonym:
+ name: synonym
+ definition_uri: https://w3id.org/biolink/vocab/synonym
+ description: Alternate human-readable names for a thing
+ in_subset:
+ - translator_minimal
+ from_schema: https://identifiers.org/brain-bican/library-generation-schema
+ aliases:
+ - alias
+ narrow_mappings:
+ - skos:altLabel
+ - gff3:Alias
+ - AGRKB:synonyms
+ - gpi:DB_Object_Synonyms
+ - HANCESTRO:0330
+ - IAO:0000136
+ - RXNORM:has_tradename
+ rank: 1000
+ is_a: node property
+ domain: named thing
+ slot_uri: biolink:synonym
+ alias: synonym
+ owner: AmplifiedCdna
+ domain_of:
+ - named thing
+ - attribute
+ - organism taxon
+ - information content entity
+ - dataset
+ - physical entity
+ - activity
+ - procedure
+ - material sample
+ - biological entity
+ - gene
+ - genome
+ range: label type
+ multivalued: true
+
+URI: AmplifiedCdnaRnaAmplificationPassFail
+| Value | +Meaning | +Description | +
|---|---|---|
| Pass | +NIMP:PD-XXXXFQ31 | +The RNA amplification passed the QA/QC | +
| Fail | +NIMP:PD-XXXXFQ31 | +The RNA amplification failed the QA/QC | +
| Low QC | +NIMP:PD-XXXXFQ31 | +The RNA amplification low passed the QA/QC | +
| Not evaluated | +NIMP:PD-XXXXFQ31 | +Library Prep not evaluated for QA/QC | +
| Name | +Description | +
|---|---|
| pass_fail_result | +Pass or Fail result based on qualitative assessment of cDNA yield and size | +
name: amplified_cdna_rna_amplification_pass_fail
+from_schema: https://identifiers.org/brain-bican/library-generation-schema
+rank: 1000
+permissible_values:
+ Pass:
+ text: Pass
+ description: The RNA amplification passed the QA/QC
+ meaning: NIMP:PD-XXXXFQ31
+ Fail:
+ text: Fail
+ description: The RNA amplification failed the QA/QC
+ meaning: NIMP:PD-XXXXFQ31
+ Low QC:
+ text: Low QC
+ description: The RNA amplification low passed the QA/QC
+ meaning: NIMP:PD-XXXXFQ31
+ Not evaluated:
+ text: Not evaluated
+ description: Library Prep not evaluated for QA/QC
+ meaning: NIMP:PD-XXXXFQ31
+
+A subset of slots/attributes that are required for analysis.
+URI: Analysis
+| Slot | +Description | +
|---|---|
| average_size_bp | +Average size of the library in terms of base pairs | +
| cell_prep_type | +The type of cell preparation | +
| enrichment_population | +Actual percentage of cells as a result of using set of fluorescent marker lab... | +
| input_quantity | +Number of enriched or dissociated cells/nuclei going into the barcoding proce... | +
| input_quantity_ng | +Amount of cDNA going into library construction in nanograms | +
| local_tube_id | +Library Pool Tube local name | +
| number_of_expected_cells | +Expected number of cells/nuclei of a barcoded_cell_sample that will be barcod... | +
| pass_fail_result | +Pass or Fail result based on qualitative assessment of cDNA yield and size | +
| pcr_cycles | +Number of PCR cycles used during cDNA amplification for this cDNA | +
| percent_cdna_longer_than_400bp | +QC metric to measure mRNA degradation of cDNA | +
| port_well | +Specific position of the loaded port of the 10x chip | +
| quantity_fmol | +Amount of library generated in terms of femtomoles | +
| quantity_ng | +Amount of cDNA produced after cDNA amplification measured in nanograms | +
| r1_r2_index | +Name of the pair of library indexes used for sequencing | +
| set | +cDNA amplification set, containing multiple amplified_cDNA_names that were pr... | +
An anatomical annotation set is a versioned release of a set of anatomical annotations anchored in the same anatomical space that divides the space into distinct segments following some annotation criteria or parcellation scheme. For example, the anatomical annotation set of 3D image based reference atlases (e.g. Allen Mouse CCF) can be expressed as a set of label indices of single multi-valued image annotations or as a set of segmentation masks (ref: ILX:0777108, RRID:SCR_023499)
+URI: AnS:AnatomicalAnnotationSet
+| Name | +Cardinality and Range | +Description | +Inheritance | +
|---|---|---|---|
| parameterizes | +1 String or AnatomicalSpace or String |
+Reference to the anatomical space for which the anatomical annotation set is ... | +direct | +
| version | +1 String |
++ | VersionedNamedThing | +
| revision_of | +0..1 VersionedNamedThing or AnatomicalAnnotationSet or String |
++ | VersionedNamedThing | +
| id | +1 Uriorcurie |
++ | NamedThing | +
| name | +1 String |
++ | NamedThing | +
| description | +1 String |
++ | NamedThing | +
| category | +* Uriorcurie |
++ | NamedThing | +
| used by | +used in | +type | +used | +
|---|---|---|---|
| AnatomicalAnnotationSet | +revision_of | +any_of[range] | +AnatomicalAnnotationSet | +
| ParcellationAnnotation | +part_of_anatomical_annotation_set | +any_of[range] | +AnatomicalAnnotationSet | +
| ParcellationAtlas | +has_anatomical_annotation_set | +any_of[range] | +AnatomicalAnnotationSet | +
| Mapping Type | +Mapped Value | +
|---|---|
| self | +AnS:AnatomicalAnnotationSet | +
| native | +AnS:AnatomicalAnnotationSet | +
name: AnatomicalAnnotationSet
+description: 'An anatomical annotation set is a versioned release of a set of anatomical
+ annotations anchored in the same anatomical space that divides the space into distinct
+ segments following some annotation criteria or parcellation scheme. For example,
+ the anatomical annotation set of 3D image based reference atlases (e.g. Allen Mouse
+ CCF) can be expressed as a set of label indices of single multi-valued image annotations
+ or as a set of segmentation masks (ref: ILX:0777108, RRID:SCR_023499)'
+from_schema: https://w3id.org/my-org/anatomical-structure-schema
+is_a: VersionedNamedThing
+slot_usage:
+ revision_of:
+ name: revision_of
+ any_of:
+ - range: AnatomicalAnnotationSet
+ - range: string
+attributes:
+ parameterizes:
+ name: parameterizes
+ description: Reference to the anatomical space for which the anatomical annotation
+ set is anchored
+ from_schema: https://w3id.org/my-org/anatomical-structure-schema
+ rank: 1000
+ domain_of:
+ - AnatomicalAnnotationSet
+ required: true
+ any_of:
+ - range: AnatomicalSpace
+ - range: string
+
+name: AnatomicalAnnotationSet
+description: 'An anatomical annotation set is a versioned release of a set of anatomical
+ annotations anchored in the same anatomical space that divides the space into distinct
+ segments following some annotation criteria or parcellation scheme. For example,
+ the anatomical annotation set of 3D image based reference atlases (e.g. Allen Mouse
+ CCF) can be expressed as a set of label indices of single multi-valued image annotations
+ or as a set of segmentation masks (ref: ILX:0777108, RRID:SCR_023499)'
+from_schema: https://w3id.org/my-org/anatomical-structure-schema
+is_a: VersionedNamedThing
+slot_usage:
+ revision_of:
+ name: revision_of
+ any_of:
+ - range: AnatomicalAnnotationSet
+ - range: string
+attributes:
+ parameterizes:
+ name: parameterizes
+ description: Reference to the anatomical space for which the anatomical annotation
+ set is anchored
+ from_schema: https://w3id.org/my-org/anatomical-structure-schema
+ rank: 1000
+ alias: parameterizes
+ owner: AnatomicalAnnotationSet
+ domain_of:
+ - AnatomicalAnnotationSet
+ range: string
+ required: true
+ any_of:
+ - range: AnatomicalSpace
+ - range: string
+ version:
+ name: version
+ from_schema: https://w3id.org/my-org/anatomical-structure-schema
+ rank: 1000
+ alias: version
+ owner: AnatomicalAnnotationSet
+ domain_of:
+ - VersionedNamedThing
+ range: string
+ required: true
+ revision_of:
+ name: revision_of
+ from_schema: https://w3id.org/my-org/anatomical-structure-schema
+ rank: 1000
+ alias: revision_of
+ owner: AnatomicalAnnotationSet
+ domain_of:
+ - VersionedNamedThing
+ range: VersionedNamedThing
+ any_of:
+ - range: AnatomicalAnnotationSet
+ - range: string
+ id:
+ name: id
+ from_schema: https://w3id.org/my-org/anatomical-structure-schema
+ rank: 1000
+ identifier: true
+ alias: id
+ owner: AnatomicalAnnotationSet
+ domain_of:
+ - NamedThing
+ range: uriorcurie
+ required: true
+ name:
+ name: name
+ from_schema: https://w3id.org/my-org/anatomical-structure-schema
+ rank: 1000
+ alias: name
+ owner: AnatomicalAnnotationSet
+ domain_of:
+ - NamedThing
+ range: string
+ required: true
+ description:
+ name: description
+ from_schema: https://w3id.org/my-org/anatomical-structure-schema
+ rank: 1000
+ alias: description
+ owner: AnatomicalAnnotationSet
+ domain_of:
+ - NamedThing
+ range: string
+ required: true
+ category:
+ name: category
+ from_schema: https://w3id.org/my-org/anatomical-structure-schema
+ rank: 1000
+ designates_type: true
+ alias: category
+ owner: AnatomicalAnnotationSet
+ domain_of:
+ - NamedThing
+ is_class_field: true
+ range: uriorcurie
+ multivalued: true
+
+An anatomical space is versioned release of a mathematical space with a defined mapping between the anatomical axes and the mathematical axes. An anatomical space may be defined by a reference image chosen as the biological reference for an anatomical structure of interest derived from a single or multiple specimens (ref: ILX:0777106, RRID:SCR_023499)
+URI: AnS:AnatomicalSpace
+| Name | +Cardinality and Range | +Description | +Inheritance | +
|---|---|---|---|
| measures | +1 String or ImageDataset or String |
+Reference to the specific image dataset used to define the anatomical space | +direct | +
| version | +1 String |
++ | VersionedNamedThing | +
| revision_of | +0..1 VersionedNamedThing or AnatomicalSpace or String |
++ | VersionedNamedThing | +
| id | +1 Uriorcurie |
++ | NamedThing | +
| name | +1 String |
++ | NamedThing | +
| description | +1 String |
++ | NamedThing | +
| category | +* Uriorcurie |
++ | NamedThing | +
| used by | +used in | +type | +used | +
|---|---|---|---|
| AnatomicalSpace | +revision_of | +any_of[range] | +AnatomicalSpace | +
| AnatomicalAnnotationSet | +parameterizes | +any_of[range] | +AnatomicalSpace | +
| ParcellationAtlas | +has_anatomical_space | +any_of[range] | +AnatomicalSpace | +
| Mapping Type | +Mapped Value | +
|---|---|
| self | +AnS:AnatomicalSpace | +
| native | +AnS:AnatomicalSpace | +
name: AnatomicalSpace
+description: 'An anatomical space is versioned release of a mathematical space with
+ a defined mapping between the anatomical axes and the mathematical axes. An anatomical
+ space may be defined by a reference image chosen as the biological reference for
+ an anatomical structure of interest derived from a single or multiple specimens
+ (ref: ILX:0777106, RRID:SCR_023499)'
+from_schema: https://w3id.org/my-org/anatomical-structure-schema
+is_a: VersionedNamedThing
+slot_usage:
+ revision_of:
+ name: revision_of
+ any_of:
+ - range: AnatomicalSpace
+ - range: string
+attributes:
+ measures:
+ name: measures
+ description: Reference to the specific image dataset used to define the anatomical
+ space.
+ from_schema: https://w3id.org/my-org/anatomical-structure-schema
+ rank: 1000
+ domain_of:
+ - AnatomicalSpace
+ required: true
+ any_of:
+ - range: ImageDataset
+ - range: string
+
+name: AnatomicalSpace
+description: 'An anatomical space is versioned release of a mathematical space with
+ a defined mapping between the anatomical axes and the mathematical axes. An anatomical
+ space may be defined by a reference image chosen as the biological reference for
+ an anatomical structure of interest derived from a single or multiple specimens
+ (ref: ILX:0777106, RRID:SCR_023499)'
+from_schema: https://w3id.org/my-org/anatomical-structure-schema
+is_a: VersionedNamedThing
+slot_usage:
+ revision_of:
+ name: revision_of
+ any_of:
+ - range: AnatomicalSpace
+ - range: string
+attributes:
+ measures:
+ name: measures
+ description: Reference to the specific image dataset used to define the anatomical
+ space.
+ from_schema: https://w3id.org/my-org/anatomical-structure-schema
+ rank: 1000
+ alias: measures
+ owner: AnatomicalSpace
+ domain_of:
+ - AnatomicalSpace
+ range: string
+ required: true
+ any_of:
+ - range: ImageDataset
+ - range: string
+ version:
+ name: version
+ from_schema: https://w3id.org/my-org/anatomical-structure-schema
+ rank: 1000
+ alias: version
+ owner: AnatomicalSpace
+ domain_of:
+ - VersionedNamedThing
+ range: string
+ required: true
+ revision_of:
+ name: revision_of
+ from_schema: https://w3id.org/my-org/anatomical-structure-schema
+ rank: 1000
+ alias: revision_of
+ owner: AnatomicalSpace
+ domain_of:
+ - VersionedNamedThing
+ range: VersionedNamedThing
+ any_of:
+ - range: AnatomicalSpace
+ - range: string
+ id:
+ name: id
+ from_schema: https://w3id.org/my-org/anatomical-structure-schema
+ rank: 1000
+ identifier: true
+ alias: id
+ owner: AnatomicalSpace
+ domain_of:
+ - NamedThing
+ range: uriorcurie
+ required: true
+ name:
+ name: name
+ from_schema: https://w3id.org/my-org/anatomical-structure-schema
+ rank: 1000
+ alias: name
+ owner: AnatomicalSpace
+ domain_of:
+ - NamedThing
+ range: string
+ required: true
+ description:
+ name: description
+ from_schema: https://w3id.org/my-org/anatomical-structure-schema
+ rank: 1000
+ alias: description
+ owner: AnatomicalSpace
+ domain_of:
+ - NamedThing
+ range: string
+ required: true
+ category:
+ name: category
+ from_schema: https://w3id.org/my-org/anatomical-structure-schema
+ rank: 1000
+ designates_type: true
+ alias: category
+ owner: AnatomicalSpace
+ domain_of:
+ - NamedThing
+ is_class_field: true
+ range: uriorcurie
+ multivalued: true
+
+Biolink Model root class for entity annotations.
+URI: biolink:Annotation
+| Name | +Cardinality and Range | +Description | +Inheritance | +
|---|---|---|---|
| + | + | + | + |
| Mapping Type | +Mapped Value | +
|---|---|
| self | +biolink:Annotation | +
| native | +bican:Annotation | +
name: annotation
+definition_uri: https://w3id.org/biolink/vocab/Annotation
+description: Biolink Model root class for entity annotations.
+from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
+abstract: true
+class_uri: biolink:Annotation
+
+name: annotation
+definition_uri: https://w3id.org/biolink/vocab/Annotation
+description: Biolink Model root class for entity annotations.
+from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
+abstract: true
+class_uri: biolink:Annotation
+
+URI: bican:AnnotationCollection
+| Name | +Cardinality and Range | +Description | +Inheritance | +
|---|---|---|---|
| annotations | +* GeneAnnotation |
++ | direct | +
| genome_annotations | +* GenomeAnnotation |
++ | direct | +
| genome_assemblies | +* GenomeAssembly |
++ | direct | +
| Mapping Type | +Mapped Value | +
|---|---|
| self | +bican:AnnotationCollection | +
| native | +bican:AnnotationCollection | +
name: annotation collection
+from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
+attributes:
+ annotations:
+ name: annotations
+ from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
+ rank: 1000
+ domain_of:
+ - annotation collection
+ range: gene annotation
+ multivalued: true
+ inlined: true
+ inlined_as_list: true
+ genome_annotations:
+ name: genome_annotations
+ from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
+ rank: 1000
+ domain_of:
+ - annotation collection
+ range: genome annotation
+ multivalued: true
+ inlined: true
+ inlined_as_list: true
+ genome_assemblies:
+ name: genome_assemblies
+ from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
+ rank: 1000
+ domain_of:
+ - annotation collection
+ range: genome assembly
+ multivalued: true
+ inlined: true
+ inlined_as_list: true
+tree_root: true
+
+name: annotation collection
+from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
+attributes:
+ annotations:
+ name: annotations
+ from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
+ rank: 1000
+ alias: annotations
+ owner: annotation collection
+ domain_of:
+ - annotation collection
+ range: gene annotation
+ multivalued: true
+ inlined: true
+ inlined_as_list: true
+ genome_annotations:
+ name: genome_annotations
+ from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
+ rank: 1000
+ alias: genome_annotations
+ owner: annotation collection
+ domain_of:
+ - annotation collection
+ range: genome annotation
+ multivalued: true
+ inlined: true
+ inlined_as_list: true
+ genome_assemblies:
+ name: genome_assemblies
+ from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
+ rank: 1000
+ alias: genome_assemblies
+ owner: annotation collection
+ domain_of:
+ - annotation collection
+ range: genome assembly
+ multivalued: true
+ inlined: true
+ inlined_as_list: true
+tree_root: true
+
+A property or characteristic of an entity. For example, an apple may have properties such as color, shape, age, crispiness. An environmental sample may have attributes such as depth, lat, long, material.
+URI: biolink:Attribute
+| Name | +Cardinality and Range | +Description | +Inheritance | +
|---|---|---|---|
| id | +1 String |
+A unique identifier for an entity | +direct | +
| category | +* Uriorcurie |
+Name of the high level ontology class in which this entity is categorized | +direct | +
| type | +* String |
++ | direct | +
| description | +0..1 NarrativeText |
+a human-readable description of an entity | +direct | +
| has_attribute | +* Attribute |
+connects any entity to an attribute | +direct | +
| deprecated | +0..1 Boolean |
+A boolean flag indicating that an entity is no longer considered current or v... | +direct | +
| provided_by | +* String |
+The value in this node property represents the knowledge provider that create... | +direct | +
| xref | +* Uriorcurie |
+A database cross reference or alternative identifier for a NamedThing or edge... | +direct | +
| full_name | +0..1 LabelType |
+a long-form human readable name for a thing | +direct | +
| synonym | +* LabelType |
+Alternate human-readable names for a thing | +direct | +
| attribute_name | +0..1 LabelType |
+The human-readable 'attribute name' can be set to a string which reflects its... | +direct | +
| has_attribute_type | +1 OntologyClass |
+connects an attribute to a class that describes it | +direct | +
| has_quantitative_value | +* QuantityValue |
+connects an attribute to a value | +direct | +
| has_qualitative_value | +0..1 NamedThing |
+connects an attribute to a value | +direct | +
| iri | +0..1 IriType |
+An IRI for an entity | +direct | +
| name | +0..1 LabelType |
+The human-readable 'attribute name' can be set to a string which reflects its... | +NamedThing, Entity, Attribute | +
Instances of this class should have identifiers with one of the following prefixes:
+EDAM-DATA
+EDAM-FORMAT
+EDAM-OPERATION
+EDAM-TOPIC
+| Mapping Type | +Mapped Value | +
|---|---|
| self | +biolink:Attribute | +
| native | +bican:Attribute | +
| exact | +SIO:000614 | +
name: attribute
+id_prefixes:
+- EDAM-DATA
+- EDAM-FORMAT
+- EDAM-OPERATION
+- EDAM-TOPIC
+definition_uri: https://w3id.org/biolink/vocab/Attribute
+description: A property or characteristic of an entity. For example, an apple may
+ have properties such as color, shape, age, crispiness. An environmental sample may
+ have attributes such as depth, lat, long, material.
+in_subset:
+- samples
+from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
+exact_mappings:
+- SIO:000614
+is_a: named thing
+mixins:
+- ontology class
+slots:
+- id
+- category
+- type
+- description
+- has attribute
+- deprecated
+- provided by
+- xref
+- full name
+- synonym
+- attribute_name
+- has attribute type
+- has quantitative value
+- has qualitative value
+- iri
+slot_usage:
+ name:
+ name: name
+ description: The human-readable 'attribute name' can be set to a string which
+ reflects its context of interpretation, e.g. SEPIO evidence/provenance/confidence
+ annotation or it can default to the name associated with the 'has attribute
+ type' slot ontology term.
+class_uri: biolink:Attribute
+
+name: attribute
+id_prefixes:
+- EDAM-DATA
+- EDAM-FORMAT
+- EDAM-OPERATION
+- EDAM-TOPIC
+definition_uri: https://w3id.org/biolink/vocab/Attribute
+description: A property or characteristic of an entity. For example, an apple may
+ have properties such as color, shape, age, crispiness. An environmental sample may
+ have attributes such as depth, lat, long, material.
+in_subset:
+- samples
+from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
+exact_mappings:
+- SIO:000614
+is_a: named thing
+mixins:
+- ontology class
+slot_usage:
+ name:
+ name: name
+ description: The human-readable 'attribute name' can be set to a string which
+ reflects its context of interpretation, e.g. SEPIO evidence/provenance/confidence
+ annotation or it can default to the name associated with the 'has attribute
+ type' slot ontology term.
+attributes:
+ id:
+ name: id
+ definition_uri: https://w3id.org/biolink/vocab/id
+ description: A unique identifier for an entity. Must be either a CURIE shorthand
+ for a URI or a complete URI
+ in_subset:
+ - translator_minimal
+ from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
+ exact_mappings:
+ - AGRKB:primaryId
+ - gff3:ID
+ - gpi:DB_Object_ID
+ rank: 1000
+ domain: entity
+ slot_uri: biolink:id
+ identifier: true
+ alias: id
+ owner: attribute
+ domain_of:
+ - ontology class
+ - entity
+ - attribute
+ - named thing
+ - taxonomic rank
+ - organism taxon
+ - information content entity
+ - dataset
+ - physical entity
+ - activity
+ - procedure
+ - material sample
+ - biological entity
+ - gene
+ - genome
+ range: string
+ required: true
+ category:
+ name: category
+ definition_uri: https://w3id.org/biolink/vocab/category
+ description: Name of the high level ontology class in which this entity is categorized.
+ Corresponds to the label for the biolink entity type class. In a neo4j database
+ this MAY correspond to the neo4j label tag. In an RDF database it should be
+ a biolink model class URI. This field is multi-valued. It should include values
+ for ancestors of the biolink class; for example, a protein such as Shh would
+ have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`.
+ In an RDF database, nodes will typically have an rdf:type triples. This can
+ be to the most specific biolink class, or potentially to a class more specific
+ than something in biolink. For example, a sequence feature `f` may have a rdf:type
+ assertion to a SO class such as TF_binding_site, which is more specific than
+ anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity,
+ biolink:NamedThing}
+ in_subset:
+ - translator_minimal
+ from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
+ rank: 1000
+ is_a: type
+ domain: entity
+ slot_uri: biolink:category
+ designates_type: true
+ alias: category
+ owner: attribute
+ domain_of:
+ - entity
+ - attribute
+ - named thing
+ - organism taxon
+ - information content entity
+ - dataset
+ - physical entity
+ - activity
+ - procedure
+ - material sample
+ - biological entity
+ - gene
+ - genome
+ is_class_field: true
+ range: uriorcurie
+ multivalued: true
+ type:
+ name: type
+ definition_uri: https://w3id.org/biolink/vocab/type
+ from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
+ mappings:
+ - rdf:type
+ exact_mappings:
+ - gff3:type
+ - gpi:DB_Object_Type
+ rank: 1000
+ domain: entity
+ slot_uri: rdf:type
+ alias: type
+ owner: attribute
+ domain_of:
+ - entity
+ - attribute
+ - named thing
+ - organism taxon
+ - information content entity
+ - dataset
+ - physical entity
+ - activity
+ - procedure
+ - material sample
+ - biological entity
+ - gene
+ - genome
+ range: string
+ multivalued: true
+ description:
+ name: description
+ definition_uri: https://w3id.org/biolink/vocab/description
+ description: a human-readable description of an entity
+ in_subset:
+ - translator_minimal
+ from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
+ aliases:
+ - definition
+ mappings:
+ - dct:description
+ exact_mappings:
+ - IAO:0000115
+ - skos:definitions
+ narrow_mappings:
+ - gff3:Description
+ rank: 1000
+ slot_uri: dct:description
+ alias: description
+ owner: attribute
+ domain_of:
+ - entity
+ - attribute
+ - named thing
+ - organism taxon
+ - information content entity
+ - dataset
+ - physical entity
+ - activity
+ - procedure
+ - material sample
+ - biological entity
+ - gene
+ - genome
+ range: narrative text
+ has attribute:
+ name: has attribute
+ definition_uri: https://w3id.org/biolink/vocab/has_attribute
+ description: connects any entity to an attribute
+ in_subset:
+ - samples
+ from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
+ exact_mappings:
+ - SIO:000008
+ close_mappings:
+ - OBI:0001927
+ narrow_mappings:
+ - OBAN:association_has_subject_property
+ - OBAN:association_has_object_property
+ - CPT:has_possibly_included_panel_element
+ - DRUGBANK:category
+ - EFO:is_executed_in
+ - HANCESTRO:0301
+ - LOINC:has_action_guidance
+ - LOINC:has_adjustment
+ - LOINC:has_aggregation_view
+ - LOINC:has_approach_guidance
+ - LOINC:has_divisor
+ - LOINC:has_exam
+ - LOINC:has_method
+ - LOINC:has_modality_subtype
+ - LOINC:has_object_guidance
+ - LOINC:has_scale
+ - LOINC:has_suffix
+ - LOINC:has_time_aspect
+ - LOINC:has_time_modifier
+ - LOINC:has_timing_of
+ - NCIT:R88
+ - NCIT:eo_disease_has_property_or_attribute
+ - NCIT:has_data_element
+ - NCIT:has_pharmaceutical_administration_method
+ - NCIT:has_pharmaceutical_basic_dose_form
+ - NCIT:has_pharmaceutical_intended_site
+ - NCIT:has_pharmaceutical_release_characteristics
+ - NCIT:has_pharmaceutical_state_of_matter
+ - NCIT:has_pharmaceutical_transformation
+ - NCIT:is_qualified_by
+ - NCIT:qualifier_applies_to
+ - NCIT:role_has_domain
+ - NCIT:role_has_range
+ - INO:0000154
+ - HANCESTRO:0308
+ - OMIM:has_inheritance_type
+ - orphanet:C016
+ - orphanet:C017
+ - RO:0000053
+ - RO:0000086
+ - RO:0000087
+ - SNOMED:has_access
+ - SNOMED:has_clinical_course
+ - SNOMED:has_count_of_base_of_active_ingredient
+ - SNOMED:has_dose_form_administration_method
+ - SNOMED:has_dose_form_release_characteristic
+ - SNOMED:has_dose_form_transformation
+ - SNOMED:has_finding_context
+ - SNOMED:has_finding_informer
+ - SNOMED:has_inherent_attribute
+ - SNOMED:has_intent
+ - SNOMED:has_interpretation
+ - SNOMED:has_laterality
+ - SNOMED:has_measurement_method
+ - SNOMED:has_method
+ - SNOMED:has_priority
+ - SNOMED:has_procedure_context
+ - SNOMED:has_process_duration
+ - SNOMED:has_property
+ - SNOMED:has_revision_status
+ - SNOMED:has_scale_type
+ - SNOMED:has_severity
+ - SNOMED:has_specimen
+ - SNOMED:has_state_of_matter
+ - SNOMED:has_subject_relationship_context
+ - SNOMED:has_surgical_approach
+ - SNOMED:has_technique
+ - SNOMED:has_temporal_context
+ - SNOMED:has_time_aspect
+ - SNOMED:has_units
+ - UMLS:has_structural_class
+ - UMLS:has_supported_concept_property
+ - UMLS:has_supported_concept_relationship
+ - UMLS:may_be_qualified_by
+ rank: 1000
+ domain: entity
+ slot_uri: biolink:has_attribute
+ alias: has_attribute
+ owner: attribute
+ domain_of:
+ - entity
+ - attribute
+ - named thing
+ - organism taxon
+ - information content entity
+ - dataset
+ - physical entity
+ - activity
+ - procedure
+ - material sample
+ - biological entity
+ - gene
+ - genome
+ range: attribute
+ multivalued: true
+ deprecated:
+ name: deprecated
+ definition_uri: https://w3id.org/biolink/vocab/deprecated
+ description: A boolean flag indicating that an entity is no longer considered
+ current or valid.
+ from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
+ exact_mappings:
+ - oboInOwl:ObsoleteClass
+ rank: 1000
+ slot_uri: biolink:deprecated
+ alias: deprecated
+ owner: attribute
+ domain_of:
+ - entity
+ - attribute
+ - named thing
+ - organism taxon
+ - information content entity
+ - dataset
+ - physical entity
+ - activity
+ - procedure
+ - material sample
+ - biological entity
+ - gene
+ - genome
+ range: boolean
+ provided by:
+ name: provided by
+ definition_uri: https://w3id.org/biolink/vocab/provided_by
+ description: The value in this node property represents the knowledge provider
+ that created or assembled the node and all of its attributes. Used internally
+ to represent how a particular node made its way into a knowledge provider or
+ graph.
+ from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
+ rank: 1000
+ is_a: node property
+ domain: named thing
+ slot_uri: biolink:provided_by
+ alias: provided_by
+ owner: attribute
+ domain_of:
+ - named thing
+ - attribute
+ - organism taxon
+ - information content entity
+ - dataset
+ - physical entity
+ - activity
+ - procedure
+ - material sample
+ - biological entity
+ - gene
+ - genome
+ range: string
+ multivalued: true
+ xref:
+ name: xref
+ definition_uri: https://w3id.org/biolink/vocab/xref
+ description: A database cross reference or alternative identifier for a NamedThing
+ or edge between two NamedThings. This property should point to a database record
+ or webpage that supports the existence of the edge, or gives more detail about
+ the edge. This property can be used on a node or edge to provide multiple URIs
+ or CURIE cross references.
+ in_subset:
+ - translator_minimal
+ from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
+ aliases:
+ - dbxref
+ - Dbxref
+ - DbXref
+ - record_url
+ - source_record_urls
+ narrow_mappings:
+ - gff3:Dbxref
+ - gpi:DB_Xrefs
+ rank: 1000
+ domain: named thing
+ slot_uri: biolink:xref
+ alias: xref
+ owner: attribute
+ domain_of:
+ - named thing
+ - gene
+ - attribute
+ - organism taxon
+ - information content entity
+ - dataset
+ - physical entity
+ - activity
+ - procedure
+ - material sample
+ - biological entity
+ - genome
+ range: uriorcurie
+ multivalued: true
+ full name:
+ name: full name
+ definition_uri: https://w3id.org/biolink/vocab/full_name
+ description: a long-form human readable name for a thing
+ from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
+ rank: 1000
+ is_a: node property
+ domain: named thing
+ slot_uri: biolink:full_name
+ alias: full_name
+ owner: attribute
+ domain_of:
+ - named thing
+ - attribute
+ - organism taxon
+ - information content entity
+ - dataset
+ - physical entity
+ - activity
+ - procedure
+ - material sample
+ - biological entity
+ - gene
+ - genome
+ range: label type
+ synonym:
+ name: synonym
+ definition_uri: https://w3id.org/biolink/vocab/synonym
+ description: Alternate human-readable names for a thing
+ in_subset:
+ - translator_minimal
+ from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
+ aliases:
+ - alias
+ narrow_mappings:
+ - skos:altLabel
+ - gff3:Alias
+ - AGRKB:synonyms
+ - gpi:DB_Object_Synonyms
+ - HANCESTRO:0330
+ - IAO:0000136
+ - RXNORM:has_tradename
+ rank: 1000
+ is_a: node property
+ domain: named thing
+ slot_uri: biolink:synonym
+ alias: synonym
+ owner: attribute
+ domain_of:
+ - named thing
+ - attribute
+ - organism taxon
+ - information content entity
+ - dataset
+ - physical entity
+ - activity
+ - procedure
+ - material sample
+ - biological entity
+ - gene
+ - genome
+ range: label type
+ multivalued: true
+ attribute_name:
+ name: attribute_name
+ definition_uri: https://w3id.org/biolink/vocab/name
+ description: The human-readable 'attribute name' can be set to a string which
+ reflects its context of interpretation, e.g. SEPIO evidence/provenance/confidence
+ annotation or it can default to the name associated with the 'has attribute
+ type' slot ontology term.
+ in_subset:
+ - translator_minimal
+ - samples
+ from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
+ aliases:
+ - label
+ - display name
+ - title
+ mappings:
+ - rdfs:label
+ exact_mappings:
+ - gff3:Name
+ - gpi:DB_Object_Name
+ narrow_mappings:
+ - dct:title
+ - WIKIDATA_PROPERTY:P1476
+ rank: 1000
+ is_a: name
+ domain: attribute
+ slot_uri: rdfs:label
+ alias: name
+ owner: attribute
+ domain_of:
+ - attribute
+ is_usage_slot: true
+ usage_slot_name: name
+ range: label type
+ has attribute type:
+ name: has attribute type
+ definition_uri: https://w3id.org/biolink/vocab/has_attribute_type
+ description: connects an attribute to a class that describes it
+ in_subset:
+ - samples
+ from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
+ narrow_mappings:
+ - LOINC:has_modality_type
+ - LOINC:has_view_type
+ rank: 1000
+ domain: attribute
+ slot_uri: biolink:has_attribute_type
+ alias: has_attribute_type
+ owner: attribute
+ domain_of:
+ - attribute
+ range: ontology class
+ required: true
+ multivalued: false
+ has quantitative value:
+ name: has quantitative value
+ definition_uri: https://w3id.org/biolink/vocab/has_quantitative_value
+ description: connects an attribute to a value
+ in_subset:
+ - samples
+ from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
+ exact_mappings:
+ - qud:quantityValue
+ narrow_mappings:
+ - SNOMED:has_concentration_strength_numerator_value
+ - SNOMED:has_presentation_strength_denominator_value
+ - SNOMED:has_presentation_strength_numerator_value
+ rank: 1000
+ domain: attribute
+ slot_uri: biolink:has_quantitative_value
+ alias: has_quantitative_value
+ owner: attribute
+ domain_of:
+ - attribute
+ range: quantity value
+ multivalued: true
+ inlined: true
+ has qualitative value:
+ name: has qualitative value
+ definition_uri: https://w3id.org/biolink/vocab/has_qualitative_value
+ description: connects an attribute to a value
+ in_subset:
+ - samples
+ from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
+ rank: 1000
+ domain: attribute
+ slot_uri: biolink:has_qualitative_value
+ alias: has_qualitative_value
+ owner: attribute
+ domain_of:
+ - attribute
+ range: named thing
+ multivalued: false
+ iri:
+ name: iri
+ definition_uri: https://w3id.org/biolink/vocab/iri
+ description: An IRI for an entity. This is determined by the id using expansion
+ rules.
+ in_subset:
+ - translator_minimal
+ - samples
+ from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
+ exact_mappings:
+ - WIKIDATA_PROPERTY:P854
+ rank: 1000
+ slot_uri: biolink:iri
+ alias: iri
+ owner: attribute
+ domain_of:
+ - attribute
+ - entity
+ - named thing
+ - organism taxon
+ - information content entity
+ - dataset
+ - physical entity
+ - activity
+ - procedure
+ - material sample
+ - biological entity
+ - gene
+ - genome
+ range: iri type
+ name:
+ name: name
+ definition_uri: https://w3id.org/biolink/vocab/name
+ description: The human-readable 'attribute name' can be set to a string which
+ reflects its context of interpretation, e.g. SEPIO evidence/provenance/confidence
+ annotation or it can default to the name associated with the 'has attribute
+ type' slot ontology term.
+ in_subset:
+ - translator_minimal
+ - samples
+ from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
+ aliases:
+ - label
+ - display name
+ - title
+ mappings:
+ - rdfs:label
+ exact_mappings:
+ - gff3:Name
+ - gpi:DB_Object_Name
+ narrow_mappings:
+ - dct:title
+ - WIKIDATA_PROPERTY:P1476
+ rank: 1000
+ domain: entity
+ slot_uri: rdfs:label
+ alias: name
+ owner: attribute
+ domain_of:
+ - attribute
+ - entity
+ - macromolecular machine mixin
+ - named thing
+ - organism taxon
+ - information content entity
+ - dataset
+ - physical entity
+ - activity
+ - procedure
+ - material sample
+ - biological entity
+ - gene or gene product
+ - gene
+ - genome
+ range: label type
+class_uri: biolink:Attribute
+
+URI: AuthorityType
+| Value | +Meaning | +Description | +
|---|---|---|
| ENSEMBL | +None | ++ |
| NCBI | +None | ++ |
| Name | +Description | +
|---|---|
| authority | +The organization responsible for publishing the data | +
name: AuthorityType
+from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
+rank: 1000
+permissible_values:
+ ENSEMBL:
+ text: ENSEMBL
+ NCBI:
+ text: NCBI
+
+A collection of molecularly barcoded cells. Input will be either dissociated cell sample or enriched cell sample. Cell barcodes are only guaranteed to be unique within this one collection. One dissociated cell sample or enriched cell sample can lead to multiple barcoded cell samples. The sequences of the molecular barcodes are revealed during alignment of the resulting fastq files for the barcoded cell sample. The barcoded cell sample name and the cell level molecular barcode together uniquely identify a single cell.
+ +| Name | +Cardinality and Range | +Description | +Inheritance | +
|---|---|---|---|
| was_generated_by | +0..1 CellBarcoding |
+The barcoding process from which the barcoded cell sample is generated from | +direct | +
| was_derived_from | +* ProvEntity or DissociatedCellSample or EnrichedCellSample |
+The input dissociated or enriched cell sample(s) from which the barcoded cell... | +direct | +
| name | +0..1 LabelType |
+Name of a collection of barcoded cells | +direct | +
| number_of_expected_cells | +0..1 Integer |
+Expected number of cells/nuclei of a barcoded_cell_sample that will be barcod... | +direct | +
| id | +1 String |
+A unique identifier for an entity | +NamedThing, PhysicalEntity, MaterialSample, Entity | +
| iri | +0..1 IriType |
+An IRI for an entity | +NamedThing, PhysicalEntity, MaterialSample, Entity | +
| category | +* Uriorcurie |
+Name of the high level ontology class in which this entity is categorized | +NamedThing, PhysicalEntity, MaterialSample, Entity | +
| type | +* String |
++ | NamedThing, PhysicalEntity, MaterialSample, Entity | +
| description | +0..1 NarrativeText |
+a human-readable description of an entity | +NamedThing, PhysicalEntity, MaterialSample, Entity | +
| has_attribute | +* Attribute |
+connects any entity to an attribute | +NamedThing, PhysicalEntity, MaterialSample, Entity | +
| deprecated | +0..1 Boolean |
+A boolean flag indicating that an entity is no longer considered current or v... | +NamedThing, PhysicalEntity, MaterialSample, Entity | +
| provided_by | +* String |
+The value in this node property represents the knowledge provider that create... | +NamedThing, PhysicalEntity, MaterialSample | +
| xref | +* Uriorcurie |
+A database cross reference or alternative identifier for a NamedThing or edge... | +NamedThing, PhysicalEntity, MaterialSample | +
| full_name | +0..1 LabelType |
+a long-form human readable name for a thing | +NamedThing, PhysicalEntity, MaterialSample | +
| synonym | +* LabelType |
+Alternate human-readable names for a thing | +NamedThing, PhysicalEntity, MaterialSample | +
| used by | +used in | +type | +used | +
|---|---|---|---|
| AmplifiedCdna | +was_derived_from | +range | +BarcodedCellSample | +
| Library | +was_derived_from | +exactly_one_of[range] | +BarcodedCellSample | +
| CdnaAmplification | +used | +range | +BarcodedCellSample | +
| LibraryConstruction | +used | +exactly_one_of[range] | +BarcodedCellSample | +
| Mapping Type | +Mapped Value | +
|---|---|
| self | +bican:BarcodedCellSample | +
| native | +bican:BarcodedCellSample | +
| exact | +NIMP:Barcoded%20Cell%20Sample | +
name: BarcodedCellSample
+description: A collection of molecularly barcoded cells. Input will be either dissociated
+ cell sample or enriched cell sample. Cell barcodes are only guaranteed to be unique
+ within this one collection. One dissociated cell sample or enriched cell sample
+ can lead to multiple barcoded cell samples. The sequences of the molecular barcodes
+ are revealed during alignment of the resulting fastq files for the barcoded cell
+ sample. The barcoded cell sample name and the cell level molecular barcode together
+ uniquely identify a single cell.
+in_subset:
+- bican
+- library_generation
+from_schema: https://identifiers.org/brain-bican/library-generation-schema
+exact_mappings:
+- NIMP:Barcoded%20Cell%20Sample
+is_a: material sample
+mixins:
+- ProvEntity
+slots:
+- was_generated_by
+- was_derived_from
+- name
+slot_usage:
+ was_generated_by:
+ name: was_generated_by
+ description: The barcoding process from which the barcoded cell sample is generated
+ from.
+ range: CellBarcoding
+ was_derived_from:
+ name: was_derived_from
+ description: The input dissociated or enriched cell sample(s) from which the barcoded
+ cell sample was derived from.
+ exact_mappings:
+ - NIMP:has_parent
+ multivalued: true
+ exactly_one_of:
+ - range: DissociatedCellSample
+ - range: EnrichedCellSample
+ name:
+ name: name
+ description: Name of a collection of barcoded cells. Input will be either dissociated_cell_sample
+ or enriched_cell_sample. Cell barcodes are only guaranteed to be unique within
+ this one collection. One dissociated_cell_sample or enriched_cell_sample can
+ lead to multiple barcoded_cell_samples.
+ exact_mappings:
+ - NIMP:PD-XEMDJF38
+ slot_uri: bican:4c0e6380-e53f-4173-a474-d41e836fefe3
+ category:
+ name: category
+ pattern: ^bican:[A-Z][A-Za-z]+$
+attributes:
+ number_of_expected_cells:
+ name: number_of_expected_cells
+ local_names:
+ NIMP:
+ local_name_source: NIMP
+ local_name_value: barcoded_cell_sample_number_of_expected_cells
+ description: Expected number of cells/nuclei of a barcoded_cell_sample that will
+ be barcoded and available for sequencing. This is a derived number from 'Barcoded
+ cell input quantity count' that is dependent on the "capture rate" of the barcoding
+ method. It is usually a calculated fraction of the 'Barcoded cell input quantity
+ count' going into the barcoding method.
+ in_subset:
+ - analysis
+ from_schema: https://identifiers.org/brain-bican/library-generation-schema
+ exact_mappings:
+ - NIMP:PD-ONONEV39
+ rank: 1000
+ slot_uri: bican:f10e928d-5a2b-4943-af18-d8fe5d05528d
+ alias: expected cell capture
+ domain_of:
+ - BarcodedCellSample
+ range: integer
+
+name: BarcodedCellSample
+description: A collection of molecularly barcoded cells. Input will be either dissociated
+ cell sample or enriched cell sample. Cell barcodes are only guaranteed to be unique
+ within this one collection. One dissociated cell sample or enriched cell sample
+ can lead to multiple barcoded cell samples. The sequences of the molecular barcodes
+ are revealed during alignment of the resulting fastq files for the barcoded cell
+ sample. The barcoded cell sample name and the cell level molecular barcode together
+ uniquely identify a single cell.
+in_subset:
+- bican
+- library_generation
+from_schema: https://identifiers.org/brain-bican/library-generation-schema
+exact_mappings:
+- NIMP:Barcoded%20Cell%20Sample
+is_a: material sample
+mixins:
+- ProvEntity
+slot_usage:
+ was_generated_by:
+ name: was_generated_by
+ description: The barcoding process from which the barcoded cell sample is generated
+ from.
+ range: CellBarcoding
+ was_derived_from:
+ name: was_derived_from
+ description: The input dissociated or enriched cell sample(s) from which the barcoded
+ cell sample was derived from.
+ exact_mappings:
+ - NIMP:has_parent
+ multivalued: true
+ exactly_one_of:
+ - range: DissociatedCellSample
+ - range: EnrichedCellSample
+ name:
+ name: name
+ description: Name of a collection of barcoded cells. Input will be either dissociated_cell_sample
+ or enriched_cell_sample. Cell barcodes are only guaranteed to be unique within
+ this one collection. One dissociated_cell_sample or enriched_cell_sample can
+ lead to multiple barcoded_cell_samples.
+ exact_mappings:
+ - NIMP:PD-XEMDJF38
+ slot_uri: bican:4c0e6380-e53f-4173-a474-d41e836fefe3
+ category:
+ name: category
+ pattern: ^bican:[A-Z][A-Za-z]+$
+attributes:
+ number_of_expected_cells:
+ name: number_of_expected_cells
+ local_names:
+ NIMP:
+ local_name_source: NIMP
+ local_name_value: barcoded_cell_sample_number_of_expected_cells
+ description: Expected number of cells/nuclei of a barcoded_cell_sample that will
+ be barcoded and available for sequencing. This is a derived number from 'Barcoded
+ cell input quantity count' that is dependent on the "capture rate" of the barcoding
+ method. It is usually a calculated fraction of the 'Barcoded cell input quantity
+ count' going into the barcoding method.
+ in_subset:
+ - analysis
+ from_schema: https://identifiers.org/brain-bican/library-generation-schema
+ exact_mappings:
+ - NIMP:PD-ONONEV39
+ rank: 1000
+ slot_uri: bican:f10e928d-5a2b-4943-af18-d8fe5d05528d
+ alias: expected cell capture
+ owner: BarcodedCellSample
+ domain_of:
+ - BarcodedCellSample
+ range: integer
+ was_generated_by:
+ name: was_generated_by
+ description: The barcoding process from which the barcoded cell sample is generated
+ from.
+ from_schema: https://identifiers.org/brain-bican/library-generation-schema
+ rank: 1000
+ slot_uri: prov:wasGeneratedBy
+ alias: was_generated_by
+ owner: BarcodedCellSample
+ domain_of:
+ - TissueSample
+ - DissociatedCellSample
+ - EnrichedCellSample
+ - BarcodedCellSample
+ - AmplifiedCdna
+ - Library
+ - LibraryPool
+ - DissectionRoiPolygon
+ - ProvEntity
+ range: CellBarcoding
+ was_derived_from:
+ name: was_derived_from
+ description: The input dissociated or enriched cell sample(s) from which the barcoded
+ cell sample was derived from.
+ from_schema: https://identifiers.org/brain-bican/library-generation-schema
+ exact_mappings:
+ - NIMP:has_parent
+ rank: 1000
+ slot_uri: prov:wasDerivedFrom
+ alias: was_derived_from
+ owner: BarcodedCellSample
+ domain_of:
+ - BrainSlab
+ - TissueSample
+ - DissociatedCellSample
+ - EnrichedCellSample
+ - BarcodedCellSample
+ - AmplifiedCdna
+ - Library
+ - LibraryAliquot
+ - LibraryPool
+ - ProvEntity
+ range: ProvEntity
+ multivalued: true
+ exactly_one_of:
+ - range: DissociatedCellSample
+ - range: EnrichedCellSample
+ name:
+ name: name
+ definition_uri: https://w3id.org/biolink/vocab/name
+ description: Name of a collection of barcoded cells. Input will be either dissociated_cell_sample
+ or enriched_cell_sample. Cell barcodes are only guaranteed to be unique within
+ this one collection. One dissociated_cell_sample or enriched_cell_sample can
+ lead to multiple barcoded_cell_samples.
+ in_subset:
+ - translator_minimal
+ - samples
+ from_schema: https://identifiers.org/brain-bican/library-generation-schema
+ aliases:
+ - label
+ - display name
+ - title
+ mappings:
+ - rdfs:label
+ exact_mappings:
+ - NIMP:PD-XEMDJF38
+ narrow_mappings:
+ - dct:title
+ - WIKIDATA_PROPERTY:P1476
+ rank: 1000
+ domain: entity
+ slot_uri: bican:4c0e6380-e53f-4173-a474-d41e836fefe3
+ alias: name
+ owner: BarcodedCellSample
+ domain_of:
+ - attribute
+ - entity
+ - macromolecular machine mixin
+ - Donor
+ - BrainSlab
+ - TissueSample
+ - DissociatedCellSample
+ - EnrichedCellSample
+ - BarcodedCellSample
+ - AmplifiedCdna
+ - Library
+ - LibraryAliquot
+ - LibraryPool
+ - DissectionRoiPolygon
+ - named thing
+ - organism taxon
+ - information content entity
+ - dataset
+ - physical entity
+ - activity
+ - procedure
+ - material sample
+ - biological entity
+ - gene or gene product
+ - gene
+ - genome
+ range: label type
+ id:
+ name: id
+ definition_uri: https://w3id.org/biolink/vocab/id
+ description: A unique identifier for an entity. Must be either a CURIE shorthand
+ for a URI or a complete URI
+ in_subset:
+ - translator_minimal
+ from_schema: https://identifiers.org/brain-bican/library-generation-schema
+ exact_mappings:
+ - AGRKB:primaryId
+ - gff3:ID
+ - gpi:DB_Object_ID
+ rank: 1000
+ domain: entity
+ slot_uri: biolink:id
+ identifier: true
+ alias: id
+ owner: BarcodedCellSample
+ domain_of:
+ - ontology class
+ - entity
+ - attribute
+ - named thing
+ - taxonomic rank
+ - organism taxon
+ - information content entity
+ - dataset
+ - physical entity
+ - activity
+ - procedure
+ - material sample
+ - biological entity
+ - gene
+ - genome
+ range: string
+ required: true
+ iri:
+ name: iri
+ definition_uri: https://w3id.org/biolink/vocab/iri
+ description: An IRI for an entity. This is determined by the id using expansion
+ rules.
+ in_subset:
+ - translator_minimal
+ - samples
+ from_schema: https://identifiers.org/brain-bican/library-generation-schema
+ exact_mappings:
+ - WIKIDATA_PROPERTY:P854
+ rank: 1000
+ slot_uri: biolink:iri
+ alias: iri
+ owner: BarcodedCellSample
+ domain_of:
+ - attribute
+ - entity
+ - named thing
+ - organism taxon
+ - information content entity
+ - dataset
+ - physical entity
+ - activity
+ - procedure
+ - material sample
+ - biological entity
+ - gene
+ - genome
+ range: iri type
+ category:
+ name: category
+ definition_uri: https://w3id.org/biolink/vocab/category
+ description: Name of the high level ontology class in which this entity is categorized.
+ Corresponds to the label for the biolink entity type class. In a neo4j database
+ this MAY correspond to the neo4j label tag. In an RDF database it should be
+ a biolink model class URI. This field is multi-valued. It should include values
+ for ancestors of the biolink class; for example, a protein such as Shh would
+ have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`.
+ In an RDF database, nodes will typically have an rdf:type triples. This can
+ be to the most specific biolink class, or potentially to a class more specific
+ than something in biolink. For example, a sequence feature `f` may have a rdf:type
+ assertion to a SO class such as TF_binding_site, which is more specific than
+ anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity,
+ biolink:NamedThing}
+ in_subset:
+ - translator_minimal
+ from_schema: https://identifiers.org/brain-bican/library-generation-schema
+ rank: 1000
+ is_a: type
+ domain: entity
+ slot_uri: biolink:category
+ designates_type: true
+ alias: category
+ owner: BarcodedCellSample
+ domain_of:
+ - entity
+ - attribute
+ - named thing
+ - organism taxon
+ - information content entity
+ - dataset
+ - physical entity
+ - activity
+ - procedure
+ - material sample
+ - biological entity
+ - gene
+ - genome
+ is_class_field: true
+ range: uriorcurie
+ multivalued: true
+ pattern: ^bican:[A-Z][A-Za-z]+$
+ type:
+ name: type
+ definition_uri: https://w3id.org/biolink/vocab/type
+ from_schema: https://identifiers.org/brain-bican/library-generation-schema
+ mappings:
+ - rdf:type
+ exact_mappings:
+ - gff3:type
+ - gpi:DB_Object_Type
+ rank: 1000
+ domain: entity
+ slot_uri: rdf:type
+ alias: type
+ owner: BarcodedCellSample
+ domain_of:
+ - entity
+ - attribute
+ - named thing
+ - organism taxon
+ - information content entity
+ - dataset
+ - physical entity
+ - activity
+ - procedure
+ - material sample
+ - biological entity
+ - gene
+ - genome
+ range: string
+ multivalued: true
+ description:
+ name: description
+ definition_uri: https://w3id.org/biolink/vocab/description
+ description: a human-readable description of an entity
+ in_subset:
+ - translator_minimal
+ from_schema: https://identifiers.org/brain-bican/library-generation-schema
+ aliases:
+ - definition
+ mappings:
+ - dct:description
+ exact_mappings:
+ - IAO:0000115
+ - skos:definitions
+ narrow_mappings:
+ - gff3:Description
+ rank: 1000
+ slot_uri: dct:description
+ alias: description
+ owner: BarcodedCellSample
+ domain_of:
+ - entity
+ - attribute
+ - named thing
+ - organism taxon
+ - information content entity
+ - dataset
+ - physical entity
+ - activity
+ - procedure
+ - material sample
+ - biological entity
+ - gene
+ - genome
+ range: narrative text
+ has attribute:
+ name: has attribute
+ definition_uri: https://w3id.org/biolink/vocab/has_attribute
+ description: connects any entity to an attribute
+ in_subset:
+ - samples
+ from_schema: https://identifiers.org/brain-bican/library-generation-schema
+ exact_mappings:
+ - SIO:000008
+ close_mappings:
+ - OBI:0001927
+ narrow_mappings:
+ - OBAN:association_has_subject_property
+ - OBAN:association_has_object_property
+ - CPT:has_possibly_included_panel_element
+ - DRUGBANK:category
+ - EFO:is_executed_in
+ - HANCESTRO:0301
+ - LOINC:has_action_guidance
+ - LOINC:has_adjustment
+ - LOINC:has_aggregation_view
+ - LOINC:has_approach_guidance
+ - LOINC:has_divisor
+ - LOINC:has_exam
+ - LOINC:has_method
+ - LOINC:has_modality_subtype
+ - LOINC:has_object_guidance
+ - LOINC:has_scale
+ - LOINC:has_suffix
+ - LOINC:has_time_aspect
+ - LOINC:has_time_modifier
+ - LOINC:has_timing_of
+ - NCIT:R88
+ - NCIT:eo_disease_has_property_or_attribute
+ - NCIT:has_data_element
+ - NCIT:has_pharmaceutical_administration_method
+ - NCIT:has_pharmaceutical_basic_dose_form
+ - NCIT:has_pharmaceutical_intended_site
+ - NCIT:has_pharmaceutical_release_characteristics
+ - NCIT:has_pharmaceutical_state_of_matter
+ - NCIT:has_pharmaceutical_transformation
+ - NCIT:is_qualified_by
+ - NCIT:qualifier_applies_to
+ - NCIT:role_has_domain
+ - NCIT:role_has_range
+ - INO:0000154
+ - HANCESTRO:0308
+ - OMIM:has_inheritance_type
+ - orphanet:C016
+ - orphanet:C017
+ - RO:0000053
+ - RO:0000086
+ - RO:0000087
+ - SNOMED:has_access
+ - SNOMED:has_clinical_course
+ - SNOMED:has_count_of_base_of_active_ingredient
+ - SNOMED:has_dose_form_administration_method
+ - SNOMED:has_dose_form_release_characteristic
+ - SNOMED:has_dose_form_transformation
+ - SNOMED:has_finding_context
+ - SNOMED:has_finding_informer
+ - SNOMED:has_inherent_attribute
+ - SNOMED:has_intent
+ - SNOMED:has_interpretation
+ - SNOMED:has_laterality
+ - SNOMED:has_measurement_method
+ - SNOMED:has_method
+ - SNOMED:has_priority
+ - SNOMED:has_procedure_context
+ - SNOMED:has_process_duration
+ - SNOMED:has_property
+ - SNOMED:has_revision_status
+ - SNOMED:has_scale_type
+ - SNOMED:has_severity
+ - SNOMED:has_specimen
+ - SNOMED:has_state_of_matter
+ - SNOMED:has_subject_relationship_context
+ - SNOMED:has_surgical_approach
+ - SNOMED:has_technique
+ - SNOMED:has_temporal_context
+ - SNOMED:has_time_aspect
+ - SNOMED:has_units
+ - UMLS:has_structural_class
+ - UMLS:has_supported_concept_property
+ - UMLS:has_supported_concept_relationship
+ - UMLS:may_be_qualified_by
+ rank: 1000
+ domain: entity
+ slot_uri: biolink:has_attribute
+ alias: has_attribute
+ owner: BarcodedCellSample
+ domain_of:
+ - entity
+ - attribute
+ - named thing
+ - organism taxon
+ - information content entity
+ - dataset
+ - physical entity
+ - activity
+ - procedure
+ - material sample
+ - biological entity
+ - gene
+ - genome
+ range: attribute
+ multivalued: true
+ deprecated:
+ name: deprecated
+ definition_uri: https://w3id.org/biolink/vocab/deprecated
+ description: A boolean flag indicating that an entity is no longer considered
+ current or valid.
+ from_schema: https://identifiers.org/brain-bican/library-generation-schema
+ exact_mappings:
+ - oboInOwl:ObsoleteClass
+ rank: 1000
+ slot_uri: biolink:deprecated
+ alias: deprecated
+ owner: BarcodedCellSample
+ domain_of:
+ - entity
+ - attribute
+ - named thing
+ - organism taxon
+ - information content entity
+ - dataset
+ - physical entity
+ - activity
+ - procedure
+ - material sample
+ - biological entity
+ - gene
+ - genome
+ range: boolean
+ provided by:
+ name: provided by
+ definition_uri: https://w3id.org/biolink/vocab/provided_by
+ description: The value in this node property represents the knowledge provider
+ that created or assembled the node and all of its attributes. Used internally
+ to represent how a particular node made its way into a knowledge provider or
+ graph.
+ from_schema: https://identifiers.org/brain-bican/library-generation-schema
+ rank: 1000
+ is_a: node property
+ domain: named thing
+ slot_uri: biolink:provided_by
+ alias: provided_by
+ owner: BarcodedCellSample
+ domain_of:
+ - named thing
+ - attribute
+ - organism taxon
+ - information content entity
+ - dataset
+ - physical entity
+ - activity
+ - procedure
+ - material sample
+ - biological entity
+ - gene
+ - genome
+ range: string
+ multivalued: true
+ xref:
+ name: xref
+ definition_uri: https://w3id.org/biolink/vocab/xref
+ description: A database cross reference or alternative identifier for a NamedThing
+ or edge between two NamedThings. This property should point to a database record
+ or webpage that supports the existence of the edge, or gives more detail about
+ the edge. This property can be used on a node or edge to provide multiple URIs
+ or CURIE cross references.
+ in_subset:
+ - translator_minimal
+ from_schema: https://identifiers.org/brain-bican/library-generation-schema
+ aliases:
+ - dbxref
+ - Dbxref
+ - DbXref
+ - record_url
+ - source_record_urls
+ narrow_mappings:
+ - gff3:Dbxref
+ - gpi:DB_Xrefs
+ rank: 1000
+ domain: named thing
+ slot_uri: biolink:xref
+ alias: xref
+ owner: BarcodedCellSample
+ domain_of:
+ - named thing
+ - gene
+ - attribute
+ - organism taxon
+ - information content entity
+ - dataset
+ - physical entity
+ - activity
+ - procedure
+ - material sample
+ - biological entity
+ - genome
+ range: uriorcurie
+ multivalued: true
+ full name:
+ name: full name
+ definition_uri: https://w3id.org/biolink/vocab/full_name
+ description: a long-form human readable name for a thing
+ from_schema: https://identifiers.org/brain-bican/library-generation-schema
+ rank: 1000
+ is_a: node property
+ domain: named thing
+ slot_uri: biolink:full_name
+ alias: full_name
+ owner: BarcodedCellSample
+ domain_of:
+ - named thing
+ - attribute
+ - organism taxon
+ - information content entity
+ - dataset
+ - physical entity
+ - activity
+ - procedure
+ - material sample
+ - biological entity
+ - gene
+ - genome
+ range: label type
+ synonym:
+ name: synonym
+ definition_uri: https://w3id.org/biolink/vocab/synonym
+ description: Alternate human-readable names for a thing
+ in_subset:
+ - translator_minimal
+ from_schema: https://identifiers.org/brain-bican/library-generation-schema
+ aliases:
+ - alias
+ narrow_mappings:
+ - skos:altLabel
+ - gff3:Alias
+ - AGRKB:synonyms
+ - gpi:DB_Object_Synonyms
+ - HANCESTRO:0330
+ - IAO:0000136
+ - RXNORM:has_tradename
+ rank: 1000
+ is_a: node property
+ domain: named thing
+ slot_uri: biolink:synonym
+ alias: synonym
+ owner: BarcodedCellSample
+ domain_of:
+ - named thing
+ - attribute
+ - organism taxon
+ - information content entity
+ - dataset
+ - physical entity
+ - activity
+ - procedure
+ - material sample
+ - biological entity
+ - gene
+ - genome
+ range: label type
+ multivalued: true
+
+URI: BarcodedCellSampleTechnique
+| Value | +Meaning | +Description | +
|---|---|---|
| Multiome | +NIMP:PD-TDTDDF25 | +Multiome | +
| ATACOnly | +NIMP:PD-TDTDDF25 | +ATACOnly | +
| GEXOnly | +NIMP:PD-TDTDDF25 | +GEXOnly | +
| snm3C-seq | +NIMP:PD-TDTDDF25 | +snm3C-seq | +
| Name | +Description | +
|---|---|
| method | +Standardized nomenclature to describe the general barcoding method used | +
name: barcoded_cell_sample_technique
+from_schema: https://identifiers.org/brain-bican/library-generation-schema
+rank: 1000
+permissible_values:
+ Multiome:
+ text: Multiome
+ description: Multiome
+ meaning: NIMP:PD-TDTDDF25
+ ATACOnly:
+ text: ATACOnly
+ description: ATACOnly
+ meaning: NIMP:PD-TDTDDF25
+ GEXOnly:
+ text: GEXOnly
+ description: GEXOnly
+ meaning: NIMP:PD-TDTDDF25
+ snm3C-seq:
+ text: snm3C-seq
+ description: snm3C-seq
+ meaning: NIMP:PD-TDTDDF25
+
+A subset of classes that are associated with BICAN.
+URI: Bican
+| Class | +Description | +
|---|---|
| AmplifiedCdna | +A collection of cDNA molecules derived and amplified from an input barcoded c... | +
| BarcodedCellSample | +A collection of molecularly barcoded cells | +
| BrainSlab | +A thick flat piece of brain tissue obtained by slicing a whole brain, brain h... | +
| CdnaAmplification | +The process of creating a collection of cDNA molecules derived and amplified ... | +
| CellBarcoding | +The process of adding a molecular barcode to individual cells in a sample | +
| CellDissociation | +The process of generating dissociated cells from an input tissue sample | +
| CellEnrichment | +The process of enriching a dissociated cell sample by including or excluding ... | +
| DissectionRoiDelineation | +The process of outlining a region of interest on a brain slab image to guide ... | +
| DissectionRoiPolygon | +A polygon annotated on a brain slab image delineating a region of interest (R... | +
| DissociatedCellSample | +A collection of dissociated cells or nuclei derived from dissociation of a ti... | +
| EnrichedCellSample | +A collection of enriched cells or nuclei after enrichment process, usually vi... | +
| EnrichedCellSampleSplitting | +The process of splitting an enriched cell sample into several portions | +
| Library | +A collection of fragmented and barcode-indexed DNA molecules for sequencing | +
| LibraryAliquot | +One library in the library pool | +
| LibraryConstruction | +The process of constructing a library from input material (such as amplified ... | +
| LibraryPool | +A library pool is made up of library aliquots from multiple libraries | +
| LibraryPooling | +The process of constructing of a libray pool by combining library aliquots fr... | +
| TissueDissection | +The process of dissecting a tissue sample from a brain slab guided by a disse... | +
| TissueSample | +The final intact piece of tissue before cell or nuclei prep | +
URI: BioType
+| Value | +Meaning | +Description | +
|---|---|---|
| protein_coding | +None | ++ |
| noncoding | +None | ++ |
name: BioType
+from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
+rank: 1000
+permissible_values:
+ protein_coding:
+ text: protein_coding
+ noncoding:
+ text: noncoding
+
+| Name | +Cardinality and Range | +Description | +Inheritance | +
|---|---|---|---|
| id | +1 String |
+A unique identifier for an entity | +direct | +
| iri | +0..1 IriType |
+An IRI for an entity | +direct | +
| category | +* Uriorcurie |
+Name of the high level ontology class in which this entity is categorized | +direct | +
| type | +* String |
++ | direct | +
| name | +0..1 LabelType |
+A human-readable name for an attribute or entity | +direct | +
| description | +0..1 NarrativeText |
+a human-readable description of an entity | +direct | +
| has_attribute | +* Attribute |
+connects any entity to an attribute | +direct | +
| deprecated | +0..1 Boolean |
+A boolean flag indicating that an entity is no longer considered current or v... | +direct | +
| provided_by | +* String |
+The value in this node property represents the knowledge provider that create... | +direct | +
| xref | +* Uriorcurie |
+A database cross reference or alternative identifier for a NamedThing or edge... | +direct | +
| full_name | +0..1 LabelType |
+a long-form human readable name for a thing | +direct | +
| synonym | +* LabelType |
+Alternate human-readable names for a thing | +direct | +
| in_taxon | +* OrganismTaxon |
+connects an entity to its taxonomic classification | +direct | +
| in_taxon_label | +0..1 LabelType |
+The human readable scientific name for the taxon of the entity | +direct | +
| Mapping Type | +Mapped Value | +
|---|---|
| self | +biolink:BiologicalEntity | +
| native | +bican:BiologicalEntity | +
| narrow | +WIKIDATA:Q28845870, STY:T050, SIO:010046, STY:T129 | +
name: biological entity
+definition_uri: https://w3id.org/biolink/vocab/BiologicalEntity
+from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
+aliases:
+- bioentity
+narrow_mappings:
+- WIKIDATA:Q28845870
+- STY:T050
+- SIO:010046
+- STY:T129
+is_a: named thing
+abstract: true
+mixins:
+- thing with taxon
+slots:
+- id
+- iri
+- category
+- type
+- name
+- description
+- has attribute
+- deprecated
+- provided by
+- xref
+- full name
+- synonym
+- in taxon
+- in taxon label
+class_uri: biolink:BiologicalEntity
+
+name: biological entity
+definition_uri: https://w3id.org/biolink/vocab/BiologicalEntity
+from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
+aliases:
+- bioentity
+narrow_mappings:
+- WIKIDATA:Q28845870
+- STY:T050
+- SIO:010046
+- STY:T129
+is_a: named thing
+abstract: true
+mixins:
+- thing with taxon
+attributes:
+ id:
+ name: id
+ definition_uri: https://w3id.org/biolink/vocab/id
+ description: A unique identifier for an entity. Must be either a CURIE shorthand
+ for a URI or a complete URI
+ in_subset:
+ - translator_minimal
+ from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
+ exact_mappings:
+ - AGRKB:primaryId
+ - gff3:ID
+ - gpi:DB_Object_ID
+ rank: 1000
+ domain: entity
+ slot_uri: biolink:id
+ identifier: true
+ alias: id
+ owner: biological entity
+ domain_of:
+ - ontology class
+ - entity
+ - attribute
+ - named thing
+ - taxonomic rank
+ - organism taxon
+ - information content entity
+ - dataset
+ - physical entity
+ - activity
+ - procedure
+ - material sample
+ - biological entity
+ - gene
+ - genome
+ range: string
+ required: true
+ iri:
+ name: iri
+ definition_uri: https://w3id.org/biolink/vocab/iri
+ description: An IRI for an entity. This is determined by the id using expansion
+ rules.
+ in_subset:
+ - translator_minimal
+ - samples
+ from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
+ exact_mappings:
+ - WIKIDATA_PROPERTY:P854
+ rank: 1000
+ slot_uri: biolink:iri
+ alias: iri
+ owner: biological entity
+ domain_of:
+ - attribute
+ - entity
+ - named thing
+ - organism taxon
+ - information content entity
+ - dataset
+ - physical entity
+ - activity
+ - procedure
+ - material sample
+ - biological entity
+ - gene
+ - genome
+ range: iri type
+ category:
+ name: category
+ definition_uri: https://w3id.org/biolink/vocab/category
+ description: Name of the high level ontology class in which this entity is categorized.
+ Corresponds to the label for the biolink entity type class. In a neo4j database
+ this MAY correspond to the neo4j label tag. In an RDF database it should be
+ a biolink model class URI. This field is multi-valued. It should include values
+ for ancestors of the biolink class; for example, a protein such as Shh would
+ have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`.
+ In an RDF database, nodes will typically have an rdf:type triples. This can
+ be to the most specific biolink class, or potentially to a class more specific
+ than something in biolink. For example, a sequence feature `f` may have a rdf:type
+ assertion to a SO class such as TF_binding_site, which is more specific than
+ anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity,
+ biolink:NamedThing}
+ in_subset:
+ - translator_minimal
+ from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
+ rank: 1000
+ is_a: type
+ domain: entity
+ slot_uri: biolink:category
+ designates_type: true
+ alias: category
+ owner: biological entity
+ domain_of:
+ - entity
+ - attribute
+ - named thing
+ - organism taxon
+ - information content entity
+ - dataset
+ - physical entity
+ - activity
+ - procedure
+ - material sample
+ - biological entity
+ - gene
+ - genome
+ is_class_field: true
+ range: uriorcurie
+ multivalued: true
+ type:
+ name: type
+ definition_uri: https://w3id.org/biolink/vocab/type
+ from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
+ mappings:
+ - rdf:type
+ exact_mappings:
+ - gff3:type
+ - gpi:DB_Object_Type
+ rank: 1000
+ domain: entity
+ slot_uri: rdf:type
+ alias: type
+ owner: biological entity
+ domain_of:
+ - entity
+ - attribute
+ - named thing
+ - organism taxon
+ - information content entity
+ - dataset
+ - physical entity
+ - activity
+ - procedure
+ - material sample
+ - biological entity
+ - gene
+ - genome
+ range: string
+ multivalued: true
+ name:
+ name: name
+ definition_uri: https://w3id.org/biolink/vocab/name
+ description: A human-readable name for an attribute or entity.
+ in_subset:
+ - translator_minimal
+ - samples
+ from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
+ aliases:
+ - label
+ - display name
+ - title
+ mappings:
+ - rdfs:label
+ exact_mappings:
+ - gff3:Name
+ - gpi:DB_Object_Name
+ narrow_mappings:
+ - dct:title
+ - WIKIDATA_PROPERTY:P1476
+ rank: 1000
+ domain: entity
+ slot_uri: rdfs:label
+ alias: name
+ owner: biological entity
+ domain_of:
+ - attribute
+ - entity
+ - macromolecular machine mixin
+ - named thing
+ - organism taxon
+ - information content entity
+ - dataset
+ - physical entity
+ - activity
+ - procedure
+ - material sample
+ - biological entity
+ - gene or gene product
+ - gene
+ - genome
+ range: label type
+ description:
+ name: description
+ definition_uri: https://w3id.org/biolink/vocab/description
+ description: a human-readable description of an entity
+ in_subset:
+ - translator_minimal
+ from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
+ aliases:
+ - definition
+ mappings:
+ - dct:description
+ exact_mappings:
+ - IAO:0000115
+ - skos:definitions
+ narrow_mappings:
+ - gff3:Description
+ rank: 1000
+ slot_uri: dct:description
+ alias: description
+ owner: biological entity
+ domain_of:
+ - entity
+ - attribute
+ - named thing
+ - organism taxon
+ - information content entity
+ - dataset
+ - physical entity
+ - activity
+ - procedure
+ - material sample
+ - biological entity
+ - gene
+ - genome
+ range: narrative text
+ has attribute:
+ name: has attribute
+ definition_uri: https://w3id.org/biolink/vocab/has_attribute
+ description: connects any entity to an attribute
+ in_subset:
+ - samples
+ from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
+ exact_mappings:
+ - SIO:000008
+ close_mappings:
+ - OBI:0001927
+ narrow_mappings:
+ - OBAN:association_has_subject_property
+ - OBAN:association_has_object_property
+ - CPT:has_possibly_included_panel_element
+ - DRUGBANK:category
+ - EFO:is_executed_in
+ - HANCESTRO:0301
+ - LOINC:has_action_guidance
+ - LOINC:has_adjustment
+ - LOINC:has_aggregation_view
+ - LOINC:has_approach_guidance
+ - LOINC:has_divisor
+ - LOINC:has_exam
+ - LOINC:has_method
+ - LOINC:has_modality_subtype
+ - LOINC:has_object_guidance
+ - LOINC:has_scale
+ - LOINC:has_suffix
+ - LOINC:has_time_aspect
+ - LOINC:has_time_modifier
+ - LOINC:has_timing_of
+ - NCIT:R88
+ - NCIT:eo_disease_has_property_or_attribute
+ - NCIT:has_data_element
+ - NCIT:has_pharmaceutical_administration_method
+ - NCIT:has_pharmaceutical_basic_dose_form
+ - NCIT:has_pharmaceutical_intended_site
+ - NCIT:has_pharmaceutical_release_characteristics
+ - NCIT:has_pharmaceutical_state_of_matter
+ - NCIT:has_pharmaceutical_transformation
+ - NCIT:is_qualified_by
+ - NCIT:qualifier_applies_to
+ - NCIT:role_has_domain
+ - NCIT:role_has_range
+ - INO:0000154
+ - HANCESTRO:0308
+ - OMIM:has_inheritance_type
+ - orphanet:C016
+ - orphanet:C017
+ - RO:0000053
+ - RO:0000086
+ - RO:0000087
+ - SNOMED:has_access
+ - SNOMED:has_clinical_course
+ - SNOMED:has_count_of_base_of_active_ingredient
+ - SNOMED:has_dose_form_administration_method
+ - SNOMED:has_dose_form_release_characteristic
+ - SNOMED:has_dose_form_transformation
+ - SNOMED:has_finding_context
+ - SNOMED:has_finding_informer
+ - SNOMED:has_inherent_attribute
+ - SNOMED:has_intent
+ - SNOMED:has_interpretation
+ - SNOMED:has_laterality
+ - SNOMED:has_measurement_method
+ - SNOMED:has_method
+ - SNOMED:has_priority
+ - SNOMED:has_procedure_context
+ - SNOMED:has_process_duration
+ - SNOMED:has_property
+ - SNOMED:has_revision_status
+ - SNOMED:has_scale_type
+ - SNOMED:has_severity
+ - SNOMED:has_specimen
+ - SNOMED:has_state_of_matter
+ - SNOMED:has_subject_relationship_context
+ - SNOMED:has_surgical_approach
+ - SNOMED:has_technique
+ - SNOMED:has_temporal_context
+ - SNOMED:has_time_aspect
+ - SNOMED:has_units
+ - UMLS:has_structural_class
+ - UMLS:has_supported_concept_property
+ - UMLS:has_supported_concept_relationship
+ - UMLS:may_be_qualified_by
+ rank: 1000
+ domain: entity
+ slot_uri: biolink:has_attribute
+ alias: has_attribute
+ owner: biological entity
+ domain_of:
+ - entity
+ - attribute
+ - named thing
+ - organism taxon
+ - information content entity
+ - dataset
+ - physical entity
+ - activity
+ - procedure
+ - material sample
+ - biological entity
+ - gene
+ - genome
+ range: attribute
+ multivalued: true
+ deprecated:
+ name: deprecated
+ definition_uri: https://w3id.org/biolink/vocab/deprecated
+ description: A boolean flag indicating that an entity is no longer considered
+ current or valid.
+ from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
+ exact_mappings:
+ - oboInOwl:ObsoleteClass
+ rank: 1000
+ slot_uri: biolink:deprecated
+ alias: deprecated
+ owner: biological entity
+ domain_of:
+ - entity
+ - attribute
+ - named thing
+ - organism taxon
+ - information content entity
+ - dataset
+ - physical entity
+ - activity
+ - procedure
+ - material sample
+ - biological entity
+ - gene
+ - genome
+ range: boolean
+ provided by:
+ name: provided by
+ definition_uri: https://w3id.org/biolink/vocab/provided_by
+ description: The value in this node property represents the knowledge provider
+ that created or assembled the node and all of its attributes. Used internally
+ to represent how a particular node made its way into a knowledge provider or
+ graph.
+ from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
+ rank: 1000
+ is_a: node property
+ domain: named thing
+ slot_uri: biolink:provided_by
+ alias: provided_by
+ owner: biological entity
+ domain_of:
+ - named thing
+ - attribute
+ - organism taxon
+ - information content entity
+ - dataset
+ - physical entity
+ - activity
+ - procedure
+ - material sample
+ - biological entity
+ - gene
+ - genome
+ range: string
+ multivalued: true
+ xref:
+ name: xref
+ definition_uri: https://w3id.org/biolink/vocab/xref
+ description: A database cross reference or alternative identifier for a NamedThing
+ or edge between two NamedThings. This property should point to a database record
+ or webpage that supports the existence of the edge, or gives more detail about
+ the edge. This property can be used on a node or edge to provide multiple URIs
+ or CURIE cross references.
+ in_subset:
+ - translator_minimal
+ from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
+ aliases:
+ - dbxref
+ - Dbxref
+ - DbXref
+ - record_url
+ - source_record_urls
+ narrow_mappings:
+ - gff3:Dbxref
+ - gpi:DB_Xrefs
+ rank: 1000
+ domain: named thing
+ slot_uri: biolink:xref
+ alias: xref
+ owner: biological entity
+ domain_of:
+ - named thing
+ - gene
+ - attribute
+ - organism taxon
+ - information content entity
+ - dataset
+ - physical entity
+ - activity
+ - procedure
+ - material sample
+ - biological entity
+ - genome
+ range: uriorcurie
+ multivalued: true
+ full name:
+ name: full name
+ definition_uri: https://w3id.org/biolink/vocab/full_name
+ description: a long-form human readable name for a thing
+ from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
+ rank: 1000
+ is_a: node property
+ domain: named thing
+ slot_uri: biolink:full_name
+ alias: full_name
+ owner: biological entity
+ domain_of:
+ - named thing
+ - attribute
+ - organism taxon
+ - information content entity
+ - dataset
+ - physical entity
+ - activity
+ - procedure
+ - material sample
+ - biological entity
+ - gene
+ - genome
+ range: label type
+ synonym:
+ name: synonym
+ definition_uri: https://w3id.org/biolink/vocab/synonym
+ description: Alternate human-readable names for a thing
+ in_subset:
+ - translator_minimal
+ from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
+ aliases:
+ - alias
+ narrow_mappings:
+ - skos:altLabel
+ - gff3:Alias
+ - AGRKB:synonyms
+ - gpi:DB_Object_Synonyms
+ - HANCESTRO:0330
+ - IAO:0000136
+ - RXNORM:has_tradename
+ rank: 1000
+ is_a: node property
+ domain: named thing
+ slot_uri: biolink:synonym
+ alias: synonym
+ owner: biological entity
+ domain_of:
+ - named thing
+ - attribute
+ - organism taxon
+ - information content entity
+ - dataset
+ - physical entity
+ - activity
+ - procedure
+ - material sample
+ - biological entity
+ - gene
+ - genome
+ range: label type
+ multivalued: true
+ in taxon:
+ name: in taxon
+ definition_uri: https://w3id.org/biolink/vocab/in_taxon
+ annotations:
+ canonical_predicate:
+ tag: canonical_predicate
+ value: true
+ description: connects an entity to its taxonomic classification. Only certain
+ kinds of entities can be taxonomically classified; see 'thing with taxon'
+ in_subset:
+ - translator_minimal
+ from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
+ aliases:
+ - instance of
+ - is organism source of gene product
+ - organism has gene
+ - gene found in organism
+ - gene product has organism source
+ exact_mappings:
+ - RO:0002162
+ - WIKIDATA_PROPERTY:P703
+ narrow_mappings:
+ - RO:0002160
+ rank: 1000
+ is_a: related to at instance level
+ domain: thing with taxon
+ slot_uri: biolink:in_taxon
+ inherited: true
+ alias: in_taxon
+ owner: biological entity
+ domain_of:
+ - thing with taxon
+ - biological entity
+ - gene
+ - genome
+ range: organism taxon
+ multivalued: true
+ in taxon label:
+ name: in taxon label
+ definition_uri: https://w3id.org/biolink/vocab/in_taxon_label
+ annotations:
+ denormalized:
+ tag: denormalized
+ value: true
+ description: The human readable scientific name for the taxon of the entity.
+ in_subset:
+ - translator_minimal
+ from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
+ exact_mappings:
+ - WIKIDATA_PROPERTY:P225
+ rank: 1000
+ is_a: node property
+ domain: thing with taxon
+ slot_uri: biolink:in_taxon_label
+ alias: in_taxon_label
+ owner: biological entity
+ domain_of:
+ - thing with taxon
+ - biological entity
+ - gene
+ - genome
+ range: label type
+class_uri: biolink:BiologicalEntity
+
+URI: xsd:string
+ +| Mapping Type | +Mapped Value | +
|---|---|
| self | +xsd:string | +
| native | +bican:biological_sequence | +
A binary (true or false) value
+URI: xsd:boolean
+ +| Mapping Type | +Mapped Value | +
|---|---|
| self | +xsd:boolean | +
| native | +bican:boolean | +
| exact | +schema:Boolean | +
A thick flat piece of brain tissue obtained by slicing a whole brain, brain hemisphere or subdivision with a blade at regular interval. When multiple brain slabs are obtained from the slicing process, an ordinal is assigned to provide information about the relative positioning of the slabs.
+URI: bican:BrainSlab
+| Name | +Cardinality and Range | +Description | +Inheritance | +
|---|---|---|---|
| was_derived_from | +0..1 Donor or Donor or BrainSlab |
+The donor from which the brain slab was derived from | +direct | +
| name | +0..1 LabelType |
+Name of a thick flat piece of brain tissue obtained by slicing a whole brain,... | +direct | +
| was_generated_by | +0..1 ProvActivity |
+Generation is the completion of production of a new entity by an activity | +ProvEntity | +
| id | +1 String |
+A unique identifier for an entity | +NamedThing, PhysicalEntity, MaterialSample, Entity | +
| iri | +0..1 IriType |
+An IRI for an entity | +NamedThing, PhysicalEntity, MaterialSample, Entity | +
| category | +* Uriorcurie |
+Name of the high level ontology class in which this entity is categorized | +NamedThing, PhysicalEntity, MaterialSample, Entity | +
| type | +* String |
++ | NamedThing, PhysicalEntity, MaterialSample, Entity | +
| description | +0..1 NarrativeText |
+a human-readable description of an entity | +NamedThing, PhysicalEntity, MaterialSample, Entity | +
| has_attribute | +* Attribute |
+connects any entity to an attribute | +NamedThing, PhysicalEntity, MaterialSample, Entity | +
| deprecated | +0..1 Boolean |
+A boolean flag indicating that an entity is no longer considered current or v... | +NamedThing, PhysicalEntity, MaterialSample, Entity | +
| provided_by | +* String |
+The value in this node property represents the knowledge provider that create... | +NamedThing, PhysicalEntity, MaterialSample | +
| xref | +* Uriorcurie |
+A database cross reference or alternative identifier for a NamedThing or edge... | +NamedThing, PhysicalEntity, MaterialSample | +
| full_name | +0..1 LabelType |
+a long-form human readable name for a thing | +NamedThing, PhysicalEntity, MaterialSample | +
| synonym | +* LabelType |
+Alternate human-readable names for a thing | +NamedThing, PhysicalEntity, MaterialSample | +
| used by | +used in | +type | +used | +
|---|---|---|---|
| BrainSlab | +was_derived_from | +exactly_one_of[range] | +BrainSlab | +
| DissectionRoiDelineation | +used | +range | +BrainSlab | +
| TissueDissection | +used | +range | +BrainSlab | +
| DissectionRoiPolygon | +annotates | +range | +BrainSlab | +
| Mapping Type | +Mapped Value | +
|---|---|
| self | +bican:BrainSlab | +
| native | +bican:BrainSlab | +
| exact | +NIMP:Slab | +
name: BrainSlab
+description: A thick flat piece of brain tissue obtained by slicing a whole brain,
+ brain hemisphere or subdivision with a blade at regular interval. When multiple
+ brain slabs are obtained from the slicing process, an ordinal is assigned to provide
+ information about the relative positioning of the slabs.
+in_subset:
+- bican
+- tissue_specimen
+from_schema: https://identifiers.org/brain-bican/library-generation-schema
+exact_mappings:
+- NIMP:Slab
+is_a: material sample
+mixins:
+- ProvEntity
+slots:
+- was_derived_from
+- name
+slot_usage:
+ was_derived_from:
+ name: was_derived_from
+ description: The donor from which the brain slab was derived from.
+ exact_mappings:
+ - NIMP:has_parent
+ range: Donor
+ exactly_one_of:
+ - range: Donor
+ - range: BrainSlab
+ name:
+ name: name
+ description: Name of a thick flat piece of brain tissue obtained by slicing a
+ whole brain, brain hemisphere or subdivision with a blade at regular interval. When
+ multiple brain slabs are obtained from the slicing process, an ordinal is assigned
+ to provide information about the relative positioning of the slabs.
+ category:
+ name: category
+ pattern: ^bican:[A-Z][A-Za-z]+$
+
+name: BrainSlab
+description: A thick flat piece of brain tissue obtained by slicing a whole brain,
+ brain hemisphere or subdivision with a blade at regular interval. When multiple
+ brain slabs are obtained from the slicing process, an ordinal is assigned to provide
+ information about the relative positioning of the slabs.
+in_subset:
+- bican
+- tissue_specimen
+from_schema: https://identifiers.org/brain-bican/library-generation-schema
+exact_mappings:
+- NIMP:Slab
+is_a: material sample
+mixins:
+- ProvEntity
+slot_usage:
+ was_derived_from:
+ name: was_derived_from
+ description: The donor from which the brain slab was derived from.
+ exact_mappings:
+ - NIMP:has_parent
+ range: Donor
+ exactly_one_of:
+ - range: Donor
+ - range: BrainSlab
+ name:
+ name: name
+ description: Name of a thick flat piece of brain tissue obtained by slicing a
+ whole brain, brain hemisphere or subdivision with a blade at regular interval. When
+ multiple brain slabs are obtained from the slicing process, an ordinal is assigned
+ to provide information about the relative positioning of the slabs.
+ category:
+ name: category
+ pattern: ^bican:[A-Z][A-Za-z]+$
+attributes:
+ was_derived_from:
+ name: was_derived_from
+ description: The donor from which the brain slab was derived from.
+ from_schema: https://identifiers.org/brain-bican/library-generation-schema
+ exact_mappings:
+ - NIMP:has_parent
+ rank: 1000
+ slot_uri: prov:wasDerivedFrom
+ alias: was_derived_from
+ owner: BrainSlab
+ domain_of:
+ - BrainSlab
+ - TissueSample
+ - DissociatedCellSample
+ - EnrichedCellSample
+ - BarcodedCellSample
+ - AmplifiedCdna
+ - Library
+ - LibraryAliquot
+ - LibraryPool
+ - ProvEntity
+ range: Donor
+ exactly_one_of:
+ - range: Donor
+ - range: BrainSlab
+ name:
+ name: name
+ definition_uri: https://w3id.org/biolink/vocab/name
+ description: Name of a thick flat piece of brain tissue obtained by slicing a
+ whole brain, brain hemisphere or subdivision with a blade at regular interval. When
+ multiple brain slabs are obtained from the slicing process, an ordinal is assigned
+ to provide information about the relative positioning of the slabs.
+ in_subset:
+ - translator_minimal
+ - samples
+ from_schema: https://identifiers.org/brain-bican/library-generation-schema
+ aliases:
+ - label
+ - display name
+ - title
+ mappings:
+ - rdfs:label
+ exact_mappings:
+ - gff3:Name
+ - gpi:DB_Object_Name
+ narrow_mappings:
+ - dct:title
+ - WIKIDATA_PROPERTY:P1476
+ rank: 1000
+ domain: entity
+ slot_uri: rdfs:label
+ alias: name
+ owner: BrainSlab
+ domain_of:
+ - attribute
+ - entity
+ - macromolecular machine mixin
+ - Donor
+ - BrainSlab
+ - TissueSample
+ - DissociatedCellSample
+ - EnrichedCellSample
+ - BarcodedCellSample
+ - AmplifiedCdna
+ - Library
+ - LibraryAliquot
+ - LibraryPool
+ - DissectionRoiPolygon
+ - named thing
+ - organism taxon
+ - information content entity
+ - dataset
+ - physical entity
+ - activity
+ - procedure
+ - material sample
+ - biological entity
+ - gene or gene product
+ - gene
+ - genome
+ range: label type
+ was_generated_by:
+ name: was_generated_by
+ description: Generation is the completion of production of a new entity by an
+ activity. This entity did not exist before generation and becomes available
+ for usage after this generation.
+ from_schema: https://identifiers.org/brain-bican/library-generation-schema
+ rank: 1000
+ slot_uri: prov:wasGeneratedBy
+ alias: was_generated_by
+ owner: BrainSlab
+ domain_of:
+ - TissueSample
+ - DissociatedCellSample
+ - EnrichedCellSample
+ - BarcodedCellSample
+ - AmplifiedCdna
+ - Library
+ - LibraryPool
+ - DissectionRoiPolygon
+ - ProvEntity
+ range: ProvActivity
+ id:
+ name: id
+ definition_uri: https://w3id.org/biolink/vocab/id
+ description: A unique identifier for an entity. Must be either a CURIE shorthand
+ for a URI or a complete URI
+ in_subset:
+ - translator_minimal
+ from_schema: https://identifiers.org/brain-bican/library-generation-schema
+ exact_mappings:
+ - AGRKB:primaryId
+ - gff3:ID
+ - gpi:DB_Object_ID
+ rank: 1000
+ domain: entity
+ slot_uri: biolink:id
+ identifier: true
+ alias: id
+ owner: BrainSlab
+ domain_of:
+ - ontology class
+ - entity
+ - attribute
+ - named thing
+ - taxonomic rank
+ - organism taxon
+ - information content entity
+ - dataset
+ - physical entity
+ - activity
+ - procedure
+ - material sample
+ - biological entity
+ - gene
+ - genome
+ range: string
+ required: true
+ iri:
+ name: iri
+ definition_uri: https://w3id.org/biolink/vocab/iri
+ description: An IRI for an entity. This is determined by the id using expansion
+ rules.
+ in_subset:
+ - translator_minimal
+ - samples
+ from_schema: https://identifiers.org/brain-bican/library-generation-schema
+ exact_mappings:
+ - WIKIDATA_PROPERTY:P854
+ rank: 1000
+ slot_uri: biolink:iri
+ alias: iri
+ owner: BrainSlab
+ domain_of:
+ - attribute
+ - entity
+ - named thing
+ - organism taxon
+ - information content entity
+ - dataset
+ - physical entity
+ - activity
+ - procedure
+ - material sample
+ - biological entity
+ - gene
+ - genome
+ range: iri type
+ category:
+ name: category
+ definition_uri: https://w3id.org/biolink/vocab/category
+ description: Name of the high level ontology class in which this entity is categorized.
+ Corresponds to the label for the biolink entity type class. In a neo4j database
+ this MAY correspond to the neo4j label tag. In an RDF database it should be
+ a biolink model class URI. This field is multi-valued. It should include values
+ for ancestors of the biolink class; for example, a protein such as Shh would
+ have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`.
+ In an RDF database, nodes will typically have an rdf:type triples. This can
+ be to the most specific biolink class, or potentially to a class more specific
+ than something in biolink. For example, a sequence feature `f` may have a rdf:type
+ assertion to a SO class such as TF_binding_site, which is more specific than
+ anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity,
+ biolink:NamedThing}
+ in_subset:
+ - translator_minimal
+ from_schema: https://identifiers.org/brain-bican/library-generation-schema
+ rank: 1000
+ is_a: type
+ domain: entity
+ slot_uri: biolink:category
+ designates_type: true
+ alias: category
+ owner: BrainSlab
+ domain_of:
+ - entity
+ - attribute
+ - named thing
+ - organism taxon
+ - information content entity
+ - dataset
+ - physical entity
+ - activity
+ - procedure
+ - material sample
+ - biological entity
+ - gene
+ - genome
+ is_class_field: true
+ range: uriorcurie
+ multivalued: true
+ pattern: ^bican:[A-Z][A-Za-z]+$
+ type:
+ name: type
+ definition_uri: https://w3id.org/biolink/vocab/type
+ from_schema: https://identifiers.org/brain-bican/library-generation-schema
+ mappings:
+ - rdf:type
+ exact_mappings:
+ - gff3:type
+ - gpi:DB_Object_Type
+ rank: 1000
+ domain: entity
+ slot_uri: rdf:type
+ alias: type
+ owner: BrainSlab
+ domain_of:
+ - entity
+ - attribute
+ - named thing
+ - organism taxon
+ - information content entity
+ - dataset
+ - physical entity
+ - activity
+ - procedure
+ - material sample
+ - biological entity
+ - gene
+ - genome
+ range: string
+ multivalued: true
+ description:
+ name: description
+ definition_uri: https://w3id.org/biolink/vocab/description
+ description: a human-readable description of an entity
+ in_subset:
+ - translator_minimal
+ from_schema: https://identifiers.org/brain-bican/library-generation-schema
+ aliases:
+ - definition
+ mappings:
+ - dct:description
+ exact_mappings:
+ - IAO:0000115
+ - skos:definitions
+ narrow_mappings:
+ - gff3:Description
+ rank: 1000
+ slot_uri: dct:description
+ alias: description
+ owner: BrainSlab
+ domain_of:
+ - entity
+ - attribute
+ - named thing
+ - organism taxon
+ - information content entity
+ - dataset
+ - physical entity
+ - activity
+ - procedure
+ - material sample
+ - biological entity
+ - gene
+ - genome
+ range: narrative text
+ has attribute:
+ name: has attribute
+ definition_uri: https://w3id.org/biolink/vocab/has_attribute
+ description: connects any entity to an attribute
+ in_subset:
+ - samples
+ from_schema: https://identifiers.org/brain-bican/library-generation-schema
+ exact_mappings:
+ - SIO:000008
+ close_mappings:
+ - OBI:0001927
+ narrow_mappings:
+ - OBAN:association_has_subject_property
+ - OBAN:association_has_object_property
+ - CPT:has_possibly_included_panel_element
+ - DRUGBANK:category
+ - EFO:is_executed_in
+ - HANCESTRO:0301
+ - LOINC:has_action_guidance
+ - LOINC:has_adjustment
+ - LOINC:has_aggregation_view
+ - LOINC:has_approach_guidance
+ - LOINC:has_divisor
+ - LOINC:has_exam
+ - LOINC:has_method
+ - LOINC:has_modality_subtype
+ - LOINC:has_object_guidance
+ - LOINC:has_scale
+ - LOINC:has_suffix
+ - LOINC:has_time_aspect
+ - LOINC:has_time_modifier
+ - LOINC:has_timing_of
+ - NCIT:R88
+ - NCIT:eo_disease_has_property_or_attribute
+ - NCIT:has_data_element
+ - NCIT:has_pharmaceutical_administration_method
+ - NCIT:has_pharmaceutical_basic_dose_form
+ - NCIT:has_pharmaceutical_intended_site
+ - NCIT:has_pharmaceutical_release_characteristics
+ - NCIT:has_pharmaceutical_state_of_matter
+ - NCIT:has_pharmaceutical_transformation
+ - NCIT:is_qualified_by
+ - NCIT:qualifier_applies_to
+ - NCIT:role_has_domain
+ - NCIT:role_has_range
+ - INO:0000154
+ - HANCESTRO:0308
+ - OMIM:has_inheritance_type
+ - orphanet:C016
+ - orphanet:C017
+ - RO:0000053
+ - RO:0000086
+ - RO:0000087
+ - SNOMED:has_access
+ - SNOMED:has_clinical_course
+ - SNOMED:has_count_of_base_of_active_ingredient
+ - SNOMED:has_dose_form_administration_method
+ - SNOMED:has_dose_form_release_characteristic
+ - SNOMED:has_dose_form_transformation
+ - SNOMED:has_finding_context
+ - SNOMED:has_finding_informer
+ - SNOMED:has_inherent_attribute
+ - SNOMED:has_intent
+ - SNOMED:has_interpretation
+ - SNOMED:has_laterality
+ - SNOMED:has_measurement_method
+ - SNOMED:has_method
+ - SNOMED:has_priority
+ - SNOMED:has_procedure_context
+ - SNOMED:has_process_duration
+ - SNOMED:has_property
+ - SNOMED:has_revision_status
+ - SNOMED:has_scale_type
+ - SNOMED:has_severity
+ - SNOMED:has_specimen
+ - SNOMED:has_state_of_matter
+ - SNOMED:has_subject_relationship_context
+ - SNOMED:has_surgical_approach
+ - SNOMED:has_technique
+ - SNOMED:has_temporal_context
+ - SNOMED:has_time_aspect
+ - SNOMED:has_units
+ - UMLS:has_structural_class
+ - UMLS:has_supported_concept_property
+ - UMLS:has_supported_concept_relationship
+ - UMLS:may_be_qualified_by
+ rank: 1000
+ domain: entity
+ slot_uri: biolink:has_attribute
+ alias: has_attribute
+ owner: BrainSlab
+ domain_of:
+ - entity
+ - attribute
+ - named thing
+ - organism taxon
+ - information content entity
+ - dataset
+ - physical entity
+ - activity
+ - procedure
+ - material sample
+ - biological entity
+ - gene
+ - genome
+ range: attribute
+ multivalued: true
+ deprecated:
+ name: deprecated
+ definition_uri: https://w3id.org/biolink/vocab/deprecated
+ description: A boolean flag indicating that an entity is no longer considered
+ current or valid.
+ from_schema: https://identifiers.org/brain-bican/library-generation-schema
+ exact_mappings:
+ - oboInOwl:ObsoleteClass
+ rank: 1000
+ slot_uri: biolink:deprecated
+ alias: deprecated
+ owner: BrainSlab
+ domain_of:
+ - entity
+ - attribute
+ - named thing
+ - organism taxon
+ - information content entity
+ - dataset
+ - physical entity
+ - activity
+ - procedure
+ - material sample
+ - biological entity
+ - gene
+ - genome
+ range: boolean
+ provided by:
+ name: provided by
+ definition_uri: https://w3id.org/biolink/vocab/provided_by
+ description: The value in this node property represents the knowledge provider
+ that created or assembled the node and all of its attributes. Used internally
+ to represent how a particular node made its way into a knowledge provider or
+ graph.
+ from_schema: https://identifiers.org/brain-bican/library-generation-schema
+ rank: 1000
+ is_a: node property
+ domain: named thing
+ slot_uri: biolink:provided_by
+ alias: provided_by
+ owner: BrainSlab
+ domain_of:
+ - named thing
+ - attribute
+ - organism taxon
+ - information content entity
+ - dataset
+ - physical entity
+ - activity
+ - procedure
+ - material sample
+ - biological entity
+ - gene
+ - genome
+ range: string
+ multivalued: true
+ xref:
+ name: xref
+ definition_uri: https://w3id.org/biolink/vocab/xref
+ description: A database cross reference or alternative identifier for a NamedThing
+ or edge between two NamedThings. This property should point to a database record
+ or webpage that supports the existence of the edge, or gives more detail about
+ the edge. This property can be used on a node or edge to provide multiple URIs
+ or CURIE cross references.
+ in_subset:
+ - translator_minimal
+ from_schema: https://identifiers.org/brain-bican/library-generation-schema
+ aliases:
+ - dbxref
+ - Dbxref
+ - DbXref
+ - record_url
+ - source_record_urls
+ narrow_mappings:
+ - gff3:Dbxref
+ - gpi:DB_Xrefs
+ rank: 1000
+ domain: named thing
+ slot_uri: biolink:xref
+ alias: xref
+ owner: BrainSlab
+ domain_of:
+ - named thing
+ - gene
+ - attribute
+ - organism taxon
+ - information content entity
+ - dataset
+ - physical entity
+ - activity
+ - procedure
+ - material sample
+ - biological entity
+ - genome
+ range: uriorcurie
+ multivalued: true
+ full name:
+ name: full name
+ definition_uri: https://w3id.org/biolink/vocab/full_name
+ description: a long-form human readable name for a thing
+ from_schema: https://identifiers.org/brain-bican/library-generation-schema
+ rank: 1000
+ is_a: node property
+ domain: named thing
+ slot_uri: biolink:full_name
+ alias: full_name
+ owner: BrainSlab
+ domain_of:
+ - named thing
+ - attribute
+ - organism taxon
+ - information content entity
+ - dataset
+ - physical entity
+ - activity
+ - procedure
+ - material sample
+ - biological entity
+ - gene
+ - genome
+ range: label type
+ synonym:
+ name: synonym
+ definition_uri: https://w3id.org/biolink/vocab/synonym
+ description: Alternate human-readable names for a thing
+ in_subset:
+ - translator_minimal
+ from_schema: https://identifiers.org/brain-bican/library-generation-schema
+ aliases:
+ - alias
+ narrow_mappings:
+ - skos:altLabel
+ - gff3:Alias
+ - AGRKB:synonyms
+ - gpi:DB_Object_Synonyms
+ - HANCESTRO:0330
+ - IAO:0000136
+ - RXNORM:has_tradename
+ rank: 1000
+ is_a: node property
+ domain: named thing
+ slot_uri: biolink:synonym
+ alias: synonym
+ owner: BrainSlab
+ domain_of:
+ - named thing
+ - attribute
+ - organism taxon
+ - information content entity
+ - dataset
+ - physical entity
+ - activity
+ - procedure
+ - material sample
+ - biological entity
+ - gene
+ - genome
+ range: label type
+ multivalued: true
+
+The process of creating a collection of cDNA molecules derived and amplified from an input barcoded cell sample. A large amount of cDNA is needed to have accurate and reliable sequencing detection of gene expression. This process generates multiple copies of each mRNA transcript (expressed gene) within each cell while retaining the cell's unique barcode from the barcoding step. This is a necessary step for GEX methods but is not used for ATAC methods.
+ +| Name | +Cardinality and Range | +Description | +Inheritance | +
|---|---|---|---|
| used | +0..1 BarcodedCellSample |
+The input barcoded cell sample from which amplified cDNA was derived from | +direct | +
| pcr_cycles | +0..1 Integer |
+Number of PCR cycles used during cDNA amplification for this cDNA | +direct | +
| process_date | +0..1 Date |
+Date of cDNA amplification | +direct | +
| set | +0..1 String |
+cDNA amplification set, containing multiple amplified_cDNA_names that were pr... | +direct | +
| id | +1 String |
+A unique identifier for an entity | +NamedThing, Procedure, Entity | +
| iri | +0..1 IriType |
+An IRI for an entity | +NamedThing, Procedure, Entity | +
| category | +* Uriorcurie |
+Name of the high level ontology class in which this entity is categorized | +NamedThing, Procedure, Entity | +
| type | +* String |
++ | NamedThing, Procedure, Entity | +
| name | +0..1 LabelType |
+A human-readable name for an attribute or entity | +NamedThing, Procedure, Entity | +
| description | +0..1 NarrativeText |
+a human-readable description of an entity | +NamedThing, Procedure, Entity | +
| has_attribute | +* Attribute |
+connects any entity to an attribute | +NamedThing, Procedure, Entity | +
| deprecated | +0..1 Boolean |
+A boolean flag indicating that an entity is no longer considered current or v... | +NamedThing, Procedure, Entity | +
| provided_by | +* String |
+The value in this node property represents the knowledge provider that create... | +NamedThing, Procedure | +
| xref | +* Uriorcurie |
+A database cross reference or alternative identifier for a NamedThing or edge... | +NamedThing, Procedure | +
| full_name | +0..1 LabelType |
+a long-form human readable name for a thing | +NamedThing, Procedure | +
| synonym | +* LabelType |
+Alternate human-readable names for a thing | +NamedThing, Procedure | +
| used by | +used in | +type | +used | +
|---|---|---|---|
| AmplifiedCdna | +was_generated_by | +range | +CdnaAmplification | +
| Mapping Type | +Mapped Value | +
|---|---|
| self | +bican:CdnaAmplification | +
| native | +bican:CdnaAmplification | +
name: CdnaAmplification
+description: The process of creating a collection of cDNA molecules derived and amplified
+ from an input barcoded cell sample. A large amount of cDNA is needed to have accurate
+ and reliable sequencing detection of gene expression. This process generates multiple
+ copies of each mRNA transcript (expressed gene) within each cell while retaining
+ the cell's unique barcode from the barcoding step. This is a necessary step for
+ GEX methods but is not used for ATAC methods.
+in_subset:
+- bican
+- library_generation
+from_schema: https://identifiers.org/brain-bican/library-generation-schema
+is_a: procedure
+mixins:
+- ProvActivity
+slots:
+- used
+slot_usage:
+ used:
+ name: used
+ description: The input barcoded cell sample from which amplified cDNA was derived
+ from.
+ range: BarcodedCellSample
+ category:
+ name: category
+ pattern: ^bican:[A-Z][A-Za-z]+$
+attributes:
+ pcr_cycles:
+ name: pcr_cycles
+ local_names:
+ NIMP:
+ local_name_source: NIMP
+ local_name_value: amplified_cdna_pcr_cycles
+ description: Number of PCR cycles used during cDNA amplification for this cDNA.
+ in_subset:
+ - analysis
+ from_schema: https://identifiers.org/brain-bican/library-generation-schema
+ exact_mappings:
+ - NIMP:PD-OKOKQD38
+ rank: 1000
+ slot_uri: bican:3827634c-3f8f-4760-b358-86ce4b030238
+ alias: amplified cDNA PCR cycles
+ domain_of:
+ - CdnaAmplification
+ range: integer
+ process_date:
+ name: process_date
+ local_names:
+ NIMP:
+ local_name_source: NIMP
+ local_name_value: amplified_cdna_preparation_date
+ description: Date of cDNA amplification.
+ from_schema: https://identifiers.org/brain-bican/library-generation-schema
+ exact_mappings:
+ - NIMP:PD-BYBYBY24
+ slot_uri: bican:6cc333e7-9b98-497f-b7b1-eae904db2400
+ alias: cDNA amplification process date
+ domain_of:
+ - CellDissociation
+ - CellEnrichment
+ - CellBarcoding
+ - CdnaAmplification
+ - LibraryConstruction
+ - LibraryPooling
+ range: date
+ set:
+ name: set
+ local_names:
+ NIMP:
+ local_name_source: NIMP
+ local_name_value: cdna_amplification_set
+ description: cDNA amplification set, containing multiple amplified_cDNA_names
+ that were processed at the same time.
+ in_subset:
+ - analysis
+ from_schema: https://identifiers.org/brain-bican/library-generation-schema
+ exact_mappings:
+ - NIMP:PD-SCSCTM41
+ rank: 1000
+ slot_uri: bican:42e98a88-50b3-4ea2-871b-2142f6a0dfdd
+ alias: cDNA amplification set
+ domain_of:
+ - CdnaAmplification
+ - LibraryConstruction
+ range: string
+
+name: CdnaAmplification
+description: The process of creating a collection of cDNA molecules derived and amplified
+ from an input barcoded cell sample. A large amount of cDNA is needed to have accurate
+ and reliable sequencing detection of gene expression. This process generates multiple
+ copies of each mRNA transcript (expressed gene) within each cell while retaining
+ the cell's unique barcode from the barcoding step. This is a necessary step for
+ GEX methods but is not used for ATAC methods.
+in_subset:
+- bican
+- library_generation
+from_schema: https://identifiers.org/brain-bican/library-generation-schema
+is_a: procedure
+mixins:
+- ProvActivity
+slot_usage:
+ used:
+ name: used
+ description: The input barcoded cell sample from which amplified cDNA was derived
+ from.
+ range: BarcodedCellSample
+ category:
+ name: category
+ pattern: ^bican:[A-Z][A-Za-z]+$
+attributes:
+ pcr_cycles:
+ name: pcr_cycles
+ local_names:
+ NIMP:
+ local_name_source: NIMP
+ local_name_value: amplified_cdna_pcr_cycles
+ description: Number of PCR cycles used during cDNA amplification for this cDNA.
+ in_subset:
+ - analysis
+ from_schema: https://identifiers.org/brain-bican/library-generation-schema
+ exact_mappings:
+ - NIMP:PD-OKOKQD38
+ rank: 1000
+ slot_uri: bican:3827634c-3f8f-4760-b358-86ce4b030238
+ alias: amplified cDNA PCR cycles
+ owner: CdnaAmplification
+ domain_of:
+ - CdnaAmplification
+ range: integer
+ process_date:
+ name: process_date
+ local_names:
+ NIMP:
+ local_name_source: NIMP
+ local_name_value: amplified_cdna_preparation_date
+ description: Date of cDNA amplification.
+ from_schema: https://identifiers.org/brain-bican/library-generation-schema
+ exact_mappings:
+ - NIMP:PD-BYBYBY24
+ slot_uri: bican:6cc333e7-9b98-497f-b7b1-eae904db2400
+ alias: cDNA amplification process date
+ owner: CdnaAmplification
+ domain_of:
+ - CellDissociation
+ - CellEnrichment
+ - CellBarcoding
+ - CdnaAmplification
+ - LibraryConstruction
+ - LibraryPooling
+ range: date
+ set:
+ name: set
+ local_names:
+ NIMP:
+ local_name_source: NIMP
+ local_name_value: cdna_amplification_set
+ description: cDNA amplification set, containing multiple amplified_cDNA_names
+ that were processed at the same time.
+ in_subset:
+ - analysis
+ from_schema: https://identifiers.org/brain-bican/library-generation-schema
+ exact_mappings:
+ - NIMP:PD-SCSCTM41
+ rank: 1000
+ slot_uri: bican:42e98a88-50b3-4ea2-871b-2142f6a0dfdd
+ alias: cDNA amplification set
+ owner: CdnaAmplification
+ domain_of:
+ - CdnaAmplification
+ - LibraryConstruction
+ range: string
+ used:
+ name: used
+ description: The input barcoded cell sample from which amplified cDNA was derived
+ from.
+ from_schema: https://identifiers.org/brain-bican/library-generation-schema
+ rank: 1000
+ slot_uri: prov:used
+ alias: used
+ owner: CdnaAmplification
+ domain_of:
+ - DissectionRoiDelineation
+ - TissueDissection
+ - CellDissociation
+ - CellEnrichment
+ - EnrichedCellSampleSplitting
+ - CellBarcoding
+ - CdnaAmplification
+ - LibraryConstruction
+ - LibraryPooling
+ - ProvActivity
+ range: BarcodedCellSample
+ id:
+ name: id
+ definition_uri: https://w3id.org/biolink/vocab/id
+ description: A unique identifier for an entity. Must be either a CURIE shorthand
+ for a URI or a complete URI
+ in_subset:
+ - translator_minimal
+ from_schema: https://identifiers.org/brain-bican/library-generation-schema
+ exact_mappings:
+ - AGRKB:primaryId
+ - gff3:ID
+ - gpi:DB_Object_ID
+ rank: 1000
+ domain: entity
+ slot_uri: biolink:id
+ identifier: true
+ alias: id
+ owner: CdnaAmplification
+ domain_of:
+ - ontology class
+ - entity
+ - attribute
+ - named thing
+ - taxonomic rank
+ - organism taxon
+ - information content entity
+ - dataset
+ - physical entity
+ - activity
+ - procedure
+ - material sample
+ - biological entity
+ - gene
+ - genome
+ range: string
+ required: true
+ iri:
+ name: iri
+ definition_uri: https://w3id.org/biolink/vocab/iri
+ description: An IRI for an entity. This is determined by the id using expansion
+ rules.
+ in_subset:
+ - translator_minimal
+ - samples
+ from_schema: https://identifiers.org/brain-bican/library-generation-schema
+ exact_mappings:
+ - WIKIDATA_PROPERTY:P854
+ rank: 1000
+ slot_uri: biolink:iri
+ alias: iri
+ owner: CdnaAmplification
+ domain_of:
+ - attribute
+ - entity
+ - named thing
+ - organism taxon
+ - information content entity
+ - dataset
+ - physical entity
+ - activity
+ - procedure
+ - material sample
+ - biological entity
+ - gene
+ - genome
+ range: iri type
+ category:
+ name: category
+ definition_uri: https://w3id.org/biolink/vocab/category
+ description: Name of the high level ontology class in which this entity is categorized.
+ Corresponds to the label for the biolink entity type class. In a neo4j database
+ this MAY correspond to the neo4j label tag. In an RDF database it should be
+ a biolink model class URI. This field is multi-valued. It should include values
+ for ancestors of the biolink class; for example, a protein such as Shh would
+ have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`.
+ In an RDF database, nodes will typically have an rdf:type triples. This can
+ be to the most specific biolink class, or potentially to a class more specific
+ than something in biolink. For example, a sequence feature `f` may have a rdf:type
+ assertion to a SO class such as TF_binding_site, which is more specific than
+ anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity,
+ biolink:NamedThing}
+ in_subset:
+ - translator_minimal
+ from_schema: https://identifiers.org/brain-bican/library-generation-schema
+ rank: 1000
+ is_a: type
+ domain: entity
+ slot_uri: biolink:category
+ designates_type: true
+ alias: category
+ owner: CdnaAmplification
+ domain_of:
+ - entity
+ - attribute
+ - named thing
+ - organism taxon
+ - information content entity
+ - dataset
+ - physical entity
+ - activity
+ - procedure
+ - material sample
+ - biological entity
+ - gene
+ - genome
+ is_class_field: true
+ range: uriorcurie
+ multivalued: true
+ pattern: ^bican:[A-Z][A-Za-z]+$
+ type:
+ name: type
+ definition_uri: https://w3id.org/biolink/vocab/type
+ from_schema: https://identifiers.org/brain-bican/library-generation-schema
+ mappings:
+ - rdf:type
+ exact_mappings:
+ - gff3:type
+ - gpi:DB_Object_Type
+ rank: 1000
+ domain: entity
+ slot_uri: rdf:type
+ alias: type
+ owner: CdnaAmplification
+ domain_of:
+ - entity
+ - attribute
+ - named thing
+ - organism taxon
+ - information content entity
+ - dataset
+ - physical entity
+ - activity
+ - procedure
+ - material sample
+ - biological entity
+ - gene
+ - genome
+ range: string
+ multivalued: true
+ name:
+ name: name
+ definition_uri: https://w3id.org/biolink/vocab/name
+ description: A human-readable name for an attribute or entity.
+ in_subset:
+ - translator_minimal
+ - samples
+ from_schema: https://identifiers.org/brain-bican/library-generation-schema
+ aliases:
+ - label
+ - display name
+ - title
+ mappings:
+ - rdfs:label
+ exact_mappings:
+ - gff3:Name
+ - gpi:DB_Object_Name
+ narrow_mappings:
+ - dct:title
+ - WIKIDATA_PROPERTY:P1476
+ rank: 1000
+ domain: entity
+ slot_uri: rdfs:label
+ alias: name
+ owner: CdnaAmplification
+ domain_of:
+ - attribute
+ - entity
+ - macromolecular machine mixin
+ - Donor
+ - BrainSlab
+ - TissueSample
+ - DissociatedCellSample
+ - EnrichedCellSample
+ - BarcodedCellSample
+ - AmplifiedCdna
+ - Library
+ - LibraryAliquot
+ - LibraryPool
+ - DissectionRoiPolygon
+ - named thing
+ - organism taxon
+ - information content entity
+ - dataset
+ - physical entity
+ - activity
+ - procedure
+ - material sample
+ - biological entity
+ - gene or gene product
+ - gene
+ - genome
+ range: label type
+ description:
+ name: description
+ definition_uri: https://w3id.org/biolink/vocab/description
+ description: a human-readable description of an entity
+ in_subset:
+ - translator_minimal
+ from_schema: https://identifiers.org/brain-bican/library-generation-schema
+ aliases:
+ - definition
+ mappings:
+ - dct:description
+ exact_mappings:
+ - IAO:0000115
+ - skos:definitions
+ narrow_mappings:
+ - gff3:Description
+ rank: 1000
+ slot_uri: dct:description
+ alias: description
+ owner: CdnaAmplification
+ domain_of:
+ - entity
+ - attribute
+ - named thing
+ - organism taxon
+ - information content entity
+ - dataset
+ - physical entity
+ - activity
+ - procedure
+ - material sample
+ - biological entity
+ - gene
+ - genome
+ range: narrative text
+ has attribute:
+ name: has attribute
+ definition_uri: https://w3id.org/biolink/vocab/has_attribute
+ description: connects any entity to an attribute
+ in_subset:
+ - samples
+ from_schema: https://identifiers.org/brain-bican/library-generation-schema
+ exact_mappings:
+ - SIO:000008
+ close_mappings:
+ - OBI:0001927
+ narrow_mappings:
+ - OBAN:association_has_subject_property
+ - OBAN:association_has_object_property
+ - CPT:has_possibly_included_panel_element
+ - DRUGBANK:category
+ - EFO:is_executed_in
+ - HANCESTRO:0301
+ - LOINC:has_action_guidance
+ - LOINC:has_adjustment
+ - LOINC:has_aggregation_view
+ - LOINC:has_approach_guidance
+ - LOINC:has_divisor
+ - LOINC:has_exam
+ - LOINC:has_method
+ - LOINC:has_modality_subtype
+ - LOINC:has_object_guidance
+ - LOINC:has_scale
+ - LOINC:has_suffix
+ - LOINC:has_time_aspect
+ - LOINC:has_time_modifier
+ - LOINC:has_timing_of
+ - NCIT:R88
+ - NCIT:eo_disease_has_property_or_attribute
+ - NCIT:has_data_element
+ - NCIT:has_pharmaceutical_administration_method
+ - NCIT:has_pharmaceutical_basic_dose_form
+ - NCIT:has_pharmaceutical_intended_site
+ - NCIT:has_pharmaceutical_release_characteristics
+ - NCIT:has_pharmaceutical_state_of_matter
+ - NCIT:has_pharmaceutical_transformation
+ - NCIT:is_qualified_by
+ - NCIT:qualifier_applies_to
+ - NCIT:role_has_domain
+ - NCIT:role_has_range
+ - INO:0000154
+ - HANCESTRO:0308
+ - OMIM:has_inheritance_type
+ - orphanet:C016
+ - orphanet:C017
+ - RO:0000053
+ - RO:0000086
+ - RO:0000087
+ - SNOMED:has_access
+ - SNOMED:has_clinical_course
+ - SNOMED:has_count_of_base_of_active_ingredient
+ - SNOMED:has_dose_form_administration_method
+ - SNOMED:has_dose_form_release_characteristic
+ - SNOMED:has_dose_form_transformation
+ - SNOMED:has_finding_context
+ - SNOMED:has_finding_informer
+ - SNOMED:has_inherent_attribute
+ - SNOMED:has_intent
+ - SNOMED:has_interpretation
+ - SNOMED:has_laterality
+ - SNOMED:has_measurement_method
+ - SNOMED:has_method
+ - SNOMED:has_priority
+ - SNOMED:has_procedure_context
+ - SNOMED:has_process_duration
+ - SNOMED:has_property
+ - SNOMED:has_revision_status
+ - SNOMED:has_scale_type
+ - SNOMED:has_severity
+ - SNOMED:has_specimen
+ - SNOMED:has_state_of_matter
+ - SNOMED:has_subject_relationship_context
+ - SNOMED:has_surgical_approach
+ - SNOMED:has_technique
+ - SNOMED:has_temporal_context
+ - SNOMED:has_time_aspect
+ - SNOMED:has_units
+ - UMLS:has_structural_class
+ - UMLS:has_supported_concept_property
+ - UMLS:has_supported_concept_relationship
+ - UMLS:may_be_qualified_by
+ rank: 1000
+ domain: entity
+ slot_uri: biolink:has_attribute
+ alias: has_attribute
+ owner: CdnaAmplification
+ domain_of:
+ - entity
+ - attribute
+ - named thing
+ - organism taxon
+ - information content entity
+ - dataset
+ - physical entity
+ - activity
+ - procedure
+ - material sample
+ - biological entity
+ - gene
+ - genome
+ range: attribute
+ multivalued: true
+ deprecated:
+ name: deprecated
+ definition_uri: https://w3id.org/biolink/vocab/deprecated
+ description: A boolean flag indicating that an entity is no longer considered
+ current or valid.
+ from_schema: https://identifiers.org/brain-bican/library-generation-schema
+ exact_mappings:
+ - oboInOwl:ObsoleteClass
+ rank: 1000
+ slot_uri: biolink:deprecated
+ alias: deprecated
+ owner: CdnaAmplification
+ domain_of:
+ - entity
+ - attribute
+ - named thing
+ - organism taxon
+ - information content entity
+ - dataset
+ - physical entity
+ - activity
+ - procedure
+ - material sample
+ - biological entity
+ - gene
+ - genome
+ range: boolean
+ provided by:
+ name: provided by
+ definition_uri: https://w3id.org/biolink/vocab/provided_by
+ description: The value in this node property represents the knowledge provider
+ that created or assembled the node and all of its attributes. Used internally
+ to represent how a particular node made its way into a knowledge provider or
+ graph.
+ from_schema: https://identifiers.org/brain-bican/library-generation-schema
+ rank: 1000
+ is_a: node property
+ domain: named thing
+ slot_uri: biolink:provided_by
+ alias: provided_by
+ owner: CdnaAmplification
+ domain_of:
+ - named thing
+ - attribute
+ - organism taxon
+ - information content entity
+ - dataset
+ - physical entity
+ - activity
+ - procedure
+ - material sample
+ - biological entity
+ - gene
+ - genome
+ range: string
+ multivalued: true
+ xref:
+ name: xref
+ definition_uri: https://w3id.org/biolink/vocab/xref
+ description: A database cross reference or alternative identifier for a NamedThing
+ or edge between two NamedThings. This property should point to a database record
+ or webpage that supports the existence of the edge, or gives more detail about
+ the edge. This property can be used on a node or edge to provide multiple URIs
+ or CURIE cross references.
+ in_subset:
+ - translator_minimal
+ from_schema: https://identifiers.org/brain-bican/library-generation-schema
+ aliases:
+ - dbxref
+ - Dbxref
+ - DbXref
+ - record_url
+ - source_record_urls
+ narrow_mappings:
+ - gff3:Dbxref
+ - gpi:DB_Xrefs
+ rank: 1000
+ domain: named thing
+ slot_uri: biolink:xref
+ alias: xref
+ owner: CdnaAmplification
+ domain_of:
+ - named thing
+ - gene
+ - attribute
+ - organism taxon
+ - information content entity
+ - dataset
+ - physical entity
+ - activity
+ - procedure
+ - material sample
+ - biological entity
+ - genome
+ range: uriorcurie
+ multivalued: true
+ full name:
+ name: full name
+ definition_uri: https://w3id.org/biolink/vocab/full_name
+ description: a long-form human readable name for a thing
+ from_schema: https://identifiers.org/brain-bican/library-generation-schema
+ rank: 1000
+ is_a: node property
+ domain: named thing
+ slot_uri: biolink:full_name
+ alias: full_name
+ owner: CdnaAmplification
+ domain_of:
+ - named thing
+ - attribute
+ - organism taxon
+ - information content entity
+ - dataset
+ - physical entity
+ - activity
+ - procedure
+ - material sample
+ - biological entity
+ - gene
+ - genome
+ range: label type
+ synonym:
+ name: synonym
+ definition_uri: https://w3id.org/biolink/vocab/synonym
+ description: Alternate human-readable names for a thing
+ in_subset:
+ - translator_minimal
+ from_schema: https://identifiers.org/brain-bican/library-generation-schema
+ aliases:
+ - alias
+ narrow_mappings:
+ - skos:altLabel
+ - gff3:Alias
+ - AGRKB:synonyms
+ - gpi:DB_Object_Synonyms
+ - HANCESTRO:0330
+ - IAO:0000136
+ - RXNORM:has_tradename
+ rank: 1000
+ is_a: node property
+ domain: named thing
+ slot_uri: biolink:synonym
+ alias: synonym
+ owner: CdnaAmplification
+ domain_of:
+ - named thing
+ - attribute
+ - organism taxon
+ - information content entity
+ - dataset
+ - physical entity
+ - activity
+ - procedure
+ - material sample
+ - biological entity
+ - gene
+ - genome
+ range: label type
+ multivalued: true
+
+The process of adding a molecular barcode to individual cells in a sample. The input will be either dissociated cell sample or enriched cell sample. Cell barcodes are only guaranteed to be unique within this one collection. One dissociated cell sample or enriched cell sample can lead to multiple barcoded cell samples.
+URI: bican:CellBarcoding
+| Name | +Cardinality and Range | +Description | +Inheritance | +
|---|---|---|---|
| used | +* ProvEntity or DissociatedCellSample or EnrichedCellSample |
+The input dissociated or enriched cell sample(s) from which the barcoded cell... | +direct | +
| port_well | +0..1 String |
+Specific position of the loaded port of the 10x chip | +direct | +
| input_quantity | +0..1 Integer |
+Number of enriched or dissociated cells/nuclei going into the barcoding proce... | +direct | +
| process_date | +0..1 String |
+Date of cell barcoding process | +direct | +
| method | +0..1 BarcodedCellSampleTechnique |
+Standardized nomenclature to describe the general barcoding method used | +direct | +
| id | +1 String |
+A unique identifier for an entity | +NamedThing, Procedure, Entity | +
| iri | +0..1 IriType |
+An IRI for an entity | +NamedThing, Procedure, Entity | +
| category | +* Uriorcurie |
+Name of the high level ontology class in which this entity is categorized | +NamedThing, Procedure, Entity | +
| type | +* String |
++ | NamedThing, Procedure, Entity | +
| name | +0..1 LabelType |
+A human-readable name for an attribute or entity | +NamedThing, Procedure, Entity | +
| description | +0..1 NarrativeText |
+a human-readable description of an entity | +NamedThing, Procedure, Entity | +
| has_attribute | +* Attribute |
+connects any entity to an attribute | +NamedThing, Procedure, Entity | +
| deprecated | +0..1 Boolean |
+A boolean flag indicating that an entity is no longer considered current or v... | +NamedThing, Procedure, Entity | +
| provided_by | +* String |
+The value in this node property represents the knowledge provider that create... | +NamedThing, Procedure | +
| xref | +* Uriorcurie |
+A database cross reference or alternative identifier for a NamedThing or edge... | +NamedThing, Procedure | +
| full_name | +0..1 LabelType |
+a long-form human readable name for a thing | +NamedThing, Procedure | +
| synonym | +* LabelType |
+Alternate human-readable names for a thing | +NamedThing, Procedure | +
| used by | +used in | +type | +used | +
|---|---|---|---|
| BarcodedCellSample | +was_generated_by | +range | +CellBarcoding | +
| Mapping Type | +Mapped Value | +
|---|---|
| self | +bican:CellBarcoding | +
| native | +bican:CellBarcoding | +
name: CellBarcoding
+description: The process of adding a molecular barcode to individual cells in a sample.
+ The input will be either dissociated cell sample or enriched cell sample. Cell barcodes
+ are only guaranteed to be unique within this one collection. One dissociated cell
+ sample or enriched cell sample can lead to multiple barcoded cell samples.
+in_subset:
+- bican
+- library_generation
+from_schema: https://identifiers.org/brain-bican/library-generation-schema
+is_a: procedure
+mixins:
+- ProvActivity
+slots:
+- used
+slot_usage:
+ used:
+ name: used
+ description: The input dissociated or enriched cell sample(s) from which the barcoded
+ cell sample was derived from.
+ multivalued: true
+ exactly_one_of:
+ - range: DissociatedCellSample
+ - range: EnrichedCellSample
+ category:
+ name: category
+ pattern: ^bican:[A-Z][A-Za-z]+$
+attributes:
+ port_well:
+ name: port_well
+ local_names:
+ NIMP:
+ local_name_source: NIMP
+ local_name_value: barcoded_cell_sample_port_well
+ description: Specific position of the loaded port of the 10x chip. An Enriched
+ or Dissociated Cell Sample is loaded into a port on a chip (creating a Barcoded
+ Cell Sample). Can be left null for non-10x methods.
+ in_subset:
+ - analysis
+ from_schema: https://identifiers.org/brain-bican/library-generation-schema
+ exact_mappings:
+ - NIMP:PD-KJKJZK32
+ rank: 1000
+ slot_uri: bican:aca38100-d245-4be4-9be3-ba27192779fe
+ alias: barcoded cell sample port well
+ domain_of:
+ - CellBarcoding
+ range: string
+ input_quantity:
+ name: input_quantity
+ local_names:
+ NIMP:
+ local_name_source: NIMP
+ local_name_value: barcoded_cell_input_quantity_count
+ description: Number of enriched or dissociated cells/nuclei going into the barcoding
+ process.
+ in_subset:
+ - analysis
+ from_schema: https://identifiers.org/brain-bican/library-generation-schema
+ exact_mappings:
+ - NIMP:PD-ZZZZWQ40
+ rank: 1000
+ slot_uri: bican:aa534269-7c9b-4b63-b990-eea8cda56d0e
+ alias: barcoded cell input quantity count
+ domain_of:
+ - CellBarcoding
+ range: integer
+ process_date:
+ name: process_date
+ local_names:
+ NIMP:
+ local_name_source: NIMP
+ local_name_value: barcoded_cell_sample_preparation_date
+ description: Date of cell barcoding process.
+ from_schema: https://identifiers.org/brain-bican/library-generation-schema
+ exact_mappings:
+ - NIMP:PD-SHSHZS25
+ domain_of:
+ - CellDissociation
+ - CellEnrichment
+ - CellBarcoding
+ - CdnaAmplification
+ - LibraryConstruction
+ - LibraryPooling
+ method:
+ name: method
+ local_names:
+ NIMP:
+ local_name_source: NIMP
+ local_name_value: barcoded_cell_sample_technique
+ description: 'Standardized nomenclature to describe the general barcoding method
+ used. For example: Multiome, ATAC Only, GEX Only or snm3C-seq.'
+ from_schema: https://identifiers.org/brain-bican/library-generation-schema
+ exact_mappings:
+ - NIMP:PD-TDTDDF25
+ rank: 1000
+ domain_of:
+ - CellBarcoding
+ - LibraryConstruction
+ range: barcoded_cell_sample_technique
+
+name: CellBarcoding
+description: The process of adding a molecular barcode to individual cells in a sample.
+ The input will be either dissociated cell sample or enriched cell sample. Cell barcodes
+ are only guaranteed to be unique within this one collection. One dissociated cell
+ sample or enriched cell sample can lead to multiple barcoded cell samples.
+in_subset:
+- bican
+- library_generation
+from_schema: https://identifiers.org/brain-bican/library-generation-schema
+is_a: procedure
+mixins:
+- ProvActivity
+slot_usage:
+ used:
+ name: used
+ description: The input dissociated or enriched cell sample(s) from which the barcoded
+ cell sample was derived from.
+ multivalued: true
+ exactly_one_of:
+ - range: DissociatedCellSample
+ - range: EnrichedCellSample
+ category:
+ name: category
+ pattern: ^bican:[A-Z][A-Za-z]+$
+attributes:
+ port_well:
+ name: port_well
+ local_names:
+ NIMP:
+ local_name_source: NIMP
+ local_name_value: barcoded_cell_sample_port_well
+ description: Specific position of the loaded port of the 10x chip. An Enriched
+ or Dissociated Cell Sample is loaded into a port on a chip (creating a Barcoded
+ Cell Sample). Can be left null for non-10x methods.
+ in_subset:
+ - analysis
+ from_schema: https://identifiers.org/brain-bican/library-generation-schema
+ exact_mappings:
+ - NIMP:PD-KJKJZK32
+ rank: 1000
+ slot_uri: bican:aca38100-d245-4be4-9be3-ba27192779fe
+ alias: barcoded cell sample port well
+ owner: CellBarcoding
+ domain_of:
+ - CellBarcoding
+ range: string
+ input_quantity:
+ name: input_quantity
+ local_names:
+ NIMP:
+ local_name_source: NIMP
+ local_name_value: barcoded_cell_input_quantity_count
+ description: Number of enriched or dissociated cells/nuclei going into the barcoding
+ process.
+ in_subset:
+ - analysis
+ from_schema: https://identifiers.org/brain-bican/library-generation-schema
+ exact_mappings:
+ - NIMP:PD-ZZZZWQ40
+ rank: 1000
+ slot_uri: bican:aa534269-7c9b-4b63-b990-eea8cda56d0e
+ alias: barcoded cell input quantity count
+ owner: CellBarcoding
+ domain_of:
+ - CellBarcoding
+ range: integer
+ process_date:
+ name: process_date
+ local_names:
+ NIMP:
+ local_name_source: NIMP
+ local_name_value: barcoded_cell_sample_preparation_date
+ description: Date of cell barcoding process.
+ from_schema: https://identifiers.org/brain-bican/library-generation-schema
+ exact_mappings:
+ - NIMP:PD-SHSHZS25
+ alias: process_date
+ owner: CellBarcoding
+ domain_of:
+ - CellDissociation
+ - CellEnrichment
+ - CellBarcoding
+ - CdnaAmplification
+ - LibraryConstruction
+ - LibraryPooling
+ range: string
+ method:
+ name: method
+ local_names:
+ NIMP:
+ local_name_source: NIMP
+ local_name_value: barcoded_cell_sample_technique
+ description: 'Standardized nomenclature to describe the general barcoding method
+ used. For example: Multiome, ATAC Only, GEX Only or snm3C-seq.'
+ from_schema: https://identifiers.org/brain-bican/library-generation-schema
+ exact_mappings:
+ - NIMP:PD-TDTDDF25
+ rank: 1000
+ alias: method
+ owner: CellBarcoding
+ domain_of:
+ - CellBarcoding
+ - LibraryConstruction
+ range: barcoded_cell_sample_technique
+ used:
+ name: used
+ description: The input dissociated or enriched cell sample(s) from which the barcoded
+ cell sample was derived from.
+ from_schema: https://identifiers.org/brain-bican/library-generation-schema
+ rank: 1000
+ slot_uri: prov:used
+ alias: used
+ owner: CellBarcoding
+ domain_of:
+ - DissectionRoiDelineation
+ - TissueDissection
+ - CellDissociation
+ - CellEnrichment
+ - EnrichedCellSampleSplitting
+ - CellBarcoding
+ - CdnaAmplification
+ - LibraryConstruction
+ - LibraryPooling
+ - ProvActivity
+ range: ProvEntity
+ multivalued: true
+ exactly_one_of:
+ - range: DissociatedCellSample
+ - range: EnrichedCellSample
+ id:
+ name: id
+ definition_uri: https://w3id.org/biolink/vocab/id
+ description: A unique identifier for an entity. Must be either a CURIE shorthand
+ for a URI or a complete URI
+ in_subset:
+ - translator_minimal
+ from_schema: https://identifiers.org/brain-bican/library-generation-schema
+ exact_mappings:
+ - AGRKB:primaryId
+ - gff3:ID
+ - gpi:DB_Object_ID
+ rank: 1000
+ domain: entity
+ slot_uri: biolink:id
+ identifier: true
+ alias: id
+ owner: CellBarcoding
+ domain_of:
+ - ontology class
+ - entity
+ - attribute
+ - named thing
+ - taxonomic rank
+ - organism taxon
+ - information content entity
+ - dataset
+ - physical entity
+ - activity
+ - procedure
+ - material sample
+ - biological entity
+ - gene
+ - genome
+ range: string
+ required: true
+ iri:
+ name: iri
+ definition_uri: https://w3id.org/biolink/vocab/iri
+ description: An IRI for an entity. This is determined by the id using expansion
+ rules.
+ in_subset:
+ - translator_minimal
+ - samples
+ from_schema: https://identifiers.org/brain-bican/library-generation-schema
+ exact_mappings:
+ - WIKIDATA_PROPERTY:P854
+ rank: 1000
+ slot_uri: biolink:iri
+ alias: iri
+ owner: CellBarcoding
+ domain_of:
+ - attribute
+ - entity
+ - named thing
+ - organism taxon
+ - information content entity
+ - dataset
+ - physical entity
+ - activity
+ - procedure
+ - material sample
+ - biological entity
+ - gene
+ - genome
+ range: iri type
+ category:
+ name: category
+ definition_uri: https://w3id.org/biolink/vocab/category
+ description: Name of the high level ontology class in which this entity is categorized.
+ Corresponds to the label for the biolink entity type class. In a neo4j database
+ this MAY correspond to the neo4j label tag. In an RDF database it should be
+ a biolink model class URI. This field is multi-valued. It should include values
+ for ancestors of the biolink class; for example, a protein such as Shh would
+ have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`.
+ In an RDF database, nodes will typically have an rdf:type triples. This can
+ be to the most specific biolink class, or potentially to a class more specific
+ than something in biolink. For example, a sequence feature `f` may have a rdf:type
+ assertion to a SO class such as TF_binding_site, which is more specific than
+ anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity,
+ biolink:NamedThing}
+ in_subset:
+ - translator_minimal
+ from_schema: https://identifiers.org/brain-bican/library-generation-schema
+ rank: 1000
+ is_a: type
+ domain: entity
+ slot_uri: biolink:category
+ designates_type: true
+ alias: category
+ owner: CellBarcoding
+ domain_of:
+ - entity
+ - attribute
+ - named thing
+ - organism taxon
+ - information content entity
+ - dataset
+ - physical entity
+ - activity
+ - procedure
+ - material sample
+ - biological entity
+ - gene
+ - genome
+ is_class_field: true
+ range: uriorcurie
+ multivalued: true
+ pattern: ^bican:[A-Z][A-Za-z]+$
+ type:
+ name: type
+ definition_uri: https://w3id.org/biolink/vocab/type
+ from_schema: https://identifiers.org/brain-bican/library-generation-schema
+ mappings:
+ - rdf:type
+ exact_mappings:
+ - gff3:type
+ - gpi:DB_Object_Type
+ rank: 1000
+ domain: entity
+ slot_uri: rdf:type
+ alias: type
+ owner: CellBarcoding
+ domain_of:
+ - entity
+ - attribute
+ - named thing
+ - organism taxon
+ - information content entity
+ - dataset
+ - physical entity
+ - activity
+ - procedure
+ - material sample
+ - biological entity
+ - gene
+ - genome
+ range: string
+ multivalued: true
+ name:
+ name: name
+ definition_uri: https://w3id.org/biolink/vocab/name
+ description: A human-readable name for an attribute or entity.
+ in_subset:
+ - translator_minimal
+ - samples
+ from_schema: https://identifiers.org/brain-bican/library-generation-schema
+ aliases:
+ - label
+ - display name
+ - title
+ mappings:
+ - rdfs:label
+ exact_mappings:
+ - gff3:Name
+ - gpi:DB_Object_Name
+ narrow_mappings:
+ - dct:title
+ - WIKIDATA_PROPERTY:P1476
+ rank: 1000
+ domain: entity
+ slot_uri: rdfs:label
+ alias: name
+ owner: CellBarcoding
+ domain_of:
+ - attribute
+ - entity
+ - macromolecular machine mixin
+ - Donor
+ - BrainSlab
+ - TissueSample
+ - DissociatedCellSample
+ - EnrichedCellSample
+ - BarcodedCellSample
+ - AmplifiedCdna
+ - Library
+ - LibraryAliquot
+ - LibraryPool
+ - DissectionRoiPolygon
+ - named thing
+ - organism taxon
+ - information content entity
+ - dataset
+ - physical entity
+ - activity
+ - procedure
+ - material sample
+ - biological entity
+ - gene or gene product
+ - gene
+ - genome
+ range: label type
+ description:
+ name: description
+ definition_uri: https://w3id.org/biolink/vocab/description
+ description: a human-readable description of an entity
+ in_subset:
+ - translator_minimal
+ from_schema: https://identifiers.org/brain-bican/library-generation-schema
+ aliases:
+ - definition
+ mappings:
+ - dct:description
+ exact_mappings:
+ - IAO:0000115
+ - skos:definitions
+ narrow_mappings:
+ - gff3:Description
+ rank: 1000
+ slot_uri: dct:description
+ alias: description
+ owner: CellBarcoding
+ domain_of:
+ - entity
+ - attribute
+ - named thing
+ - organism taxon
+ - information content entity
+ - dataset
+ - physical entity
+ - activity
+ - procedure
+ - material sample
+ - biological entity
+ - gene
+ - genome
+ range: narrative text
+ has attribute:
+ name: has attribute
+ definition_uri: https://w3id.org/biolink/vocab/has_attribute
+ description: connects any entity to an attribute
+ in_subset:
+ - samples
+ from_schema: https://identifiers.org/brain-bican/library-generation-schema
+ exact_mappings:
+ - SIO:000008
+ close_mappings:
+ - OBI:0001927
+ narrow_mappings:
+ - OBAN:association_has_subject_property
+ - OBAN:association_has_object_property
+ - CPT:has_possibly_included_panel_element
+ - DRUGBANK:category
+ - EFO:is_executed_in
+ - HANCESTRO:0301
+ - LOINC:has_action_guidance
+ - LOINC:has_adjustment
+ - LOINC:has_aggregation_view
+ - LOINC:has_approach_guidance
+ - LOINC:has_divisor
+ - LOINC:has_exam
+ - LOINC:has_method
+ - LOINC:has_modality_subtype
+ - LOINC:has_object_guidance
+ - LOINC:has_scale
+ - LOINC:has_suffix
+ - LOINC:has_time_aspect
+ - LOINC:has_time_modifier
+ - LOINC:has_timing_of
+ - NCIT:R88
+ - NCIT:eo_disease_has_property_or_attribute
+ - NCIT:has_data_element
+ - NCIT:has_pharmaceutical_administration_method
+ - NCIT:has_pharmaceutical_basic_dose_form
+ - NCIT:has_pharmaceutical_intended_site
+ - NCIT:has_pharmaceutical_release_characteristics
+ - NCIT:has_pharmaceutical_state_of_matter
+ - NCIT:has_pharmaceutical_transformation
+ - NCIT:is_qualified_by
+ - NCIT:qualifier_applies_to
+ - NCIT:role_has_domain
+ - NCIT:role_has_range
+ - INO:0000154
+ - HANCESTRO:0308
+ - OMIM:has_inheritance_type
+ - orphanet:C016
+ - orphanet:C017
+ - RO:0000053
+ - RO:0000086
+ - RO:0000087
+ - SNOMED:has_access
+ - SNOMED:has_clinical_course
+ - SNOMED:has_count_of_base_of_active_ingredient
+ - SNOMED:has_dose_form_administration_method
+ - SNOMED:has_dose_form_release_characteristic
+ - SNOMED:has_dose_form_transformation
+ - SNOMED:has_finding_context
+ - SNOMED:has_finding_informer
+ - SNOMED:has_inherent_attribute
+ - SNOMED:has_intent
+ - SNOMED:has_interpretation
+ - SNOMED:has_laterality
+ - SNOMED:has_measurement_method
+ - SNOMED:has_method
+ - SNOMED:has_priority
+ - SNOMED:has_procedure_context
+ - SNOMED:has_process_duration
+ - SNOMED:has_property
+ - SNOMED:has_revision_status
+ - SNOMED:has_scale_type
+ - SNOMED:has_severity
+ - SNOMED:has_specimen
+ - SNOMED:has_state_of_matter
+ - SNOMED:has_subject_relationship_context
+ - SNOMED:has_surgical_approach
+ - SNOMED:has_technique
+ - SNOMED:has_temporal_context
+ - SNOMED:has_time_aspect
+ - SNOMED:has_units
+ - UMLS:has_structural_class
+ - UMLS:has_supported_concept_property
+ - UMLS:has_supported_concept_relationship
+ - UMLS:may_be_qualified_by
+ rank: 1000
+ domain: entity
+ slot_uri: biolink:has_attribute
+ alias: has_attribute
+ owner: CellBarcoding
+ domain_of:
+ - entity
+ - attribute
+ - named thing
+ - organism taxon
+ - information content entity
+ - dataset
+ - physical entity
+ - activity
+ - procedure
+ - material sample
+ - biological entity
+ - gene
+ - genome
+ range: attribute
+ multivalued: true
+ deprecated:
+ name: deprecated
+ definition_uri: https://w3id.org/biolink/vocab/deprecated
+ description: A boolean flag indicating that an entity is no longer considered
+ current or valid.
+ from_schema: https://identifiers.org/brain-bican/library-generation-schema
+ exact_mappings:
+ - oboInOwl:ObsoleteClass
+ rank: 1000
+ slot_uri: biolink:deprecated
+ alias: deprecated
+ owner: CellBarcoding
+ domain_of:
+ - entity
+ - attribute
+ - named thing
+ - organism taxon
+ - information content entity
+ - dataset
+ - physical entity
+ - activity
+ - procedure
+ - material sample
+ - biological entity
+ - gene
+ - genome
+ range: boolean
+ provided by:
+ name: provided by
+ definition_uri: https://w3id.org/biolink/vocab/provided_by
+ description: The value in this node property represents the knowledge provider
+ that created or assembled the node and all of its attributes. Used internally
+ to represent how a particular node made its way into a knowledge provider or
+ graph.
+ from_schema: https://identifiers.org/brain-bican/library-generation-schema
+ rank: 1000
+ is_a: node property
+ domain: named thing
+ slot_uri: biolink:provided_by
+ alias: provided_by
+ owner: CellBarcoding
+ domain_of:
+ - named thing
+ - attribute
+ - organism taxon
+ - information content entity
+ - dataset
+ - physical entity
+ - activity
+ - procedure
+ - material sample
+ - biological entity
+ - gene
+ - genome
+ range: string
+ multivalued: true
+ xref:
+ name: xref
+ definition_uri: https://w3id.org/biolink/vocab/xref
+ description: A database cross reference or alternative identifier for a NamedThing
+ or edge between two NamedThings. This property should point to a database record
+ or webpage that supports the existence of the edge, or gives more detail about
+ the edge. This property can be used on a node or edge to provide multiple URIs
+ or CURIE cross references.
+ in_subset:
+ - translator_minimal
+ from_schema: https://identifiers.org/brain-bican/library-generation-schema
+ aliases:
+ - dbxref
+ - Dbxref
+ - DbXref
+ - record_url
+ - source_record_urls
+ narrow_mappings:
+ - gff3:Dbxref
+ - gpi:DB_Xrefs
+ rank: 1000
+ domain: named thing
+ slot_uri: biolink:xref
+ alias: xref
+ owner: CellBarcoding
+ domain_of:
+ - named thing
+ - gene
+ - attribute
+ - organism taxon
+ - information content entity
+ - dataset
+ - physical entity
+ - activity
+ - procedure
+ - material sample
+ - biological entity
+ - genome
+ range: uriorcurie
+ multivalued: true
+ full name:
+ name: full name
+ definition_uri: https://w3id.org/biolink/vocab/full_name
+ description: a long-form human readable name for a thing
+ from_schema: https://identifiers.org/brain-bican/library-generation-schema
+ rank: 1000
+ is_a: node property
+ domain: named thing
+ slot_uri: biolink:full_name
+ alias: full_name
+ owner: CellBarcoding
+ domain_of:
+ - named thing
+ - attribute
+ - organism taxon
+ - information content entity
+ - dataset
+ - physical entity
+ - activity
+ - procedure
+ - material sample
+ - biological entity
+ - gene
+ - genome
+ range: label type
+ synonym:
+ name: synonym
+ definition_uri: https://w3id.org/biolink/vocab/synonym
+ description: Alternate human-readable names for a thing
+ in_subset:
+ - translator_minimal
+ from_schema: https://identifiers.org/brain-bican/library-generation-schema
+ aliases:
+ - alias
+ narrow_mappings:
+ - skos:altLabel
+ - gff3:Alias
+ - AGRKB:synonyms
+ - gpi:DB_Object_Synonyms
+ - HANCESTRO:0330
+ - IAO:0000136
+ - RXNORM:has_tradename
+ rank: 1000
+ is_a: node property
+ domain: named thing
+ slot_uri: biolink:synonym
+ alias: synonym
+ owner: CellBarcoding
+ domain_of:
+ - named thing
+ - attribute
+ - organism taxon
+ - information content entity
+ - dataset
+ - physical entity
+ - activity
+ - procedure
+ - material sample
+ - biological entity
+ - gene
+ - genome
+ range: label type
+ multivalued: true
+
+The process of generating dissociated cells from an input tissue sample. This process could also introduce a tissue-source barcode (eg cell hashing), allowing mixing of cell dissociation samples at the cell barcoding step.
+ +| Name | +Cardinality and Range | +Description | +Inheritance | +
|---|---|---|---|
| used | +* TissueSample |
+The input tissue sample(s) from which the dissociated cell sample was derived... | +direct | +
| process_date | +0..1 String |
+Date of cell dissociation process | +direct | +
| id | +1 String |
+A unique identifier for an entity | +NamedThing, Procedure, Entity | +
| iri | +0..1 IriType |
+An IRI for an entity | +NamedThing, Procedure, Entity | +
| category | +* Uriorcurie |
+Name of the high level ontology class in which this entity is categorized | +NamedThing, Procedure, Entity | +
| type | +* String |
++ | NamedThing, Procedure, Entity | +
| name | +0..1 LabelType |
+A human-readable name for an attribute or entity | +NamedThing, Procedure, Entity | +
| description | +0..1 NarrativeText |
+a human-readable description of an entity | +NamedThing, Procedure, Entity | +
| has_attribute | +* Attribute |
+connects any entity to an attribute | +NamedThing, Procedure, Entity | +
| deprecated | +0..1 Boolean |
+A boolean flag indicating that an entity is no longer considered current or v... | +NamedThing, Procedure, Entity | +
| provided_by | +* String |
+The value in this node property represents the knowledge provider that create... | +NamedThing, Procedure | +
| xref | +* Uriorcurie |
+A database cross reference or alternative identifier for a NamedThing or edge... | +NamedThing, Procedure | +
| full_name | +0..1 LabelType |
+a long-form human readable name for a thing | +NamedThing, Procedure | +
| synonym | +* LabelType |
+Alternate human-readable names for a thing | +NamedThing, Procedure | +
| used by | +used in | +type | +used | +
|---|---|---|---|
| DissociatedCellSample | +was_generated_by | +range | +CellDissociation | +
| Mapping Type | +Mapped Value | +
|---|---|
| self | +bican:CellDissociation | +
| native | +bican:CellDissociation | +
name: CellDissociation
+description: The process of generating dissociated cells from an input tissue sample.
+ This process could also introduce a tissue-source barcode (eg cell hashing), allowing
+ mixing of cell dissociation samples at the cell barcoding step.
+in_subset:
+- bican
+- library_generation
+from_schema: https://identifiers.org/brain-bican/library-generation-schema
+is_a: procedure
+mixins:
+- ProvActivity
+slots:
+- used
+slot_usage:
+ used:
+ name: used
+ description: The input tissue sample(s) from which the dissociated cell sample
+ was derived from.
+ range: TissueSample
+ multivalued: true
+ category:
+ name: category
+ pattern: ^bican:[A-Z][A-Za-z]+$
+attributes:
+ process_date:
+ name: process_date
+ local_names:
+ NIMP:
+ local_name_source: NIMP
+ local_name_value: dissociated_cell_sample_preparation_date
+ description: Date of cell dissociation process.
+ from_schema: https://identifiers.org/brain-bican/library-generation-schema
+ exact_mappings:
+ - NIMP:PD-BUBUFE27
+ rank: 1000
+ domain_of:
+ - CellDissociation
+ - CellEnrichment
+ - CellBarcoding
+ - CdnaAmplification
+ - LibraryConstruction
+ - LibraryPooling
+
+name: CellDissociation
+description: The process of generating dissociated cells from an input tissue sample.
+ This process could also introduce a tissue-source barcode (eg cell hashing), allowing
+ mixing of cell dissociation samples at the cell barcoding step.
+in_subset:
+- bican
+- library_generation
+from_schema: https://identifiers.org/brain-bican/library-generation-schema
+is_a: procedure
+mixins:
+- ProvActivity
+slot_usage:
+ used:
+ name: used
+ description: The input tissue sample(s) from which the dissociated cell sample
+ was derived from.
+ range: TissueSample
+ multivalued: true
+ category:
+ name: category
+ pattern: ^bican:[A-Z][A-Za-z]+$
+attributes:
+ process_date:
+ name: process_date
+ local_names:
+ NIMP:
+ local_name_source: NIMP
+ local_name_value: dissociated_cell_sample_preparation_date
+ description: Date of cell dissociation process.
+ from_schema: https://identifiers.org/brain-bican/library-generation-schema
+ exact_mappings:
+ - NIMP:PD-BUBUFE27
+ rank: 1000
+ alias: process_date
+ owner: CellDissociation
+ domain_of:
+ - CellDissociation
+ - CellEnrichment
+ - CellBarcoding
+ - CdnaAmplification
+ - LibraryConstruction
+ - LibraryPooling
+ range: string
+ used:
+ name: used
+ description: The input tissue sample(s) from which the dissociated cell sample
+ was derived from.
+ from_schema: https://identifiers.org/brain-bican/library-generation-schema
+ rank: 1000
+ slot_uri: prov:used
+ alias: used
+ owner: CellDissociation
+ domain_of:
+ - DissectionRoiDelineation
+ - TissueDissection
+ - CellDissociation
+ - CellEnrichment
+ - EnrichedCellSampleSplitting
+ - CellBarcoding
+ - CdnaAmplification
+ - LibraryConstruction
+ - LibraryPooling
+ - ProvActivity
+ range: TissueSample
+ multivalued: true
+ id:
+ name: id
+ definition_uri: https://w3id.org/biolink/vocab/id
+ description: A unique identifier for an entity. Must be either a CURIE shorthand
+ for a URI or a complete URI
+ in_subset:
+ - translator_minimal
+ from_schema: https://identifiers.org/brain-bican/library-generation-schema
+ exact_mappings:
+ - AGRKB:primaryId
+ - gff3:ID
+ - gpi:DB_Object_ID
+ rank: 1000
+ domain: entity
+ slot_uri: biolink:id
+ identifier: true
+ alias: id
+ owner: CellDissociation
+ domain_of:
+ - ontology class
+ - entity
+ - attribute
+ - named thing
+ - taxonomic rank
+ - organism taxon
+ - information content entity
+ - dataset
+ - physical entity
+ - activity
+ - procedure
+ - material sample
+ - biological entity
+ - gene
+ - genome
+ range: string
+ required: true
+ iri:
+ name: iri
+ definition_uri: https://w3id.org/biolink/vocab/iri
+ description: An IRI for an entity. This is determined by the id using expansion
+ rules.
+ in_subset:
+ - translator_minimal
+ - samples
+ from_schema: https://identifiers.org/brain-bican/library-generation-schema
+ exact_mappings:
+ - WIKIDATA_PROPERTY:P854
+ rank: 1000
+ slot_uri: biolink:iri
+ alias: iri
+ owner: CellDissociation
+ domain_of:
+ - attribute
+ - entity
+ - named thing
+ - organism taxon
+ - information content entity
+ - dataset
+ - physical entity
+ - activity
+ - procedure
+ - material sample
+ - biological entity
+ - gene
+ - genome
+ range: iri type
+ category:
+ name: category
+ definition_uri: https://w3id.org/biolink/vocab/category
+ description: Name of the high level ontology class in which this entity is categorized.
+ Corresponds to the label for the biolink entity type class. In a neo4j database
+ this MAY correspond to the neo4j label tag. In an RDF database it should be
+ a biolink model class URI. This field is multi-valued. It should include values
+ for ancestors of the biolink class; for example, a protein such as Shh would
+ have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`.
+ In an RDF database, nodes will typically have an rdf:type triples. This can
+ be to the most specific biolink class, or potentially to a class more specific
+ than something in biolink. For example, a sequence feature `f` may have a rdf:type
+ assertion to a SO class such as TF_binding_site, which is more specific than
+ anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity,
+ biolink:NamedThing}
+ in_subset:
+ - translator_minimal
+ from_schema: https://identifiers.org/brain-bican/library-generation-schema
+ rank: 1000
+ is_a: type
+ domain: entity
+ slot_uri: biolink:category
+ designates_type: true
+ alias: category
+ owner: CellDissociation
+ domain_of:
+ - entity
+ - attribute
+ - named thing
+ - organism taxon
+ - information content entity
+ - dataset
+ - physical entity
+ - activity
+ - procedure
+ - material sample
+ - biological entity
+ - gene
+ - genome
+ is_class_field: true
+ range: uriorcurie
+ multivalued: true
+ pattern: ^bican:[A-Z][A-Za-z]+$
+ type:
+ name: type
+ definition_uri: https://w3id.org/biolink/vocab/type
+ from_schema: https://identifiers.org/brain-bican/library-generation-schema
+ mappings:
+ - rdf:type
+ exact_mappings:
+ - gff3:type
+ - gpi:DB_Object_Type
+ rank: 1000
+ domain: entity
+ slot_uri: rdf:type
+ alias: type
+ owner: CellDissociation
+ domain_of:
+ - entity
+ - attribute
+ - named thing
+ - organism taxon
+ - information content entity
+ - dataset
+ - physical entity
+ - activity
+ - procedure
+ - material sample
+ - biological entity
+ - gene
+ - genome
+ range: string
+ multivalued: true
+ name:
+ name: name
+ definition_uri: https://w3id.org/biolink/vocab/name
+ description: A human-readable name for an attribute or entity.
+ in_subset:
+ - translator_minimal
+ - samples
+ from_schema: https://identifiers.org/brain-bican/library-generation-schema
+ aliases:
+ - label
+ - display name
+ - title
+ mappings:
+ - rdfs:label
+ exact_mappings:
+ - gff3:Name
+ - gpi:DB_Object_Name
+ narrow_mappings:
+ - dct:title
+ - WIKIDATA_PROPERTY:P1476
+ rank: 1000
+ domain: entity
+ slot_uri: rdfs:label
+ alias: name
+ owner: CellDissociation
+ domain_of:
+ - attribute
+ - entity
+ - macromolecular machine mixin
+ - Donor
+ - BrainSlab
+ - TissueSample
+ - DissociatedCellSample
+ - EnrichedCellSample
+ - BarcodedCellSample
+ - AmplifiedCdna
+ - Library
+ - LibraryAliquot
+ - LibraryPool
+ - DissectionRoiPolygon
+ - named thing
+ - organism taxon
+ - information content entity
+ - dataset
+ - physical entity
+ - activity
+ - procedure
+ - material sample
+ - biological entity
+ - gene or gene product
+ - gene
+ - genome
+ range: label type
+ description:
+ name: description
+ definition_uri: https://w3id.org/biolink/vocab/description
+ description: a human-readable description of an entity
+ in_subset:
+ - translator_minimal
+ from_schema: https://identifiers.org/brain-bican/library-generation-schema
+ aliases:
+ - definition
+ mappings:
+ - dct:description
+ exact_mappings:
+ - IAO:0000115
+ - skos:definitions
+ narrow_mappings:
+ - gff3:Description
+ rank: 1000
+ slot_uri: dct:description
+ alias: description
+ owner: CellDissociation
+ domain_of:
+ - entity
+ - attribute
+ - named thing
+ - organism taxon
+ - information content entity
+ - dataset
+ - physical entity
+ - activity
+ - procedure
+ - material sample
+ - biological entity
+ - gene
+ - genome
+ range: narrative text
+ has attribute:
+ name: has attribute
+ definition_uri: https://w3id.org/biolink/vocab/has_attribute
+ description: connects any entity to an attribute
+ in_subset:
+ - samples
+ from_schema: https://identifiers.org/brain-bican/library-generation-schema
+ exact_mappings:
+ - SIO:000008
+ close_mappings:
+ - OBI:0001927
+ narrow_mappings:
+ - OBAN:association_has_subject_property
+ - OBAN:association_has_object_property
+ - CPT:has_possibly_included_panel_element
+ - DRUGBANK:category
+ - EFO:is_executed_in
+ - HANCESTRO:0301
+ - LOINC:has_action_guidance
+ - LOINC:has_adjustment
+ - LOINC:has_aggregation_view
+ - LOINC:has_approach_guidance
+ - LOINC:has_divisor
+ - LOINC:has_exam
+ - LOINC:has_method
+ - LOINC:has_modality_subtype
+ - LOINC:has_object_guidance
+ - LOINC:has_scale
+ - LOINC:has_suffix
+ - LOINC:has_time_aspect
+ - LOINC:has_time_modifier
+ - LOINC:has_timing_of
+ - NCIT:R88
+ - NCIT:eo_disease_has_property_or_attribute
+ - NCIT:has_data_element
+ - NCIT:has_pharmaceutical_administration_method
+ - NCIT:has_pharmaceutical_basic_dose_form
+ - NCIT:has_pharmaceutical_intended_site
+ - NCIT:has_pharmaceutical_release_characteristics
+ - NCIT:has_pharmaceutical_state_of_matter
+ - NCIT:has_pharmaceutical_transformation
+ - NCIT:is_qualified_by
+ - NCIT:qualifier_applies_to
+ - NCIT:role_has_domain
+ - NCIT:role_has_range
+ - INO:0000154
+ - HANCESTRO:0308
+ - OMIM:has_inheritance_type
+ - orphanet:C016
+ - orphanet:C017
+ - RO:0000053
+ - RO:0000086
+ - RO:0000087
+ - SNOMED:has_access
+ - SNOMED:has_clinical_course
+ - SNOMED:has_count_of_base_of_active_ingredient
+ - SNOMED:has_dose_form_administration_method
+ - SNOMED:has_dose_form_release_characteristic
+ - SNOMED:has_dose_form_transformation
+ - SNOMED:has_finding_context
+ - SNOMED:has_finding_informer
+ - SNOMED:has_inherent_attribute
+ - SNOMED:has_intent
+ - SNOMED:has_interpretation
+ - SNOMED:has_laterality
+ - SNOMED:has_measurement_method
+ - SNOMED:has_method
+ - SNOMED:has_priority
+ - SNOMED:has_procedure_context
+ - SNOMED:has_process_duration
+ - SNOMED:has_property
+ - SNOMED:has_revision_status
+ - SNOMED:has_scale_type
+ - SNOMED:has_severity
+ - SNOMED:has_specimen
+ - SNOMED:has_state_of_matter
+ - SNOMED:has_subject_relationship_context
+ - SNOMED:has_surgical_approach
+ - SNOMED:has_technique
+ - SNOMED:has_temporal_context
+ - SNOMED:has_time_aspect
+ - SNOMED:has_units
+ - UMLS:has_structural_class
+ - UMLS:has_supported_concept_property
+ - UMLS:has_supported_concept_relationship
+ - UMLS:may_be_qualified_by
+ rank: 1000
+ domain: entity
+ slot_uri: biolink:has_attribute
+ alias: has_attribute
+ owner: CellDissociation
+ domain_of:
+ - entity
+ - attribute
+ - named thing
+ - organism taxon
+ - information content entity
+ - dataset
+ - physical entity
+ - activity
+ - procedure
+ - material sample
+ - biological entity
+ - gene
+ - genome
+ range: attribute
+ multivalued: true
+ deprecated:
+ name: deprecated
+ definition_uri: https://w3id.org/biolink/vocab/deprecated
+ description: A boolean flag indicating that an entity is no longer considered
+ current or valid.
+ from_schema: https://identifiers.org/brain-bican/library-generation-schema
+ exact_mappings:
+ - oboInOwl:ObsoleteClass
+ rank: 1000
+ slot_uri: biolink:deprecated
+ alias: deprecated
+ owner: CellDissociation
+ domain_of:
+ - entity
+ - attribute
+ - named thing
+ - organism taxon
+ - information content entity
+ - dataset
+ - physical entity
+ - activity
+ - procedure
+ - material sample
+ - biological entity
+ - gene
+ - genome
+ range: boolean
+ provided by:
+ name: provided by
+ definition_uri: https://w3id.org/biolink/vocab/provided_by
+ description: The value in this node property represents the knowledge provider
+ that created or assembled the node and all of its attributes. Used internally
+ to represent how a particular node made its way into a knowledge provider or
+ graph.
+ from_schema: https://identifiers.org/brain-bican/library-generation-schema
+ rank: 1000
+ is_a: node property
+ domain: named thing
+ slot_uri: biolink:provided_by
+ alias: provided_by
+ owner: CellDissociation
+ domain_of:
+ - named thing
+ - attribute
+ - organism taxon
+ - information content entity
+ - dataset
+ - physical entity
+ - activity
+ - procedure
+ - material sample
+ - biological entity
+ - gene
+ - genome
+ range: string
+ multivalued: true
+ xref:
+ name: xref
+ definition_uri: https://w3id.org/biolink/vocab/xref
+ description: A database cross reference or alternative identifier for a NamedThing
+ or edge between two NamedThings. This property should point to a database record
+ or webpage that supports the existence of the edge, or gives more detail about
+ the edge. This property can be used on a node or edge to provide multiple URIs
+ or CURIE cross references.
+ in_subset:
+ - translator_minimal
+ from_schema: https://identifiers.org/brain-bican/library-generation-schema
+ aliases:
+ - dbxref
+ - Dbxref
+ - DbXref
+ - record_url
+ - source_record_urls
+ narrow_mappings:
+ - gff3:Dbxref
+ - gpi:DB_Xrefs
+ rank: 1000
+ domain: named thing
+ slot_uri: biolink:xref
+ alias: xref
+ owner: CellDissociation
+ domain_of:
+ - named thing
+ - gene
+ - attribute
+ - organism taxon
+ - information content entity
+ - dataset
+ - physical entity
+ - activity
+ - procedure
+ - material sample
+ - biological entity
+ - genome
+ range: uriorcurie
+ multivalued: true
+ full name:
+ name: full name
+ definition_uri: https://w3id.org/biolink/vocab/full_name
+ description: a long-form human readable name for a thing
+ from_schema: https://identifiers.org/brain-bican/library-generation-schema
+ rank: 1000
+ is_a: node property
+ domain: named thing
+ slot_uri: biolink:full_name
+ alias: full_name
+ owner: CellDissociation
+ domain_of:
+ - named thing
+ - attribute
+ - organism taxon
+ - information content entity
+ - dataset
+ - physical entity
+ - activity
+ - procedure
+ - material sample
+ - biological entity
+ - gene
+ - genome
+ range: label type
+ synonym:
+ name: synonym
+ definition_uri: https://w3id.org/biolink/vocab/synonym
+ description: Alternate human-readable names for a thing
+ in_subset:
+ - translator_minimal
+ from_schema: https://identifiers.org/brain-bican/library-generation-schema
+ aliases:
+ - alias
+ narrow_mappings:
+ - skos:altLabel
+ - gff3:Alias
+ - AGRKB:synonyms
+ - gpi:DB_Object_Synonyms
+ - HANCESTRO:0330
+ - IAO:0000136
+ - RXNORM:has_tradename
+ rank: 1000
+ is_a: node property
+ domain: named thing
+ slot_uri: biolink:synonym
+ alias: synonym
+ owner: CellDissociation
+ domain_of:
+ - named thing
+ - attribute
+ - organism taxon
+ - information content entity
+ - dataset
+ - physical entity
+ - activity
+ - procedure
+ - material sample
+ - biological entity
+ - gene
+ - genome
+ range: label type
+ multivalued: true
+
+The process of enriching a dissociated cell sample by including or excluding cells of different types based on an enrichment plan using techniques such as fluorescence-activated cell sorting (FACS). This process could also introduce a tissue-source barcode (eg cell hashing), allowing mixing of cell enriched samples at the cell barcoding step.
+URI: bican:CellEnrichment
+| Name | +Cardinality and Range | +Description | +Inheritance | +
|---|---|---|---|
| used | +* DissociatedCellSample |
+The input dissociated cell sample(s) from which the enriched cell sample was ... | +direct | +
| process_date | +0..1 String |
+Date of cell enrichment process | +direct | +
| id | +1 String |
+A unique identifier for an entity | +NamedThing, Procedure, Entity | +
| iri | +0..1 IriType |
+An IRI for an entity | +NamedThing, Procedure, Entity | +
| category | +* Uriorcurie |
+Name of the high level ontology class in which this entity is categorized | +NamedThing, Procedure, Entity | +
| type | +* String |
++ | NamedThing, Procedure, Entity | +
| name | +0..1 LabelType |
+A human-readable name for an attribute or entity | +NamedThing, Procedure, Entity | +
| description | +0..1 NarrativeText |
+a human-readable description of an entity | +NamedThing, Procedure, Entity | +
| has_attribute | +* Attribute |
+connects any entity to an attribute | +NamedThing, Procedure, Entity | +
| deprecated | +0..1 Boolean |
+A boolean flag indicating that an entity is no longer considered current or v... | +NamedThing, Procedure, Entity | +
| provided_by | +* String |
+The value in this node property represents the knowledge provider that create... | +NamedThing, Procedure | +
| xref | +* Uriorcurie |
+A database cross reference or alternative identifier for a NamedThing or edge... | +NamedThing, Procedure | +
| full_name | +0..1 LabelType |
+a long-form human readable name for a thing | +NamedThing, Procedure | +
| synonym | +* LabelType |
+Alternate human-readable names for a thing | +NamedThing, Procedure | +
| used by | +used in | +type | +used | +
|---|---|---|---|
| EnrichedCellSample | +was_generated_by | +exactly_one_of[range] | +CellEnrichment | +
| Mapping Type | +Mapped Value | +
|---|---|
| self | +bican:CellEnrichment | +
| native | +bican:CellEnrichment | +
name: CellEnrichment
+description: The process of enriching a dissociated cell sample by including or excluding
+ cells of different types based on an enrichment plan using techniques such as fluorescence-activated
+ cell sorting (FACS). This process could also introduce a tissue-source barcode (eg
+ cell hashing), allowing mixing of cell enriched samples at the cell barcoding step.
+in_subset:
+- bican
+- library_generation
+from_schema: https://identifiers.org/brain-bican/library-generation-schema
+is_a: procedure
+mixins:
+- ProvActivity
+slots:
+- used
+slot_usage:
+ used:
+ name: used
+ description: The input dissociated cell sample(s) from which the enriched cell
+ sample was derived from.
+ range: DissociatedCellSample
+ multivalued: true
+ category:
+ name: category
+ pattern: ^bican:[A-Z][A-Za-z]+$
+attributes:
+ process_date:
+ name: process_date
+ local_names:
+ NIMP:
+ local_name_source: NIMP
+ local_name_value: enriched_cell_sample_preparation_date
+ description: Date of cell enrichment process.
+ from_schema: https://identifiers.org/brain-bican/library-generation-schema
+ exact_mappings:
+ - NIMP:PD-PFPFFC28
+ domain_of:
+ - CellDissociation
+ - CellEnrichment
+ - CellBarcoding
+ - CdnaAmplification
+ - LibraryConstruction
+ - LibraryPooling
+
+name: CellEnrichment
+description: The process of enriching a dissociated cell sample by including or excluding
+ cells of different types based on an enrichment plan using techniques such as fluorescence-activated
+ cell sorting (FACS). This process could also introduce a tissue-source barcode (eg
+ cell hashing), allowing mixing of cell enriched samples at the cell barcoding step.
+in_subset:
+- bican
+- library_generation
+from_schema: https://identifiers.org/brain-bican/library-generation-schema
+is_a: procedure
+mixins:
+- ProvActivity
+slot_usage:
+ used:
+ name: used
+ description: The input dissociated cell sample(s) from which the enriched cell
+ sample was derived from.
+ range: DissociatedCellSample
+ multivalued: true
+ category:
+ name: category
+ pattern: ^bican:[A-Z][A-Za-z]+$
+attributes:
+ process_date:
+ name: process_date
+ local_names:
+ NIMP:
+ local_name_source: NIMP
+ local_name_value: enriched_cell_sample_preparation_date
+ description: Date of cell enrichment process.
+ from_schema: https://identifiers.org/brain-bican/library-generation-schema
+ exact_mappings:
+ - NIMP:PD-PFPFFC28
+ alias: process_date
+ owner: CellEnrichment
+ domain_of:
+ - CellDissociation
+ - CellEnrichment
+ - CellBarcoding
+ - CdnaAmplification
+ - LibraryConstruction
+ - LibraryPooling
+ range: string
+ used:
+ name: used
+ description: The input dissociated cell sample(s) from which the enriched cell
+ sample was derived from.
+ from_schema: https://identifiers.org/brain-bican/library-generation-schema
+ rank: 1000
+ slot_uri: prov:used
+ alias: used
+ owner: CellEnrichment
+ domain_of:
+ - DissectionRoiDelineation
+ - TissueDissection
+ - CellDissociation
+ - CellEnrichment
+ - EnrichedCellSampleSplitting
+ - CellBarcoding
+ - CdnaAmplification
+ - LibraryConstruction
+ - LibraryPooling
+ - ProvActivity
+ range: DissociatedCellSample
+ multivalued: true
+ id:
+ name: id
+ definition_uri: https://w3id.org/biolink/vocab/id
+ description: A unique identifier for an entity. Must be either a CURIE shorthand
+ for a URI or a complete URI
+ in_subset:
+ - translator_minimal
+ from_schema: https://identifiers.org/brain-bican/library-generation-schema
+ exact_mappings:
+ - AGRKB:primaryId
+ - gff3:ID
+ - gpi:DB_Object_ID
+ rank: 1000
+ domain: entity
+ slot_uri: biolink:id
+ identifier: true
+ alias: id
+ owner: CellEnrichment
+ domain_of:
+ - ontology class
+ - entity
+ - attribute
+ - named thing
+ - taxonomic rank
+ - organism taxon
+ - information content entity
+ - dataset
+ - physical entity
+ - activity
+ - procedure
+ - material sample
+ - biological entity
+ - gene
+ - genome
+ range: string
+ required: true
+ iri:
+ name: iri
+ definition_uri: https://w3id.org/biolink/vocab/iri
+ description: An IRI for an entity. This is determined by the id using expansion
+ rules.
+ in_subset:
+ - translator_minimal
+ - samples
+ from_schema: https://identifiers.org/brain-bican/library-generation-schema
+ exact_mappings:
+ - WIKIDATA_PROPERTY:P854
+ rank: 1000
+ slot_uri: biolink:iri
+ alias: iri
+ owner: CellEnrichment
+ domain_of:
+ - attribute
+ - entity
+ - named thing
+ - organism taxon
+ - information content entity
+ - dataset
+ - physical entity
+ - activity
+ - procedure
+ - material sample
+ - biological entity
+ - gene
+ - genome
+ range: iri type
+ category:
+ name: category
+ definition_uri: https://w3id.org/biolink/vocab/category
+ description: Name of the high level ontology class in which this entity is categorized.
+ Corresponds to the label for the biolink entity type class. In a neo4j database
+ this MAY correspond to the neo4j label tag. In an RDF database it should be
+ a biolink model class URI. This field is multi-valued. It should include values
+ for ancestors of the biolink class; for example, a protein such as Shh would
+ have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`.
+ In an RDF database, nodes will typically have an rdf:type triples. This can
+ be to the most specific biolink class, or potentially to a class more specific
+ than something in biolink. For example, a sequence feature `f` may have a rdf:type
+ assertion to a SO class such as TF_binding_site, which is more specific than
+ anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity,
+ biolink:NamedThing}
+ in_subset:
+ - translator_minimal
+ from_schema: https://identifiers.org/brain-bican/library-generation-schema
+ rank: 1000
+ is_a: type
+ domain: entity
+ slot_uri: biolink:category
+ designates_type: true
+ alias: category
+ owner: CellEnrichment
+ domain_of:
+ - entity
+ - attribute
+ - named thing
+ - organism taxon
+ - information content entity
+ - dataset
+ - physical entity
+ - activity
+ - procedure
+ - material sample
+ - biological entity
+ - gene
+ - genome
+ is_class_field: true
+ range: uriorcurie
+ multivalued: true
+ pattern: ^bican:[A-Z][A-Za-z]+$
+ type:
+ name: type
+ definition_uri: https://w3id.org/biolink/vocab/type
+ from_schema: https://identifiers.org/brain-bican/library-generation-schema
+ mappings:
+ - rdf:type
+ exact_mappings:
+ - gff3:type
+ - gpi:DB_Object_Type
+ rank: 1000
+ domain: entity
+ slot_uri: rdf:type
+ alias: type
+ owner: CellEnrichment
+ domain_of:
+ - entity
+ - attribute
+ - named thing
+ - organism taxon
+ - information content entity
+ - dataset
+ - physical entity
+ - activity
+ - procedure
+ - material sample
+ - biological entity
+ - gene
+ - genome
+ range: string
+ multivalued: true
+ name:
+ name: name
+ definition_uri: https://w3id.org/biolink/vocab/name
+ description: A human-readable name for an attribute or entity.
+ in_subset:
+ - translator_minimal
+ - samples
+ from_schema: https://identifiers.org/brain-bican/library-generation-schema
+ aliases:
+ - label
+ - display name
+ - title
+ mappings:
+ - rdfs:label
+ exact_mappings:
+ - gff3:Name
+ - gpi:DB_Object_Name
+ narrow_mappings:
+ - dct:title
+ - WIKIDATA_PROPERTY:P1476
+ rank: 1000
+ domain: entity
+ slot_uri: rdfs:label
+ alias: name
+ owner: CellEnrichment
+ domain_of:
+ - attribute
+ - entity
+ - macromolecular machine mixin
+ - Donor
+ - BrainSlab
+ - TissueSample
+ - DissociatedCellSample
+ - EnrichedCellSample
+ - BarcodedCellSample
+ - AmplifiedCdna
+ - Library
+ - LibraryAliquot
+ - LibraryPool
+ - DissectionRoiPolygon
+ - named thing
+ - organism taxon
+ - information content entity
+ - dataset
+ - physical entity
+ - activity
+ - procedure
+ - material sample
+ - biological entity
+ - gene or gene product
+ - gene
+ - genome
+ range: label type
+ description:
+ name: description
+ definition_uri: https://w3id.org/biolink/vocab/description
+ description: a human-readable description of an entity
+ in_subset:
+ - translator_minimal
+ from_schema: https://identifiers.org/brain-bican/library-generation-schema
+ aliases:
+ - definition
+ mappings:
+ - dct:description
+ exact_mappings:
+ - IAO:0000115
+ - skos:definitions
+ narrow_mappings:
+ - gff3:Description
+ rank: 1000
+ slot_uri: dct:description
+ alias: description
+ owner: CellEnrichment
+ domain_of:
+ - entity
+ - attribute
+ - named thing
+ - organism taxon
+ - information content entity
+ - dataset
+ - physical entity
+ - activity
+ - procedure
+ - material sample
+ - biological entity
+ - gene
+ - genome
+ range: narrative text
+ has attribute:
+ name: has attribute
+ definition_uri: https://w3id.org/biolink/vocab/has_attribute
+ description: connects any entity to an attribute
+ in_subset:
+ - samples
+ from_schema: https://identifiers.org/brain-bican/library-generation-schema
+ exact_mappings:
+ - SIO:000008
+ close_mappings:
+ - OBI:0001927
+ narrow_mappings:
+ - OBAN:association_has_subject_property
+ - OBAN:association_has_object_property
+ - CPT:has_possibly_included_panel_element
+ - DRUGBANK:category
+ - EFO:is_executed_in
+ - HANCESTRO:0301
+ - LOINC:has_action_guidance
+ - LOINC:has_adjustment
+ - LOINC:has_aggregation_view
+ - LOINC:has_approach_guidance
+ - LOINC:has_divisor
+ - LOINC:has_exam
+ - LOINC:has_method
+ - LOINC:has_modality_subtype
+ - LOINC:has_object_guidance
+ - LOINC:has_scale
+ - LOINC:has_suffix
+ - LOINC:has_time_aspect
+ - LOINC:has_time_modifier
+ - LOINC:has_timing_of
+ - NCIT:R88
+ - NCIT:eo_disease_has_property_or_attribute
+ - NCIT:has_data_element
+ - NCIT:has_pharmaceutical_administration_method
+ - NCIT:has_pharmaceutical_basic_dose_form
+ - NCIT:has_pharmaceutical_intended_site
+ - NCIT:has_pharmaceutical_release_characteristics
+ - NCIT:has_pharmaceutical_state_of_matter
+ - NCIT:has_pharmaceutical_transformation
+ - NCIT:is_qualified_by
+ - NCIT:qualifier_applies_to
+ - NCIT:role_has_domain
+ - NCIT:role_has_range
+ - INO:0000154
+ - HANCESTRO:0308
+ - OMIM:has_inheritance_type
+ - orphanet:C016
+ - orphanet:C017
+ - RO:0000053
+ - RO:0000086
+ - RO:0000087
+ - SNOMED:has_access
+ - SNOMED:has_clinical_course
+ - SNOMED:has_count_of_base_of_active_ingredient
+ - SNOMED:has_dose_form_administration_method
+ - SNOMED:has_dose_form_release_characteristic
+ - SNOMED:has_dose_form_transformation
+ - SNOMED:has_finding_context
+ - SNOMED:has_finding_informer
+ - SNOMED:has_inherent_attribute
+ - SNOMED:has_intent
+ - SNOMED:has_interpretation
+ - SNOMED:has_laterality
+ - SNOMED:has_measurement_method
+ - SNOMED:has_method
+ - SNOMED:has_priority
+ - SNOMED:has_procedure_context
+ - SNOMED:has_process_duration
+ - SNOMED:has_property
+ - SNOMED:has_revision_status
+ - SNOMED:has_scale_type
+ - SNOMED:has_severity
+ - SNOMED:has_specimen
+ - SNOMED:has_state_of_matter
+ - SNOMED:has_subject_relationship_context
+ - SNOMED:has_surgical_approach
+ - SNOMED:has_technique
+ - SNOMED:has_temporal_context
+ - SNOMED:has_time_aspect
+ - SNOMED:has_units
+ - UMLS:has_structural_class
+ - UMLS:has_supported_concept_property
+ - UMLS:has_supported_concept_relationship
+ - UMLS:may_be_qualified_by
+ rank: 1000
+ domain: entity
+ slot_uri: biolink:has_attribute
+ alias: has_attribute
+ owner: CellEnrichment
+ domain_of:
+ - entity
+ - attribute
+ - named thing
+ - organism taxon
+ - information content entity
+ - dataset
+ - physical entity
+ - activity
+ - procedure
+ - material sample
+ - biological entity
+ - gene
+ - genome
+ range: attribute
+ multivalued: true
+ deprecated:
+ name: deprecated
+ definition_uri: https://w3id.org/biolink/vocab/deprecated
+ description: A boolean flag indicating that an entity is no longer considered
+ current or valid.
+ from_schema: https://identifiers.org/brain-bican/library-generation-schema
+ exact_mappings:
+ - oboInOwl:ObsoleteClass
+ rank: 1000
+ slot_uri: biolink:deprecated
+ alias: deprecated
+ owner: CellEnrichment
+ domain_of:
+ - entity
+ - attribute
+ - named thing
+ - organism taxon
+ - information content entity
+ - dataset
+ - physical entity
+ - activity
+ - procedure
+ - material sample
+ - biological entity
+ - gene
+ - genome
+ range: boolean
+ provided by:
+ name: provided by
+ definition_uri: https://w3id.org/biolink/vocab/provided_by
+ description: The value in this node property represents the knowledge provider
+ that created or assembled the node and all of its attributes. Used internally
+ to represent how a particular node made its way into a knowledge provider or
+ graph.
+ from_schema: https://identifiers.org/brain-bican/library-generation-schema
+ rank: 1000
+ is_a: node property
+ domain: named thing
+ slot_uri: biolink:provided_by
+ alias: provided_by
+ owner: CellEnrichment
+ domain_of:
+ - named thing
+ - attribute
+ - organism taxon
+ - information content entity
+ - dataset
+ - physical entity
+ - activity
+ - procedure
+ - material sample
+ - biological entity
+ - gene
+ - genome
+ range: string
+ multivalued: true
+ xref:
+ name: xref
+ definition_uri: https://w3id.org/biolink/vocab/xref
+ description: A database cross reference or alternative identifier for a NamedThing
+ or edge between two NamedThings. This property should point to a database record
+ or webpage that supports the existence of the edge, or gives more detail about
+ the edge. This property can be used on a node or edge to provide multiple URIs
+ or CURIE cross references.
+ in_subset:
+ - translator_minimal
+ from_schema: https://identifiers.org/brain-bican/library-generation-schema
+ aliases:
+ - dbxref
+ - Dbxref
+ - DbXref
+ - record_url
+ - source_record_urls
+ narrow_mappings:
+ - gff3:Dbxref
+ - gpi:DB_Xrefs
+ rank: 1000
+ domain: named thing
+ slot_uri: biolink:xref
+ alias: xref
+ owner: CellEnrichment
+ domain_of:
+ - named thing
+ - gene
+ - attribute
+ - organism taxon
+ - information content entity
+ - dataset
+ - physical entity
+ - activity
+ - procedure
+ - material sample
+ - biological entity
+ - genome
+ range: uriorcurie
+ multivalued: true
+ full name:
+ name: full name
+ definition_uri: https://w3id.org/biolink/vocab/full_name
+ description: a long-form human readable name for a thing
+ from_schema: https://identifiers.org/brain-bican/library-generation-schema
+ rank: 1000
+ is_a: node property
+ domain: named thing
+ slot_uri: biolink:full_name
+ alias: full_name
+ owner: CellEnrichment
+ domain_of:
+ - named thing
+ - attribute
+ - organism taxon
+ - information content entity
+ - dataset
+ - physical entity
+ - activity
+ - procedure
+ - material sample
+ - biological entity
+ - gene
+ - genome
+ range: label type
+ synonym:
+ name: synonym
+ definition_uri: https://w3id.org/biolink/vocab/synonym
+ description: Alternate human-readable names for a thing
+ in_subset:
+ - translator_minimal
+ from_schema: https://identifiers.org/brain-bican/library-generation-schema
+ aliases:
+ - alias
+ narrow_mappings:
+ - skos:altLabel
+ - gff3:Alias
+ - AGRKB:synonyms
+ - gpi:DB_Object_Synonyms
+ - HANCESTRO:0330
+ - IAO:0000136
+ - RXNORM:has_tradename
+ rank: 1000
+ is_a: node property
+ domain: named thing
+ slot_uri: biolink:synonym
+ alias: synonym
+ owner: CellEnrichment
+ domain_of:
+ - named thing
+ - attribute
+ - organism taxon
+ - information content entity
+ - dataset
+ - physical entity
+ - activity
+ - procedure
+ - material sample
+ - biological entity
+ - gene
+ - genome
+ range: label type
+ multivalued: true
+
+Checksum values associated with digital entities.
+URI: bican:Checksum
+| Name | +Cardinality and Range | +Description | +Inheritance | +
|---|---|---|---|
| checksum_algorithm | +0..1 DigestType |
+The type of cryptographic hash function used to calculate the checksum value | +direct | +
| value | +0..1 String |
+The checksum value obtained from a specific cryotographic hash function | +direct | +
| id | +1 String |
+A unique identifier for an entity | +Entity | +
| iri | +0..1 IriType |
+An IRI for an entity | +Entity | +
| category | +* Uriorcurie |
+Name of the high level ontology class in which this entity is categorized | +Entity | +
| type | +* String |
++ | Entity | +
| name | +0..1 LabelType |
+A human-readable name for an attribute or entity | +Entity | +
| description | +0..1 NarrativeText |
+a human-readable description of an entity | +Entity | +
| has_attribute | +* Attribute |
+connects any entity to an attribute | +Entity | +
| deprecated | +0..1 Boolean |
+A boolean flag indicating that an entity is no longer considered current or v... | +Entity | +
| used by | +used in | +type | +used | +
|---|---|---|---|
| GenomeAnnotation | +digest | +any_of[range] | +Checksum | +
| Mapping Type | +Mapped Value | +
|---|---|
| self | +bican:Checksum | +
| native | +bican:Checksum | +
name: checksum
+description: Checksum values associated with digital entities.
+from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
+is_a: entity
+slots:
+- checksum algorithm
+attributes:
+ value:
+ name: value
+ description: The checksum value obtained from a specific cryotographic hash function.
+ from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
+ rank: 1000
+ domain_of:
+ - checksum
+
+name: checksum
+description: Checksum values associated with digital entities.
+from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
+is_a: entity
+attributes:
+ value:
+ name: value
+ description: The checksum value obtained from a specific cryotographic hash function.
+ from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
+ rank: 1000
+ alias: value
+ owner: checksum
+ domain_of:
+ - checksum
+ range: string
+ checksum algorithm:
+ name: checksum algorithm
+ description: The type of cryptographic hash function used to calculate the checksum
+ value.
+ from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
+ rank: 1000
+ alias: checksum_algorithm
+ owner: checksum
+ domain_of:
+ - checksum
+ range: DigestType
+ id:
+ name: id
+ definition_uri: https://w3id.org/biolink/vocab/id
+ description: A unique identifier for an entity. Must be either a CURIE shorthand
+ for a URI or a complete URI
+ in_subset:
+ - translator_minimal
+ from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
+ exact_mappings:
+ - AGRKB:primaryId
+ - gff3:ID
+ - gpi:DB_Object_ID
+ rank: 1000
+ domain: entity
+ slot_uri: biolink:id
+ identifier: true
+ alias: id
+ owner: checksum
+ domain_of:
+ - ontology class
+ - entity
+ - attribute
+ - named thing
+ - taxonomic rank
+ - organism taxon
+ - information content entity
+ - dataset
+ - physical entity
+ - activity
+ - procedure
+ - material sample
+ - biological entity
+ - gene
+ - genome
+ range: string
+ required: true
+ iri:
+ name: iri
+ definition_uri: https://w3id.org/biolink/vocab/iri
+ description: An IRI for an entity. This is determined by the id using expansion
+ rules.
+ in_subset:
+ - translator_minimal
+ - samples
+ from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
+ exact_mappings:
+ - WIKIDATA_PROPERTY:P854
+ rank: 1000
+ slot_uri: biolink:iri
+ alias: iri
+ owner: checksum
+ domain_of:
+ - attribute
+ - entity
+ - named thing
+ - organism taxon
+ - information content entity
+ - dataset
+ - physical entity
+ - activity
+ - procedure
+ - material sample
+ - biological entity
+ - gene
+ - genome
+ range: iri type
+ category:
+ name: category
+ definition_uri: https://w3id.org/biolink/vocab/category
+ description: Name of the high level ontology class in which this entity is categorized.
+ Corresponds to the label for the biolink entity type class. In a neo4j database
+ this MAY correspond to the neo4j label tag. In an RDF database it should be
+ a biolink model class URI. This field is multi-valued. It should include values
+ for ancestors of the biolink class; for example, a protein such as Shh would
+ have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`.
+ In an RDF database, nodes will typically have an rdf:type triples. This can
+ be to the most specific biolink class, or potentially to a class more specific
+ than something in biolink. For example, a sequence feature `f` may have a rdf:type
+ assertion to a SO class such as TF_binding_site, which is more specific than
+ anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity,
+ biolink:NamedThing}
+ in_subset:
+ - translator_minimal
+ from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
+ rank: 1000
+ is_a: type
+ domain: entity
+ slot_uri: biolink:category
+ designates_type: true
+ alias: category
+ owner: checksum
+ domain_of:
+ - entity
+ - attribute
+ - named thing
+ - organism taxon
+ - information content entity
+ - dataset
+ - physical entity
+ - activity
+ - procedure
+ - material sample
+ - biological entity
+ - gene
+ - genome
+ is_class_field: true
+ range: uriorcurie
+ multivalued: true
+ type:
+ name: type
+ definition_uri: https://w3id.org/biolink/vocab/type
+ from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
+ mappings:
+ - rdf:type
+ exact_mappings:
+ - gff3:type
+ - gpi:DB_Object_Type
+ rank: 1000
+ domain: entity
+ slot_uri: rdf:type
+ alias: type
+ owner: checksum
+ domain_of:
+ - entity
+ - attribute
+ - named thing
+ - organism taxon
+ - information content entity
+ - dataset
+ - physical entity
+ - activity
+ - procedure
+ - material sample
+ - biological entity
+ - gene
+ - genome
+ range: string
+ multivalued: true
+ name:
+ name: name
+ definition_uri: https://w3id.org/biolink/vocab/name
+ description: A human-readable name for an attribute or entity.
+ in_subset:
+ - translator_minimal
+ - samples
+ from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
+ aliases:
+ - label
+ - display name
+ - title
+ mappings:
+ - rdfs:label
+ exact_mappings:
+ - gff3:Name
+ - gpi:DB_Object_Name
+ narrow_mappings:
+ - dct:title
+ - WIKIDATA_PROPERTY:P1476
+ rank: 1000
+ domain: entity
+ slot_uri: rdfs:label
+ alias: name
+ owner: checksum
+ domain_of:
+ - attribute
+ - entity
+ - macromolecular machine mixin
+ - named thing
+ - organism taxon
+ - information content entity
+ - dataset
+ - physical entity
+ - activity
+ - procedure
+ - material sample
+ - biological entity
+ - gene or gene product
+ - gene
+ - genome
+ range: label type
+ description:
+ name: description
+ definition_uri: https://w3id.org/biolink/vocab/description
+ description: a human-readable description of an entity
+ in_subset:
+ - translator_minimal
+ from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
+ aliases:
+ - definition
+ mappings:
+ - dct:description
+ exact_mappings:
+ - IAO:0000115
+ - skos:definitions
+ narrow_mappings:
+ - gff3:Description
+ rank: 1000
+ slot_uri: dct:description
+ alias: description
+ owner: checksum
+ domain_of:
+ - entity
+ - attribute
+ - named thing
+ - organism taxon
+ - information content entity
+ - dataset
+ - physical entity
+ - activity
+ - procedure
+ - material sample
+ - biological entity
+ - gene
+ - genome
+ range: narrative text
+ has attribute:
+ name: has attribute
+ definition_uri: https://w3id.org/biolink/vocab/has_attribute
+ description: connects any entity to an attribute
+ in_subset:
+ - samples
+ from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
+ exact_mappings:
+ - SIO:000008
+ close_mappings:
+ - OBI:0001927
+ narrow_mappings:
+ - OBAN:association_has_subject_property
+ - OBAN:association_has_object_property
+ - CPT:has_possibly_included_panel_element
+ - DRUGBANK:category
+ - EFO:is_executed_in
+ - HANCESTRO:0301
+ - LOINC:has_action_guidance
+ - LOINC:has_adjustment
+ - LOINC:has_aggregation_view
+ - LOINC:has_approach_guidance
+ - LOINC:has_divisor
+ - LOINC:has_exam
+ - LOINC:has_method
+ - LOINC:has_modality_subtype
+ - LOINC:has_object_guidance
+ - LOINC:has_scale
+ - LOINC:has_suffix
+ - LOINC:has_time_aspect
+ - LOINC:has_time_modifier
+ - LOINC:has_timing_of
+ - NCIT:R88
+ - NCIT:eo_disease_has_property_or_attribute
+ - NCIT:has_data_element
+ - NCIT:has_pharmaceutical_administration_method
+ - NCIT:has_pharmaceutical_basic_dose_form
+ - NCIT:has_pharmaceutical_intended_site
+ - NCIT:has_pharmaceutical_release_characteristics
+ - NCIT:has_pharmaceutical_state_of_matter
+ - NCIT:has_pharmaceutical_transformation
+ - NCIT:is_qualified_by
+ - NCIT:qualifier_applies_to
+ - NCIT:role_has_domain
+ - NCIT:role_has_range
+ - INO:0000154
+ - HANCESTRO:0308
+ - OMIM:has_inheritance_type
+ - orphanet:C016
+ - orphanet:C017
+ - RO:0000053
+ - RO:0000086
+ - RO:0000087
+ - SNOMED:has_access
+ - SNOMED:has_clinical_course
+ - SNOMED:has_count_of_base_of_active_ingredient
+ - SNOMED:has_dose_form_administration_method
+ - SNOMED:has_dose_form_release_characteristic
+ - SNOMED:has_dose_form_transformation
+ - SNOMED:has_finding_context
+ - SNOMED:has_finding_informer
+ - SNOMED:has_inherent_attribute
+ - SNOMED:has_intent
+ - SNOMED:has_interpretation
+ - SNOMED:has_laterality
+ - SNOMED:has_measurement_method
+ - SNOMED:has_method
+ - SNOMED:has_priority
+ - SNOMED:has_procedure_context
+ - SNOMED:has_process_duration
+ - SNOMED:has_property
+ - SNOMED:has_revision_status
+ - SNOMED:has_scale_type
+ - SNOMED:has_severity
+ - SNOMED:has_specimen
+ - SNOMED:has_state_of_matter
+ - SNOMED:has_subject_relationship_context
+ - SNOMED:has_surgical_approach
+ - SNOMED:has_technique
+ - SNOMED:has_temporal_context
+ - SNOMED:has_time_aspect
+ - SNOMED:has_units
+ - UMLS:has_structural_class
+ - UMLS:has_supported_concept_property
+ - UMLS:has_supported_concept_relationship
+ - UMLS:may_be_qualified_by
+ rank: 1000
+ domain: entity
+ slot_uri: biolink:has_attribute
+ alias: has_attribute
+ owner: checksum
+ domain_of:
+ - entity
+ - attribute
+ - named thing
+ - organism taxon
+ - information content entity
+ - dataset
+ - physical entity
+ - activity
+ - procedure
+ - material sample
+ - biological entity
+ - gene
+ - genome
+ range: attribute
+ multivalued: true
+ deprecated:
+ name: deprecated
+ definition_uri: https://w3id.org/biolink/vocab/deprecated
+ description: A boolean flag indicating that an entity is no longer considered
+ current or valid.
+ from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
+ exact_mappings:
+ - oboInOwl:ObsoleteClass
+ rank: 1000
+ slot_uri: biolink:deprecated
+ alias: deprecated
+ owner: checksum
+ domain_of:
+ - entity
+ - attribute
+ - named thing
+ - organism taxon
+ - information content entity
+ - dataset
+ - physical entity
+ - activity
+ - procedure
+ - material sample
+ - biological entity
+ - gene
+ - genome
+ range: boolean
+
+A union of chemical entities and children, and gene or gene product. This mixin is helpful to use when searching across chemical entities that must include genes and their children as chemical entities.
+URI: biolink:ChemicalEntityOrGeneOrGeneProduct
+| Name | +Cardinality and Range | +Description | +Inheritance | +
|---|---|---|---|
| + | + | + | + |
| mixed into | +description | +
|---|---|
| Gene | +A region (or regions) that includes all of the sequence elements necessary to... | +
| Mapping Type | +Mapped Value | +
|---|---|
| self | +biolink:ChemicalEntityOrGeneOrGeneProduct | +
| native | +bican:ChemicalEntityOrGeneOrGeneProduct | +
name: chemical entity or gene or gene product
+definition_uri: https://w3id.org/biolink/vocab/ChemicalEntityOrGeneOrGeneProduct
+description: A union of chemical entities and children, and gene or gene product.
+ This mixin is helpful to use when searching across chemical entities that must include
+ genes and their children as chemical entities.
+from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
+mixin: true
+class_uri: biolink:ChemicalEntityOrGeneOrGeneProduct
+
+name: chemical entity or gene or gene product
+definition_uri: https://w3id.org/biolink/vocab/ChemicalEntityOrGeneOrGeneProduct
+description: A union of chemical entities and children, and gene or gene product.
+ This mixin is helpful to use when searching across chemical entities that must include
+ genes and their children as chemical entities.
+from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
+mixin: true
+class_uri: biolink:ChemicalEntityOrGeneOrGeneProduct
+
+A chemical formula
+URI: xsd:string
+ +| Mapping Type | +Mapped Value | +
|---|---|
| self | +xsd:string | +
| native | +bican:chemical_formula_value | +
a compact URI
+URI: xsd:string
+ +| Mapping Type | +Mapped Value | +
|---|---|
| self | +xsd:string | +
| native | +bican:curie | +
URI: DISTANCEUNIT
+| Value | +Meaning | +Description | +
|---|---|---|
| mm | +None | ++ |
| um | +None | ++ |
| m | +None | ++ |
| Name | +Description | +
|---|---|
| unit | +A controlled vocabulary attribute defining the length unit of the x, y, and z... | +
name: DISTANCE_UNIT
+from_schema: https://w3id.org/my-org/anatomical-structure-schema
+rank: 1000
+permissible_values:
+ mm:
+ text: mm
+ title: millimeter
+ um:
+ text: um
+ title: micrometer
+ m:
+ text: m
+ title: meter
+
+an item that refers to a collection of data from a data source.
+URI: biolink:Dataset
+| Name | +Cardinality and Range | +Description | +Inheritance | +
|---|---|---|---|
| id | +1 String |
+A unique identifier for an entity | +direct | +
| iri | +0..1 IriType |
+An IRI for an entity | +direct | +
| category | +* Uriorcurie |
+Name of the high level ontology class in which this entity is categorized | +direct | +
| type | +* String |
++ | direct | +
| name | +0..1 LabelType |
+A human-readable name for an attribute or entity | +direct | +
| description | +0..1 NarrativeText |
+a human-readable description of an entity | +direct | +
| has_attribute | +* Attribute |
+connects any entity to an attribute | +direct | +
| deprecated | +0..1 Boolean |
+A boolean flag indicating that an entity is no longer considered current or v... | +direct | +
| provided_by | +* String |
+The value in this node property represents the knowledge provider that create... | +direct | +
| xref | +* Uriorcurie |
+A database cross reference or alternative identifier for a NamedThing or edge... | +direct | +
| full_name | +0..1 LabelType |
+a long-form human readable name for a thing | +direct | +
| synonym | +* LabelType |
+Alternate human-readable names for a thing | +direct | +
| license | +0..1 String |
++ | direct | +
| rights | +0..1 String |
++ | direct | +
| format | +0..1 String |
++ | direct | +
| creation_date | +0..1 Date |
+date on which an entity was created | +direct | +
| used by | +used in | +type | +used | +
|---|---|---|---|
| GenomeAnnotation | +version | +domain | +Dataset | +
| GenomeAssembly | +version | +domain | +Dataset | +
| Mapping Type | +Mapped Value | +
|---|---|
| self | +biolink:Dataset | +
| native | +bican:Dataset | +
| exact | +IAO:0000100, dctypes:Dataset, schema:dataset, dcid:Dataset | +
name: dataset
+definition_uri: https://w3id.org/biolink/vocab/Dataset
+description: an item that refers to a collection of data from a data source.
+from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
+exact_mappings:
+- IAO:0000100
+- dctypes:Dataset
+- schema:dataset
+- dcid:Dataset
+is_a: information content entity
+slots:
+- id
+- iri
+- category
+- type
+- name
+- description
+- has attribute
+- deprecated
+- provided by
+- xref
+- full name
+- synonym
+- license
+- rights
+- format
+- creation date
+class_uri: biolink:Dataset
+
+name: dataset
+definition_uri: https://w3id.org/biolink/vocab/Dataset
+description: an item that refers to a collection of data from a data source.
+from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
+exact_mappings:
+- IAO:0000100
+- dctypes:Dataset
+- schema:dataset
+- dcid:Dataset
+is_a: information content entity
+attributes:
+ id:
+ name: id
+ definition_uri: https://w3id.org/biolink/vocab/id
+ description: A unique identifier for an entity. Must be either a CURIE shorthand
+ for a URI or a complete URI
+ in_subset:
+ - translator_minimal
+ from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
+ exact_mappings:
+ - AGRKB:primaryId
+ - gff3:ID
+ - gpi:DB_Object_ID
+ rank: 1000
+ domain: entity
+ slot_uri: biolink:id
+ identifier: true
+ alias: id
+ owner: dataset
+ domain_of:
+ - ontology class
+ - entity
+ - attribute
+ - named thing
+ - taxonomic rank
+ - organism taxon
+ - information content entity
+ - dataset
+ - physical entity
+ - activity
+ - procedure
+ - material sample
+ - biological entity
+ - gene
+ - genome
+ range: string
+ required: true
+ iri:
+ name: iri
+ definition_uri: https://w3id.org/biolink/vocab/iri
+ description: An IRI for an entity. This is determined by the id using expansion
+ rules.
+ in_subset:
+ - translator_minimal
+ - samples
+ from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
+ exact_mappings:
+ - WIKIDATA_PROPERTY:P854
+ rank: 1000
+ slot_uri: biolink:iri
+ alias: iri
+ owner: dataset
+ domain_of:
+ - attribute
+ - entity
+ - named thing
+ - organism taxon
+ - information content entity
+ - dataset
+ - physical entity
+ - activity
+ - procedure
+ - material sample
+ - biological entity
+ - gene
+ - genome
+ range: iri type
+ category:
+ name: category
+ definition_uri: https://w3id.org/biolink/vocab/category
+ description: Name of the high level ontology class in which this entity is categorized.
+ Corresponds to the label for the biolink entity type class. In a neo4j database
+ this MAY correspond to the neo4j label tag. In an RDF database it should be
+ a biolink model class URI. This field is multi-valued. It should include values
+ for ancestors of the biolink class; for example, a protein such as Shh would
+ have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`.
+ In an RDF database, nodes will typically have an rdf:type triples. This can
+ be to the most specific biolink class, or potentially to a class more specific
+ than something in biolink. For example, a sequence feature `f` may have a rdf:type
+ assertion to a SO class such as TF_binding_site, which is more specific than
+ anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity,
+ biolink:NamedThing}
+ in_subset:
+ - translator_minimal
+ from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
+ rank: 1000
+ is_a: type
+ domain: entity
+ slot_uri: biolink:category
+ designates_type: true
+ alias: category
+ owner: dataset
+ domain_of:
+ - entity
+ - attribute
+ - named thing
+ - organism taxon
+ - information content entity
+ - dataset
+ - physical entity
+ - activity
+ - procedure
+ - material sample
+ - biological entity
+ - gene
+ - genome
+ is_class_field: true
+ range: uriorcurie
+ multivalued: true
+ type:
+ name: type
+ definition_uri: https://w3id.org/biolink/vocab/type
+ from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
+ mappings:
+ - rdf:type
+ exact_mappings:
+ - gff3:type
+ - gpi:DB_Object_Type
+ rank: 1000
+ domain: entity
+ slot_uri: rdf:type
+ alias: type
+ owner: dataset
+ domain_of:
+ - entity
+ - attribute
+ - named thing
+ - organism taxon
+ - information content entity
+ - dataset
+ - physical entity
+ - activity
+ - procedure
+ - material sample
+ - biological entity
+ - gene
+ - genome
+ range: string
+ multivalued: true
+ name:
+ name: name
+ definition_uri: https://w3id.org/biolink/vocab/name
+ description: A human-readable name for an attribute or entity.
+ in_subset:
+ - translator_minimal
+ - samples
+ from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
+ aliases:
+ - label
+ - display name
+ - title
+ mappings:
+ - rdfs:label
+ exact_mappings:
+ - gff3:Name
+ - gpi:DB_Object_Name
+ narrow_mappings:
+ - dct:title
+ - WIKIDATA_PROPERTY:P1476
+ rank: 1000
+ domain: entity
+ slot_uri: rdfs:label
+ alias: name
+ owner: dataset
+ domain_of:
+ - attribute
+ - entity
+ - macromolecular machine mixin
+ - named thing
+ - organism taxon
+ - information content entity
+ - dataset
+ - physical entity
+ - activity
+ - procedure
+ - material sample
+ - biological entity
+ - gene or gene product
+ - gene
+ - genome
+ range: label type
+ description:
+ name: description
+ definition_uri: https://w3id.org/biolink/vocab/description
+ description: a human-readable description of an entity
+ in_subset:
+ - translator_minimal
+ from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
+ aliases:
+ - definition
+ mappings:
+ - dct:description
+ exact_mappings:
+ - IAO:0000115
+ - skos:definitions
+ narrow_mappings:
+ - gff3:Description
+ rank: 1000
+ slot_uri: dct:description
+ alias: description
+ owner: dataset
+ domain_of:
+ - entity
+ - attribute
+ - named thing
+ - organism taxon
+ - information content entity
+ - dataset
+ - physical entity
+ - activity
+ - procedure
+ - material sample
+ - biological entity
+ - gene
+ - genome
+ range: narrative text
+ has attribute:
+ name: has attribute
+ definition_uri: https://w3id.org/biolink/vocab/has_attribute
+ description: connects any entity to an attribute
+ in_subset:
+ - samples
+ from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
+ exact_mappings:
+ - SIO:000008
+ close_mappings:
+ - OBI:0001927
+ narrow_mappings:
+ - OBAN:association_has_subject_property
+ - OBAN:association_has_object_property
+ - CPT:has_possibly_included_panel_element
+ - DRUGBANK:category
+ - EFO:is_executed_in
+ - HANCESTRO:0301
+ - LOINC:has_action_guidance
+ - LOINC:has_adjustment
+ - LOINC:has_aggregation_view
+ - LOINC:has_approach_guidance
+ - LOINC:has_divisor
+ - LOINC:has_exam
+ - LOINC:has_method
+ - LOINC:has_modality_subtype
+ - LOINC:has_object_guidance
+ - LOINC:has_scale
+ - LOINC:has_suffix
+ - LOINC:has_time_aspect
+ - LOINC:has_time_modifier
+ - LOINC:has_timing_of
+ - NCIT:R88
+ - NCIT:eo_disease_has_property_or_attribute
+ - NCIT:has_data_element
+ - NCIT:has_pharmaceutical_administration_method
+ - NCIT:has_pharmaceutical_basic_dose_form
+ - NCIT:has_pharmaceutical_intended_site
+ - NCIT:has_pharmaceutical_release_characteristics
+ - NCIT:has_pharmaceutical_state_of_matter
+ - NCIT:has_pharmaceutical_transformation
+ - NCIT:is_qualified_by
+ - NCIT:qualifier_applies_to
+ - NCIT:role_has_domain
+ - NCIT:role_has_range
+ - INO:0000154
+ - HANCESTRO:0308
+ - OMIM:has_inheritance_type
+ - orphanet:C016
+ - orphanet:C017
+ - RO:0000053
+ - RO:0000086
+ - RO:0000087
+ - SNOMED:has_access
+ - SNOMED:has_clinical_course
+ - SNOMED:has_count_of_base_of_active_ingredient
+ - SNOMED:has_dose_form_administration_method
+ - SNOMED:has_dose_form_release_characteristic
+ - SNOMED:has_dose_form_transformation
+ - SNOMED:has_finding_context
+ - SNOMED:has_finding_informer
+ - SNOMED:has_inherent_attribute
+ - SNOMED:has_intent
+ - SNOMED:has_interpretation
+ - SNOMED:has_laterality
+ - SNOMED:has_measurement_method
+ - SNOMED:has_method
+ - SNOMED:has_priority
+ - SNOMED:has_procedure_context
+ - SNOMED:has_process_duration
+ - SNOMED:has_property
+ - SNOMED:has_revision_status
+ - SNOMED:has_scale_type
+ - SNOMED:has_severity
+ - SNOMED:has_specimen
+ - SNOMED:has_state_of_matter
+ - SNOMED:has_subject_relationship_context
+ - SNOMED:has_surgical_approach
+ - SNOMED:has_technique
+ - SNOMED:has_temporal_context
+ - SNOMED:has_time_aspect
+ - SNOMED:has_units
+ - UMLS:has_structural_class
+ - UMLS:has_supported_concept_property
+ - UMLS:has_supported_concept_relationship
+ - UMLS:may_be_qualified_by
+ rank: 1000
+ domain: entity
+ slot_uri: biolink:has_attribute
+ alias: has_attribute
+ owner: dataset
+ domain_of:
+ - entity
+ - attribute
+ - named thing
+ - organism taxon
+ - information content entity
+ - dataset
+ - physical entity
+ - activity
+ - procedure
+ - material sample
+ - biological entity
+ - gene
+ - genome
+ range: attribute
+ multivalued: true
+ deprecated:
+ name: deprecated
+ definition_uri: https://w3id.org/biolink/vocab/deprecated
+ description: A boolean flag indicating that an entity is no longer considered
+ current or valid.
+ from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
+ exact_mappings:
+ - oboInOwl:ObsoleteClass
+ rank: 1000
+ slot_uri: biolink:deprecated
+ alias: deprecated
+ owner: dataset
+ domain_of:
+ - entity
+ - attribute
+ - named thing
+ - organism taxon
+ - information content entity
+ - dataset
+ - physical entity
+ - activity
+ - procedure
+ - material sample
+ - biological entity
+ - gene
+ - genome
+ range: boolean
+ provided by:
+ name: provided by
+ definition_uri: https://w3id.org/biolink/vocab/provided_by
+ description: The value in this node property represents the knowledge provider
+ that created or assembled the node and all of its attributes. Used internally
+ to represent how a particular node made its way into a knowledge provider or
+ graph.
+ from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
+ rank: 1000
+ is_a: node property
+ domain: named thing
+ slot_uri: biolink:provided_by
+ alias: provided_by
+ owner: dataset
+ domain_of:
+ - named thing
+ - attribute
+ - organism taxon
+ - information content entity
+ - dataset
+ - physical entity
+ - activity
+ - procedure
+ - material sample
+ - biological entity
+ - gene
+ - genome
+ range: string
+ multivalued: true
+ xref:
+ name: xref
+ definition_uri: https://w3id.org/biolink/vocab/xref
+ description: A database cross reference or alternative identifier for a NamedThing
+ or edge between two NamedThings. This property should point to a database record
+ or webpage that supports the existence of the edge, or gives more detail about
+ the edge. This property can be used on a node or edge to provide multiple URIs
+ or CURIE cross references.
+ in_subset:
+ - translator_minimal
+ from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
+ aliases:
+ - dbxref
+ - Dbxref
+ - DbXref
+ - record_url
+ - source_record_urls
+ narrow_mappings:
+ - gff3:Dbxref
+ - gpi:DB_Xrefs
+ rank: 1000
+ domain: named thing
+ slot_uri: biolink:xref
+ alias: xref
+ owner: dataset
+ domain_of:
+ - named thing
+ - gene
+ - attribute
+ - organism taxon
+ - information content entity
+ - dataset
+ - physical entity
+ - activity
+ - procedure
+ - material sample
+ - biological entity
+ - genome
+ range: uriorcurie
+ multivalued: true
+ full name:
+ name: full name
+ definition_uri: https://w3id.org/biolink/vocab/full_name
+ description: a long-form human readable name for a thing
+ from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
+ rank: 1000
+ is_a: node property
+ domain: named thing
+ slot_uri: biolink:full_name
+ alias: full_name
+ owner: dataset
+ domain_of:
+ - named thing
+ - attribute
+ - organism taxon
+ - information content entity
+ - dataset
+ - physical entity
+ - activity
+ - procedure
+ - material sample
+ - biological entity
+ - gene
+ - genome
+ range: label type
+ synonym:
+ name: synonym
+ definition_uri: https://w3id.org/biolink/vocab/synonym
+ description: Alternate human-readable names for a thing
+ in_subset:
+ - translator_minimal
+ from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
+ aliases:
+ - alias
+ narrow_mappings:
+ - skos:altLabel
+ - gff3:Alias
+ - AGRKB:synonyms
+ - gpi:DB_Object_Synonyms
+ - HANCESTRO:0330
+ - IAO:0000136
+ - RXNORM:has_tradename
+ rank: 1000
+ is_a: node property
+ domain: named thing
+ slot_uri: biolink:synonym
+ alias: synonym
+ owner: dataset
+ domain_of:
+ - named thing
+ - attribute
+ - organism taxon
+ - information content entity
+ - dataset
+ - physical entity
+ - activity
+ - procedure
+ - material sample
+ - biological entity
+ - gene
+ - genome
+ range: label type
+ multivalued: true
+ license:
+ name: license
+ definition_uri: https://w3id.org/biolink/vocab/license
+ from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
+ exact_mappings:
+ - dct:license
+ narrow_mappings:
+ - WIKIDATA_PROPERTY:P275
+ rank: 1000
+ is_a: node property
+ domain: information content entity
+ slot_uri: biolink:license
+ alias: license
+ owner: dataset
+ domain_of:
+ - information content entity
+ - dataset
+ range: string
+ rights:
+ name: rights
+ definition_uri: https://w3id.org/biolink/vocab/rights
+ from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
+ exact_mappings:
+ - dct:rights
+ rank: 1000
+ is_a: node property
+ domain: information content entity
+ slot_uri: biolink:rights
+ alias: rights
+ owner: dataset
+ domain_of:
+ - information content entity
+ - dataset
+ range: string
+ format:
+ name: format
+ definition_uri: https://w3id.org/biolink/vocab/format
+ from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
+ exact_mappings:
+ - dct:format
+ - WIKIDATA_PROPERTY:P2701
+ rank: 1000
+ is_a: node property
+ domain: information content entity
+ slot_uri: biolink:format
+ alias: format
+ owner: dataset
+ domain_of:
+ - information content entity
+ - dataset
+ range: string
+ creation date:
+ name: creation date
+ definition_uri: https://w3id.org/biolink/vocab/creation_date
+ description: date on which an entity was created. This can be applied to nodes
+ or edges
+ from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
+ aliases:
+ - publication date
+ exact_mappings:
+ - dct:createdOn
+ - WIKIDATA_PROPERTY:P577
+ rank: 1000
+ is_a: node property
+ domain: named thing
+ slot_uri: biolink:creation_date
+ alias: creation_date
+ owner: dataset
+ domain_of:
+ - information content entity
+ - dataset
+ range: date
+class_uri: biolink:Dataset
+
+a date (year, month and day) in an idealized calendar
+URI: xsd:date
+ +| Mapping Type | +Mapped Value | +
|---|---|
| self | +xsd:date | +
| native | +bican:date | +
| exact | +schema:Date | +
Either a date or a datetime
+ + +| Mapping Type | +Mapped Value | +
|---|---|
| self | +linkml:DateOrDatetime | +
| native | +bican:date_or_datetime | +
The combination of a date and time
+URI: xsd:dateTime
+ +| Mapping Type | +Mapped Value | +
|---|---|
| self | +xsd:dateTime | +
| native | +bican:datetime | +
| exact | +schema:DateTime | +
A real number with arbitrary precision that conforms to the xsd:decimal specification
+URI: xsd:decimal
+ +| Mapping Type | +Mapped Value | +
|---|---|
| self | +xsd:decimal | +
| native | +bican:decimal | +
| broad | +schema:Number | +
URI: DigestType
+| Value | +Meaning | +Description | +
|---|---|---|
| spdx:checksumAlgorithm_sha1 | +spdx:checksumAlgorithm_sha1 | ++ |
| spdx:checksumAlgorithm_md5 | +spdx:checksumAlgorithm_md5 | ++ |
| spdx:checksumAlgorithm_sha256 | +spdx:checksumAlgorithm_sha256 | ++ |
| Name | +Description | +
|---|---|
| checksum_algorithm | +The type of cryptographic hash function used to calculate the checksum value | +
name: DigestType
+from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
+rank: 1000
+permissible_values:
+ spdx:checksumAlgorithm_sha1:
+ text: spdx:checksumAlgorithm_sha1
+ meaning: spdx:checksumAlgorithm_sha1
+ title: SHA1
+ spdx:checksumAlgorithm_md5:
+ text: spdx:checksumAlgorithm_md5
+ meaning: spdx:checksumAlgorithm_md5
+ title: MD5
+ spdx:checksumAlgorithm_sha256:
+ text: spdx:checksumAlgorithm_sha256
+ meaning: spdx:checksumAlgorithm_sha256
+ title: SHA256
+
+The process of outlining a region of interest on a brain slab image to guide the dissection and generation of a tissue sample.
+URI: bican:DissectionRoiDelineation
+| Name | +Cardinality and Range | +Description | +Inheritance | +
|---|---|---|---|
| used | +0..1 BrainSlab |
+The brain slab that was annotated by the delineation process | +direct | +
| id | +1 String |
+A unique identifier for an entity | +NamedThing, Procedure, Entity | +
| iri | +0..1 IriType |
+An IRI for an entity | +NamedThing, Procedure, Entity | +
| category | +* Uriorcurie |
+Name of the high level ontology class in which this entity is categorized | +NamedThing, Procedure, Entity | +
| type | +* String |
++ | NamedThing, Procedure, Entity | +
| name | +0..1 LabelType |
+A human-readable name for an attribute or entity | +NamedThing, Procedure, Entity | +
| description | +0..1 NarrativeText |
+a human-readable description of an entity | +NamedThing, Procedure, Entity | +
| has_attribute | +* Attribute |
+connects any entity to an attribute | +NamedThing, Procedure, Entity | +
| deprecated | +0..1 Boolean |
+A boolean flag indicating that an entity is no longer considered current or v... | +NamedThing, Procedure, Entity | +
| provided_by | +* String |
+The value in this node property represents the knowledge provider that create... | +NamedThing, Procedure | +
| xref | +* Uriorcurie |
+A database cross reference or alternative identifier for a NamedThing or edge... | +NamedThing, Procedure | +
| full_name | +0..1 LabelType |
+a long-form human readable name for a thing | +NamedThing, Procedure | +
| synonym | +* LabelType |
+Alternate human-readable names for a thing | +NamedThing, Procedure | +
| used by | +used in | +type | +used | +
|---|---|---|---|
| DissectionRoiPolygon | +was_generated_by | +range | +DissectionRoiDelineation | +
| Mapping Type | +Mapped Value | +
|---|---|
| self | +bican:DissectionRoiDelineation | +
| native | +bican:DissectionRoiDelineation | +
name: DissectionRoiDelineation
+description: The process of outlining a region of interest on a brain slab image to
+ guide the dissection and generation of a tissue sample.
+in_subset:
+- bican
+- library_generation
+from_schema: https://identifiers.org/brain-bican/library-generation-schema
+is_a: procedure
+mixins:
+- ProvActivity
+slots:
+- used
+slot_usage:
+ used:
+ name: used
+ description: The brain slab that was annotated by the delineation process.
+ range: BrainSlab
+ category:
+ name: category
+ pattern: ^bican:[A-Z][A-Za-z]+$
+
+name: DissectionRoiDelineation
+description: The process of outlining a region of interest on a brain slab image to
+ guide the dissection and generation of a tissue sample.
+in_subset:
+- bican
+- library_generation
+from_schema: https://identifiers.org/brain-bican/library-generation-schema
+is_a: procedure
+mixins:
+- ProvActivity
+slot_usage:
+ used:
+ name: used
+ description: The brain slab that was annotated by the delineation process.
+ range: BrainSlab
+ category:
+ name: category
+ pattern: ^bican:[A-Z][A-Za-z]+$
+attributes:
+ used:
+ name: used
+ description: The brain slab that was annotated by the delineation process.
+ from_schema: https://identifiers.org/brain-bican/library-generation-schema
+ rank: 1000
+ slot_uri: prov:used
+ alias: used
+ owner: DissectionRoiDelineation
+ domain_of:
+ - DissectionRoiDelineation
+ - TissueDissection
+ - CellDissociation
+ - CellEnrichment
+ - EnrichedCellSampleSplitting
+ - CellBarcoding
+ - CdnaAmplification
+ - LibraryConstruction
+ - LibraryPooling
+ - ProvActivity
+ range: BrainSlab
+ id:
+ name: id
+ definition_uri: https://w3id.org/biolink/vocab/id
+ description: A unique identifier for an entity. Must be either a CURIE shorthand
+ for a URI or a complete URI
+ in_subset:
+ - translator_minimal
+ from_schema: https://identifiers.org/brain-bican/library-generation-schema
+ exact_mappings:
+ - AGRKB:primaryId
+ - gff3:ID
+ - gpi:DB_Object_ID
+ rank: 1000
+ domain: entity
+ slot_uri: biolink:id
+ identifier: true
+ alias: id
+ owner: DissectionRoiDelineation
+ domain_of:
+ - ontology class
+ - entity
+ - attribute
+ - named thing
+ - taxonomic rank
+ - organism taxon
+ - information content entity
+ - dataset
+ - physical entity
+ - activity
+ - procedure
+ - material sample
+ - biological entity
+ - gene
+ - genome
+ range: string
+ required: true
+ iri:
+ name: iri
+ definition_uri: https://w3id.org/biolink/vocab/iri
+ description: An IRI for an entity. This is determined by the id using expansion
+ rules.
+ in_subset:
+ - translator_minimal
+ - samples
+ from_schema: https://identifiers.org/brain-bican/library-generation-schema
+ exact_mappings:
+ - WIKIDATA_PROPERTY:P854
+ rank: 1000
+ slot_uri: biolink:iri
+ alias: iri
+ owner: DissectionRoiDelineation
+ domain_of:
+ - attribute
+ - entity
+ - named thing
+ - organism taxon
+ - information content entity
+ - dataset
+ - physical entity
+ - activity
+ - procedure
+ - material sample
+ - biological entity
+ - gene
+ - genome
+ range: iri type
+ category:
+ name: category
+ definition_uri: https://w3id.org/biolink/vocab/category
+ description: Name of the high level ontology class in which this entity is categorized.
+ Corresponds to the label for the biolink entity type class. In a neo4j database
+ this MAY correspond to the neo4j label tag. In an RDF database it should be
+ a biolink model class URI. This field is multi-valued. It should include values
+ for ancestors of the biolink class; for example, a protein such as Shh would
+ have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`.
+ In an RDF database, nodes will typically have an rdf:type triples. This can
+ be to the most specific biolink class, or potentially to a class more specific
+ than something in biolink. For example, a sequence feature `f` may have a rdf:type
+ assertion to a SO class such as TF_binding_site, which is more specific than
+ anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity,
+ biolink:NamedThing}
+ in_subset:
+ - translator_minimal
+ from_schema: https://identifiers.org/brain-bican/library-generation-schema
+ rank: 1000
+ is_a: type
+ domain: entity
+ slot_uri: biolink:category
+ designates_type: true
+ alias: category
+ owner: DissectionRoiDelineation
+ domain_of:
+ - entity
+ - attribute
+ - named thing
+ - organism taxon
+ - information content entity
+ - dataset
+ - physical entity
+ - activity
+ - procedure
+ - material sample
+ - biological entity
+ - gene
+ - genome
+ is_class_field: true
+ range: uriorcurie
+ multivalued: true
+ pattern: ^bican:[A-Z][A-Za-z]+$
+ type:
+ name: type
+ definition_uri: https://w3id.org/biolink/vocab/type
+ from_schema: https://identifiers.org/brain-bican/library-generation-schema
+ mappings:
+ - rdf:type
+ exact_mappings:
+ - gff3:type
+ - gpi:DB_Object_Type
+ rank: 1000
+ domain: entity
+ slot_uri: rdf:type
+ alias: type
+ owner: DissectionRoiDelineation
+ domain_of:
+ - entity
+ - attribute
+ - named thing
+ - organism taxon
+ - information content entity
+ - dataset
+ - physical entity
+ - activity
+ - procedure
+ - material sample
+ - biological entity
+ - gene
+ - genome
+ range: string
+ multivalued: true
+ name:
+ name: name
+ definition_uri: https://w3id.org/biolink/vocab/name
+ description: A human-readable name for an attribute or entity.
+ in_subset:
+ - translator_minimal
+ - samples
+ from_schema: https://identifiers.org/brain-bican/library-generation-schema
+ aliases:
+ - label
+ - display name
+ - title
+ mappings:
+ - rdfs:label
+ exact_mappings:
+ - gff3:Name
+ - gpi:DB_Object_Name
+ narrow_mappings:
+ - dct:title
+ - WIKIDATA_PROPERTY:P1476
+ rank: 1000
+ domain: entity
+ slot_uri: rdfs:label
+ alias: name
+ owner: DissectionRoiDelineation
+ domain_of:
+ - attribute
+ - entity
+ - macromolecular machine mixin
+ - Donor
+ - BrainSlab
+ - TissueSample
+ - DissociatedCellSample
+ - EnrichedCellSample
+ - BarcodedCellSample
+ - AmplifiedCdna
+ - Library
+ - LibraryAliquot
+ - LibraryPool
+ - DissectionRoiPolygon
+ - named thing
+ - organism taxon
+ - information content entity
+ - dataset
+ - physical entity
+ - activity
+ - procedure
+ - material sample
+ - biological entity
+ - gene or gene product
+ - gene
+ - genome
+ range: label type
+ description:
+ name: description
+ definition_uri: https://w3id.org/biolink/vocab/description
+ description: a human-readable description of an entity
+ in_subset:
+ - translator_minimal
+ from_schema: https://identifiers.org/brain-bican/library-generation-schema
+ aliases:
+ - definition
+ mappings:
+ - dct:description
+ exact_mappings:
+ - IAO:0000115
+ - skos:definitions
+ narrow_mappings:
+ - gff3:Description
+ rank: 1000
+ slot_uri: dct:description
+ alias: description
+ owner: DissectionRoiDelineation
+ domain_of:
+ - entity
+ - attribute
+ - named thing
+ - organism taxon
+ - information content entity
+ - dataset
+ - physical entity
+ - activity
+ - procedure
+ - material sample
+ - biological entity
+ - gene
+ - genome
+ range: narrative text
+ has attribute:
+ name: has attribute
+ definition_uri: https://w3id.org/biolink/vocab/has_attribute
+ description: connects any entity to an attribute
+ in_subset:
+ - samples
+ from_schema: https://identifiers.org/brain-bican/library-generation-schema
+ exact_mappings:
+ - SIO:000008
+ close_mappings:
+ - OBI:0001927
+ narrow_mappings:
+ - OBAN:association_has_subject_property
+ - OBAN:association_has_object_property
+ - CPT:has_possibly_included_panel_element
+ - DRUGBANK:category
+ - EFO:is_executed_in
+ - HANCESTRO:0301
+ - LOINC:has_action_guidance
+ - LOINC:has_adjustment
+ - LOINC:has_aggregation_view
+ - LOINC:has_approach_guidance
+ - LOINC:has_divisor
+ - LOINC:has_exam
+ - LOINC:has_method
+ - LOINC:has_modality_subtype
+ - LOINC:has_object_guidance
+ - LOINC:has_scale
+ - LOINC:has_suffix
+ - LOINC:has_time_aspect
+ - LOINC:has_time_modifier
+ - LOINC:has_timing_of
+ - NCIT:R88
+ - NCIT:eo_disease_has_property_or_attribute
+ - NCIT:has_data_element
+ - NCIT:has_pharmaceutical_administration_method
+ - NCIT:has_pharmaceutical_basic_dose_form
+ - NCIT:has_pharmaceutical_intended_site
+ - NCIT:has_pharmaceutical_release_characteristics
+ - NCIT:has_pharmaceutical_state_of_matter
+ - NCIT:has_pharmaceutical_transformation
+ - NCIT:is_qualified_by
+ - NCIT:qualifier_applies_to
+ - NCIT:role_has_domain
+ - NCIT:role_has_range
+ - INO:0000154
+ - HANCESTRO:0308
+ - OMIM:has_inheritance_type
+ - orphanet:C016
+ - orphanet:C017
+ - RO:0000053
+ - RO:0000086
+ - RO:0000087
+ - SNOMED:has_access
+ - SNOMED:has_clinical_course
+ - SNOMED:has_count_of_base_of_active_ingredient
+ - SNOMED:has_dose_form_administration_method
+ - SNOMED:has_dose_form_release_characteristic
+ - SNOMED:has_dose_form_transformation
+ - SNOMED:has_finding_context
+ - SNOMED:has_finding_informer
+ - SNOMED:has_inherent_attribute
+ - SNOMED:has_intent
+ - SNOMED:has_interpretation
+ - SNOMED:has_laterality
+ - SNOMED:has_measurement_method
+ - SNOMED:has_method
+ - SNOMED:has_priority
+ - SNOMED:has_procedure_context
+ - SNOMED:has_process_duration
+ - SNOMED:has_property
+ - SNOMED:has_revision_status
+ - SNOMED:has_scale_type
+ - SNOMED:has_severity
+ - SNOMED:has_specimen
+ - SNOMED:has_state_of_matter
+ - SNOMED:has_subject_relationship_context
+ - SNOMED:has_surgical_approach
+ - SNOMED:has_technique
+ - SNOMED:has_temporal_context
+ - SNOMED:has_time_aspect
+ - SNOMED:has_units
+ - UMLS:has_structural_class
+ - UMLS:has_supported_concept_property
+ - UMLS:has_supported_concept_relationship
+ - UMLS:may_be_qualified_by
+ rank: 1000
+ domain: entity
+ slot_uri: biolink:has_attribute
+ alias: has_attribute
+ owner: DissectionRoiDelineation
+ domain_of:
+ - entity
+ - attribute
+ - named thing
+ - organism taxon
+ - information content entity
+ - dataset
+ - physical entity
+ - activity
+ - procedure
+ - material sample
+ - biological entity
+ - gene
+ - genome
+ range: attribute
+ multivalued: true
+ deprecated:
+ name: deprecated
+ definition_uri: https://w3id.org/biolink/vocab/deprecated
+ description: A boolean flag indicating that an entity is no longer considered
+ current or valid.
+ from_schema: https://identifiers.org/brain-bican/library-generation-schema
+ exact_mappings:
+ - oboInOwl:ObsoleteClass
+ rank: 1000
+ slot_uri: biolink:deprecated
+ alias: deprecated
+ owner: DissectionRoiDelineation
+ domain_of:
+ - entity
+ - attribute
+ - named thing
+ - organism taxon
+ - information content entity
+ - dataset
+ - physical entity
+ - activity
+ - procedure
+ - material sample
+ - biological entity
+ - gene
+ - genome
+ range: boolean
+ provided by:
+ name: provided by
+ definition_uri: https://w3id.org/biolink/vocab/provided_by
+ description: The value in this node property represents the knowledge provider
+ that created or assembled the node and all of its attributes. Used internally
+ to represent how a particular node made its way into a knowledge provider or
+ graph.
+ from_schema: https://identifiers.org/brain-bican/library-generation-schema
+ rank: 1000
+ is_a: node property
+ domain: named thing
+ slot_uri: biolink:provided_by
+ alias: provided_by
+ owner: DissectionRoiDelineation
+ domain_of:
+ - named thing
+ - attribute
+ - organism taxon
+ - information content entity
+ - dataset
+ - physical entity
+ - activity
+ - procedure
+ - material sample
+ - biological entity
+ - gene
+ - genome
+ range: string
+ multivalued: true
+ xref:
+ name: xref
+ definition_uri: https://w3id.org/biolink/vocab/xref
+ description: A database cross reference or alternative identifier for a NamedThing
+ or edge between two NamedThings. This property should point to a database record
+ or webpage that supports the existence of the edge, or gives more detail about
+ the edge. This property can be used on a node or edge to provide multiple URIs
+ or CURIE cross references.
+ in_subset:
+ - translator_minimal
+ from_schema: https://identifiers.org/brain-bican/library-generation-schema
+ aliases:
+ - dbxref
+ - Dbxref
+ - DbXref
+ - record_url
+ - source_record_urls
+ narrow_mappings:
+ - gff3:Dbxref
+ - gpi:DB_Xrefs
+ rank: 1000
+ domain: named thing
+ slot_uri: biolink:xref
+ alias: xref
+ owner: DissectionRoiDelineation
+ domain_of:
+ - named thing
+ - gene
+ - attribute
+ - organism taxon
+ - information content entity
+ - dataset
+ - physical entity
+ - activity
+ - procedure
+ - material sample
+ - biological entity
+ - genome
+ range: uriorcurie
+ multivalued: true
+ full name:
+ name: full name
+ definition_uri: https://w3id.org/biolink/vocab/full_name
+ description: a long-form human readable name for a thing
+ from_schema: https://identifiers.org/brain-bican/library-generation-schema
+ rank: 1000
+ is_a: node property
+ domain: named thing
+ slot_uri: biolink:full_name
+ alias: full_name
+ owner: DissectionRoiDelineation
+ domain_of:
+ - named thing
+ - attribute
+ - organism taxon
+ - information content entity
+ - dataset
+ - physical entity
+ - activity
+ - procedure
+ - material sample
+ - biological entity
+ - gene
+ - genome
+ range: label type
+ synonym:
+ name: synonym
+ definition_uri: https://w3id.org/biolink/vocab/synonym
+ description: Alternate human-readable names for a thing
+ in_subset:
+ - translator_minimal
+ from_schema: https://identifiers.org/brain-bican/library-generation-schema
+ aliases:
+ - alias
+ narrow_mappings:
+ - skos:altLabel
+ - gff3:Alias
+ - AGRKB:synonyms
+ - gpi:DB_Object_Synonyms
+ - HANCESTRO:0330
+ - IAO:0000136
+ - RXNORM:has_tradename
+ rank: 1000
+ is_a: node property
+ domain: named thing
+ slot_uri: biolink:synonym
+ alias: synonym
+ owner: DissectionRoiDelineation
+ domain_of:
+ - named thing
+ - attribute
+ - organism taxon
+ - information content entity
+ - dataset
+ - physical entity
+ - activity
+ - procedure
+ - material sample
+ - biological entity
+ - gene
+ - genome
+ range: label type
+ multivalued: true
+
+A polygon annotated on a brain slab image delineating a region of interest (ROI) for a tissue sample dissectioning.
+URI: bican:DissectionRoiPolygon
+| Name | +Cardinality and Range | +Description | +Inheritance | +
|---|---|---|---|
| was_generated_by | +0..1 DissectionRoiDelineation |
+The delineation process from which the dissection ROI polygon was generated b... | +direct | +
| name | +0..1 LabelType |
+Name of a polygon annotated on a brain slab image delineating a region of int... | +direct | +
| annotates | +0..1 BrainSlab |
+The brain slab that was annotated by the delineation process | +direct | +
| was_derived_from | +0..1 ProvEntity |
+A derivation is a transformation of an entity into another, an update of an e... | +ProvEntity | +
| id | +1 String |
+A unique identifier for an entity | +Entity | +
| iri | +0..1 IriType |
+An IRI for an entity | +Entity | +
| category | +* Uriorcurie |
+Name of the high level ontology class in which this entity is categorized | +Entity | +
| type | +* String |
++ | Entity | +
| description | +0..1 NarrativeText |
+a human-readable description of an entity | +Entity | +
| has_attribute | +* Attribute |
+connects any entity to an attribute | +Entity | +
| deprecated | +0..1 Boolean |
+A boolean flag indicating that an entity is no longer considered current or v... | +Entity | +
| used by | +used in | +type | +used | +
|---|---|---|---|
| TissueSample | +dissection_was_guided_by | +range | +DissectionRoiPolygon | +
| TissueDissection | +was_guided_by | +range | +DissectionRoiPolygon | +
| Mapping Type | +Mapped Value | +
|---|---|
| self | +bican:DissectionRoiPolygon | +
| native | +bican:DissectionRoiPolygon | +
| exact | +NIMP:Specimen%20Dissected%20ROI | +
name: DissectionRoiPolygon
+description: A polygon annotated on a brain slab image delineating a region of interest
+ (ROI) for a tissue sample dissectioning.
+in_subset:
+- bican
+- tissue_specimen
+from_schema: https://identifiers.org/brain-bican/library-generation-schema
+exact_mappings:
+- NIMP:Specimen%20Dissected%20ROI
+is_a: entity
+mixins:
+- ProvEntity
+slots:
+- was_generated_by
+- name
+slot_usage:
+ was_generated_by:
+ name: was_generated_by
+ description: The delineation process from which the dissection ROI polygon was
+ generated by.
+ range: DissectionRoiDelineation
+ name:
+ name: name
+ description: Name of a polygon annotated on a brain slab image delineating a region
+ of interest (ROI) for a tissue sample dissectioning.
+ category:
+ name: category
+ pattern: ^bican:[A-Z][A-Za-z]+$
+attributes:
+ annotates:
+ name: annotates
+ description: The brain slab that was annotated by the delineation process.
+ from_schema: https://identifiers.org/brain-bican/library-generation-schema
+ exact_mappings:
+ - NIMP:has_parent
+ rank: 1000
+ domain_of:
+ - DissectionRoiPolygon
+ range: BrainSlab
+
+name: DissectionRoiPolygon
+description: A polygon annotated on a brain slab image delineating a region of interest
+ (ROI) for a tissue sample dissectioning.
+in_subset:
+- bican
+- tissue_specimen
+from_schema: https://identifiers.org/brain-bican/library-generation-schema
+exact_mappings:
+- NIMP:Specimen%20Dissected%20ROI
+is_a: entity
+mixins:
+- ProvEntity
+slot_usage:
+ was_generated_by:
+ name: was_generated_by
+ description: The delineation process from which the dissection ROI polygon was
+ generated by.
+ range: DissectionRoiDelineation
+ name:
+ name: name
+ description: Name of a polygon annotated on a brain slab image delineating a region
+ of interest (ROI) for a tissue sample dissectioning.
+ category:
+ name: category
+ pattern: ^bican:[A-Z][A-Za-z]+$
+attributes:
+ annotates:
+ name: annotates
+ description: The brain slab that was annotated by the delineation process.
+ from_schema: https://identifiers.org/brain-bican/library-generation-schema
+ exact_mappings:
+ - NIMP:has_parent
+ rank: 1000
+ alias: annotates
+ owner: DissectionRoiPolygon
+ domain_of:
+ - DissectionRoiPolygon
+ range: BrainSlab
+ was_generated_by:
+ name: was_generated_by
+ description: The delineation process from which the dissection ROI polygon was
+ generated by.
+ from_schema: https://identifiers.org/brain-bican/library-generation-schema
+ rank: 1000
+ slot_uri: prov:wasGeneratedBy
+ alias: was_generated_by
+ owner: DissectionRoiPolygon
+ domain_of:
+ - TissueSample
+ - DissociatedCellSample
+ - EnrichedCellSample
+ - BarcodedCellSample
+ - AmplifiedCdna
+ - Library
+ - LibraryPool
+ - DissectionRoiPolygon
+ - ProvEntity
+ range: DissectionRoiDelineation
+ name:
+ name: name
+ definition_uri: https://w3id.org/biolink/vocab/name
+ description: Name of a polygon annotated on a brain slab image delineating a region
+ of interest (ROI) for a tissue sample dissectioning.
+ in_subset:
+ - translator_minimal
+ - samples
+ from_schema: https://identifiers.org/brain-bican/library-generation-schema
+ aliases:
+ - label
+ - display name
+ - title
+ mappings:
+ - rdfs:label
+ exact_mappings:
+ - gff3:Name
+ - gpi:DB_Object_Name
+ narrow_mappings:
+ - dct:title
+ - WIKIDATA_PROPERTY:P1476
+ rank: 1000
+ domain: entity
+ slot_uri: rdfs:label
+ alias: name
+ owner: DissectionRoiPolygon
+ domain_of:
+ - attribute
+ - entity
+ - macromolecular machine mixin
+ - Donor
+ - BrainSlab
+ - TissueSample
+ - DissociatedCellSample
+ - EnrichedCellSample
+ - BarcodedCellSample
+ - AmplifiedCdna
+ - Library
+ - LibraryAliquot
+ - LibraryPool
+ - DissectionRoiPolygon
+ - named thing
+ - organism taxon
+ - information content entity
+ - dataset
+ - physical entity
+ - activity
+ - procedure
+ - material sample
+ - biological entity
+ - gene or gene product
+ - gene
+ - genome
+ range: label type
+ was_derived_from:
+ name: was_derived_from
+ description: A derivation is a transformation of an entity into another, an update
+ of an entity resulting in a new one, or the construction of a new entity based
+ on a pre-existing entity.
+ from_schema: https://identifiers.org/brain-bican/library-generation-schema
+ rank: 1000
+ slot_uri: prov:wasDerivedFrom
+ alias: was_derived_from
+ owner: DissectionRoiPolygon
+ domain_of:
+ - BrainSlab
+ - TissueSample
+ - DissociatedCellSample
+ - EnrichedCellSample
+ - BarcodedCellSample
+ - AmplifiedCdna
+ - Library
+ - LibraryAliquot
+ - LibraryPool
+ - ProvEntity
+ range: ProvEntity
+ id:
+ name: id
+ definition_uri: https://w3id.org/biolink/vocab/id
+ description: A unique identifier for an entity. Must be either a CURIE shorthand
+ for a URI or a complete URI
+ in_subset:
+ - translator_minimal
+ from_schema: https://identifiers.org/brain-bican/library-generation-schema
+ exact_mappings:
+ - AGRKB:primaryId
+ - gff3:ID
+ - gpi:DB_Object_ID
+ rank: 1000
+ domain: entity
+ slot_uri: biolink:id
+ identifier: true
+ alias: id
+ owner: DissectionRoiPolygon
+ domain_of:
+ - ontology class
+ - entity
+ - attribute
+ - named thing
+ - taxonomic rank
+ - organism taxon
+ - information content entity
+ - dataset
+ - physical entity
+ - activity
+ - procedure
+ - material sample
+ - biological entity
+ - gene
+ - genome
+ range: string
+ required: true
+ iri:
+ name: iri
+ definition_uri: https://w3id.org/biolink/vocab/iri
+ description: An IRI for an entity. This is determined by the id using expansion
+ rules.
+ in_subset:
+ - translator_minimal
+ - samples
+ from_schema: https://identifiers.org/brain-bican/library-generation-schema
+ exact_mappings:
+ - WIKIDATA_PROPERTY:P854
+ rank: 1000
+ slot_uri: biolink:iri
+ alias: iri
+ owner: DissectionRoiPolygon
+ domain_of:
+ - attribute
+ - entity
+ - named thing
+ - organism taxon
+ - information content entity
+ - dataset
+ - physical entity
+ - activity
+ - procedure
+ - material sample
+ - biological entity
+ - gene
+ - genome
+ range: iri type
+ category:
+ name: category
+ definition_uri: https://w3id.org/biolink/vocab/category
+ description: Name of the high level ontology class in which this entity is categorized.
+ Corresponds to the label for the biolink entity type class. In a neo4j database
+ this MAY correspond to the neo4j label tag. In an RDF database it should be
+ a biolink model class URI. This field is multi-valued. It should include values
+ for ancestors of the biolink class; for example, a protein such as Shh would
+ have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`.
+ In an RDF database, nodes will typically have an rdf:type triples. This can
+ be to the most specific biolink class, or potentially to a class more specific
+ than something in biolink. For example, a sequence feature `f` may have a rdf:type
+ assertion to a SO class such as TF_binding_site, which is more specific than
+ anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity,
+ biolink:NamedThing}
+ in_subset:
+ - translator_minimal
+ from_schema: https://identifiers.org/brain-bican/library-generation-schema
+ rank: 1000
+ is_a: type
+ domain: entity
+ slot_uri: biolink:category
+ designates_type: true
+ alias: category
+ owner: DissectionRoiPolygon
+ domain_of:
+ - entity
+ - attribute
+ - named thing
+ - organism taxon
+ - information content entity
+ - dataset
+ - physical entity
+ - activity
+ - procedure
+ - material sample
+ - biological entity
+ - gene
+ - genome
+ is_class_field: true
+ range: uriorcurie
+ multivalued: true
+ pattern: ^bican:[A-Z][A-Za-z]+$
+ type:
+ name: type
+ definition_uri: https://w3id.org/biolink/vocab/type
+ from_schema: https://identifiers.org/brain-bican/library-generation-schema
+ mappings:
+ - rdf:type
+ exact_mappings:
+ - gff3:type
+ - gpi:DB_Object_Type
+ rank: 1000
+ domain: entity
+ slot_uri: rdf:type
+ alias: type
+ owner: DissectionRoiPolygon
+ domain_of:
+ - entity
+ - attribute
+ - named thing
+ - organism taxon
+ - information content entity
+ - dataset
+ - physical entity
+ - activity
+ - procedure
+ - material sample
+ - biological entity
+ - gene
+ - genome
+ range: string
+ multivalued: true
+ description:
+ name: description
+ definition_uri: https://w3id.org/biolink/vocab/description
+ description: a human-readable description of an entity
+ in_subset:
+ - translator_minimal
+ from_schema: https://identifiers.org/brain-bican/library-generation-schema
+ aliases:
+ - definition
+ mappings:
+ - dct:description
+ exact_mappings:
+ - IAO:0000115
+ - skos:definitions
+ narrow_mappings:
+ - gff3:Description
+ rank: 1000
+ slot_uri: dct:description
+ alias: description
+ owner: DissectionRoiPolygon
+ domain_of:
+ - entity
+ - attribute
+ - named thing
+ - organism taxon
+ - information content entity
+ - dataset
+ - physical entity
+ - activity
+ - procedure
+ - material sample
+ - biological entity
+ - gene
+ - genome
+ range: narrative text
+ has attribute:
+ name: has attribute
+ definition_uri: https://w3id.org/biolink/vocab/has_attribute
+ description: connects any entity to an attribute
+ in_subset:
+ - samples
+ from_schema: https://identifiers.org/brain-bican/library-generation-schema
+ exact_mappings:
+ - SIO:000008
+ close_mappings:
+ - OBI:0001927
+ narrow_mappings:
+ - OBAN:association_has_subject_property
+ - OBAN:association_has_object_property
+ - CPT:has_possibly_included_panel_element
+ - DRUGBANK:category
+ - EFO:is_executed_in
+ - HANCESTRO:0301
+ - LOINC:has_action_guidance
+ - LOINC:has_adjustment
+ - LOINC:has_aggregation_view
+ - LOINC:has_approach_guidance
+ - LOINC:has_divisor
+ - LOINC:has_exam
+ - LOINC:has_method
+ - LOINC:has_modality_subtype
+ - LOINC:has_object_guidance
+ - LOINC:has_scale
+ - LOINC:has_suffix
+ - LOINC:has_time_aspect
+ - LOINC:has_time_modifier
+ - LOINC:has_timing_of
+ - NCIT:R88
+ - NCIT:eo_disease_has_property_or_attribute
+ - NCIT:has_data_element
+ - NCIT:has_pharmaceutical_administration_method
+ - NCIT:has_pharmaceutical_basic_dose_form
+ - NCIT:has_pharmaceutical_intended_site
+ - NCIT:has_pharmaceutical_release_characteristics
+ - NCIT:has_pharmaceutical_state_of_matter
+ - NCIT:has_pharmaceutical_transformation
+ - NCIT:is_qualified_by
+ - NCIT:qualifier_applies_to
+ - NCIT:role_has_domain
+ - NCIT:role_has_range
+ - INO:0000154
+ - HANCESTRO:0308
+ - OMIM:has_inheritance_type
+ - orphanet:C016
+ - orphanet:C017
+ - RO:0000053
+ - RO:0000086
+ - RO:0000087
+ - SNOMED:has_access
+ - SNOMED:has_clinical_course
+ - SNOMED:has_count_of_base_of_active_ingredient
+ - SNOMED:has_dose_form_administration_method
+ - SNOMED:has_dose_form_release_characteristic
+ - SNOMED:has_dose_form_transformation
+ - SNOMED:has_finding_context
+ - SNOMED:has_finding_informer
+ - SNOMED:has_inherent_attribute
+ - SNOMED:has_intent
+ - SNOMED:has_interpretation
+ - SNOMED:has_laterality
+ - SNOMED:has_measurement_method
+ - SNOMED:has_method
+ - SNOMED:has_priority
+ - SNOMED:has_procedure_context
+ - SNOMED:has_process_duration
+ - SNOMED:has_property
+ - SNOMED:has_revision_status
+ - SNOMED:has_scale_type
+ - SNOMED:has_severity
+ - SNOMED:has_specimen
+ - SNOMED:has_state_of_matter
+ - SNOMED:has_subject_relationship_context
+ - SNOMED:has_surgical_approach
+ - SNOMED:has_technique
+ - SNOMED:has_temporal_context
+ - SNOMED:has_time_aspect
+ - SNOMED:has_units
+ - UMLS:has_structural_class
+ - UMLS:has_supported_concept_property
+ - UMLS:has_supported_concept_relationship
+ - UMLS:may_be_qualified_by
+ rank: 1000
+ domain: entity
+ slot_uri: biolink:has_attribute
+ alias: has_attribute
+ owner: DissectionRoiPolygon
+ domain_of:
+ - entity
+ - attribute
+ - named thing
+ - organism taxon
+ - information content entity
+ - dataset
+ - physical entity
+ - activity
+ - procedure
+ - material sample
+ - biological entity
+ - gene
+ - genome
+ range: attribute
+ multivalued: true
+ deprecated:
+ name: deprecated
+ definition_uri: https://w3id.org/biolink/vocab/deprecated
+ description: A boolean flag indicating that an entity is no longer considered
+ current or valid.
+ from_schema: https://identifiers.org/brain-bican/library-generation-schema
+ exact_mappings:
+ - oboInOwl:ObsoleteClass
+ rank: 1000
+ slot_uri: biolink:deprecated
+ alias: deprecated
+ owner: DissectionRoiPolygon
+ domain_of:
+ - entity
+ - attribute
+ - named thing
+ - organism taxon
+ - information content entity
+ - dataset
+ - physical entity
+ - activity
+ - procedure
+ - material sample
+ - biological entity
+ - gene
+ - genome
+ range: boolean
+
+A collection of dissociated cells or nuclei derived from dissociation of a tissue sample.
+URI: bican:DissociatedCellSample
+| Name | +Cardinality and Range | +Description | +Inheritance | +
|---|---|---|---|
| was_generated_by | +0..1 CellDissociation |
+The cell dissociation process from which the dissociated cell sample was gene... | +direct | +
| was_derived_from | +* TissueSample |
+The input tissue sample(s) from which dissociated cell sample was derived fro... | +direct | +
| name | +0..1 LabelType |
+Name of a collection of dissociated cells or nuclei derived from dissociation... | +direct | +
| cell_prep_type | +0..1 DissociatedCellSampleCellPrepType |
+The type of cell preparation | +direct | +
| cell_source_oligo_name | +0..1 DissociatedCellSampleCellLabelBarcode |
+Name of cell source oligo used in cell plexing | +direct | +
| id | +1 String |
+A unique identifier for an entity | +NamedThing, PhysicalEntity, MaterialSample, Entity | +
| iri | +0..1 IriType |
+An IRI for an entity | +NamedThing, PhysicalEntity, MaterialSample, Entity | +
| category | +* Uriorcurie |
+Name of the high level ontology class in which this entity is categorized | +NamedThing, PhysicalEntity, MaterialSample, Entity | +
| type | +* String |
++ | NamedThing, PhysicalEntity, MaterialSample, Entity | +
| description | +0..1 NarrativeText |
+a human-readable description of an entity | +NamedThing, PhysicalEntity, MaterialSample, Entity | +
| has_attribute | +* Attribute |
+connects any entity to an attribute | +NamedThing, PhysicalEntity, MaterialSample, Entity | +
| deprecated | +0..1 Boolean |
+A boolean flag indicating that an entity is no longer considered current or v... | +NamedThing, PhysicalEntity, MaterialSample, Entity | +
| provided_by | +* String |
+The value in this node property represents the knowledge provider that create... | +NamedThing, PhysicalEntity, MaterialSample | +
| xref | +* Uriorcurie |
+A database cross reference or alternative identifier for a NamedThing or edge... | +NamedThing, PhysicalEntity, MaterialSample | +
| full_name | +0..1 LabelType |
+a long-form human readable name for a thing | +NamedThing, PhysicalEntity, MaterialSample | +
| synonym | +* LabelType |
+Alternate human-readable names for a thing | +NamedThing, PhysicalEntity, MaterialSample | +
| used by | +used in | +type | +used | +
|---|---|---|---|
| EnrichedCellSample | +was_derived_from | +exactly_one_of[range] | +DissociatedCellSample | +
| BarcodedCellSample | +was_derived_from | +exactly_one_of[range] | +DissociatedCellSample | +
| CellEnrichment | +used | +range | +DissociatedCellSample | +
| CellBarcoding | +used | +exactly_one_of[range] | +DissociatedCellSample | +
| Mapping Type | +Mapped Value | +
|---|---|
| self | +bican:DissociatedCellSample | +
| native | +bican:DissociatedCellSample | +
| exact | +NIMP:Dissociated%20Cell%20Sample | +
name: DissociatedCellSample
+description: A collection of dissociated cells or nuclei derived from dissociation
+ of a tissue sample.
+in_subset:
+- bican
+- library_generation
+from_schema: https://identifiers.org/brain-bican/library-generation-schema
+exact_mappings:
+- NIMP:Dissociated%20Cell%20Sample
+is_a: material sample
+mixins:
+- ProvEntity
+slots:
+- was_generated_by
+- was_derived_from
+- name
+slot_usage:
+ was_generated_by:
+ name: was_generated_by
+ description: The cell dissociation process from which the dissociated cell sample
+ was generated by.
+ range: CellDissociation
+ was_derived_from:
+ name: was_derived_from
+ description: The input tissue sample(s) from which dissociated cell sample was
+ derived from.
+ exact_mappings:
+ - NIMP:has_parent
+ range: TissueSample
+ multivalued: true
+ name:
+ name: name
+ description: Name of a collection of dissociated cells or nuclei derived from
+ dissociation of a tissue sample.
+ exact_mappings:
+ - NIMP:PD-RQRWHS40
+ slot_uri: bican:65e2c7da-9eb4-45b2-8ccb-d69ef9785ee2
+ category:
+ name: category
+ pattern: ^bican:[A-Z][A-Za-z]+$
+attributes:
+ cell_prep_type:
+ name: cell_prep_type
+ local_names:
+ NIMP:
+ local_name_source: NIMP
+ local_name_value: dissociated_cell_sample_cell_prep_type
+ description: 'The type of cell preparation. For example: Cells, Nuclei. This is
+ a property of dissociated_cell_sample.'
+ in_subset:
+ - analysis
+ - tracking
+ from_schema: https://identifiers.org/brain-bican/library-generation-schema
+ exact_mappings:
+ - NIMP:PD-RELLGO26
+ rank: 1000
+ slot_uri: bican:baae4ac3-f959-4594-b943-3a82ec19bd34
+ alias: dissociated cell sample cell prep type
+ domain_of:
+ - DissociatedCellSample
+ range: dissociated_cell_sample_cell_prep_type
+ cell_source_oligo_name:
+ name: cell_source_oligo_name
+ local_names:
+ NIMP:
+ local_name_source: NIMP
+ local_name_value: dissociated_cell_sample_cell_label_barcode
+ description: Name of cell source oligo used in cell plexing. The oligo molecularly
+ tags all the cells in the dissociated cell sample and allows separate dissociated
+ cell samples to be combined downstream in the barcoded cell sample. The oligo
+ name is associated with a sequence in a lookup table. This sequence will be
+ needed during alignment to associate reads with the parent source dissociated
+ cell sample.
+ from_schema: https://identifiers.org/brain-bican/library-generation-schema
+ exact_mappings:
+ - NIMP:PD-CFCFPS27
+ rank: 1000
+ slot_uri: bican:184abbaf-baff-4b5f-b51e-dd38de6006af
+ alias: dissociated cell oligo tag name
+ domain_of:
+ - DissociatedCellSample
+ - EnrichedCellSample
+ range: dissociated_cell_sample_cell_label_barcode
+
+name: DissociatedCellSample
+description: A collection of dissociated cells or nuclei derived from dissociation
+ of a tissue sample.
+in_subset:
+- bican
+- library_generation
+from_schema: https://identifiers.org/brain-bican/library-generation-schema
+exact_mappings:
+- NIMP:Dissociated%20Cell%20Sample
+is_a: material sample
+mixins:
+- ProvEntity
+slot_usage:
+ was_generated_by:
+ name: was_generated_by
+ description: The cell dissociation process from which the dissociated cell sample
+ was generated by.
+ range: CellDissociation
+ was_derived_from:
+ name: was_derived_from
+ description: The input tissue sample(s) from which dissociated cell sample was
+ derived from.
+ exact_mappings:
+ - NIMP:has_parent
+ range: TissueSample
+ multivalued: true
+ name:
+ name: name
+ description: Name of a collection of dissociated cells or nuclei derived from
+ dissociation of a tissue sample.
+ exact_mappings:
+ - NIMP:PD-RQRWHS40
+ slot_uri: bican:65e2c7da-9eb4-45b2-8ccb-d69ef9785ee2
+ category:
+ name: category
+ pattern: ^bican:[A-Z][A-Za-z]+$
+attributes:
+ cell_prep_type:
+ name: cell_prep_type
+ local_names:
+ NIMP:
+ local_name_source: NIMP
+ local_name_value: dissociated_cell_sample_cell_prep_type
+ description: 'The type of cell preparation. For example: Cells, Nuclei. This is
+ a property of dissociated_cell_sample.'
+ in_subset:
+ - analysis
+ - tracking
+ from_schema: https://identifiers.org/brain-bican/library-generation-schema
+ exact_mappings:
+ - NIMP:PD-RELLGO26
+ rank: 1000
+ slot_uri: bican:baae4ac3-f959-4594-b943-3a82ec19bd34
+ alias: dissociated cell sample cell prep type
+ owner: DissociatedCellSample
+ domain_of:
+ - DissociatedCellSample
+ range: dissociated_cell_sample_cell_prep_type
+ cell_source_oligo_name:
+ name: cell_source_oligo_name
+ local_names:
+ NIMP:
+ local_name_source: NIMP
+ local_name_value: dissociated_cell_sample_cell_label_barcode
+ description: Name of cell source oligo used in cell plexing. The oligo molecularly
+ tags all the cells in the dissociated cell sample and allows separate dissociated
+ cell samples to be combined downstream in the barcoded cell sample. The oligo
+ name is associated with a sequence in a lookup table. This sequence will be
+ needed during alignment to associate reads with the parent source dissociated
+ cell sample.
+ from_schema: https://identifiers.org/brain-bican/library-generation-schema
+ exact_mappings:
+ - NIMP:PD-CFCFPS27
+ rank: 1000
+ slot_uri: bican:184abbaf-baff-4b5f-b51e-dd38de6006af
+ alias: dissociated cell oligo tag name
+ owner: DissociatedCellSample
+ domain_of:
+ - DissociatedCellSample
+ - EnrichedCellSample
+ range: dissociated_cell_sample_cell_label_barcode
+ was_generated_by:
+ name: was_generated_by
+ description: The cell dissociation process from which the dissociated cell sample
+ was generated by.
+ from_schema: https://identifiers.org/brain-bican/library-generation-schema
+ rank: 1000
+ slot_uri: prov:wasGeneratedBy
+ alias: was_generated_by
+ owner: DissociatedCellSample
+ domain_of:
+ - TissueSample
+ - DissociatedCellSample
+ - EnrichedCellSample
+ - BarcodedCellSample
+ - AmplifiedCdna
+ - Library
+ - LibraryPool
+ - DissectionRoiPolygon
+ - ProvEntity
+ range: CellDissociation
+ was_derived_from:
+ name: was_derived_from
+ description: The input tissue sample(s) from which dissociated cell sample was
+ derived from.
+ from_schema: https://identifiers.org/brain-bican/library-generation-schema
+ exact_mappings:
+ - NIMP:has_parent
+ rank: 1000
+ slot_uri: prov:wasDerivedFrom
+ alias: was_derived_from
+ owner: DissociatedCellSample
+ domain_of:
+ - BrainSlab
+ - TissueSample
+ - DissociatedCellSample
+ - EnrichedCellSample
+ - BarcodedCellSample
+ - AmplifiedCdna
+ - Library
+ - LibraryAliquot
+ - LibraryPool
+ - ProvEntity
+ range: TissueSample
+ multivalued: true
+ name:
+ name: name
+ definition_uri: https://w3id.org/biolink/vocab/name
+ description: Name of a collection of dissociated cells or nuclei derived from
+ dissociation of a tissue sample.
+ in_subset:
+ - translator_minimal
+ - samples
+ from_schema: https://identifiers.org/brain-bican/library-generation-schema
+ aliases:
+ - label
+ - display name
+ - title
+ mappings:
+ - rdfs:label
+ exact_mappings:
+ - NIMP:PD-RQRWHS40
+ narrow_mappings:
+ - dct:title
+ - WIKIDATA_PROPERTY:P1476
+ rank: 1000
+ domain: entity
+ slot_uri: bican:65e2c7da-9eb4-45b2-8ccb-d69ef9785ee2
+ alias: name
+ owner: DissociatedCellSample
+ domain_of:
+ - attribute
+ - entity
+ - macromolecular machine mixin
+ - Donor
+ - BrainSlab
+ - TissueSample
+ - DissociatedCellSample
+ - EnrichedCellSample
+ - BarcodedCellSample
+ - AmplifiedCdna
+ - Library
+ - LibraryAliquot
+ - LibraryPool
+ - DissectionRoiPolygon
+ - named thing
+ - organism taxon
+ - information content entity
+ - dataset
+ - physical entity
+ - activity
+ - procedure
+ - material sample
+ - biological entity
+ - gene or gene product
+ - gene
+ - genome
+ range: label type
+ id:
+ name: id
+ definition_uri: https://w3id.org/biolink/vocab/id
+ description: A unique identifier for an entity. Must be either a CURIE shorthand
+ for a URI or a complete URI
+ in_subset:
+ - translator_minimal
+ from_schema: https://identifiers.org/brain-bican/library-generation-schema
+ exact_mappings:
+ - AGRKB:primaryId
+ - gff3:ID
+ - gpi:DB_Object_ID
+ rank: 1000
+ domain: entity
+ slot_uri: biolink:id
+ identifier: true
+ alias: id
+ owner: DissociatedCellSample
+ domain_of:
+ - ontology class
+ - entity
+ - attribute
+ - named thing
+ - taxonomic rank
+ - organism taxon
+ - information content entity
+ - dataset
+ - physical entity
+ - activity
+ - procedure
+ - material sample
+ - biological entity
+ - gene
+ - genome
+ range: string
+ required: true
+ iri:
+ name: iri
+ definition_uri: https://w3id.org/biolink/vocab/iri
+ description: An IRI for an entity. This is determined by the id using expansion
+ rules.
+ in_subset:
+ - translator_minimal
+ - samples
+ from_schema: https://identifiers.org/brain-bican/library-generation-schema
+ exact_mappings:
+ - WIKIDATA_PROPERTY:P854
+ rank: 1000
+ slot_uri: biolink:iri
+ alias: iri
+ owner: DissociatedCellSample
+ domain_of:
+ - attribute
+ - entity
+ - named thing
+ - organism taxon
+ - information content entity
+ - dataset
+ - physical entity
+ - activity
+ - procedure
+ - material sample
+ - biological entity
+ - gene
+ - genome
+ range: iri type
+ category:
+ name: category
+ definition_uri: https://w3id.org/biolink/vocab/category
+ description: Name of the high level ontology class in which this entity is categorized.
+ Corresponds to the label for the biolink entity type class. In a neo4j database
+ this MAY correspond to the neo4j label tag. In an RDF database it should be
+ a biolink model class URI. This field is multi-valued. It should include values
+ for ancestors of the biolink class; for example, a protein such as Shh would
+ have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`.
+ In an RDF database, nodes will typically have an rdf:type triples. This can
+ be to the most specific biolink class, or potentially to a class more specific
+ than something in biolink. For example, a sequence feature `f` may have a rdf:type
+ assertion to a SO class such as TF_binding_site, which is more specific than
+ anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity,
+ biolink:NamedThing}
+ in_subset:
+ - translator_minimal
+ from_schema: https://identifiers.org/brain-bican/library-generation-schema
+ rank: 1000
+ is_a: type
+ domain: entity
+ slot_uri: biolink:category
+ designates_type: true
+ alias: category
+ owner: DissociatedCellSample
+ domain_of:
+ - entity
+ - attribute
+ - named thing
+ - organism taxon
+ - information content entity
+ - dataset
+ - physical entity
+ - activity
+ - procedure
+ - material sample
+ - biological entity
+ - gene
+ - genome
+ is_class_field: true
+ range: uriorcurie
+ multivalued: true
+ pattern: ^bican:[A-Z][A-Za-z]+$
+ type:
+ name: type
+ definition_uri: https://w3id.org/biolink/vocab/type
+ from_schema: https://identifiers.org/brain-bican/library-generation-schema
+ mappings:
+ - rdf:type
+ exact_mappings:
+ - gff3:type
+ - gpi:DB_Object_Type
+ rank: 1000
+ domain: entity
+ slot_uri: rdf:type
+ alias: type
+ owner: DissociatedCellSample
+ domain_of:
+ - entity
+ - attribute
+ - named thing
+ - organism taxon
+ - information content entity
+ - dataset
+ - physical entity
+ - activity
+ - procedure
+ - material sample
+ - biological entity
+ - gene
+ - genome
+ range: string
+ multivalued: true
+ description:
+ name: description
+ definition_uri: https://w3id.org/biolink/vocab/description
+ description: a human-readable description of an entity
+ in_subset:
+ - translator_minimal
+ from_schema: https://identifiers.org/brain-bican/library-generation-schema
+ aliases:
+ - definition
+ mappings:
+ - dct:description
+ exact_mappings:
+ - IAO:0000115
+ - skos:definitions
+ narrow_mappings:
+ - gff3:Description
+ rank: 1000
+ slot_uri: dct:description
+ alias: description
+ owner: DissociatedCellSample
+ domain_of:
+ - entity
+ - attribute
+ - named thing
+ - organism taxon
+ - information content entity
+ - dataset
+ - physical entity
+ - activity
+ - procedure
+ - material sample
+ - biological entity
+ - gene
+ - genome
+ range: narrative text
+ has attribute:
+ name: has attribute
+ definition_uri: https://w3id.org/biolink/vocab/has_attribute
+ description: connects any entity to an attribute
+ in_subset:
+ - samples
+ from_schema: https://identifiers.org/brain-bican/library-generation-schema
+ exact_mappings:
+ - SIO:000008
+ close_mappings:
+ - OBI:0001927
+ narrow_mappings:
+ - OBAN:association_has_subject_property
+ - OBAN:association_has_object_property
+ - CPT:has_possibly_included_panel_element
+ - DRUGBANK:category
+ - EFO:is_executed_in
+ - HANCESTRO:0301
+ - LOINC:has_action_guidance
+ - LOINC:has_adjustment
+ - LOINC:has_aggregation_view
+ - LOINC:has_approach_guidance
+ - LOINC:has_divisor
+ - LOINC:has_exam
+ - LOINC:has_method
+ - LOINC:has_modality_subtype
+ - LOINC:has_object_guidance
+ - LOINC:has_scale
+ - LOINC:has_suffix
+ - LOINC:has_time_aspect
+ - LOINC:has_time_modifier
+ - LOINC:has_timing_of
+ - NCIT:R88
+ - NCIT:eo_disease_has_property_or_attribute
+ - NCIT:has_data_element
+ - NCIT:has_pharmaceutical_administration_method
+ - NCIT:has_pharmaceutical_basic_dose_form
+ - NCIT:has_pharmaceutical_intended_site
+ - NCIT:has_pharmaceutical_release_characteristics
+ - NCIT:has_pharmaceutical_state_of_matter
+ - NCIT:has_pharmaceutical_transformation
+ - NCIT:is_qualified_by
+ - NCIT:qualifier_applies_to
+ - NCIT:role_has_domain
+ - NCIT:role_has_range
+ - INO:0000154
+ - HANCESTRO:0308
+ - OMIM:has_inheritance_type
+ - orphanet:C016
+ - orphanet:C017
+ - RO:0000053
+ - RO:0000086
+ - RO:0000087
+ - SNOMED:has_access
+ - SNOMED:has_clinical_course
+ - SNOMED:has_count_of_base_of_active_ingredient
+ - SNOMED:has_dose_form_administration_method
+ - SNOMED:has_dose_form_release_characteristic
+ - SNOMED:has_dose_form_transformation
+ - SNOMED:has_finding_context
+ - SNOMED:has_finding_informer
+ - SNOMED:has_inherent_attribute
+ - SNOMED:has_intent
+ - SNOMED:has_interpretation
+ - SNOMED:has_laterality
+ - SNOMED:has_measurement_method
+ - SNOMED:has_method
+ - SNOMED:has_priority
+ - SNOMED:has_procedure_context
+ - SNOMED:has_process_duration
+ - SNOMED:has_property
+ - SNOMED:has_revision_status
+ - SNOMED:has_scale_type
+ - SNOMED:has_severity
+ - SNOMED:has_specimen
+ - SNOMED:has_state_of_matter
+ - SNOMED:has_subject_relationship_context
+ - SNOMED:has_surgical_approach
+ - SNOMED:has_technique
+ - SNOMED:has_temporal_context
+ - SNOMED:has_time_aspect
+ - SNOMED:has_units
+ - UMLS:has_structural_class
+ - UMLS:has_supported_concept_property
+ - UMLS:has_supported_concept_relationship
+ - UMLS:may_be_qualified_by
+ rank: 1000
+ domain: entity
+ slot_uri: biolink:has_attribute
+ alias: has_attribute
+ owner: DissociatedCellSample
+ domain_of:
+ - entity
+ - attribute
+ - named thing
+ - organism taxon
+ - information content entity
+ - dataset
+ - physical entity
+ - activity
+ - procedure
+ - material sample
+ - biological entity
+ - gene
+ - genome
+ range: attribute
+ multivalued: true
+ deprecated:
+ name: deprecated
+ definition_uri: https://w3id.org/biolink/vocab/deprecated
+ description: A boolean flag indicating that an entity is no longer considered
+ current or valid.
+ from_schema: https://identifiers.org/brain-bican/library-generation-schema
+ exact_mappings:
+ - oboInOwl:ObsoleteClass
+ rank: 1000
+ slot_uri: biolink:deprecated
+ alias: deprecated
+ owner: DissociatedCellSample
+ domain_of:
+ - entity
+ - attribute
+ - named thing
+ - organism taxon
+ - information content entity
+ - dataset
+ - physical entity
+ - activity
+ - procedure
+ - material sample
+ - biological entity
+ - gene
+ - genome
+ range: boolean
+ provided by:
+ name: provided by
+ definition_uri: https://w3id.org/biolink/vocab/provided_by
+ description: The value in this node property represents the knowledge provider
+ that created or assembled the node and all of its attributes. Used internally
+ to represent how a particular node made its way into a knowledge provider or
+ graph.
+ from_schema: https://identifiers.org/brain-bican/library-generation-schema
+ rank: 1000
+ is_a: node property
+ domain: named thing
+ slot_uri: biolink:provided_by
+ alias: provided_by
+ owner: DissociatedCellSample
+ domain_of:
+ - named thing
+ - attribute
+ - organism taxon
+ - information content entity
+ - dataset
+ - physical entity
+ - activity
+ - procedure
+ - material sample
+ - biological entity
+ - gene
+ - genome
+ range: string
+ multivalued: true
+ xref:
+ name: xref
+ definition_uri: https://w3id.org/biolink/vocab/xref
+ description: A database cross reference or alternative identifier for a NamedThing
+ or edge between two NamedThings. This property should point to a database record
+ or webpage that supports the existence of the edge, or gives more detail about
+ the edge. This property can be used on a node or edge to provide multiple URIs
+ or CURIE cross references.
+ in_subset:
+ - translator_minimal
+ from_schema: https://identifiers.org/brain-bican/library-generation-schema
+ aliases:
+ - dbxref
+ - Dbxref
+ - DbXref
+ - record_url
+ - source_record_urls
+ narrow_mappings:
+ - gff3:Dbxref
+ - gpi:DB_Xrefs
+ rank: 1000
+ domain: named thing
+ slot_uri: biolink:xref
+ alias: xref
+ owner: DissociatedCellSample
+ domain_of:
+ - named thing
+ - gene
+ - attribute
+ - organism taxon
+ - information content entity
+ - dataset
+ - physical entity
+ - activity
+ - procedure
+ - material sample
+ - biological entity
+ - genome
+ range: uriorcurie
+ multivalued: true
+ full name:
+ name: full name
+ definition_uri: https://w3id.org/biolink/vocab/full_name
+ description: a long-form human readable name for a thing
+ from_schema: https://identifiers.org/brain-bican/library-generation-schema
+ rank: 1000
+ is_a: node property
+ domain: named thing
+ slot_uri: biolink:full_name
+ alias: full_name
+ owner: DissociatedCellSample
+ domain_of:
+ - named thing
+ - attribute
+ - organism taxon
+ - information content entity
+ - dataset
+ - physical entity
+ - activity
+ - procedure
+ - material sample
+ - biological entity
+ - gene
+ - genome
+ range: label type
+ synonym:
+ name: synonym
+ definition_uri: https://w3id.org/biolink/vocab/synonym
+ description: Alternate human-readable names for a thing
+ in_subset:
+ - translator_minimal
+ from_schema: https://identifiers.org/brain-bican/library-generation-schema
+ aliases:
+ - alias
+ narrow_mappings:
+ - skos:altLabel
+ - gff3:Alias
+ - AGRKB:synonyms
+ - gpi:DB_Object_Synonyms
+ - HANCESTRO:0330
+ - IAO:0000136
+ - RXNORM:has_tradename
+ rank: 1000
+ is_a: node property
+ domain: named thing
+ slot_uri: biolink:synonym
+ alias: synonym
+ owner: DissociatedCellSample
+ domain_of:
+ - named thing
+ - attribute
+ - organism taxon
+ - information content entity
+ - dataset
+ - physical entity
+ - activity
+ - procedure
+ - material sample
+ - biological entity
+ - gene
+ - genome
+ range: label type
+ multivalued: true
+
+URI: DissociatedCellSampleCellLabelBarcode
+| Value | +Meaning | +Description | +
|---|---|---|
| CMO301 | +NIMP:PD-CFCFPS27 | +10x Cell Plex oligo tag for multiplexing tissue sources into a single 10x loa... | +
| CMO302 | +NIMP:PD-CFCFPS27 | +10x Cell Plex oligo tag for multiplexing tissue sources into a single 10x loa... | +
| CMO303 | +NIMP:PD-CFCFPS27 | +10x Cell Plex oligo tag for multiplexing tissue sources into a single 10x loa... | +
| CMO304 | +NIMP:PD-CFCFPS27 | +10x Cell Plex oligo tag for multiplexing tissue sources into a single 10x loa... | +
| CMO305 | +NIMP:PD-CFCFPS27 | +10x Cell Plex oligo tag for multiplexing tissue sources into a single 10x loa... | +
| CMO306 | +NIMP:PD-CFCFPS27 | +10x Cell Plex oligo tag for multiplexing tissue sources into a single 10x loa... | +
| CMO307 | +NIMP:PD-CFCFPS27 | +10x Cell Plex oligo tag for multiplexing tissue sources into a single 10x loa... | +
| CMO308 | +NIMP:PD-CFCFPS27 | +10x Cell Plex oligo tag for multiplexing tissue sources into a single 10x loa... | +
| CMO309 | +NIMP:PD-CFCFPS27 | +10x Cell Plex oligo tag for multiplexing tissue sources into a single 10x loa... | +
| CMO310 | +NIMP:PD-CFCFPS27 | +10x Cell Plex oligo tag for multiplexing tissue sources into a single 10x loa... | +
| CMO311 | +NIMP:PD-CFCFPS27 | +10x Cell Plex oligo tag for multiplexing tissue sources into a single 10x loa... | +
| CMO312 | +NIMP:PD-CFCFPS27 | +10x Cell Plex oligo tag for multiplexing tissue sources into a single 10x loa... | +
| 2nt-001 | +NIMP:PD-CFCFPS27 | +Used in conjunction with Histone antibody to capture and tag separate subcomp... | +
| 2nt-002 | +NIMP:PD-CFCFPS27 | +Used in conjunction with Histone antibody to capture and tag separate subcomp... | +
| 2nt-003 | +NIMP:PD-CFCFPS27 | +Used in conjunction with Histone antibody to capture and tag separate subcomp... | +
| 2nt-004 | +NIMP:PD-CFCFPS27 | +Used in conjunction with Histone antibody to capture and tag separate subcomp... | +
| 3nt-001 | +NIMP:PD-CFCFPS27 | +Used in conjunction with Histone antibody to capture and tag separate subcomp... | +
| 3nt-002 | +NIMP:PD-CFCFPS27 | +Used in conjunction with Histone antibody to capture and tag separate subcomp... | +
| 3nt-003 | +NIMP:PD-CFCFPS27 | +Used in conjunction with Histone antibody to capture and tag separate subcomp... | +
| 3nt-004 | +NIMP:PD-CFCFPS27 | +Used in conjunction with Histone antibody to capture and tag separate subcomp... | +
| 3nt-005 | +NIMP:PD-CFCFPS27 | +Used in conjunction with Histone antibody to capture and tag separate subcomp... | +
| 3nt-006 | +NIMP:PD-CFCFPS27 | +Used in conjunction with Histone antibody to capture and tag separate subcomp... | +
| Name | +Description | +
|---|---|
| cell_source_oligo_name | +Name of cell source oligo used in cell plexing | +
name: dissociated_cell_sample_cell_label_barcode
+from_schema: https://identifiers.org/brain-bican/library-generation-schema
+rank: 1000
+permissible_values:
+ CMO301:
+ text: CMO301
+ description: 10x Cell Plex oligo tag for multiplexing tissue sources into a single
+ 10x load.
+ meaning: NIMP:PD-CFCFPS27
+ CMO302:
+ text: CMO302
+ description: 10x Cell Plex oligo tag for multiplexing tissue sources into a single
+ 10x load.
+ meaning: NIMP:PD-CFCFPS27
+ CMO303:
+ text: CMO303
+ description: 10x Cell Plex oligo tag for multiplexing tissue sources into a single
+ 10x load.
+ meaning: NIMP:PD-CFCFPS27
+ CMO304:
+ text: CMO304
+ description: 10x Cell Plex oligo tag for multiplexing tissue sources into a single
+ 10x load.
+ meaning: NIMP:PD-CFCFPS27
+ CMO305:
+ text: CMO305
+ description: 10x Cell Plex oligo tag for multiplexing tissue sources into a single
+ 10x load.
+ meaning: NIMP:PD-CFCFPS27
+ CMO306:
+ text: CMO306
+ description: 10x Cell Plex oligo tag for multiplexing tissue sources into a single
+ 10x load.
+ meaning: NIMP:PD-CFCFPS27
+ CMO307:
+ text: CMO307
+ description: 10x Cell Plex oligo tag for multiplexing tissue sources into a single
+ 10x load.
+ meaning: NIMP:PD-CFCFPS27
+ CMO308:
+ text: CMO308
+ description: 10x Cell Plex oligo tag for multiplexing tissue sources into a single
+ 10x load.
+ meaning: NIMP:PD-CFCFPS27
+ CMO309:
+ text: CMO309
+ description: 10x Cell Plex oligo tag for multiplexing tissue sources into a single
+ 10x load.
+ meaning: NIMP:PD-CFCFPS27
+ CMO310:
+ text: CMO310
+ description: 10x Cell Plex oligo tag for multiplexing tissue sources into a single
+ 10x load.
+ meaning: NIMP:PD-CFCFPS27
+ CMO311:
+ text: CMO311
+ description: 10x Cell Plex oligo tag for multiplexing tissue sources into a single
+ 10x load.
+ meaning: NIMP:PD-CFCFPS27
+ CMO312:
+ text: CMO312
+ description: 10x Cell Plex oligo tag for multiplexing tissue sources into a single
+ 10x load.
+ meaning: NIMP:PD-CFCFPS27
+ 2nt-001:
+ text: 2nt-001
+ description: Used in conjunction with Histone antibody to capture and tag separate
+ subcomponents of the epigenome. Allows for pooling of enriched cell samples
+ into a single 10x load.
+ meaning: NIMP:PD-CFCFPS27
+ 2nt-002:
+ text: 2nt-002
+ description: Used in conjunction with Histone antibody to capture and tag separate
+ subcomponents of the epigenome. Allows for pooling of enriched cell samples
+ into a single 10x load.
+ meaning: NIMP:PD-CFCFPS27
+ 2nt-003:
+ text: 2nt-003
+ description: Used in conjunction with Histone antibody to capture and tag separate
+ subcomponents of the epigenome. Allows for pooling of enriched cell samples
+ into a single 10x load.
+ meaning: NIMP:PD-CFCFPS27
+ 2nt-004:
+ text: 2nt-004
+ description: Used in conjunction with Histone antibody to capture and tag separate
+ subcomponents of the epigenome. Allows for pooling of enriched cell samples
+ into a single 10x load.
+ meaning: NIMP:PD-CFCFPS27
+ 3nt-001:
+ text: 3nt-001
+ description: Used in conjunction with Histone antibody to capture and tag separate
+ subcomponents of the epigenome. Allows for pooling of enriched cell samples
+ into a single 10x load.
+ meaning: NIMP:PD-CFCFPS27
+ 3nt-002:
+ text: 3nt-002
+ description: Used in conjunction with Histone antibody to capture and tag separate
+ subcomponents of the epigenome. Allows for pooling of enriched cell samples
+ into a single 10x load.
+ meaning: NIMP:PD-CFCFPS27
+ 3nt-003:
+ text: 3nt-003
+ description: Used in conjunction with Histone antibody to capture and tag separate
+ subcomponents of the epigenome. Allows for pooling of enriched cell samples
+ into a single 10x load.
+ meaning: NIMP:PD-CFCFPS27
+ 3nt-004:
+ text: 3nt-004
+ description: Used in conjunction with Histone antibody to capture and tag separate
+ subcomponents of the epigenome. Allows for pooling of enriched cell samples
+ into a single 10x load.
+ meaning: NIMP:PD-CFCFPS27
+ 3nt-005:
+ text: 3nt-005
+ description: Used in conjunction with Histone antibody to capture and tag separate
+ subcomponents of the epigenome. Allows for pooling of enriched cell samples
+ into a single 10x load.
+ meaning: NIMP:PD-CFCFPS27
+ 3nt-006:
+ text: 3nt-006
+ description: Used in conjunction with Histone antibody to capture and tag separate
+ subcomponents of the epigenome. Allows for pooling of enriched cell samples
+ into a single 10x load.
+ meaning: NIMP:PD-CFCFPS27
+
+URI: DissociatedCellSampleCellPrepType
+| Value | +Meaning | +Description | +
|---|---|---|
| Nuclei | +NIMP:PD-RELLGO26 | +isolated nuclei | +
| Cells | +NIMP:PD-RELLGO26 | +isolated whole cells | +
| Name | +Description | +
|---|---|
| cell_prep_type | +The type of cell preparation | +
name: dissociated_cell_sample_cell_prep_type
+from_schema: https://identifiers.org/brain-bican/library-generation-schema
+rank: 1000
+permissible_values:
+ Nuclei:
+ text: Nuclei
+ description: isolated nuclei
+ meaning: NIMP:PD-RELLGO26
+ Cells:
+ text: Cells
+ description: isolated whole cells
+ meaning: NIMP:PD-RELLGO26
+
+A person or organism that is the source of a biological sample for scientific study. Many biological samples are generated from a single donor.
+URI: bican:Donor
+| Name | +Cardinality and Range | +Description | +Inheritance | +
|---|---|---|---|
| name | +0..1 LabelType |
+Name of person or organism that is the source of a biological sample for scie... | +direct | +
| biological_sex | +0..1 Sex |
+Biological sex of donor at birth | +direct | +
| age_at_death_description | +0..1 String |
+Text description of the age of death following typical scientific convention ... | +direct | +
| age_at_death_reference_point | +0..1 age_at_death_reference_point |
+The reference point for an age interval; for example, birth or conception | +direct | +
| age_at_death_unit | +0..1 age_at_death_unit |
+The unit used for representing the donor age from the reference point | +direct | +
| age_at_death_value | +0..1 Float |
+The value representing the donor age from the reference point | +direct | +
| species | +0..1 String |
+Species of donor | +direct | +
| in_taxon | +* OrganismTaxon |
+connects an entity to its taxonomic classification | +ThingWithTaxon | +
| in_taxon_label | +0..1 LabelType |
+The human readable scientific name for the taxon of the entity | +ThingWithTaxon | +
| was_derived_from | +0..1 ProvEntity |
+A derivation is a transformation of an entity into another, an update of an e... | +ProvEntity | +
| was_generated_by | +0..1 ProvActivity |
+Generation is the completion of production of a new entity by an activity | +ProvEntity | +
| id | +1 String |
+A unique identifier for an entity | +NamedThing, PhysicalEntity, Entity | +
| iri | +0..1 IriType |
+An IRI for an entity | +NamedThing, PhysicalEntity, Entity | +
| category | +* Uriorcurie |
+Name of the high level ontology class in which this entity is categorized | +NamedThing, PhysicalEntity, Entity | +
| type | +* String |
++ | NamedThing, PhysicalEntity, Entity | +
| description | +0..1 NarrativeText |
+a human-readable description of an entity | +NamedThing, PhysicalEntity, Entity | +
| has_attribute | +* Attribute |
+connects any entity to an attribute | +NamedThing, PhysicalEntity, Entity | +
| deprecated | +0..1 Boolean |
+A boolean flag indicating that an entity is no longer considered current or v... | +NamedThing, PhysicalEntity, Entity | +
| provided_by | +* String |
+The value in this node property represents the knowledge provider that create... | +NamedThing, PhysicalEntity | +
| xref | +* Uriorcurie |
+A database cross reference or alternative identifier for a NamedThing or edge... | +NamedThing, PhysicalEntity | +
| full_name | +0..1 LabelType |
+a long-form human readable name for a thing | +NamedThing, PhysicalEntity | +
| synonym | +* LabelType |
+Alternate human-readable names for a thing | +NamedThing, PhysicalEntity | +
| used by | +used in | +type | +used | +
|---|---|---|---|
| BrainSlab | +was_derived_from | +range | +Donor | +
| BrainSlab | +was_derived_from | +exactly_one_of[range] | +Donor | +
| TissueSample | +was_derived_from | +range | +Donor | +
| Mapping Type | +Mapped Value | +
|---|---|
| self | +bican:Donor | +
| native | +bican:Donor | +
| exact | +NIMP:Donor | +
name: Donor
+description: A person or organism that is the source of a biological sample for scientific
+ study. Many biological samples are generated from a single donor.
+from_schema: https://identifiers.org/brain-bican/library-generation-schema
+exact_mappings:
+- NIMP:Donor
+is_a: physical entity
+mixins:
+- thing with taxon
+- ProvEntity
+slots:
+- name
+slot_usage:
+ name:
+ name: name
+ description: Name of person or organism that is the source of a biological sample
+ for scientific study. Many biological samples are generated from a single donor.
+ category:
+ name: category
+ pattern: ^bican:[A-Z][A-Za-z]+$
+attributes:
+ biological_sex:
+ name: biological_sex
+ local_names:
+ NIMP:
+ local_name_source: NIMP
+ local_name_value: sex
+ description: Biological sex of donor at birth
+ from_schema: https://identifiers.org/brain-bican/library-generation-schema
+ exact_mappings:
+ - NIMP:PD-LXUBTM45
+ rank: 1000
+ slot_uri: bican:632d3d3f-f85b-4efc-a1ab-010fe417ae81
+ domain_of:
+ - Donor
+ range: sex
+ age_at_death_description:
+ name: age_at_death_description
+ local_names:
+ NIMP:
+ local_name_source: NIMP
+ local_name_value: age_at_death_description
+ description: 'Text description of the age of death following typical scientific
+ convention for the species or developmental stage. For example: P56, E11.5'
+ from_schema: https://identifiers.org/brain-bican/library-generation-schema
+ exact_mappings:
+ - NIMP:PD-ZJZJLE33
+ rank: 1000
+ slot_uri: bican:0630a265-4a63-48f4-8853-66b929002306
+ domain_of:
+ - Donor
+ age_at_death_reference_point:
+ name: age_at_death_reference_point
+ local_names:
+ NIMP:
+ local_name_source: NIMP
+ local_name_value: age_at_death_reference_point
+ description: The reference point for an age interval; for example, birth or conception.
+ from_schema: https://identifiers.org/brain-bican/library-generation-schema
+ exact_mappings:
+ - NIMP:PD-RARAGG39
+ rank: 1000
+ slot_uri: bican:3bed1f94-9d82-4ed7-afdf-79d896b24dbb
+ domain_of:
+ - Donor
+ range: age_at_death_reference_point
+ age_at_death_unit:
+ name: age_at_death_unit
+ local_names:
+ NIMP:
+ local_name_source: NIMP
+ local_name_value: age_at_death_unit
+ description: The unit used for representing the donor age from the reference point.
+ from_schema: https://identifiers.org/brain-bican/library-generation-schema
+ exact_mappings:
+ - NIMP:PD-AVAVEV39
+ rank: 1000
+ slot_uri: bican:b5436e99-f0a7-4c30-825d-56b88ee2ac1d
+ domain_of:
+ - Donor
+ range: age_at_death_unit
+ age_at_death_value:
+ name: age_at_death_value
+ local_names:
+ NIMP:
+ local_name_source: NIMP
+ local_name_value: age_at_death
+ description: The value representing the donor age from the reference point.
+ from_schema: https://identifiers.org/brain-bican/library-generation-schema
+ exact_mappings:
+ - NIMP:PD-FTFTCP24
+ rank: 1000
+ slot_uri: bican:57e24d3c-c9c7-4ef3-9809-a35802d563ec
+ domain_of:
+ - Donor
+ range: float
+ species:
+ name: species
+ local_names:
+ local_name_value:
+ local_name_source: local_name_value
+ local_name_value: donor_species
+ description: Species of donor.
+ from_schema: https://identifiers.org/brain-bican/library-generation-schema
+ rank: 1000
+ slot_uri: bican:6837cb02-6bd7-4fb8-838c-9062ead96ba4
+ alias: donor_species
+ domain_of:
+ - Donor
+
+name: Donor
+description: A person or organism that is the source of a biological sample for scientific
+ study. Many biological samples are generated from a single donor.
+from_schema: https://identifiers.org/brain-bican/library-generation-schema
+exact_mappings:
+- NIMP:Donor
+is_a: physical entity
+mixins:
+- thing with taxon
+- ProvEntity
+slot_usage:
+ name:
+ name: name
+ description: Name of person or organism that is the source of a biological sample
+ for scientific study. Many biological samples are generated from a single donor.
+ category:
+ name: category
+ pattern: ^bican:[A-Z][A-Za-z]+$
+attributes:
+ biological_sex:
+ name: biological_sex
+ local_names:
+ NIMP:
+ local_name_source: NIMP
+ local_name_value: sex
+ description: Biological sex of donor at birth
+ from_schema: https://identifiers.org/brain-bican/library-generation-schema
+ exact_mappings:
+ - NIMP:PD-LXUBTM45
+ rank: 1000
+ slot_uri: bican:632d3d3f-f85b-4efc-a1ab-010fe417ae81
+ alias: biological_sex
+ owner: Donor
+ domain_of:
+ - Donor
+ range: sex
+ age_at_death_description:
+ name: age_at_death_description
+ local_names:
+ NIMP:
+ local_name_source: NIMP
+ local_name_value: age_at_death_description
+ description: 'Text description of the age of death following typical scientific
+ convention for the species or developmental stage. For example: P56, E11.5'
+ from_schema: https://identifiers.org/brain-bican/library-generation-schema
+ exact_mappings:
+ - NIMP:PD-ZJZJLE33
+ rank: 1000
+ slot_uri: bican:0630a265-4a63-48f4-8853-66b929002306
+ alias: age_at_death_description
+ owner: Donor
+ domain_of:
+ - Donor
+ range: string
+ age_at_death_reference_point:
+ name: age_at_death_reference_point
+ local_names:
+ NIMP:
+ local_name_source: NIMP
+ local_name_value: age_at_death_reference_point
+ description: The reference point for an age interval; for example, birth or conception.
+ from_schema: https://identifiers.org/brain-bican/library-generation-schema
+ exact_mappings:
+ - NIMP:PD-RARAGG39
+ rank: 1000
+ slot_uri: bican:3bed1f94-9d82-4ed7-afdf-79d896b24dbb
+ alias: age_at_death_reference_point
+ owner: Donor
+ domain_of:
+ - Donor
+ range: age_at_death_reference_point
+ age_at_death_unit:
+ name: age_at_death_unit
+ local_names:
+ NIMP:
+ local_name_source: NIMP
+ local_name_value: age_at_death_unit
+ description: The unit used for representing the donor age from the reference point.
+ from_schema: https://identifiers.org/brain-bican/library-generation-schema
+ exact_mappings:
+ - NIMP:PD-AVAVEV39
+ rank: 1000
+ slot_uri: bican:b5436e99-f0a7-4c30-825d-56b88ee2ac1d
+ alias: age_at_death_unit
+ owner: Donor
+ domain_of:
+ - Donor
+ range: age_at_death_unit
+ age_at_death_value:
+ name: age_at_death_value
+ local_names:
+ NIMP:
+ local_name_source: NIMP
+ local_name_value: age_at_death
+ description: The value representing the donor age from the reference point.
+ from_schema: https://identifiers.org/brain-bican/library-generation-schema
+ exact_mappings:
+ - NIMP:PD-FTFTCP24
+ rank: 1000
+ slot_uri: bican:57e24d3c-c9c7-4ef3-9809-a35802d563ec
+ alias: age_at_death_value
+ owner: Donor
+ domain_of:
+ - Donor
+ range: float
+ species:
+ name: species
+ local_names:
+ local_name_value:
+ local_name_source: local_name_value
+ local_name_value: donor_species
+ description: Species of donor.
+ from_schema: https://identifiers.org/brain-bican/library-generation-schema
+ rank: 1000
+ slot_uri: bican:6837cb02-6bd7-4fb8-838c-9062ead96ba4
+ alias: donor_species
+ owner: Donor
+ domain_of:
+ - Donor
+ range: string
+ name:
+ name: name
+ definition_uri: https://w3id.org/biolink/vocab/name
+ description: Name of person or organism that is the source of a biological sample
+ for scientific study. Many biological samples are generated from a single donor.
+ in_subset:
+ - translator_minimal
+ - samples
+ from_schema: https://identifiers.org/brain-bican/library-generation-schema
+ aliases:
+ - label
+ - display name
+ - title
+ mappings:
+ - rdfs:label
+ exact_mappings:
+ - gff3:Name
+ - gpi:DB_Object_Name
+ narrow_mappings:
+ - dct:title
+ - WIKIDATA_PROPERTY:P1476
+ rank: 1000
+ domain: entity
+ slot_uri: rdfs:label
+ alias: name
+ owner: Donor
+ domain_of:
+ - attribute
+ - entity
+ - macromolecular machine mixin
+ - Donor
+ - BrainSlab
+ - TissueSample
+ - DissociatedCellSample
+ - EnrichedCellSample
+ - BarcodedCellSample
+ - AmplifiedCdna
+ - Library
+ - LibraryAliquot
+ - LibraryPool
+ - DissectionRoiPolygon
+ - named thing
+ - organism taxon
+ - information content entity
+ - dataset
+ - physical entity
+ - activity
+ - procedure
+ - material sample
+ - biological entity
+ - gene or gene product
+ - gene
+ - genome
+ range: label type
+ in taxon:
+ name: in taxon
+ definition_uri: https://w3id.org/biolink/vocab/in_taxon
+ annotations:
+ canonical_predicate:
+ tag: canonical_predicate
+ value: true
+ description: connects an entity to its taxonomic classification. Only certain
+ kinds of entities can be taxonomically classified; see 'thing with taxon'
+ in_subset:
+ - translator_minimal
+ from_schema: https://identifiers.org/brain-bican/library-generation-schema
+ aliases:
+ - instance of
+ - is organism source of gene product
+ - organism has gene
+ - gene found in organism
+ - gene product has organism source
+ exact_mappings:
+ - RO:0002162
+ - WIKIDATA_PROPERTY:P703
+ narrow_mappings:
+ - RO:0002160
+ rank: 1000
+ is_a: related to at instance level
+ domain: thing with taxon
+ slot_uri: biolink:in_taxon
+ inherited: true
+ alias: in_taxon
+ owner: Donor
+ domain_of:
+ - thing with taxon
+ - biological entity
+ - gene
+ - genome
+ range: organism taxon
+ multivalued: true
+ in taxon label:
+ name: in taxon label
+ definition_uri: https://w3id.org/biolink/vocab/in_taxon_label
+ annotations:
+ denormalized:
+ tag: denormalized
+ value: true
+ description: The human readable scientific name for the taxon of the entity.
+ in_subset:
+ - translator_minimal
+ from_schema: https://identifiers.org/brain-bican/library-generation-schema
+ exact_mappings:
+ - WIKIDATA_PROPERTY:P225
+ rank: 1000
+ is_a: node property
+ domain: thing with taxon
+ slot_uri: biolink:in_taxon_label
+ alias: in_taxon_label
+ owner: Donor
+ domain_of:
+ - thing with taxon
+ - biological entity
+ - gene
+ - genome
+ range: label type
+ was_derived_from:
+ name: was_derived_from
+ description: A derivation is a transformation of an entity into another, an update
+ of an entity resulting in a new one, or the construction of a new entity based
+ on a pre-existing entity.
+ from_schema: https://identifiers.org/brain-bican/library-generation-schema
+ rank: 1000
+ slot_uri: prov:wasDerivedFrom
+ alias: was_derived_from
+ owner: Donor
+ domain_of:
+ - BrainSlab
+ - TissueSample
+ - DissociatedCellSample
+ - EnrichedCellSample
+ - BarcodedCellSample
+ - AmplifiedCdna
+ - Library
+ - LibraryAliquot
+ - LibraryPool
+ - ProvEntity
+ range: ProvEntity
+ was_generated_by:
+ name: was_generated_by
+ description: Generation is the completion of production of a new entity by an
+ activity. This entity did not exist before generation and becomes available
+ for usage after this generation.
+ from_schema: https://identifiers.org/brain-bican/library-generation-schema
+ rank: 1000
+ slot_uri: prov:wasGeneratedBy
+ alias: was_generated_by
+ owner: Donor
+ domain_of:
+ - TissueSample
+ - DissociatedCellSample
+ - EnrichedCellSample
+ - BarcodedCellSample
+ - AmplifiedCdna
+ - Library
+ - LibraryPool
+ - DissectionRoiPolygon
+ - ProvEntity
+ range: ProvActivity
+ id:
+ name: id
+ definition_uri: https://w3id.org/biolink/vocab/id
+ description: A unique identifier for an entity. Must be either a CURIE shorthand
+ for a URI or a complete URI
+ in_subset:
+ - translator_minimal
+ from_schema: https://identifiers.org/brain-bican/library-generation-schema
+ exact_mappings:
+ - AGRKB:primaryId
+ - gff3:ID
+ - gpi:DB_Object_ID
+ rank: 1000
+ domain: entity
+ slot_uri: biolink:id
+ identifier: true
+ alias: id
+ owner: Donor
+ domain_of:
+ - ontology class
+ - entity
+ - attribute
+ - named thing
+ - taxonomic rank
+ - organism taxon
+ - information content entity
+ - dataset
+ - physical entity
+ - activity
+ - procedure
+ - material sample
+ - biological entity
+ - gene
+ - genome
+ range: string
+ required: true
+ iri:
+ name: iri
+ definition_uri: https://w3id.org/biolink/vocab/iri
+ description: An IRI for an entity. This is determined by the id using expansion
+ rules.
+ in_subset:
+ - translator_minimal
+ - samples
+ from_schema: https://identifiers.org/brain-bican/library-generation-schema
+ exact_mappings:
+ - WIKIDATA_PROPERTY:P854
+ rank: 1000
+ slot_uri: biolink:iri
+ alias: iri
+ owner: Donor
+ domain_of:
+ - attribute
+ - entity
+ - named thing
+ - organism taxon
+ - information content entity
+ - dataset
+ - physical entity
+ - activity
+ - procedure
+ - material sample
+ - biological entity
+ - gene
+ - genome
+ range: iri type
+ category:
+ name: category
+ definition_uri: https://w3id.org/biolink/vocab/category
+ description: Name of the high level ontology class in which this entity is categorized.
+ Corresponds to the label for the biolink entity type class. In a neo4j database
+ this MAY correspond to the neo4j label tag. In an RDF database it should be
+ a biolink model class URI. This field is multi-valued. It should include values
+ for ancestors of the biolink class; for example, a protein such as Shh would
+ have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`.
+ In an RDF database, nodes will typically have an rdf:type triples. This can
+ be to the most specific biolink class, or potentially to a class more specific
+ than something in biolink. For example, a sequence feature `f` may have a rdf:type
+ assertion to a SO class such as TF_binding_site, which is more specific than
+ anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity,
+ biolink:NamedThing}
+ in_subset:
+ - translator_minimal
+ from_schema: https://identifiers.org/brain-bican/library-generation-schema
+ rank: 1000
+ is_a: type
+ domain: entity
+ slot_uri: biolink:category
+ designates_type: true
+ alias: category
+ owner: Donor
+ domain_of:
+ - entity
+ - attribute
+ - named thing
+ - organism taxon
+ - information content entity
+ - dataset
+ - physical entity
+ - activity
+ - procedure
+ - material sample
+ - biological entity
+ - gene
+ - genome
+ is_class_field: true
+ range: uriorcurie
+ multivalued: true
+ pattern: ^bican:[A-Z][A-Za-z]+$
+ type:
+ name: type
+ definition_uri: https://w3id.org/biolink/vocab/type
+ from_schema: https://identifiers.org/brain-bican/library-generation-schema
+ mappings:
+ - rdf:type
+ exact_mappings:
+ - gff3:type
+ - gpi:DB_Object_Type
+ rank: 1000
+ domain: entity
+ slot_uri: rdf:type
+ alias: type
+ owner: Donor
+ domain_of:
+ - entity
+ - attribute
+ - named thing
+ - organism taxon
+ - information content entity
+ - dataset
+ - physical entity
+ - activity
+ - procedure
+ - material sample
+ - biological entity
+ - gene
+ - genome
+ range: string
+ multivalued: true
+ description:
+ name: description
+ definition_uri: https://w3id.org/biolink/vocab/description
+ description: a human-readable description of an entity
+ in_subset:
+ - translator_minimal
+ from_schema: https://identifiers.org/brain-bican/library-generation-schema
+ aliases:
+ - definition
+ mappings:
+ - dct:description
+ exact_mappings:
+ - IAO:0000115
+ - skos:definitions
+ narrow_mappings:
+ - gff3:Description
+ rank: 1000
+ slot_uri: dct:description
+ alias: description
+ owner: Donor
+ domain_of:
+ - entity
+ - attribute
+ - named thing
+ - organism taxon
+ - information content entity
+ - dataset
+ - physical entity
+ - activity
+ - procedure
+ - material sample
+ - biological entity
+ - gene
+ - genome
+ range: narrative text
+ has attribute:
+ name: has attribute
+ definition_uri: https://w3id.org/biolink/vocab/has_attribute
+ description: connects any entity to an attribute
+ in_subset:
+ - samples
+ from_schema: https://identifiers.org/brain-bican/library-generation-schema
+ exact_mappings:
+ - SIO:000008
+ close_mappings:
+ - OBI:0001927
+ narrow_mappings:
+ - OBAN:association_has_subject_property
+ - OBAN:association_has_object_property
+ - CPT:has_possibly_included_panel_element
+ - DRUGBANK:category
+ - EFO:is_executed_in
+ - HANCESTRO:0301
+ - LOINC:has_action_guidance
+ - LOINC:has_adjustment
+ - LOINC:has_aggregation_view
+ - LOINC:has_approach_guidance
+ - LOINC:has_divisor
+ - LOINC:has_exam
+ - LOINC:has_method
+ - LOINC:has_modality_subtype
+ - LOINC:has_object_guidance
+ - LOINC:has_scale
+ - LOINC:has_suffix
+ - LOINC:has_time_aspect
+ - LOINC:has_time_modifier
+ - LOINC:has_timing_of
+ - NCIT:R88
+ - NCIT:eo_disease_has_property_or_attribute
+ - NCIT:has_data_element
+ - NCIT:has_pharmaceutical_administration_method
+ - NCIT:has_pharmaceutical_basic_dose_form
+ - NCIT:has_pharmaceutical_intended_site
+ - NCIT:has_pharmaceutical_release_characteristics
+ - NCIT:has_pharmaceutical_state_of_matter
+ - NCIT:has_pharmaceutical_transformation
+ - NCIT:is_qualified_by
+ - NCIT:qualifier_applies_to
+ - NCIT:role_has_domain
+ - NCIT:role_has_range
+ - INO:0000154
+ - HANCESTRO:0308
+ - OMIM:has_inheritance_type
+ - orphanet:C016
+ - orphanet:C017
+ - RO:0000053
+ - RO:0000086
+ - RO:0000087
+ - SNOMED:has_access
+ - SNOMED:has_clinical_course
+ - SNOMED:has_count_of_base_of_active_ingredient
+ - SNOMED:has_dose_form_administration_method
+ - SNOMED:has_dose_form_release_characteristic
+ - SNOMED:has_dose_form_transformation
+ - SNOMED:has_finding_context
+ - SNOMED:has_finding_informer
+ - SNOMED:has_inherent_attribute
+ - SNOMED:has_intent
+ - SNOMED:has_interpretation
+ - SNOMED:has_laterality
+ - SNOMED:has_measurement_method
+ - SNOMED:has_method
+ - SNOMED:has_priority
+ - SNOMED:has_procedure_context
+ - SNOMED:has_process_duration
+ - SNOMED:has_property
+ - SNOMED:has_revision_status
+ - SNOMED:has_scale_type
+ - SNOMED:has_severity
+ - SNOMED:has_specimen
+ - SNOMED:has_state_of_matter
+ - SNOMED:has_subject_relationship_context
+ - SNOMED:has_surgical_approach
+ - SNOMED:has_technique
+ - SNOMED:has_temporal_context
+ - SNOMED:has_time_aspect
+ - SNOMED:has_units
+ - UMLS:has_structural_class
+ - UMLS:has_supported_concept_property
+ - UMLS:has_supported_concept_relationship
+ - UMLS:may_be_qualified_by
+ rank: 1000
+ domain: entity
+ slot_uri: biolink:has_attribute
+ alias: has_attribute
+ owner: Donor
+ domain_of:
+ - entity
+ - attribute
+ - named thing
+ - organism taxon
+ - information content entity
+ - dataset
+ - physical entity
+ - activity
+ - procedure
+ - material sample
+ - biological entity
+ - gene
+ - genome
+ range: attribute
+ multivalued: true
+ deprecated:
+ name: deprecated
+ definition_uri: https://w3id.org/biolink/vocab/deprecated
+ description: A boolean flag indicating that an entity is no longer considered
+ current or valid.
+ from_schema: https://identifiers.org/brain-bican/library-generation-schema
+ exact_mappings:
+ - oboInOwl:ObsoleteClass
+ rank: 1000
+ slot_uri: biolink:deprecated
+ alias: deprecated
+ owner: Donor
+ domain_of:
+ - entity
+ - attribute
+ - named thing
+ - organism taxon
+ - information content entity
+ - dataset
+ - physical entity
+ - activity
+ - procedure
+ - material sample
+ - biological entity
+ - gene
+ - genome
+ range: boolean
+ provided by:
+ name: provided by
+ definition_uri: https://w3id.org/biolink/vocab/provided_by
+ description: The value in this node property represents the knowledge provider
+ that created or assembled the node and all of its attributes. Used internally
+ to represent how a particular node made its way into a knowledge provider or
+ graph.
+ from_schema: https://identifiers.org/brain-bican/library-generation-schema
+ rank: 1000
+ is_a: node property
+ domain: named thing
+ slot_uri: biolink:provided_by
+ alias: provided_by
+ owner: Donor
+ domain_of:
+ - named thing
+ - attribute
+ - organism taxon
+ - information content entity
+ - dataset
+ - physical entity
+ - activity
+ - procedure
+ - material sample
+ - biological entity
+ - gene
+ - genome
+ range: string
+ multivalued: true
+ xref:
+ name: xref
+ definition_uri: https://w3id.org/biolink/vocab/xref
+ description: A database cross reference or alternative identifier for a NamedThing
+ or edge between two NamedThings. This property should point to a database record
+ or webpage that supports the existence of the edge, or gives more detail about
+ the edge. This property can be used on a node or edge to provide multiple URIs
+ or CURIE cross references.
+ in_subset:
+ - translator_minimal
+ from_schema: https://identifiers.org/brain-bican/library-generation-schema
+ aliases:
+ - dbxref
+ - Dbxref
+ - DbXref
+ - record_url
+ - source_record_urls
+ narrow_mappings:
+ - gff3:Dbxref
+ - gpi:DB_Xrefs
+ rank: 1000
+ domain: named thing
+ slot_uri: biolink:xref
+ alias: xref
+ owner: Donor
+ domain_of:
+ - named thing
+ - gene
+ - attribute
+ - organism taxon
+ - information content entity
+ - dataset
+ - physical entity
+ - activity
+ - procedure
+ - material sample
+ - biological entity
+ - genome
+ range: uriorcurie
+ multivalued: true
+ full name:
+ name: full name
+ definition_uri: https://w3id.org/biolink/vocab/full_name
+ description: a long-form human readable name for a thing
+ from_schema: https://identifiers.org/brain-bican/library-generation-schema
+ rank: 1000
+ is_a: node property
+ domain: named thing
+ slot_uri: biolink:full_name
+ alias: full_name
+ owner: Donor
+ domain_of:
+ - named thing
+ - attribute
+ - organism taxon
+ - information content entity
+ - dataset
+ - physical entity
+ - activity
+ - procedure
+ - material sample
+ - biological entity
+ - gene
+ - genome
+ range: label type
+ synonym:
+ name: synonym
+ definition_uri: https://w3id.org/biolink/vocab/synonym
+ description: Alternate human-readable names for a thing
+ in_subset:
+ - translator_minimal
+ from_schema: https://identifiers.org/brain-bican/library-generation-schema
+ aliases:
+ - alias
+ narrow_mappings:
+ - skos:altLabel
+ - gff3:Alias
+ - AGRKB:synonyms
+ - gpi:DB_Object_Synonyms
+ - HANCESTRO:0330
+ - IAO:0000136
+ - RXNORM:has_tradename
+ rank: 1000
+ is_a: node property
+ domain: named thing
+ slot_uri: biolink:synonym
+ alias: synonym
+ owner: Donor
+ domain_of:
+ - named thing
+ - attribute
+ - organism taxon
+ - information content entity
+ - dataset
+ - physical entity
+ - activity
+ - procedure
+ - material sample
+ - biological entity
+ - gene
+ - genome
+ range: label type
+ multivalued: true
+
+A real number that conforms to the xsd:double specification
+URI: xsd:double
+ +| Mapping Type | +Mapped Value | +
|---|---|
| self | +xsd:double | +
| native | +bican:double | +
| close | +schema:Float | +
A collection of enriched cells or nuclei after enrichment process, usually via fluorescence-activated cell sorting (FACS) using the enrichment plan, is applied to dissociated cell sample.
+ +| Name | +Cardinality and Range | +Description | +Inheritance | +
|---|---|---|---|
| was_generated_by | +0..1 ProvActivity or CellEnrichment or EnrichedCellSampleSplitting |
+The cell enrichment or sample splitting process from which the enriched cell ... | +direct | +
| was_derived_from | +* ProvEntity or DissociatedCellSample or EnrichedCellSample |
+The dissociated or enriched cell sample(s) from which the enriched cell sampl... | +direct | +
| name | +0..1 LabelType |
+Name of collection of enriched cells or nuclei after enrichment process (usua... | +direct | +
| enrichment_population | +0..1 String |
+Actual percentage of cells as a result of using set of fluorescent marker lab... | +direct | +
| cell_source_oligo_name | +0..1 String |
+Name of cell source oligo used in cell plexing | +direct | +
| histone_modification_marker | +0..1 String |
+Histone modification marker antibodies (eg H3K27ac, H3K27me3, H3K9me3) used i... | +direct | +
| id | +1 String |
+A unique identifier for an entity | +NamedThing, PhysicalEntity, MaterialSample, Entity | +
| iri | +0..1 IriType |
+An IRI for an entity | +NamedThing, PhysicalEntity, MaterialSample, Entity | +
| category | +* Uriorcurie |
+Name of the high level ontology class in which this entity is categorized | +NamedThing, PhysicalEntity, MaterialSample, Entity | +
| type | +* String |
++ | NamedThing, PhysicalEntity, MaterialSample, Entity | +
| description | +0..1 NarrativeText |
+a human-readable description of an entity | +NamedThing, PhysicalEntity, MaterialSample, Entity | +
| has_attribute | +* Attribute |
+connects any entity to an attribute | +NamedThing, PhysicalEntity, MaterialSample, Entity | +
| deprecated | +0..1 Boolean |
+A boolean flag indicating that an entity is no longer considered current or v... | +NamedThing, PhysicalEntity, MaterialSample, Entity | +
| provided_by | +* String |
+The value in this node property represents the knowledge provider that create... | +NamedThing, PhysicalEntity, MaterialSample | +
| xref | +* Uriorcurie |
+A database cross reference or alternative identifier for a NamedThing or edge... | +NamedThing, PhysicalEntity, MaterialSample | +
| full_name | +0..1 LabelType |
+a long-form human readable name for a thing | +NamedThing, PhysicalEntity, MaterialSample | +
| synonym | +* LabelType |
+Alternate human-readable names for a thing | +NamedThing, PhysicalEntity, MaterialSample | +
| used by | +used in | +type | +used | +
|---|---|---|---|
| EnrichedCellSample | +was_derived_from | +exactly_one_of[range] | +EnrichedCellSample | +
| BarcodedCellSample | +was_derived_from | +exactly_one_of[range] | +EnrichedCellSample | +
| EnrichedCellSampleSplitting | +used | +range | +EnrichedCellSample | +
| CellBarcoding | +used | +exactly_one_of[range] | +EnrichedCellSample | +
| Mapping Type | +Mapped Value | +
|---|---|
| self | +bican:EnrichedCellSample | +
| native | +bican:EnrichedCellSample | +
| exact | +NIMP:Enriched%20Cell%20Sample | +
name: EnrichedCellSample
+description: A collection of enriched cells or nuclei after enrichment process, usually
+ via fluorescence-activated cell sorting (FACS) using the enrichment plan, is applied
+ to dissociated cell sample.
+in_subset:
+- bican
+- library_generation
+from_schema: https://identifiers.org/brain-bican/library-generation-schema
+exact_mappings:
+- NIMP:Enriched%20Cell%20Sample
+is_a: material sample
+mixins:
+- ProvEntity
+slots:
+- was_generated_by
+- was_derived_from
+- name
+slot_usage:
+ was_generated_by:
+ name: was_generated_by
+ description: The cell enrichment or sample splitting process from which the enriched
+ cell sample was generated by.
+ exactly_one_of:
+ - range: CellEnrichment
+ - range: EnrichedCellSampleSplitting
+ was_derived_from:
+ name: was_derived_from
+ description: The dissociated or enriched cell sample(s) from which the enriched
+ cell sample was derived from.
+ exact_mappings:
+ - NIMP:has_parent
+ multivalued: true
+ exactly_one_of:
+ - range: DissociatedCellSample
+ - range: EnrichedCellSample
+ name:
+ name: name
+ description: Name of collection of enriched cells or nuclei after enrichment process
+ (usually via FACS using the Enrichment Plan) applied to dissociated_cell_sample.
+ exact_mappings:
+ - NIMP:PD-BERWTM41
+ slot_uri: bican:bb3fc701-23a7-45c1-890d-7471730e0ec1
+ category:
+ name: category
+ pattern: ^bican:[A-Z][A-Za-z]+$
+attributes:
+ enrichment_population:
+ name: enrichment_population
+ local_names:
+ NIMP:
+ local_name_source: NIMP
+ local_name_value: enrichment_population
+ description: Actual percentage of cells as a result of using set of fluorescent
+ marker label(s) to enrich dissociated_cell_sample with desired mix of cell populations. This
+ plan can also be used to describe 'No FACS' where no enrichment was performed. This
+ is a property of enriched_cell_prep_container.
+ in_subset:
+ - analysis
+ from_schema: https://identifiers.org/brain-bican/library-generation-schema
+ exact_mappings:
+ - NIMP:PD-TZTZPI37
+ rank: 1000
+ slot_uri: bican:875f1c70-f5aa-45e3-94b9-5e482f6c4830
+ alias: enrichment population
+ domain_of:
+ - EnrichedCellSample
+ range: string
+ cell_source_oligo_name:
+ name: cell_source_oligo_name
+ local_names:
+ NIMP:
+ local_name_source: NIMP
+ local_name_value: enriched_cell_sample_cell_label_barcode
+ description: Name of cell source oligo used in cell plexing. The oligo molecularly
+ tags all the cells in the enriched cell sample and allows separate enriched
+ cell samples to be combined downstream in the barcoded cell sample. The oligo
+ name is associated with a sequence in a lookup table. This sequence will be
+ needed during alignment to associate reads with the parent source enriched cell
+ sample.
+ from_schema: https://identifiers.org/brain-bican/library-generation-schema
+ exact_mappings:
+ - NIMP:PD-CFCFPS27
+ domain_of:
+ - DissociatedCellSample
+ - EnrichedCellSample
+ histone_modification_marker:
+ name: histone_modification_marker
+ local_names:
+ NIMP:
+ local_name_source: NIMP
+ local_name_value: histone_modification_marker
+ description: Histone modification marker antibodies (eg H3K27ac, H3K27me3, H3K9me3)
+ used in conjunction with an Enriched Cell Source Barcode in order to combine
+ multiple Enriched Cell Populations before Barcoded Cell Sample step for 10xMultiome
+ method. Each of the Histone antibodies captures an essential part of the epigenome.
+ from_schema: https://identifiers.org/brain-bican/library-generation-schema
+ exact_mappings:
+ - NIMP:PD-ESESLW44
+ rank: 1000
+ domain_of:
+ - EnrichedCellSample
+
+name: EnrichedCellSample
+description: A collection of enriched cells or nuclei after enrichment process, usually
+ via fluorescence-activated cell sorting (FACS) using the enrichment plan, is applied
+ to dissociated cell sample.
+in_subset:
+- bican
+- library_generation
+from_schema: https://identifiers.org/brain-bican/library-generation-schema
+exact_mappings:
+- NIMP:Enriched%20Cell%20Sample
+is_a: material sample
+mixins:
+- ProvEntity
+slot_usage:
+ was_generated_by:
+ name: was_generated_by
+ description: The cell enrichment or sample splitting process from which the enriched
+ cell sample was generated by.
+ exactly_one_of:
+ - range: CellEnrichment
+ - range: EnrichedCellSampleSplitting
+ was_derived_from:
+ name: was_derived_from
+ description: The dissociated or enriched cell sample(s) from which the enriched
+ cell sample was derived from.
+ exact_mappings:
+ - NIMP:has_parent
+ multivalued: true
+ exactly_one_of:
+ - range: DissociatedCellSample
+ - range: EnrichedCellSample
+ name:
+ name: name
+ description: Name of collection of enriched cells or nuclei after enrichment process
+ (usually via FACS using the Enrichment Plan) applied to dissociated_cell_sample.
+ exact_mappings:
+ - NIMP:PD-BERWTM41
+ slot_uri: bican:bb3fc701-23a7-45c1-890d-7471730e0ec1
+ category:
+ name: category
+ pattern: ^bican:[A-Z][A-Za-z]+$
+attributes:
+ enrichment_population:
+ name: enrichment_population
+ local_names:
+ NIMP:
+ local_name_source: NIMP
+ local_name_value: enrichment_population
+ description: Actual percentage of cells as a result of using set of fluorescent
+ marker label(s) to enrich dissociated_cell_sample with desired mix of cell populations. This
+ plan can also be used to describe 'No FACS' where no enrichment was performed. This
+ is a property of enriched_cell_prep_container.
+ in_subset:
+ - analysis
+ from_schema: https://identifiers.org/brain-bican/library-generation-schema
+ exact_mappings:
+ - NIMP:PD-TZTZPI37
+ rank: 1000
+ slot_uri: bican:875f1c70-f5aa-45e3-94b9-5e482f6c4830
+ alias: enrichment population
+ owner: EnrichedCellSample
+ domain_of:
+ - EnrichedCellSample
+ range: string
+ cell_source_oligo_name:
+ name: cell_source_oligo_name
+ local_names:
+ NIMP:
+ local_name_source: NIMP
+ local_name_value: enriched_cell_sample_cell_label_barcode
+ description: Name of cell source oligo used in cell plexing. The oligo molecularly
+ tags all the cells in the enriched cell sample and allows separate enriched
+ cell samples to be combined downstream in the barcoded cell sample. The oligo
+ name is associated with a sequence in a lookup table. This sequence will be
+ needed during alignment to associate reads with the parent source enriched cell
+ sample.
+ from_schema: https://identifiers.org/brain-bican/library-generation-schema
+ exact_mappings:
+ - NIMP:PD-CFCFPS27
+ alias: cell_source_oligo_name
+ owner: EnrichedCellSample
+ domain_of:
+ - DissociatedCellSample
+ - EnrichedCellSample
+ range: string
+ histone_modification_marker:
+ name: histone_modification_marker
+ local_names:
+ NIMP:
+ local_name_source: NIMP
+ local_name_value: histone_modification_marker
+ description: Histone modification marker antibodies (eg H3K27ac, H3K27me3, H3K9me3)
+ used in conjunction with an Enriched Cell Source Barcode in order to combine
+ multiple Enriched Cell Populations before Barcoded Cell Sample step for 10xMultiome
+ method. Each of the Histone antibodies captures an essential part of the epigenome.
+ from_schema: https://identifiers.org/brain-bican/library-generation-schema
+ exact_mappings:
+ - NIMP:PD-ESESLW44
+ rank: 1000
+ alias: histone_modification_marker
+ owner: EnrichedCellSample
+ domain_of:
+ - EnrichedCellSample
+ range: string
+ was_generated_by:
+ name: was_generated_by
+ description: The cell enrichment or sample splitting process from which the enriched
+ cell sample was generated by.
+ from_schema: https://identifiers.org/brain-bican/library-generation-schema
+ rank: 1000
+ slot_uri: prov:wasGeneratedBy
+ alias: was_generated_by
+ owner: EnrichedCellSample
+ domain_of:
+ - TissueSample
+ - DissociatedCellSample
+ - EnrichedCellSample
+ - BarcodedCellSample
+ - AmplifiedCdna
+ - Library
+ - LibraryPool
+ - DissectionRoiPolygon
+ - ProvEntity
+ range: ProvActivity
+ exactly_one_of:
+ - range: CellEnrichment
+ - range: EnrichedCellSampleSplitting
+ was_derived_from:
+ name: was_derived_from
+ description: The dissociated or enriched cell sample(s) from which the enriched
+ cell sample was derived from.
+ from_schema: https://identifiers.org/brain-bican/library-generation-schema
+ exact_mappings:
+ - NIMP:has_parent
+ rank: 1000
+ slot_uri: prov:wasDerivedFrom
+ alias: was_derived_from
+ owner: EnrichedCellSample
+ domain_of:
+ - BrainSlab
+ - TissueSample
+ - DissociatedCellSample
+ - EnrichedCellSample
+ - BarcodedCellSample
+ - AmplifiedCdna
+ - Library
+ - LibraryAliquot
+ - LibraryPool
+ - ProvEntity
+ range: ProvEntity
+ multivalued: true
+ exactly_one_of:
+ - range: DissociatedCellSample
+ - range: EnrichedCellSample
+ name:
+ name: name
+ definition_uri: https://w3id.org/biolink/vocab/name
+ description: Name of collection of enriched cells or nuclei after enrichment process
+ (usually via FACS using the Enrichment Plan) applied to dissociated_cell_sample.
+ in_subset:
+ - translator_minimal
+ - samples
+ from_schema: https://identifiers.org/brain-bican/library-generation-schema
+ aliases:
+ - label
+ - display name
+ - title
+ mappings:
+ - rdfs:label
+ exact_mappings:
+ - NIMP:PD-BERWTM41
+ narrow_mappings:
+ - dct:title
+ - WIKIDATA_PROPERTY:P1476
+ rank: 1000
+ domain: entity
+ slot_uri: bican:bb3fc701-23a7-45c1-890d-7471730e0ec1
+ alias: name
+ owner: EnrichedCellSample
+ domain_of:
+ - attribute
+ - entity
+ - macromolecular machine mixin
+ - Donor
+ - BrainSlab
+ - TissueSample
+ - DissociatedCellSample
+ - EnrichedCellSample
+ - BarcodedCellSample
+ - AmplifiedCdna
+ - Library
+ - LibraryAliquot
+ - LibraryPool
+ - DissectionRoiPolygon
+ - named thing
+ - organism taxon
+ - information content entity
+ - dataset
+ - physical entity
+ - activity
+ - procedure
+ - material sample
+ - biological entity
+ - gene or gene product
+ - gene
+ - genome
+ range: label type
+ id:
+ name: id
+ definition_uri: https://w3id.org/biolink/vocab/id
+ description: A unique identifier for an entity. Must be either a CURIE shorthand
+ for a URI or a complete URI
+ in_subset:
+ - translator_minimal
+ from_schema: https://identifiers.org/brain-bican/library-generation-schema
+ exact_mappings:
+ - AGRKB:primaryId
+ - gff3:ID
+ - gpi:DB_Object_ID
+ rank: 1000
+ domain: entity
+ slot_uri: biolink:id
+ identifier: true
+ alias: id
+ owner: EnrichedCellSample
+ domain_of:
+ - ontology class
+ - entity
+ - attribute
+ - named thing
+ - taxonomic rank
+ - organism taxon
+ - information content entity
+ - dataset
+ - physical entity
+ - activity
+ - procedure
+ - material sample
+ - biological entity
+ - gene
+ - genome
+ range: string
+ required: true
+ iri:
+ name: iri
+ definition_uri: https://w3id.org/biolink/vocab/iri
+ description: An IRI for an entity. This is determined by the id using expansion
+ rules.
+ in_subset:
+ - translator_minimal
+ - samples
+ from_schema: https://identifiers.org/brain-bican/library-generation-schema
+ exact_mappings:
+ - WIKIDATA_PROPERTY:P854
+ rank: 1000
+ slot_uri: biolink:iri
+ alias: iri
+ owner: EnrichedCellSample
+ domain_of:
+ - attribute
+ - entity
+ - named thing
+ - organism taxon
+ - information content entity
+ - dataset
+ - physical entity
+ - activity
+ - procedure
+ - material sample
+ - biological entity
+ - gene
+ - genome
+ range: iri type
+ category:
+ name: category
+ definition_uri: https://w3id.org/biolink/vocab/category
+ description: Name of the high level ontology class in which this entity is categorized.
+ Corresponds to the label for the biolink entity type class. In a neo4j database
+ this MAY correspond to the neo4j label tag. In an RDF database it should be
+ a biolink model class URI. This field is multi-valued. It should include values
+ for ancestors of the biolink class; for example, a protein such as Shh would
+ have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`.
+ In an RDF database, nodes will typically have an rdf:type triples. This can
+ be to the most specific biolink class, or potentially to a class more specific
+ than something in biolink. For example, a sequence feature `f` may have a rdf:type
+ assertion to a SO class such as TF_binding_site, which is more specific than
+ anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity,
+ biolink:NamedThing}
+ in_subset:
+ - translator_minimal
+ from_schema: https://identifiers.org/brain-bican/library-generation-schema
+ rank: 1000
+ is_a: type
+ domain: entity
+ slot_uri: biolink:category
+ designates_type: true
+ alias: category
+ owner: EnrichedCellSample
+ domain_of:
+ - entity
+ - attribute
+ - named thing
+ - organism taxon
+ - information content entity
+ - dataset
+ - physical entity
+ - activity
+ - procedure
+ - material sample
+ - biological entity
+ - gene
+ - genome
+ is_class_field: true
+ range: uriorcurie
+ multivalued: true
+ pattern: ^bican:[A-Z][A-Za-z]+$
+ type:
+ name: type
+ definition_uri: https://w3id.org/biolink/vocab/type
+ from_schema: https://identifiers.org/brain-bican/library-generation-schema
+ mappings:
+ - rdf:type
+ exact_mappings:
+ - gff3:type
+ - gpi:DB_Object_Type
+ rank: 1000
+ domain: entity
+ slot_uri: rdf:type
+ alias: type
+ owner: EnrichedCellSample
+ domain_of:
+ - entity
+ - attribute
+ - named thing
+ - organism taxon
+ - information content entity
+ - dataset
+ - physical entity
+ - activity
+ - procedure
+ - material sample
+ - biological entity
+ - gene
+ - genome
+ range: string
+ multivalued: true
+ description:
+ name: description
+ definition_uri: https://w3id.org/biolink/vocab/description
+ description: a human-readable description of an entity
+ in_subset:
+ - translator_minimal
+ from_schema: https://identifiers.org/brain-bican/library-generation-schema
+ aliases:
+ - definition
+ mappings:
+ - dct:description
+ exact_mappings:
+ - IAO:0000115
+ - skos:definitions
+ narrow_mappings:
+ - gff3:Description
+ rank: 1000
+ slot_uri: dct:description
+ alias: description
+ owner: EnrichedCellSample
+ domain_of:
+ - entity
+ - attribute
+ - named thing
+ - organism taxon
+ - information content entity
+ - dataset
+ - physical entity
+ - activity
+ - procedure
+ - material sample
+ - biological entity
+ - gene
+ - genome
+ range: narrative text
+ has attribute:
+ name: has attribute
+ definition_uri: https://w3id.org/biolink/vocab/has_attribute
+ description: connects any entity to an attribute
+ in_subset:
+ - samples
+ from_schema: https://identifiers.org/brain-bican/library-generation-schema
+ exact_mappings:
+ - SIO:000008
+ close_mappings:
+ - OBI:0001927
+ narrow_mappings:
+ - OBAN:association_has_subject_property
+ - OBAN:association_has_object_property
+ - CPT:has_possibly_included_panel_element
+ - DRUGBANK:category
+ - EFO:is_executed_in
+ - HANCESTRO:0301
+ - LOINC:has_action_guidance
+ - LOINC:has_adjustment
+ - LOINC:has_aggregation_view
+ - LOINC:has_approach_guidance
+ - LOINC:has_divisor
+ - LOINC:has_exam
+ - LOINC:has_method
+ - LOINC:has_modality_subtype
+ - LOINC:has_object_guidance
+ - LOINC:has_scale
+ - LOINC:has_suffix
+ - LOINC:has_time_aspect
+ - LOINC:has_time_modifier
+ - LOINC:has_timing_of
+ - NCIT:R88
+ - NCIT:eo_disease_has_property_or_attribute
+ - NCIT:has_data_element
+ - NCIT:has_pharmaceutical_administration_method
+ - NCIT:has_pharmaceutical_basic_dose_form
+ - NCIT:has_pharmaceutical_intended_site
+ - NCIT:has_pharmaceutical_release_characteristics
+ - NCIT:has_pharmaceutical_state_of_matter
+ - NCIT:has_pharmaceutical_transformation
+ - NCIT:is_qualified_by
+ - NCIT:qualifier_applies_to
+ - NCIT:role_has_domain
+ - NCIT:role_has_range
+ - INO:0000154
+ - HANCESTRO:0308
+ - OMIM:has_inheritance_type
+ - orphanet:C016
+ - orphanet:C017
+ - RO:0000053
+ - RO:0000086
+ - RO:0000087
+ - SNOMED:has_access
+ - SNOMED:has_clinical_course
+ - SNOMED:has_count_of_base_of_active_ingredient
+ - SNOMED:has_dose_form_administration_method
+ - SNOMED:has_dose_form_release_characteristic
+ - SNOMED:has_dose_form_transformation
+ - SNOMED:has_finding_context
+ - SNOMED:has_finding_informer
+ - SNOMED:has_inherent_attribute
+ - SNOMED:has_intent
+ - SNOMED:has_interpretation
+ - SNOMED:has_laterality
+ - SNOMED:has_measurement_method
+ - SNOMED:has_method
+ - SNOMED:has_priority
+ - SNOMED:has_procedure_context
+ - SNOMED:has_process_duration
+ - SNOMED:has_property
+ - SNOMED:has_revision_status
+ - SNOMED:has_scale_type
+ - SNOMED:has_severity
+ - SNOMED:has_specimen
+ - SNOMED:has_state_of_matter
+ - SNOMED:has_subject_relationship_context
+ - SNOMED:has_surgical_approach
+ - SNOMED:has_technique
+ - SNOMED:has_temporal_context
+ - SNOMED:has_time_aspect
+ - SNOMED:has_units
+ - UMLS:has_structural_class
+ - UMLS:has_supported_concept_property
+ - UMLS:has_supported_concept_relationship
+ - UMLS:may_be_qualified_by
+ rank: 1000
+ domain: entity
+ slot_uri: biolink:has_attribute
+ alias: has_attribute
+ owner: EnrichedCellSample
+ domain_of:
+ - entity
+ - attribute
+ - named thing
+ - organism taxon
+ - information content entity
+ - dataset
+ - physical entity
+ - activity
+ - procedure
+ - material sample
+ - biological entity
+ - gene
+ - genome
+ range: attribute
+ multivalued: true
+ deprecated:
+ name: deprecated
+ definition_uri: https://w3id.org/biolink/vocab/deprecated
+ description: A boolean flag indicating that an entity is no longer considered
+ current or valid.
+ from_schema: https://identifiers.org/brain-bican/library-generation-schema
+ exact_mappings:
+ - oboInOwl:ObsoleteClass
+ rank: 1000
+ slot_uri: biolink:deprecated
+ alias: deprecated
+ owner: EnrichedCellSample
+ domain_of:
+ - entity
+ - attribute
+ - named thing
+ - organism taxon
+ - information content entity
+ - dataset
+ - physical entity
+ - activity
+ - procedure
+ - material sample
+ - biological entity
+ - gene
+ - genome
+ range: boolean
+ provided by:
+ name: provided by
+ definition_uri: https://w3id.org/biolink/vocab/provided_by
+ description: The value in this node property represents the knowledge provider
+ that created or assembled the node and all of its attributes. Used internally
+ to represent how a particular node made its way into a knowledge provider or
+ graph.
+ from_schema: https://identifiers.org/brain-bican/library-generation-schema
+ rank: 1000
+ is_a: node property
+ domain: named thing
+ slot_uri: biolink:provided_by
+ alias: provided_by
+ owner: EnrichedCellSample
+ domain_of:
+ - named thing
+ - attribute
+ - organism taxon
+ - information content entity
+ - dataset
+ - physical entity
+ - activity
+ - procedure
+ - material sample
+ - biological entity
+ - gene
+ - genome
+ range: string
+ multivalued: true
+ xref:
+ name: xref
+ definition_uri: https://w3id.org/biolink/vocab/xref
+ description: A database cross reference or alternative identifier for a NamedThing
+ or edge between two NamedThings. This property should point to a database record
+ or webpage that supports the existence of the edge, or gives more detail about
+ the edge. This property can be used on a node or edge to provide multiple URIs
+ or CURIE cross references.
+ in_subset:
+ - translator_minimal
+ from_schema: https://identifiers.org/brain-bican/library-generation-schema
+ aliases:
+ - dbxref
+ - Dbxref
+ - DbXref
+ - record_url
+ - source_record_urls
+ narrow_mappings:
+ - gff3:Dbxref
+ - gpi:DB_Xrefs
+ rank: 1000
+ domain: named thing
+ slot_uri: biolink:xref
+ alias: xref
+ owner: EnrichedCellSample
+ domain_of:
+ - named thing
+ - gene
+ - attribute
+ - organism taxon
+ - information content entity
+ - dataset
+ - physical entity
+ - activity
+ - procedure
+ - material sample
+ - biological entity
+ - genome
+ range: uriorcurie
+ multivalued: true
+ full name:
+ name: full name
+ definition_uri: https://w3id.org/biolink/vocab/full_name
+ description: a long-form human readable name for a thing
+ from_schema: https://identifiers.org/brain-bican/library-generation-schema
+ rank: 1000
+ is_a: node property
+ domain: named thing
+ slot_uri: biolink:full_name
+ alias: full_name
+ owner: EnrichedCellSample
+ domain_of:
+ - named thing
+ - attribute
+ - organism taxon
+ - information content entity
+ - dataset
+ - physical entity
+ - activity
+ - procedure
+ - material sample
+ - biological entity
+ - gene
+ - genome
+ range: label type
+ synonym:
+ name: synonym
+ definition_uri: https://w3id.org/biolink/vocab/synonym
+ description: Alternate human-readable names for a thing
+ in_subset:
+ - translator_minimal
+ from_schema: https://identifiers.org/brain-bican/library-generation-schema
+ aliases:
+ - alias
+ narrow_mappings:
+ - skos:altLabel
+ - gff3:Alias
+ - AGRKB:synonyms
+ - gpi:DB_Object_Synonyms
+ - HANCESTRO:0330
+ - IAO:0000136
+ - RXNORM:has_tradename
+ rank: 1000
+ is_a: node property
+ domain: named thing
+ slot_uri: biolink:synonym
+ alias: synonym
+ owner: EnrichedCellSample
+ domain_of:
+ - named thing
+ - attribute
+ - organism taxon
+ - information content entity
+ - dataset
+ - physical entity
+ - activity
+ - procedure
+ - material sample
+ - biological entity
+ - gene
+ - genome
+ range: label type
+ multivalued: true
+
+The process of splitting an enriched cell sample into several portions. Each portion may be used by the same or different groups for different scientific studies.
+URI: bican:EnrichedCellSampleSplitting
+| Name | +Cardinality and Range | +Description | +Inheritance | +
|---|---|---|---|
| used | +0..1 EnrichedCellSample |
+The enrichment cell sample splitting process from which the enriched cell sam... | +direct | +
| id | +1 String |
+A unique identifier for an entity | +NamedThing, Procedure, Entity | +
| iri | +0..1 IriType |
+An IRI for an entity | +NamedThing, Procedure, Entity | +
| category | +* Uriorcurie |
+Name of the high level ontology class in which this entity is categorized | +NamedThing, Procedure, Entity | +
| type | +* String |
++ | NamedThing, Procedure, Entity | +
| name | +0..1 LabelType |
+A human-readable name for an attribute or entity | +NamedThing, Procedure, Entity | +
| description | +0..1 NarrativeText |
+a human-readable description of an entity | +NamedThing, Procedure, Entity | +
| has_attribute | +* Attribute |
+connects any entity to an attribute | +NamedThing, Procedure, Entity | +
| deprecated | +0..1 Boolean |
+A boolean flag indicating that an entity is no longer considered current or v... | +NamedThing, Procedure, Entity | +
| provided_by | +* String |
+The value in this node property represents the knowledge provider that create... | +NamedThing, Procedure | +
| xref | +* Uriorcurie |
+A database cross reference or alternative identifier for a NamedThing or edge... | +NamedThing, Procedure | +
| full_name | +0..1 LabelType |
+a long-form human readable name for a thing | +NamedThing, Procedure | +
| synonym | +* LabelType |
+Alternate human-readable names for a thing | +NamedThing, Procedure | +
| used by | +used in | +type | +used | +
|---|---|---|---|
| EnrichedCellSample | +was_generated_by | +exactly_one_of[range] | +EnrichedCellSampleSplitting | +
| Mapping Type | +Mapped Value | +
|---|---|
| self | +bican:EnrichedCellSampleSplitting | +
| native | +bican:EnrichedCellSampleSplitting | +
name: EnrichedCellSampleSplitting
+description: The process of splitting an enriched cell sample into several portions.
+ Each portion may be used by the same or different groups for different scientific
+ studies.
+in_subset:
+- bican
+- library_generation
+from_schema: https://identifiers.org/brain-bican/library-generation-schema
+is_a: procedure
+mixins:
+- ProvActivity
+slots:
+- used
+slot_usage:
+ used:
+ name: used
+ description: The enrichment cell sample splitting process from which the enriched
+ cell sample was generated by.
+ range: EnrichedCellSample
+ category:
+ name: category
+ pattern: ^bican:[A-Z][A-Za-z]+$
+
+name: EnrichedCellSampleSplitting
+description: The process of splitting an enriched cell sample into several portions.
+ Each portion may be used by the same or different groups for different scientific
+ studies.
+in_subset:
+- bican
+- library_generation
+from_schema: https://identifiers.org/brain-bican/library-generation-schema
+is_a: procedure
+mixins:
+- ProvActivity
+slot_usage:
+ used:
+ name: used
+ description: The enrichment cell sample splitting process from which the enriched
+ cell sample was generated by.
+ range: EnrichedCellSample
+ category:
+ name: category
+ pattern: ^bican:[A-Z][A-Za-z]+$
+attributes:
+ used:
+ name: used
+ description: The enrichment cell sample splitting process from which the enriched
+ cell sample was generated by.
+ from_schema: https://identifiers.org/brain-bican/library-generation-schema
+ rank: 1000
+ slot_uri: prov:used
+ alias: used
+ owner: EnrichedCellSampleSplitting
+ domain_of:
+ - DissectionRoiDelineation
+ - TissueDissection
+ - CellDissociation
+ - CellEnrichment
+ - EnrichedCellSampleSplitting
+ - CellBarcoding
+ - CdnaAmplification
+ - LibraryConstruction
+ - LibraryPooling
+ - ProvActivity
+ range: EnrichedCellSample
+ id:
+ name: id
+ definition_uri: https://w3id.org/biolink/vocab/id
+ description: A unique identifier for an entity. Must be either a CURIE shorthand
+ for a URI or a complete URI
+ in_subset:
+ - translator_minimal
+ from_schema: https://identifiers.org/brain-bican/library-generation-schema
+ exact_mappings:
+ - AGRKB:primaryId
+ - gff3:ID
+ - gpi:DB_Object_ID
+ rank: 1000
+ domain: entity
+ slot_uri: biolink:id
+ identifier: true
+ alias: id
+ owner: EnrichedCellSampleSplitting
+ domain_of:
+ - ontology class
+ - entity
+ - attribute
+ - named thing
+ - taxonomic rank
+ - organism taxon
+ - information content entity
+ - dataset
+ - physical entity
+ - activity
+ - procedure
+ - material sample
+ - biological entity
+ - gene
+ - genome
+ range: string
+ required: true
+ iri:
+ name: iri
+ definition_uri: https://w3id.org/biolink/vocab/iri
+ description: An IRI for an entity. This is determined by the id using expansion
+ rules.
+ in_subset:
+ - translator_minimal
+ - samples
+ from_schema: https://identifiers.org/brain-bican/library-generation-schema
+ exact_mappings:
+ - WIKIDATA_PROPERTY:P854
+ rank: 1000
+ slot_uri: biolink:iri
+ alias: iri
+ owner: EnrichedCellSampleSplitting
+ domain_of:
+ - attribute
+ - entity
+ - named thing
+ - organism taxon
+ - information content entity
+ - dataset
+ - physical entity
+ - activity
+ - procedure
+ - material sample
+ - biological entity
+ - gene
+ - genome
+ range: iri type
+ category:
+ name: category
+ definition_uri: https://w3id.org/biolink/vocab/category
+ description: Name of the high level ontology class in which this entity is categorized.
+ Corresponds to the label for the biolink entity type class. In a neo4j database
+ this MAY correspond to the neo4j label tag. In an RDF database it should be
+ a biolink model class URI. This field is multi-valued. It should include values
+ for ancestors of the biolink class; for example, a protein such as Shh would
+ have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`.
+ In an RDF database, nodes will typically have an rdf:type triples. This can
+ be to the most specific biolink class, or potentially to a class more specific
+ than something in biolink. For example, a sequence feature `f` may have a rdf:type
+ assertion to a SO class such as TF_binding_site, which is more specific than
+ anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity,
+ biolink:NamedThing}
+ in_subset:
+ - translator_minimal
+ from_schema: https://identifiers.org/brain-bican/library-generation-schema
+ rank: 1000
+ is_a: type
+ domain: entity
+ slot_uri: biolink:category
+ designates_type: true
+ alias: category
+ owner: EnrichedCellSampleSplitting
+ domain_of:
+ - entity
+ - attribute
+ - named thing
+ - organism taxon
+ - information content entity
+ - dataset
+ - physical entity
+ - activity
+ - procedure
+ - material sample
+ - biological entity
+ - gene
+ - genome
+ is_class_field: true
+ range: uriorcurie
+ multivalued: true
+ pattern: ^bican:[A-Z][A-Za-z]+$
+ type:
+ name: type
+ definition_uri: https://w3id.org/biolink/vocab/type
+ from_schema: https://identifiers.org/brain-bican/library-generation-schema
+ mappings:
+ - rdf:type
+ exact_mappings:
+ - gff3:type
+ - gpi:DB_Object_Type
+ rank: 1000
+ domain: entity
+ slot_uri: rdf:type
+ alias: type
+ owner: EnrichedCellSampleSplitting
+ domain_of:
+ - entity
+ - attribute
+ - named thing
+ - organism taxon
+ - information content entity
+ - dataset
+ - physical entity
+ - activity
+ - procedure
+ - material sample
+ - biological entity
+ - gene
+ - genome
+ range: string
+ multivalued: true
+ name:
+ name: name
+ definition_uri: https://w3id.org/biolink/vocab/name
+ description: A human-readable name for an attribute or entity.
+ in_subset:
+ - translator_minimal
+ - samples
+ from_schema: https://identifiers.org/brain-bican/library-generation-schema
+ aliases:
+ - label
+ - display name
+ - title
+ mappings:
+ - rdfs:label
+ exact_mappings:
+ - gff3:Name
+ - gpi:DB_Object_Name
+ narrow_mappings:
+ - dct:title
+ - WIKIDATA_PROPERTY:P1476
+ rank: 1000
+ domain: entity
+ slot_uri: rdfs:label
+ alias: name
+ owner: EnrichedCellSampleSplitting
+ domain_of:
+ - attribute
+ - entity
+ - macromolecular machine mixin
+ - Donor
+ - BrainSlab
+ - TissueSample
+ - DissociatedCellSample
+ - EnrichedCellSample
+ - BarcodedCellSample
+ - AmplifiedCdna
+ - Library
+ - LibraryAliquot
+ - LibraryPool
+ - DissectionRoiPolygon
+ - named thing
+ - organism taxon
+ - information content entity
+ - dataset
+ - physical entity
+ - activity
+ - procedure
+ - material sample
+ - biological entity
+ - gene or gene product
+ - gene
+ - genome
+ range: label type
+ description:
+ name: description
+ definition_uri: https://w3id.org/biolink/vocab/description
+ description: a human-readable description of an entity
+ in_subset:
+ - translator_minimal
+ from_schema: https://identifiers.org/brain-bican/library-generation-schema
+ aliases:
+ - definition
+ mappings:
+ - dct:description
+ exact_mappings:
+ - IAO:0000115
+ - skos:definitions
+ narrow_mappings:
+ - gff3:Description
+ rank: 1000
+ slot_uri: dct:description
+ alias: description
+ owner: EnrichedCellSampleSplitting
+ domain_of:
+ - entity
+ - attribute
+ - named thing
+ - organism taxon
+ - information content entity
+ - dataset
+ - physical entity
+ - activity
+ - procedure
+ - material sample
+ - biological entity
+ - gene
+ - genome
+ range: narrative text
+ has attribute:
+ name: has attribute
+ definition_uri: https://w3id.org/biolink/vocab/has_attribute
+ description: connects any entity to an attribute
+ in_subset:
+ - samples
+ from_schema: https://identifiers.org/brain-bican/library-generation-schema
+ exact_mappings:
+ - SIO:000008
+ close_mappings:
+ - OBI:0001927
+ narrow_mappings:
+ - OBAN:association_has_subject_property
+ - OBAN:association_has_object_property
+ - CPT:has_possibly_included_panel_element
+ - DRUGBANK:category
+ - EFO:is_executed_in
+ - HANCESTRO:0301
+ - LOINC:has_action_guidance
+ - LOINC:has_adjustment
+ - LOINC:has_aggregation_view
+ - LOINC:has_approach_guidance
+ - LOINC:has_divisor
+ - LOINC:has_exam
+ - LOINC:has_method
+ - LOINC:has_modality_subtype
+ - LOINC:has_object_guidance
+ - LOINC:has_scale
+ - LOINC:has_suffix
+ - LOINC:has_time_aspect
+ - LOINC:has_time_modifier
+ - LOINC:has_timing_of
+ - NCIT:R88
+ - NCIT:eo_disease_has_property_or_attribute
+ - NCIT:has_data_element
+ - NCIT:has_pharmaceutical_administration_method
+ - NCIT:has_pharmaceutical_basic_dose_form
+ - NCIT:has_pharmaceutical_intended_site
+ - NCIT:has_pharmaceutical_release_characteristics
+ - NCIT:has_pharmaceutical_state_of_matter
+ - NCIT:has_pharmaceutical_transformation
+ - NCIT:is_qualified_by
+ - NCIT:qualifier_applies_to
+ - NCIT:role_has_domain
+ - NCIT:role_has_range
+ - INO:0000154
+ - HANCESTRO:0308
+ - OMIM:has_inheritance_type
+ - orphanet:C016
+ - orphanet:C017
+ - RO:0000053
+ - RO:0000086
+ - RO:0000087
+ - SNOMED:has_access
+ - SNOMED:has_clinical_course
+ - SNOMED:has_count_of_base_of_active_ingredient
+ - SNOMED:has_dose_form_administration_method
+ - SNOMED:has_dose_form_release_characteristic
+ - SNOMED:has_dose_form_transformation
+ - SNOMED:has_finding_context
+ - SNOMED:has_finding_informer
+ - SNOMED:has_inherent_attribute
+ - SNOMED:has_intent
+ - SNOMED:has_interpretation
+ - SNOMED:has_laterality
+ - SNOMED:has_measurement_method
+ - SNOMED:has_method
+ - SNOMED:has_priority
+ - SNOMED:has_procedure_context
+ - SNOMED:has_process_duration
+ - SNOMED:has_property
+ - SNOMED:has_revision_status
+ - SNOMED:has_scale_type
+ - SNOMED:has_severity
+ - SNOMED:has_specimen
+ - SNOMED:has_state_of_matter
+ - SNOMED:has_subject_relationship_context
+ - SNOMED:has_surgical_approach
+ - SNOMED:has_technique
+ - SNOMED:has_temporal_context
+ - SNOMED:has_time_aspect
+ - SNOMED:has_units
+ - UMLS:has_structural_class
+ - UMLS:has_supported_concept_property
+ - UMLS:has_supported_concept_relationship
+ - UMLS:may_be_qualified_by
+ rank: 1000
+ domain: entity
+ slot_uri: biolink:has_attribute
+ alias: has_attribute
+ owner: EnrichedCellSampleSplitting
+ domain_of:
+ - entity
+ - attribute
+ - named thing
+ - organism taxon
+ - information content entity
+ - dataset
+ - physical entity
+ - activity
+ - procedure
+ - material sample
+ - biological entity
+ - gene
+ - genome
+ range: attribute
+ multivalued: true
+ deprecated:
+ name: deprecated
+ definition_uri: https://w3id.org/biolink/vocab/deprecated
+ description: A boolean flag indicating that an entity is no longer considered
+ current or valid.
+ from_schema: https://identifiers.org/brain-bican/library-generation-schema
+ exact_mappings:
+ - oboInOwl:ObsoleteClass
+ rank: 1000
+ slot_uri: biolink:deprecated
+ alias: deprecated
+ owner: EnrichedCellSampleSplitting
+ domain_of:
+ - entity
+ - attribute
+ - named thing
+ - organism taxon
+ - information content entity
+ - dataset
+ - physical entity
+ - activity
+ - procedure
+ - material sample
+ - biological entity
+ - gene
+ - genome
+ range: boolean
+ provided by:
+ name: provided by
+ definition_uri: https://w3id.org/biolink/vocab/provided_by
+ description: The value in this node property represents the knowledge provider
+ that created or assembled the node and all of its attributes. Used internally
+ to represent how a particular node made its way into a knowledge provider or
+ graph.
+ from_schema: https://identifiers.org/brain-bican/library-generation-schema
+ rank: 1000
+ is_a: node property
+ domain: named thing
+ slot_uri: biolink:provided_by
+ alias: provided_by
+ owner: EnrichedCellSampleSplitting
+ domain_of:
+ - named thing
+ - attribute
+ - organism taxon
+ - information content entity
+ - dataset
+ - physical entity
+ - activity
+ - procedure
+ - material sample
+ - biological entity
+ - gene
+ - genome
+ range: string
+ multivalued: true
+ xref:
+ name: xref
+ definition_uri: https://w3id.org/biolink/vocab/xref
+ description: A database cross reference or alternative identifier for a NamedThing
+ or edge between two NamedThings. This property should point to a database record
+ or webpage that supports the existence of the edge, or gives more detail about
+ the edge. This property can be used on a node or edge to provide multiple URIs
+ or CURIE cross references.
+ in_subset:
+ - translator_minimal
+ from_schema: https://identifiers.org/brain-bican/library-generation-schema
+ aliases:
+ - dbxref
+ - Dbxref
+ - DbXref
+ - record_url
+ - source_record_urls
+ narrow_mappings:
+ - gff3:Dbxref
+ - gpi:DB_Xrefs
+ rank: 1000
+ domain: named thing
+ slot_uri: biolink:xref
+ alias: xref
+ owner: EnrichedCellSampleSplitting
+ domain_of:
+ - named thing
+ - gene
+ - attribute
+ - organism taxon
+ - information content entity
+ - dataset
+ - physical entity
+ - activity
+ - procedure
+ - material sample
+ - biological entity
+ - genome
+ range: uriorcurie
+ multivalued: true
+ full name:
+ name: full name
+ definition_uri: https://w3id.org/biolink/vocab/full_name
+ description: a long-form human readable name for a thing
+ from_schema: https://identifiers.org/brain-bican/library-generation-schema
+ rank: 1000
+ is_a: node property
+ domain: named thing
+ slot_uri: biolink:full_name
+ alias: full_name
+ owner: EnrichedCellSampleSplitting
+ domain_of:
+ - named thing
+ - attribute
+ - organism taxon
+ - information content entity
+ - dataset
+ - physical entity
+ - activity
+ - procedure
+ - material sample
+ - biological entity
+ - gene
+ - genome
+ range: label type
+ synonym:
+ name: synonym
+ definition_uri: https://w3id.org/biolink/vocab/synonym
+ description: Alternate human-readable names for a thing
+ in_subset:
+ - translator_minimal
+ from_schema: https://identifiers.org/brain-bican/library-generation-schema
+ aliases:
+ - alias
+ narrow_mappings:
+ - skos:altLabel
+ - gff3:Alias
+ - AGRKB:synonyms
+ - gpi:DB_Object_Synonyms
+ - HANCESTRO:0330
+ - IAO:0000136
+ - RXNORM:has_tradename
+ rank: 1000
+ is_a: node property
+ domain: named thing
+ slot_uri: biolink:synonym
+ alias: synonym
+ owner: EnrichedCellSampleSplitting
+ domain_of:
+ - named thing
+ - attribute
+ - organism taxon
+ - information content entity
+ - dataset
+ - physical entity
+ - activity
+ - procedure
+ - material sample
+ - biological entity
+ - gene
+ - genome
+ range: label type
+ multivalued: true
+
+Root Biolink Model class for all things and informational relationships, real or imagined.
+URI: biolink:Entity
+| Name | +Cardinality and Range | +Description | +Inheritance | +
|---|---|---|---|
| id | +1 String |
+A unique identifier for an entity | +direct | +
| iri | +0..1 IriType |
+An IRI for an entity | +direct | +
| category | +* Uriorcurie |
+Name of the high level ontology class in which this entity is categorized | +direct | +
| type | +* String |
++ | direct | +
| name | +0..1 LabelType |
+A human-readable name for an attribute or entity | +direct | +
| description | +0..1 NarrativeText |
+a human-readable description of an entity | +direct | +
| has_attribute | +* Attribute |
+connects any entity to an attribute | +direct | +
| deprecated | +0..1 Boolean |
+A boolean flag indicating that an entity is no longer considered current or v... | +direct | +
| Mapping Type | +Mapped Value | +
|---|---|
| self | +biolink:Entity | +
| native | +bican:Entity | +
name: entity
+definition_uri: https://w3id.org/biolink/vocab/Entity
+description: Root Biolink Model class for all things and informational relationships,
+ real or imagined.
+from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
+abstract: true
+slots:
+- id
+- iri
+- category
+- type
+- name
+- description
+- has attribute
+- deprecated
+class_uri: biolink:Entity
+
+name: entity
+definition_uri: https://w3id.org/biolink/vocab/Entity
+description: Root Biolink Model class for all things and informational relationships,
+ real or imagined.
+from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
+abstract: true
+attributes:
+ id:
+ name: id
+ definition_uri: https://w3id.org/biolink/vocab/id
+ description: A unique identifier for an entity. Must be either a CURIE shorthand
+ for a URI or a complete URI
+ in_subset:
+ - translator_minimal
+ from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
+ exact_mappings:
+ - AGRKB:primaryId
+ - gff3:ID
+ - gpi:DB_Object_ID
+ rank: 1000
+ domain: entity
+ slot_uri: biolink:id
+ identifier: true
+ alias: id
+ owner: entity
+ domain_of:
+ - ontology class
+ - entity
+ - attribute
+ - named thing
+ - taxonomic rank
+ - organism taxon
+ - information content entity
+ - dataset
+ - physical entity
+ - activity
+ - procedure
+ - material sample
+ - biological entity
+ - gene
+ - genome
+ range: string
+ required: true
+ iri:
+ name: iri
+ definition_uri: https://w3id.org/biolink/vocab/iri
+ description: An IRI for an entity. This is determined by the id using expansion
+ rules.
+ in_subset:
+ - translator_minimal
+ - samples
+ from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
+ exact_mappings:
+ - WIKIDATA_PROPERTY:P854
+ rank: 1000
+ slot_uri: biolink:iri
+ alias: iri
+ owner: entity
+ domain_of:
+ - attribute
+ - entity
+ - named thing
+ - organism taxon
+ - information content entity
+ - dataset
+ - physical entity
+ - activity
+ - procedure
+ - material sample
+ - biological entity
+ - gene
+ - genome
+ range: iri type
+ category:
+ name: category
+ definition_uri: https://w3id.org/biolink/vocab/category
+ description: Name of the high level ontology class in which this entity is categorized.
+ Corresponds to the label for the biolink entity type class. In a neo4j database
+ this MAY correspond to the neo4j label tag. In an RDF database it should be
+ a biolink model class URI. This field is multi-valued. It should include values
+ for ancestors of the biolink class; for example, a protein such as Shh would
+ have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`.
+ In an RDF database, nodes will typically have an rdf:type triples. This can
+ be to the most specific biolink class, or potentially to a class more specific
+ than something in biolink. For example, a sequence feature `f` may have a rdf:type
+ assertion to a SO class such as TF_binding_site, which is more specific than
+ anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity,
+ biolink:NamedThing}
+ in_subset:
+ - translator_minimal
+ from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
+ rank: 1000
+ is_a: type
+ domain: entity
+ slot_uri: biolink:category
+ designates_type: true
+ alias: category
+ owner: entity
+ domain_of:
+ - entity
+ - attribute
+ - named thing
+ - organism taxon
+ - information content entity
+ - dataset
+ - physical entity
+ - activity
+ - procedure
+ - material sample
+ - biological entity
+ - gene
+ - genome
+ is_class_field: true
+ range: uriorcurie
+ multivalued: true
+ type:
+ name: type
+ definition_uri: https://w3id.org/biolink/vocab/type
+ from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
+ mappings:
+ - rdf:type
+ exact_mappings:
+ - gff3:type
+ - gpi:DB_Object_Type
+ rank: 1000
+ domain: entity
+ slot_uri: rdf:type
+ alias: type
+ owner: entity
+ domain_of:
+ - entity
+ - attribute
+ - named thing
+ - organism taxon
+ - information content entity
+ - dataset
+ - physical entity
+ - activity
+ - procedure
+ - material sample
+ - biological entity
+ - gene
+ - genome
+ range: string
+ multivalued: true
+ name:
+ name: name
+ definition_uri: https://w3id.org/biolink/vocab/name
+ description: A human-readable name for an attribute or entity.
+ in_subset:
+ - translator_minimal
+ - samples
+ from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
+ aliases:
+ - label
+ - display name
+ - title
+ mappings:
+ - rdfs:label
+ exact_mappings:
+ - gff3:Name
+ - gpi:DB_Object_Name
+ narrow_mappings:
+ - dct:title
+ - WIKIDATA_PROPERTY:P1476
+ rank: 1000
+ domain: entity
+ slot_uri: rdfs:label
+ alias: name
+ owner: entity
+ domain_of:
+ - attribute
+ - entity
+ - macromolecular machine mixin
+ - named thing
+ - organism taxon
+ - information content entity
+ - dataset
+ - physical entity
+ - activity
+ - procedure
+ - material sample
+ - biological entity
+ - gene or gene product
+ - gene
+ - genome
+ range: label type
+ description:
+ name: description
+ definition_uri: https://w3id.org/biolink/vocab/description
+ description: a human-readable description of an entity
+ in_subset:
+ - translator_minimal
+ from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
+ aliases:
+ - definition
+ mappings:
+ - dct:description
+ exact_mappings:
+ - IAO:0000115
+ - skos:definitions
+ narrow_mappings:
+ - gff3:Description
+ rank: 1000
+ slot_uri: dct:description
+ alias: description
+ owner: entity
+ domain_of:
+ - entity
+ - attribute
+ - named thing
+ - organism taxon
+ - information content entity
+ - dataset
+ - physical entity
+ - activity
+ - procedure
+ - material sample
+ - biological entity
+ - gene
+ - genome
+ range: narrative text
+ has attribute:
+ name: has attribute
+ definition_uri: https://w3id.org/biolink/vocab/has_attribute
+ description: connects any entity to an attribute
+ in_subset:
+ - samples
+ from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
+ exact_mappings:
+ - SIO:000008
+ close_mappings:
+ - OBI:0001927
+ narrow_mappings:
+ - OBAN:association_has_subject_property
+ - OBAN:association_has_object_property
+ - CPT:has_possibly_included_panel_element
+ - DRUGBANK:category
+ - EFO:is_executed_in
+ - HANCESTRO:0301
+ - LOINC:has_action_guidance
+ - LOINC:has_adjustment
+ - LOINC:has_aggregation_view
+ - LOINC:has_approach_guidance
+ - LOINC:has_divisor
+ - LOINC:has_exam
+ - LOINC:has_method
+ - LOINC:has_modality_subtype
+ - LOINC:has_object_guidance
+ - LOINC:has_scale
+ - LOINC:has_suffix
+ - LOINC:has_time_aspect
+ - LOINC:has_time_modifier
+ - LOINC:has_timing_of
+ - NCIT:R88
+ - NCIT:eo_disease_has_property_or_attribute
+ - NCIT:has_data_element
+ - NCIT:has_pharmaceutical_administration_method
+ - NCIT:has_pharmaceutical_basic_dose_form
+ - NCIT:has_pharmaceutical_intended_site
+ - NCIT:has_pharmaceutical_release_characteristics
+ - NCIT:has_pharmaceutical_state_of_matter
+ - NCIT:has_pharmaceutical_transformation
+ - NCIT:is_qualified_by
+ - NCIT:qualifier_applies_to
+ - NCIT:role_has_domain
+ - NCIT:role_has_range
+ - INO:0000154
+ - HANCESTRO:0308
+ - OMIM:has_inheritance_type
+ - orphanet:C016
+ - orphanet:C017
+ - RO:0000053
+ - RO:0000086
+ - RO:0000087
+ - SNOMED:has_access
+ - SNOMED:has_clinical_course
+ - SNOMED:has_count_of_base_of_active_ingredient
+ - SNOMED:has_dose_form_administration_method
+ - SNOMED:has_dose_form_release_characteristic
+ - SNOMED:has_dose_form_transformation
+ - SNOMED:has_finding_context
+ - SNOMED:has_finding_informer
+ - SNOMED:has_inherent_attribute
+ - SNOMED:has_intent
+ - SNOMED:has_interpretation
+ - SNOMED:has_laterality
+ - SNOMED:has_measurement_method
+ - SNOMED:has_method
+ - SNOMED:has_priority
+ - SNOMED:has_procedure_context
+ - SNOMED:has_process_duration
+ - SNOMED:has_property
+ - SNOMED:has_revision_status
+ - SNOMED:has_scale_type
+ - SNOMED:has_severity
+ - SNOMED:has_specimen
+ - SNOMED:has_state_of_matter
+ - SNOMED:has_subject_relationship_context
+ - SNOMED:has_surgical_approach
+ - SNOMED:has_technique
+ - SNOMED:has_temporal_context
+ - SNOMED:has_time_aspect
+ - SNOMED:has_units
+ - UMLS:has_structural_class
+ - UMLS:has_supported_concept_property
+ - UMLS:has_supported_concept_relationship
+ - UMLS:may_be_qualified_by
+ rank: 1000
+ domain: entity
+ slot_uri: biolink:has_attribute
+ alias: has_attribute
+ owner: entity
+ domain_of:
+ - entity
+ - attribute
+ - named thing
+ - organism taxon
+ - information content entity
+ - dataset
+ - physical entity
+ - activity
+ - procedure
+ - material sample
+ - biological entity
+ - gene
+ - genome
+ range: attribute
+ multivalued: true
+ deprecated:
+ name: deprecated
+ definition_uri: https://w3id.org/biolink/vocab/deprecated
+ description: A boolean flag indicating that an entity is no longer considered
+ current or valid.
+ from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
+ exact_mappings:
+ - oboInOwl:ObsoleteClass
+ rank: 1000
+ slot_uri: biolink:deprecated
+ alias: deprecated
+ owner: entity
+ domain_of:
+ - entity
+ - attribute
+ - named thing
+ - organism taxon
+ - information content entity
+ - dataset
+ - physical entity
+ - activity
+ - procedure
+ - material sample
+ - biological entity
+ - gene
+ - genome
+ range: boolean
+class_uri: biolink:Entity
+
+A real number that conforms to the xsd:float specification
+URI: xsd:float
+ +| Mapping Type | +Mapped Value | +
|---|---|
| self | +xsd:float | +
| native | +bican:float | +
| exact | +schema:Float | +
URI: UO:0000105
+ +| Mapping Type | +Mapped Value | +
|---|---|
| self | +UO:0000105 | +
| native | +bican:frequency_value | +
A region (or regions) that includes all of the sequence elements necessary to encode a functional transcript. A gene locus may include regulatory regions, transcribed regions and/or other functional sequence regions.
+URI: biolink:Gene
+| Name | +Cardinality and Range | +Description | +Inheritance | +
|---|---|---|---|
| id | +1 String |
+A unique identifier for an entity | +direct | +
| iri | +0..1 IriType |
+An IRI for an entity | +direct | +
| category | +* Uriorcurie |
+Name of the high level ontology class in which this entity is categorized | +direct | +
| type | +* String |
++ | direct | +
| name | +0..1 LabelType |
+A human-readable name for an attribute or entity | +direct | +
| description | +0..1 NarrativeText |
+a human-readable description of an entity | +direct | +
| has_attribute | +* Attribute |
+connects any entity to an attribute | +direct | +
| deprecated | +0..1 Boolean |
+A boolean flag indicating that an entity is no longer considered current or v... | +direct | +
| provided_by | +* String |
+The value in this node property represents the knowledge provider that create... | +direct | +
| full_name | +0..1 LabelType |
+a long-form human readable name for a thing | +direct | +
| synonym | +* LabelType |
+Alternate human-readable names for a thing | +direct | +
| in_taxon | +* OrganismTaxon |
+connects an entity to its taxonomic classification | +direct | +
| in_taxon_label | +0..1 LabelType |
+The human readable scientific name for the taxon of the entity | +direct | +
| symbol | +0..1 String |
+Symbol for a particular thing | +direct | +
| xref | +* Uriorcurie |
+A database cross reference or alternative identifier for a NamedThing or edge... | +direct | +
| has_biological_sequence | +0..1 BiologicalSequence |
+connects a genomic feature to its sequence | +direct | +
Instances of this class should have identifiers with one of the following prefixes:
+NCBIGene
+ENSEMBL
+HGNC
+MGI
+ZFIN
+dictyBase
+WB
+WormBase
+FB
+RGD
+SGD
+PomBase
+OMIM
+KEGG.GENES
+UMLS
+Xenbase
+AspGD
+PHARMGKB.GENE
+| Mapping Type | +Mapped Value | +
|---|---|
| self | +biolink:Gene | +
| native | +bican:Gene | +
| exact | +SO:0000704, SIO:010035, WIKIDATA:Q7187, dcid:Gene | +
| narrow | +bioschemas:gene | +
| broad | +NCIT:C45822 | +
name: gene
+id_prefixes:
+- NCBIGene
+- ENSEMBL
+- HGNC
+- MGI
+- ZFIN
+- dictyBase
+- WB
+- WormBase
+- FB
+- RGD
+- SGD
+- PomBase
+- OMIM
+- KEGG.GENES
+- UMLS
+- Xenbase
+- AspGD
+- PHARMGKB.GENE
+definition_uri: https://w3id.org/biolink/vocab/Gene
+description: A region (or regions) that includes all of the sequence elements necessary
+ to encode a functional transcript. A gene locus may include regulatory regions,
+ transcribed regions and/or other functional sequence regions.
+in_subset:
+- translator_minimal
+- model_organism_database
+from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
+exact_mappings:
+- SO:0000704
+- SIO:010035
+- WIKIDATA:Q7187
+- dcid:Gene
+narrow_mappings:
+- bioschemas:gene
+broad_mappings:
+- NCIT:C45822
+is_a: biological entity
+mixins:
+- gene or gene product
+- genomic entity
+- chemical entity or gene or gene product
+- physical essence
+- ontology class
+slots:
+- id
+- iri
+- category
+- type
+- name
+- description
+- has attribute
+- deprecated
+- provided by
+- full name
+- synonym
+- in taxon
+- in taxon label
+- symbol
+- xref
+- has biological sequence
+class_uri: biolink:Gene
+
+name: gene
+id_prefixes:
+- NCBIGene
+- ENSEMBL
+- HGNC
+- MGI
+- ZFIN
+- dictyBase
+- WB
+- WormBase
+- FB
+- RGD
+- SGD
+- PomBase
+- OMIM
+- KEGG.GENES
+- UMLS
+- Xenbase
+- AspGD
+- PHARMGKB.GENE
+definition_uri: https://w3id.org/biolink/vocab/Gene
+description: A region (or regions) that includes all of the sequence elements necessary
+ to encode a functional transcript. A gene locus may include regulatory regions,
+ transcribed regions and/or other functional sequence regions.
+in_subset:
+- translator_minimal
+- model_organism_database
+from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
+exact_mappings:
+- SO:0000704
+- SIO:010035
+- WIKIDATA:Q7187
+- dcid:Gene
+narrow_mappings:
+- bioschemas:gene
+broad_mappings:
+- NCIT:C45822
+is_a: biological entity
+mixins:
+- gene or gene product
+- genomic entity
+- chemical entity or gene or gene product
+- physical essence
+- ontology class
+attributes:
+ id:
+ name: id
+ definition_uri: https://w3id.org/biolink/vocab/id
+ description: A unique identifier for an entity. Must be either a CURIE shorthand
+ for a URI or a complete URI
+ in_subset:
+ - translator_minimal
+ from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
+ exact_mappings:
+ - AGRKB:primaryId
+ - gff3:ID
+ - gpi:DB_Object_ID
+ rank: 1000
+ domain: entity
+ slot_uri: biolink:id
+ identifier: true
+ alias: id
+ owner: gene
+ domain_of:
+ - ontology class
+ - entity
+ - attribute
+ - named thing
+ - taxonomic rank
+ - organism taxon
+ - information content entity
+ - dataset
+ - physical entity
+ - activity
+ - procedure
+ - material sample
+ - biological entity
+ - gene
+ - genome
+ range: string
+ required: true
+ iri:
+ name: iri
+ definition_uri: https://w3id.org/biolink/vocab/iri
+ description: An IRI for an entity. This is determined by the id using expansion
+ rules.
+ in_subset:
+ - translator_minimal
+ - samples
+ from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
+ exact_mappings:
+ - WIKIDATA_PROPERTY:P854
+ rank: 1000
+ slot_uri: biolink:iri
+ alias: iri
+ owner: gene
+ domain_of:
+ - attribute
+ - entity
+ - named thing
+ - organism taxon
+ - information content entity
+ - dataset
+ - physical entity
+ - activity
+ - procedure
+ - material sample
+ - biological entity
+ - gene
+ - genome
+ range: iri type
+ category:
+ name: category
+ definition_uri: https://w3id.org/biolink/vocab/category
+ description: Name of the high level ontology class in which this entity is categorized.
+ Corresponds to the label for the biolink entity type class. In a neo4j database
+ this MAY correspond to the neo4j label tag. In an RDF database it should be
+ a biolink model class URI. This field is multi-valued. It should include values
+ for ancestors of the biolink class; for example, a protein such as Shh would
+ have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`.
+ In an RDF database, nodes will typically have an rdf:type triples. This can
+ be to the most specific biolink class, or potentially to a class more specific
+ than something in biolink. For example, a sequence feature `f` may have a rdf:type
+ assertion to a SO class such as TF_binding_site, which is more specific than
+ anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity,
+ biolink:NamedThing}
+ in_subset:
+ - translator_minimal
+ from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
+ rank: 1000
+ is_a: type
+ domain: entity
+ slot_uri: biolink:category
+ designates_type: true
+ alias: category
+ owner: gene
+ domain_of:
+ - entity
+ - attribute
+ - named thing
+ - organism taxon
+ - information content entity
+ - dataset
+ - physical entity
+ - activity
+ - procedure
+ - material sample
+ - biological entity
+ - gene
+ - genome
+ is_class_field: true
+ range: uriorcurie
+ multivalued: true
+ type:
+ name: type
+ definition_uri: https://w3id.org/biolink/vocab/type
+ from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
+ mappings:
+ - rdf:type
+ exact_mappings:
+ - gff3:type
+ - gpi:DB_Object_Type
+ rank: 1000
+ domain: entity
+ slot_uri: rdf:type
+ alias: type
+ owner: gene
+ domain_of:
+ - entity
+ - attribute
+ - named thing
+ - organism taxon
+ - information content entity
+ - dataset
+ - physical entity
+ - activity
+ - procedure
+ - material sample
+ - biological entity
+ - gene
+ - genome
+ range: string
+ multivalued: true
+ name:
+ name: name
+ definition_uri: https://w3id.org/biolink/vocab/name
+ description: A human-readable name for an attribute or entity.
+ in_subset:
+ - translator_minimal
+ - samples
+ from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
+ aliases:
+ - label
+ - display name
+ - title
+ mappings:
+ - rdfs:label
+ exact_mappings:
+ - gff3:Name
+ - gpi:DB_Object_Name
+ narrow_mappings:
+ - dct:title
+ - WIKIDATA_PROPERTY:P1476
+ rank: 1000
+ domain: entity
+ slot_uri: rdfs:label
+ alias: name
+ owner: gene
+ domain_of:
+ - attribute
+ - entity
+ - macromolecular machine mixin
+ - named thing
+ - organism taxon
+ - information content entity
+ - dataset
+ - physical entity
+ - activity
+ - procedure
+ - material sample
+ - biological entity
+ - gene or gene product
+ - gene
+ - genome
+ range: label type
+ description:
+ name: description
+ definition_uri: https://w3id.org/biolink/vocab/description
+ description: a human-readable description of an entity
+ in_subset:
+ - translator_minimal
+ from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
+ aliases:
+ - definition
+ mappings:
+ - dct:description
+ exact_mappings:
+ - IAO:0000115
+ - skos:definitions
+ narrow_mappings:
+ - gff3:Description
+ rank: 1000
+ slot_uri: dct:description
+ alias: description
+ owner: gene
+ domain_of:
+ - entity
+ - attribute
+ - named thing
+ - organism taxon
+ - information content entity
+ - dataset
+ - physical entity
+ - activity
+ - procedure
+ - material sample
+ - biological entity
+ - gene
+ - genome
+ range: narrative text
+ has attribute:
+ name: has attribute
+ definition_uri: https://w3id.org/biolink/vocab/has_attribute
+ description: connects any entity to an attribute
+ in_subset:
+ - samples
+ from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
+ exact_mappings:
+ - SIO:000008
+ close_mappings:
+ - OBI:0001927
+ narrow_mappings:
+ - OBAN:association_has_subject_property
+ - OBAN:association_has_object_property
+ - CPT:has_possibly_included_panel_element
+ - DRUGBANK:category
+ - EFO:is_executed_in
+ - HANCESTRO:0301
+ - LOINC:has_action_guidance
+ - LOINC:has_adjustment
+ - LOINC:has_aggregation_view
+ - LOINC:has_approach_guidance
+ - LOINC:has_divisor
+ - LOINC:has_exam
+ - LOINC:has_method
+ - LOINC:has_modality_subtype
+ - LOINC:has_object_guidance
+ - LOINC:has_scale
+ - LOINC:has_suffix
+ - LOINC:has_time_aspect
+ - LOINC:has_time_modifier
+ - LOINC:has_timing_of
+ - NCIT:R88
+ - NCIT:eo_disease_has_property_or_attribute
+ - NCIT:has_data_element
+ - NCIT:has_pharmaceutical_administration_method
+ - NCIT:has_pharmaceutical_basic_dose_form
+ - NCIT:has_pharmaceutical_intended_site
+ - NCIT:has_pharmaceutical_release_characteristics
+ - NCIT:has_pharmaceutical_state_of_matter
+ - NCIT:has_pharmaceutical_transformation
+ - NCIT:is_qualified_by
+ - NCIT:qualifier_applies_to
+ - NCIT:role_has_domain
+ - NCIT:role_has_range
+ - INO:0000154
+ - HANCESTRO:0308
+ - OMIM:has_inheritance_type
+ - orphanet:C016
+ - orphanet:C017
+ - RO:0000053
+ - RO:0000086
+ - RO:0000087
+ - SNOMED:has_access
+ - SNOMED:has_clinical_course
+ - SNOMED:has_count_of_base_of_active_ingredient
+ - SNOMED:has_dose_form_administration_method
+ - SNOMED:has_dose_form_release_characteristic
+ - SNOMED:has_dose_form_transformation
+ - SNOMED:has_finding_context
+ - SNOMED:has_finding_informer
+ - SNOMED:has_inherent_attribute
+ - SNOMED:has_intent
+ - SNOMED:has_interpretation
+ - SNOMED:has_laterality
+ - SNOMED:has_measurement_method
+ - SNOMED:has_method
+ - SNOMED:has_priority
+ - SNOMED:has_procedure_context
+ - SNOMED:has_process_duration
+ - SNOMED:has_property
+ - SNOMED:has_revision_status
+ - SNOMED:has_scale_type
+ - SNOMED:has_severity
+ - SNOMED:has_specimen
+ - SNOMED:has_state_of_matter
+ - SNOMED:has_subject_relationship_context
+ - SNOMED:has_surgical_approach
+ - SNOMED:has_technique
+ - SNOMED:has_temporal_context
+ - SNOMED:has_time_aspect
+ - SNOMED:has_units
+ - UMLS:has_structural_class
+ - UMLS:has_supported_concept_property
+ - UMLS:has_supported_concept_relationship
+ - UMLS:may_be_qualified_by
+ rank: 1000
+ domain: entity
+ slot_uri: biolink:has_attribute
+ alias: has_attribute
+ owner: gene
+ domain_of:
+ - entity
+ - attribute
+ - named thing
+ - organism taxon
+ - information content entity
+ - dataset
+ - physical entity
+ - activity
+ - procedure
+ - material sample
+ - biological entity
+ - gene
+ - genome
+ range: attribute
+ multivalued: true
+ deprecated:
+ name: deprecated
+ definition_uri: https://w3id.org/biolink/vocab/deprecated
+ description: A boolean flag indicating that an entity is no longer considered
+ current or valid.
+ from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
+ exact_mappings:
+ - oboInOwl:ObsoleteClass
+ rank: 1000
+ slot_uri: biolink:deprecated
+ alias: deprecated
+ owner: gene
+ domain_of:
+ - entity
+ - attribute
+ - named thing
+ - organism taxon
+ - information content entity
+ - dataset
+ - physical entity
+ - activity
+ - procedure
+ - material sample
+ - biological entity
+ - gene
+ - genome
+ range: boolean
+ provided by:
+ name: provided by
+ definition_uri: https://w3id.org/biolink/vocab/provided_by
+ description: The value in this node property represents the knowledge provider
+ that created or assembled the node and all of its attributes. Used internally
+ to represent how a particular node made its way into a knowledge provider or
+ graph.
+ from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
+ rank: 1000
+ is_a: node property
+ domain: named thing
+ slot_uri: biolink:provided_by
+ alias: provided_by
+ owner: gene
+ domain_of:
+ - named thing
+ - attribute
+ - organism taxon
+ - information content entity
+ - dataset
+ - physical entity
+ - activity
+ - procedure
+ - material sample
+ - biological entity
+ - gene
+ - genome
+ range: string
+ multivalued: true
+ full name:
+ name: full name
+ definition_uri: https://w3id.org/biolink/vocab/full_name
+ description: a long-form human readable name for a thing
+ from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
+ rank: 1000
+ is_a: node property
+ domain: named thing
+ slot_uri: biolink:full_name
+ alias: full_name
+ owner: gene
+ domain_of:
+ - named thing
+ - attribute
+ - organism taxon
+ - information content entity
+ - dataset
+ - physical entity
+ - activity
+ - procedure
+ - material sample
+ - biological entity
+ - gene
+ - genome
+ range: label type
+ synonym:
+ name: synonym
+ definition_uri: https://w3id.org/biolink/vocab/synonym
+ description: Alternate human-readable names for a thing
+ in_subset:
+ - translator_minimal
+ from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
+ aliases:
+ - alias
+ narrow_mappings:
+ - skos:altLabel
+ - gff3:Alias
+ - AGRKB:synonyms
+ - gpi:DB_Object_Synonyms
+ - HANCESTRO:0330
+ - IAO:0000136
+ - RXNORM:has_tradename
+ rank: 1000
+ is_a: node property
+ domain: named thing
+ slot_uri: biolink:synonym
+ alias: synonym
+ owner: gene
+ domain_of:
+ - named thing
+ - attribute
+ - organism taxon
+ - information content entity
+ - dataset
+ - physical entity
+ - activity
+ - procedure
+ - material sample
+ - biological entity
+ - gene
+ - genome
+ range: label type
+ multivalued: true
+ in taxon:
+ name: in taxon
+ definition_uri: https://w3id.org/biolink/vocab/in_taxon
+ annotations:
+ canonical_predicate:
+ tag: canonical_predicate
+ value: true
+ description: connects an entity to its taxonomic classification. Only certain
+ kinds of entities can be taxonomically classified; see 'thing with taxon'
+ in_subset:
+ - translator_minimal
+ from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
+ aliases:
+ - instance of
+ - is organism source of gene product
+ - organism has gene
+ - gene found in organism
+ - gene product has organism source
+ exact_mappings:
+ - RO:0002162
+ - WIKIDATA_PROPERTY:P703
+ narrow_mappings:
+ - RO:0002160
+ rank: 1000
+ is_a: related to at instance level
+ domain: thing with taxon
+ slot_uri: biolink:in_taxon
+ inherited: true
+ alias: in_taxon
+ owner: gene
+ domain_of:
+ - thing with taxon
+ - biological entity
+ - gene
+ - genome
+ range: organism taxon
+ multivalued: true
+ in taxon label:
+ name: in taxon label
+ definition_uri: https://w3id.org/biolink/vocab/in_taxon_label
+ annotations:
+ denormalized:
+ tag: denormalized
+ value: true
+ description: The human readable scientific name for the taxon of the entity.
+ in_subset:
+ - translator_minimal
+ from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
+ exact_mappings:
+ - WIKIDATA_PROPERTY:P225
+ rank: 1000
+ is_a: node property
+ domain: thing with taxon
+ slot_uri: biolink:in_taxon_label
+ alias: in_taxon_label
+ owner: gene
+ domain_of:
+ - thing with taxon
+ - biological entity
+ - gene
+ - genome
+ range: label type
+ symbol:
+ name: symbol
+ definition_uri: https://w3id.org/biolink/vocab/symbol
+ description: Symbol for a particular thing
+ from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
+ exact_mappings:
+ - AGRKB:symbol
+ - gpi:DB_Object_Symbol
+ rank: 1000
+ is_a: node property
+ domain: named thing
+ slot_uri: biolink:symbol
+ alias: symbol
+ owner: gene
+ domain_of:
+ - gene
+ range: string
+ xref:
+ name: xref
+ definition_uri: https://w3id.org/biolink/vocab/xref
+ description: A database cross reference or alternative identifier for a NamedThing
+ or edge between two NamedThings. This property should point to a database record
+ or webpage that supports the existence of the edge, or gives more detail about
+ the edge. This property can be used on a node or edge to provide multiple URIs
+ or CURIE cross references.
+ in_subset:
+ - translator_minimal
+ from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
+ aliases:
+ - dbxref
+ - Dbxref
+ - DbXref
+ - record_url
+ - source_record_urls
+ narrow_mappings:
+ - gff3:Dbxref
+ - gpi:DB_Xrefs
+ rank: 1000
+ domain: named thing
+ slot_uri: biolink:xref
+ alias: xref
+ owner: gene
+ domain_of:
+ - named thing
+ - gene
+ - attribute
+ - organism taxon
+ - information content entity
+ - dataset
+ - physical entity
+ - activity
+ - procedure
+ - material sample
+ - biological entity
+ - genome
+ range: uriorcurie
+ multivalued: true
+ has biological sequence:
+ name: has biological sequence
+ definition_uri: https://w3id.org/biolink/vocab/has_biological_sequence
+ description: connects a genomic feature to its sequence
+ from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
+ rank: 1000
+ is_a: node property
+ domain: named thing
+ slot_uri: biolink:has_biological_sequence
+ alias: has_biological_sequence
+ owner: gene
+ domain_of:
+ - genomic entity
+ - gene
+ - genome
+ range: biological sequence
+class_uri: biolink:Gene
+
+An annotation describing the location, boundaries, and functions of individual genes within a genome annotation.
+URI: bican:GeneAnnotation
+| Name | +Cardinality and Range | +Description | +Inheritance | +
|---|---|---|---|
| molecular_type | +0..1 String or BioType or String |
++ | direct | +
| source_id | +0..1 String |
+The authority specific identifier | +direct | +
| referenced_in | +1 String or GenomeAnnotation or String |
+The genome annotation that this gene annotation was referenced from | +direct | +
| id | +1 String |
+A unique identifier for an entity | +OntologyClass, Entity, NamedThing, BiologicalEntity, Gene | +
| iri | +0..1 IriType |
+An IRI for an entity | +BiologicalEntity, Gene, Entity, NamedThing | +
| category | +* Uriorcurie |
+Name of the high level ontology class in which this entity is categorized | +BiologicalEntity, Gene, Entity, NamedThing | +
| type | +* String |
++ | BiologicalEntity, Gene, Entity, NamedThing | +
| name | +0..1 LabelType |
+A human-readable name for an attribute or entity | +Entity, NamedThing, BiologicalEntity, GeneOrGeneProduct, Gene, MacromolecularMachineMixin | +
| description | +0..1 NarrativeText |
+a human-readable description of an entity | +BiologicalEntity, Gene, Entity, NamedThing | +
| has_attribute | +* Attribute |
+connects any entity to an attribute | +BiologicalEntity, Gene, Entity, NamedThing | +
| deprecated | +0..1 Boolean |
+A boolean flag indicating that an entity is no longer considered current or v... | +BiologicalEntity, Gene, Entity, NamedThing | +
| provided_by | +* String |
+The value in this node property represents the knowledge provider that create... | +BiologicalEntity, Gene, NamedThing | +
| full_name | +0..1 LabelType |
+a long-form human readable name for a thing | +BiologicalEntity, Gene, NamedThing | +
| synonym | +* LabelType |
+Alternate human-readable names for a thing | +BiologicalEntity, Gene, NamedThing | +
| in_taxon | +* OrganismTaxon |
+connects an entity to its taxonomic classification | +BiologicalEntity, ThingWithTaxon, Gene | +
| in_taxon_label | +0..1 LabelType |
+The human readable scientific name for the taxon of the entity | +BiologicalEntity, ThingWithTaxon, Gene | +
| symbol | +0..1 String |
+Symbol for a particular thing | +Gene | +
| xref | +* Uriorcurie |
+A database cross reference or alternative identifier for a NamedThing or edge... | +BiologicalEntity, Gene, NamedThing | +
| has_biological_sequence | +0..1 BiologicalSequence |
+connects a genomic feature to its sequence | +Gene, GenomicEntity | +
| used by | +used in | +type | +used | +
|---|---|---|---|
| AnnotationCollection | +annotations | +range | +GeneAnnotation | +
Instances of this class should have identifiers with one of the following prefixes:
+ENSEMBL
+MGI
+NCBIGene
+| Mapping Type | +Mapped Value | +
|---|---|
| self | +bican:GeneAnnotation | +
| native | +bican:GeneAnnotation | +
name: gene annotation
+id_prefixes:
+- ENSEMBL
+- MGI
+- NCBIGene
+description: An annotation describing the location, boundaries, and functions of individual
+ genes within a genome annotation.
+from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
+is_a: gene
+slots:
+- molecular type
+- source id
+attributes:
+ referenced in:
+ name: referenced in
+ description: The genome annotation that this gene annotation was referenced from.
+ from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
+ rank: 1000
+ domain_of:
+ - gene annotation
+ required: true
+ inlined: true
+ any_of:
+ - range: genome annotation
+ - range: string
+
+name: gene annotation
+id_prefixes:
+- ENSEMBL
+- MGI
+- NCBIGene
+description: An annotation describing the location, boundaries, and functions of individual
+ genes within a genome annotation.
+from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
+is_a: gene
+attributes:
+ referenced in:
+ name: referenced in
+ description: The genome annotation that this gene annotation was referenced from.
+ from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
+ rank: 1000
+ alias: referenced_in
+ owner: gene annotation
+ domain_of:
+ - gene annotation
+ range: string
+ required: true
+ inlined: true
+ any_of:
+ - range: genome annotation
+ - range: string
+ molecular type:
+ name: molecular type
+ from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
+ rank: 1000
+ alias: molecular_type
+ owner: gene annotation
+ domain_of:
+ - gene annotation
+ range: string
+ any_of:
+ - range: BioType
+ - range: string
+ source id:
+ name: source id
+ description: The authority specific identifier.
+ from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
+ rank: 1000
+ slot_uri: schema:identifier
+ alias: source_id
+ owner: gene annotation
+ domain_of:
+ - gene annotation
+ range: string
+ id:
+ name: id
+ definition_uri: https://w3id.org/biolink/vocab/id
+ description: A unique identifier for an entity. Must be either a CURIE shorthand
+ for a URI or a complete URI
+ in_subset:
+ - translator_minimal
+ from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
+ exact_mappings:
+ - AGRKB:primaryId
+ - gff3:ID
+ - gpi:DB_Object_ID
+ rank: 1000
+ domain: entity
+ slot_uri: biolink:id
+ identifier: true
+ alias: id
+ owner: gene annotation
+ domain_of:
+ - ontology class
+ - entity
+ - attribute
+ - named thing
+ - taxonomic rank
+ - organism taxon
+ - information content entity
+ - dataset
+ - physical entity
+ - activity
+ - procedure
+ - material sample
+ - biological entity
+ - gene
+ - genome
+ range: string
+ required: true
+ iri:
+ name: iri
+ definition_uri: https://w3id.org/biolink/vocab/iri
+ description: An IRI for an entity. This is determined by the id using expansion
+ rules.
+ in_subset:
+ - translator_minimal
+ - samples
+ from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
+ exact_mappings:
+ - WIKIDATA_PROPERTY:P854
+ rank: 1000
+ slot_uri: biolink:iri
+ alias: iri
+ owner: gene annotation
+ domain_of:
+ - attribute
+ - entity
+ - named thing
+ - organism taxon
+ - information content entity
+ - dataset
+ - physical entity
+ - activity
+ - procedure
+ - material sample
+ - biological entity
+ - gene
+ - genome
+ range: iri type
+ category:
+ name: category
+ definition_uri: https://w3id.org/biolink/vocab/category
+ description: Name of the high level ontology class in which this entity is categorized.
+ Corresponds to the label for the biolink entity type class. In a neo4j database
+ this MAY correspond to the neo4j label tag. In an RDF database it should be
+ a biolink model class URI. This field is multi-valued. It should include values
+ for ancestors of the biolink class; for example, a protein such as Shh would
+ have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`.
+ In an RDF database, nodes will typically have an rdf:type triples. This can
+ be to the most specific biolink class, or potentially to a class more specific
+ than something in biolink. For example, a sequence feature `f` may have a rdf:type
+ assertion to a SO class such as TF_binding_site, which is more specific than
+ anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity,
+ biolink:NamedThing}
+ in_subset:
+ - translator_minimal
+ from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
+ rank: 1000
+ is_a: type
+ domain: entity
+ slot_uri: biolink:category
+ designates_type: true
+ alias: category
+ owner: gene annotation
+ domain_of:
+ - entity
+ - attribute
+ - named thing
+ - organism taxon
+ - information content entity
+ - dataset
+ - physical entity
+ - activity
+ - procedure
+ - material sample
+ - biological entity
+ - gene
+ - genome
+ is_class_field: true
+ range: uriorcurie
+ multivalued: true
+ type:
+ name: type
+ definition_uri: https://w3id.org/biolink/vocab/type
+ from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
+ mappings:
+ - rdf:type
+ exact_mappings:
+ - gff3:type
+ - gpi:DB_Object_Type
+ rank: 1000
+ domain: entity
+ slot_uri: rdf:type
+ alias: type
+ owner: gene annotation
+ domain_of:
+ - entity
+ - attribute
+ - named thing
+ - organism taxon
+ - information content entity
+ - dataset
+ - physical entity
+ - activity
+ - procedure
+ - material sample
+ - biological entity
+ - gene
+ - genome
+ range: string
+ multivalued: true
+ name:
+ name: name
+ definition_uri: https://w3id.org/biolink/vocab/name
+ description: A human-readable name for an attribute or entity.
+ in_subset:
+ - translator_minimal
+ - samples
+ from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
+ aliases:
+ - label
+ - display name
+ - title
+ mappings:
+ - rdfs:label
+ exact_mappings:
+ - gff3:Name
+ - gpi:DB_Object_Name
+ narrow_mappings:
+ - dct:title
+ - WIKIDATA_PROPERTY:P1476
+ rank: 1000
+ domain: entity
+ slot_uri: rdfs:label
+ alias: name
+ owner: gene annotation
+ domain_of:
+ - attribute
+ - entity
+ - macromolecular machine mixin
+ - named thing
+ - organism taxon
+ - information content entity
+ - dataset
+ - physical entity
+ - activity
+ - procedure
+ - material sample
+ - biological entity
+ - gene or gene product
+ - gene
+ - genome
+ range: label type
+ description:
+ name: description
+ definition_uri: https://w3id.org/biolink/vocab/description
+ description: a human-readable description of an entity
+ in_subset:
+ - translator_minimal
+ from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
+ aliases:
+ - definition
+ mappings:
+ - dct:description
+ exact_mappings:
+ - IAO:0000115
+ - skos:definitions
+ narrow_mappings:
+ - gff3:Description
+ rank: 1000
+ slot_uri: dct:description
+ alias: description
+ owner: gene annotation
+ domain_of:
+ - entity
+ - attribute
+ - named thing
+ - organism taxon
+ - information content entity
+ - dataset
+ - physical entity
+ - activity
+ - procedure
+ - material sample
+ - biological entity
+ - gene
+ - genome
+ range: narrative text
+ has attribute:
+ name: has attribute
+ definition_uri: https://w3id.org/biolink/vocab/has_attribute
+ description: connects any entity to an attribute
+ in_subset:
+ - samples
+ from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
+ exact_mappings:
+ - SIO:000008
+ close_mappings:
+ - OBI:0001927
+ narrow_mappings:
+ - OBAN:association_has_subject_property
+ - OBAN:association_has_object_property
+ - CPT:has_possibly_included_panel_element
+ - DRUGBANK:category
+ - EFO:is_executed_in
+ - HANCESTRO:0301
+ - LOINC:has_action_guidance
+ - LOINC:has_adjustment
+ - LOINC:has_aggregation_view
+ - LOINC:has_approach_guidance
+ - LOINC:has_divisor
+ - LOINC:has_exam
+ - LOINC:has_method
+ - LOINC:has_modality_subtype
+ - LOINC:has_object_guidance
+ - LOINC:has_scale
+ - LOINC:has_suffix
+ - LOINC:has_time_aspect
+ - LOINC:has_time_modifier
+ - LOINC:has_timing_of
+ - NCIT:R88
+ - NCIT:eo_disease_has_property_or_attribute
+ - NCIT:has_data_element
+ - NCIT:has_pharmaceutical_administration_method
+ - NCIT:has_pharmaceutical_basic_dose_form
+ - NCIT:has_pharmaceutical_intended_site
+ - NCIT:has_pharmaceutical_release_characteristics
+ - NCIT:has_pharmaceutical_state_of_matter
+ - NCIT:has_pharmaceutical_transformation
+ - NCIT:is_qualified_by
+ - NCIT:qualifier_applies_to
+ - NCIT:role_has_domain
+ - NCIT:role_has_range
+ - INO:0000154
+ - HANCESTRO:0308
+ - OMIM:has_inheritance_type
+ - orphanet:C016
+ - orphanet:C017
+ - RO:0000053
+ - RO:0000086
+ - RO:0000087
+ - SNOMED:has_access
+ - SNOMED:has_clinical_course
+ - SNOMED:has_count_of_base_of_active_ingredient
+ - SNOMED:has_dose_form_administration_method
+ - SNOMED:has_dose_form_release_characteristic
+ - SNOMED:has_dose_form_transformation
+ - SNOMED:has_finding_context
+ - SNOMED:has_finding_informer
+ - SNOMED:has_inherent_attribute
+ - SNOMED:has_intent
+ - SNOMED:has_interpretation
+ - SNOMED:has_laterality
+ - SNOMED:has_measurement_method
+ - SNOMED:has_method
+ - SNOMED:has_priority
+ - SNOMED:has_procedure_context
+ - SNOMED:has_process_duration
+ - SNOMED:has_property
+ - SNOMED:has_revision_status
+ - SNOMED:has_scale_type
+ - SNOMED:has_severity
+ - SNOMED:has_specimen
+ - SNOMED:has_state_of_matter
+ - SNOMED:has_subject_relationship_context
+ - SNOMED:has_surgical_approach
+ - SNOMED:has_technique
+ - SNOMED:has_temporal_context
+ - SNOMED:has_time_aspect
+ - SNOMED:has_units
+ - UMLS:has_structural_class
+ - UMLS:has_supported_concept_property
+ - UMLS:has_supported_concept_relationship
+ - UMLS:may_be_qualified_by
+ rank: 1000
+ domain: entity
+ slot_uri: biolink:has_attribute
+ alias: has_attribute
+ owner: gene annotation
+ domain_of:
+ - entity
+ - attribute
+ - named thing
+ - organism taxon
+ - information content entity
+ - dataset
+ - physical entity
+ - activity
+ - procedure
+ - material sample
+ - biological entity
+ - gene
+ - genome
+ range: attribute
+ multivalued: true
+ deprecated:
+ name: deprecated
+ definition_uri: https://w3id.org/biolink/vocab/deprecated
+ description: A boolean flag indicating that an entity is no longer considered
+ current or valid.
+ from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
+ exact_mappings:
+ - oboInOwl:ObsoleteClass
+ rank: 1000
+ slot_uri: biolink:deprecated
+ alias: deprecated
+ owner: gene annotation
+ domain_of:
+ - entity
+ - attribute
+ - named thing
+ - organism taxon
+ - information content entity
+ - dataset
+ - physical entity
+ - activity
+ - procedure
+ - material sample
+ - biological entity
+ - gene
+ - genome
+ range: boolean
+ provided by:
+ name: provided by
+ definition_uri: https://w3id.org/biolink/vocab/provided_by
+ description: The value in this node property represents the knowledge provider
+ that created or assembled the node and all of its attributes. Used internally
+ to represent how a particular node made its way into a knowledge provider or
+ graph.
+ from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
+ rank: 1000
+ is_a: node property
+ domain: named thing
+ slot_uri: biolink:provided_by
+ alias: provided_by
+ owner: gene annotation
+ domain_of:
+ - named thing
+ - attribute
+ - organism taxon
+ - information content entity
+ - dataset
+ - physical entity
+ - activity
+ - procedure
+ - material sample
+ - biological entity
+ - gene
+ - genome
+ range: string
+ multivalued: true
+ full name:
+ name: full name
+ definition_uri: https://w3id.org/biolink/vocab/full_name
+ description: a long-form human readable name for a thing
+ from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
+ rank: 1000
+ is_a: node property
+ domain: named thing
+ slot_uri: biolink:full_name
+ alias: full_name
+ owner: gene annotation
+ domain_of:
+ - named thing
+ - attribute
+ - organism taxon
+ - information content entity
+ - dataset
+ - physical entity
+ - activity
+ - procedure
+ - material sample
+ - biological entity
+ - gene
+ - genome
+ range: label type
+ synonym:
+ name: synonym
+ definition_uri: https://w3id.org/biolink/vocab/synonym
+ description: Alternate human-readable names for a thing
+ in_subset:
+ - translator_minimal
+ from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
+ aliases:
+ - alias
+ narrow_mappings:
+ - skos:altLabel
+ - gff3:Alias
+ - AGRKB:synonyms
+ - gpi:DB_Object_Synonyms
+ - HANCESTRO:0330
+ - IAO:0000136
+ - RXNORM:has_tradename
+ rank: 1000
+ is_a: node property
+ domain: named thing
+ slot_uri: biolink:synonym
+ alias: synonym
+ owner: gene annotation
+ domain_of:
+ - named thing
+ - attribute
+ - organism taxon
+ - information content entity
+ - dataset
+ - physical entity
+ - activity
+ - procedure
+ - material sample
+ - biological entity
+ - gene
+ - genome
+ range: label type
+ multivalued: true
+ in taxon:
+ name: in taxon
+ definition_uri: https://w3id.org/biolink/vocab/in_taxon
+ annotations:
+ canonical_predicate:
+ tag: canonical_predicate
+ value: true
+ description: connects an entity to its taxonomic classification. Only certain
+ kinds of entities can be taxonomically classified; see 'thing with taxon'
+ in_subset:
+ - translator_minimal
+ from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
+ aliases:
+ - instance of
+ - is organism source of gene product
+ - organism has gene
+ - gene found in organism
+ - gene product has organism source
+ exact_mappings:
+ - RO:0002162
+ - WIKIDATA_PROPERTY:P703
+ narrow_mappings:
+ - RO:0002160
+ rank: 1000
+ is_a: related to at instance level
+ domain: thing with taxon
+ slot_uri: biolink:in_taxon
+ inherited: true
+ alias: in_taxon
+ owner: gene annotation
+ domain_of:
+ - thing with taxon
+ - biological entity
+ - gene
+ - genome
+ range: organism taxon
+ multivalued: true
+ in taxon label:
+ name: in taxon label
+ definition_uri: https://w3id.org/biolink/vocab/in_taxon_label
+ annotations:
+ denormalized:
+ tag: denormalized
+ value: true
+ description: The human readable scientific name for the taxon of the entity.
+ in_subset:
+ - translator_minimal
+ from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
+ exact_mappings:
+ - WIKIDATA_PROPERTY:P225
+ rank: 1000
+ is_a: node property
+ domain: thing with taxon
+ slot_uri: biolink:in_taxon_label
+ alias: in_taxon_label
+ owner: gene annotation
+ domain_of:
+ - thing with taxon
+ - biological entity
+ - gene
+ - genome
+ range: label type
+ symbol:
+ name: symbol
+ definition_uri: https://w3id.org/biolink/vocab/symbol
+ description: Symbol for a particular thing
+ from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
+ exact_mappings:
+ - AGRKB:symbol
+ - gpi:DB_Object_Symbol
+ rank: 1000
+ is_a: node property
+ domain: named thing
+ slot_uri: biolink:symbol
+ alias: symbol
+ owner: gene annotation
+ domain_of:
+ - gene
+ range: string
+ xref:
+ name: xref
+ definition_uri: https://w3id.org/biolink/vocab/xref
+ description: A database cross reference or alternative identifier for a NamedThing
+ or edge between two NamedThings. This property should point to a database record
+ or webpage that supports the existence of the edge, or gives more detail about
+ the edge. This property can be used on a node or edge to provide multiple URIs
+ or CURIE cross references.
+ in_subset:
+ - translator_minimal
+ from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
+ aliases:
+ - dbxref
+ - Dbxref
+ - DbXref
+ - record_url
+ - source_record_urls
+ narrow_mappings:
+ - gff3:Dbxref
+ - gpi:DB_Xrefs
+ rank: 1000
+ domain: named thing
+ slot_uri: biolink:xref
+ alias: xref
+ owner: gene annotation
+ domain_of:
+ - named thing
+ - gene
+ - attribute
+ - organism taxon
+ - information content entity
+ - dataset
+ - physical entity
+ - activity
+ - procedure
+ - material sample
+ - biological entity
+ - genome
+ range: uriorcurie
+ multivalued: true
+ has biological sequence:
+ name: has biological sequence
+ definition_uri: https://w3id.org/biolink/vocab/has_biological_sequence
+ description: connects a genomic feature to its sequence
+ from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
+ rank: 1000
+ is_a: node property
+ domain: named thing
+ slot_uri: biolink:has_biological_sequence
+ alias: has_biological_sequence
+ owner: gene annotation
+ domain_of:
+ - genomic entity
+ - gene
+ - genome
+ range: biological sequence
+
+A union of gene loci or gene products. Frequently an identifier for one will be used as proxy for another
+URI: biolink:GeneOrGeneProduct
+| Name | +Cardinality and Range | +Description | +Inheritance | +
|---|---|---|---|
| name | +0..1 LabelType |
+A human-readable name for an attribute or entity | +direct | +
| mixed into | +description | +
|---|---|
| Gene | +A region (or regions) that includes all of the sequence elements necessary to... | +
Instances of this class should have identifiers with one of the following prefixes:
+CHEMBL.TARGET
+IUPHAR.FAMILY
+| Mapping Type | +Mapped Value | +
|---|---|
| self | +biolink:GeneOrGeneProduct | +
| native | +bican:GeneOrGeneProduct | +
name: gene or gene product
+id_prefixes:
+- CHEMBL.TARGET
+- IUPHAR.FAMILY
+definition_uri: https://w3id.org/biolink/vocab/GeneOrGeneProduct
+description: A union of gene loci or gene products. Frequently an identifier for one
+ will be used as proxy for another
+from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
+is_a: macromolecular machine mixin
+mixin: true
+slots:
+- name
+class_uri: biolink:GeneOrGeneProduct
+
+name: gene or gene product
+id_prefixes:
+- CHEMBL.TARGET
+- IUPHAR.FAMILY
+definition_uri: https://w3id.org/biolink/vocab/GeneOrGeneProduct
+description: A union of gene loci or gene products. Frequently an identifier for one
+ will be used as proxy for another
+from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
+is_a: macromolecular machine mixin
+mixin: true
+attributes:
+ name:
+ name: name
+ definition_uri: https://w3id.org/biolink/vocab/name
+ description: A human-readable name for an attribute or entity.
+ in_subset:
+ - translator_minimal
+ - samples
+ from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
+ aliases:
+ - label
+ - display name
+ - title
+ mappings:
+ - rdfs:label
+ exact_mappings:
+ - gff3:Name
+ - gpi:DB_Object_Name
+ narrow_mappings:
+ - dct:title
+ - WIKIDATA_PROPERTY:P1476
+ rank: 1000
+ domain: entity
+ slot_uri: rdfs:label
+ alias: name
+ owner: gene or gene product
+ domain_of:
+ - attribute
+ - entity
+ - macromolecular machine mixin
+ - named thing
+ - organism taxon
+ - information content entity
+ - dataset
+ - physical entity
+ - activity
+ - procedure
+ - material sample
+ - biological entity
+ - gene or gene product
+ - gene
+ - genome
+ range: label type
+class_uri: biolink:GeneOrGeneProduct
+
+A genome is the sum of genetic material within a cell or virion.
+URI: biolink:Genome
+| Name | +Cardinality and Range | +Description | +Inheritance | +
|---|---|---|---|
| id | +1 String |
+A unique identifier for an entity | +direct | +
| iri | +0..1 IriType |
+An IRI for an entity | +direct | +
| category | +* Uriorcurie |
+Name of the high level ontology class in which this entity is categorized | +direct | +
| type | +* String |
++ | direct | +
| name | +0..1 LabelType |
+A human-readable name for an attribute or entity | +direct | +
| description | +0..1 NarrativeText |
+a human-readable description of an entity | +direct | +
| has_attribute | +* Attribute |
+connects any entity to an attribute | +direct | +
| deprecated | +0..1 Boolean |
+A boolean flag indicating that an entity is no longer considered current or v... | +direct | +
| provided_by | +* String |
+The value in this node property represents the knowledge provider that create... | +direct | +
| xref | +* Uriorcurie |
+A database cross reference or alternative identifier for a NamedThing or edge... | +direct | +
| full_name | +0..1 LabelType |
+a long-form human readable name for a thing | +direct | +
| synonym | +* LabelType |
+Alternate human-readable names for a thing | +direct | +
| in_taxon | +* OrganismTaxon |
+connects an entity to its taxonomic classification | +direct | +
| in_taxon_label | +0..1 LabelType |
+The human readable scientific name for the taxon of the entity | +direct | +
| has_biological_sequence | +0..1 BiologicalSequence |
+connects a genomic feature to its sequence | +direct | +
| Mapping Type | +Mapped Value | +
|---|---|
| self | +biolink:Genome | +
| native | +bican:Genome | +
| exact | +SO:0001026, SIO:000984, WIKIDATA:Q7020 | +
| close | +dcid:GenomeAssemblyUnit | +
name: genome
+definition_uri: https://w3id.org/biolink/vocab/Genome
+description: A genome is the sum of genetic material within a cell or virion.
+in_subset:
+- model_organism_database
+from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
+exact_mappings:
+- SO:0001026
+- SIO:000984
+- WIKIDATA:Q7020
+close_mappings:
+- dcid:GenomeAssemblyUnit
+is_a: biological entity
+mixins:
+- genomic entity
+- physical essence
+- ontology class
+slots:
+- id
+- iri
+- category
+- type
+- name
+- description
+- has attribute
+- deprecated
+- provided by
+- xref
+- full name
+- synonym
+- in taxon
+- in taxon label
+- has biological sequence
+class_uri: biolink:Genome
+
+name: genome
+definition_uri: https://w3id.org/biolink/vocab/Genome
+description: A genome is the sum of genetic material within a cell or virion.
+in_subset:
+- model_organism_database
+from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
+exact_mappings:
+- SO:0001026
+- SIO:000984
+- WIKIDATA:Q7020
+close_mappings:
+- dcid:GenomeAssemblyUnit
+is_a: biological entity
+mixins:
+- genomic entity
+- physical essence
+- ontology class
+attributes:
+ id:
+ name: id
+ definition_uri: https://w3id.org/biolink/vocab/id
+ description: A unique identifier for an entity. Must be either a CURIE shorthand
+ for a URI or a complete URI
+ in_subset:
+ - translator_minimal
+ from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
+ exact_mappings:
+ - AGRKB:primaryId
+ - gff3:ID
+ - gpi:DB_Object_ID
+ rank: 1000
+ domain: entity
+ slot_uri: biolink:id
+ identifier: true
+ alias: id
+ owner: genome
+ domain_of:
+ - ontology class
+ - entity
+ - attribute
+ - named thing
+ - taxonomic rank
+ - organism taxon
+ - information content entity
+ - dataset
+ - physical entity
+ - activity
+ - procedure
+ - material sample
+ - biological entity
+ - gene
+ - genome
+ range: string
+ required: true
+ iri:
+ name: iri
+ definition_uri: https://w3id.org/biolink/vocab/iri
+ description: An IRI for an entity. This is determined by the id using expansion
+ rules.
+ in_subset:
+ - translator_minimal
+ - samples
+ from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
+ exact_mappings:
+ - WIKIDATA_PROPERTY:P854
+ rank: 1000
+ slot_uri: biolink:iri
+ alias: iri
+ owner: genome
+ domain_of:
+ - attribute
+ - entity
+ - named thing
+ - organism taxon
+ - information content entity
+ - dataset
+ - physical entity
+ - activity
+ - procedure
+ - material sample
+ - biological entity
+ - gene
+ - genome
+ range: iri type
+ category:
+ name: category
+ definition_uri: https://w3id.org/biolink/vocab/category
+ description: Name of the high level ontology class in which this entity is categorized.
+ Corresponds to the label for the biolink entity type class. In a neo4j database
+ this MAY correspond to the neo4j label tag. In an RDF database it should be
+ a biolink model class URI. This field is multi-valued. It should include values
+ for ancestors of the biolink class; for example, a protein such as Shh would
+ have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`.
+ In an RDF database, nodes will typically have an rdf:type triples. This can
+ be to the most specific biolink class, or potentially to a class more specific
+ than something in biolink. For example, a sequence feature `f` may have a rdf:type
+ assertion to a SO class such as TF_binding_site, which is more specific than
+ anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity,
+ biolink:NamedThing}
+ in_subset:
+ - translator_minimal
+ from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
+ rank: 1000
+ is_a: type
+ domain: entity
+ slot_uri: biolink:category
+ designates_type: true
+ alias: category
+ owner: genome
+ domain_of:
+ - entity
+ - attribute
+ - named thing
+ - organism taxon
+ - information content entity
+ - dataset
+ - physical entity
+ - activity
+ - procedure
+ - material sample
+ - biological entity
+ - gene
+ - genome
+ is_class_field: true
+ range: uriorcurie
+ multivalued: true
+ type:
+ name: type
+ definition_uri: https://w3id.org/biolink/vocab/type
+ from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
+ mappings:
+ - rdf:type
+ exact_mappings:
+ - gff3:type
+ - gpi:DB_Object_Type
+ rank: 1000
+ domain: entity
+ slot_uri: rdf:type
+ alias: type
+ owner: genome
+ domain_of:
+ - entity
+ - attribute
+ - named thing
+ - organism taxon
+ - information content entity
+ - dataset
+ - physical entity
+ - activity
+ - procedure
+ - material sample
+ - biological entity
+ - gene
+ - genome
+ range: string
+ multivalued: true
+ name:
+ name: name
+ definition_uri: https://w3id.org/biolink/vocab/name
+ description: A human-readable name for an attribute or entity.
+ in_subset:
+ - translator_minimal
+ - samples
+ from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
+ aliases:
+ - label
+ - display name
+ - title
+ mappings:
+ - rdfs:label
+ exact_mappings:
+ - gff3:Name
+ - gpi:DB_Object_Name
+ narrow_mappings:
+ - dct:title
+ - WIKIDATA_PROPERTY:P1476
+ rank: 1000
+ domain: entity
+ slot_uri: rdfs:label
+ alias: name
+ owner: genome
+ domain_of:
+ - attribute
+ - entity
+ - macromolecular machine mixin
+ - named thing
+ - organism taxon
+ - information content entity
+ - dataset
+ - physical entity
+ - activity
+ - procedure
+ - material sample
+ - biological entity
+ - gene or gene product
+ - gene
+ - genome
+ range: label type
+ description:
+ name: description
+ definition_uri: https://w3id.org/biolink/vocab/description
+ description: a human-readable description of an entity
+ in_subset:
+ - translator_minimal
+ from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
+ aliases:
+ - definition
+ mappings:
+ - dct:description
+ exact_mappings:
+ - IAO:0000115
+ - skos:definitions
+ narrow_mappings:
+ - gff3:Description
+ rank: 1000
+ slot_uri: dct:description
+ alias: description
+ owner: genome
+ domain_of:
+ - entity
+ - attribute
+ - named thing
+ - organism taxon
+ - information content entity
+ - dataset
+ - physical entity
+ - activity
+ - procedure
+ - material sample
+ - biological entity
+ - gene
+ - genome
+ range: narrative text
+ has attribute:
+ name: has attribute
+ definition_uri: https://w3id.org/biolink/vocab/has_attribute
+ description: connects any entity to an attribute
+ in_subset:
+ - samples
+ from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
+ exact_mappings:
+ - SIO:000008
+ close_mappings:
+ - OBI:0001927
+ narrow_mappings:
+ - OBAN:association_has_subject_property
+ - OBAN:association_has_object_property
+ - CPT:has_possibly_included_panel_element
+ - DRUGBANK:category
+ - EFO:is_executed_in
+ - HANCESTRO:0301
+ - LOINC:has_action_guidance
+ - LOINC:has_adjustment
+ - LOINC:has_aggregation_view
+ - LOINC:has_approach_guidance
+ - LOINC:has_divisor
+ - LOINC:has_exam
+ - LOINC:has_method
+ - LOINC:has_modality_subtype
+ - LOINC:has_object_guidance
+ - LOINC:has_scale
+ - LOINC:has_suffix
+ - LOINC:has_time_aspect
+ - LOINC:has_time_modifier
+ - LOINC:has_timing_of
+ - NCIT:R88
+ - NCIT:eo_disease_has_property_or_attribute
+ - NCIT:has_data_element
+ - NCIT:has_pharmaceutical_administration_method
+ - NCIT:has_pharmaceutical_basic_dose_form
+ - NCIT:has_pharmaceutical_intended_site
+ - NCIT:has_pharmaceutical_release_characteristics
+ - NCIT:has_pharmaceutical_state_of_matter
+ - NCIT:has_pharmaceutical_transformation
+ - NCIT:is_qualified_by
+ - NCIT:qualifier_applies_to
+ - NCIT:role_has_domain
+ - NCIT:role_has_range
+ - INO:0000154
+ - HANCESTRO:0308
+ - OMIM:has_inheritance_type
+ - orphanet:C016
+ - orphanet:C017
+ - RO:0000053
+ - RO:0000086
+ - RO:0000087
+ - SNOMED:has_access
+ - SNOMED:has_clinical_course
+ - SNOMED:has_count_of_base_of_active_ingredient
+ - SNOMED:has_dose_form_administration_method
+ - SNOMED:has_dose_form_release_characteristic
+ - SNOMED:has_dose_form_transformation
+ - SNOMED:has_finding_context
+ - SNOMED:has_finding_informer
+ - SNOMED:has_inherent_attribute
+ - SNOMED:has_intent
+ - SNOMED:has_interpretation
+ - SNOMED:has_laterality
+ - SNOMED:has_measurement_method
+ - SNOMED:has_method
+ - SNOMED:has_priority
+ - SNOMED:has_procedure_context
+ - SNOMED:has_process_duration
+ - SNOMED:has_property
+ - SNOMED:has_revision_status
+ - SNOMED:has_scale_type
+ - SNOMED:has_severity
+ - SNOMED:has_specimen
+ - SNOMED:has_state_of_matter
+ - SNOMED:has_subject_relationship_context
+ - SNOMED:has_surgical_approach
+ - SNOMED:has_technique
+ - SNOMED:has_temporal_context
+ - SNOMED:has_time_aspect
+ - SNOMED:has_units
+ - UMLS:has_structural_class
+ - UMLS:has_supported_concept_property
+ - UMLS:has_supported_concept_relationship
+ - UMLS:may_be_qualified_by
+ rank: 1000
+ domain: entity
+ slot_uri: biolink:has_attribute
+ alias: has_attribute
+ owner: genome
+ domain_of:
+ - entity
+ - attribute
+ - named thing
+ - organism taxon
+ - information content entity
+ - dataset
+ - physical entity
+ - activity
+ - procedure
+ - material sample
+ - biological entity
+ - gene
+ - genome
+ range: attribute
+ multivalued: true
+ deprecated:
+ name: deprecated
+ definition_uri: https://w3id.org/biolink/vocab/deprecated
+ description: A boolean flag indicating that an entity is no longer considered
+ current or valid.
+ from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
+ exact_mappings:
+ - oboInOwl:ObsoleteClass
+ rank: 1000
+ slot_uri: biolink:deprecated
+ alias: deprecated
+ owner: genome
+ domain_of:
+ - entity
+ - attribute
+ - named thing
+ - organism taxon
+ - information content entity
+ - dataset
+ - physical entity
+ - activity
+ - procedure
+ - material sample
+ - biological entity
+ - gene
+ - genome
+ range: boolean
+ provided by:
+ name: provided by
+ definition_uri: https://w3id.org/biolink/vocab/provided_by
+ description: The value in this node property represents the knowledge provider
+ that created or assembled the node and all of its attributes. Used internally
+ to represent how a particular node made its way into a knowledge provider or
+ graph.
+ from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
+ rank: 1000
+ is_a: node property
+ domain: named thing
+ slot_uri: biolink:provided_by
+ alias: provided_by
+ owner: genome
+ domain_of:
+ - named thing
+ - attribute
+ - organism taxon
+ - information content entity
+ - dataset
+ - physical entity
+ - activity
+ - procedure
+ - material sample
+ - biological entity
+ - gene
+ - genome
+ range: string
+ multivalued: true
+ xref:
+ name: xref
+ definition_uri: https://w3id.org/biolink/vocab/xref
+ description: A database cross reference or alternative identifier for a NamedThing
+ or edge between two NamedThings. This property should point to a database record
+ or webpage that supports the existence of the edge, or gives more detail about
+ the edge. This property can be used on a node or edge to provide multiple URIs
+ or CURIE cross references.
+ in_subset:
+ - translator_minimal
+ from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
+ aliases:
+ - dbxref
+ - Dbxref
+ - DbXref
+ - record_url
+ - source_record_urls
+ narrow_mappings:
+ - gff3:Dbxref
+ - gpi:DB_Xrefs
+ rank: 1000
+ domain: named thing
+ slot_uri: biolink:xref
+ alias: xref
+ owner: genome
+ domain_of:
+ - named thing
+ - gene
+ - attribute
+ - organism taxon
+ - information content entity
+ - dataset
+ - physical entity
+ - activity
+ - procedure
+ - material sample
+ - biological entity
+ - genome
+ range: uriorcurie
+ multivalued: true
+ full name:
+ name: full name
+ definition_uri: https://w3id.org/biolink/vocab/full_name
+ description: a long-form human readable name for a thing
+ from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
+ rank: 1000
+ is_a: node property
+ domain: named thing
+ slot_uri: biolink:full_name
+ alias: full_name
+ owner: genome
+ domain_of:
+ - named thing
+ - attribute
+ - organism taxon
+ - information content entity
+ - dataset
+ - physical entity
+ - activity
+ - procedure
+ - material sample
+ - biological entity
+ - gene
+ - genome
+ range: label type
+ synonym:
+ name: synonym
+ definition_uri: https://w3id.org/biolink/vocab/synonym
+ description: Alternate human-readable names for a thing
+ in_subset:
+ - translator_minimal
+ from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
+ aliases:
+ - alias
+ narrow_mappings:
+ - skos:altLabel
+ - gff3:Alias
+ - AGRKB:synonyms
+ - gpi:DB_Object_Synonyms
+ - HANCESTRO:0330
+ - IAO:0000136
+ - RXNORM:has_tradename
+ rank: 1000
+ is_a: node property
+ domain: named thing
+ slot_uri: biolink:synonym
+ alias: synonym
+ owner: genome
+ domain_of:
+ - named thing
+ - attribute
+ - organism taxon
+ - information content entity
+ - dataset
+ - physical entity
+ - activity
+ - procedure
+ - material sample
+ - biological entity
+ - gene
+ - genome
+ range: label type
+ multivalued: true
+ in taxon:
+ name: in taxon
+ definition_uri: https://w3id.org/biolink/vocab/in_taxon
+ annotations:
+ canonical_predicate:
+ tag: canonical_predicate
+ value: true
+ description: connects an entity to its taxonomic classification. Only certain
+ kinds of entities can be taxonomically classified; see 'thing with taxon'
+ in_subset:
+ - translator_minimal
+ from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
+ aliases:
+ - instance of
+ - is organism source of gene product
+ - organism has gene
+ - gene found in organism
+ - gene product has organism source
+ exact_mappings:
+ - RO:0002162
+ - WIKIDATA_PROPERTY:P703
+ narrow_mappings:
+ - RO:0002160
+ rank: 1000
+ is_a: related to at instance level
+ domain: thing with taxon
+ slot_uri: biolink:in_taxon
+ inherited: true
+ alias: in_taxon
+ owner: genome
+ domain_of:
+ - thing with taxon
+ - biological entity
+ - gene
+ - genome
+ range: organism taxon
+ multivalued: true
+ in taxon label:
+ name: in taxon label
+ definition_uri: https://w3id.org/biolink/vocab/in_taxon_label
+ annotations:
+ denormalized:
+ tag: denormalized
+ value: true
+ description: The human readable scientific name for the taxon of the entity.
+ in_subset:
+ - translator_minimal
+ from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
+ exact_mappings:
+ - WIKIDATA_PROPERTY:P225
+ rank: 1000
+ is_a: node property
+ domain: thing with taxon
+ slot_uri: biolink:in_taxon_label
+ alias: in_taxon_label
+ owner: genome
+ domain_of:
+ - thing with taxon
+ - biological entity
+ - gene
+ - genome
+ range: label type
+ has biological sequence:
+ name: has biological sequence
+ definition_uri: https://w3id.org/biolink/vocab/has_biological_sequence
+ description: connects a genomic feature to its sequence
+ from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
+ rank: 1000
+ is_a: node property
+ domain: named thing
+ slot_uri: biolink:has_biological_sequence
+ alias: has_biological_sequence
+ owner: genome
+ domain_of:
+ - genomic entity
+ - gene
+ - genome
+ range: biological sequence
+class_uri: biolink:Genome
+
+Location and nomenclature of genes and all of the coding regions in a genome assembly and the classification of genes and transcripts into types.
+ +| Name | +Cardinality and Range | +Description | +Inheritance | +
|---|---|---|---|
| version | +0..1 String |
++ | direct | +
| digest | +* String or Checksum or String |
+Stores checksum information | +direct | +
| content_url | +* String |
++ | direct | +
| authority | +0..1 AuthorityType |
+The organization responsible for publishing the data | +direct | +
| reference_assembly | +1 String or GenomeAssembly or String |
+The reference genome assembly that this genome annotation was created from | +direct | +
| id | +1 String |
+A unique identifier for an entity | +OntologyClass, Genome, Entity, NamedThing, BiologicalEntity | +
| iri | +0..1 IriType |
+An IRI for an entity | +BiologicalEntity, Genome, Entity, NamedThing | +
| category | +* Uriorcurie |
+Name of the high level ontology class in which this entity is categorized | +BiologicalEntity, Genome, Entity, NamedThing | +
| type | +* String |
++ | BiologicalEntity, Genome, Entity, NamedThing | +
| name | +0..1 LabelType |
+A human-readable name for an attribute or entity | +BiologicalEntity, Genome, Entity, NamedThing | +
| description | +0..1 NarrativeText |
+a human-readable description of an entity | +BiologicalEntity, Genome, Entity, NamedThing | +
| has_attribute | +* Attribute |
+connects any entity to an attribute | +BiologicalEntity, Genome, Entity, NamedThing | +
| deprecated | +0..1 Boolean |
+A boolean flag indicating that an entity is no longer considered current or v... | +BiologicalEntity, Genome, Entity, NamedThing | +
| provided_by | +* String |
+The value in this node property represents the knowledge provider that create... | +BiologicalEntity, Genome, NamedThing | +
| xref | +* Uriorcurie |
+A database cross reference or alternative identifier for a NamedThing or edge... | +BiologicalEntity, Genome, NamedThing | +
| full_name | +0..1 LabelType |
+a long-form human readable name for a thing | +BiologicalEntity, Genome, NamedThing | +
| synonym | +* LabelType |
+Alternate human-readable names for a thing | +BiologicalEntity, Genome, NamedThing | +
| in_taxon | +* OrganismTaxon |
+connects an entity to its taxonomic classification | +BiologicalEntity, ThingWithTaxon, Genome | +
| in_taxon_label | +0..1 LabelType |
+The human readable scientific name for the taxon of the entity | +BiologicalEntity, ThingWithTaxon, Genome | +
| has_biological_sequence | +0..1 BiologicalSequence |
+connects a genomic feature to its sequence | +Genome, GenomicEntity | +
| used by | +used in | +type | +used | +
|---|---|---|---|
| GeneAnnotation | +referenced_in | +any_of[range] | +GenomeAnnotation | +
| AnnotationCollection | +genome_annotations | +range | +GenomeAnnotation | +
| Mapping Type | +Mapped Value | +
|---|---|
| self | +bican:GenomeAnnotation | +
| native | +bican:GenomeAnnotation | +
name: genome annotation
+description: Location and nomenclature of genes and all of the coding regions in a
+ genome assembly and the classification of genes and transcripts into types.
+from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
+is_a: genome
+slots:
+- version
+- digest
+- content_url
+- authority
+attributes:
+ reference assembly:
+ name: reference assembly
+ description: The reference genome assembly that this genome annotation was created
+ from.
+ from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
+ rank: 1000
+ domain_of:
+ - genome annotation
+ required: true
+ inlined: true
+ any_of:
+ - range: genome assembly
+ - range: string
+
+name: genome annotation
+description: Location and nomenclature of genes and all of the coding regions in a
+ genome assembly and the classification of genes and transcripts into types.
+from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
+is_a: genome
+attributes:
+ reference assembly:
+ name: reference assembly
+ description: The reference genome assembly that this genome annotation was created
+ from.
+ from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
+ rank: 1000
+ alias: reference_assembly
+ owner: genome annotation
+ domain_of:
+ - genome annotation
+ range: string
+ required: true
+ inlined: true
+ any_of:
+ - range: genome assembly
+ - range: string
+ version:
+ name: version
+ definition_uri: https://w3id.org/biolink/vocab/version
+ from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
+ broad_mappings:
+ - pav:version
+ - owl:versionInfo
+ rank: 1000
+ is_a: node property
+ domain: dataset
+ slot_uri: biolink:version
+ alias: version
+ owner: genome annotation
+ domain_of:
+ - genome annotation
+ - genome assembly
+ range: string
+ digest:
+ name: digest
+ description: Stores checksum information.
+ from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
+ rank: 1000
+ alias: digest
+ owner: genome annotation
+ domain_of:
+ - genome annotation
+ range: string
+ multivalued: true
+ inlined: true
+ inlined_as_list: true
+ any_of:
+ - range: checksum
+ - range: string
+ content_url:
+ name: content_url
+ from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
+ rank: 1000
+ slot_uri: schema:url
+ alias: content_url
+ owner: genome annotation
+ domain_of:
+ - genome annotation
+ range: string
+ multivalued: true
+ authority:
+ name: authority
+ description: The organization responsible for publishing the data.
+ from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
+ rank: 1000
+ alias: authority
+ owner: genome annotation
+ domain_of:
+ - genome annotation
+ range: AuthorityType
+ id:
+ name: id
+ definition_uri: https://w3id.org/biolink/vocab/id
+ description: A unique identifier for an entity. Must be either a CURIE shorthand
+ for a URI or a complete URI
+ in_subset:
+ - translator_minimal
+ from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
+ exact_mappings:
+ - AGRKB:primaryId
+ - gff3:ID
+ - gpi:DB_Object_ID
+ rank: 1000
+ domain: entity
+ slot_uri: biolink:id
+ identifier: true
+ alias: id
+ owner: genome annotation
+ domain_of:
+ - ontology class
+ - entity
+ - attribute
+ - named thing
+ - taxonomic rank
+ - organism taxon
+ - information content entity
+ - dataset
+ - physical entity
+ - activity
+ - procedure
+ - material sample
+ - biological entity
+ - gene
+ - genome
+ range: string
+ required: true
+ iri:
+ name: iri
+ definition_uri: https://w3id.org/biolink/vocab/iri
+ description: An IRI for an entity. This is determined by the id using expansion
+ rules.
+ in_subset:
+ - translator_minimal
+ - samples
+ from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
+ exact_mappings:
+ - WIKIDATA_PROPERTY:P854
+ rank: 1000
+ slot_uri: biolink:iri
+ alias: iri
+ owner: genome annotation
+ domain_of:
+ - attribute
+ - entity
+ - named thing
+ - organism taxon
+ - information content entity
+ - dataset
+ - physical entity
+ - activity
+ - procedure
+ - material sample
+ - biological entity
+ - gene
+ - genome
+ range: iri type
+ category:
+ name: category
+ definition_uri: https://w3id.org/biolink/vocab/category
+ description: Name of the high level ontology class in which this entity is categorized.
+ Corresponds to the label for the biolink entity type class. In a neo4j database
+ this MAY correspond to the neo4j label tag. In an RDF database it should be
+ a biolink model class URI. This field is multi-valued. It should include values
+ for ancestors of the biolink class; for example, a protein such as Shh would
+ have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`.
+ In an RDF database, nodes will typically have an rdf:type triples. This can
+ be to the most specific biolink class, or potentially to a class more specific
+ than something in biolink. For example, a sequence feature `f` may have a rdf:type
+ assertion to a SO class such as TF_binding_site, which is more specific than
+ anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity,
+ biolink:NamedThing}
+ in_subset:
+ - translator_minimal
+ from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
+ rank: 1000
+ is_a: type
+ domain: entity
+ slot_uri: biolink:category
+ designates_type: true
+ alias: category
+ owner: genome annotation
+ domain_of:
+ - entity
+ - attribute
+ - named thing
+ - organism taxon
+ - information content entity
+ - dataset
+ - physical entity
+ - activity
+ - procedure
+ - material sample
+ - biological entity
+ - gene
+ - genome
+ is_class_field: true
+ range: uriorcurie
+ multivalued: true
+ type:
+ name: type
+ definition_uri: https://w3id.org/biolink/vocab/type
+ from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
+ mappings:
+ - rdf:type
+ exact_mappings:
+ - gff3:type
+ - gpi:DB_Object_Type
+ rank: 1000
+ domain: entity
+ slot_uri: rdf:type
+ alias: type
+ owner: genome annotation
+ domain_of:
+ - entity
+ - attribute
+ - named thing
+ - organism taxon
+ - information content entity
+ - dataset
+ - physical entity
+ - activity
+ - procedure
+ - material sample
+ - biological entity
+ - gene
+ - genome
+ range: string
+ multivalued: true
+ name:
+ name: name
+ definition_uri: https://w3id.org/biolink/vocab/name
+ description: A human-readable name for an attribute or entity.
+ in_subset:
+ - translator_minimal
+ - samples
+ from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
+ aliases:
+ - label
+ - display name
+ - title
+ mappings:
+ - rdfs:label
+ exact_mappings:
+ - gff3:Name
+ - gpi:DB_Object_Name
+ narrow_mappings:
+ - dct:title
+ - WIKIDATA_PROPERTY:P1476
+ rank: 1000
+ domain: entity
+ slot_uri: rdfs:label
+ alias: name
+ owner: genome annotation
+ domain_of:
+ - attribute
+ - entity
+ - macromolecular machine mixin
+ - named thing
+ - organism taxon
+ - information content entity
+ - dataset
+ - physical entity
+ - activity
+ - procedure
+ - material sample
+ - biological entity
+ - gene or gene product
+ - gene
+ - genome
+ range: label type
+ description:
+ name: description
+ definition_uri: https://w3id.org/biolink/vocab/description
+ description: a human-readable description of an entity
+ in_subset:
+ - translator_minimal
+ from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
+ aliases:
+ - definition
+ mappings:
+ - dct:description
+ exact_mappings:
+ - IAO:0000115
+ - skos:definitions
+ narrow_mappings:
+ - gff3:Description
+ rank: 1000
+ slot_uri: dct:description
+ alias: description
+ owner: genome annotation
+ domain_of:
+ - entity
+ - attribute
+ - named thing
+ - organism taxon
+ - information content entity
+ - dataset
+ - physical entity
+ - activity
+ - procedure
+ - material sample
+ - biological entity
+ - gene
+ - genome
+ range: narrative text
+ has attribute:
+ name: has attribute
+ definition_uri: https://w3id.org/biolink/vocab/has_attribute
+ description: connects any entity to an attribute
+ in_subset:
+ - samples
+ from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
+ exact_mappings:
+ - SIO:000008
+ close_mappings:
+ - OBI:0001927
+ narrow_mappings:
+ - OBAN:association_has_subject_property
+ - OBAN:association_has_object_property
+ - CPT:has_possibly_included_panel_element
+ - DRUGBANK:category
+ - EFO:is_executed_in
+ - HANCESTRO:0301
+ - LOINC:has_action_guidance
+ - LOINC:has_adjustment
+ - LOINC:has_aggregation_view
+ - LOINC:has_approach_guidance
+ - LOINC:has_divisor
+ - LOINC:has_exam
+ - LOINC:has_method
+ - LOINC:has_modality_subtype
+ - LOINC:has_object_guidance
+ - LOINC:has_scale
+ - LOINC:has_suffix
+ - LOINC:has_time_aspect
+ - LOINC:has_time_modifier
+ - LOINC:has_timing_of
+ - NCIT:R88
+ - NCIT:eo_disease_has_property_or_attribute
+ - NCIT:has_data_element
+ - NCIT:has_pharmaceutical_administration_method
+ - NCIT:has_pharmaceutical_basic_dose_form
+ - NCIT:has_pharmaceutical_intended_site
+ - NCIT:has_pharmaceutical_release_characteristics
+ - NCIT:has_pharmaceutical_state_of_matter
+ - NCIT:has_pharmaceutical_transformation
+ - NCIT:is_qualified_by
+ - NCIT:qualifier_applies_to
+ - NCIT:role_has_domain
+ - NCIT:role_has_range
+ - INO:0000154
+ - HANCESTRO:0308
+ - OMIM:has_inheritance_type
+ - orphanet:C016
+ - orphanet:C017
+ - RO:0000053
+ - RO:0000086
+ - RO:0000087
+ - SNOMED:has_access
+ - SNOMED:has_clinical_course
+ - SNOMED:has_count_of_base_of_active_ingredient
+ - SNOMED:has_dose_form_administration_method
+ - SNOMED:has_dose_form_release_characteristic
+ - SNOMED:has_dose_form_transformation
+ - SNOMED:has_finding_context
+ - SNOMED:has_finding_informer
+ - SNOMED:has_inherent_attribute
+ - SNOMED:has_intent
+ - SNOMED:has_interpretation
+ - SNOMED:has_laterality
+ - SNOMED:has_measurement_method
+ - SNOMED:has_method
+ - SNOMED:has_priority
+ - SNOMED:has_procedure_context
+ - SNOMED:has_process_duration
+ - SNOMED:has_property
+ - SNOMED:has_revision_status
+ - SNOMED:has_scale_type
+ - SNOMED:has_severity
+ - SNOMED:has_specimen
+ - SNOMED:has_state_of_matter
+ - SNOMED:has_subject_relationship_context
+ - SNOMED:has_surgical_approach
+ - SNOMED:has_technique
+ - SNOMED:has_temporal_context
+ - SNOMED:has_time_aspect
+ - SNOMED:has_units
+ - UMLS:has_structural_class
+ - UMLS:has_supported_concept_property
+ - UMLS:has_supported_concept_relationship
+ - UMLS:may_be_qualified_by
+ rank: 1000
+ domain: entity
+ slot_uri: biolink:has_attribute
+ alias: has_attribute
+ owner: genome annotation
+ domain_of:
+ - entity
+ - attribute
+ - named thing
+ - organism taxon
+ - information content entity
+ - dataset
+ - physical entity
+ - activity
+ - procedure
+ - material sample
+ - biological entity
+ - gene
+ - genome
+ range: attribute
+ multivalued: true
+ deprecated:
+ name: deprecated
+ definition_uri: https://w3id.org/biolink/vocab/deprecated
+ description: A boolean flag indicating that an entity is no longer considered
+ current or valid.
+ from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
+ exact_mappings:
+ - oboInOwl:ObsoleteClass
+ rank: 1000
+ slot_uri: biolink:deprecated
+ alias: deprecated
+ owner: genome annotation
+ domain_of:
+ - entity
+ - attribute
+ - named thing
+ - organism taxon
+ - information content entity
+ - dataset
+ - physical entity
+ - activity
+ - procedure
+ - material sample
+ - biological entity
+ - gene
+ - genome
+ range: boolean
+ provided by:
+ name: provided by
+ definition_uri: https://w3id.org/biolink/vocab/provided_by
+ description: The value in this node property represents the knowledge provider
+ that created or assembled the node and all of its attributes. Used internally
+ to represent how a particular node made its way into a knowledge provider or
+ graph.
+ from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
+ rank: 1000
+ is_a: node property
+ domain: named thing
+ slot_uri: biolink:provided_by
+ alias: provided_by
+ owner: genome annotation
+ domain_of:
+ - named thing
+ - attribute
+ - organism taxon
+ - information content entity
+ - dataset
+ - physical entity
+ - activity
+ - procedure
+ - material sample
+ - biological entity
+ - gene
+ - genome
+ range: string
+ multivalued: true
+ xref:
+ name: xref
+ definition_uri: https://w3id.org/biolink/vocab/xref
+ description: A database cross reference or alternative identifier for a NamedThing
+ or edge between two NamedThings. This property should point to a database record
+ or webpage that supports the existence of the edge, or gives more detail about
+ the edge. This property can be used on a node or edge to provide multiple URIs
+ or CURIE cross references.
+ in_subset:
+ - translator_minimal
+ from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
+ aliases:
+ - dbxref
+ - Dbxref
+ - DbXref
+ - record_url
+ - source_record_urls
+ narrow_mappings:
+ - gff3:Dbxref
+ - gpi:DB_Xrefs
+ rank: 1000
+ domain: named thing
+ slot_uri: biolink:xref
+ alias: xref
+ owner: genome annotation
+ domain_of:
+ - named thing
+ - gene
+ - attribute
+ - organism taxon
+ - information content entity
+ - dataset
+ - physical entity
+ - activity
+ - procedure
+ - material sample
+ - biological entity
+ - genome
+ range: uriorcurie
+ multivalued: true
+ full name:
+ name: full name
+ definition_uri: https://w3id.org/biolink/vocab/full_name
+ description: a long-form human readable name for a thing
+ from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
+ rank: 1000
+ is_a: node property
+ domain: named thing
+ slot_uri: biolink:full_name
+ alias: full_name
+ owner: genome annotation
+ domain_of:
+ - named thing
+ - attribute
+ - organism taxon
+ - information content entity
+ - dataset
+ - physical entity
+ - activity
+ - procedure
+ - material sample
+ - biological entity
+ - gene
+ - genome
+ range: label type
+ synonym:
+ name: synonym
+ definition_uri: https://w3id.org/biolink/vocab/synonym
+ description: Alternate human-readable names for a thing
+ in_subset:
+ - translator_minimal
+ from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
+ aliases:
+ - alias
+ narrow_mappings:
+ - skos:altLabel
+ - gff3:Alias
+ - AGRKB:synonyms
+ - gpi:DB_Object_Synonyms
+ - HANCESTRO:0330
+ - IAO:0000136
+ - RXNORM:has_tradename
+ rank: 1000
+ is_a: node property
+ domain: named thing
+ slot_uri: biolink:synonym
+ alias: synonym
+ owner: genome annotation
+ domain_of:
+ - named thing
+ - attribute
+ - organism taxon
+ - information content entity
+ - dataset
+ - physical entity
+ - activity
+ - procedure
+ - material sample
+ - biological entity
+ - gene
+ - genome
+ range: label type
+ multivalued: true
+ in taxon:
+ name: in taxon
+ definition_uri: https://w3id.org/biolink/vocab/in_taxon
+ annotations:
+ canonical_predicate:
+ tag: canonical_predicate
+ value: true
+ description: connects an entity to its taxonomic classification. Only certain
+ kinds of entities can be taxonomically classified; see 'thing with taxon'
+ in_subset:
+ - translator_minimal
+ from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
+ aliases:
+ - instance of
+ - is organism source of gene product
+ - organism has gene
+ - gene found in organism
+ - gene product has organism source
+ exact_mappings:
+ - RO:0002162
+ - WIKIDATA_PROPERTY:P703
+ narrow_mappings:
+ - RO:0002160
+ rank: 1000
+ is_a: related to at instance level
+ domain: thing with taxon
+ slot_uri: biolink:in_taxon
+ inherited: true
+ alias: in_taxon
+ owner: genome annotation
+ domain_of:
+ - thing with taxon
+ - biological entity
+ - gene
+ - genome
+ range: organism taxon
+ multivalued: true
+ in taxon label:
+ name: in taxon label
+ definition_uri: https://w3id.org/biolink/vocab/in_taxon_label
+ annotations:
+ denormalized:
+ tag: denormalized
+ value: true
+ description: The human readable scientific name for the taxon of the entity.
+ in_subset:
+ - translator_minimal
+ from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
+ exact_mappings:
+ - WIKIDATA_PROPERTY:P225
+ rank: 1000
+ is_a: node property
+ domain: thing with taxon
+ slot_uri: biolink:in_taxon_label
+ alias: in_taxon_label
+ owner: genome annotation
+ domain_of:
+ - thing with taxon
+ - biological entity
+ - gene
+ - genome
+ range: label type
+ has biological sequence:
+ name: has biological sequence
+ definition_uri: https://w3id.org/biolink/vocab/has_biological_sequence
+ description: connects a genomic feature to its sequence
+ from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
+ rank: 1000
+ is_a: node property
+ domain: named thing
+ slot_uri: biolink:has_biological_sequence
+ alias: has_biological_sequence
+ owner: genome annotation
+ domain_of:
+ - genomic entity
+ - gene
+ - genome
+ range: biological sequence
+
+Genome assembly to contain version and label information
+URI: bican:GenomeAssembly
+| Name | +Cardinality and Range | +Description | +Inheritance | +
|---|---|---|---|
| version | +0..1 String |
++ | direct | +
| strain | +0..1 String |
+The genetic variant or subtype of a species or organism | +direct | +
| in_taxon | +* OrganismTaxon |
+connects an entity to its taxonomic classification | +ThingWithTaxon | +
| in_taxon_label | +0..1 LabelType |
+The human readable scientific name for the taxon of the entity | +ThingWithTaxon | +
| id | +1 String |
+A unique identifier for an entity | +Entity, NamedThing | +
| iri | +0..1 IriType |
+An IRI for an entity | +Entity, NamedThing | +
| category | +* Uriorcurie |
+Name of the high level ontology class in which this entity is categorized | +Entity, NamedThing | +
| type | +* String |
++ | Entity, NamedThing | +
| name | +0..1 LabelType |
+A human-readable name for an attribute or entity | +Entity, NamedThing | +
| description | +0..1 NarrativeText |
+a human-readable description of an entity | +Entity, NamedThing | +
| has_attribute | +* Attribute |
+connects any entity to an attribute | +Entity, NamedThing | +
| deprecated | +0..1 Boolean |
+A boolean flag indicating that an entity is no longer considered current or v... | +Entity, NamedThing | +
| provided_by | +* String |
+The value in this node property represents the knowledge provider that create... | +NamedThing | +
| xref | +* Uriorcurie |
+A database cross reference or alternative identifier for a NamedThing or edge... | +NamedThing | +
| full_name | +0..1 LabelType |
+a long-form human readable name for a thing | +NamedThing | +
| synonym | +* LabelType |
+Alternate human-readable names for a thing | +NamedThing | +
| used by | +used in | +type | +used | +
|---|---|---|---|
| GenomeAnnotation | +reference_assembly | +any_of[range] | +GenomeAssembly | +
| AnnotationCollection | +genome_assemblies | +range | +GenomeAssembly | +
| Mapping Type | +Mapped Value | +
|---|---|
| self | +bican:GenomeAssembly | +
| native | +bican:GenomeAssembly | +
name: genome assembly
+description: Genome assembly to contain version and label information
+from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
+is_a: named thing
+mixins:
+- thing with taxon
+slots:
+- version
+- strain
+
+name: genome assembly
+description: Genome assembly to contain version and label information
+from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
+is_a: named thing
+mixins:
+- thing with taxon
+attributes:
+ version:
+ name: version
+ definition_uri: https://w3id.org/biolink/vocab/version
+ from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
+ broad_mappings:
+ - pav:version
+ - owl:versionInfo
+ rank: 1000
+ is_a: node property
+ domain: dataset
+ slot_uri: biolink:version
+ alias: version
+ owner: genome assembly
+ domain_of:
+ - genome annotation
+ - genome assembly
+ range: string
+ strain:
+ name: strain
+ description: The genetic variant or subtype of a species or organism.
+ from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
+ rank: 1000
+ alias: strain
+ owner: genome assembly
+ domain_of:
+ - genome assembly
+ range: string
+ in taxon:
+ name: in taxon
+ definition_uri: https://w3id.org/biolink/vocab/in_taxon
+ annotations:
+ canonical_predicate:
+ tag: canonical_predicate
+ value: true
+ description: connects an entity to its taxonomic classification. Only certain
+ kinds of entities can be taxonomically classified; see 'thing with taxon'
+ in_subset:
+ - translator_minimal
+ from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
+ aliases:
+ - instance of
+ - is organism source of gene product
+ - organism has gene
+ - gene found in organism
+ - gene product has organism source
+ exact_mappings:
+ - RO:0002162
+ - WIKIDATA_PROPERTY:P703
+ narrow_mappings:
+ - RO:0002160
+ rank: 1000
+ is_a: related to at instance level
+ domain: thing with taxon
+ slot_uri: biolink:in_taxon
+ inherited: true
+ alias: in_taxon
+ owner: genome assembly
+ domain_of:
+ - thing with taxon
+ - biological entity
+ - gene
+ - genome
+ range: organism taxon
+ multivalued: true
+ in taxon label:
+ name: in taxon label
+ definition_uri: https://w3id.org/biolink/vocab/in_taxon_label
+ annotations:
+ denormalized:
+ tag: denormalized
+ value: true
+ description: The human readable scientific name for the taxon of the entity.
+ in_subset:
+ - translator_minimal
+ from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
+ exact_mappings:
+ - WIKIDATA_PROPERTY:P225
+ rank: 1000
+ is_a: node property
+ domain: thing with taxon
+ slot_uri: biolink:in_taxon_label
+ alias: in_taxon_label
+ owner: genome assembly
+ domain_of:
+ - thing with taxon
+ - biological entity
+ - gene
+ - genome
+ range: label type
+ id:
+ name: id
+ definition_uri: https://w3id.org/biolink/vocab/id
+ description: A unique identifier for an entity. Must be either a CURIE shorthand
+ for a URI or a complete URI
+ in_subset:
+ - translator_minimal
+ from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
+ exact_mappings:
+ - AGRKB:primaryId
+ - gff3:ID
+ - gpi:DB_Object_ID
+ rank: 1000
+ domain: entity
+ slot_uri: biolink:id
+ identifier: true
+ alias: id
+ owner: genome assembly
+ domain_of:
+ - ontology class
+ - entity
+ - attribute
+ - named thing
+ - taxonomic rank
+ - organism taxon
+ - information content entity
+ - dataset
+ - physical entity
+ - activity
+ - procedure
+ - material sample
+ - biological entity
+ - gene
+ - genome
+ range: string
+ required: true
+ iri:
+ name: iri
+ definition_uri: https://w3id.org/biolink/vocab/iri
+ description: An IRI for an entity. This is determined by the id using expansion
+ rules.
+ in_subset:
+ - translator_minimal
+ - samples
+ from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
+ exact_mappings:
+ - WIKIDATA_PROPERTY:P854
+ rank: 1000
+ slot_uri: biolink:iri
+ alias: iri
+ owner: genome assembly
+ domain_of:
+ - attribute
+ - entity
+ - named thing
+ - organism taxon
+ - information content entity
+ - dataset
+ - physical entity
+ - activity
+ - procedure
+ - material sample
+ - biological entity
+ - gene
+ - genome
+ range: iri type
+ category:
+ name: category
+ definition_uri: https://w3id.org/biolink/vocab/category
+ description: Name of the high level ontology class in which this entity is categorized.
+ Corresponds to the label for the biolink entity type class. In a neo4j database
+ this MAY correspond to the neo4j label tag. In an RDF database it should be
+ a biolink model class URI. This field is multi-valued. It should include values
+ for ancestors of the biolink class; for example, a protein such as Shh would
+ have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`.
+ In an RDF database, nodes will typically have an rdf:type triples. This can
+ be to the most specific biolink class, or potentially to a class more specific
+ than something in biolink. For example, a sequence feature `f` may have a rdf:type
+ assertion to a SO class such as TF_binding_site, which is more specific than
+ anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity,
+ biolink:NamedThing}
+ in_subset:
+ - translator_minimal
+ from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
+ rank: 1000
+ is_a: type
+ domain: entity
+ slot_uri: biolink:category
+ designates_type: true
+ alias: category
+ owner: genome assembly
+ domain_of:
+ - entity
+ - attribute
+ - named thing
+ - organism taxon
+ - information content entity
+ - dataset
+ - physical entity
+ - activity
+ - procedure
+ - material sample
+ - biological entity
+ - gene
+ - genome
+ is_class_field: true
+ range: uriorcurie
+ multivalued: true
+ type:
+ name: type
+ definition_uri: https://w3id.org/biolink/vocab/type
+ from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
+ mappings:
+ - rdf:type
+ exact_mappings:
+ - gff3:type
+ - gpi:DB_Object_Type
+ rank: 1000
+ domain: entity
+ slot_uri: rdf:type
+ alias: type
+ owner: genome assembly
+ domain_of:
+ - entity
+ - attribute
+ - named thing
+ - organism taxon
+ - information content entity
+ - dataset
+ - physical entity
+ - activity
+ - procedure
+ - material sample
+ - biological entity
+ - gene
+ - genome
+ range: string
+ multivalued: true
+ name:
+ name: name
+ definition_uri: https://w3id.org/biolink/vocab/name
+ description: A human-readable name for an attribute or entity.
+ in_subset:
+ - translator_minimal
+ - samples
+ from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
+ aliases:
+ - label
+ - display name
+ - title
+ mappings:
+ - rdfs:label
+ exact_mappings:
+ - gff3:Name
+ - gpi:DB_Object_Name
+ narrow_mappings:
+ - dct:title
+ - WIKIDATA_PROPERTY:P1476
+ rank: 1000
+ domain: entity
+ slot_uri: rdfs:label
+ alias: name
+ owner: genome assembly
+ domain_of:
+ - attribute
+ - entity
+ - macromolecular machine mixin
+ - named thing
+ - organism taxon
+ - information content entity
+ - dataset
+ - physical entity
+ - activity
+ - procedure
+ - material sample
+ - biological entity
+ - gene or gene product
+ - gene
+ - genome
+ range: label type
+ description:
+ name: description
+ definition_uri: https://w3id.org/biolink/vocab/description
+ description: a human-readable description of an entity
+ in_subset:
+ - translator_minimal
+ from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
+ aliases:
+ - definition
+ mappings:
+ - dct:description
+ exact_mappings:
+ - IAO:0000115
+ - skos:definitions
+ narrow_mappings:
+ - gff3:Description
+ rank: 1000
+ slot_uri: dct:description
+ alias: description
+ owner: genome assembly
+ domain_of:
+ - entity
+ - attribute
+ - named thing
+ - organism taxon
+ - information content entity
+ - dataset
+ - physical entity
+ - activity
+ - procedure
+ - material sample
+ - biological entity
+ - gene
+ - genome
+ range: narrative text
+ has attribute:
+ name: has attribute
+ definition_uri: https://w3id.org/biolink/vocab/has_attribute
+ description: connects any entity to an attribute
+ in_subset:
+ - samples
+ from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
+ exact_mappings:
+ - SIO:000008
+ close_mappings:
+ - OBI:0001927
+ narrow_mappings:
+ - OBAN:association_has_subject_property
+ - OBAN:association_has_object_property
+ - CPT:has_possibly_included_panel_element
+ - DRUGBANK:category
+ - EFO:is_executed_in
+ - HANCESTRO:0301
+ - LOINC:has_action_guidance
+ - LOINC:has_adjustment
+ - LOINC:has_aggregation_view
+ - LOINC:has_approach_guidance
+ - LOINC:has_divisor
+ - LOINC:has_exam
+ - LOINC:has_method
+ - LOINC:has_modality_subtype
+ - LOINC:has_object_guidance
+ - LOINC:has_scale
+ - LOINC:has_suffix
+ - LOINC:has_time_aspect
+ - LOINC:has_time_modifier
+ - LOINC:has_timing_of
+ - NCIT:R88
+ - NCIT:eo_disease_has_property_or_attribute
+ - NCIT:has_data_element
+ - NCIT:has_pharmaceutical_administration_method
+ - NCIT:has_pharmaceutical_basic_dose_form
+ - NCIT:has_pharmaceutical_intended_site
+ - NCIT:has_pharmaceutical_release_characteristics
+ - NCIT:has_pharmaceutical_state_of_matter
+ - NCIT:has_pharmaceutical_transformation
+ - NCIT:is_qualified_by
+ - NCIT:qualifier_applies_to
+ - NCIT:role_has_domain
+ - NCIT:role_has_range
+ - INO:0000154
+ - HANCESTRO:0308
+ - OMIM:has_inheritance_type
+ - orphanet:C016
+ - orphanet:C017
+ - RO:0000053
+ - RO:0000086
+ - RO:0000087
+ - SNOMED:has_access
+ - SNOMED:has_clinical_course
+ - SNOMED:has_count_of_base_of_active_ingredient
+ - SNOMED:has_dose_form_administration_method
+ - SNOMED:has_dose_form_release_characteristic
+ - SNOMED:has_dose_form_transformation
+ - SNOMED:has_finding_context
+ - SNOMED:has_finding_informer
+ - SNOMED:has_inherent_attribute
+ - SNOMED:has_intent
+ - SNOMED:has_interpretation
+ - SNOMED:has_laterality
+ - SNOMED:has_measurement_method
+ - SNOMED:has_method
+ - SNOMED:has_priority
+ - SNOMED:has_procedure_context
+ - SNOMED:has_process_duration
+ - SNOMED:has_property
+ - SNOMED:has_revision_status
+ - SNOMED:has_scale_type
+ - SNOMED:has_severity
+ - SNOMED:has_specimen
+ - SNOMED:has_state_of_matter
+ - SNOMED:has_subject_relationship_context
+ - SNOMED:has_surgical_approach
+ - SNOMED:has_technique
+ - SNOMED:has_temporal_context
+ - SNOMED:has_time_aspect
+ - SNOMED:has_units
+ - UMLS:has_structural_class
+ - UMLS:has_supported_concept_property
+ - UMLS:has_supported_concept_relationship
+ - UMLS:may_be_qualified_by
+ rank: 1000
+ domain: entity
+ slot_uri: biolink:has_attribute
+ alias: has_attribute
+ owner: genome assembly
+ domain_of:
+ - entity
+ - attribute
+ - named thing
+ - organism taxon
+ - information content entity
+ - dataset
+ - physical entity
+ - activity
+ - procedure
+ - material sample
+ - biological entity
+ - gene
+ - genome
+ range: attribute
+ multivalued: true
+ deprecated:
+ name: deprecated
+ definition_uri: https://w3id.org/biolink/vocab/deprecated
+ description: A boolean flag indicating that an entity is no longer considered
+ current or valid.
+ from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
+ exact_mappings:
+ - oboInOwl:ObsoleteClass
+ rank: 1000
+ slot_uri: biolink:deprecated
+ alias: deprecated
+ owner: genome assembly
+ domain_of:
+ - entity
+ - attribute
+ - named thing
+ - organism taxon
+ - information content entity
+ - dataset
+ - physical entity
+ - activity
+ - procedure
+ - material sample
+ - biological entity
+ - gene
+ - genome
+ range: boolean
+ provided by:
+ name: provided by
+ definition_uri: https://w3id.org/biolink/vocab/provided_by
+ description: The value in this node property represents the knowledge provider
+ that created or assembled the node and all of its attributes. Used internally
+ to represent how a particular node made its way into a knowledge provider or
+ graph.
+ from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
+ rank: 1000
+ is_a: node property
+ domain: named thing
+ slot_uri: biolink:provided_by
+ alias: provided_by
+ owner: genome assembly
+ domain_of:
+ - named thing
+ - attribute
+ - organism taxon
+ - information content entity
+ - dataset
+ - physical entity
+ - activity
+ - procedure
+ - material sample
+ - biological entity
+ - gene
+ - genome
+ range: string
+ multivalued: true
+ xref:
+ name: xref
+ definition_uri: https://w3id.org/biolink/vocab/xref
+ description: A database cross reference or alternative identifier for a NamedThing
+ or edge between two NamedThings. This property should point to a database record
+ or webpage that supports the existence of the edge, or gives more detail about
+ the edge. This property can be used on a node or edge to provide multiple URIs
+ or CURIE cross references.
+ in_subset:
+ - translator_minimal
+ from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
+ aliases:
+ - dbxref
+ - Dbxref
+ - DbXref
+ - record_url
+ - source_record_urls
+ narrow_mappings:
+ - gff3:Dbxref
+ - gpi:DB_Xrefs
+ rank: 1000
+ domain: named thing
+ slot_uri: biolink:xref
+ alias: xref
+ owner: genome assembly
+ domain_of:
+ - named thing
+ - gene
+ - attribute
+ - organism taxon
+ - information content entity
+ - dataset
+ - physical entity
+ - activity
+ - procedure
+ - material sample
+ - biological entity
+ - genome
+ range: uriorcurie
+ multivalued: true
+ full name:
+ name: full name
+ definition_uri: https://w3id.org/biolink/vocab/full_name
+ description: a long-form human readable name for a thing
+ from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
+ rank: 1000
+ is_a: node property
+ domain: named thing
+ slot_uri: biolink:full_name
+ alias: full_name
+ owner: genome assembly
+ domain_of:
+ - named thing
+ - attribute
+ - organism taxon
+ - information content entity
+ - dataset
+ - physical entity
+ - activity
+ - procedure
+ - material sample
+ - biological entity
+ - gene
+ - genome
+ range: label type
+ synonym:
+ name: synonym
+ definition_uri: https://w3id.org/biolink/vocab/synonym
+ description: Alternate human-readable names for a thing
+ in_subset:
+ - translator_minimal
+ from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
+ aliases:
+ - alias
+ narrow_mappings:
+ - skos:altLabel
+ - gff3:Alias
+ - AGRKB:synonyms
+ - gpi:DB_Object_Synonyms
+ - HANCESTRO:0330
+ - IAO:0000136
+ - RXNORM:has_tradename
+ rank: 1000
+ is_a: node property
+ domain: named thing
+ slot_uri: biolink:synonym
+ alias: synonym
+ owner: genome assembly
+ domain_of:
+ - named thing
+ - attribute
+ - organism taxon
+ - information content entity
+ - dataset
+ - physical entity
+ - activity
+ - procedure
+ - material sample
+ - biological entity
+ - gene
+ - genome
+ range: label type
+ multivalued: true
+
+| Name | +Cardinality and Range | +Description | +Inheritance | +
|---|---|---|---|
| has_biological_sequence | +0..1 BiologicalSequence |
+connects a genomic feature to its sequence | +direct | +
| mixed into | +description | +
|---|---|
| Gene | +A region (or regions) that includes all of the sequence elements necessary to... | +
| Genome | +A genome is the sum of genetic material within a cell or virion | +
| Mapping Type | +Mapped Value | +
|---|---|
| self | +biolink:GenomicEntity | +
| native | +bican:GenomicEntity | +
| narrow | +STY:T028, GENO:0000897 | +
name: genomic entity
+definition_uri: https://w3id.org/biolink/vocab/GenomicEntity
+in_subset:
+- translator_minimal
+from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
+narrow_mappings:
+- STY:T028
+- GENO:0000897
+mixin: true
+slots:
+- has biological sequence
+class_uri: biolink:GenomicEntity
+
+name: genomic entity
+definition_uri: https://w3id.org/biolink/vocab/GenomicEntity
+in_subset:
+- translator_minimal
+from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
+narrow_mappings:
+- STY:T028
+- GENO:0000897
+mixin: true
+attributes:
+ has biological sequence:
+ name: has biological sequence
+ definition_uri: https://w3id.org/biolink/vocab/has_biological_sequence
+ description: connects a genomic feature to its sequence
+ from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
+ rank: 1000
+ is_a: node property
+ domain: named thing
+ slot_uri: biolink:has_biological_sequence
+ alias: has_biological_sequence
+ owner: genomic entity
+ domain_of:
+ - genomic entity
+ - gene
+ - genome
+ range: biological sequence
+class_uri: biolink:GenomicEntity
+
+An image dataset is versioned release of a multidimensional regular grid of measurements and metadata required for a morphological representation of an entity such as an anatomical structure (ref: OBI_0003327, RRID:SCR_006266)
+URI: AnS:ImageDataset
+| Name | +Cardinality and Range | +Description | +Inheritance | +
|---|---|---|---|
| x_direction | +0..1 ANATOMICALDIRECTION |
+A controlled vocabulary attribute defining the x axis direction in terms of a... | +direct | +
| y_direction | +0..1 ANATOMICALDIRECTION |
+A controlled vocabulary attribute defining the y axis direction in terms of a... | +direct | +
| z_direction | +0..1 ANATOMICALDIRECTION |
+A controlled vocabulary attribute defining the z axis direction in terms of a... | +direct | +
| x_size | +0..1 Integer |
+The number of pixels/voxels (size) along the x axis | +direct | +
| y_size | +0..1 Integer |
+The number of pixels/voxels (size) along the y axis | +direct | +
| z_size | +0..1 Integer |
+The number of pixels/voxels (size) along the y axis | +direct | +
| x_resolution | +0..1 Float |
+The resolution (length / pixel) in along the x axis (numerical value part) | +direct | +
| y_resolution | +0..1 Float |
+The resolution (length / pixel) in along the y axis (numerical value part) | +direct | +
| z_resolution | +0..1 Float |
+The resolution (length / pixel) in along the z axis (numerical value part) | +direct | +
| unit | +0..1 DISTANCEUNIT |
+A controlled vocabulary attribute defining the length unit of the x, y, and z... | +direct | +
| version | +1 String |
++ | VersionedNamedThing | +
| revision_of | +0..1 VersionedNamedThing or ImageDataset or String |
++ | VersionedNamedThing | +
| id | +1 Uriorcurie |
++ | NamedThing | +
| name | +1 String |
++ | NamedThing | +
| description | +1 String |
++ | NamedThing | +
| category | +* Uriorcurie |
++ | NamedThing | +
| used by | +used in | +type | +used | +
|---|---|---|---|
| ImageDataset | +revision_of | +any_of[range] | +ImageDataset | +
| AnatomicalSpace | +measures | +any_of[range] | +ImageDataset | +
| Mapping Type | +Mapped Value | +
|---|---|
| self | +AnS:ImageDataset | +
| native | +AnS:ImageDataset | +
name: ImageDataset
+description: 'An image dataset is versioned release of a multidimensional regular
+ grid of measurements and metadata required for a morphological representation of
+ an entity such as an anatomical structure (ref: OBI_0003327, RRID:SCR_006266)'
+from_schema: https://w3id.org/my-org/anatomical-structure-schema
+is_a: VersionedNamedThing
+slot_usage:
+ revision_of:
+ name: revision_of
+ any_of:
+ - range: ImageDataset
+ - range: string
+attributes:
+ x_direction:
+ name: x_direction
+ description: A controlled vocabulary attribute defining the x axis direction in
+ terms of anatomical direction.
+ from_schema: https://w3id.org/my-org/anatomical-structure-schema
+ rank: 1000
+ domain_of:
+ - ImageDataset
+ range: ANATOMICAL_DIRECTION
+ y_direction:
+ name: y_direction
+ description: A controlled vocabulary attribute defining the y axis direction in
+ terms of anatomical direction.
+ from_schema: https://w3id.org/my-org/anatomical-structure-schema
+ rank: 1000
+ domain_of:
+ - ImageDataset
+ range: ANATOMICAL_DIRECTION
+ z_direction:
+ name: z_direction
+ description: A controlled vocabulary attribute defining the z axis direction in
+ terms of anatomical direction.
+ from_schema: https://w3id.org/my-org/anatomical-structure-schema
+ rank: 1000
+ domain_of:
+ - ImageDataset
+ range: ANATOMICAL_DIRECTION
+ x_size:
+ name: x_size
+ description: The number of pixels/voxels (size) along the x axis.
+ from_schema: https://w3id.org/my-org/anatomical-structure-schema
+ rank: 1000
+ domain_of:
+ - ImageDataset
+ range: integer
+ minimum_value: 1
+ y_size:
+ name: y_size
+ description: The number of pixels/voxels (size) along the y axis.
+ from_schema: https://w3id.org/my-org/anatomical-structure-schema
+ rank: 1000
+ domain_of:
+ - ImageDataset
+ range: integer
+ minimum_value: 1
+ z_size:
+ name: z_size
+ description: The number of pixels/voxels (size) along the y axis.
+ from_schema: https://w3id.org/my-org/anatomical-structure-schema
+ rank: 1000
+ domain_of:
+ - ImageDataset
+ range: integer
+ minimum_value: 1
+ x_resolution:
+ name: x_resolution
+ description: The resolution (length / pixel) in along the x axis (numerical value
+ part).
+ from_schema: https://w3id.org/my-org/anatomical-structure-schema
+ rank: 1000
+ domain_of:
+ - ImageDataset
+ range: float
+ structured_pattern:
+ syntax: '{PositiveFloat}'
+ y_resolution:
+ name: y_resolution
+ description: The resolution (length / pixel) in along the y axis (numerical value
+ part).
+ from_schema: https://w3id.org/my-org/anatomical-structure-schema
+ rank: 1000
+ domain_of:
+ - ImageDataset
+ range: float
+ structured_pattern:
+ syntax: '{PositiveFloat}'
+ z_resolution:
+ name: z_resolution
+ description: The resolution (length / pixel) in along the z axis (numerical value
+ part).
+ from_schema: https://w3id.org/my-org/anatomical-structure-schema
+ rank: 1000
+ domain_of:
+ - ImageDataset
+ range: float
+ structured_pattern:
+ syntax: '{PositiveFloat}'
+ unit:
+ name: unit
+ description: A controlled vocabulary attribute defining the length unit of the
+ x, y, and z resolution values.
+ from_schema: https://w3id.org/my-org/anatomical-structure-schema
+ rank: 1000
+ domain_of:
+ - ImageDataset
+ range: DISTANCE_UNIT
+
+name: ImageDataset
+description: 'An image dataset is versioned release of a multidimensional regular
+ grid of measurements and metadata required for a morphological representation of
+ an entity such as an anatomical structure (ref: OBI_0003327, RRID:SCR_006266)'
+from_schema: https://w3id.org/my-org/anatomical-structure-schema
+is_a: VersionedNamedThing
+slot_usage:
+ revision_of:
+ name: revision_of
+ any_of:
+ - range: ImageDataset
+ - range: string
+attributes:
+ x_direction:
+ name: x_direction
+ description: A controlled vocabulary attribute defining the x axis direction in
+ terms of anatomical direction.
+ from_schema: https://w3id.org/my-org/anatomical-structure-schema
+ rank: 1000
+ alias: x_direction
+ owner: ImageDataset
+ domain_of:
+ - ImageDataset
+ range: ANATOMICAL_DIRECTION
+ y_direction:
+ name: y_direction
+ description: A controlled vocabulary attribute defining the y axis direction in
+ terms of anatomical direction.
+ from_schema: https://w3id.org/my-org/anatomical-structure-schema
+ rank: 1000
+ alias: y_direction
+ owner: ImageDataset
+ domain_of:
+ - ImageDataset
+ range: ANATOMICAL_DIRECTION
+ z_direction:
+ name: z_direction
+ description: A controlled vocabulary attribute defining the z axis direction in
+ terms of anatomical direction.
+ from_schema: https://w3id.org/my-org/anatomical-structure-schema
+ rank: 1000
+ alias: z_direction
+ owner: ImageDataset
+ domain_of:
+ - ImageDataset
+ range: ANATOMICAL_DIRECTION
+ x_size:
+ name: x_size
+ description: The number of pixels/voxels (size) along the x axis.
+ from_schema: https://w3id.org/my-org/anatomical-structure-schema
+ rank: 1000
+ alias: x_size
+ owner: ImageDataset
+ domain_of:
+ - ImageDataset
+ range: integer
+ minimum_value: 1
+ y_size:
+ name: y_size
+ description: The number of pixels/voxels (size) along the y axis.
+ from_schema: https://w3id.org/my-org/anatomical-structure-schema
+ rank: 1000
+ alias: y_size
+ owner: ImageDataset
+ domain_of:
+ - ImageDataset
+ range: integer
+ minimum_value: 1
+ z_size:
+ name: z_size
+ description: The number of pixels/voxels (size) along the y axis.
+ from_schema: https://w3id.org/my-org/anatomical-structure-schema
+ rank: 1000
+ alias: z_size
+ owner: ImageDataset
+ domain_of:
+ - ImageDataset
+ range: integer
+ minimum_value: 1
+ x_resolution:
+ name: x_resolution
+ description: The resolution (length / pixel) in along the x axis (numerical value
+ part).
+ from_schema: https://w3id.org/my-org/anatomical-structure-schema
+ rank: 1000
+ alias: x_resolution
+ owner: ImageDataset
+ domain_of:
+ - ImageDataset
+ range: float
+ structured_pattern:
+ syntax: '{PositiveFloat}'
+ y_resolution:
+ name: y_resolution
+ description: The resolution (length / pixel) in along the y axis (numerical value
+ part).
+ from_schema: https://w3id.org/my-org/anatomical-structure-schema
+ rank: 1000
+ alias: y_resolution
+ owner: ImageDataset
+ domain_of:
+ - ImageDataset
+ range: float
+ structured_pattern:
+ syntax: '{PositiveFloat}'
+ z_resolution:
+ name: z_resolution
+ description: The resolution (length / pixel) in along the z axis (numerical value
+ part).
+ from_schema: https://w3id.org/my-org/anatomical-structure-schema
+ rank: 1000
+ alias: z_resolution
+ owner: ImageDataset
+ domain_of:
+ - ImageDataset
+ range: float
+ structured_pattern:
+ syntax: '{PositiveFloat}'
+ unit:
+ name: unit
+ description: A controlled vocabulary attribute defining the length unit of the
+ x, y, and z resolution values.
+ from_schema: https://w3id.org/my-org/anatomical-structure-schema
+ rank: 1000
+ alias: unit
+ owner: ImageDataset
+ domain_of:
+ - ImageDataset
+ range: DISTANCE_UNIT
+ version:
+ name: version
+ from_schema: https://w3id.org/my-org/anatomical-structure-schema
+ rank: 1000
+ alias: version
+ owner: ImageDataset
+ domain_of:
+ - VersionedNamedThing
+ range: string
+ required: true
+ revision_of:
+ name: revision_of
+ from_schema: https://w3id.org/my-org/anatomical-structure-schema
+ rank: 1000
+ alias: revision_of
+ owner: ImageDataset
+ domain_of:
+ - VersionedNamedThing
+ range: VersionedNamedThing
+ any_of:
+ - range: ImageDataset
+ - range: string
+ id:
+ name: id
+ from_schema: https://w3id.org/my-org/anatomical-structure-schema
+ rank: 1000
+ identifier: true
+ alias: id
+ owner: ImageDataset
+ domain_of:
+ - NamedThing
+ range: uriorcurie
+ required: true
+ name:
+ name: name
+ from_schema: https://w3id.org/my-org/anatomical-structure-schema
+ rank: 1000
+ alias: name
+ owner: ImageDataset
+ domain_of:
+ - NamedThing
+ range: string
+ required: true
+ description:
+ name: description
+ from_schema: https://w3id.org/my-org/anatomical-structure-schema
+ rank: 1000
+ alias: description
+ owner: ImageDataset
+ domain_of:
+ - NamedThing
+ range: string
+ required: true
+ category:
+ name: category
+ from_schema: https://w3id.org/my-org/anatomical-structure-schema
+ rank: 1000
+ designates_type: true
+ alias: category
+ owner: ImageDataset
+ domain_of:
+ - NamedThing
+ is_class_field: true
+ range: uriorcurie
+ multivalued: true
+
+a piece of information that typically describes some topic of discourse or is used as support.
+URI: biolink:InformationContentEntity
+| Name | +Cardinality and Range | +Description | +Inheritance | +
|---|---|---|---|
| id | +1 String |
+A unique identifier for an entity | +direct | +
| iri | +0..1 IriType |
+An IRI for an entity | +direct | +
| category | +* Uriorcurie |
+Name of the high level ontology class in which this entity is categorized | +direct | +
| type | +* String |
++ | direct | +
| name | +0..1 LabelType |
+A human-readable name for an attribute or entity | +direct | +
| description | +0..1 NarrativeText |
+a human-readable description of an entity | +direct | +
| has_attribute | +* Attribute |
+connects any entity to an attribute | +direct | +
| deprecated | +0..1 Boolean |
+A boolean flag indicating that an entity is no longer considered current or v... | +direct | +
| provided_by | +* String |
+The value in this node property represents the knowledge provider that create... | +direct | +
| xref | +* Uriorcurie |
+A database cross reference or alternative identifier for a NamedThing or edge... | +direct | +
| full_name | +0..1 LabelType |
+a long-form human readable name for a thing | +direct | +
| synonym | +* LabelType |
+Alternate human-readable names for a thing | +direct | +
| license | +0..1 String |
++ | direct | +
| rights | +0..1 String |
++ | direct | +
| format | +0..1 String |
++ | direct | +
| creation_date | +0..1 Date |
+date on which an entity was created | +direct | +
| used by | +used in | +type | +used | +
|---|---|---|---|
| InformationContentEntity | +license | +domain | +InformationContentEntity | +
| InformationContentEntity | +rights | +domain | +InformationContentEntity | +
| InformationContentEntity | +format | +domain | +InformationContentEntity | +
| Dataset | +license | +domain | +InformationContentEntity | +
| Dataset | +rights | +domain | +InformationContentEntity | +
| Dataset | +format | +domain | +InformationContentEntity | +
Instances of this class should have identifiers with one of the following prefixes:
+| Mapping Type | +Mapped Value | +
|---|---|
| self | +biolink:InformationContentEntity | +
| native | +bican:InformationContentEntity | +
| exact | +IAO:0000030 | +
| narrow | +UMLSSG:CONC, STY:T077, STY:T078, STY:T079, STY:T080, STY:T081, STY:T082, STY:T089, STY:T102, STY:T169, STY:T171, STY:T185 | +
name: information content entity
+id_prefixes:
+- doi
+definition_uri: https://w3id.org/biolink/vocab/InformationContentEntity
+description: a piece of information that typically describes some topic of discourse
+ or is used as support.
+from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
+aliases:
+- information
+- information artefact
+- information entity
+exact_mappings:
+- IAO:0000030
+narrow_mappings:
+- UMLSSG:CONC
+- STY:T077
+- STY:T078
+- STY:T079
+- STY:T080
+- STY:T081
+- STY:T082
+- STY:T089
+- STY:T102
+- STY:T169
+- STY:T171
+- STY:T185
+is_a: named thing
+abstract: true
+slots:
+- id
+- iri
+- category
+- type
+- name
+- description
+- has attribute
+- deprecated
+- provided by
+- xref
+- full name
+- synonym
+- license
+- rights
+- format
+- creation date
+class_uri: biolink:InformationContentEntity
+
+name: information content entity
+id_prefixes:
+- doi
+definition_uri: https://w3id.org/biolink/vocab/InformationContentEntity
+description: a piece of information that typically describes some topic of discourse
+ or is used as support.
+from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
+aliases:
+- information
+- information artefact
+- information entity
+exact_mappings:
+- IAO:0000030
+narrow_mappings:
+- UMLSSG:CONC
+- STY:T077
+- STY:T078
+- STY:T079
+- STY:T080
+- STY:T081
+- STY:T082
+- STY:T089
+- STY:T102
+- STY:T169
+- STY:T171
+- STY:T185
+is_a: named thing
+abstract: true
+attributes:
+ id:
+ name: id
+ definition_uri: https://w3id.org/biolink/vocab/id
+ description: A unique identifier for an entity. Must be either a CURIE shorthand
+ for a URI or a complete URI
+ in_subset:
+ - translator_minimal
+ from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
+ exact_mappings:
+ - AGRKB:primaryId
+ - gff3:ID
+ - gpi:DB_Object_ID
+ rank: 1000
+ domain: entity
+ slot_uri: biolink:id
+ identifier: true
+ alias: id
+ owner: information content entity
+ domain_of:
+ - ontology class
+ - entity
+ - attribute
+ - named thing
+ - taxonomic rank
+ - organism taxon
+ - information content entity
+ - dataset
+ - physical entity
+ - activity
+ - procedure
+ - material sample
+ - biological entity
+ - gene
+ - genome
+ range: string
+ required: true
+ iri:
+ name: iri
+ definition_uri: https://w3id.org/biolink/vocab/iri
+ description: An IRI for an entity. This is determined by the id using expansion
+ rules.
+ in_subset:
+ - translator_minimal
+ - samples
+ from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
+ exact_mappings:
+ - WIKIDATA_PROPERTY:P854
+ rank: 1000
+ slot_uri: biolink:iri
+ alias: iri
+ owner: information content entity
+ domain_of:
+ - attribute
+ - entity
+ - named thing
+ - organism taxon
+ - information content entity
+ - dataset
+ - physical entity
+ - activity
+ - procedure
+ - material sample
+ - biological entity
+ - gene
+ - genome
+ range: iri type
+ category:
+ name: category
+ definition_uri: https://w3id.org/biolink/vocab/category
+ description: Name of the high level ontology class in which this entity is categorized.
+ Corresponds to the label for the biolink entity type class. In a neo4j database
+ this MAY correspond to the neo4j label tag. In an RDF database it should be
+ a biolink model class URI. This field is multi-valued. It should include values
+ for ancestors of the biolink class; for example, a protein such as Shh would
+ have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`.
+ In an RDF database, nodes will typically have an rdf:type triples. This can
+ be to the most specific biolink class, or potentially to a class more specific
+ than something in biolink. For example, a sequence feature `f` may have a rdf:type
+ assertion to a SO class such as TF_binding_site, which is more specific than
+ anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity,
+ biolink:NamedThing}
+ in_subset:
+ - translator_minimal
+ from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
+ rank: 1000
+ is_a: type
+ domain: entity
+ slot_uri: biolink:category
+ designates_type: true
+ alias: category
+ owner: information content entity
+ domain_of:
+ - entity
+ - attribute
+ - named thing
+ - organism taxon
+ - information content entity
+ - dataset
+ - physical entity
+ - activity
+ - procedure
+ - material sample
+ - biological entity
+ - gene
+ - genome
+ is_class_field: true
+ range: uriorcurie
+ multivalued: true
+ type:
+ name: type
+ definition_uri: https://w3id.org/biolink/vocab/type
+ from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
+ mappings:
+ - rdf:type
+ exact_mappings:
+ - gff3:type
+ - gpi:DB_Object_Type
+ rank: 1000
+ domain: entity
+ slot_uri: rdf:type
+ alias: type
+ owner: information content entity
+ domain_of:
+ - entity
+ - attribute
+ - named thing
+ - organism taxon
+ - information content entity
+ - dataset
+ - physical entity
+ - activity
+ - procedure
+ - material sample
+ - biological entity
+ - gene
+ - genome
+ range: string
+ multivalued: true
+ name:
+ name: name
+ definition_uri: https://w3id.org/biolink/vocab/name
+ description: A human-readable name for an attribute or entity.
+ in_subset:
+ - translator_minimal
+ - samples
+ from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
+ aliases:
+ - label
+ - display name
+ - title
+ mappings:
+ - rdfs:label
+ exact_mappings:
+ - gff3:Name
+ - gpi:DB_Object_Name
+ narrow_mappings:
+ - dct:title
+ - WIKIDATA_PROPERTY:P1476
+ rank: 1000
+ domain: entity
+ slot_uri: rdfs:label
+ alias: name
+ owner: information content entity
+ domain_of:
+ - attribute
+ - entity
+ - macromolecular machine mixin
+ - named thing
+ - organism taxon
+ - information content entity
+ - dataset
+ - physical entity
+ - activity
+ - procedure
+ - material sample
+ - biological entity
+ - gene or gene product
+ - gene
+ - genome
+ range: label type
+ description:
+ name: description
+ definition_uri: https://w3id.org/biolink/vocab/description
+ description: a human-readable description of an entity
+ in_subset:
+ - translator_minimal
+ from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
+ aliases:
+ - definition
+ mappings:
+ - dct:description
+ exact_mappings:
+ - IAO:0000115
+ - skos:definitions
+ narrow_mappings:
+ - gff3:Description
+ rank: 1000
+ slot_uri: dct:description
+ alias: description
+ owner: information content entity
+ domain_of:
+ - entity
+ - attribute
+ - named thing
+ - organism taxon
+ - information content entity
+ - dataset
+ - physical entity
+ - activity
+ - procedure
+ - material sample
+ - biological entity
+ - gene
+ - genome
+ range: narrative text
+ has attribute:
+ name: has attribute
+ definition_uri: https://w3id.org/biolink/vocab/has_attribute
+ description: connects any entity to an attribute
+ in_subset:
+ - samples
+ from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
+ exact_mappings:
+ - SIO:000008
+ close_mappings:
+ - OBI:0001927
+ narrow_mappings:
+ - OBAN:association_has_subject_property
+ - OBAN:association_has_object_property
+ - CPT:has_possibly_included_panel_element
+ - DRUGBANK:category
+ - EFO:is_executed_in
+ - HANCESTRO:0301
+ - LOINC:has_action_guidance
+ - LOINC:has_adjustment
+ - LOINC:has_aggregation_view
+ - LOINC:has_approach_guidance
+ - LOINC:has_divisor
+ - LOINC:has_exam
+ - LOINC:has_method
+ - LOINC:has_modality_subtype
+ - LOINC:has_object_guidance
+ - LOINC:has_scale
+ - LOINC:has_suffix
+ - LOINC:has_time_aspect
+ - LOINC:has_time_modifier
+ - LOINC:has_timing_of
+ - NCIT:R88
+ - NCIT:eo_disease_has_property_or_attribute
+ - NCIT:has_data_element
+ - NCIT:has_pharmaceutical_administration_method
+ - NCIT:has_pharmaceutical_basic_dose_form
+ - NCIT:has_pharmaceutical_intended_site
+ - NCIT:has_pharmaceutical_release_characteristics
+ - NCIT:has_pharmaceutical_state_of_matter
+ - NCIT:has_pharmaceutical_transformation
+ - NCIT:is_qualified_by
+ - NCIT:qualifier_applies_to
+ - NCIT:role_has_domain
+ - NCIT:role_has_range
+ - INO:0000154
+ - HANCESTRO:0308
+ - OMIM:has_inheritance_type
+ - orphanet:C016
+ - orphanet:C017
+ - RO:0000053
+ - RO:0000086
+ - RO:0000087
+ - SNOMED:has_access
+ - SNOMED:has_clinical_course
+ - SNOMED:has_count_of_base_of_active_ingredient
+ - SNOMED:has_dose_form_administration_method
+ - SNOMED:has_dose_form_release_characteristic
+ - SNOMED:has_dose_form_transformation
+ - SNOMED:has_finding_context
+ - SNOMED:has_finding_informer
+ - SNOMED:has_inherent_attribute
+ - SNOMED:has_intent
+ - SNOMED:has_interpretation
+ - SNOMED:has_laterality
+ - SNOMED:has_measurement_method
+ - SNOMED:has_method
+ - SNOMED:has_priority
+ - SNOMED:has_procedure_context
+ - SNOMED:has_process_duration
+ - SNOMED:has_property
+ - SNOMED:has_revision_status
+ - SNOMED:has_scale_type
+ - SNOMED:has_severity
+ - SNOMED:has_specimen
+ - SNOMED:has_state_of_matter
+ - SNOMED:has_subject_relationship_context
+ - SNOMED:has_surgical_approach
+ - SNOMED:has_technique
+ - SNOMED:has_temporal_context
+ - SNOMED:has_time_aspect
+ - SNOMED:has_units
+ - UMLS:has_structural_class
+ - UMLS:has_supported_concept_property
+ - UMLS:has_supported_concept_relationship
+ - UMLS:may_be_qualified_by
+ rank: 1000
+ domain: entity
+ slot_uri: biolink:has_attribute
+ alias: has_attribute
+ owner: information content entity
+ domain_of:
+ - entity
+ - attribute
+ - named thing
+ - organism taxon
+ - information content entity
+ - dataset
+ - physical entity
+ - activity
+ - procedure
+ - material sample
+ - biological entity
+ - gene
+ - genome
+ range: attribute
+ multivalued: true
+ deprecated:
+ name: deprecated
+ definition_uri: https://w3id.org/biolink/vocab/deprecated
+ description: A boolean flag indicating that an entity is no longer considered
+ current or valid.
+ from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
+ exact_mappings:
+ - oboInOwl:ObsoleteClass
+ rank: 1000
+ slot_uri: biolink:deprecated
+ alias: deprecated
+ owner: information content entity
+ domain_of:
+ - entity
+ - attribute
+ - named thing
+ - organism taxon
+ - information content entity
+ - dataset
+ - physical entity
+ - activity
+ - procedure
+ - material sample
+ - biological entity
+ - gene
+ - genome
+ range: boolean
+ provided by:
+ name: provided by
+ definition_uri: https://w3id.org/biolink/vocab/provided_by
+ description: The value in this node property represents the knowledge provider
+ that created or assembled the node and all of its attributes. Used internally
+ to represent how a particular node made its way into a knowledge provider or
+ graph.
+ from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
+ rank: 1000
+ is_a: node property
+ domain: named thing
+ slot_uri: biolink:provided_by
+ alias: provided_by
+ owner: information content entity
+ domain_of:
+ - named thing
+ - attribute
+ - organism taxon
+ - information content entity
+ - dataset
+ - physical entity
+ - activity
+ - procedure
+ - material sample
+ - biological entity
+ - gene
+ - genome
+ range: string
+ multivalued: true
+ xref:
+ name: xref
+ definition_uri: https://w3id.org/biolink/vocab/xref
+ description: A database cross reference or alternative identifier for a NamedThing
+ or edge between two NamedThings. This property should point to a database record
+ or webpage that supports the existence of the edge, or gives more detail about
+ the edge. This property can be used on a node or edge to provide multiple URIs
+ or CURIE cross references.
+ in_subset:
+ - translator_minimal
+ from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
+ aliases:
+ - dbxref
+ - Dbxref
+ - DbXref
+ - record_url
+ - source_record_urls
+ narrow_mappings:
+ - gff3:Dbxref
+ - gpi:DB_Xrefs
+ rank: 1000
+ domain: named thing
+ slot_uri: biolink:xref
+ alias: xref
+ owner: information content entity
+ domain_of:
+ - named thing
+ - gene
+ - attribute
+ - organism taxon
+ - information content entity
+ - dataset
+ - physical entity
+ - activity
+ - procedure
+ - material sample
+ - biological entity
+ - genome
+ range: uriorcurie
+ multivalued: true
+ full name:
+ name: full name
+ definition_uri: https://w3id.org/biolink/vocab/full_name
+ description: a long-form human readable name for a thing
+ from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
+ rank: 1000
+ is_a: node property
+ domain: named thing
+ slot_uri: biolink:full_name
+ alias: full_name
+ owner: information content entity
+ domain_of:
+ - named thing
+ - attribute
+ - organism taxon
+ - information content entity
+ - dataset
+ - physical entity
+ - activity
+ - procedure
+ - material sample
+ - biological entity
+ - gene
+ - genome
+ range: label type
+ synonym:
+ name: synonym
+ definition_uri: https://w3id.org/biolink/vocab/synonym
+ description: Alternate human-readable names for a thing
+ in_subset:
+ - translator_minimal
+ from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
+ aliases:
+ - alias
+ narrow_mappings:
+ - skos:altLabel
+ - gff3:Alias
+ - AGRKB:synonyms
+ - gpi:DB_Object_Synonyms
+ - HANCESTRO:0330
+ - IAO:0000136
+ - RXNORM:has_tradename
+ rank: 1000
+ is_a: node property
+ domain: named thing
+ slot_uri: biolink:synonym
+ alias: synonym
+ owner: information content entity
+ domain_of:
+ - named thing
+ - attribute
+ - organism taxon
+ - information content entity
+ - dataset
+ - physical entity
+ - activity
+ - procedure
+ - material sample
+ - biological entity
+ - gene
+ - genome
+ range: label type
+ multivalued: true
+ license:
+ name: license
+ definition_uri: https://w3id.org/biolink/vocab/license
+ from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
+ exact_mappings:
+ - dct:license
+ narrow_mappings:
+ - WIKIDATA_PROPERTY:P275
+ rank: 1000
+ is_a: node property
+ domain: information content entity
+ slot_uri: biolink:license
+ alias: license
+ owner: information content entity
+ domain_of:
+ - information content entity
+ - dataset
+ range: string
+ rights:
+ name: rights
+ definition_uri: https://w3id.org/biolink/vocab/rights
+ from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
+ exact_mappings:
+ - dct:rights
+ rank: 1000
+ is_a: node property
+ domain: information content entity
+ slot_uri: biolink:rights
+ alias: rights
+ owner: information content entity
+ domain_of:
+ - information content entity
+ - dataset
+ range: string
+ format:
+ name: format
+ definition_uri: https://w3id.org/biolink/vocab/format
+ from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
+ exact_mappings:
+ - dct:format
+ - WIKIDATA_PROPERTY:P2701
+ rank: 1000
+ is_a: node property
+ domain: information content entity
+ slot_uri: biolink:format
+ alias: format
+ owner: information content entity
+ domain_of:
+ - information content entity
+ - dataset
+ range: string
+ creation date:
+ name: creation date
+ definition_uri: https://w3id.org/biolink/vocab/creation_date
+ description: date on which an entity was created. This can be applied to nodes
+ or edges
+ from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
+ aliases:
+ - publication date
+ exact_mappings:
+ - dct:createdOn
+ - WIKIDATA_PROPERTY:P577
+ rank: 1000
+ is_a: node property
+ domain: named thing
+ slot_uri: biolink:creation_date
+ alias: creation_date
+ owner: information content entity
+ domain_of:
+ - information content entity
+ - dataset
+ range: date
+class_uri: biolink:InformationContentEntity
+
+An integer
+URI: xsd:integer
+ +| Mapping Type | +Mapped Value | +
|---|---|
| self | +xsd:integer | +
| native | +bican:integer | +
| exact | +schema:Integer | +
An IRI
+URI: xsd:anyURI
+ +| Mapping Type | +Mapped Value | +
|---|---|
| self | +xsd:anyURI | +
| native | +bican:iri_type | +
A string encoding a JSON Path. The value of the string MUST conform to JSON Point syntax and SHOULD dereference to zero or more valid objects within the current instance document when encoded in tree form.
+URI: xsd:string
+ +| Mapping Type | +Mapped Value | +
|---|---|
| self | +xsd:string | +
| native | +bican:jsonpath | +
A string encoding a JSON Pointer. The value of the string MUST conform to JSON Point syntax and SHOULD dereference to a valid object within the current instance document when encoded in tree form.
+URI: xsd:string
+ +| Mapping Type | +Mapped Value | +
|---|---|
| self | +xsd:string | +
| native | +bican:jsonpointer | +
A string that provides a human-readable name for an entity
+URI: xsd:string
+ +| Mapping Type | +Mapped Value | +
|---|---|
| self | +xsd:string | +
| native | +bican:label_type | +
A collection of fragmented and barcode-indexed DNA molecules for sequencing. An index or barcode is typically introduced to enable identification of library origin to allow libraries to be pooled together for sequencing.
+URI: bican:Library
+| Name | +Cardinality and Range | +Description | +Inheritance | +
|---|---|---|---|
| was_generated_by | +0..1 LibraryConstruction |
+The library construction process from which the library was generated by | +direct | +
| was_derived_from | +0..1 ProvEntity or BarcodedCellSample or AmplifiedCdna |
+The input barcoded cell sample or amplified cDNA from which the library was d... | +direct | +
| name | +0..1 LabelType |
+Name of a library, which is a collection of fragmented and barcode-indexed DN... | +direct | +
| average_size_bp | +0..1 Integer |
+Average size of the library in terms of base pairs | +direct | +
| concentration_nm | +0..1 Float |
+Concentration of library in terms of nM (nMol/L) | +direct | +
| pass_fail_result | +0..1 LibraryPrepPassFail |
+Pass or Fail result based on qualitative assessment of library yield and size | +direct | +
| quantity_fmol | +0..1 Float |
+Amount of library generated in terms of femtomoles | +direct | +
| quantity_ng | +0..1 Float |
+Amount of library generated in terms of nanograms | +direct | +
| r1_r2_index | +0..1 LibraryR1R2Index |
+Name of the pair of library indexes used for sequencing | +direct | +
| id | +1 String |
+A unique identifier for an entity | +NamedThing, PhysicalEntity, MaterialSample, Entity | +
| iri | +0..1 IriType |
+An IRI for an entity | +NamedThing, PhysicalEntity, MaterialSample, Entity | +
| category | +* Uriorcurie |
+Name of the high level ontology class in which this entity is categorized | +NamedThing, PhysicalEntity, MaterialSample, Entity | +
| type | +* String |
++ | NamedThing, PhysicalEntity, MaterialSample, Entity | +
| description | +0..1 NarrativeText |
+a human-readable description of an entity | +NamedThing, PhysicalEntity, MaterialSample, Entity | +
| has_attribute | +* Attribute |
+connects any entity to an attribute | +NamedThing, PhysicalEntity, MaterialSample, Entity | +
| deprecated | +0..1 Boolean |
+A boolean flag indicating that an entity is no longer considered current or v... | +NamedThing, PhysicalEntity, MaterialSample, Entity | +
| provided_by | +* String |
+The value in this node property represents the knowledge provider that create... | +NamedThing, PhysicalEntity, MaterialSample | +
| xref | +* Uriorcurie |
+A database cross reference or alternative identifier for a NamedThing or edge... | +NamedThing, PhysicalEntity, MaterialSample | +
| full_name | +0..1 LabelType |
+a long-form human readable name for a thing | +NamedThing, PhysicalEntity, MaterialSample | +
| synonym | +* LabelType |
+Alternate human-readable names for a thing | +NamedThing, PhysicalEntity, MaterialSample | +
| used by | +used in | +type | +used | +
|---|---|---|---|
| LibraryAliquot | +was_derived_from | +range | +Library | +
| Mapping Type | +Mapped Value | +
|---|---|
| self | +bican:Library | +
| native | +bican:Library | +
| exact | +NIMP:Library | +
name: Library
+description: A collection of fragmented and barcode-indexed DNA molecules for sequencing.
+ An index or barcode is typically introduced to enable identification of library
+ origin to allow libraries to be pooled together for sequencing.
+in_subset:
+- bican
+- library_generation
+from_schema: https://identifiers.org/brain-bican/library-generation-schema
+exact_mappings:
+- NIMP:Library
+is_a: material sample
+mixins:
+- ProvEntity
+slots:
+- was_generated_by
+- was_derived_from
+- name
+slot_usage:
+ was_generated_by:
+ name: was_generated_by
+ description: The library construction process from which the library was generated
+ by.
+ range: LibraryConstruction
+ was_derived_from:
+ name: was_derived_from
+ description: The input barcoded cell sample or amplified cDNA from which the library
+ was derived from.
+ exact_mappings:
+ - NIMP:has_parent
+ exactly_one_of:
+ - range: BarcodedCellSample
+ - range: AmplifiedCdna
+ name:
+ name: name
+ description: Name of a library, which is a collection of fragmented and barcode-indexed
+ DNA molecules for sequencing. An index or barcode is typically introduced to
+ enable identification of library origin to allow libraries to be pooled together
+ for sequencing.
+ exact_mappings:
+ - NIMP:PD-AJJUCC35
+ slot_uri: bican:f717e254-3630-4342-be7b-4d56376e7afe
+ category:
+ name: category
+ pattern: ^bican:[A-Z][A-Za-z]+$
+attributes:
+ average_size_bp:
+ name: average_size_bp
+ local_names:
+ NIMP:
+ local_name_source: NIMP
+ local_name_value: library_avg_size_bp
+ description: Average size of the library in terms of base pairs. This is used
+ to calculate the molarity before pooling and sequencing.
+ in_subset:
+ - analysis
+ from_schema: https://identifiers.org/brain-bican/library-generation-schema
+ exact_mappings:
+ - NIMP:PD-VJVJLC46
+ rank: 1000
+ slot_uri: bican:f851eba9-56d1-4472-9d0c-d7f8bc33000a
+ alias: library avg size bp
+ domain_of:
+ - Library
+ range: integer
+ concentration_nm:
+ name: concentration_nm
+ local_names:
+ NIMP:
+ local_name_source: NIMP
+ local_name_value: library_concentration_nm
+ description: Concentration of library in terms of nM (nMol/L). Number of molecules
+ is needed for accurate pooling of the libraries and for generating the number
+ of target reads/cell in sequencing.
+ from_schema: https://identifiers.org/brain-bican/library-generation-schema
+ exact_mappings:
+ - NIMP:PD-DCDCLD43
+ rank: 1000
+ slot_uri: bican:90805b3f-f380-4f23-b159-e7eaa0c8f052
+ alias: library concentration nm
+ domain_of:
+ - Library
+ range: float
+ pass_fail_result:
+ name: pass_fail_result
+ local_names:
+ NIMP:
+ local_name_source: NIMP
+ local_name_value: library_prep_pass_fail
+ description: Pass or Fail result based on qualitative assessment of library yield
+ and size.
+ in_subset:
+ - analysis
+ from_schema: https://identifiers.org/brain-bican/library-generation-schema
+ exact_mappings:
+ - NIMP:PD-QHQHQB42
+ slot_uri: bican:6817ede2-7ead-402d-9dbc-131aca627c6c
+ alias: library prep pass-fail
+ domain_of:
+ - AmplifiedCdna
+ - Library
+ range: library_prep_pass_fail
+ quantity_fmol:
+ name: quantity_fmol
+ local_names:
+ NIMP:
+ local_name_source: NIMP
+ local_name_value: library_quantification_fmol
+ description: Amount of library generated in terms of femtomoles
+ in_subset:
+ - analysis
+ from_schema: https://identifiers.org/brain-bican/library-generation-schema
+ exact_mappings:
+ - NIMP:PD-JYJYDK42
+ rank: 1000
+ slot_uri: bican:4c09ada7-c116-48bc-8fb1-0dcf5c4b939a
+ alias: library quantification fmol
+ domain_of:
+ - Library
+ range: float
+ quantity_ng:
+ name: quantity_ng
+ local_names:
+ NIMP:
+ local_name_source: NIMP
+ local_name_value: library_quantification_ng
+ description: Amount of library generated in terms of nanograms
+ from_schema: https://identifiers.org/brain-bican/library-generation-schema
+ exact_mappings:
+ - NIMP:PD-TNTNXP37
+ slot_uri: bican:318b2d3a-dae7-4c63-bfbb-93862b92f63e
+ alias: library quantification ng
+ domain_of:
+ - AmplifiedCdna
+ - Library
+ range: float
+ r1_r2_index:
+ name: r1_r2_index
+ local_names:
+ NIMP:
+ local_name_source: NIMP
+ local_name_value: library_r1_r2_index
+ description: Name of the pair of library indexes used for sequencing. Indexes
+ allow libraries to be pooled together for sequencing. Sequencing output (fastq)
+ are demultiplexed by using the indexes for each library. The name will be associated
+ with the sequences of i7, i5, and i5as, which are needed by SeqCores for demultiplexing. The
+ required direction of the sequence (sense or antisense) of the index can differ
+ depending on sequencing instruments.
+ in_subset:
+ - analysis
+ - tracking
+ from_schema: https://identifiers.org/brain-bican/library-generation-schema
+ exact_mappings:
+ - NIMP:PD-VLLMWZ60
+ rank: 1000
+ slot_uri: bican:c94b5d8a-e92d-47af-8c0e-ea3b58be4d06
+ alias: R1/R2 index name
+ domain_of:
+ - Library
+ range: library_r1_r2_index
+
+name: Library
+description: A collection of fragmented and barcode-indexed DNA molecules for sequencing.
+ An index or barcode is typically introduced to enable identification of library
+ origin to allow libraries to be pooled together for sequencing.
+in_subset:
+- bican
+- library_generation
+from_schema: https://identifiers.org/brain-bican/library-generation-schema
+exact_mappings:
+- NIMP:Library
+is_a: material sample
+mixins:
+- ProvEntity
+slot_usage:
+ was_generated_by:
+ name: was_generated_by
+ description: The library construction process from which the library was generated
+ by.
+ range: LibraryConstruction
+ was_derived_from:
+ name: was_derived_from
+ description: The input barcoded cell sample or amplified cDNA from which the library
+ was derived from.
+ exact_mappings:
+ - NIMP:has_parent
+ exactly_one_of:
+ - range: BarcodedCellSample
+ - range: AmplifiedCdna
+ name:
+ name: name
+ description: Name of a library, which is a collection of fragmented and barcode-indexed
+ DNA molecules for sequencing. An index or barcode is typically introduced to
+ enable identification of library origin to allow libraries to be pooled together
+ for sequencing.
+ exact_mappings:
+ - NIMP:PD-AJJUCC35
+ slot_uri: bican:f717e254-3630-4342-be7b-4d56376e7afe
+ category:
+ name: category
+ pattern: ^bican:[A-Z][A-Za-z]+$
+attributes:
+ average_size_bp:
+ name: average_size_bp
+ local_names:
+ NIMP:
+ local_name_source: NIMP
+ local_name_value: library_avg_size_bp
+ description: Average size of the library in terms of base pairs. This is used
+ to calculate the molarity before pooling and sequencing.
+ in_subset:
+ - analysis
+ from_schema: https://identifiers.org/brain-bican/library-generation-schema
+ exact_mappings:
+ - NIMP:PD-VJVJLC46
+ rank: 1000
+ slot_uri: bican:f851eba9-56d1-4472-9d0c-d7f8bc33000a
+ alias: library avg size bp
+ owner: Library
+ domain_of:
+ - Library
+ range: integer
+ concentration_nm:
+ name: concentration_nm
+ local_names:
+ NIMP:
+ local_name_source: NIMP
+ local_name_value: library_concentration_nm
+ description: Concentration of library in terms of nM (nMol/L). Number of molecules
+ is needed for accurate pooling of the libraries and for generating the number
+ of target reads/cell in sequencing.
+ from_schema: https://identifiers.org/brain-bican/library-generation-schema
+ exact_mappings:
+ - NIMP:PD-DCDCLD43
+ rank: 1000
+ slot_uri: bican:90805b3f-f380-4f23-b159-e7eaa0c8f052
+ alias: library concentration nm
+ owner: Library
+ domain_of:
+ - Library
+ range: float
+ pass_fail_result:
+ name: pass_fail_result
+ local_names:
+ NIMP:
+ local_name_source: NIMP
+ local_name_value: library_prep_pass_fail
+ description: Pass or Fail result based on qualitative assessment of library yield
+ and size.
+ in_subset:
+ - analysis
+ from_schema: https://identifiers.org/brain-bican/library-generation-schema
+ exact_mappings:
+ - NIMP:PD-QHQHQB42
+ slot_uri: bican:6817ede2-7ead-402d-9dbc-131aca627c6c
+ alias: library prep pass-fail
+ owner: Library
+ domain_of:
+ - AmplifiedCdna
+ - Library
+ range: library_prep_pass_fail
+ quantity_fmol:
+ name: quantity_fmol
+ local_names:
+ NIMP:
+ local_name_source: NIMP
+ local_name_value: library_quantification_fmol
+ description: Amount of library generated in terms of femtomoles
+ in_subset:
+ - analysis
+ from_schema: https://identifiers.org/brain-bican/library-generation-schema
+ exact_mappings:
+ - NIMP:PD-JYJYDK42
+ rank: 1000
+ slot_uri: bican:4c09ada7-c116-48bc-8fb1-0dcf5c4b939a
+ alias: library quantification fmol
+ owner: Library
+ domain_of:
+ - Library
+ range: float
+ quantity_ng:
+ name: quantity_ng
+ local_names:
+ NIMP:
+ local_name_source: NIMP
+ local_name_value: library_quantification_ng
+ description: Amount of library generated in terms of nanograms
+ from_schema: https://identifiers.org/brain-bican/library-generation-schema
+ exact_mappings:
+ - NIMP:PD-TNTNXP37
+ slot_uri: bican:318b2d3a-dae7-4c63-bfbb-93862b92f63e
+ alias: library quantification ng
+ owner: Library
+ domain_of:
+ - AmplifiedCdna
+ - Library
+ range: float
+ r1_r2_index:
+ name: r1_r2_index
+ local_names:
+ NIMP:
+ local_name_source: NIMP
+ local_name_value: library_r1_r2_index
+ description: Name of the pair of library indexes used for sequencing. Indexes
+ allow libraries to be pooled together for sequencing. Sequencing output (fastq)
+ are demultiplexed by using the indexes for each library. The name will be associated
+ with the sequences of i7, i5, and i5as, which are needed by SeqCores for demultiplexing. The
+ required direction of the sequence (sense or antisense) of the index can differ
+ depending on sequencing instruments.
+ in_subset:
+ - analysis
+ - tracking
+ from_schema: https://identifiers.org/brain-bican/library-generation-schema
+ exact_mappings:
+ - NIMP:PD-VLLMWZ60
+ rank: 1000
+ slot_uri: bican:c94b5d8a-e92d-47af-8c0e-ea3b58be4d06
+ alias: R1/R2 index name
+ owner: Library
+ domain_of:
+ - Library
+ range: library_r1_r2_index
+ was_generated_by:
+ name: was_generated_by
+ description: The library construction process from which the library was generated
+ by.
+ from_schema: https://identifiers.org/brain-bican/library-generation-schema
+ rank: 1000
+ slot_uri: prov:wasGeneratedBy
+ alias: was_generated_by
+ owner: Library
+ domain_of:
+ - TissueSample
+ - DissociatedCellSample
+ - EnrichedCellSample
+ - BarcodedCellSample
+ - AmplifiedCdna
+ - Library
+ - LibraryPool
+ - DissectionRoiPolygon
+ - ProvEntity
+ range: LibraryConstruction
+ was_derived_from:
+ name: was_derived_from
+ description: The input barcoded cell sample or amplified cDNA from which the library
+ was derived from.
+ from_schema: https://identifiers.org/brain-bican/library-generation-schema
+ exact_mappings:
+ - NIMP:has_parent
+ rank: 1000
+ slot_uri: prov:wasDerivedFrom
+ alias: was_derived_from
+ owner: Library
+ domain_of:
+ - BrainSlab
+ - TissueSample
+ - DissociatedCellSample
+ - EnrichedCellSample
+ - BarcodedCellSample
+ - AmplifiedCdna
+ - Library
+ - LibraryAliquot
+ - LibraryPool
+ - ProvEntity
+ range: ProvEntity
+ exactly_one_of:
+ - range: BarcodedCellSample
+ - range: AmplifiedCdna
+ name:
+ name: name
+ definition_uri: https://w3id.org/biolink/vocab/name
+ description: Name of a library, which is a collection of fragmented and barcode-indexed
+ DNA molecules for sequencing. An index or barcode is typically introduced to
+ enable identification of library origin to allow libraries to be pooled together
+ for sequencing.
+ in_subset:
+ - translator_minimal
+ - samples
+ from_schema: https://identifiers.org/brain-bican/library-generation-schema
+ aliases:
+ - label
+ - display name
+ - title
+ mappings:
+ - rdfs:label
+ exact_mappings:
+ - NIMP:PD-AJJUCC35
+ narrow_mappings:
+ - dct:title
+ - WIKIDATA_PROPERTY:P1476
+ rank: 1000
+ domain: entity
+ slot_uri: bican:f717e254-3630-4342-be7b-4d56376e7afe
+ alias: name
+ owner: Library
+ domain_of:
+ - attribute
+ - entity
+ - macromolecular machine mixin
+ - Donor
+ - BrainSlab
+ - TissueSample
+ - DissociatedCellSample
+ - EnrichedCellSample
+ - BarcodedCellSample
+ - AmplifiedCdna
+ - Library
+ - LibraryAliquot
+ - LibraryPool
+ - DissectionRoiPolygon
+ - named thing
+ - organism taxon
+ - information content entity
+ - dataset
+ - physical entity
+ - activity
+ - procedure
+ - material sample
+ - biological entity
+ - gene or gene product
+ - gene
+ - genome
+ range: label type
+ id:
+ name: id
+ definition_uri: https://w3id.org/biolink/vocab/id
+ description: A unique identifier for an entity. Must be either a CURIE shorthand
+ for a URI or a complete URI
+ in_subset:
+ - translator_minimal
+ from_schema: https://identifiers.org/brain-bican/library-generation-schema
+ exact_mappings:
+ - AGRKB:primaryId
+ - gff3:ID
+ - gpi:DB_Object_ID
+ rank: 1000
+ domain: entity
+ slot_uri: biolink:id
+ identifier: true
+ alias: id
+ owner: Library
+ domain_of:
+ - ontology class
+ - entity
+ - attribute
+ - named thing
+ - taxonomic rank
+ - organism taxon
+ - information content entity
+ - dataset
+ - physical entity
+ - activity
+ - procedure
+ - material sample
+ - biological entity
+ - gene
+ - genome
+ range: string
+ required: true
+ iri:
+ name: iri
+ definition_uri: https://w3id.org/biolink/vocab/iri
+ description: An IRI for an entity. This is determined by the id using expansion
+ rules.
+ in_subset:
+ - translator_minimal
+ - samples
+ from_schema: https://identifiers.org/brain-bican/library-generation-schema
+ exact_mappings:
+ - WIKIDATA_PROPERTY:P854
+ rank: 1000
+ slot_uri: biolink:iri
+ alias: iri
+ owner: Library
+ domain_of:
+ - attribute
+ - entity
+ - named thing
+ - organism taxon
+ - information content entity
+ - dataset
+ - physical entity
+ - activity
+ - procedure
+ - material sample
+ - biological entity
+ - gene
+ - genome
+ range: iri type
+ category:
+ name: category
+ definition_uri: https://w3id.org/biolink/vocab/category
+ description: Name of the high level ontology class in which this entity is categorized.
+ Corresponds to the label for the biolink entity type class. In a neo4j database
+ this MAY correspond to the neo4j label tag. In an RDF database it should be
+ a biolink model class URI. This field is multi-valued. It should include values
+ for ancestors of the biolink class; for example, a protein such as Shh would
+ have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`.
+ In an RDF database, nodes will typically have an rdf:type triples. This can
+ be to the most specific biolink class, or potentially to a class more specific
+ than something in biolink. For example, a sequence feature `f` may have a rdf:type
+ assertion to a SO class such as TF_binding_site, which is more specific than
+ anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity,
+ biolink:NamedThing}
+ in_subset:
+ - translator_minimal
+ from_schema: https://identifiers.org/brain-bican/library-generation-schema
+ rank: 1000
+ is_a: type
+ domain: entity
+ slot_uri: biolink:category
+ designates_type: true
+ alias: category
+ owner: Library
+ domain_of:
+ - entity
+ - attribute
+ - named thing
+ - organism taxon
+ - information content entity
+ - dataset
+ - physical entity
+ - activity
+ - procedure
+ - material sample
+ - biological entity
+ - gene
+ - genome
+ is_class_field: true
+ range: uriorcurie
+ multivalued: true
+ pattern: ^bican:[A-Z][A-Za-z]+$
+ type:
+ name: type
+ definition_uri: https://w3id.org/biolink/vocab/type
+ from_schema: https://identifiers.org/brain-bican/library-generation-schema
+ mappings:
+ - rdf:type
+ exact_mappings:
+ - gff3:type
+ - gpi:DB_Object_Type
+ rank: 1000
+ domain: entity
+ slot_uri: rdf:type
+ alias: type
+ owner: Library
+ domain_of:
+ - entity
+ - attribute
+ - named thing
+ - organism taxon
+ - information content entity
+ - dataset
+ - physical entity
+ - activity
+ - procedure
+ - material sample
+ - biological entity
+ - gene
+ - genome
+ range: string
+ multivalued: true
+ description:
+ name: description
+ definition_uri: https://w3id.org/biolink/vocab/description
+ description: a human-readable description of an entity
+ in_subset:
+ - translator_minimal
+ from_schema: https://identifiers.org/brain-bican/library-generation-schema
+ aliases:
+ - definition
+ mappings:
+ - dct:description
+ exact_mappings:
+ - IAO:0000115
+ - skos:definitions
+ narrow_mappings:
+ - gff3:Description
+ rank: 1000
+ slot_uri: dct:description
+ alias: description
+ owner: Library
+ domain_of:
+ - entity
+ - attribute
+ - named thing
+ - organism taxon
+ - information content entity
+ - dataset
+ - physical entity
+ - activity
+ - procedure
+ - material sample
+ - biological entity
+ - gene
+ - genome
+ range: narrative text
+ has attribute:
+ name: has attribute
+ definition_uri: https://w3id.org/biolink/vocab/has_attribute
+ description: connects any entity to an attribute
+ in_subset:
+ - samples
+ from_schema: https://identifiers.org/brain-bican/library-generation-schema
+ exact_mappings:
+ - SIO:000008
+ close_mappings:
+ - OBI:0001927
+ narrow_mappings:
+ - OBAN:association_has_subject_property
+ - OBAN:association_has_object_property
+ - CPT:has_possibly_included_panel_element
+ - DRUGBANK:category
+ - EFO:is_executed_in
+ - HANCESTRO:0301
+ - LOINC:has_action_guidance
+ - LOINC:has_adjustment
+ - LOINC:has_aggregation_view
+ - LOINC:has_approach_guidance
+ - LOINC:has_divisor
+ - LOINC:has_exam
+ - LOINC:has_method
+ - LOINC:has_modality_subtype
+ - LOINC:has_object_guidance
+ - LOINC:has_scale
+ - LOINC:has_suffix
+ - LOINC:has_time_aspect
+ - LOINC:has_time_modifier
+ - LOINC:has_timing_of
+ - NCIT:R88
+ - NCIT:eo_disease_has_property_or_attribute
+ - NCIT:has_data_element
+ - NCIT:has_pharmaceutical_administration_method
+ - NCIT:has_pharmaceutical_basic_dose_form
+ - NCIT:has_pharmaceutical_intended_site
+ - NCIT:has_pharmaceutical_release_characteristics
+ - NCIT:has_pharmaceutical_state_of_matter
+ - NCIT:has_pharmaceutical_transformation
+ - NCIT:is_qualified_by
+ - NCIT:qualifier_applies_to
+ - NCIT:role_has_domain
+ - NCIT:role_has_range
+ - INO:0000154
+ - HANCESTRO:0308
+ - OMIM:has_inheritance_type
+ - orphanet:C016
+ - orphanet:C017
+ - RO:0000053
+ - RO:0000086
+ - RO:0000087
+ - SNOMED:has_access
+ - SNOMED:has_clinical_course
+ - SNOMED:has_count_of_base_of_active_ingredient
+ - SNOMED:has_dose_form_administration_method
+ - SNOMED:has_dose_form_release_characteristic
+ - SNOMED:has_dose_form_transformation
+ - SNOMED:has_finding_context
+ - SNOMED:has_finding_informer
+ - SNOMED:has_inherent_attribute
+ - SNOMED:has_intent
+ - SNOMED:has_interpretation
+ - SNOMED:has_laterality
+ - SNOMED:has_measurement_method
+ - SNOMED:has_method
+ - SNOMED:has_priority
+ - SNOMED:has_procedure_context
+ - SNOMED:has_process_duration
+ - SNOMED:has_property
+ - SNOMED:has_revision_status
+ - SNOMED:has_scale_type
+ - SNOMED:has_severity
+ - SNOMED:has_specimen
+ - SNOMED:has_state_of_matter
+ - SNOMED:has_subject_relationship_context
+ - SNOMED:has_surgical_approach
+ - SNOMED:has_technique
+ - SNOMED:has_temporal_context
+ - SNOMED:has_time_aspect
+ - SNOMED:has_units
+ - UMLS:has_structural_class
+ - UMLS:has_supported_concept_property
+ - UMLS:has_supported_concept_relationship
+ - UMLS:may_be_qualified_by
+ rank: 1000
+ domain: entity
+ slot_uri: biolink:has_attribute
+ alias: has_attribute
+ owner: Library
+ domain_of:
+ - entity
+ - attribute
+ - named thing
+ - organism taxon
+ - information content entity
+ - dataset
+ - physical entity
+ - activity
+ - procedure
+ - material sample
+ - biological entity
+ - gene
+ - genome
+ range: attribute
+ multivalued: true
+ deprecated:
+ name: deprecated
+ definition_uri: https://w3id.org/biolink/vocab/deprecated
+ description: A boolean flag indicating that an entity is no longer considered
+ current or valid.
+ from_schema: https://identifiers.org/brain-bican/library-generation-schema
+ exact_mappings:
+ - oboInOwl:ObsoleteClass
+ rank: 1000
+ slot_uri: biolink:deprecated
+ alias: deprecated
+ owner: Library
+ domain_of:
+ - entity
+ - attribute
+ - named thing
+ - organism taxon
+ - information content entity
+ - dataset
+ - physical entity
+ - activity
+ - procedure
+ - material sample
+ - biological entity
+ - gene
+ - genome
+ range: boolean
+ provided by:
+ name: provided by
+ definition_uri: https://w3id.org/biolink/vocab/provided_by
+ description: The value in this node property represents the knowledge provider
+ that created or assembled the node and all of its attributes. Used internally
+ to represent how a particular node made its way into a knowledge provider or
+ graph.
+ from_schema: https://identifiers.org/brain-bican/library-generation-schema
+ rank: 1000
+ is_a: node property
+ domain: named thing
+ slot_uri: biolink:provided_by
+ alias: provided_by
+ owner: Library
+ domain_of:
+ - named thing
+ - attribute
+ - organism taxon
+ - information content entity
+ - dataset
+ - physical entity
+ - activity
+ - procedure
+ - material sample
+ - biological entity
+ - gene
+ - genome
+ range: string
+ multivalued: true
+ xref:
+ name: xref
+ definition_uri: https://w3id.org/biolink/vocab/xref
+ description: A database cross reference or alternative identifier for a NamedThing
+ or edge between two NamedThings. This property should point to a database record
+ or webpage that supports the existence of the edge, or gives more detail about
+ the edge. This property can be used on a node or edge to provide multiple URIs
+ or CURIE cross references.
+ in_subset:
+ - translator_minimal
+ from_schema: https://identifiers.org/brain-bican/library-generation-schema
+ aliases:
+ - dbxref
+ - Dbxref
+ - DbXref
+ - record_url
+ - source_record_urls
+ narrow_mappings:
+ - gff3:Dbxref
+ - gpi:DB_Xrefs
+ rank: 1000
+ domain: named thing
+ slot_uri: biolink:xref
+ alias: xref
+ owner: Library
+ domain_of:
+ - named thing
+ - gene
+ - attribute
+ - organism taxon
+ - information content entity
+ - dataset
+ - physical entity
+ - activity
+ - procedure
+ - material sample
+ - biological entity
+ - genome
+ range: uriorcurie
+ multivalued: true
+ full name:
+ name: full name
+ definition_uri: https://w3id.org/biolink/vocab/full_name
+ description: a long-form human readable name for a thing
+ from_schema: https://identifiers.org/brain-bican/library-generation-schema
+ rank: 1000
+ is_a: node property
+ domain: named thing
+ slot_uri: biolink:full_name
+ alias: full_name
+ owner: Library
+ domain_of:
+ - named thing
+ - attribute
+ - organism taxon
+ - information content entity
+ - dataset
+ - physical entity
+ - activity
+ - procedure
+ - material sample
+ - biological entity
+ - gene
+ - genome
+ range: label type
+ synonym:
+ name: synonym
+ definition_uri: https://w3id.org/biolink/vocab/synonym
+ description: Alternate human-readable names for a thing
+ in_subset:
+ - translator_minimal
+ from_schema: https://identifiers.org/brain-bican/library-generation-schema
+ aliases:
+ - alias
+ narrow_mappings:
+ - skos:altLabel
+ - gff3:Alias
+ - AGRKB:synonyms
+ - gpi:DB_Object_Synonyms
+ - HANCESTRO:0330
+ - IAO:0000136
+ - RXNORM:has_tradename
+ rank: 1000
+ is_a: node property
+ domain: named thing
+ slot_uri: biolink:synonym
+ alias: synonym
+ owner: Library
+ domain_of:
+ - named thing
+ - attribute
+ - organism taxon
+ - information content entity
+ - dataset
+ - physical entity
+ - activity
+ - procedure
+ - material sample
+ - biological entity
+ - gene
+ - genome
+ range: label type
+ multivalued: true
+
+One library in the library pool. Each library aliquot in a library pool will have a unique R1/R2 index to allow for sequencing together then separating the sequencing output by originating library aliquot through the process of demultiplexing. The resulting demultiplexed fastq files will include the library aliquot name. A given library may produce multiple library aliquots, which is done in the case of resequencing. Each library aliquot will produce a set of fastq files.
+URI: bican:LibraryAliquot
+| Name | +Cardinality and Range | +Description | +Inheritance | +
|---|---|---|---|
| was_derived_from | +0..1 Library |
+The input library from which the library aliquot was derived from | +direct | +
| name | +0..1 LabelType |
+One library in the library pool | +direct | +
| was_generated_by | +0..1 ProvActivity |
+Generation is the completion of production of a new entity by an activity | +ProvEntity | +
| id | +1 String |
+A unique identifier for an entity | +NamedThing, PhysicalEntity, MaterialSample, Entity | +
| iri | +0..1 IriType |
+An IRI for an entity | +NamedThing, PhysicalEntity, MaterialSample, Entity | +
| category | +* Uriorcurie |
+Name of the high level ontology class in which this entity is categorized | +NamedThing, PhysicalEntity, MaterialSample, Entity | +
| type | +* String |
++ | NamedThing, PhysicalEntity, MaterialSample, Entity | +
| description | +0..1 NarrativeText |
+a human-readable description of an entity | +NamedThing, PhysicalEntity, MaterialSample, Entity | +
| has_attribute | +* Attribute |
+connects any entity to an attribute | +NamedThing, PhysicalEntity, MaterialSample, Entity | +
| deprecated | +0..1 Boolean |
+A boolean flag indicating that an entity is no longer considered current or v... | +NamedThing, PhysicalEntity, MaterialSample, Entity | +
| provided_by | +* String |
+The value in this node property represents the knowledge provider that create... | +NamedThing, PhysicalEntity, MaterialSample | +
| xref | +* Uriorcurie |
+A database cross reference or alternative identifier for a NamedThing or edge... | +NamedThing, PhysicalEntity, MaterialSample | +
| full_name | +0..1 LabelType |
+a long-form human readable name for a thing | +NamedThing, PhysicalEntity, MaterialSample | +
| synonym | +* LabelType |
+Alternate human-readable names for a thing | +NamedThing, PhysicalEntity, MaterialSample | +
| used by | +used in | +type | +used | +
|---|---|---|---|
| LibraryPool | +was_derived_from | +range | +LibraryAliquot | +
| LibraryPooling | +used | +range | +LibraryAliquot | +
| Mapping Type | +Mapped Value | +
|---|---|
| self | +bican:LibraryAliquot | +
| native | +bican:LibraryAliquot | +
| exact | +NIMP:Library%20Aliquot | +
name: LibraryAliquot
+description: One library in the library pool. Each library aliquot in a library pool
+ will have a unique R1/R2 index to allow for sequencing together then separating
+ the sequencing output by originating library aliquot through the process of demultiplexing.
+ The resulting demultiplexed fastq files will include the library aliquot name. A
+ given library may produce multiple library aliquots, which is done in the case of
+ resequencing. Each library aliquot will produce a set of fastq files.
+in_subset:
+- bican
+- library_generation
+from_schema: https://identifiers.org/brain-bican/library-generation-schema
+exact_mappings:
+- NIMP:Library%20Aliquot
+is_a: material sample
+mixins:
+- ProvEntity
+slots:
+- was_derived_from
+- name
+slot_usage:
+ was_derived_from:
+ name: was_derived_from
+ description: The input library from which the library aliquot was derived from.
+ exact_mappings:
+ - NIMP:has_parent
+ range: Library
+ name:
+ name: name
+ description: One library in the library pool. Each Library_aliquot_name in a
+ library pool will have a unique R1/R2 index to allow for sequencing together
+ then separating the sequencing output by originating library aliquot through
+ the process of demultiplexing. The resulting demultiplexed fastq files will
+ include the library_aliquot_name.
+ exact_mappings:
+ - NIMP:PD-XCXCCC35
+ slot_uri: bican:34191bad-d167-4335-8224-ade897d3728e
+ category:
+ name: category
+ pattern: ^bican:[A-Z][A-Za-z]+$
+
+name: LibraryAliquot
+description: One library in the library pool. Each library aliquot in a library pool
+ will have a unique R1/R2 index to allow for sequencing together then separating
+ the sequencing output by originating library aliquot through the process of demultiplexing.
+ The resulting demultiplexed fastq files will include the library aliquot name. A
+ given library may produce multiple library aliquots, which is done in the case of
+ resequencing. Each library aliquot will produce a set of fastq files.
+in_subset:
+- bican
+- library_generation
+from_schema: https://identifiers.org/brain-bican/library-generation-schema
+exact_mappings:
+- NIMP:Library%20Aliquot
+is_a: material sample
+mixins:
+- ProvEntity
+slot_usage:
+ was_derived_from:
+ name: was_derived_from
+ description: The input library from which the library aliquot was derived from.
+ exact_mappings:
+ - NIMP:has_parent
+ range: Library
+ name:
+ name: name
+ description: One library in the library pool. Each Library_aliquot_name in a
+ library pool will have a unique R1/R2 index to allow for sequencing together
+ then separating the sequencing output by originating library aliquot through
+ the process of demultiplexing. The resulting demultiplexed fastq files will
+ include the library_aliquot_name.
+ exact_mappings:
+ - NIMP:PD-XCXCCC35
+ slot_uri: bican:34191bad-d167-4335-8224-ade897d3728e
+ category:
+ name: category
+ pattern: ^bican:[A-Z][A-Za-z]+$
+attributes:
+ was_derived_from:
+ name: was_derived_from
+ description: The input library from which the library aliquot was derived from.
+ from_schema: https://identifiers.org/brain-bican/library-generation-schema
+ exact_mappings:
+ - NIMP:has_parent
+ rank: 1000
+ slot_uri: prov:wasDerivedFrom
+ alias: was_derived_from
+ owner: LibraryAliquot
+ domain_of:
+ - BrainSlab
+ - TissueSample
+ - DissociatedCellSample
+ - EnrichedCellSample
+ - BarcodedCellSample
+ - AmplifiedCdna
+ - Library
+ - LibraryAliquot
+ - LibraryPool
+ - ProvEntity
+ range: Library
+ name:
+ name: name
+ definition_uri: https://w3id.org/biolink/vocab/name
+ description: One library in the library pool. Each Library_aliquot_name in a
+ library pool will have a unique R1/R2 index to allow for sequencing together
+ then separating the sequencing output by originating library aliquot through
+ the process of demultiplexing. The resulting demultiplexed fastq files will
+ include the library_aliquot_name.
+ in_subset:
+ - translator_minimal
+ - samples
+ from_schema: https://identifiers.org/brain-bican/library-generation-schema
+ aliases:
+ - label
+ - display name
+ - title
+ mappings:
+ - rdfs:label
+ exact_mappings:
+ - NIMP:PD-XCXCCC35
+ narrow_mappings:
+ - dct:title
+ - WIKIDATA_PROPERTY:P1476
+ rank: 1000
+ domain: entity
+ slot_uri: bican:34191bad-d167-4335-8224-ade897d3728e
+ alias: name
+ owner: LibraryAliquot
+ domain_of:
+ - attribute
+ - entity
+ - macromolecular machine mixin
+ - Donor
+ - BrainSlab
+ - TissueSample
+ - DissociatedCellSample
+ - EnrichedCellSample
+ - BarcodedCellSample
+ - AmplifiedCdna
+ - Library
+ - LibraryAliquot
+ - LibraryPool
+ - DissectionRoiPolygon
+ - named thing
+ - organism taxon
+ - information content entity
+ - dataset
+ - physical entity
+ - activity
+ - procedure
+ - material sample
+ - biological entity
+ - gene or gene product
+ - gene
+ - genome
+ range: label type
+ was_generated_by:
+ name: was_generated_by
+ description: Generation is the completion of production of a new entity by an
+ activity. This entity did not exist before generation and becomes available
+ for usage after this generation.
+ from_schema: https://identifiers.org/brain-bican/library-generation-schema
+ rank: 1000
+ slot_uri: prov:wasGeneratedBy
+ alias: was_generated_by
+ owner: LibraryAliquot
+ domain_of:
+ - TissueSample
+ - DissociatedCellSample
+ - EnrichedCellSample
+ - BarcodedCellSample
+ - AmplifiedCdna
+ - Library
+ - LibraryPool
+ - DissectionRoiPolygon
+ - ProvEntity
+ range: ProvActivity
+ id:
+ name: id
+ definition_uri: https://w3id.org/biolink/vocab/id
+ description: A unique identifier for an entity. Must be either a CURIE shorthand
+ for a URI or a complete URI
+ in_subset:
+ - translator_minimal
+ from_schema: https://identifiers.org/brain-bican/library-generation-schema
+ exact_mappings:
+ - AGRKB:primaryId
+ - gff3:ID
+ - gpi:DB_Object_ID
+ rank: 1000
+ domain: entity
+ slot_uri: biolink:id
+ identifier: true
+ alias: id
+ owner: LibraryAliquot
+ domain_of:
+ - ontology class
+ - entity
+ - attribute
+ - named thing
+ - taxonomic rank
+ - organism taxon
+ - information content entity
+ - dataset
+ - physical entity
+ - activity
+ - procedure
+ - material sample
+ - biological entity
+ - gene
+ - genome
+ range: string
+ required: true
+ iri:
+ name: iri
+ definition_uri: https://w3id.org/biolink/vocab/iri
+ description: An IRI for an entity. This is determined by the id using expansion
+ rules.
+ in_subset:
+ - translator_minimal
+ - samples
+ from_schema: https://identifiers.org/brain-bican/library-generation-schema
+ exact_mappings:
+ - WIKIDATA_PROPERTY:P854
+ rank: 1000
+ slot_uri: biolink:iri
+ alias: iri
+ owner: LibraryAliquot
+ domain_of:
+ - attribute
+ - entity
+ - named thing
+ - organism taxon
+ - information content entity
+ - dataset
+ - physical entity
+ - activity
+ - procedure
+ - material sample
+ - biological entity
+ - gene
+ - genome
+ range: iri type
+ category:
+ name: category
+ definition_uri: https://w3id.org/biolink/vocab/category
+ description: Name of the high level ontology class in which this entity is categorized.
+ Corresponds to the label for the biolink entity type class. In a neo4j database
+ this MAY correspond to the neo4j label tag. In an RDF database it should be
+ a biolink model class URI. This field is multi-valued. It should include values
+ for ancestors of the biolink class; for example, a protein such as Shh would
+ have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`.
+ In an RDF database, nodes will typically have an rdf:type triples. This can
+ be to the most specific biolink class, or potentially to a class more specific
+ than something in biolink. For example, a sequence feature `f` may have a rdf:type
+ assertion to a SO class such as TF_binding_site, which is more specific than
+ anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity,
+ biolink:NamedThing}
+ in_subset:
+ - translator_minimal
+ from_schema: https://identifiers.org/brain-bican/library-generation-schema
+ rank: 1000
+ is_a: type
+ domain: entity
+ slot_uri: biolink:category
+ designates_type: true
+ alias: category
+ owner: LibraryAliquot
+ domain_of:
+ - entity
+ - attribute
+ - named thing
+ - organism taxon
+ - information content entity
+ - dataset
+ - physical entity
+ - activity
+ - procedure
+ - material sample
+ - biological entity
+ - gene
+ - genome
+ is_class_field: true
+ range: uriorcurie
+ multivalued: true
+ pattern: ^bican:[A-Z][A-Za-z]+$
+ type:
+ name: type
+ definition_uri: https://w3id.org/biolink/vocab/type
+ from_schema: https://identifiers.org/brain-bican/library-generation-schema
+ mappings:
+ - rdf:type
+ exact_mappings:
+ - gff3:type
+ - gpi:DB_Object_Type
+ rank: 1000
+ domain: entity
+ slot_uri: rdf:type
+ alias: type
+ owner: LibraryAliquot
+ domain_of:
+ - entity
+ - attribute
+ - named thing
+ - organism taxon
+ - information content entity
+ - dataset
+ - physical entity
+ - activity
+ - procedure
+ - material sample
+ - biological entity
+ - gene
+ - genome
+ range: string
+ multivalued: true
+ description:
+ name: description
+ definition_uri: https://w3id.org/biolink/vocab/description
+ description: a human-readable description of an entity
+ in_subset:
+ - translator_minimal
+ from_schema: https://identifiers.org/brain-bican/library-generation-schema
+ aliases:
+ - definition
+ mappings:
+ - dct:description
+ exact_mappings:
+ - IAO:0000115
+ - skos:definitions
+ narrow_mappings:
+ - gff3:Description
+ rank: 1000
+ slot_uri: dct:description
+ alias: description
+ owner: LibraryAliquot
+ domain_of:
+ - entity
+ - attribute
+ - named thing
+ - organism taxon
+ - information content entity
+ - dataset
+ - physical entity
+ - activity
+ - procedure
+ - material sample
+ - biological entity
+ - gene
+ - genome
+ range: narrative text
+ has attribute:
+ name: has attribute
+ definition_uri: https://w3id.org/biolink/vocab/has_attribute
+ description: connects any entity to an attribute
+ in_subset:
+ - samples
+ from_schema: https://identifiers.org/brain-bican/library-generation-schema
+ exact_mappings:
+ - SIO:000008
+ close_mappings:
+ - OBI:0001927
+ narrow_mappings:
+ - OBAN:association_has_subject_property
+ - OBAN:association_has_object_property
+ - CPT:has_possibly_included_panel_element
+ - DRUGBANK:category
+ - EFO:is_executed_in
+ - HANCESTRO:0301
+ - LOINC:has_action_guidance
+ - LOINC:has_adjustment
+ - LOINC:has_aggregation_view
+ - LOINC:has_approach_guidance
+ - LOINC:has_divisor
+ - LOINC:has_exam
+ - LOINC:has_method
+ - LOINC:has_modality_subtype
+ - LOINC:has_object_guidance
+ - LOINC:has_scale
+ - LOINC:has_suffix
+ - LOINC:has_time_aspect
+ - LOINC:has_time_modifier
+ - LOINC:has_timing_of
+ - NCIT:R88
+ - NCIT:eo_disease_has_property_or_attribute
+ - NCIT:has_data_element
+ - NCIT:has_pharmaceutical_administration_method
+ - NCIT:has_pharmaceutical_basic_dose_form
+ - NCIT:has_pharmaceutical_intended_site
+ - NCIT:has_pharmaceutical_release_characteristics
+ - NCIT:has_pharmaceutical_state_of_matter
+ - NCIT:has_pharmaceutical_transformation
+ - NCIT:is_qualified_by
+ - NCIT:qualifier_applies_to
+ - NCIT:role_has_domain
+ - NCIT:role_has_range
+ - INO:0000154
+ - HANCESTRO:0308
+ - OMIM:has_inheritance_type
+ - orphanet:C016
+ - orphanet:C017
+ - RO:0000053
+ - RO:0000086
+ - RO:0000087
+ - SNOMED:has_access
+ - SNOMED:has_clinical_course
+ - SNOMED:has_count_of_base_of_active_ingredient
+ - SNOMED:has_dose_form_administration_method
+ - SNOMED:has_dose_form_release_characteristic
+ - SNOMED:has_dose_form_transformation
+ - SNOMED:has_finding_context
+ - SNOMED:has_finding_informer
+ - SNOMED:has_inherent_attribute
+ - SNOMED:has_intent
+ - SNOMED:has_interpretation
+ - SNOMED:has_laterality
+ - SNOMED:has_measurement_method
+ - SNOMED:has_method
+ - SNOMED:has_priority
+ - SNOMED:has_procedure_context
+ - SNOMED:has_process_duration
+ - SNOMED:has_property
+ - SNOMED:has_revision_status
+ - SNOMED:has_scale_type
+ - SNOMED:has_severity
+ - SNOMED:has_specimen
+ - SNOMED:has_state_of_matter
+ - SNOMED:has_subject_relationship_context
+ - SNOMED:has_surgical_approach
+ - SNOMED:has_technique
+ - SNOMED:has_temporal_context
+ - SNOMED:has_time_aspect
+ - SNOMED:has_units
+ - UMLS:has_structural_class
+ - UMLS:has_supported_concept_property
+ - UMLS:has_supported_concept_relationship
+ - UMLS:may_be_qualified_by
+ rank: 1000
+ domain: entity
+ slot_uri: biolink:has_attribute
+ alias: has_attribute
+ owner: LibraryAliquot
+ domain_of:
+ - entity
+ - attribute
+ - named thing
+ - organism taxon
+ - information content entity
+ - dataset
+ - physical entity
+ - activity
+ - procedure
+ - material sample
+ - biological entity
+ - gene
+ - genome
+ range: attribute
+ multivalued: true
+ deprecated:
+ name: deprecated
+ definition_uri: https://w3id.org/biolink/vocab/deprecated
+ description: A boolean flag indicating that an entity is no longer considered
+ current or valid.
+ from_schema: https://identifiers.org/brain-bican/library-generation-schema
+ exact_mappings:
+ - oboInOwl:ObsoleteClass
+ rank: 1000
+ slot_uri: biolink:deprecated
+ alias: deprecated
+ owner: LibraryAliquot
+ domain_of:
+ - entity
+ - attribute
+ - named thing
+ - organism taxon
+ - information content entity
+ - dataset
+ - physical entity
+ - activity
+ - procedure
+ - material sample
+ - biological entity
+ - gene
+ - genome
+ range: boolean
+ provided by:
+ name: provided by
+ definition_uri: https://w3id.org/biolink/vocab/provided_by
+ description: The value in this node property represents the knowledge provider
+ that created or assembled the node and all of its attributes. Used internally
+ to represent how a particular node made its way into a knowledge provider or
+ graph.
+ from_schema: https://identifiers.org/brain-bican/library-generation-schema
+ rank: 1000
+ is_a: node property
+ domain: named thing
+ slot_uri: biolink:provided_by
+ alias: provided_by
+ owner: LibraryAliquot
+ domain_of:
+ - named thing
+ - attribute
+ - organism taxon
+ - information content entity
+ - dataset
+ - physical entity
+ - activity
+ - procedure
+ - material sample
+ - biological entity
+ - gene
+ - genome
+ range: string
+ multivalued: true
+ xref:
+ name: xref
+ definition_uri: https://w3id.org/biolink/vocab/xref
+ description: A database cross reference or alternative identifier for a NamedThing
+ or edge between two NamedThings. This property should point to a database record
+ or webpage that supports the existence of the edge, or gives more detail about
+ the edge. This property can be used on a node or edge to provide multiple URIs
+ or CURIE cross references.
+ in_subset:
+ - translator_minimal
+ from_schema: https://identifiers.org/brain-bican/library-generation-schema
+ aliases:
+ - dbxref
+ - Dbxref
+ - DbXref
+ - record_url
+ - source_record_urls
+ narrow_mappings:
+ - gff3:Dbxref
+ - gpi:DB_Xrefs
+ rank: 1000
+ domain: named thing
+ slot_uri: biolink:xref
+ alias: xref
+ owner: LibraryAliquot
+ domain_of:
+ - named thing
+ - gene
+ - attribute
+ - organism taxon
+ - information content entity
+ - dataset
+ - physical entity
+ - activity
+ - procedure
+ - material sample
+ - biological entity
+ - genome
+ range: uriorcurie
+ multivalued: true
+ full name:
+ name: full name
+ definition_uri: https://w3id.org/biolink/vocab/full_name
+ description: a long-form human readable name for a thing
+ from_schema: https://identifiers.org/brain-bican/library-generation-schema
+ rank: 1000
+ is_a: node property
+ domain: named thing
+ slot_uri: biolink:full_name
+ alias: full_name
+ owner: LibraryAliquot
+ domain_of:
+ - named thing
+ - attribute
+ - organism taxon
+ - information content entity
+ - dataset
+ - physical entity
+ - activity
+ - procedure
+ - material sample
+ - biological entity
+ - gene
+ - genome
+ range: label type
+ synonym:
+ name: synonym
+ definition_uri: https://w3id.org/biolink/vocab/synonym
+ description: Alternate human-readable names for a thing
+ in_subset:
+ - translator_minimal
+ from_schema: https://identifiers.org/brain-bican/library-generation-schema
+ aliases:
+ - alias
+ narrow_mappings:
+ - skos:altLabel
+ - gff3:Alias
+ - AGRKB:synonyms
+ - gpi:DB_Object_Synonyms
+ - HANCESTRO:0330
+ - IAO:0000136
+ - RXNORM:has_tradename
+ rank: 1000
+ is_a: node property
+ domain: named thing
+ slot_uri: biolink:synonym
+ alias: synonym
+ owner: LibraryAliquot
+ domain_of:
+ - named thing
+ - attribute
+ - organism taxon
+ - information content entity
+ - dataset
+ - physical entity
+ - activity
+ - procedure
+ - material sample
+ - biological entity
+ - gene
+ - genome
+ range: label type
+ multivalued: true
+
+The process of constructing a library from input material (such as amplified cDNA or barcoded cell sample) derived from one or more cell samples. cDNA is fragmented into smaller pieces appropriate for sequencing and at the same time a library index barcode is incorporated to enable identification of library origin, allowing libraries to be pooled together for sequencing.
+URI: bican:LibraryConstruction
+| Name | +Cardinality and Range | +Description | +Inheritance | +
|---|---|---|---|
| used | +0..1 ProvEntity or BarcodedCellSample or AmplifiedCdna |
+The input barcoded cell sample or amplified cDNA from which the library was d... | +direct | +
| method | +0..1 LibraryTechnique |
+Standardized nomenclature to describe the specific library method used | +direct | +
| process_date | +0..1 Date |
+Date of library construction | +direct | +
| input_quantity_ng | +0..1 Float |
+Amount of cDNA going into library construction in nanograms | +direct | +
| set | +0..1 String |
+Library set, containing multiple library_names that were processed at the sam... | +direct | +
| id | +1 String |
+A unique identifier for an entity | +NamedThing, Procedure, Entity | +
| iri | +0..1 IriType |
+An IRI for an entity | +NamedThing, Procedure, Entity | +
| category | +* Uriorcurie |
+Name of the high level ontology class in which this entity is categorized | +NamedThing, Procedure, Entity | +
| type | +* String |
++ | NamedThing, Procedure, Entity | +
| name | +0..1 LabelType |
+A human-readable name for an attribute or entity | +NamedThing, Procedure, Entity | +
| description | +0..1 NarrativeText |
+a human-readable description of an entity | +NamedThing, Procedure, Entity | +
| has_attribute | +* Attribute |
+connects any entity to an attribute | +NamedThing, Procedure, Entity | +
| deprecated | +0..1 Boolean |
+A boolean flag indicating that an entity is no longer considered current or v... | +NamedThing, Procedure, Entity | +
| provided_by | +* String |
+The value in this node property represents the knowledge provider that create... | +NamedThing, Procedure | +
| xref | +* Uriorcurie |
+A database cross reference or alternative identifier for a NamedThing or edge... | +NamedThing, Procedure | +
| full_name | +0..1 LabelType |
+a long-form human readable name for a thing | +NamedThing, Procedure | +
| synonym | +* LabelType |
+Alternate human-readable names for a thing | +NamedThing, Procedure | +
| used by | +used in | +type | +used | +
|---|---|---|---|
| Library | +was_generated_by | +range | +LibraryConstruction | +
| Mapping Type | +Mapped Value | +
|---|---|
| self | +bican:LibraryConstruction | +
| native | +bican:LibraryConstruction | +
name: LibraryConstruction
+description: The process of constructing a library from input material (such as amplified
+ cDNA or barcoded cell sample) derived from one or more cell samples. cDNA is fragmented
+ into smaller pieces appropriate for sequencing and at the same time a library index
+ barcode is incorporated to enable identification of library origin, allowing libraries
+ to be pooled together for sequencing.
+in_subset:
+- bican
+- library_generation
+from_schema: https://identifiers.org/brain-bican/library-generation-schema
+is_a: procedure
+mixins:
+- ProvActivity
+slots:
+- used
+slot_usage:
+ used:
+ name: used
+ description: The input barcoded cell sample or amplified cDNA from which the library
+ was derived from.
+ exactly_one_of:
+ - range: BarcodedCellSample
+ - range: AmplifiedCdna
+ category:
+ name: category
+ pattern: ^bican:[A-Z][A-Za-z]+$
+attributes:
+ method:
+ name: method
+ local_names:
+ NIMP:
+ local_name_source: NIMP
+ local_name_value: library_technique
+ description: Standardized nomenclature to describe the specific library method
+ used. This specifies the alignment method required for the library. For example,
+ 10xV3.1 (for RNASeq single assay), 10xMult-GEX (for RNASeq multiome assay),
+ and 10xMult-ATAC (for ATACSeq multiome assay).
+ in_subset:
+ - analysis
+ - tracking
+ - alignment
+ from_schema: https://identifiers.org/brain-bican/library-generation-schema
+ exact_mappings:
+ - NIMP:PD-AJAJCN35
+ slot_uri: bican:7b60d59e-fdd7-4b27-a2d4-cae9b69103a6
+ alias: library method
+ domain_of:
+ - CellBarcoding
+ - LibraryConstruction
+ range: library_technique
+ process_date:
+ name: process_date
+ local_names:
+ NIMP:
+ local_name_source: NIMP
+ local_name_value: library_preparation_date
+ description: Date of library construction.
+ from_schema: https://identifiers.org/brain-bican/library-generation-schema
+ exact_mappings:
+ - NIMP:PD-JCJCNM35
+ slot_uri: bican:9c2f575d-1b64-451d-894f-656861afe07a
+ alias: library creation date
+ domain_of:
+ - CellDissociation
+ - CellEnrichment
+ - CellBarcoding
+ - CdnaAmplification
+ - LibraryConstruction
+ - LibraryPooling
+ range: date
+ input_quantity_ng:
+ name: input_quantity_ng
+ local_names:
+ NIMP:
+ local_name_source: NIMP
+ local_name_value: library_input_ng
+ description: Amount of cDNA going into library construction in nanograms.
+ in_subset:
+ - analysis
+ from_schema: https://identifiers.org/brain-bican/library-generation-schema
+ exact_mappings:
+ - NIMP:PD-AFAFXP37
+ rank: 1000
+ slot_uri: bican:e4d31d97-722d-4771-a0e4-e6062190f2c1
+ alias: library input ng
+ domain_of:
+ - LibraryConstruction
+ range: float
+ set:
+ name: set
+ local_names:
+ NIMP:
+ local_name_source: NIMP
+ local_name_value: library_prep_set
+ description: Library set, containing multiple library_names that were processed
+ at the same time.
+ in_subset:
+ - analysis
+ from_schema: https://identifiers.org/brain-bican/library-generation-schema
+ exact_mappings:
+ - NIMP:PD-PCPCVR50
+ slot_uri: bican:b124ffa9-9134-4a61-a30d-bb191b2fc7fa
+ alias: library prep set
+ domain_of:
+ - CdnaAmplification
+ - LibraryConstruction
+ range: string
+
+name: LibraryConstruction
+description: The process of constructing a library from input material (such as amplified
+ cDNA or barcoded cell sample) derived from one or more cell samples. cDNA is fragmented
+ into smaller pieces appropriate for sequencing and at the same time a library index
+ barcode is incorporated to enable identification of library origin, allowing libraries
+ to be pooled together for sequencing.
+in_subset:
+- bican
+- library_generation
+from_schema: https://identifiers.org/brain-bican/library-generation-schema
+is_a: procedure
+mixins:
+- ProvActivity
+slot_usage:
+ used:
+ name: used
+ description: The input barcoded cell sample or amplified cDNA from which the library
+ was derived from.
+ exactly_one_of:
+ - range: BarcodedCellSample
+ - range: AmplifiedCdna
+ category:
+ name: category
+ pattern: ^bican:[A-Z][A-Za-z]+$
+attributes:
+ method:
+ name: method
+ local_names:
+ NIMP:
+ local_name_source: NIMP
+ local_name_value: library_technique
+ description: Standardized nomenclature to describe the specific library method
+ used. This specifies the alignment method required for the library. For example,
+ 10xV3.1 (for RNASeq single assay), 10xMult-GEX (for RNASeq multiome assay),
+ and 10xMult-ATAC (for ATACSeq multiome assay).
+ in_subset:
+ - analysis
+ - tracking
+ - alignment
+ from_schema: https://identifiers.org/brain-bican/library-generation-schema
+ exact_mappings:
+ - NIMP:PD-AJAJCN35
+ slot_uri: bican:7b60d59e-fdd7-4b27-a2d4-cae9b69103a6
+ alias: library method
+ owner: LibraryConstruction
+ domain_of:
+ - CellBarcoding
+ - LibraryConstruction
+ range: library_technique
+ process_date:
+ name: process_date
+ local_names:
+ NIMP:
+ local_name_source: NIMP
+ local_name_value: library_preparation_date
+ description: Date of library construction.
+ from_schema: https://identifiers.org/brain-bican/library-generation-schema
+ exact_mappings:
+ - NIMP:PD-JCJCNM35
+ slot_uri: bican:9c2f575d-1b64-451d-894f-656861afe07a
+ alias: library creation date
+ owner: LibraryConstruction
+ domain_of:
+ - CellDissociation
+ - CellEnrichment
+ - CellBarcoding
+ - CdnaAmplification
+ - LibraryConstruction
+ - LibraryPooling
+ range: date
+ input_quantity_ng:
+ name: input_quantity_ng
+ local_names:
+ NIMP:
+ local_name_source: NIMP
+ local_name_value: library_input_ng
+ description: Amount of cDNA going into library construction in nanograms.
+ in_subset:
+ - analysis
+ from_schema: https://identifiers.org/brain-bican/library-generation-schema
+ exact_mappings:
+ - NIMP:PD-AFAFXP37
+ rank: 1000
+ slot_uri: bican:e4d31d97-722d-4771-a0e4-e6062190f2c1
+ alias: library input ng
+ owner: LibraryConstruction
+ domain_of:
+ - LibraryConstruction
+ range: float
+ set:
+ name: set
+ local_names:
+ NIMP:
+ local_name_source: NIMP
+ local_name_value: library_prep_set
+ description: Library set, containing multiple library_names that were processed
+ at the same time.
+ in_subset:
+ - analysis
+ from_schema: https://identifiers.org/brain-bican/library-generation-schema
+ exact_mappings:
+ - NIMP:PD-PCPCVR50
+ slot_uri: bican:b124ffa9-9134-4a61-a30d-bb191b2fc7fa
+ alias: library prep set
+ owner: LibraryConstruction
+ domain_of:
+ - CdnaAmplification
+ - LibraryConstruction
+ range: string
+ used:
+ name: used
+ description: The input barcoded cell sample or amplified cDNA from which the library
+ was derived from.
+ from_schema: https://identifiers.org/brain-bican/library-generation-schema
+ rank: 1000
+ slot_uri: prov:used
+ alias: used
+ owner: LibraryConstruction
+ domain_of:
+ - DissectionRoiDelineation
+ - TissueDissection
+ - CellDissociation
+ - CellEnrichment
+ - EnrichedCellSampleSplitting
+ - CellBarcoding
+ - CdnaAmplification
+ - LibraryConstruction
+ - LibraryPooling
+ - ProvActivity
+ range: ProvEntity
+ exactly_one_of:
+ - range: BarcodedCellSample
+ - range: AmplifiedCdna
+ id:
+ name: id
+ definition_uri: https://w3id.org/biolink/vocab/id
+ description: A unique identifier for an entity. Must be either a CURIE shorthand
+ for a URI or a complete URI
+ in_subset:
+ - translator_minimal
+ from_schema: https://identifiers.org/brain-bican/library-generation-schema
+ exact_mappings:
+ - AGRKB:primaryId
+ - gff3:ID
+ - gpi:DB_Object_ID
+ rank: 1000
+ domain: entity
+ slot_uri: biolink:id
+ identifier: true
+ alias: id
+ owner: LibraryConstruction
+ domain_of:
+ - ontology class
+ - entity
+ - attribute
+ - named thing
+ - taxonomic rank
+ - organism taxon
+ - information content entity
+ - dataset
+ - physical entity
+ - activity
+ - procedure
+ - material sample
+ - biological entity
+ - gene
+ - genome
+ range: string
+ required: true
+ iri:
+ name: iri
+ definition_uri: https://w3id.org/biolink/vocab/iri
+ description: An IRI for an entity. This is determined by the id using expansion
+ rules.
+ in_subset:
+ - translator_minimal
+ - samples
+ from_schema: https://identifiers.org/brain-bican/library-generation-schema
+ exact_mappings:
+ - WIKIDATA_PROPERTY:P854
+ rank: 1000
+ slot_uri: biolink:iri
+ alias: iri
+ owner: LibraryConstruction
+ domain_of:
+ - attribute
+ - entity
+ - named thing
+ - organism taxon
+ - information content entity
+ - dataset
+ - physical entity
+ - activity
+ - procedure
+ - material sample
+ - biological entity
+ - gene
+ - genome
+ range: iri type
+ category:
+ name: category
+ definition_uri: https://w3id.org/biolink/vocab/category
+ description: Name of the high level ontology class in which this entity is categorized.
+ Corresponds to the label for the biolink entity type class. In a neo4j database
+ this MAY correspond to the neo4j label tag. In an RDF database it should be
+ a biolink model class URI. This field is multi-valued. It should include values
+ for ancestors of the biolink class; for example, a protein such as Shh would
+ have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`.
+ In an RDF database, nodes will typically have an rdf:type triples. This can
+ be to the most specific biolink class, or potentially to a class more specific
+ than something in biolink. For example, a sequence feature `f` may have a rdf:type
+ assertion to a SO class such as TF_binding_site, which is more specific than
+ anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity,
+ biolink:NamedThing}
+ in_subset:
+ - translator_minimal
+ from_schema: https://identifiers.org/brain-bican/library-generation-schema
+ rank: 1000
+ is_a: type
+ domain: entity
+ slot_uri: biolink:category
+ designates_type: true
+ alias: category
+ owner: LibraryConstruction
+ domain_of:
+ - entity
+ - attribute
+ - named thing
+ - organism taxon
+ - information content entity
+ - dataset
+ - physical entity
+ - activity
+ - procedure
+ - material sample
+ - biological entity
+ - gene
+ - genome
+ is_class_field: true
+ range: uriorcurie
+ multivalued: true
+ pattern: ^bican:[A-Z][A-Za-z]+$
+ type:
+ name: type
+ definition_uri: https://w3id.org/biolink/vocab/type
+ from_schema: https://identifiers.org/brain-bican/library-generation-schema
+ mappings:
+ - rdf:type
+ exact_mappings:
+ - gff3:type
+ - gpi:DB_Object_Type
+ rank: 1000
+ domain: entity
+ slot_uri: rdf:type
+ alias: type
+ owner: LibraryConstruction
+ domain_of:
+ - entity
+ - attribute
+ - named thing
+ - organism taxon
+ - information content entity
+ - dataset
+ - physical entity
+ - activity
+ - procedure
+ - material sample
+ - biological entity
+ - gene
+ - genome
+ range: string
+ multivalued: true
+ name:
+ name: name
+ definition_uri: https://w3id.org/biolink/vocab/name
+ description: A human-readable name for an attribute or entity.
+ in_subset:
+ - translator_minimal
+ - samples
+ from_schema: https://identifiers.org/brain-bican/library-generation-schema
+ aliases:
+ - label
+ - display name
+ - title
+ mappings:
+ - rdfs:label
+ exact_mappings:
+ - gff3:Name
+ - gpi:DB_Object_Name
+ narrow_mappings:
+ - dct:title
+ - WIKIDATA_PROPERTY:P1476
+ rank: 1000
+ domain: entity
+ slot_uri: rdfs:label
+ alias: name
+ owner: LibraryConstruction
+ domain_of:
+ - attribute
+ - entity
+ - macromolecular machine mixin
+ - Donor
+ - BrainSlab
+ - TissueSample
+ - DissociatedCellSample
+ - EnrichedCellSample
+ - BarcodedCellSample
+ - AmplifiedCdna
+ - Library
+ - LibraryAliquot
+ - LibraryPool
+ - DissectionRoiPolygon
+ - named thing
+ - organism taxon
+ - information content entity
+ - dataset
+ - physical entity
+ - activity
+ - procedure
+ - material sample
+ - biological entity
+ - gene or gene product
+ - gene
+ - genome
+ range: label type
+ description:
+ name: description
+ definition_uri: https://w3id.org/biolink/vocab/description
+ description: a human-readable description of an entity
+ in_subset:
+ - translator_minimal
+ from_schema: https://identifiers.org/brain-bican/library-generation-schema
+ aliases:
+ - definition
+ mappings:
+ - dct:description
+ exact_mappings:
+ - IAO:0000115
+ - skos:definitions
+ narrow_mappings:
+ - gff3:Description
+ rank: 1000
+ slot_uri: dct:description
+ alias: description
+ owner: LibraryConstruction
+ domain_of:
+ - entity
+ - attribute
+ - named thing
+ - organism taxon
+ - information content entity
+ - dataset
+ - physical entity
+ - activity
+ - procedure
+ - material sample
+ - biological entity
+ - gene
+ - genome
+ range: narrative text
+ has attribute:
+ name: has attribute
+ definition_uri: https://w3id.org/biolink/vocab/has_attribute
+ description: connects any entity to an attribute
+ in_subset:
+ - samples
+ from_schema: https://identifiers.org/brain-bican/library-generation-schema
+ exact_mappings:
+ - SIO:000008
+ close_mappings:
+ - OBI:0001927
+ narrow_mappings:
+ - OBAN:association_has_subject_property
+ - OBAN:association_has_object_property
+ - CPT:has_possibly_included_panel_element
+ - DRUGBANK:category
+ - EFO:is_executed_in
+ - HANCESTRO:0301
+ - LOINC:has_action_guidance
+ - LOINC:has_adjustment
+ - LOINC:has_aggregation_view
+ - LOINC:has_approach_guidance
+ - LOINC:has_divisor
+ - LOINC:has_exam
+ - LOINC:has_method
+ - LOINC:has_modality_subtype
+ - LOINC:has_object_guidance
+ - LOINC:has_scale
+ - LOINC:has_suffix
+ - LOINC:has_time_aspect
+ - LOINC:has_time_modifier
+ - LOINC:has_timing_of
+ - NCIT:R88
+ - NCIT:eo_disease_has_property_or_attribute
+ - NCIT:has_data_element
+ - NCIT:has_pharmaceutical_administration_method
+ - NCIT:has_pharmaceutical_basic_dose_form
+ - NCIT:has_pharmaceutical_intended_site
+ - NCIT:has_pharmaceutical_release_characteristics
+ - NCIT:has_pharmaceutical_state_of_matter
+ - NCIT:has_pharmaceutical_transformation
+ - NCIT:is_qualified_by
+ - NCIT:qualifier_applies_to
+ - NCIT:role_has_domain
+ - NCIT:role_has_range
+ - INO:0000154
+ - HANCESTRO:0308
+ - OMIM:has_inheritance_type
+ - orphanet:C016
+ - orphanet:C017
+ - RO:0000053
+ - RO:0000086
+ - RO:0000087
+ - SNOMED:has_access
+ - SNOMED:has_clinical_course
+ - SNOMED:has_count_of_base_of_active_ingredient
+ - SNOMED:has_dose_form_administration_method
+ - SNOMED:has_dose_form_release_characteristic
+ - SNOMED:has_dose_form_transformation
+ - SNOMED:has_finding_context
+ - SNOMED:has_finding_informer
+ - SNOMED:has_inherent_attribute
+ - SNOMED:has_intent
+ - SNOMED:has_interpretation
+ - SNOMED:has_laterality
+ - SNOMED:has_measurement_method
+ - SNOMED:has_method
+ - SNOMED:has_priority
+ - SNOMED:has_procedure_context
+ - SNOMED:has_process_duration
+ - SNOMED:has_property
+ - SNOMED:has_revision_status
+ - SNOMED:has_scale_type
+ - SNOMED:has_severity
+ - SNOMED:has_specimen
+ - SNOMED:has_state_of_matter
+ - SNOMED:has_subject_relationship_context
+ - SNOMED:has_surgical_approach
+ - SNOMED:has_technique
+ - SNOMED:has_temporal_context
+ - SNOMED:has_time_aspect
+ - SNOMED:has_units
+ - UMLS:has_structural_class
+ - UMLS:has_supported_concept_property
+ - UMLS:has_supported_concept_relationship
+ - UMLS:may_be_qualified_by
+ rank: 1000
+ domain: entity
+ slot_uri: biolink:has_attribute
+ alias: has_attribute
+ owner: LibraryConstruction
+ domain_of:
+ - entity
+ - attribute
+ - named thing
+ - organism taxon
+ - information content entity
+ - dataset
+ - physical entity
+ - activity
+ - procedure
+ - material sample
+ - biological entity
+ - gene
+ - genome
+ range: attribute
+ multivalued: true
+ deprecated:
+ name: deprecated
+ definition_uri: https://w3id.org/biolink/vocab/deprecated
+ description: A boolean flag indicating that an entity is no longer considered
+ current or valid.
+ from_schema: https://identifiers.org/brain-bican/library-generation-schema
+ exact_mappings:
+ - oboInOwl:ObsoleteClass
+ rank: 1000
+ slot_uri: biolink:deprecated
+ alias: deprecated
+ owner: LibraryConstruction
+ domain_of:
+ - entity
+ - attribute
+ - named thing
+ - organism taxon
+ - information content entity
+ - dataset
+ - physical entity
+ - activity
+ - procedure
+ - material sample
+ - biological entity
+ - gene
+ - genome
+ range: boolean
+ provided by:
+ name: provided by
+ definition_uri: https://w3id.org/biolink/vocab/provided_by
+ description: The value in this node property represents the knowledge provider
+ that created or assembled the node and all of its attributes. Used internally
+ to represent how a particular node made its way into a knowledge provider or
+ graph.
+ from_schema: https://identifiers.org/brain-bican/library-generation-schema
+ rank: 1000
+ is_a: node property
+ domain: named thing
+ slot_uri: biolink:provided_by
+ alias: provided_by
+ owner: LibraryConstruction
+ domain_of:
+ - named thing
+ - attribute
+ - organism taxon
+ - information content entity
+ - dataset
+ - physical entity
+ - activity
+ - procedure
+ - material sample
+ - biological entity
+ - gene
+ - genome
+ range: string
+ multivalued: true
+ xref:
+ name: xref
+ definition_uri: https://w3id.org/biolink/vocab/xref
+ description: A database cross reference or alternative identifier for a NamedThing
+ or edge between two NamedThings. This property should point to a database record
+ or webpage that supports the existence of the edge, or gives more detail about
+ the edge. This property can be used on a node or edge to provide multiple URIs
+ or CURIE cross references.
+ in_subset:
+ - translator_minimal
+ from_schema: https://identifiers.org/brain-bican/library-generation-schema
+ aliases:
+ - dbxref
+ - Dbxref
+ - DbXref
+ - record_url
+ - source_record_urls
+ narrow_mappings:
+ - gff3:Dbxref
+ - gpi:DB_Xrefs
+ rank: 1000
+ domain: named thing
+ slot_uri: biolink:xref
+ alias: xref
+ owner: LibraryConstruction
+ domain_of:
+ - named thing
+ - gene
+ - attribute
+ - organism taxon
+ - information content entity
+ - dataset
+ - physical entity
+ - activity
+ - procedure
+ - material sample
+ - biological entity
+ - genome
+ range: uriorcurie
+ multivalued: true
+ full name:
+ name: full name
+ definition_uri: https://w3id.org/biolink/vocab/full_name
+ description: a long-form human readable name for a thing
+ from_schema: https://identifiers.org/brain-bican/library-generation-schema
+ rank: 1000
+ is_a: node property
+ domain: named thing
+ slot_uri: biolink:full_name
+ alias: full_name
+ owner: LibraryConstruction
+ domain_of:
+ - named thing
+ - attribute
+ - organism taxon
+ - information content entity
+ - dataset
+ - physical entity
+ - activity
+ - procedure
+ - material sample
+ - biological entity
+ - gene
+ - genome
+ range: label type
+ synonym:
+ name: synonym
+ definition_uri: https://w3id.org/biolink/vocab/synonym
+ description: Alternate human-readable names for a thing
+ in_subset:
+ - translator_minimal
+ from_schema: https://identifiers.org/brain-bican/library-generation-schema
+ aliases:
+ - alias
+ narrow_mappings:
+ - skos:altLabel
+ - gff3:Alias
+ - AGRKB:synonyms
+ - gpi:DB_Object_Synonyms
+ - HANCESTRO:0330
+ - IAO:0000136
+ - RXNORM:has_tradename
+ rank: 1000
+ is_a: node property
+ domain: named thing
+ slot_uri: biolink:synonym
+ alias: synonym
+ owner: LibraryConstruction
+ domain_of:
+ - named thing
+ - attribute
+ - organism taxon
+ - information content entity
+ - dataset
+ - physical entity
+ - activity
+ - procedure
+ - material sample
+ - biological entity
+ - gene
+ - genome
+ range: label type
+ multivalued: true
+
+A subset of classes that are associated with library generation.
+URI: LibraryGeneration
+| Class | +Description | +
|---|---|
| AmplifiedCdna | +A collection of cDNA molecules derived and amplified from an input barcoded c... | +
| BarcodedCellSample | +A collection of molecularly barcoded cells | +
| CdnaAmplification | +The process of creating a collection of cDNA molecules derived and amplified ... | +
| CellBarcoding | +The process of adding a molecular barcode to individual cells in a sample | +
| CellDissociation | +The process of generating dissociated cells from an input tissue sample | +
| CellEnrichment | +The process of enriching a dissociated cell sample by including or excluding ... | +
| DissectionRoiDelineation | +The process of outlining a region of interest on a brain slab image to guide ... | +
| DissociatedCellSample | +A collection of dissociated cells or nuclei derived from dissociation of a ti... | +
| EnrichedCellSample | +A collection of enriched cells or nuclei after enrichment process, usually vi... | +
| EnrichedCellSampleSplitting | +The process of splitting an enriched cell sample into several portions | +
| Library | +A collection of fragmented and barcode-indexed DNA molecules for sequencing | +
| LibraryAliquot | +One library in the library pool | +
| LibraryConstruction | +The process of constructing a library from input material (such as amplified ... | +
| LibraryPool | +A library pool is made up of library aliquots from multiple libraries | +
| LibraryPooling | +The process of constructing of a libray pool by combining library aliquots fr... | +
| TissueDissection | +The process of dissecting a tissue sample from a brain slab guided by a disse... | +
| TissueSample | +The final intact piece of tissue before cell or nuclei prep | +
A library pool is made up of library aliquots from multiple libraries. Each library aliquot in a library pool will have a unique R1/R2 index to allow for sequencing together then separating the sequencing output by originating library aliquot through the process of demultiplexing.
+URI: bican:LibraryPool
+| Name | +Cardinality and Range | +Description | +Inheritance | +
|---|---|---|---|
| was_generated_by | +0..1 LibraryPooling |
+The pooling process from which the library pool was generated by | +direct | +
| was_derived_from | +* LibraryAliquot |
+The input aliquot(s) from which the library pool was derived from | +direct | +
| name | +0..1 LabelType |
+Library lab's library pool name | +direct | +
| local_tube_id | +0..1 String |
+Library Pool Tube local name | +direct | +
| id | +1 String |
+A unique identifier for an entity | +NamedThing, PhysicalEntity, MaterialSample, Entity | +
| iri | +0..1 IriType |
+An IRI for an entity | +NamedThing, PhysicalEntity, MaterialSample, Entity | +
| category | +* Uriorcurie |
+Name of the high level ontology class in which this entity is categorized | +NamedThing, PhysicalEntity, MaterialSample, Entity | +
| type | +* String |
++ | NamedThing, PhysicalEntity, MaterialSample, Entity | +
| description | +0..1 NarrativeText |
+a human-readable description of an entity | +NamedThing, PhysicalEntity, MaterialSample, Entity | +
| has_attribute | +* Attribute |
+connects any entity to an attribute | +NamedThing, PhysicalEntity, MaterialSample, Entity | +
| deprecated | +0..1 Boolean |
+A boolean flag indicating that an entity is no longer considered current or v... | +NamedThing, PhysicalEntity, MaterialSample, Entity | +
| provided_by | +* String |
+The value in this node property represents the knowledge provider that create... | +NamedThing, PhysicalEntity, MaterialSample | +
| xref | +* Uriorcurie |
+A database cross reference or alternative identifier for a NamedThing or edge... | +NamedThing, PhysicalEntity, MaterialSample | +
| full_name | +0..1 LabelType |
+a long-form human readable name for a thing | +NamedThing, PhysicalEntity, MaterialSample | +
| synonym | +* LabelType |
+Alternate human-readable names for a thing | +NamedThing, PhysicalEntity, MaterialSample | +
| Mapping Type | +Mapped Value | +
|---|---|
| self | +bican:LibraryPool | +
| native | +bican:LibraryPool | +
| exact | +NIMP:Library%20Pool | +
name: LibraryPool
+description: A library pool is made up of library aliquots from multiple libraries.
+ Each library aliquot in a library pool will have a unique R1/R2 index to allow for
+ sequencing together then separating the sequencing output by originating library
+ aliquot through the process of demultiplexing.
+in_subset:
+- bican
+- library_generation
+from_schema: https://identifiers.org/brain-bican/library-generation-schema
+exact_mappings:
+- NIMP:Library%20Pool
+is_a: material sample
+mixins:
+- ProvEntity
+slots:
+- was_generated_by
+- was_derived_from
+- name
+slot_usage:
+ was_generated_by:
+ name: was_generated_by
+ description: The pooling process from which the library pool was generated by.
+ range: LibraryPooling
+ was_derived_from:
+ name: was_derived_from
+ description: The input aliquot(s) from which the library pool was derived from.
+ exact_mappings:
+ - NIMP:has_parent
+ range: LibraryAliquot
+ multivalued: true
+ name:
+ name: name
+ description: Library lab's library pool name. For some labs this may be the same
+ as "Libray pool tube local name". Other labs distinguish between the local
+ tube label of the library pool and the library pool name provided to SeqCore
+ for tracking. Local Pool Name is used to communicate sequencing status between
+ SeqCore and Library Labs.
+ exact_mappings:
+ - NIMP:PD-KKIAPA48
+ slot_uri: bican:29e0578b-6427-4c93-b29b-bde27fbadeec
+ category:
+ name: category
+ pattern: ^bican:[A-Z][A-Za-z]+$
+attributes:
+ local_tube_id:
+ name: local_tube_id
+ local_names:
+ NIMP:
+ local_name_source: NIMP
+ local_name_value: library_pool_local_tube_id
+ description: Library Pool Tube local name. Label of the tube containing the library
+ pool, which is made up of multiple library_aliquots. This is a Library Lab
+ local tube name, before the pool is aliquoted to the Seq Core provided tube
+ 'Library Pool Tube Name'.
+ in_subset:
+ - analysis
+ - tracking
+ from_schema: https://identifiers.org/brain-bican/library-generation-schema
+ exact_mappings:
+ - NIMP:PD-WNYWPA48
+ rank: 1000
+ slot_uri: bican:f1fdea98-7849-4def-a62f-a04cbbf98922
+ alias: library_pool_tube_internal_label
+ domain_of:
+ - LibraryPool
+ range: string
+
+name: LibraryPool
+description: A library pool is made up of library aliquots from multiple libraries.
+ Each library aliquot in a library pool will have a unique R1/R2 index to allow for
+ sequencing together then separating the sequencing output by originating library
+ aliquot through the process of demultiplexing.
+in_subset:
+- bican
+- library_generation
+from_schema: https://identifiers.org/brain-bican/library-generation-schema
+exact_mappings:
+- NIMP:Library%20Pool
+is_a: material sample
+mixins:
+- ProvEntity
+slot_usage:
+ was_generated_by:
+ name: was_generated_by
+ description: The pooling process from which the library pool was generated by.
+ range: LibraryPooling
+ was_derived_from:
+ name: was_derived_from
+ description: The input aliquot(s) from which the library pool was derived from.
+ exact_mappings:
+ - NIMP:has_parent
+ range: LibraryAliquot
+ multivalued: true
+ name:
+ name: name
+ description: Library lab's library pool name. For some labs this may be the same
+ as "Libray pool tube local name". Other labs distinguish between the local
+ tube label of the library pool and the library pool name provided to SeqCore
+ for tracking. Local Pool Name is used to communicate sequencing status between
+ SeqCore and Library Labs.
+ exact_mappings:
+ - NIMP:PD-KKIAPA48
+ slot_uri: bican:29e0578b-6427-4c93-b29b-bde27fbadeec
+ category:
+ name: category
+ pattern: ^bican:[A-Z][A-Za-z]+$
+attributes:
+ local_tube_id:
+ name: local_tube_id
+ local_names:
+ NIMP:
+ local_name_source: NIMP
+ local_name_value: library_pool_local_tube_id
+ description: Library Pool Tube local name. Label of the tube containing the library
+ pool, which is made up of multiple library_aliquots. This is a Library Lab
+ local tube name, before the pool is aliquoted to the Seq Core provided tube
+ 'Library Pool Tube Name'.
+ in_subset:
+ - analysis
+ - tracking
+ from_schema: https://identifiers.org/brain-bican/library-generation-schema
+ exact_mappings:
+ - NIMP:PD-WNYWPA48
+ rank: 1000
+ slot_uri: bican:f1fdea98-7849-4def-a62f-a04cbbf98922
+ alias: library_pool_tube_internal_label
+ owner: LibraryPool
+ domain_of:
+ - LibraryPool
+ range: string
+ was_generated_by:
+ name: was_generated_by
+ description: The pooling process from which the library pool was generated by.
+ from_schema: https://identifiers.org/brain-bican/library-generation-schema
+ rank: 1000
+ slot_uri: prov:wasGeneratedBy
+ alias: was_generated_by
+ owner: LibraryPool
+ domain_of:
+ - TissueSample
+ - DissociatedCellSample
+ - EnrichedCellSample
+ - BarcodedCellSample
+ - AmplifiedCdna
+ - Library
+ - LibraryPool
+ - DissectionRoiPolygon
+ - ProvEntity
+ range: LibraryPooling
+ was_derived_from:
+ name: was_derived_from
+ description: The input aliquot(s) from which the library pool was derived from.
+ from_schema: https://identifiers.org/brain-bican/library-generation-schema
+ exact_mappings:
+ - NIMP:has_parent
+ rank: 1000
+ slot_uri: prov:wasDerivedFrom
+ alias: was_derived_from
+ owner: LibraryPool
+ domain_of:
+ - BrainSlab
+ - TissueSample
+ - DissociatedCellSample
+ - EnrichedCellSample
+ - BarcodedCellSample
+ - AmplifiedCdna
+ - Library
+ - LibraryAliquot
+ - LibraryPool
+ - ProvEntity
+ range: LibraryAliquot
+ multivalued: true
+ name:
+ name: name
+ definition_uri: https://w3id.org/biolink/vocab/name
+ description: Library lab's library pool name. For some labs this may be the same
+ as "Libray pool tube local name". Other labs distinguish between the local
+ tube label of the library pool and the library pool name provided to SeqCore
+ for tracking. Local Pool Name is used to communicate sequencing status between
+ SeqCore and Library Labs.
+ in_subset:
+ - translator_minimal
+ - samples
+ from_schema: https://identifiers.org/brain-bican/library-generation-schema
+ aliases:
+ - label
+ - display name
+ - title
+ mappings:
+ - rdfs:label
+ exact_mappings:
+ - NIMP:PD-KKIAPA48
+ narrow_mappings:
+ - dct:title
+ - WIKIDATA_PROPERTY:P1476
+ rank: 1000
+ domain: entity
+ slot_uri: bican:29e0578b-6427-4c93-b29b-bde27fbadeec
+ alias: name
+ owner: LibraryPool
+ domain_of:
+ - attribute
+ - entity
+ - macromolecular machine mixin
+ - Donor
+ - BrainSlab
+ - TissueSample
+ - DissociatedCellSample
+ - EnrichedCellSample
+ - BarcodedCellSample
+ - AmplifiedCdna
+ - Library
+ - LibraryAliquot
+ - LibraryPool
+ - DissectionRoiPolygon
+ - named thing
+ - organism taxon
+ - information content entity
+ - dataset
+ - physical entity
+ - activity
+ - procedure
+ - material sample
+ - biological entity
+ - gene or gene product
+ - gene
+ - genome
+ range: label type
+ id:
+ name: id
+ definition_uri: https://w3id.org/biolink/vocab/id
+ description: A unique identifier for an entity. Must be either a CURIE shorthand
+ for a URI or a complete URI
+ in_subset:
+ - translator_minimal
+ from_schema: https://identifiers.org/brain-bican/library-generation-schema
+ exact_mappings:
+ - AGRKB:primaryId
+ - gff3:ID
+ - gpi:DB_Object_ID
+ rank: 1000
+ domain: entity
+ slot_uri: biolink:id
+ identifier: true
+ alias: id
+ owner: LibraryPool
+ domain_of:
+ - ontology class
+ - entity
+ - attribute
+ - named thing
+ - taxonomic rank
+ - organism taxon
+ - information content entity
+ - dataset
+ - physical entity
+ - activity
+ - procedure
+ - material sample
+ - biological entity
+ - gene
+ - genome
+ range: string
+ required: true
+ iri:
+ name: iri
+ definition_uri: https://w3id.org/biolink/vocab/iri
+ description: An IRI for an entity. This is determined by the id using expansion
+ rules.
+ in_subset:
+ - translator_minimal
+ - samples
+ from_schema: https://identifiers.org/brain-bican/library-generation-schema
+ exact_mappings:
+ - WIKIDATA_PROPERTY:P854
+ rank: 1000
+ slot_uri: biolink:iri
+ alias: iri
+ owner: LibraryPool
+ domain_of:
+ - attribute
+ - entity
+ - named thing
+ - organism taxon
+ - information content entity
+ - dataset
+ - physical entity
+ - activity
+ - procedure
+ - material sample
+ - biological entity
+ - gene
+ - genome
+ range: iri type
+ category:
+ name: category
+ definition_uri: https://w3id.org/biolink/vocab/category
+ description: Name of the high level ontology class in which this entity is categorized.
+ Corresponds to the label for the biolink entity type class. In a neo4j database
+ this MAY correspond to the neo4j label tag. In an RDF database it should be
+ a biolink model class URI. This field is multi-valued. It should include values
+ for ancestors of the biolink class; for example, a protein such as Shh would
+ have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`.
+ In an RDF database, nodes will typically have an rdf:type triples. This can
+ be to the most specific biolink class, or potentially to a class more specific
+ than something in biolink. For example, a sequence feature `f` may have a rdf:type
+ assertion to a SO class such as TF_binding_site, which is more specific than
+ anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity,
+ biolink:NamedThing}
+ in_subset:
+ - translator_minimal
+ from_schema: https://identifiers.org/brain-bican/library-generation-schema
+ rank: 1000
+ is_a: type
+ domain: entity
+ slot_uri: biolink:category
+ designates_type: true
+ alias: category
+ owner: LibraryPool
+ domain_of:
+ - entity
+ - attribute
+ - named thing
+ - organism taxon
+ - information content entity
+ - dataset
+ - physical entity
+ - activity
+ - procedure
+ - material sample
+ - biological entity
+ - gene
+ - genome
+ is_class_field: true
+ range: uriorcurie
+ multivalued: true
+ pattern: ^bican:[A-Z][A-Za-z]+$
+ type:
+ name: type
+ definition_uri: https://w3id.org/biolink/vocab/type
+ from_schema: https://identifiers.org/brain-bican/library-generation-schema
+ mappings:
+ - rdf:type
+ exact_mappings:
+ - gff3:type
+ - gpi:DB_Object_Type
+ rank: 1000
+ domain: entity
+ slot_uri: rdf:type
+ alias: type
+ owner: LibraryPool
+ domain_of:
+ - entity
+ - attribute
+ - named thing
+ - organism taxon
+ - information content entity
+ - dataset
+ - physical entity
+ - activity
+ - procedure
+ - material sample
+ - biological entity
+ - gene
+ - genome
+ range: string
+ multivalued: true
+ description:
+ name: description
+ definition_uri: https://w3id.org/biolink/vocab/description
+ description: a human-readable description of an entity
+ in_subset:
+ - translator_minimal
+ from_schema: https://identifiers.org/brain-bican/library-generation-schema
+ aliases:
+ - definition
+ mappings:
+ - dct:description
+ exact_mappings:
+ - IAO:0000115
+ - skos:definitions
+ narrow_mappings:
+ - gff3:Description
+ rank: 1000
+ slot_uri: dct:description
+ alias: description
+ owner: LibraryPool
+ domain_of:
+ - entity
+ - attribute
+ - named thing
+ - organism taxon
+ - information content entity
+ - dataset
+ - physical entity
+ - activity
+ - procedure
+ - material sample
+ - biological entity
+ - gene
+ - genome
+ range: narrative text
+ has attribute:
+ name: has attribute
+ definition_uri: https://w3id.org/biolink/vocab/has_attribute
+ description: connects any entity to an attribute
+ in_subset:
+ - samples
+ from_schema: https://identifiers.org/brain-bican/library-generation-schema
+ exact_mappings:
+ - SIO:000008
+ close_mappings:
+ - OBI:0001927
+ narrow_mappings:
+ - OBAN:association_has_subject_property
+ - OBAN:association_has_object_property
+ - CPT:has_possibly_included_panel_element
+ - DRUGBANK:category
+ - EFO:is_executed_in
+ - HANCESTRO:0301
+ - LOINC:has_action_guidance
+ - LOINC:has_adjustment
+ - LOINC:has_aggregation_view
+ - LOINC:has_approach_guidance
+ - LOINC:has_divisor
+ - LOINC:has_exam
+ - LOINC:has_method
+ - LOINC:has_modality_subtype
+ - LOINC:has_object_guidance
+ - LOINC:has_scale
+ - LOINC:has_suffix
+ - LOINC:has_time_aspect
+ - LOINC:has_time_modifier
+ - LOINC:has_timing_of
+ - NCIT:R88
+ - NCIT:eo_disease_has_property_or_attribute
+ - NCIT:has_data_element
+ - NCIT:has_pharmaceutical_administration_method
+ - NCIT:has_pharmaceutical_basic_dose_form
+ - NCIT:has_pharmaceutical_intended_site
+ - NCIT:has_pharmaceutical_release_characteristics
+ - NCIT:has_pharmaceutical_state_of_matter
+ - NCIT:has_pharmaceutical_transformation
+ - NCIT:is_qualified_by
+ - NCIT:qualifier_applies_to
+ - NCIT:role_has_domain
+ - NCIT:role_has_range
+ - INO:0000154
+ - HANCESTRO:0308
+ - OMIM:has_inheritance_type
+ - orphanet:C016
+ - orphanet:C017
+ - RO:0000053
+ - RO:0000086
+ - RO:0000087
+ - SNOMED:has_access
+ - SNOMED:has_clinical_course
+ - SNOMED:has_count_of_base_of_active_ingredient
+ - SNOMED:has_dose_form_administration_method
+ - SNOMED:has_dose_form_release_characteristic
+ - SNOMED:has_dose_form_transformation
+ - SNOMED:has_finding_context
+ - SNOMED:has_finding_informer
+ - SNOMED:has_inherent_attribute
+ - SNOMED:has_intent
+ - SNOMED:has_interpretation
+ - SNOMED:has_laterality
+ - SNOMED:has_measurement_method
+ - SNOMED:has_method
+ - SNOMED:has_priority
+ - SNOMED:has_procedure_context
+ - SNOMED:has_process_duration
+ - SNOMED:has_property
+ - SNOMED:has_revision_status
+ - SNOMED:has_scale_type
+ - SNOMED:has_severity
+ - SNOMED:has_specimen
+ - SNOMED:has_state_of_matter
+ - SNOMED:has_subject_relationship_context
+ - SNOMED:has_surgical_approach
+ - SNOMED:has_technique
+ - SNOMED:has_temporal_context
+ - SNOMED:has_time_aspect
+ - SNOMED:has_units
+ - UMLS:has_structural_class
+ - UMLS:has_supported_concept_property
+ - UMLS:has_supported_concept_relationship
+ - UMLS:may_be_qualified_by
+ rank: 1000
+ domain: entity
+ slot_uri: biolink:has_attribute
+ alias: has_attribute
+ owner: LibraryPool
+ domain_of:
+ - entity
+ - attribute
+ - named thing
+ - organism taxon
+ - information content entity
+ - dataset
+ - physical entity
+ - activity
+ - procedure
+ - material sample
+ - biological entity
+ - gene
+ - genome
+ range: attribute
+ multivalued: true
+ deprecated:
+ name: deprecated
+ definition_uri: https://w3id.org/biolink/vocab/deprecated
+ description: A boolean flag indicating that an entity is no longer considered
+ current or valid.
+ from_schema: https://identifiers.org/brain-bican/library-generation-schema
+ exact_mappings:
+ - oboInOwl:ObsoleteClass
+ rank: 1000
+ slot_uri: biolink:deprecated
+ alias: deprecated
+ owner: LibraryPool
+ domain_of:
+ - entity
+ - attribute
+ - named thing
+ - organism taxon
+ - information content entity
+ - dataset
+ - physical entity
+ - activity
+ - procedure
+ - material sample
+ - biological entity
+ - gene
+ - genome
+ range: boolean
+ provided by:
+ name: provided by
+ definition_uri: https://w3id.org/biolink/vocab/provided_by
+ description: The value in this node property represents the knowledge provider
+ that created or assembled the node and all of its attributes. Used internally
+ to represent how a particular node made its way into a knowledge provider or
+ graph.
+ from_schema: https://identifiers.org/brain-bican/library-generation-schema
+ rank: 1000
+ is_a: node property
+ domain: named thing
+ slot_uri: biolink:provided_by
+ alias: provided_by
+ owner: LibraryPool
+ domain_of:
+ - named thing
+ - attribute
+ - organism taxon
+ - information content entity
+ - dataset
+ - physical entity
+ - activity
+ - procedure
+ - material sample
+ - biological entity
+ - gene
+ - genome
+ range: string
+ multivalued: true
+ xref:
+ name: xref
+ definition_uri: https://w3id.org/biolink/vocab/xref
+ description: A database cross reference or alternative identifier for a NamedThing
+ or edge between two NamedThings. This property should point to a database record
+ or webpage that supports the existence of the edge, or gives more detail about
+ the edge. This property can be used on a node or edge to provide multiple URIs
+ or CURIE cross references.
+ in_subset:
+ - translator_minimal
+ from_schema: https://identifiers.org/brain-bican/library-generation-schema
+ aliases:
+ - dbxref
+ - Dbxref
+ - DbXref
+ - record_url
+ - source_record_urls
+ narrow_mappings:
+ - gff3:Dbxref
+ - gpi:DB_Xrefs
+ rank: 1000
+ domain: named thing
+ slot_uri: biolink:xref
+ alias: xref
+ owner: LibraryPool
+ domain_of:
+ - named thing
+ - gene
+ - attribute
+ - organism taxon
+ - information content entity
+ - dataset
+ - physical entity
+ - activity
+ - procedure
+ - material sample
+ - biological entity
+ - genome
+ range: uriorcurie
+ multivalued: true
+ full name:
+ name: full name
+ definition_uri: https://w3id.org/biolink/vocab/full_name
+ description: a long-form human readable name for a thing
+ from_schema: https://identifiers.org/brain-bican/library-generation-schema
+ rank: 1000
+ is_a: node property
+ domain: named thing
+ slot_uri: biolink:full_name
+ alias: full_name
+ owner: LibraryPool
+ domain_of:
+ - named thing
+ - attribute
+ - organism taxon
+ - information content entity
+ - dataset
+ - physical entity
+ - activity
+ - procedure
+ - material sample
+ - biological entity
+ - gene
+ - genome
+ range: label type
+ synonym:
+ name: synonym
+ definition_uri: https://w3id.org/biolink/vocab/synonym
+ description: Alternate human-readable names for a thing
+ in_subset:
+ - translator_minimal
+ from_schema: https://identifiers.org/brain-bican/library-generation-schema
+ aliases:
+ - alias
+ narrow_mappings:
+ - skos:altLabel
+ - gff3:Alias
+ - AGRKB:synonyms
+ - gpi:DB_Object_Synonyms
+ - HANCESTRO:0330
+ - IAO:0000136
+ - RXNORM:has_tradename
+ rank: 1000
+ is_a: node property
+ domain: named thing
+ slot_uri: biolink:synonym
+ alias: synonym
+ owner: LibraryPool
+ domain_of:
+ - named thing
+ - attribute
+ - organism taxon
+ - information content entity
+ - dataset
+ - physical entity
+ - activity
+ - procedure
+ - material sample
+ - biological entity
+ - gene
+ - genome
+ range: label type
+ multivalued: true
+
+The process of constructing of a libray pool by combining library aliquots from a set of input libraries. Each library aliquot in a library pool will have a unique R1/R2 index to allow for sequencing together then separating the sequencing output by originating library aliquot through the process of demultiplexing.
+URI: bican:LibraryPooling
+| Name | +Cardinality and Range | +Description | +Inheritance | +
|---|---|---|---|
| used | +* LibraryAliquot |
+The input aliquot(s) from which the library pool was derived from | +direct | +
| process_date | +0..1 String |
+Date of library pooling process | +direct | +
| id | +1 String |
+A unique identifier for an entity | +NamedThing, Procedure, Entity | +
| iri | +0..1 IriType |
+An IRI for an entity | +NamedThing, Procedure, Entity | +
| category | +* Uriorcurie |
+Name of the high level ontology class in which this entity is categorized | +NamedThing, Procedure, Entity | +
| type | +* String |
++ | NamedThing, Procedure, Entity | +
| name | +0..1 LabelType |
+A human-readable name for an attribute or entity | +NamedThing, Procedure, Entity | +
| description | +0..1 NarrativeText |
+a human-readable description of an entity | +NamedThing, Procedure, Entity | +
| has_attribute | +* Attribute |
+connects any entity to an attribute | +NamedThing, Procedure, Entity | +
| deprecated | +0..1 Boolean |
+A boolean flag indicating that an entity is no longer considered current or v... | +NamedThing, Procedure, Entity | +
| provided_by | +* String |
+The value in this node property represents the knowledge provider that create... | +NamedThing, Procedure | +
| xref | +* Uriorcurie |
+A database cross reference or alternative identifier for a NamedThing or edge... | +NamedThing, Procedure | +
| full_name | +0..1 LabelType |
+a long-form human readable name for a thing | +NamedThing, Procedure | +
| synonym | +* LabelType |
+Alternate human-readable names for a thing | +NamedThing, Procedure | +
| used by | +used in | +type | +used | +
|---|---|---|---|
| LibraryPool | +was_generated_by | +range | +LibraryPooling | +
| Mapping Type | +Mapped Value | +
|---|---|
| self | +bican:LibraryPooling | +
| native | +bican:LibraryPooling | +
name: LibraryPooling
+description: The process of constructing of a libray pool by combining library aliquots
+ from a set of input libraries. Each library aliquot in a library pool will have
+ a unique R1/R2 index to allow for sequencing together then separating the sequencing
+ output by originating library aliquot through the process of demultiplexing.
+in_subset:
+- bican
+- library_generation
+from_schema: https://identifiers.org/brain-bican/library-generation-schema
+is_a: procedure
+mixins:
+- ProvActivity
+slots:
+- used
+slot_usage:
+ used:
+ name: used
+ description: The input aliquot(s) from which the library pool was derived from.
+ range: LibraryAliquot
+ multivalued: true
+ category:
+ name: category
+ pattern: ^bican:[A-Z][A-Za-z]+$
+attributes:
+ process_date:
+ name: process_date
+ local_names:
+ NIMP:
+ local_name_source: NIMP
+ local_name_value: library_pool_preparation_date
+ description: Date of library pooling process.
+ from_schema: https://identifiers.org/brain-bican/library-generation-schema
+ exact_mappings:
+ - NIMP:PD-XUXUNM35
+ domain_of:
+ - CellDissociation
+ - CellEnrichment
+ - CellBarcoding
+ - CdnaAmplification
+ - LibraryConstruction
+ - LibraryPooling
+
+name: LibraryPooling
+description: The process of constructing of a libray pool by combining library aliquots
+ from a set of input libraries. Each library aliquot in a library pool will have
+ a unique R1/R2 index to allow for sequencing together then separating the sequencing
+ output by originating library aliquot through the process of demultiplexing.
+in_subset:
+- bican
+- library_generation
+from_schema: https://identifiers.org/brain-bican/library-generation-schema
+is_a: procedure
+mixins:
+- ProvActivity
+slot_usage:
+ used:
+ name: used
+ description: The input aliquot(s) from which the library pool was derived from.
+ range: LibraryAliquot
+ multivalued: true
+ category:
+ name: category
+ pattern: ^bican:[A-Z][A-Za-z]+$
+attributes:
+ process_date:
+ name: process_date
+ local_names:
+ NIMP:
+ local_name_source: NIMP
+ local_name_value: library_pool_preparation_date
+ description: Date of library pooling process.
+ from_schema: https://identifiers.org/brain-bican/library-generation-schema
+ exact_mappings:
+ - NIMP:PD-XUXUNM35
+ alias: process_date
+ owner: LibraryPooling
+ domain_of:
+ - CellDissociation
+ - CellEnrichment
+ - CellBarcoding
+ - CdnaAmplification
+ - LibraryConstruction
+ - LibraryPooling
+ range: string
+ used:
+ name: used
+ description: The input aliquot(s) from which the library pool was derived from.
+ from_schema: https://identifiers.org/brain-bican/library-generation-schema
+ rank: 1000
+ slot_uri: prov:used
+ alias: used
+ owner: LibraryPooling
+ domain_of:
+ - DissectionRoiDelineation
+ - TissueDissection
+ - CellDissociation
+ - CellEnrichment
+ - EnrichedCellSampleSplitting
+ - CellBarcoding
+ - CdnaAmplification
+ - LibraryConstruction
+ - LibraryPooling
+ - ProvActivity
+ range: LibraryAliquot
+ multivalued: true
+ id:
+ name: id
+ definition_uri: https://w3id.org/biolink/vocab/id
+ description: A unique identifier for an entity. Must be either a CURIE shorthand
+ for a URI or a complete URI
+ in_subset:
+ - translator_minimal
+ from_schema: https://identifiers.org/brain-bican/library-generation-schema
+ exact_mappings:
+ - AGRKB:primaryId
+ - gff3:ID
+ - gpi:DB_Object_ID
+ rank: 1000
+ domain: entity
+ slot_uri: biolink:id
+ identifier: true
+ alias: id
+ owner: LibraryPooling
+ domain_of:
+ - ontology class
+ - entity
+ - attribute
+ - named thing
+ - taxonomic rank
+ - organism taxon
+ - information content entity
+ - dataset
+ - physical entity
+ - activity
+ - procedure
+ - material sample
+ - biological entity
+ - gene
+ - genome
+ range: string
+ required: true
+ iri:
+ name: iri
+ definition_uri: https://w3id.org/biolink/vocab/iri
+ description: An IRI for an entity. This is determined by the id using expansion
+ rules.
+ in_subset:
+ - translator_minimal
+ - samples
+ from_schema: https://identifiers.org/brain-bican/library-generation-schema
+ exact_mappings:
+ - WIKIDATA_PROPERTY:P854
+ rank: 1000
+ slot_uri: biolink:iri
+ alias: iri
+ owner: LibraryPooling
+ domain_of:
+ - attribute
+ - entity
+ - named thing
+ - organism taxon
+ - information content entity
+ - dataset
+ - physical entity
+ - activity
+ - procedure
+ - material sample
+ - biological entity
+ - gene
+ - genome
+ range: iri type
+ category:
+ name: category
+ definition_uri: https://w3id.org/biolink/vocab/category
+ description: Name of the high level ontology class in which this entity is categorized.
+ Corresponds to the label for the biolink entity type class. In a neo4j database
+ this MAY correspond to the neo4j label tag. In an RDF database it should be
+ a biolink model class URI. This field is multi-valued. It should include values
+ for ancestors of the biolink class; for example, a protein such as Shh would
+ have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`.
+ In an RDF database, nodes will typically have an rdf:type triples. This can
+ be to the most specific biolink class, or potentially to a class more specific
+ than something in biolink. For example, a sequence feature `f` may have a rdf:type
+ assertion to a SO class such as TF_binding_site, which is more specific than
+ anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity,
+ biolink:NamedThing}
+ in_subset:
+ - translator_minimal
+ from_schema: https://identifiers.org/brain-bican/library-generation-schema
+ rank: 1000
+ is_a: type
+ domain: entity
+ slot_uri: biolink:category
+ designates_type: true
+ alias: category
+ owner: LibraryPooling
+ domain_of:
+ - entity
+ - attribute
+ - named thing
+ - organism taxon
+ - information content entity
+ - dataset
+ - physical entity
+ - activity
+ - procedure
+ - material sample
+ - biological entity
+ - gene
+ - genome
+ is_class_field: true
+ range: uriorcurie
+ multivalued: true
+ pattern: ^bican:[A-Z][A-Za-z]+$
+ type:
+ name: type
+ definition_uri: https://w3id.org/biolink/vocab/type
+ from_schema: https://identifiers.org/brain-bican/library-generation-schema
+ mappings:
+ - rdf:type
+ exact_mappings:
+ - gff3:type
+ - gpi:DB_Object_Type
+ rank: 1000
+ domain: entity
+ slot_uri: rdf:type
+ alias: type
+ owner: LibraryPooling
+ domain_of:
+ - entity
+ - attribute
+ - named thing
+ - organism taxon
+ - information content entity
+ - dataset
+ - physical entity
+ - activity
+ - procedure
+ - material sample
+ - biological entity
+ - gene
+ - genome
+ range: string
+ multivalued: true
+ name:
+ name: name
+ definition_uri: https://w3id.org/biolink/vocab/name
+ description: A human-readable name for an attribute or entity.
+ in_subset:
+ - translator_minimal
+ - samples
+ from_schema: https://identifiers.org/brain-bican/library-generation-schema
+ aliases:
+ - label
+ - display name
+ - title
+ mappings:
+ - rdfs:label
+ exact_mappings:
+ - gff3:Name
+ - gpi:DB_Object_Name
+ narrow_mappings:
+ - dct:title
+ - WIKIDATA_PROPERTY:P1476
+ rank: 1000
+ domain: entity
+ slot_uri: rdfs:label
+ alias: name
+ owner: LibraryPooling
+ domain_of:
+ - attribute
+ - entity
+ - macromolecular machine mixin
+ - Donor
+ - BrainSlab
+ - TissueSample
+ - DissociatedCellSample
+ - EnrichedCellSample
+ - BarcodedCellSample
+ - AmplifiedCdna
+ - Library
+ - LibraryAliquot
+ - LibraryPool
+ - DissectionRoiPolygon
+ - named thing
+ - organism taxon
+ - information content entity
+ - dataset
+ - physical entity
+ - activity
+ - procedure
+ - material sample
+ - biological entity
+ - gene or gene product
+ - gene
+ - genome
+ range: label type
+ description:
+ name: description
+ definition_uri: https://w3id.org/biolink/vocab/description
+ description: a human-readable description of an entity
+ in_subset:
+ - translator_minimal
+ from_schema: https://identifiers.org/brain-bican/library-generation-schema
+ aliases:
+ - definition
+ mappings:
+ - dct:description
+ exact_mappings:
+ - IAO:0000115
+ - skos:definitions
+ narrow_mappings:
+ - gff3:Description
+ rank: 1000
+ slot_uri: dct:description
+ alias: description
+ owner: LibraryPooling
+ domain_of:
+ - entity
+ - attribute
+ - named thing
+ - organism taxon
+ - information content entity
+ - dataset
+ - physical entity
+ - activity
+ - procedure
+ - material sample
+ - biological entity
+ - gene
+ - genome
+ range: narrative text
+ has attribute:
+ name: has attribute
+ definition_uri: https://w3id.org/biolink/vocab/has_attribute
+ description: connects any entity to an attribute
+ in_subset:
+ - samples
+ from_schema: https://identifiers.org/brain-bican/library-generation-schema
+ exact_mappings:
+ - SIO:000008
+ close_mappings:
+ - OBI:0001927
+ narrow_mappings:
+ - OBAN:association_has_subject_property
+ - OBAN:association_has_object_property
+ - CPT:has_possibly_included_panel_element
+ - DRUGBANK:category
+ - EFO:is_executed_in
+ - HANCESTRO:0301
+ - LOINC:has_action_guidance
+ - LOINC:has_adjustment
+ - LOINC:has_aggregation_view
+ - LOINC:has_approach_guidance
+ - LOINC:has_divisor
+ - LOINC:has_exam
+ - LOINC:has_method
+ - LOINC:has_modality_subtype
+ - LOINC:has_object_guidance
+ - LOINC:has_scale
+ - LOINC:has_suffix
+ - LOINC:has_time_aspect
+ - LOINC:has_time_modifier
+ - LOINC:has_timing_of
+ - NCIT:R88
+ - NCIT:eo_disease_has_property_or_attribute
+ - NCIT:has_data_element
+ - NCIT:has_pharmaceutical_administration_method
+ - NCIT:has_pharmaceutical_basic_dose_form
+ - NCIT:has_pharmaceutical_intended_site
+ - NCIT:has_pharmaceutical_release_characteristics
+ - NCIT:has_pharmaceutical_state_of_matter
+ - NCIT:has_pharmaceutical_transformation
+ - NCIT:is_qualified_by
+ - NCIT:qualifier_applies_to
+ - NCIT:role_has_domain
+ - NCIT:role_has_range
+ - INO:0000154
+ - HANCESTRO:0308
+ - OMIM:has_inheritance_type
+ - orphanet:C016
+ - orphanet:C017
+ - RO:0000053
+ - RO:0000086
+ - RO:0000087
+ - SNOMED:has_access
+ - SNOMED:has_clinical_course
+ - SNOMED:has_count_of_base_of_active_ingredient
+ - SNOMED:has_dose_form_administration_method
+ - SNOMED:has_dose_form_release_characteristic
+ - SNOMED:has_dose_form_transformation
+ - SNOMED:has_finding_context
+ - SNOMED:has_finding_informer
+ - SNOMED:has_inherent_attribute
+ - SNOMED:has_intent
+ - SNOMED:has_interpretation
+ - SNOMED:has_laterality
+ - SNOMED:has_measurement_method
+ - SNOMED:has_method
+ - SNOMED:has_priority
+ - SNOMED:has_procedure_context
+ - SNOMED:has_process_duration
+ - SNOMED:has_property
+ - SNOMED:has_revision_status
+ - SNOMED:has_scale_type
+ - SNOMED:has_severity
+ - SNOMED:has_specimen
+ - SNOMED:has_state_of_matter
+ - SNOMED:has_subject_relationship_context
+ - SNOMED:has_surgical_approach
+ - SNOMED:has_technique
+ - SNOMED:has_temporal_context
+ - SNOMED:has_time_aspect
+ - SNOMED:has_units
+ - UMLS:has_structural_class
+ - UMLS:has_supported_concept_property
+ - UMLS:has_supported_concept_relationship
+ - UMLS:may_be_qualified_by
+ rank: 1000
+ domain: entity
+ slot_uri: biolink:has_attribute
+ alias: has_attribute
+ owner: LibraryPooling
+ domain_of:
+ - entity
+ - attribute
+ - named thing
+ - organism taxon
+ - information content entity
+ - dataset
+ - physical entity
+ - activity
+ - procedure
+ - material sample
+ - biological entity
+ - gene
+ - genome
+ range: attribute
+ multivalued: true
+ deprecated:
+ name: deprecated
+ definition_uri: https://w3id.org/biolink/vocab/deprecated
+ description: A boolean flag indicating that an entity is no longer considered
+ current or valid.
+ from_schema: https://identifiers.org/brain-bican/library-generation-schema
+ exact_mappings:
+ - oboInOwl:ObsoleteClass
+ rank: 1000
+ slot_uri: biolink:deprecated
+ alias: deprecated
+ owner: LibraryPooling
+ domain_of:
+ - entity
+ - attribute
+ - named thing
+ - organism taxon
+ - information content entity
+ - dataset
+ - physical entity
+ - activity
+ - procedure
+ - material sample
+ - biological entity
+ - gene
+ - genome
+ range: boolean
+ provided by:
+ name: provided by
+ definition_uri: https://w3id.org/biolink/vocab/provided_by
+ description: The value in this node property represents the knowledge provider
+ that created or assembled the node and all of its attributes. Used internally
+ to represent how a particular node made its way into a knowledge provider or
+ graph.
+ from_schema: https://identifiers.org/brain-bican/library-generation-schema
+ rank: 1000
+ is_a: node property
+ domain: named thing
+ slot_uri: biolink:provided_by
+ alias: provided_by
+ owner: LibraryPooling
+ domain_of:
+ - named thing
+ - attribute
+ - organism taxon
+ - information content entity
+ - dataset
+ - physical entity
+ - activity
+ - procedure
+ - material sample
+ - biological entity
+ - gene
+ - genome
+ range: string
+ multivalued: true
+ xref:
+ name: xref
+ definition_uri: https://w3id.org/biolink/vocab/xref
+ description: A database cross reference or alternative identifier for a NamedThing
+ or edge between two NamedThings. This property should point to a database record
+ or webpage that supports the existence of the edge, or gives more detail about
+ the edge. This property can be used on a node or edge to provide multiple URIs
+ or CURIE cross references.
+ in_subset:
+ - translator_minimal
+ from_schema: https://identifiers.org/brain-bican/library-generation-schema
+ aliases:
+ - dbxref
+ - Dbxref
+ - DbXref
+ - record_url
+ - source_record_urls
+ narrow_mappings:
+ - gff3:Dbxref
+ - gpi:DB_Xrefs
+ rank: 1000
+ domain: named thing
+ slot_uri: biolink:xref
+ alias: xref
+ owner: LibraryPooling
+ domain_of:
+ - named thing
+ - gene
+ - attribute
+ - organism taxon
+ - information content entity
+ - dataset
+ - physical entity
+ - activity
+ - procedure
+ - material sample
+ - biological entity
+ - genome
+ range: uriorcurie
+ multivalued: true
+ full name:
+ name: full name
+ definition_uri: https://w3id.org/biolink/vocab/full_name
+ description: a long-form human readable name for a thing
+ from_schema: https://identifiers.org/brain-bican/library-generation-schema
+ rank: 1000
+ is_a: node property
+ domain: named thing
+ slot_uri: biolink:full_name
+ alias: full_name
+ owner: LibraryPooling
+ domain_of:
+ - named thing
+ - attribute
+ - organism taxon
+ - information content entity
+ - dataset
+ - physical entity
+ - activity
+ - procedure
+ - material sample
+ - biological entity
+ - gene
+ - genome
+ range: label type
+ synonym:
+ name: synonym
+ definition_uri: https://w3id.org/biolink/vocab/synonym
+ description: Alternate human-readable names for a thing
+ in_subset:
+ - translator_minimal
+ from_schema: https://identifiers.org/brain-bican/library-generation-schema
+ aliases:
+ - alias
+ narrow_mappings:
+ - skos:altLabel
+ - gff3:Alias
+ - AGRKB:synonyms
+ - gpi:DB_Object_Synonyms
+ - HANCESTRO:0330
+ - IAO:0000136
+ - RXNORM:has_tradename
+ rank: 1000
+ is_a: node property
+ domain: named thing
+ slot_uri: biolink:synonym
+ alias: synonym
+ owner: LibraryPooling
+ domain_of:
+ - named thing
+ - attribute
+ - organism taxon
+ - information content entity
+ - dataset
+ - physical entity
+ - activity
+ - procedure
+ - material sample
+ - biological entity
+ - gene
+ - genome
+ range: label type
+ multivalued: true
+
+URI: LibraryPrepPassFail
+| Value | +Meaning | +Description | +
|---|---|---|
| Pass | +NIMP:PD-QHQHQB42 | +Library Prep passed the QA/QC | +
| Fail | +NIMP:PD-QHQHQB42 | +Library Prep failed the QA/QC | +
| Low QC | +NIMP:PD-QHQHQB42 | +Library Prep low passed the QA/QC | +
| Not evaluated | +NIMP:PD-QHQHQB42 | +Library Prep not evaluated for QA/QC | +
name: library_prep_pass_fail
+from_schema: https://identifiers.org/brain-bican/library-generation-schema
+rank: 1000
+permissible_values:
+ Pass:
+ text: Pass
+ description: Library Prep passed the QA/QC
+ meaning: NIMP:PD-QHQHQB42
+ Fail:
+ text: Fail
+ description: Library Prep failed the QA/QC
+ meaning: NIMP:PD-QHQHQB42
+ Low QC:
+ text: Low QC
+ description: Library Prep low passed the QA/QC
+ meaning: NIMP:PD-QHQHQB42
+ Not evaluated:
+ text: Not evaluated
+ description: Library Prep not evaluated for QA/QC
+ meaning: NIMP:PD-QHQHQB42
+
+URI: LibraryR1R2Index
+| Value | +Meaning | +Description | +
|---|---|---|
| SI-TT-A1 | +NIMP:PD-VLLMWZ60 | +10x Dual Index TT Set A | +
| SI-TT-A2 | +NIMP:PD-VLLMWZ60 | +10x Dual Index TT Set A | +
| SI-TT-A3 | +NIMP:PD-VLLMWZ60 | +10x Dual Index TT Set A | +
| SI-TT-A4 | +NIMP:PD-VLLMWZ60 | +10x Dual Index TT Set A | +
| SI-TT-A5 | +NIMP:PD-VLLMWZ60 | +10x Dual Index TT Set A | +
| SI-TT-A6 | +NIMP:PD-VLLMWZ60 | +10x Dual Index TT Set A | +
| SI-TT-A7 | +NIMP:PD-VLLMWZ60 | +10x Dual Index TT Set A | +
| SI-TT-A8 | +NIMP:PD-VLLMWZ60 | +10x Dual Index TT Set A | +
| SI-TT-A9 | +NIMP:PD-VLLMWZ60 | +10x Dual Index TT Set A | +
| SI-TT-A10 | +NIMP:PD-VLLMWZ60 | +10x Dual Index TT Set A | +
| SI-TT-A11 | +NIMP:PD-VLLMWZ60 | +10x Dual Index TT Set A | +
| SI-TT-A12 | +NIMP:PD-VLLMWZ60 | +10x Dual Index TT Set A | +
| SI-TT-B1 | +NIMP:PD-VLLMWZ60 | +10x Dual Index TT Set A | +
| SI-TT-B2 | +NIMP:PD-VLLMWZ60 | +10x Dual Index TT Set A | +
| SI-TT-B3 | +NIMP:PD-VLLMWZ60 | +10x Dual Index TT Set A | +
| SI-TT-B4 | +NIMP:PD-VLLMWZ60 | +10x Dual Index TT Set A | +
| SI-TT-B5 | +NIMP:PD-VLLMWZ60 | +10x Dual Index TT Set A | +
| SI-TT-B6 | +NIMP:PD-VLLMWZ60 | +10x Dual Index TT Set A | +
| SI-TT-B7 | +NIMP:PD-VLLMWZ60 | +10x Dual Index TT Set A | +
| SI-TT-B8 | +NIMP:PD-VLLMWZ60 | +10x Dual Index TT Set A | +
| SI-TT-B9 | +NIMP:PD-VLLMWZ60 | +10x Dual Index TT Set A | +
| SI-TT-B10 | +NIMP:PD-VLLMWZ60 | +10x Dual Index TT Set A | +
| SI-TT-B11 | +NIMP:PD-VLLMWZ60 | +10x Dual Index TT Set A | +
| SI-TT-B12 | +NIMP:PD-VLLMWZ60 | +10x Dual Index TT Set A | +
| SI-TT-C1 | +NIMP:PD-VLLMWZ60 | +10x Dual Index TT Set A | +
| SI-TT-C2 | +NIMP:PD-VLLMWZ60 | +10x Dual Index TT Set A | +
| SI-TT-C3 | +NIMP:PD-VLLMWZ60 | +10x Dual Index TT Set A | +
| SI-TT-C4 | +NIMP:PD-VLLMWZ60 | +10x Dual Index TT Set A | +
| SI-TT-C5 | +NIMP:PD-VLLMWZ60 | +10x Dual Index TT Set A | +
| SI-TT-C6 | +NIMP:PD-VLLMWZ60 | +10x Dual Index TT Set A | +
| SI-TT-C7 | +NIMP:PD-VLLMWZ60 | +10x Dual Index TT Set A | +
| SI-TT-C8 | +NIMP:PD-VLLMWZ60 | +10x Dual Index TT Set A | +
| SI-TT-C9 | +NIMP:PD-VLLMWZ60 | +10x Dual Index TT Set A | +
| SI-TT-C10 | +NIMP:PD-VLLMWZ60 | +10x Dual Index TT Set A | +
| SI-TT-C11 | +NIMP:PD-VLLMWZ60 | +10x Dual Index TT Set A | +
| SI-TT-C12 | +NIMP:PD-VLLMWZ60 | +10x Dual Index TT Set A | +
| SI-TT-D1 | +NIMP:PD-VLLMWZ60 | +10x Dual Index TT Set A | +
| SI-TT-D2 | +NIMP:PD-VLLMWZ60 | +10x Dual Index TT Set A | +
| SI-TT-D3 | +NIMP:PD-VLLMWZ60 | +10x Dual Index TT Set A | +
| SI-TT-D4 | +NIMP:PD-VLLMWZ60 | +10x Dual Index TT Set A | +
| SI-TT-D5 | +NIMP:PD-VLLMWZ60 | +10x Dual Index TT Set A | +
| SI-TT-D6 | +NIMP:PD-VLLMWZ60 | +10x Dual Index TT Set A | +
| SI-TT-D7 | +NIMP:PD-VLLMWZ60 | +10x Dual Index TT Set A | +
| SI-TT-D8 | +NIMP:PD-VLLMWZ60 | +10x Dual Index TT Set A | +
| SI-TT-D9 | +NIMP:PD-VLLMWZ60 | +10x Dual Index TT Set A | +
| SI-TT-D10 | +NIMP:PD-VLLMWZ60 | +10x Dual Index TT Set A | +
| SI-TT-D11 | +NIMP:PD-VLLMWZ60 | +10x Dual Index TT Set A | +
| SI-TT-D12 | +NIMP:PD-VLLMWZ60 | +10x Dual Index TT Set A | +
| SI-TT-E1 | +NIMP:PD-VLLMWZ60 | +10x Dual Index TT Set A | +
| SI-TT-E2 | +NIMP:PD-VLLMWZ60 | +10x Dual Index TT Set A | +
| SI-TT-E3 | +NIMP:PD-VLLMWZ60 | +10x Dual Index TT Set A | +
| SI-TT-E4 | +NIMP:PD-VLLMWZ60 | +10x Dual Index TT Set A | +
| SI-TT-E5 | +NIMP:PD-VLLMWZ60 | +10x Dual Index TT Set A | +
| SI-TT-E6 | +NIMP:PD-VLLMWZ60 | +10x Dual Index TT Set A | +
| SI-TT-E7 | +NIMP:PD-VLLMWZ60 | +10x Dual Index TT Set A | +
| SI-TT-E8 | +NIMP:PD-VLLMWZ60 | +10x Dual Index TT Set A | +
| SI-TT-E9 | +NIMP:PD-VLLMWZ60 | +10x Dual Index TT Set A | +
| SI-TT-E10 | +NIMP:PD-VLLMWZ60 | +10x Dual Index TT Set A | +
| SI-TT-E11 | +NIMP:PD-VLLMWZ60 | +10x Dual Index TT Set A | +
| SI-TT-E12 | +NIMP:PD-VLLMWZ60 | +10x Dual Index TT Set A | +
| SI-TT-F1 | +NIMP:PD-VLLMWZ60 | +10x Dual Index TT Set A | +
| SI-TT-F2 | +NIMP:PD-VLLMWZ60 | +10x Dual Index TT Set A | +
| SI-TT-F3 | +NIMP:PD-VLLMWZ60 | +10x Dual Index TT Set A | +
| SI-TT-F4 | +NIMP:PD-VLLMWZ60 | +10x Dual Index TT Set A | +
| SI-TT-F5 | +NIMP:PD-VLLMWZ60 | +10x Dual Index TT Set A | +
| SI-TT-F6 | +NIMP:PD-VLLMWZ60 | +10x Dual Index TT Set A | +
| SI-TT-F7 | +NIMP:PD-VLLMWZ60 | +10x Dual Index TT Set A | +
| SI-TT-F8 | +NIMP:PD-VLLMWZ60 | +10x Dual Index TT Set A | +
| SI-TT-F9 | +NIMP:PD-VLLMWZ60 | +10x Dual Index TT Set A | +
| SI-TT-F10 | +NIMP:PD-VLLMWZ60 | +10x Dual Index TT Set A | +
| SI-TT-F11 | +NIMP:PD-VLLMWZ60 | +10x Dual Index TT Set A | +
| SI-TT-F12 | +NIMP:PD-VLLMWZ60 | +10x Dual Index TT Set A | +
| SI-TT-G1 | +NIMP:PD-VLLMWZ60 | +10x Dual Index TT Set A | +
| SI-TT-G2 | +NIMP:PD-VLLMWZ60 | +10x Dual Index TT Set A | +
| SI-TT-G3 | +NIMP:PD-VLLMWZ60 | +10x Dual Index TT Set A | +
| SI-TT-G4 | +NIMP:PD-VLLMWZ60 | +10x Dual Index TT Set A | +
| SI-TT-G5 | +NIMP:PD-VLLMWZ60 | +10x Dual Index TT Set A | +
| SI-TT-G6 | +NIMP:PD-VLLMWZ60 | +10x Dual Index TT Set A | +
| SI-TT-G7 | +NIMP:PD-VLLMWZ60 | +10x Dual Index TT Set A | +
| SI-TT-G8 | +NIMP:PD-VLLMWZ60 | +10x Dual Index TT Set A | +
| SI-TT-G9 | +NIMP:PD-VLLMWZ60 | +10x Dual Index TT Set A | +
| SI-TT-G10 | +NIMP:PD-VLLMWZ60 | +10x Dual Index TT Set A | +
| SI-TT-G11 | +NIMP:PD-VLLMWZ60 | +10x Dual Index TT Set A | +
| SI-TT-G12 | +NIMP:PD-VLLMWZ60 | +10x Dual Index TT Set A | +
| SI-TT-H1 | +NIMP:PD-VLLMWZ60 | +10x Dual Index TT Set A | +
| SI-TT-H2 | +NIMP:PD-VLLMWZ60 | +10x Dual Index TT Set A | +
| SI-TT-H3 | +NIMP:PD-VLLMWZ60 | +10x Dual Index TT Set A | +
| SI-TT-H4 | +NIMP:PD-VLLMWZ60 | +10x Dual Index TT Set A | +
| SI-TT-H5 | +NIMP:PD-VLLMWZ60 | +10x Dual Index TT Set A | +
| SI-TT-H6 | +NIMP:PD-VLLMWZ60 | +10x Dual Index TT Set A | +
| SI-TT-H7 | +NIMP:PD-VLLMWZ60 | +10x Dual Index TT Set A | +
| SI-TT-H8 | +NIMP:PD-VLLMWZ60 | +10x Dual Index TT Set A | +
| SI-TT-H9 | +NIMP:PD-VLLMWZ60 | +10x Dual Index TT Set A | +
| SI-TT-H10 | +NIMP:PD-VLLMWZ60 | +10x Dual Index TT Set A | +
| SI-TT-H11 | +NIMP:PD-VLLMWZ60 | +10x Dual Index TT Set A | +
| SI-TT-H12 | +NIMP:PD-VLLMWZ60 | +10x Dual Index TT Set A | +
| SI-NN-A1 | +NIMP:PD-VLLMWZ60 | +10x Dual Index NN Set A | +
| SI-NN-A2 | +NIMP:PD-VLLMWZ60 | +10x Dual Index NN Set A | +
| SI-NN-A3 | +NIMP:PD-VLLMWZ60 | +10x Dual Index NN Set A | +
| SI-NN-A4 | +NIMP:PD-VLLMWZ60 | +10x Dual Index NN Set A | +
| SI-NN-A5 | +NIMP:PD-VLLMWZ60 | +10x Dual Index NN Set A | +
| SI-NN-A6 | +NIMP:PD-VLLMWZ60 | +10x Dual Index NN Set A | +
| SI-NN-A7 | +NIMP:PD-VLLMWZ60 | +10x Dual Index NN Set A | +
| SI-NN-A8 | +NIMP:PD-VLLMWZ60 | +10x Dual Index NN Set A | +
| SI-NN-A9 | +NIMP:PD-VLLMWZ60 | +10x Dual Index NN Set A | +
| SI-NN-A10 | +NIMP:PD-VLLMWZ60 | +10x Dual Index NN Set A | +
| SI-NN-A11 | +NIMP:PD-VLLMWZ60 | +10x Dual Index NN Set A | +
| SI-NN-A12 | +NIMP:PD-VLLMWZ60 | +10x Dual Index NN Set A | +
| SI-NN-B1 | +NIMP:PD-VLLMWZ60 | +10x Dual Index NN Set A | +
| SI-NN-B2 | +NIMP:PD-VLLMWZ60 | +10x Dual Index NN Set A | +
| SI-NN-B3 | +NIMP:PD-VLLMWZ60 | +10x Dual Index NN Set A | +
| SI-NN-B4 | +NIMP:PD-VLLMWZ60 | +10x Dual Index NN Set A | +
| SI-NN-B5 | +NIMP:PD-VLLMWZ60 | +10x Dual Index NN Set A | +
| SI-NN-B6 | +NIMP:PD-VLLMWZ60 | +10x Dual Index NN Set A | +
| SI-NN-B7 | +NIMP:PD-VLLMWZ60 | +10x Dual Index NN Set A | +
| SI-NN-B8 | +NIMP:PD-VLLMWZ60 | +10x Dual Index NN Set A | +
| SI-NN-B9 | +NIMP:PD-VLLMWZ60 | +10x Dual Index NN Set A | +
| SI-NN-B10 | +NIMP:PD-VLLMWZ60 | +10x Dual Index NN Set A | +
| SI-NN-B11 | +NIMP:PD-VLLMWZ60 | +10x Dual Index NN Set A | +
| SI-NN-B12 | +NIMP:PD-VLLMWZ60 | +10x Dual Index NN Set A | +
| SI-NN-C1 | +NIMP:PD-VLLMWZ60 | +10x Dual Index NN Set A | +
| SI-NN-C2 | +NIMP:PD-VLLMWZ60 | +10x Dual Index NN Set A | +
| SI-NN-C3 | +NIMP:PD-VLLMWZ60 | +10x Dual Index NN Set A | +
| SI-NN-C4 | +NIMP:PD-VLLMWZ60 | +10x Dual Index NN Set A | +
| SI-NN-C5 | +NIMP:PD-VLLMWZ60 | +10x Dual Index NN Set A | +
| SI-NN-C6 | +NIMP:PD-VLLMWZ60 | +10x Dual Index NN Set A | +
| SI-NN-C7 | +NIMP:PD-VLLMWZ60 | +10x Dual Index NN Set A | +
| SI-NN-C8 | +NIMP:PD-VLLMWZ60 | +10x Dual Index NN Set A | +
| SI-NN-C9 | +NIMP:PD-VLLMWZ60 | +10x Dual Index NN Set A | +
| SI-NN-C10 | +NIMP:PD-VLLMWZ60 | +10x Dual Index NN Set A | +
| SI-NN-C11 | +NIMP:PD-VLLMWZ60 | +10x Dual Index NN Set A | +
| SI-NN-C12 | +NIMP:PD-VLLMWZ60 | +10x Dual Index NN Set A | +
| SI-NN-D1 | +NIMP:PD-VLLMWZ60 | +10x Dual Index NN Set A | +
| SI-NN-D2 | +NIMP:PD-VLLMWZ60 | +10x Dual Index NN Set A | +
| SI-NN-D3 | +NIMP:PD-VLLMWZ60 | +10x Dual Index NN Set A | +
| SI-NN-D4 | +NIMP:PD-VLLMWZ60 | +10x Dual Index NN Set A | +
| SI-NN-D5 | +NIMP:PD-VLLMWZ60 | +10x Dual Index NN Set A | +
| SI-NN-D6 | +NIMP:PD-VLLMWZ60 | +10x Dual Index NN Set A | +
| SI-NN-D7 | +NIMP:PD-VLLMWZ60 | +10x Dual Index NN Set A | +
| SI-NN-D8 | +NIMP:PD-VLLMWZ60 | +10x Dual Index NN Set A | +
| SI-NN-D9 | +NIMP:PD-VLLMWZ60 | +10x Dual Index NN Set A | +
| SI-NN-D10 | +NIMP:PD-VLLMWZ60 | +10x Dual Index NN Set A | +
| SI-NN-D11 | +NIMP:PD-VLLMWZ60 | +10x Dual Index NN Set A | +
| SI-NN-D12 | +NIMP:PD-VLLMWZ60 | +10x Dual Index NN Set A | +
| SI-NN-E1 | +NIMP:PD-VLLMWZ60 | +10x Dual Index NN Set A | +
| SI-NN-E2 | +NIMP:PD-VLLMWZ60 | +10x Dual Index NN Set A | +
| SI-NN-E3 | +NIMP:PD-VLLMWZ60 | +10x Dual Index NN Set A | +
| SI-NN-E4 | +NIMP:PD-VLLMWZ60 | +10x Dual Index NN Set A | +
| SI-NN-E5 | +NIMP:PD-VLLMWZ60 | +10x Dual Index NN Set A | +
| SI-NN-E6 | +NIMP:PD-VLLMWZ60 | +10x Dual Index NN Set A | +
| SI-NN-E7 | +NIMP:PD-VLLMWZ60 | +10x Dual Index NN Set A | +
| SI-NN-E8 | +NIMP:PD-VLLMWZ60 | +10x Dual Index NN Set A | +
| SI-NN-E9 | +NIMP:PD-VLLMWZ60 | +10x Dual Index NN Set A | +
| SI-NN-E10 | +NIMP:PD-VLLMWZ60 | +10x Dual Index NN Set A | +
| SI-NN-E11 | +NIMP:PD-VLLMWZ60 | +10x Dual Index NN Set A | +
| SI-NN-E12 | +NIMP:PD-VLLMWZ60 | +10x Dual Index NN Set A | +
| SI-NN-F1 | +NIMP:PD-VLLMWZ60 | +10x Dual Index NN Set A | +
| SI-NN-F2 | +NIMP:PD-VLLMWZ60 | +10x Dual Index NN Set A | +
| SI-NN-F3 | +NIMP:PD-VLLMWZ60 | +10x Dual Index NN Set A | +
| SI-NN-F4 | +NIMP:PD-VLLMWZ60 | +10x Dual Index NN Set A | +
| SI-NN-F5 | +NIMP:PD-VLLMWZ60 | +10x Dual Index NN Set A | +
| SI-NN-F6 | +NIMP:PD-VLLMWZ60 | +10x Dual Index NN Set A | +
| SI-NN-F7 | +NIMP:PD-VLLMWZ60 | +10x Dual Index NN Set A | +
| SI-NN-F8 | +NIMP:PD-VLLMWZ60 | +10x Dual Index NN Set A | +
| SI-NN-F9 | +NIMP:PD-VLLMWZ60 | +10x Dual Index NN Set A | +
| SI-NN-F10 | +NIMP:PD-VLLMWZ60 | +10x Dual Index NN Set A | +
| SI-NN-F11 | +NIMP:PD-VLLMWZ60 | +10x Dual Index NN Set A | +
| SI-NN-F12 | +NIMP:PD-VLLMWZ60 | +10x Dual Index NN Set A | +
| SI-NN-G1 | +NIMP:PD-VLLMWZ60 | +10x Dual Index NN Set A | +
| SI-NN-G2 | +NIMP:PD-VLLMWZ60 | +10x Dual Index NN Set A | +
| SI-NN-G3 | +NIMP:PD-VLLMWZ60 | +10x Dual Index NN Set A | +
| SI-NN-G4 | +NIMP:PD-VLLMWZ60 | +10x Dual Index NN Set A | +
| SI-NN-G5 | +NIMP:PD-VLLMWZ60 | +10x Dual Index NN Set A | +
| SI-NN-G6 | +NIMP:PD-VLLMWZ60 | +10x Dual Index NN Set A | +
| SI-NN-G7 | +NIMP:PD-VLLMWZ60 | +10x Dual Index NN Set A | +
| SI-NN-G8 | +NIMP:PD-VLLMWZ60 | +10x Dual Index NN Set A | +
| SI-NN-G9 | +NIMP:PD-VLLMWZ60 | +10x Dual Index NN Set A | +
| SI-NN-G10 | +NIMP:PD-VLLMWZ60 | +10x Dual Index NN Set A | +
| SI-NN-G11 | +NIMP:PD-VLLMWZ60 | +10x Dual Index NN Set A | +
| SI-NN-G12 | +NIMP:PD-VLLMWZ60 | +10x Dual Index NN Set A | +
| SI-NN-H1 | +NIMP:PD-VLLMWZ60 | +10x Dual Index NN Set A | +
| SI-NN-H2 | +NIMP:PD-VLLMWZ60 | +10x Dual Index NN Set A | +
| SI-NN-H3 | +NIMP:PD-VLLMWZ60 | +10x Dual Index NN Set A | +
| SI-NN-H4 | +NIMP:PD-VLLMWZ60 | +10x Dual Index NN Set A | +
| SI-NN-H5 | +NIMP:PD-VLLMWZ60 | +10x Dual Index NN Set A | +
| SI-NN-H6 | +NIMP:PD-VLLMWZ60 | +10x Dual Index NN Set A | +
| SI-NN-H7 | +NIMP:PD-VLLMWZ60 | +10x Dual Index NN Set A | +
| SI-NN-H8 | +NIMP:PD-VLLMWZ60 | +10x Dual Index NN Set A | +
| SI-NN-H9 | +NIMP:PD-VLLMWZ60 | +10x Dual Index NN Set A | +
| SI-NN-H10 | +NIMP:PD-VLLMWZ60 | +10x Dual Index NN Set A | +
| SI-NN-H11 | +NIMP:PD-VLLMWZ60 | +10x Dual Index NN Set A | +
| SI-NN-H12 | +NIMP:PD-VLLMWZ60 | +10x Dual Index NN Set A | +
| SI-NA-A1 | +NIMP:PD-VLLMWZ60 | +10x Single Index N Set A | +
| SI-NA-B1 | +NIMP:PD-VLLMWZ60 | +10x Single Index N Set A | +
| SI-NA-C1 | +NIMP:PD-VLLMWZ60 | +10x Single Index N Set A | +
| SI-NA-D1 | +NIMP:PD-VLLMWZ60 | +10x Single Index N Set A | +
| SI-NA-E1 | +NIMP:PD-VLLMWZ60 | +10x Single Index N Set A | +
| SI-NA-F1 | +NIMP:PD-VLLMWZ60 | +10x Single Index N Set A | +
| SI-NA-G1 | +NIMP:PD-VLLMWZ60 | +10x Single Index N Set A | +
| SI-NA-H1 | +NIMP:PD-VLLMWZ60 | +10x Single Index N Set A | +
| SI-NA-A2 | +NIMP:PD-VLLMWZ60 | +10x Single Index N Set A | +
| SI-NA-B2 | +NIMP:PD-VLLMWZ60 | +10x Single Index N Set A | +
| SI-NA-C2 | +NIMP:PD-VLLMWZ60 | +10x Single Index N Set A | +
| SI-NA-D2 | +NIMP:PD-VLLMWZ60 | +10x Single Index N Set A | +
| SI-NA-E2 | +NIMP:PD-VLLMWZ60 | +10x Single Index N Set A | +
| SI-NA-F2 | +NIMP:PD-VLLMWZ60 | +10x Single Index N Set A | +
| SI-NA-G2 | +NIMP:PD-VLLMWZ60 | +10x Single Index N Set A | +
| SI-NA-H2 | +NIMP:PD-VLLMWZ60 | +10x Single Index N Set A | +
| SI-NA-A3 | +NIMP:PD-VLLMWZ60 | +10x Single Index N Set A | +
| SI-NA-B3 | +NIMP:PD-VLLMWZ60 | +10x Single Index N Set A | +
| SI-NA-C3 | +NIMP:PD-VLLMWZ60 | +10x Single Index N Set A | +
| SI-NA-D3 | +NIMP:PD-VLLMWZ60 | +10x Single Index N Set A | +
| SI-NA-E3 | +NIMP:PD-VLLMWZ60 | +10x Single Index N Set A | +
| SI-NA-F3 | +NIMP:PD-VLLMWZ60 | +10x Single Index N Set A | +
| SI-NA-G3 | +NIMP:PD-VLLMWZ60 | +10x Single Index N Set A | +
| SI-NA-H3 | +NIMP:PD-VLLMWZ60 | +10x Single Index N Set A | +
| SI-NA-A4 | +NIMP:PD-VLLMWZ60 | +10x Single Index N Set A | +
| SI-NA-B4 | +NIMP:PD-VLLMWZ60 | +10x Single Index N Set A | +
| SI-NA-C4 | +NIMP:PD-VLLMWZ60 | +10x Single Index N Set A | +
| SI-NA-D4 | +NIMP:PD-VLLMWZ60 | +10x Single Index N Set A | +
| SI-NA-E4 | +NIMP:PD-VLLMWZ60 | +10x Single Index N Set A | +
| SI-NA-F4 | +NIMP:PD-VLLMWZ60 | +10x Single Index N Set A | +
| SI-NA-G4 | +NIMP:PD-VLLMWZ60 | +10x Single Index N Set A | +
| SI-NA-H4 | +NIMP:PD-VLLMWZ60 | +10x Single Index N Set A | +
| SI-NA-A5 | +NIMP:PD-VLLMWZ60 | +10x Single Index N Set A | +
| SI-NA-B5 | +NIMP:PD-VLLMWZ60 | +10x Single Index N Set A | +
| SI-NA-C5 | +NIMP:PD-VLLMWZ60 | +10x Single Index N Set A | +
| SI-NA-D5 | +NIMP:PD-VLLMWZ60 | +10x Single Index N Set A | +
| SI-NA-E5 | +NIMP:PD-VLLMWZ60 | +10x Single Index N Set A | +
| SI-NA-F5 | +NIMP:PD-VLLMWZ60 | +10x Single Index N Set A | +
| SI-NA-G5 | +NIMP:PD-VLLMWZ60 | +10x Single Index N Set A | +
| SI-NA-H5 | +NIMP:PD-VLLMWZ60 | +10x Single Index N Set A | +
| SI-NA-A6 | +NIMP:PD-VLLMWZ60 | +10x Single Index N Set A | +
| SI-NA-B6 | +NIMP:PD-VLLMWZ60 | +10x Single Index N Set A | +
| SI-NA-C6 | +NIMP:PD-VLLMWZ60 | +10x Single Index N Set A | +
| SI-NA-D6 | +NIMP:PD-VLLMWZ60 | +10x Single Index N Set A | +
| SI-NA-E6 | +NIMP:PD-VLLMWZ60 | +10x Single Index N Set A | +
| SI-NA-F6 | +NIMP:PD-VLLMWZ60 | +10x Single Index N Set A | +
| SI-NA-G6 | +NIMP:PD-VLLMWZ60 | +10x Single Index N Set A | +
| SI-NA-H6 | +NIMP:PD-VLLMWZ60 | +10x Single Index N Set A | +
| SI-NA-A7 | +NIMP:PD-VLLMWZ60 | +10x Single Index N Set A | +
| SI-NA-B7 | +NIMP:PD-VLLMWZ60 | +10x Single Index N Set A | +
| SI-NA-C7 | +NIMP:PD-VLLMWZ60 | +10x Single Index N Set A | +
| SI-NA-D7 | +NIMP:PD-VLLMWZ60 | +10x Single Index N Set A | +
| SI-NA-E7 | +NIMP:PD-VLLMWZ60 | +10x Single Index N Set A | +
| SI-NA-F7 | +NIMP:PD-VLLMWZ60 | +10x Single Index N Set A | +
| SI-NA-G7 | +NIMP:PD-VLLMWZ60 | +10x Single Index N Set A | +
| SI-NA-H7 | +NIMP:PD-VLLMWZ60 | +10x Single Index N Set A | +
| SI-NA-A8 | +NIMP:PD-VLLMWZ60 | +10x Single Index N Set A | +
| SI-NA-B8 | +NIMP:PD-VLLMWZ60 | +10x Single Index N Set A | +
| SI-NA-C8 | +NIMP:PD-VLLMWZ60 | +10x Single Index N Set A | +
| SI-NA-D8 | +NIMP:PD-VLLMWZ60 | +10x Single Index N Set A | +
| SI-NA-E8 | +NIMP:PD-VLLMWZ60 | +10x Single Index N Set A | +
| SI-NA-F8 | +NIMP:PD-VLLMWZ60 | +10x Single Index N Set A | +
| SI-NA-G8 | +NIMP:PD-VLLMWZ60 | +10x Single Index N Set A | +
| SI-NA-H8 | +NIMP:PD-VLLMWZ60 | +10x Single Index N Set A | +
| SI-NA-A9 | +NIMP:PD-VLLMWZ60 | +10x Single Index N Set A | +
| SI-NA-B9 | +NIMP:PD-VLLMWZ60 | +10x Single Index N Set A | +
| SI-NA-C9 | +NIMP:PD-VLLMWZ60 | +10x Single Index N Set A | +
| SI-NA-D9 | +NIMP:PD-VLLMWZ60 | +10x Single Index N Set A | +
| SI-NA-E9 | +NIMP:PD-VLLMWZ60 | +10x Single Index N Set A | +
| SI-NA-F9 | +NIMP:PD-VLLMWZ60 | +10x Single Index N Set A | +
| SI-NA-G9 | +NIMP:PD-VLLMWZ60 | +10x Single Index N Set A | +
| SI-NA-H9 | +NIMP:PD-VLLMWZ60 | +10x Single Index N Set A | +
| SI-NA-A10 | +NIMP:PD-VLLMWZ60 | +10x Single Index N Set A | +
| SI-NA-B10 | +NIMP:PD-VLLMWZ60 | +10x Single Index N Set A | +
| SI-NA-C10 | +NIMP:PD-VLLMWZ60 | +10x Single Index N Set A | +
| SI-NA-D10 | +NIMP:PD-VLLMWZ60 | +10x Single Index N Set A | +
| SI-NA-E10 | +NIMP:PD-VLLMWZ60 | +10x Single Index N Set A | +
| SI-NA-F10 | +NIMP:PD-VLLMWZ60 | +10x Single Index N Set A | +
| SI-NA-G10 | +NIMP:PD-VLLMWZ60 | +10x Single Index N Set A | +
| SI-NA-H10 | +NIMP:PD-VLLMWZ60 | +10x Single Index N Set A | +
| SI-NA-A11 | +NIMP:PD-VLLMWZ60 | +10x Single Index N Set A | +
| SI-NA-B11 | +NIMP:PD-VLLMWZ60 | +10x Single Index N Set A | +
| SI-NA-C11 | +NIMP:PD-VLLMWZ60 | +10x Single Index N Set A | +
| SI-NA-D11 | +NIMP:PD-VLLMWZ60 | +10x Single Index N Set A | +
| SI-NA-E11 | +NIMP:PD-VLLMWZ60 | +10x Single Index N Set A | +
| SI-NA-F11 | +NIMP:PD-VLLMWZ60 | +10x Single Index N Set A | +
| SI-NA-G11 | +NIMP:PD-VLLMWZ60 | +10x Single Index N Set A | +
| SI-NA-H11 | +NIMP:PD-VLLMWZ60 | +10x Single Index N Set A | +
| SI-NA-A12 | +NIMP:PD-VLLMWZ60 | +10x Single Index N Set A | +
| SI-NA-B12 | +NIMP:PD-VLLMWZ60 | +10x Single Index N Set A | +
| SI-NA-C12 | +NIMP:PD-VLLMWZ60 | +10x Single Index N Set A | +
| SI-NA-D12 | +NIMP:PD-VLLMWZ60 | +10x Single Index N Set A | +
| SI-NA-E12 | +NIMP:PD-VLLMWZ60 | +10x Single Index N Set A | +
| SI-NA-F12 | +NIMP:PD-VLLMWZ60 | +10x Single Index N Set A | +
| SI-NA-G12 | +NIMP:PD-VLLMWZ60 | +10x Single Index N Set A | +
| SI-NA-H12 | +NIMP:PD-VLLMWZ60 | +10x Single Index N Set A | +
| SetB-A1 | +NIMP:PD-VLLMWZ60 | +NeryLab 384_SetB | +
| SetB-A10 | +NIMP:PD-VLLMWZ60 | +NeryLab 384_SetB | +
| SetB-A11 | +NIMP:PD-VLLMWZ60 | +NeryLab 384_SetB | +
| SetB-A12 | +NIMP:PD-VLLMWZ60 | +NeryLab 384_SetB | +
| SetB-A13 | +NIMP:PD-VLLMWZ60 | +NeryLab 384_SetB | +
| SetB-A14 | +NIMP:PD-VLLMWZ60 | +NeryLab 384_SetB | +
| SetB-A15 | +NIMP:PD-VLLMWZ60 | +NeryLab 384_SetB | +
| SetB-A16 | +NIMP:PD-VLLMWZ60 | +NeryLab 384_SetB | +
| SetB-A17 | +NIMP:PD-VLLMWZ60 | +NeryLab 384_SetB | +
| SetB-A18 | +NIMP:PD-VLLMWZ60 | +NeryLab 384_SetB | +
| SetB-A19 | +NIMP:PD-VLLMWZ60 | +NeryLab 384_SetB | +
| SetB-A2 | +NIMP:PD-VLLMWZ60 | +NeryLab 384_SetB | +
| SetB-A20 | +NIMP:PD-VLLMWZ60 | +NeryLab 384_SetB | +
| SetB-A21 | +NIMP:PD-VLLMWZ60 | +NeryLab 384_SetB | +
| SetB-A22 | +NIMP:PD-VLLMWZ60 | +NeryLab 384_SetB | +
| SetB-A23 | +NIMP:PD-VLLMWZ60 | +NeryLab 384_SetB | +
| SetB-A24 | +NIMP:PD-VLLMWZ60 | +NeryLab 384_SetB | +
| SetB-A3 | +NIMP:PD-VLLMWZ60 | +NeryLab 384_SetB | +
| SetB-A4 | +NIMP:PD-VLLMWZ60 | +NeryLab 384_SetB | +
| SetB-A5 | +NIMP:PD-VLLMWZ60 | +NeryLab 384_SetB | +
| SetB-A6 | +NIMP:PD-VLLMWZ60 | +NeryLab 384_SetB | +
| SetB-A7 | +NIMP:PD-VLLMWZ60 | +NeryLab 384_SetB | +
| SetB-A8 | +NIMP:PD-VLLMWZ60 | +NeryLab 384_SetB | +
| SetB-A9 | +NIMP:PD-VLLMWZ60 | +NeryLab 384_SetB | +
| SetB-B1 | +NIMP:PD-VLLMWZ60 | +NeryLab 384_SetB | +
| SetB-B10 | +NIMP:PD-VLLMWZ60 | +NeryLab 384_SetB | +
| SetB-B11 | +NIMP:PD-VLLMWZ60 | +NeryLab 384_SetB | +
| SetB-B12 | +NIMP:PD-VLLMWZ60 | +NeryLab 384_SetB | +
| SetB-B13 | +NIMP:PD-VLLMWZ60 | +NeryLab 384_SetB | +
| SetB-B14 | +NIMP:PD-VLLMWZ60 | +NeryLab 384_SetB | +
| SetB-B15 | +NIMP:PD-VLLMWZ60 | +NeryLab 384_SetB | +
| SetB-B16 | +NIMP:PD-VLLMWZ60 | +NeryLab 384_SetB | +
| SetB-B17 | +NIMP:PD-VLLMWZ60 | +NeryLab 384_SetB | +
| SetB-B18 | +NIMP:PD-VLLMWZ60 | +NeryLab 384_SetB | +
| SetB-B19 | +NIMP:PD-VLLMWZ60 | +NeryLab 384_SetB | +
| SetB-B2 | +NIMP:PD-VLLMWZ60 | +NeryLab 384_SetB | +
| SetB-B20 | +NIMP:PD-VLLMWZ60 | +NeryLab 384_SetB | +
| SetB-B21 | +NIMP:PD-VLLMWZ60 | +NeryLab 384_SetB | +
| SetB-B22 | +NIMP:PD-VLLMWZ60 | +NeryLab 384_SetB | +
| SetB-B23 | +NIMP:PD-VLLMWZ60 | +NeryLab 384_SetB | +
| SetB-B24 | +NIMP:PD-VLLMWZ60 | +NeryLab 384_SetB | +
| SetB-B3 | +NIMP:PD-VLLMWZ60 | +NeryLab 384_SetB | +
| SetB-B4 | +NIMP:PD-VLLMWZ60 | +NeryLab 384_SetB | +
| SetB-B5 | +NIMP:PD-VLLMWZ60 | +NeryLab 384_SetB | +
| SetB-B6 | +NIMP:PD-VLLMWZ60 | +NeryLab 384_SetB | +
| SetB-B7 | +NIMP:PD-VLLMWZ60 | +NeryLab 384_SetB | +
| SetB-B8 | +NIMP:PD-VLLMWZ60 | +NeryLab 384_SetB | +
| SetB-B9 | +NIMP:PD-VLLMWZ60 | +NeryLab 384_SetB | +
| SetB-C1 | +NIMP:PD-VLLMWZ60 | +NeryLab 384_SetB | +
| SetB-C10 | +NIMP:PD-VLLMWZ60 | +NeryLab 384_SetB | +
| SetB-C11 | +NIMP:PD-VLLMWZ60 | +NeryLab 384_SetB | +
| SetB-C12 | +NIMP:PD-VLLMWZ60 | +NeryLab 384_SetB | +
| SetB-C13 | +NIMP:PD-VLLMWZ60 | +NeryLab 384_SetB | +
| SetB-C14 | +NIMP:PD-VLLMWZ60 | +NeryLab 384_SetB | +
| SetB-C15 | +NIMP:PD-VLLMWZ60 | +NeryLab 384_SetB | +
| SetB-C16 | +NIMP:PD-VLLMWZ60 | +NeryLab 384_SetB | +
| SetB-C17 | +NIMP:PD-VLLMWZ60 | +NeryLab 384_SetB | +
| SetB-C18 | +NIMP:PD-VLLMWZ60 | +NeryLab 384_SetB | +
| SetB-C19 | +NIMP:PD-VLLMWZ60 | +NeryLab 384_SetB | +
| SetB-C2 | +NIMP:PD-VLLMWZ60 | +NeryLab 384_SetB | +
| SetB-C20 | +NIMP:PD-VLLMWZ60 | +NeryLab 384_SetB | +
| SetB-C21 | +NIMP:PD-VLLMWZ60 | +NeryLab 384_SetB | +
| SetB-C22 | +NIMP:PD-VLLMWZ60 | +NeryLab 384_SetB | +
| SetB-C23 | +NIMP:PD-VLLMWZ60 | +NeryLab 384_SetB | +
| SetB-C24 | +NIMP:PD-VLLMWZ60 | +NeryLab 384_SetB | +
| SetB-C3 | +NIMP:PD-VLLMWZ60 | +NeryLab 384_SetB | +
| SetB-C4 | +NIMP:PD-VLLMWZ60 | +NeryLab 384_SetB | +
| SetB-C5 | +NIMP:PD-VLLMWZ60 | +NeryLab 384_SetB | +
| SetB-C6 | +NIMP:PD-VLLMWZ60 | +NeryLab 384_SetB | +
| SetB-C7 | +NIMP:PD-VLLMWZ60 | +NeryLab 384_SetB | +
| SetB-C8 | +NIMP:PD-VLLMWZ60 | +NeryLab 384_SetB | +
| SetB-C9 | +NIMP:PD-VLLMWZ60 | +NeryLab 384_SetB | +
| SetB-D1 | +NIMP:PD-VLLMWZ60 | +NeryLab 384_SetB | +
| SetB-D10 | +NIMP:PD-VLLMWZ60 | +NeryLab 384_SetB | +
| SetB-D11 | +NIMP:PD-VLLMWZ60 | +NeryLab 384_SetB | +
| SetB-D12 | +NIMP:PD-VLLMWZ60 | +NeryLab 384_SetB | +
| SetB-D13 | +NIMP:PD-VLLMWZ60 | +NeryLab 384_SetB | +
| SetB-D14 | +NIMP:PD-VLLMWZ60 | +NeryLab 384_SetB | +
| SetB-D15 | +NIMP:PD-VLLMWZ60 | +NeryLab 384_SetB | +
| SetB-D16 | +NIMP:PD-VLLMWZ60 | +NeryLab 384_SetB | +
| SetB-D17 | +NIMP:PD-VLLMWZ60 | +NeryLab 384_SetB | +
| SetB-D18 | +NIMP:PD-VLLMWZ60 | +NeryLab 384_SetB | +
| SetB-D19 | +NIMP:PD-VLLMWZ60 | +NeryLab 384_SetB | +
| SetB-D2 | +NIMP:PD-VLLMWZ60 | +NeryLab 384_SetB | +
| SetB-D20 | +NIMP:PD-VLLMWZ60 | +NeryLab 384_SetB | +
| SetB-D21 | +NIMP:PD-VLLMWZ60 | +NeryLab 384_SetB | +
| SetB-D22 | +NIMP:PD-VLLMWZ60 | +NeryLab 384_SetB | +
| SetB-D23 | +NIMP:PD-VLLMWZ60 | +NeryLab 384_SetB | +
| SetB-D24 | +NIMP:PD-VLLMWZ60 | +NeryLab 384_SetB | +
| SetB-D3 | +NIMP:PD-VLLMWZ60 | +NeryLab 384_SetB | +
| SetB-D4 | +NIMP:PD-VLLMWZ60 | +NeryLab 384_SetB | +
| SetB-D5 | +NIMP:PD-VLLMWZ60 | +NeryLab 384_SetB | +
| SetB-D6 | +NIMP:PD-VLLMWZ60 | +NeryLab 384_SetB | +
| SetB-D7 | +NIMP:PD-VLLMWZ60 | +NeryLab 384_SetB | +
| SetB-D8 | +NIMP:PD-VLLMWZ60 | +NeryLab 384_SetB | +
| SetB-D9 | +NIMP:PD-VLLMWZ60 | +NeryLab 384_SetB | +
| SetB-E1 | +NIMP:PD-VLLMWZ60 | +NeryLab 384_SetB | +
| SetB-E10 | +NIMP:PD-VLLMWZ60 | +NeryLab 384_SetB | +
| SetB-E11 | +NIMP:PD-VLLMWZ60 | +NeryLab 384_SetB | +
| SetB-E12 | +NIMP:PD-VLLMWZ60 | +NeryLab 384_SetB | +
| SetB-E13 | +NIMP:PD-VLLMWZ60 | +NeryLab 384_SetB | +
| SetB-E14 | +NIMP:PD-VLLMWZ60 | +NeryLab 384_SetB | +
| SetB-E15 | +NIMP:PD-VLLMWZ60 | +NeryLab 384_SetB | +
| SetB-E16 | +NIMP:PD-VLLMWZ60 | +NeryLab 384_SetB | +
| SetB-E17 | +NIMP:PD-VLLMWZ60 | +NeryLab 384_SetB | +
| SetB-E18 | +NIMP:PD-VLLMWZ60 | +NeryLab 384_SetB | +
| SetB-E19 | +NIMP:PD-VLLMWZ60 | +NeryLab 384_SetB | +
| SetB-E2 | +NIMP:PD-VLLMWZ60 | +NeryLab 384_SetB | +
| SetB-E20 | +NIMP:PD-VLLMWZ60 | +NeryLab 384_SetB | +
| SetB-E21 | +NIMP:PD-VLLMWZ60 | +NeryLab 384_SetB | +
| SetB-E22 | +NIMP:PD-VLLMWZ60 | +NeryLab 384_SetB | +
| SetB-E23 | +NIMP:PD-VLLMWZ60 | +NeryLab 384_SetB | +
| SetB-E24 | +NIMP:PD-VLLMWZ60 | +NeryLab 384_SetB | +
| SetB-E3 | +NIMP:PD-VLLMWZ60 | +NeryLab 384_SetB | +
| SetB-E4 | +NIMP:PD-VLLMWZ60 | +NeryLab 384_SetB | +
| SetB-E5 | +NIMP:PD-VLLMWZ60 | +NeryLab 384_SetB | +
| SetB-E6 | +NIMP:PD-VLLMWZ60 | +NeryLab 384_SetB | +
| SetB-E7 | +NIMP:PD-VLLMWZ60 | +NeryLab 384_SetB | +
| SetB-E8 | +NIMP:PD-VLLMWZ60 | +NeryLab 384_SetB | +
| SetB-E9 | +NIMP:PD-VLLMWZ60 | +NeryLab 384_SetB | +
| SetB-F1 | +NIMP:PD-VLLMWZ60 | +NeryLab 384_SetB | +
| SetB-F10 | +NIMP:PD-VLLMWZ60 | +NeryLab 384_SetB | +
| SetB-F11 | +NIMP:PD-VLLMWZ60 | +NeryLab 384_SetB | +
| SetB-F12 | +NIMP:PD-VLLMWZ60 | +NeryLab 384_SetB | +
| SetB-F13 | +NIMP:PD-VLLMWZ60 | +NeryLab 384_SetB | +
| SetB-F14 | +NIMP:PD-VLLMWZ60 | +NeryLab 384_SetB | +
| SetB-F15 | +NIMP:PD-VLLMWZ60 | +NeryLab 384_SetB | +
| SetB-F16 | +NIMP:PD-VLLMWZ60 | +NeryLab 384_SetB | +
| SetB-F17 | +NIMP:PD-VLLMWZ60 | +NeryLab 384_SetB | +
| SetB-F18 | +NIMP:PD-VLLMWZ60 | +NeryLab 384_SetB | +
| SetB-F19 | +NIMP:PD-VLLMWZ60 | +NeryLab 384_SetB | +
| SetB-F2 | +NIMP:PD-VLLMWZ60 | +NeryLab 384_SetB | +
| SetB-F20 | +NIMP:PD-VLLMWZ60 | +NeryLab 384_SetB | +
| SetB-F21 | +NIMP:PD-VLLMWZ60 | +NeryLab 384_SetB | +
| SetB-F22 | +NIMP:PD-VLLMWZ60 | +NeryLab 384_SetB | +
| SetB-F23 | +NIMP:PD-VLLMWZ60 | +NeryLab 384_SetB | +
| SetB-F24 | +NIMP:PD-VLLMWZ60 | +NeryLab 384_SetB | +
| SetB-F3 | +NIMP:PD-VLLMWZ60 | +NeryLab 384_SetB | +
| SetB-F4 | +NIMP:PD-VLLMWZ60 | +NeryLab 384_SetB | +
| SetB-F5 | +NIMP:PD-VLLMWZ60 | +NeryLab 384_SetB | +
| SetB-F6 | +NIMP:PD-VLLMWZ60 | +NeryLab 384_SetB | +
| SetB-F7 | +NIMP:PD-VLLMWZ60 | +NeryLab 384_SetB | +
| SetB-F8 | +NIMP:PD-VLLMWZ60 | +NeryLab 384_SetB | +
| SetB-F9 | +NIMP:PD-VLLMWZ60 | +NeryLab 384_SetB | +
| SetB-G1 | +NIMP:PD-VLLMWZ60 | +NeryLab 384_SetB | +
| SetB-G10 | +NIMP:PD-VLLMWZ60 | +NeryLab 384_SetB | +
| SetB-G11 | +NIMP:PD-VLLMWZ60 | +NeryLab 384_SetB | +
| SetB-G12 | +NIMP:PD-VLLMWZ60 | +NeryLab 384_SetB | +
| SetB-G13 | +NIMP:PD-VLLMWZ60 | +NeryLab 384_SetB | +
| SetB-G14 | +NIMP:PD-VLLMWZ60 | +NeryLab 384_SetB | +
| SetB-G15 | +NIMP:PD-VLLMWZ60 | +NeryLab 384_SetB | +
| SetB-G16 | +NIMP:PD-VLLMWZ60 | +NeryLab 384_SetB | +
| SetB-G17 | +NIMP:PD-VLLMWZ60 | +NeryLab 384_SetB | +
| SetB-G18 | +NIMP:PD-VLLMWZ60 | +NeryLab 384_SetB | +
| SetB-G19 | +NIMP:PD-VLLMWZ60 | +NeryLab 384_SetB | +
| SetB-G2 | +NIMP:PD-VLLMWZ60 | +NeryLab 384_SetB | +
| SetB-G20 | +NIMP:PD-VLLMWZ60 | +NeryLab 384_SetB | +
| SetB-G21 | +NIMP:PD-VLLMWZ60 | +NeryLab 384_SetB | +
| SetB-G22 | +NIMP:PD-VLLMWZ60 | +NeryLab 384_SetB | +
| SetB-G23 | +NIMP:PD-VLLMWZ60 | +NeryLab 384_SetB | +
| SetB-G24 | +NIMP:PD-VLLMWZ60 | +NeryLab 384_SetB | +
| SetB-G3 | +NIMP:PD-VLLMWZ60 | +NeryLab 384_SetB | +
| SetB-G4 | +NIMP:PD-VLLMWZ60 | +NeryLab 384_SetB | +
| SetB-G5 | +NIMP:PD-VLLMWZ60 | +NeryLab 384_SetB | +
| SetB-G6 | +NIMP:PD-VLLMWZ60 | +NeryLab 384_SetB | +
| SetB-G7 | +NIMP:PD-VLLMWZ60 | +NeryLab 384_SetB | +
| SetB-G8 | +NIMP:PD-VLLMWZ60 | +NeryLab 384_SetB | +
| SetB-G9 | +NIMP:PD-VLLMWZ60 | +NeryLab 384_SetB | +
| SetB-H1 | +NIMP:PD-VLLMWZ60 | +NeryLab 384_SetB | +
| SetB-H10 | +NIMP:PD-VLLMWZ60 | +NeryLab 384_SetB | +
| SetB-H11 | +NIMP:PD-VLLMWZ60 | +NeryLab 384_SetB | +
| SetB-H12 | +NIMP:PD-VLLMWZ60 | +NeryLab 384_SetB | +
| SetB-H13 | +NIMP:PD-VLLMWZ60 | +NeryLab 384_SetB | +
| SetB-H14 | +NIMP:PD-VLLMWZ60 | +NeryLab 384_SetB | +
| SetB-H15 | +NIMP:PD-VLLMWZ60 | +NeryLab 384_SetB | +
| SetB-H16 | +NIMP:PD-VLLMWZ60 | +NeryLab 384_SetB | +
| SetB-H17 | +NIMP:PD-VLLMWZ60 | +NeryLab 384_SetB | +
| SetB-H18 | +NIMP:PD-VLLMWZ60 | +NeryLab 384_SetB | +
| SetB-H19 | +NIMP:PD-VLLMWZ60 | +NeryLab 384_SetB | +
| SetB-H2 | +NIMP:PD-VLLMWZ60 | +NeryLab 384_SetB | +
| SetB-H20 | +NIMP:PD-VLLMWZ60 | +NeryLab 384_SetB | +
| SetB-H21 | +NIMP:PD-VLLMWZ60 | +NeryLab 384_SetB | +
| SetB-H22 | +NIMP:PD-VLLMWZ60 | +NeryLab 384_SetB | +
| SetB-H23 | +NIMP:PD-VLLMWZ60 | +NeryLab 384_SetB | +
| SetB-H24 | +NIMP:PD-VLLMWZ60 | +NeryLab 384_SetB | +
| SetB-H3 | +NIMP:PD-VLLMWZ60 | +NeryLab 384_SetB | +
| SetB-H4 | +NIMP:PD-VLLMWZ60 | +NeryLab 384_SetB | +
| SetB-H5 | +NIMP:PD-VLLMWZ60 | +NeryLab 384_SetB | +
| SetB-H6 | +NIMP:PD-VLLMWZ60 | +NeryLab 384_SetB | +
| SetB-H7 | +NIMP:PD-VLLMWZ60 | +NeryLab 384_SetB | +
| SetB-H8 | +NIMP:PD-VLLMWZ60 | +NeryLab 384_SetB | +
| SetB-H9 | +NIMP:PD-VLLMWZ60 | +NeryLab 384_SetB | +
| SetB-I1 | +NIMP:PD-VLLMWZ60 | +NeryLab 384_SetB | +
| SetB-I10 | +NIMP:PD-VLLMWZ60 | +NeryLab 384_SetB | +
| SetB-I11 | +NIMP:PD-VLLMWZ60 | +NeryLab 384_SetB | +
| SetB-I12 | +NIMP:PD-VLLMWZ60 | +NeryLab 384_SetB | +
| SetB-I13 | +NIMP:PD-VLLMWZ60 | +NeryLab 384_SetB | +
| SetB-I14 | +NIMP:PD-VLLMWZ60 | +NeryLab 384_SetB | +
| SetB-I15 | +NIMP:PD-VLLMWZ60 | +NeryLab 384_SetB | +
| SetB-I16 | +NIMP:PD-VLLMWZ60 | +NeryLab 384_SetB | +
| SetB-I17 | +NIMP:PD-VLLMWZ60 | +NeryLab 384_SetB | +
| SetB-I18 | +NIMP:PD-VLLMWZ60 | +NeryLab 384_SetB | +
| SetB-I19 | +NIMP:PD-VLLMWZ60 | +NeryLab 384_SetB | +
| SetB-I2 | +NIMP:PD-VLLMWZ60 | +NeryLab 384_SetB | +
| SetB-I20 | +NIMP:PD-VLLMWZ60 | +NeryLab 384_SetB | +
| SetB-I21 | +NIMP:PD-VLLMWZ60 | +NeryLab 384_SetB | +
| SetB-I22 | +NIMP:PD-VLLMWZ60 | +NeryLab 384_SetB | +
| SetB-I23 | +NIMP:PD-VLLMWZ60 | +NeryLab 384_SetB | +
| SetB-I24 | +NIMP:PD-VLLMWZ60 | +NeryLab 384_SetB | +
| SetB-I3 | +NIMP:PD-VLLMWZ60 | +NeryLab 384_SetB | +
| SetB-I4 | +NIMP:PD-VLLMWZ60 | +NeryLab 384_SetB | +
| SetB-I5 | +NIMP:PD-VLLMWZ60 | +NeryLab 384_SetB | +
| SetB-I6 | +NIMP:PD-VLLMWZ60 | +NeryLab 384_SetB | +
| SetB-I7 | +NIMP:PD-VLLMWZ60 | +NeryLab 384_SetB | +
| SetB-I8 | +NIMP:PD-VLLMWZ60 | +NeryLab 384_SetB/# | +
| Name | +Description | +
|---|---|
| r1_r2_index | +Name of the pair of library indexes used for sequencing | +
name: library_r1_r2_index
+from_schema: https://identifiers.org/brain-bican/library-generation-schema
+rank: 1000
+permissible_values:
+ SI-TT-A1:
+ text: SI-TT-A1
+ description: 10x Dual Index TT Set A. Used with 10xV3.1, 10xV3.1_HT, and 10xMultiome;GEX
+ meaning: NIMP:PD-VLLMWZ60
+ SI-TT-A2:
+ text: SI-TT-A2
+ description: 10x Dual Index TT Set A. Used with 10xV3.1, 10xV3.1_HT, and 10xMultiome;GEX
+ meaning: NIMP:PD-VLLMWZ60
+ SI-TT-A3:
+ text: SI-TT-A3
+ description: 10x Dual Index TT Set A. Used with 10xV3.1, 10xV3.1_HT, and 10xMultiome;GEX
+ meaning: NIMP:PD-VLLMWZ60
+ SI-TT-A4:
+ text: SI-TT-A4
+ description: 10x Dual Index TT Set A. Used with 10xV3.1, 10xV3.1_HT, and 10xMultiome;GEX
+ meaning: NIMP:PD-VLLMWZ60
+ SI-TT-A5:
+ text: SI-TT-A5
+ description: 10x Dual Index TT Set A. Used with 10xV3.1, 10xV3.1_HT, and 10xMultiome;GEX
+ meaning: NIMP:PD-VLLMWZ60
+ SI-TT-A6:
+ text: SI-TT-A6
+ description: 10x Dual Index TT Set A. Used with 10xV3.1, 10xV3.1_HT, and 10xMultiome;GEX
+ meaning: NIMP:PD-VLLMWZ60
+ SI-TT-A7:
+ text: SI-TT-A7
+ description: 10x Dual Index TT Set A. Used with 10xV3.1, 10xV3.1_HT, and 10xMultiome;GEX
+ meaning: NIMP:PD-VLLMWZ60
+ SI-TT-A8:
+ text: SI-TT-A8
+ description: 10x Dual Index TT Set A. Used with 10xV3.1, 10xV3.1_HT, and 10xMultiome;GEX
+ meaning: NIMP:PD-VLLMWZ60
+ SI-TT-A9:
+ text: SI-TT-A9
+ description: 10x Dual Index TT Set A. Used with 10xV3.1, 10xV3.1_HT, and 10xMultiome;GEX
+ meaning: NIMP:PD-VLLMWZ60
+ SI-TT-A10:
+ text: SI-TT-A10
+ description: 10x Dual Index TT Set A. Used with 10xV3.1, 10xV3.1_HT, and 10xMultiome;GEX
+ meaning: NIMP:PD-VLLMWZ60
+ SI-TT-A11:
+ text: SI-TT-A11
+ description: 10x Dual Index TT Set A. Used with 10xV3.1, 10xV3.1_HT, and 10xMultiome;GEX
+ meaning: NIMP:PD-VLLMWZ60
+ SI-TT-A12:
+ text: SI-TT-A12
+ description: 10x Dual Index TT Set A. Used with 10xV3.1, 10xV3.1_HT, and 10xMultiome;GEX
+ meaning: NIMP:PD-VLLMWZ60
+ SI-TT-B1:
+ text: SI-TT-B1
+ description: 10x Dual Index TT Set A. Used with 10xV3.1, 10xV3.1_HT, and 10xMultiome;GEX
+ meaning: NIMP:PD-VLLMWZ60
+ SI-TT-B2:
+ text: SI-TT-B2
+ description: 10x Dual Index TT Set A. Used with 10xV3.1, 10xV3.1_HT, and 10xMultiome;GEX
+ meaning: NIMP:PD-VLLMWZ60
+ SI-TT-B3:
+ text: SI-TT-B3
+ description: 10x Dual Index TT Set A. Used with 10xV3.1, 10xV3.1_HT, and 10xMultiome;GEX
+ meaning: NIMP:PD-VLLMWZ60
+ SI-TT-B4:
+ text: SI-TT-B4
+ description: 10x Dual Index TT Set A. Used with 10xV3.1, 10xV3.1_HT, and 10xMultiome;GEX
+ meaning: NIMP:PD-VLLMWZ60
+ SI-TT-B5:
+ text: SI-TT-B5
+ description: 10x Dual Index TT Set A. Used with 10xV3.1, 10xV3.1_HT, and 10xMultiome;GEX
+ meaning: NIMP:PD-VLLMWZ60
+ SI-TT-B6:
+ text: SI-TT-B6
+ description: 10x Dual Index TT Set A. Used with 10xV3.1, 10xV3.1_HT, and 10xMultiome;GEX
+ meaning: NIMP:PD-VLLMWZ60
+ SI-TT-B7:
+ text: SI-TT-B7
+ description: 10x Dual Index TT Set A. Used with 10xV3.1, 10xV3.1_HT, and 10xMultiome;GEX
+ meaning: NIMP:PD-VLLMWZ60
+ SI-TT-B8:
+ text: SI-TT-B8
+ description: 10x Dual Index TT Set A. Used with 10xV3.1, 10xV3.1_HT, and 10xMultiome;GEX
+ meaning: NIMP:PD-VLLMWZ60
+ SI-TT-B9:
+ text: SI-TT-B9
+ description: 10x Dual Index TT Set A. Used with 10xV3.1, 10xV3.1_HT, and 10xMultiome;GEX
+ meaning: NIMP:PD-VLLMWZ60
+ SI-TT-B10:
+ text: SI-TT-B10
+ description: 10x Dual Index TT Set A. Used with 10xV3.1, 10xV3.1_HT, and 10xMultiome;GEX
+ meaning: NIMP:PD-VLLMWZ60
+ SI-TT-B11:
+ text: SI-TT-B11
+ description: 10x Dual Index TT Set A. Used with 10xV3.1, 10xV3.1_HT, and 10xMultiome;GEX
+ meaning: NIMP:PD-VLLMWZ60
+ SI-TT-B12:
+ text: SI-TT-B12
+ description: 10x Dual Index TT Set A. Used with 10xV3.1, 10xV3.1_HT, and 10xMultiome;GEX
+ meaning: NIMP:PD-VLLMWZ60
+ SI-TT-C1:
+ text: SI-TT-C1
+ description: 10x Dual Index TT Set A. Used with 10xV3.1, 10xV3.1_HT, and 10xMultiome;GEX
+ meaning: NIMP:PD-VLLMWZ60
+ SI-TT-C2:
+ text: SI-TT-C2
+ description: 10x Dual Index TT Set A. Used with 10xV3.1, 10xV3.1_HT, and 10xMultiome;GEX
+ meaning: NIMP:PD-VLLMWZ60
+ SI-TT-C3:
+ text: SI-TT-C3
+ description: 10x Dual Index TT Set A. Used with 10xV3.1, 10xV3.1_HT, and 10xMultiome;GEX
+ meaning: NIMP:PD-VLLMWZ60
+ SI-TT-C4:
+ text: SI-TT-C4
+ description: 10x Dual Index TT Set A. Used with 10xV3.1, 10xV3.1_HT, and 10xMultiome;GEX
+ meaning: NIMP:PD-VLLMWZ60
+ SI-TT-C5:
+ text: SI-TT-C5
+ description: 10x Dual Index TT Set A. Used with 10xV3.1, 10xV3.1_HT, and 10xMultiome;GEX
+ meaning: NIMP:PD-VLLMWZ60
+ SI-TT-C6:
+ text: SI-TT-C6
+ description: 10x Dual Index TT Set A. Used with 10xV3.1, 10xV3.1_HT, and 10xMultiome;GEX
+ meaning: NIMP:PD-VLLMWZ60
+ SI-TT-C7:
+ text: SI-TT-C7
+ description: 10x Dual Index TT Set A. Used with 10xV3.1, 10xV3.1_HT, and 10xMultiome;GEX
+ meaning: NIMP:PD-VLLMWZ60
+ SI-TT-C8:
+ text: SI-TT-C8
+ description: 10x Dual Index TT Set A. Used with 10xV3.1, 10xV3.1_HT, and 10xMultiome;GEX
+ meaning: NIMP:PD-VLLMWZ60
+ SI-TT-C9:
+ text: SI-TT-C9
+ description: 10x Dual Index TT Set A. Used with 10xV3.1, 10xV3.1_HT, and 10xMultiome;GEX
+ meaning: NIMP:PD-VLLMWZ60
+ SI-TT-C10:
+ text: SI-TT-C10
+ description: 10x Dual Index TT Set A. Used with 10xV3.1, 10xV3.1_HT, and 10xMultiome;GEX
+ meaning: NIMP:PD-VLLMWZ60
+ SI-TT-C11:
+ text: SI-TT-C11
+ description: 10x Dual Index TT Set A. Used with 10xV3.1, 10xV3.1_HT, and 10xMultiome;GEX
+ meaning: NIMP:PD-VLLMWZ60
+ SI-TT-C12:
+ text: SI-TT-C12
+ description: 10x Dual Index TT Set A. Used with 10xV3.1, 10xV3.1_HT, and 10xMultiome;GEX
+ meaning: NIMP:PD-VLLMWZ60
+ SI-TT-D1:
+ text: SI-TT-D1
+ description: 10x Dual Index TT Set A. Used with 10xV3.1, 10xV3.1_HT, and 10xMultiome;GEX
+ meaning: NIMP:PD-VLLMWZ60
+ SI-TT-D2:
+ text: SI-TT-D2
+ description: 10x Dual Index TT Set A. Used with 10xV3.1, 10xV3.1_HT, and 10xMultiome;GEX
+ meaning: NIMP:PD-VLLMWZ60
+ SI-TT-D3:
+ text: SI-TT-D3
+ description: 10x Dual Index TT Set A. Used with 10xV3.1, 10xV3.1_HT, and 10xMultiome;GEX
+ meaning: NIMP:PD-VLLMWZ60
+ SI-TT-D4:
+ text: SI-TT-D4
+ description: 10x Dual Index TT Set A. Used with 10xV3.1, 10xV3.1_HT, and 10xMultiome;GEX
+ meaning: NIMP:PD-VLLMWZ60
+ SI-TT-D5:
+ text: SI-TT-D5
+ description: 10x Dual Index TT Set A. Used with 10xV3.1, 10xV3.1_HT, and 10xMultiome;GEX
+ meaning: NIMP:PD-VLLMWZ60
+ SI-TT-D6:
+ text: SI-TT-D6
+ description: 10x Dual Index TT Set A. Used with 10xV3.1, 10xV3.1_HT, and 10xMultiome;GEX
+ meaning: NIMP:PD-VLLMWZ60
+ SI-TT-D7:
+ text: SI-TT-D7
+ description: 10x Dual Index TT Set A. Used with 10xV3.1, 10xV3.1_HT, and 10xMultiome;GEX
+ meaning: NIMP:PD-VLLMWZ60
+ SI-TT-D8:
+ text: SI-TT-D8
+ description: 10x Dual Index TT Set A. Used with 10xV3.1, 10xV3.1_HT, and 10xMultiome;GEX
+ meaning: NIMP:PD-VLLMWZ60
+ SI-TT-D9:
+ text: SI-TT-D9
+ description: 10x Dual Index TT Set A. Used with 10xV3.1, 10xV3.1_HT, and 10xMultiome;GEX
+ meaning: NIMP:PD-VLLMWZ60
+ SI-TT-D10:
+ text: SI-TT-D10
+ description: 10x Dual Index TT Set A. Used with 10xV3.1, 10xV3.1_HT, and 10xMultiome;GEX
+ meaning: NIMP:PD-VLLMWZ60
+ SI-TT-D11:
+ text: SI-TT-D11
+ description: 10x Dual Index TT Set A. Used with 10xV3.1, 10xV3.1_HT, and 10xMultiome;GEX
+ meaning: NIMP:PD-VLLMWZ60
+ SI-TT-D12:
+ text: SI-TT-D12
+ description: 10x Dual Index TT Set A. Used with 10xV3.1, 10xV3.1_HT, and 10xMultiome;GEX
+ meaning: NIMP:PD-VLLMWZ60
+ SI-TT-E1:
+ text: SI-TT-E1
+ description: 10x Dual Index TT Set A. Used with 10xV3.1, 10xV3.1_HT, and 10xMultiome;GEX
+ meaning: NIMP:PD-VLLMWZ60
+ SI-TT-E2:
+ text: SI-TT-E2
+ description: 10x Dual Index TT Set A. Used with 10xV3.1, 10xV3.1_HT, and 10xMultiome;GEX
+ meaning: NIMP:PD-VLLMWZ60
+ SI-TT-E3:
+ text: SI-TT-E3
+ description: 10x Dual Index TT Set A. Used with 10xV3.1, 10xV3.1_HT, and 10xMultiome;GEX
+ meaning: NIMP:PD-VLLMWZ60
+ SI-TT-E4:
+ text: SI-TT-E4
+ description: 10x Dual Index TT Set A. Used with 10xV3.1, 10xV3.1_HT, and 10xMultiome;GEX
+ meaning: NIMP:PD-VLLMWZ60
+ SI-TT-E5:
+ text: SI-TT-E5
+ description: 10x Dual Index TT Set A. Used with 10xV3.1, 10xV3.1_HT, and 10xMultiome;GEX
+ meaning: NIMP:PD-VLLMWZ60
+ SI-TT-E6:
+ text: SI-TT-E6
+ description: 10x Dual Index TT Set A. Used with 10xV3.1, 10xV3.1_HT, and 10xMultiome;GEX
+ meaning: NIMP:PD-VLLMWZ60
+ SI-TT-E7:
+ text: SI-TT-E7
+ description: 10x Dual Index TT Set A. Used with 10xV3.1, 10xV3.1_HT, and 10xMultiome;GEX
+ meaning: NIMP:PD-VLLMWZ60
+ SI-TT-E8:
+ text: SI-TT-E8
+ description: 10x Dual Index TT Set A. Used with 10xV3.1, 10xV3.1_HT, and 10xMultiome;GEX
+ meaning: NIMP:PD-VLLMWZ60
+ SI-TT-E9:
+ text: SI-TT-E9
+ description: 10x Dual Index TT Set A. Used with 10xV3.1, 10xV3.1_HT, and 10xMultiome;GEX
+ meaning: NIMP:PD-VLLMWZ60
+ SI-TT-E10:
+ text: SI-TT-E10
+ description: 10x Dual Index TT Set A. Used with 10xV3.1, 10xV3.1_HT, and 10xMultiome;GEX
+ meaning: NIMP:PD-VLLMWZ60
+ SI-TT-E11:
+ text: SI-TT-E11
+ description: 10x Dual Index TT Set A. Used with 10xV3.1, 10xV3.1_HT, and 10xMultiome;GEX
+ meaning: NIMP:PD-VLLMWZ60
+ SI-TT-E12:
+ text: SI-TT-E12
+ description: 10x Dual Index TT Set A. Used with 10xV3.1, 10xV3.1_HT, and 10xMultiome;GEX
+ meaning: NIMP:PD-VLLMWZ60
+ SI-TT-F1:
+ text: SI-TT-F1
+ description: 10x Dual Index TT Set A. Used with 10xV3.1, 10xV3.1_HT, and 10xMultiome;GEX
+ meaning: NIMP:PD-VLLMWZ60
+ SI-TT-F2:
+ text: SI-TT-F2
+ description: 10x Dual Index TT Set A. Used with 10xV3.1, 10xV3.1_HT, and 10xMultiome;GEX
+ meaning: NIMP:PD-VLLMWZ60
+ SI-TT-F3:
+ text: SI-TT-F3
+ description: 10x Dual Index TT Set A. Used with 10xV3.1, 10xV3.1_HT, and 10xMultiome;GEX
+ meaning: NIMP:PD-VLLMWZ60
+ SI-TT-F4:
+ text: SI-TT-F4
+ description: 10x Dual Index TT Set A. Used with 10xV3.1, 10xV3.1_HT, and 10xMultiome;GEX
+ meaning: NIMP:PD-VLLMWZ60
+ SI-TT-F5:
+ text: SI-TT-F5
+ description: 10x Dual Index TT Set A. Used with 10xV3.1, 10xV3.1_HT, and 10xMultiome;GEX
+ meaning: NIMP:PD-VLLMWZ60
+ SI-TT-F6:
+ text: SI-TT-F6
+ description: 10x Dual Index TT Set A. Used with 10xV3.1, 10xV3.1_HT, and 10xMultiome;GEX
+ meaning: NIMP:PD-VLLMWZ60
+ SI-TT-F7:
+ text: SI-TT-F7
+ description: 10x Dual Index TT Set A. Used with 10xV3.1, 10xV3.1_HT, and 10xMultiome;GEX
+ meaning: NIMP:PD-VLLMWZ60
+ SI-TT-F8:
+ text: SI-TT-F8
+ description: 10x Dual Index TT Set A. Used with 10xV3.1, 10xV3.1_HT, and 10xMultiome;GEX
+ meaning: NIMP:PD-VLLMWZ60
+ SI-TT-F9:
+ text: SI-TT-F9
+ description: 10x Dual Index TT Set A. Used with 10xV3.1, 10xV3.1_HT, and 10xMultiome;GEX
+ meaning: NIMP:PD-VLLMWZ60
+ SI-TT-F10:
+ text: SI-TT-F10
+ description: 10x Dual Index TT Set A. Used with 10xV3.1, 10xV3.1_HT, and 10xMultiome;GEX
+ meaning: NIMP:PD-VLLMWZ60
+ SI-TT-F11:
+ text: SI-TT-F11
+ description: 10x Dual Index TT Set A. Used with 10xV3.1, 10xV3.1_HT, and 10xMultiome;GEX
+ meaning: NIMP:PD-VLLMWZ60
+ SI-TT-F12:
+ text: SI-TT-F12
+ description: 10x Dual Index TT Set A. Used with 10xV3.1, 10xV3.1_HT, and 10xMultiome;GEX
+ meaning: NIMP:PD-VLLMWZ60
+ SI-TT-G1:
+ text: SI-TT-G1
+ description: 10x Dual Index TT Set A. Used with 10xV3.1, 10xV3.1_HT, and 10xMultiome;GEX
+ meaning: NIMP:PD-VLLMWZ60
+ SI-TT-G2:
+ text: SI-TT-G2
+ description: 10x Dual Index TT Set A. Used with 10xV3.1, 10xV3.1_HT, and 10xMultiome;GEX
+ meaning: NIMP:PD-VLLMWZ60
+ SI-TT-G3:
+ text: SI-TT-G3
+ description: 10x Dual Index TT Set A. Used with 10xV3.1, 10xV3.1_HT, and 10xMultiome;GEX
+ meaning: NIMP:PD-VLLMWZ60
+ SI-TT-G4:
+ text: SI-TT-G4
+ description: 10x Dual Index TT Set A. Used with 10xV3.1, 10xV3.1_HT, and 10xMultiome;GEX
+ meaning: NIMP:PD-VLLMWZ60
+ SI-TT-G5:
+ text: SI-TT-G5
+ description: 10x Dual Index TT Set A. Used with 10xV3.1, 10xV3.1_HT, and 10xMultiome;GEX
+ meaning: NIMP:PD-VLLMWZ60
+ SI-TT-G6:
+ text: SI-TT-G6
+ description: 10x Dual Index TT Set A. Used with 10xV3.1, 10xV3.1_HT, and 10xMultiome;GEX
+ meaning: NIMP:PD-VLLMWZ60
+ SI-TT-G7:
+ text: SI-TT-G7
+ description: 10x Dual Index TT Set A. Used with 10xV3.1, 10xV3.1_HT, and 10xMultiome;GEX
+ meaning: NIMP:PD-VLLMWZ60
+ SI-TT-G8:
+ text: SI-TT-G8
+ description: 10x Dual Index TT Set A. Used with 10xV3.1, 10xV3.1_HT, and 10xMultiome;GEX
+ meaning: NIMP:PD-VLLMWZ60
+ SI-TT-G9:
+ text: SI-TT-G9
+ description: 10x Dual Index TT Set A. Used with 10xV3.1, 10xV3.1_HT, and 10xMultiome;GEX
+ meaning: NIMP:PD-VLLMWZ60
+ SI-TT-G10:
+ text: SI-TT-G10
+ description: 10x Dual Index TT Set A. Used with 10xV3.1, 10xV3.1_HT, and 10xMultiome;GEX
+ meaning: NIMP:PD-VLLMWZ60
+ SI-TT-G11:
+ text: SI-TT-G11
+ description: 10x Dual Index TT Set A. Used with 10xV3.1, 10xV3.1_HT, and 10xMultiome;GEX
+ meaning: NIMP:PD-VLLMWZ60
+ SI-TT-G12:
+ text: SI-TT-G12
+ description: 10x Dual Index TT Set A. Used with 10xV3.1, 10xV3.1_HT, and 10xMultiome;GEX
+ meaning: NIMP:PD-VLLMWZ60
+ SI-TT-H1:
+ text: SI-TT-H1
+ description: 10x Dual Index TT Set A. Used with 10xV3.1, 10xV3.1_HT, and 10xMultiome;GEX
+ meaning: NIMP:PD-VLLMWZ60
+ SI-TT-H2:
+ text: SI-TT-H2
+ description: 10x Dual Index TT Set A. Used with 10xV3.1, 10xV3.1_HT, and 10xMultiome;GEX
+ meaning: NIMP:PD-VLLMWZ60
+ SI-TT-H3:
+ text: SI-TT-H3
+ description: 10x Dual Index TT Set A. Used with 10xV3.1, 10xV3.1_HT, and 10xMultiome;GEX
+ meaning: NIMP:PD-VLLMWZ60
+ SI-TT-H4:
+ text: SI-TT-H4
+ description: 10x Dual Index TT Set A. Used with 10xV3.1, 10xV3.1_HT, and 10xMultiome;GEX
+ meaning: NIMP:PD-VLLMWZ60
+ SI-TT-H5:
+ text: SI-TT-H5
+ description: 10x Dual Index TT Set A. Used with 10xV3.1, 10xV3.1_HT, and 10xMultiome;GEX
+ meaning: NIMP:PD-VLLMWZ60
+ SI-TT-H6:
+ text: SI-TT-H6
+ description: 10x Dual Index TT Set A. Used with 10xV3.1, 10xV3.1_HT, and 10xMultiome;GEX
+ meaning: NIMP:PD-VLLMWZ60
+ SI-TT-H7:
+ text: SI-TT-H7
+ description: 10x Dual Index TT Set A. Used with 10xV3.1, 10xV3.1_HT, and 10xMultiome;GEX
+ meaning: NIMP:PD-VLLMWZ60
+ SI-TT-H8:
+ text: SI-TT-H8
+ description: 10x Dual Index TT Set A. Used with 10xV3.1, 10xV3.1_HT, and 10xMultiome;GEX
+ meaning: NIMP:PD-VLLMWZ60
+ SI-TT-H9:
+ text: SI-TT-H9
+ description: 10x Dual Index TT Set A. Used with 10xV3.1, 10xV3.1_HT, and 10xMultiome;GEX
+ meaning: NIMP:PD-VLLMWZ60
+ SI-TT-H10:
+ text: SI-TT-H10
+ description: 10x Dual Index TT Set A. Used with 10xV3.1, 10xV3.1_HT, and 10xMultiome;GEX
+ meaning: NIMP:PD-VLLMWZ60
+ SI-TT-H11:
+ text: SI-TT-H11
+ description: 10x Dual Index TT Set A. Used with 10xV3.1, 10xV3.1_HT, and 10xMultiome;GEX
+ meaning: NIMP:PD-VLLMWZ60
+ SI-TT-H12:
+ text: SI-TT-H12
+ description: 10x Dual Index TT Set A. Used with 10xV3.1, 10xV3.1_HT, and 10xMultiome;GEX
+ meaning: NIMP:PD-VLLMWZ60
+ SI-NN-A1:
+ text: SI-NN-A1
+ description: 10x Dual Index NN Set A. Used with 10xV3.1_CellPlex;GEX and 10xV3.1-HT_CellPlex;GEX
+ meaning: NIMP:PD-VLLMWZ60
+ SI-NN-A2:
+ text: SI-NN-A2
+ description: 10x Dual Index NN Set A. Used with 10xV3.1_CellPlex;GEX and 10xV3.1-HT_CellPlex;GEX
+ meaning: NIMP:PD-VLLMWZ60
+ SI-NN-A3:
+ text: SI-NN-A3
+ description: 10x Dual Index NN Set A. Used with 10xV3.1_CellPlex;GEX and 10xV3.1-HT_CellPlex;GEX
+ meaning: NIMP:PD-VLLMWZ60
+ SI-NN-A4:
+ text: SI-NN-A4
+ description: 10x Dual Index NN Set A. Used with 10xV3.1_CellPlex;GEX and 10xV3.1-HT_CellPlex;GEX
+ meaning: NIMP:PD-VLLMWZ60
+ SI-NN-A5:
+ text: SI-NN-A5
+ description: 10x Dual Index NN Set A. Used with 10xV3.1_CellPlex;GEX and 10xV3.1-HT_CellPlex;GEX
+ meaning: NIMP:PD-VLLMWZ60
+ SI-NN-A6:
+ text: SI-NN-A6
+ description: 10x Dual Index NN Set A. Used with 10xV3.1_CellPlex;GEX and 10xV3.1-HT_CellPlex;GEX
+ meaning: NIMP:PD-VLLMWZ60
+ SI-NN-A7:
+ text: SI-NN-A7
+ description: 10x Dual Index NN Set A. Used with 10xV3.1_CellPlex;GEX and 10xV3.1-HT_CellPlex;GEX
+ meaning: NIMP:PD-VLLMWZ60
+ SI-NN-A8:
+ text: SI-NN-A8
+ description: 10x Dual Index NN Set A. Used with 10xV3.1_CellPlex;GEX and 10xV3.1-HT_CellPlex;GEX
+ meaning: NIMP:PD-VLLMWZ60
+ SI-NN-A9:
+ text: SI-NN-A9
+ description: 10x Dual Index NN Set A. Used with 10xV3.1_CellPlex;GEX and 10xV3.1-HT_CellPlex;GEX
+ meaning: NIMP:PD-VLLMWZ60
+ SI-NN-A10:
+ text: SI-NN-A10
+ description: 10x Dual Index NN Set A. Used with 10xV3.1_CellPlex;GEX and 10xV3.1-HT_CellPlex;GEX
+ meaning: NIMP:PD-VLLMWZ60
+ SI-NN-A11:
+ text: SI-NN-A11
+ description: 10x Dual Index NN Set A. Used with 10xV3.1_CellPlex;GEX and 10xV3.1-HT_CellPlex;GEX
+ meaning: NIMP:PD-VLLMWZ60
+ SI-NN-A12:
+ text: SI-NN-A12
+ description: 10x Dual Index NN Set A. Used with 10xV3.1_CellPlex;GEX and 10xV3.1-HT_CellPlex;GEX
+ meaning: NIMP:PD-VLLMWZ60
+ SI-NN-B1:
+ text: SI-NN-B1
+ description: 10x Dual Index NN Set A. Used with 10xV3.1_CellPlex;GEX and 10xV3.1-HT_CellPlex;GEX
+ meaning: NIMP:PD-VLLMWZ60
+ SI-NN-B2:
+ text: SI-NN-B2
+ description: 10x Dual Index NN Set A. Used with 10xV3.1_CellPlex;GEX and 10xV3.1-HT_CellPlex;GEX
+ meaning: NIMP:PD-VLLMWZ60
+ SI-NN-B3:
+ text: SI-NN-B3
+ description: 10x Dual Index NN Set A. Used with 10xV3.1_CellPlex;GEX and 10xV3.1-HT_CellPlex;GEX
+ meaning: NIMP:PD-VLLMWZ60
+ SI-NN-B4:
+ text: SI-NN-B4
+ description: 10x Dual Index NN Set A. Used with 10xV3.1_CellPlex;GEX and 10xV3.1-HT_CellPlex;GEX
+ meaning: NIMP:PD-VLLMWZ60
+ SI-NN-B5:
+ text: SI-NN-B5
+ description: 10x Dual Index NN Set A. Used with 10xV3.1_CellPlex;GEX and 10xV3.1-HT_CellPlex;GEX
+ meaning: NIMP:PD-VLLMWZ60
+ SI-NN-B6:
+ text: SI-NN-B6
+ description: 10x Dual Index NN Set A. Used with 10xV3.1_CellPlex;GEX and 10xV3.1-HT_CellPlex;GEX
+ meaning: NIMP:PD-VLLMWZ60
+ SI-NN-B7:
+ text: SI-NN-B7
+ description: 10x Dual Index NN Set A. Used with 10xV3.1_CellPlex;GEX and 10xV3.1-HT_CellPlex;GEX
+ meaning: NIMP:PD-VLLMWZ60
+ SI-NN-B8:
+ text: SI-NN-B8
+ description: 10x Dual Index NN Set A. Used with 10xV3.1_CellPlex;GEX and 10xV3.1-HT_CellPlex;GEX
+ meaning: NIMP:PD-VLLMWZ60
+ SI-NN-B9:
+ text: SI-NN-B9
+ description: 10x Dual Index NN Set A. Used with 10xV3.1_CellPlex;GEX and 10xV3.1-HT_CellPlex;GEX
+ meaning: NIMP:PD-VLLMWZ60
+ SI-NN-B10:
+ text: SI-NN-B10
+ description: 10x Dual Index NN Set A. Used with 10xV3.1_CellPlex;GEX and 10xV3.1-HT_CellPlex;GEX
+ meaning: NIMP:PD-VLLMWZ60
+ SI-NN-B11:
+ text: SI-NN-B11
+ description: 10x Dual Index NN Set A. Used with 10xV3.1_CellPlex;GEX and 10xV3.1-HT_CellPlex;GEX
+ meaning: NIMP:PD-VLLMWZ60
+ SI-NN-B12:
+ text: SI-NN-B12
+ description: 10x Dual Index NN Set A. Used with 10xV3.1_CellPlex;GEX and 10xV3.1-HT_CellPlex;GEX
+ meaning: NIMP:PD-VLLMWZ60
+ SI-NN-C1:
+ text: SI-NN-C1
+ description: 10x Dual Index NN Set A. Used with 10xV3.1_CellPlex;GEX and 10xV3.1-HT_CellPlex;GEX
+ meaning: NIMP:PD-VLLMWZ60
+ SI-NN-C2:
+ text: SI-NN-C2
+ description: 10x Dual Index NN Set A. Used with 10xV3.1_CellPlex;GEX and 10xV3.1-HT_CellPlex;GEX
+ meaning: NIMP:PD-VLLMWZ60
+ SI-NN-C3:
+ text: SI-NN-C3
+ description: 10x Dual Index NN Set A. Used with 10xV3.1_CellPlex;GEX and 10xV3.1-HT_CellPlex;GEX
+ meaning: NIMP:PD-VLLMWZ60
+ SI-NN-C4:
+ text: SI-NN-C4
+ description: 10x Dual Index NN Set A. Used with 10xV3.1_CellPlex;GEX and 10xV3.1-HT_CellPlex;GEX
+ meaning: NIMP:PD-VLLMWZ60
+ SI-NN-C5:
+ text: SI-NN-C5
+ description: 10x Dual Index NN Set A. Used with 10xV3.1_CellPlex;GEX and 10xV3.1-HT_CellPlex;GEX
+ meaning: NIMP:PD-VLLMWZ60
+ SI-NN-C6:
+ text: SI-NN-C6
+ description: 10x Dual Index NN Set A. Used with 10xV3.1_CellPlex;GEX and 10xV3.1-HT_CellPlex;GEX
+ meaning: NIMP:PD-VLLMWZ60
+ SI-NN-C7:
+ text: SI-NN-C7
+ description: 10x Dual Index NN Set A. Used with 10xV3.1_CellPlex;GEX and 10xV3.1-HT_CellPlex;GEX
+ meaning: NIMP:PD-VLLMWZ60
+ SI-NN-C8:
+ text: SI-NN-C8
+ description: 10x Dual Index NN Set A. Used with 10xV3.1_CellPlex;GEX and 10xV3.1-HT_CellPlex;GEX
+ meaning: NIMP:PD-VLLMWZ60
+ SI-NN-C9:
+ text: SI-NN-C9
+ description: 10x Dual Index NN Set A. Used with 10xV3.1_CellPlex;GEX and 10xV3.1-HT_CellPlex;GEX
+ meaning: NIMP:PD-VLLMWZ60
+ SI-NN-C10:
+ text: SI-NN-C10
+ description: 10x Dual Index NN Set A. Used with 10xV3.1_CellPlex;GEX and 10xV3.1-HT_CellPlex;GEX
+ meaning: NIMP:PD-VLLMWZ60
+ SI-NN-C11:
+ text: SI-NN-C11
+ description: 10x Dual Index NN Set A. Used with 10xV3.1_CellPlex;GEX and 10xV3.1-HT_CellPlex;GEX
+ meaning: NIMP:PD-VLLMWZ60
+ SI-NN-C12:
+ text: SI-NN-C12
+ description: 10x Dual Index NN Set A. Used with 10xV3.1_CellPlex;GEX and 10xV3.1-HT_CellPlex;GEX
+ meaning: NIMP:PD-VLLMWZ60
+ SI-NN-D1:
+ text: SI-NN-D1
+ description: 10x Dual Index NN Set A. Used with 10xV3.1_CellPlex;GEX and 10xV3.1-HT_CellPlex;GEX
+ meaning: NIMP:PD-VLLMWZ60
+ SI-NN-D2:
+ text: SI-NN-D2
+ description: 10x Dual Index NN Set A. Used with 10xV3.1_CellPlex;GEX and 10xV3.1-HT_CellPlex;GEX
+ meaning: NIMP:PD-VLLMWZ60
+ SI-NN-D3:
+ text: SI-NN-D3
+ description: 10x Dual Index NN Set A. Used with 10xV3.1_CellPlex;GEX and 10xV3.1-HT_CellPlex;GEX
+ meaning: NIMP:PD-VLLMWZ60
+ SI-NN-D4:
+ text: SI-NN-D4
+ description: 10x Dual Index NN Set A. Used with 10xV3.1_CellPlex;GEX and 10xV3.1-HT_CellPlex;GEX
+ meaning: NIMP:PD-VLLMWZ60
+ SI-NN-D5:
+ text: SI-NN-D5
+ description: 10x Dual Index NN Set A. Used with 10xV3.1_CellPlex;GEX and 10xV3.1-HT_CellPlex;GEX
+ meaning: NIMP:PD-VLLMWZ60
+ SI-NN-D6:
+ text: SI-NN-D6
+ description: 10x Dual Index NN Set A. Used with 10xV3.1_CellPlex;GEX and 10xV3.1-HT_CellPlex;GEX
+ meaning: NIMP:PD-VLLMWZ60
+ SI-NN-D7:
+ text: SI-NN-D7
+ description: 10x Dual Index NN Set A. Used with 10xV3.1_CellPlex;GEX and 10xV3.1-HT_CellPlex;GEX
+ meaning: NIMP:PD-VLLMWZ60
+ SI-NN-D8:
+ text: SI-NN-D8
+ description: 10x Dual Index NN Set A. Used with 10xV3.1_CellPlex;GEX and 10xV3.1-HT_CellPlex;GEX
+ meaning: NIMP:PD-VLLMWZ60
+ SI-NN-D9:
+ text: SI-NN-D9
+ description: 10x Dual Index NN Set A. Used with 10xV3.1_CellPlex;GEX and 10xV3.1-HT_CellPlex;GEX
+ meaning: NIMP:PD-VLLMWZ60
+ SI-NN-D10:
+ text: SI-NN-D10
+ description: 10x Dual Index NN Set A. Used with 10xV3.1_CellPlex;GEX and 10xV3.1-HT_CellPlex;GEX
+ meaning: NIMP:PD-VLLMWZ60
+ SI-NN-D11:
+ text: SI-NN-D11
+ description: 10x Dual Index NN Set A. Used with 10xV3.1_CellPlex;GEX and 10xV3.1-HT_CellPlex;GEX
+ meaning: NIMP:PD-VLLMWZ60
+ SI-NN-D12:
+ text: SI-NN-D12
+ description: 10x Dual Index NN Set A. Used with 10xV3.1_CellPlex;GEX and 10xV3.1-HT_CellPlex;GEX
+ meaning: NIMP:PD-VLLMWZ60
+ SI-NN-E1:
+ text: SI-NN-E1
+ description: 10x Dual Index NN Set A. Used with 10xV3.1_CellPlex;GEX and 10xV3.1-HT_CellPlex;GEX
+ meaning: NIMP:PD-VLLMWZ60
+ SI-NN-E2:
+ text: SI-NN-E2
+ description: 10x Dual Index NN Set A. Used with 10xV3.1_CellPlex;GEX and 10xV3.1-HT_CellPlex;GEX
+ meaning: NIMP:PD-VLLMWZ60
+ SI-NN-E3:
+ text: SI-NN-E3
+ description: 10x Dual Index NN Set A. Used with 10xV3.1_CellPlex;GEX and 10xV3.1-HT_CellPlex;GEX
+ meaning: NIMP:PD-VLLMWZ60
+ SI-NN-E4:
+ text: SI-NN-E4
+ description: 10x Dual Index NN Set A. Used with 10xV3.1_CellPlex;GEX and 10xV3.1-HT_CellPlex;GEX
+ meaning: NIMP:PD-VLLMWZ60
+ SI-NN-E5:
+ text: SI-NN-E5
+ description: 10x Dual Index NN Set A. Used with 10xV3.1_CellPlex;GEX and 10xV3.1-HT_CellPlex;GEX
+ meaning: NIMP:PD-VLLMWZ60
+ SI-NN-E6:
+ text: SI-NN-E6
+ description: 10x Dual Index NN Set A. Used with 10xV3.1_CellPlex;GEX and 10xV3.1-HT_CellPlex;GEX
+ meaning: NIMP:PD-VLLMWZ60
+ SI-NN-E7:
+ text: SI-NN-E7
+ description: 10x Dual Index NN Set A. Used with 10xV3.1_CellPlex;GEX and 10xV3.1-HT_CellPlex;GEX
+ meaning: NIMP:PD-VLLMWZ60
+ SI-NN-E8:
+ text: SI-NN-E8
+ description: 10x Dual Index NN Set A. Used with 10xV3.1_CellPlex;GEX and 10xV3.1-HT_CellPlex;GEX
+ meaning: NIMP:PD-VLLMWZ60
+ SI-NN-E9:
+ text: SI-NN-E9
+ description: 10x Dual Index NN Set A. Used with 10xV3.1_CellPlex;GEX and 10xV3.1-HT_CellPlex;GEX
+ meaning: NIMP:PD-VLLMWZ60
+ SI-NN-E10:
+ text: SI-NN-E10
+ description: 10x Dual Index NN Set A. Used with 10xV3.1_CellPlex;GEX and 10xV3.1-HT_CellPlex;GEX
+ meaning: NIMP:PD-VLLMWZ60
+ SI-NN-E11:
+ text: SI-NN-E11
+ description: 10x Dual Index NN Set A. Used with 10xV3.1_CellPlex;GEX and 10xV3.1-HT_CellPlex;GEX
+ meaning: NIMP:PD-VLLMWZ60
+ SI-NN-E12:
+ text: SI-NN-E12
+ description: 10x Dual Index NN Set A. Used with 10xV3.1_CellPlex;GEX and 10xV3.1-HT_CellPlex;GEX
+ meaning: NIMP:PD-VLLMWZ60
+ SI-NN-F1:
+ text: SI-NN-F1
+ description: 10x Dual Index NN Set A. Used with 10xV3.1_CellPlex;GEX and 10xV3.1-HT_CellPlex;GEX
+ meaning: NIMP:PD-VLLMWZ60
+ SI-NN-F2:
+ text: SI-NN-F2
+ description: 10x Dual Index NN Set A. Used with 10xV3.1_CellPlex;GEX and 10xV3.1-HT_CellPlex;GEX
+ meaning: NIMP:PD-VLLMWZ60
+ SI-NN-F3:
+ text: SI-NN-F3
+ description: 10x Dual Index NN Set A. Used with 10xV3.1_CellPlex;GEX and 10xV3.1-HT_CellPlex;GEX
+ meaning: NIMP:PD-VLLMWZ60
+ SI-NN-F4:
+ text: SI-NN-F4
+ description: 10x Dual Index NN Set A. Used with 10xV3.1_CellPlex;GEX and 10xV3.1-HT_CellPlex;GEX
+ meaning: NIMP:PD-VLLMWZ60
+ SI-NN-F5:
+ text: SI-NN-F5
+ description: 10x Dual Index NN Set A. Used with 10xV3.1_CellPlex;GEX and 10xV3.1-HT_CellPlex;GEX
+ meaning: NIMP:PD-VLLMWZ60
+ SI-NN-F6:
+ text: SI-NN-F6
+ description: 10x Dual Index NN Set A. Used with 10xV3.1_CellPlex;GEX and 10xV3.1-HT_CellPlex;GEX
+ meaning: NIMP:PD-VLLMWZ60
+ SI-NN-F7:
+ text: SI-NN-F7
+ description: 10x Dual Index NN Set A. Used with 10xV3.1_CellPlex;GEX and 10xV3.1-HT_CellPlex;GEX
+ meaning: NIMP:PD-VLLMWZ60
+ SI-NN-F8:
+ text: SI-NN-F8
+ description: 10x Dual Index NN Set A. Used with 10xV3.1_CellPlex;GEX and 10xV3.1-HT_CellPlex;GEX
+ meaning: NIMP:PD-VLLMWZ60
+ SI-NN-F9:
+ text: SI-NN-F9
+ description: 10x Dual Index NN Set A. Used with 10xV3.1_CellPlex;GEX and 10xV3.1-HT_CellPlex;GEX
+ meaning: NIMP:PD-VLLMWZ60
+ SI-NN-F10:
+ text: SI-NN-F10
+ description: 10x Dual Index NN Set A. Used with 10xV3.1_CellPlex;GEX and 10xV3.1-HT_CellPlex;GEX
+ meaning: NIMP:PD-VLLMWZ60
+ SI-NN-F11:
+ text: SI-NN-F11
+ description: 10x Dual Index NN Set A. Used with 10xV3.1_CellPlex;GEX and 10xV3.1-HT_CellPlex;GEX
+ meaning: NIMP:PD-VLLMWZ60
+ SI-NN-F12:
+ text: SI-NN-F12
+ description: 10x Dual Index NN Set A. Used with 10xV3.1_CellPlex;GEX and 10xV3.1-HT_CellPlex;GEX
+ meaning: NIMP:PD-VLLMWZ60
+ SI-NN-G1:
+ text: SI-NN-G1
+ description: 10x Dual Index NN Set A. Used with 10xV3.1_CellPlex;GEX and 10xV3.1-HT_CellPlex;GEX
+ meaning: NIMP:PD-VLLMWZ60
+ SI-NN-G2:
+ text: SI-NN-G2
+ description: 10x Dual Index NN Set A. Used with 10xV3.1_CellPlex;GEX and 10xV3.1-HT_CellPlex;GEX
+ meaning: NIMP:PD-VLLMWZ60
+ SI-NN-G3:
+ text: SI-NN-G3
+ description: 10x Dual Index NN Set A. Used with 10xV3.1_CellPlex;GEX and 10xV3.1-HT_CellPlex;GEX
+ meaning: NIMP:PD-VLLMWZ60
+ SI-NN-G4:
+ text: SI-NN-G4
+ description: 10x Dual Index NN Set A. Used with 10xV3.1_CellPlex;GEX and 10xV3.1-HT_CellPlex;GEX
+ meaning: NIMP:PD-VLLMWZ60
+ SI-NN-G5:
+ text: SI-NN-G5
+ description: 10x Dual Index NN Set A. Used with 10xV3.1_CellPlex;GEX and 10xV3.1-HT_CellPlex;GEX
+ meaning: NIMP:PD-VLLMWZ60
+ SI-NN-G6:
+ text: SI-NN-G6
+ description: 10x Dual Index NN Set A. Used with 10xV3.1_CellPlex;GEX and 10xV3.1-HT_CellPlex;GEX
+ meaning: NIMP:PD-VLLMWZ60
+ SI-NN-G7:
+ text: SI-NN-G7
+ description: 10x Dual Index NN Set A. Used with 10xV3.1_CellPlex;GEX and 10xV3.1-HT_CellPlex;GEX
+ meaning: NIMP:PD-VLLMWZ60
+ SI-NN-G8:
+ text: SI-NN-G8
+ description: 10x Dual Index NN Set A. Used with 10xV3.1_CellPlex;GEX and 10xV3.1-HT_CellPlex;GEX
+ meaning: NIMP:PD-VLLMWZ60
+ SI-NN-G9:
+ text: SI-NN-G9
+ description: 10x Dual Index NN Set A. Used with 10xV3.1_CellPlex;GEX and 10xV3.1-HT_CellPlex;GEX
+ meaning: NIMP:PD-VLLMWZ60
+ SI-NN-G10:
+ text: SI-NN-G10
+ description: 10x Dual Index NN Set A. Used with 10xV3.1_CellPlex;GEX and 10xV3.1-HT_CellPlex;GEX
+ meaning: NIMP:PD-VLLMWZ60
+ SI-NN-G11:
+ text: SI-NN-G11
+ description: 10x Dual Index NN Set A. Used with 10xV3.1_CellPlex;GEX and 10xV3.1-HT_CellPlex;GEX
+ meaning: NIMP:PD-VLLMWZ60
+ SI-NN-G12:
+ text: SI-NN-G12
+ description: 10x Dual Index NN Set A. Used with 10xV3.1_CellPlex;GEX and 10xV3.1-HT_CellPlex;GEX
+ meaning: NIMP:PD-VLLMWZ60
+ SI-NN-H1:
+ text: SI-NN-H1
+ description: 10x Dual Index NN Set A. Used with 10xV3.1_CellPlex;GEX and 10xV3.1-HT_CellPlex;GEX
+ meaning: NIMP:PD-VLLMWZ60
+ SI-NN-H2:
+ text: SI-NN-H2
+ description: 10x Dual Index NN Set A. Used with 10xV3.1_CellPlex;GEX and 10xV3.1-HT_CellPlex;GEX
+ meaning: NIMP:PD-VLLMWZ60
+ SI-NN-H3:
+ text: SI-NN-H3
+ description: 10x Dual Index NN Set A. Used with 10xV3.1_CellPlex;GEX and 10xV3.1-HT_CellPlex;GEX
+ meaning: NIMP:PD-VLLMWZ60
+ SI-NN-H4:
+ text: SI-NN-H4
+ description: 10x Dual Index NN Set A. Used with 10xV3.1_CellPlex;GEX and 10xV3.1-HT_CellPlex;GEX
+ meaning: NIMP:PD-VLLMWZ60
+ SI-NN-H5:
+ text: SI-NN-H5
+ description: 10x Dual Index NN Set A. Used with 10xV3.1_CellPlex;GEX and 10xV3.1-HT_CellPlex;GEX
+ meaning: NIMP:PD-VLLMWZ60
+ SI-NN-H6:
+ text: SI-NN-H6
+ description: 10x Dual Index NN Set A. Used with 10xV3.1_CellPlex;GEX and 10xV3.1-HT_CellPlex;GEX
+ meaning: NIMP:PD-VLLMWZ60
+ SI-NN-H7:
+ text: SI-NN-H7
+ description: 10x Dual Index NN Set A. Used with 10xV3.1_CellPlex;GEX and 10xV3.1-HT_CellPlex;GEX
+ meaning: NIMP:PD-VLLMWZ60
+ SI-NN-H8:
+ text: SI-NN-H8
+ description: 10x Dual Index NN Set A. Used with 10xV3.1_CellPlex;GEX and 10xV3.1-HT_CellPlex;GEX
+ meaning: NIMP:PD-VLLMWZ60
+ SI-NN-H9:
+ text: SI-NN-H9
+ description: 10x Dual Index NN Set A. Used with 10xV3.1_CellPlex;GEX and 10xV3.1-HT_CellPlex;GEX
+ meaning: NIMP:PD-VLLMWZ60
+ SI-NN-H10:
+ text: SI-NN-H10
+ description: 10x Dual Index NN Set A. Used with 10xV3.1_CellPlex;GEX and 10xV3.1-HT_CellPlex;GEX
+ meaning: NIMP:PD-VLLMWZ60
+ SI-NN-H11:
+ text: SI-NN-H11
+ description: 10x Dual Index NN Set A. Used with 10xV3.1_CellPlex;GEX and 10xV3.1-HT_CellPlex;GEX
+ meaning: NIMP:PD-VLLMWZ60
+ SI-NN-H12:
+ text: SI-NN-H12
+ description: 10x Dual Index NN Set A. Used with 10xV3.1_CellPlex;GEX and 10xV3.1-HT_CellPlex;GEX
+ meaning: NIMP:PD-VLLMWZ60
+ SI-NA-A1:
+ text: SI-NA-A1
+ description: 10x Single Index N Set A. Used with 10xATAC_v2.0 and 10xMultiome;ATAC
+ meaning: NIMP:PD-VLLMWZ60
+ SI-NA-B1:
+ text: SI-NA-B1
+ description: 10x Single Index N Set A. Used with 10xATAC_v2.0 and 10xMultiome;ATAC
+ meaning: NIMP:PD-VLLMWZ60
+ SI-NA-C1:
+ text: SI-NA-C1
+ description: 10x Single Index N Set A. Used with 10xATAC_v2.0 and 10xMultiome;ATAC
+ meaning: NIMP:PD-VLLMWZ60
+ SI-NA-D1:
+ text: SI-NA-D1
+ description: 10x Single Index N Set A. Used with 10xATAC_v2.0 and 10xMultiome;ATAC
+ meaning: NIMP:PD-VLLMWZ60
+ SI-NA-E1:
+ text: SI-NA-E1
+ description: 10x Single Index N Set A. Used with 10xATAC_v2.0 and 10xMultiome;ATAC
+ meaning: NIMP:PD-VLLMWZ60
+ SI-NA-F1:
+ text: SI-NA-F1
+ description: 10x Single Index N Set A. Used with 10xATAC_v2.0 and 10xMultiome;ATAC
+ meaning: NIMP:PD-VLLMWZ60
+ SI-NA-G1:
+ text: SI-NA-G1
+ description: 10x Single Index N Set A. Used with 10xATAC_v2.0 and 10xMultiome;ATAC
+ meaning: NIMP:PD-VLLMWZ60
+ SI-NA-H1:
+ text: SI-NA-H1
+ description: 10x Single Index N Set A. Used with 10xATAC_v2.0 and 10xMultiome;ATAC
+ meaning: NIMP:PD-VLLMWZ60
+ SI-NA-A2:
+ text: SI-NA-A2
+ description: 10x Single Index N Set A. Used with 10xATAC_v2.0 and 10xMultiome;ATAC
+ meaning: NIMP:PD-VLLMWZ60
+ SI-NA-B2:
+ text: SI-NA-B2
+ description: 10x Single Index N Set A. Used with 10xATAC_v2.0 and 10xMultiome;ATAC
+ meaning: NIMP:PD-VLLMWZ60
+ SI-NA-C2:
+ text: SI-NA-C2
+ description: 10x Single Index N Set A. Used with 10xATAC_v2.0 and 10xMultiome;ATAC
+ meaning: NIMP:PD-VLLMWZ60
+ SI-NA-D2:
+ text: SI-NA-D2
+ description: 10x Single Index N Set A. Used with 10xATAC_v2.0 and 10xMultiome;ATAC
+ meaning: NIMP:PD-VLLMWZ60
+ SI-NA-E2:
+ text: SI-NA-E2
+ description: 10x Single Index N Set A. Used with 10xATAC_v2.0 and 10xMultiome;ATAC
+ meaning: NIMP:PD-VLLMWZ60
+ SI-NA-F2:
+ text: SI-NA-F2
+ description: 10x Single Index N Set A. Used with 10xATAC_v2.0 and 10xMultiome;ATAC
+ meaning: NIMP:PD-VLLMWZ60
+ SI-NA-G2:
+ text: SI-NA-G2
+ description: 10x Single Index N Set A. Used with 10xATAC_v2.0 and 10xMultiome;ATAC
+ meaning: NIMP:PD-VLLMWZ60
+ SI-NA-H2:
+ text: SI-NA-H2
+ description: 10x Single Index N Set A. Used with 10xATAC_v2.0 and 10xMultiome;ATAC
+ meaning: NIMP:PD-VLLMWZ60
+ SI-NA-A3:
+ text: SI-NA-A3
+ description: 10x Single Index N Set A. Used with 10xATAC_v2.0 and 10xMultiome;ATAC
+ meaning: NIMP:PD-VLLMWZ60
+ SI-NA-B3:
+ text: SI-NA-B3
+ description: 10x Single Index N Set A. Used with 10xATAC_v2.0 and 10xMultiome;ATAC
+ meaning: NIMP:PD-VLLMWZ60
+ SI-NA-C3:
+ text: SI-NA-C3
+ description: 10x Single Index N Set A. Used with 10xATAC_v2.0 and 10xMultiome;ATAC
+ meaning: NIMP:PD-VLLMWZ60
+ SI-NA-D3:
+ text: SI-NA-D3
+ description: 10x Single Index N Set A. Used with 10xATAC_v2.0 and 10xMultiome;ATAC
+ meaning: NIMP:PD-VLLMWZ60
+ SI-NA-E3:
+ text: SI-NA-E3
+ description: 10x Single Index N Set A. Used with 10xATAC_v2.0 and 10xMultiome;ATAC
+ meaning: NIMP:PD-VLLMWZ60
+ SI-NA-F3:
+ text: SI-NA-F3
+ description: 10x Single Index N Set A. Used with 10xATAC_v2.0 and 10xMultiome;ATAC
+ meaning: NIMP:PD-VLLMWZ60
+ SI-NA-G3:
+ text: SI-NA-G3
+ description: 10x Single Index N Set A. Used with 10xATAC_v2.0 and 10xMultiome;ATAC
+ meaning: NIMP:PD-VLLMWZ60
+ SI-NA-H3:
+ text: SI-NA-H3
+ description: 10x Single Index N Set A. Used with 10xATAC_v2.0 and 10xMultiome;ATAC
+ meaning: NIMP:PD-VLLMWZ60
+ SI-NA-A4:
+ text: SI-NA-A4
+ description: 10x Single Index N Set A. Used with 10xATAC_v2.0 and 10xMultiome;ATAC
+ meaning: NIMP:PD-VLLMWZ60
+ SI-NA-B4:
+ text: SI-NA-B4
+ description: 10x Single Index N Set A. Used with 10xATAC_v2.0 and 10xMultiome;ATAC
+ meaning: NIMP:PD-VLLMWZ60
+ SI-NA-C4:
+ text: SI-NA-C4
+ description: 10x Single Index N Set A. Used with 10xATAC_v2.0 and 10xMultiome;ATAC
+ meaning: NIMP:PD-VLLMWZ60
+ SI-NA-D4:
+ text: SI-NA-D4
+ description: 10x Single Index N Set A. Used with 10xATAC_v2.0 and 10xMultiome;ATAC
+ meaning: NIMP:PD-VLLMWZ60
+ SI-NA-E4:
+ text: SI-NA-E4
+ description: 10x Single Index N Set A. Used with 10xATAC_v2.0 and 10xMultiome;ATAC
+ meaning: NIMP:PD-VLLMWZ60
+ SI-NA-F4:
+ text: SI-NA-F4
+ description: 10x Single Index N Set A. Used with 10xATAC_v2.0 and 10xMultiome;ATAC
+ meaning: NIMP:PD-VLLMWZ60
+ SI-NA-G4:
+ text: SI-NA-G4
+ description: 10x Single Index N Set A. Used with 10xATAC_v2.0 and 10xMultiome;ATAC
+ meaning: NIMP:PD-VLLMWZ60
+ SI-NA-H4:
+ text: SI-NA-H4
+ description: 10x Single Index N Set A. Used with 10xATAC_v2.0 and 10xMultiome;ATAC
+ meaning: NIMP:PD-VLLMWZ60
+ SI-NA-A5:
+ text: SI-NA-A5
+ description: 10x Single Index N Set A. Used with 10xATAC_v2.0 and 10xMultiome;ATAC
+ meaning: NIMP:PD-VLLMWZ60
+ SI-NA-B5:
+ text: SI-NA-B5
+ description: 10x Single Index N Set A. Used with 10xATAC_v2.0 and 10xMultiome;ATAC
+ meaning: NIMP:PD-VLLMWZ60
+ SI-NA-C5:
+ text: SI-NA-C5
+ description: 10x Single Index N Set A. Used with 10xATAC_v2.0 and 10xMultiome;ATAC
+ meaning: NIMP:PD-VLLMWZ60
+ SI-NA-D5:
+ text: SI-NA-D5
+ description: 10x Single Index N Set A. Used with 10xATAC_v2.0 and 10xMultiome;ATAC
+ meaning: NIMP:PD-VLLMWZ60
+ SI-NA-E5:
+ text: SI-NA-E5
+ description: 10x Single Index N Set A. Used with 10xATAC_v2.0 and 10xMultiome;ATAC
+ meaning: NIMP:PD-VLLMWZ60
+ SI-NA-F5:
+ text: SI-NA-F5
+ description: 10x Single Index N Set A. Used with 10xATAC_v2.0 and 10xMultiome;ATAC
+ meaning: NIMP:PD-VLLMWZ60
+ SI-NA-G5:
+ text: SI-NA-G5
+ description: 10x Single Index N Set A. Used with 10xATAC_v2.0 and 10xMultiome;ATAC
+ meaning: NIMP:PD-VLLMWZ60
+ SI-NA-H5:
+ text: SI-NA-H5
+ description: 10x Single Index N Set A. Used with 10xATAC_v2.0 and 10xMultiome;ATAC
+ meaning: NIMP:PD-VLLMWZ60
+ SI-NA-A6:
+ text: SI-NA-A6
+ description: 10x Single Index N Set A. Used with 10xATAC_v2.0 and 10xMultiome;ATAC
+ meaning: NIMP:PD-VLLMWZ60
+ SI-NA-B6:
+ text: SI-NA-B6
+ description: 10x Single Index N Set A. Used with 10xATAC_v2.0 and 10xMultiome;ATAC
+ meaning: NIMP:PD-VLLMWZ60
+ SI-NA-C6:
+ text: SI-NA-C6
+ description: 10x Single Index N Set A. Used with 10xATAC_v2.0 and 10xMultiome;ATAC
+ meaning: NIMP:PD-VLLMWZ60
+ SI-NA-D6:
+ text: SI-NA-D6
+ description: 10x Single Index N Set A. Used with 10xATAC_v2.0 and 10xMultiome;ATAC
+ meaning: NIMP:PD-VLLMWZ60
+ SI-NA-E6:
+ text: SI-NA-E6
+ description: 10x Single Index N Set A. Used with 10xATAC_v2.0 and 10xMultiome;ATAC
+ meaning: NIMP:PD-VLLMWZ60
+ SI-NA-F6:
+ text: SI-NA-F6
+ description: 10x Single Index N Set A. Used with 10xATAC_v2.0 and 10xMultiome;ATAC
+ meaning: NIMP:PD-VLLMWZ60
+ SI-NA-G6:
+ text: SI-NA-G6
+ description: 10x Single Index N Set A. Used with 10xATAC_v2.0 and 10xMultiome;ATAC
+ meaning: NIMP:PD-VLLMWZ60
+ SI-NA-H6:
+ text: SI-NA-H6
+ description: 10x Single Index N Set A. Used with 10xATAC_v2.0 and 10xMultiome;ATAC
+ meaning: NIMP:PD-VLLMWZ60
+ SI-NA-A7:
+ text: SI-NA-A7
+ description: 10x Single Index N Set A. Used with 10xATAC_v2.0 and 10xMultiome;ATAC
+ meaning: NIMP:PD-VLLMWZ60
+ SI-NA-B7:
+ text: SI-NA-B7
+ description: 10x Single Index N Set A. Used with 10xATAC_v2.0 and 10xMultiome;ATAC
+ meaning: NIMP:PD-VLLMWZ60
+ SI-NA-C7:
+ text: SI-NA-C7
+ description: 10x Single Index N Set A. Used with 10xATAC_v2.0 and 10xMultiome;ATAC
+ meaning: NIMP:PD-VLLMWZ60
+ SI-NA-D7:
+ text: SI-NA-D7
+ description: 10x Single Index N Set A. Used with 10xATAC_v2.0 and 10xMultiome;ATAC
+ meaning: NIMP:PD-VLLMWZ60
+ SI-NA-E7:
+ text: SI-NA-E7
+ description: 10x Single Index N Set A. Used with 10xATAC_v2.0 and 10xMultiome;ATAC
+ meaning: NIMP:PD-VLLMWZ60
+ SI-NA-F7:
+ text: SI-NA-F7
+ description: 10x Single Index N Set A. Used with 10xATAC_v2.0 and 10xMultiome;ATAC
+ meaning: NIMP:PD-VLLMWZ60
+ SI-NA-G7:
+ text: SI-NA-G7
+ description: 10x Single Index N Set A. Used with 10xATAC_v2.0 and 10xMultiome;ATAC
+ meaning: NIMP:PD-VLLMWZ60
+ SI-NA-H7:
+ text: SI-NA-H7
+ description: 10x Single Index N Set A. Used with 10xATAC_v2.0 and 10xMultiome;ATAC
+ meaning: NIMP:PD-VLLMWZ60
+ SI-NA-A8:
+ text: SI-NA-A8
+ description: 10x Single Index N Set A. Used with 10xATAC_v2.0 and 10xMultiome;ATAC
+ meaning: NIMP:PD-VLLMWZ60
+ SI-NA-B8:
+ text: SI-NA-B8
+ description: 10x Single Index N Set A. Used with 10xATAC_v2.0 and 10xMultiome;ATAC
+ meaning: NIMP:PD-VLLMWZ60
+ SI-NA-C8:
+ text: SI-NA-C8
+ description: 10x Single Index N Set A. Used with 10xATAC_v2.0 and 10xMultiome;ATAC
+ meaning: NIMP:PD-VLLMWZ60
+ SI-NA-D8:
+ text: SI-NA-D8
+ description: 10x Single Index N Set A. Used with 10xATAC_v2.0 and 10xMultiome;ATAC
+ meaning: NIMP:PD-VLLMWZ60
+ SI-NA-E8:
+ text: SI-NA-E8
+ description: 10x Single Index N Set A. Used with 10xATAC_v2.0 and 10xMultiome;ATAC
+ meaning: NIMP:PD-VLLMWZ60
+ SI-NA-F8:
+ text: SI-NA-F8
+ description: 10x Single Index N Set A. Used with 10xATAC_v2.0 and 10xMultiome;ATAC
+ meaning: NIMP:PD-VLLMWZ60
+ SI-NA-G8:
+ text: SI-NA-G8
+ description: 10x Single Index N Set A. Used with 10xATAC_v2.0 and 10xMultiome;ATAC
+ meaning: NIMP:PD-VLLMWZ60
+ SI-NA-H8:
+ text: SI-NA-H8
+ description: 10x Single Index N Set A. Used with 10xATAC_v2.0 and 10xMultiome;ATAC
+ meaning: NIMP:PD-VLLMWZ60
+ SI-NA-A9:
+ text: SI-NA-A9
+ description: 10x Single Index N Set A. Used with 10xATAC_v2.0 and 10xMultiome;ATAC
+ meaning: NIMP:PD-VLLMWZ60
+ SI-NA-B9:
+ text: SI-NA-B9
+ description: 10x Single Index N Set A. Used with 10xATAC_v2.0 and 10xMultiome;ATAC
+ meaning: NIMP:PD-VLLMWZ60
+ SI-NA-C9:
+ text: SI-NA-C9
+ description: 10x Single Index N Set A. Used with 10xATAC_v2.0 and 10xMultiome;ATAC
+ meaning: NIMP:PD-VLLMWZ60
+ SI-NA-D9:
+ text: SI-NA-D9
+ description: 10x Single Index N Set A. Used with 10xATAC_v2.0 and 10xMultiome;ATAC
+ meaning: NIMP:PD-VLLMWZ60
+ SI-NA-E9:
+ text: SI-NA-E9
+ description: 10x Single Index N Set A. Used with 10xATAC_v2.0 and 10xMultiome;ATAC
+ meaning: NIMP:PD-VLLMWZ60
+ SI-NA-F9:
+ text: SI-NA-F9
+ description: 10x Single Index N Set A. Used with 10xATAC_v2.0 and 10xMultiome;ATAC
+ meaning: NIMP:PD-VLLMWZ60
+ SI-NA-G9:
+ text: SI-NA-G9
+ description: 10x Single Index N Set A. Used with 10xATAC_v2.0 and 10xMultiome;ATAC
+ meaning: NIMP:PD-VLLMWZ60
+ SI-NA-H9:
+ text: SI-NA-H9
+ description: 10x Single Index N Set A. Used with 10xATAC_v2.0 and 10xMultiome;ATAC
+ meaning: NIMP:PD-VLLMWZ60
+ SI-NA-A10:
+ text: SI-NA-A10
+ description: 10x Single Index N Set A. Used with 10xATAC_v2.0 and 10xMultiome;ATAC
+ meaning: NIMP:PD-VLLMWZ60
+ SI-NA-B10:
+ text: SI-NA-B10
+ description: 10x Single Index N Set A. Used with 10xATAC_v2.0 and 10xMultiome;ATAC
+ meaning: NIMP:PD-VLLMWZ60
+ SI-NA-C10:
+ text: SI-NA-C10
+ description: 10x Single Index N Set A. Used with 10xATAC_v2.0 and 10xMultiome;ATAC
+ meaning: NIMP:PD-VLLMWZ60
+ SI-NA-D10:
+ text: SI-NA-D10
+ description: 10x Single Index N Set A. Used with 10xATAC_v2.0 and 10xMultiome;ATAC
+ meaning: NIMP:PD-VLLMWZ60
+ SI-NA-E10:
+ text: SI-NA-E10
+ description: 10x Single Index N Set A. Used with 10xATAC_v2.0 and 10xMultiome;ATAC
+ meaning: NIMP:PD-VLLMWZ60
+ SI-NA-F10:
+ text: SI-NA-F10
+ description: 10x Single Index N Set A. Used with 10xATAC_v2.0 and 10xMultiome;ATAC
+ meaning: NIMP:PD-VLLMWZ60
+ SI-NA-G10:
+ text: SI-NA-G10
+ description: 10x Single Index N Set A. Used with 10xATAC_v2.0 and 10xMultiome;ATAC
+ meaning: NIMP:PD-VLLMWZ60
+ SI-NA-H10:
+ text: SI-NA-H10
+ description: 10x Single Index N Set A. Used with 10xATAC_v2.0 and 10xMultiome;ATAC
+ meaning: NIMP:PD-VLLMWZ60
+ SI-NA-A11:
+ text: SI-NA-A11
+ description: 10x Single Index N Set A. Used with 10xATAC_v2.0 and 10xMultiome;ATAC
+ meaning: NIMP:PD-VLLMWZ60
+ SI-NA-B11:
+ text: SI-NA-B11
+ description: 10x Single Index N Set A. Used with 10xATAC_v2.0 and 10xMultiome;ATAC
+ meaning: NIMP:PD-VLLMWZ60
+ SI-NA-C11:
+ text: SI-NA-C11
+ description: 10x Single Index N Set A. Used with 10xATAC_v2.0 and 10xMultiome;ATAC
+ meaning: NIMP:PD-VLLMWZ60
+ SI-NA-D11:
+ text: SI-NA-D11
+ description: 10x Single Index N Set A. Used with 10xATAC_v2.0 and 10xMultiome;ATAC
+ meaning: NIMP:PD-VLLMWZ60
+ SI-NA-E11:
+ text: SI-NA-E11
+ description: 10x Single Index N Set A. Used with 10xATAC_v2.0 and 10xMultiome;ATAC
+ meaning: NIMP:PD-VLLMWZ60
+ SI-NA-F11:
+ text: SI-NA-F11
+ description: 10x Single Index N Set A. Used with 10xATAC_v2.0 and 10xMultiome;ATAC
+ meaning: NIMP:PD-VLLMWZ60
+ SI-NA-G11:
+ text: SI-NA-G11
+ description: 10x Single Index N Set A. Used with 10xATAC_v2.0 and 10xMultiome;ATAC
+ meaning: NIMP:PD-VLLMWZ60
+ SI-NA-H11:
+ text: SI-NA-H11
+ description: 10x Single Index N Set A. Used with 10xATAC_v2.0 and 10xMultiome;ATAC
+ meaning: NIMP:PD-VLLMWZ60
+ SI-NA-A12:
+ text: SI-NA-A12
+ description: 10x Single Index N Set A. Used with 10xATAC_v2.0 and 10xMultiome;ATAC
+ meaning: NIMP:PD-VLLMWZ60
+ SI-NA-B12:
+ text: SI-NA-B12
+ description: 10x Single Index N Set A. Used with 10xATAC_v2.0 and 10xMultiome;ATAC
+ meaning: NIMP:PD-VLLMWZ60
+ SI-NA-C12:
+ text: SI-NA-C12
+ description: 10x Single Index N Set A. Used with 10xATAC_v2.0 and 10xMultiome;ATAC
+ meaning: NIMP:PD-VLLMWZ60
+ SI-NA-D12:
+ text: SI-NA-D12
+ description: 10x Single Index N Set A. Used with 10xATAC_v2.0 and 10xMultiome;ATAC
+ meaning: NIMP:PD-VLLMWZ60
+ SI-NA-E12:
+ text: SI-NA-E12
+ description: 10x Single Index N Set A. Used with 10xATAC_v2.0 and 10xMultiome;ATAC
+ meaning: NIMP:PD-VLLMWZ60
+ SI-NA-F12:
+ text: SI-NA-F12
+ description: 10x Single Index N Set A. Used with 10xATAC_v2.0 and 10xMultiome;ATAC
+ meaning: NIMP:PD-VLLMWZ60
+ SI-NA-G12:
+ text: SI-NA-G12
+ description: 10x Single Index N Set A. Used with 10xATAC_v2.0 and 10xMultiome;ATAC
+ meaning: NIMP:PD-VLLMWZ60
+ SI-NA-H12:
+ text: SI-NA-H12
+ description: 10x Single Index N Set A. Used with 10xATAC_v2.0 and 10xMultiome;ATAC
+ meaning: NIMP:PD-VLLMWZ60
+ SetB-A1:
+ text: SetB-A1
+ description: NeryLab 384_SetB
+ meaning: NIMP:PD-VLLMWZ60
+ SetB-A10:
+ text: SetB-A10
+ description: NeryLab 384_SetB
+ meaning: NIMP:PD-VLLMWZ60
+ SetB-A11:
+ text: SetB-A11
+ description: NeryLab 384_SetB
+ meaning: NIMP:PD-VLLMWZ60
+ SetB-A12:
+ text: SetB-A12
+ description: NeryLab 384_SetB
+ meaning: NIMP:PD-VLLMWZ60
+ SetB-A13:
+ text: SetB-A13
+ description: NeryLab 384_SetB
+ meaning: NIMP:PD-VLLMWZ60
+ SetB-A14:
+ text: SetB-A14
+ description: NeryLab 384_SetB
+ meaning: NIMP:PD-VLLMWZ60
+ SetB-A15:
+ text: SetB-A15
+ description: NeryLab 384_SetB
+ meaning: NIMP:PD-VLLMWZ60
+ SetB-A16:
+ text: SetB-A16
+ description: NeryLab 384_SetB
+ meaning: NIMP:PD-VLLMWZ60
+ SetB-A17:
+ text: SetB-A17
+ description: NeryLab 384_SetB
+ meaning: NIMP:PD-VLLMWZ60
+ SetB-A18:
+ text: SetB-A18
+ description: NeryLab 384_SetB
+ meaning: NIMP:PD-VLLMWZ60
+ SetB-A19:
+ text: SetB-A19
+ description: NeryLab 384_SetB
+ meaning: NIMP:PD-VLLMWZ60
+ SetB-A2:
+ text: SetB-A2
+ description: NeryLab 384_SetB
+ meaning: NIMP:PD-VLLMWZ60
+ SetB-A20:
+ text: SetB-A20
+ description: NeryLab 384_SetB
+ meaning: NIMP:PD-VLLMWZ60
+ SetB-A21:
+ text: SetB-A21
+ description: NeryLab 384_SetB
+ meaning: NIMP:PD-VLLMWZ60
+ SetB-A22:
+ text: SetB-A22
+ description: NeryLab 384_SetB
+ meaning: NIMP:PD-VLLMWZ60
+ SetB-A23:
+ text: SetB-A23
+ description: NeryLab 384_SetB
+ meaning: NIMP:PD-VLLMWZ60
+ SetB-A24:
+ text: SetB-A24
+ description: NeryLab 384_SetB
+ meaning: NIMP:PD-VLLMWZ60
+ SetB-A3:
+ text: SetB-A3
+ description: NeryLab 384_SetB
+ meaning: NIMP:PD-VLLMWZ60
+ SetB-A4:
+ text: SetB-A4
+ description: NeryLab 384_SetB
+ meaning: NIMP:PD-VLLMWZ60
+ SetB-A5:
+ text: SetB-A5
+ description: NeryLab 384_SetB
+ meaning: NIMP:PD-VLLMWZ60
+ SetB-A6:
+ text: SetB-A6
+ description: NeryLab 384_SetB
+ meaning: NIMP:PD-VLLMWZ60
+ SetB-A7:
+ text: SetB-A7
+ description: NeryLab 384_SetB
+ meaning: NIMP:PD-VLLMWZ60
+ SetB-A8:
+ text: SetB-A8
+ description: NeryLab 384_SetB
+ meaning: NIMP:PD-VLLMWZ60
+ SetB-A9:
+ text: SetB-A9
+ description: NeryLab 384_SetB
+ meaning: NIMP:PD-VLLMWZ60
+ SetB-B1:
+ text: SetB-B1
+ description: NeryLab 384_SetB
+ meaning: NIMP:PD-VLLMWZ60
+ SetB-B10:
+ text: SetB-B10
+ description: NeryLab 384_SetB
+ meaning: NIMP:PD-VLLMWZ60
+ SetB-B11:
+ text: SetB-B11
+ description: NeryLab 384_SetB
+ meaning: NIMP:PD-VLLMWZ60
+ SetB-B12:
+ text: SetB-B12
+ description: NeryLab 384_SetB
+ meaning: NIMP:PD-VLLMWZ60
+ SetB-B13:
+ text: SetB-B13
+ description: NeryLab 384_SetB
+ meaning: NIMP:PD-VLLMWZ60
+ SetB-B14:
+ text: SetB-B14
+ description: NeryLab 384_SetB
+ meaning: NIMP:PD-VLLMWZ60
+ SetB-B15:
+ text: SetB-B15
+ description: NeryLab 384_SetB
+ meaning: NIMP:PD-VLLMWZ60
+ SetB-B16:
+ text: SetB-B16
+ description: NeryLab 384_SetB
+ meaning: NIMP:PD-VLLMWZ60
+ SetB-B17:
+ text: SetB-B17
+ description: NeryLab 384_SetB
+ meaning: NIMP:PD-VLLMWZ60
+ SetB-B18:
+ text: SetB-B18
+ description: NeryLab 384_SetB
+ meaning: NIMP:PD-VLLMWZ60
+ SetB-B19:
+ text: SetB-B19
+ description: NeryLab 384_SetB
+ meaning: NIMP:PD-VLLMWZ60
+ SetB-B2:
+ text: SetB-B2
+ description: NeryLab 384_SetB
+ meaning: NIMP:PD-VLLMWZ60
+ SetB-B20:
+ text: SetB-B20
+ description: NeryLab 384_SetB
+ meaning: NIMP:PD-VLLMWZ60
+ SetB-B21:
+ text: SetB-B21
+ description: NeryLab 384_SetB
+ meaning: NIMP:PD-VLLMWZ60
+ SetB-B22:
+ text: SetB-B22
+ description: NeryLab 384_SetB
+ meaning: NIMP:PD-VLLMWZ60
+ SetB-B23:
+ text: SetB-B23
+ description: NeryLab 384_SetB
+ meaning: NIMP:PD-VLLMWZ60
+ SetB-B24:
+ text: SetB-B24
+ description: NeryLab 384_SetB
+ meaning: NIMP:PD-VLLMWZ60
+ SetB-B3:
+ text: SetB-B3
+ description: NeryLab 384_SetB
+ meaning: NIMP:PD-VLLMWZ60
+ SetB-B4:
+ text: SetB-B4
+ description: NeryLab 384_SetB
+ meaning: NIMP:PD-VLLMWZ60
+ SetB-B5:
+ text: SetB-B5
+ description: NeryLab 384_SetB
+ meaning: NIMP:PD-VLLMWZ60
+ SetB-B6:
+ text: SetB-B6
+ description: NeryLab 384_SetB
+ meaning: NIMP:PD-VLLMWZ60
+ SetB-B7:
+ text: SetB-B7
+ description: NeryLab 384_SetB
+ meaning: NIMP:PD-VLLMWZ60
+ SetB-B8:
+ text: SetB-B8
+ description: NeryLab 384_SetB
+ meaning: NIMP:PD-VLLMWZ60
+ SetB-B9:
+ text: SetB-B9
+ description: NeryLab 384_SetB
+ meaning: NIMP:PD-VLLMWZ60
+ SetB-C1:
+ text: SetB-C1
+ description: NeryLab 384_SetB
+ meaning: NIMP:PD-VLLMWZ60
+ SetB-C10:
+ text: SetB-C10
+ description: NeryLab 384_SetB
+ meaning: NIMP:PD-VLLMWZ60
+ SetB-C11:
+ text: SetB-C11
+ description: NeryLab 384_SetB
+ meaning: NIMP:PD-VLLMWZ60
+ SetB-C12:
+ text: SetB-C12
+ description: NeryLab 384_SetB
+ meaning: NIMP:PD-VLLMWZ60
+ SetB-C13:
+ text: SetB-C13
+ description: NeryLab 384_SetB
+ meaning: NIMP:PD-VLLMWZ60
+ SetB-C14:
+ text: SetB-C14
+ description: NeryLab 384_SetB
+ meaning: NIMP:PD-VLLMWZ60
+ SetB-C15:
+ text: SetB-C15
+ description: NeryLab 384_SetB
+ meaning: NIMP:PD-VLLMWZ60
+ SetB-C16:
+ text: SetB-C16
+ description: NeryLab 384_SetB
+ meaning: NIMP:PD-VLLMWZ60
+ SetB-C17:
+ text: SetB-C17
+ description: NeryLab 384_SetB
+ meaning: NIMP:PD-VLLMWZ60
+ SetB-C18:
+ text: SetB-C18
+ description: NeryLab 384_SetB
+ meaning: NIMP:PD-VLLMWZ60
+ SetB-C19:
+ text: SetB-C19
+ description: NeryLab 384_SetB
+ meaning: NIMP:PD-VLLMWZ60
+ SetB-C2:
+ text: SetB-C2
+ description: NeryLab 384_SetB
+ meaning: NIMP:PD-VLLMWZ60
+ SetB-C20:
+ text: SetB-C20
+ description: NeryLab 384_SetB
+ meaning: NIMP:PD-VLLMWZ60
+ SetB-C21:
+ text: SetB-C21
+ description: NeryLab 384_SetB
+ meaning: NIMP:PD-VLLMWZ60
+ SetB-C22:
+ text: SetB-C22
+ description: NeryLab 384_SetB
+ meaning: NIMP:PD-VLLMWZ60
+ SetB-C23:
+ text: SetB-C23
+ description: NeryLab 384_SetB
+ meaning: NIMP:PD-VLLMWZ60
+ SetB-C24:
+ text: SetB-C24
+ description: NeryLab 384_SetB
+ meaning: NIMP:PD-VLLMWZ60
+ SetB-C3:
+ text: SetB-C3
+ description: NeryLab 384_SetB
+ meaning: NIMP:PD-VLLMWZ60
+ SetB-C4:
+ text: SetB-C4
+ description: NeryLab 384_SetB
+ meaning: NIMP:PD-VLLMWZ60
+ SetB-C5:
+ text: SetB-C5
+ description: NeryLab 384_SetB
+ meaning: NIMP:PD-VLLMWZ60
+ SetB-C6:
+ text: SetB-C6
+ description: NeryLab 384_SetB
+ meaning: NIMP:PD-VLLMWZ60
+ SetB-C7:
+ text: SetB-C7
+ description: NeryLab 384_SetB
+ meaning: NIMP:PD-VLLMWZ60
+ SetB-C8:
+ text: SetB-C8
+ description: NeryLab 384_SetB
+ meaning: NIMP:PD-VLLMWZ60
+ SetB-C9:
+ text: SetB-C9
+ description: NeryLab 384_SetB
+ meaning: NIMP:PD-VLLMWZ60
+ SetB-D1:
+ text: SetB-D1
+ description: NeryLab 384_SetB
+ meaning: NIMP:PD-VLLMWZ60
+ SetB-D10:
+ text: SetB-D10
+ description: NeryLab 384_SetB
+ meaning: NIMP:PD-VLLMWZ60
+ SetB-D11:
+ text: SetB-D11
+ description: NeryLab 384_SetB
+ meaning: NIMP:PD-VLLMWZ60
+ SetB-D12:
+ text: SetB-D12
+ description: NeryLab 384_SetB
+ meaning: NIMP:PD-VLLMWZ60
+ SetB-D13:
+ text: SetB-D13
+ description: NeryLab 384_SetB
+ meaning: NIMP:PD-VLLMWZ60
+ SetB-D14:
+ text: SetB-D14
+ description: NeryLab 384_SetB
+ meaning: NIMP:PD-VLLMWZ60
+ SetB-D15:
+ text: SetB-D15
+ description: NeryLab 384_SetB
+ meaning: NIMP:PD-VLLMWZ60
+ SetB-D16:
+ text: SetB-D16
+ description: NeryLab 384_SetB
+ meaning: NIMP:PD-VLLMWZ60
+ SetB-D17:
+ text: SetB-D17
+ description: NeryLab 384_SetB
+ meaning: NIMP:PD-VLLMWZ60
+ SetB-D18:
+ text: SetB-D18
+ description: NeryLab 384_SetB
+ meaning: NIMP:PD-VLLMWZ60
+ SetB-D19:
+ text: SetB-D19
+ description: NeryLab 384_SetB
+ meaning: NIMP:PD-VLLMWZ60
+ SetB-D2:
+ text: SetB-D2
+ description: NeryLab 384_SetB
+ meaning: NIMP:PD-VLLMWZ60
+ SetB-D20:
+ text: SetB-D20
+ description: NeryLab 384_SetB
+ meaning: NIMP:PD-VLLMWZ60
+ SetB-D21:
+ text: SetB-D21
+ description: NeryLab 384_SetB
+ meaning: NIMP:PD-VLLMWZ60
+ SetB-D22:
+ text: SetB-D22
+ description: NeryLab 384_SetB
+ meaning: NIMP:PD-VLLMWZ60
+ SetB-D23:
+ text: SetB-D23
+ description: NeryLab 384_SetB
+ meaning: NIMP:PD-VLLMWZ60
+ SetB-D24:
+ text: SetB-D24
+ description: NeryLab 384_SetB
+ meaning: NIMP:PD-VLLMWZ60
+ SetB-D3:
+ text: SetB-D3
+ description: NeryLab 384_SetB
+ meaning: NIMP:PD-VLLMWZ60
+ SetB-D4:
+ text: SetB-D4
+ description: NeryLab 384_SetB
+ meaning: NIMP:PD-VLLMWZ60
+ SetB-D5:
+ text: SetB-D5
+ description: NeryLab 384_SetB
+ meaning: NIMP:PD-VLLMWZ60
+ SetB-D6:
+ text: SetB-D6
+ description: NeryLab 384_SetB
+ meaning: NIMP:PD-VLLMWZ60
+ SetB-D7:
+ text: SetB-D7
+ description: NeryLab 384_SetB
+ meaning: NIMP:PD-VLLMWZ60
+ SetB-D8:
+ text: SetB-D8
+ description: NeryLab 384_SetB
+ meaning: NIMP:PD-VLLMWZ60
+ SetB-D9:
+ text: SetB-D9
+ description: NeryLab 384_SetB
+ meaning: NIMP:PD-VLLMWZ60
+ SetB-E1:
+ text: SetB-E1
+ description: NeryLab 384_SetB
+ meaning: NIMP:PD-VLLMWZ60
+ SetB-E10:
+ text: SetB-E10
+ description: NeryLab 384_SetB
+ meaning: NIMP:PD-VLLMWZ60
+ SetB-E11:
+ text: SetB-E11
+ description: NeryLab 384_SetB
+ meaning: NIMP:PD-VLLMWZ60
+ SetB-E12:
+ text: SetB-E12
+ description: NeryLab 384_SetB
+ meaning: NIMP:PD-VLLMWZ60
+ SetB-E13:
+ text: SetB-E13
+ description: NeryLab 384_SetB
+ meaning: NIMP:PD-VLLMWZ60
+ SetB-E14:
+ text: SetB-E14
+ description: NeryLab 384_SetB
+ meaning: NIMP:PD-VLLMWZ60
+ SetB-E15:
+ text: SetB-E15
+ description: NeryLab 384_SetB
+ meaning: NIMP:PD-VLLMWZ60
+ SetB-E16:
+ text: SetB-E16
+ description: NeryLab 384_SetB
+ meaning: NIMP:PD-VLLMWZ60
+ SetB-E17:
+ text: SetB-E17
+ description: NeryLab 384_SetB
+ meaning: NIMP:PD-VLLMWZ60
+ SetB-E18:
+ text: SetB-E18
+ description: NeryLab 384_SetB
+ meaning: NIMP:PD-VLLMWZ60
+ SetB-E19:
+ text: SetB-E19
+ description: NeryLab 384_SetB
+ meaning: NIMP:PD-VLLMWZ60
+ SetB-E2:
+ text: SetB-E2
+ description: NeryLab 384_SetB
+ meaning: NIMP:PD-VLLMWZ60
+ SetB-E20:
+ text: SetB-E20
+ description: NeryLab 384_SetB
+ meaning: NIMP:PD-VLLMWZ60
+ SetB-E21:
+ text: SetB-E21
+ description: NeryLab 384_SetB
+ meaning: NIMP:PD-VLLMWZ60
+ SetB-E22:
+ text: SetB-E22
+ description: NeryLab 384_SetB
+ meaning: NIMP:PD-VLLMWZ60
+ SetB-E23:
+ text: SetB-E23
+ description: NeryLab 384_SetB
+ meaning: NIMP:PD-VLLMWZ60
+ SetB-E24:
+ text: SetB-E24
+ description: NeryLab 384_SetB
+ meaning: NIMP:PD-VLLMWZ60
+ SetB-E3:
+ text: SetB-E3
+ description: NeryLab 384_SetB
+ meaning: NIMP:PD-VLLMWZ60
+ SetB-E4:
+ text: SetB-E4
+ description: NeryLab 384_SetB
+ meaning: NIMP:PD-VLLMWZ60
+ SetB-E5:
+ text: SetB-E5
+ description: NeryLab 384_SetB
+ meaning: NIMP:PD-VLLMWZ60
+ SetB-E6:
+ text: SetB-E6
+ description: NeryLab 384_SetB
+ meaning: NIMP:PD-VLLMWZ60
+ SetB-E7:
+ text: SetB-E7
+ description: NeryLab 384_SetB
+ meaning: NIMP:PD-VLLMWZ60
+ SetB-E8:
+ text: SetB-E8
+ description: NeryLab 384_SetB
+ meaning: NIMP:PD-VLLMWZ60
+ SetB-E9:
+ text: SetB-E9
+ description: NeryLab 384_SetB
+ meaning: NIMP:PD-VLLMWZ60
+ SetB-F1:
+ text: SetB-F1
+ description: NeryLab 384_SetB
+ meaning: NIMP:PD-VLLMWZ60
+ SetB-F10:
+ text: SetB-F10
+ description: NeryLab 384_SetB
+ meaning: NIMP:PD-VLLMWZ60
+ SetB-F11:
+ text: SetB-F11
+ description: NeryLab 384_SetB
+ meaning: NIMP:PD-VLLMWZ60
+ SetB-F12:
+ text: SetB-F12
+ description: NeryLab 384_SetB
+ meaning: NIMP:PD-VLLMWZ60
+ SetB-F13:
+ text: SetB-F13
+ description: NeryLab 384_SetB
+ meaning: NIMP:PD-VLLMWZ60
+ SetB-F14:
+ text: SetB-F14
+ description: NeryLab 384_SetB
+ meaning: NIMP:PD-VLLMWZ60
+ SetB-F15:
+ text: SetB-F15
+ description: NeryLab 384_SetB
+ meaning: NIMP:PD-VLLMWZ60
+ SetB-F16:
+ text: SetB-F16
+ description: NeryLab 384_SetB
+ meaning: NIMP:PD-VLLMWZ60
+ SetB-F17:
+ text: SetB-F17
+ description: NeryLab 384_SetB
+ meaning: NIMP:PD-VLLMWZ60
+ SetB-F18:
+ text: SetB-F18
+ description: NeryLab 384_SetB
+ meaning: NIMP:PD-VLLMWZ60
+ SetB-F19:
+ text: SetB-F19
+ description: NeryLab 384_SetB
+ meaning: NIMP:PD-VLLMWZ60
+ SetB-F2:
+ text: SetB-F2
+ description: NeryLab 384_SetB
+ meaning: NIMP:PD-VLLMWZ60
+ SetB-F20:
+ text: SetB-F20
+ description: NeryLab 384_SetB
+ meaning: NIMP:PD-VLLMWZ60
+ SetB-F21:
+ text: SetB-F21
+ description: NeryLab 384_SetB
+ meaning: NIMP:PD-VLLMWZ60
+ SetB-F22:
+ text: SetB-F22
+ description: NeryLab 384_SetB
+ meaning: NIMP:PD-VLLMWZ60
+ SetB-F23:
+ text: SetB-F23
+ description: NeryLab 384_SetB
+ meaning: NIMP:PD-VLLMWZ60
+ SetB-F24:
+ text: SetB-F24
+ description: NeryLab 384_SetB
+ meaning: NIMP:PD-VLLMWZ60
+ SetB-F3:
+ text: SetB-F3
+ description: NeryLab 384_SetB
+ meaning: NIMP:PD-VLLMWZ60
+ SetB-F4:
+ text: SetB-F4
+ description: NeryLab 384_SetB
+ meaning: NIMP:PD-VLLMWZ60
+ SetB-F5:
+ text: SetB-F5
+ description: NeryLab 384_SetB
+ meaning: NIMP:PD-VLLMWZ60
+ SetB-F6:
+ text: SetB-F6
+ description: NeryLab 384_SetB
+ meaning: NIMP:PD-VLLMWZ60
+ SetB-F7:
+ text: SetB-F7
+ description: NeryLab 384_SetB
+ meaning: NIMP:PD-VLLMWZ60
+ SetB-F8:
+ text: SetB-F8
+ description: NeryLab 384_SetB
+ meaning: NIMP:PD-VLLMWZ60
+ SetB-F9:
+ text: SetB-F9
+ description: NeryLab 384_SetB
+ meaning: NIMP:PD-VLLMWZ60
+ SetB-G1:
+ text: SetB-G1
+ description: NeryLab 384_SetB
+ meaning: NIMP:PD-VLLMWZ60
+ SetB-G10:
+ text: SetB-G10
+ description: NeryLab 384_SetB
+ meaning: NIMP:PD-VLLMWZ60
+ SetB-G11:
+ text: SetB-G11
+ description: NeryLab 384_SetB
+ meaning: NIMP:PD-VLLMWZ60
+ SetB-G12:
+ text: SetB-G12
+ description: NeryLab 384_SetB
+ meaning: NIMP:PD-VLLMWZ60
+ SetB-G13:
+ text: SetB-G13
+ description: NeryLab 384_SetB
+ meaning: NIMP:PD-VLLMWZ60
+ SetB-G14:
+ text: SetB-G14
+ description: NeryLab 384_SetB
+ meaning: NIMP:PD-VLLMWZ60
+ SetB-G15:
+ text: SetB-G15
+ description: NeryLab 384_SetB
+ meaning: NIMP:PD-VLLMWZ60
+ SetB-G16:
+ text: SetB-G16
+ description: NeryLab 384_SetB
+ meaning: NIMP:PD-VLLMWZ60
+ SetB-G17:
+ text: SetB-G17
+ description: NeryLab 384_SetB
+ meaning: NIMP:PD-VLLMWZ60
+ SetB-G18:
+ text: SetB-G18
+ description: NeryLab 384_SetB
+ meaning: NIMP:PD-VLLMWZ60
+ SetB-G19:
+ text: SetB-G19
+ description: NeryLab 384_SetB
+ meaning: NIMP:PD-VLLMWZ60
+ SetB-G2:
+ text: SetB-G2
+ description: NeryLab 384_SetB
+ meaning: NIMP:PD-VLLMWZ60
+ SetB-G20:
+ text: SetB-G20
+ description: NeryLab 384_SetB
+ meaning: NIMP:PD-VLLMWZ60
+ SetB-G21:
+ text: SetB-G21
+ description: NeryLab 384_SetB
+ meaning: NIMP:PD-VLLMWZ60
+ SetB-G22:
+ text: SetB-G22
+ description: NeryLab 384_SetB
+ meaning: NIMP:PD-VLLMWZ60
+ SetB-G23:
+ text: SetB-G23
+ description: NeryLab 384_SetB
+ meaning: NIMP:PD-VLLMWZ60
+ SetB-G24:
+ text: SetB-G24
+ description: NeryLab 384_SetB
+ meaning: NIMP:PD-VLLMWZ60
+ SetB-G3:
+ text: SetB-G3
+ description: NeryLab 384_SetB
+ meaning: NIMP:PD-VLLMWZ60
+ SetB-G4:
+ text: SetB-G4
+ description: NeryLab 384_SetB
+ meaning: NIMP:PD-VLLMWZ60
+ SetB-G5:
+ text: SetB-G5
+ description: NeryLab 384_SetB
+ meaning: NIMP:PD-VLLMWZ60
+ SetB-G6:
+ text: SetB-G6
+ description: NeryLab 384_SetB
+ meaning: NIMP:PD-VLLMWZ60
+ SetB-G7:
+ text: SetB-G7
+ description: NeryLab 384_SetB
+ meaning: NIMP:PD-VLLMWZ60
+ SetB-G8:
+ text: SetB-G8
+ description: NeryLab 384_SetB
+ meaning: NIMP:PD-VLLMWZ60
+ SetB-G9:
+ text: SetB-G9
+ description: NeryLab 384_SetB
+ meaning: NIMP:PD-VLLMWZ60
+ SetB-H1:
+ text: SetB-H1
+ description: NeryLab 384_SetB
+ meaning: NIMP:PD-VLLMWZ60
+ SetB-H10:
+ text: SetB-H10
+ description: NeryLab 384_SetB
+ meaning: NIMP:PD-VLLMWZ60
+ SetB-H11:
+ text: SetB-H11
+ description: NeryLab 384_SetB
+ meaning: NIMP:PD-VLLMWZ60
+ SetB-H12:
+ text: SetB-H12
+ description: NeryLab 384_SetB
+ meaning: NIMP:PD-VLLMWZ60
+ SetB-H13:
+ text: SetB-H13
+ description: NeryLab 384_SetB
+ meaning: NIMP:PD-VLLMWZ60
+ SetB-H14:
+ text: SetB-H14
+ description: NeryLab 384_SetB
+ meaning: NIMP:PD-VLLMWZ60
+ SetB-H15:
+ text: SetB-H15
+ description: NeryLab 384_SetB
+ meaning: NIMP:PD-VLLMWZ60
+ SetB-H16:
+ text: SetB-H16
+ description: NeryLab 384_SetB
+ meaning: NIMP:PD-VLLMWZ60
+ SetB-H17:
+ text: SetB-H17
+ description: NeryLab 384_SetB
+ meaning: NIMP:PD-VLLMWZ60
+ SetB-H18:
+ text: SetB-H18
+ description: NeryLab 384_SetB
+ meaning: NIMP:PD-VLLMWZ60
+ SetB-H19:
+ text: SetB-H19
+ description: NeryLab 384_SetB
+ meaning: NIMP:PD-VLLMWZ60
+ SetB-H2:
+ text: SetB-H2
+ description: NeryLab 384_SetB
+ meaning: NIMP:PD-VLLMWZ60
+ SetB-H20:
+ text: SetB-H20
+ description: NeryLab 384_SetB
+ meaning: NIMP:PD-VLLMWZ60
+ SetB-H21:
+ text: SetB-H21
+ description: NeryLab 384_SetB
+ meaning: NIMP:PD-VLLMWZ60
+ SetB-H22:
+ text: SetB-H22
+ description: NeryLab 384_SetB
+ meaning: NIMP:PD-VLLMWZ60
+ SetB-H23:
+ text: SetB-H23
+ description: NeryLab 384_SetB
+ meaning: NIMP:PD-VLLMWZ60
+ SetB-H24:
+ text: SetB-H24
+ description: NeryLab 384_SetB
+ meaning: NIMP:PD-VLLMWZ60
+ SetB-H3:
+ text: SetB-H3
+ description: NeryLab 384_SetB
+ meaning: NIMP:PD-VLLMWZ60
+ SetB-H4:
+ text: SetB-H4
+ description: NeryLab 384_SetB
+ meaning: NIMP:PD-VLLMWZ60
+ SetB-H5:
+ text: SetB-H5
+ description: NeryLab 384_SetB
+ meaning: NIMP:PD-VLLMWZ60
+ SetB-H6:
+ text: SetB-H6
+ description: NeryLab 384_SetB
+ meaning: NIMP:PD-VLLMWZ60
+ SetB-H7:
+ text: SetB-H7
+ description: NeryLab 384_SetB
+ meaning: NIMP:PD-VLLMWZ60
+ SetB-H8:
+ text: SetB-H8
+ description: NeryLab 384_SetB
+ meaning: NIMP:PD-VLLMWZ60
+ SetB-H9:
+ text: SetB-H9
+ description: NeryLab 384_SetB
+ meaning: NIMP:PD-VLLMWZ60
+ SetB-I1:
+ text: SetB-I1
+ description: NeryLab 384_SetB
+ meaning: NIMP:PD-VLLMWZ60
+ SetB-I10:
+ text: SetB-I10
+ description: NeryLab 384_SetB
+ meaning: NIMP:PD-VLLMWZ60
+ SetB-I11:
+ text: SetB-I11
+ description: NeryLab 384_SetB
+ meaning: NIMP:PD-VLLMWZ60
+ SetB-I12:
+ text: SetB-I12
+ description: NeryLab 384_SetB
+ meaning: NIMP:PD-VLLMWZ60
+ SetB-I13:
+ text: SetB-I13
+ description: NeryLab 384_SetB
+ meaning: NIMP:PD-VLLMWZ60
+ SetB-I14:
+ text: SetB-I14
+ description: NeryLab 384_SetB
+ meaning: NIMP:PD-VLLMWZ60
+ SetB-I15:
+ text: SetB-I15
+ description: NeryLab 384_SetB
+ meaning: NIMP:PD-VLLMWZ60
+ SetB-I16:
+ text: SetB-I16
+ description: NeryLab 384_SetB
+ meaning: NIMP:PD-VLLMWZ60
+ SetB-I17:
+ text: SetB-I17
+ description: NeryLab 384_SetB
+ meaning: NIMP:PD-VLLMWZ60
+ SetB-I18:
+ text: SetB-I18
+ description: NeryLab 384_SetB
+ meaning: NIMP:PD-VLLMWZ60
+ SetB-I19:
+ text: SetB-I19
+ description: NeryLab 384_SetB
+ meaning: NIMP:PD-VLLMWZ60
+ SetB-I2:
+ text: SetB-I2
+ description: NeryLab 384_SetB
+ meaning: NIMP:PD-VLLMWZ60
+ SetB-I20:
+ text: SetB-I20
+ description: NeryLab 384_SetB
+ meaning: NIMP:PD-VLLMWZ60
+ SetB-I21:
+ text: SetB-I21
+ description: NeryLab 384_SetB
+ meaning: NIMP:PD-VLLMWZ60
+ SetB-I22:
+ text: SetB-I22
+ description: NeryLab 384_SetB
+ meaning: NIMP:PD-VLLMWZ60
+ SetB-I23:
+ text: SetB-I23
+ description: NeryLab 384_SetB
+ meaning: NIMP:PD-VLLMWZ60
+ SetB-I24:
+ text: SetB-I24
+ description: NeryLab 384_SetB
+ meaning: NIMP:PD-VLLMWZ60
+ SetB-I3:
+ text: SetB-I3
+ description: NeryLab 384_SetB
+ meaning: NIMP:PD-VLLMWZ60
+ SetB-I4:
+ text: SetB-I4
+ description: NeryLab 384_SetB
+ meaning: NIMP:PD-VLLMWZ60
+ SetB-I5:
+ text: SetB-I5
+ description: NeryLab 384_SetB
+ meaning: NIMP:PD-VLLMWZ60
+ SetB-I6:
+ text: SetB-I6
+ description: NeryLab 384_SetB
+ meaning: NIMP:PD-VLLMWZ60
+ SetB-I7:
+ text: SetB-I7
+ description: NeryLab 384_SetB
+ meaning: NIMP:PD-VLLMWZ60
+ SetB-I8:
+ text: SetB-I8
+ description: NeryLab 384_SetB/#
+ meaning: NIMP:PD-VLLMWZ60
+
+URI: LibraryTechnique
+| Value | +Meaning | +Description | +
|---|---|---|
| SMARTSeqSC | +NIMP:PD-AJAJCN35 | +SMARTSeqSC | +
| SmartSeq3 | +NIMP:PD-AJAJCN35 | +SmartSeq3 | +
| 10xV3.1 | +NIMP:PD-AJAJCN35 | +10xV3 | +
| 10xV3.1_HT | +NIMP:PD-AJAJCN35 | +10xV3 | +
| 10xMultiome;GEX | +NIMP:PD-AJAJCN35 | +10xMultiome;GEX | +
| 10xMultiome;ATAC | +NIMP:PD-AJAJCN35 | +10xMultiome;ATAC | +
| 10xATAC_V2.0 | +NIMP:PD-AJAJCN35 | +10xATAC_V2 | +
| 10XMultiome-CellHashing;GEX | +NIMP:PD-AJAJCN35 | +10XMultiome-CellHashing;GEX | +
| 10XMultiome-CellHashing;ATAC | +NIMP:PD-AJAJCN35 | +10XMultiome-CellHashing;ATAC | +
| 10XMultiome-Cell Hashing;Barcode | +NIMP:PD-AJAJCN35 | +10XMultiome-Cell Hashing;Barcode | +
| 10xV3.1_CellPlex;GEX | +NIMP:PD-AJAJCN35 | +10xV3 | +
| 10xV3.1_CellPlex;Barcode | +NIMP:PD-AJAJCN35 | +10xV3 | +
| 10xV3.1_HT_CellPlex;GEX | +NIMP:PD-AJAJCN35 | +10xV3 | +
| 10xV3.1_HT_CellPlex;Barcode | +NIMP:PD-AJAJCN35 | +10xV3 | +
| MethylC-Seq | +NIMP:PD-AJAJCN35 | +MethylC-Seq | +
| snm3C-seq | +NIMP:PD-AJAJCN35 | +snm3C-seq | +
| snmCT-seq | +NIMP:PD-AJAJCN35 | +snmCT-seq | +
| scATAC-seq | +NIMP:PD-AJAJCN35 | +scATAC-seq | +
| MERFISH | +NIMP:PD-AJAJCN35 | +MERFISH | +
| Slide-seq MERFISH | +NIMP:PD-AJAJCN35 | +Slide-seq MERFISH | +
| whole brain MERFISH | +NIMP:PD-AJAJCN35 | +whole brain MERFISH | +
| DBiT RNA-seq | +NIMP:PD-AJAJCN35 | +DBiT RNA-seq | +
| DBiT ATAC-seq | +NIMP:PD-AJAJCN35 | +DBiT ATAC-seq | +
name: library_technique
+from_schema: https://identifiers.org/brain-bican/library-generation-schema
+rank: 1000
+permissible_values:
+ SMARTSeqSC:
+ text: SMARTSeqSC
+ description: SMARTSeqSC
+ meaning: NIMP:PD-AJAJCN35
+ SmartSeq3:
+ text: SmartSeq3
+ description: SmartSeq3
+ meaning: NIMP:PD-AJAJCN35
+ 10xV3.1:
+ text: 10xV3.1
+ description: 10xV3.1
+ meaning: NIMP:PD-AJAJCN35
+ 10xV3.1_HT:
+ text: 10xV3.1_HT
+ description: 10xV3.1_HT
+ meaning: NIMP:PD-AJAJCN35
+ 10xMultiome;GEX:
+ text: 10xMultiome;GEX
+ description: 10xMultiome;GEX
+ meaning: NIMP:PD-AJAJCN35
+ 10xMultiome;ATAC:
+ text: 10xMultiome;ATAC
+ description: 10xMultiome;ATAC
+ meaning: NIMP:PD-AJAJCN35
+ 10xATAC_V2.0:
+ text: 10xATAC_V2.0
+ description: 10xATAC_V2.0
+ meaning: NIMP:PD-AJAJCN35
+ 10XMultiome-CellHashing;GEX:
+ text: 10XMultiome-CellHashing;GEX
+ description: 10XMultiome-CellHashing;GEX
+ meaning: NIMP:PD-AJAJCN35
+ 10XMultiome-CellHashing;ATAC:
+ text: 10XMultiome-CellHashing;ATAC
+ description: 10XMultiome-CellHashing;ATAC
+ meaning: NIMP:PD-AJAJCN35
+ 10XMultiome-Cell Hashing;Barcode:
+ text: 10XMultiome-Cell Hashing;Barcode
+ description: 10XMultiome-Cell Hashing;Barcode
+ meaning: NIMP:PD-AJAJCN35
+ 10xV3.1_CellPlex;GEX:
+ text: 10xV3.1_CellPlex;GEX
+ description: 10xV3.1_CellPlex;GEX
+ meaning: NIMP:PD-AJAJCN35
+ 10xV3.1_CellPlex;Barcode:
+ text: 10xV3.1_CellPlex;Barcode
+ description: 10xV3.1_CellPlex;Barcode
+ meaning: NIMP:PD-AJAJCN35
+ 10xV3.1_HT_CellPlex;GEX:
+ text: 10xV3.1_HT_CellPlex;GEX
+ description: 10xV3.1_HT_CellPlex;GEX
+ meaning: NIMP:PD-AJAJCN35
+ 10xV3.1_HT_CellPlex;Barcode:
+ text: 10xV3.1_HT_CellPlex;Barcode
+ description: 10xV3.1_HT_CellPlex;Barcode
+ meaning: NIMP:PD-AJAJCN35
+ MethylC-Seq:
+ text: MethylC-Seq
+ description: MethylC-Seq
+ meaning: NIMP:PD-AJAJCN35
+ snm3C-seq:
+ text: snm3C-seq
+ description: snm3C-seq
+ meaning: NIMP:PD-AJAJCN35
+ snmCT-seq:
+ text: snmCT-seq
+ description: snmCT-seq
+ meaning: NIMP:PD-AJAJCN35
+ scATAC-seq:
+ text: scATAC-seq
+ description: scATAC-seq
+ meaning: NIMP:PD-AJAJCN35
+ MERFISH:
+ text: MERFISH
+ description: MERFISH
+ meaning: NIMP:PD-AJAJCN35
+ Slide-seq MERFISH:
+ text: Slide-seq MERFISH
+ description: Slide-seq MERFISH
+ meaning: NIMP:PD-AJAJCN35
+ whole brain MERFISH:
+ text: whole brain MERFISH
+ description: whole brain MERFISH
+ meaning: NIMP:PD-AJAJCN35
+ DBiT RNA-seq:
+ text: DBiT RNA-seq
+ description: DBiT RNA-seq
+ meaning: NIMP:PD-AJAJCN35
+ DBiT ATAC-seq:
+ text: DBiT ATAC-seq
+ description: DBiT ATAC-seq
+ meaning: NIMP:PD-AJAJCN35
+
+A union of gene locus, gene product, and macromolecular complex. These are the basic units of function in a cell. They either carry out individual biological activities, or they encode molecules which do this.
+URI: biolink:MacromolecularMachineMixin
+| Name | +Cardinality and Range | +Description | +Inheritance | +
|---|---|---|---|
| name | +0..1 LabelType |
+A human-readable name for an attribute or entity | +direct | +
| mixed into | +description | +
|---|---|
| + | + |
| Mapping Type | +Mapped Value | +
|---|---|
| self | +biolink:MacromolecularMachineMixin | +
| native | +bican:MacromolecularMachineMixin | +
name: macromolecular machine mixin
+definition_uri: https://w3id.org/biolink/vocab/MacromolecularMachineMixin
+description: A union of gene locus, gene product, and macromolecular complex. These
+ are the basic units of function in a cell. They either carry out individual biological
+ activities, or they encode molecules which do this.
+from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
+mixin: true
+slots:
+- name
+class_uri: biolink:MacromolecularMachineMixin
+
+name: macromolecular machine mixin
+definition_uri: https://w3id.org/biolink/vocab/MacromolecularMachineMixin
+description: A union of gene locus, gene product, and macromolecular complex. These
+ are the basic units of function in a cell. They either carry out individual biological
+ activities, or they encode molecules which do this.
+from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
+mixin: true
+attributes:
+ name:
+ name: name
+ definition_uri: https://w3id.org/biolink/vocab/name
+ description: A human-readable name for an attribute or entity.
+ in_subset:
+ - translator_minimal
+ - samples
+ from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
+ aliases:
+ - label
+ - display name
+ - title
+ mappings:
+ - rdfs:label
+ exact_mappings:
+ - gff3:Name
+ - gpi:DB_Object_Name
+ narrow_mappings:
+ - dct:title
+ - WIKIDATA_PROPERTY:P1476
+ rank: 1000
+ domain: entity
+ slot_uri: rdfs:label
+ alias: name
+ owner: macromolecular machine mixin
+ domain_of:
+ - attribute
+ - entity
+ - macromolecular machine mixin
+ - named thing
+ - organism taxon
+ - information content entity
+ - dataset
+ - physical entity
+ - activity
+ - procedure
+ - material sample
+ - biological entity
+ - gene or gene product
+ - gene
+ - genome
+ range: label type
+class_uri: biolink:MacromolecularMachineMixin
+
+A sample is a limited quantity of something (e.g. an individual or set of individuals from a population, or a portion of a substance) to be used for testing, analysis, inspection, investigation, demonstration, or trial use. [SIO]
+ +| Name | +Cardinality and Range | +Description | +Inheritance | +
|---|---|---|---|
| id | +1 String |
+A unique identifier for an entity | +direct | +
| iri | +0..1 IriType |
+An IRI for an entity | +direct | +
| category | +* Uriorcurie |
+Name of the high level ontology class in which this entity is categorized | +direct | +
| type | +* String |
++ | direct | +
| name | +0..1 LabelType |
+A human-readable name for an attribute or entity | +direct | +
| description | +0..1 NarrativeText |
+a human-readable description of an entity | +direct | +
| has_attribute | +* Attribute |
+connects any entity to an attribute | +direct | +
| deprecated | +0..1 Boolean |
+A boolean flag indicating that an entity is no longer considered current or v... | +direct | +
| provided_by | +* String |
+The value in this node property represents the knowledge provider that create... | +direct | +
| xref | +* Uriorcurie |
+A database cross reference or alternative identifier for a NamedThing or edge... | +direct | +
| full_name | +0..1 LabelType |
+a long-form human readable name for a thing | +direct | +
| synonym | +* LabelType |
+Alternate human-readable names for a thing | +direct | +
Instances of this class should have identifiers with one of the following prefixes:
+BIOSAMPLE
+GOLD.META
+| Mapping Type | +Mapped Value | +
|---|---|
| self | +biolink:MaterialSample | +
| native | +bican:MaterialSample | +
| exact | +OBI:0000747, SIO:001050 | +
name: material sample
+id_prefixes:
+- BIOSAMPLE
+- GOLD.META
+definition_uri: https://w3id.org/biolink/vocab/MaterialSample
+description: A sample is a limited quantity of something (e.g. an individual or set
+ of individuals from a population, or a portion of a substance) to be used for testing,
+ analysis, inspection, investigation, demonstration, or trial use. [SIO]
+from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
+aliases:
+- biospecimen
+- sample
+- biosample
+- physical sample
+exact_mappings:
+- OBI:0000747
+- SIO:001050
+is_a: physical entity
+mixins:
+- subject of investigation
+slots:
+- id
+- iri
+- category
+- type
+- name
+- description
+- has attribute
+- deprecated
+- provided by
+- xref
+- full name
+- synonym
+class_uri: biolink:MaterialSample
+
+name: material sample
+id_prefixes:
+- BIOSAMPLE
+- GOLD.META
+definition_uri: https://w3id.org/biolink/vocab/MaterialSample
+description: A sample is a limited quantity of something (e.g. an individual or set
+ of individuals from a population, or a portion of a substance) to be used for testing,
+ analysis, inspection, investigation, demonstration, or trial use. [SIO]
+from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
+aliases:
+- biospecimen
+- sample
+- biosample
+- physical sample
+exact_mappings:
+- OBI:0000747
+- SIO:001050
+is_a: physical entity
+mixins:
+- subject of investigation
+attributes:
+ id:
+ name: id
+ definition_uri: https://w3id.org/biolink/vocab/id
+ description: A unique identifier for an entity. Must be either a CURIE shorthand
+ for a URI or a complete URI
+ in_subset:
+ - translator_minimal
+ from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
+ exact_mappings:
+ - AGRKB:primaryId
+ - gff3:ID
+ - gpi:DB_Object_ID
+ rank: 1000
+ domain: entity
+ slot_uri: biolink:id
+ identifier: true
+ alias: id
+ owner: material sample
+ domain_of:
+ - ontology class
+ - entity
+ - attribute
+ - named thing
+ - taxonomic rank
+ - organism taxon
+ - information content entity
+ - dataset
+ - physical entity
+ - activity
+ - procedure
+ - material sample
+ - biological entity
+ - gene
+ - genome
+ range: string
+ required: true
+ iri:
+ name: iri
+ definition_uri: https://w3id.org/biolink/vocab/iri
+ description: An IRI for an entity. This is determined by the id using expansion
+ rules.
+ in_subset:
+ - translator_minimal
+ - samples
+ from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
+ exact_mappings:
+ - WIKIDATA_PROPERTY:P854
+ rank: 1000
+ slot_uri: biolink:iri
+ alias: iri
+ owner: material sample
+ domain_of:
+ - attribute
+ - entity
+ - named thing
+ - organism taxon
+ - information content entity
+ - dataset
+ - physical entity
+ - activity
+ - procedure
+ - material sample
+ - biological entity
+ - gene
+ - genome
+ range: iri type
+ category:
+ name: category
+ definition_uri: https://w3id.org/biolink/vocab/category
+ description: Name of the high level ontology class in which this entity is categorized.
+ Corresponds to the label for the biolink entity type class. In a neo4j database
+ this MAY correspond to the neo4j label tag. In an RDF database it should be
+ a biolink model class URI. This field is multi-valued. It should include values
+ for ancestors of the biolink class; for example, a protein such as Shh would
+ have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`.
+ In an RDF database, nodes will typically have an rdf:type triples. This can
+ be to the most specific biolink class, or potentially to a class more specific
+ than something in biolink. For example, a sequence feature `f` may have a rdf:type
+ assertion to a SO class such as TF_binding_site, which is more specific than
+ anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity,
+ biolink:NamedThing}
+ in_subset:
+ - translator_minimal
+ from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
+ rank: 1000
+ is_a: type
+ domain: entity
+ slot_uri: biolink:category
+ designates_type: true
+ alias: category
+ owner: material sample
+ domain_of:
+ - entity
+ - attribute
+ - named thing
+ - organism taxon
+ - information content entity
+ - dataset
+ - physical entity
+ - activity
+ - procedure
+ - material sample
+ - biological entity
+ - gene
+ - genome
+ is_class_field: true
+ range: uriorcurie
+ multivalued: true
+ type:
+ name: type
+ definition_uri: https://w3id.org/biolink/vocab/type
+ from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
+ mappings:
+ - rdf:type
+ exact_mappings:
+ - gff3:type
+ - gpi:DB_Object_Type
+ rank: 1000
+ domain: entity
+ slot_uri: rdf:type
+ alias: type
+ owner: material sample
+ domain_of:
+ - entity
+ - attribute
+ - named thing
+ - organism taxon
+ - information content entity
+ - dataset
+ - physical entity
+ - activity
+ - procedure
+ - material sample
+ - biological entity
+ - gene
+ - genome
+ range: string
+ multivalued: true
+ name:
+ name: name
+ definition_uri: https://w3id.org/biolink/vocab/name
+ description: A human-readable name for an attribute or entity.
+ in_subset:
+ - translator_minimal
+ - samples
+ from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
+ aliases:
+ - label
+ - display name
+ - title
+ mappings:
+ - rdfs:label
+ exact_mappings:
+ - gff3:Name
+ - gpi:DB_Object_Name
+ narrow_mappings:
+ - dct:title
+ - WIKIDATA_PROPERTY:P1476
+ rank: 1000
+ domain: entity
+ slot_uri: rdfs:label
+ alias: name
+ owner: material sample
+ domain_of:
+ - attribute
+ - entity
+ - macromolecular machine mixin
+ - named thing
+ - organism taxon
+ - information content entity
+ - dataset
+ - physical entity
+ - activity
+ - procedure
+ - material sample
+ - biological entity
+ - gene or gene product
+ - gene
+ - genome
+ range: label type
+ description:
+ name: description
+ definition_uri: https://w3id.org/biolink/vocab/description
+ description: a human-readable description of an entity
+ in_subset:
+ - translator_minimal
+ from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
+ aliases:
+ - definition
+ mappings:
+ - dct:description
+ exact_mappings:
+ - IAO:0000115
+ - skos:definitions
+ narrow_mappings:
+ - gff3:Description
+ rank: 1000
+ slot_uri: dct:description
+ alias: description
+ owner: material sample
+ domain_of:
+ - entity
+ - attribute
+ - named thing
+ - organism taxon
+ - information content entity
+ - dataset
+ - physical entity
+ - activity
+ - procedure
+ - material sample
+ - biological entity
+ - gene
+ - genome
+ range: narrative text
+ has attribute:
+ name: has attribute
+ definition_uri: https://w3id.org/biolink/vocab/has_attribute
+ description: connects any entity to an attribute
+ in_subset:
+ - samples
+ from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
+ exact_mappings:
+ - SIO:000008
+ close_mappings:
+ - OBI:0001927
+ narrow_mappings:
+ - OBAN:association_has_subject_property
+ - OBAN:association_has_object_property
+ - CPT:has_possibly_included_panel_element
+ - DRUGBANK:category
+ - EFO:is_executed_in
+ - HANCESTRO:0301
+ - LOINC:has_action_guidance
+ - LOINC:has_adjustment
+ - LOINC:has_aggregation_view
+ - LOINC:has_approach_guidance
+ - LOINC:has_divisor
+ - LOINC:has_exam
+ - LOINC:has_method
+ - LOINC:has_modality_subtype
+ - LOINC:has_object_guidance
+ - LOINC:has_scale
+ - LOINC:has_suffix
+ - LOINC:has_time_aspect
+ - LOINC:has_time_modifier
+ - LOINC:has_timing_of
+ - NCIT:R88
+ - NCIT:eo_disease_has_property_or_attribute
+ - NCIT:has_data_element
+ - NCIT:has_pharmaceutical_administration_method
+ - NCIT:has_pharmaceutical_basic_dose_form
+ - NCIT:has_pharmaceutical_intended_site
+ - NCIT:has_pharmaceutical_release_characteristics
+ - NCIT:has_pharmaceutical_state_of_matter
+ - NCIT:has_pharmaceutical_transformation
+ - NCIT:is_qualified_by
+ - NCIT:qualifier_applies_to
+ - NCIT:role_has_domain
+ - NCIT:role_has_range
+ - INO:0000154
+ - HANCESTRO:0308
+ - OMIM:has_inheritance_type
+ - orphanet:C016
+ - orphanet:C017
+ - RO:0000053
+ - RO:0000086
+ - RO:0000087
+ - SNOMED:has_access
+ - SNOMED:has_clinical_course
+ - SNOMED:has_count_of_base_of_active_ingredient
+ - SNOMED:has_dose_form_administration_method
+ - SNOMED:has_dose_form_release_characteristic
+ - SNOMED:has_dose_form_transformation
+ - SNOMED:has_finding_context
+ - SNOMED:has_finding_informer
+ - SNOMED:has_inherent_attribute
+ - SNOMED:has_intent
+ - SNOMED:has_interpretation
+ - SNOMED:has_laterality
+ - SNOMED:has_measurement_method
+ - SNOMED:has_method
+ - SNOMED:has_priority
+ - SNOMED:has_procedure_context
+ - SNOMED:has_process_duration
+ - SNOMED:has_property
+ - SNOMED:has_revision_status
+ - SNOMED:has_scale_type
+ - SNOMED:has_severity
+ - SNOMED:has_specimen
+ - SNOMED:has_state_of_matter
+ - SNOMED:has_subject_relationship_context
+ - SNOMED:has_surgical_approach
+ - SNOMED:has_technique
+ - SNOMED:has_temporal_context
+ - SNOMED:has_time_aspect
+ - SNOMED:has_units
+ - UMLS:has_structural_class
+ - UMLS:has_supported_concept_property
+ - UMLS:has_supported_concept_relationship
+ - UMLS:may_be_qualified_by
+ rank: 1000
+ domain: entity
+ slot_uri: biolink:has_attribute
+ alias: has_attribute
+ owner: material sample
+ domain_of:
+ - entity
+ - attribute
+ - named thing
+ - organism taxon
+ - information content entity
+ - dataset
+ - physical entity
+ - activity
+ - procedure
+ - material sample
+ - biological entity
+ - gene
+ - genome
+ range: attribute
+ multivalued: true
+ deprecated:
+ name: deprecated
+ definition_uri: https://w3id.org/biolink/vocab/deprecated
+ description: A boolean flag indicating that an entity is no longer considered
+ current or valid.
+ from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
+ exact_mappings:
+ - oboInOwl:ObsoleteClass
+ rank: 1000
+ slot_uri: biolink:deprecated
+ alias: deprecated
+ owner: material sample
+ domain_of:
+ - entity
+ - attribute
+ - named thing
+ - organism taxon
+ - information content entity
+ - dataset
+ - physical entity
+ - activity
+ - procedure
+ - material sample
+ - biological entity
+ - gene
+ - genome
+ range: boolean
+ provided by:
+ name: provided by
+ definition_uri: https://w3id.org/biolink/vocab/provided_by
+ description: The value in this node property represents the knowledge provider
+ that created or assembled the node and all of its attributes. Used internally
+ to represent how a particular node made its way into a knowledge provider or
+ graph.
+ from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
+ rank: 1000
+ is_a: node property
+ domain: named thing
+ slot_uri: biolink:provided_by
+ alias: provided_by
+ owner: material sample
+ domain_of:
+ - named thing
+ - attribute
+ - organism taxon
+ - information content entity
+ - dataset
+ - physical entity
+ - activity
+ - procedure
+ - material sample
+ - biological entity
+ - gene
+ - genome
+ range: string
+ multivalued: true
+ xref:
+ name: xref
+ definition_uri: https://w3id.org/biolink/vocab/xref
+ description: A database cross reference or alternative identifier for a NamedThing
+ or edge between two NamedThings. This property should point to a database record
+ or webpage that supports the existence of the edge, or gives more detail about
+ the edge. This property can be used on a node or edge to provide multiple URIs
+ or CURIE cross references.
+ in_subset:
+ - translator_minimal
+ from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
+ aliases:
+ - dbxref
+ - Dbxref
+ - DbXref
+ - record_url
+ - source_record_urls
+ narrow_mappings:
+ - gff3:Dbxref
+ - gpi:DB_Xrefs
+ rank: 1000
+ domain: named thing
+ slot_uri: biolink:xref
+ alias: xref
+ owner: material sample
+ domain_of:
+ - named thing
+ - gene
+ - attribute
+ - organism taxon
+ - information content entity
+ - dataset
+ - physical entity
+ - activity
+ - procedure
+ - material sample
+ - biological entity
+ - genome
+ range: uriorcurie
+ multivalued: true
+ full name:
+ name: full name
+ definition_uri: https://w3id.org/biolink/vocab/full_name
+ description: a long-form human readable name for a thing
+ from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
+ rank: 1000
+ is_a: node property
+ domain: named thing
+ slot_uri: biolink:full_name
+ alias: full_name
+ owner: material sample
+ domain_of:
+ - named thing
+ - attribute
+ - organism taxon
+ - information content entity
+ - dataset
+ - physical entity
+ - activity
+ - procedure
+ - material sample
+ - biological entity
+ - gene
+ - genome
+ range: label type
+ synonym:
+ name: synonym
+ definition_uri: https://w3id.org/biolink/vocab/synonym
+ description: Alternate human-readable names for a thing
+ in_subset:
+ - translator_minimal
+ from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
+ aliases:
+ - alias
+ narrow_mappings:
+ - skos:altLabel
+ - gff3:Alias
+ - AGRKB:synonyms
+ - gpi:DB_Object_Synonyms
+ - HANCESTRO:0330
+ - IAO:0000136
+ - RXNORM:has_tradename
+ rank: 1000
+ is_a: node property
+ domain: named thing
+ slot_uri: biolink:synonym
+ alias: synonym
+ owner: material sample
+ domain_of:
+ - named thing
+ - attribute
+ - organism taxon
+ - information content entity
+ - dataset
+ - physical entity
+ - activity
+ - procedure
+ - material sample
+ - biological entity
+ - gene
+ - genome
+ range: label type
+ multivalued: true
+class_uri: biolink:MaterialSample
+
+Subset that is relevant for a typical Model Organism Database (MOD)
+ +| Class | +Description | +
|---|---|
| Gene | +A region (or regions) that includes all of the sequence elements necessary to... | +
| Genome | +A genome is the sum of genetic material within a cell or virion | +
| OrganismTaxon | +A classification of a set of organisms | +
a databased entity or concept/class
+URI: biolink:NamedThing
+| Name | +Cardinality and Range | +Description | +Inheritance | +
|---|---|---|---|
| id | +1 String |
+A unique identifier for an entity | +direct | +
| iri | +0..1 IriType |
+An IRI for an entity | +direct | +
| category | +* Uriorcurie |
+Name of the high level ontology class in which this entity is categorized | +direct | +
| type | +* String |
++ | direct | +
| name | +0..1 LabelType |
+A human-readable name for an attribute or entity | +direct | +
| description | +0..1 NarrativeText |
+a human-readable description of an entity | +direct | +
| has_attribute | +* Attribute |
+connects any entity to an attribute | +direct | +
| deprecated | +0..1 Boolean |
+A boolean flag indicating that an entity is no longer considered current or v... | +direct | +
| provided_by | +* String |
+The value in this node property represents the knowledge provider that create... | +direct | +
| xref | +* Uriorcurie |
+A database cross reference or alternative identifier for a NamedThing or edge... | +direct | +
| full_name | +0..1 LabelType |
+a long-form human readable name for a thing | +direct | +
| synonym | +* LabelType |
+Alternate human-readable names for a thing | +direct | +
| Mapping Type | +Mapped Value | +
|---|---|
| self | +biolink:NamedThing | +
| native | +bican:NamedThing | +
| exact | +BFO:0000001, WIKIDATA:Q35120, UMLSSG:OBJC, STY:T071, dcid:Thing | +
name: named thing
+definition_uri: https://w3id.org/biolink/vocab/NamedThing
+description: a databased entity or concept/class
+from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
+exact_mappings:
+- BFO:0000001
+- WIKIDATA:Q35120
+- UMLSSG:OBJC
+- STY:T071
+- dcid:Thing
+is_a: entity
+slots:
+- id
+- iri
+- category
+- type
+- name
+- description
+- has attribute
+- deprecated
+- provided by
+- xref
+- full name
+- synonym
+class_uri: biolink:NamedThing
+
+name: named thing
+definition_uri: https://w3id.org/biolink/vocab/NamedThing
+description: a databased entity or concept/class
+from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
+exact_mappings:
+- BFO:0000001
+- WIKIDATA:Q35120
+- UMLSSG:OBJC
+- STY:T071
+- dcid:Thing
+is_a: entity
+attributes:
+ id:
+ name: id
+ definition_uri: https://w3id.org/biolink/vocab/id
+ description: A unique identifier for an entity. Must be either a CURIE shorthand
+ for a URI or a complete URI
+ in_subset:
+ - translator_minimal
+ from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
+ exact_mappings:
+ - AGRKB:primaryId
+ - gff3:ID
+ - gpi:DB_Object_ID
+ rank: 1000
+ domain: entity
+ slot_uri: biolink:id
+ identifier: true
+ alias: id
+ owner: named thing
+ domain_of:
+ - ontology class
+ - entity
+ - attribute
+ - named thing
+ - taxonomic rank
+ - organism taxon
+ - information content entity
+ - dataset
+ - physical entity
+ - activity
+ - procedure
+ - material sample
+ - biological entity
+ - gene
+ - genome
+ range: string
+ required: true
+ iri:
+ name: iri
+ definition_uri: https://w3id.org/biolink/vocab/iri
+ description: An IRI for an entity. This is determined by the id using expansion
+ rules.
+ in_subset:
+ - translator_minimal
+ - samples
+ from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
+ exact_mappings:
+ - WIKIDATA_PROPERTY:P854
+ rank: 1000
+ slot_uri: biolink:iri
+ alias: iri
+ owner: named thing
+ domain_of:
+ - attribute
+ - entity
+ - named thing
+ - organism taxon
+ - information content entity
+ - dataset
+ - physical entity
+ - activity
+ - procedure
+ - material sample
+ - biological entity
+ - gene
+ - genome
+ range: iri type
+ category:
+ name: category
+ definition_uri: https://w3id.org/biolink/vocab/category
+ description: Name of the high level ontology class in which this entity is categorized.
+ Corresponds to the label for the biolink entity type class. In a neo4j database
+ this MAY correspond to the neo4j label tag. In an RDF database it should be
+ a biolink model class URI. This field is multi-valued. It should include values
+ for ancestors of the biolink class; for example, a protein such as Shh would
+ have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`.
+ In an RDF database, nodes will typically have an rdf:type triples. This can
+ be to the most specific biolink class, or potentially to a class more specific
+ than something in biolink. For example, a sequence feature `f` may have a rdf:type
+ assertion to a SO class such as TF_binding_site, which is more specific than
+ anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity,
+ biolink:NamedThing}
+ in_subset:
+ - translator_minimal
+ from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
+ rank: 1000
+ is_a: type
+ domain: entity
+ slot_uri: biolink:category
+ designates_type: true
+ alias: category
+ owner: named thing
+ domain_of:
+ - entity
+ - attribute
+ - named thing
+ - organism taxon
+ - information content entity
+ - dataset
+ - physical entity
+ - activity
+ - procedure
+ - material sample
+ - biological entity
+ - gene
+ - genome
+ is_class_field: true
+ range: uriorcurie
+ multivalued: true
+ type:
+ name: type
+ definition_uri: https://w3id.org/biolink/vocab/type
+ from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
+ mappings:
+ - rdf:type
+ exact_mappings:
+ - gff3:type
+ - gpi:DB_Object_Type
+ rank: 1000
+ domain: entity
+ slot_uri: rdf:type
+ alias: type
+ owner: named thing
+ domain_of:
+ - entity
+ - attribute
+ - named thing
+ - organism taxon
+ - information content entity
+ - dataset
+ - physical entity
+ - activity
+ - procedure
+ - material sample
+ - biological entity
+ - gene
+ - genome
+ range: string
+ multivalued: true
+ name:
+ name: name
+ definition_uri: https://w3id.org/biolink/vocab/name
+ description: A human-readable name for an attribute or entity.
+ in_subset:
+ - translator_minimal
+ - samples
+ from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
+ aliases:
+ - label
+ - display name
+ - title
+ mappings:
+ - rdfs:label
+ exact_mappings:
+ - gff3:Name
+ - gpi:DB_Object_Name
+ narrow_mappings:
+ - dct:title
+ - WIKIDATA_PROPERTY:P1476
+ rank: 1000
+ domain: entity
+ slot_uri: rdfs:label
+ alias: name
+ owner: named thing
+ domain_of:
+ - attribute
+ - entity
+ - macromolecular machine mixin
+ - named thing
+ - organism taxon
+ - information content entity
+ - dataset
+ - physical entity
+ - activity
+ - procedure
+ - material sample
+ - biological entity
+ - gene or gene product
+ - gene
+ - genome
+ range: label type
+ description:
+ name: description
+ definition_uri: https://w3id.org/biolink/vocab/description
+ description: a human-readable description of an entity
+ in_subset:
+ - translator_minimal
+ from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
+ aliases:
+ - definition
+ mappings:
+ - dct:description
+ exact_mappings:
+ - IAO:0000115
+ - skos:definitions
+ narrow_mappings:
+ - gff3:Description
+ rank: 1000
+ slot_uri: dct:description
+ alias: description
+ owner: named thing
+ domain_of:
+ - entity
+ - attribute
+ - named thing
+ - organism taxon
+ - information content entity
+ - dataset
+ - physical entity
+ - activity
+ - procedure
+ - material sample
+ - biological entity
+ - gene
+ - genome
+ range: narrative text
+ has attribute:
+ name: has attribute
+ definition_uri: https://w3id.org/biolink/vocab/has_attribute
+ description: connects any entity to an attribute
+ in_subset:
+ - samples
+ from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
+ exact_mappings:
+ - SIO:000008
+ close_mappings:
+ - OBI:0001927
+ narrow_mappings:
+ - OBAN:association_has_subject_property
+ - OBAN:association_has_object_property
+ - CPT:has_possibly_included_panel_element
+ - DRUGBANK:category
+ - EFO:is_executed_in
+ - HANCESTRO:0301
+ - LOINC:has_action_guidance
+ - LOINC:has_adjustment
+ - LOINC:has_aggregation_view
+ - LOINC:has_approach_guidance
+ - LOINC:has_divisor
+ - LOINC:has_exam
+ - LOINC:has_method
+ - LOINC:has_modality_subtype
+ - LOINC:has_object_guidance
+ - LOINC:has_scale
+ - LOINC:has_suffix
+ - LOINC:has_time_aspect
+ - LOINC:has_time_modifier
+ - LOINC:has_timing_of
+ - NCIT:R88
+ - NCIT:eo_disease_has_property_or_attribute
+ - NCIT:has_data_element
+ - NCIT:has_pharmaceutical_administration_method
+ - NCIT:has_pharmaceutical_basic_dose_form
+ - NCIT:has_pharmaceutical_intended_site
+ - NCIT:has_pharmaceutical_release_characteristics
+ - NCIT:has_pharmaceutical_state_of_matter
+ - NCIT:has_pharmaceutical_transformation
+ - NCIT:is_qualified_by
+ - NCIT:qualifier_applies_to
+ - NCIT:role_has_domain
+ - NCIT:role_has_range
+ - INO:0000154
+ - HANCESTRO:0308
+ - OMIM:has_inheritance_type
+ - orphanet:C016
+ - orphanet:C017
+ - RO:0000053
+ - RO:0000086
+ - RO:0000087
+ - SNOMED:has_access
+ - SNOMED:has_clinical_course
+ - SNOMED:has_count_of_base_of_active_ingredient
+ - SNOMED:has_dose_form_administration_method
+ - SNOMED:has_dose_form_release_characteristic
+ - SNOMED:has_dose_form_transformation
+ - SNOMED:has_finding_context
+ - SNOMED:has_finding_informer
+ - SNOMED:has_inherent_attribute
+ - SNOMED:has_intent
+ - SNOMED:has_interpretation
+ - SNOMED:has_laterality
+ - SNOMED:has_measurement_method
+ - SNOMED:has_method
+ - SNOMED:has_priority
+ - SNOMED:has_procedure_context
+ - SNOMED:has_process_duration
+ - SNOMED:has_property
+ - SNOMED:has_revision_status
+ - SNOMED:has_scale_type
+ - SNOMED:has_severity
+ - SNOMED:has_specimen
+ - SNOMED:has_state_of_matter
+ - SNOMED:has_subject_relationship_context
+ - SNOMED:has_surgical_approach
+ - SNOMED:has_technique
+ - SNOMED:has_temporal_context
+ - SNOMED:has_time_aspect
+ - SNOMED:has_units
+ - UMLS:has_structural_class
+ - UMLS:has_supported_concept_property
+ - UMLS:has_supported_concept_relationship
+ - UMLS:may_be_qualified_by
+ rank: 1000
+ domain: entity
+ slot_uri: biolink:has_attribute
+ alias: has_attribute
+ owner: named thing
+ domain_of:
+ - entity
+ - attribute
+ - named thing
+ - organism taxon
+ - information content entity
+ - dataset
+ - physical entity
+ - activity
+ - procedure
+ - material sample
+ - biological entity
+ - gene
+ - genome
+ range: attribute
+ multivalued: true
+ deprecated:
+ name: deprecated
+ definition_uri: https://w3id.org/biolink/vocab/deprecated
+ description: A boolean flag indicating that an entity is no longer considered
+ current or valid.
+ from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
+ exact_mappings:
+ - oboInOwl:ObsoleteClass
+ rank: 1000
+ slot_uri: biolink:deprecated
+ alias: deprecated
+ owner: named thing
+ domain_of:
+ - entity
+ - attribute
+ - named thing
+ - organism taxon
+ - information content entity
+ - dataset
+ - physical entity
+ - activity
+ - procedure
+ - material sample
+ - biological entity
+ - gene
+ - genome
+ range: boolean
+ provided by:
+ name: provided by
+ definition_uri: https://w3id.org/biolink/vocab/provided_by
+ description: The value in this node property represents the knowledge provider
+ that created or assembled the node and all of its attributes. Used internally
+ to represent how a particular node made its way into a knowledge provider or
+ graph.
+ from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
+ rank: 1000
+ is_a: node property
+ domain: named thing
+ slot_uri: biolink:provided_by
+ alias: provided_by
+ owner: named thing
+ domain_of:
+ - named thing
+ - attribute
+ - organism taxon
+ - information content entity
+ - dataset
+ - physical entity
+ - activity
+ - procedure
+ - material sample
+ - biological entity
+ - gene
+ - genome
+ range: string
+ multivalued: true
+ xref:
+ name: xref
+ definition_uri: https://w3id.org/biolink/vocab/xref
+ description: A database cross reference or alternative identifier for a NamedThing
+ or edge between two NamedThings. This property should point to a database record
+ or webpage that supports the existence of the edge, or gives more detail about
+ the edge. This property can be used on a node or edge to provide multiple URIs
+ or CURIE cross references.
+ in_subset:
+ - translator_minimal
+ from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
+ aliases:
+ - dbxref
+ - Dbxref
+ - DbXref
+ - record_url
+ - source_record_urls
+ narrow_mappings:
+ - gff3:Dbxref
+ - gpi:DB_Xrefs
+ rank: 1000
+ domain: named thing
+ slot_uri: biolink:xref
+ alias: xref
+ owner: named thing
+ domain_of:
+ - named thing
+ - gene
+ - attribute
+ - organism taxon
+ - information content entity
+ - dataset
+ - physical entity
+ - activity
+ - procedure
+ - material sample
+ - biological entity
+ - genome
+ range: uriorcurie
+ multivalued: true
+ full name:
+ name: full name
+ definition_uri: https://w3id.org/biolink/vocab/full_name
+ description: a long-form human readable name for a thing
+ from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
+ rank: 1000
+ is_a: node property
+ domain: named thing
+ slot_uri: biolink:full_name
+ alias: full_name
+ owner: named thing
+ domain_of:
+ - named thing
+ - attribute
+ - organism taxon
+ - information content entity
+ - dataset
+ - physical entity
+ - activity
+ - procedure
+ - material sample
+ - biological entity
+ - gene
+ - genome
+ range: label type
+ synonym:
+ name: synonym
+ definition_uri: https://w3id.org/biolink/vocab/synonym
+ description: Alternate human-readable names for a thing
+ in_subset:
+ - translator_minimal
+ from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
+ aliases:
+ - alias
+ narrow_mappings:
+ - skos:altLabel
+ - gff3:Alias
+ - AGRKB:synonyms
+ - gpi:DB_Object_Synonyms
+ - HANCESTRO:0330
+ - IAO:0000136
+ - RXNORM:has_tradename
+ rank: 1000
+ is_a: node property
+ domain: named thing
+ slot_uri: biolink:synonym
+ alias: synonym
+ owner: named thing
+ domain_of:
+ - named thing
+ - attribute
+ - organism taxon
+ - information content entity
+ - dataset
+ - physical entity
+ - activity
+ - procedure
+ - material sample
+ - biological entity
+ - gene
+ - genome
+ range: label type
+ multivalued: true
+class_uri: biolink:NamedThing
+
+A string that provides a human-readable description of something
+URI: xsd:string
+ +| Mapping Type | +Mapped Value | +
|---|---|
| self | +xsd:string | +
| native | +bican:narrative_text | +
Prefix part of CURIE
+URI: xsd:string
+ +| Mapping Type | +Mapped Value | +
|---|---|
| self | +xsd:string | +
| native | +bican:ncname | +
A URI, CURIE or BNODE that represents a node in a model.
+URI: shex:nonLiteral
+ +| Mapping Type | +Mapped Value | +
|---|---|
| self | +shex:nonLiteral | +
| native | +bican:nodeidentifier | +
A URI or CURIE that represents an object in the model.
+URI: shex:iri
+ +| Mapping Type | +Mapped Value | +
|---|---|
| self | +shex:iri | +
| native | +bican:objectidentifier | +
A processual entity.
+URI: biolink:Occurrent
+| Name | +Cardinality and Range | +Description | +Inheritance | +
|---|---|---|---|
| + | + | + | + |
| mixed into | +description | +
|---|---|
| + | + |
| Mapping Type | +Mapped Value | +
|---|---|
| self | +biolink:Occurrent | +
| native | +bican:Occurrent | +
| exact | +BFO:0000003 | +
name: occurrent
+definition_uri: https://w3id.org/biolink/vocab/Occurrent
+description: A processual entity.
+from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
+exact_mappings:
+- BFO:0000003
+is_a: physical essence or occurrent
+mixin: true
+class_uri: biolink:Occurrent
+
+name: occurrent
+definition_uri: https://w3id.org/biolink/vocab/Occurrent
+description: A processual entity.
+from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
+exact_mappings:
+- BFO:0000003
+is_a: physical essence or occurrent
+mixin: true
+class_uri: biolink:Occurrent
+
+a concept or class in an ontology, vocabulary or thesaurus. Note that nodes in a biolink compatible KG can be considered both instances of biolink classes, and OWL classes in their own right. In general you should not need to use this class directly. Instead, use the appropriate biolink class. For example, for the GO concept of endocytosis (GO:0006897), use bl:BiologicalProcess as the type.
+ +| Name | +Cardinality and Range | +Description | +Inheritance | +
|---|---|---|---|
| id | +1 String |
+A unique identifier for an entity | +direct | +
| mixed into | +description | +
|---|---|
| Attribute | +A property or characteristic of an entity | +
| Gene | +A region (or regions) that includes all of the sequence elements necessary to... | +
| Genome | +A genome is the sum of genetic material within a cell or virion | +
| used by | +used in | +type | +used | +
|---|---|---|---|
| Attribute | +has_attribute_type | +range | +OntologyClass | +
| Value | +
|---|
| UBERON:0000955 | +
Instances of this class should have identifiers with one of the following prefixes:
+MESH
+UMLS
+KEGG.BRITE
+| Mapping Type | +Mapped Value | +
|---|---|
| self | +biolink:OntologyClass | +
| native | +bican:OntologyClass | +
| exact | +owl:Class, schema:Class | +
name: ontology class
+id_prefixes:
+- MESH
+- UMLS
+- KEGG.BRITE
+definition_uri: https://w3id.org/biolink/vocab/OntologyClass
+description: a concept or class in an ontology, vocabulary or thesaurus. Note that
+ nodes in a biolink compatible KG can be considered both instances of biolink classes,
+ and OWL classes in their own right. In general you should not need to use this class
+ directly. Instead, use the appropriate biolink class. For example, for the GO concept
+ of endocytosis (GO:0006897), use bl:BiologicalProcess as the type.
+comments:
+- This is modeled as a mixin. 'ontology class' should not be the primary type of a
+ node in the KG. Instead you should use an informative bioloink category, such as
+ AnatomicalEntity (for Uberon classes), ChemicalSubstance (for CHEBI or CHEMBL),
+ etc
+- Note that formally this is a metaclass. Instances of this class are instances in
+ the graph, but can be the object of 'type' edges. For example, if we had a node
+ in the graph representing a specific brain of a specific patient (e.g brain001),
+ this could have a category of bl:Sample, and by typed more specifically with an
+ ontology class UBERON:nnn, which has as category bl:AnatomicalEntity
+examples:
+- value: UBERON:0000955
+ description: the class 'brain' from the Uberon anatomy ontology
+from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
+see_also:
+- https://github.com/biolink/biolink-model/issues/486
+exact_mappings:
+- owl:Class
+- schema:Class
+mixin: true
+slots:
+- id
+class_uri: biolink:OntologyClass
+
+name: ontology class
+id_prefixes:
+- MESH
+- UMLS
+- KEGG.BRITE
+definition_uri: https://w3id.org/biolink/vocab/OntologyClass
+description: a concept or class in an ontology, vocabulary or thesaurus. Note that
+ nodes in a biolink compatible KG can be considered both instances of biolink classes,
+ and OWL classes in their own right. In general you should not need to use this class
+ directly. Instead, use the appropriate biolink class. For example, for the GO concept
+ of endocytosis (GO:0006897), use bl:BiologicalProcess as the type.
+comments:
+- This is modeled as a mixin. 'ontology class' should not be the primary type of a
+ node in the KG. Instead you should use an informative bioloink category, such as
+ AnatomicalEntity (for Uberon classes), ChemicalSubstance (for CHEBI or CHEMBL),
+ etc
+- Note that formally this is a metaclass. Instances of this class are instances in
+ the graph, but can be the object of 'type' edges. For example, if we had a node
+ in the graph representing a specific brain of a specific patient (e.g brain001),
+ this could have a category of bl:Sample, and by typed more specifically with an
+ ontology class UBERON:nnn, which has as category bl:AnatomicalEntity
+examples:
+- value: UBERON:0000955
+ description: the class 'brain' from the Uberon anatomy ontology
+from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
+see_also:
+- https://github.com/biolink/biolink-model/issues/486
+exact_mappings:
+- owl:Class
+- schema:Class
+mixin: true
+attributes:
+ id:
+ name: id
+ definition_uri: https://w3id.org/biolink/vocab/id
+ description: A unique identifier for an entity. Must be either a CURIE shorthand
+ for a URI or a complete URI
+ in_subset:
+ - translator_minimal
+ from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
+ exact_mappings:
+ - AGRKB:primaryId
+ - gff3:ID
+ - gpi:DB_Object_ID
+ rank: 1000
+ domain: entity
+ slot_uri: biolink:id
+ identifier: true
+ alias: id
+ owner: ontology class
+ domain_of:
+ - ontology class
+ - entity
+ - attribute
+ - named thing
+ - taxonomic rank
+ - organism taxon
+ - information content entity
+ - dataset
+ - physical entity
+ - activity
+ - procedure
+ - material sample
+ - biological entity
+ - gene
+ - genome
+ range: string
+ required: true
+class_uri: biolink:OntologyClass
+
+A classification of a set of organisms. Example instances: NCBITaxon:9606 (Homo sapiens), NCBITaxon:2 (Bacteria). Can also be used to represent strains or subspecies.
+ +| Name | +Cardinality and Range | +Description | +Inheritance | +
|---|---|---|---|
| id | +1 String |
+A unique identifier for an entity | +direct | +
| iri | +0..1 IriType |
+An IRI for an entity | +direct | +
| category | +* Uriorcurie |
+Name of the high level ontology class in which this entity is categorized | +direct | +
| type | +* String |
++ | direct | +
| name | +0..1 LabelType |
+A human-readable name for an attribute or entity | +direct | +
| description | +0..1 NarrativeText |
+a human-readable description of an entity | +direct | +
| has_attribute | +* Attribute |
+connects any entity to an attribute | +direct | +
| deprecated | +0..1 Boolean |
+A boolean flag indicating that an entity is no longer considered current or v... | +direct | +
| provided_by | +* String |
+The value in this node property represents the knowledge provider that create... | +direct | +
| xref | +* Uriorcurie |
+A database cross reference or alternative identifier for a NamedThing or edge... | +direct | +
| full_name | +0..1 LabelType |
+a long-form human readable name for a thing | +direct | +
| synonym | +* LabelType |
+Alternate human-readable names for a thing | +direct | +
| has_taxonomic_rank | +0..1 TaxonomicRank |
++ | direct | +
| used by | +used in | +type | +used | +
|---|---|---|---|
| GeneAnnotation | +in_taxon | +range | +OrganismTaxon | +
| GenomeAnnotation | +in_taxon | +range | +OrganismTaxon | +
| GenomeAssembly | +in_taxon | +range | +OrganismTaxon | +
| ThingWithTaxon | +in_taxon | +range | +OrganismTaxon | +
| BiologicalEntity | +in_taxon | +range | +OrganismTaxon | +
| Gene | +in_taxon | +range | +OrganismTaxon | +
| Genome | +in_taxon | +range | +OrganismTaxon | +
Instances of this class should have identifiers with one of the following prefixes:
+NCBITaxon
+MESH
+UMLS
+| Mapping Type | +Mapped Value | +
|---|---|
| self | +biolink:OrganismTaxon | +
| native | +bican:OrganismTaxon | +
| exact | +WIKIDATA:Q16521, STY:T001, bioschemas:Taxon | +
| narrow | +dcid:BiologicalSpecies | +
name: organism taxon
+id_prefixes:
+- NCBITaxon
+- MESH
+- UMLS
+definition_uri: https://w3id.org/biolink/vocab/OrganismTaxon
+description: 'A classification of a set of organisms. Example instances: NCBITaxon:9606
+ (Homo sapiens), NCBITaxon:2 (Bacteria). Can also be used to represent strains or
+ subspecies.'
+in_subset:
+- model_organism_database
+from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
+aliases:
+- taxon
+- taxonomic classification
+exact_mappings:
+- WIKIDATA:Q16521
+- STY:T001
+- bioschemas:Taxon
+narrow_mappings:
+- dcid:BiologicalSpecies
+is_a: named thing
+values_from:
+- NCBITaxon
+slots:
+- id
+- iri
+- category
+- type
+- name
+- description
+- has attribute
+- deprecated
+- provided by
+- xref
+- full name
+- synonym
+- has taxonomic rank
+class_uri: biolink:OrganismTaxon
+
+name: organism taxon
+id_prefixes:
+- NCBITaxon
+- MESH
+- UMLS
+definition_uri: https://w3id.org/biolink/vocab/OrganismTaxon
+description: 'A classification of a set of organisms. Example instances: NCBITaxon:9606
+ (Homo sapiens), NCBITaxon:2 (Bacteria). Can also be used to represent strains or
+ subspecies.'
+in_subset:
+- model_organism_database
+from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
+aliases:
+- taxon
+- taxonomic classification
+exact_mappings:
+- WIKIDATA:Q16521
+- STY:T001
+- bioschemas:Taxon
+narrow_mappings:
+- dcid:BiologicalSpecies
+is_a: named thing
+values_from:
+- NCBITaxon
+attributes:
+ id:
+ name: id
+ definition_uri: https://w3id.org/biolink/vocab/id
+ description: A unique identifier for an entity. Must be either a CURIE shorthand
+ for a URI or a complete URI
+ in_subset:
+ - translator_minimal
+ from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
+ exact_mappings:
+ - AGRKB:primaryId
+ - gff3:ID
+ - gpi:DB_Object_ID
+ rank: 1000
+ domain: entity
+ slot_uri: biolink:id
+ identifier: true
+ alias: id
+ owner: organism taxon
+ domain_of:
+ - ontology class
+ - entity
+ - attribute
+ - named thing
+ - taxonomic rank
+ - organism taxon
+ - information content entity
+ - dataset
+ - physical entity
+ - activity
+ - procedure
+ - material sample
+ - biological entity
+ - gene
+ - genome
+ range: string
+ required: true
+ iri:
+ name: iri
+ definition_uri: https://w3id.org/biolink/vocab/iri
+ description: An IRI for an entity. This is determined by the id using expansion
+ rules.
+ in_subset:
+ - translator_minimal
+ - samples
+ from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
+ exact_mappings:
+ - WIKIDATA_PROPERTY:P854
+ rank: 1000
+ slot_uri: biolink:iri
+ alias: iri
+ owner: organism taxon
+ domain_of:
+ - attribute
+ - entity
+ - named thing
+ - organism taxon
+ - information content entity
+ - dataset
+ - physical entity
+ - activity
+ - procedure
+ - material sample
+ - biological entity
+ - gene
+ - genome
+ range: iri type
+ category:
+ name: category
+ definition_uri: https://w3id.org/biolink/vocab/category
+ description: Name of the high level ontology class in which this entity is categorized.
+ Corresponds to the label for the biolink entity type class. In a neo4j database
+ this MAY correspond to the neo4j label tag. In an RDF database it should be
+ a biolink model class URI. This field is multi-valued. It should include values
+ for ancestors of the biolink class; for example, a protein such as Shh would
+ have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`.
+ In an RDF database, nodes will typically have an rdf:type triples. This can
+ be to the most specific biolink class, or potentially to a class more specific
+ than something in biolink. For example, a sequence feature `f` may have a rdf:type
+ assertion to a SO class such as TF_binding_site, which is more specific than
+ anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity,
+ biolink:NamedThing}
+ in_subset:
+ - translator_minimal
+ from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
+ rank: 1000
+ is_a: type
+ domain: entity
+ slot_uri: biolink:category
+ designates_type: true
+ alias: category
+ owner: organism taxon
+ domain_of:
+ - entity
+ - attribute
+ - named thing
+ - organism taxon
+ - information content entity
+ - dataset
+ - physical entity
+ - activity
+ - procedure
+ - material sample
+ - biological entity
+ - gene
+ - genome
+ is_class_field: true
+ range: uriorcurie
+ multivalued: true
+ type:
+ name: type
+ definition_uri: https://w3id.org/biolink/vocab/type
+ from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
+ mappings:
+ - rdf:type
+ exact_mappings:
+ - gff3:type
+ - gpi:DB_Object_Type
+ rank: 1000
+ domain: entity
+ slot_uri: rdf:type
+ alias: type
+ owner: organism taxon
+ domain_of:
+ - entity
+ - attribute
+ - named thing
+ - organism taxon
+ - information content entity
+ - dataset
+ - physical entity
+ - activity
+ - procedure
+ - material sample
+ - biological entity
+ - gene
+ - genome
+ range: string
+ multivalued: true
+ name:
+ name: name
+ definition_uri: https://w3id.org/biolink/vocab/name
+ description: A human-readable name for an attribute or entity.
+ in_subset:
+ - translator_minimal
+ - samples
+ from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
+ aliases:
+ - label
+ - display name
+ - title
+ mappings:
+ - rdfs:label
+ exact_mappings:
+ - gff3:Name
+ - gpi:DB_Object_Name
+ narrow_mappings:
+ - dct:title
+ - WIKIDATA_PROPERTY:P1476
+ rank: 1000
+ domain: entity
+ slot_uri: rdfs:label
+ alias: name
+ owner: organism taxon
+ domain_of:
+ - attribute
+ - entity
+ - macromolecular machine mixin
+ - named thing
+ - organism taxon
+ - information content entity
+ - dataset
+ - physical entity
+ - activity
+ - procedure
+ - material sample
+ - biological entity
+ - gene or gene product
+ - gene
+ - genome
+ range: label type
+ description:
+ name: description
+ definition_uri: https://w3id.org/biolink/vocab/description
+ description: a human-readable description of an entity
+ in_subset:
+ - translator_minimal
+ from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
+ aliases:
+ - definition
+ mappings:
+ - dct:description
+ exact_mappings:
+ - IAO:0000115
+ - skos:definitions
+ narrow_mappings:
+ - gff3:Description
+ rank: 1000
+ slot_uri: dct:description
+ alias: description
+ owner: organism taxon
+ domain_of:
+ - entity
+ - attribute
+ - named thing
+ - organism taxon
+ - information content entity
+ - dataset
+ - physical entity
+ - activity
+ - procedure
+ - material sample
+ - biological entity
+ - gene
+ - genome
+ range: narrative text
+ has attribute:
+ name: has attribute
+ definition_uri: https://w3id.org/biolink/vocab/has_attribute
+ description: connects any entity to an attribute
+ in_subset:
+ - samples
+ from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
+ exact_mappings:
+ - SIO:000008
+ close_mappings:
+ - OBI:0001927
+ narrow_mappings:
+ - OBAN:association_has_subject_property
+ - OBAN:association_has_object_property
+ - CPT:has_possibly_included_panel_element
+ - DRUGBANK:category
+ - EFO:is_executed_in
+ - HANCESTRO:0301
+ - LOINC:has_action_guidance
+ - LOINC:has_adjustment
+ - LOINC:has_aggregation_view
+ - LOINC:has_approach_guidance
+ - LOINC:has_divisor
+ - LOINC:has_exam
+ - LOINC:has_method
+ - LOINC:has_modality_subtype
+ - LOINC:has_object_guidance
+ - LOINC:has_scale
+ - LOINC:has_suffix
+ - LOINC:has_time_aspect
+ - LOINC:has_time_modifier
+ - LOINC:has_timing_of
+ - NCIT:R88
+ - NCIT:eo_disease_has_property_or_attribute
+ - NCIT:has_data_element
+ - NCIT:has_pharmaceutical_administration_method
+ - NCIT:has_pharmaceutical_basic_dose_form
+ - NCIT:has_pharmaceutical_intended_site
+ - NCIT:has_pharmaceutical_release_characteristics
+ - NCIT:has_pharmaceutical_state_of_matter
+ - NCIT:has_pharmaceutical_transformation
+ - NCIT:is_qualified_by
+ - NCIT:qualifier_applies_to
+ - NCIT:role_has_domain
+ - NCIT:role_has_range
+ - INO:0000154
+ - HANCESTRO:0308
+ - OMIM:has_inheritance_type
+ - orphanet:C016
+ - orphanet:C017
+ - RO:0000053
+ - RO:0000086
+ - RO:0000087
+ - SNOMED:has_access
+ - SNOMED:has_clinical_course
+ - SNOMED:has_count_of_base_of_active_ingredient
+ - SNOMED:has_dose_form_administration_method
+ - SNOMED:has_dose_form_release_characteristic
+ - SNOMED:has_dose_form_transformation
+ - SNOMED:has_finding_context
+ - SNOMED:has_finding_informer
+ - SNOMED:has_inherent_attribute
+ - SNOMED:has_intent
+ - SNOMED:has_interpretation
+ - SNOMED:has_laterality
+ - SNOMED:has_measurement_method
+ - SNOMED:has_method
+ - SNOMED:has_priority
+ - SNOMED:has_procedure_context
+ - SNOMED:has_process_duration
+ - SNOMED:has_property
+ - SNOMED:has_revision_status
+ - SNOMED:has_scale_type
+ - SNOMED:has_severity
+ - SNOMED:has_specimen
+ - SNOMED:has_state_of_matter
+ - SNOMED:has_subject_relationship_context
+ - SNOMED:has_surgical_approach
+ - SNOMED:has_technique
+ - SNOMED:has_temporal_context
+ - SNOMED:has_time_aspect
+ - SNOMED:has_units
+ - UMLS:has_structural_class
+ - UMLS:has_supported_concept_property
+ - UMLS:has_supported_concept_relationship
+ - UMLS:may_be_qualified_by
+ rank: 1000
+ domain: entity
+ slot_uri: biolink:has_attribute
+ alias: has_attribute
+ owner: organism taxon
+ domain_of:
+ - entity
+ - attribute
+ - named thing
+ - organism taxon
+ - information content entity
+ - dataset
+ - physical entity
+ - activity
+ - procedure
+ - material sample
+ - biological entity
+ - gene
+ - genome
+ range: attribute
+ multivalued: true
+ deprecated:
+ name: deprecated
+ definition_uri: https://w3id.org/biolink/vocab/deprecated
+ description: A boolean flag indicating that an entity is no longer considered
+ current or valid.
+ from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
+ exact_mappings:
+ - oboInOwl:ObsoleteClass
+ rank: 1000
+ slot_uri: biolink:deprecated
+ alias: deprecated
+ owner: organism taxon
+ domain_of:
+ - entity
+ - attribute
+ - named thing
+ - organism taxon
+ - information content entity
+ - dataset
+ - physical entity
+ - activity
+ - procedure
+ - material sample
+ - biological entity
+ - gene
+ - genome
+ range: boolean
+ provided by:
+ name: provided by
+ definition_uri: https://w3id.org/biolink/vocab/provided_by
+ description: The value in this node property represents the knowledge provider
+ that created or assembled the node and all of its attributes. Used internally
+ to represent how a particular node made its way into a knowledge provider or
+ graph.
+ from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
+ rank: 1000
+ is_a: node property
+ domain: named thing
+ slot_uri: biolink:provided_by
+ alias: provided_by
+ owner: organism taxon
+ domain_of:
+ - named thing
+ - attribute
+ - organism taxon
+ - information content entity
+ - dataset
+ - physical entity
+ - activity
+ - procedure
+ - material sample
+ - biological entity
+ - gene
+ - genome
+ range: string
+ multivalued: true
+ xref:
+ name: xref
+ definition_uri: https://w3id.org/biolink/vocab/xref
+ description: A database cross reference or alternative identifier for a NamedThing
+ or edge between two NamedThings. This property should point to a database record
+ or webpage that supports the existence of the edge, or gives more detail about
+ the edge. This property can be used on a node or edge to provide multiple URIs
+ or CURIE cross references.
+ in_subset:
+ - translator_minimal
+ from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
+ aliases:
+ - dbxref
+ - Dbxref
+ - DbXref
+ - record_url
+ - source_record_urls
+ narrow_mappings:
+ - gff3:Dbxref
+ - gpi:DB_Xrefs
+ rank: 1000
+ domain: named thing
+ slot_uri: biolink:xref
+ alias: xref
+ owner: organism taxon
+ domain_of:
+ - named thing
+ - gene
+ - attribute
+ - organism taxon
+ - information content entity
+ - dataset
+ - physical entity
+ - activity
+ - procedure
+ - material sample
+ - biological entity
+ - genome
+ range: uriorcurie
+ multivalued: true
+ full name:
+ name: full name
+ definition_uri: https://w3id.org/biolink/vocab/full_name
+ description: a long-form human readable name for a thing
+ from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
+ rank: 1000
+ is_a: node property
+ domain: named thing
+ slot_uri: biolink:full_name
+ alias: full_name
+ owner: organism taxon
+ domain_of:
+ - named thing
+ - attribute
+ - organism taxon
+ - information content entity
+ - dataset
+ - physical entity
+ - activity
+ - procedure
+ - material sample
+ - biological entity
+ - gene
+ - genome
+ range: label type
+ synonym:
+ name: synonym
+ definition_uri: https://w3id.org/biolink/vocab/synonym
+ description: Alternate human-readable names for a thing
+ in_subset:
+ - translator_minimal
+ from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
+ aliases:
+ - alias
+ narrow_mappings:
+ - skos:altLabel
+ - gff3:Alias
+ - AGRKB:synonyms
+ - gpi:DB_Object_Synonyms
+ - HANCESTRO:0330
+ - IAO:0000136
+ - RXNORM:has_tradename
+ rank: 1000
+ is_a: node property
+ domain: named thing
+ slot_uri: biolink:synonym
+ alias: synonym
+ owner: organism taxon
+ domain_of:
+ - named thing
+ - attribute
+ - organism taxon
+ - information content entity
+ - dataset
+ - physical entity
+ - activity
+ - procedure
+ - material sample
+ - biological entity
+ - gene
+ - genome
+ range: label type
+ multivalued: true
+ has taxonomic rank:
+ name: has taxonomic rank
+ definition_uri: https://w3id.org/biolink/vocab/has_taxonomic_rank
+ from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
+ mappings:
+ - WIKIDATA:P105
+ rank: 1000
+ is_a: node property
+ domain: named thing
+ slot_uri: biolink:has_taxonomic_rank
+ alias: has_taxonomic_rank
+ owner: organism taxon
+ domain_of:
+ - organism taxon
+ range: taxonomic rank
+ multivalued: false
+class_uri: biolink:OrganismTaxon
+
+A parcellation annotation defines a specific segment of an anatomical space denoted by an internal identifier and is a unique and exclusive member of a versioned release anatomical annotation set. For example, in the case where the anatomical annotation set is a single multi-value image mask (e.g. Allen Mouse CCF), a specific annotation corresponds to a specific label index (internal identifier) in the mask.
+URI: AnS:ParcellationAnnotation
+| Name | +Cardinality and Range | +Description | +Inheritance | +
|---|---|---|---|
| part_of_anatomical_annotation_set | +1 String or AnatomicalAnnotationSet or String |
++ | direct | +
| internal_identifier | +1 String |
+An identifier that uniquely denotes a specific parcellation annotation within... | +direct | +
| voxel_count | +0..1 Integer |
+The number of voxels (3D pixels) spanned by the parcellation annotation (opti... | +direct | +
| used by | +used in | +type | +used | +
|---|---|---|---|
| ParcellationAnnotationTermMap | +subject_parcellation_annotation | +any_of[range] | +ParcellationAnnotation | +
| Mapping Type | +Mapped Value | +
|---|---|
| self | +AnS:ParcellationAnnotation | +
| native | +AnS:ParcellationAnnotation | +
name: ParcellationAnnotation
+description: A parcellation annotation defines a specific segment of an anatomical
+ space denoted by an internal identifier and is a unique and exclusive member of
+ a versioned release anatomical annotation set. For example, in the case where the
+ anatomical annotation set is a single multi-value image mask (e.g. Allen Mouse CCF),
+ a specific annotation corresponds to a specific label index (internal identifier)
+ in the mask.
+from_schema: https://w3id.org/my-org/anatomical-structure-schema
+attributes:
+ part_of_anatomical_annotation_set:
+ name: part_of_anatomical_annotation_set
+ from_schema: https://w3id.org/my-org/anatomical-structure-schema
+ rank: 1000
+ domain_of:
+ - ParcellationAnnotation
+ required: true
+ any_of:
+ - range: AnatomicalAnnotationSet
+ - range: string
+ internal_identifier:
+ name: internal_identifier
+ description: An identifier that uniquely denotes a specific parcellation annotation
+ within the context of an anatomical annotation set
+ from_schema: https://w3id.org/my-org/anatomical-structure-schema
+ rank: 1000
+ domain_of:
+ - ParcellationAnnotation
+ required: true
+ voxel_count:
+ name: voxel_count
+ description: The number of voxels (3D pixels) spanned by the parcellation annotation
+ (optional).
+ from_schema: https://w3id.org/my-org/anatomical-structure-schema
+ rank: 1000
+ domain_of:
+ - ParcellationAnnotation
+ range: integer
+ minimum_value: 0
+
+name: ParcellationAnnotation
+description: A parcellation annotation defines a specific segment of an anatomical
+ space denoted by an internal identifier and is a unique and exclusive member of
+ a versioned release anatomical annotation set. For example, in the case where the
+ anatomical annotation set is a single multi-value image mask (e.g. Allen Mouse CCF),
+ a specific annotation corresponds to a specific label index (internal identifier)
+ in the mask.
+from_schema: https://w3id.org/my-org/anatomical-structure-schema
+attributes:
+ part_of_anatomical_annotation_set:
+ name: part_of_anatomical_annotation_set
+ from_schema: https://w3id.org/my-org/anatomical-structure-schema
+ rank: 1000
+ alias: part_of_anatomical_annotation_set
+ owner: ParcellationAnnotation
+ domain_of:
+ - ParcellationAnnotation
+ range: string
+ required: true
+ any_of:
+ - range: AnatomicalAnnotationSet
+ - range: string
+ internal_identifier:
+ name: internal_identifier
+ description: An identifier that uniquely denotes a specific parcellation annotation
+ within the context of an anatomical annotation set
+ from_schema: https://w3id.org/my-org/anatomical-structure-schema
+ rank: 1000
+ alias: internal_identifier
+ owner: ParcellationAnnotation
+ domain_of:
+ - ParcellationAnnotation
+ range: string
+ required: true
+ voxel_count:
+ name: voxel_count
+ description: The number of voxels (3D pixels) spanned by the parcellation annotation
+ (optional).
+ from_schema: https://w3id.org/my-org/anatomical-structure-schema
+ rank: 1000
+ alias: voxel_count
+ owner: ParcellationAnnotation
+ domain_of:
+ - ParcellationAnnotation
+ range: integer
+ minimum_value: 0
+
+The parcellation annotation term map table defines the relationship between parcellation annotations and parcellation terms. A parcellation term is uniquely denoted by a parcellation term identifier and the parcellation terminology it belongs to. A parcellation term can be spatially parameterized by the union of one or more parcellation annotations within a versioned release of an anatomical annotation set. For example, annotations defining individual cortical layers in cortical region R (R1, R2/3, R4, etc) can be combined to define the parent region R.
+URI: AnS:ParcellationAnnotationTermMap
+| Name | +Cardinality and Range | +Description | +Inheritance | +
|---|---|---|---|
| subject_parcellation_annotation | +1 String or ParcellationAnnotation or String |
+Reference to the parcellation annotation that is the subject of the associati... | +direct | +
| subject_parcellation_term | +1 String or ParcellationTerm or String |
+Reference to the parcellation term that is the subject of the association | +direct | +
| Mapping Type | +Mapped Value | +
|---|---|
| self | +AnS:ParcellationAnnotationTermMap | +
| native | +AnS:ParcellationAnnotationTermMap | +
name: ParcellationAnnotationTermMap
+description: The parcellation annotation term map table defines the relationship between
+ parcellation annotations and parcellation terms. A parcellation term is uniquely
+ denoted by a parcellation term identifier and the parcellation terminology it belongs
+ to. A parcellation term can be spatially parameterized by the union of one or more
+ parcellation annotations within a versioned release of an anatomical annotation
+ set. For example, annotations defining individual cortical layers in cortical region R
+ (R1, R2/3, R4, etc) can be combined to define the parent region R.
+from_schema: https://w3id.org/my-org/anatomical-structure-schema
+attributes:
+ subject_parcellation_annotation:
+ name: subject_parcellation_annotation
+ description: Reference to the parcellation annotation that is the subject of the
+ association.
+ from_schema: https://w3id.org/my-org/anatomical-structure-schema
+ rank: 1000
+ domain_of:
+ - ParcellationAnnotationTermMap
+ required: true
+ any_of:
+ - range: ParcellationAnnotation
+ - range: string
+ subject_parcellation_term:
+ name: subject_parcellation_term
+ description: Reference to the parcellation term that is the subject of the association.
+ from_schema: https://w3id.org/my-org/anatomical-structure-schema
+ domain_of:
+ - ParcellationColorAssignment
+ - ParcellationAnnotationTermMap
+ required: true
+ any_of:
+ - range: ParcellationTerm
+ - range: string
+
+name: ParcellationAnnotationTermMap
+description: The parcellation annotation term map table defines the relationship between
+ parcellation annotations and parcellation terms. A parcellation term is uniquely
+ denoted by a parcellation term identifier and the parcellation terminology it belongs
+ to. A parcellation term can be spatially parameterized by the union of one or more
+ parcellation annotations within a versioned release of an anatomical annotation
+ set. For example, annotations defining individual cortical layers in cortical region R
+ (R1, R2/3, R4, etc) can be combined to define the parent region R.
+from_schema: https://w3id.org/my-org/anatomical-structure-schema
+attributes:
+ subject_parcellation_annotation:
+ name: subject_parcellation_annotation
+ description: Reference to the parcellation annotation that is the subject of the
+ association.
+ from_schema: https://w3id.org/my-org/anatomical-structure-schema
+ rank: 1000
+ alias: subject_parcellation_annotation
+ owner: ParcellationAnnotationTermMap
+ domain_of:
+ - ParcellationAnnotationTermMap
+ range: string
+ required: true
+ any_of:
+ - range: ParcellationAnnotation
+ - range: string
+ subject_parcellation_term:
+ name: subject_parcellation_term
+ description: Reference to the parcellation term that is the subject of the association.
+ from_schema: https://w3id.org/my-org/anatomical-structure-schema
+ alias: subject_parcellation_term
+ owner: ParcellationAnnotationTermMap
+ domain_of:
+ - ParcellationColorAssignment
+ - ParcellationAnnotationTermMap
+ range: string
+ required: true
+ any_of:
+ - range: ParcellationTerm
+ - range: string
+
+A parcellation atlas is a versioned release reference used to guide experiments or deal with the spatial relationship between objects or the location of objects within the context of some anatomical structure. An atlas is minimally defined by a notion of space (either implicit or explicit) and an annotation set. Reference atlases usually have additional parts that make them more useful in certain situations, such as a well defined coordinate system, delineations indicating the boundaries of various regions or cell populations, landmarks, and labels and names to make it easier to communicate about well known and useful locations (ref: ILX:0777109, RRID:SCR_023499).
+ +| Name | +Cardinality and Range | +Description | +Inheritance | +
|---|---|---|---|
| has_anatomical_space | +1 String or AnatomicalSpace or String |
+Reference to the anatomical space component of the parcellation atlas | +direct | +
| has_anatomical_annotation_set | +1 String or AnatomicalAnnotationSet or String |
+Reference to the anatomical annotation set component of the parcellation atla... | +direct | +
| has_parcellation_terminology | +1 String or ParcellationTerminology or String |
+Reference to the parcellation terminology component of the parcellation atlas | +direct | +
| specialization_of | +0..1 String or ParcellationAtlas or String |
+Reference to the general (non versioned) parcellation atlas for which the par... | +direct | +
| version | +1 String |
++ | VersionedNamedThing | +
| revision_of | +0..1 VersionedNamedThing or ParcellationAtlas or String |
++ | VersionedNamedThing | +
| id | +1 Uriorcurie |
++ | NamedThing | +
| name | +1 String |
++ | NamedThing | +
| description | +1 String |
++ | NamedThing | +
| category | +* Uriorcurie |
++ | NamedThing | +
| used by | +used in | +type | +used | +
|---|---|---|---|
| ParcellationAtlas | +specialization_of | +any_of[range] | +ParcellationAtlas | +
| ParcellationAtlas | +revision_of | +any_of[range] | +ParcellationAtlas | +
| Mapping Type | +Mapped Value | +
|---|---|
| self | +AnS:ParcellationAtlas | +
| native | +AnS:ParcellationAtlas | +
name: ParcellationAtlas
+description: 'A parcellation atlas is a versioned release reference used to guide
+ experiments or deal with the spatial relationship between objects or the location
+ of objects within the context of some anatomical structure. An atlas is minimally
+ defined by a notion of space (either implicit or explicit) and an annotation set.
+ Reference atlases usually have additional parts that make them more useful in certain
+ situations, such as a well defined coordinate system, delineations indicating the
+ boundaries of various regions or cell populations, landmarks, and labels and names
+ to make it easier to communicate about well known and useful locations (ref: ILX:0777109,
+ RRID:SCR_023499).'
+from_schema: https://w3id.org/my-org/anatomical-structure-schema
+is_a: VersionedNamedThing
+slot_usage:
+ revision_of:
+ name: revision_of
+ any_of:
+ - range: ParcellationAtlas
+ - range: string
+attributes:
+ has_anatomical_space:
+ name: has_anatomical_space
+ description: Reference to the anatomical space component of the parcellation atlas
+ from_schema: https://w3id.org/my-org/anatomical-structure-schema
+ rank: 1000
+ domain_of:
+ - ParcellationAtlas
+ required: true
+ any_of:
+ - range: AnatomicalSpace
+ - range: string
+ has_anatomical_annotation_set:
+ name: has_anatomical_annotation_set
+ description: Reference to the anatomical annotation set component of the parcellation
+ atlas
+ from_schema: https://w3id.org/my-org/anatomical-structure-schema
+ rank: 1000
+ domain_of:
+ - ParcellationAtlas
+ required: true
+ any_of:
+ - range: AnatomicalAnnotationSet
+ - range: string
+ has_parcellation_terminology:
+ name: has_parcellation_terminology
+ description: Reference to the parcellation terminology component of the parcellation
+ atlas
+ from_schema: https://w3id.org/my-org/anatomical-structure-schema
+ rank: 1000
+ domain_of:
+ - ParcellationAtlas
+ required: true
+ any_of:
+ - range: ParcellationTerminology
+ - range: string
+ specialization_of:
+ name: specialization_of
+ description: Reference to the general (non versioned) parcellation atlas for which
+ the parcellation atlas is a specific version release of.
+ from_schema: https://w3id.org/my-org/anatomical-structure-schema
+ rank: 1000
+ domain_of:
+ - ParcellationAtlas
+ any_of:
+ - range: ParcellationAtlas
+ - range: string
+
+name: ParcellationAtlas
+description: 'A parcellation atlas is a versioned release reference used to guide
+ experiments or deal with the spatial relationship between objects or the location
+ of objects within the context of some anatomical structure. An atlas is minimally
+ defined by a notion of space (either implicit or explicit) and an annotation set.
+ Reference atlases usually have additional parts that make them more useful in certain
+ situations, such as a well defined coordinate system, delineations indicating the
+ boundaries of various regions or cell populations, landmarks, and labels and names
+ to make it easier to communicate about well known and useful locations (ref: ILX:0777109,
+ RRID:SCR_023499).'
+from_schema: https://w3id.org/my-org/anatomical-structure-schema
+is_a: VersionedNamedThing
+slot_usage:
+ revision_of:
+ name: revision_of
+ any_of:
+ - range: ParcellationAtlas
+ - range: string
+attributes:
+ has_anatomical_space:
+ name: has_anatomical_space
+ description: Reference to the anatomical space component of the parcellation atlas
+ from_schema: https://w3id.org/my-org/anatomical-structure-schema
+ rank: 1000
+ alias: has_anatomical_space
+ owner: ParcellationAtlas
+ domain_of:
+ - ParcellationAtlas
+ range: string
+ required: true
+ any_of:
+ - range: AnatomicalSpace
+ - range: string
+ has_anatomical_annotation_set:
+ name: has_anatomical_annotation_set
+ description: Reference to the anatomical annotation set component of the parcellation
+ atlas
+ from_schema: https://w3id.org/my-org/anatomical-structure-schema
+ rank: 1000
+ alias: has_anatomical_annotation_set
+ owner: ParcellationAtlas
+ domain_of:
+ - ParcellationAtlas
+ range: string
+ required: true
+ any_of:
+ - range: AnatomicalAnnotationSet
+ - range: string
+ has_parcellation_terminology:
+ name: has_parcellation_terminology
+ description: Reference to the parcellation terminology component of the parcellation
+ atlas
+ from_schema: https://w3id.org/my-org/anatomical-structure-schema
+ rank: 1000
+ alias: has_parcellation_terminology
+ owner: ParcellationAtlas
+ domain_of:
+ - ParcellationAtlas
+ range: string
+ required: true
+ any_of:
+ - range: ParcellationTerminology
+ - range: string
+ specialization_of:
+ name: specialization_of
+ description: Reference to the general (non versioned) parcellation atlas for which
+ the parcellation atlas is a specific version release of.
+ from_schema: https://w3id.org/my-org/anatomical-structure-schema
+ rank: 1000
+ alias: specialization_of
+ owner: ParcellationAtlas
+ domain_of:
+ - ParcellationAtlas
+ range: string
+ any_of:
+ - range: ParcellationAtlas
+ - range: string
+ version:
+ name: version
+ from_schema: https://w3id.org/my-org/anatomical-structure-schema
+ rank: 1000
+ alias: version
+ owner: ParcellationAtlas
+ domain_of:
+ - VersionedNamedThing
+ range: string
+ required: true
+ revision_of:
+ name: revision_of
+ from_schema: https://w3id.org/my-org/anatomical-structure-schema
+ rank: 1000
+ alias: revision_of
+ owner: ParcellationAtlas
+ domain_of:
+ - VersionedNamedThing
+ range: VersionedNamedThing
+ any_of:
+ - range: ParcellationAtlas
+ - range: string
+ id:
+ name: id
+ from_schema: https://w3id.org/my-org/anatomical-structure-schema
+ rank: 1000
+ identifier: true
+ alias: id
+ owner: ParcellationAtlas
+ domain_of:
+ - NamedThing
+ range: uriorcurie
+ required: true
+ name:
+ name: name
+ from_schema: https://w3id.org/my-org/anatomical-structure-schema
+ rank: 1000
+ alias: name
+ owner: ParcellationAtlas
+ domain_of:
+ - NamedThing
+ range: string
+ required: true
+ description:
+ name: description
+ from_schema: https://w3id.org/my-org/anatomical-structure-schema
+ rank: 1000
+ alias: description
+ owner: ParcellationAtlas
+ domain_of:
+ - NamedThing
+ range: string
+ required: true
+ category:
+ name: category
+ from_schema: https://w3id.org/my-org/anatomical-structure-schema
+ rank: 1000
+ designates_type: true
+ alias: category
+ owner: ParcellationAtlas
+ domain_of:
+ - NamedThing
+ is_class_field: true
+ range: uriorcurie
+ multivalued: true
+
+The parcellation color assignment associates hex color value to a parcellation term within a versioned release of a color scheme. A parcellation term is uniquely denoted by a parcellation term identifier and the parcellation terminology it belongs to.
+URI: AnS:ParcellationColorAssignment
+| Name | +Cardinality and Range | +Description | +Inheritance | +
|---|---|---|---|
| part_of_parcellation_color_scheme | +1 String or ParcellationColorScheme or String |
+Reference to the parcellation color scheme for which the color assignment is ... | +direct | +
| subject_parcellation_term | +1 String or ParcellationTerm or String |
+Reference to the parcellation term identifier for which the color assignment ... | +direct | +
| color | +0..1 String |
+A string representing to hex triplet code of a color | +direct | +
| Mapping Type | +Mapped Value | +
|---|---|
| self | +AnS:ParcellationColorAssignment | +
| native | +AnS:ParcellationColorAssignment | +
name: ParcellationColorAssignment
+description: The parcellation color assignment associates hex color value to a parcellation
+ term within a versioned release of a color scheme. A parcellation term is uniquely
+ denoted by a parcellation term identifier and the parcellation terminology it belongs
+ to.
+from_schema: https://w3id.org/my-org/anatomical-structure-schema
+attributes:
+ part_of_parcellation_color_scheme:
+ name: part_of_parcellation_color_scheme
+ description: Reference to the parcellation color scheme for which the color assignment
+ is part of.
+ from_schema: https://w3id.org/my-org/anatomical-structure-schema
+ rank: 1000
+ domain_of:
+ - ParcellationColorAssignment
+ required: true
+ any_of:
+ - range: ParcellationColorScheme
+ - range: string
+ subject_parcellation_term:
+ name: subject_parcellation_term
+ description: Reference to the parcellation term identifier for which the color
+ assignment is about.
+ from_schema: https://w3id.org/my-org/anatomical-structure-schema
+ rank: 1000
+ domain_of:
+ - ParcellationColorAssignment
+ - ParcellationAnnotationTermMap
+ required: true
+ any_of:
+ - range: ParcellationTerm
+ - range: string
+ color:
+ name: color
+ description: A string representing to hex triplet code of a color
+ from_schema: https://w3id.org/my-org/anatomical-structure-schema
+ rank: 1000
+ domain_of:
+ - ParcellationColorAssignment
+ range: string
+ structured_pattern:
+ syntax: '{ColorHexTriplet}'
+
+name: ParcellationColorAssignment
+description: The parcellation color assignment associates hex color value to a parcellation
+ term within a versioned release of a color scheme. A parcellation term is uniquely
+ denoted by a parcellation term identifier and the parcellation terminology it belongs
+ to.
+from_schema: https://w3id.org/my-org/anatomical-structure-schema
+attributes:
+ part_of_parcellation_color_scheme:
+ name: part_of_parcellation_color_scheme
+ description: Reference to the parcellation color scheme for which the color assignment
+ is part of.
+ from_schema: https://w3id.org/my-org/anatomical-structure-schema
+ rank: 1000
+ alias: part_of_parcellation_color_scheme
+ owner: ParcellationColorAssignment
+ domain_of:
+ - ParcellationColorAssignment
+ range: string
+ required: true
+ any_of:
+ - range: ParcellationColorScheme
+ - range: string
+ subject_parcellation_term:
+ name: subject_parcellation_term
+ description: Reference to the parcellation term identifier for which the color
+ assignment is about.
+ from_schema: https://w3id.org/my-org/anatomical-structure-schema
+ rank: 1000
+ alias: subject_parcellation_term
+ owner: ParcellationColorAssignment
+ domain_of:
+ - ParcellationColorAssignment
+ - ParcellationAnnotationTermMap
+ range: string
+ required: true
+ any_of:
+ - range: ParcellationTerm
+ - range: string
+ color:
+ name: color
+ description: A string representing to hex triplet code of a color
+ from_schema: https://w3id.org/my-org/anatomical-structure-schema
+ rank: 1000
+ alias: color
+ owner: ParcellationColorAssignment
+ domain_of:
+ - ParcellationColorAssignment
+ range: string
+ structured_pattern:
+ syntax: '{ColorHexTriplet}'
+
+A parcellation color scheme is a versioned release color palette that can be used to visualize a parcellation terminology or its related parcellation annotation. A parcellation terminology may have zero or more parcellation color schemes and each color scheme is in context of a specific parcellation terminology, where each parcellation term is assigned a hex color value. A parcellation color scheme is defined as a part of one and only one parcellation terminology.
+URI: AnS:ParcellationColorScheme
+| Name | +Cardinality and Range | +Description | +Inheritance | +
|---|---|---|---|
| subject_parcellation_terminology | +1 String or ParcellationTerminology or String |
+Reference to the parcellation terminology for which the parcellation color sc... | +direct | +
| version | +1 String |
++ | VersionedNamedThing | +
| revision_of | +0..1 VersionedNamedThing or ParcellationColorScheme or String |
++ | VersionedNamedThing | +
| id | +1 Uriorcurie |
++ | NamedThing | +
| name | +1 String |
++ | NamedThing | +
| description | +1 String |
++ | NamedThing | +
| category | +* Uriorcurie |
++ | NamedThing | +
| used by | +used in | +type | +used | +
|---|---|---|---|
| ParcellationColorScheme | +revision_of | +any_of[range] | +ParcellationColorScheme | +
| ParcellationColorAssignment | +part_of_parcellation_color_scheme | +any_of[range] | +ParcellationColorScheme | +
| Mapping Type | +Mapped Value | +
|---|---|
| self | +AnS:ParcellationColorScheme | +
| native | +AnS:ParcellationColorScheme | +
name: ParcellationColorScheme
+description: A parcellation color scheme is a versioned release color palette that
+ can be used to visualize a parcellation terminology or its related parcellation
+ annotation. A parcellation terminology may have zero or more parcellation color
+ schemes and each color scheme is in context of a specific parcellation terminology,
+ where each parcellation term is assigned a hex color value. A parcellation color
+ scheme is defined as a part of one and only one parcellation terminology.
+from_schema: https://w3id.org/my-org/anatomical-structure-schema
+is_a: VersionedNamedThing
+slot_usage:
+ revision_of:
+ name: revision_of
+ any_of:
+ - range: ParcellationColorScheme
+ - range: string
+attributes:
+ subject_parcellation_terminology:
+ name: subject_parcellation_terminology
+ description: Reference to the parcellation terminology for which the parcellation
+ color scheme is in context of.
+ from_schema: https://w3id.org/my-org/anatomical-structure-schema
+ rank: 1000
+ domain_of:
+ - ParcellationColorScheme
+ required: true
+ any_of:
+ - range: ParcellationTerminology
+ - range: string
+
+name: ParcellationColorScheme
+description: A parcellation color scheme is a versioned release color palette that
+ can be used to visualize a parcellation terminology or its related parcellation
+ annotation. A parcellation terminology may have zero or more parcellation color
+ schemes and each color scheme is in context of a specific parcellation terminology,
+ where each parcellation term is assigned a hex color value. A parcellation color
+ scheme is defined as a part of one and only one parcellation terminology.
+from_schema: https://w3id.org/my-org/anatomical-structure-schema
+is_a: VersionedNamedThing
+slot_usage:
+ revision_of:
+ name: revision_of
+ any_of:
+ - range: ParcellationColorScheme
+ - range: string
+attributes:
+ subject_parcellation_terminology:
+ name: subject_parcellation_terminology
+ description: Reference to the parcellation terminology for which the parcellation
+ color scheme is in context of.
+ from_schema: https://w3id.org/my-org/anatomical-structure-schema
+ rank: 1000
+ alias: subject_parcellation_terminology
+ owner: ParcellationColorScheme
+ domain_of:
+ - ParcellationColorScheme
+ range: string
+ required: true
+ any_of:
+ - range: ParcellationTerminology
+ - range: string
+ version:
+ name: version
+ from_schema: https://w3id.org/my-org/anatomical-structure-schema
+ rank: 1000
+ alias: version
+ owner: ParcellationColorScheme
+ domain_of:
+ - VersionedNamedThing
+ range: string
+ required: true
+ revision_of:
+ name: revision_of
+ from_schema: https://w3id.org/my-org/anatomical-structure-schema
+ rank: 1000
+ alias: revision_of
+ owner: ParcellationColorScheme
+ domain_of:
+ - VersionedNamedThing
+ range: VersionedNamedThing
+ any_of:
+ - range: ParcellationColorScheme
+ - range: string
+ id:
+ name: id
+ from_schema: https://w3id.org/my-org/anatomical-structure-schema
+ rank: 1000
+ identifier: true
+ alias: id
+ owner: ParcellationColorScheme
+ domain_of:
+ - NamedThing
+ range: uriorcurie
+ required: true
+ name:
+ name: name
+ from_schema: https://w3id.org/my-org/anatomical-structure-schema
+ rank: 1000
+ alias: name
+ owner: ParcellationColorScheme
+ domain_of:
+ - NamedThing
+ range: string
+ required: true
+ description:
+ name: description
+ from_schema: https://w3id.org/my-org/anatomical-structure-schema
+ rank: 1000
+ alias: description
+ owner: ParcellationColorScheme
+ domain_of:
+ - NamedThing
+ range: string
+ required: true
+ category:
+ name: category
+ from_schema: https://w3id.org/my-org/anatomical-structure-schema
+ rank: 1000
+ designates_type: true
+ alias: category
+ owner: ParcellationColorScheme
+ domain_of:
+ - NamedThing
+ is_class_field: true
+ range: uriorcurie
+ multivalued: true
+
+A parcellation term is an individual term within a specific parcellation terminology describing a single anatomical entity by a persistent identifier, name, symbol and description. A parcellation term is a unique and exclusive member of a versioned release parcellation terminology. Although term identifiers must be unique within the context of one versioned release of a parcellation terminology, they can be reused in different parcellation terminology versions enabling the representation of terminology updates and modifications over time.
+URI: AnS:ParcellationTerm
+| Name | +Cardinality and Range | +Description | +Inheritance | +
|---|---|---|---|
| symbol | +0..1 String |
+Symbol representing a parcellation term | +direct | +
| part_of_parcellation_term_set | +1 String or ParcellationTermSet or String |
+Reference to the parcellation term set for which the parcellation term is par... | +direct | +
| ordinal | +0..1 Integer |
+Ordinal of the parcellation term among other terms within the context of the ... | +direct | +
| has_parent_parcellation_term | +0..1 String or ParcellationTerm or String |
+Reference to the parent parcellation term for which the parcellation term is ... | +direct | +
| id | +1 Uriorcurie |
++ | NamedThing | +
| name | +1 String |
++ | NamedThing | +
| description | +1 String |
++ | NamedThing | +
| category | +* Uriorcurie |
++ | NamedThing | +
| used by | +used in | +type | +used | +
|---|---|---|---|
| ParcellationTerm | +has_parent_parcellation_term | +any_of[range] | +ParcellationTerm | +
| ParcellationColorAssignment | +subject_parcellation_term | +any_of[range] | +ParcellationTerm | +
| ParcellationAnnotationTermMap | +subject_parcellation_term | +any_of[range] | +ParcellationTerm | +
| Mapping Type | +Mapped Value | +
|---|---|
| self | +AnS:ParcellationTerm | +
| native | +AnS:ParcellationTerm | +
name: ParcellationTerm
+description: A parcellation term is an individual term within a specific parcellation
+ terminology describing a single anatomical entity by a persistent identifier, name,
+ symbol and description. A parcellation term is a unique and exclusive member of
+ a versioned release parcellation terminology. Although term identifiers must be
+ unique within the context of one versioned release of a parcellation terminology, they
+ can be reused in different parcellation terminology versions enabling the representation
+ of terminology updates and modifications over time.
+from_schema: https://w3id.org/my-org/anatomical-structure-schema
+is_a: NamedThing
+attributes:
+ symbol:
+ name: symbol
+ description: Symbol representing a parcellation term.
+ from_schema: https://w3id.org/my-org/anatomical-structure-schema
+ rank: 1000
+ domain_of:
+ - ParcellationTerm
+ part_of_parcellation_term_set:
+ name: part_of_parcellation_term_set
+ description: Reference to the parcellation term set for which the parcellation
+ term is part of.
+ from_schema: https://w3id.org/my-org/anatomical-structure-schema
+ rank: 1000
+ domain_of:
+ - ParcellationTerm
+ required: true
+ any_of:
+ - range: ParcellationTermSet
+ - range: string
+ ordinal:
+ name: ordinal
+ description: Ordinal of the parcellation term among other terms within the context
+ of the associated parcellation terminology.
+ from_schema: https://w3id.org/my-org/anatomical-structure-schema
+ domain_of:
+ - ParcellationTermSet
+ - ParcellationTerm
+ range: integer
+ minimum_value: 0
+ has_parent_parcellation_term:
+ name: has_parent_parcellation_term
+ description: Reference to the parent parcellation term for which the parcellation
+ term is a child ( spatially part) of
+ from_schema: https://w3id.org/my-org/anatomical-structure-schema
+ rank: 1000
+ domain_of:
+ - ParcellationTerm
+ any_of:
+ - range: ParcellationTerm
+ - range: string
+
+name: ParcellationTerm
+description: A parcellation term is an individual term within a specific parcellation
+ terminology describing a single anatomical entity by a persistent identifier, name,
+ symbol and description. A parcellation term is a unique and exclusive member of
+ a versioned release parcellation terminology. Although term identifiers must be
+ unique within the context of one versioned release of a parcellation terminology, they
+ can be reused in different parcellation terminology versions enabling the representation
+ of terminology updates and modifications over time.
+from_schema: https://w3id.org/my-org/anatomical-structure-schema
+is_a: NamedThing
+attributes:
+ symbol:
+ name: symbol
+ description: Symbol representing a parcellation term.
+ from_schema: https://w3id.org/my-org/anatomical-structure-schema
+ rank: 1000
+ alias: symbol
+ owner: ParcellationTerm
+ domain_of:
+ - ParcellationTerm
+ range: string
+ part_of_parcellation_term_set:
+ name: part_of_parcellation_term_set
+ description: Reference to the parcellation term set for which the parcellation
+ term is part of.
+ from_schema: https://w3id.org/my-org/anatomical-structure-schema
+ rank: 1000
+ alias: part_of_parcellation_term_set
+ owner: ParcellationTerm
+ domain_of:
+ - ParcellationTerm
+ range: string
+ required: true
+ any_of:
+ - range: ParcellationTermSet
+ - range: string
+ ordinal:
+ name: ordinal
+ description: Ordinal of the parcellation term among other terms within the context
+ of the associated parcellation terminology.
+ from_schema: https://w3id.org/my-org/anatomical-structure-schema
+ alias: ordinal
+ owner: ParcellationTerm
+ domain_of:
+ - ParcellationTermSet
+ - ParcellationTerm
+ range: integer
+ minimum_value: 0
+ has_parent_parcellation_term:
+ name: has_parent_parcellation_term
+ description: Reference to the parent parcellation term for which the parcellation
+ term is a child ( spatially part) of
+ from_schema: https://w3id.org/my-org/anatomical-structure-schema
+ rank: 1000
+ alias: has_parent_parcellation_term
+ owner: ParcellationTerm
+ domain_of:
+ - ParcellationTerm
+ range: string
+ any_of:
+ - range: ParcellationTerm
+ - range: string
+ id:
+ name: id
+ from_schema: https://w3id.org/my-org/anatomical-structure-schema
+ rank: 1000
+ identifier: true
+ alias: id
+ owner: ParcellationTerm
+ domain_of:
+ - NamedThing
+ range: uriorcurie
+ required: true
+ name:
+ name: name
+ from_schema: https://w3id.org/my-org/anatomical-structure-schema
+ rank: 1000
+ alias: name
+ owner: ParcellationTerm
+ domain_of:
+ - NamedThing
+ range: string
+ required: true
+ description:
+ name: description
+ from_schema: https://w3id.org/my-org/anatomical-structure-schema
+ rank: 1000
+ alias: description
+ owner: ParcellationTerm
+ domain_of:
+ - NamedThing
+ range: string
+ required: true
+ category:
+ name: category
+ from_schema: https://w3id.org/my-org/anatomical-structure-schema
+ rank: 1000
+ designates_type: true
+ alias: category
+ owner: ParcellationTerm
+ domain_of:
+ - NamedThing
+ is_class_field: true
+ range: uriorcurie
+ multivalued: true
+
+A parcellation term set is the set of parcellation terms within a specific parcellation terminology. A parcellation term set belongs to one and only one parcellation terminology and each parcellation term in a parcellation terminology belongs to one and only one term set. If the parcellation terminology is a taxonomy, parcellation term sets can be used to represent taxonomic ranks. For consistency, if the terminology does not have the notion of taxonomic ranks, all terms are grouped into a single parcellation term set.
+ +| Name | +Cardinality and Range | +Description | +Inheritance | +
|---|---|---|---|
| part_of_parcellation_terminology | +1 String or ParcellationTerminology or String |
+Reference to the parcellation terminology for which the parcellation term set... | +direct | +
| ordinal | +0..1 Integer |
+Ordinal of the parcellation term set among other term sets within the context... | +direct | +
| has_parent_parcellation_term_set | +0..1 String or ParcellationTermSet or String |
+Reference to the parent parcellation term set for which the parcellation term... | +direct | +
| id | +1 Uriorcurie |
++ | NamedThing | +
| name | +1 String |
++ | NamedThing | +
| description | +1 String |
++ | NamedThing | +
| category | +* Uriorcurie |
++ | NamedThing | +
| used by | +used in | +type | +used | +
|---|---|---|---|
| ParcellationTermSet | +has_parent_parcellation_term_set | +any_of[range] | +ParcellationTermSet | +
| ParcellationTerm | +part_of_parcellation_term_set | +any_of[range] | +ParcellationTermSet | +
| Mapping Type | +Mapped Value | +
|---|---|
| self | +AnS:ParcellationTermSet | +
| native | +AnS:ParcellationTermSet | +
name: ParcellationTermSet
+description: A parcellation term set is the set of parcellation terms within a specific
+ parcellation terminology. A parcellation term set belongs to one and only one parcellation
+ terminology and each parcellation term in a parcellation terminology belongs to
+ one and only one term set. If the parcellation terminology is a taxonomy, parcellation
+ term sets can be used to represent taxonomic ranks. For consistency, if the terminology
+ does not have the notion of taxonomic ranks, all terms are grouped into a single
+ parcellation term set.
+from_schema: https://w3id.org/my-org/anatomical-structure-schema
+is_a: NamedThing
+attributes:
+ part_of_parcellation_terminology:
+ name: part_of_parcellation_terminology
+ description: Reference to the parcellation terminology for which the parcellation
+ term set partitions.
+ from_schema: https://w3id.org/my-org/anatomical-structure-schema
+ rank: 1000
+ domain_of:
+ - ParcellationTermSet
+ required: true
+ any_of:
+ - range: ParcellationTerminology
+ - range: string
+ ordinal:
+ name: ordinal
+ description: Ordinal of the parcellation term set among other term sets within
+ the context of the associated parcellation terminology.
+ from_schema: https://w3id.org/my-org/anatomical-structure-schema
+ rank: 1000
+ domain_of:
+ - ParcellationTermSet
+ - ParcellationTerm
+ range: integer
+ minimum_value: 0
+ has_parent_parcellation_term_set:
+ name: has_parent_parcellation_term_set
+ description: Reference to the parent parcellation term set for which the parcellation
+ term set is a child (lower taxonomic rank) of.
+ from_schema: https://w3id.org/my-org/anatomical-structure-schema
+ rank: 1000
+ domain_of:
+ - ParcellationTermSet
+ any_of:
+ - range: ParcellationTermSet
+ - range: string
+
+name: ParcellationTermSet
+description: A parcellation term set is the set of parcellation terms within a specific
+ parcellation terminology. A parcellation term set belongs to one and only one parcellation
+ terminology and each parcellation term in a parcellation terminology belongs to
+ one and only one term set. If the parcellation terminology is a taxonomy, parcellation
+ term sets can be used to represent taxonomic ranks. For consistency, if the terminology
+ does not have the notion of taxonomic ranks, all terms are grouped into a single
+ parcellation term set.
+from_schema: https://w3id.org/my-org/anatomical-structure-schema
+is_a: NamedThing
+attributes:
+ part_of_parcellation_terminology:
+ name: part_of_parcellation_terminology
+ description: Reference to the parcellation terminology for which the parcellation
+ term set partitions.
+ from_schema: https://w3id.org/my-org/anatomical-structure-schema
+ rank: 1000
+ alias: part_of_parcellation_terminology
+ owner: ParcellationTermSet
+ domain_of:
+ - ParcellationTermSet
+ range: string
+ required: true
+ any_of:
+ - range: ParcellationTerminology
+ - range: string
+ ordinal:
+ name: ordinal
+ description: Ordinal of the parcellation term set among other term sets within
+ the context of the associated parcellation terminology.
+ from_schema: https://w3id.org/my-org/anatomical-structure-schema
+ rank: 1000
+ alias: ordinal
+ owner: ParcellationTermSet
+ domain_of:
+ - ParcellationTermSet
+ - ParcellationTerm
+ range: integer
+ minimum_value: 0
+ has_parent_parcellation_term_set:
+ name: has_parent_parcellation_term_set
+ description: Reference to the parent parcellation term set for which the parcellation
+ term set is a child (lower taxonomic rank) of.
+ from_schema: https://w3id.org/my-org/anatomical-structure-schema
+ rank: 1000
+ alias: has_parent_parcellation_term_set
+ owner: ParcellationTermSet
+ domain_of:
+ - ParcellationTermSet
+ range: string
+ any_of:
+ - range: ParcellationTermSet
+ - range: string
+ id:
+ name: id
+ from_schema: https://w3id.org/my-org/anatomical-structure-schema
+ rank: 1000
+ identifier: true
+ alias: id
+ owner: ParcellationTermSet
+ domain_of:
+ - NamedThing
+ range: uriorcurie
+ required: true
+ name:
+ name: name
+ from_schema: https://w3id.org/my-org/anatomical-structure-schema
+ rank: 1000
+ alias: name
+ owner: ParcellationTermSet
+ domain_of:
+ - NamedThing
+ range: string
+ required: true
+ description:
+ name: description
+ from_schema: https://w3id.org/my-org/anatomical-structure-schema
+ rank: 1000
+ alias: description
+ owner: ParcellationTermSet
+ domain_of:
+ - NamedThing
+ range: string
+ required: true
+ category:
+ name: category
+ from_schema: https://w3id.org/my-org/anatomical-structure-schema
+ rank: 1000
+ designates_type: true
+ alias: category
+ owner: ParcellationTermSet
+ domain_of:
+ - NamedThing
+ is_class_field: true
+ range: uriorcurie
+ multivalued: true
+
+A parcellation terminology is a versioned release set of terms that can be used to label annotations in an atlas, providing human readability and context and allowing communication about brain locations and structural properties. Typically, a terminology is a set of descriptive anatomical terms following a specific naming convention and/or approach to organization scheme. The terminology may be a flat list of controlled vocabulary, a taxonomy and partonomy, or an ontology (ref: ILX:0777107, RRID:SCR_023499)
+URI: AnS:ParcellationTerminology
+| Name | +Cardinality and Range | +Description | +Inheritance | +
|---|---|---|---|
| version | +1 String |
++ | VersionedNamedThing | +
| revision_of | +0..1 VersionedNamedThing or ParcellationTerminology or String |
++ | VersionedNamedThing | +
| id | +1 Uriorcurie |
++ | NamedThing | +
| name | +1 String |
++ | NamedThing | +
| description | +1 String |
++ | NamedThing | +
| category | +* Uriorcurie |
++ | NamedThing | +
| used by | +used in | +type | +used | +
|---|---|---|---|
| ParcellationTerminology | +revision_of | +any_of[range] | +ParcellationTerminology | +
| ParcellationTermSet | +part_of_parcellation_terminology | +any_of[range] | +ParcellationTerminology | +
| ParcellationColorScheme | +subject_parcellation_terminology | +any_of[range] | +ParcellationTerminology | +
| ParcellationAtlas | +has_parcellation_terminology | +any_of[range] | +ParcellationTerminology | +
| Mapping Type | +Mapped Value | +
|---|---|
| self | +AnS:ParcellationTerminology | +
| native | +AnS:ParcellationTerminology | +
name: ParcellationTerminology
+description: 'A parcellation terminology is a versioned release set of terms that
+ can be used to label annotations in an atlas, providing human readability and context
+ and allowing communication about brain locations and structural properties. Typically,
+ a terminology is a set of descriptive anatomical terms following a specific naming
+ convention and/or approach to organization scheme. The terminology may be a flat
+ list of controlled vocabulary, a taxonomy and partonomy, or an ontology (ref: ILX:0777107,
+ RRID:SCR_023499)'
+from_schema: https://w3id.org/my-org/anatomical-structure-schema
+is_a: VersionedNamedThing
+slot_usage:
+ revision_of:
+ name: revision_of
+ any_of:
+ - range: ParcellationTerminology
+ - range: string
+
+name: ParcellationTerminology
+description: 'A parcellation terminology is a versioned release set of terms that
+ can be used to label annotations in an atlas, providing human readability and context
+ and allowing communication about brain locations and structural properties. Typically,
+ a terminology is a set of descriptive anatomical terms following a specific naming
+ convention and/or approach to organization scheme. The terminology may be a flat
+ list of controlled vocabulary, a taxonomy and partonomy, or an ontology (ref: ILX:0777107,
+ RRID:SCR_023499)'
+from_schema: https://w3id.org/my-org/anatomical-structure-schema
+is_a: VersionedNamedThing
+slot_usage:
+ revision_of:
+ name: revision_of
+ any_of:
+ - range: ParcellationTerminology
+ - range: string
+attributes:
+ version:
+ name: version
+ from_schema: https://w3id.org/my-org/anatomical-structure-schema
+ rank: 1000
+ alias: version
+ owner: ParcellationTerminology
+ domain_of:
+ - VersionedNamedThing
+ range: string
+ required: true
+ revision_of:
+ name: revision_of
+ from_schema: https://w3id.org/my-org/anatomical-structure-schema
+ rank: 1000
+ alias: revision_of
+ owner: ParcellationTerminology
+ domain_of:
+ - VersionedNamedThing
+ range: VersionedNamedThing
+ any_of:
+ - range: ParcellationTerminology
+ - range: string
+ id:
+ name: id
+ from_schema: https://w3id.org/my-org/anatomical-structure-schema
+ rank: 1000
+ identifier: true
+ alias: id
+ owner: ParcellationTerminology
+ domain_of:
+ - NamedThing
+ range: uriorcurie
+ required: true
+ name:
+ name: name
+ from_schema: https://w3id.org/my-org/anatomical-structure-schema
+ rank: 1000
+ alias: name
+ owner: ParcellationTerminology
+ domain_of:
+ - NamedThing
+ range: string
+ required: true
+ description:
+ name: description
+ from_schema: https://w3id.org/my-org/anatomical-structure-schema
+ rank: 1000
+ alias: description
+ owner: ParcellationTerminology
+ domain_of:
+ - NamedThing
+ range: string
+ required: true
+ category:
+ name: category
+ from_schema: https://w3id.org/my-org/anatomical-structure-schema
+ rank: 1000
+ designates_type: true
+ alias: category
+ owner: ParcellationTerminology
+ domain_of:
+ - NamedThing
+ is_class_field: true
+ range: uriorcurie
+ multivalued: true
+
+URI: UO:0000187
+ +| Mapping Type | +Mapped Value | +
|---|---|
| self | +UO:0000187 | +
| native | +bican:percentage_frequency_value | +
An entity that has material reality (a.k.a. physical essence).
+ +| Name | +Cardinality and Range | +Description | +Inheritance | +
|---|---|---|---|
| id | +1 String |
+A unique identifier for an entity | +direct | +
| iri | +0..1 IriType |
+An IRI for an entity | +direct | +
| category | +* Uriorcurie |
+Name of the high level ontology class in which this entity is categorized | +direct | +
| type | +* String |
++ | direct | +
| name | +0..1 LabelType |
+A human-readable name for an attribute or entity | +direct | +
| description | +0..1 NarrativeText |
+a human-readable description of an entity | +direct | +
| has_attribute | +* Attribute |
+connects any entity to an attribute | +direct | +
| deprecated | +0..1 Boolean |
+A boolean flag indicating that an entity is no longer considered current or v... | +direct | +
| provided_by | +* String |
+The value in this node property represents the knowledge provider that create... | +direct | +
| xref | +* Uriorcurie |
+A database cross reference or alternative identifier for a NamedThing or edge... | +direct | +
| full_name | +0..1 LabelType |
+a long-form human readable name for a thing | +direct | +
| synonym | +* LabelType |
+Alternate human-readable names for a thing | +direct | +
| Mapping Type | +Mapped Value | +
|---|---|
| self | +biolink:PhysicalEntity | +
| native | +bican:PhysicalEntity | +
| exact | +STY:T072 | +
| narrow | +STY:T073 | +
name: physical entity
+definition_uri: https://w3id.org/biolink/vocab/PhysicalEntity
+description: An entity that has material reality (a.k.a. physical essence).
+from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
+exact_mappings:
+- STY:T072
+narrow_mappings:
+- STY:T073
+is_a: named thing
+mixins:
+- physical essence
+slots:
+- id
+- iri
+- category
+- type
+- name
+- description
+- has attribute
+- deprecated
+- provided by
+- xref
+- full name
+- synonym
+class_uri: biolink:PhysicalEntity
+
+name: physical entity
+definition_uri: https://w3id.org/biolink/vocab/PhysicalEntity
+description: An entity that has material reality (a.k.a. physical essence).
+from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
+exact_mappings:
+- STY:T072
+narrow_mappings:
+- STY:T073
+is_a: named thing
+mixins:
+- physical essence
+attributes:
+ id:
+ name: id
+ definition_uri: https://w3id.org/biolink/vocab/id
+ description: A unique identifier for an entity. Must be either a CURIE shorthand
+ for a URI or a complete URI
+ in_subset:
+ - translator_minimal
+ from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
+ exact_mappings:
+ - AGRKB:primaryId
+ - gff3:ID
+ - gpi:DB_Object_ID
+ rank: 1000
+ domain: entity
+ slot_uri: biolink:id
+ identifier: true
+ alias: id
+ owner: physical entity
+ domain_of:
+ - ontology class
+ - entity
+ - attribute
+ - named thing
+ - taxonomic rank
+ - organism taxon
+ - information content entity
+ - dataset
+ - physical entity
+ - activity
+ - procedure
+ - material sample
+ - biological entity
+ - gene
+ - genome
+ range: string
+ required: true
+ iri:
+ name: iri
+ definition_uri: https://w3id.org/biolink/vocab/iri
+ description: An IRI for an entity. This is determined by the id using expansion
+ rules.
+ in_subset:
+ - translator_minimal
+ - samples
+ from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
+ exact_mappings:
+ - WIKIDATA_PROPERTY:P854
+ rank: 1000
+ slot_uri: biolink:iri
+ alias: iri
+ owner: physical entity
+ domain_of:
+ - attribute
+ - entity
+ - named thing
+ - organism taxon
+ - information content entity
+ - dataset
+ - physical entity
+ - activity
+ - procedure
+ - material sample
+ - biological entity
+ - gene
+ - genome
+ range: iri type
+ category:
+ name: category
+ definition_uri: https://w3id.org/biolink/vocab/category
+ description: Name of the high level ontology class in which this entity is categorized.
+ Corresponds to the label for the biolink entity type class. In a neo4j database
+ this MAY correspond to the neo4j label tag. In an RDF database it should be
+ a biolink model class URI. This field is multi-valued. It should include values
+ for ancestors of the biolink class; for example, a protein such as Shh would
+ have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`.
+ In an RDF database, nodes will typically have an rdf:type triples. This can
+ be to the most specific biolink class, or potentially to a class more specific
+ than something in biolink. For example, a sequence feature `f` may have a rdf:type
+ assertion to a SO class such as TF_binding_site, which is more specific than
+ anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity,
+ biolink:NamedThing}
+ in_subset:
+ - translator_minimal
+ from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
+ rank: 1000
+ is_a: type
+ domain: entity
+ slot_uri: biolink:category
+ designates_type: true
+ alias: category
+ owner: physical entity
+ domain_of:
+ - entity
+ - attribute
+ - named thing
+ - organism taxon
+ - information content entity
+ - dataset
+ - physical entity
+ - activity
+ - procedure
+ - material sample
+ - biological entity
+ - gene
+ - genome
+ is_class_field: true
+ range: uriorcurie
+ multivalued: true
+ type:
+ name: type
+ definition_uri: https://w3id.org/biolink/vocab/type
+ from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
+ mappings:
+ - rdf:type
+ exact_mappings:
+ - gff3:type
+ - gpi:DB_Object_Type
+ rank: 1000
+ domain: entity
+ slot_uri: rdf:type
+ alias: type
+ owner: physical entity
+ domain_of:
+ - entity
+ - attribute
+ - named thing
+ - organism taxon
+ - information content entity
+ - dataset
+ - physical entity
+ - activity
+ - procedure
+ - material sample
+ - biological entity
+ - gene
+ - genome
+ range: string
+ multivalued: true
+ name:
+ name: name
+ definition_uri: https://w3id.org/biolink/vocab/name
+ description: A human-readable name for an attribute or entity.
+ in_subset:
+ - translator_minimal
+ - samples
+ from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
+ aliases:
+ - label
+ - display name
+ - title
+ mappings:
+ - rdfs:label
+ exact_mappings:
+ - gff3:Name
+ - gpi:DB_Object_Name
+ narrow_mappings:
+ - dct:title
+ - WIKIDATA_PROPERTY:P1476
+ rank: 1000
+ domain: entity
+ slot_uri: rdfs:label
+ alias: name
+ owner: physical entity
+ domain_of:
+ - attribute
+ - entity
+ - macromolecular machine mixin
+ - named thing
+ - organism taxon
+ - information content entity
+ - dataset
+ - physical entity
+ - activity
+ - procedure
+ - material sample
+ - biological entity
+ - gene or gene product
+ - gene
+ - genome
+ range: label type
+ description:
+ name: description
+ definition_uri: https://w3id.org/biolink/vocab/description
+ description: a human-readable description of an entity
+ in_subset:
+ - translator_minimal
+ from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
+ aliases:
+ - definition
+ mappings:
+ - dct:description
+ exact_mappings:
+ - IAO:0000115
+ - skos:definitions
+ narrow_mappings:
+ - gff3:Description
+ rank: 1000
+ slot_uri: dct:description
+ alias: description
+ owner: physical entity
+ domain_of:
+ - entity
+ - attribute
+ - named thing
+ - organism taxon
+ - information content entity
+ - dataset
+ - physical entity
+ - activity
+ - procedure
+ - material sample
+ - biological entity
+ - gene
+ - genome
+ range: narrative text
+ has attribute:
+ name: has attribute
+ definition_uri: https://w3id.org/biolink/vocab/has_attribute
+ description: connects any entity to an attribute
+ in_subset:
+ - samples
+ from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
+ exact_mappings:
+ - SIO:000008
+ close_mappings:
+ - OBI:0001927
+ narrow_mappings:
+ - OBAN:association_has_subject_property
+ - OBAN:association_has_object_property
+ - CPT:has_possibly_included_panel_element
+ - DRUGBANK:category
+ - EFO:is_executed_in
+ - HANCESTRO:0301
+ - LOINC:has_action_guidance
+ - LOINC:has_adjustment
+ - LOINC:has_aggregation_view
+ - LOINC:has_approach_guidance
+ - LOINC:has_divisor
+ - LOINC:has_exam
+ - LOINC:has_method
+ - LOINC:has_modality_subtype
+ - LOINC:has_object_guidance
+ - LOINC:has_scale
+ - LOINC:has_suffix
+ - LOINC:has_time_aspect
+ - LOINC:has_time_modifier
+ - LOINC:has_timing_of
+ - NCIT:R88
+ - NCIT:eo_disease_has_property_or_attribute
+ - NCIT:has_data_element
+ - NCIT:has_pharmaceutical_administration_method
+ - NCIT:has_pharmaceutical_basic_dose_form
+ - NCIT:has_pharmaceutical_intended_site
+ - NCIT:has_pharmaceutical_release_characteristics
+ - NCIT:has_pharmaceutical_state_of_matter
+ - NCIT:has_pharmaceutical_transformation
+ - NCIT:is_qualified_by
+ - NCIT:qualifier_applies_to
+ - NCIT:role_has_domain
+ - NCIT:role_has_range
+ - INO:0000154
+ - HANCESTRO:0308
+ - OMIM:has_inheritance_type
+ - orphanet:C016
+ - orphanet:C017
+ - RO:0000053
+ - RO:0000086
+ - RO:0000087
+ - SNOMED:has_access
+ - SNOMED:has_clinical_course
+ - SNOMED:has_count_of_base_of_active_ingredient
+ - SNOMED:has_dose_form_administration_method
+ - SNOMED:has_dose_form_release_characteristic
+ - SNOMED:has_dose_form_transformation
+ - SNOMED:has_finding_context
+ - SNOMED:has_finding_informer
+ - SNOMED:has_inherent_attribute
+ - SNOMED:has_intent
+ - SNOMED:has_interpretation
+ - SNOMED:has_laterality
+ - SNOMED:has_measurement_method
+ - SNOMED:has_method
+ - SNOMED:has_priority
+ - SNOMED:has_procedure_context
+ - SNOMED:has_process_duration
+ - SNOMED:has_property
+ - SNOMED:has_revision_status
+ - SNOMED:has_scale_type
+ - SNOMED:has_severity
+ - SNOMED:has_specimen
+ - SNOMED:has_state_of_matter
+ - SNOMED:has_subject_relationship_context
+ - SNOMED:has_surgical_approach
+ - SNOMED:has_technique
+ - SNOMED:has_temporal_context
+ - SNOMED:has_time_aspect
+ - SNOMED:has_units
+ - UMLS:has_structural_class
+ - UMLS:has_supported_concept_property
+ - UMLS:has_supported_concept_relationship
+ - UMLS:may_be_qualified_by
+ rank: 1000
+ domain: entity
+ slot_uri: biolink:has_attribute
+ alias: has_attribute
+ owner: physical entity
+ domain_of:
+ - entity
+ - attribute
+ - named thing
+ - organism taxon
+ - information content entity
+ - dataset
+ - physical entity
+ - activity
+ - procedure
+ - material sample
+ - biological entity
+ - gene
+ - genome
+ range: attribute
+ multivalued: true
+ deprecated:
+ name: deprecated
+ definition_uri: https://w3id.org/biolink/vocab/deprecated
+ description: A boolean flag indicating that an entity is no longer considered
+ current or valid.
+ from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
+ exact_mappings:
+ - oboInOwl:ObsoleteClass
+ rank: 1000
+ slot_uri: biolink:deprecated
+ alias: deprecated
+ owner: physical entity
+ domain_of:
+ - entity
+ - attribute
+ - named thing
+ - organism taxon
+ - information content entity
+ - dataset
+ - physical entity
+ - activity
+ - procedure
+ - material sample
+ - biological entity
+ - gene
+ - genome
+ range: boolean
+ provided by:
+ name: provided by
+ definition_uri: https://w3id.org/biolink/vocab/provided_by
+ description: The value in this node property represents the knowledge provider
+ that created or assembled the node and all of its attributes. Used internally
+ to represent how a particular node made its way into a knowledge provider or
+ graph.
+ from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
+ rank: 1000
+ is_a: node property
+ domain: named thing
+ slot_uri: biolink:provided_by
+ alias: provided_by
+ owner: physical entity
+ domain_of:
+ - named thing
+ - attribute
+ - organism taxon
+ - information content entity
+ - dataset
+ - physical entity
+ - activity
+ - procedure
+ - material sample
+ - biological entity
+ - gene
+ - genome
+ range: string
+ multivalued: true
+ xref:
+ name: xref
+ definition_uri: https://w3id.org/biolink/vocab/xref
+ description: A database cross reference or alternative identifier for a NamedThing
+ or edge between two NamedThings. This property should point to a database record
+ or webpage that supports the existence of the edge, or gives more detail about
+ the edge. This property can be used on a node or edge to provide multiple URIs
+ or CURIE cross references.
+ in_subset:
+ - translator_minimal
+ from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
+ aliases:
+ - dbxref
+ - Dbxref
+ - DbXref
+ - record_url
+ - source_record_urls
+ narrow_mappings:
+ - gff3:Dbxref
+ - gpi:DB_Xrefs
+ rank: 1000
+ domain: named thing
+ slot_uri: biolink:xref
+ alias: xref
+ owner: physical entity
+ domain_of:
+ - named thing
+ - gene
+ - attribute
+ - organism taxon
+ - information content entity
+ - dataset
+ - physical entity
+ - activity
+ - procedure
+ - material sample
+ - biological entity
+ - genome
+ range: uriorcurie
+ multivalued: true
+ full name:
+ name: full name
+ definition_uri: https://w3id.org/biolink/vocab/full_name
+ description: a long-form human readable name for a thing
+ from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
+ rank: 1000
+ is_a: node property
+ domain: named thing
+ slot_uri: biolink:full_name
+ alias: full_name
+ owner: physical entity
+ domain_of:
+ - named thing
+ - attribute
+ - organism taxon
+ - information content entity
+ - dataset
+ - physical entity
+ - activity
+ - procedure
+ - material sample
+ - biological entity
+ - gene
+ - genome
+ range: label type
+ synonym:
+ name: synonym
+ definition_uri: https://w3id.org/biolink/vocab/synonym
+ description: Alternate human-readable names for a thing
+ in_subset:
+ - translator_minimal
+ from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
+ aliases:
+ - alias
+ narrow_mappings:
+ - skos:altLabel
+ - gff3:Alias
+ - AGRKB:synonyms
+ - gpi:DB_Object_Synonyms
+ - HANCESTRO:0330
+ - IAO:0000136
+ - RXNORM:has_tradename
+ rank: 1000
+ is_a: node property
+ domain: named thing
+ slot_uri: biolink:synonym
+ alias: synonym
+ owner: physical entity
+ domain_of:
+ - named thing
+ - attribute
+ - organism taxon
+ - information content entity
+ - dataset
+ - physical entity
+ - activity
+ - procedure
+ - material sample
+ - biological entity
+ - gene
+ - genome
+ range: label type
+ multivalued: true
+class_uri: biolink:PhysicalEntity
+
+Semantic mixin concept. Pertains to entities that have physical properties such as mass, volume, or charge.
+ +| Name | +Cardinality and Range | +Description | +Inheritance | +
|---|---|---|---|
| + | + | + | + |
| mixed into | +description | +
|---|---|
| PhysicalEntity | +An entity that has material reality (a | +
| Gene | +A region (or regions) that includes all of the sequence elements necessary to... | +
| Genome | +A genome is the sum of genetic material within a cell or virion | +
| Mapping Type | +Mapped Value | +
|---|---|
| self | +biolink:PhysicalEssence | +
| native | +bican:PhysicalEssence | +
name: physical essence
+definition_uri: https://w3id.org/biolink/vocab/PhysicalEssence
+description: Semantic mixin concept. Pertains to entities that have physical properties
+ such as mass, volume, or charge.
+from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
+is_a: physical essence or occurrent
+mixin: true
+class_uri: biolink:PhysicalEssence
+
+name: physical essence
+definition_uri: https://w3id.org/biolink/vocab/PhysicalEssence
+description: Semantic mixin concept. Pertains to entities that have physical properties
+ such as mass, volume, or charge.
+from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
+is_a: physical essence or occurrent
+mixin: true
+class_uri: biolink:PhysicalEssence
+
+Either a physical or processual entity.
+URI: biolink:PhysicalEssenceOrOccurrent
+| Name | +Cardinality and Range | +Description | +Inheritance | +
|---|---|---|---|
| + | + | + | + |
| mixed into | +description | +
|---|---|
| + | + |
| Mapping Type | +Mapped Value | +
|---|---|
| self | +biolink:PhysicalEssenceOrOccurrent | +
| native | +bican:PhysicalEssenceOrOccurrent | +
name: physical essence or occurrent
+definition_uri: https://w3id.org/biolink/vocab/PhysicalEssenceOrOccurrent
+description: Either a physical or processual entity.
+from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
+mixin: true
+class_uri: biolink:PhysicalEssenceOrOccurrent
+
+name: physical essence or occurrent
+definition_uri: https://w3id.org/biolink/vocab/PhysicalEssenceOrOccurrent
+description: Either a physical or processual entity.
+from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
+mixin: true
+class_uri: biolink:PhysicalEssenceOrOccurrent
+
+A CURIE from the biolink related_to hierarchy. For example, biolink:related_to, biolink:causes, biolink:treats.
+URI: xsd:anyURI
+ +| Mapping Type | +Mapped Value | +
|---|---|
| self | +xsd:anyURI | +
| native | +bican:predicate_type | +
A series of actions conducted in a certain order or manner
+URI: biolink:Procedure
+| Name | +Cardinality and Range | +Description | +Inheritance | +
|---|---|---|---|
| id | +1 String |
+A unique identifier for an entity | +direct | +
| iri | +0..1 IriType |
+An IRI for an entity | +direct | +
| category | +* Uriorcurie |
+Name of the high level ontology class in which this entity is categorized | +direct | +
| type | +* String |
++ | direct | +
| name | +0..1 LabelType |
+A human-readable name for an attribute or entity | +direct | +
| description | +0..1 NarrativeText |
+a human-readable description of an entity | +direct | +
| has_attribute | +* Attribute |
+connects any entity to an attribute | +direct | +
| deprecated | +0..1 Boolean |
+A boolean flag indicating that an entity is no longer considered current or v... | +direct | +
| provided_by | +* String |
+The value in this node property represents the knowledge provider that create... | +direct | +
| xref | +* Uriorcurie |
+A database cross reference or alternative identifier for a NamedThing or edge... | +direct | +
| full_name | +0..1 LabelType |
+a long-form human readable name for a thing | +direct | +
| synonym | +* LabelType |
+Alternate human-readable names for a thing | +direct | +
Instances of this class should have identifiers with one of the following prefixes:
+| Mapping Type | +Mapped Value | +
|---|---|
| self | +biolink:Procedure | +
| native | +bican:Procedure | +
| exact | +UMLSSG:PROC, dcid:MedicalProcedure | +
| narrow | +STY:T059, STY:T060, STY:T061, STY:T063 | +
name: procedure
+id_prefixes:
+- CPT
+definition_uri: https://w3id.org/biolink/vocab/Procedure
+description: A series of actions conducted in a certain order or manner
+from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
+exact_mappings:
+- UMLSSG:PROC
+- dcid:MedicalProcedure
+narrow_mappings:
+- STY:T059
+- STY:T060
+- STY:T061
+- STY:T063
+is_a: named thing
+mixins:
+- activity and behavior
+slots:
+- id
+- iri
+- category
+- type
+- name
+- description
+- has attribute
+- deprecated
+- provided by
+- xref
+- full name
+- synonym
+class_uri: biolink:Procedure
+
+name: procedure
+id_prefixes:
+- CPT
+definition_uri: https://w3id.org/biolink/vocab/Procedure
+description: A series of actions conducted in a certain order or manner
+from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
+exact_mappings:
+- UMLSSG:PROC
+- dcid:MedicalProcedure
+narrow_mappings:
+- STY:T059
+- STY:T060
+- STY:T061
+- STY:T063
+is_a: named thing
+mixins:
+- activity and behavior
+attributes:
+ id:
+ name: id
+ definition_uri: https://w3id.org/biolink/vocab/id
+ description: A unique identifier for an entity. Must be either a CURIE shorthand
+ for a URI or a complete URI
+ in_subset:
+ - translator_minimal
+ from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
+ exact_mappings:
+ - AGRKB:primaryId
+ - gff3:ID
+ - gpi:DB_Object_ID
+ rank: 1000
+ domain: entity
+ slot_uri: biolink:id
+ identifier: true
+ alias: id
+ owner: procedure
+ domain_of:
+ - ontology class
+ - entity
+ - attribute
+ - named thing
+ - taxonomic rank
+ - organism taxon
+ - information content entity
+ - dataset
+ - physical entity
+ - activity
+ - procedure
+ - material sample
+ - biological entity
+ - gene
+ - genome
+ range: string
+ required: true
+ iri:
+ name: iri
+ definition_uri: https://w3id.org/biolink/vocab/iri
+ description: An IRI for an entity. This is determined by the id using expansion
+ rules.
+ in_subset:
+ - translator_minimal
+ - samples
+ from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
+ exact_mappings:
+ - WIKIDATA_PROPERTY:P854
+ rank: 1000
+ slot_uri: biolink:iri
+ alias: iri
+ owner: procedure
+ domain_of:
+ - attribute
+ - entity
+ - named thing
+ - organism taxon
+ - information content entity
+ - dataset
+ - physical entity
+ - activity
+ - procedure
+ - material sample
+ - biological entity
+ - gene
+ - genome
+ range: iri type
+ category:
+ name: category
+ definition_uri: https://w3id.org/biolink/vocab/category
+ description: Name of the high level ontology class in which this entity is categorized.
+ Corresponds to the label for the biolink entity type class. In a neo4j database
+ this MAY correspond to the neo4j label tag. In an RDF database it should be
+ a biolink model class URI. This field is multi-valued. It should include values
+ for ancestors of the biolink class; for example, a protein such as Shh would
+ have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`.
+ In an RDF database, nodes will typically have an rdf:type triples. This can
+ be to the most specific biolink class, or potentially to a class more specific
+ than something in biolink. For example, a sequence feature `f` may have a rdf:type
+ assertion to a SO class such as TF_binding_site, which is more specific than
+ anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity,
+ biolink:NamedThing}
+ in_subset:
+ - translator_minimal
+ from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
+ rank: 1000
+ is_a: type
+ domain: entity
+ slot_uri: biolink:category
+ designates_type: true
+ alias: category
+ owner: procedure
+ domain_of:
+ - entity
+ - attribute
+ - named thing
+ - organism taxon
+ - information content entity
+ - dataset
+ - physical entity
+ - activity
+ - procedure
+ - material sample
+ - biological entity
+ - gene
+ - genome
+ is_class_field: true
+ range: uriorcurie
+ multivalued: true
+ type:
+ name: type
+ definition_uri: https://w3id.org/biolink/vocab/type
+ from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
+ mappings:
+ - rdf:type
+ exact_mappings:
+ - gff3:type
+ - gpi:DB_Object_Type
+ rank: 1000
+ domain: entity
+ slot_uri: rdf:type
+ alias: type
+ owner: procedure
+ domain_of:
+ - entity
+ - attribute
+ - named thing
+ - organism taxon
+ - information content entity
+ - dataset
+ - physical entity
+ - activity
+ - procedure
+ - material sample
+ - biological entity
+ - gene
+ - genome
+ range: string
+ multivalued: true
+ name:
+ name: name
+ definition_uri: https://w3id.org/biolink/vocab/name
+ description: A human-readable name for an attribute or entity.
+ in_subset:
+ - translator_minimal
+ - samples
+ from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
+ aliases:
+ - label
+ - display name
+ - title
+ mappings:
+ - rdfs:label
+ exact_mappings:
+ - gff3:Name
+ - gpi:DB_Object_Name
+ narrow_mappings:
+ - dct:title
+ - WIKIDATA_PROPERTY:P1476
+ rank: 1000
+ domain: entity
+ slot_uri: rdfs:label
+ alias: name
+ owner: procedure
+ domain_of:
+ - attribute
+ - entity
+ - macromolecular machine mixin
+ - named thing
+ - organism taxon
+ - information content entity
+ - dataset
+ - physical entity
+ - activity
+ - procedure
+ - material sample
+ - biological entity
+ - gene or gene product
+ - gene
+ - genome
+ range: label type
+ description:
+ name: description
+ definition_uri: https://w3id.org/biolink/vocab/description
+ description: a human-readable description of an entity
+ in_subset:
+ - translator_minimal
+ from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
+ aliases:
+ - definition
+ mappings:
+ - dct:description
+ exact_mappings:
+ - IAO:0000115
+ - skos:definitions
+ narrow_mappings:
+ - gff3:Description
+ rank: 1000
+ slot_uri: dct:description
+ alias: description
+ owner: procedure
+ domain_of:
+ - entity
+ - attribute
+ - named thing
+ - organism taxon
+ - information content entity
+ - dataset
+ - physical entity
+ - activity
+ - procedure
+ - material sample
+ - biological entity
+ - gene
+ - genome
+ range: narrative text
+ has attribute:
+ name: has attribute
+ definition_uri: https://w3id.org/biolink/vocab/has_attribute
+ description: connects any entity to an attribute
+ in_subset:
+ - samples
+ from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
+ exact_mappings:
+ - SIO:000008
+ close_mappings:
+ - OBI:0001927
+ narrow_mappings:
+ - OBAN:association_has_subject_property
+ - OBAN:association_has_object_property
+ - CPT:has_possibly_included_panel_element
+ - DRUGBANK:category
+ - EFO:is_executed_in
+ - HANCESTRO:0301
+ - LOINC:has_action_guidance
+ - LOINC:has_adjustment
+ - LOINC:has_aggregation_view
+ - LOINC:has_approach_guidance
+ - LOINC:has_divisor
+ - LOINC:has_exam
+ - LOINC:has_method
+ - LOINC:has_modality_subtype
+ - LOINC:has_object_guidance
+ - LOINC:has_scale
+ - LOINC:has_suffix
+ - LOINC:has_time_aspect
+ - LOINC:has_time_modifier
+ - LOINC:has_timing_of
+ - NCIT:R88
+ - NCIT:eo_disease_has_property_or_attribute
+ - NCIT:has_data_element
+ - NCIT:has_pharmaceutical_administration_method
+ - NCIT:has_pharmaceutical_basic_dose_form
+ - NCIT:has_pharmaceutical_intended_site
+ - NCIT:has_pharmaceutical_release_characteristics
+ - NCIT:has_pharmaceutical_state_of_matter
+ - NCIT:has_pharmaceutical_transformation
+ - NCIT:is_qualified_by
+ - NCIT:qualifier_applies_to
+ - NCIT:role_has_domain
+ - NCIT:role_has_range
+ - INO:0000154
+ - HANCESTRO:0308
+ - OMIM:has_inheritance_type
+ - orphanet:C016
+ - orphanet:C017
+ - RO:0000053
+ - RO:0000086
+ - RO:0000087
+ - SNOMED:has_access
+ - SNOMED:has_clinical_course
+ - SNOMED:has_count_of_base_of_active_ingredient
+ - SNOMED:has_dose_form_administration_method
+ - SNOMED:has_dose_form_release_characteristic
+ - SNOMED:has_dose_form_transformation
+ - SNOMED:has_finding_context
+ - SNOMED:has_finding_informer
+ - SNOMED:has_inherent_attribute
+ - SNOMED:has_intent
+ - SNOMED:has_interpretation
+ - SNOMED:has_laterality
+ - SNOMED:has_measurement_method
+ - SNOMED:has_method
+ - SNOMED:has_priority
+ - SNOMED:has_procedure_context
+ - SNOMED:has_process_duration
+ - SNOMED:has_property
+ - SNOMED:has_revision_status
+ - SNOMED:has_scale_type
+ - SNOMED:has_severity
+ - SNOMED:has_specimen
+ - SNOMED:has_state_of_matter
+ - SNOMED:has_subject_relationship_context
+ - SNOMED:has_surgical_approach
+ - SNOMED:has_technique
+ - SNOMED:has_temporal_context
+ - SNOMED:has_time_aspect
+ - SNOMED:has_units
+ - UMLS:has_structural_class
+ - UMLS:has_supported_concept_property
+ - UMLS:has_supported_concept_relationship
+ - UMLS:may_be_qualified_by
+ rank: 1000
+ domain: entity
+ slot_uri: biolink:has_attribute
+ alias: has_attribute
+ owner: procedure
+ domain_of:
+ - entity
+ - attribute
+ - named thing
+ - organism taxon
+ - information content entity
+ - dataset
+ - physical entity
+ - activity
+ - procedure
+ - material sample
+ - biological entity
+ - gene
+ - genome
+ range: attribute
+ multivalued: true
+ deprecated:
+ name: deprecated
+ definition_uri: https://w3id.org/biolink/vocab/deprecated
+ description: A boolean flag indicating that an entity is no longer considered
+ current or valid.
+ from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
+ exact_mappings:
+ - oboInOwl:ObsoleteClass
+ rank: 1000
+ slot_uri: biolink:deprecated
+ alias: deprecated
+ owner: procedure
+ domain_of:
+ - entity
+ - attribute
+ - named thing
+ - organism taxon
+ - information content entity
+ - dataset
+ - physical entity
+ - activity
+ - procedure
+ - material sample
+ - biological entity
+ - gene
+ - genome
+ range: boolean
+ provided by:
+ name: provided by
+ definition_uri: https://w3id.org/biolink/vocab/provided_by
+ description: The value in this node property represents the knowledge provider
+ that created or assembled the node and all of its attributes. Used internally
+ to represent how a particular node made its way into a knowledge provider or
+ graph.
+ from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
+ rank: 1000
+ is_a: node property
+ domain: named thing
+ slot_uri: biolink:provided_by
+ alias: provided_by
+ owner: procedure
+ domain_of:
+ - named thing
+ - attribute
+ - organism taxon
+ - information content entity
+ - dataset
+ - physical entity
+ - activity
+ - procedure
+ - material sample
+ - biological entity
+ - gene
+ - genome
+ range: string
+ multivalued: true
+ xref:
+ name: xref
+ definition_uri: https://w3id.org/biolink/vocab/xref
+ description: A database cross reference or alternative identifier for a NamedThing
+ or edge between two NamedThings. This property should point to a database record
+ or webpage that supports the existence of the edge, or gives more detail about
+ the edge. This property can be used on a node or edge to provide multiple URIs
+ or CURIE cross references.
+ in_subset:
+ - translator_minimal
+ from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
+ aliases:
+ - dbxref
+ - Dbxref
+ - DbXref
+ - record_url
+ - source_record_urls
+ narrow_mappings:
+ - gff3:Dbxref
+ - gpi:DB_Xrefs
+ rank: 1000
+ domain: named thing
+ slot_uri: biolink:xref
+ alias: xref
+ owner: procedure
+ domain_of:
+ - named thing
+ - gene
+ - attribute
+ - organism taxon
+ - information content entity
+ - dataset
+ - physical entity
+ - activity
+ - procedure
+ - material sample
+ - biological entity
+ - genome
+ range: uriorcurie
+ multivalued: true
+ full name:
+ name: full name
+ definition_uri: https://w3id.org/biolink/vocab/full_name
+ description: a long-form human readable name for a thing
+ from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
+ rank: 1000
+ is_a: node property
+ domain: named thing
+ slot_uri: biolink:full_name
+ alias: full_name
+ owner: procedure
+ domain_of:
+ - named thing
+ - attribute
+ - organism taxon
+ - information content entity
+ - dataset
+ - physical entity
+ - activity
+ - procedure
+ - material sample
+ - biological entity
+ - gene
+ - genome
+ range: label type
+ synonym:
+ name: synonym
+ definition_uri: https://w3id.org/biolink/vocab/synonym
+ description: Alternate human-readable names for a thing
+ in_subset:
+ - translator_minimal
+ from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
+ aliases:
+ - alias
+ narrow_mappings:
+ - skos:altLabel
+ - gff3:Alias
+ - AGRKB:synonyms
+ - gpi:DB_Object_Synonyms
+ - HANCESTRO:0330
+ - IAO:0000136
+ - RXNORM:has_tradename
+ rank: 1000
+ is_a: node property
+ domain: named thing
+ slot_uri: biolink:synonym
+ alias: synonym
+ owner: procedure
+ domain_of:
+ - named thing
+ - attribute
+ - organism taxon
+ - information content entity
+ - dataset
+ - physical entity
+ - activity
+ - procedure
+ - material sample
+ - biological entity
+ - gene
+ - genome
+ range: label type
+ multivalued: true
+class_uri: biolink:Procedure
+
+A subset of classes that are associated with processing.
+URI: ProcessingElements
+An activity is something that occurs over a period of time and acts upon or with entities; it may include consuming, processing, transforming, modifying, relocating, using, or generating entities.
+URI: prov:Activity
+| Name | +Cardinality and Range | +Description | +Inheritance | +
|---|---|---|---|
| used | +0..1 ProvEntity |
+Usage is the beginning of utilizing an entity by an activity | +direct | +
| mixed into | +description | +
|---|---|
| DissectionRoiDelineation | +The process of outlining a region of interest on a brain slab image to guide ... | +
| TissueDissection | +The process of dissecting a tissue sample from a brain slab guided by a disse... | +
| CellDissociation | +The process of generating dissociated cells from an input tissue sample | +
| CellEnrichment | +The process of enriching a dissociated cell sample by including or excluding ... | +
| EnrichedCellSampleSplitting | +The process of splitting an enriched cell sample into several portions | +
| CellBarcoding | +The process of adding a molecular barcode to individual cells in a sample | +
| CdnaAmplification | +The process of creating a collection of cDNA molecules derived and amplified ... | +
| LibraryConstruction | +The process of constructing a library from input material (such as amplified ... | +
| LibraryPooling | +The process of constructing of a libray pool by combining library aliquots fr... | +
| used by | +used in | +type | +used | +
|---|---|---|---|
| Donor | +was_generated_by | +range | +ProvActivity | +
| BrainSlab | +was_generated_by | +range | +ProvActivity | +
| EnrichedCellSample | +was_generated_by | +range | +ProvActivity | +
| LibraryAliquot | +was_generated_by | +range | +ProvActivity | +
| ProvEntity | +was_generated_by | +range | +ProvActivity | +
| Mapping Type | +Mapped Value | +
|---|---|
| self | +prov:Activity | +
| native | +bican:ProvActivity | +
name: ProvActivity
+description: An activity is something that occurs over a period of time and acts upon
+ or with entities; it may include consuming, processing, transforming, modifying,
+ relocating, using, or generating entities.
+from_schema: https://identifiers.org/brain-bican/library-generation-schema
+mixin: true
+slots:
+- used
+class_uri: prov:Activity
+
+name: ProvActivity
+description: An activity is something that occurs over a period of time and acts upon
+ or with entities; it may include consuming, processing, transforming, modifying,
+ relocating, using, or generating entities.
+from_schema: https://identifiers.org/brain-bican/library-generation-schema
+mixin: true
+attributes:
+ used:
+ name: used
+ description: Usage is the beginning of utilizing an entity by an activity. Before
+ usage, the activity had not begun to utilize this entity and could not have
+ been affected by the entity.
+ from_schema: https://identifiers.org/brain-bican/library-generation-schema
+ rank: 1000
+ slot_uri: prov:used
+ alias: used
+ owner: ProvActivity
+ domain_of:
+ - DissectionRoiDelineation
+ - TissueDissection
+ - CellDissociation
+ - CellEnrichment
+ - EnrichedCellSampleSplitting
+ - CellBarcoding
+ - CdnaAmplification
+ - LibraryConstruction
+ - LibraryPooling
+ - ProvActivity
+ range: ProvEntity
+class_uri: prov:Activity
+
+An entity is a physical, digital, conceptual, or other kind of thing with some fixed aspects; entities may be real or imaginary.
+URI: prov:Entity
+| Name | +Cardinality and Range | +Description | +Inheritance | +
|---|---|---|---|
| was_derived_from | +0..1 ProvEntity |
+A derivation is a transformation of an entity into another, an update of an e... | +direct | +
| was_generated_by | +0..1 ProvActivity |
+Generation is the completion of production of a new entity by an activity | +direct | +
| mixed into | +description | +
|---|---|
| Donor | +A person or organism that is the source of a biological sample for scientific... | +
| BrainSlab | +A thick flat piece of brain tissue obtained by slicing a whole brain, brain h... | +
| TissueSample | +The final intact piece of tissue before cell or nuclei prep | +
| DissociatedCellSample | +A collection of dissociated cells or nuclei derived from dissociation of a ti... | +
| EnrichedCellSample | +A collection of enriched cells or nuclei after enrichment process, usually vi... | +
| BarcodedCellSample | +A collection of molecularly barcoded cells | +
| AmplifiedCdna | +A collection of cDNA molecules derived and amplified from an input barcoded c... | +
| Library | +A collection of fragmented and barcode-indexed DNA molecules for sequencing | +
| LibraryAliquot | +One library in the library pool | +
| LibraryPool | +A library pool is made up of library aliquots from multiple libraries | +
| DissectionRoiPolygon | +A polygon annotated on a brain slab image delineating a region of interest (R... | +
| used by | +used in | +type | +used | +
|---|---|---|---|
| Donor | +was_derived_from | +range | +ProvEntity | +
| EnrichedCellSample | +was_derived_from | +range | +ProvEntity | +
| BarcodedCellSample | +was_derived_from | +range | +ProvEntity | +
| Library | +was_derived_from | +range | +ProvEntity | +
| CellBarcoding | +used | +range | +ProvEntity | +
| LibraryConstruction | +used | +range | +ProvEntity | +
| DissectionRoiPolygon | +was_derived_from | +range | +ProvEntity | +
| ProvActivity | +used | +range | +ProvEntity | +
| ProvEntity | +was_derived_from | +range | +ProvEntity | +
| Mapping Type | +Mapped Value | +
|---|---|
| self | +prov:Entity | +
| native | +bican:ProvEntity | +
name: ProvEntity
+description: An entity is a physical, digital, conceptual, or other kind of thing
+ with some fixed aspects; entities may be real or imaginary.
+from_schema: https://identifiers.org/brain-bican/library-generation-schema
+mixin: true
+slots:
+- was_derived_from
+- was_generated_by
+class_uri: prov:Entity
+
+name: ProvEntity
+description: An entity is a physical, digital, conceptual, or other kind of thing
+ with some fixed aspects; entities may be real or imaginary.
+from_schema: https://identifiers.org/brain-bican/library-generation-schema
+mixin: true
+attributes:
+ was_derived_from:
+ name: was_derived_from
+ description: A derivation is a transformation of an entity into another, an update
+ of an entity resulting in a new one, or the construction of a new entity based
+ on a pre-existing entity.
+ from_schema: https://identifiers.org/brain-bican/library-generation-schema
+ rank: 1000
+ slot_uri: prov:wasDerivedFrom
+ alias: was_derived_from
+ owner: ProvEntity
+ domain_of:
+ - BrainSlab
+ - TissueSample
+ - DissociatedCellSample
+ - EnrichedCellSample
+ - BarcodedCellSample
+ - AmplifiedCdna
+ - Library
+ - LibraryAliquot
+ - LibraryPool
+ - ProvEntity
+ range: ProvEntity
+ was_generated_by:
+ name: was_generated_by
+ description: Generation is the completion of production of a new entity by an
+ activity. This entity did not exist before generation and becomes available
+ for usage after this generation.
+ from_schema: https://identifiers.org/brain-bican/library-generation-schema
+ rank: 1000
+ slot_uri: prov:wasGeneratedBy
+ alias: was_generated_by
+ owner: ProvEntity
+ domain_of:
+ - TissueSample
+ - DissociatedCellSample
+ - EnrichedCellSample
+ - BarcodedCellSample
+ - AmplifiedCdna
+ - Library
+ - LibraryPool
+ - DissectionRoiPolygon
+ - ProvEntity
+ range: ProvActivity
+class_uri: prov:Entity
+
+A value of an attribute that is quantitative and measurable, expressed as a combination of a unit and a numeric value
+ +| Name | +Cardinality and Range | +Description | +Inheritance | +
|---|---|---|---|
| has_unit | +0..1 Unit |
+connects a quantity value to a unit | +direct | +
| has_numeric_value | +0..1 Double |
+connects a quantity value to a number | +direct | +
| used by | +used in | +type | +used | +
|---|---|---|---|
| QuantityValue | +has_unit | +domain | +QuantityValue | +
| QuantityValue | +has_numeric_value | +domain | +QuantityValue | +
| Attribute | +has_quantitative_value | +range | +QuantityValue | +
| Mapping Type | +Mapped Value | +
|---|---|
| self | +biolink:QuantityValue | +
| native | +bican:QuantityValue | +
name: quantity value
+definition_uri: https://w3id.org/biolink/vocab/QuantityValue
+description: A value of an attribute that is quantitative and measurable, expressed
+ as a combination of a unit and a numeric value
+from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
+is_a: annotation
+slots:
+- has unit
+- has numeric value
+class_uri: biolink:QuantityValue
+
+name: quantity value
+definition_uri: https://w3id.org/biolink/vocab/QuantityValue
+description: A value of an attribute that is quantitative and measurable, expressed
+ as a combination of a unit and a numeric value
+from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
+is_a: annotation
+attributes:
+ has unit:
+ name: has unit
+ definition_uri: https://w3id.org/biolink/vocab/has_unit
+ description: connects a quantity value to a unit
+ in_subset:
+ - samples
+ from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
+ exact_mappings:
+ - qud:unit
+ - IAO:0000039
+ close_mappings:
+ - EFO:0001697
+ - UO-PROPERTY:is_unit_of
+ narrow_mappings:
+ - SNOMED:has_concentration_strength_denominator_unit
+ - SNOMED:has_concentration_strength_numerator_unit
+ - SNOMED:has_presentation_strength_denominator_unit
+ - SNOMED:has_presentation_strength_numerator_unit
+ - SNOMED:has_unit_of_presentation
+ rank: 1000
+ domain: quantity value
+ slot_uri: biolink:has_unit
+ alias: has_unit
+ owner: quantity value
+ domain_of:
+ - quantity value
+ range: unit
+ multivalued: false
+ has numeric value:
+ name: has numeric value
+ definition_uri: https://w3id.org/biolink/vocab/has_numeric_value
+ description: connects a quantity value to a number
+ in_subset:
+ - samples
+ from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
+ exact_mappings:
+ - qud:quantityValue
+ rank: 1000
+ domain: quantity value
+ slot_uri: biolink:has_numeric_value
+ alias: has_numeric_value
+ owner: quantity value
+ domain_of:
+ - quantity value
+ range: double
+ multivalued: false
+class_uri: biolink:QuantityValue
+
+URI: UO:0010006
+ +| Mapping Type | +Mapped Value | +
|---|---|
| self | +UO:0010006 | +
| native | +bican:quotient | +
Sample/biosample datamodel
+URI: Samples
+| Class | +Description | +
|---|---|
| Attribute | +A property or characteristic of an entity | +
| Name | +Cardinality and Range | +Description | +
|---|---|---|
| attribute_name | +0..1 LabelType |
+The human-readable 'attribute name' can be set to a string which reflects its... | +
| has_attribute | +* Attribute |
+connects any entity to an attribute | +
| has_attribute_type | +1 OntologyClass |
+connects an attribute to a class that describes it | +
| has_qualitative_value | +0..1 NamedThing |
+connects an attribute to a value | +
| has_quantitative_value | +* QuantityValue |
+connects an attribute to a value | +
| iri | +0..1 IriType |
+An IRI for an entity | +
| name | +0..1 LabelType |
+The human-readable 'attribute name' can be set to a string which reflects its... | +
| Slot | +Description | +
|---|---|
| attribute_name | +The human-readable 'attribute name' can be set to a string which reflects its... | +
| has_attribute | +connects any entity to an attribute | +
| has_attribute_type | +connects an attribute to a class that describes it | +
| has_numeric_value | +connects a quantity value to a number | +
| has_qualitative_value | +connects an attribute to a value | +
| has_quantitative_value | +connects an attribute to a value | +
| has_unit | +connects a quantity value to a unit | +
| iri | +An IRI for an entity | +
| name | +A human-readable name for an attribute or entity | +
A subset of classes that are associated with sequencing.
+URI: SequencingElements
+URI: Sex
+| Value | +Meaning | +Description | +
|---|---|---|
| 1 | +NIMP:PD-LXUBTM45 | +Male | +
| 2 | +NIMP:PD-LXUBTM45 | +Female | +
| 7 | +NIMP:PD-LXUBTM45 | +Other | +
| 8 | +NIMP:PD-LXUBTM45 | +Unknown | +
| 9 | +NIMP:PD-LXUBTM45 | +Not Reported | +
| Name | +Description | +
|---|---|
| biological_sex | +Biological sex of donor at birth | +
name: sex
+from_schema: https://identifiers.org/brain-bican/library-generation-schema
+rank: 1000
+permissible_values:
+ '1':
+ text: '1'
+ description: Male
+ meaning: NIMP:PD-LXUBTM45
+ '2':
+ text: '2'
+ description: Female
+ meaning: NIMP:PD-LXUBTM45
+ '7':
+ text: '7'
+ description: Other
+ meaning: NIMP:PD-LXUBTM45
+ '8':
+ text: '8'
+ description: Unknown
+ meaning: NIMP:PD-LXUBTM45
+ '9':
+ text: '9'
+ description: Not Reported
+ meaning: NIMP:PD-LXUBTM45
+
+A string encoding a SPARQL Property Path. The value of the string MUST conform to SPARQL syntax and SHOULD dereference to zero or more valid objects within the current instance document when encoded as RDF.
+URI: xsd:string
+ +| Mapping Type | +Mapped Value | +
|---|---|
| self | +xsd:string | +
| native | +bican:sparqlpath | +
A character string
+URI: xsd:string
+ +| Mapping Type | +Mapped Value | +
|---|---|
| self | +xsd:string | +
| native | +bican:string | +
| exact | +schema:Text | +
An entity that has the role of being studied in an investigation, study, or experiment
+URI: biolink:SubjectOfInvestigation
+| Name | +Cardinality and Range | +Description | +Inheritance | +
|---|---|---|---|
| + | + | + | + |
| mixed into | +description | +
|---|---|
| MaterialSample | +A sample is a limited quantity of something (e | +
| Mapping Type | +Mapped Value | +
|---|---|
| self | +biolink:SubjectOfInvestigation | +
| native | +bican:SubjectOfInvestigation | +
name: subject of investigation
+definition_uri: https://w3id.org/biolink/vocab/SubjectOfInvestigation
+description: An entity that has the role of being studied in an investigation, study,
+ or experiment
+from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
+mixin: true
+class_uri: biolink:SubjectOfInvestigation
+
+name: subject of investigation
+definition_uri: https://w3id.org/biolink/vocab/SubjectOfInvestigation
+description: An entity that has the role of being studied in an investigation, study,
+ or experiment
+from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
+mixin: true
+class_uri: biolink:SubjectOfInvestigation
+
+URI: xsd:string
+ +| Mapping Type | +Mapped Value | +
|---|---|
| self | +xsd:string | +
| native | +bican:symbol_type | +
A descriptor for the rank within a taxonomic classification. Example instance: TAXRANK:0000017 (kingdom)
+ +| Name | +Cardinality and Range | +Description | +Inheritance | +
|---|---|---|---|
| id | +1 String |
+A unique identifier for an entity | +direct | +
| used by | +used in | +type | +used | +
|---|---|---|---|
| OrganismTaxon | +has_taxonomic_rank | +range | +TaxonomicRank | +
Instances of this class should have identifiers with one of the following prefixes:
+| Mapping Type | +Mapped Value | +
|---|---|
| self | +biolink:TaxonomicRank | +
| native | +bican:TaxonomicRank | +
| undefined | +WIKIDATA:Q427626 | +
name: taxonomic rank
+id_prefixes:
+- TAXRANK
+definition_uri: https://w3id.org/biolink/vocab/TaxonomicRank
+description: 'A descriptor for the rank within a taxonomic classification. Example
+ instance: TAXRANK:0000017 (kingdom)'
+from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
+mappings:
+- WIKIDATA:Q427626
+is_a: ontology class
+slots:
+- id
+class_uri: biolink:TaxonomicRank
+
+name: taxonomic rank
+id_prefixes:
+- TAXRANK
+definition_uri: https://w3id.org/biolink/vocab/TaxonomicRank
+description: 'A descriptor for the rank within a taxonomic classification. Example
+ instance: TAXRANK:0000017 (kingdom)'
+from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
+mappings:
+- WIKIDATA:Q427626
+is_a: ontology class
+attributes:
+ id:
+ name: id
+ definition_uri: https://w3id.org/biolink/vocab/id
+ description: A unique identifier for an entity. Must be either a CURIE shorthand
+ for a URI or a complete URI
+ in_subset:
+ - translator_minimal
+ from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
+ exact_mappings:
+ - AGRKB:primaryId
+ - gff3:ID
+ - gpi:DB_Object_ID
+ rank: 1000
+ domain: entity
+ slot_uri: biolink:id
+ identifier: true
+ alias: id
+ owner: taxonomic rank
+ domain_of:
+ - ontology class
+ - entity
+ - attribute
+ - named thing
+ - taxonomic rank
+ - organism taxon
+ - information content entity
+ - dataset
+ - physical entity
+ - activity
+ - procedure
+ - material sample
+ - biological entity
+ - gene
+ - genome
+ range: string
+ required: true
+class_uri: biolink:TaxonomicRank
+
+TBD
+URI: Testing
+A mixin that can be used on any entity that can be taxonomically classified. This includes individual organisms; genes, their products and other molecular entities; body parts; biological processes
+ +| Name | +Cardinality and Range | +Description | +Inheritance | +
|---|---|---|---|
| in_taxon | +* OrganismTaxon |
+connects an entity to its taxonomic classification | +direct | +
| in_taxon_label | +0..1 LabelType |
+The human readable scientific name for the taxon of the entity | +direct | +
| mixed into | +description | +
|---|---|
| GenomeAssembly | +Genome assembly to contain version and label information | +
| BiologicalEntity | ++ |
| used by | +used in | +type | +used | +
|---|---|---|---|
| GeneAnnotation | +in_taxon | +domain | +ThingWithTaxon | +
| GeneAnnotation | +in_taxon_label | +domain | +ThingWithTaxon | +
| GenomeAnnotation | +in_taxon | +domain | +ThingWithTaxon | +
| GenomeAnnotation | +in_taxon_label | +domain | +ThingWithTaxon | +
| GenomeAssembly | +in_taxon | +domain | +ThingWithTaxon | +
| GenomeAssembly | +in_taxon_label | +domain | +ThingWithTaxon | +
| ThingWithTaxon | +in_taxon | +domain | +ThingWithTaxon | +
| ThingWithTaxon | +in_taxon_label | +domain | +ThingWithTaxon | +
| BiologicalEntity | +in_taxon | +domain | +ThingWithTaxon | +
| BiologicalEntity | +in_taxon_label | +domain | +ThingWithTaxon | +
| Gene | +in_taxon | +domain | +ThingWithTaxon | +
| Gene | +in_taxon_label | +domain | +ThingWithTaxon | +
| Genome | +in_taxon | +domain | +ThingWithTaxon | +
| Genome | +in_taxon_label | +domain | +ThingWithTaxon | +
| Mapping Type | +Mapped Value | +
|---|---|
| self | +biolink:ThingWithTaxon | +
| native | +bican:ThingWithTaxon | +
name: thing with taxon
+definition_uri: https://w3id.org/biolink/vocab/ThingWithTaxon
+description: A mixin that can be used on any entity that can be taxonomically classified.
+ This includes individual organisms; genes, their products and other molecular entities;
+ body parts; biological processes
+from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
+mixin: true
+slots:
+- in taxon
+- in taxon label
+class_uri: biolink:ThingWithTaxon
+
+name: thing with taxon
+definition_uri: https://w3id.org/biolink/vocab/ThingWithTaxon
+description: A mixin that can be used on any entity that can be taxonomically classified.
+ This includes individual organisms; genes, their products and other molecular entities;
+ body parts; biological processes
+from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
+mixin: true
+attributes:
+ in taxon:
+ name: in taxon
+ definition_uri: https://w3id.org/biolink/vocab/in_taxon
+ annotations:
+ canonical_predicate:
+ tag: canonical_predicate
+ value: true
+ description: connects an entity to its taxonomic classification. Only certain
+ kinds of entities can be taxonomically classified; see 'thing with taxon'
+ in_subset:
+ - translator_minimal
+ from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
+ aliases:
+ - instance of
+ - is organism source of gene product
+ - organism has gene
+ - gene found in organism
+ - gene product has organism source
+ exact_mappings:
+ - RO:0002162
+ - WIKIDATA_PROPERTY:P703
+ narrow_mappings:
+ - RO:0002160
+ rank: 1000
+ is_a: related to at instance level
+ domain: thing with taxon
+ slot_uri: biolink:in_taxon
+ inherited: true
+ alias: in_taxon
+ owner: thing with taxon
+ domain_of:
+ - thing with taxon
+ - biological entity
+ - gene
+ - genome
+ range: organism taxon
+ multivalued: true
+ in taxon label:
+ name: in taxon label
+ definition_uri: https://w3id.org/biolink/vocab/in_taxon_label
+ annotations:
+ denormalized:
+ tag: denormalized
+ value: true
+ description: The human readable scientific name for the taxon of the entity.
+ in_subset:
+ - translator_minimal
+ from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
+ exact_mappings:
+ - WIKIDATA_PROPERTY:P225
+ rank: 1000
+ is_a: node property
+ domain: thing with taxon
+ slot_uri: biolink:in_taxon_label
+ alias: in_taxon_label
+ owner: thing with taxon
+ domain_of:
+ - thing with taxon
+ - biological entity
+ - gene
+ - genome
+ range: label type
+class_uri: biolink:ThingWithTaxon
+
+A time object represents a (local) time of day, independent of any particular day
+URI: xsd:time
+ +| Mapping Type | +Mapped Value | +
|---|---|
| self | +xsd:time | +
| native | +bican:time | +
| exact | +schema:Time | +
URI: xsd:time
+ +| Mapping Type | +Mapped Value | +
|---|---|
| self | +xsd:time | +
| native | +bican:time_type | +
The process of dissecting a tissue sample from a brain slab guided by a dissection region of interest (ROI) delineation.
+ +| Name | +Cardinality and Range | +Description | +Inheritance | +
|---|---|---|---|
| used | +0..1 BrainSlab |
+The brain slab from which the tissue sample was dissected from | +direct | +
| was_guided_by | +0..1 DissectionRoiPolygon |
+The dissection ROI polygon which was used to guide the tissue dissection | +direct | +
| id | +1 String |
+A unique identifier for an entity | +NamedThing, Procedure, Entity | +
| iri | +0..1 IriType |
+An IRI for an entity | +NamedThing, Procedure, Entity | +
| category | +* Uriorcurie |
+Name of the high level ontology class in which this entity is categorized | +NamedThing, Procedure, Entity | +
| type | +* String |
++ | NamedThing, Procedure, Entity | +
| name | +0..1 LabelType |
+A human-readable name for an attribute or entity | +NamedThing, Procedure, Entity | +
| description | +0..1 NarrativeText |
+a human-readable description of an entity | +NamedThing, Procedure, Entity | +
| has_attribute | +* Attribute |
+connects any entity to an attribute | +NamedThing, Procedure, Entity | +
| deprecated | +0..1 Boolean |
+A boolean flag indicating that an entity is no longer considered current or v... | +NamedThing, Procedure, Entity | +
| provided_by | +* String |
+The value in this node property represents the knowledge provider that create... | +NamedThing, Procedure | +
| xref | +* Uriorcurie |
+A database cross reference or alternative identifier for a NamedThing or edge... | +NamedThing, Procedure | +
| full_name | +0..1 LabelType |
+a long-form human readable name for a thing | +NamedThing, Procedure | +
| synonym | +* LabelType |
+Alternate human-readable names for a thing | +NamedThing, Procedure | +
| used by | +used in | +type | +used | +
|---|---|---|---|
| TissueSample | +was_generated_by | +range | +TissueDissection | +
| Mapping Type | +Mapped Value | +
|---|---|
| self | +bican:TissueDissection | +
| native | +bican:TissueDissection | +
name: TissueDissection
+description: The process of dissecting a tissue sample from a brain slab guided by
+ a dissection region of interest (ROI) delineation.
+in_subset:
+- bican
+- library_generation
+from_schema: https://identifiers.org/brain-bican/library-generation-schema
+is_a: procedure
+mixins:
+- ProvActivity
+slots:
+- used
+slot_usage:
+ used:
+ name: used
+ description: The brain slab from which the tissue sample was dissected from.
+ range: BrainSlab
+ category:
+ name: category
+ pattern: ^bican:[A-Z][A-Za-z]+$
+attributes:
+ was_guided_by:
+ name: was_guided_by
+ description: The dissection ROI polygon which was used to guide the tissue dissection.
+ from_schema: https://identifiers.org/brain-bican/library-generation-schema
+ rank: 1000
+ domain_of:
+ - TissueDissection
+ range: DissectionRoiPolygon
+
+name: TissueDissection
+description: The process of dissecting a tissue sample from a brain slab guided by
+ a dissection region of interest (ROI) delineation.
+in_subset:
+- bican
+- library_generation
+from_schema: https://identifiers.org/brain-bican/library-generation-schema
+is_a: procedure
+mixins:
+- ProvActivity
+slot_usage:
+ used:
+ name: used
+ description: The brain slab from which the tissue sample was dissected from.
+ range: BrainSlab
+ category:
+ name: category
+ pattern: ^bican:[A-Z][A-Za-z]+$
+attributes:
+ was_guided_by:
+ name: was_guided_by
+ description: The dissection ROI polygon which was used to guide the tissue dissection.
+ from_schema: https://identifiers.org/brain-bican/library-generation-schema
+ rank: 1000
+ alias: was_guided_by
+ owner: TissueDissection
+ domain_of:
+ - TissueDissection
+ range: DissectionRoiPolygon
+ used:
+ name: used
+ description: The brain slab from which the tissue sample was dissected from.
+ from_schema: https://identifiers.org/brain-bican/library-generation-schema
+ rank: 1000
+ slot_uri: prov:used
+ alias: used
+ owner: TissueDissection
+ domain_of:
+ - DissectionRoiDelineation
+ - TissueDissection
+ - CellDissociation
+ - CellEnrichment
+ - EnrichedCellSampleSplitting
+ - CellBarcoding
+ - CdnaAmplification
+ - LibraryConstruction
+ - LibraryPooling
+ - ProvActivity
+ range: BrainSlab
+ id:
+ name: id
+ definition_uri: https://w3id.org/biolink/vocab/id
+ description: A unique identifier for an entity. Must be either a CURIE shorthand
+ for a URI or a complete URI
+ in_subset:
+ - translator_minimal
+ from_schema: https://identifiers.org/brain-bican/library-generation-schema
+ exact_mappings:
+ - AGRKB:primaryId
+ - gff3:ID
+ - gpi:DB_Object_ID
+ rank: 1000
+ domain: entity
+ slot_uri: biolink:id
+ identifier: true
+ alias: id
+ owner: TissueDissection
+ domain_of:
+ - ontology class
+ - entity
+ - attribute
+ - named thing
+ - taxonomic rank
+ - organism taxon
+ - information content entity
+ - dataset
+ - physical entity
+ - activity
+ - procedure
+ - material sample
+ - biological entity
+ - gene
+ - genome
+ range: string
+ required: true
+ iri:
+ name: iri
+ definition_uri: https://w3id.org/biolink/vocab/iri
+ description: An IRI for an entity. This is determined by the id using expansion
+ rules.
+ in_subset:
+ - translator_minimal
+ - samples
+ from_schema: https://identifiers.org/brain-bican/library-generation-schema
+ exact_mappings:
+ - WIKIDATA_PROPERTY:P854
+ rank: 1000
+ slot_uri: biolink:iri
+ alias: iri
+ owner: TissueDissection
+ domain_of:
+ - attribute
+ - entity
+ - named thing
+ - organism taxon
+ - information content entity
+ - dataset
+ - physical entity
+ - activity
+ - procedure
+ - material sample
+ - biological entity
+ - gene
+ - genome
+ range: iri type
+ category:
+ name: category
+ definition_uri: https://w3id.org/biolink/vocab/category
+ description: Name of the high level ontology class in which this entity is categorized.
+ Corresponds to the label for the biolink entity type class. In a neo4j database
+ this MAY correspond to the neo4j label tag. In an RDF database it should be
+ a biolink model class URI. This field is multi-valued. It should include values
+ for ancestors of the biolink class; for example, a protein such as Shh would
+ have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`.
+ In an RDF database, nodes will typically have an rdf:type triples. This can
+ be to the most specific biolink class, or potentially to a class more specific
+ than something in biolink. For example, a sequence feature `f` may have a rdf:type
+ assertion to a SO class such as TF_binding_site, which is more specific than
+ anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity,
+ biolink:NamedThing}
+ in_subset:
+ - translator_minimal
+ from_schema: https://identifiers.org/brain-bican/library-generation-schema
+ rank: 1000
+ is_a: type
+ domain: entity
+ slot_uri: biolink:category
+ designates_type: true
+ alias: category
+ owner: TissueDissection
+ domain_of:
+ - entity
+ - attribute
+ - named thing
+ - organism taxon
+ - information content entity
+ - dataset
+ - physical entity
+ - activity
+ - procedure
+ - material sample
+ - biological entity
+ - gene
+ - genome
+ is_class_field: true
+ range: uriorcurie
+ multivalued: true
+ pattern: ^bican:[A-Z][A-Za-z]+$
+ type:
+ name: type
+ definition_uri: https://w3id.org/biolink/vocab/type
+ from_schema: https://identifiers.org/brain-bican/library-generation-schema
+ mappings:
+ - rdf:type
+ exact_mappings:
+ - gff3:type
+ - gpi:DB_Object_Type
+ rank: 1000
+ domain: entity
+ slot_uri: rdf:type
+ alias: type
+ owner: TissueDissection
+ domain_of:
+ - entity
+ - attribute
+ - named thing
+ - organism taxon
+ - information content entity
+ - dataset
+ - physical entity
+ - activity
+ - procedure
+ - material sample
+ - biological entity
+ - gene
+ - genome
+ range: string
+ multivalued: true
+ name:
+ name: name
+ definition_uri: https://w3id.org/biolink/vocab/name
+ description: A human-readable name for an attribute or entity.
+ in_subset:
+ - translator_minimal
+ - samples
+ from_schema: https://identifiers.org/brain-bican/library-generation-schema
+ aliases:
+ - label
+ - display name
+ - title
+ mappings:
+ - rdfs:label
+ exact_mappings:
+ - gff3:Name
+ - gpi:DB_Object_Name
+ narrow_mappings:
+ - dct:title
+ - WIKIDATA_PROPERTY:P1476
+ rank: 1000
+ domain: entity
+ slot_uri: rdfs:label
+ alias: name
+ owner: TissueDissection
+ domain_of:
+ - attribute
+ - entity
+ - macromolecular machine mixin
+ - Donor
+ - BrainSlab
+ - TissueSample
+ - DissociatedCellSample
+ - EnrichedCellSample
+ - BarcodedCellSample
+ - AmplifiedCdna
+ - Library
+ - LibraryAliquot
+ - LibraryPool
+ - DissectionRoiPolygon
+ - named thing
+ - organism taxon
+ - information content entity
+ - dataset
+ - physical entity
+ - activity
+ - procedure
+ - material sample
+ - biological entity
+ - gene or gene product
+ - gene
+ - genome
+ range: label type
+ description:
+ name: description
+ definition_uri: https://w3id.org/biolink/vocab/description
+ description: a human-readable description of an entity
+ in_subset:
+ - translator_minimal
+ from_schema: https://identifiers.org/brain-bican/library-generation-schema
+ aliases:
+ - definition
+ mappings:
+ - dct:description
+ exact_mappings:
+ - IAO:0000115
+ - skos:definitions
+ narrow_mappings:
+ - gff3:Description
+ rank: 1000
+ slot_uri: dct:description
+ alias: description
+ owner: TissueDissection
+ domain_of:
+ - entity
+ - attribute
+ - named thing
+ - organism taxon
+ - information content entity
+ - dataset
+ - physical entity
+ - activity
+ - procedure
+ - material sample
+ - biological entity
+ - gene
+ - genome
+ range: narrative text
+ has attribute:
+ name: has attribute
+ definition_uri: https://w3id.org/biolink/vocab/has_attribute
+ description: connects any entity to an attribute
+ in_subset:
+ - samples
+ from_schema: https://identifiers.org/brain-bican/library-generation-schema
+ exact_mappings:
+ - SIO:000008
+ close_mappings:
+ - OBI:0001927
+ narrow_mappings:
+ - OBAN:association_has_subject_property
+ - OBAN:association_has_object_property
+ - CPT:has_possibly_included_panel_element
+ - DRUGBANK:category
+ - EFO:is_executed_in
+ - HANCESTRO:0301
+ - LOINC:has_action_guidance
+ - LOINC:has_adjustment
+ - LOINC:has_aggregation_view
+ - LOINC:has_approach_guidance
+ - LOINC:has_divisor
+ - LOINC:has_exam
+ - LOINC:has_method
+ - LOINC:has_modality_subtype
+ - LOINC:has_object_guidance
+ - LOINC:has_scale
+ - LOINC:has_suffix
+ - LOINC:has_time_aspect
+ - LOINC:has_time_modifier
+ - LOINC:has_timing_of
+ - NCIT:R88
+ - NCIT:eo_disease_has_property_or_attribute
+ - NCIT:has_data_element
+ - NCIT:has_pharmaceutical_administration_method
+ - NCIT:has_pharmaceutical_basic_dose_form
+ - NCIT:has_pharmaceutical_intended_site
+ - NCIT:has_pharmaceutical_release_characteristics
+ - NCIT:has_pharmaceutical_state_of_matter
+ - NCIT:has_pharmaceutical_transformation
+ - NCIT:is_qualified_by
+ - NCIT:qualifier_applies_to
+ - NCIT:role_has_domain
+ - NCIT:role_has_range
+ - INO:0000154
+ - HANCESTRO:0308
+ - OMIM:has_inheritance_type
+ - orphanet:C016
+ - orphanet:C017
+ - RO:0000053
+ - RO:0000086
+ - RO:0000087
+ - SNOMED:has_access
+ - SNOMED:has_clinical_course
+ - SNOMED:has_count_of_base_of_active_ingredient
+ - SNOMED:has_dose_form_administration_method
+ - SNOMED:has_dose_form_release_characteristic
+ - SNOMED:has_dose_form_transformation
+ - SNOMED:has_finding_context
+ - SNOMED:has_finding_informer
+ - SNOMED:has_inherent_attribute
+ - SNOMED:has_intent
+ - SNOMED:has_interpretation
+ - SNOMED:has_laterality
+ - SNOMED:has_measurement_method
+ - SNOMED:has_method
+ - SNOMED:has_priority
+ - SNOMED:has_procedure_context
+ - SNOMED:has_process_duration
+ - SNOMED:has_property
+ - SNOMED:has_revision_status
+ - SNOMED:has_scale_type
+ - SNOMED:has_severity
+ - SNOMED:has_specimen
+ - SNOMED:has_state_of_matter
+ - SNOMED:has_subject_relationship_context
+ - SNOMED:has_surgical_approach
+ - SNOMED:has_technique
+ - SNOMED:has_temporal_context
+ - SNOMED:has_time_aspect
+ - SNOMED:has_units
+ - UMLS:has_structural_class
+ - UMLS:has_supported_concept_property
+ - UMLS:has_supported_concept_relationship
+ - UMLS:may_be_qualified_by
+ rank: 1000
+ domain: entity
+ slot_uri: biolink:has_attribute
+ alias: has_attribute
+ owner: TissueDissection
+ domain_of:
+ - entity
+ - attribute
+ - named thing
+ - organism taxon
+ - information content entity
+ - dataset
+ - physical entity
+ - activity
+ - procedure
+ - material sample
+ - biological entity
+ - gene
+ - genome
+ range: attribute
+ multivalued: true
+ deprecated:
+ name: deprecated
+ definition_uri: https://w3id.org/biolink/vocab/deprecated
+ description: A boolean flag indicating that an entity is no longer considered
+ current or valid.
+ from_schema: https://identifiers.org/brain-bican/library-generation-schema
+ exact_mappings:
+ - oboInOwl:ObsoleteClass
+ rank: 1000
+ slot_uri: biolink:deprecated
+ alias: deprecated
+ owner: TissueDissection
+ domain_of:
+ - entity
+ - attribute
+ - named thing
+ - organism taxon
+ - information content entity
+ - dataset
+ - physical entity
+ - activity
+ - procedure
+ - material sample
+ - biological entity
+ - gene
+ - genome
+ range: boolean
+ provided by:
+ name: provided by
+ definition_uri: https://w3id.org/biolink/vocab/provided_by
+ description: The value in this node property represents the knowledge provider
+ that created or assembled the node and all of its attributes. Used internally
+ to represent how a particular node made its way into a knowledge provider or
+ graph.
+ from_schema: https://identifiers.org/brain-bican/library-generation-schema
+ rank: 1000
+ is_a: node property
+ domain: named thing
+ slot_uri: biolink:provided_by
+ alias: provided_by
+ owner: TissueDissection
+ domain_of:
+ - named thing
+ - attribute
+ - organism taxon
+ - information content entity
+ - dataset
+ - physical entity
+ - activity
+ - procedure
+ - material sample
+ - biological entity
+ - gene
+ - genome
+ range: string
+ multivalued: true
+ xref:
+ name: xref
+ definition_uri: https://w3id.org/biolink/vocab/xref
+ description: A database cross reference or alternative identifier for a NamedThing
+ or edge between two NamedThings. This property should point to a database record
+ or webpage that supports the existence of the edge, or gives more detail about
+ the edge. This property can be used on a node or edge to provide multiple URIs
+ or CURIE cross references.
+ in_subset:
+ - translator_minimal
+ from_schema: https://identifiers.org/brain-bican/library-generation-schema
+ aliases:
+ - dbxref
+ - Dbxref
+ - DbXref
+ - record_url
+ - source_record_urls
+ narrow_mappings:
+ - gff3:Dbxref
+ - gpi:DB_Xrefs
+ rank: 1000
+ domain: named thing
+ slot_uri: biolink:xref
+ alias: xref
+ owner: TissueDissection
+ domain_of:
+ - named thing
+ - gene
+ - attribute
+ - organism taxon
+ - information content entity
+ - dataset
+ - physical entity
+ - activity
+ - procedure
+ - material sample
+ - biological entity
+ - genome
+ range: uriorcurie
+ multivalued: true
+ full name:
+ name: full name
+ definition_uri: https://w3id.org/biolink/vocab/full_name
+ description: a long-form human readable name for a thing
+ from_schema: https://identifiers.org/brain-bican/library-generation-schema
+ rank: 1000
+ is_a: node property
+ domain: named thing
+ slot_uri: biolink:full_name
+ alias: full_name
+ owner: TissueDissection
+ domain_of:
+ - named thing
+ - attribute
+ - organism taxon
+ - information content entity
+ - dataset
+ - physical entity
+ - activity
+ - procedure
+ - material sample
+ - biological entity
+ - gene
+ - genome
+ range: label type
+ synonym:
+ name: synonym
+ definition_uri: https://w3id.org/biolink/vocab/synonym
+ description: Alternate human-readable names for a thing
+ in_subset:
+ - translator_minimal
+ from_schema: https://identifiers.org/brain-bican/library-generation-schema
+ aliases:
+ - alias
+ narrow_mappings:
+ - skos:altLabel
+ - gff3:Alias
+ - AGRKB:synonyms
+ - gpi:DB_Object_Synonyms
+ - HANCESTRO:0330
+ - IAO:0000136
+ - RXNORM:has_tradename
+ rank: 1000
+ is_a: node property
+ domain: named thing
+ slot_uri: biolink:synonym
+ alias: synonym
+ owner: TissueDissection
+ domain_of:
+ - named thing
+ - attribute
+ - organism taxon
+ - information content entity
+ - dataset
+ - physical entity
+ - activity
+ - procedure
+ - material sample
+ - biological entity
+ - gene
+ - genome
+ range: label type
+ multivalued: true
+
+The final intact piece of tissue before cell or nuclei prep. This piece of tissue will be used in dissociation and has an region of interest polygon (ROI) associated with it.
+URI: bican:TissueSample
+| Name | +Cardinality and Range | +Description | +Inheritance | +
|---|---|---|---|
| was_derived_from | +0..1 Donor |
+The donor or brain slab from which the tissue sample was derived from | +direct | +
| was_generated_by | +0..1 TissueDissection |
+The dissection process from which the tissue sample was generated by | +direct | +
| name | +0..1 LabelType |
+Identifier name for final intact piece of tissue before cell or nuclei prep | +direct | +
| dissection_was_guided_by | +0..1 DissectionRoiPolygon |
+The dissection ROI polygon that was used to guide the dissection | +direct | +
| structure | +* String |
+Strucure of tissue sample | +direct | +
| id | +1 String |
+A unique identifier for an entity | +NamedThing, PhysicalEntity, MaterialSample, Entity | +
| iri | +0..1 IriType |
+An IRI for an entity | +NamedThing, PhysicalEntity, MaterialSample, Entity | +
| category | +* Uriorcurie |
+Name of the high level ontology class in which this entity is categorized | +NamedThing, PhysicalEntity, MaterialSample, Entity | +
| type | +* String |
++ | NamedThing, PhysicalEntity, MaterialSample, Entity | +
| description | +0..1 NarrativeText |
+a human-readable description of an entity | +NamedThing, PhysicalEntity, MaterialSample, Entity | +
| has_attribute | +* Attribute |
+connects any entity to an attribute | +NamedThing, PhysicalEntity, MaterialSample, Entity | +
| deprecated | +0..1 Boolean |
+A boolean flag indicating that an entity is no longer considered current or v... | +NamedThing, PhysicalEntity, MaterialSample, Entity | +
| provided_by | +* String |
+The value in this node property represents the knowledge provider that create... | +NamedThing, PhysicalEntity, MaterialSample | +
| xref | +* Uriorcurie |
+A database cross reference or alternative identifier for a NamedThing or edge... | +NamedThing, PhysicalEntity, MaterialSample | +
| full_name | +0..1 LabelType |
+a long-form human readable name for a thing | +NamedThing, PhysicalEntity, MaterialSample | +
| synonym | +* LabelType |
+Alternate human-readable names for a thing | +NamedThing, PhysicalEntity, MaterialSample | +
| used by | +used in | +type | +used | +
|---|---|---|---|
| DissociatedCellSample | +was_derived_from | +range | +TissueSample | +
| CellDissociation | +used | +range | +TissueSample | +
| Mapping Type | +Mapped Value | +
|---|---|
| self | +bican:TissueSample | +
| native | +bican:TissueSample | +
| exact | +NIMP:Tissue | +
name: TissueSample
+description: The final intact piece of tissue before cell or nuclei prep. This piece
+ of tissue will be used in dissociation and has an region of interest polygon (ROI)
+ associated with it.
+in_subset:
+- bican
+- library_generation
+from_schema: https://identifiers.org/brain-bican/library-generation-schema
+exact_mappings:
+- NIMP:Tissue
+is_a: material sample
+mixins:
+- ProvEntity
+slots:
+- was_derived_from
+- was_generated_by
+- name
+slot_usage:
+ was_derived_from:
+ name: was_derived_from
+ description: The donor or brain slab from which the tissue sample was derived
+ from.
+ exact_mappings:
+ - NIMP:has_parent
+ range: Donor
+ was_generated_by:
+ name: was_generated_by
+ description: The dissection process from which the tissue sample was generated
+ by.
+ range: TissueDissection
+ name:
+ name: name
+ description: Identifier name for final intact piece of tissue before cell or nuclei
+ prep. This piece of tissue will be used in dissociation and has an ROI associated
+ with it.
+ exact_mappings:
+ - NIMP:PD-LJCRCC35
+ slot_uri: bican:2e4ca2fc-2d77-4d19-af45-d0fb7bbc2269
+ category:
+ name: category
+ pattern: ^bican:[A-Z][A-Za-z]+$
+attributes:
+ dissection_was_guided_by:
+ name: dissection_was_guided_by
+ description: The dissection ROI polygon that was used to guide the dissection.
+ from_schema: https://identifiers.org/brain-bican/library-generation-schema
+ exact_mappings:
+ - NIMP:has_parent
+ rank: 1000
+ domain_of:
+ - TissueSample
+ range: DissectionRoiPolygon
+ structure:
+ name: structure
+ local_names:
+ local_name_value:
+ local_name_source: local_name_value
+ local_name_value: structure
+ description: Strucure of tissue sample.
+ from_schema: https://identifiers.org/brain-bican/library-generation-schema
+ rank: 1000
+ alias: tissue_sample_structure
+ domain_of:
+ - TissueSample
+ multivalued: true
+
+name: TissueSample
+description: The final intact piece of tissue before cell or nuclei prep. This piece
+ of tissue will be used in dissociation and has an region of interest polygon (ROI)
+ associated with it.
+in_subset:
+- bican
+- library_generation
+from_schema: https://identifiers.org/brain-bican/library-generation-schema
+exact_mappings:
+- NIMP:Tissue
+is_a: material sample
+mixins:
+- ProvEntity
+slot_usage:
+ was_derived_from:
+ name: was_derived_from
+ description: The donor or brain slab from which the tissue sample was derived
+ from.
+ exact_mappings:
+ - NIMP:has_parent
+ range: Donor
+ was_generated_by:
+ name: was_generated_by
+ description: The dissection process from which the tissue sample was generated
+ by.
+ range: TissueDissection
+ name:
+ name: name
+ description: Identifier name for final intact piece of tissue before cell or nuclei
+ prep. This piece of tissue will be used in dissociation and has an ROI associated
+ with it.
+ exact_mappings:
+ - NIMP:PD-LJCRCC35
+ slot_uri: bican:2e4ca2fc-2d77-4d19-af45-d0fb7bbc2269
+ category:
+ name: category
+ pattern: ^bican:[A-Z][A-Za-z]+$
+attributes:
+ dissection_was_guided_by:
+ name: dissection_was_guided_by
+ description: The dissection ROI polygon that was used to guide the dissection.
+ from_schema: https://identifiers.org/brain-bican/library-generation-schema
+ exact_mappings:
+ - NIMP:has_parent
+ rank: 1000
+ alias: dissection_was_guided_by
+ owner: TissueSample
+ domain_of:
+ - TissueSample
+ range: DissectionRoiPolygon
+ structure:
+ name: structure
+ local_names:
+ local_name_value:
+ local_name_source: local_name_value
+ local_name_value: structure
+ description: Strucure of tissue sample.
+ from_schema: https://identifiers.org/brain-bican/library-generation-schema
+ rank: 1000
+ alias: tissue_sample_structure
+ owner: TissueSample
+ domain_of:
+ - TissueSample
+ range: string
+ multivalued: true
+ was_derived_from:
+ name: was_derived_from
+ description: The donor or brain slab from which the tissue sample was derived
+ from.
+ from_schema: https://identifiers.org/brain-bican/library-generation-schema
+ exact_mappings:
+ - NIMP:has_parent
+ rank: 1000
+ slot_uri: prov:wasDerivedFrom
+ alias: was_derived_from
+ owner: TissueSample
+ domain_of:
+ - BrainSlab
+ - TissueSample
+ - DissociatedCellSample
+ - EnrichedCellSample
+ - BarcodedCellSample
+ - AmplifiedCdna
+ - Library
+ - LibraryAliquot
+ - LibraryPool
+ - ProvEntity
+ range: Donor
+ was_generated_by:
+ name: was_generated_by
+ description: The dissection process from which the tissue sample was generated
+ by.
+ from_schema: https://identifiers.org/brain-bican/library-generation-schema
+ rank: 1000
+ slot_uri: prov:wasGeneratedBy
+ alias: was_generated_by
+ owner: TissueSample
+ domain_of:
+ - TissueSample
+ - DissociatedCellSample
+ - EnrichedCellSample
+ - BarcodedCellSample
+ - AmplifiedCdna
+ - Library
+ - LibraryPool
+ - DissectionRoiPolygon
+ - ProvEntity
+ range: TissueDissection
+ name:
+ name: name
+ definition_uri: https://w3id.org/biolink/vocab/name
+ description: Identifier name for final intact piece of tissue before cell or nuclei
+ prep. This piece of tissue will be used in dissociation and has an ROI associated
+ with it.
+ in_subset:
+ - translator_minimal
+ - samples
+ from_schema: https://identifiers.org/brain-bican/library-generation-schema
+ aliases:
+ - label
+ - display name
+ - title
+ mappings:
+ - rdfs:label
+ exact_mappings:
+ - NIMP:PD-LJCRCC35
+ narrow_mappings:
+ - dct:title
+ - WIKIDATA_PROPERTY:P1476
+ rank: 1000
+ domain: entity
+ slot_uri: bican:2e4ca2fc-2d77-4d19-af45-d0fb7bbc2269
+ alias: name
+ owner: TissueSample
+ domain_of:
+ - attribute
+ - entity
+ - macromolecular machine mixin
+ - Donor
+ - BrainSlab
+ - TissueSample
+ - DissociatedCellSample
+ - EnrichedCellSample
+ - BarcodedCellSample
+ - AmplifiedCdna
+ - Library
+ - LibraryAliquot
+ - LibraryPool
+ - DissectionRoiPolygon
+ - named thing
+ - organism taxon
+ - information content entity
+ - dataset
+ - physical entity
+ - activity
+ - procedure
+ - material sample
+ - biological entity
+ - gene or gene product
+ - gene
+ - genome
+ range: label type
+ id:
+ name: id
+ definition_uri: https://w3id.org/biolink/vocab/id
+ description: A unique identifier for an entity. Must be either a CURIE shorthand
+ for a URI or a complete URI
+ in_subset:
+ - translator_minimal
+ from_schema: https://identifiers.org/brain-bican/library-generation-schema
+ exact_mappings:
+ - AGRKB:primaryId
+ - gff3:ID
+ - gpi:DB_Object_ID
+ rank: 1000
+ domain: entity
+ slot_uri: biolink:id
+ identifier: true
+ alias: id
+ owner: TissueSample
+ domain_of:
+ - ontology class
+ - entity
+ - attribute
+ - named thing
+ - taxonomic rank
+ - organism taxon
+ - information content entity
+ - dataset
+ - physical entity
+ - activity
+ - procedure
+ - material sample
+ - biological entity
+ - gene
+ - genome
+ range: string
+ required: true
+ iri:
+ name: iri
+ definition_uri: https://w3id.org/biolink/vocab/iri
+ description: An IRI for an entity. This is determined by the id using expansion
+ rules.
+ in_subset:
+ - translator_minimal
+ - samples
+ from_schema: https://identifiers.org/brain-bican/library-generation-schema
+ exact_mappings:
+ - WIKIDATA_PROPERTY:P854
+ rank: 1000
+ slot_uri: biolink:iri
+ alias: iri
+ owner: TissueSample
+ domain_of:
+ - attribute
+ - entity
+ - named thing
+ - organism taxon
+ - information content entity
+ - dataset
+ - physical entity
+ - activity
+ - procedure
+ - material sample
+ - biological entity
+ - gene
+ - genome
+ range: iri type
+ category:
+ name: category
+ definition_uri: https://w3id.org/biolink/vocab/category
+ description: Name of the high level ontology class in which this entity is categorized.
+ Corresponds to the label for the biolink entity type class. In a neo4j database
+ this MAY correspond to the neo4j label tag. In an RDF database it should be
+ a biolink model class URI. This field is multi-valued. It should include values
+ for ancestors of the biolink class; for example, a protein such as Shh would
+ have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`.
+ In an RDF database, nodes will typically have an rdf:type triples. This can
+ be to the most specific biolink class, or potentially to a class more specific
+ than something in biolink. For example, a sequence feature `f` may have a rdf:type
+ assertion to a SO class such as TF_binding_site, which is more specific than
+ anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity,
+ biolink:NamedThing}
+ in_subset:
+ - translator_minimal
+ from_schema: https://identifiers.org/brain-bican/library-generation-schema
+ rank: 1000
+ is_a: type
+ domain: entity
+ slot_uri: biolink:category
+ designates_type: true
+ alias: category
+ owner: TissueSample
+ domain_of:
+ - entity
+ - attribute
+ - named thing
+ - organism taxon
+ - information content entity
+ - dataset
+ - physical entity
+ - activity
+ - procedure
+ - material sample
+ - biological entity
+ - gene
+ - genome
+ is_class_field: true
+ range: uriorcurie
+ multivalued: true
+ pattern: ^bican:[A-Z][A-Za-z]+$
+ type:
+ name: type
+ definition_uri: https://w3id.org/biolink/vocab/type
+ from_schema: https://identifiers.org/brain-bican/library-generation-schema
+ mappings:
+ - rdf:type
+ exact_mappings:
+ - gff3:type
+ - gpi:DB_Object_Type
+ rank: 1000
+ domain: entity
+ slot_uri: rdf:type
+ alias: type
+ owner: TissueSample
+ domain_of:
+ - entity
+ - attribute
+ - named thing
+ - organism taxon
+ - information content entity
+ - dataset
+ - physical entity
+ - activity
+ - procedure
+ - material sample
+ - biological entity
+ - gene
+ - genome
+ range: string
+ multivalued: true
+ description:
+ name: description
+ definition_uri: https://w3id.org/biolink/vocab/description
+ description: a human-readable description of an entity
+ in_subset:
+ - translator_minimal
+ from_schema: https://identifiers.org/brain-bican/library-generation-schema
+ aliases:
+ - definition
+ mappings:
+ - dct:description
+ exact_mappings:
+ - IAO:0000115
+ - skos:definitions
+ narrow_mappings:
+ - gff3:Description
+ rank: 1000
+ slot_uri: dct:description
+ alias: description
+ owner: TissueSample
+ domain_of:
+ - entity
+ - attribute
+ - named thing
+ - organism taxon
+ - information content entity
+ - dataset
+ - physical entity
+ - activity
+ - procedure
+ - material sample
+ - biological entity
+ - gene
+ - genome
+ range: narrative text
+ has attribute:
+ name: has attribute
+ definition_uri: https://w3id.org/biolink/vocab/has_attribute
+ description: connects any entity to an attribute
+ in_subset:
+ - samples
+ from_schema: https://identifiers.org/brain-bican/library-generation-schema
+ exact_mappings:
+ - SIO:000008
+ close_mappings:
+ - OBI:0001927
+ narrow_mappings:
+ - OBAN:association_has_subject_property
+ - OBAN:association_has_object_property
+ - CPT:has_possibly_included_panel_element
+ - DRUGBANK:category
+ - EFO:is_executed_in
+ - HANCESTRO:0301
+ - LOINC:has_action_guidance
+ - LOINC:has_adjustment
+ - LOINC:has_aggregation_view
+ - LOINC:has_approach_guidance
+ - LOINC:has_divisor
+ - LOINC:has_exam
+ - LOINC:has_method
+ - LOINC:has_modality_subtype
+ - LOINC:has_object_guidance
+ - LOINC:has_scale
+ - LOINC:has_suffix
+ - LOINC:has_time_aspect
+ - LOINC:has_time_modifier
+ - LOINC:has_timing_of
+ - NCIT:R88
+ - NCIT:eo_disease_has_property_or_attribute
+ - NCIT:has_data_element
+ - NCIT:has_pharmaceutical_administration_method
+ - NCIT:has_pharmaceutical_basic_dose_form
+ - NCIT:has_pharmaceutical_intended_site
+ - NCIT:has_pharmaceutical_release_characteristics
+ - NCIT:has_pharmaceutical_state_of_matter
+ - NCIT:has_pharmaceutical_transformation
+ - NCIT:is_qualified_by
+ - NCIT:qualifier_applies_to
+ - NCIT:role_has_domain
+ - NCIT:role_has_range
+ - INO:0000154
+ - HANCESTRO:0308
+ - OMIM:has_inheritance_type
+ - orphanet:C016
+ - orphanet:C017
+ - RO:0000053
+ - RO:0000086
+ - RO:0000087
+ - SNOMED:has_access
+ - SNOMED:has_clinical_course
+ - SNOMED:has_count_of_base_of_active_ingredient
+ - SNOMED:has_dose_form_administration_method
+ - SNOMED:has_dose_form_release_characteristic
+ - SNOMED:has_dose_form_transformation
+ - SNOMED:has_finding_context
+ - SNOMED:has_finding_informer
+ - SNOMED:has_inherent_attribute
+ - SNOMED:has_intent
+ - SNOMED:has_interpretation
+ - SNOMED:has_laterality
+ - SNOMED:has_measurement_method
+ - SNOMED:has_method
+ - SNOMED:has_priority
+ - SNOMED:has_procedure_context
+ - SNOMED:has_process_duration
+ - SNOMED:has_property
+ - SNOMED:has_revision_status
+ - SNOMED:has_scale_type
+ - SNOMED:has_severity
+ - SNOMED:has_specimen
+ - SNOMED:has_state_of_matter
+ - SNOMED:has_subject_relationship_context
+ - SNOMED:has_surgical_approach
+ - SNOMED:has_technique
+ - SNOMED:has_temporal_context
+ - SNOMED:has_time_aspect
+ - SNOMED:has_units
+ - UMLS:has_structural_class
+ - UMLS:has_supported_concept_property
+ - UMLS:has_supported_concept_relationship
+ - UMLS:may_be_qualified_by
+ rank: 1000
+ domain: entity
+ slot_uri: biolink:has_attribute
+ alias: has_attribute
+ owner: TissueSample
+ domain_of:
+ - entity
+ - attribute
+ - named thing
+ - organism taxon
+ - information content entity
+ - dataset
+ - physical entity
+ - activity
+ - procedure
+ - material sample
+ - biological entity
+ - gene
+ - genome
+ range: attribute
+ multivalued: true
+ deprecated:
+ name: deprecated
+ definition_uri: https://w3id.org/biolink/vocab/deprecated
+ description: A boolean flag indicating that an entity is no longer considered
+ current or valid.
+ from_schema: https://identifiers.org/brain-bican/library-generation-schema
+ exact_mappings:
+ - oboInOwl:ObsoleteClass
+ rank: 1000
+ slot_uri: biolink:deprecated
+ alias: deprecated
+ owner: TissueSample
+ domain_of:
+ - entity
+ - attribute
+ - named thing
+ - organism taxon
+ - information content entity
+ - dataset
+ - physical entity
+ - activity
+ - procedure
+ - material sample
+ - biological entity
+ - gene
+ - genome
+ range: boolean
+ provided by:
+ name: provided by
+ definition_uri: https://w3id.org/biolink/vocab/provided_by
+ description: The value in this node property represents the knowledge provider
+ that created or assembled the node and all of its attributes. Used internally
+ to represent how a particular node made its way into a knowledge provider or
+ graph.
+ from_schema: https://identifiers.org/brain-bican/library-generation-schema
+ rank: 1000
+ is_a: node property
+ domain: named thing
+ slot_uri: biolink:provided_by
+ alias: provided_by
+ owner: TissueSample
+ domain_of:
+ - named thing
+ - attribute
+ - organism taxon
+ - information content entity
+ - dataset
+ - physical entity
+ - activity
+ - procedure
+ - material sample
+ - biological entity
+ - gene
+ - genome
+ range: string
+ multivalued: true
+ xref:
+ name: xref
+ definition_uri: https://w3id.org/biolink/vocab/xref
+ description: A database cross reference or alternative identifier for a NamedThing
+ or edge between two NamedThings. This property should point to a database record
+ or webpage that supports the existence of the edge, or gives more detail about
+ the edge. This property can be used on a node or edge to provide multiple URIs
+ or CURIE cross references.
+ in_subset:
+ - translator_minimal
+ from_schema: https://identifiers.org/brain-bican/library-generation-schema
+ aliases:
+ - dbxref
+ - Dbxref
+ - DbXref
+ - record_url
+ - source_record_urls
+ narrow_mappings:
+ - gff3:Dbxref
+ - gpi:DB_Xrefs
+ rank: 1000
+ domain: named thing
+ slot_uri: biolink:xref
+ alias: xref
+ owner: TissueSample
+ domain_of:
+ - named thing
+ - gene
+ - attribute
+ - organism taxon
+ - information content entity
+ - dataset
+ - physical entity
+ - activity
+ - procedure
+ - material sample
+ - biological entity
+ - genome
+ range: uriorcurie
+ multivalued: true
+ full name:
+ name: full name
+ definition_uri: https://w3id.org/biolink/vocab/full_name
+ description: a long-form human readable name for a thing
+ from_schema: https://identifiers.org/brain-bican/library-generation-schema
+ rank: 1000
+ is_a: node property
+ domain: named thing
+ slot_uri: biolink:full_name
+ alias: full_name
+ owner: TissueSample
+ domain_of:
+ - named thing
+ - attribute
+ - organism taxon
+ - information content entity
+ - dataset
+ - physical entity
+ - activity
+ - procedure
+ - material sample
+ - biological entity
+ - gene
+ - genome
+ range: label type
+ synonym:
+ name: synonym
+ definition_uri: https://w3id.org/biolink/vocab/synonym
+ description: Alternate human-readable names for a thing
+ in_subset:
+ - translator_minimal
+ from_schema: https://identifiers.org/brain-bican/library-generation-schema
+ aliases:
+ - alias
+ narrow_mappings:
+ - skos:altLabel
+ - gff3:Alias
+ - AGRKB:synonyms
+ - gpi:DB_Object_Synonyms
+ - HANCESTRO:0330
+ - IAO:0000136
+ - RXNORM:has_tradename
+ rank: 1000
+ is_a: node property
+ domain: named thing
+ slot_uri: biolink:synonym
+ alias: synonym
+ owner: TissueSample
+ domain_of:
+ - named thing
+ - attribute
+ - organism taxon
+ - information content entity
+ - dataset
+ - physical entity
+ - activity
+ - procedure
+ - material sample
+ - biological entity
+ - gene
+ - genome
+ range: label type
+ multivalued: true
+
+A subset of classes that are associated with tissue specimens.
+URI: TissueSpecimen
+| Class | +Description | +
|---|---|
| BrainSlab | +A thick flat piece of brain tissue obtained by slicing a whole brain, brain h... | +
| DissectionRoiPolygon | +A polygon annotated on a brain slab image delineating a region of interest (R... | +
A subset of slots/attributes that are required for tracking.
+URI: Tracking
+| Slot | +Description | +
|---|---|
| cell_prep_type | +The type of cell preparation | +
| local_tube_id | +Library Pool Tube local name | +
| r1_r2_index | +Name of the pair of library indexes used for sequencing | +
Minimum subset of translator work
+URI: TranslatorMinimal
+| Class | +Description | +
|---|---|
| Gene | +A region (or regions) that includes all of the sequence elements necessary to... | +
| GenomicEntity | ++ |
| Name | +Cardinality and Range | +Description | +
|---|---|---|
| category | +* Uriorcurie |
+Name of the high level ontology class in which this entity is categorized | +
| description | +0..1 NarrativeText |
+a human-readable description of an entity | +
| id | +1 String |
+A unique identifier for an entity identifier | +
| in_taxon | +* OrganismTaxon |
+connects an entity to its taxonomic classification | +
| in_taxon_label | +0..1 LabelType |
+The human readable scientific name for the taxon of the entity | +
| iri | +0..1 IriType |
+An IRI for an entity | +
| name | +0..1 LabelType |
+A human-readable name for an attribute or entity | +
| synonym | +* LabelType |
+Alternate human-readable names for a thing | +
| xref | +* Uriorcurie |
+A database cross reference or alternative identifier for a NamedThing or edge... | +
| Slot | +Description | +
|---|---|
| attribute_name | +The human-readable 'attribute name' can be set to a string which reflects its... | +
| category | +Name of the high level ontology class in which this entity is categorized | +
| description | +a human-readable description of an entity | +
| id | +A unique identifier for an entity | +
| in_taxon | +connects an entity to its taxonomic classification | +
| in_taxon_label | +The human readable scientific name for the taxon of the entity | +
| iri | +An IRI for an entity | +
| name | +A human-readable name for an attribute or entity | +
| synonym | +Alternate human-readable names for a thing | +
| xref | +A database cross reference or alternative identifier for a NamedThing or edge... | +
URI: UO:0000000
+ +Instances of this class should have identifiers with one of the following prefixes:
+| Mapping Type | +Mapped Value | +
|---|---|
| self | +UO:0000000 | +
| native | +bican:unit | +
| exact | +qud:Unit | +
a complete URI
+URI: xsd:anyURI
+ +| Mapping Type | +Mapped Value | +
|---|---|
| self | +xsd:anyURI | +
| native | +bican:uri | +
| close | +schema:URL | +
a URI or a CURIE
+URI: xsd:anyURI
+ +| Mapping Type | +Mapped Value | +
|---|---|
| self | +xsd:anyURI | +
| native | +bican:uriorcurie | +
Core base entity for Anatomical Structure schema representing an versioned named thing.
+| Name | +Cardinality and Range | +Description | +Inheritance | +
|---|---|---|---|
| version | +1 String |
++ | direct | +
| revision_of | +0..1 VersionedNamedThing |
++ | direct | +
| id | +1 Uriorcurie |
++ | NamedThing | +
| name | +1 String |
++ | NamedThing | +
| description | +1 String |
++ | NamedThing | +
| category | +* Uriorcurie |
++ | NamedThing | +
| used by | +used in | +type | +used | +
|---|---|---|---|
| ImageDataset | +revision_of | +range | +VersionedNamedThing | +
| AnatomicalSpace | +revision_of | +range | +VersionedNamedThing | +
| ParcellationTerminology | +revision_of | +range | +VersionedNamedThing | +
| ParcellationColorScheme | +revision_of | +range | +VersionedNamedThing | +
| AnatomicalAnnotationSet | +revision_of | +range | +VersionedNamedThing | +
| ParcellationAtlas | +revision_of | +range | +VersionedNamedThing | +
| VersionedNamedThing | +revision_of | +range | +VersionedNamedThing | +
| Mapping Type | +Mapped Value | +
|---|---|
| self | +AnS:VersionedNamedThing | +
| native | +AnS:VersionedNamedThing | +
name: VersionedNamedThing
+description: Core base entity for Anatomical Structure schema representing an versioned
+ named thing.
+from_schema: https://w3id.org/my-org/anatomical-structure-schema
+is_a: NamedThing
+abstract: true
+slots:
+- version
+- revision_of
+
+name: VersionedNamedThing
+description: Core base entity for Anatomical Structure schema representing an versioned
+ named thing.
+from_schema: https://w3id.org/my-org/anatomical-structure-schema
+is_a: NamedThing
+abstract: true
+attributes:
+ version:
+ name: version
+ from_schema: https://w3id.org/my-org/anatomical-structure-schema
+ rank: 1000
+ alias: version
+ owner: VersionedNamedThing
+ domain_of:
+ - VersionedNamedThing
+ range: string
+ required: true
+ revision_of:
+ name: revision_of
+ from_schema: https://w3id.org/my-org/anatomical-structure-schema
+ rank: 1000
+ alias: revision_of
+ owner: VersionedNamedThing
+ domain_of:
+ - VersionedNamedThing
+ range: VersionedNamedThing
+ id:
+ name: id
+ from_schema: https://w3id.org/my-org/anatomical-structure-schema
+ rank: 1000
+ identifier: true
+ alias: id
+ owner: VersionedNamedThing
+ domain_of:
+ - NamedThing
+ range: uriorcurie
+ required: true
+ name:
+ name: name
+ from_schema: https://w3id.org/my-org/anatomical-structure-schema
+ rank: 1000
+ alias: name
+ owner: VersionedNamedThing
+ domain_of:
+ - NamedThing
+ range: string
+ required: true
+ description:
+ name: description
+ from_schema: https://w3id.org/my-org/anatomical-structure-schema
+ rank: 1000
+ alias: description
+ owner: VersionedNamedThing
+ domain_of:
+ - NamedThing
+ range: string
+ required: true
+ category:
+ name: category
+ from_schema: https://w3id.org/my-org/anatomical-structure-schema
+ rank: 1000
+ designates_type: true
+ alias: category
+ owner: VersionedNamedThing
+ domain_of:
+ - NamedThing
+ is_class_field: true
+ range: uriorcurie
+ multivalued: true
+
+Text description of the age of death following typical scientific convention for the species or developmental stage. For example: P56, E11.5
+URI: bican:0630a265-4a63-48f4-8853-66b929002306
+ + +| Name | +Description | +Modifies Slot | +
|---|---|---|
| Donor | +A person or organism that is the source of a biological sample for scientific... | +no | +
| Mapping Type | +Mapped Value | +
|---|---|
| self | +bican:0630a265-4a63-48f4-8853-66b929002306 | +
| native | +bican:age_at_death_description | +
| exact | +NIMP:PD-ZJZJLE33 | +
name: age_at_death_description
+local_names:
+ NIMP:
+ local_name_source: NIMP
+ local_name_value: age_at_death_description
+description: 'Text description of the age of death following typical scientific convention
+ for the species or developmental stage. For example: P56, E11.5'
+from_schema: https://identifiers.org/brain-bican/library-generation-schema
+exact_mappings:
+- NIMP:PD-ZJZJLE33
+rank: 1000
+slot_uri: bican:0630a265-4a63-48f4-8853-66b929002306
+alias: age_at_death_description
+owner: Donor
+domain_of:
+- Donor
+range: string
+
+The reference point for an age interval; for example, birth or conception.
+URI: bican:3bed1f94-9d82-4ed7-afdf-79d896b24dbb
+ + +| Name | +Description | +Modifies Slot | +
|---|---|---|
| Donor | +A person or organism that is the source of a biological sample for scientific... | +no | +
| used by | +used in | +type | +used | +
|---|---|---|---|
| Donor | +age_at_death_reference_point | +range | +age_at_death_reference_point | +
| Mapping Type | +Mapped Value | +
|---|---|
| self | +bican:3bed1f94-9d82-4ed7-afdf-79d896b24dbb | +
| native | +bican:age_at_death_reference_point | +
| exact | +NIMP:PD-RARAGG39 | +
name: age_at_death_reference_point
+local_names:
+ NIMP:
+ local_name_source: NIMP
+ local_name_value: age_at_death_reference_point
+description: The reference point for an age interval; for example, birth or conception.
+from_schema: https://identifiers.org/brain-bican/library-generation-schema
+exact_mappings:
+- NIMP:PD-RARAGG39
+rank: 1000
+slot_uri: bican:3bed1f94-9d82-4ed7-afdf-79d896b24dbb
+alias: age_at_death_reference_point
+owner: Donor
+domain_of:
+- Donor
+range: age_at_death_reference_point
+
+The unit used for representing the donor age from the reference point.
+URI: bican:b5436e99-f0a7-4c30-825d-56b88ee2ac1d
+ + +| Name | +Description | +Modifies Slot | +
|---|---|---|
| Donor | +A person or organism that is the source of a biological sample for scientific... | +no | +
| used by | +used in | +type | +used | +
|---|---|---|---|
| Donor | +age_at_death_unit | +range | +age_at_death_unit | +
| Mapping Type | +Mapped Value | +
|---|---|
| self | +bican:b5436e99-f0a7-4c30-825d-56b88ee2ac1d | +
| native | +bican:age_at_death_unit | +
| exact | +NIMP:PD-AVAVEV39 | +
name: age_at_death_unit
+local_names:
+ NIMP:
+ local_name_source: NIMP
+ local_name_value: age_at_death_unit
+description: The unit used for representing the donor age from the reference point.
+from_schema: https://identifiers.org/brain-bican/library-generation-schema
+exact_mappings:
+- NIMP:PD-AVAVEV39
+rank: 1000
+slot_uri: bican:b5436e99-f0a7-4c30-825d-56b88ee2ac1d
+alias: age_at_death_unit
+owner: Donor
+domain_of:
+- Donor
+range: age_at_death_unit
+
+The value representing the donor age from the reference point.
+URI: bican:57e24d3c-c9c7-4ef3-9809-a35802d563ec
+ + +| Name | +Description | +Modifies Slot | +
|---|---|---|
| Donor | +A person or organism that is the source of a biological sample for scientific... | +no | +
| Mapping Type | +Mapped Value | +
|---|---|
| self | +bican:57e24d3c-c9c7-4ef3-9809-a35802d563ec | +
| native | +bican:age_at_death_value | +
| exact | +NIMP:PD-FTFTCP24 | +
name: age_at_death_value
+local_names:
+ NIMP:
+ local_name_source: NIMP
+ local_name_value: age_at_death
+description: The value representing the donor age from the reference point.
+from_schema: https://identifiers.org/brain-bican/library-generation-schema
+exact_mappings:
+- NIMP:PD-FTFTCP24
+rank: 1000
+slot_uri: bican:57e24d3c-c9c7-4ef3-9809-a35802d563ec
+alias: age_at_death_value
+owner: Donor
+domain_of:
+- Donor
+range: float
+
+The Anatomical Structure schema is designed to represent types and relationships of anatomical brain structures.
+URI: https://w3id.org/my-org/anatomical-structure-schema
+ + + + + + + + + + + + + +The brain slab that was annotated by the delineation process.
+URI: bican:annotates
+ + +| Name | +Description | +Modifies Slot | +
|---|---|---|
| DissectionRoiPolygon | +A polygon annotated on a brain slab image delineating a region of interest (R... | +no | +
| Mapping Type | +Mapped Value | +
|---|---|
| self | +bican:annotates | +
| native | +bican:annotates | +
| exact | +NIMP:has_parent | +
name: annotates
+description: The brain slab that was annotated by the delineation process.
+from_schema: https://identifiers.org/brain-bican/library-generation-schema
+exact_mappings:
+- NIMP:has_parent
+rank: 1000
+alias: annotates
+owner: DissectionRoiPolygon
+domain_of:
+- DissectionRoiPolygon
+range: BrainSlab
+
+URI: bican:annotations
+ + +| Name | +Description | +Modifies Slot | +
|---|---|---|
| AnnotationCollection | ++ | no | +
Range: GeneAnnotation
+Multivalued: True
+| Mapping Type | +Mapped Value | +
|---|---|
| self | +bican:annotations | +
| native | +bican:annotations | +
name: annotations
+from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
+rank: 1000
+alias: annotations
+owner: annotation collection
+domain_of:
+- annotation collection
+range: gene annotation
+multivalued: true
+inlined: true
+inlined_as_list: true
+
+