From 9ec2c00b6d1d8e7736d8d1bba5019fe9b054663c Mon Sep 17 00:00:00 2001 From: Robert Allaway Date: Wed, 25 Oct 2023 13:46:58 -0500 Subject: [PATCH 01/97] convert list to list like --- nf_research_tools.rdb.model.csv | 28 ++++++++++++++-------------- 1 file changed, 14 insertions(+), 14 deletions(-) diff --git a/nf_research_tools.rdb.model.csv b/nf_research_tools.rdb.model.csv index 9f9a2d02..6595a272 100644 --- a/nf_research_tools.rdb.model.csv +++ b/nf_research_tools.rdb.model.csv @@ -4,10 +4,10 @@ resource,"A tool used in the research process (i.e. animal model, cell line, etc resourceId,A unique identifier for the resource.,,,TRUE,,resource,,, rrid,"The RRID, a standard resource identifier that will facilitate interoperability with other databases, and is an increasingly-used identifier for publications https://scicrunch.org/resources if available",,,FALSE,,resource,,, resourceName,The “canonical” name of the resource,,,TRUE,,resource,,, -synonyms,Synonyms of the resource,,,FALSE,,resource,,,list +synonyms,Synonyms of the resource,,,FALSE,,resource,,,list like resourceType,"Type of resource. (e.g. animal model, antibody, plasmid, etc.)","Animal Model, Cell Line, Antibody, Genetic Reagent, Biobank",,TRUE,,resource,,, description,Free text description/summary/overview/purpose of the resource.,,,FALSE,,resource,,, -usageRequirements,Any known restrictions on use of the resource. ,"non-commercial use only, re-distribution not permitted, generation of germ line transmitting chimeras not permitted, creation of functional gametes not permitted, generation of interspecies chimeras not permitted, human cloning not permitted, cannot be used for treatment purposes, IRB documentation required, special licencing restrictions (see vendor for more information), unknown",,FALSE,,resource,,,list +usageRequirements,Any known restrictions on use of the resource. ,"non-commercial use only, re-distribution not permitted, generation of germ line transmitting chimeras not permitted, creation of functional gametes not permitted, generation of interspecies chimeras not permitted, human cloning not permitted, cannot be used for treatment purposes, IRB documentation required, special licencing restrictions (see vendor for more information), unknown",,FALSE,,resource,,,list like howToAcquire,How to acquire a particular resource. ,,,TRUE,,resource,,, dateAdded,The date that the resource was originally added.,,,TRUE,,resource,,, dateModified,The last update of the resource metadata (not including observations).,,,TRUE,,resource,,, @@ -17,9 +17,9 @@ insertName,Name of the main gene insert in the plasmid.,,,TRUE,,geneticReagent,, insertEntrezId,The entrez gene id for the gene insert,,,TRUE,,geneticReagent,,, gRNAshRNASequence,"The sequence of the gRNA or shRNA for the gene insert, if present. ",,,FALSE,,geneticReagent,,, insertSize,"Size, in bp, of the gene insert as it is in the plasmid.",,,FALSE,,geneticReagent,,, -insertSpecies,Species of the insert,"Homo sapiens, Mus musculus, Rattus norvegicus",,TRUE,,geneticReagent,,,list -nTerminalTag,Any tags on the N terminal 5' end of the gene insert in the plasmid. Only tags that are in frame,,,FALSE,,geneticReagent,,,list -cTerminalTag,Any tags on the C terminal 3' end of the gene insert in the plasmid. Only tags that are in frame,,,FALSE,,geneticReagent,,,list +insertSpecies,Species of the insert,"Homo sapiens, Mus musculus, Rattus norvegicus",,TRUE,,geneticReagent,,,list like +nTerminalTag,Any tags on the N terminal 5' end of the gene insert in the plasmid. Only tags that are in frame,,,FALSE,,geneticReagent,,,list like +cTerminalTag,Any tags on the C terminal 3' end of the gene insert in the plasmid. Only tags that are in frame,,,FALSE,,geneticReagent,,,list like cloningMethod,"How the vector was constructed. (e.g. restriction enzyme, TOPO cloning, etc.)","Restriction Enzyme, TOPO cloning, Gateway Cloning, Ligation Independent Cloning, Gibson Cloning, Unknown",,FALSE,,geneticReagent,,, 5primeCloningSite,"If Restriction Enzyme was selected as the cloning method, specifies what enzyme was used on the 5' (N-terminal) end of the insert",,cloningMethod,FALSE,,geneticReagent,,, 5primeSiteDestroyed,"If 5' site was destroyed during cloning. (e.g. yes, no, unknown).","Yes, No, Unknown",,FALSE,,geneticReagent,,, @@ -29,7 +29,7 @@ promoter,Promoter driving the expression of the insert in the plasmid,,,FALSE,,g 5primer,Primer to sequence the 5' end (N-terminal) of the insert,,,FALSE,,geneticReagent,,, 3primer,Primer to sequence the 3' end (C-terminal) of the insert.,,,FALSE,,geneticReagent,,, vectorBackbone,Name of the backbone the plasmid is built on. (e.g pGBT9),,,FALSE,,geneticReagent,,, -vectorType,"Primary function of the plasmid. (e.g. mammalian expression, bacterial expression, etc.)","Mammalian Expression, Bacterial Expression, Gateway Entry Clone, Lentiviral, Adenoviral, AAV, RNAi, Luciferase, Cre/Lox, Yeast Expression, Worm Expression, Insect Expression, Plant Expression, Mouse Targeting, CRISPR, TALEN, Synthetic Biology, Transfer Vector, Unspecified, Other",,FALSE,,geneticReagent,,,list +vectorType,"Primary function of the plasmid. (e.g. mammalian expression, bacterial expression, etc.)","Mammalian Expression, Bacterial Expression, Gateway Entry Clone, Lentiviral, Adenoviral, AAV, RNAi, Luciferase, Cre/Lox, Yeast Expression, Worm Expression, Insect Expression, Plant Expression, Mouse Targeting, CRISPR, TALEN, Synthetic Biology, Transfer Vector, Unspecified, Other",,FALSE,,geneticReagent,,,list like backboneSize,Size in bp of the backbone without the insert,,,FALSE,,geneticReagent,,, totalSize,Size of vector with insert. Derived from insertSize and backboneSize.,,,FALSE,,geneticReagent,,, bacterialResistance,"Antibiotic(s) that should be used for selection in bacteria. (e.g. ampicillin, kanamycin, etc.)","Ampicillin, Kanamycin, Chloramphenicol, Tetracycline, Spectinomycin, Hygromycin, Bleocin(Zeocin), Gentamycin, Streptomycin, Nourseothricin(clonNat), Ampicillin and Bleocin (Zeocin), Ampicillin and Kanamycin, Ampicillin and Tetracycline, Ampicillin and Streptomycin, Ampicillin and Spectinomycin, Chloramphenicol and Ampicillin, Chloramphenicol and Bleocin (Zeocin), Chloramphenicol and Tetracycline, Chloramphenicol and Kanamycin, Chloramphenicol and Spectinomycin, Chloramphenicol and Gentamycin, Spectinomycin and Streptomycin, Other",,FALSE,,geneticReagent,,, @@ -50,12 +50,12 @@ biobank,"A large collection of biological or medical data and tissue samples, am biobankName,The name of the biobank. ,,,TRUE,,biobank,,, biobankId,A unique identifier for the biobank.,,,TRUE,,biobank,,, biobankURL,A URL for the biobank landing page.,,,TRUE,,biobank,,, -specimenType,The types of specimens that are banked.,"human tissue, xenograft tumors, cell lines",,TRUE,,biobank,,,list -specimenTissueType,The types of tissues that are banked.,"blood, tumor, cerebrospinal fluid, nerve, skin, bone, brain",,TRUE,,biobank,,,list -tumorType,"The types of tumors that are banked, if applicable.","cutaneous neurofibroma, plexiform neurofibroma, schwannoma, meningioma, malignant peripheral nerve sheath tumor, low grade glioma, high grade glioma, pheochromocytoma, optic nerve glioma, atypical neurofibroma, neurofibroma NOS, diffuse infiltrating neurofibroma, brain NOS",,TRUE,,biobank,,,list -diseaseType,"The diseases of the banked specimens, if applicable.","Neurofibromatosis type 1, Neurofibromatosis type 2, Schwannomatosis",,TRUE,,biobank,,,list -specimenPreparationMethod,The preservation methods used by the biobank.,"Fresh collected, Flash frozen, FFPE, Cryopreserved, OCT, RNA later, Formalin-fixed, Ethanol",,TRUE,,biobank,,,list -specimenFormat,How the specimens have been processed in preparation for distribution.,"whole tumor, slide, whole cell lysate, DNA, RNA",,TRUE,,biobank,,,list +specimenType,The types of specimens that are banked.,"human tissue, xenograft tumors, cell lines",,TRUE,,biobank,,,list like +specimenTissueType,The types of tissues that are banked.,"blood, tumor, cerebrospinal fluid, nerve, skin, bone, brain",,TRUE,,biobank,,,list like +tumorType,"The types of tumors that are banked, if applicable.","cutaneous neurofibroma, plexiform neurofibroma, schwannoma, meningioma, malignant peripheral nerve sheath tumor, low grade glioma, high grade glioma, pheochromocytoma, optic nerve glioma, atypical neurofibroma, neurofibroma NOS, diffuse infiltrating neurofibroma, brain NOS",,TRUE,,biobank,,,list like +diseaseType,"The diseases of the banked specimens, if applicable.","Neurofibromatosis type 1, Neurofibromatosis type 2, Schwannomatosis",,TRUE,,biobank,,,list like +specimenPreparationMethod,The preservation methods used by the biobank.,"Fresh collected, Flash frozen, FFPE, Cryopreserved, OCT, RNA later, Formalin-fixed, Ethanol",,TRUE,,biobank,,,list like +specimenFormat,How the specimens have been processed in preparation for distribution.,"whole tumor, slide, whole cell lysate, DNA, RNA",,TRUE,,biobank,,,list like observation,"A remark, statement, or comment based on the resource.",,"Component, observationId, resourceId, publicationId, observationSubmitterName, synapseId, observationText, observationType, observationPhase, observationTime, observationTimeUnits, reliabilityRating, easeOfUseRating, observationLink",FALSE,,observation,"observationId, resourceId, publicationId, observationSubmitterName, synapseId, observationText, observationType, observationPhase, observationTime, observationTimeUnits, reliabilityRating, easeOfUseRating, observationLink","resource, investigator, publication", observationId,A unique identifier for the observation.,,,TRUE,,observation,,, observationSubmitterName,The name of the person submitting the observation. ,,,TRUE,,observation,,, @@ -71,7 +71,7 @@ observationLink,"A link/reference related to the observation being recorded. If resourceApplication,"Applications the resource can be used for. (i.e. western blot, immunofluorescence, etc.)",,"Component, resourceApplicationId, resourceId, source, applications, links",FALSE,,resourceApplication,"resourceApplicationId, resourceId, source, applications, links",resource, resourceApplicationId,A unique identifier for resrouce Application,,,TRUE,,resourceApplication,,, source,"The source of resource application information (e.g. Vendor, Community)","Community-reported, Investigator-reported, Vendor-reported",,TRUE,,resourceApplication,,, -applications,"One or more uses for the resource (e.g. western blot, immunofluorescence)","Western Blot, Immunofluorescence, ELISA, Immunohistochemistry, Immunoprecipitation, Tumor Growth Studies, Immunohistochemistry (Paraffin-Embedded), Immunocytochemistry, Immunohistochemistry (Frozen Sections), Flow Cytometry, Affinity Purification, Microarray",,TRUE,,resourceApplication,,,list +applications,"One or more uses for the resource (e.g. western blot, immunofluorescence)","Western Blot, Immunofluorescence, ELISA, Immunohistochemistry, Immunoprecipitation, Tumor Growth Studies, Immunohistochemistry (Paraffin-Embedded), Immunocytochemistry, Immunohistochemistry (Frozen Sections), Flow Cytometry, Affinity Purification, Microarray",,TRUE,,resourceApplication,,,list like links,shareable links related to the resource,,,FALSE,,resourceApplication,,,list antibody,"A blood protein produced in response to and counteracting a specific antigen. Antibodies combine chemically with substances which the body recognizes as alien, such as bacteria, viruses, and foreign substances in the blood.",,"Component, antibodyId, uniprotId, targetAntigen, clonality, cloneId, reactiveSpecies, conjugate, hostOrganism",FALSE,,antibody,,, antibodyId,A unique identifier for the antibody.,,,TRUE,,antibody,"antibodyId, uniprotId, targetAntigen, clonality, cloneId, reactiveSpecies, conjugate, hostOrganism",, @@ -142,7 +142,7 @@ investigatorSynapseId,The synapse identifier for the investigator.,,,FALSE,,inve publication,Initial publication associated with the resource.,,"Component, publicationId, publicationTitle, authors, abstract, journal, publicationDate, pmid, doi, citation, publicationDateUnix",FALSE,,publication,"publicationId, publicationTitle, authors, abstract, journal, publicationDate, pmid, doi, citation, publicationDateUnix",, publicationId,A unique identifier for the publication.,,,FALSE,,publication,,, publicationTitle,The title of the publication associated with the resource.,,,TRUE,,publication,,, -authors,Writers of the publication.,,,FALSE,,publication,,,list +authors,Writers of the publication.,,,FALSE,,publication,,,list like abstract,"A brief, comprehensive summary of the contents of a publication.",,,FALSE,,publication,,, journal,The name of the periodical publication in which the paper was published.,,,FALSE,,publication,,, publicationDate,The date of the paper's publication.,,,FALSE,,publication,,, From fddb02fc62488a923b09a043b86f4dd3c1d938e2 Mon Sep 17 00:00:00 2001 From: Robert Allaway Date: Wed, 25 Oct 2023 13:52:36 -0500 Subject: [PATCH 02/97] Update nf_research_tools.rdb.model.csv From 54b694f06f780d5fd25099a0821cc5037eba7a0b Mon Sep 17 00:00:00 2001 From: Robert Allaway Date: Wed, 25 Oct 2023 13:53:12 -0500 Subject: [PATCH 03/97] Update nf_research_tools.rdb.model.csv --- nf_research_tools.rdb.model.csv | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/nf_research_tools.rdb.model.csv b/nf_research_tools.rdb.model.csv index 6595a272..ac08d9ea 100644 --- a/nf_research_tools.rdb.model.csv +++ b/nf_research_tools.rdb.model.csv @@ -4,7 +4,7 @@ resource,"A tool used in the research process (i.e. animal model, cell line, etc resourceId,A unique identifier for the resource.,,,TRUE,,resource,,, rrid,"The RRID, a standard resource identifier that will facilitate interoperability with other databases, and is an increasingly-used identifier for publications https://scicrunch.org/resources if available",,,FALSE,,resource,,, resourceName,The “canonical” name of the resource,,,TRUE,,resource,,, -synonyms,Synonyms of the resource,,,FALSE,,resource,,,list like +synonyms,Synonyms of the resource,,,FALSE,,resource,,,list resourceType,"Type of resource. (e.g. animal model, antibody, plasmid, etc.)","Animal Model, Cell Line, Antibody, Genetic Reagent, Biobank",,TRUE,,resource,,, description,Free text description/summary/overview/purpose of the resource.,,,FALSE,,resource,,, usageRequirements,Any known restrictions on use of the resource. ,"non-commercial use only, re-distribution not permitted, generation of germ line transmitting chimeras not permitted, creation of functional gametes not permitted, generation of interspecies chimeras not permitted, human cloning not permitted, cannot be used for treatment purposes, IRB documentation required, special licencing restrictions (see vendor for more information), unknown",,FALSE,,resource,,,list like From b6516f9f02dea4b69104c0bfcb984f31cf951bca Mon Sep 17 00:00:00 2001 From: Robert Allaway Date: Wed, 25 Oct 2023 13:53:30 -0500 Subject: [PATCH 04/97] Update nf_research_tools.rdb.model.csv --- nf_research_tools.rdb.model.csv | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/nf_research_tools.rdb.model.csv b/nf_research_tools.rdb.model.csv index ac08d9ea..6595a272 100644 --- a/nf_research_tools.rdb.model.csv +++ b/nf_research_tools.rdb.model.csv @@ -4,7 +4,7 @@ resource,"A tool used in the research process (i.e. animal model, cell line, etc resourceId,A unique identifier for the resource.,,,TRUE,,resource,,, rrid,"The RRID, a standard resource identifier that will facilitate interoperability with other databases, and is an increasingly-used identifier for publications https://scicrunch.org/resources if available",,,FALSE,,resource,,, resourceName,The “canonical” name of the resource,,,TRUE,,resource,,, -synonyms,Synonyms of the resource,,,FALSE,,resource,,,list +synonyms,Synonyms of the resource,,,FALSE,,resource,,,list like resourceType,"Type of resource. (e.g. animal model, antibody, plasmid, etc.)","Animal Model, Cell Line, Antibody, Genetic Reagent, Biobank",,TRUE,,resource,,, description,Free text description/summary/overview/purpose of the resource.,,,FALSE,,resource,,, usageRequirements,Any known restrictions on use of the resource. ,"non-commercial use only, re-distribution not permitted, generation of germ line transmitting chimeras not permitted, creation of functional gametes not permitted, generation of interspecies chimeras not permitted, human cloning not permitted, cannot be used for treatment purposes, IRB documentation required, special licencing restrictions (see vendor for more information), unknown",,FALSE,,resource,,,list like From 341f0535f3720fc02305e87ab0a04a6ed68c598e Mon Sep 17 00:00:00 2001 From: Robert Allaway Date: Wed, 25 Oct 2023 13:56:58 -0500 Subject: [PATCH 05/97] Update nf_research_tools.rdb.model.csv --- nf_research_tools.rdb.model.csv | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/nf_research_tools.rdb.model.csv b/nf_research_tools.rdb.model.csv index 6595a272..ac08d9ea 100644 --- a/nf_research_tools.rdb.model.csv +++ b/nf_research_tools.rdb.model.csv @@ -4,7 +4,7 @@ resource,"A tool used in the research process (i.e. animal model, cell line, etc resourceId,A unique identifier for the resource.,,,TRUE,,resource,,, rrid,"The RRID, a standard resource identifier that will facilitate interoperability with other databases, and is an increasingly-used identifier for publications https://scicrunch.org/resources if available",,,FALSE,,resource,,, resourceName,The “canonical” name of the resource,,,TRUE,,resource,,, -synonyms,Synonyms of the resource,,,FALSE,,resource,,,list like +synonyms,Synonyms of the resource,,,FALSE,,resource,,,list resourceType,"Type of resource. (e.g. animal model, antibody, plasmid, etc.)","Animal Model, Cell Line, Antibody, Genetic Reagent, Biobank",,TRUE,,resource,,, description,Free text description/summary/overview/purpose of the resource.,,,FALSE,,resource,,, usageRequirements,Any known restrictions on use of the resource. ,"non-commercial use only, re-distribution not permitted, generation of germ line transmitting chimeras not permitted, creation of functional gametes not permitted, generation of interspecies chimeras not permitted, human cloning not permitted, cannot be used for treatment purposes, IRB documentation required, special licencing restrictions (see vendor for more information), unknown",,FALSE,,resource,,,list like From a179887131b0fac22370d7c163c80539128565ce Mon Sep 17 00:00:00 2001 From: Robert Allaway Date: Wed, 25 Oct 2023 13:57:07 -0500 Subject: [PATCH 06/97] Update nf_research_tools.rdb.model.csv --- nf_research_tools.rdb.model.csv | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/nf_research_tools.rdb.model.csv b/nf_research_tools.rdb.model.csv index ac08d9ea..6595a272 100644 --- a/nf_research_tools.rdb.model.csv +++ b/nf_research_tools.rdb.model.csv @@ -4,7 +4,7 @@ resource,"A tool used in the research process (i.e. animal model, cell line, etc resourceId,A unique identifier for the resource.,,,TRUE,,resource,,, rrid,"The RRID, a standard resource identifier that will facilitate interoperability with other databases, and is an increasingly-used identifier for publications https://scicrunch.org/resources if available",,,FALSE,,resource,,, resourceName,The “canonical” name of the resource,,,TRUE,,resource,,, -synonyms,Synonyms of the resource,,,FALSE,,resource,,,list +synonyms,Synonyms of the resource,,,FALSE,,resource,,,list like resourceType,"Type of resource. (e.g. animal model, antibody, plasmid, etc.)","Animal Model, Cell Line, Antibody, Genetic Reagent, Biobank",,TRUE,,resource,,, description,Free text description/summary/overview/purpose of the resource.,,,FALSE,,resource,,, usageRequirements,Any known restrictions on use of the resource. ,"non-commercial use only, re-distribution not permitted, generation of germ line transmitting chimeras not permitted, creation of functional gametes not permitted, generation of interspecies chimeras not permitted, human cloning not permitted, cannot be used for treatment purposes, IRB documentation required, special licencing restrictions (see vendor for more information), unknown",,FALSE,,resource,,,list like From f3b3ea8029eacaaa219adf2dd1e08acec4ce3df3 Mon Sep 17 00:00:00 2001 From: Robert Allaway Date: Wed, 25 Oct 2023 13:58:30 -0500 Subject: [PATCH 07/97] Update nf_research_tools.rdb.model.csv --- nf_research_tools.rdb.model.csv | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/nf_research_tools.rdb.model.csv b/nf_research_tools.rdb.model.csv index 6595a272..ac08d9ea 100644 --- a/nf_research_tools.rdb.model.csv +++ b/nf_research_tools.rdb.model.csv @@ -4,7 +4,7 @@ resource,"A tool used in the research process (i.e. animal model, cell line, etc resourceId,A unique identifier for the resource.,,,TRUE,,resource,,, rrid,"The RRID, a standard resource identifier that will facilitate interoperability with other databases, and is an increasingly-used identifier for publications https://scicrunch.org/resources if available",,,FALSE,,resource,,, resourceName,The “canonical” name of the resource,,,TRUE,,resource,,, -synonyms,Synonyms of the resource,,,FALSE,,resource,,,list like +synonyms,Synonyms of the resource,,,FALSE,,resource,,,list resourceType,"Type of resource. (e.g. animal model, antibody, plasmid, etc.)","Animal Model, Cell Line, Antibody, Genetic Reagent, Biobank",,TRUE,,resource,,, description,Free text description/summary/overview/purpose of the resource.,,,FALSE,,resource,,, usageRequirements,Any known restrictions on use of the resource. ,"non-commercial use only, re-distribution not permitted, generation of germ line transmitting chimeras not permitted, creation of functional gametes not permitted, generation of interspecies chimeras not permitted, human cloning not permitted, cannot be used for treatment purposes, IRB documentation required, special licencing restrictions (see vendor for more information), unknown",,FALSE,,resource,,,list like From a8dc317391c00bcb0362606fb56fea8c10e2c15b Mon Sep 17 00:00:00 2001 From: Robert Allaway Date: Wed, 25 Oct 2023 13:58:39 -0500 Subject: [PATCH 08/97] Update nf_research_tools.rdb.model.csv --- nf_research_tools.rdb.model.csv | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/nf_research_tools.rdb.model.csv b/nf_research_tools.rdb.model.csv index ac08d9ea..6595a272 100644 --- a/nf_research_tools.rdb.model.csv +++ b/nf_research_tools.rdb.model.csv @@ -4,7 +4,7 @@ resource,"A tool used in the research process (i.e. animal model, cell line, etc resourceId,A unique identifier for the resource.,,,TRUE,,resource,,, rrid,"The RRID, a standard resource identifier that will facilitate interoperability with other databases, and is an increasingly-used identifier for publications https://scicrunch.org/resources if available",,,FALSE,,resource,,, resourceName,The “canonical” name of the resource,,,TRUE,,resource,,, -synonyms,Synonyms of the resource,,,FALSE,,resource,,,list +synonyms,Synonyms of the resource,,,FALSE,,resource,,,list like resourceType,"Type of resource. (e.g. animal model, antibody, plasmid, etc.)","Animal Model, Cell Line, Antibody, Genetic Reagent, Biobank",,TRUE,,resource,,, description,Free text description/summary/overview/purpose of the resource.,,,FALSE,,resource,,, usageRequirements,Any known restrictions on use of the resource. ,"non-commercial use only, re-distribution not permitted, generation of germ line transmitting chimeras not permitted, creation of functional gametes not permitted, generation of interspecies chimeras not permitted, human cloning not permitted, cannot be used for treatment purposes, IRB documentation required, special licencing restrictions (see vendor for more information), unknown",,FALSE,,resource,,,list like From cf6623e60f1d97e4851ad1bad63f72fd3175c404 Mon Sep 17 00:00:00 2001 From: "nf-osi[bot]" Date: Wed, 25 Oct 2023 19:00:30 +0000 Subject: [PATCH 09/97] Add changes --- nf-research-tools.jsonld | 10613 +++++++++++++++---------------------- 1 file changed, 4369 insertions(+), 6244 deletions(-) diff --git a/nf-research-tools.jsonld b/nf-research-tools.jsonld index 4bb6d379..f58838ad 100644 --- a/nf-research-tools.jsonld +++ b/nf-research-tools.jsonld @@ -7,2062 +7,6 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ - { - "@id": "schema:Text", - "@type": [ - "schema:DataType", - "rdfs:Class" - ], - "rdfs:comment": "Data type: Text.", - "rdfs:label": "Text" - }, - { - "@id": "schema:Number", - "@type": [ - "schema:DataType", - "rdfs:Class" - ], - "rdfs:comment": "Data type: Number.", - "rdfs:label": "Number" - }, - { - "@id": "schema:Integer", - "@type": "rdfs:Class", - "rdfs:comment": "Data type: Integer.", - "rdfs:label": "Integer", - "rdfs:subClassOf": { - "@id": "schema:Number" - } - }, - { - "@id": "schema:Thing", - "@type": "rdfs:Class", - "rdfs:comment": "Thing", - "rdfs:label": "Thing", - "schema:isPartOf": { - "@id": "http://schema.org" - } - }, - { - "@id": "bts:BiologicalEntity", - "@type": "rdfs:Class", - "rdfs:comment": null, - "rdfs:label": "BiologicalEntity", - "rdfs:subClassOf": { - "@id": "schema:Thing" - }, - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - } - }, - { - "@id": "bts:OntologyClass", - "@type": "rdfs:Class", - "rdfs:comment": "a concept or class in an ontology, vocabulary or thesaurus", - "rdfs:label": "OntologyClass", - "rdfs:subClassOf": { - "@id": "schema:Thing" - }, - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - } - }, - { - "@id": "bts:RelationshipType", - "@type": "rdfs:Class", - "rdfs:comment": "An OWL property used as an edge label", - "rdfs:label": "RelationshipType", - "rdfs:subClassOf": { - "@id": "bts:OntologyClass" - }, - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - } - }, - { - "@id": "bts:GeneOntologyClass", - "@type": "rdfs:Class", - "rdfs:comment": "an ontology class that describes a functional aspect of a gene, gene prodoct or complex", - "rdfs:label": "GeneOntologyClass", - "rdfs:subClassOf": { - "@id": "bts:OntologyClass" - }, - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - } - }, - { - "@id": "bts:OrganismTaxon", - "@type": "rdfs:Class", - "rdfs:comment": null, - "rdfs:label": "OrganismTaxon", - "rdfs:subClassOf": { - "@id": "bts:OntologyClass" - }, - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - } - }, - { - "@id": "bts:OrganismalEntity", - "@type": "rdfs:Class", - "rdfs:comment": "A named entity that is either a part of an organism, a whole organism, population or clade of organisms, excluding molecular entities", - "rdfs:label": "OrganismalEntity", - "rdfs:subClassOf": { - "@id": "bts:BiologicalEntity" - }, - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - } - }, - { - "@id": "bts:IndividualOrganism", - "@type": "rdfs:Class", - "rdfs:comment": null, - "rdfs:label": "IndividualOrganism", - "rdfs:subClassOf": { - "@id": "bts:OrganismalEntity" - }, - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - } - }, - { - "@id": "bts:Case", - "@type": "rdfs:Class", - "rdfs:comment": "An individual organism that has a patient role in some clinical context.", - "rdfs:label": "Case", - "rdfs:subClassOf": { - "@id": "bts:IndividualOrganism" - }, - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - } - }, - { - "@id": "bts:PopulationOfIndividualOrganisms", - "@type": "rdfs:Class", - "rdfs:comment": null, - "rdfs:label": "PopulationOfIndividualOrganisms", - "rdfs:subClassOf": { - "@id": "bts:OrganismalEntity" - }, - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - } - }, - { - "@id": "bts:Biosample", - "@type": "rdfs:Class", - "rdfs:comment": null, - "rdfs:label": "Biosample", - "rdfs:subClassOf": { - "@id": "bts:OrganismalEntity" - }, - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - } - }, - { - "@id": "bts:DiseaseOrPhenotypicFeature", - "@type": "rdfs:Class", - "rdfs:comment": "Either one of a disease or an individual phenotypic feature. 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"@id": "http://schema.biothings.io" - } - }, - { - "@id": "bts:Cell", - "@type": "rdfs:Class", - "rdfs:comment": null, - "rdfs:label": "Cell", - "rdfs:subClassOf": { - "@id": "bts:AnatomicalEntity" - }, - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - } - }, - { - "@id": "bts:CellLine", - "@type": "rdfs:Class", - "rdfs:comment": "A cell culture selected for uniformity from a cell population derived from a usually homogeneous tissue source (such as an organ).", - "rdfs:label": "CellLine", - "rdfs:subClassOf": [ - { - "@id": "bts:CellLine" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "cellLine", - "sms:required": "sms:false", - "sms:requiresComponent": [ - { - "@id": "bts:Donor" - } - ], - "sms:requiresDependency": [ - { - "@id": "bts:Component" - }, - { - "@id": "bts:cellLineId" - }, - { - "@id": "bts:donorId" - }, - { - "@id": "bts:organ" - }, - { - "@id": "bts:tissue" - }, - { - "@id": "bts:cellLineCategory" - }, - { - "@id": "bts:originYear" - 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{ - "@id": "bts:Disease" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": { - "@id": "schema:Integer" - } - }, - { - "@id": "bts:umls", - "@type": "rdf:Property", - "rdfs:comment": "Refseq ID for gene, protein or transcript", - "rdfs:label": "umls", - "schema:domainIncludes": { - "@id": "bts:Disease" - }, - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": { - "@id": "schema:Text" - } - }, - { - "@id": "bts:homologousTo", - "@type": "rdf:Property", - "rdfs:comment": "Shared ancestry between protein or gene", - "rdfs:label": "homologousTo", - "schema:domainIncludes": { - "@id": "bts:GeneOrGeneProduct" - }, - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": { - "@id": "bts:GeneOrGeneProduct" - } - }, - { - "@id": "bts:molecularlyInteractsWith", - "@type": "rdf:Property", - "rdfs:comment": null, - "rdfs:label": "molecularlyInteractsWith", - "schema:domainIncludes": { - 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"@id": "bts:MolecularEntity" - }, - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": { - "@id": "bts:MolecularEntity" - } - }, - { - "@id": "bts:decreasesAbundanceOf", - "@type": "rdf:Property", - "rdfs:comment": "holds between two molecular entities where the action or effect of one decreases the amount of the other within a system of interest", - "rdfs:label": "decreasesAbundanceOf", - "schema:domainIncludes": { - "@id": "bts:MolecularEntity" - }, - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": { - "@id": "bts:MolecularEntity" - } - }, - { - "@id": "bts:affectsActivityOf", - "@type": "rdf:Property", - "rdfs:comment": "holds between two molecular entities where the action or effect of one changes the activity of the other within a system of interest", - "rdfs:label": "affectsActivityOf", - "schema:domainIncludes": { - "@id": "bts:MolecularEntity" - }, - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": { - "@id": "bts:MolecularEntity" - } - }, - { - "@id": "bts:increasesActivityOf", - "@type": "rdf:Property", - "rdfs:comment": "holds between two molecular entities where the action or effect of one increases the activity of the other within a system of interest", - "rdfs:label": "increasesActivityOf", - "schema:domainIncludes": { - "@id": "bts:MolecularEntity" - }, - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": { - "@id": "bts:MolecularEntity" - } - }, - { - "@id": "bts:decreasesActivityOf", - "@type": "rdf:Property", - "rdfs:comment": "holds between two molecular entities where the action or effect of one decreases the activity of the other within a system of interest", - "rdfs:label": "decreasesActivityOf", - "schema:domainIncludes": { - "@id": "bts:MolecularEntity" - }, - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": { - "@id": "bts:MolecularEntity" - } - }, - { - "@id": "bts:affectsExpressionOf", - "@type": "rdf:Property", - "rdfs:comment": "holds between two molecular entities where the action or effect of one changes the level of expression of the other within a system of interest", - "rdfs:label": "affectsExpressionOf", - "schema:domainIncludes": { - "@id": "bts:MolecularEntity" - }, - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": { - "@id": "bts:GenomicEntity" - } - }, - { - "@id": "bts:increasesExpressionOf", - "@type": "rdf:Property", - "rdfs:comment": "holds between two molecular entities where the action or effect of one increases the level of expression of the other within a system of interest", - "rdfs:label": "increasesExpressionOf", - "schema:domainIncludes": { - "@id": "bts:MolecularEntity" - }, - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": { - "@id": "bts:GenomicEntity" - } - }, - { - "@id": "bts:decreasesExpressionOf", - "@type": "rdf:Property", - "rdfs:comment": "holds between two molecular entities where the action or effect of one decreases the level of expression of the other within a system of interest", - "rdfs:label": "decreasesExpressionOf", - "schema:domainIncludes": { - "@id": "bts:MolecularEntity" - }, - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": { - "@id": "bts:GenomicEntity" - } - }, - { - "@id": "bts:affectsFoldingOf", - "@type": "rdf:Property", - "rdfs:comment": "holds between two molecular entities where the action or effect of one changes the rate or quality of folding of the other ", - "rdfs:label": "affectsFoldingOf", - "schema:domainIncludes": { - "@id": "bts:MolecularEntity" - }, - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": { - "@id": "bts:MolecularEntity" - } - }, - { - "@id": "bts:increasesFoldingOf", - "@type": "rdf:Property", - "rdfs:comment": "holds between two molecular entities where the action or effect of one increases the rate or quality of folding of the other ", - "rdfs:label": "increasesFoldingOf", - "schema:domainIncludes": { - "@id": "bts:MolecularEntity" - }, - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": { - "@id": "bts:MolecularEntity" - } - }, - { - "@id": "bts:decreasesFoldingOf", - "@type": "rdf:Property", - "rdfs:comment": "holds between two molecular entities where the action or effect of one decreases the rate or quality of folding of the other ", - "rdfs:label": "decreasesFoldingOf", - "schema:domainIncludes": { - "@id": "bts:MolecularEntity" - }, - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": { - "@id": "bts:MolecularEntity" - } - }, - { - "@id": "bts:affectsLocalizationOf", - "@type": "rdf:Property", - "rdfs:comment": "holds between two molecular entities where the action or effect of one changes the localization of the other within a system of interest", - "rdfs:label": "affectsLocalizationOf", - "schema:domainIncludes": { - "@id": "bts:MolecularEntity" - }, - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": { - "@id": "bts:MolecularEntity" - } - }, - { - "@id": "bts:increasesLocalizationOf", - "@type": "rdf:Property", - "rdfs:comment": "holds between two molecular entities where the action or effect of one increases the proper localization of the other within a system of interest", - "rdfs:label": "increasesLocalizationOf", - "schema:domainIncludes": { - "@id": "bts:MolecularEntity" - }, - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": { - "@id": "bts:MolecularEntity" - } - }, - { - "@id": "bts:decreasesLocalizationOf", - "@type": "rdf:Property", - "rdfs:comment": "holds between two molecular entities where the action or effect of one decreases the proper localization of the other within a system of interest", - "rdfs:label": "decreasesLocalizationOf", - "schema:domainIncludes": { - "@id": "bts:MolecularEntity" - }, - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": { - "@id": "bts:MolecularEntity" - } - }, - { - "@id": "bts:affectsMetabolicProcessingOf", - "@type": "rdf:Property", - "rdfs:comment": "holds between two molecular entities where the action or effect of one impacts the metabolic processing of the other within a system of interest", - "rdfs:label": "affectsMetabolicProcessingOf", - "schema:domainIncludes": { - "@id": "bts:MolecularEntity" - }, - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": { - "@id": "bts:MolecularEntity" - } - }, - { - "@id": "bts:increasesMetabolicProcessingOf", - "@type": "rdf:Property", - "rdfs:comment": "holds between two molecular entities where the action or effect of one increases the rate of metabolic processing of the other within a system of interest", - "rdfs:label": "increasesMetabolicProcessingOf", - "schema:domainIncludes": { - "@id": "bts:MolecularEntity" - }, - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": { - "@id": "bts:MolecularEntity" - } - }, - { - "@id": "bts:decreasesMetabolicProcessingOf", - "@type": "rdf:Property", - "rdfs:comment": "holds between two molecular entities where the action or effect of one decreases the rate of metabolic processing of the other within a system of interest", - "rdfs:label": "decreasesMetabolicProcessingOf", - "schema:domainIncludes": { - "@id": "bts:MolecularEntity" - }, - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": { - "@id": "bts:MolecularEntity" - } - }, - { - "@id": "bts:affectsMolecularModificationOf", - "@type": "rdf:Property", - "rdfs:comment": "holds between two molecular entities where the action or effect of one leads changes in the molecular modification(s) of the other (e.g. via post-translational modifications of proteins such as the addition of phosphoryl group, or via redox reaction that adds or subtracts electrons)", - "rdfs:label": "affectsMolecularModificationOf", - "schema:domainIncludes": { - "@id": "bts:MolecularEntity" - }, - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": { - "@id": "bts:MolecularEntity" - } - }, - { - "@id": "bts:increasesMolecularModificationOf", - "@type": "rdf:Property", - "rdfs:comment": "holds between two molecular entities where the action or effect of one leads to increased molecular modification(s) of the other (e.g. via post-translational modifications of proteins such as the addition of phosphoryl group, or via redox reaction that adds or subtracts electrons)", - "rdfs:label": "increasesMolecularModificationOf", - "schema:domainIncludes": { - "@id": "bts:MolecularEntity" - }, - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": { - "@id": "bts:MolecularEntity" - } - }, - { - "@id": "bts:decreasesMolecularModificationOf", - "@type": "rdf:Property", - "rdfs:comment": "holds between two molecular entities where the action or effect of one leads to decreased molecular modification(s) of the other (e.g. via post-translational modifications of proteins such as the addition of phosphoryl group, or via redox reaction that adds or subtracts electrons)", - 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}, - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": { - "@id": "bts:MolecularEntity" - } - }, - { - "@id": "bts:decreasesSynthesisOf", - "@type": "rdf:Property", - "rdfs:comment": "holds between two molecular entities where the action or effect of one decreases the rate of chemical synthesis of the other", - "rdfs:label": "decreasesSynthesisOf", - "schema:domainIncludes": { - "@id": "bts:MolecularEntity" - }, - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": { - "@id": "bts:MolecularEntity" - } - }, - { - "@id": "bts:affectsDegradationOf", - "@type": "rdf:Property", - "rdfs:comment": "holds between two molecular entities where the action or effect of one impacts the rate of degradation of the other within a system of interest", - "rdfs:label": "affectsDegradationOf", - "schema:domainIncludes": { - "@id": "bts:MolecularEntity" - }, - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": { - "@id": "bts:MolecularEntity" - } - }, - { - "@id": "bts:increasesDegradationOf", - "@type": "rdf:Property", - "rdfs:comment": "holds between two molecular entities where the action or effect of one increases the rate of degradation of the other within a system of interest", - "rdfs:label": "increasesDegradationOf", - "schema:domainIncludes": { - "@id": "bts:MolecularEntity" - }, - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": { - "@id": "bts:MolecularEntity" - } - }, - { - "@id": "bts:decreasesDegradationOf", - "@type": "rdf:Property", - "rdfs:comment": "holds between two molecular entities where the action or effect of one decreases the rate of degradation of the other within a system of interest", - "rdfs:label": "decreasesDegradationOf", - "schema:domainIncludes": { - "@id": "bts:MolecularEntity" - }, - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": { - "@id": "bts:MolecularEntity" - } - }, - { - "@id": "bts:affectsMutationRateOf", - "@type": "rdf:Property", - "rdfs:comment": "holds between a molecular entity and a genomic entity where the action or effect of the molecular entity impacts the rate of mutation of the genomic entity within a system of interest", - "rdfs:label": "affectsMutationRateOf", - "schema:domainIncludes": { - "@id": "bts:MolecularEntity" - }, - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": { - "@id": "bts:GenomicEntity" - } - }, - { - "@id": "bts:increasesMutationRateOf", - "@type": "rdf:Property", - "rdfs:comment": "holds between a molecular entity and a genomic entity where the action or effect of the molecular entity increases the rate of mutation of the genomic entity within a system of interest", - "rdfs:label": "increasesMutationRateOf", - "schema:domainIncludes": { - "@id": "bts:MolecularEntity" - }, - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": { - "@id": "bts:GenomicEntity" - } - }, - { - "@id": "bts:decreasesMutationRateOf", - "@type": "rdf:Property", - "rdfs:comment": "holds between a molecular entity and a genomic entity where the action or effect of the molecular entity decreases the rate of mutation of the genomic entity within a system of interest", - "rdfs:label": "decreasesMutationRateOf", - "schema:domainIncludes": { - "@id": "bts:MolecularEntity" - }, - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": { - "@id": "bts:GenomicEntity" - } - }, - { - "@id": "bts:affectsResponseTo", - "@type": "rdf:Property", - "rdfs:comment": "holds between two molecular entities where the action or effect of one impacts the susceptibility of a biological entity or system (e.g. an organism, cell, cellular component, macromolecular machine, biological or pathological process) to the other", - "rdfs:label": "affectsResponseTo", - "schema:domainIncludes": { - "@id": "bts:MolecularEntity" - }, - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": { - "@id": "bts:MolecularEntity" - } - }, - { - "@id": "bts:increasesResponseTo", - "@type": "rdf:Property", - "rdfs:comment": "holds between two molecular entities where the action or effect of one increases the susceptibility of a biological entity or system (e.g. an organism, cell, cellular component, macromolecular machine, biological or pathological process) to the other", - "rdfs:label": "increasesResponseTo", - "schema:domainIncludes": { - "@id": "bts:MolecularEntity" - }, - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": { - "@id": "bts:MolecularEntity" - } - }, - { - "@id": "bts:decreasesResponseTo", - "@type": "rdf:Property", - "rdfs:comment": "holds between two molecular entities where the action or effect of one decreases the susceptibility of a biological entity or system (e.g. an organism, cell, cellular component, macromolecular machine, biological or pathological process) to the other", - "rdfs:label": "decreasesResponseTo", - "schema:domainIncludes": { - "@id": "bts:MolecularEntity" - }, - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": { - "@id": "bts:MolecularEntity" - } - }, - { - "@id": "bts:affectsSplicingOf", - "@type": "rdf:Property", - "rdfs:comment": "holds between a molecular entity and an mRNA where the action or effect of the molecular entity impacts the splicing of the mRNA", - "rdfs:label": "affectsSplicingOf", - "schema:domainIncludes": { - "@id": "bts:MolecularEntity" - }, - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": { - "@id": "bts:Transcript" - } - }, - { - "@id": "bts:increasesSplicingOf", - "@type": "rdf:Property", - "rdfs:comment": "holds between a molecular entity and an mRNA where the action or effect of the molecular entity increases the proper splicing of the mRNA", - "rdfs:label": "increasesSplicingOf", - "schema:domainIncludes": { - "@id": "bts:MolecularEntity" - }, - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": { - "@id": "bts:Transcript" - } - }, - { - "@id": "bts:decreasesSplicingOf", - "@type": "rdf:Property", - "rdfs:comment": "holds between a molecular entity and an mRNA where the action or effect of the molecular entity decreases the proper splicing of the mRNA", - "rdfs:label": "decreasesSplicingOf", - "schema:domainIncludes": { - "@id": "bts:MolecularEntity" - }, - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": { - "@id": "bts:Transcript" - } - }, - { - "@id": "bts:affectsStabilityOf", - "@type": "rdf:Property", - "rdfs:comment": "holds between two molecular entities where the action or effect of one impacts the stability of the other within a system of interest", - "rdfs:label": "affectsStabilityOf", - "schema:domainIncludes": { - "@id": "bts:MolecularEntity" - }, - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": { - "@id": "bts:MolecularEntity" - } - }, - { - "@id": "bts:increasesStabilityOf", - "@type": "rdf:Property", - "rdfs:comment": "holds between two molecular entities where the action or effect of one increases the stability of the other within a system of interest", - "rdfs:label": "increasesStabilityOf", - "schema:domainIncludes": { - "@id": "bts:MolecularEntity" - }, - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": { - "@id": "bts:MolecularEntity" - } - }, - { - "@id": "bts:decreasesStabilityOf", - "@type": "rdf:Property", - "rdfs:comment": "holds between two molecular entities where the action or effect of one decreases the stability of the other within a system of interest", - "rdfs:label": "decreasesStabilityOf", - "schema:domainIncludes": { - "@id": "bts:MolecularEntity" - }, - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": { - "@id": "bts:MolecularEntity" - } - }, - { - "@id": "bts:affectsTransportOf", - "@type": "rdf:Property", - "rdfs:comment": "holds between two molecular entities where the action or effect of one impacts the rate of transport of the other across some boundary in a system of interest", - "rdfs:label": "affectsTransportOf", - "schema:domainIncludes": { - "@id": "bts:MolecularEntity" - }, - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": { - "@id": "bts:MolecularEntity" - } - }, - { - "@id": "bts:increasesTransportOf", - "@type": "rdf:Property", - "rdfs:comment": "holds between two molecular entities where the action or effect of one increases the rate of transport of the other across some boundary in a system of interest", - "rdfs:label": "increasesTransportOf", - "schema:domainIncludes": { - "@id": "bts:MolecularEntity" - }, - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": { - "@id": "bts:MolecularEntity" - } - }, - { - "@id": "bts:decreasesTransportOf", - "@type": "rdf:Property", - "rdfs:comment": "holds between two molecular entities where the action or effect of one decreases the rate of transport of the other across some boundary in a system of interest", - "rdfs:label": "decreasesTransportOf", - "schema:domainIncludes": { - "@id": "bts:MolecularEntity" - }, - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": { - "@id": "bts:MolecularEntity" - } - }, - { - "@id": "bts:affectsSecretionOf", - "@type": "rdf:Property", - "rdfs:comment": "holds between two molecular entities where the action or effect of one impacts the rate of secretion of the other out of a cell, gland, or organ", - "rdfs:label": "affectsSecretionOf", - "schema:domainIncludes": { - "@id": "bts:MolecularEntity" - }, - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": { - "@id": "bts:MolecularEntity" - } - }, - { - "@id": "bts:increasesSecretionOf", - "@type": "rdf:Property", - "rdfs:comment": "holds between two molecular entities where the action or effect of one increases the rate of secretion of the other out of a cell, gland, or organ", - "rdfs:label": "increasesSecretionOf", - "schema:domainIncludes": { - "@id": "bts:MolecularEntity" - }, - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": { - "@id": "bts:MolecularEntity" - } - }, - { - "@id": "bts:decreasesSecretionOf", - "@type": "rdf:Property", - "rdfs:comment": "holds between two molecular entities where the action or effect of one decreases the rate of secretion of the other out of a cell, gland, or organ", - "rdfs:label": "decreasesSecretionOf", - "schema:domainIncludes": { - "@id": "bts:MolecularEntity" - }, - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": { - "@id": "bts:MolecularEntity" - } - }, - { - "@id": "bts:affectsUptakeOf", - "@type": "rdf:Property", - "rdfs:comment": "holds between two molecular entities where the action or effect of one impacts the rate of uptake of the other into of a cell, gland, or organ", - "rdfs:label": "affectsUptakeOf", - "schema:domainIncludes": { - "@id": "bts:MolecularEntity" - }, - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": { - "@id": "bts:MolecularEntity" - } - }, - { - "@id": "bts:increasesUptakeOf", - "@type": "rdf:Property", - "rdfs:comment": "holds between two molecular entities where the action or effect of one increases the rate of uptake of the other into of a cell, gland, or organ", - "rdfs:label": "increasesUptakeOf", - "schema:domainIncludes": { - "@id": "bts:MolecularEntity" - }, - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": { - "@id": "bts:MolecularEntity" - } - }, - { - "@id": "bts:decreasesUptakeOf", - "@type": "rdf:Property", - "rdfs:comment": "holds between two molecular entities where the action or effect of one decreases the rate of uptake of the other into of a cell, gland, or organ", - "rdfs:label": "decreasesUptakeOf", - "schema:domainIncludes": { - "@id": "bts:MolecularEntity" - }, - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": { - "@id": "bts:MolecularEntity" - } - }, - { - "@id": "bts:regulates,ProcessToProcess", - "@type": "rdf:Property", - "rdfs:comment": null, - "rdfs:label": "regulates,ProcessToProcess", - "schema:domainIncludes": { - "@id": "bts:Occurrent" - }, - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": { - "@id": "bts:Occurrent" - } - }, - { - "@id": "bts:regulates,EntityToEntity", - "@type": "rdf:Property", - "rdfs:comment": null, - "rdfs:label": "regulates,EntityToEntity", - "schema:domainIncludes": { - "@id": "bts:MolecularEntity" - }, - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": { - "@id": "bts:MolecularEntity" - } - }, - { - "@id": "bts:hasGeneProduct", - "@type": "rdf:Property", - "rdfs:comment": "holds between a gene and a transcribed and/or translated product generated from it", - "rdfs:label": "hasGeneProduct", - "schema:domainIncludes": { - "@id": "bts:Gene" - }, - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": { - "@id": "bts:GeneProduct" - } - }, - { - "@id": "bts:inPathwayWith", - "@type": "rdf:Property", - "rdfs:comment": "holds between two genes or gene products that are part of in the same biological pathway", - "rdfs:label": "inPathwayWith", - "schema:domainIncludes": { - "@id": "bts:GeneOrGeneProduct" - }, - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": { - "@id": "bts:GeneOrGeneProduct" - } - }, - { - "@id": "bts:inComplexWith", - "@type": "rdf:Property", - "rdfs:comment": "holds between two genes or gene products that are part of (or code for products that are part of) in the same macromolecular complex", - "rdfs:label": "inComplexWith", - "schema:domainIncludes": { - "@id": "bts:GeneOrGeneProduct" - }, - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": { - "@id": "bts:GeneOrGeneProduct" - } - }, - { - "@id": "bts:inCellPopulationWith", - "@type": "rdf:Property", - "rdfs:comment": "holds between two genes or gene products that are expressed in the same cell type or population ", - "rdfs:label": "inCellPopulationWith", - "schema:domainIncludes": { - "@id": "bts:GeneOrGeneProduct" - }, - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": { - "@id": "bts:GeneOrGeneProduct" - } - }, - { - "@id": "bts:geneAssociatedWithCondition", - "@type": "rdf:Property", - "rdfs:comment": "holds between a gene and a disease or phenotypic feature that the gene or its alleles/products may influence, contribute to, or correlate with", - "rdfs:label": "geneAssociatedWithCondition", - "schema:domainIncludes": { - "@id": "bts:Gene" - }, - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": { - "@id": "bts:DiseaseOrPhenotypicFeature" - } - }, - { - "@id": "bts:treats", - "@type": "rdf:Property", - "rdfs:comment": "holds between a therapeutic procedure or chemical substance and a disease or phenotypic feature that it is used to treat", - "rdfs:label": "treats", - "schema:domainIncludes": { - "@id": "bts:Treatment" - }, - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": { - "@id": "bts:DiseaseOrPhenotypicFeature" - } - }, - { - "@id": "bts:correlatedWith", - "@type": "rdf:Property", - "rdfs:comment": "holds between a disease or phenotypic feature and a measurable molecular entity that is used as an indicator of the presence or state of the disease or feature.", - "rdfs:label": "correlatedWith", - "schema:domainIncludes": { - "@id": "bts:DiseaseOrPhenotypicFeature" - }, - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": { - "@id": "bts:MolecularEntity" - } - }, - { - "@id": "bts:hasBiomarker", - "@type": "rdf:Property", - "rdfs:comment": "holds between a disease or phenotypic feature and a measurable molecular entity that is used as an indicator of the presence or state of the disease or feature.", - "rdfs:label": "hasBiomarker", - "schema:domainIncludes": { - "@id": "bts:DiseaseOrPhenotypicFeature" - }, - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": { - "@id": "bts:MolecularEntity" - } - }, - { - "@id": "bts:biomarkerFor", - "@type": "rdf:Property", - "rdfs:comment": "holds between a measurable molecular entity and a disease or phenotypic feature, where the entity is used as an indicator of the presence or state of the disease or feature.", - "rdfs:label": "biomarkerFor", - "schema:domainIncludes": { - "@id": "bts:MolecularEntity" - }, - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": { - "@id": "bts:DiseaseOrPhenotypicFeature" - } - }, - { - "@id": "bts:expressedIn", - "@type": "rdf:Property", - "rdfs:comment": "holds between a gene or gene product and an anatomical entity in which it is expressed", - "rdfs:label": "expressedIn", - "schema:domainIncludes": { - "@id": "bts:GeneOrGeneProduct" - }, - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": { - "@id": "bts:AnatomicalEntity" - } - }, - { - "@id": "bts:expresses", - "@type": "rdf:Property", - "rdfs:comment": "holds between an anatomical entity and gene or gene product that is expressed there", - "rdfs:label": "expresses", - "schema:domainIncludes": { - "@id": "bts:AnatomicalEntity" - }, - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": { - "@id": "bts:GeneOrGeneProduct" - } - }, - { - "@id": "bts:hasPhenotype", - "@type": "rdf:Property", - "rdfs:comment": "holds between a biological entity and a phenotype, where a phenotype is construed broadly as any kind of quality of an organism part, a collection of these qualities, or a change in quality or qualities (e.g. abnormally increased temperature). ", - "rdfs:label": "hasPhenotype", - "schema:domainIncludes": { - "@id": "bts:BiologicalEntity" - }, - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": { - "@id": "bts:DiseaseOrPhenotypicFeature" - } - }, - { - "@id": "bts:precedes", - "@type": "rdf:Property", - "rdfs:comment": "holds between two processes, where one completes before the other begins", - "rdfs:label": "precedes", - "schema:domainIncludes": { - "@id": "bts:Occurrent" - }, - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": { - "@id": "bts:Occurrent" - } - }, - { - "@id": "bts:subclassOf", - "@type": "rdf:Property", - "rdfs:comment": "holds between two classes where the domain class is a specialization of the range class", - "rdfs:label": "subclassOf", - "schema:domainIncludes": { - "@id": "bts:OntologyClass" - }, - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": { - "@id": "bts:OntologyClass" - } - }, { "@id": "bts:Component", "@type": "rdfs:Class", @@ -2070,7 +14,7 @@ "rdfs:label": "Component", "rdfs:subClassOf": [ { - "@id": "schema:Thing" + "@id": "bts:Thing" } ], "schema:isPartOf": { @@ -2193,6 +137,89 @@ "sms:required": "sms:true", "sms:validationRules": [] }, + { + "@id": "bts:geneticReagentId", + "@type": "rdf:Property", + "rdfs:comment": "A unique identifier for the reagent.", + "rdfs:label": "geneticReagentId", + "schema:domainIncludes": [ + { + "@id": "bts:Resource" + }, + { + "@id": "bts:GeneticReagent" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "geneticReagentId", + "sms:required": "sms:true", + "sms:validationRules": [] + }, + { + "@id": "bts:antibodyId", + "@type": "rdf:Property", + "rdfs:comment": "A unique identifier for the antibody.", + "rdfs:label": "antibodyId", + "schema:domainIncludes": [ + { + "@id": "bts:Resource" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "antibodyId", + "sms:required": "sms:true", + "sms:validationRules": [] + }, + { + "@id": "bts:cellLineId", + "@type": "rdf:Property", + "rdfs:comment": "A unique identifier for the cell line.", + "rdfs:label": "cellLineId", + "schema:domainIncludes": [ + { + "@id": "bts:Resource" + }, + { + "@id": "bts:CellLine" + }, + { + "@id": "bts:Mutation" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "cellLineId", + "sms:required": "sms:true", + "sms:validationRules": [] + }, + { + "@id": "bts:animalModelId", + "@type": "rdf:Property", + "rdfs:comment": "A unique identifier for the animal model.", + "rdfs:label": "animalModelId", + "schema:domainIncludes": [ + { + "@id": "bts:Resource" + }, + { + "@id": "bts:Mutation" + }, + { + "@id": "bts:AnimalModel" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "animalModelId", + "sms:required": "sms:true", + "sms:validationRules": [] + }, { "@id": "bts:rrid", "@type": "rdf:Property", @@ -2243,7 +270,7 @@ "sms:displayName": "synonyms", "sms:required": "sms:false", "sms:validationRules": [ - "list" + "list like" ] }, { @@ -2300,7 +327,7 @@ { "@id": "bts:usageRequirements", "@type": "rdf:Property", - "rdfs:comment": "Any known restrictions on use of the resource. ", + "rdfs:comment": "Any known restrictions on use of the resource.", "rdfs:label": "usageRequirements", "schema:domainIncludes": [ { @@ -2345,13 +372,13 @@ "sms:displayName": "usageRequirements", "sms:required": "sms:false", "sms:validationRules": [ - "list" + "list like" ] }, { "@id": "bts:howToAcquire", "@type": "rdf:Property", - "rdfs:comment": "How to acquire a particular resource. ", + "rdfs:comment": "How to acquire a particular resource.", "rdfs:label": "howToAcquire", "schema:domainIncludes": [ { @@ -2402,17 +429,17 @@ { "@id": "bts:GeneticReagent", "@type": "rdfs:Class", - "rdfs:comment": "Genetic reagents.", + "rdfs:comment": "TBD", "rdfs:label": "GeneticReagent", "rdfs:subClassOf": [ { - "@id": "bts:GeneticReagent" + "@id": "bts:resourceType" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "geneticReagent", + "sms:displayName": "Genetic Reagent", "sms:required": "sms:false", "sms:requiresDependency": [ { @@ -2500,452 +527,427 @@ "sms:validationRules": [] }, { - "@id": "bts:geneticReagentId", - "@type": "rdf:Property", - "rdfs:comment": "A unique identifier for the reagent.", - "rdfs:label": "geneticReagentId", - "schema:domainIncludes": [ - { - "@id": "bts:Resource" - }, + "@id": "bts:Antibody", + "@type": "rdfs:Class", + "rdfs:comment": "TBD", + "rdfs:label": "Antibody", + "rdfs:subClassOf": [ { - "@id": "bts:GeneticReagent" + "@id": "bts:resourceType" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "geneticReagentId", - "sms:required": "sms:true", - "sms:validationRules": [] - }, - { - "@id": "bts:insertName", - "@type": "rdf:Property", - "rdfs:comment": "Name of the main gene insert in the plasmid.", - "rdfs:label": "insertName", - "schema:domainIncludes": [ + "sms:displayName": "Antibody", + "sms:required": "sms:false", + "sms:requiresDependency": [ { - "@id": "bts:GeneticReagent" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "insertName", - "sms:required": "sms:true", - "sms:validationRules": [] - }, - { - "@id": "bts:insertEntrezId", - "@type": "rdf:Property", - "rdfs:comment": "The entrez gene id for the gene insert", - "rdfs:label": "insertEntrezId", - "schema:domainIncludes": [ + "@id": "bts:Component" + }, { - "@id": "bts:GeneticReagent" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "insertEntrezId", - "sms:required": "sms:true", - "sms:validationRules": [] - }, - { - "@id": "bts:gRNAshRNASequence", - "@type": "rdf:Property", - "rdfs:comment": "The sequence of the gRNA or shRNA for the gene insert, if present. ", - "rdfs:label": "gRNAshRNASequence", - "schema:domainIncludes": [ + "@id": "bts:antibodyId" + }, { - "@id": "bts:GeneticReagent" + "@id": "bts:uniprotId" + }, + { + "@id": "bts:targetAntigen" + }, + { + "@id": "bts:clonality" + }, + { + "@id": "bts:cloneId" + }, + { + "@id": "bts:reactiveSpecies" + }, + { + "@id": "bts:conjugate" + }, + { + "@id": "bts:hostOrganism" } ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "gRNAshRNASequence", - "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:insertSize", - "@type": "rdf:Property", - "rdfs:comment": "Size, in bp, of the gene insert as it is in the plasmid.", - "rdfs:label": "insertSize", - "schema:domainIncludes": [ + "@id": "bts:CellLine", + "@type": "rdfs:Class", + "rdfs:comment": "TBD", + "rdfs:label": "CellLine", + "rdfs:subClassOf": [ { - "@id": "bts:GeneticReagent" + "@id": "bts:resourceType" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "insertSize", + "sms:displayName": "Cell Line", "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:insertSpecies", - "@type": "rdf:Property", - "rdfs:comment": "Species of the insert", - "rdfs:label": "insertSpecies", - "schema:domainIncludes": [ + "sms:requiresComponent": [ { - "@id": "bts:GeneticReagent" + "@id": "bts:Donor" } ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ + "sms:requiresDependency": [ { - "@id": "bts:Homosapiens" + "@id": "bts:Component" + }, + { + "@id": "bts:cellLineId" + }, + { + "@id": "bts:donorId" + }, + { + "@id": "bts:organ" + }, + { + "@id": "bts:tissue" + }, + { + "@id": "bts:cellLineCategory" + }, + { + "@id": "bts:originYear" + }, + { + "@id": "bts:strProfile" + }, + { + "@id": "bts:populationDoublingTime" + }, + { + "@id": "bts:resistance" + }, + { + "@id": "bts:contaminatedMisidentified" }, { - "@id": "bts:Musmusculus" + "@id": "bts:cellLineGeneticDisorder" }, { - "@id": "bts:Rattusnorvegicus" + "@id": "bts:cellLineManifestation" } ], - "sms:displayName": "insertSpecies", - "sms:required": "sms:true", - "sms:validationRules": [ - "list" - ] + "sms:validationRules": [] }, { - "@id": "bts:nTerminalTag", - "@type": "rdf:Property", - "rdfs:comment": "Any tags on the N terminal 5' end of the gene insert in the plasmid. Only tags that are in frame", - "rdfs:label": "nTerminalTag", - "schema:domainIncludes": [ + "@id": "bts:AnimalModel", + "@type": "rdfs:Class", + "rdfs:comment": "TBD", + "rdfs:label": "AnimalModel", + "rdfs:subClassOf": [ { - "@id": "bts:GeneticReagent" + "@id": "bts:resourceType" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "nTerminalTag", + "sms:displayName": "Animal Model", "sms:required": "sms:false", - "sms:validationRules": [ - "list" - ] + "sms:requiresComponent": [ + { + "@id": "bts:Donor" + } + ], + "sms:requiresDependency": [ + { + "@id": "bts:Component" + }, + { + "@id": "bts:animalModelId" + }, + { + "@id": "bts:donorId" + }, + { + "@id": "bts:transplantationDonorId" + }, + { + "@id": "bts:animalState" + }, + { + "@id": "bts:backgroundStrain" + }, + { + "@id": "bts:backgroundSubstrain" + }, + { + "@id": "bts:strainNomenclature" + }, + { + "@id": "bts:generation" + }, + { + "@id": "bts:transplantationType" + }, + { + "@id": "bts:animalModelGeneticDisorder" + }, + { + "@id": "bts:animalModelOfManifestation" + } + ], + "sms:validationRules": [] }, { - "@id": "bts:cTerminalTag", - "@type": "rdf:Property", - "rdfs:comment": "Any tags on the C terminal 3' end of the gene insert in the plasmid. Only tags that are in frame", - "rdfs:label": "cTerminalTag", - "schema:domainIncludes": [ + "@id": "bts:Biobank", + "@type": "rdfs:Class", + "rdfs:comment": "A large collection of biological or medical data and tissue samples, amassed for research purposes.", + "rdfs:label": "Biobank", + "rdfs:subClassOf": [ { - "@id": "bts:GeneticReagent" + "@id": "bts:resourceType" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "cTerminalTag", + "sms:displayName": "biobank", "sms:required": "sms:false", - "sms:validationRules": [ - "list" - ] - }, - { - "@id": "bts:cloningMethod", - "@type": "rdf:Property", - "rdfs:comment": "How the vector was constructed. (e.g. restriction enzyme, TOPO cloning, etc.)", - "rdfs:label": "cloningMethod", - "schema:domainIncludes": [ + "sms:requiresComponent": [ { - "@id": "bts:GeneticReagent" + "@id": "bts:Resource" } ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ + "sms:requiresDependency": [ { - "@id": "bts:RestrictionEnzyme" + "@id": "bts:Component" }, { - "@id": "bts:TOPOcloning" + "@id": "bts:biobankId" }, { - "@id": "bts:GatewayCloning" + "@id": "bts:resourceId" }, { - "@id": "bts:LigationIndependentCloning" + "@id": "bts:biobankName" }, { - "@id": "bts:GibsonCloning" + "@id": "bts:biobankURL" }, { - "@id": "bts:Unknown" + "@id": "bts:specimenType" + }, + { + "@id": "bts:specimenTissueType" + }, + { + "@id": "bts:tumorType" + }, + { + "@id": "bts:diseaseType" + }, + { + "@id": "bts:specimenPreparationMethod" + }, + { + "@id": "bts:specimenFormat" } ], - "sms:displayName": "cloningMethod", - "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:5primeCloningSite", - "@type": "rdf:Property", - "rdfs:comment": "If Restriction Enzyme was selected as the cloning method, specifies what enzyme was used on the 5' (N-terminal) end of the insert", - "rdfs:label": "5primeCloningSite", - "schema:domainIncludes": [ + "@id": "bts:Non-commercialuseonly", + "@type": "rdfs:Class", + "rdfs:comment": "TBD", + "rdfs:label": "Non-commercialuseonly", + "rdfs:subClassOf": [ { - "@id": "bts:GeneticReagent" + "@id": "bts:usageRequirements" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "5primeCloningSite", + "sms:displayName": "non-commercial use only", "sms:required": "sms:false", - "sms:requiresDependency": [ - { - "@id": "bts:cloningMethod" - } - ], "sms:validationRules": [] }, { - "@id": "bts:5primeSiteDestroyed", - "@type": "rdf:Property", - "rdfs:comment": "If 5' site was destroyed during cloning. (e.g. yes, no, unknown).", - "rdfs:label": "5primeSiteDestroyed", - "schema:domainIncludes": [ + "@id": "bts:Re-distributionnotpermitted", + "@type": "rdfs:Class", + "rdfs:comment": "TBD", + "rdfs:label": "Re-distributionnotpermitted", + "rdfs:subClassOf": [ { - "@id": "bts:GeneticReagent" + "@id": "bts:usageRequirements" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "schema:rangeIncludes": [ - { - "@id": "bts:Yes" - }, - { - "@id": "bts:No" - }, - { - "@id": "bts:Unknown" - } - ], - "sms:displayName": "5primeSiteDestroyed", + "sms:displayName": "re-distribution not permitted", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:3primeCloningSite", - "@type": "rdf:Property", - "rdfs:comment": "If Restriction Enzyme was selected as the cloning method, specifies what enzyme was used on the 3' (C-terminal) end of the insert", - "rdfs:label": "3primeCloningSite", - "schema:domainIncludes": [ + "@id": "bts:Generationofgermlinetransmittingchimerasnotpermitted", + "@type": "rdfs:Class", + "rdfs:comment": "TBD", + "rdfs:label": "Generationofgermlinetransmittingchimerasnotpermitted", + "rdfs:subClassOf": [ { - "@id": "bts:GeneticReagent" + "@id": "bts:usageRequirements" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "3primeCloningSite", + "sms:displayName": "generation of germ line transmitting chimeras not permitted", "sms:required": "sms:false", - "sms:requiresDependency": [ - { - "@id": "bts:cloningMethod" - } - ], "sms:validationRules": [] }, { - "@id": "bts:3primeSiteDestroyed", - "@type": "rdf:Property", - "rdfs:comment": "If 3' site was destroyed during cloning. (e.g. yes, no, unknown)", - "rdfs:label": "3primeSiteDestroyed", - "schema:domainIncludes": [ + "@id": "bts:Creationoffunctionalgametesnotpermitted", + "@type": "rdfs:Class", + "rdfs:comment": "TBD", + "rdfs:label": "Creationoffunctionalgametesnotpermitted", + "rdfs:subClassOf": [ { - "@id": "bts:GeneticReagent" + "@id": "bts:usageRequirements" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "schema:rangeIncludes": [ - { - "@id": "bts:Yes" - }, - { - "@id": "bts:No" - }, - { - "@id": "bts:Unknown" - } - ], - "sms:displayName": "3primeSiteDestroyed", + "sms:displayName": "creation of functional gametes not permitted", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:promoter", - "@type": "rdf:Property", - "rdfs:comment": "Promoter driving the expression of the insert in the plasmid", - "rdfs:label": "promoter", - "schema:domainIncludes": [ + "@id": "bts:Generationofinterspecieschimerasnotpermitted", + "@type": "rdfs:Class", + "rdfs:comment": "TBD", + "rdfs:label": "Generationofinterspecieschimerasnotpermitted", + "rdfs:subClassOf": [ { - "@id": "bts:GeneticReagent" + "@id": "bts:usageRequirements" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "promoter", + "sms:displayName": "generation of interspecies chimeras not permitted", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:5primer", - "@type": "rdf:Property", - "rdfs:comment": "Primer to sequence the 5' end (N-terminal) of the insert", - "rdfs:label": "5primer", - "schema:domainIncludes": [ + "@id": "bts:Humancloningnotpermitted", + "@type": "rdfs:Class", + "rdfs:comment": "TBD", + "rdfs:label": "Humancloningnotpermitted", + "rdfs:subClassOf": [ { - "@id": "bts:GeneticReagent" + "@id": "bts:usageRequirements" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "5primer", + "sms:displayName": "human cloning not permitted", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:3primer", - "@type": "rdf:Property", - "rdfs:comment": "Primer to sequence the 3' end (C-terminal) of the insert.", - "rdfs:label": "3primer", - "schema:domainIncludes": [ + "@id": "bts:Cannotbeusedfortreatmentpurposes", + "@type": "rdfs:Class", + "rdfs:comment": "TBD", + "rdfs:label": "Cannotbeusedfortreatmentpurposes", + "rdfs:subClassOf": [ { - "@id": "bts:GeneticReagent" + "@id": "bts:usageRequirements" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "3primer", + "sms:displayName": "cannot be used for treatment purposes", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:vectorBackbone", - "@type": "rdf:Property", - "rdfs:comment": "Name of the backbone the plasmid is built on. (e.g pGBT9)", - "rdfs:label": "vectorBackbone", - "schema:domainIncludes": [ + "@id": "bts:IRBdocumentationrequired", + "@type": "rdfs:Class", + "rdfs:comment": "TBD", + "rdfs:label": "IRBdocumentationrequired", + "rdfs:subClassOf": [ { - "@id": "bts:GeneticReagent" + "@id": "bts:usageRequirements" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "vectorBackbone", + "sms:displayName": "IRB documentation required", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:vectorType", - "@type": "rdf:Property", - "rdfs:comment": "Primary function of the plasmid. (e.g. mammalian expression, bacterial expression, etc.)", - "rdfs:label": "vectorType", - "schema:domainIncludes": [ + "@id": "bts:Speciallicencingrestrictions(seevendorformoreinformation)", + "@type": "rdfs:Class", + "rdfs:comment": "TBD", + "rdfs:label": "Speciallicencingrestrictions(seevendorformoreinformation)", + "rdfs:subClassOf": [ { - "@id": "bts:GeneticReagent" + "@id": "bts:usageRequirements" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "schema:rangeIncludes": [ - { - "@id": "bts:MammalianExpression" - }, - { - "@id": "bts:BacterialExpression" - }, - { - "@id": "bts:GatewayEntryClone" - }, - { - "@id": "bts:Lentiviral" - }, - { - "@id": "bts:Adenoviral" - }, - { - "@id": "bts:AAV" - }, - { - "@id": "bts:RNAi" - }, - { - "@id": "bts:Luciferase" - }, - { - "@id": "bts:Cre/Lox" - }, - { - "@id": "bts:YeastExpression" - }, - { - "@id": "bts:WormExpression" - }, - { - "@id": "bts:InsectExpression" - }, + "sms:displayName": "special licencing restrictions (see vendor for more information)", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:Unknown", + "@type": "rdfs:Class", + "rdfs:comment": "TBD", + "rdfs:label": "Unknown", + "rdfs:subClassOf": [ { - "@id": "bts:PlantExpression" + "@id": "bts:clonality" }, { - "@id": "bts:MouseTargeting" + "@id": "bts:5primeSiteDestroyed" }, { - "@id": "bts:CRISPR" + "@id": "bts:3primeSiteDestroyed" }, { - "@id": "bts:TALEN" + "@id": "bts:copyNumber" }, { - "@id": "bts:SyntheticBiology" + "@id": "bts:hazardous" }, { - "@id": "bts:TransferVector" + "@id": "bts:sex" }, { - "@id": "bts:Unspecified" + "@id": "bts:cloningMethod" }, { - "@id": "bts:Other" + "@id": "bts:usageRequirements" } ], - "sms:displayName": "vectorType", + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Unknown", "sms:required": "sms:false", - "sms:validationRules": [ - "list" - ] + "sms:validationRules": [] }, { - "@id": "bts:backboneSize", + "@id": "bts:insertName", "@type": "rdf:Property", - "rdfs:comment": "Size in bp of the backbone without the insert", - "rdfs:label": "backboneSize", + "rdfs:comment": "Name of the main gene insert in the plasmid.", + "rdfs:label": "insertName", "schema:domainIncludes": [ { "@id": "bts:GeneticReagent" @@ -2954,15 +956,15 @@ "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "backboneSize", - "sms:required": "sms:false", + "sms:displayName": "insertName", + "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:totalSize", + "@id": "bts:insertEntrezId", "@type": "rdf:Property", - "rdfs:comment": "Size of vector with insert. Derived from insertSize and backboneSize.", - "rdfs:label": "totalSize", + "rdfs:comment": "The entrez gene id for the gene insert", + "rdfs:label": "insertEntrezId", "schema:domainIncludes": [ { "@id": "bts:GeneticReagent" @@ -2971,15 +973,15 @@ "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "totalSize", - "sms:required": "sms:false", + "sms:displayName": "insertEntrezId", + "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:bacterialResistance", + "@id": "bts:gRNAshRNASequence", "@type": "rdf:Property", - "rdfs:comment": "Antibiotic(s) that should be used for selection in bacteria. (e.g. ampicillin, kanamycin, etc.)", - "rdfs:label": "bacterialResistance", + "rdfs:comment": "The sequence of the gRNA or shRNA for the gene insert, if present.", + "rdfs:label": "gRNAshRNASequence", "schema:domainIncludes": [ { "@id": "bts:GeneticReagent" @@ -2988,86 +990,32 @@ "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "schema:rangeIncludes": [ - { - "@id": "bts:Ampicillin" - }, - { - "@id": "bts:Kanamycin" - }, - { - "@id": "bts:Chloramphenicol" - }, - { - "@id": "bts:Tetracycline" - }, - { - "@id": "bts:Spectinomycin" - }, - { - "@id": "bts:Hygromycin" - }, - { - "@id": "bts:Bleocin(Zeocin)" - }, - { - "@id": "bts:Gentamycin" - }, - { - "@id": "bts:Streptomycin" - }, - { - "@id": "bts:Nourseothricin(clonNat)" - }, - { - "@id": "bts:AmpicillinandBleocin(Zeocin)" - }, - { - "@id": "bts:AmpicillinandKanamycin" - }, - { - "@id": "bts:AmpicillinandTetracycline" - }, - { - "@id": "bts:AmpicillinandStreptomycin" - }, - { - "@id": "bts:AmpicillinandSpectinomycin" - }, - { - "@id": "bts:ChloramphenicolandAmpicillin" - }, - { - "@id": "bts:ChloramphenicolandBleocin(Zeocin)" - }, - { - "@id": "bts:ChloramphenicolandTetracycline" - }, - { - "@id": "bts:ChloramphenicolandKanamycin" - }, - { - "@id": "bts:ChloramphenicolandSpectinomycin" - }, - { - "@id": "bts:ChloramphenicolandGentamycin" - }, - { - "@id": "bts:SpectinomycinandStreptomycin" - }, + "sms:displayName": "gRNAshRNASequence", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:insertSize", + "@type": "rdf:Property", + "rdfs:comment": "Size, in bp, of the gene insert as it is in the plasmid.", + "rdfs:label": "insertSize", + "schema:domainIncludes": [ { - "@id": "bts:Other" + "@id": "bts:GeneticReagent" } ], - "sms:displayName": "bacterialResistance", + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "insertSize", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:selectableMarker", + "@id": "bts:insertSpecies", "@type": "rdf:Property", - "rdfs:comment": "Are there any additional selection markers on this plasmid, for example, any mammalian selection markers or fluorescent proteins?", - "rdfs:label": "selectableMarker", + "rdfs:comment": "Species of the insert", + "rdfs:label": "insertSpecies", "schema:domainIncludes": [ { "@id": "bts:GeneticReagent" @@ -3078,51 +1026,26 @@ }, "schema:rangeIncludes": [ { - "@id": "bts:Neomycin" - }, - { - "@id": "bts:Puromycin" - }, - { - "@id": "bts:Hygromycin" - }, - { - "@id": "bts:Zeocin" - }, - { - "@id": "bts:Blasticidin" - }, - { - "@id": "bts:Gentamicin" - }, - { - "@id": "bts:TRP1" - }, - { - "@id": "bts:LEU1" - }, - { - "@id": "bts:URA3" - }, - { - "@id": "bts:HIS3" + "@id": "bts:Homosapiens" }, { - "@id": "bts:Basta" + "@id": "bts:Musmusculus" }, { - "@id": "bts:Other" + "@id": "bts:Rattusnorvegicus" } ], - "sms:displayName": "selectableMarker", - "sms:required": "sms:false", - "sms:validationRules": [] + "sms:displayName": "insertSpecies", + "sms:required": "sms:true", + "sms:validationRules": [ + "list like" + ] }, { - "@id": "bts:copyNumber", + "@id": "bts:nTerminalTag", "@type": "rdf:Property", - "rdfs:comment": "If a plasmid produces a sufficient amount of DNA from a normal miniprep or if plasmid requires special growth conditions or it is difficult to grow. (e.g. high copy, low copy, unknown).", - "rdfs:label": "copyNumber", + "rdfs:comment": "Any tags on the N terminal 5' end of the gene insert in the plasmid. Only tags that are in frame", + "rdfs:label": "nTerminalTag", "schema:domainIncludes": [ { "@id": "bts:GeneticReagent" @@ -3131,26 +1054,17 @@ "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "schema:rangeIncludes": [ - { - "@id": "bts:HighCopy" - }, - { - "@id": "bts:LowCopy" - }, - { - "@id": "bts:Unknown" - } - ], - "sms:displayName": "copyNumber", + "sms:displayName": "nTerminalTag", "sms:required": "sms:false", - "sms:validationRules": [] + "sms:validationRules": [ + "list like" + ] }, { - "@id": "bts:growthTemp", + "@id": "bts:cTerminalTag", "@type": "rdf:Property", - "rdfs:comment": "At what temperature should the bacteria hosting the plasmid be grown", - "rdfs:label": "growthTemp", + "rdfs:comment": "Any tags on the C terminal 3' end of the gene insert in the plasmid. Only tags that are in frame", + "rdfs:label": "cTerminalTag", "schema:domainIncludes": [ { "@id": "bts:GeneticReagent" @@ -3159,26 +1073,17 @@ "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "schema:rangeIncludes": [ - { - "@id": "bts:37C" - }, - { - "@id": "bts:30C" - }, - { - "@id": "bts:RoomTemperature" - } - ], - "sms:displayName": "growthTemp", + "sms:displayName": "cTerminalTag", "sms:required": "sms:false", - "sms:validationRules": [] + "sms:validationRules": [ + "list like" + ] }, { - "@id": "bts:growthStrain", + "@id": "bts:cloningMethod", "@type": "rdf:Property", - "rdfs:comment": "The E.Coli strain that should be used to distribute the plasmid. (e.g. DH5alpha, NEB Stable, etc.)", - "rdfs:label": "growthStrain", + "rdfs:comment": "How the vector was constructed. (e.g. restriction enzyme, TOPO cloning, etc.)", + "rdfs:label": "cloningMethod", "schema:domainIncludes": [ { "@id": "bts:GeneticReagent" @@ -3189,33 +1094,33 @@ }, "schema:rangeIncludes": [ { - "@id": "bts:DH5alpha" + "@id": "bts:RestrictionEnzyme" }, { - "@id": "bts:DH10B" + "@id": "bts:TOPOcloning" }, { - "@id": "bts:NEBStable" + "@id": "bts:GatewayCloning" }, { - "@id": "bts:CcdbSurvival" + "@id": "bts:LigationIndependentCloning" }, { - "@id": "bts:Pir1" + "@id": "bts:GibsonCloning" }, { - "@id": "bts:Other" + "@id": "bts:Unknown" } ], - "sms:displayName": "growthStrain", + "sms:displayName": "cloningMethod", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:hazardous", + "@id": "bts:5primeCloningSite", "@type": "rdf:Property", - "rdfs:comment": "Does the unmodified plasmid DNA, either in purified form or when introduced into bacterial or mammalian cells require handling at Biosafety Level 2 or higher?", - "rdfs:label": "hazardous", + "rdfs:comment": "If Restriction Enzyme was selected as the cloning method, specifies what enzyme was used on the 5' (N-terminal) end of the insert", + "rdfs:label": "5primeCloningSite", "schema:domainIncludes": [ { "@id": "bts:GeneticReagent" @@ -3224,318 +1129,274 @@ "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "schema:rangeIncludes": [ - { - "@id": "bts:Yes" - }, - { - "@id": "bts:No" - }, - { - "@id": "bts:Unknown" - } - ], - "sms:displayName": "hazardous", - "sms:required": "sms:true", + "sms:displayName": "5primeCloningSite", + "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:VendorItem", - "@type": "rdfs:Class", - "rdfs:comment": "The resource item associated with a vendor.", - "rdfs:label": "VendorItem", - "rdfs:subClassOf": [ + "@id": "bts:5primeSiteDestroyed", + "@type": "rdf:Property", + "rdfs:comment": "If 5' site was destroyed during cloning. (e.g. yes, no, unknown).", + "rdfs:label": "5primeSiteDestroyed", + "schema:domainIncludes": [ { - "@id": "bts:VendorItem" + "@id": "bts:GeneticReagent" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "vendorItem", - "sms:required": "sms:false", - "sms:requiresComponent": [ - { - "@id": "bts:Resource" - }, - { - "@id": "bts:Vendor" - } - ], - "sms:requiresDependency": [ - { - "@id": "bts:Component" - }, - { - "@id": "bts:vendorItemId" - }, - { - "@id": "bts:vendorId" - }, + "schema:rangeIncludes": [ { - "@id": "bts:resourceId" + "@id": "bts:Yes" }, { - "@id": "bts:catalogNumber" + "@id": "bts:No" }, { - "@id": "bts:catalogNumberURL" + "@id": "bts:Unknown" } ], + "sms:displayName": "5primeSiteDestroyed", + "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:vendorItemId", + "@id": "bts:3primeCloningSite", "@type": "rdf:Property", - "rdfs:comment": "A unique identifier for the resource associated with a vendor. ", - "rdfs:label": "vendorItemId", + "rdfs:comment": "If Restriction Enzyme was selected as the cloning method, specifies what enzyme was used on the 3' (C-terminal) end of the insert", + "rdfs:label": "3primeCloningSite", "schema:domainIncludes": [ { - "@id": "bts:VendorItem" + "@id": "bts:GeneticReagent" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "vendorItemId", - "sms:required": "sms:true", + "sms:displayName": "3primeCloningSite", + "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:catalogNumber", + "@id": "bts:3primeSiteDestroyed", "@type": "rdf:Property", - "rdfs:comment": "The catalog number associated with the resource pertaining to the vendor that sells the resource.", - "rdfs:label": "catalogNumber", + "rdfs:comment": "If 3' site was destroyed during cloning. (e.g. yes, no, unknown)", + "rdfs:label": "3primeSiteDestroyed", "schema:domainIncludes": [ { - "@id": "bts:VendorItem" + "@id": "bts:GeneticReagent" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "catalogNumber", - "sms:required": "sms:true", + "schema:rangeIncludes": [ + { + "@id": "bts:Yes" + }, + { + "@id": "bts:No" + }, + { + "@id": "bts:Unknown" + } + ], + "sms:displayName": "3primeSiteDestroyed", + "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:catalogNumberURL", + "@id": "bts:promoter", "@type": "rdf:Property", - "rdfs:comment": "The url linking to the resource on the vendor's website. ", - "rdfs:label": "catalogNumberURL", + "rdfs:comment": "Promoter driving the expression of the insert in the plasmid", + "rdfs:label": "promoter", "schema:domainIncludes": [ { - "@id": "bts:VendorItem" + "@id": "bts:GeneticReagent" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "catalogNumberURL", + "sms:displayName": "promoter", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:Vendor", - "@type": "rdfs:Class", - "rdfs:comment": "A person or compnay offering the resource for sale.", - "rdfs:label": "Vendor", - "rdfs:subClassOf": [ + "@id": "bts:5primer", + "@type": "rdf:Property", + "rdfs:comment": "Primer to sequence the 5' end (N-terminal) of the insert", + "rdfs:label": "5primer", + "schema:domainIncludes": [ { - "@id": "bts:Vendor" + "@id": "bts:GeneticReagent" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "vendor", + "sms:displayName": "5primer", "sms:required": "sms:false", - "sms:requiresDependency": [ - { - "@id": "bts:Component" - }, - { - "@id": "bts:vendorId" - }, - { - "@id": "bts:vendorName" - }, - { - "@id": "bts:vendorURL" - } - ], "sms:validationRules": [] }, { - "@id": "bts:vendorId", + "@id": "bts:3primer", "@type": "rdf:Property", - "rdfs:comment": "A unique identifier for the vendor.", - "rdfs:label": "vendorId", + "rdfs:comment": "Primer to sequence the 3' end (C-terminal) of the insert.", + "rdfs:label": "3primer", "schema:domainIncludes": [ { - "@id": "bts:VendorItem" - }, - { - "@id": "bts:Vendor" + "@id": "bts:GeneticReagent" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "vendorId", - "sms:required": "sms:true", + "sms:displayName": "3primer", + "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:vendorName", + "@id": "bts:vectorBackbone", "@type": "rdf:Property", - "rdfs:comment": "The name of the vendor.", - "rdfs:label": "vendorName", + "rdfs:comment": "Name of the backbone the plasmid is built on. (e.g pGBT9)", + "rdfs:label": "vectorBackbone", "schema:domainIncludes": [ { - "@id": "bts:Vendor" + "@id": "bts:GeneticReagent" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "vendorName", + "sms:displayName": "vectorBackbone", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:vendorURL", + "@id": "bts:vectorType", "@type": "rdf:Property", - "rdfs:comment": "The vendor website url associated with the resource.", - "rdfs:label": "vendorURL", + "rdfs:comment": "Primary function of the plasmid. (e.g. mammalian expression, bacterial expression, etc.)", + "rdfs:label": "vectorType", "schema:domainIncludes": [ { - "@id": "bts:Vendor" + "@id": "bts:GeneticReagent" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "vendorURL", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:Biobank", - "@type": "rdfs:Class", - "rdfs:comment": "A large collection of biological or medical data and tissue samples, amassed for research purposes.", - "rdfs:label": "Biobank", - "rdfs:subClassOf": [ + "schema:rangeIncludes": [ + { + "@id": "bts:MammalianExpression" + }, + { + "@id": "bts:BacterialExpression" + }, + { + "@id": "bts:GatewayEntryClone" + }, + { + "@id": "bts:Lentiviral" + }, + { + "@id": "bts:Adenoviral" + }, { - "@id": "bts:Biobank" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "biobank", - "sms:required": "sms:false", - "sms:requiresComponent": [ + "@id": "bts:AAV" + }, { - "@id": "bts:Resource" - } - ], - "sms:requiresDependency": [ + "@id": "bts:RNAi" + }, { - "@id": "bts:Component" + "@id": "bts:Luciferase" }, { - "@id": "bts:biobankId" + "@id": "bts:Cre/Lox" }, { - "@id": "bts:resourceId" + "@id": "bts:YeastExpression" }, { - "@id": "bts:biobankName" + "@id": "bts:WormExpression" }, { - "@id": "bts:biobankURL" + "@id": "bts:InsectExpression" }, { - "@id": "bts:specimenType" + "@id": "bts:PlantExpression" }, { - "@id": "bts:specimenTissueType" + "@id": "bts:MouseTargeting" }, { - "@id": "bts:tumorType" + "@id": "bts:CRISPR" }, { - "@id": "bts:diseaseType" + "@id": "bts:TALEN" }, { - "@id": "bts:specimenPreparationMethod" + "@id": "bts:SyntheticBiology" }, { - "@id": "bts:specimenFormat" - } - ], - "sms:validationRules": [] - }, - { - "@id": "bts:biobankName", - "@type": "rdf:Property", - "rdfs:comment": "The name of the biobank. ", - "rdfs:label": "biobankName", - "schema:domainIncludes": [ + "@id": "bts:TransferVector" + }, { - "@id": "bts:Biobank" + "@id": "bts:Unspecified" + }, + { + "@id": "bts:Other" } ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "biobankName", - "sms:required": "sms:true", - "sms:validationRules": [] + "sms:displayName": "vectorType", + "sms:required": "sms:false", + "sms:validationRules": [ + "list like" + ] }, { - "@id": "bts:biobankId", + "@id": "bts:backboneSize", "@type": "rdf:Property", - "rdfs:comment": "A unique identifier for the biobank.", - "rdfs:label": "biobankId", + "rdfs:comment": "Size in bp of the backbone without the insert", + "rdfs:label": "backboneSize", "schema:domainIncludes": [ { - "@id": "bts:Biobank" + "@id": "bts:GeneticReagent" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "biobankId", - "sms:required": "sms:true", + "sms:displayName": "backboneSize", + "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:biobankURL", + "@id": "bts:totalSize", "@type": "rdf:Property", - "rdfs:comment": "A URL for the biobank landing page.", - "rdfs:label": "biobankURL", + "rdfs:comment": "Size of vector with insert. Derived from insertSize and backboneSize.", + "rdfs:label": "totalSize", "schema:domainIncludes": [ { - "@id": "bts:Biobank" + "@id": "bts:GeneticReagent" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "biobankURL", - "sms:required": "sms:true", + "sms:displayName": "totalSize", + "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:specimenType", + "@id": "bts:bacterialResistance", "@type": "rdf:Property", - "rdfs:comment": "The types of specimens that are banked.", - "rdfs:label": "specimenType", + "rdfs:comment": "Antibiotic(s) that should be used for selection in bacteria. (e.g. ampicillin, kanamycin, etc.)", + "rdfs:label": "bacterialResistance", "schema:domainIncludes": [ { - "@id": "bts:Biobank" + "@id": "bts:GeneticReagent" } ], "schema:isPartOf": { @@ -3543,71 +1404,87 @@ }, "schema:rangeIncludes": [ { - "@id": "bts:Humantissue" + "@id": "bts:Ampicillin" }, { - "@id": "bts:Xenografttumors" + "@id": "bts:Kanamycin" }, { - "@id": "bts:Celllines" - } - ], - "sms:displayName": "specimenType", - "sms:required": "sms:true", - "sms:validationRules": [ - "list" - ] - }, - { - "@id": "bts:specimenTissueType", - "@type": "rdf:Property", - "rdfs:comment": "The types of tissues that are banked.", - "rdfs:label": "specimenTissueType", - "schema:domainIncludes": [ + "@id": "bts:Chloramphenicol" + }, { - "@id": "bts:Biobank" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ + "@id": "bts:Tetracycline" + }, { - "@id": "bts:Blood" + "@id": "bts:Spectinomycin" }, { - "@id": "bts:Tumor" + "@id": "bts:Hygromycin" }, { - "@id": "bts:Cerebrospinalfluid" + "@id": "bts:Bleocin(Zeocin)" }, { - "@id": "bts:Nerve" + "@id": "bts:Gentamycin" }, { - "@id": "bts:Skin" + "@id": "bts:Streptomycin" }, { - "@id": "bts:Bone" + "@id": "bts:Nourseothricin(clonNat)" }, { - "@id": "bts:Brain" + "@id": "bts:AmpicillinandBleocin(Zeocin)" + }, + { + "@id": "bts:AmpicillinandKanamycin" + }, + { + "@id": "bts:AmpicillinandTetracycline" + }, + { + "@id": "bts:AmpicillinandStreptomycin" + }, + { + "@id": "bts:AmpicillinandSpectinomycin" + }, + { + "@id": "bts:ChloramphenicolandAmpicillin" + }, + { + "@id": "bts:ChloramphenicolandBleocin(Zeocin)" + }, + { + "@id": "bts:ChloramphenicolandTetracycline" + }, + { + "@id": "bts:ChloramphenicolandKanamycin" + }, + { + "@id": "bts:ChloramphenicolandSpectinomycin" + }, + { + "@id": "bts:ChloramphenicolandGentamycin" + }, + { + "@id": "bts:SpectinomycinandStreptomycin" + }, + { + "@id": "bts:Other" } ], - "sms:displayName": "specimenTissueType", - "sms:required": "sms:true", - "sms:validationRules": [ - "list" - ] + "sms:displayName": "bacterialResistance", + "sms:required": "sms:false", + "sms:validationRules": [] }, { - "@id": "bts:tumorType", + "@id": "bts:selectableMarker", "@type": "rdf:Property", - "rdfs:comment": "The types of tumors that are banked, if applicable.", - "rdfs:label": "tumorType", + "rdfs:comment": "Are there any additional selection markers on this plasmid, for example, any mammalian selection markers or fluorescent proteins?", + "rdfs:label": "selectableMarker", "schema:domainIncludes": [ { - "@id": "bts:Biobank" + "@id": "bts:GeneticReagent" } ], "schema:isPartOf": { @@ -3615,59 +1492,82 @@ }, "schema:rangeIncludes": [ { - "@id": "bts:Cutaneousneurofibroma" + "@id": "bts:Neomycin" }, { - "@id": "bts:Plexiformneurofibroma" + "@id": "bts:Puromycin" }, { - "@id": "bts:Schwannoma" + "@id": "bts:Hygromycin" }, { - "@id": "bts:Meningioma" + "@id": "bts:Zeocin" }, { - "@id": "bts:Malignantperipheralnervesheathtumor" + "@id": "bts:Blasticidin" }, { - "@id": "bts:Lowgradeglioma" + "@id": "bts:Gentamicin" }, { - "@id": "bts:Highgradeglioma" + "@id": "bts:TRP1" }, { - "@id": "bts:Pheochromocytoma" + "@id": "bts:LEU1" }, { - "@id": "bts:Opticnerveglioma" + "@id": "bts:URA3" }, { - "@id": "bts:Atypicalneurofibroma" + "@id": "bts:HIS3" }, { - "@id": "bts:NeurofibromaNOS" + "@id": "bts:Basta" }, { - "@id": "bts:Diffuseinfiltratingneurofibroma" + "@id": "bts:Other" + } + ], + "sms:displayName": "selectableMarker", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:copyNumber", + "@type": "rdf:Property", + "rdfs:comment": "If a plasmid produces a sufficient amount of DNA from a normal miniprep or if plasmid requires special growth conditions or it is difficult to grow. (e.g. high copy, low copy, unknown).", + "rdfs:label": "copyNumber", + "schema:domainIncludes": [ + { + "@id": "bts:GeneticReagent" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ + { + "@id": "bts:HighCopy" }, { - "@id": "bts:BrainNOS" + "@id": "bts:LowCopy" + }, + { + "@id": "bts:Unknown" } ], - "sms:displayName": "tumorType", - "sms:required": "sms:true", - "sms:validationRules": [ - "list" - ] + "sms:displayName": "copyNumber", + "sms:required": "sms:false", + "sms:validationRules": [] }, { - "@id": "bts:diseaseType", + "@id": "bts:growthTemp", "@type": "rdf:Property", - "rdfs:comment": "The diseases of the banked specimens, if applicable.", - "rdfs:label": "diseaseType", + "rdfs:comment": "At what temperature should the bacteria hosting the plasmid be grown", + "rdfs:label": "growthTemp", "schema:domainIncludes": [ { - "@id": "bts:Biobank" + "@id": "bts:GeneticReagent" } ], "schema:isPartOf": { @@ -3675,29 +1575,27 @@ }, "schema:rangeIncludes": [ { - "@id": "bts:Neurofibromatosistype1" + "@id": "bts:37C" }, { - "@id": "bts:Neurofibromatosistype2" + "@id": "bts:30C" }, { - "@id": "bts:Schwannomatosis" + "@id": "bts:RoomTemperature" } ], - "sms:displayName": "diseaseType", - "sms:required": "sms:true", - "sms:validationRules": [ - "list" - ] + "sms:displayName": "growthTemp", + "sms:required": "sms:false", + "sms:validationRules": [] }, { - "@id": "bts:specimenPreparationMethod", + "@id": "bts:growthStrain", "@type": "rdf:Property", - "rdfs:comment": "The preservation methods used by the biobank.", - "rdfs:label": "specimenPreparationMethod", + "rdfs:comment": "The E.Coli strain that should be used to distribute the plasmid. (e.g. DH5alpha, NEB Stable, etc.)", + "rdfs:label": "growthStrain", "schema:domainIncludes": [ { - "@id": "bts:Biobank" + "@id": "bts:GeneticReagent" } ], "schema:isPartOf": { @@ -3705,44 +1603,36 @@ }, "schema:rangeIncludes": [ { - "@id": "bts:Freshcollected" - }, - { - "@id": "bts:Flashfrozen" - }, - { - "@id": "bts:FFPE" + "@id": "bts:DH5alpha" }, { - "@id": "bts:Cryopreserved" + "@id": "bts:DH10B" }, { - "@id": "bts:OCT" + "@id": "bts:NEBStable" }, { - "@id": "bts:RNAlater" + "@id": "bts:CcdbSurvival" }, { - "@id": "bts:Formalin-fixed" + "@id": "bts:Pir1" }, { - "@id": "bts:Ethanol" + "@id": "bts:Other" } ], - "sms:displayName": "specimenPreparationMethod", - "sms:required": "sms:true", - "sms:validationRules": [ - "list" - ] + "sms:displayName": "growthStrain", + "sms:required": "sms:false", + "sms:validationRules": [] }, { - "@id": "bts:specimenFormat", + "@id": "bts:hazardous", "@type": "rdf:Property", - "rdfs:comment": "How the specimens have been processed in preparation for distribution.", - "rdfs:label": "specimenFormat", + "rdfs:comment": "Does the unmodified plasmid DNA, either in purified form or when introduced into bacterial or mammalian cells require handling at Biosafety Level 2 or higher?", + "rdfs:label": "hazardous", "schema:domainIncludes": [ { - "@id": "bts:Biobank" + "@id": "bts:GeneticReagent" } ], "schema:isPartOf": { @@ -3750,2224 +1640,1660 @@ }, "schema:rangeIncludes": [ { - "@id": "bts:Wholetumor" - }, - { - "@id": "bts:Slide" - }, - { - "@id": "bts:Wholecelllysate" + "@id": "bts:Yes" }, { - "@id": "bts:DNA" + "@id": "bts:No" }, { - "@id": "bts:RNA" + "@id": "bts:Unknown" } ], - "sms:displayName": "specimenFormat", + "sms:displayName": "hazardous", "sms:required": "sms:true", - "sms:validationRules": [ - "list" - ] + "sms:validationRules": [] }, { - "@id": "bts:Observation", + "@id": "bts:Homosapiens", "@type": "rdfs:Class", - "rdfs:comment": "A remark, statement, or comment based on the resource.", - "rdfs:label": "Observation", + "rdfs:comment": "TBD", + "rdfs:label": "Homosapiens", "rdfs:subClassOf": [ { - "@id": "bts:Observation" + "@id": "bts:insertSpecies" + }, + { + "@id": "bts:species" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "observation", + "sms:displayName": "Homo sapiens", "sms:required": "sms:false", - "sms:requiresComponent": [ - { - "@id": "bts:Resource" - }, + "sms:validationRules": [] + }, + { + "@id": "bts:Musmusculus", + "@type": "rdfs:Class", + "rdfs:comment": "TBD", + "rdfs:label": "Musmusculus", + "rdfs:subClassOf": [ { - "@id": "bts:Investigator" + "@id": "bts:insertSpecies" }, { - "@id": "bts:Publication" + "@id": "bts:species" } ], - "sms:requiresDependency": [ - { - "@id": "bts:Component" - }, + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Mus musculus", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:Rattusnorvegicus", + "@type": "rdfs:Class", + "rdfs:comment": "TBD", + "rdfs:label": "Rattusnorvegicus", + "rdfs:subClassOf": [ { - "@id": "bts:observationId" + "@id": "bts:insertSpecies" }, { - "@id": "bts:resourceId" - }, + "@id": "bts:species" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Rattus norvegicus", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:RestrictionEnzyme", + "@type": "rdfs:Class", + "rdfs:comment": "TBD", + "rdfs:label": "RestrictionEnzyme", + "rdfs:subClassOf": [ { - "@id": "bts:publicationId" - }, + "@id": "bts:cloningMethod" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Restriction Enzyme", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:TOPOcloning", + "@type": "rdfs:Class", + "rdfs:comment": "TBD", + "rdfs:label": "TOPOcloning", + "rdfs:subClassOf": [ { - "@id": "bts:observationSubmitterName" - }, + "@id": "bts:cloningMethod" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "TOPO cloning", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:GatewayCloning", + "@type": "rdfs:Class", + "rdfs:comment": "TBD", + "rdfs:label": "GatewayCloning", + "rdfs:subClassOf": [ { - 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[ NCI ]", - "rdfs:label": "cellLineGeneticDisorder", - "schema:domainIncludes": [ + "@id": "bts:LEU1", + "@type": "rdfs:Class", + "rdfs:comment": "TBD", + "rdfs:label": "LEU1", + "rdfs:subClassOf": [ { - "@id": "bts:CellLine" + "@id": "bts:selectableMarker" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "schema:rangeIncludes": [ - { - "@id": "bts:Neurofibromatosistype1" - }, - { - "@id": "bts:Neurofibromatosistype2" - }, - { - "@id": "bts:Schwannomatosis" - }, - { - "@id": "bts:Noknowndisease" - } - ], - "sms:displayName": "cellLineGeneticDisorder", + "sms:displayName": "LEU1", "sms:required": "sms:false", - "sms:validationRules": [ - "list" - ] + "sms:validationRules": [] }, { - "@id": "bts:cellLineManifestation", - "@type": "rdf:Property", - "rdfs:comment": "Manifestations/symptoms that this resource is used to model (e.g. tumor type, behavioral phenotype, etc.)", - "rdfs:label": "cellLineManifestation", - "schema:domainIncludes": [ + "@id": "bts:URA3", + "@type": "rdfs:Class", + "rdfs:comment": "TBD", + "rdfs:label": "URA3", + "rdfs:subClassOf": [ { - "@id": "bts:CellLine" + "@id": "bts:selectableMarker" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "cellLineManifestation", + "sms:displayName": "URA3", "sms:required": "sms:false", - "sms:validationRules": [ - "list" - ] + "sms:validationRules": [] }, { - "@id": "bts:MutationDetails", + "@id": "bts:HIS3", "@type": "rdfs:Class", - "rdfs:comment": "The changing of the structure of a gene, resulting in a variant form that may be transmitted to subsequent generations", - "rdfs:label": "MutationDetails", + "rdfs:comment": "TBD", + "rdfs:label": "HIS3", "rdfs:subClassOf": [ { - "@id": "bts:MutationDetails" + "@id": "bts:selectableMarker" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "mutationDetails", + "sms:displayName": "HIS3", "sms:required": "sms:false", - "sms:requiresDependency": [ - { - "@id": "bts:Component" - }, - { - "@id": "bts:mutationDetailsId" - }, - { - "@id": "bts:externalMutationID" - }, - { - "@id": "bts:alleleType" - }, - { - "@id": "bts:mutationType" - }, - { - "@id": "bts:mutationMethod" - }, - { - "@id": "bts:affectedGeneSymbol" - }, - { - "@id": "bts:affectedGeneName" - }, - { - "@id": "bts:sequenceVariation" - }, - { - "@id": "bts:proteinVariation" - }, - { - "@id": "bts:animalModelMutation" - }, - { - "@id": "bts:humanClinVarMutation" - }, - { - "@id": "bts:chromosome" - } - ], "sms:validationRules": [] }, { - "@id": "bts:mutationDetailsId", - "@type": "rdf:Property", - "rdfs:comment": "A unique identifier for mutation.", - "rdfs:label": "mutationDetailsId", - "schema:domainIncludes": [ - { - "@id": "bts:MutationDetails" - }, + "@id": "bts:Basta", + "@type": "rdfs:Class", + "rdfs:comment": "TBD", + "rdfs:label": "Basta", + "rdfs:subClassOf": [ { - "@id": "bts:Mutation" + "@id": "bts:selectableMarker" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "mutationDetailsId", + "sms:displayName": "Basta", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:externalMutationID", - "@type": "rdf:Property", - "rdfs:comment": "An identifier from an organism database such as MGI or other curated variant resource, if available. 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", - "rdfs:label": "sequenceVariation", - "schema:domainIncludes": [ + "@id": "bts:VendorItem", + "@type": "rdfs:Class", + "rdfs:comment": "The resource item associated with a vendor.", + "rdfs:label": "VendorItem", + "rdfs:subClassOf": [ { - "@id": "bts:MutationDetails" + "@id": "bts:Thing" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "sequenceVariation", + "sms:displayName": "vendorItem", "sms:required": "sms:false", + "sms:requiresComponent": [ + { + "@id": "bts:Resource" + }, + { + "@id": "bts:Vendor" + } + ], + "sms:requiresDependency": [ + { + "@id": "bts:Component" + }, + { + "@id": "bts:vendorItemId" + }, + { + "@id": "bts:vendorId" + }, + { + "@id": "bts:resourceId" + }, + { + "@id": "bts:catalogNumber" + }, + { + "@id": "bts:catalogNumberURL" + } + ], "sms:validationRules": [] }, { - "@id": "bts:proteinVariation", + "@id": "bts:vendorItemId", "@type": "rdf:Property", - "rdfs:comment": "The protein consequence of the mutation described in sequence variations. (e.g. p.Asn58fs). See http://varnomen.hgvs.org/recommendations/protein/ for the Protein Variation nomenclature.", - "rdfs:label": "proteinVariation", + "rdfs:comment": "A unique identifier for the resource associated with a vendor.", + "rdfs:label": "vendorItemId", "schema:domainIncludes": [ { - "@id": "bts:MutationDetails" + "@id": "bts:VendorItem" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "proteinVariation", - "sms:required": "sms:false", + "sms:displayName": "vendorItemId", + "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:animalModelMutation", + "@id": "bts:vendorId", "@type": "rdf:Property", - "rdfs:comment": "A description of the specific mutation(s) created in the genome. (e.g. A neomycin resistance cassette replaced the first 42 codons of exon 31, the exon 31 splice acceptor site, and approximately 2 kb of intron 30.)", - "rdfs:label": "animalModelMutation", + "rdfs:comment": "A unique identifier for the vendor.", + "rdfs:label": "vendorId", "schema:domainIncludes": [ { - "@id": "bts:MutationDetails" + "@id": "bts:VendorItem" + }, + { + "@id": "bts:Vendor" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "animalModelMutation", - "sms:required": "sms:false", + "sms:displayName": "vendorId", + "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:humanClinVarMutation", + "@id": "bts:catalogNumber", "@type": "rdf:Property", - "rdfs:comment": "The human equivalent, of the mutation being described in ClinVar/HGVS notation. Can be used to link animal model mutations to the mutation they are modeling in human disease. ", - "rdfs:label": "humanClinVarMutation", + "rdfs:comment": "The catalog number associated with the resource pertaining to the vendor that sells the resource.", + "rdfs:label": "catalogNumber", "schema:domainIncludes": [ { - "@id": "bts:MutationDetails" + "@id": "bts:VendorItem" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "humanClinVarMutation", - "sms:required": "sms:false", + "sms:displayName": "catalogNumber", + "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:chromosome", + "@id": "bts:catalogNumberURL", "@type": "rdf:Property", - "rdfs:comment": "Chromosome number of affected gene. (e.g. 11)", - "rdfs:label": "chromosome", + "rdfs:comment": "The url linking to the resource on the vendor's website.", + "rdfs:label": "catalogNumberURL", "schema:domainIncludes": [ { - "@id": "bts:MutationDetails" + "@id": "bts:VendorItem" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "chromosome", + "sms:displayName": "catalogNumberURL", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:Mutation", + "@id": "bts:Vendor", "@type": "rdfs:Class", - "rdfs:comment": "(intermediary table)", - "rdfs:label": "Mutation", + "rdfs:comment": "A person or compnay offering the resource for sale.", + "rdfs:label": "Vendor", "rdfs:subClassOf": [ { - "@id": "bts:Mutation" + "@id": "bts:Thing" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "mutation", + "sms:displayName": "vendor", "sms:required": "sms:false", - "sms:requiresComponent": [ - { - "@id": "bts:MutationDetails" - }, - { - "@id": "bts:AnimalModel" - }, - { - "@id": "bts:CellLine" - } - ], "sms:requiresDependency": [ { "@id": "bts:Component" }, { - "@id": "bts:mutationId" - }, - { - "@id": "bts:mutationDetailsId" + "@id": "bts:vendorId" }, { - "@id": "bts:animalModelId" + "@id": "bts:vendorName" }, { - "@id": "bts:cellLineId" + "@id": "bts:vendorURL" } ], "sms:validationRules": [] }, { - "@id": "bts:mutationId", + "@id": "bts:vendorName", "@type": "rdf:Property", - "rdfs:comment": "A unique identifier for the mutation burden of the resource.", - "rdfs:label": "mutationId", + "rdfs:comment": "The name of the vendor.", + "rdfs:label": "vendorName", "schema:domainIncludes": [ { - "@id": "bts:Mutation" + "@id": "bts:Vendor" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "mutationId", + "sms:displayName": "vendorName", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:AnimalModel", - "@type": "rdfs:Class", - "rdfs:comment": "An animal sufficiently like humans in its anatomy, physiology, or response to a pathogen to be used in medical research in order to obtain results that can be extrapolated to human medicine.", - "rdfs:label": "AnimalModel", - "rdfs:subClassOf": [ + "@id": "bts:vendorURL", + "@type": "rdf:Property", + "rdfs:comment": "The vendor website url associated with the resource.", + "rdfs:label": "vendorURL", + "schema:domainIncludes": [ { - "@id": "bts:AnimalModel" + "@id": "bts:Vendor" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "animalModel", + "sms:displayName": "vendorURL", "sms:required": "sms:false", - "sms:requiresComponent": [ - { - "@id": "bts:Donor" - } - ], - "sms:requiresDependency": [ - { - "@id": "bts:Component" - }, - { - "@id": "bts:animalModelId" - }, - { - "@id": "bts:donorId" - }, - { - "@id": "bts:transplantationDonorId" - }, - { - "@id": "bts:animalState" - }, - { - "@id": "bts:backgroundStrain" - }, - { - "@id": "bts:backgroundSubstrain" - }, - { - "@id": "bts:strainNomenclature" - }, - { - "@id": "bts:generation" - }, - { - "@id": "bts:transplantationType" - }, - { - "@id": "bts:animalModelGeneticDisorder" - }, - { - "@id": "bts:animalModelOfManifestation" - } - ], "sms:validationRules": [] }, { - "@id": "bts:animalModelId", + "@id": "bts:biobankId", "@type": "rdf:Property", - "rdfs:comment": "A unique identifier for the animal model.", - "rdfs:label": "animalModelId", + "rdfs:comment": "A unique identifier for the biobank.", + "rdfs:label": "biobankId", "schema:domainIncludes": [ { - "@id": "bts:Resource" - }, - { - "@id": "bts:Mutation" - }, - { - "@id": "bts:AnimalModel" + "@id": "bts:Biobank" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "animalModelId", + "sms:displayName": "biobankId", "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:animalState", + "@id": "bts:biobankName", "@type": "rdf:Property", - "rdfs:comment": "State the animal is in according to the vendor/developer. (e.g. embryo, sperm, live)", - "rdfs:label": "animalState", + "rdfs:comment": "The name of the biobank.", + "rdfs:label": "biobankName", "schema:domainIncludes": [ { - "@id": "bts:AnimalModel" + "@id": "bts:Biobank" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "animalState", - "sms:required": "sms:false", + "sms:displayName": "biobankName", + "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:backgroundStrain", + "@id": "bts:biobankURL", "@type": "rdf:Property", - "rdfs:comment": "An assigned name that describes the genetic make-up (all its alleles at all loci) except the mutated gene of interest and a very small amount of other genetic material, generally from one or two other strains. Correct strain nomenclature indicates what a mutant strain’s background is.", - "rdfs:label": "backgroundStrain", + "rdfs:comment": "A URL for the biobank landing page.", + "rdfs:label": "biobankURL", "schema:domainIncludes": [ { - "@id": "bts:AnimalModel" + "@id": "bts:Biobank" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "backgroundStrain", - "sms:required": "sms:false", + "sms:displayName": "biobankURL", + "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:backgroundSubstrain", + "@id": "bts:specimenType", "@type": "rdf:Property", - "rdfs:comment": "The substrain is a particular variety of a strain. For example, a C57BL/6 mice may have a substrain of C57BL/6J, C57BL/6Tac, or another substrain. ", - "rdfs:label": "backgroundSubstrain", + "rdfs:comment": "The types of specimens that are banked.", + "rdfs:label": "specimenType", "schema:domainIncludes": [ { - "@id": "bts:AnimalModel" + "@id": "bts:Biobank" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "backgroundSubstrain", - "sms:required": "sms:false", - "sms:validationRules": [] + "schema:rangeIncludes": [ + { + "@id": "bts:Humantissue" + }, + { + "@id": "bts:Xenografttumors" + }, + { + "@id": "bts:Celllines" + } + ], + "sms:displayName": "specimenType", + "sms:required": "sms:true", + "sms:validationRules": [ + "list like" + ] }, { - "@id": "bts:strainNomenclature", + "@id": "bts:specimenTissueType", "@type": "rdf:Property", - "rdfs:comment": "The standard nomenclature for the strain. (e.g. B6.129S2-NF1tm1Tyj/J). Set by the International Committee on Standardized Genetic Nomenclature for Mice. See http://www.informatics.jax.org/mgihome/nomen/strains.shtml for nomenclature information.", - "rdfs:label": "strainNomenclature", + "rdfs:comment": "The types of tissues that are banked.", + "rdfs:label": "specimenTissueType", "schema:domainIncludes": [ { - "@id": "bts:AnimalModel" + "@id": "bts:Biobank" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "strainNomenclature", - "sms:required": "sms:false", - "sms:validationRules": [] + "schema:rangeIncludes": [ + { + "@id": "bts:Blood" + }, + { + "@id": "bts:Tumor" + }, + { + "@id": "bts:Cerebrospinalfluid" + }, + { + "@id": "bts:Nerve" + }, + { + "@id": "bts:Skin" + }, + { + "@id": "bts:Bone" + }, + { + "@id": "bts:Brain" + } + ], + "sms:displayName": "specimenTissueType", + "sms:required": "sms:true", + "sms:validationRules": [ + "list like" + ] }, { - "@id": "bts:generation", + "@id": "bts:tumorType", "@type": "rdf:Property", - "rdfs:comment": "The generation of the animal model. (e.g. 13)", - "rdfs:label": "generation", + "rdfs:comment": "The types of tumors that are banked, if applicable.", + "rdfs:label": "tumorType", "schema:domainIncludes": [ { - "@id": "bts:AnimalModel" + "@id": "bts:Biobank" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "generation", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:transplantationType", - "@type": "rdf:Property", - "rdfs:comment": "Type of transplantation involved in the experiment, derived from MESH", - "rdfs:label": "transplantationType", - "schema:domainIncludes": [ + "schema:rangeIncludes": [ + { + "@id": "bts:Cutaneousneurofibroma" + }, + { + "@id": "bts:Plexiformneurofibroma" + }, + { + "@id": "bts:Schwannoma" + }, + { + "@id": "bts:Meningioma" + }, { - "@id": "bts:AnimalModel" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ + "@id": "bts:Malignantperipheralnervesheathtumor" + }, { - "@id": "bts:Allograft" + "@id": "bts:Lowgradeglioma" }, { - "@id": "bts:Xenograft" + "@id": "bts:Highgradeglioma" }, { - "@id": "bts:Autograft" + "@id": "bts:Pheochromocytoma" }, { - "@id": "bts:Isograft" - } - ], - "sms:displayName": "transplantationType", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:transplantationDonorId", - "@type": "rdf:Property", - "rdfs:comment": "The donor indentifier number for the transplantion donor. ", - "rdfs:label": "transplantationDonorId", - "schema:domainIncludes": [ + "@id": "bts:Opticnerveglioma" + }, { - "@id": "bts:Donor" + "@id": "bts:Atypicalneurofibroma" }, { - "@id": "bts:AnimalModel" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "transplantationDonorId", - "sms:required": "sms:false", - "sms:requiresDependency": [ + "@id": "bts:NeurofibromaNOS" + }, { - "@id": "bts:donorId" + "@id": "bts:Diffuseinfiltratingneurofibroma" + }, + { + "@id": "bts:BrainNOS" } ], - "sms:validationRules": [] + "sms:displayName": "tumorType", + "sms:required": "sms:true", + "sms:validationRules": [ + "list like" + ] }, { - "@id": "bts:animalModelGeneticDisorder", + "@id": "bts:diseaseType", "@type": "rdf:Property", - "rdfs:comment": "Genetic diseases are diseases in which inherited genes predispose to increased risk. The genetic disorders associated with cancer often result from an alteration or mutation in a single gene. The diseases range from rare dominant cancer family syndrome to familial tendencies in which low-penetrance genes may interact with other genes or environmental factors to induce cancer. Research may involve clinical, epidemiologic, and laboratory studies of persons, families, and populations at high risk of these disorders. [ NCI ]", - "rdfs:label": "animalModelGeneticDisorder", + "rdfs:comment": "The diseases of the banked specimens, if applicable.", + "rdfs:label": "diseaseType", "schema:domainIncludes": [ { - "@id": "bts:AnimalModel" + "@id": "bts:Biobank" } ], "schema:isPartOf": { @@ -5982,6023 +3308,6822 @@ }, { "@id": "bts:Schwannomatosis" - }, - { - "@id": "bts:Noknowndisease" } ], - "sms:displayName": "animalModelGeneticDisorder", + "sms:displayName": "diseaseType", "sms:required": "sms:true", "sms:validationRules": [ - "list" + "list like" ] }, { - "@id": "bts:animalModelOfManifestation", + "@id": "bts:specimenPreparationMethod", "@type": "rdf:Property", - "rdfs:comment": "Manifestations/symptoms that this resource is used to model (e.g. tumor type, behavioral phenotype, etc.) ", - "rdfs:label": "animalModelOfManifestation", + "rdfs:comment": "The preservation methods used by the biobank.", + "rdfs:label": "specimenPreparationMethod", "schema:domainIncludes": [ { - "@id": "bts:AnimalModel" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "animalModelOfManifestation", - "sms:required": "sms:true", - "sms:validationRules": [ - "list" - ] - }, - { - "@id": "bts:Development", - "@type": "rdfs:Class", - "rdfs:comment": "resourceId, investigatorId, publicationId, funderId (intermediary table)", - "rdfs:label": "Development", - "rdfs:subClassOf": [ - { - "@id": "bts:Development" + "@id": "bts:Biobank" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "development", - "sms:required": "sms:false", - "sms:requiresComponent": [ - { - "@id": "bts:Resource" - }, + "schema:rangeIncludes": [ { - "@id": "bts:Investigator" + "@id": "bts:Freshcollected" }, { - "@id": "bts:Publication" + "@id": "bts:Flashfrozen" }, { - "@id": "bts:Funder" - } - ], - "sms:requiresDependency": [ - { - "@id": "bts:Component" + "@id": "bts:FFPE" }, { - "@id": "bts:developmentId" + "@id": "bts:Cryopreserved" }, { - "@id": "bts:resourceId" + "@id": "bts:OCT" }, { - "@id": "bts:investigatorId" + "@id": "bts:RNAlater" }, { - "@id": "bts:publicationId" + "@id": "bts:Formalin-fixed" }, { - "@id": "bts:funderId" + "@id": "bts:Ethanol" } ], - "sms:validationRules": [] + "sms:displayName": "specimenPreparationMethod", + "sms:required": "sms:true", + "sms:validationRules": [ + "list like" + ] }, { - "@id": "bts:developmentId", + "@id": "bts:specimenFormat", "@type": "rdf:Property", - "rdfs:comment": "A unique identifier for the development of the resource.", - "rdfs:label": "developmentId", + "rdfs:comment": "How the specimens have been processed in preparation for distribution.", + "rdfs:label": "specimenFormat", "schema:domainIncludes": [ { - "@id": "bts:Development" + "@id": "bts:Biobank" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "developmentId", + "schema:rangeIncludes": [ + { + "@id": "bts:Wholetumor" + }, + { + "@id": "bts:Slide" + }, + { + "@id": "bts:Wholecelllysate" + }, + { + "@id": "bts:DNA" + }, + { + "@id": "bts:RNA" + } + ], + "sms:displayName": "specimenFormat", "sms:required": "sms:true", - "sms:validationRules": [] + "sms:validationRules": [ + "list like" + ] }, { - "@id": "bts:Funder", + "@id": "bts:Humantissue", "@type": "rdfs:Class", - "rdfs:comment": "A person or organization that provides money for a particular resource.", - "rdfs:label": "Funder", + "rdfs:comment": "TBD", + "rdfs:label": "Humantissue", "rdfs:subClassOf": [ { - "@id": "bts:Funder" + "@id": "bts:specimenType" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "funder", + "sms:displayName": "human tissue", "sms:required": "sms:false", - "sms:requiresDependency": [ - { - "@id": "bts:Component" - }, - { - "@id": "bts:funderId" - }, + "sms:validationRules": [] + }, + { + "@id": "bts:Xenografttumors", + "@type": "rdfs:Class", + "rdfs:comment": "TBD", + "rdfs:label": "Xenografttumors", + "rdfs:subClassOf": [ { - "@id": "bts:funderName" + "@id": "bts:specimenType" } ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "xenograft tumors", + "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:funderId", - "@type": "rdf:Property", - "rdfs:comment": "A unique identifier for the funder of the resource.", - "rdfs:label": "funderId", - "schema:domainIncludes": [ - { - "@id": "bts:Development" - }, + "@id": "bts:Celllines", + "@type": "rdfs:Class", + "rdfs:comment": "TBD", + "rdfs:label": "Celllines", + "rdfs:subClassOf": [ { - "@id": "bts:Funder" + "@id": "bts:specimenType" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "funderId", + "sms:displayName": "cell lines", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:funderName", - "@type": "rdf:Property", - "rdfs:comment": "The name of the person or agency that funded the development of the resource.", - "rdfs:label": "funderName", - "schema:domainIncludes": [ + "@id": "bts:Blood", + "@type": "rdfs:Class", + "rdfs:comment": "TBD", + "rdfs:label": "Blood", + "rdfs:subClassOf": [ { - "@id": "bts:Funder" + "@id": "bts:specimenTissueType" + }, + { + "@id": "bts:organ" + }, + { + "@id": "bts:tissue" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "funderName", + "sms:displayName": "Blood", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:Investigator", + "@id": "bts:Tumor", "@type": "rdfs:Class", - "rdfs:comment": "A person who carries out a formal inquiry or investigation into the development of the resource.", - "rdfs:label": "Investigator", + "rdfs:comment": "TBD", + "rdfs:label": "Tumor", "rdfs:subClassOf": [ { - "@id": "bts:Investigator" + "@id": "bts:specimenTissueType" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "investigator", + "sms:displayName": "tumor", "sms:required": "sms:false", - "sms:requiresDependency": [ - { - "@id": "bts:Component" - }, - { - "@id": "bts:investigatorId" - }, - { - "@id": "bts:orcid" - }, - { - "@id": "bts:investigatorName" - }, - { - "@id": "bts:institution" - }, - { - "@id": "bts:investigatorWebsite" - }, + "sms:validationRules": [] + }, + { + "@id": "bts:Cerebrospinalfluid", + "@type": "rdfs:Class", + "rdfs:comment": "TBD", + "rdfs:label": "Cerebrospinalfluid", + "rdfs:subClassOf": [ { - 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The genetic disorders associated with cancer often result from an alteration or mutation in a single gene. The diseases range from rare dominant cancer family syndrome to familial tendencies in which low-penetrance genes may interact with other genes or environmental factors to induce cancer. Research may involve clinical, epidemiologic, and laboratory studies of persons, families, and populations at high risk of these disorders. 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"@id": "bts:MutationDetails" + "@id": "bts:AnimalModel" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "QTL", - "sms:required": "sms:false", - "sms:validationRules": [] + "sms:displayName": "animalModelOfManifestation", + "sms:required": "sms:true", + "sms:validationRules": [ + "list" + ] }, { - "@id": "bts:Radiationinduced", + "@id": "bts:Allograft", "@type": "rdfs:Class", "rdfs:comment": "TBD", - "rdfs:label": "Radiationinduced", + "rdfs:label": "Allograft", "rdfs:subClassOf": [ { - "@id": "bts:MutationDetails" + "@id": "bts:transplantationType" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Radiation induced", + "sms:displayName": "allograft", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:Spontaneous", + "@id": "bts:Xenograft", "@type": "rdfs:Class", "rdfs:comment": "TBD", - "rdfs:label": "Spontaneous", + "rdfs:label": "Xenograft", "rdfs:subClassOf": [ { - "@id": "bts:MutationDetails" + "@id": "bts:transplantationType" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Spontaneous", + "sms:displayName": "xenograft", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:Targeted", + "@id": "bts:Autograft", "@type": "rdfs:Class", "rdfs:comment": "TBD", - "rdfs:label": "Targeted", + "rdfs:label": "Autograft", "rdfs:subClassOf": [ { - "@id": "bts:MutationDetails" + "@id": "bts:transplantationType" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Targeted", + "sms:displayName": "autograft", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:Transgenic", + "@id": "bts:Isograft", "@type": "rdfs:Class", "rdfs:comment": "TBD", - "rdfs:label": "Transgenic", + "rdfs:label": "Isograft", "rdfs:subClassOf": [ { - "@id": "bts:MutationDetails" + "@id": "bts:transplantationType" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Transgenic", + "sms:displayName": "isograft", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:Transposoninduced", + "@id": "bts:Development", "@type": "rdfs:Class", - "rdfs:comment": "TBD", - "rdfs:label": "Transposoninduced", + "rdfs:comment": "resourceId, investigatorId, publicationId, funderId (intermediary table)", + "rdfs:label": "Development", "rdfs:subClassOf": [ { - "@id": "bts:MutationDetails" + "@id": "bts:Thing" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Transposon induced", + "sms:displayName": "development", "sms:required": "sms:false", + "sms:requiresComponent": [ + { + "@id": "bts:Resource" + }, + { + "@id": "bts:Investigator" + }, + { + "@id": "bts:Publication" + }, + { + "@id": "bts:Funder" + } + ], + "sms:requiresDependency": [ + { + "@id": "bts:Component" + }, + { + "@id": "bts:developmentId" + }, + { + "@id": "bts:resourceId" + }, + { + "@id": "bts:investigatorId" + }, + { + "@id": "bts:publicationId" + }, + { + "@id": "bts:funderId" + } + ], "sms:validationRules": [] }, { - "@id": "bts:Conditionalready", - "@type": "rdfs:Class", - "rdfs:comment": "TBD", - "rdfs:label": "Conditionalready", - "rdfs:subClassOf": [ + "@id": "bts:developmentId", + "@type": "rdf:Property", + "rdfs:comment": "A unique identifier for the development of the resource.", + "rdfs:label": "developmentId", + "schema:domainIncludes": [ { - "@id": "bts:MutationDetails" + "@id": "bts:Development" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Conditional ready", - "sms:required": "sms:false", + "sms:displayName": "developmentId", + "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:Constitutivelyactive", - "@type": "rdfs:Class", - "rdfs:comment": "TBD", - "rdfs:label": "Constitutivelyactive", - "rdfs:subClassOf": [ + "@id": "bts:investigatorId", + "@type": "rdf:Property", + "rdfs:comment": "A unique identifier for the investigator.", + "rdfs:label": "investigatorId", + "schema:domainIncludes": [ { - "@id": "bts:MutationDetails" + "@id": "bts:Development" + }, + { + "@id": "bts:Investigator" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Constitutively active", - "sms:required": "sms:false", + "sms:displayName": "investigatorId", + "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:Dominantnegative", - "@type": "rdfs:Class", - "rdfs:comment": "TBD", - "rdfs:label": "Dominantnegative", - "rdfs:subClassOf": [ + "@id": "bts:funderId", + "@type": "rdf:Property", + "rdfs:comment": "A unique identifier for the funder of the resource.", + "rdfs:label": "funderId", + "schema:domainIncludes": [ { - "@id": "bts:MutationDetails" + "@id": "bts:Development" + }, + { + "@id": "bts:Funder" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Dominant negative", + "sms:displayName": "funderId", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:Humanizedsequence", + "@id": "bts:Funder", "@type": "rdfs:Class", - "rdfs:comment": "TBD", - "rdfs:label": "Humanizedsequence", + "rdfs:comment": "A person or organization that provides money for a particular resource.", + "rdfs:label": "Funder", "rdfs:subClassOf": [ { - "@id": "bts:MutationDetails" + "@id": "bts:Thing" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Humanized sequence", + "sms:displayName": "funder", "sms:required": "sms:false", + "sms:requiresDependency": [ + { + "@id": "bts:Component" + }, + { + "@id": "bts:funderId" + }, + { + "@id": "bts:funderName" + } + ], "sms:validationRules": [] }, { - "@id": "bts:Hypomorph", - "@type": "rdfs:Class", - "rdfs:comment": "TBD", - "rdfs:label": "Hypomorph", - "rdfs:subClassOf": [ + "@id": "bts:funderName", + "@type": "rdf:Property", + "rdfs:comment": "The name of the person or agency that funded the development of the resource.", + "rdfs:label": "funderName", + "schema:domainIncludes": [ { - "@id": "bts:MutationDetails" + "@id": "bts:Funder" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Hypomorph", + "sms:displayName": "funderName", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:Inducible", - "@type": "rdfs:Class", - "rdfs:comment": "TBD", - "rdfs:label": "Inducible", - "rdfs:subClassOf": [ + "@id": "bts:orcid", + "@type": "rdf:Property", + "rdfs:comment": "The orcidId of the investigator that developed the resource", + "rdfs:label": "orcid", + "schema:domainIncludes": [ { - "@id": "bts:MutationDetails" + "@id": "bts:Investigator" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Inducible", + "sms:displayName": "orcid", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:Insertedexpressedsequence", - "@type": "rdfs:Class", - "rdfs:comment": "TBD", - "rdfs:label": "Insertedexpressedsequence", - "rdfs:subClassOf": [ + "@id": "bts:investigatorName", + "@type": "rdf:Property", + "rdfs:comment": "The name of the investigator responsible for devleoping the resource.", + "rdfs:label": "investigatorName", + "schema:domainIncludes": [ { - "@id": "bts:MutationDetails" + "@id": "bts:Investigator" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Inserted expressed sequence", - "sms:required": "sms:false", + "sms:displayName": "investigatorName", + "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:Knockdown", - "@type": "rdfs:Class", - "rdfs:comment": "TBD", - "rdfs:label": "Knockdown", - "rdfs:subClassOf": [ + "@id": "bts:institution", + "@type": "rdf:Property", + "rdfs:comment": "The insitution of the investator", + "rdfs:label": "institution", + "schema:domainIncludes": [ { - "@id": "bts:MutationDetails" + "@id": "bts:Investigator" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Knockdown", + "sms:displayName": "institution", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:Modifiedisoform(s)", - "@type": "rdfs:Class", - "rdfs:comment": "TBD", - "rdfs:label": "Modifiedisoform(s)", - "rdfs:subClassOf": [ + "@id": "bts:investigatorWebsite", + "@type": "rdf:Property", + "rdfs:comment": "The url to the investigator's laboratory website corresponding to the resource.", + "rdfs:label": "investigatorWebsite", + "schema:domainIncludes": [ { - "@id": "bts:MutationDetails" + "@id": "bts:Investigator" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Modified isoform(s)", + "sms:displayName": "investigatorWebsite", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:Nofunctionalchange", - "@type": "rdfs:Class", - "rdfs:comment": "TBD", - "rdfs:label": "Nofunctionalchange", - "rdfs:subClassOf": [ + "@id": "bts:investigatorSynapseId", + "@type": "rdf:Property", + "rdfs:comment": "The synapse identifier for the investigator.", + "rdfs:label": "investigatorSynapseId", + "schema:domainIncludes": [ { - "@id": "bts:MutationDetails" + "@id": "bts:Investigator" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "No functional change", + "sms:displayName": "investigatorSynapseId", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:Null/knockout", - "@type": "rdfs:Class", - "rdfs:comment": "TBD", - "rdfs:label": "Null/knockout", - "rdfs:subClassOf": [ + "@id": "bts:publicationTitle", + "@type": "rdf:Property", + "rdfs:comment": "The title of the publication associated with the resource.", + "rdfs:label": "publicationTitle", + "schema:domainIncludes": [ { - "@id": "bts:MutationDetails" + "@id": "bts:Publication" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Null/knockout", - "sms:required": "sms:false", + "sms:displayName": "publicationTitle", + "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:Recombinase", - "@type": "rdfs:Class", - "rdfs:comment": "TBD", - "rdfs:label": "Recombinase", - "rdfs:subClassOf": [ + "@id": "bts:authors", + "@type": "rdf:Property", + "rdfs:comment": "Writers of the publication.", + "rdfs:label": "authors", + "schema:domainIncludes": [ { - "@id": "bts:MutationDetails" + "@id": "bts:Publication" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Recombinase", + "sms:displayName": "authors", "sms:required": "sms:false", - "sms:validationRules": [] + "sms:validationRules": [ + "list like" + ] }, { - "@id": "bts:Reporter", - "@type": "rdfs:Class", - "rdfs:comment": "TBD", - "rdfs:label": "Reporter", - "rdfs:subClassOf": [ + "@id": "bts:abstract", + "@type": "rdf:Property", + "rdfs:comment": "A brief, comprehensive summary of the contents of a publication.", + "rdfs:label": "abstract", + "schema:domainIncludes": [ { - "@id": "bts:MutationDetails" + "@id": "bts:Publication" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Reporter", + "sms:displayName": "abstract", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:RMCE-Ready", - "@type": "rdfs:Class", - "rdfs:comment": "TBD", - "rdfs:label": "RMCE-Ready", - "rdfs:subClassOf": [ + "@id": "bts:journal", + "@type": "rdf:Property", + "rdfs:comment": "The name of the periodical publication in which the paper was published.", + "rdfs:label": "journal", + "schema:domainIncludes": [ { - "@id": "bts:MutationDetails" + "@id": "bts:Publication" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "RMCE-Ready", + "sms:displayName": "journal", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:Transactivator", - "@type": "rdfs:Class", - "rdfs:comment": "TBD", - "rdfs:label": "Transactivator", - "rdfs:subClassOf": [ + "@id": "bts:publicationDate", + "@type": "rdf:Property", + "rdfs:comment": "The date of the paper's publication.", + "rdfs:label": "publicationDate", + "schema:domainIncludes": [ { - "@id": "bts:MutationDetails" + "@id": "bts:Publication" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Transactivator", + "sms:displayName": "publicationDate", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:Transposase", - "@type": "rdfs:Class", - "rdfs:comment": "TBD", - "rdfs:label": "Transposase", - "rdfs:subClassOf": [ + "@id": "bts:pmid", + "@type": "rdf:Property", + "rdfs:comment": "The PubMed Identifier associated with the publication.", + "rdfs:label": "pmid", + "schema:domainIncludes": [ { - "@id": "bts:MutationDetails" + "@id": "bts:Publication" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Transposase", + "sms:displayName": "pmid", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:Transposonconcatemer", - "@type": "rdfs:Class", - "rdfs:comment": "TBD", - "rdfs:label": "Transposonconcatemer", - "rdfs:subClassOf": [ + "@id": "bts:doi", + "@type": "rdf:Property", + "rdfs:comment": "The digital object identifier associated with the publication in the form of https://www.doi.org/{doi} to comply with CrossRef DOI display guidelines.", + "rdfs:label": "doi", + "schema:domainIncludes": [ { - "@id": "bts:MutationDetails" + "@id": "bts:Publication" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Transposon concatemer", + "sms:displayName": "doi", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:Allograft", - "@type": "rdfs:Class", - "rdfs:comment": "TBD", - "rdfs:label": "Allograft", - "rdfs:subClassOf": [ + "@id": "bts:citation", + "@type": "rdf:Property", + "rdfs:comment": "A merged citation for the publication, used to render citation on details pages.", + "rdfs:label": "citation", + "schema:domainIncludes": [ { - "@id": "bts:AnimalModel" + "@id": "bts:Publication" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "allograft", - "sms:required": "sms:false", + "sms:displayName": "citation", + "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:Xenograft", - "@type": "rdfs:Class", - "rdfs:comment": "TBD", - "rdfs:label": "Xenograft", - "rdfs:subClassOf": [ + "@id": "bts:publicationDateUnix", + "@type": "rdf:Property", + "rdfs:comment": "The date of the paper's publication in UNIX time", + "rdfs:label": "publicationDateUnix", + "schema:domainIncludes": [ { - "@id": "bts:AnimalModel" + "@id": "bts:Publication" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "xenograft", + "sms:displayName": "publicationDateUnix", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:Autograft", + "@id": "bts:Usage", "@type": "rdfs:Class", - "rdfs:comment": "TBD", - "rdfs:label": "Autograft", + "rdfs:comment": "Publications referencing the resource's use.", + "rdfs:label": "Usage", "rdfs:subClassOf": [ { - "@id": "bts:AnimalModel" + "@id": "bts:Thing" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "autograft", + "sms:displayName": "usage", "sms:required": "sms:false", + "sms:requiresComponent": [ + { + "@id": "bts:Publication" + }, + { + "@id": "bts:Resource" + } + ], + "sms:requiresDependency": [ + { + "@id": "bts:Component" + }, + { + "@id": "bts:usageId" + }, + { + "@id": "bts:publicationId" + }, + { + "@id": "bts:resourceId" + } + ], "sms:validationRules": [] }, { - "@id": "bts:Isograft", - "@type": "rdfs:Class", - "rdfs:comment": "TBD", - "rdfs:label": "Isograft", - "rdfs:subClassOf": [ + "@id": "bts:usageId", + "@type": "rdf:Property", + "rdfs:comment": "A unique identifier for the usage of the resource.", + "rdfs:label": "usageId", + "schema:domainIncludes": [ { - "@id": "bts:AnimalModel" + "@id": "bts:Usage" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "isograft", - "sms:required": "sms:false", + "sms:displayName": "usageId", + "sms:required": "sms:true", "sms:validationRules": [] } ], From dcf6c34706053ee8946e52c3d6f41bf043b06bf2 Mon Sep 17 00:00:00 2001 From: Robert Allaway Date: Wed, 25 Oct 2023 14:13:59 -0500 Subject: [PATCH 10/97] remove biobank dependson --- nf_research_tools.rdb.model.csv | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/nf_research_tools.rdb.model.csv b/nf_research_tools.rdb.model.csv index 6595a272..ca52d24d 100644 --- a/nf_research_tools.rdb.model.csv +++ b/nf_research_tools.rdb.model.csv @@ -46,7 +46,7 @@ vendor,A person or compnay offering the resource for sale.,,"Component, vendorId vendorId,A unique identifier for the vendor.,,,TRUE,,vendor,,, vendorName,The name of the vendor.,,,FALSE,,vendor,,, vendorURL,The vendor website url associated with the resource.,,,FALSE,,vendor,,, -biobank,"A large collection of biological or medical data and tissue samples, amassed for research purposes.",,"Component, biobankId, resourceId, biobankName, biobankURL, specimenType, specimenTissueType, tumorType, diseaseType, specimenPreparationMethod, specimenFormat",FALSE,,biobank,"biobankId, resourceId, biobankName, biobankURL, specimenType, specimenTissueType, tumorType, diseaseType, specimenPreparationMethod, specimenFormat",resource, +biobank,"A large collection of biological or medical data and tissue samples, amassed for research purposes.",,"Component, biobankId, resourceId, biobankName, biobankURL, specimenType, specimenTissueType, tumorType, diseaseType, specimenPreparationMethod, specimenFormat",FALSE,,biobank,"biobankId, resourceId, biobankName, biobankURL, specimenType, specimenTissueType, tumorType, diseaseType, specimenPreparationMethod, specimenFormat",, biobankName,The name of the biobank. ,,,TRUE,,biobank,,, biobankId,A unique identifier for the biobank.,,,TRUE,,biobank,,, biobankURL,A URL for the biobank landing page.,,,TRUE,,biobank,,, From ab06341fd18a2a74fa9e4d250edd1d21cc92c5fa Mon Sep 17 00:00:00 2001 From: "nf-osi[bot]" Date: Wed, 25 Oct 2023 19:15:32 +0000 Subject: [PATCH 11/97] Add changes --- nf-research-tools.jsonld | 5 ----- 1 file changed, 5 deletions(-) diff --git a/nf-research-tools.jsonld b/nf-research-tools.jsonld index f58838ad..f5eabb28 100644 --- a/nf-research-tools.jsonld +++ b/nf-research-tools.jsonld @@ -710,11 +710,6 @@ }, "sms:displayName": "biobank", "sms:required": "sms:false", - "sms:requiresComponent": [ - { - "@id": "bts:Resource" - } - ], "sms:requiresDependency": [ { "@id": "bts:Component" From 67f955dbf0c6d866409fbe8c15d037f8bde4f453 Mon Sep 17 00:00:00 2001 From: Robert Allaway Date: Wed, 25 Oct 2023 15:32:49 -0500 Subject: [PATCH 12/97] Update nf_research_tools.rdb.model.csv --- nf_research_tools.rdb.model.csv | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/nf_research_tools.rdb.model.csv b/nf_research_tools.rdb.model.csv index ca52d24d..57d369d7 100644 --- a/nf_research_tools.rdb.model.csv +++ b/nf_research_tools.rdb.model.csv @@ -7,7 +7,7 @@ resourceName,The “canonical” name of the resource,,,TRUE,,resource,,, synonyms,Synonyms of the resource,,,FALSE,,resource,,,list like resourceType,"Type of resource. (e.g. animal model, antibody, plasmid, etc.)","Animal Model, Cell Line, Antibody, Genetic Reagent, Biobank",,TRUE,,resource,,, description,Free text description/summary/overview/purpose of the resource.,,,FALSE,,resource,,, -usageRequirements,Any known restrictions on use of the resource. ,"non-commercial use only, re-distribution not permitted, generation of germ line transmitting chimeras not permitted, creation of functional gametes not permitted, generation of interspecies chimeras not permitted, human cloning not permitted, cannot be used for treatment purposes, IRB documentation required, special licencing restrictions (see vendor for more information), unknown",,FALSE,,resource,,,list like +usageRequirements,Any known restrictions on use of the resource. ,"data sharing required, non-commercial use only, re-distribution not permitted, generation of germ line transmitting chimeras not permitted, creation of functional gametes not permitted, generation of interspecies chimeras not permitted, human cloning not permitted, cannot be used for treatment purposes, IRB documentation required, special licencing restrictions (see vendor for more information), unknown",,FALSE,,resource,,,list like howToAcquire,How to acquire a particular resource. ,,,TRUE,,resource,,, dateAdded,The date that the resource was originally added.,,,TRUE,,resource,,, dateModified,The last update of the resource metadata (not including observations).,,,TRUE,,resource,,, @@ -86,7 +86,7 @@ donor,"A person, animal, etc. who is the contributor of the resource.",,"Compone donorId,A uniqe identifier for donor.,,,TRUE,,donor,,, parentDonorId,The ID of the parent donor.,,donorId,FALSE,,donor,,, species,The species of the individual the resource was derived from.,"Homo sapiens, Mus musculus, Mus musculus (humanized), Rattus norvegicus, Drosophila melanogaster, Rhesus macaque, Pan troglodytes, Gallus gallus, Sus scrofa, Oryctolagus cuniculus,Danio rerio,Escherichia coli",,TRUE,,donor,,, -sex,The sex of the indiviudal from which the resource was derived from.,"Male, Female, Unknown",,FALSE,,donor,,, +sex,The sex of the individual from which the resource was derived from.,"Male, Female, Unknown",,FALSE,,donor,,, age,That age of the individual from which the resource was derived from.,,,FALSE,,donor,,, race,The ethnicity of the individual the resource was derived from.,,,FALSE,,donor,,, cellLine,A cell culture selected for uniformity from a cell population derived from a usually homogeneous tissue source (such as an organ).,,"Component, cellLineId, donorId, organ, tissue, cellLineCategory, originYear, strProfile, populationDoublingTime, resistance, contaminatedMisidentified, cellLineGeneticDisorder, cellLineManifestation",FALSE,,cellLine,"cellLineId, donorId, organ, tissue, cellLineCategory, originYear, strProfile, populationDoublingTime, resistance, contaminatedMisidentified, cellLineGeneticDisorder, cellLineManifestation",donor, From 2e16ee3cc4831c05ff7e7b9b1c70d018e2647aea Mon Sep 17 00:00:00 2001 From: "nf-osi[bot]" Date: Wed, 25 Oct 2023 20:34:33 +0000 Subject: [PATCH 13/97] Add changes --- nf-research-tools.jsonld | 22 +++++++++++++++++++++- 1 file changed, 21 insertions(+), 1 deletion(-) diff --git a/nf-research-tools.jsonld b/nf-research-tools.jsonld index f5eabb28..220131d9 100644 --- a/nf-research-tools.jsonld +++ b/nf-research-tools.jsonld @@ -338,6 +338,9 @@ "@id": "http://schema.biothings.io" }, "schema:rangeIncludes": [ + { + "@id": "bts:Datasharingrequired" + }, { "@id": "bts:Non-commercialuseonly" }, @@ -747,6 +750,23 @@ ], "sms:validationRules": [] }, + { + "@id": "bts:Datasharingrequired", + "@type": "rdfs:Class", + "rdfs:comment": "TBD", + "rdfs:label": "Datasharingrequired", + "rdfs:subClassOf": [ + { + "@id": "bts:usageRequirements" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "data sharing required", + "sms:required": "sms:false", + "sms:validationRules": [] + }, { "@id": "bts:Non-commercialuseonly", "@type": "rdfs:Class", @@ -6871,7 +6891,7 @@ { "@id": "bts:sex", "@type": "rdf:Property", - "rdfs:comment": "The sex of the indiviudal from which the resource was derived from.", + "rdfs:comment": "The sex of the individual from which the resource was derived from.", "rdfs:label": "sex", "schema:domainIncludes": [ { From bfa7ef6534da1896f6c99b288f83fbb6559a257f Mon Sep 17 00:00:00 2001 From: Robert Allaway Date: Wed, 25 Oct 2023 15:45:15 -0500 Subject: [PATCH 14/97] add new selectable markers --- nf_research_tools.rdb.model.csv | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/nf_research_tools.rdb.model.csv b/nf_research_tools.rdb.model.csv index 57d369d7..31fe8fa9 100644 --- a/nf_research_tools.rdb.model.csv +++ b/nf_research_tools.rdb.model.csv @@ -33,7 +33,7 @@ vectorType,"Primary function of the plasmid. (e.g. mammalian expression, bacteri backboneSize,Size in bp of the backbone without the insert,,,FALSE,,geneticReagent,,, totalSize,Size of vector with insert. Derived from insertSize and backboneSize.,,,FALSE,,geneticReagent,,, bacterialResistance,"Antibiotic(s) that should be used for selection in bacteria. (e.g. ampicillin, kanamycin, etc.)","Ampicillin, Kanamycin, Chloramphenicol, Tetracycline, Spectinomycin, Hygromycin, Bleocin(Zeocin), Gentamycin, Streptomycin, Nourseothricin(clonNat), Ampicillin and Bleocin (Zeocin), Ampicillin and Kanamycin, Ampicillin and Tetracycline, Ampicillin and Streptomycin, Ampicillin and Spectinomycin, Chloramphenicol and Ampicillin, Chloramphenicol and Bleocin (Zeocin), Chloramphenicol and Tetracycline, Chloramphenicol and Kanamycin, Chloramphenicol and Spectinomycin, Chloramphenicol and Gentamycin, Spectinomycin and Streptomycin, Other",,FALSE,,geneticReagent,,, -selectableMarker,"Are there any additional selection markers on this plasmid, for example, any mammalian selection markers or fluorescent proteins?","Neomycin, Puromycin, Hygromycin, Zeocin, Blasticidin, Gentamicin, TRP1, LEU1, URA3, HIS3, Basta, Other",,FALSE,,geneticReagent,,, +selectableMarker,"Are there any additional selection markers on this plasmid, for example, any mammalian selection markers or fluorescent proteins?","Neomycin, Puromycin, Hygromycin, Kanamycin, Chloramphenicol, Zeocin, Blasticidin, Gentamicin, TRP1, LEU1, LEU2, URA3, HIS3, Basta, Other",,FALSE,,geneticReagent,,, copyNumber,"If a plasmid produces a sufficient amount of DNA from a normal miniprep or if plasmid requires special growth conditions or it is difficult to grow. (e.g. high copy, low copy, unknown).","High Copy, Low Copy, Unknown",,FALSE,,geneticReagent,,, growthTemp,At what temperature should the bacteria hosting the plasmid be grown,"37 C, 30 C, Room Temperature",,FALSE,,geneticReagent,,, growthStrain,"The E.Coli strain that should be used to distribute the plasmid. (e.g. DH5alpha, NEB Stable, etc.)","DH5alpha, DH10B, NEB Stable, ccdb Survival, Pir1, Other",,FALSE,,geneticReagent,,, From 59f9219fa465ee94ffb718e4bc3bbce5181c8ea8 Mon Sep 17 00:00:00 2001 From: Robert Allaway Date: Wed, 25 Oct 2023 15:46:48 -0500 Subject: [PATCH 15/97] update vectorType --- nf_research_tools.rdb.model.csv | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/nf_research_tools.rdb.model.csv b/nf_research_tools.rdb.model.csv index 31fe8fa9..beaf33c9 100644 --- a/nf_research_tools.rdb.model.csv +++ b/nf_research_tools.rdb.model.csv @@ -29,7 +29,7 @@ promoter,Promoter driving the expression of the insert in the plasmid,,,FALSE,,g 5primer,Primer to sequence the 5' end (N-terminal) of the insert,,,FALSE,,geneticReagent,,, 3primer,Primer to sequence the 3' end (C-terminal) of the insert.,,,FALSE,,geneticReagent,,, vectorBackbone,Name of the backbone the plasmid is built on. (e.g pGBT9),,,FALSE,,geneticReagent,,, -vectorType,"Primary function of the plasmid. (e.g. mammalian expression, bacterial expression, etc.)","Mammalian Expression, Bacterial Expression, Gateway Entry Clone, Lentiviral, Adenoviral, AAV, RNAi, Luciferase, Cre/Lox, Yeast Expression, Worm Expression, Insect Expression, Plant Expression, Mouse Targeting, CRISPR, TALEN, Synthetic Biology, Transfer Vector, Unspecified, Other",,FALSE,,geneticReagent,,,list like +vectorType,"Primary function of the plasmid. (e.g. mammalian expression, bacterial expression, etc.)","Mammalian Expression, Bacterial Expression, Gateway Entry Clone, Lentiviral, Adenoviral, AAV, RNAi, Luciferase, Cre/Lox, Yeast Expression, Worm Expression, Insect Expression, Plant Expression, Mouse Targeting, CRISPR, TALEN, Synthetic Biology, Transfer Vector, Transposon Vector, Unspecified, Other",,FALSE,,geneticReagent,,,list like backboneSize,Size in bp of the backbone without the insert,,,FALSE,,geneticReagent,,, totalSize,Size of vector with insert. Derived from insertSize and backboneSize.,,,FALSE,,geneticReagent,,, bacterialResistance,"Antibiotic(s) that should be used for selection in bacteria. (e.g. ampicillin, kanamycin, etc.)","Ampicillin, Kanamycin, Chloramphenicol, Tetracycline, Spectinomycin, Hygromycin, Bleocin(Zeocin), Gentamycin, Streptomycin, Nourseothricin(clonNat), Ampicillin and Bleocin (Zeocin), Ampicillin and Kanamycin, Ampicillin and Tetracycline, Ampicillin and Streptomycin, Ampicillin and Spectinomycin, Chloramphenicol and Ampicillin, Chloramphenicol and Bleocin (Zeocin), Chloramphenicol and Tetracycline, Chloramphenicol and Kanamycin, Chloramphenicol and Spectinomycin, Chloramphenicol and Gentamycin, Spectinomycin and Streptomycin, Other",,FALSE,,geneticReagent,,, From 03a78509044b09815aad7099f41d23484d22d8cb Mon Sep 17 00:00:00 2001 From: "nf-osi[bot]" Date: Wed, 25 Oct 2023 20:48:43 +0000 Subject: [PATCH 16/97] Add changes --- nf-research-tools.jsonld | 56 ++++++++++++++++++++++++++++++++++++++-- 1 file changed, 54 insertions(+), 2 deletions(-) diff --git a/nf-research-tools.jsonld b/nf-research-tools.jsonld index 220131d9..f90bea0b 100644 --- a/nf-research-tools.jsonld +++ b/nf-research-tools.jsonld @@ -1357,6 +1357,9 @@ { "@id": "bts:TransferVector" }, + { + "@id": "bts:TransposonVector" + }, { "@id": "bts:Unspecified" }, @@ -1515,6 +1518,12 @@ { "@id": "bts:Hygromycin" }, + { + "@id": "bts:Kanamycin" + }, + { + "@id": "bts:Chloramphenicol" + }, { "@id": "bts:Zeocin" }, @@ -1530,6 +1539,9 @@ { "@id": "bts:LEU1" }, + { + "@id": "bts:LEU2" + }, { "@id": "bts:URA3" }, @@ -2165,6 +2177,23 @@ "sms:required": "sms:false", "sms:validationRules": [] }, + { + "@id": "bts:TransposonVector", + "@type": "rdfs:Class", + "rdfs:comment": "TBD", + "rdfs:label": "TransposonVector", + "rdfs:subClassOf": [ + { + "@id": "bts:vectorType" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Transposon Vector", + "sms:required": "sms:false", + "sms:validationRules": [] + }, { "@id": "bts:Unspecified", "@type": "rdfs:Class", @@ -2195,10 +2224,10 @@ "@id": "bts:growthStrain" }, { - "@id": "bts:selectableMarker" + "@id": "bts:mutationType" }, { - "@id": "bts:mutationType" + "@id": "bts:selectableMarker" }, { "@id": "bts:reactiveSpecies" @@ -2245,6 +2274,9 @@ "rdfs:subClassOf": [ { "@id": "bts:bacterialResistance" + }, + { + "@id": "bts:selectableMarker" } ], "schema:isPartOf": { @@ -2262,6 +2294,9 @@ "rdfs:subClassOf": [ { "@id": "bts:bacterialResistance" + }, + { + "@id": "bts:selectableMarker" } ], "schema:isPartOf": { @@ -2716,6 +2751,23 @@ "sms:required": "sms:false", "sms:validationRules": [] }, + { + "@id": "bts:LEU2", + "@type": "rdfs:Class", + "rdfs:comment": "TBD", + "rdfs:label": "LEU2", + "rdfs:subClassOf": [ + { + "@id": "bts:selectableMarker" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "LEU2", + "sms:required": "sms:false", + "sms:validationRules": [] + }, { "@id": "bts:URA3", "@type": "rdfs:Class", From aed7fa3453efc76cfd75ee1b537c7835a989b214 Mon Sep 17 00:00:00 2001 From: Robert Allaway Date: Wed, 25 Oct 2023 16:27:05 -0500 Subject: [PATCH 17/97] replace list of organs with NCIT values --- nf_research_tools.rdb.model.csv | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/nf_research_tools.rdb.model.csv b/nf_research_tools.rdb.model.csv index beaf33c9..4dab9e14 100644 --- a/nf_research_tools.rdb.model.csv +++ b/nf_research_tools.rdb.model.csv @@ -91,7 +91,7 @@ age,That age of the individual from which the resource was derived from.,,,FALSE race,The ethnicity of the individual the resource was derived from.,,,FALSE,,donor,,, cellLine,A cell culture selected for uniformity from a cell population derived from a usually homogeneous tissue source (such as an organ).,,"Component, cellLineId, donorId, organ, tissue, cellLineCategory, originYear, strProfile, populationDoublingTime, resistance, contaminatedMisidentified, cellLineGeneticDisorder, cellLineManifestation",FALSE,,cellLine,"cellLineId, donorId, organ, tissue, cellLineCategory, originYear, strProfile, populationDoublingTime, resistance, contaminatedMisidentified, cellLineGeneticDisorder, cellLineManifestation",donor, cellLineId,A unique identifier for the cell line.,,,TRUE,,cellLine,,, -organ,The organ the cell line is derived from.,"Blood, Bone marrow, Brain, Breast, Bursa of fabricius, Colon, Kidney, Lung, Lymph node, Mammary gland, Nerves, Nose, Ovary, Pancreas, Prostate, Skin, Spleen",,FALSE,,cellLine,,, +organ,The organ the cell line is derived from.,"Biliary Tract, Bladder, Bone Marrow, Brain, Breast, Bronchial Tree, Duct, Epididymis, Esophagus, Fallopian Tube, Gallbladder, Gland, Gonad, Heart, Intestine, Kidney, Liver, Lung, Lymph Node, Ear, Eye, Nose, Tongue, Pancreas, Penis, Seminal Vesicle, Skin, Spermatic Cord, Spinal Cord, Spleen, Stomach, Thymus Gland, Tonsil, Trachea, Tracheobronchial Tree, Ureter, Urethra, Uterus, Vagina, Vulva",,FALSE,,cellLine,,, tissue,The tissue the cell line is derived from.,"Blood, Bone marrow, Buccal mucosa, Buffy coat, Cerebral cortex, Dorsal root ganglion, Embryonic tissue, Meninges, Nerve tissue, Optic nerve, Plasma, Primary tumor, Sciatic nerve, Serum, Splenocyte, Unspecified, Whole brain",,FALSE,,cellLine,,, cellLineCategory,The category to which the cell line belongs.,"Cancer cell line, Conditionally immortalized cell line, Embryonic stem cell, Factor-dependent cell line, Finite cell line, Hybridoma, Induced pluripotent stem cell, Somatic stem cell, Spontaneously immortalized cell line, Stromal cell line, Telomerase immortalized cell line, Transformed cell line, Undefined cell line type",,FALSE,,cellLine,,, originYear,The year the cell line orginated.,,,FALSE,,cellLine,,, From e2c3ff619b8f78f24e59579031a212c1fe8ed02f Mon Sep 17 00:00:00 2001 From: "nf-osi[bot]" Date: Wed, 25 Oct 2023 21:29:01 +0000 Subject: [PATCH 18/97] Add changes --- nf-research-tools.jsonld | 564 ++++++++++++++++++++++++++++++++++++--- 1 file changed, 526 insertions(+), 38 deletions(-) diff --git a/nf-research-tools.jsonld b/nf-research-tools.jsonld index f90bea0b..38d84fcd 100644 --- a/nf-research-tools.jsonld +++ b/nf-research-tools.jsonld @@ -3524,9 +3524,6 @@ { "@id": "bts:specimenTissueType" }, - { - "@id": "bts:organ" - }, { "@id": "bts:tissue" } @@ -7204,10 +7201,13 @@ }, "schema:rangeIncludes": [ { - "@id": "bts:Blood" + "@id": "bts:BiliaryTract" }, { - "@id": "bts:Bonemarrow" + "@id": "bts:Bladder" + }, + { + "@id": "bts:BoneMarrow" }, { "@id": "bts:Brain" @@ -7216,43 +7216,109 @@ "@id": "bts:Breast" }, { - "@id": "bts:Bursaoffabricius" + "@id": "bts:BronchialTree" + }, + { + "@id": "bts:Duct" + }, + { + "@id": "bts:Epididymis" + }, + { + "@id": "bts:Esophagus" }, { - "@id": "bts:Colon" + "@id": "bts:FallopianTube" + }, + { + "@id": "bts:Gallbladder" + }, + { + "@id": "bts:Gland" + }, + { + "@id": "bts:Gonad" + }, + { + "@id": "bts:Heart" + }, + { + "@id": "bts:Intestine" }, { "@id": "bts:Kidney" }, + { + "@id": "bts:Liver" + }, { "@id": "bts:Lung" }, { - "@id": "bts:Lymphnode" + "@id": "bts:LymphNode" }, { - "@id": "bts:Mammarygland" + "@id": "bts:Ear" }, { - "@id": "bts:Nerves" + "@id": "bts:Eye" }, { "@id": "bts:Nose" }, { - "@id": "bts:Ovary" + "@id": "bts:Tongue" }, { "@id": "bts:Pancreas" }, { - "@id": "bts:Prostate" + "@id": "bts:Penis" + }, + { + "@id": "bts:SeminalVesicle" }, { "@id": "bts:Skin" }, + { + "@id": "bts:SpermaticCord" + }, + { + "@id": "bts:SpinalCord" + }, { "@id": "bts:Spleen" + }, + { + "@id": "bts:Stomach" + }, + { + "@id": "bts:ThymusGland" + }, + { + "@id": "bts:Tonsil" + }, + { + "@id": "bts:Trachea" + }, + { + "@id": "bts:TracheobronchialTree" + }, + { + "@id": "bts:Ureter" + }, + { + "@id": "bts:Urethra" + }, + { + "@id": "bts:Uterus" + }, + { + "@id": "bts:Vagina" + }, + { + "@id": "bts:Vulva" } ], "sms:displayName": "organ", @@ -7527,22 +7593,53 @@ ] }, { - "@id": "bts:Bonemarrow", + "@id": "bts:BiliaryTract", "@type": "rdfs:Class", "rdfs:comment": "TBD", - "rdfs:label": "Bonemarrow", + "rdfs:label": "BiliaryTract", "rdfs:subClassOf": [ { "@id": "bts:organ" - }, + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Biliary Tract", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:Bladder", + "@type": "rdfs:Class", + "rdfs:comment": "TBD", + "rdfs:label": "Bladder", + "rdfs:subClassOf": [ { - "@id": "bts:tissue" + "@id": "bts:organ" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Bone marrow", + "sms:displayName": "Bladder", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:BoneMarrow", + "@type": "rdfs:Class", + "rdfs:comment": "TBD", + "rdfs:label": "BoneMarrow", + "rdfs:subClassOf": [ + { + "@id": "bts:organ" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Bone Marrow", "sms:required": "sms:false", "sms:validationRules": [] }, @@ -7564,10 +7661,95 @@ "sms:validationRules": [] }, { - "@id": "bts:Bursaoffabricius", + "@id": "bts:BronchialTree", + "@type": "rdfs:Class", + "rdfs:comment": "TBD", + "rdfs:label": "BronchialTree", + "rdfs:subClassOf": [ + { + "@id": "bts:organ" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Bronchial Tree", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:Duct", + "@type": "rdfs:Class", + "rdfs:comment": "TBD", + "rdfs:label": "Duct", + "rdfs:subClassOf": [ + { + "@id": "bts:organ" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Duct", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:Epididymis", + "@type": "rdfs:Class", + "rdfs:comment": "TBD", + "rdfs:label": "Epididymis", + "rdfs:subClassOf": [ + { + "@id": "bts:organ" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Epididymis", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:Esophagus", + "@type": "rdfs:Class", + "rdfs:comment": "TBD", + "rdfs:label": "Esophagus", + "rdfs:subClassOf": [ + { + "@id": "bts:organ" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Esophagus", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:FallopianTube", + "@type": "rdfs:Class", + "rdfs:comment": "TBD", + "rdfs:label": "FallopianTube", + "rdfs:subClassOf": [ + { + "@id": "bts:organ" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Fallopian Tube", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:Gallbladder", "@type": "rdfs:Class", "rdfs:comment": "TBD", - "rdfs:label": "Bursaoffabricius", + "rdfs:label": "Gallbladder", "rdfs:subClassOf": [ { "@id": "bts:organ" @@ -7576,15 +7758,15 @@ "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Bursa of fabricius", + "sms:displayName": "Gallbladder", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:Colon", + "@id": "bts:Gland", "@type": "rdfs:Class", "rdfs:comment": "TBD", - "rdfs:label": "Colon", + "rdfs:label": "Gland", "rdfs:subClassOf": [ { "@id": "bts:organ" @@ -7593,7 +7775,58 @@ "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Colon", + "sms:displayName": "Gland", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:Gonad", + "@type": "rdfs:Class", + "rdfs:comment": "TBD", + "rdfs:label": "Gonad", + "rdfs:subClassOf": [ + { + "@id": "bts:organ" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Gonad", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:Heart", + "@type": "rdfs:Class", + "rdfs:comment": "TBD", + "rdfs:label": "Heart", + "rdfs:subClassOf": [ + { + "@id": "bts:organ" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Heart", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:Intestine", + "@type": "rdfs:Class", + "rdfs:comment": "TBD", + "rdfs:label": "Intestine", + "rdfs:subClassOf": [ + { + "@id": "bts:organ" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Intestine", "sms:required": "sms:false", "sms:validationRules": [] }, @@ -7614,6 +7847,23 @@ "sms:required": "sms:false", "sms:validationRules": [] }, + { + "@id": "bts:Liver", + "@type": "rdfs:Class", + "rdfs:comment": "TBD", + "rdfs:label": "Liver", + "rdfs:subClassOf": [ + { + "@id": "bts:organ" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Liver", + "sms:required": "sms:false", + "sms:validationRules": [] + }, { "@id": "bts:Lung", "@type": "rdfs:Class", @@ -7632,10 +7882,10 @@ "sms:validationRules": [] }, { - "@id": "bts:Lymphnode", + "@id": "bts:LymphNode", "@type": "rdfs:Class", "rdfs:comment": "TBD", - "rdfs:label": "Lymphnode", + "rdfs:label": "LymphNode", "rdfs:subClassOf": [ { "@id": "bts:organ" @@ -7644,15 +7894,15 @@ "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Lymph node", + "sms:displayName": "Lymph Node", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:Mammarygland", + "@id": "bts:Ear", "@type": "rdfs:Class", "rdfs:comment": "TBD", - "rdfs:label": "Mammarygland", + "rdfs:label": "Ear", "rdfs:subClassOf": [ { "@id": "bts:organ" @@ -7661,15 +7911,15 @@ "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Mammary gland", + "sms:displayName": "Ear", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:Nerves", + "@id": "bts:Eye", "@type": "rdfs:Class", "rdfs:comment": "TBD", - "rdfs:label": "Nerves", + "rdfs:label": "Eye", "rdfs:subClassOf": [ { "@id": "bts:organ" @@ -7678,7 +7928,7 @@ "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Nerves", + "sms:displayName": "Eye", "sms:required": "sms:false", "sms:validationRules": [] }, @@ -7700,10 +7950,10 @@ "sms:validationRules": [] }, { - "@id": "bts:Ovary", + "@id": "bts:Tongue", "@type": "rdfs:Class", "rdfs:comment": "TBD", - "rdfs:label": "Ovary", + "rdfs:label": "Tongue", "rdfs:subClassOf": [ { "@id": "bts:organ" @@ -7712,7 +7962,7 @@ "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Ovary", + "sms:displayName": "Tongue", "sms:required": "sms:false", "sms:validationRules": [] }, @@ -7734,10 +7984,27 @@ "sms:validationRules": [] }, { - "@id": "bts:Prostate", + "@id": "bts:Penis", + "@type": "rdfs:Class", + "rdfs:comment": "TBD", + "rdfs:label": "Penis", + "rdfs:subClassOf": [ + { + "@id": "bts:organ" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Penis", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:SeminalVesicle", "@type": "rdfs:Class", "rdfs:comment": "TBD", - "rdfs:label": "Prostate", + "rdfs:label": "SeminalVesicle", "rdfs:subClassOf": [ { "@id": "bts:organ" @@ -7746,7 +8013,41 @@ "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Prostate", + "sms:displayName": "Seminal Vesicle", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:SpermaticCord", + "@type": "rdfs:Class", + "rdfs:comment": "TBD", + "rdfs:label": "SpermaticCord", + "rdfs:subClassOf": [ + { + "@id": "bts:organ" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Spermatic Cord", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:SpinalCord", + "@type": "rdfs:Class", + "rdfs:comment": "TBD", + "rdfs:label": "SpinalCord", + "rdfs:subClassOf": [ + { + "@id": "bts:organ" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Spinal Cord", "sms:required": "sms:false", "sms:validationRules": [] }, @@ -7767,6 +8068,193 @@ "sms:required": "sms:false", "sms:validationRules": [] }, + { + "@id": "bts:Stomach", + "@type": "rdfs:Class", + "rdfs:comment": "TBD", + "rdfs:label": "Stomach", + "rdfs:subClassOf": [ + { + "@id": "bts:organ" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Stomach", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:ThymusGland", + "@type": "rdfs:Class", + "rdfs:comment": "TBD", + "rdfs:label": "ThymusGland", + "rdfs:subClassOf": [ + { + "@id": "bts:organ" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Thymus Gland", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:Tonsil", + "@type": "rdfs:Class", + "rdfs:comment": "TBD", + "rdfs:label": "Tonsil", + "rdfs:subClassOf": [ + { + "@id": "bts:organ" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Tonsil", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:Trachea", + "@type": "rdfs:Class", + "rdfs:comment": "TBD", + "rdfs:label": "Trachea", + "rdfs:subClassOf": [ + { + "@id": "bts:organ" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Trachea", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:TracheobronchialTree", + "@type": "rdfs:Class", + "rdfs:comment": "TBD", + "rdfs:label": "TracheobronchialTree", + "rdfs:subClassOf": [ + { + "@id": "bts:organ" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Tracheobronchial Tree", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:Ureter", + "@type": "rdfs:Class", + "rdfs:comment": "TBD", + "rdfs:label": "Ureter", + "rdfs:subClassOf": [ + { + "@id": "bts:organ" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Ureter", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:Urethra", + "@type": "rdfs:Class", + "rdfs:comment": "TBD", + "rdfs:label": "Urethra", + "rdfs:subClassOf": [ + { + "@id": "bts:organ" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Urethra", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:Uterus", + "@type": "rdfs:Class", + "rdfs:comment": "TBD", + "rdfs:label": "Uterus", + "rdfs:subClassOf": [ + { + "@id": "bts:organ" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Uterus", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:Vagina", + "@type": "rdfs:Class", + "rdfs:comment": "TBD", + "rdfs:label": "Vagina", + "rdfs:subClassOf": [ + { + "@id": "bts:organ" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Vagina", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:Vulva", + "@type": "rdfs:Class", + "rdfs:comment": "TBD", + "rdfs:label": "Vulva", + "rdfs:subClassOf": [ + { + "@id": "bts:organ" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Vulva", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:Bonemarrow", + "@type": "rdfs:Class", + "rdfs:comment": "TBD", + "rdfs:label": "Bonemarrow", + "rdfs:subClassOf": [ + { + "@id": "bts:tissue" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Bone marrow", + "sms:required": "sms:false", + "sms:validationRules": [] + }, { "@id": "bts:Buccalmucosa", "@type": "rdfs:Class", From 4d5fac8f9b42a56c5ca7d21dce3e9281fb9b2ec1 Mon Sep 17 00:00:00 2001 From: Robert Allaway Date: Thu, 26 Oct 2023 09:57:25 -0500 Subject: [PATCH 19/97] rename tool details tables this is to avoid collision of resourceType valid values and tool-type-components --- nf_research_tools.rdb.model.csv | 142 ++++++++++++++++---------------- 1 file changed, 71 insertions(+), 71 deletions(-) diff --git a/nf_research_tools.rdb.model.csv b/nf_research_tools.rdb.model.csv index 4dab9e14..32f86294 100644 --- a/nf_research_tools.rdb.model.csv +++ b/nf_research_tools.rdb.model.csv @@ -5,39 +5,39 @@ resourceId,A unique identifier for the resource.,,,TRUE,,resource,,, rrid,"The RRID, a standard resource identifier that will facilitate interoperability with other databases, and is an increasingly-used identifier for publications https://scicrunch.org/resources if available",,,FALSE,,resource,,, resourceName,The “canonical” name of the resource,,,TRUE,,resource,,, synonyms,Synonyms of the resource,,,FALSE,,resource,,,list like -resourceType,"Type of resource. (e.g. animal model, antibody, plasmid, etc.)","Animal Model, Cell Line, Antibody, Genetic Reagent, Biobank",,TRUE,,resource,,, +resourceType,"Type of resource. (e.g. animal model, antibodyDetails, plasmid, etc.)","Animal Model, Cell Line, Antibody, Genetic Reagent, Biobank",,TRUE,,resource,,, description,Free text description/summary/overview/purpose of the resource.,,,FALSE,,resource,,, usageRequirements,Any known restrictions on use of the resource. ,"data sharing required, non-commercial use only, re-distribution not permitted, generation of germ line transmitting chimeras not permitted, creation of functional gametes not permitted, generation of interspecies chimeras not permitted, human cloning not permitted, cannot be used for treatment purposes, IRB documentation required, special licencing restrictions (see vendor for more information), unknown",,FALSE,,resource,,,list like howToAcquire,How to acquire a particular resource. ,,,TRUE,,resource,,, dateAdded,The date that the resource was originally added.,,,TRUE,,resource,,, dateModified,The last update of the resource metadata (not including observations).,,,TRUE,,resource,,, -geneticReagent,Genetic reagents.,,"Component, geneticReagentId, insertName, insertEntrezId, gRNAshRNASequence, insertSize, insertSpecies, nTerminalTag, cTerminalTag, cloningMethod, 5primeCloningSite, 5primeSiteDestroyed, 3primeCloningSite, 3primeSiteDestroyed, promoter, 5primer, 3primer, vectorBackbone, vectorType, backboneSize, totalSize, bacterialResistance, selectableMarker, copyNumber, growthTemp, growthStrain, hazardous",FALSE,,geneticReagent,"geneticReagentId, insertName, insertEntrezId, gRNAshRNASequence, insertSize, insertSpecies, nTerminalTag, cTerminalTag, cloningMethod, 5primeCloningSite, 5primeSiteDestroyed, 3primeCloningSite, 3primeSiteDestroyed, promoter, 5primer, 3primer, vectorBackbone, vectorType, backboneSize, totalSize, bacterialResistance, selectableMarker, copyNumber, growthTemp, growthStrain, hazardous",, -geneticReagentId,A unique identifier for the reagent.,,,TRUE,,geneticReagent,,, -insertName,Name of the main gene insert in the plasmid.,,,TRUE,,geneticReagent,,, -insertEntrezId,The entrez gene id for the gene insert,,,TRUE,,geneticReagent,,, -gRNAshRNASequence,"The sequence of the gRNA or shRNA for the gene insert, if present. ",,,FALSE,,geneticReagent,,, -insertSize,"Size, in bp, of the gene insert as it is in the plasmid.",,,FALSE,,geneticReagent,,, -insertSpecies,Species of the insert,"Homo sapiens, Mus musculus, Rattus norvegicus",,TRUE,,geneticReagent,,,list like -nTerminalTag,Any tags on the N terminal 5' end of the gene insert in the plasmid. Only tags that are in frame,,,FALSE,,geneticReagent,,,list like -cTerminalTag,Any tags on the C terminal 3' end of the gene insert in the plasmid. Only tags that are in frame,,,FALSE,,geneticReagent,,,list like -cloningMethod,"How the vector was constructed. (e.g. restriction enzyme, TOPO cloning, etc.)","Restriction Enzyme, TOPO cloning, Gateway Cloning, Ligation Independent Cloning, Gibson Cloning, Unknown",,FALSE,,geneticReagent,,, -5primeCloningSite,"If Restriction Enzyme was selected as the cloning method, specifies what enzyme was used on the 5' (N-terminal) end of the insert",,cloningMethod,FALSE,,geneticReagent,,, -5primeSiteDestroyed,"If 5' site was destroyed during cloning. (e.g. yes, no, unknown).","Yes, No, Unknown",,FALSE,,geneticReagent,,, -3primeCloningSite,"If Restriction Enzyme was selected as the cloning method, specifies what enzyme was used on the 3' (C-terminal) end of the insert",,cloningMethod,FALSE,,geneticReagent,,, -3primeSiteDestroyed,"If 3' site was destroyed during cloning. (e.g. yes, no, unknown)","Yes, No, Unknown",,FALSE,,geneticReagent,,, -promoter,Promoter driving the expression of the insert in the plasmid,,,FALSE,,geneticReagent,,, -5primer,Primer to sequence the 5' end (N-terminal) of the insert,,,FALSE,,geneticReagent,,, -3primer,Primer to sequence the 3' end (C-terminal) of the insert.,,,FALSE,,geneticReagent,,, -vectorBackbone,Name of the backbone the plasmid is built on. (e.g pGBT9),,,FALSE,,geneticReagent,,, -vectorType,"Primary function of the plasmid. (e.g. mammalian expression, bacterial expression, etc.)","Mammalian Expression, Bacterial Expression, Gateway Entry Clone, Lentiviral, Adenoviral, AAV, RNAi, Luciferase, Cre/Lox, Yeast Expression, Worm Expression, Insect Expression, Plant Expression, Mouse Targeting, CRISPR, TALEN, Synthetic Biology, Transfer Vector, Transposon Vector, Unspecified, Other",,FALSE,,geneticReagent,,,list like -backboneSize,Size in bp of the backbone without the insert,,,FALSE,,geneticReagent,,, -totalSize,Size of vector with insert. Derived from insertSize and backboneSize.,,,FALSE,,geneticReagent,,, -bacterialResistance,"Antibiotic(s) that should be used for selection in bacteria. (e.g. ampicillin, kanamycin, etc.)","Ampicillin, Kanamycin, Chloramphenicol, Tetracycline, Spectinomycin, Hygromycin, Bleocin(Zeocin), Gentamycin, Streptomycin, Nourseothricin(clonNat), Ampicillin and Bleocin (Zeocin), Ampicillin and Kanamycin, Ampicillin and Tetracycline, Ampicillin and Streptomycin, Ampicillin and Spectinomycin, Chloramphenicol and Ampicillin, Chloramphenicol and Bleocin (Zeocin), Chloramphenicol and Tetracycline, Chloramphenicol and Kanamycin, Chloramphenicol and Spectinomycin, Chloramphenicol and Gentamycin, Spectinomycin and Streptomycin, Other",,FALSE,,geneticReagent,,, -selectableMarker,"Are there any additional selection markers on this plasmid, for example, any mammalian selection markers or fluorescent proteins?","Neomycin, Puromycin, Hygromycin, Kanamycin, Chloramphenicol, Zeocin, Blasticidin, Gentamicin, TRP1, LEU1, LEU2, URA3, HIS3, Basta, Other",,FALSE,,geneticReagent,,, -copyNumber,"If a plasmid produces a sufficient amount of DNA from a normal miniprep or if plasmid requires special growth conditions or it is difficult to grow. (e.g. high copy, low copy, unknown).","High Copy, Low Copy, Unknown",,FALSE,,geneticReagent,,, -growthTemp,At what temperature should the bacteria hosting the plasmid be grown,"37 C, 30 C, Room Temperature",,FALSE,,geneticReagent,,, -growthStrain,"The E.Coli strain that should be used to distribute the plasmid. (e.g. DH5alpha, NEB Stable, etc.)","DH5alpha, DH10B, NEB Stable, ccdb Survival, Pir1, Other",,FALSE,,geneticReagent,,, -hazardous,"Does the unmodified plasmid DNA, either in purified form or when introduced into bacterial or mammalian cells require handling at Biosafety Level 2 or higher?","Yes, No, Unknown",,TRUE,,geneticReagent,,, +geneticReagentDetails,Genetic reagents.,,"Component, geneticReagentId, insertName, insertEntrezId, gRNAshRNASequence, insertSize, insertSpecies, nTerminalTag, cTerminalTag, cloningMethod, 5primeCloningSite, 5primeSiteDestroyed, 3primeCloningSite, 3primeSiteDestroyed, promoter, 5primer, 3primer, vectorBackbone, vectorType, backboneSize, totalSize, bacterialResistance, selectableMarker, copyNumber, growthTemp, growthStrain, hazardous",FALSE,,geneticReagentDetails,"geneticReagentId, insertName, insertEntrezId, gRNAshRNASequence, insertSize, insertSpecies, nTerminalTag, cTerminalTag, cloningMethod, 5primeCloningSite, 5primeSiteDestroyed, 3primeCloningSite, 3primeSiteDestroyed, promoter, 5primer, 3primer, vectorBackbone, vectorType, backboneSize, totalSize, bacterialResistance, selectableMarker, copyNumber, growthTemp, growthStrain, hazardous",, +geneticReagentId,A unique identifier for the reagent.,,,TRUE,,geneticReagentDetails,,, +insertName,Name of the main gene insert in the plasmid.,,,TRUE,,geneticReagentDetails,,, +insertEntrezId,The entrez gene id for the gene insert,,,TRUE,,geneticReagentDetails,,, +gRNAshRNASequence,"The sequence of the gRNA or shRNA for the gene insert, if present. ",,,FALSE,,geneticReagentDetails,,, +insertSize,"Size, in bp, of the gene insert as it is in the plasmid.",,,FALSE,,geneticReagentDetails,,, +insertSpecies,Species of the insert,"Homo sapiens, Mus musculus, Rattus norvegicus",,TRUE,,geneticReagentDetails,,,list like +nTerminalTag,Any tags on the N terminal 5' end of the gene insert in the plasmid. Only tags that are in frame,,,FALSE,,geneticReagentDetails,,,list like +cTerminalTag,Any tags on the C terminal 3' end of the gene insert in the plasmid. Only tags that are in frame,,,FALSE,,geneticReagentDetails,,,list like +cloningMethod,"How the vector was constructed. (e.g. restriction enzyme, TOPO cloning, etc.)","Restriction Enzyme, TOPO cloning, Gateway Cloning, Ligation Independent Cloning, Gibson Cloning, Unknown",,FALSE,,geneticReagentDetails,,, +5primeCloningSite,"If Restriction Enzyme was selected as the cloning method, specifies what enzyme was used on the 5' (N-terminal) end of the insert",,cloningMethod,FALSE,,geneticReagentDetails,,, +5primeSiteDestroyed,"If 5' site was destroyed during cloning. (e.g. yes, no, unknown).","Yes, No, Unknown",,FALSE,,geneticReagentDetails,,, +3primeCloningSite,"If Restriction Enzyme was selected as the cloning method, specifies what enzyme was used on the 3' (C-terminal) end of the insert",,cloningMethod,FALSE,,geneticReagentDetails,,, +3primeSiteDestroyed,"If 3' site was destroyed during cloning. (e.g. yes, no, unknown)","Yes, No, Unknown",,FALSE,,geneticReagentDetails,,, +promoter,Promoter driving the expression of the insert in the plasmid,,,FALSE,,geneticReagentDetails,,, +5primer,Primer to sequence the 5' end (N-terminal) of the insert,,,FALSE,,geneticReagentDetails,,, +3primer,Primer to sequence the 3' end (C-terminal) of the insert.,,,FALSE,,geneticReagentDetails,,, +vectorBackbone,Name of the backbone the plasmid is built on. (e.g pGBT9),,,FALSE,,geneticReagentDetails,,, +vectorType,"Primary function of the plasmid. (e.g. mammalian expression, bacterial expression, etc.)","Mammalian Expression, Bacterial Expression, Gateway Entry Clone, Lentiviral, Adenoviral, AAV, RNAi, Luciferase, Cre/Lox, Yeast Expression, Worm Expression, Insect Expression, Plant Expression, Mouse Targeting, CRISPR, TALEN, Synthetic Biology, Transfer Vector, Transposon Vector, Unspecified, Other",,FALSE,,geneticReagentDetails,,,list like +backboneSize,Size in bp of the backbone without the insert,,,FALSE,,geneticReagentDetails,,, +totalSize,Size of vector with insert. Derived from insertSize and backboneSize.,,,FALSE,,geneticReagentDetails,,, +bacterialResistance,"Antibiotic(s) that should be used for selection in bacteria. (e.g. ampicillin, kanamycin, etc.)","Ampicillin, Kanamycin, Chloramphenicol, Tetracycline, Spectinomycin, Hygromycin, Bleocin(Zeocin), Gentamycin, Streptomycin, Nourseothricin(clonNat), Ampicillin and Bleocin (Zeocin), Ampicillin and Kanamycin, Ampicillin and Tetracycline, Ampicillin and Streptomycin, Ampicillin and Spectinomycin, Chloramphenicol and Ampicillin, Chloramphenicol and Bleocin (Zeocin), Chloramphenicol and Tetracycline, Chloramphenicol and Kanamycin, Chloramphenicol and Spectinomycin, Chloramphenicol and Gentamycin, Spectinomycin and Streptomycin, Other",,FALSE,,geneticReagentDetails,,, +selectableMarker,"Are there any additional selection markers on this plasmid, for example, any mammalian selection markers or fluorescent proteins?","Neomycin, Puromycin, Hygromycin, Kanamycin, Chloramphenicol, Zeocin, Blasticidin, Gentamicin, TRP1, LEU1, LEU2, URA3, HIS3, Basta, Other",,FALSE,,geneticReagentDetails,,, +copyNumber,"If a plasmid produces a sufficient amount of DNA from a normal miniprep or if plasmid requires special growth conditions or it is difficult to grow. (e.g. high copy, low copy, unknown).","High Copy, Low Copy, Unknown",,FALSE,,geneticReagentDetails,,, +growthTemp,At what temperature should the bacteria hosting the plasmid be grown,"37 C, 30 C, Room Temperature",,FALSE,,geneticReagentDetails,,, +growthStrain,"The E.Coli strain that should be used to distribute the plasmid. (e.g. DH5alpha, NEB Stable, etc.)","DH5alpha, DH10B, NEB Stable, ccdb Survival, Pir1, Other",,FALSE,,geneticReagentDetails,,, +hazardous,"Does the unmodified plasmid DNA, either in purified form or when introduced into bacterial or mammalian cells require handling at Biosafety Level 2 or higher?","Yes, No, Unknown",,TRUE,,geneticReagentDetails,,, vendorItem,The resource item associated with a vendor.,,"Component, vendorItemId, vendorId, resourceId, catalogNumber, catalogNumberURL",FALSE,,vendorItem,"vendorItemId, vendorId, resourceId, catalogNumber, catalogNumberURL","resource,vendor", vendorItemId,A unique identifier for the resource associated with a vendor. ,,,TRUE,,vendorItem,,, catalogNumber,The catalog number associated with the resource pertaining to the vendor that sells the resource.,,,TRUE,,vendorItem,,, @@ -46,16 +46,16 @@ vendor,A person or compnay offering the resource for sale.,,"Component, vendorId vendorId,A unique identifier for the vendor.,,,TRUE,,vendor,,, vendorName,The name of the vendor.,,,FALSE,,vendor,,, vendorURL,The vendor website url associated with the resource.,,,FALSE,,vendor,,, -biobank,"A large collection of biological or medical data and tissue samples, amassed for research purposes.",,"Component, biobankId, resourceId, biobankName, biobankURL, specimenType, specimenTissueType, tumorType, diseaseType, specimenPreparationMethod, specimenFormat",FALSE,,biobank,"biobankId, resourceId, biobankName, biobankURL, specimenType, specimenTissueType, tumorType, diseaseType, specimenPreparationMethod, specimenFormat",, -biobankName,The name of the biobank. ,,,TRUE,,biobank,,, -biobankId,A unique identifier for the biobank.,,,TRUE,,biobank,,, -biobankURL,A URL for the biobank landing page.,,,TRUE,,biobank,,, -specimenType,The types of specimens that are banked.,"human tissue, xenograft tumors, cell lines",,TRUE,,biobank,,,list like -specimenTissueType,The types of tissues that are banked.,"blood, tumor, cerebrospinal fluid, nerve, skin, bone, brain",,TRUE,,biobank,,,list like -tumorType,"The types of tumors that are banked, if applicable.","cutaneous neurofibroma, plexiform neurofibroma, schwannoma, meningioma, malignant peripheral nerve sheath tumor, low grade glioma, high grade glioma, pheochromocytoma, optic nerve glioma, atypical neurofibroma, neurofibroma NOS, diffuse infiltrating neurofibroma, brain NOS",,TRUE,,biobank,,,list like -diseaseType,"The diseases of the banked specimens, if applicable.","Neurofibromatosis type 1, Neurofibromatosis type 2, Schwannomatosis",,TRUE,,biobank,,,list like -specimenPreparationMethod,The preservation methods used by the biobank.,"Fresh collected, Flash frozen, FFPE, Cryopreserved, OCT, RNA later, Formalin-fixed, Ethanol",,TRUE,,biobank,,,list like -specimenFormat,How the specimens have been processed in preparation for distribution.,"whole tumor, slide, whole cell lysate, DNA, RNA",,TRUE,,biobank,,,list like +biobankDetails,"A large collection of biological or medical data and tissue samples, amassed for research purposes.",,"Component, biobankId, resourceId, biobankName, biobankURL, specimenType, specimenTissueType, tumorType, diseaseType, specimenPreparationMethod, specimenFormat",FALSE,,biobankDetails,"biobankId, resourceId, biobankName, biobankURL, specimenType, specimenTissueType, tumorType, diseaseType, specimenPreparationMethod, specimenFormat",, +biobankName,The name of the biobankDetails. ,,,TRUE,,biobankDetails,,, +biobankId,A unique identifier for the biobankDetails.,,,TRUE,,biobankDetails,,, +biobankURL,A URL for the biobankDetails landing page.,,,TRUE,,biobankDetails,,, +specimenType,The types of specimens that are banked.,"human tissue, xenograft tumors, cell lines",,TRUE,,biobankDetails,,,list like +specimenTissueType,The types of tissues that are banked.,"blood, tumor, cerebrospinal fluid, nerve, skin, bone, brain",,TRUE,,biobankDetails,,,list like +tumorType,"The types of tumors that are banked, if applicable.","cutaneous neurofibroma, plexiform neurofibroma, schwannoma, meningioma, malignant peripheral nerve sheath tumor, low grade glioma, high grade glioma, pheochromocytoma, optic nerve glioma, atypical neurofibroma, neurofibroma NOS, diffuse infiltrating neurofibroma, brain NOS",,TRUE,,biobankDetails,,,list like +diseaseType,"The diseases of the banked specimens, if applicable.","Neurofibromatosis type 1, Neurofibromatosis type 2, Schwannomatosis",,TRUE,,biobankDetails,,,list like +specimenPreparationMethod,The preservation methods used by the biobankDetails.,"Fresh collected, Flash frozen, FFPE, Cryopreserved, OCT, RNA later, Formalin-fixed, Ethanol",,TRUE,,biobankDetails,,,list like +specimenFormat,How the specimens have been processed in preparation for distribution.,"whole tumor, slide, whole cell lysate, DNA, RNA",,TRUE,,biobankDetails,,,list like observation,"A remark, statement, or comment based on the resource.",,"Component, observationId, resourceId, publicationId, observationSubmitterName, synapseId, observationText, observationType, observationPhase, observationTime, observationTimeUnits, reliabilityRating, easeOfUseRating, observationLink",FALSE,,observation,"observationId, resourceId, publicationId, observationSubmitterName, synapseId, observationText, observationType, observationPhase, observationTime, observationTimeUnits, reliabilityRating, easeOfUseRating, observationLink","resource, investigator, publication", observationId,A unique identifier for the observation.,,,TRUE,,observation,,, observationSubmitterName,The name of the person submitting the observation. ,,,TRUE,,observation,,, @@ -73,15 +73,15 @@ resourceApplicationId,A unique identifier for resrouce Application,,,TRUE,,resou source,"The source of resource application information (e.g. Vendor, Community)","Community-reported, Investigator-reported, Vendor-reported",,TRUE,,resourceApplication,,, applications,"One or more uses for the resource (e.g. western blot, immunofluorescence)","Western Blot, Immunofluorescence, ELISA, Immunohistochemistry, Immunoprecipitation, Tumor Growth Studies, Immunohistochemistry (Paraffin-Embedded), Immunocytochemistry, Immunohistochemistry (Frozen Sections), Flow Cytometry, Affinity Purification, Microarray",,TRUE,,resourceApplication,,,list like links,shareable links related to the resource,,,FALSE,,resourceApplication,,,list -antibody,"A blood protein produced in response to and counteracting a specific antigen. Antibodies combine chemically with substances which the body recognizes as alien, such as bacteria, viruses, and foreign substances in the blood.",,"Component, antibodyId, uniprotId, targetAntigen, clonality, cloneId, reactiveSpecies, conjugate, hostOrganism",FALSE,,antibody,,, -antibodyId,A unique identifier for the antibody.,,,TRUE,,antibody,"antibodyId, uniprotId, targetAntigen, clonality, cloneId, reactiveSpecies, conjugate, hostOrganism",, -uniprotId,The uniprotId of the antibody.,,,TRUE,,antibody,,, -targetAntigen,Antigen that is targeted by antibody. (e.g. Neurofibromin 1 human),,,TRUE,,antibody,,, -clonality,They type of clonality of the antibody,"Unknown, Cocktail, Control, Isotype Control, Monoclonal, Monoclonal Secondary, Polyclonal, Polyclonal Secondary, OligoClonal, Recombinant, Recombinant Monoclonal, Recombinant Monoclonal Secondary, Recombinant Polyclonal, Recombinant Polyclonal Secondary",,TRUE,,antibody,,, -cloneId,Identification of clone (e.g. 2D1),,,FALSE,,antibody,,, -reactiveSpecies,Species the antibody has been shown to crossreact with the target protein. ,"Avian, Bovine, Canine, Chicken, Cow, Dog, Donkey, Feline, Fish, Guinea pig, Hamster, Human, Monkey, Mouse, Non-human primate, Other, Pig, Porcine, Rabbit, Rat, Rodent, Sheep, Simian, Zebrafish",,TRUE,,antibody,,,list -conjugate,Is the antibody conjugated or nonconjugated,"Conjugated, Nonconjugated",,TRUE,,antibody,,, -hostOrganism,The species of the organism that hosts the antibody,"Mouse, Rabbit",,TRUE,,antibody,,, +antibodyDetails,"A blood protein produced in response to and counteracting a specific antigen. Antibodies combine chemically with substances which the body recognizes as alien, such as bacteria, viruses, and foreign substances in the blood.",,"Component, antibodyId, uniprotId, targetAntigen, clonality, cloneId, reactiveSpecies, conjugate, hostOrganism",FALSE,,antibodyDetails,,, +antibodyId,A unique identifier for the antibodyDetails.,,,TRUE,,antibodyDetails,"antibodyId, uniprotId, targetAntigen, clonality, cloneId, reactiveSpecies, conjugate, hostOrganism",, +uniprotId,The uniprotId of the antibodyDetails.,,,TRUE,,antibodyDetails,,, +targetAntigen,Antigen that is targeted by antibodyDetails. (e.g. Neurofibromin 1 human),,,TRUE,,antibodyDetails,,, +clonality,They type of clonality of the antibodyDetails,"Unknown, Cocktail, Control, Isotype Control, Monoclonal, Monoclonal Secondary, Polyclonal, Polyclonal Secondary, OligoClonal, Recombinant, Recombinant Monoclonal, Recombinant Monoclonal Secondary, Recombinant Polyclonal, Recombinant Polyclonal Secondary",,TRUE,,antibodyDetails,,, +cloneId,Identification of clone (e.g. 2D1),,,FALSE,,antibodyDetails,,, +reactiveSpecies,Species the antibodyDetails has been shown to crossreact with the target protein. ,"Avian, Bovine, Canine, Chicken, Cow, Dog, Donkey, Feline, Fish, Guinea pig, Hamster, Human, Monkey, Mouse, Non-human primate, Other, Pig, Porcine, Rabbit, Rat, Rodent, Sheep, Simian, Zebrafish",,TRUE,,antibodyDetails,,,list +conjugate,Is the antibodyDetails conjugated or nonconjugated,"Conjugated, Nonconjugated",,TRUE,,antibodyDetails,,, +hostOrganism,The species of the organism that hosts the antibodyDetails,"Mouse, Rabbit",,TRUE,,antibodyDetails,,, donor,"A person, animal, etc. who is the contributor of the resource.",,"Component, donorId, parentDonorId, transplantationDonorId, species, sex, age, race",FALSE,,donor,"donorId, parentDonorId, transplantationDonorId, species, sex, age, race",, donorId,A uniqe identifier for donor.,,,TRUE,,donor,,, parentDonorId,The ID of the parent donor.,,donorId,FALSE,,donor,,, @@ -89,18 +89,18 @@ species,The species of the individual the resource was derived from.,"Homo sapie sex,The sex of the individual from which the resource was derived from.,"Male, Female, Unknown",,FALSE,,donor,,, age,That age of the individual from which the resource was derived from.,,,FALSE,,donor,,, race,The ethnicity of the individual the resource was derived from.,,,FALSE,,donor,,, -cellLine,A cell culture selected for uniformity from a cell population derived from a usually homogeneous tissue source (such as an organ).,,"Component, cellLineId, donorId, organ, tissue, cellLineCategory, originYear, strProfile, populationDoublingTime, resistance, contaminatedMisidentified, cellLineGeneticDisorder, cellLineManifestation",FALSE,,cellLine,"cellLineId, donorId, organ, tissue, cellLineCategory, originYear, strProfile, populationDoublingTime, resistance, contaminatedMisidentified, cellLineGeneticDisorder, cellLineManifestation",donor, -cellLineId,A unique identifier for the cell line.,,,TRUE,,cellLine,,, -organ,The organ the cell line is derived from.,"Biliary Tract, Bladder, Bone Marrow, Brain, Breast, Bronchial Tree, Duct, Epididymis, Esophagus, Fallopian Tube, Gallbladder, Gland, Gonad, Heart, Intestine, Kidney, Liver, Lung, Lymph Node, Ear, Eye, Nose, Tongue, Pancreas, Penis, Seminal Vesicle, Skin, Spermatic Cord, Spinal Cord, Spleen, Stomach, Thymus Gland, Tonsil, Trachea, Tracheobronchial Tree, Ureter, Urethra, Uterus, Vagina, Vulva",,FALSE,,cellLine,,, -tissue,The tissue the cell line is derived from.,"Blood, Bone marrow, Buccal mucosa, Buffy coat, Cerebral cortex, Dorsal root ganglion, Embryonic tissue, Meninges, Nerve tissue, Optic nerve, Plasma, Primary tumor, Sciatic nerve, Serum, Splenocyte, Unspecified, Whole brain",,FALSE,,cellLine,,, -cellLineCategory,The category to which the cell line belongs.,"Cancer cell line, Conditionally immortalized cell line, Embryonic stem cell, Factor-dependent cell line, Finite cell line, Hybridoma, Induced pluripotent stem cell, Somatic stem cell, Spontaneously immortalized cell line, Stromal cell line, Telomerase immortalized cell line, Transformed cell line, Undefined cell line type",,FALSE,,cellLine,,, -originYear,The year the cell line orginated.,,,FALSE,,cellLine,,, -strProfile,Short tandem repeat profile information.,,,FALSE,,cellLine,,, -populationDoublingTime,Time for cell line to double,,,FALSE,,cellLine,,, -resistance,List of compounds if a cell line has been selected for.,,,FALSE,,cellLine,,,list -contaminatedMisidentified,If a cell line has been contaminated or misidentified,,,FALSE,,cellLine,,, -cellLineGeneticDisorder,"Genetic diseases are diseases in which inherited genes predispose to increased risk. The genetic disorders associated with cancer often result from an alteration or mutation in a single gene. The diseases range from rare dominant cancer family syndrome to familial tendencies in which low-penetrance genes may interact with other genes or environmental factors to induce cancer. Research may involve clinical, epidemiologic, and laboratory studies of persons, families, and populations at high risk of these disorders. [ NCI ]","Neurofibromatosis type 1, Neurofibromatosis type 2, Schwannomatosis, No known disease",,FALSE,http://purl.obolibrary.org/obo/NCIT_C3101,cellLine,,,list -cellLineManifestation,"Manifestations/symptoms that this resource is used to model (e.g. tumor type, behavioral phenotype, etc.)",,,FALSE,,cellLine,,,list +cellLineDetails,A cell culture selected for uniformity from a cell population derived from a usually homogeneous tissue source (such as an organ).,,"Component, cellLineId, donorId, organ, tissue, cellLineCategory, originYear, strProfile, populationDoublingTime, resistance, contaminatedMisidentified, cellLineGeneticDisorder, cellLineManifestation",FALSE,,cellLineDetails,"cellLineId, donorId, organ, tissue, cellLineCategory, originYear, strProfile, populationDoublingTime, resistance, contaminatedMisidentified, cellLineGeneticDisorder, cellLineManifestation",donor, +cellLineId,A unique identifier for the cell line.,,,TRUE,,cellLineDetails,,, +organ,The organ the cell line is derived from.,"Biliary Tract, Bladder, Bone Marrow, Brain, Breast, Bronchial Tree, Duct, Epididymis, Esophagus, Fallopian Tube, Gallbladder, Gland, Gonad, Heart, Intestine, Kidney, Liver, Lung, Lymph Node, Ear, Eye, Nose, Tongue, Pancreas, Penis, Seminal Vesicle, Skin, Spermatic Cord, Spinal Cord, Spleen, Stomach, Thymus Gland, Tonsil, Trachea, Tracheobronchial Tree, Ureter, Urethra, Uterus, Vagina, Vulva",,FALSE,,cellLineDetails,,, +tissue,The tissue the cell line is derived from.,"Blood, Bone marrow, Buccal mucosa, Buffy coat, Cerebral cortex, Dorsal root ganglion, Embryonic tissue, Meninges, Nerve tissue, Optic nerve, Plasma, Primary tumor, Sciatic nerve, Serum, Splenocyte, Unspecified, Whole brain",,FALSE,,cellLineDetails,,, +cellLineCategory,The category to which the cell line belongs.,"Cancer cell line, Conditionally immortalized cell line, Embryonic stem cell, Factor-dependent cell line, Finite cell line, Hybridoma, Induced pluripotent stem cell, Somatic stem cell, Spontaneously immortalized cell line, Stromal cell line, Telomerase immortalized cell line, Transformed cell line, Undefined cell line type",,FALSE,,cellLineDetails,,, +originYear,The year the cell line orginated.,,,FALSE,,cellLineDetails,,, +strProfile,Short tandem repeat profile information.,,,FALSE,,cellLineDetails,,, +populationDoublingTime,Time for cell line to double,,,FALSE,,cellLineDetails,,, +resistance,List of compounds if a cell line has been selected for.,,,FALSE,,cellLineDetails,,,list +contaminatedMisidentified,If a cell line has been contaminated or misidentified,,,FALSE,,cellLineDetails,,, +cellLineGeneticDisorder,"Genetic diseases are diseases in which inherited genes predispose to increased risk. The genetic disorders associated with cancer often result from an alteration or mutation in a single gene. The diseases range from rare dominant cancer family syndrome to familial tendencies in which low-penetrance genes may interact with other genes or environmental factors to induce cancer. Research may involve clinical, epidemiologic, and laboratory studies of persons, families, and populations at high risk of these disorders. [ NCI ]","Neurofibromatosis type 1, Neurofibromatosis type 2, Schwannomatosis, No known disease",,FALSE,http://purl.obolibrary.org/obo/NCIT_C3101,cellLineDetails,,,list +cellLineManifestation,"Manifestations/symptoms that this resource is used to model (e.g. tumor type, behavioral phenotype, etc.)",,,FALSE,,cellLineDetails,,,list mutationDetails,"The changing of the structure of a gene, resulting in a variant form that may be transmitted to subsequent generations",,"Component, mutationDetailsId, externalMutationID, alleleType, mutationType, mutationMethod, affectedGeneSymbol, affectedGeneName, sequenceVariation, proteinVariation, animalModelMutation, humanClinVarMutation, chromosome",FALSE,,mutationDetails,"mutationDetailsId, externalMutationID, alleleType, mutationType, mutationMethod, affectedGeneSymbol, affectedGeneName, sequenceVariation, proteinVariation, animalModelMutation, humanClinVarMutation, chromosome",, mutationDetailsId,A unique identifier for mutation.,,,FALSE,,mutationDetails,,, externalMutationID,"An identifier from an organism database such as MGI or other curated variant resource, if available. ",,,FALSE,,mutationDetails,,, @@ -114,19 +114,19 @@ proteinVariation,The protein consequence of the mutation described in sequence v animalModelMutation,"A description of the specific mutation(s) created in the genome. (e.g. A neomycin resistance cassette replaced the first 42 codons of exon 31, the exon 31 splice acceptor site, and approximately 2 kb of intron 30.)",,,FALSE,,mutationDetails,,, humanClinVarMutation,"The human equivalent, of the mutation being described in ClinVar/HGVS notation. Can be used to link animal model mutations to the mutation they are modeling in human disease. ",,,FALSE,,mutationDetails,,, chromosome,Chromosome number of affected gene. (e.g. 11),,,FALSE,,mutationDetails,,, -mutation,(intermediary table),,"Component, mutationId, mutationDetailsId, animalModelId, cellLineId",FALSE,,mutation,"mutationId, mutationDetailsId, animalModelId, cellLineId","mutationDetails, animalModel, cellLine", +mutation,(intermediary table),,"Component, mutationId, mutationDetailsId, animalModelId, cellLineId",FALSE,,mutation,"mutationId, mutationDetailsId, animalModelId, cellLineId","mutationDetails, animalModelDetails, cellLineDetails", mutationId,A unique identifier for the mutation burden of the resource.,,,FALSE,,mutation,,, -animalModel,"An animal sufficiently like humans in its anatomy, physiology, or response to a pathogen to be used in medical research in order to obtain results that can be extrapolated to human medicine.",,"Component, animalModelId, donorId, transplantationDonorId, animalState, backgroundStrain, backgroundSubstrain, strainNomenclature, generation, transplantationType, animalModelGeneticDisorder, animalModelOfManifestation",FALSE,,animalModel,"animalModelId, donorId, animalState, backgroundStrain, backgroundSubstrain, strainNomenclature, generation, transplantationType, transplantationDonorId, animalModelGeneticDisorder, animalModelOfManifestation",donor, -animalModelId,A unique identifier for the animal model.,,,TRUE,,animalModel,,, -animalState,"State the animal is in according to the vendor/developer. (e.g. embryo, sperm, live)",,,FALSE,,animalModel,,, -backgroundStrain,"An assigned name that describes the genetic make-up (all its alleles at all loci) except the mutated gene of interest and a very small amount of other genetic material, generally from one or two other strains. Correct strain nomenclature indicates what a mutant strain’s background is.",,,FALSE,,animalModel,,, -backgroundSubstrain,"The substrain is a particular variety of a strain. For example, a C57BL/6 mice may have a substrain of C57BL/6J, C57BL/6Tac, or another substrain. ",,,FALSE,Sage Bionetworks,animalModel,,, -strainNomenclature,The standard nomenclature for the strain. (e.g. B6.129S2-NF1tm1Tyj/J). Set by the International Committee on Standardized Genetic Nomenclature for Mice. See http://www.informatics.jax.org/mgihome/nomen/strains.shtml for nomenclature information.,,,FALSE,http://www.informatics.jax.org/mgihome/nomen/strains.shtml,animalModel,,, -generation,The generation of the animal model. (e.g. 13),,,FALSE,,animalModel,,, -transplantationType,"Type of transplantation involved in the experiment, derived from MESH","allograft, xenograft, autograft, isograft",,FALSE,,animalModel,,, -transplantationDonorId,The donor indentifier number for the transplantion donor. ,,donorId,FALSE,,animalModel,,, -animalModelGeneticDisorder,"Genetic diseases are diseases in which inherited genes predispose to increased risk. The genetic disorders associated with cancer often result from an alteration or mutation in a single gene. The diseases range from rare dominant cancer family syndrome to familial tendencies in which low-penetrance genes may interact with other genes or environmental factors to induce cancer. Research may involve clinical, epidemiologic, and laboratory studies of persons, families, and populations at high risk of these disorders. [ NCI ]","Neurofibromatosis type 1, Neurofibromatosis type 2, Schwannomatosis, No known disease",,TRUE,http://purl.obolibrary.org/obo/NCIT_C3101,animalModel,,,list -animalModelOfManifestation,"Manifestations/symptoms that this resource is used to model (e.g. tumor type, behavioral phenotype, etc.) ",,,TRUE,,animalModel,,,list +animalModelDetails,"An animal sufficiently like humans in its anatomy, physiology, or response to a pathogen to be used in medical research in order to obtain results that can be extrapolated to human medicine.",,"Component, animalModelId, donorId, transplantationDonorId, animalState, backgroundStrain, backgroundSubstrain, strainNomenclature, generation, transplantationType, animalModelGeneticDisorder, animalModelOfManifestation",FALSE,,animalModelDetails,"animalModelId, donorId, animalState, backgroundStrain, backgroundSubstrain, strainNomenclature, generation, transplantationType, transplantationDonorId, animalModelGeneticDisorder, animalModelOfManifestation",donor, +animalModelId,A unique identifier for the animal model.,,,TRUE,,animalModelDetails,,, +animalState,"State the animal is in according to the vendor/developer. (e.g. embryo, sperm, live)",,,FALSE,,animalModelDetails,,, +backgroundStrain,"An assigned name that describes the genetic make-up (all its alleles at all loci) except the mutated gene of interest and a very small amount of other genetic material, generally from one or two other strains. Correct strain nomenclature indicates what a mutant strain’s background is.",,,FALSE,,animalModelDetails,,, +backgroundSubstrain,"The substrain is a particular variety of a strain. For example, a C57BL/6 mice may have a substrain of C57BL/6J, C57BL/6Tac, or another substrain. ",,,FALSE,Sage Bionetworks,animalModelDetails,,, +strainNomenclature,The standard nomenclature for the strain. (e.g. B6.129S2-NF1tm1Tyj/J). Set by the International Committee on Standardized Genetic Nomenclature for Mice. See http://www.informatics.jax.org/mgihome/nomen/strains.shtml for nomenclature information.,,,FALSE,http://www.informatics.jax.org/mgihome/nomen/strains.shtml,animalModelDetails,,, +generation,The generation of the animal model. (e.g. 13),,,FALSE,,animalModelDetails,,, +transplantationType,"Type of transplantation involved in the experiment, derived from MESH","allograft, xenograft, autograft, isograft",,FALSE,,animalModelDetails,,, +transplantationDonorId,The donor indentifier number for the transplantion donor. ,,donorId,FALSE,,animalModelDetails,,, +animalModelGeneticDisorder,"Genetic diseases are diseases in which inherited genes predispose to increased risk. The genetic disorders associated with cancer often result from an alteration or mutation in a single gene. The diseases range from rare dominant cancer family syndrome to familial tendencies in which low-penetrance genes may interact with other genes or environmental factors to induce cancer. Research may involve clinical, epidemiologic, and laboratory studies of persons, families, and populations at high risk of these disorders. [ NCI ]","Neurofibromatosis type 1, Neurofibromatosis type 2, Schwannomatosis, No known disease",,TRUE,http://purl.obolibrary.org/obo/NCIT_C3101,animalModelDetails,,,list +animalModelOfManifestation,"Manifestations/symptoms that this resource is used to model (e.g. tumor type, behavioral phenotype, etc.) ",,,TRUE,,animalModelDetails,,,list development,"resourceId, investigatorId, publicationId, funderId (intermediary table)",,"Component, developmentId, resourceId, investigatorId, publicationId, funderId",FALSE,,development,"developmentId, resourceId, investigatorId, publicationId, funderId","resource, investigator, publication, funder", developmentId,A unique identifier for the development of the resource.,,,TRUE,,development,,, funder,A person or organization that provides money for a particular resource.,,"Component, funderId, funderName",FALSE,,funder,"funderId, funderName",, From c00a5679002429aa7e223348a1dd15cb09656eb8 Mon Sep 17 00:00:00 2001 From: "nf-osi[bot]" Date: Thu, 26 Oct 2023 14:59:25 +0000 Subject: [PATCH 20/97] Add changes --- nf-research-tools.jsonld | 707 ++++++++++++++++++++++----------------- 1 file changed, 396 insertions(+), 311 deletions(-) diff --git a/nf-research-tools.jsonld b/nf-research-tools.jsonld index 38d84fcd..c80a7cd6 100644 --- a/nf-research-tools.jsonld +++ b/nf-research-tools.jsonld @@ -115,7 +115,7 @@ "@id": "bts:VendorItem" }, { - "@id": "bts:Biobank" + "@id": "bts:BiobankDetails" }, { "@id": "bts:Observation" @@ -147,7 +147,7 @@ "@id": "bts:Resource" }, { - "@id": "bts:GeneticReagent" + "@id": "bts:GeneticReagentDetails" } ], "schema:isPartOf": { @@ -160,7 +160,7 @@ { "@id": "bts:antibodyId", "@type": "rdf:Property", - "rdfs:comment": "A unique identifier for the antibody.", + "rdfs:comment": "A unique identifier for the antibodyDetails.", "rdfs:label": "antibodyId", "schema:domainIncludes": [ { @@ -184,7 +184,7 @@ "@id": "bts:Resource" }, { - "@id": "bts:CellLine" + "@id": "bts:CellLineDetails" }, { "@id": "bts:Mutation" @@ -210,7 +210,7 @@ "@id": "bts:Mutation" }, { - "@id": "bts:AnimalModel" + "@id": "bts:AnimalModelDetails" } ], "schema:isPartOf": { @@ -276,7 +276,7 @@ { "@id": "bts:resourceType", "@type": "rdf:Property", - "rdfs:comment": "Type of resource. (e.g. animal model, antibody, plasmid, etc.)", + "rdfs:comment": "Type of resource. (e.g. animal model, antibodyDetails, plasmid, etc.)", "rdfs:label": "resourceType", "schema:domainIncludes": [ { @@ -444,89 +444,6 @@ }, "sms:displayName": "Genetic Reagent", "sms:required": "sms:false", - "sms:requiresDependency": [ - { - "@id": "bts:Component" - }, - { - "@id": "bts:geneticReagentId" - }, - { - "@id": "bts:insertName" - }, - { - "@id": "bts:insertEntrezId" - }, - { - "@id": "bts:gRNAshRNASequence" - }, - { - "@id": "bts:insertSize" - }, - { - "@id": "bts:insertSpecies" - }, - { - "@id": "bts:nTerminalTag" - }, - { - "@id": "bts:cTerminalTag" - }, - { - "@id": "bts:cloningMethod" - }, - { - "@id": "bts:5primeCloningSite" - }, - { - "@id": "bts:5primeSiteDestroyed" - }, - { - "@id": "bts:3primeCloningSite" - }, - { - "@id": "bts:3primeSiteDestroyed" - }, - { - "@id": "bts:promoter" - }, - { - "@id": "bts:5primer" - }, - { - "@id": "bts:3primer" - }, - { - "@id": "bts:vectorBackbone" - }, - { - "@id": "bts:vectorType" - }, - { - "@id": "bts:backboneSize" - }, - { - "@id": "bts:totalSize" - }, - { - "@id": "bts:bacterialResistance" - }, - { - "@id": "bts:selectableMarker" - }, - { - "@id": "bts:copyNumber" - }, - { - "@id": "bts:growthTemp" - }, - { - "@id": "bts:growthStrain" - }, - { - "@id": "bts:hazardous" - } - ], "sms:validationRules": [] }, { @@ -544,35 +461,6 @@ }, "sms:displayName": "Antibody", "sms:required": "sms:false", - "sms:requiresDependency": [ - { - "@id": "bts:Component" - }, - { - "@id": "bts:antibodyId" - }, - { - "@id": "bts:uniprotId" - }, - { - "@id": "bts:targetAntigen" - }, - { - "@id": "bts:clonality" - }, - { - "@id": "bts:cloneId" - }, - { - "@id": "bts:reactiveSpecies" - }, - { - "@id": "bts:conjugate" - }, - { - "@id": "bts:hostOrganism" - } - ], "sms:validationRules": [] }, { @@ -590,52 +478,6 @@ }, "sms:displayName": "Cell Line", "sms:required": "sms:false", - "sms:requiresComponent": [ - { - "@id": "bts:Donor" - } - ], - "sms:requiresDependency": [ - { - "@id": "bts:Component" - }, - { - "@id": "bts:cellLineId" - }, - { - "@id": "bts:donorId" - }, - { - "@id": "bts:organ" - }, - { - "@id": "bts:tissue" - }, - { - "@id": "bts:cellLineCategory" - }, - { - "@id": "bts:originYear" - }, - { - "@id": "bts:strProfile" - }, - { - "@id": "bts:populationDoublingTime" - }, - { - "@id": "bts:resistance" - }, - { - "@id": "bts:contaminatedMisidentified" - }, - { - "@id": "bts:cellLineGeneticDisorder" - }, - { - "@id": "bts:cellLineManifestation" - } - ], "sms:validationRules": [] }, { @@ -653,55 +495,12 @@ }, "sms:displayName": "Animal Model", "sms:required": "sms:false", - "sms:requiresComponent": [ - { - "@id": "bts:Donor" - } - ], - "sms:requiresDependency": [ - { - "@id": "bts:Component" - }, - { - "@id": "bts:animalModelId" - }, - { - "@id": "bts:donorId" - }, - { - "@id": "bts:transplantationDonorId" - }, - { - "@id": "bts:animalState" - }, - { - "@id": "bts:backgroundStrain" - }, - { - "@id": "bts:backgroundSubstrain" - }, - { - "@id": "bts:strainNomenclature" - }, - { - "@id": "bts:generation" - }, - { - "@id": "bts:transplantationType" - }, - { - "@id": "bts:animalModelGeneticDisorder" - }, - { - "@id": "bts:animalModelOfManifestation" - } - ], "sms:validationRules": [] }, { "@id": "bts:Biobank", "@type": "rdfs:Class", - "rdfs:comment": "A large collection of biological or medical data and tissue samples, amassed for research purposes.", + "rdfs:comment": "TBD", "rdfs:label": "Biobank", "rdfs:subClassOf": [ { @@ -711,43 +510,8 @@ "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "biobank", + "sms:displayName": "Biobank", "sms:required": "sms:false", - "sms:requiresDependency": [ - { - "@id": "bts:Component" - }, - { - "@id": "bts:biobankId" - }, - { - "@id": "bts:resourceId" - }, - { - "@id": "bts:biobankName" - }, - { - "@id": "bts:biobankURL" - }, - { - "@id": "bts:specimenType" - }, - { - "@id": "bts:specimenTissueType" - }, - { - "@id": "bts:tumorType" - }, - { - "@id": "bts:diseaseType" - }, - { - "@id": "bts:specimenPreparationMethod" - }, - { - "@id": "bts:specimenFormat" - } - ], "sms:validationRules": [] }, { @@ -958,6 +722,106 @@ "sms:required": "sms:false", "sms:validationRules": [] }, + { + "@id": "bts:GeneticReagentDetails", + "@type": "rdfs:Class", + "rdfs:comment": "Genetic reagents.", + "rdfs:label": "GeneticReagentDetails", + "rdfs:subClassOf": [ + { + "@id": "bts:Thing" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "geneticReagentDetails", + "sms:required": "sms:false", + "sms:requiresDependency": [ + { + "@id": "bts:Component" + }, + { + "@id": "bts:geneticReagentId" + }, + { + "@id": "bts:insertName" + }, + { + "@id": "bts:insertEntrezId" + }, + { + "@id": "bts:gRNAshRNASequence" + }, + { + "@id": "bts:insertSize" + }, + { + "@id": "bts:insertSpecies" + }, + { + "@id": "bts:nTerminalTag" + }, + { + "@id": "bts:cTerminalTag" + }, + { + "@id": "bts:cloningMethod" + }, + { + "@id": "bts:5primeCloningSite" + }, + { + "@id": "bts:5primeSiteDestroyed" + }, + { + "@id": "bts:3primeCloningSite" + }, + { + "@id": "bts:3primeSiteDestroyed" + }, + { + "@id": "bts:promoter" + }, + { + "@id": "bts:5primer" + }, + { + "@id": "bts:3primer" + }, + { + "@id": "bts:vectorBackbone" + }, + { + "@id": "bts:vectorType" + }, + { + "@id": "bts:backboneSize" + }, + { + "@id": "bts:totalSize" + }, + { + "@id": "bts:bacterialResistance" + }, + { + "@id": "bts:selectableMarker" + }, + { + "@id": "bts:copyNumber" + }, + { + "@id": "bts:growthTemp" + }, + { + "@id": "bts:growthStrain" + }, + { + "@id": "bts:hazardous" + } + ], + "sms:validationRules": [] + }, { "@id": "bts:insertName", "@type": "rdf:Property", @@ -965,7 +829,7 @@ "rdfs:label": "insertName", "schema:domainIncludes": [ { - "@id": "bts:GeneticReagent" + "@id": "bts:GeneticReagentDetails" } ], "schema:isPartOf": { @@ -982,7 +846,7 @@ "rdfs:label": "insertEntrezId", "schema:domainIncludes": [ { - "@id": "bts:GeneticReagent" + "@id": "bts:GeneticReagentDetails" } ], "schema:isPartOf": { @@ -999,7 +863,7 @@ "rdfs:label": "gRNAshRNASequence", "schema:domainIncludes": [ { - "@id": "bts:GeneticReagent" + "@id": "bts:GeneticReagentDetails" } ], "schema:isPartOf": { @@ -1016,7 +880,7 @@ "rdfs:label": "insertSize", "schema:domainIncludes": [ { - "@id": "bts:GeneticReagent" + "@id": "bts:GeneticReagentDetails" } ], "schema:isPartOf": { @@ -1033,7 +897,7 @@ "rdfs:label": "insertSpecies", "schema:domainIncludes": [ { - "@id": "bts:GeneticReagent" + "@id": "bts:GeneticReagentDetails" } ], "schema:isPartOf": { @@ -1063,7 +927,7 @@ "rdfs:label": "nTerminalTag", "schema:domainIncludes": [ { - "@id": "bts:GeneticReagent" + "@id": "bts:GeneticReagentDetails" } ], "schema:isPartOf": { @@ -1082,7 +946,7 @@ "rdfs:label": "cTerminalTag", "schema:domainIncludes": [ { - "@id": "bts:GeneticReagent" + "@id": "bts:GeneticReagentDetails" } ], "schema:isPartOf": { @@ -1101,7 +965,7 @@ "rdfs:label": "cloningMethod", "schema:domainIncludes": [ { - "@id": "bts:GeneticReagent" + "@id": "bts:GeneticReagentDetails" } ], "schema:isPartOf": { @@ -1138,7 +1002,7 @@ "rdfs:label": "5primeCloningSite", "schema:domainIncludes": [ { - "@id": "bts:GeneticReagent" + "@id": "bts:GeneticReagentDetails" } ], "schema:isPartOf": { @@ -1155,7 +1019,7 @@ "rdfs:label": "5primeSiteDestroyed", "schema:domainIncludes": [ { - "@id": "bts:GeneticReagent" + "@id": "bts:GeneticReagentDetails" } ], "schema:isPartOf": { @@ -1183,7 +1047,7 @@ "rdfs:label": "3primeCloningSite", "schema:domainIncludes": [ { - "@id": "bts:GeneticReagent" + "@id": "bts:GeneticReagentDetails" } ], "schema:isPartOf": { @@ -1200,7 +1064,7 @@ "rdfs:label": "3primeSiteDestroyed", "schema:domainIncludes": [ { - "@id": "bts:GeneticReagent" + "@id": "bts:GeneticReagentDetails" } ], "schema:isPartOf": { @@ -1228,7 +1092,7 @@ "rdfs:label": "promoter", "schema:domainIncludes": [ { - "@id": "bts:GeneticReagent" + "@id": "bts:GeneticReagentDetails" } ], "schema:isPartOf": { @@ -1245,7 +1109,7 @@ "rdfs:label": "5primer", "schema:domainIncludes": [ { - "@id": "bts:GeneticReagent" + "@id": "bts:GeneticReagentDetails" } ], "schema:isPartOf": { @@ -1262,7 +1126,7 @@ "rdfs:label": "3primer", "schema:domainIncludes": [ { - "@id": "bts:GeneticReagent" + "@id": "bts:GeneticReagentDetails" } ], "schema:isPartOf": { @@ -1279,7 +1143,7 @@ "rdfs:label": "vectorBackbone", "schema:domainIncludes": [ { - "@id": "bts:GeneticReagent" + "@id": "bts:GeneticReagentDetails" } ], "schema:isPartOf": { @@ -1296,7 +1160,7 @@ "rdfs:label": "vectorType", "schema:domainIncludes": [ { - "@id": "bts:GeneticReagent" + "@id": "bts:GeneticReagentDetails" } ], "schema:isPartOf": { @@ -1380,7 +1244,7 @@ "rdfs:label": "backboneSize", "schema:domainIncludes": [ { - "@id": "bts:GeneticReagent" + "@id": "bts:GeneticReagentDetails" } ], "schema:isPartOf": { @@ -1397,7 +1261,7 @@ "rdfs:label": "totalSize", "schema:domainIncludes": [ { - "@id": "bts:GeneticReagent" + "@id": "bts:GeneticReagentDetails" } ], "schema:isPartOf": { @@ -1414,7 +1278,7 @@ "rdfs:label": "bacterialResistance", "schema:domainIncludes": [ { - "@id": "bts:GeneticReagent" + "@id": "bts:GeneticReagentDetails" } ], "schema:isPartOf": { @@ -1502,7 +1366,7 @@ "rdfs:label": "selectableMarker", "schema:domainIncludes": [ { - "@id": "bts:GeneticReagent" + "@id": "bts:GeneticReagentDetails" } ], "schema:isPartOf": { @@ -1566,7 +1430,7 @@ "rdfs:label": "copyNumber", "schema:domainIncludes": [ { - "@id": "bts:GeneticReagent" + "@id": "bts:GeneticReagentDetails" } ], "schema:isPartOf": { @@ -1594,7 +1458,7 @@ "rdfs:label": "growthTemp", "schema:domainIncludes": [ { - "@id": "bts:GeneticReagent" + "@id": "bts:GeneticReagentDetails" } ], "schema:isPartOf": { @@ -1622,7 +1486,7 @@ "rdfs:label": "growthStrain", "schema:domainIncludes": [ { - "@id": "bts:GeneticReagent" + "@id": "bts:GeneticReagentDetails" } ], "schema:isPartOf": { @@ -1659,7 +1523,7 @@ "rdfs:label": "hazardous", "schema:domainIncludes": [ { - "@id": "bts:GeneticReagent" + "@id": "bts:GeneticReagentDetails" } ], "schema:isPartOf": { @@ -3170,14 +3034,66 @@ "sms:required": "sms:false", "sms:validationRules": [] }, + { + "@id": "bts:BiobankDetails", + "@type": "rdfs:Class", + "rdfs:comment": "A large collection of biological or medical data and tissue samples, amassed for research purposes.", + "rdfs:label": "BiobankDetails", + "rdfs:subClassOf": [ + { + "@id": "bts:Thing" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "biobankDetails", + "sms:required": "sms:false", + "sms:requiresDependency": [ + { + "@id": "bts:Component" + }, + { + "@id": "bts:biobankId" + }, + { + "@id": "bts:resourceId" + }, + { + "@id": "bts:biobankName" + }, + { + "@id": "bts:biobankURL" + }, + { + "@id": "bts:specimenType" + }, + { + "@id": "bts:specimenTissueType" + }, + { + "@id": "bts:tumorType" + }, + { + "@id": "bts:diseaseType" + }, + { + "@id": "bts:specimenPreparationMethod" + }, + { + "@id": "bts:specimenFormat" + } + ], + "sms:validationRules": [] + }, { "@id": "bts:biobankId", "@type": "rdf:Property", - "rdfs:comment": "A unique identifier for the biobank.", + "rdfs:comment": "A unique identifier for the biobankDetails.", "rdfs:label": "biobankId", "schema:domainIncludes": [ { - "@id": "bts:Biobank" + "@id": "bts:BiobankDetails" } ], "schema:isPartOf": { @@ -3190,11 +3106,11 @@ { "@id": "bts:biobankName", "@type": "rdf:Property", - "rdfs:comment": "The name of the biobank.", + "rdfs:comment": "The name of the biobankDetails.", "rdfs:label": "biobankName", "schema:domainIncludes": [ { - "@id": "bts:Biobank" + "@id": "bts:BiobankDetails" } ], "schema:isPartOf": { @@ -3207,11 +3123,11 @@ { "@id": "bts:biobankURL", "@type": "rdf:Property", - "rdfs:comment": "A URL for the biobank landing page.", + "rdfs:comment": "A URL for the biobankDetails landing page.", "rdfs:label": "biobankURL", "schema:domainIncludes": [ { - "@id": "bts:Biobank" + "@id": "bts:BiobankDetails" } ], "schema:isPartOf": { @@ -3228,7 +3144,7 @@ "rdfs:label": "specimenType", "schema:domainIncludes": [ { - "@id": "bts:Biobank" + "@id": "bts:BiobankDetails" } ], "schema:isPartOf": { @@ -3258,7 +3174,7 @@ "rdfs:label": "specimenTissueType", "schema:domainIncludes": [ { - "@id": "bts:Biobank" + "@id": "bts:BiobankDetails" } ], "schema:isPartOf": { @@ -3300,7 +3216,7 @@ "rdfs:label": "tumorType", "schema:domainIncludes": [ { - "@id": "bts:Biobank" + "@id": "bts:BiobankDetails" } ], "schema:isPartOf": { @@ -3360,7 +3276,7 @@ "rdfs:label": "diseaseType", "schema:domainIncludes": [ { - "@id": "bts:Biobank" + "@id": "bts:BiobankDetails" } ], "schema:isPartOf": { @@ -3386,11 +3302,11 @@ { "@id": "bts:specimenPreparationMethod", "@type": "rdf:Property", - "rdfs:comment": "The preservation methods used by the biobank.", + "rdfs:comment": "The preservation methods used by the biobankDetails.", "rdfs:label": "specimenPreparationMethod", "schema:domainIncludes": [ { - "@id": "bts:Biobank" + "@id": "bts:BiobankDetails" } ], "schema:isPartOf": { @@ -3435,7 +3351,7 @@ "rdfs:label": "specimenFormat", "schema:domainIncludes": [ { - "@id": "bts:Biobank" + "@id": "bts:BiobankDetails" } ], "schema:isPartOf": { @@ -5872,10 +5788,56 @@ "sms:required": "sms:false", "sms:validationRules": [] }, + { + "@id": "bts:AntibodyDetails", + "@type": "rdfs:Class", + "rdfs:comment": "A blood protein produced in response to and counteracting a specific antigen. Antibodies combine chemically with substances which the body recognizes as alien, such as bacteria, viruses, and foreign substances in the blood.", + "rdfs:label": "AntibodyDetails", + "rdfs:subClassOf": [ + { + "@id": "bts:Thing" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "antibodyDetails", + "sms:required": "sms:false", + "sms:requiresDependency": [ + { + "@id": "bts:Component" + }, + { + "@id": "bts:antibodyId" + }, + { + "@id": "bts:uniprotId" + }, + { + "@id": "bts:targetAntigen" + }, + { + "@id": "bts:clonality" + }, + { + "@id": "bts:cloneId" + }, + { + "@id": "bts:reactiveSpecies" + }, + { + "@id": "bts:conjugate" + }, + { + "@id": "bts:hostOrganism" + } + ], + "sms:validationRules": [] + }, { "@id": "bts:uniprotId", "@type": "rdf:Property", - "rdfs:comment": "The uniprotId of the antibody.", + "rdfs:comment": "The uniprotId of the antibodyDetails.", "rdfs:label": "uniprotId", "schema:domainIncludes": [ { @@ -5892,7 +5854,7 @@ { "@id": "bts:targetAntigen", "@type": "rdf:Property", - "rdfs:comment": "Antigen that is targeted by antibody. (e.g. Neurofibromin 1 human)", + "rdfs:comment": "Antigen that is targeted by antibodyDetails. (e.g. Neurofibromin 1 human)", "rdfs:label": "targetAntigen", "schema:domainIncludes": [ { @@ -5909,7 +5871,7 @@ { "@id": "bts:clonality", "@type": "rdf:Property", - "rdfs:comment": "They type of clonality of the antibody", + "rdfs:comment": "They type of clonality of the antibodyDetails", "rdfs:label": "clonality", "schema:domainIncludes": [ { @@ -5987,7 +5949,7 @@ { "@id": "bts:reactiveSpecies", "@type": "rdf:Property", - "rdfs:comment": "Species the antibody has been shown to crossreact with the target protein.", + "rdfs:comment": "Species the antibodyDetails has been shown to crossreact with the target protein.", "rdfs:label": "reactiveSpecies", "schema:domainIncludes": [ { @@ -6080,7 +6042,7 @@ { "@id": "bts:conjugate", "@type": "rdf:Property", - "rdfs:comment": "Is the antibody conjugated or nonconjugated", + "rdfs:comment": "Is the antibodyDetails conjugated or nonconjugated", "rdfs:label": "conjugate", "schema:domainIncludes": [ { @@ -6105,7 +6067,7 @@ { "@id": "bts:hostOrganism", "@type": "rdf:Property", - "rdfs:comment": "The species of the organism that hosts the antibody", + "rdfs:comment": "The species of the organism that hosts the antibodyDetails", "rdfs:label": "hostOrganism", "schema:domainIncludes": [ { @@ -6832,10 +6794,10 @@ "@id": "bts:Donor" }, { - "@id": "bts:CellLine" + "@id": "bts:CellLineDetails" }, { - "@id": "bts:AnimalModel" + "@id": "bts:AnimalModelDetails" } ], "schema:isPartOf": { @@ -6872,7 +6834,7 @@ "@id": "bts:Donor" }, { - "@id": "bts:AnimalModel" + "@id": "bts:AnimalModelDetails" } ], "schema:isPartOf": { @@ -7186,6 +7148,69 @@ "sms:required": "sms:false", "sms:validationRules": [] }, + { + "@id": "bts:CellLineDetails", + "@type": "rdfs:Class", + "rdfs:comment": "A cell culture selected for uniformity from a cell population derived from a usually homogeneous tissue source (such as an organ).", + "rdfs:label": "CellLineDetails", + "rdfs:subClassOf": [ + { + "@id": "bts:Thing" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "cellLineDetails", + "sms:required": "sms:false", + "sms:requiresComponent": [ + { + "@id": "bts:Donor" + } + ], + "sms:requiresDependency": [ + { + "@id": "bts:Component" + }, + { + "@id": "bts:cellLineId" + }, + { + "@id": "bts:donorId" + }, + { + "@id": "bts:organ" + }, + { + "@id": "bts:tissue" + }, + { + "@id": "bts:cellLineCategory" + }, + { + "@id": "bts:originYear" + }, + { + "@id": "bts:strProfile" + }, + { + "@id": "bts:populationDoublingTime" + }, + { + "@id": "bts:resistance" + }, + { + "@id": "bts:contaminatedMisidentified" + }, + { + "@id": "bts:cellLineGeneticDisorder" + }, + { + "@id": "bts:cellLineManifestation" + } + ], + "sms:validationRules": [] + }, { "@id": "bts:organ", "@type": "rdf:Property", @@ -7193,7 +7218,7 @@ "rdfs:label": "organ", "schema:domainIncludes": [ { - "@id": "bts:CellLine" + "@id": "bts:CellLineDetails" } ], "schema:isPartOf": { @@ -7332,7 +7357,7 @@ "rdfs:label": "tissue", "schema:domainIncludes": [ { - "@id": "bts:CellLine" + "@id": "bts:CellLineDetails" } ], "schema:isPartOf": { @@ -7402,7 +7427,7 @@ "rdfs:label": "cellLineCategory", "schema:domainIncludes": [ { - "@id": "bts:CellLine" + "@id": "bts:CellLineDetails" } ], "schema:isPartOf": { @@ -7460,7 +7485,7 @@ "rdfs:label": "originYear", "schema:domainIncludes": [ { - "@id": "bts:CellLine" + "@id": "bts:CellLineDetails" } ], "schema:isPartOf": { @@ -7477,7 +7502,7 @@ "rdfs:label": "strProfile", "schema:domainIncludes": [ { - "@id": "bts:CellLine" + "@id": "bts:CellLineDetails" } ], "schema:isPartOf": { @@ -7494,7 +7519,7 @@ "rdfs:label": "populationDoublingTime", "schema:domainIncludes": [ { - "@id": "bts:CellLine" + "@id": "bts:CellLineDetails" } ], "schema:isPartOf": { @@ -7511,7 +7536,7 @@ "rdfs:label": "resistance", "schema:domainIncludes": [ { - "@id": "bts:CellLine" + "@id": "bts:CellLineDetails" } ], "schema:isPartOf": { @@ -7530,7 +7555,7 @@ "rdfs:label": "contaminatedMisidentified", "schema:domainIncludes": [ { - "@id": "bts:CellLine" + "@id": "bts:CellLineDetails" } ], "schema:isPartOf": { @@ -7547,7 +7572,7 @@ "rdfs:label": "cellLineGeneticDisorder", "schema:domainIncludes": [ { - "@id": "bts:CellLine" + "@id": "bts:CellLineDetails" } ], "schema:isPartOf": { @@ -7580,7 +7605,7 @@ "rdfs:label": "cellLineManifestation", "schema:domainIncludes": [ { - "@id": "bts:CellLine" + "@id": "bts:CellLineDetails" } ], "schema:isPartOf": { @@ -9954,10 +9979,10 @@ "@id": "bts:MutationDetails" }, { - "@id": "bts:AnimalModel" + "@id": "bts:AnimalModelDetails" }, { - "@id": "bts:CellLine" + "@id": "bts:CellLineDetails" } ], "sms:requiresDependency": [ @@ -9996,6 +10021,66 @@ "sms:required": "sms:false", "sms:validationRules": [] }, + { + "@id": "bts:AnimalModelDetails", + "@type": "rdfs:Class", + "rdfs:comment": "An animal sufficiently like humans in its anatomy, physiology, or response to a pathogen to be used in medical research in order to obtain results that can be extrapolated to human medicine.", + "rdfs:label": "AnimalModelDetails", + "rdfs:subClassOf": [ + { + "@id": "bts:Thing" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "animalModelDetails", + "sms:required": "sms:false", + "sms:requiresComponent": [ + { + "@id": "bts:Donor" + } + ], + "sms:requiresDependency": [ + { + "@id": "bts:Component" + }, + { + "@id": "bts:animalModelId" + }, + { + "@id": "bts:donorId" + }, + { + "@id": "bts:transplantationDonorId" + }, + { + "@id": "bts:animalState" + }, + { + "@id": "bts:backgroundStrain" + }, + { + "@id": "bts:backgroundSubstrain" + }, + { + "@id": "bts:strainNomenclature" + }, + { + "@id": "bts:generation" + }, + { + "@id": "bts:transplantationType" + }, + { + "@id": "bts:animalModelGeneticDisorder" + }, + { + "@id": "bts:animalModelOfManifestation" + } + ], + "sms:validationRules": [] + }, { "@id": "bts:animalState", "@type": "rdf:Property", @@ -10003,7 +10088,7 @@ "rdfs:label": "animalState", "schema:domainIncludes": [ { - "@id": "bts:AnimalModel" + "@id": "bts:AnimalModelDetails" } ], "schema:isPartOf": { @@ -10020,7 +10105,7 @@ "rdfs:label": "backgroundStrain", "schema:domainIncludes": [ { - "@id": "bts:AnimalModel" + "@id": "bts:AnimalModelDetails" } ], "schema:isPartOf": { @@ -10037,7 +10122,7 @@ "rdfs:label": "backgroundSubstrain", "schema:domainIncludes": [ { - "@id": "bts:AnimalModel" + "@id": "bts:AnimalModelDetails" } ], "schema:isPartOf": { @@ -10054,7 +10139,7 @@ "rdfs:label": "strainNomenclature", "schema:domainIncludes": [ { - "@id": "bts:AnimalModel" + "@id": "bts:AnimalModelDetails" } ], "schema:isPartOf": { @@ -10071,7 +10156,7 @@ "rdfs:label": "generation", "schema:domainIncludes": [ { - "@id": "bts:AnimalModel" + "@id": "bts:AnimalModelDetails" } ], "schema:isPartOf": { @@ -10088,7 +10173,7 @@ "rdfs:label": "transplantationType", "schema:domainIncludes": [ { - "@id": "bts:AnimalModel" + "@id": "bts:AnimalModelDetails" } ], "schema:isPartOf": { @@ -10119,7 +10204,7 @@ "rdfs:label": "animalModelGeneticDisorder", "schema:domainIncludes": [ { - "@id": "bts:AnimalModel" + "@id": "bts:AnimalModelDetails" } ], "schema:isPartOf": { @@ -10152,7 +10237,7 @@ "rdfs:label": "animalModelOfManifestation", "schema:domainIncludes": [ { - "@id": "bts:AnimalModel" + "@id": "bts:AnimalModelDetails" } ], "schema:isPartOf": { From 48acb1424a613bb8d235b2100e2bd55942d048b4 Mon Sep 17 00:00:00 2001 From: Robert Allaway Date: Thu, 26 Oct 2023 10:49:40 -0500 Subject: [PATCH 21/97] fix bad find and replaces --- nf_research_tools.rdb.model.csv | 24 ++++++++++++------------ 1 file changed, 12 insertions(+), 12 deletions(-) diff --git a/nf_research_tools.rdb.model.csv b/nf_research_tools.rdb.model.csv index 32f86294..4a32ec25 100644 --- a/nf_research_tools.rdb.model.csv +++ b/nf_research_tools.rdb.model.csv @@ -5,7 +5,7 @@ resourceId,A unique identifier for the resource.,,,TRUE,,resource,,, rrid,"The RRID, a standard resource identifier that will facilitate interoperability with other databases, and is an increasingly-used identifier for publications https://scicrunch.org/resources if available",,,FALSE,,resource,,, resourceName,The “canonical” name of the resource,,,TRUE,,resource,,, synonyms,Synonyms of the resource,,,FALSE,,resource,,,list like -resourceType,"Type of resource. (e.g. animal model, antibodyDetails, plasmid, etc.)","Animal Model, Cell Line, Antibody, Genetic Reagent, Biobank",,TRUE,,resource,,, +resourceType,"Type of resource. (e.g. animal model, antibody, plasmid, etc.)","Animal Model, Cell Line, Antibody, Genetic Reagent, Biobank",,TRUE,,resource,,, description,Free text description/summary/overview/purpose of the resource.,,,FALSE,,resource,,, usageRequirements,Any known restrictions on use of the resource. ,"data sharing required, non-commercial use only, re-distribution not permitted, generation of germ line transmitting chimeras not permitted, creation of functional gametes not permitted, generation of interspecies chimeras not permitted, human cloning not permitted, cannot be used for treatment purposes, IRB documentation required, special licencing restrictions (see vendor for more information), unknown",,FALSE,,resource,,,list like howToAcquire,How to acquire a particular resource. ,,,TRUE,,resource,,, @@ -47,14 +47,14 @@ vendorId,A unique identifier for the vendor.,,,TRUE,,vendor,,, vendorName,The name of the vendor.,,,FALSE,,vendor,,, vendorURL,The vendor website url associated with the resource.,,,FALSE,,vendor,,, biobankDetails,"A large collection of biological or medical data and tissue samples, amassed for research purposes.",,"Component, biobankId, resourceId, biobankName, biobankURL, specimenType, specimenTissueType, tumorType, diseaseType, specimenPreparationMethod, specimenFormat",FALSE,,biobankDetails,"biobankId, resourceId, biobankName, biobankURL, specimenType, specimenTissueType, tumorType, diseaseType, specimenPreparationMethod, specimenFormat",, -biobankName,The name of the biobankDetails. ,,,TRUE,,biobankDetails,,, -biobankId,A unique identifier for the biobankDetails.,,,TRUE,,biobankDetails,,, -biobankURL,A URL for the biobankDetails landing page.,,,TRUE,,biobankDetails,,, +biobankName,The name of the biobank. ,,,TRUE,,biobankDetails,,, +biobankId,A unique identifier for the biobank.,,,TRUE,,biobankDetails,,, +biobankURL,A URL for the biobank landing page.,,,TRUE,,biobankDetails,,, specimenType,The types of specimens that are banked.,"human tissue, xenograft tumors, cell lines",,TRUE,,biobankDetails,,,list like specimenTissueType,The types of tissues that are banked.,"blood, tumor, cerebrospinal fluid, nerve, skin, bone, brain",,TRUE,,biobankDetails,,,list like tumorType,"The types of tumors that are banked, if applicable.","cutaneous neurofibroma, plexiform neurofibroma, schwannoma, meningioma, malignant peripheral nerve sheath tumor, low grade glioma, high grade glioma, pheochromocytoma, optic nerve glioma, atypical neurofibroma, neurofibroma NOS, diffuse infiltrating neurofibroma, brain NOS",,TRUE,,biobankDetails,,,list like diseaseType,"The diseases of the banked specimens, if applicable.","Neurofibromatosis type 1, Neurofibromatosis type 2, Schwannomatosis",,TRUE,,biobankDetails,,,list like -specimenPreparationMethod,The preservation methods used by the biobankDetails.,"Fresh collected, Flash frozen, FFPE, Cryopreserved, OCT, RNA later, Formalin-fixed, Ethanol",,TRUE,,biobankDetails,,,list like +specimenPreparationMethod,The preservation methods used by the biobank.,"Fresh collected, Flash frozen, FFPE, Cryopreserved, OCT, RNA later, Formalin-fixed, Ethanol",,TRUE,,biobankDetails,,,list like specimenFormat,How the specimens have been processed in preparation for distribution.,"whole tumor, slide, whole cell lysate, DNA, RNA",,TRUE,,biobankDetails,,,list like observation,"A remark, statement, or comment based on the resource.",,"Component, observationId, resourceId, publicationId, observationSubmitterName, synapseId, observationText, observationType, observationPhase, observationTime, observationTimeUnits, reliabilityRating, easeOfUseRating, observationLink",FALSE,,observation,"observationId, resourceId, publicationId, observationSubmitterName, synapseId, observationText, observationType, observationPhase, observationTime, observationTimeUnits, reliabilityRating, easeOfUseRating, observationLink","resource, investigator, publication", observationId,A unique identifier for the observation.,,,TRUE,,observation,,, @@ -74,14 +74,14 @@ source,"The source of resource application information (e.g. Vendor, Community)" applications,"One or more uses for the resource (e.g. western blot, immunofluorescence)","Western Blot, Immunofluorescence, ELISA, Immunohistochemistry, Immunoprecipitation, Tumor Growth Studies, Immunohistochemistry (Paraffin-Embedded), Immunocytochemistry, Immunohistochemistry (Frozen Sections), Flow Cytometry, Affinity Purification, Microarray",,TRUE,,resourceApplication,,,list like links,shareable links related to the resource,,,FALSE,,resourceApplication,,,list antibodyDetails,"A blood protein produced in response to and counteracting a specific antigen. Antibodies combine chemically with substances which the body recognizes as alien, such as bacteria, viruses, and foreign substances in the blood.",,"Component, antibodyId, uniprotId, targetAntigen, clonality, cloneId, reactiveSpecies, conjugate, hostOrganism",FALSE,,antibodyDetails,,, -antibodyId,A unique identifier for the antibodyDetails.,,,TRUE,,antibodyDetails,"antibodyId, uniprotId, targetAntigen, clonality, cloneId, reactiveSpecies, conjugate, hostOrganism",, -uniprotId,The uniprotId of the antibodyDetails.,,,TRUE,,antibodyDetails,,, -targetAntigen,Antigen that is targeted by antibodyDetails. (e.g. Neurofibromin 1 human),,,TRUE,,antibodyDetails,,, -clonality,They type of clonality of the antibodyDetails,"Unknown, Cocktail, Control, Isotype Control, Monoclonal, Monoclonal Secondary, Polyclonal, Polyclonal Secondary, OligoClonal, Recombinant, Recombinant Monoclonal, Recombinant Monoclonal Secondary, Recombinant Polyclonal, Recombinant Polyclonal Secondary",,TRUE,,antibodyDetails,,, +antibodyId,A unique identifier for the antibody.,,,TRUE,,antibodyDetails,"antibodyId, uniprotId, targetAntigen, clonality, cloneId, reactiveSpecies, conjugate, hostOrganism",, +uniprotId,The uniprotId of the antibody.,,,TRUE,,antibodyDetails,,, +targetAntigen,Antigen that is targeted by antibody. (e.g. Neurofibromin 1 human),,,TRUE,,antibodyDetails,,, +clonality,They type of clonality of the antibody,"Unknown, Cocktail, Control, Isotype Control, Monoclonal, Monoclonal Secondary, Polyclonal, Polyclonal Secondary, OligoClonal, Recombinant, Recombinant Monoclonal, Recombinant Monoclonal Secondary, Recombinant Polyclonal, Recombinant Polyclonal Secondary",,TRUE,,antibodyDetails,,, cloneId,Identification of clone (e.g. 2D1),,,FALSE,,antibodyDetails,,, -reactiveSpecies,Species the antibodyDetails has been shown to crossreact with the target protein. ,"Avian, Bovine, Canine, Chicken, Cow, Dog, Donkey, Feline, Fish, Guinea pig, Hamster, Human, Monkey, Mouse, Non-human primate, Other, Pig, Porcine, Rabbit, Rat, Rodent, Sheep, Simian, Zebrafish",,TRUE,,antibodyDetails,,,list -conjugate,Is the antibodyDetails conjugated or nonconjugated,"Conjugated, Nonconjugated",,TRUE,,antibodyDetails,,, -hostOrganism,The species of the organism that hosts the antibodyDetails,"Mouse, Rabbit",,TRUE,,antibodyDetails,,, +reactiveSpecies,Species the antibody has been shown to crossreact with the target protein. ,"Avian, Bovine, Canine, Chicken, Cow, Dog, Donkey, Feline, Fish, Guinea pig, Hamster, Human, Monkey, Mouse, Non-human primate, Other, Pig, Porcine, Rabbit, Rat, Rodent, Sheep, Simian, Zebrafish",,TRUE,,antibodyDetails,,,list +conjugate,Is the antibody conjugated or nonconjugated,"Conjugated, Nonconjugated",,TRUE,,antibodyDetails,,, +hostOrganism,The species of the organism that hosts the antibody,"Mouse, Rabbit",,TRUE,,antibodyDetails,,, donor,"A person, animal, etc. who is the contributor of the resource.",,"Component, donorId, parentDonorId, transplantationDonorId, species, sex, age, race",FALSE,,donor,"donorId, parentDonorId, transplantationDonorId, species, sex, age, race",, donorId,A uniqe identifier for donor.,,,TRUE,,donor,,, parentDonorId,The ID of the parent donor.,,donorId,FALSE,,donor,,, From 6e72fb57086235fb37bcf1d921c4f71795788ee8 Mon Sep 17 00:00:00 2001 From: "nf-osi[bot]" Date: Thu, 26 Oct 2023 15:51:23 +0000 Subject: [PATCH 22/97] Add changes --- nf-research-tools.jsonld | 24 ++++++++++++------------ 1 file changed, 12 insertions(+), 12 deletions(-) diff --git a/nf-research-tools.jsonld b/nf-research-tools.jsonld index c80a7cd6..c6ed4f0e 100644 --- a/nf-research-tools.jsonld +++ b/nf-research-tools.jsonld @@ -160,7 +160,7 @@ { "@id": "bts:antibodyId", "@type": "rdf:Property", - "rdfs:comment": "A unique identifier for the antibodyDetails.", + "rdfs:comment": "A unique identifier for the antibody.", "rdfs:label": "antibodyId", "schema:domainIncludes": [ { @@ -276,7 +276,7 @@ { "@id": "bts:resourceType", "@type": "rdf:Property", - "rdfs:comment": "Type of resource. (e.g. animal model, antibodyDetails, plasmid, etc.)", + "rdfs:comment": "Type of resource. (e.g. animal model, antibody, plasmid, etc.)", "rdfs:label": "resourceType", "schema:domainIncludes": [ { @@ -3089,7 +3089,7 @@ { "@id": "bts:biobankId", "@type": "rdf:Property", - "rdfs:comment": "A unique identifier for the biobankDetails.", + "rdfs:comment": "A unique identifier for the biobank.", "rdfs:label": "biobankId", "schema:domainIncludes": [ { @@ -3106,7 +3106,7 @@ { "@id": "bts:biobankName", "@type": "rdf:Property", - "rdfs:comment": "The name of the biobankDetails.", + "rdfs:comment": "The name of the biobank.", "rdfs:label": "biobankName", "schema:domainIncludes": [ { @@ -3123,7 +3123,7 @@ { "@id": "bts:biobankURL", "@type": "rdf:Property", - "rdfs:comment": "A URL for the biobankDetails landing page.", + "rdfs:comment": "A URL for the biobank landing page.", "rdfs:label": "biobankURL", "schema:domainIncludes": [ { @@ -3302,7 +3302,7 @@ { "@id": "bts:specimenPreparationMethod", "@type": "rdf:Property", - "rdfs:comment": "The preservation methods used by the biobankDetails.", + "rdfs:comment": "The preservation methods used by the biobank.", "rdfs:label": "specimenPreparationMethod", "schema:domainIncludes": [ { @@ -5837,7 +5837,7 @@ { "@id": "bts:uniprotId", "@type": "rdf:Property", - "rdfs:comment": "The uniprotId of the antibodyDetails.", + "rdfs:comment": "The uniprotId of the antibody.", "rdfs:label": "uniprotId", "schema:domainIncludes": [ { @@ -5854,7 +5854,7 @@ { "@id": "bts:targetAntigen", "@type": "rdf:Property", - "rdfs:comment": "Antigen that is targeted by antibodyDetails. (e.g. Neurofibromin 1 human)", + "rdfs:comment": "Antigen that is targeted by antibody. (e.g. Neurofibromin 1 human)", "rdfs:label": "targetAntigen", "schema:domainIncludes": [ { @@ -5871,7 +5871,7 @@ { "@id": "bts:clonality", "@type": "rdf:Property", - "rdfs:comment": "They type of clonality of the antibodyDetails", + "rdfs:comment": "They type of clonality of the antibody", "rdfs:label": "clonality", "schema:domainIncludes": [ { @@ -5949,7 +5949,7 @@ { "@id": "bts:reactiveSpecies", "@type": "rdf:Property", - "rdfs:comment": "Species the antibodyDetails has been shown to crossreact with the target protein.", + "rdfs:comment": "Species the antibody has been shown to crossreact with the target protein.", "rdfs:label": "reactiveSpecies", "schema:domainIncludes": [ { @@ -6042,7 +6042,7 @@ { "@id": "bts:conjugate", "@type": "rdf:Property", - "rdfs:comment": "Is the antibodyDetails conjugated or nonconjugated", + "rdfs:comment": "Is the antibody conjugated or nonconjugated", "rdfs:label": "conjugate", "schema:domainIncludes": [ { @@ -6067,7 +6067,7 @@ { "@id": "bts:hostOrganism", "@type": "rdf:Property", - "rdfs:comment": "The species of the organism that hosts the antibodyDetails", + "rdfs:comment": "The species of the organism that hosts the antibody", "rdfs:label": "hostOrganism", "schema:domainIncludes": [ { From fbb44bee89db580945e767af9e344abd6c47c167 Mon Sep 17 00:00:00 2001 From: Robert Allaway Date: Thu, 26 Oct 2023 11:34:32 -0500 Subject: [PATCH 23/97] remove requirement for resourcetype ID --- nf_research_tools.rdb.model.csv | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/nf_research_tools.rdb.model.csv b/nf_research_tools.rdb.model.csv index 4a32ec25..86ce76bb 100644 --- a/nf_research_tools.rdb.model.csv +++ b/nf_research_tools.rdb.model.csv @@ -12,7 +12,7 @@ howToAcquire,How to acquire a particular resource. ,,,TRUE,,resource,,, dateAdded,The date that the resource was originally added.,,,TRUE,,resource,,, dateModified,The last update of the resource metadata (not including observations).,,,TRUE,,resource,,, geneticReagentDetails,Genetic reagents.,,"Component, geneticReagentId, insertName, insertEntrezId, gRNAshRNASequence, insertSize, insertSpecies, nTerminalTag, cTerminalTag, cloningMethod, 5primeCloningSite, 5primeSiteDestroyed, 3primeCloningSite, 3primeSiteDestroyed, promoter, 5primer, 3primer, vectorBackbone, vectorType, backboneSize, totalSize, bacterialResistance, selectableMarker, copyNumber, growthTemp, growthStrain, hazardous",FALSE,,geneticReagentDetails,"geneticReagentId, insertName, insertEntrezId, gRNAshRNASequence, insertSize, insertSpecies, nTerminalTag, cTerminalTag, cloningMethod, 5primeCloningSite, 5primeSiteDestroyed, 3primeCloningSite, 3primeSiteDestroyed, promoter, 5primer, 3primer, vectorBackbone, vectorType, backboneSize, totalSize, bacterialResistance, selectableMarker, copyNumber, growthTemp, growthStrain, hazardous",, -geneticReagentId,A unique identifier for the reagent.,,,TRUE,,geneticReagentDetails,,, +geneticReagentId,A unique identifier for the reagent.,,,FALSE,,geneticReagentDetails,,, insertName,Name of the main gene insert in the plasmid.,,,TRUE,,geneticReagentDetails,,, insertEntrezId,The entrez gene id for the gene insert,,,TRUE,,geneticReagentDetails,,, gRNAshRNASequence,"The sequence of the gRNA or shRNA for the gene insert, if present. ",,,FALSE,,geneticReagentDetails,,, @@ -74,7 +74,7 @@ source,"The source of resource application information (e.g. Vendor, Community)" applications,"One or more uses for the resource (e.g. western blot, immunofluorescence)","Western Blot, Immunofluorescence, ELISA, Immunohistochemistry, Immunoprecipitation, Tumor Growth Studies, Immunohistochemistry (Paraffin-Embedded), Immunocytochemistry, Immunohistochemistry (Frozen Sections), Flow Cytometry, Affinity Purification, Microarray",,TRUE,,resourceApplication,,,list like links,shareable links related to the resource,,,FALSE,,resourceApplication,,,list antibodyDetails,"A blood protein produced in response to and counteracting a specific antigen. Antibodies combine chemically with substances which the body recognizes as alien, such as bacteria, viruses, and foreign substances in the blood.",,"Component, antibodyId, uniprotId, targetAntigen, clonality, cloneId, reactiveSpecies, conjugate, hostOrganism",FALSE,,antibodyDetails,,, -antibodyId,A unique identifier for the antibody.,,,TRUE,,antibodyDetails,"antibodyId, uniprotId, targetAntigen, clonality, cloneId, reactiveSpecies, conjugate, hostOrganism",, +antibodyId,A unique identifier for the antibody.,,,FALSE,,antibodyDetails,"antibodyId, uniprotId, targetAntigen, clonality, cloneId, reactiveSpecies, conjugate, hostOrganism",, uniprotId,The uniprotId of the antibody.,,,TRUE,,antibodyDetails,,, targetAntigen,Antigen that is targeted by antibody. (e.g. Neurofibromin 1 human),,,TRUE,,antibodyDetails,,, clonality,They type of clonality of the antibody,"Unknown, Cocktail, Control, Isotype Control, Monoclonal, Monoclonal Secondary, Polyclonal, Polyclonal Secondary, OligoClonal, Recombinant, Recombinant Monoclonal, Recombinant Monoclonal Secondary, Recombinant Polyclonal, Recombinant Polyclonal Secondary",,TRUE,,antibodyDetails,,, @@ -90,7 +90,7 @@ sex,The sex of the individual from which the resource was derived from.,"Male, F age,That age of the individual from which the resource was derived from.,,,FALSE,,donor,,, race,The ethnicity of the individual the resource was derived from.,,,FALSE,,donor,,, cellLineDetails,A cell culture selected for uniformity from a cell population derived from a usually homogeneous tissue source (such as an organ).,,"Component, cellLineId, donorId, organ, tissue, cellLineCategory, originYear, strProfile, populationDoublingTime, resistance, contaminatedMisidentified, cellLineGeneticDisorder, cellLineManifestation",FALSE,,cellLineDetails,"cellLineId, donorId, organ, tissue, cellLineCategory, originYear, strProfile, populationDoublingTime, resistance, contaminatedMisidentified, cellLineGeneticDisorder, cellLineManifestation",donor, -cellLineId,A unique identifier for the cell line.,,,TRUE,,cellLineDetails,,, +cellLineId,A unique identifier for the cell line.,,,FALSE,,cellLineDetails,,, organ,The organ the cell line is derived from.,"Biliary Tract, Bladder, Bone Marrow, Brain, Breast, Bronchial Tree, Duct, Epididymis, Esophagus, Fallopian Tube, Gallbladder, Gland, Gonad, Heart, Intestine, Kidney, Liver, Lung, Lymph Node, Ear, Eye, Nose, Tongue, Pancreas, Penis, Seminal Vesicle, Skin, Spermatic Cord, Spinal Cord, Spleen, Stomach, Thymus Gland, Tonsil, Trachea, Tracheobronchial Tree, Ureter, Urethra, Uterus, Vagina, Vulva",,FALSE,,cellLineDetails,,, tissue,The tissue the cell line is derived from.,"Blood, Bone marrow, Buccal mucosa, Buffy coat, Cerebral cortex, Dorsal root ganglion, Embryonic tissue, Meninges, Nerve tissue, Optic nerve, Plasma, Primary tumor, Sciatic nerve, Serum, Splenocyte, Unspecified, Whole brain",,FALSE,,cellLineDetails,,, cellLineCategory,The category to which the cell line belongs.,"Cancer cell line, Conditionally immortalized cell line, Embryonic stem cell, Factor-dependent cell line, Finite cell line, Hybridoma, Induced pluripotent stem cell, Somatic stem cell, Spontaneously immortalized cell line, Stromal cell line, Telomerase immortalized cell line, Transformed cell line, Undefined cell line type",,FALSE,,cellLineDetails,,, @@ -117,7 +117,7 @@ chromosome,Chromosome number of affected gene. (e.g. 11),,,FALSE,,mutationDetail mutation,(intermediary table),,"Component, mutationId, mutationDetailsId, animalModelId, cellLineId",FALSE,,mutation,"mutationId, mutationDetailsId, animalModelId, cellLineId","mutationDetails, animalModelDetails, cellLineDetails", mutationId,A unique identifier for the mutation burden of the resource.,,,FALSE,,mutation,,, animalModelDetails,"An animal sufficiently like humans in its anatomy, physiology, or response to a pathogen to be used in medical research in order to obtain results that can be extrapolated to human medicine.",,"Component, animalModelId, donorId, transplantationDonorId, animalState, backgroundStrain, backgroundSubstrain, strainNomenclature, generation, transplantationType, animalModelGeneticDisorder, animalModelOfManifestation",FALSE,,animalModelDetails,"animalModelId, donorId, animalState, backgroundStrain, backgroundSubstrain, strainNomenclature, generation, transplantationType, transplantationDonorId, animalModelGeneticDisorder, animalModelOfManifestation",donor, -animalModelId,A unique identifier for the animal model.,,,TRUE,,animalModelDetails,,, +animalModelId,A unique identifier for the animal model.,,,FALSE,,animalModelDetails,,, animalState,"State the animal is in according to the vendor/developer. (e.g. embryo, sperm, live)",,,FALSE,,animalModelDetails,,, backgroundStrain,"An assigned name that describes the genetic make-up (all its alleles at all loci) except the mutated gene of interest and a very small amount of other genetic material, generally from one or two other strains. Correct strain nomenclature indicates what a mutant strain’s background is.",,,FALSE,,animalModelDetails,,, backgroundSubstrain,"The substrain is a particular variety of a strain. For example, a C57BL/6 mice may have a substrain of C57BL/6J, C57BL/6Tac, or another substrain. ",,,FALSE,Sage Bionetworks,animalModelDetails,,, From 180b6e55932d4efc2d150994e5899adf981cc823 Mon Sep 17 00:00:00 2001 From: "nf-osi[bot]" Date: Thu, 26 Oct 2023 16:36:31 +0000 Subject: [PATCH 24/97] Add changes --- nf-research-tools.jsonld | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/nf-research-tools.jsonld b/nf-research-tools.jsonld index c6ed4f0e..dce66793 100644 --- a/nf-research-tools.jsonld +++ b/nf-research-tools.jsonld @@ -154,7 +154,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "geneticReagentId", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -171,7 +171,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "antibodyId", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -194,7 +194,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "cellLineId", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -217,7 +217,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "animalModelId", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { From 0ff5f9a0a3da652122fd24d70a5157b0137e831d Mon Sep 17 00:00:00 2001 From: Robert Allaway Date: Thu, 26 Oct 2023 12:28:48 -0500 Subject: [PATCH 25/97] Update nf_research_tools.rdb.model.csv --- nf_research_tools.rdb.model.csv | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/nf_research_tools.rdb.model.csv b/nf_research_tools.rdb.model.csv index 86ce76bb..d3d6f1e2 100644 --- a/nf_research_tools.rdb.model.csv +++ b/nf_research_tools.rdb.model.csv @@ -6,6 +6,10 @@ rrid,"The RRID, a standard resource identifier that will facilitate interoperabi resourceName,The “canonical” name of the resource,,,TRUE,,resource,,, synonyms,Synonyms of the resource,,,FALSE,,resource,,,list like resourceType,"Type of resource. (e.g. animal model, antibody, plasmid, etc.)","Animal Model, Cell Line, Antibody, Genetic Reagent, Biobank",,TRUE,,resource,,, +Animal Model,,,animalModelId,,,resourceType,,, +Cell Line,,,cellLineId,,,resourceType,,, +Genetic Reagent,,,geneticReagentId,,,resourceType,,, +Biobank,,,biobankId,,,resourceType,,, description,Free text description/summary/overview/purpose of the resource.,,,FALSE,,resource,,, usageRequirements,Any known restrictions on use of the resource. ,"data sharing required, non-commercial use only, re-distribution not permitted, generation of germ line transmitting chimeras not permitted, creation of functional gametes not permitted, generation of interspecies chimeras not permitted, human cloning not permitted, cannot be used for treatment purposes, IRB documentation required, special licencing restrictions (see vendor for more information), unknown",,FALSE,,resource,,,list like howToAcquire,How to acquire a particular resource. ,,,TRUE,,resource,,, From 615eceec9b3ea15c1e1fde4339351faa1dd7fdbd Mon Sep 17 00:00:00 2001 From: "nf-osi[bot]" Date: Thu, 26 Oct 2023 17:30:21 +0000 Subject: [PATCH 26/97] Add changes --- nf-research-tools.jsonld | 54 +++++++++++++++++++++++++++------------- 1 file changed, 37 insertions(+), 17 deletions(-) diff --git a/nf-research-tools.jsonld b/nf-research-tools.jsonld index dce66793..c038207f 100644 --- a/nf-research-tools.jsonld +++ b/nf-research-tools.jsonld @@ -444,6 +444,11 @@ }, "sms:displayName": "Genetic Reagent", "sms:required": "sms:false", + "sms:requiresDependency": [ + { + "@id": "bts:geneticReagentId" + } + ], "sms:validationRules": [] }, { @@ -478,6 +483,11 @@ }, "sms:displayName": "Cell Line", "sms:required": "sms:false", + "sms:requiresDependency": [ + { + "@id": "bts:cellLineId" + } + ], "sms:validationRules": [] }, { @@ -495,6 +505,11 @@ }, "sms:displayName": "Animal Model", "sms:required": "sms:false", + "sms:requiresDependency": [ + { + "@id": "bts:animalModelId" + } + ], "sms:validationRules": [] }, { @@ -512,6 +527,28 @@ }, "sms:displayName": "Biobank", "sms:required": "sms:false", + "sms:requiresDependency": [ + { + "@id": "bts:biobankId" + } + ], + "sms:validationRules": [] + }, + { + "@id": "bts:biobankId", + "@type": "rdf:Property", + "rdfs:comment": "A unique identifier for the biobank.", + "rdfs:label": "biobankId", + "schema:domainIncludes": [ + { + "@id": "bts:BiobankDetails" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "biobankId", + "sms:required": "sms:true", "sms:validationRules": [] }, { @@ -3086,23 +3123,6 @@ ], "sms:validationRules": [] }, - { - "@id": "bts:biobankId", - "@type": "rdf:Property", - "rdfs:comment": "A unique identifier for the biobank.", - "rdfs:label": "biobankId", - "schema:domainIncludes": [ - { - "@id": "bts:BiobankDetails" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "biobankId", - "sms:required": "sms:true", - "sms:validationRules": [] - }, { "@id": "bts:biobankName", "@type": "rdf:Property", From 89379110f9c2bc9edeacfcf3e6e311e909455cd7 Mon Sep 17 00:00:00 2001 From: Robert Allaway Date: Thu, 26 Oct 2023 13:12:41 -0500 Subject: [PATCH 27/97] Update nf_research_tools.rdb.model.csv --- nf_research_tools.rdb.model.csv | 12 ++++++------ 1 file changed, 6 insertions(+), 6 deletions(-) diff --git a/nf_research_tools.rdb.model.csv b/nf_research_tools.rdb.model.csv index d3d6f1e2..84d572d7 100644 --- a/nf_research_tools.rdb.model.csv +++ b/nf_research_tools.rdb.model.csv @@ -1,6 +1,6 @@ Attribute,Description,Valid Values,DependsOn,Required,Source,Parent,Properties,DependsOn Component,Validation Rules Component,Type of submitted information.,,,TRUE,,,,, -resource,"A tool used in the research process (i.e. animal model, cell line, etc.)",,"Component, resourceId, geneticReagentId, antibodyId, cellLineId, animalModelId, rrid, resourceName, synonyms, resourceType, description, usageRequirements, howToAcquire, dateAdded, dateModified",FALSE,,,"resourceId, geneticReagentId, antibodyId, cellLineId, animalModelId, rrid, resourceName, synonyms, resourceType, description, usageRequirements, howToAcquire, dateAdded, dateModified","geneticReagent, antibody, cellLine, animalModel", +resource,"A tool used in the research process (i.e. animal model, cell line, etc.)",,"Component, resourceId, geneticReagentId, antibodyId, cellLineId, animalModelId, biobankId, rrid, resourceName, synonyms, resourceType, description, usageRequirements, howToAcquire, dateAdded, dateModified",FALSE,,,"resourceId, geneticReagentId, antibodyId, cellLineId, animalModelId, biobankId, rrid, resourceName, synonyms, resourceType, description, usageRequirements, howToAcquire, dateAdded, dateModified","geneticReagent, antibody, cellLine, animalModel", resourceId,A unique identifier for the resource.,,,TRUE,,resource,,, rrid,"The RRID, a standard resource identifier that will facilitate interoperability with other databases, and is an increasingly-used identifier for publications https://scicrunch.org/resources if available",,,FALSE,,resource,,, resourceName,The “canonical” name of the resource,,,TRUE,,resource,,, @@ -11,12 +11,12 @@ Cell Line,,,cellLineId,,,resourceType,,, Genetic Reagent,,,geneticReagentId,,,resourceType,,, Biobank,,,biobankId,,,resourceType,,, description,Free text description/summary/overview/purpose of the resource.,,,FALSE,,resource,,, -usageRequirements,Any known restrictions on use of the resource. ,"data sharing required, non-commercial use only, re-distribution not permitted, generation of germ line transmitting chimeras not permitted, creation of functional gametes not permitted, generation of interspecies chimeras not permitted, human cloning not permitted, cannot be used for treatment purposes, IRB documentation required, special licencing restrictions (see vendor for more information), unknown",,FALSE,,resource,,,list like +usageRequirements,Any known restrictions on use of the resource. ,"data sharin g required, non-commercial use only, re-distribution not permitted, generation of germ line transmitting chimeras not permitted, creation of functional gametes not permitted, generation of interspecies chimeras not permitted, human cloning not permitted, cannot be used for treatment purposes, IRB documentation required, special licencing restrictions (see vendor for more information), unknown",,FALSE,,resource,,,list like howToAcquire,How to acquire a particular resource. ,,,TRUE,,resource,,, dateAdded,The date that the resource was originally added.,,,TRUE,,resource,,, dateModified,The last update of the resource metadata (not including observations).,,,TRUE,,resource,,, geneticReagentDetails,Genetic reagents.,,"Component, geneticReagentId, insertName, insertEntrezId, gRNAshRNASequence, insertSize, insertSpecies, nTerminalTag, cTerminalTag, cloningMethod, 5primeCloningSite, 5primeSiteDestroyed, 3primeCloningSite, 3primeSiteDestroyed, promoter, 5primer, 3primer, vectorBackbone, vectorType, backboneSize, totalSize, bacterialResistance, selectableMarker, copyNumber, growthTemp, growthStrain, hazardous",FALSE,,geneticReagentDetails,"geneticReagentId, insertName, insertEntrezId, gRNAshRNASequence, insertSize, insertSpecies, nTerminalTag, cTerminalTag, cloningMethod, 5primeCloningSite, 5primeSiteDestroyed, 3primeCloningSite, 3primeSiteDestroyed, promoter, 5primer, 3primer, vectorBackbone, vectorType, backboneSize, totalSize, bacterialResistance, selectableMarker, copyNumber, growthTemp, growthStrain, hazardous",, -geneticReagentId,A unique identifier for the reagent.,,,FALSE,,geneticReagentDetails,,, +geneticReagentId,A unique identifier for the reagent.,,,TRUE,,geneticReagentDetails,,, insertName,Name of the main gene insert in the plasmid.,,,TRUE,,geneticReagentDetails,,, insertEntrezId,The entrez gene id for the gene insert,,,TRUE,,geneticReagentDetails,,, gRNAshRNASequence,"The sequence of the gRNA or shRNA for the gene insert, if present. ",,,FALSE,,geneticReagentDetails,,, @@ -78,7 +78,7 @@ source,"The source of resource application information (e.g. Vendor, Community)" applications,"One or more uses for the resource (e.g. western blot, immunofluorescence)","Western Blot, Immunofluorescence, ELISA, Immunohistochemistry, Immunoprecipitation, Tumor Growth Studies, Immunohistochemistry (Paraffin-Embedded), Immunocytochemistry, Immunohistochemistry (Frozen Sections), Flow Cytometry, Affinity Purification, Microarray",,TRUE,,resourceApplication,,,list like links,shareable links related to the resource,,,FALSE,,resourceApplication,,,list antibodyDetails,"A blood protein produced in response to and counteracting a specific antigen. Antibodies combine chemically with substances which the body recognizes as alien, such as bacteria, viruses, and foreign substances in the blood.",,"Component, antibodyId, uniprotId, targetAntigen, clonality, cloneId, reactiveSpecies, conjugate, hostOrganism",FALSE,,antibodyDetails,,, -antibodyId,A unique identifier for the antibody.,,,FALSE,,antibodyDetails,"antibodyId, uniprotId, targetAntigen, clonality, cloneId, reactiveSpecies, conjugate, hostOrganism",, +antibodyId,A unique identifier for the antibody.,,,TRUE,,antibodyDetails,"antibodyId, uniprotId, targetAntigen, clonality, cloneId, reactiveSpecies, conjugate, hostOrganism",, uniprotId,The uniprotId of the antibody.,,,TRUE,,antibodyDetails,,, targetAntigen,Antigen that is targeted by antibody. (e.g. Neurofibromin 1 human),,,TRUE,,antibodyDetails,,, clonality,They type of clonality of the antibody,"Unknown, Cocktail, Control, Isotype Control, Monoclonal, Monoclonal Secondary, Polyclonal, Polyclonal Secondary, OligoClonal, Recombinant, Recombinant Monoclonal, Recombinant Monoclonal Secondary, Recombinant Polyclonal, Recombinant Polyclonal Secondary",,TRUE,,antibodyDetails,,, @@ -94,7 +94,7 @@ sex,The sex of the individual from which the resource was derived from.,"Male, F age,That age of the individual from which the resource was derived from.,,,FALSE,,donor,,, race,The ethnicity of the individual the resource was derived from.,,,FALSE,,donor,,, cellLineDetails,A cell culture selected for uniformity from a cell population derived from a usually homogeneous tissue source (such as an organ).,,"Component, cellLineId, donorId, organ, tissue, cellLineCategory, originYear, strProfile, populationDoublingTime, resistance, contaminatedMisidentified, cellLineGeneticDisorder, cellLineManifestation",FALSE,,cellLineDetails,"cellLineId, donorId, organ, tissue, cellLineCategory, originYear, strProfile, populationDoublingTime, resistance, contaminatedMisidentified, cellLineGeneticDisorder, cellLineManifestation",donor, -cellLineId,A unique identifier for the cell line.,,,FALSE,,cellLineDetails,,, +cellLineId,A unique identifier for the cell line.,,,TRUE,,cellLineDetails,,, organ,The organ the cell line is derived from.,"Biliary Tract, Bladder, Bone Marrow, Brain, Breast, Bronchial Tree, Duct, Epididymis, Esophagus, Fallopian Tube, Gallbladder, Gland, Gonad, Heart, Intestine, Kidney, Liver, Lung, Lymph Node, Ear, Eye, Nose, Tongue, Pancreas, Penis, Seminal Vesicle, Skin, Spermatic Cord, Spinal Cord, Spleen, Stomach, Thymus Gland, Tonsil, Trachea, Tracheobronchial Tree, Ureter, Urethra, Uterus, Vagina, Vulva",,FALSE,,cellLineDetails,,, tissue,The tissue the cell line is derived from.,"Blood, Bone marrow, Buccal mucosa, Buffy coat, Cerebral cortex, Dorsal root ganglion, Embryonic tissue, Meninges, Nerve tissue, Optic nerve, Plasma, Primary tumor, Sciatic nerve, Serum, Splenocyte, Unspecified, Whole brain",,FALSE,,cellLineDetails,,, cellLineCategory,The category to which the cell line belongs.,"Cancer cell line, Conditionally immortalized cell line, Embryonic stem cell, Factor-dependent cell line, Finite cell line, Hybridoma, Induced pluripotent stem cell, Somatic stem cell, Spontaneously immortalized cell line, Stromal cell line, Telomerase immortalized cell line, Transformed cell line, Undefined cell line type",,FALSE,,cellLineDetails,,, @@ -121,7 +121,7 @@ chromosome,Chromosome number of affected gene. (e.g. 11),,,FALSE,,mutationDetail mutation,(intermediary table),,"Component, mutationId, mutationDetailsId, animalModelId, cellLineId",FALSE,,mutation,"mutationId, mutationDetailsId, animalModelId, cellLineId","mutationDetails, animalModelDetails, cellLineDetails", mutationId,A unique identifier for the mutation burden of the resource.,,,FALSE,,mutation,,, animalModelDetails,"An animal sufficiently like humans in its anatomy, physiology, or response to a pathogen to be used in medical research in order to obtain results that can be extrapolated to human medicine.",,"Component, animalModelId, donorId, transplantationDonorId, animalState, backgroundStrain, backgroundSubstrain, strainNomenclature, generation, transplantationType, animalModelGeneticDisorder, animalModelOfManifestation",FALSE,,animalModelDetails,"animalModelId, donorId, animalState, backgroundStrain, backgroundSubstrain, strainNomenclature, generation, transplantationType, transplantationDonorId, animalModelGeneticDisorder, animalModelOfManifestation",donor, -animalModelId,A unique identifier for the animal model.,,,FALSE,,animalModelDetails,,, +animalModelId,A unique identifier for the animal model.,,,TRUE,,animalModelDetails,,, animalState,"State the animal is in according to the vendor/developer. (e.g. embryo, sperm, live)",,,FALSE,,animalModelDetails,,, backgroundStrain,"An assigned name that describes the genetic make-up (all its alleles at all loci) except the mutated gene of interest and a very small amount of other genetic material, generally from one or two other strains. Correct strain nomenclature indicates what a mutant strain’s background is.",,,FALSE,,animalModelDetails,,, backgroundSubstrain,"The substrain is a particular variety of a strain. For example, a C57BL/6 mice may have a substrain of C57BL/6J, C57BL/6Tac, or another substrain. ",,,FALSE,Sage Bionetworks,animalModelDetails,,, From 20fb02682a52ccaefc40da4204dd750c5a4b61fb Mon Sep 17 00:00:00 2001 From: "nf-osi[bot]" Date: Thu, 26 Oct 2023 18:14:24 +0000 Subject: [PATCH 28/97] Add changes --- nf-research-tools.jsonld | 50 ++++++++++++++++++++++------------------ 1 file changed, 28 insertions(+), 22 deletions(-) diff --git a/nf-research-tools.jsonld b/nf-research-tools.jsonld index c038207f..2ac9e2b3 100644 --- a/nf-research-tools.jsonld +++ b/nf-research-tools.jsonld @@ -72,6 +72,9 @@ { "@id": "bts:animalModelId" }, + { + "@id": "bts:biobankId" + }, { "@id": "bts:rrid" }, @@ -154,7 +157,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "geneticReagentId", - "sms:required": "sms:false", + "sms:required": "sms:true", "sms:validationRules": [] }, { @@ -171,7 +174,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "antibodyId", - "sms:required": "sms:false", + "sms:required": "sms:true", "sms:validationRules": [] }, { @@ -194,7 +197,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "cellLineId", - "sms:required": "sms:false", + "sms:required": "sms:true", "sms:validationRules": [] }, { @@ -217,7 +220,27 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "animalModelId", - "sms:required": "sms:false", + "sms:required": "sms:true", + "sms:validationRules": [] + }, + { + "@id": "bts:biobankId", + "@type": "rdf:Property", + "rdfs:comment": "A unique identifier for the biobank.", + "rdfs:label": "biobankId", + "schema:domainIncludes": [ + { + "@id": "bts:Resource" + }, + { + "@id": "bts:BiobankDetails" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "biobankId", + "sms:required": "sms:true", "sms:validationRules": [] }, { @@ -534,23 +557,6 @@ ], "sms:validationRules": [] }, - { - "@id": "bts:biobankId", - "@type": "rdf:Property", - "rdfs:comment": "A unique identifier for the biobank.", - "rdfs:label": "biobankId", - "schema:domainIncludes": [ - { - "@id": "bts:BiobankDetails" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "biobankId", - "sms:required": "sms:true", - "sms:validationRules": [] - }, { "@id": "bts:Datasharingrequired", "@type": "rdfs:Class", @@ -564,7 +570,7 @@ "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "data sharing required", + "sms:displayName": "data sharin g required", "sms:required": "sms:false", "sms:validationRules": [] }, From 924199620b2190cd602444f8dee7bb6fe74e2999 Mon Sep 17 00:00:00 2001 From: Robert Allaway Date: Thu, 26 Oct 2023 13:19:59 -0500 Subject: [PATCH 29/97] fix extra space --- nf_research_tools.rdb.model.csv | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/nf_research_tools.rdb.model.csv b/nf_research_tools.rdb.model.csv index 84d572d7..d900d8a9 100644 --- a/nf_research_tools.rdb.model.csv +++ b/nf_research_tools.rdb.model.csv @@ -11,7 +11,7 @@ Cell Line,,,cellLineId,,,resourceType,,, Genetic Reagent,,,geneticReagentId,,,resourceType,,, Biobank,,,biobankId,,,resourceType,,, description,Free text description/summary/overview/purpose of the resource.,,,FALSE,,resource,,, -usageRequirements,Any known restrictions on use of the resource. ,"data sharin g required, non-commercial use only, re-distribution not permitted, generation of germ line transmitting chimeras not permitted, creation of functional gametes not permitted, generation of interspecies chimeras not permitted, human cloning not permitted, cannot be used for treatment purposes, IRB documentation required, special licencing restrictions (see vendor for more information), unknown",,FALSE,,resource,,,list like +usageRequirements,Any known restrictions on use of the resource. ,"data sharing required, non-commercial use only, re-distribution not permitted, generation of germ line transmitting chimeras not permitted, creation of functional gametes not permitted, generation of interspecies chimeras not permitted, human cloning not permitted, cannot be used for treatment purposes, IRB documentation required, special licencing restrictions (see vendor for more information), unknown",,FALSE,,resource,,,list like howToAcquire,How to acquire a particular resource. ,,,TRUE,,resource,,, dateAdded,The date that the resource was originally added.,,,TRUE,,resource,,, dateModified,The last update of the resource metadata (not including observations).,,,TRUE,,resource,,, From 53fb9e6427cd37cc4a32ef3321db5ae33e3c7e8b Mon Sep 17 00:00:00 2001 From: "nf-osi[bot]" Date: Thu, 26 Oct 2023 18:22:52 +0000 Subject: [PATCH 30/97] Add changes --- nf-research-tools.jsonld | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/nf-research-tools.jsonld b/nf-research-tools.jsonld index 2ac9e2b3..4dd97a34 100644 --- a/nf-research-tools.jsonld +++ b/nf-research-tools.jsonld @@ -570,7 +570,7 @@ "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "data sharin g required", + "sms:displayName": "data sharing required", "sms:required": "sms:false", "sms:validationRules": [] }, From c8325f2f93fcb71cbd1f3ce1bd2de5b292fecb68 Mon Sep 17 00:00:00 2001 From: Robert Allaway Date: Thu, 26 Oct 2023 13:27:51 -0500 Subject: [PATCH 31/97] Update nf_research_tools.rdb.model.csv --- nf_research_tools.rdb.model.csv | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/nf_research_tools.rdb.model.csv b/nf_research_tools.rdb.model.csv index d900d8a9..8177424a 100644 --- a/nf_research_tools.rdb.model.csv +++ b/nf_research_tools.rdb.model.csv @@ -1,6 +1,6 @@ Attribute,Description,Valid Values,DependsOn,Required,Source,Parent,Properties,DependsOn Component,Validation Rules Component,Type of submitted information.,,,TRUE,,,,, -resource,"A tool used in the research process (i.e. animal model, cell line, etc.)",,"Component, resourceId, geneticReagentId, antibodyId, cellLineId, animalModelId, biobankId, rrid, resourceName, synonyms, resourceType, description, usageRequirements, howToAcquire, dateAdded, dateModified",FALSE,,,"resourceId, geneticReagentId, antibodyId, cellLineId, animalModelId, biobankId, rrid, resourceName, synonyms, resourceType, description, usageRequirements, howToAcquire, dateAdded, dateModified","geneticReagent, antibody, cellLine, animalModel", +resource,"A tool used in the research process (i.e. animal model, cell line, etc.)",,"Component, resourceId, rrid, resourceName, synonyms, resourceType, description, usageRequirements, howToAcquire, dateAdded, dateModified",FALSE,,,"resourceId, rrid, resourceName, synonyms, resourceType, description, usageRequirements, howToAcquire, dateAdded, dateModified","geneticReagent, antibody, cellLine, animalModel", resourceId,A unique identifier for the resource.,,,TRUE,,resource,,, rrid,"The RRID, a standard resource identifier that will facilitate interoperability with other databases, and is an increasingly-used identifier for publications https://scicrunch.org/resources if available",,,FALSE,,resource,,, resourceName,The “canonical” name of the resource,,,TRUE,,resource,,, From fed2c30376d7cd339b89c677fe05e5b6ff085ee4 Mon Sep 17 00:00:00 2001 From: "nf-osi[bot]" Date: Thu, 26 Oct 2023 18:30:06 +0000 Subject: [PATCH 32/97] Add changes --- nf-research-tools.jsonld | 209 +++++++++++++++++---------------------- 1 file changed, 91 insertions(+), 118 deletions(-) diff --git a/nf-research-tools.jsonld b/nf-research-tools.jsonld index 4dd97a34..c4099add 100644 --- a/nf-research-tools.jsonld +++ b/nf-research-tools.jsonld @@ -60,21 +60,6 @@ { "@id": "bts:resourceId" }, - { - "@id": "bts:geneticReagentId" - }, - { - "@id": "bts:antibodyId" - }, - { - "@id": "bts:cellLineId" - }, - { - "@id": "bts:animalModelId" - }, - { - "@id": "bts:biobankId" - }, { "@id": "bts:rrid" }, @@ -140,109 +125,6 @@ "sms:required": "sms:true", "sms:validationRules": [] }, - { - "@id": "bts:geneticReagentId", - "@type": "rdf:Property", - "rdfs:comment": "A unique identifier for the reagent.", - "rdfs:label": "geneticReagentId", - "schema:domainIncludes": [ - { - "@id": "bts:Resource" - }, - { - "@id": "bts:GeneticReagentDetails" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "geneticReagentId", - "sms:required": "sms:true", - "sms:validationRules": [] - }, - { - "@id": "bts:antibodyId", - "@type": "rdf:Property", - "rdfs:comment": "A unique identifier for the antibody.", - "rdfs:label": "antibodyId", - "schema:domainIncludes": [ - { - "@id": "bts:Resource" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "antibodyId", - "sms:required": "sms:true", - "sms:validationRules": [] - }, - { - "@id": "bts:cellLineId", - "@type": "rdf:Property", - "rdfs:comment": "A unique identifier for the cell line.", - "rdfs:label": "cellLineId", - "schema:domainIncludes": [ - { - "@id": "bts:Resource" - }, - { - "@id": "bts:CellLineDetails" - }, - { - "@id": "bts:Mutation" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "cellLineId", - "sms:required": "sms:true", - "sms:validationRules": [] - }, - { - "@id": "bts:animalModelId", - "@type": "rdf:Property", - "rdfs:comment": "A unique identifier for the animal model.", - "rdfs:label": "animalModelId", - "schema:domainIncludes": [ - { - "@id": "bts:Resource" - }, - { - "@id": "bts:Mutation" - }, - { - "@id": "bts:AnimalModelDetails" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "animalModelId", - "sms:required": "sms:true", - "sms:validationRules": [] - }, - { - "@id": "bts:biobankId", - "@type": "rdf:Property", - "rdfs:comment": "A unique identifier for the biobank.", - "rdfs:label": "biobankId", - "schema:domainIncludes": [ - { - "@id": "bts:Resource" - }, - { - "@id": "bts:BiobankDetails" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "biobankId", - "sms:required": "sms:true", - "sms:validationRules": [] - }, { "@id": "bts:rrid", "@type": "rdf:Property", @@ -557,6 +439,80 @@ ], "sms:validationRules": [] }, + { + "@id": "bts:animalModelId", + "@type": "rdf:Property", + "rdfs:comment": "A unique identifier for the animal model.", + "rdfs:label": "animalModelId", + "schema:domainIncludes": [ + { + "@id": "bts:Mutation" + }, + { + "@id": "bts:AnimalModelDetails" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "animalModelId", + "sms:required": "sms:true", + "sms:validationRules": [] + }, + { + "@id": "bts:cellLineId", + "@type": "rdf:Property", + "rdfs:comment": "A unique identifier for the cell line.", + "rdfs:label": "cellLineId", + "schema:domainIncludes": [ + { + "@id": "bts:CellLineDetails" + }, + { + "@id": "bts:Mutation" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "cellLineId", + "sms:required": "sms:true", + "sms:validationRules": [] + }, + { + "@id": "bts:geneticReagentId", + "@type": "rdf:Property", + "rdfs:comment": "A unique identifier for the reagent.", + "rdfs:label": "geneticReagentId", + "schema:domainIncludes": [ + { + "@id": "bts:GeneticReagentDetails" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "geneticReagentId", + "sms:required": "sms:true", + "sms:validationRules": [] + }, + { + "@id": "bts:biobankId", + "@type": "rdf:Property", + "rdfs:comment": "A unique identifier for the biobank.", + "rdfs:label": "biobankId", + "schema:domainIncludes": [ + { + "@id": "bts:BiobankDetails" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "biobankId", + "sms:required": "sms:true", + "sms:validationRules": [] + }, { "@id": "bts:Datasharingrequired", "@type": "rdfs:Class", @@ -5860,6 +5816,23 @@ ], "sms:validationRules": [] }, + { + "@id": "bts:antibodyId", + "@type": "rdfs:Class", + "rdfs:comment": "A unique identifier for the antibody.", + "rdfs:label": "antibodyId", + "rdfs:subClassOf": [ + { + "@id": "bts:AntibodyDetails" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "antibodyId", + "sms:required": "sms:true", + "sms:validationRules": [] + }, { "@id": "bts:uniprotId", "@type": "rdf:Property", From 679e900e72eabcfc216a853b02a622f56b52c3c4 Mon Sep 17 00:00:00 2001 From: Robert Allaway Date: Thu, 26 Oct 2023 13:32:05 -0500 Subject: [PATCH 33/97] Update nf_research_tools.rdb.model.csv --- nf_research_tools.rdb.model.csv | 1 + 1 file changed, 1 insertion(+) diff --git a/nf_research_tools.rdb.model.csv b/nf_research_tools.rdb.model.csv index 8177424a..a6ed1218 100644 --- a/nf_research_tools.rdb.model.csv +++ b/nf_research_tools.rdb.model.csv @@ -9,6 +9,7 @@ resourceType,"Type of resource. (e.g. animal model, antibody, plasmid, etc.)","A Animal Model,,,animalModelId,,,resourceType,,, Cell Line,,,cellLineId,,,resourceType,,, Genetic Reagent,,,geneticReagentId,,,resourceType,,, +Antibody,,,antibodyId,,,resourceType,,, Biobank,,,biobankId,,,resourceType,,, description,Free text description/summary/overview/purpose of the resource.,,,FALSE,,resource,,, usageRequirements,Any known restrictions on use of the resource. ,"data sharing required, non-commercial use only, re-distribution not permitted, generation of germ line transmitting chimeras not permitted, creation of functional gametes not permitted, generation of interspecies chimeras not permitted, human cloning not permitted, cannot be used for treatment purposes, IRB documentation required, special licencing restrictions (see vendor for more information), unknown",,FALSE,,resource,,,list like From 8c87309188c964446692891372f69774bace2574 Mon Sep 17 00:00:00 2001 From: "nf-osi[bot]" Date: Thu, 26 Oct 2023 18:33:57 +0000 Subject: [PATCH 34/97] Add changes --- nf-research-tools.jsonld | 39 ++++++++++++++++++++++----------------- 1 file changed, 22 insertions(+), 17 deletions(-) diff --git a/nf-research-tools.jsonld b/nf-research-tools.jsonld index c4099add..42521628 100644 --- a/nf-research-tools.jsonld +++ b/nf-research-tools.jsonld @@ -371,6 +371,11 @@ }, "sms:displayName": "Antibody", "sms:required": "sms:false", + "sms:requiresDependency": [ + { + "@id": "bts:antibodyId" + } + ], "sms:validationRules": [] }, { @@ -496,6 +501,23 @@ "sms:required": "sms:true", "sms:validationRules": [] }, + { + "@id": "bts:antibodyId", + "@type": "rdfs:Class", + "rdfs:comment": "A unique identifier for the antibody.", + "rdfs:label": "antibodyId", + "rdfs:subClassOf": [ + { + "@id": "bts:AntibodyDetails" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "antibodyId", + "sms:required": "sms:true", + "sms:validationRules": [] + }, { "@id": "bts:biobankId", "@type": "rdf:Property", @@ -5816,23 +5838,6 @@ ], "sms:validationRules": [] }, - { - "@id": "bts:antibodyId", - "@type": "rdfs:Class", - "rdfs:comment": "A unique identifier for the antibody.", - "rdfs:label": "antibodyId", - "rdfs:subClassOf": [ - { - "@id": "bts:AntibodyDetails" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "antibodyId", - "sms:required": "sms:true", - "sms:validationRules": [] - }, { "@id": "bts:uniprotId", "@type": "rdf:Property", From 50abb57805ec4a1ffcc2c4ff8a525aa48a5de1f0 Mon Sep 17 00:00:00 2001 From: Robert Allaway Date: Thu, 26 Oct 2023 13:43:07 -0500 Subject: [PATCH 35/97] set requirement for insertEntrezId to false --- nf_research_tools.rdb.model.csv | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/nf_research_tools.rdb.model.csv b/nf_research_tools.rdb.model.csv index a6ed1218..b3925a48 100644 --- a/nf_research_tools.rdb.model.csv +++ b/nf_research_tools.rdb.model.csv @@ -19,7 +19,7 @@ dateModified,The last update of the resource metadata (not including observation geneticReagentDetails,Genetic reagents.,,"Component, geneticReagentId, insertName, insertEntrezId, gRNAshRNASequence, insertSize, insertSpecies, nTerminalTag, cTerminalTag, cloningMethod, 5primeCloningSite, 5primeSiteDestroyed, 3primeCloningSite, 3primeSiteDestroyed, promoter, 5primer, 3primer, vectorBackbone, vectorType, backboneSize, totalSize, bacterialResistance, selectableMarker, copyNumber, growthTemp, growthStrain, hazardous",FALSE,,geneticReagentDetails,"geneticReagentId, insertName, insertEntrezId, gRNAshRNASequence, insertSize, insertSpecies, nTerminalTag, cTerminalTag, cloningMethod, 5primeCloningSite, 5primeSiteDestroyed, 3primeCloningSite, 3primeSiteDestroyed, promoter, 5primer, 3primer, vectorBackbone, vectorType, backboneSize, totalSize, bacterialResistance, selectableMarker, copyNumber, growthTemp, growthStrain, hazardous",, geneticReagentId,A unique identifier for the reagent.,,,TRUE,,geneticReagentDetails,,, insertName,Name of the main gene insert in the plasmid.,,,TRUE,,geneticReagentDetails,,, -insertEntrezId,The entrez gene id for the gene insert,,,TRUE,,geneticReagentDetails,,, +insertEntrezId,The entrez gene id for the gene insert,,,FALSE,,geneticReagentDetails,,, gRNAshRNASequence,"The sequence of the gRNA or shRNA for the gene insert, if present. ",,,FALSE,,geneticReagentDetails,,, insertSize,"Size, in bp, of the gene insert as it is in the plasmid.",,,FALSE,,geneticReagentDetails,,, insertSpecies,Species of the insert,"Homo sapiens, Mus musculus, Rattus norvegicus",,TRUE,,geneticReagentDetails,,,list like From 2eecad9732ce7ff4762ee1020a5db31113544260 Mon Sep 17 00:00:00 2001 From: "nf-osi[bot]" Date: Thu, 26 Oct 2023 18:45:30 +0000 Subject: [PATCH 36/97] Add changes --- nf-research-tools.jsonld | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/nf-research-tools.jsonld b/nf-research-tools.jsonld index 42521628..b64d33c0 100644 --- a/nf-research-tools.jsonld +++ b/nf-research-tools.jsonld @@ -874,7 +874,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "insertEntrezId", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { From 5f8a67c49fa8da02c7fd03da900da443f4252188 Mon Sep 17 00:00:00 2001 From: Robert Allaway Date: Thu, 26 Oct 2023 13:48:39 -0500 Subject: [PATCH 37/97] Switch more list -> list like validation --- nf_research_tools.rdb.model.csv | 16 ++++++++-------- 1 file changed, 8 insertions(+), 8 deletions(-) diff --git a/nf_research_tools.rdb.model.csv b/nf_research_tools.rdb.model.csv index b3925a48..83edb8ee 100644 --- a/nf_research_tools.rdb.model.csv +++ b/nf_research_tools.rdb.model.csv @@ -84,7 +84,7 @@ uniprotId,The uniprotId of the antibody.,,,TRUE,,antibodyDetails,,, targetAntigen,Antigen that is targeted by antibody. (e.g. Neurofibromin 1 human),,,TRUE,,antibodyDetails,,, clonality,They type of clonality of the antibody,"Unknown, Cocktail, Control, Isotype Control, Monoclonal, Monoclonal Secondary, Polyclonal, Polyclonal Secondary, OligoClonal, Recombinant, Recombinant Monoclonal, Recombinant Monoclonal Secondary, Recombinant Polyclonal, Recombinant Polyclonal Secondary",,TRUE,,antibodyDetails,,, cloneId,Identification of clone (e.g. 2D1),,,FALSE,,antibodyDetails,,, -reactiveSpecies,Species the antibody has been shown to crossreact with the target protein. ,"Avian, Bovine, Canine, Chicken, Cow, Dog, Donkey, Feline, Fish, Guinea pig, Hamster, Human, Monkey, Mouse, Non-human primate, Other, Pig, Porcine, Rabbit, Rat, Rodent, Sheep, Simian, Zebrafish",,TRUE,,antibodyDetails,,,list +reactiveSpecies,Species the antibody has been shown to crossreact with the target protein. ,"Avian, Bovine, Canine, Chicken, Cow, Dog, Donkey, Feline, Fish, Guinea pig, Hamster, Human, Monkey, Mouse, Non-human primate, Other, Pig, Porcine, Rabbit, Rat, Rodent, Sheep, Simian, Zebrafish",,TRUE,,antibodyDetails,,,list like conjugate,Is the antibody conjugated or nonconjugated,"Conjugated, Nonconjugated",,TRUE,,antibodyDetails,,, hostOrganism,The species of the organism that hosts the antibody,"Mouse, Rabbit",,TRUE,,antibodyDetails,,, donor,"A person, animal, etc. who is the contributor of the resource.",,"Component, donorId, parentDonorId, transplantationDonorId, species, sex, age, race",FALSE,,donor,"donorId, parentDonorId, transplantationDonorId, species, sex, age, race",, @@ -102,16 +102,16 @@ cellLineCategory,The category to which the cell line belongs.,"Cancer cell line, originYear,The year the cell line orginated.,,,FALSE,,cellLineDetails,,, strProfile,Short tandem repeat profile information.,,,FALSE,,cellLineDetails,,, populationDoublingTime,Time for cell line to double,,,FALSE,,cellLineDetails,,, -resistance,List of compounds if a cell line has been selected for.,,,FALSE,,cellLineDetails,,,list +resistance,List of compounds if a cell line has been selected for.,,,FALSE,,cellLineDetails,,,list like contaminatedMisidentified,If a cell line has been contaminated or misidentified,,,FALSE,,cellLineDetails,,, -cellLineGeneticDisorder,"Genetic diseases are diseases in which inherited genes predispose to increased risk. The genetic disorders associated with cancer often result from an alteration or mutation in a single gene. The diseases range from rare dominant cancer family syndrome to familial tendencies in which low-penetrance genes may interact with other genes or environmental factors to induce cancer. Research may involve clinical, epidemiologic, and laboratory studies of persons, families, and populations at high risk of these disorders. [ NCI ]","Neurofibromatosis type 1, Neurofibromatosis type 2, Schwannomatosis, No known disease",,FALSE,http://purl.obolibrary.org/obo/NCIT_C3101,cellLineDetails,,,list -cellLineManifestation,"Manifestations/symptoms that this resource is used to model (e.g. tumor type, behavioral phenotype, etc.)",,,FALSE,,cellLineDetails,,,list +cellLineGeneticDisorder,"Genetic diseases are diseases in which inherited genes predispose to increased risk. The genetic disorders associated with cancer often result from an alteration or mutation in a single gene. The diseases range from rare dominant cancer family syndrome to familial tendencies in which low-penetrance genes may interact with other genes or environmental factors to induce cancer. Research may involve clinical, epidemiologic, and laboratory studies of persons, families, and populations at high risk of these disorders. [ NCI ]","Neurofibromatosis type 1, Neurofibromatosis type 2, Schwannomatosis, No known disease",,FALSE,http://purl.obolibrary.org/obo/NCIT_C3101,cellLineDetails,,,list like +cellLineManifestation,"Manifestations/symptoms that this resource is used to model (e.g. tumor type, behavioral phenotype, etc.)",,,FALSE,,cellLineDetails,,,list like mutationDetails,"The changing of the structure of a gene, resulting in a variant form that may be transmitted to subsequent generations",,"Component, mutationDetailsId, externalMutationID, alleleType, mutationType, mutationMethod, affectedGeneSymbol, affectedGeneName, sequenceVariation, proteinVariation, animalModelMutation, humanClinVarMutation, chromosome",FALSE,,mutationDetails,"mutationDetailsId, externalMutationID, alleleType, mutationType, mutationMethod, affectedGeneSymbol, affectedGeneName, sequenceVariation, proteinVariation, animalModelMutation, humanClinVarMutation, chromosome",, mutationDetailsId,A unique identifier for mutation.,,,FALSE,,mutationDetails,,, externalMutationID,"An identifier from an organism database such as MGI or other curated variant resource, if available. ",,,FALSE,,mutationDetails,,, -mutationType,"The type of the mutation, vocabulary aligned with MGI mutation types. ","Disruption caused by insertion of vector, Duplication, Insertion, Insertion of gene trap vector, Intergenic deletion, Intragenic deletion, Inversion, Loss of heterozygosity (unspecified mechanism), Not Applicable, Not Specified, Nucleotide repeat expansion, Nucleotide substitutions, Other, Single point mutation, Translocation, Transposon insertion, Undefined, Viral insertion",,FALSE,,mutationDetails,,,list -mutationMethod,"The method used to alter the resource, vocabulary aligned with and expanded upon MGI allele origin types. ","Chemically induced (ENU), Chemically induced (other), Chemically and radiation induced, Endonuclease-mediated (CRISPR), Endonuclease-mediated (TALEN), Gene trapped, QTL, Radiation induced, Spontaneous, Targeted, Transgenic, Transposon induced",,FALSE,,mutationDetails,,,list -alleleType,"The type of genetic alteration of the resource, vocabulary aligned with MGI allele subtypes. ","Conditional ready, Constitutively active, Dominant negative, Humanized sequence, Hypomorph, Inducible, Inserted expressed sequence, Knockdown, Modified isoform(s), No functional change, Null/knockout, Recombinase, Reporter, RMCE-Ready, Transactivator, Transposase, Transposon concatemer",,FALSE,,mutationDetails,,,list +mutationType,"The type of the mutation, vocabulary aligned with MGI mutation types. ","Disruption caused by insertion of vector, Duplication, Insertion, Insertion of gene trap vector, Intergenic deletion, Intragenic deletion, Inversion, Loss of heterozygosity (unspecified mechanism), Not Applicable, Not Specified, Nucleotide repeat expansion, Nucleotide substitutions, Other, Single point mutation, Translocation, Transposon insertion, Undefined, Viral insertion",,FALSE,,mutationDetails,,,list like +mutationMethod,"The method used to alter the resource, vocabulary aligned with and expanded upon MGI allele origin types. ","Chemically induced (ENU), Chemically induced (other), Chemically and radiation induced, Endonuclease-mediated (CRISPR), Endonuclease-mediated (TALEN), Gene trapped, QTL, Radiation induced, Spontaneous, Targeted, Transgenic, Transposon induced",,FALSE,,mutationDetails,,,list like +alleleType,"The type of genetic alteration of the resource, vocabulary aligned with MGI allele subtypes. ","Conditional ready, Constitutively active, Dominant negative, Humanized sequence, Hypomorph, Inducible, Inserted expressed sequence, Knockdown, Modified isoform(s), No functional change, Null/knockout, Recombinase, Reporter, RMCE-Ready, Transactivator, Transposase, Transposon concatemer",,FALSE,,mutationDetails,,,list like affectedGeneSymbol,"The gene symbol for the mutated gene. (e.g. NF1, SUZ12, SMARCB1, P53, etc.)",,,FALSE,,mutationDetails,,, affectedGeneName,Gene name for the affected gene (e.g. neurofibromin 1),,,FALSE,,mutationDetails,,, sequenceVariation,Important sequence variations (e.g. g.123_127del). See http://varnomen.hgvs.org/ for the sequence variation nomenclature. ,,,FALSE,http://varnomen.hgvs.org/,mutationDetails,,, @@ -131,7 +131,7 @@ generation,The generation of the animal model. (e.g. 13),,,FALSE,,animalModelDet transplantationType,"Type of transplantation involved in the experiment, derived from MESH","allograft, xenograft, autograft, isograft",,FALSE,,animalModelDetails,,, transplantationDonorId,The donor indentifier number for the transplantion donor. ,,donorId,FALSE,,animalModelDetails,,, animalModelGeneticDisorder,"Genetic diseases are diseases in which inherited genes predispose to increased risk. The genetic disorders associated with cancer often result from an alteration or mutation in a single gene. The diseases range from rare dominant cancer family syndrome to familial tendencies in which low-penetrance genes may interact with other genes or environmental factors to induce cancer. Research may involve clinical, epidemiologic, and laboratory studies of persons, families, and populations at high risk of these disorders. [ NCI ]","Neurofibromatosis type 1, Neurofibromatosis type 2, Schwannomatosis, No known disease",,TRUE,http://purl.obolibrary.org/obo/NCIT_C3101,animalModelDetails,,,list -animalModelOfManifestation,"Manifestations/symptoms that this resource is used to model (e.g. tumor type, behavioral phenotype, etc.) ",,,TRUE,,animalModelDetails,,,list +animalModelOfManifestation,"Manifestations/symptoms that this resource is used to model (e.g. tumor type, behavioral phenotype, etc.) ",,,TRUE,,animalModelDetails,,,list like development,"resourceId, investigatorId, publicationId, funderId (intermediary table)",,"Component, developmentId, resourceId, investigatorId, publicationId, funderId",FALSE,,development,"developmentId, resourceId, investigatorId, publicationId, funderId","resource, investigator, publication, funder", developmentId,A unique identifier for the development of the resource.,,,TRUE,,development,,, funder,A person or organization that provides money for a particular resource.,,"Component, funderId, funderName",FALSE,,funder,"funderId, funderName",, From 4b7cc9ad6c4dac466688f7b77c41105faa4a0274 Mon Sep 17 00:00:00 2001 From: "nf-osi[bot]" Date: Thu, 26 Oct 2023 18:50:17 +0000 Subject: [PATCH 38/97] Add changes --- nf-research-tools.jsonld | 16 ++++++++-------- 1 file changed, 8 insertions(+), 8 deletions(-) diff --git a/nf-research-tools.jsonld b/nf-research-tools.jsonld index b64d33c0..7cb94a3e 100644 --- a/nf-research-tools.jsonld +++ b/nf-research-tools.jsonld @@ -6040,7 +6040,7 @@ "sms:displayName": "reactiveSpecies", "sms:required": "sms:true", "sms:validationRules": [ - "list" + "list like" ] }, { @@ -7549,7 +7549,7 @@ "sms:displayName": "resistance", "sms:required": "sms:false", "sms:validationRules": [ - "list" + "list like" ] }, { @@ -7599,7 +7599,7 @@ "sms:displayName": "cellLineGeneticDisorder", "sms:required": "sms:false", "sms:validationRules": [ - "list" + "list like" ] }, { @@ -7618,7 +7618,7 @@ "sms:displayName": "cellLineManifestation", "sms:required": "sms:false", "sms:validationRules": [ - "list" + "list like" ] }, { @@ -8927,7 +8927,7 @@ "sms:displayName": "alleleType", "sms:required": "sms:false", "sms:validationRules": [ - "list" + "list like" ] }, { @@ -9002,7 +9002,7 @@ "sms:displayName": "mutationType", "sms:required": "sms:false", "sms:validationRules": [ - "list" + "list like" ] }, { @@ -9059,7 +9059,7 @@ "sms:displayName": "mutationMethod", "sms:required": "sms:false", "sms:validationRules": [ - "list" + "list like" ] }, { @@ -10250,7 +10250,7 @@ "sms:displayName": "animalModelOfManifestation", "sms:required": "sms:true", "sms:validationRules": [ - "list" + "list like" ] }, { From cffe50452812762af5c98cbecd7ec88cf2fc48f4 Mon Sep 17 00:00:00 2001 From: Robert Allaway Date: Thu, 26 Oct 2023 13:55:44 -0500 Subject: [PATCH 39/97] update biobank valid values --- nf_research_tools.rdb.model.csv | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/nf_research_tools.rdb.model.csv b/nf_research_tools.rdb.model.csv index 83edb8ee..f1bcb9b9 100644 --- a/nf_research_tools.rdb.model.csv +++ b/nf_research_tools.rdb.model.csv @@ -57,10 +57,10 @@ biobankId,A unique identifier for the biobank.,,,TRUE,,biobankDetails,,, biobankURL,A URL for the biobank landing page.,,,TRUE,,biobankDetails,,, specimenType,The types of specimens that are banked.,"human tissue, xenograft tumors, cell lines",,TRUE,,biobankDetails,,,list like specimenTissueType,The types of tissues that are banked.,"blood, tumor, cerebrospinal fluid, nerve, skin, bone, brain",,TRUE,,biobankDetails,,,list like -tumorType,"The types of tumors that are banked, if applicable.","cutaneous neurofibroma, plexiform neurofibroma, schwannoma, meningioma, malignant peripheral nerve sheath tumor, low grade glioma, high grade glioma, pheochromocytoma, optic nerve glioma, atypical neurofibroma, neurofibroma NOS, diffuse infiltrating neurofibroma, brain NOS",,TRUE,,biobankDetails,,,list like +tumorType,"The types of tumors that are banked, if applicable.","cutaneous neurofibroma, plexiform neurofibroma, atypical neurofibroma, schwannoma, meningioma, malignant peripheral nerve sheath tumor, low grade glioma, high grade glioma, pheochromocytoma, optic nerve glioma, atypical neurofibroma, neurofibroma NOS, diffuse infiltrating neurofibroma, brain NOS, other",,TRUE,,biobankDetails,,,list like diseaseType,"The diseases of the banked specimens, if applicable.","Neurofibromatosis type 1, Neurofibromatosis type 2, Schwannomatosis",,TRUE,,biobankDetails,,,list like specimenPreparationMethod,The preservation methods used by the biobank.,"Fresh collected, Flash frozen, FFPE, Cryopreserved, OCT, RNA later, Formalin-fixed, Ethanol",,TRUE,,biobankDetails,,,list like -specimenFormat,How the specimens have been processed in preparation for distribution.,"whole tumor, slide, whole cell lysate, DNA, RNA",,TRUE,,biobankDetails,,,list like +specimenFormat,How the specimens have been processed in preparation for distribution.,"whole tumor, slide, cells, whole cell lysate, DNA, RNA",,TRUE,,biobankDetails,,,list like observation,"A remark, statement, or comment based on the resource.",,"Component, observationId, resourceId, publicationId, observationSubmitterName, synapseId, observationText, observationType, observationPhase, observationTime, observationTimeUnits, reliabilityRating, easeOfUseRating, observationLink",FALSE,,observation,"observationId, resourceId, publicationId, observationSubmitterName, synapseId, observationText, observationType, observationPhase, observationTime, observationTimeUnits, reliabilityRating, easeOfUseRating, observationLink","resource, investigator, publication", observationId,A unique identifier for the observation.,,,TRUE,,observation,,, observationSubmitterName,The name of the person submitting the observation. ,,,TRUE,,observation,,, From b01d7b8ed22abb50ea66a39bb4dd710440638303 Mon Sep 17 00:00:00 2001 From: "nf-osi[bot]" Date: Thu, 26 Oct 2023 18:58:10 +0000 Subject: [PATCH 40/97] Add changes --- nf-research-tools.jsonld | 68 +++++++++++++++++++++++++++------------- 1 file changed, 47 insertions(+), 21 deletions(-) diff --git a/nf-research-tools.jsonld b/nf-research-tools.jsonld index 7cb94a3e..5ea323ae 100644 --- a/nf-research-tools.jsonld +++ b/nf-research-tools.jsonld @@ -2114,6 +2114,9 @@ { "@id": "bts:selectableMarker" }, + { + "@id": "bts:tumorType" + }, { "@id": "bts:reactiveSpecies" }, @@ -2130,7 +2133,7 @@ "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Other", + "sms:displayName": "other", "sms:required": "sms:false", "sms:validationRules": [] }, @@ -3233,6 +3236,9 @@ { "@id": "bts:Plexiformneurofibroma" }, + { + "@id": "bts:Atypicalneurofibroma" + }, { "@id": "bts:Schwannoma" }, @@ -3254,9 +3260,6 @@ { "@id": "bts:Opticnerveglioma" }, - { - "@id": "bts:Atypicalneurofibroma" - }, { "@id": "bts:NeurofibromaNOS" }, @@ -3265,6 +3268,9 @@ }, { "@id": "bts:BrainNOS" + }, + { + "@id": "bts:Other" } ], "sms:displayName": "tumorType", @@ -3368,6 +3374,9 @@ { "@id": "bts:Slide" }, + { + "@id": "bts:Cells" + }, { "@id": "bts:Wholecelllysate" }, @@ -3597,6 +3606,23 @@ "sms:required": "sms:false", "sms:validationRules": [] }, + { + "@id": "bts:Atypicalneurofibroma", + "@type": "rdfs:Class", + "rdfs:comment": "TBD", + "rdfs:label": "Atypicalneurofibroma", + "rdfs:subClassOf": [ + { + "@id": "bts:tumorType" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "atypical neurofibroma", + "sms:required": "sms:false", + "sms:validationRules": [] + }, { "@id": "bts:Schwannoma", "@type": "rdfs:Class", @@ -3716,23 +3742,6 @@ "sms:required": "sms:false", "sms:validationRules": [] }, - { - "@id": "bts:Atypicalneurofibroma", - "@type": "rdfs:Class", - "rdfs:comment": "TBD", - "rdfs:label": "Atypicalneurofibroma", - "rdfs:subClassOf": [ - { - "@id": "bts:tumorType" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "atypical neurofibroma", - "sms:required": "sms:false", - "sms:validationRules": [] - }, { "@id": "bts:NeurofibromaNOS", "@type": "rdfs:Class", @@ -4023,6 +4032,23 @@ "sms:required": "sms:false", "sms:validationRules": [] }, + { + "@id": "bts:Cells", + "@type": "rdfs:Class", + "rdfs:comment": "TBD", + "rdfs:label": "Cells", + "rdfs:subClassOf": [ + { + "@id": "bts:specimenFormat" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "cells", + "sms:required": "sms:false", + "sms:validationRules": [] + }, { "@id": "bts:Wholecelllysate", "@type": "rdfs:Class", From 3f84d8829ea9cac806433af620e42515ec68b3b5 Mon Sep 17 00:00:00 2001 From: Robert Allaway Date: Thu, 26 Oct 2023 13:58:44 -0500 Subject: [PATCH 41/97] consistent tissue.specimen capitalization --- nf_research_tools.rdb.model.csv | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/nf_research_tools.rdb.model.csv b/nf_research_tools.rdb.model.csv index f1bcb9b9..23edbda9 100644 --- a/nf_research_tools.rdb.model.csv +++ b/nf_research_tools.rdb.model.csv @@ -56,7 +56,7 @@ biobankName,The name of the biobank. ,,,TRUE,,biobankDetails,,, biobankId,A unique identifier for the biobank.,,,TRUE,,biobankDetails,,, biobankURL,A URL for the biobank landing page.,,,TRUE,,biobankDetails,,, specimenType,The types of specimens that are banked.,"human tissue, xenograft tumors, cell lines",,TRUE,,biobankDetails,,,list like -specimenTissueType,The types of tissues that are banked.,"blood, tumor, cerebrospinal fluid, nerve, skin, bone, brain",,TRUE,,biobankDetails,,,list like +specimenTissueType,The types of tissues that are banked.,"Blood, Tumor, Cerebrospinal Fluid, Nerve, Skin, Bone, Brain",,TRUE,,biobankDetails,,,list like tumorType,"The types of tumors that are banked, if applicable.","cutaneous neurofibroma, plexiform neurofibroma, atypical neurofibroma, schwannoma, meningioma, malignant peripheral nerve sheath tumor, low grade glioma, high grade glioma, pheochromocytoma, optic nerve glioma, atypical neurofibroma, neurofibroma NOS, diffuse infiltrating neurofibroma, brain NOS, other",,TRUE,,biobankDetails,,,list like diseaseType,"The diseases of the banked specimens, if applicable.","Neurofibromatosis type 1, Neurofibromatosis type 2, Schwannomatosis",,TRUE,,biobankDetails,,,list like specimenPreparationMethod,The preservation methods used by the biobank.,"Fresh collected, Flash frozen, FFPE, Cryopreserved, OCT, RNA later, Formalin-fixed, Ethanol",,TRUE,,biobankDetails,,,list like From dd4bf06785e3aeb04a7bdb8a2ff30c105d28df27 Mon Sep 17 00:00:00 2001 From: "nf-osi[bot]" Date: Thu, 26 Oct 2023 19:01:03 +0000 Subject: [PATCH 42/97] Add changes --- nf-research-tools.jsonld | 14 +++++++------- 1 file changed, 7 insertions(+), 7 deletions(-) diff --git a/nf-research-tools.jsonld b/nf-research-tools.jsonld index 5ea323ae..45965ccf 100644 --- a/nf-research-tools.jsonld +++ b/nf-research-tools.jsonld @@ -3195,7 +3195,7 @@ "@id": "bts:Tumor" }, { - "@id": "bts:Cerebrospinalfluid" + "@id": "bts:CerebrospinalFluid" }, { "@id": "bts:Nerve" @@ -3477,15 +3477,15 @@ "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "tumor", + "sms:displayName": "Tumor", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:Cerebrospinalfluid", + "@id": "bts:CerebrospinalFluid", "@type": "rdfs:Class", "rdfs:comment": "TBD", - "rdfs:label": "Cerebrospinalfluid", + "rdfs:label": "CerebrospinalFluid", "rdfs:subClassOf": [ { "@id": "bts:specimenTissueType" @@ -3494,7 +3494,7 @@ "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "cerebrospinal fluid", + "sms:displayName": "Cerebrospinal Fluid", "sms:required": "sms:false", "sms:validationRules": [] }, @@ -3511,7 +3511,7 @@ "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "nerve", + "sms:displayName": "Nerve", "sms:required": "sms:false", "sms:validationRules": [] }, @@ -3548,7 +3548,7 @@ "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "bone", + "sms:displayName": "Bone", "sms:required": "sms:false", "sms:validationRules": [] }, From 6717664e5d35fc5d456cddc4c9b3867c4dbc3c54 Mon Sep 17 00:00:00 2001 From: Robert Allaway Date: Thu, 26 Oct 2023 14:05:47 -0500 Subject: [PATCH 43/97] replace disease -> genetic disorder --- nf_research_tools.rdb.model.csv | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/nf_research_tools.rdb.model.csv b/nf_research_tools.rdb.model.csv index 23edbda9..312ecc6e 100644 --- a/nf_research_tools.rdb.model.csv +++ b/nf_research_tools.rdb.model.csv @@ -104,7 +104,7 @@ strProfile,Short tandem repeat profile information.,,,FALSE,,cellLineDetails,,, populationDoublingTime,Time for cell line to double,,,FALSE,,cellLineDetails,,, resistance,List of compounds if a cell line has been selected for.,,,FALSE,,cellLineDetails,,,list like contaminatedMisidentified,If a cell line has been contaminated or misidentified,,,FALSE,,cellLineDetails,,, -cellLineGeneticDisorder,"Genetic diseases are diseases in which inherited genes predispose to increased risk. The genetic disorders associated with cancer often result from an alteration or mutation in a single gene. The diseases range from rare dominant cancer family syndrome to familial tendencies in which low-penetrance genes may interact with other genes or environmental factors to induce cancer. Research may involve clinical, epidemiologic, and laboratory studies of persons, families, and populations at high risk of these disorders. [ NCI ]","Neurofibromatosis type 1, Neurofibromatosis type 2, Schwannomatosis, No known disease",,FALSE,http://purl.obolibrary.org/obo/NCIT_C3101,cellLineDetails,,,list like +cellLineGeneticDisorder,"Genetic diseases are diseases in which inherited genes predispose to increased risk. The genetic disorders associated with cancer often result from an alteration or mutation in a single gene. The diseases range from rare dominant cancer family syndrome to familial tendencies in which low-penetrance genes may interact with other genes or environmental factors to induce cancer. Research may involve clinical, epidemiologic, and laboratory studies of persons, families, and populations at high risk of these disorders. [ NCI ]","Neurofibromatosis type 1, Neurofibromatosis type 2, Schwannomatosis, No known genetic disorder",,FALSE,http://purl.obolibrary.org/obo/NCIT_C3101,cellLineDetails,,,list like cellLineManifestation,"Manifestations/symptoms that this resource is used to model (e.g. tumor type, behavioral phenotype, etc.)",,,FALSE,,cellLineDetails,,,list like mutationDetails,"The changing of the structure of a gene, resulting in a variant form that may be transmitted to subsequent generations",,"Component, mutationDetailsId, externalMutationID, alleleType, mutationType, mutationMethod, affectedGeneSymbol, affectedGeneName, sequenceVariation, proteinVariation, animalModelMutation, humanClinVarMutation, chromosome",FALSE,,mutationDetails,"mutationDetailsId, externalMutationID, alleleType, mutationType, mutationMethod, affectedGeneSymbol, affectedGeneName, sequenceVariation, proteinVariation, animalModelMutation, humanClinVarMutation, chromosome",, mutationDetailsId,A unique identifier for mutation.,,,FALSE,,mutationDetails,,, @@ -130,7 +130,7 @@ strainNomenclature,The standard nomenclature for the strain. (e.g. B6.129S2-NF1t generation,The generation of the animal model. (e.g. 13),,,FALSE,,animalModelDetails,,, transplantationType,"Type of transplantation involved in the experiment, derived from MESH","allograft, xenograft, autograft, isograft",,FALSE,,animalModelDetails,,, transplantationDonorId,The donor indentifier number for the transplantion donor. ,,donorId,FALSE,,animalModelDetails,,, -animalModelGeneticDisorder,"Genetic diseases are diseases in which inherited genes predispose to increased risk. The genetic disorders associated with cancer often result from an alteration or mutation in a single gene. The diseases range from rare dominant cancer family syndrome to familial tendencies in which low-penetrance genes may interact with other genes or environmental factors to induce cancer. Research may involve clinical, epidemiologic, and laboratory studies of persons, families, and populations at high risk of these disorders. [ NCI ]","Neurofibromatosis type 1, Neurofibromatosis type 2, Schwannomatosis, No known disease",,TRUE,http://purl.obolibrary.org/obo/NCIT_C3101,animalModelDetails,,,list +animalModelGeneticDisorder,"Genetic diseases are diseases in which inherited genes predispose to increased risk. The genetic disorders associated with cancer often result from an alteration or mutation in a single gene. The diseases range from rare dominant cancer family syndrome to familial tendencies in which low-penetrance genes may interact with other genes or environmental factors to induce cancer. Research may involve clinical, epidemiologic, and laboratory studies of persons, families, and populations at high risk of these disorders. [ NCI ]","Neurofibromatosis type 1, Neurofibromatosis type 2, Schwannomatosis, No known genetic disorder",,TRUE,http://purl.obolibrary.org/obo/NCIT_C3101,animalModelDetails,,,list animalModelOfManifestation,"Manifestations/symptoms that this resource is used to model (e.g. tumor type, behavioral phenotype, etc.) ",,,TRUE,,animalModelDetails,,,list like development,"resourceId, investigatorId, publicationId, funderId (intermediary table)",,"Component, developmentId, resourceId, investigatorId, publicationId, funderId",FALSE,,development,"developmentId, resourceId, investigatorId, publicationId, funderId","resource, investigator, publication, funder", developmentId,A unique identifier for the development of the resource.,,,TRUE,,development,,, From bc8e2d9f794531f0cb06a5e45cacb97c13c8163c Mon Sep 17 00:00:00 2001 From: "nf-osi[bot]" Date: Thu, 26 Oct 2023 19:07:32 +0000 Subject: [PATCH 44/97] Add changes --- nf-research-tools.jsonld | 10 +++++----- 1 file changed, 5 insertions(+), 5 deletions(-) diff --git a/nf-research-tools.jsonld b/nf-research-tools.jsonld index 45965ccf..194116fc 100644 --- a/nf-research-tools.jsonld +++ b/nf-research-tools.jsonld @@ -7619,7 +7619,7 @@ "@id": "bts:Schwannomatosis" }, { - "@id": "bts:Noknowndisease" + "@id": "bts:Noknowngeneticdisorder" } ], "sms:displayName": "cellLineGeneticDisorder", @@ -8770,10 +8770,10 @@ "sms:validationRules": [] }, { - "@id": "bts:Noknowndisease", + "@id": "bts:Noknowngeneticdisorder", "@type": "rdfs:Class", "rdfs:comment": "TBD", - "rdfs:label": "Noknowndisease", + "rdfs:label": "Noknowngeneticdisorder", "rdfs:subClassOf": [ { "@id": "bts:cellLineGeneticDisorder" @@ -8785,7 +8785,7 @@ "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "No known disease", + "sms:displayName": "No known genetic disorder", "sms:required": "sms:false", "sms:validationRules": [] }, @@ -10251,7 +10251,7 @@ "@id": "bts:Schwannomatosis" }, { - "@id": "bts:Noknowndisease" + "@id": "bts:Noknowngeneticdisorder" } ], "sms:displayName": "animalModelGeneticDisorder", From e4cb122f80d2176aa690590f9c2208d62fedf7e3 Mon Sep 17 00:00:00 2001 From: Robert Allaway Date: Thu, 26 Oct 2023 14:11:31 -0500 Subject: [PATCH 45/97] add hybrid cell line --- nf_research_tools.rdb.model.csv | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/nf_research_tools.rdb.model.csv b/nf_research_tools.rdb.model.csv index 312ecc6e..ac0bdbf5 100644 --- a/nf_research_tools.rdb.model.csv +++ b/nf_research_tools.rdb.model.csv @@ -98,7 +98,7 @@ cellLineDetails,A cell culture selected for uniformity from a cell population de cellLineId,A unique identifier for the cell line.,,,TRUE,,cellLineDetails,,, organ,The organ the cell line is derived from.,"Biliary Tract, Bladder, Bone Marrow, Brain, Breast, Bronchial Tree, Duct, Epididymis, Esophagus, Fallopian Tube, Gallbladder, Gland, Gonad, Heart, Intestine, Kidney, Liver, Lung, Lymph Node, Ear, Eye, Nose, Tongue, Pancreas, Penis, Seminal Vesicle, Skin, Spermatic Cord, Spinal Cord, Spleen, Stomach, Thymus Gland, Tonsil, Trachea, Tracheobronchial Tree, Ureter, Urethra, Uterus, Vagina, Vulva",,FALSE,,cellLineDetails,,, tissue,The tissue the cell line is derived from.,"Blood, Bone marrow, Buccal mucosa, Buffy coat, Cerebral cortex, Dorsal root ganglion, Embryonic tissue, Meninges, Nerve tissue, Optic nerve, Plasma, Primary tumor, Sciatic nerve, Serum, Splenocyte, Unspecified, Whole brain",,FALSE,,cellLineDetails,,, -cellLineCategory,The category to which the cell line belongs.,"Cancer cell line, Conditionally immortalized cell line, Embryonic stem cell, Factor-dependent cell line, Finite cell line, Hybridoma, Induced pluripotent stem cell, Somatic stem cell, Spontaneously immortalized cell line, Stromal cell line, Telomerase immortalized cell line, Transformed cell line, Undefined cell line type",,FALSE,,cellLineDetails,,, +cellLineCategory,The category to which the cell line belongs.,"Cancer cell line, Conditionally immortalized cell line, Embryonic stem cell, Factor-dependent cell line, Finite cell line, Hybridoma, Hybrid cell line, Induced pluripotent stem cell, Somatic stem cell, Spontaneously immortalized cell line, Stromal cell line, Telomerase immortalized cell line, Transformed cell line, Undefined cell line type",,FALSE,,cellLineDetails,,, originYear,The year the cell line orginated.,,,FALSE,,cellLineDetails,,, strProfile,Short tandem repeat profile information.,,,FALSE,,cellLineDetails,,, populationDoublingTime,Time for cell line to double,,,FALSE,,cellLineDetails,,, From 3d2532af177df84571f5e153388f2b27f3e12ed5 Mon Sep 17 00:00:00 2001 From: Robert Allaway Date: Thu, 26 Oct 2023 14:12:10 -0500 Subject: [PATCH 46/97] Update nf_research_tools.rdb.model.csv --- nf_research_tools.rdb.model.csv | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/nf_research_tools.rdb.model.csv b/nf_research_tools.rdb.model.csv index ac0bdbf5..de659303 100644 --- a/nf_research_tools.rdb.model.csv +++ b/nf_research_tools.rdb.model.csv @@ -97,7 +97,7 @@ race,The ethnicity of the individual the resource was derived from.,,,FALSE,,don cellLineDetails,A cell culture selected for uniformity from a cell population derived from a usually homogeneous tissue source (such as an organ).,,"Component, cellLineId, donorId, organ, tissue, cellLineCategory, originYear, strProfile, populationDoublingTime, resistance, contaminatedMisidentified, cellLineGeneticDisorder, cellLineManifestation",FALSE,,cellLineDetails,"cellLineId, donorId, organ, tissue, cellLineCategory, originYear, strProfile, populationDoublingTime, resistance, contaminatedMisidentified, cellLineGeneticDisorder, cellLineManifestation",donor, cellLineId,A unique identifier for the cell line.,,,TRUE,,cellLineDetails,,, organ,The organ the cell line is derived from.,"Biliary Tract, Bladder, Bone Marrow, Brain, Breast, Bronchial Tree, Duct, Epididymis, Esophagus, Fallopian Tube, Gallbladder, Gland, Gonad, Heart, Intestine, Kidney, Liver, Lung, Lymph Node, Ear, Eye, Nose, Tongue, Pancreas, Penis, Seminal Vesicle, Skin, Spermatic Cord, Spinal Cord, Spleen, Stomach, Thymus Gland, Tonsil, Trachea, Tracheobronchial Tree, Ureter, Urethra, Uterus, Vagina, Vulva",,FALSE,,cellLineDetails,,, -tissue,The tissue the cell line is derived from.,"Blood, Bone marrow, Buccal mucosa, Buffy coat, Cerebral cortex, Dorsal root ganglion, Embryonic tissue, Meninges, Nerve tissue, Optic nerve, Plasma, Primary tumor, Sciatic nerve, Serum, Splenocyte, Unspecified, Whole brain",,FALSE,,cellLineDetails,,, +tissue,The tissue the cell line is derived from.,"Blood, Bone marrow, Buccal mucosa, Buffy coat, Cerebral cortex, Dorsal root ganglion, Embryonic tissue, Meninges, Nerve tissue, Optic nerve, Plasma, Primary tumor, Sciatic nerve, Serum, Splenocyte, Unspecified, Urine, Whole brain",,FALSE,,cellLineDetails,,, cellLineCategory,The category to which the cell line belongs.,"Cancer cell line, Conditionally immortalized cell line, Embryonic stem cell, Factor-dependent cell line, Finite cell line, Hybridoma, Hybrid cell line, Induced pluripotent stem cell, Somatic stem cell, Spontaneously immortalized cell line, Stromal cell line, Telomerase immortalized cell line, Transformed cell line, Undefined cell line type",,FALSE,,cellLineDetails,,, originYear,The year the cell line orginated.,,,FALSE,,cellLineDetails,,, strProfile,Short tandem repeat profile information.,,,FALSE,,cellLineDetails,,, From 56b6e2da0b27a5517d6ec2f32bc979a0ee707d6d Mon Sep 17 00:00:00 2001 From: "nf-osi[bot]" Date: Thu, 26 Oct 2023 19:14:20 +0000 Subject: [PATCH 47/97] Add changes --- nf-research-tools.jsonld | 40 ++++++++++++++++++++++++++++++++++++++++ 1 file changed, 40 insertions(+) diff --git a/nf-research-tools.jsonld b/nf-research-tools.jsonld index 194116fc..ea1560ea 100644 --- a/nf-research-tools.jsonld +++ b/nf-research-tools.jsonld @@ -7442,6 +7442,9 @@ { "@id": "bts:Unspecified" }, + { + "@id": "bts:Urine" + }, { "@id": "bts:Wholebrain" } @@ -7482,6 +7485,9 @@ { "@id": "bts:Hybridoma" }, + { + "@id": "bts:Hybridcellline" + }, { "@id": "bts:Inducedpluripotentstemcell" }, @@ -8531,6 +8537,23 @@ "sms:required": "sms:false", "sms:validationRules": [] }, + { + "@id": "bts:Urine", + "@type": "rdfs:Class", + "rdfs:comment": "TBD", + "rdfs:label": "Urine", + "rdfs:subClassOf": [ + { + "@id": "bts:tissue" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Urine", + "sms:required": "sms:false", + "sms:validationRules": [] + }, { "@id": "bts:Wholebrain", "@type": "rdfs:Class", @@ -8650,6 +8673,23 @@ "sms:required": "sms:false", "sms:validationRules": [] }, + { + "@id": "bts:Hybridcellline", + "@type": "rdfs:Class", + "rdfs:comment": "TBD", + "rdfs:label": "Hybridcellline", + "rdfs:subClassOf": [ + { + "@id": "bts:cellLineCategory" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Hybrid cell line", + "sms:required": "sms:false", + "sms:validationRules": [] + }, { "@id": "bts:Inducedpluripotentstemcell", "@type": "rdfs:Class", From 7daf02fe7e091cec8c6fef849f5f609031677251 Mon Sep 17 00:00:00 2001 From: Robert Allaway Date: Thu, 26 Oct 2023 14:52:55 -0500 Subject: [PATCH 48/97] Remove unused reactivespecies terms --- nf_research_tools.rdb.model.csv | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/nf_research_tools.rdb.model.csv b/nf_research_tools.rdb.model.csv index de659303..31f307ec 100644 --- a/nf_research_tools.rdb.model.csv +++ b/nf_research_tools.rdb.model.csv @@ -84,7 +84,7 @@ uniprotId,The uniprotId of the antibody.,,,TRUE,,antibodyDetails,,, targetAntigen,Antigen that is targeted by antibody. (e.g. Neurofibromin 1 human),,,TRUE,,antibodyDetails,,, clonality,They type of clonality of the antibody,"Unknown, Cocktail, Control, Isotype Control, Monoclonal, Monoclonal Secondary, Polyclonal, Polyclonal Secondary, OligoClonal, Recombinant, Recombinant Monoclonal, Recombinant Monoclonal Secondary, Recombinant Polyclonal, Recombinant Polyclonal Secondary",,TRUE,,antibodyDetails,,, cloneId,Identification of clone (e.g. 2D1),,,FALSE,,antibodyDetails,,, -reactiveSpecies,Species the antibody has been shown to crossreact with the target protein. ,"Avian, Bovine, Canine, Chicken, Cow, Dog, Donkey, Feline, Fish, Guinea pig, Hamster, Human, Monkey, Mouse, Non-human primate, Other, Pig, Porcine, Rabbit, Rat, Rodent, Sheep, Simian, Zebrafish",,TRUE,,antibodyDetails,,,list like +reactiveSpecies,Species the antibody has been shown to crossreact with the target protein. ,"Human, Mouse, Rat, Chicken, Rabbit, Pig, Dog, Zebrafish, Fish, Non-human primate, Guinea pig, Hamster, Cow, Monkey, Avian, Horse, Rodent, Drosophila",,TRUE,,antibodyDetails,,,list like conjugate,Is the antibody conjugated or nonconjugated,"Conjugated, Nonconjugated",,TRUE,,antibodyDetails,,, hostOrganism,The species of the organism that hosts the antibody,"Mouse, Rabbit",,TRUE,,antibodyDetails,,, donor,"A person, animal, etc. who is the contributor of the resource.",,"Component, donorId, parentDonorId, transplantationDonorId, species, sex, age, race",FALSE,,donor,"donorId, parentDonorId, transplantationDonorId, species, sex, age, race",, @@ -130,7 +130,7 @@ strainNomenclature,The standard nomenclature for the strain. (e.g. B6.129S2-NF1t generation,The generation of the animal model. (e.g. 13),,,FALSE,,animalModelDetails,,, transplantationType,"Type of transplantation involved in the experiment, derived from MESH","allograft, xenograft, autograft, isograft",,FALSE,,animalModelDetails,,, transplantationDonorId,The donor indentifier number for the transplantion donor. ,,donorId,FALSE,,animalModelDetails,,, -animalModelGeneticDisorder,"Genetic diseases are diseases in which inherited genes predispose to increased risk. The genetic disorders associated with cancer often result from an alteration or mutation in a single gene. The diseases range from rare dominant cancer family syndrome to familial tendencies in which low-penetrance genes may interact with other genes or environmental factors to induce cancer. Research may involve clinical, epidemiologic, and laboratory studies of persons, families, and populations at high risk of these disorders. [ NCI ]","Neurofibromatosis type 1, Neurofibromatosis type 2, Schwannomatosis, No known genetic disorder",,TRUE,http://purl.obolibrary.org/obo/NCIT_C3101,animalModelDetails,,,list +animalModelGeneticDisorder,"Genetic diseases are diseases in which inherited genes predispose to increased risk. The genetic disorders associated with cancer often result from an alteration or mutation in a single gene. The diseases range from rare dominant cancer family syndrome to familial tendencies in which low-penetrance genes may interact with other genes or environmental factors to induce cancer. Research may involve clinical, epidemiologic, and laboratory studies of persons, families, and populations at high risk of these disorders. [ NCI ]","Neurofibromatosis type 1, Neurofibromatosis type 2, Schwannomatosis, No known genetic disorder",,TRUE,http://purl.obolibrary.org/obo/NCIT_C3101,animalModelDetails,,,list like animalModelOfManifestation,"Manifestations/symptoms that this resource is used to model (e.g. tumor type, behavioral phenotype, etc.) ",,,TRUE,,animalModelDetails,,,list like development,"resourceId, investigatorId, publicationId, funderId (intermediary table)",,"Component, developmentId, resourceId, investigatorId, publicationId, funderId",FALSE,,development,"developmentId, resourceId, investigatorId, publicationId, funderId","resource, investigator, publication, funder", developmentId,A unique identifier for the development of the resource.,,,TRUE,,development,,, From 30f5be89df02b5476e87554370da302c9b3d3d12 Mon Sep 17 00:00:00 2001 From: Robert Allaway Date: Thu, 26 Oct 2023 14:53:35 -0500 Subject: [PATCH 49/97] Update nf_research_tools.rdb.model.csv --- nf_research_tools.rdb.model.csv | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/nf_research_tools.rdb.model.csv b/nf_research_tools.rdb.model.csv index 31f307ec..e18e8ef2 100644 --- a/nf_research_tools.rdb.model.csv +++ b/nf_research_tools.rdb.model.csv @@ -80,7 +80,7 @@ applications,"One or more uses for the resource (e.g. western blot, immunofluore links,shareable links related to the resource,,,FALSE,,resourceApplication,,,list antibodyDetails,"A blood protein produced in response to and counteracting a specific antigen. Antibodies combine chemically with substances which the body recognizes as alien, such as bacteria, viruses, and foreign substances in the blood.",,"Component, antibodyId, uniprotId, targetAntigen, clonality, cloneId, reactiveSpecies, conjugate, hostOrganism",FALSE,,antibodyDetails,,, antibodyId,A unique identifier for the antibody.,,,TRUE,,antibodyDetails,"antibodyId, uniprotId, targetAntigen, clonality, cloneId, reactiveSpecies, conjugate, hostOrganism",, -uniprotId,The uniprotId of the antibody.,,,TRUE,,antibodyDetails,,, +uniprotId,The uniprotId of the protein targeted by the antibody.,,,FALSE,,antibodyDetails,,, targetAntigen,Antigen that is targeted by antibody. (e.g. Neurofibromin 1 human),,,TRUE,,antibodyDetails,,, clonality,They type of clonality of the antibody,"Unknown, Cocktail, Control, Isotype Control, Monoclonal, Monoclonal Secondary, Polyclonal, Polyclonal Secondary, OligoClonal, Recombinant, Recombinant Monoclonal, Recombinant Monoclonal Secondary, Recombinant Polyclonal, Recombinant Polyclonal Secondary",,TRUE,,antibodyDetails,,, cloneId,Identification of clone (e.g. 2D1),,,FALSE,,antibodyDetails,,, From 9c173eaa14fc58539e58850051e512cc07ff1565 Mon Sep 17 00:00:00 2001 From: "nf-osi[bot]" Date: Thu, 26 Oct 2023 19:55:40 +0000 Subject: [PATCH 50/97] Add changes --- nf-research-tools.jsonld | 242 +++++++++++---------------------------- 1 file changed, 68 insertions(+), 174 deletions(-) diff --git a/nf-research-tools.jsonld b/nf-research-tools.jsonld index ea1560ea..fce20349 100644 --- a/nf-research-tools.jsonld +++ b/nf-research-tools.jsonld @@ -2117,9 +2117,6 @@ { "@id": "bts:tumorType" }, - { - "@id": "bts:reactiveSpecies" - }, { "@id": "bts:observationType" }, @@ -5867,7 +5864,7 @@ { "@id": "bts:uniprotId", "@type": "rdf:Property", - "rdfs:comment": "The uniprotId of the antibody.", + "rdfs:comment": "The uniprotId of the protein targeted by the antibody.", "rdfs:label": "uniprotId", "schema:domainIncludes": [ { @@ -5878,7 +5875,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "uniprotId", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -5991,32 +5988,35 @@ }, "schema:rangeIncludes": [ { - "@id": "bts:Avian" + "@id": "bts:Human" }, { - "@id": "bts:Bovine" + "@id": "bts:Mouse" }, { - "@id": "bts:Canine" + "@id": "bts:Rat" }, { "@id": "bts:Chicken" }, { - "@id": "bts:Cow" + "@id": "bts:Rabbit" }, { - "@id": "bts:Dog" + "@id": "bts:Pig" }, { - "@id": "bts:Donkey" + "@id": "bts:Dog" }, { - "@id": "bts:Feline" + "@id": "bts:Zebrafish" }, { "@id": "bts:Fish" }, + { + "@id": "bts:Non-humanprimate" + }, { "@id": "bts:Guineapig" }, @@ -6024,43 +6024,22 @@ "@id": "bts:Hamster" }, { - "@id": "bts:Human" + "@id": "bts:Cow" }, { "@id": "bts:Monkey" }, { - "@id": "bts:Mouse" - }, - { - "@id": "bts:Non-humanprimate" - }, - { - "@id": "bts:Other" - }, - { - "@id": "bts:Pig" - }, - { - "@id": "bts:Porcine" - }, - { - "@id": "bts:Rabbit" + "@id": "bts:Avian" }, { - "@id": "bts:Rat" + "@id": "bts:Horse" }, { "@id": "bts:Rodent" }, { - "@id": "bts:Sheep" - }, - { - "@id": "bts:Simian" - }, - { - "@id": "bts:Zebrafish" + "@id": "bts:Drosophila" } ], "sms:displayName": "reactiveSpecies", @@ -6341,10 +6320,10 @@ "sms:validationRules": [] }, { - "@id": "bts:Avian", + "@id": "bts:Human", "@type": "rdfs:Class", "rdfs:comment": "TBD", - "rdfs:label": "Avian", + "rdfs:label": "Human", "rdfs:subClassOf": [ { "@id": "bts:reactiveSpecies" @@ -6353,16 +6332,19 @@ "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Avian", + "sms:displayName": "Human", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:Bovine", + "@id": "bts:Mouse", "@type": "rdfs:Class", "rdfs:comment": "TBD", - "rdfs:label": "Bovine", + "rdfs:label": "Mouse", "rdfs:subClassOf": [ + { + "@id": "bts:hostOrganism" + }, { "@id": "bts:reactiveSpecies" } @@ -6370,15 +6352,15 @@ "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Bovine", + "sms:displayName": "Mouse", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:Canine", + "@id": "bts:Rat", "@type": "rdfs:Class", "rdfs:comment": "TBD", - "rdfs:label": "Canine", + "rdfs:label": "Rat", "rdfs:subClassOf": [ { "@id": "bts:reactiveSpecies" @@ -6387,7 +6369,7 @@ "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Canine", + "sms:displayName": "Rat", "sms:required": "sms:false", "sms:validationRules": [] }, @@ -6409,11 +6391,14 @@ "sms:validationRules": [] }, { - "@id": "bts:Cow", + "@id": "bts:Rabbit", "@type": "rdfs:Class", "rdfs:comment": "TBD", - "rdfs:label": "Cow", + "rdfs:label": "Rabbit", "rdfs:subClassOf": [ + { + "@id": "bts:hostOrganism" + }, { "@id": "bts:reactiveSpecies" } @@ -6421,15 +6406,15 @@ "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Cow", + "sms:displayName": "Rabbit", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:Dog", + "@id": "bts:Pig", "@type": "rdfs:Class", "rdfs:comment": "TBD", - "rdfs:label": "Dog", + "rdfs:label": "Pig", "rdfs:subClassOf": [ { "@id": "bts:reactiveSpecies" @@ -6438,15 +6423,15 @@ "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Dog", + "sms:displayName": "Pig", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:Donkey", + "@id": "bts:Dog", "@type": "rdfs:Class", "rdfs:comment": "TBD", - "rdfs:label": "Donkey", + "rdfs:label": "Dog", "rdfs:subClassOf": [ { "@id": "bts:reactiveSpecies" @@ -6455,15 +6440,15 @@ "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Donkey", + "sms:displayName": "Dog", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:Feline", + "@id": "bts:Zebrafish", "@type": "rdfs:Class", "rdfs:comment": "TBD", - "rdfs:label": "Feline", + "rdfs:label": "Zebrafish", "rdfs:subClassOf": [ { "@id": "bts:reactiveSpecies" @@ -6472,7 +6457,7 @@ "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Feline", + "sms:displayName": "Zebrafish", "sms:required": "sms:false", "sms:validationRules": [] }, @@ -6493,94 +6478,6 @@ "sms:required": "sms:false", "sms:validationRules": [] }, - { - "@id": "bts:Guineapig", - "@type": "rdfs:Class", - "rdfs:comment": "TBD", - "rdfs:label": "Guineapig", - "rdfs:subClassOf": [ - { - "@id": "bts:reactiveSpecies" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Guinea pig", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:Hamster", - "@type": "rdfs:Class", - "rdfs:comment": "TBD", - "rdfs:label": "Hamster", - "rdfs:subClassOf": [ - { - "@id": "bts:reactiveSpecies" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Hamster", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:Human", - "@type": "rdfs:Class", - "rdfs:comment": "TBD", - "rdfs:label": "Human", - "rdfs:subClassOf": [ - { - "@id": "bts:reactiveSpecies" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Human", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:Monkey", - "@type": "rdfs:Class", - "rdfs:comment": "TBD", - "rdfs:label": "Monkey", - "rdfs:subClassOf": [ - { - "@id": "bts:reactiveSpecies" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Monkey", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:Mouse", - "@type": "rdfs:Class", - "rdfs:comment": "TBD", - "rdfs:label": "Mouse", - "rdfs:subClassOf": [ - { - "@id": "bts:hostOrganism" - }, - { - "@id": "bts:reactiveSpecies" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Mouse", - "sms:required": "sms:false", - "sms:validationRules": [] - }, { "@id": "bts:Non-humanprimate", "@type": "rdfs:Class", @@ -6599,10 +6496,10 @@ "sms:validationRules": [] }, { - "@id": "bts:Pig", + "@id": "bts:Guineapig", "@type": "rdfs:Class", "rdfs:comment": "TBD", - "rdfs:label": "Pig", + "rdfs:label": "Guineapig", "rdfs:subClassOf": [ { "@id": "bts:reactiveSpecies" @@ -6611,15 +6508,15 @@ "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Pig", + "sms:displayName": "Guinea pig", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:Porcine", + "@id": "bts:Hamster", "@type": "rdfs:Class", "rdfs:comment": "TBD", - "rdfs:label": "Porcine", + "rdfs:label": "Hamster", "rdfs:subClassOf": [ { "@id": "bts:reactiveSpecies" @@ -6628,19 +6525,16 @@ "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Porcine", + "sms:displayName": "Hamster", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:Rabbit", + "@id": "bts:Cow", "@type": "rdfs:Class", "rdfs:comment": "TBD", - "rdfs:label": "Rabbit", + "rdfs:label": "Cow", "rdfs:subClassOf": [ - { - "@id": "bts:hostOrganism" - }, { "@id": "bts:reactiveSpecies" } @@ -6648,15 +6542,15 @@ "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Rabbit", + "sms:displayName": "Cow", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:Rat", + "@id": "bts:Monkey", "@type": "rdfs:Class", "rdfs:comment": "TBD", - "rdfs:label": "Rat", + "rdfs:label": "Monkey", "rdfs:subClassOf": [ { "@id": "bts:reactiveSpecies" @@ -6665,15 +6559,15 @@ "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Rat", + "sms:displayName": "Monkey", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:Rodent", + "@id": "bts:Avian", "@type": "rdfs:Class", "rdfs:comment": "TBD", - "rdfs:label": "Rodent", + "rdfs:label": "Avian", "rdfs:subClassOf": [ { "@id": "bts:reactiveSpecies" @@ -6682,15 +6576,15 @@ "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Rodent", + "sms:displayName": "Avian", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:Sheep", + "@id": "bts:Horse", "@type": "rdfs:Class", "rdfs:comment": "TBD", - "rdfs:label": "Sheep", + "rdfs:label": "Horse", "rdfs:subClassOf": [ { "@id": "bts:reactiveSpecies" @@ -6699,15 +6593,15 @@ "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Sheep", + "sms:displayName": "Horse", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:Simian", + "@id": "bts:Rodent", "@type": "rdfs:Class", "rdfs:comment": "TBD", - "rdfs:label": "Simian", + "rdfs:label": "Rodent", "rdfs:subClassOf": [ { "@id": "bts:reactiveSpecies" @@ -6716,15 +6610,15 @@ "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Simian", + "sms:displayName": "Rodent", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:Zebrafish", + "@id": "bts:Drosophila", "@type": "rdfs:Class", "rdfs:comment": "TBD", - "rdfs:label": "Zebrafish", + "rdfs:label": "Drosophila", "rdfs:subClassOf": [ { "@id": "bts:reactiveSpecies" @@ -6733,7 +6627,7 @@ "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Zebrafish", + "sms:displayName": "Drosophila", "sms:required": "sms:false", "sms:validationRules": [] }, @@ -10297,7 +10191,7 @@ "sms:displayName": "animalModelGeneticDisorder", "sms:required": "sms:true", "sms:validationRules": [ - "list" + "list like" ] }, { From 28ebed832e60cbcaee0283f0c038c82282831d8c Mon Sep 17 00:00:00 2001 From: Robert Allaway Date: Thu, 26 Oct 2023 15:36:49 -0500 Subject: [PATCH 51/97] add yeast donor --- nf_research_tools.rdb.model.csv | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/nf_research_tools.rdb.model.csv b/nf_research_tools.rdb.model.csv index e18e8ef2..75f5f358 100644 --- a/nf_research_tools.rdb.model.csv +++ b/nf_research_tools.rdb.model.csv @@ -90,7 +90,7 @@ hostOrganism,The species of the organism that hosts the antibody,"Mouse, Rabbit" donor,"A person, animal, etc. who is the contributor of the resource.",,"Component, donorId, parentDonorId, transplantationDonorId, species, sex, age, race",FALSE,,donor,"donorId, parentDonorId, transplantationDonorId, species, sex, age, race",, donorId,A uniqe identifier for donor.,,,TRUE,,donor,,, parentDonorId,The ID of the parent donor.,,donorId,FALSE,,donor,,, -species,The species of the individual the resource was derived from.,"Homo sapiens, Mus musculus, Mus musculus (humanized), Rattus norvegicus, Drosophila melanogaster, Rhesus macaque, Pan troglodytes, Gallus gallus, Sus scrofa, Oryctolagus cuniculus,Danio rerio,Escherichia coli",,TRUE,,donor,,, +species,The species of the individual the resource was derived from.,"Homo sapiens, Mus musculus, Mus musculus (humanized), Rattus norvegicus, Drosophila melanogaster, Saccharomyces cerevisiae, Rhesus macaque, Pan troglodytes, Gallus gallus, Sus scrofa, Oryctolagus cuniculus,Danio rerio,Escherichia coli",,TRUE,,donor,,, sex,The sex of the individual from which the resource was derived from.,"Male, Female, Unknown",,FALSE,,donor,,, age,That age of the individual from which the resource was derived from.,,,FALSE,,donor,,, race,The ethnicity of the individual the resource was derived from.,,,FALSE,,donor,,, From eba5640e84d4635a641819bbc32ac087a2f1dbae Mon Sep 17 00:00:00 2001 From: Robert Allaway Date: Thu, 26 Oct 2023 15:38:25 -0500 Subject: [PATCH 52/97] yet another list to list like --- nf_research_tools.rdb.model.csv | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/nf_research_tools.rdb.model.csv b/nf_research_tools.rdb.model.csv index 75f5f358..2988659a 100644 --- a/nf_research_tools.rdb.model.csv +++ b/nf_research_tools.rdb.model.csv @@ -77,7 +77,7 @@ resourceApplication,"Applications the resource can be used for. (i.e. western bl resourceApplicationId,A unique identifier for resrouce Application,,,TRUE,,resourceApplication,,, source,"The source of resource application information (e.g. Vendor, Community)","Community-reported, Investigator-reported, Vendor-reported",,TRUE,,resourceApplication,,, applications,"One or more uses for the resource (e.g. western blot, immunofluorescence)","Western Blot, Immunofluorescence, ELISA, Immunohistochemistry, Immunoprecipitation, Tumor Growth Studies, Immunohistochemistry (Paraffin-Embedded), Immunocytochemistry, Immunohistochemistry (Frozen Sections), Flow Cytometry, Affinity Purification, Microarray",,TRUE,,resourceApplication,,,list like -links,shareable links related to the resource,,,FALSE,,resourceApplication,,,list +links,shareable links related to the resource,,,FALSE,,resourceApplication,,,list like antibodyDetails,"A blood protein produced in response to and counteracting a specific antigen. Antibodies combine chemically with substances which the body recognizes as alien, such as bacteria, viruses, and foreign substances in the blood.",,"Component, antibodyId, uniprotId, targetAntigen, clonality, cloneId, reactiveSpecies, conjugate, hostOrganism",FALSE,,antibodyDetails,,, antibodyId,A unique identifier for the antibody.,,,TRUE,,antibodyDetails,"antibodyId, uniprotId, targetAntigen, clonality, cloneId, reactiveSpecies, conjugate, hostOrganism",, uniprotId,The uniprotId of the protein targeted by the antibody.,,,FALSE,,antibodyDetails,,, From 2bca84b81edc8c6a31d4a8b971a65ceb57e4d323 Mon Sep 17 00:00:00 2001 From: "nf-osi[bot]" Date: Thu, 26 Oct 2023 20:39:59 +0000 Subject: [PATCH 53/97] Add changes --- nf-research-tools.jsonld | 22 +++++++++++++++++++++- 1 file changed, 21 insertions(+), 1 deletion(-) diff --git a/nf-research-tools.jsonld b/nf-research-tools.jsonld index fce20349..235cd039 100644 --- a/nf-research-tools.jsonld +++ b/nf-research-tools.jsonld @@ -5557,7 +5557,7 @@ "sms:displayName": "links", "sms:required": "sms:false", "sms:validationRules": [ - "list" + "list like" ] }, { @@ -6797,6 +6797,9 @@ { "@id": "bts:Drosophilamelanogaster" }, + { + "@id": "bts:Saccharomycescerevisiae" + }, { "@id": "bts:Rhesusmacaque" }, @@ -6919,6 +6922,23 @@ "sms:required": "sms:false", "sms:validationRules": [] }, + { + "@id": "bts:Saccharomycescerevisiae", + "@type": "rdfs:Class", + "rdfs:comment": "TBD", + "rdfs:label": "Saccharomycescerevisiae", + "rdfs:subClassOf": [ + { + "@id": "bts:species" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Saccharomyces cerevisiae", + "sms:required": "sms:false", + "sms:validationRules": [] + }, { "@id": "bts:Rhesusmacaque", "@type": "rdfs:Class", From 8b453e7c21a771e020f760380dab480f34596f74 Mon Sep 17 00:00:00 2001 From: Robert Allaway Date: Thu, 26 Oct 2023 15:41:28 -0500 Subject: [PATCH 54/97] Update nf_research_tools.rdb.model.csv --- nf_research_tools.rdb.model.csv | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/nf_research_tools.rdb.model.csv b/nf_research_tools.rdb.model.csv index 2988659a..fcda12fb 100644 --- a/nf_research_tools.rdb.model.csv +++ b/nf_research_tools.rdb.model.csv @@ -138,7 +138,7 @@ funder,A person or organization that provides money for a particular resource.,, funderId,A unique identifier for the funder of the resource.,,,FALSE,,funder,,, funderName,The name of the person or agency that funded the development of the resource.,,,FALSE,,funder,,, investigator,A person who carries out a formal inquiry or investigation into the development of the resource.,,"Component, investigatorId, orcid, investigatorName, institution, investigatorWebsite, investigatorSynapseId",FALSE,,investigator,"investigatorId, orcid, investigatorName, institution, investigatorWebsite, investigatorSynapseId",, -investigatorId,A unique identifier for the investigator.,,,TRUE,,investigator,,, +investigatorId,A unique identifier for the investigator.,,,FALSE,,investigator,,, orcid,The orcidId of the investigator that developed the resource,,,FALSE,,investigator,,, investigatorName,The name of the investigator responsible for devleoping the resource.,,,TRUE,,investigator,,, institution,The insitution of the investator,,,FALSE,,investigator,,, From 4e5fd38e2c89d476d9b06d48b3d57f3eac429e68 Mon Sep 17 00:00:00 2001 From: "nf-osi[bot]" Date: Thu, 26 Oct 2023 20:43:11 +0000 Subject: [PATCH 55/97] Add changes --- nf-research-tools.jsonld | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/nf-research-tools.jsonld b/nf-research-tools.jsonld index 235cd039..8ed5117c 100644 --- a/nf-research-tools.jsonld +++ b/nf-research-tools.jsonld @@ -10386,7 +10386,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "investigatorId", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { From 50789b0cc8ed4fa79f51999513873e7c7bec0330 Mon Sep 17 00:00:00 2001 From: Robert Allaway Date: Thu, 26 Oct 2023 15:47:46 -0500 Subject: [PATCH 56/97] moar donor species --- nf_research_tools.rdb.model.csv | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/nf_research_tools.rdb.model.csv b/nf_research_tools.rdb.model.csv index fcda12fb..8d29c686 100644 --- a/nf_research_tools.rdb.model.csv +++ b/nf_research_tools.rdb.model.csv @@ -90,7 +90,7 @@ hostOrganism,The species of the organism that hosts the antibody,"Mouse, Rabbit" donor,"A person, animal, etc. who is the contributor of the resource.",,"Component, donorId, parentDonorId, transplantationDonorId, species, sex, age, race",FALSE,,donor,"donorId, parentDonorId, transplantationDonorId, species, sex, age, race",, donorId,A uniqe identifier for donor.,,,TRUE,,donor,,, parentDonorId,The ID of the parent donor.,,donorId,FALSE,,donor,,, -species,The species of the individual the resource was derived from.,"Homo sapiens, Mus musculus, Mus musculus (humanized), Rattus norvegicus, Drosophila melanogaster, Saccharomyces cerevisiae, Rhesus macaque, Pan troglodytes, Gallus gallus, Sus scrofa, Oryctolagus cuniculus,Danio rerio,Escherichia coli",,TRUE,,donor,,, +species,The species of the individual the resource was derived from.,"Homo sapiens, Mus musculus, Mus musculus (humanized), Rattus norvegicus, Drosophila melanogaster, Saccharomyces cerevisiae, Rhesus macaque, Cricetulus griseus, Xenopus laevis, Canis lupus familiaris, Pan troglodytes, Gallus gallus, Sus scrofa, Oryctolagus cuniculus,Danio rerio,Escherichia coli",,TRUE,,donor,,,list like sex,The sex of the individual from which the resource was derived from.,"Male, Female, Unknown",,FALSE,,donor,,, age,That age of the individual from which the resource was derived from.,,,FALSE,,donor,,, race,The ethnicity of the individual the resource was derived from.,,,FALSE,,donor,,, From a5c852dd848228a70380f87ac51b2888f5711107 Mon Sep 17 00:00:00 2001 From: "nf-osi[bot]" Date: Thu, 26 Oct 2023 20:49:30 +0000 Subject: [PATCH 57/97] Add changes --- nf-research-tools.jsonld | 64 +++++++++++++++++++++++++++++++++++++++- 1 file changed, 63 insertions(+), 1 deletion(-) diff --git a/nf-research-tools.jsonld b/nf-research-tools.jsonld index 8ed5117c..edb7ef72 100644 --- a/nf-research-tools.jsonld +++ b/nf-research-tools.jsonld @@ -6803,6 +6803,15 @@ { "@id": "bts:Rhesusmacaque" }, + { + "@id": "bts:Cricetulusgriseus" + }, + { + "@id": "bts:Xenopuslaevis" + }, + { + "@id": "bts:Canislupusfamiliaris" + }, { "@id": "bts:Pantroglodytes" }, @@ -6824,7 +6833,9 @@ ], "sms:displayName": "species", "sms:required": "sms:true", - "sms:validationRules": [] + "sms:validationRules": [ + "list like" + ] }, { "@id": "bts:sex", @@ -6956,6 +6967,57 @@ "sms:required": "sms:false", "sms:validationRules": [] }, + { + "@id": "bts:Cricetulusgriseus", + "@type": "rdfs:Class", + "rdfs:comment": "TBD", + "rdfs:label": "Cricetulusgriseus", + "rdfs:subClassOf": [ + { + "@id": "bts:species" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Cricetulus griseus", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:Xenopuslaevis", + "@type": "rdfs:Class", + "rdfs:comment": "TBD", + "rdfs:label": "Xenopuslaevis", + "rdfs:subClassOf": [ + { + "@id": "bts:species" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Xenopus laevis", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:Canislupusfamiliaris", + "@type": "rdfs:Class", + "rdfs:comment": "TBD", + "rdfs:label": "Canislupusfamiliaris", + "rdfs:subClassOf": [ + { + "@id": "bts:species" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Canis lupus familiaris", + "sms:required": "sms:false", + "sms:validationRules": [] + }, { "@id": "bts:Pantroglodytes", "@type": "rdfs:Class", From e48d7601b868c47e484c3b9d8525e0b47786e878 Mon Sep 17 00:00:00 2001 From: Robert Allaway Date: Thu, 26 Oct 2023 15:53:10 -0500 Subject: [PATCH 58/97] add new mutationType --- nf_research_tools.rdb.model.csv | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/nf_research_tools.rdb.model.csv b/nf_research_tools.rdb.model.csv index 8d29c686..1b1f038b 100644 --- a/nf_research_tools.rdb.model.csv +++ b/nf_research_tools.rdb.model.csv @@ -109,7 +109,7 @@ cellLineManifestation,"Manifestations/symptoms that this resource is used to mod mutationDetails,"The changing of the structure of a gene, resulting in a variant form that may be transmitted to subsequent generations",,"Component, mutationDetailsId, externalMutationID, alleleType, mutationType, mutationMethod, affectedGeneSymbol, affectedGeneName, sequenceVariation, proteinVariation, animalModelMutation, humanClinVarMutation, chromosome",FALSE,,mutationDetails,"mutationDetailsId, externalMutationID, alleleType, mutationType, mutationMethod, affectedGeneSymbol, affectedGeneName, sequenceVariation, proteinVariation, animalModelMutation, humanClinVarMutation, chromosome",, mutationDetailsId,A unique identifier for mutation.,,,FALSE,,mutationDetails,,, externalMutationID,"An identifier from an organism database such as MGI or other curated variant resource, if available. ",,,FALSE,,mutationDetails,,, -mutationType,"The type of the mutation, vocabulary aligned with MGI mutation types. ","Disruption caused by insertion of vector, Duplication, Insertion, Insertion of gene trap vector, Intergenic deletion, Intragenic deletion, Inversion, Loss of heterozygosity (unspecified mechanism), Not Applicable, Not Specified, Nucleotide repeat expansion, Nucleotide substitutions, Other, Single point mutation, Translocation, Transposon insertion, Undefined, Viral insertion",,FALSE,,mutationDetails,,,list like +mutationType,"The type of the mutation, vocabulary aligned with MGI mutation types, and expanded to include additional types. ","Disruption caused by insertion of vector, Duplication, Insertion, Insertion of gene trap vector, Intergenic deletion, Intragenic deletion, Inversion, Loss of heterozygosity (unspecified mechanism), Not Applicable, Not Specified, Nucleotide repeat expansion, Nucleotide substitutions, Other, Single point mutation, Translocation, Transposon insertion, Undefined, Viral insertion, Microdeletion, Homozygous deletion, Loss of heterozygosity (mitotic recombination), Loss of heterozygosity (deletion), Stable knockdown, Exogenous DNA expression",,FALSE,,mutationDetails,,,list like mutationMethod,"The method used to alter the resource, vocabulary aligned with and expanded upon MGI allele origin types. ","Chemically induced (ENU), Chemically induced (other), Chemically and radiation induced, Endonuclease-mediated (CRISPR), Endonuclease-mediated (TALEN), Gene trapped, QTL, Radiation induced, Spontaneous, Targeted, Transgenic, Transposon induced",,FALSE,,mutationDetails,,,list like alleleType,"The type of genetic alteration of the resource, vocabulary aligned with MGI allele subtypes. ","Conditional ready, Constitutively active, Dominant negative, Humanized sequence, Hypomorph, Inducible, Inserted expressed sequence, Knockdown, Modified isoform(s), No functional change, Null/knockout, Recombinase, Reporter, RMCE-Ready, Transactivator, Transposase, Transposon concatemer",,FALSE,,mutationDetails,,,list like affectedGeneSymbol,"The gene symbol for the mutated gene. (e.g. NF1, SUZ12, SMARCB1, P53, etc.)",,,FALSE,,mutationDetails,,, From 22c5bb9399254f365e8dd3cc212ba48001773fc1 Mon Sep 17 00:00:00 2001 From: Robert Allaway Date: Thu, 26 Oct 2023 15:54:01 -0500 Subject: [PATCH 59/97] Update nf_research_tools.rdb.model.csv --- nf_research_tools.rdb.model.csv | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/nf_research_tools.rdb.model.csv b/nf_research_tools.rdb.model.csv index 1b1f038b..e06d97c0 100644 --- a/nf_research_tools.rdb.model.csv +++ b/nf_research_tools.rdb.model.csv @@ -110,7 +110,7 @@ mutationDetails,"The changing of the structure of a gene, resulting in a variant mutationDetailsId,A unique identifier for mutation.,,,FALSE,,mutationDetails,,, externalMutationID,"An identifier from an organism database such as MGI or other curated variant resource, if available. ",,,FALSE,,mutationDetails,,, mutationType,"The type of the mutation, vocabulary aligned with MGI mutation types, and expanded to include additional types. ","Disruption caused by insertion of vector, Duplication, Insertion, Insertion of gene trap vector, Intergenic deletion, Intragenic deletion, Inversion, Loss of heterozygosity (unspecified mechanism), Not Applicable, Not Specified, Nucleotide repeat expansion, Nucleotide substitutions, Other, Single point mutation, Translocation, Transposon insertion, Undefined, Viral insertion, Microdeletion, Homozygous deletion, Loss of heterozygosity (mitotic recombination), Loss of heterozygosity (deletion), Stable knockdown, Exogenous DNA expression",,FALSE,,mutationDetails,,,list like -mutationMethod,"The method used to alter the resource, vocabulary aligned with and expanded upon MGI allele origin types. ","Chemically induced (ENU), Chemically induced (other), Chemically and radiation induced, Endonuclease-mediated (CRISPR), Endonuclease-mediated (TALEN), Gene trapped, QTL, Radiation induced, Spontaneous, Targeted, Transgenic, Transposon induced",,FALSE,,mutationDetails,,,list like +mutationMethod,"The method used to alter the resource, vocabulary aligned with and expanded upon MGI allele origin types. ","Chemically induced (ENU), Chemically induced (other), Chemically and radiation induced, Endonuclease-mediated (CRISPR), Endonuclease-mediated (TALEN), Gene trapped, QTL, Radiation induced, Spontaneous, Targeted, Transgenic, Transposon induced, Unknown",,FALSE,,mutationDetails,,,list like alleleType,"The type of genetic alteration of the resource, vocabulary aligned with MGI allele subtypes. ","Conditional ready, Constitutively active, Dominant negative, Humanized sequence, Hypomorph, Inducible, Inserted expressed sequence, Knockdown, Modified isoform(s), No functional change, Null/knockout, Recombinase, Reporter, RMCE-Ready, Transactivator, Transposase, Transposon concatemer",,FALSE,,mutationDetails,,,list like affectedGeneSymbol,"The gene symbol for the mutated gene. (e.g. NF1, SUZ12, SMARCB1, P53, etc.)",,,FALSE,,mutationDetails,,, affectedGeneName,Gene name for the affected gene (e.g. neurofibromin 1),,,FALSE,,mutationDetails,,, From 0562d0f48411ad5feaf1c3434a2a966669d1071c Mon Sep 17 00:00:00 2001 From: "nf-osi[bot]" Date: Thu, 26 Oct 2023 20:56:05 +0000 Subject: [PATCH 60/97] Add changes --- nf-research-tools.jsonld | 128 ++++++++++++++++++++++++++++++++++++++- 1 file changed, 127 insertions(+), 1 deletion(-) diff --git a/nf-research-tools.jsonld b/nf-research-tools.jsonld index edb7ef72..ee0b6ddf 100644 --- a/nf-research-tools.jsonld +++ b/nf-research-tools.jsonld @@ -734,6 +734,9 @@ }, { "@id": "bts:usageRequirements" + }, + { + "@id": "bts:mutationMethod" } ], "schema:isPartOf": { @@ -8975,7 +8978,7 @@ { "@id": "bts:mutationType", "@type": "rdf:Property", - "rdfs:comment": "The type of the mutation, vocabulary aligned with MGI mutation types.", + "rdfs:comment": "The type of the mutation, vocabulary aligned with MGI mutation types, and expanded to include additional types.", "rdfs:label": "mutationType", "schema:domainIncludes": [ { @@ -9039,6 +9042,24 @@ }, { "@id": "bts:Viralinsertion" + }, + { + "@id": "bts:Microdeletion" + }, + { + "@id": "bts:Homozygousdeletion" + }, + { + "@id": "bts:Lossofheterozygosity(mitoticrecombination)" + }, + { + "@id": "bts:Lossofheterozygosity(deletion)" + }, + { + "@id": "bts:Stableknockdown" + }, + { + "@id": "bts:ExogenousDNAexpression" } ], "sms:displayName": "mutationType", @@ -9096,6 +9117,9 @@ }, { "@id": "bts:Transposoninduced" + }, + { + "@id": "bts:Unknown" } ], "sms:displayName": "mutationMethod", @@ -9512,6 +9536,108 @@ "sms:required": "sms:false", "sms:validationRules": [] }, + { + "@id": "bts:Microdeletion", + "@type": "rdfs:Class", + "rdfs:comment": "TBD", + "rdfs:label": "Microdeletion", + "rdfs:subClassOf": [ + { + "@id": "bts:mutationType" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Microdeletion", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:Homozygousdeletion", + "@type": "rdfs:Class", + "rdfs:comment": "TBD", + "rdfs:label": "Homozygousdeletion", + "rdfs:subClassOf": [ + { + "@id": "bts:mutationType" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Homozygous deletion", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:Lossofheterozygosity(mitoticrecombination)", + "@type": "rdfs:Class", + "rdfs:comment": "TBD", + "rdfs:label": "Lossofheterozygosity(mitoticrecombination)", + "rdfs:subClassOf": [ + { + "@id": "bts:mutationType" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Loss of heterozygosity (mitotic recombination)", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:Lossofheterozygosity(deletion)", + "@type": "rdfs:Class", + "rdfs:comment": "TBD", + "rdfs:label": "Lossofheterozygosity(deletion)", + "rdfs:subClassOf": [ + { + "@id": "bts:mutationType" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Loss of heterozygosity (deletion)", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:Stableknockdown", + "@type": "rdfs:Class", + "rdfs:comment": "TBD", + "rdfs:label": "Stableknockdown", + "rdfs:subClassOf": [ + { + "@id": "bts:mutationType" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Stable knockdown", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:ExogenousDNAexpression", + "@type": "rdfs:Class", + "rdfs:comment": "TBD", + "rdfs:label": "ExogenousDNAexpression", + "rdfs:subClassOf": [ + { + "@id": "bts:mutationType" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Exogenous DNA expression", + "sms:required": "sms:false", + "sms:validationRules": [] + }, { "@id": "bts:Chemicallyinduced(ENU)", "@type": "rdfs:Class", From 247e4a49ecdbf57e4e61b7e2070e164e6a163dc8 Mon Sep 17 00:00:00 2001 From: Robert Allaway Date: Thu, 26 Oct 2023 15:56:19 -0500 Subject: [PATCH 61/97] Update nf_research_tools.rdb.model.csv --- nf_research_tools.rdb.model.csv | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/nf_research_tools.rdb.model.csv b/nf_research_tools.rdb.model.csv index e06d97c0..766d6db7 100644 --- a/nf_research_tools.rdb.model.csv +++ b/nf_research_tools.rdb.model.csv @@ -119,7 +119,7 @@ proteinVariation,The protein consequence of the mutation described in sequence v animalModelMutation,"A description of the specific mutation(s) created in the genome. (e.g. A neomycin resistance cassette replaced the first 42 codons of exon 31, the exon 31 splice acceptor site, and approximately 2 kb of intron 30.)",,,FALSE,,mutationDetails,,, humanClinVarMutation,"The human equivalent, of the mutation being described in ClinVar/HGVS notation. Can be used to link animal model mutations to the mutation they are modeling in human disease. ",,,FALSE,,mutationDetails,,, chromosome,Chromosome number of affected gene. (e.g. 11),,,FALSE,,mutationDetails,,, -mutation,(intermediary table),,"Component, mutationId, mutationDetailsId, animalModelId, cellLineId",FALSE,,mutation,"mutationId, mutationDetailsId, animalModelId, cellLineId","mutationDetails, animalModelDetails, cellLineDetails", +mutation,(intermediary table),,"Component, mutationId, mutationDetailsId, animalModelId, cellLineId",FALSE,,mutation,"mutationId, mutationDetailsId","mutationDetails, animalModelDetails, cellLineDetails", mutationId,A unique identifier for the mutation burden of the resource.,,,FALSE,,mutation,,, animalModelDetails,"An animal sufficiently like humans in its anatomy, physiology, or response to a pathogen to be used in medical research in order to obtain results that can be extrapolated to human medicine.",,"Component, animalModelId, donorId, transplantationDonorId, animalState, backgroundStrain, backgroundSubstrain, strainNomenclature, generation, transplantationType, animalModelGeneticDisorder, animalModelOfManifestation",FALSE,,animalModelDetails,"animalModelId, donorId, animalState, backgroundStrain, backgroundSubstrain, strainNomenclature, generation, transplantationType, transplantationDonorId, animalModelGeneticDisorder, animalModelOfManifestation",donor, animalModelId,A unique identifier for the animal model.,,,TRUE,,animalModelDetails,,, From 9f5239305643bfafde5dbac9b96fe473cf2c5cb7 Mon Sep 17 00:00:00 2001 From: "nf-osi[bot]" Date: Thu, 26 Oct 2023 20:58:06 +0000 Subject: [PATCH 62/97] Add changes --- nf-research-tools.jsonld | 6 ------ 1 file changed, 6 deletions(-) diff --git a/nf-research-tools.jsonld b/nf-research-tools.jsonld index ee0b6ddf..ca82b728 100644 --- a/nf-research-tools.jsonld +++ b/nf-research-tools.jsonld @@ -450,9 +450,6 @@ "rdfs:comment": "A unique identifier for the animal model.", "rdfs:label": "animalModelId", "schema:domainIncludes": [ - { - "@id": "bts:Mutation" - }, { "@id": "bts:AnimalModelDetails" } @@ -472,9 +469,6 @@ "schema:domainIncludes": [ { "@id": "bts:CellLineDetails" - }, - { - "@id": "bts:Mutation" } ], "schema:isPartOf": { From d3435ba559eed61828b7a93e9aac0674fe1c7466 Mon Sep 17 00:00:00 2001 From: Robert Allaway Date: Thu, 26 Oct 2023 16:01:02 -0500 Subject: [PATCH 63/97] Update nf_research_tools.rdb.model.csv --- nf_research_tools.rdb.model.csv | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/nf_research_tools.rdb.model.csv b/nf_research_tools.rdb.model.csv index 766d6db7..08eeb644 100644 --- a/nf_research_tools.rdb.model.csv +++ b/nf_research_tools.rdb.model.csv @@ -119,7 +119,7 @@ proteinVariation,The protein consequence of the mutation described in sequence v animalModelMutation,"A description of the specific mutation(s) created in the genome. (e.g. A neomycin resistance cassette replaced the first 42 codons of exon 31, the exon 31 splice acceptor site, and approximately 2 kb of intron 30.)",,,FALSE,,mutationDetails,,, humanClinVarMutation,"The human equivalent, of the mutation being described in ClinVar/HGVS notation. Can be used to link animal model mutations to the mutation they are modeling in human disease. ",,,FALSE,,mutationDetails,,, chromosome,Chromosome number of affected gene. (e.g. 11),,,FALSE,,mutationDetails,,, -mutation,(intermediary table),,"Component, mutationId, mutationDetailsId, animalModelId, cellLineId",FALSE,,mutation,"mutationId, mutationDetailsId","mutationDetails, animalModelDetails, cellLineDetails", +mutation,(intermediary table),,"Component, mutationId, mutationDetailsId",FALSE,,mutation,"mutationId, mutationDetailsId, animalModelId, cellLineId","mutationDetails, animalModelDetails, cellLineDetails", mutationId,A unique identifier for the mutation burden of the resource.,,,FALSE,,mutation,,, animalModelDetails,"An animal sufficiently like humans in its anatomy, physiology, or response to a pathogen to be used in medical research in order to obtain results that can be extrapolated to human medicine.",,"Component, animalModelId, donorId, transplantationDonorId, animalState, backgroundStrain, backgroundSubstrain, strainNomenclature, generation, transplantationType, animalModelGeneticDisorder, animalModelOfManifestation",FALSE,,animalModelDetails,"animalModelId, donorId, animalState, backgroundStrain, backgroundSubstrain, strainNomenclature, generation, transplantationType, transplantationDonorId, animalModelGeneticDisorder, animalModelOfManifestation",donor, animalModelId,A unique identifier for the animal model.,,,TRUE,,animalModelDetails,,, From 8ef779fc81569afe1b0e0dcc623c23dbd3b29477 Mon Sep 17 00:00:00 2001 From: "nf-osi[bot]" Date: Thu, 26 Oct 2023 21:02:39 +0000 Subject: [PATCH 64/97] Add changes --- nf-research-tools.jsonld | 12 ++++++------ 1 file changed, 6 insertions(+), 6 deletions(-) diff --git a/nf-research-tools.jsonld b/nf-research-tools.jsonld index ca82b728..cf22b0cb 100644 --- a/nf-research-tools.jsonld +++ b/nf-research-tools.jsonld @@ -450,6 +450,9 @@ "rdfs:comment": "A unique identifier for the animal model.", "rdfs:label": "animalModelId", "schema:domainIncludes": [ + { + "@id": "bts:Mutation" + }, { "@id": "bts:AnimalModelDetails" } @@ -469,6 +472,9 @@ "schema:domainIncludes": [ { "@id": "bts:CellLineDetails" + }, + { + "@id": "bts:Mutation" } ], "schema:isPartOf": { @@ -10160,12 +10166,6 @@ }, { "@id": "bts:mutationDetailsId" - }, - { - "@id": "bts:animalModelId" - }, - { - "@id": "bts:cellLineId" } ], "sms:validationRules": [] From d9b8be3fcf35bb2a960f3a71108be85c9ae01c43 Mon Sep 17 00:00:00 2001 From: Robert Allaway Date: Thu, 26 Oct 2023 16:08:39 -0500 Subject: [PATCH 65/97] Update nf_research_tools.rdb.model.csv --- nf_research_tools.rdb.model.csv | 12 ++++++------ 1 file changed, 6 insertions(+), 6 deletions(-) diff --git a/nf_research_tools.rdb.model.csv b/nf_research_tools.rdb.model.csv index 08eeb644..9ec82867 100644 --- a/nf_research_tools.rdb.model.csv +++ b/nf_research_tools.rdb.model.csv @@ -17,7 +17,7 @@ howToAcquire,How to acquire a particular resource. ,,,TRUE,,resource,,, dateAdded,The date that the resource was originally added.,,,TRUE,,resource,,, dateModified,The last update of the resource metadata (not including observations).,,,TRUE,,resource,,, geneticReagentDetails,Genetic reagents.,,"Component, geneticReagentId, insertName, insertEntrezId, gRNAshRNASequence, insertSize, insertSpecies, nTerminalTag, cTerminalTag, cloningMethod, 5primeCloningSite, 5primeSiteDestroyed, 3primeCloningSite, 3primeSiteDestroyed, promoter, 5primer, 3primer, vectorBackbone, vectorType, backboneSize, totalSize, bacterialResistance, selectableMarker, copyNumber, growthTemp, growthStrain, hazardous",FALSE,,geneticReagentDetails,"geneticReagentId, insertName, insertEntrezId, gRNAshRNASequence, insertSize, insertSpecies, nTerminalTag, cTerminalTag, cloningMethod, 5primeCloningSite, 5primeSiteDestroyed, 3primeCloningSite, 3primeSiteDestroyed, promoter, 5primer, 3primer, vectorBackbone, vectorType, backboneSize, totalSize, bacterialResistance, selectableMarker, copyNumber, growthTemp, growthStrain, hazardous",, -geneticReagentId,A unique identifier for the reagent.,,,TRUE,,geneticReagentDetails,,, +geneticReagentId,A unique identifier for the reagent.,,,FALSE,,geneticReagentDetails,,, insertName,Name of the main gene insert in the plasmid.,,,TRUE,,geneticReagentDetails,,, insertEntrezId,The entrez gene id for the gene insert,,,FALSE,,geneticReagentDetails,,, gRNAshRNASequence,"The sequence of the gRNA or shRNA for the gene insert, if present. ",,,FALSE,,geneticReagentDetails,,, @@ -53,7 +53,7 @@ vendorName,The name of the vendor.,,,FALSE,,vendor,,, vendorURL,The vendor website url associated with the resource.,,,FALSE,,vendor,,, biobankDetails,"A large collection of biological or medical data and tissue samples, amassed for research purposes.",,"Component, biobankId, resourceId, biobankName, biobankURL, specimenType, specimenTissueType, tumorType, diseaseType, specimenPreparationMethod, specimenFormat",FALSE,,biobankDetails,"biobankId, resourceId, biobankName, biobankURL, specimenType, specimenTissueType, tumorType, diseaseType, specimenPreparationMethod, specimenFormat",, biobankName,The name of the biobank. ,,,TRUE,,biobankDetails,,, -biobankId,A unique identifier for the biobank.,,,TRUE,,biobankDetails,,, +biobankId,A unique identifier for the biobank.,,,FALSE,,biobankDetails,,, biobankURL,A URL for the biobank landing page.,,,TRUE,,biobankDetails,,, specimenType,The types of specimens that are banked.,"human tissue, xenograft tumors, cell lines",,TRUE,,biobankDetails,,,list like specimenTissueType,The types of tissues that are banked.,"Blood, Tumor, Cerebrospinal Fluid, Nerve, Skin, Bone, Brain",,TRUE,,biobankDetails,,,list like @@ -79,7 +79,7 @@ source,"The source of resource application information (e.g. Vendor, Community)" applications,"One or more uses for the resource (e.g. western blot, immunofluorescence)","Western Blot, Immunofluorescence, ELISA, Immunohistochemistry, Immunoprecipitation, Tumor Growth Studies, Immunohistochemistry (Paraffin-Embedded), Immunocytochemistry, Immunohistochemistry (Frozen Sections), Flow Cytometry, Affinity Purification, Microarray",,TRUE,,resourceApplication,,,list like links,shareable links related to the resource,,,FALSE,,resourceApplication,,,list like antibodyDetails,"A blood protein produced in response to and counteracting a specific antigen. Antibodies combine chemically with substances which the body recognizes as alien, such as bacteria, viruses, and foreign substances in the blood.",,"Component, antibodyId, uniprotId, targetAntigen, clonality, cloneId, reactiveSpecies, conjugate, hostOrganism",FALSE,,antibodyDetails,,, -antibodyId,A unique identifier for the antibody.,,,TRUE,,antibodyDetails,"antibodyId, uniprotId, targetAntigen, clonality, cloneId, reactiveSpecies, conjugate, hostOrganism",, +antibodyId,A unique identifier for the antibody.,,,FALSE,,antibodyDetails,"antibodyId, uniprotId, targetAntigen, clonality, cloneId, reactiveSpecies, conjugate, hostOrganism",, uniprotId,The uniprotId of the protein targeted by the antibody.,,,FALSE,,antibodyDetails,,, targetAntigen,Antigen that is targeted by antibody. (e.g. Neurofibromin 1 human),,,TRUE,,antibodyDetails,,, clonality,They type of clonality of the antibody,"Unknown, Cocktail, Control, Isotype Control, Monoclonal, Monoclonal Secondary, Polyclonal, Polyclonal Secondary, OligoClonal, Recombinant, Recombinant Monoclonal, Recombinant Monoclonal Secondary, Recombinant Polyclonal, Recombinant Polyclonal Secondary",,TRUE,,antibodyDetails,,, @@ -95,7 +95,7 @@ sex,The sex of the individual from which the resource was derived from.,"Male, F age,That age of the individual from which the resource was derived from.,,,FALSE,,donor,,, race,The ethnicity of the individual the resource was derived from.,,,FALSE,,donor,,, cellLineDetails,A cell culture selected for uniformity from a cell population derived from a usually homogeneous tissue source (such as an organ).,,"Component, cellLineId, donorId, organ, tissue, cellLineCategory, originYear, strProfile, populationDoublingTime, resistance, contaminatedMisidentified, cellLineGeneticDisorder, cellLineManifestation",FALSE,,cellLineDetails,"cellLineId, donorId, organ, tissue, cellLineCategory, originYear, strProfile, populationDoublingTime, resistance, contaminatedMisidentified, cellLineGeneticDisorder, cellLineManifestation",donor, -cellLineId,A unique identifier for the cell line.,,,TRUE,,cellLineDetails,,, +cellLineId,A unique identifier for the cell line.,,,FALSE,,cellLineDetails,,, organ,The organ the cell line is derived from.,"Biliary Tract, Bladder, Bone Marrow, Brain, Breast, Bronchial Tree, Duct, Epididymis, Esophagus, Fallopian Tube, Gallbladder, Gland, Gonad, Heart, Intestine, Kidney, Liver, Lung, Lymph Node, Ear, Eye, Nose, Tongue, Pancreas, Penis, Seminal Vesicle, Skin, Spermatic Cord, Spinal Cord, Spleen, Stomach, Thymus Gland, Tonsil, Trachea, Tracheobronchial Tree, Ureter, Urethra, Uterus, Vagina, Vulva",,FALSE,,cellLineDetails,,, tissue,The tissue the cell line is derived from.,"Blood, Bone marrow, Buccal mucosa, Buffy coat, Cerebral cortex, Dorsal root ganglion, Embryonic tissue, Meninges, Nerve tissue, Optic nerve, Plasma, Primary tumor, Sciatic nerve, Serum, Splenocyte, Unspecified, Urine, Whole brain",,FALSE,,cellLineDetails,,, cellLineCategory,The category to which the cell line belongs.,"Cancer cell line, Conditionally immortalized cell line, Embryonic stem cell, Factor-dependent cell line, Finite cell line, Hybridoma, Hybrid cell line, Induced pluripotent stem cell, Somatic stem cell, Spontaneously immortalized cell line, Stromal cell line, Telomerase immortalized cell line, Transformed cell line, Undefined cell line type",,FALSE,,cellLineDetails,,, @@ -119,10 +119,10 @@ proteinVariation,The protein consequence of the mutation described in sequence v animalModelMutation,"A description of the specific mutation(s) created in the genome. (e.g. A neomycin resistance cassette replaced the first 42 codons of exon 31, the exon 31 splice acceptor site, and approximately 2 kb of intron 30.)",,,FALSE,,mutationDetails,,, humanClinVarMutation,"The human equivalent, of the mutation being described in ClinVar/HGVS notation. Can be used to link animal model mutations to the mutation they are modeling in human disease. ",,,FALSE,,mutationDetails,,, chromosome,Chromosome number of affected gene. (e.g. 11),,,FALSE,,mutationDetails,,, -mutation,(intermediary table),,"Component, mutationId, mutationDetailsId",FALSE,,mutation,"mutationId, mutationDetailsId, animalModelId, cellLineId","mutationDetails, animalModelDetails, cellLineDetails", +mutation,(intermediary table),,"Component, mutationId, mutationDetailsId, animalModelId, cellLineId",FALSE,,mutation,"mutationId, mutationDetailsId, animalModelId, cellLineId","mutationDetails, animalModelDetails, cellLineDetails", mutationId,A unique identifier for the mutation burden of the resource.,,,FALSE,,mutation,,, animalModelDetails,"An animal sufficiently like humans in its anatomy, physiology, or response to a pathogen to be used in medical research in order to obtain results that can be extrapolated to human medicine.",,"Component, animalModelId, donorId, transplantationDonorId, animalState, backgroundStrain, backgroundSubstrain, strainNomenclature, generation, transplantationType, animalModelGeneticDisorder, animalModelOfManifestation",FALSE,,animalModelDetails,"animalModelId, donorId, animalState, backgroundStrain, backgroundSubstrain, strainNomenclature, generation, transplantationType, transplantationDonorId, animalModelGeneticDisorder, animalModelOfManifestation",donor, -animalModelId,A unique identifier for the animal model.,,,TRUE,,animalModelDetails,,, +animalModelId,A unique identifier for the animal model.,,,FALSE,,animalModelDetails,,, animalState,"State the animal is in according to the vendor/developer. (e.g. embryo, sperm, live)",,,FALSE,,animalModelDetails,,, backgroundStrain,"An assigned name that describes the genetic make-up (all its alleles at all loci) except the mutated gene of interest and a very small amount of other genetic material, generally from one or two other strains. Correct strain nomenclature indicates what a mutant strain’s background is.",,,FALSE,,animalModelDetails,,, backgroundSubstrain,"The substrain is a particular variety of a strain. For example, a C57BL/6 mice may have a substrain of C57BL/6J, C57BL/6Tac, or another substrain. ",,,FALSE,Sage Bionetworks,animalModelDetails,,, From ec6b9fd76392833e67a8a6cfb2fc37ab0c6987e0 Mon Sep 17 00:00:00 2001 From: "nf-osi[bot]" Date: Thu, 26 Oct 2023 21:10:40 +0000 Subject: [PATCH 66/97] Add changes --- nf-research-tools.jsonld | 16 +++++++++++----- 1 file changed, 11 insertions(+), 5 deletions(-) diff --git a/nf-research-tools.jsonld b/nf-research-tools.jsonld index cf22b0cb..bff0d4c6 100644 --- a/nf-research-tools.jsonld +++ b/nf-research-tools.jsonld @@ -461,7 +461,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "animalModelId", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -481,7 +481,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "cellLineId", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -498,7 +498,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "geneticReagentId", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -515,7 +515,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "antibodyId", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -532,7 +532,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "biobankId", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -10166,6 +10166,12 @@ }, { "@id": "bts:mutationDetailsId" + }, + { + "@id": "bts:animalModelId" + }, + { + "@id": "bts:cellLineId" } ], "sms:validationRules": [] From 6051ad1eca6590304c43535b1b155ce1f4053615 Mon Sep 17 00:00:00 2001 From: Robert Allaway Date: Thu, 26 Oct 2023 16:12:27 -0500 Subject: [PATCH 67/97] add new resource appliations --- nf_research_tools.rdb.model.csv | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/nf_research_tools.rdb.model.csv b/nf_research_tools.rdb.model.csv index 9ec82867..196463e6 100644 --- a/nf_research_tools.rdb.model.csv +++ b/nf_research_tools.rdb.model.csv @@ -76,7 +76,7 @@ observationLink,"A link/reference related to the observation being recorded. If resourceApplication,"Applications the resource can be used for. (i.e. western blot, immunofluorescence, etc.)",,"Component, resourceApplicationId, resourceId, source, applications, links",FALSE,,resourceApplication,"resourceApplicationId, resourceId, source, applications, links",resource, resourceApplicationId,A unique identifier for resrouce Application,,,TRUE,,resourceApplication,,, source,"The source of resource application information (e.g. Vendor, Community)","Community-reported, Investigator-reported, Vendor-reported",,TRUE,,resourceApplication,,, -applications,"One or more uses for the resource (e.g. western blot, immunofluorescence)","Western Blot, Immunofluorescence, ELISA, Immunohistochemistry, Immunoprecipitation, Tumor Growth Studies, Immunohistochemistry (Paraffin-Embedded), Immunocytochemistry, Immunohistochemistry (Frozen Sections), Flow Cytometry, Affinity Purification, Microarray",,TRUE,,resourceApplication,,,list like +applications,"One or more uses for the resource (e.g. western blot, immunofluorescence)","Western Blot, Immunofluorescence, ELISA, Immunohistochemistry, Immunoprecipitation, Immunochromatography, Tumor Growth Studies, Gold Immunochromatographic Assay, Immunoelectron Microscopy, Immunogold Silver Staining, Immunohistochemistry (Paraffin-Embedded), Immunocytochemistry, Immunohistochemistry (Frozen Sections), Flow Cytometry, Affinity Purification, Microarray",,TRUE,,resourceApplication,,,list like links,shareable links related to the resource,,,FALSE,,resourceApplication,,,list like antibodyDetails,"A blood protein produced in response to and counteracting a specific antigen. Antibodies combine chemically with substances which the body recognizes as alien, such as bacteria, viruses, and foreign substances in the blood.",,"Component, antibodyId, uniprotId, targetAntigen, clonality, cloneId, reactiveSpecies, conjugate, hostOrganism",FALSE,,antibodyDetails,,, antibodyId,A unique identifier for the antibody.,,,FALSE,,antibodyDetails,"antibodyId, uniprotId, targetAntigen, clonality, cloneId, reactiveSpecies, conjugate, hostOrganism",, From 50691cb9cf17af26f38f3159f5a87316365cc557 Mon Sep 17 00:00:00 2001 From: "nf-osi[bot]" Date: Thu, 26 Oct 2023 21:13:57 +0000 Subject: [PATCH 68/97] Add changes --- nf-research-tools.jsonld | 80 ++++++++++++++++++++++++++++++++++++++++ 1 file changed, 80 insertions(+) diff --git a/nf-research-tools.jsonld b/nf-research-tools.jsonld index bff0d4c6..b0d6a466 100644 --- a/nf-research-tools.jsonld +++ b/nf-research-tools.jsonld @@ -5516,9 +5516,21 @@ { "@id": "bts:Immunoprecipitation" }, + { + "@id": "bts:Immunochromatography" + }, { "@id": "bts:TumorGrowthStudies" }, + { + "@id": "bts:GoldImmunochromatographicAssay" + }, + { + "@id": "bts:ImmunoelectronMicroscopy" + }, + { + "@id": "bts:ImmunogoldSilverStaining" + }, { "@id": "bts:Immunohistochemistry(Paraffin-Embedded)" }, @@ -5699,6 +5711,23 @@ "sms:required": "sms:false", "sms:validationRules": [] }, + { + "@id": "bts:Immunochromatography", + "@type": "rdfs:Class", + "rdfs:comment": "TBD", + "rdfs:label": "Immunochromatography", + "rdfs:subClassOf": [ + { + "@id": "bts:applications" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Immunochromatography", + "sms:required": "sms:false", + "sms:validationRules": [] + }, { "@id": "bts:TumorGrowthStudies", "@type": "rdfs:Class", @@ -5716,6 +5745,57 @@ "sms:required": "sms:false", "sms:validationRules": [] }, + { + "@id": "bts:GoldImmunochromatographicAssay", + "@type": "rdfs:Class", + "rdfs:comment": "TBD", + "rdfs:label": "GoldImmunochromatographicAssay", + "rdfs:subClassOf": [ + { + "@id": "bts:applications" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Gold Immunochromatographic Assay", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:ImmunoelectronMicroscopy", + "@type": "rdfs:Class", + "rdfs:comment": "TBD", + "rdfs:label": "ImmunoelectronMicroscopy", + "rdfs:subClassOf": [ + { + "@id": "bts:applications" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Immunoelectron Microscopy", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:ImmunogoldSilverStaining", + "@type": "rdfs:Class", + "rdfs:comment": "TBD", + "rdfs:label": "ImmunogoldSilverStaining", + "rdfs:subClassOf": [ + { + "@id": "bts:applications" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Immunogold Silver Staining", + "sms:required": "sms:false", + "sms:validationRules": [] + }, { "@id": "bts:Immunohistochemistry(Paraffin-Embedded)", "@type": "rdfs:Class", From cf26a28e70f52979babaa1083fcc6d709c7a975f Mon Sep 17 00:00:00 2001 From: Robert Allaway Date: Thu, 26 Oct 2023 18:12:33 -0500 Subject: [PATCH 69/97] Update nf_research_tools.rdb.model.csv --- nf_research_tools.rdb.model.csv | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/nf_research_tools.rdb.model.csv b/nf_research_tools.rdb.model.csv index 196463e6..d7b8016e 100644 --- a/nf_research_tools.rdb.model.csv +++ b/nf_research_tools.rdb.model.csv @@ -1,6 +1,6 @@ Attribute,Description,Valid Values,DependsOn,Required,Source,Parent,Properties,DependsOn Component,Validation Rules Component,Type of submitted information.,,,TRUE,,,,, -resource,"A tool used in the research process (i.e. animal model, cell line, etc.)",,"Component, resourceId, rrid, resourceName, synonyms, resourceType, description, usageRequirements, howToAcquire, dateAdded, dateModified",FALSE,,,"resourceId, rrid, resourceName, synonyms, resourceType, description, usageRequirements, howToAcquire, dateAdded, dateModified","geneticReagent, antibody, cellLine, animalModel", +resource,"A tool used in the research process (i.e. animal model, cell line, etc.)",,"Component, resourceId, rrid, resourceName, synonyms, resourceType, description, aiSummary, usageRequirements, howToAcquire, dateAdded, dateModified",FALSE,,,"resourceId, rrid, resourceName, synonyms, resourceType, description, aiSummary, usageRequirements, howToAcquire, dateAdded, dateModified","geneticReagent, antibody, cellLine, animalModel", resourceId,A unique identifier for the resource.,,,TRUE,,resource,,, rrid,"The RRID, a standard resource identifier that will facilitate interoperability with other databases, and is an increasingly-used identifier for publications https://scicrunch.org/resources if available",,,FALSE,,resource,,, resourceName,The “canonical” name of the resource,,,TRUE,,resource,,, @@ -12,6 +12,7 @@ Genetic Reagent,,,geneticReagentId,,,resourceType,,, Antibody,,,antibodyId,,,resourceType,,, Biobank,,,biobankId,,,resourceType,,, description,Free text description/summary/overview/purpose of the resource.,,,FALSE,,resource,,, +aiSummary,A large language model-generated summary of the resource (currently generated with gpt-3.5-turbo).,,,FALSE,,resource,,, usageRequirements,Any known restrictions on use of the resource. ,"data sharing required, non-commercial use only, re-distribution not permitted, generation of germ line transmitting chimeras not permitted, creation of functional gametes not permitted, generation of interspecies chimeras not permitted, human cloning not permitted, cannot be used for treatment purposes, IRB documentation required, special licencing restrictions (see vendor for more information), unknown",,FALSE,,resource,,,list like howToAcquire,How to acquire a particular resource. ,,,TRUE,,resource,,, dateAdded,The date that the resource was originally added.,,,TRUE,,resource,,, From b774d1e6991fcfc3e58e95607e73a3fca1cecd11 Mon Sep 17 00:00:00 2001 From: "nf-osi[bot]" Date: Thu, 26 Oct 2023 23:14:25 +0000 Subject: [PATCH 70/97] Add changes --- nf-research-tools.jsonld | 20 ++++++++++++++++++++ 1 file changed, 20 insertions(+) diff --git a/nf-research-tools.jsonld b/nf-research-tools.jsonld index b0d6a466..1656bc09 100644 --- a/nf-research-tools.jsonld +++ b/nf-research-tools.jsonld @@ -75,6 +75,9 @@ { "@id": "bts:description" }, + { + "@id": "bts:aiSummary" + }, { "@id": "bts:usageRequirements" }, @@ -229,6 +232,23 @@ "sms:required": "sms:false", "sms:validationRules": [] }, + { + "@id": "bts:aiSummary", + "@type": "rdf:Property", + "rdfs:comment": "A large language model-generated summary of the resource (currently generated with gpt-3.5-turbo).", + "rdfs:label": "aiSummary", + "schema:domainIncludes": [ + { + "@id": "bts:Resource" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "aiSummary", + "sms:required": "sms:false", + "sms:validationRules": [] + }, { "@id": "bts:usageRequirements", "@type": "rdf:Property", From b2dddcc63bf32ee923b9d129ead1aad64f5ab7aa Mon Sep 17 00:00:00 2001 From: Robert Allaway Date: Tue, 7 Nov 2023 15:51:08 -0600 Subject: [PATCH 71/97] fix phase caps --- nf_research_tools.rdb.model.csv | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/nf_research_tools.rdb.model.csv b/nf_research_tools.rdb.model.csv index d7b8016e..2ec7248e 100644 --- a/nf_research_tools.rdb.model.csv +++ b/nf_research_tools.rdb.model.csv @@ -67,8 +67,8 @@ observationId,A unique identifier for the observation.,,,TRUE,,observation,,, observationSubmitterName,The name of the person submitting the observation. ,,,TRUE,,observation,,, synapseId,The synapse identifier for the person submitting the observation. ,,,FALSE,,observation,,, observationText,Free text observation about the resource.,,,TRUE,,observation,,, -observationType,Type of observation,"Body Length, Body weight, Coat Color, Disease Susceptibility, Feed Intake, Feeding Behavior, Growth rate, Motor Activity, Organ Development, Reflex Development, Reproductive Behavior, Social Behavior, Swimming Behavior, Tumor Growth, Issue, Depositor Comment, Usage Instructions, General Comment or Review, Other",,TRUE,,observation,,, -observationPhase,What t=0 for the observationTime is,"Adolescent, Adult, Death Phase, Embryo, Juvenile, Larval, Log Phase, Neonatal, Postnatal, Prenatal, Pupal, Stationary Phase, Weanling",,FALSE,,observation,,, +observationType,Type of observation,"Body Length, Body Weight, Coat Color, Disease Susceptibility, Feed Intake, Feeding Behavior, Growth Rate, Motor Activity, Organ Development, Reflex Development, Reproductive Behavior, Social Behavior, Swimming Behavior, Tumor Growth, Issue, Depositor Comment, Usage Instructions, General Comment or Review, Other",,TRUE,,observation,,, +observationPhase,What t=0 for the observationTime is,"adolescent, adult, death phase, embryo, juvenile, larval, log phase, neonatal, postnatal, prenatal, pupal, stationary phase, weanling",,FALSE,,observation,,, observationTime,When the observation was.,,,FALSE,,observation,,, observationTimeUnits,The unit of time pertaining to the observation,"days, weeks, months, years, hours, minutes, seconds, milliseconds",,FALSE,,observation,,, reliabilityRating,A 1-5 rating of the reliability of the resource; does the resource produce consistent and reliable results? Does the resource reasonably recapitulate the human disease it is intended to model? ,"1,2,3,4,5",,FALSE,,observation,,, From 2f388aa4e8342e6abaed79e0a606f6e9ae4862d1 Mon Sep 17 00:00:00 2001 From: Robert Allaway Date: Tue, 7 Nov 2023 15:51:44 -0600 Subject: [PATCH 72/97] make observationType list friendly --- nf_research_tools.rdb.model.csv | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/nf_research_tools.rdb.model.csv b/nf_research_tools.rdb.model.csv index 2ec7248e..25c6f455 100644 --- a/nf_research_tools.rdb.model.csv +++ b/nf_research_tools.rdb.model.csv @@ -67,7 +67,7 @@ observationId,A unique identifier for the observation.,,,TRUE,,observation,,, observationSubmitterName,The name of the person submitting the observation. ,,,TRUE,,observation,,, synapseId,The synapse identifier for the person submitting the observation. ,,,FALSE,,observation,,, observationText,Free text observation about the resource.,,,TRUE,,observation,,, -observationType,Type of observation,"Body Length, Body Weight, Coat Color, Disease Susceptibility, Feed Intake, Feeding Behavior, Growth Rate, Motor Activity, Organ Development, Reflex Development, Reproductive Behavior, Social Behavior, Swimming Behavior, Tumor Growth, Issue, Depositor Comment, Usage Instructions, General Comment or Review, Other",,TRUE,,observation,,, +observationType,Type of observation,"Body Length, Body Weight, Coat Color, Disease Susceptibility, Feed Intake, Feeding Behavior, Growth Rate, Motor Activity, Organ Development, Reflex Development, Reproductive Behavior, Social Behavior, Swimming Behavior, Tumor Growth, Issue, Depositor Comment, Usage Instructions, General Comment or Review, Other",,TRUE,,observation,,,list like observationPhase,What t=0 for the observationTime is,"adolescent, adult, death phase, embryo, juvenile, larval, log phase, neonatal, postnatal, prenatal, pupal, stationary phase, weanling",,FALSE,,observation,,, observationTime,When the observation was.,,,FALSE,,observation,,, observationTimeUnits,The unit of time pertaining to the observation,"days, weeks, months, years, hours, minutes, seconds, milliseconds",,FALSE,,observation,,, From 5e3b5f389a8fe75ac6e6ab94692536a43b6c324c Mon Sep 17 00:00:00 2001 From: "nf-osi[bot]" Date: Tue, 7 Nov 2023 21:53:42 +0000 Subject: [PATCH 73/97] Add changes --- nf-research-tools.jsonld | 64 +++++++++++++++++++++------------------- 1 file changed, 33 insertions(+), 31 deletions(-) diff --git a/nf-research-tools.jsonld b/nf-research-tools.jsonld index 1656bc09..2f7b6dd6 100644 --- a/nf-research-tools.jsonld +++ b/nf-research-tools.jsonld @@ -4304,7 +4304,7 @@ "@id": "bts:BodyLength" }, { - "@id": "bts:Bodyweight" + "@id": "bts:BodyWeight" }, { "@id": "bts:CoatColor" @@ -4319,7 +4319,7 @@ "@id": "bts:FeedingBehavior" }, { - "@id": "bts:Growthrate" + "@id": "bts:GrowthRate" }, { "@id": "bts:MotorActivity" @@ -4360,7 +4360,9 @@ ], "sms:displayName": "observationType", "sms:required": "sms:true", - "sms:validationRules": [] + "sms:validationRules": [ + "list like" + ] }, { "@id": "bts:observationPhase", @@ -4383,7 +4385,7 @@ "@id": "bts:Adult" }, { - "@id": "bts:DeathPhase" + "@id": "bts:Deathphase" }, { "@id": "bts:Embryo" @@ -4395,7 +4397,7 @@ "@id": "bts:Larval" }, { - "@id": "bts:LogPhase" + "@id": "bts:Logphase" }, { "@id": "bts:Neonatal" @@ -4410,7 +4412,7 @@ "@id": "bts:Pupal" }, { - "@id": "bts:StationaryPhase" + "@id": "bts:Stationaryphase" }, { "@id": "bts:Weanling" @@ -4675,10 +4677,10 @@ "sms:validationRules": [] }, { - "@id": "bts:Bodyweight", + "@id": "bts:BodyWeight", "@type": "rdfs:Class", "rdfs:comment": "TBD", - "rdfs:label": "Bodyweight", + "rdfs:label": "BodyWeight", "rdfs:subClassOf": [ { "@id": "bts:observationType" @@ -4687,7 +4689,7 @@ "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Body weight", + "sms:displayName": "Body Weight", "sms:required": "sms:false", "sms:validationRules": [] }, @@ -4760,10 +4762,10 @@ "sms:validationRules": [] }, { - "@id": "bts:Growthrate", + "@id": "bts:GrowthRate", "@type": "rdfs:Class", "rdfs:comment": "TBD", - "rdfs:label": "Growthrate", + "rdfs:label": "GrowthRate", "rdfs:subClassOf": [ { "@id": "bts:observationType" @@ -4772,7 +4774,7 @@ "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Growth rate", + "sms:displayName": "Growth Rate", "sms:required": "sms:false", "sms:validationRules": [] }, @@ -4976,7 +4978,7 @@ "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Adolescent", + "sms:displayName": "adolescent", "sms:required": "sms:false", "sms:validationRules": [] }, @@ -4993,15 +4995,15 @@ "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Adult", + "sms:displayName": "adult", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:DeathPhase", + "@id": "bts:Deathphase", "@type": "rdfs:Class", "rdfs:comment": "TBD", - "rdfs:label": "DeathPhase", + "rdfs:label": "Deathphase", "rdfs:subClassOf": [ { "@id": "bts:observationPhase" @@ -5010,7 +5012,7 @@ "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Death Phase", + "sms:displayName": "death phase", "sms:required": "sms:false", "sms:validationRules": [] }, @@ -5027,7 +5029,7 @@ "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Embryo", + "sms:displayName": "embryo", "sms:required": "sms:false", "sms:validationRules": [] }, @@ -5044,7 +5046,7 @@ "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Juvenile", + "sms:displayName": "juvenile", "sms:required": "sms:false", "sms:validationRules": [] }, @@ -5061,15 +5063,15 @@ "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Larval", + "sms:displayName": "larval", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:LogPhase", + "@id": "bts:Logphase", "@type": "rdfs:Class", "rdfs:comment": "TBD", - "rdfs:label": "LogPhase", + "rdfs:label": "Logphase", "rdfs:subClassOf": [ { "@id": "bts:observationPhase" @@ -5078,7 +5080,7 @@ "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Log Phase", + "sms:displayName": "log phase", "sms:required": "sms:false", "sms:validationRules": [] }, @@ -5095,7 +5097,7 @@ "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Neonatal", + "sms:displayName": "neonatal", "sms:required": "sms:false", "sms:validationRules": [] }, @@ -5112,7 +5114,7 @@ "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Postnatal", + "sms:displayName": "postnatal", "sms:required": "sms:false", "sms:validationRules": [] }, @@ -5129,7 +5131,7 @@ "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Prenatal", + "sms:displayName": "prenatal", "sms:required": "sms:false", "sms:validationRules": [] }, @@ -5146,15 +5148,15 @@ "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Pupal", + "sms:displayName": "pupal", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:StationaryPhase", + "@id": "bts:Stationaryphase", "@type": "rdfs:Class", "rdfs:comment": "TBD", - "rdfs:label": "StationaryPhase", + "rdfs:label": "Stationaryphase", "rdfs:subClassOf": [ { "@id": "bts:observationPhase" @@ -5163,7 +5165,7 @@ "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Stationary Phase", + "sms:displayName": "stationary phase", "sms:required": "sms:false", "sms:validationRules": [] }, @@ -5180,7 +5182,7 @@ "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Weanling", + "sms:displayName": "weanling", "sms:required": "sms:false", "sms:validationRules": [] }, From ac6141d7d9a698d84a717e717ce15558d480b36e Mon Sep 17 00:00:00 2001 From: Robert Allaway Date: Tue, 7 Nov 2023 16:04:31 -0600 Subject: [PATCH 74/97] Update nf_research_tools.rdb.model.csv --- nf_research_tools.rdb.model.csv | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/nf_research_tools.rdb.model.csv b/nf_research_tools.rdb.model.csv index 25c6f455..c3d84ab7 100644 --- a/nf_research_tools.rdb.model.csv +++ b/nf_research_tools.rdb.model.csv @@ -85,7 +85,7 @@ uniprotId,The uniprotId of the protein targeted by the antibody.,,,FALSE,,antibo targetAntigen,Antigen that is targeted by antibody. (e.g. Neurofibromin 1 human),,,TRUE,,antibodyDetails,,, clonality,They type of clonality of the antibody,"Unknown, Cocktail, Control, Isotype Control, Monoclonal, Monoclonal Secondary, Polyclonal, Polyclonal Secondary, OligoClonal, Recombinant, Recombinant Monoclonal, Recombinant Monoclonal Secondary, Recombinant Polyclonal, Recombinant Polyclonal Secondary",,TRUE,,antibodyDetails,,, cloneId,Identification of clone (e.g. 2D1),,,FALSE,,antibodyDetails,,, -reactiveSpecies,Species the antibody has been shown to crossreact with the target protein. ,"Human, Mouse, Rat, Chicken, Rabbit, Pig, Dog, Zebrafish, Fish, Non-human primate, Guinea pig, Hamster, Cow, Monkey, Avian, Horse, Rodent, Drosophila",,TRUE,,antibodyDetails,,,list like +reactiveSpecies,Species the antibody has been shown to crossreact with the target protein. ,"Human, Mouse, Rat, Chicken, Rabbit, Pig, Dog, Zebrafish, Fish, Non-human primate, Guinea pig, Hamster, Cow, Monkey, Avian, Horse, Rodent, Drosophila, Unknown",,TRUE,,antibodyDetails,,,list like conjugate,Is the antibody conjugated or nonconjugated,"Conjugated, Nonconjugated",,TRUE,,antibodyDetails,,, hostOrganism,The species of the organism that hosts the antibody,"Mouse, Rabbit",,TRUE,,antibodyDetails,,, donor,"A person, animal, etc. who is the contributor of the resource.",,"Component, donorId, parentDonorId, transplantationDonorId, species, sex, age, race",FALSE,,donor,"donorId, parentDonorId, transplantationDonorId, species, sex, age, race",, @@ -97,7 +97,7 @@ age,That age of the individual from which the resource was derived from.,,,FALSE race,The ethnicity of the individual the resource was derived from.,,,FALSE,,donor,,, cellLineDetails,A cell culture selected for uniformity from a cell population derived from a usually homogeneous tissue source (such as an organ).,,"Component, cellLineId, donorId, organ, tissue, cellLineCategory, originYear, strProfile, populationDoublingTime, resistance, contaminatedMisidentified, cellLineGeneticDisorder, cellLineManifestation",FALSE,,cellLineDetails,"cellLineId, donorId, organ, tissue, cellLineCategory, originYear, strProfile, populationDoublingTime, resistance, contaminatedMisidentified, cellLineGeneticDisorder, cellLineManifestation",donor, cellLineId,A unique identifier for the cell line.,,,FALSE,,cellLineDetails,,, -organ,The organ the cell line is derived from.,"Biliary Tract, Bladder, Bone Marrow, Brain, Breast, Bronchial Tree, Duct, Epididymis, Esophagus, Fallopian Tube, Gallbladder, Gland, Gonad, Heart, Intestine, Kidney, Liver, Lung, Lymph Node, Ear, Eye, Nose, Tongue, Pancreas, Penis, Seminal Vesicle, Skin, Spermatic Cord, Spinal Cord, Spleen, Stomach, Thymus Gland, Tonsil, Trachea, Tracheobronchial Tree, Ureter, Urethra, Uterus, Vagina, Vulva",,FALSE,,cellLineDetails,,, +organ,The organ the cell line is derived from.,"Biliary Tract, Bladder, Bone Marrow, Brain, Breast, Bronchial Tree, Duct, Epididymis, Esophagus, Fallopian Tube, Gallbladder, Gland, Gonad, Heart, Intestine, Kidney, Liver, Lung, Lymph Node, Ear, Eye, Nose, Tongue, Pancreas, Penis, Seminal Vesicle, Skin, Spermatic Cord, Spinal Cord, Spleen, Stomach, Thymus Gland, Thyroid Gland, Tonsil, Trachea, Tracheobronchial Tree, Ureter, Urethra, Uterus, Vagina, Vulva",,FALSE,,cellLineDetails,,, tissue,The tissue the cell line is derived from.,"Blood, Bone marrow, Buccal mucosa, Buffy coat, Cerebral cortex, Dorsal root ganglion, Embryonic tissue, Meninges, Nerve tissue, Optic nerve, Plasma, Primary tumor, Sciatic nerve, Serum, Splenocyte, Unspecified, Urine, Whole brain",,FALSE,,cellLineDetails,,, cellLineCategory,The category to which the cell line belongs.,"Cancer cell line, Conditionally immortalized cell line, Embryonic stem cell, Factor-dependent cell line, Finite cell line, Hybridoma, Hybrid cell line, Induced pluripotent stem cell, Somatic stem cell, Spontaneously immortalized cell line, Stromal cell line, Telomerase immortalized cell line, Transformed cell line, Undefined cell line type",,FALSE,,cellLineDetails,,, originYear,The year the cell line orginated.,,,FALSE,,cellLineDetails,,, From 2fa04ba0d386c0075b39e64c31dd578b43ec38d1 Mon Sep 17 00:00:00 2001 From: "nf-osi[bot]" Date: Tue, 7 Nov 2023 22:06:02 +0000 Subject: [PATCH 75/97] Add changes --- nf-research-tools.jsonld | 26 ++++++++++++++++++++++++++ 1 file changed, 26 insertions(+) diff --git a/nf-research-tools.jsonld b/nf-research-tools.jsonld index 2f7b6dd6..8d7e0c0d 100644 --- a/nf-research-tools.jsonld +++ b/nf-research-tools.jsonld @@ -757,6 +757,9 @@ }, { "@id": "bts:mutationMethod" + }, + { + "@id": "bts:reactiveSpecies" } ], "schema:isPartOf": { @@ -6145,6 +6148,9 @@ }, { "@id": "bts:Drosophila" + }, + { + "@id": "bts:Unknown" } ], "sms:displayName": "reactiveSpecies", @@ -7432,6 +7438,9 @@ { "@id": "bts:ThymusGland" }, + { + "@id": "bts:ThyroidGland" + }, { "@id": "bts:Tonsil" }, @@ -8244,6 +8253,23 @@ "sms:required": "sms:false", "sms:validationRules": [] }, + { + "@id": "bts:ThyroidGland", + "@type": "rdfs:Class", + "rdfs:comment": "TBD", + "rdfs:label": "ThyroidGland", + "rdfs:subClassOf": [ + { + "@id": "bts:organ" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Thyroid Gland", + "sms:required": "sms:false", + "sms:validationRules": [] + }, { "@id": "bts:Tonsil", "@type": "rdfs:Class", From 4b989ce98371a8f58cfad6d9f03de7109bbdb98c Mon Sep 17 00:00:00 2001 From: Robert Allaway Date: Tue, 7 Nov 2023 17:10:50 -0600 Subject: [PATCH 76/97] Update nf_research_tools.rdb.model.csv --- nf_research_tools.rdb.model.csv | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/nf_research_tools.rdb.model.csv b/nf_research_tools.rdb.model.csv index c3d84ab7..8f8f1cb5 100644 --- a/nf_research_tools.rdb.model.csv +++ b/nf_research_tools.rdb.model.csv @@ -58,7 +58,7 @@ biobankId,A unique identifier for the biobank.,,,FALSE,,biobankDetails,,, biobankURL,A URL for the biobank landing page.,,,TRUE,,biobankDetails,,, specimenType,The types of specimens that are banked.,"human tissue, xenograft tumors, cell lines",,TRUE,,biobankDetails,,,list like specimenTissueType,The types of tissues that are banked.,"Blood, Tumor, Cerebrospinal Fluid, Nerve, Skin, Bone, Brain",,TRUE,,biobankDetails,,,list like -tumorType,"The types of tumors that are banked, if applicable.","cutaneous neurofibroma, plexiform neurofibroma, atypical neurofibroma, schwannoma, meningioma, malignant peripheral nerve sheath tumor, low grade glioma, high grade glioma, pheochromocytoma, optic nerve glioma, atypical neurofibroma, neurofibroma NOS, diffuse infiltrating neurofibroma, brain NOS, other",,TRUE,,biobankDetails,,,list like +tumorType,"The types of tumors that are banked, if applicable.","cutaneous neurofibroma, plexiform neurofibroma, atypical neurofibroma, schwannoma, meningioma, malignant peripheral nerve sheath tumor, low grade glioma, high grade glioma, pheochromocytoma, optic nerve glioma, atypical neurofibroma, neurofibroma NOS, diffuse infiltrating neurofibroma, brain NOS, Other",,TRUE,,biobankDetails,,,list like diseaseType,"The diseases of the banked specimens, if applicable.","Neurofibromatosis type 1, Neurofibromatosis type 2, Schwannomatosis",,TRUE,,biobankDetails,,,list like specimenPreparationMethod,The preservation methods used by the biobank.,"Fresh collected, Flash frozen, FFPE, Cryopreserved, OCT, RNA later, Formalin-fixed, Ethanol",,TRUE,,biobankDetails,,,list like specimenFormat,How the specimens have been processed in preparation for distribution.,"whole tumor, slide, cells, whole cell lysate, DNA, RNA",,TRUE,,biobankDetails,,,list like @@ -67,7 +67,7 @@ observationId,A unique identifier for the observation.,,,TRUE,,observation,,, observationSubmitterName,The name of the person submitting the observation. ,,,TRUE,,observation,,, synapseId,The synapse identifier for the person submitting the observation. ,,,FALSE,,observation,,, observationText,Free text observation about the resource.,,,TRUE,,observation,,, -observationType,Type of observation,"Body Length, Body Weight, Coat Color, Disease Susceptibility, Feed Intake, Feeding Behavior, Growth Rate, Motor Activity, Organ Development, Reflex Development, Reproductive Behavior, Social Behavior, Swimming Behavior, Tumor Growth, Issue, Depositor Comment, Usage Instructions, General Comment or Review, Other",,TRUE,,observation,,,list like +observationType,Type of observation,"Body Length, Body Weight, Coat Color, Disease Susceptibility, Feed Intake, Feeding Behavior, Growth Rate, Motor Activity, Organ Development, Reflex Development, Reproductive Behavior, Social Behavior, Swimming Behavior, Tumor Growth, Issue, Depositor Comment, Usage Instructions, General Comment or Review, Lifespan, Other",,TRUE,,observation,,,list like observationPhase,What t=0 for the observationTime is,"adolescent, adult, death phase, embryo, juvenile, larval, log phase, neonatal, postnatal, prenatal, pupal, stationary phase, weanling",,FALSE,,observation,,, observationTime,When the observation was.,,,FALSE,,observation,,, observationTimeUnits,The unit of time pertaining to the observation,"days, weeks, months, years, hours, minutes, seconds, milliseconds",,FALSE,,observation,,, From c6d6c28edcb59a4cee9fa5ed6cea0ac294b5fedc Mon Sep 17 00:00:00 2001 From: "nf-osi[bot]" Date: Tue, 7 Nov 2023 23:12:09 +0000 Subject: [PATCH 77/97] Add changes --- nf-research-tools.jsonld | 22 +++++++++++++++++++++- 1 file changed, 21 insertions(+), 1 deletion(-) diff --git a/nf-research-tools.jsonld b/nf-research-tools.jsonld index 8d7e0c0d..e4291b4a 100644 --- a/nf-research-tools.jsonld +++ b/nf-research-tools.jsonld @@ -2156,7 +2156,7 @@ "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "other", + "sms:displayName": "Other", "sms:required": "sms:false", "sms:validationRules": [] }, @@ -4357,6 +4357,9 @@ { "@id": "bts:GeneralCommentorReview" }, + { + "@id": "bts:Lifespan" + }, { "@id": "bts:Other" } @@ -4968,6 +4971,23 @@ "sms:required": "sms:false", "sms:validationRules": [] }, + { + "@id": "bts:Lifespan", + "@type": "rdfs:Class", + "rdfs:comment": "TBD", + "rdfs:label": "Lifespan", + "rdfs:subClassOf": [ + { + "@id": "bts:observationType" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Lifespan", + "sms:required": "sms:false", + "sms:validationRules": [] + }, { "@id": "bts:Adolescent", "@type": "rdfs:Class", From 9c911812e6865a2ae2748e36240686c1c541a98e Mon Sep 17 00:00:00 2001 From: Robert Allaway Date: Tue, 7 Nov 2023 17:13:42 -0600 Subject: [PATCH 78/97] Update nf_research_tools.rdb.model.csv --- nf_research_tools.rdb.model.csv | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/nf_research_tools.rdb.model.csv b/nf_research_tools.rdb.model.csv index 8f8f1cb5..f881c3a7 100644 --- a/nf_research_tools.rdb.model.csv +++ b/nf_research_tools.rdb.model.csv @@ -87,7 +87,7 @@ clonality,They type of clonality of the antibody,"Unknown, Cocktail, Control, Is cloneId,Identification of clone (e.g. 2D1),,,FALSE,,antibodyDetails,,, reactiveSpecies,Species the antibody has been shown to crossreact with the target protein. ,"Human, Mouse, Rat, Chicken, Rabbit, Pig, Dog, Zebrafish, Fish, Non-human primate, Guinea pig, Hamster, Cow, Monkey, Avian, Horse, Rodent, Drosophila, Unknown",,TRUE,,antibodyDetails,,,list like conjugate,Is the antibody conjugated or nonconjugated,"Conjugated, Nonconjugated",,TRUE,,antibodyDetails,,, -hostOrganism,The species of the organism that hosts the antibody,"Mouse, Rabbit",,TRUE,,antibodyDetails,,, +hostOrganism,The species of the organism that hosts the antibody,"Mouse, Rabbit, Unknown",,TRUE,,antibodyDetails,,, donor,"A person, animal, etc. who is the contributor of the resource.",,"Component, donorId, parentDonorId, transplantationDonorId, species, sex, age, race",FALSE,,donor,"donorId, parentDonorId, transplantationDonorId, species, sex, age, race",, donorId,A uniqe identifier for donor.,,,TRUE,,donor,,, parentDonorId,The ID of the parent donor.,,donorId,FALSE,,donor,,, From 09d5663aa299aa554066009bb32e7bbc50fdbe29 Mon Sep 17 00:00:00 2001 From: "nf-osi[bot]" Date: Tue, 7 Nov 2023 23:15:01 +0000 Subject: [PATCH 79/97] Add changes --- nf-research-tools.jsonld | 6 ++++++ 1 file changed, 6 insertions(+) diff --git a/nf-research-tools.jsonld b/nf-research-tools.jsonld index e4291b4a..f7ef54ca 100644 --- a/nf-research-tools.jsonld +++ b/nf-research-tools.jsonld @@ -746,6 +746,9 @@ { "@id": "bts:hazardous" }, + { + "@id": "bts:hostOrganism" + }, { "@id": "bts:sex" }, @@ -6223,6 +6226,9 @@ }, { "@id": "bts:Rabbit" + }, + { + "@id": "bts:Unknown" } ], "sms:displayName": "hostOrganism", From 9228ef982c5c998d7577f9750806e67762a42dd0 Mon Sep 17 00:00:00 2001 From: Robert Allaway Date: Tue, 7 Nov 2023 18:19:18 -0600 Subject: [PATCH 80/97] update caps for vendor url --- nf_research_tools.rdb.model.csv | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/nf_research_tools.rdb.model.csv b/nf_research_tools.rdb.model.csv index f881c3a7..a82a8e4d 100644 --- a/nf_research_tools.rdb.model.csv +++ b/nf_research_tools.rdb.model.csv @@ -48,10 +48,10 @@ vendorItem,The resource item associated with a vendor.,,"Component, vendorItemId vendorItemId,A unique identifier for the resource associated with a vendor. ,,,TRUE,,vendorItem,,, catalogNumber,The catalog number associated with the resource pertaining to the vendor that sells the resource.,,,TRUE,,vendorItem,,, catalogNumberURL,The url linking to the resource on the vendor's website. ,,,FALSE,,vendorItem,,, -vendor,A person or compnay offering the resource for sale.,,"Component, vendorId, vendorName, vendorURL",FALSE,,vendor,"vendorId, vendorName, vendorURL",, +vendor,A person or compnay offering the resource for sale.,,"Component, vendorId, vendorName, vendorUrl",FALSE,,vendor,"vendorId, vendorName, vendorUrl",, vendorId,A unique identifier for the vendor.,,,TRUE,,vendor,,, vendorName,The name of the vendor.,,,FALSE,,vendor,,, -vendorURL,The vendor website url associated with the resource.,,,FALSE,,vendor,,, +vendorUrl,The vendor website url associated with the resource.,,,FALSE,,vendor,,, biobankDetails,"A large collection of biological or medical data and tissue samples, amassed for research purposes.",,"Component, biobankId, resourceId, biobankName, biobankURL, specimenType, specimenTissueType, tumorType, diseaseType, specimenPreparationMethod, specimenFormat",FALSE,,biobankDetails,"biobankId, resourceId, biobankName, biobankURL, specimenType, specimenTissueType, tumorType, diseaseType, specimenPreparationMethod, specimenFormat",, biobankName,The name of the biobank. ,,,TRUE,,biobankDetails,,, biobankId,A unique identifier for the biobank.,,,FALSE,,biobankDetails,,, From fb63db672336cda6eba3392d8151de93669681cd Mon Sep 17 00:00:00 2001 From: "nf-osi[bot]" Date: Wed, 8 Nov 2023 00:21:34 +0000 Subject: [PATCH 81/97] Add changes --- nf-research-tools.jsonld | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/nf-research-tools.jsonld b/nf-research-tools.jsonld index f7ef54ca..85de3ed7 100644 --- a/nf-research-tools.jsonld +++ b/nf-research-tools.jsonld @@ -3045,7 +3045,7 @@ "@id": "bts:vendorName" }, { - "@id": "bts:vendorURL" + "@id": "bts:vendorUrl" } ], "sms:validationRules": [] @@ -3068,10 +3068,10 @@ "sms:validationRules": [] }, { - "@id": "bts:vendorURL", + "@id": "bts:vendorUrl", "@type": "rdf:Property", "rdfs:comment": "The vendor website url associated with the resource.", - "rdfs:label": "vendorURL", + "rdfs:label": "vendorUrl", "schema:domainIncludes": [ { "@id": "bts:Vendor" @@ -3080,7 +3080,7 @@ "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "vendorURL", + "sms:displayName": "vendorUrl", "sms:required": "sms:false", "sms:validationRules": [] }, From c3002796348a84871dfa857e0d6fc9e8e898f4ed Mon Sep 17 00:00:00 2001 From: Robert Allaway Date: Thu, 9 Nov 2023 08:49:05 -0600 Subject: [PATCH 82/97] Update nf_research_tools.rdb.model.csv --- nf_research_tools.rdb.model.csv | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/nf_research_tools.rdb.model.csv b/nf_research_tools.rdb.model.csv index a82a8e4d..39a9e9c5 100644 --- a/nf_research_tools.rdb.model.csv +++ b/nf_research_tools.rdb.model.csv @@ -1,6 +1,6 @@ Attribute,Description,Valid Values,DependsOn,Required,Source,Parent,Properties,DependsOn Component,Validation Rules Component,Type of submitted information.,,,TRUE,,,,, -resource,"A tool used in the research process (i.e. animal model, cell line, etc.)",,"Component, resourceId, rrid, resourceName, synonyms, resourceType, description, aiSummary, usageRequirements, howToAcquire, dateAdded, dateModified",FALSE,,,"resourceId, rrid, resourceName, synonyms, resourceType, description, aiSummary, usageRequirements, howToAcquire, dateAdded, dateModified","geneticReagent, antibody, cellLine, animalModel", +resource,"A tool used in the research process (i.e. animal model, cell line, etc.)",,"Component, resourceId, rrid, resourceName, synonyms, resourceType, description, aiSummary, usageRequirements, howToAcquire, dateAdded, dateModified",FALSE,,,"resourceId, rrid, resourceName, synonyms, resourceType, description, aiSummary, usageRequirements, howToAcquire, dateAdded, dateModified","geneticReagentDetails, antibodyDetails, cellLineDetails, animalModelDetails", resourceId,A unique identifier for the resource.,,,TRUE,,resource,,, rrid,"The RRID, a standard resource identifier that will facilitate interoperability with other databases, and is an increasingly-used identifier for publications https://scicrunch.org/resources if available",,,FALSE,,resource,,, resourceName,The “canonical” name of the resource,,,TRUE,,resource,,, From 9ad1b0e362e38c9fe6e69aa09883e7f8ab5dc226 Mon Sep 17 00:00:00 2001 From: "nf-osi[bot]" Date: Thu, 9 Nov 2023 14:50:50 +0000 Subject: [PATCH 83/97] Add changes --- nf-research-tools.jsonld | 626 +++++++++++++++++++-------------------- 1 file changed, 313 insertions(+), 313 deletions(-) diff --git a/nf-research-tools.jsonld b/nf-research-tools.jsonld index 85de3ed7..40ba7b35 100644 --- a/nf-research-tools.jsonld +++ b/nf-research-tools.jsonld @@ -41,16 +41,16 @@ "sms:required": "sms:false", "sms:requiresComponent": [ { - "@id": "bts:GeneticReagent" + "@id": "bts:GeneticReagentDetails" }, { - "@id": "bts:Antibody" + "@id": "bts:AntibodyDetails" }, { - "@id": "bts:CellLine" + "@id": "bts:CellLineDetails" }, { - "@id": "bts:AnimalModel" + "@id": "bts:AnimalModelDetails" } ], "sms:requiresDependency": [ @@ -355,32 +355,279 @@ "sms:validationRules": [] }, { - "@id": "bts:GeneticReagent", + "@id": "bts:GeneticReagentDetails", "@type": "rdfs:Class", - "rdfs:comment": "TBD", - "rdfs:label": "GeneticReagent", + "rdfs:comment": "Genetic reagents.", + "rdfs:label": "GeneticReagentDetails", "rdfs:subClassOf": [ { - "@id": "bts:resourceType" + "@id": "bts:Thing" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Genetic Reagent", + "sms:displayName": "geneticReagentDetails", "sms:required": "sms:false", "sms:requiresDependency": [ + { + "@id": "bts:Component" + }, { "@id": "bts:geneticReagentId" + }, + { + "@id": "bts:insertName" + }, + { + "@id": "bts:insertEntrezId" + }, + { + "@id": "bts:gRNAshRNASequence" + }, + { + "@id": "bts:insertSize" + }, + { + "@id": "bts:insertSpecies" + }, + { + "@id": "bts:nTerminalTag" + }, + { + "@id": "bts:cTerminalTag" + }, + { + "@id": "bts:cloningMethod" + }, + { + "@id": "bts:5primeCloningSite" + }, + { + "@id": "bts:5primeSiteDestroyed" + }, + { + "@id": "bts:3primeCloningSite" + }, + { + "@id": "bts:3primeSiteDestroyed" + }, + { + "@id": "bts:promoter" + }, + { + "@id": "bts:5primer" + }, + { + "@id": "bts:3primer" + }, + { + "@id": "bts:vectorBackbone" + }, + { + "@id": "bts:vectorType" + }, + { + "@id": "bts:backboneSize" + }, + { + "@id": "bts:totalSize" + }, + { + "@id": "bts:bacterialResistance" + }, + { + "@id": "bts:selectableMarker" + }, + { + "@id": "bts:copyNumber" + }, + { + "@id": "bts:growthTemp" + }, + { + "@id": "bts:growthStrain" + }, + { + "@id": "bts:hazardous" } ], "sms:validationRules": [] }, { - "@id": "bts:Antibody", + "@id": "bts:AntibodyDetails", + "@type": "rdfs:Class", + "rdfs:comment": "A blood protein produced in response to and counteracting a specific antigen. Antibodies combine chemically with substances which the body recognizes as alien, such as bacteria, viruses, and foreign substances in the blood.", + "rdfs:label": "AntibodyDetails", + "rdfs:subClassOf": [ + { + "@id": "bts:Thing" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "antibodyDetails", + "sms:required": "sms:false", + "sms:requiresDependency": [ + { + "@id": "bts:Component" + }, + { + "@id": "bts:antibodyId" + }, + { + "@id": "bts:uniprotId" + }, + { + "@id": "bts:targetAntigen" + }, + { + "@id": "bts:clonality" + }, + { + "@id": "bts:cloneId" + }, + { + "@id": "bts:reactiveSpecies" + }, + { + "@id": "bts:conjugate" + }, + { + "@id": "bts:hostOrganism" + } + ], + "sms:validationRules": [] + }, + { + "@id": "bts:CellLineDetails", + "@type": "rdfs:Class", + "rdfs:comment": "A cell culture selected for uniformity from a cell population derived from a usually homogeneous tissue source (such as an organ).", + "rdfs:label": "CellLineDetails", + "rdfs:subClassOf": [ + { + "@id": "bts:Thing" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "cellLineDetails", + "sms:required": "sms:false", + "sms:requiresComponent": [ + { + "@id": "bts:Donor" + } + ], + "sms:requiresDependency": [ + { + "@id": "bts:Component" + }, + { + "@id": "bts:cellLineId" + }, + { + "@id": "bts:donorId" + }, + { + "@id": "bts:organ" + }, + { + "@id": "bts:tissue" + }, + { + "@id": "bts:cellLineCategory" + }, + { + "@id": "bts:originYear" + }, + { + "@id": "bts:strProfile" + }, + { + "@id": "bts:populationDoublingTime" + }, + { + "@id": "bts:resistance" + }, + { + "@id": "bts:contaminatedMisidentified" + }, + { + "@id": "bts:cellLineGeneticDisorder" + }, + { + "@id": "bts:cellLineManifestation" + } + ], + "sms:validationRules": [] + }, + { + "@id": "bts:AnimalModelDetails", + "@type": "rdfs:Class", + "rdfs:comment": "An animal sufficiently like humans in its anatomy, physiology, or response to a pathogen to be used in medical research in order to obtain results that can be extrapolated to human medicine.", + "rdfs:label": "AnimalModelDetails", + "rdfs:subClassOf": [ + { + "@id": "bts:Thing" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "animalModelDetails", + "sms:required": "sms:false", + "sms:requiresComponent": [ + { + "@id": "bts:Donor" + } + ], + "sms:requiresDependency": [ + { + "@id": "bts:Component" + }, + { + "@id": "bts:animalModelId" + }, + { + "@id": "bts:donorId" + }, + { + "@id": "bts:transplantationDonorId" + }, + { + "@id": "bts:animalState" + }, + { + "@id": "bts:backgroundStrain" + }, + { + "@id": "bts:backgroundSubstrain" + }, + { + "@id": "bts:strainNomenclature" + }, + { + "@id": "bts:generation" + }, + { + "@id": "bts:transplantationType" + }, + { + "@id": "bts:animalModelGeneticDisorder" + }, + { + "@id": "bts:animalModelOfManifestation" + } + ], + "sms:validationRules": [] + }, + { + "@id": "bts:AnimalModel", "@type": "rdfs:Class", "rdfs:comment": "TBD", - "rdfs:label": "Antibody", + "rdfs:label": "AnimalModel", "rdfs:subClassOf": [ { "@id": "bts:resourceType" @@ -389,11 +636,11 @@ "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Antibody", + "sms:displayName": "Animal Model", "sms:required": "sms:false", "sms:requiresDependency": [ { - "@id": "bts:antibodyId" + "@id": "bts:animalModelId" } ], "sms:validationRules": [] @@ -421,10 +668,10 @@ "sms:validationRules": [] }, { - "@id": "bts:AnimalModel", + "@id": "bts:Antibody", "@type": "rdfs:Class", "rdfs:comment": "TBD", - "rdfs:label": "AnimalModel", + "rdfs:label": "Antibody", "rdfs:subClassOf": [ { "@id": "bts:resourceType" @@ -433,11 +680,33 @@ "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Animal Model", + "sms:displayName": "Antibody", "sms:required": "sms:false", "sms:requiresDependency": [ { - "@id": "bts:animalModelId" + "@id": "bts:antibodyId" + } + ], + "sms:validationRules": [] + }, + { + "@id": "bts:GeneticReagent", + "@type": "rdfs:Class", + "rdfs:comment": "TBD", + "rdfs:label": "GeneticReagent", + "rdfs:subClassOf": [ + { + "@id": "bts:resourceType" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Genetic Reagent", + "sms:required": "sms:false", + "sms:requiresDependency": [ + { + "@id": "bts:geneticReagentId" } ], "sms:validationRules": [] @@ -710,166 +979,66 @@ }, { "@id": "bts:Speciallicencingrestrictions(seevendorformoreinformation)", - "@type": "rdfs:Class", - "rdfs:comment": "TBD", - "rdfs:label": "Speciallicencingrestrictions(seevendorformoreinformation)", - "rdfs:subClassOf": [ - { - "@id": "bts:usageRequirements" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "special licencing restrictions (see vendor for more information)", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:Unknown", - "@type": "rdfs:Class", - "rdfs:comment": "TBD", - "rdfs:label": "Unknown", - "rdfs:subClassOf": [ - { - "@id": "bts:clonality" - }, - { - "@id": "bts:5primeSiteDestroyed" - }, - { - "@id": "bts:3primeSiteDestroyed" - }, - { - "@id": "bts:copyNumber" - }, - { - "@id": "bts:hazardous" - }, - { - "@id": "bts:hostOrganism" - }, - { - "@id": "bts:sex" - }, - { - "@id": "bts:cloningMethod" - }, - { - "@id": "bts:usageRequirements" - }, - { - "@id": "bts:mutationMethod" - }, - { - "@id": "bts:reactiveSpecies" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Unknown", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:GeneticReagentDetails", - "@type": "rdfs:Class", - "rdfs:comment": "Genetic reagents.", - "rdfs:label": "GeneticReagentDetails", + "@type": "rdfs:Class", + "rdfs:comment": "TBD", + "rdfs:label": "Speciallicencingrestrictions(seevendorformoreinformation)", "rdfs:subClassOf": [ { - "@id": "bts:Thing" + "@id": "bts:usageRequirements" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "geneticReagentDetails", + "sms:displayName": "special licencing restrictions (see vendor for more information)", "sms:required": "sms:false", - "sms:requiresDependency": [ - { - "@id": "bts:Component" - }, - { - "@id": "bts:geneticReagentId" - }, - { - "@id": "bts:insertName" - }, - { - "@id": "bts:insertEntrezId" - }, - { - "@id": "bts:gRNAshRNASequence" - }, - { - "@id": "bts:insertSize" - }, - { - "@id": "bts:insertSpecies" - }, - { - "@id": "bts:nTerminalTag" - }, - { - "@id": "bts:cTerminalTag" - }, - { - "@id": "bts:cloningMethod" - }, + "sms:validationRules": [] + }, + { + "@id": "bts:Unknown", + "@type": "rdfs:Class", + "rdfs:comment": "TBD", + "rdfs:label": "Unknown", + "rdfs:subClassOf": [ { - "@id": "bts:5primeCloningSite" + "@id": "bts:clonality" }, { "@id": "bts:5primeSiteDestroyed" }, - { - "@id": "bts:3primeCloningSite" - }, { "@id": "bts:3primeSiteDestroyed" }, { - "@id": "bts:promoter" - }, - { - "@id": "bts:5primer" - }, - { - "@id": "bts:3primer" - }, - { - "@id": "bts:vectorBackbone" - }, - { - "@id": "bts:vectorType" - }, - { - "@id": "bts:backboneSize" + "@id": "bts:copyNumber" }, { - "@id": "bts:totalSize" + "@id": "bts:hazardous" }, { - "@id": "bts:bacterialResistance" + "@id": "bts:hostOrganism" }, { - "@id": "bts:selectableMarker" + "@id": "bts:sex" }, { - "@id": "bts:copyNumber" + "@id": "bts:cloningMethod" }, { - "@id": "bts:growthTemp" + "@id": "bts:usageRequirements" }, { - "@id": "bts:growthStrain" + "@id": "bts:mutationMethod" }, { - "@id": "bts:hazardous" + "@id": "bts:reactiveSpecies" } ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Unknown", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -5946,52 +6115,6 @@ "sms:required": "sms:false", "sms:validationRules": [] }, - { - "@id": "bts:AntibodyDetails", - "@type": "rdfs:Class", - "rdfs:comment": "A blood protein produced in response to and counteracting a specific antigen. Antibodies combine chemically with substances which the body recognizes as alien, such as bacteria, viruses, and foreign substances in the blood.", - "rdfs:label": "AntibodyDetails", - "rdfs:subClassOf": [ - { - "@id": "bts:Thing" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "antibodyDetails", - "sms:required": "sms:false", - "sms:requiresDependency": [ - { - "@id": "bts:Component" - }, - { - "@id": "bts:antibodyId" - }, - { - "@id": "bts:uniprotId" - }, - { - "@id": "bts:targetAntigen" - }, - { - "@id": "bts:clonality" - }, - { - "@id": "bts:cloneId" - }, - { - "@id": "bts:reactiveSpecies" - }, - { - "@id": "bts:conjugate" - }, - { - "@id": "bts:hostOrganism" - } - ], - "sms:validationRules": [] - }, { "@id": "bts:uniprotId", "@type": "rdf:Property", @@ -7291,69 +7414,6 @@ "sms:required": "sms:false", "sms:validationRules": [] }, - { - "@id": "bts:CellLineDetails", - "@type": "rdfs:Class", - "rdfs:comment": "A cell culture selected for uniformity from a cell population derived from a usually homogeneous tissue source (such as an organ).", - "rdfs:label": "CellLineDetails", - "rdfs:subClassOf": [ - { - "@id": "bts:Thing" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "cellLineDetails", - "sms:required": "sms:false", - "sms:requiresComponent": [ - { - "@id": "bts:Donor" - } - ], - "sms:requiresDependency": [ - { - "@id": "bts:Component" - }, - { - "@id": "bts:cellLineId" - }, - { - "@id": "bts:donorId" - }, - { - "@id": "bts:organ" - }, - { - "@id": "bts:tissue" - }, - { - "@id": "bts:cellLineCategory" - }, - { - "@id": "bts:originYear" - }, - { - "@id": "bts:strProfile" - }, - { - "@id": "bts:populationDoublingTime" - }, - { - "@id": "bts:resistance" - }, - { - "@id": "bts:contaminatedMisidentified" - }, - { - "@id": "bts:cellLineGeneticDisorder" - }, - { - "@id": "bts:cellLineManifestation" - } - ], - "sms:validationRules": [] - }, { "@id": "bts:organ", "@type": "rdf:Property", @@ -10347,66 +10407,6 @@ "sms:required": "sms:false", "sms:validationRules": [] }, - { - "@id": "bts:AnimalModelDetails", - "@type": "rdfs:Class", - "rdfs:comment": "An animal sufficiently like humans in its anatomy, physiology, or response to a pathogen to be used in medical research in order to obtain results that can be extrapolated to human medicine.", - "rdfs:label": "AnimalModelDetails", - "rdfs:subClassOf": [ - { - "@id": "bts:Thing" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "animalModelDetails", - "sms:required": "sms:false", - "sms:requiresComponent": [ - { - "@id": "bts:Donor" - } - ], - "sms:requiresDependency": [ - { - "@id": "bts:Component" - }, - { - "@id": "bts:animalModelId" - }, - { - "@id": "bts:donorId" - }, - { - "@id": "bts:transplantationDonorId" - }, - { - "@id": "bts:animalState" - }, - { - "@id": "bts:backgroundStrain" - }, - { - "@id": "bts:backgroundSubstrain" - }, - { - "@id": "bts:strainNomenclature" - }, - { - "@id": "bts:generation" - }, - { - "@id": "bts:transplantationType" - }, - { - "@id": "bts:animalModelGeneticDisorder" - }, - { - "@id": "bts:animalModelOfManifestation" - } - ], - "sms:validationRules": [] - }, { "@id": "bts:animalState", "@type": "rdf:Property", From 7aee9446ffecfc2a46e5788930d38d3eb5b07279 Mon Sep 17 00:00:00 2001 From: Robert Allaway Date: Thu, 9 Nov 2023 08:57:22 -0600 Subject: [PATCH 84/97] Update nf_research_tools.rdb.model.csv --- nf_research_tools.rdb.model.csv | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/nf_research_tools.rdb.model.csv b/nf_research_tools.rdb.model.csv index 39a9e9c5..9dd21bf5 100644 --- a/nf_research_tools.rdb.model.csv +++ b/nf_research_tools.rdb.model.csv @@ -79,7 +79,7 @@ resourceApplicationId,A unique identifier for resrouce Application,,,TRUE,,resou source,"The source of resource application information (e.g. Vendor, Community)","Community-reported, Investigator-reported, Vendor-reported",,TRUE,,resourceApplication,,, applications,"One or more uses for the resource (e.g. western blot, immunofluorescence)","Western Blot, Immunofluorescence, ELISA, Immunohistochemistry, Immunoprecipitation, Immunochromatography, Tumor Growth Studies, Gold Immunochromatographic Assay, Immunoelectron Microscopy, Immunogold Silver Staining, Immunohistochemistry (Paraffin-Embedded), Immunocytochemistry, Immunohistochemistry (Frozen Sections), Flow Cytometry, Affinity Purification, Microarray",,TRUE,,resourceApplication,,,list like links,shareable links related to the resource,,,FALSE,,resourceApplication,,,list like -antibodyDetails,"A blood protein produced in response to and counteracting a specific antigen. Antibodies combine chemically with substances which the body recognizes as alien, such as bacteria, viruses, and foreign substances in the blood.",,"Component, antibodyId, uniprotId, targetAntigen, clonality, cloneId, reactiveSpecies, conjugate, hostOrganism",FALSE,,antibodyDetails,,, +antibodyDetails,"A blood protein produced in response to and counteracting a specific antigen. Antibodies combine chemically with substances which the body recognizes as alien, such as bacteria, viruses, and foreign substances in the blood.",,"Component, antibodyId, uniprotId, targetAntigen, clonality, cloneId, reactiveSpecies, conjugate, hostOrganism",FALSE,,antibodyDetails,"antibodyId, uniprotId, targetAntigen, clonality, cloneId, reactiveSpecies, conjugate, hostOrganism",, antibodyId,A unique identifier for the antibody.,,,FALSE,,antibodyDetails,"antibodyId, uniprotId, targetAntigen, clonality, cloneId, reactiveSpecies, conjugate, hostOrganism",, uniprotId,The uniprotId of the protein targeted by the antibody.,,,FALSE,,antibodyDetails,,, targetAntigen,Antigen that is targeted by antibody. (e.g. Neurofibromin 1 human),,,TRUE,,antibodyDetails,,, From 898b5c23b7dba2bf4ad5aca04072be54e7cbd869 Mon Sep 17 00:00:00 2001 From: "nf-osi[bot]" Date: Thu, 9 Nov 2023 14:58:45 +0000 Subject: [PATCH 85/97] Add changes --- nf-research-tools.jsonld | 25 +++++++++++++++++++++++-- 1 file changed, 23 insertions(+), 2 deletions(-) diff --git a/nf-research-tools.jsonld b/nf-research-tools.jsonld index 40ba7b35..72202fd4 100644 --- a/nf-research-tools.jsonld +++ b/nf-research-tools.jsonld @@ -792,10 +792,10 @@ }, { "@id": "bts:antibodyId", - "@type": "rdfs:Class", + "@type": "rdf:Property", "rdfs:comment": "A unique identifier for the antibody.", "rdfs:label": "antibodyId", - "rdfs:subClassOf": [ + "schema:domainIncludes": [ { "@id": "bts:AntibodyDetails" } @@ -6121,6 +6121,9 @@ "rdfs:comment": "The uniprotId of the protein targeted by the antibody.", "rdfs:label": "uniprotId", "schema:domainIncludes": [ + { + "@id": "bts:AntibodyDetails" + }, { "@id": "bts:antibodyId" } @@ -6138,6 +6141,9 @@ "rdfs:comment": "Antigen that is targeted by antibody. (e.g. Neurofibromin 1 human)", "rdfs:label": "targetAntigen", "schema:domainIncludes": [ + { + "@id": "bts:AntibodyDetails" + }, { "@id": "bts:antibodyId" } @@ -6155,6 +6161,9 @@ "rdfs:comment": "They type of clonality of the antibody", "rdfs:label": "clonality", "schema:domainIncludes": [ + { + "@id": "bts:AntibodyDetails" + }, { "@id": "bts:antibodyId" } @@ -6216,6 +6225,9 @@ "rdfs:comment": "Identification of clone (e.g. 2D1)", "rdfs:label": "cloneId", "schema:domainIncludes": [ + { + "@id": "bts:AntibodyDetails" + }, { "@id": "bts:antibodyId" } @@ -6233,6 +6245,9 @@ "rdfs:comment": "Species the antibody has been shown to crossreact with the target protein.", "rdfs:label": "reactiveSpecies", "schema:domainIncludes": [ + { + "@id": "bts:AntibodyDetails" + }, { "@id": "bts:antibodyId" } @@ -6311,6 +6326,9 @@ "rdfs:comment": "Is the antibody conjugated or nonconjugated", "rdfs:label": "conjugate", "schema:domainIncludes": [ + { + "@id": "bts:AntibodyDetails" + }, { "@id": "bts:antibodyId" } @@ -6336,6 +6354,9 @@ "rdfs:comment": "The species of the organism that hosts the antibody", "rdfs:label": "hostOrganism", "schema:domainIncludes": [ + { + "@id": "bts:AntibodyDetails" + }, { "@id": "bts:antibodyId" } From f3926a5ec993ea1378aed41d3db19487448d8f77 Mon Sep 17 00:00:00 2001 From: Robert Allaway Date: Thu, 9 Nov 2023 09:11:55 -0600 Subject: [PATCH 86/97] Update nf_research_tools.rdb.model.csv --- nf_research_tools.rdb.model.csv | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/nf_research_tools.rdb.model.csv b/nf_research_tools.rdb.model.csv index 9dd21bf5..73f86af7 100644 --- a/nf_research_tools.rdb.model.csv +++ b/nf_research_tools.rdb.model.csv @@ -1,6 +1,6 @@ Attribute,Description,Valid Values,DependsOn,Required,Source,Parent,Properties,DependsOn Component,Validation Rules Component,Type of submitted information.,,,TRUE,,,,, -resource,"A tool used in the research process (i.e. animal model, cell line, etc.)",,"Component, resourceId, rrid, resourceName, synonyms, resourceType, description, aiSummary, usageRequirements, howToAcquire, dateAdded, dateModified",FALSE,,,"resourceId, rrid, resourceName, synonyms, resourceType, description, aiSummary, usageRequirements, howToAcquire, dateAdded, dateModified","geneticReagentDetails, antibodyDetails, cellLineDetails, animalModelDetails", +resource,"A tool used in the research process (i.e. animal model, cell line, etc.)",,"Component, resourceId, rrid, resourceName, synonyms, resourceType, description, aiSummary, usageRequirements, howToAcquire, dateAdded, dateModified",FALSE,,,"resourceId, animalModelId, antibodyId, cellLineId, geneticReagentId, biobankId, rrid, resourceName, synonyms, resourceType, description, aiSummary, usageRequirements, howToAcquire, dateAdded, dateModified","geneticReagentDetails, antibodyDetails, cellLineDetails, animalModelDetails", resourceId,A unique identifier for the resource.,,,TRUE,,resource,,, rrid,"The RRID, a standard resource identifier that will facilitate interoperability with other databases, and is an increasingly-used identifier for publications https://scicrunch.org/resources if available",,,FALSE,,resource,,, resourceName,The “canonical” name of the resource,,,TRUE,,resource,,, From 3e8604cbea0d78d69b1edab38007b93985a4cda8 Mon Sep 17 00:00:00 2001 From: "nf-osi[bot]" Date: Thu, 9 Nov 2023 15:13:34 +0000 Subject: [PATCH 87/97] Add changes --- nf-research-tools.jsonld | 197 +++++++++++++++++++++------------------ 1 file changed, 106 insertions(+), 91 deletions(-) diff --git a/nf-research-tools.jsonld b/nf-research-tools.jsonld index 72202fd4..d70171b0 100644 --- a/nf-research-tools.jsonld +++ b/nf-research-tools.jsonld @@ -623,6 +623,112 @@ ], "sms:validationRules": [] }, + { + "@id": "bts:animalModelId", + "@type": "rdf:Property", + "rdfs:comment": "A unique identifier for the animal model.", + "rdfs:label": "animalModelId", + "schema:domainIncludes": [ + { + "@id": "bts:Resource" + }, + { + "@id": "bts:Mutation" + }, + { + "@id": "bts:AnimalModelDetails" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "animalModelId", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:antibodyId", + "@type": "rdf:Property", + "rdfs:comment": "A unique identifier for the antibody.", + "rdfs:label": "antibodyId", + "schema:domainIncludes": [ + { + "@id": "bts:Resource" + }, + { + "@id": "bts:AntibodyDetails" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "antibodyId", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:cellLineId", + "@type": "rdf:Property", + "rdfs:comment": "A unique identifier for the cell line.", + "rdfs:label": "cellLineId", + "schema:domainIncludes": [ + { + "@id": "bts:Resource" + }, + { + "@id": "bts:CellLineDetails" + }, + { + "@id": "bts:Mutation" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "cellLineId", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:geneticReagentId", + "@type": "rdf:Property", + "rdfs:comment": "A unique identifier for the reagent.", + "rdfs:label": "geneticReagentId", + "schema:domainIncludes": [ + { + "@id": "bts:Resource" + }, + { + "@id": "bts:GeneticReagentDetails" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "geneticReagentId", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:biobankId", + "@type": "rdf:Property", + "rdfs:comment": "A unique identifier for the biobank.", + "rdfs:label": "biobankId", + "schema:domainIncludes": [ + { + "@id": "bts:Resource" + }, + { + "@id": "bts:BiobankDetails" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "biobankId", + "sms:required": "sms:false", + "sms:validationRules": [] + }, { "@id": "bts:AnimalModel", "@type": "rdfs:Class", @@ -733,97 +839,6 @@ ], "sms:validationRules": [] }, - { - "@id": "bts:animalModelId", - "@type": "rdf:Property", - "rdfs:comment": "A unique identifier for the animal model.", - "rdfs:label": "animalModelId", - "schema:domainIncludes": [ - { - "@id": "bts:Mutation" - }, - { - "@id": "bts:AnimalModelDetails" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "animalModelId", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:cellLineId", - "@type": "rdf:Property", - "rdfs:comment": "A unique identifier for the cell line.", - "rdfs:label": "cellLineId", - "schema:domainIncludes": [ - { - "@id": "bts:CellLineDetails" - }, - { - "@id": "bts:Mutation" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "cellLineId", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:geneticReagentId", - "@type": "rdf:Property", - "rdfs:comment": "A unique identifier for the reagent.", - "rdfs:label": "geneticReagentId", - "schema:domainIncludes": [ - { - "@id": "bts:GeneticReagentDetails" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "geneticReagentId", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:antibodyId", - "@type": "rdf:Property", - "rdfs:comment": "A unique identifier for the antibody.", - "rdfs:label": "antibodyId", - "schema:domainIncludes": [ - { - "@id": "bts:AntibodyDetails" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "antibodyId", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:biobankId", - "@type": "rdf:Property", - "rdfs:comment": "A unique identifier for the biobank.", - "rdfs:label": "biobankId", - "schema:domainIncludes": [ - { - "@id": "bts:BiobankDetails" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "biobankId", - "sms:required": "sms:false", - "sms:validationRules": [] - }, { "@id": "bts:Datasharingrequired", "@type": "rdfs:Class", From b1c6dbdd262454689accd46d0fbb7c8bced19434 Mon Sep 17 00:00:00 2001 From: Robert Allaway Date: Thu, 9 Nov 2023 09:29:16 -0600 Subject: [PATCH 88/97] Update nf_research_tools.rdb.model.csv --- nf_research_tools.rdb.model.csv | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/nf_research_tools.rdb.model.csv b/nf_research_tools.rdb.model.csv index 73f86af7..a0b92b3a 100644 --- a/nf_research_tools.rdb.model.csv +++ b/nf_research_tools.rdb.model.csv @@ -1,6 +1,6 @@ Attribute,Description,Valid Values,DependsOn,Required,Source,Parent,Properties,DependsOn Component,Validation Rules Component,Type of submitted information.,,,TRUE,,,,, -resource,"A tool used in the research process (i.e. animal model, cell line, etc.)",,"Component, resourceId, rrid, resourceName, synonyms, resourceType, description, aiSummary, usageRequirements, howToAcquire, dateAdded, dateModified",FALSE,,,"resourceId, animalModelId, antibodyId, cellLineId, geneticReagentId, biobankId, rrid, resourceName, synonyms, resourceType, description, aiSummary, usageRequirements, howToAcquire, dateAdded, dateModified","geneticReagentDetails, antibodyDetails, cellLineDetails, animalModelDetails", +resource,"A tool used in the research process (i.e. animal model, cell line, etc.)",,"Component, resourceId, rrid, resourceName, synonyms, resourceType, description, aiSummary, usageRequirements, howToAcquire, dateAdded, dateModified",FALSE,,,"resourceId, animalModelId, antibodyId, cellLineId, geneticReagentId, biobankId, rrid, resourceName, synonyms, resourceType, description, aiSummary, usageRequirements, howToAcquire, dateAdded, dateModified","geneticReagentDetails, antibodyDetails, cellLineDetails, animalModelDetails, biobankDetails", resourceId,A unique identifier for the resource.,,,TRUE,,resource,,, rrid,"The RRID, a standard resource identifier that will facilitate interoperability with other databases, and is an increasingly-used identifier for publications https://scicrunch.org/resources if available",,,FALSE,,resource,,, resourceName,The “canonical” name of the resource,,,TRUE,,resource,,, From e43d49185406609498a97a76b8841e70fb36f514 Mon Sep 17 00:00:00 2001 From: "nf-osi[bot]" Date: Thu, 9 Nov 2023 15:31:30 +0000 Subject: [PATCH 89/97] Add changes --- nf-research-tools.jsonld | 107 ++++++++++++++++++++------------------- 1 file changed, 55 insertions(+), 52 deletions(-) diff --git a/nf-research-tools.jsonld b/nf-research-tools.jsonld index d70171b0..23c04407 100644 --- a/nf-research-tools.jsonld +++ b/nf-research-tools.jsonld @@ -51,6 +51,9 @@ }, { "@id": "bts:AnimalModelDetails" + }, + { + "@id": "bts:BiobankDetails" } ], "sms:requiresDependency": [ @@ -623,6 +626,58 @@ ], "sms:validationRules": [] }, + { + "@id": "bts:BiobankDetails", + "@type": "rdfs:Class", + "rdfs:comment": "A large collection of biological or medical data and tissue samples, amassed for research purposes.", + "rdfs:label": "BiobankDetails", + "rdfs:subClassOf": [ + { + "@id": "bts:Thing" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "biobankDetails", + "sms:required": "sms:false", + "sms:requiresDependency": [ + { + "@id": "bts:Component" + }, + { + "@id": "bts:biobankId" + }, + { + "@id": "bts:resourceId" + }, + { + "@id": "bts:biobankName" + }, + { + "@id": "bts:biobankURL" + }, + { + "@id": "bts:specimenType" + }, + { + "@id": "bts:specimenTissueType" + }, + { + "@id": "bts:tumorType" + }, + { + "@id": "bts:diseaseType" + }, + { + "@id": "bts:specimenPreparationMethod" + }, + { + "@id": "bts:specimenFormat" + } + ], + "sms:validationRules": [] + }, { "@id": "bts:animalModelId", "@type": "rdf:Property", @@ -3268,58 +3323,6 @@ "sms:required": "sms:false", "sms:validationRules": [] }, - { - "@id": "bts:BiobankDetails", - "@type": "rdfs:Class", - "rdfs:comment": "A large collection of biological or medical data and tissue samples, amassed for research purposes.", - "rdfs:label": "BiobankDetails", - "rdfs:subClassOf": [ - { - "@id": "bts:Thing" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "biobankDetails", - "sms:required": "sms:false", - "sms:requiresDependency": [ - { - "@id": "bts:Component" - }, - { - "@id": "bts:biobankId" - }, - { - "@id": "bts:resourceId" - }, - { - "@id": "bts:biobankName" - }, - { - "@id": "bts:biobankURL" - }, - { - "@id": "bts:specimenType" - }, - { - "@id": "bts:specimenTissueType" - }, - { - "@id": "bts:tumorType" - }, - { - "@id": "bts:diseaseType" - }, - { - "@id": "bts:specimenPreparationMethod" - }, - { - "@id": "bts:specimenFormat" - } - ], - "sms:validationRules": [] - }, { "@id": "bts:biobankName", "@type": "rdf:Property", From 7c3e89dd2dd92329064a3d35ccf17384264f0bc9 Mon Sep 17 00:00:00 2001 From: Robert Allaway Date: Thu, 9 Nov 2023 11:19:09 -0600 Subject: [PATCH 90/97] Update nf_research_tools.rdb.model.csv --- nf_research_tools.rdb.model.csv | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/nf_research_tools.rdb.model.csv b/nf_research_tools.rdb.model.csv index a0b92b3a..7575c2ef 100644 --- a/nf_research_tools.rdb.model.csv +++ b/nf_research_tools.rdb.model.csv @@ -52,7 +52,8 @@ vendor,A person or compnay offering the resource for sale.,,"Component, vendorId vendorId,A unique identifier for the vendor.,,,TRUE,,vendor,,, vendorName,The name of the vendor.,,,FALSE,,vendor,,, vendorUrl,The vendor website url associated with the resource.,,,FALSE,,vendor,,, -biobankDetails,"A large collection of biological or medical data and tissue samples, amassed for research purposes.",,"Component, biobankId, resourceId, biobankName, biobankURL, specimenType, specimenTissueType, tumorType, diseaseType, specimenPreparationMethod, specimenFormat",FALSE,,biobankDetails,"biobankId, resourceId, biobankName, biobankURL, specimenType, specimenTissueType, tumorType, diseaseType, specimenPreparationMethod, specimenFormat",, +biobankDetails,"A large collection of biological or medical data and tissue samples, amassed for research purposes.",,"Component, biobankId, resourceId, biobankName, biobankURL, specimenType, specimenTissueType, tumorType, diseaseType, specimenPreparationMethod, specimenFormat",FALSE,,biobankDetails,"biobankId, resourceId, biobankName, biobankURL, specimenType, specimenTissueType, tumorType, diseaseType, specimenPreparationMethod, specimenFormat",resource, + biobankName,The name of the biobank. ,,,TRUE,,biobankDetails,,, biobankId,A unique identifier for the biobank.,,,FALSE,,biobankDetails,,, biobankURL,A URL for the biobank landing page.,,,TRUE,,biobankDetails,,, From 85fb09b04f09f67687dbff959edca5a22879370b Mon Sep 17 00:00:00 2001 From: "nf-osi[bot]" Date: Thu, 9 Nov 2023 17:20:28 +0000 Subject: [PATCH 91/97] Add changes --- nf-research-tools.jsonld | 5 +++++ 1 file changed, 5 insertions(+) diff --git a/nf-research-tools.jsonld b/nf-research-tools.jsonld index 23c04407..7a22de7f 100644 --- a/nf-research-tools.jsonld +++ b/nf-research-tools.jsonld @@ -641,6 +641,11 @@ }, "sms:displayName": "biobankDetails", "sms:required": "sms:false", + "sms:requiresComponent": [ + { + "@id": "bts:Resource" + } + ], "sms:requiresDependency": [ { "@id": "bts:Component" From b44b94050641712621f6d472ce03ed7e922394bf Mon Sep 17 00:00:00 2001 From: Robert Allaway Date: Thu, 9 Nov 2023 11:33:26 -0600 Subject: [PATCH 92/97] Update nf_research_tools.rdb.model.csv --- nf_research_tools.rdb.model.csv | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/nf_research_tools.rdb.model.csv b/nf_research_tools.rdb.model.csv index 7575c2ef..a0b92b3a 100644 --- a/nf_research_tools.rdb.model.csv +++ b/nf_research_tools.rdb.model.csv @@ -52,8 +52,7 @@ vendor,A person or compnay offering the resource for sale.,,"Component, vendorId vendorId,A unique identifier for the vendor.,,,TRUE,,vendor,,, vendorName,The name of the vendor.,,,FALSE,,vendor,,, vendorUrl,The vendor website url associated with the resource.,,,FALSE,,vendor,,, -biobankDetails,"A large collection of biological or medical data and tissue samples, amassed for research purposes.",,"Component, biobankId, resourceId, biobankName, biobankURL, specimenType, specimenTissueType, tumorType, diseaseType, specimenPreparationMethod, specimenFormat",FALSE,,biobankDetails,"biobankId, resourceId, biobankName, biobankURL, specimenType, specimenTissueType, tumorType, diseaseType, specimenPreparationMethod, specimenFormat",resource, - +biobankDetails,"A large collection of biological or medical data and tissue samples, amassed for research purposes.",,"Component, biobankId, resourceId, biobankName, biobankURL, specimenType, specimenTissueType, tumorType, diseaseType, specimenPreparationMethod, specimenFormat",FALSE,,biobankDetails,"biobankId, resourceId, biobankName, biobankURL, specimenType, specimenTissueType, tumorType, diseaseType, specimenPreparationMethod, specimenFormat",, biobankName,The name of the biobank. ,,,TRUE,,biobankDetails,,, biobankId,A unique identifier for the biobank.,,,FALSE,,biobankDetails,,, biobankURL,A URL for the biobank landing page.,,,TRUE,,biobankDetails,,, From 7a27047032ab50625391ee5c406a07aaf11729fe Mon Sep 17 00:00:00 2001 From: "nf-osi[bot]" Date: Thu, 9 Nov 2023 17:35:23 +0000 Subject: [PATCH 93/97] Add changes --- nf-research-tools.jsonld | 5 ----- 1 file changed, 5 deletions(-) diff --git a/nf-research-tools.jsonld b/nf-research-tools.jsonld index 7a22de7f..23c04407 100644 --- a/nf-research-tools.jsonld +++ b/nf-research-tools.jsonld @@ -641,11 +641,6 @@ }, "sms:displayName": "biobankDetails", "sms:required": "sms:false", - "sms:requiresComponent": [ - { - "@id": "bts:Resource" - } - ], "sms:requiresDependency": [ { "@id": "bts:Component" From 042044cdbcb02db402ec10d5e6255bcfcfec6f57 Mon Sep 17 00:00:00 2001 From: Robert Allaway Date: Mon, 14 Oct 2024 14:26:46 -0500 Subject: [PATCH 94/97] Update nf_research_tools.rdb.model.csv --- nf_research_tools.rdb.model.csv | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/nf_research_tools.rdb.model.csv b/nf_research_tools.rdb.model.csv index a0b92b3a..8947043a 100644 --- a/nf_research_tools.rdb.model.csv +++ b/nf_research_tools.rdb.model.csv @@ -138,12 +138,11 @@ developmentId,A unique identifier for the development of the resource.,,,TRUE,,d funder,A person or organization that provides money for a particular resource.,,"Component, funderId, funderName",FALSE,,funder,"funderId, funderName",, funderId,A unique identifier for the funder of the resource.,,,FALSE,,funder,,, funderName,The name of the person or agency that funded the development of the resource.,,,FALSE,,funder,,, -investigator,A person who carries out a formal inquiry or investigation into the development of the resource.,,"Component, investigatorId, orcid, investigatorName, institution, investigatorWebsite, investigatorSynapseId",FALSE,,investigator,"investigatorId, orcid, investigatorName, institution, investigatorWebsite, investigatorSynapseId",, +investigator,A person who carries out a formal inquiry or investigation into the development of the resource.,,"Component, investigatorId, orcid, investigatorName, institution, investigatorSynapseId",FALSE,,investigator,"investigatorId, orcid, investigatorName, institution, investigatorSynapseId",, investigatorId,A unique identifier for the investigator.,,,FALSE,,investigator,,, orcid,The orcidId of the investigator that developed the resource,,,FALSE,,investigator,,, investigatorName,The name of the investigator responsible for devleoping the resource.,,,TRUE,,investigator,,, institution,The insitution of the investator,,,FALSE,,investigator,,, -investigatorWebsite,The url to the investigator's laboratory website corresponding to the resource.,,,FALSE,,investigator,,, investigatorSynapseId,The synapse identifier for the investigator.,,,FALSE,,investigator,,, publication,Initial publication associated with the resource.,,"Component, publicationId, publicationTitle, authors, abstract, journal, publicationDate, pmid, doi, citation, publicationDateUnix",FALSE,,publication,"publicationId, publicationTitle, authors, abstract, journal, publicationDate, pmid, doi, citation, publicationDateUnix",, publicationId,A unique identifier for the publication.,,,FALSE,,publication,,, From 613d7c0dc651f16832755f92a6958d3a20341c74 Mon Sep 17 00:00:00 2001 From: Robert Allaway Date: Mon, 14 Oct 2024 14:40:29 -0500 Subject: [PATCH 95/97] Update nf_research_tools.rdb.model.csv From 8ac72763970109e00434bb88cbb4a3151bfb4e85 Mon Sep 17 00:00:00 2001 From: Robert Allaway Date: Mon, 14 Oct 2024 14:42:35 -0500 Subject: [PATCH 96/97] Update nf_research_tools.rdb.model.csv --- nf_research_tools.rdb.model.csv | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/nf_research_tools.rdb.model.csv b/nf_research_tools.rdb.model.csv index 8947043a..5ab0832c 100644 --- a/nf_research_tools.rdb.model.csv +++ b/nf_research_tools.rdb.model.csv @@ -141,7 +141,7 @@ funderName,The name of the person or agency that funded the development of the r investigator,A person who carries out a formal inquiry or investigation into the development of the resource.,,"Component, investigatorId, orcid, investigatorName, institution, investigatorSynapseId",FALSE,,investigator,"investigatorId, orcid, investigatorName, institution, investigatorSynapseId",, investigatorId,A unique identifier for the investigator.,,,FALSE,,investigator,,, orcid,The orcidId of the investigator that developed the resource,,,FALSE,,investigator,,, -investigatorName,The name of the investigator responsible for devleoping the resource.,,,TRUE,,investigator,,, +investigatorName,The name of the investigator responsible for developing the resource.,,,TRUE,,investigator,,, institution,The insitution of the investator,,,FALSE,,investigator,,, investigatorSynapseId,The synapse identifier for the investigator.,,,FALSE,,investigator,,, publication,Initial publication associated with the resource.,,"Component, publicationId, publicationTitle, authors, abstract, journal, publicationDate, pmid, doi, citation, publicationDateUnix",FALSE,,publication,"publicationId, publicationTitle, authors, abstract, journal, publicationDate, pmid, doi, citation, publicationDateUnix",, From b62a74b1ce7dfd4c6a13ce8097ab3e57b6c209fc Mon Sep 17 00:00:00 2001 From: Robert Allaway Date: Mon, 14 Oct 2024 15:07:31 -0500 Subject: [PATCH 97/97] Update nf_research_tools.rdb.model.csv --- nf_research_tools.rdb.model.csv | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/nf_research_tools.rdb.model.csv b/nf_research_tools.rdb.model.csv index 5ab0832c..84ea37f6 100644 --- a/nf_research_tools.rdb.model.csv +++ b/nf_research_tools.rdb.model.csv @@ -48,7 +48,7 @@ vendorItem,The resource item associated with a vendor.,,"Component, vendorItemId vendorItemId,A unique identifier for the resource associated with a vendor. ,,,TRUE,,vendorItem,,, catalogNumber,The catalog number associated with the resource pertaining to the vendor that sells the resource.,,,TRUE,,vendorItem,,, catalogNumberURL,The url linking to the resource on the vendor's website. ,,,FALSE,,vendorItem,,, -vendor,A person or compnay offering the resource for sale.,,"Component, vendorId, vendorName, vendorUrl",FALSE,,vendor,"vendorId, vendorName, vendorUrl",, +vendor,A person or company offering the resource for sale.,,"Component, vendorId, vendorName, vendorUrl",FALSE,,vendor,"vendorId, vendorName, vendorUrl",, vendorId,A unique identifier for the vendor.,,,TRUE,,vendor,,, vendorName,The name of the vendor.,,,FALSE,,vendor,,, vendorUrl,The vendor website url associated with the resource.,,,FALSE,,vendor,,,