From d77172050122bf4d5b48cd1d487fb58a8b163620 Mon Sep 17 00:00:00 2001 From: Deepak Unni Date: Tue, 21 Sep 2021 22:48:49 +0000 Subject: [PATCH] Regenerate artifacts from biolink-model.yaml --- biolink-model.graphql | 48 + biolink-model.owl.ttl | 773 +++++++-------- biolink-model.proto | 152 ++- biolink-model.shex | 4 +- biolink-model.ttl | 803 +++++++++------- biolink/model.py | 23 +- context.jsonld | 14 +- contextn.jsonld | 16 +- golr-views/RNA_product_config.yaml | 9 + golr-views/RNA_product_isoform_config.yaml | 9 + golr-views/chemical_entity_config.yaml | 9 + golr-views/chemical_mixture_config.yaml | 9 + golr-views/coding_sequence_config.yaml | 9 + .../complex_molecular_mixture_config.yaml | 9 + golr-views/drug_config.yaml | 9 + ...environmental_food_contaminant_config.yaml | 9 + golr-views/exon_config.yaml | 9 + golr-views/food_additive_config.yaml | 9 + golr-views/food_config.yaml | 9 + golr-views/macronutrient_config.yaml | 9 + golr-views/microRNA_config.yaml | 9 + golr-views/micronutrient_config.yaml | 9 + golr-views/molecular_entity_config.yaml | 9 + golr-views/molecular_mixture_config.yaml | 9 + golr-views/noncoding_RNA_product_config.yaml | 9 + golr-views/nucleic_acid_entity_config.yaml | 9 + golr-views/nutrient_config.yaml | 9 + golr-views/processed_material_config.yaml | 9 + golr-views/siRNA_config.yaml | 9 + golr-views/small_molecule_config.yaml | 9 + golr-views/transcript_config.yaml | 9 + golr-views/vitamin_config.yaml | 9 + graphviz/RNA_product.gv | 130 +-- graphviz/RNA_product.svg | 188 ++-- graphviz/RNA_product_isoform.gv | 124 ++- graphviz/RNA_product_isoform.svg | 184 ++-- graphviz/chemical_entity.gv | 107 ++- graphviz/chemical_entity.svg | 136 +-- graphviz/chemical_mixture.gv | 102 +- graphviz/chemical_mixture.svg | 140 +-- graphviz/coding_sequence.gv | 105 ++- graphviz/coding_sequence.svg | 150 +-- graphviz/complex_molecular_mixture.gv | 100 +- graphviz/complex_molecular_mixture.svg | 140 +-- graphviz/drug.gv | 113 ++- graphviz/drug.svg | 152 +-- graphviz/environmental_food_contaminant.gv | 83 +- graphviz/environmental_food_contaminant.svg | 112 ++- graphviz/exon.gv | 109 ++- graphviz/exon.svg | 150 +-- graphviz/food.gv | 104 +- graphviz/food.svg | 140 +-- graphviz/food_additive.gv | 86 +- graphviz/food_additive.svg | 112 ++- graphviz/macronutrient.gv | 86 +- graphviz/macronutrient.svg | 112 ++- graphviz/microRNA.gv | 119 ++- graphviz/microRNA.svg | 176 ++-- graphviz/micronutrient.gv | 86 +- graphviz/micronutrient.svg | 112 ++- graphviz/molecular_entity.gv | 94 +- graphviz/molecular_entity.svg | 126 ++- graphviz/molecular_mixture.gv | 102 +- graphviz/molecular_mixture.svg | 140 +-- graphviz/noncoding_RNA_product.gv | 117 ++- graphviz/noncoding_RNA_product.svg | 178 ++-- graphviz/nucleic_acid_entity.gv | 127 +-- graphviz/nucleic_acid_entity.svg | 172 ++-- graphviz/nutrient.gv | 87 +- graphviz/nutrient.svg | 112 ++- graphviz/processed_material.gv | 101 +- graphviz/processed_material.svg | 140 +-- graphviz/siRNA.gv | 119 ++- graphviz/siRNA.svg | 176 ++-- graphviz/small_molecule.gv | 94 +- graphviz/small_molecule.svg | 138 +-- graphviz/transcript.gv | 107 ++- graphviz/transcript.svg | 150 +-- graphviz/vitamin.gv | 88 +- graphviz/vitamin.svg | 112 ++- json-schema/biolink-model.json | 888 +++++++++++------- 81 files changed, 5315 insertions(+), 3560 deletions(-) diff --git a/biolink-model.graphql b/biolink-model.graphql index 9969acd306..de6a1d0ecc 100644 --- a/biolink-model.graphql +++ b/biolink-model.graphql @@ -495,6 +495,8 @@ type ChemicalEntity implements PhysicalEssence, ChemicalOrDrugOrTreatment, Chemi category: [NamedThing]! tradeName: ChemicalEntity availableFrom: [DrugAvailabilityEnum] + maxToleratedDose: String + isToxic: Boolean } interface ChemicalEntityOrGeneOrGeneProduct @@ -528,6 +530,8 @@ type ChemicalMixture category: [NamedThing]! tradeName: ChemicalEntity availableFrom: [DrugAvailabilityEnum] + maxToleratedDose: String + isToxic: Boolean isSupplement: ChemicalMixture highestFDAApprovalStatus: String } @@ -752,6 +756,8 @@ type CodingSequence category: [NamedThing]! tradeName: ChemicalEntity availableFrom: [DrugAvailabilityEnum] + maxToleratedDose: String + isToxic: Boolean isMetabolite: Boolean inTaxon: [OrganismTaxon] hasBiologicalSequence: BiologicalSequence @@ -788,6 +794,8 @@ type ComplexMolecularMixture category: [NamedThing]! tradeName: ChemicalEntity availableFrom: [DrugAvailabilityEnum] + maxToleratedDose: String + isToxic: Boolean isSupplement: ChemicalMixture highestFDAApprovalStatus: String } @@ -1040,6 +1048,8 @@ type Drug implements ChemicalOrDrugOrTreatment, OntologyClass category: [NamedThing]! tradeName: ChemicalEntity availableFrom: [DrugAvailabilityEnum] + maxToleratedDose: String + isToxic: Boolean isSupplement: ChemicalMixture highestFDAApprovalStatus: String } @@ -1206,6 +1216,8 @@ type EnvironmentalFoodContaminant category: [NamedThing]! tradeName: ChemicalEntity availableFrom: [DrugAvailabilityEnum] + maxToleratedDose: String + isToxic: Boolean } type EnvironmentalProcess implements Occurrent @@ -1268,6 +1280,8 @@ type Exon category: [NamedThing]! tradeName: ChemicalEntity availableFrom: [DrugAvailabilityEnum] + maxToleratedDose: String + isToxic: Boolean isMetabolite: Boolean inTaxon: [OrganismTaxon] hasBiologicalSequence: BiologicalSequence @@ -1361,6 +1375,8 @@ type Food category: [NamedThing]! tradeName: ChemicalEntity availableFrom: [DrugAvailabilityEnum] + maxToleratedDose: String + isToxic: Boolean isSupplement: ChemicalMixture highestFDAApprovalStatus: String } @@ -1378,6 +1394,8 @@ type FoodAdditive category: [NamedThing]! tradeName: ChemicalEntity availableFrom: [DrugAvailabilityEnum] + maxToleratedDose: String + isToxic: Boolean } interface FrequencyQualifierMixin @@ -2183,6 +2201,8 @@ type Macronutrient category: [NamedThing]! tradeName: ChemicalEntity availableFrom: [DrugAvailabilityEnum] + maxToleratedDose: String + isToxic: Boolean } type MaterialSample implements SubjectOfInvestigation @@ -2256,6 +2276,8 @@ type Micronutrient category: [NamedThing]! tradeName: ChemicalEntity availableFrom: [DrugAvailabilityEnum] + maxToleratedDose: String + isToxic: Boolean } type MicroRNA @@ -2271,6 +2293,8 @@ type MicroRNA category: [NamedThing]! tradeName: ChemicalEntity availableFrom: [DrugAvailabilityEnum] + maxToleratedDose: String + isToxic: Boolean isMetabolite: Boolean inTaxon: [OrganismTaxon] hasBiologicalSequence: BiologicalSequence @@ -2313,6 +2337,8 @@ type MolecularEntity category: [NamedThing]! tradeName: ChemicalEntity availableFrom: [DrugAvailabilityEnum] + maxToleratedDose: String + isToxic: Boolean isMetabolite: Boolean } @@ -2329,6 +2355,8 @@ type MolecularMixture category: [NamedThing]! tradeName: ChemicalEntity availableFrom: [DrugAvailabilityEnum] + maxToleratedDose: String + isToxic: Boolean isSupplement: ChemicalMixture highestFDAApprovalStatus: String } @@ -2383,6 +2411,8 @@ type NoncodingRNAProduct category: [NamedThing]! tradeName: ChemicalEntity availableFrom: [DrugAvailabilityEnum] + maxToleratedDose: String + isToxic: Boolean isMetabolite: Boolean inTaxon: [OrganismTaxon] hasBiologicalSequence: BiologicalSequence @@ -2403,6 +2433,8 @@ type NucleicAcidEntity implements GenomicEntity, PhysicalEssence, OntologyClass category: [NamedThing]! tradeName: ChemicalEntity availableFrom: [DrugAvailabilityEnum] + maxToleratedDose: String + isToxic: Boolean isMetabolite: Boolean inTaxon: [OrganismTaxon] hasBiologicalSequence: BiologicalSequence @@ -2421,6 +2453,8 @@ type Nutrient category: [NamedThing]! tradeName: ChemicalEntity availableFrom: [DrugAvailabilityEnum] + maxToleratedDose: String + isToxic: Boolean } interface Occurrent @@ -2896,6 +2930,8 @@ type ProcessedMaterial category: [NamedThing]! tradeName: ChemicalEntity availableFrom: [DrugAvailabilityEnum] + maxToleratedDose: String + isToxic: Boolean isSupplement: ChemicalMixture highestFDAApprovalStatus: String } @@ -3043,6 +3079,8 @@ type RNAProduct implements GeneProductMixin category: [NamedThing]! tradeName: ChemicalEntity availableFrom: [DrugAvailabilityEnum] + maxToleratedDose: String + isToxic: Boolean isMetabolite: Boolean inTaxon: [OrganismTaxon] hasBiologicalSequence: BiologicalSequence @@ -3063,6 +3101,8 @@ type RNAProductIsoform implements GeneProductIsoformMixin category: [NamedThing]! tradeName: ChemicalEntity availableFrom: [DrugAvailabilityEnum] + maxToleratedDose: String + isToxic: Boolean isMetabolite: Boolean inTaxon: [OrganismTaxon] hasBiologicalSequence: BiologicalSequence @@ -3199,6 +3239,8 @@ type SiRNA category: [NamedThing]! tradeName: ChemicalEntity availableFrom: [DrugAvailabilityEnum] + maxToleratedDose: String + isToxic: Boolean isMetabolite: Boolean inTaxon: [OrganismTaxon] hasBiologicalSequence: BiologicalSequence @@ -3218,6 +3260,8 @@ type SmallMolecule category: [NamedThing]! tradeName: ChemicalEntity availableFrom: [DrugAvailabilityEnum] + maxToleratedDose: String + isToxic: Boolean isMetabolite: Boolean id: String! } @@ -3322,6 +3366,8 @@ type Transcript category: [NamedThing]! tradeName: ChemicalEntity availableFrom: [DrugAvailabilityEnum] + maxToleratedDose: String + isToxic: Boolean isMetabolite: Boolean inTaxon: [OrganismTaxon] hasBiologicalSequence: BiologicalSequence @@ -3525,6 +3571,8 @@ type Vitamin category: [NamedThing]! tradeName: ChemicalEntity availableFrom: [DrugAvailabilityEnum] + maxToleratedDose: String + isToxic: Boolean } type Zygosity diff --git a/biolink-model.owl.ttl b/biolink-model.owl.ttl index f5700113c0..f4ebf017a4 100644 --- a/biolink-model.owl.ttl +++ b/biolink-model.owl.ttl @@ -11,13 +11,13 @@ a owl:Ontology ; rdfs:label "Biolink-Model" ; dcterms:license "https://creativecommons.org/publicdomain/zero/1.0/" ; - pav:version "2.2.4" ; + pav:version "2.2.5" ; skos:definition "Entity and association taxonomy and datamodel for life-sciences data" ; - linkml:generation_date "2021-09-02 18:53" ; + linkml:generation_date "2021-09-21 22:44" ; linkml:metamodel_version "1.7.0" ; linkml:source_file "biolink-model.yaml" ; - linkml:source_file_date "Thu Sep 2 18:51:32 2021" ; - linkml:source_file_size 314029 . + linkml:source_file_date "Tue Sep 21 22:41:10 2021" ; + linkml:source_file_size 314894 . a owl:Class, linkml:ClassDefinition ; @@ -68,21 +68,21 @@ linkml:ClassDefinition ; rdfs:label "case to phenotypic feature association" ; rdfs:subClassOf [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass ; - owl:onProperty ], - [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass ; owl:onProperty ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass ; - owl:onProperty ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass ; owl:onProperty ], + [ a owl:Restriction ; + owl:maxQualifiedCardinality 1 ; + owl:onClass ; + owl:onProperty ], + [ a owl:Restriction ; + owl:maxQualifiedCardinality 1 ; + owl:onClass ; + owl:onProperty ], , , ; @@ -161,6 +161,10 @@ owl:maxQualifiedCardinality 1 ; owl:onClass ; owl:onProperty ], + [ a owl:Restriction ; + owl:maxQualifiedCardinality 1 ; + owl:onClass ; + owl:onProperty ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass ; @@ -169,10 +173,6 @@ owl:maxQualifiedCardinality 1 ; owl:onClass ; owl:onProperty ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass ; - owl:onProperty ], , , ; @@ -291,12 +291,12 @@ linkml:ClassDefinition ; rdfs:label "genome" ; rdfs:subClassOf [ a owl:Restriction ; + owl:allValuesFrom ; + owl:onProperty ], + [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass ; owl:onProperty ], - [ a owl:Restriction ; - owl:allValuesFrom ; - owl:onProperty ], , , , @@ -310,13 +310,13 @@ linkml:ClassDefinition ; rdfs:label "genomic background exposure" ; rdfs:subClassOf [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass ; - owl:onProperty ], - [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass ; owl:onProperty ], + [ a owl:Restriction ; + owl:maxQualifiedCardinality 1 ; + owl:onClass ; + owl:onProperty ], [ a owl:Restriction ; owl:allValuesFrom ; owl:onProperty ], @@ -389,7 +389,7 @@ linkml:ClassDefinition ; rdfs:label "hospitalization" ; rdfs:subClassOf ; - skos:exactMatch , + skos:exactMatch , . a owl:Class, @@ -2496,10 +2496,6 @@ linkml:variant_to_population_association_subject a owl:ObjectProperty, owl:maxQualifiedCardinality 1 ; owl:onClass ; owl:onProperty ], - [ a owl:Restriction ; - owl:onClass ; - owl:onProperty ; - owl:qualifiedCardinality 1 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass ; @@ -2508,6 +2504,10 @@ linkml:variant_to_population_association_subject a owl:ObjectProperty, owl:maxQualifiedCardinality 1 ; owl:onClass ; owl:onProperty ], + [ a owl:Restriction ; + owl:onClass ; + owl:onProperty ; + owl:qualifiedCardinality 1 ], , , . @@ -2687,25 +2687,25 @@ linkml:variant_to_population_association_subject a owl:ObjectProperty, linkml:ClassDefinition ; rdfs:label "exposure event to phenotypic feature association" ; rdfs:subClassOf [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass ; - owl:onProperty ], + owl:onClass ; + owl:onProperty ; + owl:qualifiedCardinality 1 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass ; owl:onProperty ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; - owl:onClass ; - owl:onProperty ], + owl:onClass ; + owl:onProperty ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass ; owl:onProperty ], [ a owl:Restriction ; - owl:onClass ; - owl:onProperty ; - owl:qualifiedCardinality 1 ], + owl:maxQualifiedCardinality 1 ; + owl:onClass ; + owl:onProperty ], , ; skos:definition "Any association between an environment and a phenotypic feature, where being in the environment influences the phenotype." . @@ -2716,19 +2716,19 @@ linkml:variant_to_population_association_subject a owl:ObjectProperty, rdfs:subClassOf [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass linkml:Integer ; - owl:onProperty ], + owl:onProperty ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:Integer ; - owl:onProperty ], + owl:onClass linkml:Double ; + owl:onProperty ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass linkml:Double ; owl:onProperty ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:Double ; - owl:onProperty ], + owl:onClass linkml:Integer ; + owl:onProperty ], , linkml:mixin . @@ -2760,21 +2760,21 @@ linkml:variant_to_population_association_subject a owl:ObjectProperty, linkml:ClassDefinition ; rdfs:label "gene to gene coexpression association" ; rdfs:subClassOf [ a owl:Restriction ; - owl:onClass ; - owl:onProperty ; - owl:qualifiedCardinality 1 ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass ; - owl:onProperty ], - [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass ; owl:onProperty ], + [ a owl:Restriction ; + owl:onClass ; + owl:onProperty ; + owl:qualifiedCardinality 1 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass ; owl:onProperty ], + [ a owl:Restriction ; + owl:maxQualifiedCardinality 1 ; + owl:onClass ; + owl:onProperty ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass ; @@ -2797,25 +2797,25 @@ linkml:variant_to_population_association_subject a owl:ObjectProperty, linkml:ClassDefinition ; rdfs:label "gene to phenotypic feature association" ; rdfs:subClassOf [ a owl:Restriction ; + owl:maxQualifiedCardinality 1 ; + owl:onClass ; + owl:onProperty ], + [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass ; owl:onProperty ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; - owl:onClass ; - owl:onProperty ], + owl:onClass ; + owl:onProperty ], [ a owl:Restriction ; owl:onClass ; owl:onProperty ; owl:qualifiedCardinality 1 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; - owl:onClass ; - owl:onProperty ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass ; - owl:onProperty ], + owl:onClass ; + owl:onProperty ], , , ; @@ -2838,11 +2838,11 @@ linkml:variant_to_population_association_subject a owl:ObjectProperty, rdfs:subClassOf [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass linkml:Float ; - owl:onProperty ], + owl:onProperty ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass linkml:Float ; - owl:onProperty ], + owl:onProperty ], ; skos:definition "a location that can be described in lat/long coordinates" ; skos:exactMatch , @@ -2897,6 +2897,14 @@ linkml:variant_to_population_association_subject a owl:ObjectProperty, linkml:ClassDefinition ; rdfs:label "organismal entity as a model of disease association" ; rdfs:subClassOf [ a owl:Restriction ; + owl:onClass ; + owl:onProperty ; + owl:qualifiedCardinality 1 ], + [ a owl:Restriction ; + owl:maxQualifiedCardinality 1 ; + owl:onClass ; + owl:onProperty ], + [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass ; owl:onProperty ], @@ -2904,14 +2912,6 @@ linkml:variant_to_population_association_subject a owl:ObjectProperty, owl:maxQualifiedCardinality 1 ; owl:onClass ; owl:onProperty ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass ; - owl:onProperty ], - [ a owl:Restriction ; - owl:onClass ; - owl:onProperty ; - owl:qualifiedCardinality 1 ], , , . @@ -3010,24 +3010,24 @@ linkml:variant_to_population_association_subject a owl:ObjectProperty, rdfs:label "variant to gene expression association" ; rdfs:subClassOf [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; - owl:onClass ; - owl:onProperty ], + owl:onClass ; + owl:onProperty ], + [ a owl:Restriction ; + owl:onClass ; + owl:onProperty ; + owl:qualifiedCardinality 1 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass ; owl:onProperty ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; - owl:onClass ; - owl:onProperty ], - [ a owl:Restriction ; - owl:onClass ; - owl:onProperty ; - owl:qualifiedCardinality 1 ], + owl:onClass ; + owl:onProperty ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; - owl:onClass ; - owl:onProperty ], + owl:onClass ; + owl:onProperty ], , ; skos:definition "An association between a variant and expression of a gene (i.e. e-QTL)" . @@ -3037,24 +3037,24 @@ linkml:variant_to_population_association_subject a owl:ObjectProperty, rdfs:label "variant to phenotypic feature association" ; rdfs:subClassOf [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; - owl:onClass ; - owl:onProperty ], + owl:onClass ; + owl:onProperty ], [ a owl:Restriction ; owl:onClass ; owl:onProperty ; owl:qualifiedCardinality 1 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; - owl:onClass ; - owl:onProperty ], + owl:onClass ; + owl:onProperty ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass ; owl:onProperty ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; - owl:onClass ; - owl:onProperty ], + owl:onClass ; + owl:onProperty ], , , . @@ -3297,6 +3297,7 @@ linkml:variant_to_population_association_subject a owl:ObjectProperty, rdfs:label "consumed by" ; rdfs:domain ; rdfs:range ; + rdfs:subPropertyOf ; owl:inverseOf . a owl:ObjectProperty, @@ -4279,14 +4280,6 @@ linkml:variant_to_population_association_subject a owl:ObjectProperty, owl:inverseOf ; skos:definition "holds between a sequence variant and a gene, such the sequence variant causes a disruption of the translational reading frame, because the number of nucleotides inserted or deleted is not a multiple of three." . - a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "is input of" ; - rdfs:domain ; - rdfs:range ; - rdfs:subPropertyOf ; - owl:inverseOf . - a owl:ObjectProperty, linkml:SlotDefinition ; rdfs:label "is metabolite" ; @@ -4391,6 +4384,14 @@ linkml:variant_to_population_association_subject a owl:ObjectProperty, owl:inverseOf ; skos:definition "holds between a sequence variant and a gene, such the sequence variant is in the coding sequence of the gene, but results in the same amino acid sequence" . + a owl:ObjectProperty, + linkml:SlotDefinition ; + rdfs:label "is toxic" ; + rdfs:domain ; + rdfs:range linkml:Boolean ; + rdfs:subPropertyOf ; + skos:definition "" . + a owl:ObjectProperty, linkml:SlotDefinition ; rdfs:label "keywords" ; @@ -4473,6 +4474,14 @@ linkml:variant_to_population_association_subject a owl:ObjectProperty, owl:inverseOf ; skos:definition "that part of a phenomenon which is directly observable or visibly expressed, or which gives evidence to the underlying process; used in SemMedDB for linking things like dysfunctions and processes to some disease or syndrome" . + a owl:ObjectProperty, + linkml:SlotDefinition ; + rdfs:label "max tolerated dose" ; + rdfs:domain ; + rdfs:range linkml:String ; + rdfs:subPropertyOf ; + skos:definition "The highest dose of a drug or treatment that does not cause unacceptable side effects. The maximum tolerated dose is determined in clinical trials by testing increasing doses on different groups of people until the highest dose with acceptable side effects is found. Also called MTD." . + a owl:ObjectProperty, linkml:SlotDefinition ; rdfs:label "mesh terms" ; @@ -5125,7 +5134,7 @@ linkml:variant_to_gene_association_predicate a owl:ObjectProperty, rdfs:subClassOf [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass linkml:String ; - owl:onProperty ], + owl:onProperty ], [ a owl:Restriction ; owl:onClass linkml:Uriorcurie ; owl:onProperty ; @@ -5133,11 +5142,11 @@ linkml:variant_to_gene_association_predicate a owl:ObjectProperty, [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass linkml:String ; - owl:onProperty ], + owl:onProperty ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass linkml:String ; - owl:onProperty ], + owl:onProperty ], . a owl:Class, @@ -5156,29 +5165,29 @@ linkml:variant_to_gene_association_predicate a owl:ObjectProperty, linkml:ClassDefinition ; rdfs:label "behavior to behavioral feature association" ; rdfs:subClassOf [ a owl:Restriction ; + owl:maxQualifiedCardinality 1 ; + owl:onClass ; + owl:onProperty ], + [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass ; owl:onProperty ], - [ a owl:Restriction ; - owl:onClass ; - owl:onProperty ; - owl:qualifiedCardinality 1 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass ; owl:onProperty ], + [ a owl:Restriction ; + owl:maxQualifiedCardinality 1 ; + owl:onClass ; + owl:onProperty ], [ a owl:Restriction ; owl:onClass ; owl:onProperty ; owl:qualifiedCardinality 1 ], [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass ; - owl:onProperty ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass ; - owl:onProperty ], + owl:onClass ; + owl:onProperty ; + owl:qualifiedCardinality 1 ], , ; skos:definition "An association between an mixture behavior and a behavioral feature manifested by the individual exhibited or has exhibited the behavior." . @@ -5195,11 +5204,11 @@ linkml:variant_to_gene_association_predicate a owl:ObjectProperty, rdfs:label "book" ; rdfs:subClassOf [ a owl:Restriction ; owl:onClass linkml:String ; - owl:onProperty ; + owl:onProperty ; owl:qualifiedCardinality 1 ], [ a owl:Restriction ; owl:onClass linkml:String ; - owl:onProperty ; + owl:onProperty ; owl:qualifiedCardinality 1 ], ; skos:definition "This class may rarely be instantiated except if use cases of a given knowledge graph support its utility." . @@ -5208,6 +5217,10 @@ linkml:variant_to_gene_association_predicate a owl:ObjectProperty, linkml:ClassDefinition ; rdfs:label "book chapter" ; rdfs:subClassOf [ a owl:Restriction ; + owl:onClass linkml:Uriorcurie ; + owl:onProperty ; + owl:qualifiedCardinality 1 ], + [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass linkml:String ; owl:onProperty ], @@ -5215,10 +5228,6 @@ linkml:variant_to_gene_association_predicate a owl:ObjectProperty, owl:maxQualifiedCardinality 1 ; owl:onClass linkml:String ; owl:onProperty ], - [ a owl:Restriction ; - owl:onClass linkml:Uriorcurie ; - owl:onProperty ; - owl:qualifiedCardinality 1 ], . a owl:Class, @@ -5391,13 +5400,13 @@ linkml:variant_to_gene_association_predicate a owl:ObjectProperty, linkml:ClassDefinition ; rdfs:label "gene to go term association" ; rdfs:subClassOf [ a owl:Restriction ; - owl:onClass ; - owl:onProperty ; - owl:qualifiedCardinality 1 ], - [ a owl:Restriction ; owl:onClass ; owl:onProperty ; owl:qualifiedCardinality 1 ], + [ a owl:Restriction ; + owl:onClass ; + owl:onProperty ; + owl:qualifiedCardinality 1 ], ; skos:altLabel "functional association" ; skos:exactMatch . @@ -5406,6 +5415,14 @@ linkml:variant_to_gene_association_predicate a owl:ObjectProperty, linkml:ClassDefinition ; rdfs:label "genotype to phenotypic feature association" ; rdfs:subClassOf [ a owl:Restriction ; + owl:maxQualifiedCardinality 1 ; + owl:onClass ; + owl:onProperty ], + [ a owl:Restriction ; + owl:maxQualifiedCardinality 1 ; + owl:onClass ; + owl:onProperty ], + [ a owl:Restriction ; owl:onClass ; owl:onProperty ; owl:qualifiedCardinality 1 ], @@ -5413,10 +5430,6 @@ linkml:variant_to_gene_association_predicate a owl:ObjectProperty, owl:onClass ; owl:onProperty ; owl:qualifiedCardinality 1 ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass ; - owl:onProperty ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass ; @@ -5425,10 +5438,6 @@ linkml:variant_to_gene_association_predicate a owl:ObjectProperty, owl:maxQualifiedCardinality 1 ; owl:onClass ; owl:onProperty ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass ; - owl:onProperty ], , , ; @@ -5490,11 +5499,11 @@ linkml:variant_to_gene_association_predicate a owl:ObjectProperty, linkml:ClassDefinition ; rdfs:label "RNA product" ; rdfs:subClassOf [ a owl:Restriction ; - owl:allValuesFrom ; - owl:onProperty ], - [ a owl:Restriction ; owl:allValuesFrom ; owl:onProperty ], + [ a owl:Restriction ; + owl:allValuesFrom ; + owl:onProperty ], , ; skos:exactMatch , @@ -5504,34 +5513,34 @@ linkml:variant_to_gene_association_predicate a owl:ObjectProperty, linkml:ClassDefinition ; rdfs:label "reaction to participant association" ; rdfs:subClassOf [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass ; - owl:onProperty ], - [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass linkml:Integer ; owl:onProperty ], + [ a owl:Restriction ; + owl:maxQualifiedCardinality 1 ; + owl:onClass ; + owl:onProperty ], [ a owl:Restriction ; owl:onClass ; owl:onProperty ; owl:qualifiedCardinality 1 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; - owl:onClass ; - owl:onProperty ], - . + owl:onClass ; + owl:onProperty ], + . a owl:Class, linkml:ClassDefinition ; rdfs:label "sequence variant modulates treatment association" ; rdfs:subClassOf [ a owl:Restriction ; - owl:onClass ; - owl:onProperty ; - owl:qualifiedCardinality 1 ], - [ a owl:Restriction ; owl:onClass ; owl:onProperty ; owl:qualifiedCardinality 1 ], + [ a owl:Restriction ; + owl:onClass ; + owl:onProperty ; + owl:qualifiedCardinality 1 ], ; skos:definition "An association between a sequence variant and a treatment or health intervention. The treatment object itself encompasses both the disease and the drug used." ; skos:note "An alternate way to model the same information could be via a qualifier" . @@ -5540,10 +5549,6 @@ linkml:variant_to_gene_association_predicate a owl:ObjectProperty, linkml:ClassDefinition ; rdfs:label "serial" ; rdfs:subClassOf [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty ], - [ a owl:Restriction ; owl:onClass linkml:String ; owl:onProperty ; owl:qualifiedCardinality 1 ], @@ -5555,6 +5560,10 @@ linkml:variant_to_gene_association_predicate a owl:ObjectProperty, owl:maxQualifiedCardinality 1 ; owl:onClass linkml:String ; owl:onProperty ], + [ a owl:Restriction ; + owl:maxQualifiedCardinality 1 ; + owl:onClass linkml:String ; + owl:onProperty ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass linkml:String ; @@ -5586,18 +5595,18 @@ linkml:variant_to_gene_association_predicate a owl:ObjectProperty, linkml:ClassDefinition ; rdfs:label "treatment" ; rdfs:subClassOf [ a owl:Restriction ; - owl:allValuesFrom ; - owl:onProperty ], - [ a owl:Restriction ; owl:allValuesFrom ; owl:onProperty ], + [ a owl:Restriction ; + owl:allValuesFrom ; + owl:onProperty ], + [ a owl:Restriction ; + owl:allValuesFrom ; + owl:onProperty ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass ; owl:onProperty ], - [ a owl:Restriction ; - owl:allValuesFrom ; - owl:onProperty ], , , ; @@ -5744,6 +5753,14 @@ linkml:variant_to_gene_association_predicate a owl:ObjectProperty, rdfs:range ; skos:definition "An IRI for an entity. This is determined by the id using expansion rules." . + a owl:ObjectProperty, + linkml:SlotDefinition ; + rdfs:label "is input of" ; + rdfs:domain ; + rdfs:range ; + rdfs:subPropertyOf ; + owl:inverseOf . + a owl:ObjectProperty, linkml:SlotDefinition ; rdfs:label "issue" ; @@ -5939,10 +5956,6 @@ linkml:publication_type a owl:ObjectProperty, linkml:ClassDefinition ; rdfs:label "anatomical entity to anatomical entity part of association" ; rdfs:subClassOf [ a owl:Restriction ; - owl:onClass ; - owl:onProperty ; - owl:qualifiedCardinality 1 ], - [ a owl:Restriction ; owl:onClass ; owl:onProperty ; owl:qualifiedCardinality 1 ], @@ -5950,6 +5963,10 @@ linkml:publication_type a owl:ObjectProperty, owl:onClass ; owl:onProperty ; owl:qualifiedCardinality 1 ], + [ a owl:Restriction ; + owl:onClass ; + owl:onProperty ; + owl:qualifiedCardinality 1 ], ; skos:definition "A relationship between two anatomical entities where the relationship is mereological, i.e the two entities are related by parthood. This includes relationships between cellular components and cells, between cells and tissues, tissues and whole organisms" . @@ -6004,11 +6021,11 @@ linkml:publication_type a owl:ObjectProperty, rdfs:subClassOf [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass linkml:String ; - owl:onProperty ], + owl:onProperty ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass linkml:String ; - owl:onProperty ], + owl:onProperty ], ; skos:definition "an item that holds summary level information about a dataset." . @@ -6056,10 +6073,6 @@ linkml:publication_type a owl:ObjectProperty, linkml:ClassDefinition ; rdfs:label "gene regulatory relationship" ; rdfs:subClassOf [ a owl:Restriction ; - owl:onClass ; - owl:onProperty ; - owl:qualifiedCardinality 1 ], - [ a owl:Restriction ; owl:onClass ; owl:onProperty ; owl:qualifiedCardinality 1 ], @@ -6067,6 +6080,10 @@ linkml:publication_type a owl:ObjectProperty, owl:onClass ; owl:onProperty ; owl:qualifiedCardinality 1 ], + [ a owl:Restriction ; + owl:onClass ; + owl:onProperty ; + owl:qualifiedCardinality 1 ], ; skos:definition "A regulatory relationship between two genes" . @@ -6074,14 +6091,6 @@ linkml:publication_type a owl:ObjectProperty, linkml:ClassDefinition ; rdfs:label "gene to disease association" ; rdfs:subClassOf [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass ; - owl:onProperty ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass ; - owl:onProperty ], - [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass ; owl:onProperty ], @@ -6089,6 +6098,14 @@ linkml:publication_type a owl:ObjectProperty, owl:onClass ; owl:onProperty ; owl:qualifiedCardinality 1 ], + [ a owl:Restriction ; + owl:maxQualifiedCardinality 1 ; + owl:onClass ; + owl:onProperty ], + [ a owl:Restriction ; + owl:maxQualifiedCardinality 1 ; + owl:onClass ; + owl:onProperty ], , , ; @@ -6108,6 +6125,10 @@ linkml:publication_type a owl:ObjectProperty, linkml:ClassDefinition ; rdfs:label "gene to gene product relationship" ; rdfs:subClassOf [ a owl:Restriction ; + owl:onClass ; + owl:onProperty ; + owl:qualifiedCardinality 1 ], + [ a owl:Restriction ; owl:onClass ; owl:onProperty ; owl:qualifiedCardinality 1 ], @@ -6115,10 +6136,6 @@ linkml:publication_type a owl:ObjectProperty, owl:onClass ; owl:onProperty ; owl:qualifiedCardinality 1 ], - [ a owl:Restriction ; - owl:onClass ; - owl:onProperty ; - owl:qualifiedCardinality 1 ], ; skos:definition "A gene is transcribed and potentially translated to a gene product" . @@ -6171,16 +6188,16 @@ linkml:publication_type a owl:ObjectProperty, linkml:ClassDefinition ; rdfs:label "genotype to variant association" ; rdfs:subClassOf [ a owl:Restriction ; - owl:onClass ; - owl:onProperty ; + owl:onClass ; + owl:onProperty ; owl:qualifiedCardinality 1 ], [ a owl:Restriction ; owl:onClass ; owl:onProperty ; owl:qualifiedCardinality 1 ], [ a owl:Restriction ; - owl:onClass ; - owl:onProperty ; + owl:onClass ; + owl:onProperty ; owl:qualifiedCardinality 1 ], ; skos:definition "Any association between a genotype and a sequence variant." . @@ -6207,16 +6224,16 @@ linkml:publication_type a owl:ObjectProperty, linkml:ClassDefinition ; rdfs:label "named thing to information content entity association" ; rdfs:subClassOf [ a owl:Restriction ; - owl:onClass ; - owl:onProperty ; + owl:onClass ; + owl:onProperty ; owl:qualifiedCardinality 1 ], [ a owl:Restriction ; owl:onClass ; owl:onProperty ; owl:qualifiedCardinality 1 ], [ a owl:Restriction ; - owl:onClass ; - owl:onProperty ; + owl:onClass ; + owl:onProperty ; owl:qualifiedCardinality 1 ], ; skos:definition "association between a named thing and a information content entity where the specific context of the relationship between that named thing and the publication is unknown. For example, model organisms databases often capture the knowledge that a gene is found in a journal article, but not specifically the context in which that gene was documented in the article. In these cases, this association with the accompanying predicate 'mentions' could be used. Conversely, for more specific associations (like 'gene to disease association', the publication should be captured as an edge property)." . @@ -6235,10 +6252,6 @@ linkml:publication_type a owl:ObjectProperty, linkml:ClassDefinition ; rdfs:label "organism taxon to environment association" ; rdfs:subClassOf [ a owl:Restriction ; - owl:onClass ; - owl:onProperty ; - owl:qualifiedCardinality 1 ], - [ a owl:Restriction ; owl:onClass ; owl:onProperty ; owl:qualifiedCardinality 1 ], @@ -6246,6 +6259,10 @@ linkml:publication_type a owl:ObjectProperty, owl:onClass ; owl:onProperty ; owl:qualifiedCardinality 1 ], + [ a owl:Restriction ; + owl:onClass ; + owl:onProperty ; + owl:qualifiedCardinality 1 ], , . @@ -6256,14 +6273,14 @@ linkml:publication_type a owl:ObjectProperty, owl:onClass ; owl:onProperty ; owl:qualifiedCardinality 1 ], - [ a owl:Restriction ; - owl:onClass ; - owl:onProperty ; - owl:qualifiedCardinality 1 ], [ a owl:Restriction ; owl:onClass ; owl:onProperty ; owl:qualifiedCardinality 1 ], + [ a owl:Restriction ; + owl:onClass ; + owl:onProperty ; + owl:qualifiedCardinality 1 ], ; skos:definition "A child-parent relationship between two taxa. For example: Homo sapiens subclass_of Homo" . @@ -6288,13 +6305,13 @@ linkml:publication_type a owl:ObjectProperty, linkml:ClassDefinition ; rdfs:label "pairwise gene to gene interaction" ; rdfs:subClassOf [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty ], - [ a owl:Restriction ; owl:onClass ; owl:onProperty ; owl:qualifiedCardinality 1 ], + [ a owl:Restriction ; + owl:maxQualifiedCardinality 1 ; + owl:onClass linkml:String ; + owl:onProperty ], ; skos:definition "An interaction between two genes or two gene products. May be physical (e.g. protein binding) or genetic (between genes). May be symmetric (e.g. protein interaction) or directed (e.g. phosphorylation)" . @@ -6316,10 +6333,6 @@ linkml:publication_type a owl:ObjectProperty, linkml:ClassDefinition ; rdfs:label "population to population association" ; rdfs:subClassOf [ a owl:Restriction ; - owl:onClass ; - owl:onProperty ; - owl:qualifiedCardinality 1 ], - [ a owl:Restriction ; owl:onClass ; owl:onProperty ; owl:qualifiedCardinality 1 ], @@ -6327,6 +6340,10 @@ linkml:publication_type a owl:ObjectProperty, owl:onClass ; owl:onProperty ; owl:qualifiedCardinality 1 ], + [ a owl:Restriction ; + owl:onClass ; + owl:onProperty ; + owl:qualifiedCardinality 1 ], ; skos:definition "An association between a two populations" . @@ -6367,14 +6384,14 @@ linkml:publication_type a owl:ObjectProperty, owl:onClass ; owl:onProperty ; owl:qualifiedCardinality 1 ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty ], [ a owl:Restriction ; owl:onClass ; owl:onProperty ; owl:qualifiedCardinality 1 ], + [ a owl:Restriction ; + owl:maxQualifiedCardinality 1 ; + owl:onClass linkml:String ; + owl:onProperty ], . a owl:Class, @@ -6881,11 +6898,11 @@ linkml:sequence_feature_relationship_subject a owl:ObjectProperty, rdfs:label "anatomical entity to anatomical entity association" ; rdfs:subClassOf [ a owl:Restriction ; owl:onClass ; - owl:onProperty ; + owl:onProperty ; owl:qualifiedCardinality 1 ], [ a owl:Restriction ; owl:onClass ; - owl:onProperty ; + owl:onProperty ; owl:qualifiedCardinality 1 ], . @@ -6933,10 +6950,6 @@ linkml:sequence_feature_relationship_subject a owl:ObjectProperty, linkml:ClassDefinition ; rdfs:label "contributor association" ; rdfs:subClassOf [ a owl:Restriction ; - owl:onClass ; - owl:onProperty ; - owl:qualifiedCardinality 1 ], - [ a owl:Restriction ; owl:onClass ; owl:onProperty ; owl:qualifiedCardinality 1 ], @@ -6944,6 +6957,10 @@ linkml:sequence_feature_relationship_subject a owl:ObjectProperty, owl:onClass ; owl:onProperty ; owl:qualifiedCardinality 1 ], + [ a owl:Restriction ; + owl:onClass ; + owl:onProperty ; + owl:qualifiedCardinality 1 ], [ a owl:Restriction ; owl:allValuesFrom ; owl:onProperty ], @@ -6954,6 +6971,10 @@ linkml:sequence_feature_relationship_subject a owl:ObjectProperty, linkml:ClassDefinition ; rdfs:label "dataset version" ; rdfs:subClassOf [ a owl:Restriction ; + owl:maxQualifiedCardinality 1 ; + owl:onClass ; + owl:onProperty ], + [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass ; owl:onProperty ], @@ -6961,10 +6982,6 @@ linkml:sequence_feature_relationship_subject a owl:ObjectProperty, owl:maxQualifiedCardinality 1 ; owl:onClass linkml:String ; owl:onProperty ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass ; - owl:onProperty ], ; skos:definition "an item that holds version level information about a dataset." . @@ -6973,18 +6990,8 @@ linkml:sequence_feature_relationship_subject a owl:ObjectProperty, rdfs:label "entity" ; rdfs:subClassOf [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; - owl:onClass ; - owl:onProperty ], - [ a owl:Restriction ; - owl:allValuesFrom ; - owl:onProperty ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty ], - [ a owl:Restriction ; - owl:allValuesFrom ; - owl:onProperty ], + owl:onClass ; + owl:onProperty ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass ; @@ -6993,17 +7000,27 @@ linkml:sequence_feature_relationship_subject a owl:ObjectProperty, owl:onClass linkml:String ; owl:onProperty ; owl:qualifiedCardinality 1 ], + [ a owl:Restriction ; + owl:allValuesFrom ; + owl:onProperty ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; - owl:onClass ; - owl:onProperty ], + owl:onClass ; + owl:onProperty ], + [ a owl:Restriction ; + owl:maxQualifiedCardinality 1 ; + owl:onClass ; + owl:onProperty ], + [ a owl:Restriction ; + owl:maxQualifiedCardinality 1 ; + owl:onClass linkml:String ; + owl:onProperty ], [ a owl:Restriction ; owl:allValuesFrom ; owl:onProperty ], [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass ; - owl:onProperty ] ; + owl:allValuesFrom ; + owl:onProperty ] ; skos:definition "Root Biolink Model class for all things and informational relationships, real or imagined." . a owl:Class, @@ -7026,6 +7043,10 @@ linkml:sequence_feature_relationship_subject a owl:ObjectProperty, linkml:ClassDefinition ; rdfs:label "genotype to disease association" ; rdfs:subClassOf [ a owl:Restriction ; + owl:onClass ; + owl:onProperty ; + owl:qualifiedCardinality 1 ], + [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass ; owl:onProperty ], @@ -7034,21 +7055,17 @@ linkml:sequence_feature_relationship_subject a owl:ObjectProperty, owl:onClass ; owl:onProperty ], [ a owl:Restriction ; - owl:onClass ; - owl:onProperty ; + owl:onClass ; + owl:onProperty ; owl:qualifiedCardinality 1 ], [ a owl:Restriction ; owl:onClass ; - owl:onProperty ; + owl:onProperty ; owl:qualifiedCardinality 1 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass ; owl:onProperty ], - [ a owl:Restriction ; - owl:onClass ; - owl:onProperty ; - owl:qualifiedCardinality 1 ], , , ; @@ -7109,14 +7126,14 @@ linkml:sequence_feature_relationship_subject a owl:ObjectProperty, owl:onClass ; owl:onProperty ; owl:qualifiedCardinality 1 ], - [ a owl:Restriction ; - owl:onClass ; - owl:onProperty ; - owl:qualifiedCardinality 1 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass linkml:String ; owl:onProperty ], + [ a owl:Restriction ; + owl:onClass ; + owl:onProperty ; + owl:qualifiedCardinality 1 ], ; skos:definition "An interaction relationship between two taxa. This may be a symbiotic relationship (encompassing mutualism and parasitism), or it may be non-symbiotic. Example: plague transmitted_by flea; cattle domesticated_by Homo sapiens; plague infects Homo sapiens" . @@ -7148,24 +7165,24 @@ linkml:sequence_feature_relationship_subject a owl:ObjectProperty, rdfs:label "variant to disease association" ; rdfs:subClassOf [ a owl:Restriction ; owl:onClass ; - owl:onProperty ; + owl:onProperty ; owl:qualifiedCardinality 1 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass ; owl:onProperty ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass ; - owl:onProperty ], [ a owl:Restriction ; owl:onClass ; owl:onProperty ; owl:qualifiedCardinality 1 ], [ a owl:Restriction ; owl:onClass ; - owl:onProperty ; + owl:onProperty ; owl:qualifiedCardinality 1 ], + [ a owl:Restriction ; + owl:maxQualifiedCardinality 1 ; + owl:onClass ; + owl:onProperty ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass ; @@ -7298,17 +7315,17 @@ linkml:functional_association_object a owl:ObjectProperty, rdfs:label "gene to expression site association" ; rdfs:seeAlso "https://github.com/monarch-initiative/ingest-artifacts/tree/master/sources/BGee" ; rdfs:subClassOf [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass ; - owl:onProperty ], + owl:onClass ; + owl:onProperty ; + owl:qualifiedCardinality 1 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass ; owl:onProperty ], [ a owl:Restriction ; - owl:onClass ; - owl:onProperty ; - owl:qualifiedCardinality 1 ], + owl:maxQualifiedCardinality 1 ; + owl:onClass ; + owl:onProperty ], [ a owl:Restriction ; owl:onClass ; owl:onProperty ; @@ -7362,29 +7379,29 @@ linkml:functional_association_object a owl:ObjectProperty, linkml:ClassDefinition ; rdfs:label "pairwise molecular interaction" ; rdfs:subClassOf [ a owl:Restriction ; - owl:onClass ; - owl:onProperty ; - owl:qualifiedCardinality 1 ], - [ a owl:Restriction ; - owl:onClass ; - owl:onProperty ; - owl:qualifiedCardinality 1 ], - [ a owl:Restriction ; owl:onClass ; owl:onProperty ; owl:qualifiedCardinality 1 ], + [ a owl:Restriction ; + owl:maxQualifiedCardinality 1 ; + owl:onClass linkml:String ; + owl:onProperty ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass ; owl:onProperty ], [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty ], + owl:onClass ; + owl:onProperty ; + owl:qualifiedCardinality 1 ], [ a owl:Restriction ; owl:onClass linkml:String ; owl:onProperty ; owl:qualifiedCardinality 1 ], + [ a owl:Restriction ; + owl:onClass ; + owl:onProperty ; + owl:qualifiedCardinality 1 ], ; skos:definition "An interaction at the molecular level between two physical entities" . @@ -7416,33 +7433,33 @@ linkml:functional_association_object a owl:ObjectProperty, linkml:ClassDefinition ; rdfs:label "variant to population association" ; rdfs:subClassOf [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:Integer ; - owl:onProperty ], - [ a owl:Restriction ; - owl:onClass ; - owl:onProperty ; + owl:onClass ; + owl:onProperty ; owl:qualifiedCardinality 1 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass linkml:Double ; owl:onProperty ], [ a owl:Restriction ; - owl:onClass ; - owl:onProperty ; + owl:onClass ; + owl:onProperty ; owl:qualifiedCardinality 1 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:Double ; - owl:onProperty ], + owl:onClass linkml:Integer ; + owl:onProperty ], + [ a owl:Restriction ; + owl:maxQualifiedCardinality 1 ; + owl:onClass ; + owl:onProperty ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass linkml:Integer ; owl:onProperty ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; - owl:onClass ; - owl:onProperty ], + owl:onClass linkml:Double ; + owl:onProperty ], , , , @@ -7526,15 +7543,6 @@ linkml:functional_association_object a owl:ObjectProperty, rdfs:subPropertyOf ; skos:definition "Alternate CURIEs for a thing" . -linkml:Boolean a owl:Class, - linkml:TypeDefinition ; - rdfs:label "boolean" ; - rdfs:subClassOf [ a owl:Restriction ; - owl:onDataRange xsd:boolean ; - owl:onProperty linkml:topValue ; - owl:qualifiedCardinality 1 ] ; - skos:definition "A binary (true or false) value" . - a owl:Class, linkml:ClassDefinition ; rdfs:label "chemical mixture" ; @@ -7669,11 +7677,11 @@ linkml:Float a owl:Class, linkml:ClassDefinition ; rdfs:label "gene product mixin" ; rdfs:subClassOf [ a owl:Restriction ; - owl:allValuesFrom ; - owl:onProperty ], - [ a owl:Restriction ; owl:allValuesFrom ; owl:onProperty ], + [ a owl:Restriction ; + owl:allValuesFrom ; + owl:onProperty ], , linkml:mixin ; skos:definition "The functional molecular product of a single gene locus. Gene products are either proteins or functional RNA molecules." ; @@ -7685,13 +7693,13 @@ linkml:Float a owl:Class, linkml:ClassDefinition ; rdfs:label "model to disease association mixin" ; rdfs:subClassOf [ a owl:Restriction ; - owl:onClass ; - owl:onProperty ; - owl:qualifiedCardinality 1 ], - [ a owl:Restriction ; owl:onClass ; owl:onProperty ; owl:qualifiedCardinality 1 ], + [ a owl:Restriction ; + owl:onClass ; + owl:onProperty ; + owl:qualifiedCardinality 1 ], linkml:mixin ; skos:definition "This mixin is used for any association class for which the subject (source node) plays the role of a 'model', in that it recapitulates some features of the disease in a way that is useful for studying the disease outside a patient carrying the disease" . @@ -7713,6 +7721,15 @@ linkml:Float a owl:Class, owl:inverseOf ; skos:definition "holds between a continuant and a process, where the continuant is somehow involved in the process" . +linkml:Boolean a owl:Class, + linkml:TypeDefinition ; + rdfs:label "boolean" ; + rdfs:subClassOf [ a owl:Restriction ; + owl:onDataRange xsd:boolean ; + owl:onProperty linkml:topValue ; + owl:qualifiedCardinality 1 ] ; + skos:definition "A binary (true or false) value" . + a owl:Class, linkml:ClassDefinition ; rdfs:label "genomic entity" ; @@ -7782,13 +7799,13 @@ linkml:Float a owl:Class, linkml:ClassDefinition ; rdfs:label "entity to phenotypic feature association mixin" ; rdfs:subClassOf [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass ; - owl:onProperty ], - [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass ; owl:onProperty ], + [ a owl:Restriction ; + owl:maxQualifiedCardinality 1 ; + owl:onClass ; + owl:onProperty ], [ a owl:Restriction ; owl:onClass ; owl:onProperty ; @@ -7806,11 +7823,11 @@ linkml:Float a owl:Class, linkml:ClassDefinition ; rdfs:label "molecular activity" ; rdfs:subClassOf [ a owl:Restriction ; - owl:allValuesFrom ; - owl:onProperty ], - [ a owl:Restriction ; owl:allValuesFrom ; owl:onProperty ], + [ a owl:Restriction ; + owl:allValuesFrom ; + owl:onProperty ], [ a owl:Restriction ; owl:allValuesFrom ; owl:onProperty ], @@ -7919,20 +7936,20 @@ linkml:Double a owl:Class, linkml:ClassDefinition ; rdfs:label "agent" ; rdfs:subClassOf [ a owl:Restriction ; - owl:allValuesFrom linkml:Uriorcurie ; - owl:onProperty ], - [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass ; owl:onProperty ], [ a owl:Restriction ; - owl:onClass linkml:String ; - owl:onProperty ; - owl:qualifiedCardinality 1 ], + owl:allValuesFrom linkml:Uriorcurie ; + owl:onProperty ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass linkml:String ; owl:onProperty ], + [ a owl:Restriction ; + owl:onClass linkml:String ; + owl:onProperty ; + owl:qualifiedCardinality 1 ], ; skos:altLabel "group" ; skos:definition "person, group, organization or project that provides a piece of information (i.e. a knowledge association)" ; @@ -7949,14 +7966,14 @@ linkml:Double a owl:Class, linkml:ClassDefinition ; rdfs:label "biological process or activity" ; rdfs:subClassOf [ a owl:Restriction ; + owl:allValuesFrom ; + owl:onProperty ], + [ a owl:Restriction ; owl:allValuesFrom ; owl:onProperty ], [ a owl:Restriction ; owl:allValuesFrom ; owl:onProperty ], - [ a owl:Restriction ; - owl:allValuesFrom ; - owl:onProperty ], , , ; @@ -7980,37 +7997,37 @@ linkml:Double a owl:Class, linkml:ClassDefinition ; rdfs:label "genomic sequence localization" ; rdfs:subClassOf [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:Integer ; - owl:onProperty ], - [ a owl:Restriction ; - owl:onClass ; - owl:onProperty ; - owl:qualifiedCardinality 1 ], - [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass ; owl:onProperty ], + [ a owl:Restriction ; + owl:maxQualifiedCardinality 1 ; + owl:onClass ; + owl:onProperty ], [ a owl:Restriction ; owl:onClass ; - owl:onProperty ; + owl:onProperty ; owl:qualifiedCardinality 1 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass linkml:Integer ; owl:onProperty ], + [ a owl:Restriction ; + owl:onClass ; + owl:onProperty ; + owl:qualifiedCardinality 1 ], + [ a owl:Restriction ; + owl:onClass ; + owl:onProperty ; + owl:qualifiedCardinality 1 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; - owl:onClass ; - owl:onProperty ], + owl:onClass linkml:Integer ; + owl:onProperty ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass ; owl:onProperty ], - [ a owl:Restriction ; - owl:onClass ; - owl:onProperty ; - owl:qualifiedCardinality 1 ], ; skos:definition "A relationship between a sequence feature and a nucleic acid entity it is localized to. The reference entity may be a chromosome, chromosome region or information entity such as a contig." . @@ -8058,27 +8075,27 @@ linkml:Uriorcurie a owl:Class, rdfs:label "attribute" ; rdfs:subClassOf [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; - owl:onClass ; - owl:onProperty ], + owl:onClass ; + owl:onProperty ], [ a owl:Restriction ; owl:allValuesFrom ; owl:onProperty ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass ; - owl:onProperty ], [ a owl:Restriction ; owl:onClass ; owl:onProperty ; owl:qualifiedCardinality 1 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; - owl:onClass ; - owl:onProperty ], + owl:onClass ; + owl:onProperty ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass ; - owl:onProperty ], + owl:onProperty ], + [ a owl:Restriction ; + owl:maxQualifiedCardinality 1 ; + owl:onClass ; + owl:onProperty ], , ; skos:definition "A property or characteristic of an entity. For example, an apple may have properties such as color, shape, age, crispiness. An environmental sample may have attributes such as depth, lat, long, material." ; @@ -8089,15 +8106,15 @@ linkml:Uriorcurie a owl:Class, rdfs:label "genotype" ; rdfs:subClassOf [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; - owl:onClass ; - owl:onProperty ], + owl:onClass ; + owl:onProperty ], [ a owl:Restriction ; owl:allValuesFrom ; owl:onProperty ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; - owl:onClass ; - owl:onProperty ], + owl:onClass ; + owl:onProperty ], , , , @@ -8169,6 +8186,10 @@ linkml:topValue a owl:DatatypeProperty ; linkml:ClassDefinition ; rdfs:label "information content entity" ; rdfs:subClassOf [ a owl:Restriction ; + owl:maxQualifiedCardinality 1 ; + owl:onClass linkml:String ; + owl:onProperty ], + [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass linkml:String ; owl:onProperty ], @@ -8180,10 +8201,6 @@ linkml:topValue a owl:DatatypeProperty ; owl:maxQualifiedCardinality 1 ; owl:onClass linkml:String ; owl:onProperty ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty ], ; skos:altLabel "information", "information artefact", @@ -8290,35 +8307,35 @@ linkml:Integer a owl:Class, linkml:ClassDefinition ; rdfs:label "publication" ; rdfs:subClassOf [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty ], + owl:allValuesFrom linkml:String ; + owl:onProperty ], [ a owl:Restriction ; owl:allValuesFrom linkml:String ; owl:onProperty ], [ a owl:Restriction ; owl:allValuesFrom linkml:String ; - owl:onProperty ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass ; - owl:onProperty ], + owl:onProperty ], [ a owl:Restriction ; owl:allValuesFrom linkml:Uriorcurie ; owl:onProperty ], [ a owl:Restriction ; owl:onClass linkml:String ; - owl:onProperty ; + owl:onProperty ; owl:qualifiedCardinality 1 ], - [ a owl:Restriction ; - owl:allValuesFrom linkml:String ; - owl:onProperty ], [ a owl:Restriction ; owl:allValuesFrom ; owl:onProperty ], [ a owl:Restriction ; + owl:maxQualifiedCardinality 1 ; owl:onClass linkml:String ; - owl:onProperty ; + owl:onProperty ], + [ a owl:Restriction ; + owl:maxQualifiedCardinality 1 ; + owl:onClass ; + owl:onProperty ], + [ a owl:Restriction ; + owl:onClass linkml:String ; + owl:onProperty ; owl:qualifiedCardinality 1 ], ; skos:definition "Any published piece of information. Can refer to a whole publication, its encompassing publication (i.e. journal or book) or to a part of a publication, if of significant knowledge scope (e.g. a figure, figure legend, or section highlighted by NLP). The scope is intended to be general and include information published on the web, as well as printed materials, either directly or in one of the Publication Biolink category subclasses." ; @@ -8432,9 +8449,6 @@ linkml:TypeDefinition a owl:Class ; linkml:ClassDefinition ; rdfs:label "gene" ; rdfs:subClassOf [ a owl:Restriction ; - owl:allValuesFrom ; - owl:onProperty ], - [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass linkml:String ; owl:onProperty ], @@ -8442,6 +8456,9 @@ linkml:TypeDefinition a owl:Class ; owl:maxQualifiedCardinality 1 ; owl:onClass ; owl:onProperty ], + [ a owl:Restriction ; + owl:allValuesFrom ; + owl:onProperty ], [ a owl:Restriction ; owl:allValuesFrom ; owl:onProperty ], @@ -8513,6 +8530,12 @@ linkml:TypeDefinition a owl:Class ; skos:definition "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; skos:editorialNote "Has a value from the Biolink related_to hierarchy. In RDF, this corresponds to rdf:predicate and in Neo4j this corresponds to the relationship type. The convention is for an edge label in snake_case form. For example, biolink:related_to, biolink:causes, biolink:treats" . + a owl:Class, + linkml:TypeDefinition ; + rdfs:label "predicate type" ; + rdfs:subClassOf linkml:Uriorcurie ; + skos:definition "A CURIE from the biolink related_to hierarchy. For example, biolink:related_to, biolink:causes, biolink:treats." . + a owl:ObjectProperty, linkml:SlotDefinition ; rdfs:label "node property" ; @@ -8520,12 +8543,6 @@ linkml:TypeDefinition a owl:Class ; rdfs:range linkml:String ; skos:definition "A grouping for any property that holds between a node and a value" . - a owl:Class, - linkml:TypeDefinition ; - rdfs:label "predicate type" ; - rdfs:subClassOf linkml:Uriorcurie ; - skos:definition "A CURIE from the biolink related_to hierarchy. For example, biolink:related_to, biolink:causes, biolink:treats." . - a owl:ObjectProperty, owl:SymmetricProperty, linkml:SlotDefinition ; @@ -8546,38 +8563,38 @@ linkml:TypeDefinition a owl:Class ; linkml:ClassDefinition ; rdfs:label "association" ; rdfs:subClassOf [ a owl:Restriction ; - owl:allValuesFrom ; - owl:onProperty ], - [ a owl:Restriction ; - owl:onClass ; - owl:onProperty ; - owl:qualifiedCardinality 1 ], - [ a owl:Restriction ; owl:onClass ; owl:onProperty ; owl:qualifiedCardinality 1 ], + [ a owl:Restriction ; + owl:allValuesFrom ; + owl:onProperty ], [ a owl:Restriction ; owl:onClass ; owl:onProperty ; owl:qualifiedCardinality 1 ], - [ a owl:Restriction ; - owl:allValuesFrom ; - owl:onProperty ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass linkml:String ; - owl:onProperty ], + owl:onProperty ], [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:Boolean ; - owl:onProperty ], + owl:allValuesFrom ; + owl:onProperty ], + [ a owl:Restriction ; + owl:onClass ; + owl:onProperty ; + owl:qualifiedCardinality 1 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass linkml:String ; - owl:onProperty ], + owl:onProperty ], [ a owl:Restriction ; owl:allValuesFrom ; owl:onProperty ], + [ a owl:Restriction ; + owl:maxQualifiedCardinality 1 ; + owl:onClass linkml:Boolean ; + owl:onProperty ], ; skos:definition "A typed association between two entities, supported by evidence" ; skos:exactMatch , @@ -8606,12 +8623,20 @@ linkml:String a owl:Class, linkml:ClassDefinition ; rdfs:label "chemical entity" ; rdfs:subClassOf [ a owl:Restriction ; + owl:allValuesFrom ; + owl:onProperty ], + [ a owl:Restriction ; + owl:maxQualifiedCardinality 1 ; + owl:onClass linkml:Boolean ; + owl:onProperty ], + [ a owl:Restriction ; + owl:maxQualifiedCardinality 1 ; + owl:onClass linkml:String ; + owl:onProperty ], + [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass ; owl:onProperty ], - [ a owl:Restriction ; - owl:allValuesFrom ; - owl:onProperty ], , , , diff --git a/biolink-model.proto b/biolink-model.proto index 9e5e1d2adb..497fd26822 100644 --- a/biolink-model.proto +++ b/biolink-model.proto @@ -421,6 +421,8 @@ message ChemicalEntity repeated category NamedThing = 9 optional tradeName ChemicalEntity = 10 repeated availableFrom DrugAvailabilityEnum = 11 + optional maxToleratedDose String = 12 + optional isToxic Boolean = 13 } // A chemical exposure is an intake of a particular chemical entity. message ChemicalExposure @@ -441,8 +443,10 @@ message ChemicalMixture repeated category NamedThing = 9 optional tradeName ChemicalEntity = 10 repeated availableFrom DrugAvailabilityEnum = 11 - optional isSupplement ChemicalMixture = 12 - optional highestFDAApprovalStatus String = 13 + optional maxToleratedDose String = 12 + optional isToxic Boolean = 13 + optional isSupplement ChemicalMixture = 14 + optional highestFDAApprovalStatus String = 15 } // A relationship between two chemical entities. This can encompass actual interactions as well as temporal causal edges, e.g. one chemical converted to another. message ChemicalToChemicalAssociation @@ -656,9 +660,11 @@ message CodingSequence repeated category NamedThing = 9 optional tradeName ChemicalEntity = 10 repeated availableFrom DrugAvailabilityEnum = 11 - optional isMetabolite Boolean = 12 - repeated inTaxon OrganismTaxon = 13 - optional hasBiologicalSequence BiologicalSequence = 14 + optional maxToleratedDose String = 12 + optional isToxic Boolean = 13 + optional isMetabolite Boolean = 14 + repeated inTaxon OrganismTaxon = 15 + optional hasBiologicalSequence BiologicalSequence = 16 } // A group of people banded together or treated as a group who share common characteristics. A cohort 'study' is a particular form of longitudinal study that samples a cohort, performing a cross-section at intervals through time. message Cohort @@ -688,8 +694,10 @@ message ComplexMolecularMixture repeated category NamedThing = 9 optional tradeName ChemicalEntity = 10 repeated availableFrom DrugAvailabilityEnum = 11 - optional isSupplement ChemicalMixture = 12 - optional highestFDAApprovalStatus String = 13 + optional maxToleratedDose String = 12 + optional isToxic Boolean = 13 + optional isSupplement ChemicalMixture = 14 + optional highestFDAApprovalStatus String = 15 } // Level of confidence in a statement message ConfidenceLevel @@ -925,8 +933,10 @@ message Drug repeated category NamedThing = 9 optional tradeName ChemicalEntity = 10 repeated availableFrom DrugAvailabilityEnum = 11 - optional isSupplement ChemicalMixture = 12 - optional highestFDAApprovalStatus String = 13 + optional maxToleratedDose String = 12 + optional isToxic Boolean = 13 + optional isSupplement ChemicalMixture = 14 + optional highestFDAApprovalStatus String = 15 } // A drug exposure is an intake of a particular drug. message DrugExposure @@ -1029,6 +1039,8 @@ message EnvironmentalFoodContaminant repeated category NamedThing = 9 optional tradeName ChemicalEntity = 10 repeated availableFrom DrugAvailabilityEnum = 11 + optional maxToleratedDose String = 12 + optional isToxic Boolean = 13 } message EnvironmentalProcess { @@ -1086,9 +1098,11 @@ message Exon repeated category NamedThing = 9 optional tradeName ChemicalEntity = 10 repeated availableFrom DrugAvailabilityEnum = 11 - optional isMetabolite Boolean = 12 - repeated inTaxon OrganismTaxon = 13 - optional hasBiologicalSequence BiologicalSequence = 14 + optional maxToleratedDose String = 12 + optional isToxic Boolean = 13 + optional isMetabolite Boolean = 14 + repeated inTaxon OrganismTaxon = 15 + optional hasBiologicalSequence BiologicalSequence = 16 } // A transcript is formed from multiple exons message ExonToTranscriptRelationship @@ -1170,8 +1184,10 @@ message Food repeated category NamedThing = 9 optional tradeName ChemicalEntity = 10 repeated availableFrom DrugAvailabilityEnum = 11 - optional isSupplement ChemicalMixture = 12 - optional highestFDAApprovalStatus String = 13 + optional maxToleratedDose String = 12 + optional isToxic Boolean = 13 + optional isSupplement ChemicalMixture = 14 + optional highestFDAApprovalStatus String = 15 } message FoodAdditive { @@ -1186,6 +1202,8 @@ message FoodAdditive repeated category NamedThing = 9 optional tradeName ChemicalEntity = 10 repeated availableFrom DrugAvailabilityEnum = 11 + optional maxToleratedDose String = 12 + optional isToxic Boolean = 13 } // An association between a macromolecular machine mixin (gene, gene product or complex of gene products) and either a molecular activity, a biological process or a cellular location in which a function is executed. message FunctionalAssociation @@ -1860,6 +1878,8 @@ message Macronutrient repeated category NamedThing = 9 optional tradeName ChemicalEntity = 10 repeated availableFrom DrugAvailabilityEnum = 11 + optional maxToleratedDose String = 12 + optional isToxic Boolean = 13 } // A sample is a limited quantity of something (e.g. an individual or set of individuals from a population, or a portion of a substance) to be used for testing, analysis, inspection, investigation, demonstration, or trial use. [SIO] message MaterialSample @@ -1927,6 +1947,8 @@ message Micronutrient repeated category NamedThing = 9 optional tradeName ChemicalEntity = 10 repeated availableFrom DrugAvailabilityEnum = 11 + optional maxToleratedDose String = 12 + optional isToxic Boolean = 13 } message MicroRNA { @@ -1941,11 +1963,13 @@ message MicroRNA repeated category NamedThing = 9 optional tradeName ChemicalEntity = 10 repeated availableFrom DrugAvailabilityEnum = 11 - optional isMetabolite Boolean = 12 - repeated inTaxon OrganismTaxon = 13 - optional hasBiologicalSequence BiologicalSequence = 14 - repeated synonym LabelType = 15 - repeated xref IriType = 16 + optional maxToleratedDose String = 12 + optional isToxic Boolean = 13 + optional isMetabolite Boolean = 14 + repeated inTaxon OrganismTaxon = 15 + optional hasBiologicalSequence BiologicalSequence = 16 + repeated synonym LabelType = 17 + repeated xref IriType = 18 } // An execution of a molecular function carried out by a gene product or macromolecular complex. message MolecularActivity @@ -1977,7 +2001,9 @@ message MolecularEntity repeated category NamedThing = 9 optional tradeName ChemicalEntity = 10 repeated availableFrom DrugAvailabilityEnum = 11 - optional isMetabolite Boolean = 12 + optional maxToleratedDose String = 12 + optional isToxic Boolean = 13 + optional isMetabolite Boolean = 14 } // A molecular mixture is a chemical mixture composed of two or more molecular entities with known concentration and stoichiometry. message MolecularMixture @@ -1993,8 +2019,10 @@ message MolecularMixture repeated category NamedThing = 9 optional tradeName ChemicalEntity = 10 repeated availableFrom DrugAvailabilityEnum = 11 - optional isSupplement ChemicalMixture = 12 - optional highestFDAApprovalStatus String = 13 + optional maxToleratedDose String = 12 + optional isToxic Boolean = 13 + optional isSupplement ChemicalMixture = 14 + optional highestFDAApprovalStatus String = 15 } // a databased entity or concept/class message NamedThing @@ -2042,11 +2070,13 @@ message NoncodingRNAProduct repeated category NamedThing = 9 optional tradeName ChemicalEntity = 10 repeated availableFrom DrugAvailabilityEnum = 11 - optional isMetabolite Boolean = 12 - repeated inTaxon OrganismTaxon = 13 - optional hasBiologicalSequence BiologicalSequence = 14 - repeated synonym LabelType = 15 - repeated xref IriType = 16 + optional maxToleratedDose String = 12 + optional isToxic Boolean = 13 + optional isMetabolite Boolean = 14 + repeated inTaxon OrganismTaxon = 15 + optional hasBiologicalSequence BiologicalSequence = 16 + repeated synonym LabelType = 17 + repeated xref IriType = 18 } // A nucleic acid entity is a molecular entity characterized by availability in gene databases of nucleotide-based sequence representations of its precise sequence; for convenience of representation, partial sequences of various kinds are included. message NucleicAcidEntity @@ -2062,9 +2092,11 @@ message NucleicAcidEntity repeated category NamedThing = 9 optional tradeName ChemicalEntity = 10 repeated availableFrom DrugAvailabilityEnum = 11 - optional isMetabolite Boolean = 12 - repeated inTaxon OrganismTaxon = 13 - optional hasBiologicalSequence BiologicalSequence = 14 + optional maxToleratedDose String = 12 + optional isToxic Boolean = 13 + optional isMetabolite Boolean = 14 + repeated inTaxon OrganismTaxon = 15 + optional hasBiologicalSequence BiologicalSequence = 16 } message Nutrient { @@ -2079,6 +2111,8 @@ message Nutrient repeated category NamedThing = 9 optional tradeName ChemicalEntity = 10 repeated availableFrom DrugAvailabilityEnum = 11 + optional maxToleratedDose String = 12 + optional isToxic Boolean = 13 } // The age group in which (disease) symptom manifestations appear message Onset @@ -2455,8 +2489,10 @@ message ProcessedMaterial repeated category NamedThing = 9 optional tradeName ChemicalEntity = 10 repeated availableFrom DrugAvailabilityEnum = 11 - optional isSupplement ChemicalMixture = 12 - optional highestFDAApprovalStatus String = 13 + optional maxToleratedDose String = 12 + optional isToxic Boolean = 13 + optional isSupplement ChemicalMixture = 14 + optional highestFDAApprovalStatus String = 15 } // A gene product that is composed of a chain of amino acid sequences and is produced by ribosome-mediated translation of mRNA message Protein @@ -2591,11 +2627,13 @@ message RNAProduct repeated category NamedThing = 9 optional tradeName ChemicalEntity = 10 repeated availableFrom DrugAvailabilityEnum = 11 - optional isMetabolite Boolean = 12 - repeated inTaxon OrganismTaxon = 13 - optional hasBiologicalSequence BiologicalSequence = 14 - repeated synonym LabelType = 15 - repeated xref IriType = 16 + optional maxToleratedDose String = 12 + optional isToxic Boolean = 13 + optional isMetabolite Boolean = 14 + repeated inTaxon OrganismTaxon = 15 + optional hasBiologicalSequence BiologicalSequence = 16 + repeated synonym LabelType = 17 + repeated xref IriType = 18 } // Represents a protein that is a specific isoform of the canonical or reference RNA message RNAProductIsoform @@ -2611,11 +2649,13 @@ message RNAProductIsoform repeated category NamedThing = 9 optional tradeName ChemicalEntity = 10 repeated availableFrom DrugAvailabilityEnum = 11 - optional isMetabolite Boolean = 12 - repeated inTaxon OrganismTaxon = 13 - optional hasBiologicalSequence BiologicalSequence = 14 - repeated synonym LabelType = 15 - repeated xref IriType = 16 + optional maxToleratedDose String = 12 + optional isToxic Boolean = 13 + optional isMetabolite Boolean = 14 + repeated inTaxon OrganismTaxon = 15 + optional hasBiologicalSequence BiologicalSequence = 16 + repeated synonym LabelType = 17 + repeated xref IriType = 18 } // An association between a sequence feature and a nucleic acid entity it is localized to. message SequenceAssociation @@ -2723,11 +2763,13 @@ message SiRNA repeated category NamedThing = 9 optional tradeName ChemicalEntity = 10 repeated availableFrom DrugAvailabilityEnum = 11 - optional isMetabolite Boolean = 12 - repeated inTaxon OrganismTaxon = 13 - optional hasBiologicalSequence BiologicalSequence = 14 - repeated synonym LabelType = 15 - repeated xref IriType = 16 + optional maxToleratedDose String = 12 + optional isToxic Boolean = 13 + optional isMetabolite Boolean = 14 + repeated inTaxon OrganismTaxon = 15 + optional hasBiologicalSequence BiologicalSequence = 16 + repeated synonym LabelType = 17 + repeated xref IriType = 18 } // A small molecule entity is a molecular entity characterized by availability in small-molecule databases of SMILES, InChI, IUPAC, or other unambiguous representation of its precise chemical structure; for convenience of representation, any valid chemical representation is included, even if it is not strictly molecular (e.g., sodium ion). message SmallMolecule @@ -2742,8 +2784,10 @@ message SmallMolecule repeated category NamedThing = 8 optional tradeName ChemicalEntity = 9 repeated availableFrom DrugAvailabilityEnum = 10 - optional isMetabolite Boolean = 11 - id String = 12 + optional maxToleratedDose String = 11 + optional isToxic Boolean = 12 + optional isMetabolite Boolean = 13 + id String = 14 } // SNVs are single nucleotide positions in genomic DNA at which different sequence alternatives exist message Snv @@ -2824,9 +2868,11 @@ message Transcript repeated category NamedThing = 9 optional tradeName ChemicalEntity = 10 repeated availableFrom DrugAvailabilityEnum = 11 - optional isMetabolite Boolean = 12 - repeated inTaxon OrganismTaxon = 13 - optional hasBiologicalSequence BiologicalSequence = 14 + optional maxToleratedDose String = 12 + optional isToxic Boolean = 13 + optional isMetabolite Boolean = 14 + repeated inTaxon OrganismTaxon = 15 + optional hasBiologicalSequence BiologicalSequence = 16 } // A gene is a collection of transcripts message TranscriptToGeneRelationship @@ -3014,6 +3060,8 @@ message Vitamin repeated category NamedThing = 9 optional tradeName ChemicalEntity = 10 repeated availableFrom DrugAvailabilityEnum = 11 + optional maxToleratedDose String = 12 + optional isToxic Boolean = 13 } message Zygosity { diff --git a/biolink-model.shex b/biolink-model.shex index c0e4d6a543..3ee8d1707d 100644 --- a/biolink-model.shex +++ b/biolink-model.shex @@ -469,7 +469,9 @@ linkml:Nodeidentifier NONLITERAL & ; rdf:type [ ] ? ; @ ? ; - @ * + @ * ; + @linkml:String ? ; + @linkml:Boolean ? ) ; rdf:type [ ] ) diff --git a/biolink-model.ttl b/biolink-model.ttl index e76846b964..125cf157b0 100644 --- a/biolink-model.ttl +++ b/biolink-model.ttl @@ -13,7 +13,7 @@ a linkml:SchemaDefinition ; dcterms:license "https://creativecommons.org/publicdomain/zero/1.0/" ; - pav:version "2.2.4" ; + pav:version "2.2.5" ; skos:definition "Entity and association taxonomy and datamodel for life-sciences data" ; linkml:classes , , @@ -294,220 +294,226 @@ , , ; - linkml:generation_date "2021-09-02 18:54"^^xsd:dateTime ; + linkml:generation_date "2021-09-21 22:44"^^xsd:dateTime ; linkml:id ; linkml:imports linkml:types ; linkml:metamodel_version "1.7.0" ; - linkml:prefixes [ linkml:prefix_prefix "ScopusID" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "UBERGRAPH" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "VANDF" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "KEGG.RCLASS" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "COG" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "isbn" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "OBOREL" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "PATO-PROPERTY" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "GAMMA" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "CLINVAR" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "HCPCS" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "WIKIDATA" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "alliancegenome" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "doi" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "ExO" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "WIKIDATA_PROPERTY" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "SEMMEDDB" ; - linkml:prefix_reference ], + linkml:prefixes [ linkml:prefix_prefix "EFO" ; + linkml:prefix_reference ], [ linkml:prefix_prefix "UBERON_CORE" ; linkml:prefix_reference ], - [ linkml:prefix_prefix "CHADO" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "CID" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "HANCESTRO" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "CAID" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "Xenbase" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "ICD9" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "XPO" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "biolink" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "MetaCyc" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "NCBIGene" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "INO" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "UMLSSG" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "gpi" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "KEGG.GENE" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "Aeolus" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "GTOPDB" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "EDAM-FORMAT" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "PathWhiz" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "GTEx" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "DrugCentral" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "foodb.compound" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "KEGG.DGROUP" ; - linkml:prefix_reference ], + [ linkml:prefix_prefix "PATO-PROPERTY" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "prov" ; + linkml:prefix_reference ], [ linkml:prefix_prefix "chembio" ; linkml:prefix_reference ], - [ linkml:prefix_prefix "ECTO" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "mirbase" ; - linkml:prefix_reference ], + [ linkml:prefix_prefix "PANTHER.FAMILY" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "LOINC" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "ICD0" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "REPODB" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "MI" ; + linkml:prefix_reference ], [ linkml:prefix_prefix "medgen" ; linkml:prefix_reference ], - [ linkml:prefix_prefix "EDAM-DATA" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "dct" ; - linkml:prefix_reference dcterms: ], - [ linkml:prefix_prefix "pav" ; - linkml:prefix_reference pav: ], - [ linkml:prefix_prefix "COAR_RESOURCE" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "interpro" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "os" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "GOREL" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "MESH" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "SNPEFF" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "CTD" ; - linkml:prefix_reference ], [ linkml:prefix_prefix "ORPHA" ; linkml:prefix_reference ], - [ linkml:prefix_prefix "KEGG.ENZYME" ; + [ linkml:prefix_prefix "NLMID" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "ICD10" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "MESH" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "WBVocab" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "GOREL" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "MSigDB" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "Xenbase" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "KEGG.GENE" ; linkml:prefix_reference ], + [ linkml:prefix_prefix "XPO" ; + linkml:prefix_reference ], [ linkml:prefix_prefix "ORCID" ; linkml:prefix_reference ], - [ linkml:prefix_prefix "PANTHER.FAMILY" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "STY" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "SIO" ; - linkml:prefix_reference ], + [ linkml:prefix_prefix "GAMMA" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "COAR_RESOURCE" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "CTD" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "issn" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "dcat" ; + linkml:prefix_reference ], [ linkml:prefix_prefix "RXCUI" ; linkml:prefix_reference ], - [ linkml:prefix_prefix "schema" ; - linkml:prefix_reference schema: ], - [ linkml:prefix_prefix "prov" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "PHAROS" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "oboformat" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "DGIdb" ; - linkml:prefix_reference ], [ linkml:prefix_prefix "gff3" ; linkml:prefix_reference ], + [ linkml:prefix_prefix "HANCESTRO" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "STY" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "wgs" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "CLINVAR" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "INO" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "dct" ; + linkml:prefix_reference dcterms: ], [ linkml:prefix_prefix "CHEMBL.MECHANISM" ; linkml:prefix_reference ], + [ linkml:prefix_prefix "DGIdb" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "VANDF" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "EDAM-FORMAT" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "os" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "NCBIGene" ; + linkml:prefix_reference ], [ linkml:prefix_prefix "GSID" ; linkml:prefix_reference ], - [ linkml:prefix_prefix "EFO" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "KEGG.BRITE" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "NLMID" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "OBAN" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "GOP" ; - linkml:prefix_reference ], + [ linkml:prefix_prefix "WIKIDATA_PROPERTY" ; + linkml:prefix_reference ], [ linkml:prefix_prefix "VMC" ; linkml:prefix_reference ], - [ linkml:prefix_prefix "qud" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "ResearchID" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "RO" ; + [ linkml:prefix_prefix "SNOMED" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "CHADO" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "OBOREL" ; linkml:prefix_reference ], + [ linkml:prefix_prefix "KEGG.BRITE" ; + linkml:prefix_reference ], [ linkml:prefix_prefix "gtpo" ; linkml:prefix_reference ], - [ linkml:prefix_prefix "EDAM-OPERATION" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "ChemBank" ; - linkml:prefix_reference ], + [ linkml:prefix_prefix "SNOMEDCT" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "interpro" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "linkml" ; + linkml:prefix_reference linkml: ], + [ linkml:prefix_prefix "ECTO" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "WIKIDATA" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "RXNORM" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "doi" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "CID" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "ICD9" ; + linkml:prefix_reference ], [ linkml:prefix_prefix "HsapDv" ; linkml:prefix_reference ], - [ linkml:prefix_prefix "CPT" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "apollo" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "RTXKG1" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "isni" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "issn" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "WBVocab" ; - linkml:prefix_reference ], + [ linkml:prefix_prefix "oboformat" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "ResearchID" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "COG" ; + linkml:prefix_reference ], [ linkml:prefix_prefix "MAXO" ; linkml:prefix_reference ], + [ linkml:prefix_prefix "qud" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "RO" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "isbn" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "PDQ" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "foodb.compound" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "SNPEFF" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "SIO" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "GOP" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "PHAROS" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "hetio" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "EDAM-DATA" ; + linkml:prefix_reference ], [ linkml:prefix_prefix "EDAM-TOPIC" ; linkml:prefix_reference ], - [ linkml:prefix_prefix "ICD0" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "dcat" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "LOINC" ; - linkml:prefix_reference ], + [ linkml:prefix_prefix "MetaCyc" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "UBERGRAPH" ; + linkml:prefix_reference ], [ linkml:prefix_prefix "foaf" ; linkml:prefix_reference ], - [ linkml:prefix_prefix "REPODB" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "MSigDB" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "linkml" ; - linkml:prefix_reference linkml: ], - [ linkml:prefix_prefix "RXNORM" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "NDDF" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "MI" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "PDQ" ; - linkml:prefix_reference ], + [ linkml:prefix_prefix "isni" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "CPT" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "mirbase" ; + linkml:prefix_reference ], [ linkml:prefix_prefix "fabio" ; linkml:prefix_reference ], - [ linkml:prefix_prefix "ICD10" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "hetio" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "wgs" ; - linkml:prefix_reference ] ; + [ linkml:prefix_prefix "schema" ; + linkml:prefix_reference schema: ], + [ linkml:prefix_prefix "Aeolus" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "GTEx" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "KEGG.ENZYME" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "OBAN" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "pav" ; + linkml:prefix_reference pav: ], + [ linkml:prefix_prefix "RTXKG1" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "apollo" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "DrugCentral" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "HCPCS" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "gpi" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "ScopusID" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "EDAM-OPERATION" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "UMLSSG" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "PathWhiz" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "alliancegenome" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "KEGG.DGROUP" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "CAID" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "KEGG.RCLASS" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "ChemBank" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "FYPO" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "ExO" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "biolink" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "GTOPDB" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "NDDF" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "SEMMEDDB" ; + linkml:prefix_reference ] ; linkml:slots , , , @@ -872,6 +878,7 @@ , , , + , , , , @@ -896,6 +903,7 @@ , , , + , , , , @@ -1115,8 +1123,8 @@ , ; linkml:source_file "biolink-model.yaml" ; - linkml:source_file_date "Thu Sep 2 18:51:32 2021"^^xsd:dateTime ; - linkml:source_file_size 314029 ; + linkml:source_file_date "Tue Sep 21 22:41:10 2021"^^xsd:dateTime ; + linkml:source_file_size 314894 ; linkml:subsets , , , @@ -1947,14 +1955,14 @@ linkml:domain ; linkml:domain_of ; linkml:examples [ a linkml:Example ; - skos:definition "abnormal circulating bilirubin level" ; - skos:example "MP:0001569" ], - [ a linkml:Example ; skos:definition "Hyperkinesis" ; skos:example "HP:0002487" ], [ a linkml:Example ; skos:definition "axon morphology variant" ; - skos:example "WBPhenotype:0000180" ] ; + skos:example "WBPhenotype:0000180" ], + [ a linkml:Example ; + skos:definition "abnormal circulating bilirubin level" ; + skos:example "MP:0001569" ] ; linkml:is_a ; linkml:is_usage_slot true ; linkml:owner ; @@ -3685,6 +3693,8 @@ , , , + , + , , , , @@ -3810,6 +3820,8 @@ , , , + , + , , , , @@ -3879,6 +3891,8 @@ , , , + , + , , , , @@ -3898,6 +3912,8 @@ , , , + , + , , , , @@ -4147,6 +4163,8 @@ , , , + , + , , , , @@ -4203,6 +4221,8 @@ , , , + , + , , , , @@ -4407,6 +4427,8 @@ , , , + , + , , , , @@ -4457,6 +4479,8 @@ , , , + , + , , , , @@ -4530,6 +4554,8 @@ , , , + , + , , , , @@ -4594,6 +4620,8 @@ , , , + , + , , , , @@ -5120,6 +5148,8 @@ , , , + , + , , , , @@ -5266,6 +5296,8 @@ , , , + , + , , , , @@ -5312,6 +5344,8 @@ , , , + , + , , , , @@ -5355,6 +5389,8 @@ , , , + , + , , , , @@ -5681,15 +5717,6 @@ linkml:range ; linkml:slot_uri . - a linkml:TypeDefinition ; - skos:definition "A binary (true or false) value" ; - skos:inScheme linkml:types ; - linkml:base "Bool" ; - linkml:definition_uri linkml:Boolean ; - linkml:imported_from "linkml:types" ; - linkml:repr "bool" ; - linkml:uri xsd:boolean . - a linkml:TypeDefinition ; skos:definition "A primitive type in which the value denotes a class within the biolink model. The value must be a URI or a CURIE. In a Neo4j representation, the value should be the CURIE for the biolink class, for example biolink:Gene. For an RDF representation, the value should be a URI such as https://w3id.org/biolink/vocab/Gene" ; skos:inScheme ; @@ -5802,14 +5829,6 @@ linkml:slot_uri ; linkml:symmetric true . - a linkml:SlotDefinition ; - owl:inverseOf ; - skos:inScheme ; - linkml:definition_uri ; - linkml:domain ; - linkml:range ; - linkml:slot_uri . - a linkml:SlotDefinition ; skos:exactMatch pav:createdWith ; skos:inScheme ; @@ -5996,6 +6015,9 @@ skos:definition "holds between two genes whose phenotypic effects are dependent on each other in some way - such that their combined phenotypic effects are the result of some interaction between the activity of their gene products. Examples include epistasis and synthetic lethality." ; skos:exactMatch ; skos:inScheme ; + linkml:annotations [ a linkml:Annotation ; + skos:example "True" ; + linkml:tag ] ; linkml:definition_uri ; linkml:domain ; linkml:inherited true ; @@ -6153,8 +6175,8 @@ skos:exactMatch ; skos:inScheme ; skos:narrowMatch , - , - ; + , + ; linkml:definition_uri ; linkml:domain ; linkml:is_a ; @@ -6214,11 +6236,11 @@ skos:exactMatch , ; skos:inScheme ; - skos:narrowMatch , - , - , - , - ; + skos:narrowMatch , + , + , + , + ; linkml:definition_uri ; linkml:domain ; linkml:domain_of ; @@ -6918,6 +6940,8 @@ , , , + , + , , , , @@ -6939,6 +6963,8 @@ , , , + , + , , , , @@ -6979,6 +7005,8 @@ , , , + , + , , , , @@ -7244,6 +7272,15 @@ linkml:range ; linkml:slot_uri . + a linkml:TypeDefinition ; + skos:definition "A binary (true or false) value" ; + skos:inScheme linkml:types ; + linkml:base "Bool" ; + linkml:definition_uri linkml:Boolean ; + linkml:imported_from "linkml:types" ; + linkml:repr "bool" ; + linkml:uri xsd:boolean . + a linkml:SlotDefinition ; OIO:inSubset ; owl:inverseOf ; @@ -7454,6 +7491,19 @@ linkml:range ; linkml:slot_uri . + a linkml:SlotDefinition ; + owl:inverseOf ; + skos:inScheme ; + linkml:definition_uri ; + linkml:domain ; + linkml:inherited true ; + linkml:inlined true ; + linkml:is_a ; + linkml:multivalued true ; + linkml:owner ; + linkml:range ; + linkml:slot_uri . + a linkml:SlotDefinition ; owl:inverseOf ; skos:inScheme ; @@ -8082,11 +8132,11 @@ linkml:inherited true ; linkml:is_a ; linkml:local_names [ a linkml:LocalName ; - skos:altLabel "positively regulates" ; - linkml:local_name_source "translator" ], - [ a linkml:LocalName ; skos:altLabel "activity directly positively regulates activity of" ; - linkml:local_name_source "ro" ] ; + linkml:local_name_source "ro" ], + [ a linkml:LocalName ; + skos:altLabel "positively regulates" ; + linkml:local_name_source "translator" ] ; linkml:mixins ; linkml:multivalued true ; linkml:owner ; @@ -9076,20 +9126,6 @@ linkml:range ; linkml:slot_uri . - a linkml:SlotDefinition ; - OIO:inSubset ; - owl:inverseOf ; - skos:inScheme ; - linkml:definition_uri ; - linkml:domain ; - linkml:inherited true ; - linkml:inlined true ; - linkml:is_a ; - linkml:multivalued true ; - linkml:owner ; - linkml:range ; - linkml:slot_uri . - a linkml:SlotDefinition ; OIO:inSubset ; owl:inverseOf ; @@ -9364,13 +9400,13 @@ , , , - , - , - , , , , - ; + , + , + , + ; linkml:annotations [ a linkml:Annotation ; skos:example "True" ; linkml:tag ] ; @@ -9394,7 +9430,7 @@ , ; skos:inScheme ; - skos:narrowMatch ; + skos:narrowMatch ; linkml:definition_uri ; linkml:domain ; linkml:inherited true ; @@ -9425,7 +9461,7 @@ , ; skos:inScheme ; - skos:narrowMatch ; + skos:narrowMatch ; linkml:annotations [ a linkml:Annotation ; skos:example "True" ; linkml:tag ] ; @@ -9636,21 +9672,21 @@ OIO:inSubset ; owl:inverseOf ; skos:closeMatch , - , - ; + , + ; skos:definition "holds between a process and a material entity or site within which the process occurs" ; skos:exactMatch , - , - ; + , + ; skos:inScheme ; skos:narrowMatch , , , - , - , - , , , + , + , + , , , , @@ -9747,7 +9783,7 @@ ; skos:definition "holds between two processes, where one completes before the other begins" ; skos:exactMatch , - , + , , ; skos:inScheme ; @@ -9896,8 +9932,8 @@ ; skos:inScheme ; skos:narrowMatch , - , - ; + , + ; skos:relatedMatch ; linkml:annotations [ a linkml:Annotation ; skos:example "True" ; @@ -10103,7 +10139,7 @@ , , , - ; + ; linkml:definition_uri ; linkml:domain ; linkml:inherited true ; @@ -10990,6 +11026,8 @@ , , , + , + , , , , @@ -11259,11 +11297,11 @@ linkml:domain ; linkml:domain_of ; linkml:examples [ a linkml:Example ; - skos:definition "postsynaptic membrane" ; - skos:example "GO:0045211" ], - [ a linkml:Example ; skos:definition "kinase activity" ; - skos:example "GO:0016301" ] ; + skos:example "GO:0016301" ], + [ a linkml:Example ; + skos:definition "postsynaptic membrane" ; + skos:example "GO:0045211" ] ; linkml:inlined true ; linkml:is_a ; linkml:is_usage_slot true ; @@ -11382,7 +11420,7 @@ skos:editorialNote "check the range" ; skos:exactMatch , , - ; + ; skos:inScheme ; skos:narrowMatch , , @@ -11467,6 +11505,20 @@ linkml:range ; linkml:slot_uri . + a linkml:SlotDefinition ; + OIO:inSubset ; + owl:inverseOf ; + skos:inScheme ; + linkml:definition_uri ; + linkml:domain ; + linkml:inherited true ; + linkml:inlined true ; + linkml:is_a ; + linkml:multivalued true ; + linkml:owner ; + linkml:range ; + linkml:slot_uri . + a linkml:SlotDefinition ; skos:definition "issue of a newspaper, a scientific journal or magazine for reference purpose" ; skos:exactMatch ; @@ -11701,7 +11753,7 @@ a linkml:SlotDefinition ; skos:definition "holds between two entities with a temporal relationship" ; - skos:exactMatch ; + skos:exactMatch ; skos:inScheme ; skos:narrowMatch , , @@ -11781,7 +11833,7 @@ , , , - ; + ; skos:relatedMatch ; linkml:annotations [ a linkml:Annotation ; skos:example "True" ; @@ -12343,7 +12395,7 @@ ; skos:definition "holds between two entities where the occurrence, existence, or activity of one causes the occurrence or generation of the other" ; skos:exactMatch , - , + , , , ; @@ -12365,14 +12417,14 @@ , , , - , - , , , , , , - ; + , + , + ; linkml:annotations [ a linkml:Annotation ; skos:example "True" ; linkml:tag ] ; @@ -12408,7 +12460,7 @@ ; skos:inScheme ; skos:narrowMatch , - ; + ; linkml:annotations [ a linkml:Annotation ; skos:example "True" ; linkml:tag ] ; @@ -13101,10 +13153,10 @@ linkml:is_a ; linkml:local_names [ a linkml:LocalName ; skos:altLabel "population" ; - linkml:local_name_source "agr" ], + linkml:local_name_source "ga4gh" ], [ a linkml:LocalName ; skos:altLabel "population" ; - linkml:local_name_source "ga4gh" ] ; + linkml:local_name_source "agr" ] ; linkml:mixins ; linkml:slot_usage [ ] ; linkml:slots , @@ -13475,9 +13527,9 @@ , , , - , - , , + , + , rdfs:subPropertyOf ; linkml:annotations [ a linkml:Annotation ; skos:example "True" ; @@ -13701,6 +13753,7 @@ linkml:id_prefixes "APO", "EFO", "FBcv", + "FYPO", "HP", "MEDDRA", "MESH", @@ -13823,9 +13876,9 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t , , , - , - , , + , + , ; linkml:annotations [ a linkml:Annotation ; skos:example "True" ; @@ -13879,9 +13932,9 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t , , , - , , , + , ; linkml:annotations [ a linkml:Annotation ; skos:example "True" ; @@ -14209,19 +14262,19 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t , , , - , - , - , - , - , - , - , - , - , , , , , + , + , + , + , + , + , + , + , + , , , , @@ -14392,9 +14445,6 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t , , , - , - , - , , , , @@ -14402,7 +14452,10 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t , , , - ; + , + , + , + ; linkml:annotations [ a linkml:Annotation ; skos:example "True" ; linkml:tag ] ; @@ -14435,7 +14488,7 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t , , , - ; + ; linkml:definition_uri ; linkml:domain ; linkml:inherited true ; @@ -14549,6 +14602,8 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t , , , + , + , , , , @@ -15116,6 +15171,8 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t , , , + , + , , , , @@ -15378,15 +15435,15 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t , , , - , - , - , - , - , - , - , - , - ; + , + , + , + , + , + , + , + , + ; linkml:annotations [ a linkml:Annotation ; skos:example "True" ; linkml:tag ] ; @@ -15501,6 +15558,8 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t , , , + , + , , , , @@ -15818,9 +15877,9 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t skos:definition "connects an attribute to a value" ; skos:exactMatch ; skos:inScheme ; - skos:narrowMatch , - , - ; + skos:narrowMatch , + , + ; linkml:definition_uri ; linkml:domain ; linkml:domain_of ; @@ -16258,10 +16317,10 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t , , , - , , , , + , ; skos:relatedMatch ; linkml:annotations [ a linkml:Annotation ; @@ -16288,6 +16347,28 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t linkml:range ; linkml:slot_uri . + a linkml:SlotDefinition ; + skos:definition "" ; + skos:inScheme ; + linkml:definition_uri ; + linkml:domain ; + linkml:domain_of ; + linkml:is_a ; + linkml:owner ; + linkml:range ; + linkml:slot_uri . + + a linkml:SlotDefinition ; + skos:definition "The highest dose of a drug or treatment that does not cause unacceptable side effects. The maximum tolerated dose is determined in clinical trials by testing increasing doses on different groups of people until the highest dose with acceptable side effects is found. Also called MTD." ; + skos:inScheme ; + linkml:definition_uri ; + linkml:domain ; + linkml:domain_of ; + linkml:is_a ; + linkml:owner ; + linkml:range ; + linkml:slot_uri . + a linkml:SubsetDefinition ; skos:definition "Subset that is relevant for a typical Model Organism Database (MOD)" ; skos:inScheme ; @@ -16379,6 +16460,8 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t , , , + , + , , , , @@ -16432,6 +16515,8 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t , , , + , + , , , , @@ -16842,17 +16927,6 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t , , , - , - , - , - , - , - , - , - , - , - , - , , , , @@ -16866,6 +16940,17 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t , , , + , + , + , + , + , + , + , + , + , + , + , , , , @@ -16950,11 +17035,11 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t linkml:domain_of ; linkml:is_a ; linkml:local_names [ a linkml:LocalName ; - skos:altLabel "predicate" ; - linkml:local_name_source "translator" ], - [ a linkml:LocalName ; skos:altLabel "annotation predicate" ; - linkml:local_name_source "ga4gh" ] ; + linkml:local_name_source "ga4gh" ], + [ a linkml:LocalName ; + skos:altLabel "predicate" ; + linkml:local_name_source "translator" ] ; linkml:owner ; linkml:range ; linkml:required true ; @@ -17004,35 +17089,6 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t , , , - , - , - , - , - , - , - , - , - , - , - , - , - , - , - , - , - , - , - , - , - , - , - , - , - , - , - , - , - , , , , @@ -17040,6 +17096,35 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t , , , + , + , + , + , + , + , + , + , + , + , + , + , + , + , + , + , + , + , + , + , + , + , + , + , + , + , + , + , + , ; linkml:definition_uri ; linkml:domain ; @@ -17061,11 +17146,11 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t linkml:domain_of ; linkml:is_a ; linkml:local_names [ a linkml:LocalName ; - skos:altLabel "descriptor" ; - linkml:local_name_source "ga4gh" ], - [ a linkml:LocalName ; skos:altLabel "node with incoming relationship" ; - linkml:local_name_source "neo4j" ] ; + linkml:local_name_source "neo4j" ], + [ a linkml:LocalName ; + skos:altLabel "descriptor" ; + linkml:local_name_source "ga4gh" ] ; linkml:owner ; linkml:range ; linkml:required true ; @@ -17186,6 +17271,27 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t skos:inScheme ; linkml:definition_uri . + a linkml:ClassDefinition ; + skos:definition "a databased entity or concept/class" ; + skos:exactMatch , + , + , + ; + skos:inScheme ; + linkml:class_uri ; + linkml:definition_uri ; + linkml:is_a ; + linkml:slot_usage [ ] ; + linkml:slots , + , + , + , + , + , + , + , + . + a linkml:ClassDefinition ; OIO:inSubset ; skos:definition "A chemical entity is a physical entity that pertains to chemistry or biochemistry." ; @@ -17211,6 +17317,8 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t , , , + , + , , , , @@ -17218,26 +17326,5 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t , . - a linkml:ClassDefinition ; - skos:definition "a databased entity or concept/class" ; - skos:exactMatch , - , - , - ; - skos:inScheme ; - linkml:class_uri ; - linkml:definition_uri ; - linkml:is_a ; - linkml:slot_usage [ ] ; - linkml:slots , - , - , - , - , - , - , - , - . - diff --git a/biolink/model.py b/biolink/model.py index 0a29ed75c2..8e58db95fc 100644 --- a/biolink/model.py +++ b/biolink/model.py @@ -1,5 +1,5 @@ # Auto generated from biolink-model.yaml by pythongen.py version: 0.9.0 -# Generation date: 2021-09-02 18:54 +# Generation date: 2021-09-21 22:45 # Schema: Biolink-Model # # id: https://w3id.org/biolink/biolink-model @@ -84,6 +84,7 @@ FBCV = CurieNamespace('FBcv', 'http://purl.obolibrary.org/obo/FBcv_') FMA = CurieNamespace('FMA', 'http://purl.obolibrary.org/obo/FMA_') FOODON = CurieNamespace('FOODON', 'http://purl.obolibrary.org/obo/FOODON_') +FYPO = CurieNamespace('FYPO', 'http://purl.obolibrary.org/obo/FYPO_') GAMMA = CurieNamespace('GAMMA', 'http://translator.renci.org/GAMMA_') GENEPIO = CurieNamespace('GENEPIO', 'http://purl.obolibrary.org/obo/GENEPIO_') GENO = CurieNamespace('GENO', 'http://purl.obolibrary.org/obo/GENO_') @@ -195,8 +196,8 @@ SIO = CurieNamespace('SIO', 'http://semanticscience.org/resource/SIO_') SMART = CurieNamespace('SMART', 'http://identifiers.org/smart/') SMPDB = CurieNamespace('SMPDB', 'http://identifiers.org/smpdb/') -SNOMED = CurieNamespace('SNOMED', 'http://purl.obolibrary.org/obo/SNOMED_') -SNOMEDCT = CurieNamespace('SNOMEDCT', 'http://identifiers.org/snomedct/') +SNOMED = CurieNamespace('SNOMED', 'http://www.snomedbrowser.com/Codes/Details/') +SNOMEDCT = CurieNamespace('SNOMEDCT', 'http://www.snomedbrowser.com/Codes/Details/') SNPEFF = CurieNamespace('SNPEFF', 'http://translator.ncats.nih.gov/SNPEFF_') SO = CurieNamespace('SO', 'http://purl.obolibrary.org/obo/SO_') STATO = CurieNamespace('STATO', 'http://purl.obolibrary.org/obo/STATO_') @@ -2352,6 +2353,8 @@ class ChemicalEntity(NamedThing): category: Union[Union[str, NamedThingId], List[Union[str, NamedThingId]]] = None trade_name: Optional[Union[str, ChemicalEntityId]] = None available_from: Optional[Union[Union[str, "DrugAvailabilityEnum"], List[Union[str, "DrugAvailabilityEnum"]]]] = empty_list() + max_tolerated_dose: Optional[str] = None + is_toxic: Optional[Union[bool, Bool]] = None def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): if self._is_empty(self.id): @@ -2366,6 +2369,12 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.available_from = [self.available_from] if self.available_from is not None else [] self.available_from = [v if isinstance(v, DrugAvailabilityEnum) else DrugAvailabilityEnum(v) for v in self.available_from] + if self.max_tolerated_dose is not None and not isinstance(self.max_tolerated_dose, str): + self.max_tolerated_dose = str(self.max_tolerated_dose) + + if self.is_toxic is not None and not isinstance(self.is_toxic, Bool): + self.is_toxic = Bool(self.is_toxic) + super().__post_init__(**kwargs) @@ -8293,6 +8302,12 @@ class slots: slots.available_from = Slot(uri=BIOLINK.available_from, name="available from", curie=BIOLINK.curie('available_from'), model_uri=BIOLINK.available_from, domain=NamedThing, range=Optional[Union[Union[str, "DrugAvailabilityEnum"], List[Union[str, "DrugAvailabilityEnum"]]]]) +slots.is_toxic = Slot(uri=BIOLINK.is_toxic, name="is toxic", curie=BIOLINK.curie('is_toxic'), + model_uri=BIOLINK.is_toxic, domain=NamedThing, range=Optional[Union[bool, Bool]]) + +slots.max_tolerated_dose = Slot(uri=BIOLINK.max_tolerated_dose, name="max tolerated dose", curie=BIOLINK.curie('max_tolerated_dose'), + model_uri=BIOLINK.max_tolerated_dose, domain=NamedThing, range=Optional[str]) + slots.animal_model_available_from = Slot(uri=BIOLINK.animal_model_available_from, name="animal model available from", curie=BIOLINK.curie('animal_model_available_from'), model_uri=BIOLINK.animal_model_available_from, domain=NamedThing, range=Optional[Union[Union[str, DiseaseOrPhenotypicFeatureId], List[Union[str, DiseaseOrPhenotypicFeatureId]]]]) @@ -9035,7 +9050,7 @@ class slots: model_uri=BIOLINK.consumes, domain=None, range=Optional[Union[Union[str, BiologicalProcessOrActivityId], List[Union[str, BiologicalProcessOrActivityId]]]]) slots.consumed_by = Slot(uri=BIOLINK.consumed_by, name="consumed by", curie=BIOLINK.curie('consumed_by'), - model_uri=BIOLINK.consumed_by, domain=BiologicalProcessOrActivity, range=Optional[Union[dict, Occurrent]]) + model_uri=BIOLINK.consumed_by, domain=BiologicalProcessOrActivity, range=Optional[Union[Union[dict, Occurrent], List[Union[dict, Occurrent]]]]) slots.temporally_related_to = Slot(uri=BIOLINK.temporally_related_to, name="temporally related to", curie=BIOLINK.curie('temporally_related_to'), model_uri=BIOLINK.temporally_related_to, domain=None, range=Optional[Union[Union[dict, "Occurrent"], List[Union[dict, "Occurrent"]]]]) diff --git a/context.jsonld b/context.jsonld index 24b0889d86..2c96a33745 100644 --- a/context.jsonld +++ b/context.jsonld @@ -1,5 +1,5 @@ { - "_comments": "Auto generated from biolink-model.yaml by jsonldcontextgen.py version: 0.1.1\n Generation date: 2021-09-20 15:59\n Schema: Biolink-Model\n \n id: https://w3id.org/biolink/biolink-model\n description: Entity and association taxonomy and datamodel for life-sciences data\n license: https://creativecommons.org/publicdomain/zero/1.0/\n ", + "_comments": "Auto generated from biolink-model.yaml by jsonldcontextgen.py version: 0.1.1\n Generation date: 2021-09-21 22:44\n Schema: Biolink-Model\n \n id: https://w3id.org/biolink/biolink-model\n description: Entity and association taxonomy and datamodel for life-sciences data\n license: https://creativecommons.org/publicdomain/zero/1.0/\n ", "@context": { "APO": { "@id": "http://purl.obolibrary.org/obo/APO_", @@ -147,6 +147,10 @@ "@id": "http://purl.obolibrary.org/obo/FOODON_", "@prefix": true }, + "FYPO": { + "@id": "http://purl.obolibrary.org/obo/FYPO_", + "@prefix": true + }, "GAMMA": { "@id": "http://translator.renci.org/GAMMA_", "@prefix": true @@ -387,10 +391,7 @@ }, "SMART": "http://identifiers.org/smart/", "SMPDB": "http://identifiers.org/smpdb/", - "SNOMED": { - "@id": "http://purl.obolibrary.org/obo/SNOMED_", - "@prefix": true - }, + "SNOMED": "http://www.snomedbrowser.com/Codes/Details/", "SNOMEDCT": "http://www.snomedbrowser.com/Codes/Details/", "SNPEFF": { "@id": "http://translator.ncats.nih.gov/SNPEFF_", @@ -1287,6 +1288,9 @@ "is_synonymous_variant_of": { "@type": "@id" }, + "is_toxic": { + "@type": "xsd:boolean" + }, "knowledge_source": { "@type": "@id" }, diff --git a/contextn.jsonld b/contextn.jsonld index 65b3ca5dc5..3cb994ed8f 100644 --- a/contextn.jsonld +++ b/contextn.jsonld @@ -1,5 +1,5 @@ { - "_comments": "Auto generated from biolink-model.yaml by jsonldcontextgen.py version: 0.1.1\n Generation date: 2021-09-02 18:53\n Schema: Biolink-Model\n \n id: https://w3id.org/biolink/biolink-model\n description: Entity and association taxonomy and datamodel for life-sciences data\n license: https://creativecommons.org/publicdomain/zero/1.0/\n ", + "_comments": "Auto generated from biolink-model.yaml by jsonldcontextgen.py version: 0.1.1\n Generation date: 2021-09-21 22:44\n Schema: Biolink-Model\n \n id: https://w3id.org/biolink/biolink-model\n description: Entity and association taxonomy and datamodel for life-sciences data\n license: https://creativecommons.org/publicdomain/zero/1.0/\n ", "@context": { "APO": { "@id": "http://purl.obolibrary.org/obo/APO_", @@ -147,6 +147,10 @@ "@id": "http://purl.obolibrary.org/obo/FOODON_", "@prefix": true }, + "FYPO": { + "@id": "http://purl.obolibrary.org/obo/FYPO_", + "@prefix": true + }, "GAMMA": { "@id": "http://translator.renci.org/GAMMA_", "@prefix": true @@ -387,11 +391,8 @@ }, "SMART": "http://identifiers.org/smart/", "SMPDB": "http://identifiers.org/smpdb/", - "SNOMED": { - "@id": "http://purl.obolibrary.org/obo/SNOMED_", - "@prefix": true - }, - "SNOMEDCT": "http://identifiers.org/snomedct/", + "SNOMED": "http://www.snomedbrowser.com/Codes/Details/", + "SNOMEDCT": "http://www.snomedbrowser.com/Codes/Details/", "SNPEFF": { "@id": "http://translator.ncats.nih.gov/SNPEFF_", "@prefix": true @@ -1273,6 +1274,9 @@ "is_synonymous_variant_of": { "@type": "@id" }, + "is_toxic": { + "@type": "xsd:boolean" + }, "knowledge_source": { "@type": "@id" }, diff --git a/golr-views/RNA_product_config.yaml b/golr-views/RNA_product_config.yaml index ccc403f554..d0c49b7391 100644 --- a/golr-views/RNA_product_config.yaml +++ b/golr-views/RNA_product_config.yaml @@ -44,6 +44,15 @@ fields: description: '' display_name: available from cardinality: multi +- id: max_tolerated_dose + description: The highest dose of a drug or treatment that does not cause unacceptable + side effects. The maximum tolerated dose is determined in clinical trials by testing + increasing doses on different groups of people until the highest dose with acceptable + side effects is found. Also called MTD. + display_name: max tolerated dose +- id: is_toxic + description: '' + display_name: is toxic - id: is_metabolite description: indicates whether a molecular entity is a metabolite display_name: is metabolite diff --git a/golr-views/RNA_product_isoform_config.yaml b/golr-views/RNA_product_isoform_config.yaml index 961d44af2e..e567feb54b 100644 --- a/golr-views/RNA_product_isoform_config.yaml +++ b/golr-views/RNA_product_isoform_config.yaml @@ -46,6 +46,15 @@ fields: description: '' display_name: available from cardinality: multi +- id: max_tolerated_dose + description: The highest dose of a drug or treatment that does not cause unacceptable + side effects. The maximum tolerated dose is determined in clinical trials by testing + increasing doses on different groups of people until the highest dose with acceptable + side effects is found. Also called MTD. + display_name: max tolerated dose +- id: is_toxic + description: '' + display_name: is toxic - id: is_metabolite description: indicates whether a molecular entity is a metabolite display_name: is metabolite diff --git a/golr-views/chemical_entity_config.yaml b/golr-views/chemical_entity_config.yaml index 91be89e968..03d1bb0947 100644 --- a/golr-views/chemical_entity_config.yaml +++ b/golr-views/chemical_entity_config.yaml @@ -46,3 +46,12 @@ fields: description: '' display_name: available from cardinality: multi +- id: max_tolerated_dose + description: The highest dose of a drug or treatment that does not cause unacceptable + side effects. The maximum tolerated dose is determined in clinical trials by testing + increasing doses on different groups of people until the highest dose with acceptable + side effects is found. Also called MTD. + display_name: max tolerated dose +- id: is_toxic + description: '' + display_name: is toxic diff --git a/golr-views/chemical_mixture_config.yaml b/golr-views/chemical_mixture_config.yaml index 39fd93c7c0..d49c511d30 100644 --- a/golr-views/chemical_mixture_config.yaml +++ b/golr-views/chemical_mixture_config.yaml @@ -46,6 +46,15 @@ fields: description: '' display_name: available from cardinality: multi +- id: max_tolerated_dose + description: The highest dose of a drug or treatment that does not cause unacceptable + side effects. The maximum tolerated dose is determined in clinical trials by testing + increasing doses on different groups of people until the highest dose with acceptable + side effects is found. Also called MTD. + display_name: max tolerated dose +- id: is_toxic + description: '' + display_name: is toxic - id: is_supplement description: '' display_name: is supplement diff --git a/golr-views/coding_sequence_config.yaml b/golr-views/coding_sequence_config.yaml index 4423d58f85..54193710e9 100644 --- a/golr-views/coding_sequence_config.yaml +++ b/golr-views/coding_sequence_config.yaml @@ -44,6 +44,15 @@ fields: description: '' display_name: available from cardinality: multi +- id: max_tolerated_dose + description: The highest dose of a drug or treatment that does not cause unacceptable + side effects. The maximum tolerated dose is determined in clinical trials by testing + increasing doses on different groups of people until the highest dose with acceptable + side effects is found. Also called MTD. + display_name: max tolerated dose +- id: is_toxic + description: '' + display_name: is toxic - id: is_metabolite description: indicates whether a molecular entity is a metabolite display_name: is metabolite diff --git a/golr-views/complex_molecular_mixture_config.yaml b/golr-views/complex_molecular_mixture_config.yaml index d43298f76e..8b5ebf712b 100644 --- a/golr-views/complex_molecular_mixture_config.yaml +++ b/golr-views/complex_molecular_mixture_config.yaml @@ -46,6 +46,15 @@ fields: description: '' display_name: available from cardinality: multi +- id: max_tolerated_dose + description: The highest dose of a drug or treatment that does not cause unacceptable + side effects. The maximum tolerated dose is determined in clinical trials by testing + increasing doses on different groups of people until the highest dose with acceptable + side effects is found. Also called MTD. + display_name: max tolerated dose +- id: is_toxic + description: '' + display_name: is toxic - id: is_supplement description: '' display_name: is supplement diff --git a/golr-views/drug_config.yaml b/golr-views/drug_config.yaml index 49b1409137..e63c977e6d 100644 --- a/golr-views/drug_config.yaml +++ b/golr-views/drug_config.yaml @@ -46,6 +46,15 @@ fields: description: '' display_name: available from cardinality: multi +- id: max_tolerated_dose + description: The highest dose of a drug or treatment that does not cause unacceptable + side effects. The maximum tolerated dose is determined in clinical trials by testing + increasing doses on different groups of people until the highest dose with acceptable + side effects is found. Also called MTD. + display_name: max tolerated dose +- id: is_toxic + description: '' + display_name: is toxic - id: is_supplement description: '' display_name: is supplement diff --git a/golr-views/environmental_food_contaminant_config.yaml b/golr-views/environmental_food_contaminant_config.yaml index 7a69238fd7..fafe61eebf 100644 --- a/golr-views/environmental_food_contaminant_config.yaml +++ b/golr-views/environmental_food_contaminant_config.yaml @@ -44,3 +44,12 @@ fields: description: '' display_name: available from cardinality: multi +- id: max_tolerated_dose + description: The highest dose of a drug or treatment that does not cause unacceptable + side effects. The maximum tolerated dose is determined in clinical trials by testing + increasing doses on different groups of people until the highest dose with acceptable + side effects is found. Also called MTD. + display_name: max tolerated dose +- id: is_toxic + description: '' + display_name: is toxic diff --git a/golr-views/exon_config.yaml b/golr-views/exon_config.yaml index 8d750b6dbf..57868eac46 100644 --- a/golr-views/exon_config.yaml +++ b/golr-views/exon_config.yaml @@ -46,6 +46,15 @@ fields: description: '' display_name: available from cardinality: multi +- id: max_tolerated_dose + description: The highest dose of a drug or treatment that does not cause unacceptable + side effects. The maximum tolerated dose is determined in clinical trials by testing + increasing doses on different groups of people until the highest dose with acceptable + side effects is found. Also called MTD. + display_name: max tolerated dose +- id: is_toxic + description: '' + display_name: is toxic - id: is_metabolite description: indicates whether a molecular entity is a metabolite display_name: is metabolite diff --git a/golr-views/food_additive_config.yaml b/golr-views/food_additive_config.yaml index 395b72024a..67bfee27eb 100644 --- a/golr-views/food_additive_config.yaml +++ b/golr-views/food_additive_config.yaml @@ -44,3 +44,12 @@ fields: description: '' display_name: available from cardinality: multi +- id: max_tolerated_dose + description: The highest dose of a drug or treatment that does not cause unacceptable + side effects. The maximum tolerated dose is determined in clinical trials by testing + increasing doses on different groups of people until the highest dose with acceptable + side effects is found. Also called MTD. + display_name: max tolerated dose +- id: is_toxic + description: '' + display_name: is toxic diff --git a/golr-views/food_config.yaml b/golr-views/food_config.yaml index 5a517b78e5..20bf235fbf 100644 --- a/golr-views/food_config.yaml +++ b/golr-views/food_config.yaml @@ -45,6 +45,15 @@ fields: description: '' display_name: available from cardinality: multi +- id: max_tolerated_dose + description: The highest dose of a drug or treatment that does not cause unacceptable + side effects. The maximum tolerated dose is determined in clinical trials by testing + increasing doses on different groups of people until the highest dose with acceptable + side effects is found. Also called MTD. + display_name: max tolerated dose +- id: is_toxic + description: '' + display_name: is toxic - id: is_supplement description: '' display_name: is supplement diff --git a/golr-views/macronutrient_config.yaml b/golr-views/macronutrient_config.yaml index 18b513aa79..a52f652ec9 100644 --- a/golr-views/macronutrient_config.yaml +++ b/golr-views/macronutrient_config.yaml @@ -44,3 +44,12 @@ fields: description: '' display_name: available from cardinality: multi +- id: max_tolerated_dose + description: The highest dose of a drug or treatment that does not cause unacceptable + side effects. The maximum tolerated dose is determined in clinical trials by testing + increasing doses on different groups of people until the highest dose with acceptable + side effects is found. Also called MTD. + display_name: max tolerated dose +- id: is_toxic + description: '' + display_name: is toxic diff --git a/golr-views/microRNA_config.yaml b/golr-views/microRNA_config.yaml index f4026b7eef..90654f1a72 100644 --- a/golr-views/microRNA_config.yaml +++ b/golr-views/microRNA_config.yaml @@ -44,6 +44,15 @@ fields: description: '' display_name: available from cardinality: multi +- id: max_tolerated_dose + description: The highest dose of a drug or treatment that does not cause unacceptable + side effects. The maximum tolerated dose is determined in clinical trials by testing + increasing doses on different groups of people until the highest dose with acceptable + side effects is found. Also called MTD. + display_name: max tolerated dose +- id: is_toxic + description: '' + display_name: is toxic - id: is_metabolite description: indicates whether a molecular entity is a metabolite display_name: is metabolite diff --git a/golr-views/micronutrient_config.yaml b/golr-views/micronutrient_config.yaml index 77e3696107..1b07927ffd 100644 --- a/golr-views/micronutrient_config.yaml +++ b/golr-views/micronutrient_config.yaml @@ -44,3 +44,12 @@ fields: description: '' display_name: available from cardinality: multi +- id: max_tolerated_dose + description: The highest dose of a drug or treatment that does not cause unacceptable + side effects. The maximum tolerated dose is determined in clinical trials by testing + increasing doses on different groups of people until the highest dose with acceptable + side effects is found. Also called MTD. + display_name: max tolerated dose +- id: is_toxic + description: '' + display_name: is toxic diff --git a/golr-views/molecular_entity_config.yaml b/golr-views/molecular_entity_config.yaml index 3cf1f12b4c..afc2d3c25b 100644 --- a/golr-views/molecular_entity_config.yaml +++ b/golr-views/molecular_entity_config.yaml @@ -46,6 +46,15 @@ fields: description: '' display_name: available from cardinality: multi +- id: max_tolerated_dose + description: The highest dose of a drug or treatment that does not cause unacceptable + side effects. The maximum tolerated dose is determined in clinical trials by testing + increasing doses on different groups of people until the highest dose with acceptable + side effects is found. Also called MTD. + display_name: max tolerated dose +- id: is_toxic + description: '' + display_name: is toxic - id: is_metabolite description: indicates whether a molecular entity is a metabolite display_name: is metabolite diff --git a/golr-views/molecular_mixture_config.yaml b/golr-views/molecular_mixture_config.yaml index 3271990436..0ba88dcb1c 100644 --- a/golr-views/molecular_mixture_config.yaml +++ b/golr-views/molecular_mixture_config.yaml @@ -46,6 +46,15 @@ fields: description: '' display_name: available from cardinality: multi +- id: max_tolerated_dose + description: The highest dose of a drug or treatment that does not cause unacceptable + side effects. The maximum tolerated dose is determined in clinical trials by testing + increasing doses on different groups of people until the highest dose with acceptable + side effects is found. Also called MTD. + display_name: max tolerated dose +- id: is_toxic + description: '' + display_name: is toxic - id: is_supplement description: '' display_name: is supplement diff --git a/golr-views/noncoding_RNA_product_config.yaml b/golr-views/noncoding_RNA_product_config.yaml index 9e80f09ae8..7d0b752ba0 100644 --- a/golr-views/noncoding_RNA_product_config.yaml +++ b/golr-views/noncoding_RNA_product_config.yaml @@ -44,6 +44,15 @@ fields: description: '' display_name: available from cardinality: multi +- id: max_tolerated_dose + description: The highest dose of a drug or treatment that does not cause unacceptable + side effects. The maximum tolerated dose is determined in clinical trials by testing + increasing doses on different groups of people until the highest dose with acceptable + side effects is found. Also called MTD. + display_name: max tolerated dose +- id: is_toxic + description: '' + display_name: is toxic - id: is_metabolite description: indicates whether a molecular entity is a metabolite display_name: is metabolite diff --git a/golr-views/nucleic_acid_entity_config.yaml b/golr-views/nucleic_acid_entity_config.yaml index b5953d6e11..03d85d33fb 100644 --- a/golr-views/nucleic_acid_entity_config.yaml +++ b/golr-views/nucleic_acid_entity_config.yaml @@ -47,6 +47,15 @@ fields: description: '' display_name: available from cardinality: multi +- id: max_tolerated_dose + description: The highest dose of a drug or treatment that does not cause unacceptable + side effects. The maximum tolerated dose is determined in clinical trials by testing + increasing doses on different groups of people until the highest dose with acceptable + side effects is found. Also called MTD. + display_name: max tolerated dose +- id: is_toxic + description: '' + display_name: is toxic - id: is_metabolite description: indicates whether a molecular entity is a metabolite display_name: is metabolite diff --git a/golr-views/nutrient_config.yaml b/golr-views/nutrient_config.yaml index cc0f6d4afb..e27c7d255d 100644 --- a/golr-views/nutrient_config.yaml +++ b/golr-views/nutrient_config.yaml @@ -44,3 +44,12 @@ fields: description: '' display_name: available from cardinality: multi +- id: max_tolerated_dose + description: The highest dose of a drug or treatment that does not cause unacceptable + side effects. The maximum tolerated dose is determined in clinical trials by testing + increasing doses on different groups of people until the highest dose with acceptable + side effects is found. Also called MTD. + display_name: max tolerated dose +- id: is_toxic + description: '' + display_name: is toxic diff --git a/golr-views/processed_material_config.yaml b/golr-views/processed_material_config.yaml index 8cbcb22cfe..dbdef374d3 100644 --- a/golr-views/processed_material_config.yaml +++ b/golr-views/processed_material_config.yaml @@ -47,6 +47,15 @@ fields: description: '' display_name: available from cardinality: multi +- id: max_tolerated_dose + description: The highest dose of a drug or treatment that does not cause unacceptable + side effects. The maximum tolerated dose is determined in clinical trials by testing + increasing doses on different groups of people until the highest dose with acceptable + side effects is found. Also called MTD. + display_name: max tolerated dose +- id: is_toxic + description: '' + display_name: is toxic - id: is_supplement description: '' display_name: is supplement diff --git a/golr-views/siRNA_config.yaml b/golr-views/siRNA_config.yaml index 8d1888af71..777f4746c2 100644 --- a/golr-views/siRNA_config.yaml +++ b/golr-views/siRNA_config.yaml @@ -48,6 +48,15 @@ fields: description: '' display_name: available from cardinality: multi +- id: max_tolerated_dose + description: The highest dose of a drug or treatment that does not cause unacceptable + side effects. The maximum tolerated dose is determined in clinical trials by testing + increasing doses on different groups of people until the highest dose with acceptable + side effects is found. Also called MTD. + display_name: max tolerated dose +- id: is_toxic + description: '' + display_name: is toxic - id: is_metabolite description: indicates whether a molecular entity is a metabolite display_name: is metabolite diff --git a/golr-views/small_molecule_config.yaml b/golr-views/small_molecule_config.yaml index f1d2582d1d..1c78a0def5 100644 --- a/golr-views/small_molecule_config.yaml +++ b/golr-views/small_molecule_config.yaml @@ -45,6 +45,15 @@ fields: description: '' display_name: available from cardinality: multi +- id: max_tolerated_dose + description: The highest dose of a drug or treatment that does not cause unacceptable + side effects. The maximum tolerated dose is determined in clinical trials by testing + increasing doses on different groups of people until the highest dose with acceptable + side effects is found. Also called MTD. + display_name: max tolerated dose +- id: is_toxic + description: '' + display_name: is toxic - id: is_metabolite description: indicates whether a molecular entity is a metabolite display_name: is metabolite diff --git a/golr-views/transcript_config.yaml b/golr-views/transcript_config.yaml index ecdbe42fc6..6a44e09fe1 100644 --- a/golr-views/transcript_config.yaml +++ b/golr-views/transcript_config.yaml @@ -45,6 +45,15 @@ fields: description: '' display_name: available from cardinality: multi +- id: max_tolerated_dose + description: The highest dose of a drug or treatment that does not cause unacceptable + side effects. The maximum tolerated dose is determined in clinical trials by testing + increasing doses on different groups of people until the highest dose with acceptable + side effects is found. Also called MTD. + display_name: max tolerated dose +- id: is_toxic + description: '' + display_name: is toxic - id: is_metabolite description: indicates whether a molecular entity is a metabolite display_name: is metabolite diff --git a/golr-views/vitamin_config.yaml b/golr-views/vitamin_config.yaml index 12147ed899..188555e3c6 100644 --- a/golr-views/vitamin_config.yaml +++ b/golr-views/vitamin_config.yaml @@ -44,3 +44,12 @@ fields: description: '' display_name: available from cardinality: multi +- id: max_tolerated_dose + description: The highest dose of a drug or treatment that does not cause unacceptable + side effects. The maximum tolerated dose is determined in clinical trials by testing + increasing doses on different groups of people until the highest dose with acceptable + side effects is found. Also called MTD. + display_name: max tolerated dose +- id: is_toxic + description: '' + display_name: is toxic diff --git a/graphviz/RNA_product.gv b/graphviz/RNA_product.gv index 1208e91932..7213be4c61 100644 --- a/graphviz/RNA_product.gv +++ b/graphviz/RNA_product.gv @@ -1,23 +1,23 @@ digraph { - graph [bb="0,0,2587.4,123"]; + graph [bb="0,0,2794.4,123"]; node [label="\N"]; "RNA product" [height=0.5, label="RNA product", - pos="1170.2,105", + pos="1285.2,105", width=1.9679]; transcript [height=0.5, pos="57.195,18", width=1.5887]; "RNA product" -> transcript [label=is_a, - lp="367.19,61.5", - pos="e,98.933,30.487 1099.5,103.34 957.75,101.5 628.5,94.583 353.19,69 250.37,59.445 224.46,56.243 123.19,36 118.51,35.064 113.66,34 \ -108.82,32.872"]; + lp="368.19,61.5", + pos="e,98.933,30.491 1214.4,103.85 1058.6,102.98 674.37,97.809 354.19,69 250.9,59.706 224.9,56.298 123.19,36 118.51,35.065 113.66,34.002 \ +108.82,32.875"]; "gene product mixin" [height=0.5, pos="233.19,18", width=2.7984]; "RNA product" -> "gene product mixin" [label=uses, - lp="486.69,61.5", - pos="e,288.32,33.214 1099.3,104.14 972.56,103.58 698.86,98.649 470.19,69 411.41,61.377 345.5,46.988 298.13,35.596"]; + lp="487.69,61.5", + pos="e,288.07,33.205 1214.1,104.85 1072.2,105.69 744.17,103.31 471.19,69 411.94,61.553 345.51,47.073 297.93,35.603"]; id [color=blue, height=0.5, label=string, @@ -25,9 +25,9 @@ digraph { width=1.0652]; "RNA product" -> id [color=blue, label=id, - lp="600.19,61.5", - pos="e,419.19,29.954 1099.7,103.11 990.64,100.96 774.68,93.683 593.19,69 523.4,59.508 505.98,55.131 438.19,36 435.09,35.124 431.89,34.151 \ -428.7,33.129", + lp="602.19,61.5", + pos="e,419.19,29.966 1214.3,104.05 1089,103.33 820.01,98.147 595.19,69 524.48,59.833 506.84,55.278 438.19,36 435.09,35.128 431.89,34.158 \ +428.69,33.138", style=solid]; iri [color=blue, height=0.5, @@ -36,9 +36,8 @@ digraph { width=1.2277]; "RNA product" -> iri [color=blue, label=iri, - lp="694.19,61.5", - pos="e,524.49,29.913 1100.1,102.39 1005.6,99.441 832.37,91.248 686.19,69 622.57,59.316 607.27,53.009 545.19,36 541.62,35.02 537.93,33.96 \ -534.23,32.865", + lp="690.19,61.5", + pos="e,524.21,29.992 1214.2,103.97 1101.1,103 873.06,97.295 682.19,69 630.37,61.317 572.35,44.986 534,33.071", style=solid]; type [color=blue, height=0.5, @@ -47,9 +46,9 @@ digraph { width=1.0652]; "RNA product" -> type [color=blue, label=type, - lp="799.19,61.5", - pos="e,620.84,29.989 1101.3,100.59 1023.7,96.085 893.79,86.591 783.19,69 718.35,58.686 702.18,54.534 639.19,36 636.29,35.146 633.31,34.209 \ -630.32,33.227", + lp="796.19,61.5", + pos="e,620.85,29.968 1214.5,102.68 1116.5,100.04 934.01,92.177 780.19,69 716.55,59.411 700.9,54.31 639.19,36 636.29,35.139 633.31,34.197 \ +630.32,33.212", style=solid]; name [color=blue, height=0.5, @@ -58,8 +57,8 @@ digraph { width=1.5707]; "RNA product" -> name [color=blue, label=name, - lp="895.19,61.5", - pos="e,741.89,31.738 1102.9,99.253 1042.8,94.246 952.5,84.837 875.19,69 832.68,60.29 785.4,45.995 751.51,34.917", + lp="898.19,61.5", + pos="e,741.81,31.852 1215.1,102.13 1133.6,99.001 995.17,90.716 878.19,69 834.55,60.897 786.1,46.402 751.6,35.098", style=solid]; description [color=blue, height=0.5, @@ -68,8 +67,8 @@ digraph { width=2.0943]; "RNA product" -> description [color=blue, label=description, - lp="996.69,61.5", - pos="e,881.71,34.858 1103.9,98.299 1061,93.364 1004.4,84.49 956.19,69 933.46,61.696 909.45,49.994 890.55,39.747", + lp="1001.7,61.5", + pos="e,882.55,35.021 1214.7,103.1 1148.2,100.69 1046.3,92.935 961.19,69 937.01,62.199 911.51,50.33 891.57,39.863", style=solid]; source [color=blue, height=0.5, @@ -78,8 +77,8 @@ digraph { width=1.5707]; "RNA product" -> source [color=blue, label=source, - lp="1085.2,61.5", - pos="e,1020,35.382 1119.2,92.414 1100.3,86.894 1079,79.217 1061.2,69 1048.9,61.951 1036.9,51.852 1027.2,42.574", + lp="1095.2,61.5", + pos="e,1021.9,35.367 1215.8,101.15 1172.8,97.349 1117,88.665 1071.2,69 1056.1,62.508 1041.3,51.813 1029.5,41.977", style=solid]; "provided by" [color=blue, height=0.5, @@ -88,8 +87,8 @@ digraph { width=1.0291]; "RNA product" -> "provided by" [color=blue, label="provided by", - lp="1159.7,61.5", - pos="e,1113.3,36.192 1136.8,89.062 1129,83.885 1121.6,77.254 1117.2,69 1113.5,62.168 1112.4,54.012 1112.5,46.289", + lp="1174.7,61.5", + pos="e,1118.1,36.109 1223.2,96.228 1186.8,90.478 1145.5,81.473 1132.2,69 1125.8,63.014 1122.1,54.417 1120,46.035", style=solid]; "has attribute" [color=blue, height=0.5, @@ -98,16 +97,16 @@ digraph { width=1.4443]; "RNA product" -> "has attribute" [color=blue, label="has attribute", - lp="1258.2,61.5", - pos="e,1218.3,35.908 1187.3,87.481 1192.5,81.925 1198,75.484 1202.2,69 1206.9,61.737 1211.1,53.287 1214.5,45.422", + lp="1272.2,61.5", + pos="e,1220.5,36.342 1247.3,89.659 1238.6,84.504 1230.3,77.733 1225.2,69 1221.3,62.31 1220,54.197 1219.9,46.47", style=solid]; category [height=0.5, pos="1345.2,18", width=1.4263]; "RNA product" -> category [color=blue, label=category, - lp="1356.7,61.5", - pos="e,1337.1,35.789 1222.1,92.74 1258.4,84.552 1301.8,74.052 1309.2,69 1318.4,62.779 1326,53.415 1331.8,44.467", + lp="1363.7,61.5", + pos="e,1339.7,36.124 1306.1,87.577 1312.1,82.122 1318.4,75.713 1323.2,69 1328.3,61.869 1332.6,53.37 1336,45.42", style=solid]; "trade name" [color=blue, height=0.5, @@ -116,9 +115,8 @@ digraph { width=2.2748]; "RNA product" -> "trade name" [color=blue, label="trade name", - lp="1472.2,61.5", - pos="e,1468.9,35.129 1221.1,92.375 1230.4,90.436 1240.1,88.554 1249.2,87 1312.3,76.252 1330.8,87.113 1392.2,69 1415.8,62.056 1440.6,50.297 \ -1460.1,39.927", + lp="1473.2,61.5", + pos="e,1468.4,35.019 1332.4,91.541 1353.2,85.542 1377.7,77.749 1399.2,69 1419.7,60.66 1441.6,49.537 1459.5,39.9", style=solid]; "available from" [color=blue, height=0.5, @@ -127,68 +125,90 @@ digraph { width=3.2858]; "RNA product" -> "available from" [color=blue, label="available from", - lp="1640.7,61.5", - pos="e,1664.1,34.395 1220.1,92.108 1229.7,90.148 1239.7,88.327 1249.2,87 1367.4,70.399 1399.3,87.761 1517.2,69 1563.7,61.593 1615.3,48.305 \ -1654.1,37.288", + lp="1635.7,61.5", + pos="e,1662.2,34.282 1336.1,92.308 1345.4,90.376 1355.1,88.513 1364.2,87 1432.2,75.739 1450.4,81.545 1518.2,69 1563.5,60.608 1613.9,47.676 \ +1652.2,37.066", + style=solid]; + "max tolerated dose" [color=blue, + height=0.5, + label=string, + pos="1889.2,18", + width=1.0652]; + "RNA product" -> "max tolerated dose" [color=blue, + label="max tolerated dose", + lp="1844.2,61.5", + pos="e,1860.2,29.922 1334.7,92.101 1344.4,90.117 1354.6,88.288 1364.2,87 1508.5,67.63 1547,88.701 1691.2,69 1758.8,59.761 1775.6,54.764 \ +1841.2,36 1844.3,35.113 1847.5,34.133 1850.7,33.106", + style=solid]; + "is toxic" [color=blue, + height=0.5, + label=boolean, + pos="1992.2,18", + width=1.2999]; + "RNA product" -> "is toxic" [color=blue, + label="is toxic", + lp="1974.2,61.5", + pos="e,1974.6,34.897 1334.3,92.015 1344.1,90.011 1354.4,88.198 1364.2,87 1425.2,79.503 1858.7,87.77 1917.2,69 1935.2,63.223 1952.9,51.75 \ +1966.6,41.25", style=solid]; "is metabolite" [color=blue, height=0.5, label=boolean, - pos="1897.2,18", + pos="2104.2,18", width=1.2999]; "RNA product" -> "is metabolite" [color=blue, label="is metabolite", - lp="1822.2,61.5", - pos="e,1862.4,30.171 1219.7,91.988 1229.4,90.014 1239.6,88.217 1249.2,87 1446.4,61.994 1499.1,95.171 1696.2,69 1750.9,61.735 1812.3,45.207 \ -1852.6,33.136", + lp="2092.2,61.5", + pos="e,2081.5,33.973 1334.3,91.98 1344.1,89.98 1354.4,88.176 1364.2,87 1505.4,69.962 1866.2,103.63 2004.2,69 2028.5,62.91 2053.6,50.275 \ +2072.7,39.231", style=solid]; "in taxon" [color=blue, height=0.5, label="organism taxon", - pos="2045.2,18", + pos="2252.2,18", width=2.3109]; "RNA product" -> "in taxon" [color=blue, label="in taxon", - lp="1970.2,61.5", - pos="e,2004.8,33.894 1219.3,91.986 1229.1,89.985 1239.4,88.18 1249.2,87 1524.6,53.676 1599.1,112.07 1873.2,69 1915.1,62.409 1961.3,48.628 \ -1995.2,37.2", + lp="2216.2,61.5", + pos="e,2225.1,35.224 1334.3,91.942 1344.1,89.944 1354.4,88.152 1364.2,87 1536.2,66.696 1974.5,107.9 2143.2,69 2168.7,63.119 2195.5,50.952 \ +2216.1,40.093", style=solid]; "has biological sequence" [color=blue, height=0.5, label="biological sequence", - pos="2248.2,18", + pos="2455.2,18", width=2.8164]; "RNA product" -> "has biological sequence" [color=blue, label="has biological sequence", - lp="2176.7,61.5", - pos="e,2193.2,33.145 1219.3,91.948 1229.1,89.95 1239.4,88.155 1249.2,87 1582.1,47.566 1670.1,106.66 2003.2,69 2064.9,62.018 2134.2,47.213 \ -2183.3,35.515", + lp="2414.7,61.5", + pos="e,2406.6,33.959 1334.3,91.92 1344.1,89.925 1354.4,88.138 1364.2,87 1755,41.409 1859.1,119.7 2249.2,69 2299.8,62.428 2356,48.32 2396.9,\ +36.761", style=solid]; synonym [color=blue, height=0.5, label="label type", - pos="2424.2,18", + pos="2631.2,18", width=1.5707]; "RNA product" -> synonym [color=blue, label=synonym, - lp="2360.2,61.5", - pos="e,2390.8,32.611 1219.3,91.9 1229.1,89.906 1239.4,88.125 1249.2,87 1473.5,61.125 2042.3,105.24 2265.2,69 2305.6,62.434 2349.8,47.871 \ -2381.4,36.147", + lp="2586.2,61.5", + pos="e,2602.6,33.588 1334.3,91.885 1344.1,89.893 1354.4,88.116 1364.2,87 1489.9,72.617 2379,93.414 2503.2,69 2534.7,62.798 2568.6,49.267 \ +2593.5,37.843", style=solid]; xref [color=blue, height=0.5, label="iri type", - pos="2543.2,18", + pos="2750.2,18", width=1.2277]; "RNA product" -> xref [color=blue, label=xref, - lp="2468.7,61.5", - pos="e,2514.3,31.825 1219.3,91.884 1229.1,89.892 1239.4,88.115 1249.2,87 1502.5,58.046 2145,112.57 2396.2,69 2434.3,62.397 2475.8,47.519 \ -2504.9,35.7", + lp="2686.7,61.5", + pos="e,2723.6,32.654 1334.3,91.874 1344.1,89.882 1354.4,88.109 1364.2,87 1503.1,71.219 2485,95.861 2622.2,69 2654.6,62.659 2689.3,48.572 \ +2714.5,36.961", style=solid]; "named thing_category" [color=blue, height=0.5, label="named thing", - pos="1328.2,105", + pos="1443.2,105", width=1.9318]; } diff --git a/graphviz/RNA_product.svg b/graphviz/RNA_product.svg index 67edddfeae..6419d663af 100644 --- a/graphviz/RNA_product.svg +++ b/graphviz/RNA_product.svg @@ -4,16 +4,16 @@ - + %3 - + RNA product - -RNA product + +RNA product @@ -24,9 +24,9 @@ RNA product->transcript - - -is_a + + +is_a @@ -37,9 +37,9 @@ RNA product->gene product mixin - - -uses + + +uses @@ -50,9 +50,9 @@ RNA product->id - - -id + + +id @@ -63,9 +63,9 @@ RNA product->iri - - -iri + + +iri @@ -76,9 +76,9 @@ RNA product->type - - -type + + +type @@ -89,9 +89,9 @@ RNA product->name - - -name + + +name @@ -102,9 +102,9 @@ RNA product->description - - -description + + +description @@ -115,9 +115,9 @@ RNA product->source - - -source + + +source @@ -128,9 +128,9 @@ RNA product->provided by - - -provided by + + +provided by @@ -141,9 +141,9 @@ RNA product->has attribute - - -has attribute + + +has attribute @@ -154,9 +154,9 @@ RNA product->category - - -category + + +category @@ -167,9 +167,9 @@ RNA product->trade name - - -trade name + + +trade name @@ -180,80 +180,106 @@ RNA product->available from - - -available from + + +available from - + +max tolerated dose + +string + + + +RNA product->max tolerated dose + + +max tolerated dose + + + +is toxic + +boolean + + + +RNA product->is toxic + + +is toxic + + + is metabolite - -boolean + +boolean - + RNA product->is metabolite - - -is metabolite + + +is metabolite - + in taxon - -organism taxon + +organism taxon - + RNA product->in taxon - - -in taxon + + +in taxon - + has biological sequence - -biological sequence + +biological sequence - + RNA product->has biological sequence - - -has biological sequence + + +has biological sequence - + synonym - -label type + +label type - + RNA product->synonym - - -synonym + + +synonym - + xref - -iri type + +iri type - + RNA product->xref - - -xref + + +xref named thing_category - -named thing + +named thing diff --git a/graphviz/RNA_product_isoform.gv b/graphviz/RNA_product_isoform.gv index 6e7b2db845..8a0bf65ca1 100644 --- a/graphviz/RNA_product_isoform.gv +++ b/graphviz/RNA_product_isoform.gv @@ -1,23 +1,23 @@ digraph { - graph [bb="0,0,2691,123"]; + graph [bb="0,0,2898,123"]; node [label="\N"]; "RNA product isoform" [height=0.5, label="RNA product isoform", - pos="1273.8,105", + pos="1388.8,105", width=3.015]; "RNA product" [height=0.5, pos="70.844,18", width=1.9679]; "RNA product isoform" -> "RNA product" [label=is_a, lp="457.84,61.5", - pos="e,121.92,30.626 1166.9,101.88 1008.7,98.209 703.04,89.036 443.84,69 313.19,58.9 280.2,56.978 150.84,36 144.68,35.001 138.28,33.843 \ + pos="e,121.92,30.626 1281,102.64 1105.4,99.832 746.72,91.633 443.84,69 313.16,59.235 280.2,56.978 150.84,36 144.68,35.001 138.28,33.843 \ 131.89,32.611"]; "gene product isoform mixin" [height=0.5, pos="298.84,18", width=3.8635]; "RNA product isoform" -> "gene product isoform mixin" [label=uses, - lp="590.34,61.5", - pos="e,366.29,33.792 1165.9,102.94 1028.1,100.6 782.51,93.083 573.84,69 506.68,61.248 431.17,47.124 376.29,35.86"]; + lp="591.34,61.5", + pos="e,365.96,33.804 1280.2,104.02 1123.8,102.99 826.3,97.051 574.84,69 507.19,61.453 431.12,47.238 376,35.888"]; id [color=blue, height=0.5, label=string, @@ -25,9 +25,9 @@ digraph { width=1.0652]; "RNA product isoform" -> id [color=blue, label=id, - lp="703.84,61.5", - pos="e,522.84,29.954 1166.5,102.27 1050.3,99.282 859.68,91.147 696.84,69 627.05,59.508 609.63,55.131 541.84,36 538.74,35.124 535.54,34.151 \ -532.35,33.129", + lp="705.84,61.5", + pos="e,522.84,29.966 1280.5,103.73 1144.2,102.2 903.29,95.506 698.84,69 628.13,59.833 610.49,55.278 541.84,36 538.74,35.128 535.54,34.158 \ +532.34,33.138", style=solid]; iri [color=blue, height=0.5, @@ -36,9 +36,8 @@ digraph { width=1.2277]; "RNA product isoform" -> iri [color=blue, label=iri, - lp="797.84,61.5", - pos="e,628.14,29.913 1167.6,101.13 1069.1,97.335 918.94,88.649 789.84,69 726.22,59.316 710.92,53.009 648.84,36 645.27,35.02 641.57,33.96 \ -637.87,32.865", + lp="793.84,61.5", + pos="e,627.86,29.992 1280.4,103.51 1159.2,101.62 957.52,94.45 785.84,69 734.02,61.317 676,44.986 637.65,33.071", style=solid]; type [color=blue, height=0.5, @@ -47,9 +46,9 @@ digraph { width=1.0652]; "RNA product isoform" -> type [color=blue, label=type, - lp="902.84,61.5", - pos="e,724.49,29.989 1172.3,98.58 1094,93.49 983.12,84.313 886.84,69 822,58.686 805.83,54.534 742.84,36 739.94,35.146 736.96,34.209 733.97,\ -33.227", + lp="899.84,61.5", + pos="e,724.5,29.968 1281.9,101.57 1179.3,98.064 1020.3,89.558 883.84,69 820.2,59.411 804.54,54.31 742.84,36 739.94,35.139 736.96,34.197 \ +733.97,33.212", style=solid]; name [color=blue, height=0.5, @@ -58,8 +57,8 @@ digraph { width=1.5707]; "RNA product isoform" -> name [color=blue, label=name, - lp="998.84,61.5", - pos="e,845.53,31.738 1177.5,96.689 1119.6,91.272 1044.5,82.456 978.84,69 936.33,60.29 889.04,45.995 855.16,34.917", + lp="1001.8,61.5", + pos="e,845.46,31.852 1283.5,100.59 1200.9,96.567 1083.3,87.836 981.84,69 938.2,60.897 889.75,46.402 855.25,35.098", style=solid]; description [color=blue, height=0.5, @@ -68,8 +67,8 @@ digraph { width=2.0943]; "RNA product isoform" -> description [color=blue, label=description, - lp="1100.3,61.5", - pos="e,985.36,34.858 1182.6,95.158 1144.1,89.874 1099.2,81.639 1059.8,69 1037.1,61.696 1013.1,49.994 994.2,39.747", + lp="1105.3,61.5", + pos="e,986.2,35.021 1282.5,101.4 1218.4,97.662 1135.8,88.953 1064.8,69 1040.7,62.199 1015.2,50.33 995.22,39.863", style=solid]; source [color=blue, height=0.5, @@ -78,8 +77,8 @@ digraph { width=1.5707]; "RNA product isoform" -> source [color=blue, label=source, - lp="1188.8,61.5", - pos="e,1123.6,35.382 1214.5,89.877 1197.8,84.615 1180.1,77.737 1164.8,69 1152.5,61.951 1140.6,51.852 1130.9,42.574", + lp="1198.8,61.5", + pos="e,1125.6,35.367 1289.1,97.819 1252.1,92.938 1210.5,84.286 1174.8,69 1159.7,62.508 1144.9,51.813 1133.2,41.977", style=solid]; "provided by" [color=blue, height=0.5, @@ -88,8 +87,8 @@ digraph { width=1.0291]; "RNA product isoform" -> "provided by" [color=blue, label="provided by", - lp="1263.3,61.5", - pos="e,1217,36.192 1238.8,87.944 1231.6,82.941 1225,76.671 1220.8,69 1217.2,62.168 1216.1,54.012 1216.2,46.289", + lp="1278.3,61.5", + pos="e,1221.7,36.109 1307.8,92.978 1277.1,87.284 1246.9,79.332 1235.8,69 1229.4,63.014 1225.7,54.417 1223.6,46.035", style=solid]; "has attribute" [color=blue, height=0.5, @@ -98,16 +97,16 @@ digraph { width=1.4443]; "RNA product isoform" -> "has attribute" [color=blue, label="has attribute", - lp="1361.8,61.5", - pos="e,1322,35.908 1291.3,87.125 1296.4,81.651 1301.7,75.346 1305.8,69 1310.6,61.737 1314.7,53.287 1318.1,45.422", + lp="1375.8,61.5", + pos="e,1324.2,36.342 1348.5,88.142 1340.7,83.196 1333.5,76.901 1328.8,69 1324.9,62.31 1323.6,54.197 1323.6,46.47", style=solid]; category [height=0.5, pos="1448.8,18", width=1.4263]; "RNA product isoform" -> category [color=blue, label=category, - lp="1460.3,61.5", - pos="e,1440.7,35.789 1356.5,93.174 1376.1,87.99 1396.2,80.327 1412.8,69 1422,62.779 1429.6,53.415 1435.5,44.467", + lp="1467.3,61.5", + pos="e,1443.3,36.124 1410.1,87.22 1416.1,81.843 1422.2,75.568 1426.8,69 1431.9,61.869 1436.2,53.37 1439.6,45.42", style=solid]; "trade name" [color=blue, height=0.5, @@ -116,8 +115,8 @@ digraph { width=2.2748]; "RNA product isoform" -> "trade name" [color=blue, label="trade name", - lp="1575.8,61.5", - pos="e,1572.1,35.114 1351.4,92.319 1412.6,83.014 1488.8,71.196 1495.8,69 1519.1,61.741 1543.8,50.081 1563.2,39.846", + lp="1576.8,61.5", + pos="e,1572,35.019 1443.5,89.381 1462.5,83.72 1483.9,76.734 1502.8,69 1523.3,60.66 1545.3,49.537 1563.1,39.9", style=solid]; "available from" [color=blue, height=0.5, @@ -126,68 +125,89 @@ digraph { width=3.2858]; "RNA product isoform" -> "available from" [color=blue, label="available from", - lp="1744.3,61.5", - pos="e,1767.3,34.356 1350.2,92.16 1363.7,90.277 1377.7,88.469 1390.8,87 1492.7,75.622 1519.7,85.673 1620.8,69 1667.2,61.363 1718.6,48.15 \ -1757.3,37.225", + lp="1739.3,61.5", + pos="e,1764.5,34.151 1467.6,92.575 1529.1,83.571 1606.8,72.044 1621.8,69 1666.6,59.963 1716.4,47.224 1754.6,36.867", + style=solid]; + "max tolerated dose" [color=blue, + height=0.5, + label=string, + pos="1992.8,18", + width=1.0652]; + "RNA product isoform" -> "max tolerated dose" [color=blue, + label="max tolerated dose", + lp="1947.8,61.5", + pos="e,1963.8,29.922 1464.6,92.071 1478.3,90.175 1492.5,88.386 1505.8,87 1633.9,73.736 1667.4,86.879 1794.8,69 1862.4,59.517 1879.2,54.764 \ +1944.8,36 1947.9,35.113 1951.1,34.133 1954.3,33.106", + style=solid]; + "is toxic" [color=blue, + height=0.5, + label=boolean, + pos="2095.8,18", + width=1.2999]; + "RNA product isoform" -> "is toxic" [color=blue, + label="is toxic", + lp="2077.8,61.5", + pos="e,2078.2,34.883 1463.6,91.896 1477.6,89.982 1492.1,88.231 1505.8,87 1562.9,81.876 1966.3,86.547 2020.8,69 2038.9,63.202 2056.6,51.727 \ +2070.3,41.232", style=solid]; "is metabolite" [color=blue, height=0.5, label=boolean, - pos="2000.8,18", + pos="2207.8,18", width=1.2999]; "RNA product isoform" -> "is metabolite" [color=blue, label="is metabolite", - lp="1925.8,61.5", - pos="e,1966.1,30.13 1348.9,91.954 1362.8,90.047 1377.3,88.283 1390.8,87 1572,69.897 1619.5,93.287 1799.8,69 1854.5,61.633 1915.9,45.125 \ -1956.3,33.087", + lp="2195.8,61.5", + pos="e,2185.1,33.96 1463.3,91.883 1477.4,89.957 1492,88.205 1505.8,87 1639.2,75.359 1978.1,101.69 2107.8,69 2132.1,62.888 2157.3,50.254 \ +2176.3,39.215", style=solid]; "in taxon" [color=blue, height=0.5, label="organism taxon", - pos="2148.8,18", + pos="2355.8,18", width=2.3109]; "RNA product isoform" -> "in taxon" [color=blue, label="in taxon", - lp="2073.8,61.5", - pos="e,2108.5,33.872 1348.3,91.892 1362.4,89.965 1377,88.211 1390.8,87 1650.4,64.23 1719.5,109.69 1976.8,69 2018.8,62.37 2064.9,48.591 \ -2098.8,37.174", + lp="2319.8,61.5", + pos="e,2328.7,35.214 1463.3,91.82 1477.4,89.9 1492,88.166 1505.8,87 1587.9,80.066 2166.6,87.55 2246.8,69 2272.4,63.104 2299.1,50.937 \ +2319.7,40.082", style=solid]; "has biological sequence" [color=blue, height=0.5, label="biological sequence", - pos="2351.8,18", + pos="2558.8,18", width=2.8164]; "RNA product isoform" -> "has biological sequence" [color=blue, label="has biological sequence", - lp="2280.3,61.5", - pos="e,2296.8,33.124 1348.3,91.829 1362.4,89.908 1377,88.172 1390.8,87 1708,60.067 1790.6,104.97 2106.8,69 2168.6,61.979 2237.9,47.178 \ -2287,35.492", + lp="2518.3,61.5", + pos="e,2510.3,33.946 1463,91.828 1477.2,89.894 1491.9,88.154 1505.8,87 1693.5,71.435 2166.2,93.346 2352.8,69 2403.4,62.405 2459.6,48.299 \ +2500.5,36.746", style=solid]; synonym [color=blue, height=0.5, label="label type", - pos="2527.8,18", + pos="2734.8,18", width=1.5707]; "RNA product isoform" -> synonym [color=blue, label=synonym, - lp="2463.8,61.5", - pos="e,2494.4,32.604 1348,91.796 1362.2,89.865 1376.9,88.134 1390.8,87 1607.5,69.337 2154.3,103.96 2368.8,69 2409.2,62.42 2453.5,47.859 \ -2485,36.138", + lp="2689.8,61.5", + pos="e,2706.2,33.583 1463,91.773 1477.2,89.844 1491.9,88.12 1505.8,87 1627.8,77.184 2486.8,92.632 2606.8,69 2638.4,62.789 2672.2,49.259 \ +2697.1,37.838", style=solid]; xref [color=blue, height=0.5, label="iri type", - pos="2646.8,18", + pos="2853.8,18", width=1.2277]; "RNA product isoform" -> xref [color=blue, label=xref, - lp="2572.3,61.5", - pos="e,2618,31.82 1348,91.772 1362.2,89.843 1376.9,88.119 1390.8,87 1513.7,77.12 2378.4,90.098 2499.8,69 2537.9,62.387 2579.4,47.51 2608.6,\ -35.694", + lp="2790.3,61.5", + pos="e,2827.2,32.65 1462.6,91.798 1476.9,89.853 1491.8,88.117 1505.8,87 1641,76.231 2592.8,95.08 2725.8,69 2758.2,62.652 2793,48.565 \ +2818.1,36.957", style=solid]; "named thing_category" [color=blue, height=0.5, label="named thing", - pos="1469.8,105", + pos="1584.8,105", width=1.9318]; } diff --git a/graphviz/RNA_product_isoform.svg b/graphviz/RNA_product_isoform.svg index 2f0c46000f..181ce51fd8 100644 --- a/graphviz/RNA_product_isoform.svg +++ b/graphviz/RNA_product_isoform.svg @@ -4,16 +4,16 @@ - + %3 - + RNA product isoform - -RNA product isoform + +RNA product isoform @@ -24,7 +24,7 @@ RNA product isoform->RNA product - + is_a @@ -37,9 +37,9 @@ RNA product isoform->gene product isoform mixin - - -uses + + +uses @@ -50,9 +50,9 @@ RNA product isoform->id - - -id + + +id @@ -63,9 +63,9 @@ RNA product isoform->iri - - -iri + + +iri @@ -76,9 +76,9 @@ RNA product isoform->type - - -type + + +type @@ -89,9 +89,9 @@ RNA product isoform->name - - -name + + +name @@ -102,9 +102,9 @@ RNA product isoform->description - - -description + + +description @@ -115,9 +115,9 @@ RNA product isoform->source - - -source + + +source @@ -128,9 +128,9 @@ RNA product isoform->provided by - - -provided by + + +provided by @@ -141,9 +141,9 @@ RNA product isoform->has attribute - - -has attribute + + +has attribute @@ -154,9 +154,9 @@ RNA product isoform->category - - -category + + +category @@ -167,9 +167,9 @@ RNA product isoform->trade name - - -trade name + + +trade name @@ -180,80 +180,106 @@ RNA product isoform->available from - - -available from + + +available from - + +max tolerated dose + +string + + + +RNA product isoform->max tolerated dose + + +max tolerated dose + + + +is toxic + +boolean + + + +RNA product isoform->is toxic + + +is toxic + + + is metabolite - -boolean + +boolean - + RNA product isoform->is metabolite - - -is metabolite + + +is metabolite - + in taxon - -organism taxon + +organism taxon - + RNA product isoform->in taxon - - -in taxon + + +in taxon - + has biological sequence - -biological sequence + +biological sequence - + RNA product isoform->has biological sequence - - -has biological sequence + + +has biological sequence - + synonym - -label type + +label type - + RNA product isoform->synonym - - -synonym + + +synonym - + xref - -iri type + +iri type - + RNA product isoform->xref - - -xref + + +xref named thing_category - -named thing + +named thing diff --git a/graphviz/chemical_entity.gv b/graphviz/chemical_entity.gv index 2984283909..77418e1270 100644 --- a/graphviz/chemical_entity.gv +++ b/graphviz/chemical_entity.gv @@ -1,41 +1,42 @@ digraph { - graph [bb="0,0,2985.8,123"]; + graph [bb="0,0,3225.3,123"]; node [label="\N"]; "chemical entity" [height=0.5, label="chemical entity", - pos="1801.5,105", + pos="1933.5,105", width=2.2748]; "named thing" [height=0.5, pos="69.544,18", width=1.9318]; "chemical entity" -> "named thing" [label=is_a, - lp="523.54,61.5", - pos="e,119.53,30.709 1719.8,103.6 1515.6,102.21 966.5,96.047 509.54,69 348.71,59.48 307.81,60.325 148.54,36 142.36,35.055 135.92,33.923 \ -129.52,32.697"]; + lp="519.54,61.5", + pos="e,119.53,30.701 1851.8,103.93 1633.1,103.33 1017.1,98.877 505.54,69 346.47,59.709 306.05,60.137 148.54,36 142.36,35.052 135.92,33.917 \ +129.52,32.691"]; "physical essence" [height=0.5, pos="245.54,18", width=2.4553]; "chemical entity" -> "physical essence" [label=uses, - lp="679.04,61.5", - pos="e,307.6,30.825 1719.4,104.2 1497,103.87 864.82,97.162 343.54,36 335.16,35.017 326.41,33.789 317.73,32.446"]; + lp="921.04,61.5", + pos="e,307.6,30.854 1852.8,101.93 1679.2,97.342 1257.6,85.388 904.54,69 655.05,57.421 591.65,64.724 343.54,36 335.16,35.029 326.41,33.81 \ +317.73,32.472"]; "chemical or drug or treatment" [height=0.5, pos="503.54,18", width=4.2066]; "chemical entity" -> "chemical or drug or treatment" [label=uses, - lp="1118,61.5", - pos="e,609.34,30.937 1722.1,100.52 1536.6,92.11 1060.5,68.93 663.54,36 649.29,34.818 634.35,33.429 619.55,31.963"]; + lp="1169,61.5", + pos="e,608.9,30.979 1853.2,101.17 1652.4,93.787 1112.5,71.954 663.54,36 649.18,34.85 634.1,33.472 619.19,32.007"]; "chemical entity or gene or gene product" [height=0.5, pos="869.54,18", width=5.4703]; "chemical entity" -> "chemical entity or gene or gene product" [label=uses, - lp="1408,61.5", - pos="e,1003.8,31.241 1727.2,97.224 1572.9,83.145 1215.1,50.517 1013.8,32.158"]; + lp="1492,61.5", + pos="e,1010,30.64 1857.8,98.095 1708.2,86.417 1364.5,59.465 1075.5,36 1057.6,34.541 1038.7,33 1020,31.466"]; "chemical entity or protein or polypeptide" [height=0.5, pos="1285.5,18", width=5.5967]; "chemical entity" -> "chemical entity or protein or polypeptide" [label=uses, - lp="1591,61.5", - pos="e,1377.1,34.082 1738,93.535 1650.3,79.091 1491.3,52.888 1387,35.715"]; + lp="1645,61.5", + pos="e,1381.9,33.849 1861.4,96.345 1799.5,89.635 1708.1,79.359 1628.5,69 1549.2,58.67 1459.8,45.587 1392.1,35.395"]; id [color=blue, height=0.5, label=string, @@ -43,8 +44,8 @@ digraph { width=1.0652]; "chemical entity" -> id [color=blue, label=id, - lp="1696.5,61.5", - pos="e,1572.9,29.556 1756.8,89.892 1714.2,76.378 1648.3,55.251 1591.5,36 1588.6,35.01 1585.6,33.975 1582.6,32.924", + lp="1729.5,61.5", + pos="e,1572.5,29.922 1867.9,94.235 1798.4,83.152 1686.1,63.041 1591.5,36 1588.4,35.113 1585.2,34.133 1582.1,33.106", style=solid]; iri [color=blue, height=0.5, @@ -53,8 +54,9 @@ digraph { width=1.2277]; "chemical entity" -> iri [color=blue, label=iri, - lp="1740.5,61.5", - pos="e,1670,32.808 1772,88.012 1745.6,73.711 1706.9,52.741 1679,37.673", + lp="1816.5,61.5", + pos="e,1678.2,29.681 1884.5,90.495 1861.4,84.082 1833.5,76.249 1808.5,69 1759.5,54.785 1747.3,50.997 1698.5,36 1695.1,34.926 1691.4,33.805 \ +1687.8,32.674", style=solid]; type [color=blue, height=0.5, @@ -63,8 +65,8 @@ digraph { width=1.0652]; "chemical entity" -> type [color=blue, label=type, - lp="1793.5,61.5", - pos="e,1756.3,35.31 1790.2,86.799 1782.1,74.463 1771,57.656 1761.9,43.862", + lp="1867.5,61.5", + pos="e,1772.3,31.117 1899.5,88.607 1866.1,73.52 1815.5,50.612 1781.5,35.24", style=solid]; name [color=blue, height=0.5, @@ -73,8 +75,8 @@ digraph { width=1.5707]; "chemical entity" -> name [color=blue, label=name, - lp="1853.5,61.5", - pos="e,1847.2,35.885 1813.1,86.799 1821.2,74.622 1832.3,58.089 1841.5,44.398", + lp="1920.5,61.5", + pos="e,1873.1,35.469 1918.7,87.207 1907.7,74.669 1892.4,57.35 1880,43.302", style=solid]; description [color=blue, height=0.5, @@ -83,8 +85,8 @@ digraph { width=2.0943]; "chemical entity" -> description [color=blue, label=description, - lp="1958,61.5", - pos="e,1972.2,33.922 1838.6,88.804 1873.2,74.557 1925.2,53.213 1962.6,37.879", + lp="2016,61.5", + pos="e,1993.8,35.758 1948.4,87.207 1959.4,74.75 1974.5,57.573 1986.9,43.574", style=solid]; source [color=blue, height=0.5, @@ -93,9 +95,8 @@ digraph { width=1.5707]; "chemical entity" -> source [color=blue, label=source, - lp="2079.5,61.5", - pos="e,2123,32.058 1861.1,92.535 1871.2,90.641 1881.7,88.732 1891.5,87 1940.8,78.361 1953.9,80.66 2002.5,69 2040.5,59.9 2082.5,46.198 \ -2113.4,35.438", + lp="2118.5,61.5", + pos="e,2132.6,34.075 1988.1,91.557 2010.8,85.707 2037.3,78.023 2060.5,69 2082.2,60.602 2105.3,48.916 2123.7,38.953", style=solid]; "provided by" [color=blue, height=0.5, @@ -104,9 +105,9 @@ digraph { width=1.0291]; "chemical entity" -> "provided by" [color=blue, label="provided by", - lp="2212,61.5", - pos="e,2242.4,29.784 1859.5,92.14 1870.1,90.225 1881.1,88.412 1891.5,87 1987,74.043 2012.8,86.154 2107.5,69 2160.7,59.379 2173.2,52.711 \ -2224.5,36 2227.3,35.111 2230.1,34.161 2232.9,33.182", + lp="2231,61.5", + pos="e,2245,31.378 1992.5,92.494 2002.9,90.585 2013.5,88.682 2023.5,87 2078,77.871 2093.2,83.433 2146.5,69 2177.6,60.596 2211.4,46.635 \ +2235.8,35.599", style=solid]; "has attribute" [color=blue, height=0.5, @@ -115,18 +116,18 @@ digraph { width=1.4443]; "chemical entity" -> "has attribute" [color=blue, label="has attribute", - lp="2349.5,61.5", - pos="e,2350.6,33.551 1858.5,92.018 1869.4,90.067 1880.8,88.271 1891.5,87 2053.7,67.799 2099.3,105.18 2258.5,69 2287.5,62.411 2318.5,49.216 \ -2341.5,38.035", + lp="2362.5,61.5", + pos="e,2354,34.138 1991,92.12 2001.8,90.184 2013,88.368 2023.5,87 2135.8,72.473 2168.4,98.881 2277.5,69 2301.4,62.482 2326.2,50.099 2345.2,\ +39.287", style=solid]; category [height=0.5, pos="2498.5,18", width=1.4263]; "chemical entity" -> category [color=blue, label=category, - lp="2472,61.5", - pos="e,2475.9,34.161 1858.5,91.899 1869.4,89.959 1880.8,88.198 1891.5,87 2004,74.46 2291,97.392 2400.5,69 2424.2,62.865 2448.7,50.358 \ -2467.3,39.388", + lp="2478,61.5", + pos="e,2478.2,34.817 1990.5,91.993 2001.4,90.044 2012.8,88.256 2023.5,87 2109.7,76.924 2330.4,93.719 2413.5,69 2433.8,62.991 2454.2,51.187 \ +2470,40.557", style=solid]; "trade name" [color=blue, height=0.5, @@ -135,9 +136,9 @@ digraph { width=2.2748]; "chemical entity" -> "trade name" [color=blue, label="trade name", - lp="2604.5,61.5", - pos="e,2615.4,34.412 1858,91.932 1869.1,89.962 1880.6,88.182 1891.5,87 2027.7,72.245 2372.9,94.041 2507.5,69 2541.6,62.673 2578.4,49.518 \ -2606,38.289", + lp="2608.5,61.5", + pos="e,2616.3,34.587 1990.5,91.911 2001.4,89.97 2012.8,88.205 2023.5,87 2240.1,62.708 2299.7,111.12 2513.5,69 2545.9,62.634 2580.7,49.702 \ +2607,38.585", style=solid]; "available from" [color=blue, height=0.5, @@ -146,13 +147,35 @@ digraph { width=3.2858]; "chemical entity" -> "available from" [color=blue, label="available from", - lp="2786,61.5", - pos="e,2814.8,34.255 1858,91.884 1869.1,89.918 1880.6,88.152 1891.5,87 2226.7,51.609 2315.2,110.88 2649.5,69 2702.6,62.352 2761.7,48.378 \ -2805,36.889", + lp="2783,61.5", + pos="e,2815.8,34.188 1990,91.926 2001.1,89.957 2012.6,88.179 2023.5,87 2302,56.91 2375.8,105.05 2653.5,69 2705.6,62.25 2763.4,48.33 2805.9,\ +36.888", + style=solid]; + "max tolerated dose" [color=blue, + height=0.5, + label=string, + pos="3042.5,18", + width=1.0652]; + "chemical entity" -> "max tolerated dose" [color=blue, + label="max tolerated dose", + lp="2997.5,61.5", + pos="e,3013.6,29.96 1990,91.869 2001.1,89.905 2012.6,88.143 2023.5,87 2383.9,49.249 2478.6,110.67 2838.5,69 2908.9,60.849 2926.3,55.205 \ +2994.5,36 2997.6,35.126 3000.8,34.155 3004,33.133", + style=solid]; + "is toxic" [color=blue, + height=0.5, + label=boolean, + pos="3178.5,18", + width=1.2999]; + "chemical entity" -> "is toxic" [color=blue, + label="is toxic", + lp="3139.5,61.5", + pos="e,3154.7,33.576 1990,91.827 2001.1,89.866 2012.6,88.117 2023.5,87 2139.3,75.16 2957.1,95.002 3070.5,69 3097.1,62.913 3124.9,49.839 \ +3145.7,38.586", style=solid]; "named thing_category" [color=blue, height=0.5, label="named thing", - pos="1970.5,105", + pos="2102.5,105", width=1.9318]; } diff --git a/graphviz/chemical_entity.svg b/graphviz/chemical_entity.svg index 0587f8f271..7c5f19161f 100644 --- a/graphviz/chemical_entity.svg +++ b/graphviz/chemical_entity.svg @@ -4,16 +4,16 @@ - + %3 - + chemical entity - -chemical entity + +chemical entity @@ -24,9 +24,9 @@ chemical entity->named thing - - -is_a + + +is_a @@ -37,9 +37,9 @@ chemical entity->physical essence - - -uses + + +uses @@ -50,9 +50,9 @@ chemical entity->chemical or drug or treatment - - -uses + + +uses @@ -63,9 +63,9 @@ chemical entity->chemical entity or gene or gene product - - -uses + + +uses @@ -76,9 +76,9 @@ chemical entity->chemical entity or protein or polypeptide - - -uses + + +uses @@ -89,9 +89,9 @@ chemical entity->id - - -id + + +id @@ -102,9 +102,9 @@ chemical entity->iri - - -iri + + +iri @@ -115,9 +115,9 @@ chemical entity->type - - -type + + +type @@ -128,9 +128,9 @@ chemical entity->name - - -name + + +name @@ -141,9 +141,9 @@ chemical entity->description - - -description + + +description @@ -154,9 +154,9 @@ chemical entity->source - - -source + + +source @@ -167,9 +167,9 @@ chemical entity->provided by - - -provided by + + +provided by @@ -180,9 +180,9 @@ chemical entity->has attribute - - -has attribute + + +has attribute @@ -193,9 +193,9 @@ chemical entity->category - - -category + + +category @@ -206,9 +206,9 @@ chemical entity->trade name - - -trade name + + +trade name @@ -219,15 +219,41 @@ chemical entity->available from - - -available from + + +available from + + + +max tolerated dose + +string + + + +chemical entity->max tolerated dose + + +max tolerated dose + + + +is toxic + +boolean + + + +chemical entity->is toxic + + +is toxic named thing_category - -named thing + +named thing diff --git a/graphviz/chemical_mixture.gv b/graphviz/chemical_mixture.gv index 3cbcaf757f..939ed6e886 100644 --- a/graphviz/chemical_mixture.gv +++ b/graphviz/chemical_mixture.gv @@ -1,16 +1,16 @@ digraph { - graph [bb="0,0,2009.9,123"]; + graph [bb="0,0,2251.9,123"]; node [label="\N"]; "chemical mixture" [height=0.5, label="chemical mixture", - pos="889.89,105", + pos="999.89,105", width=2.5276]; "chemical entity" [height=0.5, pos="81.893,18", width=2.2748]; "chemical mixture" -> "chemical entity" [label=is_a, - lp="321.89,61.5", - pos="e,131.75,32.407 799.22,102.96 684.36,100.64 480.57,93.14 307.89,69 250.91,61.034 186.98,46.34 141.69,34.934"]; + lp="318.89,61.5", + pos="e,131.05,32.558 908.92,104.34 775.71,103.72 520.06,98.323 304.89,69 248.61,61.33 185.53,46.6 140.86,35.106"]; id [color=blue, height=0.5, label=string, @@ -18,9 +18,9 @@ digraph { width=1.0652]; "chemical mixture" -> id [color=blue, label=id, - lp="434.89,61.5", - pos="e,248.88,29.984 801.39,100.66 708.13,96.351 557.14,87.148 427.89,69 355.99,58.904 337.83,55.499 267.89,36 264.78,35.133 261.59,34.168 \ -258.39,33.151", + lp="429.89,61.5", + pos="e,248.89,29.954 909.54,102.68 795.61,100.07 593.93,92.263 422.89,69 353.1,59.508 335.68,55.131 267.89,36 264.79,35.124 261.59,34.151 \ +258.39,33.129", style=solid]; iri [color=blue, height=0.5, @@ -29,9 +29,9 @@ digraph { width=1.2277]; "chemical mixture" -> iri [color=blue, label=iri, - lp="535.89,61.5", - pos="e,354.17,30.005 804.7,98.566 731.12,93.205 622.1,83.663 527.89,69 459.16,58.301 442.14,53.797 374.89,36 371.31,35.052 367.61,34.014 \ -363.9,32.933", + lp="523.89,61.5", + pos="e,354.19,29.913 910.22,101.74 812.7,98.307 652.49,89.79 515.89,69 452.27,59.316 436.96,53.009 374.89,36 371.32,35.02 367.62,33.96 \ +363.92,32.865", style=solid]; type [color=blue, height=0.5, @@ -40,8 +40,9 @@ digraph { width=1.0652]; "chemical mixture" -> type [color=blue, label=type, - lp="621.89,61.5", - pos="e,450.55,29.968 808.2,97.071 722.35,88.346 584.05,70.176 468.89,36 465.99,35.139 463.01,34.197 460.02,33.212", + lp="628.89,61.5", + pos="e,450.54,29.989 913.02,99.507 834.31,94.64 715.33,85.293 612.89,69 548.05,58.686 531.88,54.534 468.89,36 465.99,35.146 463.01,34.209 \ +460.02,33.227", style=solid]; name [color=blue, height=0.5, @@ -50,8 +51,8 @@ digraph { width=1.5707]; "chemical mixture" -> name [color=blue, label=name, - lp="720.89,61.5", - pos="e,572.48,31.607 821.27,93.154 785.24,86.99 740.46,78.592 700.89,69 660.47,59.2 615.31,45.409 582.31,34.792", + lp="724.89,61.5", + pos="e,571.58,31.738 916.33,97.852 856.93,92.568 775.5,83.465 704.89,69 662.38,60.29 615.09,45.995 581.21,34.917", style=solid]; description [color=blue, height=0.5, @@ -60,8 +61,8 @@ digraph { width=2.0943]; "chemical mixture" -> description [color=blue, label=description, - lp="815.39,61.5", - pos="e,710.54,35.167 836.68,90.351 816.94,84.631 794.58,77.355 774.89,69 755.87,60.93 735.68,49.953 719.25,40.34", + lp="826.39,61.5", + pos="e,711.4,34.858 919.29,96.562 878.61,91.374 828.9,82.82 785.89,69 763.16,61.696 739.15,49.994 720.25,39.747", style=solid]; source [color=blue, height=0.5, @@ -70,8 +71,8 @@ digraph { width=1.5707]; "chemical mixture" -> source [color=blue, label=source, - lp="889.89,61.5", - pos="e,845.82,35.885 878.76,86.799 870.88,74.622 860.19,58.089 851.33,44.398", + lp="914.89,61.5", + pos="e,849.67,35.382 943.67,90.839 926.11,85.463 907.11,78.279 890.89,69 878.57,61.951 866.6,51.852 856.91,42.574", style=solid]; "provided by" [color=blue, height=0.5, @@ -80,8 +81,8 @@ digraph { width=1.0291]; "chemical mixture" -> "provided by" [color=blue, label="provided by", - lp="970.39,61.5", - pos="e,938.09,35.59 904.38,86.943 908.89,81.359 913.76,75.036 917.89,69 923.19,61.262 928.48,52.512 933.07,44.519", + lp="989.39,61.5", + pos="e,943.01,36.192 965.39,88.321 957.98,83.258 951.12,76.866 946.89,69 943.22,62.168 942.11,54.012 942.22,46.289", style=solid]; "has attribute" [color=blue, height=0.5, @@ -90,17 +91,16 @@ digraph { width=1.4443]; "chemical mixture" -> "has attribute" [color=blue, label="has attribute", - lp="1078.9,61.5", - pos="e,1045.1,36.182 960.09,93.451 979.64,88.254 1000.1,80.515 1016.9,69 1026,62.769 1033.7,53.565 1039.7,44.747", + lp="1087.9,61.5", + pos="e,1048,35.908 1017.4,87.125 1022.5,81.651 1027.8,75.346 1031.9,69 1036.6,61.737 1040.8,53.287 1044.2,45.422", style=solid]; category [height=0.5, pos="1174.9,18", width=1.4263]; "chemical mixture" -> category [color=blue, label=category, - lp="1180.4,61.5", - pos="e,1164.5,35.818 955.46,92.463 966.92,90.558 978.75,88.663 989.89,87 1051.9,77.741 1074.3,98.132 1129.9,69 1141.1,63.128 1150.9,53.278 \ -1158.4,43.866", + lp="1186.4,61.5", + pos="e,1166.8,35.789 1064.3,92.203 1094.4,85.81 1126.4,77.495 1138.9,69 1148.1,62.779 1155.7,53.415 1161.5,44.467", style=solid]; "trade name" [color=blue, height=0.5, @@ -109,9 +109,9 @@ digraph { width=2.2748]; "chemical mixture" -> "trade name" [color=blue, label="trade name", - lp="1297.9,61.5", - pos="e,1297.9,34.994 954.05,92.225 965.94,90.29 978.27,88.448 989.89,87 1089.9,74.544 1118.3,94.227 1215.9,69 1241.3,62.442 1268,50.384 \ -1288.8,39.753", + lp="1301.9,61.5", + pos="e,1298.1,35.195 1066,92.548 1077.3,90.652 1088.9,88.739 1099.9,87 1154,78.407 1169.5,85.057 1221.9,69 1245.2,61.856 1269.9,50.202 \ +1289.3,39.941", style=solid]; "available from" [color=blue, height=0.5, @@ -120,35 +120,57 @@ digraph { width=3.2858]; "chemical mixture" -> "available from" [color=blue, label="available from", - lp="1467.4,61.5", - pos="e,1493.6,34.372 953.48,92.039 965.54,90.098 978.08,88.301 989.89,87 1146,69.806 1187.5,92.068 1342.9,69 1390.9,61.869 1444.2,48.346 \ -1483.9,37.16", + lp="1470.4,61.5", + pos="e,1493.8,34.315 1064,92.161 1075.9,90.232 1088.3,88.409 1099.9,87 1209.2,73.761 1238.2,86.607 1346.9,69 1393.4,61.461 1445,48.178 \ +1483.7,37.198", + style=solid]; + "max tolerated dose" [color=blue, + height=0.5, + label=string, + pos="1718.9,18", + width=1.0652]; + "chemical mixture" -> "max tolerated dose" [color=blue, + label="max tolerated dose", + lp="1675.9,61.5", + pos="e,1689.9,29.887 1063.2,91.998 1075.3,90.048 1088,88.259 1099.9,87 1288.3,67.081 1338.1,94.13 1525.9,69 1591.4,60.236 1607.4,54.397 \ +1670.9,36 1674,35.102 1677.2,34.114 1680.4,33.081", + style=solid]; + "is toxic" [color=blue, + height=0.5, + label=boolean, + pos="1821.9,18", + width=1.2999]; + "chemical mixture" -> "is toxic" [color=blue, + label="is toxic", + lp="1805.9,61.5", + pos="e,1804.9,34.923 1062.7,91.944 1075,89.973 1087.8,88.19 1099.9,87 1171.7,79.937 1680.3,91.29 1748.9,69 1766.6,63.261 1783.8,51.79 \ +1797.1,41.282", style=solid]; "is supplement" [color=blue, height=0.5, label="chemical mixture", - pos="1770.9,18", + pos="1977.9,18", width=2.5276]; "chemical mixture" -> "is supplement" [color=blue, label="is supplement", - lp="1663.4,61.5", - pos="e,1716.6,32.632 952.93,91.959 965.15,90 977.89,88.217 989.89,87 1225.7,63.084 1287.5,96.516 1522.9,69 1585.9,61.63 1656.9,46.643 \ -1706.7,34.99", + lp="1942.4,61.5", + pos="e,1943.1,34.703 1062.7,91.912 1075,89.944 1087.8,88.17 1099.9,87 1262.7,71.25 1675,98.532 1835.9,69 1869.7,62.796 1906.2,49.774 \ +1933.8,38.574", style=solid]; "highest FDA approval status" [color=blue, height=0.5, label=string, - pos="1917.9,18", + pos="2124.9,18", width=1.0652]; "chemical mixture" -> "highest FDA approval status" [color=blue, label="highest FDA approval status", - lp="1907.4,61.5", - pos="e,1889.3,30.049 952.65,91.914 964.96,89.946 977.8,88.171 989.89,87 1312,55.798 1396.5,107.29 1717.9,69 1787,60.771 1804,55.207 1870.9,\ -36 1873.8,35.164 1876.8,34.241 1879.8,33.269", + lp="2149.4,61.5", + pos="e,2099.7,31.91 1062.4,91.912 1074.8,89.931 1087.7,88.152 1099.9,87 1298.4,68.241 1801.3,107.87 1996.9,69 2029.9,62.442 2065.4,47.942 \ +2090.6,36.237", style=solid]; "named thing_category" [color=blue, height=0.5, label="named thing", - pos="1068.9,105", + pos="1178.9,105", width=1.9318]; } diff --git a/graphviz/chemical_mixture.svg b/graphviz/chemical_mixture.svg index 46c89dbdc5..15187c5c1f 100644 --- a/graphviz/chemical_mixture.svg +++ b/graphviz/chemical_mixture.svg @@ -4,16 +4,16 @@ - + %3 - + chemical mixture - -chemical mixture + +chemical mixture @@ -24,9 +24,9 @@ chemical mixture->chemical entity - - -is_a + + +is_a @@ -37,9 +37,9 @@ chemical mixture->id - - -id + + +id @@ -50,9 +50,9 @@ chemical mixture->iri - - -iri + + +iri @@ -63,9 +63,9 @@ chemical mixture->type - - -type + + +type @@ -76,9 +76,9 @@ chemical mixture->name - - -name + + +name @@ -89,9 +89,9 @@ chemical mixture->description - - -description + + +description @@ -102,9 +102,9 @@ chemical mixture->source - - -source + + +source @@ -115,9 +115,9 @@ chemical mixture->provided by - - -provided by + + +provided by @@ -128,9 +128,9 @@ chemical mixture->has attribute - - -has attribute + + +has attribute @@ -141,9 +141,9 @@ chemical mixture->category - - -category + + +category @@ -154,9 +154,9 @@ chemical mixture->trade name - - -trade name + + +trade name @@ -167,41 +167,67 @@ chemical mixture->available from - - -available from + + +available from - + +max tolerated dose + +string + + + +chemical mixture->max tolerated dose + + +max tolerated dose + + + +is toxic + +boolean + + + +chemical mixture->is toxic + + +is toxic + + + is supplement - -chemical mixture + +chemical mixture - + chemical mixture->is supplement - - -is supplement + + +is supplement - + highest FDA approval status - -string + +string - + chemical mixture->highest FDA approval status - - -highest FDA approval status + + +highest FDA approval status named thing_category - -named thing + +named thing diff --git a/graphviz/coding_sequence.gv b/graphviz/coding_sequence.gv index d5a1e22ecc..c85a7fc610 100644 --- a/graphviz/coding_sequence.gv +++ b/graphviz/coding_sequence.gv @@ -1,16 +1,16 @@ digraph { - graph [bb="0,0,2206.9,123"]; + graph [bb="0,0,2413.9,123"]; node [label="\N"]; "coding sequence" [height=0.5, label="coding sequence", - pos="973.54,105", + pos="1082.5,105", width=2.4373]; "nucleic acid entity" [height=0.5, pos="95.542,18", width=2.6539]; "coding sequence" -> "nucleic acid entity" [label=is_a, - lp="348.54,61.5", - pos="e,150.19,32.9 886.08,103.39 762.63,101.59 530.49,94.712 334.54,69 274.9,61.173 207.94,46.66 160.1,35.278"]; + lp="349.54,61.5", + pos="e,149.93,32.907 994.75,104.38 854.75,103.98 572.53,99.046 335.54,69 275.43,61.379 207.95,46.77 159.89,35.302"]; id [color=blue, height=0.5, label=string, @@ -18,9 +18,9 @@ digraph { width=1.0652]; "coding sequence" -> id [color=blue, label=id, - lp="461.54,61.5", - pos="e,276.53,29.979 886.85,101.79 783.5,98.317 605.75,89.691 454.54,69 383.04,59.216 365.05,55.425 295.54,36 292.43,35.132 289.24,34.165 \ -286.04,33.146", + lp="462.54,61.5", + pos="e,276.53,29.984 995.19,103.19 873.7,101.13 647.03,93.953 455.54,69 383.54,59.618 365.48,55.499 295.54,36 292.43,35.133 289.24,34.168 \ +286.04,33.151", style=solid]; iri [color=blue, height=0.5, @@ -29,9 +29,8 @@ digraph { width=1.2277]; "coding sequence" -> iri [color=blue, label=iri, - lp="561.54,61.5", - pos="e,381.82,29.991 888.69,100.22 803.59,95.661 668.95,86.342 553.54,69 485.61,58.792 468.93,53.665 402.54,36 398.96,35.047 395.26,34.005 \ -391.56,32.922", + lp="551.54,61.5", + pos="e,381.93,29.82 995.26,102.75 888.27,100.21 701.69,92.478 543.54,69 490.43,61.116 430.84,44.688 391.67,32.81", style=solid]; type [color=blue, height=0.5, @@ -40,8 +39,9 @@ digraph { width=1.0652]; "coding sequence" -> type [color=blue, label=type, - lp="654.54,61.5", - pos="e,478.18,30.023 890.18,99.243 793.78,92.117 631.1,75.059 496.54,36 493.64,35.156 490.65,34.227 487.66,33.251", + lp="656.54,61.5", + pos="e,478.19,29.989 996.97,100.93 907.62,96.868 763.61,87.871 640.54,69 575.64,59.049 559.53,54.534 496.54,36 493.64,35.146 490.65,34.209 \ +487.66,33.227", style=solid]; name [color=blue, height=0.5, @@ -51,7 +51,7 @@ digraph { "coding sequence" -> name [color=blue, label=name, lp="759.54,61.5", - pos="e,600.86,31.346 899.33,95.346 853.11,89.352 792.55,80.403 739.54,69 695.31,59.485 645.83,45.188 610.45,34.315", + pos="e,600.07,31.655 998.78,99.527 928.97,94.827 827.15,85.713 739.54,69 694.82,60.468 645,45.928 609.64,34.72", style=solid]; description [color=blue, height=0.5, @@ -60,8 +60,8 @@ digraph { width=2.0943]; "coding sequence" -> description [color=blue, label=description, - lp="860.04,61.5", - pos="e,741.81,34.76 909.38,92.612 881.4,86.833 848.46,78.915 819.54,69 796.1,60.962 770.94,49.37 750.92,39.37", + lp="864.04,61.5", + pos="e,741.35,34.764 999.64,98.921 948.18,94.272 881.12,85.481 823.54,69 798.34,61.788 771.51,49.83 750.54,39.417", style=solid]; source [color=blue, height=0.5, @@ -70,8 +70,8 @@ digraph { width=1.5707]; "coding sequence" -> source [color=blue, label=source, - lp="946.54,61.5", - pos="e,881.09,35.223 948.83,87.72 940.37,81.971 930.93,75.353 922.54,69 911.28,60.474 899.25,50.609 888.94,41.906", + lp="956.54,61.5", + pos="e,880.9,35.187 1013.5,93.757 987.39,88.386 957.88,80.46 932.54,69 917.06,61.999 901.52,51.348 889.02,41.673", style=solid]; "provided by" [color=blue, height=0.5, @@ -80,8 +80,8 @@ digraph { width=1.0291]; "coding sequence" -> "provided by" [color=blue, label="provided by", - lp="1017,61.5", - pos="e,974.34,36.175 973.74,86.799 973.88,75.163 974.06,59.548 974.22,46.237", + lp="1036,61.5", + pos="e,977.41,36.214 1027.9,90.703 1015.4,85.58 1003,78.564 993.54,69 987.32,62.709 983.1,54.176 980.25,45.94", style=solid]; "has attribute" [color=blue, height=0.5, @@ -90,16 +90,16 @@ digraph { width=1.4443]; "coding sequence" -> "has attribute" [color=blue, label="has attribute", - lp="1117.5,61.5", - pos="e,1077.5,36.207 1025.1,90.43 1037.5,85.285 1049.9,78.327 1059.5,69 1066.1,62.632 1070.8,53.979 1074.2,45.661", + lp="1129.5,61.5", + pos="e,1081.7,36.175 1082.3,86.799 1082.2,75.163 1082,59.548 1081.9,46.237", style=solid]; category [height=0.5, pos="1202.5,18", width=1.4263]; "coding sequence" -> category [color=blue, label=category, - lp="1216,61.5", - pos="e,1195.3,36.05 1037.6,92.647 1094.2,82.603 1167.8,69.461 1168.5,69 1177.6,63.147 1184.8,53.974 1190.3,45.075", + lp="1223,61.5", + pos="e,1198.7,36.344 1141.5,91.557 1155.6,86.401 1169.6,79.156 1180.5,69 1187.2,62.776 1192,54.158 1195.3,45.829", style=solid]; "trade name" [color=blue, height=0.5, @@ -108,9 +108,8 @@ digraph { width=2.2748]; "coding sequence" -> "trade name" [color=blue, label="trade name", - lp="1330.5,61.5", - pos="e,1327.3,35.115 1035.7,92.283 1046.9,90.365 1058.6,88.513 1069.5,87 1150.1,75.905 1173.4,91.243 1251.5,69 1274.9,62.368 1299.3,50.581 \ -1318.4,40.117", + lp="1332.5,61.5", + pos="e,1327.9,35.129 1145.7,92.358 1191.7,83.721 1247.8,72.809 1258.5,69 1279.5,61.582 1301.5,50.229 1319.1,40.215", style=solid]; "available from" [color=blue, height=0.5, @@ -119,46 +118,68 @@ digraph { width=3.2858]; "coding sequence" -> "available from" [color=blue, label="available from", - lp="1498,61.5", - pos="e,1522.1,34.398 1034.8,92.049 1046.3,90.119 1058.3,88.324 1069.5,87 1204.8,71.095 1240.9,89.933 1375.5,69 1422,61.768 1473.6,48.404 \ -1512.1,37.311", + lp="1499,61.5", + pos="e,1521.4,34.319 1144.6,92.207 1155.9,90.297 1167.6,88.467 1178.5,87 1266.6,75.247 1290,84.131 1377.5,69 1423,61.139 1473.4,48 1511.5,\ +37.164", + style=solid]; + "max tolerated dose" [color=blue, + height=0.5, + label=string, + pos="1746.5,18", + width=1.0652]; + "coding sequence" -> "max tolerated dose" [color=blue, + label="max tolerated dose", + lp="1703.5,61.5", + pos="e,1717.5,29.88 1143.6,91.991 1155.1,90.055 1167.2,88.272 1178.5,87 1344.8,68.376 1388.8,91.775 1554.5,69 1619.6,60.062 1635.5,54.324 \ +1698.5,36 1701.6,35.099 1704.8,34.11 1708,33.076", + style=solid]; + "is toxic" [color=blue, + height=0.5, + label=boolean, + pos="1849.5,18", + width=1.2999]; + "coding sequence" -> "is toxic" [color=blue, + label="is toxic", + lp="1833.5,61.5", + pos="e,1832.5,34.909 1143,91.913 1154.8,89.958 1167,88.188 1178.5,87 1244.7,80.186 1713.3,89.615 1776.5,69 1794.2,63.24 1811.5,51.768 \ +1824.8,41.264", style=solid]; "is metabolite" [color=blue, height=0.5, label=boolean, - pos="1754.5,18", + pos="1961.5,18", width=1.2999]; "coding sequence" -> "is metabolite" [color=blue, label="is metabolite", - lp="1679.5,61.5", - pos="e,1719.8,30.205 1034.3,91.935 1046,89.992 1058.1,88.22 1069.5,87 1283.6,64.178 1340.1,97.006 1553.5,69 1608.3,61.819 1669.6,45.274 \ -1710,33.176", + lp="1950.5,61.5", + pos="e,1939.3,33.986 1143,91.877 1154.8,89.926 1167,88.166 1178.5,87 1254.3,79.341 1789.8,87.765 1863.5,69 1887.4,62.932 1912.1,50.297 \ +1930.7,39.248", style=solid]; "in taxon" [color=blue, height=0.5, label="organism taxon", - pos="1902.5,18", + pos="2109.5,18", width=2.3109]; "coding sequence" -> "in taxon" [color=blue, label="in taxon", - lp="1827.5,61.5", - pos="e,1862.5,33.793 1034,91.886 1045.8,89.934 1058,88.172 1069.5,87 1215.7,72.148 1585.4,91.694 1730.5,69 1772.6,62.421 1818.9,48.568 \ -1852.9,37.108", + lp="2074.5,61.5", + pos="e,2082.7,35.234 1142.8,91.879 1154.6,89.914 1166.9,88.149 1178.5,87 1269.6,77.999 1912.4,89.65 2001.5,69 2026.9,63.135 2053.4,50.968 \ +2073.8,40.106", style=solid]; "has biological sequence" [color=blue, height=0.5, label="biological sequence", - pos="2105.5,18", + pos="2312.5,18", width=2.8164]; "coding sequence" -> "has biological sequence" [color=blue, label="has biological sequence", - lp="2040,61.5", - pos="e,2050.5,33.163 1033.8,91.887 1045.6,89.922 1057.9,88.154 1069.5,87 1419.5,52.241 1511.1,108.31 1860.5,69 1922.3,62.053 1991.6,47.243 \ -2040.7,35.535", + lp="2272,61.5", + pos="e,2264.2,33.974 1142.8,91.856 1154.6,89.893 1166.9,88.135 1178.5,87 1384,66.937 1902.8,95.624 2107.5,69 2157.9,62.454 2213.8,48.344 \ +2254.5,36.777", style=solid]; "named thing_category" [color=blue, height=0.5, label="named thing", - pos="1148.5,105", + pos="1257.5,105", width=1.9318]; } diff --git a/graphviz/coding_sequence.svg b/graphviz/coding_sequence.svg index 261bff9b33..ebf762b5d5 100644 --- a/graphviz/coding_sequence.svg +++ b/graphviz/coding_sequence.svg @@ -4,16 +4,16 @@ - + %3 - + coding sequence - -coding sequence + +coding sequence @@ -24,9 +24,9 @@ coding sequence->nucleic acid entity - - -is_a + + +is_a @@ -37,9 +37,9 @@ coding sequence->id - + -id +id @@ -50,9 +50,9 @@ coding sequence->iri - - -iri + + +iri @@ -63,9 +63,9 @@ coding sequence->type - - -type + + +type @@ -76,8 +76,8 @@ coding sequence->name - - + + name @@ -89,9 +89,9 @@ coding sequence->description - - -description + + +description @@ -102,9 +102,9 @@ coding sequence->source - - -source + + +source @@ -115,9 +115,9 @@ coding sequence->provided by - - -provided by + + +provided by @@ -128,9 +128,9 @@ coding sequence->has attribute - - -has attribute + + +has attribute @@ -141,9 +141,9 @@ coding sequence->category - - -category + + +category @@ -154,9 +154,9 @@ coding sequence->trade name - - -trade name + + +trade name @@ -167,54 +167,80 @@ coding sequence->available from - - -available from + + +available from - + +max tolerated dose + +string + + + +coding sequence->max tolerated dose + + +max tolerated dose + + + +is toxic + +boolean + + + +coding sequence->is toxic + + +is toxic + + + is metabolite - -boolean + +boolean - + coding sequence->is metabolite - - -is metabolite + + +is metabolite - + in taxon - -organism taxon + +organism taxon - + coding sequence->in taxon - - -in taxon + + +in taxon - + has biological sequence - -biological sequence + +biological sequence - + coding sequence->has biological sequence - - -has biological sequence + + +has biological sequence named thing_category - -named thing + +named thing diff --git a/graphviz/complex_molecular_mixture.gv b/graphviz/complex_molecular_mixture.gv index 71f6f62e12..64b12eca5f 100644 --- a/graphviz/complex_molecular_mixture.gv +++ b/graphviz/complex_molecular_mixture.gv @@ -1,16 +1,16 @@ digraph { - graph [bb="0,0,2028,123"]; + graph [bb="0,0,2270,123"]; node [label="\N"]; "complex molecular mixture" [height=0.5, label="complex molecular mixture", - pos="907.99,105", + pos="1018,105", width=3.8274]; "chemical mixture" [height=0.5, pos="90.992,18", width=2.5276]; "complex molecular mixture" -> "chemical mixture" [label=is_a, - lp="339.99,61.5", - pos="e,144.26,32.716 772.49,101.58 654.18,98.104 478.08,89.635 325.99,69 267.14,61.016 201.07,46.448 154,35.088"]; + lp="336.99,61.5", + pos="e,143.09,32.761 880.58,103.62 739.95,101.71 515.38,94.405 322.99,69 264.77,61.311 199.46,46.683 153,35.227"]; id [color=blue, height=0.5, label=string, @@ -18,9 +18,9 @@ digraph { width=1.0652]; "complex molecular mixture" -> id [color=blue, label=id, - lp="452.99,61.5", - pos="e,266.98,29.984 778.57,98.626 685.68,93.691 557.71,84.687 445.99,69 374.09,58.904 355.93,55.499 285.99,36 282.88,35.133 279.69,34.168 \ -276.49,33.151", + lp="447.99,61.5", + pos="e,266.99,29.954 882.78,101.49 765.49,97.958 591.4,89.456 440.99,69 371.2,59.508 353.78,55.131 285.99,36 282.89,35.124 279.69,34.151 \ +276.49,33.129", style=solid]; iri [color=blue, height=0.5, @@ -29,9 +29,9 @@ digraph { width=1.2277]; "complex molecular mixture" -> iri [color=blue, label=iri, - lp="553.99,61.5", - pos="e,372.27,30.005 788.53,95.954 717.76,90.316 626.47,81.527 545.99,69 477.26,58.301 460.24,53.797 392.99,36 389.41,35.052 385.71,34.014 \ -382,32.933", + lp="541.99,61.5", + pos="e,372.29,29.913 885.38,100.05 787.76,95.77 652.05,86.97 533.99,69 470.36,59.316 455.06,53.009 392.99,36 389.42,35.02 385.72,33.96 \ +382.02,32.865", style=solid]; type [color=blue, height=0.5, @@ -40,8 +40,9 @@ digraph { width=1.0652]; "complex molecular mixture" -> type [color=blue, label=type, - lp="639.99,61.5", - pos="e,468.65,29.968 798.12,94.059 712.14,84.424 590.27,66.647 486.99,36 484.09,35.139 481.11,34.197 478.12,33.212", + lp="646.99,61.5", + pos="e,468.64,29.989 894.16,97.075 817.94,91.755 718.44,82.909 630.99,69 566.15,58.686 549.98,54.534 486.99,36 484.09,35.146 481.1,34.209 \ +478.11,33.227", style=solid]; name [color=blue, height=0.5, @@ -50,8 +51,8 @@ digraph { width=1.5707]; "complex molecular mixture" -> name [color=blue, label=name, - lp="738.99,61.5", - pos="e,590.58,31.607 824.78,90.616 791.68,84.767 753.37,77.334 718.99,69 678.57,59.2 633.41,45.409 600.41,34.792", + lp="742.99,61.5", + pos="e,589.68,31.738 903.46,94.926 848.52,89.426 781.98,81.085 722.99,69 680.47,60.29 633.19,45.995 599.31,34.917", style=solid]; description [color=blue, height=0.5, @@ -60,8 +61,8 @@ digraph { width=2.0943]; "complex molecular mixture" -> description [color=blue, label=description, - lp="833.49,61.5", - pos="e,728.64,35.167 848.93,88.633 830.71,83.201 810.76,76.54 792.99,69 773.97,60.93 753.78,49.953 737.35,40.34", + lp="844.49,61.5", + pos="e,729.5,34.858 913.39,93.236 878.1,87.941 838.85,80.2 803.99,69 781.26,61.696 757.25,49.994 738.35,39.747", style=solid]; source [color=blue, height=0.5, @@ -70,8 +71,8 @@ digraph { width=1.5707]; "complex molecular mixture" -> source [color=blue, label=source, - lp="907.99,61.5", - pos="e,863.92,35.885 896.86,86.799 888.98,74.622 878.28,58.089 869.43,44.398", + lp="932.99,61.5", + pos="e,867.77,35.382 955.55,88.877 939.8,83.753 923.31,77.194 908.99,69 896.67,61.951 884.7,51.852 875.01,42.574", style=solid]; "provided by" [color=blue, height=0.5, @@ -80,8 +81,8 @@ digraph { width=1.0291]; "complex molecular mixture" -> "provided by" [color=blue, label="provided by", - lp="988.49,61.5", - pos="e,956.19,35.59 922.48,86.943 926.99,81.359 931.86,75.036 935.99,69 941.29,61.262 946.58,52.512 951.17,44.519", + lp="1007.5,61.5", + pos="e,961.11,36.192 982.39,87.561 975.41,82.623 969.01,76.477 964.99,69 961.32,62.168 960.21,54.012 960.32,46.289", style=solid]; "has attribute" [color=blue, height=0.5, @@ -90,16 +91,16 @@ digraph { width=1.4443]; "complex molecular mixture" -> "has attribute" [color=blue, label="has attribute", - lp="1097,61.5", - pos="e,1063.2,36.182 988.8,90.394 1005,85.35 1021.2,78.445 1035,69 1044.1,62.769 1051.8,53.565 1057.8,44.747", + lp="1106,61.5", + pos="e,1066.1,35.908 1035.5,87.125 1040.6,81.651 1045.9,75.346 1050,69 1054.7,61.737 1058.9,53.287 1062.3,45.422", style=solid]; category [height=0.5, pos="1193,18", width=1.4263]; "complex molecular mixture" -> category [color=blue, label=category, - lp="1198.5,61.5", - pos="e,1182.5,35.743 1008.1,92.632 1068.2,85.246 1135.3,75.768 1148,69 1159.1,63.033 1168.9,53.169 1176.5,43.771", + lp="1204.5,61.5", + pos="e,1184.9,35.789 1107.6,91.246 1124.9,86.142 1142.3,78.998 1157,69 1166.1,62.779 1173.8,53.415 1179.6,44.467", style=solid]; "trade name" [color=blue, height=0.5, @@ -108,9 +109,8 @@ digraph { width=2.2748]; "complex molecular mixture" -> "trade name" [color=blue, label="trade name", - lp="1316,61.5", - pos="e,1315.5,35.065 1006.1,92.351 1022.1,90.516 1038.5,88.675 1054,87 1133.9,78.35 1156.4,89.914 1234,69 1259.1,62.233 1285.7,50.29 \ -1306.5,39.773", + lp="1320,61.5", + pos="e,1316.2,35.114 1112.6,91.873 1161.7,85.013 1216.4,76.361 1240,69 1263.3,61.741 1287.9,50.081 1307.4,39.846", style=solid]; "available from" [color=blue, height=0.5, @@ -119,35 +119,57 @@ digraph { width=3.2858]; "complex molecular mixture" -> "available from" [color=blue, label="available from", - lp="1485.5,61.5", - pos="e,1511.3,34.382 1004.1,92.014 1020.7,90.169 1037.8,88.412 1054,87 1190.2,75.091 1225.9,89.585 1361,69 1408.8,61.711 1461.9,48.265 \ -1501.5,37.152", + lp="1488.5,61.5", + pos="e,1511,34.314 1115.7,92.256 1131.8,90.424 1148.4,88.608 1164,87 1253.2,77.813 1276.6,84.08 1365,69 1411.1,61.13 1462.3,47.992 1501,\ +37.158", + style=solid]; + "max tolerated dose" [color=blue, + height=0.5, + label=string, + pos="1737,18", + width=1.0652]; + "complex molecular mixture" -> "max tolerated dose" [color=blue, + label="max tolerated dose", + lp="1694,61.5", + pos="e,1708,29.887 1113.3,91.947 1130.2,90.087 1147.6,88.342 1164,87 1332.5,73.214 1376.5,91.849 1544,69 1609.5,60.068 1625.5,54.397 \ +1689,36 1692.1,35.102 1695.3,34.114 1698.5,33.081", + style=solid]; + "is toxic" [color=blue, + height=0.5, + label=boolean, + pos="1840,18", + width=1.2999]; + "complex molecular mixture" -> "is toxic" [color=blue, + label="is toxic", + lp="1824,61.5", + pos="e,1823,34.91 1112.1,91.834 1129.4,89.95 1147.2,88.226 1164,87 1230.8,82.119 1703.3,89.779 1767,69 1784.6,63.242 1801.9,51.77 1815.2,\ +41.266", style=solid]; "is supplement" [color=blue, height=0.5, label="chemical mixture", - pos="1789,18", + pos="1996,18", width=2.5276]; "complex molecular mixture" -> "is supplement" [color=blue, label="is supplement", - lp="1681.5,61.5", - pos="e,1734.7,32.581 1002.5,91.889 1019.6,90.012 1037.3,88.276 1054,87 1270,70.462 1325.9,94.487 1541,69 1604,61.53 1674.9,46.555 1724.7,\ -34.932", + lp="1960.5,61.5", + pos="e,1961.2,34.686 1112.1,91.782 1129.4,89.903 1147.2,88.195 1164,87 1317,76.119 1703.1,96.81 1854,69 1887.8,62.769 1924.3,49.747 1951.9,\ +38.554", style=solid]; "highest FDA approval status" [color=blue, height=0.5, label=string, - pos="1936,18", + pos="2143,18", width=1.0652]; "complex molecular mixture" -> "highest FDA approval status" [color=blue, label="highest FDA approval status", - lp="1925.5,61.5", - pos="e,1907.4,30.049 1002.1,91.786 1019.4,89.907 1037.2,88.197 1054,87 1356.4,65.444 1434.9,105.12 1736,69 1805.1,60.713 1822.1,55.207 \ -1889,36 1891.9,35.164 1894.9,34.241 1897.9,33.269", + lp="2167.5,61.5", + pos="e,2117.8,31.901 1111.7,91.756 1129.1,89.868 1147.1,88.162 1164,87 1258.3,80.524 1922.2,87.49 2015,69 2048,62.424 2083.5,47.926 2108.7,\ +36.226", style=solid]; "named thing_category" [color=blue, height=0.5, label="named thing", - pos="1133,105", + pos="1243,105", width=1.9318]; } diff --git a/graphviz/complex_molecular_mixture.svg b/graphviz/complex_molecular_mixture.svg index 862ee98f1b..e02e11cf72 100644 --- a/graphviz/complex_molecular_mixture.svg +++ b/graphviz/complex_molecular_mixture.svg @@ -4,16 +4,16 @@ - + %3 - + complex molecular mixture - -complex molecular mixture + +complex molecular mixture @@ -24,9 +24,9 @@ complex molecular mixture->chemical mixture - - -is_a + + +is_a @@ -37,9 +37,9 @@ complex molecular mixture->id - - -id + + +id @@ -50,9 +50,9 @@ complex molecular mixture->iri - - -iri + + +iri @@ -63,9 +63,9 @@ complex molecular mixture->type - - -type + + +type @@ -76,9 +76,9 @@ complex molecular mixture->name - - -name + + +name @@ -89,9 +89,9 @@ complex molecular mixture->description - - -description + + +description @@ -102,9 +102,9 @@ complex molecular mixture->source - - -source + + +source @@ -115,9 +115,9 @@ complex molecular mixture->provided by - - -provided by + + +provided by @@ -128,9 +128,9 @@ complex molecular mixture->has attribute - - -has attribute + + +has attribute @@ -141,9 +141,9 @@ complex molecular mixture->category - - -category + + +category @@ -154,9 +154,9 @@ complex molecular mixture->trade name - - -trade name + + +trade name @@ -167,41 +167,67 @@ complex molecular mixture->available from - - -available from + + +available from - + +max tolerated dose + +string + + + +complex molecular mixture->max tolerated dose + + +max tolerated dose + + + +is toxic + +boolean + + + +complex molecular mixture->is toxic + + +is toxic + + + is supplement - -chemical mixture + +chemical mixture - + complex molecular mixture->is supplement - - -is supplement + + +is supplement - + highest FDA approval status - -string + +string - + complex molecular mixture->highest FDA approval status - - -highest FDA approval status + + +highest FDA approval status named thing_category - -named thing + +named thing diff --git a/graphviz/drug.gv b/graphviz/drug.gv index ba7ff971f4..bb4695e207 100644 --- a/graphviz/drug.gv +++ b/graphviz/drug.gv @@ -1,28 +1,29 @@ digraph { - graph [bb="0,0,2530.2,123"]; + graph [bb="0,0,2773.2,123"]; node [label="\N"]; drug [height=0.5, label=drug, - pos="1281.2,105", + pos="1411.2,105", width=0.9027]; "molecular mixture" [height=0.5, pos="96.191,18", width=2.672]; drug -> "molecular mixture" [label=is_a, - lp="542.19,61.5", - pos="e,164.8,30.708 1248.4,103.41 1116.6,100.73 612.85,87.484 202.19,36 193.3,34.885 184,33.588 174.77,32.218"]; + lp="568.19,61.5", + pos="e,164.81,30.677 1378.5,103.28 1264.6,100.66 875.11,90.581 554.19,69 397.42,58.457 358.07,55.785 202.19,36 193.3,34.871 184,33.566 \ +174.77,32.192"]; "chemical or drug or treatment" [height=0.5, pos="362.19,18", width=4.2066]; drug -> "chemical or drug or treatment" [label=uses, - lp="730.69,61.5", - pos="e,446.96,32.968 1248.8,102.9 1162.1,99.769 917.05,89.636 714.19,69 626.84,60.114 527.87,45.664 457.18,34.578"]; + lp="726.69,61.5", + pos="e,444.9,33.091 1378.6,103.45 1278.6,101.52 967.02,93.808 710.19,69 623.33,60.61 524.95,45.997 455.01,34.728"]; "ontology class" [height=0.5, pos="608.19,18", width=2.1304]; drug -> "ontology class" [label=uses, - lp="847.69,61.5", - pos="e,656.97,32.053 1248.8,103.07 1174.6,100.59 986.56,92.338 831.19,69 774.83,60.535 711.52,45.828 666.79,34.549"]; + lp="840.69,61.5", + pos="e,655.37,32.336 1378.5,103.97 1289.3,103.47 1033.9,99.298 824.19,69 769.59,61.109 708.41,46.38 665.15,34.944"]; id [color=blue, height=0.5, label=string, @@ -30,8 +31,9 @@ digraph { width=1.0652]; drug -> id [color=blue, label=id, - lp="943.19,61.5", - pos="e,770.18,29.996 1248.9,102.51 1169.4,98.213 958.28,82.918 789.19,36 786.08,35.137 782.88,34.175 779.68,33.159", + lp="956.19,61.5", + pos="e,770.18,29.984 1378.8,102.97 1303.3,100.26 1109.5,91.51 949.19,69 877.29,58.904 859.13,55.499 789.19,36 786.08,35.133 782.89,34.168 \ +779.69,33.151", style=solid]; iri [color=blue, height=0.5, @@ -40,9 +42,9 @@ digraph { width=1.2277]; drug -> iri [color=blue, label=iri, - lp="1049.2,61.5", - pos="e,875.48,29.946 1249.6,100.2 1203.6,94.485 1115.5,82.851 1041.2,69 976.22,56.888 959.99,53.271 896.19,36 892.61,35.031 888.92,33.979 \ -885.22,32.889", + lp="1057.2,61.5", + pos="e,875.47,30.005 1379.1,102.15 1315.7,98.225 1170.2,87.839 1049.2,69 980.46,58.301 963.44,53.797 896.19,36 892.61,35.052 888.91,34.014 \ +885.2,32.933", style=solid]; type [color=blue, height=0.5, @@ -51,8 +53,8 @@ digraph { width=1.0652]; drug -> type [color=blue, label=type, - lp="1125.2,61.5", - pos="e,972.12,29.97 1250.7,98.296 1197.3,88.002 1083.7,64.698 990.19,36 987.43,35.153 984.59,34.238 981.75,33.289", + lp="1143.2,61.5", + pos="e,971.85,29.968 1379.1,101.64 1307.9,95.801 1131.6,77.969 990.19,36 987.29,35.139 984.31,34.197 981.32,33.212", style=solid]; name [color=blue, height=0.5, @@ -61,8 +63,8 @@ digraph { width=1.5707]; drug -> name [color=blue, label=name, - lp="1202.2,61.5", - pos="e,1091.1,32.19 1254.9,94.083 1217.1,79.773 1146.6,53.147 1100.5,35.754", + lp="1242.2,61.5", + pos="e,1093.8,31.607 1380.2,99.329 1342.6,93.414 1277.3,82.366 1222.2,69 1181.8,59.2 1136.6,45.409 1103.6,34.792", style=solid]; description [color=blue, height=0.5, @@ -71,8 +73,8 @@ digraph { width=2.0943]; drug -> description [color=blue, label=description, - lp="1288.7,61.5", - pos="e,1221.1,35.949 1267.4,88.41 1256.4,75.874 1240.6,58.031 1227.9,43.576", + lp="1336.7,61.5", + pos="e,1231.8,35.167 1381.8,96.885 1358.2,90.744 1324.4,80.982 1296.2,69 1277.2,60.93 1257,49.953 1240.5,40.34", style=solid]; source [color=blue, height=0.5, @@ -81,8 +83,8 @@ digraph { width=1.5707]; drug -> source [color=blue, label=source, - lp="1367.2,61.5", - pos="e,1351,36.066 1304.3,92.207 1314.2,86.285 1325.2,78.367 1333.2,69 1339,62.169 1343.6,53.628 1347.2,45.547", + lp="1411.2,61.5", + pos="e,1367.1,35.92 1400.6,87.611 1392.7,75.422 1381.8,58.556 1372.8,44.596", style=solid]; "provided by" [color=blue, height=0.5, @@ -91,9 +93,8 @@ digraph { width=1.0291]; drug -> "provided by" [color=blue, label="provided by", - lp="1463.7,61.5", - pos="e,1450.4,33.913 1305.7,93.139 1311.1,90.951 1316.8,88.78 1322.2,87 1353.9,76.571 1364.7,82.661 1395.2,69 1411.9,61.53 1428.8,50.208 \ -1442.2,40.225", + lp="1491.7,61.5", + pos="e,1459.4,35.59 1424.5,88.352 1429.4,82.437 1434.7,75.55 1439.2,69 1444.5,61.262 1449.8,52.512 1454.4,44.519", style=solid]; "has attribute" [color=blue, height=0.5, @@ -102,18 +103,18 @@ digraph { width=1.4443]; drug -> "has attribute" [color=blue, label="has attribute", - lp="1583.2,61.5", - pos="e,1559.4,35.26 1305.1,92.706 1310.6,90.49 1316.5,88.416 1322.2,87 1403.6,66.701 1432.1,99.789 1510.2,69 1525.6,62.932 1540.4,52.073 \ -1552,42.021", + lp="1602.2,61.5", + pos="e,1566.9,35.95 1435.6,92.993 1441,90.814 1446.7,88.683 1452.2,87 1489.5,75.471 1505.3,90.074 1538.2,69 1547.6,62.968 1555.4,53.641 \ +1561.5,44.669", style=solid]; category [height=0.5, pos="1696.2,18", width=1.4263]; drug -> category [color=blue, label=category, - lp="1690.7,61.5", - pos="e,1681.2,35.711 1305,92.546 1310.6,90.338 1316.5,88.309 1322.2,87 1389.9,71.482 1569.4,93.994 1634.2,69 1648.9,63.314 1662.9,52.742 \ -1673.8,42.779", + lp="1703.7,61.5", + pos="e,1686.5,35.98 1435.1,92.68 1440.6,90.465 1446.5,88.399 1452.2,87 1495.7,76.288 1613.3,89.506 1653.2,69 1664.1,63.388 1673.4,53.71 \ +1680.6,44.355", style=solid]; "trade name" [color=blue, height=0.5, @@ -122,9 +123,9 @@ digraph { width=2.2748]; drug -> "trade name" [color=blue, label="trade name", - lp="1812.2,61.5", - pos="e,1817.3,34.782 1305,92.491 1310.5,90.286 1316.5,88.271 1322.2,87 1497.6,47.989 1550.7,107.91 1726.2,69 1754.7,62.686 1785,50.14 \ -1808.2,39.195", + lp="1821.2,61.5", + pos="e,1819.8,35.141 1435,92.567 1440.6,90.359 1446.5,88.323 1452.2,87 1576.7,58.131 1615.3,100.39 1739.2,69 1764.2,62.664 1790.5,50.612 \ +1810.9,39.928", style=solid]; "available from" [color=blue, height=0.5, @@ -133,35 +134,57 @@ digraph { width=3.2858]; drug -> "available from" [color=blue, label="available from", - lp="1984.7,61.5", - pos="e,2014,34.365 1305,92.444 1310.5,90.242 1316.5,88.24 1322.2,87 1438.5,61.813 1739.3,84.983 1857.2,69 1907.3,62.2 1963,48.473 2004.2,\ -37.119", + lp="1989.7,61.5", + pos="e,2015.9,34.365 1435,92.486 1440.5,90.281 1446.5,88.268 1452.2,87 1632,47.122 1683.9,95.576 1866.2,69 1914,62.034 1966.9,48.432 \ +2006.2,37.172", + style=solid]; + "max tolerated dose" [color=blue, + height=0.5, + label=string, + pos="2240.2,18", + width=1.0652]; + drug -> "max tolerated dose" [color=blue, + label="max tolerated dose", + lp="2196.2,61.5", + pos="e,2211.2,29.901 1435,92.43 1440.5,90.229 1446.5,88.231 1452.2,87 1581.1,59.298 1914.4,85.514 2045.2,69 2111.6,60.613 2127.9,54.544 \ +2192.2,36 2195.3,35.106 2198.5,34.122 2201.7,33.091", + style=solid]; + "is toxic" [color=blue, + height=0.5, + label=boolean, + pos="2343.2,18", + width=1.2999]; + drug -> "is toxic" [color=blue, + label="is toxic", + lp="2326.2,61.5", + pos="e,2325.9,34.959 1435,92.395 1440.5,90.195 1446.5,88.207 1452.2,87 1541,68.29 2182.7,96.537 2269.2,69 2287.1,63.315 2304.6,51.847 \ +2318,41.327", style=solid]; "is supplement" [color=blue, height=0.5, label="chemical mixture", - pos="2292.2,18", + pos="2499.2,18", width=2.5276]; drug -> "is supplement" [color=blue, label="is supplement", - lp="2181.7,61.5", - pos="e,2238,32.532 1305,92.408 1310.5,90.207 1316.5,88.215 1322.2,87 1478.3,53.875 1881.6,86.595 2040.2,69 2104.8,61.832 2177.6,46.613 \ -2228.2,34.838", + lp="2463.7,61.5", + pos="e,2464.2,34.749 1435,92.386 1440.5,90.187 1446.5,88.201 1452.2,87 1648.9,45.806 2158.4,104.6 2356.2,69 2390.2,62.872 2427,49.847 \ +2454.8,38.628", style=solid]; "highest FDA approval status" [color=blue, height=0.5, label=string, - pos="2439.2,18", + pos="2646.2,18", width=1.0652]; drug -> "highest FDA approval status" [color=blue, label="highest FDA approval status", - lp="2427.7,61.5", - pos="e,2410.6,30.067 1305,92.385 1310.5,90.186 1316.5,88.2 1322.2,87 1421.6,66.186 2135.3,80.562 2236.2,69 2306.6,60.933 2324,55.432 \ -2392.2,36 2395.1,35.17 2398.1,34.251 2401.1,33.282", + lp="2670.7,61.5", + pos="e,2621,31.935 1435,92.373 1440.5,90.175 1446.5,88.192 1452.2,87 1684.2,38.777 2285.7,114.82 2518.2,69 2551.2,62.494 2586.7,47.989 \ +2611.9,36.269", style=solid]; "named thing_category" [color=blue, height=0.5, label="named thing", - pos="1401.2,105", + pos="1531.2,105", width=1.9318]; } diff --git a/graphviz/drug.svg b/graphviz/drug.svg index 16e1445d0b..7105d0d4e9 100644 --- a/graphviz/drug.svg +++ b/graphviz/drug.svg @@ -4,16 +4,16 @@ - + %3 - + drug - -drug + +drug @@ -24,9 +24,9 @@ drug->molecular mixture - - -is_a + + +is_a @@ -37,9 +37,9 @@ drug->chemical or drug or treatment - - -uses + + +uses @@ -50,9 +50,9 @@ drug->ontology class - - -uses + + +uses @@ -63,9 +63,9 @@ drug->id - - -id + + +id @@ -76,9 +76,9 @@ drug->iri - - -iri + + +iri @@ -89,9 +89,9 @@ drug->type - - -type + + +type @@ -102,9 +102,9 @@ drug->name - - -name + + +name @@ -115,9 +115,9 @@ drug->description - - -description + + +description @@ -128,9 +128,9 @@ drug->source - - -source + + +source @@ -141,9 +141,9 @@ drug->provided by - - -provided by + + +provided by @@ -154,9 +154,9 @@ drug->has attribute - - -has attribute + + +has attribute @@ -167,9 +167,9 @@ drug->category - - -category + + +category @@ -180,9 +180,9 @@ drug->trade name - - -trade name + + +trade name @@ -193,41 +193,67 @@ drug->available from - - -available from + + +available from - + +max tolerated dose + +string + + + +drug->max tolerated dose + + +max tolerated dose + + + +is toxic + +boolean + + + +drug->is toxic + + +is toxic + + + is supplement - -chemical mixture + +chemical mixture - + drug->is supplement - - -is supplement + + +is supplement - + highest FDA approval status - -string + +string - + drug->highest FDA approval status - - -highest FDA approval status + + +highest FDA approval status named thing_category - -named thing + +named thing diff --git a/graphviz/environmental_food_contaminant.gv b/graphviz/environmental_food_contaminant.gv index 3d8b131dce..2b80a7ebb5 100644 --- a/graphviz/environmental_food_contaminant.gv +++ b/graphviz/environmental_food_contaminant.gv @@ -1,16 +1,16 @@ digraph { - graph [bb="0,0,1662.2,123"]; + graph [bb="0,0,1901.7,123"]; node [label="\N"]; "environmental food contaminant" [height=0.5, label="environmental food contaminant", - pos="759.89,105", + pos="889.89,105", width=4.4954]; "chemical entity" [height=0.5, pos="81.893,18", width=2.2748]; "environmental food contaminant" -> "chemical entity" [label=is_a, - lp="328.89,61.5", - pos="e,133.36,32.105 613.04,97.366 526.04,92.213 413.81,83.439 314.89,69 256.16,60.427 190.07,45.759 143.33,34.52"]; + lp="321.89,61.5", + pos="e,131.75,32.407 731.44,101.21 614.03,97.508 450.37,88.918 307.89,69 250.91,61.034 186.98,46.34 141.69,34.934"]; id [color=blue, height=0.5, label=string, @@ -18,8 +18,9 @@ digraph { width=1.0652]; "environmental food contaminant" -> id [color=blue, label=id, - lp="421.89,61.5", - pos="e,248.88,29.996 624.81,95.08 524.84,86.141 386.09,68.796 267.89,36 264.78,35.137 261.58,34.175 258.39,33.159", + lp="434.89,61.5", + pos="e,248.88,29.984 742.17,97.625 651.23,92.508 532.44,83.681 427.89,69 355.99,58.904 337.83,55.499 267.89,36 264.78,35.133 261.59,34.168 \ +258.39,33.151", style=solid]; iri [color=blue, height=0.5, @@ -28,9 +29,9 @@ digraph { width=1.2277]; "environmental food contaminant" -> iri [color=blue, label=iri, - lp="527.89,61.5", - pos="e,354.18,29.946 658,90.952 615.22,85.004 565.01,77.411 519.89,69 454.92,56.888 438.69,53.271 374.89,36 371.31,35.031 367.62,33.979 \ -363.92,32.889", + lp="535.89,61.5", + pos="e,354.17,30.005 756.19,94.798 687.68,89.142 603.07,80.701 527.89,69 459.16,58.301 442.14,53.797 374.89,36 371.31,35.052 367.61,34.014 \ +363.9,32.933", style=solid]; type [color=blue, height=0.5, @@ -39,8 +40,8 @@ digraph { width=1.0652]; "environmental food contaminant" -> type [color=blue, label=type, - lp="603.89,61.5", - pos="e,450.83,29.97 683.46,89.121 624.33,76.894 540.69,58.037 468.89,36 466.13,35.153 463.29,34.238 460.45,33.289", + lp="621.89,61.5", + pos="e,450.55,29.968 769.66,92.879 684.44,82.999 568.08,65.436 468.89,36 465.99,35.139 463.01,34.197 460.02,33.212", style=solid]; name [color=blue, height=0.5, @@ -49,8 +50,8 @@ digraph { width=1.5707]; "environmental food contaminant" -> name [color=blue, label=name, - lp="680.89,61.5", - pos="e,570.02,32.27 716.51,87.611 677.11,72.726 619.24,50.863 579.47,35.839", + lp="720.89,61.5", + pos="e,572.48,31.607 801.96,89.778 769.98,84.064 733.65,76.941 700.89,69 660.47,59.2 615.31,45.409 582.31,34.792", style=solid]; description [color=blue, height=0.5, @@ -59,8 +60,8 @@ digraph { width=2.0943]; "environmental food contaminant" -> description [color=blue, label=description, - lp="767.39,61.5", - pos="e,699.79,35.885 744.72,86.799 733.77,74.39 718.83,57.458 706.61,43.618", + lp="815.39,61.5", + pos="e,710.54,35.167 829.65,88.279 811.75,82.912 792.28,76.377 774.89,69 755.87,60.93 735.68,49.953 719.25,40.34", style=solid]; source [color=blue, height=0.5, @@ -69,8 +70,8 @@ digraph { width=1.5707]; "environmental food contaminant" -> source [color=blue, label=source, - lp="845.89,61.5", - pos="e,829.68,36.066 790.75,87.262 798.34,82.125 805.97,75.963 811.89,69 817.7,62.169 822.34,53.628 825.89,45.547", + lp="889.89,61.5", + pos="e,845.82,35.885 878.76,86.799 870.88,74.622 860.19,58.089 851.33,44.398", style=solid]; "provided by" [color=blue, height=0.5, @@ -79,8 +80,8 @@ digraph { width=1.0291]; "environmental food contaminant" -> "provided by" [color=blue, label="provided by", - lp="942.39,61.5", - pos="e,928.64,33.821 823.02,88.334 839.94,83.143 857.95,76.687 873.89,69 890.24,61.12 907.04,49.867 920.4,40.03", + lp="970.39,61.5", + pos="e,938.09,35.59 904.38,86.943 908.89,81.359 913.76,75.036 917.89,69 923.19,61.262 928.48,52.512 933.07,44.519", style=solid]; "has attribute" [color=blue, height=0.5, @@ -89,17 +90,16 @@ digraph { width=1.4443]; "environmental food contaminant" -> "has attribute" [color=blue, label="has attribute", - lp="1061.9,61.5", - pos="e,1037.8,35.19 872.73,92.071 919.46,86.035 967.67,78.064 988.89,69 1004,62.548 1018.7,51.756 1030.3,41.846", + lp="1078.9,61.5", + pos="e,1045.1,36.182 973.36,89.548 988.66,84.585 1003.9,77.928 1016.9,69 1026,62.769 1033.7,53.565 1039.7,44.747", style=solid]; category [height=0.5, pos="1174.9,18", width=1.4263]; "environmental food contaminant" -> category [color=blue, label=category, - lp="1169.4,61.5", - pos="e,1159.8,35.491 875.57,92.407 893.75,90.592 912.33,88.742 929.89,87 1011.2,78.934 1037.3,99.947 1112.9,69 1127.5,63.017 1141.4,52.413 \ -1152.4,42.506", + lp="1180.4,61.5", + pos="e,1164.4,35.743 998.31,91.603 1056.1,84.382 1117.8,75.457 1129.9,69 1141,63.033 1150.8,53.169 1158.4,43.771", style=solid]; "trade name" [color=blue, height=0.5, @@ -108,9 +108,8 @@ digraph { width=2.2748]; "environmental food contaminant" -> "trade name" [color=blue, label="trade name", - lp="1290.9,61.5", - pos="e,1295.5,34.836 873.23,92.12 892.14,90.294 911.57,88.516 929.89,87 1052,76.905 1085.6,96.757 1204.9,69 1233.1,62.435 1263.2,50.016 \ -1286.3,39.197", + lp="1297.9,61.5", + pos="e,1297.4,35.003 1006,92.415 1095.4,83.346 1205.6,71.814 1215.9,69 1241,62.142 1267.6,50.195 1288.3,39.7", style=solid]; "available from" [color=blue, height=0.5, @@ -119,13 +118,35 @@ digraph { width=3.2858]; "environmental food contaminant" -> "available from" [color=blue, label="available from", - lp="1463.4,61.5", - pos="e,1492.3,34.328 871.84,91.917 891.18,90.083 911.11,88.355 929.89,87 1110,74.009 1157,94.224 1335.9,69 1385.8,61.957 1441.3,48.315 \ -1482.4,37.059", + lp="1467.4,61.5", + pos="e,1493.2,34.31 1003.2,92.091 1022.1,90.269 1041.6,88.499 1059.9,87 1185.5,76.728 1218.3,88.29 1342.9,69 1390.7,61.592 1443.8,48.153 \ +1483.4,37.072", + style=solid]; + "max tolerated dose" [color=blue, + height=0.5, + label=string, + pos="1718.9,18", + width=1.0652]; + "environmental food contaminant" -> "max tolerated dose" [color=blue, + label="max tolerated dose", + lp="1674.9,61.5", + pos="e,1689.9,29.908 1001.4,91.873 1020.9,90.033 1041,88.314 1059.9,87 1265.3,72.748 1318.7,95.516 1522.9,69 1589.7,60.322 1606.1,54.617 \ +1670.9,36 1674,35.109 1677.2,34.126 1680.4,33.096", + style=solid]; + "is toxic" [color=blue, + height=0.5, + label=boolean, + pos="1854.9,18", + width=1.2999]; + "environmental food contaminant" -> "is toxic" [color=blue, + label="is toxic", + lp="1815.9,61.5", + pos="e,1830.9,33.747 999.99,91.798 1019.9,89.931 1040.5,88.221 1059.9,87 1136.2,82.192 1673.5,86.556 1747.9,69 1774,62.836 1801.4,49.896 \ +1821.9,38.724", style=solid]; "named thing_category" [color=blue, height=0.5, label="named thing", - pos="1008.9,105", + pos="1138.9,105", width=1.9318]; } diff --git a/graphviz/environmental_food_contaminant.svg b/graphviz/environmental_food_contaminant.svg index bdeb03e2d5..474c126d4d 100644 --- a/graphviz/environmental_food_contaminant.svg +++ b/graphviz/environmental_food_contaminant.svg @@ -4,16 +4,16 @@ - + %3 - + environmental food contaminant - -environmental food contaminant + +environmental food contaminant @@ -24,9 +24,9 @@ environmental food contaminant->chemical entity - - -is_a + + +is_a @@ -37,9 +37,9 @@ environmental food contaminant->id - - -id + + +id @@ -50,9 +50,9 @@ environmental food contaminant->iri - - -iri + + +iri @@ -63,9 +63,9 @@ environmental food contaminant->type - - -type + + +type @@ -76,9 +76,9 @@ environmental food contaminant->name - - -name + + +name @@ -89,9 +89,9 @@ environmental food contaminant->description - - -description + + +description @@ -102,9 +102,9 @@ environmental food contaminant->source - - -source + + +source @@ -115,9 +115,9 @@ environmental food contaminant->provided by - - -provided by + + +provided by @@ -128,9 +128,9 @@ environmental food contaminant->has attribute - - -has attribute + + +has attribute @@ -141,9 +141,9 @@ environmental food contaminant->category - - -category + + +category @@ -154,9 +154,9 @@ environmental food contaminant->trade name - - -trade name + + +trade name @@ -167,15 +167,41 @@ environmental food contaminant->available from - - -available from + + +available from + + + +max tolerated dose + +string + + + +environmental food contaminant->max tolerated dose + + +max tolerated dose + + + +is toxic + +boolean + + + +environmental food contaminant->is toxic + + +is toxic named thing_category - -named thing + +named thing diff --git a/graphviz/exon.gv b/graphviz/exon.gv index 1f15a2988c..914ff7cb8a 100644 --- a/graphviz/exon.gv +++ b/graphviz/exon.gv @@ -1,16 +1,16 @@ digraph { - graph [bb="0,0,2206.9,123"]; + graph [bb="0,0,2413.9,123"]; node [label="\N"]; exon [height=0.5, label=exon, - pos="973.54,105", + pos="1082.5,105", width=0.9027]; "nucleic acid entity" [height=0.5, pos="95.542,18", width=2.6539]; exon -> "nucleic acid entity" [label=is_a, - lp="348.54,61.5", - pos="e,150.19,32.9 940.8,103.95 846.33,103.44 565.33,99.283 334.54,69 274.9,61.173 207.94,46.66 160.1,35.278"]; + lp="349.54,61.5", + pos="e,149.93,32.907 1050,104.31 945.62,104.92 610.2,103.82 335.54,69 275.43,61.379 207.95,46.77 159.89,35.302"]; id [color=blue, height=0.5, label=string, @@ -18,9 +18,9 @@ digraph { width=1.0652]; exon -> id [color=blue, label=id, - lp="461.54,61.5", - pos="e,276.53,29.979 940.89,103.35 858.81,101.39 637.29,94.007 454.54,69 383.04,59.216 365.05,55.425 295.54,36 292.43,35.132 289.24,34.165 \ -286.04,33.146", + lp="462.54,61.5", + pos="e,276.53,29.984 1050.1,103.87 957.07,103.15 681.76,98.479 455.54,69 383.54,59.618 365.48,55.499 295.54,36 292.43,35.133 289.24,34.168 \ +286.04,33.151", style=solid]; iri [color=blue, height=0.5, @@ -29,9 +29,8 @@ digraph { width=1.2277]; exon -> iri [color=blue, label=iri, - lp="561.54,61.5", - pos="e,381.82,29.991 941.23,102.76 870.58,99.738 697.17,90.583 553.54,69 485.61,58.792 468.93,53.665 402.54,36 398.96,35.047 395.26,34.005 \ -391.56,32.922", + lp="551.54,61.5", + pos="e,381.93,29.82 1049.8,103.75 965.5,102.7 733.93,97.263 543.54,69 490.43,61.116 430.84,44.688 391.67,32.81", style=solid]; type [color=blue, height=0.5, @@ -40,8 +39,9 @@ digraph { width=1.0652]; exon -> type [color=blue, label=type, - lp="654.54,61.5", - pos="e,478.18,30.023 941.07,102.52 863,98.285 659.22,83.221 496.54,36 493.64,35.156 490.65,34.227 487.66,33.251", + lp="656.54,61.5", + pos="e,478.19,29.989 1050.2,103.06 976.89,100.57 792.72,92.333 640.54,69 575.64,59.049 559.53,54.534 496.54,36 493.64,35.146 490.65,34.209 \ +487.66,33.227", style=solid]; name [color=blue, height=0.5, @@ -51,7 +51,7 @@ digraph { exon -> name [color=blue, label=name, lp="759.54,61.5", - pos="e,600.86,31.346 941.9,100.56 896.71,95.353 811.22,84.42 739.54,69 695.31,59.485 645.83,45.188 610.45,34.315", + pos="e,600.07,31.655 1050.1,102.57 988.92,99.455 852.43,90.536 739.54,69 694.82,60.468 645,45.928 609.64,34.72", style=solid]; description [color=blue, height=0.5, @@ -60,8 +60,8 @@ digraph { width=2.0943]; exon -> description [color=blue, label=description, - lp="860.04,61.5", - pos="e,741.81,34.76 942.62,98.98 911.13,93.406 861.17,83.273 819.54,69 796.1,60.962 770.94,49.37 750.92,39.37", + lp="864.04,61.5", + pos="e,741.35,34.764 1050,102.61 1000.3,99.828 902.93,91.724 823.54,69 798.34,61.788 771.51,49.83 750.54,39.417", style=solid]; source [color=blue, height=0.5, @@ -70,8 +70,8 @@ digraph { width=1.5707]; exon -> source [color=blue, label=source, - lp="946.54,61.5", - pos="e,881.09,35.223 953.38,90.793 943.88,84.411 932.47,76.52 922.54,69 911.28,60.474 899.25,50.609 888.94,41.906", + lp="956.54,61.5", + pos="e,880.9,35.187 1050.9,100.28 1019.8,95.779 971.28,86.521 932.54,69 917.06,61.999 901.52,51.348 889.02,41.673", style=solid]; "provided by" [color=blue, height=0.5, @@ -80,8 +80,8 @@ digraph { width=1.0291]; exon -> "provided by" [color=blue, label="provided by", - lp="1017,61.5", - pos="e,974.34,36.175 973.74,86.799 973.88,75.163 974.06,59.548 974.22,46.237", + lp="1036,61.5", + pos="e,977.41,36.214 1051.8,98.51 1032.8,93.67 1009.2,84.822 993.54,69 987.32,62.709 983.1,54.176 980.25,45.94", style=solid]; "has attribute" [color=blue, height=0.5, @@ -90,18 +90,17 @@ digraph { width=1.4443]; exon -> "has attribute" [color=blue, label="has attribute", - lp="1117.5,61.5", - pos="e,1077.5,36.226 998.67,93.521 1003.9,91.353 1009.4,89.093 1014.5,87 1034.5,78.875 1044.1,83.97 1059.5,69 1066.1,62.652 1070.8,54.003 \ -1074.2,45.684", + lp="1129.5,61.5", + pos="e,1081.7,36.175 1082.3,86.799 1082.2,75.163 1082,59.548 1081.9,46.237", style=solid]; category [height=0.5, pos="1202.5,18", width=1.4263]; exon -> category [color=blue, label=category, - lp="1216,61.5", - pos="e,1195.4,36.29 997.44,92.794 1003,90.573 1008.9,88.476 1014.5,87 1081.2,69.637 1109.6,104.72 1168.5,69 1177.8,63.368 1185.2,54.117 \ -1190.6,45.094", + lp="1223,61.5", + pos="e,1198.9,35.983 1107.6,93.222 1112.8,91.075 1118.3,88.9 1123.5,87 1148.5,77.904 1160.8,86.738 1180.5,69 1187.4,62.81 1192.3,54.058 \ +1195.6,45.602", style=solid]; "trade name" [color=blue, height=0.5, @@ -110,9 +109,9 @@ digraph { width=2.2748]; exon -> "trade name" [color=blue, label="trade name", - lp="1330.5,61.5", - pos="e,1327.4,35.296 997.4,92.623 1002.9,90.411 1008.8,88.36 1014.5,87 1117.3,62.462 1149.6,96.748 1251.5,69 1274.9,62.634 1299.4,50.858 \ -1318.5,40.333", + lp="1335.5,61.5", + pos="e,1328.4,35.374 1106.9,92.686 1112.3,90.527 1118,88.481 1123.5,87 1182,71.275 1200.9,87.38 1258.5,69 1279.9,62.205 1302.1,50.785 \ +1319.7,40.573", style=solid]; "available from" [color=blue, height=0.5, @@ -121,46 +120,68 @@ digraph { width=3.2858]; exon -> "available from" [color=blue, label="available from", - lp="1498,61.5", - pos="e,1522.6,34.404 997.37,92.513 1002.9,90.307 1008.8,88.286 1014.5,87 1171.3,51.717 1216.7,92.974 1375.5,69 1422.2,61.952 1474,48.511 \ -1512.5,37.338", + lp="1502,61.5", + pos="e,1522.6,34.5 1106.4,92.598 1111.9,90.388 1117.8,88.344 1123.5,87 1235,60.73 1267.6,87.579 1380.5,69 1425.6,61.597 1475.4,48.375 \ +1512.9,37.387", + style=solid]; + "max tolerated dose" [color=blue, + height=0.5, + label=string, + pos="1746.5,18", + width=1.0652]; + exon -> "max tolerated dose" [color=blue, + label="max tolerated dose", + lp="1705.5,61.5", + pos="e,1717.5,29.858 1106.4,92.477 1111.9,90.273 1117.8,88.262 1123.5,87 1312.1,45.387 1366.3,95.113 1557.5,69 1621.3,60.295 1636.8,54.104 \ +1698.5,36 1701.6,35.092 1704.8,34.098 1708,33.06", + style=solid]; + "is toxic" [color=blue, + height=0.5, + label=boolean, + pos="1849.5,18", + width=1.2999]; + exon -> "is toxic" [color=blue, + label="is toxic", + lp="1834.5,61.5", + pos="e,1833.1,34.92 1106.4,92.418 1111.9,90.217 1117.8,88.222 1123.5,87 1194.7,71.804 1709.4,91.938 1778.5,69 1795.7,63.311 1812.3,52.002 \ +1825.2,41.576", style=solid]; "is metabolite" [color=blue, height=0.5, label=boolean, - pos="1754.5,18", + pos="1961.5,18", width=1.2999]; exon -> "is metabolite" [color=blue, label="is metabolite", - lp="1679.5,61.5", - pos="e,1719.8,30.246 997.36,92.443 1002.9,90.241 1008.8,88.239 1014.5,87 1131.7,61.64 1434.7,84.367 1553.5,69 1608.3,61.923 1669.6,45.357 \ -1710,33.226", + lp="1951.5,61.5", + pos="e,1939.6,34 1106.3,92.405 1111.9,90.204 1117.8,88.213 1123.5,87 1284.7,52.877 1705,109.77 1864.5,69 1888.2,62.955 1912.6,50.32 1931.1,\ +39.265", style=solid]; "in taxon" [color=blue, height=0.5, label="organism taxon", - pos="1902.5,18", + pos="2109.5,18", width=2.3109]; exon -> "in taxon" [color=blue, label="in taxon", - lp="1827.5,61.5", - pos="e,1862.5,33.818 997.35,92.408 1002.9,90.208 1008.8,88.216 1014.5,87 1170.2,53.962 1573.3,93.417 1730.5,69 1772.6,62.465 1818.9,48.609 \ -1852.9,37.136", + lp="2074.5,61.5", + pos="e,2083,35.245 1106.3,92.388 1111.9,90.189 1117.8,88.202 1123.5,87 1314.8,46.89 1812.3,113.31 2002.5,69 2027.7,63.152 2053.9,50.986 \ +2074.1,40.119", style=solid]; "has biological sequence" [color=blue, height=0.5, label="biological sequence", - pos="2105.5,18", + pos="2312.5,18", width=2.8164]; exon -> "has biological sequence" [color=blue, label="has biological sequence", - lp="2040,61.5", - pos="e,2050.5,33.186 997.35,92.392 1002.9,90.192 1008.8,88.205 1014.5,87 1198.6,48.322 1673.7,89.885 1860.5,69 1922.3,62.099 1991.6,47.283 \ -2040.7,35.561", + lp="2272,61.5", + pos="e,2264.6,33.869 1106.3,92.379 1111.9,90.18 1117.8,88.196 1123.5,87 1230.6,64.667 1999.1,83.041 2107.5,69 2158.1,62.46 2214.2,48.275 \ +2254.9,36.679", style=solid]; "named thing_category" [color=blue, height=0.5, label="named thing", - pos="1093.5,105", + pos="1202.5,105", width=1.9318]; } diff --git a/graphviz/exon.svg b/graphviz/exon.svg index d99446c8c1..d977c6d9cb 100644 --- a/graphviz/exon.svg +++ b/graphviz/exon.svg @@ -4,16 +4,16 @@ - + %3 - + exon - -exon + +exon @@ -24,9 +24,9 @@ exon->nucleic acid entity - - -is_a + + +is_a @@ -37,9 +37,9 @@ exon->id - + -id +id @@ -50,9 +50,9 @@ exon->iri - - -iri + + +iri @@ -63,9 +63,9 @@ exon->type - - -type + + +type @@ -76,8 +76,8 @@ exon->name - - + + name @@ -89,9 +89,9 @@ exon->description - - -description + + +description @@ -102,9 +102,9 @@ exon->source - - -source + + +source @@ -115,9 +115,9 @@ exon->provided by - - -provided by + + +provided by @@ -128,9 +128,9 @@ exon->has attribute - - -has attribute + + +has attribute @@ -141,9 +141,9 @@ exon->category - - -category + + +category @@ -154,9 +154,9 @@ exon->trade name - - -trade name + + +trade name @@ -167,54 +167,80 @@ exon->available from - - -available from + + +available from - + +max tolerated dose + +string + + + +exon->max tolerated dose + + +max tolerated dose + + + +is toxic + +boolean + + + +exon->is toxic + + +is toxic + + + is metabolite - -boolean + +boolean - + exon->is metabolite - - -is metabolite + + +is metabolite - + in taxon - -organism taxon + +organism taxon - + exon->in taxon - - -in taxon + + +in taxon - + has biological sequence - -biological sequence + +biological sequence - + exon->has biological sequence - - -has biological sequence + + +has biological sequence named thing_category - -named thing + +named thing diff --git a/graphviz/food.gv b/graphviz/food.gv index 62e0aa1cd3..d7dc7e8b4b 100644 --- a/graphviz/food.gv +++ b/graphviz/food.gv @@ -1,16 +1,16 @@ digraph { - graph [bb="0,0,2028,123"]; + graph [bb="0,0,2270,123"]; node [label="\N"]; food [height=0.5, label=food, - pos="907.99,105", + pos="1018,105", width=0.84854]; "chemical mixture" [height=0.5, pos="90.992,18", width=2.5276]; food -> "chemical mixture" [label=is_a, - lp="339.99,61.5", - pos="e,144.26,32.716 877.23,103.77 790.27,102.76 535.38,97.409 325.99,69 267.14,61.016 201.07,46.448 154,35.088"]; + lp="336.99,61.5", + pos="e,143.09,32.761 987.35,104.22 889.83,104.55 578.11,102.69 322.99,69 264.77,61.311 199.46,46.683 153,35.227"]; id [color=blue, height=0.5, label=string, @@ -18,9 +18,9 @@ digraph { width=1.0652]; food -> id [color=blue, label=id, - lp="452.99,61.5", - pos="e,266.98,29.984 877.58,103.04 803.45,100.41 607.7,91.706 445.99,69 374.09,58.904 355.93,55.499 285.99,36 282.88,35.133 279.69,34.168 \ -276.49,33.151", + lp="447.99,61.5", + pos="e,266.99,29.954 987.49,103.75 901.28,102.69 648.58,97.233 440.99,69 371.2,59.508 353.78,55.131 285.99,36 282.89,35.124 279.69,34.151 \ +276.49,33.129", style=solid]; iri [color=blue, height=0.5, @@ -29,9 +29,9 @@ digraph { width=1.2277]; food -> iri [color=blue, label=iri, - lp="553.99,61.5", - pos="e,372.27,30.005 877.33,102.24 814.76,98.385 667.96,87.984 545.99,69 477.26,58.301 460.24,53.797 392.99,36 389.41,35.052 385.71,34.014 \ -382,32.933", + lp="541.99,61.5", + pos="e,372.29,29.913 987.51,103.46 910.87,101.75 704.11,94.893 533.99,69 470.36,59.316 455.06,53.009 392.99,36 389.42,35.02 385.72,33.96 \ +382.02,32.865", style=solid]; type [color=blue, height=0.5, @@ -40,8 +40,9 @@ digraph { width=1.0652]; food -> type [color=blue, label=type, - lp="639.99,61.5", - pos="e,468.65,29.968 877.8,101.8 807.83,96.112 629.66,78.338 486.99,36 484.09,35.139 481.11,34.197 478.12,33.212", + lp="646.99,61.5", + pos="e,468.64,29.989 987.46,102.64 921.87,99.421 762.74,89.956 630.99,69 566.15,58.686 549.98,54.534 486.99,36 484.09,35.146 481.1,34.209 \ +478.11,33.227", style=solid]; name [color=blue, height=0.5, @@ -50,8 +51,8 @@ digraph { width=1.5707]; food -> name [color=blue, label=name, - lp="738.99,61.5", - pos="e,590.58,31.607 878.64,99.587 841.3,93.739 774.94,82.562 718.99,69 678.57,59.2 633.41,45.409 600.41,34.792", + lp="742.99,61.5", + pos="e,589.68,31.738 987.57,102.08 933.77,98.317 818.48,88.563 722.99,69 680.47,60.29 633.19,45.995 599.31,34.917", style=solid]; description [color=blue, height=0.5, @@ -60,8 +61,8 @@ digraph { width=2.0943]; food -> description [color=blue, label=description, - lp="833.49,61.5", - pos="e,728.64,35.167 879.99,97.256 856.34,91.142 821.81,81.227 792.99,69 773.97,60.93 753.78,49.953 737.35,40.34", + lp="844.49,61.5", + pos="e,729.5,34.858 987.56,101.88 945.45,98.312 867.43,89.384 803.99,69 781.26,61.696 757.25,49.994 738.35,39.747", style=solid]; source [color=blue, height=0.5, @@ -70,8 +71,8 @@ digraph { width=1.5707]; food -> source [color=blue, label=source, - lp="907.99,61.5", - pos="e,863.86,35.789 897.65,88.012 889.73,75.783 878.67,58.677 869.53,44.556", + lp="932.99,61.5", + pos="e,867.77,35.382 989.33,98.26 966.53,92.898 934.35,83.512 908.99,69 896.67,61.951 884.7,51.852 875.01,42.574", style=solid]; "provided by" [color=blue, height=0.5, @@ -80,8 +81,8 @@ digraph { width=1.0291]; food -> "provided by" [color=blue, label="provided by", - lp="988.49,61.5", - pos="e,956.19,35.59 921.05,88.699 925.94,82.707 931.42,75.679 935.99,69 941.29,61.262 946.58,52.512 951.17,44.519", + lp="1007.5,61.5", + pos="e,961.11,36.192 993.21,94.153 982.5,88.507 971.05,80.264 964.99,69 961.32,62.168 960.21,54.012 960.32,46.289", style=solid]; "has attribute" [color=blue, height=0.5, @@ -90,18 +91,17 @@ digraph { width=1.4443]; food -> "has attribute" [color=blue, label="has attribute", - lp="1099,61.5", - pos="e,1063.7,35.969 931.2,92.94 936.32,90.765 941.78,88.649 946.99,87 985.05,74.958 1001.3,90.467 1035,69 1044.4,62.99 1052.3,53.667 \ -1058.3,44.692", + lp="1106,61.5", + pos="e,1066.1,35.908 1033.5,89.223 1039.2,83.295 1045.3,76.174 1050,69 1054.7,61.737 1058.9,53.287 1062.3,45.422", style=solid]; category [height=0.5, pos="1193,18", width=1.4263]; food -> category [color=blue, label=category, - lp="1200.5,61.5", - pos="e,1183.3,35.984 930.65,92.663 935.91,90.449 941.55,88.387 946.99,87 990.87,75.806 1109.7,89.691 1150,69 1160.9,63.393 1170.2,53.716 \ -1177.4,44.36", + lp="1204.5,61.5", + pos="e,1185.1,36.059 1041.2,92.846 1046.3,90.677 1051.8,88.587 1057,87 1100.2,73.889 1118.8,93.081 1157,69 1166.4,63.097 1174,53.794 \ +1179.9,44.805", style=solid]; "trade name" [color=blue, height=0.5, @@ -110,9 +110,9 @@ digraph { width=2.2748]; food -> "trade name" [color=blue, label="trade name", - lp="1318,61.5", - pos="e,1316.6,35.145 930.63,92.557 935.88,90.349 941.53,88.316 946.99,87 1072.1,56.83 1111.2,100.58 1236,69 1261,62.669 1287.3,50.618 \ -1307.7,39.933", + lp="1320,61.5", + pos="e,1317.2,35.109 1040.7,92.702 1045.9,90.486 1051.6,88.414 1057,87 1136.1,66.42 1161.3,91.043 1240,69 1263.8,62.33 1288.8,50.465 \ +1308.4,39.968", style=solid]; "available from" [color=blue, height=0.5, @@ -121,35 +121,57 @@ digraph { width=3.2858]; food -> "available from" [color=blue, label="available from", - lp="1486.5,61.5", - pos="e,1512.7,34.368 930.61,92.48 935.86,90.276 941.52,88.264 946.99,87 1127.3,45.323 1179.9,95.685 1363,69 1410.8,62.039 1463.7,48.437 \ -1503,37.175", + lp="1488.5,61.5", + pos="e,1512.3,34.399 1040.6,92.542 1045.9,90.334 1051.5,88.306 1057,87 1190.4,55.109 1229.5,89.961 1365,69 1411.7,61.771 1463.5,48.407 \ +1502.3,37.313", + style=solid]; + "max tolerated dose" [color=blue, + height=0.5, + label=string, + pos="1737,18", + width=1.0652]; + food -> "max tolerated dose" [color=blue, + label="max tolerated dose", + lp="1694,61.5", + pos="e,1708,29.887 1040.2,92.629 1045.6,90.358 1051.4,88.28 1057,87 1162.6,62.944 1436.6,83.077 1544,69 1609.5,60.409 1625.5,54.397 1689,\ +36 1692.1,35.102 1695.3,34.114 1698.5,33.081", + style=solid]; + "is toxic" [color=blue, + height=0.5, + label=boolean, + pos="1840,18", + width=1.2999]; + food -> "is toxic" [color=blue, + label="is toxic", + lp="1824,61.5", + pos="e,1823,34.937 1040.2,92.582 1045.5,90.313 1051.4,88.247 1057,87 1134,69.917 1691.9,93.295 1767,69 1784.7,63.282 1801.9,51.812 1815.2,\ +41.299", style=solid]; "is supplement" [color=blue, height=0.5, label="chemical mixture", - pos="1789,18", + pos="1996,18", width=2.5276]; food -> "is supplement" [color=blue, label="is supplement", - lp="1681.5,61.5", - pos="e,1735.4,32.574 930.18,92.602 935.55,90.332 941.37,88.261 946.99,87 1076.1,58.048 1410.6,84.177 1542,69 1605,61.721 1675.9,46.645 \ -1725.5,34.941", + lp="1960.5,61.5", + pos="e,1961.2,34.722 1040.2,92.57 1045.5,90.302 1051.4,88.239 1057,87 1230,48.889 1679.7,100.82 1854,69 1887.8,62.828 1924.3,49.804 1951.9,\ +38.596", style=solid]; "highest FDA approval status" [color=blue, height=0.5, label=string, - pos="1936,18", + pos="2143,18", width=1.0652]; food -> "highest FDA approval status" [color=blue, label="highest FDA approval status", - lp="1925.5,61.5", - pos="e,1907.4,30.049 930.18,92.571 935.55,90.303 941.37,88.24 946.99,87 1118.3,49.252 1561.8,89.581 1736,69 1805.1,60.837 1822.1,55.207 \ -1889,36 1891.9,35.164 1894.9,34.241 1897.9,33.269", + lp="2167.5,61.5", + pos="e,2117.8,31.92 1040.2,92.555 1045.5,90.287 1051.4,88.229 1057,87 1265,41.588 1806.1,110.38 2015,69 2048,62.463 2083.5,47.961 2108.7,\ +36.25", style=solid]; "named thing_category" [color=blue, height=0.5, label="named thing", - pos="1026,105", + pos="1136,105", width=1.9318]; } diff --git a/graphviz/food.svg b/graphviz/food.svg index effb3caf10..0b74393793 100644 --- a/graphviz/food.svg +++ b/graphviz/food.svg @@ -4,16 +4,16 @@ - + %3 - + food - -food + +food @@ -24,9 +24,9 @@ food->chemical mixture - - -is_a + + +is_a @@ -37,9 +37,9 @@ food->id - - -id + + +id @@ -50,9 +50,9 @@ food->iri - - -iri + + +iri @@ -63,9 +63,9 @@ food->type - - -type + + +type @@ -76,9 +76,9 @@ food->name - - -name + + +name @@ -89,9 +89,9 @@ food->description - - -description + + +description @@ -102,9 +102,9 @@ food->source - - -source + + +source @@ -115,9 +115,9 @@ food->provided by - - -provided by + + +provided by @@ -128,9 +128,9 @@ food->has attribute - - -has attribute + + +has attribute @@ -141,9 +141,9 @@ food->category - - -category + + +category @@ -154,9 +154,9 @@ food->trade name - - -trade name + + +trade name @@ -167,41 +167,67 @@ food->available from - - -available from + + +available from - + +max tolerated dose + +string + + + +food->max tolerated dose + + +max tolerated dose + + + +is toxic + +boolean + + + +food->is toxic + + +is toxic + + + is supplement - -chemical mixture + +chemical mixture - + food->is supplement - - -is supplement + + +is supplement - + highest FDA approval status - -string + +string - + food->highest FDA approval status - - -highest FDA approval status + + +highest FDA approval status named thing_category - -named thing + +named thing diff --git a/graphviz/food_additive.gv b/graphviz/food_additive.gv index 5883142ecc..8e8cf60535 100644 --- a/graphviz/food_additive.gv +++ b/graphviz/food_additive.gv @@ -1,16 +1,16 @@ digraph { - graph [bb="0,0,1662.2,123"]; + graph [bb="0,0,1901.7,123"]; node [label="\N"]; "food additive" [height=0.5, label="food additive", - pos="759.89,105", + pos="889.89,105", width=1.9859]; "chemical entity" [height=0.5, pos="81.893,18", width=2.2748]; "food additive" -> "chemical entity" [label=is_a, - lp="328.89,61.5", - pos="e,133.36,32.105 689.82,101.37 601.88,97.407 446.6,88.224 314.89,69 256.16,60.427 190.07,45.759 143.33,34.52"]; + lp="321.89,61.5", + pos="e,131.75,32.407 818.31,103.32 708.13,101.46 490.6,94.542 307.89,69 250.91,61.034 186.98,46.34 141.69,34.934"]; id [color=blue, height=0.5, label=string, @@ -18,8 +18,9 @@ digraph { width=1.0652]; "food additive" -> id [color=blue, label=id, - lp="421.89,61.5", - pos="e,248.88,29.996 690.67,100.26 594.36,93.741 415.17,76.866 267.89,36 264.78,35.137 261.58,34.175 258.39,33.159", + lp="434.89,61.5", + pos="e,248.88,29.984 819.54,101.47 728.71,97.558 565.9,88.378 427.89,69 355.99,58.904 337.83,55.499 267.89,36 264.78,35.133 261.59,34.168 \ +258.39,33.151", style=solid]; iri [color=blue, height=0.5, @@ -28,9 +29,9 @@ digraph { width=1.2277]; "food additive" -> iri [color=blue, label=iri, - lp="527.89,61.5", - pos="e,354.18,29.946 697.26,96.243 648.7,89.898 579.81,80.169 519.89,69 454.92,56.888 438.69,53.271 374.89,36 371.31,35.031 367.62,33.979 \ -363.92,32.889", + lp="535.89,61.5", + pos="e,354.17,30.005 821.21,99.742 748.17,94.659 629.43,84.804 527.89,69 459.16,58.301 442.14,53.797 374.89,36 371.31,35.052 367.61,34.014 \ +363.9,32.933", style=solid]; type [color=blue, height=0.5, @@ -39,8 +40,8 @@ digraph { width=1.0652]; "food additive" -> type [color=blue, label=type, - lp="603.89,61.5", - pos="e,450.83,29.97 704.86,93.477 645.9,81.662 549.86,60.854 468.89,36 466.13,35.153 463.29,34.238 460.45,33.289", + lp="621.89,61.5", + pos="e,450.55,29.968 823.09,98.543 739.06,90.472 590.98,72.229 468.89,36 465.99,35.139 463.01,34.197 460.02,33.212", style=solid]; name [color=blue, height=0.5, @@ -49,8 +50,8 @@ digraph { width=1.5707]; "food additive" -> name [color=blue, label=name, - lp="680.89,61.5", - pos="e,570,32.261 721.98,89.677 682.67,74.828 621.26,51.628 579.61,35.893", + lp="720.89,61.5", + pos="e,572.48,31.607 830.8,94.767 793.35,88.495 744.03,79.457 700.89,69 660.47,59.2 615.31,45.409 582.31,34.792", style=solid]; description [color=blue, height=0.5, @@ -59,8 +60,8 @@ digraph { width=2.0943]; "food additive" -> description [color=blue, label=description, - lp="767.39,61.5", - pos="e,699.68,35.758 745.08,87.207 734.08,74.75 718.93,57.573 706.58,43.574", + lp="815.39,61.5", + pos="e,710.54,35.167 841.53,91.742 820.67,85.83 796.22,78.048 774.89,69 755.87,60.93 735.68,49.953 719.25,40.34", style=solid]; source [color=blue, height=0.5, @@ -69,8 +70,8 @@ digraph { width=1.5707]; "food additive" -> source [color=blue, label=source, - lp="845.89,61.5", - pos="e,829.68,36.066 788.86,88.525 797.05,83.147 805.48,76.544 811.89,69 817.7,62.169 822.34,53.628 825.89,45.547", + lp="889.89,61.5", + pos="e,845.74,35.758 879.03,87.207 871.12,74.983 860.27,58.214 851.3,44.362", style=solid]; "provided by" [color=blue, height=0.5, @@ -79,8 +80,8 @@ digraph { width=1.0291]; "food additive" -> "provided by" [color=blue, label="provided by", - lp="942.39,61.5", - pos="e,928.64,33.821 810.23,92.088 830.53,86.384 853.84,78.665 873.89,69 890.24,61.12 907.04,49.867 920.4,40.03", + lp="970.39,61.5", + pos="e,938.09,35.59 904.09,87.299 908.68,81.628 913.67,75.165 917.89,69 923.19,61.262 928.48,52.512 933.07,44.519", style=solid]; "has attribute" [color=blue, height=0.5, @@ -89,18 +90,17 @@ digraph { width=1.4443]; "food additive" -> "has attribute" [color=blue, label="has attribute", - lp="1061.9,61.5", - pos="e,1037.8,35.365 811.41,92.348 820.85,90.412 830.65,88.537 839.89,87 905.69,76.057 927.15,94.234 988.89,69 1004.1,62.786 1018.8,52.017 \ -1030.4,42.062", + lp="1078.9,61.5", + pos="e,1045.1,36.182 943.33,92.945 972.33,86.236 1004.7,77.378 1016.9,69 1026,62.769 1033.7,53.565 1039.7,44.747", style=solid]; category [height=0.5, pos="1174.9,18", width=1.4263]; "food additive" -> category [color=blue, label=category, - lp="1169.4,61.5", - pos="e,1159.8,35.666 810.48,92.104 820.2,90.145 830.33,88.325 839.89,87 900.12,78.66 1056.3,91.113 1112.9,69 1127.6,63.253 1141.5,52.675 \ -1152.5,42.724", + lp="1180.4,61.5", + pos="e,1164.5,35.889 940.97,92.373 950.55,90.412 960.5,88.522 969.89,87 1040.5,75.549 1066.3,101.73 1129.9,69 1141.1,63.217 1150.9,53.38 \ +1158.5,43.954", style=solid]; "trade name" [color=blue, height=0.5, @@ -109,9 +109,9 @@ digraph { width=2.2748]; "food additive" -> "trade name" [color=blue, label="trade name", - lp="1290.9,61.5", - pos="e,1295.5,34.982 810.04,92.062 819.89,90.081 830.18,88.264 839.89,87 1001,66.053 1046.4,104.53 1204.9,69 1233.2,62.663 1263.3,50.244 \ -1286.4,39.369", + lp="1297.9,61.5", + pos="e,1298,35.048 940.49,92.16 950.21,90.195 960.33,88.359 969.89,87 1078.4,71.571 1109.7,96.104 1215.9,69 1241.3,62.523 1268.1,50.468 \ +1288.9,39.818", style=solid]; "available from" [color=blue, height=0.5, @@ -120,13 +120,35 @@ digraph { width=3.2858]; "food additive" -> "available from" [color=blue, label="available from", - lp="1463.4,61.5", - pos="e,1492.7,34.326 809.6,92.047 819.58,90.041 830.03,88.218 839.89,87 1058.8,59.973 1117.3,98.928 1335.9,69 1386,62.134 1441.7,48.411 \ -1482.9,37.076", + lp="1467.4,61.5", + pos="e,1493.6,34.411 940.04,92.054 949.89,90.073 960.18,88.258 969.89,87 1134.5,65.682 1178.7,93.148 1342.9,69 1390.9,61.934 1444.2,48.408 \ +1483.9,37.204", + style=solid]; + "max tolerated dose" [color=blue, + height=0.5, + label=string, + pos="1718.9,18", + width=1.0652]; + "food additive" -> "max tolerated dose" [color=blue, + label="max tolerated dose", + lp="1674.9,61.5", + pos="e,1689.9,29.908 939.59,92.017 949.57,90.014 960.03,88.199 969.89,87 1214,57.327 1278.9,99.893 1522.9,69 1589.8,60.534 1606.1,54.617 \ +1670.9,36 1674,35.109 1677.2,34.126 1680.4,33.096", + style=solid]; + "is toxic" [color=blue, + height=0.5, + label=boolean, + pos="1854.9,18", + width=1.2999]; + "food additive" -> "is toxic" [color=blue, + label="is toxic", + lp="1815.9,61.5", + pos="e,1830.9,33.77 939.59,91.944 949.57,89.946 960.02,88.153 969.89,87 1141.7,66.94 1579.5,108.45 1747.9,69 1774,62.875 1801.4,49.934 \ +1822,38.753", style=solid]; "named thing_category" [color=blue, height=0.5, label="named thing", - pos="918.89,105", + pos="1048.9,105", width=1.9318]; } diff --git a/graphviz/food_additive.svg b/graphviz/food_additive.svg index 94d88b8717..97713947db 100644 --- a/graphviz/food_additive.svg +++ b/graphviz/food_additive.svg @@ -4,16 +4,16 @@ - + %3 - + food additive - -food additive + +food additive @@ -24,9 +24,9 @@ food additive->chemical entity - - -is_a + + +is_a @@ -37,9 +37,9 @@ food additive->id - - -id + + +id @@ -50,9 +50,9 @@ food additive->iri - - -iri + + +iri @@ -63,9 +63,9 @@ food additive->type - - -type + + +type @@ -76,9 +76,9 @@ food additive->name - - -name + + +name @@ -89,9 +89,9 @@ food additive->description - - -description + + +description @@ -102,9 +102,9 @@ food additive->source - - -source + + +source @@ -115,9 +115,9 @@ food additive->provided by - - -provided by + + +provided by @@ -128,9 +128,9 @@ food additive->has attribute - - -has attribute + + +has attribute @@ -141,9 +141,9 @@ food additive->category - - -category + + +category @@ -154,9 +154,9 @@ food additive->trade name - - -trade name + + +trade name @@ -167,15 +167,41 @@ food additive->available from - - -available from + + +available from + + + +max tolerated dose + +string + + + +food additive->max tolerated dose + + +max tolerated dose + + + +is toxic + +boolean + + + +food additive->is toxic + + +is toxic named thing_category - -named thing + +named thing diff --git a/graphviz/macronutrient.gv b/graphviz/macronutrient.gv index 867f3435e0..fb848841c5 100644 --- a/graphviz/macronutrient.gv +++ b/graphviz/macronutrient.gv @@ -1,16 +1,16 @@ digraph { - graph [bb="0,0,1596,123"]; + graph [bb="0,0,1835.5,123"]; node [label="\N"]; macronutrient [height=0.5, label=macronutrient, - pos="693.75,105", + pos="823.75,105", width=2.1484]; nutrient [height=0.5, pos="48.746,18", width=1.354]; macronutrient -> nutrient [label=is_a, - lp="262.75,61.5", - pos="e,84.832,30.148 617.76,101.49 528.85,97.751 377.41,88.895 248.75,69 195.11,60.706 134.83,44.693 94.611,33.016"]; + lp="255.75,61.5", + pos="e,84.212,30.556 746.55,103.76 634.66,102.41 421.16,96.098 241.75,69 190.38,61.242 132.9,45.394 94.139,33.609"]; id [color=blue, height=0.5, label=string, @@ -18,8 +18,9 @@ digraph { width=1.0652]; macronutrient -> id [color=blue, label=id, - lp="355.75,61.5", - pos="e,182.73,29.996 619.15,99.887 521.66,93.114 346.32,76.116 201.75,36 198.64,35.137 195.44,34.175 192.24,33.159", + lp="368.75,61.5", + pos="e,182.73,29.984 747.8,101.22 655.99,97.183 496.96,87.987 361.75,69 289.84,58.904 271.69,55.499 201.75,36 198.64,35.133 195.44,34.168 \ +192.24,33.151", style=solid]; iri [color=blue, height=0.5, @@ -28,9 +29,9 @@ digraph { width=1.2277]; macronutrient -> iri [color=blue, label=iri, - lp="461.75,61.5", - pos="e,288.04,29.946 627.3,95.743 578.99,89.393 512.11,79.88 453.75,69 388.77,56.888 372.54,53.271 308.75,36 305.17,35.031 301.47,33.979 \ -297.77,32.889", + lp="469.75,61.5", + pos="e,288.02,30.005 749.94,99.383 676.56,94.202 560.94,84.44 461.75,69 393.01,58.301 375.99,53.797 308.75,36 305.16,35.052 301.46,34.014 \ +297.76,32.933", style=solid]; type [color=blue, height=0.5, @@ -39,8 +40,8 @@ digraph { width=1.0652]; macronutrient -> type [color=blue, label=type, - lp="537.75,61.5", - pos="e,384.68,29.97 635.98,92.928 576.81,81.024 482.47,60.473 402.75,36 399.98,35.153 397.15,34.238 394.3,33.289", + lp="555.75,61.5", + pos="e,384.4,29.968 752.11,98.074 667.32,89.776 522.52,71.545 402.75,36 399.84,35.139 396.86,34.197 393.87,33.212", style=solid]; name [color=blue, height=0.5, @@ -49,8 +50,8 @@ digraph { width=1.5707]; macronutrient -> name [color=blue, label=name, - lp="614.75,61.5", - pos="e,503.96,32.304 655.07,89.388 615.75,74.535 554.9,51.546 513.52,35.914", + lp="654.75,61.5", + pos="e,506.33,31.607 761.24,94.193 724.25,87.95 676.58,79.142 634.75,69 594.32,59.2 549.16,45.409 516.16,34.792", style=solid]; description [color=blue, height=0.5, @@ -59,8 +60,8 @@ digraph { width=2.0943]; macronutrient -> description [color=blue, label=description, - lp="701.25,61.5", - pos="e,633.53,35.758 678.93,87.207 667.94,74.75 652.78,57.573 640.43,43.574", + lp="749.25,61.5", + pos="e,644.39,35.167 773.68,91.259 753.2,85.408 729.49,77.803 708.75,69 689.73,60.93 669.53,49.953 653.1,40.34", style=solid]; source [color=blue, height=0.5, @@ -69,8 +70,8 @@ digraph { width=1.5707]; macronutrient -> source [color=blue, label=source, - lp="779.75,61.5", - pos="e,763.54,36.066 723.25,88.169 731.27,82.856 739.47,76.378 745.75,69 751.55,62.169 756.2,53.628 759.74,45.547", + lp="823.75,61.5", + pos="e,779.67,35.885 812.62,86.799 804.74,74.622 794.04,58.089 785.18,44.398", style=solid]; "provided by" [color=blue, height=0.5, @@ -79,8 +80,8 @@ digraph { width=1.0291]; macronutrient -> "provided by" [color=blue, label="provided by", - lp="876.25,61.5", - pos="e,862.5,33.821 745.79,91.606 765.68,85.952 788.26,78.395 807.75,69 824.09,61.12 840.89,49.867 854.25,40.03", + lp="904.25,61.5", + pos="e,871.94,35.59 837.94,87.299 842.53,81.628 847.53,75.165 851.75,69 857.04,61.262 862.33,52.512 866.92,44.519", style=solid]; "has attribute" [color=blue, height=0.5, @@ -89,18 +90,17 @@ digraph { width=1.4443]; macronutrient -> "has attribute" [color=blue, label="has attribute", - lp="995.75,61.5", - pos="e,971.68,35.337 749.62,92.366 759.63,90.45 769.98,88.578 779.75,87 842.98,76.783 863.51,93.381 922.75,69 937.94,62.748 952.64,51.976 \ -964.2,42.027", + lp="1012.7,61.5", + pos="e,978.96,36.182 879.54,92.396 907.91,85.757 938.86,77.151 950.75,69 959.83,62.769 967.55,53.565 973.55,44.747", style=solid]; category [height=0.5, pos="1108.7,18", width=1.4263]; macronutrient -> category [color=blue, label=category, - lp="1103.2,61.5", - pos="e,1093.7,35.658 748.17,92.152 758.61,90.189 769.49,88.354 779.75,87 838.7,79.218 991.37,90.67 1046.7,69 1061.5,63.242 1075.4,52.663 \ -1086.3,42.714", + lp="1114.2,61.5", + pos="e,1098.3,35.869 879.15,92.382 889.3,90.443 899.82,88.558 909.75,87 977.82,76.31 1002.5,100.65 1063.7,69 1075,63.192 1084.8,53.352 \ +1092.3,43.93", style=solid]; "trade name" [color=blue, height=0.5, @@ -109,9 +109,9 @@ digraph { width=2.2748]; macronutrient -> "trade name" [color=blue, label="trade name", - lp="1224.7,61.5", - pos="e,1229.4,34.975 747.69,92.095 758.27,90.112 769.32,88.285 779.75,87 938.3,67.459 982.87,104.02 1138.7,69 1167,62.651 1197.1,50.232 \ -1220.2,39.36", + lp="1231.7,61.5", + pos="e,1231.8,35.033 878.63,92.128 888.94,90.191 899.64,88.373 909.75,87 1015.7,72.602 1046.1,95.541 1149.7,69 1175.1,62.5 1201.9,50.444 \ +1222.7,39.8", style=solid]; "available from" [color=blue, height=0.5, @@ -120,13 +120,35 @@ digraph { width=3.2858]; macronutrient -> "available from" [color=blue, label="available from", - lp="1397.2,61.5", - pos="e,1426.6,34.32 747.67,91.984 758.26,90.01 769.31,88.215 779.75,87 996.21,61.791 1053.8,98.614 1269.7,69 1319.9,62.123 1375.6,48.4 \ -1416.7,37.069", + lp="1401.2,61.5", + pos="e,1427.5,34.4 877.69,92.086 888.27,90.103 899.32,88.279 909.75,87 1071.8,67.112 1115.2,92.824 1276.7,69 1324.8,61.915 1378.1,48.39 \ +1417.7,37.191", + style=solid]; + "max tolerated dose" [color=blue, + height=0.5, + label=string, + pos="1652.7,18", + width=1.0652]; + macronutrient -> "max tolerated dose" [color=blue, + label="max tolerated dose", + lp="1608.7,61.5", + pos="e,1623.7,29.908 877.67,91.952 888.26,89.981 899.31,88.195 909.75,87 1151.4,59.324 1215.4,99.601 1456.7,69 1523.6,60.522 1540,54.617 \ +1604.7,36 1607.8,35.109 1611,34.126 1614.2,33.096", + style=solid]; + "is toxic" [color=blue, + height=0.5, + label=boolean, + pos="1788.7,18", + width=1.2999]; + macronutrient -> "is toxic" [color=blue, + label="is toxic", + lp="1749.7,61.5", + pos="e,1764.7,33.768 877.2,91.957 887.93,89.959 899.16,88.161 909.75,87 1080.3,68.292 1514.7,108.16 1681.7,69 1707.9,62.873 1735.3,49.932 \ +1755.8,38.751", style=solid]; "named thing_category" [color=blue, height=0.5, label="named thing", - pos="858.75,105", + pos="988.75,105", width=1.9318]; } diff --git a/graphviz/macronutrient.svg b/graphviz/macronutrient.svg index 2d5a0eec3c..967a9aa7d8 100644 --- a/graphviz/macronutrient.svg +++ b/graphviz/macronutrient.svg @@ -4,16 +4,16 @@ - + %3 - + macronutrient - -macronutrient + +macronutrient @@ -24,9 +24,9 @@ macronutrient->nutrient - - -is_a + + +is_a @@ -37,9 +37,9 @@ macronutrient->id - - -id + + +id @@ -50,9 +50,9 @@ macronutrient->iri - - -iri + + +iri @@ -63,9 +63,9 @@ macronutrient->type - - -type + + +type @@ -76,9 +76,9 @@ macronutrient->name - - -name + + +name @@ -89,9 +89,9 @@ macronutrient->description - - -description + + +description @@ -102,9 +102,9 @@ macronutrient->source - - -source + + +source @@ -115,9 +115,9 @@ macronutrient->provided by - - -provided by + + +provided by @@ -128,9 +128,9 @@ macronutrient->has attribute - - -has attribute + + +has attribute @@ -141,9 +141,9 @@ macronutrient->category - - -category + + +category @@ -154,9 +154,9 @@ macronutrient->trade name - - -trade name + + +trade name @@ -167,15 +167,41 @@ macronutrient->available from - - -available from + + +available from + + + +max tolerated dose + +string + + + +macronutrient->max tolerated dose + + +max tolerated dose + + + +is toxic + +boolean + + + +macronutrient->is toxic + + +is toxic named thing_category - -named thing + +named thing diff --git a/graphviz/microRNA.gv b/graphviz/microRNA.gv index 7e8bcad04f..faeb826b99 100644 --- a/graphviz/microRNA.gv +++ b/graphviz/microRNA.gv @@ -1,16 +1,16 @@ digraph { - graph [bb="0,0,2496.7,123"]; + graph [bb="0,0,2703.7,123"]; node [label="\N"]; microRNA [height=0.5, label=microRNA, - pos="1134.5,105", + pos="1254.5,105", width=1.6068]; "noncoding RNA product" [height=0.5, pos="121.54,18", width=3.3761]; microRNA -> "noncoding RNA product" [label=is_a, - lp="401.54,61.5", - pos="e,184.58,33.411 1076.7,104.02 950.87,103.47 643.19,98.87 387.54,69 321.77,61.316 247.81,46.941 194.6,35.57"]; + lp="398.54,61.5", + pos="e,183.58,33.479 1196.5,104.62 1056.5,105.46 688.85,103.85 384.54,69 319.36,61.535 246.1,47.101 193.49,35.653"]; id [color=blue, height=0.5, label=string, @@ -18,9 +18,9 @@ digraph { width=1.0652]; microRNA -> id [color=blue, label=id, - lp="514.54,61.5", - pos="e,328.53,29.984 1076.8,103.62 965.96,102.26 715.92,96.154 507.54,69 435.54,59.618 417.48,55.499 347.54,36 344.43,35.133 341.23,34.168 \ -338.03,33.151", + lp="513.54,61.5", + pos="e,328.53,29.979 1196.6,104.39 1070.5,104.57 762.24,101.31 506.54,69 434.94,59.952 417.05,55.425 347.54,36 344.43,35.132 341.23,34.165 \ +338.04,33.146", style=solid]; iri [color=blue, height=0.5, @@ -29,8 +29,8 @@ digraph { width=1.2277]; microRNA -> iri [color=blue, label=iri, - lp="603.54,61.5", - pos="e,433.92,29.82 1076.8,103.37 977.76,101.59 769.46,94.818 595.54,69 542.43,61.116 482.84,44.688 443.67,32.81", + lp="601.54,61.5", + pos="e,433.9,30.049 1196.3,104.43 1080.7,104.5 814.49,100.81 593.54,69 541.18,61.461 482.54,45.101 443.79,33.141", style=solid]; type [color=blue, height=0.5, @@ -40,7 +40,7 @@ digraph { microRNA -> type [color=blue, label=type, lp="708.54,61.5", - pos="e,530.19,29.989 1077.4,102.14 992.83,98.797 829.69,90.029 692.54,69 627.64,59.049 611.53,54.534 548.54,36 545.64,35.146 542.65,34.209 \ + pos="e,530.19,29.989 1196.8,103.5 1094.6,101.93 875.4,95.466 692.54,69 627.56,59.595 611.53,54.534 548.54,36 545.64,35.146 542.65,34.209 \ 539.66,33.227", style=solid]; name [color=blue, @@ -50,8 +50,8 @@ digraph { width=1.5707]; microRNA -> name [color=blue, label=name, - lp="811.54,61.5", - pos="e,652.06,31.655 1078,101.24 1009.6,97.219 891.35,88.04 791.54,69 746.81,60.468 697,45.928 661.64,34.72", + lp="812.54,61.5", + pos="e,651.54,31.719 1196.8,103.29 1108.9,101.38 936.51,94.415 792.54,69 747.18,60.992 696.74,46.25 661.17,34.84", style=solid]; description [color=blue, height=0.5, @@ -60,8 +60,8 @@ digraph { width=2.0943]; microRNA -> description [color=blue, label=description, - lp="916.04,61.5", - pos="e,793.34,34.764 1078,101.07 1024.9,97.214 943.59,88.478 875.54,69 850.34,61.788 823.51,49.83 802.54,39.417", + lp="918.04,61.5", + pos="e,793.33,34.87 1196.7,104.39 1121.8,103.59 987.91,97.721 877.54,69 851.5,62.223 823.85,50.083 802.41,39.462", style=solid]; source [color=blue, height=0.5, @@ -70,8 +70,8 @@ digraph { width=1.5707]; microRNA -> source [color=blue, label=source, - lp="1008.5,61.5", - pos="e,932.9,35.187 1082.6,97.017 1052.9,91.787 1015.6,83.05 984.54,69 969.06,61.999 953.52,51.348 941.02,41.673", + lp="1015.5,61.5", + pos="e,933.81,35.006 1196.9,103.58 1142.4,101.51 1059.2,93.997 991.54,69 973.83,62.455 956.03,51.266 942.01,41.13", style=solid]; "provided by" [color=blue, height=0.5, @@ -80,8 +80,8 @@ digraph { width=1.0291]; microRNA -> "provided by" [color=blue, label="provided by", - lp="1088,61.5", - pos="e,1029.4,36.214 1088.7,94.003 1073.3,88.731 1057.2,80.808 1045.5,69 1039.3,62.709 1035.1,54.176 1032.2,45.94", + lp="1100,61.5", + pos="e,1032.8,36.035 1199.5,99.261 1149.5,94.061 1080.2,84.351 1057.5,69 1048.9,63.129 1042.2,53.953 1037.3,45.055", style=solid]; "has attribute" [color=blue, height=0.5, @@ -90,16 +90,16 @@ digraph { width=1.4443]; microRNA -> "has attribute" [color=blue, label="has attribute", - lp="1181.5,61.5", - pos="e,1133.7,36.175 1134.3,86.799 1134.2,75.163 1134,59.548 1133.9,46.237", + lp="1203.5,61.5", + pos="e,1137.8,36.353 1206.3,94.979 1189,89.765 1170.3,81.627 1156.5,69 1149.8,62.786 1144.8,54.17 1141.3,45.84", style=solid]; category [height=0.5, pos="1254.5,18", width=1.4263]; microRNA -> category [color=blue, label=category, - lp="1275,61.5", - pos="e,1250.6,36.344 1176.7,92.567 1199.2,85.765 1224,76.94 1232.5,69 1239.2,62.776 1244,54.158 1247.3,45.829", + lp="1286,61.5", + pos="e,1254.5,36.175 1254.5,86.799 1254.5,75.163 1254.5,59.548 1254.5,46.237", style=solid]; "trade name" [color=blue, height=0.5, @@ -108,9 +108,8 @@ digraph { width=2.2748]; microRNA -> "trade name" [color=blue, label="trade name", - lp="1387.5,61.5", - pos="e,1380.3,35.15 1176.7,92.55 1184.6,90.572 1192.8,88.63 1200.5,87 1249,76.811 1263.6,84.74 1310.5,69 1331.8,61.89 1354,50.45 1371.6,\ -40.306", + lp="1388.5,61.5", + pos="e,1379.3,35.143 1283.4,89.359 1295.3,83.217 1309.2,75.909 1321.5,69 1337.7,59.957 1355.4,49.52 1370.4,40.529", style=solid]; "available from" [color=blue, height=0.5, @@ -119,68 +118,90 @@ digraph { width=3.2858]; microRNA -> "available from" [color=blue, label="available from", - lp="1553,61.5", - pos="e,1574.6,34.397 1175.5,92.27 1183.7,90.245 1192.4,88.359 1200.5,87 1302.6,70.037 1330.6,86.164 1432.5,69 1477.5,61.428 1527.4,48.213 \ -1564.9,37.27", + lp="1549,61.5", + pos="e,1571.5,34.202 1296.7,92.523 1304.6,90.548 1312.8,88.614 1320.5,87 1370.3,76.646 1383.8,79.484 1433.5,69 1476.7,59.899 1524.8,47.219 \ +1561.8,36.906", + style=solid]; + "max tolerated dose" [color=blue, + height=0.5, + label=string, + pos="1798.5,18", + width=1.0652]; + microRNA -> "max tolerated dose" [color=blue, + label="max tolerated dose", + lp="1755.5,61.5", + pos="e,1769.5,29.895 1295.5,92.178 1303.7,90.161 1312.4,88.301 1320.5,87 1445.4,67.138 1479.4,86.999 1604.5,69 1670.4,59.533 1686.6,54.47 \ +1750.5,36 1753.6,35.104 1756.8,34.118 1760,33.086", + style=solid]; + "is toxic" [color=blue, + height=0.5, + label=boolean, + pos="1901.5,18", + width=1.2999]; + microRNA -> "is toxic" [color=blue, + label="is toxic", + lp="1885.5,61.5", + pos="e,1884.5,34.877 1295.1,92.083 1303.4,90.047 1312.2,88.204 1320.5,87 1432.3,70.817 1721.2,104.32 1828.5,69 1846.2,63.193 1863.4,51.719 \ +1876.7,41.225", style=solid]; "is metabolite" [color=blue, height=0.5, label=boolean, - pos="1806.5,18", + pos="2013.5,18", width=1.2999]; microRNA -> "is metabolite" [color=blue, label="is metabolite", - lp="1733.5,61.5", - pos="e,1772,30.231 1175.1,92.14 1183.5,90.099 1192.2,88.24 1200.5,87 1380.1,60.218 1428.7,93.648 1608.5,69 1662.3,61.632 1722.5,45.206 \ -1762.3,33.184", + lp="2002.5,61.5", + pos="e,1991.3,33.958 1295.1,92.049 1303.4,90.016 1312.2,88.182 1320.5,87 1451.5,68.388 1787.4,101.86 1915.5,69 1939.4,62.884 1964.1,50.25 \ +1982.7,39.213", style=solid]; "in taxon" [color=blue, height=0.5, label="organism taxon", - pos="1954.5,18", + pos="2161.5,18", width=2.3109]; microRNA -> "in taxon" [color=blue, label="in taxon", - lp="1880.5,61.5", - pos="e,1914.7,33.874 1175.1,92.053 1183.4,90.019 1192.2,88.184 1200.5,87 1457.6,50.39 1528.1,109.97 1784.5,69 1826,62.374 1871.6,48.595 \ -1905.1,37.177", + lp="2126.5,61.5", + pos="e,2134.7,35.212 1295.1,92.012 1303.4,89.982 1312.2,88.158 1320.5,87 1481.9,64.534 1894.9,106 2053.5,69 2078.8,63.101 2105.3,50.934 \ +2125.8,40.079", style=solid]; "has biological sequence" [color=blue, height=0.5, label="biological sequence", - pos="2157.5,18", + pos="2364.5,18", width=2.8164]; microRNA -> "has biological sequence" [color=blue, label="has biological sequence", - lp="2086,61.5", - pos="e,2102.3,33.242 1175.1,92.017 1183.4,89.986 1192.2,88.161 1200.5,87 1514.5,43.184 1598.6,104.96 1913.5,69 1974.8,62.002 2043.6,47.274 \ -2092.5,35.606", + lp="2324,61.5", + pos="e,2316.2,33.945 1295.1,91.992 1303.4,89.963 1312.2,88.145 1320.5,87 1690,36.146 1789.7,117.48 2159.5,69 2209.9,62.402 2265.8,48.296 \ +2306.5,36.744", style=solid]; synonym [color=blue, height=0.5, label="label type", - pos="2333.5,18", + pos="2540.5,18", width=1.5707]; microRNA -> synonym [color=blue, label=synonym, - lp="2269.5,61.5", - pos="e,2300.1,32.603 1175.1,91.973 1183.4,89.945 1192.2,88.133 1200.5,87 1415,57.802 1960.9,103.83 2174.5,69 2214.9,62.419 2259.2,47.858 \ -2290.7,36.137", + lp="2495.5,61.5", + pos="e,2511.9,33.582 1294.7,92.045 1303.2,89.984 1312.1,88.141 1320.5,87 1440.8,70.753 2293.5,92.447 2412.5,69 2444.1,62.787 2477.9,49.257 \ +2502.8,37.836", style=solid]; xref [color=blue, height=0.5, label="iri type", - pos="2452.5,18", + pos="2659.5,18", width=1.2277]; microRNA -> xref [color=blue, label=xref, - lp="2378,61.5", - pos="e,2423.7,31.819 1174.7,92.044 1183.2,89.983 1192.1,88.14 1200.5,87 1443.9,54.143 2063.6,111.05 2305.5,69 2343.6,62.386 2385.1,47.509 \ -2414.3,35.693", + lp="2596,61.5", + pos="e,2632.9,32.649 1294.7,92.035 1303.2,89.975 1312.1,88.134 1320.5,87 1453.9,69.091 2399.5,94.894 2531.5,69 2563.9,62.65 2598.7,48.564 \ +2623.8,36.956", style=solid]; "named thing_category" [color=blue, height=0.5, label="named thing", - pos="1279.5,105", + pos="1399.5,105", width=1.9318]; } diff --git a/graphviz/microRNA.svg b/graphviz/microRNA.svg index 5eb13bbb2e..a1bffab3e4 100644 --- a/graphviz/microRNA.svg +++ b/graphviz/microRNA.svg @@ -4,16 +4,16 @@ - + %3 - + microRNA - -microRNA + +microRNA @@ -24,9 +24,9 @@ microRNA->noncoding RNA product - - -is_a + + +is_a @@ -37,9 +37,9 @@ microRNA->id - + -id +id @@ -50,9 +50,9 @@ microRNA->iri - - -iri + + +iri @@ -63,7 +63,7 @@ microRNA->type - + type @@ -76,9 +76,9 @@ microRNA->name - - -name + + +name @@ -89,9 +89,9 @@ microRNA->description - - -description + + +description @@ -102,9 +102,9 @@ microRNA->source - - -source + + +source @@ -115,9 +115,9 @@ microRNA->provided by - - -provided by + + +provided by @@ -128,9 +128,9 @@ microRNA->has attribute - - -has attribute + + +has attribute @@ -141,9 +141,9 @@ microRNA->category - - -category + + +category @@ -154,9 +154,9 @@ microRNA->trade name - - -trade name + + +trade name @@ -167,80 +167,106 @@ microRNA->available from - - -available from + + +available from - + +max tolerated dose + +string + + + +microRNA->max tolerated dose + + +max tolerated dose + + + +is toxic + +boolean + + + +microRNA->is toxic + + +is toxic + + + is metabolite - -boolean + +boolean - + microRNA->is metabolite - - -is metabolite + + +is metabolite - + in taxon - -organism taxon + +organism taxon - + microRNA->in taxon - - -in taxon + + +in taxon - + has biological sequence - -biological sequence + +biological sequence - + microRNA->has biological sequence - - -has biological sequence + + +has biological sequence - + synonym - -label type + +label type - + microRNA->synonym - - -synonym + + +synonym - + xref - -iri type + +iri type - + microRNA->xref - - -xref + + +xref named thing_category - -named thing + +named thing diff --git a/graphviz/micronutrient.gv b/graphviz/micronutrient.gv index 5a76450f5c..d15adf4ce9 100644 --- a/graphviz/micronutrient.gv +++ b/graphviz/micronutrient.gv @@ -1,16 +1,16 @@ digraph { - graph [bb="0,0,1596,123"]; + graph [bb="0,0,1835.5,123"]; node [label="\N"]; micronutrient [height=0.5, label=micronutrient, - pos="693.75,105", + pos="823.75,105", width=2.0943]; nutrient [height=0.5, pos="48.746,18", width=1.354]; micronutrient -> nutrient [label=is_a, - lp="262.75,61.5", - pos="e,84.832,30.148 619.73,101.57 531.1,97.882 378.37,89.043 248.75,69 195.11,60.706 134.83,44.693 94.611,33.016"]; + lp="255.75,61.5", + pos="e,84.212,30.556 748.42,103.78 637.04,102.48 422.16,96.249 241.75,69 190.38,61.242 132.9,45.394 94.139,33.609"]; id [color=blue, height=0.5, label=string, @@ -18,8 +18,9 @@ digraph { width=1.0652]; micronutrient -> id [color=blue, label=id, - lp="355.75,61.5", - pos="e,182.73,29.996 621.24,100.03 524.18,93.357 347.36,76.405 201.75,36 198.64,35.137 195.44,34.175 192.24,33.159", + lp="368.75,61.5", + pos="e,182.73,29.984 749.82,101.31 658.34,97.318 497.96,88.127 361.75,69 289.84,58.904 271.69,55.499 201.75,36 198.64,35.133 195.44,34.168 \ +192.24,33.151", style=solid]; iri [color=blue, height=0.5, @@ -28,9 +29,9 @@ digraph { width=1.2277]; micronutrient -> iri [color=blue, label=iri, - lp="461.75,61.5", - pos="e,288.04,29.946 628.58,95.912 580.18,89.561 512.63,79.976 453.75,69 388.77,56.888 372.54,53.271 308.75,36 305.17,35.031 301.47,33.979 \ -297.77,32.889", + lp="469.75,61.5", + pos="e,288.02,30.005 751.66,99.505 678.38,94.355 561.72,84.561 461.75,69 393.01,58.301 375.99,53.797 308.75,36 305.16,35.052 301.46,34.014 \ +297.76,32.933", style=solid]; type [color=blue, height=0.5, @@ -39,8 +40,8 @@ digraph { width=1.0652]; micronutrient -> type [color=blue, label=type, - lp="537.75,61.5", - pos="e,384.68,29.97 636.81,93.094 577.7,81.215 482.85,60.588 402.75,36 399.98,35.153 397.15,34.238 394.3,33.289", + lp="555.75,61.5", + pos="e,384.4,29.968 753.61,98.221 669.04,89.991 523.23,71.755 402.75,36 399.84,35.139 396.86,34.197 393.87,33.212", style=solid]; name [color=blue, height=0.5, @@ -49,8 +50,8 @@ digraph { width=1.5707]; micronutrient -> name [color=blue, label=name, - lp="614.75,61.5", - pos="e,503.68,32.198 655.32,89.485 615.93,74.604 554.73,51.483 513.25,35.814", + lp="654.75,61.5", + pos="e,506.33,31.607 762.53,94.41 725.36,88.155 677.07,79.26 634.75,69 594.32,59.2 549.16,45.409 516.16,34.792", style=solid]; description [color=blue, height=0.5, @@ -59,8 +60,8 @@ digraph { width=2.0943]; micronutrient -> description [color=blue, label=description, - lp="701.25,61.5", - pos="e,633.53,35.758 678.93,87.207 667.94,74.75 652.78,57.573 640.43,43.574", + lp="749.25,61.5", + pos="e,644.39,35.167 774.25,91.421 753.64,85.549 729.69,77.885 708.75,69 689.73,60.93 669.53,49.953 653.1,40.34", style=solid]; source [color=blue, height=0.5, @@ -69,8 +70,8 @@ digraph { width=1.5707]; micronutrient -> source [color=blue, label=source, - lp="779.75,61.5", - pos="e,763.54,36.066 722.98,88.347 731.09,83.002 739.4,76.461 745.75,69 751.55,62.169 756.2,53.628 759.74,45.547", + lp="823.75,61.5", + pos="e,779.67,35.885 812.62,86.799 804.74,74.622 794.04,58.089 785.18,44.398", style=solid]; "provided by" [color=blue, height=0.5, @@ -79,8 +80,8 @@ digraph { width=1.0291]; micronutrient -> "provided by" [color=blue, label="provided by", - lp="876.25,61.5", - pos="e,862.5,33.821 745.22,91.768 765.25,86.097 788.07,78.485 807.75,69 824.09,61.12 840.89,49.867 854.25,40.03", + lp="904.25,61.5", + pos="e,871.94,35.59 837.94,87.299 842.53,81.628 847.53,75.165 851.75,69 857.04,61.262 862.33,52.512 866.92,44.519", style=solid]; "has attribute" [color=blue, height=0.5, @@ -89,18 +90,17 @@ digraph { width=1.4443]; micronutrient -> "has attribute" [color=blue, label="has attribute", - lp="995.75,61.5", - pos="e,971.68,35.347 747.86,92.418 757.78,90.475 768.05,88.58 777.75,87 841.84,76.552 862.67,93.665 922.75,69 937.94,62.761 952.64,51.99 \ -964.21,42.039", + lp="1012.7,61.5", + pos="e,978.96,36.182 878.53,92.632 907.17,85.962 938.72,77.248 950.75,69 959.83,62.769 967.55,53.565 973.55,44.747", style=solid]; category [height=0.5, pos="1108.7,18", width=1.4263]; micronutrient -> category [color=blue, label=category, - lp="1103.2,61.5", - pos="e,1093.7,35.661 746.89,92.136 757.09,90.174 767.72,88.344 777.75,87 837.13,79.04 990.95,90.818 1046.7,69 1061.5,63.246 1075.4,52.667 \ -1086.3,42.717", + lp="1114.2,61.5", + pos="e,1098.3,35.876 877.85,92.349 887.77,90.413 898.05,88.538 907.75,87 976.68,76.068 1001.7,101.01 1063.7,69 1075,63.201 1084.8,53.362 \ +1092.3,43.938", style=solid]; "trade name" [color=blue, height=0.5, @@ -109,9 +109,9 @@ digraph { width=2.2748]; micronutrient -> "trade name" [color=blue, label="trade name", - lp="1224.7,61.5", - pos="e,1229.4,34.977 746.42,92.084 756.76,90.101 767.56,88.277 777.75,87 937.14,67.011 982,104.19 1138.7,69 1167,62.655 1197.1,50.236 \ -1220.2,39.363", + lp="1231.7,61.5", + pos="e,1231.8,35.038 876.9,92.196 887.1,90.228 897.72,88.381 907.75,87 1014.6,72.274 1045.3,95.729 1149.7,69 1175.1,62.508 1201.9,50.452 \ +1222.7,39.806", style=solid]; "available from" [color=blue, height=0.5, @@ -120,13 +120,35 @@ digraph { width=3.2858]; micronutrient -> "available from" [color=blue, label="available from", - lp="1397.2,61.5", - pos="e,1426.6,34.322 746.41,91.976 756.75,90.003 767.55,88.21 777.75,87 995.03,61.212 1053,98.719 1269.7,69 1319.9,62.126 1375.6,48.404 \ -1416.7,37.071", + lp="1401.2,61.5", + pos="e,1427.5,34.403 876.42,92.075 886.76,90.093 897.56,88.272 907.75,87 1070.7,66.657 1114.3,92.932 1276.7,69 1324.8,61.922 1378.1,48.396 \ +1417.7,37.195", + style=solid]; + "max tolerated dose" [color=blue, + height=0.5, + label=string, + pos="1652.7,18", + width=1.0652]; + micronutrient -> "max tolerated dose" [color=blue, + label="max tolerated dose", + lp="1608.7,61.5", + pos="e,1623.7,29.908 876.4,91.945 886.75,89.974 897.55,88.191 907.75,87 1150.2,58.689 1214.6,99.698 1456.7,69 1523.6,60.526 1540,54.617 \ +1604.7,36 1607.8,35.109 1611,34.126 1614.2,33.096", + style=solid]; + "is toxic" [color=blue, + height=0.5, + label=boolean, + pos="1788.7,18", + width=1.2999]; + micronutrient -> "is toxic" [color=blue, + label="is toxic", + lp="1749.7,61.5", + pos="e,1764.7,33.769 875.95,91.953 886.42,89.955 897.4,88.159 907.75,87 1078.7,67.862 1514.2,108.26 1681.7,69 1707.9,62.874 1735.3,49.933 \ +1755.8,38.752", style=solid]; "named thing_category" [color=blue, height=0.5, label="named thing", - pos="856.75,105", + pos="986.75,105", width=1.9318]; } diff --git a/graphviz/micronutrient.svg b/graphviz/micronutrient.svg index cb98e6533f..611cf7267f 100644 --- a/graphviz/micronutrient.svg +++ b/graphviz/micronutrient.svg @@ -4,16 +4,16 @@ - + %3 - + micronutrient - -micronutrient + +micronutrient @@ -24,9 +24,9 @@ micronutrient->nutrient - - -is_a + + +is_a @@ -37,9 +37,9 @@ micronutrient->id - - -id + + +id @@ -50,9 +50,9 @@ micronutrient->iri - - -iri + + +iri @@ -63,9 +63,9 @@ micronutrient->type - - -type + + +type @@ -76,9 +76,9 @@ micronutrient->name - - -name + + +name @@ -89,9 +89,9 @@ micronutrient->description - - -description + + +description @@ -102,9 +102,9 @@ micronutrient->source - - -source + + +source @@ -115,9 +115,9 @@ micronutrient->provided by - - -provided by + + +provided by @@ -128,9 +128,9 @@ micronutrient->has attribute - - -has attribute + + +has attribute @@ -141,9 +141,9 @@ micronutrient->category - - -category + + +category @@ -154,9 +154,9 @@ micronutrient->trade name - - -trade name + + +trade name @@ -167,15 +167,41 @@ micronutrient->available from - - -available from + + +available from + + + +max tolerated dose + +string + + + +micronutrient->max tolerated dose + + +max tolerated dose + + + +is toxic + +boolean + + + +micronutrient->is toxic + + +is toxic named thing_category - -named thing + +named thing diff --git a/graphviz/molecular_entity.gv b/graphviz/molecular_entity.gv index b77a1fa6db..e297d906ff 100644 --- a/graphviz/molecular_entity.gv +++ b/graphviz/molecular_entity.gv @@ -1,16 +1,16 @@ digraph { - graph [bb="0,0,1773.7,123"]; + graph [bb="0,0,1984.7,123"]; node [label="\N"]; "molecular entity" [height=0.5, label="molecular entity", - pos="834.89,105", + pos="945.89,105", width=2.4192]; "chemical entity" [height=0.5, pos="81.893,18", width=2.2748]; "molecular entity" -> "chemical entity" [label=is_a, - lp="319.89,61.5", - pos="e,131.75,32.441 748.34,102.35 643.23,99.4 460.77,91.274 305.89,69 249.61,60.905 186.47,46.298 141.6,34.954"]; + lp="320.89,61.5", + pos="e,131.51,32.488 858.9,103.74 735.54,102.35 502.95,95.968 306.89,69 250.14,61.193 186.49,46.48 141.41,35.027"]; id [color=blue, height=0.5, label=string, @@ -18,9 +18,9 @@ digraph { width=1.0652]; "molecular entity" -> id [color=blue, label=id, - lp="430.89,61.5", - pos="e,248.89,29.96 751.1,99.902 667.8,95.115 536.53,85.645 423.89,69 353.79,58.64 336.11,55.205 267.89,36 264.79,35.126 261.59,34.155 \ -258.39,33.133", + lp="433.89,61.5", + pos="e,248.88,29.979 860.12,101.82 756.91,98.368 578.55,89.752 426.89,69 355.39,59.216 337.4,55.425 267.89,36 264.79,35.132 261.59,34.165 \ +258.39,33.146", style=solid]; iri [color=blue, height=0.5, @@ -29,9 +29,9 @@ digraph { width=1.2277]; "molecular entity" -> iri [color=blue, label=iri, - lp="521.89,61.5", - pos="e,354.2,29.896 754.37,98.016 689.21,92.504 595.24,83.035 513.89,69 451.32,58.205 436.1,52.878 374.89,36 371.32,35.015 367.63,33.951 \ -363.93,32.852", + lp="533.89,61.5", + pos="e,354.17,29.991 861.84,100.26 776.78,95.719 641.66,86.397 525.89,69 457.96,58.792 441.28,53.665 374.89,36 371.31,35.047 367.61,34.005 \ +363.91,32.922", style=solid]; type [color=blue, height=0.5, @@ -40,9 +40,8 @@ digraph { width=1.0652]; "molecular entity" -> type [color=blue, label=type, - lp="618.89,61.5", - pos="e,450.82,30.003 762.75,94.852 716.81,88.599 656.14,79.549 602.89,69 542.73,57.079 527.59,53.789 468.89,36 466.13,35.162 463.29,34.255 \ -460.44,33.311", + lp="626.89,61.5", + pos="e,450.53,30.023 862.96,99.274 766.62,92.168 603.65,75.117 468.89,36 465.99,35.156 463,34.227 460.01,33.251", style=solid]; name [color=blue, height=0.5, @@ -51,8 +50,8 @@ digraph { width=1.5707]; "molecular entity" -> name [color=blue, label=name, - lp="703.89,61.5", - pos="e,570.72,32.101 775.76,91.672 747.75,85.483 713.93,77.5 683.89,69 648.75,59.054 609.61,45.838 580.28,35.491", + lp="731.89,61.5", + pos="e,573.21,31.346 871.95,95.38 825.69,89.386 765,80.425 711.89,69 667.66,59.485 618.18,45.188 582.8,34.315", style=solid]; description [color=blue, height=0.5, @@ -61,8 +60,8 @@ digraph { width=2.0943]; "molecular entity" -> description [color=blue, label=description, - lp="790.39,61.5", - pos="e,703.57,35.515 792.77,89.217 778.75,83.632 763.3,76.734 749.89,69 736.5,61.273 722.76,51.1 711.39,41.949", + lp="832.39,61.5", + pos="e,714.17,34.76 882.1,92.69 854.05,86.904 820.94,78.96 791.89,69 768.45,60.962 743.29,49.37 723.27,39.37", style=solid]; source [color=blue, height=0.5, @@ -71,8 +70,8 @@ digraph { width=1.5707]; "molecular entity" -> source [color=blue, label=source, - lp="858.89,61.5", - pos="e,834.89,36.175 834.89,86.799 834.89,75.163 834.89,59.548 834.89,46.237", + lp="918.89,61.5", + pos="e,853.44,35.223 921.18,87.72 912.72,81.971 903.28,75.353 894.89,69 883.63,60.474 871.6,50.609 861.29,41.906", style=solid]; "provided by" [color=blue, height=0.5, @@ -81,8 +80,8 @@ digraph { width=1.0291]; "molecular entity" -> "provided by" [color=blue, label="provided by", - lp="948.39,61.5", - pos="e,929.68,34.142 860.38,87.597 868.94,81.893 878.45,75.334 886.89,69 898.73,60.117 911.39,49.717 922.01,40.71", + lp="989.39,61.5", + pos="e,946.69,36.175 946.1,86.799 946.23,75.163 946.42,59.548 946.57,46.237", style=solid]; "has attribute" [color=blue, height=0.5, @@ -91,17 +90,16 @@ digraph { width=1.4443]; "molecular entity" -> "has attribute" [color=blue, label="has attribute", - lp="1065.9,61.5", - pos="e,1038.9,35.363 900.14,93.019 936.69,86.226 978.2,77.255 994.89,69 1008.3,62.361 1021.2,52.013 1031.6,42.449", + lp="1089.9,61.5", + pos="e,1049.9,36.207 997.49,90.43 1009.9,85.285 1022.3,78.327 1031.9,69 1038.4,62.632 1043.2,53.979 1046.5,45.661", style=solid]; category [height=0.5, pos="1174.9,18", width=1.4263]; "molecular entity" -> category [color=blue, label=category, - lp="1172.4,61.5", - pos="e,1161,35.5 896.75,92.308 908.08,90.376 919.82,88.513 930.89,87 1013.2,75.75 1040.5,101.65 1116.9,69 1130.7,63.087 1143.7,52.632 \ -1153.8,42.806", + lp="1188.4,61.5", + pos="e,1167.6,36.05 1009.7,92.695 1066.3,82.644 1140.2,69.461 1140.9,69 1149.9,63.147 1157.2,53.974 1162.6,45.075", style=solid]; "trade name" [color=blue, height=0.5, @@ -110,9 +108,9 @@ digraph { width=2.2748]; "molecular entity" -> "trade name" [color=blue, label="trade name", - lp="1292.9,61.5", - pos="e,1296.3,34.85 895.94,92.148 907.51,90.197 919.55,88.369 930.89,87 1053.4,72.221 1087.9,97.467 1207.9,69 1235.4,62.486 1264.6,50.148 \ -1287.1,39.358", + lp="1302.9,61.5", + pos="e,1299.7,35.115 1007.8,92.327 1019.1,90.393 1030.8,88.525 1041.9,87 1122.4,75.905 1145.7,91.243 1223.9,69 1247.2,62.368 1271.6,50.581 \ +1290.7,40.117", style=solid]; "available from" [color=blue, height=0.5, @@ -121,24 +119,46 @@ digraph { width=3.2858]; "molecular entity" -> "available from" [color=blue, label="available from", - lp="1464.4,61.5", - pos="e,1492.8,34.335 895.4,92.044 907.14,90.077 919.37,88.27 930.89,87 1110.9,67.171 1158.6,94.474 1337.9,69 1387.4,61.969 1442.3,48.327 \ -1483,37.067", + lp="1470.4,61.5", + pos="e,1494.5,34.398 1006.9,92.092 1018.5,90.146 1030.5,88.334 1041.9,87 1177.2,71.095 1213.3,89.933 1347.9,69 1394.4,61.768 1445.9,48.404 \ +1484.5,37.311", + style=solid]; + "max tolerated dose" [color=blue, + height=0.5, + label=string, + pos="1718.9,18", + width=1.0652]; + "molecular entity" -> "max tolerated dose" [color=blue, + label="max tolerated dose", + lp="1675.9,61.5", + pos="e,1689.9,29.887 1006.4,91.978 1018.1,90.018 1030.4,88.229 1041.9,87 1255.9,64.178 1312.5,97.006 1525.9,69 1591.4,60.401 1607.4,54.397 \ +1670.9,36 1674,35.102 1677.2,34.114 1680.4,33.081", + style=solid]; + "is toxic" [color=blue, + height=0.5, + label=boolean, + pos="1825.9,18", + width=1.2999]; + "molecular entity" -> "is toxic" [color=blue, + label="is toxic", + lp="1806.9,61.5", + pos="e,1808.1,34.7 1006.1,91.912 1017.9,89.944 1030.3,88.17 1041.9,87 1120.1,79.127 1673.8,92.274 1748.9,69 1767.4,63.253 1785.7,51.666 \ +1799.9,41.092", style=solid]; "is metabolite" [color=blue, height=0.5, label=boolean, - pos="1726.9,18", + pos="1937.9,18", width=1.2999]; "molecular entity" -> "is metabolite" [color=blue, label="is metabolite", - lp="1646.9,61.5", - pos="e,1691.8,30.074 895.13,91.96 906.95,89.988 919.28,88.2 930.89,87 1191.4,60.096 1260,101.09 1519.9,69 1576.7,61.989 1640.4,45.185 \ -1682,32.989", + lp="1923.9,61.5", + pos="e,1915.3,33.773 1005.9,91.929 1017.8,89.946 1030.2,88.162 1041.9,87 1129.8,78.271 1751.1,90.102 1836.9,69 1861.7,62.909 1887.4,50.056 \ +1906.7,38.908", style=solid]; "named thing_category" [color=blue, height=0.5, label="named thing", - pos="1009.9,105", + pos="1120.9,105", width=1.9318]; } diff --git a/graphviz/molecular_entity.svg b/graphviz/molecular_entity.svg index 4645837eeb..2ab72abd16 100644 --- a/graphviz/molecular_entity.svg +++ b/graphviz/molecular_entity.svg @@ -4,16 +4,16 @@ - + %3 - + molecular entity - -molecular entity + +molecular entity @@ -24,9 +24,9 @@ molecular entity->chemical entity - - -is_a + + +is_a @@ -37,9 +37,9 @@ molecular entity->id - - -id + + +id @@ -50,9 +50,9 @@ molecular entity->iri - - -iri + + +iri @@ -63,9 +63,9 @@ molecular entity->type - - -type + + +type @@ -76,9 +76,9 @@ molecular entity->name - - -name + + +name @@ -89,9 +89,9 @@ molecular entity->description - - -description + + +description @@ -102,9 +102,9 @@ molecular entity->source - - -source + + +source @@ -115,9 +115,9 @@ molecular entity->provided by - - -provided by + + +provided by @@ -128,9 +128,9 @@ molecular entity->has attribute - - -has attribute + + +has attribute @@ -141,9 +141,9 @@ molecular entity->category - - -category + + +category @@ -154,9 +154,9 @@ molecular entity->trade name - - -trade name + + +trade name @@ -167,28 +167,54 @@ molecular entity->available from - - -available from + + +available from - + +max tolerated dose + +string + + + +molecular entity->max tolerated dose + + +max tolerated dose + + + +is toxic + +boolean + + + +molecular entity->is toxic + + +is toxic + + + is metabolite - -boolean + +boolean - + molecular entity->is metabolite - - -is metabolite + + +is metabolite named thing_category - -named thing + +named thing diff --git a/graphviz/molecular_mixture.gv b/graphviz/molecular_mixture.gv index 7ba3a77b1c..62c948045c 100644 --- a/graphviz/molecular_mixture.gv +++ b/graphviz/molecular_mixture.gv @@ -1,16 +1,16 @@ digraph { - graph [bb="0,0,2028,123"]; + graph [bb="0,0,2270,123"]; node [label="\N"]; "molecular mixture" [height=0.5, label="molecular mixture", - pos="907.99,105", + pos="1018,105", width=2.672]; "chemical mixture" [height=0.5, pos="90.992,18", width=2.5276]; "molecular mixture" -> "chemical mixture" [label=is_a, - lp="339.99,61.5", - pos="e,144.26,32.716 812.55,102.63 696.91,99.967 496.39,92.118 325.99,69 267.14,61.016 201.07,46.448 154,35.088"]; + lp="336.99,61.5", + pos="e,143.09,32.761 921.71,104.06 787.14,103.04 535.44,97.054 322.99,69 264.77,61.311 199.46,46.683 153,35.227"]; id [color=blue, height=0.5, label=string, @@ -18,9 +18,9 @@ digraph { width=1.0652]; "molecular mixture" -> id [color=blue, label=id, - lp="452.99,61.5", - pos="e,266.98,29.984 814.7,100.43 721.12,96.037 573.04,86.84 445.99,69 374.09,58.904 355.93,55.499 285.99,36 282.88,35.133 279.69,34.168 \ -276.49,33.151", + lp="447.99,61.5", + pos="e,266.99,29.954 922.61,102.56 807.85,99.836 609.55,91.925 440.99,69 371.2,59.508 353.78,55.131 285.99,36 282.89,35.124 279.69,34.151 \ +276.49,33.129", style=solid]; iri [color=blue, height=0.5, @@ -29,9 +29,9 @@ digraph { width=1.2277]; "molecular mixture" -> iri [color=blue, label=iri, - lp="553.99,61.5", - pos="e,372.27,30.005 818.74,98.269 745.25,92.856 638.48,83.396 545.99,69 477.26,58.301 460.24,53.797 392.99,36 389.41,35.052 385.71,34.014 \ -382,32.933", + lp="541.99,61.5", + pos="e,372.29,29.913 923.36,101.57 825.43,98.018 668.29,89.442 533.99,69 470.36,59.316 455.06,53.009 392.99,36 389.42,35.02 385.72,33.96 \ +382.02,32.865", style=solid]; type [color=blue, height=0.5, @@ -40,8 +40,9 @@ digraph { width=1.0652]; "molecular mixture" -> type [color=blue, label=type, - lp="639.99,61.5", - pos="e,468.65,29.968 822.29,96.661 736.19,87.782 600.38,69.649 486.99,36 484.09,35.139 481.11,34.197 478.12,33.212", + lp="646.99,61.5", + pos="e,468.64,29.989 926.47,99.217 847.77,94.272 731.43,84.975 630.99,69 566.15,58.686 549.98,54.534 486.99,36 484.09,35.146 481.1,34.209 \ +478.11,33.227", style=solid]; name [color=blue, height=0.5, @@ -50,8 +51,8 @@ digraph { width=1.5707]; "molecular mixture" -> name [color=blue, label=name, - lp="738.99,61.5", - pos="e,590.58,31.607 837.15,92.773 801.5,86.646 757.75,78.395 718.99,69 678.57,59.2 633.41,45.409 600.41,34.792", + lp="742.99,61.5", + pos="e,589.68,31.738 930.25,97.477 871.25,92.142 791.96,83.129 722.99,69 680.47,60.29 633.19,45.995 599.31,34.917", style=solid]; description [color=blue, height=0.5, @@ -60,8 +61,8 @@ digraph { width=2.0943]; "molecular mixture" -> description [color=blue, label=description, - lp="833.49,61.5", - pos="e,728.64,35.167 853.91,90.099 834.39,84.417 812.4,77.233 792.99,69 773.97,60.93 753.78,49.953 737.35,40.34", + lp="844.49,61.5", + pos="e,729.5,34.858 934.06,96.133 894.02,90.907 845.84,82.446 803.99,69 781.26,61.696 757.25,49.994 738.35,39.747", style=solid]; source [color=blue, height=0.5, @@ -70,8 +71,8 @@ digraph { width=1.5707]; "molecular mixture" -> source [color=blue, label=source, - lp="907.99,61.5", - pos="e,863.92,35.885 896.86,86.799 888.98,74.622 878.28,58.089 869.43,44.398", + lp="932.99,61.5", + pos="e,867.77,35.382 960.65,90.494 943.4,85.157 924.86,78.082 908.99,69 896.67,61.951 884.7,51.852 875.01,42.574", style=solid]; "provided by" [color=blue, height=0.5, @@ -80,8 +81,8 @@ digraph { width=1.0291]; "molecular mixture" -> "provided by" [color=blue, label="provided by", - lp="988.49,61.5", - pos="e,956.19,35.59 922.48,86.943 926.99,81.359 931.86,75.036 935.99,69 941.29,61.262 946.58,52.512 951.17,44.519", + lp="1007.5,61.5", + pos="e,961.11,36.192 983.21,88.133 975.91,83.1 969.17,76.768 964.99,69 961.32,62.168 960.21,54.012 960.32,46.289", style=solid]; "has attribute" [color=blue, height=0.5, @@ -90,17 +91,16 @@ digraph { width=1.4443]; "molecular mixture" -> "has attribute" [color=blue, label="has attribute", - lp="1097,61.5", - pos="e,1063.2,36.182 979.84,93.007 998.89,87.816 1018.7,80.192 1035,69 1044.1,62.769 1051.8,53.565 1057.8,44.747", + lp="1106,61.5", + pos="e,1066.1,35.908 1035.5,87.125 1040.6,81.651 1045.9,75.346 1050,69 1054.7,61.737 1058.9,53.287 1062.3,45.422", style=solid]; category [height=0.5, pos="1193,18", width=1.4263]; "molecular mixture" -> category [color=blue, label=category, - lp="1198.5,61.5", - pos="e,1182.6,35.797 977.42,92.478 989.28,90.591 1001.5,88.699 1013,87 1072.9,78.162 1094.4,97.234 1148,69 1159.2,63.102 1169,53.248 \ -1176.5,43.839", + lp="1204.5,61.5", + pos="e,1184.9,35.789 1096,94.374 1117,89.196 1139,81.236 1157,69 1166.1,62.779 1173.8,53.415 1179.6,44.467", style=solid]; "trade name" [color=blue, height=0.5, @@ -109,9 +109,9 @@ digraph { width=2.2748]; "molecular mixture" -> "trade name" [color=blue, label="trade name", - lp="1316,61.5", - pos="e,1316,34.979 975.94,92.192 988.25,90.284 1001,88.459 1013,87 1110.8,75.116 1138.6,93.758 1234,69 1259.3,62.419 1286.1,50.361 1306.9,\ -39.736", + lp="1320,61.5", + pos="e,1316.2,35.144 1088,92.584 1099.7,90.703 1111.7,88.785 1123,87 1175,78.796 1189.7,84.568 1240,69 1263.3,61.784 1287.9,50.126 1307.4,\ +39.882", style=solid]; "available from" [color=blue, height=0.5, @@ -120,35 +120,57 @@ digraph { width=3.2858]; "molecular mixture" -> "available from" [color=blue, label="available from", - lp="1485.5,61.5", - pos="e,1511.7,34.361 975.06,92.026 987.63,90.099 1000.7,88.31 1013,87 1167,70.6 1207.8,91.798 1361,69 1409,61.851 1462.3,48.329 1502,\ -37.148", + lp="1488.5,61.5", + pos="e,1511.5,34.411 1085.7,92.166 1098,90.249 1110.9,88.427 1123,87 1230.1,74.37 1258.5,86.332 1365,69 1411.3,61.452 1462.8,48.236 1501.4,\ +37.287", + style=solid]; + "max tolerated dose" [color=blue, + height=0.5, + label=string, + pos="1737,18", + width=1.0652]; + "molecular mixture" -> "max tolerated dose" [color=blue, + label="max tolerated dose", + lp="1694,61.5", + pos="e,1708,29.887 1084.8,91.979 1097.4,90.044 1110.6,88.265 1123,87 1309.3,68.001 1358.4,93.882 1544,69 1609.5,60.219 1625.5,54.397 \ +1689,36 1692.1,35.102 1695.3,34.114 1698.5,33.081", + style=solid]; + "is toxic" [color=blue, + height=0.5, + label=boolean, + pos="1840,18", + width=1.2999]; + "molecular mixture" -> "is toxic" [color=blue, + label="is toxic", + lp="1824,61.5", + pos="e,1823,34.922 1084.2,91.916 1097,89.961 1110.4,88.19 1123,87 1194.3,80.265 1698.9,91.126 1767,69 1784.7,63.259 1801.9,51.788 1815.2,\ +41.28", style=solid]; "is supplement" [color=blue, height=0.5, label="chemical mixture", - pos="1789,18", + pos="1996,18", width=2.5276]; "molecular mixture" -> "is supplement" [color=blue, label="is supplement", - lp="1681.5,61.5", - pos="e,1734.7,32.627 974.48,91.935 987.23,89.991 1000.5,88.22 1013,87 1246.7,64.191 1307.8,96.295 1541,69 1604,61.62 1675,46.634 1724.8,\ -34.984", + lp="1960.5,61.5", + pos="e,1961.2,34.701 1084.2,91.882 1097,89.93 1110.4,88.169 1123,87 1284.8,71.98 1694.2,98.345 1854,69 1887.8,62.793 1924.3,49.771 1951.9,\ +38.572", style=solid]; "highest FDA approval status" [color=blue, height=0.5, label=string, - pos="1936,18", + pos="2143,18", width=1.0652]; "molecular mixture" -> "highest FDA approval status" [color=blue, label="highest FDA approval status", - lp="1925.5,61.5", - pos="e,1907.4,30.049 974.19,91.885 987.02,89.932 1000.4,88.171 1013,87 1333,57.245 1416.8,107.05 1736,69 1805.1,60.765 1822.1,55.207 \ -1889,36 1891.9,35.164 1894.9,34.241 1897.9,33.269", + lp="2167.5,61.5", + pos="e,2117.8,31.909 1083.9,91.879 1096.8,89.914 1110.3,88.15 1123,87 1320.4,69.112 1820.5,107.67 2015,69 2048,62.44 2083.5,47.94 2108.7,\ +36.236", style=solid]; "named thing_category" [color=blue, height=0.5, label="named thing", - pos="1092,105", + pos="1202,105", width=1.9318]; } diff --git a/graphviz/molecular_mixture.svg b/graphviz/molecular_mixture.svg index b0cd43aa1e..298a225929 100644 --- a/graphviz/molecular_mixture.svg +++ b/graphviz/molecular_mixture.svg @@ -4,16 +4,16 @@ - + %3 - + molecular mixture - -molecular mixture + +molecular mixture @@ -24,9 +24,9 @@ molecular mixture->chemical mixture - - -is_a + + +is_a @@ -37,9 +37,9 @@ molecular mixture->id - - -id + + +id @@ -50,9 +50,9 @@ molecular mixture->iri - - -iri + + +iri @@ -63,9 +63,9 @@ molecular mixture->type - - -type + + +type @@ -76,9 +76,9 @@ molecular mixture->name - - -name + + +name @@ -89,9 +89,9 @@ molecular mixture->description - - -description + + +description @@ -102,9 +102,9 @@ molecular mixture->source - - -source + + +source @@ -115,9 +115,9 @@ molecular mixture->provided by - - -provided by + + +provided by @@ -128,9 +128,9 @@ molecular mixture->has attribute - - -has attribute + + +has attribute @@ -141,9 +141,9 @@ molecular mixture->category - - -category + + +category @@ -154,9 +154,9 @@ molecular mixture->trade name - - -trade name + + +trade name @@ -167,41 +167,67 @@ molecular mixture->available from - - -available from + + +available from - + +max tolerated dose + +string + + + +molecular mixture->max tolerated dose + + +max tolerated dose + + + +is toxic + +boolean + + + +molecular mixture->is toxic + + +is toxic + + + is supplement - -chemical mixture + +chemical mixture - + molecular mixture->is supplement - - -is supplement + + +is supplement - + highest FDA approval status - -string + +string - + molecular mixture->highest FDA approval status - - -highest FDA approval status + + +highest FDA approval status named thing_category - -named thing + +named thing diff --git a/graphviz/noncoding_RNA_product.gv b/graphviz/noncoding_RNA_product.gv index a899278041..318a7e2c7a 100644 --- a/graphviz/noncoding_RNA_product.gv +++ b/graphviz/noncoding_RNA_product.gv @@ -1,16 +1,16 @@ digraph { - graph [bb="0,0,2395,123"]; + graph [bb="0,0,2602,123"]; node [label="\N"]; "noncoding RNA product" [height=0.5, label="noncoding RNA product", - pos="1032.8,105", + pos="1152.8,105", width=3.3761]; "RNA product" [height=0.5, pos="70.844,18", width=1.9679]; "noncoding RNA product" -> "RNA product" [label=is_a, - lp="299.84,61.5", - pos="e,115.7,31.945 913.97,101.06 734.67,96.182 403.51,85.301 285.84,69 230.55,61.34 168.58,46.211 125.43,34.591"]; + lp="296.84,61.5", + pos="e,115.45,32.154 1032.7,102.01 828.98,98.156 424,88.304 282.84,69 228.56,61.576 167.82,46.54 125.31,34.886"]; id [color=blue, height=0.5, label=string, @@ -18,9 +18,9 @@ digraph { width=1.0652]; "noncoding RNA product" -> id [color=blue, label=id, - lp="412.84,61.5", - pos="e,226.83,29.984 912.16,102.54 785.54,99.776 580.98,91.822 405.84,69 333.84,59.618 315.78,55.499 245.84,36 242.74,35.133 239.54,34.168 \ -236.34,33.151", + lp="411.84,61.5", + pos="e,226.83,29.979 1031.2,104.19 882.77,103.07 624.43,96.748 404.84,69 333.24,59.952 315.35,55.425 245.84,36 242.74,35.132 239.54,34.165 \ +236.34,33.146", style=solid]; iri [color=blue, height=0.5, @@ -29,8 +29,8 @@ digraph { width=1.2277]; "noncoding RNA product" -> iri [color=blue, label=iri, - lp="501.84,61.5", - pos="e,332.23,29.82 912.89,101.87 803.26,98.591 636.92,90.24 493.84,69 440.73,61.116 381.14,44.688 341.97,32.81", + lp="499.84,61.5", + pos="e,332.2,30.049 1031.3,104.1 898.2,102.7 678.81,95.92 491.84,69 439.48,61.461 380.85,45.101 342.1,33.141", style=solid]; type [color=blue, height=0.5, @@ -40,7 +40,7 @@ digraph { "noncoding RNA product" -> type [color=blue, label=type, lp="606.84,61.5", - pos="e,428.49,29.989 916.91,99.459 827.44,94.837 700.79,85.858 590.84,69 525.94,59.049 509.83,54.534 446.84,36 443.94,35.146 440.96,34.209 \ + pos="e,428.49,29.989 1032.8,102.18 918.58,99.116 742.26,90.915 590.84,69 525.86,59.595 509.83,54.534 446.84,36 443.94,35.146 440.96,34.209 \ 437.97,33.227", style=solid]; name [color=blue, @@ -50,8 +50,8 @@ digraph { width=1.5707]; "noncoding RNA product" -> name [color=blue, label=name, - lp="709.84,61.5", - pos="e,550.37,31.655 921.69,97.566 854.21,92.447 766.57,83.638 689.84,69 645.12,60.468 595.3,45.928 559.94,34.72", + lp="710.84,61.5", + pos="e,549.85,31.719 1033.3,101.44 939.58,97.87 806.1,89.346 690.84,69 645.48,60.992 595.04,46.25 559.47,34.84", style=solid]; description [color=blue, height=0.5, @@ -60,8 +60,8 @@ digraph { width=2.0943]; "noncoding RNA product" -> description [color=blue, label=description, - lp="814.34,61.5", - pos="e,691.65,34.764 925.56,96.51 878.38,91.431 822.7,82.984 773.84,69 748.65,61.788 721.81,49.83 700.84,39.417", + lp="816.34,61.5", + pos="e,691.64,34.87 1032.3,102.7 957.42,99.474 859.81,90.851 775.84,69 749.8,62.223 722.15,50.083 700.72,39.462", style=solid]; source [color=blue, height=0.5, @@ -70,8 +70,8 @@ digraph { width=1.5707]; "noncoding RNA product" -> source [color=blue, label=source, - lp="906.84,61.5", - pos="e,831.2,35.187 952.7,91.358 929.54,86.107 904.65,78.863 882.84,69 867.37,61.999 851.82,51.348 839.33,41.673", + lp="913.84,61.5", + pos="e,832.11,35.006 1036.6,99.633 989.85,95.05 936.18,86.13 889.84,69 872.14,62.455 854.34,51.266 840.32,41.13", style=solid]; "provided by" [color=blue, height=0.5, @@ -80,8 +80,8 @@ digraph { width=1.0291]; "noncoding RNA product" -> "provided by" [color=blue, label="provided by", - lp="986.34,61.5", - pos="e,927.72,36.214 974.49,89.129 963.26,84.169 952.36,77.62 943.84,69 937.62,62.709 933.4,54.176 930.55,45.94", + lp="998.34,61.5", + pos="e,931.1,36.035 1055.5,94.191 1014.5,88.553 972.52,80.306 955.84,69 947.19,63.129 940.49,53.953 935.58,45.055", style=solid]; "has attribute" [color=blue, height=0.5, @@ -90,16 +90,16 @@ digraph { width=1.4443]; "noncoding RNA product" -> "has attribute" [color=blue, label="has attribute", - lp="1079.8,61.5", - pos="e,1032,36.175 1032.6,86.799 1032.5,75.163 1032.3,59.548 1032.2,46.237", + lp="1101.8,61.5", + pos="e,1036.1,36.353 1089.1,89.568 1076.7,84.579 1064.6,77.906 1054.8,69 1048.1,62.786 1043.1,54.17 1039.6,45.84", style=solid]; category [height=0.5, pos="1152.8,18", width=1.4263]; "noncoding RNA product" -> category [color=blue, label=category, - lp="1173.3,61.5", - pos="e,1149,36.344 1096.9,89.588 1109.2,84.602 1121.3,77.925 1130.8,69 1137.5,62.776 1142.3,54.158 1145.6,45.829", + lp="1184.3,61.5", + pos="e,1152.8,36.175 1152.8,86.799 1152.8,75.163 1152.8,59.548 1152.8,46.237", style=solid]; "trade name" [color=blue, height=0.5, @@ -108,8 +108,8 @@ digraph { width=2.2748]; "noncoding RNA product" -> "trade name" [color=blue, label="trade name", - lp="1282.8,61.5", - pos="e,1278.2,35.129 1118.3,92.108 1147.5,86.711 1180.1,79.193 1208.8,69 1229.8,61.582 1251.8,50.229 1269.4,40.215", + lp="1286.8,61.5", + pos="e,1277.6,35.143 1185.1,87.624 1196.2,81.867 1208.6,75.269 1219.8,69 1236,59.957 1253.7,49.52 1268.7,40.529", style=solid]; "available from" [color=blue, height=0.5, @@ -118,68 +118,89 @@ digraph { width=3.2858]; "noncoding RNA product" -> "available from" [color=blue, label="available from", - lp="1444.3,61.5", - pos="e,1470.8,34.291 1119.9,92.358 1134.2,90.514 1148.9,88.667 1162.8,87 1236.1,78.217 1255.3,82.24 1327.8,69 1372.9,60.777 1423,47.778 \ -1460.9,37.095", + lp="1441.3,61.5", + pos="e,1468,34.151 1226.7,90.671 1259,84.54 1297.4,76.884 1331.8,69 1374.1,59.322 1421.2,46.935 1457.9,36.911", + style=solid]; + "max tolerated dose" [color=blue, + height=0.5, + label=string, + pos="1696.8,18", + width=1.0652]; + "noncoding RNA product" -> "max tolerated dose" [color=blue, + label="max tolerated dose", + lp="1650.8,61.5", + pos="e,1667.8,29.935 1238.8,92.193 1253.5,90.338 1268.6,88.531 1282.8,87 1377.7,76.809 1402.5,83.155 1496.8,69 1565.2,58.748 1582.4,54.911 \ +1648.8,36 1651.9,35.117 1655.1,34.141 1658.3,33.115", + style=solid]; + "is toxic" [color=blue, + height=0.5, + label=boolean, + pos="1799.8,18", + width=1.2999]; + "noncoding RNA product" -> "is toxic" [color=blue, + label="is toxic", + lp="1781.8,61.5", + pos="e,1782,34.849 1236.6,91.925 1252,90.032 1267.9,88.282 1282.8,87 1380.6,78.633 1630.5,99.047 1723.8,69 1742,63.15 1760,51.673 1773.9,\ +41.189", style=solid]; "is metabolite" [color=blue, height=0.5, label=boolean, - pos="1704.8,18", + pos="1911.8,18", width=1.2999]; "noncoding RNA product" -> "is metabolite" [color=blue, label="is metabolite", - lp="1627.8,61.5", - pos="e,1670,30.026 1117.4,91.994 1132.5,90.118 1148.1,88.355 1162.8,87 1312.2,73.266 1351.2,89.285 1499.8,69 1567,59.827 1583.2,53.197 \ -1648.8,36 1652.6,35.014 1656.5,33.942 1660.4,32.833", + lp="1899.8,61.5", + pos="e,1889.1,33.93 1236.3,91.884 1251.7,89.983 1267.8,88.24 1282.8,87 1400.1,77.363 1697.8,97.967 1811.8,69 1836.1,62.838 1861.3,50.204 \ +1880.3,39.178", style=solid]; "in taxon" [color=blue, height=0.5, label="organism taxon", - pos="1852.8,18", + pos="2059.8,18", width=2.3109]; "noncoding RNA product" -> "in taxon" [color=blue, label="in taxon", - lp="1771.8,61.5", - pos="e,1812,33.818 1116.3,91.895 1131.7,89.993 1147.8,88.247 1162.8,87 1391.5,68.101 1452.2,104.96 1678.8,69 1721.2,62.276 1767.9,48.504 \ -1802.2,37.113", + lp="2023.8,61.5", + pos="e,2032.7,35.192 1235.9,91.839 1251.5,89.93 1267.6,88.196 1282.8,87 1430.9,75.357 1806.2,102.64 1950.8,69 1976.3,63.07 2003.1,50.902 \ +2023.7,40.055", style=solid]; "has biological sequence" [color=blue, height=0.5, label="biological sequence", - pos="2055.8,18", + pos="2262.8,18", width=2.8164]; "noncoding RNA product" -> "has biological sequence" [color=blue, label="has biological sequence", - lp="1980.3,61.5", - pos="e,1999.5,33.068 1115.9,91.853 1131.5,89.942 1147.6,88.204 1162.8,87 1447.4,64.465 1521.2,101 1804.8,69 1868.2,61.856 1939.3,47.021 \ -1989.7,35.356", + lp="2222.3,61.5", + pos="e,2214.3,33.918 1235.9,91.793 1251.5,89.889 1267.6,88.168 1282.8,87 1454.4,73.827 1886.3,91.42 2056.8,69 2107.4,62.354 2163.6,48.253 \ +2204.5,36.714", style=solid]; synonym [color=blue, height=0.5, label="label type", - pos="2231.8,18", + pos="2438.8,18", width=1.5707]; "noncoding RNA product" -> synonym [color=blue, label=synonym, - lp="2164.8,61.5", - pos="e,2197.8,32.47 1115.6,91.794 1131.2,89.876 1147.5,88.15 1162.8,87 1363.7,71.922 1870,100.83 2068.8,69 2110.3,62.363 2155.8,47.734 \ -2188.2,36.004", + lp="2393.8,61.5", + pos="e,2410.2,33.573 1235.6,91.764 1251.2,89.849 1267.5,88.132 1282.8,87 1396.8,78.58 2198.8,91.131 2310.8,69 2342.4,62.771 2376.2,49.241 \ +2401.1,37.825", style=solid]; xref [color=blue, height=0.5, label="iri type", - pos="2350.8,18", + pos="2557.8,18", width=1.2277]; "noncoding RNA product" -> xref [color=blue, label=xref, - lp="2274.3,61.5", - pos="e,2321.6,31.694 1115.6,91.762 1131.2,89.848 1147.5,88.131 1162.8,87 1277.9,78.508 2087.1,88.464 2200.8,69 2239.7,62.342 2282.2,47.396 \ -2312.1,35.569", + lp="2494.3,61.5", + pos="e,2531.2,32.643 1235.6,91.742 1251.2,89.829 1267.5,88.118 1282.8,87 1410,77.721 2304.8,93.578 2429.8,69 2462.2,62.636 2497,48.551 \ +2522.1,36.947", style=solid]; "named thing_category" [color=blue, height=0.5, label="named thing", - pos="1241.8,105", + pos="1361.8,105", width=1.9318]; } diff --git a/graphviz/noncoding_RNA_product.svg b/graphviz/noncoding_RNA_product.svg index e42e56d10d..9e58e7168a 100644 --- a/graphviz/noncoding_RNA_product.svg +++ b/graphviz/noncoding_RNA_product.svg @@ -4,16 +4,16 @@ - + %3 - + noncoding RNA product - -noncoding RNA product + +noncoding RNA product @@ -24,9 +24,9 @@ noncoding RNA product->RNA product - - -is_a + + +is_a @@ -37,9 +37,9 @@ noncoding RNA product->id - - -id + + +id @@ -50,9 +50,9 @@ noncoding RNA product->iri - - -iri + + +iri @@ -63,7 +63,7 @@ noncoding RNA product->type - + type @@ -76,9 +76,9 @@ noncoding RNA product->name - - -name + + +name @@ -89,9 +89,9 @@ noncoding RNA product->description - - -description + + +description @@ -102,9 +102,9 @@ noncoding RNA product->source - - -source + + +source @@ -115,9 +115,9 @@ noncoding RNA product->provided by - - -provided by + + +provided by @@ -128,9 +128,9 @@ noncoding RNA product->has attribute - - -has attribute + + +has attribute @@ -141,9 +141,9 @@ noncoding RNA product->category - - -category + + +category @@ -154,9 +154,9 @@ noncoding RNA product->trade name - - -trade name + + +trade name @@ -167,80 +167,106 @@ noncoding RNA product->available from - - -available from + + +available from - + +max tolerated dose + +string + + + +noncoding RNA product->max tolerated dose + + +max tolerated dose + + + +is toxic + +boolean + + + +noncoding RNA product->is toxic + + +is toxic + + + is metabolite - -boolean + +boolean - + noncoding RNA product->is metabolite - - -is metabolite + + +is metabolite - + in taxon - -organism taxon + +organism taxon - + noncoding RNA product->in taxon - - -in taxon + + +in taxon - + has biological sequence - -biological sequence + +biological sequence - + noncoding RNA product->has biological sequence - - -has biological sequence + + +has biological sequence - + synonym - -label type + +label type - + noncoding RNA product->synonym - - -synonym + + +synonym - + xref - -iri type + +iri type - + noncoding RNA product->xref - - -xref + + +xref named thing_category - -named thing + +named thing diff --git a/graphviz/nucleic_acid_entity.gv b/graphviz/nucleic_acid_entity.gv index 4b030f0caf..b44d479f79 100644 --- a/graphviz/nucleic_acid_entity.gv +++ b/graphviz/nucleic_acid_entity.gv @@ -1,37 +1,36 @@ digraph { - graph [bb="0,0,2733.5,123"]; + graph [bb="0,0,2940.5,123"]; node [label="\N"]; "nucleic acid entity" [height=0.5, label="nucleic acid entity", - pos="1314.1,105", + pos="1444.1,105", width=2.6539]; "molecular entity" [height=0.5, pos="87.092,18", width=2.4192]; "nucleic acid entity" -> "molecular entity" [label=is_a, - lp="461.09,61.5", - pos="e,149.76,30.571 1219,102.77 1059.3,100.12 727.09,92.11 447.09,69 329.25,59.273 300.01,53.648 183.09,36 175.5,34.854 167.59,33.581 \ -159.7,32.261"]; + lp="457.09,61.5", + pos="e,149.76,30.554 1348.7,103.56 1170.5,102.1 775.01,95.811 443.09,69 326.99,59.622 298.25,53.494 183.09,36 175.5,34.847 167.59,33.569 \ +159.71,32.247"]; "genomic entity" [height=0.5, pos="272.09,18", width=2.2206]; "nucleic acid entity" -> "genomic entity" [label=uses, - lp="630.59,61.5", - pos="e,329.93,30.561 1220,101.68 1085.4,97.814 830.41,88.485 614.09,69 501.15,58.827 473.05,53.979 361.09,36 354.31,34.911 347.25,33.698 \ -340.21,32.437"]; + lp="620.59,61.5", + pos="e,329.94,30.517 1349.1,102.93 1193.3,100.52 873.61,92.863 604.09,69 495.53,59.388 468.66,53.564 361.09,36 354.31,34.893 347.26,33.669 \ +340.21,32.4"]; "physical essence" [height=0.5, pos="458.09,18", width=2.4553]; "nucleic acid entity" -> "physical essence" [label=uses, - lp="763.59,61.5", - pos="e,522.53,30.323 1220.5,101.34 1107.9,97.411 913.14,88.337 747.09,69 661.09,58.985 640.4,50.807 555.09,36 547.77,34.729 540.14,33.4 \ -532.52,32.069"]; + lp="759.59,61.5", + pos="e,516.74,31.48 1349.1,102.98 1214.1,100.69 958.94,93.228 743.09,69 668.68,60.648 584.31,45.072 526.8,33.515"]; "ontology class" [height=0.5, pos="641.09,18", width=2.1304]; "nucleic acid entity" -> "ontology class" [label=uses, - lp="880.59,61.5", - pos="e,689.87,32.053 1221,100.65 1129.7,96.441 986.72,87.42 864.09,69 807.73,60.535 744.42,45.828 699.69,34.549"]; + lp="873.59,61.5", + pos="e,688.27,32.336 1348.8,103.22 1232.2,101.14 1029.2,93.877 857.09,69 802.49,61.109 741.32,46.38 698.05,34.944"]; id [color=blue, height=0.5, label=string, @@ -39,8 +38,9 @@ digraph { width=1.0652]; "nucleic acid entity" -> id [color=blue, label=id, - lp="976.09,61.5", - pos="e,803.08,29.996 1224.2,98.786 1124.4,91.346 959.4,74.099 822.09,36 818.98,35.137 815.78,34.175 812.59,33.159", + lp="989.09,61.5", + pos="e,803.08,29.984 1351.2,100.46 1257.7,96.065 1109.3,86.868 982.09,69 910.19,58.904 892.03,55.499 822.09,36 818.98,35.133 815.79,34.168 \ +812.59,33.151", style=solid]; iri [color=blue, height=0.5, @@ -49,9 +49,9 @@ digraph { width=1.2277]; "nucleic acid entity" -> iri [color=blue, label=iri, - lp="1082.1,61.5", - pos="e,908.38,29.946 1236.8,94.309 1189.7,88.002 1128.2,79.089 1074.1,69 1009.1,56.888 992.89,53.271 929.09,36 925.51,35.031 921.82,33.979 \ -918.12,32.889", + lp="1090.1,61.5", + pos="e,908.37,30.005 1355.2,98.297 1281.7,92.888 1174.7,83.42 1082.1,69 1013.4,58.301 996.34,53.797 929.09,36 925.51,35.052 921.81,34.014 \ +918.1,32.933", style=solid]; type [color=blue, height=0.5, @@ -60,8 +60,8 @@ digraph { width=1.0652]; "nucleic acid entity" -> type [color=blue, label=type, - lp="1158.1,61.5", - pos="e,1005,29.97 1249.8,91.618 1190.4,79.549 1100,59.598 1023.1,36 1020.3,35.153 1017.5,34.238 1014.6,33.289", + lp="1176.1,61.5", + pos="e,1004.7,29.968 1358.8,96.702 1272.7,87.839 1136.7,69.702 1023.1,36 1020.2,35.139 1017.2,34.197 1014.2,33.212", style=solid]; name [color=blue, height=0.5, @@ -70,8 +70,8 @@ digraph { width=1.5707]; "nucleic acid entity" -> name [color=blue, label=name, - lp="1235.1,61.5", - pos="e,1124,32.186 1273.3,88.607 1233.8,73.681 1174.1,51.1 1133.4,35.735", + lp="1275.1,61.5", + pos="e,1126.7,31.607 1373.2,92.773 1337.6,86.646 1293.8,78.395 1255.1,69 1214.7,59.2 1169.5,45.409 1136.5,34.792", style=solid]; description [color=blue, height=0.5, @@ -80,8 +80,8 @@ digraph { width=2.0943]; "nucleic acid entity" -> description [color=blue, label=description, - lp="1321.6,61.5", - pos="e,1253.9,35.758 1299.3,87.207 1288.3,74.75 1273.1,57.573 1260.8,43.574", + lp="1369.6,61.5", + pos="e,1264.7,35.167 1390,90.099 1370.5,84.417 1348.5,77.233 1329.1,69 1310.1,60.93 1289.9,49.953 1273.4,40.34", style=solid]; source [color=blue, height=0.5, @@ -90,8 +90,8 @@ digraph { width=1.5707]; "nucleic acid entity" -> source [color=blue, label=source, - lp="1400.1,61.5", - pos="e,1383.9,36.066 1344.1,87.809 1352,82.565 1360,76.212 1366.1,69 1371.9,62.169 1376.5,53.628 1380.1,45.547", + lp="1444.1,61.5", + pos="e,1400,35.885 1433,86.799 1425.1,74.622 1414.4,58.089 1405.5,44.398", style=solid]; "provided by" [color=blue, height=0.5, @@ -100,8 +100,8 @@ digraph { width=1.0291]; "nucleic acid entity" -> "provided by" [color=blue, label="provided by", - lp="1496.6,61.5", - pos="e,1482.8,33.821 1370.5,90.359 1389.3,84.858 1410,77.721 1428.1,69 1444.4,61.12 1461.2,49.867 1474.6,40.03", + lp="1524.6,61.5", + pos="e,1492.3,35.59 1458.6,86.943 1463.1,81.359 1468,75.036 1472.1,69 1477.4,61.262 1482.7,52.512 1487.3,44.519", style=solid]; "has attribute" [color=blue, height=0.5, @@ -110,18 +110,17 @@ digraph { width=1.4443]; "nucleic acid entity" -> "has attribute" [color=blue, label="has attribute", - lp="1616.1,61.5", - pos="e,1592,35.238 1383.2,92.523 1394.8,90.64 1406.8,88.737 1418.1,87 1473.6,78.472 1491.4,90.824 1543.1,69 1558.2,62.613 1572.9,51.827 \ -1584.5,41.905", + lp="1633.1,61.5", + pos="e,1599.3,36.182 1515.9,93.007 1535,87.816 1554.8,80.192 1571.1,69 1580.2,62.769 1587.9,53.565 1593.9,44.747", style=solid]; category [height=0.5, pos="1729.1,18", width=1.4263]; "nucleic acid entity" -> category [color=blue, label=category, - lp="1723.6,61.5", - pos="e,1714,35.632 1381.1,92.138 1393.4,90.224 1406.1,88.411 1418.1,87 1473.2,80.519 1615.5,89.341 1667.1,69 1681.8,63.207 1695.7,52.624 \ -1706.6,42.681", + lp="1734.6,61.5", + pos="e,1718.7,35.801 1512.9,92.457 1524.6,90.572 1536.7,88.686 1548.1,87 1608.4,78.081 1630.1,97.414 1684.1,69 1695.3,63.107 1705.1,53.254 \ +1712.6,43.845", style=solid]; "trade name" [color=blue, height=0.5, @@ -130,9 +129,9 @@ digraph { width=2.2748]; "nucleic acid entity" -> "trade name" [color=blue, label="trade name", - lp="1845.1,61.5", - pos="e,1849.7,34.951 1380.5,92.032 1393,90.104 1405.9,88.314 1418.1,87 1569,70.734 1611.1,102.46 1759.1,69 1787.3,62.614 1817.5,50.195 \ -1840.6,39.332", + lp="1852.1,61.5", + pos="e,1852.1,34.982 1511.4,92.181 1523.6,90.274 1536.2,88.452 1548.1,87 1646.4,75.006 1674.3,93.852 1770.1,69 1795.4,62.424 1822.2,50.366 \ +1843,39.739", style=solid]; "available from" [color=blue, height=0.5, @@ -141,46 +140,68 @@ digraph { width=3.2858]; "nucleic acid entity" -> "available from" [color=blue, label="available from", - lp="2017.6,61.5", - pos="e,2046.9,34.299 1380.2,91.929 1392.8,89.999 1405.8,88.234 1418.1,87 1627,66.027 1682.1,97.673 1890.1,69 1940.2,62.088 1995.9,48.368 \ -2037.1,37.046", + lp="2021.6,61.5", + pos="e,2047.8,34.364 1510.5,92.02 1523,90.093 1535.9,88.306 1548.1,87 1702.5,70.447 1743.5,91.852 1897.1,69 1945.1,61.855 1998.4,48.333 \ +2038.1,37.151", + style=solid]; + "max tolerated dose" [color=blue, + height=0.5, + label=string, + pos="2273.1,18", + width=1.0652]; + "nucleic acid entity" -> "max tolerated dose" [color=blue, + label="max tolerated dose", + lp="2229.1,61.5", + pos="e,2244.1,29.908 1509.9,91.931 1522.6,89.988 1535.7,88.217 1548.1,87 1782.2,63.978 1843.7,98.726 2077.1,69 2143.9,60.484 2160.3,54.617 \ +2225.1,36 2228.2,35.109 2231.4,34.126 2234.6,33.096", + style=solid]; + "is toxic" [color=blue, + height=0.5, + label=boolean, + pos="2376.1,18", + width=1.2999]; + "nucleic acid entity" -> "is toxic" [color=blue, + label="is toxic", + lp="2359.1,61.5", + pos="e,2358.8,34.948 1509.7,91.872 1522.4,89.921 1535.6,88.163 1548.1,87 1631.5,79.222 2222.3,94.488 2302.1,69 2320,63.298 2337.4,51.829 \ +2350.9,41.313", style=solid]; "is metabolite" [color=blue, height=0.5, label=boolean, - pos="2281.1,18", + pos="2488.1,18", width=1.2999]; "nucleic acid entity" -> "is metabolite" [color=blue, label="is metabolite", - lp="2201.1,61.5", - pos="e,2246.2,30.001 1379.9,91.865 1392.6,89.928 1405.7,88.177 1418.1,87 1708,59.448 1784,104.05 2073.1,69 2130.4,62.049 2194.9,45.088 \ -2236.6,32.847", + lp="2476.1,61.5", + pos="e,2465.6,34.021 1509.7,91.847 1522.4,89.898 1535.6,88.148 1548.1,87 1641.2,78.44 2298.4,91.629 2389.1,69 2413.2,62.991 2438.1,50.355 \ +2456.9,39.291", style=solid]; "in taxon" [color=blue, height=0.5, label="organism taxon", - pos="2429.1,18", + pos="2636.1,18", width=2.3109]; "nucleic acid entity" -> "in taxon" [color=blue, label="in taxon", - lp="2351.1,61.5", - pos="e,2388.3,33.735 1379.7,91.849 1392.4,89.9 1405.6,88.149 1418.1,87 1602.7,70.006 2068.8,96.417 2252.1,69 2295.7,62.482 2343.7,48.458 \ -2378.7,36.916", + lp="2600.1,61.5", + pos="e,2609,35.263 1509.7,91.817 1522.4,89.871 1535.6,88.129 1548.1,87 1656.4,77.199 2421,93.192 2527.1,69 2552.6,63.179 2579.4,51.013 \ +2600,40.14", style=solid]; "has biological sequence" [color=blue, height=0.5, label="biological sequence", - pos="2632.1,18", + pos="2839.1,18", width=2.8164]; "nucleic acid entity" -> "has biological sequence" [color=blue, label="has biological sequence", - lp="2565.6,61.5", - pos="e,2576.9,33.108 1379.7,91.819 1392.4,89.873 1405.6,88.13 1418.1,87 1845.7,48.264 1957.2,115.62 2384.1,69 2446.8,62.152 2517.2,47.253 \ -2566.9,35.49", + lp="2798.6,61.5", + pos="e,2791,33.892 1509.4,91.842 1522.2,89.88 1535.5,88.126 1548.1,87 1788.3,65.492 2393.9,99.627 2633.1,69 2683.8,62.501 2740.2,48.313 \ +2781.2,36.705", style=solid]; "named thing_category" [color=blue, height=0.5, label="named thing", - pos="1497.1,105", + pos="1627.1,105", width=1.9318]; } diff --git a/graphviz/nucleic_acid_entity.svg b/graphviz/nucleic_acid_entity.svg index 35a9a60adf..d9dc95bf6b 100644 --- a/graphviz/nucleic_acid_entity.svg +++ b/graphviz/nucleic_acid_entity.svg @@ -4,16 +4,16 @@ - + %3 - + nucleic acid entity - -nucleic acid entity + +nucleic acid entity @@ -24,9 +24,9 @@ nucleic acid entity->molecular entity - - -is_a + + +is_a @@ -37,9 +37,9 @@ nucleic acid entity->genomic entity - - -uses + + +uses @@ -50,9 +50,9 @@ nucleic acid entity->physical essence - - -uses + + +uses @@ -63,9 +63,9 @@ nucleic acid entity->ontology class - - -uses + + +uses @@ -76,9 +76,9 @@ nucleic acid entity->id - - -id + + +id @@ -89,9 +89,9 @@ nucleic acid entity->iri - - -iri + + +iri @@ -102,9 +102,9 @@ nucleic acid entity->type - - -type + + +type @@ -115,9 +115,9 @@ nucleic acid entity->name - - -name + + +name @@ -128,9 +128,9 @@ nucleic acid entity->description - - -description + + +description @@ -141,9 +141,9 @@ nucleic acid entity->source - - -source + + +source @@ -154,9 +154,9 @@ nucleic acid entity->provided by - - -provided by + + +provided by @@ -167,9 +167,9 @@ nucleic acid entity->has attribute - - -has attribute + + +has attribute @@ -180,9 +180,9 @@ nucleic acid entity->category - - -category + + +category @@ -193,9 +193,9 @@ nucleic acid entity->trade name - - -trade name + + +trade name @@ -206,54 +206,80 @@ nucleic acid entity->available from - - -available from + + +available from - + +max tolerated dose + +string + + + +nucleic acid entity->max tolerated dose + + +max tolerated dose + + + +is toxic + +boolean + + + +nucleic acid entity->is toxic + + +is toxic + + + is metabolite - -boolean + +boolean - + nucleic acid entity->is metabolite - - -is metabolite + + +is metabolite - + in taxon - -organism taxon + +organism taxon - + nucleic acid entity->in taxon - - -in taxon + + +in taxon - + has biological sequence - -biological sequence + +biological sequence - + nucleic acid entity->has biological sequence - - -has biological sequence + + +has biological sequence named thing_category - -named thing + +named thing diff --git a/graphviz/nutrient.gv b/graphviz/nutrient.gv index d3deb77ea9..23ebc60c0f 100644 --- a/graphviz/nutrient.gv +++ b/graphviz/nutrient.gv @@ -1,16 +1,16 @@ digraph { - graph [bb="0,0,1662.2,123"]; + graph [bb="0,0,1901.7,123"]; node [label="\N"]; nutrient [height=0.5, label=nutrient, - pos="759.89,105", + pos="889.89,105", width=1.354]; "chemical entity" [height=0.5, pos="81.893,18", width=2.2748]; nutrient -> "chemical entity" [label=is_a, - lp="328.89,61.5", - pos="e,133.36,32.105 711.59,102.3 629.64,98.958 458.29,89.931 314.89,69 256.16,60.427 190.07,45.759 143.33,34.52"]; + lp="321.89,61.5", + pos="e,131.75,32.407 840.96,103.66 740.55,102.38 504.13,96.434 307.89,69 250.91,61.034 186.98,46.34 141.69,34.934"]; id [color=blue, height=0.5, label=string, @@ -18,8 +18,9 @@ digraph { width=1.0652]; nutrient -> id [color=blue, label=id, - lp="421.89,61.5", - pos="e,248.88,29.996 711.89,101.61 622.87,96.257 426.8,80.093 267.89,36 264.78,35.137 261.58,34.175 258.39,33.159", + lp="434.89,61.5", + pos="e,248.88,29.984 841.45,102.37 757.09,99.071 577.85,90.056 427.89,69 355.99,58.904 337.83,55.499 267.89,36 264.78,35.133 261.59,34.168 \ +258.39,33.151", style=solid]; iri [color=blue, height=0.5, @@ -28,9 +29,9 @@ digraph { width=1.2277]; nutrient -> iri [color=blue, label=iri, - lp="527.89,61.5", - pos="e,354.18,29.946 714.15,98.422 665.73,92.262 587.16,81.539 519.89,69 454.92,56.888 438.69,53.271 374.89,36 371.31,35.031 367.62,33.979 \ -363.92,32.889", + lp="535.89,61.5", + pos="e,354.17,30.005 842.24,101.16 772.8,96.625 639.88,86.431 527.89,69 459.16,58.301 442.14,53.797 374.89,36 371.31,35.052 367.61,34.014 \ +363.9,32.933", style=solid]; type [color=blue, height=0.5, @@ -39,8 +40,8 @@ digraph { width=1.0652]; nutrient -> type [color=blue, label=type, - lp="603.89,61.5", - pos="e,450.83,29.97 717.49,95.983 660.4,84.762 555.94,62.719 468.89,36 466.13,35.153 463.29,34.238 460.45,33.289", + lp="621.89,61.5", + pos="e,450.55,29.968 842.61,100.34 763.77,93.371 601.09,75.231 468.89,36 465.99,35.139 463.01,34.197 460.02,33.212", style=solid]; name [color=blue, height=0.5, @@ -49,8 +50,8 @@ digraph { width=1.5707]; nutrient -> name [color=blue, label=name, - lp="680.89,61.5", - pos="e,569.87,32.214 727.18,91.64 688.2,76.915 622.89,52.244 579.35,35.797", + lp="720.89,61.5", + pos="e,572.48,31.607 845.69,97.219 807.2,90.982 750.03,80.911 700.89,69 660.47,59.2 615.31,45.409 582.31,34.792", style=solid]; description [color=blue, height=0.5, @@ -59,8 +60,8 @@ digraph { width=2.0943]; nutrient -> description [color=blue, label=description, - lp="767.39,61.5", - pos="e,699.82,35.92 745.43,87.611 734.47,75.19 719.23,57.911 706.78,43.801", + lp="815.39,61.5", + pos="e,710.54,35.167 850.57,94.253 828.01,88.115 799.39,79.393 774.89,69 755.87,60.93 735.68,49.953 719.25,40.34", style=solid]; source [color=blue, height=0.5, @@ -69,8 +70,8 @@ digraph { width=1.5707]; nutrient -> source [color=blue, label=source, - lp="845.89,61.5", - pos="e,829.68,36.066 786.7,89.915 795.56,84.301 804.91,77.207 811.89,69 817.7,62.169 822.34,53.628 825.89,45.547", + lp="889.89,61.5", + pos="e,845.74,35.758 879.03,87.207 871.12,74.983 860.27,58.214 851.3,44.362", style=solid]; "provided by" [color=blue, height=0.5, @@ -79,8 +80,8 @@ digraph { width=1.0291]; nutrient -> "provided by" [color=blue, label="provided by", - lp="942.39,61.5", - pos="e,928.64,33.821 796.52,93.045 828.45,83.447 870.24,70.759 873.89,69 890.24,61.12 907.04,49.867 920.4,40.03", + lp="970.39,61.5", + pos="e,938.09,35.59 903.8,87.652 908.47,81.897 913.59,75.293 917.89,69 923.19,61.262 928.48,52.512 933.07,44.519", style=solid]; "has attribute" [color=blue, height=0.5, @@ -89,18 +90,18 @@ digraph { width=1.4443]; nutrient -> "has attribute" [color=blue, label="has attribute", - lp="1061.9,61.5", - pos="e,1038.1,35.212 794.91,92.447 802.12,90.382 809.7,88.435 816.89,87 892.27,71.952 917.51,97.508 988.89,69 1004.3,62.865 1019.1,51.999 \ -1030.7,41.961", + lp="1079.9,61.5", + pos="e,1045.4,35.77 926.32,92.91 933.14,90.897 940.23,88.851 946.89,87 977.85,78.408 990.25,86.944 1016.9,69 1026.2,62.757 1034,53.389 \ +1040,44.443", style=solid]; category [height=0.5, pos="1174.9,18", width=1.4263]; nutrient -> category [color=blue, label=category, - lp="1169.4,61.5", - pos="e,1159.9,35.694 794.56,92.287 801.86,90.209 809.57,88.297 816.89,87 881.78,75.507 1051.4,92.812 1112.9,69 1127.6,63.291 1141.6,52.717 \ -1152.5,42.758", + lp="1181.4,61.5", + pos="e,1164.9,35.949 924.9,92.408 932.11,90.347 939.7,88.411 946.89,87 1027.5,71.185 1057.8,106.46 1130.9,69 1141.9,63.35 1151.4,53.666 \ +1158.8,44.316", style=solid]; "trade name" [color=blue, height=0.5, @@ -109,9 +110,9 @@ digraph { width=2.2748]; nutrient -> "trade name" [color=blue, label="trade name", - lp="1290.9,61.5", - pos="e,1296,34.766 794.54,92.206 801.85,90.133 809.56,88.244 816.89,87 987.09,58.117 1036.4,106.52 1204.9,69 1233.4,62.66 1263.7,50.114 \ -1286.9,39.175", + lp="1298.9,61.5", + pos="e,1298.2,35.106 924.56,92.32 931.87,90.239 939.58,88.318 946.89,87 1065.3,65.681 1100.3,98.559 1216.9,69 1242.1,62.61 1268.6,50.557 \ +1289.2,39.886", style=solid]; "available from" [color=blue, height=0.5, @@ -120,13 +121,35 @@ digraph { width=3.2858]; nutrient -> "available from" [color=blue, label="available from", - lp="1463.4,61.5", - pos="e,1492.7,34.35 794.53,92.139 801.84,90.071 809.56,88.201 816.89,87 1044.7,49.714 1107.2,100.13 1335.9,69 1386,62.174 1441.7,48.449 \ -1482.9,37.102", + lp="1468.4,61.5", + pos="e,1493.9,34.455 924.54,92.2 931.85,90.127 939.56,88.24 946.89,87 1121,57.54 1169.1,94.546 1343.9,69 1391.7,62.009 1444.7,48.478 \ +1484.2,37.254", + style=solid]; + "max tolerated dose" [color=blue, + height=0.5, + label=string, + pos="1718.9,18", + width=1.0652]; + nutrient -> "max tolerated dose" [color=blue, + label="max tolerated dose", + lp="1674.9,61.5", + pos="e,1689.9,29.901 924.22,92.206 931.62,90.105 939.45,88.205 946.89,87 1200.2,45.993 1269.4,101.24 1523.9,69 1590.3,60.585 1606.6,54.544 \ +1670.9,36 1674,35.106 1677.2,34.122 1680.4,33.091", + style=solid]; + "is toxic" [color=blue, + height=0.5, + label=boolean, + pos="1854.9,18", + width=1.2999]; + nutrient -> "is toxic" [color=blue, + label="is toxic", + lp="1815.9,61.5", + pos="e,1830.9,33.775 924.22,92.156 931.61,90.059 939.45,88.172 946.89,87 1122.8,59.31 1574.5,109.56 1747.9,69 1774,62.884 1801.4,49.943 \ +1822,38.759", style=solid]; "named thing_category" [color=blue, height=0.5, label="named thing", - pos="895.89,105", + pos="1025.9,105", width=1.9318]; } diff --git a/graphviz/nutrient.svg b/graphviz/nutrient.svg index 05b06568ab..7b945888ff 100644 --- a/graphviz/nutrient.svg +++ b/graphviz/nutrient.svg @@ -4,16 +4,16 @@ - + %3 - + nutrient - -nutrient + +nutrient @@ -24,9 +24,9 @@ nutrient->chemical entity - - -is_a + + +is_a @@ -37,9 +37,9 @@ nutrient->id - - -id + + +id @@ -50,9 +50,9 @@ nutrient->iri - - -iri + + +iri @@ -63,9 +63,9 @@ nutrient->type - - -type + + +type @@ -76,9 +76,9 @@ nutrient->name - - -name + + +name @@ -89,9 +89,9 @@ nutrient->description - - -description + + +description @@ -102,9 +102,9 @@ nutrient->source - - -source + + +source @@ -115,9 +115,9 @@ nutrient->provided by - - -provided by + + +provided by @@ -128,9 +128,9 @@ nutrient->has attribute - - -has attribute + + +has attribute @@ -141,9 +141,9 @@ nutrient->category - - -category + + +category @@ -154,9 +154,9 @@ nutrient->trade name - - -trade name + + +trade name @@ -167,15 +167,41 @@ nutrient->available from - - -available from + + +available from + + + +max tolerated dose + +string + + + +nutrient->max tolerated dose + + +max tolerated dose + + + +is toxic + +boolean + + + +nutrient->is toxic + + +is toxic named thing_category - -named thing + +named thing diff --git a/graphviz/processed_material.gv b/graphviz/processed_material.gv index ce48c10700..bf50b33520 100644 --- a/graphviz/processed_material.gv +++ b/graphviz/processed_material.gv @@ -1,16 +1,16 @@ digraph { - graph [bb="0,0,2028,123"]; + graph [bb="0,0,2270,123"]; node [label="\N"]; "processed material" [height=0.5, label="processed material", - pos="907.99,105", + pos="1018,105", width=2.7623]; "chemical mixture" [height=0.5, pos="90.992,18", width=2.5276]; "processed material" -> "chemical mixture" [label=is_a, - lp="339.99,61.5", - pos="e,144.26,32.716 809.21,102.55 693.08,99.815 494.76,91.897 325.99,69 267.14,61.016 201.07,46.448 154,35.088"]; + lp="336.99,61.5", + pos="e,143.09,32.761 918.56,104.04 783.24,102.94 533.79,96.837 322.99,69 264.77,61.311 199.46,46.683 153,35.227"]; id [color=blue, height=0.5, label=string, @@ -18,9 +18,9 @@ digraph { width=1.0652]; "processed material" -> id [color=blue, label=id, - lp="452.99,61.5", - pos="e,266.98,29.984 811.6,100.29 717.87,95.834 571.65,86.645 445.99,69 374.09,58.904 355.93,55.499 285.99,36 282.88,35.133 279.69,34.168 \ -276.49,33.151", + lp="447.99,61.5", + pos="e,266.99,29.954 919.29,102.48 804.05,99.683 607.93,91.705 440.99,69 371.2,59.508 353.78,55.131 285.99,36 282.89,35.124 279.69,34.151 \ +276.49,33.129", style=solid]; iri [color=blue, height=0.5, @@ -29,9 +29,9 @@ digraph { width=1.2277]; "processed material" -> iri [color=blue, label=iri, - lp="553.99,61.5", - pos="e,372.27,30.005 816.13,98.076 742.73,92.632 637.39,83.226 545.99,69 477.26,58.301 460.24,53.797 392.99,36 389.41,35.052 385.71,34.014 \ -382,32.933", + lp="541.99,61.5", + pos="e,372.29,29.913 920.15,101.45 822.03,97.83 666.84,89.22 533.99,69 470.36,59.316 455.06,53.009 392.99,36 389.42,35.02 385.72,33.96 \ +382.02,32.865", style=solid]; type [color=blue, height=0.5, @@ -40,8 +40,9 @@ digraph { width=1.0652]; "processed material" -> type [color=blue, label=type, - lp="639.99,61.5", - pos="e,468.65,29.968 820.26,96.451 734.07,87.497 599.49,69.386 486.99,36 484.09,35.139 481.11,34.197 478.12,33.212", + lp="646.99,61.5", + pos="e,468.64,29.989 923.71,99.043 845.08,94.056 730.26,84.79 630.99,69 566.15,58.686 549.98,54.534 486.99,36 484.09,35.146 481.1,34.209 \ +478.11,33.227", style=solid]; name [color=blue, height=0.5, @@ -50,8 +51,8 @@ digraph { width=1.5707]; "processed material" -> name [color=blue, label=name, - lp="738.99,61.5", - pos="e,590.58,31.607 835.8,92.541 800.41,86.438 757.26,78.277 718.99,69 678.57,59.2 633.41,45.409 600.41,34.792", + lp="742.99,61.5", + pos="e,589.68,31.738 927.97,97.27 869.22,91.91 791.07,82.948 722.99,69 680.47,60.29 633.19,45.995 599.31,34.917", style=solid]; description [color=blue, height=0.5, @@ -60,8 +61,8 @@ digraph { width=2.0943]; "processed material" -> description [color=blue, label=description, - lp="833.49,61.5", - pos="e,728.64,35.167 853.33,89.93 833.95,84.275 812.2,77.151 792.99,69 773.97,60.93 753.78,49.953 737.35,40.34", + lp="844.49,61.5", + pos="e,729.5,34.858 932,95.862 892.37,90.615 845.12,82.215 803.99,69 781.26,61.696 757.25,49.994 738.35,39.747", style=solid]; source [color=blue, height=0.5, @@ -70,8 +71,8 @@ digraph { width=1.5707]; "processed material" -> source [color=blue, label=source, - lp="907.99,61.5", - pos="e,863.92,35.885 896.86,86.799 888.98,74.622 878.28,58.089 869.43,44.398", + lp="932.99,61.5", + pos="e,867.77,35.382 960.08,90.319 943,85.003 924.69,77.983 908.99,69 896.67,61.951 884.7,51.852 875.01,42.574", style=solid]; "provided by" [color=blue, height=0.5, @@ -80,8 +81,8 @@ digraph { width=1.0291]; "processed material" -> "provided by" [color=blue, label="provided by", - lp="988.49,61.5", - pos="e,956.19,35.59 922.48,86.943 926.99,81.359 931.86,75.036 935.99,69 941.29,61.262 946.58,52.512 951.17,44.519", + lp="1007.5,61.5", + pos="e,961.11,36.192 983.21,88.133 975.91,83.1 969.17,76.768 964.99,69 961.32,62.168 960.21,54.012 960.32,46.289", style=solid]; "has attribute" [color=blue, height=0.5, @@ -90,17 +91,16 @@ digraph { width=1.4443]; "processed material" -> "has attribute" [color=blue, label="has attribute", - lp="1097,61.5", - pos="e,1063.2,36.182 980.83,92.734 999.58,87.551 1019,79.998 1035,69 1044.1,62.769 1051.8,53.565 1057.8,44.747", + lp="1106,61.5", + pos="e,1066.1,35.908 1035.5,87.125 1040.6,81.651 1045.9,75.346 1050,69 1054.7,61.737 1058.9,53.287 1062.3,45.422", style=solid]; category [height=0.5, pos="1193,18", width=1.4263]; "processed material" -> category [color=blue, label=category, - lp="1198.5,61.5", - pos="e,1182.5,35.784 979.71,92.5 991.81,90.619 1004.3,88.724 1016,87 1074.6,78.396 1095.7,96.696 1148,69 1159.2,63.085 1168.9,53.228 \ -1176.5,43.823", + lp="1204.5,61.5", + pos="e,1184.9,35.789 1097.4,94.015 1118,88.83 1139.4,80.956 1157,69 1166.1,62.779 1173.8,53.415 1179.6,44.467", style=solid]; "trade name" [color=blue, height=0.5, @@ -109,9 +109,8 @@ digraph { width=2.2748]; "processed material" -> "trade name" [color=blue, label="trade name", - lp="1316,61.5", - pos="e,1316,34.97 978.18,92.183 990.75,90.286 1003.7,88.468 1016,87 1112.5,75.434 1139.9,93.476 1234,69 1259.3,62.405 1286.1,50.347 1306.9,\ -39.724", + lp="1320,61.5", + pos="e,1316.2,35.114 1090.3,92.62 1155,82.429 1239.8,69.072 1240,69 1263.3,61.741 1287.9,50.081 1307.4,39.846", style=solid]; "available from" [color=blue, height=0.5, @@ -120,35 +119,57 @@ digraph { width=3.2858]; "processed material" -> "available from" [color=blue, label="available from", - lp="1485.5,61.5", - pos="e,1511.7,34.355 977.28,92.002 990.12,90.089 1003.4,88.312 1016,87 1168.7,71.041 1209.1,91.636 1361,69 1409,61.84 1462.3,48.319 1502,\ -37.141", + lp="1488.5,61.5", + pos="e,1511.5,34.398 1087.9,92.152 1100.5,90.248 1113.6,88.435 1126,87 1231.8,74.708 1259.9,86.167 1365,69 1411.3,61.431 1462.8,48.216 \ +1501.4,37.272", + style=solid]; + "max tolerated dose" [color=blue, + height=0.5, + label=string, + pos="1737,18", + width=1.0652]; + "processed material" -> "max tolerated dose" [color=blue, + label="max tolerated dose", + lp="1694,61.5", + pos="e,1708,29.887 1087,91.951 1099.9,90.031 1113.3,88.264 1126,87 1311,68.514 1359.7,93.733 1544,69 1609.5,60.209 1625.5,54.397 1689,\ +36 1692.1,35.102 1695.3,34.114 1698.5,33.081", + style=solid]; + "is toxic" [color=blue, + height=0.5, + label=boolean, + pos="1840,18", + width=1.2999]; + "processed material" -> "is toxic" [color=blue, + label="is toxic", + lp="1824,61.5", + pos="e,1823,34.921 1086.4,91.882 1099.5,89.943 1113.1,88.187 1126,87 1196.9,80.447 1699.2,91.028 1767,69 1784.7,63.258 1801.9,51.787 \ +1815.2,41.279", style=solid]; "is supplement" [color=blue, height=0.5, label="chemical mixture", - pos="1789,18", + pos="1996,18", width=2.5276]; "processed material" -> "is supplement" [color=blue, label="is supplement", - lp="1681.5,61.5", - pos="e,1734.7,32.624 976.68,91.903 989.7,89.975 1003.2,88.218 1016,87 1248.4,64.807 1309.1,96.163 1541,69 1604,61.614 1675,46.629 1724.8,\ -34.98", + lp="1960.5,61.5", + pos="e,1961.2,34.7 1086.4,91.847 1099.5,89.911 1113.1,88.166 1126,87 1287.2,72.387 1694.8,98.233 1854,69 1887.8,62.792 1924.3,49.769 \ +1951.9,38.571", style=solid]; "highest FDA approval status" [color=blue, height=0.5, label=string, - pos="1936,18", + pos="2143,18", width=1.0652]; "processed material" -> "highest FDA approval status" [color=blue, label="highest FDA approval status", - lp="1925.5,61.5", - pos="e,1907.4,30.049 976.38,91.85 989.49,89.914 1003.1,88.167 1016,87 1334.8,58.051 1418.1,106.91 1736,69 1805.1,60.761 1822.1,55.207 \ -1889,36 1891.9,35.164 1894.9,34.241 1897.9,33.269", + lp="2167.5,61.5", + pos="e,2117.8,31.909 1086.1,91.843 1099.3,89.895 1113,88.145 1126,87 1224.4,78.299 1918.1,88.272 2015,69 2048,62.439 2083.5,47.939 2108.7,\ +36.235", style=solid]; "named thing_category" [color=blue, height=0.5, label="named thing", - pos="1095,105", + pos="1205,105", width=1.9318]; } diff --git a/graphviz/processed_material.svg b/graphviz/processed_material.svg index 4fd3b3cc22..85f1cf1aa1 100644 --- a/graphviz/processed_material.svg +++ b/graphviz/processed_material.svg @@ -4,16 +4,16 @@ - + %3 - + processed material - -processed material + +processed material @@ -24,9 +24,9 @@ processed material->chemical mixture - - -is_a + + +is_a @@ -37,9 +37,9 @@ processed material->id - - -id + + +id @@ -50,9 +50,9 @@ processed material->iri - - -iri + + +iri @@ -63,9 +63,9 @@ processed material->type - - -type + + +type @@ -76,9 +76,9 @@ processed material->name - - -name + + +name @@ -89,9 +89,9 @@ processed material->description - - -description + + +description @@ -102,9 +102,9 @@ processed material->source - - -source + + +source @@ -115,9 +115,9 @@ processed material->provided by - - -provided by + + +provided by @@ -128,9 +128,9 @@ processed material->has attribute - - -has attribute + + +has attribute @@ -141,9 +141,9 @@ processed material->category - - -category + + +category @@ -154,9 +154,9 @@ processed material->trade name - - -trade name + + +trade name @@ -167,41 +167,67 @@ processed material->available from - - -available from + + +available from - + +max tolerated dose + +string + + + +processed material->max tolerated dose + + +max tolerated dose + + + +is toxic + +boolean + + + +processed material->is toxic + + +is toxic + + + is supplement - -chemical mixture + +chemical mixture - + processed material->is supplement - - -is supplement + + +is supplement - + highest FDA approval status - -string + +string - + processed material->highest FDA approval status - - -highest FDA approval status + + +highest FDA approval status named thing_category - -named thing + +named thing diff --git a/graphviz/siRNA.gv b/graphviz/siRNA.gv index 52bdaf401b..8034ef3f57 100644 --- a/graphviz/siRNA.gv +++ b/graphviz/siRNA.gv @@ -1,16 +1,16 @@ digraph { - graph [bb="0,0,2496.7,123"]; + graph [bb="0,0,2703.7,123"]; node [label="\N"]; siRNA [height=0.5, label=siRNA, - pos="1134.5,105", + pos="1254.5,105", width=1.1013]; "noncoding RNA product" [height=0.5, pos="121.54,18", width=3.3761]; siRNA -> "noncoding RNA product" [label=is_a, - lp="401.54,61.5", - pos="e,184.58,33.411 1094.7,104.08 982.82,103.87 656.41,100.41 387.54,69 321.77,61.316 247.81,46.941 194.6,35.57"]; + lp="398.54,61.5", + pos="e,183.58,33.479 1214.5,104.49 1090.6,105.54 702.92,105.47 384.54,69 319.36,61.535 246.1,47.101 193.49,35.653"]; id [color=blue, height=0.5, label=string, @@ -18,9 +18,9 @@ digraph { width=1.0652]; siRNA -> id [color=blue, label=id, - lp="514.54,61.5", - pos="e,328.53,29.984 1094.7,103.81 995.29,102.9 728.08,97.739 507.54,69 435.54,59.618 417.48,55.499 347.54,36 344.43,35.133 341.23,34.168 \ -338.03,33.151", + lp="513.54,61.5", + pos="e,328.53,29.979 1214.6,104.34 1102.5,104.83 775.46,102.98 506.54,69 434.94,59.952 417.05,55.425 347.54,36 344.43,35.132 341.23,34.165 \ +338.04,33.146", style=solid]; iri [color=blue, height=0.5, @@ -29,8 +29,8 @@ digraph { width=1.2277]; siRNA -> iri [color=blue, label=iri, - lp="603.54,61.5", - pos="e,433.92,29.82 1094.7,103.66 1005.1,102.4 780.82,96.505 595.54,69 542.43,61.116 482.84,44.688 443.67,32.81", + lp="601.54,61.5", + pos="e,433.9,30.049 1214.8,104.38 1111.7,104.83 827.28,102.65 593.54,69 541.18,61.461 482.54,45.101 443.79,33.141", style=solid]; type [color=blue, height=0.5, @@ -40,7 +40,7 @@ digraph { siRNA -> type [color=blue, label=type, lp="708.54,61.5", - pos="e,530.19,29.989 1095,102.81 1017.4,100.04 839.96,91.604 692.54,69 627.64,59.049 611.53,54.534 548.54,36 545.64,35.146 542.65,34.209 \ + pos="e,530.19,29.989 1214.8,103.75 1122.6,102.67 887.01,97.146 692.54,69 627.56,59.595 611.53,54.534 548.54,36 545.64,35.146 542.65,34.209 \ 539.66,33.227", style=solid]; name [color=blue, @@ -50,8 +50,8 @@ digraph { width=1.5707]; siRNA -> name [color=blue, label=name, - lp="811.54,61.5", - pos="e,652.06,31.655 1095.1,102.21 1031,98.788 900.31,89.751 791.54,69 746.81,60.468 697,45.928 661.64,34.72", + lp="812.54,61.5", + pos="e,651.54,31.719 1215,103.64 1134.7,102.32 947.2,96.303 792.54,69 747.18,60.992 696.74,46.25 661.17,34.84", style=solid]; description [color=blue, height=0.5, @@ -60,8 +60,8 @@ digraph { width=2.0943]; siRNA -> description [color=blue, label=description, - lp="916.04,61.5", - pos="e,793.34,34.764 1095.2,102.21 1043.8,99.087 951.44,90.726 875.54,69 850.34,61.788 823.51,49.83 802.54,39.417", + lp="918.04,61.5", + pos="e,793.33,34.87 1214.7,104.49 1145.2,104.43 997.45,100.2 877.54,69 851.5,62.223 823.85,50.083 802.41,39.462", style=solid]; source [color=blue, height=0.5, @@ -70,8 +70,8 @@ digraph { width=1.5707]; siRNA -> source [color=blue, label=source, - lp="1008.5,61.5", - pos="e,932.9,35.187 1096.9,99.373 1065.7,94.582 1020.8,85.419 984.54,69 969.06,61.999 953.52,51.348 941.02,41.673", + lp="1015.5,61.5", + pos="e,933.81,35.006 1214.9,104.1 1162.3,103.04 1067.1,96.952 991.54,69 973.83,62.455 956.03,51.266 942.01,41.13", style=solid]; "provided by" [color=blue, height=0.5, @@ -80,8 +80,8 @@ digraph { width=1.0291]; siRNA -> "provided by" [color=blue, label="provided by", - lp="1088,61.5", - pos="e,1029.4,36.214 1098.6,97.111 1080.7,92.03 1059.8,83.405 1045.5,69 1039.3,62.709 1035.1,54.176 1032.2,45.94", + lp="1100,61.5", + pos="e,1032.8,36.035 1215.8,100.87 1166,96.207 1082.8,86.106 1057.5,69 1048.9,63.129 1042.2,53.953 1037.3,45.055", style=solid]; "has attribute" [color=blue, height=0.5, @@ -90,16 +90,16 @@ digraph { width=1.4443]; siRNA -> "has attribute" [color=blue, label="has attribute", - lp="1181.5,61.5", - pos="e,1133.7,36.175 1134.3,86.799 1134.2,75.163 1134,59.548 1133.9,46.237", + lp="1203.5,61.5", + pos="e,1137.8,36.353 1217.9,98.098 1197.7,93.229 1173.5,84.494 1156.5,69 1149.8,62.786 1144.8,54.17 1141.3,45.84", style=solid]; category [height=0.5, pos="1254.5,18", width=1.4263]; siRNA -> category [color=blue, label=category, - lp="1275,61.5", - pos="e,1250.6,36.344 1164.9,93.246 1193.5,83.073 1232.2,69.31 1232.5,69 1239.2,62.776 1244,54.158 1247.3,45.829", + lp="1286,61.5", + pos="e,1254.5,36.175 1254.5,86.799 1254.5,75.163 1254.5,59.548 1254.5,46.237", style=solid]; "trade name" [color=blue, height=0.5, @@ -108,9 +108,8 @@ digraph { width=2.2748]; siRNA -> "trade name" [color=blue, label="trade name", - lp="1387.5,61.5", - pos="e,1380.4,35.319 1163.7,92.623 1169.9,90.52 1176.4,88.513 1182.5,87 1238.3,73.342 1255.9,86.64 1310.5,69 1331.8,62.129 1354.1,50.704 \ -1371.6,40.508", + lp="1388.5,61.5", + pos="e,1379.3,35.143 1280.2,91.034 1292.7,84.574 1308,76.548 1321.5,69 1337.7,59.957 1355.4,49.52 1370.4,40.529", style=solid]; "available from" [color=blue, height=0.5, @@ -119,68 +118,90 @@ digraph { width=3.2858]; siRNA -> "available from" [color=blue, label="available from", - lp="1553,61.5", - pos="e,1574.6,34.473 1163.1,92.47 1169.4,90.324 1176.1,88.339 1182.5,87 1291.6,64.2 1322.6,87.183 1432.5,69 1477.6,61.553 1527.4,48.333 \ -1564.9,37.357", + lp="1549,61.5", + pos="e,1572.3,34.277 1283.7,92.608 1289.9,90.506 1296.4,88.504 1302.5,87 1359.6,73.118 1375.9,80.499 1433.5,69 1477.1,60.3 1525.6,47.497 \ +1562.7,37.024", + style=solid]; + "max tolerated dose" [color=blue, + height=0.5, + label=string, + pos="1798.5,18", + width=1.0652]; + siRNA -> "max tolerated dose" [color=blue, + label="max tolerated dose", + lp="1755.5,61.5", + pos="e,1769.5,29.895 1283.1,92.411 1289.4,90.268 1296.1,88.299 1302.5,87 1434.3,60.292 1471.4,87.884 1604.5,69 1670.4,59.657 1686.6,54.47 \ +1750.5,36 1753.6,35.104 1756.8,34.118 1760,33.086", + style=solid]; + "is toxic" [color=blue, + height=0.5, + label=boolean, + pos="1901.5,18", + width=1.2999]; + siRNA -> "is toxic" [color=blue, + label="is toxic", + lp="1885.5,61.5", + pos="e,1884.5,34.885 1282.8,92.374 1289.2,90.205 1296,88.235 1302.5,87 1417.5,65.222 1717.4,105.5 1828.5,69 1846.2,63.204 1863.4,51.73 \ +1876.7,41.234", style=solid]; "is metabolite" [color=blue, height=0.5, label=boolean, - pos="1806.5,18", + pos="2013.5,18", width=1.2999]; siRNA -> "is metabolite" [color=blue, label="is metabolite", - lp="1733.5,61.5", - pos="e,1772,30.251 1163.1,92.326 1169.4,90.189 1176.1,88.244 1182.5,87 1368.6,50.968 1420.8,94.559 1608.5,69 1662.3,61.682 1722.5,45.246 \ -1762.3,33.209", + lp="2002.5,61.5", + pos="e,1991.3,33.964 1282.8,92.35 1289.2,90.183 1296,88.219 1302.5,87 1436.5,61.949 1783.5,102.79 1915.5,69 1939.4,62.895 1964.1,50.261 \ +1982.7,39.22", style=solid]; "in taxon" [color=blue, height=0.5, label="organism taxon", - pos="1954.5,18", + pos="2161.5,18", width=2.3109]; siRNA -> "in taxon" [color=blue, label="in taxon", - lp="1880.5,61.5", - pos="e,1914.7,33.884 1162.8,92.353 1169.2,90.185 1176,88.221 1182.5,87 1445.6,37.726 1520.2,111.11 1784.5,69 1826,62.393 1871.6,48.613 \ -1905.1,37.189", + lp="2126.5,61.5", + pos="e,2134.7,35.217 1282.8,92.324 1289.2,90.158 1296,88.201 1302.5,87 1466.7,56.757 1891,106.86 2053.5,69 2078.8,63.108 2105.3,50.941 \ +2125.8,40.085", style=solid]; "has biological sequence" [color=blue, height=0.5, label="biological sequence", - pos="2157.5,18", + pos="2364.5,18", width=2.8164]; siRNA -> "has biological sequence" [color=blue, label="has biological sequence", - lp="2086,61.5", - pos="e,2102.3,33.252 1162.8,92.327 1169.2,90.161 1176,88.203 1182.5,87 1342.3,57.509 1752.1,87.382 1913.5,69 1974.8,62.021 2043.6,47.291 \ -2092.5,35.617", + lp="2324,61.5", + pos="e,2316.2,33.951 1282.8,92.309 1289.2,90.144 1296,88.192 1302.5,87 1489.9,52.768 1970.7,93.715 2159.5,69 2209.9,62.413 2265.8,48.307 \ +2306.5,36.752", style=solid]; synonym [color=blue, height=0.5, label="label type", - pos="2333.5,18", + pos="2540.5,18", width=1.5707]; siRNA -> synonym [color=blue, label=synonym, - lp="2269.5,61.5", - pos="e,2300.1,32.607 1162.8,92.295 1169.2,90.131 1176,88.182 1182.5,87 1399.5,47.687 1956.9,104.43 2174.5,69 2214.9,62.425 2259.2,47.864 \ -2290.7,36.142", + lp="2495.5,61.5", + pos="e,2511.9,33.584 1282.8,92.286 1289.2,90.122 1296,88.176 1302.5,87 1545.3,43.247 2170.5,116.63 2412.5,69 2444.1,62.791 2477.9,49.261 \ +2502.8,37.839", style=solid]; xref [color=blue, height=0.5, label="iri type", - pos="2452.5,18", + pos="2659.5,18", width=1.2277]; siRNA -> xref [color=blue, label=xref, - lp="2378,61.5", - pos="e,2423.7,31.822 1162.8,92.285 1169.2,90.121 1176,88.175 1182.5,87 1428.2,42.757 2059.6,111.7 2305.5,69 2343.6,62.391 2385.1,47.514 \ -2414.3,35.696", + lp="2596,61.5", + pos="e,2632.9,32.651 1282.8,92.278 1289.2,90.115 1296,88.171 1302.5,87 1437,62.884 2397.5,95.265 2531.5,69 2563.9,62.653 2598.7,48.567 \ +2623.8,36.958", style=solid]; "named thing_category" [color=blue, height=0.5, label="named thing", - pos="1261.5,105", + pos="1381.5,105", width=1.9318]; } diff --git a/graphviz/siRNA.svg b/graphviz/siRNA.svg index 09b0791984..dfcc8c828e 100644 --- a/graphviz/siRNA.svg +++ b/graphviz/siRNA.svg @@ -4,16 +4,16 @@ - + %3 - + siRNA - -siRNA + +siRNA @@ -24,9 +24,9 @@ siRNA->noncoding RNA product - - -is_a + + +is_a @@ -37,9 +37,9 @@ siRNA->id - + -id +id @@ -50,9 +50,9 @@ siRNA->iri - - -iri + + +iri @@ -63,7 +63,7 @@ siRNA->type - + type @@ -76,9 +76,9 @@ siRNA->name - - -name + + +name @@ -89,9 +89,9 @@ siRNA->description - - -description + + +description @@ -102,9 +102,9 @@ siRNA->source - - -source + + +source @@ -115,9 +115,9 @@ siRNA->provided by - - -provided by + + +provided by @@ -128,9 +128,9 @@ siRNA->has attribute - - -has attribute + + +has attribute @@ -141,9 +141,9 @@ siRNA->category - - -category + + +category @@ -154,9 +154,9 @@ siRNA->trade name - - -trade name + + +trade name @@ -167,80 +167,106 @@ siRNA->available from - - -available from + + +available from - + +max tolerated dose + +string + + + +siRNA->max tolerated dose + + +max tolerated dose + + + +is toxic + +boolean + + + +siRNA->is toxic + + +is toxic + + + is metabolite - -boolean + +boolean - + siRNA->is metabolite - - -is metabolite + + +is metabolite - + in taxon - -organism taxon + +organism taxon - + siRNA->in taxon - - -in taxon + + +in taxon - + has biological sequence - -biological sequence + +biological sequence - + siRNA->has biological sequence - - -has biological sequence + + +has biological sequence - + synonym - -label type + +label type - + siRNA->synonym - - -synonym + + +synonym - + xref - -iri type + +iri type - + siRNA->xref - - -xref + + +xref named thing_category - -named thing + +named thing diff --git a/graphviz/small_molecule.gv b/graphviz/small_molecule.gv index 38e822708f..6214b013b4 100644 --- a/graphviz/small_molecule.gv +++ b/graphviz/small_molecule.gv @@ -1,16 +1,16 @@ digraph { - graph [bb="0,0,1773.1,123"]; + graph [bb="0,0,1980.1,123"]; node [label="\N"]; "small molecule" [height=0.5, label="small molecule", - pos="861.09,105", + pos="970.09,105", width=2.2206]; "molecular entity" [height=0.5, pos="87.092,18", width=2.4192]; "small molecule" -> "molecular entity" [label=is_a, - lp="342.09,61.5", - pos="e,140.33,32.267 781.73,102.23 677.3,99.113 488.21,90.759 328.09,69 267.22,60.727 198.7,45.976 150.33,34.633"]; + lp="343.09,61.5", + pos="e,140.05,32.322 890.3,103.46 768.71,101.77 529.97,95.087 329.09,69 267.6,61.014 198.4,46.106 149.8,34.639"]; iri [color=blue, height=0.5, label="iri type", @@ -18,9 +18,8 @@ digraph { width=1.2277]; "small molecule" -> iri [color=blue, label=iri, - lp="449.09,61.5", - pos="e,269.37,29.991 783.33,100.6 698.75,96.18 559.76,86.831 441.09,69 373.16,58.792 356.48,53.665 290.09,36 286.51,35.047 282.81,34.005 \ -279.11,32.922", + lp="439.09,61.5", + pos="e,269.48,29.82 890.66,102.93 785.14,100.58 593.19,93.063 431.09,69 377.98,61.116 318.39,44.688 279.22,32.81", style=solid]; type [color=blue, height=0.5, @@ -29,8 +28,9 @@ digraph { width=1.0652]; "small molecule" -> type [color=blue, label=type, - lp="542.09,61.5", - pos="e,365.73,30.023 784.52,99.736 689.12,92.919 521.86,75.992 384.09,36 381.19,35.156 378.2,34.227 375.21,33.251", + lp="544.09,61.5", + pos="e,365.74,29.989 891.85,101.26 803.2,97.361 654.59,88.396 528.09,69 463.19,59.049 447.08,54.534 384.09,36 381.19,35.146 378.2,34.209 \ +375.22,33.227", style=solid]; name [color=blue, height=0.5, @@ -40,7 +40,7 @@ digraph { "small molecule" -> name [color=blue, label=name, lp="647.09,61.5", - pos="e,488.41,31.346 791.82,95.982 745.03,89.993 682.01,80.814 627.09,69 582.86,59.485 533.38,45.188 498,34.315", + pos="e,487.62,31.655 893.25,99.985 823.37,95.431 717.64,86.273 627.09,69 582.37,60.468 532.55,45.928 497.19,34.72", style=solid]; description [color=blue, height=0.5, @@ -49,8 +49,8 @@ digraph { width=2.0943]; "small molecule" -> description [color=blue, label=description, - lp="747.59,61.5", - pos="e,629.36,34.76 800.29,93.301 771.62,87.469 737.18,79.315 707.09,69 683.65,60.962 658.49,49.37 638.47,39.37", + lp="751.59,61.5", + pos="e,628.9,34.764 893.82,99.505 841.59,95.023 771.18,86.199 711.09,69 685.89,61.788 659.06,49.83 638.09,39.417", style=solid]; source [color=blue, height=0.5, @@ -59,8 +59,8 @@ digraph { width=1.5707]; "small molecule" -> source [color=blue, label=source, - lp="834.09,61.5", - pos="e,768.64,35.223 836.38,87.72 827.92,81.971 818.48,75.353 810.09,69 798.83,60.474 786.8,50.609 776.49,41.906", + lp="844.09,61.5", + pos="e,768.45,35.187 904.79,94.514 877.79,89.139 846.65,81.011 820.09,69 804.61,61.999 789.07,51.348 776.58,41.673", style=solid]; "provided by" [color=blue, height=0.5, @@ -69,8 +69,8 @@ digraph { width=1.0291]; "small molecule" -> "provided by" [color=blue, label="provided by", - lp="904.59,61.5", - pos="e,861.89,36.175 861.29,86.799 861.43,75.163 861.62,59.548 861.77,46.237", + lp="923.59,61.5", + pos="e,864.96,36.214 917.29,91.448 904.16,86.267 891.01,79.037 881.09,69 874.87,62.709 870.65,54.176 867.8,45.94", style=solid]; "has attribute" [color=blue, height=0.5, @@ -79,17 +79,16 @@ digraph { width=1.4443]; "small molecule" -> "has attribute" [color=blue, label="has attribute", - lp="1005.1,61.5", - pos="e,965.07,36.207 911.35,90.981 924.19,85.785 937.15,78.664 947.09,69 953.64,62.632 958.38,53.979 961.74,45.661", + lp="1017.1,61.5", + pos="e,969.29,36.175 969.89,86.799 969.75,75.163 969.57,59.548 969.41,46.237", style=solid]; category [height=0.5, pos="1090.1,18", width=1.4263]; "small molecule" -> category [color=blue, label=category, - lp="1103.6,61.5", - pos="e,1082.9,36.092 919.28,92.554 929.22,90.658 939.45,88.743 949.09,87 996.55,78.426 1015.5,95.029 1056.1,69 1065.2,63.136 1072.5,53.84 \ -1078,44.847", + lp="1110.6,61.5", + pos="e,1086.2,36.344 1027,92.292 1041.8,87.097 1056.7,79.648 1068.1,69 1074.8,62.776 1079.5,54.158 1082.9,45.829", style=solid]; "trade name" [color=blue, height=0.5, @@ -98,9 +97,8 @@ digraph { width=2.2748]; "small molecule" -> "trade name" [color=blue, label="trade name", - lp="1218.1,61.5", - pos="e,1214.9,35.147 917.76,92.22 928.15,90.297 938.93,88.46 949.09,87 1033.1,74.942 1057.5,92.043 1139.1,69 1162.4,62.416 1186.9,50.631 \ -1206,40.156", + lp="1220.1,61.5", + pos="e,1215.4,35.129 1028.4,92.615 1078.5,82.789 1143.2,70.014 1146.1,69 1167,61.582 1189.1,50.229 1206.7,40.215", style=solid]; "available from" [color=blue, height=0.5, @@ -109,38 +107,60 @@ digraph { width=3.2858]; "small molecule" -> "available from" [color=blue, label="available from", - lp="1385.6,61.5", - pos="e,1409.7,34.419 916.78,92.079 927.46,90.122 938.59,88.309 949.09,87 1087.8,69.705 1125,90.375 1263.1,69 1309.6,61.803 1361.1,48.437 \ -1399.7,37.335", + lp="1387.6,61.5", + pos="e,1408.9,34.368 1026.8,92.155 1037.1,90.239 1047.9,88.421 1058.1,87 1149.6,74.225 1174.1,84.577 1265.1,69 1310.6,61.218 1361,48.076 \ +1399,37.219", + style=solid]; + "max tolerated dose" [color=blue, + height=0.5, + label=string, + pos="1634.1,18", + width=1.0652]; + "small molecule" -> "max tolerated dose" [color=blue, + label="max tolerated dose", + lp="1592.1,61.5", + pos="e,1605.1,29.873 1025.8,91.99 1036.5,90.041 1047.6,88.254 1058.1,87 1228.2,66.702 1273.4,92.354 1443.1,69 1507.7,60.108 1523.5,54.25 \ +1586.1,36 1589.2,35.097 1592.4,34.106 1595.6,33.07", + style=solid]; + "is toxic" [color=blue, + height=0.5, + label=boolean, + pos="1737.1,18", + width=1.2999]; + "small molecule" -> "is toxic" [color=blue, + label="is toxic", + lp="1721.1,61.5", + pos="e,1720.3,34.91 1025.3,91.93 1036.1,89.961 1047.4,88.181 1058.1,87 1125.2,79.577 1601,90.117 1665.1,69 1682.4,63.296 1699.3,51.985 \ +1712.3,41.563", style=solid]; "is metabolite" [color=blue, height=0.5, label=boolean, - pos="1642.1,18", + pos="1849.1,18", width=1.2999]; "small molecule" -> "is metabolite" [color=blue, label="is metabolite", - lp="1567.1,61.5", - pos="e,1607.3,30.211 916.76,91.903 927.44,89.963 938.58,88.2 949.09,87 1166.5,62.175 1224.1,97.403 1441.1,69 1495.8,61.835 1557.2,45.288 \ -1597.5,33.184", + lp="1838.1,61.5", + pos="e,1826.9,33.988 1025.3,91.899 1036.1,89.932 1047.4,88.162 1058.1,87 1211.2,70.334 1601.8,106.94 1751.1,69 1775,62.935 1799.6,50.301 \ +1818.3,39.25", style=solid]; id [height=0.5, - pos="1746.1,18", + pos="1953.1,18", width=0.75]; "small molecule" -> id [color=blue, label=id, - lp="1675.1,61.5", - pos="e,1725,29.845 916.27,91.907 927.11,89.939 938.42,88.167 949.09,87 1096.9,70.841 1472.3,98.495 1618.1,69 1652.9,61.951 1690.6,46.175 \ -1715.9,34.216", + lp="1923.1,61.5", + pos="e,1939.5,33.965 1025.3,91.862 1036.1,89.898 1047.4,88.139 1058.1,87 1149.9,77.206 1802.1,100.01 1889.1,69 1905.3,63.23 1920.6,51.621 \ +1932.1,41.041", style=solid]; "named thing_category" [color=blue, height=0.5, label="named thing", - pos="1028.1,105", + pos="1137.1,105", width=1.9318]; "small molecule_id" [color=blue, height=0.5, label=string, - pos="1154.1,105", + pos="1263.1,105", width=1.0652]; } diff --git a/graphviz/small_molecule.svg b/graphviz/small_molecule.svg index bbaa1cf9ab..4d756b97c6 100644 --- a/graphviz/small_molecule.svg +++ b/graphviz/small_molecule.svg @@ -4,16 +4,16 @@ - + %3 - + small molecule - -small molecule + +small molecule @@ -24,9 +24,9 @@ small molecule->molecular entity - - -is_a + + +is_a @@ -37,9 +37,9 @@ small molecule->iri - - -iri + + +iri @@ -50,9 +50,9 @@ small molecule->type - - -type + + +type @@ -63,8 +63,8 @@ small molecule->name - - + + name @@ -76,9 +76,9 @@ small molecule->description - - -description + + +description @@ -89,9 +89,9 @@ small molecule->source - - -source + + +source @@ -102,9 +102,9 @@ small molecule->provided by - - -provided by + + +provided by @@ -115,9 +115,9 @@ small molecule->has attribute - - -has attribute + + +has attribute @@ -128,9 +128,9 @@ small molecule->category - - -category + + +category @@ -141,9 +141,9 @@ small molecule->trade name - - -trade name + + +trade name @@ -154,47 +154,73 @@ small molecule->available from - - -available from + + +available from - + +max tolerated dose + +string + + + +small molecule->max tolerated dose + + +max tolerated dose + + + +is toxic + +boolean + + + +small molecule->is toxic + + +is toxic + + + is metabolite - -boolean + +boolean - + small molecule->is metabolite - - -is metabolite + + +is metabolite - + id - -id + +id - + small molecule->id - - -id + + +id named thing_category - -named thing + +named thing - + small molecule_id - -string + +string diff --git a/graphviz/transcript.gv b/graphviz/transcript.gv index a49f1c674c..82042eb990 100644 --- a/graphviz/transcript.gv +++ b/graphviz/transcript.gv @@ -1,16 +1,16 @@ digraph { - graph [bb="0,0,2206.9,123"]; + graph [bb="0,0,2413.9,123"]; node [label="\N"]; transcript [height=0.5, label=transcript, - pos="973.54,105", + pos="1082.5,105", width=1.5887]; "nucleic acid entity" [height=0.5, pos="95.542,18", width=2.6539]; transcript -> "nucleic acid entity" [label=is_a, - lp="348.54,61.5", - pos="e,150.19,32.9 916.43,103.77 804.36,102.67 547.98,97.007 334.54,69 274.9,61.173 207.94,46.66 160.1,35.278"]; + lp="349.54,61.5", + pos="e,149.93,32.907 1025.1,104.4 899.51,104.6 591.21,101.41 335.54,69 275.43,61.379 207.95,46.77 159.89,35.302"]; id [color=blue, height=0.5, label=string, @@ -18,9 +18,9 @@ digraph { width=1.0652]; transcript -> id [color=blue, label=id, - lp="461.54,61.5", - pos="e,276.53,29.979 916.45,102.71 820.6,99.974 621.41,91.833 454.54,69 383.04,59.216 365.05,55.425 295.54,36 292.43,35.132 289.24,34.165 \ -286.04,33.146", + lp="462.54,61.5", + pos="e,276.53,29.984 1025.2,103.62 914.61,102.28 664.19,96.19 455.54,69 383.54,59.618 365.48,55.499 295.54,36 292.43,35.133 289.24,34.168 \ +286.04,33.151", style=solid]; iri [color=blue, height=0.5, @@ -29,9 +29,8 @@ digraph { width=1.2277]; transcript -> iri [color=blue, label=iri, - lp="561.54,61.5", - pos="e,381.82,29.991 917.22,101.67 836.37,97.793 682.88,88.435 553.54,69 485.61,58.792 468.93,53.665 402.54,36 398.96,35.047 395.26,34.005 \ -391.56,32.922", + lp="551.54,61.5", + pos="e,381.93,29.82 1025.6,103.38 926.87,101.63 717.92,94.887 543.54,69 490.43,61.116 430.84,44.688 391.67,32.81", style=solid]; type [color=blue, height=0.5, @@ -40,8 +39,9 @@ digraph { width=1.0652]; transcript -> type [color=blue, label=type, - lp="654.54,61.5", - pos="e,478.18,30.023 917.38,101.12 827.09,95.353 644.76,79.023 496.54,36 493.64,35.156 490.65,34.227 487.66,33.251", + lp="656.54,61.5", + pos="e,478.19,29.989 1025.7,102.16 941.28,98.821 777.88,90.058 640.54,69 575.64,59.049 559.53,54.534 496.54,36 493.64,35.146 490.65,34.209 \ +487.66,33.227", style=solid]; name [color=blue, height=0.5, @@ -51,7 +51,7 @@ digraph { transcript -> name [color=blue, label=name, lp="759.54,61.5", - pos="e,600.86,31.346 920.69,98.038 873.03,92.203 801.18,82.261 739.54,69 695.31,59.485 645.83,45.188 610.45,34.315", + pos="e,600.07,31.655 1026.6,101.28 958.3,97.273 839.64,88.096 739.54,69 694.82,60.468 645,45.928 609.64,34.72", style=solid]; description [color=blue, height=0.5, @@ -60,8 +60,8 @@ digraph { width=2.0943]; transcript -> description [color=blue, label=description, - lp="860.04,61.5", - pos="e,741.81,34.76 924.59,95.649 893.95,89.744 853.91,80.783 819.54,69 796.1,60.962 770.94,49.37 750.92,39.37", + lp="864.04,61.5", + pos="e,741.35,34.764 1026.5,101.1 973.4,97.27 891.81,88.54 823.54,69 798.34,61.788 771.51,49.83 750.54,39.417", style=solid]; source [color=blue, height=0.5, @@ -70,8 +70,8 @@ digraph { width=1.5707]; transcript -> source [color=blue, label=source, - lp="946.54,61.5", - pos="e,881.09,35.223 949.86,88.42 941.14,82.512 931.27,75.612 922.54,69 911.28,60.474 899.25,50.609 888.94,41.906", + lp="956.54,61.5", + pos="e,880.9,35.187 1030.9,97.079 1001.2,91.855 963.73,83.105 932.54,69 917.06,61.999 901.52,51.348 889.02,41.673", style=solid]; "provided by" [color=blue, height=0.5, @@ -80,8 +80,8 @@ digraph { width=1.0291]; transcript -> "provided by" [color=blue, label="provided by", - lp="1017,61.5", - pos="e,974.34,36.175 973.74,86.799 973.88,75.163 974.06,59.548 974.22,46.237", + lp="1036,61.5", + pos="e,977.41,36.214 1036.7,94.003 1021.3,88.731 1005.2,80.808 993.54,69 987.32,62.709 983.1,54.176 980.25,45.94", style=solid]; "has attribute" [color=blue, height=0.5, @@ -90,17 +90,16 @@ digraph { width=1.4443]; transcript -> "has attribute" [color=blue, label="has attribute", - lp="1117.5,61.5", - pos="e,1077.5,36.207 1017.6,93.368 1032.3,88.036 1048,80.238 1059.5,69 1066.1,62.632 1070.8,53.979 1074.2,45.661", + lp="1129.5,61.5", + pos="e,1081.7,36.175 1082.3,86.799 1082.2,75.163 1082,59.548 1081.9,46.237", style=solid]; category [height=0.5, pos="1202.5,18", width=1.4263]; transcript -> category [color=blue, label=category, - lp="1216,61.5", - pos="e,1195.4,36.202 1015.3,92.488 1023.3,90.494 1031.6,88.562 1039.5,87 1096.3,75.762 1119.4,99.56 1168.5,69 1177.8,63.264 1185.1,53.994 \ -1190.5,44.984", + lp="1223,61.5", + pos="e,1198.7,36.344 1124.4,92.646 1147,85.834 1172,76.971 1180.5,69 1187.2,62.776 1192,54.158 1195.3,45.829", style=solid]; "trade name" [color=blue, height=0.5, @@ -109,9 +108,9 @@ digraph { width=2.2748]; transcript -> "trade name" [color=blue, label="trade name", - lp="1330.5,61.5", - pos="e,1327.4,35.225 1014.5,92.317 1022.7,90.288 1031.4,88.388 1039.5,87 1132.8,71.151 1160.4,94.244 1251.5,69 1274.9,62.53 1299.3,50.75 \ -1318.4,40.248", + lp="1335.5,61.5", + pos="e,1328.3,35.15 1124.3,92.639 1132.3,90.63 1140.7,88.655 1148.5,87 1197,76.811 1211.6,84.74 1258.5,69 1279.8,61.89 1302,50.45 1319.6,\ +40.306", style=solid]; "available from" [color=blue, height=0.5, @@ -120,46 +119,68 @@ digraph { width=3.2858]; transcript -> "available from" [color=blue, label="available from", - lp="1498,61.5", - pos="e,1522.2,34.471 1014.1,92.201 1022.5,90.156 1031.2,88.279 1039.5,87 1187.3,64.237 1227.7,91.592 1375.5,69 1422.1,61.89 1473.6,48.52 \ -1512.1,37.394", + lp="1501,61.5", + pos="e,1522.6,34.397 1123.5,92.27 1131.7,90.245 1140.4,88.359 1148.5,87 1250.6,70.037 1278.6,86.164 1380.5,69 1425.5,61.428 1475.4,48.213 \ +1512.9,37.27", + style=solid]; + "max tolerated dose" [color=blue, + height=0.5, + label=string, + pos="1746.5,18", + width=1.0652]; + transcript -> "max tolerated dose" [color=blue, + label="max tolerated dose", + lp="1704.5,61.5", + pos="e,1717.5,29.866 1123.1,92.14 1131.5,90.099 1140.2,88.24 1148.5,87 1328.1,60.218 1376.7,93.648 1556.5,69 1620.7,60.201 1636.4,54.177 \ +1698.5,36 1701.6,35.095 1704.8,34.102 1708,33.065", + style=solid]; + "is toxic" [color=blue, + height=0.5, + label=boolean, + pos="1849.5,18", + width=1.2999]; + transcript -> "is toxic" [color=blue, + label="is toxic", + lp="1833.5,61.5", + pos="e,1832.8,34.916 1122.7,92.125 1131.2,90.058 1140.1,88.192 1148.5,87 1217.8,77.219 1711.1,90.848 1777.5,69 1794.9,63.305 1811.7,51.995 \ +1824.8,41.57", style=solid]; "is metabolite" [color=blue, height=0.5, label=boolean, - pos="1754.5,18", + pos="1961.5,18", width=1.2999]; transcript -> "is metabolite" [color=blue, label="is metabolite", - lp="1679.5,61.5", - pos="e,1719.8,30.228 1013.7,92.167 1022.2,90.097 1031.1,88.219 1039.5,87 1265.8,54.299 1326.9,98.494 1553.5,69 1608.3,61.878 1669.6,45.322 \ -1710,33.205", + lp="1950.5,61.5", + pos="e,1939.3,33.994 1122.7,92.102 1131.2,90.037 1140.1,88.177 1148.5,87 1306,65.036 1709.5,108.09 1863.5,69 1887.4,62.945 1912.1,50.31 \ +1930.7,39.257", style=solid]; "in taxon" [color=blue, height=0.5, label="organism taxon", - pos="1902.5,18", + pos="2109.5,18", width=2.3109]; transcript -> "in taxon" [color=blue, label="in taxon", - lp="1827.5,61.5", - pos="e,1862.5,33.807 1013.7,92.108 1022.2,90.042 1031.1,88.181 1039.5,87 1343.8,44.413 1427,116.27 1730.5,69 1772.6,62.446 1818.9,48.591 \ -1852.9,37.124", + lp="2074.5,61.5", + pos="e,2082.7,35.24 1122.7,92.076 1131.2,90.012 1140.1,88.16 1148.5,87 1336.4,61.182 1816.8,111.73 2001.5,69 2026.9,63.144 2053.4,50.978 \ +2073.8,40.113", style=solid]; "has biological sequence" [color=blue, height=0.5, label="biological sequence", - pos="2105.5,18", + pos="2312.5,18", width=2.8164]; transcript -> "has biological sequence" [color=blue, label="has biological sequence", - lp="2040,61.5", - pos="e,2050.5,33.176 1013.7,92.081 1022.2,90.017 1031.1,88.164 1039.5,87 1220.3,62.076 1679.2,89.327 1860.5,69 1922.3,62.079 1991.6,47.266 \ -2040.7,35.55", + lp="2272,61.5", + pos="e,2264.2,33.982 1122.7,92.06 1131.2,89.998 1140.1,88.15 1148.5,87 1359.7,58.221 1896.2,96.42 2107.5,69 2157.9,62.47 2213.8,48.358 \ +2254.5,36.787", style=solid]; "named thing_category" [color=blue, height=0.5, label="named thing", - pos="1118.5,105", + pos="1227.5,105", width=1.9318]; } diff --git a/graphviz/transcript.svg b/graphviz/transcript.svg index dab1b87765..2e1beb4707 100644 --- a/graphviz/transcript.svg +++ b/graphviz/transcript.svg @@ -4,16 +4,16 @@ - + %3 - + transcript - -transcript + +transcript @@ -24,9 +24,9 @@ transcript->nucleic acid entity - - -is_a + + +is_a @@ -37,9 +37,9 @@ transcript->id - + -id +id @@ -50,9 +50,9 @@ transcript->iri - - -iri + + +iri @@ -63,9 +63,9 @@ transcript->type - - -type + + +type @@ -76,8 +76,8 @@ transcript->name - - + + name @@ -89,9 +89,9 @@ transcript->description - - -description + + +description @@ -102,9 +102,9 @@ transcript->source - - -source + + +source @@ -115,9 +115,9 @@ transcript->provided by - - -provided by + + +provided by @@ -128,9 +128,9 @@ transcript->has attribute - - -has attribute + + +has attribute @@ -141,9 +141,9 @@ transcript->category - - -category + + +category @@ -154,9 +154,9 @@ transcript->trade name - - -trade name + + +trade name @@ -167,54 +167,80 @@ transcript->available from - - -available from + + +available from - + +max tolerated dose + +string + + + +transcript->max tolerated dose + + +max tolerated dose + + + +is toxic + +boolean + + + +transcript->is toxic + + +is toxic + + + is metabolite - -boolean + +boolean - + transcript->is metabolite - - -is metabolite + + +is metabolite - + in taxon - -organism taxon + +organism taxon - + transcript->in taxon - - -in taxon + + +in taxon - + has biological sequence - -biological sequence + +biological sequence - + transcript->has biological sequence - - -has biological sequence + + +has biological sequence named thing_category - -named thing + +named thing diff --git a/graphviz/vitamin.gv b/graphviz/vitamin.gv index 2cb024555f..c61a569f15 100644 --- a/graphviz/vitamin.gv +++ b/graphviz/vitamin.gv @@ -1,16 +1,16 @@ digraph { - graph [bb="0,0,1649.7,123"]; + graph [bb="0,0,1889.2,123"]; node [label="\N"]; vitamin [height=0.5, label=vitamin, - pos="747.39,105", + pos="877.39,105", width=1.2818]; micronutrient [height=0.5, pos="75.393,18", width=2.0943]; vitamin -> micronutrient [label=is_a, - lp="316.39,61.5", - pos="e,124.18,31.799 701.68,102.49 620.78,99.355 447.27,90.547 302.39,69 244.57,60.4 179.49,45.521 133.89,34.224"]; + lp="309.39,61.5", + pos="e,122.61,32.088 831.11,103.78 732.24,102.74 493.31,97.248 295.39,69 239.34,60.999 176.43,46.09 132.29,34.626"]; id [color=blue, height=0.5, label=string, @@ -18,8 +18,9 @@ digraph { width=1.0652]; vitamin -> id [color=blue, label=id, - lp="409.39,61.5", - pos="e,236.38,29.996 701.8,101.76 613.96,96.55 415.76,80.497 255.39,36 252.28,35.137 249.09,34.175 245.89,33.159", + lp="422.39,61.5", + pos="e,236.38,29.984 831.61,102.47 748.4,99.261 566.94,90.28 415.39,69 343.49,58.904 325.33,55.499 255.39,36 252.29,35.133 249.09,34.168 \ +245.89,33.151", style=solid]; iri [color=blue, height=0.5, @@ -28,9 +29,9 @@ digraph { width=1.2277]; vitamin -> iri [color=blue, label=iri, - lp="515.39,61.5", - pos="e,341.68,29.946 703.87,98.703 655.65,92.591 575.69,81.732 507.39,69 442.42,56.888 426.19,53.271 362.39,36 358.81,35.031 355.12,33.979 \ -351.42,32.889", + lp="523.39,61.5", + pos="e,341.67,30.005 832.03,101.31 763.26,96.851 628.63,86.625 515.39,69 446.66,58.301 429.64,53.797 362.39,36 358.81,35.052 355.11,34.014 \ +351.41,32.933", style=solid]; type [color=blue, height=0.5, @@ -39,8 +40,8 @@ digraph { width=1.0652]; vitamin -> type [color=blue, label=type, - lp="591.39,61.5", - pos="e,438.33,29.97 706.44,96.268 649.69,85.138 544.18,62.947 456.39,36 453.63,35.153 450.8,34.238 447.95,33.289", + lp="609.39,61.5", + pos="e,438.05,29.968 832.62,100.56 754.77,93.758 590.01,75.652 456.39,36 453.49,35.139 450.51,34.197 447.52,33.212", style=solid]; name [color=blue, height=0.5, @@ -49,8 +50,8 @@ digraph { width=1.5707]; vitamin -> name [color=blue, label=name, - lp="668.39,61.5", - pos="e,557.53,32.275 715.16,91.822 676.3,77.141 610.77,52.388 567.06,35.873", + lp="708.39,61.5", + pos="e,559.98,31.607 835.08,97.525 796.59,91.314 738.34,81.108 688.39,69 647.97,59.2 602.81,45.409 569.81,34.792", style=solid]; description [color=blue, height=0.5, @@ -59,8 +60,8 @@ digraph { width=2.0943]; vitamin -> description [color=blue, label=description, - lp="754.89,61.5", - pos="e,687.32,35.92 732.93,87.611 721.97,75.19 706.73,57.911 694.28,43.801", + lp="802.89,61.5", + pos="e,698.04,35.167 839.39,94.611 816.63,88.457 787.37,79.597 762.39,69 743.37,60.93 723.18,49.953 706.75,40.34", style=solid]; source [color=blue, height=0.5, @@ -69,8 +70,8 @@ digraph { width=1.5707]; vitamin -> source [color=blue, label=source, - lp="833.39,61.5", - pos="e,817.18,36.066 773.93,90.084 782.87,84.444 792.34,77.29 799.39,69 805.2,62.169 809.84,53.628 813.39,45.547", + lp="877.39,61.5", + pos="e,833.24,35.758 866.53,87.207 858.62,74.983 847.77,58.214 838.8,44.362", style=solid]; "provided by" [color=blue, height=0.5, @@ -79,9 +80,8 @@ digraph { width=1.0291]; vitamin -> "provided by" [color=blue, label="provided by", - lp="929.89,61.5", - pos="e,916.15,33.831 782.3,93.189 788.97,91.13 795.9,88.995 802.39,87 828.6,78.952 836.69,80.883 861.39,69 877.75,61.135 894.55,49.882 \ -907.91,40.043", + lp="957.89,61.5", + pos="e,925.59,35.59 891.3,87.652 895.97,81.897 901.09,75.293 905.39,69 910.69,61.262 915.98,52.512 920.57,44.519", style=solid]; "has attribute" [color=blue, height=0.5, @@ -90,18 +90,18 @@ digraph { width=1.4443]; vitamin -> "has attribute" [color=blue, label="has attribute", - lp="1049.4,61.5", - pos="e,1025.6,35.218 780.86,92.509 787.91,90.414 795.34,88.44 802.39,87 878.57,71.445 904.18,97.793 976.39,69 991.76,62.874 1006.6,52.009 \ -1018.2,41.969", + lp="1068.4,61.5", + pos="e,1033,35.797 911.93,93.009 918.69,90.945 925.75,88.855 932.39,87 964.16,78.126 976.97,87.334 1004.4,69 1013.7,62.788 1021.5,53.426 \ +1027.5,44.477", style=solid]; category [height=0.5, pos="1162.4,18", width=1.4263]; vitamin -> category [color=blue, label=category, - lp="1156.9,61.5", - pos="e,1147.4,35.696 780.52,92.362 787.66,90.25 795.22,88.307 802.39,87 867.66,75.119 1038.5,92.959 1100.4,69 1115.1,63.294 1129.1,52.72 \ -1140,42.761", + lp="1169.9,61.5", + pos="e,1152.7,35.951 910.85,92.47 917.9,90.378 925.34,88.415 932.39,87 973.33,78.793 1082.3,88.213 1119.4,69 1130.3,63.352 1139.6,53.668 \ +1146.7,44.318", style=solid]; "trade name" [color=blue, height=0.5, @@ -110,9 +110,9 @@ digraph { width=2.2748]; vitamin -> "trade name" [color=blue, label="trade name", - lp="1278.4,61.5", - pos="e,1283.5,34.768 780.51,92.283 787.65,90.177 795.21,88.256 802.39,87 973.32,57.14 1023,106.7 1192.4,69 1220.9,62.664 1251.2,50.117 \ -1274.4,39.178", + lp="1286.4,61.5", + pos="e,1286,35.115 910.53,92.392 917.66,90.279 925.22,88.326 932.39,87 1052,64.895 1087.6,99.049 1205.4,69 1230.4,62.624 1256.7,50.571 \ +1277.1,39.897", style=solid]; "available from" [color=blue, height=0.5, @@ -121,13 +121,35 @@ digraph { width=3.2858]; vitamin -> "available from" [color=blue, label="available from", - lp="1450.9,61.5", - pos="e,1480.2,34.352 780.21,92.306 787.43,90.17 795.1,88.231 802.39,87 1030.9,48.451 1093.8,100.23 1323.4,69 1373.5,62.177 1429.2,48.452 \ -1470.4,37.105", + lp="1455.9,61.5", + pos="e,1481.4,34.459 910.51,92.278 917.64,90.172 925.21,88.252 932.39,87 1107.3,56.543 1155.7,94.655 1331.4,69 1379.2,62.014 1432.3,48.483 \ +1471.7,37.258", + style=solid]; + "max tolerated dose" [color=blue, + height=0.5, + label=string, + pos="1706.4,18", + width=1.0652]; + vitamin -> "max tolerated dose" [color=blue, + label="max tolerated dose", + lp="1662.4,61.5", + pos="e,1677.4,29.901 910.2,92.287 917.43,90.152 925.1,88.218 932.39,87 1186.3,44.604 1256,101.34 1511.4,69 1577.8,60.589 1594.1,54.544 \ +1658.4,36 1661.5,35.106 1664.7,34.122 1667.9,33.091", + style=solid]; + "is toxic" [color=blue, + height=0.5, + label=boolean, + pos="1842.4,18", + width=1.2999]; + vitamin -> "is toxic" [color=blue, + label="is toxic", + lp="1803.4,61.5", + pos="e,1818.4,33.775 910.19,92.239 917.42,90.107 925.09,88.186 932.39,87 1108.6,58.371 1561.6,109.65 1735.4,69 1761.5,62.885 1788.9,49.944 \ +1809.5,38.759", style=solid]; "named thing_category" [color=blue, height=0.5, label="named thing", - pos="881.39,105", + pos="1011.4,105", width=1.9318]; } diff --git a/graphviz/vitamin.svg b/graphviz/vitamin.svg index eabc980077..f8d9ab1a75 100644 --- a/graphviz/vitamin.svg +++ b/graphviz/vitamin.svg @@ -4,16 +4,16 @@ - + %3 - + vitamin - -vitamin + +vitamin @@ -24,9 +24,9 @@ vitamin->micronutrient - - -is_a + + +is_a @@ -37,9 +37,9 @@ vitamin->id - - -id + + +id @@ -50,9 +50,9 @@ vitamin->iri - - -iri + + +iri @@ -63,9 +63,9 @@ vitamin->type - - -type + + +type @@ -76,9 +76,9 @@ vitamin->name - - -name + + +name @@ -89,9 +89,9 @@ vitamin->description - - -description + + +description @@ -102,9 +102,9 @@ vitamin->source - - -source + + +source @@ -115,9 +115,9 @@ vitamin->provided by - - -provided by + + +provided by @@ -128,9 +128,9 @@ vitamin->has attribute - - -has attribute + + +has attribute @@ -141,9 +141,9 @@ vitamin->category - - -category + + +category @@ -154,9 +154,9 @@ vitamin->trade name - - -trade name + + +trade name @@ -167,15 +167,41 @@ vitamin->available from - - -available from + + +available from + + + +max tolerated dose + +string + + + +vitamin->max tolerated dose + + +max tolerated dose + + + +is toxic + +boolean + + + +vitamin->is toxic + + +is toxic named thing_category - -named thing + +named thing diff --git a/json-schema/biolink-model.json b/json-schema/biolink-model.json index 97d0e860c0..aad14ee3f8 100644 --- a/json-schema/biolink-model.json +++ b/json-schema/biolink-model.json @@ -1,8 +1,5 @@ { - "$id": "https://w3id.org/biolink/biolink-model", - "$schema": "http://json-schema.org/draft-07/schema#", - "additionalProperties": true, - "definitions": { + "$defs": { "Activity": { "additionalProperties": false, "description": "An activity is something that occurs over a period of time and acts upon or with entities; it may include consuming, processing, transforming, modifying, relocating, using, or generating entities.", @@ -20,7 +17,7 @@ "has_attribute": { "description": "connects any entity to an attribute", "items": { - "$ref": "#/definitions/Attribute" + "$ref": "#/$defs/Attribute" }, "type": "array" }, @@ -86,7 +83,7 @@ "has_attribute": { "description": "connects any entity to an attribute", "items": { - "$ref": "#/definitions/Attribute" + "$ref": "#/$defs/Attribute" }, "type": "array" }, @@ -141,7 +138,7 @@ "has_attribute": { "description": "may often be an organism attribute", "items": { - "$ref": "#/definitions/Attribute" + "$ref": "#/$defs/Attribute" }, "type": "array" }, @@ -203,7 +200,7 @@ "has_attribute": { "description": "connects any entity to an attribute", "items": { - "$ref": "#/definitions/Attribute" + "$ref": "#/$defs/Attribute" }, "type": "array" }, @@ -247,7 +244,7 @@ "qualifiers": { "description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": { - "$ref": "#/definitions/OntologyClass" + "$ref": "#/$defs/OntologyClass" }, "type": "array" }, @@ -293,7 +290,7 @@ "has_attribute": { "description": "connects any entity to an attribute", "items": { - "$ref": "#/definitions/Attribute" + "$ref": "#/$defs/Attribute" }, "type": "array" }, @@ -337,7 +334,7 @@ "qualifiers": { "description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": { - "$ref": "#/definitions/OntologyClass" + "$ref": "#/$defs/OntologyClass" }, "type": "array" }, @@ -398,7 +395,7 @@ "has_attribute": { "description": "connects any entity to an attribute", "items": { - "$ref": "#/definitions/Attribute" + "$ref": "#/$defs/Attribute" }, "type": "array" }, @@ -510,7 +507,7 @@ "has_attribute": { "description": "connects any entity to an attribute", "items": { - "$ref": "#/definitions/Attribute" + "$ref": "#/$defs/Attribute" }, "type": "array" }, @@ -555,7 +552,7 @@ "qualifiers": { "description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": { - "$ref": "#/definitions/OntologyClass" + "$ref": "#/$defs/OntologyClass" }, "type": "array" }, @@ -589,7 +586,7 @@ "description": "A property or characteristic of an entity. For example, an apple may have properties such as color, shape, age, crispiness. An environmental sample may have attributes such as depth, lat, long, material.", "properties": { "has_attribute_type": { - "$ref": "#/definitions/OntologyClass", + "$ref": "#/$defs/OntologyClass", "description": "connects an attribute to a class that describes it" }, "has_qualitative_value": { @@ -599,7 +596,7 @@ "has_quantitative_value": { "description": "connects an attribute to a value", "items": { - "$ref": "#/definitions/QuantityValue" + "$ref": "#/$defs/QuantityValue" }, "type": "array" }, @@ -646,7 +643,7 @@ "has_attribute": { "description": "connects any entity to an attribute", "items": { - "$ref": "#/definitions/Attribute" + "$ref": "#/$defs/Attribute" }, "type": "array" }, @@ -719,7 +716,7 @@ "has_attribute": { "description": "connects any entity to an attribute", "items": { - "$ref": "#/definitions/Attribute" + "$ref": "#/$defs/Attribute" }, "type": "array" }, @@ -744,7 +741,7 @@ "type": "string" }, "onset_qualifier": { - "$ref": "#/definitions/Onset", + "$ref": "#/$defs/Onset", "description": "a qualifier used in a phenotypic association to state when the phenotype appears is in the subject" }, "predicate": { @@ -768,7 +765,7 @@ "qualifiers": { "description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": { - "$ref": "#/definitions/OntologyClass" + "$ref": "#/$defs/OntologyClass" }, "type": "array" }, @@ -776,11 +773,11 @@ "type": "string" }, "severity_qualifier": { - "$ref": "#/definitions/SeverityValue", + "$ref": "#/$defs/SeverityValue", "description": "a qualifier used in a phenotypic association to state how severe the phenotype is in the subject" }, "sex_qualifier": { - "$ref": "#/definitions/BiologicalSex", + "$ref": "#/$defs/BiologicalSex", "description": "a qualifier used in a phenotypic association to state whether the association is specific to a particular sex." }, "source": { @@ -836,7 +833,7 @@ "has_attribute": { "description": "connects any entity to an attribute", "items": { - "$ref": "#/definitions/Attribute" + "$ref": "#/$defs/Attribute" }, "type": "array" }, @@ -913,7 +910,7 @@ "has_attribute": { "description": "connects any entity to an attribute", "items": { - "$ref": "#/definitions/Attribute" + "$ref": "#/$defs/Attribute" }, "type": "array" }, @@ -989,7 +986,7 @@ "has_attribute": { "description": "connects any entity to an attribute", "items": { - "$ref": "#/definitions/Attribute" + "$ref": "#/$defs/Attribute" }, "type": "array" }, @@ -1046,7 +1043,7 @@ "description": "", "properties": { "has_attribute_type": { - "$ref": "#/definitions/OntologyClass", + "$ref": "#/$defs/OntologyClass", "description": "connects an attribute to a class that describes it" }, "has_qualitative_value": { @@ -1056,7 +1053,7 @@ "has_quantitative_value": { "description": "connects an attribute to a value", "items": { - "$ref": "#/definitions/QuantityValue" + "$ref": "#/$defs/QuantityValue" }, "type": "array" }, @@ -1125,7 +1122,7 @@ "has_attribute": { "description": "connects any entity to an attribute", "items": { - "$ref": "#/definitions/Attribute" + "$ref": "#/$defs/Attribute" }, "type": "array" }, @@ -1239,7 +1236,7 @@ "has_attribute": { "description": "connects any entity to an attribute", "items": { - "$ref": "#/definitions/Attribute" + "$ref": "#/$defs/Attribute" }, "type": "array" }, @@ -1343,7 +1340,7 @@ "has_attribute": { "description": "may often be an organism attribute", "items": { - "$ref": "#/definitions/Attribute" + "$ref": "#/$defs/Attribute" }, "type": "array" }, @@ -1409,7 +1406,7 @@ "has_attribute": { "description": "connects any entity to an attribute", "items": { - "$ref": "#/definitions/Attribute" + "$ref": "#/$defs/Attribute" }, "type": "array" }, @@ -1434,7 +1431,7 @@ "type": "string" }, "onset_qualifier": { - "$ref": "#/definitions/Onset", + "$ref": "#/$defs/Onset", "description": "a qualifier used in a phenotypic association to state when the phenotype appears is in the subject" }, "predicate": { @@ -1458,7 +1455,7 @@ "qualifiers": { "description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": { - "$ref": "#/definitions/OntologyClass" + "$ref": "#/$defs/OntologyClass" }, "type": "array" }, @@ -1466,11 +1463,11 @@ "type": "string" }, "severity_qualifier": { - "$ref": "#/definitions/SeverityValue", + "$ref": "#/$defs/SeverityValue", "description": "a qualifier used in a phenotypic association to state how severe the phenotype is in the subject" }, "sex_qualifier": { - "$ref": "#/definitions/BiologicalSex", + "$ref": "#/$defs/BiologicalSex", "description": "a qualifier used in a phenotypic association to state whether the association is specific to a particular sex." }, "source": { @@ -1512,7 +1509,7 @@ "has_attribute": { "description": "may often be an organism attribute", "items": { - "$ref": "#/definitions/Attribute" + "$ref": "#/$defs/Attribute" }, "type": "array" }, @@ -1574,7 +1571,7 @@ "has_attribute": { "description": "may often be an organism attribute", "items": { - "$ref": "#/definitions/Attribute" + "$ref": "#/$defs/Attribute" }, "type": "array" }, @@ -1633,7 +1630,7 @@ "has_attribute": { "description": "connects any entity to an attribute", "items": { - "$ref": "#/definitions/Attribute" + "$ref": "#/$defs/Attribute" }, "type": "array" }, @@ -1658,7 +1655,7 @@ "type": "string" }, "onset_qualifier": { - "$ref": "#/definitions/Onset", + "$ref": "#/$defs/Onset", "description": "a qualifier used in a phenotypic association to state when the phenotype appears is in the subject" }, "predicate": { @@ -1682,7 +1679,7 @@ "qualifiers": { "description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": { - "$ref": "#/definitions/OntologyClass" + "$ref": "#/$defs/OntologyClass" }, "type": "array" }, @@ -1690,7 +1687,7 @@ "type": "string" }, "severity_qualifier": { - "$ref": "#/definitions/SeverityValue", + "$ref": "#/$defs/SeverityValue", "description": "a qualifier used in a phenotypic association to state how severe the phenotype is in the subject" }, "source": { @@ -1732,7 +1729,7 @@ "has_attribute": { "description": "connects any entity to an attribute", "items": { - "$ref": "#/definitions/Attribute" + "$ref": "#/$defs/Attribute" }, "type": "array" }, @@ -1777,7 +1774,7 @@ "qualifiers": { "description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": { - "$ref": "#/definitions/OntologyClass" + "$ref": "#/$defs/OntologyClass" }, "type": "array" }, @@ -1822,7 +1819,7 @@ "has_attribute": { "description": "may often be an organism attribute", "items": { - "$ref": "#/definitions/Attribute" + "$ref": "#/$defs/Attribute" }, "type": "array" }, @@ -1873,7 +1870,7 @@ "properties": { "available_from": { "items": { - "$ref": "#/definitions/DrugAvailabilityEnum" + "$ref": "#/$defs/DrugAvailabilityEnum" }, "type": "array" }, @@ -1890,7 +1887,7 @@ "has_attribute": { "description": "connects any entity to an attribute", "items": { - "$ref": "#/definitions/Attribute" + "$ref": "#/$defs/Attribute" }, "type": "array" }, @@ -1902,6 +1899,13 @@ "description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string" }, + "is_toxic": { + "type": "boolean" + }, + "max_tolerated_dose": { + "description": "The highest dose of a drug or treatment that does not cause unacceptable side effects. The maximum tolerated dose is determined in clinical trials by testing increasing doses on different groups of people until the highest dose with acceptable side effects is found. Also called MTD.", + "type": "string" + }, "name": { "description": "A human-readable name for an attribute or entity.", "type": "string" @@ -1951,7 +1955,7 @@ "properties": { "available_from": { "items": { - "$ref": "#/definitions/DrugAvailabilityEnum" + "$ref": "#/$defs/DrugAvailabilityEnum" }, "type": "array" }, @@ -1968,7 +1972,7 @@ "has_attribute": { "description": "connects any entity to an attribute", "items": { - "$ref": "#/definitions/Attribute" + "$ref": "#/$defs/Attribute" }, "type": "array" }, @@ -1987,6 +1991,13 @@ "is_supplement": { "type": "string" }, + "is_toxic": { + "type": "boolean" + }, + "max_tolerated_dose": { + "description": "The highest dose of a drug or treatment that does not cause unacceptable side effects. The maximum tolerated dose is determined in clinical trials by testing increasing doses on different groups of people until the highest dose with acceptable side effects is found. Also called MTD.", + "type": "string" + }, "name": { "description": "A human-readable name for an attribute or entity.", "type": "string" @@ -2041,7 +2052,7 @@ "has_attribute": { "description": "connects any entity to an attribute", "items": { - "$ref": "#/definitions/Attribute" + "$ref": "#/$defs/Attribute" }, "type": "array" }, @@ -2086,7 +2097,7 @@ "qualifiers": { "description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": { - "$ref": "#/definitions/OntologyClass" + "$ref": "#/$defs/OntologyClass" }, "type": "array" }, @@ -2122,7 +2133,7 @@ "catalyst_qualifier": { "description": "this connects the derivation edge to the chemical entity that catalyzes the reaction that causes the subject chemical to transform into the object chemical.", "items": { - "$ref": "#/definitions/MacromolecularMachineMixin" + "$ref": "#/$defs/MacromolecularMachineMixin" }, "type": "array" }, @@ -2139,7 +2150,7 @@ "has_attribute": { "description": "connects any entity to an attribute", "items": { - "$ref": "#/definitions/Attribute" + "$ref": "#/$defs/Attribute" }, "type": "array" }, @@ -2183,7 +2194,7 @@ "qualifiers": { "description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": { - "$ref": "#/definitions/OntologyClass" + "$ref": "#/$defs/OntologyClass" }, "type": "array" }, @@ -2229,7 +2240,7 @@ "has_attribute": { "description": "connects any entity to an attribute", "items": { - "$ref": "#/definitions/Attribute" + "$ref": "#/$defs/Attribute" }, "type": "array" }, @@ -2274,7 +2285,7 @@ "qualifiers": { "description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": { - "$ref": "#/definitions/OntologyClass" + "$ref": "#/$defs/OntologyClass" }, "type": "array" }, @@ -2320,7 +2331,7 @@ "has_attribute": { "description": "connects any entity to an attribute", "items": { - "$ref": "#/definitions/Attribute" + "$ref": "#/$defs/Attribute" }, "type": "array" }, @@ -2341,7 +2352,7 @@ "type": "boolean" }, "object": { - "$ref": "#/definitions/GeneOrGeneProduct", + "$ref": "#/$defs/GeneOrGeneProduct", "description": "the gene or gene product that is affected by the chemical." }, "predicate": { @@ -2365,7 +2376,7 @@ "qualifiers": { "description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": { - "$ref": "#/definitions/OntologyClass" + "$ref": "#/$defs/OntologyClass" }, "type": "array" }, @@ -2411,7 +2422,7 @@ "has_attribute": { "description": "connects any entity to an attribute", "items": { - "$ref": "#/definitions/Attribute" + "$ref": "#/$defs/Attribute" }, "type": "array" }, @@ -2456,7 +2467,7 @@ "qualifiers": { "description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": { - "$ref": "#/definitions/OntologyClass" + "$ref": "#/$defs/OntologyClass" }, "type": "array" }, @@ -2490,7 +2501,7 @@ "description": "Attributes relating to a clinical manifestation", "properties": { "has_attribute_type": { - "$ref": "#/definitions/OntologyClass", + "$ref": "#/$defs/OntologyClass", "description": "connects an attribute to a class that describes it" }, "has_qualitative_value": { @@ -2500,7 +2511,7 @@ "has_quantitative_value": { "description": "connects an attribute to a value", "items": { - "$ref": "#/definitions/QuantityValue" + "$ref": "#/$defs/QuantityValue" }, "type": "array" }, @@ -2528,7 +2539,7 @@ "description": "The course a disease typically takes from its onset, progression in time, and eventual resolution or death of the affected individual", "properties": { "has_attribute_type": { - "$ref": "#/definitions/OntologyClass", + "$ref": "#/$defs/OntologyClass", "description": "connects an attribute to a class that describes it" }, "has_qualitative_value": { @@ -2538,7 +2549,7 @@ "has_quantitative_value": { "description": "connects an attribute to a value", "items": { - "$ref": "#/definitions/QuantityValue" + "$ref": "#/$defs/QuantityValue" }, "type": "array" }, @@ -2578,7 +2589,7 @@ "has_attribute": { "description": "connects any entity to an attribute", "items": { - "$ref": "#/definitions/Attribute" + "$ref": "#/$defs/Attribute" }, "type": "array" }, @@ -2632,7 +2643,7 @@ }, "has_attribute": { "items": { - "$ref": "#/definitions/ClinicalAttribute" + "$ref": "#/$defs/ClinicalAttribute" }, "type": "array" }, @@ -2694,7 +2705,7 @@ "has_attribute": { "description": "connects any entity to an attribute", "items": { - "$ref": "#/definitions/Attribute" + "$ref": "#/$defs/Attribute" }, "type": "array" }, @@ -2737,7 +2748,7 @@ "description": "A clinical measurement is a special kind of attribute which results from a laboratory observation from a subject individual or sample. Measurements can be connected to their subject by the 'has attribute' slot.", "properties": { "has_attribute_type": { - "$ref": "#/definitions/OntologyClass" + "$ref": "#/$defs/OntologyClass" }, "has_qualitative_value": { "description": "connects an attribute to a value", @@ -2746,7 +2757,7 @@ "has_quantitative_value": { "description": "connects an attribute to a value", "items": { - "$ref": "#/definitions/QuantityValue" + "$ref": "#/$defs/QuantityValue" }, "type": "array" }, @@ -2774,7 +2785,7 @@ "description": "Used to characterize and specify the phenotypic abnormalities defined in the phenotypic abnormality sub-ontology, with respect to severity, laterality, and other aspects", "properties": { "has_attribute_type": { - "$ref": "#/definitions/OntologyClass", + "$ref": "#/$defs/OntologyClass", "description": "connects an attribute to a class that describes it" }, "has_qualitative_value": { @@ -2784,7 +2795,7 @@ "has_quantitative_value": { "description": "connects an attribute to a value", "items": { - "$ref": "#/definitions/QuantityValue" + "$ref": "#/$defs/QuantityValue" }, "type": "array" }, @@ -2824,7 +2835,7 @@ "has_attribute": { "description": "connects any entity to an attribute", "items": { - "$ref": "#/definitions/Attribute" + "$ref": "#/$defs/Attribute" }, "type": "array" }, @@ -2868,7 +2879,7 @@ "properties": { "available_from": { "items": { - "$ref": "#/definitions/DrugAvailabilityEnum" + "$ref": "#/$defs/DrugAvailabilityEnum" }, "type": "array" }, @@ -2885,7 +2896,7 @@ "has_attribute": { "description": "connects any entity to an attribute", "items": { - "$ref": "#/definitions/Attribute" + "$ref": "#/$defs/Attribute" }, "type": "array" }, @@ -2912,6 +2923,13 @@ "description": "indicates whether a molecular entity is a metabolite", "type": "boolean" }, + "is_toxic": { + "type": "boolean" + }, + "max_tolerated_dose": { + "description": "The highest dose of a drug or treatment that does not cause unacceptable side effects. The maximum tolerated dose is determined in clinical trials by testing increasing doses on different groups of people until the highest dose with acceptable side effects is found. Also called MTD.", + "type": "string" + }, "name": { "description": "A human-readable name for an attribute or entity.", "type": "string" @@ -2958,7 +2976,7 @@ "has_attribute": { "description": "may often be an organism attribute", "items": { - "$ref": "#/definitions/Attribute" + "$ref": "#/$defs/Attribute" }, "type": "array" }, @@ -3017,7 +3035,7 @@ "properties": { "available_from": { "items": { - "$ref": "#/definitions/DrugAvailabilityEnum" + "$ref": "#/$defs/DrugAvailabilityEnum" }, "type": "array" }, @@ -3034,7 +3052,7 @@ "has_attribute": { "description": "connects any entity to an attribute", "items": { - "$ref": "#/definitions/Attribute" + "$ref": "#/$defs/Attribute" }, "type": "array" }, @@ -3053,6 +3071,13 @@ "is_supplement": { "type": "string" }, + "is_toxic": { + "type": "boolean" + }, + "max_tolerated_dose": { + "description": "The highest dose of a drug or treatment that does not cause unacceptable side effects. The maximum tolerated dose is determined in clinical trials by testing increasing doses on different groups of people until the highest dose with acceptable side effects is found. Also called MTD.", + "type": "string" + }, "name": { "description": "A human-readable name for an attribute or entity.", "type": "string" @@ -3107,7 +3132,7 @@ "has_attribute": { "description": "connects any entity to an attribute", "items": { - "$ref": "#/definitions/Attribute" + "$ref": "#/$defs/Attribute" }, "type": "array" }, @@ -3168,7 +3193,7 @@ "has_attribute": { "description": "connects any entity to an attribute", "items": { - "$ref": "#/definitions/Attribute" + "$ref": "#/$defs/Attribute" }, "type": "array" }, @@ -3213,7 +3238,7 @@ "qualifiers": { "description": "this field can be used to annotate special characteristics of an agent relationship, such as the fact that a given author agent of a publication is the 'corresponding author'", "items": { - "$ref": "#/definitions/OntologyClass" + "$ref": "#/$defs/OntologyClass" }, "type": "array" }, @@ -3267,7 +3292,7 @@ "has_attribute": { "description": "connects any entity to an attribute", "items": { - "$ref": "#/definitions/Attribute" + "$ref": "#/$defs/Attribute" }, "type": "array" }, @@ -3339,7 +3364,7 @@ "has_attribute": { "description": "connects any entity to an attribute", "items": { - "$ref": "#/definitions/Attribute" + "$ref": "#/$defs/Attribute" }, "type": "array" }, @@ -3408,7 +3433,7 @@ "has_attribute": { "description": "connects any entity to an attribute", "items": { - "$ref": "#/definitions/Attribute" + "$ref": "#/$defs/Attribute" }, "type": "array" }, @@ -3483,7 +3508,7 @@ "has_attribute": { "description": "connects any entity to an attribute", "items": { - "$ref": "#/definitions/Attribute" + "$ref": "#/$defs/Attribute" }, "type": "array" }, @@ -3553,7 +3578,7 @@ "has_attribute": { "description": "connects any entity to an attribute", "items": { - "$ref": "#/definitions/Attribute" + "$ref": "#/$defs/Attribute" }, "type": "array" }, @@ -3608,7 +3633,7 @@ "has_attribute": { "description": "connects any entity to an attribute", "items": { - "$ref": "#/definitions/Attribute" + "$ref": "#/$defs/Attribute" }, "type": "array" }, @@ -3670,7 +3695,7 @@ "has_attribute": { "description": "connects any entity to an attribute", "items": { - "$ref": "#/definitions/Attribute" + "$ref": "#/$defs/Attribute" }, "type": "array" }, @@ -3754,7 +3779,7 @@ "has_attribute": { "description": "connects any entity to an attribute", "items": { - "$ref": "#/definitions/Attribute" + "$ref": "#/$defs/Attribute" }, "type": "array" }, @@ -3799,7 +3824,7 @@ "qualifiers": { "description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": { - "$ref": "#/definitions/OntologyClass" + "$ref": "#/$defs/OntologyClass" }, "type": "array" }, @@ -3845,7 +3870,7 @@ "has_attribute": { "description": "connects any entity to an attribute", "items": { - "$ref": "#/definitions/Attribute" + "$ref": "#/$defs/Attribute" }, "type": "array" }, @@ -3890,7 +3915,7 @@ "qualifiers": { "description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": { - "$ref": "#/definitions/OntologyClass" + "$ref": "#/$defs/OntologyClass" }, "type": "array" }, @@ -3940,7 +3965,7 @@ "has_attribute": { "description": "connects any entity to an attribute", "items": { - "$ref": "#/definitions/Attribute" + "$ref": "#/$defs/Attribute" }, "type": "array" }, @@ -3965,7 +3990,7 @@ "type": "string" }, "onset_qualifier": { - "$ref": "#/definitions/Onset", + "$ref": "#/$defs/Onset", "description": "a qualifier used in a phenotypic association to state when the phenotype appears is in the subject" }, "predicate": { @@ -3989,7 +4014,7 @@ "qualifiers": { "description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": { - "$ref": "#/definitions/OntologyClass" + "$ref": "#/$defs/OntologyClass" }, "type": "array" }, @@ -3997,11 +4022,11 @@ "type": "string" }, "severity_qualifier": { - "$ref": "#/definitions/SeverityValue", + "$ref": "#/$defs/SeverityValue", "description": "a qualifier used in a phenotypic association to state how severe the phenotype is in the subject" }, "sex_qualifier": { - "$ref": "#/definitions/BiologicalSex", + "$ref": "#/$defs/BiologicalSex", "description": "a qualifier used in a phenotypic association to state whether the association is specific to a particular sex." }, "source": { @@ -4032,7 +4057,7 @@ "properties": { "available_from": { "items": { - "$ref": "#/definitions/DrugAvailabilityEnum" + "$ref": "#/$defs/DrugAvailabilityEnum" }, "type": "array" }, @@ -4049,7 +4074,7 @@ "has_attribute": { "description": "connects any entity to an attribute", "items": { - "$ref": "#/definitions/Attribute" + "$ref": "#/$defs/Attribute" }, "type": "array" }, @@ -4068,6 +4093,13 @@ "is_supplement": { "type": "string" }, + "is_toxic": { + "type": "boolean" + }, + "max_tolerated_dose": { + "description": "The highest dose of a drug or treatment that does not cause unacceptable side effects. The maximum tolerated dose is determined in clinical trials by testing increasing doses on different groups of people until the highest dose with acceptable side effects is found. Also called MTD.", + "type": "string" + }, "name": { "description": "A human-readable name for an attribute or entity.", "type": "string" @@ -4137,7 +4169,7 @@ "has_attribute": { "description": "connects any entity to an attribute", "items": { - "$ref": "#/definitions/Attribute" + "$ref": "#/$defs/Attribute" }, "type": "array" }, @@ -4158,7 +4190,7 @@ "type": "boolean" }, "object": { - "$ref": "#/definitions/GeneOrGeneProduct", + "$ref": "#/$defs/GeneOrGeneProduct", "description": "the gene or gene product that is affected by the drug" }, "predicate": { @@ -4182,7 +4214,7 @@ "qualifiers": { "description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": { - "$ref": "#/definitions/OntologyClass" + "$ref": "#/$defs/OntologyClass" }, "type": "array" }, @@ -4237,7 +4269,7 @@ "description": "", "properties": { "FDA_approval_status": { - "$ref": "#/definitions/FDAApprovalStatusEnum" + "$ref": "#/$defs/FDAApprovalStatusEnum" }, "category": { "items": { @@ -4252,7 +4284,7 @@ "has_attribute": { "description": "connects any entity to an attribute", "items": { - "$ref": "#/definitions/Attribute" + "$ref": "#/$defs/Attribute" }, "type": "array" }, @@ -4297,7 +4329,7 @@ "qualifiers": { "description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": { - "$ref": "#/definitions/OntologyClass" + "$ref": "#/$defs/OntologyClass" }, "type": "array" }, @@ -4331,7 +4363,7 @@ "description": "", "properties": { "FDA_approval_status": { - "$ref": "#/definitions/FDAApprovalStatusEnum" + "$ref": "#/$defs/FDAApprovalStatusEnum" }, "category": { "items": { @@ -4346,7 +4378,7 @@ "has_attribute": { "description": "connects any entity to an attribute", "items": { - "$ref": "#/definitions/Attribute" + "$ref": "#/$defs/Attribute" }, "type": "array" }, @@ -4391,7 +4423,7 @@ "qualifiers": { "description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": { - "$ref": "#/definitions/OntologyClass" + "$ref": "#/$defs/OntologyClass" }, "type": "array" }, @@ -4451,7 +4483,7 @@ "has_attribute": { "description": "connects any entity to an attribute", "items": { - "$ref": "#/definitions/Attribute" + "$ref": "#/$defs/Attribute" }, "type": "array" }, @@ -4495,7 +4527,7 @@ "properties": { "available_from": { "items": { - "$ref": "#/definitions/DrugAvailabilityEnum" + "$ref": "#/$defs/DrugAvailabilityEnum" }, "type": "array" }, @@ -4512,7 +4544,7 @@ "has_attribute": { "description": "connects any entity to an attribute", "items": { - "$ref": "#/definitions/Attribute" + "$ref": "#/$defs/Attribute" }, "type": "array" }, @@ -4524,6 +4556,13 @@ "description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string" }, + "is_toxic": { + "type": "boolean" + }, + "max_tolerated_dose": { + "description": "The highest dose of a drug or treatment that does not cause unacceptable side effects. The maximum tolerated dose is determined in clinical trials by testing increasing doses on different groups of people until the highest dose with acceptable side effects is found. Also called MTD.", + "type": "string" + }, "name": { "description": "A human-readable name for an attribute or entity.", "type": "string" @@ -4570,7 +4609,7 @@ "has_attribute": { "description": "connects any entity to an attribute", "items": { - "$ref": "#/definitions/Attribute" + "$ref": "#/$defs/Attribute" }, "type": "array" }, @@ -4633,7 +4672,7 @@ "has_attribute": { "description": "connects any entity to an attribute", "items": { - "$ref": "#/definitions/Attribute" + "$ref": "#/$defs/Attribute" }, "type": "array" }, @@ -4696,7 +4735,7 @@ "has_attribute": { "description": "connects any entity to an attribute", "items": { - "$ref": "#/definitions/Attribute" + "$ref": "#/$defs/Attribute" }, "type": "array" }, @@ -4746,7 +4785,7 @@ "properties": { "available_from": { "items": { - "$ref": "#/definitions/DrugAvailabilityEnum" + "$ref": "#/$defs/DrugAvailabilityEnum" }, "type": "array" }, @@ -4763,7 +4802,7 @@ "has_attribute": { "description": "connects any entity to an attribute", "items": { - "$ref": "#/definitions/Attribute" + "$ref": "#/$defs/Attribute" }, "type": "array" }, @@ -4790,6 +4829,13 @@ "description": "indicates whether a molecular entity is a metabolite", "type": "boolean" }, + "is_toxic": { + "type": "boolean" + }, + "max_tolerated_dose": { + "description": "The highest dose of a drug or treatment that does not cause unacceptable side effects. The maximum tolerated dose is determined in clinical trials by testing increasing doses on different groups of people until the highest dose with acceptable side effects is found. Also called MTD.", + "type": "string" + }, "name": { "description": "A human-readable name for an attribute or entity.", "type": "string" @@ -4836,7 +4882,7 @@ "has_attribute": { "description": "connects any entity to an attribute", "items": { - "$ref": "#/definitions/Attribute" + "$ref": "#/$defs/Attribute" }, "type": "array" }, @@ -4880,7 +4926,7 @@ "qualifiers": { "description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": { - "$ref": "#/definitions/OntologyClass" + "$ref": "#/$defs/OntologyClass" }, "type": "array" }, @@ -4933,7 +4979,7 @@ "has_attribute": { "description": "connects any entity to an attribute", "items": { - "$ref": "#/definitions/Attribute" + "$ref": "#/$defs/Attribute" }, "type": "array" }, @@ -4987,7 +5033,7 @@ "qualifiers": { "description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": { - "$ref": "#/definitions/OntologyClass" + "$ref": "#/$defs/OntologyClass" }, "type": "array" }, @@ -5037,7 +5083,7 @@ "has_attribute": { "description": "connects any entity to an attribute", "items": { - "$ref": "#/definitions/Attribute" + "$ref": "#/$defs/Attribute" }, "type": "array" }, @@ -5062,7 +5108,7 @@ "type": "string" }, "onset_qualifier": { - "$ref": "#/definitions/Onset", + "$ref": "#/$defs/Onset", "description": "a qualifier used in a phenotypic association to state when the phenotype appears is in the subject" }, "predicate": { @@ -5086,7 +5132,7 @@ "qualifiers": { "description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": { - "$ref": "#/definitions/OntologyClass" + "$ref": "#/$defs/OntologyClass" }, "type": "array" }, @@ -5094,11 +5140,11 @@ "type": "string" }, "severity_qualifier": { - "$ref": "#/definitions/SeverityValue", + "$ref": "#/$defs/SeverityValue", "description": "a qualifier used in a phenotypic association to state how severe the phenotype is in the subject" }, "sex_qualifier": { - "$ref": "#/definitions/BiologicalSex", + "$ref": "#/$defs/BiologicalSex", "description": "a qualifier used in a phenotypic association to state whether the association is specific to a particular sex." }, "source": { @@ -5106,7 +5152,7 @@ "type": "string" }, "subject": { - "$ref": "#/definitions/ExposureEvent" + "$ref": "#/$defs/ExposureEvent" }, "type": { "description": "rdf:type of biolink:Association should be fixed at rdf:Statement", @@ -5150,7 +5196,7 @@ "properties": { "available_from": { "items": { - "$ref": "#/definitions/DrugAvailabilityEnum" + "$ref": "#/$defs/DrugAvailabilityEnum" }, "type": "array" }, @@ -5167,7 +5213,7 @@ "has_attribute": { "description": "connects any entity to an attribute", "items": { - "$ref": "#/definitions/Attribute" + "$ref": "#/$defs/Attribute" }, "type": "array" }, @@ -5186,6 +5232,13 @@ "is_supplement": { "type": "string" }, + "is_toxic": { + "type": "boolean" + }, + "max_tolerated_dose": { + "description": "The highest dose of a drug or treatment that does not cause unacceptable side effects. The maximum tolerated dose is determined in clinical trials by testing increasing doses on different groups of people until the highest dose with acceptable side effects is found. Also called MTD.", + "type": "string" + }, "name": { "description": "A human-readable name for an attribute or entity.", "type": "string" @@ -5221,7 +5274,7 @@ "properties": { "available_from": { "items": { - "$ref": "#/definitions/DrugAvailabilityEnum" + "$ref": "#/$defs/DrugAvailabilityEnum" }, "type": "array" }, @@ -5238,7 +5291,7 @@ "has_attribute": { "description": "connects any entity to an attribute", "items": { - "$ref": "#/definitions/Attribute" + "$ref": "#/$defs/Attribute" }, "type": "array" }, @@ -5250,6 +5303,13 @@ "description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string" }, + "is_toxic": { + "type": "boolean" + }, + "max_tolerated_dose": { + "description": "The highest dose of a drug or treatment that does not cause unacceptable side effects. The maximum tolerated dose is determined in clinical trials by testing increasing doses on different groups of people until the highest dose with acceptable side effects is found. Also called MTD.", + "type": "string" + }, "name": { "description": "A human-readable name for an attribute or entity.", "type": "string" @@ -5296,7 +5356,7 @@ "has_attribute": { "description": "connects any entity to an attribute", "items": { - "$ref": "#/definitions/Attribute" + "$ref": "#/$defs/Attribute" }, "type": "array" }, @@ -5317,7 +5377,7 @@ "type": "boolean" }, "object": { - "$ref": "#/definitions/GeneOntologyClass", + "$ref": "#/$defs/GeneOntologyClass", "description": "class describing the activity, process or localization of the gene product" }, "predicate": { @@ -5341,7 +5401,7 @@ "qualifiers": { "description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": { - "$ref": "#/definitions/OntologyClass" + "$ref": "#/$defs/OntologyClass" }, "type": "array" }, @@ -5353,7 +5413,7 @@ "type": "string" }, "subject": { - "$ref": "#/definitions/MacromolecularMachineMixin", + "$ref": "#/$defs/MacromolecularMachineMixin", "description": "gene, product or macromolecular complex mixin that has the function associated with the GO term" }, "type": { @@ -5387,7 +5447,7 @@ "has_attribute": { "description": "connects any entity to an attribute", "items": { - "$ref": "#/definitions/Attribute" + "$ref": "#/$defs/Attribute" }, "type": "array" }, @@ -5475,7 +5535,7 @@ "has_attribute": { "description": "connects any entity to an attribute", "items": { - "$ref": "#/definitions/Attribute" + "$ref": "#/$defs/Attribute" }, "type": "array" }, @@ -5500,7 +5560,7 @@ "type": "string" }, "onset_qualifier": { - "$ref": "#/definitions/Onset", + "$ref": "#/$defs/Onset", "description": "a qualifier used in a phenotypic association to state when the phenotype appears is in the subject" }, "predicate": { @@ -5524,7 +5584,7 @@ "qualifiers": { "description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": { - "$ref": "#/definitions/OntologyClass" + "$ref": "#/$defs/OntologyClass" }, "type": "array" }, @@ -5532,7 +5592,7 @@ "type": "string" }, "severity_qualifier": { - "$ref": "#/definitions/SeverityValue", + "$ref": "#/$defs/SeverityValue", "description": "a qualifier used in a phenotypic association to state how severe the phenotype is in the subject" }, "source": { @@ -5540,7 +5600,7 @@ "type": "string" }, "subject": { - "$ref": "#/definitions/GeneOrGeneProduct", + "$ref": "#/$defs/GeneOrGeneProduct", "description": "A gene that has a role in modeling the disease. This may be a model organism ortholog of a known disease gene, or it may be a gene whose mutants recapitulate core features of the disease." }, "type": { @@ -5574,7 +5634,7 @@ "has_attribute": { "description": "connects any entity to an attribute", "items": { - "$ref": "#/definitions/Attribute" + "$ref": "#/$defs/Attribute" }, "type": "array" }, @@ -5640,7 +5700,7 @@ "has_attribute": { "description": "connects any entity to an attribute", "items": { - "$ref": "#/definitions/Attribute" + "$ref": "#/$defs/Attribute" }, "type": "array" }, @@ -5665,7 +5725,7 @@ "type": "string" }, "onset_qualifier": { - "$ref": "#/definitions/Onset", + "$ref": "#/$defs/Onset", "description": "a qualifier used in a phenotypic association to state when the phenotype appears is in the subject" }, "predicate": { @@ -5689,7 +5749,7 @@ "qualifiers": { "description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": { - "$ref": "#/definitions/OntologyClass" + "$ref": "#/$defs/OntologyClass" }, "type": "array" }, @@ -5701,7 +5761,7 @@ "type": "string" }, "severity_qualifier": { - "$ref": "#/definitions/SeverityValue", + "$ref": "#/$defs/SeverityValue", "description": "a qualifier used in a phenotypic association to state how severe the phenotype is in the subject" }, "source": { @@ -5709,7 +5769,7 @@ "type": "string" }, "subject": { - "$ref": "#/definitions/GeneOrGeneProduct", + "$ref": "#/$defs/GeneOrGeneProduct", "description": "A gene that has a role in modeling the disease. This may be a model organism ortholog of a known disease gene, or it may be a gene whose mutants recapitulate core features of the disease." }, "type": { @@ -5743,7 +5803,7 @@ "has_attribute": { "description": "connects any entity to an attribute", "items": { - "$ref": "#/definitions/Attribute" + "$ref": "#/$defs/Attribute" }, "type": "array" }, @@ -5764,7 +5824,7 @@ "type": "boolean" }, "object": { - "$ref": "#/definitions/GeneOrGeneProduct" + "$ref": "#/$defs/GeneOrGeneProduct" }, "predicate": { "description": "the direction is always from regulator to regulated", @@ -5787,7 +5847,7 @@ "qualifiers": { "description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": { - "$ref": "#/definitions/OntologyClass" + "$ref": "#/$defs/OntologyClass" }, "type": "array" }, @@ -5799,7 +5859,7 @@ "type": "string" }, "subject": { - "$ref": "#/definitions/GeneOrGeneProduct" + "$ref": "#/$defs/GeneOrGeneProduct" }, "type": { "description": "rdf:type of biolink:Association should be fixed at rdf:Statement", @@ -5836,7 +5896,7 @@ "has_attribute": { "description": "connects any entity to an attribute", "items": { - "$ref": "#/definitions/Attribute" + "$ref": "#/$defs/Attribute" }, "type": "array" }, @@ -5861,7 +5921,7 @@ "type": "string" }, "onset_qualifier": { - "$ref": "#/definitions/Onset", + "$ref": "#/$defs/Onset", "description": "a qualifier used in a phenotypic association to state when the phenotype appears is in the subject" }, "predicate": { @@ -5885,7 +5945,7 @@ "qualifiers": { "description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": { - "$ref": "#/definitions/OntologyClass" + "$ref": "#/$defs/OntologyClass" }, "type": "array" }, @@ -5893,7 +5953,7 @@ "type": "string" }, "severity_qualifier": { - "$ref": "#/definitions/SeverityValue", + "$ref": "#/$defs/SeverityValue", "description": "a qualifier used in a phenotypic association to state how severe the phenotype is in the subject" }, "source": { @@ -5901,7 +5961,7 @@ "type": "string" }, "subject": { - "$ref": "#/definitions/GeneOrGeneProduct", + "$ref": "#/$defs/GeneOrGeneProduct", "description": "gene in which variation is correlated with the disease, may be protective or causative or associative, or as a model" }, "type": { @@ -5935,7 +5995,7 @@ "has_attribute": { "description": "connects any entity to an attribute", "items": { - "$ref": "#/definitions/Attribute" + "$ref": "#/$defs/Attribute" }, "type": "array" }, @@ -5980,12 +6040,12 @@ "qualifiers": { "description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": { - "$ref": "#/definitions/OntologyClass" + "$ref": "#/$defs/OntologyClass" }, "type": "array" }, "quantifier_qualifier": { - "$ref": "#/definitions/OntologyClass", + "$ref": "#/$defs/OntologyClass", "description": "can be used to indicate magnitude, or also ranking" }, "relation": { @@ -6000,7 +6060,7 @@ "type": "string" }, "subject": { - "$ref": "#/definitions/GeneOrGeneProduct", + "$ref": "#/$defs/GeneOrGeneProduct", "description": "gene in which variation is correlated with the phenotypic feature" }, "type": { @@ -6038,7 +6098,7 @@ "has_attribute": { "description": "connects any entity to an attribute", "items": { - "$ref": "#/definitions/Attribute" + "$ref": "#/$defs/Attribute" }, "type": "array" }, @@ -6059,7 +6119,7 @@ "type": "boolean" }, "object": { - "$ref": "#/definitions/GeneOrGeneProduct", + "$ref": "#/$defs/GeneOrGeneProduct", "description": "the object gene in the association. If the relation is symmetric, subject vs object is arbitrary. We allow a gene product to stand as a proxy for the gene or vice versa." }, "phenotypic_state": { @@ -6086,12 +6146,12 @@ "qualifiers": { "description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": { - "$ref": "#/definitions/OntologyClass" + "$ref": "#/$defs/OntologyClass" }, "type": "array" }, "quantifier_qualifier": { - "$ref": "#/definitions/OntologyClass", + "$ref": "#/$defs/OntologyClass", "description": "Optional quantitative value indicating degree of expression." }, "relation": { @@ -6106,7 +6166,7 @@ "type": "string" }, "subject": { - "$ref": "#/definitions/GeneOrGeneProduct", + "$ref": "#/$defs/GeneOrGeneProduct", "description": "the subject gene in the association. If the relation is symmetric, subject vs object is arbitrary. We allow a gene product to stand as a proxy for the gene or vice versa." }, "type": { @@ -6140,7 +6200,7 @@ "has_attribute": { "description": "connects any entity to an attribute", "items": { - "$ref": "#/definitions/Attribute" + "$ref": "#/$defs/Attribute" }, "type": "array" }, @@ -6161,7 +6221,7 @@ "type": "boolean" }, "object": { - "$ref": "#/definitions/GeneOrGeneProduct", + "$ref": "#/$defs/GeneOrGeneProduct", "description": "the object gene in the association. If the relation is symmetric, subject vs object is arbitrary. We allow a gene product to stand as a proxy for the gene or vice versa." }, "predicate": { @@ -6185,7 +6245,7 @@ "qualifiers": { "description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": { - "$ref": "#/definitions/OntologyClass" + "$ref": "#/$defs/OntologyClass" }, "type": "array" }, @@ -6197,7 +6257,7 @@ "type": "string" }, "subject": { - "$ref": "#/definitions/GeneOrGeneProduct", + "$ref": "#/$defs/GeneOrGeneProduct", "description": "the subject gene in the association. If the relation is symmetric, subject vs object is arbitrary. We allow a gene product to stand as a proxy for the gene or vice versa." }, "type": { @@ -6231,7 +6291,7 @@ "has_attribute": { "description": "connects any entity to an attribute", "items": { - "$ref": "#/definitions/Attribute" + "$ref": "#/$defs/Attribute" }, "type": "array" }, @@ -6252,7 +6312,7 @@ "type": "boolean" }, "object": { - "$ref": "#/definitions/GeneProductMixin" + "$ref": "#/$defs/GeneProductMixin" }, "predicate": { "type": "string" @@ -6274,7 +6334,7 @@ "qualifiers": { "description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": { - "$ref": "#/definitions/OntologyClass" + "$ref": "#/$defs/OntologyClass" }, "type": "array" }, @@ -6319,7 +6379,7 @@ "has_attribute": { "description": "connects any entity to an attribute", "items": { - "$ref": "#/definitions/Attribute" + "$ref": "#/$defs/Attribute" }, "type": "array" }, @@ -6340,7 +6400,7 @@ "type": "boolean" }, "object": { - "$ref": "#/definitions/GeneOntologyClass", + "$ref": "#/$defs/GeneOntologyClass", "description": "class describing the activity, process or localization of the gene product" }, "predicate": { @@ -6364,7 +6424,7 @@ "qualifiers": { "description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": { - "$ref": "#/definitions/OntologyClass" + "$ref": "#/$defs/OntologyClass" }, "type": "array" }, @@ -6414,7 +6474,7 @@ "has_attribute": { "description": "connects any entity to an attribute", "items": { - "$ref": "#/definitions/Attribute" + "$ref": "#/$defs/Attribute" }, "type": "array" }, @@ -6439,7 +6499,7 @@ "type": "string" }, "onset_qualifier": { - "$ref": "#/definitions/Onset", + "$ref": "#/$defs/Onset", "description": "a qualifier used in a phenotypic association to state when the phenotype appears is in the subject" }, "predicate": { @@ -6463,7 +6523,7 @@ "qualifiers": { "description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": { - "$ref": "#/definitions/OntologyClass" + "$ref": "#/$defs/OntologyClass" }, "type": "array" }, @@ -6471,11 +6531,11 @@ "type": "string" }, "severity_qualifier": { - "$ref": "#/definitions/SeverityValue", + "$ref": "#/$defs/SeverityValue", "description": "a qualifier used in a phenotypic association to state how severe the phenotype is in the subject" }, "sex_qualifier": { - "$ref": "#/definitions/BiologicalSex", + "$ref": "#/$defs/BiologicalSex", "description": "a qualifier used in a phenotypic association to state whether the association is specific to a particular sex." }, "source": { @@ -6483,7 +6543,7 @@ "type": "string" }, "subject": { - "$ref": "#/definitions/GeneOrGeneProduct", + "$ref": "#/$defs/GeneOrGeneProduct", "description": "gene in which variation is correlated with the phenotypic feature" }, "type": { @@ -6517,7 +6577,7 @@ "has_attribute": { "description": "connects any entity to an attribute", "items": { - "$ref": "#/definitions/Attribute" + "$ref": "#/$defs/Attribute" }, "type": "array" }, @@ -6617,13 +6677,13 @@ "type": "integer" }, "genome_build": { - "$ref": "#/definitions/StrandEnum", + "$ref": "#/$defs/StrandEnum", "description": "The version of the genome on which a feature is located. For example, GRCh38 for Homo sapiens." }, "has_attribute": { "description": "connects any entity to an attribute", "items": { - "$ref": "#/definitions/Attribute" + "$ref": "#/$defs/Attribute" }, "type": "array" }, @@ -6647,7 +6707,7 @@ "type": "string" }, "phase": { - "$ref": "#/definitions/PhaseEnum", + "$ref": "#/$defs/PhaseEnum", "description": "The phase for a coding sequence entity. For example, phase of a CDS as represented in a GFF3 with a value of 0, 1 or 2." }, "predicate": { @@ -6670,7 +6730,7 @@ "qualifiers": { "description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": { - "$ref": "#/definitions/OntologyClass" + "$ref": "#/$defs/OntologyClass" }, "type": "array" }, @@ -6686,7 +6746,7 @@ "type": "integer" }, "strand": { - "$ref": "#/definitions/StrandEnum", + "$ref": "#/$defs/StrandEnum", "description": "The strand on which a feature is located. Has a value of '+' (sense strand or forward strand) or '-' (anti-sense strand or reverse strand)." }, "subject": { @@ -6723,7 +6783,7 @@ "has_attribute": { "description": "connects any entity to an attribute", "items": { - "$ref": "#/definitions/Attribute" + "$ref": "#/$defs/Attribute" }, "type": "array" }, @@ -6732,7 +6792,7 @@ "type": "string" }, "has_zygosity": { - "$ref": "#/definitions/Zygosity" + "$ref": "#/$defs/Zygosity" }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", @@ -6796,7 +6856,7 @@ "has_attribute": { "description": "connects any entity to an attribute", "items": { - "$ref": "#/definitions/Attribute" + "$ref": "#/$defs/Attribute" }, "type": "array" }, @@ -6821,7 +6881,7 @@ "type": "string" }, "onset_qualifier": { - "$ref": "#/definitions/Onset", + "$ref": "#/$defs/Onset", "description": "a qualifier used in a phenotypic association to state when the phenotype appears is in the subject" }, "predicate": { @@ -6845,7 +6905,7 @@ "qualifiers": { "description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": { - "$ref": "#/definitions/OntologyClass" + "$ref": "#/$defs/OntologyClass" }, "type": "array" }, @@ -6853,7 +6913,7 @@ "type": "string" }, "severity_qualifier": { - "$ref": "#/definitions/SeverityValue", + "$ref": "#/$defs/SeverityValue", "description": "a qualifier used in a phenotypic association to state how severe the phenotype is in the subject" }, "source": { @@ -6899,7 +6959,7 @@ "has_attribute": { "description": "connects any entity to an attribute", "items": { - "$ref": "#/definitions/Attribute" + "$ref": "#/$defs/Attribute" }, "type": "array" }, @@ -6924,7 +6984,7 @@ "type": "string" }, "onset_qualifier": { - "$ref": "#/definitions/Onset", + "$ref": "#/$defs/Onset", "description": "a qualifier used in a phenotypic association to state when the phenotype appears is in the subject" }, "predicate": { @@ -6948,7 +7008,7 @@ "qualifiers": { "description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": { - "$ref": "#/definitions/OntologyClass" + "$ref": "#/$defs/OntologyClass" }, "type": "array" }, @@ -6956,7 +7016,7 @@ "type": "string" }, "severity_qualifier": { - "$ref": "#/definitions/SeverityValue", + "$ref": "#/$defs/SeverityValue", "description": "a qualifier used in a phenotypic association to state how severe the phenotype is in the subject" }, "source": { @@ -6998,7 +7058,7 @@ "has_attribute": { "description": "connects any entity to an attribute", "items": { - "$ref": "#/definitions/Attribute" + "$ref": "#/$defs/Attribute" }, "type": "array" }, @@ -7043,7 +7103,7 @@ "qualifiers": { "description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": { - "$ref": "#/definitions/OntologyClass" + "$ref": "#/$defs/OntologyClass" }, "type": "array" }, @@ -7089,7 +7149,7 @@ "has_attribute": { "description": "connects any entity to an attribute", "items": { - "$ref": "#/definitions/Attribute" + "$ref": "#/$defs/Attribute" }, "type": "array" }, @@ -7133,7 +7193,7 @@ "qualifiers": { "description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": { - "$ref": "#/definitions/OntologyClass" + "$ref": "#/$defs/OntologyClass" }, "type": "array" }, @@ -7183,7 +7243,7 @@ "has_attribute": { "description": "connects any entity to an attribute", "items": { - "$ref": "#/definitions/Attribute" + "$ref": "#/$defs/Attribute" }, "type": "array" }, @@ -7208,7 +7268,7 @@ "type": "string" }, "onset_qualifier": { - "$ref": "#/definitions/Onset", + "$ref": "#/$defs/Onset", "description": "a qualifier used in a phenotypic association to state when the phenotype appears is in the subject" }, "predicate": { @@ -7231,7 +7291,7 @@ "qualifiers": { "description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": { - "$ref": "#/definitions/OntologyClass" + "$ref": "#/$defs/OntologyClass" }, "type": "array" }, @@ -7239,11 +7299,11 @@ "type": "string" }, "severity_qualifier": { - "$ref": "#/definitions/SeverityValue", + "$ref": "#/$defs/SeverityValue", "description": "a qualifier used in a phenotypic association to state how severe the phenotype is in the subject" }, "sex_qualifier": { - "$ref": "#/definitions/BiologicalSex", + "$ref": "#/$defs/BiologicalSex", "description": "a qualifier used in a phenotypic association to state whether the association is specific to a particular sex." }, "source": { @@ -7285,7 +7345,7 @@ "has_attribute": { "description": "connects any entity to an attribute", "items": { - "$ref": "#/definitions/Attribute" + "$ref": "#/$defs/Attribute" }, "type": "array" }, @@ -7330,7 +7390,7 @@ "qualifiers": { "description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": { - "$ref": "#/definitions/OntologyClass" + "$ref": "#/$defs/OntologyClass" }, "type": "array" }, @@ -7364,7 +7424,7 @@ "description": "An attribute corresponding to the genotypic sex of the individual, based upon genotypic composition of sex chromosomes.", "properties": { "has_attribute_type": { - "$ref": "#/definitions/OntologyClass", + "$ref": "#/$defs/OntologyClass", "description": "connects an attribute to a class that describes it" }, "has_qualitative_value": { @@ -7374,7 +7434,7 @@ "has_quantitative_value": { "description": "connects an attribute to a value", "items": { - "$ref": "#/definitions/QuantityValue" + "$ref": "#/$defs/QuantityValue" }, "type": "array" }, @@ -7428,7 +7488,7 @@ "has_attribute": { "description": "connects any entity to an attribute", "items": { - "$ref": "#/definitions/Attribute" + "$ref": "#/$defs/Attribute" }, "type": "array" }, @@ -7491,7 +7551,7 @@ "has_attribute": { "description": "connects any entity to an attribute", "items": { - "$ref": "#/definitions/Attribute" + "$ref": "#/$defs/Attribute" }, "type": "array" }, @@ -7559,7 +7619,7 @@ "has_attribute": { "description": "may often be an organism attribute", "items": { - "$ref": "#/definitions/Attribute" + "$ref": "#/$defs/Attribute" }, "type": "array" }, @@ -7621,7 +7681,7 @@ "has_attribute": { "description": "connects any entity to an attribute", "items": { - "$ref": "#/definitions/Attribute" + "$ref": "#/$defs/Attribute" }, "type": "array" }, @@ -7687,7 +7747,7 @@ "has_attribute": { "description": "connects any entity to an attribute", "items": { - "$ref": "#/definitions/Attribute" + "$ref": "#/$defs/Attribute" }, "type": "array" }, @@ -7750,7 +7810,7 @@ "has_attribute": { "description": "may often be an organism attribute", "items": { - "$ref": "#/definitions/Attribute" + "$ref": "#/$defs/Attribute" }, "type": "array" }, @@ -7820,7 +7880,7 @@ "has_attribute": { "description": "connects any entity to an attribute", "items": { - "$ref": "#/definitions/Attribute" + "$ref": "#/$defs/Attribute" }, "type": "array" }, @@ -7869,7 +7929,7 @@ "description": "The pattern or 'mode' in which a particular genetic trait or disorder is passed from one generation to the next, e.g. autosomal dominant, autosomal recessive, etc.", "properties": { "has_attribute_type": { - "$ref": "#/definitions/OntologyClass", + "$ref": "#/$defs/OntologyClass", "description": "connects an attribute to a class that describes it" }, "has_qualitative_value": { @@ -7879,7 +7939,7 @@ "has_quantitative_value": { "description": "connects an attribute to a value", "items": { - "$ref": "#/definitions/QuantityValue" + "$ref": "#/$defs/QuantityValue" }, "type": "array" }, @@ -7919,7 +7979,7 @@ "has_attribute": { "description": "may often be an organism attribute", "items": { - "$ref": "#/definitions/Attribute" + "$ref": "#/$defs/Attribute" }, "type": "array" }, @@ -7991,7 +8051,7 @@ "has_attribute": { "description": "connects any entity to an attribute", "items": { - "$ref": "#/definitions/Attribute" + "$ref": "#/$defs/Attribute" }, "type": "array" }, @@ -8035,7 +8095,7 @@ "qualifiers": { "description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": { - "$ref": "#/definitions/OntologyClass" + "$ref": "#/$defs/OntologyClass" }, "type": "array" }, @@ -8047,7 +8107,7 @@ "type": "string" }, "subject": { - "$ref": "#/definitions/MacromolecularMachineMixin", + "$ref": "#/$defs/MacromolecularMachineMixin", "description": "gene, product or macromolecular complex mixin that has the function associated with the GO term" }, "type": { @@ -8081,7 +8141,7 @@ "has_attribute": { "description": "connects any entity to an attribute", "items": { - "$ref": "#/definitions/Attribute" + "$ref": "#/$defs/Attribute" }, "type": "array" }, @@ -8125,7 +8185,7 @@ "qualifiers": { "description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": { - "$ref": "#/definitions/OntologyClass" + "$ref": "#/$defs/OntologyClass" }, "type": "array" }, @@ -8137,7 +8197,7 @@ "type": "string" }, "subject": { - "$ref": "#/definitions/MacromolecularMachineMixin", + "$ref": "#/$defs/MacromolecularMachineMixin", "description": "gene, product or macromolecular complex mixin that has the function associated with the GO term" }, "type": { @@ -8171,7 +8231,7 @@ "has_attribute": { "description": "connects any entity to an attribute", "items": { - "$ref": "#/definitions/Attribute" + "$ref": "#/$defs/Attribute" }, "type": "array" }, @@ -8215,7 +8275,7 @@ "qualifiers": { "description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": { - "$ref": "#/definitions/OntologyClass" + "$ref": "#/$defs/OntologyClass" }, "type": "array" }, @@ -8227,7 +8287,7 @@ "type": "string" }, "subject": { - "$ref": "#/definitions/MacromolecularMachineMixin", + "$ref": "#/$defs/MacromolecularMachineMixin", "description": "gene, product or macromolecular complex mixin that has the function associated with the GO term" }, "type": { @@ -8250,7 +8310,7 @@ "properties": { "available_from": { "items": { - "$ref": "#/definitions/DrugAvailabilityEnum" + "$ref": "#/$defs/DrugAvailabilityEnum" }, "type": "array" }, @@ -8267,7 +8327,7 @@ "has_attribute": { "description": "connects any entity to an attribute", "items": { - "$ref": "#/definitions/Attribute" + "$ref": "#/$defs/Attribute" }, "type": "array" }, @@ -8279,6 +8339,13 @@ "description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string" }, + "is_toxic": { + "type": "boolean" + }, + "max_tolerated_dose": { + "description": "The highest dose of a drug or treatment that does not cause unacceptable side effects. The maximum tolerated dose is determined in clinical trials by testing increasing doses on different groups of people until the highest dose with acceptable side effects is found. Also called MTD.", + "type": "string" + }, "name": { "description": "A human-readable name for an attribute or entity.", "type": "string" @@ -8325,7 +8392,7 @@ "has_attribute": { "description": "connects any entity to an attribute", "items": { - "$ref": "#/definitions/Attribute" + "$ref": "#/$defs/Attribute" }, "type": "array" }, @@ -8380,7 +8447,7 @@ "has_attribute": { "description": "connects any entity to an attribute", "items": { - "$ref": "#/definitions/Attribute" + "$ref": "#/$defs/Attribute" }, "type": "array" }, @@ -8425,7 +8492,7 @@ "qualifiers": { "description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": { - "$ref": "#/definitions/OntologyClass" + "$ref": "#/$defs/OntologyClass" }, "type": "array" }, @@ -8471,7 +8538,7 @@ "has_attribute": { "description": "connects any entity to an attribute", "items": { - "$ref": "#/definitions/Attribute" + "$ref": "#/$defs/Attribute" }, "type": "array" }, @@ -8516,7 +8583,7 @@ "qualifiers": { "description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": { - "$ref": "#/definitions/OntologyClass" + "$ref": "#/$defs/OntologyClass" }, "type": "array" }, @@ -8551,7 +8618,7 @@ "properties": { "available_from": { "items": { - "$ref": "#/definitions/DrugAvailabilityEnum" + "$ref": "#/$defs/DrugAvailabilityEnum" }, "type": "array" }, @@ -8568,7 +8635,7 @@ "has_attribute": { "description": "connects any entity to an attribute", "items": { - "$ref": "#/definitions/Attribute" + "$ref": "#/$defs/Attribute" }, "type": "array" }, @@ -8595,6 +8662,13 @@ "description": "indicates whether a molecular entity is a metabolite", "type": "boolean" }, + "is_toxic": { + "type": "boolean" + }, + "max_tolerated_dose": { + "description": "The highest dose of a drug or treatment that does not cause unacceptable side effects. The maximum tolerated dose is determined in clinical trials by testing increasing doses on different groups of people until the highest dose with acceptable side effects is found. Also called MTD.", + "type": "string" + }, "name": { "description": "A human-readable name for an attribute or entity.", "type": "string" @@ -8644,7 +8718,7 @@ "properties": { "available_from": { "items": { - "$ref": "#/definitions/DrugAvailabilityEnum" + "$ref": "#/$defs/DrugAvailabilityEnum" }, "type": "array" }, @@ -8661,7 +8735,7 @@ "has_attribute": { "description": "connects any entity to an attribute", "items": { - "$ref": "#/definitions/Attribute" + "$ref": "#/$defs/Attribute" }, "type": "array" }, @@ -8673,6 +8747,13 @@ "description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string" }, + "is_toxic": { + "type": "boolean" + }, + "max_tolerated_dose": { + "description": "The highest dose of a drug or treatment that does not cause unacceptable side effects. The maximum tolerated dose is determined in clinical trials by testing increasing doses on different groups of people until the highest dose with acceptable side effects is found. Also called MTD.", + "type": "string" + }, "name": { "description": "A human-readable name for an attribute or entity.", "type": "string" @@ -8719,14 +8800,14 @@ "enabled_by": { "description": "The gene product, gene, or complex that catalyzes the reaction", "items": { - "$ref": "#/definitions/MacromolecularMachineMixin" + "$ref": "#/$defs/MacromolecularMachineMixin" }, "type": "array" }, "has_attribute": { "description": "connects any entity to an attribute", "items": { - "$ref": "#/definitions/Attribute" + "$ref": "#/$defs/Attribute" }, "type": "array" }, @@ -8784,7 +8865,7 @@ "properties": { "available_from": { "items": { - "$ref": "#/definitions/DrugAvailabilityEnum" + "$ref": "#/$defs/DrugAvailabilityEnum" }, "type": "array" }, @@ -8801,7 +8882,7 @@ "has_attribute": { "description": "connects any entity to an attribute", "items": { - "$ref": "#/definitions/Attribute" + "$ref": "#/$defs/Attribute" }, "type": "array" }, @@ -8817,6 +8898,13 @@ "description": "indicates whether a molecular entity is a metabolite", "type": "boolean" }, + "is_toxic": { + "type": "boolean" + }, + "max_tolerated_dose": { + "description": "The highest dose of a drug or treatment that does not cause unacceptable side effects. The maximum tolerated dose is determined in clinical trials by testing increasing doses on different groups of people until the highest dose with acceptable side effects is found. Also called MTD.", + "type": "string" + }, "name": { "description": "A human-readable name for an attribute or entity.", "type": "string" @@ -8852,7 +8940,7 @@ "properties": { "available_from": { "items": { - "$ref": "#/definitions/DrugAvailabilityEnum" + "$ref": "#/$defs/DrugAvailabilityEnum" }, "type": "array" }, @@ -8869,7 +8957,7 @@ "has_attribute": { "description": "connects any entity to an attribute", "items": { - "$ref": "#/definitions/Attribute" + "$ref": "#/$defs/Attribute" }, "type": "array" }, @@ -8888,6 +8976,13 @@ "is_supplement": { "type": "string" }, + "is_toxic": { + "type": "boolean" + }, + "max_tolerated_dose": { + "description": "The highest dose of a drug or treatment that does not cause unacceptable side effects. The maximum tolerated dose is determined in clinical trials by testing increasing doses on different groups of people until the highest dose with acceptable side effects is found. Also called MTD.", + "type": "string" + }, "name": { "description": "A human-readable name for an attribute or entity.", "type": "string" @@ -8942,7 +9037,7 @@ "has_attribute": { "description": "connects any entity to an attribute", "items": { - "$ref": "#/definitions/Attribute" + "$ref": "#/$defs/Attribute" }, "type": "array" }, @@ -8997,7 +9092,7 @@ "has_attribute": { "description": "connects any entity to an attribute", "items": { - "$ref": "#/definitions/Attribute" + "$ref": "#/$defs/Attribute" }, "type": "array" }, @@ -9040,7 +9135,7 @@ "qualifiers": { "description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": { - "$ref": "#/definitions/OntologyClass" + "$ref": "#/$defs/OntologyClass" }, "type": "array" }, @@ -9074,7 +9169,7 @@ "properties": { "available_from": { "items": { - "$ref": "#/definitions/DrugAvailabilityEnum" + "$ref": "#/$defs/DrugAvailabilityEnum" }, "type": "array" }, @@ -9091,7 +9186,7 @@ "has_attribute": { "description": "connects any entity to an attribute", "items": { - "$ref": "#/definitions/Attribute" + "$ref": "#/$defs/Attribute" }, "type": "array" }, @@ -9118,6 +9213,13 @@ "description": "indicates whether a molecular entity is a metabolite", "type": "boolean" }, + "is_toxic": { + "type": "boolean" + }, + "max_tolerated_dose": { + "description": "The highest dose of a drug or treatment that does not cause unacceptable side effects. The maximum tolerated dose is determined in clinical trials by testing increasing doses on different groups of people until the highest dose with acceptable side effects is found. Also called MTD.", + "type": "string" + }, "name": { "description": "A human-readable name for an attribute or entity.", "type": "string" @@ -9167,7 +9269,7 @@ "properties": { "available_from": { "items": { - "$ref": "#/definitions/DrugAvailabilityEnum" + "$ref": "#/$defs/DrugAvailabilityEnum" }, "type": "array" }, @@ -9184,7 +9286,7 @@ "has_attribute": { "description": "connects any entity to an attribute", "items": { - "$ref": "#/definitions/Attribute" + "$ref": "#/$defs/Attribute" }, "type": "array" }, @@ -9211,6 +9313,13 @@ "description": "indicates whether a molecular entity is a metabolite", "type": "boolean" }, + "is_toxic": { + "type": "boolean" + }, + "max_tolerated_dose": { + "description": "The highest dose of a drug or treatment that does not cause unacceptable side effects. The maximum tolerated dose is determined in clinical trials by testing increasing doses on different groups of people until the highest dose with acceptable side effects is found. Also called MTD.", + "type": "string" + }, "name": { "description": "A human-readable name for an attribute or entity.", "type": "string" @@ -9246,7 +9355,7 @@ "properties": { "available_from": { "items": { - "$ref": "#/definitions/DrugAvailabilityEnum" + "$ref": "#/$defs/DrugAvailabilityEnum" }, "type": "array" }, @@ -9263,7 +9372,7 @@ "has_attribute": { "description": "connects any entity to an attribute", "items": { - "$ref": "#/definitions/Attribute" + "$ref": "#/$defs/Attribute" }, "type": "array" }, @@ -9275,6 +9384,13 @@ "description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string" }, + "is_toxic": { + "type": "boolean" + }, + "max_tolerated_dose": { + "description": "The highest dose of a drug or treatment that does not cause unacceptable side effects. The maximum tolerated dose is determined in clinical trials by testing increasing doses on different groups of people until the highest dose with acceptable side effects is found. Also called MTD.", + "type": "string" + }, "name": { "description": "A human-readable name for an attribute or entity.", "type": "string" @@ -9309,7 +9425,7 @@ "description": "The age group in which (disease) symptom manifestations appear", "properties": { "has_attribute_type": { - "$ref": "#/definitions/OntologyClass", + "$ref": "#/$defs/OntologyClass", "description": "connects an attribute to a class that describes it" }, "has_qualitative_value": { @@ -9319,7 +9435,7 @@ "has_quantitative_value": { "description": "connects an attribute to a value", "items": { - "$ref": "#/definitions/QuantityValue" + "$ref": "#/$defs/QuantityValue" }, "type": "array" }, @@ -9347,7 +9463,7 @@ "description": "describes a characteristic of an organismal entity.", "properties": { "has_attribute_type": { - "$ref": "#/definitions/OntologyClass", + "$ref": "#/$defs/OntologyClass", "description": "connects an attribute to a class that describes it" }, "has_qualitative_value": { @@ -9357,7 +9473,7 @@ "has_quantitative_value": { "description": "connects an attribute to a value", "items": { - "$ref": "#/definitions/QuantityValue" + "$ref": "#/$defs/QuantityValue" }, "type": "array" }, @@ -9397,12 +9513,12 @@ "has_attribute": { "description": "connects any entity to an attribute", "items": { - "$ref": "#/definitions/Attribute" + "$ref": "#/$defs/Attribute" }, "type": "array" }, "has_taxonomic_rank": { - "$ref": "#/definitions/TaxonomicRank" + "$ref": "#/$defs/TaxonomicRank" }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", @@ -9466,7 +9582,7 @@ "has_attribute": { "description": "connects any entity to an attribute", "items": { - "$ref": "#/definitions/Attribute" + "$ref": "#/$defs/Attribute" }, "type": "array" }, @@ -9510,7 +9626,7 @@ "qualifiers": { "description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": { - "$ref": "#/definitions/OntologyClass" + "$ref": "#/$defs/OntologyClass" }, "type": "array" }, @@ -9556,7 +9672,7 @@ "has_attribute": { "description": "connects any entity to an attribute", "items": { - "$ref": "#/definitions/Attribute" + "$ref": "#/$defs/Attribute" }, "type": "array" }, @@ -9600,7 +9716,7 @@ "qualifiers": { "description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": { - "$ref": "#/definitions/OntologyClass" + "$ref": "#/$defs/OntologyClass" }, "type": "array" }, @@ -9646,7 +9762,7 @@ "has_attribute": { "description": "connects any entity to an attribute", "items": { - "$ref": "#/definitions/Attribute" + "$ref": "#/$defs/Attribute" }, "type": "array" }, @@ -9691,7 +9807,7 @@ "qualifiers": { "description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": { - "$ref": "#/definitions/OntologyClass" + "$ref": "#/$defs/OntologyClass" }, "type": "array" }, @@ -9740,7 +9856,7 @@ "has_attribute": { "description": "connects any entity to an attribute", "items": { - "$ref": "#/definitions/Attribute" + "$ref": "#/$defs/Attribute" }, "type": "array" }, @@ -9765,7 +9881,7 @@ "type": "string" }, "onset_qualifier": { - "$ref": "#/definitions/Onset", + "$ref": "#/$defs/Onset", "description": "a qualifier used in a phenotypic association to state when the phenotype appears is in the subject" }, "predicate": { @@ -9789,7 +9905,7 @@ "qualifiers": { "description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": { - "$ref": "#/definitions/OntologyClass" + "$ref": "#/$defs/OntologyClass" }, "type": "array" }, @@ -9797,7 +9913,7 @@ "type": "string" }, "severity_qualifier": { - "$ref": "#/definitions/SeverityValue", + "$ref": "#/$defs/SeverityValue", "description": "a qualifier used in a phenotypic association to state how severe the phenotype is in the subject" }, "source": { @@ -9839,7 +9955,7 @@ "has_attribute": { "description": "connects any entity to an attribute", "items": { - "$ref": "#/definitions/Attribute" + "$ref": "#/$defs/Attribute" }, "type": "array" }, @@ -9860,7 +9976,7 @@ "type": "boolean" }, "object": { - "$ref": "#/definitions/GeneOrGeneProduct", + "$ref": "#/$defs/GeneOrGeneProduct", "description": "the object gene in the association. If the relation is symmetric, subject vs object is arbitrary. We allow a gene product to stand as a proxy for the gene or vice versa." }, "predicate": { @@ -9883,7 +9999,7 @@ "qualifiers": { "description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": { - "$ref": "#/definitions/OntologyClass" + "$ref": "#/$defs/OntologyClass" }, "type": "array" }, @@ -9896,7 +10012,7 @@ "type": "string" }, "subject": { - "$ref": "#/definitions/GeneOrGeneProduct", + "$ref": "#/$defs/GeneOrGeneProduct", "description": "the subject gene in the association. If the relation is symmetric, subject vs object is arbitrary. We allow a gene product to stand as a proxy for the gene or vice versa." }, "type": { @@ -9930,7 +10046,7 @@ "has_attribute": { "description": "connects any entity to an attribute", "items": { - "$ref": "#/definitions/Attribute" + "$ref": "#/$defs/Attribute" }, "type": "array" }, @@ -9939,7 +10055,7 @@ "type": "string" }, "interacting_molecules_category": { - "$ref": "#/definitions/OntologyClass" + "$ref": "#/$defs/OntologyClass" }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", @@ -9976,7 +10092,7 @@ "qualifiers": { "description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": { - "$ref": "#/definitions/OntologyClass" + "$ref": "#/$defs/OntologyClass" }, "type": "array" }, @@ -10044,7 +10160,7 @@ "has_attribute": { "description": "may often be an organism attribute", "items": { - "$ref": "#/definitions/Attribute" + "$ref": "#/$defs/Attribute" }, "type": "array" }, @@ -10113,7 +10229,7 @@ "has_attribute": { "description": "connects any entity to an attribute", "items": { - "$ref": "#/definitions/Attribute" + "$ref": "#/$defs/Attribute" }, "type": "array" }, @@ -10211,7 +10327,7 @@ "has_attribute": { "description": "connects any entity to an attribute", "items": { - "$ref": "#/definitions/Attribute" + "$ref": "#/$defs/Attribute" }, "type": "array" }, @@ -10290,7 +10406,7 @@ "has_attribute": { "description": "connects any entity to an attribute", "items": { - "$ref": "#/definitions/Attribute" + "$ref": "#/$defs/Attribute" }, "type": "array" }, @@ -10345,7 +10461,7 @@ "has_attribute": { "description": "connects any entity to an attribute", "items": { - "$ref": "#/definitions/Attribute" + "$ref": "#/$defs/Attribute" }, "type": "array" }, @@ -10395,7 +10511,7 @@ "description": "A property of a phenotype", "properties": { "has_attribute_type": { - "$ref": "#/definitions/OntologyClass", + "$ref": "#/$defs/OntologyClass", "description": "connects an attribute to a class that describes it" }, "has_qualitative_value": { @@ -10405,7 +10521,7 @@ "has_quantitative_value": { "description": "connects an attribute to a value", "items": { - "$ref": "#/definitions/QuantityValue" + "$ref": "#/$defs/QuantityValue" }, "type": "array" }, @@ -10433,7 +10549,7 @@ "description": "An attribute corresponding to the phenotypic sex of the individual, based upon the reproductive organs present.", "properties": { "has_attribute_type": { - "$ref": "#/definitions/OntologyClass", + "$ref": "#/$defs/OntologyClass", "description": "connects an attribute to a class that describes it" }, "has_qualitative_value": { @@ -10443,7 +10559,7 @@ "has_quantitative_value": { "description": "connects an attribute to a value", "items": { - "$ref": "#/definitions/QuantityValue" + "$ref": "#/$defs/QuantityValue" }, "type": "array" }, @@ -10483,7 +10599,7 @@ "has_attribute": { "description": "connects any entity to an attribute", "items": { - "$ref": "#/definitions/Attribute" + "$ref": "#/$defs/Attribute" }, "type": "array" }, @@ -10545,7 +10661,7 @@ "has_attribute": { "description": "connects any entity to an attribute", "items": { - "$ref": "#/definitions/Attribute" + "$ref": "#/$defs/Attribute" }, "type": "array" }, @@ -10614,7 +10730,7 @@ "has_attribute": { "description": "connects any entity to an attribute", "items": { - "$ref": "#/definitions/Attribute" + "$ref": "#/$defs/Attribute" }, "type": "array" }, @@ -10669,7 +10785,7 @@ "has_attribute": { "description": "connects any entity to an attribute", "items": { - "$ref": "#/definitions/Attribute" + "$ref": "#/$defs/Attribute" }, "type": "array" }, @@ -10731,7 +10847,7 @@ "has_attribute": { "description": "may often be an organism attribute", "items": { - "$ref": "#/definitions/Attribute" + "$ref": "#/$defs/Attribute" }, "type": "array" }, @@ -10793,7 +10909,7 @@ "has_attribute": { "description": "connects any entity to an attribute", "items": { - "$ref": "#/definitions/Attribute" + "$ref": "#/$defs/Attribute" }, "type": "array" }, @@ -10838,7 +10954,7 @@ "qualifiers": { "description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": { - "$ref": "#/definitions/OntologyClass" + "$ref": "#/$defs/OntologyClass" }, "type": "array" }, @@ -10897,7 +11013,7 @@ "has_attribute": { "description": "connects any entity to an attribute", "items": { - "$ref": "#/definitions/Attribute" + "$ref": "#/$defs/Attribute" }, "type": "array" }, @@ -10941,7 +11057,7 @@ "properties": { "available_from": { "items": { - "$ref": "#/definitions/DrugAvailabilityEnum" + "$ref": "#/$defs/DrugAvailabilityEnum" }, "type": "array" }, @@ -10958,7 +11074,7 @@ "has_attribute": { "description": "connects any entity to an attribute", "items": { - "$ref": "#/definitions/Attribute" + "$ref": "#/$defs/Attribute" }, "type": "array" }, @@ -10977,6 +11093,13 @@ "is_supplement": { "type": "string" }, + "is_toxic": { + "type": "boolean" + }, + "max_tolerated_dose": { + "description": "The highest dose of a drug or treatment that does not cause unacceptable side effects. The maximum tolerated dose is determined in clinical trials by testing increasing doses on different groups of people until the highest dose with acceptable side effects is found. Also called MTD.", + "type": "string" + }, "name": { "description": "A human-readable name for an attribute or entity.", "type": "string" @@ -11023,7 +11146,7 @@ "has_attribute": { "description": "connects any entity to an attribute", "items": { - "$ref": "#/definitions/Attribute" + "$ref": "#/$defs/Attribute" }, "type": "array" }, @@ -11099,7 +11222,7 @@ "has_attribute": { "description": "connects any entity to an attribute", "items": { - "$ref": "#/definitions/Attribute" + "$ref": "#/$defs/Attribute" }, "type": "array" }, @@ -11190,7 +11313,7 @@ "has_attribute": { "description": "connects any entity to an attribute", "items": { - "$ref": "#/definitions/Attribute" + "$ref": "#/$defs/Attribute" }, "type": "array" }, @@ -11291,7 +11414,7 @@ "properties": { "available_from": { "items": { - "$ref": "#/definitions/DrugAvailabilityEnum" + "$ref": "#/$defs/DrugAvailabilityEnum" }, "type": "array" }, @@ -11308,7 +11431,7 @@ "has_attribute": { "description": "connects any entity to an attribute", "items": { - "$ref": "#/definitions/Attribute" + "$ref": "#/$defs/Attribute" }, "type": "array" }, @@ -11335,6 +11458,13 @@ "description": "indicates whether a molecular entity is a metabolite", "type": "boolean" }, + "is_toxic": { + "type": "boolean" + }, + "max_tolerated_dose": { + "description": "The highest dose of a drug or treatment that does not cause unacceptable side effects. The maximum tolerated dose is determined in clinical trials by testing increasing doses on different groups of people until the highest dose with acceptable side effects is found. Also called MTD.", + "type": "string" + }, "name": { "description": "A human-readable name for an attribute or entity.", "type": "string" @@ -11384,7 +11514,7 @@ "properties": { "available_from": { "items": { - "$ref": "#/definitions/DrugAvailabilityEnum" + "$ref": "#/$defs/DrugAvailabilityEnum" }, "type": "array" }, @@ -11401,7 +11531,7 @@ "has_attribute": { "description": "connects any entity to an attribute", "items": { - "$ref": "#/definitions/Attribute" + "$ref": "#/$defs/Attribute" }, "type": "array" }, @@ -11428,6 +11558,13 @@ "description": "indicates whether a molecular entity is a metabolite", "type": "boolean" }, + "is_toxic": { + "type": "boolean" + }, + "max_tolerated_dose": { + "description": "The highest dose of a drug or treatment that does not cause unacceptable side effects. The maximum tolerated dose is determined in clinical trials by testing increasing doses on different groups of people until the highest dose with acceptable side effects is found. Also called MTD.", + "type": "string" + }, "name": { "description": "A human-readable name for an attribute or entity.", "type": "string" @@ -11508,7 +11645,7 @@ "has_attribute": { "description": "connects any entity to an attribute", "items": { - "$ref": "#/definitions/Attribute" + "$ref": "#/$defs/Attribute" }, "type": "array" }, @@ -11529,7 +11666,7 @@ "type": "boolean" }, "object": { - "$ref": "#/definitions/GeneOrGeneProduct" + "$ref": "#/$defs/GeneOrGeneProduct" }, "predicate": { "description": "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.", @@ -11552,16 +11689,16 @@ "qualifiers": { "description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": { - "$ref": "#/definitions/OntologyClass" + "$ref": "#/$defs/OntologyClass" }, "type": "array" }, "reaction_direction": { - "$ref": "#/definitions/ReactionDirectionEnum", + "$ref": "#/$defs/ReactionDirectionEnum", "description": "the direction of a reaction as constrained by the direction_enum (ie: left_to_right, neutral, etc.)" }, "reaction_side": { - "$ref": "#/definitions/ReactionSideEnum", + "$ref": "#/$defs/ReactionSideEnum", "description": "the side of a reaction being modeled (ie: left or right)" }, "relation": { @@ -11609,7 +11746,7 @@ "has_attribute": { "description": "connects any entity to an attribute", "items": { - "$ref": "#/definitions/Attribute" + "$ref": "#/$defs/Attribute" }, "type": "array" }, @@ -11654,16 +11791,16 @@ "qualifiers": { "description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": { - "$ref": "#/definitions/OntologyClass" + "$ref": "#/$defs/OntologyClass" }, "type": "array" }, "reaction_direction": { - "$ref": "#/definitions/ReactionDirectionEnum", + "$ref": "#/$defs/ReactionDirectionEnum", "description": "the direction of a reaction as constrained by the direction_enum (ie: left_to_right, neutral, etc.)" }, "reaction_side": { - "$ref": "#/definitions/ReactionSideEnum", + "$ref": "#/$defs/ReactionSideEnum", "description": "the side of a reaction being modeled (ie: left or right)" }, "relation": { @@ -11711,7 +11848,7 @@ "has_attribute": { "description": "connects any entity to an attribute", "items": { - "$ref": "#/definitions/Attribute" + "$ref": "#/$defs/Attribute" }, "type": "array" }, @@ -11785,7 +11922,7 @@ "has_attribute": { "description": "connects any entity to an attribute", "items": { - "$ref": "#/definitions/Attribute" + "$ref": "#/$defs/Attribute" }, "type": "array" }, @@ -11830,7 +11967,7 @@ "qualifiers": { "description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": { - "$ref": "#/definitions/OntologyClass" + "$ref": "#/$defs/OntologyClass" }, "type": "array" }, @@ -11885,7 +12022,7 @@ "has_attribute": { "description": "connects any entity to an attribute", "items": { - "$ref": "#/definitions/Attribute" + "$ref": "#/$defs/Attribute" }, "type": "array" }, @@ -11929,7 +12066,7 @@ "qualifiers": { "description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": { - "$ref": "#/definitions/OntologyClass" + "$ref": "#/$defs/OntologyClass" }, "type": "array" }, @@ -11974,7 +12111,7 @@ "has_attribute": { "description": "connects any entity to an attribute", "items": { - "$ref": "#/definitions/Attribute" + "$ref": "#/$defs/Attribute" }, "type": "array" }, @@ -12061,7 +12198,7 @@ "has_attribute": { "description": "connects any entity to an attribute", "items": { - "$ref": "#/definitions/Attribute" + "$ref": "#/$defs/Attribute" }, "type": "array" }, @@ -12156,7 +12293,7 @@ "description": "describes the severity of a phenotypic feature or disease", "properties": { "has_attribute_type": { - "$ref": "#/definitions/OntologyClass", + "$ref": "#/$defs/OntologyClass", "description": "connects an attribute to a class that describes it" }, "has_qualitative_value": { @@ -12166,7 +12303,7 @@ "has_quantitative_value": { "description": "connects an attribute to a value", "items": { - "$ref": "#/definitions/QuantityValue" + "$ref": "#/$defs/QuantityValue" }, "type": "array" }, @@ -12195,7 +12332,7 @@ "properties": { "available_from": { "items": { - "$ref": "#/definitions/DrugAvailabilityEnum" + "$ref": "#/$defs/DrugAvailabilityEnum" }, "type": "array" }, @@ -12212,7 +12349,7 @@ "has_attribute": { "description": "connects any entity to an attribute", "items": { - "$ref": "#/definitions/Attribute" + "$ref": "#/$defs/Attribute" }, "type": "array" }, @@ -12239,6 +12376,13 @@ "description": "indicates whether a molecular entity is a metabolite", "type": "boolean" }, + "is_toxic": { + "type": "boolean" + }, + "max_tolerated_dose": { + "description": "The highest dose of a drug or treatment that does not cause unacceptable side effects. The maximum tolerated dose is determined in clinical trials by testing increasing doses on different groups of people until the highest dose with acceptable side effects is found. Also called MTD.", + "type": "string" + }, "name": { "description": "A human-readable name for an attribute or entity.", "type": "string" @@ -12288,7 +12432,7 @@ "properties": { "available_from": { "items": { - "$ref": "#/definitions/DrugAvailabilityEnum" + "$ref": "#/$defs/DrugAvailabilityEnum" }, "type": "array" }, @@ -12305,7 +12449,7 @@ "has_attribute": { "description": "connects any entity to an attribute", "items": { - "$ref": "#/definitions/Attribute" + "$ref": "#/$defs/Attribute" }, "type": "array" }, @@ -12320,6 +12464,13 @@ "description": "indicates whether a molecular entity is a metabolite", "type": "boolean" }, + "is_toxic": { + "type": "boolean" + }, + "max_tolerated_dose": { + "description": "The highest dose of a drug or treatment that does not cause unacceptable side effects. The maximum tolerated dose is determined in clinical trials by testing increasing doses on different groups of people until the highest dose with acceptable side effects is found. Also called MTD.", + "type": "string" + }, "name": { "description": "A human-readable name for an attribute or entity.", "type": "string" @@ -12366,7 +12517,7 @@ "has_attribute": { "description": "connects any entity to an attribute", "items": { - "$ref": "#/definitions/Attribute" + "$ref": "#/$defs/Attribute" }, "type": "array" }, @@ -12426,7 +12577,7 @@ "description": "Attributes relating to a socioeconomic manifestation", "properties": { "has_attribute_type": { - "$ref": "#/definitions/OntologyClass", + "$ref": "#/$defs/OntologyClass", "description": "connects an attribute to a class that describes it" }, "has_qualitative_value": { @@ -12436,7 +12587,7 @@ "has_quantitative_value": { "description": "connects an attribute to a value", "items": { - "$ref": "#/definitions/QuantityValue" + "$ref": "#/$defs/QuantityValue" }, "type": "array" }, @@ -12465,7 +12616,7 @@ "properties": { "has_attribute": { "items": { - "$ref": "#/definitions/SocioeconomicAttribute" + "$ref": "#/$defs/SocioeconomicAttribute" }, "type": "array" }, @@ -12517,7 +12668,7 @@ "has_attribute": { "description": "may often be an organism attribute", "items": { - "$ref": "#/definitions/Attribute" + "$ref": "#/$defs/Attribute" }, "type": "array" }, @@ -12579,7 +12730,7 @@ "has_attribute": { "description": "connects any entity to an attribute", "items": { - "$ref": "#/definitions/Attribute" + "$ref": "#/$defs/Attribute" }, "type": "array" }, @@ -12624,7 +12775,7 @@ "qualifiers": { "description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": { - "$ref": "#/definitions/OntologyClass" + "$ref": "#/$defs/OntologyClass" }, "type": "array" }, @@ -12666,7 +12817,7 @@ "properties": { "available_from": { "items": { - "$ref": "#/definitions/DrugAvailabilityEnum" + "$ref": "#/$defs/DrugAvailabilityEnum" }, "type": "array" }, @@ -12683,7 +12834,7 @@ "has_attribute": { "description": "connects any entity to an attribute", "items": { - "$ref": "#/definitions/Attribute" + "$ref": "#/$defs/Attribute" }, "type": "array" }, @@ -12710,6 +12861,13 @@ "description": "indicates whether a molecular entity is a metabolite", "type": "boolean" }, + "is_toxic": { + "type": "boolean" + }, + "max_tolerated_dose": { + "description": "The highest dose of a drug or treatment that does not cause unacceptable side effects. The maximum tolerated dose is determined in clinical trials by testing increasing doses on different groups of people until the highest dose with acceptable side effects is found. Also called MTD.", + "type": "string" + }, "name": { "description": "A human-readable name for an attribute or entity.", "type": "string" @@ -12756,7 +12914,7 @@ "has_attribute": { "description": "connects any entity to an attribute", "items": { - "$ref": "#/definitions/Attribute" + "$ref": "#/$defs/Attribute" }, "type": "array" }, @@ -12800,7 +12958,7 @@ "qualifiers": { "description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": { - "$ref": "#/definitions/OntologyClass" + "$ref": "#/$defs/OntologyClass" }, "type": "array" }, @@ -12845,7 +13003,7 @@ "has_attribute": { "description": "connects any entity to an attribute", "items": { - "$ref": "#/definitions/Attribute" + "$ref": "#/$defs/Attribute" }, "type": "array" }, @@ -12930,7 +13088,7 @@ "has_attribute": { "description": "connects any entity to an attribute", "items": { - "$ref": "#/definitions/Attribute" + "$ref": "#/$defs/Attribute" }, "type": "array" }, @@ -12955,7 +13113,7 @@ "type": "string" }, "onset_qualifier": { - "$ref": "#/definitions/Onset", + "$ref": "#/$defs/Onset", "description": "a qualifier used in a phenotypic association to state when the phenotype appears is in the subject" }, "predicate": { @@ -12979,7 +13137,7 @@ "qualifiers": { "description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": { - "$ref": "#/definitions/OntologyClass" + "$ref": "#/$defs/OntologyClass" }, "type": "array" }, @@ -12987,7 +13145,7 @@ "type": "string" }, "severity_qualifier": { - "$ref": "#/definitions/SeverityValue", + "$ref": "#/$defs/SeverityValue", "description": "a qualifier used in a phenotypic association to state how severe the phenotype is in the subject" }, "source": { @@ -13033,7 +13191,7 @@ "has_attribute": { "description": "connects any entity to an attribute", "items": { - "$ref": "#/definitions/Attribute" + "$ref": "#/$defs/Attribute" }, "type": "array" }, @@ -13058,7 +13216,7 @@ "type": "string" }, "onset_qualifier": { - "$ref": "#/definitions/Onset", + "$ref": "#/$defs/Onset", "description": "a qualifier used in a phenotypic association to state when the phenotype appears is in the subject" }, "predicate": { @@ -13082,7 +13240,7 @@ "qualifiers": { "description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": { - "$ref": "#/definitions/OntologyClass" + "$ref": "#/$defs/OntologyClass" }, "type": "array" }, @@ -13090,7 +13248,7 @@ "type": "string" }, "severity_qualifier": { - "$ref": "#/definitions/SeverityValue", + "$ref": "#/$defs/SeverityValue", "description": "a qualifier used in a phenotypic association to state how severe the phenotype is in the subject" }, "source": { @@ -13132,7 +13290,7 @@ "has_attribute": { "description": "connects any entity to an attribute", "items": { - "$ref": "#/definitions/Attribute" + "$ref": "#/$defs/Attribute" }, "type": "array" }, @@ -13175,7 +13333,7 @@ "qualifiers": { "description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": { - "$ref": "#/definitions/OntologyClass" + "$ref": "#/$defs/OntologyClass" }, "type": "array" }, @@ -13225,7 +13383,7 @@ "has_attribute": { "description": "connects any entity to an attribute", "items": { - "$ref": "#/definitions/Attribute" + "$ref": "#/$defs/Attribute" }, "type": "array" }, @@ -13272,12 +13430,12 @@ "qualifiers": { "description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": { - "$ref": "#/definitions/OntologyClass" + "$ref": "#/$defs/OntologyClass" }, "type": "array" }, "quantifier_qualifier": { - "$ref": "#/definitions/OntologyClass", + "$ref": "#/$defs/OntologyClass", "description": "Optional quantitative value indicating degree of expression." }, "relation": { @@ -13330,7 +13488,7 @@ "has_attribute": { "description": "connects any entity to an attribute", "items": { - "$ref": "#/definitions/Attribute" + "$ref": "#/$defs/Attribute" }, "type": "array" }, @@ -13355,7 +13513,7 @@ "type": "string" }, "onset_qualifier": { - "$ref": "#/definitions/Onset", + "$ref": "#/$defs/Onset", "description": "a qualifier used in a phenotypic association to state when the phenotype appears is in the subject" }, "predicate": { @@ -13379,7 +13537,7 @@ "qualifiers": { "description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": { - "$ref": "#/definitions/OntologyClass" + "$ref": "#/$defs/OntologyClass" }, "type": "array" }, @@ -13387,11 +13545,11 @@ "type": "string" }, "severity_qualifier": { - "$ref": "#/definitions/SeverityValue", + "$ref": "#/$defs/SeverityValue", "description": "a qualifier used in a phenotypic association to state how severe the phenotype is in the subject" }, "sex_qualifier": { - "$ref": "#/definitions/BiologicalSex", + "$ref": "#/$defs/BiologicalSex", "description": "a qualifier used in a phenotypic association to state whether the association is specific to a particular sex." }, "source": { @@ -13437,7 +13595,7 @@ "has_attribute": { "description": "connects any entity to an attribute", "items": { - "$ref": "#/definitions/Attribute" + "$ref": "#/$defs/Attribute" }, "type": "array" }, @@ -13498,7 +13656,7 @@ "qualifiers": { "description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": { - "$ref": "#/definitions/OntologyClass" + "$ref": "#/$defs/OntologyClass" }, "type": "array" }, @@ -13533,7 +13691,7 @@ "properties": { "available_from": { "items": { - "$ref": "#/definitions/DrugAvailabilityEnum" + "$ref": "#/$defs/DrugAvailabilityEnum" }, "type": "array" }, @@ -13550,7 +13708,7 @@ "has_attribute": { "description": "connects any entity to an attribute", "items": { - "$ref": "#/definitions/Attribute" + "$ref": "#/$defs/Attribute" }, "type": "array" }, @@ -13562,6 +13720,13 @@ "description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string" }, + "is_toxic": { + "type": "boolean" + }, + "max_tolerated_dose": { + "description": "The highest dose of a drug or treatment that does not cause unacceptable side effects. The maximum tolerated dose is determined in clinical trials by testing increasing doses on different groups of people until the highest dose with acceptable side effects is found. Also called MTD.", + "type": "string" + }, "name": { "description": "A human-readable name for an attribute or entity.", "type": "string" @@ -13596,7 +13761,7 @@ "description": "", "properties": { "has_attribute_type": { - "$ref": "#/definitions/OntologyClass", + "$ref": "#/$defs/OntologyClass", "description": "connects an attribute to a class that describes it" }, "has_qualitative_value": { @@ -13606,7 +13771,7 @@ "has_quantitative_value": { "description": "connects an attribute to a value", "items": { - "$ref": "#/definitions/QuantityValue" + "$ref": "#/$defs/QuantityValue" }, "type": "array" }, @@ -13630,6 +13795,9 @@ "type": "object" } }, + "$id": "https://w3id.org/biolink/biolink-model", + "$schema": "http://json-schema.org/draft-07/schema#", + "additionalProperties": true, "properties": {}, "title": "Biolink-Model", "type": "object"