From d9ae8e8c2f88021be314d19d18edf465ba063f79 Mon Sep 17 00:00:00 2001 From: GitHub Action Date: Mon, 23 May 2022 23:00:15 +0000 Subject: [PATCH] Regenerate artifacts from biolink-model.yaml --- biolink-model.graphql | 122 +- biolink-model.owl.ttl | 904 +++++----- biolink-model.proto | 317 ++-- biolink-model.shex | 82 +- biolink-model.shexj | 163 +- biolink-model.ttl | 1213 +++++++------- biolink-modeln.shex | 82 +- biolink-modeln.shexj | 163 +- biolink/model.py | 370 +++-- context.jsonld | 6 +- contextn.jsonld | 6 +- golr-views/RNA_product_config.yaml | 2 +- golr-views/RNA_product_isoform_config.yaml | 2 +- golr-views/activity_config.yaml | 2 +- golr-views/agent_config.yaml | 2 +- golr-views/anatomical_entity_config.yaml | 2 +- ...l_entity_ontogenic_association_config.yaml | 2 +- ...cal_entity_part_of_association_config.yaml | 2 +- golr-views/article_config.yaml | 2 +- golr-views/association_config.yaml | 2 +- golr-views/attribute_config.yaml | 40 +- golr-views/behavior_config.yaml | 2 +- ...behavioral_feature_association_config.yaml | 2 +- golr-views/behavioral_feature_config.yaml | 2 +- golr-views/biological_process_config.yaml | 2 +- ...biological_process_or_activity_config.yaml | 2 +- golr-views/biological_sex_config.yaml | 40 +- golr-views/book_chapter_config.yaml | 2 +- golr-views/book_config.yaml | 2 +- golr-views/case_config.yaml | 2 +- ...phenotypic_feature_association_config.yaml | 2 +- golr-views/cell_config.yaml | 2 +- ...a_model_of_disease_association_config.yaml | 2 +- golr-views/cell_line_config.yaml | 2 +- ...phenotypic_feature_association_config.yaml | 2 +- golr-views/cellular_component_config.yaml | 2 +- golr-views/chemical_entity_config.yaml | 2 +- golr-views/chemical_exposure_config.yaml | 2 +- golr-views/chemical_mixture_config.yaml | 2 +- golr-views/chemical_role_config.yaml | 40 +- ...emical_to_chemical_association_config.yaml | 2 +- ...hemical_derivation_association_config.yaml | 2 +- ...phenotypic_feature_association_config.yaml | 2 +- .../chemical_to_gene_association_config.yaml | 2 +- ...hemical_to_pathway_association_config.yaml | 2 +- golr-views/clinical_attribute_config.yaml | 40 +- golr-views/clinical_course_config.yaml | 40 +- golr-views/clinical_entity_config.yaml | 2 +- golr-views/clinical_finding_config.yaml | 2 +- golr-views/clinical_intervention_config.yaml | 2 +- golr-views/clinical_measurement_config.yaml | 40 +- golr-views/clinical_modifier_config.yaml | 40 +- golr-views/clinical_trial_config.yaml | 2 +- golr-views/coding_sequence_config.yaml | 2 +- golr-views/cohort_config.yaml | 2 +- .../complex_molecular_mixture_config.yaml | 2 +- golr-views/confidence_level_config.yaml | 2 +- .../contributor_association_config.yaml | 2 +- golr-views/dataset_config.yaml | 2 +- golr-views/dataset_distribution_config.yaml | 2 +- golr-views/dataset_summary_config.yaml | 2 +- golr-views/dataset_version_config.yaml | 2 +- golr-views/device_config.yaml | 2 +- golr-views/disease_config.yaml | 2 +- .../disease_or_phenotypic_feature_config.yaml | 2 +- ...eature_to_location_association_config.yaml | 2 +- ..._to_exposure_event_association_config.yaml | 2 +- ...phenotypic_feature_association_config.yaml | 2 +- golr-views/drug_config.yaml | 2 +- golr-views/drug_exposure_config.yaml | 2 +- .../drug_to_gene_association_config.yaml | 2 +- ...g_to_gene_interaction_exposure_config.yaml | 2 +- ...le_gene_to_disease_association_config.yaml | 2 +- .../entity_to_disease_association_config.yaml | 2 +- ...phenotypic_feature_association_config.yaml | 2 +- golr-views/environmental_feature_config.yaml | 2 +- ...environmental_food_contaminant_config.yaml | 2 +- golr-views/environmental_process_config.yaml | 2 +- golr-views/event_config.yaml | 2 +- golr-views/evidence_type_config.yaml | 2 +- golr-views/exon_config.yaml | 2 +- ...xon_to_transcript_relationship_config.yaml | 2 +- ...e_event_to_outcome_association_config.yaml | 2 +- ...phenotypic_feature_association_config.yaml | 2 +- golr-views/food_additive_config.yaml | 2 +- golr-views/food_config.yaml | 2 +- golr-views/functional_association_config.yaml | 2 +- ...a_model_of_disease_association_config.yaml | 2 +- golr-views/gene_config.yaml | 2 +- golr-views/gene_family_config.yaml | 2 +- ...ributes_to_disease_association_config.yaml | 2 +- .../gene_regulatory_relationship_config.yaml | 2 +- .../gene_to_disease_association_config.yaml | 2 +- ...to_expression_site_association_config.yaml | 2 +- ..._gene_coexpression_association_config.yaml | 2 +- ...e_to_gene_homology_association_config.yaml | 2 +- ...e_to_gene_product_relationship_config.yaml | 2 +- .../gene_to_go_term_association_config.yaml | 2 +- ...phenotypic_feature_association_config.yaml | 2 +- golr-views/genome_config.yaml | 2 +- .../genomic_background_exposure_config.yaml | 6 +- .../genomic_sequence_localization_config.yaml | 2 +- ...a_model_of_disease_association_config.yaml | 2 +- golr-views/genotype_config.yaml | 2 +- ...enotype_to_disease_association_config.yaml | 2 +- .../genotype_to_gene_association_config.yaml | 2 +- ...e_to_genotype_part_association_config.yaml | 2 +- ...phenotypic_feature_association_config.yaml | 2 +- ...enotype_to_variant_association_config.yaml | 2 +- golr-views/genotypic_sex_config.yaml | 40 +- .../geographic_location_at_time_config.yaml | 2 +- golr-views/geographic_location_config.yaml | 2 +- .../gross_anatomical_structure_config.yaml | 2 +- golr-views/haplotype_config.yaml | 2 +- golr-views/hospitalization_config.yaml | 2 +- golr-views/individual_organism_config.yaml | 2 +- ...ity_to_named_thing_association_config.yaml | 2 +- golr-views/information_resource_config.yaml | 2 +- golr-views/inheritance_config.yaml | 40 +- golr-views/life_stage_config.yaml | 2 +- ...biological_process_association_config.yaml | 2 +- ...cellular_component_association_config.yaml | 2 +- ...molecular_activity_association_config.yaml | 2 +- golr-views/macronutrient_config.yaml | 2 +- golr-views/material_sample_config.yaml | 2 +- ..._sample_derivation_association_config.yaml | 2 +- ...phenotypic_feature_association_config.yaml | 2 +- golr-views/microRNA_config.yaml | 2 +- golr-views/micronutrient_config.yaml | 2 +- golr-views/molecular_activity_config.yaml | 2 +- ...to_chemical_entity_association_config.yaml | 2 +- ...molecular_activity_association_config.yaml | 2 +- golr-views/molecular_entity_config.yaml | 2 +- golr-views/molecular_mixture_config.yaml | 2 +- golr-views/named_thing_config.yaml | 2 +- golr-views/noncoding_RNA_product_config.yaml | 2 +- golr-views/nucleic_acid_entity_config.yaml | 2 +- .../nucleic_acid_sequence_motif_config.yaml | 2 +- golr-views/nutrient_config.yaml | 2 +- golr-views/onset_config.yaml | 40 +- golr-views/organism_attribute_config.yaml | 40 +- golr-views/organism_taxon_config.yaml | 2 +- ..._to_organism_taxon_interaction_config.yaml | 2 +- ..._organism_taxon_specialization_config.yaml | 2 +- ...ganism_to_organism_association_config.yaml | 2 +- ...a_model_of_disease_association_config.yaml | 2 +- ...rwise_gene_to_gene_interaction_config.yaml | 2 +- ...pairwise_molecular_interaction_config.yaml | 2 +- ...hological_anatomical_structure_config.yaml | 2 +- golr-views/pathological_process_config.yaml | 2 +- golr-views/pathway_config.yaml | 2 +- golr-views/phenomenon_config.yaml | 2 +- golr-views/phenotypic_feature_config.yaml | 2 +- golr-views/phenotypic_quality_config.yaml | 40 +- golr-views/phenotypic_sex_config.yaml | 40 +- golr-views/physical_entity_config.yaml | 2 +- golr-views/physiological_process_config.yaml | 2 +- golr-views/planetary_entity_config.yaml | 2 +- golr-views/polypeptide_config.yaml | 2 +- ...lation_of_individual_organisms_config.yaml | 2 +- ...tion_to_population_association_config.yaml | 2 +- golr-views/procedure_config.yaml | 2 +- golr-views/processed_material_config.yaml | 2 +- golr-views/protein_config.yaml | 2 +- golr-views/protein_domain_config.yaml | 2 +- golr-views/protein_family_config.yaml | 2 +- golr-views/protein_isoform_config.yaml | 2 +- golr-views/publication_config.yaml | 2 +- golr-views/quantity_value_config.yaml | 2 +- ...action_to_catalyst_association_config.yaml | 2 +- ...ion_to_participant_association_config.yaml | 2 +- golr-views/reagent_targeted_gene_config.yaml | 2 +- golr-views/sequence_association_config.yaml | 2 +- .../sequence_feature_relationship_config.yaml | 2 +- golr-views/sequence_variant_config.yaml | 2 +- golr-views/serial_config.yaml | 2 +- golr-views/severity_value_config.yaml | 40 +- golr-views/siRNA_config.yaml | 2 +- golr-views/small_molecule_config.yaml | 2 +- golr-views/snv_config.yaml | 2 +- .../socioeconomic_attribute_config.yaml | 40 +- golr-views/socioeconomic_exposure_config.yaml | 2 +- golr-views/study_population_config.yaml | 2 +- .../taxon_to_taxon_association_config.yaml | 2 +- golr-views/transcript_config.yaml | 2 +- ...ranscript_to_gene_relationship_config.yaml | 2 +- golr-views/treatment_config.yaml | 2 +- ...a_model_of_disease_association_config.yaml | 2 +- ...variant_to_disease_association_config.yaml | 2 +- .../variant_to_gene_association_config.yaml | 2 +- ...to_gene_expression_association_config.yaml | 2 +- ...phenotypic_feature_association_config.yaml | 2 +- ...iant_to_population_association_config.yaml | 2 +- golr-views/vitamin_config.yaml | 2 +- golr-views/zygosity_config.yaml | 40 +- graphviz/attribute.gv | 143 +- graphviz/attribute.svg | 225 ++- graphviz/biological_sex.gv | 126 +- graphviz/biological_sex.svg | 203 ++- graphviz/chemical_role.gv | 126 +- graphviz/chemical_role.svg | 203 ++- graphviz/clinical_attribute.gv | 125 +- graphviz/clinical_attribute.svg | 203 ++- graphviz/clinical_course.gv | 125 +- graphviz/clinical_course.svg | 203 ++- graphviz/clinical_measurement.gv | 126 +- graphviz/clinical_measurement.svg | 209 ++- graphviz/clinical_modifier.gv | 125 +- graphviz/clinical_modifier.svg | 203 ++- graphviz/gene_ontology_class.gv | 10 +- graphviz/gene_ontology_class.svg | 25 +- graphviz/genomic_background_exposure.gv | 55 +- graphviz/genomic_background_exposure.svg | 85 +- graphviz/genotypic_sex.gv | 125 +- graphviz/genotypic_sex.svg | 203 ++- graphviz/inheritance.gv | 127 +- graphviz/inheritance.svg | 203 ++- graphviz/onset.gv | 128 +- graphviz/onset.svg | 203 ++- graphviz/ontology_class.gv | 14 +- graphviz/ontology_class.svg | 25 +- graphviz/organism_attribute.gv | 125 +- graphviz/organism_attribute.svg | 203 ++- graphviz/phenotypic_quality.gv | 125 +- graphviz/phenotypic_quality.svg | 203 ++- graphviz/phenotypic_sex.gv | 125 +- graphviz/phenotypic_sex.svg | 203 ++- graphviz/relationship_type.gv | 20 +- graphviz/relationship_type.svg | 33 +- graphviz/severity_value.gv | 125 +- graphviz/severity_value.svg | 203 ++- graphviz/socioeconomic_attribute.gv | 125 +- graphviz/socioeconomic_attribute.svg | 203 ++- graphviz/taxonomic_rank.gv | 20 +- graphviz/taxonomic_rank.svg | 33 +- graphviz/unclassified_ontology_class.gv | 10 +- graphviz/unclassified_ontology_class.svg | 25 +- graphviz/zygosity.gv | 127 +- graphviz/zygosity.svg | 203 ++- json-schema/biolink-model.json | 1476 ++++++++++++----- prefix-map/biolink-model-prefix-map.json | 4 +- 241 files changed, 7962 insertions(+), 3585 deletions(-) diff --git a/biolink-model.graphql b/biolink-model.graphql index 404b8bc098..e9b0b1db5b 100644 --- a/biolink-model.graphql +++ b/biolink-model.graphql @@ -1,5 +1,5 @@ # metamodel_version: 1.7.0 -# version: 2.3.1 +# version: 2.4.0 type Activity implements ActivityAndBehavior { id: String! @@ -188,6 +188,13 @@ type Association type Attribute implements OntologyClass { + id: String! + type: String + description: NarrativeText + hasAttribute: [Attribute] + providedBy: [String] + xref: [Uriorcurie] + category: [CategoryType]! name: LabelType hasAttributeType: OntologyClass! hasQuantitativeValue: [QuantityValue] @@ -314,6 +321,13 @@ type BiologicalProcessOrActivity implements Occurrent, OntologyClass type BiologicalSex { + id: String! + type: String + description: NarrativeText + hasAttribute: [Attribute] + providedBy: [String] + xref: [Uriorcurie] + category: [CategoryType]! name: LabelType hasAttributeType: OntologyClass! hasQuantitativeValue: [QuantityValue] @@ -588,6 +602,13 @@ interface ChemicalOrDrugOrTreatment type ChemicalRole { + id: String! + type: String + description: NarrativeText + hasAttribute: [Attribute] + providedBy: [String] + xref: [Uriorcurie] + category: [CategoryType]! name: LabelType hasAttributeType: OntologyClass! hasQuantitativeValue: [QuantityValue] @@ -723,6 +744,13 @@ type ChemicalToPathwayAssociation implements ChemicalToEntityAssociationMixin type ClinicalAttribute { + id: String! + type: String + description: NarrativeText + hasAttribute: [Attribute] + providedBy: [String] + xref: [Uriorcurie] + category: [CategoryType]! name: LabelType hasAttributeType: OntologyClass! hasQuantitativeValue: [QuantityValue] @@ -733,6 +761,13 @@ type ClinicalAttribute type ClinicalCourse { + id: String! + type: String + description: NarrativeText + hasAttribute: [Attribute] + providedBy: [String] + xref: [Uriorcurie] + category: [CategoryType]! name: LabelType hasAttributeType: OntologyClass! hasQuantitativeValue: [QuantityValue] @@ -786,6 +821,13 @@ type ClinicalIntervention type ClinicalMeasurement { + id: String! + type: String + description: NarrativeText + hasAttribute: [Attribute] + providedBy: [String] + xref: [Uriorcurie] + category: [CategoryType]! name: LabelType hasQuantitativeValue: [QuantityValue] hasQualitativeValue: NamedThing @@ -796,6 +838,13 @@ type ClinicalMeasurement type ClinicalModifier { + id: String! + type: String + description: NarrativeText + hasAttribute: [Attribute] + providedBy: [String] + xref: [Uriorcurie] + category: [CategoryType]! name: LabelType hasAttributeType: OntologyClass! hasQuantitativeValue: [QuantityValue] @@ -1697,7 +1746,7 @@ type GeneHasVariantThatContributesToDiseaseAssociation subject: GeneOrGeneProduct! } -interface GeneOntologyClass +type GeneOntologyClass { } @@ -1967,6 +2016,7 @@ type GenomicBackgroundExposure implements ExposureEvent, GeneGroupingMixin, Phys hasGeneOrGeneProduct: [Gene] inTaxon: [OrganismTaxon] hasBiologicalSequence: BiologicalSequence + id: String! } interface GenomicEntity @@ -2175,6 +2225,13 @@ type GenotypeToVariantAssociation type GenotypicSex { + id: String! + type: String + description: NarrativeText + hasAttribute: [Attribute] + providedBy: [String] + xref: [Uriorcurie] + category: [CategoryType]! name: LabelType hasAttributeType: OntologyClass! hasQuantitativeValue: [QuantityValue] @@ -2346,6 +2403,13 @@ type InformationResource type Inheritance { + id: String! + type: String + description: NarrativeText + hasAttribute: [Attribute] + providedBy: [String] + xref: [Uriorcurie] + category: [CategoryType]! name: LabelType hasAttributeType: OntologyClass! hasQuantitativeValue: [QuantityValue] @@ -2793,6 +2857,13 @@ interface Occurrent type Onset { + id: String! + type: String + description: NarrativeText + hasAttribute: [Attribute] + providedBy: [String] + xref: [Uriorcurie] + category: [CategoryType]! name: LabelType hasAttributeType: OntologyClass! hasQuantitativeValue: [QuantityValue] @@ -2803,10 +2874,18 @@ type Onset interface OntologyClass { + id: String! } type OrganismAttribute { + id: String! + type: String + description: NarrativeText + hasAttribute: [Attribute] + providedBy: [String] + xref: [Uriorcurie] + category: [CategoryType]! name: LabelType hasAttributeType: OntologyClass! hasQuantitativeValue: [QuantityValue] @@ -3148,6 +3227,13 @@ type PhenotypicFeature type PhenotypicQuality { + id: String! + type: String + description: NarrativeText + hasAttribute: [Attribute] + providedBy: [String] + xref: [Uriorcurie] + category: [CategoryType]! name: LabelType hasAttributeType: OntologyClass! hasQuantitativeValue: [QuantityValue] @@ -3158,6 +3244,13 @@ type PhenotypicQuality type PhenotypicSex { + id: String! + type: String + description: NarrativeText + hasAttribute: [Attribute] + providedBy: [String] + xref: [Uriorcurie] + category: [CategoryType]! name: LabelType hasAttributeType: OntologyClass! hasQuantitativeValue: [QuantityValue] @@ -3474,6 +3567,7 @@ interface RelationshipQuantifier type RelationshipType { + id: String! } type RNAProduct implements GeneProductMixin @@ -3640,6 +3734,13 @@ type Serial type SeverityValue { + id: String! + type: String + description: NarrativeText + hasAttribute: [Attribute] + providedBy: [String] + xref: [Uriorcurie] + category: [CategoryType]! name: LabelType hasAttributeType: OntologyClass! hasQuantitativeValue: [QuantityValue] @@ -3710,6 +3811,13 @@ type Snv type SocioeconomicAttribute { + id: String! + type: String + description: NarrativeText + hasAttribute: [Attribute] + providedBy: [String] + xref: [Uriorcurie] + category: [CategoryType]! name: LabelType hasAttributeType: OntologyClass! hasQuantitativeValue: [QuantityValue] @@ -3776,6 +3884,7 @@ type TaxonToTaxonAssociation type TaxonomicRank { + id: String! } interface ThingWithTaxon @@ -3846,7 +3955,7 @@ type Treatment implements ExposureEvent, ChemicalOrDrugOrTreatment timepoint: TimeType } -interface UnclassifiedOntologyClass +type UnclassifiedOntologyClass { } @@ -4033,6 +4142,13 @@ type Vitamin type Zygosity { + id: String! + type: String + description: NarrativeText + hasAttribute: [Attribute] + providedBy: [String] + xref: [Uriorcurie] + category: [CategoryType]! name: LabelType hasAttributeType: OntologyClass! hasQuantitativeValue: [QuantityValue] diff --git a/biolink-model.owl.ttl b/biolink-model.owl.ttl index bacdb79393..7186a93dd5 100644 --- a/biolink-model.owl.ttl +++ b/biolink-model.owl.ttl @@ -90,6 +90,7 @@ biolink:FrequencyQualifierMixin, biolink:GeneExpressionMixin, biolink:GeneGroupingMixin, + biolink:GeneOntologyClass, biolink:GeneToEntityAssociationMixin, biolink:GenotypeToEntityAssociationMixin, biolink:MacromolecularMachineMixin, @@ -104,14 +105,15 @@ biolink:RelationshipQuantifier, biolink:SubjectOfInvestigation, biolink:ThingWithTaxon, + biolink:UnclassifiedOntologyClass, biolink:VariantToEntityAssociationMixin ; dct:license "https://creativecommons.org/publicdomain/zero/1.0/" ; - pav:version "2.3.1" ; - linkml:generation_date "2022-05-23T16:31:27" ; + pav:version "2.4.0" ; + linkml:generation_date "2022-05-23T22:57:56" ; linkml:metamodel_version "1.7.0" ; linkml:source_file "biolink-model.yaml" ; - linkml:source_file_date "2022-05-23T16:27:31" ; - linkml:source_file_size 345250 . + linkml:source_file_date "2022-05-23T22:55:47" ; + linkml:source_file_size 344965 . biolink:Activity a owl:Class ; rdfs:label "activity" ; @@ -131,13 +133,13 @@ biolink:Activity a owl:Class ; biolink:AnatomicalEntityToAnatomicalEntityOntogenicAssociation a owl:Class ; rdfs:label "anatomical entity to anatomical entity ontogenic association" ; rdfs:subClassOf [ a owl:Restriction ; - owl:onClass biolink:AnatomicalEntity ; - owl:onProperty rdf:object ; - owl:qualifiedCardinality 1 ], - [ a owl:Restriction ; owl:onClass biolink:PredicateType ; owl:onProperty rdf:predicate ; owl:qualifiedCardinality 1 ], + [ a owl:Restriction ; + owl:onClass biolink:AnatomicalEntity ; + owl:onProperty rdf:object ; + owl:qualifiedCardinality 1 ], [ a owl:Restriction ; owl:onClass biolink:AnatomicalEntity ; owl:onProperty rdf:subject ; @@ -147,10 +149,6 @@ biolink:AnatomicalEntityToAnatomicalEntityOntogenicAssociation a owl:Class ; biolink:AnatomicalEntityToAnatomicalEntityPartOfAssociation a owl:Class ; rdfs:label "anatomical entity to anatomical entity part of association" ; rdfs:subClassOf [ a owl:Restriction ; - owl:onClass biolink:AnatomicalEntity ; - owl:onProperty rdf:subject ; - owl:qualifiedCardinality 1 ], - [ a owl:Restriction ; owl:onClass biolink:AnatomicalEntity ; owl:onProperty rdf:object ; owl:qualifiedCardinality 1 ], @@ -158,6 +156,10 @@ biolink:AnatomicalEntityToAnatomicalEntityPartOfAssociation a owl:Class ; owl:onClass biolink:PredicateType ; owl:onProperty rdf:predicate ; owl:qualifiedCardinality 1 ], + [ a owl:Restriction ; + owl:onClass biolink:AnatomicalEntity ; + owl:onProperty rdf:subject ; + owl:qualifiedCardinality 1 ], biolink:AnatomicalEntityToAnatomicalEntityAssociation . biolink:Article a owl:Class ; @@ -165,47 +167,47 @@ biolink:Article a owl:Class ; rdfs:subClassOf [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass linkml:String ; - owl:onProperty biolink:issue ], - [ a owl:Restriction ; - owl:onClass linkml:Uriorcurie ; - owl:onProperty biolink:published_in ; - owl:qualifiedCardinality 1 ], + owl:onProperty biolink:volume ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass linkml:String ; owl:onProperty biolink:iso_abbreviation ], + [ a owl:Restriction ; + owl:onClass linkml:Uriorcurie ; + owl:onProperty biolink:published_in ; + owl:qualifiedCardinality 1 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass linkml:String ; - owl:onProperty biolink:volume ], + owl:onProperty biolink:issue ], biolink:Publication . biolink:BehaviorToBehavioralFeatureAssociation a owl:Class ; rdfs:label "behavior to behavioral feature association" ; rdfs:subClassOf [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass biolink:FrequencyValue ; - owl:onProperty biolink:frequency_qualifier ], - [ a owl:Restriction ; owl:onClass biolink:Behavior ; owl:onProperty rdf:subject ; owl:qualifiedCardinality 1 ], + [ a owl:Restriction ; + owl:maxQualifiedCardinality 1 ; + owl:onClass biolink:BiologicalSex ; + owl:onProperty biolink:sex_qualifier ], + [ a owl:Restriction ; + owl:maxQualifiedCardinality 1 ; + owl:onClass biolink:SeverityValue ; + owl:onProperty biolink:severity_qualifier ], [ a owl:Restriction ; owl:onClass biolink:BehavioralFeature ; owl:onProperty rdf:object ; owl:qualifiedCardinality 1 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; - owl:onClass biolink:BiologicalSex ; - owl:onProperty biolink:sex_qualifier ], + owl:onClass biolink:FrequencyValue ; + owl:onProperty biolink:frequency_qualifier ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass biolink:Onset ; owl:onProperty biolink:onset_qualifier ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass biolink:SeverityValue ; - owl:onProperty biolink:severity_qualifier ], biolink:Association, biolink:EntityToPhenotypicFeatureAssociationMixin . @@ -277,21 +279,21 @@ biolink:Cell a owl:Class ; biolink:CellLineAsAModelOfDiseaseAssociation a owl:Class ; rdfs:label "cell line as a model of disease association" ; rdfs:subClassOf [ a owl:Restriction ; + owl:maxQualifiedCardinality 1 ; + owl:onClass biolink:FrequencyValue ; + owl:onProperty biolink:frequency_qualifier ], + [ a owl:Restriction ; owl:onClass biolink:CellLine ; owl:onProperty rdf:subject ; owl:qualifiedCardinality 1 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; - owl:onClass biolink:FrequencyValue ; - owl:onProperty biolink:frequency_qualifier ], + owl:onClass biolink:Onset ; + owl:onProperty biolink:onset_qualifier ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass biolink:SeverityValue ; owl:onProperty biolink:severity_qualifier ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass biolink:Onset ; - owl:onProperty biolink:onset_qualifier ], biolink:CellLineToDiseaseOrPhenotypicFeatureAssociation, biolink:EntityToDiseaseAssociationMixin, biolink:ModelToDiseaseAssociationMixin . @@ -299,6 +301,13 @@ biolink:CellLineAsAModelOfDiseaseAssociation a owl:Class ; biolink:ChemicalToChemicalDerivationAssociation a owl:Class ; rdfs:label "chemical to chemical derivation association" ; rdfs:subClassOf [ a owl:Restriction ; + owl:allValuesFrom biolink:MacromolecularMachineMixin ; + owl:onProperty biolink:catalyst_qualifier ], + [ a owl:Restriction ; + owl:onClass biolink:ChemicalEntity ; + owl:onProperty rdf:object ; + owl:qualifiedCardinality 1 ], + [ a owl:Restriction ; owl:onClass biolink:PredicateType ; owl:onProperty rdf:predicate ; owl:qualifiedCardinality 1 ], @@ -306,13 +315,6 @@ biolink:ChemicalToChemicalDerivationAssociation a owl:Class ; owl:onClass biolink:ChemicalEntity ; owl:onProperty rdf:subject ; owl:qualifiedCardinality 1 ], - [ a owl:Restriction ; - owl:onClass biolink:ChemicalEntity ; - owl:onProperty rdf:object ; - owl:qualifiedCardinality 1 ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:MacromolecularMachineMixin ; - owl:onProperty biolink:catalyst_qualifier ], biolink:ChemicalToChemicalAssociation . biolink:ChemicalToDiseaseOrPhenotypicFeatureAssociation a owl:Class ; @@ -386,20 +388,20 @@ biolink:ComplexMolecularMixture a owl:Class ; biolink:ContributorAssociation a owl:Class ; rdfs:label "contributor association" ; rdfs:subClassOf [ a owl:Restriction ; - owl:onClass biolink:InformationContentEntity ; - owl:onProperty rdf:subject ; - owl:qualifiedCardinality 1 ], + owl:allValuesFrom biolink:OntologyClass ; + owl:onProperty biolink:qualifiers ], [ a owl:Restriction ; owl:onClass biolink:PredicateType ; owl:onProperty rdf:predicate ; owl:qualifiedCardinality 1 ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:OntologyClass ; - owl:onProperty biolink:qualifiers ], [ a owl:Restriction ; owl:onClass biolink:Agent ; owl:onProperty rdf:object ; owl:qualifiedCardinality 1 ], + [ a owl:Restriction ; + owl:onClass biolink:InformationContentEntity ; + owl:onProperty rdf:subject ; + owl:qualifiedCardinality 1 ], biolink:Association . biolink:DiseaseOrPhenotypicFeatureExposure a owl:Class ; @@ -433,14 +435,6 @@ biolink:DiseaseToExposureEventAssociation a owl:Class ; biolink:DiseaseToPhenotypicFeatureAssociation a owl:Class ; rdfs:label "disease to phenotypic feature association" ; rdfs:subClassOf [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass biolink:BiologicalSex ; - owl:onProperty biolink:sex_qualifier ], - [ a owl:Restriction ; - owl:onClass biolink:Disease ; - owl:onProperty rdf:subject ; - owl:qualifiedCardinality 1 ], - [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass biolink:SeverityValue ; owl:onProperty biolink:severity_qualifier ], @@ -452,10 +446,18 @@ biolink:DiseaseToPhenotypicFeatureAssociation a owl:Class ; owl:onClass biolink:PhenotypicFeature ; owl:onProperty rdf:object ; owl:qualifiedCardinality 1 ], + [ a owl:Restriction ; + owl:maxQualifiedCardinality 1 ; + owl:onClass biolink:BiologicalSex ; + owl:onProperty biolink:sex_qualifier ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass biolink:Onset ; owl:onProperty biolink:onset_qualifier ], + [ a owl:Restriction ; + owl:onClass biolink:Disease ; + owl:onProperty rdf:subject ; + owl:qualifiedCardinality 1 ], biolink:Association, biolink:DiseaseToEntityAssociationMixin, biolink:EntityToPhenotypicFeatureAssociationMixin ; @@ -482,12 +484,12 @@ biolink:DrugToGeneInteractionExposure a owl:Class ; biolink:DruggableGeneToDiseaseAssociation a owl:Class ; rdfs:label "druggable gene to disease association" ; rdfs:subClassOf [ a owl:Restriction ; + owl:allValuesFrom biolink:DruggableGeneCategoryEnum ; + owl:onProperty biolink:has_evidence ], + [ a owl:Restriction ; owl:onClass biolink:GeneOrGeneProduct ; owl:onProperty rdf:subject ; owl:qualifiedCardinality 1 ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:DruggableGeneCategoryEnum ; - owl:onProperty biolink:has_evidence ], [ a owl:Restriction ; owl:onClass biolink:PredicateType ; owl:onProperty rdf:predicate ; @@ -554,13 +556,13 @@ biolink:ExonToTranscriptRelationship a owl:Class ; biolink:ExposureEventToOutcomeAssociation a owl:Class ; rdfs:label "exposure event to outcome association" ; rdfs:subClassOf [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass biolink:TimeType ; - owl:onProperty biolink:has_temporal_context ], - [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass biolink:PopulationOfIndividualOrganisms ; owl:onProperty biolink:has_population_context ], + [ a owl:Restriction ; + owl:maxQualifiedCardinality 1 ; + owl:onClass biolink:TimeType ; + owl:onProperty biolink:has_temporal_context ], biolink:Association, biolink:EntityToOutcomeAssociationMixin, biolink:ExposureEventToEntityAssociationMixin . @@ -569,16 +571,16 @@ biolink:ExposureEventToPhenotypicFeatureAssociation a owl:Class ; rdfs:label "exposure event to phenotypic feature association" ; rdfs:subClassOf [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; - owl:onClass biolink:BiologicalSex ; - owl:onProperty biolink:sex_qualifier ], + owl:onClass biolink:FrequencyValue ; + owl:onProperty biolink:frequency_qualifier ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass biolink:SeverityValue ; owl:onProperty biolink:severity_qualifier ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; - owl:onClass biolink:FrequencyValue ; - owl:onProperty biolink:frequency_qualifier ], + owl:onClass biolink:BiologicalSex ; + owl:onProperty biolink:sex_qualifier ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass biolink:Onset ; @@ -641,10 +643,6 @@ biolink:GeneHasVariantThatContributesToDiseaseAssociation a owl:Class ; biolink:GeneRegulatoryRelationship a owl:Class ; rdfs:label "gene regulatory relationship" ; rdfs:subClassOf [ a owl:Restriction ; - owl:onClass biolink:GeneOrGeneProduct ; - owl:onProperty rdf:object ; - owl:qualifiedCardinality 1 ], - [ a owl:Restriction ; owl:onClass biolink:PredicateType ; owl:onProperty rdf:predicate ; owl:qualifiedCardinality 1 ], @@ -652,6 +650,10 @@ biolink:GeneRegulatoryRelationship a owl:Class ; owl:onClass biolink:GeneOrGeneProduct ; owl:onProperty rdf:subject ; owl:qualifiedCardinality 1 ], + [ a owl:Restriction ; + owl:onClass biolink:GeneOrGeneProduct ; + owl:onProperty rdf:object ; + owl:qualifiedCardinality 1 ], biolink:Association . biolink:GeneToExpressionSiteAssociation a owl:Class ; @@ -659,8 +661,8 @@ biolink:GeneToExpressionSiteAssociation a owl:Class ; rdfs:seeAlso "https://github.com/monarch-initiative/ingest-artifacts/tree/master/sources/BGee" ; rdfs:subClassOf [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; - owl:onClass biolink:OntologyClass ; - owl:onProperty biolink:quantifier_qualifier ], + owl:onClass biolink:LifeStage ; + owl:onProperty biolink:stage_qualifier ], [ a owl:Restriction ; owl:onClass biolink:PredicateType ; owl:onProperty rdf:predicate ; @@ -671,8 +673,8 @@ biolink:GeneToExpressionSiteAssociation a owl:Class ; owl:qualifiedCardinality 1 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; - owl:onClass biolink:LifeStage ; - owl:onProperty biolink:stage_qualifier ], + owl:onClass biolink:OntologyClass ; + owl:onProperty biolink:quantifier_qualifier ], [ a owl:Restriction ; owl:onClass biolink:AnatomicalEntity ; owl:onProperty rdf:object ; @@ -683,10 +685,6 @@ biolink:GeneToExpressionSiteAssociation a owl:Class ; biolink:GeneToGeneCoexpressionAssociation a owl:Class ; rdfs:label "gene to gene coexpression association" ; rdfs:subClassOf [ a owl:Restriction ; - owl:onClass biolink:PredicateType ; - owl:onProperty rdf:predicate ; - owl:qualifiedCardinality 1 ], - [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass biolink:OntologyClass ; owl:onProperty biolink:quantifier_qualifier ], @@ -695,13 +693,17 @@ biolink:GeneToGeneCoexpressionAssociation a owl:Class ; owl:onClass biolink:AnatomicalEntity ; owl:onProperty biolink:expression_site ], [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass biolink:LifeStage ; - owl:onProperty biolink:stage_qualifier ], + owl:onClass biolink:PredicateType ; + owl:onProperty rdf:predicate ; + owl:qualifiedCardinality 1 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass biolink:DiseaseOrPhenotypicFeature ; owl:onProperty biolink:phenotypic_state ], + [ a owl:Restriction ; + owl:maxQualifiedCardinality 1 ; + owl:onClass biolink:LifeStage ; + owl:onProperty biolink:stage_qualifier ], biolink:GeneExpressionMixin, biolink:GeneToGeneAssociation . @@ -724,6 +726,10 @@ biolink:GeneToGeneHomologyAssociation a owl:Class ; biolink:GeneToGeneProductRelationship a owl:Class ; rdfs:label "gene to gene product relationship" ; rdfs:subClassOf [ a owl:Restriction ; + owl:onClass biolink:Gene ; + owl:onProperty rdf:subject ; + owl:qualifiedCardinality 1 ], + [ a owl:Restriction ; owl:onClass biolink:GeneProductMixin ; owl:onProperty rdf:object ; owl:qualifiedCardinality 1 ], @@ -731,22 +737,18 @@ biolink:GeneToGeneProductRelationship a owl:Class ; owl:onClass biolink:PredicateType ; owl:onProperty rdf:predicate ; owl:qualifiedCardinality 1 ], - [ a owl:Restriction ; - owl:onClass biolink:Gene ; - owl:onProperty rdf:subject ; - owl:qualifiedCardinality 1 ], biolink:SequenceFeatureRelationship . biolink:GeneToGoTermAssociation a owl:Class ; rdfs:label "gene to go term association" ; rdfs:subClassOf [ a owl:Restriction ; - owl:onClass biolink:GeneOntologyClass ; - owl:onProperty rdf:object ; - owl:qualifiedCardinality 1 ], - [ a owl:Restriction ; owl:onClass biolink:Gene ; owl:onProperty rdf:subject ; owl:qualifiedCardinality 1 ], + [ a owl:Restriction ; + owl:onClass biolink:GeneOntologyClass ; + owl:onProperty rdf:object ; + owl:qualifiedCardinality 1 ], biolink:FunctionalAssociation ; skos:altLabel "functional association" ; skos:exactMatch WBVocab:Gene-GO-Association . @@ -754,29 +756,29 @@ biolink:GeneToGoTermAssociation a owl:Class ; biolink:GeneToPhenotypicFeatureAssociation a owl:Class ; rdfs:label "gene to phenotypic feature association" ; rdfs:subClassOf [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass biolink:SeverityValue ; - owl:onProperty biolink:severity_qualifier ], - [ a owl:Restriction ; owl:onClass biolink:PhenotypicFeature ; owl:onProperty rdf:object ; owl:qualifiedCardinality 1 ], [ a owl:Restriction ; - owl:onClass biolink:GeneOrGeneProduct ; - owl:onProperty rdf:subject ; - owl:qualifiedCardinality 1 ], + owl:maxQualifiedCardinality 1 ; + owl:onClass biolink:Onset ; + owl:onProperty biolink:onset_qualifier ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; - owl:onClass biolink:BiologicalSex ; - owl:onProperty biolink:sex_qualifier ], + owl:onClass biolink:SeverityValue ; + owl:onProperty biolink:severity_qualifier ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; - owl:onClass biolink:Onset ; - owl:onProperty biolink:onset_qualifier ], + owl:onClass biolink:BiologicalSex ; + owl:onProperty biolink:sex_qualifier ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass biolink:FrequencyValue ; owl:onProperty biolink:frequency_qualifier ], + [ a owl:Restriction ; + owl:onClass biolink:GeneOrGeneProduct ; + owl:onProperty rdf:subject ; + owl:qualifiedCardinality 1 ], biolink:Association, biolink:EntityToPhenotypicFeatureAssociationMixin, biolink:GeneToEntityAssociationMixin ; @@ -803,19 +805,23 @@ biolink:Genome a owl:Class ; biolink:GenomicBackgroundExposure a owl:Class ; rdfs:label "genomic background exposure" ; rdfs:subClassOf [ a owl:Restriction ; + owl:onClass linkml:String ; + owl:onProperty biolink:id ; + owl:qualifiedCardinality 1 ], + [ a owl:Restriction ; owl:allValuesFrom biolink:OrganismTaxon ; owl:onProperty biolink:in_taxon ], [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass biolink:BiologicalSequence ; - owl:onProperty biolink:has_biological_sequence ], + owl:allValuesFrom biolink:Gene ; + owl:onProperty biolink:has_gene_or_gene_product ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass biolink:TimeType ; owl:onProperty biolink:timepoint ], [ a owl:Restriction ; - owl:allValuesFrom biolink:Gene ; - owl:onProperty biolink:has_gene_or_gene_product ], + owl:maxQualifiedCardinality 1 ; + owl:onClass biolink:BiologicalSequence ; + owl:onProperty biolink:has_biological_sequence ], biolink:ExposureEvent, biolink:GeneGroupingMixin, biolink:GenomicEntity, @@ -835,22 +841,26 @@ biolink:GenotypeAsAModelOfDiseaseAssociation a owl:Class ; biolink:GenotypeToGeneAssociation a owl:Class ; rdfs:label "genotype to gene association" ; rdfs:subClassOf [ a owl:Restriction ; - owl:onClass biolink:Genotype ; - owl:onProperty rdf:subject ; + owl:onClass biolink:PredicateType ; + owl:onProperty rdf:predicate ; owl:qualifiedCardinality 1 ], [ a owl:Restriction ; owl:onClass biolink:Gene ; owl:onProperty rdf:object ; owl:qualifiedCardinality 1 ], [ a owl:Restriction ; - owl:onClass biolink:PredicateType ; - owl:onProperty rdf:predicate ; + owl:onClass biolink:Genotype ; + owl:onProperty rdf:subject ; owl:qualifiedCardinality 1 ], biolink:Association . biolink:GenotypeToGenotypePartAssociation a owl:Class ; rdfs:label "genotype to genotype part association" ; rdfs:subClassOf [ a owl:Restriction ; + owl:onClass biolink:PredicateType ; + owl:onProperty rdf:predicate ; + owl:qualifiedCardinality 1 ], + [ a owl:Restriction ; owl:onClass biolink:Genotype ; owl:onProperty rdf:object ; owl:qualifiedCardinality 1 ], @@ -858,10 +868,6 @@ biolink:GenotypeToGenotypePartAssociation a owl:Class ; owl:onClass biolink:Genotype ; owl:onProperty rdf:subject ; owl:qualifiedCardinality 1 ], - [ a owl:Restriction ; - owl:onClass biolink:PredicateType ; - owl:onProperty rdf:predicate ; - owl:qualifiedCardinality 1 ], biolink:Association . biolink:GenotypeToPhenotypicFeatureAssociation a owl:Class ; @@ -870,6 +876,14 @@ biolink:GenotypeToPhenotypicFeatureAssociation a owl:Class ; owl:maxQualifiedCardinality 1 ; owl:onClass biolink:Onset ; owl:onProperty biolink:onset_qualifier ], + [ a owl:Restriction ; + owl:onClass biolink:Genotype ; + owl:onProperty rdf:subject ; + owl:qualifiedCardinality 1 ], + [ a owl:Restriction ; + owl:maxQualifiedCardinality 1 ; + owl:onClass biolink:BiologicalSex ; + owl:onProperty biolink:sex_qualifier ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass biolink:SeverityValue ; @@ -878,18 +892,10 @@ biolink:GenotypeToPhenotypicFeatureAssociation a owl:Class ; owl:onClass biolink:PredicateType ; owl:onProperty rdf:predicate ; owl:qualifiedCardinality 1 ], - [ a owl:Restriction ; - owl:onClass biolink:Genotype ; - owl:onProperty rdf:subject ; - owl:qualifiedCardinality 1 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass biolink:FrequencyValue ; owl:onProperty biolink:frequency_qualifier ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass biolink:BiologicalSex ; - owl:onProperty biolink:sex_qualifier ], biolink:Association, biolink:EntityToPhenotypicFeatureAssociationMixin, biolink:GenotypeToEntityAssociationMixin . @@ -897,16 +903,16 @@ biolink:GenotypeToPhenotypicFeatureAssociation a owl:Class ; biolink:GenotypeToVariantAssociation a owl:Class ; rdfs:label "genotype to variant association" ; rdfs:subClassOf [ a owl:Restriction ; - owl:onClass biolink:SequenceVariant ; - owl:onProperty rdf:object ; + owl:onClass biolink:PredicateType ; + owl:onProperty rdf:predicate ; owl:qualifiedCardinality 1 ], [ a owl:Restriction ; owl:onClass biolink:Genotype ; owl:onProperty rdf:subject ; owl:qualifiedCardinality 1 ], [ a owl:Restriction ; - owl:onClass biolink:PredicateType ; - owl:onProperty rdf:predicate ; + owl:onClass biolink:SequenceVariant ; + owl:onProperty rdf:object ; owl:qualifiedCardinality 1 ], biolink:Association . @@ -957,12 +963,12 @@ biolink:GrossAnatomicalStructure a owl:Class ; biolink:Haplotype a owl:Class ; rdfs:label "haplotype" ; rdfs:subClassOf [ a owl:Restriction ; + owl:allValuesFrom biolink:OrganismTaxon ; + owl:onProperty biolink:in_taxon ], + [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass biolink:BiologicalSequence ; owl:onProperty biolink:has_biological_sequence ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:OrganismTaxon ; - owl:onProperty biolink:in_taxon ], biolink:BiologicalEntity, biolink:GenomicEntity, biolink:OntologyClass, @@ -987,14 +993,14 @@ biolink:InformationContentEntityToNamedThingAssociation a owl:Class ; owl:onClass biolink:NamedThing ; owl:onProperty rdf:object ; owl:qualifiedCardinality 1 ], - [ a owl:Restriction ; - owl:onClass biolink:PredicateType ; - owl:onProperty rdf:predicate ; - owl:qualifiedCardinality 1 ], [ a owl:Restriction ; owl:onClass biolink:NamedThing ; owl:onProperty rdf:subject ; owl:qualifiedCardinality 1 ], + [ a owl:Restriction ; + owl:onClass biolink:PredicateType ; + owl:onProperty rdf:predicate ; + owl:qualifiedCardinality 1 ], biolink:Association . biolink:Inheritance a owl:Class ; @@ -1108,13 +1114,13 @@ biolink:NucleicAcidSequenceMotif a owl:Class ; biolink:OrganismTaxonToEnvironmentAssociation a owl:Class ; rdfs:label "organism taxon to environment association" ; rdfs:subClassOf [ a owl:Restriction ; - owl:onClass biolink:OrganismTaxon ; - owl:onProperty rdf:subject ; - owl:qualifiedCardinality 1 ], - [ a owl:Restriction ; owl:onClass biolink:NamedThing ; owl:onProperty rdf:object ; owl:qualifiedCardinality 1 ], + [ a owl:Restriction ; + owl:onClass biolink:OrganismTaxon ; + owl:onProperty rdf:subject ; + owl:qualifiedCardinality 1 ], [ a owl:Restriction ; owl:onClass biolink:PredicateType ; owl:onProperty rdf:predicate ; @@ -1125,21 +1131,21 @@ biolink:OrganismTaxonToEnvironmentAssociation a owl:Class ; biolink:OrganismTaxonToOrganismTaxonInteraction a owl:Class ; rdfs:label "organism taxon to organism taxon interaction" ; rdfs:subClassOf [ a owl:Restriction ; - owl:onClass biolink:OrganismTaxon ; - owl:onProperty rdf:subject ; + owl:onClass biolink:PredicateType ; + owl:onProperty rdf:predicate ; owl:qualifiedCardinality 1 ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty biolink:associated_environmental_context ], [ a owl:Restriction ; owl:onClass biolink:OrganismTaxon ; owl:onProperty rdf:object ; owl:qualifiedCardinality 1 ], [ a owl:Restriction ; - owl:onClass biolink:PredicateType ; - owl:onProperty rdf:predicate ; + owl:onClass biolink:OrganismTaxon ; + owl:onProperty rdf:subject ; owl:qualifiedCardinality 1 ], + [ a owl:Restriction ; + owl:maxQualifiedCardinality 1 ; + owl:onClass linkml:String ; + owl:onProperty biolink:associated_environmental_context ], biolink:OrganismTaxonToOrganismTaxonAssociation . biolink:OrganismTaxonToOrganismTaxonSpecialization a owl:Class ; @@ -1148,14 +1154,14 @@ biolink:OrganismTaxonToOrganismTaxonSpecialization a owl:Class ; owl:onClass biolink:OrganismTaxon ; owl:onProperty rdf:object ; owl:qualifiedCardinality 1 ], - [ a owl:Restriction ; - owl:onClass biolink:OrganismTaxon ; - owl:onProperty rdf:subject ; - owl:qualifiedCardinality 1 ], [ a owl:Restriction ; owl:onClass biolink:PredicateType ; owl:onProperty rdf:predicate ; owl:qualifiedCardinality 1 ], + [ a owl:Restriction ; + owl:onClass biolink:OrganismTaxon ; + owl:onProperty rdf:subject ; + owl:qualifiedCardinality 1 ], biolink:OrganismTaxonToOrganismTaxonAssociation . biolink:OrganismToOrganismAssociation a owl:Class ; @@ -1174,20 +1180,20 @@ biolink:OrganismalEntityAsAModelOfDiseaseAssociation a owl:Class ; rdfs:label "organismal entity as a model of disease association" ; rdfs:subClassOf [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; - owl:onClass biolink:SeverityValue ; - owl:onProperty biolink:severity_qualifier ], + owl:onClass biolink:Onset ; + owl:onProperty biolink:onset_qualifier ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass biolink:FrequencyValue ; owl:onProperty biolink:frequency_qualifier ], + [ a owl:Restriction ; + owl:maxQualifiedCardinality 1 ; + owl:onClass biolink:SeverityValue ; + owl:onProperty biolink:severity_qualifier ], [ a owl:Restriction ; owl:onClass biolink:OrganismalEntity ; owl:onProperty rdf:subject ; owl:qualifiedCardinality 1 ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass biolink:Onset ; - owl:onProperty biolink:onset_qualifier ], biolink:Association, biolink:EntityToDiseaseAssociationMixin, biolink:ModelToDiseaseAssociationMixin . @@ -1198,22 +1204,22 @@ biolink:PairwiseMolecularInteraction a owl:Class ; owl:onClass biolink:PredicateType ; owl:onProperty rdf:predicate ; owl:qualifiedCardinality 1 ], - [ a owl:Restriction ; - owl:onClass biolink:MolecularEntity ; - owl:onProperty rdf:object ; - owl:qualifiedCardinality 1 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass biolink:OntologyClass ; owl:onProperty biolink:interacting_molecules_category ], [ a owl:Restriction ; - owl:onClass linkml:String ; - owl:onProperty biolink:id ; + owl:onClass biolink:MolecularEntity ; + owl:onProperty rdf:object ; owl:qualifiedCardinality 1 ], [ a owl:Restriction ; owl:onClass biolink:MolecularEntity ; owl:onProperty rdf:subject ; owl:qualifiedCardinality 1 ], + [ a owl:Restriction ; + owl:onClass linkml:String ; + owl:onProperty biolink:id ; + owl:qualifiedCardinality 1 ], biolink:PairwiseGeneToGeneInteraction . biolink:PathognomonicityQuantifier a owl:Class ; @@ -1304,10 +1310,6 @@ biolink:PhysiologicalProcess a owl:Class ; biolink:PopulationToPopulationAssociation a owl:Class ; rdfs:label "population to population association" ; rdfs:subClassOf [ a owl:Restriction ; - owl:onClass biolink:PopulationOfIndividualOrganisms ; - owl:onProperty rdf:object ; - owl:qualifiedCardinality 1 ], - [ a owl:Restriction ; owl:onClass biolink:PopulationOfIndividualOrganisms ; owl:onProperty rdf:subject ; owl:qualifiedCardinality 1 ], @@ -1315,6 +1317,10 @@ biolink:PopulationToPopulationAssociation a owl:Class ; owl:onClass biolink:PredicateType ; owl:onProperty rdf:predicate ; owl:qualifiedCardinality 1 ], + [ a owl:Restriction ; + owl:onClass biolink:PopulationOfIndividualOrganisms ; + owl:onProperty rdf:object ; + owl:qualifiedCardinality 1 ], biolink:Association . biolink:PredicateQualifierEnum a owl:Class ; @@ -1415,23 +1421,19 @@ biolink:SequenceEnum a owl:Class ; biolink:SequenceVariantModulatesTreatmentAssociation a owl:Class ; rdfs:label "sequence variant modulates treatment association" ; rdfs:subClassOf [ a owl:Restriction ; - owl:onClass biolink:Treatment ; - owl:onProperty rdf:object ; - owl:qualifiedCardinality 1 ], - [ a owl:Restriction ; owl:onClass biolink:SequenceVariant ; owl:onProperty rdf:subject ; owl:qualifiedCardinality 1 ], + [ a owl:Restriction ; + owl:onClass biolink:Treatment ; + owl:onProperty rdf:object ; + owl:qualifiedCardinality 1 ], biolink:Association ; skos:note "An alternate way to model the same information could be via a qualifier" . biolink:Serial a owl:Class ; rdfs:label "serial" ; rdfs:subClassOf [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty biolink:issue ], - [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass linkml:String ; owl:onProperty biolink:iso_abbreviation ], @@ -1441,12 +1443,16 @@ biolink:Serial a owl:Class ; owl:onProperty biolink:volume ], [ a owl:Restriction ; owl:onClass linkml:String ; - owl:onProperty biolink:id ; + owl:onProperty rdf:type ; owl:qualifiedCardinality 1 ], [ a owl:Restriction ; owl:onClass linkml:String ; - owl:onProperty rdf:type ; + owl:onProperty biolink:id ; owl:qualifiedCardinality 1 ], + [ a owl:Restriction ; + owl:maxQualifiedCardinality 1 ; + owl:onClass linkml:String ; + owl:onProperty biolink:issue ], biolink:Publication ; skos:altLabel "journal" . @@ -1492,16 +1498,16 @@ biolink:Snv a owl:Class ; biolink:SocioeconomicExposure a owl:Class ; rdfs:label "socioeconomic exposure" ; - rdfs:subClassOf [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass biolink:TimeType ; - owl:onProperty biolink:timepoint ], - [ a owl:Class ; + rdfs:subClassOf [ a owl:Class ; owl:intersectionOf ( [ a owl:Restriction ; owl:allValuesFrom biolink:SocioeconomicAttribute ; owl:onProperty biolink:has_attribute ] [ a owl:Restriction ; owl:onProperty biolink:has_attribute ; owl:someValuesFrom biolink:SocioeconomicAttribute ] ) ], + [ a owl:Restriction ; + owl:maxQualifiedCardinality 1 ; + owl:onClass biolink:TimeType ; + owl:onProperty biolink:timepoint ], biolink:ExposureEvent . biolink:SocioeconomicOutcome a owl:Class ; @@ -1512,11 +1518,11 @@ biolink:TaxonToTaxonAssociation a owl:Class ; rdfs:label "taxon to taxon association" ; rdfs:subClassOf [ a owl:Restriction ; owl:onClass biolink:OrganismTaxon ; - owl:onProperty rdf:object ; + owl:onProperty rdf:subject ; owl:qualifiedCardinality 1 ], [ a owl:Restriction ; owl:onClass biolink:OrganismTaxon ; - owl:onProperty rdf:subject ; + owl:onProperty rdf:object ; owl:qualifiedCardinality 1 ], biolink:Association . @@ -1532,11 +1538,6 @@ biolink:TranscriptToGeneRelationship a owl:Class ; owl:qualifiedCardinality 1 ], biolink:SequenceFeatureRelationship . -biolink:UnclassifiedOntologyClass a owl:Class ; - rdfs:label "unclassified ontology class" ; - rdfs:subClassOf biolink:OntologyClass, - linkml:mixin . - biolink:VariantAsAModelOfDiseaseAssociation a owl:Class ; rdfs:label "variant as a model of disease association" ; rdfs:subClassOf [ a owl:Restriction ; @@ -1550,14 +1551,6 @@ biolink:VariantAsAModelOfDiseaseAssociation a owl:Class ; biolink:VariantToGeneExpressionAssociation a owl:Class ; rdfs:label "variant to gene expression association" ; rdfs:subClassOf [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass biolink:DiseaseOrPhenotypicFeature ; - owl:onProperty biolink:phenotypic_state ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass biolink:LifeStage ; - owl:onProperty biolink:stage_qualifier ], - [ a owl:Restriction ; owl:onClass biolink:PredicateType ; owl:onProperty rdf:predicate ; owl:qualifiedCardinality 1 ], @@ -1565,10 +1558,18 @@ biolink:VariantToGeneExpressionAssociation a owl:Class ; owl:maxQualifiedCardinality 1 ; owl:onClass biolink:OntologyClass ; owl:onProperty biolink:quantifier_qualifier ], + [ a owl:Restriction ; + owl:maxQualifiedCardinality 1 ; + owl:onClass biolink:DiseaseOrPhenotypicFeature ; + owl:onProperty biolink:phenotypic_state ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass biolink:AnatomicalEntity ; owl:onProperty biolink:expression_site ], + [ a owl:Restriction ; + owl:maxQualifiedCardinality 1 ; + owl:onClass biolink:LifeStage ; + owl:onProperty biolink:stage_qualifier ], biolink:GeneExpressionMixin, biolink:VariantToGeneAssociation . @@ -1576,24 +1577,24 @@ biolink:VariantToPhenotypicFeatureAssociation a owl:Class ; rdfs:label "variant to phenotypic feature association" ; rdfs:subClassOf [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; - owl:onClass biolink:BiologicalSex ; - owl:onProperty biolink:sex_qualifier ], + owl:onClass biolink:Onset ; + owl:onProperty biolink:onset_qualifier ], [ a owl:Restriction ; owl:onClass biolink:SequenceVariant ; owl:onProperty rdf:subject ; owl:qualifiedCardinality 1 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; - owl:onClass biolink:Onset ; - owl:onProperty biolink:onset_qualifier ], + owl:onClass biolink:FrequencyValue ; + owl:onProperty biolink:frequency_qualifier ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass biolink:SeverityValue ; owl:onProperty biolink:severity_qualifier ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; - owl:onClass biolink:FrequencyValue ; - owl:onProperty biolink:frequency_qualifier ], + owl:onClass biolink:BiologicalSex ; + owl:onProperty biolink:sex_qualifier ], biolink:Association, biolink:EntityToPhenotypicFeatureAssociationMixin, biolink:VariantToEntityAssociationMixin . @@ -1601,18 +1602,6 @@ biolink:VariantToPhenotypicFeatureAssociation a owl:Class ; biolink:VariantToPopulationAssociation a owl:Class ; rdfs:label "variant to population association" ; rdfs:subClassOf [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:Double ; - owl:onProperty biolink:has_percentage ], - [ a owl:Restriction ; - owl:onClass biolink:PopulationOfIndividualOrganisms ; - owl:onProperty rdf:object ; - owl:qualifiedCardinality 1 ], - [ a owl:Restriction ; - owl:onClass biolink:SequenceVariant ; - owl:onProperty rdf:subject ; - owl:qualifiedCardinality 1 ], - [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass biolink:FrequencyValue ; owl:onProperty biolink:frequency_qualifier ], @@ -1623,11 +1612,23 @@ biolink:VariantToPopulationAssociation a owl:Class ; [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass linkml:Integer ; - owl:onProperty biolink:has_total ], + owl:onProperty biolink:has_count ], + [ a owl:Restriction ; + owl:maxQualifiedCardinality 1 ; + owl:onClass linkml:Double ; + owl:onProperty biolink:has_percentage ], + [ a owl:Restriction ; + owl:onClass biolink:SequenceVariant ; + owl:onProperty rdf:subject ; + owl:qualifiedCardinality 1 ], + [ a owl:Restriction ; + owl:onClass biolink:PopulationOfIndividualOrganisms ; + owl:onProperty rdf:object ; + owl:qualifiedCardinality 1 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass linkml:Integer ; - owl:onProperty biolink:has_count ], + owl:onProperty biolink:has_total ], biolink:Association, biolink:FrequencyQualifierMixin, biolink:FrequencyQuantifier, @@ -2108,10 +2109,6 @@ biolink:BehavioralFeature a owl:Class ; biolink:BookChapter a owl:Class ; rdfs:label "book chapter" ; rdfs:subClassOf [ a owl:Restriction ; - owl:onClass linkml:Uriorcurie ; - owl:onProperty biolink:published_in ; - owl:qualifiedCardinality 1 ], - [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass linkml:String ; owl:onProperty biolink:volume ], @@ -2119,6 +2116,10 @@ biolink:BookChapter a owl:Class ; owl:maxQualifiedCardinality 1 ; owl:onClass linkml:String ; owl:onProperty biolink:chapter ], + [ a owl:Restriction ; + owl:onClass linkml:Uriorcurie ; + owl:onProperty biolink:published_in ; + owl:qualifiedCardinality 1 ], biolink:Publication . biolink:Case a owl:Class ; @@ -2140,12 +2141,12 @@ biolink:CellLineToDiseaseOrPhenotypicFeatureAssociation a owl:Class ; biolink:ChemicalExposure a owl:Class ; rdfs:label "chemical exposure" ; rdfs:subClassOf [ a owl:Restriction ; + owl:allValuesFrom biolink:QuantityValue ; + owl:onProperty biolink:has_quantitative_value ], + [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass biolink:TimeType ; owl:onProperty biolink:timepoint ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:QuantityValue ; - owl:onProperty biolink:has_quantitative_value ], biolink:ExposureEvent ; skos:exactMatch ECTO:9000000, SIO:001399 . @@ -2242,10 +2243,6 @@ biolink:Exon a owl:Class ; biolink:FrequencyQuantifier a owl:Class ; rdfs:label "frequency quantifier" ; rdfs:subClassOf [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:Double ; - owl:onProperty biolink:has_percentage ], - [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass linkml:Integer ; owl:onProperty biolink:has_total ], @@ -2257,31 +2254,35 @@ biolink:FrequencyQuantifier a owl:Class ; owl:maxQualifiedCardinality 1 ; owl:onClass linkml:Double ; owl:onProperty biolink:has_quotient ], + [ a owl:Restriction ; + owl:maxQualifiedCardinality 1 ; + owl:onClass linkml:Double ; + owl:onProperty biolink:has_percentage ], biolink:RelationshipQuantifier, linkml:mixin . biolink:GenotypeToDiseaseAssociation a owl:Class ; rdfs:label "genotype to disease association" ; rdfs:subClassOf [ a owl:Restriction ; - owl:onClass biolink:PredicateType ; - owl:onProperty rdf:predicate ; - owl:qualifiedCardinality 1 ], - [ a owl:Restriction ; - owl:onClass biolink:NamedThing ; - owl:onProperty rdf:subject ; - owl:qualifiedCardinality 1 ], - [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass biolink:FrequencyValue ; owl:onProperty biolink:frequency_qualifier ], + [ a owl:Restriction ; + owl:maxQualifiedCardinality 1 ; + owl:onClass biolink:Onset ; + owl:onProperty biolink:onset_qualifier ], + [ a owl:Restriction ; + owl:onClass biolink:PredicateType ; + owl:onProperty rdf:predicate ; + owl:qualifiedCardinality 1 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass biolink:SeverityValue ; owl:onProperty biolink:severity_qualifier ], [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass biolink:Onset ; - owl:onProperty biolink:onset_qualifier ], + owl:onClass biolink:NamedThing ; + owl:onProperty rdf:subject ; + owl:qualifiedCardinality 1 ], [ a owl:Restriction ; owl:onClass biolink:NamedThing ; owl:onProperty rdf:object ; @@ -2356,21 +2357,21 @@ biolink:Polypeptide a owl:Class ; biolink:ReactionToParticipantAssociation a owl:Class ; rdfs:label "reaction to participant association" ; rdfs:subClassOf [ a owl:Restriction ; - owl:onClass biolink:MolecularEntity ; - owl:onProperty rdf:subject ; - owl:qualifiedCardinality 1 ], - [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; - owl:onClass biolink:ReactionSideEnum ; - owl:onProperty biolink:reaction_side ], + owl:onClass linkml:Integer ; + owl:onProperty biolink:stoichiometry ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass biolink:ReactionDirectionEnum ; owl:onProperty biolink:reaction_direction ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:Integer ; - owl:onProperty biolink:stoichiometry ], + owl:onClass biolink:ReactionSideEnum ; + owl:onProperty biolink:reaction_side ], + [ a owl:Restriction ; + owl:onClass biolink:MolecularEntity ; + owl:onProperty rdf:subject ; + owl:qualifiedCardinality 1 ], biolink:ChemicalToChemicalAssociation . biolink:SequenceAssociation a owl:Class ; @@ -2399,18 +2400,18 @@ biolink:TaxonomicRank a owl:Class ; biolink:Treatment a owl:Class ; rdfs:label "treatment" ; rdfs:subClassOf [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass biolink:TimeType ; - owl:onProperty biolink:timepoint ], + owl:allValuesFrom biolink:Procedure ; + owl:onProperty biolink:has_procedure ], [ a owl:Restriction ; owl:allValuesFrom biolink:Device ; owl:onProperty biolink:has_device ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:Procedure ; - owl:onProperty biolink:has_procedure ], [ a owl:Restriction ; owl:allValuesFrom biolink:Drug ; owl:onProperty biolink:has_drug ], + [ a owl:Restriction ; + owl:maxQualifiedCardinality 1 ; + owl:onClass biolink:TimeType ; + owl:onProperty biolink:timepoint ], biolink:ChemicalOrDrugOrTreatment, biolink:ExposureEvent, biolink:NamedThing ; @@ -2420,19 +2421,22 @@ biolink:Treatment a owl:Class ; skos:exactMatch , SIO:001398 . +biolink:UnclassifiedOntologyClass a owl:Class ; + rdfs:label "unclassified ontology class" . + biolink:VariantToDiseaseAssociation a owl:Class ; rdfs:label "variant to disease association" ; rdfs:subClassOf [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; - owl:onClass biolink:FrequencyValue ; - owl:onProperty biolink:frequency_qualifier ], + owl:onClass biolink:SeverityValue ; + owl:onProperty biolink:severity_qualifier ], [ a owl:Restriction ; owl:onClass biolink:NamedThing ; owl:onProperty rdf:object ; owl:qualifiedCardinality 1 ], [ a owl:Restriction ; - owl:onClass biolink:NamedThing ; - owl:onProperty rdf:subject ; + owl:onClass biolink:PredicateType ; + owl:onProperty rdf:predicate ; owl:qualifiedCardinality 1 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; @@ -2440,11 +2444,11 @@ biolink:VariantToDiseaseAssociation a owl:Class ; owl:onProperty biolink:onset_qualifier ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; - owl:onClass biolink:SeverityValue ; - owl:onProperty biolink:severity_qualifier ], + owl:onClass biolink:FrequencyValue ; + owl:onProperty biolink:frequency_qualifier ], [ a owl:Restriction ; - owl:onClass biolink:PredicateType ; - owl:onProperty rdf:predicate ; + owl:onClass biolink:NamedThing ; + owl:onProperty rdf:subject ; owl:qualifiedCardinality 1 ], biolink:Association, biolink:EntityToDiseaseAssociationMixin, @@ -3893,6 +3897,11 @@ biolink:interacting_molecules_category a owl:ObjectProperty ; skos:exactMatch MI:1046 ; linkml:examples "Example(value='MI:1048', description='smallmolecule-protein')" . +biolink:iri a owl:ObjectProperty ; + rdfs:label "iri" ; + rdfs:range biolink:IriType ; + skos:exactMatch WIKIDATA_PROPERTY:P854 . + biolink:is_active_ingredient_of a owl:ObjectProperty ; rdfs:label "is active ingredient of" ; rdfs:domain biolink:MolecularEntity ; @@ -4532,6 +4541,10 @@ biolink:sequence_variant_qualifier a owl:ObjectProperty ; rdfs:range biolink:SequenceVariant ; rdfs:subPropertyOf biolink:association_slot . +biolink:source a owl:ObjectProperty ; + rdfs:label "source" ; + rdfs:range linkml:String . + biolink:source_web_page a owl:ObjectProperty ; rdfs:label "source web page" ; rdfs:domain biolink:DatasetSummary ; @@ -4799,14 +4812,17 @@ biolink:AnatomicalEntityToAnatomicalEntityAssociation a owl:Class ; rdfs:label "anatomical entity to anatomical entity association" ; rdfs:subClassOf [ a owl:Restriction ; owl:onClass biolink:AnatomicalEntity ; - owl:onProperty rdf:object ; + owl:onProperty rdf:subject ; owl:qualifiedCardinality 1 ], [ a owl:Restriction ; owl:onClass biolink:AnatomicalEntity ; - owl:onProperty rdf:subject ; + owl:onProperty rdf:object ; owl:qualifiedCardinality 1 ], biolink:Association . +biolink:Annotation a owl:Class ; + rdfs:label "annotation" . + biolink:CaseToEntityAssociationMixin a owl:Class ; rdfs:label "case to entity association mixin" ; rdfs:subClassOf [ a owl:Restriction ; @@ -4917,13 +4933,13 @@ biolink:EntityToExposureEventAssociationMixin a owl:Class ; biolink:EntityToFeatureOrDiseaseQualifiersMixin a owl:Class ; rdfs:label "entity to feature or disease qualifiers mixin" ; rdfs:subClassOf [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass biolink:Onset ; - owl:onProperty biolink:onset_qualifier ], - [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass biolink:SeverityValue ; owl:onProperty biolink:severity_qualifier ], + [ a owl:Restriction ; + owl:maxQualifiedCardinality 1 ; + owl:onClass biolink:Onset ; + owl:onProperty biolink:onset_qualifier ], biolink:FrequencyQualifierMixin, linkml:mixin . @@ -4989,16 +5005,15 @@ biolink:FDA_approval_status a owl:ObjectProperty ; rdfs:range biolink:FDAApprovalStatusEnum ; rdfs:subPropertyOf biolink:association_slot . -biolink:GeneOntologyClass a owl:Class ; - rdfs:label "gene ontology class" ; - rdfs:subClassOf biolink:OntologyClass, - linkml:mixin . - biolink:GeneProductIsoformMixin a owl:Class ; rdfs:label "gene product isoform mixin" ; rdfs:subClassOf biolink:GeneProductMixin, linkml:mixin . +biolink:IriType a owl:Class ; + rdfs:label "iri type" ; + rdfs:subClassOf linkml:Uriorcurie . + a owl:Class ; rdfs:label "InverseAllSome" . @@ -5045,11 +5060,11 @@ biolink:OrganismTaxonToOrganismTaxonAssociation a owl:Class ; rdfs:label "organism taxon to organism taxon association" ; rdfs:subClassOf [ a owl:Restriction ; owl:onClass biolink:OrganismTaxon ; - owl:onProperty rdf:subject ; + owl:onProperty rdf:object ; owl:qualifiedCardinality 1 ], [ a owl:Restriction ; owl:onClass biolink:OrganismTaxon ; - owl:onProperty rdf:object ; + owl:onProperty rdf:subject ; owl:qualifiedCardinality 1 ], biolink:Association, biolink:OrganismTaxonToEntityAssociation . @@ -5309,11 +5324,6 @@ biolink:interbase_coordinate a owl:ObjectProperty ; "space-based", "zero-based" . -biolink:iri a owl:ObjectProperty ; - rdfs:label "iri" ; - rdfs:range biolink:IriType ; - skos:exactMatch WIKIDATA_PROPERTY:P854 . - biolink:iso_abbreviation a owl:ObjectProperty . biolink:issue a owl:ObjectProperty ; @@ -5446,10 +5456,6 @@ biolink:similar_to a owl:ObjectProperty, skos:exactMatch RO:HOM0000000, . -biolink:source a owl:ObjectProperty ; - rdfs:label "source" ; - rdfs:range linkml:String . - biolink:temporally_related_to a owl:ObjectProperty, owl:SymmetricProperty ; rdfs:label "temporally related to" ; @@ -5549,9 +5555,6 @@ biolink:ActivityAndBehavior a owl:Class ; linkml:mixin ; skos:exactMatch UMLSSG:ACTI . -biolink:Annotation a owl:Class ; - rdfs:label "annotation" . - biolink:CellularComponent a owl:Class ; rdfs:label "cellular component" ; rdfs:subClassOf biolink:AnatomicalEntity ; @@ -5607,10 +5610,6 @@ biolink:DiseaseToEntityAssociationMixin a owl:Class ; biolink:Entity a owl:Class ; rdfs:label "entity" ; rdfs:subClassOf [ a owl:Restriction ; - owl:onClass linkml:String ; - owl:onProperty biolink:id ; - owl:qualifiedCardinality 1 ], - [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass biolink:LabelType ; owl:onProperty rdfs:label ], @@ -5623,8 +5622,13 @@ biolink:Entity a owl:Class ; owl:onClass biolink:NarrativeText ; owl:onProperty dct:description ], [ a owl:Restriction ; - owl:allValuesFrom biolink:Attribute ; - owl:onProperty biolink:has_attribute ], + owl:maxQualifiedCardinality 1 ; + owl:onClass biolink:IriType ; + owl:onProperty biolink:iri ], + [ a owl:Restriction ; + owl:onClass linkml:String ; + owl:onProperty biolink:id ; + owl:qualifiedCardinality 1 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass linkml:String ; @@ -5633,9 +5637,8 @@ biolink:Entity a owl:Class ; owl:allValuesFrom biolink:CategoryType ; owl:onProperty biolink:category ], [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass biolink:IriType ; - owl:onProperty biolink:iri ] . + owl:allValuesFrom biolink:Attribute ; + owl:onProperty biolink:has_attribute ] . biolink:FDAApprovalStatusEnum a owl:Class ; rdfs:label "FDA_approval_status_enum" ; @@ -5667,14 +5670,6 @@ biolink:FrequencyQualifierMixin a owl:Class ; biolink:GeneExpressionMixin a owl:Class ; rdfs:label "gene expression mixin" ; rdfs:subClassOf [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass biolink:OntologyClass ; - owl:onProperty biolink:quantifier_qualifier ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass biolink:AnatomicalEntity ; - owl:onProperty biolink:expression_site ], - [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass biolink:LifeStage ; owl:onProperty biolink:stage_qualifier ], @@ -5682,8 +5677,19 @@ biolink:GeneExpressionMixin a owl:Class ; owl:maxQualifiedCardinality 1 ; owl:onClass biolink:DiseaseOrPhenotypicFeature ; owl:onProperty biolink:phenotypic_state ], + [ a owl:Restriction ; + owl:maxQualifiedCardinality 1 ; + owl:onClass biolink:OntologyClass ; + owl:onProperty biolink:quantifier_qualifier ], + [ a owl:Restriction ; + owl:maxQualifiedCardinality 1 ; + owl:onClass biolink:AnatomicalEntity ; + owl:onProperty biolink:expression_site ], linkml:mixin . +biolink:GeneOntologyClass a owl:Class ; + rdfs:label "gene ontology class" . + biolink:GeneToDiseaseAssociation a owl:Class ; rdfs:label "gene to disease association" ; rdfs:subClassOf [ a owl:Restriction ; @@ -5691,21 +5697,21 @@ biolink:GeneToDiseaseAssociation a owl:Class ; owl:onClass biolink:SeverityValue ; owl:onProperty biolink:severity_qualifier ], [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass biolink:FrequencyValue ; - owl:onProperty biolink:frequency_qualifier ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass biolink:Onset ; - owl:onProperty biolink:onset_qualifier ], + owl:onClass biolink:GeneOrGeneProduct ; + owl:onProperty rdf:subject ; + owl:qualifiedCardinality 1 ], [ a owl:Restriction ; owl:onClass biolink:Disease ; owl:onProperty rdf:object ; owl:qualifiedCardinality 1 ], [ a owl:Restriction ; - owl:onClass biolink:GeneOrGeneProduct ; - owl:onProperty rdf:subject ; - owl:qualifiedCardinality 1 ], + owl:maxQualifiedCardinality 1 ; + owl:onClass biolink:Onset ; + owl:onProperty biolink:onset_qualifier ], + [ a owl:Restriction ; + owl:maxQualifiedCardinality 1 ; + owl:onClass biolink:FrequencyValue ; + owl:onProperty biolink:frequency_qualifier ], biolink:Association, biolink:EntityToDiseaseAssociationMixin, biolink:GeneToEntityAssociationMixin ; @@ -5717,11 +5723,11 @@ biolink:GeneToGeneAssociation a owl:Class ; rdfs:label "gene to gene association" ; rdfs:subClassOf [ a owl:Restriction ; owl:onClass biolink:GeneOrGeneProduct ; - owl:onProperty rdf:object ; + owl:onProperty rdf:subject ; owl:qualifiedCardinality 1 ], [ a owl:Restriction ; owl:onClass biolink:GeneOrGeneProduct ; - owl:onProperty rdf:subject ; + owl:onProperty rdf:object ; owl:qualifiedCardinality 1 ], biolink:Association ; skos:altLabel "molecular or genetic interaction" . @@ -5747,10 +5753,6 @@ biolink:IndividualOrganism a owl:Class ; skos:narrowMatch foaf:Person, WIKIDATA:Q795052 . -biolink:IriType a owl:Class ; - rdfs:label "iri type" ; - rdfs:subClassOf linkml:Uriorcurie . - biolink:OrganismTaxonToEntityAssociation a owl:Class ; rdfs:label "organism taxon to entity association" ; rdfs:subClassOf [ a owl:Restriction ; @@ -6279,6 +6281,10 @@ biolink:ClinicalAttribute a owl:Class ; biolink:DatasetVersion a owl:Class ; rdfs:label "dataset version" ; rdfs:subClassOf [ a owl:Restriction ; + owl:maxQualifiedCardinality 1 ; + owl:onClass linkml:String ; + owl:onProperty pav:version ], + [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass biolink:DatasetDistribution ; owl:onProperty dct:distribution ], @@ -6286,10 +6292,6 @@ biolink:DatasetVersion a owl:Class ; owl:maxQualifiedCardinality 1 ; owl:onClass biolink:Dataset ; owl:onProperty dct:source ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty pav:version ], biolink:InformationContentEntity . biolink:EntityToDiseaseOrPhenotypicFeatureAssociationMixin a owl:Class ; @@ -6732,14 +6734,14 @@ biolink:Dataset a owl:Class ; biolink:QuantityValue a owl:Class ; rdfs:label "quantity value" ; - rdfs:subClassOf [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:Double ; - owl:onProperty biolink:has_numeric_value ], - [ a owl:Restriction ; + rdfs:subClassOf [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass biolink:Unit ; owl:onProperty biolink:has_unit ], + [ a owl:Restriction ; + owl:maxQualifiedCardinality 1 ; + owl:onClass linkml:Double ; + owl:onProperty biolink:has_numeric_value ], biolink:Annotation . biolink:VariantToEntityAssociationMixin a owl:Class ; @@ -6810,6 +6812,9 @@ biolink:sequence_localization_attribute a owl:ObjectProperty ; biolink:ChemicalMixture a owl:Class ; rdfs:label "chemical mixture" ; rdfs:subClassOf [ a owl:Restriction ; + owl:allValuesFrom biolink:DrugDeliveryEnum ; + owl:onProperty biolink:routes_of_delivery ], + [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass biolink:ChemicalMixture ; owl:onProperty biolink:is_supplement ], @@ -6821,9 +6826,6 @@ biolink:ChemicalMixture a owl:Class ; owl:maxQualifiedCardinality 1 ; owl:onClass linkml:String ; owl:onProperty biolink:highest_FDA_approval_status ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:DrugDeliveryEnum ; - owl:onProperty biolink:routes_of_delivery ], biolink:ChemicalEntity ; skos:closeMatch dcid:ChemicalCompound ; skos:narrowMatch , @@ -6839,11 +6841,11 @@ biolink:GeneGroupingMixin a owl:Class ; biolink:GeneProductMixin a owl:Class ; rdfs:label "gene product mixin" ; rdfs:subClassOf [ a owl:Restriction ; - owl:allValuesFrom biolink:LabelType ; - owl:onProperty biolink:synonym ], - [ a owl:Restriction ; owl:allValuesFrom linkml:Uriorcurie ; owl:onProperty biolink:xref ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:LabelType ; + owl:onProperty biolink:synonym ], biolink:GeneOrGeneProduct, linkml:mixin ; skos:exactMatch , @@ -7014,29 +7016,29 @@ biolink:part_of a owl:ObjectProperty ; biolink:EntityToPhenotypicFeatureAssociationMixin a owl:Class ; rdfs:label "entity to phenotypic feature association mixin" ; rdfs:subClassOf [ a owl:Restriction ; - owl:onClass biolink:PhenotypicFeature ; - owl:onProperty rdf:object ; - owl:qualifiedCardinality 1 ], - [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass biolink:BiologicalSex ; owl:onProperty biolink:sex_qualifier ], + [ a owl:Restriction ; + owl:onClass biolink:PhenotypicFeature ; + owl:onProperty rdf:object ; + owl:qualifiedCardinality 1 ], biolink:EntityToFeatureOrDiseaseQualifiersMixin, linkml:mixin . biolink:Genotype a owl:Class ; rdfs:label "genotype" ; rdfs:subClassOf [ a owl:Restriction ; + owl:maxQualifiedCardinality 1 ; + owl:onClass biolink:Zygosity ; + owl:onProperty biolink:has_zygosity ], + [ a owl:Restriction ; owl:allValuesFrom biolink:OrganismTaxon ; owl:onProperty biolink:in_taxon ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass biolink:BiologicalSequence ; owl:onProperty biolink:has_biological_sequence ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass biolink:Zygosity ; - owl:onProperty biolink:has_zygosity ], biolink:BiologicalEntity, biolink:GenomicEntity, biolink:OntologyClass, @@ -7130,12 +7132,12 @@ biolink:MolecularActivity a owl:Class ; rdfs:subClassOf [ a owl:Restriction ; owl:allValuesFrom biolink:MolecularEntity ; owl:onProperty biolink:has_input ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:MacromolecularMachineMixin ; - owl:onProperty biolink:enabled_by ], [ a owl:Restriction ; owl:allValuesFrom biolink:MolecularEntity ; owl:onProperty biolink:has_output ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:MacromolecularMachineMixin ; + owl:onProperty biolink:enabled_by ], biolink:BiologicalProcessOrActivity, biolink:Occurrent, biolink:OntologyClass ; @@ -7152,8 +7154,6 @@ biolink:has_sequence_variant a owl:ObjectProperty ; rdfs:subPropertyOf biolink:related_to_at_instance_level ; owl:inverseOf biolink:is_sequence_variant_of . -biolink:id a owl:ObjectProperty . - biolink:is_sequence_variant_of a owl:ObjectProperty ; rdfs:label "is sequence variant of" ; rdfs:domain biolink:SequenceVariant ; @@ -7174,14 +7174,14 @@ biolink:sex_qualifier a owl:ObjectProperty ; biolink:BiologicalProcessOrActivity a owl:Class ; rdfs:label "biological process or activity" ; rdfs:subClassOf [ a owl:Restriction ; + owl:allValuesFrom biolink:BiologicalProcessOrActivity ; + owl:onProperty biolink:has_input ], + [ a owl:Restriction ; owl:allValuesFrom biolink:PhysicalEntity ; owl:onProperty biolink:enabled_by ], [ a owl:Restriction ; owl:allValuesFrom biolink:BiologicalProcessOrActivity ; owl:onProperty biolink:has_output ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:BiologicalProcessOrActivity ; - owl:onProperty biolink:has_input ], biolink:BiologicalEntity, biolink:Occurrent, biolink:OntologyClass . @@ -7205,34 +7205,34 @@ biolink:GenomicSequenceLocalization a owl:Class ; owl:maxQualifiedCardinality 1 ; owl:onClass linkml:Integer ; owl:onProperty biolink:start_interbase_coordinate ], + [ a owl:Restriction ; + owl:onClass biolink:PredicateType ; + owl:onProperty rdf:predicate ; + owl:qualifiedCardinality 1 ], [ a owl:Restriction ; owl:onClass biolink:NucleicAcidEntity ; owl:onProperty rdf:object ; owl:qualifiedCardinality 1 ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass biolink:PhaseEnum ; - owl:onProperty biolink:phase ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass biolink:StrandEnum ; owl:onProperty biolink:genome_build ], [ a owl:Restriction ; - owl:onClass biolink:NucleicAcidEntity ; - owl:onProperty rdf:subject ; - owl:qualifiedCardinality 1 ], + owl:maxQualifiedCardinality 1 ; + owl:onClass linkml:Integer ; + owl:onProperty biolink:end_interbase_coordinate ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass biolink:StrandEnum ; owl:onProperty biolink:strand ], - [ a owl:Restriction ; - owl:onClass biolink:PredicateType ; - owl:onProperty rdf:predicate ; - owl:qualifiedCardinality 1 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:Integer ; - owl:onProperty biolink:end_interbase_coordinate ], + owl:onClass biolink:PhaseEnum ; + owl:onProperty biolink:phase ], + [ a owl:Restriction ; + owl:onClass biolink:NucleicAcidEntity ; + owl:onProperty rdf:subject ; + owl:qualifiedCardinality 1 ], biolink:SequenceAssociation ; skos:broadMatch dcid:Chromosome ; skos:exactMatch dcid:GenomeAnnotation . @@ -7252,32 +7252,26 @@ biolink:Outcome a owl:Class ; rdfs:label "outcome" ; rdfs:subClassOf linkml:mixin . +biolink:id a owl:ObjectProperty . + biolink:Attribute a owl:Class ; rdfs:label "attribute" ; rdfs:subClassOf [ a owl:Restriction ; - owl:allValuesFrom biolink:QuantityValue ; - owl:onProperty biolink:has_quantitative_value ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass biolink:LabelType ; - owl:onProperty rdfs:label ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass biolink:NamedThing ; - owl:onProperty biolink:has_qualitative_value ], - [ a owl:Restriction ; owl:onClass biolink:OntologyClass ; owl:onProperty biolink:has_attribute_type ; owl:qualifiedCardinality 1 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; - owl:onClass biolink:IriType ; - owl:onProperty biolink:iri ], + owl:onClass biolink:NamedThing ; + owl:onProperty biolink:has_qualitative_value ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty biolink:source ], - biolink:Annotation, + owl:onClass biolink:LabelType ; + owl:onProperty rdfs:label ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:QuantityValue ; + owl:onProperty biolink:has_quantitative_value ], + biolink:NamedThing, biolink:OntologyClass ; skos:exactMatch SIO:000614 . @@ -7318,20 +7312,20 @@ biolink:ThingWithTaxon a owl:Class ; biolink:Agent a owl:Class ; rdfs:label "agent" ; rdfs:subClassOf [ a owl:Restriction ; + owl:allValuesFrom linkml:Uriorcurie ; + owl:onProperty biolink:affiliation ], + [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass biolink:LabelType ; owl:onProperty rdfs:label ], [ a owl:Restriction ; - owl:allValuesFrom linkml:Uriorcurie ; - owl:onProperty biolink:affiliation ], + owl:maxQualifiedCardinality 1 ; + owl:onClass linkml:String ; + owl:onProperty biolink:address ], [ a owl:Restriction ; owl:onClass linkml:String ; owl:onProperty biolink:id ; owl:qualifiedCardinality 1 ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty biolink:address ], biolink:AdministrativeEntity ; skos:altLabel "group" ; skos:exactMatch dct:Agent, @@ -7403,14 +7397,14 @@ biolink:InformationContentEntity a owl:Class ; owl:maxQualifiedCardinality 1 ; owl:onClass linkml:String ; owl:onProperty biolink:license ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:Date ; - owl:onProperty biolink:creation_date ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass linkml:String ; owl:onProperty biolink:format ], + [ a owl:Restriction ; + owl:maxQualifiedCardinality 1 ; + owl:onClass linkml:Date ; + owl:onProperty biolink:creation_date ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass linkml:String ; @@ -7500,30 +7494,30 @@ biolink:Publication a owl:Class ; owl:allValuesFrom linkml:String ; owl:onProperty biolink:keywords ], [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty biolink:summary ], + owl:allValuesFrom linkml:Uriorcurie ; + owl:onProperty biolink:mesh_terms ], [ a owl:Restriction ; owl:allValuesFrom linkml:String ; owl:onProperty biolink:pages ], [ a owl:Restriction ; - owl:onClass linkml:String ; - owl:onProperty biolink:id ; - owl:qualifiedCardinality 1 ], - [ a owl:Restriction ; - owl:allValuesFrom linkml:Uriorcurie ; - owl:onProperty biolink:mesh_terms ], + owl:allValuesFrom linkml:String ; + owl:onProperty biolink:authors ], [ a owl:Restriction ; + owl:maxQualifiedCardinality 1 ; owl:onClass linkml:String ; - owl:onProperty dct:type ; - owl:qualifiedCardinality 1 ], + owl:onProperty biolink:summary ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass biolink:LabelType ; owl:onProperty rdfs:label ], [ a owl:Restriction ; - owl:allValuesFrom linkml:String ; - owl:onProperty biolink:authors ], + owl:onClass linkml:String ; + owl:onProperty dct:type ; + owl:qualifiedCardinality 1 ], + [ a owl:Restriction ; + owl:onClass linkml:String ; + owl:onProperty biolink:id ; + owl:qualifiedCardinality 1 ], biolink:InformationContentEntity ; skos:exactMatch IAO:0000311 ; skos:narrowMatch STY:T170, @@ -7587,15 +7581,15 @@ biolink:affects a owl:ObjectProperty ; biolink:SequenceVariant a owl:Class ; rdfs:label "sequence variant" ; rdfs:subClassOf [ a owl:Restriction ; + owl:allValuesFrom biolink:Gene ; + owl:onProperty biolink:has_gene ], + [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass biolink:BiologicalSequence ; owl:onProperty biolink:has_biological_sequence ], [ a owl:Restriction ; owl:allValuesFrom biolink:OrganismTaxon ; owl:onProperty biolink:in_taxon ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:Gene ; - owl:onProperty biolink:has_gene ], [ a owl:Restriction ; owl:onClass linkml:String ; owl:onProperty biolink:id ; @@ -7666,16 +7660,9 @@ biolink:association_slot a owl:ObjectProperty ; biolink:ChemicalEntity a owl:Class ; rdfs:label "chemical entity" ; rdfs:subClassOf [ a owl:Restriction ; - owl:allValuesFrom biolink:ChemicalRole ; - owl:onProperty biolink:has_chemical_role ], - [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass linkml:String ; owl:onProperty biolink:max_tolerated_dose ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:Boolean ; - owl:onProperty biolink:is_toxic ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass biolink:ChemicalEntity ; @@ -7683,6 +7670,13 @@ biolink:ChemicalEntity a owl:Class ; [ a owl:Restriction ; owl:allValuesFrom biolink:DrugAvailabilityEnum ; owl:onProperty biolink:available_from ], + [ a owl:Restriction ; + owl:maxQualifiedCardinality 1 ; + owl:onClass linkml:Boolean ; + owl:onProperty biolink:is_toxic ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:ChemicalRole ; + owl:onProperty biolink:has_chemical_role ], biolink:ChemicalEntityOrGeneOrGeneProduct, biolink:ChemicalEntityOrProteinOrPolypeptide, biolink:ChemicalOrDrugOrTreatment, @@ -7714,22 +7708,36 @@ biolink:NucleicAcidEntity a owl:Class ; skos:narrowMatch STY:T086, STY:T114 . +biolink:OntologyClass a owl:Class ; + rdfs:label "ontology class" ; + rdfs:seeAlso "https://github.com/biolink/biolink-model/issues/486" ; + rdfs:subClassOf [ a owl:Restriction ; + owl:onClass linkml:String ; + owl:onProperty biolink:id ; + owl:qualifiedCardinality 1 ], + linkml:mixin ; + skos:exactMatch schema1:Class, + owl:Class ; + skos:note "Note that formally this is a metaclass. Instances of this class are instances in the graph, but can be the object of 'type' edges. For example, if we had a node in the graph representing a specific brain of a specific patient (e.g brain001), this could have a category of bl:Sample, and by typed more specifically with an ontology class UBERON:nnn, which has as category bl:AnatomicalEntity", + "This is modeled as a mixin. 'ontology class' should not be the primary type of a node in the KG. Instead you should use an informative bioloink category, such as AnatomicalEntity (for Uberon classes), ChemicalSubstance (for CHEBI or CHEMBL), etc" ; + linkml:examples "Example(value='UBERON:0000955', description=\"the class 'brain' from the Uberon anatomy ontology\")" . + biolink:Gene a owl:Class ; rdfs:label "gene" ; rdfs:subClassOf [ a owl:Restriction ; - owl:allValuesFrom biolink:LabelType ; - owl:onProperty biolink:synonym ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:OrganismTaxon ; - owl:onProperty biolink:in_taxon ], + owl:maxQualifiedCardinality 1 ; + owl:onClass biolink:BiologicalSequence ; + owl:onProperty biolink:has_biological_sequence ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass linkml:String ; owl:onProperty biolink:symbol ], [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass biolink:BiologicalSequence ; - owl:onProperty biolink:has_biological_sequence ], + owl:allValuesFrom biolink:OrganismTaxon ; + owl:onProperty biolink:in_taxon ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:LabelType ; + owl:onProperty biolink:synonym ], biolink:BiologicalEntity, biolink:ChemicalEntityOrGeneOrGeneProduct, biolink:GeneOrGeneProduct, @@ -7749,16 +7757,6 @@ biolink:Occurrent a owl:Class ; linkml:mixin ; skos:exactMatch . -biolink:OntologyClass a owl:Class ; - rdfs:label "ontology class" ; - rdfs:seeAlso "https://github.com/biolink/biolink-model/issues/486" ; - rdfs:subClassOf linkml:mixin ; - skos:exactMatch schema1:Class, - owl:Class ; - skos:note "Note that formally this is a metaclass. Instances of this class are instances in the graph, but can be the object of 'type' edges. For example, if we had a node in the graph representing a specific brain of a specific patient (e.g brain001), this could have a category of bl:Sample, and by typed more specifically with an ontology class UBERON:nnn, which has as category bl:AnatomicalEntity", - "This is modeled as a mixin. 'ontology class' should not be the primary type of a node in the KG. Instead you should use an informative bioloink category, such as AnatomicalEntity (for Uberon classes), ChemicalSubstance (for CHEBI or CHEMBL), etc" ; - linkml:examples "Example(value='UBERON:0000955', description=\"the class 'brain' from the Uberon anatomy ontology\")" . - biolink:GeneOrGeneProduct a owl:Class ; rdfs:label "gene or gene product" ; rdfs:subClassOf biolink:MacromolecularMachineMixin, @@ -7783,51 +7781,51 @@ biolink:related_to_at_instance_level a owl:ObjectProperty, biolink:Association a owl:Class ; rdfs:label "association" ; rdfs:subClassOf [ a owl:Restriction ; + owl:allValuesFrom biolink:CategoryType ; + owl:onProperty biolink:category ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:InformationResource ; + owl:onProperty biolink:knowledge_source ], + [ a owl:Restriction ; + owl:onClass biolink:NamedThing ; + owl:onProperty rdf:object ; + owl:qualifiedCardinality 1 ], + [ a owl:Restriction ; owl:onClass biolink:NamedThing ; owl:onProperty rdf:subject ; owl:qualifiedCardinality 1 ], [ a owl:Restriction ; owl:allValuesFrom biolink:InformationResource ; owl:onProperty biolink:aggregator_knowledge_source ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass biolink:InformationResource ; - owl:onProperty biolink:primary_knowledge_source ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:Publication ; - owl:onProperty biolink:publications ], [ a owl:Restriction ; owl:allValuesFrom biolink:OntologyClass ; owl:onProperty biolink:qualifiers ], + [ a owl:Restriction ; + owl:onClass biolink:PredicateType ; + owl:onProperty rdf:predicate ; + owl:qualifiedCardinality 1 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass linkml:String ; owl:onProperty rdf:type ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:Publication ; + owl:onProperty biolink:publications ], [ a owl:Restriction ; owl:allValuesFrom biolink:EvidenceType ; owl:onProperty biolink:has_evidence ], [ a owl:Restriction ; - owl:onClass biolink:NamedThing ; - owl:onProperty rdf:object ; - owl:qualifiedCardinality 1 ], + owl:maxQualifiedCardinality 1 ; + owl:onClass linkml:Boolean ; + owl:onProperty biolink:negated ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass biolink:InformationResource ; owl:onProperty biolink:original_knowledge_source ], - [ a owl:Restriction ; - owl:onClass biolink:PredicateType ; - owl:onProperty rdf:predicate ; - owl:qualifiedCardinality 1 ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:InformationResource ; - owl:onProperty biolink:knowledge_source ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:CategoryType ; - owl:onProperty biolink:category ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:Boolean ; - owl:onProperty biolink:negated ], + owl:onClass biolink:InformationResource ; + owl:onProperty biolink:primary_knowledge_source ], biolink:Entity ; skos:exactMatch OBAN:association, rdf:Statement, @@ -7840,15 +7838,15 @@ biolink:ChemicalEntityOrGeneOrGeneProduct a owl:Class ; biolink:NamedThing a owl:Class ; rdfs:label "named thing" ; - rdfs:subClassOf [ a owl:Class ; + rdfs:subClassOf [ a owl:Restriction ; + owl:allValuesFrom linkml:Uriorcurie ; + owl:onProperty biolink:xref ], + [ a owl:Class ; owl:intersectionOf ( [ a owl:Restriction ; owl:allValuesFrom biolink:CategoryType ; owl:onProperty biolink:category ] [ a owl:Restriction ; owl:onProperty biolink:category ; owl:someValuesFrom biolink:CategoryType ] ) ], - [ a owl:Restriction ; - owl:allValuesFrom linkml:Uriorcurie ; - owl:onProperty biolink:xref ], [ a owl:Restriction ; owl:allValuesFrom linkml:String ; owl:onProperty biolink:provided_by ], diff --git a/biolink-model.proto b/biolink-model.proto index 3b74199699..f4a1729ac9 100644 --- a/biolink-model.proto +++ b/biolink-model.proto @@ -1,5 +1,5 @@ // metamodel_version: 1.7.0 -// version: 2.3.1 +// version: 2.4.0 // 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. message Activity { @@ -143,12 +143,19 @@ message Association // 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. message Attribute { - optional name LabelType = 1 - hasAttributeType OntologyClass = 2 - repeated hasQuantitativeValue QuantityValue = 3 - optional hasQualitativeValue NamedThing = 4 - optional iri IriType = 5 - optional source String = 6 + id String = 1 + optional type String = 2 + optional description NarrativeText = 3 + repeated hasAttribute Attribute = 4 + repeated providedBy String = 5 + repeated xref Uriorcurie = 6 + repeated category CategoryType = 7 + optional name LabelType = 8 + hasAttributeType OntologyClass = 9 + repeated hasQuantitativeValue QuantityValue = 10 + optional hasQualitativeValue NamedThing = 11 + optional iri IriType = 12 + optional source String = 13 } message Behavior { @@ -249,12 +256,19 @@ message BiologicalProcessOrActivity } message BiologicalSex { - optional name LabelType = 1 - hasAttributeType OntologyClass = 2 - repeated hasQuantitativeValue QuantityValue = 3 - optional hasQualitativeValue NamedThing = 4 - optional iri IriType = 5 - optional source String = 6 + id String = 1 + optional type String = 2 + optional description NarrativeText = 3 + repeated hasAttribute Attribute = 4 + repeated providedBy String = 5 + repeated xref Uriorcurie = 6 + repeated category CategoryType = 7 + optional name LabelType = 8 + hasAttributeType OntologyClass = 9 + repeated hasQuantitativeValue QuantityValue = 10 + optional hasQualitativeValue NamedThing = 11 + optional iri IriType = 12 + optional source String = 13 } // An external biotic exposure is an intake of (sometimes pathological) biological organisms (including viruses). message BioticExposure @@ -491,12 +505,19 @@ message ChemicalMixture } message ChemicalRole { - optional name LabelType = 1 - hasAttributeType OntologyClass = 2 - repeated hasQuantitativeValue QuantityValue = 3 - optional hasQualitativeValue NamedThing = 4 - optional iri IriType = 5 - optional source String = 6 + id String = 1 + optional type String = 2 + optional description NarrativeText = 3 + repeated hasAttribute Attribute = 4 + repeated providedBy String = 5 + repeated xref Uriorcurie = 6 + repeated category CategoryType = 7 + optional name LabelType = 8 + hasAttributeType OntologyClass = 9 + repeated hasQuantitativeValue QuantityValue = 10 + optional hasQualitativeValue NamedThing = 11 + optional iri IriType = 12 + optional source String = 13 } // 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 @@ -624,22 +645,36 @@ message ChemicalToPathwayAssociation // Attributes relating to a clinical manifestation message ClinicalAttribute { - optional name LabelType = 1 - hasAttributeType OntologyClass = 2 - repeated hasQuantitativeValue QuantityValue = 3 - optional hasQualitativeValue NamedThing = 4 - optional iri IriType = 5 - optional source String = 6 + id String = 1 + optional type String = 2 + optional description NarrativeText = 3 + repeated hasAttribute Attribute = 4 + repeated providedBy String = 5 + repeated xref Uriorcurie = 6 + repeated category CategoryType = 7 + optional name LabelType = 8 + hasAttributeType OntologyClass = 9 + repeated hasQuantitativeValue QuantityValue = 10 + optional hasQualitativeValue NamedThing = 11 + optional iri IriType = 12 + optional source String = 13 } // The course a disease typically takes from its onset, progression in time, and eventual resolution or death of the affected individual message ClinicalCourse { - optional name LabelType = 1 - hasAttributeType OntologyClass = 2 - repeated hasQuantitativeValue QuantityValue = 3 - optional hasQualitativeValue NamedThing = 4 - optional iri IriType = 5 - optional source String = 6 + id String = 1 + optional type String = 2 + optional description NarrativeText = 3 + repeated hasAttribute Attribute = 4 + repeated providedBy String = 5 + repeated xref Uriorcurie = 6 + repeated category CategoryType = 7 + optional name LabelType = 8 + hasAttributeType OntologyClass = 9 + repeated hasQuantitativeValue QuantityValue = 10 + optional hasQualitativeValue NamedThing = 11 + optional iri IriType = 12 + optional source String = 13 } // Any entity or process that exists in the clinical domain and outside the biological realm. Diseases are placed under biological entities message ClinicalEntity @@ -686,22 +721,36 @@ message ClinicalIntervention // 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. message ClinicalMeasurement { - optional name LabelType = 1 - repeated hasQuantitativeValue QuantityValue = 2 - optional hasQualitativeValue NamedThing = 3 - optional iri IriType = 4 - optional source String = 5 - hasAttributeType OntologyClass = 6 + id String = 1 + optional type String = 2 + optional description NarrativeText = 3 + repeated hasAttribute Attribute = 4 + repeated providedBy String = 5 + repeated xref Uriorcurie = 6 + repeated category CategoryType = 7 + optional name LabelType = 8 + repeated hasQuantitativeValue QuantityValue = 9 + optional hasQualitativeValue NamedThing = 10 + optional iri IriType = 11 + optional source String = 12 + hasAttributeType OntologyClass = 13 } // Used to characterize and specify the phenotypic abnormalities defined in the phenotypic abnormality sub-ontology, with respect to severity, laterality, and other aspects message ClinicalModifier { - optional name LabelType = 1 - hasAttributeType OntologyClass = 2 - repeated hasQuantitativeValue QuantityValue = 3 - optional hasQualitativeValue NamedThing = 4 - optional iri IriType = 5 - optional source String = 6 + id String = 1 + optional type String = 2 + optional description NarrativeText = 3 + repeated hasAttribute Attribute = 4 + repeated providedBy String = 5 + repeated xref Uriorcurie = 6 + repeated category CategoryType = 7 + optional name LabelType = 8 + hasAttributeType OntologyClass = 9 + repeated hasQuantitativeValue QuantityValue = 10 + optional hasQualitativeValue NamedThing = 11 + optional iri IriType = 12 + optional source String = 13 } message ClinicalTrial { @@ -1688,6 +1737,7 @@ message GenomicBackgroundExposure repeated hasGeneOrGeneProduct Gene = 2 repeated inTaxon OrganismTaxon = 3 optional hasBiologicalSequence BiologicalSequence = 4 + id String = 5 } // 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. message GenomicSequenceLocalization @@ -1883,12 +1933,19 @@ message GenotypeToVariantAssociation // An attribute corresponding to the genotypic sex of the individual, based upon genotypic composition of sex chromosomes. message GenotypicSex { - optional name LabelType = 1 - hasAttributeType OntologyClass = 2 - repeated hasQuantitativeValue QuantityValue = 3 - optional hasQualitativeValue NamedThing = 4 - optional iri IriType = 5 - optional source String = 6 + id String = 1 + optional type String = 2 + optional description NarrativeText = 3 + repeated hasAttribute Attribute = 4 + repeated providedBy String = 5 + repeated xref Uriorcurie = 6 + repeated category CategoryType = 7 + optional name LabelType = 8 + hasAttributeType OntologyClass = 9 + repeated hasQuantitativeValue QuantityValue = 10 + optional hasQualitativeValue NamedThing = 11 + optional iri IriType = 12 + optional source String = 13 } // A geographic exposure is a factor relating to geographic proximity to some impactful entity. message GeographicExposure @@ -2030,12 +2087,19 @@ message InformationResource // 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. message Inheritance { - optional name LabelType = 1 - hasAttributeType OntologyClass = 2 - repeated hasQuantitativeValue QuantityValue = 3 - optional hasQualitativeValue NamedThing = 4 - optional iri IriType = 5 - optional source String = 6 + id String = 1 + optional type String = 2 + optional description NarrativeText = 3 + repeated hasAttribute Attribute = 4 + repeated providedBy String = 5 + repeated xref Uriorcurie = 6 + repeated category CategoryType = 7 + optional name LabelType = 8 + hasAttributeType OntologyClass = 9 + repeated hasQuantitativeValue QuantityValue = 10 + optional hasQualitativeValue NamedThing = 11 + optional iri IriType = 12 + optional source String = 13 } // A stage of development or growth of an organism, including post-natal adult stages message LifeStage @@ -2438,22 +2502,36 @@ message Nutrient // The age group in which (disease) symptom manifestations appear message Onset { - optional name LabelType = 1 - hasAttributeType OntologyClass = 2 - repeated hasQuantitativeValue QuantityValue = 3 - optional hasQualitativeValue NamedThing = 4 - optional iri IriType = 5 - optional source String = 6 + id String = 1 + optional type String = 2 + optional description NarrativeText = 3 + repeated hasAttribute Attribute = 4 + repeated providedBy String = 5 + repeated xref Uriorcurie = 6 + repeated category CategoryType = 7 + optional name LabelType = 8 + hasAttributeType OntologyClass = 9 + repeated hasQuantitativeValue QuantityValue = 10 + optional hasQualitativeValue NamedThing = 11 + optional iri IriType = 12 + optional source String = 13 } // describes a characteristic of an organismal entity. message OrganismAttribute { - optional name LabelType = 1 - hasAttributeType OntologyClass = 2 - repeated hasQuantitativeValue QuantityValue = 3 - optional hasQualitativeValue NamedThing = 4 - optional iri IriType = 5 - optional source String = 6 + id String = 1 + optional type String = 2 + optional description NarrativeText = 3 + repeated hasAttribute Attribute = 4 + repeated providedBy String = 5 + repeated xref Uriorcurie = 6 + repeated category CategoryType = 7 + optional name LabelType = 8 + hasAttributeType OntologyClass = 9 + repeated hasQuantitativeValue QuantityValue = 10 + optional hasQualitativeValue NamedThing = 11 + optional iri IriType = 12 + optional source String = 13 } // A classification of a set of organisms. Example instances: NCBITaxon:9606 (Homo sapiens), NCBITaxon:2 (Bacteria). Can also be used to represent strains or subspecies. message OrganismTaxon @@ -2701,22 +2779,36 @@ message PhenotypicFeature // A property of a phenotype message PhenotypicQuality { - optional name LabelType = 1 - hasAttributeType OntologyClass = 2 - repeated hasQuantitativeValue QuantityValue = 3 - optional hasQualitativeValue NamedThing = 4 - optional iri IriType = 5 - optional source String = 6 + id String = 1 + optional type String = 2 + optional description NarrativeText = 3 + repeated hasAttribute Attribute = 4 + repeated providedBy String = 5 + repeated xref Uriorcurie = 6 + repeated category CategoryType = 7 + optional name LabelType = 8 + hasAttributeType OntologyClass = 9 + repeated hasQuantitativeValue QuantityValue = 10 + optional hasQualitativeValue NamedThing = 11 + optional iri IriType = 12 + optional source String = 13 } // An attribute corresponding to the phenotypic sex of the individual, based upon the reproductive organs present. message PhenotypicSex { - optional name LabelType = 1 - hasAttributeType OntologyClass = 2 - repeated hasQuantitativeValue QuantityValue = 3 - optional hasQualitativeValue NamedThing = 4 - optional iri IriType = 5 - optional source String = 6 + id String = 1 + optional type String = 2 + optional description NarrativeText = 3 + repeated hasAttribute Attribute = 4 + repeated providedBy String = 5 + repeated xref Uriorcurie = 6 + repeated category CategoryType = 7 + optional name LabelType = 8 + hasAttributeType OntologyClass = 9 + repeated hasQuantitativeValue QuantityValue = 10 + optional hasQualitativeValue NamedThing = 11 + optional iri IriType = 12 + optional source String = 13 } // An entity that has material reality (a.k.a. physical essence). message PhysicalEntity @@ -3008,6 +3100,11 @@ message ReagentTargetedGene repeated inTaxon OrganismTaxon = 11 optional hasBiologicalSequence BiologicalSequence = 12 } +// An OWL property used as an edge label +message RelationshipType + { + id String = 1 + } message RNAProduct { id String = 1 @@ -3145,12 +3242,19 @@ message Serial // describes the severity of a phenotypic feature or disease message SeverityValue { - optional name LabelType = 1 - hasAttributeType OntologyClass = 2 - repeated hasQuantitativeValue QuantityValue = 3 - optional hasQualitativeValue NamedThing = 4 - optional iri IriType = 5 - optional source String = 6 + id String = 1 + optional type String = 2 + optional description NarrativeText = 3 + repeated hasAttribute Attribute = 4 + repeated providedBy String = 5 + repeated xref Uriorcurie = 6 + repeated category CategoryType = 7 + optional name LabelType = 8 + hasAttributeType OntologyClass = 9 + repeated hasQuantitativeValue QuantityValue = 10 + optional hasQualitativeValue NamedThing = 11 + optional iri IriType = 12 + optional source String = 13 } // A small RNA molecule that is the product of a longer exogenous or endogenous dsRNA, which is either a bimolecular duplex or very long hairpin, processed (via the Dicer pathway) such that numerous siRNAs accumulate from both strands of the dsRNA. SRNAs trigger the cleavage of their target molecules. message SiRNA @@ -3215,12 +3319,19 @@ message Snv // Attributes relating to a socioeconomic manifestation message SocioeconomicAttribute { - optional name LabelType = 1 - hasAttributeType OntologyClass = 2 - repeated hasQuantitativeValue QuantityValue = 3 - optional hasQualitativeValue NamedThing = 4 - optional iri IriType = 5 - optional source String = 6 + id String = 1 + optional type String = 2 + optional description NarrativeText = 3 + repeated hasAttribute Attribute = 4 + repeated providedBy String = 5 + repeated xref Uriorcurie = 6 + repeated category CategoryType = 7 + optional name LabelType = 8 + hasAttributeType OntologyClass = 9 + repeated hasQuantitativeValue QuantityValue = 10 + optional hasQualitativeValue NamedThing = 11 + optional iri IriType = 12 + optional source String = 13 } // A socioeconomic exposure is a factor relating to social and financial status of an affected individual (e.g. poverty). message SocioeconomicExposure @@ -3265,6 +3376,11 @@ message TaxonToTaxonAssociation subject OrganismTaxon = 18 object OrganismTaxon = 19 } +// A descriptor for the rank within a taxonomic classification. Example instance: TAXRANK:0000017 (kingdom) +message TaxonomicRank + { + id String = 1 + } // An RNA synthesized on a DNA or RNA template by an RNA polymerase. message Transcript { @@ -3502,11 +3618,18 @@ message Vitamin } message Zygosity { - optional name LabelType = 1 - hasAttributeType OntologyClass = 2 - repeated hasQuantitativeValue QuantityValue = 3 - optional hasQualitativeValue NamedThing = 4 - optional iri IriType = 5 - optional source String = 6 + id String = 1 + optional type String = 2 + optional description NarrativeText = 3 + repeated hasAttribute Attribute = 4 + repeated providedBy String = 5 + repeated xref Uriorcurie = 6 + repeated category CategoryType = 7 + optional name LabelType = 8 + hasAttributeType OntologyClass = 9 + repeated hasQuantitativeValue QuantityValue = 10 + optional hasQualitativeValue NamedThing = 11 + optional iri IriType = 12 + optional source String = 13 } diff --git a/biolink-model.shex b/biolink-model.shex index 1fe8d33e30..262bbfe6a0 100644 --- a/biolink-model.shex +++ b/biolink-model.shex @@ -1,5 +1,5 @@ # metamodel_version: 1.7.0 -# version: 2.3.1 +# version: 2.4.0 BASE PREFIX dcterms: PREFIX rdf: @@ -156,15 +156,13 @@ linkml:Nodeidentifier NONLITERAL } ( - @ OR @ + { + ( $ rdf:type . * ; + rdf:type [ ] ? + ) + } OR @ ) - { - ( $ rdf:type . * ; - rdf:type [ ] ? - ) -} -
CLOSED { ( $ ( & ; rdf:type [ ] ? ; @@ -219,18 +217,16 @@ linkml:Nodeidentifier NONLITERAL ( CLOSED { - ( $ ( & ; - rdf:type [ ] ? ; + ( $ ( & ; + rdf:type [ ] ? ; & ; rdf:type [ ] ? ; rdfs:label @ ? ; @ ; @ * ; - @ ? ; - @ ? ; - @linkml:String ? + @ ? ) ; - rdf:type [ ] ? + rdf:type [ ] ) } OR @ OR @ OR @ OR @ OR @ OR @ OR @ @@ -339,7 +335,7 @@ linkml:Nodeidentifier NONLITERAL ( $ ( & ; rdf:type [ ] ? ) ; - rdf:type [ ] ? + rdf:type [ ] ) } OR @ OR @ ) @@ -545,7 +541,7 @@ linkml:Nodeidentifier NONLITERAL ( $ ( & ; rdf:type [ ] ? ) ; - rdf:type [ ] ? + rdf:type [ ] ) } @@ -630,7 +626,7 @@ linkml:Nodeidentifier NONLITERAL ( $ ( & ; rdf:type [ ] ? ) ; - rdf:type [ ] ? + rdf:type [ ] ) } OR @ OR @ OR @ ) @@ -640,7 +636,7 @@ linkml:Nodeidentifier NONLITERAL ( $ ( & ; rdf:type [ ] ? ) ; - rdf:type [ ] ? + rdf:type [ ] ) } OR @ ) @@ -679,7 +675,7 @@ linkml:Nodeidentifier NONLITERAL rdf:type [ ] ? ; @ ) ; - rdf:type [ ] ? + rdf:type [ ] ) } @@ -687,7 +683,7 @@ linkml:Nodeidentifier NONLITERAL ( $ ( & ; rdf:type [ ] ? ) ; - rdf:type [ ] ? + rdf:type [ ] ) } @@ -1287,10 +1283,8 @@ linkml:Nodeidentifier NONLITERAL ) } - { - ( $ ( & ; - rdf:type [ ] ? - ) ; + CLOSED { + ( $ rdf:type . * ; rdf:type [ ] ? ) } @@ -1486,7 +1480,7 @@ linkml:Nodeidentifier NONLITERAL @ * ; @ ? ) ; - rdf:type [ ] ? + rdf:type [ ] ) } @@ -1626,7 +1620,7 @@ linkml:Nodeidentifier NONLITERAL ( $ ( & ; rdf:type [ ] ? ) ; - rdf:type [ ] ? + rdf:type [ ] ) } @@ -1754,7 +1748,7 @@ linkml:Nodeidentifier NONLITERAL ( $ ( & ; rdf:type [ ] ? ) ; - rdf:type [ ] ? + rdf:type [ ] ) } @@ -1973,9 +1967,9 @@ linkml:Nodeidentifier NONLITERAL ) ; rdf:type [ ] ) - } OR @ OR @ OR @ OR @ OR @ OR @ OR - @ OR @ OR @ OR @ OR @ OR @ OR - @ OR @ + } OR @ OR @ OR @ OR @ OR @ OR @ OR + @ OR @ OR @ OR @ OR @ OR @ OR + @ OR @ OR @ ) ( @@ -2038,17 +2032,17 @@ linkml:Nodeidentifier NONLITERAL ( $ ( & ; rdf:type [ ] ? ) ; - rdf:type [ ] ? + rdf:type [ ] ) } ( - @ OR @ OR @ OR @ + @ OR @ ) { ( $ rdf:type . * ; - rdf:type [ ] ? + rdf:type [ ] ) } @@ -2057,7 +2051,7 @@ linkml:Nodeidentifier NONLITERAL ( $ ( & ; rdf:type [ ] ? ) ; - rdf:type [ ] ? + rdf:type [ ] ) } OR @ OR @ ) @@ -2299,7 +2293,7 @@ linkml:Nodeidentifier NONLITERAL ( $ ( & ; rdf:type [ ] ? ) ; - rdf:type [ ] ? + rdf:type [ ] ) } @@ -2307,7 +2301,7 @@ linkml:Nodeidentifier NONLITERAL ( $ ( & ; rdf:type [ ] ? ) ; - rdf:type [ ] ? + rdf:type [ ] ) } @@ -2551,7 +2545,7 @@ linkml:Nodeidentifier NONLITERAL ( $ ( & ; rdf:type [ ] ? ) ; - rdf:type [ ] ? + rdf:type [ ] ) } @@ -2653,7 +2647,7 @@ linkml:Nodeidentifier NONLITERAL ( $ ( & ; rdf:type [ ] ? ) ; - rdf:type [ ] ? + rdf:type [ ] ) } @@ -2685,7 +2679,7 @@ linkml:Nodeidentifier NONLITERAL ( $ ( & ; rdf:type [ ] ? ) ; - rdf:type [ ] ? + rdf:type [ ] ) } @@ -2747,7 +2741,7 @@ linkml:Nodeidentifier NONLITERAL ( $ ( & ; rdf:type [ ] ? ) ; - rdf:type [ ] ? + rdf:type [ ] ) } @@ -2795,10 +2789,8 @@ linkml:Nodeidentifier NONLITERAL ) } - { - ( $ ( & ; - rdf:type [ ] ? - ) ; + CLOSED { + ( $ rdf:type . * ; rdf:type [ ] ? ) } @@ -2921,7 +2913,7 @@ linkml:Nodeidentifier NONLITERAL ( $ ( & ; rdf:type [ ] ? ) ; - rdf:type [ ] ? + rdf:type [ ] ) } diff --git a/biolink-model.shexj b/biolink-model.shexj index bf8059e104..750035b9a8 100644 --- a/biolink-model.shexj +++ b/biolink-model.shexj @@ -1,5 +1,5 @@ # metamodel_version: 1.7.0 -# version: 2.3.1 +# version: 2.4.0 { "type": "Schema", "@context": [ @@ -603,38 +603,36 @@ "type": "ShapeOr", "id": "https://w3id.org/biolink/vocab/Annotation", "shapeExprs": [ - "https://w3id.org/biolink/vocab/Attribute", + { + "type": "Shape", + "closed": false, + "expression": { + "type": "EachOf", + "expressions": [ + { + "type": "TripleConstraint", + "id": "https://w3id.org/biolink/vocab/Annotation_tes", + "predicate": "http://www.w3.org/1999/02/22-rdf-syntax-ns#type", + "min": 0, + "max": -1 + }, + { + "type": "TripleConstraint", + "predicate": "http://www.w3.org/1999/02/22-rdf-syntax-ns#type", + "valueExpr": { + "type": "NodeConstraint", + "values": [ + "https://w3id.org/biolink/vocab/Annotation" + ] + }, + "min": 0 + } + ] + } + }, "https://w3id.org/biolink/vocab/QuantityValue" ] }, - { - "type": "Shape", - "id": "https://w3id.org/biolink/vocab/Annotation_struct", - "closed": false, - "expression": { - "type": "EachOf", - "expressions": [ - { - "type": "TripleConstraint", - "id": "https://w3id.org/biolink/vocab/Annotation_tes", - "predicate": "http://www.w3.org/1999/02/22-rdf-syntax-ns#type", - "min": 0, - "max": -1 - }, - { - "type": "TripleConstraint", - "predicate": "http://www.w3.org/1999/02/22-rdf-syntax-ns#type", - "valueExpr": { - "type": "NodeConstraint", - "values": [ - "https://w3id.org/biolink/vocab/Annotation" - ] - }, - "min": 0 - } - ] - } - }, { "type": "Shape", "id": "https://w3id.org/biolink/vocab/Article", @@ -897,14 +895,14 @@ "type": "EachOf", "id": "https://w3id.org/biolink/vocab/Attribute_tes", "expressions": [ - "https://w3id.org/biolink/vocab/Annotation_tes", + "https://w3id.org/biolink/vocab/NamedThing_tes", { "type": "TripleConstraint", "predicate": "http://www.w3.org/1999/02/22-rdf-syntax-ns#type", "valueExpr": { "type": "NodeConstraint", "values": [ - "https://w3id.org/biolink/vocab/Annotation" + "https://w3id.org/biolink/vocab/NamedThing" ] }, "min": 0 @@ -948,20 +946,6 @@ "valueExpr": "https://w3id.org/biolink/vocab/NamedThing", "min": 0, "max": 1 - }, - { - "type": "TripleConstraint", - "predicate": "https://w3id.org/biolink/vocab/iri", - "valueExpr": "https://w3id.org/biolink/vocab/IriType", - "min": 0, - "max": 1 - }, - { - "type": "TripleConstraint", - "predicate": "https://w3id.org/biolink/vocab/source", - "valueExpr": "https://w3id.org/linkml/String", - "min": 0, - "max": 1 } ] }, @@ -974,7 +958,7 @@ "https://w3id.org/biolink/vocab/Attribute" ] }, - "min": 0 + "min": 1 } ] } @@ -1527,7 +1511,7 @@ "https://w3id.org/biolink/vocab/BiologicalSex" ] }, - "min": 0 + "min": 1 } ] } @@ -2582,7 +2566,7 @@ "https://w3id.org/biolink/vocab/ChemicalRole" ] }, - "min": 0 + "min": 1 } ] } @@ -3023,7 +3007,7 @@ "https://w3id.org/biolink/vocab/ClinicalAttribute" ] }, - "min": 0 + "min": 1 } ] } @@ -3070,7 +3054,7 @@ "https://w3id.org/biolink/vocab/ClinicalCourse" ] }, - "min": 0 + "min": 1 } ] } @@ -3256,7 +3240,7 @@ "https://w3id.org/biolink/vocab/ClinicalMeasurement" ] }, - "min": 0 + "min": 1 } ] } @@ -3295,7 +3279,7 @@ "https://w3id.org/biolink/vocab/ClinicalModifier" ] }, - "min": 0 + "min": 1 } ] } @@ -6360,27 +6344,16 @@ { "type": "Shape", "id": "https://w3id.org/biolink/vocab/GeneOntologyClass", - "closed": false, + "closed": true, "expression": { "type": "EachOf", "expressions": [ { - "type": "EachOf", + "type": "TripleConstraint", "id": "https://w3id.org/biolink/vocab/GeneOntologyClass_tes", - "expressions": [ - "https://w3id.org/biolink/vocab/OntologyClass_tes", - { - "type": "TripleConstraint", - "predicate": "http://www.w3.org/1999/02/22-rdf-syntax-ns#type", - "valueExpr": { - "type": "NodeConstraint", - "values": [ - "https://w3id.org/biolink/vocab/OntologyClass" - ] - }, - "min": 0 - } - ] + "predicate": "http://www.w3.org/1999/02/22-rdf-syntax-ns#type", + "min": 0, + "max": -1 }, { "type": "TripleConstraint", @@ -7433,7 +7406,7 @@ "https://w3id.org/biolink/vocab/GenomicBackgroundExposure" ] }, - "min": 0 + "min": 1 } ] } @@ -8204,7 +8177,7 @@ "https://w3id.org/biolink/vocab/GenotypicSex" ] }, - "min": 0 + "min": 1 } ] } @@ -8849,7 +8822,7 @@ "https://w3id.org/biolink/vocab/Inheritance" ] }, - "min": 0 + "min": 1 } ] } @@ -9950,6 +9923,7 @@ }, "https://w3id.org/biolink/vocab/Activity", "https://w3id.org/biolink/vocab/AdministrativeEntity", + "https://w3id.org/biolink/vocab/Attribute", "https://w3id.org/biolink/vocab/BiologicalEntity", "https://w3id.org/biolink/vocab/ChemicalEntity", "https://w3id.org/biolink/vocab/ClinicalEntity", @@ -10271,7 +10245,7 @@ "https://w3id.org/biolink/vocab/Onset" ] }, - "min": 0 + "min": 1 } ] } @@ -10280,10 +10254,8 @@ "type": "ShapeOr", "id": "https://w3id.org/biolink/vocab/OntologyClass", "shapeExprs": [ - "https://w3id.org/biolink/vocab/GeneOntologyClass", "https://w3id.org/biolink/vocab/RelationshipType", - "https://w3id.org/biolink/vocab/TaxonomicRank", - "https://w3id.org/biolink/vocab/UnclassifiedOntologyClass" + "https://w3id.org/biolink/vocab/TaxonomicRank" ] }, { @@ -10309,7 +10281,7 @@ "https://w3id.org/biolink/vocab/OntologyClass" ] }, - "min": 0 + "min": 1 } ] } @@ -10351,7 +10323,7 @@ "https://w3id.org/biolink/vocab/OrganismAttribute" ] }, - "min": 0 + "min": 1 } ] } @@ -11576,7 +11548,7 @@ "https://w3id.org/biolink/vocab/PhenotypicQuality" ] }, - "min": 0 + "min": 1 } ] } @@ -11615,7 +11587,7 @@ "https://w3id.org/biolink/vocab/PhenotypicSex" ] }, - "min": 0 + "min": 1 } ] } @@ -12848,7 +12820,7 @@ "https://w3id.org/biolink/vocab/RelationshipType" ] }, - "min": 0 + "min": 1 } ] } @@ -13370,7 +13342,7 @@ "https://w3id.org/biolink/vocab/SeverityValue" ] }, - "min": 0 + "min": 1 } ] } @@ -13526,7 +13498,7 @@ "https://w3id.org/biolink/vocab/SocioeconomicAttribute" ] }, - "min": 0 + "min": 1 } ] } @@ -13828,7 +13800,7 @@ "https://w3id.org/biolink/vocab/TaxonomicRank" ] }, - "min": 0 + "min": 1 } ] } @@ -14060,27 +14032,16 @@ { "type": "Shape", "id": "https://w3id.org/biolink/vocab/UnclassifiedOntologyClass", - "closed": false, + "closed": true, "expression": { "type": "EachOf", "expressions": [ { - "type": "EachOf", + "type": "TripleConstraint", "id": "https://w3id.org/biolink/vocab/UnclassifiedOntologyClass_tes", - "expressions": [ - "https://w3id.org/biolink/vocab/OntologyClass_tes", - { - "type": "TripleConstraint", - "predicate": "http://www.w3.org/1999/02/22-rdf-syntax-ns#type", - "valueExpr": { - "type": "NodeConstraint", - "values": [ - "https://w3id.org/biolink/vocab/OntologyClass" - ] - }, - "min": 0 - } - ] + "predicate": "http://www.w3.org/1999/02/22-rdf-syntax-ns#type", + "min": 0, + "max": -1 }, { "type": "TripleConstraint", @@ -14758,7 +14719,7 @@ "https://w3id.org/biolink/vocab/Zygosity" ] }, - "min": 0 + "min": 1 } ] } diff --git a/biolink-model.ttl b/biolink-model.ttl index 3a509d2c6c..ede2661ad1 100644 --- a/biolink-model.ttl +++ b/biolink-model.ttl @@ -17,7 +17,7 @@ a linkml:SchemaDefinition ; dcterms:license "https://creativecommons.org/publicdomain/zero/1.0/" ; - pav:version "2.3.1" ; + pav:version "2.4.0" ; skos:definition "Entity and association taxonomy and datamodel for life-sciences data" ; linkml:classes , , @@ -307,252 +307,254 @@ , , ; - linkml:generation_date "2022-05-23T16:31:39"^^xsd:dateTime ; + linkml:generation_date "2022-05-23T22:58:04"^^xsd:dateTime ; linkml:id ; linkml:imports linkml:types ; linkml:metamodel_version "1.7.0" ; - linkml:prefixes [ linkml:prefix_prefix "dcat" ; - linkml:prefix_reference dcat: ], - [ linkml:prefix_prefix "NBO-PROPERTY" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "CAID" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "PHAROS" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "pav" ; - linkml:prefix_reference pav: ], - [ linkml:prefix_prefix "metacyc.reaction" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "EDAM-DATA" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "PathWhiz" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "KEGG.PATHWAY" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "SEED.REACTION" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "NCIT-OBO" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "qud" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "DOID-PROPERTY" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "doi" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "HANCESTRO" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "foodb.compound" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "NDDF" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "LOINC" ; - linkml:prefix_reference ], + linkml:prefixes [ linkml:prefix_prefix "PANTHER.FAMILY" ; + linkml:prefix_reference ], [ linkml:prefix_prefix "COG" ; linkml:prefix_reference ], - [ linkml:prefix_prefix "medgen" ; - linkml:prefix_reference ], + [ linkml:prefix_prefix "CTD.GENE" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "ScopusID" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "WIKIDATA_PROPERTY" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "VMC" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "GAMMA" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "XPO" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "gff3" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "UO-PROPERTY" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "NCIT-OBO" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "REPODB" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "ResearchID" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "METANETX.REACTION" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "KEGG.RCLASS" ; + linkml:prefix_reference ], [ linkml:prefix_prefix "GOP" ; linkml:prefix_reference ], - [ linkml:prefix_prefix "ICD10" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "GSID" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "STY" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "PANTHER.FAMILY" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "ExO" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "foaf" ; - linkml:prefix_reference foaf: ], - [ linkml:prefix_prefix "CLINVAR" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "interpro" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "DrugCentral" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "CPT" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "alliancegenome" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "PomBase" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "prov" ; - linkml:prefix_reference prov: ], - [ linkml:prefix_prefix "WIKIDATA" ; - linkml:prefix_reference ], + [ linkml:prefix_prefix "KEGG.PATHWAY" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "GTEx" ; + linkml:prefix_reference ], [ linkml:prefix_prefix "CTD.CHEMICAL" ; linkml:prefix_reference ], - [ linkml:prefix_prefix "HCPCS" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "fabio" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "RO" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "gpi" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "mirbase" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "UBERON_NONAMESPACE" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "ORPHA" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "isni" ; - linkml:prefix_reference ], + [ linkml:prefix_prefix "MI" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "interpro" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "bioschemas" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "RXCUI" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "NBO-PROPERTY" ; + linkml:prefix_reference ], [ linkml:prefix_prefix "WBbt" ; linkml:prefix_reference ], - [ linkml:prefix_prefix "COAR_RESOURCE" ; - linkml:prefix_reference ], + [ linkml:prefix_prefix "dcid" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "CPT" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "WBls" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "issn" ; + linkml:prefix_reference ], [ linkml:prefix_prefix "EDAM-TOPIC" ; linkml:prefix_reference ], + [ linkml:prefix_prefix "PHAROS" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "metacyc.reaction" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "CTD.DISEASE" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "ChemBank" ; + linkml:prefix_reference ], [ linkml:prefix_prefix "dct" ; linkml:prefix_reference dcterms: ], - [ linkml:prefix_prefix "ICD9" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "MESH" ; - linkml:prefix_reference ], + [ linkml:prefix_prefix "HCPCS" ; + linkml:prefix_reference ], [ linkml:prefix_prefix "DGIdb" ; linkml:prefix_reference ], - [ linkml:prefix_prefix "MSigDB" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "EFO" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "oboformat" ; - linkml:prefix_reference OIO: ], - [ linkml:prefix_prefix "CTD.GENE" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "INO" ; - linkml:prefix_reference ], + [ linkml:prefix_prefix "isbn" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "FYPO" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "AspGD" ; + linkml:prefix_reference ], [ linkml:prefix_prefix "CTD" ; linkml:prefix_reference ], - [ linkml:prefix_prefix "ECTO" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "REPODB" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "SIO" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "XPO" ; - linkml:prefix_reference ], + [ linkml:prefix_prefix "WIKIDATA" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "NCBIGene" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "prov" ; + linkml:prefix_reference prov: ], + [ linkml:prefix_prefix "MAXO" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "DrugCentral" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "RXNORM" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "CHEMBL.MECHANISM" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "SEED.REACTION" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "SNOMEDCT" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "schema" ; + linkml:prefix_reference schema1: ], + [ linkml:prefix_prefix "foodb.compound" ; + linkml:prefix_reference ], [ linkml:prefix_prefix "HsapDv" ; linkml:prefix_reference ], - [ linkml:prefix_prefix "SEMMEDDB" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "isbn" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "wgs" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "Xenbase" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "os" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "MmusDv" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "GOREL" ; - linkml:prefix_reference ], [ linkml:prefix_prefix "EDAM-FORMAT" ; linkml:prefix_reference ], - [ linkml:prefix_prefix "ResearchID" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "GTOPDB" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "GTEx" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "CID" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "MI" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "RXNORM" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "FYPO" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "CTD.DISEASE" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "ORCID" ; - linkml:prefix_reference ], + [ linkml:prefix_prefix "foodb.food" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "os" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "PathWhiz" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "PomBase" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "SIO" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "fabio" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "KEGG.ENZYME" ; + linkml:prefix_reference ], [ linkml:prefix_prefix "KEGG.DGROUP" ; linkml:prefix_reference ], + [ linkml:prefix_prefix "FYECO" ; + linkml:prefix_reference ], [ linkml:prefix_prefix "UMLSSG" ; linkml:prefix_reference ], - [ linkml:prefix_prefix "UO-PROPERTY" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "KEGG.RCLASS" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "ChemBank" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "OMIM.PS" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "CHEMBL.MECHANISM" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "AspGD" ; - linkml:prefix_reference ], + [ linkml:prefix_prefix "EDAM-OPERATION" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "GSID" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "CHADO" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "LOINC" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "linkml" ; + linkml:prefix_reference linkml: ], + [ linkml:prefix_prefix "HANCESTRO" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "COAR_RESOURCE" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "UBERGRAPH" ; + linkml:prefix_reference ], [ linkml:prefix_prefix "mmmp.biomaps" ; linkml:prefix_reference ], + [ linkml:prefix_prefix "ECTO" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "foaf" ; + linkml:prefix_reference foaf: ], + [ linkml:prefix_prefix "doi" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "ExO" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "isni" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "Xenbase" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "EFO" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "dcat" ; + linkml:prefix_reference dcat: ], + [ linkml:prefix_prefix "oboformat" ; + linkml:prefix_reference OIO: ], + [ linkml:prefix_prefix "OBOREL" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "medgen" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "CAID" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "KEGG.BRITE" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "UBERON_NONAMESPACE" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "ICD10" ; + linkml:prefix_reference ], [ linkml:prefix_prefix "UBERON_CORE" ; linkml:prefix_reference ], - [ linkml:prefix_prefix "bioschemas" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "GAMMA" ; - linkml:prefix_reference ], [ linkml:prefix_prefix "apollo" ; linkml:prefix_reference ], - [ linkml:prefix_prefix "NLMID" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "schema" ; - linkml:prefix_reference schema1: ], - [ linkml:prefix_prefix "RXCUI" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "WBVocab" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "issn" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "dcid" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "gff3" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "KEGG.BRITE" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "METANETX.REACTION" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "CHADO" ; - linkml:prefix_reference ], + [ linkml:prefix_prefix "mirbase" ; + linkml:prefix_reference ], [ linkml:prefix_prefix "VANDF" ; linkml:prefix_reference ], - [ linkml:prefix_prefix "ScopusID" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "NCBIGene" ; - linkml:prefix_reference ], + [ linkml:prefix_prefix "ORCID" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "ORPHA" ; + linkml:prefix_reference ], [ linkml:prefix_prefix "KEGG.GENE" ; linkml:prefix_reference ], - [ linkml:prefix_prefix "EDAM-OPERATION" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "UBERGRAPH" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "SNOMED" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "WIKIDATA_PROPERTY" ; - linkml:prefix_reference ], + [ linkml:prefix_prefix "GTOPDB" ; + linkml:prefix_reference ], [ linkml:prefix_prefix "OBAN" ; linkml:prefix_reference ], - [ linkml:prefix_prefix "MAXO" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "WBls" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "FYECO" ; - linkml:prefix_reference ], + [ linkml:prefix_prefix "MSigDB" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "GOREL" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "NLMID" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "OMIM.PS" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "EDAM-DATA" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "ICD9" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "CID" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "RO" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "wgs" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "STY" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "SNOMED" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "pav" ; + linkml:prefix_reference pav: ], + [ linkml:prefix_prefix "CLINVAR" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "INO" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "gpi" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "WBVocab" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "NDDF" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "qud" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "DOID-PROPERTY" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "alliancegenome" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "MESH" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "SEMMEDDB" ; + linkml:prefix_reference ], [ linkml:prefix_prefix "gtpo" ; linkml:prefix_reference ], - [ linkml:prefix_prefix "SNOMEDCT" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "KEGG.ENZYME" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "VMC" ; - linkml:prefix_reference ], + [ linkml:prefix_prefix "MmusDv" ; + linkml:prefix_reference ], [ linkml:prefix_prefix "biolink" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "OBOREL" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "linkml" ; - linkml:prefix_reference linkml: ] ; + linkml:prefix_reference ] ; linkml:slots , , , @@ -1201,8 +1203,8 @@ , ; linkml:source_file "biolink-model.yaml" ; - linkml:source_file_date "2022-05-23T16:27:31"^^xsd:dateTime ; - linkml:source_file_size 345250 ; + linkml:source_file_date "2022-05-23T22:55:47"^^xsd:dateTime ; + linkml:source_file_size 344965 ; linkml:subsets , , , @@ -1365,6 +1367,11 @@ linkml:permissible_values , . + a linkml:SubsetDefinition ; + skos:definition "TBD" ; + skos:inScheme ; + linkml:definition_uri . + a linkml:TypeDefinition ; skos:definition "a complete URI" ; skos:inScheme linkml:types ; @@ -2071,7 +2078,6 @@ linkml:definition_uri ; linkml:domain ; linkml:domain_of ; - linkml:inlined true ; linkml:is_a ; linkml:is_usage_slot true ; linkml:multivalued true ; @@ -2090,7 +2096,6 @@ linkml:definition_uri ; linkml:domain ; linkml:domain_of ; - linkml:inlined true ; linkml:is_a ; linkml:is_usage_slot true ; linkml:owner ; @@ -2155,7 +2160,6 @@ linkml:definition_uri ; linkml:domain ; linkml:domain_of ; - linkml:inlined true ; linkml:is_a ; linkml:is_usage_slot true ; linkml:local_names [ linkml:ga4gh [ skos:altLabel "annotation qualifier" ; @@ -2479,11 +2483,11 @@ linkml:domain ; linkml:domain_of ; linkml:examples [ a linkml:Example ; - skos:definition "abnormal brain ventricle size" ; - skos:example "MP:0013229" ], - [ a linkml:Example ; skos:definition "Ehlers-Danlos syndrome, vascular type" ; - skos:example "MONDO:0017314" ] ; + skos:example "MONDO:0017314" ], + [ a linkml:Example ; + skos:definition "abnormal brain ventricle size" ; + skos:example "MP:0013229" ] ; linkml:is_a ; linkml:is_usage_slot true ; linkml:local_names [ linkml:ga4gh [ skos:altLabel "descriptor" ; @@ -2553,14 +2557,14 @@ linkml:domain ; linkml:domain_of ; linkml:examples [ a linkml:Example ; + skos:definition "Hyperkinesis" ; + skos:example "HP:0002487" ], + [ a linkml:Example ; skos:definition "axon morphology variant" ; skos:example "WBPhenotype:0000180" ], [ a linkml:Example ; skos:definition "abnormal circulating bilirubin level" ; - skos:example "MP:0001569" ], - [ a linkml:Example ; - skos:definition "Hyperkinesis" ; - skos:example "HP:0002487" ] ; + skos:example "MP:0001569" ] ; linkml:is_a ; linkml:is_usage_slot true ; linkml:local_names [ linkml:ga4gh [ skos:altLabel "descriptor" ; @@ -2852,7 +2856,6 @@ linkml:definition_uri ; linkml:domain ; linkml:domain_of ; - linkml:inlined true ; linkml:is_a ; linkml:is_usage_slot true ; linkml:owner ; @@ -4039,7 +4042,6 @@ linkml:definition_uri ; linkml:domain ; linkml:domain_of ; - linkml:inlined true ; linkml:is_a ; linkml:is_usage_slot true ; linkml:owner ; @@ -4753,7 +4755,6 @@ linkml:definition_uri ; linkml:domain ; linkml:domain_of ; - linkml:inlined true ; linkml:is_a ; linkml:is_usage_slot true ; linkml:multivalued true ; @@ -5595,6 +5596,7 @@ linkml:slot_usage [ ] ; linkml:slots , , + , , . @@ -5607,11 +5609,18 @@ linkml:is_a ; linkml:slot_usage [ ] ; linkml:slots , + , + , , , , + , , - . + , + , + , + , + . a linkml:ClassDefinition ; skos:closeMatch ; @@ -5733,11 +5742,18 @@ linkml:is_a ; linkml:slot_usage [ ] ; linkml:slots , + , + , , , , + , , - . + , + , + , + , + . a linkml:ClassDefinition ; OIO:inSubset ; @@ -6000,11 +6016,18 @@ linkml:is_a ; linkml:slot_usage [ ] ; linkml:slots , + , + , , , , + , , - . + , + , + , + , + . a linkml:ClassDefinition ; skos:definition "An attribute corresponding to the phenotypic sex of the individual, based upon the reproductive organs present." ; @@ -6015,11 +6038,18 @@ linkml:is_a ; linkml:slot_usage [ ] ; linkml:slots , + , + , , , , + , , - . + , + , + , + , + . a linkml:ClassDefinition ; skos:altLabel "physiology" ; @@ -6216,7 +6246,8 @@ linkml:class_uri ; linkml:definition_uri ; linkml:is_a ; - linkml:slot_usage [ ] . + linkml:slot_usage [ ] ; + linkml:slots . a linkml:ClassDefinition ; skos:inScheme ; @@ -6295,13 +6326,10 @@ linkml:slot_usage [ ] . a linkml:ClassDefinition ; - OIO:inSubset ; - skos:definition "this is used for nodes that are taken from an ontology but are not typed using an existing biolink class" ; skos:inScheme ; linkml:class_uri ; linkml:definition_uri ; - linkml:is_a ; - linkml:mixin true ; + linkml:deprecated "True" ; linkml:slot_usage [ ] . a linkml:ClassDefinition ; @@ -6595,11 +6623,11 @@ linkml:domain ; linkml:domain_of ; linkml:examples [ a linkml:Example ; - skos:definition "ti282a allele from ZFIN" ; - skos:example "ZFIN:ZDB-ALT-980203-1091" ], - [ a linkml:Example ; skos:definition "NM_007294.3(BRCA1):c.2521C>T (p.Arg841Trp)" ; - skos:example "ClinVarVariant:17681" ] ; + skos:example "ClinVarVariant:17681" ], + [ a linkml:Example ; + skos:definition "ti282a allele from ZFIN" ; + skos:example "ZFIN:ZDB-ALT-980203-1091" ] ; linkml:identifier true ; linkml:is_a ; linkml:is_usage_slot true ; @@ -6640,11 +6668,6 @@ linkml:range ; linkml:slot_uri . - a linkml:SubsetDefinition ; - skos:definition "TBD" ; - skos:inScheme ; - linkml:definition_uri . - a linkml:TypeDefinition ; skos:inScheme ; linkml:base "XSDTime" ; @@ -6791,6 +6814,14 @@ , . + a linkml:ClassDefinition ; + skos:definition "Biolink Model root class for entity annotations." ; + skos:inScheme ; + linkml:abstract true ; + linkml:class_uri ; + linkml:definition_uri ; + linkml:slot_usage [ ] . + a linkml:ClassDefinition ; skos:exactMatch , ; @@ -6866,11 +6897,18 @@ linkml:is_a ; linkml:slot_usage [ ] ; linkml:slots , + , + , , , , + , , - . + , + , + , + , + . a linkml:ClassDefinition ; skos:definition "The course a disease typically takes from its onset, progression in time, and eventual resolution or death of the affected individual" ; @@ -6881,11 +6919,18 @@ linkml:is_a ; linkml:slot_usage [ ] ; linkml:slots , + , + , , , , + , , - . + , + , + , + , + . a linkml:ClassDefinition ; skos:inScheme ; @@ -6913,11 +6958,18 @@ linkml:is_a ; linkml:slot_usage [ ] ; linkml:slots , + , + , , , , + , , - . + , + , + , + , + . a linkml:ClassDefinition ; skos:exactMatch , @@ -7213,11 +7265,18 @@ linkml:is_a ; linkml:slot_usage [ ] ; linkml:slots , + , + , , , , + , , - . + , + , + , + , + . a linkml:ClassDefinition ; skos:exactMatch , @@ -7347,11 +7406,18 @@ linkml:is_a ; linkml:slot_usage [ ] ; linkml:slots , + , + , , , , + , , - . + , + , + , + , + . a linkml:ClassDefinition ; skos:definition "Attributes relating to a socioeconomic manifestation" ; @@ -7361,11 +7427,18 @@ linkml:is_a ; linkml:slot_usage [ ] ; linkml:slots , + , + , , , , + , , - . + , + , + , + , + . a linkml:ClassDefinition ; skos:inScheme ; @@ -7411,11 +7484,18 @@ linkml:is_a ; linkml:slot_usage [ ] ; linkml:slots , + , + , , , , + , , - . + , + , + , + , + . a linkml:SlotDefinition ; skos:definition "the particulars of the place where someone or an organization is situated. For now, this slot is a simple text \"blob\" containing all relevant details of the given location for fitness of purpose. For the moment, this \"address\" can include other contact details such as email and phone number(?)." ; @@ -7599,7 +7679,6 @@ skos:inScheme ; linkml:definition_uri ; linkml:domain ; - linkml:inlined true ; linkml:is_a ; linkml:owner ; linkml:range ; @@ -7774,7 +7853,6 @@ linkml:definition_uri ; linkml:domain ; linkml:domain_of ; - linkml:inlined true ; linkml:is_a ; linkml:is_usage_slot true ; linkml:owner ; @@ -7993,7 +8071,6 @@ skos:inScheme ; linkml:definition_uri ; linkml:domain ; - linkml:inlined true ; linkml:is_a ; linkml:owner ; linkml:range ; @@ -8102,7 +8179,6 @@ linkml:examples [ a linkml:Example ; skos:definition "smallmolecule-protein" ; skos:example "MI:1048" ] ; - linkml:inlined true ; linkml:is_a ; linkml:owner ; linkml:range ; @@ -8324,11 +8400,11 @@ skos:exactMatch ; skos:inScheme ; linkml:annotations [ a linkml:Annotation ; - skos:example "biolink:negatively correlated with" ; - linkml:tag ns1:opposite_of ], - [ a linkml:Annotation ; skos:example "True" ; - linkml:tag ns1:canonical_predicate ] ; + linkml:tag ns1:canonical_predicate ], + [ a linkml:Annotation ; + skos:example "biolink:negatively correlated with" ; + linkml:tag ns1:opposite_of ] ; linkml:definition_uri ; linkml:domain ; linkml:inherited true ; @@ -8504,14 +8580,6 @@ linkml:slot_uri ; linkml:symmetric true . - a linkml:ClassDefinition ; - skos:definition "Biolink Model root class for entity annotations." ; - skos:inScheme ; - linkml:abstract true ; - linkml:class_uri ; - linkml:definition_uri ; - linkml:slot_usage [ ] . - a linkml:ClassDefinition ; skos:exactMatch ; skos:inScheme ; @@ -8599,13 +8667,10 @@ linkml:slot_uri . a linkml:ClassDefinition ; - OIO:inSubset ; - skos:definition "an ontology class that describes a functional aspect of a gene, gene prodoct or complex" ; skos:inScheme ; linkml:class_uri ; linkml:definition_uri ; - linkml:is_a ; - linkml:mixin true ; + linkml:deprecated "True" ; linkml:slot_usage [ ] . a linkml:ClassDefinition ; @@ -8740,11 +8805,18 @@ linkml:is_a ; linkml:slot_usage [ ] ; linkml:slots , + , + , , , , + , , - . + , + , + , + , + . a linkml:ClassDefinition ; skos:exactMatch , @@ -8784,7 +8856,8 @@ linkml:definition_uri ; linkml:id_prefixes "TAXRANK" ; linkml:is_a ; - linkml:slot_usage [ ] . + linkml:slot_usage [ ] ; + linkml:slots . a linkml:SlotDefinition ; owl:inverseOf ; @@ -9302,11 +9375,11 @@ skos:exactMatch ; skos:inScheme ; linkml:annotations [ a linkml:Annotation ; - skos:example "biolink:treats" ; - linkml:tag ns1:opposite_of ], - [ a linkml:Annotation ; skos:example "True" ; - linkml:tag ns1:canonical_predicate ] ; + linkml:tag ns1:canonical_predicate ], + [ a linkml:Annotation ; + skos:example "biolink:treats" ; + linkml:tag ns1:opposite_of ] ; linkml:definition_uri ; linkml:domain ; linkml:inherited true ; @@ -9348,11 +9421,11 @@ skos:inScheme ; skos:relatedMatch ; linkml:annotations [ a linkml:Annotation ; - skos:example "biolink:increases abundance of" ; - linkml:tag ns1:opposite_of ], - [ a linkml:Annotation ; skos:example "True" ; - linkml:tag ns1:canonical_predicate ] ; + linkml:tag ns1:canonical_predicate ], + [ a linkml:Annotation ; + skos:example "biolink:increases abundance of" ; + linkml:tag ns1:opposite_of ] ; linkml:definition_uri ; linkml:domain ; linkml:inherited true ; @@ -9401,11 +9474,11 @@ , ; linkml:annotations [ a linkml:Annotation ; - skos:example "biolink:increases activity of" ; - linkml:tag ns1:opposite_of ], - [ a linkml:Annotation ; skos:example "True" ; - linkml:tag ns1:canonical_predicate ] ; + linkml:tag ns1:canonical_predicate ], + [ a linkml:Annotation ; + skos:example "biolink:increases activity of" ; + linkml:tag ns1:opposite_of ] ; linkml:definition_uri ; linkml:domain ; linkml:inherited true ; @@ -9426,11 +9499,11 @@ skos:narrowMatch , ; linkml:annotations [ a linkml:Annotation ; - skos:example "True" ; - linkml:tag ns1:canonical_predicate ], - [ a linkml:Annotation ; skos:example "increases degredation of" ; - linkml:tag ns1:opposite_of ] ; + linkml:tag ns1:opposite_of ], + [ a linkml:Annotation ; + skos:example "True" ; + linkml:tag ns1:canonical_predicate ] ; linkml:definition_uri ; linkml:domain ; linkml:inherited true ; @@ -9468,11 +9541,11 @@ skos:exactMatch ; skos:inScheme ; linkml:annotations [ a linkml:Annotation ; - skos:example "biolink:increases folding of" ; - linkml:tag ns1:opposite_of ], - [ a linkml:Annotation ; skos:example "True" ; - linkml:tag ns1:canonical_predicate ] ; + linkml:tag ns1:canonical_predicate ], + [ a linkml:Annotation ; + skos:example "biolink:increases folding of" ; + linkml:tag ns1:opposite_of ] ; linkml:definition_uri ; linkml:domain ; linkml:inherited true ; @@ -9490,11 +9563,11 @@ skos:exactMatch ; skos:inScheme ; linkml:annotations [ a linkml:Annotation ; - skos:example "biolink:increases localization of" ; - linkml:tag ns1:opposite_of ], - [ a linkml:Annotation ; skos:example "True" ; - linkml:tag ns1:canonical_predicate ] ; + linkml:tag ns1:canonical_predicate ], + [ a linkml:Annotation ; + skos:example "biolink:increases localization of" ; + linkml:tag ns1:opposite_of ] ; linkml:definition_uri ; linkml:domain ; linkml:inherited true ; @@ -9513,11 +9586,11 @@ skos:exactMatch ; skos:inScheme ; linkml:annotations [ a linkml:Annotation ; - skos:example "biolink:increases metabolic processing of" ; - linkml:tag ns1:opposite_of ], - [ a linkml:Annotation ; skos:example "True" ; - linkml:tag ns1:canonical_predicate ] ; + linkml:tag ns1:canonical_predicate ], + [ a linkml:Annotation ; + skos:example "biolink:increases metabolic processing of" ; + linkml:tag ns1:opposite_of ] ; linkml:definition_uri ; linkml:domain ; linkml:inherited true ; @@ -9535,11 +9608,11 @@ skos:exactMatch ; skos:inScheme ; linkml:annotations [ a linkml:Annotation ; - skos:example "biolink:increases molecular interaction" ; - linkml:tag ns1:opposite_of ], - [ a linkml:Annotation ; skos:example "True" ; - linkml:tag ns1:canonical_predicate ] ; + linkml:tag ns1:canonical_predicate ], + [ a linkml:Annotation ; + skos:example "biolink:increases molecular interaction" ; + linkml:tag ns1:opposite_of ] ; linkml:definition_uri ; linkml:domain ; linkml:inherited true ; @@ -9589,11 +9662,11 @@ , ; linkml:annotations [ a linkml:Annotation ; - skos:example "biolink:increases molecular modification of" ; - linkml:tag ns1:opposite_of ], - [ a linkml:Annotation ; skos:example "True" ; - linkml:tag ns1:canonical_predicate ] ; + linkml:tag ns1:canonical_predicate ], + [ a linkml:Annotation ; + skos:example "biolink:increases molecular modification of" ; + linkml:tag ns1:opposite_of ] ; linkml:definition_uri ; linkml:domain ; linkml:inherited true ; @@ -9613,11 +9686,11 @@ skos:exactMatch ; skos:inScheme ; linkml:annotations [ a linkml:Annotation ; - skos:example "biolink:increases mutation rate of" ; - linkml:tag ns1:opposite_of ], - [ a linkml:Annotation ; skos:example "True" ; - linkml:tag ns1:canonical_predicate ] ; + linkml:tag ns1:canonical_predicate ], + [ a linkml:Annotation ; + skos:example "biolink:increases mutation rate of" ; + linkml:tag ns1:opposite_of ] ; linkml:definition_uri ; linkml:domain ; linkml:inherited true ; @@ -9661,11 +9734,11 @@ skos:exactMatch ; skos:inScheme ; linkml:annotations [ a linkml:Annotation ; - skos:example "True" ; - linkml:tag ns1:canonical_predicate ], - [ a linkml:Annotation ; skos:example "biolink:increases secretion of" ; - linkml:tag ns1:opposite_of ] ; + linkml:tag ns1:opposite_of ], + [ a linkml:Annotation ; + skos:example "True" ; + linkml:tag ns1:canonical_predicate ] ; linkml:definition_uri ; linkml:domain ; linkml:inherited true ; @@ -9685,11 +9758,11 @@ skos:exactMatch ; skos:inScheme ; linkml:annotations [ a linkml:Annotation ; - skos:example "biolink:increases splicing of" ; - linkml:tag ns1:opposite_of ], - [ a linkml:Annotation ; skos:example "True" ; - linkml:tag ns1:canonical_predicate ] ; + linkml:tag ns1:canonical_predicate ], + [ a linkml:Annotation ; + skos:example "biolink:increases splicing of" ; + linkml:tag ns1:opposite_of ] ; linkml:definition_uri ; linkml:domain ; linkml:inherited true ; @@ -9707,11 +9780,11 @@ skos:exactMatch ; skos:inScheme ; linkml:annotations [ a linkml:Annotation ; - skos:example "increases stability of" ; - linkml:tag ns1:opposite_of ], - [ a linkml:Annotation ; skos:example "True" ; - linkml:tag ns1:canonical_predicate ] ; + linkml:tag ns1:canonical_predicate ], + [ a linkml:Annotation ; + skos:example "increases stability of" ; + linkml:tag ns1:opposite_of ] ; linkml:definition_uri ; linkml:domain ; linkml:inherited true ; @@ -9730,11 +9803,11 @@ skos:exactMatch ; skos:inScheme ; linkml:annotations [ a linkml:Annotation ; - skos:example "True" ; - linkml:tag ns1:canonical_predicate ], - [ a linkml:Annotation ; skos:example "biolink:increases synthesis of" ; - linkml:tag ns1:opposite_of ] ; + linkml:tag ns1:opposite_of ], + [ a linkml:Annotation ; + skos:example "True" ; + linkml:tag ns1:canonical_predicate ] ; linkml:definition_uri ; linkml:domain ; linkml:inherited true ; @@ -9753,11 +9826,11 @@ skos:exactMatch ; skos:inScheme ; linkml:annotations [ a linkml:Annotation ; - skos:example "True" ; - linkml:tag ns1:canonical_predicate ], - [ a linkml:Annotation ; skos:example "biolink:increases transport of" ; - linkml:tag ns1:opposite_of ] ; + linkml:tag ns1:opposite_of ], + [ a linkml:Annotation ; + skos:example "True" ; + linkml:tag ns1:canonical_predicate ] ; linkml:definition_uri ; linkml:domain ; linkml:inherited true ; @@ -9777,11 +9850,11 @@ skos:exactMatch ; skos:inScheme ; linkml:annotations [ a linkml:Annotation ; - skos:example "biolink:increases uptake of" ; - linkml:tag ns1:opposite_of ], - [ a linkml:Annotation ; skos:example "True" ; - linkml:tag ns1:canonical_predicate ] ; + linkml:tag ns1:canonical_predicate ], + [ a linkml:Annotation ; + skos:example "biolink:increases uptake of" ; + linkml:tag ns1:opposite_of ] ; linkml:definition_uri ; linkml:domain ; linkml:inherited true ; @@ -10017,11 +10090,11 @@ , ; linkml:annotations [ a linkml:Annotation ; - skos:example "True" ; - linkml:tag ns1:canonical_predicate ], - [ a linkml:Annotation ; skos:example "biolink:entity negatively regulates entity" ; - linkml:tag ns1:opposite_of ] ; + linkml:tag ns1:opposite_of ], + [ a linkml:Annotation ; + skos:example "True" ; + linkml:tag ns1:canonical_predicate ] ; linkml:definition_uri ; linkml:domain ; linkml:inherited true ; @@ -10246,11 +10319,11 @@ skos:inScheme ; skos:mappingRelation ; linkml:annotations [ a linkml:Annotation ; - skos:example "True" ; - linkml:tag ns1:canonical_predicate ], - [ a linkml:Annotation ; skos:example "biolink:is excipient of" ; - linkml:tag ns1:opposite_of ] ; + linkml:tag ns1:opposite_of ], + [ a linkml:Annotation ; + skos:example "True" ; + linkml:tag ns1:canonical_predicate ] ; linkml:definition_uri ; linkml:domain ; linkml:inherited true ; @@ -10319,11 +10392,11 @@ skos:exactMatch ; skos:inScheme ; linkml:annotations [ a linkml:Annotation ; - skos:example "biolink:has not completed" ; - linkml:tag ns1:opposite_of ], - [ a linkml:Annotation ; skos:example "True" ; - linkml:tag ns1:canonical_predicate ] ; + linkml:tag ns1:canonical_predicate ], + [ a linkml:Annotation ; + skos:example "biolink:has not completed" ; + linkml:tag ns1:opposite_of ] ; linkml:definition_uri ; linkml:domain ; linkml:inherited true ; @@ -10414,11 +10487,11 @@ skos:inScheme ; skos:narrowMatch ; linkml:annotations [ a linkml:Annotation ; - skos:example "True" ; - linkml:tag ns1:canonical_predicate ], - [ a linkml:Annotation ; skos:example "biolink:has decreased amount" ; - linkml:tag ns1:opposite_of ] ; + linkml:tag ns1:opposite_of ], + [ a linkml:Annotation ; + skos:example "True" ; + linkml:tag ns1:canonical_predicate ] ; linkml:definition_uri ; linkml:domain ; linkml:inherited true ; @@ -10483,7 +10556,6 @@ linkml:definition_uri ; linkml:domain ; linkml:inherited true ; - linkml:inlined true ; linkml:is_a ; linkml:multivalued true ; linkml:owner ; @@ -10733,7 +10805,6 @@ linkml:definition_uri ; linkml:domain ; linkml:domain_of ; - linkml:inlined true ; linkml:is_a ; linkml:owner ; linkml:range ; @@ -10758,11 +10829,11 @@ skos:inScheme ; skos:relatedMatch ; linkml:annotations [ a linkml:Annotation ; - skos:example "True" ; - linkml:tag ns1:canonical_predicate ], - [ a linkml:Annotation ; skos:example "biolink:decreases abundance of" ; - linkml:tag ns1:opposite_of ] ; + linkml:tag ns1:opposite_of ], + [ a linkml:Annotation ; + skos:example "True" ; + linkml:tag ns1:canonical_predicate ] ; linkml:definition_uri ; linkml:domain ; linkml:inherited true ; @@ -10826,11 +10897,11 @@ skos:relatedMatch , ; linkml:annotations [ a linkml:Annotation ; - skos:example "decreases degredation of" ; - linkml:tag ns1:opposite_of ], - [ a linkml:Annotation ; skos:example "True" ; - linkml:tag ns1:canonical_predicate ] ; + linkml:tag ns1:canonical_predicate ], + [ a linkml:Annotation ; + skos:example "decreases degredation of" ; + linkml:tag ns1:opposite_of ] ; linkml:definition_uri ; linkml:domain ; linkml:inherited true ; @@ -10866,11 +10937,11 @@ skos:exactMatch ; skos:inScheme ; linkml:annotations [ a linkml:Annotation ; - skos:example "biolink:decreases folding of" ; - linkml:tag ns1:opposite_of ], - [ a linkml:Annotation ; skos:example "True" ; - linkml:tag ns1:canonical_predicate ] ; + linkml:tag ns1:canonical_predicate ], + [ a linkml:Annotation ; + skos:example "biolink:decreases folding of" ; + linkml:tag ns1:opposite_of ] ; linkml:definition_uri ; linkml:domain ; linkml:inherited true ; @@ -10888,11 +10959,11 @@ skos:exactMatch ; skos:inScheme ; linkml:annotations [ a linkml:Annotation ; - skos:example "True" ; - linkml:tag ns1:canonical_predicate ], - [ a linkml:Annotation ; skos:example "biolink:decreases localization of" ; - linkml:tag ns1:opposite_of ] ; + linkml:tag ns1:opposite_of ], + [ a linkml:Annotation ; + skos:example "True" ; + linkml:tag ns1:canonical_predicate ] ; linkml:definition_uri ; linkml:domain ; linkml:inherited true ; @@ -10912,11 +10983,11 @@ skos:inScheme ; skos:narrowMatch ; linkml:annotations [ a linkml:Annotation ; - skos:example "biolink:decreases metabolic processing of" ; - linkml:tag ns1:opposite_of ], - [ a linkml:Annotation ; skos:example "True" ; - linkml:tag ns1:canonical_predicate ] ; + linkml:tag ns1:canonical_predicate ], + [ a linkml:Annotation ; + skos:example "biolink:decreases metabolic processing of" ; + linkml:tag ns1:opposite_of ] ; linkml:definition_uri ; linkml:domain ; linkml:inherited true ; @@ -10934,11 +11005,11 @@ skos:exactMatch ; skos:inScheme ; linkml:annotations [ a linkml:Annotation ; - skos:example "True" ; - linkml:tag ns1:canonical_predicate ], - [ a linkml:Annotation ; skos:example "biolink:decreases molecular interaction" ; - linkml:tag ns1:opposite_of ] ; + linkml:tag ns1:opposite_of ], + [ a linkml:Annotation ; + skos:example "True" ; + linkml:tag ns1:canonical_predicate ] ; linkml:definition_uri ; linkml:domain ; linkml:inherited true ; @@ -10989,11 +11060,11 @@ , ; linkml:annotations [ a linkml:Annotation ; - skos:example "biolink:decreases molecular modification of" ; - linkml:tag ns1:opposite_of ], - [ a linkml:Annotation ; skos:example "True" ; - linkml:tag ns1:canonical_predicate ] ; + linkml:tag ns1:canonical_predicate ], + [ a linkml:Annotation ; + skos:example "biolink:decreases molecular modification of" ; + linkml:tag ns1:opposite_of ] ; linkml:definition_uri ; linkml:domain ; linkml:inherited true ; @@ -11013,11 +11084,11 @@ skos:exactMatch ; skos:inScheme ; linkml:annotations [ a linkml:Annotation ; - skos:example "True" ; - linkml:tag ns1:canonical_predicate ], - [ a linkml:Annotation ; skos:example "biolink:decreases mutation rate of" ; - linkml:tag ns1:opposite_of ] ; + linkml:tag ns1:opposite_of ], + [ a linkml:Annotation ; + skos:example "True" ; + linkml:tag ns1:canonical_predicate ] ; linkml:definition_uri ; linkml:domain ; linkml:inherited true ; @@ -11105,11 +11176,11 @@ skos:definition "holds between two chemical or gene/gene product entities where the action or effect of one increases the stability of the other within a system of interest" ; skos:inScheme ; linkml:annotations [ a linkml:Annotation ; - skos:example "decreases stability of" ; - linkml:tag ns1:opposite_of ], - [ a linkml:Annotation ; skos:example "True" ; - linkml:tag ns1:canonical_predicate ] ; + linkml:tag ns1:canonical_predicate ], + [ a linkml:Annotation ; + skos:example "decreases stability of" ; + linkml:tag ns1:opposite_of ] ; linkml:definition_uri ; linkml:domain ; linkml:inherited true ; @@ -11152,11 +11223,11 @@ skos:definition "holds between two chemical or gene/gene product entities where the action or effect of one increases the rate of transport of the other across some boundary in a system of interest" ; skos:inScheme ; linkml:annotations [ a linkml:Annotation ; - skos:example "True" ; - linkml:tag ns1:canonical_predicate ], - [ a linkml:Annotation ; skos:example "biolink:decreases transport of" ; - linkml:tag ns1:opposite_of ] ; + linkml:tag ns1:opposite_of ], + [ a linkml:Annotation ; + skos:example "True" ; + linkml:tag ns1:canonical_predicate ] ; linkml:definition_uri ; linkml:domain ; linkml:inherited true ; @@ -11444,11 +11515,11 @@ skos:inScheme ; skos:narrowMatch ; linkml:annotations [ a linkml:Annotation ; - skos:example "biolink:has part" ; - linkml:tag ns1:opposite_of ], - [ a linkml:Annotation ; skos:example "True" ; - linkml:tag ns1:canonical_predicate ] ; + linkml:tag ns1:canonical_predicate ], + [ a linkml:Annotation ; + skos:example "biolink:has part" ; + linkml:tag ns1:opposite_of ] ; linkml:definition_uri ; linkml:domain ; linkml:inherited true ; @@ -11960,11 +12031,11 @@ skos:exactMatch ; skos:inScheme ; linkml:annotations [ a linkml:Annotation ; - skos:example "True" ; - linkml:tag ns1:canonical_predicate ], - [ a linkml:Annotation ; skos:example "biolink:process positively regulates process" ; - linkml:tag ns1:opposite_of ] ; + linkml:tag ns1:opposite_of ], + [ a linkml:Annotation ; + skos:example "True" ; + linkml:tag ns1:canonical_predicate ] ; linkml:definition_uri ; linkml:domain ; linkml:inherited true ; @@ -12325,7 +12396,6 @@ linkml:definition_uri ; linkml:domain ; linkml:inherited true ; - linkml:inlined true ; linkml:is_a ; linkml:multivalued true ; linkml:owner ; @@ -12432,11 +12502,11 @@ skos:definition "x (amino acid chain/polypeptide) is the ribosomal translation of y (transcript) if and only if a ribosome reads y (transcript) through a series of triplet codon-amino acid adaptor activities (GO:0030533) and produces x (amino acid chain/polypeptide)" ; skos:inScheme ; linkml:annotations [ a linkml:Annotation ; - skos:example "True" ; - linkml:tag ns1:canonical_predicate ], - [ a linkml:Annotation ; skos:example "biolink:translation of" ; - linkml:tag ns1:opposite_of ] ; + linkml:tag ns1:opposite_of ], + [ a linkml:Annotation ; + skos:example "True" ; + linkml:tag ns1:canonical_predicate ] ; linkml:definition_uri ; linkml:domain ; linkml:inherited true ; @@ -12550,11 +12620,18 @@ linkml:is_a ; linkml:slot_usage [ ] ; linkml:slots , + , + , , , , + , , - . + , + , + , + , + . a linkml:ClassDefinition ; skos:inScheme ; @@ -12730,10 +12807,17 @@ linkml:slot_usage [ ] ; linkml:slots , , + , + , , , + , , - . + , + , + , + , + . a linkml:ClassDefinition ; skos:definition "An association between either a disease or a phenotypic feature and an anatomical entity, where the disease/feature manifests in that site." ; @@ -13418,11 +13502,11 @@ skos:exactMatch ; skos:inScheme ; linkml:annotations [ a linkml:Annotation ; - skos:example "biolink:exacerbates" ; - linkml:tag ns1:opposite_of ], - [ a linkml:Annotation ; skos:example "True" ; - linkml:tag ns1:canonical_predicate ] ; + linkml:tag ns1:canonical_predicate ], + [ a linkml:Annotation ; + skos:example "biolink:exacerbates" ; + linkml:tag ns1:opposite_of ] ; linkml:definition_uri ; linkml:domain ; linkml:inherited true ; @@ -14211,7 +14295,6 @@ linkml:definition_uri ; linkml:domain ; linkml:inherited true ; - linkml:inlined true ; linkml:is_a ; linkml:multivalued true ; linkml:owner ; @@ -14391,11 +14474,18 @@ linkml:is_a ; linkml:slot_usage [ ] ; linkml:slots , + , + , , , , + , , - . + , + , + , + , + . a linkml:ClassDefinition ; skos:definition "an item that holds distribution level information about a dataset." ; @@ -14950,11 +15040,11 @@ , ; linkml:annotations [ a linkml:Annotation ; - skos:example "True" ; - linkml:tag ns1:canonical_predicate ], - [ a linkml:Annotation ; skos:example "biolink:prevents" ; - linkml:tag ns1:opposite_of ] ; + linkml:tag ns1:opposite_of ], + [ a linkml:Annotation ; + skos:example "True" ; + linkml:tag ns1:canonical_predicate ] ; linkml:definition_uri ; linkml:domain ; linkml:inherited true ; @@ -15061,11 +15151,11 @@ linkml:inlined true ; linkml:is_a ; linkml:local_names [ a linkml:LocalName ; - skos:altLabel "regulates" ; - linkml:local_name_source "translator" ], - [ a linkml:LocalName ; skos:altLabel "activity directly regulates activity of" ; - linkml:local_name_source "ro" ] ; + linkml:local_name_source "ro" ], + [ a linkml:LocalName ; + skos:altLabel "regulates" ; + linkml:local_name_source "translator" ] ; linkml:mixins ; linkml:multivalued true ; linkml:owner ; @@ -15142,7 +15232,6 @@ skos:mappingRelation ; linkml:definition_uri ; linkml:domain ; - linkml:inlined true ; linkml:is_a ; linkml:owner ; linkml:range ; @@ -16684,7 +16773,6 @@ linkml:domain ; linkml:domain_of , ; - linkml:inlined true ; linkml:is_a ; linkml:owner ; linkml:range ; @@ -16992,11 +17080,11 @@ , ; linkml:annotations [ a linkml:Annotation ; - skos:example "biolink:lacks part" ; - linkml:tag ns1:opposite_of ], - [ a linkml:Annotation ; skos:example "True" ; - linkml:tag ns1:canonical_predicate ] ; + linkml:tag ns1:canonical_predicate ], + [ a linkml:Annotation ; + skos:example "biolink:lacks part" ; + linkml:tag ns1:opposite_of ] ; linkml:definition_uri ; linkml:domain ; linkml:inherited true ; @@ -17358,7 +17446,6 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t linkml:definition_uri ; linkml:domain ; linkml:domain_of ; - linkml:inlined true ; linkml:is_a ; linkml:owner ; linkml:range ; @@ -18495,7 +18582,6 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t linkml:definition_uri ; linkml:domain ; linkml:domain_of ; - linkml:inlined true ; linkml:is_a ; linkml:is_usage_slot true ; linkml:multivalued true ; @@ -19150,7 +19236,6 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t linkml:definition_uri ; linkml:domain ; linkml:domain_of ; - linkml:inlined true ; linkml:owner ; linkml:range ; linkml:required true ; @@ -19289,7 +19374,6 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t linkml:definition_uri ; linkml:domain ; linkml:domain_of ; - linkml:inlined true ; linkml:is_a ; linkml:owner ; linkml:range ; @@ -19301,7 +19385,6 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t linkml:definition_uri ; linkml:domain ; linkml:domain_of ; - linkml:inlined true ; linkml:is_a ; linkml:owner ; linkml:range ; @@ -19364,15 +19447,22 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t "EDAM-FORMAT", "EDAM-OPERATION", "EDAM-TOPIC" ; - linkml:is_a ; + linkml:is_a ; linkml:mixins ; linkml:slot_usage [ ] ; linkml:slots , + , + , , , , + , , - . + , + , + , + , + . a linkml:SlotDefinition ; owl:inverseOf ; @@ -19455,7 +19545,6 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t linkml:definition_uri ; linkml:domain ; linkml:domain_of ; - linkml:inlined true ; linkml:is_a ; linkml:multivalued true ; linkml:owner ; @@ -19708,6 +19797,26 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t , . + a linkml:ClassDefinition ; + rdfs:seeAlso ; + skos:definition "a concept or class in an ontology, vocabulary or thesaurus. Note that nodes in a biolink compatible KG can be considered both instances of biolink classes, and OWL classes in their own right. In general you should not need to use this class directly. Instead, use the appropriate biolink class. For example, for the GO concept of endocytosis (GO:0006897), use bl:BiologicalProcess as the type." ; + skos:exactMatch schema1:Class, + owl:Class ; + skos:inScheme ; + skos:note "Note that formally this is a metaclass. Instances of this class are instances in the graph, but can be the object of 'type' edges. For example, if we had a node in the graph representing a specific brain of a specific patient (e.g brain001), this could have a category of bl:Sample, and by typed more specifically with an ontology class UBERON:nnn, which has as category bl:AnatomicalEntity", + "This is modeled as a mixin. 'ontology class' should not be the primary type of a node in the KG. Instead you should use an informative bioloink category, such as AnatomicalEntity (for Uberon classes), ChemicalSubstance (for CHEBI or CHEMBL), etc" ; + linkml:class_uri ; + linkml:definition_uri ; + linkml:examples [ a linkml:Example ; + skos:definition "the class 'brain' from the Uberon anatomy ontology" ; + skos:example "UBERON:0000955" ] ; + linkml:id_prefixes "KEGG.BRITE", + "MESH", + "UMLS" ; + linkml:mixin true ; + linkml:slot_usage [ ] ; + linkml:slots . + a linkml:ClassDefinition ; OIO:inSubset ; skos:altLabel "locus" ; @@ -19759,25 +19868,6 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t , . - a linkml:ClassDefinition ; - rdfs:seeAlso ; - skos:definition "a concept or class in an ontology, vocabulary or thesaurus. Note that nodes in a biolink compatible KG can be considered both instances of biolink classes, and OWL classes in their own right. In general you should not need to use this class directly. Instead, use the appropriate biolink class. For example, for the GO concept of endocytosis (GO:0006897), use bl:BiologicalProcess as the type." ; - skos:exactMatch schema1:Class, - owl:Class ; - skos:inScheme ; - skos:note "Note that formally this is a metaclass. Instances of this class are instances in the graph, but can be the object of 'type' edges. For example, if we had a node in the graph representing a specific brain of a specific patient (e.g brain001), this could have a category of bl:Sample, and by typed more specifically with an ontology class UBERON:nnn, which has as category bl:AnatomicalEntity", - "This is modeled as a mixin. 'ontology class' should not be the primary type of a node in the KG. Instead you should use an informative bioloink category, such as AnatomicalEntity (for Uberon classes), ChemicalSubstance (for CHEBI or CHEMBL), etc" ; - linkml:class_uri ; - linkml:definition_uri ; - linkml:examples [ a linkml:Example ; - skos:definition "the class 'brain' from the Uberon anatomy ontology" ; - skos:example "UBERON:0000955" ] ; - linkml:id_prefixes "KEGG.BRITE", - "MESH", - "UMLS" ; - linkml:mixin true ; - linkml:slot_usage [ ] . - a linkml:ClassDefinition ; OIO:inSubset ; skos:altLabel "allele" ; @@ -19792,11 +19882,11 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t skos:inScheme ; skos:note "This class is for modeling the specific state at a locus. A single DBSNP rs ID could correspond to more than one sequence variants (e.g CIViC:1252 and CIViC:1253, two distinct BRCA2 alleles for rs28897743)" ; linkml:alt_descriptions [ a linkml:AltDescription ; - skos:definition "An entity that describes a single affected, endogenous allele. These can be of any type that matches that definition" ; - linkml:source "AGR" ], - [ a linkml:AltDescription ; skos:definition "A contiguous change at a Location" ; - linkml:source "VMC" ] ; + linkml:source "VMC" ], + [ a linkml:AltDescription ; + skos:definition "An entity that describes a single affected, endogenous allele. These can be of any type that matches that definition" ; + linkml:source "AGR" ] ; linkml:class_uri ; linkml:definition_uri ; linkml:id_prefixes "CAID", @@ -20117,7 +20207,6 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t linkml:definition_uri ; linkml:domain ; linkml:domain_of ; - linkml:inlined true ; linkml:is_a ; linkml:local_names [ a linkml:LocalName ; skos:altLabel "annotation qualifier" ; @@ -20179,6 +20268,37 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t linkml:range ; linkml:slot_uri . + a linkml:ClassDefinition ; + skos:definition "A typed association between two entities, supported by evidence" ; + skos:exactMatch rdf:Statement, + owl:Axiom, + ; + skos:inScheme ; + skos:note "This is roughly the model used by biolink and ontobio at the moment" ; + linkml:class_uri ; + linkml:definition_uri ; + linkml:is_a ; + linkml:slot_usage [ ] ; + linkml:slots , + , + , + , + , + , + , + , + , + , + , + , + , + , + , + , + , + , + . + a linkml:SlotDefinition ; skos:exactMatch , , @@ -20212,37 +20332,6 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t linkml:range ; linkml:slot_uri . - a linkml:ClassDefinition ; - skos:definition "A typed association between two entities, supported by evidence" ; - skos:exactMatch rdf:Statement, - owl:Axiom, - ; - skos:inScheme ; - skos:note "This is roughly the model used by biolink and ontobio at the moment" ; - linkml:class_uri ; - linkml:definition_uri ; - linkml:is_a ; - linkml:slot_usage [ ] ; - linkml:slots , - , - , - , - , - , - , - , - , - , - , - , - , - , - , - , - , - , - . - a linkml:SlotDefinition ; 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" ; @@ -20255,16 +20344,66 @@ 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 "annotation predicate" ; - linkml:local_name_source "ga4gh" ], - [ a linkml:LocalName ; skos:altLabel "predicate" ; - linkml:local_name_source "translator" ] ; + linkml:local_name_source "translator" ], + [ a linkml:LocalName ; + skos:altLabel "annotation predicate" ; + linkml:local_name_source "ga4gh" ] ; linkml:owner ; linkml:range ; linkml:required true ; linkml:slot_uri rdf:predicate . + a linkml:SlotDefinition ; + skos:definition "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + skos:exactMatch , + owl:annotatedTarget ; + skos:inScheme ; + skos:mappingRelation rdf:object ; + linkml:definition_uri ; + linkml:domain ; + linkml:domain_of ; + linkml:is_a ; + linkml:local_names [ a linkml:LocalName ; + skos:altLabel "node with incoming relationship" ; + linkml:local_name_source "neo4j" ], + [ a linkml:LocalName ; + skos:altLabel "descriptor" ; + linkml:local_name_source "ga4gh" ] ; + linkml:owner ; + linkml:range ; + linkml:required true ; + linkml:slot_uri rdf:object . + + a linkml:SlotDefinition ; + OIO:inSubset , + ; + skos:altLabel "display name", + "label", + "title" ; + skos:definition "A human-readable name for an attribute or entity." ; + skos:exactMatch , + ; + skos:inScheme ; + skos:mappingRelation rdfs:label ; + skos:narrowMatch dcterms:title, + ; + linkml:definition_uri ; + linkml:domain_of , + , + ; + linkml:owner ; + linkml:range ; + linkml:slot_uri rdfs:label . + + a linkml:ClassDefinition ; + skos:definition "A union of chemical entities and children, and gene or gene product. This mixin is helpful to use when searching across chemical entities that must include genes and their children as chemical entities." ; + skos:inScheme ; + linkml:class_uri ; + linkml:definition_uri ; + linkml:mixin true ; + linkml:slot_usage [ ] . + a linkml:SlotDefinition ; OIO:inSubset ; skos:closeMatch ; @@ -20348,33 +20487,11 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t linkml:definition_uri ; linkml:domain ; linkml:domain_of ; - linkml:inlined true ; linkml:multivalued true ; linkml:owner ; linkml:range ; linkml:slot_uri . - a linkml:SlotDefinition ; - skos:definition "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; - skos:exactMatch , - owl:annotatedTarget ; - skos:inScheme ; - skos:mappingRelation rdf:object ; - linkml:definition_uri ; - linkml:domain ; - linkml:domain_of ; - linkml:is_a ; - linkml:local_names [ a linkml:LocalName ; - skos:altLabel "node with incoming relationship" ; - linkml:local_name_source "neo4j" ], - [ a linkml:LocalName ; - skos:altLabel "descriptor" ; - linkml:local_name_source "ga4gh" ] ; - linkml:owner ; - linkml:range ; - linkml:required true ; - linkml:slot_uri rdf:object . - a linkml:SlotDefinition ; OIO:inSubset ; skos:altLabel "definition" ; @@ -20390,50 +20507,6 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t linkml:range ; linkml:slot_uri dcterms:description . - a linkml:SlotDefinition ; - OIO:inSubset , - ; - skos:altLabel "display name", - "label", - "title" ; - skos:definition "A human-readable name for an attribute or entity." ; - skos:exactMatch , - ; - skos:inScheme ; - skos:mappingRelation rdfs:label ; - skos:narrowMatch dcterms:title, - ; - linkml:definition_uri ; - linkml:domain_of , - , - ; - linkml:owner ; - linkml:range ; - linkml:slot_uri rdfs:label . - - a linkml:ClassDefinition ; - skos:definition "A union of chemical entities and children, and gene or gene product. This mixin is helpful to use when searching across chemical entities that must include genes and their children as chemical entities." ; - skos:inScheme ; - linkml:class_uri ; - linkml:definition_uri ; - linkml:mixin true ; - linkml:slot_usage [ ] . - - a linkml:SlotDefinition ; - OIO:inSubset ; - skos:definition "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - skos:exactMatch , - , - ; - skos:inScheme ; - linkml:definition_uri ; - linkml:domain_of ; - linkml:identifier true ; - linkml:owner ; - linkml:range ; - linkml:required true ; - linkml:slot_uri . - a linkml:SlotDefinition ; OIO:inSubset , ; @@ -20468,16 +20541,32 @@ 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 "annotation subject" ; - linkml:local_name_source "ga4gh" ], - [ a linkml:LocalName ; skos:altLabel "node with outgoing relationship" ; - linkml:local_name_source "neo4j" ] ; + linkml:local_name_source "neo4j" ], + [ a linkml:LocalName ; + skos:altLabel "annotation subject" ; + linkml:local_name_source "ga4gh" ] ; linkml:owner ; linkml:range ; linkml:required true ; linkml:slot_uri rdf:subject . + a linkml:SlotDefinition ; + OIO:inSubset ; + skos:definition "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + skos:exactMatch , + , + ; + skos:inScheme ; + linkml:definition_uri ; + linkml:domain_of , + ; + linkml:identifier true ; + linkml:owner ; + linkml:range ; + linkml:required true ; + linkml:slot_uri . + a linkml:SubsetDefinition ; skos:definition "Minimum subset of translator work" ; skos:inScheme ; diff --git a/biolink-modeln.shex b/biolink-modeln.shex index 0e1b5b6dfd..60e26a1d8c 100644 --- a/biolink-modeln.shex +++ b/biolink-modeln.shex @@ -1,5 +1,5 @@ # metamodel_version: 1.7.0 -# version: 2.3.1 +# version: 2.4.0 BASE PREFIX rdf: PREFIX xsd: @@ -152,15 +152,13 @@ linkml:Nodeidentifier NONLITERAL } ( - @ OR @ + { + ( $ rdf:type . * ; + rdf:type [ ] ? + ) + } OR @ ) - { - ( $ rdf:type . * ; - rdf:type [ ] ? - ) -} -
CLOSED { ( $ ( & ; rdf:type [ ] ? ; @@ -215,18 +213,16 @@ linkml:Nodeidentifier NONLITERAL ( CLOSED { - ( $ ( & ; - rdf:type [ ] ? ; + ( $ ( & ; + rdf:type [ ] ? ; & ; rdf:type [ ] ? ; @ ? ; @ ; @ * ; - @ ? ; - @ ? ; - @linkml:String ? + @ ? ) ; - rdf:type [ ] ? + rdf:type [ ] ) } OR @ OR @ OR @ OR @ OR @ OR @ OR @ @@ -335,7 +331,7 @@ linkml:Nodeidentifier NONLITERAL ( $ ( & ; rdf:type [ ] ? ) ; - rdf:type [ ] ? + rdf:type [ ] ) } OR @ OR @ ) @@ -541,7 +537,7 @@ linkml:Nodeidentifier NONLITERAL ( $ ( & ; rdf:type [ ] ? ) ; - rdf:type [ ] ? + rdf:type [ ] ) } @@ -626,7 +622,7 @@ linkml:Nodeidentifier NONLITERAL ( $ ( & ; rdf:type [ ] ? ) ; - rdf:type [ ] ? + rdf:type [ ] ) } OR @ OR @ OR @ ) @@ -636,7 +632,7 @@ linkml:Nodeidentifier NONLITERAL ( $ ( & ; rdf:type [ ] ? ) ; - rdf:type [ ] ? + rdf:type [ ] ) } OR @ ) @@ -675,7 +671,7 @@ linkml:Nodeidentifier NONLITERAL rdf:type [ ] ? ; @ ) ; - rdf:type [ ] ? + rdf:type [ ] ) } @@ -683,7 +679,7 @@ linkml:Nodeidentifier NONLITERAL ( $ ( & ; rdf:type [ ] ? ) ; - rdf:type [ ] ? + rdf:type [ ] ) } @@ -1283,10 +1279,8 @@ linkml:Nodeidentifier NONLITERAL ) } - { - ( $ ( & ; - rdf:type [ ] ? - ) ; + CLOSED { + ( $ rdf:type . * ; rdf:type [ ] ? ) } @@ -1482,7 +1476,7 @@ linkml:Nodeidentifier NONLITERAL @ * ; @ ? ) ; - rdf:type [ ] ? + rdf:type [ ] ) } @@ -1622,7 +1616,7 @@ linkml:Nodeidentifier NONLITERAL ( $ ( & ; rdf:type [ ] ? ) ; - rdf:type [ ] ? + rdf:type [ ] ) } @@ -1750,7 +1744,7 @@ linkml:Nodeidentifier NONLITERAL ( $ ( & ; rdf:type [ ] ? ) ; - rdf:type [ ] ? + rdf:type [ ] ) } @@ -1969,9 +1963,9 @@ linkml:Nodeidentifier NONLITERAL ) ; rdf:type [ ] ) - } OR @ OR @ OR @ OR @ OR @ OR @ OR - @ OR @ OR @ OR @ OR @ OR @ OR - @ OR @ + } OR @ OR @ OR @ OR @ OR @ OR @ OR + @ OR @ OR @ OR @ OR @ OR @ OR + @ OR @ OR @ ) ( @@ -2034,17 +2028,17 @@ linkml:Nodeidentifier NONLITERAL ( $ ( & ; rdf:type [ ] ? ) ; - rdf:type [ ] ? + rdf:type [ ] ) } ( - @ OR @ OR @ OR @ + @ OR @ ) { ( $ rdf:type . * ; - rdf:type [ ] ? + rdf:type [ ] ) } @@ -2053,7 +2047,7 @@ linkml:Nodeidentifier NONLITERAL ( $ ( & ; rdf:type [ ] ? ) ; - rdf:type [ ] ? + rdf:type [ ] ) } OR @ OR @ ) @@ -2295,7 +2289,7 @@ linkml:Nodeidentifier NONLITERAL ( $ ( & ; rdf:type [ ] ? ) ; - rdf:type [ ] ? + rdf:type [ ] ) } @@ -2303,7 +2297,7 @@ linkml:Nodeidentifier NONLITERAL ( $ ( & ; rdf:type [ ] ? ) ; - rdf:type [ ] ? + rdf:type [ ] ) } @@ -2547,7 +2541,7 @@ linkml:Nodeidentifier NONLITERAL ( $ ( & ; rdf:type [ ] ? ) ; - rdf:type [ ] ? + rdf:type [ ] ) } @@ -2649,7 +2643,7 @@ linkml:Nodeidentifier NONLITERAL ( $ ( & ; rdf:type [ ] ? ) ; - rdf:type [ ] ? + rdf:type [ ] ) } @@ -2681,7 +2675,7 @@ linkml:Nodeidentifier NONLITERAL ( $ ( & ; rdf:type [ ] ? ) ; - rdf:type [ ] ? + rdf:type [ ] ) } @@ -2743,7 +2737,7 @@ linkml:Nodeidentifier NONLITERAL ( $ ( & ; rdf:type [ ] ? ) ; - rdf:type [ ] ? + rdf:type [ ] ) } @@ -2791,10 +2785,8 @@ linkml:Nodeidentifier NONLITERAL ) } - { - ( $ ( & ; - rdf:type [ ] ? - ) ; + CLOSED { + ( $ rdf:type . * ; rdf:type [ ] ? ) } @@ -2917,7 +2909,7 @@ linkml:Nodeidentifier NONLITERAL ( $ ( & ; rdf:type [ ] ? ) ; - rdf:type [ ] ? + rdf:type [ ] ) } diff --git a/biolink-modeln.shexj b/biolink-modeln.shexj index 32d856271c..0a3888fc0d 100644 --- a/biolink-modeln.shexj +++ b/biolink-modeln.shexj @@ -1,5 +1,5 @@ # metamodel_version: 1.7.0 -# version: 2.3.1 +# version: 2.4.0 { "type": "Schema", "@context": [ @@ -603,38 +603,36 @@ "type": "ShapeOr", "id": "https://w3id.org/biolink/vocab/Annotation", "shapeExprs": [ - "https://w3id.org/biolink/vocab/Attribute", + { + "type": "Shape", + "closed": false, + "expression": { + "type": "EachOf", + "expressions": [ + { + "type": "TripleConstraint", + "id": "https://w3id.org/biolink/vocab/Annotation_tes", + "predicate": "http://www.w3.org/1999/02/22-rdf-syntax-ns#type", + "min": 0, + "max": -1 + }, + { + "type": "TripleConstraint", + "predicate": "http://www.w3.org/1999/02/22-rdf-syntax-ns#type", + "valueExpr": { + "type": "NodeConstraint", + "values": [ + "https://w3id.org/biolink/vocab/Annotation" + ] + }, + "min": 0 + } + ] + } + }, "https://w3id.org/biolink/vocab/QuantityValue" ] }, - { - "type": "Shape", - "id": "https://w3id.org/biolink/vocab/Annotation_struct", - "closed": false, - "expression": { - "type": "EachOf", - "expressions": [ - { - "type": "TripleConstraint", - "id": "https://w3id.org/biolink/vocab/Annotation_tes", - "predicate": "http://www.w3.org/1999/02/22-rdf-syntax-ns#type", - "min": 0, - "max": -1 - }, - { - "type": "TripleConstraint", - "predicate": "http://www.w3.org/1999/02/22-rdf-syntax-ns#type", - "valueExpr": { - "type": "NodeConstraint", - "values": [ - "https://w3id.org/biolink/vocab/Annotation" - ] - }, - "min": 0 - } - ] - } - }, { "type": "Shape", "id": "https://w3id.org/biolink/vocab/Article", @@ -897,14 +895,14 @@ "type": "EachOf", "id": "https://w3id.org/biolink/vocab/Attribute_tes", "expressions": [ - "https://w3id.org/biolink/vocab/Annotation_tes", + "https://w3id.org/biolink/vocab/NamedThing_tes", { "type": "TripleConstraint", "predicate": "http://www.w3.org/1999/02/22-rdf-syntax-ns#type", "valueExpr": { "type": "NodeConstraint", "values": [ - "https://w3id.org/biolink/vocab/Annotation" + "https://w3id.org/biolink/vocab/NamedThing" ] }, "min": 0 @@ -948,20 +946,6 @@ "valueExpr": "https://w3id.org/biolink/vocab/NamedThing", "min": 0, "max": 1 - }, - { - "type": "TripleConstraint", - "predicate": "https://w3id.org/biolink/vocab/iri", - "valueExpr": "https://w3id.org/biolink/vocab/IriType", - "min": 0, - "max": 1 - }, - { - "type": "TripleConstraint", - "predicate": "https://w3id.org/biolink/vocab/source", - "valueExpr": "https://w3id.org/linkml/String", - "min": 0, - "max": 1 } ] }, @@ -974,7 +958,7 @@ "https://w3id.org/biolink/vocab/Attribute" ] }, - "min": 0 + "min": 1 } ] } @@ -1527,7 +1511,7 @@ "https://w3id.org/biolink/vocab/BiologicalSex" ] }, - "min": 0 + "min": 1 } ] } @@ -2582,7 +2566,7 @@ "https://w3id.org/biolink/vocab/ChemicalRole" ] }, - "min": 0 + "min": 1 } ] } @@ -3023,7 +3007,7 @@ "https://w3id.org/biolink/vocab/ClinicalAttribute" ] }, - "min": 0 + "min": 1 } ] } @@ -3070,7 +3054,7 @@ "https://w3id.org/biolink/vocab/ClinicalCourse" ] }, - "min": 0 + "min": 1 } ] } @@ -3256,7 +3240,7 @@ "https://w3id.org/biolink/vocab/ClinicalMeasurement" ] }, - "min": 0 + "min": 1 } ] } @@ -3295,7 +3279,7 @@ "https://w3id.org/biolink/vocab/ClinicalModifier" ] }, - "min": 0 + "min": 1 } ] } @@ -6360,27 +6344,16 @@ { "type": "Shape", "id": "https://w3id.org/biolink/vocab/GeneOntologyClass", - "closed": false, + "closed": true, "expression": { "type": "EachOf", "expressions": [ { - "type": "EachOf", + "type": "TripleConstraint", "id": "https://w3id.org/biolink/vocab/GeneOntologyClass_tes", - "expressions": [ - "https://w3id.org/biolink/vocab/OntologyClass_tes", - { - "type": "TripleConstraint", - "predicate": "http://www.w3.org/1999/02/22-rdf-syntax-ns#type", - "valueExpr": { - "type": "NodeConstraint", - "values": [ - "https://w3id.org/biolink/vocab/OntologyClass" - ] - }, - "min": 0 - } - ] + "predicate": "http://www.w3.org/1999/02/22-rdf-syntax-ns#type", + "min": 0, + "max": -1 }, { "type": "TripleConstraint", @@ -7433,7 +7406,7 @@ "https://w3id.org/biolink/vocab/GenomicBackgroundExposure" ] }, - "min": 0 + "min": 1 } ] } @@ -8204,7 +8177,7 @@ "https://w3id.org/biolink/vocab/GenotypicSex" ] }, - "min": 0 + "min": 1 } ] } @@ -8849,7 +8822,7 @@ "https://w3id.org/biolink/vocab/Inheritance" ] }, - "min": 0 + "min": 1 } ] } @@ -9950,6 +9923,7 @@ }, "https://w3id.org/biolink/vocab/Activity", "https://w3id.org/biolink/vocab/AdministrativeEntity", + "https://w3id.org/biolink/vocab/Attribute", "https://w3id.org/biolink/vocab/BiologicalEntity", "https://w3id.org/biolink/vocab/ChemicalEntity", "https://w3id.org/biolink/vocab/ClinicalEntity", @@ -10271,7 +10245,7 @@ "https://w3id.org/biolink/vocab/Onset" ] }, - "min": 0 + "min": 1 } ] } @@ -10280,10 +10254,8 @@ "type": "ShapeOr", "id": "https://w3id.org/biolink/vocab/OntologyClass", "shapeExprs": [ - "https://w3id.org/biolink/vocab/GeneOntologyClass", "https://w3id.org/biolink/vocab/RelationshipType", - "https://w3id.org/biolink/vocab/TaxonomicRank", - "https://w3id.org/biolink/vocab/UnclassifiedOntologyClass" + "https://w3id.org/biolink/vocab/TaxonomicRank" ] }, { @@ -10309,7 +10281,7 @@ "https://w3id.org/biolink/vocab/OntologyClass" ] }, - "min": 0 + "min": 1 } ] } @@ -10351,7 +10323,7 @@ "https://w3id.org/biolink/vocab/OrganismAttribute" ] }, - "min": 0 + "min": 1 } ] } @@ -11576,7 +11548,7 @@ "https://w3id.org/biolink/vocab/PhenotypicQuality" ] }, - "min": 0 + "min": 1 } ] } @@ -11615,7 +11587,7 @@ "https://w3id.org/biolink/vocab/PhenotypicSex" ] }, - "min": 0 + "min": 1 } ] } @@ -12848,7 +12820,7 @@ "https://w3id.org/biolink/vocab/RelationshipType" ] }, - "min": 0 + "min": 1 } ] } @@ -13370,7 +13342,7 @@ "https://w3id.org/biolink/vocab/SeverityValue" ] }, - "min": 0 + "min": 1 } ] } @@ -13526,7 +13498,7 @@ "https://w3id.org/biolink/vocab/SocioeconomicAttribute" ] }, - "min": 0 + "min": 1 } ] } @@ -13828,7 +13800,7 @@ "https://w3id.org/biolink/vocab/TaxonomicRank" ] }, - "min": 0 + "min": 1 } ] } @@ -14060,27 +14032,16 @@ { "type": "Shape", "id": "https://w3id.org/biolink/vocab/UnclassifiedOntologyClass", - "closed": false, + "closed": true, "expression": { "type": "EachOf", "expressions": [ { - "type": "EachOf", + "type": "TripleConstraint", "id": "https://w3id.org/biolink/vocab/UnclassifiedOntologyClass_tes", - "expressions": [ - "https://w3id.org/biolink/vocab/OntologyClass_tes", - { - "type": "TripleConstraint", - "predicate": "http://www.w3.org/1999/02/22-rdf-syntax-ns#type", - "valueExpr": { - "type": "NodeConstraint", - "values": [ - "https://w3id.org/biolink/vocab/OntologyClass" - ] - }, - "min": 0 - } - ] + "predicate": "http://www.w3.org/1999/02/22-rdf-syntax-ns#type", + "min": 0, + "max": -1 }, { "type": "TripleConstraint", @@ -14758,7 +14719,7 @@ "https://w3id.org/biolink/vocab/Zygosity" ] }, - "min": 0 + "min": 1 } ] } diff --git a/biolink/model.py b/biolink/model.py index 7eae057da9..10db514f7f 100644 --- a/biolink/model.py +++ b/biolink/model.py @@ -1,7 +1,5 @@ # Auto generated from biolink-model.yaml by pythongen.py version: 0.9.0 - -# Generation date: 2022-05-23T16:31:53 - +# Generation date: 2022-05-23T22:58:14 # Schema: Biolink-Model # # id: https://w3id.org/biolink/biolink-model @@ -28,7 +26,7 @@ from linkml_runtime.utils.metamodelcore import Bool, URIorCURIE, XSDDate, XSDTime metamodel_version = "1.7.0" -version = "2.3.1" +version = "2.4.0" # Overwrite dataclasses _init_fn to add **kwargs in __init__ dataclasses._init_fn = dataclasses_init_fn_with_kwargs @@ -394,35 +392,35 @@ class OntologyClassId(extended_str): pass -class AttributeId(extended_str): +class EntityId(extended_str): pass -class ChemicalRoleId(AttributeId): +class NamedThingId(EntityId): pass -class BiologicalSexId(AttributeId): +class AttributeId(NamedThingId): pass -class PhenotypicSexId(BiologicalSexId): +class ChemicalRoleId(AttributeId): pass -class GenotypicSexId(BiologicalSexId): +class BiologicalSexId(AttributeId): pass -class SeverityValueId(AttributeId): +class PhenotypicSexId(BiologicalSexId): pass -class EntityId(extended_str): +class GenotypicSexId(BiologicalSexId): pass -class NamedThingId(EntityId): +class SeverityValueId(AttributeId): pass @@ -1222,172 +1220,6 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): super().__post_init__(**kwargs) -@dataclass -class Attribute(Annotation): - """ - 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. - """ - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = BIOLINK.Attribute - class_class_curie: ClassVar[str] = "biolink:Attribute" - class_name: ClassVar[str] = "attribute" - class_model_uri: ClassVar[URIRef] = BIOLINK.Attribute - - id: Union[str, AttributeId] = None - has_attribute_type: Union[str, OntologyClassId] = None - name: Optional[Union[str, LabelType]] = None - has_quantitative_value: Optional[Union[Union[dict, QuantityValue], List[Union[dict, QuantityValue]]]] = empty_list() - has_qualitative_value: Optional[Union[str, NamedThingId]] = None - iri: Optional[Union[str, IriType]] = None - source: Optional[str] = None - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self._is_empty(self.id): - self.MissingRequiredField("id") - if not isinstance(self.id, AttributeId): - self.id = AttributeId(self.id) - - if self._is_empty(self.has_attribute_type): - self.MissingRequiredField("has_attribute_type") - if not isinstance(self.has_attribute_type, OntologyClassId): - self.has_attribute_type = OntologyClassId(self.has_attribute_type) - - if self.name is not None and not isinstance(self.name, LabelType): - self.name = LabelType(self.name) - - if not isinstance(self.has_quantitative_value, list): - self.has_quantitative_value = [self.has_quantitative_value] if self.has_quantitative_value is not None else [] - self.has_quantitative_value = [v if isinstance(v, QuantityValue) else QuantityValue(**as_dict(v)) for v in self.has_quantitative_value] - - if self.has_qualitative_value is not None and not isinstance(self.has_qualitative_value, NamedThingId): - self.has_qualitative_value = NamedThingId(self.has_qualitative_value) - - if self.iri is not None and not isinstance(self.iri, IriType): - self.iri = IriType(self.iri) - - if self.source is not None and not isinstance(self.source, str): - self.source = str(self.source) - - super().__post_init__(**kwargs) - - -@dataclass -class ChemicalRole(Attribute): - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = BIOLINK.ChemicalRole - class_class_curie: ClassVar[str] = "biolink:ChemicalRole" - class_name: ClassVar[str] = "chemical role" - class_model_uri: ClassVar[URIRef] = BIOLINK.ChemicalRole - - id: Union[str, ChemicalRoleId] = None - has_attribute_type: Union[str, OntologyClassId] = None - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self._is_empty(self.id): - self.MissingRequiredField("id") - if not isinstance(self.id, ChemicalRoleId): - self.id = ChemicalRoleId(self.id) - - super().__post_init__(**kwargs) - - -@dataclass -class BiologicalSex(Attribute): - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = BIOLINK.BiologicalSex - class_class_curie: ClassVar[str] = "biolink:BiologicalSex" - class_name: ClassVar[str] = "biological sex" - class_model_uri: ClassVar[URIRef] = BIOLINK.BiologicalSex - - id: Union[str, BiologicalSexId] = None - has_attribute_type: Union[str, OntologyClassId] = None - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self._is_empty(self.id): - self.MissingRequiredField("id") - if not isinstance(self.id, BiologicalSexId): - self.id = BiologicalSexId(self.id) - - super().__post_init__(**kwargs) - - -@dataclass -class PhenotypicSex(BiologicalSex): - """ - An attribute corresponding to the phenotypic sex of the individual, based upon the reproductive organs present. - """ - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = BIOLINK.PhenotypicSex - class_class_curie: ClassVar[str] = "biolink:PhenotypicSex" - class_name: ClassVar[str] = "phenotypic sex" - class_model_uri: ClassVar[URIRef] = BIOLINK.PhenotypicSex - - id: Union[str, PhenotypicSexId] = None - has_attribute_type: Union[str, OntologyClassId] = None - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self._is_empty(self.id): - self.MissingRequiredField("id") - if not isinstance(self.id, PhenotypicSexId): - self.id = PhenotypicSexId(self.id) - - super().__post_init__(**kwargs) - - -@dataclass -class GenotypicSex(BiologicalSex): - """ - An attribute corresponding to the genotypic sex of the individual, based upon genotypic composition of sex - chromosomes. - """ - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = BIOLINK.GenotypicSex - class_class_curie: ClassVar[str] = "biolink:GenotypicSex" - class_name: ClassVar[str] = "genotypic sex" - class_model_uri: ClassVar[URIRef] = BIOLINK.GenotypicSex - - id: Union[str, GenotypicSexId] = None - has_attribute_type: Union[str, OntologyClassId] = None - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self._is_empty(self.id): - self.MissingRequiredField("id") - if not isinstance(self.id, GenotypicSexId): - self.id = GenotypicSexId(self.id) - - super().__post_init__(**kwargs) - - -@dataclass -class SeverityValue(Attribute): - """ - describes the severity of a phenotypic feature or disease - """ - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = BIOLINK.SeverityValue - class_class_curie: ClassVar[str] = "biolink:SeverityValue" - class_name: ClassVar[str] = "severity value" - class_model_uri: ClassVar[URIRef] = BIOLINK.SeverityValue - - id: Union[str, SeverityValueId] = None - has_attribute_type: Union[str, OntologyClassId] = None - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self._is_empty(self.id): - self.MissingRequiredField("id") - if not isinstance(self.id, SeverityValueId): - self.id = SeverityValueId(self.id) - - super().__post_init__(**kwargs) - - class RelationshipQuantifier(YAMLRoot): _inherited_slots: ClassVar[List[str]] = [] @@ -1560,6 +1392,178 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): super().__post_init__(**kwargs) +@dataclass +class Attribute(NamedThing): + """ + 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. + """ + _inherited_slots: ClassVar[List[str]] = [] + + class_class_uri: ClassVar[URIRef] = BIOLINK.Attribute + class_class_curie: ClassVar[str] = "biolink:Attribute" + class_name: ClassVar[str] = "attribute" + class_model_uri: ClassVar[URIRef] = BIOLINK.Attribute + + id: Union[str, AttributeId] = None + category: Union[Union[str, CategoryType], List[Union[str, CategoryType]]] = None + has_attribute_type: Union[str, OntologyClassId] = None + name: Optional[Union[str, LabelType]] = None + has_quantitative_value: Optional[Union[Union[dict, QuantityValue], List[Union[dict, QuantityValue]]]] = empty_list() + has_qualitative_value: Optional[Union[str, NamedThingId]] = None + iri: Optional[Union[str, IriType]] = None + source: Optional[str] = None + + def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): + if self._is_empty(self.id): + self.MissingRequiredField("id") + if not isinstance(self.id, AttributeId): + self.id = AttributeId(self.id) + + if self._is_empty(self.has_attribute_type): + self.MissingRequiredField("has_attribute_type") + if not isinstance(self.has_attribute_type, OntologyClassId): + self.has_attribute_type = OntologyClassId(self.has_attribute_type) + + if self.name is not None and not isinstance(self.name, LabelType): + self.name = LabelType(self.name) + + if not isinstance(self.has_quantitative_value, list): + self.has_quantitative_value = [self.has_quantitative_value] if self.has_quantitative_value is not None else [] + self.has_quantitative_value = [v if isinstance(v, QuantityValue) else QuantityValue(**as_dict(v)) for v in self.has_quantitative_value] + + if self.has_qualitative_value is not None and not isinstance(self.has_qualitative_value, NamedThingId): + self.has_qualitative_value = NamedThingId(self.has_qualitative_value) + + if self.iri is not None and not isinstance(self.iri, IriType): + self.iri = IriType(self.iri) + + if self.source is not None and not isinstance(self.source, str): + self.source = str(self.source) + + super().__post_init__(**kwargs) + + +@dataclass +class ChemicalRole(Attribute): + _inherited_slots: ClassVar[List[str]] = [] + + class_class_uri: ClassVar[URIRef] = BIOLINK.ChemicalRole + class_class_curie: ClassVar[str] = "biolink:ChemicalRole" + class_name: ClassVar[str] = "chemical role" + class_model_uri: ClassVar[URIRef] = BIOLINK.ChemicalRole + + id: Union[str, ChemicalRoleId] = None + category: Union[Union[str, CategoryType], List[Union[str, CategoryType]]] = None + has_attribute_type: Union[str, OntologyClassId] = None + + def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): + if self._is_empty(self.id): + self.MissingRequiredField("id") + if not isinstance(self.id, ChemicalRoleId): + self.id = ChemicalRoleId(self.id) + + super().__post_init__(**kwargs) + + +@dataclass +class BiologicalSex(Attribute): + _inherited_slots: ClassVar[List[str]] = [] + + class_class_uri: ClassVar[URIRef] = BIOLINK.BiologicalSex + class_class_curie: ClassVar[str] = "biolink:BiologicalSex" + class_name: ClassVar[str] = "biological sex" + class_model_uri: ClassVar[URIRef] = BIOLINK.BiologicalSex + + id: Union[str, BiologicalSexId] = None + category: Union[Union[str, CategoryType], List[Union[str, CategoryType]]] = None + has_attribute_type: Union[str, OntologyClassId] = None + + def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): + if self._is_empty(self.id): + self.MissingRequiredField("id") + if not isinstance(self.id, BiologicalSexId): + self.id = BiologicalSexId(self.id) + + super().__post_init__(**kwargs) + + +@dataclass +class PhenotypicSex(BiologicalSex): + """ + An attribute corresponding to the phenotypic sex of the individual, based upon the reproductive organs present. + """ + _inherited_slots: ClassVar[List[str]] = [] + + class_class_uri: ClassVar[URIRef] = BIOLINK.PhenotypicSex + class_class_curie: ClassVar[str] = "biolink:PhenotypicSex" + class_name: ClassVar[str] = "phenotypic sex" + class_model_uri: ClassVar[URIRef] = BIOLINK.PhenotypicSex + + id: Union[str, PhenotypicSexId] = None + category: Union[Union[str, CategoryType], List[Union[str, CategoryType]]] = None + has_attribute_type: Union[str, OntologyClassId] = None + + def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): + if self._is_empty(self.id): + self.MissingRequiredField("id") + if not isinstance(self.id, PhenotypicSexId): + self.id = PhenotypicSexId(self.id) + + super().__post_init__(**kwargs) + + +@dataclass +class GenotypicSex(BiologicalSex): + """ + An attribute corresponding to the genotypic sex of the individual, based upon genotypic composition of sex + chromosomes. + """ + _inherited_slots: ClassVar[List[str]] = [] + + class_class_uri: ClassVar[URIRef] = BIOLINK.GenotypicSex + class_class_curie: ClassVar[str] = "biolink:GenotypicSex" + class_name: ClassVar[str] = "genotypic sex" + class_model_uri: ClassVar[URIRef] = BIOLINK.GenotypicSex + + id: Union[str, GenotypicSexId] = None + category: Union[Union[str, CategoryType], List[Union[str, CategoryType]]] = None + has_attribute_type: Union[str, OntologyClassId] = None + + def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): + if self._is_empty(self.id): + self.MissingRequiredField("id") + if not isinstance(self.id, GenotypicSexId): + self.id = GenotypicSexId(self.id) + + super().__post_init__(**kwargs) + + +@dataclass +class SeverityValue(Attribute): + """ + describes the severity of a phenotypic feature or disease + """ + _inherited_slots: ClassVar[List[str]] = [] + + class_class_uri: ClassVar[URIRef] = BIOLINK.SeverityValue + class_class_curie: ClassVar[str] = "biolink:SeverityValue" + class_name: ClassVar[str] = "severity value" + class_model_uri: ClassVar[URIRef] = BIOLINK.SeverityValue + + id: Union[str, SeverityValueId] = None + category: Union[Union[str, CategoryType], List[Union[str, CategoryType]]] = None + has_attribute_type: Union[str, OntologyClassId] = None + + def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): + if self._is_empty(self.id): + self.MissingRequiredField("id") + if not isinstance(self.id, SeverityValueId): + self.id = SeverityValueId(self.id) + + super().__post_init__(**kwargs) + + @dataclass class RelationshipType(OntologyClass): """ @@ -3166,6 +3170,7 @@ class OrganismAttribute(Attribute): class_model_uri: ClassVar[URIRef] = BIOLINK.OrganismAttribute id: Union[str, OrganismAttributeId] = None + category: Union[Union[str, CategoryType], List[Union[str, CategoryType]]] = None has_attribute_type: Union[str, OntologyClassId] = None def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): @@ -3190,6 +3195,7 @@ class PhenotypicQuality(OrganismAttribute): class_model_uri: ClassVar[URIRef] = BIOLINK.PhenotypicQuality id: Union[str, PhenotypicQualityId] = None + category: Union[Union[str, CategoryType], List[Union[str, CategoryType]]] = None has_attribute_type: Union[str, OntologyClassId] = None def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): @@ -3215,6 +3221,7 @@ class Inheritance(OrganismAttribute): class_model_uri: ClassVar[URIRef] = BIOLINK.Inheritance id: Union[str, InheritanceId] = None + category: Union[Union[str, CategoryType], List[Union[str, CategoryType]]] = None has_attribute_type: Union[str, OntologyClassId] = None def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): @@ -4197,6 +4204,7 @@ class Zygosity(Attribute): class_model_uri: ClassVar[URIRef] = BIOLINK.Zygosity id: Union[str, ZygosityId] = None + category: Union[Union[str, CategoryType], List[Union[str, CategoryType]]] = None has_attribute_type: Union[str, OntologyClassId] = None def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): @@ -4368,6 +4376,7 @@ class ClinicalAttribute(Attribute): class_model_uri: ClassVar[URIRef] = BIOLINK.ClinicalAttribute id: Union[str, ClinicalAttributeId] = None + category: Union[Union[str, CategoryType], List[Union[str, CategoryType]]] = None has_attribute_type: Union[str, OntologyClassId] = None def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): @@ -4393,6 +4402,7 @@ class ClinicalMeasurement(ClinicalAttribute): class_model_uri: ClassVar[URIRef] = BIOLINK.ClinicalMeasurement id: Union[str, ClinicalMeasurementId] = None + category: Union[Union[str, CategoryType], List[Union[str, CategoryType]]] = None has_attribute_type: Union[str, OntologyClassId] = None def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): @@ -4423,6 +4433,7 @@ class ClinicalModifier(ClinicalAttribute): class_model_uri: ClassVar[URIRef] = BIOLINK.ClinicalModifier id: Union[str, ClinicalModifierId] = None + category: Union[Union[str, CategoryType], List[Union[str, CategoryType]]] = None has_attribute_type: Union[str, OntologyClassId] = None def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): @@ -4448,6 +4459,7 @@ class ClinicalCourse(ClinicalAttribute): class_model_uri: ClassVar[URIRef] = BIOLINK.ClinicalCourse id: Union[str, ClinicalCourseId] = None + category: Union[Union[str, CategoryType], List[Union[str, CategoryType]]] = None has_attribute_type: Union[str, OntologyClassId] = None def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): @@ -4472,6 +4484,7 @@ class Onset(ClinicalCourse): class_model_uri: ClassVar[URIRef] = BIOLINK.Onset id: Union[str, OnsetId] = None + category: Union[Union[str, CategoryType], List[Union[str, CategoryType]]] = None has_attribute_type: Union[str, OntologyClassId] = None def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): @@ -4614,6 +4627,7 @@ class SocioeconomicAttribute(Attribute): class_model_uri: ClassVar[URIRef] = BIOLINK.SocioeconomicAttribute id: Union[str, SocioeconomicAttributeId] = None + category: Union[Union[str, CategoryType], List[Union[str, CategoryType]]] = None has_attribute_type: Union[str, OntologyClassId] = None def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): diff --git a/context.jsonld b/context.jsonld index 3ab23c2674..4d28f478f1 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: 2022-05-23T16:31:11\n Schema: Biolink-Model\n metamodel version: 1.7.0\n model version: 2.3.1\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: 2022-05-23T22:57:43\n Schema: Biolink-Model\n metamodel version: 1.7.0\n model version: 2.4.0\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_", @@ -518,8 +518,8 @@ "fabio": "http://purl.org/spar/fabio/", "faldo": "http://biohackathon.org/resource/faldo#", "foaf": "http://xmlns.com/foaf/0.1/", - "foodb.compound": "http://foodb.ca/compounds/", - "foodb.food": "http://example.org/UNKNOWN/foodb.food/", + "foodb.compound": "http://foodb.ca/foods/", + "foodb.food": "http://foodb.ca/compounds/", "gff3": "https://github.com/The-Sequence-Ontology/Specifications/blob/master/gff3.md#", "gpi": "https://github.com/geneontology/go-annotation/blob/master/specs/gpad-gpi-2-0.md#", "gtpo": "https://rdf.guidetopharmacology.org/ns/gtpo#", diff --git a/contextn.jsonld b/contextn.jsonld index 28f1385e42..83487b92ee 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: 2022-05-20T22:58:46\n Schema: Biolink-Model\n metamodel version: 1.7.0\n model version: 2.3.0\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: 2022-05-23T22:57:47\n Schema: Biolink-Model\n metamodel version: 1.7.0\n model version: 2.4.0\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_", @@ -518,8 +518,8 @@ "fabio": "http://purl.org/spar/fabio/", "faldo": "http://biohackathon.org/resource/faldo#", "foaf": "http://xmlns.com/foaf/0.1/", - "foodb.compound": "http://foodb.ca/compounds/", - "foodb.food": "http://example.org/UNKNOWN/foodb.food/", + "foodb.compound": "http://foodb.ca/foods/", + "foodb.food": "http://foodb.ca/compounds/", "gff3": "https://github.com/The-Sequence-Ontology/Specifications/blob/master/gff3.md#", "gpi": "https://github.com/geneontology/go-annotation/blob/master/specs/gpad-gpi-2-0.md#", "gtpo": "https://rdf.guidetopharmacology.org/ns/gtpo#", diff --git a/golr-views/RNA_product_config.yaml b/golr-views/RNA_product_config.yaml index 9a6f38171e..701905df33 100644 --- a/golr-views/RNA_product_config.yaml +++ b/golr-views/RNA_product_config.yaml @@ -1,4 +1,4 @@ -# metamodel_version: 1.7.0# version: 2.3.1id: RNA_product +# metamodel_version: 1.7.0# version: 2.4.0id: RNA_product schema_generating: true display_name: RNA product document_category: RNA product diff --git a/golr-views/RNA_product_isoform_config.yaml b/golr-views/RNA_product_isoform_config.yaml index 19966322c6..bfbabfa068 100644 --- a/golr-views/RNA_product_isoform_config.yaml +++ b/golr-views/RNA_product_isoform_config.yaml @@ -1,4 +1,4 @@ -# metamodel_version: 1.7.0# version: 2.3.1id: RNA_product_isoform +# metamodel_version: 1.7.0# version: 2.4.0id: RNA_product_isoform schema_generating: true description: Represents a protein that is a specific isoform of the canonical or reference RNA diff --git a/golr-views/activity_config.yaml b/golr-views/activity_config.yaml index e79537314c..aef2007fc5 100644 --- a/golr-views/activity_config.yaml +++ b/golr-views/activity_config.yaml @@ -1,4 +1,4 @@ -# metamodel_version: 1.7.0# version: 2.3.1id: activity +# metamodel_version: 1.7.0# version: 2.4.0id: activity schema_generating: true 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, diff --git a/golr-views/agent_config.yaml b/golr-views/agent_config.yaml index 89bb6ecd5f..ab033ad905 100644 --- a/golr-views/agent_config.yaml +++ b/golr-views/agent_config.yaml @@ -1,4 +1,4 @@ -# metamodel_version: 1.7.0# version: 2.3.1id: agent +# metamodel_version: 1.7.0# version: 2.4.0id: agent schema_generating: true description: person, group, organization or project that provides a piece of information (i.e. a knowledge association) diff --git a/golr-views/anatomical_entity_config.yaml b/golr-views/anatomical_entity_config.yaml index 6e93eb12cc..1aac262522 100644 --- a/golr-views/anatomical_entity_config.yaml +++ b/golr-views/anatomical_entity_config.yaml @@ -1,4 +1,4 @@ -# metamodel_version: 1.7.0# version: 2.3.1id: anatomical_entity +# metamodel_version: 1.7.0# version: 2.4.0id: anatomical_entity schema_generating: true description: A subcellular location, cell type or gross anatomical part display_name: anatomical entity diff --git a/golr-views/anatomical_entity_to_anatomical_entity_ontogenic_association_config.yaml b/golr-views/anatomical_entity_to_anatomical_entity_ontogenic_association_config.yaml index 8bf0156561..a6c1cb4d5f 100644 --- a/golr-views/anatomical_entity_to_anatomical_entity_ontogenic_association_config.yaml +++ b/golr-views/anatomical_entity_to_anatomical_entity_ontogenic_association_config.yaml @@ -1,4 +1,4 @@ -# metamodel_version: 1.7.0# version: 2.3.1id: anatomical_entity_to_anatomical_entity_ontogenic_association +# metamodel_version: 1.7.0# version: 2.4.0id: anatomical_entity_to_anatomical_entity_ontogenic_association schema_generating: true description: A relationship between two anatomical entities where the relationship is ontogenic, i.e. the two entities are related by development. A number of different diff --git a/golr-views/anatomical_entity_to_anatomical_entity_part_of_association_config.yaml b/golr-views/anatomical_entity_to_anatomical_entity_part_of_association_config.yaml index f59d7cb9f3..297cd6091f 100644 --- a/golr-views/anatomical_entity_to_anatomical_entity_part_of_association_config.yaml +++ b/golr-views/anatomical_entity_to_anatomical_entity_part_of_association_config.yaml @@ -1,4 +1,4 @@ -# metamodel_version: 1.7.0# version: 2.3.1id: anatomical_entity_to_anatomical_entity_part_of_association +# metamodel_version: 1.7.0# version: 2.4.0id: anatomical_entity_to_anatomical_entity_part_of_association schema_generating: true description: A relationship between two anatomical entities where the relationship is mereological, i.e the two entities are related by parthood. This includes relationships diff --git a/golr-views/article_config.yaml b/golr-views/article_config.yaml index 0703060eb3..c30c60eefc 100644 --- a/golr-views/article_config.yaml +++ b/golr-views/article_config.yaml @@ -1,4 +1,4 @@ -# metamodel_version: 1.7.0# version: 2.3.1id: article +# metamodel_version: 1.7.0# version: 2.4.0id: article schema_generating: true display_name: article document_category: article diff --git a/golr-views/association_config.yaml b/golr-views/association_config.yaml index a274e80228..7338d7cddd 100644 --- a/golr-views/association_config.yaml +++ b/golr-views/association_config.yaml @@ -1,4 +1,4 @@ -# metamodel_version: 1.7.0# version: 2.3.1id: association +# metamodel_version: 1.7.0# version: 2.4.0id: association schema_generating: true description: A typed association between two entities, supported by evidence display_name: association diff --git a/golr-views/attribute_config.yaml b/golr-views/attribute_config.yaml index d5db89cd1a..9ab7d3ecd3 100644 --- a/golr-views/attribute_config.yaml +++ b/golr-views/attribute_config.yaml @@ -1,4 +1,4 @@ -# metamodel_version: 1.7.0# version: 2.3.1id: attribute +# metamodel_version: 1.7.0# version: 2.4.0id: attribute schema_generating: true 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 @@ -7,6 +7,44 @@ display_name: attribute document_category: attribute weight: 20 fields: +- id: id + description: A unique identifier for an entity. Must be either a CURIE shorthand + for a URI or a complete URI + display_name: id +- id: type + display_name: type +- id: description + description: a human-readable description of an entity + display_name: description +- id: has_attribute + description: connects any entity to an attribute + display_name: has attribute + cardinality: multi +- id: provided_by + description: The value in this node property represents the knowledge provider that + created or assembled the node and all of its attributes. Used internally to represent + how a particular node made its way into a knowledge provider or graph. + display_name: provided by + cardinality: multi +- id: xref + description: Alternate CURIEs for a thing + display_name: xref + cardinality: multi +- id: category + description: "Name of the high level ontology class in which this entity is categorized.\ + \ Corresponds to the label for the biolink entity type class.\n * In a neo4j database\ + \ this MAY correspond to the neo4j label tag.\n * In an RDF database it should\ + \ be a biolink model class URI.\nThis field is multi-valued. It should include\ + \ values for ancestors of the biolink class; for example, a protein such as Shh\ + \ would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`,\ + \ ...\nIn an RDF database, nodes will typically have an rdf:type triples. This\ + \ can be to the most specific biolink class, or potentially to a class more specific\ + \ than something in biolink. For example, a sequence feature `f` may have a rdf:type\ + \ assertion to a SO class such as TF_binding_site, which is more specific than\ + \ anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity,\ + \ biolink:NamedThing}" + display_name: named thing_category + cardinality: multi - id: name description: The human-readable 'attribute name' can be set to a string which reflects its context of interpretation, e.g. SEPIO evidence/provenance/confidence annotation diff --git a/golr-views/behavior_config.yaml b/golr-views/behavior_config.yaml index 7606b4ed84..f3d1beaf86 100644 --- a/golr-views/behavior_config.yaml +++ b/golr-views/behavior_config.yaml @@ -1,4 +1,4 @@ -# metamodel_version: 1.7.0# version: 2.3.1id: behavior +# metamodel_version: 1.7.0# version: 2.4.0id: behavior schema_generating: true display_name: behavior document_category: behavior diff --git a/golr-views/behavior_to_behavioral_feature_association_config.yaml b/golr-views/behavior_to_behavioral_feature_association_config.yaml index 6743a16abc..b8eeb1f8a3 100644 --- a/golr-views/behavior_to_behavioral_feature_association_config.yaml +++ b/golr-views/behavior_to_behavioral_feature_association_config.yaml @@ -1,4 +1,4 @@ -# metamodel_version: 1.7.0# version: 2.3.1id: behavior_to_behavioral_feature_association +# metamodel_version: 1.7.0# version: 2.4.0id: behavior_to_behavioral_feature_association schema_generating: true description: An association between an mixture behavior and a behavioral feature manifested by the individual exhibited or has exhibited the behavior. diff --git a/golr-views/behavioral_feature_config.yaml b/golr-views/behavioral_feature_config.yaml index 37746d33ec..702db54c92 100644 --- a/golr-views/behavioral_feature_config.yaml +++ b/golr-views/behavioral_feature_config.yaml @@ -1,4 +1,4 @@ -# metamodel_version: 1.7.0# version: 2.3.1id: behavioral_feature +# metamodel_version: 1.7.0# version: 2.4.0id: behavioral_feature schema_generating: true description: A phenotypic feature which is behavioral in nature. display_name: behavioral feature diff --git a/golr-views/biological_process_config.yaml b/golr-views/biological_process_config.yaml index 351f95416a..f258672462 100644 --- a/golr-views/biological_process_config.yaml +++ b/golr-views/biological_process_config.yaml @@ -1,4 +1,4 @@ -# metamodel_version: 1.7.0# version: 2.3.1id: biological_process +# metamodel_version: 1.7.0# version: 2.4.0id: biological_process schema_generating: true description: One or more causally connected executions of molecular functions display_name: biological process diff --git a/golr-views/biological_process_or_activity_config.yaml b/golr-views/biological_process_or_activity_config.yaml index 0d7e9bdd4c..253ff5d767 100644 --- a/golr-views/biological_process_or_activity_config.yaml +++ b/golr-views/biological_process_or_activity_config.yaml @@ -1,4 +1,4 @@ -# metamodel_version: 1.7.0# version: 2.3.1id: biological_process_or_activity +# metamodel_version: 1.7.0# version: 2.4.0id: biological_process_or_activity schema_generating: true description: Either an individual molecular activity, or a collection of causally connected molecular activities in a biological system. diff --git a/golr-views/biological_sex_config.yaml b/golr-views/biological_sex_config.yaml index bd9832c8df..3694f43748 100644 --- a/golr-views/biological_sex_config.yaml +++ b/golr-views/biological_sex_config.yaml @@ -1,9 +1,47 @@ -# metamodel_version: 1.7.0# version: 2.3.1id: biological_sex +# metamodel_version: 1.7.0# version: 2.4.0id: biological_sex schema_generating: true display_name: biological sex document_category: biological sex weight: 20 fields: +- id: id + description: A unique identifier for an entity. Must be either a CURIE shorthand + for a URI or a complete URI + display_name: id +- id: type + display_name: type +- id: description + description: a human-readable description of an entity + display_name: description +- id: has_attribute + description: connects any entity to an attribute + display_name: has attribute + cardinality: multi +- id: provided_by + description: The value in this node property represents the knowledge provider that + created or assembled the node and all of its attributes. Used internally to represent + how a particular node made its way into a knowledge provider or graph. + display_name: provided by + cardinality: multi +- id: xref + description: Alternate CURIEs for a thing + display_name: xref + cardinality: multi +- id: category + description: "Name of the high level ontology class in which this entity is categorized.\ + \ Corresponds to the label for the biolink entity type class.\n * In a neo4j database\ + \ this MAY correspond to the neo4j label tag.\n * In an RDF database it should\ + \ be a biolink model class URI.\nThis field is multi-valued. It should include\ + \ values for ancestors of the biolink class; for example, a protein such as Shh\ + \ would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`,\ + \ ...\nIn an RDF database, nodes will typically have an rdf:type triples. This\ + \ can be to the most specific biolink class, or potentially to a class more specific\ + \ than something in biolink. For example, a sequence feature `f` may have a rdf:type\ + \ assertion to a SO class such as TF_binding_site, which is more specific than\ + \ anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity,\ + \ biolink:NamedThing}" + display_name: named thing_category + cardinality: multi - id: name description: The human-readable 'attribute name' can be set to a string which reflects its context of interpretation, e.g. SEPIO evidence/provenance/confidence annotation diff --git a/golr-views/book_chapter_config.yaml b/golr-views/book_chapter_config.yaml index f97c97a96a..0009719455 100644 --- a/golr-views/book_chapter_config.yaml +++ b/golr-views/book_chapter_config.yaml @@ -1,4 +1,4 @@ -# metamodel_version: 1.7.0# version: 2.3.1id: book_chapter +# metamodel_version: 1.7.0# version: 2.4.0id: book_chapter schema_generating: true display_name: book chapter document_category: book chapter diff --git a/golr-views/book_config.yaml b/golr-views/book_config.yaml index 625819e376..c3a263924b 100644 --- a/golr-views/book_config.yaml +++ b/golr-views/book_config.yaml @@ -1,4 +1,4 @@ -# metamodel_version: 1.7.0# version: 2.3.1id: book +# metamodel_version: 1.7.0# version: 2.4.0id: book schema_generating: true description: This class may rarely be instantiated except if use cases of a given knowledge graph support its utility. diff --git a/golr-views/case_config.yaml b/golr-views/case_config.yaml index 97cce4e9d4..d75424af00 100644 --- a/golr-views/case_config.yaml +++ b/golr-views/case_config.yaml @@ -1,4 +1,4 @@ -# metamodel_version: 1.7.0# version: 2.3.1id: case +# metamodel_version: 1.7.0# version: 2.4.0id: case schema_generating: true description: An individual (human) organism that has a patient role in some clinical context. diff --git a/golr-views/case_to_phenotypic_feature_association_config.yaml b/golr-views/case_to_phenotypic_feature_association_config.yaml index 43cd695c96..7c3a57e76e 100644 --- a/golr-views/case_to_phenotypic_feature_association_config.yaml +++ b/golr-views/case_to_phenotypic_feature_association_config.yaml @@ -1,4 +1,4 @@ -# metamodel_version: 1.7.0# version: 2.3.1id: case_to_phenotypic_feature_association +# metamodel_version: 1.7.0# version: 2.4.0id: case_to_phenotypic_feature_association schema_generating: true description: An association between a case (e.g. individual patient) and a phenotypic feature in which the individual has or has had the phenotype. diff --git a/golr-views/cell_config.yaml b/golr-views/cell_config.yaml index f9d09c21d0..e59e7b4ed2 100644 --- a/golr-views/cell_config.yaml +++ b/golr-views/cell_config.yaml @@ -1,4 +1,4 @@ -# metamodel_version: 1.7.0# version: 2.3.1id: cell +# metamodel_version: 1.7.0# version: 2.4.0id: cell schema_generating: true display_name: cell document_category: cell diff --git a/golr-views/cell_line_as_a_model_of_disease_association_config.yaml b/golr-views/cell_line_as_a_model_of_disease_association_config.yaml index 6a4bcb101e..24a6d4034e 100644 --- a/golr-views/cell_line_as_a_model_of_disease_association_config.yaml +++ b/golr-views/cell_line_as_a_model_of_disease_association_config.yaml @@ -1,4 +1,4 @@ -# metamodel_version: 1.7.0# version: 2.3.1id: cell_line_as_a_model_of_disease_association +# metamodel_version: 1.7.0# version: 2.4.0id: cell_line_as_a_model_of_disease_association schema_generating: true display_name: cell line as a model of disease association document_category: cell line as a model of disease association diff --git a/golr-views/cell_line_config.yaml b/golr-views/cell_line_config.yaml index ab5915b95b..31a577367e 100644 --- a/golr-views/cell_line_config.yaml +++ b/golr-views/cell_line_config.yaml @@ -1,4 +1,4 @@ -# metamodel_version: 1.7.0# version: 2.3.1id: cell_line +# metamodel_version: 1.7.0# version: 2.4.0id: cell_line schema_generating: true display_name: cell line document_category: cell line diff --git a/golr-views/cell_line_to_disease_or_phenotypic_feature_association_config.yaml b/golr-views/cell_line_to_disease_or_phenotypic_feature_association_config.yaml index 7025b74b1d..1a92ab75ed 100644 --- a/golr-views/cell_line_to_disease_or_phenotypic_feature_association_config.yaml +++ b/golr-views/cell_line_to_disease_or_phenotypic_feature_association_config.yaml @@ -1,4 +1,4 @@ -# metamodel_version: 1.7.0# version: 2.3.1id: cell_line_to_disease_or_phenotypic_feature_association +# metamodel_version: 1.7.0# version: 2.4.0id: cell_line_to_disease_or_phenotypic_feature_association schema_generating: true description: An relationship between a cell line and a disease or a phenotype, where the cell line is derived from an individual with that disease or phenotype. diff --git a/golr-views/cellular_component_config.yaml b/golr-views/cellular_component_config.yaml index afb1053511..c663c4b442 100644 --- a/golr-views/cellular_component_config.yaml +++ b/golr-views/cellular_component_config.yaml @@ -1,4 +1,4 @@ -# metamodel_version: 1.7.0# version: 2.3.1id: cellular_component +# metamodel_version: 1.7.0# version: 2.4.0id: cellular_component schema_generating: true description: A location in or around a cell display_name: cellular component diff --git a/golr-views/chemical_entity_config.yaml b/golr-views/chemical_entity_config.yaml index 9f767eeabc..361c8ed154 100644 --- a/golr-views/chemical_entity_config.yaml +++ b/golr-views/chemical_entity_config.yaml @@ -1,4 +1,4 @@ -# metamodel_version: 1.7.0# version: 2.3.1id: chemical_entity +# metamodel_version: 1.7.0# version: 2.4.0id: chemical_entity schema_generating: true description: A chemical entity is a physical entity that pertains to chemistry or biochemistry. diff --git a/golr-views/chemical_exposure_config.yaml b/golr-views/chemical_exposure_config.yaml index 26d74c33e3..f2ad5318ee 100644 --- a/golr-views/chemical_exposure_config.yaml +++ b/golr-views/chemical_exposure_config.yaml @@ -1,4 +1,4 @@ -# metamodel_version: 1.7.0# version: 2.3.1id: chemical_exposure +# metamodel_version: 1.7.0# version: 2.4.0id: chemical_exposure schema_generating: true description: A chemical exposure is an intake of a particular chemical entity. display_name: chemical exposure diff --git a/golr-views/chemical_mixture_config.yaml b/golr-views/chemical_mixture_config.yaml index bd087e6657..a08db7555e 100644 --- a/golr-views/chemical_mixture_config.yaml +++ b/golr-views/chemical_mixture_config.yaml @@ -1,4 +1,4 @@ -# metamodel_version: 1.7.0# version: 2.3.1id: chemical_mixture +# metamodel_version: 1.7.0# version: 2.4.0id: chemical_mixture schema_generating: true description: A chemical mixture is a chemical entity composed of two or more molecular entities. diff --git a/golr-views/chemical_role_config.yaml b/golr-views/chemical_role_config.yaml index 091b3d6367..af16c27236 100644 --- a/golr-views/chemical_role_config.yaml +++ b/golr-views/chemical_role_config.yaml @@ -1,9 +1,47 @@ -# metamodel_version: 1.7.0# version: 2.3.1id: chemical_role +# metamodel_version: 1.7.0# version: 2.4.0id: chemical_role schema_generating: true display_name: chemical role document_category: chemical role weight: 20 fields: +- id: id + description: A unique identifier for an entity. Must be either a CURIE shorthand + for a URI or a complete URI + display_name: id +- id: type + display_name: type +- id: description + description: a human-readable description of an entity + display_name: description +- id: has_attribute + description: connects any entity to an attribute + display_name: has attribute + cardinality: multi +- id: provided_by + description: The value in this node property represents the knowledge provider that + created or assembled the node and all of its attributes. Used internally to represent + how a particular node made its way into a knowledge provider or graph. + display_name: provided by + cardinality: multi +- id: xref + description: Alternate CURIEs for a thing + display_name: xref + cardinality: multi +- id: category + description: "Name of the high level ontology class in which this entity is categorized.\ + \ Corresponds to the label for the biolink entity type class.\n * In a neo4j database\ + \ this MAY correspond to the neo4j label tag.\n * In an RDF database it should\ + \ be a biolink model class URI.\nThis field is multi-valued. It should include\ + \ values for ancestors of the biolink class; for example, a protein such as Shh\ + \ would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`,\ + \ ...\nIn an RDF database, nodes will typically have an rdf:type triples. This\ + \ can be to the most specific biolink class, or potentially to a class more specific\ + \ than something in biolink. For example, a sequence feature `f` may have a rdf:type\ + \ assertion to a SO class such as TF_binding_site, which is more specific than\ + \ anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity,\ + \ biolink:NamedThing}" + display_name: named thing_category + cardinality: multi - id: name description: The human-readable 'attribute name' can be set to a string which reflects its context of interpretation, e.g. SEPIO evidence/provenance/confidence annotation diff --git a/golr-views/chemical_to_chemical_association_config.yaml b/golr-views/chemical_to_chemical_association_config.yaml index 4f3143786f..4b68d294b6 100644 --- a/golr-views/chemical_to_chemical_association_config.yaml +++ b/golr-views/chemical_to_chemical_association_config.yaml @@ -1,4 +1,4 @@ -# metamodel_version: 1.7.0# version: 2.3.1id: chemical_to_chemical_association +# metamodel_version: 1.7.0# version: 2.4.0id: chemical_to_chemical_association schema_generating: true description: A relationship between two chemical entities. This can encompass actual interactions as well as temporal causal edges, e.g. one chemical converted to another. diff --git a/golr-views/chemical_to_chemical_derivation_association_config.yaml b/golr-views/chemical_to_chemical_derivation_association_config.yaml index 036f88b32c..aef7e5b9cb 100644 --- a/golr-views/chemical_to_chemical_derivation_association_config.yaml +++ b/golr-views/chemical_to_chemical_derivation_association_config.yaml @@ -1,4 +1,4 @@ -# metamodel_version: 1.7.0# version: 2.3.1id: chemical_to_chemical_derivation_association +# metamodel_version: 1.7.0# version: 2.4.0id: chemical_to_chemical_derivation_association schema_generating: true description: "A causal relationship between two chemical entities, where the subject\ \ represents the upstream entity and the object represents the downstream. For any\ diff --git a/golr-views/chemical_to_disease_or_phenotypic_feature_association_config.yaml b/golr-views/chemical_to_disease_or_phenotypic_feature_association_config.yaml index 2a557ade1c..e0706787b6 100644 --- a/golr-views/chemical_to_disease_or_phenotypic_feature_association_config.yaml +++ b/golr-views/chemical_to_disease_or_phenotypic_feature_association_config.yaml @@ -1,4 +1,4 @@ -# metamodel_version: 1.7.0# version: 2.3.1id: chemical_to_disease_or_phenotypic_feature_association +# metamodel_version: 1.7.0# version: 2.4.0id: chemical_to_disease_or_phenotypic_feature_association schema_generating: true description: An interaction between a chemical entity and a phenotype or disease, where the presence of the chemical gives rise to or exacerbates the phenotype. diff --git a/golr-views/chemical_to_gene_association_config.yaml b/golr-views/chemical_to_gene_association_config.yaml index f1815d54b7..1a64cd6f9f 100644 --- a/golr-views/chemical_to_gene_association_config.yaml +++ b/golr-views/chemical_to_gene_association_config.yaml @@ -1,4 +1,4 @@ -# metamodel_version: 1.7.0# version: 2.3.1id: chemical_to_gene_association +# metamodel_version: 1.7.0# version: 2.4.0id: chemical_to_gene_association schema_generating: true description: An interaction between a chemical entity and a gene or gene product. display_name: chemical to gene association diff --git a/golr-views/chemical_to_pathway_association_config.yaml b/golr-views/chemical_to_pathway_association_config.yaml index b27ac9377b..786b3f9264 100644 --- a/golr-views/chemical_to_pathway_association_config.yaml +++ b/golr-views/chemical_to_pathway_association_config.yaml @@ -1,4 +1,4 @@ -# metamodel_version: 1.7.0# version: 2.3.1id: chemical_to_pathway_association +# metamodel_version: 1.7.0# version: 2.4.0id: chemical_to_pathway_association schema_generating: true description: An interaction between a chemical entity and a biological process or pathway. diff --git a/golr-views/clinical_attribute_config.yaml b/golr-views/clinical_attribute_config.yaml index 29d86285c1..8baf139a81 100644 --- a/golr-views/clinical_attribute_config.yaml +++ b/golr-views/clinical_attribute_config.yaml @@ -1,10 +1,48 @@ -# metamodel_version: 1.7.0# version: 2.3.1id: clinical_attribute +# metamodel_version: 1.7.0# version: 2.4.0id: clinical_attribute schema_generating: true description: Attributes relating to a clinical manifestation display_name: clinical attribute document_category: clinical attribute weight: 20 fields: +- id: id + description: A unique identifier for an entity. Must be either a CURIE shorthand + for a URI or a complete URI + display_name: id +- id: type + display_name: type +- id: description + description: a human-readable description of an entity + display_name: description +- id: has_attribute + description: connects any entity to an attribute + display_name: has attribute + cardinality: multi +- id: provided_by + description: The value in this node property represents the knowledge provider that + created or assembled the node and all of its attributes. Used internally to represent + how a particular node made its way into a knowledge provider or graph. + display_name: provided by + cardinality: multi +- id: xref + description: Alternate CURIEs for a thing + display_name: xref + cardinality: multi +- id: category + description: "Name of the high level ontology class in which this entity is categorized.\ + \ Corresponds to the label for the biolink entity type class.\n * In a neo4j database\ + \ this MAY correspond to the neo4j label tag.\n * In an RDF database it should\ + \ be a biolink model class URI.\nThis field is multi-valued. It should include\ + \ values for ancestors of the biolink class; for example, a protein such as Shh\ + \ would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`,\ + \ ...\nIn an RDF database, nodes will typically have an rdf:type triples. This\ + \ can be to the most specific biolink class, or potentially to a class more specific\ + \ than something in biolink. For example, a sequence feature `f` may have a rdf:type\ + \ assertion to a SO class such as TF_binding_site, which is more specific than\ + \ anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity,\ + \ biolink:NamedThing}" + display_name: named thing_category + cardinality: multi - id: name description: The human-readable 'attribute name' can be set to a string which reflects its context of interpretation, e.g. SEPIO evidence/provenance/confidence annotation diff --git a/golr-views/clinical_course_config.yaml b/golr-views/clinical_course_config.yaml index 9dff6db106..6cca9bdca8 100644 --- a/golr-views/clinical_course_config.yaml +++ b/golr-views/clinical_course_config.yaml @@ -1,4 +1,4 @@ -# metamodel_version: 1.7.0# version: 2.3.1id: clinical_course +# metamodel_version: 1.7.0# version: 2.4.0id: clinical_course schema_generating: true description: The course a disease typically takes from its onset, progression in time, and eventual resolution or death of the affected individual @@ -6,6 +6,44 @@ display_name: clinical course document_category: clinical course weight: 20 fields: +- id: id + description: A unique identifier for an entity. Must be either a CURIE shorthand + for a URI or a complete URI + display_name: id +- id: type + display_name: type +- id: description + description: a human-readable description of an entity + display_name: description +- id: has_attribute + description: connects any entity to an attribute + display_name: has attribute + cardinality: multi +- id: provided_by + description: The value in this node property represents the knowledge provider that + created or assembled the node and all of its attributes. Used internally to represent + how a particular node made its way into a knowledge provider or graph. + display_name: provided by + cardinality: multi +- id: xref + description: Alternate CURIEs for a thing + display_name: xref + cardinality: multi +- id: category + description: "Name of the high level ontology class in which this entity is categorized.\ + \ Corresponds to the label for the biolink entity type class.\n * In a neo4j database\ + \ this MAY correspond to the neo4j label tag.\n * In an RDF database it should\ + \ be a biolink model class URI.\nThis field is multi-valued. It should include\ + \ values for ancestors of the biolink class; for example, a protein such as Shh\ + \ would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`,\ + \ ...\nIn an RDF database, nodes will typically have an rdf:type triples. This\ + \ can be to the most specific biolink class, or potentially to a class more specific\ + \ than something in biolink. For example, a sequence feature `f` may have a rdf:type\ + \ assertion to a SO class such as TF_binding_site, which is more specific than\ + \ anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity,\ + \ biolink:NamedThing}" + display_name: named thing_category + cardinality: multi - id: name description: The human-readable 'attribute name' can be set to a string which reflects its context of interpretation, e.g. SEPIO evidence/provenance/confidence annotation diff --git a/golr-views/clinical_entity_config.yaml b/golr-views/clinical_entity_config.yaml index 77bbe582f8..b827aaa060 100644 --- a/golr-views/clinical_entity_config.yaml +++ b/golr-views/clinical_entity_config.yaml @@ -1,4 +1,4 @@ -# metamodel_version: 1.7.0# version: 2.3.1id: clinical_entity +# metamodel_version: 1.7.0# version: 2.4.0id: clinical_entity schema_generating: true description: Any entity or process that exists in the clinical domain and outside the biological realm. Diseases are placed under biological entities diff --git a/golr-views/clinical_finding_config.yaml b/golr-views/clinical_finding_config.yaml index 72e4f57c1f..c9864d517e 100644 --- a/golr-views/clinical_finding_config.yaml +++ b/golr-views/clinical_finding_config.yaml @@ -1,4 +1,4 @@ -# metamodel_version: 1.7.0# version: 2.3.1id: clinical_finding +# metamodel_version: 1.7.0# version: 2.4.0id: clinical_finding schema_generating: true description: this category is currently considered broad enough to tag clinical lab measurements and other biological attributes taken as 'clinical traits' with some diff --git a/golr-views/clinical_intervention_config.yaml b/golr-views/clinical_intervention_config.yaml index e0a87d3250..32b86a8955 100644 --- a/golr-views/clinical_intervention_config.yaml +++ b/golr-views/clinical_intervention_config.yaml @@ -1,4 +1,4 @@ -# metamodel_version: 1.7.0# version: 2.3.1id: clinical_intervention +# metamodel_version: 1.7.0# version: 2.4.0id: clinical_intervention schema_generating: true display_name: clinical intervention document_category: clinical intervention diff --git a/golr-views/clinical_measurement_config.yaml b/golr-views/clinical_measurement_config.yaml index 0a72ed4fb4..a1d8d9aa41 100644 --- a/golr-views/clinical_measurement_config.yaml +++ b/golr-views/clinical_measurement_config.yaml @@ -1,4 +1,4 @@ -# metamodel_version: 1.7.0# version: 2.3.1id: clinical_measurement +# metamodel_version: 1.7.0# version: 2.4.0id: clinical_measurement schema_generating: true 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 @@ -7,6 +7,44 @@ display_name: clinical measurement document_category: clinical measurement weight: 20 fields: +- id: id + description: A unique identifier for an entity. Must be either a CURIE shorthand + for a URI or a complete URI + display_name: id +- id: type + display_name: type +- id: description + description: a human-readable description of an entity + display_name: description +- id: has_attribute + description: connects any entity to an attribute + display_name: has attribute + cardinality: multi +- id: provided_by + description: The value in this node property represents the knowledge provider that + created or assembled the node and all of its attributes. Used internally to represent + how a particular node made its way into a knowledge provider or graph. + display_name: provided by + cardinality: multi +- id: xref + description: Alternate CURIEs for a thing + display_name: xref + cardinality: multi +- id: category + description: "Name of the high level ontology class in which this entity is categorized.\ + \ Corresponds to the label for the biolink entity type class.\n * In a neo4j database\ + \ this MAY correspond to the neo4j label tag.\n * In an RDF database it should\ + \ be a biolink model class URI.\nThis field is multi-valued. It should include\ + \ values for ancestors of the biolink class; for example, a protein such as Shh\ + \ would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`,\ + \ ...\nIn an RDF database, nodes will typically have an rdf:type triples. This\ + \ can be to the most specific biolink class, or potentially to a class more specific\ + \ than something in biolink. For example, a sequence feature `f` may have a rdf:type\ + \ assertion to a SO class such as TF_binding_site, which is more specific than\ + \ anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity,\ + \ biolink:NamedThing}" + display_name: named thing_category + cardinality: multi - id: name description: The human-readable 'attribute name' can be set to a string which reflects its context of interpretation, e.g. SEPIO evidence/provenance/confidence annotation diff --git a/golr-views/clinical_modifier_config.yaml b/golr-views/clinical_modifier_config.yaml index 7b13ba93ee..afe0018065 100644 --- a/golr-views/clinical_modifier_config.yaml +++ b/golr-views/clinical_modifier_config.yaml @@ -1,4 +1,4 @@ -# metamodel_version: 1.7.0# version: 2.3.1id: clinical_modifier +# metamodel_version: 1.7.0# version: 2.4.0id: clinical_modifier schema_generating: true description: Used to characterize and specify the phenotypic abnormalities defined in the phenotypic abnormality sub-ontology, with respect to severity, laterality, @@ -7,6 +7,44 @@ display_name: clinical modifier document_category: clinical modifier weight: 20 fields: +- id: id + description: A unique identifier for an entity. Must be either a CURIE shorthand + for a URI or a complete URI + display_name: id +- id: type + display_name: type +- id: description + description: a human-readable description of an entity + display_name: description +- id: has_attribute + description: connects any entity to an attribute + display_name: has attribute + cardinality: multi +- id: provided_by + description: The value in this node property represents the knowledge provider that + created or assembled the node and all of its attributes. Used internally to represent + how a particular node made its way into a knowledge provider or graph. + display_name: provided by + cardinality: multi +- id: xref + description: Alternate CURIEs for a thing + display_name: xref + cardinality: multi +- id: category + description: "Name of the high level ontology class in which this entity is categorized.\ + \ Corresponds to the label for the biolink entity type class.\n * In a neo4j database\ + \ this MAY correspond to the neo4j label tag.\n * In an RDF database it should\ + \ be a biolink model class URI.\nThis field is multi-valued. It should include\ + \ values for ancestors of the biolink class; for example, a protein such as Shh\ + \ would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`,\ + \ ...\nIn an RDF database, nodes will typically have an rdf:type triples. This\ + \ can be to the most specific biolink class, or potentially to a class more specific\ + \ than something in biolink. For example, a sequence feature `f` may have a rdf:type\ + \ assertion to a SO class such as TF_binding_site, which is more specific than\ + \ anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity,\ + \ biolink:NamedThing}" + display_name: named thing_category + cardinality: multi - id: name description: The human-readable 'attribute name' can be set to a string which reflects its context of interpretation, e.g. SEPIO evidence/provenance/confidence annotation diff --git a/golr-views/clinical_trial_config.yaml b/golr-views/clinical_trial_config.yaml index ada2136dd5..7fe8f7161c 100644 --- a/golr-views/clinical_trial_config.yaml +++ b/golr-views/clinical_trial_config.yaml @@ -1,4 +1,4 @@ -# metamodel_version: 1.7.0# version: 2.3.1id: clinical_trial +# metamodel_version: 1.7.0# version: 2.4.0id: clinical_trial schema_generating: true display_name: clinical trial document_category: clinical trial diff --git a/golr-views/coding_sequence_config.yaml b/golr-views/coding_sequence_config.yaml index b3514dbe46..bf0cf6c153 100644 --- a/golr-views/coding_sequence_config.yaml +++ b/golr-views/coding_sequence_config.yaml @@ -1,4 +1,4 @@ -# metamodel_version: 1.7.0# version: 2.3.1id: coding_sequence +# metamodel_version: 1.7.0# version: 2.4.0id: coding_sequence schema_generating: true display_name: coding sequence document_category: coding sequence diff --git a/golr-views/cohort_config.yaml b/golr-views/cohort_config.yaml index 9d55bf579f..7c4da0178a 100644 --- a/golr-views/cohort_config.yaml +++ b/golr-views/cohort_config.yaml @@ -1,4 +1,4 @@ -# metamodel_version: 1.7.0# version: 2.3.1id: cohort +# metamodel_version: 1.7.0# version: 2.4.0id: cohort schema_generating: true description: 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 diff --git a/golr-views/complex_molecular_mixture_config.yaml b/golr-views/complex_molecular_mixture_config.yaml index 91cc095d80..b7b9fd9712 100644 --- a/golr-views/complex_molecular_mixture_config.yaml +++ b/golr-views/complex_molecular_mixture_config.yaml @@ -1,4 +1,4 @@ -# metamodel_version: 1.7.0# version: 2.3.1id: complex_molecular_mixture +# metamodel_version: 1.7.0# version: 2.4.0id: complex_molecular_mixture schema_generating: true description: A complex molecular mixture is a chemical mixture composed of two or more molecular entities with unknown concentration and stoichiometry. diff --git a/golr-views/confidence_level_config.yaml b/golr-views/confidence_level_config.yaml index 9819198e63..7536cb798b 100644 --- a/golr-views/confidence_level_config.yaml +++ b/golr-views/confidence_level_config.yaml @@ -1,4 +1,4 @@ -# metamodel_version: 1.7.0# version: 2.3.1id: confidence_level +# metamodel_version: 1.7.0# version: 2.4.0id: confidence_level schema_generating: true description: Level of confidence in a statement display_name: confidence level diff --git a/golr-views/contributor_association_config.yaml b/golr-views/contributor_association_config.yaml index a80ad994d7..70544b6436 100644 --- a/golr-views/contributor_association_config.yaml +++ b/golr-views/contributor_association_config.yaml @@ -1,4 +1,4 @@ -# metamodel_version: 1.7.0# version: 2.3.1id: contributor_association +# metamodel_version: 1.7.0# version: 2.4.0id: contributor_association schema_generating: true description: Any association between an entity (such as a publication) and various agents that contribute to its realisation diff --git a/golr-views/dataset_config.yaml b/golr-views/dataset_config.yaml index 09218184df..37dc73b9be 100644 --- a/golr-views/dataset_config.yaml +++ b/golr-views/dataset_config.yaml @@ -1,4 +1,4 @@ -# metamodel_version: 1.7.0# version: 2.3.1id: dataset +# metamodel_version: 1.7.0# version: 2.4.0id: dataset schema_generating: true description: an item that refers to a collection of data from a data source. display_name: dataset diff --git a/golr-views/dataset_distribution_config.yaml b/golr-views/dataset_distribution_config.yaml index 3093a7aa69..1007d1e6ba 100644 --- a/golr-views/dataset_distribution_config.yaml +++ b/golr-views/dataset_distribution_config.yaml @@ -1,4 +1,4 @@ -# metamodel_version: 1.7.0# version: 2.3.1id: dataset_distribution +# metamodel_version: 1.7.0# version: 2.4.0id: dataset_distribution schema_generating: true description: an item that holds distribution level information about a dataset. display_name: dataset distribution diff --git a/golr-views/dataset_summary_config.yaml b/golr-views/dataset_summary_config.yaml index c1d3f1adf3..306d37f113 100644 --- a/golr-views/dataset_summary_config.yaml +++ b/golr-views/dataset_summary_config.yaml @@ -1,4 +1,4 @@ -# metamodel_version: 1.7.0# version: 2.3.1id: dataset_summary +# metamodel_version: 1.7.0# version: 2.4.0id: dataset_summary schema_generating: true description: an item that holds summary level information about a dataset. display_name: dataset summary diff --git a/golr-views/dataset_version_config.yaml b/golr-views/dataset_version_config.yaml index ce282811c6..cd3d02467a 100644 --- a/golr-views/dataset_version_config.yaml +++ b/golr-views/dataset_version_config.yaml @@ -1,4 +1,4 @@ -# metamodel_version: 1.7.0# version: 2.3.1id: dataset_version +# metamodel_version: 1.7.0# version: 2.4.0id: dataset_version schema_generating: true description: an item that holds version level information about a dataset. display_name: dataset version diff --git a/golr-views/device_config.yaml b/golr-views/device_config.yaml index 37d81cd4f8..17dc30b5d2 100644 --- a/golr-views/device_config.yaml +++ b/golr-views/device_config.yaml @@ -1,4 +1,4 @@ -# metamodel_version: 1.7.0# version: 2.3.1id: device +# metamodel_version: 1.7.0# version: 2.4.0id: device schema_generating: true description: A thing made or adapted for a particular purpose, especially a piece of mechanical or electronic equipment diff --git a/golr-views/disease_config.yaml b/golr-views/disease_config.yaml index 58b283c982..0d45b81350 100644 --- a/golr-views/disease_config.yaml +++ b/golr-views/disease_config.yaml @@ -1,4 +1,4 @@ -# metamodel_version: 1.7.0# version: 2.3.1id: disease +# metamodel_version: 1.7.0# version: 2.4.0id: disease schema_generating: true display_name: disease document_category: disease diff --git a/golr-views/disease_or_phenotypic_feature_config.yaml b/golr-views/disease_or_phenotypic_feature_config.yaml index 9a1aca3287..d9cd5b7724 100644 --- a/golr-views/disease_or_phenotypic_feature_config.yaml +++ b/golr-views/disease_or_phenotypic_feature_config.yaml @@ -1,4 +1,4 @@ -# metamodel_version: 1.7.0# version: 2.3.1id: disease_or_phenotypic_feature +# metamodel_version: 1.7.0# version: 2.4.0id: disease_or_phenotypic_feature schema_generating: true description: Either one of a disease or an individual phenotypic feature. Some knowledge resources such as Monarch treat these as distinct, others such as MESH conflate. diff --git a/golr-views/disease_or_phenotypic_feature_to_location_association_config.yaml b/golr-views/disease_or_phenotypic_feature_to_location_association_config.yaml index 5b0ad4f7d8..937b2ebec3 100644 --- a/golr-views/disease_or_phenotypic_feature_to_location_association_config.yaml +++ b/golr-views/disease_or_phenotypic_feature_to_location_association_config.yaml @@ -1,4 +1,4 @@ -# metamodel_version: 1.7.0# version: 2.3.1id: disease_or_phenotypic_feature_to_location_association +# metamodel_version: 1.7.0# version: 2.4.0id: disease_or_phenotypic_feature_to_location_association schema_generating: true description: An association between either a disease or a phenotypic feature and an anatomical entity, where the disease/feature manifests in that site. diff --git a/golr-views/disease_to_exposure_event_association_config.yaml b/golr-views/disease_to_exposure_event_association_config.yaml index 92bbc8eefd..5b51e1ab18 100644 --- a/golr-views/disease_to_exposure_event_association_config.yaml +++ b/golr-views/disease_to_exposure_event_association_config.yaml @@ -1,4 +1,4 @@ -# metamodel_version: 1.7.0# version: 2.3.1id: disease_to_exposure_event_association +# metamodel_version: 1.7.0# version: 2.4.0id: disease_to_exposure_event_association schema_generating: true description: An association between an exposure event and a disease. display_name: disease to exposure event association diff --git a/golr-views/disease_to_phenotypic_feature_association_config.yaml b/golr-views/disease_to_phenotypic_feature_association_config.yaml index f5912b8fc8..143931faef 100644 --- a/golr-views/disease_to_phenotypic_feature_association_config.yaml +++ b/golr-views/disease_to_phenotypic_feature_association_config.yaml @@ -1,4 +1,4 @@ -# metamodel_version: 1.7.0# version: 2.3.1id: disease_to_phenotypic_feature_association +# metamodel_version: 1.7.0# version: 2.4.0id: disease_to_phenotypic_feature_association schema_generating: true description: An association between a disease and a phenotypic feature in which the phenotypic feature is associated with the disease in some way. diff --git a/golr-views/drug_config.yaml b/golr-views/drug_config.yaml index 1ed37f0699..4dda45e52f 100644 --- a/golr-views/drug_config.yaml +++ b/golr-views/drug_config.yaml @@ -1,4 +1,4 @@ -# metamodel_version: 1.7.0# version: 2.3.1id: drug +# metamodel_version: 1.7.0# version: 2.4.0id: drug schema_generating: true description: A substance intended for use in the diagnosis, cure, mitigation, treatment, or prevention of disease diff --git a/golr-views/drug_exposure_config.yaml b/golr-views/drug_exposure_config.yaml index 1a20efa4ac..3e1c14ea10 100644 --- a/golr-views/drug_exposure_config.yaml +++ b/golr-views/drug_exposure_config.yaml @@ -1,4 +1,4 @@ -# metamodel_version: 1.7.0# version: 2.3.1id: drug_exposure +# metamodel_version: 1.7.0# version: 2.4.0id: drug_exposure schema_generating: true description: A drug exposure is an intake of a particular drug. display_name: drug exposure diff --git a/golr-views/drug_to_gene_association_config.yaml b/golr-views/drug_to_gene_association_config.yaml index 30d7d5c868..c6fb204302 100644 --- a/golr-views/drug_to_gene_association_config.yaml +++ b/golr-views/drug_to_gene_association_config.yaml @@ -1,4 +1,4 @@ -# metamodel_version: 1.7.0# version: 2.3.1id: drug_to_gene_association +# metamodel_version: 1.7.0# version: 2.4.0id: drug_to_gene_association schema_generating: true description: An interaction between a drug and a gene or gene product. display_name: drug to gene association diff --git a/golr-views/drug_to_gene_interaction_exposure_config.yaml b/golr-views/drug_to_gene_interaction_exposure_config.yaml index 97adf84ee8..47c999154a 100644 --- a/golr-views/drug_to_gene_interaction_exposure_config.yaml +++ b/golr-views/drug_to_gene_interaction_exposure_config.yaml @@ -1,4 +1,4 @@ -# metamodel_version: 1.7.0# version: 2.3.1id: drug_to_gene_interaction_exposure +# metamodel_version: 1.7.0# version: 2.4.0id: drug_to_gene_interaction_exposure schema_generating: true description: drug to gene interaction exposure is a drug exposure is where the interactions of the drug with specific genes are known to constitute an 'exposure' to the organism, diff --git a/golr-views/druggable_gene_to_disease_association_config.yaml b/golr-views/druggable_gene_to_disease_association_config.yaml index f7b713e7e9..97c58121a7 100644 --- a/golr-views/druggable_gene_to_disease_association_config.yaml +++ b/golr-views/druggable_gene_to_disease_association_config.yaml @@ -1,4 +1,4 @@ -# metamodel_version: 1.7.0# version: 2.3.1id: druggable_gene_to_disease_association +# metamodel_version: 1.7.0# version: 2.4.0id: druggable_gene_to_disease_association schema_generating: true display_name: druggable gene to disease association document_category: druggable gene to disease association diff --git a/golr-views/entity_to_disease_association_config.yaml b/golr-views/entity_to_disease_association_config.yaml index aa21ae1413..7f7c3206b7 100644 --- a/golr-views/entity_to_disease_association_config.yaml +++ b/golr-views/entity_to_disease_association_config.yaml @@ -1,4 +1,4 @@ -# metamodel_version: 1.7.0# version: 2.3.1id: entity_to_disease_association +# metamodel_version: 1.7.0# version: 2.4.0id: entity_to_disease_association schema_generating: true display_name: entity to disease association document_category: entity to disease association diff --git a/golr-views/entity_to_phenotypic_feature_association_config.yaml b/golr-views/entity_to_phenotypic_feature_association_config.yaml index 16f87bc69e..40745e6eaf 100644 --- a/golr-views/entity_to_phenotypic_feature_association_config.yaml +++ b/golr-views/entity_to_phenotypic_feature_association_config.yaml @@ -1,4 +1,4 @@ -# metamodel_version: 1.7.0# version: 2.3.1id: entity_to_phenotypic_feature_association +# metamodel_version: 1.7.0# version: 2.4.0id: entity_to_phenotypic_feature_association schema_generating: true display_name: entity to phenotypic feature association document_category: entity to phenotypic feature association diff --git a/golr-views/environmental_feature_config.yaml b/golr-views/environmental_feature_config.yaml index 4257511e88..880abed2ce 100644 --- a/golr-views/environmental_feature_config.yaml +++ b/golr-views/environmental_feature_config.yaml @@ -1,4 +1,4 @@ -# metamodel_version: 1.7.0# version: 2.3.1id: environmental_feature +# metamodel_version: 1.7.0# version: 2.4.0id: environmental_feature schema_generating: true display_name: environmental feature document_category: environmental feature diff --git a/golr-views/environmental_food_contaminant_config.yaml b/golr-views/environmental_food_contaminant_config.yaml index 6b47031d14..01e8aa865d 100644 --- a/golr-views/environmental_food_contaminant_config.yaml +++ b/golr-views/environmental_food_contaminant_config.yaml @@ -1,4 +1,4 @@ -# metamodel_version: 1.7.0# version: 2.3.1id: environmental_food_contaminant +# metamodel_version: 1.7.0# version: 2.4.0id: environmental_food_contaminant schema_generating: true display_name: environmental food contaminant document_category: environmental food contaminant diff --git a/golr-views/environmental_process_config.yaml b/golr-views/environmental_process_config.yaml index 0df798eba4..e58344ba86 100644 --- a/golr-views/environmental_process_config.yaml +++ b/golr-views/environmental_process_config.yaml @@ -1,4 +1,4 @@ -# metamodel_version: 1.7.0# version: 2.3.1id: environmental_process +# metamodel_version: 1.7.0# version: 2.4.0id: environmental_process schema_generating: true display_name: environmental process document_category: environmental process diff --git a/golr-views/event_config.yaml b/golr-views/event_config.yaml index 91cb6bf794..bc73a64b2c 100644 --- a/golr-views/event_config.yaml +++ b/golr-views/event_config.yaml @@ -1,4 +1,4 @@ -# metamodel_version: 1.7.0# version: 2.3.1id: event +# metamodel_version: 1.7.0# version: 2.4.0id: event schema_generating: true description: Something that happens at a given place and time. display_name: event diff --git a/golr-views/evidence_type_config.yaml b/golr-views/evidence_type_config.yaml index e6fc944713..3a51816273 100644 --- a/golr-views/evidence_type_config.yaml +++ b/golr-views/evidence_type_config.yaml @@ -1,4 +1,4 @@ -# metamodel_version: 1.7.0# version: 2.3.1id: evidence_type +# metamodel_version: 1.7.0# version: 2.4.0id: evidence_type schema_generating: true description: Class of evidence that supports an association display_name: evidence type diff --git a/golr-views/exon_config.yaml b/golr-views/exon_config.yaml index 17afc0f2ca..f7bcd4b1f5 100644 --- a/golr-views/exon_config.yaml +++ b/golr-views/exon_config.yaml @@ -1,4 +1,4 @@ -# metamodel_version: 1.7.0# version: 2.3.1id: exon +# metamodel_version: 1.7.0# version: 2.4.0id: exon schema_generating: true description: A region of the transcript sequence within a gene which is not removed from the primary RNA transcript by RNA splicing. diff --git a/golr-views/exon_to_transcript_relationship_config.yaml b/golr-views/exon_to_transcript_relationship_config.yaml index 99c2cdac54..1be12e9825 100644 --- a/golr-views/exon_to_transcript_relationship_config.yaml +++ b/golr-views/exon_to_transcript_relationship_config.yaml @@ -1,4 +1,4 @@ -# metamodel_version: 1.7.0# version: 2.3.1id: exon_to_transcript_relationship +# metamodel_version: 1.7.0# version: 2.4.0id: exon_to_transcript_relationship schema_generating: true description: A transcript is formed from multiple exons display_name: exon to transcript relationship diff --git a/golr-views/exposure_event_to_outcome_association_config.yaml b/golr-views/exposure_event_to_outcome_association_config.yaml index d0c58a339d..a4e8625bc2 100644 --- a/golr-views/exposure_event_to_outcome_association_config.yaml +++ b/golr-views/exposure_event_to_outcome_association_config.yaml @@ -1,4 +1,4 @@ -# metamodel_version: 1.7.0# version: 2.3.1id: exposure_event_to_outcome_association +# metamodel_version: 1.7.0# version: 2.4.0id: exposure_event_to_outcome_association schema_generating: true description: An association between an exposure event and an outcome. display_name: exposure event to outcome association diff --git a/golr-views/exposure_event_to_phenotypic_feature_association_config.yaml b/golr-views/exposure_event_to_phenotypic_feature_association_config.yaml index 53e870ae0b..159ccb0299 100644 --- a/golr-views/exposure_event_to_phenotypic_feature_association_config.yaml +++ b/golr-views/exposure_event_to_phenotypic_feature_association_config.yaml @@ -1,4 +1,4 @@ -# metamodel_version: 1.7.0# version: 2.3.1id: exposure_event_to_phenotypic_feature_association +# metamodel_version: 1.7.0# version: 2.4.0id: exposure_event_to_phenotypic_feature_association schema_generating: true description: Any association between an environment and a phenotypic feature, where being in the environment influences the phenotype. diff --git a/golr-views/food_additive_config.yaml b/golr-views/food_additive_config.yaml index c506585f4e..eb31e29135 100644 --- a/golr-views/food_additive_config.yaml +++ b/golr-views/food_additive_config.yaml @@ -1,4 +1,4 @@ -# metamodel_version: 1.7.0# version: 2.3.1id: food_additive +# metamodel_version: 1.7.0# version: 2.4.0id: food_additive schema_generating: true display_name: food additive document_category: food additive diff --git a/golr-views/food_config.yaml b/golr-views/food_config.yaml index 2c75b7708a..6c3b3bc284 100644 --- a/golr-views/food_config.yaml +++ b/golr-views/food_config.yaml @@ -1,4 +1,4 @@ -# metamodel_version: 1.7.0# version: 2.3.1id: food +# metamodel_version: 1.7.0# version: 2.4.0id: food schema_generating: true description: A substance consumed by a living organism as a source of nutrition display_name: food diff --git a/golr-views/functional_association_config.yaml b/golr-views/functional_association_config.yaml index 2c8b30fd51..1035671ee1 100644 --- a/golr-views/functional_association_config.yaml +++ b/golr-views/functional_association_config.yaml @@ -1,4 +1,4 @@ -# metamodel_version: 1.7.0# version: 2.3.1id: functional_association +# metamodel_version: 1.7.0# version: 2.4.0id: functional_association schema_generating: true description: An association between a macromolecular machine mixin (gene, gene product or complex of gene products) and either a molecular activity, a biological process diff --git a/golr-views/gene_as_a_model_of_disease_association_config.yaml b/golr-views/gene_as_a_model_of_disease_association_config.yaml index 0d391aa2d8..fd2365cd75 100644 --- a/golr-views/gene_as_a_model_of_disease_association_config.yaml +++ b/golr-views/gene_as_a_model_of_disease_association_config.yaml @@ -1,4 +1,4 @@ -# metamodel_version: 1.7.0# version: 2.3.1id: gene_as_a_model_of_disease_association +# metamodel_version: 1.7.0# version: 2.4.0id: gene_as_a_model_of_disease_association schema_generating: true display_name: gene as a model of disease association document_category: gene as a model of disease association diff --git a/golr-views/gene_config.yaml b/golr-views/gene_config.yaml index 84354c58df..81f21d5850 100644 --- a/golr-views/gene_config.yaml +++ b/golr-views/gene_config.yaml @@ -1,4 +1,4 @@ -# metamodel_version: 1.7.0# version: 2.3.1id: gene +# metamodel_version: 1.7.0# version: 2.4.0id: gene schema_generating: true description: A region (or regions) that includes all of the sequence elements necessary to encode a functional transcript. A gene locus may include regulatory regions, diff --git a/golr-views/gene_family_config.yaml b/golr-views/gene_family_config.yaml index 823ae7522b..1e383c0447 100644 --- a/golr-views/gene_family_config.yaml +++ b/golr-views/gene_family_config.yaml @@ -1,4 +1,4 @@ -# metamodel_version: 1.7.0# version: 2.3.1id: gene_family +# metamodel_version: 1.7.0# version: 2.4.0id: gene_family schema_generating: true description: any grouping of multiple genes or gene products related by common descent display_name: gene family diff --git a/golr-views/gene_has_variant_that_contributes_to_disease_association_config.yaml b/golr-views/gene_has_variant_that_contributes_to_disease_association_config.yaml index f6bb2cc74d..7e3b7de505 100644 --- a/golr-views/gene_has_variant_that_contributes_to_disease_association_config.yaml +++ b/golr-views/gene_has_variant_that_contributes_to_disease_association_config.yaml @@ -1,4 +1,4 @@ -# metamodel_version: 1.7.0# version: 2.3.1id: gene_has_variant_that_contributes_to_disease_association +# metamodel_version: 1.7.0# version: 2.4.0id: gene_has_variant_that_contributes_to_disease_association schema_generating: true display_name: gene has variant that contributes to disease association document_category: gene has variant that contributes to disease association diff --git a/golr-views/gene_regulatory_relationship_config.yaml b/golr-views/gene_regulatory_relationship_config.yaml index 072112cf1d..072933f99d 100644 --- a/golr-views/gene_regulatory_relationship_config.yaml +++ b/golr-views/gene_regulatory_relationship_config.yaml @@ -1,4 +1,4 @@ -# metamodel_version: 1.7.0# version: 2.3.1id: gene_regulatory_relationship +# metamodel_version: 1.7.0# version: 2.4.0id: gene_regulatory_relationship schema_generating: true description: A regulatory relationship between two genes display_name: gene regulatory relationship diff --git a/golr-views/gene_to_disease_association_config.yaml b/golr-views/gene_to_disease_association_config.yaml index 1151c81bc7..be2d2c598f 100644 --- a/golr-views/gene_to_disease_association_config.yaml +++ b/golr-views/gene_to_disease_association_config.yaml @@ -1,4 +1,4 @@ -# metamodel_version: 1.7.0# version: 2.3.1id: gene_to_disease_association +# metamodel_version: 1.7.0# version: 2.4.0id: gene_to_disease_association schema_generating: true display_name: gene to disease association document_category: gene to disease association diff --git a/golr-views/gene_to_expression_site_association_config.yaml b/golr-views/gene_to_expression_site_association_config.yaml index 2eac65051f..62eca21617 100644 --- a/golr-views/gene_to_expression_site_association_config.yaml +++ b/golr-views/gene_to_expression_site_association_config.yaml @@ -1,4 +1,4 @@ -# metamodel_version: 1.7.0# version: 2.3.1id: gene_to_expression_site_association +# metamodel_version: 1.7.0# version: 2.4.0id: gene_to_expression_site_association schema_generating: true description: An association between a gene and a gene expression site, possibly qualified by stage/timing info. diff --git a/golr-views/gene_to_gene_coexpression_association_config.yaml b/golr-views/gene_to_gene_coexpression_association_config.yaml index 87a9ecb566..9a12cc938f 100644 --- a/golr-views/gene_to_gene_coexpression_association_config.yaml +++ b/golr-views/gene_to_gene_coexpression_association_config.yaml @@ -1,4 +1,4 @@ -# metamodel_version: 1.7.0# version: 2.3.1id: gene_to_gene_coexpression_association +# metamodel_version: 1.7.0# version: 2.4.0id: gene_to_gene_coexpression_association schema_generating: true description: Indicates that two genes are co-expressed, generally under the same conditions. display_name: gene to gene coexpression association diff --git a/golr-views/gene_to_gene_homology_association_config.yaml b/golr-views/gene_to_gene_homology_association_config.yaml index 74a27e47b9..124a468983 100644 --- a/golr-views/gene_to_gene_homology_association_config.yaml +++ b/golr-views/gene_to_gene_homology_association_config.yaml @@ -1,4 +1,4 @@ -# metamodel_version: 1.7.0# version: 2.3.1id: gene_to_gene_homology_association +# metamodel_version: 1.7.0# version: 2.4.0id: gene_to_gene_homology_association schema_generating: true description: A homology association between two genes. May be orthology (in which case the species of subject and object should differ) or paralogy (in which case diff --git a/golr-views/gene_to_gene_product_relationship_config.yaml b/golr-views/gene_to_gene_product_relationship_config.yaml index a79bc4a0c3..1bf4562327 100644 --- a/golr-views/gene_to_gene_product_relationship_config.yaml +++ b/golr-views/gene_to_gene_product_relationship_config.yaml @@ -1,4 +1,4 @@ -# metamodel_version: 1.7.0# version: 2.3.1id: gene_to_gene_product_relationship +# metamodel_version: 1.7.0# version: 2.4.0id: gene_to_gene_product_relationship schema_generating: true description: A gene is transcribed and potentially translated to a gene product display_name: gene to gene product relationship diff --git a/golr-views/gene_to_go_term_association_config.yaml b/golr-views/gene_to_go_term_association_config.yaml index b46ef553e1..30153ff0f9 100644 --- a/golr-views/gene_to_go_term_association_config.yaml +++ b/golr-views/gene_to_go_term_association_config.yaml @@ -1,4 +1,4 @@ -# metamodel_version: 1.7.0# version: 2.3.1id: gene_to_go_term_association +# metamodel_version: 1.7.0# version: 2.4.0id: gene_to_go_term_association schema_generating: true display_name: gene to go term association document_category: gene to go term association diff --git a/golr-views/gene_to_phenotypic_feature_association_config.yaml b/golr-views/gene_to_phenotypic_feature_association_config.yaml index 1e40cc337f..6fa9c66bdd 100644 --- a/golr-views/gene_to_phenotypic_feature_association_config.yaml +++ b/golr-views/gene_to_phenotypic_feature_association_config.yaml @@ -1,4 +1,4 @@ -# metamodel_version: 1.7.0# version: 2.3.1id: gene_to_phenotypic_feature_association +# metamodel_version: 1.7.0# version: 2.4.0id: gene_to_phenotypic_feature_association schema_generating: true display_name: gene to phenotypic feature association document_category: gene to phenotypic feature association diff --git a/golr-views/genome_config.yaml b/golr-views/genome_config.yaml index 10ee194875..2c7e62c6bc 100644 --- a/golr-views/genome_config.yaml +++ b/golr-views/genome_config.yaml @@ -1,4 +1,4 @@ -# metamodel_version: 1.7.0# version: 2.3.1id: genome +# metamodel_version: 1.7.0# version: 2.4.0id: genome schema_generating: true description: A genome is the sum of genetic material within a cell or virion. display_name: genome diff --git a/golr-views/genomic_background_exposure_config.yaml b/golr-views/genomic_background_exposure_config.yaml index 7dfe061f4a..024497c13b 100644 --- a/golr-views/genomic_background_exposure_config.yaml +++ b/golr-views/genomic_background_exposure_config.yaml @@ -1,4 +1,4 @@ -# metamodel_version: 1.7.0# version: 2.3.1id: genomic_background_exposure +# metamodel_version: 1.7.0# version: 2.4.0id: genomic_background_exposure schema_generating: true description: A genomic background exposure is where an individual's specific genomic background of genes, sequence variants or other pre-existing genomic conditions @@ -22,3 +22,7 @@ fields: - id: has_biological_sequence description: connects a genomic feature to its sequence display_name: has biological sequence +- id: id + description: A unique identifier for an entity. Must be either a CURIE shorthand + for a URI or a complete URI + display_name: id diff --git a/golr-views/genomic_sequence_localization_config.yaml b/golr-views/genomic_sequence_localization_config.yaml index d186d3193b..4a3558528e 100644 --- a/golr-views/genomic_sequence_localization_config.yaml +++ b/golr-views/genomic_sequence_localization_config.yaml @@ -1,4 +1,4 @@ -# metamodel_version: 1.7.0# version: 2.3.1id: genomic_sequence_localization +# metamodel_version: 1.7.0# version: 2.4.0id: genomic_sequence_localization schema_generating: true description: 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 diff --git a/golr-views/genotype_as_a_model_of_disease_association_config.yaml b/golr-views/genotype_as_a_model_of_disease_association_config.yaml index 6aaca74787..aa6d74d9c1 100644 --- a/golr-views/genotype_as_a_model_of_disease_association_config.yaml +++ b/golr-views/genotype_as_a_model_of_disease_association_config.yaml @@ -1,4 +1,4 @@ -# metamodel_version: 1.7.0# version: 2.3.1id: genotype_as_a_model_of_disease_association +# metamodel_version: 1.7.0# version: 2.4.0id: genotype_as_a_model_of_disease_association schema_generating: true display_name: genotype as a model of disease association document_category: genotype as a model of disease association diff --git a/golr-views/genotype_config.yaml b/golr-views/genotype_config.yaml index 656f922d75..f14945ed3b 100644 --- a/golr-views/genotype_config.yaml +++ b/golr-views/genotype_config.yaml @@ -1,4 +1,4 @@ -# metamodel_version: 1.7.0# version: 2.3.1id: genotype +# metamodel_version: 1.7.0# version: 2.4.0id: genotype schema_generating: true description: An information content entity that describes a genome by specifying the total variation in genomic sequence and/or gene expression, relative to some established diff --git a/golr-views/genotype_to_disease_association_config.yaml b/golr-views/genotype_to_disease_association_config.yaml index 4bb54226c2..e1bba41b6d 100644 --- a/golr-views/genotype_to_disease_association_config.yaml +++ b/golr-views/genotype_to_disease_association_config.yaml @@ -1,4 +1,4 @@ -# metamodel_version: 1.7.0# version: 2.3.1id: genotype_to_disease_association +# metamodel_version: 1.7.0# version: 2.4.0id: genotype_to_disease_association schema_generating: true display_name: genotype to disease association document_category: genotype to disease association diff --git a/golr-views/genotype_to_gene_association_config.yaml b/golr-views/genotype_to_gene_association_config.yaml index 24e2283922..f1e70acad2 100644 --- a/golr-views/genotype_to_gene_association_config.yaml +++ b/golr-views/genotype_to_gene_association_config.yaml @@ -1,4 +1,4 @@ -# metamodel_version: 1.7.0# version: 2.3.1id: genotype_to_gene_association +# metamodel_version: 1.7.0# version: 2.4.0id: genotype_to_gene_association schema_generating: true description: Any association between a genotype and a gene. The genotype have have multiple variants in that gene or a single one. There is no assumption of cardinality diff --git a/golr-views/genotype_to_genotype_part_association_config.yaml b/golr-views/genotype_to_genotype_part_association_config.yaml index 6547e4e5ce..d024309711 100644 --- a/golr-views/genotype_to_genotype_part_association_config.yaml +++ b/golr-views/genotype_to_genotype_part_association_config.yaml @@ -1,4 +1,4 @@ -# metamodel_version: 1.7.0# version: 2.3.1id: genotype_to_genotype_part_association +# metamodel_version: 1.7.0# version: 2.4.0id: genotype_to_genotype_part_association schema_generating: true description: Any association between one genotype and a genotypic entity that is a sub-component of it diff --git a/golr-views/genotype_to_phenotypic_feature_association_config.yaml b/golr-views/genotype_to_phenotypic_feature_association_config.yaml index 0de956f648..21354f886c 100644 --- a/golr-views/genotype_to_phenotypic_feature_association_config.yaml +++ b/golr-views/genotype_to_phenotypic_feature_association_config.yaml @@ -1,4 +1,4 @@ -# metamodel_version: 1.7.0# version: 2.3.1id: genotype_to_phenotypic_feature_association +# metamodel_version: 1.7.0# version: 2.4.0id: genotype_to_phenotypic_feature_association schema_generating: true description: Any association between one genotype and a phenotypic feature, where having the genotype confers the phenotype, either in isolation or through environment diff --git a/golr-views/genotype_to_variant_association_config.yaml b/golr-views/genotype_to_variant_association_config.yaml index 7019798969..bb2fe8cff0 100644 --- a/golr-views/genotype_to_variant_association_config.yaml +++ b/golr-views/genotype_to_variant_association_config.yaml @@ -1,4 +1,4 @@ -# metamodel_version: 1.7.0# version: 2.3.1id: genotype_to_variant_association +# metamodel_version: 1.7.0# version: 2.4.0id: genotype_to_variant_association schema_generating: true description: Any association between a genotype and a sequence variant. display_name: genotype to variant association diff --git a/golr-views/genotypic_sex_config.yaml b/golr-views/genotypic_sex_config.yaml index 79e06e5ac0..1540c00631 100644 --- a/golr-views/genotypic_sex_config.yaml +++ b/golr-views/genotypic_sex_config.yaml @@ -1,4 +1,4 @@ -# metamodel_version: 1.7.0# version: 2.3.1id: genotypic_sex +# metamodel_version: 1.7.0# version: 2.4.0id: genotypic_sex schema_generating: true description: An attribute corresponding to the genotypic sex of the individual, based upon genotypic composition of sex chromosomes. @@ -6,6 +6,44 @@ display_name: genotypic sex document_category: genotypic sex weight: 20 fields: +- id: id + description: A unique identifier for an entity. Must be either a CURIE shorthand + for a URI or a complete URI + display_name: id +- id: type + display_name: type +- id: description + description: a human-readable description of an entity + display_name: description +- id: has_attribute + description: connects any entity to an attribute + display_name: has attribute + cardinality: multi +- id: provided_by + description: The value in this node property represents the knowledge provider that + created or assembled the node and all of its attributes. Used internally to represent + how a particular node made its way into a knowledge provider or graph. + display_name: provided by + cardinality: multi +- id: xref + description: Alternate CURIEs for a thing + display_name: xref + cardinality: multi +- id: category + description: "Name of the high level ontology class in which this entity is categorized.\ + \ Corresponds to the label for the biolink entity type class.\n * In a neo4j database\ + \ this MAY correspond to the neo4j label tag.\n * In an RDF database it should\ + \ be a biolink model class URI.\nThis field is multi-valued. It should include\ + \ values for ancestors of the biolink class; for example, a protein such as Shh\ + \ would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`,\ + \ ...\nIn an RDF database, nodes will typically have an rdf:type triples. This\ + \ can be to the most specific biolink class, or potentially to a class more specific\ + \ than something in biolink. For example, a sequence feature `f` may have a rdf:type\ + \ assertion to a SO class such as TF_binding_site, which is more specific than\ + \ anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity,\ + \ biolink:NamedThing}" + display_name: named thing_category + cardinality: multi - id: name description: The human-readable 'attribute name' can be set to a string which reflects its context of interpretation, e.g. SEPIO evidence/provenance/confidence annotation diff --git a/golr-views/geographic_location_at_time_config.yaml b/golr-views/geographic_location_at_time_config.yaml index b01701483d..d03233861c 100644 --- a/golr-views/geographic_location_at_time_config.yaml +++ b/golr-views/geographic_location_at_time_config.yaml @@ -1,4 +1,4 @@ -# metamodel_version: 1.7.0# version: 2.3.1id: geographic_location_at_time +# metamodel_version: 1.7.0# version: 2.4.0id: geographic_location_at_time schema_generating: true description: a location that can be described in lat/long coordinates, for a particular time diff --git a/golr-views/geographic_location_config.yaml b/golr-views/geographic_location_config.yaml index e9ce433de9..f3866acfd0 100644 --- a/golr-views/geographic_location_config.yaml +++ b/golr-views/geographic_location_config.yaml @@ -1,4 +1,4 @@ -# metamodel_version: 1.7.0# version: 2.3.1id: geographic_location +# metamodel_version: 1.7.0# version: 2.4.0id: geographic_location schema_generating: true description: a location that can be described in lat/long coordinates display_name: geographic location diff --git a/golr-views/gross_anatomical_structure_config.yaml b/golr-views/gross_anatomical_structure_config.yaml index ab14bffe8a..73c14d83da 100644 --- a/golr-views/gross_anatomical_structure_config.yaml +++ b/golr-views/gross_anatomical_structure_config.yaml @@ -1,4 +1,4 @@ -# metamodel_version: 1.7.0# version: 2.3.1id: gross_anatomical_structure +# metamodel_version: 1.7.0# version: 2.4.0id: gross_anatomical_structure schema_generating: true display_name: gross anatomical structure document_category: gross anatomical structure diff --git a/golr-views/haplotype_config.yaml b/golr-views/haplotype_config.yaml index a8e494ab3b..060b0f96b0 100644 --- a/golr-views/haplotype_config.yaml +++ b/golr-views/haplotype_config.yaml @@ -1,4 +1,4 @@ -# metamodel_version: 1.7.0# version: 2.3.1id: haplotype +# metamodel_version: 1.7.0# version: 2.4.0id: haplotype schema_generating: true description: A set of zero or more Alleles on a single instance of a Sequence[VMC] display_name: haplotype diff --git a/golr-views/hospitalization_config.yaml b/golr-views/hospitalization_config.yaml index a2b15e83ba..37203b70ff 100644 --- a/golr-views/hospitalization_config.yaml +++ b/golr-views/hospitalization_config.yaml @@ -1,4 +1,4 @@ -# metamodel_version: 1.7.0# version: 2.3.1id: hospitalization +# metamodel_version: 1.7.0# version: 2.4.0id: hospitalization schema_generating: true display_name: hospitalization document_category: hospitalization diff --git a/golr-views/individual_organism_config.yaml b/golr-views/individual_organism_config.yaml index 1dff077ef7..d170f24837 100644 --- a/golr-views/individual_organism_config.yaml +++ b/golr-views/individual_organism_config.yaml @@ -1,4 +1,4 @@ -# metamodel_version: 1.7.0# version: 2.3.1id: individual_organism +# metamodel_version: 1.7.0# version: 2.4.0id: individual_organism schema_generating: true description: 'An instance of an organism. For example, Richard Nixon, Charles Darwin, my pet cat. Example ID: ORCID:0000-0002-5355-2576' diff --git a/golr-views/information_content_entity_to_named_thing_association_config.yaml b/golr-views/information_content_entity_to_named_thing_association_config.yaml index 8ef73596ba..2856d80adf 100644 --- a/golr-views/information_content_entity_to_named_thing_association_config.yaml +++ b/golr-views/information_content_entity_to_named_thing_association_config.yaml @@ -1,4 +1,4 @@ -# metamodel_version: 1.7.0# version: 2.3.1id: information_content_entity_to_named_thing_association +# metamodel_version: 1.7.0# version: 2.4.0id: information_content_entity_to_named_thing_association schema_generating: true description: association between a named thing and a information content entity where the specific context of the relationship between that named thing and the publication diff --git a/golr-views/information_resource_config.yaml b/golr-views/information_resource_config.yaml index 995c907f13..62f1ba5099 100644 --- a/golr-views/information_resource_config.yaml +++ b/golr-views/information_resource_config.yaml @@ -1,4 +1,4 @@ -# metamodel_version: 1.7.0# version: 2.3.1id: information_resource +# metamodel_version: 1.7.0# version: 2.4.0id: information_resource schema_generating: true description: A database or knowledgebase and its supporting ecosystem of interfaces and services that deliver content to consumers (e.g. web portals, APIs, query endpoints, diff --git a/golr-views/inheritance_config.yaml b/golr-views/inheritance_config.yaml index cef96cda14..36868c46b2 100644 --- a/golr-views/inheritance_config.yaml +++ b/golr-views/inheritance_config.yaml @@ -1,4 +1,4 @@ -# metamodel_version: 1.7.0# version: 2.3.1id: inheritance +# metamodel_version: 1.7.0# version: 2.4.0id: inheritance schema_generating: true 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, @@ -7,6 +7,44 @@ display_name: inheritance document_category: inheritance weight: 20 fields: +- id: id + description: A unique identifier for an entity. Must be either a CURIE shorthand + for a URI or a complete URI + display_name: id +- id: type + display_name: type +- id: description + description: a human-readable description of an entity + display_name: description +- id: has_attribute + description: connects any entity to an attribute + display_name: has attribute + cardinality: multi +- id: provided_by + description: The value in this node property represents the knowledge provider that + created or assembled the node and all of its attributes. Used internally to represent + how a particular node made its way into a knowledge provider or graph. + display_name: provided by + cardinality: multi +- id: xref + description: Alternate CURIEs for a thing + display_name: xref + cardinality: multi +- id: category + description: "Name of the high level ontology class in which this entity is categorized.\ + \ Corresponds to the label for the biolink entity type class.\n * In a neo4j database\ + \ this MAY correspond to the neo4j label tag.\n * In an RDF database it should\ + \ be a biolink model class URI.\nThis field is multi-valued. It should include\ + \ values for ancestors of the biolink class; for example, a protein such as Shh\ + \ would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`,\ + \ ...\nIn an RDF database, nodes will typically have an rdf:type triples. This\ + \ can be to the most specific biolink class, or potentially to a class more specific\ + \ than something in biolink. For example, a sequence feature `f` may have a rdf:type\ + \ assertion to a SO class such as TF_binding_site, which is more specific than\ + \ anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity,\ + \ biolink:NamedThing}" + display_name: named thing_category + cardinality: multi - id: name description: The human-readable 'attribute name' can be set to a string which reflects its context of interpretation, e.g. SEPIO evidence/provenance/confidence annotation diff --git a/golr-views/life_stage_config.yaml b/golr-views/life_stage_config.yaml index 6c4c49ff6e..054ffbfb68 100644 --- a/golr-views/life_stage_config.yaml +++ b/golr-views/life_stage_config.yaml @@ -1,4 +1,4 @@ -# metamodel_version: 1.7.0# version: 2.3.1id: life_stage +# metamodel_version: 1.7.0# version: 2.4.0id: life_stage schema_generating: true description: A stage of development or growth of an organism, including post-natal adult stages diff --git a/golr-views/macromolecular_machine_to_biological_process_association_config.yaml b/golr-views/macromolecular_machine_to_biological_process_association_config.yaml index d88c086f0f..bda3e1d56c 100644 --- a/golr-views/macromolecular_machine_to_biological_process_association_config.yaml +++ b/golr-views/macromolecular_machine_to_biological_process_association_config.yaml @@ -1,4 +1,4 @@ -# metamodel_version: 1.7.0# version: 2.3.1id: macromolecular_machine_to_biological_process_association +# metamodel_version: 1.7.0# version: 2.4.0id: macromolecular_machine_to_biological_process_association schema_generating: true description: A functional association between a macromolecular machine (gene, gene product or complex) and a biological process or pathway (as represented in the GO diff --git a/golr-views/macromolecular_machine_to_cellular_component_association_config.yaml b/golr-views/macromolecular_machine_to_cellular_component_association_config.yaml index 4ffd169d9e..51cc1a0ed3 100644 --- a/golr-views/macromolecular_machine_to_cellular_component_association_config.yaml +++ b/golr-views/macromolecular_machine_to_cellular_component_association_config.yaml @@ -1,4 +1,4 @@ -# metamodel_version: 1.7.0# version: 2.3.1id: macromolecular_machine_to_cellular_component_association +# metamodel_version: 1.7.0# version: 2.4.0id: macromolecular_machine_to_cellular_component_association schema_generating: true description: A functional association between a macromolecular machine (gene, gene product or complex) and a cellular component (as represented in the GO cellular diff --git a/golr-views/macromolecular_machine_to_molecular_activity_association_config.yaml b/golr-views/macromolecular_machine_to_molecular_activity_association_config.yaml index 0d4345f784..b802e237ef 100644 --- a/golr-views/macromolecular_machine_to_molecular_activity_association_config.yaml +++ b/golr-views/macromolecular_machine_to_molecular_activity_association_config.yaml @@ -1,4 +1,4 @@ -# metamodel_version: 1.7.0# version: 2.3.1id: macromolecular_machine_to_molecular_activity_association +# metamodel_version: 1.7.0# version: 2.4.0id: macromolecular_machine_to_molecular_activity_association schema_generating: true description: A functional association between a macromolecular machine (gene, gene product or complex) and a molecular activity (as represented in the GO molecular diff --git a/golr-views/macronutrient_config.yaml b/golr-views/macronutrient_config.yaml index 5c10321fec..c227849e9c 100644 --- a/golr-views/macronutrient_config.yaml +++ b/golr-views/macronutrient_config.yaml @@ -1,4 +1,4 @@ -# metamodel_version: 1.7.0# version: 2.3.1id: macronutrient +# metamodel_version: 1.7.0# version: 2.4.0id: macronutrient schema_generating: true display_name: macronutrient document_category: macronutrient diff --git a/golr-views/material_sample_config.yaml b/golr-views/material_sample_config.yaml index 2208b544ec..fbc2eab620 100644 --- a/golr-views/material_sample_config.yaml +++ b/golr-views/material_sample_config.yaml @@ -1,4 +1,4 @@ -# metamodel_version: 1.7.0# version: 2.3.1id: material_sample +# metamodel_version: 1.7.0# version: 2.4.0id: material_sample schema_generating: true description: A sample is a limited quantity of something (e.g. an individual or set of individuals from a population, or a portion of a substance) to be used for testing, diff --git a/golr-views/material_sample_derivation_association_config.yaml b/golr-views/material_sample_derivation_association_config.yaml index ee2808c6de..b376af9aa6 100644 --- a/golr-views/material_sample_derivation_association_config.yaml +++ b/golr-views/material_sample_derivation_association_config.yaml @@ -1,4 +1,4 @@ -# metamodel_version: 1.7.0# version: 2.3.1id: material_sample_derivation_association +# metamodel_version: 1.7.0# version: 2.4.0id: material_sample_derivation_association schema_generating: true description: An association between a material sample and the material entity from which it is derived. diff --git a/golr-views/material_sample_to_disease_or_phenotypic_feature_association_config.yaml b/golr-views/material_sample_to_disease_or_phenotypic_feature_association_config.yaml index 7bbbcde7e1..d8c704fc87 100644 --- a/golr-views/material_sample_to_disease_or_phenotypic_feature_association_config.yaml +++ b/golr-views/material_sample_to_disease_or_phenotypic_feature_association_config.yaml @@ -1,4 +1,4 @@ -# metamodel_version: 1.7.0# version: 2.3.1id: material_sample_to_disease_or_phenotypic_feature_association +# metamodel_version: 1.7.0# version: 2.4.0id: material_sample_to_disease_or_phenotypic_feature_association schema_generating: true description: An association between a material sample and a disease or phenotype. display_name: material sample to disease or phenotypic feature association diff --git a/golr-views/microRNA_config.yaml b/golr-views/microRNA_config.yaml index 6e1257f28f..ac6270f8ee 100644 --- a/golr-views/microRNA_config.yaml +++ b/golr-views/microRNA_config.yaml @@ -1,4 +1,4 @@ -# metamodel_version: 1.7.0# version: 2.3.1id: microRNA +# metamodel_version: 1.7.0# version: 2.4.0id: microRNA schema_generating: true display_name: microRNA document_category: microRNA diff --git a/golr-views/micronutrient_config.yaml b/golr-views/micronutrient_config.yaml index 5d3bc3b855..377e5aeabc 100644 --- a/golr-views/micronutrient_config.yaml +++ b/golr-views/micronutrient_config.yaml @@ -1,4 +1,4 @@ -# metamodel_version: 1.7.0# version: 2.3.1id: micronutrient +# metamodel_version: 1.7.0# version: 2.4.0id: micronutrient schema_generating: true display_name: micronutrient document_category: micronutrient diff --git a/golr-views/molecular_activity_config.yaml b/golr-views/molecular_activity_config.yaml index 758e133424..6f632e2a5b 100644 --- a/golr-views/molecular_activity_config.yaml +++ b/golr-views/molecular_activity_config.yaml @@ -1,4 +1,4 @@ -# metamodel_version: 1.7.0# version: 2.3.1id: molecular_activity +# metamodel_version: 1.7.0# version: 2.4.0id: molecular_activity schema_generating: true description: An execution of a molecular function carried out by a gene product or macromolecular complex. diff --git a/golr-views/molecular_activity_to_chemical_entity_association_config.yaml b/golr-views/molecular_activity_to_chemical_entity_association_config.yaml index 64ffb0abd1..cb6e36d94d 100644 --- a/golr-views/molecular_activity_to_chemical_entity_association_config.yaml +++ b/golr-views/molecular_activity_to_chemical_entity_association_config.yaml @@ -1,4 +1,4 @@ -# metamodel_version: 1.7.0# version: 2.3.1id: molecular_activity_to_chemical_entity_association +# metamodel_version: 1.7.0# version: 2.4.0id: molecular_activity_to_chemical_entity_association schema_generating: true description: Added in response to capturing relationship between microbiome activities as measured via measurements of blood analytes as collected via blood and stool diff --git a/golr-views/molecular_activity_to_molecular_activity_association_config.yaml b/golr-views/molecular_activity_to_molecular_activity_association_config.yaml index f2953fb34c..9f6d20ae7e 100644 --- a/golr-views/molecular_activity_to_molecular_activity_association_config.yaml +++ b/golr-views/molecular_activity_to_molecular_activity_association_config.yaml @@ -1,4 +1,4 @@ -# metamodel_version: 1.7.0# version: 2.3.1id: molecular_activity_to_molecular_activity_association +# metamodel_version: 1.7.0# version: 2.4.0id: molecular_activity_to_molecular_activity_association schema_generating: true description: Added in response to capturing relationship between microbiome activities as measured via measurements of blood analytes as collected via blood and stool diff --git a/golr-views/molecular_entity_config.yaml b/golr-views/molecular_entity_config.yaml index 95422d2d92..e5e1a9081f 100644 --- a/golr-views/molecular_entity_config.yaml +++ b/golr-views/molecular_entity_config.yaml @@ -1,4 +1,4 @@ -# metamodel_version: 1.7.0# version: 2.3.1id: molecular_entity +# metamodel_version: 1.7.0# version: 2.4.0id: molecular_entity schema_generating: true description: A molecular entity is a chemical entity composed of individual or covalently bonded atoms. diff --git a/golr-views/molecular_mixture_config.yaml b/golr-views/molecular_mixture_config.yaml index a14e199ddd..e4be4ca51e 100644 --- a/golr-views/molecular_mixture_config.yaml +++ b/golr-views/molecular_mixture_config.yaml @@ -1,4 +1,4 @@ -# metamodel_version: 1.7.0# version: 2.3.1id: molecular_mixture +# metamodel_version: 1.7.0# version: 2.4.0id: molecular_mixture schema_generating: true description: A molecular mixture is a chemical mixture composed of two or more molecular entities with known concentration and stoichiometry. diff --git a/golr-views/named_thing_config.yaml b/golr-views/named_thing_config.yaml index c8c3da2ae4..1536ee71a1 100644 --- a/golr-views/named_thing_config.yaml +++ b/golr-views/named_thing_config.yaml @@ -1,4 +1,4 @@ -# metamodel_version: 1.7.0# version: 2.3.1id: named_thing +# metamodel_version: 1.7.0# version: 2.4.0id: named_thing schema_generating: true description: a databased entity or concept/class display_name: named thing diff --git a/golr-views/noncoding_RNA_product_config.yaml b/golr-views/noncoding_RNA_product_config.yaml index cf4f1cc4dc..b8f9c1d89b 100644 --- a/golr-views/noncoding_RNA_product_config.yaml +++ b/golr-views/noncoding_RNA_product_config.yaml @@ -1,4 +1,4 @@ -# metamodel_version: 1.7.0# version: 2.3.1id: noncoding_RNA_product +# metamodel_version: 1.7.0# version: 2.4.0id: noncoding_RNA_product schema_generating: true display_name: noncoding RNA product document_category: noncoding RNA product diff --git a/golr-views/nucleic_acid_entity_config.yaml b/golr-views/nucleic_acid_entity_config.yaml index bcf44ca3c4..6c5a58529e 100644 --- a/golr-views/nucleic_acid_entity_config.yaml +++ b/golr-views/nucleic_acid_entity_config.yaml @@ -1,4 +1,4 @@ -# metamodel_version: 1.7.0# version: 2.3.1id: nucleic_acid_entity +# metamodel_version: 1.7.0# version: 2.4.0id: nucleic_acid_entity schema_generating: true description: A nucleic acid entity is a molecular entity characterized by availability in gene databases of nucleotide-based sequence representations of its precise sequence; diff --git a/golr-views/nucleic_acid_sequence_motif_config.yaml b/golr-views/nucleic_acid_sequence_motif_config.yaml index da765b427b..f7949edfd4 100644 --- a/golr-views/nucleic_acid_sequence_motif_config.yaml +++ b/golr-views/nucleic_acid_sequence_motif_config.yaml @@ -1,4 +1,4 @@ -# metamodel_version: 1.7.0# version: 2.3.1id: nucleic_acid_sequence_motif +# metamodel_version: 1.7.0# version: 2.4.0id: nucleic_acid_sequence_motif schema_generating: true description: A linear nucleotide sequence pattern that is widespread and has, or is conjectured to have, a biological significance. e.g. the TATA box promoter motif, diff --git a/golr-views/nutrient_config.yaml b/golr-views/nutrient_config.yaml index 38345d1077..af28b30cb7 100644 --- a/golr-views/nutrient_config.yaml +++ b/golr-views/nutrient_config.yaml @@ -1,4 +1,4 @@ -# metamodel_version: 1.7.0# version: 2.3.1id: nutrient +# metamodel_version: 1.7.0# version: 2.4.0id: nutrient schema_generating: true display_name: nutrient document_category: nutrient diff --git a/golr-views/onset_config.yaml b/golr-views/onset_config.yaml index bd45c4518b..24bf045930 100644 --- a/golr-views/onset_config.yaml +++ b/golr-views/onset_config.yaml @@ -1,10 +1,48 @@ -# metamodel_version: 1.7.0# version: 2.3.1id: onset +# metamodel_version: 1.7.0# version: 2.4.0id: onset schema_generating: true description: The age group in which (disease) symptom manifestations appear display_name: onset document_category: onset weight: 20 fields: +- id: id + description: A unique identifier for an entity. Must be either a CURIE shorthand + for a URI or a complete URI + display_name: id +- id: type + display_name: type +- id: description + description: a human-readable description of an entity + display_name: description +- id: has_attribute + description: connects any entity to an attribute + display_name: has attribute + cardinality: multi +- id: provided_by + description: The value in this node property represents the knowledge provider that + created or assembled the node and all of its attributes. Used internally to represent + how a particular node made its way into a knowledge provider or graph. + display_name: provided by + cardinality: multi +- id: xref + description: Alternate CURIEs for a thing + display_name: xref + cardinality: multi +- id: category + description: "Name of the high level ontology class in which this entity is categorized.\ + \ Corresponds to the label for the biolink entity type class.\n * In a neo4j database\ + \ this MAY correspond to the neo4j label tag.\n * In an RDF database it should\ + \ be a biolink model class URI.\nThis field is multi-valued. It should include\ + \ values for ancestors of the biolink class; for example, a protein such as Shh\ + \ would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`,\ + \ ...\nIn an RDF database, nodes will typically have an rdf:type triples. This\ + \ can be to the most specific biolink class, or potentially to a class more specific\ + \ than something in biolink. For example, a sequence feature `f` may have a rdf:type\ + \ assertion to a SO class such as TF_binding_site, which is more specific than\ + \ anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity,\ + \ biolink:NamedThing}" + display_name: named thing_category + cardinality: multi - id: name description: The human-readable 'attribute name' can be set to a string which reflects its context of interpretation, e.g. SEPIO evidence/provenance/confidence annotation diff --git a/golr-views/organism_attribute_config.yaml b/golr-views/organism_attribute_config.yaml index dc65d0d887..6242d3b288 100644 --- a/golr-views/organism_attribute_config.yaml +++ b/golr-views/organism_attribute_config.yaml @@ -1,10 +1,48 @@ -# metamodel_version: 1.7.0# version: 2.3.1id: organism_attribute +# metamodel_version: 1.7.0# version: 2.4.0id: organism_attribute schema_generating: true description: describes a characteristic of an organismal entity. display_name: organism attribute document_category: organism attribute weight: 20 fields: +- id: id + description: A unique identifier for an entity. Must be either a CURIE shorthand + for a URI or a complete URI + display_name: id +- id: type + display_name: type +- id: description + description: a human-readable description of an entity + display_name: description +- id: has_attribute + description: connects any entity to an attribute + display_name: has attribute + cardinality: multi +- id: provided_by + description: The value in this node property represents the knowledge provider that + created or assembled the node and all of its attributes. Used internally to represent + how a particular node made its way into a knowledge provider or graph. + display_name: provided by + cardinality: multi +- id: xref + description: Alternate CURIEs for a thing + display_name: xref + cardinality: multi +- id: category + description: "Name of the high level ontology class in which this entity is categorized.\ + \ Corresponds to the label for the biolink entity type class.\n * In a neo4j database\ + \ this MAY correspond to the neo4j label tag.\n * In an RDF database it should\ + \ be a biolink model class URI.\nThis field is multi-valued. It should include\ + \ values for ancestors of the biolink class; for example, a protein such as Shh\ + \ would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`,\ + \ ...\nIn an RDF database, nodes will typically have an rdf:type triples. This\ + \ can be to the most specific biolink class, or potentially to a class more specific\ + \ than something in biolink. For example, a sequence feature `f` may have a rdf:type\ + \ assertion to a SO class such as TF_binding_site, which is more specific than\ + \ anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity,\ + \ biolink:NamedThing}" + display_name: named thing_category + cardinality: multi - id: name description: The human-readable 'attribute name' can be set to a string which reflects its context of interpretation, e.g. SEPIO evidence/provenance/confidence annotation diff --git a/golr-views/organism_taxon_config.yaml b/golr-views/organism_taxon_config.yaml index 815ca7ef58..f0aa17cd7b 100644 --- a/golr-views/organism_taxon_config.yaml +++ b/golr-views/organism_taxon_config.yaml @@ -1,4 +1,4 @@ -# metamodel_version: 1.7.0# version: 2.3.1id: organism_taxon +# metamodel_version: 1.7.0# version: 2.4.0id: organism_taxon schema_generating: true description: 'A classification of a set of organisms. Example instances: NCBITaxon:9606 (Homo sapiens), NCBITaxon:2 (Bacteria). Can also be used to represent strains or diff --git a/golr-views/organism_taxon_to_organism_taxon_interaction_config.yaml b/golr-views/organism_taxon_to_organism_taxon_interaction_config.yaml index 9964d3cd41..ae224df98d 100644 --- a/golr-views/organism_taxon_to_organism_taxon_interaction_config.yaml +++ b/golr-views/organism_taxon_to_organism_taxon_interaction_config.yaml @@ -1,4 +1,4 @@ -# metamodel_version: 1.7.0# version: 2.3.1id: organism_taxon_to_organism_taxon_interaction +# metamodel_version: 1.7.0# version: 2.4.0id: organism_taxon_to_organism_taxon_interaction schema_generating: true description: 'An interaction relationship between two taxa. This may be a symbiotic relationship (encompassing mutualism and parasitism), or it may be non-symbiotic. diff --git a/golr-views/organism_taxon_to_organism_taxon_specialization_config.yaml b/golr-views/organism_taxon_to_organism_taxon_specialization_config.yaml index 8fbcae909f..466cb9a672 100644 --- a/golr-views/organism_taxon_to_organism_taxon_specialization_config.yaml +++ b/golr-views/organism_taxon_to_organism_taxon_specialization_config.yaml @@ -1,4 +1,4 @@ -# metamodel_version: 1.7.0# version: 2.3.1id: organism_taxon_to_organism_taxon_specialization +# metamodel_version: 1.7.0# version: 2.4.0id: organism_taxon_to_organism_taxon_specialization schema_generating: true description: 'A child-parent relationship between two taxa. For example: Homo sapiens subclass_of Homo' diff --git a/golr-views/organism_to_organism_association_config.yaml b/golr-views/organism_to_organism_association_config.yaml index ba32019702..cd3c719ce3 100644 --- a/golr-views/organism_to_organism_association_config.yaml +++ b/golr-views/organism_to_organism_association_config.yaml @@ -1,4 +1,4 @@ -# metamodel_version: 1.7.0# version: 2.3.1id: organism_to_organism_association +# metamodel_version: 1.7.0# version: 2.4.0id: organism_to_organism_association schema_generating: true display_name: organism to organism association document_category: organism to organism association diff --git a/golr-views/organismal_entity_as_a_model_of_disease_association_config.yaml b/golr-views/organismal_entity_as_a_model_of_disease_association_config.yaml index 7bed3d4141..e5bbdceb40 100644 --- a/golr-views/organismal_entity_as_a_model_of_disease_association_config.yaml +++ b/golr-views/organismal_entity_as_a_model_of_disease_association_config.yaml @@ -1,4 +1,4 @@ -# metamodel_version: 1.7.0# version: 2.3.1id: organismal_entity_as_a_model_of_disease_association +# metamodel_version: 1.7.0# version: 2.4.0id: organismal_entity_as_a_model_of_disease_association schema_generating: true display_name: organismal entity as a model of disease association document_category: organismal entity as a model of disease association diff --git a/golr-views/pairwise_gene_to_gene_interaction_config.yaml b/golr-views/pairwise_gene_to_gene_interaction_config.yaml index 237e84c1a4..ad558e337f 100644 --- a/golr-views/pairwise_gene_to_gene_interaction_config.yaml +++ b/golr-views/pairwise_gene_to_gene_interaction_config.yaml @@ -1,4 +1,4 @@ -# metamodel_version: 1.7.0# version: 2.3.1id: pairwise_gene_to_gene_interaction +# metamodel_version: 1.7.0# version: 2.4.0id: pairwise_gene_to_gene_interaction schema_generating: true description: 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 diff --git a/golr-views/pairwise_molecular_interaction_config.yaml b/golr-views/pairwise_molecular_interaction_config.yaml index 7dfa6a33b8..7cc7bcb7a4 100644 --- a/golr-views/pairwise_molecular_interaction_config.yaml +++ b/golr-views/pairwise_molecular_interaction_config.yaml @@ -1,4 +1,4 @@ -# metamodel_version: 1.7.0# version: 2.3.1id: pairwise_molecular_interaction +# metamodel_version: 1.7.0# version: 2.4.0id: pairwise_molecular_interaction schema_generating: true description: An interaction at the molecular level between two physical entities display_name: pairwise molecular interaction diff --git a/golr-views/pathological_anatomical_structure_config.yaml b/golr-views/pathological_anatomical_structure_config.yaml index f31d27fb64..10f2eab0cc 100644 --- a/golr-views/pathological_anatomical_structure_config.yaml +++ b/golr-views/pathological_anatomical_structure_config.yaml @@ -1,4 +1,4 @@ -# metamodel_version: 1.7.0# version: 2.3.1id: pathological_anatomical_structure +# metamodel_version: 1.7.0# version: 2.4.0id: pathological_anatomical_structure schema_generating: true description: An anatomical structure with the potential of have an abnormal or deleterious effect at the subcellular, cellular, multicellular, or organismal level. diff --git a/golr-views/pathological_process_config.yaml b/golr-views/pathological_process_config.yaml index b4d91d613e..4df81a624b 100644 --- a/golr-views/pathological_process_config.yaml +++ b/golr-views/pathological_process_config.yaml @@ -1,4 +1,4 @@ -# metamodel_version: 1.7.0# version: 2.3.1id: pathological_process +# metamodel_version: 1.7.0# version: 2.4.0id: pathological_process schema_generating: true description: A biologic function or a process having an abnormal or deleterious effect at the subcellular, cellular, multicellular, or organismal level. diff --git a/golr-views/pathway_config.yaml b/golr-views/pathway_config.yaml index e3ce359383..f143e62d97 100644 --- a/golr-views/pathway_config.yaml +++ b/golr-views/pathway_config.yaml @@ -1,4 +1,4 @@ -# metamodel_version: 1.7.0# version: 2.3.1id: pathway +# metamodel_version: 1.7.0# version: 2.4.0id: pathway schema_generating: true display_name: pathway document_category: pathway diff --git a/golr-views/phenomenon_config.yaml b/golr-views/phenomenon_config.yaml index fe63218897..b8f1c2579a 100644 --- a/golr-views/phenomenon_config.yaml +++ b/golr-views/phenomenon_config.yaml @@ -1,4 +1,4 @@ -# metamodel_version: 1.7.0# version: 2.3.1id: phenomenon +# metamodel_version: 1.7.0# version: 2.4.0id: phenomenon schema_generating: true description: a fact or situation that is observed to exist or happen, especially one whose cause or explanation is in question diff --git a/golr-views/phenotypic_feature_config.yaml b/golr-views/phenotypic_feature_config.yaml index 00215b7d2c..3d6014862d 100644 --- a/golr-views/phenotypic_feature_config.yaml +++ b/golr-views/phenotypic_feature_config.yaml @@ -1,4 +1,4 @@ -# metamodel_version: 1.7.0# version: 2.3.1id: phenotypic_feature +# metamodel_version: 1.7.0# version: 2.4.0id: phenotypic_feature schema_generating: true description: A combination of entity and quality that makes up a phenotyping statement. display_name: phenotypic feature diff --git a/golr-views/phenotypic_quality_config.yaml b/golr-views/phenotypic_quality_config.yaml index 5180338af2..afd34b4315 100644 --- a/golr-views/phenotypic_quality_config.yaml +++ b/golr-views/phenotypic_quality_config.yaml @@ -1,10 +1,48 @@ -# metamodel_version: 1.7.0# version: 2.3.1id: phenotypic_quality +# metamodel_version: 1.7.0# version: 2.4.0id: phenotypic_quality schema_generating: true description: A property of a phenotype display_name: phenotypic quality document_category: phenotypic quality weight: 20 fields: +- id: id + description: A unique identifier for an entity. Must be either a CURIE shorthand + for a URI or a complete URI + display_name: id +- id: type + display_name: type +- id: description + description: a human-readable description of an entity + display_name: description +- id: has_attribute + description: connects any entity to an attribute + display_name: has attribute + cardinality: multi +- id: provided_by + description: The value in this node property represents the knowledge provider that + created or assembled the node and all of its attributes. Used internally to represent + how a particular node made its way into a knowledge provider or graph. + display_name: provided by + cardinality: multi +- id: xref + description: Alternate CURIEs for a thing + display_name: xref + cardinality: multi +- id: category + description: "Name of the high level ontology class in which this entity is categorized.\ + \ Corresponds to the label for the biolink entity type class.\n * In a neo4j database\ + \ this MAY correspond to the neo4j label tag.\n * In an RDF database it should\ + \ be a biolink model class URI.\nThis field is multi-valued. It should include\ + \ values for ancestors of the biolink class; for example, a protein such as Shh\ + \ would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`,\ + \ ...\nIn an RDF database, nodes will typically have an rdf:type triples. This\ + \ can be to the most specific biolink class, or potentially to a class more specific\ + \ than something in biolink. For example, a sequence feature `f` may have a rdf:type\ + \ assertion to a SO class such as TF_binding_site, which is more specific than\ + \ anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity,\ + \ biolink:NamedThing}" + display_name: named thing_category + cardinality: multi - id: name description: The human-readable 'attribute name' can be set to a string which reflects its context of interpretation, e.g. SEPIO evidence/provenance/confidence annotation diff --git a/golr-views/phenotypic_sex_config.yaml b/golr-views/phenotypic_sex_config.yaml index 932c576cfc..0e7e6c6cb9 100644 --- a/golr-views/phenotypic_sex_config.yaml +++ b/golr-views/phenotypic_sex_config.yaml @@ -1,4 +1,4 @@ -# metamodel_version: 1.7.0# version: 2.3.1id: phenotypic_sex +# metamodel_version: 1.7.0# version: 2.4.0id: phenotypic_sex schema_generating: true description: An attribute corresponding to the phenotypic sex of the individual, based upon the reproductive organs present. @@ -6,6 +6,44 @@ display_name: phenotypic sex document_category: phenotypic sex weight: 20 fields: +- id: id + description: A unique identifier for an entity. Must be either a CURIE shorthand + for a URI or a complete URI + display_name: id +- id: type + display_name: type +- id: description + description: a human-readable description of an entity + display_name: description +- id: has_attribute + description: connects any entity to an attribute + display_name: has attribute + cardinality: multi +- id: provided_by + description: The value in this node property represents the knowledge provider that + created or assembled the node and all of its attributes. Used internally to represent + how a particular node made its way into a knowledge provider or graph. + display_name: provided by + cardinality: multi +- id: xref + description: Alternate CURIEs for a thing + display_name: xref + cardinality: multi +- id: category + description: "Name of the high level ontology class in which this entity is categorized.\ + \ Corresponds to the label for the biolink entity type class.\n * In a neo4j database\ + \ this MAY correspond to the neo4j label tag.\n * In an RDF database it should\ + \ be a biolink model class URI.\nThis field is multi-valued. It should include\ + \ values for ancestors of the biolink class; for example, a protein such as Shh\ + \ would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`,\ + \ ...\nIn an RDF database, nodes will typically have an rdf:type triples. This\ + \ can be to the most specific biolink class, or potentially to a class more specific\ + \ than something in biolink. For example, a sequence feature `f` may have a rdf:type\ + \ assertion to a SO class such as TF_binding_site, which is more specific than\ + \ anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity,\ + \ biolink:NamedThing}" + display_name: named thing_category + cardinality: multi - id: name description: The human-readable 'attribute name' can be set to a string which reflects its context of interpretation, e.g. SEPIO evidence/provenance/confidence annotation diff --git a/golr-views/physical_entity_config.yaml b/golr-views/physical_entity_config.yaml index 8dc1434aac..f05de34f85 100644 --- a/golr-views/physical_entity_config.yaml +++ b/golr-views/physical_entity_config.yaml @@ -1,4 +1,4 @@ -# metamodel_version: 1.7.0# version: 2.3.1id: physical_entity +# metamodel_version: 1.7.0# version: 2.4.0id: physical_entity schema_generating: true description: An entity that has material reality (a.k.a. physical essence). display_name: physical entity diff --git a/golr-views/physiological_process_config.yaml b/golr-views/physiological_process_config.yaml index 017493daf0..3cb535b8e7 100644 --- a/golr-views/physiological_process_config.yaml +++ b/golr-views/physiological_process_config.yaml @@ -1,4 +1,4 @@ -# metamodel_version: 1.7.0# version: 2.3.1id: physiological_process +# metamodel_version: 1.7.0# version: 2.4.0id: physiological_process schema_generating: true display_name: physiological process document_category: physiological process diff --git a/golr-views/planetary_entity_config.yaml b/golr-views/planetary_entity_config.yaml index 3289fb1c08..7a57cd492d 100644 --- a/golr-views/planetary_entity_config.yaml +++ b/golr-views/planetary_entity_config.yaml @@ -1,4 +1,4 @@ -# metamodel_version: 1.7.0# version: 2.3.1id: planetary_entity +# metamodel_version: 1.7.0# version: 2.4.0id: planetary_entity schema_generating: true description: Any entity or process that exists at the level of the whole planet display_name: planetary entity diff --git a/golr-views/polypeptide_config.yaml b/golr-views/polypeptide_config.yaml index 3208d730e7..c66a1f3923 100644 --- a/golr-views/polypeptide_config.yaml +++ b/golr-views/polypeptide_config.yaml @@ -1,4 +1,4 @@ -# metamodel_version: 1.7.0# version: 2.3.1id: polypeptide +# metamodel_version: 1.7.0# version: 2.4.0id: polypeptide schema_generating: true description: A polypeptide is a molecular entity characterized by availability in protein databases of amino-acid-based sequence representations of its precise primary diff --git a/golr-views/population_of_individual_organisms_config.yaml b/golr-views/population_of_individual_organisms_config.yaml index f2aa0b3e4d..f3e42608cb 100644 --- a/golr-views/population_of_individual_organisms_config.yaml +++ b/golr-views/population_of_individual_organisms_config.yaml @@ -1,4 +1,4 @@ -# metamodel_version: 1.7.0# version: 2.3.1id: population_of_individual_organisms +# metamodel_version: 1.7.0# version: 2.4.0id: population_of_individual_organisms schema_generating: true description: A collection of individuals from the same taxonomic class distinguished by one or more characteristics. Characteristics can include, but are not limited diff --git a/golr-views/population_to_population_association_config.yaml b/golr-views/population_to_population_association_config.yaml index c7c4798e38..9671868c44 100644 --- a/golr-views/population_to_population_association_config.yaml +++ b/golr-views/population_to_population_association_config.yaml @@ -1,4 +1,4 @@ -# metamodel_version: 1.7.0# version: 2.3.1id: population_to_population_association +# metamodel_version: 1.7.0# version: 2.4.0id: population_to_population_association schema_generating: true description: An association between a two populations display_name: population to population association diff --git a/golr-views/procedure_config.yaml b/golr-views/procedure_config.yaml index d9c75f8aef..eb37d4c481 100644 --- a/golr-views/procedure_config.yaml +++ b/golr-views/procedure_config.yaml @@ -1,4 +1,4 @@ -# metamodel_version: 1.7.0# version: 2.3.1id: procedure +# metamodel_version: 1.7.0# version: 2.4.0id: procedure schema_generating: true description: A series of actions conducted in a certain order or manner display_name: procedure diff --git a/golr-views/processed_material_config.yaml b/golr-views/processed_material_config.yaml index 22721870f0..e2a8dc6354 100644 --- a/golr-views/processed_material_config.yaml +++ b/golr-views/processed_material_config.yaml @@ -1,4 +1,4 @@ -# metamodel_version: 1.7.0# version: 2.3.1id: processed_material +# metamodel_version: 1.7.0# version: 2.4.0id: processed_material schema_generating: true description: A chemical entity (often a mixture) processed for consumption for nutritional, medical or technical use. Is a material entity that is created or changed during diff --git a/golr-views/protein_config.yaml b/golr-views/protein_config.yaml index 7aa0b2e4da..092d832ba2 100644 --- a/golr-views/protein_config.yaml +++ b/golr-views/protein_config.yaml @@ -1,4 +1,4 @@ -# metamodel_version: 1.7.0# version: 2.3.1id: protein +# metamodel_version: 1.7.0# version: 2.4.0id: protein schema_generating: true description: A gene product that is composed of a chain of amino acid sequences and is produced by ribosome-mediated translation of mRNA diff --git a/golr-views/protein_domain_config.yaml b/golr-views/protein_domain_config.yaml index 8066d25a50..dbc35451de 100644 --- a/golr-views/protein_domain_config.yaml +++ b/golr-views/protein_domain_config.yaml @@ -1,4 +1,4 @@ -# metamodel_version: 1.7.0# version: 2.3.1id: protein_domain +# metamodel_version: 1.7.0# version: 2.4.0id: protein_domain schema_generating: true description: A conserved part of protein sequence and (tertiary) structure that can evolve, function, and exist independently of the rest of the protein chain. Protein diff --git a/golr-views/protein_family_config.yaml b/golr-views/protein_family_config.yaml index a5d0be0523..d8f0b4762e 100644 --- a/golr-views/protein_family_config.yaml +++ b/golr-views/protein_family_config.yaml @@ -1,4 +1,4 @@ -# metamodel_version: 1.7.0# version: 2.3.1id: protein_family +# metamodel_version: 1.7.0# version: 2.4.0id: protein_family schema_generating: true display_name: protein family document_category: protein family diff --git a/golr-views/protein_isoform_config.yaml b/golr-views/protein_isoform_config.yaml index 52d8b3ded2..748de91dd9 100644 --- a/golr-views/protein_isoform_config.yaml +++ b/golr-views/protein_isoform_config.yaml @@ -1,4 +1,4 @@ -# metamodel_version: 1.7.0# version: 2.3.1id: protein_isoform +# metamodel_version: 1.7.0# version: 2.4.0id: protein_isoform schema_generating: true description: Represents a protein that is a specific isoform of the canonical or reference protein. See https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4114032/ diff --git a/golr-views/publication_config.yaml b/golr-views/publication_config.yaml index 65de3a18d8..a9f2ed24dd 100644 --- a/golr-views/publication_config.yaml +++ b/golr-views/publication_config.yaml @@ -1,4 +1,4 @@ -# metamodel_version: 1.7.0# version: 2.3.1id: publication +# metamodel_version: 1.7.0# version: 2.4.0id: publication schema_generating: true description: 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, diff --git a/golr-views/quantity_value_config.yaml b/golr-views/quantity_value_config.yaml index 966506afea..f395377b98 100644 --- a/golr-views/quantity_value_config.yaml +++ b/golr-views/quantity_value_config.yaml @@ -1,4 +1,4 @@ -# metamodel_version: 1.7.0# version: 2.3.1id: quantity_value +# metamodel_version: 1.7.0# version: 2.4.0id: quantity_value schema_generating: true description: A value of an attribute that is quantitative and measurable, expressed as a combination of a unit and a numeric value diff --git a/golr-views/reaction_to_catalyst_association_config.yaml b/golr-views/reaction_to_catalyst_association_config.yaml index 9ba6396863..4d3769171a 100644 --- a/golr-views/reaction_to_catalyst_association_config.yaml +++ b/golr-views/reaction_to_catalyst_association_config.yaml @@ -1,4 +1,4 @@ -# metamodel_version: 1.7.0# version: 2.3.1id: reaction_to_catalyst_association +# metamodel_version: 1.7.0# version: 2.4.0id: reaction_to_catalyst_association schema_generating: true display_name: reaction to catalyst association document_category: reaction to catalyst association diff --git a/golr-views/reaction_to_participant_association_config.yaml b/golr-views/reaction_to_participant_association_config.yaml index 27a46e5288..bb4b4e760c 100644 --- a/golr-views/reaction_to_participant_association_config.yaml +++ b/golr-views/reaction_to_participant_association_config.yaml @@ -1,4 +1,4 @@ -# metamodel_version: 1.7.0# version: 2.3.1id: reaction_to_participant_association +# metamodel_version: 1.7.0# version: 2.4.0id: reaction_to_participant_association schema_generating: true display_name: reaction to participant association document_category: reaction to participant association diff --git a/golr-views/reagent_targeted_gene_config.yaml b/golr-views/reagent_targeted_gene_config.yaml index be89d4acdc..254c0d45d1 100644 --- a/golr-views/reagent_targeted_gene_config.yaml +++ b/golr-views/reagent_targeted_gene_config.yaml @@ -1,4 +1,4 @@ -# metamodel_version: 1.7.0# version: 2.3.1id: reagent_targeted_gene +# metamodel_version: 1.7.0# version: 2.4.0id: reagent_targeted_gene schema_generating: true description: A gene altered in its expression level in the context of some experiment as a result of being targeted by gene-knockdown reagent(s) such as a morpholino diff --git a/golr-views/sequence_association_config.yaml b/golr-views/sequence_association_config.yaml index 90c3f2f1a3..8a0bfa698f 100644 --- a/golr-views/sequence_association_config.yaml +++ b/golr-views/sequence_association_config.yaml @@ -1,4 +1,4 @@ -# metamodel_version: 1.7.0# version: 2.3.1id: sequence_association +# metamodel_version: 1.7.0# version: 2.4.0id: sequence_association schema_generating: true description: An association between a sequence feature and a nucleic acid entity it is localized to. diff --git a/golr-views/sequence_feature_relationship_config.yaml b/golr-views/sequence_feature_relationship_config.yaml index 26dde39d9b..9e749035d7 100644 --- a/golr-views/sequence_feature_relationship_config.yaml +++ b/golr-views/sequence_feature_relationship_config.yaml @@ -1,4 +1,4 @@ -# metamodel_version: 1.7.0# version: 2.3.1id: sequence_feature_relationship +# metamodel_version: 1.7.0# version: 2.4.0id: sequence_feature_relationship schema_generating: true description: For example, a particular exon is part of a particular transcript or gene diff --git a/golr-views/sequence_variant_config.yaml b/golr-views/sequence_variant_config.yaml index 4cee43dc88..ca590cf596 100644 --- a/golr-views/sequence_variant_config.yaml +++ b/golr-views/sequence_variant_config.yaml @@ -1,4 +1,4 @@ -# metamodel_version: 1.7.0# version: 2.3.1id: sequence_variant +# metamodel_version: 1.7.0# version: 2.4.0id: sequence_variant schema_generating: true description: An allele that varies in its sequence from what is considered the reference allele at that locus. diff --git a/golr-views/serial_config.yaml b/golr-views/serial_config.yaml index b452b5d06a..058c7a8914 100644 --- a/golr-views/serial_config.yaml +++ b/golr-views/serial_config.yaml @@ -1,4 +1,4 @@ -# metamodel_version: 1.7.0# version: 2.3.1id: serial +# metamodel_version: 1.7.0# version: 2.4.0id: serial schema_generating: true description: This class may rarely be instantiated except if use cases of a given knowledge graph support its utility. diff --git a/golr-views/severity_value_config.yaml b/golr-views/severity_value_config.yaml index 9fb0debbd3..1a09e0b6e1 100644 --- a/golr-views/severity_value_config.yaml +++ b/golr-views/severity_value_config.yaml @@ -1,10 +1,48 @@ -# metamodel_version: 1.7.0# version: 2.3.1id: severity_value +# metamodel_version: 1.7.0# version: 2.4.0id: severity_value schema_generating: true description: describes the severity of a phenotypic feature or disease display_name: severity value document_category: severity value weight: 20 fields: +- id: id + description: A unique identifier for an entity. Must be either a CURIE shorthand + for a URI or a complete URI + display_name: id +- id: type + display_name: type +- id: description + description: a human-readable description of an entity + display_name: description +- id: has_attribute + description: connects any entity to an attribute + display_name: has attribute + cardinality: multi +- id: provided_by + description: The value in this node property represents the knowledge provider that + created or assembled the node and all of its attributes. Used internally to represent + how a particular node made its way into a knowledge provider or graph. + display_name: provided by + cardinality: multi +- id: xref + description: Alternate CURIEs for a thing + display_name: xref + cardinality: multi +- id: category + description: "Name of the high level ontology class in which this entity is categorized.\ + \ Corresponds to the label for the biolink entity type class.\n * In a neo4j database\ + \ this MAY correspond to the neo4j label tag.\n * In an RDF database it should\ + \ be a biolink model class URI.\nThis field is multi-valued. It should include\ + \ values for ancestors of the biolink class; for example, a protein such as Shh\ + \ would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`,\ + \ ...\nIn an RDF database, nodes will typically have an rdf:type triples. This\ + \ can be to the most specific biolink class, or potentially to a class more specific\ + \ than something in biolink. For example, a sequence feature `f` may have a rdf:type\ + \ assertion to a SO class such as TF_binding_site, which is more specific than\ + \ anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity,\ + \ biolink:NamedThing}" + display_name: named thing_category + cardinality: multi - id: name description: The human-readable 'attribute name' can be set to a string which reflects its context of interpretation, e.g. SEPIO evidence/provenance/confidence annotation diff --git a/golr-views/siRNA_config.yaml b/golr-views/siRNA_config.yaml index 0911bca2aa..179ce763d6 100644 --- a/golr-views/siRNA_config.yaml +++ b/golr-views/siRNA_config.yaml @@ -1,4 +1,4 @@ -# metamodel_version: 1.7.0# version: 2.3.1id: siRNA +# metamodel_version: 1.7.0# version: 2.4.0id: siRNA schema_generating: true description: A small RNA molecule that is the product of a longer exogenous or endogenous dsRNA, which is either a bimolecular duplex or very long hairpin, processed (via diff --git a/golr-views/small_molecule_config.yaml b/golr-views/small_molecule_config.yaml index 242d65be60..b0caa91927 100644 --- a/golr-views/small_molecule_config.yaml +++ b/golr-views/small_molecule_config.yaml @@ -1,4 +1,4 @@ -# metamodel_version: 1.7.0# version: 2.3.1id: small_molecule +# metamodel_version: 1.7.0# version: 2.4.0id: small_molecule schema_generating: true description: A small molecule entity is a molecular entity characterized by availability in small-molecule databases of SMILES, InChI, IUPAC, or other unambiguous representation diff --git a/golr-views/snv_config.yaml b/golr-views/snv_config.yaml index 7ce6b362f7..9ea8f37936 100644 --- a/golr-views/snv_config.yaml +++ b/golr-views/snv_config.yaml @@ -1,4 +1,4 @@ -# metamodel_version: 1.7.0# version: 2.3.1id: snv +# metamodel_version: 1.7.0# version: 2.4.0id: snv schema_generating: true description: SNVs are single nucleotide positions in genomic DNA at which different sequence alternatives exist diff --git a/golr-views/socioeconomic_attribute_config.yaml b/golr-views/socioeconomic_attribute_config.yaml index 13a4012e76..23663c0933 100644 --- a/golr-views/socioeconomic_attribute_config.yaml +++ b/golr-views/socioeconomic_attribute_config.yaml @@ -1,10 +1,48 @@ -# metamodel_version: 1.7.0# version: 2.3.1id: socioeconomic_attribute +# metamodel_version: 1.7.0# version: 2.4.0id: socioeconomic_attribute schema_generating: true description: Attributes relating to a socioeconomic manifestation display_name: socioeconomic attribute document_category: socioeconomic attribute weight: 20 fields: +- id: id + description: A unique identifier for an entity. Must be either a CURIE shorthand + for a URI or a complete URI + display_name: id +- id: type + display_name: type +- id: description + description: a human-readable description of an entity + display_name: description +- id: has_attribute + description: connects any entity to an attribute + display_name: has attribute + cardinality: multi +- id: provided_by + description: The value in this node property represents the knowledge provider that + created or assembled the node and all of its attributes. Used internally to represent + how a particular node made its way into a knowledge provider or graph. + display_name: provided by + cardinality: multi +- id: xref + description: Alternate CURIEs for a thing + display_name: xref + cardinality: multi +- id: category + description: "Name of the high level ontology class in which this entity is categorized.\ + \ Corresponds to the label for the biolink entity type class.\n * In a neo4j database\ + \ this MAY correspond to the neo4j label tag.\n * In an RDF database it should\ + \ be a biolink model class URI.\nThis field is multi-valued. It should include\ + \ values for ancestors of the biolink class; for example, a protein such as Shh\ + \ would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`,\ + \ ...\nIn an RDF database, nodes will typically have an rdf:type triples. This\ + \ can be to the most specific biolink class, or potentially to a class more specific\ + \ than something in biolink. For example, a sequence feature `f` may have a rdf:type\ + \ assertion to a SO class such as TF_binding_site, which is more specific than\ + \ anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity,\ + \ biolink:NamedThing}" + display_name: named thing_category + cardinality: multi - id: name description: The human-readable 'attribute name' can be set to a string which reflects its context of interpretation, e.g. SEPIO evidence/provenance/confidence annotation diff --git a/golr-views/socioeconomic_exposure_config.yaml b/golr-views/socioeconomic_exposure_config.yaml index b5b72c504c..e92d909dfd 100644 --- a/golr-views/socioeconomic_exposure_config.yaml +++ b/golr-views/socioeconomic_exposure_config.yaml @@ -1,4 +1,4 @@ -# metamodel_version: 1.7.0# version: 2.3.1id: socioeconomic_exposure +# metamodel_version: 1.7.0# version: 2.4.0id: socioeconomic_exposure schema_generating: true description: A socioeconomic exposure is a factor relating to social and financial status of an affected individual (e.g. poverty). diff --git a/golr-views/study_population_config.yaml b/golr-views/study_population_config.yaml index 5b0722b0d0..d7c870170d 100644 --- a/golr-views/study_population_config.yaml +++ b/golr-views/study_population_config.yaml @@ -1,4 +1,4 @@ -# metamodel_version: 1.7.0# version: 2.3.1id: study_population +# metamodel_version: 1.7.0# version: 2.4.0id: study_population schema_generating: true description: A group of people banded together or treated as a group as participants in a research study. diff --git a/golr-views/taxon_to_taxon_association_config.yaml b/golr-views/taxon_to_taxon_association_config.yaml index fb60dc7252..6032a10b67 100644 --- a/golr-views/taxon_to_taxon_association_config.yaml +++ b/golr-views/taxon_to_taxon_association_config.yaml @@ -1,4 +1,4 @@ -# metamodel_version: 1.7.0# version: 2.3.1id: taxon_to_taxon_association +# metamodel_version: 1.7.0# version: 2.4.0id: taxon_to_taxon_association schema_generating: true display_name: taxon to taxon association document_category: taxon to taxon association diff --git a/golr-views/transcript_config.yaml b/golr-views/transcript_config.yaml index 6a64be8a70..8918335baf 100644 --- a/golr-views/transcript_config.yaml +++ b/golr-views/transcript_config.yaml @@ -1,4 +1,4 @@ -# metamodel_version: 1.7.0# version: 2.3.1id: transcript +# metamodel_version: 1.7.0# version: 2.4.0id: transcript schema_generating: true description: An RNA synthesized on a DNA or RNA template by an RNA polymerase. display_name: transcript diff --git a/golr-views/transcript_to_gene_relationship_config.yaml b/golr-views/transcript_to_gene_relationship_config.yaml index fbcf3ad6d7..6d7e6bb399 100644 --- a/golr-views/transcript_to_gene_relationship_config.yaml +++ b/golr-views/transcript_to_gene_relationship_config.yaml @@ -1,4 +1,4 @@ -# metamodel_version: 1.7.0# version: 2.3.1id: transcript_to_gene_relationship +# metamodel_version: 1.7.0# version: 2.4.0id: transcript_to_gene_relationship schema_generating: true description: A gene is a collection of transcripts display_name: transcript to gene relationship diff --git a/golr-views/treatment_config.yaml b/golr-views/treatment_config.yaml index 1fb9954227..3c446ce375 100644 --- a/golr-views/treatment_config.yaml +++ b/golr-views/treatment_config.yaml @@ -1,4 +1,4 @@ -# metamodel_version: 1.7.0# version: 2.3.1id: treatment +# metamodel_version: 1.7.0# version: 2.4.0id: treatment schema_generating: true description: A treatment is targeted at a disease or phenotype and may involve multiple drug 'exposures', medical devices and/or procedures diff --git a/golr-views/variant_as_a_model_of_disease_association_config.yaml b/golr-views/variant_as_a_model_of_disease_association_config.yaml index 014d8fa0b9..6ae64c7a12 100644 --- a/golr-views/variant_as_a_model_of_disease_association_config.yaml +++ b/golr-views/variant_as_a_model_of_disease_association_config.yaml @@ -1,4 +1,4 @@ -# metamodel_version: 1.7.0# version: 2.3.1id: variant_as_a_model_of_disease_association +# metamodel_version: 1.7.0# version: 2.4.0id: variant_as_a_model_of_disease_association schema_generating: true display_name: variant as a model of disease association document_category: variant as a model of disease association diff --git a/golr-views/variant_to_disease_association_config.yaml b/golr-views/variant_to_disease_association_config.yaml index f1c68ae536..fb50d9b8da 100644 --- a/golr-views/variant_to_disease_association_config.yaml +++ b/golr-views/variant_to_disease_association_config.yaml @@ -1,4 +1,4 @@ -# metamodel_version: 1.7.0# version: 2.3.1id: variant_to_disease_association +# metamodel_version: 1.7.0# version: 2.4.0id: variant_to_disease_association schema_generating: true display_name: variant to disease association document_category: variant to disease association diff --git a/golr-views/variant_to_gene_association_config.yaml b/golr-views/variant_to_gene_association_config.yaml index 2a30f7634e..27da29c166 100644 --- a/golr-views/variant_to_gene_association_config.yaml +++ b/golr-views/variant_to_gene_association_config.yaml @@ -1,4 +1,4 @@ -# metamodel_version: 1.7.0# version: 2.3.1id: variant_to_gene_association +# metamodel_version: 1.7.0# version: 2.4.0id: variant_to_gene_association schema_generating: true description: An association between a variant and a gene, where the variant has a genetic association with the gene (i.e. is in linkage disequilibrium) diff --git a/golr-views/variant_to_gene_expression_association_config.yaml b/golr-views/variant_to_gene_expression_association_config.yaml index 8b934d23c1..942d223581 100644 --- a/golr-views/variant_to_gene_expression_association_config.yaml +++ b/golr-views/variant_to_gene_expression_association_config.yaml @@ -1,4 +1,4 @@ -# metamodel_version: 1.7.0# version: 2.3.1id: variant_to_gene_expression_association +# metamodel_version: 1.7.0# version: 2.4.0id: variant_to_gene_expression_association schema_generating: true description: An association between a variant and expression of a gene (i.e. e-QTL) display_name: variant to gene expression association diff --git a/golr-views/variant_to_phenotypic_feature_association_config.yaml b/golr-views/variant_to_phenotypic_feature_association_config.yaml index 922029ba99..cbff50d366 100644 --- a/golr-views/variant_to_phenotypic_feature_association_config.yaml +++ b/golr-views/variant_to_phenotypic_feature_association_config.yaml @@ -1,4 +1,4 @@ -# metamodel_version: 1.7.0# version: 2.3.1id: variant_to_phenotypic_feature_association +# metamodel_version: 1.7.0# version: 2.4.0id: variant_to_phenotypic_feature_association schema_generating: true display_name: variant to phenotypic feature association document_category: variant to phenotypic feature association diff --git a/golr-views/variant_to_population_association_config.yaml b/golr-views/variant_to_population_association_config.yaml index d5eea8bd5d..c9833befe9 100644 --- a/golr-views/variant_to_population_association_config.yaml +++ b/golr-views/variant_to_population_association_config.yaml @@ -1,4 +1,4 @@ -# metamodel_version: 1.7.0# version: 2.3.1id: variant_to_population_association +# metamodel_version: 1.7.0# version: 2.4.0id: variant_to_population_association schema_generating: true description: An association between a variant and a population, where the variant has particular frequency in the population diff --git a/golr-views/vitamin_config.yaml b/golr-views/vitamin_config.yaml index 283a1896f4..6b4a2a08a7 100644 --- a/golr-views/vitamin_config.yaml +++ b/golr-views/vitamin_config.yaml @@ -1,4 +1,4 @@ -# metamodel_version: 1.7.0# version: 2.3.1id: vitamin +# metamodel_version: 1.7.0# version: 2.4.0id: vitamin schema_generating: true display_name: vitamin document_category: vitamin diff --git a/golr-views/zygosity_config.yaml b/golr-views/zygosity_config.yaml index e996cd84e7..446cfe64c6 100644 --- a/golr-views/zygosity_config.yaml +++ b/golr-views/zygosity_config.yaml @@ -1,9 +1,47 @@ -# metamodel_version: 1.7.0# version: 2.3.1id: zygosity +# metamodel_version: 1.7.0# version: 2.4.0id: zygosity schema_generating: true display_name: zygosity document_category: zygosity weight: 20 fields: +- id: id + description: A unique identifier for an entity. Must be either a CURIE shorthand + for a URI or a complete URI + display_name: id +- id: type + display_name: type +- id: description + description: a human-readable description of an entity + display_name: description +- id: has_attribute + description: connects any entity to an attribute + display_name: has attribute + cardinality: multi +- id: provided_by + description: The value in this node property represents the knowledge provider that + created or assembled the node and all of its attributes. Used internally to represent + how a particular node made its way into a knowledge provider or graph. + display_name: provided by + cardinality: multi +- id: xref + description: Alternate CURIEs for a thing + display_name: xref + cardinality: multi +- id: category + description: "Name of the high level ontology class in which this entity is categorized.\ + \ Corresponds to the label for the biolink entity type class.\n * In a neo4j database\ + \ this MAY correspond to the neo4j label tag.\n * In an RDF database it should\ + \ be a biolink model class URI.\nThis field is multi-valued. It should include\ + \ values for ancestors of the biolink class; for example, a protein such as Shh\ + \ would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`,\ + \ ...\nIn an RDF database, nodes will typically have an rdf:type triples. This\ + \ can be to the most specific biolink class, or potentially to a class more specific\ + \ than something in biolink. For example, a sequence feature `f` may have a rdf:type\ + \ assertion to a SO class such as TF_binding_site, which is more specific than\ + \ anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity,\ + \ biolink:NamedThing}" + display_name: named thing_category + cardinality: multi - id: name description: The human-readable 'attribute name' can be set to a string which reflects its context of interpretation, e.g. SEPIO evidence/provenance/confidence annotation diff --git a/graphviz/attribute.gv b/graphviz/attribute.gv index 56f425ee80..30e6de49a9 100644 --- a/graphviz/attribute.gv +++ b/graphviz/attribute.gv @@ -1,87 +1,162 @@ digraph { - graph [bb="0,0,1124.8,123"]; + graph [bb="0,0,1971.9,123"]; node [label="\N"]; attribute [height=0.5, label=attribute, - pos="553.44,105", + pos="961.54,105", width=1.4443]; - annotation [height=0.5, - pos="60.445,18", - width=1.679]; - attribute -> annotation [label=is_a, - lp="297.44,61.5", - pos="e,105.31,30.263 504.49,98.878 450.26,92.92 360.31,82.195 283.44,69 214.46,57.157 197.66,51.708 129.44,36 124.8,34.932 120,33.799 \ -115.17,32.646"]; + "named thing" [height=0.5, + pos="69.544,18", + width=1.9318]; + attribute -> "named thing" [label=is_a, + lp="346.54,61.5", + pos="e,119.14,30.638 909.59,103.23 801.71,101.17 545.74,93.854 332.54,69 262.07,60.784 182.12,44.586 129.06,32.848"]; "ontology class" [height=0.5, - pos="215.44,18", + pos="233.54,18", width=2.1304]; attribute -> "ontology class" [label=uses, - lp="381.94,61.5", - pos="e,254.17,33.544 506.31,97.071 468.04,91.006 412.86,81.253 365.44,69 330.94,60.083 292.86,47.351 263.7,36.967"]; + lp="454.04,61.5", + pos="e,279.27,32.625 909.53,103.51 815,101.96 608.96,95.526 437.54,69 386.61,61.118 329.73,46.697 289,35.361"]; + id [color=blue, + height=0.5, + label=string, + pos="366.54,18", + width=1.0652]; + attribute -> id [color=blue, + label=id, + lp="541.54,61.5", + pos="e,395.49,29.825 909.88,102.87 829.18,100.41 668.58,92.709 534.54,69 489.13,60.968 438.62,44.924 404.95,33.169", + style=solid]; + type [color=blue, + height=0.5, + label=string, + pos="461.54,18", + width=1.0652]; + attribute -> type [color=blue, + label=type, + lp="619.54,61.5", + pos="e,488.72,30.794 909.65,102.82 839.46,100.35 710.71,92.688 603.54,69 566.79,60.876 526.45,46.068 498.19,34.668", + style=solid]; + description [color=blue, + height=0.5, + label="narrative text", + pos="593.54,18", + width=2.0943]; + attribute -> description [color=blue, + label=description, + lp="707.04,61.5", + pos="e,612.23,35.594 910.77,100.91 838.54,96.024 710.06,85.345 666.54,69 649.91,62.752 633.41,51.943 620.31,41.97", + style=solid]; + "has attribute" [color=blue, + height=0.5, + label=attribute, + pos="738.54,18", + width=1.4443]; + attribute -> "has attribute" [color=blue, + label="has attribute", + lp="810.54,61.5", + pos="e,742.74,35.971 911.16,100.24 860.38,95.551 786.35,86.014 763.54,69 755.74,63.181 750.22,54.25 746.38,45.537", + style=solid]; + "provided by" [color=blue, + height=0.5, + label=string, + pos="846.54,18", + width=1.0652]; + attribute -> "provided by" [color=blue, + label="provided by", + lp="915.04,61.5", + pos="e,851.99,36.267 919.61,94.312 903.46,88.951 885.75,80.887 872.54,69 865.46,62.627 860.01,53.869 855.97,45.463", + style=solid]; + xref [color=blue, + height=0.5, + label=uriorcurie, + pos="960.54,18", + width=1.5887]; + attribute -> xref [color=blue, + label=xref, + lp="976.04,61.5", + pos="e,960.75,36.175 961.34,86.799 961.2,75.163 961.02,59.548 960.86,46.237", + style=solid]; + category [height=0.5, + pos="1087.5,18", + width=1.4263]; + attribute -> category [color=blue, + label=category, + lp="1064,61.5", + pos="e,1064.9,34.278 984.36,88.607 1004.5,75.008 1034.1,55.052 1056.4,39.991", + style=solid]; name [height=0.5, - pos="346.44,18", + pos="1193.5,18", width=1.011]; attribute -> name [color=blue, label=name, - lp="450.44,61.5", - pos="e,366.7,33.103 510.66,94.729 486.57,88.796 456.24,80.12 430.44,69 411.29,60.743 391.17,48.893 375.43,38.801", + lp="1152.5,61.5", + pos="e,1171.9,32.604 1000.2,92.962 1007.6,90.924 1015.3,88.855 1022.5,87 1056.6,78.281 1066.6,81.356 1099.5,69 1121.6,60.699 1145.1,48.234 \ +1163,37.826", style=solid]; "has attribute type" [color=blue, height=0.5, label="ontology class", - pos="477.44,18", + pos="1324.5,18", width=2.1304]; attribute -> "has attribute type" [color=blue, label="has attribute type", - lp="543.44,61.5", - pos="e,473.52,36.068 511.78,93.946 498.92,88.696 486.13,80.801 478.44,69 474.1,62.322 472.74,54.005 472.78,46.084", + lp="1295.5,61.5", + pos="e,1287.8,33.836 999.4,92.469 1007,90.428 1015,88.484 1022.5,87 1090.2,73.71 1109.3,84.111 1176.5,69 1211.4,61.172 1249.5,48.177 \ +1278.3,37.396", style=solid]; "has quantitative value" [color=blue, height=0.5, label="quantity value", - pos="649.44,18", + pos="1496.5,18", width=2.1484]; attribute -> "has quantitative value" [color=blue, label="has quantitative value", - lp="702.44,61.5", - pos="e,637.71,35.909 580.11,89.385 589.53,83.631 599.89,76.583 608.44,69 616.76,61.627 624.78,52.479 631.48,44.032", + lp="1493.5,61.5", + pos="e,1464.3,34.441 998.68,92.259 1006.5,90.182 1014.7,88.278 1022.5,87 1172.8,62.421 1215.6,100.33 1364.5,69 1395.8,62.425 1429.5,49.582 \ +1455,38.56", style=solid]; "has qualitative value" [color=blue, height=0.5, label="named thing", - pos="814.44,18", + pos="1661.5,18", width=1.9318]; attribute -> "has qualitative value" [color=blue, label="has qualitative value", - lp="874.94,61.5", - pos="e,809.39,36.264 590.96,92.483 598.67,90.416 606.78,88.459 614.44,87 652.2,79.816 754.35,90.135 786.44,69 794.87,63.455 801.01,54.465 \ -805.35,45.625", + lp="1687,61.5", + pos="e,1640.8,35.396 998.33,92.223 1006.2,90.121 1014.6,88.216 1022.5,87 1144.5,68.303 1459.1,103.65 1577.5,69 1597.2,63.263 1616.9,51.866 \ +1632.3,41.4", style=solid]; iri [color=blue, height=0.5, label="iri type", - pos="985.44,18", + pos="1832.5,18", width=1.2277]; attribute -> iri [color=blue, label=iri, - lp="977.44,61.5", - pos="e,979.37,36.023 590.58,92.262 598.39,90.185 606.63,88.28 614.44,87 651.67,80.9 920.85,87.98 953.44,69 962.7,63.612 969.71,54.36 \ -974.78,45.27", + lp="1802.5,61.5", + pos="e,1817.2,34.928 998.32,92.173 1006.2,90.074 1014.6,88.183 1022.5,87 1104.2,74.822 1687.5,95.968 1765.5,69 1781.8,63.378 1797.4,52.23 \ +1809.4,41.884", style=solid]; source [color=blue, height=0.5, label=string, - pos="1086.4,18", + pos="1933.5,18", width=1.0652]; attribute -> source [color=blue, label=source, - lp="1050.4,61.5", - pos="e,1065.6,33.123 590.57,92.231 598.39,90.156 606.63,88.26 614.44,87 779.18,60.437 828.28,112.21 989.44,69 1013.5,62.549 1038.4,49.535 \ -1057,38.401", + lp="1886.5,61.5", + pos="e,1909.4,32.355 998.32,92.164 1006.2,90.066 1014.6,88.178 1022.5,87 1196.7,61.17 1642.4,105.74 1814.5,69 1844.8,62.546 1877,48.523 \ +1900.3,36.965", style=solid]; + "named thing_category" [color=blue, + height=0.5, + label="category type", + pos="1106.5,105", + width=2.0762]; attribute_name [color=blue, height=0.5, label="label type", - pos="680.44,105", + pos="1255.5,105", width=1.5707]; } diff --git a/graphviz/attribute.svg b/graphviz/attribute.svg index e70be9e731..488c6ae642 100644 --- a/graphviz/attribute.svg +++ b/graphviz/attribute.svg @@ -4,126 +4,223 @@ - + %3 - + attribute - -attribute + +attribute - + -annotation - -annotation +named thing + +named thing - + -attribute->annotation - - -is_a +attribute->named thing + + +is_a ontology class - -ontology class + +ontology class attribute->ontology class - - -uses + + +uses - + +id + +string + + + +attribute->id + + +id + + + +type + +string + + + +attribute->type + + +type + + + +description + +narrative text + + + +attribute->description + + +description + + + +has attribute + +attribute + + + +attribute->has attribute + + +has attribute + + + +provided by + +string + + + +attribute->provided by + + +provided by + + + +xref + +uriorcurie + + + +attribute->xref + + +xref + + + +category + +category + + + +attribute->category + + +category + + + name - -name + +name - + attribute->name - - -name + + +name - + has attribute type - -ontology class + +ontology class - + attribute->has attribute type - - -has attribute type + + +has attribute type - + has quantitative value - -quantity value + +quantity value - + attribute->has quantitative value - - -has quantitative value + + +has quantitative value - + has qualitative value - -named thing + +named thing - + attribute->has qualitative value - - -has qualitative value + + +has qualitative value - + iri - -iri type + +iri type - + attribute->iri - - -iri + + +iri - + source - -string + +string - + attribute->source - - -source + + +source + + + +named thing_category + +category type - + attribute_name - -label type + +label type diff --git a/graphviz/biological_sex.gv b/graphviz/biological_sex.gv index 37ce087059..3c765e22ae 100644 --- a/graphviz/biological_sex.gv +++ b/graphviz/biological_sex.gv @@ -1,79 +1,155 @@ digraph { - graph [bb="0,0,937.34,123"]; + graph [bb="0,0,1765.3,123"]; node [label="\N"]; "biological sex" [height=0.5, label="biological sex", - pos="443,105", + pos="819,105", width=2.0401]; attribute [height=0.5, pos="51.995,18", width=1.4443]; "biological sex" -> attribute [label=is_a, - lp="204,61.5", - pos="e,83.2,32.445 374.34,98.437 323.03,93.333 251.44,84.202 190,69 156.51,60.715 119.85,47.21 92.734,36.323"]; + lp="253,61.5", + pos="e,88.065,31.025 745.25,104.16 634.58,103.35 419.3,97.767 239,69 189.95,61.175 135.21,45.72 97.693,34.053"]; + id [color=blue, + height=0.5, + label=string, + pos="160,18", + width=1.0652]; + "biological sex" -> id [color=blue, + label=id, + lp="341,61.5", + pos="e,189.38,29.712 745.78,102.9 650.4,100.52 478.71,92.962 334,69 286.72,61.172 234.05,44.936 199.17,33.082", + style=solid]; + type [color=blue, + height=0.5, + label=string, + pos="255,18", + width=1.0652]; + "biological sex" -> type [color=blue, + label=type, + lp="422,61.5", + pos="e,282.82,30.508 745.93,102.77 662.85,100.23 523.48,92.486 406,69 366.34,61.073 322.64,45.853 292.5,34.278", + style=solid]; 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attribute_name [color=blue, height=0.5, label="label type", - pos="591,105", + pos="1134,105", width=1.5707]; } diff --git a/graphviz/biological_sex.svg b/graphviz/biological_sex.svg index 5f64a15aee..2019c8daf1 100644 --- a/graphviz/biological_sex.svg +++ b/graphviz/biological_sex.svg @@ -4,16 +4,16 @@ - + %3 - + biological sex - -biological sex + +biological sex @@ -24,93 +24,190 @@ biological sex->attribute - - -is_a + + +is_a - + +id + +string + + + +biological sex->id + + +id + + + +type + +string + + + +biological sex->type + + +type + + + +description + +narrative text + + + +biological sex->description + + +description + + + +has attribute + +attribute + + + +biological sex->has attribute + + +has attribute + + + +provided by + +string + + + +biological sex->provided by + + +provided by + + + +xref + +uriorcurie + + + +biological sex->xref + + +xref + + + +category + +category + + + +biological sex->category + + +category + + + name - -name + +name - + biological sex->name - - -name + + +name - + has attribute type - -ontology class + +ontology class - + biological sex->has attribute type - - -has attribute type + + +has attribute type - + has quantitative value - -quantity value + +quantity value - + biological sex->has quantitative value - - -has quantitative value + + +has quantitative value - + has qualitative value - -named thing + +named thing - + biological sex->has qualitative value - - -has qualitative value + + +has qualitative value - + iri - -iri type + +iri type - + biological sex->iri - - -iri + + +iri - + source - -string + +string - + biological sex->source - - -source + + +source + + + +named thing_category + +category type - + attribute_name - -label type + +label type diff --git a/graphviz/chemical_role.gv b/graphviz/chemical_role.gv index 9fd4eabf9a..22a39ca541 100644 --- a/graphviz/chemical_role.gv +++ b/graphviz/chemical_role.gv @@ -1,79 +1,155 @@ digraph { - graph [bb="0,0,937.34,123"]; 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attribute_name [color=blue, height=0.5, label="label type", - pos="590,105", + pos="1134,105", width=1.5707]; } diff --git a/graphviz/chemical_role.svg b/graphviz/chemical_role.svg index c97a5fa02f..46b2bddef8 100644 --- a/graphviz/chemical_role.svg +++ b/graphviz/chemical_role.svg @@ -4,16 +4,16 @@ - + %3 - + chemical role - -chemical role + +chemical role @@ -24,93 +24,190 @@ chemical role->attribute - - -is_a + + +is_a - + +id + +string + + + +chemical role->id + + +id + + + +type + +string + + + +chemical role->type + + +type + + + +description + +narrative text + + + +chemical role->description + + +description + + + +has attribute + +attribute + + + +chemical role->has attribute + + +has attribute + + + +provided by + +string + + + +chemical role->provided by + + +provided by + + + +xref + +uriorcurie + + + +chemical role->xref + + +xref + + + +category + +category + + + +chemical role->category + + +category + + + name - -name + +name - + chemical role->name - - -name + + +name - + has attribute type - -ontology class + +ontology class - + chemical role->has attribute type - - -has attribute type + + +has attribute type - + has quantitative value - -quantity value + +quantity value - + chemical role->has quantitative value - - -has quantitative value + + +has quantitative value - + has qualitative value - -named thing + +named thing - + chemical role->has qualitative value - - -has qualitative value + + +has qualitative value - + iri - -iri type + +iri type - + chemical role->iri - - -iri + + +iri - + source - -string + +string - + chemical role->source - - -source + + +source + + + +named thing_category + +category type - + attribute_name - -label type + +label type diff --git a/graphviz/clinical_attribute.gv b/graphviz/clinical_attribute.gv index 6dca278c59..e3bd6c4584 100644 --- a/graphviz/clinical_attribute.gv +++ b/graphviz/clinical_attribute.gv @@ -1,79 +1,154 @@ digraph { - graph [bb="0,0,937.34,123"]; 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"clinical measurement" -> source [color=blue, label=source, - lp="765.74,61.5", - pos="e,770.53,33.922 612.19,91.874 651.32,85.072 694.48,76.476 712.74,69 730.41,61.765 748.35,50.212 762.35,40.032", + lp="1554.7,61.5", + pos="e,1567.6,33.195 966.78,91.931 981.03,90.013 995.82,88.252 1009.7,87 1116.3,77.423 1387.2,95.939 1490.7,69 1515,62.675 1540.2,49.657 \ +1559,38.49", style=solid]; "has attribute type" [height=0.5, - pos="939.74,18", + pos="1739.7,18", width=2.6359]; "clinical measurement" -> "has attribute type" [color=blue, label="has attribute type", - lp="907.74,61.5", - pos="e,901.32,34.534 615.42,92.471 628.55,90.613 642.02,88.732 654.74,87 716.47,78.595 733.08,83.163 793.74,69 827.12,61.208 863.59,48.719 \ -891.74,38.172", + lp="1709.7,61.5", + pos="e,1701.5,34.488 966.78,91.863 981.02,89.951 995.81,88.21 1009.7,87 1136.7,75.975 1457.2,90.536 1582.7,69 1620.3,62.564 1661.2,49.305 \ +1691.9,38.058", style=solid]; + "named thing_category" [color=blue, + height=0.5, + label="category type", + pos="1093.7,105", + width=2.0762]; attribute_name [color=blue, height=0.5, label="label type", - pos="720.74,105", + pos="1242.7,105", width=1.5707]; "clinical measurement_has attribute type" [color=blue, height=0.5, label="ontology class", - pos="871.74,105", + pos="1393.7,105", width=2.1304]; } diff --git a/graphviz/clinical_measurement.svg b/graphviz/clinical_measurement.svg index ed6b31d247..ae818bb306 100644 --- a/graphviz/clinical_measurement.svg +++ b/graphviz/clinical_measurement.svg @@ -4,16 +4,16 @@ - + %3 - + clinical measurement - -clinical measurement + +clinical measurement @@ -24,99 +24,196 @@ clinical measurement->clinical attribute - - -is_a + + +is_a - + +id + +string + + + +clinical measurement->id + + +id + + + +type + +string + + + +clinical measurement->type + + +type + + + +description + +narrative text + + + +clinical measurement->description + + +description + + + +has attribute + +attribute + + + +clinical measurement->has attribute + + +has attribute + + + +provided by + +string + + + +clinical measurement->provided by + + +provided by + + + +xref + +uriorcurie + + + +clinical measurement->xref + + +xref + + + +category + +category + + + +clinical measurement->category + + +category + + + name - -name + +name - + clinical measurement->name - - -name + + +name - + has quantitative value - -quantity value + +quantity value - + clinical measurement->has quantitative value - - -has quantitative value + + +has quantitative value - + has qualitative value - -named thing + +named thing - + clinical measurement->has qualitative value - - -has qualitative value + + +has qualitative value - + iri - -iri type + +iri type - + clinical measurement->iri - - -iri + + +iri - + source - -string + +string - + clinical measurement->source - - -source + + +source - + has attribute type - -has attribute type + +has attribute type - + clinical measurement->has attribute type - - -has attribute type + + +has attribute type + + + +named thing_category + +category type - + attribute_name - -label type + +label type - + clinical measurement_has attribute type - -ontology class + +ontology class diff --git a/graphviz/clinical_modifier.gv b/graphviz/clinical_modifier.gv index c7a8466750..e0c0daf038 100644 --- a/graphviz/clinical_modifier.gv +++ b/graphviz/clinical_modifier.gv @@ -1,79 +1,154 @@ digraph { - graph [bb="0,0,1009.1,123"]; 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"has quantitative value" [color=blue, height=0.5, label="quantity value", - pos="532.74,18", + pos="1361.7,18", width=2.1484]; "clinical modifier" -> "has quantitative value" [color=blue, label="has quantitative value", - lp="595.74,61.5", - pos="e,522.72,35.892 513.27,86.643 512.9,76.915 513.18,64.636 515.74,54 516.44,51.106 517.4,48.171 518.51,45.296", + lp="1364.7,61.5", + pos="e,1331,34.66 950.77,92.146 962.02,90.207 973.72,88.383 984.74,87 1097,72.909 1128.5,94.627 1238.7,69 1267.5,62.325 1298.2,49.842 \ +1321.7,39.019", style=solid]; "has qualitative value" [color=blue, height=0.5, label="named thing", - pos="697.74,18", + pos="1526.7,18", width=1.9318]; "clinical modifier" -> "has qualitative value" [color=blue, label="has qualitative value", - lp="762.24,61.5", - pos="e,694.36,36.279 575.24,92.177 619.19,83.373 671.67,72.326 675.74,69 682.92,63.134 687.82,54.457 691.14,45.972", + lp="1556.2,61.5", + pos="e,1507.7,35.35 949.98,91.986 961.47,90.025 973.45,88.234 984.74,87 1087.3,75.791 1350.3,99.928 1448.7,69 1467,63.251 1485.2,52.008 \ +1499.4,41.638", style=solid]; iri [color=blue, height=0.5, label="iri type", - pos="869.74,18", + pos="1697.7,18", width=1.2277]; "clinical modifier" -> iri [color=blue, label=iri, - lp="863.74,61.5", - pos="e,864.6,35.888 574.78,92.206 586.03,90.262 597.72,88.42 608.74,87 660.03,80.39 796.97,96.526 840.74,69 849.57,63.45 856.01,54.168 \ -860.54,45.098", + lp="1669.7,61.5", + pos="e,1683,35.386 949.72,91.928 961.28,89.959 973.36,88.18 984.74,87 1056.6,79.55 1566.9,93.725 1634.7,69 1649.9,63.463 1664.3,52.694 \ +1675.4,42.565", style=solid]; source [color=blue, height=0.5, label=string, - pos="970.74,18", + pos="1798.7,18", width=1.0652]; "clinical modifier" -> source [color=blue, label=source, - lp="935.74,61.5", - pos="e,949.94,33.23 574.51,92.158 585.85,90.206 597.63,88.375 608.74,87 726.78,72.394 761.3,101.4 875.74,69 898.95,62.428 922.98,49.72 \ -941.06,38.76", + lp="1752.7,61.5", + pos="e,1775,32.332 949.46,91.954 961.11,89.969 973.28,88.178 984.74,87 1138.9,71.167 1530.4,102.03 1681.7,69 1711.5,62.502 1743.2,48.482 \ +1766.1,36.937", style=solid]; + "named thing_category" [color=blue, + height=0.5, + label="category type", + pos="1068.7,105", + width=2.0762]; attribute_name [color=blue, height=0.5, label="label type", - pos="674.74,105", + pos="1217.7,105", width=1.5707]; } diff --git a/graphviz/clinical_modifier.svg b/graphviz/clinical_modifier.svg index e0b7eaa56b..031aa2cd1e 100644 --- a/graphviz/clinical_modifier.svg +++ b/graphviz/clinical_modifier.svg @@ -4,16 +4,16 @@ - + %3 - + clinical modifier - -clinical modifier + +clinical modifier @@ -24,93 +24,190 @@ clinical modifier->clinical attribute - - -is_a + + +is_a - + +id + +string + + + +clinical modifier->id + + +id + + + +type + +string + + + +clinical modifier->type + + +type + + + +description + +narrative text + + + +clinical modifier->description + + +description + + + +has attribute + +attribute + + + +clinical modifier->has attribute + + +has attribute + + + +provided by + +string + + + +clinical modifier->provided by + + +provided by + + + +xref + +uriorcurie + + + +clinical modifier->xref + + +xref + + + +category + +category + + + +clinical modifier->category + + +category + + + name - -name + +name - + clinical modifier->name - - -name + + +name - + has attribute type - -ontology class + +ontology class - + clinical modifier->has attribute type - - -has attribute type + + +has attribute type - + has quantitative value - -quantity value + +quantity value - + clinical modifier->has quantitative value - - -has quantitative value + + +has quantitative value - + has qualitative value - -named thing + +named thing - + clinical modifier->has qualitative value - - -has qualitative value + + +has qualitative value - + iri - -iri type + +iri type - + clinical modifier->iri - - -iri + + +iri - + source - -string + +string - + clinical modifier->source - - -source + + +source + + + +named thing_category + +category type - + attribute_name - -label type + +label type diff --git a/graphviz/gene_ontology_class.gv b/graphviz/gene_ontology_class.gv index 1a9ed8ecdf..02bfc2af55 100644 --- a/graphviz/gene_ontology_class.gv +++ b/graphviz/gene_ontology_class.gv @@ -1,14 +1,8 @@ digraph { - graph [bb="0,0,204.08,123"]; + graph [bb="0,0,204.08,36"]; node [label="\N"]; "gene ontology class" [height=0.5, label="gene ontology class", - pos="102.04,105", - width=2.8345]; - "ontology class" [height=0.5, pos="102.04,18", - width=2.1304]; - "gene ontology class" -> "ontology class" [label=is_a, - lp="116.04,61.5", - pos="e,102.04,36.175 102.04,86.799 102.04,75.163 102.04,59.548 102.04,46.237"]; + width=2.8345]; } diff --git a/graphviz/gene_ontology_class.svg b/graphviz/gene_ontology_class.svg index 7c32c26288..164bdb005e 100644 --- a/graphviz/gene_ontology_class.svg +++ b/graphviz/gene_ontology_class.svg @@ -4,29 +4,16 @@ - - + + %3 - + gene ontology class - -gene ontology class - - - -ontology class - -ontology class - - - -gene ontology class->ontology class - - -is_a + +gene ontology class diff --git a/graphviz/genomic_background_exposure.gv b/graphviz/genomic_background_exposure.gv index 7f90cd97a9..a90b09187f 100644 --- a/graphviz/genomic_background_exposure.gv +++ b/graphviz/genomic_background_exposure.gv @@ -1,40 +1,40 @@ digraph { - graph [bb="0,0,1585.3,123"]; + graph [bb="0,0,1668.2,123"]; node [label="\N"]; "genomic background exposure" [height=0.5, label="genomic background exposure", - pos="861.89,105", + pos="906.89,105", width=4.2427]; "exposure event" [height=0.5, pos="81.893,18", width=2.2748]; "genomic background exposure" -> "exposure event" [label=uses, - lp="453.39,61.5", - pos="e,140.35,30.785 734.61,94.997 595.83,84.356 367.4,64.43 171.89,36 164.86,34.977 157.54,33.794 150.25,32.537"]; + lp="450.39,61.5", + pos="e,139.86,30.728 775.31,95.836 627.88,85.758 381.99,66.161 171.89,36 164.75,34.975 157.31,33.779 149.91,32.505"]; "gene grouping mixin" [height=0.5, pos="287.89,18", width=2.9608]; "genomic background exposure" -> "gene grouping mixin" [label=uses, - lp="639.39,61.5", - pos="e,364.72,30.528 769.95,90.597 725.52,84.104 671.43,76.176 622.89,69 538.65,56.545 442.52,42.181 374.9,32.054"]; + lp="655.39,61.5", + pos="e,365.25,30.428 809,91.177 707.59,77.799 544.57,56.02 403.89,36 394.62,34.68 384.93,33.286 375.28,31.886"]; "physical essence" [height=0.5, pos="500.89,18", width=2.4553]; "genomic background exposure" -> "physical essence" [label=uses, - lp="720.39,61.5", - pos="e,556.45,32.082 796.94,88.706 731.67,73.339 631.64,49.787 566.24,34.387"]; + lp="745.39,61.5", + pos="e,560.29,31.435 835.24,88.999 760.56,73.364 644.31,49.026 570.42,33.557"]; "genomic entity" [height=0.5, pos="686.89,18", width=2.2206]; "genomic background exposure" -> "genomic entity" [label=uses, - lp="801.39,61.5", - pos="e,718.9,34.546 827.74,87.409 799.16,73.53 758.31,53.689 727.96,38.945"]; + lp="827.39,61.5", + pos="e,725.5,33.915 864.47,87.611 827.41,73.291 773.63,52.513 734.98,37.579"]; "ontology class" [height=0.5, pos="861.89,18", width=2.1304]; "genomic background exposure" -> "ontology class" [label=uses, - lp="878.39,61.5", - pos="e,861.89,36.175 861.89,86.799 861.89,75.163 861.89,59.548 861.89,46.237"]; + lp="904.39,61.5", + pos="e,870.83,35.885 897.79,86.799 891.4,74.738 882.75,58.403 875.55,44.79"]; timepoint [color=blue, height=0.5, label="time type", @@ -42,8 +42,8 @@ digraph { width=1.5346]; "genomic background exposure" -> timepoint [color=blue, label=timepoint, - lp="980.89,61.5", - pos="e,985.33,34.049 891.53,87.207 915.97,73.357 950.7,53.674 976.58,39.01", + lp="988.89,61.5", + pos="e,984.01,33.744 921.09,86.66 929.91,76.476 941.85,63.734 953.89,54 960.39,48.751 967.74,43.72 974.98,39.192", style=solid]; "has gene or gene product" [color=blue, height=0.5, @@ -52,27 +52,38 @@ digraph { width=0.92075]; "genomic background exposure" -> "has gene or gene product" [color=blue, label="has gene or gene product", - lp="1145.4,61.5", - pos="e,1096.4,31.971 944.61,89.808 969.21,84.489 995.96,77.596 1019.9,69 1043.5,60.509 1068.7,47.55 1087.7,36.953", + lp="1138.4,61.5", + pos="e,1093.2,30.278 970.36,88.617 988.07,83.365 1007.1,76.806 1023.9,69 1035,63.865 1036.3,60.042 1046.9,54 1058.8,47.235 1072.1,40.446 \ +1084,34.671", style=solid]; "in taxon" [color=blue, height=0.5, label="organism taxon", - pos="1280.9,18", + pos="1251.9,18", width=2.3109]; "genomic background exposure" -> "in taxon" [color=blue, label="in taxon", - lp="1287.9,61.5", - pos="e,1272.1,35.949 1012.5,102 1100.7,98.536 1202.1,89.916 1240.9,69 1251.3,63.407 1259.9,53.862 1266.5,44.602", + lp="1271.9,61.5", + pos="e,1248.9,36.147 1057.8,101.93 1128.1,98.158 1202.2,89.246 1229.9,69 1237.6,63.382 1242.6,54.494 1245.9,45.761", style=solid]; "has biological sequence" [color=blue, height=0.5, label="biological sequence", - pos="1483.9,18", + pos="1454.9,18", width=2.8164]; "genomic background exposure" -> "has biological sequence" [color=blue, label="has biological sequence", - lp="1465.4,61.5", - pos="e,1442.3,34.551 1010.8,100.98 1101.1,97.093 1218.4,88.376 1320.9,69 1359.1,61.774 1401,48.792 1432.8,37.867", + lp="1444.4,61.5", + pos="e,1416.1,34.722 1052.2,99.384 1128.1,94.924 1222.2,86.169 1304.9,69 1339.7,61.78 1377.6,49.087 1406.6,38.298", + style=solid]; + id [color=blue, + height=0.5, + label=string, + pos="1629.9,18", + width=1.0652]; + "genomic background exposure" -> id [color=blue, + label=id, + lp="1575.9,61.5", + pos="e,1608.6,33.304 1058.7,102.76 1214.8,100.2 1446.9,92.419 1532.9,69 1556.8,62.497 1581.5,49.612 1600.1,38.552", style=solid]; } diff --git a/graphviz/genomic_background_exposure.svg b/graphviz/genomic_background_exposure.svg index b7d7a0a7e3..b0574ed34f 100644 --- a/graphviz/genomic_background_exposure.svg +++ b/graphviz/genomic_background_exposure.svg @@ -4,16 +4,16 @@ - + %3 - + genomic background exposure - -genomic background exposure + +genomic background exposure @@ -24,9 +24,9 @@ genomic background exposure->exposure event - - -uses + + +uses @@ -37,9 +37,9 @@ genomic background exposure->gene grouping mixin - - -uses + + +uses @@ -50,9 +50,9 @@ genomic background exposure->physical essence - - -uses + + +uses @@ -63,9 +63,9 @@ genomic background exposure->genomic entity - - -uses + + +uses @@ -76,9 +76,9 @@ genomic background exposure->ontology class - - -uses + + +uses @@ -89,9 +89,9 @@ genomic background exposure->timepoint - - -timepoint + + +timepoint @@ -102,35 +102,48 @@ genomic background exposure->has gene or gene product - - -has gene or gene product + + +has gene or gene product in taxon - -organism taxon + +organism taxon genomic background exposure->in taxon - - -in taxon + + +in taxon has biological sequence - -biological sequence + +biological sequence genomic background exposure->has biological sequence - - -has biological sequence + + +has biological sequence + + + +id + +string + + + +genomic background exposure->id + + +id diff --git a/graphviz/genotypic_sex.gv b/graphviz/genotypic_sex.gv index aa5abd10d8..66806bf396 100644 --- a/graphviz/genotypic_sex.gv +++ b/graphviz/genotypic_sex.gv @@ -1,79 +1,154 @@ digraph { - graph [bb="0,0,980.79,123"]; + graph [bb="0,0,1808.8,123"]; node [label="\N"]; "genotypic sex" [height=0.5, label="genotypic sex", - pos="486.44,105", + pos="862.44,105", width=2.0762]; "biological sex" [height=0.5, pos="73.443,18", width=2.0401]; "genotypic sex" -> "biological sex" [label=is_a, - lp="247.44,61.5", - pos="e,112.73,33.279 417.98,97.628 366.76,92.114 295.21,82.824 233.44,69 195.64,60.54 153.9,47.362 122.53,36.658"]; + lp="296.44,61.5", + pos="e,118.66,32.237 787.85,103.65 677.02,102.19 462.55,95.768 282.44,69 229.49,61.13 170.23,46.373 128.38,34.922"]; + id [color=blue, + height=0.5, + label=string, + pos="203.44,18", + width=1.0652]; + "genotypic sex" -> id [color=blue, + label=id, + lp="384.44,61.5", + pos="e,232.83,29.712 787.99,102.87 692.36,100.45 521.53,92.858 377.44,69 330.17,61.172 277.49,44.936 242.61,33.082", + style=solid]; + type [color=blue, + height=0.5, + label=string, + pos="298.44,18", + width=1.0652]; + "genotypic sex" -> type [color=blue, + label=type, + lp="465.44,61.5", + pos="e,326.27,30.508 788.25,102.73 705.04,100.16 566.4,92.38 449.44,69 409.79,61.073 366.09,45.853 335.95,34.278", + style=solid]; 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+ "named thing_category" [color=blue, + height=0.5, + label="category type", + pos="1011,105", + width=2.0762]; attribute_name [color=blue, height=0.5, label="label type", - pos="616,105", + pos="1160,105", width=1.5707]; } diff --git a/graphviz/organism_attribute.svg b/graphviz/organism_attribute.svg index addd7617c4..e3f36f0960 100644 --- a/graphviz/organism_attribute.svg +++ b/graphviz/organism_attribute.svg @@ -4,16 +4,16 @@ - + %3 - + organism attribute - -organism attribute + +organism attribute @@ -24,93 +24,190 @@ organism attribute->attribute - - -is_a + + +is_a - + +id + +string + + + +organism attribute->id + + +id + + + +type + +string + + + +organism attribute->type + + +type + + + +description + +narrative text + + + +organism attribute->description + + +description + + + +has attribute + +attribute + + + +organism attribute->has attribute + + +has attribute + + + +provided by + +string + + + +organism attribute->provided by + + +provided by + + + +xref + +uriorcurie + + + +organism attribute->xref + + +xref + + + +category + +category + + + +organism attribute->category + + +category + + + name - -name + +name - + organism attribute->name - - -name + + +name - + has attribute type - -ontology class + +ontology class - + organism attribute->has attribute type - - -has attribute type + + +has attribute type - + has quantitative value - -quantity value + +quantity value - + organism attribute->has quantitative value - - -has quantitative value + + +has quantitative value - + has qualitative value - -named thing + +named thing - + organism attribute->has qualitative value - - -has qualitative value + + +has qualitative value - + iri - -iri type + +iri type - + organism attribute->iri - - -iri + + +iri - + source - -string + +string - + organism attribute->source - - -source + + +source + + + +named thing_category + +category type - + attribute_name - -label type + +label type diff --git a/graphviz/phenotypic_quality.gv b/graphviz/phenotypic_quality.gv index 312b224c1e..9caa26ead5 100644 --- a/graphviz/phenotypic_quality.gv +++ b/graphviz/phenotypic_quality.gv @@ -1,79 +1,154 @@ digraph { - graph [bb="0,0,1031.1,123"]; 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+ "named thing_category" [color=blue, + height=0.5, + label="category type", + pos="1035.4,105", + width=2.0762]; attribute_name [color=blue, height=0.5, label="label type", - pos="641.44,105", + pos="1184.4,105", width=1.5707]; } diff --git a/graphviz/phenotypic_sex.svg b/graphviz/phenotypic_sex.svg index 82e74b9303..c338fd1394 100644 --- a/graphviz/phenotypic_sex.svg +++ b/graphviz/phenotypic_sex.svg @@ -4,16 +4,16 @@ - + %3 - + phenotypic sex - -phenotypic sex + +phenotypic sex @@ -24,93 +24,190 @@ phenotypic sex->biological sex - - -is_a + + +is_a - + +id + +string + + + +phenotypic sex->id + + +id + + + +type + +string + + + +phenotypic sex->type + + +type + + + +description + +narrative text + + + +phenotypic sex->description + + +description + + + +has attribute + +attribute + + + +phenotypic sex->has attribute + + +has attribute + + + +provided by + +string + + + +phenotypic sex->provided by + + +provided by + + + +xref + +uriorcurie + + + +phenotypic sex->xref + + +xref + + + +category + +category + + + +phenotypic sex->category + + +category + + + name - -name + +name - + phenotypic sex->name - - -name + + +name - + has attribute type - -ontology class + +ontology class - + phenotypic sex->has attribute type - - -has attribute type + + +has attribute type - + has quantitative value - -quantity value + +quantity value - + phenotypic sex->has quantitative value - - -has quantitative value + + +has quantitative value - + has qualitative value - -named thing + +named thing - + phenotypic sex->has qualitative value - - -has qualitative value + + +has qualitative value - + iri - -iri type + +iri type - + phenotypic sex->iri - - -iri + + +iri - + source - -string + +string - + phenotypic sex->source - - -source + + +source + + + +named thing_category + +category type - + attribute_name - -label type + +label type diff --git a/graphviz/relationship_type.gv b/graphviz/relationship_type.gv index ee0d83ff68..ffb521687e 100644 --- a/graphviz/relationship_type.gv +++ b/graphviz/relationship_type.gv @@ -1,14 +1,24 @@ digraph { - graph [bb="0,0,179.38,123"]; + graph [bb="0,0,248.04,123"]; node [label="\N"]; "relationship type" [height=0.5, label="relationship type", - pos="89.692,105", + pos="142.69,105", width=2.4914]; "ontology class" [height=0.5, - pos="89.692,18", + pos="76.693,18", width=2.1304]; "relationship type" -> "ontology class" [label=is_a, - lp="103.69,61.5", - pos="e,89.692,36.175 89.692,86.799 89.692,75.163 89.692,59.548 89.692,46.237"]; + lp="127.69,61.5", + pos="e,89.804,35.885 129.34,86.799 119.79,74.506 106.8,57.774 96.111,44.007"]; + id [color=blue, + height=0.5, + label=string, + pos="209.69,18", + width=1.0652]; + "relationship type" -> id [color=blue, + label=id, + lp="186.69,61.5", + pos="e,197.06,35.025 156.25,86.799 166.13,74.265 179.65,57.116 190.62,43.201", + style=solid]; } diff --git a/graphviz/relationship_type.svg b/graphviz/relationship_type.svg index 00fdd74a57..7298e534c9 100644 --- a/graphviz/relationship_type.svg +++ b/graphviz/relationship_type.svg @@ -4,29 +4,42 @@ - + %3 - + relationship type - -relationship type + +relationship type ontology class - -ontology class + +ontology class relationship type->ontology class - - -is_a + + +is_a + + + +id + +string + + + +relationship type->id + + +id diff --git a/graphviz/severity_value.gv b/graphviz/severity_value.gv index 39cefea343..ce6e04b8c9 100644 --- a/graphviz/severity_value.gv +++ b/graphviz/severity_value.gv @@ -1,79 +1,154 @@ digraph { - graph [bb="0,0,937.34,123"]; + graph [bb="0,0,1765.3,123"]; node [label="\N"]; "severity value" [height=0.5, label="severity value", - pos="443,105", + pos="819,105", width=2.1123]; attribute [height=0.5, pos="51.995,18", width=1.4443]; "severity value" -> attribute [label=is_a, - lp="204,61.5", - pos="e,83.2,32.445 372.44,98.247 321.27,93.108 250.69,84.016 190,69 156.51,60.715 119.85,47.21 92.734,36.323"]; + lp="253,61.5", + pos="e,88.065,31.025 742.94,104.14 631.61,103.27 418.06,97.569 239,69 189.95,61.175 135.21,45.72 97.693,34.053"]; + id [color=blue, + height=0.5, + label=string, + pos="160,18", + width=1.0652]; + "severity value" -> id [color=blue, + label=id, + lp="341,61.5", + pos="e,189.38,29.712 743.3,102.84 647.43,100.39 477.46,92.755 334,69 286.72,61.172 234.05,44.936 199.17,33.082", + style=solid]; + type [color=blue, + height=0.5, + label=string, + pos="255,18", + width=1.0652]; + "severity value" -> type [color=blue, + label=type, + lp="422,61.5", + pos="e,282.82,30.508 743.29,102.69 659.92,100.06 522.25,92.239 406,69 366.34,61.073 322.64,45.853 292.5,34.278", + style=solid]; + description [color=blue, + height=0.5, + label="narrative text", + pos="387,18", + width=2.0943]; + "severity value" -> description [color=blue, + label=description, + lp="514.5,61.5", + pos="e,409.38,35.406 745.6,100.16 659.66,95.028 522.85,84.723 474,69 454.13,62.606 433.8,51.245 417.79,40.967", + style=solid]; + "has attribute" [color=blue, + height=0.5, + label=attribute, + pos="532,18", + width=1.4443]; + "severity value" -> "has attribute" [color=blue, + label="has attribute", + lp="624,61.5", + pos="e,542.46,35.748 747.2,99.021 686.75,93.85 605.68,84.332 577,69 565.84,63.04 556.07,53.176 548.51,43.778", + style=solid]; + "provided by" [color=blue, + height=0.5, + label=string, + pos="640,18", + width=1.0652]; + "severity value" -> "provided by" [color=blue, + label="provided by", + lp="736.5,61.5", + pos="e,653.59,35.116 760.13,93.581 738.45,88.21 714.25,80.331 694,69 681.68,62.11 669.93,51.856 660.57,42.424", + style=solid]; + xref [color=blue, + height=0.5, + label=uriorcurie, + pos="754,18", + width=1.5887]; 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iri [color=blue, height=0.5, label="iri type", - pos="798,18", + pos="1626,18", width=1.2277]; "socioeconomic attribute" -> iri [color=blue, label=iri, - lp="792,61.5", - pos="e,792.63,36.323 529.61,92.3 544.41,90.433 559.64,88.594 574,87 617.25,82.199 732.33,92.433 769,69 777.56,63.524 783.89,54.548 788.41,\ -45.701", + lp="1598,61.5", + pos="e,1611.2,35.377 902.73,91.872 918.41,89.96 934.68,88.216 950,87 1017.9,81.609 1499,92.372 1563,69 1578.2,63.45 1592.5,52.68 1603.7,\ +42.553", style=solid]; source [color=blue, height=0.5, label=string, - pos="899,18", + pos="1727,18", width=1.0652]; "socioeconomic attribute" -> source [color=blue, label=source, - lp="864,61.5", - pos="e,878.17,33.157 529.24,92.173 544.15,90.31 559.51,88.506 574,87 675.98,76.399 705.49,97.463 804,69 827.17,62.303 851.2,49.596 869.29,\ -38.668", + lp="1681,61.5", + pos="e,1703.2,32.321 902.72,91.846 918.4,89.936 934.68,88.2 950,87 1096.3,75.544 1466.7,100.38 1610,69 1639.8,62.48 1671.4,48.462 1694.3,\ +36.923", style=solid]; + "named thing_category" [color=blue, + height=0.5, + label="category type", + pos="1034,105", + width=2.0762]; attribute_name [color=blue, height=0.5, label="label type", - pos="640,105", + pos="1183,105", width=1.5707]; } diff --git a/graphviz/socioeconomic_attribute.svg b/graphviz/socioeconomic_attribute.svg index c99d93d925..916c64984f 100644 --- a/graphviz/socioeconomic_attribute.svg +++ b/graphviz/socioeconomic_attribute.svg @@ -4,16 +4,16 @@ - + %3 - + socioeconomic attribute - -socioeconomic attribute + +socioeconomic attribute @@ -24,93 +24,190 @@ socioeconomic attribute->attribute - - -is_a + + +is_a - + +id + +string + + + +socioeconomic attribute->id + + +id + + + +type + +string + + + +socioeconomic attribute->type + + +type + + + +description + +narrative text + + + +socioeconomic attribute->description + + +description + + + +has attribute + +attribute + + + +socioeconomic attribute->has attribute + + +has attribute + + + +provided by + +string + + + +socioeconomic attribute->provided by + + +provided by + + + +xref + +uriorcurie + + + +socioeconomic attribute->xref + + +xref + + + +category + +category + + + +socioeconomic attribute->category + + +category + + + name - -name + +name - + socioeconomic attribute->name - - -name + + +name - + has attribute type - -ontology class + +ontology class - + socioeconomic attribute->has attribute type - - -has attribute type + + +has attribute type - + has quantitative value - -quantity value + +quantity value - + socioeconomic attribute->has quantitative value - - -has quantitative value + + +has quantitative value - + has qualitative value - -named thing + +named thing - + socioeconomic attribute->has qualitative value - - -has qualitative value + + +has qualitative value - + iri - -iri type + +iri type - + socioeconomic attribute->iri - - -iri + + +iri - + source - -string + +string - + socioeconomic attribute->source - - -source + + +source + + + +named thing_category + +category type - + attribute_name - -label type + +label type diff --git a/graphviz/taxonomic_rank.gv b/graphviz/taxonomic_rank.gv index c73a8a1319..ee4cb959b0 100644 --- a/graphviz/taxonomic_rank.gv +++ b/graphviz/taxonomic_rank.gv @@ -1,14 +1,24 @@ digraph { - graph [bb="0,0,165.09,123"]; + graph [bb="0,0,248.04,123"]; node [label="\N"]; "taxonomic rank" [height=0.5, label="taxonomic rank", - pos="82.543,105", + pos="142.69,105", width=2.2929]; "ontology class" [height=0.5, - pos="82.543,18", + pos="76.693,18", width=2.1304]; "taxonomic rank" -> "ontology class" [label=is_a, - lp="96.543,61.5", - pos="e,82.543,36.175 82.543,86.799 82.543,75.163 82.543,59.548 82.543,46.237"]; + lp="127.69,61.5", + pos="e,89.706,35.758 129.65,87.207 120.07,74.866 106.89,57.894 96.08,43.967"]; + id [color=blue, + height=0.5, + label=string, + pos="209.69,18", + width=1.0652]; + "taxonomic rank" -> id [color=blue, + label=id, + lp="186.69,61.5", + pos="e,196.94,35.182 155.93,87.207 165.78,74.706 179.38,57.452 190.44,43.426", + style=solid]; } diff --git a/graphviz/taxonomic_rank.svg b/graphviz/taxonomic_rank.svg index 1afee122da..3b27179d00 100644 --- a/graphviz/taxonomic_rank.svg +++ b/graphviz/taxonomic_rank.svg @@ -4,29 +4,42 @@ - + %3 - + taxonomic rank - -taxonomic rank + +taxonomic rank ontology class - -ontology class + +ontology class taxonomic rank->ontology class - - -is_a + + +is_a + + + +id + +string + + + +taxonomic rank->id + + +id diff --git a/graphviz/unclassified_ontology_class.gv b/graphviz/unclassified_ontology_class.gv index 339f1e28df..4f5261f6e9 100644 --- a/graphviz/unclassified_ontology_class.gv +++ b/graphviz/unclassified_ontology_class.gv @@ -1,14 +1,8 @@ digraph { - graph [bb="0,0,267.78,123"]; + graph [bb="0,0,267.78,36"]; node [label="\N"]; "unclassified ontology class" [height=0.5, label="unclassified ontology class", - pos="133.89,105", - width=3.7191]; - "ontology class" [height=0.5, pos="133.89,18", - width=2.1304]; - "unclassified ontology class" -> "ontology class" [label=is_a, - lp="147.89,61.5", - pos="e,133.89,36.175 133.89,86.799 133.89,75.163 133.89,59.548 133.89,46.237"]; + width=3.7191]; } diff --git a/graphviz/unclassified_ontology_class.svg b/graphviz/unclassified_ontology_class.svg index 978db2f0a1..d2e2417137 100644 --- a/graphviz/unclassified_ontology_class.svg +++ b/graphviz/unclassified_ontology_class.svg @@ -4,29 +4,16 @@ - - + + %3 - + unclassified ontology class - -unclassified ontology class - - - -ontology class - -ontology class - - - -unclassified ontology class->ontology class - - -is_a + +unclassified ontology class diff --git a/graphviz/zygosity.gv b/graphviz/zygosity.gv index 9295fe05a3..09af01fc86 100644 --- a/graphviz/zygosity.gv +++ b/graphviz/zygosity.gv @@ -1,80 +1,155 @@ digraph { - graph [bb="0,0,937.34,123"]; + graph [bb="0,0,1765.3,123"]; node [label="\N"]; zygosity [height=0.5, label=zygosity, - pos="443,105", + pos="819,105", width=1.3721]; attribute [height=0.5, pos="51.995,18", width=1.4443]; zygosity -> attribute [label=is_a, - lp="204,61.5", - pos="e,83.2,32.445 394.87,100.37 343.54,95.801 260.16,86.359 190,69 156.51,60.715 119.85,47.21 92.734,36.323"]; + lp="253,61.5", + pos="e,88.065,31.025 769.37,104.27 668.7,104.09 433.5,100.03 239,69 189.95,61.175 135.21,45.72 97.693,34.053"]; + id [color=blue, + height=0.5, + label=string, + pos="160,18", + width=1.0652]; + zygosity -> id [color=blue, + label=id, + lp="341,61.5", + pos="e,189.38,29.712 769.77,103.43 681.75,101.76 491.82,95.134 334,69 286.72,61.172 234.05,44.936 199.17,33.082", + style=solid]; + type [color=blue, + height=0.5, + label=string, + pos="255,18", + width=1.0652]; + zygosity -> type [color=blue, + label=type, + lp="422,61.5", + pos="e,282.82,30.508 769.54,103.4 691.53,101.64 535.48,94.883 406,69 366.34,61.073 322.64,45.853 292.5,34.278", + style=solid]; + description [color=blue, + height=0.5, + label="narrative text", + pos="387,18", + width=2.0943]; + zygosity -> description [color=blue, + label=description, + lp="514.5,61.5", + pos="e,409.38,35.406 770.3,101.57 688.67,97.086 527.87,86.337 474,69 454.13,62.606 433.8,51.245 417.79,40.967", + style=solid]; + "has attribute" [color=blue, + height=0.5, + label=attribute, + pos="532,18", + width=1.4443]; + zygosity -> "has attribute" [color=blue, + label="has attribute", + lp="624,61.5", + pos="e,542.46,35.748 770.7,100.91 709.95,96.349 609.61,86.433 577,69 565.84,63.04 556.07,53.176 548.51,43.778", + style=solid]; + "provided by" [color=blue, + height=0.5, + label=string, + pos="640,18", + width=1.0652]; + zygosity -> "provided by" [color=blue, + label="provided by", + lp="736.5,61.5", + pos="e,653.59,35.116 774.79,96.938 749.93,91.695 718.97,82.972 694,69 681.68,62.11 669.93,51.856 660.57,42.424", + style=solid]; + xref [color=blue, + height=0.5, + label=uriorcurie, + pos="754,18", + width=1.5887]; + zygosity -> xref [color=blue, + label=xref, + lp="805.5,61.5", + pos="e,766.81,35.758 806.15,87.207 796.72,74.866 783.74,57.894 773.09,43.967", + style=solid]; + category [height=0.5, + pos="881,18", + width=1.4263]; + zygosity -> category [color=blue, + label=category, + lp="885.5,61.5", + pos="e,868.77,35.758 831.24,87.207 840.25,74.866 852.63,57.894 862.78,43.967", + style=solid]; name [height=0.5, - pos="158,18", + pos="987,18", width=1.011]; zygosity -> name [color=blue, label=name, - lp="274,61.5", - pos="e,179.66,32.671 396.18,99.253 357.32,94.39 301.01,85.189 254,69 231.04,61.096 206.81,48.438 188.44,37.836", + lp="965,61.5", + pos="e,970.11,34.206 855.46,92.831 879.8,85.122 909.39,75.183 921,69 935.63,61.203 950.48,50.278 962.38,40.628", style=solid]; "has attribute type" [color=blue, height=0.5, label="ontology class", - pos="289,18", + pos="1118,18", width=2.1304]; zygosity -> "has attribute type" [color=blue, label="has attribute type", - lp="373,61.5", - pos="e,291.41,36.104 394.11,102.18 365.88,98.703 331.44,90.006 308,69 301.24,62.942 296.87,54.221 294.05,45.753", + lp="1098,61.5", + pos="e,1084.4,34.26 855.32,92.594 862.46,90.566 869.93,88.596 877,87 926.17,75.888 940.33,82.183 989,69 1018.4,61.043 1050.3,48.717 1075,\ +38.295", style=solid]; "has quantitative value" [color=blue, height=0.5, label="quantity value", - pos="461,18", + pos="1290,18", width=2.1484]; zygosity -> "has quantitative value" [color=blue, label="has quantitative value", - lp="524,61.5", - pos="e,450.97,35.892 441.53,86.643 441.15,76.915 441.44,64.636 444,54 444.69,51.106 445.65,48.171 446.76,45.296", + lp="1293,61.5", + pos="e,1259.6,34.62 854.28,92.3 861.71,90.22 869.55,88.305 877,87 1004.2,64.7 1041.1,97.691 1167,69 1195.8,62.428 1226.7,49.882 1250.2,\ +39.002", style=solid]; "has qualitative value" [color=blue, height=0.5, label="named thing", - pos="626,18", + pos="1455,18", width=1.9318]; zygosity -> "has qualitative value" [color=blue, label="has qualitative value", - lp="690.5,61.5", - pos="e,622.72,36.415 479.34,92.671 486.48,90.637 493.94,88.644 501,87 546.25,76.448 567.42,97.663 604,69 611.29,63.282 616.22,54.641 \ -619.53,46.143", + lp="1484.5,61.5", + pos="e,1436,35.368 853.94,92.236 861.47,90.133 869.43,88.225 877,87 986.75,69.226 1270.9,102.18 1377,69 1395.3,63.276 1413.5,52.036 1427.7,\ +41.66", style=solid]; iri [color=blue, height=0.5, label="iri type", - pos="798,18", + pos="1626,18", width=1.2277]; zygosity -> iri [color=blue, label=iri, - lp="792,61.5", - pos="e,792.88,35.926 478.28,92.329 485.72,90.247 493.56,88.324 501,87 559.76,76.543 718.3,100.51 769,69 777.85,63.496 784.3,54.222 788.83,\ -45.147", + lp="1598,61.5", + pos="e,1611.2,35.394 853.94,92.179 861.46,90.08 869.43,88.188 877,87 952.32,75.178 1491.3,95.041 1563,69 1578.2,63.474 1592.6,52.706 \ +1603.7,42.575", style=solid]; source [color=blue, height=0.5, label=string, - pos="899,18", + pos="1727,18", width=1.0652]; zygosity -> source [color=blue, label=source, - lp="864,61.5", - pos="e,878.21,33.284 478.28,92.284 485.71,90.206 493.55,88.295 501,87 633.9,63.881 674.05,105.23 804,69 827.23,62.521 851.26,49.811 869.33,\ -38.828", + lp="1681,61.5", + pos="e,1703.2,32.342 853.93,92.17 861.46,90.071 869.43,88.181 877,87 1038,61.872 1450.8,103.64 1610,69 1639.8,62.521 1671.4,48.499 1694.3,\ +36.949", style=solid]; + "named thing_category" [color=blue, + height=0.5, + label="category type", + pos="961,105", + width=2.0762]; attribute_name [color=blue, height=0.5, label="label type", - pos="567,105", + pos="1110,105", width=1.5707]; } diff --git a/graphviz/zygosity.svg b/graphviz/zygosity.svg index 996899d44e..9717da8da0 100644 --- a/graphviz/zygosity.svg +++ b/graphviz/zygosity.svg @@ -4,16 +4,16 @@ - + %3 - + zygosity - -zygosity + +zygosity @@ -24,93 +24,190 @@ zygosity->attribute - - -is_a + + +is_a - + +id + +string + + + +zygosity->id + + +id + + + +type + +string + + + +zygosity->type + + +type + + + +description + +narrative text + + + +zygosity->description + + +description + + + +has attribute + +attribute + + + +zygosity->has attribute + + +has attribute + + + +provided by + +string + + + +zygosity->provided by + + +provided by + + + +xref + +uriorcurie + + + +zygosity->xref + + +xref + + + +category + +category + + + +zygosity->category + + +category + + + name - -name + +name - + zygosity->name - - -name + + +name - + has attribute type - -ontology class + +ontology class - + zygosity->has attribute type - - -has attribute type + + +has attribute type - + has quantitative value - -quantity value + +quantity value - + zygosity->has quantitative value - - -has quantitative value + + +has quantitative value - + has qualitative value - -named thing + +named thing - + zygosity->has qualitative value - - -has qualitative value + + +has qualitative value - + iri - -iri type + +iri type - + zygosity->iri - - -iri + + +iri - + source - -string + +string - + zygosity->source - - -source + + +source + + + +named thing_category + +category type - + attribute_name - -label type + +label type diff --git a/json-schema/biolink-model.json b/json-schema/biolink-model.json index a8d5953eeb..3f7da984d9 100644 --- a/json-schema/biolink-model.json +++ b/json-schema/biolink-model.json @@ -19,7 +19,7 @@ "has_attribute": { "description": "connects any entity to an attribute", "items": { - "$ref": "#/$defs/Attribute" + "type": "string" }, "type": "array" }, @@ -93,7 +93,7 @@ "has_attribute": { "description": "connects any entity to an attribute", "items": { - "$ref": "#/$defs/Attribute" + "type": "string" }, "type": "array" }, @@ -156,7 +156,7 @@ "has_attribute": { "description": "may often be an organism attribute", "items": { - "$ref": "#/$defs/Attribute" + "type": "string" }, "type": "array" }, @@ -232,7 +232,7 @@ "has_attribute": { "description": "connects any entity to an attribute", "items": { - "$ref": "#/$defs/Attribute" + "type": "string" }, "type": "array" }, @@ -292,7 +292,7 @@ "qualifiers": { "description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": { - "$ref": "#/$defs/OntologyClass" + "type": "string" }, "type": "array" }, @@ -342,7 +342,7 @@ "has_attribute": { "description": "connects any entity to an attribute", "items": { - "$ref": "#/$defs/Attribute" + "type": "string" }, "type": "array" }, @@ -402,7 +402,7 @@ "qualifiers": { "description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": { - "$ref": "#/$defs/OntologyClass" + "type": "string" }, "type": "array" }, @@ -461,7 +461,7 @@ "has_attribute": { "description": "connects any entity to an attribute", "items": { - "$ref": "#/$defs/Attribute" + "type": "string" }, "type": "array" }, @@ -580,7 +580,7 @@ "has_attribute": { "description": "connects any entity to an attribute", "items": { - "$ref": "#/$defs/Attribute" + "type": "string" }, "type": "array" }, @@ -640,7 +640,7 @@ "qualifiers": { "description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": { - "$ref": "#/$defs/OntologyClass" + "type": "string" }, "type": "array" }, @@ -669,9 +669,28 @@ "additionalProperties": false, "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": { + "category": { + "description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", + "items": { + "type": "string" + }, + "pattern": "^biolink:\\d+$", + "type": "array" + }, + "description": { + "description": "a human-readable description of an entity", + "type": "string" + }, + "has_attribute": { + "description": "connects any entity to an attribute", + "items": { + "type": "string" + }, + "type": "array" + }, "has_attribute_type": { - "$ref": "#/$defs/OntologyClass", - "description": "connects an attribute to a class that describes it" + "description": "connects an attribute to a class that describes it", + "type": "string" }, "has_qualitative_value": { "description": "connects an attribute to a value", @@ -684,6 +703,10 @@ }, "type": "array" }, + "id": { + "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", + "type": "string" + }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string" @@ -692,11 +715,30 @@ "description": "The human-readable 'attribute name' can be set to a string which reflects its context of interpretation, e.g. SEPIO evidence/provenance/confidence annotation or it can default to the name associated with the 'has attribute type' slot ontology term.", "type": "string" }, + "provided_by": { + "description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", + "items": { + "type": "string" + }, + "type": "array" + }, "source": { "type": "string" + }, + "type": { + "type": "string" + }, + "xref": { + "description": "Alternate CURIEs for a thing", + "items": { + "type": "string" + }, + "type": "array" } }, "required": [ + "id", + "category", "has_attribute_type" ], "title": "Attribute", @@ -728,7 +770,7 @@ "has_attribute": { "description": "connects any entity to an attribute", "items": { - "$ref": "#/$defs/Attribute" + "type": "string" }, "type": "array" }, @@ -815,7 +857,7 @@ "has_attribute": { "description": "connects any entity to an attribute", "items": { - "$ref": "#/$defs/Attribute" + "type": "string" }, "type": "array" }, @@ -854,8 +896,8 @@ "type": "string" }, "onset_qualifier": { - "$ref": "#/$defs/Onset", - "description": "a qualifier used in a phenotypic association to state when the phenotype appears is in the subject" + "description": "a qualifier used in a phenotypic association to state when the phenotype appears is in the subject", + "type": "string" }, "original_knowledge_source": { "description": "The Information Resource that created the original record of the knowledge expressed in an Association (e.g. via curation of the knowledge from the literature, or generation of the knowledge de novo through computation, reasoning, inference over data).", @@ -879,17 +921,17 @@ "qualifiers": { "description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": { - "$ref": "#/$defs/OntologyClass" + "type": "string" }, "type": "array" }, "severity_qualifier": { - "$ref": "#/$defs/SeverityValue", - "description": "a qualifier used in a phenotypic association to state how severe the phenotype is in the subject" + "description": "a qualifier used in a phenotypic association to state how severe the phenotype is in the subject", + "type": "string" }, "sex_qualifier": { - "$ref": "#/$defs/BiologicalSex", - "description": "a qualifier used in a phenotypic association to state whether the association is specific to a particular sex." + "description": "a qualifier used in a phenotypic association to state whether the association is specific to a particular sex.", + "type": "string" }, "source": { "type": "string" @@ -945,7 +987,7 @@ "has_attribute": { "description": "connects any entity to an attribute", "items": { - "$ref": "#/$defs/Attribute" + "type": "string" }, "type": "array" }, @@ -1030,7 +1072,7 @@ "has_attribute": { "description": "connects any entity to an attribute", "items": { - "$ref": "#/$defs/Attribute" + "type": "string" }, "type": "array" }, @@ -1114,7 +1156,7 @@ "has_attribute": { "description": "connects any entity to an attribute", "items": { - "$ref": "#/$defs/Attribute" + "type": "string" }, "type": "array" }, @@ -1176,9 +1218,28 @@ "additionalProperties": false, "description": "", "properties": { + "category": { + "description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", + "items": { + "type": "string" + }, + "pattern": "^biolink:\\d+$", + "type": "array" + }, + "description": { + "description": "a human-readable description of an entity", + "type": "string" + }, + "has_attribute": { + "description": "connects any entity to an attribute", + "items": { + "type": "string" + }, + "type": "array" + }, "has_attribute_type": { - "$ref": "#/$defs/OntologyClass", - "description": "connects an attribute to a class that describes it" + "description": "connects an attribute to a class that describes it", + "type": "string" }, "has_qualitative_value": { "description": "connects an attribute to a value", @@ -1191,6 +1252,10 @@ }, "type": "array" }, + "id": { + "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", + "type": "string" + }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string" @@ -1199,11 +1264,30 @@ "description": "The human-readable 'attribute name' can be set to a string which reflects its context of interpretation, e.g. SEPIO evidence/provenance/confidence annotation or it can default to the name associated with the 'has attribute type' slot ontology term.", "type": "string" }, + "provided_by": { + "description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", + "items": { + "type": "string" + }, + "type": "array" + }, "source": { "type": "string" + }, + "type": { + "type": "string" + }, + "xref": { + "description": "Alternate CURIEs for a thing", + "items": { + "type": "string" + }, + "type": "array" } }, "required": [ + "id", + "category", "has_attribute_type" ], "title": "BiologicalSex", @@ -1257,7 +1341,7 @@ "has_attribute": { "description": "connects any entity to an attribute", "items": { - "$ref": "#/$defs/Attribute" + "type": "string" }, "type": "array" }, @@ -1372,7 +1456,7 @@ "has_attribute": { "description": "connects any entity to an attribute", "items": { - "$ref": "#/$defs/Attribute" + "type": "string" }, "type": "array" }, @@ -1477,7 +1561,7 @@ "has_attribute": { "description": "may often be an organism attribute", "items": { - "$ref": "#/$defs/Attribute" + "type": "string" }, "type": "array" }, @@ -1557,7 +1641,7 @@ "has_attribute": { "description": "connects any entity to an attribute", "items": { - "$ref": "#/$defs/Attribute" + "type": "string" }, "type": "array" }, @@ -1596,8 +1680,8 @@ "type": "string" }, "onset_qualifier": { - "$ref": "#/$defs/Onset", - "description": "a qualifier used in a phenotypic association to state when the phenotype appears is in the subject" + "description": "a qualifier used in a phenotypic association to state when the phenotype appears is in the subject", + "type": "string" }, "original_knowledge_source": { "description": "The Information Resource that created the original record of the knowledge expressed in an Association (e.g. via curation of the knowledge from the literature, or generation of the knowledge de novo through computation, reasoning, inference over data).", @@ -1621,17 +1705,17 @@ "qualifiers": { "description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": { - "$ref": "#/$defs/OntologyClass" + "type": "string" }, "type": "array" }, "severity_qualifier": { - "$ref": "#/$defs/SeverityValue", - "description": "a qualifier used in a phenotypic association to state how severe the phenotype is in the subject" + "description": "a qualifier used in a phenotypic association to state how severe the phenotype is in the subject", + "type": "string" }, "sex_qualifier": { - "$ref": "#/$defs/BiologicalSex", - "description": "a qualifier used in a phenotypic association to state whether the association is specific to a particular sex." + "description": "a qualifier used in a phenotypic association to state whether the association is specific to a particular sex.", + "type": "string" }, "source": { "type": "string" @@ -1673,7 +1757,7 @@ "has_attribute": { "description": "may often be an organism attribute", "items": { - "$ref": "#/$defs/Attribute" + "type": "string" }, "type": "array" }, @@ -1743,7 +1827,7 @@ "has_attribute": { "description": "may often be an organism attribute", "items": { - "$ref": "#/$defs/Attribute" + "type": "string" }, "type": "array" }, @@ -1816,7 +1900,7 @@ "has_attribute": { "description": "connects any entity to an attribute", "items": { - "$ref": "#/$defs/Attribute" + "type": "string" }, "type": "array" }, @@ -1855,8 +1939,8 @@ "type": "string" }, "onset_qualifier": { - "$ref": "#/$defs/Onset", - "description": "a qualifier used in a phenotypic association to state when the phenotype appears is in the subject" + "description": "a qualifier used in a phenotypic association to state when the phenotype appears is in the subject", + "type": "string" }, "original_knowledge_source": { "description": "The Information Resource that created the original record of the knowledge expressed in an Association (e.g. via curation of the knowledge from the literature, or generation of the knowledge de novo through computation, reasoning, inference over data).", @@ -1880,13 +1964,13 @@ "qualifiers": { "description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": { - "$ref": "#/$defs/OntologyClass" + "type": "string" }, "type": "array" }, "severity_qualifier": { - "$ref": "#/$defs/SeverityValue", - "description": "a qualifier used in a phenotypic association to state how severe the phenotype is in the subject" + "description": "a qualifier used in a phenotypic association to state how severe the phenotype is in the subject", + "type": "string" }, "source": { "type": "string" @@ -1934,7 +2018,7 @@ "has_attribute": { "description": "connects any entity to an attribute", "items": { - "$ref": "#/$defs/Attribute" + "type": "string" }, "type": "array" }, @@ -1994,7 +2078,7 @@ "qualifiers": { "description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": { - "$ref": "#/$defs/OntologyClass" + "type": "string" }, "type": "array" }, @@ -2038,7 +2122,7 @@ "has_attribute": { "description": "may often be an organism attribute", "items": { - "$ref": "#/$defs/Attribute" + "type": "string" }, "type": "array" }, @@ -2114,14 +2198,14 @@ "has_attribute": { "description": "connects any entity to an attribute", "items": { - "$ref": "#/$defs/Attribute" + "type": "string" }, "type": "array" }, "has_chemical_role": { "description": "\tA role is particular behaviour which a material entity may exhibit.", "items": { - "$ref": "#/$defs/ChemicalRole" + "type": "string" }, "type": "array" }, @@ -2225,14 +2309,14 @@ "has_attribute": { "description": "connects any entity to an attribute", "items": { - "$ref": "#/$defs/Attribute" + "type": "string" }, "type": "array" }, "has_chemical_role": { "description": "\tA role is particular behaviour which a material entity may exhibit.", "items": { - "$ref": "#/$defs/ChemicalRole" + "type": "string" }, "type": "array" }, @@ -2304,9 +2388,28 @@ "additionalProperties": false, "description": "", "properties": { + "category": { + "description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", + "items": { + "type": "string" + }, + "pattern": "^biolink:\\d+$", + "type": "array" + }, + "description": { + "description": "a human-readable description of an entity", + "type": "string" + }, + "has_attribute": { + "description": "connects any entity to an attribute", + "items": { + "type": "string" + }, + "type": "array" + }, "has_attribute_type": { - "$ref": "#/$defs/OntologyClass", - "description": "connects an attribute to a class that describes it" + "description": "connects an attribute to a class that describes it", + "type": "string" }, "has_qualitative_value": { "description": "connects an attribute to a value", @@ -2319,6 +2422,10 @@ }, "type": "array" }, + "id": { + "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", + "type": "string" + }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string" @@ -2327,11 +2434,30 @@ "description": "The human-readable 'attribute name' can be set to a string which reflects its context of interpretation, e.g. SEPIO evidence/provenance/confidence annotation or it can default to the name associated with the 'has attribute type' slot ontology term.", "type": "string" }, + "provided_by": { + "description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", + "items": { + "type": "string" + }, + "type": "array" + }, "source": { "type": "string" + }, + "type": { + "type": "string" + }, + "xref": { + "description": "Alternate CURIEs for a thing", + "items": { + "type": "string" + }, + "type": "array" } }, "required": [ + "id", + "category", "has_attribute_type" ], "title": "ChemicalRole", @@ -2370,7 +2496,7 @@ "has_attribute": { "description": "connects any entity to an attribute", "items": { - "$ref": "#/$defs/Attribute" + "type": "string" }, "type": "array" }, @@ -2430,7 +2556,7 @@ "qualifiers": { "description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": { - "$ref": "#/$defs/OntologyClass" + "type": "string" }, "type": "array" }, @@ -2487,7 +2613,7 @@ "has_attribute": { "description": "connects any entity to an attribute", "items": { - "$ref": "#/$defs/Attribute" + "type": "string" }, "type": "array" }, @@ -2547,7 +2673,7 @@ "qualifiers": { "description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": { - "$ref": "#/$defs/OntologyClass" + "type": "string" }, "type": "array" }, @@ -2597,7 +2723,7 @@ "has_attribute": { "description": "connects any entity to an attribute", "items": { - "$ref": "#/$defs/Attribute" + "type": "string" }, "type": "array" }, @@ -2657,7 +2783,7 @@ "qualifiers": { "description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": { - "$ref": "#/$defs/OntologyClass" + "type": "string" }, "type": "array" }, @@ -2707,7 +2833,7 @@ "has_attribute": { "description": "connects any entity to an attribute", "items": { - "$ref": "#/$defs/Attribute" + "type": "string" }, "type": "array" }, @@ -2767,7 +2893,7 @@ "qualifiers": { "description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": { - "$ref": "#/$defs/OntologyClass" + "type": "string" }, "type": "array" }, @@ -2817,7 +2943,7 @@ "has_attribute": { "description": "connects any entity to an attribute", "items": { - "$ref": "#/$defs/Attribute" + "type": "string" }, "type": "array" }, @@ -2877,7 +3003,7 @@ "qualifiers": { "description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": { - "$ref": "#/$defs/OntologyClass" + "type": "string" }, "type": "array" }, @@ -2906,9 +3032,28 @@ "additionalProperties": false, "description": "Attributes relating to a clinical manifestation", "properties": { + "category": { + "description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", + "items": { + "type": "string" + }, + "pattern": "^biolink:\\d+$", + "type": "array" + }, + "description": { + "description": "a human-readable description of an entity", + "type": "string" + }, + "has_attribute": { + "description": "connects any entity to an attribute", + "items": { + "type": "string" + }, + "type": "array" + }, "has_attribute_type": { - "$ref": "#/$defs/OntologyClass", - "description": "connects an attribute to a class that describes it" + "description": "connects an attribute to a class that describes it", + "type": "string" }, "has_qualitative_value": { "description": "connects an attribute to a value", @@ -2921,6 +3066,10 @@ }, "type": "array" }, + "id": { + "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", + "type": "string" + }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string" @@ -2929,11 +3078,30 @@ "description": "The human-readable 'attribute name' can be set to a string which reflects its context of interpretation, e.g. SEPIO evidence/provenance/confidence annotation or it can default to the name associated with the 'has attribute type' slot ontology term.", "type": "string" }, + "provided_by": { + "description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", + "items": { + "type": "string" + }, + "type": "array" + }, "source": { "type": "string" + }, + "type": { + "type": "string" + }, + "xref": { + "description": "Alternate CURIEs for a thing", + "items": { + "type": "string" + }, + "type": "array" } }, "required": [ + "id", + "category", "has_attribute_type" ], "title": "ClinicalAttribute", @@ -2943,9 +3111,28 @@ "additionalProperties": false, "description": "The course a disease typically takes from its onset, progression in time, and eventual resolution or death of the affected individual", "properties": { + "category": { + "description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", + "items": { + "type": "string" + }, + "pattern": "^biolink:\\d+$", + "type": "array" + }, + "description": { + "description": "a human-readable description of an entity", + "type": "string" + }, + "has_attribute": { + "description": "connects any entity to an attribute", + "items": { + "type": "string" + }, + "type": "array" + }, "has_attribute_type": { - "$ref": "#/$defs/OntologyClass", - "description": "connects an attribute to a class that describes it" + "description": "connects an attribute to a class that describes it", + "type": "string" }, "has_qualitative_value": { "description": "connects an attribute to a value", @@ -2958,6 +3145,10 @@ }, "type": "array" }, + "id": { + "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", + "type": "string" + }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string" @@ -2966,11 +3157,30 @@ "description": "The human-readable 'attribute name' can be set to a string which reflects its context of interpretation, e.g. SEPIO evidence/provenance/confidence annotation or it can default to the name associated with the 'has attribute type' slot ontology term.", "type": "string" }, + "provided_by": { + "description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", + "items": { + "type": "string" + }, + "type": "array" + }, "source": { "type": "string" + }, + "type": { + "type": "string" + }, + "xref": { + "description": "Alternate CURIEs for a thing", + "items": { + "type": "string" + }, + "type": "array" } }, "required": [ + "id", + "category", "has_attribute_type" ], "title": "ClinicalCourse", @@ -2995,7 +3205,7 @@ "has_attribute": { "description": "connects any entity to an attribute", "items": { - "$ref": "#/$defs/Attribute" + "type": "string" }, "type": "array" }, @@ -3058,7 +3268,7 @@ "has_attribute": { "description": "connects any entity to an attribute", "items": { - "$ref": "#/$defs/ClinicalAttribute" + "type": "string" }, "type": "array" }, @@ -3128,7 +3338,7 @@ "has_attribute": { "description": "connects any entity to an attribute", "items": { - "$ref": "#/$defs/Attribute" + "type": "string" }, "type": "array" }, @@ -3176,9 +3386,28 @@ "additionalProperties": false, "description": "A clinical measurement is a special kind of attribute which results from a laboratory observation from a subject individual or sample. Measurements can be connected to their subject by the 'has attribute' slot.", "properties": { + "category": { + "description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", + "items": { + "type": "string" + }, + "pattern": "^biolink:\\d+$", + "type": "array" + }, + "description": { + "description": "a human-readable description of an entity", + "type": "string" + }, + "has_attribute": { + "description": "connects any entity to an attribute", + "items": { + "type": "string" + }, + "type": "array" + }, "has_attribute_type": { - "$ref": "#/$defs/OntologyClass", - "description": "connects an attribute to a class that describes it" + "description": "connects an attribute to a class that describes it", + "type": "string" }, "has_qualitative_value": { "description": "connects an attribute to a value", @@ -3191,6 +3420,10 @@ }, "type": "array" }, + "id": { + "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", + "type": "string" + }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string" @@ -3199,11 +3432,30 @@ "description": "The human-readable 'attribute name' can be set to a string which reflects its context of interpretation, e.g. SEPIO evidence/provenance/confidence annotation or it can default to the name associated with the 'has attribute type' slot ontology term.", "type": "string" }, + "provided_by": { + "description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", + "items": { + "type": "string" + }, + "type": "array" + }, "source": { "type": "string" + }, + "type": { + "type": "string" + }, + "xref": { + "description": "Alternate CURIEs for a thing", + "items": { + "type": "string" + }, + "type": "array" } }, "required": [ + "id", + "category", "has_attribute_type" ], "title": "ClinicalMeasurement", @@ -3213,9 +3465,28 @@ "additionalProperties": false, "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": { + "category": { + "description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", + "items": { + "type": "string" + }, + "pattern": "^biolink:\\d+$", + "type": "array" + }, + "description": { + "description": "a human-readable description of an entity", + "type": "string" + }, + "has_attribute": { + "description": "connects any entity to an attribute", + "items": { + "type": "string" + }, + "type": "array" + }, "has_attribute_type": { - "$ref": "#/$defs/OntologyClass", - "description": "connects an attribute to a class that describes it" + "description": "connects an attribute to a class that describes it", + "type": "string" }, "has_qualitative_value": { "description": "connects an attribute to a value", @@ -3228,6 +3499,10 @@ }, "type": "array" }, + "id": { + "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", + "type": "string" + }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string" @@ -3236,11 +3511,30 @@ "description": "The human-readable 'attribute name' can be set to a string which reflects its context of interpretation, e.g. SEPIO evidence/provenance/confidence annotation or it can default to the name associated with the 'has attribute type' slot ontology term.", "type": "string" }, + "provided_by": { + "description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", + "items": { + "type": "string" + }, + "type": "array" + }, "source": { "type": "string" + }, + "type": { + "type": "string" + }, + "xref": { + "description": "Alternate CURIEs for a thing", + "items": { + "type": "string" + }, + "type": "array" } }, "required": [ + "id", + "category", "has_attribute_type" ], "title": "ClinicalModifier", @@ -3265,7 +3559,7 @@ "has_attribute": { "description": "connects any entity to an attribute", "items": { - "$ref": "#/$defs/Attribute" + "type": "string" }, "type": "array" }, @@ -3334,7 +3628,7 @@ "has_attribute": { "description": "connects any entity to an attribute", "items": { - "$ref": "#/$defs/Attribute" + "type": "string" }, "type": "array" }, @@ -3345,7 +3639,7 @@ "has_chemical_role": { "description": "\tA role is particular behaviour which a material entity may exhibit.", "items": { - "$ref": "#/$defs/ChemicalRole" + "type": "string" }, "type": "array" }, @@ -3429,7 +3723,7 @@ "has_attribute": { "description": "may often be an organism attribute", "items": { - "$ref": "#/$defs/Attribute" + "type": "string" }, "type": "array" }, @@ -3517,14 +3811,14 @@ "has_attribute": { "description": "connects any entity to an attribute", "items": { - "$ref": "#/$defs/Attribute" + "type": "string" }, "type": "array" }, "has_chemical_role": { "description": "\tA role is particular behaviour which a material entity may exhibit.", "items": { - "$ref": "#/$defs/ChemicalRole" + "type": "string" }, "type": "array" }, @@ -3619,7 +3913,7 @@ "has_attribute": { "description": "connects any entity to an attribute", "items": { - "$ref": "#/$defs/Attribute" + "type": "string" }, "type": "array" }, @@ -3694,7 +3988,7 @@ "has_attribute": { "description": "connects any entity to an attribute", "items": { - "$ref": "#/$defs/Attribute" + "type": "string" }, "type": "array" }, @@ -3754,7 +4048,7 @@ "qualifiers": { "description": "this field can be used to annotate special characteristics of an agent relationship, such as the fact that a given author agent of a publication is the 'corresponding author'", "items": { - "$ref": "#/$defs/OntologyClass" + "type": "string" }, "type": "array" }, @@ -3806,7 +4100,7 @@ "has_attribute": { "description": "connects any entity to an attribute", "items": { - "$ref": "#/$defs/Attribute" + "type": "string" }, "type": "array" }, @@ -3886,7 +4180,7 @@ "has_attribute": { "description": "connects any entity to an attribute", "items": { - "$ref": "#/$defs/Attribute" + "type": "string" }, "type": "array" }, @@ -3963,7 +4257,7 @@ "has_attribute": { "description": "connects any entity to an attribute", "items": { - "$ref": "#/$defs/Attribute" + "type": "string" }, "type": "array" }, @@ -4046,7 +4340,7 @@ "has_attribute": { "description": "connects any entity to an attribute", "items": { - "$ref": "#/$defs/Attribute" + "type": "string" }, "type": "array" }, @@ -4124,7 +4418,7 @@ "has_attribute": { "description": "connects any entity to an attribute", "items": { - "$ref": "#/$defs/Attribute" + "type": "string" }, "type": "array" }, @@ -4187,7 +4481,7 @@ "has_attribute": { "description": "connects any entity to an attribute", "items": { - "$ref": "#/$defs/Attribute" + "type": "string" }, "type": "array" }, @@ -4257,7 +4551,7 @@ "has_attribute": { "description": "connects any entity to an attribute", "items": { - "$ref": "#/$defs/Attribute" + "type": "string" }, "type": "array" }, @@ -4355,7 +4649,7 @@ "has_attribute": { "description": "connects any entity to an attribute", "items": { - "$ref": "#/$defs/Attribute" + "type": "string" }, "type": "array" }, @@ -4415,7 +4709,7 @@ "qualifiers": { "description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": { - "$ref": "#/$defs/OntologyClass" + "type": "string" }, "type": "array" }, @@ -4465,7 +4759,7 @@ "has_attribute": { "description": "connects any entity to an attribute", "items": { - "$ref": "#/$defs/Attribute" + "type": "string" }, "type": "array" }, @@ -4525,7 +4819,7 @@ "qualifiers": { "description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": { - "$ref": "#/$defs/OntologyClass" + "type": "string" }, "type": "array" }, @@ -4579,7 +4873,7 @@ "has_attribute": { "description": "connects any entity to an attribute", "items": { - "$ref": "#/$defs/Attribute" + "type": "string" }, "type": "array" }, @@ -4618,8 +4912,8 @@ "type": "string" }, "onset_qualifier": { - "$ref": "#/$defs/Onset", - "description": "a qualifier used in a phenotypic association to state when the phenotype appears is in the subject" + "description": "a qualifier used in a phenotypic association to state when the phenotype appears is in the subject", + "type": "string" }, "original_knowledge_source": { "description": "The Information Resource that created the original record of the knowledge expressed in an Association (e.g. via curation of the knowledge from the literature, or generation of the knowledge de novo through computation, reasoning, inference over data).", @@ -4643,17 +4937,17 @@ "qualifiers": { "description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": { - "$ref": "#/$defs/OntologyClass" + "type": "string" }, "type": "array" }, "severity_qualifier": { - "$ref": "#/$defs/SeverityValue", - "description": "a qualifier used in a phenotypic association to state how severe the phenotype is in the subject" + "description": "a qualifier used in a phenotypic association to state how severe the phenotype is in the subject", + "type": "string" }, "sex_qualifier": { - "$ref": "#/$defs/BiologicalSex", - "description": "a qualifier used in a phenotypic association to state whether the association is specific to a particular sex." + "description": "a qualifier used in a phenotypic association to state whether the association is specific to a particular sex.", + "type": "string" }, "source": { "type": "string" @@ -4705,14 +4999,14 @@ "has_attribute": { "description": "connects any entity to an attribute", "items": { - "$ref": "#/$defs/Attribute" + "type": "string" }, "type": "array" }, "has_chemical_role": { "description": "\tA role is particular behaviour which a material entity may exhibit.", "items": { - "$ref": "#/$defs/ChemicalRole" + "type": "string" }, "type": "array" }, @@ -4846,7 +5140,7 @@ "has_attribute": { "description": "connects any entity to an attribute", "items": { - "$ref": "#/$defs/Attribute" + "type": "string" }, "type": "array" }, @@ -4906,7 +5200,7 @@ "qualifiers": { "description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": { - "$ref": "#/$defs/OntologyClass" + "type": "string" }, "type": "array" }, @@ -4999,7 +5293,7 @@ "has_attribute": { "description": "connects any entity to an attribute", "items": { - "$ref": "#/$defs/Attribute" + "type": "string" }, "type": "array" }, @@ -5038,8 +5332,8 @@ "type": "string" }, "onset_qualifier": { - "$ref": "#/$defs/Onset", - "description": "a qualifier used in a phenotypic association to state when the phenotype appears is in the subject" + "description": "a qualifier used in a phenotypic association to state when the phenotype appears is in the subject", + "type": "string" }, "original_knowledge_source": { "description": "The Information Resource that created the original record of the knowledge expressed in an Association (e.g. via curation of the knowledge from the literature, or generation of the knowledge de novo through computation, reasoning, inference over data).", @@ -5063,13 +5357,13 @@ "qualifiers": { "description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": { - "$ref": "#/$defs/OntologyClass" + "type": "string" }, "type": "array" }, "severity_qualifier": { - "$ref": "#/$defs/SeverityValue", - "description": "a qualifier used in a phenotypic association to state how severe the phenotype is in the subject" + "description": "a qualifier used in a phenotypic association to state how severe the phenotype is in the subject", + "type": "string" }, "source": { "type": "string" @@ -5120,7 +5414,7 @@ "has_attribute": { "description": "connects any entity to an attribute", "items": { - "$ref": "#/$defs/Attribute" + "type": "string" }, "type": "array" }, @@ -5180,7 +5474,7 @@ "qualifiers": { "description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": { - "$ref": "#/$defs/OntologyClass" + "type": "string" }, "type": "array" }, @@ -5233,7 +5527,7 @@ "has_attribute": { "description": "connects any entity to an attribute", "items": { - "$ref": "#/$defs/Attribute" + "type": "string" }, "type": "array" }, @@ -5293,7 +5587,7 @@ "qualifiers": { "description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": { - "$ref": "#/$defs/OntologyClass" + "type": "string" }, "type": "array" }, @@ -5351,7 +5645,7 @@ "has_attribute": { "description": "connects any entity to an attribute", "items": { - "$ref": "#/$defs/Attribute" + "type": "string" }, "type": "array" }, @@ -5420,14 +5714,14 @@ "has_attribute": { "description": "connects any entity to an attribute", "items": { - "$ref": "#/$defs/Attribute" + "type": "string" }, "type": "array" }, "has_chemical_role": { "description": "\tA role is particular behaviour which a material entity may exhibit.", "items": { - "$ref": "#/$defs/ChemicalRole" + "type": "string" }, "type": "array" }, @@ -5500,7 +5794,7 @@ "has_attribute": { "description": "connects any entity to an attribute", "items": { - "$ref": "#/$defs/Attribute" + "type": "string" }, "type": "array" }, @@ -5571,7 +5865,7 @@ "has_attribute": { "description": "connects any entity to an attribute", "items": { - "$ref": "#/$defs/Attribute" + "type": "string" }, "type": "array" }, @@ -5642,7 +5936,7 @@ "has_attribute": { "description": "connects any entity to an attribute", "items": { - "$ref": "#/$defs/Attribute" + "type": "string" }, "type": "array" }, @@ -5717,7 +6011,7 @@ "has_attribute": { "description": "connects any entity to an attribute", "items": { - "$ref": "#/$defs/Attribute" + "type": "string" }, "type": "array" }, @@ -5728,7 +6022,7 @@ "has_chemical_role": { "description": "\tA role is particular behaviour which a material entity may exhibit.", "items": { - "$ref": "#/$defs/ChemicalRole" + "type": "string" }, "type": "array" }, @@ -5818,7 +6112,7 @@ "has_attribute": { "description": "connects any entity to an attribute", "items": { - "$ref": "#/$defs/Attribute" + "type": "string" }, "type": "array" }, @@ -5878,7 +6172,7 @@ "qualifiers": { "description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": { - "$ref": "#/$defs/OntologyClass" + "type": "string" }, "type": "array" }, @@ -5936,7 +6230,7 @@ "has_attribute": { "description": "connects any entity to an attribute", "items": { - "$ref": "#/$defs/Attribute" + "type": "string" }, "type": "array" }, @@ -6005,7 +6299,7 @@ "qualifiers": { "description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": { - "$ref": "#/$defs/OntologyClass" + "type": "string" }, "type": "array" }, @@ -6059,7 +6353,7 @@ "has_attribute": { "description": "connects any entity to an attribute", "items": { - "$ref": "#/$defs/Attribute" + "type": "string" }, "type": "array" }, @@ -6098,8 +6392,8 @@ "type": "string" }, "onset_qualifier": { - "$ref": "#/$defs/Onset", - "description": "a qualifier used in a phenotypic association to state when the phenotype appears is in the subject" + "description": "a qualifier used in a phenotypic association to state when the phenotype appears is in the subject", + "type": "string" }, "original_knowledge_source": { "description": "The Information Resource that created the original record of the knowledge expressed in an Association (e.g. via curation of the knowledge from the literature, or generation of the knowledge de novo through computation, reasoning, inference over data).", @@ -6123,17 +6417,17 @@ "qualifiers": { "description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": { - "$ref": "#/$defs/OntologyClass" + "type": "string" }, "type": "array" }, "severity_qualifier": { - "$ref": "#/$defs/SeverityValue", - "description": "a qualifier used in a phenotypic association to state how severe the phenotype is in the subject" + "description": "a qualifier used in a phenotypic association to state how severe the phenotype is in the subject", + "type": "string" }, "sex_qualifier": { - "$ref": "#/$defs/BiologicalSex", - "description": "a qualifier used in a phenotypic association to state whether the association is specific to a particular sex." + "description": "a qualifier used in a phenotypic association to state whether the association is specific to a particular sex.", + "type": "string" }, "source": { "type": "string" @@ -6207,14 +6501,14 @@ "has_attribute": { "description": "connects any entity to an attribute", "items": { - "$ref": "#/$defs/Attribute" + "type": "string" }, "type": "array" }, "has_chemical_role": { "description": "\tA role is particular behaviour which a material entity may exhibit.", "items": { - "$ref": "#/$defs/ChemicalRole" + "type": "string" }, "type": "array" }, @@ -6307,14 +6601,14 @@ "has_attribute": { "description": "connects any entity to an attribute", "items": { - "$ref": "#/$defs/Attribute" + "type": "string" }, "type": "array" }, "has_chemical_role": { "description": "\tA role is particular behaviour which a material entity may exhibit.", "items": { - "$ref": "#/$defs/ChemicalRole" + "type": "string" }, "type": "array" }, @@ -6393,7 +6687,7 @@ "has_attribute": { "description": "connects any entity to an attribute", "items": { - "$ref": "#/$defs/Attribute" + "type": "string" }, "type": "array" }, @@ -6453,7 +6747,7 @@ "qualifiers": { "description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": { - "$ref": "#/$defs/OntologyClass" + "type": "string" }, "type": "array" }, @@ -6497,7 +6791,7 @@ "has_attribute": { "description": "connects any entity to an attribute", "items": { - "$ref": "#/$defs/Attribute" + "type": "string" }, "type": "array" }, @@ -6592,7 +6886,7 @@ "has_attribute": { "description": "connects any entity to an attribute", "items": { - "$ref": "#/$defs/Attribute" + "type": "string" }, "type": "array" }, @@ -6631,8 +6925,8 @@ "type": "string" }, "onset_qualifier": { - "$ref": "#/$defs/Onset", - "description": "a qualifier used in a phenotypic association to state when the phenotype appears is in the subject" + "description": "a qualifier used in a phenotypic association to state when the phenotype appears is in the subject", + "type": "string" }, "original_knowledge_source": { "description": "The Information Resource that created the original record of the knowledge expressed in an Association (e.g. via curation of the knowledge from the literature, or generation of the knowledge de novo through computation, reasoning, inference over data).", @@ -6656,13 +6950,13 @@ "qualifiers": { "description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": { - "$ref": "#/$defs/OntologyClass" + "type": "string" }, "type": "array" }, "severity_qualifier": { - "$ref": "#/$defs/SeverityValue", - "description": "a qualifier used in a phenotypic association to state how severe the phenotype is in the subject" + "description": "a qualifier used in a phenotypic association to state how severe the phenotype is in the subject", + "type": "string" }, "source": { "type": "string" @@ -6704,7 +6998,7 @@ "has_attribute": { "description": "connects any entity to an attribute", "items": { - "$ref": "#/$defs/Attribute" + "type": "string" }, "type": "array" }, @@ -6784,7 +7078,7 @@ "has_attribute": { "description": "connects any entity to an attribute", "items": { - "$ref": "#/$defs/Attribute" + "type": "string" }, "type": "array" }, @@ -6823,8 +7117,8 @@ "type": "string" }, "onset_qualifier": { - "$ref": "#/$defs/Onset", - "description": "a qualifier used in a phenotypic association to state when the phenotype appears is in the subject" + "description": "a qualifier used in a phenotypic association to state when the phenotype appears is in the subject", + "type": "string" }, "original_knowledge_source": { "description": "The Information Resource that created the original record of the knowledge expressed in an Association (e.g. via curation of the knowledge from the literature, or generation of the knowledge de novo through computation, reasoning, inference over data).", @@ -6848,7 +7142,7 @@ "qualifiers": { "description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": { - "$ref": "#/$defs/OntologyClass" + "type": "string" }, "type": "array" }, @@ -6857,8 +7151,8 @@ "type": "string" }, "severity_qualifier": { - "$ref": "#/$defs/SeverityValue", - "description": "a qualifier used in a phenotypic association to state how severe the phenotype is in the subject" + "description": "a qualifier used in a phenotypic association to state how severe the phenotype is in the subject", + "type": "string" }, "source": { "type": "string" @@ -6881,6 +7175,14 @@ "title": "GeneHasVariantThatContributesToDiseaseAssociation", "type": "object" }, + "GeneOntologyClass": { + "additionalProperties": false, + "description": "", + "properties": {}, + "required": [], + "title": "GeneOntologyClass", + "type": "object" + }, "GeneRegulatoryRelationship": { "additionalProperties": false, "description": "A regulatory relationship between two genes", @@ -6906,7 +7208,7 @@ "has_attribute": { "description": "connects any entity to an attribute", "items": { - "$ref": "#/$defs/Attribute" + "type": "string" }, "type": "array" }, @@ -6966,7 +7268,7 @@ "qualifiers": { "description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": { - "$ref": "#/$defs/OntologyClass" + "type": "string" }, "type": "array" }, @@ -7020,7 +7322,7 @@ "has_attribute": { "description": "connects any entity to an attribute", "items": { - "$ref": "#/$defs/Attribute" + "type": "string" }, "type": "array" }, @@ -7059,8 +7361,8 @@ "type": "string" }, "onset_qualifier": { - "$ref": "#/$defs/Onset", - "description": "a qualifier used in a phenotypic association to state when the phenotype appears is in the subject" + "description": "a qualifier used in a phenotypic association to state when the phenotype appears is in the subject", + "type": "string" }, "original_knowledge_source": { "description": "The Information Resource that created the original record of the knowledge expressed in an Association (e.g. via curation of the knowledge from the literature, or generation of the knowledge de novo through computation, reasoning, inference over data).", @@ -7084,13 +7386,13 @@ "qualifiers": { "description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": { - "$ref": "#/$defs/OntologyClass" + "type": "string" }, "type": "array" }, "severity_qualifier": { - "$ref": "#/$defs/SeverityValue", - "description": "a qualifier used in a phenotypic association to state how severe the phenotype is in the subject" + "description": "a qualifier used in a phenotypic association to state how severe the phenotype is in the subject", + "type": "string" }, "source": { "type": "string" @@ -7138,7 +7440,7 @@ "has_attribute": { "description": "connects any entity to an attribute", "items": { - "$ref": "#/$defs/Attribute" + "type": "string" }, "type": "array" }, @@ -7198,13 +7500,13 @@ "qualifiers": { "description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": { - "$ref": "#/$defs/OntologyClass" + "type": "string" }, "type": "array" }, "quantifier_qualifier": { - "$ref": "#/$defs/OntologyClass", - "description": "can be used to indicate magnitude, or also ranking" + "description": "can be used to indicate magnitude, or also ranking", + "type": "string" }, "source": { "type": "string" @@ -7260,7 +7562,7 @@ "has_attribute": { "description": "connects any entity to an attribute", "items": { - "$ref": "#/$defs/Attribute" + "type": "string" }, "type": "array" }, @@ -7324,13 +7626,13 @@ "qualifiers": { "description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": { - "$ref": "#/$defs/OntologyClass" + "type": "string" }, "type": "array" }, "quantifier_qualifier": { - "$ref": "#/$defs/OntologyClass", - "description": "Optional quantitative value indicating degree of expression." + "description": "Optional quantitative value indicating degree of expression.", + "type": "string" }, "source": { "type": "string" @@ -7382,7 +7684,7 @@ "has_attribute": { "description": "connects any entity to an attribute", "items": { - "$ref": "#/$defs/Attribute" + "type": "string" }, "type": "array" }, @@ -7442,7 +7744,7 @@ "qualifiers": { "description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": { - "$ref": "#/$defs/OntologyClass" + "type": "string" }, "type": "array" }, @@ -7492,7 +7794,7 @@ "has_attribute": { "description": "connects any entity to an attribute", "items": { - "$ref": "#/$defs/Attribute" + "type": "string" }, "type": "array" }, @@ -7552,7 +7854,7 @@ "qualifiers": { "description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": { - "$ref": "#/$defs/OntologyClass" + "type": "string" }, "type": "array" }, @@ -7602,7 +7904,7 @@ "has_attribute": { "description": "connects any entity to an attribute", "items": { - "$ref": "#/$defs/Attribute" + "type": "string" }, "type": "array" }, @@ -7662,7 +7964,7 @@ "qualifiers": { "description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": { - "$ref": "#/$defs/OntologyClass" + "type": "string" }, "type": "array" }, @@ -7716,7 +8018,7 @@ "has_attribute": { "description": "connects any entity to an attribute", "items": { - "$ref": "#/$defs/Attribute" + "type": "string" }, "type": "array" }, @@ -7755,8 +8057,8 @@ "type": "string" }, "onset_qualifier": { - "$ref": "#/$defs/Onset", - "description": "a qualifier used in a phenotypic association to state when the phenotype appears is in the subject" + "description": "a qualifier used in a phenotypic association to state when the phenotype appears is in the subject", + "type": "string" }, "original_knowledge_source": { "description": "The Information Resource that created the original record of the knowledge expressed in an Association (e.g. via curation of the knowledge from the literature, or generation of the knowledge de novo through computation, reasoning, inference over data).", @@ -7780,17 +8082,17 @@ "qualifiers": { "description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": { - "$ref": "#/$defs/OntologyClass" + "type": "string" }, "type": "array" }, "severity_qualifier": { - "$ref": "#/$defs/SeverityValue", - "description": "a qualifier used in a phenotypic association to state how severe the phenotype is in the subject" + "description": "a qualifier used in a phenotypic association to state how severe the phenotype is in the subject", + "type": "string" }, "sex_qualifier": { - "$ref": "#/$defs/BiologicalSex", - "description": "a qualifier used in a phenotypic association to state whether the association is specific to a particular sex." + "description": "a qualifier used in a phenotypic association to state whether the association is specific to a particular sex.", + "type": "string" }, "source": { "type": "string" @@ -7832,7 +8134,7 @@ "has_attribute": { "description": "connects any entity to an attribute", "items": { - "$ref": "#/$defs/Attribute" + "type": "string" }, "type": "array" }, @@ -7902,6 +8204,10 @@ }, "type": "array" }, + "id": { + "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", + "type": "string" + }, "in_taxon": { "description": "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'", "items": { @@ -7915,7 +8221,9 @@ "type": "string" } }, - "required": [], + "required": [ + "id" + ], "title": "GenomicBackgroundExposure", "type": "object" }, @@ -7952,7 +8260,7 @@ "has_attribute": { "description": "connects any entity to an attribute", "items": { - "$ref": "#/$defs/Attribute" + "type": "string" }, "type": "array" }, @@ -8016,7 +8324,7 @@ "qualifiers": { "description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": { - "$ref": "#/$defs/OntologyClass" + "type": "string" }, "type": "array" }, @@ -8068,7 +8376,7 @@ "has_attribute": { "description": "connects any entity to an attribute", "items": { - "$ref": "#/$defs/Attribute" + "type": "string" }, "type": "array" }, @@ -8077,7 +8385,7 @@ "type": "string" }, "has_zygosity": { - "$ref": "#/$defs/Zygosity" + "type": "string" }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", @@ -8155,7 +8463,7 @@ "has_attribute": { "description": "connects any entity to an attribute", "items": { - "$ref": "#/$defs/Attribute" + "type": "string" }, "type": "array" }, @@ -8194,8 +8502,8 @@ "type": "string" }, "onset_qualifier": { - "$ref": "#/$defs/Onset", - "description": "a qualifier used in a phenotypic association to state when the phenotype appears is in the subject" + "description": "a qualifier used in a phenotypic association to state when the phenotype appears is in the subject", + "type": "string" }, "original_knowledge_source": { "description": "The Information Resource that created the original record of the knowledge expressed in an Association (e.g. via curation of the knowledge from the literature, or generation of the knowledge de novo through computation, reasoning, inference over data).", @@ -8219,13 +8527,13 @@ "qualifiers": { "description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": { - "$ref": "#/$defs/OntologyClass" + "type": "string" }, "type": "array" }, "severity_qualifier": { - "$ref": "#/$defs/SeverityValue", - "description": "a qualifier used in a phenotypic association to state how severe the phenotype is in the subject" + "description": "a qualifier used in a phenotypic association to state how severe the phenotype is in the subject", + "type": "string" }, "source": { "type": "string" @@ -8277,7 +8585,7 @@ "has_attribute": { "description": "connects any entity to an attribute", "items": { - "$ref": "#/$defs/Attribute" + "type": "string" }, "type": "array" }, @@ -8316,8 +8624,8 @@ "type": "string" }, "onset_qualifier": { - "$ref": "#/$defs/Onset", - "description": "a qualifier used in a phenotypic association to state when the phenotype appears is in the subject" + "description": "a qualifier used in a phenotypic association to state when the phenotype appears is in the subject", + "type": "string" }, "original_knowledge_source": { "description": "The Information Resource that created the original record of the knowledge expressed in an Association (e.g. via curation of the knowledge from the literature, or generation of the knowledge de novo through computation, reasoning, inference over data).", @@ -8341,13 +8649,13 @@ "qualifiers": { "description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": { - "$ref": "#/$defs/OntologyClass" + "type": "string" }, "type": "array" }, "severity_qualifier": { - "$ref": "#/$defs/SeverityValue", - "description": "a qualifier used in a phenotypic association to state how severe the phenotype is in the subject" + "description": "a qualifier used in a phenotypic association to state how severe the phenotype is in the subject", + "type": "string" }, "source": { "type": "string" @@ -8395,7 +8703,7 @@ "has_attribute": { "description": "connects any entity to an attribute", "items": { - "$ref": "#/$defs/Attribute" + "type": "string" }, "type": "array" }, @@ -8455,7 +8763,7 @@ "qualifiers": { "description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": { - "$ref": "#/$defs/OntologyClass" + "type": "string" }, "type": "array" }, @@ -8505,7 +8813,7 @@ "has_attribute": { "description": "connects any entity to an attribute", "items": { - "$ref": "#/$defs/Attribute" + "type": "string" }, "type": "array" }, @@ -8565,7 +8873,7 @@ "qualifiers": { "description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": { - "$ref": "#/$defs/OntologyClass" + "type": "string" }, "type": "array" }, @@ -8619,7 +8927,7 @@ "has_attribute": { "description": "connects any entity to an attribute", "items": { - "$ref": "#/$defs/Attribute" + "type": "string" }, "type": "array" }, @@ -8658,8 +8966,8 @@ "type": "string" }, "onset_qualifier": { - "$ref": "#/$defs/Onset", - "description": "a qualifier used in a phenotypic association to state when the phenotype appears is in the subject" + "description": "a qualifier used in a phenotypic association to state when the phenotype appears is in the subject", + "type": "string" }, "original_knowledge_source": { "description": "The Information Resource that created the original record of the knowledge expressed in an Association (e.g. via curation of the knowledge from the literature, or generation of the knowledge de novo through computation, reasoning, inference over data).", @@ -8683,17 +8991,17 @@ "qualifiers": { "description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": { - "$ref": "#/$defs/OntologyClass" + "type": "string" }, "type": "array" }, "severity_qualifier": { - "$ref": "#/$defs/SeverityValue", - "description": "a qualifier used in a phenotypic association to state how severe the phenotype is in the subject" + "description": "a qualifier used in a phenotypic association to state how severe the phenotype is in the subject", + "type": "string" }, "sex_qualifier": { - "$ref": "#/$defs/BiologicalSex", - "description": "a qualifier used in a phenotypic association to state whether the association is specific to a particular sex." + "description": "a qualifier used in a phenotypic association to state whether the association is specific to a particular sex.", + "type": "string" }, "source": { "type": "string" @@ -8741,7 +9049,7 @@ "has_attribute": { "description": "connects any entity to an attribute", "items": { - "$ref": "#/$defs/Attribute" + "type": "string" }, "type": "array" }, @@ -8801,7 +9109,7 @@ "qualifiers": { "description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": { - "$ref": "#/$defs/OntologyClass" + "type": "string" }, "type": "array" }, @@ -8830,9 +9138,28 @@ "additionalProperties": false, "description": "An attribute corresponding to the genotypic sex of the individual, based upon genotypic composition of sex chromosomes.", "properties": { + "category": { + "description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", + "items": { + "type": "string" + }, + "pattern": "^biolink:\\d+$", + "type": "array" + }, + "description": { + "description": "a human-readable description of an entity", + "type": "string" + }, + "has_attribute": { + "description": "connects any entity to an attribute", + "items": { + "type": "string" + }, + "type": "array" + }, "has_attribute_type": { - "$ref": "#/$defs/OntologyClass", - "description": "connects an attribute to a class that describes it" + "description": "connects an attribute to a class that describes it", + "type": "string" }, "has_qualitative_value": { "description": "connects an attribute to a value", @@ -8845,6 +9172,10 @@ }, "type": "array" }, + "id": { + "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", + "type": "string" + }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string" @@ -8853,11 +9184,30 @@ "description": "The human-readable 'attribute name' can be set to a string which reflects its context of interpretation, e.g. SEPIO evidence/provenance/confidence annotation or it can default to the name associated with the 'has attribute type' slot ontology term.", "type": "string" }, + "provided_by": { + "description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", + "items": { + "type": "string" + }, + "type": "array" + }, "source": { "type": "string" + }, + "type": { + "type": "string" + }, + "xref": { + "description": "Alternate CURIEs for a thing", + "items": { + "type": "string" + }, + "type": "array" } }, "required": [ + "id", + "category", "has_attribute_type" ], "title": "GenotypicSex", @@ -8896,7 +9246,7 @@ "has_attribute": { "description": "connects any entity to an attribute", "items": { - "$ref": "#/$defs/Attribute" + "type": "string" }, "type": "array" }, @@ -8967,7 +9317,7 @@ "has_attribute": { "description": "connects any entity to an attribute", "items": { - "$ref": "#/$defs/Attribute" + "type": "string" }, "type": "array" }, @@ -9043,7 +9393,7 @@ "has_attribute": { "description": "may often be an organism attribute", "items": { - "$ref": "#/$defs/Attribute" + "type": "string" }, "type": "array" }, @@ -9113,7 +9463,7 @@ "has_attribute": { "description": "connects any entity to an attribute", "items": { - "$ref": "#/$defs/Attribute" + "type": "string" }, "type": "array" }, @@ -9187,7 +9537,7 @@ "has_attribute": { "description": "connects any entity to an attribute", "items": { - "$ref": "#/$defs/Attribute" + "type": "string" }, "type": "array" }, @@ -9258,7 +9608,7 @@ "has_attribute": { "description": "may often be an organism attribute", "items": { - "$ref": "#/$defs/Attribute" + "type": "string" }, "type": "array" }, @@ -9334,7 +9684,7 @@ "has_attribute": { "description": "connects any entity to an attribute", "items": { - "$ref": "#/$defs/Attribute" + "type": "string" }, "type": "array" }, @@ -9394,7 +9744,7 @@ "qualifiers": { "description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": { - "$ref": "#/$defs/OntologyClass" + "type": "string" }, "type": "array" }, @@ -9446,7 +9796,7 @@ "has_attribute": { "description": "connects any entity to an attribute", "items": { - "$ref": "#/$defs/Attribute" + "type": "string" }, "type": "array" }, @@ -9500,9 +9850,28 @@ "additionalProperties": false, "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": { + "category": { + "description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", + "items": { + "type": "string" + }, + "pattern": "^biolink:\\d+$", + "type": "array" + }, + "description": { + "description": "a human-readable description of an entity", + "type": "string" + }, + "has_attribute": { + "description": "connects any entity to an attribute", + "items": { + "type": "string" + }, + "type": "array" + }, "has_attribute_type": { - "$ref": "#/$defs/OntologyClass", - "description": "connects an attribute to a class that describes it" + "description": "connects an attribute to a class that describes it", + "type": "string" }, "has_qualitative_value": { "description": "connects an attribute to a value", @@ -9515,6 +9884,10 @@ }, "type": "array" }, + "id": { + "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", + "type": "string" + }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string" @@ -9523,11 +9896,30 @@ "description": "The human-readable 'attribute name' can be set to a string which reflects its context of interpretation, e.g. SEPIO evidence/provenance/confidence annotation or it can default to the name associated with the 'has attribute type' slot ontology term.", "type": "string" }, + "provided_by": { + "description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", + "items": { + "type": "string" + }, + "type": "array" + }, "source": { "type": "string" + }, + "type": { + "type": "string" + }, + "xref": { + "description": "Alternate CURIEs for a thing", + "items": { + "type": "string" + }, + "type": "array" } }, "required": [ + "id", + "category", "has_attribute_type" ], "title": "Inheritance", @@ -9552,7 +9944,7 @@ "has_attribute": { "description": "may often be an organism attribute", "items": { - "$ref": "#/$defs/Attribute" + "type": "string" }, "type": "array" }, @@ -9638,7 +10030,7 @@ "has_attribute": { "description": "connects any entity to an attribute", "items": { - "$ref": "#/$defs/Attribute" + "type": "string" }, "type": "array" }, @@ -9698,7 +10090,7 @@ "qualifiers": { "description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": { - "$ref": "#/$defs/OntologyClass" + "type": "string" }, "type": "array" }, @@ -9748,7 +10140,7 @@ "has_attribute": { "description": "connects any entity to an attribute", "items": { - "$ref": "#/$defs/Attribute" + "type": "string" }, "type": "array" }, @@ -9808,7 +10200,7 @@ "qualifiers": { "description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": { - "$ref": "#/$defs/OntologyClass" + "type": "string" }, "type": "array" }, @@ -9858,7 +10250,7 @@ "has_attribute": { "description": "connects any entity to an attribute", "items": { - "$ref": "#/$defs/Attribute" + "type": "string" }, "type": "array" }, @@ -9918,7 +10310,7 @@ "qualifiers": { "description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": { - "$ref": "#/$defs/OntologyClass" + "type": "string" }, "type": "array" }, @@ -9968,14 +10360,14 @@ "has_attribute": { "description": "connects any entity to an attribute", "items": { - "$ref": "#/$defs/Attribute" + "type": "string" }, "type": "array" }, "has_chemical_role": { "description": "\tA role is particular behaviour which a material entity may exhibit.", "items": { - "$ref": "#/$defs/ChemicalRole" + "type": "string" }, "type": "array" }, @@ -10048,7 +10440,7 @@ "has_attribute": { "description": "connects any entity to an attribute", "items": { - "$ref": "#/$defs/Attribute" + "type": "string" }, "type": "array" }, @@ -10117,7 +10509,7 @@ "has_attribute": { "description": "connects any entity to an attribute", "items": { - "$ref": "#/$defs/Attribute" + "type": "string" }, "type": "array" }, @@ -10177,7 +10569,7 @@ "qualifiers": { "description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": { - "$ref": "#/$defs/OntologyClass" + "type": "string" }, "type": "array" }, @@ -10227,7 +10619,7 @@ "has_attribute": { "description": "connects any entity to an attribute", "items": { - "$ref": "#/$defs/Attribute" + "type": "string" }, "type": "array" }, @@ -10287,7 +10679,7 @@ "qualifiers": { "description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": { - "$ref": "#/$defs/OntologyClass" + "type": "string" }, "type": "array" }, @@ -10337,7 +10729,7 @@ "has_attribute": { "description": "connects any entity to an attribute", "items": { - "$ref": "#/$defs/Attribute" + "type": "string" }, "type": "array" }, @@ -10348,7 +10740,7 @@ "has_chemical_role": { "description": "\tA role is particular behaviour which a material entity may exhibit.", "items": { - "$ref": "#/$defs/ChemicalRole" + "type": "string" }, "type": "array" }, @@ -10445,14 +10837,14 @@ "has_attribute": { "description": "connects any entity to an attribute", "items": { - "$ref": "#/$defs/Attribute" + "type": "string" }, "type": "array" }, "has_chemical_role": { "description": "\tA role is particular behaviour which a material entity may exhibit.", "items": { - "$ref": "#/$defs/ChemicalRole" + "type": "string" }, "type": "array" }, @@ -10532,7 +10924,7 @@ "has_attribute": { "description": "connects any entity to an attribute", "items": { - "$ref": "#/$defs/Attribute" + "type": "string" }, "type": "array" }, @@ -10615,7 +11007,7 @@ "has_attribute": { "description": "connects any entity to an attribute", "items": { - "$ref": "#/$defs/Attribute" + "type": "string" }, "type": "array" }, @@ -10675,7 +11067,7 @@ "qualifiers": { "description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": { - "$ref": "#/$defs/OntologyClass" + "type": "string" }, "type": "array" }, @@ -10725,7 +11117,7 @@ "has_attribute": { "description": "connects any entity to an attribute", "items": { - "$ref": "#/$defs/Attribute" + "type": "string" }, "type": "array" }, @@ -10785,7 +11177,7 @@ "qualifiers": { "description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": { - "$ref": "#/$defs/OntologyClass" + "type": "string" }, "type": "array" }, @@ -10835,14 +11227,14 @@ "has_attribute": { "description": "connects any entity to an attribute", "items": { - "$ref": "#/$defs/Attribute" + "type": "string" }, "type": "array" }, "has_chemical_role": { "description": "\tA role is particular behaviour which a material entity may exhibit.", "items": { - "$ref": "#/$defs/ChemicalRole" + "type": "string" }, "type": "array" }, @@ -10929,14 +11321,14 @@ "has_attribute": { "description": "connects any entity to an attribute", "items": { - "$ref": "#/$defs/Attribute" + "type": "string" }, "type": "array" }, "has_chemical_role": { "description": "\tA role is particular behaviour which a material entity may exhibit.", "items": { - "$ref": "#/$defs/ChemicalRole" + "type": "string" }, "type": "array" }, @@ -11031,7 +11423,7 @@ "has_attribute": { "description": "connects any entity to an attribute", "items": { - "$ref": "#/$defs/Attribute" + "type": "string" }, "type": "array" }, @@ -11100,7 +11492,7 @@ "has_attribute": { "description": "connects any entity to an attribute", "items": { - "$ref": "#/$defs/Attribute" + "type": "string" }, "type": "array" }, @@ -11111,7 +11503,7 @@ "has_chemical_role": { "description": "\tA role is particular behaviour which a material entity may exhibit.", "items": { - "$ref": "#/$defs/ChemicalRole" + "type": "string" }, "type": "array" }, @@ -11208,7 +11600,7 @@ "has_attribute": { "description": "connects any entity to an attribute", "items": { - "$ref": "#/$defs/Attribute" + "type": "string" }, "type": "array" }, @@ -11219,7 +11611,7 @@ "has_chemical_role": { "description": "\tA role is particular behaviour which a material entity may exhibit.", "items": { - "$ref": "#/$defs/ChemicalRole" + "type": "string" }, "type": "array" }, @@ -11303,7 +11695,7 @@ "has_attribute": { "description": "connects any entity to an attribute", "items": { - "$ref": "#/$defs/Attribute" + "type": "string" }, "type": "array" }, @@ -11372,14 +11764,14 @@ "has_attribute": { "description": "connects any entity to an attribute", "items": { - "$ref": "#/$defs/Attribute" + "type": "string" }, "type": "array" }, "has_chemical_role": { "description": "\tA role is particular behaviour which a material entity may exhibit.", "items": { - "$ref": "#/$defs/ChemicalRole" + "type": "string" }, "type": "array" }, @@ -11437,9 +11829,28 @@ "additionalProperties": false, "description": "The age group in which (disease) symptom manifestations appear", "properties": { + "category": { + "description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", + "items": { + "type": "string" + }, + "pattern": "^biolink:\\d+$", + "type": "array" + }, + "description": { + "description": "a human-readable description of an entity", + "type": "string" + }, + "has_attribute": { + "description": "connects any entity to an attribute", + "items": { + "type": "string" + }, + "type": "array" + }, "has_attribute_type": { - "$ref": "#/$defs/OntologyClass", - "description": "connects an attribute to a class that describes it" + "description": "connects an attribute to a class that describes it", + "type": "string" }, "has_qualitative_value": { "description": "connects an attribute to a value", @@ -11452,6 +11863,10 @@ }, "type": "array" }, + "id": { + "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", + "type": "string" + }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string" @@ -11460,11 +11875,30 @@ "description": "The human-readable 'attribute name' can be set to a string which reflects its context of interpretation, e.g. SEPIO evidence/provenance/confidence annotation or it can default to the name associated with the 'has attribute type' slot ontology term.", "type": "string" }, + "provided_by": { + "description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", + "items": { + "type": "string" + }, + "type": "array" + }, "source": { "type": "string" + }, + "type": { + "type": "string" + }, + "xref": { + "description": "Alternate CURIEs for a thing", + "items": { + "type": "string" + }, + "type": "array" } }, "required": [ + "id", + "category", "has_attribute_type" ], "title": "Onset", @@ -11474,9 +11908,28 @@ "additionalProperties": false, "description": "describes a characteristic of an organismal entity.", "properties": { + "category": { + "description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", + "items": { + "type": "string" + }, + "pattern": "^biolink:\\d+$", + "type": "array" + }, + "description": { + "description": "a human-readable description of an entity", + "type": "string" + }, + "has_attribute": { + "description": "connects any entity to an attribute", + "items": { + "type": "string" + }, + "type": "array" + }, "has_attribute_type": { - "$ref": "#/$defs/OntologyClass", - "description": "connects an attribute to a class that describes it" + "description": "connects an attribute to a class that describes it", + "type": "string" }, "has_qualitative_value": { "description": "connects an attribute to a value", @@ -11489,6 +11942,10 @@ }, "type": "array" }, + "id": { + "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", + "type": "string" + }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string" @@ -11497,11 +11954,30 @@ "description": "The human-readable 'attribute name' can be set to a string which reflects its context of interpretation, e.g. SEPIO evidence/provenance/confidence annotation or it can default to the name associated with the 'has attribute type' slot ontology term.", "type": "string" }, + "provided_by": { + "description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", + "items": { + "type": "string" + }, + "type": "array" + }, "source": { "type": "string" + }, + "type": { + "type": "string" + }, + "xref": { + "description": "Alternate CURIEs for a thing", + "items": { + "type": "string" + }, + "type": "array" } }, "required": [ + "id", + "category", "has_attribute_type" ], "title": "OrganismAttribute", @@ -11526,12 +12002,12 @@ "has_attribute": { "description": "connects any entity to an attribute", "items": { - "$ref": "#/$defs/Attribute" + "type": "string" }, "type": "array" }, "has_taxonomic_rank": { - "$ref": "#/$defs/TaxonomicRank" + "type": "string" }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", @@ -11602,7 +12078,7 @@ "has_attribute": { "description": "connects any entity to an attribute", "items": { - "$ref": "#/$defs/Attribute" + "type": "string" }, "type": "array" }, @@ -11662,7 +12138,7 @@ "qualifiers": { "description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": { - "$ref": "#/$defs/OntologyClass" + "type": "string" }, "type": "array" }, @@ -11712,7 +12188,7 @@ "has_attribute": { "description": "connects any entity to an attribute", "items": { - "$ref": "#/$defs/Attribute" + "type": "string" }, "type": "array" }, @@ -11772,7 +12248,7 @@ "qualifiers": { "description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": { - "$ref": "#/$defs/OntologyClass" + "type": "string" }, "type": "array" }, @@ -11822,7 +12298,7 @@ "has_attribute": { "description": "connects any entity to an attribute", "items": { - "$ref": "#/$defs/Attribute" + "type": "string" }, "type": "array" }, @@ -11882,7 +12358,7 @@ "qualifiers": { "description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": { - "$ref": "#/$defs/OntologyClass" + "type": "string" }, "type": "array" }, @@ -11936,7 +12412,7 @@ "has_attribute": { "description": "connects any entity to an attribute", "items": { - "$ref": "#/$defs/Attribute" + "type": "string" }, "type": "array" }, @@ -11975,8 +12451,8 @@ "type": "string" }, "onset_qualifier": { - "$ref": "#/$defs/Onset", - "description": "a qualifier used in a phenotypic association to state when the phenotype appears is in the subject" + "description": "a qualifier used in a phenotypic association to state when the phenotype appears is in the subject", + "type": "string" }, "original_knowledge_source": { "description": "The Information Resource that created the original record of the knowledge expressed in an Association (e.g. via curation of the knowledge from the literature, or generation of the knowledge de novo through computation, reasoning, inference over data).", @@ -12000,13 +12476,13 @@ "qualifiers": { "description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": { - "$ref": "#/$defs/OntologyClass" + "type": "string" }, "type": "array" }, "severity_qualifier": { - "$ref": "#/$defs/SeverityValue", - "description": "a qualifier used in a phenotypic association to state how severe the phenotype is in the subject" + "description": "a qualifier used in a phenotypic association to state how severe the phenotype is in the subject", + "type": "string" }, "source": { "type": "string" @@ -12054,7 +12530,7 @@ "has_attribute": { "description": "connects any entity to an attribute", "items": { - "$ref": "#/$defs/Attribute" + "type": "string" }, "type": "array" }, @@ -12114,7 +12590,7 @@ "qualifiers": { "description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": { - "$ref": "#/$defs/OntologyClass" + "type": "string" }, "type": "array" }, @@ -12164,7 +12640,7 @@ "has_attribute": { "description": "connects any entity to an attribute", "items": { - "$ref": "#/$defs/Attribute" + "type": "string" }, "type": "array" }, @@ -12180,7 +12656,7 @@ "type": "string" }, "interacting_molecules_category": { - "$ref": "#/$defs/OntologyClass" + "type": "string" }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", @@ -12227,7 +12703,7 @@ "qualifiers": { "description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": { - "$ref": "#/$defs/OntologyClass" + "type": "string" }, "type": "array" }, @@ -12293,7 +12769,7 @@ "has_attribute": { "description": "may often be an organism attribute", "items": { - "$ref": "#/$defs/Attribute" + "type": "string" }, "type": "array" }, @@ -12370,7 +12846,7 @@ "has_attribute": { "description": "connects any entity to an attribute", "items": { - "$ref": "#/$defs/Attribute" + "type": "string" }, "type": "array" }, @@ -12476,7 +12952,7 @@ "has_attribute": { "description": "connects any entity to an attribute", "items": { - "$ref": "#/$defs/Attribute" + "type": "string" }, "type": "array" }, @@ -12563,7 +13039,7 @@ "has_attribute": { "description": "connects any entity to an attribute", "items": { - "$ref": "#/$defs/Attribute" + "type": "string" }, "type": "array" }, @@ -12626,7 +13102,7 @@ "has_attribute": { "description": "connects any entity to an attribute", "items": { - "$ref": "#/$defs/Attribute" + "type": "string" }, "type": "array" }, @@ -12681,9 +13157,28 @@ "additionalProperties": false, "description": "A property of a phenotype", "properties": { + "category": { + "description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", + "items": { + "type": "string" + }, + "pattern": "^biolink:\\d+$", + "type": "array" + }, + "description": { + "description": "a human-readable description of an entity", + "type": "string" + }, + "has_attribute": { + "description": "connects any entity to an attribute", + "items": { + "type": "string" + }, + "type": "array" + }, "has_attribute_type": { - "$ref": "#/$defs/OntologyClass", - "description": "connects an attribute to a class that describes it" + "description": "connects an attribute to a class that describes it", + "type": "string" }, "has_qualitative_value": { "description": "connects an attribute to a value", @@ -12696,6 +13191,10 @@ }, "type": "array" }, + "id": { + "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", + "type": "string" + }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string" @@ -12704,11 +13203,30 @@ "description": "The human-readable 'attribute name' can be set to a string which reflects its context of interpretation, e.g. SEPIO evidence/provenance/confidence annotation or it can default to the name associated with the 'has attribute type' slot ontology term.", "type": "string" }, + "provided_by": { + "description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", + "items": { + "type": "string" + }, + "type": "array" + }, "source": { "type": "string" + }, + "type": { + "type": "string" + }, + "xref": { + "description": "Alternate CURIEs for a thing", + "items": { + "type": "string" + }, + "type": "array" } }, "required": [ + "id", + "category", "has_attribute_type" ], "title": "PhenotypicQuality", @@ -12718,9 +13236,28 @@ "additionalProperties": false, "description": "An attribute corresponding to the phenotypic sex of the individual, based upon the reproductive organs present.", "properties": { + "category": { + "description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", + "items": { + "type": "string" + }, + "pattern": "^biolink:\\d+$", + "type": "array" + }, + "description": { + "description": "a human-readable description of an entity", + "type": "string" + }, + "has_attribute": { + "description": "connects any entity to an attribute", + "items": { + "type": "string" + }, + "type": "array" + }, "has_attribute_type": { - "$ref": "#/$defs/OntologyClass", - "description": "connects an attribute to a class that describes it" + "description": "connects an attribute to a class that describes it", + "type": "string" }, "has_qualitative_value": { "description": "connects an attribute to a value", @@ -12733,6 +13270,10 @@ }, "type": "array" }, + "id": { + "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", + "type": "string" + }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string" @@ -12741,11 +13282,30 @@ "description": "The human-readable 'attribute name' can be set to a string which reflects its context of interpretation, e.g. SEPIO evidence/provenance/confidence annotation or it can default to the name associated with the 'has attribute type' slot ontology term.", "type": "string" }, + "provided_by": { + "description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", + "items": { + "type": "string" + }, + "type": "array" + }, "source": { "type": "string" + }, + "type": { + "type": "string" + }, + "xref": { + "description": "Alternate CURIEs for a thing", + "items": { + "type": "string" + }, + "type": "array" } }, "required": [ + "id", + "category", "has_attribute_type" ], "title": "PhenotypicSex", @@ -12770,7 +13330,7 @@ "has_attribute": { "description": "connects any entity to an attribute", "items": { - "$ref": "#/$defs/Attribute" + "type": "string" }, "type": "array" }, @@ -12840,7 +13400,7 @@ "has_attribute": { "description": "connects any entity to an attribute", "items": { - "$ref": "#/$defs/Attribute" + "type": "string" }, "type": "array" }, @@ -12917,7 +13477,7 @@ "has_attribute": { "description": "connects any entity to an attribute", "items": { - "$ref": "#/$defs/Attribute" + "type": "string" }, "type": "array" }, @@ -12980,7 +13540,7 @@ "has_attribute": { "description": "connects any entity to an attribute", "items": { - "$ref": "#/$defs/Attribute" + "type": "string" }, "type": "array" }, @@ -13050,7 +13610,7 @@ "has_attribute": { "description": "may often be an organism attribute", "items": { - "$ref": "#/$defs/Attribute" + "type": "string" }, "type": "array" }, @@ -13126,7 +13686,7 @@ "has_attribute": { "description": "connects any entity to an attribute", "items": { - "$ref": "#/$defs/Attribute" + "type": "string" }, "type": "array" }, @@ -13186,7 +13746,7 @@ "qualifiers": { "description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": { - "$ref": "#/$defs/OntologyClass" + "type": "string" }, "type": "array" }, @@ -13243,7 +13803,7 @@ "has_attribute": { "description": "connects any entity to an attribute", "items": { - "$ref": "#/$defs/Attribute" + "type": "string" }, "type": "array" }, @@ -13316,14 +13876,14 @@ "has_attribute": { "description": "connects any entity to an attribute", "items": { - "$ref": "#/$defs/Attribute" + "type": "string" }, "type": "array" }, "has_chemical_role": { "description": "\tA role is particular behaviour which a material entity may exhibit.", "items": { - "$ref": "#/$defs/ChemicalRole" + "type": "string" }, "type": "array" }, @@ -13410,7 +13970,7 @@ "has_attribute": { "description": "connects any entity to an attribute", "items": { - "$ref": "#/$defs/Attribute" + "type": "string" }, "type": "array" }, @@ -13487,7 +14047,7 @@ "has_attribute": { "description": "connects any entity to an attribute", "items": { - "$ref": "#/$defs/Attribute" + "type": "string" }, "type": "array" }, @@ -13557,7 +14117,7 @@ "has_attribute": { "description": "connects any entity to an attribute", "items": { - "$ref": "#/$defs/Attribute" + "type": "string" }, "type": "array" }, @@ -13627,7 +14187,7 @@ "has_attribute": { "description": "connects any entity to an attribute", "items": { - "$ref": "#/$defs/Attribute" + "type": "string" }, "type": "array" }, @@ -13719,7 +14279,7 @@ "has_attribute": { "description": "connects any entity to an attribute", "items": { - "$ref": "#/$defs/Attribute" + "type": "string" }, "type": "array" }, @@ -13838,7 +14398,7 @@ "has_attribute": { "description": "connects any entity to an attribute", "items": { - "$ref": "#/$defs/Attribute" + "type": "string" }, "type": "array" }, @@ -13849,7 +14409,7 @@ "has_chemical_role": { "description": "\tA role is particular behaviour which a material entity may exhibit.", "items": { - "$ref": "#/$defs/ChemicalRole" + "type": "string" }, "type": "array" }, @@ -13946,7 +14506,7 @@ "has_attribute": { "description": "connects any entity to an attribute", "items": { - "$ref": "#/$defs/Attribute" + "type": "string" }, "type": "array" }, @@ -13957,7 +14517,7 @@ "has_chemical_role": { "description": "\tA role is particular behaviour which a material entity may exhibit.", "items": { - "$ref": "#/$defs/ChemicalRole" + "type": "string" }, "type": "array" }, @@ -14074,7 +14634,7 @@ "has_attribute": { "description": "connects any entity to an attribute", "items": { - "$ref": "#/$defs/Attribute" + "type": "string" }, "type": "array" }, @@ -14134,7 +14694,7 @@ "qualifiers": { "description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": { - "$ref": "#/$defs/OntologyClass" + "type": "string" }, "type": "array" }, @@ -14196,7 +14756,7 @@ "has_attribute": { "description": "connects any entity to an attribute", "items": { - "$ref": "#/$defs/Attribute" + "type": "string" }, "type": "array" }, @@ -14256,7 +14816,7 @@ "qualifiers": { "description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": { - "$ref": "#/$defs/OntologyClass" + "type": "string" }, "type": "array" }, @@ -14312,7 +14872,7 @@ "has_attribute": { "description": "connects any entity to an attribute", "items": { - "$ref": "#/$defs/Attribute" + "type": "string" }, "type": "array" }, @@ -14370,8 +14930,15 @@ "RelationshipType": { "additionalProperties": false, "description": "An OWL property used as an edge label", - "properties": {}, - "required": [], + "properties": { + "id": { + "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", + "type": "string" + } + }, + "required": [ + "id" + ], "title": "RelationshipType", "type": "object" }, @@ -14400,7 +14967,7 @@ "has_attribute": { "description": "connects any entity to an attribute", "items": { - "$ref": "#/$defs/Attribute" + "type": "string" }, "type": "array" }, @@ -14460,7 +15027,7 @@ "qualifiers": { "description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": { - "$ref": "#/$defs/OntologyClass" + "type": "string" }, "type": "array" }, @@ -14519,7 +15086,7 @@ "has_attribute": { "description": "connects any entity to an attribute", "items": { - "$ref": "#/$defs/Attribute" + "type": "string" }, "type": "array" }, @@ -14579,7 +15146,7 @@ "qualifiers": { "description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": { - "$ref": "#/$defs/OntologyClass" + "type": "string" }, "type": "array" }, @@ -14623,7 +15190,7 @@ "has_attribute": { "description": "connects any entity to an attribute", "items": { - "$ref": "#/$defs/Attribute" + "type": "string" }, "type": "array" }, @@ -14719,7 +15286,7 @@ "has_attribute": { "description": "connects any entity to an attribute", "items": { - "$ref": "#/$defs/Attribute" + "type": "string" }, "type": "array" }, @@ -14812,9 +15379,28 @@ "additionalProperties": false, "description": "describes the severity of a phenotypic feature or disease", "properties": { + "category": { + "description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", + "items": { + "type": "string" + }, + "pattern": "^biolink:\\d+$", + "type": "array" + }, + "description": { + "description": "a human-readable description of an entity", + "type": "string" + }, + "has_attribute": { + "description": "connects any entity to an attribute", + "items": { + "type": "string" + }, + "type": "array" + }, "has_attribute_type": { - "$ref": "#/$defs/OntologyClass", - "description": "connects an attribute to a class that describes it" + "description": "connects an attribute to a class that describes it", + "type": "string" }, "has_qualitative_value": { "description": "connects an attribute to a value", @@ -14827,6 +15413,10 @@ }, "type": "array" }, + "id": { + "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", + "type": "string" + }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string" @@ -14835,11 +15425,30 @@ "description": "The human-readable 'attribute name' can be set to a string which reflects its context of interpretation, e.g. SEPIO evidence/provenance/confidence annotation or it can default to the name associated with the 'has attribute type' slot ontology term.", "type": "string" }, + "provided_by": { + "description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", + "items": { + "type": "string" + }, + "type": "array" + }, "source": { "type": "string" + }, + "type": { + "type": "string" + }, + "xref": { + "description": "Alternate CURIEs for a thing", + "items": { + "type": "string" + }, + "type": "array" } }, "required": [ + "id", + "category", "has_attribute_type" ], "title": "SeverityValue", @@ -14870,7 +15479,7 @@ "has_attribute": { "description": "connects any entity to an attribute", "items": { - "$ref": "#/$defs/Attribute" + "type": "string" }, "type": "array" }, @@ -14881,7 +15490,7 @@ "has_chemical_role": { "description": "\tA role is particular behaviour which a material entity may exhibit.", "items": { - "$ref": "#/$defs/ChemicalRole" + "type": "string" }, "type": "array" }, @@ -14978,14 +15587,14 @@ "has_attribute": { "description": "connects any entity to an attribute", "items": { - "$ref": "#/$defs/Attribute" + "type": "string" }, "type": "array" }, "has_chemical_role": { "description": "\tA role is particular behaviour which a material entity may exhibit.", "items": { - "$ref": "#/$defs/ChemicalRole" + "type": "string" }, "type": "array" }, @@ -15062,7 +15671,7 @@ "has_attribute": { "description": "connects any entity to an attribute", "items": { - "$ref": "#/$defs/Attribute" + "type": "string" }, "type": "array" }, @@ -15128,9 +15737,28 @@ "additionalProperties": false, "description": "Attributes relating to a socioeconomic manifestation", "properties": { + "category": { + "description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", + "items": { + "type": "string" + }, + "pattern": "^biolink:\\d+$", + "type": "array" + }, + "description": { + "description": "a human-readable description of an entity", + "type": "string" + }, + "has_attribute": { + "description": "connects any entity to an attribute", + "items": { + "type": "string" + }, + "type": "array" + }, "has_attribute_type": { - "$ref": "#/$defs/OntologyClass", - "description": "connects an attribute to a class that describes it" + "description": "connects an attribute to a class that describes it", + "type": "string" }, "has_qualitative_value": { "description": "connects an attribute to a value", @@ -15143,6 +15771,10 @@ }, "type": "array" }, + "id": { + "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", + "type": "string" + }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string" @@ -15151,11 +15783,30 @@ "description": "The human-readable 'attribute name' can be set to a string which reflects its context of interpretation, e.g. SEPIO evidence/provenance/confidence annotation or it can default to the name associated with the 'has attribute type' slot ontology term.", "type": "string" }, + "provided_by": { + "description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", + "items": { + "type": "string" + }, + "type": "array" + }, "source": { "type": "string" + }, + "type": { + "type": "string" + }, + "xref": { + "description": "Alternate CURIEs for a thing", + "items": { + "type": "string" + }, + "type": "array" } }, "required": [ + "id", + "category", "has_attribute_type" ], "title": "SocioeconomicAttribute", @@ -15168,7 +15819,7 @@ "has_attribute": { "description": "connects any entity to an attribute", "items": { - "$ref": "#/$defs/SocioeconomicAttribute" + "type": "string" }, "type": "array" }, @@ -15222,7 +15873,7 @@ "has_attribute": { "description": "may often be an organism attribute", "items": { - "$ref": "#/$defs/Attribute" + "type": "string" }, "type": "array" }, @@ -15298,7 +15949,7 @@ "has_attribute": { "description": "connects any entity to an attribute", "items": { - "$ref": "#/$defs/Attribute" + "type": "string" }, "type": "array" }, @@ -15358,7 +16009,7 @@ "qualifiers": { "description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": { - "$ref": "#/$defs/OntologyClass" + "type": "string" }, "type": "array" }, @@ -15386,8 +16037,15 @@ "TaxonomicRank": { "additionalProperties": false, "description": "A descriptor for the rank within a taxonomic classification. Example instance: TAXRANK:0000017 (kingdom)", - "properties": {}, - "required": [], + "properties": { + "id": { + "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", + "type": "string" + } + }, + "required": [ + "id" + ], "title": "TaxonomicRank", "type": "object" }, @@ -15416,7 +16074,7 @@ "has_attribute": { "description": "connects any entity to an attribute", "items": { - "$ref": "#/$defs/Attribute" + "type": "string" }, "type": "array" }, @@ -15427,7 +16085,7 @@ "has_chemical_role": { "description": "\tA role is particular behaviour which a material entity may exhibit.", "items": { - "$ref": "#/$defs/ChemicalRole" + "type": "string" }, "type": "array" }, @@ -15517,7 +16175,7 @@ "has_attribute": { "description": "connects any entity to an attribute", "items": { - "$ref": "#/$defs/Attribute" + "type": "string" }, "type": "array" }, @@ -15577,7 +16235,7 @@ "qualifiers": { "description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": { - "$ref": "#/$defs/OntologyClass" + "type": "string" }, "type": "array" }, @@ -15621,7 +16279,7 @@ "has_attribute": { "description": "connects any entity to an attribute", "items": { - "$ref": "#/$defs/Attribute" + "type": "string" }, "type": "array" }, @@ -15691,6 +16349,14 @@ "title": "Treatment", "type": "object" }, + "UnclassifiedOntologyClass": { + "additionalProperties": false, + "description": "", + "properties": {}, + "required": [], + "title": "UnclassifiedOntologyClass", + "type": "object" + }, "VariantAsAModelOfDiseaseAssociation": { "additionalProperties": false, "description": "", @@ -15720,7 +16386,7 @@ "has_attribute": { "description": "connects any entity to an attribute", "items": { - "$ref": "#/$defs/Attribute" + "type": "string" }, "type": "array" }, @@ -15759,8 +16425,8 @@ "type": "string" }, "onset_qualifier": { - "$ref": "#/$defs/Onset", - "description": "a qualifier used in a phenotypic association to state when the phenotype appears is in the subject" + "description": "a qualifier used in a phenotypic association to state when the phenotype appears is in the subject", + "type": "string" }, "original_knowledge_source": { "description": "The Information Resource that created the original record of the knowledge expressed in an Association (e.g. via curation of the knowledge from the literature, or generation of the knowledge de novo through computation, reasoning, inference over data).", @@ -15784,13 +16450,13 @@ "qualifiers": { "description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": { - "$ref": "#/$defs/OntologyClass" + "type": "string" }, "type": "array" }, "severity_qualifier": { - "$ref": "#/$defs/SeverityValue", - "description": "a qualifier used in a phenotypic association to state how severe the phenotype is in the subject" + "description": "a qualifier used in a phenotypic association to state how severe the phenotype is in the subject", + "type": "string" }, "source": { "type": "string" @@ -15842,7 +16508,7 @@ "has_attribute": { "description": "connects any entity to an attribute", "items": { - "$ref": "#/$defs/Attribute" + "type": "string" }, "type": "array" }, @@ -15881,8 +16547,8 @@ "type": "string" }, "onset_qualifier": { - "$ref": "#/$defs/Onset", - "description": "a qualifier used in a phenotypic association to state when the phenotype appears is in the subject" + "description": "a qualifier used in a phenotypic association to state when the phenotype appears is in the subject", + "type": "string" }, "original_knowledge_source": { "description": "The Information Resource that created the original record of the knowledge expressed in an Association (e.g. via curation of the knowledge from the literature, or generation of the knowledge de novo through computation, reasoning, inference over data).", @@ -15906,13 +16572,13 @@ "qualifiers": { "description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": { - "$ref": "#/$defs/OntologyClass" + "type": "string" }, "type": "array" }, "severity_qualifier": { - "$ref": "#/$defs/SeverityValue", - "description": "a qualifier used in a phenotypic association to state how severe the phenotype is in the subject" + "description": "a qualifier used in a phenotypic association to state how severe the phenotype is in the subject", + "type": "string" }, "source": { "type": "string" @@ -15960,7 +16626,7 @@ "has_attribute": { "description": "connects any entity to an attribute", "items": { - "$ref": "#/$defs/Attribute" + "type": "string" }, "type": "array" }, @@ -16020,7 +16686,7 @@ "qualifiers": { "description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": { - "$ref": "#/$defs/OntologyClass" + "type": "string" }, "type": "array" }, @@ -16074,7 +16740,7 @@ "has_attribute": { "description": "connects any entity to an attribute", "items": { - "$ref": "#/$defs/Attribute" + "type": "string" }, "type": "array" }, @@ -16138,13 +16804,13 @@ "qualifiers": { "description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": { - "$ref": "#/$defs/OntologyClass" + "type": "string" }, "type": "array" }, "quantifier_qualifier": { - "$ref": "#/$defs/OntologyClass", - "description": "Optional quantitative value indicating degree of expression." + "description": "Optional quantitative value indicating degree of expression.", + "type": "string" }, "source": { "type": "string" @@ -16200,7 +16866,7 @@ "has_attribute": { "description": "connects any entity to an attribute", "items": { - "$ref": "#/$defs/Attribute" + "type": "string" }, "type": "array" }, @@ -16239,8 +16905,8 @@ "type": "string" }, "onset_qualifier": { - "$ref": "#/$defs/Onset", - "description": "a qualifier used in a phenotypic association to state when the phenotype appears is in the subject" + "description": "a qualifier used in a phenotypic association to state when the phenotype appears is in the subject", + "type": "string" }, "original_knowledge_source": { "description": "The Information Resource that created the original record of the knowledge expressed in an Association (e.g. via curation of the knowledge from the literature, or generation of the knowledge de novo through computation, reasoning, inference over data).", @@ -16264,17 +16930,17 @@ "qualifiers": { "description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": { - "$ref": "#/$defs/OntologyClass" + "type": "string" }, "type": "array" }, "severity_qualifier": { - "$ref": "#/$defs/SeverityValue", - "description": "a qualifier used in a phenotypic association to state how severe the phenotype is in the subject" + "description": "a qualifier used in a phenotypic association to state how severe the phenotype is in the subject", + "type": "string" }, "sex_qualifier": { - "$ref": "#/$defs/BiologicalSex", - "description": "a qualifier used in a phenotypic association to state whether the association is specific to a particular sex." + "description": "a qualifier used in a phenotypic association to state whether the association is specific to a particular sex.", + "type": "string" }, "source": { "type": "string" @@ -16326,7 +16992,7 @@ "has_attribute": { "description": "connects any entity to an attribute", "items": { - "$ref": "#/$defs/Attribute" + "type": "string" }, "type": "array" }, @@ -16402,7 +17068,7 @@ "qualifiers": { "description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": { - "$ref": "#/$defs/OntologyClass" + "type": "string" }, "type": "array" }, @@ -16452,14 +17118,14 @@ "has_attribute": { "description": "connects any entity to an attribute", "items": { - "$ref": "#/$defs/Attribute" + "type": "string" }, "type": "array" }, "has_chemical_role": { "description": "\tA role is particular behaviour which a material entity may exhibit.", "items": { - "$ref": "#/$defs/ChemicalRole" + "type": "string" }, "type": "array" }, @@ -16517,9 +17183,28 @@ "additionalProperties": false, "description": "", "properties": { + "category": { + "description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", + "items": { + "type": "string" + }, + "pattern": "^biolink:\\d+$", + "type": "array" + }, + "description": { + "description": "a human-readable description of an entity", + "type": "string" + }, + "has_attribute": { + "description": "connects any entity to an attribute", + "items": { + "type": "string" + }, + "type": "array" + }, "has_attribute_type": { - "$ref": "#/$defs/OntologyClass", - "description": "connects an attribute to a class that describes it" + "description": "connects an attribute to a class that describes it", + "type": "string" }, "has_qualitative_value": { "description": "connects an attribute to a value", @@ -16532,6 +17217,10 @@ }, "type": "array" }, + "id": { + "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", + "type": "string" + }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string" @@ -16540,11 +17229,30 @@ "description": "The human-readable 'attribute name' can be set to a string which reflects its context of interpretation, e.g. SEPIO evidence/provenance/confidence annotation or it can default to the name associated with the 'has attribute type' slot ontology term.", "type": "string" }, + "provided_by": { + "description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", + "items": { + "type": "string" + }, + "type": "array" + }, "source": { "type": "string" + }, + "type": { + "type": "string" + }, + "xref": { + "description": "Alternate CURIEs for a thing", + "items": { + "type": "string" + }, + "type": "array" } }, "required": [ + "id", + "category", "has_attribute_type" ], "title": "Zygosity", @@ -16559,6 +17267,6 @@ "required": [], "title": "Biolink-Model", "type": "object", - "version": "2.3.1" + "version": "2.4.0" } diff --git a/prefix-map/biolink-model-prefix-map.json b/prefix-map/biolink-model-prefix-map.json index dade1ba786..ba2a6a90ab 100644 --- a/prefix-map/biolink-model-prefix-map.json +++ b/prefix-map/biolink-model-prefix-map.json @@ -225,8 +225,8 @@ "fabio": "http://purl.org/spar/fabio/", "faldo": "http://biohackathon.org/resource/faldo#", "foaf": "http://xmlns.com/foaf/0.1/", - "foodb.compound": "http://foodb.ca/compounds/", - "foodb.food": "http://example.org/UNKNOWN/foodb.food/", + "foodb.compound": "http://foodb.ca/foods/", + "foodb.food": "http://foodb.ca/compounds/", "gff3": "https://github.com/The-Sequence-Ontology/Specifications/blob/master/gff3.md#", "gpi": "https://github.com/geneontology/go-annotation/blob/master/specs/gpad-gpi-2-0.md#", "gtpo": "https://rdf.guidetopharmacology.org/ns/gtpo#",