diff --git a/erdiagram-autogen/kbmodel.md b/erdiagram-autogen/kbmodel.md index 2e9df27d..a1da6f22 100644 --- a/erdiagram-autogen/kbmodel.md +++ b/erdiagram-autogen/kbmodel.md @@ -1,9 +1,22 @@ ```mermaid erDiagram LibraryPool { - integer tube_avg_size + integer avg_size_bp float tube_contents - string tube_internal_label + string id + iri_type iri + category_typeList category + stringList type + label_type name + narrative_text description +} +Agent { + uriorcurieList affiliation + string address + stringList provided_by + uriorcurieList xref + label_type full_name + label_typeList synonym string id iri_type iri category_typeList category @@ -47,9 +60,9 @@ LibraryAliquoting { Library { string method datetime creation_date - integer avg_size - float input_amount - boolean library_prep_pass + float input_quantity + boolean process_pass + integer avg_size_bp float quantification_fmol float quantification_ng float quantification_nm @@ -78,10 +91,10 @@ LibraryConstruction { } AmplifiedCdna { string method - float amplified_quantity + float input_quantity + boolean process_pass integer pcr_cycles float percent_cdna_longer_than_400bp - boolean rna_amplification_pass string id iri_type iri category_typeList category @@ -146,7 +159,7 @@ CellEnrichment { DissociatedCellSample { string cell_prep_type string facs_population_plan - integer number_of_cells_collected + integer num_cells_collected string id iri_type iri category_typeList category @@ -168,7 +181,7 @@ CellDissociation { } TissueSample { string roi_plan - string region_of_interest_label + string roi_label string id iri_type iri category_typeList category @@ -189,7 +202,6 @@ TissueDissecting { narrative_text description } BrainSection { - string barcode integer ordinal string id iri_type iri @@ -211,7 +223,6 @@ BrainSegmentSectioning { narrative_text description } BrainSegment { - string barcode string anatomical_division string id iri_type iri @@ -234,17 +245,26 @@ BrainExtraction { } Donor { SexType sex - date date_of_birth - date date_of_death - string age_at_death + date birth_date + date death_date + string death_age string full_genotype label_type in_taxon_label + uriorcurieList affiliation + string address + stringList provided_by + uriorcurieList xref + label_type full_name + label_typeList synonym string id iri_type iri category_typeList category stringList type label_type name narrative_text description +} +ProvEntity { + } Activity { stringList provided_by @@ -265,9 +285,6 @@ Entity { stringList type label_type name narrative_text description -} -ProvEntity { - } ProvActivity { @@ -338,74 +355,95 @@ Checksum { LibraryPool ||--}o LibraryAliquot : "wasDerivedFrom" LibraryPool ||--}o LibraryPooling : "wasGeneratedBy" +LibraryPool ||--}o Agent : "wasAttributedTo" LibraryPool ||--}o Attribute : "has attribute" +Agent ||--}o Attribute : "has attribute" LibraryPooling ||--}o LibraryAliquot : "used" LibraryPooling ||--}o LibraryPool : "generated" +LibraryPooling ||--}o Agent : "wasAssociatedWith" LibraryPooling ||--}o Attribute : "has attribute" LibraryAliquot ||--}o Library : "wasDerivedFrom" LibraryAliquot ||--}o LibraryAliquoting : "wasGeneratedBy" +LibraryAliquot ||--}o Agent : "wasAttributedTo" LibraryAliquot ||--}o Attribute : "has attribute" LibraryAliquoting ||--}o Library : "used" LibraryAliquoting ||--}o LibraryAliquot : "generated" +LibraryAliquoting ||--}o Agent : "wasAssociatedWith" LibraryAliquoting ||--}o Attribute : "has attribute" Library ||--}o AmplifiedCdna : "wasDerivedFrom" Library ||--}o LibraryConstruction : "wasGeneratedBy" +Library ||--}o Agent : "wasAttributedTo" Library ||--}o Attribute : "has attribute" LibraryConstruction ||--}o AmplifiedCdna : "used" LibraryConstruction ||--}o Library : "generated" +LibraryConstruction ||--}o Agent : "wasAssociatedWith" LibraryConstruction ||--}o Attribute : "has attribute" AmplifiedCdna ||--}o BarcodedCellSample : "wasDerivedFrom" AmplifiedCdna ||--}o CdnaAmplification : "wasGeneratedBy" +AmplifiedCdna ||--}o Agent : "wasAttributedTo" AmplifiedCdna ||--}o Attribute : "has attribute" CdnaAmplification ||--}o BarcodedCellSample : "used" CdnaAmplification ||--}o AmplifiedCdna : "generated" +CdnaAmplification ||--}o Agent : "wasAssociatedWith" CdnaAmplification ||--}o Attribute : "has attribute" BarcodedCellSample ||--}o EnrichedCellSample : "wasDerivedFrom" BarcodedCellSample ||--}o CellBarcoding : "wasGeneratedBy" +BarcodedCellSample ||--}o Agent : "wasAttributedTo" BarcodedCellSample ||--}o Attribute : "has attribute" CellBarcoding ||--}o EnrichedCellSample : "used" CellBarcoding ||--}o BarcodedCellSample : "generated" +CellBarcoding ||--}o Agent : "wasAssociatedWith" CellBarcoding ||--}o Attribute : "has attribute" EnrichedCellSample ||--}o DissociatedCellSample : "wasDerivedFrom" EnrichedCellSample ||--}o CellEnrichment : "wasGeneratedBy" +EnrichedCellSample ||--}o Agent : "wasAttributedTo" EnrichedCellSample ||--}o Attribute : "has attribute" CellEnrichment ||--}o DissociatedCellSample : "used" CellEnrichment ||--}o EnrichedCellSample : "generated" +CellEnrichment ||--}o Agent : "wasAssociatedWith" CellEnrichment ||--}o Attribute : "has attribute" DissociatedCellSample ||--}o TissueSample : "wasDerivedFrom" DissociatedCellSample ||--}o CellDissociation : "wasGeneratedBy" +DissociatedCellSample ||--}o Agent : "wasAttributedTo" DissociatedCellSample ||--}o Attribute : "has attribute" CellDissociation ||--}o TissueSample : "used" CellDissociation ||--}o DissociatedCellSample : "generated" +CellDissociation ||--}o Agent : "wasAssociatedWith" CellDissociation ||--}o Attribute : "has attribute" TissueSample ||--}o BrainSection : "wasDerivedFrom" TissueSample ||--}o TissueDissecting : "wasGeneratedBy" +TissueSample ||--}o Agent : "wasAttributedTo" TissueSample ||--}o Attribute : "has attribute" TissueDissecting ||--}o BrainSection : "used" TissueDissecting ||--}o TissueSample : "generated" +TissueDissecting ||--}o Agent : "wasAssociatedWith" TissueDissecting ||--}o Attribute : "has attribute" BrainSection ||--}o BrainSegment : "wasDerivedFrom" BrainSection ||--}o BrainSegmentSectioning : "wasGeneratedBy" +BrainSection ||--}o Agent : "wasAttributedTo" BrainSection ||--}o Attribute : "has attribute" BrainSegmentSectioning ||--}o BrainSegment : "used" BrainSegmentSectioning ||--}o BrainSection : "generated" +BrainSegmentSectioning ||--}o Agent : "wasAssociatedWith" BrainSegmentSectioning ||--}o Attribute : "has attribute" BrainSegment ||--}o Donor : "wasDerivedFrom" BrainSegment ||--}o BrainExtraction : "wasGeneratedBy" +BrainSegment ||--}o Agent : "wasAttributedTo" BrainSegment ||--}o Attribute : "has attribute" BrainExtraction ||--}o Donor : "used" BrainExtraction ||--}o BrainSegment : "generated" +BrainExtraction ||--}o Agent : "wasAssociatedWith" BrainExtraction ||--}o Attribute : "has attribute" Donor ||--}o OrganismTaxon : "in taxon" -Donor ||--}o Entity : "wasDerivedFrom" -Donor ||--}o Activity : "wasGeneratedBy" Donor ||--}o Attribute : "has attribute" -Activity ||--}o Attribute : "has attribute" -Entity ||--}o Attribute : "has attribute" ProvEntity ||--}o Entity : "wasDerivedFrom" ProvEntity ||--}o Activity : "wasGeneratedBy" +ProvEntity ||--}o Agent : "wasAttributedTo" +Activity ||--}o Attribute : "has attribute" +Entity ||--}o Attribute : "has attribute" ProvActivity ||--}o Entity : "used" ProvActivity ||--}o Entity : "generated" +ProvActivity ||--}o Agent : "wasAssociatedWith" AnnotationCollection ||--}o GeneAnnotation : "annotations" AnnotationCollection ||--}o GenomeAnnotation : "genome_annotations" AnnotationCollection ||--}o GenomeAssembly : "genome_assemblies" diff --git a/json-schema-autogen/kbmodel.json b/json-schema-autogen/kbmodel.json index 2db0e351..13808c61 100644 --- a/json-schema-autogen/kbmodel.json +++ b/json-schema-autogen/kbmodel.json @@ -252,10 +252,6 @@ "additionalProperties": false, "description": "", "properties": { - "amplified_quantity": { - "description": "Amount of cDNA amplified (ng).", - "type": "number" - }, "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": { @@ -278,6 +274,10 @@ "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string" }, + "input_quantity": { + "description": "The amount of input cDNA (ng) amplified.", + "type": "number" + }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string" @@ -297,7 +297,8 @@ "description": "The percentage of cDNA fragments that are longer than 400bp.", "type": "number" }, - "rna_amplification_pass": { + "process_pass": { + "description": "Indicates whether the rna amplification process passed or failed.", "type": "boolean" }, "type": { @@ -306,6 +307,12 @@ }, "type": "array" }, + "wasAttributedTo": { + "items": { + "$ref": "#/$defs/Agent" + }, + "type": "array" + }, "wasDerivedFrom": { "items": { "$ref": "#/$defs/BarcodedCellSample" @@ -1349,6 +1356,12 @@ }, "type": "array" }, + "wasAttributedTo": { + "items": { + "$ref": "#/$defs/Agent" + }, + "type": "array" + }, "wasDerivedFrom": { "items": { "$ref": "#/$defs/EnrichedCellSample" @@ -2607,6 +2620,12 @@ }, "type": "array" }, + "wasAssociatedWith": { + "items": { + "$ref": "#/$defs/Agent" + }, + "type": "array" + }, "xref": { "description": "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.", "items": { @@ -2626,10 +2645,6 @@ "additionalProperties": false, "description": "", "properties": { - "barcode": { - "description": "The unique identifier of the object.", - "type": "string" - }, "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": { @@ -2670,6 +2685,12 @@ }, "type": "array" }, + "wasAttributedTo": { + "items": { + "$ref": "#/$defs/Agent" + }, + "type": "array" + }, "wasDerivedFrom": { "items": { "$ref": "#/$defs/BrainSegment" @@ -2696,10 +2717,6 @@ "anatomical_division": { "type": "string" }, - "barcode": { - "description": "The unique identifier of the object.", - "type": "string" - }, "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": { @@ -2736,6 +2753,12 @@ }, "type": "array" }, + "wasAttributedTo": { + "items": { + "$ref": "#/$defs/Agent" + }, + "type": "array" + }, "wasDerivedFrom": { "items": { "$ref": "#/$defs/Donor" @@ -2826,6 +2849,12 @@ }, "type": "array" }, + "wasAssociatedWith": { + "items": { + "$ref": "#/$defs/Agent" + }, + "type": "array" + }, "xref": { "description": "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.", "items": { @@ -3460,6 +3489,12 @@ }, "type": "array" }, + "wasAssociatedWith": { + "items": { + "$ref": "#/$defs/Agent" + }, + "type": "array" + }, "xref": { "description": "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.", "items": { @@ -3631,6 +3666,12 @@ }, "type": "array" }, + "wasAssociatedWith": { + "items": { + "$ref": "#/$defs/Agent" + }, + "type": "array" + }, "xref": { "description": "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.", "items": { @@ -3717,6 +3758,12 @@ }, "type": "array" }, + "wasAssociatedWith": { + "items": { + "$ref": "#/$defs/Agent" + }, + "type": "array" + }, "xref": { "description": "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.", "items": { @@ -3803,6 +3850,12 @@ }, "type": "array" }, + "wasAssociatedWith": { + "items": { + "$ref": "#/$defs/Agent" + }, + "type": "array" + }, "xref": { "description": "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.", "items": { @@ -10331,7 +10384,7 @@ "description": "A human-readable name for an attribute or entity.", "type": "string" }, - "number_of_cells_collected": { + "num_cells_collected": { "type": "integer" }, "type": { @@ -10340,6 +10393,12 @@ }, "type": "array" }, + "wasAttributedTo": { + "items": { + "$ref": "#/$defs/Agent" + }, + "type": "array" + }, "wasDerivedFrom": { "items": { "$ref": "#/$defs/TissueSample" @@ -10363,23 +10422,35 @@ "additionalProperties": false, "description": "A person or organism that is the source of a biological sample.", "properties": { - "age_at_death": { - "description": "The age of the donor at the time of death.", + "address": { + "description": "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(?).", "type": "string" }, - "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}", + "affiliation": { + "description": "a professional relationship between one provider (often a person) within another provider (often an organization). Target provider identity should be specified by a CURIE. Providers may have multiple affiliations.", "items": { "type": "string" }, "type": "array" }, - "date_of_birth": { + "birth_date": { "description": "The date of birth of the donor.", "format": "date", "type": "string" }, - "date_of_death": { + "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": { + "pattern": "^biolink:[A-Z][A-Za-z]+$", + "type": "string" + }, + "type": "array" + }, + "death_age": { + "description": "The age of the donor at the time of death (ISO 8601 format).", + "type": "string" + }, + "death_date": { "description": "The date of death of the donor.", "format": "date", "type": "string" @@ -10392,6 +10463,10 @@ "description": "The full genotype of the donor.", "type": "string" }, + "full_name": { + "description": "a long-form human readable name for a thing", + "type": "string" + }, "has_attribute": { "description": "connects any entity to an attribute", "items": { @@ -10400,7 +10475,7 @@ "type": "array" }, "id": { - "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", + "description": "Different classes of agents have distinct preferred identifiers. For publishers, use the ISBN publisher code. See https://grp.isbn-international.org/ for publisher code lookups. For editors, authors and individual providers, use the individual's ORCID if available; Otherwise, a ScopusID, ResearchID or Google Scholar ID ('GSID') may be used if the author ORCID is unknown. Institutional agents could be identified by an International Standard Name Identifier ('ISNI') code.", "type": "string" }, "in_taxon": { @@ -10419,33 +10494,43 @@ "type": "string" }, "name": { - "description": "A human-readable name for an attribute or entity.", + "description": "it is recommended that an author's 'name' property be formatted as \"surname, firstname initial.\"", "type": "string" }, + "provided_by": { + "description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", + "items": { + "type": "string" + }, + "type": "array" + }, "sex": { "$ref": "#/$defs/SexType" }, - "type": { + "synonym": { + "description": "Alternate human-readable names for a thing", "items": { "type": "string" }, "type": "array" }, - "wasDerivedFrom": { + "type": { "items": { - "$ref": "#/$defs/Entity" + "type": "string" }, "type": "array" }, - "wasGeneratedBy": { + "xref": { + "description": "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.", "items": { - "$ref": "#/$defs/Activity" + "type": "string" }, "type": "array" } }, "required": [ - "id" + "id", + "category" ], "title": "Donor", "type": "object" @@ -11364,6 +11449,12 @@ }, "type": "array" }, + "wasAttributedTo": { + "items": { + "$ref": "#/$defs/Agent" + }, + "type": "array" + }, "wasDerivedFrom": { "items": { "$ref": "#/$defs/DissociatedCellSample" @@ -19446,8 +19537,8 @@ "additionalProperties": false, "description": "", "properties": { - "avg_size": { - "description": "The average size (bp) of the library fragments. bp stands for base pairs.", + "avg_size_bp": { + "description": "The average size (bp) of the library fragments.", "type": "integer" }, "category": { @@ -19477,7 +19568,7 @@ "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string" }, - "input_amount": { + "input_quantity": { "description": "The amount of input material (ng) used to create the library.", "type": "number" }, @@ -19485,9 +19576,6 @@ "description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string" }, - "library_prep_pass": { - "type": "boolean" - }, "method": { "type": "string" }, @@ -19495,6 +19583,10 @@ "description": "A human-readable name for an attribute or entity.", "type": "string" }, + "process_pass": { + "description": "Indicates whether the library prep process passed or failed.", + "type": "boolean" + }, "quantification_fmol": { "type": "number" }, @@ -19522,6 +19614,12 @@ }, "type": "array" }, + "wasAttributedTo": { + "items": { + "$ref": "#/$defs/Agent" + }, + "type": "array" + }, "wasDerivedFrom": { "items": { "$ref": "#/$defs/AmplifiedCdna" @@ -19585,6 +19683,12 @@ }, "type": "array" }, + "wasAttributedTo": { + "items": { + "$ref": "#/$defs/Agent" + }, + "type": "array" + }, "wasDerivedFrom": { "items": { "$ref": "#/$defs/Library" @@ -19675,6 +19779,12 @@ }, "type": "array" }, + "wasAssociatedWith": { + "items": { + "$ref": "#/$defs/Agent" + }, + "type": "array" + }, "xref": { "description": "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.", "items": { @@ -19761,6 +19871,12 @@ }, "type": "array" }, + "wasAssociatedWith": { + "items": { + "$ref": "#/$defs/Agent" + }, + "type": "array" + }, "xref": { "description": "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.", "items": { @@ -19780,6 +19896,10 @@ "additionalProperties": false, "description": "", "properties": { + "avg_size_bp": { + "description": "The average size (bp) of the library fragments in the tube.", + "type": "integer" + }, "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": { @@ -19810,23 +19930,22 @@ "description": "A human-readable name for an attribute or entity.", "type": "string" }, - "tube_avg_size": { - "description": "The average size (bp) of the library fragments in the tube.", - "type": "integer" - }, "tube_contents": { "description": "The content concentration (nm).", "type": "number" }, - "tube_internal_label": { - "type": "string" - }, "type": { "items": { "type": "string" }, "type": "array" }, + "wasAttributedTo": { + "items": { + "$ref": "#/$defs/Agent" + }, + "type": "array" + }, "wasDerivedFrom": { "items": { "$ref": "#/$defs/LibraryAliquot" @@ -19917,6 +20036,12 @@ }, "type": "array" }, + "wasAssociatedWith": { + "items": { + "$ref": "#/$defs/Agent" + }, + "type": "array" + }, "xref": { "description": "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.", "items": { @@ -26941,46 +27066,6 @@ "title": "ProteinIsoform", "type": "object" }, - "ProvActivity": { - "additionalProperties": false, - "description": "Based off prov:Activity; an activity is something that occurs over a period of time and acts upon or with entities; it may include consuming, processing, transforming, modifying, relocating, using, or generating entities.", - "properties": { - "generated": { - "items": { - "$ref": "#/$defs/Entity" - }, - "type": "array" - }, - "used": { - "items": { - "$ref": "#/$defs/Entity" - }, - "type": "array" - } - }, - "title": "ProvActivity", - "type": "object" - }, - "ProvEntity": { - "additionalProperties": false, - "description": "Based off prov:Entity; an entity is a physical, digital, conceptual, or other kind of thing with some fixed aspects; entities may be real or imaginary.", - "properties": { - "wasDerivedFrom": { - "items": { - "$ref": "#/$defs/Entity" - }, - "type": "array" - }, - "wasGeneratedBy": { - "items": { - "$ref": "#/$defs/Activity" - }, - "type": "array" - } - }, - "title": "ProvEntity", - "type": "object" - }, "Publication": { "additionalProperties": false, "description": "Any \u2018published\u2019 piece of information. Publications are considered broadly to include any document or document part made available in print or on the web - which may include scientific journal issues, individual articles, and books - as well as things like pre-prints, white papers, patents, drug labels, web pages, protocol documents, and even a part of a publication if of significant knowledge scope (e.g. a figure, figure legend, or section highlighted by NLP).", @@ -30006,6 +30091,12 @@ }, "type": "array" }, + "wasAssociatedWith": { + "items": { + "$ref": "#/$defs/Agent" + }, + "type": "array" + }, "xref": { "description": "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.", "items": { @@ -30055,7 +30146,7 @@ "description": "A human-readable name for an attribute or entity.", "type": "string" }, - "region_of_interest_label": { + "roi_label": { "description": "The label of the region of interest.", "type": "string" }, @@ -30068,6 +30159,12 @@ }, "type": "array" }, + "wasAttributedTo": { + "items": { + "$ref": "#/$defs/Agent" + }, + "type": "array" + }, "wasDerivedFrom": { "items": { "$ref": "#/$defs/BrainSection" diff --git a/jsonld-context-autogen/kbmodel.context.jsonld b/jsonld-context-autogen/kbmodel.context.jsonld index 3d459257..781a0215 100644 --- a/jsonld-context-autogen/kbmodel.context.jsonld +++ b/jsonld-context-autogen/kbmodel.context.jsonld @@ -646,18 +646,12 @@ "@type": "@id", "@id": "biolink:amount_or_activity_increased_by" }, - "amplified_quantity": { - "@type": "xsd:float" - }, "pcr_cycles": { "@type": "xsd:integer" }, "percent_cdna_longer_than_400bp": { "@type": "xsd:float" }, - "rna_amplification_pass": { - "@type": "xsd:boolean" - }, "anatomical_context_qualifier": { "@id": "biolink:anatomical_context_qualifier" }, @@ -728,8 +722,8 @@ }, "@id": "biolink:available_from" }, - "barcode": { - "@id": "schema:identifier" + "avg_size_bp": { + "@type": "xsd:integer" }, "base_coordinate": { "@type": "xsd:integer", @@ -746,6 +740,9 @@ "@type": "@id", "@id": "biolink:biomarker_for" }, + "birth_date": { + "@type": "xsd:date" + }, "bonferonni_adjusted_p_value": { "@type": "xsd:float", "@id": "biolink:bonferonni_adjusted_p_value" @@ -918,10 +915,7 @@ "dataset_download_url": { "@id": "dcat:downloadURL" }, - "date_of_birth": { - "@type": "xsd:date" - }, - "date_of_death": { + "death_date": { "@type": "xsd:date" }, "decreased_amount_in": { @@ -992,7 +986,7 @@ "@type": "@id", "@id": "biolink:disrupts" }, - "number_of_cells_collected": { + "num_cells_collected": { "@type": "xsd:integer" }, "distribution_download_url": { @@ -1505,6 +1499,9 @@ "ingest_date": { "@id": "biolink:ingest_date" }, + "input_quantity": { + "@type": "xsd:float" + }, "interacting_molecules_category": { "@type": "@id", "@id": "biolink:interacting_molecules_category" @@ -1625,9 +1622,6 @@ "knowledge_source": { "@id": "biolink:knowledge_source" }, - "label": { - "@id": "schema:name" - }, "lacks_part": { "@type": "@id", "@id": "biolink:lacks_part" @@ -1636,15 +1630,6 @@ "@type": "xsd:float", "@id": "biolink:latitude" }, - "avg_size": { - "@type": "xsd:integer" - }, - "input_amount": { - "@type": "xsd:float" - }, - "library_prep_pass": { - "@type": "xsd:boolean" - }, "quantification_fmol": { "@type": "xsd:float" }, @@ -1654,12 +1639,6 @@ "quantification_nm": { "@type": "xsd:float" }, - "input_quantity": { - "@type": "xsd:integer" - }, - "tube_avg_size": { - "@type": "xsd:integer" - }, "tube_contents": { "@type": "xsd:float" }, @@ -1977,6 +1956,9 @@ "primary_knowledge_source": { "@id": "biolink:primary_knowledge_source" }, + "process_pass": { + "@type": "xsd:boolean" + }, "produced_by": { "@type": "@id", "@id": "biolink:produced_by" @@ -2433,6 +2415,14 @@ "volume": { "@id": "biolink:volume" }, + "wasAssociatedWith": { + "@type": "@id", + "@id": "prov:wasAssociatedWith" + }, + "wasAttributedTo": { + "@type": "@id", + "@id": "prov:wasAttributedTo" + }, "wasDerivedFrom": { "@type": "@id", "@id": "prov:wasDerivedFrom" diff --git a/models_py-autogen/kbmodel.py b/models_py-autogen/kbmodel.py index 8b50c526..cec823e9 100644 --- a/models_py-autogen/kbmodel.py +++ b/models_py-autogen/kbmodel.py @@ -447,18 +447,20 @@ class AnnotationCollection(ConfiguredBaseModel): class ProvActivity(ConfiguredBaseModel): """ - Based off prov:Activity; 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. + Based off prov:Activity; 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. """ - used: Optional[List[Union[Entity,Checksum,Donor,BrainSegment,BrainSection,TissueSample,DissociatedCellSample,EnrichedCellSample,BarcodedCellSample,AmplifiedCdna,Library,LibraryAliquot,LibraryPool,NamedThing,Association,ChemicalEntityAssessesNamedThingAssociation,ContributorAssociation,GenotypeToGenotypePartAssociation,GenotypeToGeneAssociation,GenotypeToVariantAssociation,GeneToGeneAssociation,GeneToGeneFamilyAssociation,CellLineToDiseaseOrPhenotypicFeatureAssociation,ChemicalToChemicalAssociation,ChemicalToDiseaseOrPhenotypicFeatureAssociation,ChemicalOrDrugOrTreatmentToDiseaseOrPhenotypicFeatureAssociation,GeneToPathwayAssociation,MolecularActivityToPathwayAssociation,ChemicalToPathwayAssociation,NamedThingAssociatedWithLikelihoodOfNamedThingAssociation,ChemicalGeneInteractionAssociation,ChemicalAffectsGeneAssociation,DrugToGeneAssociation,MaterialSampleDerivationAssociation,MaterialSampleToDiseaseOrPhenotypicFeatureAssociation,DiseaseToExposureEventAssociation,ExposureEventToOutcomeAssociation,InformationContentEntityToNamedThingAssociation,DiseaseOrPhenotypicFeatureToLocationAssociation,DiseaseOrPhenotypicFeatureToGeneticInheritanceAssociation,GenotypeToPhenotypicFeatureAssociation,ExposureEventToPhenotypicFeatureAssociation,DiseaseToPhenotypicFeatureAssociation,CaseToPhenotypicFeatureAssociation,BehaviorToBehavioralFeatureAssociation,GeneToDiseaseOrPhenotypicFeatureAssociation,VariantToGeneAssociation,VariantToPopulationAssociation,PopulationToPopulationAssociation,VariantToPhenotypicFeatureAssociation,VariantToDiseaseAssociation,GenotypeToDiseaseAssociation,OrganismalEntityAsAModelOfDiseaseAssociation,OrganismToOrganismAssociation,TaxonToTaxonAssociation,GeneToExpressionSiteAssociation,SequenceVariantModulatesTreatmentAssociation,FunctionalAssociation,MolecularActivityToChemicalEntityAssociation,MolecularActivityToMolecularActivityAssociation,EntityToDiseaseAssociation,EntityToPhenotypicFeatureAssociation,SequenceAssociation,SequenceFeatureRelationship,ChemicalEntityOrGeneOrGeneProductRegulatesGeneAssociation,AnatomicalEntityToAnatomicalEntityAssociation,OrganismTaxonToOrganismTaxonAssociation,OrganismTaxonToEnvironmentAssociation,OrganismTaxonToOrganismTaxonSpecialization,OrganismTaxonToOrganismTaxonInteraction,AnatomicalEntityToAnatomicalEntityPartOfAssociation,AnatomicalEntityToAnatomicalEntityOntogenicAssociation,TranscriptToGeneRelationship,GeneToGeneProductRelationship,ExonToTranscriptRelationship,GenomicSequenceLocalization,MacromolecularMachineToMolecularActivityAssociation,MacromolecularMachineToBiologicalProcessAssociation,MacromolecularMachineToCellularComponentAssociation,GeneToGoTermAssociation,GenotypeAsAModelOfDiseaseAssociation,VariantAsAModelOfDiseaseAssociation,VariantToGeneExpressionAssociation,GeneToPhenotypicFeatureAssociation,GeneToDiseaseAssociation,CausalGeneToDiseaseAssociation,CorrelatedGeneToDiseaseAssociation,DruggableGeneToDiseaseAssociation,GeneAsAModelOfDiseaseAssociation,GeneHasVariantThatContributesToDiseaseAssociation,ChemicalOrDrugOrTreatmentSideEffectDiseaseOrPhenotypicFeatureAssociation,ReactionToParticipantAssociation,ChemicalToChemicalDerivationAssociation,ReactionToCatalystAssociation,CellLineAsAModelOfDiseaseAssociation,GeneToGeneHomologyAssociation,GeneToGeneCoexpressionAssociation,PairwiseGeneToGeneInteraction,PairwiseMolecularInteraction,GenomeAssembly,Attribute,OrganismTaxon,Event,AdministrativeEntity,InformationContentEntity,PhysicalEntity,Activity,Procedure,Phenomenon,Device,DiagnosticAid,PlanetaryEntity,BiologicalEntity,ChemicalEntity,ClinicalEntity,Treatment,ClinicalTrial,ClinicalIntervention,Hospitalization,MolecularEntity,ChemicalMixture,EnvironmentalFoodContaminant,FoodAdditive,MolecularMixture,ComplexMolecularMixture,ProcessedMaterial,Food,Drug,SmallMolecule,NucleicAcidEntity,Exon,Transcript,CodingSequence,RNAProduct,RNAProductIsoform,NoncodingRNAProduct,MicroRNA,SiRNA,RegulatoryRegion,BiologicalProcessOrActivity,GeneticInheritance,OrganismalEntity,DiseaseOrPhenotypicFeature,Gene,MacromolecularComplex,NucleosomeModification,Genome,Polypeptide,ProteinDomain,PosttranslationalModification,ProteinFamily,NucleicAcidSequenceMotif,GeneFamily,Genotype,Haplotype,SequenceVariant,ReagentTargetedGene,Snv,Protein,ProteinIsoform,GenomeAnnotation,GeneAnnotation,Disease,PhenotypicFeature,BehavioralFeature,ClinicalFinding,Bacterium,Virus,CellularOrganism,LifeStage,IndividualOrganism,PopulationOfIndividualOrganisms,AnatomicalEntity,CellLine,CellularComponent,Cell,GrossAnatomicalStructure,PathologicalAnatomicalStructure,StudyPopulation,Cohort,Case,Mammal,Plant,Invertebrate,Vertebrate,Fungus,Human,MolecularActivity,BiologicalProcess,Pathway,PhysiologicalProcess,Behavior,PathologicalProcess,AccessibleDnaRegion,TranscriptionFactorBindingSite,EnvironmentalProcess,EnvironmentalFeature,GeographicLocation,GeographicLocationAtTime,BrainExtraction,BrainSegmentSectioning,TissueDissecting,CellDissociation,CellEnrichment,CellBarcoding,CdnaAmplification,LibraryConstruction,LibraryAliquoting,LibraryPooling,Study,MaterialSample,StudyResult,StudyVariable,CommonDataElement,Dataset,DatasetDistribution,DatasetVersion,DatasetSummary,ConfidenceLevel,EvidenceType,Publication,RetrievalSource,Book,BookChapter,Serial,Article,Patent,WebPage,PreprintPublication,DrugLabel,JournalArticle,ConceptCountAnalysisResult,ObservedExpectedFrequencyAnalysisResult,RelativeFrequencyAnalysisResult,TextMiningResult,ChiSquaredAnalysisResult,LogOddsAnalysisResult,Agent,ChemicalRole,BiologicalSex,SeverityValue,OrganismAttribute,Zygosity,ClinicalAttribute,SocioeconomicAttribute,GenomicBackgroundExposure,PathologicalProcessExposure,PathologicalAnatomicalExposure,DiseaseOrPhenotypicFeatureExposure,ChemicalExposure,ComplexChemicalExposure,BioticExposure,EnvironmentalExposure,BehavioralExposure,SocioeconomicExposure,GeographicExposure,DrugExposure,DrugToGeneInteractionExposure,ClinicalMeasurement,ClinicalModifier,ClinicalCourse,Onset,PhenotypicQuality,PhenotypicSex,GenotypicSex]]] = Field(default_factory=list) - generated: Optional[List[Union[Entity,Checksum,Donor,BrainSegment,BrainSection,TissueSample,DissociatedCellSample,EnrichedCellSample,BarcodedCellSample,AmplifiedCdna,Library,LibraryAliquot,LibraryPool,NamedThing,Association,ChemicalEntityAssessesNamedThingAssociation,ContributorAssociation,GenotypeToGenotypePartAssociation,GenotypeToGeneAssociation,GenotypeToVariantAssociation,GeneToGeneAssociation,GeneToGeneFamilyAssociation,CellLineToDiseaseOrPhenotypicFeatureAssociation,ChemicalToChemicalAssociation,ChemicalToDiseaseOrPhenotypicFeatureAssociation,ChemicalOrDrugOrTreatmentToDiseaseOrPhenotypicFeatureAssociation,GeneToPathwayAssociation,MolecularActivityToPathwayAssociation,ChemicalToPathwayAssociation,NamedThingAssociatedWithLikelihoodOfNamedThingAssociation,ChemicalGeneInteractionAssociation,ChemicalAffectsGeneAssociation,DrugToGeneAssociation,MaterialSampleDerivationAssociation,MaterialSampleToDiseaseOrPhenotypicFeatureAssociation,DiseaseToExposureEventAssociation,ExposureEventToOutcomeAssociation,InformationContentEntityToNamedThingAssociation,DiseaseOrPhenotypicFeatureToLocationAssociation,DiseaseOrPhenotypicFeatureToGeneticInheritanceAssociation,GenotypeToPhenotypicFeatureAssociation,ExposureEventToPhenotypicFeatureAssociation,DiseaseToPhenotypicFeatureAssociation,CaseToPhenotypicFeatureAssociation,BehaviorToBehavioralFeatureAssociation,GeneToDiseaseOrPhenotypicFeatureAssociation,VariantToGeneAssociation,VariantToPopulationAssociation,PopulationToPopulationAssociation,VariantToPhenotypicFeatureAssociation,VariantToDiseaseAssociation,GenotypeToDiseaseAssociation,OrganismalEntityAsAModelOfDiseaseAssociation,OrganismToOrganismAssociation,TaxonToTaxonAssociation,GeneToExpressionSiteAssociation,SequenceVariantModulatesTreatmentAssociation,FunctionalAssociation,MolecularActivityToChemicalEntityAssociation,MolecularActivityToMolecularActivityAssociation,EntityToDiseaseAssociation,EntityToPhenotypicFeatureAssociation,SequenceAssociation,SequenceFeatureRelationship,ChemicalEntityOrGeneOrGeneProductRegulatesGeneAssociation,AnatomicalEntityToAnatomicalEntityAssociation,OrganismTaxonToOrganismTaxonAssociation,OrganismTaxonToEnvironmentAssociation,OrganismTaxonToOrganismTaxonSpecialization,OrganismTaxonToOrganismTaxonInteraction,AnatomicalEntityToAnatomicalEntityPartOfAssociation,AnatomicalEntityToAnatomicalEntityOntogenicAssociation,TranscriptToGeneRelationship,GeneToGeneProductRelationship,ExonToTranscriptRelationship,GenomicSequenceLocalization,MacromolecularMachineToMolecularActivityAssociation,MacromolecularMachineToBiologicalProcessAssociation,MacromolecularMachineToCellularComponentAssociation,GeneToGoTermAssociation,GenotypeAsAModelOfDiseaseAssociation,VariantAsAModelOfDiseaseAssociation,VariantToGeneExpressionAssociation,GeneToPhenotypicFeatureAssociation,GeneToDiseaseAssociation,CausalGeneToDiseaseAssociation,CorrelatedGeneToDiseaseAssociation,DruggableGeneToDiseaseAssociation,GeneAsAModelOfDiseaseAssociation,GeneHasVariantThatContributesToDiseaseAssociation,ChemicalOrDrugOrTreatmentSideEffectDiseaseOrPhenotypicFeatureAssociation,ReactionToParticipantAssociation,ChemicalToChemicalDerivationAssociation,ReactionToCatalystAssociation,CellLineAsAModelOfDiseaseAssociation,GeneToGeneHomologyAssociation,GeneToGeneCoexpressionAssociation,PairwiseGeneToGeneInteraction,PairwiseMolecularInteraction,GenomeAssembly,Attribute,OrganismTaxon,Event,AdministrativeEntity,InformationContentEntity,PhysicalEntity,Activity,Procedure,Phenomenon,Device,DiagnosticAid,PlanetaryEntity,BiologicalEntity,ChemicalEntity,ClinicalEntity,Treatment,ClinicalTrial,ClinicalIntervention,Hospitalization,MolecularEntity,ChemicalMixture,EnvironmentalFoodContaminant,FoodAdditive,MolecularMixture,ComplexMolecularMixture,ProcessedMaterial,Food,Drug,SmallMolecule,NucleicAcidEntity,Exon,Transcript,CodingSequence,RNAProduct,RNAProductIsoform,NoncodingRNAProduct,MicroRNA,SiRNA,RegulatoryRegion,BiologicalProcessOrActivity,GeneticInheritance,OrganismalEntity,DiseaseOrPhenotypicFeature,Gene,MacromolecularComplex,NucleosomeModification,Genome,Polypeptide,ProteinDomain,PosttranslationalModification,ProteinFamily,NucleicAcidSequenceMotif,GeneFamily,Genotype,Haplotype,SequenceVariant,ReagentTargetedGene,Snv,Protein,ProteinIsoform,GenomeAnnotation,GeneAnnotation,Disease,PhenotypicFeature,BehavioralFeature,ClinicalFinding,Bacterium,Virus,CellularOrganism,LifeStage,IndividualOrganism,PopulationOfIndividualOrganisms,AnatomicalEntity,CellLine,CellularComponent,Cell,GrossAnatomicalStructure,PathologicalAnatomicalStructure,StudyPopulation,Cohort,Case,Mammal,Plant,Invertebrate,Vertebrate,Fungus,Human,MolecularActivity,BiologicalProcess,Pathway,PhysiologicalProcess,Behavior,PathologicalProcess,AccessibleDnaRegion,TranscriptionFactorBindingSite,EnvironmentalProcess,EnvironmentalFeature,GeographicLocation,GeographicLocationAtTime,BrainExtraction,BrainSegmentSectioning,TissueDissecting,CellDissociation,CellEnrichment,CellBarcoding,CdnaAmplification,LibraryConstruction,LibraryAliquoting,LibraryPooling,Study,MaterialSample,StudyResult,StudyVariable,CommonDataElement,Dataset,DatasetDistribution,DatasetVersion,DatasetSummary,ConfidenceLevel,EvidenceType,Publication,RetrievalSource,Book,BookChapter,Serial,Article,Patent,WebPage,PreprintPublication,DrugLabel,JournalArticle,ConceptCountAnalysisResult,ObservedExpectedFrequencyAnalysisResult,RelativeFrequencyAnalysisResult,TextMiningResult,ChiSquaredAnalysisResult,LogOddsAnalysisResult,Agent,ChemicalRole,BiologicalSex,SeverityValue,OrganismAttribute,Zygosity,ClinicalAttribute,SocioeconomicAttribute,GenomicBackgroundExposure,PathologicalProcessExposure,PathologicalAnatomicalExposure,DiseaseOrPhenotypicFeatureExposure,ChemicalExposure,ComplexChemicalExposure,BioticExposure,EnvironmentalExposure,BehavioralExposure,SocioeconomicExposure,GeographicExposure,DrugExposure,DrugToGeneInteractionExposure,ClinicalMeasurement,ClinicalModifier,ClinicalCourse,Onset,PhenotypicQuality,PhenotypicSex,GenotypicSex]]] = Field(default_factory=list) + used: Optional[List[Union[Entity,Checksum,BrainSegment,BrainSection,TissueSample,DissociatedCellSample,EnrichedCellSample,BarcodedCellSample,AmplifiedCdna,Library,LibraryAliquot,LibraryPool,NamedThing,Association,ChemicalEntityAssessesNamedThingAssociation,ContributorAssociation,GenotypeToGenotypePartAssociation,GenotypeToGeneAssociation,GenotypeToVariantAssociation,GeneToGeneAssociation,GeneToGeneFamilyAssociation,CellLineToDiseaseOrPhenotypicFeatureAssociation,ChemicalToChemicalAssociation,ChemicalToDiseaseOrPhenotypicFeatureAssociation,ChemicalOrDrugOrTreatmentToDiseaseOrPhenotypicFeatureAssociation,GeneToPathwayAssociation,MolecularActivityToPathwayAssociation,ChemicalToPathwayAssociation,NamedThingAssociatedWithLikelihoodOfNamedThingAssociation,ChemicalGeneInteractionAssociation,ChemicalAffectsGeneAssociation,DrugToGeneAssociation,MaterialSampleDerivationAssociation,MaterialSampleToDiseaseOrPhenotypicFeatureAssociation,DiseaseToExposureEventAssociation,ExposureEventToOutcomeAssociation,InformationContentEntityToNamedThingAssociation,DiseaseOrPhenotypicFeatureToLocationAssociation,DiseaseOrPhenotypicFeatureToGeneticInheritanceAssociation,GenotypeToPhenotypicFeatureAssociation,ExposureEventToPhenotypicFeatureAssociation,DiseaseToPhenotypicFeatureAssociation,CaseToPhenotypicFeatureAssociation,BehaviorToBehavioralFeatureAssociation,GeneToDiseaseOrPhenotypicFeatureAssociation,VariantToGeneAssociation,VariantToPopulationAssociation,PopulationToPopulationAssociation,VariantToPhenotypicFeatureAssociation,VariantToDiseaseAssociation,GenotypeToDiseaseAssociation,OrganismalEntityAsAModelOfDiseaseAssociation,OrganismToOrganismAssociation,TaxonToTaxonAssociation,GeneToExpressionSiteAssociation,SequenceVariantModulatesTreatmentAssociation,FunctionalAssociation,MolecularActivityToChemicalEntityAssociation,MolecularActivityToMolecularActivityAssociation,EntityToDiseaseAssociation,EntityToPhenotypicFeatureAssociation,SequenceAssociation,SequenceFeatureRelationship,ChemicalEntityOrGeneOrGeneProductRegulatesGeneAssociation,AnatomicalEntityToAnatomicalEntityAssociation,OrganismTaxonToOrganismTaxonAssociation,OrganismTaxonToEnvironmentAssociation,OrganismTaxonToOrganismTaxonSpecialization,OrganismTaxonToOrganismTaxonInteraction,AnatomicalEntityToAnatomicalEntityPartOfAssociation,AnatomicalEntityToAnatomicalEntityOntogenicAssociation,TranscriptToGeneRelationship,GeneToGeneProductRelationship,ExonToTranscriptRelationship,GenomicSequenceLocalization,MacromolecularMachineToMolecularActivityAssociation,MacromolecularMachineToBiologicalProcessAssociation,MacromolecularMachineToCellularComponentAssociation,GeneToGoTermAssociation,GenotypeAsAModelOfDiseaseAssociation,VariantAsAModelOfDiseaseAssociation,VariantToGeneExpressionAssociation,GeneToPhenotypicFeatureAssociation,GeneToDiseaseAssociation,CausalGeneToDiseaseAssociation,CorrelatedGeneToDiseaseAssociation,DruggableGeneToDiseaseAssociation,GeneAsAModelOfDiseaseAssociation,GeneHasVariantThatContributesToDiseaseAssociation,ChemicalOrDrugOrTreatmentSideEffectDiseaseOrPhenotypicFeatureAssociation,ReactionToParticipantAssociation,ChemicalToChemicalDerivationAssociation,ReactionToCatalystAssociation,CellLineAsAModelOfDiseaseAssociation,GeneToGeneHomologyAssociation,GeneToGeneCoexpressionAssociation,PairwiseGeneToGeneInteraction,PairwiseMolecularInteraction,GenomeAssembly,Attribute,OrganismTaxon,Event,AdministrativeEntity,InformationContentEntity,PhysicalEntity,Activity,Procedure,Phenomenon,Device,DiagnosticAid,PlanetaryEntity,BiologicalEntity,ChemicalEntity,ClinicalEntity,Treatment,ClinicalTrial,ClinicalIntervention,Hospitalization,MolecularEntity,ChemicalMixture,EnvironmentalFoodContaminant,FoodAdditive,MolecularMixture,ComplexMolecularMixture,ProcessedMaterial,Food,Drug,SmallMolecule,NucleicAcidEntity,Exon,Transcript,CodingSequence,RNAProduct,RNAProductIsoform,NoncodingRNAProduct,MicroRNA,SiRNA,RegulatoryRegion,BiologicalProcessOrActivity,GeneticInheritance,OrganismalEntity,DiseaseOrPhenotypicFeature,Gene,MacromolecularComplex,NucleosomeModification,Genome,Polypeptide,ProteinDomain,PosttranslationalModification,ProteinFamily,NucleicAcidSequenceMotif,GeneFamily,Genotype,Haplotype,SequenceVariant,ReagentTargetedGene,Snv,Protein,ProteinIsoform,GenomeAnnotation,GeneAnnotation,Disease,PhenotypicFeature,BehavioralFeature,ClinicalFinding,Bacterium,Virus,CellularOrganism,LifeStage,IndividualOrganism,PopulationOfIndividualOrganisms,AnatomicalEntity,CellLine,CellularComponent,Cell,GrossAnatomicalStructure,PathologicalAnatomicalStructure,StudyPopulation,Cohort,Case,Mammal,Plant,Invertebrate,Vertebrate,Fungus,Human,MolecularActivity,BiologicalProcess,Pathway,PhysiologicalProcess,Behavior,PathologicalProcess,AccessibleDnaRegion,TranscriptionFactorBindingSite,EnvironmentalProcess,EnvironmentalFeature,GeographicLocation,GeographicLocationAtTime,BrainExtraction,BrainSegmentSectioning,TissueDissecting,CellDissociation,CellEnrichment,CellBarcoding,CdnaAmplification,LibraryConstruction,LibraryAliquoting,LibraryPooling,Study,MaterialSample,StudyResult,StudyVariable,CommonDataElement,Dataset,DatasetDistribution,DatasetVersion,DatasetSummary,ConfidenceLevel,EvidenceType,Publication,RetrievalSource,Book,BookChapter,Serial,Article,Patent,WebPage,PreprintPublication,DrugLabel,JournalArticle,ConceptCountAnalysisResult,ObservedExpectedFrequencyAnalysisResult,RelativeFrequencyAnalysisResult,TextMiningResult,ChiSquaredAnalysisResult,LogOddsAnalysisResult,Agent,Donor,ChemicalRole,BiologicalSex,SeverityValue,OrganismAttribute,Zygosity,ClinicalAttribute,SocioeconomicAttribute,GenomicBackgroundExposure,PathologicalProcessExposure,PathologicalAnatomicalExposure,DiseaseOrPhenotypicFeatureExposure,ChemicalExposure,ComplexChemicalExposure,BioticExposure,EnvironmentalExposure,BehavioralExposure,SocioeconomicExposure,GeographicExposure,DrugExposure,DrugToGeneInteractionExposure,ClinicalMeasurement,ClinicalModifier,ClinicalCourse,Onset,PhenotypicQuality,PhenotypicSex,GenotypicSex]]] = Field(default_factory=list) + generated: Optional[List[Union[Entity,Checksum,BrainSegment,BrainSection,TissueSample,DissociatedCellSample,EnrichedCellSample,BarcodedCellSample,AmplifiedCdna,Library,LibraryAliquot,LibraryPool,NamedThing,Association,ChemicalEntityAssessesNamedThingAssociation,ContributorAssociation,GenotypeToGenotypePartAssociation,GenotypeToGeneAssociation,GenotypeToVariantAssociation,GeneToGeneAssociation,GeneToGeneFamilyAssociation,CellLineToDiseaseOrPhenotypicFeatureAssociation,ChemicalToChemicalAssociation,ChemicalToDiseaseOrPhenotypicFeatureAssociation,ChemicalOrDrugOrTreatmentToDiseaseOrPhenotypicFeatureAssociation,GeneToPathwayAssociation,MolecularActivityToPathwayAssociation,ChemicalToPathwayAssociation,NamedThingAssociatedWithLikelihoodOfNamedThingAssociation,ChemicalGeneInteractionAssociation,ChemicalAffectsGeneAssociation,DrugToGeneAssociation,MaterialSampleDerivationAssociation,MaterialSampleToDiseaseOrPhenotypicFeatureAssociation,DiseaseToExposureEventAssociation,ExposureEventToOutcomeAssociation,InformationContentEntityToNamedThingAssociation,DiseaseOrPhenotypicFeatureToLocationAssociation,DiseaseOrPhenotypicFeatureToGeneticInheritanceAssociation,GenotypeToPhenotypicFeatureAssociation,ExposureEventToPhenotypicFeatureAssociation,DiseaseToPhenotypicFeatureAssociation,CaseToPhenotypicFeatureAssociation,BehaviorToBehavioralFeatureAssociation,GeneToDiseaseOrPhenotypicFeatureAssociation,VariantToGeneAssociation,VariantToPopulationAssociation,PopulationToPopulationAssociation,VariantToPhenotypicFeatureAssociation,VariantToDiseaseAssociation,GenotypeToDiseaseAssociation,OrganismalEntityAsAModelOfDiseaseAssociation,OrganismToOrganismAssociation,TaxonToTaxonAssociation,GeneToExpressionSiteAssociation,SequenceVariantModulatesTreatmentAssociation,FunctionalAssociation,MolecularActivityToChemicalEntityAssociation,MolecularActivityToMolecularActivityAssociation,EntityToDiseaseAssociation,EntityToPhenotypicFeatureAssociation,SequenceAssociation,SequenceFeatureRelationship,ChemicalEntityOrGeneOrGeneProductRegulatesGeneAssociation,AnatomicalEntityToAnatomicalEntityAssociation,OrganismTaxonToOrganismTaxonAssociation,OrganismTaxonToEnvironmentAssociation,OrganismTaxonToOrganismTaxonSpecialization,OrganismTaxonToOrganismTaxonInteraction,AnatomicalEntityToAnatomicalEntityPartOfAssociation,AnatomicalEntityToAnatomicalEntityOntogenicAssociation,TranscriptToGeneRelationship,GeneToGeneProductRelationship,ExonToTranscriptRelationship,GenomicSequenceLocalization,MacromolecularMachineToMolecularActivityAssociation,MacromolecularMachineToBiologicalProcessAssociation,MacromolecularMachineToCellularComponentAssociation,GeneToGoTermAssociation,GenotypeAsAModelOfDiseaseAssociation,VariantAsAModelOfDiseaseAssociation,VariantToGeneExpressionAssociation,GeneToPhenotypicFeatureAssociation,GeneToDiseaseAssociation,CausalGeneToDiseaseAssociation,CorrelatedGeneToDiseaseAssociation,DruggableGeneToDiseaseAssociation,GeneAsAModelOfDiseaseAssociation,GeneHasVariantThatContributesToDiseaseAssociation,ChemicalOrDrugOrTreatmentSideEffectDiseaseOrPhenotypicFeatureAssociation,ReactionToParticipantAssociation,ChemicalToChemicalDerivationAssociation,ReactionToCatalystAssociation,CellLineAsAModelOfDiseaseAssociation,GeneToGeneHomologyAssociation,GeneToGeneCoexpressionAssociation,PairwiseGeneToGeneInteraction,PairwiseMolecularInteraction,GenomeAssembly,Attribute,OrganismTaxon,Event,AdministrativeEntity,InformationContentEntity,PhysicalEntity,Activity,Procedure,Phenomenon,Device,DiagnosticAid,PlanetaryEntity,BiologicalEntity,ChemicalEntity,ClinicalEntity,Treatment,ClinicalTrial,ClinicalIntervention,Hospitalization,MolecularEntity,ChemicalMixture,EnvironmentalFoodContaminant,FoodAdditive,MolecularMixture,ComplexMolecularMixture,ProcessedMaterial,Food,Drug,SmallMolecule,NucleicAcidEntity,Exon,Transcript,CodingSequence,RNAProduct,RNAProductIsoform,NoncodingRNAProduct,MicroRNA,SiRNA,RegulatoryRegion,BiologicalProcessOrActivity,GeneticInheritance,OrganismalEntity,DiseaseOrPhenotypicFeature,Gene,MacromolecularComplex,NucleosomeModification,Genome,Polypeptide,ProteinDomain,PosttranslationalModification,ProteinFamily,NucleicAcidSequenceMotif,GeneFamily,Genotype,Haplotype,SequenceVariant,ReagentTargetedGene,Snv,Protein,ProteinIsoform,GenomeAnnotation,GeneAnnotation,Disease,PhenotypicFeature,BehavioralFeature,ClinicalFinding,Bacterium,Virus,CellularOrganism,LifeStage,IndividualOrganism,PopulationOfIndividualOrganisms,AnatomicalEntity,CellLine,CellularComponent,Cell,GrossAnatomicalStructure,PathologicalAnatomicalStructure,StudyPopulation,Cohort,Case,Mammal,Plant,Invertebrate,Vertebrate,Fungus,Human,MolecularActivity,BiologicalProcess,Pathway,PhysiologicalProcess,Behavior,PathologicalProcess,AccessibleDnaRegion,TranscriptionFactorBindingSite,EnvironmentalProcess,EnvironmentalFeature,GeographicLocation,GeographicLocationAtTime,BrainExtraction,BrainSegmentSectioning,TissueDissecting,CellDissociation,CellEnrichment,CellBarcoding,CdnaAmplification,LibraryConstruction,LibraryAliquoting,LibraryPooling,Study,MaterialSample,StudyResult,StudyVariable,CommonDataElement,Dataset,DatasetDistribution,DatasetVersion,DatasetSummary,ConfidenceLevel,EvidenceType,Publication,RetrievalSource,Book,BookChapter,Serial,Article,Patent,WebPage,PreprintPublication,DrugLabel,JournalArticle,ConceptCountAnalysisResult,ObservedExpectedFrequencyAnalysisResult,RelativeFrequencyAnalysisResult,TextMiningResult,ChiSquaredAnalysisResult,LogOddsAnalysisResult,Agent,Donor,ChemicalRole,BiologicalSex,SeverityValue,OrganismAttribute,Zygosity,ClinicalAttribute,SocioeconomicAttribute,GenomicBackgroundExposure,PathologicalProcessExposure,PathologicalAnatomicalExposure,DiseaseOrPhenotypicFeatureExposure,ChemicalExposure,ComplexChemicalExposure,BioticExposure,EnvironmentalExposure,BehavioralExposure,SocioeconomicExposure,GeographicExposure,DrugExposure,DrugToGeneInteractionExposure,ClinicalMeasurement,ClinicalModifier,ClinicalCourse,Onset,PhenotypicQuality,PhenotypicSex,GenotypicSex]]] = Field(default_factory=list) + wasAssociatedWith: Optional[List[Union[Agent,Donor]]] = Field(default_factory=list) class ProvEntity(ConfiguredBaseModel): """ - Based off prov:Entity; an entity is a physical, digital, conceptual, or other kind of thing with some fixed aspects; entities may be real or imaginary. + Based off prov:Entity; an entity is a physical, digital, conceptual, or other kind of thing with some fixed aspects; entities may be real or imaginary. """ - wasDerivedFrom: Optional[List[Union[Entity,Checksum,Donor,BrainSegment,BrainSection,TissueSample,DissociatedCellSample,EnrichedCellSample,BarcodedCellSample,AmplifiedCdna,Library,LibraryAliquot,LibraryPool,NamedThing,Association,ChemicalEntityAssessesNamedThingAssociation,ContributorAssociation,GenotypeToGenotypePartAssociation,GenotypeToGeneAssociation,GenotypeToVariantAssociation,GeneToGeneAssociation,GeneToGeneFamilyAssociation,CellLineToDiseaseOrPhenotypicFeatureAssociation,ChemicalToChemicalAssociation,ChemicalToDiseaseOrPhenotypicFeatureAssociation,ChemicalOrDrugOrTreatmentToDiseaseOrPhenotypicFeatureAssociation,GeneToPathwayAssociation,MolecularActivityToPathwayAssociation,ChemicalToPathwayAssociation,NamedThingAssociatedWithLikelihoodOfNamedThingAssociation,ChemicalGeneInteractionAssociation,ChemicalAffectsGeneAssociation,DrugToGeneAssociation,MaterialSampleDerivationAssociation,MaterialSampleToDiseaseOrPhenotypicFeatureAssociation,DiseaseToExposureEventAssociation,ExposureEventToOutcomeAssociation,InformationContentEntityToNamedThingAssociation,DiseaseOrPhenotypicFeatureToLocationAssociation,DiseaseOrPhenotypicFeatureToGeneticInheritanceAssociation,GenotypeToPhenotypicFeatureAssociation,ExposureEventToPhenotypicFeatureAssociation,DiseaseToPhenotypicFeatureAssociation,CaseToPhenotypicFeatureAssociation,BehaviorToBehavioralFeatureAssociation,GeneToDiseaseOrPhenotypicFeatureAssociation,VariantToGeneAssociation,VariantToPopulationAssociation,PopulationToPopulationAssociation,VariantToPhenotypicFeatureAssociation,VariantToDiseaseAssociation,GenotypeToDiseaseAssociation,OrganismalEntityAsAModelOfDiseaseAssociation,OrganismToOrganismAssociation,TaxonToTaxonAssociation,GeneToExpressionSiteAssociation,SequenceVariantModulatesTreatmentAssociation,FunctionalAssociation,MolecularActivityToChemicalEntityAssociation,MolecularActivityToMolecularActivityAssociation,EntityToDiseaseAssociation,EntityToPhenotypicFeatureAssociation,SequenceAssociation,SequenceFeatureRelationship,ChemicalEntityOrGeneOrGeneProductRegulatesGeneAssociation,AnatomicalEntityToAnatomicalEntityAssociation,OrganismTaxonToOrganismTaxonAssociation,OrganismTaxonToEnvironmentAssociation,OrganismTaxonToOrganismTaxonSpecialization,OrganismTaxonToOrganismTaxonInteraction,AnatomicalEntityToAnatomicalEntityPartOfAssociation,AnatomicalEntityToAnatomicalEntityOntogenicAssociation,TranscriptToGeneRelationship,GeneToGeneProductRelationship,ExonToTranscriptRelationship,GenomicSequenceLocalization,MacromolecularMachineToMolecularActivityAssociation,MacromolecularMachineToBiologicalProcessAssociation,MacromolecularMachineToCellularComponentAssociation,GeneToGoTermAssociation,GenotypeAsAModelOfDiseaseAssociation,VariantAsAModelOfDiseaseAssociation,VariantToGeneExpressionAssociation,GeneToPhenotypicFeatureAssociation,GeneToDiseaseAssociation,CausalGeneToDiseaseAssociation,CorrelatedGeneToDiseaseAssociation,DruggableGeneToDiseaseAssociation,GeneAsAModelOfDiseaseAssociation,GeneHasVariantThatContributesToDiseaseAssociation,ChemicalOrDrugOrTreatmentSideEffectDiseaseOrPhenotypicFeatureAssociation,ReactionToParticipantAssociation,ChemicalToChemicalDerivationAssociation,ReactionToCatalystAssociation,CellLineAsAModelOfDiseaseAssociation,GeneToGeneHomologyAssociation,GeneToGeneCoexpressionAssociation,PairwiseGeneToGeneInteraction,PairwiseMolecularInteraction,GenomeAssembly,Attribute,OrganismTaxon,Event,AdministrativeEntity,InformationContentEntity,PhysicalEntity,Activity,Procedure,Phenomenon,Device,DiagnosticAid,PlanetaryEntity,BiologicalEntity,ChemicalEntity,ClinicalEntity,Treatment,ClinicalTrial,ClinicalIntervention,Hospitalization,MolecularEntity,ChemicalMixture,EnvironmentalFoodContaminant,FoodAdditive,MolecularMixture,ComplexMolecularMixture,ProcessedMaterial,Food,Drug,SmallMolecule,NucleicAcidEntity,Exon,Transcript,CodingSequence,RNAProduct,RNAProductIsoform,NoncodingRNAProduct,MicroRNA,SiRNA,RegulatoryRegion,BiologicalProcessOrActivity,GeneticInheritance,OrganismalEntity,DiseaseOrPhenotypicFeature,Gene,MacromolecularComplex,NucleosomeModification,Genome,Polypeptide,ProteinDomain,PosttranslationalModification,ProteinFamily,NucleicAcidSequenceMotif,GeneFamily,Genotype,Haplotype,SequenceVariant,ReagentTargetedGene,Snv,Protein,ProteinIsoform,GenomeAnnotation,GeneAnnotation,Disease,PhenotypicFeature,BehavioralFeature,ClinicalFinding,Bacterium,Virus,CellularOrganism,LifeStage,IndividualOrganism,PopulationOfIndividualOrganisms,AnatomicalEntity,CellLine,CellularComponent,Cell,GrossAnatomicalStructure,PathologicalAnatomicalStructure,StudyPopulation,Cohort,Case,Mammal,Plant,Invertebrate,Vertebrate,Fungus,Human,MolecularActivity,BiologicalProcess,Pathway,PhysiologicalProcess,Behavior,PathologicalProcess,AccessibleDnaRegion,TranscriptionFactorBindingSite,EnvironmentalProcess,EnvironmentalFeature,GeographicLocation,GeographicLocationAtTime,BrainExtraction,BrainSegmentSectioning,TissueDissecting,CellDissociation,CellEnrichment,CellBarcoding,CdnaAmplification,LibraryConstruction,LibraryAliquoting,LibraryPooling,Study,MaterialSample,StudyResult,StudyVariable,CommonDataElement,Dataset,DatasetDistribution,DatasetVersion,DatasetSummary,ConfidenceLevel,EvidenceType,Publication,RetrievalSource,Book,BookChapter,Serial,Article,Patent,WebPage,PreprintPublication,DrugLabel,JournalArticle,ConceptCountAnalysisResult,ObservedExpectedFrequencyAnalysisResult,RelativeFrequencyAnalysisResult,TextMiningResult,ChiSquaredAnalysisResult,LogOddsAnalysisResult,Agent,ChemicalRole,BiologicalSex,SeverityValue,OrganismAttribute,Zygosity,ClinicalAttribute,SocioeconomicAttribute,GenomicBackgroundExposure,PathologicalProcessExposure,PathologicalAnatomicalExposure,DiseaseOrPhenotypicFeatureExposure,ChemicalExposure,ComplexChemicalExposure,BioticExposure,EnvironmentalExposure,BehavioralExposure,SocioeconomicExposure,GeographicExposure,DrugExposure,DrugToGeneInteractionExposure,ClinicalMeasurement,ClinicalModifier,ClinicalCourse,Onset,PhenotypicQuality,PhenotypicSex,GenotypicSex]]] = Field(default_factory=list) + wasDerivedFrom: Optional[List[Union[Entity,Checksum,BrainSegment,BrainSection,TissueSample,DissociatedCellSample,EnrichedCellSample,BarcodedCellSample,AmplifiedCdna,Library,LibraryAliquot,LibraryPool,NamedThing,Association,ChemicalEntityAssessesNamedThingAssociation,ContributorAssociation,GenotypeToGenotypePartAssociation,GenotypeToGeneAssociation,GenotypeToVariantAssociation,GeneToGeneAssociation,GeneToGeneFamilyAssociation,CellLineToDiseaseOrPhenotypicFeatureAssociation,ChemicalToChemicalAssociation,ChemicalToDiseaseOrPhenotypicFeatureAssociation,ChemicalOrDrugOrTreatmentToDiseaseOrPhenotypicFeatureAssociation,GeneToPathwayAssociation,MolecularActivityToPathwayAssociation,ChemicalToPathwayAssociation,NamedThingAssociatedWithLikelihoodOfNamedThingAssociation,ChemicalGeneInteractionAssociation,ChemicalAffectsGeneAssociation,DrugToGeneAssociation,MaterialSampleDerivationAssociation,MaterialSampleToDiseaseOrPhenotypicFeatureAssociation,DiseaseToExposureEventAssociation,ExposureEventToOutcomeAssociation,InformationContentEntityToNamedThingAssociation,DiseaseOrPhenotypicFeatureToLocationAssociation,DiseaseOrPhenotypicFeatureToGeneticInheritanceAssociation,GenotypeToPhenotypicFeatureAssociation,ExposureEventToPhenotypicFeatureAssociation,DiseaseToPhenotypicFeatureAssociation,CaseToPhenotypicFeatureAssociation,BehaviorToBehavioralFeatureAssociation,GeneToDiseaseOrPhenotypicFeatureAssociation,VariantToGeneAssociation,VariantToPopulationAssociation,PopulationToPopulationAssociation,VariantToPhenotypicFeatureAssociation,VariantToDiseaseAssociation,GenotypeToDiseaseAssociation,OrganismalEntityAsAModelOfDiseaseAssociation,OrganismToOrganismAssociation,TaxonToTaxonAssociation,GeneToExpressionSiteAssociation,SequenceVariantModulatesTreatmentAssociation,FunctionalAssociation,MolecularActivityToChemicalEntityAssociation,MolecularActivityToMolecularActivityAssociation,EntityToDiseaseAssociation,EntityToPhenotypicFeatureAssociation,SequenceAssociation,SequenceFeatureRelationship,ChemicalEntityOrGeneOrGeneProductRegulatesGeneAssociation,AnatomicalEntityToAnatomicalEntityAssociation,OrganismTaxonToOrganismTaxonAssociation,OrganismTaxonToEnvironmentAssociation,OrganismTaxonToOrganismTaxonSpecialization,OrganismTaxonToOrganismTaxonInteraction,AnatomicalEntityToAnatomicalEntityPartOfAssociation,AnatomicalEntityToAnatomicalEntityOntogenicAssociation,TranscriptToGeneRelationship,GeneToGeneProductRelationship,ExonToTranscriptRelationship,GenomicSequenceLocalization,MacromolecularMachineToMolecularActivityAssociation,MacromolecularMachineToBiologicalProcessAssociation,MacromolecularMachineToCellularComponentAssociation,GeneToGoTermAssociation,GenotypeAsAModelOfDiseaseAssociation,VariantAsAModelOfDiseaseAssociation,VariantToGeneExpressionAssociation,GeneToPhenotypicFeatureAssociation,GeneToDiseaseAssociation,CausalGeneToDiseaseAssociation,CorrelatedGeneToDiseaseAssociation,DruggableGeneToDiseaseAssociation,GeneAsAModelOfDiseaseAssociation,GeneHasVariantThatContributesToDiseaseAssociation,ChemicalOrDrugOrTreatmentSideEffectDiseaseOrPhenotypicFeatureAssociation,ReactionToParticipantAssociation,ChemicalToChemicalDerivationAssociation,ReactionToCatalystAssociation,CellLineAsAModelOfDiseaseAssociation,GeneToGeneHomologyAssociation,GeneToGeneCoexpressionAssociation,PairwiseGeneToGeneInteraction,PairwiseMolecularInteraction,GenomeAssembly,Attribute,OrganismTaxon,Event,AdministrativeEntity,InformationContentEntity,PhysicalEntity,Activity,Procedure,Phenomenon,Device,DiagnosticAid,PlanetaryEntity,BiologicalEntity,ChemicalEntity,ClinicalEntity,Treatment,ClinicalTrial,ClinicalIntervention,Hospitalization,MolecularEntity,ChemicalMixture,EnvironmentalFoodContaminant,FoodAdditive,MolecularMixture,ComplexMolecularMixture,ProcessedMaterial,Food,Drug,SmallMolecule,NucleicAcidEntity,Exon,Transcript,CodingSequence,RNAProduct,RNAProductIsoform,NoncodingRNAProduct,MicroRNA,SiRNA,RegulatoryRegion,BiologicalProcessOrActivity,GeneticInheritance,OrganismalEntity,DiseaseOrPhenotypicFeature,Gene,MacromolecularComplex,NucleosomeModification,Genome,Polypeptide,ProteinDomain,PosttranslationalModification,ProteinFamily,NucleicAcidSequenceMotif,GeneFamily,Genotype,Haplotype,SequenceVariant,ReagentTargetedGene,Snv,Protein,ProteinIsoform,GenomeAnnotation,GeneAnnotation,Disease,PhenotypicFeature,BehavioralFeature,ClinicalFinding,Bacterium,Virus,CellularOrganism,LifeStage,IndividualOrganism,PopulationOfIndividualOrganisms,AnatomicalEntity,CellLine,CellularComponent,Cell,GrossAnatomicalStructure,PathologicalAnatomicalStructure,StudyPopulation,Cohort,Case,Mammal,Plant,Invertebrate,Vertebrate,Fungus,Human,MolecularActivity,BiologicalProcess,Pathway,PhysiologicalProcess,Behavior,PathologicalProcess,AccessibleDnaRegion,TranscriptionFactorBindingSite,EnvironmentalProcess,EnvironmentalFeature,GeographicLocation,GeographicLocationAtTime,BrainExtraction,BrainSegmentSectioning,TissueDissecting,CellDissociation,CellEnrichment,CellBarcoding,CdnaAmplification,LibraryConstruction,LibraryAliquoting,LibraryPooling,Study,MaterialSample,StudyResult,StudyVariable,CommonDataElement,Dataset,DatasetDistribution,DatasetVersion,DatasetSummary,ConfidenceLevel,EvidenceType,Publication,RetrievalSource,Book,BookChapter,Serial,Article,Patent,WebPage,PreprintPublication,DrugLabel,JournalArticle,ConceptCountAnalysisResult,ObservedExpectedFrequencyAnalysisResult,RelativeFrequencyAnalysisResult,TextMiningResult,ChiSquaredAnalysisResult,LogOddsAnalysisResult,Agent,Donor,ChemicalRole,BiologicalSex,SeverityValue,OrganismAttribute,Zygosity,ClinicalAttribute,SocioeconomicAttribute,GenomicBackgroundExposure,PathologicalProcessExposure,PathologicalAnatomicalExposure,DiseaseOrPhenotypicFeatureExposure,ChemicalExposure,ComplexChemicalExposure,BioticExposure,EnvironmentalExposure,BehavioralExposure,SocioeconomicExposure,GeographicExposure,DrugExposure,DrugToGeneInteractionExposure,ClinicalMeasurement,ClinicalModifier,ClinicalCourse,Onset,PhenotypicQuality,PhenotypicSex,GenotypicSex]]] = Field(default_factory=list) wasGeneratedBy: Optional[List[Union[Activity,BrainExtraction,BrainSegmentSectioning,TissueDissecting,CellDissociation,CellEnrichment,CellBarcoding,CdnaAmplification,LibraryConstruction,LibraryAliquoting,LibraryPooling,Study]]] = Field(default_factory=list) + wasAttributedTo: Optional[List[Union[Agent,Donor]]] = Field(default_factory=list) class MappingCollection(ConfiguredBaseModel): @@ -590,10 +592,10 @@ class Checksum(Entity): class BrainSegment(Entity, ProvEntity): - barcode: Optional[str] = Field(None, description="""The unique identifier of the object.""") anatomical_division: Optional[str] = Field(None) wasDerivedFrom: Optional[List[Donor]] = Field(default_factory=list) wasGeneratedBy: Optional[List[BrainExtraction]] = Field(default_factory=list) + wasAttributedTo: Optional[List[Union[Agent,Donor]]] = Field(default_factory=list) id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://identifiers.org/brain-bican/vocab/BrainSegment","bican:BrainSegment"]] = Field(["bican:BrainSegment"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. @@ -609,10 +611,10 @@ class BrainSegment(Entity, ProvEntity): class BrainSection(Entity, ProvEntity): - barcode: Optional[str] = Field(None, description="""The unique identifier of the object.""") ordinal: Optional[int] = Field(None, description="""The ordinal number of the section.""") wasDerivedFrom: Optional[List[BrainSegment]] = Field(default_factory=list) wasGeneratedBy: Optional[List[BrainSegmentSectioning]] = Field(default_factory=list) + wasAttributedTo: Optional[List[Union[Agent,Donor]]] = Field(default_factory=list) id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://identifiers.org/brain-bican/vocab/BrainSection","bican:BrainSection"]] = Field(["bican:BrainSection"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. @@ -629,9 +631,10 @@ class BrainSection(Entity, ProvEntity): class TissueSample(Entity, ProvEntity): roi_plan: Optional[str] = Field(None) - region_of_interest_label: Optional[str] = Field(None, description="""The label of the region of interest.""") + roi_label: Optional[str] = Field(None, description="""The label of the region of interest.""") wasDerivedFrom: Optional[List[BrainSection]] = Field(default_factory=list) wasGeneratedBy: Optional[List[TissueDissecting]] = Field(default_factory=list) + wasAttributedTo: Optional[List[Union[Agent,Donor]]] = Field(default_factory=list) id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://identifiers.org/brain-bican/vocab/TissueSample","bican:TissueSample"]] = Field(["bican:TissueSample"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. @@ -649,9 +652,10 @@ class DissociatedCellSample(Entity, ProvEntity): cell_prep_type: Optional[str] = Field(None) facs_population_plan: Optional[str] = Field(None) - number_of_cells_collected: Optional[int] = Field(None) + num_cells_collected: Optional[int] = Field(None) wasDerivedFrom: Optional[List[TissueSample]] = Field(default_factory=list) wasGeneratedBy: Optional[List[CellDissociation]] = Field(default_factory=list) + wasAttributedTo: Optional[List[Union[Agent,Donor]]] = Field(default_factory=list) id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://identifiers.org/brain-bican/vocab/DissociatedCellSample","bican:DissociatedCellSample"]] = Field(["bican:DissociatedCellSample"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. @@ -669,6 +673,7 @@ class EnrichedCellSample(Entity, ProvEntity): wasDerivedFrom: Optional[List[DissociatedCellSample]] = Field(default_factory=list) wasGeneratedBy: Optional[List[CellEnrichment]] = Field(default_factory=list) + wasAttributedTo: Optional[List[Union[Agent,Donor]]] = Field(default_factory=list) id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://identifiers.org/brain-bican/vocab/EnrichedCellSample","bican:EnrichedCellSample"]] = Field(["bican:EnrichedCellSample"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. @@ -688,6 +693,7 @@ class BarcodedCellSample(Entity, ProvEntity): sample_quality_count: Optional[str] = Field(None) wasDerivedFrom: Optional[List[EnrichedCellSample]] = Field(default_factory=list) wasGeneratedBy: Optional[List[CellBarcoding]] = Field(default_factory=list) + wasAttributedTo: Optional[List[Union[Agent,Donor]]] = Field(default_factory=list) id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://identifiers.org/brain-bican/vocab/BarcodedCellSample","bican:BarcodedCellSample"]] = Field(["bican:BarcodedCellSample"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. @@ -704,12 +710,13 @@ class BarcodedCellSample(Entity, ProvEntity): class AmplifiedCdna(Entity, ProvEntity): method: Optional[str] = Field(None) - amplified_quantity: Optional[float] = Field(None, description="""Amount of cDNA amplified (ng).""") + input_quantity: Optional[float] = Field(None, description="""The amount of input cDNA (ng) amplified.""") + process_pass: Optional[bool] = Field(None, description="""Indicates whether the rna amplification process passed or failed.""") pcr_cycles: Optional[int] = Field(None, description="""Number of PCR cycles used to amplify the cDNA.""") percent_cdna_longer_than_400bp: Optional[float] = Field(None, description="""The percentage of cDNA fragments that are longer than 400bp.""") - rna_amplification_pass: Optional[bool] = Field(None) wasDerivedFrom: Optional[List[BarcodedCellSample]] = Field(default_factory=list) wasGeneratedBy: Optional[List[CdnaAmplification]] = Field(default_factory=list) + wasAttributedTo: Optional[List[Union[Agent,Donor]]] = Field(default_factory=list) id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://identifiers.org/brain-bican/vocab/AmplifiedCdna","bican:AmplifiedCdna"]] = Field(["bican:AmplifiedCdna"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. @@ -727,9 +734,9 @@ class Library(Entity, ProvEntity): method: Optional[str] = Field(None) creation_date: Optional[datetime ] = Field(None, description="""The date and time the object was created.""") - avg_size: Optional[int] = Field(None, description="""The average size (bp) of the library fragments. bp stands for base pairs.""") - input_amount: Optional[float] = Field(None, description="""The amount of input material (ng) used to create the library.""") - library_prep_pass: Optional[bool] = Field(None) + input_quantity: Optional[float] = Field(None, description="""The amount of input material (ng) used to create the library.""") + process_pass: Optional[bool] = Field(None, description="""Indicates whether the library prep process passed or failed.""") + avg_size_bp: Optional[int] = Field(None, description="""The average size (bp) of the library fragments.""") quantification_fmol: Optional[float] = Field(None) quantification_ng: Optional[float] = Field(None) quantification_nm: Optional[float] = Field(None) @@ -739,6 +746,7 @@ class Library(Entity, ProvEntity): r2_sequence: Optional[str] = Field(None) wasDerivedFrom: Optional[List[AmplifiedCdna]] = Field(default_factory=list) wasGeneratedBy: Optional[List[LibraryConstruction]] = Field(default_factory=list) + wasAttributedTo: Optional[List[Union[Agent,Donor]]] = Field(default_factory=list) id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://identifiers.org/brain-bican/vocab/Library","bican:Library"]] = Field(["bican:Library"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. @@ -757,6 +765,7 @@ class LibraryAliquot(Entity, ProvEntity): input_quantity: Optional[int] = Field(None, description="""The amount of input material (fmol) used to create the library aliquot.""") wasDerivedFrom: Optional[List[Library]] = Field(default_factory=list) wasGeneratedBy: Optional[List[LibraryAliquoting]] = Field(default_factory=list) + wasAttributedTo: Optional[List[Union[Agent,Donor]]] = Field(default_factory=list) id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://identifiers.org/brain-bican/vocab/LibraryAliquot","bican:LibraryAliquot"]] = Field(["bican:LibraryAliquot"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. @@ -772,11 +781,11 @@ class LibraryAliquot(Entity, ProvEntity): class LibraryPool(Entity, ProvEntity): - tube_avg_size: Optional[int] = Field(None, description="""The average size (bp) of the library fragments in the tube.""") + avg_size_bp: Optional[int] = Field(None, description="""The average size (bp) of the library fragments in the tube.""") tube_contents: Optional[float] = Field(None, description="""The content concentration (nm).""") - tube_internal_label: Optional[str] = Field(None) wasDerivedFrom: Optional[List[LibraryAliquot]] = Field(default_factory=list) wasGeneratedBy: Optional[List[LibraryPooling]] = Field(default_factory=list) + wasAttributedTo: Optional[List[Union[Agent,Donor]]] = Field(default_factory=list) id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://identifiers.org/brain-bican/vocab/LibraryPool","bican:LibraryPool"]] = Field(["bican:LibraryPool"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. @@ -1873,6 +1882,7 @@ class BrainExtraction(Activity, ProvActivity): """ used: Optional[List[Donor]] = Field(default_factory=list) generated: Optional[List[BrainSegment]] = Field(default_factory=list) + wasAssociatedWith: Optional[List[Union[Agent,Donor]]] = Field(default_factory=list) provided_by: Optional[List[str]] = Field(None, 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.""") xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") full_name: Optional[str] = Field(None, description="""a long-form human readable name for a thing""") @@ -1896,6 +1906,7 @@ class BrainSegmentSectioning(Activity, ProvActivity): """ used: Optional[List[BrainSegment]] = Field(default_factory=list) generated: Optional[List[BrainSection]] = Field(default_factory=list) + wasAssociatedWith: Optional[List[Union[Agent,Donor]]] = Field(default_factory=list) provided_by: Optional[List[str]] = Field(None, 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.""") xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") full_name: Optional[str] = Field(None, description="""a long-form human readable name for a thing""") @@ -1919,6 +1930,7 @@ class TissueDissecting(Activity, ProvActivity): """ used: Optional[List[BrainSection]] = Field(default_factory=list) generated: Optional[List[TissueSample]] = Field(default_factory=list) + wasAssociatedWith: Optional[List[Union[Agent,Donor]]] = Field(default_factory=list) provided_by: Optional[List[str]] = Field(None, 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.""") xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") full_name: Optional[str] = Field(None, description="""a long-form human readable name for a thing""") @@ -1942,6 +1954,7 @@ class CellDissociation(Activity, ProvActivity): """ used: Optional[List[TissueSample]] = Field(default_factory=list) generated: Optional[List[DissociatedCellSample]] = Field(default_factory=list) + wasAssociatedWith: Optional[List[Union[Agent,Donor]]] = Field(default_factory=list) provided_by: Optional[List[str]] = Field(None, 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.""") xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") full_name: Optional[str] = Field(None, description="""a long-form human readable name for a thing""") @@ -1965,6 +1978,7 @@ class CellEnrichment(Activity, ProvActivity): """ used: Optional[List[DissociatedCellSample]] = Field(default_factory=list) generated: Optional[List[EnrichedCellSample]] = Field(default_factory=list) + wasAssociatedWith: Optional[List[Union[Agent,Donor]]] = Field(default_factory=list) provided_by: Optional[List[str]] = Field(None, 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.""") xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") full_name: Optional[str] = Field(None, description="""a long-form human readable name for a thing""") @@ -1988,6 +2002,7 @@ class CellBarcoding(Activity, ProvActivity): """ used: Optional[List[EnrichedCellSample]] = Field(default_factory=list) generated: Optional[List[BarcodedCellSample]] = Field(default_factory=list) + wasAssociatedWith: Optional[List[Union[Agent,Donor]]] = Field(default_factory=list) provided_by: Optional[List[str]] = Field(None, 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.""") xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") full_name: Optional[str] = Field(None, description="""a long-form human readable name for a thing""") @@ -2011,6 +2026,7 @@ class CdnaAmplification(Activity, ProvActivity): """ used: Optional[List[BarcodedCellSample]] = Field(default_factory=list) generated: Optional[List[AmplifiedCdna]] = Field(default_factory=list) + wasAssociatedWith: Optional[List[Union[Agent,Donor]]] = Field(default_factory=list) provided_by: Optional[List[str]] = Field(None, 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.""") xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") full_name: Optional[str] = Field(None, description="""a long-form human readable name for a thing""") @@ -2034,6 +2050,7 @@ class LibraryConstruction(Activity, ProvActivity): """ used: Optional[List[AmplifiedCdna]] = Field(default_factory=list) generated: Optional[List[Library]] = Field(default_factory=list) + wasAssociatedWith: Optional[List[Union[Agent,Donor]]] = Field(default_factory=list) provided_by: Optional[List[str]] = Field(None, 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.""") xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") full_name: Optional[str] = Field(None, description="""a long-form human readable name for a thing""") @@ -2057,6 +2074,7 @@ class LibraryAliquoting(Activity, ProvActivity): """ used: Optional[List[Library]] = Field(default_factory=list) generated: Optional[List[LibraryAliquot]] = Field(default_factory=list) + wasAssociatedWith: Optional[List[Union[Agent,Donor]]] = Field(default_factory=list) provided_by: Optional[List[str]] = Field(None, 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.""") xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") full_name: Optional[str] = Field(None, description="""a long-form human readable name for a thing""") @@ -2080,6 +2098,7 @@ class LibraryPooling(Activity, ProvActivity): """ used: Optional[List[LibraryAliquot]] = Field(default_factory=list) generated: Optional[List[LibraryPool]] = Field(default_factory=list) + wasAssociatedWith: Optional[List[Union[Agent,Donor]]] = Field(default_factory=list) provided_by: Optional[List[str]] = Field(None, 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.""") xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") full_name: Optional[str] = Field(None, description="""a long-form human readable name for a thing""") @@ -2369,20 +2388,24 @@ class GenomeAssembly(ThingWithTaxon, NamedThing): has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") -class Donor(ThingWithTaxon, Entity, ProvEntity): +class Donor(ThingWithTaxon, Agent): """ A person or organism that is the source of a biological sample. """ sex: Optional[SexType] = Field(None) - date_of_birth: Optional[date] = Field(None, description="""The date of birth of the donor.""") - date_of_death: Optional[date] = Field(None, description="""The date of death of the donor.""") - age_at_death: Optional[str] = Field(None, description="""The age of the donor at the time of death.""") + birth_date: Optional[date] = Field(None, description="""The date of birth of the donor.""") + death_date: Optional[date] = Field(None, description="""The date of death of the donor.""") + death_age: Optional[str] = Field(None, description="""The age of the donor at the time of death (ISO 8601 format).""") full_genotype: Optional[str] = Field(None, description="""The full genotype of the donor.""") in_taxon: Optional[List[str]] = Field(None, description="""connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'""") in_taxon_label: Optional[str] = Field(None, description="""The human readable scientific name for the taxon of the entity.""") - wasDerivedFrom: Optional[List[Union[Entity,Checksum,Donor,BrainSegment,BrainSection,TissueSample,DissociatedCellSample,EnrichedCellSample,BarcodedCellSample,AmplifiedCdna,Library,LibraryAliquot,LibraryPool,NamedThing,Association,ChemicalEntityAssessesNamedThingAssociation,ContributorAssociation,GenotypeToGenotypePartAssociation,GenotypeToGeneAssociation,GenotypeToVariantAssociation,GeneToGeneAssociation,GeneToGeneFamilyAssociation,CellLineToDiseaseOrPhenotypicFeatureAssociation,ChemicalToChemicalAssociation,ChemicalToDiseaseOrPhenotypicFeatureAssociation,ChemicalOrDrugOrTreatmentToDiseaseOrPhenotypicFeatureAssociation,GeneToPathwayAssociation,MolecularActivityToPathwayAssociation,ChemicalToPathwayAssociation,NamedThingAssociatedWithLikelihoodOfNamedThingAssociation,ChemicalGeneInteractionAssociation,ChemicalAffectsGeneAssociation,DrugToGeneAssociation,MaterialSampleDerivationAssociation,MaterialSampleToDiseaseOrPhenotypicFeatureAssociation,DiseaseToExposureEventAssociation,ExposureEventToOutcomeAssociation,InformationContentEntityToNamedThingAssociation,DiseaseOrPhenotypicFeatureToLocationAssociation,DiseaseOrPhenotypicFeatureToGeneticInheritanceAssociation,GenotypeToPhenotypicFeatureAssociation,ExposureEventToPhenotypicFeatureAssociation,DiseaseToPhenotypicFeatureAssociation,CaseToPhenotypicFeatureAssociation,BehaviorToBehavioralFeatureAssociation,GeneToDiseaseOrPhenotypicFeatureAssociation,VariantToGeneAssociation,VariantToPopulationAssociation,PopulationToPopulationAssociation,VariantToPhenotypicFeatureAssociation,VariantToDiseaseAssociation,GenotypeToDiseaseAssociation,OrganismalEntityAsAModelOfDiseaseAssociation,OrganismToOrganismAssociation,TaxonToTaxonAssociation,GeneToExpressionSiteAssociation,SequenceVariantModulatesTreatmentAssociation,FunctionalAssociation,MolecularActivityToChemicalEntityAssociation,MolecularActivityToMolecularActivityAssociation,EntityToDiseaseAssociation,EntityToPhenotypicFeatureAssociation,SequenceAssociation,SequenceFeatureRelationship,ChemicalEntityOrGeneOrGeneProductRegulatesGeneAssociation,AnatomicalEntityToAnatomicalEntityAssociation,OrganismTaxonToOrganismTaxonAssociation,OrganismTaxonToEnvironmentAssociation,OrganismTaxonToOrganismTaxonSpecialization,OrganismTaxonToOrganismTaxonInteraction,AnatomicalEntityToAnatomicalEntityPartOfAssociation,AnatomicalEntityToAnatomicalEntityOntogenicAssociation,TranscriptToGeneRelationship,GeneToGeneProductRelationship,ExonToTranscriptRelationship,GenomicSequenceLocalization,MacromolecularMachineToMolecularActivityAssociation,MacromolecularMachineToBiologicalProcessAssociation,MacromolecularMachineToCellularComponentAssociation,GeneToGoTermAssociation,GenotypeAsAModelOfDiseaseAssociation,VariantAsAModelOfDiseaseAssociation,VariantToGeneExpressionAssociation,GeneToPhenotypicFeatureAssociation,GeneToDiseaseAssociation,CausalGeneToDiseaseAssociation,CorrelatedGeneToDiseaseAssociation,DruggableGeneToDiseaseAssociation,GeneAsAModelOfDiseaseAssociation,GeneHasVariantThatContributesToDiseaseAssociation,ChemicalOrDrugOrTreatmentSideEffectDiseaseOrPhenotypicFeatureAssociation,ReactionToParticipantAssociation,ChemicalToChemicalDerivationAssociation,ReactionToCatalystAssociation,CellLineAsAModelOfDiseaseAssociation,GeneToGeneHomologyAssociation,GeneToGeneCoexpressionAssociation,PairwiseGeneToGeneInteraction,PairwiseMolecularInteraction,GenomeAssembly,Attribute,OrganismTaxon,Event,AdministrativeEntity,InformationContentEntity,PhysicalEntity,Activity,Procedure,Phenomenon,Device,DiagnosticAid,PlanetaryEntity,BiologicalEntity,ChemicalEntity,ClinicalEntity,Treatment,ClinicalTrial,ClinicalIntervention,Hospitalization,MolecularEntity,ChemicalMixture,EnvironmentalFoodContaminant,FoodAdditive,MolecularMixture,ComplexMolecularMixture,ProcessedMaterial,Food,Drug,SmallMolecule,NucleicAcidEntity,Exon,Transcript,CodingSequence,RNAProduct,RNAProductIsoform,NoncodingRNAProduct,MicroRNA,SiRNA,RegulatoryRegion,BiologicalProcessOrActivity,GeneticInheritance,OrganismalEntity,DiseaseOrPhenotypicFeature,Gene,MacromolecularComplex,NucleosomeModification,Genome,Polypeptide,ProteinDomain,PosttranslationalModification,ProteinFamily,NucleicAcidSequenceMotif,GeneFamily,Genotype,Haplotype,SequenceVariant,ReagentTargetedGene,Snv,Protein,ProteinIsoform,GenomeAnnotation,GeneAnnotation,Disease,PhenotypicFeature,BehavioralFeature,ClinicalFinding,Bacterium,Virus,CellularOrganism,LifeStage,IndividualOrganism,PopulationOfIndividualOrganisms,AnatomicalEntity,CellLine,CellularComponent,Cell,GrossAnatomicalStructure,PathologicalAnatomicalStructure,StudyPopulation,Cohort,Case,Mammal,Plant,Invertebrate,Vertebrate,Fungus,Human,MolecularActivity,BiologicalProcess,Pathway,PhysiologicalProcess,Behavior,PathologicalProcess,AccessibleDnaRegion,TranscriptionFactorBindingSite,EnvironmentalProcess,EnvironmentalFeature,GeographicLocation,GeographicLocationAtTime,BrainExtraction,BrainSegmentSectioning,TissueDissecting,CellDissociation,CellEnrichment,CellBarcoding,CdnaAmplification,LibraryConstruction,LibraryAliquoting,LibraryPooling,Study,MaterialSample,StudyResult,StudyVariable,CommonDataElement,Dataset,DatasetDistribution,DatasetVersion,DatasetSummary,ConfidenceLevel,EvidenceType,Publication,RetrievalSource,Book,BookChapter,Serial,Article,Patent,WebPage,PreprintPublication,DrugLabel,JournalArticle,ConceptCountAnalysisResult,ObservedExpectedFrequencyAnalysisResult,RelativeFrequencyAnalysisResult,TextMiningResult,ChiSquaredAnalysisResult,LogOddsAnalysisResult,Agent,ChemicalRole,BiologicalSex,SeverityValue,OrganismAttribute,Zygosity,ClinicalAttribute,SocioeconomicAttribute,GenomicBackgroundExposure,PathologicalProcessExposure,PathologicalAnatomicalExposure,DiseaseOrPhenotypicFeatureExposure,ChemicalExposure,ComplexChemicalExposure,BioticExposure,EnvironmentalExposure,BehavioralExposure,SocioeconomicExposure,GeographicExposure,DrugExposure,DrugToGeneInteractionExposure,ClinicalMeasurement,ClinicalModifier,ClinicalCourse,Onset,PhenotypicQuality,PhenotypicSex,GenotypicSex]]] = Field(default_factory=list) - wasGeneratedBy: Optional[List[Union[Activity,BrainExtraction,BrainSegmentSectioning,TissueDissecting,CellDissociation,CellEnrichment,CellBarcoding,CdnaAmplification,LibraryConstruction,LibraryAliquoting,LibraryPooling,Study]]] = Field(default_factory=list) - id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") + affiliation: Optional[List[str]] = Field(default_factory=list, description="""a professional relationship between one provider (often a person) within another provider (often an organization). Target provider identity should be specified by a CURIE. Providers may have multiple affiliations.""") + address: Optional[str] = Field(None, description="""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(?).""") + provided_by: Optional[List[str]] = Field(None, 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.""") + xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") + full_name: Optional[str] = Field(None, description="""a long-form human readable name for a thing""") + synonym: Optional[List[str]] = Field(default_factory=list, description="""Alternate human-readable names for a thing""") + id: str = Field(..., description="""Different classes of agents have distinct preferred identifiers. For publishers, use the ISBN publisher code. See https://grp.isbn-international.org/ for publisher code lookups. For editors, authors and individual providers, use the individual's ORCID if available; Otherwise, a ScopusID, ResearchID or Google Scholar ID ('GSID') may be used if the author ORCID is unknown. Institutional agents could be identified by an International Standard Name Identifier ('ISNI') code.""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://identifiers.org/brain-bican/vocab/Donor","bican:Donor"]] = Field(["bican:Donor"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. @@ -2390,7 +2413,7 @@ class Donor(ThingWithTaxon, Entity, ProvEntity): This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") type: Optional[List[str]] = Field(default_factory=list) - name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") + name: Optional[str] = Field(None, description="""it is recommended that an author's 'name' property be formatted as \"surname, firstname initial.\"""") description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""")