diff --git a/bioschemasdrafts.json b/bioschemasdrafts.json index cc33ebb..8719947 100644 --- a/bioschemasdrafts.json +++ b/bioschemasdrafts.json @@ -10,7 +10,7 @@ "bioschemastypesdrafts": "https://discovery.biothings.io/view/bioschemastypesdrafts/", "bioschemasdeprecated": "https://discovery.biothings.io/view/bioschemasdeprecated/", "dct": "http://purl.org/dc/terms/", - "@dateModified": "12/12/2023, 08:33:51", + "@dateModified": "12/21/2023, 10:12:00", "dwc": "http://rs.tdwg.org/dwc/terms/", "ppeo:hasGrowthFacility": "http://purl.org/ppeo/PPEO.owl#hasGrowthFacility" }, @@ -700,8 +700,8 @@ }, "additional_type": "https://bioschemas.org/profiles#nav-draft", "schema:schemaVersion": [ - "https://github.com/BioSchemas/specifications/blob/master/Gene/jsonld/Gene_v1.1-DRAFT.json", - "https://bioschemas.org/profiles/Gene/1.1-DRAFT" + "https://bioschemas.org/profiles/Gene/1.1-DRAFT", + "https://github.com/BioSchemas/specifications/blob/master/Gene/jsonld/Gene_v1.1-DRAFT.json" ] }, { @@ -1905,8 +1905,8 @@ }, "additional_type": "https://bioschemas.org/profiles#nav-draft", "schema:schemaVersion": [ - "https://github.com/BioSchemas/specifications/tree/master/ChemicalSubstance/jsonld/ChemicalSubstance_v0.5-DRAFT.json", - "https://bioschemas.org/profiles/ChemicalSubstance/0.5-DRAFT" + "https://bioschemas.org/profiles/ChemicalSubstance/0.5-DRAFT", + "https://github.com/BioSchemas/specifications/tree/master/ChemicalSubstance/jsonld/ChemicalSubstance_v0.5-DRAFT.json" ] }, { @@ -2775,8 +2775,8 @@ }, "additional_type": "https://bioschemas.org/profiles#nav-draft", "schema:schemaVersion": [ - "https://bioschemas.org/profiles/ComputationalTool/1.1-DRAFT", - "https://github.com/BioSchemas/specifications/tree/master/ComputationalTool/jsonld/ComputationalTool_v1.1-DRAFT.json" + "https://github.com/BioSchemas/specifications/tree/master/ComputationalTool/jsonld/ComputationalTool_v1.1-DRAFT.json", + "https://bioschemas.org/profiles/ComputationalTool/1.1-DRAFT" ] }, { @@ -5031,8 +5031,8 @@ }, "additional_type": "https://bioschemas.org/profiles#nav-draft", "schema:schemaVersion": [ - "https://bioschemas.org/profiles/ComputationalWorkflow/1.1-DRAFT", - "https://github.com/BioSchemas/specifications/tree/master/ComputationalWorkflow/jsonld/ComputationalWorkflow_v1.1-DRAFT.json" + "https://github.com/BioSchemas/specifications/tree/master/ComputationalWorkflow/jsonld/ComputationalWorkflow_v1.1-DRAFT.json", + "https://bioschemas.org/profiles/ComputationalWorkflow/1.1-DRAFT" ] }, { @@ -7923,8 +7923,8 @@ }, "additional_type": "https://bioschemas.org/profiles#nav-draft", "schema:schemaVersion": [ - "https://bioschemas.org/profiles/DataCatalog/0.4-DRAFT", - "https://github.com/BioSchemas/specifications/tree/master/DataCatalog/jsonld/DataCatalog_v0.4-DRAFT.json" + "https://github.com/BioSchemas/specifications/tree/master/DataCatalog/jsonld/DataCatalog_v0.4-DRAFT.json", + "https://bioschemas.org/profiles/DataCatalog/0.4-DRAFT" ] }, { @@ -7932,8 +7932,8 @@ "@type": "rdfs:Class", "rdfs:comment": "A guide for how to describe datasets in the life-sciences using Schema.org-like annotation. Version 1.1-DRAFT.

Summary of Changes


Key changes since 1.0-RELEASE:", "schema:schemaVersion": [ - "https://bioschemas.org/profiles/Dataset/1.1-DRAFT", - "https://github.com/BioSchemas/specifications/tree/master/Dataset/jsonld/Dataset_v1.1-DRAFT.json" + "https://github.com/BioSchemas/specifications/tree/master/Dataset/jsonld/Dataset_v1.1-DRAFT.json", + "https://bioschemas.org/profiles/Dataset/1.1-DRAFT" ], "rdfs:label": "Dataset", "rdfs:subClassOf": { @@ -8932,8 +8932,8 @@ }, "additional_type": "https://bioschemas.org/profiles#nav-draft", "schema:schemaVersion": [ - "https://bioschemas.org/profiles/Disease/0.2-DRAFT", - "https://github.com/BioSchemas/specifications/tree/master/Disease/jsonld/Disease_v0.2-DRAFT.json" + "https://github.com/BioSchemas/specifications/tree/master/Disease/jsonld/Disease_v0.2-DRAFT.json", + "https://bioschemas.org/profiles/Disease/0.2-DRAFT" ] }, { @@ -8941,8 +8941,8 @@ "@type": "rdfs:Class", "rdfs:comment": "Specification for describing an event in the Life Sciences Specification for describing a Life Science event. This includes conferences, workshops, meetings, courses, receptions, networking and prizegivings. Version 0.3-DRAFT.

Summary of Changes

Changes since 0.2-DRAFT-2019_06_14", "schema:schemaVersion": [ - "https://github.com/BioSchemas/specifications/tree/master/Event/jsonld/Event_v0.3-DRAFT.json", - "https://bioschemas.org/profiles/Event/0.3-DRAFT" + "https://bioschemas.org/profiles/Event/0.3-DRAFT", + "https://github.com/BioSchemas/specifications/tree/master/Event/jsonld/Event_v0.3-DRAFT.json" ], "rdfs:label": "Event", "rdfs:subClassOf": { @@ -10002,8 +10002,8 @@ }, "additional_type": "https://bioschemas.org/profiles#nav-draft", "schema:schemaVersion": [ - "https://bioschemas.org/profiles/FormalParameter/1.1-DRAFT", - "https://github.com/BioSchemas/specifications/tree/master/FormalParameter/jsonld/FormalParameter_v1.1-DRAFT.json" + "https://github.com/BioSchemas/specifications/tree/master/FormalParameter/jsonld/FormalParameter_v1.1-DRAFT.json", + "https://bioschemas.org/profiles/FormalParameter/1.1-DRAFT" ] }, { @@ -10011,8 +10011,8 @@ "@type": "rdfs:Class", "rdfs:comment": "Bioschemas profile, based on Biotea model, describing a Journal in Life Sciences. A Journal is a collection of publication issues, publication volumes or scholarly articles, or possibly, although no commonly, any mix from those mentioned. Version 0.3-DRAFT

Summary of Changes


Changes since previous draft 0.2 Journal profile: ", "schema:schemaVersion": [ - "https://github.com/BioSchemas/specifications/tree/master/Journal/jsonld/Journal_v0.3-DRAFT.json", - "https://bioschemas.org/profiles/Journal/0.3-DRAFT" + "https://bioschemas.org/profiles/Journal/0.3-DRAFT", + "https://github.com/BioSchemas/specifications/tree/master/Journal/jsonld/Journal_v0.3-DRAFT.json" ], "rdfs:label": "Journal", "rdfs:subClassOf": { @@ -10535,91 +10535,125 @@ "additional_type": "https://bioschemas.org/profiles#nav-draft" }, { - "@id": "bioschemasdrafts:LabProtocol", + "@id": "bioschemasdrafts:MolecularEntity", "@type": "rdfs:Class", - "rdfs:comment": "Bioschemas profile describing a LabProtocol in Life Sciences. An experimental LabProtocol is a sequence of tasks and operations executed to perform experimental research in biological and biomedical areas. This LabProtocol profile specification presents the markup for describing a LabProtocol type according to Bioschemas. An experimental LabProtocol is a sequence of tasks and operations executed to perform experimental research in biological and biomedical areas. Version 0.7-DRAFT.

Summary of Changes


Changes since previous draft 0.5 of the LabProtocols profile: ", - "schema:schemaVersion": [ - "https://bioschemas.org/profiles/LabProtocol/0.7-DRAFT", - "https://github.com/BioSchemas/specifications/tree/master/LabProtocol/jsonld/LabProtocol_v0.7-DRAFT.json" - ], - "rdfs:label": "LabProtocol", + "rdfs:comment": "Bioschemas profile describing a MolecularEntity. Any constitutionally or isotopically distinct atom, molecule, ion, ion pair, radical, radical ion, complex, conformer etc., identifiable as a separately distinguishable entity. (Source: ChEBI:23367) Version 0.7-DRAFT.

Summary of Changes


Changes since 0.6-DRAFT:", + "rdfs:label": "MolecularEntity", "rdfs:subClassOf": { - "@id": "bioschemastypesdrafts:LabProtocol" + "@id": "schema:MolecularEntity" }, "$validation": { "$schema": "http://json-schema.org/draft-07/schema#", "type": "object", "properties": { - "author": { - "description": " The author of this content or rating. Please note that author is special in that HTML 5 provides a special mechanism for indicating authorship via the rel tag. That is equivalent to this and may be used interchangeably.", - "anyOf": [ + "inChI": { + "description": "Non-proprietary identifier for molecular entity that can be used in printed and electronic data sources thus enabling easier linking of diverse data compilations.", + "type": "string", + "owl:cardinality": "one" + }, + "inChIKey": { + "description": "InChIKey is a hashed version of the full InChI (using the SHA-256 algorithm).", + "type": "string", + "owl:cardinality": "one" + }, + "iupacName": { + "description": "Systematic method of naming chemical compounds as recommended by the International Union of Pure and Applied Chemistry (IUPAC).", + "type": "string", + "owl:cardinality": "one" + }, + "molecularFormula": { + "description": "The empirical formula is the simplest whole number ratio of all the atoms in a molecule.", + "type": "string", + "owl:cardinality": "one" + }, + "molecularWeight": { + "description": "This is the molecular weight of the entity being described, not of the parent. Units should be included in the form \u2018 ', for example '12 amu' or as '.", + "oneOf": [ { - "$ref": "#/definitions/organization" + "$ref": "#/definitions/quantitativeValue" }, { - "type": "array", - "items": { - "$ref": "#/definitions/organization" - } - }, + "type": "string" + } + ], + "owl:cardinality": "one" + }, + "smiles": { + "description": "A specification in form of a line notation for describing the structure of chemical species using short ASCII strings. Double bond stereochemistry \\ indicators may need to be escaped in the string in formats where the backslash is an escape character.", + "oneOf": [ { - "$ref": "#/definitions/person" + "type": "string" }, { "type": "array", "items": { - "$ref": "#/definitions/person" + "type": "string" } } ], "owl:cardinality": "many" }, - "bioSampleUsed": { - "description": " BioSample used in the protocol. It could be a record in a Dataset describing the sample or a physical object corresponding to the sample or a URL pointing to the type of sample used. ", - "anyOf": [ + "chemicalRole": { + "description": "A role played by the BioChemEntity within a chemical context.", + "oneOf": [ { - "$ref": "#/definitions/biosample" + "$ref": "#/definitions/definedTerm" }, { "type": "array", "items": { - "$ref": "#/definitions/biosample" + "$ref": "#/definitions/definedTerm" } - }, + } + ], + "owl:cardinality": "many" + }, + "monoisotopicMolecularWeight": { + "description": "The monoisotopic mass is the sum of the masses of the atoms in a molecule using the unbound, ground-state, rest mass of the principal (most abundant) isotope for each element instead of the isotopic average mass. Please include the units the form \u2018 ', for example '770.230488 g/mol' or as '.", + "oneOf": [ { - "$ref": "#/definitions/taxon" + "$ref": "#/definitions/quantitativeValue" }, { - "type": "array", - "items": { - "$ref": "#/definitions/taxon" - } - }, + "type": "string" + } + ], + "owl:cardinality": "one" + }, + "potentialUse": { + "description": "Intended use of the BioChemEntity by humans.", + "oneOf": [ { - "$ref": "#/definitions/biochementity" + "$ref": "#/definitions/definedTerm" }, { "type": "array", "items": { - "$ref": "#/definitions/biochementity" + "$ref": "#/definitions/definedTerm" } - }, + } + ], + "owl:cardinality": "many" + }, + "associatedDisease": { + "description": "Disease associated to this BioChemEntity. Such a disease can be a MedicalCondition or a URL. If you want to add an evidence supporting the association, please use PropertyValue.", + "anyOf": [ { - "$ref": "#/definitions/definedterm" + "$ref": "#/definitions/medicalCondition" }, { "type": "array", "items": { - "$ref": "#/definitions/definedterm" + "$ref": "#/definitions/medicalCondition" } }, { - "type": "string" + "$ref": "#/definitions/propertyValue" }, { "type": "array", "items": { - "type": "string" + "$ref": "#/definitions/propertyValue" } }, { @@ -10636,135 +10670,94 @@ ], "owl:cardinality": "many" }, - "citation": { - "description": " A citation or reference to another creative work, such as another publication, web page, scholarly article, etc.", - "anyOf": [ - { - "$ref": "#/definitions/creativework" - }, - { - "type": "array", - "items": { - "$ref": "#/definitions/creativework" - } - }, + "bioChemInteraction": { + "description": "A BioChemEntity that is know to interact with this item.", + "oneOf": [ { - "type": "string" + "$ref": "#/definitions/bioChemEntity" }, { "type": "array", "items": { - "type": "string" + "$ref": "#/definitions/bioChemEntity" } } ], "owl:cardinality": "many" }, - "dateCreated": { - "description": " The date on which the CreativeWork was created or the item was added to a DataFeed.", - "oneOf": [ - { - "type": "string", - "format": "date" - }, - { - "$ref": "#/definitions/datetime" - } - ], - "owl:cardinality": "one" - }, - "dateModified": { - "description": "Last modified date The date on which the CreativeWork was most recently modified or when the item's entry was modified within a DataFeed.", + "bioChemSimilarity": { + "description": "A similar molecular entity, e.g., obtained by fingerprint similarity algorithm.", "oneOf": [ { - "type": "string", - "format": "date" + "$ref": "#/definitions/bioChemEntity" }, { - "$ref": "#/definitions/datetime" + "type": "array", + "items": { + "$ref": "#/definitions/bioChemEntity" + } } ], - "owl:cardinality": "one" + "owl:cardinality": "many" }, - "datePublished": { - "description": "Many is used to cover original printed and electronic publication dates. Date of first broadcast/publication.", + "biologicalRole": { + "description": "A role played by the molecular entity within a biological context.", "oneOf": [ { - "type": "string", - "format": "date" + "$ref": "#/definitions/definedTerm" }, { "type": "array", "items": { - "type": "string", - "format": "date" + "$ref": "#/definitions/definedTerm" } } ], "owl:cardinality": "many" }, - "description": { - "description": " A description of the item.", - "type": "string", - "owl:cardinality": "one" - }, - "headline": { - "description": "Main title of the LabProtocol Headline of the article.", - "type": "string", - "owl:cardinality": "one" - }, - "identifier": { - "description": " The identifier property represents any kind of identifier for any kind of Thing, such as ISBNs, GTIN codes, UUIDs etc. Schema.org provides dedicated properties for representing many of these, either as textual strings or as URL (URI) links. See [background notes](http://schema.org/docs/datamodel.html#identifierBg) for more details.", + "hasBioChemEntityPart": { + "description": "Indicates a BioChemEntity that (in some sense) has this BioChemEntity as a part. Inverse property: isPartOfBioChemEntity", "oneOf": [ { - "$ref": "#/definitions/propertyvalue" - }, - { - "type": "string" + "$ref": "#/definitions/bioChemEntity" }, { - "type": "string", - "format": "uri" + "type": "array", + "items": { + "$ref": "#/definitions/bioChemEntity" + } } ], - "owl:cardinality": "one" + "owl:cardinality": "many" }, - "isBasedOn": { - "description": "Note: Bioschemas has removed Product from the Expected Types A resource that was used in the creation of this resource. This term can be repeated for multiple sources. For example, http://example.com/great-multiplication-intro.html. Supersedes isBasedOnUrl.", + "hasMolecularFunction": { + "description": "Molecular function performed by this BioChemEntity; please use PropertyValue if you want to include any evidence.", "anyOf": [ { - "$ref": "#/definitions/creativework" + "$ref": "#/definitions/definedTerm" }, { "type": "array", "items": { - "$ref": "#/definitions/creativework" + "$ref": "#/definitions/definedTerm" } }, { - "type": "string", - "format": "uri" + "$ref": "#/definitions/propertyValue" }, { "type": "array", "items": { - "type": "string", - "format": "uri" + "$ref": "#/definitions/propertyValue" } - } - ], - "owl:cardinality": "many" - }, - "isPartOf": { - "description": " Indicates an item or CreativeWork that this item, or CreativeWork (in some sense), is part of. Inverse property: hasPart.", - "anyOf": [ + }, { - "$ref": "#/definitions/creativework" + "type": "string" }, { "type": "array", "items": { - "$ref": "#/definitions/creativework" + "type": "string" } }, { @@ -10781,32 +10774,25 @@ ], "owl:cardinality": "many" }, - "keywords": { - "description": " Keywords or tags used to describe this content. Multiple entries in a keywords list are typically delimited by commas.", - "oneOf": [ + "hasRepresentation": { + "description": "A common representation such as a protein sequence or chemical structure for this entity. For images use schema.org/image.", + "anyOf": [ { - "$ref": "#/definitions/definedterm" + "$ref": "#/definitions/definedTerm" }, { - "type": "string" + "type": "array", + "items": { + "$ref": "#/definitions/definedTerm" + } }, { - "type": "string", - "format": "uri" - } - ], - "owl:cardinality": "one" - }, - "labEquipmentUsed": { - "description": " A laboratory equipment used by a person to follow one or more steps described in this LabProtocol. ", - "anyOf": [ - { - "$ref": "#/definitions/definedterm" + "$ref": "#/definitions/propertyValue" }, { "type": "array", "items": { - "$ref": "#/definitions/definedterm" + "$ref": "#/definitions/propertyValue" } }, { @@ -10832,174 +10818,143 @@ ], "owl:cardinality": "many" }, - "license": { - "description": " A license document that applies to this content, typically indicated by URL.", + "isEncodedByBioChemEntity": { + "description": "Another BioChemEntity encoding this one. Inverse property: encodesBioChemEntity.", "oneOf": [ { - "$ref": "#/definitions/creativework" + "$ref": "#/definitions/gene" }, { - "type": "string", - "format": "uri" + "type": "array", + "items": { + "$ref": "#/definitions/gene" + } } ], - "owl:cardinality": "one" - }, - "performTime": { - "description": " The length of time it takes to perform instructions or a direction (not including time to prepare the supplies), in ISO 8601 duration format.", - "$ref": "#/definitions/duration", - "owl:cardinality": "one" - }, - "prepTime": { - "description": " The length of time it takes to prepare the items to be used in instructions or a direction, in ISO 8601 duration format.", - "$ref": "#/definitions/duration", - "owl:cardinality": "one" + "owl:cardinality": "many" }, - "protocolAdvantage": { - "description": " Situations where the Protocol has been successfully employed including advantageous elements (e.g. better yield, shorter running time) (see more information here)", + "isInvolvedInBiologicalProcess": { + "description": "Biological process this BioChemEntity is involved in; please use PropertyValue if you want to include any evidence.", "anyOf": [ { - "$ref": "#/definitions/creativework" + "$ref": "#/definitions/definedTerm" }, { "type": "array", "items": { - "$ref": "#/definitions/creativework" + "$ref": "#/definitions/definedTerm" } }, { - "type": "string" + "$ref": "#/definitions/propertyValue" }, { "type": "array", "items": { - "type": "string" + "$ref": "#/definitions/propertyValue" } - } - ], - "owl:cardinality": "many" - }, - "protocolApplication": { - "description": " Applications of the protocol list the full diversity of the applications of the method and support if is possible to extend the range of applications of the protocol. e.g. northern blot assays, sequencing, etc. (see more information here)", - "anyOf": [ + }, { - "$ref": "#/definitions/creativework" + "type": "string" }, { "type": "array", "items": { - "$ref": "#/definitions/creativework" + "type": "string" } }, { - "type": "string" + "type": "string", + "format": "uri" }, { "type": "array", "items": { - "type": "string" + "type": "string", + "format": "uri" } } ], "owl:cardinality": "many" }, - "protocolLimitation": { - "description": " Situations where the Protocol would be unreliable or otherwise unsuccessful (see more information here)", + "isLocatedInSubcellularLocation": { + "description": "Subcellular location where this BioChemEntity is located; please use PropertyValue if you want to include any evidence.", "anyOf": [ { - "$ref": "#/definitions/creativework" + "$ref": "#/definitions/definedTerm" }, { "type": "array", "items": { - "$ref": "#/definitions/creativework" + "$ref": "#/definitions/definedTerm" } }, { - "type": "string" + "$ref": "#/definitions/propertyValue" }, { "type": "array", "items": { - "type": "string" + "$ref": "#/definitions/propertyValue" } - } - ], - "owl:cardinality": "many" - }, - "protocolOutcome": { - "description": " Outcome or expected result by a protocol execution (see more information here)", - "anyOf": [ + }, { - "$ref": "#/definitions/creativework" + "type": "string" }, { "type": "array", "items": { - "$ref": "#/definitions/creativework" + "type": "string" } }, { - "type": "string" + "type": "string", + "format": "uri" }, { "type": "array", "items": { - "type": "string" + "type": "string", + "format": "uri" } } ], "owl:cardinality": "many" }, - "protocolPurpose": { - "description": " The purpose of the protocol enables readers to make a decision as to the suitability of the protocol to their experimental problem. (see more information here)", + "isPartOfBioChemEntity": { + "description": "Indicates a BioChemEntity that is (in some sense) a part of this BioChemEntity. Inverse property: hasBioChemEntityPart", "oneOf": [ { - "$ref": "#/definitions/creativework" + "$ref": "#/definitions/bioChemEntity" }, { - "type": "string" + "type": "array", + "items": { + "$ref": "#/definitions/bioChemEntity" + } } ], - "owl:cardinality": "one" + "owl:cardinality": "many" }, - "reagentUsed": { - "description": " Reagents used in the protocol. ChEBI and PubChem entities can be used whenever available. Commercial names are also acceptable. A reagent is defined as 'A substance used in a chemical reaction to detect, measure, examine, or produce other substances' in CHEBI:33893", + "taxonomicRange": { + "description": "The taxonomic grouping of the organism that expresses, encodes, or in someway related to the BioChemEntity.", "anyOf": [ { - "$ref": "#/definitions/molecularentity" - }, - { - "type": "array", - "items": { - "$ref": "#/definitions/molecularentity" - } - }, - { - "$ref": "#/definitions/chemicalsubstance" - }, - { - "type": "array", - "items": { - "$ref": "#/definitions/chemicalsubstance" - } - }, - { - "$ref": "#/definitions/biochementity" + "$ref": "#/definitions/definedTerm" }, { "type": "array", "items": { - "$ref": "#/definitions/biochementity" + "$ref": "#/definitions/definedTerm" } }, { - "$ref": "#/definitions/definedterm" + "$ref": "#/definitions/taxon" }, { "type": "array", "items": { - "$ref": "#/definitions/definedterm" + "$ref": "#/definitions/taxon" } }, { @@ -11025,80 +10980,74 @@ ], "owl:cardinality": "many" }, - "softwareUsed": { - "description": " Software or tool used as part of the lab protocol to complete a part of it.", - "anyOf": [ - { - "$ref": "#/definitions/softwareapplication" - }, - { - "type": "array", - "items": { - "$ref": "#/definitions/softwareapplication" - } - }, + "alternateName": { + "description": "An alias for the item.", + "oneOf": [ { - "type": "string", - "format": "uri" + "type": "string" }, { "type": "array", "items": { - "type": "string", - "format": "uri" + "type": "string" } } ], "owl:cardinality": "many" }, - "step": { - "description": " A single step item (as HowToStep, text, document, video, etc.) or a HowToSection.", + "description": { + "description": "A description of the item.", + "type": "string", + "owl:cardinality": "one" + }, + "disambiguatingDescription": { + "description": "A sub property of description. A short description of the item used to disambiguate from other, similar items. Information from other properties (in particular, name) may be necessary for the description to be useful for disambiguation.", + "type": "string", + "owl:cardinality": "one" + }, + "identifier": { + "description": "The identifier property represents any kind of identifier for any kind of Thing, such as ISBNs, GTIN codes, UUIDs etc. Schema.org provides dedicated properties for representing many of these, either as textual strings or as URL (URI) links. See background notes for more details.", "anyOf": [ { - "$ref": "#/definitions/creativework" - }, - { - "type": "array", - "items": { - "$ref": "#/definitions/creativework" - } - }, - { - "$ref": "#/definitions/howtosection" + "$ref": "#/definitions/definedTerm" }, { - "type": "array", - "items": { - "$ref": "#/definitions/howtosection" - } + "$ref": "#/definitions/propertyValue" }, { - "$ref": "#/definitions/howtostep" + "type": "string" }, { - "type": "array", - "items": { - "$ref": "#/definitions/howtostep" - } - }, + "type": "string", + "format": "uri" + } + ], + "owl:cardinality": "one" + }, + "image": { + "description": "An image of the item. This can be a URL or a fully described ImageObject.", + "oneOf": [ { - "type": "string" + "type": "string", + "format": "uri" }, { "type": "array", "items": { - "type": "string" + "type": "string", + "format": "uri" } } ], "owl:cardinality": "many" }, - "totalTime": { - "description": " The total time required to perform instructions or a direction (including time to prepare the supplies), in ISO 8601 duration format.", - "$ref": "#/definitions/duration", + "name": { + "description": "The name of the item.", + "type": "string", "owl:cardinality": "one" }, "sameAs": { + "description": "URL of a reference Web page that unambiguously indicates the item's identity. E.g. the URL of the item's Wikipedia page, Wikidata entry, or official website.", "oneOf": [ { "type": "string", @@ -11112,124 +11061,88 @@ } } ], - "description": "URL of additional sources for the dataset", + "owl:cardinality": "many" + }, + "subjectOf": { + "description": "A CreativeWork or Event about this Thing. Inverse property: about", + "oneOf": [ + { + "$ref": "#/definitions/creativework" + }, + { + "type": "array", + "items": { + "$ref": "#/definitions/creativework" + } + }, + { + "$ref": "#/definitions/event" + }, + { + "type": "array", + "items": { + "$ref": "#/definitions/event" + } + } + ], "owl:cardinality": "many" }, "conformsTo": { - "description": "This is used to state the Bioschemas profile that the markup relates to. The identifier can be the url for the version of this bioschemas class on github: https://github.com/BioSchemas/specifications/tree/master/LabProtocol/jsonld/LabProtocol_v0.7-DRAFT.json", + "description": "This is used to state the Bioschemas profile that the markup relates to. The identifier can be the url for the version of this bioschemas class on github: https://github.com/BioSchemas/specifications/tree/master/MolecularEntity/jsonld/MolecularEntity_v0.7-DRAFT.json", "$ref": "#/definitions/conformsDefinition" } }, "required": [ - "bioSampleUsed", - "headline", - "keywords", - "labEquipmentUsed", - "protocolPurpose", - "reagentUsed", "conformsTo" ], "recommended": [ - "author", - "citation", - "identifier", - "isPartOf", - "license", - "protocolAdvantage", - "protocolApplication", - "protocolLimitation", - "protocolOutcome", - "softwareUsed", - "step", - "totalTime", + "inChIKey", + "iupacName", + "molecularFormula", + "molecularWeight", "sameAs" ], "optional": [ - "dateCreated", - "dateModified", - "datePublished", + "identifier", + "alternateName", + "associatedDisease", + "bioChemInteraction", + "bioChemSimilarity", + "biologicalRole", + "chemicalRole", "description", - "isBasedOn", - "performTime", - "prepTime" + "disambiguatingDescription", + "hasBioChemEntityPart", + "hasMolecularFunction", + "hasRepresentation", + "image", + "isEncodedByBioChemEntity", + "isInvolvedInBiologicalProcess", + "isLocatedInSubcellularLocation", + "isPartOfBioChemEntity", + "monoisotopicMolecularWeight", + "potentialUse", + "taxonomicRange", + "subjectOf" + ], + "anyOf": [ + { + "required": [ + "name" + ] + }, + { + "required": [ + "inChI" + ] + }, + { + "required": [ + "smiles" + ] + } ], "definitions": { - "organization": { - "@type": "Organization", - "type": "object", - "properties": { - "name": { - "type": "string" - }, - "legalName": { - "type": "string" - }, - "description": { - "type": "string" - }, - "sameAs": { - "type": "string", - "format": "uri" - } - } - }, - "person": { - "@type": "Person", - "type": "object", - "properties": { - "name": { - "type": "string" - }, - "url": { - "type": "string", - "format": "uri" - }, - "mainEntityOfPage": { - "anyOf": [ - { - "type": "string", - "format": "uri" - }, - { - "type": "array", - "items": { - "type": "string", - "format": "uri" - } - }, - { - "$ref": "#/definitions/creativework" - }, - { - "type": "array", - "items": { - "$ref": "#/definitions/creativework" - } - } - ] - } - }, - "required": [ - "name" - ] - }, - "creativework": { - "@type": "CreativeWork", - "type": "object", - "properties": { - "name": { - "type": "string" - }, - "identifier": { - "type": "string" - }, - "url": { - "type": "string", - "format": "uri" - } - }, - "required": [] - }, "taxon": { "@type": "bioschemas:Taxon", "type": "object", @@ -11240,12 +11153,12 @@ "taxonRank": { "anyOf": [ { - "$ref": "#/definitions/propertyvalue" + "$ref": "#/definitions/propertyValue" }, { "type": "array", "items": { - "$ref": "#/definitions/propertyvalue" + "$ref": "#/definitions/propertyValue" } }, { @@ -11276,24 +11189,20 @@ "taxonRank" ] }, - "biochementity": { - "@type": "bioschemas:BioChemEntity", + "propertyValue": { + "@type": "PropertyValue", "type": "object", "properties": { - "url": { - "type": "string", - "format": "uri" - }, "name": { "type": "string" }, - "identifier": { + "value": { "type": "string" } }, "required": [] }, - "definedterm": { + "definedTerm": { "@type": "DefinedTerm", "type": "object", "properties": { @@ -11306,93 +11215,47 @@ }, "termCode": { "type": "string" - }, - "identifier": { - "type": "string" - }, - "inDefinedTermSet": { - "$ref": "#/definitions/definedtermset" } }, "required": [] }, - "biosample": { - "@type": "bioschemas:BioSample", + "medicalCondition": { + "@type": "MedicalCondition", "type": "object", "properties": { + "url": { + "type": "string", + "format": "uri" + }, "name": { "type": "string" } }, "required": [] }, - "definedtermset": { - "@type": "DefinedTermSet", + "bioChemEntity": { + "@type": "bioschemas:BioChemEntity", "type": "object", "properties": { - "name": { - "type": "string" - }, - "identifier": { - "type": "string" - }, "url": { "type": "string", "format": "uri" - } - }, - "required": [] - }, - "datetime": { - "@type": "schema:DateTime", - "type": "object", - "properties": { + }, "name": { "type": "string" } }, "required": [] }, - "propertyvalue": { - "@type": "PropertyValue", + "gene": { + "@type": "bioschemas:Gene", "type": "object", "properties": { - "name": { - "type": "string" - }, - "value": { - "oneOf": [ - { - "type": "string" - }, - { - "type": "boolean" - }, - { - "type": "number" - } - ] - }, "identifier": { - "type": "string" - }, - "valuereference": { - "oneOf": [ + "anyOf": [ { - "$ref": "#/definitions/categorycode" + "$ref": "#/definitions/propertyValue" }, - { - "type": "array", - "items": [ - { - "$ref": "#/definitions/categorycode" - } - ] - } - ] - }, - "unitCode": { - "oneOf": [ { "type": "string" }, @@ -11402,84 +11265,27 @@ } ] }, - "unitText": { - "type": "string" - } - }, - "required": [ - "name", - "value" - ], - "recommended": [ - "valueReference" - ], - "optional": [ - "unitCode", - "unitText" - ] - }, - "categorycode": { - "@type": "CategoryCode", - "type": "object", - "properties": { - "name": { - "type": "string" - }, - "codeValue": { - "type": "string" - }, - "url": { - "type": "string" - } - }, - "required": [ - "name", - "codeValue", - "url" - ] - }, - "duration": { - "@type": "schema:Duration", - "type": "object", - "properties": { - "name": { - "type": "string" - } - }, - "required": [] - }, - "molecularentity": { - "@type": "bioschemas:MolecularEntity", - "type": "object", - "properties": { "name": { "type": "string" } }, "required": [] }, - "chemicalsubstance": { - "@type": "bioschemas:ChemicalSubstance", + "quantitativeValue": { + "@type": "QuantitativeValue", "type": "object", "properties": { - "name": { + "value": { "type": "string" - } - }, - "required": [] - }, - "softwareapplication": { - "@type": "schema:SoftwareApplication", - "type": "object", - "properties": { - "name": { + }, + "unitText": { "type": "string" } }, "required": [] }, - "howtosection": { - "@type": "schema:HowToSection", + "creativework": { + "@type": "CreativeWork", "type": "object", "properties": { "name": { @@ -11488,8 +11294,8 @@ }, "required": [] }, - "howtostep": { - "@type": "schema:HowToStep", + "event": { + "@type": "Event", "type": "object", "properties": { "name": { @@ -11507,7 +11313,7 @@ "oneOf": [ { "enum": [ - "https://github.com/BioSchemas/specifications/tree/master/LabProtocol/jsonld/LabProtocol_v0.7-DRAFT.json" + "https://github.com/BioSchemas/specifications/tree/master/MolecularEntity/jsonld/MolecularEntity_v0.7-DRAFT.json" ] }, { @@ -11523,234 +11329,288 @@ } } }, - "additional_type": "https://bioschemas.org/profiles#nav-draft" + "additional_type": "https://bioschemas.org/profiles#nav-draft", + "schema:schemaVersion": [ + "https://bioschemas.org/profiles/MolecularEntity/0.7-DRAFT", + "https://github.com/BioSchemas/specifications/tree/master/MolecularEntity/jsonld/MolecularEntity_v0.7-DRAFT.json" + ] }, { - "@id": "bioschemasdrafts:MolecularEntity", + "@id": "bioschemasdrafts:Organization", "@type": "rdfs:Class", - "rdfs:comment": "Bioschemas profile describing a MolecularEntity. Any constitutionally or isotopically distinct atom, molecule, ion, ion pair, radical, radical ion, complex, conformer etc., identifiable as a separately distinguishable entity. (Source: ChEBI:23367) Version 0.7-DRAFT.

Summary of Changes


Changes since 0.6-DRAFT:", - "rdfs:label": "MolecularEntity", + "rdfs:comment": "Bioschemas specification for describing a Organization in the life-science. Provides a way to describe bioscience organizations on the World Wide Web. It defines metadata terms that can be used in the code of web pages and applications, and builds on top of existing technologies and standards. The goal of the specification is to make it easier to discover, exchange and integrate life science organization profiles across the Internet. Version: 0.3-DRAFT.

Summary of Changes


Changes since 0.2-DRAFT.", + "schema:schemaVersion": [ + "https://bioschemas.org/profiles/Organization/0.3-DRAFT", + "https://github.com/BioSchemas/specifications/tree/master/Organization/jsonld/Organization_v0.3-DRAFT.json" + ], + "rdfs:label": "Organization", "rdfs:subClassOf": { - "@id": "schema:MolecularEntity" + "@id": "schema:Organization" }, "$validation": { "$schema": "http://json-schema.org/draft-07/schema#", "type": "object", "properties": { - "inChI": { - "description": "Non-proprietary identifier for molecular entity that can be used in printed and electronic data sources thus enabling easier linking of diverse data compilations.", - "type": "string", - "owl:cardinality": "one" - }, - "inChIKey": { - "description": "InChIKey is a hashed version of the full InChI (using the SHA-256 algorithm).", - "type": "string", - "owl:cardinality": "one" - }, - "iupacName": { - "description": "Systematic method of naming chemical compounds as recommended by the International Union of Pure and Applied Chemistry (IUPAC).", - "type": "string", - "owl:cardinality": "one" - }, - "molecularFormula": { - "description": "The empirical formula is the simplest whole number ratio of all the atoms in a molecule.", + "alternateName": { + "description": " An alias for the item.", "type": "string", "owl:cardinality": "one" }, - "molecularWeight": { - "description": "This is the molecular weight of the entity being described, not of the parent. Units should be included in the form \u2018 ', for example '12 amu' or as '.", - "oneOf": [ - { - "$ref": "#/definitions/quantitativeValue" - }, - { - "type": "string" - } - ], - "owl:cardinality": "one" - }, - "smiles": { - "description": "A specification in form of a line notation for describing the structure of chemical species using short ASCII strings. Double bond stereochemistry \\ indicators may need to be escaped in the string in formats where the backslash is an escape character.", + "attachment": { + "description": "Any files or related websites which give more information about this organization, e.g., flyers, third party sites, ... ", "oneOf": [ { - "type": "string" + "type": "string", + "format": "uri" }, { "type": "array", "items": { - "type": "string" + "type": "string", + "format": "uri" } } ], "owl:cardinality": "many" }, - "chemicalRole": { - "description": "A role played by the BioChemEntity within a chemical context.", + "budget": { + "description": "The annual (or total - for a project) budget for the organization. ", + "$ref": "#/definitions/pricespecification", + "owl:cardinality": "one" + }, + "contactPoint": { + "description": " A contact point for a person or organization. Supersedes contactPoints.", "oneOf": [ { - "$ref": "#/definitions/definedTerm" + "$ref": "#/definitions/contactpoint" }, { "type": "array", "items": { - "$ref": "#/definitions/definedTerm" + "$ref": "#/definitions/contactpoint" } } ], "owl:cardinality": "many" }, - "monoisotopicMolecularWeight": { - "description": "The monoisotopic mass is the sum of the masses of the atoms in a molecule using the unbound, ground-state, rest mass of the principal (most abundant) isotope for each element instead of the isotopic average mass. Please include the units the form \u2018 ', for example '770.230488 g/mol' or as '.", + "dateModified": { + "description": "The date when the organization information was last modified. The date on which the CreativeWork was most recently modified or when the item's entry was modified within a DataFeed.", "oneOf": [ { - "$ref": "#/definitions/quantitativeValue" + "type": "string", + "format": "date" }, { - "type": "string" + "$ref": "#/definitions/datetime" } ], "owl:cardinality": "one" }, - "potentialUse": { - "description": "Intended use of the BioChemEntity by humans.", + "department": { + "description": " A relationship between an organization and a department of that organization, also described as an organization (allowing different urls, logos, opening hours). For example: a store with a pharmacy, or a bakery with a cafe.", "oneOf": [ { - "$ref": "#/definitions/definedTerm" + "$ref": "#/definitions/organization" }, { "type": "array", "items": { - "$ref": "#/definitions/definedTerm" + "$ref": "#/definitions/organization" } } ], "owl:cardinality": "many" }, - "associatedDisease": { - "description": "Disease associated to this BioChemEntity. Such a disease can be a MedicalCondition or a URL. If you want to add an evidence supporting the association, please use PropertyValue.", + "description": { + "description": " A description of the item.", + "type": "string", + "owl:cardinality": "one" + }, + "dissolutionDate": { + "description": " The date that this organization was dissolved.", + "type": "string", + "format": "date", + "owl:cardinality": "one" + }, + "founderMember": { + "description": "For an alliance or collaboration or project, the founding members. NOTE: schema/Organization has founder but this has a type of Person not Person and Organization ", "anyOf": [ { - "$ref": "#/definitions/medicalCondition" + "$ref": "#/definitions/organization" }, { "type": "array", "items": { - "$ref": "#/definitions/medicalCondition" + "$ref": "#/definitions/organization" } }, { - "$ref": "#/definitions/propertyValue" + "$ref": "#/definitions/person" }, { "type": "array", "items": { - "$ref": "#/definitions/propertyValue" + "$ref": "#/definitions/person" } + } + ], + "owl:cardinality": "many" + }, + "foundingDate": { + "description": " The date that this organization was founded.", + "type": "string", + "format": "date", + "owl:cardinality": "one" + }, + "fundingModel": { + "description": "A description of how the organization is funded. ", + "type": "string", + "owl:cardinality": "one" + }, + "keywords": { + "description": " Keywords or tags used to describe this content. Multiple entries in a keywords list are typically delimited by commas.", + "type": "string", + "owl:cardinality": "one" + }, + "legalName": { + "description": " The official name of the organization, e.g. the registered company name.", + "type": "string", + "owl:cardinality": "one" + }, + "location": { + "description": " The location of for example where the event is happening, an organization is located, or where an action takes place.", + "oneOf": [ + { + "$ref": "#/definitions/place" + }, + { + "$ref": "#/definitions/postaladdress" + }, + { + "type": "string" + } + ], + "owl:cardinality": "one" + }, + "logo": { + "description": " An associated logo.", + "oneOf": [ + { + "$ref": "#/definitions/imageobject" }, { "type": "string", "format": "uri" + } + ], + "owl:cardinality": "one" + }, + "member": { + "description": " A member of an Organization or a ProgramMembership. Organizations can be members of organizations; ProgramMembership is typically for individuals. Supersedes members, musicGroupMember.\nInverse property: memberOf.", + "anyOf": [ + { + "$ref": "#/definitions/organization" }, { "type": "array", "items": { - "type": "string", - "format": "uri" + "$ref": "#/definitions/organization" } - } - ], - "owl:cardinality": "many" - }, - "bioChemInteraction": { - "description": "A BioChemEntity that is know to interact with this item.", - "oneOf": [ + }, { - "$ref": "#/definitions/bioChemEntity" + "$ref": "#/definitions/person" }, { "type": "array", "items": { - "$ref": "#/definitions/bioChemEntity" + "$ref": "#/definitions/person" } } ], "owl:cardinality": "many" }, - "bioChemSimilarity": { - "description": "A similar molecular entity, e.g., obtained by fingerprint similarity algorithm.", - "oneOf": [ + "memberOf": { + "description": " An Organization (or ProgramMembership) to which this Person or Organization belongs.\nInverse property: member.", + "anyOf": [ { - "$ref": "#/definitions/bioChemEntity" + "$ref": "#/definitions/organization" }, { "type": "array", "items": { - "$ref": "#/definitions/bioChemEntity" + "$ref": "#/definitions/organization" } - } - ], - "owl:cardinality": "many" - }, - "biologicalRole": { - "description": "A role played by the molecular entity within a biological context.", - "oneOf": [ + }, { - "$ref": "#/definitions/definedTerm" + "$ref": "#/definitions/programmembership" }, { "type": "array", "items": { - "$ref": "#/definitions/definedTerm" + "$ref": "#/definitions/programmembership" } } ], "owl:cardinality": "many" }, - "hasBioChemEntityPart": { - "description": "Indicates a BioChemEntity that (in some sense) has this BioChemEntity as a part. Inverse property: isPartOfBioChemEntity", + "membershipCategory": { + "description": "Defines a membership category and associated fees (for projects and alliances etc.). ", "oneOf": [ { - "$ref": "#/definitions/bioChemEntity" + "$ref": "#/definitions/offer" }, { "type": "array", "items": { - "$ref": "#/definitions/bioChemEntity" + "$ref": "#/definitions/offer" } } ], "owl:cardinality": "many" }, - "hasMolecularFunction": { - "description": "Molecular function performed by this BioChemEntity; please use PropertyValue if you want to include any evidence.", + "name": { + "description": " The name of the item.", + "type": "string", + "owl:cardinality": "one" + }, + "owns": { + "description": " Products owned by the organization or person.", "anyOf": [ { - "$ref": "#/definitions/definedTerm" - }, - { - "type": "array", - "items": { - "$ref": "#/definitions/definedTerm" - } - }, - { - "$ref": "#/definitions/propertyValue" + "$ref": "#/definitions/ownershipinfo" }, { "type": "array", "items": { - "$ref": "#/definitions/propertyValue" + "$ref": "#/definitions/ownershipinfo" } }, { - "type": "string" + "$ref": "#/definitions/product" }, { "type": "array", "items": { - "type": "string" + "$ref": "#/definitions/product" } - }, + } + ], + "owl:cardinality": "many" + }, + "parentOrganization": { + "description": " The larger organization that this organization is a subOrganization of, if any. Supersedes branchOf.\nInverse property: subOrganization.", + "$ref": "#/definitions/organization", + "owl:cardinality": "one" + }, + "sameAs": { + "description": " URL of a reference Web page that unambiguously indicates the item's identity. E.g. the URL of the item's Wikipedia page, Wikidata entry, or official website.", + "type": "string", + "format": "uri", + "owl:cardinality": "one" + }, + "socialMedia": { + "description": "Link to social media websites like twitter or facebook. ", + "oneOf": [ { "type": "string", "format": "uri" @@ -11765,86 +11625,29 @@ ], "owl:cardinality": "many" }, - "hasRepresentation": { - "description": "A common representation such as a protein sequence or chemical structure for this entity. For images use schema.org/image.", - "anyOf": [ + "status": { + "description": "To record if the organization is still alive, and if it were are project or alliance, what the outcome was, or if it has closed down or merged, why and when.\nNote: There is a health-lifesci.status, but this is not related to the current status property ", + "type": "string", + "owl:cardinality": "one" + }, + "subOrganization": { + "description": " A relationship between two organizations where the first includes the second, e.g., as a subsidiary. See also: the more specific 'department' property.\nInverse property: parentOrganization.", + "oneOf": [ { - "$ref": "#/definitions/definedTerm" + "$ref": "#/definitions/organization" }, { "type": "array", "items": { - "$ref": "#/definitions/definedTerm" - } - }, - { - "$ref": "#/definitions/propertyValue" - }, - { - "type": "array", - "items": { - "$ref": "#/definitions/propertyValue" - } - }, - { - "type": "string" - }, - { - "type": "array", - "items": { - "type": "string" - } - }, - { - "type": "string", - "format": "uri" - }, - { - "type": "array", - "items": { - "type": "string", - "format": "uri" - } - } - ], - "owl:cardinality": "many" - }, - "isEncodedByBioChemEntity": { - "description": "Another BioChemEntity encoding this one. Inverse property: encodesBioChemEntity.", - "oneOf": [ - { - "$ref": "#/definitions/gene" - }, - { - "type": "array", - "items": { - "$ref": "#/definitions/gene" + "$ref": "#/definitions/organization" } } ], "owl:cardinality": "many" }, - "isInvolvedInBiologicalProcess": { - "description": "Biological process this BioChemEntity is involved in; please use PropertyValue if you want to include any evidence.", + "topic": { + "description": "Scientific topics that describe the organization and its activities, ideally using an ontology term from EDAM:Topic. ", "anyOf": [ - { - "$ref": "#/definitions/definedTerm" - }, - { - "type": "array", - "items": { - "$ref": "#/definitions/definedTerm" - } - }, - { - "$ref": "#/definitions/propertyValue" - }, - { - "type": "array", - "items": { - "$ref": "#/definitions/propertyValue" - } - }, { "type": "string" }, @@ -11868,27 +11671,9 @@ ], "owl:cardinality": "many" }, - "isLocatedInSubcellularLocation": { - "description": "Subcellular location where this BioChemEntity is located; please use PropertyValue if you want to include any evidence.", + "type": { + "description": "The type of the organization should be selected from the Controlled Vocabulary column. ", "anyOf": [ - { - "$ref": "#/definitions/definedTerm" - }, - { - "type": "array", - "items": { - "$ref": "#/definitions/definedTerm" - } - }, - { - "$ref": "#/definitions/propertyValue" - }, - { - "type": "array", - "items": { - "$ref": "#/definitions/propertyValue" - } - }, { "type": "string" }, @@ -11912,51 +11697,9 @@ ], "owl:cardinality": "many" }, - "isPartOfBioChemEntity": { - "description": "Indicates a BioChemEntity that is (in some sense) a part of this BioChemEntity. Inverse property: hasBioChemEntityPart", + "url": { + "description": " URL of the item.", "oneOf": [ - { - "$ref": "#/definitions/bioChemEntity" - }, - { - "type": "array", - "items": { - "$ref": "#/definitions/bioChemEntity" - } - } - ], - "owl:cardinality": "many" - }, - "taxonomicRange": { - "description": "The taxonomic grouping of the organism that expresses, encodes, or in someway related to the BioChemEntity.", - "anyOf": [ - { - "$ref": "#/definitions/definedTerm" - }, - { - "type": "array", - "items": { - "$ref": "#/definitions/definedTerm" - } - }, - { - "$ref": "#/definitions/taxon" - }, - { - "type": "array", - "items": { - "$ref": "#/definitions/taxon" - } - }, - { - "type": "string" - }, - { - "type": "array", - "items": { - "type": "string" - } - }, { "type": "string", "format": "uri" @@ -11971,312 +11714,240 @@ ], "owl:cardinality": "many" }, - "alternateName": { - "description": "An alias for the item.", - "oneOf": [ - { + "conformsTo": { + "description": "This is used to state the Bioschemas profile that the markup relates to. The identifier can be the url for the version of this bioschemas class on github: https://github.com/BioSchemas/specifications/tree/master/Organization/jsonld/Organization_v0.3-DRAFT.json", + "$ref": "#/definitions/conformsDefinition" + } + }, + "required": [ + "description", + "legalName", + "name", + "sameAs", + "topic", + "type", + "conformsTo" + ], + "recommended": [ + "alternateName", + "contactPoint", + "fundingModel", + "keywords", + "location", + "logo", + "member", + "memberOf", + "membershipCategory", + "status", + "url", + "sameAs" + ], + "optional": [ + "attachment", + "budget", + "dateModified", + "department", + "dissolutionDate", + "founderMember", + "foundingDate", + "owns", + "parentOrganization", + "socialMedia", + "subOrganization" + ], + "definitions": { + "pricespecification": { + "@type": "schema:PriceSpecification", + "type": "object", + "properties": { + "name": { "type": "string" - }, - { - "type": "array", - "items": { - "type": "string" - } } - ], - "owl:cardinality": "many" + }, + "required": [] }, - "description": { - "description": "A description of the item.", - "type": "string", - "owl:cardinality": "one" + "contactpoint": { + "@type": "schema:ContactPoint", + "type": "object", + "properties": { + "name": { + "type": "string" + } + }, + "required": [] }, - "disambiguatingDescription": { - "description": "A sub property of description. A short description of the item used to disambiguate from other, similar items. Information from other properties (in particular, name) may be necessary for the description to be useful for disambiguation.", - "type": "string", - "owl:cardinality": "one" + "datetime": { + "@type": "schema:DateTime", + "type": "object", + "properties": { + "name": { + "type": "string" + } + }, + "required": [] }, - "identifier": { - "description": "The identifier property represents any kind of identifier for any kind of Thing, such as ISBNs, GTIN codes, UUIDs etc. Schema.org provides dedicated properties for representing many of these, either as textual strings or as URL (URI) links. See background notes for more details.", - "anyOf": [ - { - "$ref": "#/definitions/definedTerm" + "organization": { + "@type": "Organization", + "type": "object", + "properties": { + "name": { + "type": "string" }, - { - "$ref": "#/definitions/propertyValue" + "legalName": { + "type": "string" }, - { + "description": { "type": "string" }, - { + "sameAs": { "type": "string", "format": "uri" } - ], - "owl:cardinality": "one" + } }, - "image": { - "description": "An image of the item. This can be a URL or a fully described ImageObject.", - "oneOf": [ - { + "person": { + "@type": "Person", + "type": "object", + "properties": { + "name": { + "type": "string" + }, + "url": { "type": "string", "format": "uri" }, - { - "type": "array", - "items": { - "type": "string", - "format": "uri" - } - } - ], - "owl:cardinality": "many" - }, - "name": { - "description": "The name of the item.", - "type": "string", - "owl:cardinality": "one" - }, - "sameAs": { - "description": "URL of a reference Web page that unambiguously indicates the item's identity. E.g. the URL of the item's Wikipedia page, Wikidata entry, or official website.", - "oneOf": [ - { - "type": "string", - "format": "uri" - }, - { - "type": "array", - "items": { - "type": "string", - "format": "uri" - } - } - ], - "owl:cardinality": "many" - }, - "subjectOf": { - "description": "A CreativeWork or Event about this Thing. Inverse property: about", - "oneOf": [ - { - "$ref": "#/definitions/creativework" - }, - { - "type": "array", - "items": { - "$ref": "#/definitions/creativework" - } - }, - { - "$ref": "#/definitions/event" - }, - { - "type": "array", - "items": { - "$ref": "#/definitions/event" - } - } - ], - "owl:cardinality": "many" - }, - "conformsTo": { - "description": "This is used to state the Bioschemas profile that the markup relates to. The identifier can be the url for the version of this bioschemas class on github: https://github.com/BioSchemas/specifications/tree/master/MolecularEntity/jsonld/MolecularEntity_v0.7-DRAFT.json", - "$ref": "#/definitions/conformsDefinition" - } - }, - "required": [ - "conformsTo" - ], - "recommended": [ - "inChIKey", - "iupacName", - "molecularFormula", - "molecularWeight", - "sameAs" - ], - "optional": [ - "identifier", - "alternateName", - "associatedDisease", - "bioChemInteraction", - "bioChemSimilarity", - "biologicalRole", - "chemicalRole", - "description", - "disambiguatingDescription", - "hasBioChemEntityPart", - "hasMolecularFunction", - "hasRepresentation", - "image", - "isEncodedByBioChemEntity", - "isInvolvedInBiologicalProcess", - "isLocatedInSubcellularLocation", - "isPartOfBioChemEntity", - "monoisotopicMolecularWeight", - "potentialUse", - "taxonomicRange", - "subjectOf" - ], - "anyOf": [ - { - "required": [ - "name" - ] - }, - { - "required": [ - "inChI" - ] - }, - { - "required": [ - "smiles" - ] - } - ], - "definitions": { - "taxon": { - "@type": "bioschemas:Taxon", - "type": "object", - "properties": { - "name": { - "type": "string" - }, - "taxonRank": { + "mainEntityOfPage": { "anyOf": [ { - "$ref": "#/definitions/propertyValue" - }, - { - "type": "array", - "items": { - "$ref": "#/definitions/propertyValue" - } - }, - { - "type": "string" + "type": "string", + "format": "uri" }, { "type": "array", "items": { - "type": "string" + "type": "string", + "format": "uri" } }, { - "type": "string", - "format": "uri" + "$ref": "#/definitions/creativework" }, { "type": "array", "items": { - "type": "string", - "format": "uri" + "$ref": "#/definitions/creativework" } } ] } }, "required": [ - "name", - "taxonRank" + "name" ] }, - "propertyValue": { - "@type": "PropertyValue", + "creativework": { + "@type": "CreativeWork", "type": "object", "properties": { "name": { "type": "string" }, - "value": { + "identifier": { "type": "string" + }, + "url": { + "type": "string", + "format": "uri" } }, "required": [] }, - "definedTerm": { - "@type": "DefinedTerm", + "place": { + "@type": "Place", "type": "object", "properties": { - "url": { - "type": "string", - "format": "uri" - }, "name": { "type": "string" }, - "termCode": { + "address": { + "oneOf": [ + { + "type": "string" + }, + { + "$ref": "#/definitions/postaladdress" + } + ] + }, + "identifier": { "type": "string" + }, + "url": { + "type": "string", + "format": "uri" } - }, - "required": [] + } }, - "medicalCondition": { - "@type": "MedicalCondition", + "postaladdress": { + "@type": "PostalAddress", "type": "object", "properties": { - "url": { - "type": "string", - "format": "uri" + "addressCountry": { + "type": "string" }, - "name": { + "addressLocality": { + "type": "string" + }, + "addressRegion": { + "type": "string" + }, + "postOfficeBoxNumber": { + "type": "string" + }, + "postalCode": { + "type": "string" + }, + "streetAddress": { "type": "string" } - }, - "required": [] + } }, - "bioChemEntity": { - "@type": "bioschemas:BioChemEntity", + "imageobject": { + "@type": "ImageObject", "type": "object", "properties": { + "name": { + "type": "string" + }, "url": { "type": "string", "format": "uri" - }, - "name": { - "type": "string" } }, "required": [] }, - "gene": { - "@type": "bioschemas:Gene", + "programmembership": { + "@type": "schema:ProgramMembership", "type": "object", "properties": { - "identifier": { - "anyOf": [ - { - "$ref": "#/definitions/propertyValue" - }, - { - "type": "string" - }, - { - "type": "string", - "format": "uri" - } - ] - }, "name": { "type": "string" } }, "required": [] }, - "quantitativeValue": { - "@type": "QuantitativeValue", + "offer": { + "@type": "schema:Offer", "type": "object", "properties": { - "value": { - "type": "string" - }, - "unitText": { + "name": { "type": "string" } }, "required": [] }, - "creativework": { - "@type": "CreativeWork", + "ownershipinfo": { + "@type": "schema:OwnershipInfo", "type": "object", "properties": { "name": { @@ -12285,8 +11956,8 @@ }, "required": [] }, - "event": { - "@type": "Event", + "product": { + "@type": "schema:Product", "type": "object", "properties": { "name": { @@ -12304,7 +11975,7 @@ "oneOf": [ { "enum": [ - "https://github.com/BioSchemas/specifications/tree/master/MolecularEntity/jsonld/MolecularEntity_v0.7-DRAFT.json" + "https://github.com/BioSchemas/specifications/tree/master/Organization/jsonld/Organization_v0.3-DRAFT.json" ] }, { @@ -12320,171 +11991,132 @@ } } }, - "additional_type": "https://bioschemas.org/profiles#nav-draft", - "schema:schemaVersion": [ - "https://bioschemas.org/profiles/MolecularEntity/0.7-DRAFT", - "https://github.com/BioSchemas/specifications/tree/master/MolecularEntity/jsonld/MolecularEntity_v0.7-DRAFT.json" - ] + "additional_type": "https://bioschemas.org/profiles#nav-draft" }, { - "@id": "bioschemasdrafts:Organization", + "@id": "bioschemasdrafts:Person", "@type": "rdfs:Class", - "rdfs:comment": "Bioschemas specification for describing a Organization in the life-science. Provides a way to describe bioscience organizations on the World Wide Web. It defines metadata terms that can be used in the code of web pages and applications, and builds on top of existing technologies and standards. The goal of the specification is to make it easier to discover, exchange and integrate life science organization profiles across the Internet. Version: 0.3-DRAFT.

Summary of Changes


Changes since 0.2-DRAFT.", + "rdfs:comment": "A specification for describing people in life sciences The Life Science Person specification provides a way to describe bioscience events on the World Wide Web. It defines a set of metadata and vocabularies, built on top of existing technologies and standards, that can be used to represent the profile information of people in Web pages and applications. The goal of the specification is to make it easier to discover, life science profile information. Version: 0.3-DRAFT.

Summary of Changes


Changes since 0.2-DRAFT-2019_07_19:. ", "schema:schemaVersion": [ - "https://bioschemas.org/profiles/Organization/0.3-DRAFT", - "https://github.com/BioSchemas/specifications/tree/master/Organization/jsonld/Organization_v0.3-DRAFT.json" + "https://github.com/BioSchemas/specifications/tree/master/Person/jsonld/Person_v0.3-DRAFT.json", + "https://bioschemas.org/profiles/Person/0.3-DRAFT" ], - "rdfs:label": "Organization", + "rdfs:label": "Person", "rdfs:subClassOf": { - "@id": "schema:Organization" + "@id": "schema:Person" }, "$validation": { "$schema": "http://json-schema.org/draft-07/schema#", "type": "object", "properties": { - "alternateName": { - "description": " An alias for the item.", - "type": "string", - "owl:cardinality": "one" - }, - "attachment": { - "description": "Any files or related websites which give more information about this organization, e.g., flyers, third party sites, ... ", + "advisor": { + "description": "A person who has been an educational, professional or personal advisor to the person. ", "oneOf": [ { - "type": "string", - "format": "uri" + "$ref": "#/definitions/person" }, { "type": "array", "items": { - "type": "string", - "format": "uri" + "$ref": "#/definitions/person" } } ], "owl:cardinality": "many" }, - "budget": { - "description": "The annual (or total - for a project) budget for the organization. ", - "$ref": "#/definitions/pricespecification", + "curriculumVitae": { + "description": "A link or body of text describing the person's notable achievements, employment history, and contact details. ", + "oneOf": [ + { + "type": "string" + }, + { + "type": "string", + "format": "uri" + } + ], "owl:cardinality": "one" }, - "contactPoint": { - "description": " A contact point for a person or organization. Supersedes contactPoints.", + "description": { + "description": " A description of the item.", "oneOf": [ { - "$ref": "#/definitions/contactpoint" + "type": "string" }, { "type": "array", "items": { - "$ref": "#/definitions/contactpoint" + "type": "string" } } ], "owl:cardinality": "many" }, - "dateModified": { - "description": "The date when the organization information was last modified. The date on which the CreativeWork was most recently modified or when the item's entry was modified within a DataFeed.", + "email": { + "description": " Email address.", "oneOf": [ { - "type": "string", - "format": "date" + "$ref": "#/definitions/organization" }, { - "$ref": "#/definitions/datetime" + "$ref": "#/definitions/contactpoint" + }, + { + "$ref": "#/definitions/place" } ], "owl:cardinality": "one" }, - "department": { - "description": " A relationship between an organization and a department of that organization, also described as an organization (allowing different urls, logos, opening hours). For example: a store with a pharmacy, or a bakery with a cafe.", + "experience": { + "description": "A textual description of the professional experiences a person has acquired. ", "oneOf": [ { - "$ref": "#/definitions/organization" + "type": "string" }, { "type": "array", "items": { - "$ref": "#/definitions/organization" + "type": "string" } } ], "owl:cardinality": "many" }, - "description": { - "description": " A description of the item.", - "type": "string", - "owl:cardinality": "one" - }, - "dissolutionDate": { - "description": " The date that this organization was dissolved.", + "expertise": { + "description": "A textual description of the topic which a person has the most expertise in. This should make use of an ontology such as the EDAM ontology ", "type": "string", - "format": "date", + "format": "uri", "owl:cardinality": "one" }, - "founderMember": { - "description": "For an alliance or collaboration or project, the founding members. NOTE: schema/Organization has founder but this has a type of Person not Person and Organization ", - "anyOf": [ - { - "$ref": "#/definitions/organization" - }, - { - "type": "array", - "items": { - "$ref": "#/definitions/organization" - } - }, + "funding": { + "description": "Textual description of current or past funding ths person has acquired ", + "oneOf": [ { - "$ref": "#/definitions/person" + "type": "string" }, { "type": "array", "items": { - "$ref": "#/definitions/person" + "type": "string" } } ], "owl:cardinality": "many" }, - "foundingDate": { - "description": " The date that this organization was founded.", - "type": "string", - "format": "date", - "owl:cardinality": "one" - }, - "fundingModel": { - "description": "A description of how the organization is funded. ", - "type": "string", - "owl:cardinality": "one" - }, - "keywords": { - "description": " Keywords or tags used to describe this content. Multiple entries in a keywords list are typically delimited by commas.", - "type": "string", - "owl:cardinality": "one" - }, - "legalName": { - "description": " The official name of the organization, e.g. the registered company name.", - "type": "string", - "owl:cardinality": "one" - }, - "location": { - "description": " The location of for example where the event is happening, an organization is located, or where an action takes place.", + "homeLocation": { + "description": " A contact location for a person's residence.", "oneOf": [ { - "$ref": "#/definitions/place" - }, - { - "$ref": "#/definitions/postaladdress" + "$ref": "#/definitions/contactpoint" }, { - "type": "string" + "$ref": "#/definitions/place" } ], "owl:cardinality": "one" }, - "logo": { - "description": " An associated logo.", + "image": { + "description": " An image of the item. This can be a URL or a fully described ImageObject.", "oneOf": [ { "$ref": "#/definitions/imageobject" @@ -12496,112 +12128,94 @@ ], "owl:cardinality": "one" }, - "member": { - "description": " A member of an Organization or a ProgramMembership. Organizations can be members of organizations; ProgramMembership is typically for individuals. Supersedes members, musicGroupMember.\nInverse property: memberOf.", + "interest": { + "description": "Any interests held by the person. These should be single words or short phrases that relate to a person ", "anyOf": [ { - "$ref": "#/definitions/organization" + "type": "string" }, { "type": "array", "items": { - "$ref": "#/definitions/organization" + "type": "string" } }, { - "$ref": "#/definitions/person" + "type": "string", + "format": "uri" }, { "type": "array", "items": { - "$ref": "#/definitions/person" + "type": "string", + "format": "uri" } } ], "owl:cardinality": "many" }, - "memberOf": { - "description": " An Organization (or ProgramMembership) to which this Person or Organization belongs.\nInverse property: member.", - "anyOf": [ + "internatonalActivities": { + "description": "Global connetions related to teaching and scholarly work in the past 3 years ", + "oneOf": [ { - "$ref": "#/definitions/organization" + "type": "string" }, { "type": "array", "items": { - "$ref": "#/definitions/organization" + "type": "string" } - }, + } + ], + "owl:cardinality": "many" + }, + "journalReferee": { + "description": "Which journals this person is a reeree of ", + "oneOf": [ { - "$ref": "#/definitions/programmembership" + "$ref": "#/definitions/creativework" }, { "type": "array", "items": { - "$ref": "#/definitions/programmembership" + "$ref": "#/definitions/creativework" } } ], "owl:cardinality": "many" }, - "membershipCategory": { - "description": "Defines a membership category and associated fees (for projects and alliances etc.). ", + "keywords": { + "description": "Keywords to describe the person. These should be single words or short phrases that relate to a person. Keywords or tags used to describe this content. Multiple entries in a keywords list are typically delimited by commas.", "oneOf": [ { - "$ref": "#/definitions/offer" + "type": "string" }, { "type": "array", "items": { - "$ref": "#/definitions/offer" + "type": "string" } } ], "owl:cardinality": "many" }, - "name": { - "description": " The name of the item.", - "type": "string", + "knowsLanguage": { + "description": "A list of languages spoken by the Person Of a Person, and less typically of an Organization, to indicate a known language. We do not distinguish skill levels or reading/writing/speaking/signing here. Use language codes from the IETF BCP 47 standard.", + "$ref": "#/definitions/language", "owl:cardinality": "one" }, - "owns": { - "description": " Products owned by the organization or person.", + "mainEntityOfPage": { + "description": " Indicates a page (or other CreativeWork) for which this thing is the main entity being described. See background notes for details.\nInverse property: mainEntity.", "anyOf": [ { - "$ref": "#/definitions/ownershipinfo" + "$ref": "#/definitions/creativework" }, { "type": "array", "items": { - "$ref": "#/definitions/ownershipinfo" + "$ref": "#/definitions/creativework" } }, - { - "$ref": "#/definitions/product" - }, - { - "type": "array", - "items": { - "$ref": "#/definitions/product" - } - } - ], - "owl:cardinality": "many" - }, - "parentOrganization": { - "description": " The larger organization that this organization is a subOrganization of, if any. Supersedes branchOf.\nInverse property: subOrganization.", - "$ref": "#/definitions/organization", - "owl:cardinality": "one" - }, - "sameAs": { - "description": " URL of a reference Web page that unambiguously indicates the item's identity. E.g. the URL of the item's Wikipedia page, Wikidata entry, or official website.", - "type": "string", - "format": "uri", - "owl:cardinality": "one" - }, - "socialMedia": { - "description": "Link to social media websites like twitter or facebook. ", - "oneOf": [ { "type": "string", "format": "uri" @@ -12616,14 +12230,9 @@ ], "owl:cardinality": "many" }, - "status": { - "description": "To record if the organization is still alive, and if it were are project or alliance, what the outcome was, or if it has closed down or merged, why and when.\nNote: There is a health-lifesci.status, but this is not related to the current status property ", - "type": "string", - "owl:cardinality": "one" - }, - "subOrganization": { - "description": " A relationship between two organizations where the first includes the second, e.g., as a subsidiary. See also: the more specific 'department' property.\nInverse property: parentOrganization.", - "oneOf": [ + "memberOf": { + "description": " An Organization (or ProgramMembership) to which this Person or Organization belongs.\nInverse property: member.", + "anyOf": [ { "$ref": "#/definitions/organization" }, @@ -12632,64 +12241,68 @@ "items": { "$ref": "#/definitions/organization" } - } - ], - "owl:cardinality": "many" - }, - "topic": { - "description": "Scientific topics that describe the organization and its activities, ideally using an ontology term from EDAM:Topic. ", - "anyOf": [ - { - "type": "string" - }, - { - "type": "array", - "items": { - "type": "string" - } }, { - "type": "string", - "format": "uri" + "$ref": "#/definitions/programmembership" }, { "type": "array", "items": { - "type": "string", - "format": "uri" + "$ref": "#/definitions/programmembership" } } ], "owl:cardinality": "many" }, - "type": { - "description": "The type of the organization should be selected from the Controlled Vocabulary column. ", - "anyOf": [ + "name": { + "description": " The name of the item.", + "type": "string", + "owl:cardinality": "one" + }, + "orcid": { + "description": "The url of ID of the person's ORCID (see http://orcid.org) ", + "oneOf": [ { "type": "string" }, + { + "type": "string", + "format": "uri" + } + ], + "owl:cardinality": "one" + }, + "works": { + "description": "All or notable publications, presentations, training materials, research outputs or any other body of work attributed to this person. ", + "oneOf": [ + { + "$ref": "#/definitions/creativework" + }, { "type": "array", "items": { - "type": "string" + "$ref": "#/definitions/creativework" } - }, + } + ], + "owl:cardinality": "many" + }, + "worksFor": { + "description": " Organizations that the person works for.", + "oneOf": [ { - "type": "string", - "format": "uri" + "$ref": "#/definitions/organization" }, { "type": "array", "items": { - "type": "string", - "format": "uri" + "$ref": "#/definitions/organization" } } ], "owl:cardinality": "many" }, - "url": { - "description": " URL of the item.", + "sameAs": { "oneOf": [ { "type": "string", @@ -12703,99 +12316,43 @@ } } ], + "description": "URL of additional sources for the dataset", "owl:cardinality": "many" }, "conformsTo": { - "description": "This is used to state the Bioschemas profile that the markup relates to. The identifier can be the url for the version of this bioschemas class on github: https://github.com/BioSchemas/specifications/tree/master/Organization/jsonld/Organization_v0.3-DRAFT.json", + "description": "This is used to state the Bioschemas profile that the markup relates to. The identifier can be the url for the version of this bioschemas class on github: https://github.com/BioSchemas/specifications/tree/master/Person/jsonld/Person_v0.3-DRAFT.json", "$ref": "#/definitions/conformsDefinition" } }, "required": [ "description", - "legalName", + "mainEntityOfPage", "name", - "sameAs", - "topic", - "type", "conformsTo" ], "recommended": [ - "alternateName", - "contactPoint", - "fundingModel", - "keywords", - "location", - "logo", - "member", + "email", + "expertise", + "homeLocation", + "image", "memberOf", - "membershipCategory", - "status", - "url", + "orcid", + "worksFor", "sameAs" ], "optional": [ - "attachment", - "budget", - "dateModified", - "department", - "dissolutionDate", - "founderMember", - "foundingDate", - "owns", - "parentOrganization", - "socialMedia", - "subOrganization" + "advisor", + "curriculumVitae", + "experience", + "funding", + "interest", + "internatonalActivities", + "journalReferee", + "keywords", + "knowsLanguage", + "works" ], "definitions": { - "pricespecification": { - "@type": "schema:PriceSpecification", - "type": "object", - "properties": { - "name": { - "type": "string" - } - }, - "required": [] - }, - "contactpoint": { - "@type": "schema:ContactPoint", - "type": "object", - "properties": { - "name": { - "type": "string" - } - }, - "required": [] - }, - "datetime": { - "@type": "schema:DateTime", - "type": "object", - "properties": { - "name": { - "type": "string" - } - }, - "required": [] - }, - "organization": { - "@type": "Organization", - "type": "object", - "properties": { - "name": { - "type": "string" - }, - "legalName": { - "type": "string" - }, - "description": { - "type": "string" - }, - "sameAs": { - "type": "string", - "format": "uri" - } - } - }, "person": { "@type": "Person", "type": "object", @@ -12853,6 +12410,25 @@ }, "required": [] }, + "organization": { + "@type": "Organization", + "type": "object", + "properties": { + "name": { + "type": "string" + }, + "legalName": { + "type": "string" + }, + "description": { + "type": "string" + }, + "sameAs": { + "type": "string", + "format": "uri" + } + } + }, "place": { "@type": "Place", "type": "object", @@ -12879,29 +12455,15 @@ } } }, - "postaladdress": { - "@type": "PostalAddress", + "contactpoint": { + "@type": "schema:ContactPoint", "type": "object", "properties": { - "addressCountry": { - "type": "string" - }, - "addressLocality": { - "type": "string" - }, - "addressRegion": { - "type": "string" - }, - "postOfficeBoxNumber": { - "type": "string" - }, - "postalCode": { - "type": "string" - }, - "streetAddress": { + "name": { "type": "string" } - } + }, + "required": [] }, "imageobject": { "@type": "ImageObject", @@ -12917,8 +12479,8 @@ }, "required": [] }, - "programmembership": { - "@type": "schema:ProgramMembership", + "language": { + "@type": "Language", "type": "object", "properties": { "name": { @@ -12927,8 +12489,8 @@ }, "required": [] }, - "offer": { - "@type": "schema:Offer", + "programmembership": { + "@type": "ProgramMembership", "type": "object", "properties": { "name": { @@ -12937,21 +12499,26 @@ }, "required": [] }, - "ownershipinfo": { - "@type": "schema:OwnershipInfo", + "postaladdress": { + "@type": "schema:PostalAddress", "type": "object", "properties": { - "name": { + "addressCountry": { "type": "string" - } - }, - "required": [] - }, - "product": { - "@type": "schema:Product", - "type": "object", - "properties": { - "name": { + }, + "addressLocality": { + "type": "string" + }, + "addressRegion": { + "type": "string" + }, + "postOfficeBoxNumber": { + "type": "string" + }, + "postalCode": { + "type": "string" + }, + "streetAddress": { "type": "string" } }, @@ -12966,7 +12533,7 @@ "oneOf": [ { "enum": [ - "https://github.com/BioSchemas/specifications/tree/master/Organization/jsonld/Organization_v0.3-DRAFT.json" + "https://github.com/BioSchemas/specifications/tree/master/Person/jsonld/Person_v0.3-DRAFT.json" ] }, { @@ -12985,150 +12552,140 @@ "additional_type": "https://bioschemas.org/profiles#nav-draft" }, { - "@id": "bioschemasdrafts:Person", + "@id": "bioschemasdrafts:Phenotype", "@type": "rdfs:Class", - "rdfs:comment": "A specification for describing people in life sciences The Life Science Person specification provides a way to describe bioscience events on the World Wide Web. It defines a set of metadata and vocabularies, built on top of existing technologies and standards, that can be used to represent the profile information of people in Web pages and applications. The goal of the specification is to make it easier to discover, life science profile information. Version: 0.3-DRAFT.

Summary of Changes


Changes since 0.2-DRAFT-2019_07_19:. ", + "rdfs:comment": "Bioschemas profile describing a Phenotype in Life Sciences This Phenotype type specification presents the markup for describing a Phenotype. Version 0.2-DRAFT.

Summary of Changes


Changes from Previous Version:", "schema:schemaVersion": [ - "https://github.com/BioSchemas/specifications/tree/master/Person/jsonld/Person_v0.3-DRAFT.json", - "https://bioschemas.org/profiles/Person/0.3-DRAFT" + "https://github.com/BioSchemas/specifications/tree/master/Phenotype/jsonld/Phenotype_v0.2-DRAFT.json", + "https://bioschemas.org/profiles/Phenotype/0.2-DRAFT" ], - "rdfs:label": "Person", + "rdfs:label": "Phenotype", "rdfs:subClassOf": { - "@id": "schema:Person" + "@id": "bioschemastypesdrafts:Phenotype" }, "$validation": { "$schema": "http://json-schema.org/draft-07/schema#", "type": "object", "properties": { - "advisor": { - "description": "A person who has been an educational, professional or personal advisor to the person. ", + "additionalProperty": { + "description": "Before using this property, make sure none of the existing ones covers your case. Whenever possible, please use a property coined in a third-party well-know vocabulary. Please always use (i) property name to specify the name of the property, (ii) additionalType (if possible) to better specify the nature of the property (e.g., link to the third-party well-known vocabulary term), and (iii) value to link to the object/range of this property. A property-value pair representing an additional characteristics of the entitity, e.g. a product feature or another characteristic for which there is no matching property in schema.org.\n\nNote: Publishers should be aware that applications designed to use specific schema.org properties (e.g. http://schema.org/width, http://schema.org/color, http://schema.org/gtin13, ...) will typically expect such data to be provided using those properties, rather than using the generic property/value mechanism.", "oneOf": [ { - "$ref": "#/definitions/person" + "$ref": "#/definitions/propertyvalue" }, { "type": "array", "items": { - "$ref": "#/definitions/person" + "$ref": "#/definitions/propertyvalue" } } ], "owl:cardinality": "many" }, - "curriculumVitae": { - "description": "A link or body of text describing the person's notable achievements, employment history, and contact details. ", + "alternateName": { + "description": " An alias for the item.", "oneOf": [ { "type": "string" }, { - "type": "string", - "format": "uri" + "type": "array", + "items": { + "type": "string" + } } ], - "owl:cardinality": "one" + "owl:cardinality": "many" }, - "description": { - "description": " A description of the item.", + "anatomicalLocation": { + "description": " Any part of an organism, typically a component of an anatomical system. Organs, tissues, and cells are all anatomical locations.", "oneOf": [ { - "type": "string" + "$ref": "#/definitions/definedterm" }, { "type": "array", "items": { - "type": "string" + "$ref": "#/definitions/definedterm" } } ], "owl:cardinality": "many" }, - "email": { - "description": " Email address.", - "oneOf": [ + "associatedDisease": { + "description": " Disease associated to this BioChemEntity. Such a disease can be a MedicalCondition or a URL. If you want to add an evidence supporting the association, please use PropertyValue.", + "anyOf": [ { - "$ref": "#/definitions/organization" + "$ref": "#/definitions/medicalcondition" }, { - "$ref": "#/definitions/contactpoint" + "type": "array", + "items": { + "$ref": "#/definitions/medicalcondition" + } }, { - "$ref": "#/definitions/place" - } - ], - "owl:cardinality": "one" - }, - "experience": { - "description": "A textual description of the professional experiences a person has acquired. ", - "oneOf": [ - { - "type": "string" + "$ref": "#/definitions/propertyvalue" }, { "type": "array", "items": { - "type": "string" + "$ref": "#/definitions/propertyvalue" } - } - ], - "owl:cardinality": "many" - }, - "expertise": { - "description": "A textual description of the topic which a person has the most expertise in. This should make use of an ontology such as the EDAM ontology ", - "type": "string", - "format": "uri", - "owl:cardinality": "one" - }, - "funding": { - "description": "Textual description of current or past funding ths person has acquired ", - "oneOf": [ + }, { - "type": "string" + "type": "string", + "format": "uri" }, { "type": "array", "items": { - "type": "string" + "type": "string", + "format": "uri" } } ], "owl:cardinality": "many" }, - "homeLocation": { - "description": " A contact location for a person's residence.", + "bioChemAssociation": { + "description": " BioChemEntity, e.g., gene, associated to this Phenotype and relevant for its characterization, particularly useful for the molecular basis of this Phenotype.", "oneOf": [ { - "$ref": "#/definitions/contactpoint" + "$ref": "#/definitions/biochementity" }, { - "$ref": "#/definitions/place" + "type": "array", + "items": { + "$ref": "#/definitions/biochementity" + } } ], + "owl:cardinality": "many" + }, + "description": { + "description": " A description of the item.", + "type": "string", "owl:cardinality": "one" }, - "image": { - "description": " An image of the item. This can be a URL or a fully described ImageObject.", - "oneOf": [ + "hasMolecularFunction": { + "description": " Molecular function performed by this Phenotype.", + "anyOf": [ { - "$ref": "#/definitions/imageobject" + "$ref": "#/definitions/definedterm" }, { - "type": "string", - "format": "uri" - } - ], - "owl:cardinality": "one" - }, - "interest": { - "description": "Any interests held by the person. These should be single words or short phrases that relate to a person ", - "anyOf": [ + "type": "array", + "items": { + "$ref": "#/definitions/definedterm" + } + }, { - "type": "string" + "$ref": "#/definitions/propertyvalue" }, { "type": "array", "items": { - "type": "string" + "$ref": "#/definitions/propertyvalue" } }, { @@ -13145,66 +12702,67 @@ ], "owl:cardinality": "many" }, - "internatonalActivities": { - "description": "Global connetions related to teaching and scholarly work in the past 3 years ", + "identifier": { + "description": " The identifier property represents any kind of identifier for any kind of Thing, such as ISBNs, GTIN codes, UUIDs etc. Schema.org provides dedicated properties for representing many of these, either as textual strings or as URL (URI) links. See [background notes](http://schema.org/docs/datamodel.html#identifierBg) for more details.", "oneOf": [ + { + "$ref": "#/definitions/propertyvalue" + }, { "type": "string" }, { - "type": "array", - "items": { - "type": "string" - } + "type": "string", + "format": "uri" } ], - "owl:cardinality": "many" + "owl:cardinality": "one" }, - "journalReferee": { - "description": "Which journals this person is a reeree of ", - "oneOf": [ + "image": { + "description": " An image of the item. This can be a URL or a fully described ImageObject.", + "anyOf": [ { - "$ref": "#/definitions/creativework" + "$ref": "#/definitions/imageobject" }, { "type": "array", "items": { - "$ref": "#/definitions/creativework" + "$ref": "#/definitions/imageobject" } - } - ], - "owl:cardinality": "many" - }, - "keywords": { - "description": "Keywords to describe the person. These should be single words or short phrases that relate to a person. Keywords or tags used to describe this content. Multiple entries in a keywords list are typically delimited by commas.", - "oneOf": [ + }, { - "type": "string" + "type": "string", + "format": "uri" }, { "type": "array", "items": { - "type": "string" + "type": "string", + "format": "uri" } } ], "owl:cardinality": "many" }, - "knowsLanguage": { - "description": "A list of languages spoken by the Person Of a Person, and less typically of an Organization, to indicate a known language. We do not distinguish skill levels or reading/writing/speaking/signing here. Use language codes from the IETF BCP 47 standard.", - "$ref": "#/definitions/language", - "owl:cardinality": "one" - }, - "mainEntityOfPage": { - "description": " Indicates a page (or other CreativeWork) for which this thing is the main entity being described. See background notes for details.\nInverse property: mainEntity.", + "isInvolvedInBiologicalProcess": { + "description": " Biological process this Phenotype is involved in.", "anyOf": [ { - "$ref": "#/definitions/creativework" + "$ref": "#/definitions/definedterm" }, { "type": "array", "items": { - "$ref": "#/definitions/creativework" + "$ref": "#/definitions/definedterm" + } + }, + { + "$ref": "#/definitions/propertyvalue" + }, + { + "type": "array", + "items": { + "$ref": "#/definitions/propertyvalue" } }, { @@ -13221,40 +12779,46 @@ ], "owl:cardinality": "many" }, - "memberOf": { - "description": " An Organization (or ProgramMembership) to which this Person or Organization belongs.\nInverse property: member.", + "isLocatedInSubcellularLocation": { + "description": " Subcellular location where this Phenotype is located.", "anyOf": [ { - "$ref": "#/definitions/organization" + "$ref": "#/definitions/definedterm" }, { "type": "array", "items": { - "$ref": "#/definitions/organization" + "$ref": "#/definitions/definedterm" } }, { - "$ref": "#/definitions/programmembership" + "$ref": "#/definitions/propertyvalue" }, { "type": "array", "items": { - "$ref": "#/definitions/programmembership" + "$ref": "#/definitions/propertyvalue" + } + }, + { + "type": "string", + "format": "uri" + }, + { + "type": "array", + "items": { + "type": "string", + "format": "uri" } } ], "owl:cardinality": "many" }, - "name": { - "description": " The name of the item.", - "type": "string", - "owl:cardinality": "one" - }, - "orcid": { - "description": "The url of ID of the person's ORCID (see http://orcid.org) ", + "mainEntityOfPage": { + "description": "Link via DataRecord to the main DataRecord representing this entity in a dataset. It is usually preferred to use mainEntity from a DataRecord to point to its corresponding entity. Indicates a page (or other CreativeWork) for which this thing is the main entity being described. See [background notes](http://schema.org/docs/datamodel.html#mainEntityBackground) for details.\nInverse property: mainEntity.", "oneOf": [ { - "type": "string" + "$ref": "#/definitions/creativework" }, { "type": "string", @@ -13263,180 +12827,210 @@ ], "owl:cardinality": "one" }, - "works": { - "description": "All or notable publications, presentations, training materials, research outputs or any other body of work attributed to this person. ", + "name": { + "description": " The name of the item.", + "type": "string", + "owl:cardinality": "one" + }, + "sameAs": { + "description": " URL of a reference Web page that unambiguously indicates the item's identity. E.g. the URL of the item's Wikipedia page, Wikidata entry, or official website.", "oneOf": [ { - "$ref": "#/definitions/creativework" + "type": "string", + "format": "uri" }, { "type": "array", "items": { - "$ref": "#/definitions/creativework" + "type": "string", + "format": "uri" } } ], "owl:cardinality": "many" }, - "worksFor": { - "description": " Organizations that the person works for.", + "taxonomicRange": { + "description": " The taxonomic grouping of the organism that expresses the Phenotype.", "oneOf": [ { - "$ref": "#/definitions/organization" + "$ref": "#/definitions/taxon" }, { - "type": "array", - "items": { - "$ref": "#/definitions/organization" - } + "type": "string" + }, + { + "type": "string", + "format": "uri" } ], - "owl:cardinality": "many" + "owl:cardinality": "one" }, - "sameAs": { + "url": { + "description": "Link to the official webpage associated to this entity. URL of the item.", + "type": "string", + "format": "uri", + "owl:cardinality": "one" + }, + "valueReference": { + "description": " A DefinedTerm in this code set.", "oneOf": [ { - "type": "string", - "format": "uri" + "$ref": "#/definitions/definedterm" }, { "type": "array", "items": { - "type": "string", - "format": "uri" + "$ref": "#/definitions/definedterm" } } ], - "description": "URL of additional sources for the dataset", "owl:cardinality": "many" }, "conformsTo": { - "description": "This is used to state the Bioschemas profile that the markup relates to. The identifier can be the url for the version of this bioschemas class on github: https://github.com/BioSchemas/specifications/tree/master/Person/jsonld/Person_v0.3-DRAFT.json", + "description": "This is used to state the Bioschemas profile that the markup relates to. The identifier can be the url for the version of this bioschemas class on github: https://github.com/BioSchemas/specifications/tree/master/Phenotype/jsonld/Phenotype_v0.2-DRAFT.json", "$ref": "#/definitions/conformsDefinition" } }, "required": [ - "description", - "mainEntityOfPage", + "identifier", "name", "conformsTo" ], "recommended": [ - "email", - "expertise", - "homeLocation", - "image", - "memberOf", - "orcid", - "worksFor", + "bioChemAssociation", + "description", + "taxonomicRange", + "url", "sameAs" ], "optional": [ - "advisor", - "curriculumVitae", - "experience", - "funding", - "interest", - "internatonalActivities", - "journalReferee", - "keywords", - "knowsLanguage", - "works" + "additionalProperty", + "alternateName", + "anatomicalLocation", + "associatedDisease", + "hasMolecularFunction", + "image", + "isInvolvedInBiologicalProcess", + "isLocatedInSubcellularLocation", + "mainEntityOfPage", + "valueReference" ], "definitions": { - "person": { - "@type": "Person", + "propertyvalue": { + "@type": "PropertyValue", "type": "object", "properties": { "name": { "type": "string" }, - "url": { - "type": "string", - "format": "uri" - }, - "mainEntityOfPage": { - "anyOf": [ + "value": { + "oneOf": [ { - "type": "string", - "format": "uri" + "type": "string" }, { - "type": "array", - "items": { - "type": "string", - "format": "uri" - } + "type": "boolean" }, { - "$ref": "#/definitions/creativework" + "type": "number" + } + ] + }, + "identifier": { + "type": "string" + }, + "valuereference": { + "oneOf": [ + { + "$ref": "#/definitions/categorycode" }, { "type": "array", - "items": { - "$ref": "#/definitions/creativework" - } + "items": [ + { + "$ref": "#/definitions/categorycode" + } + ] + } + ] + }, + "unitCode": { + "oneOf": [ + { + "type": "string" + }, + { + "type": "string", + "format": "uri" } ] + }, + "unitText": { + "type": "string" } }, "required": [ - "name" + "name", + "value" + ], + "recommended": [ + "valueReference" + ], + "optional": [ + "unitCode", + "unitText" ] }, - "creativework": { - "@type": "CreativeWork", + "categorycode": { + "@type": "CategoryCode", "type": "object", "properties": { "name": { "type": "string" }, - "identifier": { + "codeValue": { "type": "string" }, "url": { - "type": "string", - "format": "uri" + "type": "string" } }, - "required": [] + "required": [ + "name", + "codeValue", + "url" + ] }, - "organization": { - "@type": "Organization", + "definedterm": { + "@type": "DefinedTerm", "type": "object", "properties": { + "url": { + "type": "string", + "format": "uri" + }, "name": { "type": "string" }, - "legalName": { + "termCode": { "type": "string" }, - "description": { + "identifier": { "type": "string" }, - "sameAs": { - "type": "string", - "format": "uri" + "inDefinedTermSet": { + "$ref": "#/definitions/definedtermset" } - } + }, + "required": [] }, - "place": { - "@type": "Place", + "definedtermset": { + "@type": "DefinedTermSet", "type": "object", "properties": { "name": { "type": "string" }, - "address": { - "oneOf": [ - { - "type": "string" - }, - { - "$ref": "#/definitions/postaladdress" - } - ] - }, "identifier": { "type": "string" }, @@ -13444,76 +13038,119 @@ "type": "string", "format": "uri" } - } + }, + "required": [] }, - "contactpoint": { - "@type": "schema:ContactPoint", + "medicalcondition": { + "@type": "MedicalCondition", "type": "object", "properties": { + "url": { + "type": "string", + "format": "uri" + }, "name": { "type": "string" + }, + "identifier": { + "type": "string" } }, "required": [] }, - "imageobject": { - "@type": "ImageObject", + "biochementity": { + "@type": "bioschemas:BioChemEntity", "type": "object", "properties": { - "name": { - "type": "string" - }, "url": { "type": "string", "format": "uri" + }, + "name": { + "type": "string" + }, + "identifier": { + "type": "string" } }, "required": [] }, - "language": { - "@type": "Language", + "imageobject": { + "@type": "ImageObject", "type": "object", "properties": { "name": { "type": "string" + }, + "url": { + "type": "string", + "format": "uri" } }, "required": [] }, - "programmembership": { - "@type": "ProgramMembership", + "creativework": { + "@type": "CreativeWork", "type": "object", "properties": { "name": { "type": "string" + }, + "identifier": { + "type": "string" + }, + "url": { + "type": "string", + "format": "uri" } }, "required": [] }, - "postaladdress": { - "@type": "schema:PostalAddress", + "taxon": { + "@type": "bioschemas:Taxon", "type": "object", "properties": { - "addressCountry": { - "type": "string" - }, - "addressLocality": { - "type": "string" - }, - "addressRegion": { - "type": "string" - }, - "postOfficeBoxNumber": { - "type": "string" - }, - "postalCode": { + "name": { "type": "string" }, - "streetAddress": { - "type": "string" + "taxonRank": { + "anyOf": [ + { + "$ref": "#/definitions/propertyvalue" + }, + { + "type": "array", + "items": { + "$ref": "#/definitions/propertyvalue" + } + }, + { + "type": "string" + }, + { + "type": "array", + "items": { + "type": "string" + } + }, + { + "type": "string", + "format": "uri" + }, + { + "type": "array", + "items": { + "type": "string", + "format": "uri" + } + } + ] } }, - "required": [] + "required": [ + "name", + "taxonRank" + ] }, "conformsDefinition": { "@type": "CreativeWork", @@ -13524,7 +13161,7 @@ "oneOf": [ { "enum": [ - "https://github.com/BioSchemas/specifications/tree/master/Person/jsonld/Person_v0.3-DRAFT.json" + "https://github.com/BioSchemas/specifications/tree/master/Phenotype/jsonld/Phenotype_v0.2-DRAFT.json" ] }, { @@ -13543,85 +13180,107 @@ "additional_type": "https://bioschemas.org/profiles#nav-draft" }, { - "@id": "bioschemasdrafts:Phenotype", + "@id": "bioschemasdrafts:Protein", "@type": "rdfs:Class", - "rdfs:comment": "Bioschemas profile describing a Phenotype in Life Sciences This Phenotype type specification presents the markup for describing a Phenotype. Version 0.2-DRAFT.

Summary of Changes


Changes from Previous Version:", - "schema:schemaVersion": [ - "https://github.com/BioSchemas/specifications/tree/master/Phenotype/jsonld/Phenotype_v0.2-DRAFT.json", - "https://bioschemas.org/profiles/Phenotype/0.2-DRAFT" - ], - "rdfs:label": "Phenotype", + "rdfs:comment": "This Protein profile specification presents the most common properties used for a Protein plus examples on how to use them. Version 0.12-DRAFT.

Summary of Changes


Changes since 0.11-DRAFT:", + "rdfs:label": "Protein", "rdfs:subClassOf": { - "@id": "bioschemastypesdrafts:Phenotype" + "@id": "schema:Protein" }, "$validation": { "$schema": "http://json-schema.org/draft-07/schema#", "type": "object", "properties": { - "additionalProperty": { - "description": "Before using this property, make sure none of the existing ones covers your case. Whenever possible, please use a property coined in a third-party well-know vocabulary. Please always use (i) property name to specify the name of the property, (ii) additionalType (if possible) to better specify the nature of the property (e.g., link to the third-party well-known vocabulary term), and (iii) value to link to the object/range of this property. A property-value pair representing an additional characteristics of the entitity, e.g. a product feature or another characteristic for which there is no matching property in schema.org.\n\nNote: Publishers should be aware that applications designed to use specific schema.org properties (e.g. http://schema.org/width, http://schema.org/color, http://schema.org/gtin13, ...) will typically expect such data to be provided using those properties, rather than using the generic property/value mechanism.", + "hasBioPolymerSequence": { + "description": "A symbolic representation of a BioChemEnity. For example, a nucleotide sequence of a Gene or an amino acid sequence of a Protein.", "oneOf": [ { - "$ref": "#/definitions/propertyvalue" + "type": "string" }, { "type": "array", "items": { - "$ref": "#/definitions/propertyvalue" + "type": "string" } } ], "owl:cardinality": "many" }, - "alternateName": { - "description": " An alias for the item.", - "oneOf": [ - { - "type": "string" + "associatedDisease": { + "description": "Disease associated to this protein, if any.", + "anyOf": [ + { + "$ref": "#/definitions/medicalCondition" }, { "type": "array", "items": { - "type": "string" + "$ref": "#/definitions/medicalCondition" + } + }, + { + "$ref": "#/definitions/propertyValue" + }, + { + "type": "array", + "items": { + "$ref": "#/definitions/propertyValue" + } + }, + { + "type": "string", + "format": "uri" + }, + { + "type": "array", + "items": { + "type": "string", + "format": "uri" } } ], "owl:cardinality": "many" }, - "anatomicalLocation": { - "description": " Any part of an organism, typically a component of an anatomical system. Organs, tissues, and cells are all anatomical locations.", + "bioChemInteraction": { + "description": "A BioChemEntity that is know to interact with this item.", "oneOf": [ { - "$ref": "#/definitions/definedterm" + "$ref": "#/definitions/bioChemEntity" }, { "type": "array", "items": { - "$ref": "#/definitions/definedterm" + "$ref": "#/definitions/bioChemEntity" } } ], "owl:cardinality": "many" }, - "associatedDisease": { - "description": " Disease associated to this BioChemEntity. Such a disease can be a MedicalCondition or a URL. If you want to add an evidence supporting the association, please use PropertyValue.", - "anyOf": [ + "bioChemSimilarity": { + "description": "A similar molecular entity, e.g., obtained by fingerprint similarity algorithm.", + "oneOf": [ { - "$ref": "#/definitions/medicalcondition" + "$ref": "#/definitions/bioChemEntity" }, { "type": "array", "items": { - "$ref": "#/definitions/medicalcondition" + "$ref": "#/definitions/bioChemEntity" } - }, + } + ], + "owl:cardinality": "many" + }, + "hasBioChemEntityPart": { + "description": "Indicates a BioChemEntity that (in some sense) has this BioChemEntity as a part. Inverse property: isPartOfBioChemEntity", + "anyOf": [ { - "$ref": "#/definitions/propertyvalue" + "$ref": "#/definitions/bioChemEntity" }, { "type": "array", "items": { - "$ref": "#/definitions/propertyvalue" + "$ref": "#/definitions/bioChemEntity" } }, { @@ -13638,45 +13297,60 @@ ], "owl:cardinality": "many" }, - "bioChemAssociation": { - "description": " BioChemEntity, e.g., gene, associated to this Phenotype and relevant for its characterization, particularly useful for the molecular basis of this Phenotype.", - "oneOf": [ + "hasMolecularFunction": { + "description": "GO term corresponding to the Molecular Function branch of the GO ontology.", + "anyOf": [ { - "$ref": "#/definitions/biochementity" + "$ref": "#/definitions/definedTerm" }, { "type": "array", "items": { - "$ref": "#/definitions/biochementity" + "$ref": "#/definitions/definedTerm" + } + }, + { + "$ref": "#/definitions/propertyValue" + }, + { + "type": "array", + "items": { + "$ref": "#/definitions/propertyValue" + } + }, + { + "type": "string", + "format": "uri" + }, + { + "type": "array", + "items": { + "type": "string", + "format": "uri" } } ], "owl:cardinality": "many" }, - "description": { - "description": " A description of the item.", - "type": "string", - "owl:cardinality": "one" - }, - "hasMolecularFunction": { - "description": " Molecular function performed by this Phenotype.", + "hasRepresentation": { + "description": "Bioschemas Protein: This property could be used, for instance, to link to a page containing the corresponding sequence protein. If you want to better define the nature of the representation, use a PropertyValue as described in additionalProperty.", "anyOf": [ { - "$ref": "#/definitions/definedterm" + "$ref": "#/definitions/propertyValue" }, { "type": "array", "items": { - "$ref": "#/definitions/definedterm" + "$ref": "#/definitions/propertyValue" } }, { - "$ref": "#/definitions/propertyvalue" + "type": "string" }, { "type": "array", "items": { - "$ref": "#/definitions/propertyvalue" + "type": "string" } }, { @@ -13693,67 +13367,58 @@ ], "owl:cardinality": "many" }, - "identifier": { - "description": " The identifier property represents any kind of identifier for any kind of Thing, such as ISBNs, GTIN codes, UUIDs etc. Schema.org provides dedicated properties for representing many of these, either as textual strings or as URL (URI) links. See [background notes](http://schema.org/docs/datamodel.html#identifierBg) for more details.", - "oneOf": [ + "isEncodedByBioChemEntity": { + "description": "Another BioChemEntity encoding this one. Inverse property: encodesBioChemEntity.", + "anyOf": [ { - "$ref": "#/definitions/propertyvalue" + "$ref": "#/definitions/gene" }, { - "type": "string" + "type": "array", + "items": { + "$ref": "#/definitions/gene" + } }, { - "type": "string", - "format": "uri" - } - ], - "owl:cardinality": "one" - }, - "image": { - "description": " An image of the item. This can be a URL or a fully described ImageObject.", - "anyOf": [ - { - "$ref": "#/definitions/imageobject" + "$ref": "#/definitions/dna" }, { "type": "array", "items": { - "$ref": "#/definitions/imageobject" + "$ref": "#/definitions/dna" } }, { - "type": "string", - "format": "uri" + "$ref": "#/definitions/rna" }, { "type": "array", "items": { - "type": "string", - "format": "uri" + "$ref": "#/definitions/rna" } } ], "owl:cardinality": "many" }, "isInvolvedInBiologicalProcess": { - "description": " Biological process this Phenotype is involved in.", + "description": "Functional term corresponding to the biological process (typically the Biological Process branch of the GO ontology).", "anyOf": [ { - "$ref": "#/definitions/definedterm" + "$ref": "#/definitions/definedTerm" }, { "type": "array", "items": { - "$ref": "#/definitions/definedterm" + "$ref": "#/definitions/definedTerm" } }, { - "$ref": "#/definitions/propertyvalue" + "$ref": "#/definitions/propertyValue" }, { "type": "array", "items": { - "$ref": "#/definitions/propertyvalue" + "$ref": "#/definitions/propertyValue" } }, { @@ -13771,24 +13436,24 @@ "owl:cardinality": "many" }, "isLocatedInSubcellularLocation": { - "description": " Subcellular location where this Phenotype is located.", + "description": "Functional term corresponding to the subcellular location (typically the Subcellular Location branch of the GO ontology).", "anyOf": [ { - "$ref": "#/definitions/definedterm" + "$ref": "#/definitions/definedTerm" }, { "type": "array", "items": { - "$ref": "#/definitions/definedterm" + "$ref": "#/definitions/definedTerm" } }, { - "$ref": "#/definitions/propertyvalue" + "$ref": "#/definitions/propertyValue" }, { "type": "array", "items": { - "$ref": "#/definitions/propertyvalue" + "$ref": "#/definitions/propertyValue" } }, { @@ -13805,27 +13470,51 @@ ], "owl:cardinality": "many" }, - "mainEntityOfPage": { - "description": "Link via DataRecord to the main DataRecord representing this entity in a dataset. It is usually preferred to use mainEntity from a DataRecord to point to its corresponding entity. Indicates a page (or other CreativeWork) for which this thing is the main entity being described. See [background notes](http://schema.org/docs/datamodel.html#mainEntityBackground) for details.\nInverse property: mainEntity.", + "isPartOfBioChemEntity": { + "description": "For proteins, it can be used to link to protein sequence annotations such as domains, sites, regions, etc.", "oneOf": [ { - "$ref": "#/definitions/creativework" + "$ref": "#/definitions/bioChemEntity" }, { - "type": "string", - "format": "uri" + "type": "array", + "items": { + "$ref": "#/definitions/bioChemEntity" + } } ], - "owl:cardinality": "one" - }, - "name": { - "description": " The name of the item.", - "type": "string", - "owl:cardinality": "one" + "owl:cardinality": "many" }, - "sameAs": { - "description": " URL of a reference Web page that unambiguously indicates the item's identity. E.g. the URL of the item's Wikipedia page, Wikidata entry, or official website.", - "oneOf": [ + "taxonomicRange": { + "description": "For proteins, it is recommended to use this property to specify the taxon/organism corresponding to a genome including a expressed gene that can be translated to this protein. For taxon/organism, it is a good practice to use hasCategoryCode to point to a controlled vacabulary such as NCBI taxon or UniProt Taxonomy..", + "anyOf": [ + { + "type": "string" + }, + { + "type": "array", + "items": { + "type": "string" + } + }, + { + "$ref": "#/definitions/definedTerm" + }, + { + "type": "array", + "items": { + "$ref": "#/definitions/definedTerm" + } + }, + { + "$ref": "#/definitions/taxon" + }, + { + "type": "array", + "items": { + "$ref": "#/definitions/taxon" + } + }, { "type": "string", "format": "uri" @@ -13840,11 +13529,21 @@ ], "owl:cardinality": "many" }, - "taxonomicRange": { - "description": " The taxonomic grouping of the organism that expresses the Phenotype.", - "oneOf": [ + "alternateName": { + "description": "An alias for the item.", + "type": "string", + "owl:cardinality": "one" + }, + "description": { + "description": "Protein function. We recommend to start the description with \u201cFunction: [\u2026]\u201d.", + "type": "string", + "owl:cardinality": "one" + }, + "identifier": { + "description": "The identifier property represents any kind of identifier for any kind of Thing, such as ISBNs, GTIN codes, UUIDs etc. Schema.org provides dedicated properties for representing many of these, either as textual strings or as URL (URI) links. See background notes for more details.", + "anyOf": [ { - "$ref": "#/definitions/taxon" + "$ref": "#/definitions/propertyValue" }, { "type": "string" @@ -13856,143 +13555,178 @@ ], "owl:cardinality": "one" }, - "url": { - "description": "Link to the official webpage associated to this entity. URL of the item.", - "type": "string", - "format": "uri", - "owl:cardinality": "one" - }, - "valueReference": { - "description": " A DefinedTerm in this code set.", + "image": { + "description": "An image of the item. This can be a URL or a fully described ImageObject.", "oneOf": [ { - "$ref": "#/definitions/definedterm" + "type": "string" }, { "type": "array", "items": { - "$ref": "#/definitions/definedterm" + "type": "string" } } ], "owl:cardinality": "many" }, - "conformsTo": { - "description": "This is used to state the Bioschemas profile that the markup relates to. The identifier can be the url for the version of this bioschemas class on github: https://github.com/BioSchemas/specifications/tree/master/Phenotype/jsonld/Phenotype_v0.2-DRAFT.json", - "$ref": "#/definitions/conformsDefinition" - } - }, - "required": [ - "identifier", - "name", - "conformsTo" - ], - "recommended": [ - "bioChemAssociation", - "description", - "taxonomicRange", - "url", + "mainEntityOfPage": { + "description": "Link to the main DataRecord representing this entity in a dataset.", + "type": "string", + "format": "uri", + "owl:cardinality": "one" + }, + "name": { + "description": "The name of the item.", + "type": "string", + "owl:cardinality": "one" + }, + "sameAs": { + "description": "Link to any resource other than the Record and the official webpage, for instance a Wikipedia page.", + "oneOf": [ + { + "type": "string", + "format": "uri" + }, + { + "type": "array", + "items": { + "type": "string", + "format": "uri" + } + } + ], + "owl:cardinality": "many" + }, + "url": { + "description": "Link to the official webpage associated to this entity.", + "type": "string", + "format": "uri", + "owl:cardinality": "one" + }, + "hasSequenceAnnotation": { + "description": "The taxonomic grouping of the organism that expresses, encodes, or in someway related to the BioChemEntity.", + "anyOf": [ + { + "$ref": "#/definitions/sequenceAnnotation" + }, + { + "type": "array", + "items": { + "$ref": "#/definitions/sequenceAnnotation" + } + }, + { + "type": "string", + "format": "uri" + }, + { + "type": "array", + "items": { + "type": "string", + "format": "uri" + } + } + ], + "owl:cardinality": "many" + }, + "conformsTo": { + "description": "This is used to state the Bioschemas profile that the markup relates to. The identifier can be the url for the version of this bioschemas class on github: https://github.com/BioSchemas/specifications/tree/master/Protein/jsonld/Protein_v0.12-DRAFT.json", + "$ref": "#/definitions/conformsDefinition" + } + }, + "required": [ + "identifier", + "name", + "conformsTo" + ], + "recommended": [ + "associatedDisease", + "description", + "hasSequenceAnnotation", + "isEncodedByBioChemEntity", + "taxonomicRange", + "url", "sameAs" ], "optional": [ - "additionalProperty", "alternateName", - "anatomicalLocation", - "associatedDisease", + "bioChemInteraction", + "bioChemSimilarity", + "hasBioChemEntityPart", + "hasBioPolymerSequence", "hasMolecularFunction", + "hasRepresentation", "image", "isInvolvedInBiologicalProcess", "isLocatedInSubcellularLocation", - "mainEntityOfPage", - "valueReference" + "isPartOfBioChemEntity", + "mainEntityOfPage" ], "definitions": { - "propertyvalue": { - "@type": "PropertyValue", + "taxon": { + "@type": "Taxon", "type": "object", "properties": { "name": { "type": "string" }, - "value": { - "oneOf": [ + "taxonRank": { + "anyOf": [ { - "type": "string" + "$ref": "#/definitions/propertyValue" }, { - "type": "boolean" + "type": "array", + "items": { + "$ref": "#/definitions/propertyValue" + } }, { - "type": "number" - } - ] - }, - "identifier": { - "type": "string" - }, - "valuereference": { - "oneOf": [ - { - "$ref": "#/definitions/categorycode" + "type": "string" }, { "type": "array", - "items": [ - { - "$ref": "#/definitions/categorycode" - } - ] - } - ] - }, - "unitCode": { - "oneOf": [ - { - "type": "string" + "items": { + "type": "string" + } }, { "type": "string", "format": "uri" + }, + { + "type": "array", + "items": { + "type": "string", + "format": "uri" + } } ] - }, - "unitText": { - "type": "string" } }, "required": [ "name", - "value" - ], - "recommended": [ - "valueReference" - ], - "optional": [ - "unitCode", - "unitText" + "taxonRank" ] }, - "categorycode": { - "@type": "CategoryCode", + "propertyValue": { + "@type": "PropertyValue", "type": "object", "properties": { "name": { "type": "string" }, - "codeValue": { + "value": { "type": "string" }, - "url": { + "identifier": { "type": "string" } }, - "required": [ - "name", - "codeValue", - "url" - ] + "required": [] }, - "definedterm": { + "definedTerm": { "@type": "DefinedTerm", "type": "object", "properties": { @@ -14008,32 +13742,29 @@ }, "identifier": { "type": "string" - }, - "inDefinedTermSet": { - "$ref": "#/definitions/definedtermset" } }, "required": [] }, - "definedtermset": { - "@type": "DefinedTermSet", + "medicalCondition": { + "@type": "MedicalCondition", "type": "object", "properties": { + "url": { + "type": "string", + "format": "uri" + }, "name": { "type": "string" }, "identifier": { "type": "string" - }, - "url": { - "type": "string", - "format": "uri" } }, "required": [] }, - "medicalcondition": { - "@type": "MedicalCondition", + "bioChemEntity": { + "@type": "bioschemastypes:BioChemEntity", "type": "object", "properties": { "url": { @@ -14049,99 +13780,108 @@ }, "required": [] }, - "biochementity": { - "@type": "bioschemas:BioChemEntity", + "gene": { + "@type": "Gene", "type": "object", "properties": { - "url": { - "type": "string", - "format": "uri" + "identifier": { + "anyOf": [ + { + "$ref": "#/definitions/propertyValue" + }, + { + "type": "string" + }, + { + "type": "string", + "format": "uri" + } + ] }, "name": { "type": "string" - }, - "identifier": { - "type": "string" } }, "required": [] }, - "imageobject": { - "@type": "ImageObject", + "quantitativeValue": { + "@type": "QuantitativeValue", "type": "object", "properties": { - "name": { + "value": { "type": "string" }, - "url": { - "type": "string", - "format": "uri" + "unitText": { + "type": "string" } }, "required": [] }, - "creativework": { - "@type": "CreativeWork", + "dna": { + "@type": "bioschemastypesdrafts:DNA", "type": "object", "properties": { - "name": { - "type": "string" + "encodesBioChemEntity": { + "oneOf": [ + { + "$ref": "#/definitions/bioChemEntity" + }, + { + "type": "array", + "items": { + "$ref": "#/definitions/bioChemEntity" + } + } + ] }, - "identifier": { + "hasSequence": { "type": "string" - }, - "url": { - "type": "string", - "format": "uri" } }, "required": [] }, - "taxon": { - "@type": "bioschemas:Taxon", + "rna": { + "@type": "bioschemastypesdrafts:RNA", "type": "object", "properties": { - "name": { - "type": "string" - }, - "taxonRank": { - "anyOf": [ + "encodesBioChemEntity": { + "oneOf": [ { - "$ref": "#/definitions/propertyvalue" + "$ref": "#/definitions/bioChemEntity" }, { "type": "array", "items": { - "$ref": "#/definitions/propertyvalue" - } - }, - { - "type": "string" - }, - { - "type": "array", - "items": { - "type": "string" - } - }, - { - "type": "string", - "format": "uri" - }, - { - "type": "array", - "items": { - "type": "string", - "format": "uri" + "$ref": "#/definitions/bioChemEntity" } } ] + }, + "hasSequence": { + "type": "string" } }, - "required": [ - "name", - "taxonRank" - ] + "required": [] + }, + "sequenceAnnotation": { + "@type": "bioschemastypesdrafts:SequenceAnnotation", + "type": "object", + "properties": { + "sequenceLocation": { + "$ref": "#/definitions/sequenceRange" + } + }, + "required": [] + }, + "sequenceRange": { + "@type": "bioschemastypesdrafts:SequenceRange", + "type": "object", + "properties": { + "rangeStart": { + "type": "integer" + } + }, + "required": [] }, "conformsDefinition": { "@type": "CreativeWork", @@ -14152,7 +13892,7 @@ "oneOf": [ { "enum": [ - "https://github.com/BioSchemas/specifications/tree/master/Phenotype/jsonld/Phenotype_v0.2-DRAFT.json" + "https://github.com/BioSchemas/specifications/tree/master/Protein/jsonld/Protein_v0.12-DRAFT.json" ] }, { @@ -14168,54 +13908,85 @@ } } }, - "additional_type": "https://bioschemas.org/profiles#nav-draft" + "additional_type": "https://bioschemas.org/profiles#nav-draft", + "schema:schemaVersion": [ + "https://github.com/BioSchemas/specifications/tree/master/Protein/jsonld/Protein_v0.12-DRAFT.json", + "https://bioschemas.org/profiles/Protein/0.12-DRAFT" + ] }, { - "@id": "bioschemasdrafts:Protein", + "@id": "bioschemasdrafts:ProteinStructure", "@type": "rdfs:Class", - "rdfs:comment": "This Protein profile specification presents the most common properties used for a Protein plus examples on how to use them. Version 0.12-DRAFT.

Summary of Changes


Changes since 0.11-DRAFT:", - "rdfs:label": "Protein", + "rdfs:comment": "This profile specification presents the BioChemEntity usage when describing a Protein structure. Version 0.6-DRAFT.

Summary of Changes


Changes since 0.5-DRAFT-2018_08_15:", + "schema:schemaVersion": [ + "https://github.com/BioSchemas/specifications/tree/master/ProteinStructure/jsonld/ProteinStructure_v0.6-DRAFT.json", + "https://bioschemas.org/profiles/ProteinStructure/0.6-DRAFT" + ], + "rdfs:label": "ProteinStructure", "rdfs:subClassOf": { - "@id": "schema:Protein" + "@id": "bioschemastypes:BioChemEntity" }, "$validation": { "$schema": "http://json-schema.org/draft-07/schema#", "type": "object", "properties": { - "hasBioPolymerSequence": { - "description": "A symbolic representation of a BioChemEnity. For example, a nucleotide sequence of a Gene or an amino acid sequence of a Protein.", + "identifier": { + "description": " The identifier property represents any kind of identifier for any kind of Thing, such as ISBNs, GTIN codes, UUIDs etc. Schema.org provides dedicated properties for representing many of these, either as textual strings or as URL (URI) links. See [background notes](http://schema.org/docs/datamodel.html#identifierBg) for more details.", "oneOf": [ + { + "$ref": "#/definitions/propertyvalue" + }, { "type": "string" }, { - "type": "array", - "items": { - "type": "string" - } + "type": "string", + "format": "uri" } ], - "owl:cardinality": "many" + "owl:cardinality": "one" }, - "associatedDisease": { - "description": "Disease associated to this protein, if any.", - "anyOf": [ + "alternateName": { + "description": " An alias for the item.", + "oneOf": [ { - "$ref": "#/definitions/medicalCondition" + "type": "string" }, { "type": "array", "items": { - "$ref": "#/definitions/medicalCondition" + "type": "string" } - }, + } + ], + "owl:cardinality": "many" + }, + "description": { + "description": " A description of the item.", + "type": "string", + "owl:cardinality": "one" + }, + "name": { + "description": " The name of the item.", + "type": "string", + "owl:cardinality": "one" + }, + "url": { + "description": "Link to the official webpage associated to this entity. URL of the item.", + "type": "string", + "format": "uri", + "owl:cardinality": "one" + }, + "image": { + "description": " An image of the item. This can be a URL or a fully described ImageObject.", + "anyOf": [ { - "$ref": "#/definitions/propertyValue" + "$ref": "#/definitions/imageobject" }, { "type": "array", "items": { - "$ref": "#/definitions/propertyValue" + "$ref": "#/definitions/imageobject" } }, { @@ -14232,118 +14003,100 @@ ], "owl:cardinality": "many" }, - "bioChemInteraction": { - "description": "A BioChemEntity that is know to interact with this item.", - "oneOf": [ + "boundMolecule": { + "description": "Bound molecules.", + "anyOf": [ { - "$ref": "#/definitions/bioChemEntity" + "type": "string", + "format": "uri" }, { "type": "array", "items": { - "$ref": "#/definitions/bioChemEntity" + "type": "string", + "format": "uri" } - } - ], - "owl:cardinality": "many" - }, - "bioChemSimilarity": { - "description": "A similar molecular entity, e.g., obtained by fingerprint similarity algorithm.", - "oneOf": [ + }, { - "$ref": "#/definitions/bioChemEntity" + "type": "string" }, { "type": "array", "items": { - "$ref": "#/definitions/bioChemEntity" + "type": "string" } } ], "owl:cardinality": "many" }, - "hasBioChemEntityPart": { - "description": "Indicates a BioChemEntity that (in some sense) has this BioChemEntity as a part. Inverse property: isPartOfBioChemEntity", + "expressionSystem": { + "description": " Organism where this protein structure is expressed.", "anyOf": [ { - "$ref": "#/definitions/bioChemEntity" + "$ref": "#/definitions/biochementity" }, { "type": "array", "items": { - "$ref": "#/definitions/bioChemEntity" + "$ref": "#/definitions/biochementity" } }, { - "type": "string", - "format": "uri" + "$ref": "#/definitions/taxon" }, { "type": "array", "items": { - "type": "string", - "format": "uri" + "$ref": "#/definitions/taxon" } } ], "owl:cardinality": "many" }, - "hasMolecularFunction": { - "description": "GO term corresponding to the Molecular Function branch of the GO ontology.", + "structureDeterminationMethod": { + "description": " Method used to determine the protein structure.", "anyOf": [ { - "$ref": "#/definitions/definedTerm" - }, - { - "type": "array", - "items": { - "$ref": "#/definitions/definedTerm" - } - }, - { - "$ref": "#/definitions/propertyValue" + "type": "string", + "format": "uri" }, { "type": "array", "items": { - "$ref": "#/definitions/propertyValue" + "type": "string", + "format": "uri" } }, { - "type": "string", - "format": "uri" + "type": "string" }, { "type": "array", "items": { - "type": "string", - "format": "uri" + "type": "string" } } ], "owl:cardinality": "many" }, - "hasRepresentation": { - "description": "Bioschemas Protein: This property could be used, for instance, to link to a page containing the corresponding sequence protein. If you want to better define the nature of the representation, use a PropertyValue as described in additionalProperty.", - "anyOf": [ - { - "$ref": "#/definitions/propertyValue" - }, - { - "type": "array", - "items": { - "$ref": "#/definitions/propertyValue" - } - }, + "additionalProperty": { + "description": "As much a possible, do not use it! Alternatively, consider reusing properties/relations already coined in controlled vocabularies. We recommed to look at the [OBO Relations Ontology (RO)](http://obofoundry.org/ontology/ro.html) or the [Semanticscience Integrated Ontology (SIO)](http://sio.semanticscience.org/) as starting points. A property-value pair representing an additional characteristics of the entitity, e.g. a product feature or another characteristic for which there is no matching property in schema.org. Note: Publishers should be aware that applications designed to use specific schema.org properties (e.g. http://schema.org/width, http://schema.org/color, http://schema.org/gtin13, ...) will typically expect such data to be provided using those properties, rather than using the generic property/value mechanism.", + "oneOf": [ { - "type": "string" + "$ref": "#/definitions/propertyvalue" }, { "type": "array", "items": { - "type": "string" + "$ref": "#/definitions/propertyvalue" } - }, + } + ], + "owl:cardinality": "many" + }, + "additionalType": { + "description": "Should be set to any of the values listed in the Controlled Vocabulary. An additional type for the item, typically used for adding more specific types from external vocabularies in microdata syntax. This is a relationship between something and a class that the thing is in. In RDFa syntax, it is better to use the native RDFa syntax - the 'typeof' attribute - for multiple types. Schema.org tools may have only weaker understanding of extra types, in particular those defined externally.", + "oneOf": [ { "type": "string", "format": "uri" @@ -14358,58 +14111,66 @@ ], "owl:cardinality": "many" }, - "isEncodedByBioChemEntity": { - "description": "Another BioChemEntity encoding this one. Inverse property: encodesBioChemEntity.", + "contains": { + "description": "Indicates a BioChemEntity that is (in some sense) a part of this BioChemEntity. Inverse property: isContainedIn. ", "anyOf": [ { - "$ref": "#/definitions/gene" + "$ref": "#/definitions/biochementity" }, { "type": "array", "items": { - "$ref": "#/definitions/gene" + "$ref": "#/definitions/biochementity" } }, { - "$ref": "#/definitions/dna" + "type": "string", + "format": "uri" }, { "type": "array", "items": { - "$ref": "#/definitions/dna" + "type": "string", + "format": "uri" } - }, + } + ], + "owl:cardinality": "many" + }, + "hasCategoryCode": { + "description": "A Category code contained in this code set. A controlled vocabulary term equivalent to this entity. For instance, an organism coined in NCBI taxonomy can be represented as a BioChemEntity. As it also exists as a term in an ontology, it would be nice to capture that information via categoryCode. ", + "oneOf": [ { - "$ref": "#/definitions/rna" + "$ref": "#/definitions/categorycode" }, { "type": "array", "items": { - "$ref": "#/definitions/rna" + "$ref": "#/definitions/categorycode" } } ], "owl:cardinality": "many" }, - "isInvolvedInBiologicalProcess": { - "description": "Functional term corresponding to the biological process (typically the Biological Process branch of the GO ontology).", + "hasRepresentation": { + "description": "Representation of this entity. For instance, a chemical structure or sequence. A representation for this entity other than, for instance, an image (use image property for that) or the main web page/record (use mainEntityOfPage for that), and see background notes, for sameAs and url).", "anyOf": [ { - "$ref": "#/definitions/definedTerm" + "$ref": "#/definitions/propertyvalue" }, { "type": "array", "items": { - "$ref": "#/definitions/definedTerm" + "$ref": "#/definitions/propertyvalue" } }, { - "$ref": "#/definitions/propertyValue" + "type": "string" }, { "type": "array", "items": { - "$ref": "#/definitions/propertyValue" + "type": "string" } }, { @@ -14426,25 +14187,16 @@ ], "owl:cardinality": "many" }, - "isLocatedInSubcellularLocation": { - "description": "Functional term corresponding to the subcellular location (typically the Subcellular Location branch of the GO ontology).", + "isContainedIn": { + "description": "Indicates a BioChemEntity that this BioChemEntity is (in some sense) a part of. Inverse property: contains. ", "anyOf": [ { - "$ref": "#/definitions/definedTerm" + "$ref": "#/definitions/biochementity" }, { "type": "array", "items": { - "$ref": "#/definitions/definedTerm" - } - }, - { - "$ref": "#/definitions/propertyValue" - }, - { - "type": "array", - "items": { - "$ref": "#/definitions/propertyValue" + "$ref": "#/definitions/biochementity" } }, { @@ -14461,49 +14213,34 @@ ], "owl:cardinality": "many" }, - "isPartOfBioChemEntity": { - "description": "For proteins, it can be used to link to protein sequence annotations such as domains, sites, regions, etc.", - "oneOf": [ - { - "$ref": "#/definitions/bioChemEntity" - }, - { - "type": "array", - "items": { - "$ref": "#/definitions/bioChemEntity" - } - } - ], - "owl:cardinality": "many" - }, - "taxonomicRange": { - "description": "For proteins, it is recommended to use this property to specify the taxon/organism corresponding to a genome including a expressed gene that can be translated to this protein. For taxon/organism, it is a good practice to use hasCategoryCode to point to a controlled vacabulary such as NCBI taxon or UniProt Taxonomy..", + "location": { + "description": "The location can refer to a position in the chromosome or sequence or to a physical place where, for instance, a sample is stored. Using [additionalType](http://bioschemas.org/devSpecs/ProteinStructure/#additionalType) is advised to make this distinction. For instance, [FALDO](https://github.com/OBF/FALDO) can be used for sequence co-ordinates.\n**Note:** The list of Expected Types has been extended as schema.org/location only has Place, PostalAddress and Text. The location of for example where the event is happening, an organization is located, or where an action takes place.", "anyOf": [ { - "type": "string" + "$ref": "#/definitions/place" }, { "type": "array", "items": { - "type": "string" + "$ref": "#/definitions/place" } }, { - "$ref": "#/definitions/definedTerm" + "$ref": "#/definitions/postaladdress" }, { "type": "array", "items": { - "$ref": "#/definitions/definedTerm" + "$ref": "#/definitions/postaladdress" } }, { - "$ref": "#/definitions/taxon" + "$ref": "#/definitions/propertyvalue" }, { "type": "array", "items": { - "$ref": "#/definitions/taxon" + "$ref": "#/definitions/propertyvalue" } }, { @@ -14516,39 +14253,7 @@ "type": "string", "format": "uri" } - } - ], - "owl:cardinality": "many" - }, - "alternateName": { - "description": "An alias for the item.", - "type": "string", - "owl:cardinality": "one" - }, - "description": { - "description": "Protein function. We recommend to start the description with \u201cFunction: [\u2026]\u201d.", - "type": "string", - "owl:cardinality": "one" - }, - "identifier": { - "description": "The identifier property represents any kind of identifier for any kind of Thing, such as ISBNs, GTIN codes, UUIDs etc. Schema.org provides dedicated properties for representing many of these, either as textual strings or as URL (URI) links. See background notes for more details.", - "anyOf": [ - { - "$ref": "#/definitions/propertyValue" - }, - { - "type": "string" }, - { - "type": "string", - "format": "uri" - } - ], - "owl:cardinality": "one" - }, - "image": { - "description": "An image of the item. This can be a URL or a fully described ImageObject.", - "oneOf": [ { "type": "string" }, @@ -14562,51 +14267,21 @@ "owl:cardinality": "many" }, "mainEntityOfPage": { - "description": "Link to the main DataRecord representing this entity in a dataset.", - "type": "string", - "format": "uri", - "owl:cardinality": "one" - }, - "name": { - "description": "The name of the item.", - "type": "string", - "owl:cardinality": "one" - }, - "sameAs": { - "description": "Link to any resource other than the Record and the official webpage, for instance a Wikipedia page.", + "description": "Link via DataRecord or [URL](http://schema.org/url) to the main Record representing this entity in a dataset.\n**Note:** Bioschemas has replaced DataRecord with CreativeWork in the Expected Types. Indicates a page (or other CreativeWork) for which this thing is the main entity being described. See background notes for details.", "oneOf": [ { "type": "string", "format": "uri" }, { - "type": "array", - "items": { - "type": "string", - "format": "uri" - } + "$ref": "#/definitions/creativework" } ], - "owl:cardinality": "many" - }, - "url": { - "description": "Link to the official webpage associated to this entity.", - "type": "string", - "format": "uri", "owl:cardinality": "one" }, - "hasSequenceAnnotation": { - "description": "The taxonomic grouping of the organism that expresses, encodes, or in someway related to the BioChemEntity.", - "anyOf": [ - { - "$ref": "#/definitions/sequenceAnnotation" - }, - { - "type": "array", - "items": { - "$ref": "#/definitions/sequenceAnnotation" - } - }, + "sameAs": { + "description": "Link to any resource other than the Record and the official webpage, for instance a Wikipedia page. URL of a reference Web page that unambiguously indicates the item's identity. E.g. the URL of the item's Wikipedia page, Wikidata entry, or official website.", + "oneOf": [ { "type": "string", "format": "uri" @@ -14622,103 +14297,103 @@ "owl:cardinality": "many" }, "conformsTo": { - "description": "This is used to state the Bioschemas profile that the markup relates to. The identifier can be the url for the version of this bioschemas class on github: https://github.com/BioSchemas/specifications/tree/master/Protein/jsonld/Protein_v0.12-DRAFT.json", + "description": "This is used to state the Bioschemas profile that the markup relates to. The identifier can be the url for the version of this bioschemas class on github: https://github.com/BioSchemas/specifications/tree/master/ProteinStructure/jsonld/ProteinStructure_v0.6-DRAFT.json", "$ref": "#/definitions/conformsDefinition" } }, "required": [ "identifier", - "name", "conformsTo" ], "recommended": [ - "associatedDisease", + "alternateName", "description", - "hasSequenceAnnotation", - "isEncodedByBioChemEntity", - "taxonomicRange", + "name", "url", + "image", + "boundMolecule", + "expressionSystem", + "structureDeterminationMethod", "sameAs" ], "optional": [ - "alternateName", - "bioChemInteraction", - "bioChemSimilarity", - "hasBioChemEntityPart", - "hasBioPolymerSequence", - "hasMolecularFunction", + "additionalProperty", + "additionalType", + "contains", + "hasCategoryCode", "hasRepresentation", - "image", - "isInvolvedInBiologicalProcess", - "isLocatedInSubcellularLocation", - "isPartOfBioChemEntity", + "isContainedIn", + "location", "mainEntityOfPage" ], "definitions": { - "taxon": { - "@type": "Taxon", + "propertyvalue": { + "@type": "PropertyValue", "type": "object", "properties": { "name": { "type": "string" }, - "taxonRank": { - "anyOf": [ + "value": { + "oneOf": [ { - "$ref": "#/definitions/propertyValue" + "type": "string" }, { - "type": "array", - "items": { - "$ref": "#/definitions/propertyValue" - } + "type": "boolean" }, { - "type": "string" + "type": "number" + } + ] + }, + "identifier": { + "type": "string" + }, + "valuereference": { + "oneOf": [ + { + "$ref": "#/definitions/categorycode" }, { "type": "array", - "items": { - "type": "string" - } + "items": [ + { + "$ref": "#/definitions/categorycode" + } + ] + } + ] + }, + "unitCode": { + "oneOf": [ + { + "type": "string" }, { "type": "string", "format": "uri" - }, - { - "type": "array", - "items": { - "type": "string", - "format": "uri" - } } ] + }, + "unitText": { + "type": "string" } }, "required": [ "name", - "taxonRank" + "value" + ], + "recommended": [ + "valueReference" + ], + "optional": [ + "unitCode", + "unitText" ] }, - "propertyValue": { - "@type": "PropertyValue", - "type": "object", - "properties": { - "name": { - "type": "string" - }, - "value": { - "type": "string" - }, - "identifier": { - "type": "string" - } - }, - "required": [] - }, - "definedTerm": { - "@type": "DefinedTerm", + "biochementity": { + "@type": "bioschemasdrafts:BioChemEntity", "type": "object", "properties": { "url": { @@ -14728,148 +14403,124 @@ "name": { "type": "string" }, - "termCode": { - "type": "string" - }, "identifier": { "type": "string" } }, "required": [] }, - "medicalCondition": { - "@type": "MedicalCondition", + "imageobject": { + "@type": "ImageObject", "type": "object", "properties": { - "url": { - "type": "string", - "format": "uri" - }, "name": { "type": "string" }, - "identifier": { - "type": "string" - } - }, - "required": [] - }, - "bioChemEntity": { - "@type": "bioschemastypes:BioChemEntity", - "type": "object", - "properties": { "url": { "type": "string", "format": "uri" - }, - "name": { - "type": "string" - }, - "identifier": { - "type": "string" } }, "required": [] }, - "gene": { - "@type": "Gene", + "taxon": { + "@type": "Taxon", "type": "object", "properties": { - "identifier": { - "anyOf": [ - { - "$ref": "#/definitions/propertyValue" + "name": { + "type": "string" + }, + "taxonRank": { + "anyOf": [ + { + "$ref": "#/definitions/propertyvalue" }, { - "type": "string" + "type": "array", + "items": { + "$ref": "#/definitions/propertyvalue" + } }, { "type": "string", "format": "uri" + }, + { + "type": "array", + "items": { + "type": "string", + "format": "uri" + } + }, + { + "type": "string" + }, + { + "type": "array", + "items": { + "type": "string" + } } ] - }, - "name": { - "type": "string" } }, "required": [] }, - "quantitativeValue": { - "@type": "QuantitativeValue", + "categorycode": { + "@type": "CategoryCode", "type": "object", "properties": { - "value": { + "name": { "type": "string" }, - "unitText": { + "codeValue": { "type": "string" - } - }, - "required": [] - }, - "dna": { - "@type": "bioschemastypesdrafts:DNA", - "type": "object", - "properties": { - "encodesBioChemEntity": { - "oneOf": [ - { - "$ref": "#/definitions/bioChemEntity" - }, - { - "type": "array", - "items": { - "$ref": "#/definitions/bioChemEntity" - } - } - ] }, - "hasSequence": { + "url": { "type": "string" } }, - "required": [] + "required": [ + "name", + "codeValue", + "url" + ] }, - "rna": { - "@type": "bioschemastypesdrafts:RNA", + "place": { + "@type": "Place", "type": "object", "properties": { - "encodesBioChemEntity": { - "oneOf": [ - { - "$ref": "#/definitions/bioChemEntity" - }, - { - "type": "array", - "items": { - "$ref": "#/definitions/bioChemEntity" - } - } - ] - }, - "hasSequence": { + "name": { "type": "string" } }, "required": [] }, - "sequenceAnnotation": { - "@type": "bioschemastypesdrafts:SequenceAnnotation", + "postaladdress": { + "@type": "PostalAddress", "type": "object", "properties": { - "sequenceLocation": { - "$ref": "#/definitions/sequenceRange" + "streetAddress": { + "type": "string" + }, + "postalCode": { + "type": "string" + }, + "postOfficeBoxNumber": { + "type": "string" + }, + "addressRegion": { + "type": "string" } }, "required": [] }, - "sequenceRange": { - "@type": "bioschemastypesdrafts:SequenceRange", + "creativework": { + "@type": "schema:CreativeWork", "type": "object", "properties": { - "rangeStart": { - "type": "integer" + "name": { + "type": "string" } }, "required": [] @@ -14883,7 +14534,7 @@ "oneOf": [ { "enum": [ - "https://github.com/BioSchemas/specifications/tree/master/Protein/jsonld/Protein_v0.12-DRAFT.json" + "https://github.com/BioSchemas/specifications/tree/master/ProteinStructure/jsonld/ProteinStructure_v0.6-DRAFT.json" ] }, { @@ -14899,113 +14550,85 @@ } } }, - "additional_type": "https://bioschemas.org/profiles#nav-draft", - "schema:schemaVersion": [ - "https://bioschemas.org/profiles/Protein/0.12-DRAFT", - "https://github.com/BioSchemas/specifications/tree/master/Protein/jsonld/Protein_v0.12-DRAFT.json" - ] + "additional_type": "https://bioschemas.org/profiles#nav-draft" }, { - "@id": "bioschemasdrafts:ProteinStructure", + "@id": "bioschemasdrafts:PublicationIssue", "@type": "rdfs:Class", - "rdfs:comment": "This profile specification presents the BioChemEntity usage when describing a Protein structure. Version 0.6-DRAFT.

Summary of Changes


Changes since 0.5-DRAFT-2018_08_15:", + "rdfs:comment": "Bioschemas profile, based on Biotea model, describing a PublicationIssue in Life Sciences. A PublicationIssue is a collection of publication scholarly articles published as a collection in a publication volume or a journal. Version 0.3-DRAFT.

Summary of Changes


Changes since previous draft 0.2-DRAFT-2020_12_03 of the PublicationIssue profile: ", "schema:schemaVersion": [ - "https://bioschemas.org/profiles/ProteinStructure/0.6-DRAFT", - "https://github.com/BioSchemas/specifications/tree/master/ProteinStructure/jsonld/ProteinStructure_v0.6-DRAFT.json" + "https://bioschemas.org/profiles/PublicationIssue/0.3-DRAFT", + "https://github.com/BioSchemas/specifications/tree/master/PublicationIssue/jsonld/PublicationIssue_v0.3-DRAFT.json" ], - "rdfs:label": "ProteinStructure", + "rdfs:label": "PublicationIssue", "rdfs:subClassOf": { - "@id": "bioschemastypes:BioChemEntity" + "@id": "schema:PublicationIssue" }, "$validation": { "$schema": "http://json-schema.org/draft-07/schema#", "type": "object", "properties": { - "identifier": { - "description": " The identifier property represents any kind of identifier for any kind of Thing, such as ISBNs, GTIN codes, UUIDs etc. Schema.org provides dedicated properties for representing many of these, either as textual strings or as URL (URI) links. See [background notes](http://schema.org/docs/datamodel.html#identifierBg) for more details.", + "about": { + "description": "Describes what this issue is about. The subject matter of the content.\n Inverse property: subjectOf.", + "$ref": "#/definitions/thing", + "owl:cardinality": "one" + }, + "editor": { + "description": " Specifies the Person who edited the CreativeWork.", "oneOf": [ { - "$ref": "#/definitions/propertyvalue" - }, - { - "type": "string" + "$ref": "#/definitions/person" }, { - "type": "string", - "format": "uri" + "type": "array", + "items": { + "$ref": "#/definitions/person" + } } ], - "owl:cardinality": "one" + "owl:cardinality": "many" }, - "alternateName": { - "description": " An alias for the item.", + "hasPart": { + "description": "A PublicationIssue has part ScholarlyArticle. Indicates an item or CreativeWork that is part of this item, or CreativeWork (in some sense).\n Inverse property: isPartOf.", "oneOf": [ { - "type": "string" + "$ref": "#/definitions/scholarlyarticle" }, { "type": "array", "items": { - "type": "string" + "$ref": "#/definitions/scholarlyarticle" } } ], "owl:cardinality": "many" }, - "description": { - "description": " A description of the item.", - "type": "string", - "owl:cardinality": "one" - }, - "name": { - "description": " The name of the item.", - "type": "string", - "owl:cardinality": "one" - }, - "url": { - "description": "Link to the official webpage associated to this entity. URL of the item.", - "type": "string", - "format": "uri", - "owl:cardinality": "one" - }, - "image": { - "description": " An image of the item. This can be a URL or a fully described ImageObject.", - "anyOf": [ + "identifier": { + "description": "Publication issues do not commonly have a global or unique identifier. We recommend here to use the URL as identifier whenever possible. The identifier property represents any kind of identifier for any kind of Thing, such as ISBNs, GTIN codes, UUIDs etc. Schema.org provides dedicated properties for representing many of these, either as textual strings or as URL (URI) links. See [background notes](http://schema.org/docs/datamodel.html#identifierBg) for more details.", + "oneOf": [ { - "$ref": "#/definitions/imageobject" + "$ref": "#/definitions/propertyvalue" }, { - "type": "array", - "items": { - "$ref": "#/definitions/imageobject" - } + "type": "string" }, { "type": "string", "format": "uri" - }, - { - "type": "array", - "items": { - "type": "string", - "format": "uri" - } } ], - "owl:cardinality": "many" + "owl:cardinality": "one" }, - "boundMolecule": { - "description": "Bound molecules.", + "inLanguage": { + "description": " The language of the content or performance or used in an action. Please use one of the language codes from the IETF BCP 47 standard. See also availableLanguage. Supersedes language.", "anyOf": [ { - "type": "string", - "format": "uri" + "$ref": "#/definitions/language" }, { "type": "array", "items": { - "type": "string", - "format": "uri" + "$ref": "#/definitions/language" } }, { @@ -15020,231 +14643,85 @@ ], "owl:cardinality": "many" }, - "expressionSystem": { - "description": " Organism where this protein structure is expressed.", + "isPartOf": { + "description": "A PublicationIssue is part of PublicationVoume or Journal. If it is part of a PublicationVolume, optionally the 'isPartOf' a Journal could explicitely indicated as well, making it easier to find the journal this issue belongs to. Indicates an item or CreativeWork that this item, or CreativeWork (in some sense), is part of.\n Inverse property: hasPart.", "anyOf": [ { - "$ref": "#/definitions/biochementity" + "$ref": "#/definitions/publicationvolume" }, { "type": "array", "items": { - "$ref": "#/definitions/biochementity" + "$ref": "#/definitions/publicationvolume" } }, { - "$ref": "#/definitions/taxon" + "$ref": "#/definitions/journal" }, { "type": "array", "items": { - "$ref": "#/definitions/taxon" + "$ref": "#/definitions/journal" } } ], "owl:cardinality": "many" }, - "structureDeterminationMethod": { - "description": " Method used to determine the protein structure.", - "anyOf": [ + "issueNumber": { + "description": " Identifies the issue of publication; for example, \"iii\" or \"2\".", + "oneOf": [ { - "type": "string", - "format": "uri" + "type": "integer" }, { - "type": "array", - "items": { - "type": "string", - "format": "uri" - } + "type": "string" + } + ], + "owl:cardinality": "one" + }, + "keywords": { + "description": " Keywords or tags used to describe this content. Multiple entries in a keywords list are typically delimited by commas.", + "oneOf": [ + { + "$ref": "#/definitions/definedterm" }, { "type": "string" }, { - "type": "array", - "items": { - "type": "string" - } + "type": "string", + "format": "uri" } ], - "owl:cardinality": "many" + "owl:cardinality": "one" }, - "additionalProperty": { - "description": "As much a possible, do not use it! Alternatively, consider reusing properties/relations already coined in controlled vocabularies. We recommed to look at the [OBO Relations Ontology (RO)](http://obofoundry.org/ontology/ro.html) or the [Semanticscience Integrated Ontology (SIO)](http://sio.semanticscience.org/) as starting points. A property-value pair representing an additional characteristics of the entitity, e.g. a product feature or another characteristic for which there is no matching property in schema.org. Note: Publishers should be aware that applications designed to use specific schema.org properties (e.g. http://schema.org/width, http://schema.org/color, http://schema.org/gtin13, ...) will typically expect such data to be provided using those properties, rather than using the generic property/value mechanism.", + "pageEnd": { + "description": " The page on which the work ends; for example \"138\" or \"xvi\".", "oneOf": [ { - "$ref": "#/definitions/propertyvalue" + "type": "integer" }, { - "type": "array", - "items": { - "$ref": "#/definitions/propertyvalue" - } - } - ], - "owl:cardinality": "many" - }, - "additionalType": { - "description": "Should be set to any of the values listed in the Controlled Vocabulary. An additional type for the item, typically used for adding more specific types from external vocabularies in microdata syntax. This is a relationship between something and a class that the thing is in. In RDFa syntax, it is better to use the native RDFa syntax - the 'typeof' attribute - for multiple types. Schema.org tools may have only weaker understanding of extra types, in particular those defined externally.", - "oneOf": [ - { - "type": "string", - "format": "uri" - }, - { - "type": "array", - "items": { - "type": "string", - "format": "uri" - } - } - ], - "owl:cardinality": "many" - }, - "contains": { - "description": "Indicates a BioChemEntity that is (in some sense) a part of this BioChemEntity. Inverse property: isContainedIn. ", - "anyOf": [ - { - "$ref": "#/definitions/biochementity" - }, - { - "type": "array", - "items": { - "$ref": "#/definitions/biochementity" - } - }, - { - "type": "string", - "format": "uri" - }, - { - "type": "array", - "items": { - "type": "string", - "format": "uri" - } + "type": "string" } ], - "owl:cardinality": "many" + "owl:cardinality": "one" }, - "hasCategoryCode": { - "description": "A Category code contained in this code set. A controlled vocabulary term equivalent to this entity. For instance, an organism coined in NCBI taxonomy can be represented as a BioChemEntity. As it also exists as a term in an ontology, it would be nice to capture that information via categoryCode. ", + "pageStart": { + "description": " The page on which the work starts; for example \"135\" or \"xiii\".", "oneOf": [ { - "$ref": "#/definitions/categorycode" - }, - { - "type": "array", - "items": { - "$ref": "#/definitions/categorycode" - } - } - ], - "owl:cardinality": "many" - }, - "hasRepresentation": { - "description": "Representation of this entity. For instance, a chemical structure or sequence. A representation for this entity other than, for instance, an image (use image property for that) or the main web page/record (use mainEntityOfPage for that), and see background notes, for sameAs and url).", - "anyOf": [ - { - "$ref": "#/definitions/propertyvalue" - }, - { - "type": "array", - "items": { - "$ref": "#/definitions/propertyvalue" - } + "type": "integer" }, { "type": "string" - }, - { - "type": "array", - "items": { - "type": "string" - } - }, - { - "type": "string", - "format": "uri" - }, - { - "type": "array", - "items": { - "type": "string", - "format": "uri" - } - } - ], - "owl:cardinality": "many" - }, - "isContainedIn": { - "description": "Indicates a BioChemEntity that this BioChemEntity is (in some sense) a part of. Inverse property: contains. ", - "anyOf": [ - { - "$ref": "#/definitions/biochementity" - }, - { - "type": "array", - "items": { - "$ref": "#/definitions/biochementity" - } - }, - { - "type": "string", - "format": "uri" - }, - { - "type": "array", - "items": { - "type": "string", - "format": "uri" - } } ], - "owl:cardinality": "many" + "owl:cardinality": "one" }, - "location": { - "description": "The location can refer to a position in the chromosome or sequence or to a physical place where, for instance, a sample is stored. Using [additionalType](http://bioschemas.org/devSpecs/ProteinStructure/#additionalType) is advised to make this distinction. For instance, [FALDO](https://github.com/OBF/FALDO) can be used for sequence co-ordinates.\n**Note:** The list of Expected Types has been extended as schema.org/location only has Place, PostalAddress and Text. The location of for example where the event is happening, an organization is located, or where an action takes place.", - "anyOf": [ - { - "$ref": "#/definitions/place" - }, - { - "type": "array", - "items": { - "$ref": "#/definitions/place" - } - }, - { - "$ref": "#/definitions/postaladdress" - }, - { - "type": "array", - "items": { - "$ref": "#/definitions/postaladdress" - } - }, - { - "$ref": "#/definitions/propertyvalue" - }, - { - "type": "array", - "items": { - "$ref": "#/definitions/propertyvalue" - } - }, - { - "type": "string", - "format": "uri" - }, - { - "type": "array", - "items": { - "type": "string", - "format": "uri" - } - }, + "pagination": { + "description": " Any description of pages that is not separated into pageStart and pageEnd; for example, \"1-6, 9, 55\" or \"10-12, 46-49\".", + "oneOf": [ { "type": "string" }, @@ -15257,21 +14734,8 @@ ], "owl:cardinality": "many" }, - "mainEntityOfPage": { - "description": "Link via DataRecord or [URL](http://schema.org/url) to the main Record representing this entity in a dataset.\n**Note:** Bioschemas has replaced DataRecord with CreativeWork in the Expected Types. Indicates a page (or other CreativeWork) for which this thing is the main entity being described. See background notes for details.", - "oneOf": [ - { - "type": "string", - "format": "uri" - }, - { - "$ref": "#/definitions/creativework" - } - ], - "owl:cardinality": "one" - }, "sameAs": { - "description": "Link to any resource other than the Record and the official webpage, for instance a Wikipedia page. URL of a reference Web page that unambiguously indicates the item's identity. E.g. the URL of the item's Wikipedia page, Wikidata entry, or official website.", + "description": "Any other URL linking to this Issue, preferrable in machine-readable format. URL of a reference Web page that unambiguously indicates the item's identity. E.g. the URL of the item's Wikipedia page, Wikidata entry, or official website.", "oneOf": [ { "type": "string", @@ -15287,58 +14751,136 @@ ], "owl:cardinality": "many" }, + "url": { + "description": "Oficial URL. URL of the item.", + "type": "string", + "format": "uri", + "owl:cardinality": "one" + }, "conformsTo": { - "description": "This is used to state the Bioschemas profile that the markup relates to. The identifier can be the url for the version of this bioschemas class on github: https://github.com/BioSchemas/specifications/tree/master/ProteinStructure/jsonld/ProteinStructure_v0.6-DRAFT.json", + "description": "This is used to state the Bioschemas profile that the markup relates to. The identifier can be the url for the version of this bioschemas class on github: https://github.com/BioSchemas/specifications/tree/master/PublicationIssue/jsonld/PublicationIssue_v0.3-DRAFT.json", "$ref": "#/definitions/conformsDefinition" } }, "required": [ - "identifier", + "issueNumber", "conformsTo" ], "recommended": [ - "alternateName", - "description", - "name", + "hasPart", + "identifier", + "isPartOf", + "pageEnd", + "pageStart", "url", - "image", - "boundMolecule", - "expressionSystem", - "structureDeterminationMethod", "sameAs" ], "optional": [ - "additionalProperty", - "additionalType", - "contains", - "hasCategoryCode", - "hasRepresentation", - "isContainedIn", - "location", - "mainEntityOfPage" + "about", + "editor", + "inLanguage", + "keywords", + "pagination" ], "definitions": { - "propertyvalue": { - "@type": "PropertyValue", + "thing": { + "@type": "schema:Thing", + "type": "object", + "properties": { + "name": { + "type": "string" + } + }, + "required": [] + }, + "person": { + "@type": "Person", "type": "object", "properties": { "name": { "type": "string" }, - "value": { - "oneOf": [ + "url": { + "type": "string", + "format": "uri" + }, + "mainEntityOfPage": { + "anyOf": [ { - "type": "string" + "type": "string", + "format": "uri" }, { - "type": "boolean" + "type": "array", + "items": { + "type": "string", + "format": "uri" + } }, { - "type": "number" + "$ref": "#/definitions/creativework" + }, + { + "type": "array", + "items": { + "$ref": "#/definitions/creativework" + } } ] - }, - "identifier": { + } + }, + "required": [ + "name" + ] + }, + "creativework": { + "@type": "CreativeWork", + "type": "object", + "properties": { + "name": { + "type": "string" + }, + "identifier": { + "type": "string" + }, + "url": { + "type": "string", + "format": "uri" + } + }, + "required": [] + }, + "scholarlyarticle": { + "@type": "bioschemas:ScholarlyArticle", + "type": "object", + "properties": { + "name": { + "type": "string" + } + }, + "required": [] + }, + "propertyvalue": { + "@type": "PropertyValue", + "type": "object", + "properties": { + "name": { + "type": "string" + }, + "value": { + "oneOf": [ + { + "type": "string" + }, + { + "type": "boolean" + }, + { + "type": "number" + } + ] + }, + "identifier": { "type": "string" }, "valuereference": { @@ -15383,102 +14925,48 @@ "unitText" ] }, - "biochementity": { - "@type": "bioschemasdrafts:BioChemEntity", + "categorycode": { + "@type": "CategoryCode", "type": "object", "properties": { - "url": { - "type": "string", - "format": "uri" - }, "name": { "type": "string" }, - "identifier": { - "type": "string" - } - }, - "required": [] - }, - "imageobject": { - "@type": "ImageObject", - "type": "object", - "properties": { - "name": { + "codeValue": { "type": "string" }, "url": { - "type": "string", - "format": "uri" + "type": "string" } }, - "required": [] + "required": [ + "name", + "codeValue", + "url" + ] }, - "taxon": { - "@type": "Taxon", + "language": { + "@type": "schema:Language", "type": "object", "properties": { "name": { "type": "string" - }, - "taxonRank": { - "anyOf": [ - { - "$ref": "#/definitions/propertyvalue" - }, - { - "type": "array", - "items": { - "$ref": "#/definitions/propertyvalue" - } - }, - { - "type": "string", - "format": "uri" - }, - { - "type": "array", - "items": { - "type": "string", - "format": "uri" - } - }, - { - "type": "string" - }, - { - "type": "array", - "items": { - "type": "string" - } - } - ] } }, "required": [] }, - "categorycode": { - "@type": "CategoryCode", + "publicationvolume": { + "@type": "bioschemas:PublicationVolume", "type": "object", "properties": { "name": { "type": "string" - }, - "codeValue": { - "type": "string" - }, - "url": { - "type": "string" } }, - "required": [ - "name", - "codeValue", - "url" - ] + "required": [] }, - "place": { - "@type": "Place", + "journal": { + "@type": "bioschemas:Journal", "type": "object", "properties": { "name": { @@ -15487,31 +14975,42 @@ }, "required": [] }, - "postaladdress": { - "@type": "PostalAddress", + "definedterm": { + "@type": "DefinedTerm", "type": "object", "properties": { - "streetAddress": { - "type": "string" + "url": { + "type": "string", + "format": "uri" }, - "postalCode": { + "name": { "type": "string" }, - "postOfficeBoxNumber": { + "termCode": { "type": "string" }, - "addressRegion": { + "identifier": { "type": "string" + }, + "inDefinedTermSet": { + "$ref": "#/definitions/definedtermset" } }, "required": [] }, - "creativework": { - "@type": "schema:CreativeWork", + "definedtermset": { + "@type": "DefinedTermSet", "type": "object", "properties": { "name": { "type": "string" + }, + "identifier": { + "type": "string" + }, + "url": { + "type": "string", + "format": "uri" } }, "required": [] @@ -15525,7 +15024,7 @@ "oneOf": [ { "enum": [ - "https://github.com/BioSchemas/specifications/tree/master/ProteinStructure/jsonld/ProteinStructure_v0.6-DRAFT.json" + "https://github.com/BioSchemas/specifications/tree/master/PublicationIssue/jsonld/PublicationIssue_v0.3-DRAFT.json" ] }, { @@ -15544,23 +15043,23 @@ "additional_type": "https://bioschemas.org/profiles#nav-draft" }, { - "@id": "bioschemasdrafts:PublicationIssue", + "@id": "bioschemasdrafts:PublicationVolume", "@type": "rdfs:Class", - "rdfs:comment": "Bioschemas profile, based on Biotea model, describing a PublicationIssue in Life Sciences. A PublicationIssue is a collection of publication scholarly articles published as a collection in a publication volume or a journal. Version 0.3-DRAFT.

Summary of Changes


Changes since previous draft 0.2-DRAFT-2020_12_03 of the PublicationIssue profile: ", + "rdfs:comment": "Bioschemas profile, based on Biotea model, describing a PublicationVolume in Life Sciences. A PublicationVolume is a collection of publication issues, or scholarly articles, or possibly, although no commonly, any mix from those mentioned. It is commonly part of a Journal. Version 0.3-DRAFT.

Summary of Changes


Changes since previous draft 0.2-DRAFT-2020_12_03 of the PublicationVolumen profile: ", "schema:schemaVersion": [ - "https://bioschemas.org/profiles/PublicationIssue/0.3-DRAFT", - "https://github.com/BioSchemas/specifications/tree/master/PublicationIssue/jsonld/PublicationIssue_v0.3-DRAFT.json" + "https://github.com/BioSchemas/specifications/tree/master/PublicationVolume/jsonld/PublicationVolume_v0.3-DRAFT.json", + "https://bioschemas.org/profiles/PublicationVolume/0.3-DRAFT" ], - "rdfs:label": "PublicationIssue", + "rdfs:label": "PublicationVolume", "rdfs:subClassOf": { - "@id": "schema:PublicationIssue" + "@id": "schema:PublicationVolume" }, "$validation": { "$schema": "http://json-schema.org/draft-07/schema#", "type": "object", "properties": { "about": { - "description": "Describes what this issue is about. The subject matter of the content.\n Inverse property: subjectOf.", + "description": "Describes what this volume is about. The subject matter of the content.\n Inverse property: subjectOf.", "$ref": "#/definitions/thing", "owl:cardinality": "one" }, @@ -15580,8 +15079,17 @@ "owl:cardinality": "many" }, "hasPart": { - "description": "A PublicationIssue has part ScholarlyArticle. Indicates an item or CreativeWork that is part of this item, or CreativeWork (in some sense).\n Inverse property: isPartOf.", - "oneOf": [ + "description": "A PublicationVolume has part PublicationIssue (a.k.a. supplements) or ScholaryArticle. We recommend to include at least the highest 'hasPart' level, i.e., PublicationIssue. It is also possible to use 'hasPart' to link as well directly to ScholarlyArticle, making it easier to find articles in this volume. Indicates an item or CreativeWork that is part of this item, or CreativeWork (in some sense).\n Inverse property: isPartOf.", + "anyOf": [ + { + "$ref": "#/definitions/publicationissue" + }, + { + "type": "array", + "items": { + "$ref": "#/definitions/publicationissue" + } + }, { "$ref": "#/definitions/scholarlyarticle" }, @@ -15595,7 +15103,7 @@ "owl:cardinality": "many" }, "identifier": { - "description": "Publication issues do not commonly have a global or unique identifier. We recommend here to use the URL as identifier whenever possible. The identifier property represents any kind of identifier for any kind of Thing, such as ISBNs, GTIN codes, UUIDs etc. Schema.org provides dedicated properties for representing many of these, either as textual strings or as URL (URI) links. See [background notes](http://schema.org/docs/datamodel.html#identifierBg) for more details.", + "description": "Volumes in a journal are commonly identified by a number thus not unique nor global. We recommend to use the URL as identifier whenever possible. The identifier property represents any kind of identifier for any kind of Thing, such as ISBNs, GTIN codes, UUIDs etc. Schema.org provides dedicated properties for representing many of these, either as textual strings or as URL (URI) links. See [background notes](http://schema.org/docs/datamodel.html#identifierBg) for more details.", "oneOf": [ { "$ref": "#/definitions/propertyvalue" @@ -15635,39 +15143,8 @@ "owl:cardinality": "many" }, "isPartOf": { - "description": "A PublicationIssue is part of PublicationVoume or Journal. If it is part of a PublicationVolume, optionally the 'isPartOf' a Journal could explicitely indicated as well, making it easier to find the journal this issue belongs to. Indicates an item or CreativeWork that this item, or CreativeWork (in some sense), is part of.\n Inverse property: hasPart.", - "anyOf": [ - { - "$ref": "#/definitions/publicationvolume" - }, - { - "type": "array", - "items": { - "$ref": "#/definitions/publicationvolume" - } - }, - { - "$ref": "#/definitions/journal" - }, - { - "type": "array", - "items": { - "$ref": "#/definitions/journal" - } - } - ], - "owl:cardinality": "many" - }, - "issueNumber": { - "description": " Identifies the issue of publication; for example, \"iii\" or \"2\".", - "oneOf": [ - { - "type": "integer" - }, - { - "type": "string" - } - ], + "description": "A PublicationVolume is part of a Journal. Indicates an item or CreativeWork that this item, or CreativeWork (in some sense), is part of.\n Inverse property: hasPart.", + "$ref": "#/definitions/journal", "owl:cardinality": "one" }, "keywords": { @@ -15726,7 +15203,7 @@ "owl:cardinality": "many" }, "sameAs": { - "description": "Any other URL linking to this Issue, preferrable in machine-readable format. URL of a reference Web page that unambiguously indicates the item's identity. E.g. the URL of the item's Wikipedia page, Wikidata entry, or official website.", + "description": "Any other URL linking to this volume, preferrable in machine-readable format. URL of a reference Web page that unambiguously indicates the item's identity. E.g. the URL of the item's Wikipedia page, Wikidata entry, or official website.", "oneOf": [ { "type": "string", @@ -15748,13 +15225,26 @@ "format": "uri", "owl:cardinality": "one" }, + "volumeNumber": { + "description": " Identifies the volume of publication or multi-part work; for example, \"iii\" or \"2\".", + "oneOf": [ + { + "type": "integer" + }, + { + "type": "string" + } + ], + "owl:cardinality": "one" + }, "conformsTo": { - "description": "This is used to state the Bioschemas profile that the markup relates to. The identifier can be the url for the version of this bioschemas class on github: https://github.com/BioSchemas/specifications/tree/master/PublicationIssue/jsonld/PublicationIssue_v0.3-DRAFT.json", + "description": "This is used to state the Bioschemas profile that the markup relates to. The identifier can be the url for the version of this bioschemas class on github: https://github.com/BioSchemas/specifications/tree/master/PublicationVolume/jsonld/PublicationVolume_v0.3-DRAFT.json", "$ref": "#/definitions/conformsDefinition" } }, "required": [ - "issueNumber", + "url", + "volumeNumber", "conformsTo" ], "recommended": [ @@ -15763,7 +15253,6 @@ "isPartOf", "pageEnd", "pageStart", - "url", "sameAs" ], "optional": [ @@ -15841,7 +15330,17 @@ }, "required": [] }, - "scholarlyarticle": { + "publicationissue": { + "@type": "bioschemas:PublicationIssue", + "type": "object", + "properties": { + "name": { + "type": "string" + } + }, + "required": [] + }, + "scholarlyarticle": { "@type": "bioschemas:ScholarlyArticle", "type": "object", "properties": { @@ -15946,16 +15445,6 @@ }, "required": [] }, - "publicationvolume": { - "@type": "bioschemas:PublicationVolume", - "type": "object", - "properties": { - "name": { - "type": "string" - } - }, - "required": [] - }, "journal": { "@type": "bioschemas:Journal", "type": "object", @@ -16015,7 +15504,7 @@ "oneOf": [ { "enum": [ - "https://github.com/BioSchemas/specifications/tree/master/PublicationIssue/jsonld/PublicationIssue_v0.3-DRAFT.json" + "https://github.com/BioSchemas/specifications/tree/master/PublicationVolume/jsonld/PublicationVolume_v0.3-DRAFT.json" ] }, { @@ -16034,67 +15523,101 @@ "additional_type": "https://bioschemas.org/profiles#nav-draft" }, { - "@id": "bioschemasdrafts:PublicationVolume", + "@id": "bioschemasdrafts:RNA", "@type": "rdfs:Class", - "rdfs:comment": "Bioschemas profile, based on Biotea model, describing a PublicationVolume in Life Sciences. A PublicationVolume is a collection of publication issues, or scholarly articles, or possibly, although no commonly, any mix from those mentioned. It is commonly part of a Journal. Version 0.3-DRAFT.

Summary of Changes


Changes since previous draft 0.2-DRAFT-2020_12_03 of the PublicationVolumen profile: ", + "rdfs:comment": " The parent class for this type has been updated to a pending class in schema.org. Version 0.2-DRAFT.

Summary of Changes

Changes since 0.1-DRAFT-2019_11_15", "schema:schemaVersion": [ - "https://github.com/BioSchemas/specifications/tree/master/PublicationVolume/jsonld/PublicationVolume_v0.3-DRAFT.json", - "https://bioschemas.org/profiles/PublicationVolume/0.3-DRAFT" + "https://bioschemas.org/profiles/RNA/0.2-DRAFT", + "https://github.com/BioSchemas/specifications/tree/master/RNA/jsonld/RNA_v0.2-DRAFT.json" ], - "rdfs:label": "PublicationVolume", + "rdfs:label": "RNA", "rdfs:subClassOf": { - "@id": "schema:PublicationVolume" + "@id": "bioschemastypesdrafts:RNA" }, "$validation": { "$schema": "http://json-schema.org/draft-07/schema#", "type": "object", "properties": { - "about": { - "description": "Describes what this volume is about. The subject matter of the content.\n Inverse property: subjectOf.", - "$ref": "#/definitions/thing", + "additionalType": { + "description": " An additional type for the item, typically used for adding more specific types from external vocabularies in microdata syntax. This is a relationship between something and a class that the thing is in. In RDFa syntax, it is better to use the native RDFa syntax - the 'typeof' attribute - for multiple types. Schema.org tools may have only weaker understanding of extra types, in particular those defined externally.", + "type": "string", + "format": "uri", "owl:cardinality": "one" }, - "editor": { - "description": " Specifies the Person who edited the CreativeWork.", + "alternateName": { + "description": " An alias for the item.", + "type": "string", + "owl:cardinality": "one" + }, + "associatedDisease": { + "description": " Disease associated to this BioChemEntity. Such disease can be a MedicalCondition or a URL. If you want to add an evidence supporting the association, please use PropertyValue.", "oneOf": [ { - "$ref": "#/definitions/person" + "$ref": "#/definitions/medicalcondition" }, { - "type": "array", - "items": { - "$ref": "#/definitions/person" - } + "$ref": "#/definitions/propertyvalue" + }, + { + "type": "string", + "format": "uri" } ], - "owl:cardinality": "many" + "owl:cardinality": "one" }, - "hasPart": { - "description": "A PublicationVolume has part PublicationIssue (a.k.a. supplements) or ScholaryArticle. We recommend to include at least the highest 'hasPart' level, i.e., PublicationIssue. It is also possible to use 'hasPart' to link as well directly to ScholarlyArticle, making it easier to find articles in this volume. Indicates an item or CreativeWork that is part of this item, or CreativeWork (in some sense).\n Inverse property: isPartOf.", - "anyOf": [ - { - "$ref": "#/definitions/publicationissue" - }, + "bioChemInteraction": { + "description": " A BioChemEntity that is known to interact with this item.", + "$ref": "#/definitions/biochementity", + "owl:cardinality": "one" + }, + "bioChemSimilarity": { + "description": " A similar molecular entity, e.g., obtained by fingerprint similarity algorithms.", + "$ref": "#/definitions/biochementity", + "owl:cardinality": "one" + }, + "biologicalRole": { + "description": " A role played by the molecular entity within a biological context.", + "$ref": "#/definitions/definedterm", + "owl:cardinality": "one" + }, + "description": { + "description": " A description of the item.", + "type": "string", + "owl:cardinality": "one" + }, + "disambiguatingDescription": { + "description": " A sub property of description. A short description of the item used to disambiguate from other, similar items. Information from other properties (in particular, name) may be necessary for the description to be useful for disambiguation.", + "type": "string", + "owl:cardinality": "one" + }, + "encodesBioChemEntity": { + "description": " Another BioChemEntity encoded by this one.\nInverse property:isEncodedByBioChemEntity.", + "$ref": "#/definitions/biochementity", + "owl:cardinality": "one" + }, + "hasBioChemEntityPart": { + "description": " Indicates a BioChemEntity that (in some sense) has this BioChemEntity as a part.\nInverse property:isPartOfBioChemEntity.", + "$ref": "#/definitions/biochementity", + "owl:cardinality": "one" + }, + "hasMolecularFunction": { + "description": " Molecular function performed by this BioChemEntity; please use PropertyValue if you want to include any evidence.", + "oneOf": [ { - "type": "array", - "items": { - "$ref": "#/definitions/publicationissue" - } + "$ref": "#/definitions/definedterm" }, { - "$ref": "#/definitions/scholarlyarticle" + "$ref": "#/definitions/propertyvalue" }, { - "type": "array", - "items": { - "$ref": "#/definitions/scholarlyarticle" - } + "type": "string", + "format": "uri" } ], - "owl:cardinality": "many" + "owl:cardinality": "one" }, - "identifier": { - "description": "Volumes in a journal are commonly identified by a number thus not unique nor global. We recommend to use the URL as identifier whenever possible. The identifier property represents any kind of identifier for any kind of Thing, such as ISBNs, GTIN codes, UUIDs etc. Schema.org provides dedicated properties for representing many of these, either as textual strings or as URL (URI) links. See [background notes](http://schema.org/docs/datamodel.html#identifierBg) for more details.", + "hasRepresentation": { + "description": " A common representation such as a protein sequence or chemical structure for this entity. For images use schema.org/image.", "oneOf": [ { "$ref": "#/definitions/propertyvalue" @@ -16109,43 +15632,44 @@ ], "owl:cardinality": "one" }, - "inLanguage": { - "description": " The language of the content or performance or used in an action. Please use one of the language codes from the IETF BCP 47 standard. See also availableLanguage. Supersedes language.", - "anyOf": [ + "hasSequence": { + "description": " Nucleotide or amino acid sequence.", + "type": "string", + "owl:cardinality": "one" + }, + "hasSequenceAnnotation": { + "description": " Pointer to a sequence annotation; please use PropertyValue if you want to include any evidence.", + "oneOf": [ { - "$ref": "#/definitions/language" + "$ref": "#/definitions/propertyvalue" }, { - "type": "array", - "items": { - "$ref": "#/definitions/language" - } + "$ref": "#/definitions/sequenceannotation" + } + ], + "owl:cardinality": "one" + }, + "identifier": { + "description": " The identifier property represents any kind of identifier for any kind ofThing, such as ISBNs, GTIN codes, UUIDs etc. Schema.org provides dedicated properties for representing many of these, either as textual strings or as URL (URI) links. Seebackground notesfor more details.", + "oneOf": [ + { + "$ref": "#/definitions/propertyvalue" }, { "type": "string" }, { - "type": "array", - "items": { - "type": "string" - } + "type": "string", + "format": "uri" } ], - "owl:cardinality": "many" - }, - "isPartOf": { - "description": "A PublicationVolume is part of a Journal. Indicates an item or CreativeWork that this item, or CreativeWork (in some sense), is part of.\n Inverse property: hasPart.", - "$ref": "#/definitions/journal", "owl:cardinality": "one" }, - "keywords": { - "description": " Keywords or tags used to describe this content. Multiple entries in a keywords list are typically delimited by commas.", + "image": { + "description": " An image of the item. This can be aURLor a fully describedImageObject.", "oneOf": [ { - "$ref": "#/definitions/definedterm" - }, - { - "type": "string" + "$ref": "#/definitions/imageobject" }, { "type": "string", @@ -16154,47 +15678,74 @@ ], "owl:cardinality": "one" }, - "pageEnd": { - "description": " The page on which the work ends; for example \"138\" or \"xvi\".", + "isCodingRNA": { + "description": " Indicates whether or not this Rna is a coding one.", + "type": "boolean", + "owl:cardinality": "one" + }, + "isEncodedByBioChemEntity": { + "description": " Another BioChemEntity encoding by this one.\nInverse property:encodesBioChemEntity.", "oneOf": [ { - "type": "integer" + "$ref": "#/definitions/gene" }, { - "type": "string" + "$ref": "#/definitions/rna" + }, + { + "$ref": "#/definitions/dna" } ], "owl:cardinality": "one" }, - "pageStart": { - "description": " The page on which the work starts; for example \"135\" or \"xiii\".", + "isInvolvedInBiologicalProcess": { + "description": " Biological process this BioChemEntity is involved in; please use PropertyValue if you want to include any evidence.", "oneOf": [ { - "type": "integer" + "$ref": "#/definitions/definedterm" }, { - "type": "string" + "$ref": "#/definitions/propertyvalue" + }, + { + "type": "string", + "format": "uri" } ], "owl:cardinality": "one" }, - "pagination": { - "description": " Any description of pages that is not separated into pageStart and pageEnd; for example, \"1-6, 9, 55\" or \"10-12, 46-49\".", + "isLocatedInSubcellularLocation": { + "description": " Subcellular location where this BioChemEntity is located; please use PropertyValue if you want to include any evidence.", "oneOf": [ { - "type": "string" + "$ref": "#/definitions/definedterm" }, { - "type": "array", - "items": { - "type": "string" - } + "$ref": "#/definitions/propertyvalue" + }, + { + "type": "string", + "format": "uri" } ], - "owl:cardinality": "many" + "owl:cardinality": "one" + }, + "isMatchedBy": { + "description": " A model matching this BioChemEntity.", + "$ref": "#/definitions/sequencematchingmodel", + "owl:cardinality": "one" + }, + "isPartOfBioChemEntity": { + "description": " Indicates a BioChemEntity that is (in some sense) a part of this BioChemEntity.\nInverse property:hasBioChemEntityPart.", + "$ref": "#/definitions/biochementity", + "owl:cardinality": "one" + }, + "name": { + "description": " The name of the item.", + "type": "string", + "owl:cardinality": "one" }, "sameAs": { - "description": "Any other URL linking to this volume, preferrable in machine-readable format. URL of a reference Web page that unambiguously indicates the item's identity. E.g. the URL of the item's Wikipedia page, Wikidata entry, or official website.", "oneOf": [ { "type": "string", @@ -16208,135 +15759,86 @@ } } ], + "description": "URL of a reference Web page that unambiguously indicates the item's identity. E.g. the URL of the item's Wikipedia page, Wikidata entry, or official website.", "owl:cardinality": "many" }, - "url": { - "description": "Oficial URL. URL of the item.", - "type": "string", - "format": "uri", - "owl:cardinality": "one" - }, - "volumeNumber": { - "description": " Identifies the volume of publication or multi-part work; for example, \"iii\" or \"2\".", + "taxonomicRange": { + "description": " The taxonomic grouping of the organism that expresses, encodes, or in someway related to the BioChemEntity.", "oneOf": [ { - "type": "integer" + "$ref": "#/definitions/taxon" + }, + { + "$ref": "#/definitions/definedterm" }, { "type": "string" + }, + { + "type": "string", + "format": "uri" } ], "owl:cardinality": "one" }, - "conformsTo": { - "description": "This is used to state the Bioschemas profile that the markup relates to. The identifier can be the url for the version of this bioschemas class on github: https://github.com/BioSchemas/specifications/tree/master/PublicationVolume/jsonld/PublicationVolume_v0.3-DRAFT.json", - "$ref": "#/definitions/conformsDefinition" + "url": { + "description": " URL of the item.", + "type": "string", + "format": "uri", + "owl:cardinality": "one" + }, + "conformsTo": { + "description": "This is used to state the Bioschemas profile that the markup relates to. The identifier can be the url for the version of this bioschemas class on github: https://github.com/BioSchemas/specifications/tree/master/RNA/jsonld/RNA_v0.2-DRAFT.json", + "$ref": "#/definitions/conformsDefinition" } }, "required": [ - "url", - "volumeNumber", "conformsTo" ], "recommended": [ - "hasPart", - "identifier", - "isPartOf", - "pageEnd", - "pageStart", "sameAs" ], "optional": [ - "about", - "editor", - "inLanguage", - "keywords", - "pagination" + "additionalType", + "alternateName", + "associatedDisease", + "bioChemInteraction", + "bioChemSimilarity", + "biologicalRole", + "description", + "disambiguatingDescription", + "encodesBioChemEntity", + "hasBioChemEntityPart", + "hasMolecularFunction", + "hasRepresentation", + "hasSequence", + "hasSequenceAnnotation", + "identifier", + "image", + "isCodingRNA", + "isEncodedByBioChemEntity", + "isInvolvedInBiologicalProcess", + "isLocatedInSubcellularLocation", + "isMatchedBy", + "isPartOfBioChemEntity", + "name", + "taxonomicRange", + "url" ], "definitions": { - "thing": { - "@type": "schema:Thing", - "type": "object", - "properties": { - "name": { - "type": "string" - } - }, - "required": [] - }, - "person": { - "@type": "Person", + "medicalcondition": { + "@type": "MedicalCondition", "type": "object", "properties": { - "name": { - "type": "string" - }, "url": { "type": "string", "format": "uri" }, - "mainEntityOfPage": { - "anyOf": [ - { - "type": "string", - "format": "uri" - }, - { - "type": "array", - "items": { - "type": "string", - "format": "uri" - } - }, - { - "$ref": "#/definitions/creativework" - }, - { - "type": "array", - "items": { - "$ref": "#/definitions/creativework" - } - } - ] - } - }, - "required": [ - "name" - ] - }, - "creativework": { - "@type": "CreativeWork", - "type": "object", - "properties": { "name": { "type": "string" }, "identifier": { "type": "string" - }, - "url": { - "type": "string", - "format": "uri" - } - }, - "required": [] - }, - "publicationissue": { - "@type": "bioschemas:PublicationIssue", - "type": "object", - "properties": { - "name": { - "type": "string" - } - }, - "required": [] - }, - "scholarlyarticle": { - "@type": "bioschemas:ScholarlyArticle", - "type": "object", - "properties": { - "name": { - "type": "string" } }, "required": [] @@ -16426,28 +15928,25 @@ "url" ] }, - "language": { - "@type": "schema:Language", + "biochementity": { + "@type": "bioschemastypesdrafts:BioChemEntity", "type": "object", "properties": { + "url": { + "type": "string", + "format": "uri" + }, "name": { "type": "string" - } - }, - "required": [] - }, - "journal": { - "@type": "bioschemas:Journal", - "type": "object", - "properties": { - "name": { + }, + "identifier": { "type": "string" } }, "required": [] }, "definedterm": { - "@type": "DefinedTerm", + "@type": "schema:DefinedTerm", "type": "object", "properties": { "url": { @@ -16486,257 +15985,626 @@ }, "required": [] }, - "conformsDefinition": { - "@type": "CreativeWork", + "sequenceannotation": { + "@type": "schema:SequenceAnnotation", + "type": "object", + "properties": { + "name": { + "type": "string" + } + }, + "required": [] + }, + "imageobject": { + "@type": "ImageObject", + "type": "object", + "properties": { + "name": { + "type": "string" + }, + "url": { + "type": "string", + "format": "uri" + } + }, + "required": [] + }, + "gene": { + "@type": "bioschemas:Gene", "type": "object", "properties": { "identifier": { - "description": "The url of the version bioschemas profile that was used. For jsonschema, set @id to the identifier", - "oneOf": [ + "anyOf": [ { - "enum": [ - "https://github.com/BioSchemas/specifications/tree/master/PublicationVolume/jsonld/PublicationVolume_v0.3-DRAFT.json" - ] + "$ref": "#/definitions/propertyvalue" + }, + { + "type": "string" }, { "type": "string", "format": "uri" } ] + }, + "name": { + "type": "string" } }, - "required": [ - "identifier" - ] - } - } - }, - "additional_type": "https://bioschemas.org/profiles#nav-draft" - }, - { - "@id": "bioschemasdrafts:RNA", - "@type": "rdfs:Class", - "rdfs:comment": " The parent class for this type has been updated to a pending class in schema.org. Version 0.2-DRAFT.

Summary of Changes

Changes since 0.1-DRAFT-2019_11_15", - "schema:schemaVersion": [ - "https://github.com/BioSchemas/specifications/tree/master/RNA/jsonld/RNA_v0.2-DRAFT.json", - "https://bioschemas.org/profiles/RNA/0.2-DRAFT" - ], - "rdfs:label": "RNA", - "rdfs:subClassOf": { - "@id": "bioschemastypesdrafts:RNA" - }, - "$validation": { - "$schema": "http://json-schema.org/draft-07/schema#", - "type": "object", - "properties": { - "additionalType": { - "description": " An additional type for the item, typically used for adding more specific types from external vocabularies in microdata syntax. This is a relationship between something and a class that the thing is in. In RDFa syntax, it is better to use the native RDFa syntax - the 'typeof' attribute - for multiple types. Schema.org tools may have only weaker understanding of extra types, in particular those defined externally.", - "type": "string", - "format": "uri", - "owl:cardinality": "one" - }, - "alternateName": { - "description": " An alias for the item.", - "type": "string", - "owl:cardinality": "one" + "required": [] }, - "associatedDisease": { - "description": " Disease associated to this BioChemEntity. Such disease can be a MedicalCondition or a URL. If you want to add an evidence supporting the association, please use PropertyValue.", - "oneOf": [ - { - "$ref": "#/definitions/medicalcondition" - }, - { - "$ref": "#/definitions/propertyvalue" - }, - { - "type": "string", - "format": "uri" + "rna": { + "@type": "bioschemastypesdrafts:RNA", + "type": "object", + "properties": { + "name": { + "type": "string" } - ], - "owl:cardinality": "one" - }, - "bioChemInteraction": { - "description": " A BioChemEntity that is known to interact with this item.", - "$ref": "#/definitions/biochementity", - "owl:cardinality": "one" + }, + "required": [] }, - "bioChemSimilarity": { - "description": " A similar molecular entity, e.g., obtained by fingerprint similarity algorithms.", - "$ref": "#/definitions/biochementity", - "owl:cardinality": "one" + "dna": { + "@type": "bioschemastypesdrafts:DNA", + "type": "object", + "properties": { + "name": { + "type": "string" + } + }, + "required": [] }, - "biologicalRole": { - "description": " A role played by the molecular entity within a biological context.", - "$ref": "#/definitions/definedterm", - "owl:cardinality": "one" - }, - "description": { - "description": " A description of the item.", - "type": "string", - "owl:cardinality": "one" - }, - "disambiguatingDescription": { - "description": " A sub property of description. A short description of the item used to disambiguate from other, similar items. Information from other properties (in particular, name) may be necessary for the description to be useful for disambiguation.", - "type": "string", - "owl:cardinality": "one" - }, - "encodesBioChemEntity": { - "description": " Another BioChemEntity encoded by this one.\nInverse property:isEncodedByBioChemEntity.", - "$ref": "#/definitions/biochementity", - "owl:cardinality": "one" - }, - "hasBioChemEntityPart": { - "description": " Indicates a BioChemEntity that (in some sense) has this BioChemEntity as a part.\nInverse property:isPartOfBioChemEntity.", - "$ref": "#/definitions/biochementity", - "owl:cardinality": "one" - }, - "hasMolecularFunction": { - "description": " Molecular function performed by this BioChemEntity; please use PropertyValue if you want to include any evidence.", - "oneOf": [ - { - "$ref": "#/definitions/definedterm" - }, - { - "$ref": "#/definitions/propertyvalue" - }, - { - "type": "string", - "format": "uri" + "sequencematchingmodel": { + "@type": "bioschemastypesdrafts:SequenceMatchingModel", + "type": "object", + "properties": { + "name": { + "type": "string" } - ], - "owl:cardinality": "one" + }, + "required": [] }, - "hasRepresentation": { - "description": " A common representation such as a protein sequence or chemical structure for this entity. For images use schema.org/image.", - "oneOf": [ - { - "$ref": "#/definitions/propertyvalue" - }, - { + "taxon": { + "@type": "bioschemas:Taxon", + "type": "object", + "properties": { + "name": { "type": "string" }, - { - "type": "string", - "format": "uri" + "taxonRank": { + "anyOf": [ + { + "$ref": "#/definitions/propertyvalue" + }, + { + "type": "array", + "items": { + "$ref": "#/definitions/propertyvalue" + } + }, + { + "type": "string" + }, + { + "type": "array", + "items": { + "type": "string" + } + }, + { + "type": "string", + "format": "uri" + }, + { + "type": "array", + "items": { + "type": "string", + "format": "uri" + } + } + ] } - ], - "owl:cardinality": "one" - }, - "hasSequence": { - "description": " Nucleotide or amino acid sequence.", - "type": "string", - "owl:cardinality": "one" + }, + "required": [ + "name", + "taxonRank" + ] }, - "hasSequenceAnnotation": { - "description": " Pointer to a sequence annotation; please use PropertyValue if you want to include any evidence.", - "oneOf": [ - { - "$ref": "#/definitions/propertyvalue" - }, - { - "$ref": "#/definitions/sequenceannotation" + "conformsDefinition": { + "@type": "CreativeWork", + "type": "object", + "properties": { + "identifier": { + "description": "The url of the version bioschemas profile that was used. For jsonschema, set @id to the identifier", + "oneOf": [ + { + "enum": [ + "https://github.com/BioSchemas/specifications/tree/master/RNA/jsonld/RNA_v0.2-DRAFT.json" + ] + }, + { + "type": "string", + "format": "uri" + } + ] } - ], - "owl:cardinality": "one" - }, - "identifier": { - "description": " The identifier property represents any kind of identifier for any kind ofThing, such as ISBNs, GTIN codes, UUIDs etc. Schema.org provides dedicated properties for representing many of these, either as textual strings or as URL (URI) links. Seebackground notesfor more details.", + }, + "required": [ + "identifier" + ] + } + } + }, + "additional_type": "https://bioschemas.org/profiles#nav-draft" + }, + { + "@id": "bioschemasdrafts:Sample", + "@type": "rdfs:Class", + "rdfs:comment": "To deliver on the identified use cases for samples, we have identified a minimal set of properties to encapsulate identification, linking, and metadata descriptions. Some of these properties are existing standard schema.org properties, others require Bioschemas extensions. Version 0.3-DRAFT

Summary of Changes

Changes since 0.2-DRAFT", + "rdfs:label": "Sample", + "rdfs:subClassOf": { + "@id": "bioschemastypesdrafts:Sample" + }, + "$validation": { + "$schema": "http://json-schema.org/draft-07/schema#", + "type": "object", + "properties": { + "additionalProperty": { + "description": "A property-value pair representing an additional characteristics of the entitity, e.g. a product feature or another characteristic for which there is no matching property in schema.org. Note: Publishers should be aware that applications designed to use specific schema.org properties (e.g. https://schema.org/width, https://schema.org/color, https://schema.org/gtin13, ...) will typically expect such data to be provided using those properties, rather than using the generic property/value mechanism. ", "oneOf": [ { - "$ref": "#/definitions/propertyvalue" + "@type": "PropertyValue", + "optional": [ + "unitCode", + "unitText" + ], + "properties": { + "identifier": { + "type": "string" + }, + "name": { + "type": "string" + }, + "unitCode": { + "oneOf": [ + { + "type": "string" + }, + { + "format": "uri", + "type": "string" + } + ] + }, + "unitText": { + "type": "string" + }, + "value": { + "oneOf": [ + { + "type": "string" + }, + { + "type": "boolean" + }, + { + "type": "number" + } + ] + }, + "valueReference": { + "oneOf": [ + { + "@type": "CategoryCode", + "properties": { + "codeValue": { + "type": "string" + }, + "name": { + "type": "string" + }, + "url": { + "type": "string" + } + }, + "required": [ + "name", + "codeValue", + "url" + ], + "type": "object" + }, + { + "items": [ + { + "@type": "CategoryCode", + "properties": { + "codeValue": { + "type": "string" + }, + "name": { + "type": "string" + }, + "url": { + "type": "string" + } + }, + "required": [ + "name", + "codeValue", + "url" + ], + "type": "object" + } + ], + "type": "array" + } + ] + } + }, + "recommended": [ + "valueReference" + ], + "required": [ + "name", + "value" + ], + "type": "object" }, { - "type": "string" - }, - { - "type": "string", - "format": "uri" - } - ], - "owl:cardinality": "one" - }, - "image": { - "description": " An image of the item. This can be aURLor a fully describedImageObject.", - "oneOf": [ - { - "$ref": "#/definitions/imageobject" - }, - { - "type": "string", - "format": "uri" + "items": { + "@type": "PropertyValue", + "optional": [ + "unitCode", + "unitText" + ], + "properties": { + "identifier": { + "type": "string" + }, + "name": { + "type": "string" + }, + "unitCode": { + "oneOf": [ + { + "type": "string" + }, + { + "format": "uri", + "type": "string" + } + ] + }, + "unitText": { + "type": "string" + }, + "value": { + "oneOf": [ + { + "type": "string" + }, + { + "type": "boolean" + }, + { + "type": "number" + } + ] + }, + "valueReference": { + "oneOf": [ + { + "@type": "CategoryCode", + "properties": { + "codeValue": { + "type": "string" + }, + "name": { + "type": "string" + }, + "url": { + "type": "string" + } + }, + "required": [ + "name", + "codeValue", + "url" + ], + "type": "object" + }, + { + "items": [ + { + "@type": "CategoryCode", + "properties": { + "codeValue": { + "type": "string" + }, + "name": { + "type": "string" + }, + "url": { + "type": "string" + } + }, + "required": [ + "name", + "codeValue", + "url" + ], + "type": "object" + } + ], + "type": "array" + } + ] + } + }, + "recommended": [ + "valueReference" + ], + "required": [ + "name", + "value" + ], + "type": "object" + }, + "type": "array" } ], - "owl:cardinality": "one" - }, - "isCodingRNA": { - "description": " Indicates whether or not this Rna is a coding one.", - "type": "boolean", - "owl:cardinality": "one" + "owl:cardinality": "many" }, - "isEncodedByBioChemEntity": { - "description": " Another BioChemEntity encoding by this one.\nInverse property:encodesBioChemEntity.", - "oneOf": [ - { - "$ref": "#/definitions/gene" - }, - { - "$ref": "#/definitions/rna" - }, - { - "$ref": "#/definitions/dna" - } - ], - "owl:cardinality": "one" + "description": { + "description": "A description of the item.", + "owl:cardinality": "one", + "type": "string" }, - "isInvolvedInBiologicalProcess": { - "description": " Biological process this BioChemEntity is involved in; please use PropertyValue if you want to include any evidence.", - "oneOf": [ - { - "$ref": "#/definitions/definedterm" - }, + "identifier": { + "description": "The identifier property represents any kind of identifier for any kind of [[Thing]], such as ISBNs, GTIN codes, UUIDs etc. Schema.org provides dedicated properties for representing many of these, either as textual strings or as URL (URI) links. See [background notes](/docs/datamodel.html#identifierBg) for more details.\n ", + "anyOf": [ { - "$ref": "#/definitions/propertyvalue" + "@type": "PropertyValue", + "optional": [ + "unitCode", + "unitText" + ], + "properties": { + "identifier": { + "type": "string" + }, + "name": { + "type": "string" + }, + "unitCode": { + "oneOf": [ + { + "type": "string" + }, + { + "format": "uri", + "type": "string" + } + ] + }, + "unitText": { + "type": "string" + }, + "value": { + "oneOf": [ + { + "type": "string" + }, + { + "type": "boolean" + }, + { + "type": "number" + } + ] + }, + "valueReference": { + "oneOf": [ + { + "@type": "CategoryCode", + "properties": { + "codeValue": { + "type": "string" + }, + "name": { + "type": "string" + }, + "url": { + "type": "string" + } + }, + "required": [ + "name", + "codeValue", + "url" + ], + "type": "object" + }, + { + "items": [ + { + "@type": "CategoryCode", + "properties": { + "codeValue": { + "type": "string" + }, + "name": { + "type": "string" + }, + "url": { + "type": "string" + } + }, + "required": [ + "name", + "codeValue", + "url" + ], + "type": "object" + } + ], + "type": "array" + } + ] + } + }, + "recommended": [ + "valueReference" + ], + "required": [ + "name", + "value" + ], + "type": "object" }, { - "type": "string", - "format": "uri" - } - ], - "owl:cardinality": "one" - }, - "isLocatedInSubcellularLocation": { - "description": " Subcellular location where this BioChemEntity is located; please use PropertyValue if you want to include any evidence.", - "oneOf": [ + "items": { + "@type": "PropertyValue", + "optional": [ + "unitCode", + "unitText" + ], + "properties": { + "identifier": { + "type": "string" + }, + "name": { + "type": "string" + }, + "unitCode": { + "oneOf": [ + { + "type": "string" + }, + { + "format": "uri", + "type": "string" + } + ] + }, + "unitText": { + "type": "string" + }, + "value": { + "oneOf": [ + { + "type": "string" + }, + { + "type": "boolean" + }, + { + "type": "number" + } + ] + }, + "valueReference": { + "oneOf": [ + { + "@type": "CategoryCode", + "properties": { + "codeValue": { + "type": "string" + }, + "name": { + "type": "string" + }, + "url": { + "type": "string" + } + }, + "required": [ + "name", + "codeValue", + "url" + ], + "type": "object" + }, + { + "items": [ + { + "@type": "CategoryCode", + "properties": { + "codeValue": { + "type": "string" + }, + "name": { + "type": "string" + }, + "url": { + "type": "string" + } + }, + "required": [ + "name", + "codeValue", + "url" + ], + "type": "object" + } + ], + "type": "array" + } + ] + } + }, + "recommended": [ + "valueReference" + ], + "required": [ + "name", + "value" + ], + "type": "object" + }, + "type": "array" + }, { - "$ref": "#/definitions/definedterm" + "type": "string" }, { - "$ref": "#/definitions/propertyvalue" + "items": { + "type": "string" + }, + "type": "array" }, { - "type": "string", - "format": "uri" + "format": "uri", + "type": "string" + }, + { + "items": { + "format": "uri", + "type": "string" + }, + "type": "array" } ], - "owl:cardinality": "one" - }, - "isMatchedBy": { - "description": " A model matching this BioChemEntity.", - "$ref": "#/definitions/sequencematchingmodel", - "owl:cardinality": "one" - }, - "isPartOfBioChemEntity": { - "description": " Indicates a BioChemEntity that is (in some sense) a part of this BioChemEntity.\nInverse property:hasBioChemEntityPart.", - "$ref": "#/definitions/biochementity", - "owl:cardinality": "one" + "owl:cardinality": "many" }, "name": { - "description": " The name of the item.", - "type": "string", - "owl:cardinality": "one" + "description": "The name of the item.", + "oneOf": [ + { + "type": "string" + }, + { + "items": { + "type": "string" + }, + "type": "array" + } + ], + "owl:cardinality": "many" }, "sameAs": { + "description": "URL of a reference Web page that unambiguously indicates the item's identity. E.g. the URL of the item's Wikipedia page, Wikidata entry, or official website.", + "owl:cardinality": "many", "oneOf": [ { "type": "string", @@ -16749,936 +16617,942 @@ "format": "uri" } } - ], - "description": "URL of a reference Web page that unambiguously indicates the item's identity. E.g. the URL of the item's Wikipedia page, Wikidata entry, or official website.", - "owl:cardinality": "many" + ] }, - "taxonomicRange": { - "description": " The taxonomic grouping of the organism that expresses, encodes, or in someway related to the BioChemEntity.", + "subjectOf": { + "description": "A CreativeWork or Event about this Thing.", "oneOf": [ { - "$ref": "#/definitions/taxon" - }, - { - "$ref": "#/definitions/definedterm" - }, - { - "type": "string" + "@type": "CreativeWork", + "properties": { + "identifier": { + "type": "string" + }, + "name": { + "type": "string" + }, + "url": { + "format": "uri", + "type": "string" + } + }, + "required": [], + "type": "object" }, { - "type": "string", - "format": "uri" + "items": { + "@type": "CreativeWork", + "properties": { + "identifier": { + "type": "string" + }, + "name": { + "type": "string" + }, + "url": { + "format": "uri", + "type": "string" + } + }, + "required": [], + "type": "object" + }, + "type": "array" } ], - "owl:cardinality": "one" + "owl:cardinality": "many" }, "url": { - "description": " URL of the item.", - "type": "string", + "description": "URL of the item.", "format": "uri", - "owl:cardinality": "one" + "owl:cardinality": "one", + "type": "string" }, "conformsTo": { - "description": "This is used to state the Bioschemas profile that the markup relates to. The identifier can be the url for the version of this bioschemas class on github: https://github.com/BioSchemas/specifications/tree/master/RNA/jsonld/RNA_v0.2-DRAFT.json", + "description": "This is used to state the Bioschemas profile that the markup relates to. The identifier can be the url for the version of this bioschemas class on github: https://github.com/BioSchemas/specifications/tree/master/Sample/jsonld/Sample_v0.3-DRAFT.json", "$ref": "#/definitions/conformsDefinition" } }, "required": [ + "identifier", "conformsTo" ], "recommended": [ - "sameAs" + "sameAs", + "url" ], "optional": [ - "additionalType", - "alternateName", - "associatedDisease", - "bioChemInteraction", - "bioChemSimilarity", - "biologicalRole", + "additionalProperty", "description", - "disambiguatingDescription", - "encodesBioChemEntity", - "hasBioChemEntityPart", - "hasMolecularFunction", - "hasRepresentation", - "hasSequence", - "hasSequenceAnnotation", - "identifier", - "image", - "isCodingRNA", - "isEncodedByBioChemEntity", - "isInvolvedInBiologicalProcess", - "isLocatedInSubcellularLocation", - "isMatchedBy", - "isPartOfBioChemEntity", "name", - "taxonomicRange", - "url" + "subjectOf" ], "definitions": { - "medicalcondition": { - "@type": "MedicalCondition", + "conformsDefinition": { + "@type": "CreativeWork", "type": "object", "properties": { - "url": { - "type": "string", - "format": "uri" - }, - "name": { - "type": "string" - }, "identifier": { - "type": "string" - } - }, - "required": [] - }, - "propertyvalue": { - "@type": "PropertyValue", - "type": "object", - "properties": { - "name": { - "type": "string" - }, - "value": { - "oneOf": [ - { - "type": "string" - }, - { - "type": "boolean" - }, - { - "type": "number" - } - ] - }, - "identifier": { - "type": "string" - }, - "valuereference": { + "description": "The url of the version bioschemas profile that was used. For jsonschema, set @id to the identifier", "oneOf": [ { - "$ref": "#/definitions/categorycode" - }, - { - "type": "array", - "items": [ - { - "$ref": "#/definitions/categorycode" - } + "enum": [ + "https://github.com/BioSchemas/specifications/tree/master/Sample/jsonld/Sample_v0.3-DRAFT.json" ] - } - ] - }, - "unitCode": { - "oneOf": [ - { - "type": "string" }, { "type": "string", "format": "uri" } ] - }, - "unitText": { - "type": "string" } }, "required": [ - "name", - "value" - ], - "recommended": [ - "valueReference" - ], - "optional": [ - "unitCode", - "unitText" + "identifier" ] - }, - "categorycode": { - "@type": "CategoryCode", - "type": "object", - "properties": { - "name": { - "type": "string" + } + } + }, + "additional_type": "https://bioschemas.org/profiles#nav-draft", + "schema:schemaVersion": [ + "https://bioschemas.org/profiles/Sample/0.3-DRAFT", + "https://github.com/BioSchemas/specifications/tree/master/Sample/jsonld/Sample_v0.3-DRAFT.json" + ] + }, + { + "@id": "bioschemasdrafts:ScholarlyArticle", + "@type": "rdfs:Class", + "rdfs:comment": "Bioschemas profile, based on Biotea model, describing a ScholarlyArticle in Life Sciences. A ScholarlyArticle is an article commonly reporting a scientific research, for instance a journal article or thesis. DOI is recommended as official idnetifier (e.g., \"@id\" in JSON-LD) Version 0.3-DRAFT.

Summary of Changes


Changes since previous draft 0.2-DRAFT-2020_12_03 of the ScholarlyArticle profile:", + "schema:schemaVersion": [ + "https://bioschemas.org/profiles/ScholarlyArticle/0.3-DRAFT", + "https://github.com/BioSchemas/specifications/tree/master/ScholarlyArticle/jsonld/ScholarlyArticle_v0.3-DRAFT.json" + ], + "rdfs:label": "ScholarlyArticle", + "rdfs:subClassOf": { + "@id": "schema:ScholarlyArticle" + }, + "$validation": { + "$schema": "http://json-schema.org/draft-07/schema#", + "type": "object", + "properties": { + "about": { + "description": "SemanticTextAnnotations derived (manually or automatically) from the text of this article The subject matter of the content.\n Inverse property: subjectOf.", + "oneOf": [ + { + "$ref": "#/definitions/thing" }, - "codeValue": { + { + "type": "array", + "items": { + "$ref": "#/definitions/thing" + } + } + ], + "owl:cardinality": "many" + }, + "abstract": { + "description": " An abstract is a short description that summarizes a CreativeWork.", + "type": "string", + "owl:cardinality": "one" + }, + "articleBody": { + "description": "If included, could be separated in paragraphs or so. The actual body of the article.", + "oneOf": [ + { "type": "string" }, - "url": { - "type": "string" + { + "type": "array", + "items": { + "type": "string" + } } - }, - "required": [ - "name", - "codeValue", - "url" - ] + ], + "owl:cardinality": "many" }, - "biochementity": { - "@type": "bioschemastypesdrafts:BioChemEntity", - "type": "object", - "properties": { - "url": { - "type": "string", - "format": "uri" + "author": { + "description": " The author of this content or rating. Please note that author is special in that HTML 5 provides a special mechanism for indicating authorship via the rel tag. That is equivalent to this and may be used interchangeably.", + "anyOf": [ + { + "$ref": "#/definitions/organization" }, - "name": { - "type": "string" + { + "type": "array", + "items": { + "$ref": "#/definitions/organization" + } }, - "identifier": { - "type": "string" + { + "$ref": "#/definitions/person" + }, + { + "type": "array", + "items": { + "$ref": "#/definitions/person" + } } - }, - "required": [] + ], + "owl:cardinality": "many" }, - "definedterm": { - "@type": "schema:DefinedTerm", - "type": "object", - "properties": { - "url": { - "type": "string", - "format": "uri" - }, - "name": { - "type": "string" + "citation": { + "description": " A citation or reference to another creative work, such as another publication, web page, scholarly article, etc.", + "anyOf": [ + { + "$ref": "#/definitions/creativework" }, - "termCode": { - "type": "string" + { + "type": "array", + "items": { + "$ref": "#/definitions/creativework" + } }, - "identifier": { + { "type": "string" }, - "inDefinedTermSet": { - "$ref": "#/definitions/definedtermset" + { + "type": "array", + "items": { + "type": "string" + } } - }, - "required": [] + ], + "owl:cardinality": "many" }, - "definedtermset": { - "@type": "DefinedTermSet", - "type": "object", - "properties": { - "name": { - "type": "string" + "correction": { + "description": " Indicates a correction to a CreativeWork, either via a CorrectionComment, textually or in another document.", + "anyOf": [ + { + "$ref": "#/definitions/correctioncomment" }, - "identifier": { + { + "type": "array", + "items": { + "$ref": "#/definitions/correctioncomment" + } + }, + { "type": "string" }, - "url": { + { + "type": "array", + "items": { + "type": "string" + } + }, + { "type": "string", "format": "uri" + }, + { + "type": "array", + "items": { + "type": "string", + "format": "uri" + } } - }, - "required": [] - }, - "sequenceannotation": { - "@type": "schema:SequenceAnnotation", - "type": "object", - "properties": { - "name": { - "type": "string" - } - }, - "required": [] + ], + "owl:cardinality": "many" }, - "imageobject": { - "@type": "ImageObject", - "type": "object", - "properties": { - "name": { - "type": "string" - }, - "url": { + "dateCreated": { + "description": " The date on which the CreativeWork was created or the item was added to a DataFeed.", + "oneOf": [ + { "type": "string", - "format": "uri" + "format": "date" + }, + { + "$ref": "#/definitions/datetime" } - }, - "required": [] + ], + "owl:cardinality": "one" }, - "gene": { - "@type": "bioschemas:Gene", - "type": "object", - "properties": { - "identifier": { - "anyOf": [ - { - "$ref": "#/definitions/propertyvalue" - }, - { - "type": "string" - }, - { - "type": "string", - "format": "uri" - } - ] + "dateModified": { + "description": " The date on which the CreativeWork was most recently modified or when the item's entry was modified within a DataFeed.", + "anyOf": [ + { + "type": "string", + "format": "date" }, - "name": { - "type": "string" + { + "type": "array", + "items": { + "type": "string", + "format": "date" + } + }, + { + "$ref": "#/definitions/datetime" + }, + { + "type": "array", + "items": { + "$ref": "#/definitions/datetime" + } } - }, - "required": [] + ], + "owl:cardinality": "many" }, - "rna": { - "@type": "bioschemastypesdrafts:RNA", - "type": "object", - "properties": { - "name": { - "type": "string" + "datePublished": { + "description": " Date of first broadcast/publication.", + "type": "string", + "format": "date", + "owl:cardinality": "one" + }, + "editor": { + "description": " Specifies the Person who edited the CreativeWork.", + "oneOf": [ + { + "$ref": "#/definitions/person" + }, + { + "type": "array", + "items": { + "$ref": "#/definitions/person" + } } - }, - "required": [] + ], + "owl:cardinality": "many" }, - "dna": { - "@type": "bioschemastypesdrafts:DNA", - "type": "object", - "properties": { - "name": { - "type": "string" + "funder": { + "description": " A person or organization that supports (sponsors) something through some kind of financial contribution.", + "oneOf": [ + { + "$ref": "#/definitions/organization" + }, + { + "$ref": "#/definitions/person" } - }, - "required": [] + ], + "owl:cardinality": "one" }, - "sequencematchingmodel": { - "@type": "bioschemastypesdrafts:SequenceMatchingModel", - "type": "object", - "properties": { - "name": { + "headline": { + "description": "Title of the article (offer for compatibility, while schema.org uses name for this purpose, some scholarly material repostitories/archives use headline) Headline of the article.", + "type": "string", + "owl:cardinality": "one" + }, + "identifier": { + "description": "A global a unique identifier for scholarly articles such as DOI. Others such as PMID and PMC are also possible. Use the namespace:id format e.g. doi, pmid and pmc . Follow community recommendations for the namespace The identifier property represents any kind of identifier for any kind of Thing, such as ISBNs, GTIN codes, UUIDs etc. Schema.org provides dedicated properties for representing many of these, either as textual strings or as URL (URI) links. See [background notes](http://schema.org/docs/datamodel.html#identifierBg) for more details.", + "anyOf": [ + { + "$ref": "#/definitions/propertyvalue" + }, + { + "type": "array", + "items": { + "$ref": "#/definitions/propertyvalue" + } + }, + { "type": "string" + }, + { + "type": "array", + "items": { + "type": "string" + } + }, + { + "type": "string", + "format": "uri" + }, + { + "type": "array", + "items": { + "type": "string", + "format": "uri" + } } - }, - "required": [] + ], + "owl:cardinality": "many" }, - "taxon": { - "@type": "bioschemas:Taxon", - "type": "object", - "properties": { - "name": { + "inLanguage": { + "description": " The language of the content or performance or used in an action. Please use one of the language codes from the IETF BCP 47 standard. See also availableLanguage. Supersedes language.", + "anyOf": [ + { + "$ref": "#/definitions/language" + }, + { + "type": "array", + "items": { + "$ref": "#/definitions/language" + } + }, + { "type": "string" }, - "taxonRank": { - "anyOf": [ - { - "$ref": "#/definitions/propertyvalue" - }, - { - "type": "array", - "items": { - "$ref": "#/definitions/propertyvalue" - } - }, - { - "type": "string" - }, - { - "type": "array", - "items": { - "type": "string" - } - }, - { - "type": "string", - "format": "uri" - }, - { - "type": "array", - "items": { - "type": "string", - "format": "uri" - } - } - ] + { + "type": "array", + "items": { + "type": "string" + } } - }, - "required": [ - "name", - "taxonRank" - ] + ], + "owl:cardinality": "many" }, - "conformsDefinition": { - "@type": "CreativeWork", - "type": "object", - "properties": { - "identifier": { - "description": "The url of the version bioschemas profile that was used. For jsonschema, set @id to the identifier", - "oneOf": [ - { - "enum": [ - "https://github.com/BioSchemas/specifications/tree/master/RNA/jsonld/RNA_v0.2-DRAFT.json" - ] - }, - { - "type": "string", - "format": "uri" - } - ] - } - }, - "required": [ - "identifier" - ] - } - } - }, - "additional_type": "https://bioschemas.org/profiles#nav-draft" - }, - { - "@id": "bioschemasdrafts:Sample", - "@type": "rdfs:Class", - "rdfs:comment": "To deliver on the identified use cases for samples, we have identified a minimal set of properties to encapsulate identification, linking, and metadata descriptions. Some of these properties are existing standard schema.org properties, others require Bioschemas extensions. Version 0.3-DRAFT

Summary of Changes

Changes since 0.2-DRAFT", - "rdfs:label": "Sample", - "rdfs:subClassOf": { - "@id": "bioschemastypesdrafts:Sample" - }, - "$validation": { - "$schema": "http://json-schema.org/draft-07/schema#", - "type": "object", - "properties": { - "additionalProperty": { - "description": "A property-value pair representing an additional characteristics of the entitity, e.g. a product feature or another characteristic for which there is no matching property in schema.org. Note: Publishers should be aware that applications designed to use specific schema.org properties (e.g. https://schema.org/width, https://schema.org/color, https://schema.org/gtin13, ...) will typically expect such data to be provided using those properties, rather than using the generic property/value mechanism. ", - "oneOf": [ + "isAccessibleForFree": { + "description": " A flag to signal that the item, event, or place is accessible for free. Supersedes free.", + "type": "boolean", + "owl:cardinality": "one" + }, + "isBasedOn": { + "description": "Link to any HTML other than the DOI one as well as to possible web services, such as PMC OAI service, providing machine-readable versions used to create this metadata. A resource that was used in the creation of this resource. This term can be repeated for multiple sources. For example, http://example.com/great-multiplication-intro.html. Supersedes isBasedOnUrl.", + "anyOf": [ { - "@type": "PropertyValue", - "optional": [ - "unitCode", - "unitText" - ], - "properties": { - "identifier": { - "type": "string" - }, - "name": { - "type": "string" - }, - "unitCode": { - "oneOf": [ - { - "type": "string" - }, - { - "format": "uri", - "type": "string" - } - ] - }, - "unitText": { - "type": "string" - }, - "value": { - "oneOf": [ - { - "type": "string" - }, - { - "type": "boolean" - }, - { - "type": "number" - } - ] - }, - "valueReference": { - "oneOf": [ - { - "@type": "CategoryCode", - "properties": { - "codeValue": { - "type": "string" - }, - "name": { - "type": "string" - }, - "url": { - "type": "string" - } - }, - "required": [ - "name", - "codeValue", - "url" - ], - "type": "object" - }, - { - "items": [ - { - "@type": "CategoryCode", - "properties": { - "codeValue": { - "type": "string" - }, - "name": { - "type": "string" - }, - "url": { - "type": "string" - } - }, - "required": [ - "name", - "codeValue", - "url" - ], - "type": "object" - } - ], - "type": "array" - } - ] - } - }, - "recommended": [ - "valueReference" - ], - "required": [ - "name", - "value" - ], - "type": "object" + "$ref": "#/definitions/creativework" }, { + "type": "array", "items": { - "@type": "PropertyValue", - "optional": [ - "unitCode", - "unitText" - ], - "properties": { - "identifier": { - "type": "string" - }, - "name": { - "type": "string" - }, - "unitCode": { - "oneOf": [ - { - "type": "string" - }, - { - "format": "uri", - "type": "string" - } - ] - }, - "unitText": { - "type": "string" - }, - "value": { - "oneOf": [ - { - "type": "string" - }, - { - "type": "boolean" - }, - { - "type": "number" - } - ] - }, - "valueReference": { - "oneOf": [ - { - "@type": "CategoryCode", - "properties": { - "codeValue": { - "type": "string" - }, - "name": { - "type": "string" - }, - "url": { - "type": "string" - } - }, - "required": [ - "name", - "codeValue", - "url" - ], - "type": "object" - }, - { - "items": [ - { - "@type": "CategoryCode", - "properties": { - "codeValue": { - "type": "string" - }, - "name": { - "type": "string" - }, - "url": { - "type": "string" - } - }, - "required": [ - "name", - "codeValue", - "url" - ], - "type": "object" - } - ], - "type": "array" - } - ] - } - }, - "recommended": [ - "valueReference" - ], - "required": [ - "name", - "value" - ], - "type": "object" - }, - "type": "array" + "$ref": "#/definitions/creativework" + } + }, + { + "$ref": "#/definitions/product" + }, + { + "type": "array", + "items": { + "$ref": "#/definitions/product" + } + }, + { + "type": "string", + "format": "uri" + }, + { + "type": "array", + "items": { + "type": "string", + "format": "uri" + } } ], "owl:cardinality": "many" }, - "description": { - "description": "A description of the item.", - "owl:cardinality": "one", - "type": "string" - }, - "identifier": { - "description": "The identifier property represents any kind of identifier for any kind of [[Thing]], such as ISBNs, GTIN codes, UUIDs etc. Schema.org provides dedicated properties for representing many of these, either as textual strings or as URL (URI) links. See [background notes](/docs/datamodel.html#identifierBg) for more details.\n ", + "isPartOf": { + "description": "We recommend at least to inlcude a link to the most granular possible level, e.g., PublicationIssue if available. It is also possible to use 'isPartOf' to directly link to the PublicationVolume or the Journal (i.e. Periodical), making it easier to find links to each other. It can also be part of another type, e.g., Dataset, if needed. Indicates an item or CreativeWork that this item, or CreativeWork (in some sense), is part of.\n Inverse property: hasPart.", "anyOf": [ { - "@type": "PropertyValue", - "optional": [ - "unitCode", - "unitText" - ], - "properties": { - "identifier": { - "type": "string" - }, - "name": { - "type": "string" - }, - "unitCode": { - "oneOf": [ - { - "type": "string" - }, - { - "format": "uri", - "type": "string" - } - ] - }, - "unitText": { - "type": "string" - }, - "value": { - "oneOf": [ - { - "type": "string" - }, - { - "type": "boolean" - }, - { - "type": "number" - } - ] - }, - "valueReference": { - "oneOf": [ - { - "@type": "CategoryCode", - "properties": { - "codeValue": { - "type": "string" - }, - "name": { - "type": "string" - }, - "url": { - "type": "string" - } - }, - "required": [ - "name", - "codeValue", - "url" - ], - "type": "object" - }, - { - "items": [ - { - "@type": "CategoryCode", - "properties": { - "codeValue": { - "type": "string" - }, - "name": { - "type": "string" - }, - "url": { - "type": "string" - } - }, - "required": [ - "name", - "codeValue", - "url" - ], - "type": "object" - } - ], - "type": "array" - } - ] - } - }, - "recommended": [ - "valueReference" - ], - "required": [ - "name", - "value" - ], - "type": "object" + "$ref": "#/definitions/publicationvolume" }, { + "type": "array", "items": { - "@type": "PropertyValue", - "optional": [ - "unitCode", - "unitText" - ], - "properties": { - "identifier": { - "type": "string" - }, - "name": { - "type": "string" - }, - "unitCode": { - "oneOf": [ - { - "type": "string" - }, - { - "format": "uri", - "type": "string" - } - ] - }, - "unitText": { - "type": "string" - }, - "value": { - "oneOf": [ - { - "type": "string" - }, - { - "type": "boolean" - }, - { - "type": "number" - } - ] - }, - "valueReference": { - "oneOf": [ - { - "@type": "CategoryCode", - "properties": { - "codeValue": { - "type": "string" - }, - "name": { - "type": "string" - }, - "url": { - "type": "string" - } - }, - "required": [ - "name", - "codeValue", - "url" - ], - "type": "object" - }, - { - "items": [ - { - "@type": "CategoryCode", - "properties": { - "codeValue": { - "type": "string" - }, - "name": { - "type": "string" - }, - "url": { - "type": "string" - } - }, - "required": [ - "name", - "codeValue", - "url" - ], - "type": "object" - } - ], - "type": "array" - } - ] + "$ref": "#/definitions/publicationvolume" + } + }, + { + "$ref": "#/definitions/publicationissue" + }, + { + "type": "array", + "items": { + "$ref": "#/definitions/publicationissue" + } + }, + { + "$ref": "#/definitions/creativework" + }, + { + "type": "array", + "items": { + "$ref": "#/definitions/creativework" + } + }, + { + "type": "string", + "format": "uri" + }, + { + "type": "array", + "items": { + "type": "string", + "format": "uri" + } + }, + { + "$ref": "#/definitions/periodical" + }, + { + "type": "array", + "items": { + "$ref": "#/definitions/periodical" + } + } + ], + "owl:cardinality": "many" + }, + "keywords": { + "description": " Keywords or tags used to describe this content. Multiple entries in a keywords list are typically delimited by commas.", + "anyOf": [ + { + "$ref": "#/definitions/definedterm" + }, + { + "type": "array", + "items": { + "$ref": "#/definitions/definedterm" + } + }, + { + "type": "string" + }, + { + "type": "array", + "items": { + "type": "string" + } + }, + { + "type": "string", + "format": "uri" + }, + { + "type": "array", + "items": { + "type": "string", + "format": "uri" + } + } + ], + "owl:cardinality": "many" + }, + "license": { + "description": " A license document that applies to this content, typically indicated by URL.", + "oneOf": [ + { + "$ref": "#/definitions/creativework" + }, + { + "type": "string", + "format": "uri" + } + ], + "owl:cardinality": "one" + }, + "name": { + "description": "Title of the article as per schema.org examples (headline is also offered as optional for compatibility purposes) The name of the item.", + "type": "string", + "owl:cardinality": "one" + }, + "pageEnd": { + "description": " The page on which the work ends; for example \"138\" or \"xvi\".", + "oneOf": [ + { + "type": "integer" + }, + { + "type": "string" + } + ], + "owl:cardinality": "one" + }, + "pageStart": { + "description": " The page on which the work starts; for example \"135\" or \"xiii\".", + "oneOf": [ + { + "type": "integer" + }, + { + "type": "string" + } + ], + "owl:cardinality": "one" + }, + "pagination": { + "description": " Any description of pages that is not separated into pageStart and pageEnd; for example, \"1-6, 9, 55\" or \"10-12, 46-49\".", + "oneOf": [ + { + "type": "string" + }, + { + "type": "array", + "items": { + "type": "string" + } + } + ], + "owl:cardinality": "many" + }, + "publisher": { + "description": " The publisher of the creative work.", + "anyOf": [ + { + "$ref": "#/definitions/organization" + }, + { + "type": "array", + "items": { + "$ref": "#/definitions/organization" + } + }, + { + "$ref": "#/definitions/person" + }, + { + "type": "array", + "items": { + "$ref": "#/definitions/person" + } + } + ], + "owl:cardinality": "many" + }, + "sameAs": { + "description": "Any other machine readable description of this article. URL of a reference Web page that unambiguously indicates the item's identity. E.g. the URL of the item's Wikipedia page, Wikidata entry, or official website.", + "oneOf": [ + { + "type": "string", + "format": "uri" + }, + { + "type": "array", + "items": { + "type": "string", + "format": "uri" + } + } + ], + "owl:cardinality": "many" + }, + "url": { + "description": "DOI if possible and any other available page displaying this article URL of the item.", + "oneOf": [ + { + "type": "string", + "format": "uri" + }, + { + "type": "array", + "items": { + "type": "string", + "format": "uri" + } + } + ], + "owl:cardinality": "many" + }, + "conformsTo": { + "description": "This is used to state the Bioschemas profile that the markup relates to. The identifier can be the url for the version of this bioschemas class on github: https://github.com/BioSchemas/specifications/tree/master/ScholarlyArticle/jsonld/ScholarlyArticle_v0.3-DRAFT.json", + "$ref": "#/definitions/conformsDefinition" + } + }, + "required": [ + "identifier", + "name", + "conformsTo" + ], + "recommended": [ + "abstract", + "author", + "citation", + "dateCreated", + "dateModified", + "datePublished", + "isPartOf", + "keywords", + "license", + "publisher", + "url", + "sameAs" + ], + "optional": [ + "about", + "articleBody", + "correction", + "editor", + "funder", + "headline", + "inLanguage", + "isAccessibleForFree", + "isBasedOn", + "pageEnd", + "pageStart", + "pagination", + "sameAs" + ], + "definitions": { + "thing": { + "@type": "schema:Thing", + "type": "object", + "properties": { + "name": { + "type": "string" + } + }, + "required": [] + }, + "organization": { + "@type": "Organization", + "type": "object", + "properties": { + "name": { + "type": "string" + }, + "legalName": { + "type": "string" + }, + "description": { + "type": "string" + }, + "sameAs": { + "type": "string", + "format": "uri" + } + } + }, + "person": { + "@type": "Person", + "type": "object", + "properties": { + "name": { + "type": "string" + }, + "url": { + "type": "string", + "format": "uri" + }, + "mainEntityOfPage": { + "anyOf": [ + { + "type": "string", + "format": "uri" + }, + { + "type": "array", + "items": { + "type": "string", + "format": "uri" } }, - "recommended": [ - "valueReference" - ], - "required": [ - "name", - "value" - ], - "type": "object" - }, - "type": "array" + { + "$ref": "#/definitions/creativework" + }, + { + "type": "array", + "items": { + "$ref": "#/definitions/creativework" + } + } + ] + } + }, + "required": [ + "name" + ] + }, + "creativework": { + "@type": "CreativeWork", + "type": "object", + "properties": { + "name": { + "type": "string" + }, + "identifier": { + "type": "string" + }, + "url": { + "type": "string", + "format": "uri" + } + }, + "required": [] + }, + "correctioncomment": { + "@type": "schema:CorrectionComment", + "type": "object", + "properties": { + "name": { + "type": "string" + } + }, + "required": [] + }, + "datetime": { + "@type": "schema:DateTime", + "type": "object", + "properties": { + "name": { + "type": "string" + } + }, + "required": [] + }, + "propertyvalue": { + "@type": "PropertyValue", + "type": "object", + "properties": { + "name": { + "type": "string" + }, + "value": { + "oneOf": [ + { + "type": "string" + }, + { + "type": "boolean" + }, + { + "type": "number" + } + ] }, - { + "identifier": { "type": "string" }, - { - "items": { - "type": "string" - }, - "type": "array" + "valuereference": { + "oneOf": [ + { + "$ref": "#/definitions/categorycode" + }, + { + "type": "array", + "items": [ + { + "$ref": "#/definitions/categorycode" + } + ] + } + ] }, - { - "format": "uri", - "type": "string" + "unitCode": { + "oneOf": [ + { + "type": "string" + }, + { + "type": "string", + "format": "uri" + } + ] }, - { - "items": { - "format": "uri", - "type": "string" - }, - "type": "array" + "unitText": { + "type": "string" } + }, + "required": [ + "name", + "value" ], - "owl:cardinality": "many" + "recommended": [ + "valueReference" + ], + "optional": [ + "unitCode", + "unitText" + ] }, - "name": { - "description": "The name of the item.", - "oneOf": [ - { + "categorycode": { + "@type": "CategoryCode", + "type": "object", + "properties": { + "name": { "type": "string" }, - { - "items": { - "type": "string" - }, - "type": "array" + "codeValue": { + "type": "string" + }, + "url": { + "type": "string" } - ], - "owl:cardinality": "many" + }, + "required": [ + "name", + "codeValue", + "url" + ] }, - "sameAs": { - "description": "URL of a reference Web page that unambiguously indicates the item's identity. E.g. the URL of the item's Wikipedia page, Wikidata entry, or official website.", - "owl:cardinality": "many", - "oneOf": [ - { + "language": { + "@type": "schema:Language", + "type": "object", + "properties": { + "name": { + "type": "string" + } + }, + "required": [] + }, + "product": { + "@type": "schema:Product", + "type": "object", + "properties": { + "name": { + "type": "string" + } + }, + "required": [] + }, + "publicationvolume": { + "@type": "bioschemas:PublicationVolume", + "type": "object", + "properties": { + "name": { + "type": "string" + } + }, + "required": [] + }, + "publicationissue": { + "@type": "bioschemas:PublicationIssue", + "type": "object", + "properties": { + "name": { + "type": "string" + } + }, + "required": [] + }, + "periodical": { + "@type": "schema:Periodical", + "type": "object", + "properties": { + "name": { + "type": "string" + } + }, + "required": [] + }, + "definedterm": { + "@type": "DefinedTerm", + "type": "object", + "properties": { + "url": { "type": "string", "format": "uri" }, - { - "type": "array", - "items": { - "type": "string", - "format": "uri" - } - } - ] - }, - "subjectOf": { - "description": "A CreativeWork or Event about this Thing.", - "oneOf": [ - { - "@type": "CreativeWork", - "properties": { - "identifier": { - "type": "string" - }, - "name": { - "type": "string" - }, - "url": { - "format": "uri", - "type": "string" - } - }, - "required": [], - "type": "object" + "name": { + "type": "string" }, - { - "items": { - "@type": "CreativeWork", - "properties": { - "identifier": { - "type": "string" - }, - "name": { - "type": "string" - }, - "url": { - "format": "uri", - "type": "string" - } - }, - "required": [], - "type": "object" - }, - "type": "array" + "termCode": { + "type": "string" + }, + "identifier": { + "type": "string" + }, + "inDefinedTermSet": { + "$ref": "#/definitions/definedtermset" } - ], - "owl:cardinality": "many" - }, - "url": { - "description": "URL of the item.", - "format": "uri", - "owl:cardinality": "one", - "type": "string" + }, + "required": [] + }, + "definedtermset": { + "@type": "DefinedTermSet", + "type": "object", + "properties": { + "name": { + "type": "string" + }, + "identifier": { + "type": "string" + }, + "url": { + "type": "string", + "format": "uri" + } + }, + "required": [] }, - "conformsTo": { - "description": "This is used to state the Bioschemas profile that the markup relates to. The identifier can be the url for the version of this bioschemas class on github: https://github.com/BioSchemas/specifications/tree/master/Sample/jsonld/Sample_v0.3-DRAFT.json", - "$ref": "#/definitions/conformsDefinition" - } - }, - "required": [ - "identifier", - "conformsTo" - ], - "recommended": [ - "sameAs", - "url" - ], - "optional": [ - "additionalProperty", - "description", - "name", - "subjectOf" - ], - "definitions": { "conformsDefinition": { "@type": "CreativeWork", "type": "object", @@ -17688,7 +17562,7 @@ "oneOf": [ { "enum": [ - "https://github.com/BioSchemas/specifications/tree/master/Sample/jsonld/Sample_v0.3-DRAFT.json" + "https://github.com/BioSchemas/specifications/tree/master/ScholarlyArticle/jsonld/ScholarlyArticle_v0.3-DRAFT.json" ] }, { @@ -17704,65 +17578,31 @@ } } }, - "additional_type": "https://bioschemas.org/profiles#nav-draft", - "schema:schemaVersion": [ - "https://github.com/BioSchemas/specifications/tree/master/Sample/jsonld/Sample_v0.3-DRAFT.json", - "https://bioschemas.org/profiles/Sample/0.3-DRAFT" - ] + "additional_type": "https://bioschemas.org/profiles#nav-draft" }, { - "@id": "bioschemasdrafts:ScholarlyArticle", + "@id": "bioschemasdrafts:SemanticTextAnnotation", "@type": "rdfs:Class", - "rdfs:comment": "Bioschemas profile, based on Biotea model, describing a ScholarlyArticle in Life Sciences. A ScholarlyArticle is an article commonly reporting a scientific research, for instance a journal article or thesis. DOI is recommended as official idnetifier (e.g., \"@id\" in JSON-LD) Version 0.3-DRAFT.

Summary of Changes


Changes since previous draft 0.2-DRAFT-2020_12_03 of the ScholarlyArticle profile:", + "rdfs:comment": "Bioschemas profile, based on Biotea model, describing a semantic annotation associated to a piece of text in a ScholarlyArticle in Life Sciences. A SemanticTextAnnotation corresponds to an expression identified in a ScholarlyArticle and associated to an ontology term. Version 0.3-DRAFT.

Summary of Changes


Changes since previous draft 0.2-DRAFT-2020_12_03 of the SemanticAnnotation profile: ", "schema:schemaVersion": [ - "https://github.com/BioSchemas/specifications/tree/master/ScholarlyArticle/jsonld/ScholarlyArticle_v0.3-DRAFT.json", - "https://bioschemas.org/profiles/ScholarlyArticle/0.3-DRAFT" + "https://github.com/BioSchemas/specifications/tree/master/SemanticTextAnnotation/jsonld/SemanticTextAnnotation_v0.3-DRAFT.json", + "https://bioschemas.org/profiles/SemanticTextAnnotation/0.3-DRAFT" ], - "rdfs:label": "ScholarlyArticle", + "rdfs:label": "SemanticTextAnnotation", "rdfs:subClassOf": { - "@id": "schema:ScholarlyArticle" + "@id": "schema:CreativeWork" }, "$validation": { "$schema": "http://json-schema.org/draft-07/schema#", "type": "object", "properties": { - "about": { - "description": "SemanticTextAnnotations derived (manually or automatically) from the text of this article The subject matter of the content.\n Inverse property: subjectOf.", - "oneOf": [ - { - "$ref": "#/definitions/thing" - }, - { - "type": "array", - "items": { - "$ref": "#/definitions/thing" - } - } - ], - "owl:cardinality": "many" - }, - "abstract": { - "description": " An abstract is a short description that summarizes a CreativeWork.", - "type": "string", + "commentCount": { + "description": "Number of times this annotation is found in the associated scholarly article. The number of comments this CreativeWork (e.g. Article, Question or Answer) has received. This is most applicable to works published in Web sites with commenting system; additional comments may exist elsewhere.", + "type": "integer", "owl:cardinality": "one" }, - "articleBody": { - "description": "If included, could be separated in paragraphs or so. The actual body of the article.", - "oneOf": [ - { - "type": "string" - }, - { - "type": "array", - "items": { - "type": "string" - } - } - ], - "owl:cardinality": "many" - }, - "author": { - "description": " The author of this content or rating. Please note that author is special in that HTML 5 provides a special mechanism for indicating authorship via the rel tag. That is equivalent to this and may be used interchangeably.", + "creator": { + "description": " The creator/author of this CreativeWork. This is the same as the Author property for CreativeWork.", "anyOf": [ { "$ref": "#/definitions/organization" @@ -17785,65 +17625,6 @@ ], "owl:cardinality": "many" }, - "citation": { - "description": " A citation or reference to another creative work, such as another publication, web page, scholarly article, etc.", - "anyOf": [ - { - "$ref": "#/definitions/creativework" - }, - { - "type": "array", - "items": { - "$ref": "#/definitions/creativework" - } - }, - { - "type": "string" - }, - { - "type": "array", - "items": { - "type": "string" - } - } - ], - "owl:cardinality": "many" - }, - "correction": { - "description": " Indicates a correction to a CreativeWork, either via a CorrectionComment, textually or in another document.", - "anyOf": [ - { - "$ref": "#/definitions/correctioncomment" - }, - { - "type": "array", - "items": { - "$ref": "#/definitions/correctioncomment" - } - }, - { - "type": "string" - }, - { - "type": "array", - "items": { - "type": "string" - } - }, - { - "type": "string", - "format": "uri" - }, - { - "type": "array", - "items": { - "type": "string", - "format": "uri" - } - } - ], - "owl:cardinality": "many" - }, "dateCreated": { "description": " The date on which the CreativeWork was created or the item was added to a DataFeed.", "oneOf": [ @@ -17859,29 +17640,16 @@ }, "dateModified": { "description": " The date on which the CreativeWork was most recently modified or when the item's entry was modified within a DataFeed.", - "anyOf": [ + "oneOf": [ { "type": "string", "format": "date" }, - { - "type": "array", - "items": { - "type": "string", - "format": "date" - } - }, { "$ref": "#/definitions/datetime" - }, - { - "type": "array", - "items": { - "$ref": "#/definitions/datetime" - } } ], - "owl:cardinality": "many" + "owl:cardinality": "one" }, "datePublished": { "description": " Date of first broadcast/publication.", @@ -17889,140 +17657,46 @@ "format": "date", "owl:cardinality": "one" }, - "editor": { - "description": " Specifies the Person who edited the CreativeWork.", - "oneOf": [ - { - "$ref": "#/definitions/person" - }, - { - "type": "array", - "items": { - "$ref": "#/definitions/person" - } - } - ], - "owl:cardinality": "many" - }, - "funder": { - "description": " A person or organization that supports (sponsors) something through some kind of financial contribution.", - "oneOf": [ - { - "$ref": "#/definitions/organization" - }, - { - "$ref": "#/definitions/person" - } - ], - "owl:cardinality": "one" - }, - "headline": { - "description": "Title of the article (offer for compatibility, while schema.org uses name for this purpose, some scholarly material repostitories/archives use headline) Headline of the article.", - "type": "string", - "owl:cardinality": "one" - }, "identifier": { - "description": "A global a unique identifier for scholarly articles such as DOI. Others such as PMID and PMC are also possible. Use the namespace:id format e.g. doi, pmid and pmc . Follow community recommendations for the namespace The identifier property represents any kind of identifier for any kind of Thing, such as ISBNs, GTIN codes, UUIDs etc. Schema.org provides dedicated properties for representing many of these, either as textual strings or as URL (URI) links. See [background notes](http://schema.org/docs/datamodel.html#identifierBg) for more details.", - "anyOf": [ + "description": "If available. The identifier property represents any kind of identifier for any kind of Thing, such as ISBNs, GTIN codes, UUIDs etc. Schema.org provides dedicated properties for representing many of these, either as textual strings or as URL (URI) links. See [background notes](http://schema.org/docs/datamodel.html#identifierBg) for more details.", + "oneOf": [ { "$ref": "#/definitions/propertyvalue" }, - { - "type": "array", - "items": { - "$ref": "#/definitions/propertyvalue" - } - }, { "type": "string" }, - { - "type": "array", - "items": { - "type": "string" - } - }, { "type": "string", "format": "uri" - }, - { - "type": "array", - "items": { - "type": "string", - "format": "uri" - } } ], - "owl:cardinality": "many" + "owl:cardinality": "one" }, "inLanguage": { "description": " The language of the content or performance or used in an action. Please use one of the language codes from the IETF BCP 47 standard. See also availableLanguage. Supersedes language.", - "anyOf": [ + "oneOf": [ { "$ref": "#/definitions/language" }, - { - "type": "array", - "items": { - "$ref": "#/definitions/language" - } - }, { "type": "string" - }, - { - "type": "array", - "items": { - "type": "string" - } } ], - "owl:cardinality": "many" - }, - "isAccessibleForFree": { - "description": " A flag to signal that the item, event, or place is accessible for free. Supersedes free.", - "type": "boolean", "owl:cardinality": "one" }, - "isBasedOn": { - "description": "Link to any HTML other than the DOI one as well as to possible web services, such as PMC OAI service, providing machine-readable versions used to create this metadata. A resource that was used in the creation of this resource. This term can be repeated for multiple sources. For example, http://example.com/great-multiplication-intro.html. Supersedes isBasedOnUrl.", - "anyOf": [ - { - "$ref": "#/definitions/creativework" - }, - { - "type": "array", - "items": { - "$ref": "#/definitions/creativework" - } - }, - { - "$ref": "#/definitions/product" - }, - { - "type": "array", - "items": { - "$ref": "#/definitions/product" - } - }, - { - "type": "string", - "format": "uri" - }, - { - "type": "array", - "items": { - "type": "string", - "format": "uri" - } - } - ], - "owl:cardinality": "many" - }, "isPartOf": { - "description": "We recommend at least to inlcude a link to the most granular possible level, e.g., PublicationIssue if available. It is also possible to use 'isPartOf' to directly link to the PublicationVolume or the Journal (i.e. Periodical), making it easier to find links to each other. It can also be part of another type, e.g., Dataset, if needed. Indicates an item or CreativeWork that this item, or CreativeWork (in some sense), is part of.\n Inverse property: hasPart.", + "description": "Dataset or collection aggregating this annotation Indicates an item or CreativeWork that this item, or CreativeWork (in some sense), is part of.\n Inverse property: hasPart.", "anyOf": [ + { + "$ref": "#/definitions/journal" + }, + { + "type": "array", + "items": { + "$ref": "#/definitions/journal" + } + }, { "$ref": "#/definitions/publicationvolume" }, @@ -18051,38 +17725,42 @@ } }, { - "type": "string", - "format": "uri" + "$ref": "#/definitions/trip" }, { "type": "array", "items": { - "type": "string", - "format": "uri" + "$ref": "#/definitions/trip" } - }, + } + ], + "owl:cardinality": "many" + }, + "mainEntity": { + "description": "Ontology terms associated to this annotation. On the DefinedTerm, use additionalType to link to a Unified Medical Language System (UMLS) semantic type (TUI) or group, and sameAs to link to the corresponding concept unique identifier (CUI), if available.\nNote: Bioschemas recommends using DefinedTerm rather than Thing (as specified in schema.org) Indicates the primary entity described in some page or other CreativeWork.\n Inverse property: mainEntityOfPage.", + "oneOf": [ { - "$ref": "#/definitions/periodical" + "$ref": "#/definitions/definedterm" }, { "type": "array", "items": { - "$ref": "#/definitions/periodical" + "$ref": "#/definitions/definedterm" } } ], "owl:cardinality": "many" }, - "keywords": { - "description": " Keywords or tags used to describe this content. Multiple entries in a keywords list are typically delimited by commas.", + "position": { + "description": " The position of an item in a series or sequence of items.", "anyOf": [ { - "$ref": "#/definitions/definedterm" + "type": "integer" }, { "type": "array", "items": { - "$ref": "#/definitions/definedterm" + "type": "integer" } }, { @@ -18093,65 +17771,24 @@ "items": { "type": "string" } - }, - { - "type": "string", - "format": "uri" - }, - { - "type": "array", - "items": { - "type": "string", - "format": "uri" - } } ], "owl:cardinality": "many" }, - "license": { - "description": " A license document that applies to this content, typically indicated by URL.", - "oneOf": [ - { - "$ref": "#/definitions/creativework" - }, - { - "type": "string", - "format": "uri" - } - ], - "owl:cardinality": "one" - }, - "name": { - "description": "Title of the article as per schema.org examples (headline is also offered as optional for compatibility purposes) The name of the item.", - "type": "string", - "owl:cardinality": "one" - }, - "pageEnd": { - "description": " The page on which the work ends; for example \"138\" or \"xvi\".", - "oneOf": [ - { - "type": "integer" - }, - { - "type": "string" - } - ], - "owl:cardinality": "one" - }, - "pageStart": { - "description": " The page on which the work starts; for example \"135\" or \"xiii\".", + "subjectOf": { + "description": "ScholarlyArticle where this annotation is located. It is also possible to link from the ScholarlyArticle to the SemanticTextAnnotation via about\nNote: For the Bioschemas case, the preferred property range is ScholarlyArticle A CreativeWork or Event about this Thing. \nInverse property: about", "oneOf": [ { - "type": "integer" + "$ref": "#/definitions/event" }, { - "type": "string" + "$ref": "#/definitions/creativework" } ], "owl:cardinality": "one" }, - "pagination": { - "description": " Any description of pages that is not separated into pageStart and pageEnd; for example, \"1-6, 9, 55\" or \"10-12, 46-49\".", + "text": { + "description": "Expression found in the text corresponding to this annotation. The textual content of this CreativeWork.", "oneOf": [ { "type": "string" @@ -18165,49 +17802,7 @@ ], "owl:cardinality": "many" }, - "publisher": { - "description": " The publisher of the creative work.", - "anyOf": [ - { - "$ref": "#/definitions/organization" - }, - { - "type": "array", - "items": { - "$ref": "#/definitions/organization" - } - }, - { - "$ref": "#/definitions/person" - }, - { - "type": "array", - "items": { - "$ref": "#/definitions/person" - } - } - ], - "owl:cardinality": "many" - }, "sameAs": { - "description": "Any other machine readable description of this article. URL of a reference Web page that unambiguously indicates the item's identity. E.g. the URL of the item's Wikipedia page, Wikidata entry, or official website.", - "oneOf": [ - { - "type": "string", - "format": "uri" - }, - { - "type": "array", - "items": { - "type": "string", - "format": "uri" - } - } - ], - "owl:cardinality": "many" - }, - "url": { - "description": "DOI if possible and any other available page displaying this article URL of the item.", "oneOf": [ { "type": "string", @@ -18221,58 +17816,35 @@ } } ], + "description": "URL of additional sources for the dataset", "owl:cardinality": "many" }, "conformsTo": { - "description": "This is used to state the Bioschemas profile that the markup relates to. The identifier can be the url for the version of this bioschemas class on github: https://github.com/BioSchemas/specifications/tree/master/ScholarlyArticle/jsonld/ScholarlyArticle_v0.3-DRAFT.json", + "description": "This is used to state the Bioschemas profile that the markup relates to. The identifier can be the url for the version of this bioschemas class on github: https://github.com/BioSchemas/specifications/tree/master/SemanticTextAnnotation/jsonld/SemanticTextAnnotation_v0.3-DRAFT.json", "$ref": "#/definitions/conformsDefinition" } }, "required": [ - "identifier", - "name", + "mainEntity", + "text", "conformsTo" ], "recommended": [ - "abstract", - "author", - "citation", - "dateCreated", - "dateModified", - "datePublished", - "isPartOf", - "keywords", - "license", - "publisher", - "url", + "subjectOf", "sameAs" ], "optional": [ - "about", - "articleBody", - "correction", - "editor", - "funder", - "headline", + "commentCount", + "creator", + "dateCreated", + "dateModified", + "datePublished", + "identifier", "inLanguage", - "isAccessibleForFree", - "isBasedOn", - "pageEnd", - "pageStart", - "pagination", - "sameAs" + "isPartOf", + "position" ], "definitions": { - "thing": { - "@type": "schema:Thing", - "type": "object", - "properties": { - "name": { - "type": "string" - } - }, - "required": [] - }, "organization": { "@type": "Organization", "type": "object", @@ -18349,16 +17921,6 @@ }, "required": [] }, - "correctioncomment": { - "@type": "schema:CorrectionComment", - "type": "object", - "properties": { - "name": { - "type": "string" - } - }, - "required": [] - }, "datetime": { "@type": "schema:DateTime", "type": "object", @@ -18464,8 +18026,8 @@ }, "required": [] }, - "product": { - "@type": "schema:Product", + "journal": { + "@type": "bioschemas:Journal", "type": "object", "properties": { "name": { @@ -18494,8 +18056,8 @@ }, "required": [] }, - "periodical": { - "@type": "schema:Periodical", + "trip": { + "@type": "schema:Trip", "type": "object", "properties": { "name": { @@ -18544,6 +18106,16 @@ }, "required": [] }, + "event": { + "@type": "bioschemas:Event", + "type": "object", + "properties": { + "name": { + "type": "string" + } + }, + "required": [] + }, "conformsDefinition": { "@type": "CreativeWork", "type": "object", @@ -18553,7 +18125,7 @@ "oneOf": [ { "enum": [ - "https://github.com/BioSchemas/specifications/tree/master/ScholarlyArticle/jsonld/ScholarlyArticle_v0.3-DRAFT.json" + "https://github.com/BioSchemas/specifications/tree/master/SemanticTextAnnotation/jsonld/SemanticTextAnnotation_v0.3-DRAFT.json" ] }, { @@ -18572,88 +18144,56 @@ "additional_type": "https://bioschemas.org/profiles#nav-draft" }, { - "@id": "bioschemasdrafts:SemanticTextAnnotation", + "@id": "bioschemasdrafts:SequenceAnnotation", "@type": "rdfs:Class", - "rdfs:comment": "Bioschemas profile, based on Biotea model, describing a semantic annotation associated to a piece of text in a ScholarlyArticle in Life Sciences. A SemanticTextAnnotation corresponds to an expression identified in a ScholarlyArticle and associated to an ontology term. Version 0.3-DRAFT.

Summary of Changes


Changes since previous draft 0.2-DRAFT-2020_12_03 of the SemanticAnnotation profile: ", - "schema:schemaVersion": [ - "https://github.com/BioSchemas/specifications/tree/master/SemanticTextAnnotation/jsonld/SemanticTextAnnotation_v0.3-DRAFT.json", - "https://bioschemas.org/profiles/SemanticTextAnnotation/0.3-DRAFT" - ], - "rdfs:label": "SemanticTextAnnotation", + "rdfs:comment": "Used to provide metadata about Sequence Annotations. The sequence can be an amino acid (protein) or nucleic acid (Gene, DNA, RNA). Version: 0.7-DRAFT (05 July 2021) Note, the parent class for this type has been updated to a pending class in schema.org.

Summary of Changes


Not available.", + "rdfs:label": "SequenceAnnotation", "rdfs:subClassOf": { - "@id": "schema:CreativeWork" + "@id": "bioschemastypesdrafts:SequenceAnnotation" }, "$validation": { "$schema": "http://json-schema.org/draft-07/schema#", "type": "object", "properties": { - "commentCount": { - "description": "Number of times this annotation is found in the associated scholarly article. The number of comments this CreativeWork (e.g. Article, Question or Answer) has received. This is most applicable to works published in Web sites with commenting system; additional comments may exist elsewhere.", - "type": "integer", - "owl:cardinality": "one" - }, - "creator": { - "description": " The creator/author of this CreativeWork. This is the same as the Author property for CreativeWork.", - "anyOf": [ - { - "$ref": "#/definitions/organization" - }, - { - "type": "array", - "items": { - "$ref": "#/definitions/organization" - } - }, + "sequenceLocation": { + "description": "A range/position location where this annotation or BioChemEntity is located reagrding another BioChemEntity, for instance a BioChemStructure in a Protein.", + "oneOf": [ { - "$ref": "#/definitions/person" + "$ref": "#/definitions/sequencerange" }, { "type": "array", "items": { - "$ref": "#/definitions/person" + "$ref": "#/definitions/sequencerange" } } ], - "owl:cardinality": "many" - }, - "dateCreated": { - "description": " The date on which the CreativeWork was created or the item was added to a DataFeed.", - "oneOf": [ - { - "type": "string", - "format": "date" - }, - { - "$ref": "#/definitions/datetime" - } - ], - "owl:cardinality": "one" + "owl:cardinality": "many" }, - "dateModified": { - "description": " The date on which the CreativeWork was most recently modified or when the item's entry was modified within a DataFeed.", + "creationMethod": { + "description": "Method used to create or obtain this annotation or BioChemEntity; please use PropertyValue if you want to include any evidence.", "oneOf": [ + { + "type": "string" + }, { "type": "string", - "format": "date" + "format": "uri" }, { - "$ref": "#/definitions/datetime" + "$ref": "#/definitions/propertyvalue" } ], "owl:cardinality": "one" }, - "datePublished": { - "description": " Date of first broadcast/publication.", - "type": "string", - "format": "date", + "sequenceOrientation": { + "description": "One of 1, 0 or -1.", + "type": "integer", "owl:cardinality": "one" }, - "identifier": { - "description": "If available. The identifier property represents any kind of identifier for any kind of Thing, such as ISBNs, GTIN codes, UUIDs etc. Schema.org provides dedicated properties for representing many of these, either as textual strings or as URL (URI) links. See [background notes](http://schema.org/docs/datamodel.html#identifierBg) for more details.", + "sequenceValue": { + "description": "value of the sequence", "oneOf": [ - { - "$ref": "#/definitions/propertyvalue" - }, { "type": "string" }, @@ -18664,136 +18204,186 @@ ], "owl:cardinality": "one" }, - "inLanguage": { - "description": " The language of the content or performance or used in an action. Please use one of the language codes from the IETF BCP 47 standard. See also availableLanguage. Supersedes language.", + "valueReference": { + "description": "A pointer to a secondary value that provides additional information on the original value, e.g. a reference temperature.", "oneOf": [ { - "$ref": "#/definitions/language" + "type": "string" }, { - "type": "string" + "type": "string", + "format": "uri" + }, + { + "$ref": "#/definitions/propertyvalue" } ], "owl:cardinality": "one" }, - "isPartOf": { - "description": "Dataset or collection aggregating this annotation Indicates an item or CreativeWork that this item, or CreativeWork (in some sense), is part of.\n Inverse property: hasPart.", - "anyOf": [ + "hasBioChemEntityPart": { + "description": "Indicates a BioChemEntity that (in some sense) has this BioChemEntity as a part. Inverse property: isPartOfBioChemEntity", + "oneOf": [ { - "$ref": "#/definitions/journal" + "$ref": "#/definitions/biochementity" }, { "type": "array", "items": { - "$ref": "#/definitions/journal" + "$ref": "#/definitions/biochementity" } + } + ], + "owl:cardinality": "many" + }, + "hasRepresentation": { + "description": "A common representation such as a protein sequence or chemical structure for this entity. For images use schema.org/image.", + "anyOf": [ + { + "type": "string" }, { - "$ref": "#/definitions/publicationvolume" + "type": "string", + "format": "uri" + }, + { + "$ref": "#/definitions/propertyvalue" }, { "type": "array", "items": { - "$ref": "#/definitions/publicationvolume" + "type": "string" } }, { - "$ref": "#/definitions/publicationissue" + "type": "array", + "items": { + "type": "string", + "format": "uri" + } }, { "type": "array", "items": { - "$ref": "#/definitions/publicationissue" + "$ref": "#/definitions/propertyvalue" } - }, + } + ], + "owl:cardinality": "many" + }, + "isPartOfBioChemEntity": { + "description": "Indicates a BioChemEntity that is (in some sense) a part of this BioChemEntity. Inverse property: hasBioChemEntityPart", + "anyOf": [ { - "$ref": "#/definitions/creativework" + "$ref": "#/definitions/biochementity" }, { "type": "array", "items": { - "$ref": "#/definitions/creativework" + "$ref": "#/definitions/biochementity" } }, { - "$ref": "#/definitions/trip" + "type": "string", + "format": "uri" }, { "type": "array", "items": { - "$ref": "#/definitions/trip" + "type": "string", + "format": "uri" } } ], "owl:cardinality": "many" }, - "mainEntity": { - "description": "Ontology terms associated to this annotation. On the DefinedTerm, use additionalType to link to a Unified Medical Language System (UMLS) semantic type (TUI) or group, and sameAs to link to the corresponding concept unique identifier (CUI), if available.\nNote: Bioschemas recommends using DefinedTerm rather than Thing (as specified in schema.org) Indicates the primary entity described in some page or other CreativeWork.\n Inverse property: mainEntityOfPage.", - "oneOf": [ + "isLocatedInSubcellularLocation": { + "description": "Subcellular location where this BioChemEntity is located; please use PropertyValue if you want to include any evidence.", + "anyOf": [ { "$ref": "#/definitions/definedterm" }, + { + "type": "string", + "format": "uri" + }, + { + "$ref": "#/definitions/propertyvalue" + }, { "type": "array", "items": { "$ref": "#/definitions/definedterm" } - } - ], - "owl:cardinality": "many" - }, - "position": { - "description": " The position of an item in a series or sequence of items.", - "anyOf": [ - { - "type": "integer" }, { "type": "array", "items": { - "type": "integer" + "type": "string", + "format": "uri" } }, - { - "type": "string" - }, { "type": "array", "items": { - "type": "string" + "$ref": "#/definitions/propertyvalue" } } ], "owl:cardinality": "many" }, - "subjectOf": { - "description": "ScholarlyArticle where this annotation is located. It is also possible to link from the ScholarlyArticle to the SemanticTextAnnotation via about\nNote: For the Bioschemas case, the preferred property range is ScholarlyArticle A CreativeWork or Event about this Thing. \nInverse property: about", + "alternateName": { + "description": "An alias for the item.", "oneOf": [ { - "$ref": "#/definitions/event" + "type": "string" }, { - "$ref": "#/definitions/creativework" + "type": "array", + "items": { + "type": "string" + } } ], + "owl:cardinality": "many" + }, + "description": { + "description": "A description of the item.", + "type": "string", "owl:cardinality": "one" }, - "text": { - "description": "Expression found in the text corresponding to this annotation. The textual content of this CreativeWork.", - "oneOf": [ + "image": { + "description": "An image of the item. This can be a [[URL]] or a fully described [[ImageObject]].", + "anyOf": [ { - "type": "string" + "type": "string", + "format": "uri" }, { "type": "array", "items": { - "type": "string" + "type": "string", + "format": "uri" + } + }, + { + "$ref": "#/definitions/imageobject" + }, + { + "type": "array", + "items": { + "$ref": "#/definitions/imageobject" } } ], "owl:cardinality": "many" }, + "name": { + "description": "The name of the item.", + "type": "string", + "owl:cardinality": "one" + }, "sameAs": { + "description": "URL of a reference Web page that unambiguously indicates the item's identity. E.g. the URL of the item's Wikipedia page, Wikidata entry, or official website.", "oneOf": [ { "type": "string", @@ -18807,120 +18397,71 @@ } } ], - "description": "URL of additional sources for the dataset", "owl:cardinality": "many" }, + "url": { + "description": "URL of the item.", + "type": "string", + "format": "uri", + "owl:cardinality": "one" + }, "conformsTo": { - "description": "This is used to state the Bioschemas profile that the markup relates to. The identifier can be the url for the version of this bioschemas class on github: https://github.com/BioSchemas/specifications/tree/master/SemanticTextAnnotation/jsonld/SemanticTextAnnotation_v0.3-DRAFT.json", + "description": "This is used to state the Bioschemas profile that the markup relates to. The identifier can be the url for the version of this bioschemas class on github: https://github.com/BioSchemas/specifications/tree/master/SequenceAnnotation/jsonld/SequenceAnnotation_v0.7-DRAFT.json", "$ref": "#/definitions/conformsDefinition" } }, "required": [ - "mainEntity", - "text", + "sequenceLocation", "conformsTo" ], "recommended": [ - "subjectOf", - "sameAs" + "creationMethod", + "sequenceOrientation", + "sequenceValue", + "description", + "image", + "name", + "sameAs", + "url" ], "optional": [ - "commentCount", - "creator", - "dateCreated", - "dateModified", - "datePublished", - "identifier", - "inLanguage", - "isPartOf", - "position" + "valueReference", + "hasBioChemEntityPart", + "hasRepresentation", + "isLocatedInSubcellularLocation", + "alternateName", + "isPartOfBioChemEntity" ], "definitions": { - "organization": { - "@type": "Organization", - "type": "object", - "properties": { - "name": { - "type": "string" - }, - "legalName": { - "type": "string" - }, - "description": { - "type": "string" - }, - "sameAs": { - "type": "string", - "format": "uri" - } - } - }, - "person": { - "@type": "Person", + "sequencerange": { + "@type": "bioschemas:SequenceRange", "type": "object", "properties": { - "name": { - "type": "string" - }, - "url": { - "type": "string", - "format": "uri" + "rangeEnd": { + "type": "integer" }, - "mainEntityOfPage": { - "anyOf": [ - { - "type": "string", - "format": "uri" - }, - { - "type": "array", - "items": { - "type": "string", - "format": "uri" - } - }, - { - "$ref": "#/definitions/creativework" - }, - { - "type": "array", - "items": { - "$ref": "#/definitions/creativework" - } - } - ] + "rangeStart": { + "type": "integer" } - }, - "required": [ - "name" - ] + } }, - "creativework": { - "@type": "CreativeWork", + "biochementity": { + "@type": "bioschemas:BioChemEntity", "type": "object", "properties": { "name": { "type": "string" - }, - "identifier": { - "type": "string" - }, - "url": { - "type": "string", - "format": "uri" } - }, - "required": [] + } }, - "datetime": { - "@type": "schema:DateTime", + "definedterm": { + "@type": "schema:DefinedTerm", "type": "object", "properties": { - "name": { + "termCode": { "type": "string" } - }, - "required": [] + } }, "propertyvalue": { "@type": "PropertyValue", @@ -19007,106 +18548,117 @@ "url" ] }, - "language": { - "@type": "schema:Language", + "imageobject": { + "@type": "ImageObject", "type": "object", "properties": { "name": { "type": "string" + }, + "url": { + "type": "string", + "format": "uri" } }, "required": [] }, - "journal": { - "@type": "bioschemas:Journal", + "conformsDefinition": { + "@type": "CreativeWork", "type": "object", "properties": { - "name": { - "type": "string" + "identifier": { + "description": "The url of the version bioschemas profile that was used. For jsonschema, set @id to the identifier", + "oneOf": [ + { + "enum": [ + "https://github.com/BioSchemas/specifications/tree/master/SequenceAnnotation/jsonld/SequenceAnnotation_v0.7-DRAFT.json" + ] + }, + { + "type": "string", + "format": "uri" + } + ] } }, - "required": [] + "required": [ + "identifier" + ] + } + } + }, + "additional_type": "https://bioschemas.org/profiles#nav-draft", + "schema:schemaVersion": [ + "https://github.com/BioSchemas/specifications/tree/master/SequenceAnnotation/jsonld/SequenceAnnotation_v0.7-DRAFT.json", + "https://bioschemas.org/profiles/SequenceAnnotation/0.7-DRAFT" + ] + }, + { + "@id": "bioschemasdrafts:SequenceRange", + "@type": "rdfs:Class", + "rdfs:comment": "Used to define the range of a subsequence, typically used in conjunction with SequenceAnnotation to define the range of the annotation on the protein or gene sequence. Version: 0.1-DRAFT.

Summary of Changes


Not available. Note, the parent class for this profile has been updated to a pending class in schema.org.", + "rdfs:label": "SequenceRange", + "rdfs:subClassOf": { + "@id": "bioschemastypesdrafts:SequenceRange" + }, + "$validation": { + "$schema": "http://json-schema.org/draft-07/schema#", + "type": "object", + "properties": { + "rangeEnd": { + "description": "Final position of the range", + "type": "integer", + "owl:cardinality": "one" }, - "publicationvolume": { - "@type": "bioschemas:PublicationVolume", - "type": "object", - "properties": { - "name": { - "type": "string" - } - }, - "required": [] + "rangeStart": { + "description": "Initial position of the range.", + "type": "integer", + "owl:cardinality": "one" }, - "publicationissue": { - "@type": "bioschemas:PublicationIssue", - "type": "object", - "properties": { - "name": { - "type": "string" - } - }, - "required": [] + "endUncertainty": { + "description": "If the initial position is not known with reasonable certainty, specify here the uncertainty type as one of \u2018<\u2019 (any position before than rangeEnd), \u2018>\u2019 (any position after rangeEnd), \u2018~\u2019 (around rangeEnd), \u2018[#-#] (to indicate a range where rangeEnd could be located)\u2019.", + "type": "string", + "owl:cardinality": "one" }, - "trip": { - "@type": "schema:Trip", - "type": "object", - "properties": { - "name": { - "type": "string" - } - }, - "required": [] + "startUncertainty": { + "description": "If the initial position is not known with reasonable certainty, specify here the uncertainty type as one of \u2018<\u2019 (any position before than rangeStart), \u2018>\u2019 (any position after rangeStart), \u2018~\u2019 (around the rangeStart), \u2018[#-#] (to indicate a range where rangeStart could be located)\u2019.", + "type": "string", + "owl:cardinality": "one" }, - "definedterm": { - "@type": "DefinedTerm", - "type": "object", - "properties": { - "url": { + "sameAs": { + "oneOf": [ + { "type": "string", "format": "uri" }, - "name": { - "type": "string" - }, - "termCode": { - "type": "string" - }, - "identifier": { - "type": "string" - }, - "inDefinedTermSet": { - "$ref": "#/definitions/definedtermset" - } - }, - "required": [] - }, - "definedtermset": { - "@type": "DefinedTermSet", - "type": "object", - "properties": { - "name": { - "type": "string" - }, - "identifier": { - "type": "string" - }, - "url": { - "type": "string", - "format": "uri" - } - }, - "required": [] - }, - "event": { - "@type": "bioschemas:Event", - "type": "object", - "properties": { - "name": { - "type": "string" + { + "type": "array", + "items": { + "type": "string", + "format": "uri" + } } - }, - "required": [] + ], + "description": "URL of a reference Web page that unambiguously indicates the item's identity. E.g. the URL of the item's Wikipedia page, Wikidata entry, or official website.", + "owl:cardinality": "many" }, + "conformsTo": { + "description": "This is used to state the Bioschemas profile that the markup relates to. The identifier can be the url for the version of this bioschemas class on github: https://github.com/BioSchemas/specifications/tree/master/SequenceRange/jsonld/SequenceRange_v0.2-DRAFT.json", + "$ref": "#/definitions/conformsDefinition" + } + }, + "required": [ + "rangeEnd", + "rangeStart", + "conformsTo" + ], + "recommended": [ + "endUncertainty", + "startUncertainty", + "sameAs" + ], + "optional": [], + "definitions": { "conformsDefinition": { "@type": "CreativeWork", "type": "object", @@ -19116,7 +18668,7 @@ "oneOf": [ { "enum": [ - "https://github.com/BioSchemas/specifications/tree/master/SemanticTextAnnotation/jsonld/SemanticTextAnnotation_v0.3-DRAFT.json" + "https://github.com/BioSchemas/specifications/tree/master/SequenceRange/jsonld/SequenceRange_v0.2-DRAFT.json" ] }, { @@ -19132,249 +18684,321 @@ } } }, - "additional_type": "https://bioschemas.org/profiles#nav-draft" + "additional_type": "https://bioschemas.org/profiles#nav-draft", + "schema:schemaVersion": [ + "https://github.com/BioSchemas/specifications/tree/master/SequenceRange/jsonld/SequenceRange_v0.2-DRAFT.json", + "https://bioschemas.org/profiles/SequenceRange/0.2-DRAFT" + ] }, { - "@id": "bioschemasdrafts:SequenceAnnotation", + "@id": "bioschemasdrafts:Study", "@type": "rdfs:Class", - "rdfs:comment": "Used to provide metadata about Sequence Annotations. The sequence can be an amino acid (protein) or nucleic acid (Gene, DNA, RNA). Version: 0.7-DRAFT (05 July 2021) Note, the parent class for this type has been updated to a pending class in schema.org.

Summary of Changes


Not available.", - "rdfs:label": "SequenceAnnotation", + "rdfs:comment": " This Study profile presents the markup when describing a Study. Version: 0.3-DRAFT.

Summary of Changes


Changes since 0.2-DRAFT:", + "schema:schemaVersion": [ + "https://bioschemas.org/profiles/Study/0.3-DRAFT", + "https://github.com/BioSchemas/specifications/tree/master/Study/jsonld/Study_v0.3-DRAFT.json" + ], + "rdfs:label": "Study", "rdfs:subClassOf": { - "@id": "bioschemastypesdrafts:SequenceAnnotation" + "@id": "bioschemastypesdrafts:Study" }, "$validation": { "$schema": "http://json-schema.org/draft-07/schema#", "type": "object", "properties": { - "sequenceLocation": { - "description": "A range/position location where this annotation or BioChemEntity is located reagrding another BioChemEntity, for instance a BioChemStructure in a Protein.", + "about": { + "description": "Use to link to the Protein, Gene, etc that the study is about The subject matter of the content.\nInverse property: subjectOf.", + "oneOf": [ + { + "$ref": "#/definitions/thing" + }, + { + "type": "array", + "items": { + "$ref": "#/definitions/thing" + } + } + ], + "owl:cardinality": "many" + }, + "additionalProperty": { + "description": "Used to provide arbirary properties of a study. A property-value pair representing an additional characteristics of the entitity, e.g. a product feature or another characteristic for which there is no matching property in schema.org.\n\nNote: Publishers should be aware that applications designed to use specific schema.org properties (e.g. http://schema.org/width, http://schema.org/color, http://schema.org/gtin13, ...) will typically expect such data to be provided using those properties, rather than using the generic property/value mechanism.", + "oneOf": [ + { + "$ref": "#/definitions/propertyvalue" + }, + { + "type": "array", + "items": { + "$ref": "#/definitions/propertyvalue" + } + } + ], + "owl:cardinality": "many" + }, + "author": { + "description": "Used to indicate the person(s) or organizations that conducted the Study. Please use creator to indicate the Research project The author of this content or rating. Please note that author is special in that HTML 5 provides a special mechanism for indicating authorship via the rel tag. That is equivalent to this and may be used interchangeably.", + "oneOf": [ + { + "$ref": "#/definitions/organization" + }, + { + "$ref": "#/definitions/person" + } + ], + "owl:cardinality": "one" + }, + "citation": { + "description": " A citation or reference to another creative work, such as another publication, web page, scholarly article, etc.", "oneOf": [ { - "$ref": "#/definitions/sequencerange" + "$ref": "#/definitions/creativework" + }, + { + "type": "string" + } + ], + "owl:cardinality": "one" + }, + "creator": { + "description": "Used to specify the research project that created the study. Please use author to indicate the organisation, or individuals that conducted the study. The creator/author of this CreativeWork. This is the same as the Author property for CreativeWork.", + "anyOf": [ + { + "$ref": "#/definitions/organization" }, { "type": "array", "items": { - "$ref": "#/definitions/sequencerange" + "$ref": "#/definitions/organization" + } + }, + { + "$ref": "#/definitions/person" + }, + { + "type": "array", + "items": { + "$ref": "#/definitions/person" } } ], "owl:cardinality": "many" }, - "creationMethod": { - "description": "Method used to create or obtain this annotation or BioChemEntity; please use PropertyValue if you want to include any evidence.", + "dateCreated": { + "description": " The date on which the CreativeWork was created or the item was added to a DataFeed.", "oneOf": [ - { - "type": "string" - }, { "type": "string", - "format": "uri" + "format": "date" }, { - "$ref": "#/definitions/propertyvalue" + "$ref": "#/definitions/datetime" } ], "owl:cardinality": "one" }, - "sequenceOrientation": { - "description": "One of 1, 0 or -1.", - "type": "integer", + "datePublished": { + "description": " Date of first broadcast/publication.", + "type": "string", + "format": "date", "owl:cardinality": "one" }, - "sequenceValue": { - "description": "value of the sequence", + "description": { + "description": " A description of the item.", + "type": "string", + "owl:cardinality": "one" + }, + "endDate": { + "description": "Used to indicate the end date of the study. (Extension of existing schema.org property) The end date and time of the item (in ISO 8601 date format).", "oneOf": [ { - "type": "string" + "type": "string", + "format": "date" }, { - "type": "string", - "format": "uri" + "$ref": "#/definitions/datetime" } ], "owl:cardinality": "one" }, - "valueReference": { - "description": "A pointer to a secondary value that provides additional information on the original value, e.g. a reference temperature.", + "identifier": { + "description": " The identifier property represents any kind of identifier for any kind of Thing, such as ISBNs, GTIN codes, UUIDs etc. Schema.org provides dedicated properties for representing many of these, either as textual strings or as URL (URI) links. See [background notes](http://schema.org/docs/datamodel.html#identifierBg) for more details.", "oneOf": [ + { + "$ref": "#/definitions/propertyvalue" + }, { "type": "string" }, { "type": "string", "format": "uri" - }, - { - "$ref": "#/definitions/propertyvalue" } ], "owl:cardinality": "one" }, - "hasBioChemEntityPart": { - "description": "Indicates a BioChemEntity that (in some sense) has this BioChemEntity as a part. Inverse property: isPartOfBioChemEntity", + "isPartOf": { + "description": "Used to indicate the project that the study is a part of. Indicates an item or CreativeWork that this item, or CreativeWork (in some sense), is part of. Inverse property: hasPart.", "oneOf": [ { - "$ref": "#/definitions/biochementity" + "$ref": "#/definitions/creativework" }, { - "type": "array", - "items": { - "$ref": "#/definitions/biochementity" - } + "type": "string", + "format": "uri" } ], - "owl:cardinality": "many" + "owl:cardinality": "one" }, - "hasRepresentation": { - "description": "A common representation such as a protein sequence or chemical structure for this entity. For images use schema.org/image.", - "anyOf": [ + "keywords": { + "description": " Keywords or tags used to describe this content. Multiple entries in a keywords list are typically delimited by commas.", + "oneOf": [ + { + "$ref": "#/definitions/definedterm" + }, { "type": "string" }, { "type": "string", "format": "uri" - }, + } + ], + "owl:cardinality": "one" + }, + "name": { + "description": " The name of the item.", + "type": "string", + "owl:cardinality": "one" + }, + "hasGrowthFacility": { + "description": "The kind of growth facility used in a plant study has growth facility", + "type": "string", + "format": "uri", + "owl:cardinality": "one" + }, + "relatedStudy": { + "description": " A study that is related to this one.", + "oneOf": [ { - "$ref": "#/definitions/propertyvalue" + "$ref": "#/definitions/study" }, { "type": "array", "items": { - "type": "string" + "$ref": "#/definitions/study" } - }, + } + ], + "owl:cardinality": "many" + }, + "startDate": { + "description": "Used to indicate the start date of the study. (Extension of existing schema.org property) The start date and time of the item (in ISO 8601 date format).", + "oneOf": [ { - "type": "array", - "items": { - "type": "string", - "format": "uri" - } + "type": "string", + "format": "date" }, { - "type": "array", - "items": { - "$ref": "#/definitions/propertyvalue" - } + "$ref": "#/definitions/datetime" } ], - "owl:cardinality": "many" + "owl:cardinality": "one" }, - "isPartOfBioChemEntity": { - "description": "Indicates a BioChemEntity that is (in some sense) a part of this BioChemEntity. Inverse property: hasBioChemEntityPart", - "anyOf": [ + "studyDomain": { + "description": "For example, in the life sciences we could have\nFunctional Genomics: http://edamontology.org/topic_0085\nProtemics: http://edamontology.org/topic_0121 Define the domain of the study. For example, the domain could be astrophysics, functional genomics or earth science. Those domains can also have an ontology reference.", + "oneOf": [ { - "$ref": "#/definitions/biochementity" + "$ref": "#/definitions/propertyvalue" }, { - "type": "array", - "items": { - "$ref": "#/definitions/biochementity" - } + "type": "string" }, { "type": "string", "format": "uri" - }, - { - "type": "array", - "items": { - "type": "string", - "format": "uri" - } } ], - "owl:cardinality": "many" + "owl:cardinality": "one" }, - "isLocatedInSubcellularLocation": { - "description": "Subcellular location where this BioChemEntity is located; please use PropertyValue if you want to include any evidence.", - "anyOf": [ + "studyLocation": { + "description": "(Reuse of property from MedicalStudy; Expected types extended.) The location in which the study is taking/took place.", + "oneOf": [ { - "$ref": "#/definitions/definedterm" + "$ref": "#/definitions/administrativearea" }, { - "type": "string", - "format": "uri" - }, + "$ref": "#/definitions/place" + } + ], + "owl:cardinality": "one" + }, + "studyProcess": { + "description": "For example, in the life sciences we could have \nRNA-seq of coding RNA from single cells: http://www.ebi.ac.uk/efo/EFO_0005684\ncase control design: http://www.ebi.ac.uk/efo/EFO_0001427 A process performed as part of an experiment or wider study, i.e. intentionally designed.\nThese processes can have ontology URL attached to.", + "anyOf": [ { "$ref": "#/definitions/propertyvalue" }, { "type": "array", "items": { - "$ref": "#/definitions/definedterm" + "$ref": "#/definitions/propertyvalue" } }, { - "type": "array", - "items": { - "type": "string", - "format": "uri" - } + "type": "string" }, { "type": "array", "items": { - "$ref": "#/definitions/propertyvalue" + "type": "string" } - } - ], - "owl:cardinality": "many" - }, - "alternateName": { - "description": "An alias for the item.", - "oneOf": [ + }, { - "type": "string" + "type": "string", + "format": "uri" }, { "type": "array", "items": { - "type": "string" + "type": "string", + "format": "uri" } } ], "owl:cardinality": "many" }, - "description": { - "description": "A description of the item.", - "type": "string", - "owl:cardinality": "one" - }, - "image": { - "description": "An image of the item. This can be a [[URL]] or a fully described [[ImageObject]].", + "studySubject": { + "description": "(Reuse of property from MedicalStudy; Expected types extended.) A subject of the study, i.e. one of the medical conditions, therapies, devices, drugs, etc. investigated by the study.", "anyOf": [ { - "type": "string", - "format": "uri" + "$ref": "#/definitions/biochementity" }, { "type": "array", "items": { - "type": "string", - "format": "uri" + "$ref": "#/definitions/biochementity" } }, { - "$ref": "#/definitions/imageobject" + "$ref": "#/definitions/medicalentity" }, { "type": "array", "items": { - "$ref": "#/definitions/imageobject" + "$ref": "#/definitions/medicalentity" } } ], "owl:cardinality": "many" }, - "name": { - "description": "The name of the item.", + "url": { + "description": " URL of the item.", "type": "string", + "format": "uri", "owl:cardinality": "one" }, "sameAs": { - "description": "URL of a reference Web page that unambiguously indicates the item's identity. E.g. the URL of the item's Wikipedia page, Wikidata entry, or official website.", "oneOf": [ { "type": "string", @@ -19388,71 +19012,53 @@ } } ], + "description": "URL of a reference Web page that unambiguously indicates the item's identity. E.g. the URL of the item's Wikipedia page, Wikidata entry, or official website.", "owl:cardinality": "many" }, - "url": { - "description": "URL of the item.", - "type": "string", - "format": "uri", - "owl:cardinality": "one" - }, "conformsTo": { - "description": "This is used to state the Bioschemas profile that the markup relates to. The identifier can be the url for the version of this bioschemas class on github: https://github.com/BioSchemas/specifications/tree/master/SequenceAnnotation/jsonld/SequenceAnnotation_v0.7-DRAFT.json", + "description": "This is used to state the Bioschemas profile that the markup relates to. The identifier can be the url for the version of this bioschemas class on github: https://github.com/BioSchemas/specifications/tree/master/Study/jsonld/Study_v0.3-DRAFT.json", "$ref": "#/definitions/conformsDefinition" } }, "required": [ - "sequenceLocation", - "conformsTo" - ], - "recommended": [ - "creationMethod", - "sequenceOrientation", - "sequenceValue", + "author", + "datePublished", "description", - "image", + "identifier", "name", - "sameAs", - "url" + "studyDomain", + "studySubject", + "conformsTo" + ], + "recommended": [ + "about", + "additionalProperty", + "citation", + "creator", + "dateCreated", + "endDate", + "keywords", + "startDate", + "studyLocation", + "studyProcess", + "url", + "sameAs" ], "optional": [ - "valueReference", - "hasBioChemEntityPart", - "hasRepresentation", - "isLocatedInSubcellularLocation", - "alternateName", - "isPartOfBioChemEntity" + "isPartOf", + "hasGrowthFacility", + "relatedStudy" ], "definitions": { - "sequencerange": { - "@type": "bioschemas:SequenceRange", - "type": "object", - "properties": { - "rangeEnd": { - "type": "integer" - }, - "rangeStart": { - "type": "integer" - } - } - }, - "biochementity": { - "@type": "bioschemas:BioChemEntity", + "thing": { + "@type": "schema:Thing", "type": "object", "properties": { "name": { "type": "string" } - } - }, - "definedterm": { - "@type": "schema:DefinedTerm", - "type": "object", - "properties": { - "termCode": { - "type": "string" - } - } + }, + "required": [] }, "propertyvalue": { "@type": "PropertyValue", @@ -19539,117 +19145,230 @@ "url" ] }, - "imageobject": { - "@type": "ImageObject", + "organization": { + "@type": "Organization", "type": "object", "properties": { "name": { "type": "string" }, - "url": { + "legalName": { + "type": "string" + }, + "description": { + "type": "string" + }, + "sameAs": { "type": "string", "format": "uri" } - }, - "required": [] + } }, - "conformsDefinition": { - "@type": "CreativeWork", + "person": { + "@type": "Person", "type": "object", "properties": { - "identifier": { - "description": "The url of the version bioschemas profile that was used. For jsonschema, set @id to the identifier", - "oneOf": [ - { - "enum": [ - "https://github.com/BioSchemas/specifications/tree/master/SequenceAnnotation/jsonld/SequenceAnnotation_v0.7-DRAFT.json" - ] - }, + "name": { + "type": "string" + }, + "url": { + "type": "string", + "format": "uri" + }, + "mainEntityOfPage": { + "anyOf": [ { "type": "string", "format": "uri" + }, + { + "type": "array", + "items": { + "type": "string", + "format": "uri" + } + }, + { + "$ref": "#/definitions/creativework" + }, + { + "type": "array", + "items": { + "$ref": "#/definitions/creativework" + } } ] } }, "required": [ - "identifier" + "name" ] - } - } - }, - "additional_type": "https://bioschemas.org/profiles#nav-draft", - "schema:schemaVersion": [ - "https://bioschemas.org/profiles/SequenceAnnotation/0.7-DRAFT", - "https://github.com/BioSchemas/specifications/tree/master/SequenceAnnotation/jsonld/SequenceAnnotation_v0.7-DRAFT.json" - ] - }, - { - "@id": "bioschemasdrafts:SequenceRange", - "@type": "rdfs:Class", - "rdfs:comment": "Used to define the range of a subsequence, typically used in conjunction with SequenceAnnotation to define the range of the annotation on the protein or gene sequence. Version: 0.1-DRAFT.

Summary of Changes


Not available. Note, the parent class for this profile has been updated to a pending class in schema.org.", - "rdfs:label": "SequenceRange", - "rdfs:subClassOf": { - "@id": "bioschemastypesdrafts:SequenceRange" - }, - "$validation": { - "$schema": "http://json-schema.org/draft-07/schema#", - "type": "object", - "properties": { - "rangeEnd": { - "description": "Final position of the range", - "type": "integer", - "owl:cardinality": "one" }, - "rangeStart": { - "description": "Initial position of the range.", - "type": "integer", - "owl:cardinality": "one" + "creativework": { + "@type": "CreativeWork", + "type": "object", + "properties": { + "name": { + "type": "string" + }, + "identifier": { + "type": "string" + }, + "url": { + "type": "string", + "format": "uri" + } + }, + "required": [] }, - "endUncertainty": { - "description": "If the initial position is not known with reasonable certainty, specify here the uncertainty type as one of \u2018<\u2019 (any position before than rangeEnd), \u2018>\u2019 (any position after rangeEnd), \u2018~\u2019 (around rangeEnd), \u2018[#-#] (to indicate a range where rangeEnd could be located)\u2019.", - "type": "string", - "owl:cardinality": "one" + "datetime": { + "@type": "schema:DateTime", + "type": "object", + "properties": { + "name": { + "type": "string" + } + }, + "required": [] }, - "startUncertainty": { - "description": "If the initial position is not known with reasonable certainty, specify here the uncertainty type as one of \u2018<\u2019 (any position before than rangeStart), \u2018>\u2019 (any position after rangeStart), \u2018~\u2019 (around the rangeStart), \u2018[#-#] (to indicate a range where rangeStart could be located)\u2019.", - "type": "string", - "owl:cardinality": "one" + "definedterm": { + "@type": "DefinedTerm", + "type": "object", + "properties": { + "url": { + "type": "string", + "format": "uri" + }, + "name": { + "type": "string" + }, + "termCode": { + "type": "string" + }, + "identifier": { + "type": "string" + }, + "inDefinedTermSet": { + "$ref": "#/definitions/definedtermset" + } + }, + "required": [] }, - "sameAs": { - "oneOf": [ - { + "definedtermset": { + "@type": "DefinedTermSet", + "type": "object", + "properties": { + "name": { + "type": "string" + }, + "identifier": { + "type": "string" + }, + "url": { + "type": "string", + "format": "uri" + } + }, + "required": [] + }, + "study": { + "@type": "bioschemas:Study", + "type": "object", + "properties": { + "name": { + "type": "string" + } + }, + "required": [] + }, + "place": { + "@type": "Place", + "type": "object", + "properties": { + "name": { + "type": "string" + }, + "address": { + "oneOf": [ + { + "type": "string" + }, + { + "$ref": "#/definitions/postaladdress" + } + ] + }, + "identifier": { + "type": "string" + }, + "url": { + "type": "string", + "format": "uri" + } + } + }, + "administrativearea": { + "@type": "schema:AdministrativeArea", + "type": "object", + "properties": { + "name": { + "type": "string" + } + }, + "required": [] + }, + "biochementity": { + "@type": "bioschemas:BioChemEntity", + "type": "object", + "properties": { + "url": { "type": "string", "format": "uri" }, - { - "type": "array", - "items": { - "type": "string", - "format": "uri" - } + "name": { + "type": "string" + }, + "identifier": { + "type": "string" } - ], - "description": "URL of a reference Web page that unambiguously indicates the item's identity. E.g. the URL of the item's Wikipedia page, Wikidata entry, or official website.", - "owl:cardinality": "many" + }, + "required": [] + }, + "medicalentity": { + "@type": "schema:MedicalEntity", + "type": "object", + "properties": { + "name": { + "type": "string" + } + }, + "required": [] + }, + "postaladdress": { + "@type": "schema:PostalAddress", + "type": "object", + "properties": { + "addressCountry": { + "type": "string" + }, + "addressLocality": { + "type": "string" + }, + "addressRegion": { + "type": "string" + }, + "postOfficeBoxNumber": { + "type": "string" + }, + "postalCode": { + "type": "string" + }, + "streetAddress": { + "type": "string" + } + }, + "required": [] }, - "conformsTo": { - "description": "This is used to state the Bioschemas profile that the markup relates to. The identifier can be the url for the version of this bioschemas class on github: https://github.com/BioSchemas/specifications/tree/master/SequenceRange/jsonld/SequenceRange_v0.2-DRAFT.json", - "$ref": "#/definitions/conformsDefinition" - } - }, - "required": [ - "rangeEnd", - "rangeStart", - "conformsTo" - ], - "recommended": [ - "endUncertainty", - "startUncertainty", - "sameAs" - ], - "optional": [], - "definitions": { "conformsDefinition": { "@type": "CreativeWork", "type": "object", @@ -19659,7 +19378,7 @@ "oneOf": [ { "enum": [ - "https://github.com/BioSchemas/specifications/tree/master/SequenceRange/jsonld/SequenceRange_v0.2-DRAFT.json" + "https://github.com/BioSchemas/specifications/tree/master/Study/jsonld/Study_v0.3-DRAFT.json" ] }, { @@ -19675,30 +19394,26 @@ } } }, - "additional_type": "https://bioschemas.org/profiles#nav-draft", - "schema:schemaVersion": [ - "https://bioschemas.org/profiles/SequenceRange/0.2-DRAFT", - "https://github.com/BioSchemas/specifications/tree/master/SequenceRange/jsonld/SequenceRange_v0.2-DRAFT.json" - ] + "additional_type": "https://bioschemas.org/profiles#nav-draft" }, { - "@id": "bioschemasdrafts:Study", + "@id": "bioschemasdrafts:TrainingMaterial", "@type": "rdfs:Class", - "rdfs:comment": " This Study profile presents the markup when describing a Study. Version: 0.3-DRAFT.

Summary of Changes


Changes since 0.2-DRAFT:", + "rdfs:comment": "A specification for describing training materials in life sciences. The Life Science Training Materials specification provides a way to describe bioscience training material on the World Wide Web. It defines a set of metadata and vocabularies, built on top of existing technologies and standards, that can be used to represent events in Web pages and applications. The goal of the specification is to make it easier to discover, exchange and integrate life science training material information across the Internet. Version: 1.1-DRAFT.

Summary of Changes


Changes since previous draft 0.9-DRAFT-2020_12_08 of the TrainingMaterials profile:", "schema:schemaVersion": [ - "https://bioschemas.org/profiles/Study/0.3-DRAFT", - "https://github.com/BioSchemas/specifications/tree/master/Study/jsonld/Study_v0.3-DRAFT.json" + "https://github.com/BioSchemas/specifications/tree/master/TrainingMaterial/jsonld/TrainingMaterial_v1.1-DRAFT.json", + "https://bioschemas.org/profiles/TrainingMaterial/1.1-DRAFT" ], - "rdfs:label": "Study", + "rdfs:label": "TrainingMaterial", "rdfs:subClassOf": { - "@id": "bioschemastypesdrafts:Study" + "@id": "schema:LearningResource" }, "$validation": { "$schema": "http://json-schema.org/draft-07/schema#", "type": "object", "properties": { "about": { - "description": "Use to link to the Protein, Gene, etc that the study is about The subject matter of the content.\nInverse property: subjectOf.", + "description": "The subject of this Training Material. Use the DefinedTerm type to add a\n controlled vocabulary term to describe the topic (such as from the EDAM\n ontology) The subject matter of the content.\n Inverse property: subjectOf.", "oneOf": [ { "$ref": "#/definitions/thing" @@ -19712,47 +19427,92 @@ ], "owl:cardinality": "many" }, - "additionalProperty": { - "description": "Used to provide arbirary properties of a study. A property-value pair representing an additional characteristics of the entitity, e.g. a product feature or another characteristic for which there is no matching property in schema.org.\n\nNote: Publishers should be aware that applications designed to use specific schema.org properties (e.g. http://schema.org/width, http://schema.org/color, http://schema.org/gtin13, ...) will typically expect such data to be provided using those properties, rather than using the generic property/value mechanism.", + "abstract": { + "description": " An abstract is a short description that summarizes a CreativeWork.", + "type": "string", + "owl:cardinality": "one" + }, + "accessibilitySummary": { + "description": " A human-readable summary of specific accessibility features or deficiencies, consistent with the other accessibility metadata but expressing subtleties such as \"short descriptions are present but long descriptions will be needed for non-visual users\" or \"short descriptions are present and no long descriptions are needed.\"", + "type": "string", + "owl:cardinality": "one" + }, + "audience": { + "description": "A succinct description of the intended target audience for your materials: e.g., graduates, postgraduates, clinicians. An intended audience, i.e. a group for whom something was created. Supersedes serviceAudience.", "oneOf": [ { - "$ref": "#/definitions/propertyvalue" + "$ref": "#/definitions/audience" }, { "type": "array", "items": { - "$ref": "#/definitions/propertyvalue" + "$ref": "#/definitions/audience" } } ], "owl:cardinality": "many" }, "author": { - "description": "Used to indicate the person(s) or organizations that conducted the Study. Please use creator to indicate the Research project The author of this content or rating. Please note that author is special in that HTML 5 provides a special mechanism for indicating authorship via the rel tag. That is equivalent to this and may be used interchangeably.", - "oneOf": [ + "description": " Those involved in the preparation, creation and/or presentation of the published work, specifically writing the initial draft The author of this content or rating. Please note that author is special in that HTML 5 provides a special mechanism for indicating authorship via the rel tag. That is equivalent to this and may be used interchangeably.", + "anyOf": [ { "$ref": "#/definitions/organization" }, + { + "type": "array", + "items": { + "$ref": "#/definitions/organization" + } + }, { "$ref": "#/definitions/person" + }, + { + "type": "array", + "items": { + "$ref": "#/definitions/person" + } } ], - "owl:cardinality": "one" + "owl:cardinality": "many" }, - "citation": { - "description": " A citation or reference to another creative work, such as another publication, web page, scholarly article, etc.", - "oneOf": [ + "competencyRequired": { + "description": " Knowledge, skill, ability or personal attribute that must be demonstrated by a person or other entity in order to do something such as earn an Educational Occupational Credential or understand a LearningResource.", + "anyOf": [ { - "$ref": "#/definitions/creativework" + "$ref": "#/definitions/definedterm" + }, + { + "type": "array", + "items": { + "$ref": "#/definitions/definedterm" + } }, { "type": "string" + }, + { + "type": "array", + "items": { + "type": "string" + } + }, + { + "type": "string", + "format": "uri" + }, + { + "type": "array", + "items": { + "type": "string", + "format": "uri" + } } ], - "owl:cardinality": "one" + "owl:cardinality": "many" }, - "creator": { - "description": "Used to specify the research project that created the study. Please use author to indicate the organisation, or individuals that conducted the study. The creator/author of this CreativeWork. This is the same as the Author property for CreativeWork.", + "contributor": { + "description": "Contributors are those that made non-authorship contributions e.g. critical review, commentary or revision A secondary contributor to the CreativeWork or Event.", "anyOf": [ { "$ref": "#/definitions/organization" @@ -19775,6 +19535,18 @@ ], "owl:cardinality": "many" }, + "creativeWorkStatus": { + "description": "The status of a training material. If this is not filled in it will be regarded as Active.\n\nOptions are 'Active', 'Under development', and 'Archived'. The status of a creative work in terms of its stage in a lifecycle. Example terms include Incomplete, Draft, Published, Obsolete. Some organizations define a set of terms for the stages of their publication lifecycle.", + "oneOf": [ + { + "$ref": "#/definitions/definedterm" + }, + { + "type": "string" + } + ], + "owl:cardinality": "one" + }, "dateCreated": { "description": " The date on which the CreativeWork was created or the item was added to a DataFeed.", "oneOf": [ @@ -19788,10 +19560,30 @@ ], "owl:cardinality": "one" }, + "dateModified": { + "description": " The date on which the CreativeWork was most recently modified or when the item's entry was modified within a DataFeed.", + "oneOf": [ + { + "type": "string", + "format": "date" + }, + { + "$ref": "#/definitions/datetime" + } + ], + "owl:cardinality": "one" + }, "datePublished": { "description": " Date of first broadcast/publication.", - "type": "string", - "format": "date", + "oneOf": [ + { + "type": "string", + "format": "date" + }, + { + "$ref": "#/definitions/datetime" + } + ], "owl:cardinality": "one" }, "description": { @@ -19799,196 +19591,304 @@ "type": "string", "owl:cardinality": "one" }, - "endDate": { - "description": "Used to indicate the end date of the study. (Extension of existing schema.org property) The end date and time of the item (in ISO 8601 date format).", + "educationalLevel": { + "description": "The students level of ability in the topic being taught. Examples of skill levels include 'beginner', 'intermediate' or 'advanced'. The level in terms of progression through an educational or training context. Examples of educational levels include 'beginner', 'intermediate' or 'advanced', and formal sets of level indicators.", "oneOf": [ + { + "$ref": "#/definitions/definedterm" + }, + { + "type": "string" + }, { "type": "string", - "format": "date" + "format": "uri" + } + ], + "owl:cardinality": "one" + }, + "hasPart": { + "description": "A sub-training material or externally referenced training material\n Indicates an item or CreativeWork that is part of this item, or CreativeWork (in some sense).\n Inverse property: isPartOf.", + "oneOf": [ + { + "$ref": "#/definitions/creativework" }, { - "$ref": "#/definitions/datetime" + "type": "array", + "items": { + "$ref": "#/definitions/creativework" + } + } + ], + "owl:cardinality": "many" + }, + "identifier": { + "description": "An identifier for this resource such as a DOI or compact URI\n The identifier property represents any kind of identifier for any kind of Thing, such as ISBNs, GTIN codes, UUIDs etc. Schema.org provides dedicated properties for representing many of these, either as textual strings or as URL (URI) links. See background notes for more details.", + "anyOf": [ + { + "$ref": "#/definitions/propertyvalue" + }, + { + "type": "array", + "items": { + "$ref": "#/definitions/propertyvalue" + } + }, + { + "type": "string" + }, + { + "type": "array", + "items": { + "type": "string" + } + }, + { + "type": "string", + "format": "uri" + }, + { + "type": "array", + "items": { + "type": "string", + "format": "uri" + } } ], - "owl:cardinality": "one" + "owl:cardinality": "many" }, - "identifier": { - "description": " The identifier property represents any kind of identifier for any kind of Thing, such as ISBNs, GTIN codes, UUIDs etc. Schema.org provides dedicated properties for representing many of these, either as textual strings or as URL (URI) links. See [background notes](http://schema.org/docs/datamodel.html#identifierBg) for more details.", - "oneOf": [ + "inLanguage": { + "description": "Defaults to English if not specified. Please choose a value from [IETF BCP 47 standard](http://tools.ietf.org/html/bcp47).\nYou can add multiple languages if the Training Material offers different translations The language of the content or performance or used in an action. Please use one of the language codes from the IETF BCP 47 standard. See also availableLanguage. Supersedes language.", + "anyOf": [ { - "$ref": "#/definitions/propertyvalue" + "$ref": "#/definitions/language" + }, + { + "type": "array", + "items": { + "$ref": "#/definitions/language" + } }, { "type": "string" }, { - "type": "string", - "format": "uri" + "type": "array", + "items": { + "type": "string" + } } ], - "owl:cardinality": "one" + "owl:cardinality": "many" }, "isPartOf": { - "description": "Used to indicate the project that the study is a part of. Indicates an item or CreativeWork that this item, or CreativeWork (in some sense), is part of. Inverse property: hasPart.", - "oneOf": [ + "description": "The Course this Training Material was/will be used in. Or a training material this training material is a part of (for example, if this is a module in a book, isPartOf can describe the book).\n\nInverse property: hasPart\n\nIf this varies in CourseInstances, use the workFeatured property Indicates an item or CreativeWork that this item, or CreativeWork (in some sense), is part of.\n Inverse property: hasPart.", + "anyOf": [ { "$ref": "#/definitions/creativework" }, + { + "type": "array", + "items": { + "$ref": "#/definitions/creativework" + } + }, { "type": "string", "format": "uri" + }, + { + "type": "array", + "items": { + "type": "string", + "format": "uri" + } } ], - "owl:cardinality": "one" + "owl:cardinality": "many" }, "keywords": { "description": " Keywords or tags used to describe this content. Multiple entries in a keywords list are typically delimited by commas.", - "oneOf": [ + "anyOf": [ { "$ref": "#/definitions/definedterm" }, + { + "type": "array", + "items": { + "$ref": "#/definitions/definedterm" + } + }, { "type": "string" }, + { + "type": "array", + "items": { + "type": "string" + } + }, { "type": "string", "format": "uri" - } - ], - "owl:cardinality": "one" - }, - "name": { - "description": " The name of the item.", - "type": "string", - "owl:cardinality": "one" - }, - "hasGrowthFacility": { - "description": "The kind of growth facility used in a plant study has growth facility", - "type": "string", - "format": "uri", - "owl:cardinality": "one" - }, - "relatedStudy": { - "description": " A study that is related to this one.", - "oneOf": [ - { - "$ref": "#/definitions/study" }, { "type": "array", "items": { - "$ref": "#/definitions/study" + "type": "string", + "format": "uri" } } ], "owl:cardinality": "many" }, - "startDate": { - "description": "Used to indicate the start date of the study. (Extension of existing schema.org property) The start date and time of the item (in ISO 8601 date format).", - "oneOf": [ + "learningResourceType": { + "description": "This may include things such as video lecture, e-Learning module, or tutorial. The predominant type or kind characterizing the learning resource. For example, 'presentation', 'handout'.", + "anyOf": [ { - "type": "string", - "format": "date" + "$ref": "#/definitions/definedterm" }, { - "$ref": "#/definitions/datetime" + "type": "array", + "items": { + "$ref": "#/definitions/definedterm" + } + }, + { + "type": "string" + }, + { + "type": "array", + "items": { + "type": "string" + } } ], - "owl:cardinality": "one" + "owl:cardinality": "many" }, - "studyDomain": { - "description": "For example, in the life sciences we could have\nFunctional Genomics: http://edamontology.org/topic_0085\nProtemics: http://edamontology.org/topic_0121 Define the domain of the study. For example, the domain could be astrophysics, functional genomics or earth science. Those domains can also have an ontology reference.", - "oneOf": [ + "license": { + "description": "If there is a licence it must be added. A license document that applies to this content, typically indicated by URL.", + "anyOf": [ { - "$ref": "#/definitions/propertyvalue" + "$ref": "#/definitions/creativework" }, { - "type": "string" + "type": "array", + "items": { + "$ref": "#/definitions/creativework" + } }, { "type": "string", "format": "uri" + }, + { + "type": "array", + "items": { + "type": "string", + "format": "uri" + } } ], - "owl:cardinality": "one" + "owl:cardinality": "many" }, - "studyLocation": { - "description": "(Reuse of property from MedicalStudy; Expected types extended.) The location in which the study is taking/took place.", + "mentions": { + "description": "Datasets, tools, technologies, entities etc, which are referred to by this training material or actively used in this training material. Indicates that the CreativeWork contains a reference to, but is not necessarily about a concept.", "oneOf": [ { - "$ref": "#/definitions/administrativearea" + "$ref": "#/definitions/thing" }, { - "$ref": "#/definitions/place" + "type": "array", + "items": { + "$ref": "#/definitions/thing" + } } ], + "owl:cardinality": "many" + }, + "name": { + "description": " The name of the item.", + "type": "string", "owl:cardinality": "one" }, - "studyProcess": { - "description": "For example, in the life sciences we could have \nRNA-seq of coding RNA from single cells: http://www.ebi.ac.uk/efo/EFO_0005684\ncase control design: http://www.ebi.ac.uk/efo/EFO_0001427 A process performed as part of an experiment or wider study, i.e. intentionally designed.\nThese processes can have ontology URL attached to.", - "anyOf": [ + "recordedAt": { + "description": "The course instance or event where this training material was or will be featured. \n\nUse isPartOf to refer to a Course, unless this training material is unique to a specific Course Instance. The Event where the CreativeWork was recorded. The CreativeWork may capture all or part of the event.\nInverse property: recordedIn.", + "oneOf": [ { - "$ref": "#/definitions/propertyvalue" + "$ref": "#/definitions/event" }, { "type": "array", "items": { - "$ref": "#/definitions/propertyvalue" + "$ref": "#/definitions/event" } - }, + } + ], + "owl:cardinality": "many" + }, + "teaches": { + "description": " The item being described is intended to help a person learn the competency or learning outcome defined by the referenced term.", + "anyOf": [ { - "type": "string" + "$ref": "#/definitions/definedterm" }, { "type": "array", "items": { - "type": "string" + "$ref": "#/definitions/definedterm" } }, { - "type": "string", - "format": "uri" + "type": "string" }, { "type": "array", "items": { - "type": "string", - "format": "uri" + "type": "string" } } ], "owl:cardinality": "many" }, - "studySubject": { - "description": "(Reuse of property from MedicalStudy; Expected types extended.) A subject of the study, i.e. one of the medical conditions, therapies, devices, drugs, etc. investigated by the study.", - "anyOf": [ + "timeRequired": { + "description": "The estimated time it takes to work through this resource.\n\nPlease specify in [ISO 8601 duration format](https://en.wikipedia.org/wiki/ISO_8601). Approximate or typical time it takes to work with or through this learning resource for the typical intended target audience, e.g. 'PT30M', 'PT1H25M'.", + "$ref": "#/definitions/duration", + "owl:cardinality": "one" + }, + "url": { + "description": "The preferred URL of the Training Material. You must provide this value if it is known. URL of the item.", + "type": "string", + "format": "uri", + "owl:cardinality": "one" + }, + "version": { + "description": "If this training material is versioned, its strongly recommended you use this property to list the version being displayed The version of the CreativeWork embodied by a specified resource.", + "oneOf": [ { - "$ref": "#/definitions/biochementity" + "type": "number" }, { - "type": "array", - "items": { - "$ref": "#/definitions/biochementity" - } - }, + "type": "string" + } + ], + "owl:cardinality": "one" + }, + "workTranslation": { + "description": " A work that is a translation of the content of this work. e.g. \u897f\u904a\u8a18 has an English workTranslation \u201cJourney to the West\u201d,a German workTranslation \u201cMonkeys Pilgerfahrt\u201d and a Vietnamese translation T\u00e2y du k\u00fd b\u00ecnh kh\u1ea3o.\nInverse property: translationOfWork.", + "oneOf": [ { - "$ref": "#/definitions/medicalentity" + "$ref": "#/definitions/creativework" }, { "type": "array", "items": { - "$ref": "#/definitions/medicalentity" + "$ref": "#/definitions/creativework" } } ], "owl:cardinality": "many" }, - "url": { - "description": " URL of the item.", - "type": "string", - "format": "uri", - "owl:cardinality": "one" - }, "sameAs": { "oneOf": [ { @@ -20007,38 +19907,45 @@ "owl:cardinality": "many" }, "conformsTo": { - "description": "This is used to state the Bioschemas profile that the markup relates to. The identifier can be the url for the version of this bioschemas class on github: https://github.com/BioSchemas/specifications/tree/master/Study/jsonld/Study_v0.3-DRAFT.json", + "description": "This is used to state the Bioschemas profile that the markup relates to. The identifier can be the url for the version of this bioschemas class on github: https://github.com/BioSchemas/specifications/tree/master/TrainingMaterial/jsonld/TrainingMaterial_v1.1-DRAFT.json", "$ref": "#/definitions/conformsDefinition" } }, "required": [ - "author", - "datePublished", "description", - "identifier", + "keywords", "name", - "studyDomain", - "studySubject", "conformsTo" ], "recommended": [ "about", - "additionalProperty", - "citation", - "creator", - "dateCreated", - "endDate", - "keywords", - "startDate", - "studyLocation", - "studyProcess", + "abstract", + "audience", + "author", + "competencyRequired", + "educationalLevel", + "identifier", + "inLanguage", + "learningResourceType", + "license", + "mentions", + "teaches", + "timeRequired", "url", "sameAs" ], "optional": [ + "accessibilitySummary", + "contributor", + "creativeWorkStatus", + "dateCreated", + "dateModified", + "datePublished", + "hasPart", "isPartOf", - "hasGrowthFacility", - "relatedStudy" + "recordedAt", + "version", + "workTranslation" ], "definitions": { "thing": { @@ -20051,90 +19958,15 @@ }, "required": [] }, - "propertyvalue": { - "@type": "PropertyValue", - "type": "object", - "properties": { - "name": { - "type": "string" - }, - "value": { - "oneOf": [ - { - "type": "string" - }, - { - "type": "boolean" - }, - { - "type": "number" - } - ] - }, - "identifier": { - "type": "string" - }, - "valuereference": { - "oneOf": [ - { - "$ref": "#/definitions/categorycode" - }, - { - "type": "array", - "items": [ - { - "$ref": "#/definitions/categorycode" - } - ] - } - ] - }, - "unitCode": { - "oneOf": [ - { - "type": "string" - }, - { - "type": "string", - "format": "uri" - } - ] - }, - "unitText": { - "type": "string" - } - }, - "required": [ - "name", - "value" - ], - "recommended": [ - "valueReference" - ], - "optional": [ - "unitCode", - "unitText" - ] - }, - "categorycode": { - "@type": "CategoryCode", + "audience": { + "@type": "schema:Audience", "type": "object", "properties": { "name": { "type": "string" - }, - "codeValue": { - "type": "string" - }, - "url": { - "type": "string" } }, - "required": [ - "name", - "codeValue", - "url" - ] + "required": [] }, "organization": { "@type": "Organization", @@ -20212,16 +20044,6 @@ }, "required": [] }, - "datetime": { - "@type": "schema:DateTime", - "type": "object", - "properties": { - "name": { - "type": "string" - } - }, - "required": [] - }, "definedterm": { "@type": "DefinedTerm", "type": "object", @@ -20262,8 +20084,8 @@ }, "required": [] }, - "study": { - "@type": "bioschemas:Study", + "datetime": { + "@type": "schema:DateTime", "type": "object", "properties": { "name": { @@ -20272,34 +20094,113 @@ }, "required": [] }, - "place": { - "@type": "Place", + "propertyvalue": { + "@type": "PropertyValue", "type": "object", "properties": { "name": { "type": "string" }, - "address": { + "value": { "oneOf": [ { "type": "string" }, { - "$ref": "#/definitions/postaladdress" + "type": "boolean" + }, + { + "type": "number" } ] }, "identifier": { "type": "string" }, + "valuereference": { + "oneOf": [ + { + "$ref": "#/definitions/categorycode" + }, + { + "type": "array", + "items": [ + { + "$ref": "#/definitions/categorycode" + } + ] + } + ] + }, + "unitCode": { + "oneOf": [ + { + "type": "string" + }, + { + "type": "string", + "format": "uri" + } + ] + }, + "unitText": { + "type": "string" + } + }, + "required": [ + "name", + "value" + ], + "recommended": [ + "valueReference" + ], + "optional": [ + "unitCode", + "unitText" + ] + }, + "categorycode": { + "@type": "CategoryCode", + "type": "object", + "properties": { + "name": { + "type": "string" + }, + "codeValue": { + "type": "string" + }, "url": { - "type": "string", - "format": "uri" + "type": "string" } - } + }, + "required": [ + "name", + "codeValue", + "url" + ] }, - "administrativearea": { - "@type": "schema:AdministrativeArea", + "language": { + "@type": "schema:Language", + "type": "object", + "properties": { + "name": { + "type": "string" + } + }, + "required": [] + }, + "event": { + "@type": "bioschemas:Event", + "type": "object", + "properties": { + "name": { + "type": "string" + } + }, + "required": [] + }, + "duration": { + "@type": "schema:Duration", "type": "object", "properties": { "name": { @@ -20308,58 +20209,109 @@ }, "required": [] }, - "biochementity": { - "@type": "bioschemas:BioChemEntity", - "type": "object", - "properties": { - "url": { + "conformsDefinition": { + "@type": "CreativeWork", + "type": "object", + "properties": { + "identifier": { + "description": "The url of the version bioschemas profile that was used. For jsonschema, set @id to the identifier", + "oneOf": [ + { + "enum": [ + "https://github.com/BioSchemas/specifications/tree/master/TrainingMaterial/jsonld/TrainingMaterial_v1.1-DRAFT.json" + ] + }, + { + "type": "string", + "format": "uri" + } + ] + } + }, + "required": [ + "identifier" + ] + } + } + }, + "additional_type": "https://bioschemas.org/profiles#nav-draft" + }, + { + "@id": "bioschemasdrafts:DefinedTerm", + "@type": "rdfs:Class", + "rdfs:comment": "A word, name, acronym, phrase, etc. with a formal definition. Use the name property for the term being defined, use termCode if the term has an alpha-numeric code allocated, use description to provide the definition of the term. This Bioschemas profile specifically helps reusing terms from terminology and ontology services. Version 0.1-DRAFT.

Summary of Changes

None--this is the first draft.", + "rdfs:label": "DefinedTerm", + "rdfs:subClassOf": { + "@id": "schema:DefinedTerm" + }, + "$validation": { + "$schema": "http://json-schema.org/draft-07/schema#", + "type": "object", + "properties": { + "termCode": { + "description": "A code that identifies this [[DefinedTerm]] within a [[DefinedTermSet]]", + "type": "string", + "owl:cardinality": "one" + }, + "inDefinedTermSet": { + "description": "A [[DefinedTermSet]] that contains this term.", + "type": "string", + "owl:cardinality": "one" + }, + "description": { + "description": "A description of the item.", + "type": "string", + "owl:cardinality": "one" + }, + "identifier": { + "description": "The identifier property represents any kind of identifier for any kind of [[Thing]], such as ISBNs, GTIN codes, UUIDs etc. Schema.org provides dedicated properties for representing many of these, either as textual strings or as URL (URI) links. See [background notes](/docs/datamodel.html#identifierBg) for more details.\n ", + "type": "string", + "owl:cardinality": "one" + }, + "name": { + "description": "The name of the item.", + "type": "string", + "owl:cardinality": "one" + }, + "sameAs": { + "description": "URL of a reference Web page that unambiguously indicates the item's identity. E.g. the URL of the item's Wikipedia page, Wikidata entry, or official website.", + "owl:cardinality": "many" + }, + "url": { + "description": "URL of the item.", + "oneOf": [ + { "type": "string", "format": "uri" }, - "name": { - "type": "string" - }, - "identifier": { - "type": "string" - } - }, - "required": [] - }, - "medicalentity": { - "@type": "schema:MedicalEntity", - "type": "object", - "properties": { - "name": { - "type": "string" - } - }, - "required": [] - }, - "postaladdress": { - "@type": "schema:PostalAddress", - "type": "object", - "properties": { - "addressCountry": { - "type": "string" - }, - "addressLocality": { - "type": "string" - }, - "addressRegion": { - "type": "string" - }, - "postOfficeBoxNumber": { - "type": "string" - }, - "postalCode": { - "type": "string" - }, - "streetAddress": { - "type": "string" + { + "type": "array", + "items": { + "type": "string", + "format": "uri" + } } - }, - "required": [] + ], + "owl:cardinality": "many" }, + "conformsTo": { + "description": "This is used to state the Bioschemas profile that the markup relates to. The identifier can be the url for the version of this bioschemas class on github: https://github.com/BioSchemas/specifications/tree/master/DefinedTerm/jsonld/DefinedTerm_v0.1-DRAFT.jsonld", + "$ref": "#/definitions/conformsDefinition" + } + }, + "required": [ + "inDefinedTermSet", + "conformsTo" + ], + "recommended": [ + "termCode", + "sameAs", + "name" + ], + "optional": [ + "description" + ], + "definitions": { "conformsDefinition": { "@type": "CreativeWork", "type": "object", @@ -20369,7 +20321,7 @@ "oneOf": [ { "enum": [ - "https://github.com/BioSchemas/specifications/tree/master/Study/jsonld/Study_v0.3-DRAFT.json" + "https://github.com/BioSchemas/specifications/tree/master/DefinedTerm/jsonld/DefinedTerm_v0.1-DRAFT.jsonld" ] }, { @@ -20385,91 +20337,111 @@ } } }, - "additional_type": "https://bioschemas.org/profiles#nav-draft" + "schemaVersion": [ + "https://schema.org/docs/releases.html#v23.0" + ], + "additional_type": "https://bioschemas.org/profiles#nav-draft", + "schema:schemaVersion": [ + "https://github.com/BioSchemas/specifications/tree/master/DefinedTerm/jsonld/DefinedTerm_v0.1-DRAFT.jsonld", + "https://bioschemas.org/profiles/DefinedTerm/0.1-DRAFT" + ] }, { - "@id": "bioschemasdrafts:TrainingMaterial", + "@id": "bioschemasdrafts:LabProtocol", "@type": "rdfs:Class", - "rdfs:comment": "A specification for describing training materials in life sciences. The Life Science Training Materials specification provides a way to describe bioscience training material on the World Wide Web. It defines a set of metadata and vocabularies, built on top of existing technologies and standards, that can be used to represent events in Web pages and applications. The goal of the specification is to make it easier to discover, exchange and integrate life science training material information across the Internet. Version: 1.1-DRAFT.

Summary of Changes


Changes since previous draft 0.9-DRAFT-2020_12_08 of the TrainingMaterials profile:", - "schema:schemaVersion": [ - "https://bioschemas.org/profiles/TrainingMaterial/1.1-DRAFT", - "https://github.com/BioSchemas/specifications/tree/master/TrainingMaterial/jsonld/TrainingMaterial_v1.1-DRAFT.json" - ], - "rdfs:label": "TrainingMaterial", + "rdfs:comment": "Bioschemas profile describing a LabProtocol in Life Sciences. An experimental LabProtocol is a sequence of tasks and operations executed to perform experimental research in biological and biomedical areas. This LabProtocol profile specification presents the markup for describing a LabProtocol type according to Bioschemas. An experimental LabProtocol is a sequence of tasks and operations executed to perform experimental research in biological and biomedical areas. Version 0.8-DRAFT.\n\n

Summary of changes

\nChanges since previous draft 0.7 of the LabProtocols profile:\n", + "rdfs:label": "LabProtocol", "rdfs:subClassOf": { - "@id": "schema:LearningResource" + "@id": "bioschemastypesdrafts:LabProtocol" }, "$validation": { "$schema": "http://json-schema.org/draft-07/schema#", "type": "object", "properties": { - "about": { - "description": "The subject of this Training Material. Use the DefinedTerm type to add a\n controlled vocabulary term to describe the topic (such as from the EDAM\n ontology) The subject matter of the content.\n Inverse property: subjectOf.", + "intendedUse": { + "description": "Purpose and intended use stated to enable users to make a decision as to the suitability of this creative work (e.g., lab protocol, machine learning model, software) to their experimental problem or own use case.\n\nSee more information here", "oneOf": [ { - "$ref": "#/definitions/thing" + "$ref": "#/definitions/definedterm" }, { - "type": "array", - "items": { - "$ref": "#/definitions/thing" - } + "type": "string" + }, + { + "type": "string", + "format": "uri" } ], - "owl:cardinality": "many" - }, - "abstract": { - "description": " An abstract is a short description that summarizes a CreativeWork.", - "type": "string", "owl:cardinality": "one" }, - "accessibilitySummary": { - "description": " A human-readable summary of specific accessibility features or deficiencies, consistent with the other accessibility metadata but expressing subtleties such as \"short descriptions are present but long descriptions will be needed for non-visual users\" or \"short descriptions are present and no long descriptions are needed.\"", + "ethicalLegalSocial": { + "description": "Considerations wrt ethical, legal and social aspects.", "type": "string", - "owl:cardinality": "one" + "owl:cardinality": "many" }, - "audience": { - "description": "A succinct description of the intended target audience for your materials: e.g., graduates, postgraduates, clinicians. An intended audience, i.e. a group for whom something was created. Supersedes serviceAudience.", - "oneOf": [ + "computationalTool": { + "description": "Computational tool or workflow used to complete a part of this protocol.", + "anyOf": [ { - "$ref": "#/definitions/audience" + "$ref": "#/definitions/softwareapplication" }, { "type": "array", "items": { - "$ref": "#/definitions/audience" + "$ref": "#/definitions/softwareapplication" } - } - ], - "owl:cardinality": "many" - }, - "author": { - "description": " Those involved in the preparation, creation and/or presentation of the published work, specifically writing the initial draft The author of this content or rating. Please note that author is special in that HTML 5 provides a special mechanism for indicating authorship via the rel tag. That is equivalent to this and may be used interchangeably.", - "anyOf": [ + }, { - "$ref": "#/definitions/organization" + "$ref": "#/definitions/softwaresourcecode" }, { "type": "array", "items": { - "$ref": "#/definitions/organization" + "$ref": "#/definitions/softwaresourcecode" } }, { - "$ref": "#/definitions/person" + "$ref": "#/definitions/workflow" }, { "type": "array", "items": { - "$ref": "#/definitions/person" + "$ref": "#/definitions/workflow" } } ], "owl:cardinality": "many" }, - "competencyRequired": { - "description": " Knowledge, skill, ability or personal attribute that must be demonstrated by a person or other entity in order to do something such as earn an Educational Occupational Credential or understand a LearningResource.", + "bioSample": { + "description": "BioSample used in the protocol. It could be a record in a Dataset describing the sample or a physical object corresponding to the sample or a URL pointing to the type of sample used.", "anyOf": [ + { + "$ref": "#/definitions/biosample" + }, + { + "type": "array", + "items": { + "$ref": "#/definitions/biosample" + } + }, + { + "$ref": "#/definitions/taxon" + }, + { + "type": "array", + "items": { + "$ref": "#/definitions/taxon" + } + }, + { + "$ref": "#/definitions/biochementity" + }, + { + "type": "array", + "items": { + "$ref": "#/definitions/biochementity" + } + }, { "$ref": "#/definitions/definedterm" }, @@ -20502,105 +20474,116 @@ ], "owl:cardinality": "many" }, - "contributor": { - "description": "Contributors are those that made non-authorship contributions e.g. critical review, commentary or revision A secondary contributor to the CreativeWork or Event.", + "labEquipment": { + "description": "A laboratory equipment used by a person to follow one or more steps described in this LabProtocol.", "anyOf": [ { - "$ref": "#/definitions/organization" + "$ref": "#/definitions/definedterm" }, { "type": "array", "items": { - "$ref": "#/definitions/organization" + "$ref": "#/definitions/definedterm" } }, { - "$ref": "#/definitions/person" + "type": "string" }, { "type": "array", "items": { - "$ref": "#/definitions/person" + "type": "string" + } + }, + { + "type": "string", + "format": "uri" + }, + { + "type": "array", + "items": { + "type": "string", + "format": "uri" } } ], "owl:cardinality": "many" }, - "creativeWorkStatus": { - "description": "The status of a training material. If this is not filled in it will be regarded as Active.\n\nOptions are 'Active', 'Under development', and 'Archived'. The status of a creative work in terms of its stage in a lifecycle. Example terms include Incomplete, Draft, Published, Obsolete. Some organizations define a set of terms for the stages of their publication lifecycle.", - "oneOf": [ + "protocolAdvantage": { + "description": "Situations where the LabProtocol has been successfully employed including advantageous elements (e.g. better yield, shorter running time).\n\nSee more information here", + "anyOf": [ { - "$ref": "#/definitions/definedterm" + "$ref": "#/definitions/creativework" }, { - "type": "string" - } - ], - "owl:cardinality": "one" - }, - "dateCreated": { - "description": " The date on which the CreativeWork was created or the item was added to a DataFeed.", - "oneOf": [ + "type": "array", + "items": { + "$ref": "#/definitions/creativework" + } + }, { - "type": "string", - "format": "date" + "type": "string" }, { - "$ref": "#/definitions/datetime" + "type": "array", + "items": { + "type": "string" + } } ], - "owl:cardinality": "one" + "owl:cardinality": "many" }, - "dateModified": { - "description": " The date on which the CreativeWork was most recently modified or when the item's entry was modified within a DataFeed.", - "oneOf": [ + "protocolApplication": { + "description": "Applications of the protocol list the full diversity of the applications of the method and support if is possible to extend the range of applications of the protocol. e.g. northern blot assays, sequencing, etc. \n\nSee more information here", + "anyOf": [ { - "type": "string", - "format": "date" + "$ref": "#/definitions/creativework" }, { - "$ref": "#/definitions/datetime" - } - ], - "owl:cardinality": "one" - }, - "datePublished": { - "description": " Date of first broadcast/publication.", - "oneOf": [ + "type": "array", + "items": { + "$ref": "#/definitions/creativework" + } + }, { - "type": "string", - "format": "date" + "type": "string" }, { - "$ref": "#/definitions/datetime" + "type": "array", + "items": { + "type": "string" + } } ], - "owl:cardinality": "one" - }, - "description": { - "description": " A description of the item.", - "type": "string", - "owl:cardinality": "one" + "owl:cardinality": "many" }, - "educationalLevel": { - "description": "The students level of ability in the topic being taught. Examples of skill levels include 'beginner', 'intermediate' or 'advanced'. The level in terms of progression through an educational or training context. Examples of educational levels include 'beginner', 'intermediate' or 'advanced', and formal sets of level indicators.", - "oneOf": [ + "protocolLimitation": { + "description": "Situations where the Protocol would be unreliable or otherwise unsuccessful.\n\nSee more information here", + "anyOf": [ { - "$ref": "#/definitions/definedterm" + "$ref": "#/definitions/creativework" + }, + { + "type": "array", + "items": { + "$ref": "#/definitions/creativework" + } }, { "type": "string" }, { - "type": "string", - "format": "uri" + "type": "array", + "items": { + "type": "string" + } } ], - "owl:cardinality": "one" + "owl:cardinality": "many" }, - "hasPart": { - "description": "A sub-training material or externally referenced training material\n Indicates an item or CreativeWork that is part of this item, or CreativeWork (in some sense).\n Inverse property: isPartOf.", - "oneOf": [ + "protocolOutcome": { + "description": "Actual outcome or result by a protocol execution. The shape of the expected outcome/result can be described using the property 'output'.\n\nSee more information here", + "anyOf": [ { "$ref": "#/definitions/creativework" }, @@ -20609,55 +20592,56 @@ "items": { "$ref": "#/definitions/creativework" } + }, + { + "type": "string" + }, + { + "type": "array", + "items": { + "type": "string" + } } ], "owl:cardinality": "many" }, - "identifier": { - "description": "An identifier for this resource such as a DOI or compact URI\n The identifier property represents any kind of identifier for any kind of Thing, such as ISBNs, GTIN codes, UUIDs etc. Schema.org provides dedicated properties for representing many of these, either as textual strings or as URL (URI) links. See background notes for more details.", + "reagent": { + "description": "Reagents used in the protocol. DefinedTerm is preferred whenever possible, e.g., ChEBI and PubChem entities can be used whenever available. Commercial names are also acceptable. A reagent is defined as \u2018A substance used in a chemical reaction to detect, measure, examine, or produce other substances\u2019 in [CHEBI:33893](https://www.ebi.ac.uk/chebi/searchId.do?chebiId=CHEBI:33893).", "anyOf": [ { - "$ref": "#/definitions/propertyvalue" + "$ref": "#/definitions/molecularentity" }, { "type": "array", "items": { - "$ref": "#/definitions/propertyvalue" + "$ref": "#/definitions/molecularentity" } }, { - "type": "string" + "$ref": "#/definitions/chemicalsubstance" }, { "type": "array", "items": { - "type": "string" + "$ref": "#/definitions/chemicalsubstance" } }, { - "type": "string", - "format": "uri" + "$ref": "#/definitions/biochementity" }, { "type": "array", "items": { - "type": "string", - "format": "uri" + "$ref": "#/definitions/biochementity" } - } - ], - "owl:cardinality": "many" - }, - "inLanguage": { - "description": "Defaults to English if not specified. Please choose a value from [IETF BCP 47 standard](http://tools.ietf.org/html/bcp47).\nYou can add multiple languages if the Training Material offers different translations The language of the content or performance or used in an action. Please use one of the language codes from the IETF BCP 47 standard. See also availableLanguage. Supersedes language.", - "anyOf": [ + }, { - "$ref": "#/definitions/language" + "$ref": "#/definitions/definedterm" }, { "type": "array", "items": { - "$ref": "#/definitions/language" + "$ref": "#/definitions/definedterm" } }, { @@ -20668,12 +20652,33 @@ "items": { "type": "string" } + }, + { + "type": "string", + "format": "uri" + }, + { + "type": "array", + "items": { + "type": "string", + "format": "uri" + } } ], "owl:cardinality": "many" }, - "isPartOf": { - "description": "The Course this Training Material was/will be used in. Or a training material this training material is a part of (for example, if this is a module in a book, isPartOf can describe the book).\n\nInverse property: hasPart\n\nIf this varies in CourseInstances, use the workFeatured property Indicates an item or CreativeWork that this item, or CreativeWork (in some sense), is part of.\n Inverse property: hasPart.", + "performTime": { + "description": "The length of time it takes to perform instructions or a direction (not including time to prepare the supplies), in [ISO 8601 duration format](http://en.wikipedia.org/wiki/ISO_8601).", + "$ref": "#/definitions/duration", + "owl:cardinality": "one" + }, + "prepTime": { + "description": "The length of time it takes to prepare the items to be used in instructions or a direction, in [ISO 8601 duration format](http://en.wikipedia.org/wiki/ISO_8601).", + "$ref": "#/definitions/duration", + "owl:cardinality": "one" + }, + "step": { + "description": "A single step item (as HowToStep, text, document, video, etc.) or a HowToSection.", "anyOf": [ { "$ref": "#/definitions/creativework" @@ -20685,29 +20690,21 @@ } }, { - "type": "string", - "format": "uri" + "$ref": "#/definitions/howtosection" }, { "type": "array", "items": { - "type": "string", - "format": "uri" + "$ref": "#/definitions/howtosection" } - } - ], - "owl:cardinality": "many" - }, - "keywords": { - "description": " Keywords or tags used to describe this content. Multiple entries in a keywords list are typically delimited by commas.", - "anyOf": [ + }, { - "$ref": "#/definitions/definedterm" + "$ref": "#/definitions/howtostep" }, { "type": "array", "items": { - "$ref": "#/definitions/definedterm" + "$ref": "#/definitions/howtostep" } }, { @@ -20718,31 +20715,49 @@ "items": { "type": "string" } + } + ], + "owl:cardinality": "many" + }, + "totalTime": { + "description": "The total time required to perform instructions or a direction (including time to prepare the supplies), in [ISO 8601 duration format](http://en.wikipedia.org/wiki/ISO_8601).", + "$ref": "#/definitions/duration", + "owl:cardinality": "one" + }, + "author": { + "description": "The author of this content or rating. Please note that author is special in that HTML 5 provides a special mechanism for indicating authorship via the rel tag. That is equivalent to this and may be used interchangeably.", + "anyOf": [ + { + "$ref": "#/definitions/organization" + }, + { + "type": "array", + "items": { + "$ref": "#/definitions/organization" + } }, { - "type": "string", - "format": "uri" + "$ref": "#/definitions/person" }, { "type": "array", "items": { - "type": "string", - "format": "uri" + "$ref": "#/definitions/person" } } ], "owl:cardinality": "many" }, - "learningResourceType": { - "description": "This may include things such as video lecture, e-Learning module, or tutorial. The predominant type or kind characterizing the learning resource. For example, 'presentation', 'handout'.", + "citation": { + "description": "A citation or reference to another creative work, such as another publication, web page, scholarly article, etc.", "anyOf": [ { - "$ref": "#/definitions/definedterm" + "$ref": "#/definitions/creativework" }, { "type": "array", "items": { - "$ref": "#/definitions/definedterm" + "$ref": "#/definitions/creativework" } }, { @@ -20757,8 +20772,47 @@ ], "owl:cardinality": "many" }, - "license": { - "description": "If there is a licence it must be added. A license document that applies to this content, typically indicated by URL.", + "dateCreated": { + "description": "The date on which the CreativeWork was created or the item was added to a DataFeed.", + "oneOf": [ + { + "type": "string", + "format": "date" + }, + { + "$ref": "#/definitions/datetime" + } + ], + "owl:cardinality": "one" + }, + "dateModified": { + "description": "The date on which the CreativeWork was most recently modified or when the item's entry was modified within a DataFeed.", + "oneOf": [ + { + "type": "string", + "format": "date" + }, + { + "$ref": "#/definitions/datetime" + } + ], + "owl:cardinality": "one" + }, + "datePublished": { + "description": "Date of first broadcast/publication.\n\n'MANY' is used to cover original printed and electronic publication dates.", + "oneOf": [ + { + "type": "string", + "format": "date" + }, + { + "$ref": "#/definitions/datetime" + } + ], + "owl:cardinality": "many" + }, + "isBasedOn": { + "description": "A resource from which this work is derived or from which it is a modification or adaption.", "anyOf": [ { "$ref": "#/definitions/creativework" @@ -20783,47 +20837,45 @@ ], "owl:cardinality": "many" }, - "mentions": { - "description": "Datasets, tools, technologies, entities etc, which are referred to by this training material or actively used in this training material. Indicates that the CreativeWork contains a reference to, but is not necessarily about a concept.", - "oneOf": [ + "isPartOf": { + "description": "Indicates an item or CreativeWork that this item, or CreativeWork (in some sense), is part of.", + "anyOf": [ { - "$ref": "#/definitions/thing" + "$ref": "#/definitions/creativework" }, { "type": "array", "items": { - "$ref": "#/definitions/thing" + "$ref": "#/definitions/creativework" } - } - ], - "owl:cardinality": "many" - }, - "name": { - "description": " The name of the item.", - "type": "string", - "owl:cardinality": "one" - }, - "recordedAt": { - "description": "The course instance or event where this training material was or will be featured. \n\nUse isPartOf to refer to a Course, unless this training material is unique to a specific Course Instance. The Event where the CreativeWork was recorded. The CreativeWork may capture all or part of the event.\nInverse property: recordedIn.", - "oneOf": [ + }, { - "$ref": "#/definitions/event" + "type": "string", + "format": "uri" }, { "type": "array", "items": { - "$ref": "#/definitions/event" + "type": "string", + "format": "uri" } } ], "owl:cardinality": "many" }, - "teaches": { - "description": " The item being described is intended to help a person learn the competency or learning outcome defined by the referenced term.", + "keywords": { + "description": "Keywords or tags used to describe this content. Multiple entries in a keywords list are typically delimited by commas.", "anyOf": [ { "$ref": "#/definitions/definedterm" }, + { + "type": "string" + }, + { + "type": "string", + "format": "uri" + }, { "type": "array", "items": { @@ -20831,56 +20883,62 @@ } }, { - "type": "string" + "type": "array", + "items": { + "type": "string" + } }, { "type": "array", "items": { - "type": "string" + "type": "string", + "format": "uri" } } ], "owl:cardinality": "many" }, - "timeRequired": { - "description": "The estimated time it takes to work through this resource.\n\nPlease specify in [ISO 8601 duration format](https://en.wikipedia.org/wiki/ISO_8601). Approximate or typical time it takes to work with or through this learning resource for the typical intended target audience, e.g. 'PT30M', 'PT1H25M'.", - "$ref": "#/definitions/duration", - "owl:cardinality": "one" - }, - "url": { - "description": "The preferred URL of the Training Material. You must provide this value if it is known. URL of the item.", - "type": "string", - "format": "uri", - "owl:cardinality": "one" - }, - "version": { - "description": "If this training material is versioned, its strongly recommended you use this property to list the version being displayed The version of the CreativeWork embodied by a specified resource.", + "license": { + "description": "A license document that applies to this content, typically indicated by URL.", "oneOf": [ { - "type": "number" + "$ref": "#/definitions/creativework" }, { - "type": "string" + "type": "string", + "format": "uri" } ], "owl:cardinality": "one" }, - "workTranslation": { - "description": " A work that is a translation of the content of this work. e.g. \u897f\u904a\u8a18 has an English workTranslation \u201cJourney to the West\u201d,a German workTranslation \u201cMonkeys Pilgerfahrt\u201d and a Vietnamese translation T\u00e2y du k\u00fd b\u00ecnh kh\u1ea3o.\nInverse property: translationOfWork.", + "description": { + "description": "A description of the item.", + "type": "string", + "owl:cardinality": "one" + }, + "identifier": { + "description": "The identifier property represents any kind of identifier for any kind of [[Thing]], such as ISBNs, GTIN codes, UUIDs etc. Schema.org provides dedicated properties for representing many of these, either as textual strings or as URL (URI) links. See [background notes](/docs/datamodel.html#identifierBg) for more details.\n ", "oneOf": [ { - "$ref": "#/definitions/creativework" + "$ref": "#/definitions/propertyvalue" + }, + { + "type": "string" }, { - "type": "array", - "items": { - "$ref": "#/definitions/creativework" - } + "type": "string", + "format": "uri" } ], "owl:cardinality": "many" }, + "name": { + "description": "The name of the item.", + "type": "string", + "owl:cardinality": "one" + }, "sameAs": { + "description": "URL of a reference Web page that unambiguously indicates the item's identity. E.g. the URL of the item's Wikipedia page, Wikidata entry, or official website.", "oneOf": [ { "type": "string", @@ -20894,71 +20952,48 @@ } } ], - "description": "URL of a reference Web page that unambiguously indicates the item's identity. E.g. the URL of the item's Wikipedia page, Wikidata entry, or official website.", "owl:cardinality": "many" }, "conformsTo": { - "description": "This is used to state the Bioschemas profile that the markup relates to. The identifier can be the url for the version of this bioschemas class on github: https://github.com/BioSchemas/specifications/tree/master/TrainingMaterial/jsonld/TrainingMaterial_v1.1-DRAFT.json", + "description": "This is used to state the Bioschemas profile that the markup relates to. The identifier can be the url for the version of this bioschemas class on github: https://github.com/BioSchemas/specifications/tree/master/LabProtocol/jsonld/LabProtocol_v0.8-DRAFT.json", "$ref": "#/definitions/conformsDefinition" } }, "required": [ - "description", + "intendedUse", + "bioSample", + "labEquipment", + "reagent", "keywords", "name", "conformsTo" ], "recommended": [ - "about", - "abstract", - "audience", + "computationalTool", + "protocolAdvantage", + "protocolApplication", + "protocolLimitation", + "protocolOutcome", + "step", + "totalTime", "author", - "competencyRequired", - "educationalLevel", - "identifier", - "inLanguage", - "learningResourceType", + "citation", "license", - "mentions", - "teaches", - "timeRequired", - "url", + "identifier", "sameAs" ], "optional": [ - "accessibilitySummary", - "contributor", - "creativeWorkStatus", + "ethicalLegalSocial", + "performTime", + "prepTime", "dateCreated", "dateModified", "datePublished", - "hasPart", + "isBasedOn", "isPartOf", - "recordedAt", - "version", - "workTranslation" + "description" ], "definitions": { - "thing": { - "@type": "schema:Thing", - "type": "object", - "properties": { - "name": { - "type": "string" - } - }, - "required": [] - }, - "audience": { - "@type": "schema:Audience", - "type": "object", - "properties": { - "name": { - "type": "string" - } - }, - "required": [] - }, "organization": { "@type": "Organization", "type": "object", @@ -21035,11 +21070,74 @@ }, "required": [] }, + "taxon": { + "@type": "bioschemas:Taxon", + "type": "object", + "properties": { + "name": { + "type": "string" + }, + "taxonRank": { + "anyOf": [ + { + "$ref": "#/definitions/propertyvalue" + }, + { + "type": "array", + "items": { + "$ref": "#/definitions/propertyvalue" + } + }, + { + "type": "string" + }, + { + "type": "array", + "items": { + "type": "string" + } + }, + { + "type": "string", + "format": "uri" + }, + { + "type": "array", + "items": { + "type": "string", + "format": "uri" + } + } + ] + } + }, + "required": [ + "name", + "taxonRank" + ] + }, + "biochementity": { + "@type": "bioschemas:BioChemEntity", + "type": "object", + "properties": { + "url": { + "type": "string", + "format": "uri" + }, + "name": { + "type": "string" + }, + "identifier": { + "type": "string" + } + }, + "required": [] + }, "definedterm": { "@type": "DefinedTerm", "type": "object", "properties": { - "url": { + "sameAs": { "type": "string", "format": "uri" }, @@ -21058,6 +21156,16 @@ }, "required": [] }, + "biosample": { + "@type": "bioschemas:BioSample", + "type": "object", + "properties": { + "name": { + "type": "string" + } + }, + "required": [] + }, "definedtermset": { "@type": "DefinedTermSet", "type": "object", @@ -21170,8 +21278,8 @@ "url" ] }, - "language": { - "@type": "schema:Language", + "duration": { + "@type": "schema:Duration", "type": "object", "properties": { "name": { @@ -21180,8 +21288,8 @@ }, "required": [] }, - "event": { - "@type": "bioschemas:Event", + "molecularentity": { + "@type": "bioschemas:MolecularEntity", "type": "object", "properties": { "name": { @@ -21190,8 +21298,8 @@ }, "required": [] }, - "duration": { - "@type": "schema:Duration", + "chemicalsubstance": { + "@type": "bioschemas:ChemicalSubstance", "type": "object", "properties": { "name": { @@ -21200,109 +21308,56 @@ }, "required": [] }, - "conformsDefinition": { - "@type": "CreativeWork", + "softwareapplication": { + "@type": "schema:SoftwareApplication", "type": "object", "properties": { - "identifier": { - "description": "The url of the version bioschemas profile that was used. For jsonschema, set @id to the identifier", - "oneOf": [ - { - "enum": [ - "https://github.com/BioSchemas/specifications/tree/master/TrainingMaterial/jsonld/TrainingMaterial_v1.1-DRAFT.json" - ] - }, - { - "type": "string", - "format": "uri" - } - ] + "name": { + "type": "string" } }, - "required": [ - "identifier" - ] - } - } - }, - "additional_type": "https://bioschemas.org/profiles#nav-draft" - }, - { - "@id": "bioschemasdrafts:DefinedTerm", - "@type": "rdfs:Class", - "rdfs:comment": "A word, name, acronym, phrase, etc. with a formal definition. Use the name property for the term being defined, use termCode if the term has an alpha-numeric code allocated, use description to provide the definition of the term. This Bioschemas profile specifically helps reusing terms from terminology and ontology services.", - "rdfs:label": "DefinedTerm", - "rdfs:subClassOf": { - "@id": "schema:DefinedTerm" - }, - "$validation": { - "$schema": "http://json-schema.org/draft-07/schema#", - "type": "object", - "properties": { - "termCode": { - "description": "A code that identifies this [[DefinedTerm]] within a [[DefinedTermSet]]", - "type": "string", - "owl:cardinality": "one" - }, - "inDefinedTermSet": { - "description": "A [[DefinedTermSet]] that contains this term.", - "type": "string", - "owl:cardinality": "one" - }, - "description": { - "description": "A description of the item.", - "type": "string", - "owl:cardinality": "one" + "required": [] }, - "identifier": { - "description": "The identifier property represents any kind of identifier for any kind of [[Thing]], such as ISBNs, GTIN codes, UUIDs etc. Schema.org provides dedicated properties for representing many of these, either as textual strings or as URL (URI) links. See [background notes](/docs/datamodel.html#identifierBg) for more details.\n ", - "type": "string", - "owl:cardinality": "one" + "softwaresourcecode": { + "@type": "schema:SoftwareSourceCode", + "type": "object", + "properties": { + "name": { + "type": "string" + } + }, + "required": [] }, - "name": { - "description": "The name of the item.", - "type": "string", - "owl:cardinality": "one" + "workflow": { + "@type": "bioschemastypes:ComputationalWorkflow", + "type": "object", + "properties": { + "name": { + "type": "string" + } + }, + "required": [] }, - "sameAs": { - "description": "URL of a reference Web page that unambiguously indicates the item's identity. E.g. the URL of the item's Wikipedia page, Wikidata entry, or official website.", - "owl:cardinality": "many" + "howtosection": { + "@type": "schema:HowToSection", + "type": "object", + "properties": { + "name": { + "type": "string" + } + }, + "required": [] }, - "url": { - "description": "URL of the item.", - "oneOf": [ - { - "type": "string", - "format": "uri" - }, - { - "type": "array", - "items": { - "type": "string", - "format": "uri" - } + "howtostep": { + "@type": "schema:HowToStep", + "type": "object", + "properties": { + "name": { + "type": "string" } - ], - "owl:cardinality": "many" + }, + "required": [] }, - "conformsTo": { - "description": "This is used to state the Bioschemas profile that the markup relates to. The identifier can be the url for the version of this bioschemas class on github: https://github.com/BioSchemas/specifications/tree/master/DefinedTerm/jsonld/DefinedTerm_v0.1-DRAFT.jsonld", - "$ref": "#/definitions/conformsDefinition" - } - }, - "required": [ - "inDefinedTermSet", - "conformsTo" - ], - "recommended": [ - "termCode", - "sameAs", - "name" - ], - "optional": [ - "description" - ], - "definitions": { "conformsDefinition": { "@type": "CreativeWork", "type": "object", @@ -21312,7 +21367,7 @@ "oneOf": [ { "enum": [ - "https://github.com/BioSchemas/specifications/tree/master/DefinedTerm/jsonld/DefinedTerm_v0.1-DRAFT.jsonld" + "https://github.com/BioSchemas/specifications/tree/master/LabProtocol/jsonld/LabProtocol_v0.8-DRAFT.json" ] }, { @@ -21333,8 +21388,8 @@ ], "additional_type": "https://bioschemas.org/profiles#nav-draft", "schema:schemaVersion": [ - "https://bioschemas.org/profiles/DefinedTerm/0.1-DRAFT", - "https://github.com/BioSchemas/specifications/tree/master/DefinedTerm/jsonld/DefinedTerm_v0.1-DRAFT.jsonld" + "https://github.com/BioSchemas/specifications/tree/master/LabProtocol/jsonld/LabProtocol_v0.8-DRAFT.json", + "https://bioschemas.org/profiles/LabProtocol/0.8-DRAFT" ] }, { @@ -21448,12 +21503,12 @@ ] }, { - "@id": "bioschemasdrafts:codeRepository", + "@id": "bioschemasdrafts:applicationSubCategory", "@type": "rdf:Property", - "rdfs:comment": "Link to the source code repository of the tool.", - "rdfs:label": "codeRepository", + "rdfs:comment": "Subcategory of the application. \"A URL to the subcategory of ComputationalWorkflow. Note that the applicationCategory is implicitly Workflow. Example: \"applicationCategory\": \"http://edamontology.org/topic_3948\"", + "rdfs:label": "applicationSubCategory", "schema:domainIncludes": { - "@id": "bioschemasdrafts:ComputationalTool" + "@id": "bioschemasdrafts:ComputationalWorkflow" }, "schema:rangeIncludes": [ { @@ -21462,26 +21517,29 @@ ] }, { - "@id": "bioschemasdrafts:programmingLanguage", - "rdfs:comment": "The main programming language(s) used to build or execute the tool. Please use terms from the ‘Programming language’ table in the Bio.Tools documentation.", + "@id": "bioschemasdrafts:featureList", "@type": "rdf:Property", - "rdfs:label": "programmingLanguage", + "rdfs:comment": "Features or modules provided by this application (and possibly required by other applications). Functionality provided by the ComputatiionalWorkflow. ", + "rdfs:label": "featureList", "schema:domainIncludes": { - "@id": "bioschemasdrafts:ComputationalTool" + "@id": "bioschemasdrafts:ComputationalWorkflow" }, "schema:rangeIncludes": [ { - "@id": "schema:ComputerLanguage" + "@id": "schema:URL" + }, + { + "@id": "schema:Text" } ] }, { - "@id": "bioschemasdrafts:applicationSubCategory", + "@id": "bioschemasdrafts:codeRepository", "@type": "rdf:Property", - "rdfs:comment": "Subcategory of the application. \"A URL to the subcategory of ComputationalWorkflow. Note that the applicationCategory is implicitly Workflow. Example: \"applicationCategory\": \"http://edamontology.org/topic_3948\"", - "rdfs:label": "applicationSubCategory", + "rdfs:comment": "Link to the source code repository of the tool.", + "rdfs:label": "codeRepository", "schema:domainIncludes": { - "@id": "bioschemasdrafts:ComputationalWorkflow" + "@id": "bioschemasdrafts:ComputationalTool" }, "schema:rangeIncludes": [ { @@ -21490,19 +21548,16 @@ ] }, { - "@id": "bioschemasdrafts:featureList", + "@id": "bioschemasdrafts:programmingLanguage", + "rdfs:comment": "The main programming language(s) used to build or execute the tool. Please use terms from the ‘Programming language’ table in the Bio.Tools documentation.", "@type": "rdf:Property", - "rdfs:comment": "Features or modules provided by this application (and possibly required by other applications). Functionality provided by the ComputatiionalWorkflow. ", - "rdfs:label": "featureList", + "rdfs:label": "programmingLanguage", "schema:domainIncludes": { - "@id": "bioschemasdrafts:ComputationalWorkflow" + "@id": "bioschemasdrafts:ComputationalTool" }, "schema:rangeIncludes": [ { - "@id": "schema:URL" - }, - { - "@id": "schema:Text" + "@id": "schema:ComputerLanguage" } ] }, @@ -21689,154 +21744,6 @@ } ] }, - { - "@id": "bioschemasdrafts:labEquipmentUsed", - "rdfs:comment": "A laboratory equipment used by a person to follow one or more steps described in this LabProtocol. Controlled Vocabulary: BAO, EFO, ERO, OBI", - "@type": "rdf:Property", - "rdfs:label": "labEquipmentUsed", - "schema:domainIncludes": { - "@id": "bioschemasdrafts:LabProtocol" - }, - "schema:rangeIncludes": [ - { - "@id": "schema:DefinedTerm" - }, - { - "@id": "schema:Text" - }, - { - "@id": "schema:URL" - } - ] - }, - { - "@id": "bioschemasdrafts:bioSampleUsed", - "rdfs:comment": "BioSample used in the protocol. It could be a record in a Dataset describing the sample or a physical object corresponding to the sample or a URL pointing to the type of sample used. Controlled Vocabulary: NCBI Taxonomy, Uberon", - "@type": "rdf:Property", - "rdfs:label": "bioSampleUsed", - "schema:domainIncludes": { - "@id": "bioschemasdrafts:LabProtocol" - }, - "schema:rangeIncludes": [ - { - "@id": "bioschemastypes:BioChemEntity" - }, - { - "@id": "bioschemastypes:BioSample" - }, - { - "@id": "schema:DefinedTerm" - }, - { - "@id": "bioschemastypes:Taxon" - }, - { - "@id": "schema:Text" - }, - { - "@id": "schema:URL" - } - ] - }, - { - "@id": "bioschemasdrafts:totalTime", - "rdfs:comment": "The total time required to perform instructions or a direction (including time to prepare the supplies), in ISO 8601 duration format.", - "@type": "rdf:Property", - "rdfs:label": "totalTime", - "schema:domainIncludes": { - "@id": "bioschemasdrafts:LabProtocol" - }, - "schema:rangeIncludes": [ - { - "@id": "schema:Duration" - } - ] - }, - { - "@id": "bioschemasdrafts:protocolPurpose", - "rdfs:comment": "BioSample used in the protocol. It could be a record in a Dataset describing the sample or a physical object corresponding to the sample or a URL pointing to the type of sample used. Controlled Vocabulary: NCBI Taxonomy, Uberon", - "@type": "rdf:Property", - "rdfs:label": "protocolPurpose", - "schema:domainIncludes": { - "@id": "bioschemasdrafts:LabProtocol" - }, - "schema:rangeIncludes": [ - { - "@id": "schema:CreativeWork" - }, - { - "@id": "schema:Text" - } - ] - }, - { - "@id": "bioschemasdrafts:reagentUsed", - "rdfs:comment": "Reagents used in the protocol. ChEBI and PubChem entities can be used whenever available. Commercial names are also acceptable. Controlled Vocabulary: ChEBI, PubChem", - "@type": "rdf:Property", - "rdfs:label": "reagentUsed", - "schema:domainIncludes": { - "@id": "bioschemasdrafts:LabProtocol" - }, - "schema:rangeIncludes": [ - { - "@id": "bioschemastypes:BioChemEntity" - }, - { - "@id": "schema:DefinedTerm" - }, - { - "@id": "schema:Text" - }, - { - "@id": "schema:URL" - } - ] - }, - { - "@id": "bioschemasdrafts:softwareUsed", - "rdfs:comment": "Software or tool used as part of the lab protocol to complete a part of it.", - "@type": "rdf:Property", - "rdfs:label": "softwareUsed", - "schema:domainIncludes": { - "@id": "bioschemasdrafts:LabProtocol" - }, - "schema:rangeIncludes": [ - { - "@id": "schema:SoftwareApplication" - }, - { - "@id": "schema:URL" - } - ] - }, - { - "@id": "bioschemasdrafts:performTime", - "rdfs:comment": "The length of time it takes to perform instructions or a direction (not including time to prepare the supplies), in ISO 8601 duration format.", - "@type": "rdf:Property", - "rdfs:label": "performTime", - "schema:domainIncludes": { - "@id": "bioschemasdrafts:LabProtocol" - }, - "schema:rangeIncludes": [ - { - "@id": "schema:Duration" - } - ] - }, - { - "@id": "bioschemasdrafts:prepTime", - "rdfs:comment": "The length of time it takes to prepare the items to be used in instructions or a direction, in ISO 8601 duration format.", - "@type": "rdf:Property", - "rdfs:label": "prepTime", - "schema:domainIncludes": { - "@id": "bioschemasdrafts:LabProtocol" - }, - "schema:rangeIncludes": [ - { - "@id": "schema:Duration" - } - ] - }, { "@id": "bioschemasdrafts:budget", "rdfs:comment": "The annual (or total - for a project) budget for the organization.", @@ -22204,10 +22111,10 @@ ] }, { - "@id": "bioschemasdrafts:attachment", - "rdfs:comment": "Any files or related websites which give more information about this event. e.g. flyers, third party sites handling tickets.", + "@id": "bioschemasdrafts:topic", + "rdfs:comment": "The scientific topic the event is about. Please use a term from EDAM: Topic.", "@type": "rdf:Property", - "rdfs:label": "attachment", + "rdfs:label": "topic", "schema:domainIncludes": [ { "@id": "bioschemasdrafts:Event" @@ -22223,21 +22130,21 @@ ] }, { - "@id": "bioschemasdrafts:keywords", - "rdfs:comment": "Keywords or tags used to describe this content. Multiple entries in a keywords list are typically delimited by commas. \n NOTE: Keywords is not part of Event.", + "@id": "rdf:type", + "rdfs:comment": "This is used by validation tools to indentify the profile used. You must use the value specified in the Controlled Vocabulary column. This is used by validation tools to indentify the profile used. You must use the value specified in the Controlled Vocabulary column.", "@type": "rdf:Property", - "rdfs:label": "keywords", + "rdfs:label": "type", "schema:domainIncludes": [ { "@id": "bioschemasdrafts:Event" }, { - "@id": "bioschemasdrafts:Person" + "@id": "bioschemasdrafts:Organization" } ], "schema:rangeIncludes": [ { - "@id": "schema:Text" + "@id": "schema:URL" } ] }, @@ -22261,57 +22168,48 @@ ] }, { - "@id": "bioschemasdrafts:hasSequenceAnnotation", - "rdfs:comment": "An annotation on the BioPolymerSequence associated with this BioChemEntity. For genes, it can be used to link to gene sequence annotations such as variants or so.", + "@id": "bioschemasdrafts:attachment", + "rdfs:comment": "Any files or related websites which give more information about this event. e.g. flyers, third party sites handling tickets.", "@type": "rdf:Property", - "rdfs:label": "hasSequenceAnnotation", + "rdfs:label": "attachment", "schema:domainIncludes": [ { - "@id": "bioschemasdrafts:Gene" - }, - { - "@id": "bioschemasdrafts:Protein" + "@id": "bioschemasdrafts:Event" }, { - "@id": "bioschemasdrafts:RNA" + "@id": "bioschemasdrafts:Organization" } ], "schema:rangeIncludes": [ - { - "@id": "bioschemastypesdrafts:SequenceAnnotation" - }, { "@id": "schema:URL" } ] }, { - "@id": "bioschemasdrafts:dateModified", - "rdfs:comment": "The date on which the CreativeWork was most recently modified or when the item\u2019s entry was modified within a DataFeed. \n NOTE: Keywords is not part of Event.", + "@id": "bioschemasdrafts:keywords", + "rdfs:comment": "Keywords or tags used to describe this content. Multiple entries in a keywords list are typically delimited by commas. \n NOTE: Keywords is not part of Event.", "@type": "rdf:Property", - "rdfs:label": "dateModified", + "rdfs:label": "keywords", "schema:domainIncludes": [ { "@id": "bioschemasdrafts:Event" }, { - "@id": "bioschemasdrafts:Organization" + "@id": "bioschemasdrafts:Person" } ], "schema:rangeIncludes": [ { - "@id": "schema:Date" - }, - { - "@id": "schema:DateTime" + "@id": "schema:Text" } ] }, { - "@id": "bioschemasdrafts:topic", - "rdfs:comment": "The scientific topic the event is about. Please use a term from EDAM: Topic.", + "@id": "bioschemasdrafts:dateModified", + "rdfs:comment": "The date on which the CreativeWork was most recently modified or when the item\u2019s entry was modified within a DataFeed. \n NOTE: Keywords is not part of Event.", "@type": "rdf:Property", - "rdfs:label": "topic", + "rdfs:label": "dateModified", "schema:domainIncludes": [ { "@id": "bioschemasdrafts:Event" @@ -22322,24 +22220,33 @@ ], "schema:rangeIncludes": [ { - "@id": "schema:URL" + "@id": "schema:Date" + }, + { + "@id": "schema:DateTime" } ] }, { - "@id": "rdf:type", - "rdfs:comment": "This is used by validation tools to indentify the profile used. You must use the value specified in the Controlled Vocabulary column. This is used by validation tools to indentify the profile used. You must use the value specified in the Controlled Vocabulary column.", + "@id": "bioschemasdrafts:hasSequenceAnnotation", + "rdfs:comment": "An annotation on the BioPolymerSequence associated with this BioChemEntity. For genes, it can be used to link to gene sequence annotations such as variants or so.", "@type": "rdf:Property", - "rdfs:label": "type", + "rdfs:label": "hasSequenceAnnotation", "schema:domainIncludes": [ { - "@id": "bioschemasdrafts:Event" + "@id": "bioschemasdrafts:Gene" }, { - "@id": "bioschemasdrafts:Organization" + "@id": "bioschemasdrafts:Protein" + }, + { + "@id": "bioschemasdrafts:RNA" } ], "schema:rangeIncludes": [ + { + "@id": "bioschemastypesdrafts:SequenceAnnotation" + }, { "@id": "schema:URL" } @@ -22393,9 +22300,6 @@ { "@id": "bioschemasdrafts:Journal" }, - { - "@id": "bioschemasdrafts:LabProtocol" - }, { "@id": "bioschemasdrafts:MolecularEntity" }, @@ -22446,6 +22350,9 @@ }, { "@id": "bioschemasdrafts:DefinedTerm" + }, + { + "@id": "bioschemasdrafts:LabProtocol" } ], "schema:rangeIncludes": [ diff --git a/draft_profile_list.txt b/draft_profile_list.txt index 7414c48..3a716a7 100644 --- a/draft_profile_list.txt +++ b/draft_profile_list.txt @@ -13,7 +13,6 @@ bioschemasdrafts Disease schema:MedicalCondition Profile 0.2-DRAFT https://githu bioschemas Event schema:Event Profile 0.3-DRAFT https://github.com/BioSchemas/specifications/tree/master/Event/jsonld/Event_v0.3-DRAFT.json bioschemas FormalParameter bioschemastypes:FormalParameter Profile 1.1-DRAFT https://github.com/BioSchemas/specifications/tree/master/FormalParameter/jsonld/FormalParameter_v1.1-DRAFT.json bioschemas Journal schema:CreativeWorkSeries Profile 0.3-DRAFT https://github.com/BioSchemas/specifications/tree/master/Journal/jsonld/Journal_v0.3-DRAFT.json -bioschemas LabProtocol bioschemastypes:LabProtocol Profile 0.7-DRAFT https://github.com/BioSchemas/specifications/tree/master/LabProtocol/jsonld/LabProtocol_v0.7-DRAFT.json bioschemas MolecularEntity schema:MolecularEntity Profile 0.7-DRAFT https://github.com/BioSchemas/specifications/tree/master/MolecularEntity/jsonld/MolecularEntity_v0.7-DRAFT.json bioschemas Organization schema:Organization Profile 0.3-DRAFT https://github.com/BioSchemas/specifications/tree/master/Organization/jsonld/Organization_v0.3-DRAFT.json bioschemas Person schema:Person Profile 0.3-DRAFT https://github.com/BioSchemas/specifications/tree/master/Person/jsonld/Person_v0.3-DRAFT.json @@ -31,3 +30,4 @@ bioschemas SequenceRange bioschemastypes:SequenceStructure Profile 0.2-DRAFT htt bioschemas Study bioschemastypes:Study Profile 0.3-DRAFT https://github.com/BioSchemas/specifications/tree/master/Study/jsonld/Study_v0.3-DRAFT.json bioschemas TrainingMaterial schema:LearningResource Profile 1.1-DRAFT https://github.com/BioSchemas/specifications/tree/master/TrainingMaterial/jsonld/TrainingMaterial_v1.1-DRAFT.json bioschemasdrafts DefinedTerm schema:DefinedTerm Profile 0.1-DRAFT https://github.com/BioSchemas/specifications/tree/master/DefinedTerm/jsonld/DefinedTerm_v0.1-DRAFT.jsonld +bioschemasdrafts LabProtocol bioschemastypes:LabProtocol Profile 0.8-DRAFT https://github.com/BioSchemas/specifications/tree/master/LabProtocol/jsonld/LabProtocol_v0.8-DRAFT.json