diff --git a/MolecularEntity/jsonld/MolecularEntity_v0.8-DRAFT.json b/MolecularEntity/jsonld/MolecularEntity_v0.8-DRAFT.json new file mode 100644 index 0000000..33e913b --- /dev/null +++ b/MolecularEntity/jsonld/MolecularEntity_v0.8-DRAFT.json @@ -0,0 +1,767 @@ +{ + "@context": { + "schema": "http://schema.org/", + "rdf": "http://www.w3.org/1999/02/22-rdf-syntax-ns#", + "rdfs": "http://www.w3.org/2000/01/rdf-schema#", + "bioschemas": "https://discovery.biothings.io/view/bioschemas/", + "owl": "http://www.w3.org/2002/07/owl/", + "dct": "http://purl.org/dc/terms/" + }, + "@graph": [ + { + "@id": "bioschemas:MolecularEntity", + "@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 0.8-DRAFT.

Summary of Changes


Changes since 0.7-DRAFT: clarify how to comply with the FAIR chemical structures principle", + "rdfs:label": "MolecularEntity", + "rdfs:subClassOf": { + "@id": "schema:MolecularEntity" + }, + "$validation": { + "$schema": "http://json-schema.org/draft-08/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.\n\nTo comply with the 'FAIR chemical structures' specification, at least one of inChI, inChIKey, iupacName, and smiles should be provided.", + "type": "string", + "owl:cardinality": "one" + }, + "inChIKey": { + "description": "InChIKey is a hashed version of the full InChI (using the SHA-256 algorithm).\n\nTo comply with the 'FAIR chemical structures' specification, at least one of inChI, inChIKey, iupacName, and smiles should be provided.", + "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).\n\nTo comply with the 'FAIR chemical structures' specification, at least one of inChI, inChIKey, iupacName, and smiles should be provided.", + "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": [ + { + "$ref": "#/definitions/quantitativeValue" + }, + { + "type": "string" + } + ], + "owl:cardinality": "one" + }, + "smiles": { + "description": "A specification in form of a line notation for describing the structure of chemical species using short ASCII strings. Double bond stereochemistry \\ indicators may need to be escaped in the string in formats where the backslash is an escape character.\n\nTo comply with the 'FAIR chemical structures' specification, at least one of inChI, inChIKey, iupacName, and smiles should be provided.", + "oneOf": [ + { + "type": "string" + }, + { + "type": "array", + "items": { + "type": "string" + } + } + ], + "owl:cardinality": "many" + }, + "chemicalRole": { + "description": "A role played by the BioChemEntity within a chemical context.", + "oneOf": [ + { + "$ref": "#/definitions/definedTerm" + }, + { + "type": "array", + "items": { + "$ref": "#/definitions/definedTerm" + } + } + ], + "owl:cardinality": "many" + }, + "monoisotopicMolecularWeight": { + "description": "The monoisotopic mass is the sum of the masses of the atoms in a molecule using the unbound, ground-state, rest mass of the principal (most abundant) isotope for each element instead of the isotopic average mass. Please include the units the form \u2018 ', for example '770.230488 g/mol' or as '.", + "oneOf": [ + { + "$ref": "#/definitions/quantitativeValue" + }, + { + "type": "string" + } + ], + "owl:cardinality": "one" + }, + "potentialUse": { + "description": "Intended use of the BioChemEntity by humans.", + "oneOf": [ + { + "$ref": "#/definitions/definedTerm" + }, + { + "type": "array", + "items": { + "$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": [ + { + "$ref": "#/definitions/medicalCondition" + }, + { + "type": "array", + "items": { + "$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" + }, + "bioChemInteraction": { + "description": "A BioChemEntity that is know to interact with this item.", + "oneOf": [ + { + "$ref": "#/definitions/bioChemEntity" + }, + { + "type": "array", + "items": { + "$ref": "#/definitions/bioChemEntity" + } + } + ], + "owl:cardinality": "many" + }, + "bioChemSimilarity": { + "description": "A similar molecular entity, e.g., obtained by fingerprint similarity algorithm.", + "oneOf": [ + { + "$ref": "#/definitions/bioChemEntity" + }, + { + "type": "array", + "items": { + "$ref": "#/definitions/bioChemEntity" + } + } + ], + "owl:cardinality": "many" + }, + "biologicalRole": { + "description": "A role played by the molecular entity within a biological context.", + "oneOf": [ + { + "$ref": "#/definitions/definedTerm" + }, + { + "type": "array", + "items": { + "$ref": "#/definitions/definedTerm" + } + } + ], + "owl:cardinality": "many" + }, + "hasBioChemEntityPart": { + "description": "Indicates a BioChemEntity that (in some sense) has this BioChemEntity as a part. Inverse property: isPartOfBioChemEntity", + "oneOf": [ + { + "$ref": "#/definitions/bioChemEntity" + }, + { + "type": "array", + "items": { + "$ref": "#/definitions/bioChemEntity" + } + } + ], + "owl:cardinality": "many" + }, + "hasMolecularFunction": { + "description": "Molecular function performed by this BioChemEntity; please use PropertyValue if you want to include any evidence.", + "anyOf": [ + { + "$ref": "#/definitions/definedTerm" + }, + { + "type": "array", + "items": { + "$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" + }, + "hasRepresentation": { + "description": "A common representation such as a protein sequence or chemical structure for this entity. For images use schema.org/image.", + "anyOf": [ + { + "$ref": "#/definitions/definedTerm" + }, + { + "type": "array", + "items": { + "$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" + } + } + ], + "owl:cardinality": "many" + }, + "isInvolvedInBiologicalProcess": { + "description": "Biological process this BioChemEntity is involved in; please use PropertyValue if you want to include any evidence.", + "anyOf": [ + { + "$ref": "#/definitions/definedTerm" + }, + { + "type": "array", + "items": { + "$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" + }, + "isLocatedInSubcellularLocation": { + "description": "Subcellular location where this BioChemEntity is located; please use PropertyValue if you want to include any evidence.", + "anyOf": [ + { + "$ref": "#/definitions/definedTerm" + }, + { + "type": "array", + "items": { + "$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" + }, + "isPartOfBioChemEntity": { + "description": "Indicates a BioChemEntity that is (in some sense) a part of this BioChemEntity. Inverse property: hasBioChemEntityPart", + "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" + }, + { + "type": "array", + "items": { + "type": "string", + "format": "uri" + } + } + ], + "owl:cardinality": "many" + }, + "alternateName": { + "description": "An alias for the item.", + "oneOf": [ + { + "type": "string" + }, + { + "type": "array", + "items": { + "type": "string" + } + } + ], + "owl:cardinality": "many" + }, + "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": [ + { + "$ref": "#/definitions/definedTerm" + }, + { + "$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", + "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" + } + }, + "required": [], + "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": { + "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" + ] + }, + "propertyValue": { + "@type": "PropertyValue", + "type": "object", + "properties": { + "name": { + "type": "string" + }, + "value": { + "type": "string" + } + }, + "required": [] + }, + "definedTerm": { + "@type": "DefinedTerm", + "type": "object", + "properties": { + "url": { + "type": "string", + "format": "uri" + }, + "name": { + "type": "string" + }, + "termCode": { + "type": "string" + } + }, + "required": [] + }, + "medicalCondition": { + "@type": "MedicalCondition", + "type": "object", + "properties": { + "url": { + "type": "string", + "format": "uri" + }, + "name": { + "type": "string" + } + }, + "required": [] + }, + "bioChemEntity": { + "@type": "bioschemas:BioChemEntity", + "type": "object", + "properties": { + "url": { + "type": "string", + "format": "uri" + }, + "name": { + "type": "string" + } + }, + "required": [] + }, + "gene": { + "@type": "bioschemas:Gene", + "type": "object", + "properties": { + "identifier": { + "anyOf": [ + { + "$ref": "#/definitions/propertyValue" + }, + { + "type": "string" + }, + { + "type": "string", + "format": "uri" + } + ] + }, + "name": { + "type": "string" + } + }, + "required": [] + }, + "quantitativeValue": { + "@type": "QuantitativeValue", + "type": "object", + "properties": { + "value": { + "type": "string" + }, + "unitText": { + "type": "string" + } + }, + "required": [] + }, + "creativework": { + "@type": "CreativeWork", + "type": "object", + "properties": { + "name": { + "type": "string" + } + }, + "required": [] + }, + "event": { + "@type": "Event", + "type": "object", + "properties": { + "name": { + "type": "string" + } + }, + "required": [] + } + } + } + } + ] +}