{ "@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#", "dct": "http://purl.org/dc/terms/", "bioschemas": "https://discovery.biothings.io/ns/bioschemas/", "bioschemastypesdrafts": "https://discovery.biothings.io/ns/bioschemastypesdrafts/", "niaid": "http://discovery.biothings.io/ns/niaid/", "nde": "https://discovery.biothings.io/ns/nde/" }, "@graph": [ { "@id": "nde:Dataset", "@type": "rdfs:Class", "rdfs:comment": "Datasets contained in the NIAID Data Ecosystem. A dataset is a collection of data of a particular experimental type. The NIAID Data Ecosystem is an environment to find and access and infectious and immune-mediated disease data and computational tools to speed the development of diagnostics, therapeutics, and vaccines. 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This topic may be assigned by a human curator or through automated algorithms.", "abstract": "topic", "anyOf": [ { "type": "array", "items": { "$ref": "#/definitions/topic" } }, { "$ref": "#/definitions/topic" }, { "type": "array", "items": { "$ref": "#/definitions/definedterm" } }, { "$ref": "#/definitions/definedterm" } ], "owl:cardinality": "many" }, "infectiousAgent": { "description": "Infectious agent(s) / pathogen(s) which are the focus of the work (like SARS-CoV-2).", "abstract": "infectious agent / pathogen", "anyOf": [ { "description": "collection of vocabulary terms defined in ontologies", "strict": false, "type": "string", "vocabulary": { "children_of": ["http://purl.obolibrary.org/obo/NCBITaxon_10239", "http://purl.obolibrary.org/obo/NCBITaxon_2"], "ontology": ["ncbitaxon"] } }, { "items": { "description": "collection of vocabulary terms defined in ontologies", "strict": false, "type": "string", "vocabulary": { "children_of": 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"items": { "type": "object", "@type": "MonetaryGrant", "description": "Funding that supports (sponsors) the collection of this dataset through some kind of financial contribution", "properties": { "funder": { "description": "An organization associated with a creator or funder of a dataset", "oneOf": [ { "type": "object", "@type": "Organization", "description": "Information about a single funder", "properties": { "name": { "type": "string", "description": "An organization associated with a creator or funder of a dataset" }, "parentOrganization": { "type": "string", "description": "name of the parent funding organization" } }, "required": [ "name" ] }, { "type": "array", "items": { "type": "object", "@type": "Organization", "description": "Information about a single funder", "properties": { "name": { "type": "string", "description": "An organization associated with a creator or funder of a dataset" }, "parentOrganization": { "type": "string", "description": "name of the parent funding 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"uri", "type": "string" }, "encodingFormat": { "description": "file type (ex: XLSX)", "type": "string" }, "dateModified": { "format": "date", "description": "date the file was modified", "type": "string" } }, "required": ["dateModified", "contentUrl"], "type": "object" } ], "owl:cardinality": "many" }, "includedInDataCatalog": { "description": "Data or tool catalog where the work is published; original source of the metadata.", "abstract": "catalog containing the work", "oneOf": [ { "$ref": "#/definitions/catalog" }, { "type": "array", "items": { "$ref": "#/definitions/catalog" } } ], "owl:cardinality": "one" }, "measurementTechnique": { "description": "A technique or technology used in a dataset corresponding to the method used for measuring the corresponding variable(s) (described using variableMeasured). For example, if variableMeasured is molecule concentration, measurementTechnique could be: \"mass spectrometry\" or \"nmr spectroscopy\" or \"colorimetry\" or \"immunofluorescence\".", "abstract": "measurement technique used to collect the dataset", "anyOf": [ { "description": "collection of vocabulary terms defined in ontologies", "strict": false, "type": "string", "vocabulary": { "children_of": ["http://edamontology.org/topic_3361", "http://purl.obolibrary.org/obo/NCIT_C20368", "http://purl.obolibrary.org/obo/MMO_0000000", "http://www.ebi.ac.uk/efo/EFO_0000001"], "ontology": ["edam", "ncit", "mmo","efo"] } }, { "items": { "description": "collection of vocabulary terms defined in ontologies", "strict": false, "type": "string", "vocabulary": { "children_of": ["http://edamontology.org/topic_3361", "http://purl.obolibrary.org/obo/NCIT_C20368", "http://purl.obolibrary.org/obo/MMO_0000000", "http://www.ebi.ac.uk/efo/EFO_0000001"], "ontology": ["edam", "ncit", "mmo","efo"] } }, "type": "array" }, { "type": "array", "items": { "$ref": "#/definitions/definedterm" } }, { "$ref": "#/definitions/definedterm" } ], "owl:cardinality": "many" }, "variableMeasured": { "description": "Variables measured within the dataset.", "oneOf": [ { "description": "collection of vocabulary terms defined in ontologies", "strict": false, "type": "string", "vocabulary": { "children_of": ["http://www.ebi.ac.uk/efo/EFO_0000001", "http://purl.obolibrary.org/obo/CMO_0000000", "http://purl.obolibrary.org/obo/NCIT_C25209"], "ontology": ["efo", "cmo","ncit"] } }, { "items": { "description": "collection of vocabulary terms defined in ontologies", "strict": false, "type": "string", "vocabulary": { "children_of": ["http://www.ebi.ac.uk/efo/EFO_0000001", "http://purl.obolibrary.org/obo/CMO_0000000", "http://purl.obolibrary.org/obo/NCIT_C25209"], "ontology": ["efo", "cmo","ncit"] } }, "type": "array" }, { "type": "array", "items": { "$ref": "#/definitions/definedterm" } }, { "$ref": "#/definitions/definedterm" } ], "owl:cardinality": "many" }, "abstract": { "description": "Short description that summarizes a work.", "abstract": "short description", "type": "string", "owl:cardinality": "one" }, "aggregateRating": { "description": "The overall rating, based on a collection of reviews or ratings, of the work. These ratings can be collected based on user reviews or through Altmetric scores of web-based citations.", "abstract": "rating of the work", "oneOf": [ { "items": { "@type": "AggregateRating", "type": "object", "properties": { "ratingCount": { "description": "Total number of ratings", "type": "integer" }, "ratingValue": { "description": "Average rating", "type": "string" }, "itemReviewed": { "description": "What is being reviewed", "type": "string" } }, "required": ["ratingValue"], "recommended": ["ratingCount", "itemReviewed"] }, "type": "array" }, { "@type": "AggregateRating", "type": "object", "properties": { "ratingCount": { "description": "Total number of ratings", "type": "integer" }, "ratingValue": { "description": "Average rating", "type": "string" }, "itemReviewed": { "description": "What is being reviewed", "type": "string" } }, "required": ["ratingValue"], "recommended": ["ratingCount", "itemReviewed"] } ], "owl:cardinality": "many" }, "author": { "description": "Author or creator of the work. The default field for the author or creator of the work.", "anyOf": [ { "type": "array", "items": { "$ref": "#/definitions/person" } }, { "$ref": "#/definitions/person" }, { "type": "array", "items": { "$ref": "#/definitions/organization" } }, { "$ref": "#/definitions/organization" } ], "owl:cardinality": "many" }, "citation": { "description": "The primary citation or reference about the dataset. Examples: a publication which describes the creation of the dataset. The original reference by the dataset creators/maintainers that should be cited when reusing the dataset. For other references to the dataset, use 'citedBy'.", "abstract": "citation to the work", "owl:cardinality": "many", "anyOf": [ { "type": "array", "items": { "$ref": "#/definitions/citation" } }, { "$ref": "#/definitions/citation" }, { "type": "array", "items": { "$ref": "#/definitions/creativework" } }, { "$ref": "#/definitions/creativework" } ] }, "conditionsOfAccess": { "description": "Conditions that affect the availability of, or method(s) of access to, the work. Options include open (freely available), restricted (may include restrictions such as on use), closed (requires registration to access), or embargoed (unpublished).", "abstract": "accessibility of the work", "type": "string", "enum": ["Closed", "Open", "Restricted", "Embargoed"], "owl:cardinality": "one" }, "creator": { "description": "The creator/author of this work; equivalent to author. Please use author by default. Use creator if author/creator in a record of this work submitted elsewhere differs from the author/creator entered into the author field.", "anyOf": [ { "type": "array", "items": { "$ref": "#/definitions/person" } }, { "$ref": "#/definitions/person" }, { "type": "array", "items": { "$ref": "#/definitions/organization" } }, { "$ref": "#/definitions/organization" } ], "owl:cardinality": "many" }, "dateCreated": { "description": "Date the work was created.", "format": "date", "type": "string", "owl:cardinality": "one" }, "dateModified": { "description": "Date the work was modified.", "format": "date", "type": "string", "owl:cardinality": "one" }, "datePublished": { "description": "Date the work was first published.", "format": "date", "type": "string", "owl:cardinality": "one" }, "hasPart": { "description": "Associated materials for the dataset, including data dictionaries and data limitation descriptions.", "abstract": "data limitations or dictionaries", "anyOf": [ { "type": "array", "items": { "$ref": "#/definitions/citation" } }, { "$ref": "#/definitions/citation" }, { "type": "array", "items": { "$ref": "#/definitions/creativework" } }, { "$ref": "#/definitions/creativework" } ], "owl:cardinality": "many" }, "inLanguage": { "description": "The language of the content of the dataset.", "owl:cardinality": "many", "oneOf": [ { "items": { "type": "object", "properties": { "name": { "type": "string", "description": "language of the work" }, "alternateName": { "type": "string" } }, "required": ["name"], "recommended": ["alternateName"] }, "type": "array" }, { "type": "object", "properties": { "name": { "type": "string", "description": "language of the work" }, "alternateName": { "type": "string" } }, "required": ["name"], "recommended": ["alternateName"] } ] }, "interactionStatistic": { "description": "The number of interactions with the work, such as page views or tool downloads.", "abstract": "views or downloads", "oneOf": [ { "items": { "@type": "InteractionCounter", "type": "object", "properties": { "interactionType": { "type": "string" }, "userInteractionCount": { "type": "integer" } }, "required": ["interactionType", "userInteractionCount"] }, "type": "array" }, { "@type": "InteractionCounter", "type": "object", "properties": { "interactionType": { "type": "string" }, "userInteractionCount": { "type": "integer" } }, "required": ["interactionType", "userInteractionCount"] } ], "owl:cardinality": "many" }, "isAccessibleForFree": { "description": "A flag to signal that the work is accessible for free.", "abstract": "accessible without charge", "type": "boolean", "owl:cardinality": "one" }, "isBasedOn": { "description": "A dataset, publication, or computational tool from which this work is derived, modified, or adapted.", "abstract": "dataset, publication, or tool used to create the work", "owl:cardinality": "many", "anyOf": [ { "type": "array", "items": { "$ref": "#/definitions/citation" } }, { "$ref": "#/definitions/citation" }, { "type": "array", "items": { "$ref": "#/definitions/creativework" } }, { "$ref": "#/definitions/creativework" } ] }, "isPartOf": { "description": "Indicates a broader study, project, or collection the work is part of.", "abstract": "study or project including the work", "owl:cardinality": "many", "anyOf": [ { "type": "array", "items": { "$ref": "#/definitions/citation" } }, { "$ref": "#/definitions/citation" }, { "type": "array", "items": { "$ref": "#/definitions/creativework" } }, { "$ref": "#/definitions/creativework" } ] }, "keywords": { "description": "Keywords or tags used to describe this work.", "abstract": "keywords or tags", "oneOf": [ { "type": "array", "items": { "type": "string" } }, { "type": "string" } ], "owl:cardinality": "many" }, "license": { "description": "A license document that applies to this work, typically indicated by URL.", "abstract": "license for use", "format": "uri", "owl:cardinality": "one", "type": "string" }, "sdPublisher": { "description": "Original publisher of the dataset metadata (like GenBank, ImmPort, etc.).", "abstract": "original metadata source", "oneOf": [ { "$ref": "#/definitions/catalog" }, { "type": "array", "items": { "$ref": "#/definitions/catalog" } } ], "owl:cardinality": "many" }, "spatialCoverage": { "description": "The place(s) which are the focus of the dataset.", "abstract": "geographic focus of the work", "oneOf": [ { "items": { "@type": "AdministrativeArea", "description": "Location information", "properties": { "administrativeType": { "description": "the type of administrative area, such as country, state, county, or city", "enum": ["province", "district", "chiefdom", "village", "city", "country", "prefecture", "sub-prefecture", "clan", "Federal Capital Territory", "state", "Local Government Area", "ward"], "type": "string" }, "alternateName": { "description": "An alias for the location", "oneOf": [ { "type": "string" }, { "items": { "type": "string" }, "type": "array" } ] }, "identifier": { "description": "An identifier for the location, preferably a Wikidata ID", "type": "string" }, "locationType": { "description": "Categorization of how the location relates to the dataset", "oneOf": [ { "enum": ["residence", "exposure", "collection", "screening", "treatment", "study location", "other", "unknown"], "type": "string" }, { "items": { "enum": ["residence", "exposure", "collection", "screening", "treatment", "study location", "other", "unknown"], "type": "string" }, "type": "array" } ] }, "name": { "description": "The name of the location", "type": "string" } }, "type": "object" }, "type": "array" }, { "@type": "AdministrativeArea", "description": "Location information", "properties": { "administrativeType": { "description": "the type of administrative area, such as country, state, county, or city", "enum": ["province", "district", "chiefdom", "village", "city", "country", "prefecture", "sub-prefecture", "clan", "Federal Capital Territory", "state", "Local Government Area", "ward"], "type": "string" }, "alternateName": { "description": "An alias for the location", "oneOf": [ { "type": "string" }, { "items": { "type": "string" }, "type": "array" } ] }, "identifier": { "description": "An identifier for the location, preferably a Wikidata ID", "type": "string" }, "locationType": { "description": "Categorization of how the location relates to the dataset", "oneOf": [ { "enum": ["residence", "exposure", "collection", "screening", "treatment", "study location", "other", "unknown"], "type": "string" }, { "items": { "enum": ["residence", "exposure", "collection", "screening", "treatment", "study location", "other", "unknown"], "type": "string" }, "type": "array" } ] }, "name": { "description": "The name of the location", "type": "string" } }, "type": "object" } ], "owl:cardinality": "many" }, "temporalCoverage": { "description": "The period of time covered within the dataset.", "abstract": "time period", "oneOf": [ { "items": { "@type": "TemporalInterval", "description": "Temporal information", "properties": { "duration": { "description": "A time interval in ISO 8601 duration format", "type": "string" }, "endDate": { "description": "An end date", "format": "date", "type": "string" }, "name": { "description": "String describing the temporal interval", "type": "string" }, "startDate": { "description": "A start date", "format": "date", "type": "string" }, "temporalType": { "description": "Categorization of how the date/temporal interval relates to the dataset", "oneOf": [ { "enum": ["exposure", "collection", "screening", "treatment", "study date", "other", "unknown"], "type": "string" }, { "items": { "enum": ["exposure", "collection", "screening", "treatment", "study date", "other", "unknown"], "type": "string" }, "type": "array" } ] } }, "type": "object" }, "type": "array" }, { "@type": "TemporalInterval", "description": "Temporal information", "properties": { "duration": { "description": "A time interval in ISO 8601 duration format", "type": "string" }, "endDate": { "description": "An end date", "format": "date", "type": "string" }, "name": { "description": "String describing the temporal interval", "type": "string" }, "startDate": { "description": "A start date", "format": "date", "type": "string" }, "temporalType": { "description": "Categorization of how the date/temporal interval relates to the dataset", "oneOf": [ { "enum": ["exposure", "collection", "screening", "treatment", "study date", "other", "unknown"], "type": "string" }, { "items": { "enum": ["exposure", "collection", "screening", "treatment", "study date", "other", "unknown"], "type": "string" }, "type": "array" } ] } }, "type": "object" } ], "owl:cardinality": "many" }, "usageInfo": { "description": "Data usage agreement, specifying the terms under which the dataset can be used. Note that this is related to but distinct from the license.", "abstract": "data usage agreement", "oneOf": [ { "type": "array", "items": { "$ref": "#/definitions/creativework" } }, { "$ref": "#/definitions/creativework" } ], "owl:cardinality": "many" }, "version": { "description": "Dataset version.", "type": "string", "owl:cardinality": "one" }, "alternateName": { "description": "An alias for the dataset name.", "oneOf": [ { "type": "string" }, { "type": "array", "items": { "type": "string" } } ], "owl:cardinality": "many" }, "description": { "description": "A description of the dataset.", "owl:cardinality": "one", "type": "string" }, "identifier": { "description": "Dataset identifier or accession number, such as a digital object identifier (DOI), sequence read archive (SRA) or GenBank accession number, etc.", "abstract": "identifier or accession number", "oneOf": [ { "type": "string" }, { "items": { "type": "string" }, "type": "array" } ], "owl:cardinality": "many" }, "mainEntityOfPage": { "description": "Website which describes the work and provides additional details.", "abstract": "associated webpage", "oneOf": [ { "items": { "type": "string", "format": "uri" }, "type": "array" }, { "type": "string", "format": "uri" } ], "owl:cardinality": "many" }, "name": { "description": "Dataset name.", "owl:cardinality": "one", "type": "string" }, "sameAs": { "description": "URL of additional sources for the work.", "oneOf": [ { "items": { "type": "string", "format": "uri" }, "type": "array" }, { "type": "string", "format": "uri" } ], "owl:cardinality": "many" }, "url": { "description": "URL of the work.", "type": "string", "format": "uri", "owl:cardinality": "one" }, "sourceOrganization": { "description": "The organization, research project, working group, or funded program on whose behalf the author/creator was working.", "anyOf": [ { "type": "array", "items": { "$ref": "#/definitions/researchproject" } }, { "$ref": "#/definitions/researchproject" }, { "type": "array", "items": { "$ref": "#/definitions/organization" } }, { "$ref": "#/definitions/organization" } ], "owl:cardinality": "many" }, "sample": { "description": "the samples used to generate the dataset", "anyOf": [ { "type": "array", "items": { "$ref": "#/definitions/samplerecord" } }, { "$ref": "#/definitions/samplerecord" }, { "type": "string", "format": "uri" }, { "type": "array", "items": { "type": "string", "format": "uri" } }, { "type": "array", "items": { "$ref": "#/definitions/samplecollection" } }, { "$ref": "#/definitions/samplecollection" } ], "owl:cardinality": "many" }, "creditText": { "description": "Text that can be used to credit person(s) and/or organization(s) associated with a published Creative Work. For example, how a user should cite the dataset.", "type": "string", "owl:cardinality": "one" } }, "required": ["date", "funding", "distribution", "includedInDataCatalog", "measurementTechnique", "author", "description", "name", "url"], "recommended": ["citedBy", "doi", "infectiousAgent", "healthCondition", "species", "variableMeasured", "citation", "conditionsOfAccess", "dateCreated", "dateModified", "datePublished", "interactionStatistic", "isBasedOn", "keywords", "license", "sdPublisher", "spatialCoverage", "temporalCoverage", "usageInfo", "identifier", "topicCategory"], "optional": ["isRelatedTo", "isSimilarTo", "isBasisFor", "nctid", "abstract", "aggregateRating", "creator", "hasPart", "inLanguage", "isAccessibleForFree", "isPartOf", "version", "alternateName", "mainEntityOfPage", "sameAs", "relationship","sourceOrganization", "sample","creditText"], "definitions": { "citation": { "description": "A citation object for a resource which is cited by the dataset (ie- is a derivative of the dataset) , related to the dataset, or from which the dataset was based on (ie- is derived from).", "@type": "ScholarlyArticle", "type": "object", "properties": { "author": { "description": "Author(s) of the publication", "anyOf": [ { "type": "array", "items": { "$ref": "#/definitions/person" } }, { "$ref": "#/definitions/person" }, { "type": "array", "items": { "$ref": "#/definitions/organization" } }, { "$ref": "#/definitions/organization" } ] }, "abstract": { "description": "Abstract of the publication", "type": "string" }, "datePublished": { "description": "Date the article was published", "format": "date", "type": "string" }, "description": { "description": "Description of the publication", "type": "string" }, "name": { "description": "Title of the publication", "type": "string" }, "identifier": { "description": "An identifier associated with the citation such as a digital object identifier (DOI), PubMed ID (PMID), or PubMed Central ID (PMCID)", "type": "string" }, "pmid": { "description": "A PubMed identifier (PMID) of the referenced publication", "abstract": "PubMed identifier", "type": "string" }, "doi": { "description": "A digital object identifier (DOI) of the referenced publication", "abstract": "digital object identifier", "type": "string" }, "issueNumber": { "description": "Issue number where the article appears", "type": "string" }, "journalName": { "description": "Journal where the article appears", "type": "string" }, "journalNameAbbrev": { "description": "Abbreviated journal name where the article appears", "type": "string" }, "pagination": { "description": "Page numbers in the journal where the article appears", "type": "string" }, "url": { "description": "The url of the article", "type": "string", "format": "uri" }, "volumeNumber": { "description": "Volume of the journal where the article appears", "type": "string" }, "citation": { "description": "The bibliographic citation string for the article as is provided", "type": "string" } }, "required": ["name"], "recommended": ["author", "datePublished", "doi", "identifier", "journalName", "pmid", "url"], "optional": ["abstract", "citation", "description", "issueNumber", "journalNameAbbrev", "pagination", "volumeNumber"] }, "creativework": { "description": "A resource", "@type": "CreativeWork", "type": "object", "properties": { "author": { "description": "Author(s) of the referenced work", "anyOf": [ { "type": "array", "items": { "$ref": "#/definitions/person" } }, { "$ref": "#/definitions/person" }, { "type": "array", "items": { "$ref": "#/definitions/organization" } }, { "$ref": "#/definitions/organization" } ] }, "abstract": { "description": "Abstract of the referenced work", "type": "string" }, "datePublished": { "description": "Date the referenced work was published", "format": "date", "type": "string" }, "description": { "description": "Description of the referenced work", "type": "string" }, "hasPart": { "description": "A portion of the work", "oneOf": [ { "$ref": "#/definitions/citation" } ] }, "includedInDataCatalog": { "description": "Data or tool catalog which houses the work", "oneOf": [ { "$ref": "#/definitions/catalog" } ] }, "name": { "description": "Name or title", "type": "string" }, "identifier": { "description": "An identifier associated with the work", "type": "string" }, "relationship": { "description": "How the works are related", "type": "string" }, "doi": { "description": "A digital object identifier (DOI) of the referenced work", "abstract": "digital object identifier", "type": "string" }, "url": { "description": "The url of the work", "type": "string", "format": "uri" }, "citation": { "description": "The bibliographic citation for the referenced work as is provided", "type": "string" } }, "required": ["name"], "recommended": ["author", "datePublished", "doi", "identifier", "includedInDataCatalog", "relationship", "url"], "optional": ["abstract", "citation", "description", "hasPart"] }, "topic": { "description": "Topic assigned to the work.", "type": "string", "vocabulary": { "ontology": ["edam"], "children_of": ["http://edamontology.org/topic_0003"] }, "strict": true }, "catalog": { "@type": "DataCatalog", "description": "Data or tool catalog", "type": "object", "properties": { "name": { "description": "Data or tool catalog name", "type": "string" }, "url": { "description": "Link to data or tool catalog", "type": "string", "format": "uri" }, "versionDate": { "description": "date the metadata was harvested from the catalog", "type": "string", "format": "date" }, "archivedAt": { "description": "The url(s) of one or more datasets, tools, resources or other items listed in a DataCatalog or ResourceCatalog", "oneOf": [ { "items": { "type": "string", "format": "uri" }, "type": "array" }, { "type": "string", "format": "uri" } ] } }, "required": ["name", "url"], "recommended": ["versionDate", "archivedAt"] }, "organization": { "@type": "Organization", "description": "Reusable organization definition", "properties": { "affiliation": { "type": "object", "properties": { "name": { "description": "Name of the affiliation, such as a university", "type": "string" }, "sameAs": { "description": "Alias for the affiliation", "type": "string" }, "url": { "description": "URL of the affiliation", "type": "string", "format": "uri" } }, "required": ["name"], "optional": ["sameAs", "url"] }, "alternateName": { "description": "Alias of the name", "oneOf": [ { "type": "array", "items": { "type": "string" } }, { "type": "string" } ] }, "name": { "description": "Name of the organization", "type": "string" }, "parentOrganization": { "description": "Name of the parent organization. For instance, the parentOrganization of NIAID is the National Institutes of health (NIH)", "type": "string" }, "email": { "description": "Email address of the organization", "type": "string" }, "identifier": { "description": "Unique identifier of the organization", "type": "string" }, "role": { "description": "What role the organization played in creating the dataset", "type": "string" }, "url": { "description": "Link to the organization", "type": "string", "format": "uri" } }, "required": ["name"], "recommended": ["identifier"], "optional": ["affiliation", "alternateName", "email", "parentOrganization", "role", "url"], "type": "object" }, "researchproject": { "@type": "ResearchProject", "description": "a type of organization definition", "properties": { "alternateName": { "description": "Alias of the name", "oneOf": [ { "type": "array", "items": { "type": "string" } }, { "type": "string" } ] }, "name": { "description": "Name of the organization", "type": "string" }, "parentOrganization": { "description": "Name of the parent organization. For instance, the parentOrganization of NIAID is the National Institutes of health (NIH)", "type": "string" }, "email": { "description": "Email address of the organization", "type": "string" }, "identifier": { "description": "Unique identifier of the organization", "type": "string" }, "url": { "description": "Link to the organization", "type": "string", "format": "uri" } }, "required": ["name"], "recommended": ["identifier", "url", "parentOrganization"], "optional": ["alternateName", "email", "role"], "type": "object" }, "person": { "@type": "Person", "description": "Reusable person definition", "properties": { "affiliation": { "type": "object", "properties": { "name": { "description": "Name of the affiliation, such as a university", "type": "string" }, "sameAs": { "description": "Alias for the affiliation", "type": "string" }, "url": { "description": "URL of the affiliation", "type": "string", "format": "uri" } }, "required": ["name"], "optional": ["sameAs", "url"] }, "name": { "description": "Name of the person", "type": "string" }, "email": { "description": "Email address of the person", "type": "string" }, "familyName": { "description": "Family name (surname) of the person", "type": "string" }, "givenName": { "description": "Given (first) name of the person", "type": "string" }, "identifier": { "description": "Unique identifier of the person, like an ORCID ID", "type": "string" }, "role": { "description": "Role the person played in creating the dataset", "type": "string" }, "title": { "description": "Title of the person", "type": "string" }, "url": { "description": "Link to the homepage or other web content describing the person", "type": "string", "format": "uri" } }, "required": ["name"], "recommended": ["familyName", "givenName ", "identifier "], "optional": ["affiliation", "email", "role", "title", "url"], "type": "object" }, "definedterm": { "@type": "DefinedTerm", "type": "object", "properties": { "name": { "description": "The name 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 for more details.", "owl:cardinality": "one", "type": "string" }, "url": { "description": "URL of the item.", "owl:cardinality": "one", "type": "string", "format": "uri" }, "curatedBy": { "description": "The person, organization, or catalog that curated this DefinedTerm for the metadata property", "anyOf": [ { "$ref": "#/definitions/person" }, { "$ref": "#/definitions/organization" }, { "$ref": "#/definitions/catalog" }, { "$ref": "#/definitions/researchproject" }, { "$ref": "#/definitions/softwareapplication" } ] }, "termCode": { "description": "A code that identifies this DefinedTerm within a DefinedTermSet.", "type": "string" }, "description": { "description": "A description of the item.", "type": "string" }, "inDefinedTermSet": { "description": "A DefinedTermSet that contains this term.", "type": "string" }, "originalName": { "description": "The original name of the item, before any metadata standardization/normalization", "type": "string" }, "isCurated": { "description": "A boolean indicator describing whether or not this DefinedTerm was curated as the value of a property.", "type": "boolean" } }, "required": [] }, "softwareapplication": { "@type": "SoftwareApplication", "description": "Reusable software or algorithm definition", "properties": { "name": { "description": "name of the software, computational tool, or algorithm.", "type": "string" }, "dateModified": { "description": "date the software, computational tool, or algorithm was run", "type": "string", "format": "date" }, "url": { "description": "url of the software, computational tool, or algorithm", "type": "string", "format": "uri" } }, "required": ["name"], "recommended": ["url"], "optional": ["dateModified"], "type": "object" }, "samplerecord": { "@type": "Sample", "description": "reusable sample object", "type": "object", "properties": { "url": { "description": "Link to sample", "type": "string", "format": "uri" }, "identifier": { "description": "an identifier for the sample", "type": "string" }, "includedInDataCatalog": { "description": "Data or resource catalog where the sample is listed", "oneOf": [ { "$ref": "#/definitions/catalog" }, { "type": "array", "items": { "$ref": "#/definitions/catalog" } } ] }, "associatedPhenotype": { "description": "one or more observable traits or conditions relevant to the source of the sample.", "anyOf": [ { "description": "collection of vocabulary terms defined in ontologies", "strict": false, "type": "string", "vocabulary": { "children_of": ["http://purl.obolibrary.org/obo/UPHENO_0001001", "http://purl.obolibrary.org/obo/PATO_0000001"], "ontology": ["UPHENO","PATO"] } }, { "items": { "description": "collection of vocabulary terms defined in ontologies", "strict": false, "type": "string", "vocabulary": { "children_of": ["http://purl.obolibrary.org/obo/UPHENO_0001001", "http://purl.obolibrary.org/obo/PATO_0000001"], "ontology": ["UPHENO","PATO"] } }, "type": "array" }, { "type": "array", "items": { "$ref": "#/definitions/definedterm" } }, { "$ref": "#/definitions/definedterm" } ], "owl:cardinality": "many" }, "associatedGenotype": { "description": "One or more genetic variants or molecular features observed or inferred from the sample.", "anyOf": [ { "description": "collection of vocabulary terms defined in ontologies", "strict": false, "type": "string", "vocabulary": { "children_of": ["http://purl.obolibrary.org/obo/NCIT_C16612", "http://purl.obolibrary.org/obo/NCIT_C20181","http://purl.obolibrary.org/obo/NCIT_C17649"], "ontology": ["NCIT"] } }, { "items": { "description": "collection of vocabulary terms defined in ontologies", "strict": false, "type": "string", "vocabulary": { "children_of": ["http://purl.obolibrary.org/obo/NCIT_C16612", "http://purl.obolibrary.org/obo/NCIT_C20181","http://purl.obolibrary.org/obo/NCIT_C17649"], "ontology": ["NCIT"] } }, "type": "array" }, { "type": "array", "items": { "$ref": "#/definitions/definedterm" } }, { "$ref": "#/definitions/definedterm" } ], "owl:cardinality": "many" }, "cellType": { "description": "The type of cell represented in or derived from the biological sample, based on morphology, lineage, or molecular markers.", "anyOf": [ { "description": "collection of vocabulary terms defined in ontologies", "strict": false, "type": "string", "vocabulary": { "children_of": ["http://purl.obolibrary.org/obo/CL_0000000", "http://purl.obolibrary.org/obo/CLO_0000031"], "ontology": ["CL","CLO"] } }, { "items": { "description": "collection of vocabulary terms defined in ontologies", "strict": false, "type": "string", "vocabulary": { "children_of": ["http://purl.obolibrary.org/obo/CL_0000000", "http://purl.obolibrary.org/obo/CLO_0000031"], "ontology": ["CL","CLO"] } }, "type": "array" }, { "type": "array", "items": { "$ref": "#/definitions/definedterm" } }, { "$ref": "#/definitions/definedterm" } ], "owl:cardinality": "many" }, "anatomicalSystem": { "description": "Indicate the anatomical system from which the sample is collect, e.g. circulatory, digestive, endocrine, immune and other systems.", "anyOf": [ { "description": "collection of vocabulary terms defined in ontologies", "strict": false, "type": "string", "vocabulary": { "children_of": ["http://purl.obolibrary.org/obo/UBERON_0000467"], "ontology": ["UBERON"] } }, { "items": { "description": "collection of vocabulary terms defined in ontologies", "strict": false, "type": "string", "vocabulary": { "children_of": ["http://purl.obolibrary.org/obo/UBERON_0000467"], "ontology": ["UBERON"] } }, "type": "array" }, { "type": "array", "items": { "$ref": "#/definitions/definedterm" } }, { "$ref": "#/definitions/definedterm" } ], "owl:cardinality": "many" }, "anatomicalStructure": { "description": "Indicate the organ, tissues the sample was collected from.", "anyOf": [ { "description": "collection of vocabulary terms defined in ontologies", "strict": false, "type": "string", "vocabulary": { "children_of": ["http://purl.obolibrary.org/obo/UBERON_0001062"], "ontology": ["UBERON"] } }, { "items": { "description": "collection of vocabulary terms defined in ontologies", "strict": false, "type": "string", "vocabulary": { "children_of": ["http://purl.obolibrary.org/obo/UBERON_0001062"], "ontology": ["UBERON"] } }, "type": "array" }, { "type": "array", "items": { "$ref": "#/definitions/definedterm" } }, { "$ref": "#/definitions/definedterm" } ], "owl:cardinality": "many" }, "sex": { "description": "The biological sex of the individual from which the sample was obtained.", "anyOf": [ { "description": "collection of vocabulary terms defined in ontologies", "strict": false, "type": "string", "vocabulary": { "children_of": ["http://purl.obolibrary.org/obo/PATO_0000047"], "ontology": ["PATO"] } }, { "items": { "description": "collection of vocabulary terms defined in ontologies", "strict": false, "type": "string", "vocabulary": { "children_of": ["http://purl.obolibrary.org/obo/PATO_0000047"], "ontology": ["PATO"] } }, "type": "array" }, { "type": "array", "items": { "$ref": "#/definitions/definedterm" } }, { "$ref": "#/definitions/definedterm" } ], "owl:cardinality": "many" }, "developmentalStage": { "description": "A temporal subdivision of a developmental process, indicating the age or stage of the object when the sample was created.", "anyOf": [ { "description": "collection of vocabulary terms defined in ontologies", "strict": false, "type": "string", "vocabulary": { "children_of": ["http://purl.obolibrary.org/obo/UBERON_0000104","http://purl.obolibrary.org/obo/NCIT_C48308"], "ontology": ["UBERON","NCIT"] } }, { "items": { "description": "collection of vocabulary terms defined in ontologies", "strict": false, "type": "string", "vocabulary": { "children_of": ["http://purl.obolibrary.org/obo/UBERON_0000104","http://purl.obolibrary.org/obo/NCIT_C48308"], "ontology": ["UBERON","NCIT"] } }, "type": "array" }, { "type": "array", "items": { "$ref": "#/definitions/definedterm" } }, { "$ref": "#/definitions/definedterm" }, { "type": "array", "items": { "$ref": "#/definitions/quantitativevalue" } }, { "$ref": "#/definitions/quantitativevalue" } ], "owl:cardinality": "many" }, "sampleAvailability": { "description": "A flag to signal that the sample is available for reuse.", "abstract": "availability of the sample", "type": "boolean", "owl:cardinality": "one" }, "sampleQuantity": { "description": "A numeric value for a measurement of the size of a sample. If completely unknown, set value = 0, and unitText = 'unknown'", "oneOf": [ { "type": "array", "items": { "$ref": "#/definitions/quantitativevalue" } }, { "$ref": "#/definitions/quantitativevalue" } ], "owl:cardinality": "many" }, "sampleType": { "description": "The type of sample or specimen.", "anyOf": [ { "description": "collection of vocabulary terms defined in ontologies", "strict": false, "type": "string", "vocabulary": { "children_of": ["http://purl.obolibrary.org/obo/BFO_0000040"], "ontology": ["OBI"] } }, { "items": { "description": "collection of vocabulary terms defined in ontologies", "strict": false, "type": "string", "vocabulary": { "children_of": ["http://purl.obolibrary.org/obo/BFO_0000040"], "ontology": ["OBI"] } }, "type": "array" }, { "type": "array", "items": { "$ref": "#/definitions/definedterm" } }, { "$ref": "#/definitions/definedterm" } ], "owl:cardinality": "many" } }, "recommended": ["url", "identifier", "includedInDataCatalog", "associatedPhenotype", "associatedGenotype", "cellType", "sampleType", "anatomicalSystem", "anatomicalStructure", "sex", "developmentalStage", "sampleAvailability", "sampleQuantity"] }, "samplecollection": { "@type": "SampleCollection", "description": "reusable sampleCollection object", "type": "object", "properties": { "url": { "description": "Link to sample", "type": "string", "format": "uri" }, "identifier": { "description": "an identifier for the sample", "type": "string" }, "includedInDataCatalog": { "description": "Data or resource catalog where the sample is listed", "oneOf": [ { "$ref": "#/definitions/catalog" }, { "type": "array", "items": { "$ref": "#/definitions/catalog" } } ] }, "aggregateElement": { "description": "Aggregate information about the samples in the Sample Collection formatted as a sample object.", "oneOf": [ { "$ref": "#/definitions/samplerecord" }, { "type": "array", "items": { "$ref": "#/definitions/samplerecord" } } ] }, "itemListElement": { "description": "Samples listed in the sample collection", "oneOf": [ { "$ref": "#/definitions/minsampleinfo" }, { "type": "array", "items": { "$ref": "#/definitions/minsampleinfo" } } ] }, "numberOfItems": { "description": "The number of sample records in the sample collection. Min/max estimates can be used in lieu of actual number. If completely unknown, set value = 0, and unitText = 'unknown'", "anyOf": [ { "type": "array", "items": { "$ref": "#/definitions/propertyvalue" } }, { "$ref": "#/definitions/propertyvalue" }, { "type": "array", "items": { "$ref": "#/definitions/quantitativevalue" } }, { "$ref": "#/definitions/quantitativevalue" } ], "owl:cardinality": "many" } }, "recommended": ["url", "identifier", "includedInDataCatalog", "aggregateElement","itemListElement","numberOfItems"] }, "minsampleinfo": { "@type": "Sample", "description": "reusable sample object", "type": "object", "properties": { "url": { "description": "Link to sample", "type": "string", "format": "uri" }, "identifier": { "description": "an identifier for the sample", "type": "string" }, "includedInDataCatalog": { "description": "Data or resource catalog where the sample is listed", "oneOf": [ { "$ref": "#/definitions/catalog" }, { "type": "array", "items": { "$ref": "#/definitions/catalog" } } ] } }, "recommended": ["url", "identifier", "includedInDataCatalog"] }, "quantitativevalue": { "@type": "QuantitativeValue", "description": "A numeric value and unit for a property with potentially different units", "type": "object", "properties": { "value": { "description": "A numeric value for the property", "type": "number" }, "maxValue": { "description": "An estimated maximum numberic value if the actual value is not known. Ignore if actual numeric value is known.", "type": "number" }, "minValue": { "description": "An estimated minumum numeric value if the actual value is not known. Ignore if actual numeric value is known.", "type": "number" }, "unitText": { "description": "A unit associated with the value. E.g.- 'records' for the number of records in a database.", "type": "string" } }, "required" : ["unitText"], "recommended": ["value"], "optional": ["maxValue","minValue"] }, "propertyvalue": { "@type": "PropertyValue", "description": "A numeric value and unit for a property with potentially different units", "type": "object", "properties": { "value": { "description": "A numeric value for the property", "type": "number" }, "maxValue": { "description": "An estimated maximum numberic value if the actual value is not known. Ignore if actual numeric value is known.", "type": "number" }, "minValue": { "description": "An estimated minumum numeric value if the actual value is not known. Ignore if actual numeric value is known.", "type": "number" }, "unitText": { "description": "A unit associated with the value. E.g.- 'records' for the number of records in a database.", "type": "string" }, "propertyID": { "description": "A commonly used identifier for the characteristic represented by the property, e.g. a manufacturer or a standard code for a property. propertyID can be (1) a prefixed string, mainly meant to be used with standards for product properties; (2) a site-specific, non-prefixed string (e.g. the primary key of the property or the vendor-specific ID of the property), or (3) a URL indicating the type of the property, either pointing to an external vocabulary, or a Web resource that describes the property (e.g. a glossary entry). Standards bodies should promote a standard prefix for the identifiers of properties from their standards.", "oneOf": [ {"type": "string"}, { "type": "string", "format": "uri" } ] } }, "required" : ["unitText"], "recommended": ["value","propertyID"], "optional": ["maxValue","minValue"] } } } }, { "@id": "nde:ComputationalTool", "@type": "rdfs:Class", "rdfs:comment": "ComputationalTools (software, workflows, computational tools, code) contained in the NIAID Data Ecosystem. The NIAID Data Ecosystem is a secure environment to find, access and analyze immune-mediated and infectious disease data and computational tools to speed the development of diagnostics, therapeutics, and vaccines. The NIAID Data Ecosystem Discovery Portal harvests metadata from dataset repository and harmonizes them to this schema to enable easy cross-platform dataset searching and filtering.", "abstract": "ComputationalTools (software, workflows, computational tools, code) contained in the NIAID Data Ecosystem.", "rdfs:label": "ComputationalTool", "rdfs:subClassOf": { "@id": "niaid:ComputationalTool" }, "schema:schemaVersion":["https://schema.org/docs/releases.html#v18.0","v1.9 - 2025.09.03"], "dct:provenance":"Changes since previous version: Update 'citation' and 'citedBy' descriptions. Added the creditText property as optional.", "$validation": { "$schema": "http://json-schema.org/draft-07/schema#", "type": "object", "properties": { "citedBy": { "description": "Publications, datasets, or computational tools that cite the work. Examples: a publication which uses the tool on a new dataset. For the primary publication, use the 'citation' property.", "anyOf": [ { "type": "array", "items": { "$ref": "#/definitions/citation" } }, { "$ref": "#/definitions/citation" }, { "type": "array", "items": { "$ref": "#/definitions/creativework" } }, { "$ref": "#/definitions/creativework" } ], "owl:cardinality": "many" }, "date": { "description": "Date the work has changed: most recent date of dateModified, datePublished, and dateCreated.", "abstract": "date changed", "owl:cardinality": "one", "format": "date", "type": "string" }, "doi": { "description": "Digital object identifier (DOI) for the work, not any associated publications.", "abstract": "digital object identifier", "owl:cardinality": "one", "type": "string" }, "includedInDataCatalog": { "description": "Data or tool catalog where the work is published; original source of the metadata.", "abstract": "catalog containing the work", "$ref": "#/definitions/catalog" }, "isBasisFor": { "description": "A computational tool which reuses the computational tool.", "owl:cardinality": "many", "anyOf": [ { "type": "array", "items": { "$ref": "#/definitions/citation" } }, { "$ref": "#/definitions/citation" }, { "type": "array", "items": { "$ref": "#/definitions/creativework" } }, { "$ref": "#/definitions/creativework" } ] }, "isRelatedTo": { "description": "Computational tools which are related to the given computational tool. These linkages are created via human curation.", "abstract": "related records (via curation)", "anyOf": [ { "type": "array", "items": { "$ref": "#/definitions/citation" } }, { "$ref": "#/definitions/citation" }, { "type": "array", "items": { "$ref": "#/definitions/creativework" } }, { "$ref": "#/definitions/creativework" } ], "owl:cardinality": "many" }, "isSimilarTo": { "description": "Datasets or computational tools which are similar to the work, based on terms in the names, descriptions, authors, measurementTechniques, infectiousAgents, healthConditions, etc.", "abstract": "similar records (auto-assigned)", "anyOf": [ { "type": "array", "items": { "$ref": "#/definitions/citation" } }, { "$ref": "#/definitions/citation" }, { "type": "array", "items": { "$ref": "#/definitions/creativework" } }, { "$ref": "#/definitions/creativework" } ], "owl:cardinality": "many" }, "topicCategory": { "description": "Topic of the work. This topic may be assigned by a human curator or through automated algorithms.", "abstract": "topic", "anyOf": [ { "type": "array", "items": { "$ref": "#/definitions/topic" } }, { "$ref": "#/definitions/topic" }, { "type": "array", "items": { "$ref": "#/definitions/definedterm" } }, { "$ref": "#/definitions/definedterm" } ], "owl:cardinality": "many" }, "infectiousAgent": { "description": "Infectious agent(s) / pathogen(s) which are the focus of the work (like SARS-CoV-2).", "abstract": "infectious agent / pathogen", "anyOf": [ { "description": "collection of vocabulary terms defined in ontologies", "strict": false, "type": "string", "vocabulary": { "children_of": ["http://purl.obolibrary.org/obo/NCBITaxon_10239", "http://purl.obolibrary.org/obo/NCBITaxon_2"], "ontology": ["ncbitaxon"] } }, { "items": { "description": "collection of vocabulary terms defined in ontologies", "strict": false, "type": "string", "vocabulary": { "children_of": ["http://purl.obolibrary.org/obo/NCBITaxon_10239", "http://purl.obolibrary.org/obo/NCBITaxon_2"], "ontology": ["ncbitaxon"] } }, "type": "array" }, { "type": "array", "items": { "$ref": "#/definitions/definedterm" } }, { "$ref": "#/definitions/definedterm" } ], "owl:cardinality": "many" }, "healthCondition": { "description": "The health condition(s) /infectious disease(s) which are the focus of the work (like COVID-19, coronavirus).", "abstract": "health condition/disease", "anyOf": [ { "description": "collection of vocabulary terms defined in ontologies", "strict": false, "type": "string", "vocabulary": { "children_of": ["http://purl.obolibrary.org/obo/MONDO_0000001", "http://purl.obolibrary.org/obo/DOID_4", "http://purl.obolibrary.org/obo/HP_0000001", "http://purl.obolibrary.org/obo/NCIT_C7057"], "ontology": ["mondo","hpo","doid","ncit"] } }, { "items": { "description": "collection of vocabulary terms defined in ontologies", "strict": false, "type": "string", "vocabulary": { "children_of": ["http://purl.obolibrary.org/obo/MONDO_0000001", "http://purl.obolibrary.org/obo/DOID_4", "http://purl.obolibrary.org/obo/HP_0000001", "http://purl.obolibrary.org/obo/NCIT_C7057"], "ontology": ["mondo","hpo","doid","ncit"] } }, "type": "array" }, { "type": "array", "items": { "$ref": "#/definitions/definedterm" } }, { "$ref": "#/definitions/definedterm" } ], "owl:cardinality": "many" }, "funding": { "description": "Funding that supports (sponsors) the development of this computational tool through some kind of financial contribution.", "abstract": "funding source (grant, contract, etc.)", "oneOf": [ { "type": "object", "@type": "MonetaryGrant", "description": "Funding that supports (sponsors) the development of this computational tool through some kind of financial contribution", "properties": { "funder": { "description": "An organization associated with a creator or funder of a computational tool", "oneOf": [ { "type": "object", "@type": "Organization", "description": "Information about a single funder", "properties": { "name": { "type": "string", "description": "An organization associated with a creator or funder of a computational tool" }, "parentOrganization": { "type": "string", "description": "name of the parent funding organization" } }, "required": [ "name" ] }, { "type": "array", "items": { "type": "object", "@type": "Organization", "description": "Information about a single funder", "properties": { "name": { "type": "string", "description": "An organization associated with a creator or funder of a computational tool" }, "parentOrganization": { "type": "string", "description": "name of the parent funding organization" } }, "required": [ "name" ] } } ] }, "description": { "type": "string", "description": "description about the funding award / grant" }, "url": { "type": "string", "description": "award / grant URL" }, "identifier": { "type": "string", "description": "Unique identifier(s) for the grant(s) used to fund the development of this computational tool" } }, "required": [ "funder", "identifier" ] }, { "type": "array", "items": { "type": "object", "@type": "MonetaryGrant", "description": "Funding that supports (sponsors) the development of this computational tool through some kind of financial contribution", "properties": { "funder": { "description": "An organization associated with a creator or funder of a computational tool", "oneOf": [ { "type": "object", "@type": "Organization", "description": "Information about a single funder", "properties": { "name": { "type": "string", "description": "An organization associated with a creator or funder of a computational tool" }, "parentOrganization": { "type": "string", "description": "name of the parent funding organization" } }, "required": [ "name" ] }, { "type": "array", "items": { "type": "object", "@type": "Organization", "description": "Information about a single funder", "properties": { "name": { "type": "string", "description": "An organization associated with a creator or funder of a computational tool" }, "parentOrganization": { "type": "string", "description": "name of the parent funding organization" } }, "required": [ "name" ] } } ] }, "description": { "type": "string", "description": "description about the funding award / grant" }, "url": { "type": "string", "description": "award / grant URL" }, "identifier": { "type": "string", "description": "Unique identifier(s) for the grant(s) used to fund the development of this computational tool" } }, "required": [ "funder", "identifier" ] } } ], "owl:cardinality": "many" }, "species": { "description": "Species / host organism from which the dataset has been collected.", "abstract": "species/host organism", "anyOf": [ { "description": "collection of vocabulary terms defined in ontologies", "strict": false, "type": "string", "vocabulary": { "children_of": ["http://purl.obolibrary.org/obo/NCBITaxon_131567", "http://purl.obolibrary.org/obo/NCBITaxon_10239"], "ontology": ["ncbitaxon"] } }, { "items": { "description": "collection of vocabulary terms defined in ontologies", "strict": false, "type": "string", "vocabulary": { "children_of": ["http://purl.obolibrary.org/obo/NCBITaxon_131567", "http://purl.obolibrary.org/obo/NCBITaxon_10239"], "ontology": ["ncbitaxon"] } }, "type": "array" }, { "type": "array", "items": { "$ref": "#/definitions/definedterm" } }, { "$ref": "#/definitions/definedterm" } ], "owl:cardinality": "many" }, "availableOnDevice": { "description": "Device or platform required to run the application, such as Bioconda, Docker, or Singularity.", "abstract": "platform to run the application", "owl:cardinality": "many", "oneOf": [ { "items": { "type": "string" }, "type": "array" }, { "type": "string" } ] }, "codeRepository": { "description": "Link to the source code repository of the tool such as GitHub.", "abstract": "source code link", "oneOf": [ { "format": "uri", "type": "string" }, { "items": { "format": "uri", "type": "string" }, "type": "array" } ], "owl:cardinality": "many" }, "programmingLanguage": { "description": "The main programming language(s) used to build or execute the tool.", "abstract": "programming language", "oneOf": [ { "type": "string" }, { "items": { "type": "string" }, "type": "array" } ], "owl:cardinality": "many" }, "input": { "description": "software input, such as a file or parameter.", "abstract": "input file/parameter", "owl:cardinality": "many", "anyOf": [ { "type": "array", "items": { "$ref": "#/definitions/formalparameter" } }, { "$ref": "#/definitions/formalparameter" }, { "type": "array", "items": { "$ref": "#/definitions/definedterm" } }, { "$ref": "#/definitions/definedterm" } ] }, "output": { "description": "Output of the computational tool.", "owl:cardinality": "many", "anyOf": [ { "type": "array", "items": { "$ref": "#/definitions/formalparameter" } }, { "$ref": "#/definitions/formalparameter" }, { "type": "array", "items": { "$ref": "#/definitions/definedterm" } }, { "$ref": "#/definitions/definedterm" } ] }, "applicationCategory": { "description": "Type of software application, e.g. 'Command-line tool', 'Database portal', 'Desktop application', 'Library', 'Ontology', 'Plug-in', 'Script', 'SPARQL endpoint', 'Suite', 'Web application', 'Web API', 'Web service', 'Workbench', 'Workflow'.", "abstract": "type of software application", "anyOf": [ { "type": "string" }, { "items": { "type": "string" }, "type": "array" }, { "type": "array", "items": { "$ref": "#/definitions/definedterm" } }, { "$ref": "#/definitions/definedterm" } ], "owl:cardinality": "many" }, "applicationSubCategory": { "description": "A subcategory of the computational tool, like gene regulation.", "abstract": "software subcategory", "anyOf": [ { "@type": "DefinedTerm", "strict": false, "type": "object", "vocabulary": { "children_of": ["http://edamontology.org/topic_3361"], "ontology": ["edam"], "property": { "identifier": { "type": "string" }, "name": { "type": "string", "description": "Subcategory of the tool (ex: cytometry)" }, "url": { "format": "uri", "type": "string" } } } }, { "items": { "@type": "DefinedTerm", "strict": false, "type": "object", "vocabulary": { "children_of": ["http://edamontology.org/topic_3361"], "ontology": ["edam"], "property": { "identifier": { "type": "string" }, "name": { "type": "string", "description": "Subcategory of the tool (ex: cytometry)" }, "url": { "format": "uri", "type": "string" } } } }, "type": "array" }, { "type": "array", "items": { "$ref": "#/definitions/definedterm" } }, { "$ref": "#/definitions/definedterm" }, { "type": "string" }, { "type": "array", "items": { "type": "string" } } ], "owl:cardinality": "many" }, "applicationSuite": { "description": "The name of the application suite to which the application belongs (e.g. Excel belongs to Office).", "abstract": "software suite for the tool", "owl:cardinality": "many", "oneOf": [ { "type": "array", "items": { "type": "string" } }, { "type": "string" } ] }, "downloadUrl": { "description": "URL to download the computational tool.", "owl:cardinality": "many", "oneOf": [ { "items": { "type": "string", "format": "uri" }, "type": "array" }, { "type": "string", "format": "uri" } ] }, "featureList": { "description": "Features or modules provided by this application (and possibly required by other applications).", "abstract": "features of the tool", "anyOf": [ { "@type": "DefinedTerm", "strict": false, "type": "object", "vocabulary": { "children_of": ["http://edamontology.org/operation_0004"], "ontology": ["edam"], "property": { "identifier": { "type": "string" }, "name": { "type": "string" }, "url": { "format": "uri", "type": "string" } } } }, { "items": { "@type": "DefinedTerm", "strict": false, "type": "object", "vocabulary": { "children_of": ["http://edamontology.org/operation_0004"], "ontology": ["edam"], "property": { "identifier": { "type": "string" }, "name": { "type": "string" }, "url": { "format": "uri", "type": "string" } } } }, "type": "array" }, { "format": "uri", "type": "string" }, { "items": { "format": "uri", "type": "string" }, "type": "array" } ], "owl:cardinality": "many" }, "operatingSystem": { "description": "Operating systems supported (Windows 7, OSX 10.6, Android 1.6).", "abstract": "operative systems supported", "owl:cardinality": "many", "oneOf": [ { "type": "string" }, { "type": "array", "items": { "type": "string" } } ] }, "processorRequirements": { "description": "Processor architecture required to run the application (e.g. IA64).", "abstract": "processor requirements", "owl:cardinality": "many", "oneOf": [ { "type": "string" }, { "type": "array", "items": { "type": "string" } } ] }, "softwareAddOn": { "description": "Additional content for a software application.", "owl:cardinality": "many", "oneOf": [ { "type": "array", "items": { "$ref": "#/definitions/creativework" } }, { "$ref": "#/definitions/creativework" } ] }, "softwareHelp": { "description": "URL to access software application help.", "oneOf": [ { "@type": "CreativeWork", "properties": { "url": { "format": "uri", "type": "string" } }, "type": "object" }, { "items": { "@type": "CreativeWork", "properties": { "url": { "format": "uri", "type": "string" } }, "type": "object" }, "type": "array" } ], "owl:cardinality": "many" }, "softwareRequirements": { "description": "Component dependency requirements for application. This includes runtime environments and shared libraries that are not included in the application distribution package, but required to run the application (Examples: DirectX, Java or .NET runtime).", "abstract": "requirements of tool", "owl:cardinality": "many", "oneOf": [ { "type": "array", "items": { "type": "string" } }, { "type": "string" } ] }, "softwareVersion": { "description": "Software version.", "type": "string", "owl:cardinality": "one" }, "aggregateRating": { "description": "The overall rating, based on a collection of reviews or ratings, of the work. These ratings can be collected based on user reviews or through Altmetric scores of web-based citations.", "abstract": "rating of the work", "oneOf": [ { "items": { "@type": "AggregateRating", "type": "object", "properties": { "ratingCount": { "description": "Total number of ratings", "type": "integer" }, "ratingValue": { "description": "Average rating", "type": "string" }, "itemReviewed": { "description": "What is being reviewed", "type": "string" } }, "required": ["ratingValue"], "recommended": ["ratingCount", "itemReviewed"] }, "type": "array" }, { "@type": "AggregateRating", "type": "object", "properties": { "ratingCount": { "description": "Total number of ratings", "type": "integer" }, "ratingValue": { "description": "Average rating", "type": "string" }, "itemReviewed": { "description": "What is being reviewed", "type": "string" } }, "required": ["ratingValue"], "recommended": ["ratingCount", "itemReviewed"] } ], "owl:cardinality": "many" }, "author": { "description": "Author or creator of the work. The default field for the author or creator of the work.", "anyOf": [ { "type": "array", "items": { "$ref": "#/definitions/person" } }, { "$ref": "#/definitions/person" }, { "type": "array", "items": { "$ref": "#/definitions/organization" } }, { "$ref": "#/definitions/organization" } ], "owl:cardinality": "many" }, "citation": { "description": "The primary citation or reference about the computational tool. Examples: a publication which describes the development, features and/or application of the tool. The original reference by the tool developers/maintainers that should be cited when reusing the tool. For other references to the tool, use 'citedBy'. ", "abstract": "citation to the work", "anyOf": [ { "type": "array", "items": { "$ref": "#/definitions/citation" } }, { "$ref": "#/definitions/citation" }, { "type": "array", "items": { "$ref": "#/definitions/creativework" } }, { "$ref": "#/definitions/creativework" } ], "owl:cardinality": "many" }, "conditionsOfAccess": { "description": "Conditions that affect the availability of, or method(s) of access to, the work. Options include open (freely available), restricted (may include restrictions such as on use), closed (requires registration to access), or embargoed (unpublished).", "abstract": "accessibility of the work", "owl:cardinality": "one", "type": "string", "enum": ["Closed", "Open", "Restricted", "Embargoed"] }, "contributor": { "description": "A secondary contributor to the developement or maintenance of the computational tool.", "abstract": "contributor to development or maintenance", "oneOf": [ { "type": "array", "items": { "$ref": "#/definitions/person" } }, { "type": "array", "items": { "$ref": "#/definitions/organization" } } ], "owl:cardinality": "many" }, "creator": { "description": "The creator/author of this work; equivalent to author. Please use author by default. Use creator if author/creator in a record of this work submitted elsewhere differs from the author/creator entered into the author field.", "anyOf": [ { "type": "array", "items": { "$ref": "#/definitions/person" } }, { "$ref": "#/definitions/person" }, { "type": "array", "items": { "$ref": "#/definitions/organization" } }, { "$ref": "#/definitions/organization" } ], "owl:cardinality": "many" }, "dateCreated": { "description": "Date the work was created.", "owl:cardinality": "one", "format": "date", "type": "string" }, "dateModified": { "description": "Date the work was modified.", "format": "date", "owl:cardinality": "one", "type": "string" }, "datePublished": { "description": "Date the work was first published.", "owl:cardinality": "one", "format": "date", "type": "string" }, "discussionUrl": { "description": "A link to a webpage containing the comments about the computational tool.", "abstract": "link to tool discussion page", "owl:cardinality": "many", "type": "string", "format": "uri" }, "hasPart": { "description": "An item that is part of this computational tool.", "anyOf": [ { "type": "array", "items": { "$ref": "#/definitions/citation" } }, { "$ref": "#/definitions/citation" }, { "type": "array", "items": { "$ref": "#/definitions/creativework" } }, { "$ref": "#/definitions/creativework" } ], "owl:cardinality": "many" }, "inLanguage": { "description": "The language of the computational tool (not programming language).", "owl:cardinality": "many", "oneOf": [ { "items": { "type": "object", "properties": { "name": { "type": "string", "description": "language of the work" }, "alternateName": { "type": "string" } }, "required": ["name"], "recommended": ["alternateName"] }, "type": "array" }, { "type": "object", "properties": { "name": { "type": "string", "description": "language of the work" }, "alternateName": { "type": "string" } }, "required": ["name"], "recommended": ["alternateName"] } ] }, "interactionStatistic": { "description": "The number of interactions with the work, such as page views or tool downloads.", "abstract": "views or downloads", "owl:cardinality": "many", "oneOf": [ { "items": { "@type": "InteractionCounter", "type": "object", "properties": { "interactionType": { "type": "string" }, "userInteractionCount": { "type": "integer" } }, "required": ["interactionType", "userInteractionCount"] }, "type": "array" }, { "@type": "InteractionCounter", "type": "object", "properties": { "interactionType": { "type": "string" }, "userInteractionCount": { "type": "integer" } }, "required": ["interactionType", "userInteractionCount"] } ] }, "isAccessibleForFree": { "description": "A flag to signal that the work is accessible for free.", "abstract": "accessible without charge", "owl:cardinality": "one", "type": "boolean" }, "isBasedOn": { "description": "A dataset, publication, or computational tool from which this work is derived, modified, or adapted.", "abstract": "dataset, publication, or tool used to create the work", "anyOf": [ { "type": "array", "items": { "$ref": "#/definitions/citation" } }, { "$ref": "#/definitions/citation" }, { "type": "array", "items": { "$ref": "#/definitions/creativework" } }, { "$ref": "#/definitions/creativework" } ], "owl:cardinality": "many" }, "isPartOf": { "description": "Indicates a broader study, project, or collection the work is part of.", "abstract": "study or project including the work", "anyOf": [ { "type": "array", "items": { "$ref": "#/definitions/citation" } }, { "$ref": "#/definitions/citation" }, { "type": "array", "items": { "$ref": "#/definitions/creativework" } }, { "$ref": "#/definitions/creativework" } ], "owl:cardinality": "many" }, "keywords": { "description": "Keywords or tags used to describe this work.", "abstract": "keywords or tags", "oneOf": [ { "type": "array", "items": { "type": "string" } }, { "type": "string" } ] }, "license": { "description": "A license document that applies to this work, typically indicated by URL.", "abstract": "license for use", "format": "uri", "owl:cardinality": "one", "type": "string" }, "sdPublisher": { "description": "Original publisher of the computational tool metadata (like GitHub, Dockstore, etc.).", "abstract": "original metadata source", "oneOf": [ { "$ref": "#/definitions/catalog" }, { "type": "array", "items": { "$ref": "#/definitions/catalog" } } ], "owl:cardinality": "many" }, "thumbnailUrl": { "description": "A thumbnail image of the computational tool.", "owl:cardinality": "many", "type": "string", "format": "uri" }, "description": { "description": "A description of the computational tool.", "owl:cardinality": "one", "type": "string" }, "identifier": { "description": "Identifier for the computational tool.", "owl:cardinality": "many", "oneOf": [ { "type": "string" }, { "type": "array", "items": { "type": "string" } } ] }, "mainEntityOfPage": { "description": "Website which describes the work and provides additional details.", "abstract": "associated webpage", "owl:cardinality": "many", "oneOf": [ { "items": { "type": "string", "format": "uri" }, "type": "array" }, { "type": "string", "format": "uri" } ] }, "name": { "description": "Computational tool name.", "owl:cardinality": "one", "type": "string" }, "sameAs": { "description": "URL of additional sources for the work.", "owl:cardinality": "many", "oneOf": [ { "items": { "type": "string", "format": "uri" }, "type": "array" }, { "type": "string", "format": "uri" } ] }, "url": { "description": "URL of the work.", "format": "uri", "owl:cardinality": "one", "type": "string" }, "sourceOrganization": { "description": "The organization, research project, working group, or funded program on whose behalf the author/creator was working.", "anyOf": [ { "type": "array", "items": { "$ref": "#/definitions/researchproject" } }, { "$ref": "#/definitions/researchproject" }, { "type": "array", "items": { "$ref": "#/definitions/organization" } }, { "$ref": "#/definitions/organization" } ], "owl:cardinality": "many" }, "creditText": { "description": "Text that can be used to credit person(s) and/or organization(s) associated with a published Creative Work. For example, how a user should cite the tool.", "type": "string", "owl:cardinality": "one" } }, "required": ["date", "includedInDataCatalog", "funding", "author", "description", "name"], "recommended": ["citedBy", "doi", "topicCategory", "codeRepository", "programmingLanguage", "applicationCategory", "applicationSubCategory", "input", "output", "featureList", "operatingSystem", "softwareRequirements", "softwareVersion", "citation", "conditionsOfAccess", "dateModified", "interactionStatistic", "license", "identifier", "url"], "optional": ["isBasisFor", "isRelatedTo", "isSimilarTo", "infectiousAgent", "healthCondition", "species", "applicationSuite", "availableOnDevice", "downloadUrl", "processorRequirements", "softwareAddOn", "softwareHelp", "aggregateRating", "contributor", "creator", "dateCreated", "datePublished", "discussionUrl", "hasPart", "inLanguage", "isAccessibleForFree", "isBasedOn", "isPartOf", "keywords", "provider", "sdPublisher", "thumbnailUrl", "mainEntityOfPage", "sameAs","sourceOrganization", "creditText"], "definitions": { "citation": { "description": "A citation object for a resource which is cited by the dataset (ie- is a derivative of the dataset) , related to the dataset, or from which the dataset was based on (ie- is derived from).", "@type": "ScholarlyArticle", "type": "object", "properties": { "author": { "description": "Author(s) of the publication", "anyOf": [ { "type": "array", "items": { "$ref": "#/definitions/person" } }, { "$ref": "#/definitions/person" }, { "type": "array", "items": { "$ref": "#/definitions/organization" } }, { "$ref": "#/definitions/organization" } ] }, "abstract": { "description": "Abstract of the publication", "type": "string" }, "datePublished": { "description": "Date the article was published", "format": "date", "type": "string" }, "description": { "description": "Description of the publication", "type": "string" }, "name": { "description": "Title of the publication", "type": "string" }, "identifier": { "description": "An identifier associated with the citation such as a digital object identifier (DOI), PubMed ID (PMID), or PubMed Central ID (PMCID)", "type": "string" }, "pmid": { "description": "A PubMed identifier (PMID) of the referenced publication", "abstract": "PubMed identifier", "type": "string" }, "doi": { "description": "A digital object identifier (DOI) of the referenced publication", "abstract": "digital object identifier", "type": "string" }, "issueNumber": { "description": "Issue number where the article appears", "type": "string" }, "journalName": { "description": "Journal where the article appears", "type": "string" }, "journalNameAbbrev": { "description": "Abbreviated journal name where the article appears", "type": "string" }, "pagination": { "description": "Page numbers in the journal where the article appears", "type": "string" }, "url": { "description": "The url of the arrticle", "type": "string", "format": "uri" }, "volumeNumber": { "description": "Volume of the journal where the article appears", "type": "string" }, "citation": { "description": "The bibliographic citation string for the article as is provided", "type": "string" } }, "required": ["name"], "recommended": ["author", "datePublished", "doi", "identifier", "journalName", "pmid", "url"], "optional": ["abstract", "citation", "description", "issueNumber", "journalNameAbbrev", "pagination", "volumeNumber"] }, "catalog": { "@type": "DataCatalog", "description": "Data or tool catalog", "type": "object", "properties": { "name": { "description": "Data or tool catalog name", "type": "string" }, "url": { "description": "Link to data or tool catalog", "type": "string", "format": "uri" }, "versionDate": { "description": "date the metadata was harvested from the catalog", "type": "string", "format": "date" }, "archivedAt": { "description": "The url(s) of one or more datasets, tools, resources or other items listed in a DataCatalog or ResourceCatalog", "oneOf": [ { "items": { "type": "string", "format": "uri" }, "type": "array" }, { "type": "string", "format": "uri" } ] } }, "required": ["name", "url"], "recommended": ["versionDate", "archivedAt"] }, "creativework": { "description": "A resource", "@type": "CreativeWork", "type": "object", "properties": { "author": { "description": "Author(s) of the referenced work", "anyOf": [ { "type": "array", "items": { "$ref": "#/definitions/person" } }, { "$ref": "#/definitions/person" }, { "type": "array", "items": { "$ref": "#/definitions/organization" } }, { "$ref": "#/definitions/organization" } ] }, "abstract": { "description": "Abstract of the referenced work", "type": "string" }, "additionalType": { "description": "Additional type of the referenced work, such as a Sample, Run, Experiment, or BioProject", "oneOf": [ { "items": { "properties": { "name": { "type": "string" }, "url": { "format": "uri", "type": "string" } }, "required": ["name"], "recommended": ["url"], "type": "object" }, "type": "array" } ] }, "datePublished": { "description": "Date the referenced work was published", "format": "date", "type": "string" }, "description": { "description": "Description of the referenced work", "type": "string" }, "hasPart": { "description": "A portion of the work", "oneOf": [ { "$ref": "#/definitions/citation" } ] }, "includedInDataCatalog": { "description": "Data or tool catalog which houses the work", "oneOf": [ { "$ref": "#/definitions/catalog" } ] }, "name": { "description": "Name or title", "type": "string" }, "identifier": { "description": "An identifier associated with the work", "type": "string" }, "relationship": { "description": "How the works are related", "type": "string" }, "doi": { "description": "A digital object identifier (DOI) of the referenced work", "abstract": "digital object identifier", "type": "string" }, "url": { "description": "The url of the work", "type": "string", "format": "uri" }, "citation": { "description": "The bibliographic citation for the referenced work as is provided", "type": "string" } }, "required": ["name"], "recommended": ["author", "datePublished", "doi", "identifier", "includedInDataCatalog", "relationship", "url"], "optional": ["abstract", "citation", "description", "hasPart"] }, "topic": { "description": "Topic assigned to the work.", "type": "string", "vocabulary": { "ontology": ["edam"], "children_of": ["http://edamontology.org/topic_0003"] }, "strict": true }, "organization": { "@type": "Organization", "description": "Reusable organization definition", "properties": { "affiliation": { "type": "object", "properties": { "name": { "description": "Name of the affiliation, such as a university", "type": "string" }, "sameAs": { "description": "Alias for the affiliation", "type": "string" }, "url": { "description": "URL of the affiliation", "type": "string", "format": "uri" } }, "required": ["name"], "optional": ["sameAs", "url"] }, "alternateName": { "description": "Alias of the name", "oneOf": [ { "type": "array", "items": { "type": "string" } }, { "type": "string" } ] }, "name": { "description": "Name of the organization", "type": "string" }, "parentOrganization": { "description": "Name of the parent organization. For instance, the parentOrganization of NIAID is the National Institutes of health (NIH)", "type": "string" }, "email": { "description": "Email address of the organization", "type": "string" }, "identifier": { "description": "Unique identifier of the organization", "type": "string" }, "role": { "description": "What role the organization played in creating the dataset", "type": "string" }, "url": { "description": "Link to the organization", "type": "string", "format": "uri" } }, "required": ["name"], "recommended": ["identifier"], "optional": ["affiliation", "alternateName", "email", "parentOrganization", "role", "url"], "type": "object" }, "researchproject": { "@type": "ResearchProject", "description": "a type of organization definition", "properties": { "alternateName": { "description": "Alias of the name", "oneOf": [ { "type": "array", "items": { "type": "string" } }, { "type": "string" } ] }, "name": { "description": "Name of the organization", "type": "string" }, "parentOrganization": { "description": "Name of the parent organization. For instance, the parentOrganization of NIAID is the National Institutes of health (NIH)", "type": "string" }, "email": { "description": "Email address of the organization", "type": "string" }, "identifier": { "description": "Unique identifier of the organization", "type": "string" }, "url": { "description": "Link to the organization", "type": "string", "format": "uri" } }, "required": ["name"], "recommended": ["identifier", "url", "parentOrganization"], "optional": ["alternateName", "email", "role"], "type": "object" }, "person": { "@type": "Person", "description": "Reusable person definition", "properties": { "affiliation": { "type": "object", "properties": { "name": { "description": "Name of the affiliation, such as a university", "type": "string" }, "sameAs": { "description": "Alias for the affiliation", "type": "string" }, "url": { "description": "URL of the affiliation", "type": "string", "format": "uri" } }, "required": ["name"], "optional": ["sameAs", "url"] }, "name": { "description": "Name of the person", "type": "string" }, "email": { "description": "Email address of the person", "type": "string" }, "familyName": { "description": "Family name (surname) of the person", "type": "string" }, "givenName": { "description": "Given (first) name of the person", "type": "string" }, "identifier": { "description": "Unique identifier of the person, like an ORCID ID", "type": "string" }, "role": { "description": "Role the person played in creating the computational tool", "type": "string" }, "title": { "description": "Title of the person", "type": "string" }, "url": { "description": "Link to the homepage or other web content describing the person", "type": "string", "format": "uri" } }, "required": ["name"], "recommended": ["familyName", "givenName ", "identifier "], "optional": ["affiliation", "email", "role", "title", "url"], "type": "object" }, "definedterm": { "@type": "DefinedTerm", "type": "object", "properties": { "name": { "description": "The name 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 for more details.", "owl:cardinality": "one", "type": "string" }, "url": { "description": "URL of the item.", "owl:cardinality": "one", "type": "string", "format": "uri" }, "curatedBy": { "description": "The person, organization, or catalog that curated this DefinedTerm for the metadata property", "anyOf": [ { "$ref": "#/definitions/person" }, { "$ref": "#/definitions/organization" }, { "$ref": "#/definitions/catalog" }, { "$ref": "#/definitions/researchproject" }, { "$ref": "#/definitions/softwareapplication" } ] }, "termCode": { "description": "A code that identifies this DefinedTerm within a DefinedTermSet.", "type": "string" }, "description": { "description": "A description of the item.", "type": "string" }, "inDefinedTermSet": { "description": "A DefinedTermSet that contains this term.", "type": "string" }, "originalName": { "description": "The original name of the item, before any metadata standardization/normalization", "type": "string" }, "isCurated": { "description": "A boolean indicator describing whether or not this DefinedTerm was curated as the value of a property.", "type": "boolean" } }, "required": [] }, "softwareapplication": { "@type": "SoftwareApplication", "description": "Reusable software or algorithm definition", "properties": { "name": { "description": "name of the software, computational tool, or algorithm.", "type": "string" }, "dateModified": { "description": "date the software, computational tool, or algorithm was run", "type": "string", "format": "date" }, "url": { "description": "url of the software, computational tool, or algorithm", "type": "string", "format": "uri" } }, "required": ["name"], "recommended": ["url"], "optional": ["dateModified"], "type": "object" }, "formalparameter": { "@type": "FormalParameter", "description": "Reusable input or output parameter definition", "properties": { "name": { "type": "string", "description": "Name of the software input" }, "identifier": { "description": "An ontology identifier or url of the software input our output", "anyOf": [ { "type": "string" }, { "type": "array", "items": { "type": "string" } }, { "type": "string", "format": "uri" }, { "type": "array", "items": { "type": "string", "format": "uri" } } ] }, "description": { "type": "string", "description": "Description of the software input or output" }, "encodingFormat": { "description": "File type of the software input our output", "anyOf": [ { "type": "string" }, { "type": "array", "items": { "type": "string" } }, { "type": "array", "items": { "$ref": "#/definitions/definedterm" } }, { "$ref": "#/definitions/definedterm" } ] } }, "required": ["name"], "recommended": ["encodingFormat"] } } } }, { "@id": "nde:ResourceCatalog", "@type": "rdfs:Class", "rdfs:comment": "ResourceCatalogs (collections of scientific information or research outputs) contained in the NIAID Data Ecosystem. Resource catalogs include databases, repositories, knowledge bases, citation indices, software indices, browser-based data portals (web portals), etc. The NIAID Data Ecosystem is an environment to find and access and infectious and immune-mediated disease data, resources and computational tools to speed the development of diagnostics, therapeutics, and vaccines. The NIAID Data Ecosystem Discovery Portal harvests metadata from dataset repository and harmonizes them to this schema to enable easy cross-platform dataset searching and filtering.", "abstract": "ResourceCatalogs (collections of scientific information or research outputs) contained in the NIAID Data Ecosystem. Resource catalogs include databases, repositories, knowledge bases, citation indices, software indices, browser-based data portals (web portals), etc.", "rdfs:label": "ResourceCatalog", "rdfs:subClassOf": { "@id": "schema:Collection" }, "schema:schemaVersion":["https://schema.org/docs/releases.html#v18.0","v2.0 - 2025.12.08"], "dct:provenance":"Changes since previous version: Add description for the 'about' field.", "$validation": { "$schema": "http://json-schema.org/draft-07/schema#", "type": "object", "properties": { "about": { "description": "The entity type or class encapsulated by the records in this resource. For example, if a repository has a record on CDK2, and metadata about the genetic sequence, epigentic annotation, gene locus, etc-- the entity type would be Gene, and the resource contains data 'about' Genes. These should be formatted as DefinedTerm objects (mapped to ontology terms) for easier standardization.", "oneOf": [ { "type": "array", "items": { "$ref": "#/definitions/definedterm" } }, { "$ref": "#/definitions/definedterm" } ], "owl:cardinality": "many" }, "citedBy": { "description": "Publications, datasets, or computational tools that cite the work. Examples: a publication which uses information or content of the resource catalog for secondary analysis, or a computational tool which relies on the content of the resource catalog. For the primary citation, use the 'citation' field.", "anyOf": [ { "type": "array", "items": { "$ref": "#/definitions/citation" } }, { "$ref": "#/definitions/citation" }, { "type": "array", "items": { "$ref": "#/definitions/creativework" } }, { "$ref": "#/definitions/creativework" } ], "owl:cardinality": "many" }, "date": { "description": "Date the work has changed: most recent date of dateModified, datePublished, and dateCreated.", "abstract": "date changed", "format": "date", "type": "string", "owl:cardinality": "one" }, "doi": { "description": "Digital Object Identifier (DOI) for the work, not any associated publications.", "abstract": "digital object identifier", "type": "string", "owl:cardinality": "one" }, "isRelatedTo": { "description": "Resources which are related to the given resource catalog. These linkages are created via human curation.", "abstract": "related datasets (via curation)", "anyOf": [ { "type": "array", "items": { "$ref": "#/definitions/citation" } }, { "$ref": "#/definitions/citation" }, { "type": "array", "items": { "$ref": "#/definitions/creativework" } }, { "$ref": "#/definitions/creativework" } ], "owl:cardinality": "many" }, "isSimilarTo": { "description": "Resource catalogs which are similar to the work, based on terms in the names, descriptions, authors, measurementTechniques, infectiousAgents, healthConditions, etc.", "abstract": "similar datasets (auto-assigned)", "anyOf": [ { "type": "array", "items": { "$ref": "#/definitions/citation" } }, { "$ref": "#/definitions/citation" }, { "type": "array", "items": { "$ref": "#/definitions/creativework" } }, { "$ref": "#/definitions/creativework" } ], "owl:cardinality": "many" }, "isBasisFor": { "description": "A resource catalog which uses the resource catalog.", "anyOf": [ { "type": "array", "items": { "$ref": "#/definitions/citation" } }, { "$ref": "#/definitions/citation" }, { "type": "array", "items": { "$ref": "#/definitions/creativework" } }, { "$ref": "#/definitions/creativework" } ], "owl:cardinality": "many" }, "relationship": { "description": "How an associated work is related to the resource catalog.", "type": "string", "owl:cardinality": "one" }, "topicCategory": { "description": "Topic of the work. This topic may be assigned by a human curator or through automated algorithms.", "abstract": "topic", "anyOf": [ { "type": "array", "items": { "$ref": "#/definitions/topic" } }, { "$ref": "#/definitions/topic" }, { "type": "array", "items": { "$ref": "#/definitions/definedterm" } }, { "$ref": "#/definitions/definedterm" } ], "owl:cardinality": "many" }, "infectiousAgent": { "description": "Infectious agent(s) / pathogen(s) which are the focus of the work (like SARS-CoV-2).", "abstract": "infectious agent / pathogen", "anyOf": [ { "description": "collection of vocabulary terms defined in ontologies", "strict": false, "type": "string", "vocabulary": { "children_of": ["http://purl.obolibrary.org/obo/NCBITaxon_10239", "http://purl.obolibrary.org/obo/NCBITaxon_2"], "ontology": ["ncbitaxon"] } }, { "items": { "description": "collection of vocabulary terms defined in ontologies", "strict": false, "type": "string", "vocabulary": { "children_of": ["http://purl.obolibrary.org/obo/NCBITaxon_10239", "http://purl.obolibrary.org/obo/NCBITaxon_2"], "ontology": ["ncbitaxon"] } }, "type": "array" }, { "type": "array", "items": { "$ref": "#/definitions/definedterm" } }, { "$ref": "#/definitions/definedterm" } ], "owl:cardinality": "many" }, "healthCondition": { "description": "The health condition(s) /infectious disease(s) which are the focus of the work (like COVID-19, coronavirus).", "abstract": "health condition/disease", "anyOf": [ { "description": "collection of vocabulary terms defined in ontologies", "strict": false, "type": "string", "vocabulary": { "children_of": ["http://purl.obolibrary.org/obo/MONDO_0000001", "http://purl.obolibrary.org/obo/DOID_4", "http://purl.obolibrary.org/obo/HP_0000001", "http://purl.obolibrary.org/obo/NCIT_C7057"], "ontology": ["mondo","hpo","doid","ncit"] } }, { "items": { "description": "collection of vocabulary terms defined in ontologies", "strict": false, "type": "string", "vocabulary": { "children_of": ["http://purl.obolibrary.org/obo/MONDO_0000001", "http://purl.obolibrary.org/obo/DOID_4", "http://purl.obolibrary.org/obo/HP_0000001", "http://purl.obolibrary.org/obo/NCIT_C7057"], "ontology": ["mondo","hpo","doid","ncit"] } }, "type": "array" }, { "type": "array", "items": { "$ref": "#/definitions/definedterm" } }, { "$ref": "#/definitions/definedterm" } ], "owl:cardinality": "many" }, "funding": { "description": "Funding that supports (sponsors) the creation or maintenance of the resource catalog through some kind of financial contribution.", "abstract": "funding source (grant, contract, etc.)", "oneOf": [ { "type": "object", "@type": "MonetaryGrant", "description": "Funding that supports (sponsors) the creation or maintenance of the resource catalog through some kind of financial contribution", "properties": { "funder": { "description": "An organization associated with a creator or funder of a resource catalog", "oneOf": [ { "type": "object", "@type": "Organization", "description": "Information about a single funder", "properties": { "name": { "type": "string", "description": "An organization associated with a creator or funder of a resource catalog" }, "parentOrganization": { "type": "string", "description": "name of the parent funding organization" } }, "required": [ "name" ] }, { "type": "array", "items": { "type": "object", "@type": "Organization", "description": "Information about a single funder", "properties": { "name": { "type": "string", "description": "An organization associated with a creator or funder of a dataset" }, "parentOrganization": { "type": "string", "description": "name of the parent funding organization" } }, "required": [ "name" ] } } ] }, "description": { "type": "string", "description": "description about the funding award / grant" }, "url": { "type": "string", "description": "award / grant URL" }, "identifier": { "type": "string", "description": "Unique identifier(s) for the grant(s) used to fund the resource catalog" } }, "required": [ "funder", "identifier" ] }, { "type": "array", "items": { "type": "object", "@type": "MonetaryGrant", "description": "Funding that supports (sponsors) the creation or maintenance of the resource catalog through some kind of financial contribution", "properties": { "funder": { "description": "An organization associated with a creator or funder of a resource catalog", "oneOf": [ { "type": "object", "@type": "Organization", "description": "Information about a single funder", "properties": { "name": { "type": "string", "description": "An organization associated with a creator or funder of a resource catalog" }, "parentOrganization": { "type": "string", "description": "name of the parent funding organization" } }, "required": [ "name" ] }, { "type": "array", "items": { "type": "object", "@type": "Organization", "description": "Information about a single funder", "properties": { "name": { "type": "string", "description": "An organization associated with a creator or funder of a resource catalog" }, "parentOrganization": { "type": "string", "description": "name of the parent funding organization" } }, "required": [ "name" ] } } ] }, "description": { "type": "string", "description": "description about the funding award / grant" }, "url": { "type": "string", "description": "award / grant URL" }, "identifier": { "type": "string", "description": "Unique identifier(s) for the grant(s) used to fund the resource catalog" } }, "required": [ "funder", "identifier" ] } } ], "owl:cardinality": "many" }, "species": { "description": "Species / host organism from which the dataset has been collected.", "abstract": "species/host organism", "anyOf": [ { "description": "collection of vocabulary terms defined in ontologies", "strict": false, "type": "string", "vocabulary": { "children_of": ["http://purl.obolibrary.org/obo/NCBITaxon_131567", "http://purl.obolibrary.org/obo/NCBITaxon_10239"], "ontology": ["ncbitaxon"] } }, { "items": { "description": "collection of vocabulary terms defined in ontologies", "strict": false, "type": "string", "vocabulary": { "children_of": ["http://purl.obolibrary.org/obo/NCBITaxon_131567", "http://purl.obolibrary.org/obo/NCBITaxon_10239"], "ontology": ["ncbitaxon"] } }, "type": "array" }, { "type": "array", "items": { "$ref": "#/definitions/definedterm" } }, { "$ref": "#/definitions/definedterm" } ], "owl:cardinality": "many" }, "distribution": { "description": "A downloadable form of the resource catalog, at a specific location, in a specific format.", "abstract": "download link", "oneOf": [ { "items": { "@type": "DataDownload", "description": "A downloadable form of the resource catalog.", "properties": { "contentUrl": { "format": "uri", "type": "string" }, "encodingFormat": { "description": "file type (ex: XLSX)", "type": "string" }, "dateModified": { "format": "date", "description": "date the file was modified", "type": "string" } }, "required": ["dateModified", "contentUrl"], "type": "object" }, "type": "array" }, { "@type": "DataDownload", "description": "A downloadable form of the resource catalog.", "properties": { "contentUrl": { "format": "uri", "type": "string" }, "encodingFormat": { "description": "file type (ex: XLSX)", "type": "string" }, "dateModified": { "format": "date", "description": "date the file was modified", "type": "string" } }, "required": ["dateModified", "contentUrl"], "type": "object" } ], "owl:cardinality": "many" }, "includedInDataCatalog": { "description": "A resource catalog where the resource catalog is published.", "abstract": "catalog containing the work", "oneOf": [ { "$ref": "#/definitions/catalog" }, { "type": "array", "items": { "$ref": "#/definitions/catalog" } } ], "owl:cardinality": "one" }, "measurementTechnique": { "description": "A technique or technology used in a dataset corresponding to the method used for measuring the corresponding variable(s) (described using variableMeasured). For example, if variableMeasured is molecule concentration, measurementTechnique could be: \"mass spectrometry\" or \"nmr spectroscopy\" or \"colorimetry\" or \"immunofluorescence\".", "abstract": "measurement technique used to collect the dataset", "anyOf": [ { "description": "collection of vocabulary terms defined in ontologies", "strict": false, "type": "string", "vocabulary": { "children_of": ["http://edamontology.org/topic_3361", "http://purl.obolibrary.org/obo/NCIT_C20368", "http://purl.obolibrary.org/obo/MMO_0000000", "http://www.ebi.ac.uk/efo/EFO_0000001"], "ontology": ["edam", "ncit", "mmo","efo"] } }, { "items": { "description": "collection of vocabulary terms defined in ontologies", "strict": false, "type": "string", "vocabulary": { "children_of": ["http://edamontology.org/topic_3361", "http://purl.obolibrary.org/obo/NCIT_C20368", "http://purl.obolibrary.org/obo/MMO_0000000", "http://www.ebi.ac.uk/efo/EFO_0000001"], "ontology": ["edam", "ncit", "mmo","efo"] } }, "type": "array" }, { "type": "array", "items": { "$ref": "#/definitions/definedterm" } }, { "$ref": "#/definitions/definedterm" } ], "owl:cardinality": "many" }, "variableMeasured": { "description": "Variables measured within the dataset.", "oneOf": [ { "description": "collection of vocabulary terms defined in ontologies", "strict": false, "type": "string", "vocabulary": { "children_of": ["http://www.ebi.ac.uk/efo/EFO_0000001", "http://purl.obolibrary.org/obo/CMO_0000000", "http://purl.obolibrary.org/obo/NCIT_C25209"], "ontology": ["efo", "cmo","ncit"] } }, { "items": { "description": "collection of vocabulary terms defined in ontologies", "strict": false, "type": "string", "vocabulary": { "children_of": ["http://www.ebi.ac.uk/efo/EFO_0000001", "http://purl.obolibrary.org/obo/CMO_0000000", "http://purl.obolibrary.org/obo/NCIT_C25209"], "ontology": ["efo", "cmo","ncit"] } }, "type": "array" }, { "type": "array", "items": { "$ref": "#/definitions/definedterm" } }, { "$ref": "#/definitions/definedterm" } ], "owl:cardinality": "many" }, "abstract": { "description": "Short description that summarizes a work.", "abstract": "short description", "type": "string", "owl:cardinality": "one" }, "aggregateRating": { "description": "The overall rating, based on a collection of reviews or ratings, of the work. These ratings can be collected based on user reviews or through Altmetric scores of web-based citations.", "abstract": "rating of the work", "oneOf": [ { "items": { "@type": "AggregateRating", "type": "object", "properties": { "ratingCount": { "description": "Total number of ratings", "type": "integer" }, "ratingValue": { "description": "Average rating", "type": "string" }, "itemReviewed": { "description": "What is being reviewed", "type": "string" } }, "required": ["ratingValue"], "recommended": ["ratingCount", "itemReviewed"] }, "type": "array" }, { "@type": "AggregateRating", "type": "object", "properties": { "ratingCount": { "description": "Total number of ratings", "type": "integer" }, "ratingValue": { "description": "Average rating", "type": "string" }, "itemReviewed": { "description": "What is being reviewed", "type": "string" } }, "required": ["ratingValue"], "recommended": ["ratingCount", "itemReviewed"] } ], "owl:cardinality": "many" }, "author": { "description": "Author or creator of the work. The default field for the author or creator of the work.", "abstract": "Author or creator of the work", "anyOf": [ { "type": "array", "items": { "$ref": "#/definitions/person" } }, { "$ref": "#/definitions/person" }, { "type": "array", "items": { "$ref": "#/definitions/organization" } }, { "$ref": "#/definitions/organization" } ], "owl:cardinality": "many" }, "citation": { "description": "The primary citation or reference about the resource catalog. Examples: a publication which describes the development of or improvements to the resource catalog. The original reference by the resource catalog developers/maintainers that should be cited when using the resource. For all other references to the resource catalog, use 'citedBy'.", "abstract": "citation to the work", "owl:cardinality": "many", "anyOf": [ { "type": "array", "items": { "$ref": "#/definitions/citation" } }, { "$ref": "#/definitions/citation" }, { "type": "array", "items": { "$ref": "#/definitions/creativework" } }, { "$ref": "#/definitions/creativework" } ] }, "genre": { "description": "Whether the resource is IID domain specific or generalist.", "abstract": "Whether the work is IID domain specific or generalist", "type": "string", "enum": ["IID", "Generalist", "Basic science", "Biomedical", "Other", "Metadata"], "owl:cardinality": "one" }, "conditionsOfAccess": { "description": "Conditions that affect the availability of, or method(s) of access to, the work. Options include open (freely available), restricted (may include restrictions such as on use), closed (requires registration to access), or embargoed (unpublished).", "abstract": "accessibility of the work", "type": "string", "enum": ["Closed", "Open", "Restricted", "Embargoed"], "owl:cardinality": "one" }, "creator": { "description": "The creator/author of this work; equivalent to author. Please use author by default. Use creator if author/creator in a record of this work submitted elsewhere differs from the author/creator entered into the author field.", "abstract": "The creator/author of this work; equivalent to author", "anyOf": [ { "type": "array", "items": { "$ref": "#/definitions/person" } }, { "$ref": "#/definitions/person" }, { "type": "array", "items": { "$ref": "#/definitions/organization" } }, { "$ref": "#/definitions/organization" } ], "owl:cardinality": "many" }, "dateCreated": { "description": "Date the work was created.", "format": "date", "type": "string", "owl:cardinality": "one" }, "dateModified": { "description": "Date the work was modified", "format": "date", "type": "string", "owl:cardinality": "one" }, "datePublished": { "description": "Date the work was first published", "format": "date", "type": "string", "owl:cardinality": "one" }, "hasAPI": { "description": "The resource has an API through which important content may be accessed.", "abstract": "API availability", "type": "boolean", "owl:cardinality": "one" }, "hasDownload": { "description": "The resource provides downloads of its contents. Options: All content (e.g. entire data builds, tools, etc.), Partial content (just data, or just tools, etc.), Record-level (individual records, or selections of records), No downloads (information is viewable but not downloadable, users must resort to copy/paste, screenshots, etc.), Prohibited (downloading, copy/pasting, screenshotting the data is prohibited).", "abstract": "Download availability", "type": "string", "enum": ["All content", "Partial content", "Record-level", "No downloads", "Prohibited"], "owl:cardinality": "one" }, "hasPart": { "description": "Associated materials for the resource catalog, including data dictionaries and data limitation descriptions", "abstract": "data limitations or dictionaries", "anyOf": [ { "type": "array", "items": { "$ref": "#/definitions/citation" } }, { "$ref": "#/definitions/citation" }, { "type": "array", "items": { "$ref": "#/definitions/creativework" } }, { "$ref": "#/definitions/creativework" } ], "owl:cardinality": "many" }, "inLanguage": { "description": "The language of the content of the resource catalog.", "oneOf": [ { "items": { "type": "object", "properties": { "name": { "type": "string", "description": "language of the work" }, "alternateName": { "type": "string" } }, "required": ["name"], "recommended": ["alternateName"] }, "type": "array" }, { "type": "object", "properties": { "name": { "type": "string", "description": "language of the work" }, "alternateName": { "type": "string" } }, "required": ["name"], "recommended": ["alternateName"] } ], "owl:cardinality": "many" }, "interactionStatistic": { "description": "The number of interactions with the work, such as page views or tool downloads.", "abstract": "views or downloads", "oneOf": [ { "items": { "@type": "InteractionCounter", "type": "object", "properties": { "interactionType": { "type": "string" }, "userInteractionCount": { "type": "integer" } }, "required": ["interactionType", "userInteractionCount"] }, "type": "array" }, { "@type": "InteractionCounter", "type": "object", "properties": { "interactionType": { "type": "string" }, "userInteractionCount": { "type": "integer" } }, "required": ["interactionType", "userInteractionCount"] } ], "owl:cardinality": "many" }, "isAccessibleForFree": { "description": "A flag to signal that the work is accessible for free.", "abstract": "accessible without charge", "type": "boolean", "owl:cardinality": "one" }, "isBasedOn": { "description": "A dataset, publication, or computational tool from which this work is derived, modified, or adapted.", "abstract": "dataset, publication, or tool used to create the work", "owl:cardinality": "many", "anyOf": [ { "type": "array", "items": { "$ref": "#/definitions/citation" } }, { "$ref": "#/definitions/citation" }, { "type": "array", "items": { "$ref": "#/definitions/creativework" } }, { "$ref": "#/definitions/creativework" } ] }, "isPartOf": { "description": "Indicates a broader study, project, or collection the work is part of.", "abstract": "study or project including the work", "owl:cardinality": "many", "anyOf": [ { "type": "array", "items": { "$ref": "#/definitions/citation" } }, { "$ref": "#/definitions/citation" }, { "type": "array", "items": { "$ref": "#/definitions/creativework" } }, { "$ref": "#/definitions/creativework" } ] }, "keywords": { "description": "Keywords or tags used to describe this work.", "abstract": "keywords or tags", "oneOf": [ { "type": "array", "items": { "type": "string" } }, { "type": "string" } ], "owl:cardinality": "many" }, "license": { "description": "A license document that applies to this work, typically indicated by URL.", "abstract": "license for use", "format": "uri", "owl:cardinality": "one", "type": "string" }, "sdPublisher": { "description": "Original publisher of the resource catalog metadata (like GenBank, ImmPort, etc.).", "abstract": "original metadata source", "oneOf": [ { "$ref": "#/definitions/catalog" }, { "type": "array", "items": { "$ref": "#/definitions/catalog" } } ], "owl:cardinality": "many" }, "spatialCoverage": { "description": "The place(s) which are the focus of the resource catalog.", "abstract": "geographic focus of the work", "oneOf": [ { "items": { "@type": "AdministrativeArea", "description": "Location information", "properties": { "administrativeType": { "description": "the type of administrative area, such as country, state, county, or city", "enum": ["province", "district", "chiefdom", "village", "city", "country", "prefecture", "sub-prefecture", "clan", "Federal Capital Territory", "state", "Local Government Area", "ward"], "type": "string" }, "alternateName": { "description": "An alias for the location", "oneOf": [ { "type": "string" }, { "items": { "type": "string" }, "type": "array" } ] }, "identifier": { "description": "An identifier for the location, preferably a Wikidata ID", "type": "string" }, "locationType": { "description": "Categorization of how the location relates to the dataset", "oneOf": [ { "enum": ["residence", "exposure", "collection", "screening", "treatment", "study location", "other", "unknown"], "type": "string" }, { "items": { "enum": ["residence", "exposure", "collection", "screening", "treatment", "study location", "other", "unknown"], "type": "string" }, "type": "array" } ] }, "name": { "description": "The name of the location", "type": "string" } }, "type": "object" }, "type": "array" }, { "@type": "AdministrativeArea", "description": "Location information", "properties": { "administrativeType": { "description": "the type of administrative area, such as country, state, county, or city", "enum": ["province", "district", "chiefdom", "village", "city", "country", "prefecture", "sub-prefecture", "clan", "Federal Capital Territory", "state", "Local Government Area", "ward"], "type": "string" }, "alternateName": { "description": "An alias for the location", "oneOf": [ { "type": "string" }, { "items": { "type": "string" }, "type": "array" } ] }, "identifier": { "description": "An identifier for the location, preferably a Wikidata ID", "type": "string" }, "locationType": { "description": "Categorization of how the location relates to the dataset", "oneOf": [ { "enum": ["residence", "exposure", "collection", "screening", "treatment", "study location", "other", "unknown"], "type": "string" }, { "items": { "enum": ["residence", "exposure", "collection", "screening", "treatment", "study location", "other", "unknown"], "type": "string" }, "type": "array" } ] }, "name": { "description": "The name of the location", "type": "string" } }, "type": "object" } ], "owl:cardinality": "many" }, "temporalCoverage": { "description": "The period of time covered within the resource catalog.", "abstract": "time period", "oneOf": [ { "items": { "@type": "TemporalInterval", "description": "Temporal information", "properties": { "duration": { "description": "A time interval in ISO 8601 duration format", "type": "string" }, "endDate": { "description": "An end date", "format": "date", "type": "string" }, "name": { "description": "String describing the temporal interval", "type": "string" }, "startDate": { "description": "A start date", "format": "date", "type": "string" }, "temporalType": { "description": "Categorization of how the date/temporal interval relates to the dataset", "oneOf": [ { "enum": ["exposure", "collection", "screening", "treatment", "study date", "other", "unknown"], "type": "string" }, { "items": { "enum": ["exposure", "collection", "screening", "treatment", "study date", "other", "unknown"], "type": "string" }, "type": "array" } ] } }, "type": "object" }, "type": "array" }, { "@type": "TemporalInterval", "description": "Temporal information", "properties": { "duration": { "description": "A time interval in ISO 8601 duration format", "type": "string" }, "endDate": { "description": "An end date", "format": "date", "type": "string" }, "name": { "description": "String describing the temporal interval", "type": "string" }, "startDate": { "description": "A start date", "format": "date", "type": "string" }, "temporalType": { "description": "Categorization of how the date/temporal interval relates to the dataset", "oneOf": [ { "enum": ["exposure", "collection", "screening", "treatment", "study date", "other", "unknown"], "type": "string" }, { "items": { "enum": ["exposure", "collection", "screening", "treatment", "study date", "other", "unknown"], "type": "string" }, "type": "array" } ] } }, "type": "object" } ], "owl:cardinality": "many" }, "usageInfo": { "description": "Data usage agreement, specifying the terms under which the content from the resource catalog can be used. Note that this is related to but distinct from the license.", "abstract": "data usage agreement", "oneOf": [ { "type": "array", "items": { "$ref": "#/definitions/creativework" } }, { "$ref": "#/definitions/creativework" } ], "owl:cardinality": "many" }, "version": { "description": "Resource catalog version.", "type": "string", "owl:cardinality": "one" }, "alternateName": { "description": "An alias for the resource catalog name.", "oneOf": [ { "type": "string" }, { "type": "array", "items": { "type": "string" } } ], "owl:cardinality": "many" }, "description": { "description": "A description of the resource catalog.", "owl:cardinality": "one", "type": "string" }, "identifier": { "description": "Resource catalog identifier or accession number, such as a digital object identifier (DOI), etc.", "abstract": "identifier", "oneOf": [ { "type": "string" }, { "items": { "type": "string" }, "type": "array" } ], "owl:cardinality": "many" }, "mainEntityOfPage": { "description": "Website which describes the work and provides additional details.", "abstract": "associated webpage", "oneOf": [ { "items": { "type": "string", "format": "uri" }, "type": "array" }, { "type": "string", "format": "uri" } ], "owl:cardinality": "many" }, "name": { "description": "Resource catalog name.", "owl:cardinality": "one", "type": "string" }, "sameAs": { "description": "URL of additional sources for the work.", "oneOf": [ { "items": { "type": "string", "format": "uri" }, "type": "array" }, { "type": "string", "format": "uri" } ], "owl:cardinality": "many" }, "url": { "description": "URL of the work.", "type": "string", "format": "uri", "owl:cardinality": "one" }, "collectionSize": { "description": "The number of records, datasets, tools, items, pages, etc. in the resource catalog. Min/max estimates can be used in lieu of actual number. If completely unknown, set value = 0, and unitText = 'unknown'", "anyOf": [ { "type": "array", "items": { "$ref": "#/definitions/propertyvalue" } }, { "$ref": "#/definitions/propertyvalue" }, { "type": "array", "items": { "$ref": "#/definitions/quantitativevalue" } }, { "$ref": "#/definitions/quantitativevalue" } ], "owl:cardinality": "many" }, "collectionType": { "description": "The type of resource/resource catalog that best describes the work.", "anyOf": [ { "type": "string", "enum": ["Knowledge Base", "Ontology", "Terminology", "Database", "Dataset", "Metadata Catalog", "Archive", "Cloud Ecosystem", "Corpus", "Repository", "Controlled Vocabulary", "Registry", "Data Dictionary", "Data Mart", "Data Warehouse", "Data Store", "Data Collection", "Portal"] }, { "$ref": "#/definitions/collectiontypes" } ], "owl:cardinality": "one" }, "sourceOrganization": { "description": "The organization, research project, working group, or funded program on whose behalf the author/creator was working.", "anyOf": [ { "type": "array", "items": { "$ref": "#/definitions/researchproject" } }, { "$ref": "#/definitions/researchproject" }, { "type": "array", "items": { "$ref": "#/definitions/organization" } }, { "$ref": "#/definitions/organization" } ], "owl:cardinality": "many" }, "archivedAt": { "description": "The url(s) of one or more datasets, tools, resources or other items listed in a DataCatalog or ResourceCatalog", "oneOf": [ { "items": { "type": "string", "format": "uri" }, "type": "array" }, { "type": "string", "format": "uri" } ], "owl:cardinality": "many" }, "creditText": { "description": "Text that can be used to credit person(s) and/or organization(s) associated with a published Creative Work. For example, how a user should cite the resource.", "type": "string", "owl:cardinality": "one" } }, "required": ["date", "funding", "measurementTechnique", "description", "name", "url", "about","genre", "includedInDataCatalog"], "recommended": ["author", "citedBy", "doi", "infectiousAgent", "healthCondition", "species", "variableMeasured", "citation", "conditionsOfAccess", "dateCreated", "dateModified", "datePublished", "interactionStatistic", "isBasedOn", "keywords", "license", "sdPublisher", "spatialCoverage", "temporalCoverage", "usageInfo", "identifier", "topicCategory", "collectionSize", "hasAPI", "hasDownload", "collectionType"], "optional": ["isRelatedTo", "isSimilarTo", "isBasisFor", "distribution", "abstract", "aggregateRating", "creator", "hasPart", "inLanguage", "isAccessibleForFree", "isPartOf", "version", "alternateName", "mainEntityOfPage", "sameAs", "relationship", "sourceOrganization", "archivedAt","creditText"], "definitions": { "citation": { "description": "A citation object for a publication which is cited by the resource catalog (ie- is a derivative of the resource catalog), related to the resource catalog, or from which the resource catalog was based on (ie- is derived from).", "@type": "ScholarlyArticle", "type": "object", "properties": { "author": { "description": "Author(s) of the publication", "anyOf": [ { "type": "array", "items": { "$ref": "#/definitions/person" } }, { "$ref": "#/definitions/person" }, { "type": "array", "items": { "$ref": "#/definitions/organization" } }, { "$ref": "#/definitions/organization" } ] }, "abstract": { "description": "Abstract of the publication", "type": "string" }, "datePublished": { "description": "Date the article was published", "format": "date", "type": "string" }, "description": { "description": "Description of the publication", "type": "string" }, "name": { "description": "Title of the publication", "type": "string" }, "identifier": { "description": "An identifier associated with the citation such as a digital object identifier (DOI), PubMed ID (PMID), or PubMed Central ID (PMCID)", "type": "string" }, "pmid": { "description": "A PubMed identifier (PMID) of the referenced publication", "abstract": "PubMed identifier", "type": "string" }, "doi": { "description": "A digital object identifier (DOI) of the referenced publication", "abstract": "digital object identifier", "type": "string" }, "issueNumber": { "description": "Issue number where the article appears", "type": "string" }, "journalName": { "description": "Journal where the article appears", "type": "string" }, "journalNameAbbrev": { "description": "Abbreviated journal name where the article appears", "type": "string" }, "pagination": { "description": "Page numbers in the journal where the article appears", "type": "string" }, "url": { "description": "The url of the article", "type": "string", "format": "uri" }, "volumeNumber": { "description": "Volume of the journal where the article appears", "type": "string" }, "citation": { "description": "The bibliographic citation string for the article as is provided", "type": "string" } }, "required": ["name"], "recommended": ["author", "datePublished", "doi", "identifier", "journalName", "pmid", "url"], "optional": ["abstract", "citation", "description", "issueNumber", "journalNameAbbrev", "pagination", "volumeNumber"] }, "creativework": { "description": "A resource", "@type": "CreativeWork", "type": "object", "properties": { "author": { "description": "Author(s) of the referenced work", "anyOf": [ { "type": "array", "items": { "$ref": "#/definitions/person" } }, { "$ref": "#/definitions/person" }, { "type": "array", "items": { "$ref": "#/definitions/organization" } }, { "$ref": "#/definitions/organization" } ] }, "abstract": { "description": "Abstract of the referenced work", "type": "string" }, "datePublished": { "description": "Date the referenced work was published", "format": "date", "type": "string" }, "description": { "description": "Description of the referenced work", "type": "string" }, "hasPart": { "description": "A portion of the work", "oneOf": [ { "$ref": "#/definitions/citation" } ] }, "includedInDataCatalog": { "description": "Data, resource or tool catalog which houses the work", "oneOf": [ { "$ref": "#/definitions/catalog" } ] }, "name": { "description": "Name or title", "type": "string" }, "identifier": { "description": "An identifier associated with the work", "type": "string" }, "relationship": { "description": "How the works are related", "type": "string" }, "doi": { "description": "A digital object identifier (DOI) of the referenced work", "abstract": "digital object identifier", "type": "string" }, "url": { "description": "The url of the work", "type": "string", "format": "uri" }, "citation": { "description": "The bibliographic citation for the referenced work as is provided", "type": "string" } }, "required": ["name"], "recommended": ["author", "datePublished", "doi", "identifier", "includedInDataCatalog", "relationship", "url"], "optional": ["abstract", "citation", "description", "hasPart"] }, "topic": { "description": "Topic assigned to the work.", "type": "string", "vocabulary": { "ontology": ["edam"], "children_of": ["http://edamontology.org/topic_0003"] }, "strict": true }, "catalog": { "@type": "DataCatalog", "description": "Data, resource or tool catalog", "type": "object", "properties": { "name": { "description": "Data, resource or tool catalog name", "type": "string" }, "url": { "description": "Link to data, resource or tool catalog", "type": "string", "format": "uri" }, "versionDate": { "description": "date the metadata was harvested from the catalog", "type": "string", "format": "date" }, "archivedAt": { "description": "The url(s) of one or more datasets, tools, resources or other items listed in a DataCatalog or ResourceCatalog", "oneOf": [ { "items": { "type": "string", "format": "uri" }, "type": "array" }, { "type": "string", "format": "uri" } ] } }, "required": ["name", "url"], "recommended": ["versionDate", "archivedAt"] }, "organization": { "@type": "Organization", "description": "Reusable organization definition", "properties": { "affiliation": { "type": "object", "properties": { "name": { "description": "Name of the affiliation, such as a university", "type": "string" }, "sameAs": { "description": "Alias for the affiliation", "type": "string" }, "url": { "description": "URL of the affiliation", "type": "string", "format": "uri" } }, "required": ["name"], "optional": ["sameAs", "url"] }, "alternateName": { "description": "Alias of the name", "oneOf": [ { "type": "array", "items": { "type": "string" } }, { "type": "string" } ] }, "name": { "description": "Name of the organization", "type": "string" }, "parentOrganization": { "description": "Name of the parent organization. For instance, the parentOrganization of NIAID is the National Institutes of health (NIH)", "type": "string" }, "email": { "description": "Email address of the organization", "type": "string" }, "identifier": { "description": "Unique identifier of the organization", "type": "string" }, "role": { "description": "What role the organization played in creating the dataset", "type": "string" }, "url": { "description": "Link to the organization", "type": "string", "format": "uri" } }, "required": ["name"], "recommended": ["identifier"], "optional": ["affiliation", "alternateName", "email", "parentOrganization", "role", "url"], "type": "object" }, "researchproject": { "@type": "ResearchProject", "description": "a type of organization definition", "properties": { "alternateName": { "description": "Alias of the name", "oneOf": [ { "type": "array", "items": { "type": "string" } }, { "type": "string" } ] }, "name": { "description": "Name of the organization", "type": "string" }, "parentOrganization": { "description": "Name of the parent organization. For instance, the parentOrganization of NIAID is the National Institutes of health (NIH)", "type": "string" }, "email": { "description": "Email address of the organization", "type": "string" }, "identifier": { "description": "Unique identifier of the organization", "type": "string" }, "url": { "description": "Link to the organization", "type": "string", "format": "uri" } }, "required": ["name"], "recommended": ["identifier", "url", "parentOrganization"], "optional": ["alternateName", "email", "role"], "type": "object" }, "person": { "@type": "Person", "description": "Reusable person definition", "properties": { "affiliation": { "type": "object", "properties": { "name": { "description": "Name of the affiliation, such as a university", "type": "string" }, "sameAs": { "description": "Alias for the affiliation", "type": "string" }, "url": { "description": "URL of the affiliation", "type": "string", "format": "uri" } }, "required": ["name"], "optional": ["sameAs", "url"] }, "name": { "description": "Name of the person", "type": "string" }, "email": { "description": "Email address of the person", "type": "string" }, "familyName": { "description": "Family name (surname) of the person", "type": "string" }, "givenName": { "description": "Given (first) name of the person", "type": "string" }, "identifier": { "description": "Unique identifier of the person, like an ORCID ID", "type": "string" }, "role": { "description": "Role the person played in creating the resource catalog", "type": "string" }, "title": { "description": "Title of the person", "type": "string" }, "url": { "description": "Link to the homepage or other web content describing the person", "type": "string", "format": "uri" } }, "required": ["name"], "recommended": ["familyName", "givenName ", "identifier "], "optional": ["affiliation", "email", "role", "title", "url"], "type": "object" }, "propertyvalue": { "@type": "PropertyValue", "description": "A numeric value and unit for a property with potentially different units", "type": "object", "properties": { "value": { "description": "A numeric value for the property", "type": "number" }, "maxValue": { "description": "An estimated maximum numberic value if the actual value is not known. Ignore if actual numeric value is known.", "type": "number" }, "minValue": { "description": "An estimated minumum numeric value if the actual value is not known. Ignore if actual numeric value is known.", "type": "number" }, "unitText": { "description": "A unit associated with the value. E.g.- 'records' for the number of records in a database.", "type": "string" }, "propertyID": { "description": "A commonly used identifier for the characteristic represented by the property, e.g. a manufacturer or a standard code for a property. propertyID can be (1) a prefixed string, mainly meant to be used with standards for product properties; (2) a site-specific, non-prefixed string (e.g. the primary key of the property or the vendor-specific ID of the property), or (3) a URL indicating the type of the property, either pointing to an external vocabulary, or a Web resource that describes the property (e.g. a glossary entry). Standards bodies should promote a standard prefix for the identifiers of properties from their standards.", "oneOf": [ {"type": "string"}, { "type": "string", "format": "uri" } ] } }, "required" : ["unitText"], "recommended": ["value","propertyID"], "optional": ["maxValue","minValue"] }, "quantitativevalue": { "@type": "QuantitativeValue", "description": "A numeric value and unit for a property with potentially different units", "type": "object", "properties": { "value": { "description": "A numeric value for the property", "type": "number" }, "maxValue": { "description": "An estimated maximum numberic value if the actual value is not known. Ignore if actual numeric value is known.", "type": "number" }, "minValue": { "description": "An estimated minumum numeric value if the actual value is not known. Ignore if actual numeric value is known.", "type": "number" }, "unitText": { "description": "A unit associated with the value. E.g.- 'records' for the number of records in a database.", "type": "string" } }, "required" : ["unitText"], "recommended": ["value"], "optional": ["maxValue","minValue"] }, "collectiontypes": { "description": "potential ontology-linked resource types", "@type": "DefinedTerm", "type": "string", "vocabulary": { "ontology": ["ncit"], "children_of": ["http://purl.obolibrary.org/obo/NCIT_C16048"] }, "strict": false }, "definedterm": { "@type": "DefinedTerm", "type": "object", "properties": { "name": { "description": "The name 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 for more details.", "owl:cardinality": "one", "type": "string" }, "url": { "description": "URL of the item.", "owl:cardinality": "one", "type": "string", "format": "uri" }, "curatedBy": { "description": "The person, organization, or catalog that curated this DefinedTerm for the metadata property", "anyOf": [ { "$ref": "#/definitions/person" }, { "$ref": "#/definitions/organization" }, { "$ref": "#/definitions/catalog" }, { "$ref": "#/definitions/researchproject" }, { "$ref": "#/definitions/softwareapplication" } ] }, "termCode": { "description": "A code that identifies this DefinedTerm within a DefinedTermSet.", "type": "string" }, "description": { "description": "A description of the item.", "type": "string" }, "inDefinedTermSet": { "description": "A DefinedTermSet that contains this term.", "type": "string" }, "originalName": { "description": "The original name of the item, before any metadata standardization/normalization", "type": "string" }, "isCurated": { "description": "A boolean indicator describing whether or not this DefinedTerm was curated as the value of a property.", "type": "boolean" } }, "required": [] }, "softwareapplication": { "@type": "SoftwareApplication", "description": "Reusable software or algorithm definition", "properties": { "name": { "description": "name of the software, computational tool, or algorithm.", "type": "string" }, "dateModified": { "description": "date the software, computational tool, or algorithm was run", "type": "string", "format": "date" }, "url": { "description": "url of the software, computational tool, or algorithm", "type": "string", "format": "uri" } }, "required": ["name"], "recommended": ["url"], "optional": ["dateModified"], "type": "object" } } } }, { "@id": "nde:DefinedTerm", "@type": "rdfs:Class", "rdfs:comment": "A word, name, acronym, phrase, etc. with a formal definition. Often used in the context of category or subject classification, glossaries or dictionaries, product or creative work types, etc. Use the name property for the term being defined, use termCode if the term has an alpha-numeric code allocated, use description to provide the definition of the term.", "rdfs:label": "DefinedTerm", "rdfs:subClassOf": { "@id": "schema:DefinedTerm" }, "schema:schemaVersion":["https://schema.org/docs/releases.html#v18.0","v1.2 - 2025.05.29"], "dct:provenance":"Changes since previous version: Replace includedInDataCatalog.dataset with includedInDataCatalog.archivedAt.", "$validation": { "$schema": "http://json-schema.org/draft-07/schema#", "type": "object", "properties": { "name": { "description": "The name of the item.", "owl:cardinality": "one", "type": "string" }, "identifier": { "description": "The identifier property represents any kind of identifier for any kind of Thing, such as ISBNs, GTIN codes, UUIDs etc. Schema.org provides dedicated properties for representing many of these, either as textual strings or as URL (URI) links. See background notes for more details.", "owl:cardinality": "one", "type": "string" }, "url": { "description": "URL of the item.", "owl:cardinality": "one", "type": "string", "format": "uri" }, "curatedBy": { "description": "The person, organization, or catalog that curated this DefinedTerm for the metadata property", "anyOf": [ { "$ref": "#/definitions/person" }, { "$ref": "#/definitions/organization" }, { "$ref": "#/definitions/catalog" }, { "$ref": "#/definitions/researchproject" }, { "$ref": "#/definitions/softwareapplication" } ] }, "termCode": { "description": "A code that identifies this DefinedTerm within a DefinedTermSet.", "type": "string" }, "description": { "description": "A description of the item.", "type": "string" }, "inDefinedTermSet": { "description": "A DefinedTermSet that contains this term.", "type": "string" }, "originalName": { "description": "The original name of the item, before any metadata standardization/normalization", "type": "string" }, "isCurated": { "description": "A boolean indicator describing whether or not this DefinedTerm was curated as the value of a property.", "type": "boolean" } }, "required": [], "recommended": [ "description", "curatedBy", "isCurated" ], "optional": [ "termCode", "inDefinedTermSet", "originalName" ], "anyOf": [ {"required":["name"]}, {"required":["identifier"]}, {"required":["url"]} ], "definitions": { "catalog": { "@type": "DataCatalog", "description": "Data, resource or tool catalog", "type": "object", "properties": { "name": { "description": "Data, resource or tool catalog name", "type": "string" }, "url": { "description": "Link to data, resource or tool catalog", "type": "string", "format": "uri" }, "versionDate": { "description": "date the metadata was harvested from the catalog", "type": "string", "format": "date" }, "archivedAt": { "description": "The url(s) of one or more datasets, tools, resources or other items listed in a DataCatalog or ResourceCatalog", "oneOf": [ { "items": { "type": "string", "format": "uri" }, "type": "array" }, { "type": "string", "format": "uri" } ] } }, "required": ["name", "url"], "recommended": ["versionDate", "archivedAt"] }, "organization": { "@type": "Organization", "description": "Reusable organization definition", "properties": { "affiliation": { "type": "object", "properties": { "name": { "description": "Name of the affiliation, such as a university", "type": "string" }, "sameAs": { "description": "Alias for the affiliation", "type": "string" }, "url": { "description": "URL of the affiliation", "type": "string", "format": "uri" } }, "required": ["name"], "optional": ["sameAs", "url"] }, "alternateName": { "description": "Alias of the name", "oneOf": [ { "type": "array", "items": { "type": "string" } }, { "type": "string" } ] }, "name": { "description": "Name of the organization", "type": "string" }, "parentOrganization": { "description": "Name of the parent organization. For instance, the parentOrganization of NIAID is the National Institutes of health (NIH)", "type": "string" }, "email": { "description": "Email address of the organization", "type": "string" }, "identifier": { "description": "Unique identifier of the organization", "type": "string" }, "role": { "description": "What role the organization played in creating the dataset", "type": "string" }, "url": { "description": "Link to the organization", "type": "string", "format": "uri" } }, "required": ["name"], "recommended": ["identifier"], "optional": ["affiliation", "alternateName", "email", "parentOrganization", "role", "url"], "type": "object" }, "researchproject": { "@type": "ResearchProject", "description": "a type of organization definition", "properties": { "alternateName": { "description": "Alias of the name", "oneOf": [ { "type": "array", "items": { "type": "string" } }, { "type": "string" } ] }, "name": { "description": "Name of the organization", "type": "string" }, "parentOrganization": { "description": "Name of the parent organization. For instance, the parentOrganization of NIAID is the National Institutes of health (NIH)", "type": "string" }, "email": { "description": "Email address of the organization", "type": "string" }, "identifier": { "description": "Unique identifier of the organization", "type": "string" }, "url": { "description": "Link to the organization", "type": "string", "format": "uri" } }, "required": ["name"], "recommended": ["identifier", "url", "parentOrganization"], "optional": ["alternateName", "email", "role"], "type": "object" }, "person": { "@type": "Person", "description": "Reusable person definition", "properties": { "affiliation": { "type": "object", "properties": { "name": { "description": "Name of the affiliation, such as a university", "type": "string" }, "sameAs": { "description": "Alias for the affiliation", "type": "string" }, "url": { "description": "URL of the affiliation", "type": "string", "format": "uri" } }, "required": ["name"], "optional": ["sameAs", "url"] }, "name": { "description": "Name of the person", "type": "string" }, "email": { "description": "Email address of the person", "type": "string" }, "familyName": { "description": "Family name (surname) of the person", "type": "string" }, "givenName": { "description": "Given (first) name of the person", "type": "string" }, "identifier": { "description": "Unique identifier of the person, like an ORCID ID", "type": "string" }, "role": { "description": "Role the person played in creating the resource catalog", "type": "string" }, "title": { "description": "Title of the person", "type": "string" }, "url": { "description": "Link to the homepage or other web content describing the person", "type": "string", "format": "uri" } }, "required": ["name"], "recommended": ["familyName", "givenName ", "identifier "], "optional": ["affiliation", "email", "role", "title", "url"], "type": "object" }, "softwareapplication": { "@type": "SoftwareApplication", "description": "Reusable software or algorithm definition", "properties": { "name": { "description": "name of the software, computational tool, or algorithm.", "type": "string" }, "dateModified": { "description": "date the software, computational tool, or algorithm was run", "type": "string", "format": "date" }, "url": { "description": "url of the software, computational tool, or algorithm", "type": "string", "format": "uri" } }, "required": ["name"], "recommended": ["url"], "optional": ["dateModified"], "type": "object" } } } }, { "@id": "nde:Sample", "@type": "rdfs:Class", "rdfs:comment": "Samples contained in the NIAID Data Ecosystem. A Sample is a material entity taken from a larger source, system, or environment, collected for the purpose of analysis, testing, identification, or demonstration. The NIAID Data Ecosystem Discovery Portal harvests metadata from repositories and harmonizes them to this schema to enable easy cross-platform sample searching and filtering.", "abstract": "Samples contained in the NIAID Data Ecosystem. A sample is a material entity taken from a larger source.", "rdfs:label": "Sample", "rdfs:subClassOf": [ { "@id": "bioschemastypesdrafts:BioSample" }, { "@id": "schema:CreativeWork" } ], "schema:schemaVersion":["https://schema.org/docs/releases.html#v18.0","v0.5 - 2026.02.04"], "dct:provenance":"Changes since previous version: Allow DefinedTerm as an expected type for experimentalPurpose.", "$validation": { "$schema": "http://json-schema.org/draft-07/schema#", "type": "object", "properties": { "name": { "description": "Sample name.", "owl:cardinality": "one", "type": "string" }, "description": { "description": "A description of the sample.", "owl:cardinality": "one", "type": "string" }, "identifier": { "description": "Sample identifier or accession number, such as a digital object identifier (DOI), sequence read archive (SRA) or GenBank accession number, etc.", "abstract": "identifier or accession number", "oneOf": [ { "type": "string" }, { "items": { "type": "string" }, "type": "array" } ], "owl:cardinality": "many" }, "sameAs": { "description": "URL of additional sources for the work.", "oneOf": [ { "items": { "type": "string", "format": "uri" }, "type": "array" }, { "type": "string", "format": "uri" } ], "owl:cardinality": "many" }, "url": { "description": "URL of the work.", "type": "string", "format": "uri", "owl:cardinality": "one" }, "usageInfo": { "description": "The terms under which the sample can be used. Note that this is related to but distinct from the license.", "abstract": "sample usage agreement", "oneOf": [ { "type": "array", "items": { "$ref": "#/definitions/creativework" } }, { "$ref": "#/definitions/creativework" } ], "owl:cardinality": "many" }, "license": { "description": "A license document that applies to this work, typically indicated by URL.", "abstract": "license for use", "format": "uri", "owl:cardinality": "one", "type": "string" }, "conditionsOfAccess": { "description": "Conditions that affect the availability of, or method(s) of access to, the sample. Options include open (freely available), restricted (may include restrictions such as on use), closed (requires registration to access), or embargoed (unpublished).", "abstract": "accessibility of the work", "type": "string", "enum": ["Closed", "Open", "Restricted", "Embargoed"], "owl:cardinality": "one" }, "isAccessibleForFree": { "description": "A flag to signal that the sample may be requested at no cost (not including shipping).", "abstract": "accessible without charge", "type": "boolean", "owl:cardinality": "one" }, "includedInDataCatalog": { "description": "Data or resource catalog where the sample is listed; original source of the metadata.", "abstract": "catalog containing the work", "oneOf": [ { "$ref": "#/definitions/catalog" }, { "type": "array", "items": { "$ref": "#/definitions/catalog" } } ], "owl:cardinality": "one" }, "associatedPhenotype": { "description": "one or more observable traits or conditions relevant to the source of the sample.", "anyOf": [ { "description": "collection of vocabulary terms defined in ontologies", "strict": false, "type": "string", "vocabulary": { "children_of": ["http://purl.obolibrary.org/obo/UPHENO_0001001", "http://purl.obolibrary.org/obo/PATO_0000001"], "ontology": ["UPHENO","PATO"] } }, { "items": { "description": "collection of vocabulary terms defined in ontologies", "strict": false, "type": "string", "vocabulary": { "children_of": ["http://purl.obolibrary.org/obo/UPHENO_0001001", "http://purl.obolibrary.org/obo/PATO_0000001"], "ontology": ["UPHENO","PATO"] } }, "type": "array" }, { "type": "array", "items": { "$ref": "#/definitions/definedterm" } }, { "$ref": "#/definitions/definedterm" }, { "type": "array", "items": { "$ref": "#/definitions/quantitativevalue" } }, { "$ref": "#/definitions/quantitativevalue" } ], "owl:cardinality": "many" }, "associatedGenotype": { "description": "One or more genetic variants or molecular features observed or inferred from the sample.", "anyOf": [ { "description": "collection of vocabulary terms defined in ontologies", "strict": false, "type": "string", "vocabulary": { "children_of": ["http://purl.obolibrary.org/obo/NCIT_C16612", "http://purl.obolibrary.org/obo/NCIT_C20181","http://purl.obolibrary.org/obo/NCIT_C17649"], "ontology": ["NCIT"] } }, { "items": { "description": "collection of vocabulary terms defined in ontologies", "strict": false, "type": "string", "vocabulary": { "children_of": ["http://purl.obolibrary.org/obo/NCIT_C16612", "http://purl.obolibrary.org/obo/NCIT_C20181","http://purl.obolibrary.org/obo/NCIT_C17649"], "ontology": ["NCIT"] } }, "type": "array" }, { "type": "array", "items": { "$ref": "#/definitions/definedterm" } }, { "$ref": "#/definitions/definedterm" } ], "owl:cardinality": "many" }, "cellType": { "description": "The type of cell represented in or derived from the biological sample, based on morphology, lineage, or molecular markers.", "anyOf": [ { "description": "collection of vocabulary terms defined in ontologies", "strict": false, "type": "string", "vocabulary": { "children_of": ["http://purl.obolibrary.org/obo/CL_0000000", "http://purl.obolibrary.org/obo/CLO_0000031"], "ontology": ["CL","CLO"] } }, { "items": { "description": "collection of vocabulary terms defined in ontologies", "strict": false, "type": "string", "vocabulary": { "children_of": ["http://purl.obolibrary.org/obo/CL_0000000", "http://purl.obolibrary.org/obo/CLO_0000031"], "ontology": ["CL","CLO"] } }, "type": "array" }, { "type": "array", "items": { "$ref": "#/definitions/definedterm" } }, { "$ref": "#/definitions/definedterm" } ], "owl:cardinality": "many" }, "infectiousAgent": { "description": "Infectious agent(s) / pathogen(s) which are the focus of the work (like SARS-CoV-2).", "abstract": "infectious agent / pathogen", "anyOf": [ { "description": "collection of vocabulary terms defined in ontologies", "strict": false, "type": "string", "vocabulary": { "children_of": ["http://purl.obolibrary.org/obo/NCBITaxon_10239", "http://purl.obolibrary.org/obo/NCBITaxon_2"], "ontology": ["ncbitaxon"] } }, { "items": { "description": "collection of vocabulary terms defined in ontologies", "strict": false, "type": "string", "vocabulary": { "children_of": ["http://purl.obolibrary.org/obo/NCBITaxon_10239", "http://purl.obolibrary.org/obo/NCBITaxon_2"], "ontology": ["ncbitaxon"] } }, "type": "array" }, { "type": "array", "items": { "$ref": "#/definitions/definedterm" } }, { "$ref": "#/definitions/definedterm" } ], "owl:cardinality": "many" }, "healthCondition": { "description": "The health condition(s) /infectious disease(s) which are the focus of the work (like COVID-19, coronavirus).", "abstract": "health condition/disease", "anyOf": [ { "description": "collection of vocabulary terms defined in ontologies", "strict": false, "type": "string", "vocabulary": { "children_of": ["http://purl.obolibrary.org/obo/MONDO_0000001", "http://purl.obolibrary.org/obo/DOID_4", "http://purl.obolibrary.org/obo/HP_0000001", "http://purl.obolibrary.org/obo/NCIT_C7057"], "ontology": ["mondo","hpo","doid","ncit"] } }, { "items": { "description": "collection of vocabulary terms defined in ontologies", "strict": false, "type": "string", "vocabulary": { "children_of": ["http://purl.obolibrary.org/obo/MONDO_0000001", "http://purl.obolibrary.org/obo/DOID_4", "http://purl.obolibrary.org/obo/HP_0000001", "http://purl.obolibrary.org/obo/NCIT_C7057"], "ontology": ["mondo","hpo","doid","ncit"] } }, "type": "array" }, { "type": "array", "items": { "$ref": "#/definitions/definedterm" } }, { "$ref": "#/definitions/definedterm" } ], "owl:cardinality": "many" }, "funding": { "description": "Funding that supports (sponsors) the collection of this dataset through some kind of financial contribution.", "abstract": "funding source (grant, contract, etc.)", "oneOf": [ { "type": "object", "@type": "MonetaryGrant", "description": "Funding that supports (sponsors) the collection of this dataset through some kind of financial contribution", "properties": { "funder": { "description": "An organization associated with a creator or funder of a dataset", "oneOf": [ { "type": "object", "@type": "Organization", "description": "Information about a single funder", "properties": { "name": { "type": "string", "description": "An organization associated with a creator or funder of a dataset" }, "parentOrganization": { "type": "string", "description": "name of the parent funding organization" } }, "required": [ "name" ] }, { "type": "array", "items": { "type": "object", "@type": "Organization", "description": "Information about a single funder", "properties": { "name": { "type": "string", "description": "An organization associated with a creator or funder of a dataset" }, "parentOrganization": { "type": "string", "description": "name of the parent funding organization" } }, "required": [ "name" ] } } ] }, "description": { "type": "string", "description": "description about the funding award / grant" }, "url": { "type": "string", "description": "award / grant URL" }, "identifier": { "type": "string", "description": "Unique identifier(s) for the grant(s) used to fund the Dataset" } }, "required": [ "funder", "identifier" ] }, { "type": "array", "items": { "type": "object", "@type": "MonetaryGrant", "description": "Funding that supports (sponsors) the collection of this dataset through some kind of financial contribution", "properties": { "funder": { "description": "An organization associated with a creator or funder of a dataset", "oneOf": [ { "type": "object", "@type": "Organization", "description": "Information about a single funder", "properties": { "name": { "type": "string", "description": "An organization associated with a creator or funder of a dataset" }, "parentOrganization": { "type": "string", "description": "name of the parent funding organization" } }, "required": [ "name" ] }, { "type": "array", "items": { "type": "object", "@type": "Organization", "description": "Information about a single funder", "properties": { "name": { "type": "string", "description": "An organization associated with a creator or funder of a dataset" }, "parentOrganization": { "type": "string", "description": "name of the parent funding organization" } }, "required": [ "name" ] } } ] }, "description": { "type": "string", "description": "description about the funding award / grant" }, "url": { "type": "string", "description": "award / grant URL" }, "identifier": { "type": "string", "description": "Unique identifier(s) for the grant(s) used to fund the Dataset" } }, "required": [ "funder", "identifier" ] } } ], "owl:cardinality": "many" }, "species": { "description": "Species / host organism from which the dataset has been collected.", "abstract": "species/host organism", "anyOf": [ { "description": "collection of vocabulary terms defined in ontologies", "strict": false, "type": "string", "vocabulary": { "children_of": ["http://purl.obolibrary.org/obo/NCBITaxon_131567", "http://purl.obolibrary.org/obo/NCBITaxon_10239"], "ontology": ["ncbitaxon"] } }, { "items": { "description": "collection of vocabulary terms defined in ontologies", "strict": false, "type": "string", "vocabulary": { "children_of": ["http://purl.obolibrary.org/obo/NCBITaxon_131567", "http://purl.obolibrary.org/obo/NCBITaxon_10239"], "ontology": ["ncbitaxon"] } }, "type": "array" }, { "type": "array", "items": { "$ref": "#/definitions/definedterm" } }, { "$ref": "#/definitions/definedterm" } ], "owl:cardinality": "many" }, "citedBy": { "description": "Publications, datasets, or computational tools that cite the sample. Examples: a dataset which reuses the sample in a secondary study.", "anyOf": [ { "type": "array", "items": { "$ref": "#/definitions/citation" } }, { "$ref": "#/definitions/citation" }, { "type": "array", "items": { "$ref": "#/definitions/creativework" } }, { "$ref": "#/definitions/creativework" } ], "owl:cardinality": "many" }, "isRelatedTo": { "description": "Datasets, resources, or samples which are related to the given sample; often sample involved in the same study. These linkages are created via human curation.", "abstract": "related resources or samples (via curation)", "anyOf": [ { "type": "array", "items": { "$ref": "#/definitions/citation" } }, { "$ref": "#/definitions/citation" }, { "type": "array", "items": { "$ref": "#/definitions/creativework" } }, { "$ref": "#/definitions/creativework" }, { "type": "array", "items": { "$ref": "#/definitions/sample" } }, { "$ref": "#/definitions/sample" } ], "owl:cardinality": "many" }, "isSimilarTo": { "description": "Datasets, resources, or samples which are similar to the sample, based on terms in the names, descriptions, authors, measurementTechniques, infectiousAgents, healthConditions, etc.", "abstract": "similar resources of samples (auto-assigned)", "anyOf": [ { "type": "array", "items": { "$ref": "#/definitions/citation" } }, { "$ref": "#/definitions/citation" }, { "type": "array", "items": { "$ref": "#/definitions/creativework" } }, { "$ref": "#/definitions/creativework" }, { "type": "array", "items": { "$ref": "#/definitions/sample" } }, { "$ref": "#/definitions/sample" } ], "owl:cardinality": "many" }, "isBasisFor": { "description": "A resource or sample which reuses the sample. For example, a sample of a cell line that was created by knocking out a gene from this cell line sample. Another example would be a sample of infected tissue that was derived from this tissue sample by infecting it with a virus.", "anyOf": [ { "type": "array", "items": { "$ref": "#/definitions/citation" } }, { "$ref": "#/definitions/citation" }, { "type": "array", "items": { "$ref": "#/definitions/creativework" } }, { "$ref": "#/definitions/creativework" }, { "type": "array", "items": { "$ref": "#/definitions/sample" } }, { "$ref": "#/definitions/sample" } ], "owl:cardinality": "many" }, "isBasedOn": { "description": "A resource or sample from which this sample is derived, modified, or adapted. For example a sample of a cell line, which was infected by virus sample in order to create the sample. ", "abstract": "resource or sample used to create the sample.", "owl:cardinality": "many", "anyOf": [ { "type": "array", "items": { "$ref": "#/definitions/citation" } }, { "$ref": "#/definitions/citation" }, { "type": "array", "items": { "$ref": "#/definitions/creativework" } }, { "$ref": "#/definitions/creativework" }, { "type": "array", "items": { "$ref": "#/definitions/sample" } }, { "$ref": "#/definitions/sample" } ] }, "hasPart": { "description": "Associated materials that constitute the sample. For example, other samples (if sample was created by pooling samples), additives, cryoprotective agents, etc. Use 'hasPart' for samples that were generated by pooling other samples. For example, a synthetic microbiome sample may use 'hasPart' to list the individual microbial samples used to generate it.", "abstract": "Associated materials or samples that constitute the sample", "anyOf": [ { "type": "array", "items": { "$ref": "#/definitions/citation" } }, { "$ref": "#/definitions/citation" }, { "type": "array", "items": { "$ref": "#/definitions/creativework" } }, { "$ref": "#/definitions/creativework" }, { "type": "array", "items": { "$ref": "#/definitions/sample" } }, { "$ref": "#/definitions/sample" } ], "owl:cardinality": "many" }, "isPartOf": { "description": "Associated materials the sample may help constitute. For example, the pooled sample that used this sample. Use 'isPartOf' for pooled samples generated from this sample. For example, a microbial sample that was used to generate a synthetic microbiome sample.", "abstract": "study or project including the work", "owl:cardinality": "many", "anyOf": [ { "type": "array", "items": { "$ref": "#/definitions/citation" } }, { "$ref": "#/definitions/citation" }, { "type": "array", "items": { "$ref": "#/definitions/creativework" } }, { "$ref": "#/definitions/creativework" }, { "type": "array", "items": { "$ref": "#/definitions/sample" } }, { "$ref": "#/definitions/sample" } ] }, "anatomicalSystem": { "description": "Indicate the anatomical system from which the sample is collect, e.g. circulatory, digestive, endocrine, immune and other systems.", "anyOf": [ { "description": "collection of vocabulary terms defined in ontologies", "strict": false, "type": "string", "vocabulary": { "children_of": ["http://purl.obolibrary.org/obo/UBERON_0000467"], "ontology": ["UBERON"] } }, { "items": { "description": "collection of vocabulary terms defined in ontologies", "strict": false, "type": "string", "vocabulary": { "children_of": ["http://purl.obolibrary.org/obo/UBERON_0000467"], "ontology": ["UBERON"] } }, "type": "array" }, { "type": "array", "items": { "$ref": "#/definitions/definedterm" } }, { "$ref": "#/definitions/definedterm" } ], "owl:cardinality": "many" }, "anatomicalStructure": { "description": "Indicate the organ, tissues the sample was collected from.", "anyOf": [ { "description": "collection of vocabulary terms defined in ontologies", "strict": false, "type": "string", "vocabulary": { "children_of": ["http://purl.obolibrary.org/obo/UBERON_0001062"], "ontology": ["UBERON"] } }, { "items": { "description": "collection of vocabulary terms defined in ontologies", "strict": false, "type": "string", "vocabulary": { "children_of": ["http://purl.obolibrary.org/obo/UBERON_0001062"], "ontology": ["UBERON"] } }, "type": "array" }, { "type": "array", "items": { "$ref": "#/definitions/definedterm" } }, { "$ref": "#/definitions/definedterm" } ], "owl:cardinality": "many" }, "sex": { "description": "The biological sex of the individual from which the sample was obtained.", "anyOf": [ { "description": "collection of vocabulary terms defined in ontologies", "strict": false, "type": "string", "vocabulary": { "children_of": ["http://purl.obolibrary.org/obo/PATO_0000047"], "ontology": ["PATO"] } }, { "items": { "description": "collection of vocabulary terms defined in ontologies", "strict": false, "type": "string", "vocabulary": { "children_of": ["http://purl.obolibrary.org/obo/PATO_0000047"], "ontology": ["PATO"] } }, "type": "array" }, { "type": "array", "items": { "$ref": "#/definitions/definedterm" } }, { "$ref": "#/definitions/definedterm" } ], "owl:cardinality": "many" }, "developmentalStage": { "description": "A temporal subdivision of a developmental process, indicating the age or stage of the object when the sample was created.", "anyOf": [ { "description": "collection of vocabulary terms defined in ontologies", "strict": false, "type": "string", "vocabulary": { "children_of": ["http://purl.obolibrary.org/obo/UBERON_0000104","http://purl.obolibrary.org/obo/NCIT_C48308"], "ontology": ["UBERON","NCIT"] } }, { "items": { "description": "collection of vocabulary terms defined in ontologies", "strict": false, "type": "string", "vocabulary": { "children_of": ["http://purl.obolibrary.org/obo/UBERON_0000104","http://purl.obolibrary.org/obo/NCIT_C48308"], "ontology": ["UBERON","NCIT"] } }, "type": "array" }, { "type": "array", "items": { "$ref": "#/definitions/definedterm" } }, { "$ref": "#/definitions/definedterm" }, { "type": "array", "items": { "$ref": "#/definitions/quantitativevalue" } }, { "$ref": "#/definitions/quantitativevalue" } ], "owl:cardinality": "many" }, "sampleAvailability": { "description": "A flag to signal that the sample is available for reuse.", "abstract": "availability of the sample", "type": "boolean", "owl:cardinality": "one" }, "sampleProcess": { "description": "The processing technique that was applied to the sample, methods used to prepare the samples.", "anyOf": [ { "description": "collection of vocabulary terms defined in ontologies", "strict": false, "type": "string", "vocabulary": { "children_of": ["http://purl.obolibrary.org/obo/OBI_0000094","http://purl.obolibrary.org/obo/NCIT_C48177","http://purl.obolibrary.org/obo/NCIT_C16680"], "ontology": ["OBI","NCIT"] } }, { "items": { "description": "collection of vocabulary terms defined in ontologies", "strict": false, "type": "string", "vocabulary": { "children_of": ["http://purl.obolibrary.org/obo/OBI_0000094","http://purl.obolibrary.org/obo/NCIT_C48177","http://purl.obolibrary.org/obo/NCIT_C16680"], "ontology": ["OBI","NCIT"] } }, "type": "array" }, { "type": "array", "items": { "$ref": "#/definitions/definedterm" } }, { "$ref": "#/definitions/definedterm" }, { "type": "array", "items": { "$ref": "#/definitions/creativework" } }, { "$ref": "#/definitions/creativework" }, { "type":"string" } ], "owl:cardinality": "many" }, "sampleQuantity": { "description": "A numeric value for a measurement of the size of a sample. If completely unknown, set value = 0, and unitText = 'unknown'", "oneOf": [ { "type": "array", "items": { "$ref": "#/definitions/quantitativevalue" } }, { "$ref": "#/definitions/quantitativevalue" } ], "owl:cardinality": "many" }, "sampleState": { "description": "Specify the condition, composition or state of the sample, for example dried, frozen, passage number.", "anyOf": [ { "type": "string" }, { "type": "array", "items": { "$ref": "#/definitions/quantitativevalue" } }, { "$ref": "#/definitions/quantitativevalue" } ], "owl:cardinality": "many" }, "sampleStorageTemperature": { "description": "The temperature at which the sample is stored.", "oneOf": [ { "type": "array", "items": { "$ref": "#/definitions/quantitativevalue" } }, { "$ref": "#/definitions/quantitativevalue" } ], "owl:cardinality": "one" }, "sampleType": { "description": "The type of sample or specimen.", "anyOf": [ { "description": "collection of vocabulary terms defined in ontologies", "strict": false, "type": "string", "vocabulary": { "children_of": ["http://purl.obolibrary.org/obo/BFO_0000040"], "ontology": ["OBI"] } }, { "items": { "description": "collection of vocabulary terms defined in ontologies", "strict": false, "type": "string", "vocabulary": { "children_of": ["http://purl.obolibrary.org/obo/BFO_0000040"], "ontology": ["OBI"] } }, "type": "array" }, { "type": "array", "items": { "$ref": "#/definitions/definedterm" } }, { "$ref": "#/definitions/definedterm" } ], "owl:cardinality": "many" }, "distribution": { "description": "A downloadable form of this dataset, at a specific location, in a specific format.", "abstract": "download link", "oneOf": [ { "items": { "@type": "DataDownload", "description": "A dataset in downloadable form.", "properties": { "contentUrl": { "format": "uri", "type": "string" }, "encodingFormat": { "description": "file type (ex: XLSX)", "type": "string" }, "dateModified": { "format": "date", "description": "date the file was modified", "type": "string" } }, "required": ["dateModified", "contentUrl"], "type": "object" }, "type": "array" }, { "@type": "DataDownload", "description": "A dataset in downloadable form.", "properties": { "contentUrl": { "format": "uri", "type": "string" }, "encodingFormat": { "description": "file type (ex: XLSX)", "type": "string" }, "dateModified": { "format": "date", "description": "date the file was modified", "type": "string" } }, "required": ["dateModified", "contentUrl"], "type": "object" } ], "owl:cardinality": "many" }, "measurementTechnique": { "description": "A technique or technology used in the collection or processing of the sample corresponding to the method used for measuring the corresponding variable(s) (described using variableMeasured). For example, if variableMeasured is cell density or cell counts, measurementTechnique could be: \"centrifugation\" or \"flow cytometry\".", "abstract": "measurement technique used to collect, process, or generate the sample", "anyOf": [ { "description": "collection of vocabulary terms defined in ontologies", "strict": false, "type": "string", "vocabulary": { "children_of": ["http://edamontology.org/topic_3361", "http://purl.obolibrary.org/obo/NCIT_C20368", "http://purl.obolibrary.org/obo/MMO_0000000", "http://www.ebi.ac.uk/efo/EFO_0000001"], "ontology": ["edam", "ncit", "mmo","efo"] } }, { "items": { "description": "collection of vocabulary terms defined in ontologies", "strict": false, "type": "string", "vocabulary": { "children_of": ["http://edamontology.org/topic_3361", "http://purl.obolibrary.org/obo/NCIT_C20368", "http://purl.obolibrary.org/obo/MMO_0000000", "http://www.ebi.ac.uk/efo/EFO_0000001"], "ontology": ["edam", "ncit", "mmo","efo"] } }, "type": "array" }, { "type": "array", "items": { "$ref": "#/definitions/definedterm" } }, { "$ref": "#/definitions/definedterm" } ], "owl:cardinality": "many" }, "variableMeasured": { "description": "Variables measured within the sample.", "oneOf": [ { "description": "collection of vocabulary terms defined in ontologies", "strict": false, "type": "string", "vocabulary": { "children_of": ["http://www.ebi.ac.uk/efo/EFO_0000001", "http://purl.obolibrary.org/obo/CMO_0000000", "http://purl.obolibrary.org/obo/NCIT_C25209"], "ontology": ["efo", "cmo","ncit"] } }, { "items": { "description": "collection of vocabulary terms defined in ontologies", "strict": false, "type": "string", "vocabulary": { "children_of": ["http://www.ebi.ac.uk/efo/EFO_0000001", "http://purl.obolibrary.org/obo/CMO_0000000", "http://purl.obolibrary.org/obo/NCIT_C25209"], "ontology": ["efo", "cmo","ncit"] } }, "type": "array" }, { "type": "array", "items": { "$ref": "#/definitions/definedterm" } }, { "$ref": "#/definitions/definedterm" } ], "owl:cardinality": "many" }, "collectionMethod": { "description": "Provide information about the conditions and methods of acquisition of samples. ", "anyOf": [ { "type": "string", "format": "uri" }, { "items": { "type": "string", "format": "uri" }, "type": "array" }, { "type": "string" }, { "items": { "type": "string" }, "type": "array" }, { "type": "array", "items": { "$ref": "#/definitions/definedterm" } }, { "$ref": "#/definitions/definedterm" } ], "owl:cardinality": "many" }, "instrument": { "description": "Provide description of instruments and devices used in collecting, processing and analysis of samples.", "anyOf": [ { "type": "string", "format": "uri" }, { "items": { "type": "string", "format": "uri" }, "type": "array" }, { "type": "string" }, { "items": { "type": "string" }, "type": "array" }, { "type": "array", "items": { "$ref": "#/definitions/definedterm" } }, { "$ref": "#/definitions/definedterm" } ], "owl:cardinality": "many" }, "environmentalSystem": { "description": "A category or description of the habitat that describes elements of an ecosystem where the sample was collected. Where possible use controlled vocabulary such as ENVO.", "anyOf": [ { "description": "collection of vocabulary terms defined in ontologies", "strict": false, "type": "string", "vocabulary": { "children_of": ["http://purl.obolibrary.org/obo/ENVO_00010483","http://purl.obolibrary.org/obo/NCIT_C62574"], "ontology": ["ENVO","NCIT"] } }, { "items": { "description": "collection of vocabulary terms defined in ontologies", "strict": false, "type": "string", "vocabulary": { "children_of": ["http://purl.obolibrary.org/obo/ENVO_00010483","http://purl.obolibrary.org/obo/NCIT_C62574"], "ontology": ["ENVO","NCIT"] } }, "type": "array" }, { "type": "array", "items": { "$ref": "#/definitions/definedterm" } }, { "$ref": "#/definitions/definedterm" } ], "owl:cardinality": "many" }, "experimentalPurpose": { "description": "Describe the planned or executed experimental procedures involving the samples.", "anyOf": [ { "type": "string" }, { "items": { "type": "string" }, "type": "array" }, { "type": "array", "items": { "$ref": "#/definitions/definedterm" } }, { "$ref": "#/definitions/definedterm" } ], "owl:cardinality": "many" }, "aggregateRating": { "description": "The overall rating, based on a collection of reviews or ratings, of the work. These ratings can be collected based on user reviews or through Altmetric scores of web-based citations.", "abstract": "rating of the work", "oneOf": [ { "items": { "@type": "AggregateRating", "type": "object", "properties": { "ratingCount": { "description": "Total number of ratings", "type": "integer" }, "ratingValue": { "description": "Average rating", "type": "string" }, "itemReviewed": { "description": "What is being reviewed", "type": "string" } }, "required": ["ratingValue"], "recommended": ["ratingCount", "itemReviewed"] }, "type": "array" }, { "@type": "AggregateRating", "type": "object", "properties": { "ratingCount": { "description": "Total number of ratings", "type": "integer" }, "ratingValue": { "description": "Average rating", "type": "string" }, "itemReviewed": { "description": "What is being reviewed", "type": "string" } }, "required": ["ratingValue"], "recommended": ["ratingCount", "itemReviewed"] } ], "owl:cardinality": "many" }, "author": { "description": "A person or organization responsible for the collection, processing, or maintenance of the sample: Populated from collector, contributor, and maintainer.", "anyOf": [ { "type": "array", "items": { "$ref": "#/definitions/person" } }, { "$ref": "#/definitions/person" }, { "type": "array", "items": { "$ref": "#/definitions/organization" } }, { "$ref": "#/definitions/organization" } ], "owl:cardinality": "many" }, "collector": { "description": "The Person or Organization who collected the Sample.", "anyOf": [ { "type": "array", "items": { "$ref": "#/definitions/person" } }, { "$ref": "#/definitions/person" }, { "type": "array", "items": { "$ref": "#/definitions/organization" } }, { "$ref": "#/definitions/organization" } ], "owl:cardinality": "many" }, "contributor": { "description": "Person or organization that contributes to the work.", "anyOf": [ { "type": "array", "items": { "$ref": "#/definitions/person" } }, { "$ref": "#/definitions/person" }, { "type": "array", "items": { "$ref": "#/definitions/organization" } }, { "$ref": "#/definitions/organization" } ], "owl:cardinality": "many" }, "maintainer": { "description": "The Person or Organization who is responsible for the Sample.", "anyOf": [ { "type": "array", "items": { "$ref": "#/definitions/person" } }, { "$ref": "#/definitions/person" }, { "type": "array", "items": { "$ref": "#/definitions/organization" } }, { "$ref": "#/definitions/organization" } ], "owl:cardinality": "many" }, "locationOfOrigin": { "description": "The location from which the sample was originally collected.", "oneOf": [ { "items": { "@type": "AdministrativeArea", "description": "Location information", "properties": { "administrativeType": { "description": "the type of administrative area, such as country, state, county, or city", "enum": ["province", "district", "chiefdom", "village", "city", "country", "prefecture", "sub-prefecture", "clan", "Federal Capital Territory", "state", "Local Government Area", "ward"], "type": "string" }, "alternateName": { "description": "An alias for the location", "oneOf": [ { "type": "string" }, { "items": { "type": "string" }, "type": "array" } ] }, "identifier": { "description": "An identifier for the location, preferably a Wikidata ID", "type": "string" }, "locationType": { "description": "Categorization of how the location relates to the dataset", "const": "collection" }, "name": { "description": "The name of the location", "type": "string" } }, "type": "object" }, "type": "array" }, { "@type": "AdministrativeArea", "type": "object", "description": "Location information", "properties": { "administrativeType": { "description": "the type of administrative area, such as country, state, county, or city", "enum": ["province", "district", "chiefdom", "village", "city", "country", "prefecture", "sub-prefecture", "clan", "Federal Capital Territory", "state", "Local Government Area", "ward"], "type": "string" }, "alternateName": { "description": "An alias for the location", "oneOf": [ { "type": "string" }, { "items": { "type": "string" }, "type": "array" } ] }, "identifier": { "description": "An identifier for the location, preferably a Wikidata ID", "type": "string" }}, "locationType": { "description": "Categorization of how the location relates to the dataset", "const": "collection" }, "name": { "description": "The name of the location", "type": "string" } } ], "owl:cardinality": "many" }, "itemLocation": { "description": "The location where the sample is stored and/or may be ordered.", "oneOf": [ { "type": "array", "items": { "@type": "AdministrativeArea", "description": "Location information", "type": "object", "properties": { "administrativeType": { "description": "the type of administrative area, such as country, state, county, or city", "enum": ["province", "district", "chiefdom", "village", "city", "country", "prefecture", "sub-prefecture", "clan", "Federal Capital Territory", "state", "Local Government Area", "ward"], "type": "string" }, "alternateName": { "description": "An alias for the location", "oneOf": [ { "type": "string" }, { "items": { "type": "string" }, "type": "array" } ] }, "identifier": { "description": "An identifier for the location, preferably a Wikidata ID", "type": "string" }, "locationType": { "description": "Categorization of how the location relates to the dataset", "const": "storage" }, "name": { "description": "The name of the location", "type": "string" } } } }, { "@type": "AdministrativeArea", "type": "object", "description": "Location information", "properties": { "administrativeType": { "description": "the type of administrative area, such as country, state, county, or city", "enum": ["province", "district", "chiefdom", "village", "city", "country", "prefecture", "sub-prefecture", "clan", "Federal Capital Territory", "state", "Local Government Area", "ward"], "type": "string" }, "alternateName": { "description": "An alias for the location", "oneOf": [ { "type": "string" }, { "items": { "type": "string" }, "type": "array" } ] }, "identifier": { "description": "An identifier for the location, preferably a Wikidata ID", "type": "string" }}, "locationType": { "description": "Categorization of how the location relates to the dataset", "const": "storage" }, "name": { "description": "The name of the location", "type": "string" } } ], "owl:cardinality": "many" }, "citation": { "description": "The primary citation or reference to a publication, dataset, or computational tool which uses the sample. Examples: a publication which describes the creation/collection/processing of the sample. The original reference by the sample collectors/processors/maintainers that should be cited when reusing the sample. For all other references by others reusing the sample, use 'citedBy'.", "abstract": "primary citation to the work", "owl:cardinality": "many", "anyOf": [ { "type": "array", "items": { "$ref": "#/definitions/citation" } }, { "$ref": "#/definitions/citation" }, { "type": "array", "items": { "$ref": "#/definitions/creativework" } }, { "$ref": "#/definitions/creativework" } ] }, "date": { "description": "Date the sample has changed: most recent date of dateModified, dateProcessed, and dateCollected.", "abstract": "date changed", "format": "date", "type": "string", "owl:cardinality": "one" }, "dateCreated": { "description": "Date the work was created.", "format": "date", "type": "string", "owl:cardinality": "one" }, "dateModified": { "description": "Date the work was modified.", "format": "date", "type": "string", "owl:cardinality": "one" }, "datePublished": { "description": "Date the work was first published.", "format": "date", "type": "string", "owl:cardinality": "one" }, "dateCollected": { "description": "The date on which the sample was collected.", "format": "date", "type": "string", "owl:cardinality": "one" }, "dateProcessed": { "description": "The date the sample was processed or used in a method.", "format": "date", "type": "string", "owl:cardinality": "one" }, "interactionStatistic": { "description": "The number of interactions with the work, such as page views or tool downloads.", "abstract": "views or downloads", "oneOf": [ { "items": { "@type": "InteractionCounter", "type": "object", "properties": { "interactionType": { "type": "string" }, "userInteractionCount": { "type": "integer" } }, "required": ["interactionType", "userInteractionCount"] }, "type": "array" }, { "@type": "InteractionCounter", "type": "object", "properties": { "interactionType": { "type": "string" }, "userInteractionCount": { "type": "integer" } }, "required": ["interactionType", "userInteractionCount"] } ], "owl:cardinality": "many" }, "keywords": { "description": "Keywords or tags used to describe this work.", "abstract": "keywords or tags", "oneOf": [ { "type": "array", "items": { "type": "string" } }, { "type": "string" } ], "owl:cardinality": "many" }, "sdPublisher": { "description": "Original publisher of the sample metadata (like NCBI GEO, SRA, etc.).", "abstract": "original metadata source", "oneOf": [ { "$ref": "#/definitions/catalog" }, { "type": "array", "items": { "$ref": "#/definitions/catalog" } } ], "owl:cardinality": "many" }, "spatialCoverage": { "description": "The place(s) which are the focus of the sample.", "abstract": "geographic focus of the work", "oneOf": [ { "items": { "@type": "AdministrativeArea", "description": "Location information", "properties": { "administrativeType": { "description": "the type of administrative area, such as country, state, county, or city", "enum": ["province", "district", "chiefdom", "village", "city", "country", "prefecture", "sub-prefecture", "clan", "Federal Capital Territory", "state", "Local Government Area", "ward"], "type": "string" }, "alternateName": { "description": "An alias for the location", "oneOf": [ { "type": "string" }, { "items": { "type": "string" }, "type": "array" } ] }, "identifier": { "description": "An identifier for the location, preferably a Wikidata ID", "type": "string" }, "locationType": { "description": "Categorization of how the location relates to the dataset", "oneOf": [ { "enum": ["residence", "exposure", "collection", "screening", "treatment", "study location", "other", "unknown"], "type": "string" }, { "items": { "enum": ["residence", "exposure", "collection", "screening", "treatment", "study location", "other", "unknown"], "type": "string" }, "type": "array" } ] }, "name": { "description": "The name of the location", "type": "string" } }, "type": "object" }, "type": "array" }, { "@type": "AdministrativeArea", "description": "Location information", "properties": { "administrativeType": { "description": "the type of administrative area, such as country, state, county, or city", "enum": ["province", "district", "chiefdom", "village", "city", "country", "prefecture", "sub-prefecture", "clan", "Federal Capital Territory", "state", "Local Government Area", "ward"], "type": "string" }, "alternateName": { "description": "An alias for the location", "oneOf": [ { "type": "string" }, { "items": { "type": "string" }, "type": "array" } ] }, "identifier": { "description": "An identifier for the location, preferably a Wikidata ID", "type": "string" }, "locationType": { "description": "Categorization of how the location relates to the dataset", "oneOf": [ { "enum": ["residence", "exposure", "collection", "screening", "treatment", "study location", "other", "unknown"], "type": "string" }, { "items": { "enum": ["residence", "exposure", "collection", "screening", "treatment", "study location", "other", "unknown"], "type": "string" }, "type": "array" } ] }, "name": { "description": "The name of the location", "type": "string" } }, "type": "object" } ], "owl:cardinality": "many" }, "temporalCoverage": { "description": "The period of time covered during sampling.", "abstract": "time period", "oneOf": [ { "items": { "@type": "TemporalInterval", "description": "Temporal information", "properties": { "duration": { "description": "A time interval in ISO 8601 duration format", "type": "string" }, "endDate": { "description": "An end date", "format": "date", "type": "string" }, "name": { "description": "String describing the temporal interval", "type": "string" }, "startDate": { "description": "A start date", "format": "date", "type": "string" }, "temporalType": { "description": "Categorization of how the date/temporal interval relates to the dataset", "oneOf": [ { "enum": ["exposure", "collection", "screening", "treatment", "study date", "other", "unknown"], "type": "string" }, { "items": { "enum": ["exposure", "collection", "screening", "treatment", "study date", "other", "unknown"], "type": "string" }, "type": "array" } ] } }, "type": "object" }, "type": "array" }, { "@type": "TemporalInterval", "description": "Temporal information", "properties": { "duration": { "description": "A time interval in ISO 8601 duration format", "type": "string" }, "endDate": { "description": "An end date", "format": "date", "type": "string" }, "name": { "description": "String describing the temporal interval", "type": "string" }, "startDate": { "description": "A start date", "format": "date", "type": "string" }, "temporalType": { "description": "Categorization of how the date/temporal interval relates to the dataset", "oneOf": [ { "enum": ["exposure", "collection", "screening", "treatment", "study date", "other", "unknown"], "type": "string" }, { "items": { "enum": ["exposure", "collection", "screening", "treatment", "study date", "other", "unknown"], "type": "string" }, "type": "array" } ] } }, "type": "object" } ], "owl:cardinality": "many" }, "sourceOrganization": { "description": "The organization, research project, working group, or funded program on whose behalf the author/creator was working.", "anyOf": [ { "type": "array", "items": { "$ref": "#/definitions/researchproject" } }, { "$ref": "#/definitions/researchproject" }, { "type": "array", "items": { "$ref": "#/definitions/organization" } }, { "$ref": "#/definitions/organization" } ], "owl:cardinality": "many" }, "topicCategory": { "description": "Topic of the work. This topic may be assigned by a human curator or through automated algorithms.", "abstract": "topic", "anyOf": [ { "type": "array", "items": { "$ref": "#/definitions/topic" } }, { "$ref": "#/definitions/topic" }, { "type": "array", "items": { "$ref": "#/definitions/definedterm" } }, { "$ref": "#/definitions/definedterm" } ], "owl:cardinality": "many" }, "creditText": { "description": "Text that can be used to credit person(s) and/or organization(s) associated with a published Creative Work. For example, how a user should cite the sample.", "type": "string", "owl:cardinality": "one" }, "additionalProperty": { "description": "Other Property/Value pairs that describe the sample.", "anyOf": [ { "type": "array", "items": { "$ref": "#/definitions/propertyvalue" } }, { "$ref": "#/definitions/propertyvalue" } ], "owl:cardinality": "many" } }, "required": ["name", "url", "identifier", "includedInDataCatalog", "author", "date"], "recommended": ["description", "sameAs", "conditionsOfAccess", "usageInfo", "license", "cellType", "infectiousAgent", "species", "healthCondition", "funding", "creditText", "anatomicalStructure", "sex", "developmentalStage", "sampleAvailability", "sampleProcess", "sampleType", "collectionMethod", "instrument", "collector", "contributor", "locationOfOrigin", "citation", "dateModified", "dateCollected", "dateProcessed", "interactionStatistic", "keywords", "sdPublisher", "sourceOrganization", "topicCategory", "creditText"], "optional": ["associatedPhenotype", "associatedGenotype", "citedBy", "isRelatedTo", "isSimilarTo", "isBasisFor", "isBasedOn", "hasPart","isPartOf", "anatomicalSystem", "sampleQuantity", "sampleState", "sampleStorageTemperature", "distribution", "measurementTechnique", "variableMeasured", "environmentalSystem", "aggregateRating", "experimentalPurpose", "maintainer", "itemLocation", "dateCreated", "datePublished", "spatialCoverage", "temporalCoverage", "additionalProperty"], "definitions": { "citation": { "description": "A citation object for a resource which is cited by the dataset (ie- is a derivative of the dataset) , related to the dataset, or from which the dataset was based on (ie- is derived from).", "@type": "ScholarlyArticle", "type": "object", "properties": { "author": { "description": "Author(s) of the publication", "anyOf": [ { "type": "array", "items": { "$ref": "#/definitions/person" } }, { "$ref": "#/definitions/person" }, { "type": "array", "items": { "$ref": "#/definitions/organization" } }, { "$ref": "#/definitions/organization" } ] }, "abstract": { "description": "Abstract of the publication", "type": "string" }, "datePublished": { "description": "Date the article was published", "format": "date", "type": "string" }, "description": { "description": "Description of the publication", "type": "string" }, "name": { "description": "Title of the publication", "type": "string" }, "identifier": { "description": "An identifier associated with the citation such as a digital object identifier (DOI), PubMed ID (PMID), or PubMed Central ID (PMCID)", "type": "string" }, "pmid": { "description": "A PubMed identifier (PMID) of the referenced publication", "abstract": "PubMed identifier", "type": "string" }, "doi": { "description": "A digital object identifier (DOI) of the referenced publication", "abstract": "digital object identifier", "type": "string" }, "issueNumber": { "description": "Issue number where the article appears", "type": "string" }, "journalName": { "description": "Journal where the article appears", "type": "string" }, "journalNameAbbrev": { "description": "Abbreviated journal name where the article appears", "type": "string" }, "pagination": { "description": "Page numbers in the journal where the article appears", "type": "string" }, "url": { "description": "The url of the article", "type": "string", "format": "uri" }, "volumeNumber": { "description": "Volume of the journal where the article appears", "type": "string" }, "citation": { "description": "The bibliographic citation string for the article as is provided", "type": "string" } }, "required": ["name"], "recommended": ["author", "datePublished", "doi", "identifier", "journalName", "pmid", "url"], "optional": ["abstract", "citation", "description", "issueNumber", "journalNameAbbrev", "pagination", "volumeNumber"] }, "creativework": { "description": "A resource", "@type": "CreativeWork", "type": "object", "properties": { "author": { "description": "Author(s) of the referenced work", "anyOf": [ { "type": "array", "items": { "$ref": "#/definitions/person" } }, { "$ref": "#/definitions/person" }, { "type": "array", "items": { "$ref": "#/definitions/organization" } }, { "$ref": "#/definitions/organization" } ] }, "abstract": { "description": "Abstract of the referenced work", "type": "string" }, "datePublished": { "description": "Date the referenced work was published", "format": "date", "type": "string" }, "description": { "description": "Description of the referenced work", "type": "string" }, "hasPart": { "description": "A portion of the work", "oneOf": [ { "$ref": "#/definitions/citation" } ] }, "includedInDataCatalog": { "description": "Data or tool catalog which houses the work", "oneOf": [ { "$ref": "#/definitions/catalog" } ] }, "name": { "description": "Name or title", "type": "string" }, "identifier": { "description": "An identifier associated with the work", "type": "string" }, "relationship": { "description": "How the works are related", "type": "string" }, "doi": { "description": "A digital object identifier (DOI) of the referenced work", "abstract": "digital object identifier", "type": "string" }, "url": { "description": "The url of the work", "type": "string", "format": "uri" }, "citation": { "description": "The bibliographic citation for the referenced work as is provided", "type": "string" } }, "required": ["name"], "recommended": ["author", "datePublished", "doi", "identifier", "includedInDataCatalog", "relationship", "url"], "optional": ["abstract", "citation", "description", "hasPart"] }, "topic": { "description": "Topic assigned to the work.", "type": "string", "vocabulary": { "ontology": ["edam"], "children_of": ["http://edamontology.org/topic_0003"] }, "strict": true }, "catalog": { "@type": "DataCatalog", "description": "Data or tool catalog", "type": "object", "properties": { "name": { "description": "Data or tool catalog name", "type": "string" }, "url": { "description": "Link to data or tool catalog", "type": "string", "format": "uri" }, "versionDate": { "description": "date the metadata was harvested from the catalog", "type": "string", "format": "date" }, "archivedAt": { "description": "The url(s) of one or more datasets, tools, resources or other items listed in a DataCatalog or ResourceCatalog", "oneOf": [ { "items": { "type": "string", "format": "uri" }, "type": "array" }, { "type": "string", "format": "uri" } ] } }, "required": ["name", "url"], "recommended": ["versionDate", "archivedAt"] }, "organization": { "@type": "Organization", "description": "Reusable organization definition", "properties": { "affiliation": { "type": "object", "properties": { "name": { "description": "Name of the affiliation, such as a university", "type": "string" }, "sameAs": { "description": "Alias for the affiliation", "type": "string" }, "url": { "description": "URL of the affiliation", "type": "string", "format": "uri" } }, "required": ["name"], "optional": ["sameAs", "url"] }, "alternateName": { "description": "Alias of the name", "oneOf": [ { "type": "array", "items": { "type": "string" } }, { "type": "string" } ] }, "name": { "description": "Name of the organization", "type": "string" }, "parentOrganization": { "description": "Name of the parent organization. For instance, the parentOrganization of NIAID is the National Institutes of health (NIH)", "type": "string" }, "email": { "description": "Email address of the organization", "type": "string" }, "identifier": { "description": "Unique identifier of the organization", "type": "string" }, "role": { "description": "What role the organization played in creating the dataset", "type": "string" }, "url": { "description": "Link to the organization", "type": "string", "format": "uri" } }, "required": ["name"], "recommended": ["identifier"], "optional": ["affiliation", "alternateName", "email", "parentOrganization", "role", "url"], "type": "object" }, "researchproject": { "@type": "ResearchProject", "description": "a type of organization definition", "properties": { "alternateName": { "description": "Alias of the name", "oneOf": [ { "type": "array", "items": { "type": "string" } }, { "type": "string" } ] }, "name": { "description": "Name of the organization", "type": "string" }, "parentOrganization": { "description": "Name of the parent organization. For instance, the parentOrganization of NIAID is the National Institutes of health (NIH)", "type": "string" }, "email": { "description": "Email address of the organization", "type": "string" }, "identifier": { "description": "Unique identifier of the organization", "type": "string" }, "url": { "description": "Link to the organization", "type": "string", "format": "uri" } }, "required": ["name"], "recommended": ["identifier", "url", "parentOrganization"], "optional": ["alternateName", "email", "role"], "type": "object" }, "person": { "@type": "Person", "description": "Reusable person definition", "properties": { "affiliation": { "type": "object", "properties": { "name": { "description": "Name of the affiliation, such as a university", "type": "string" }, "sameAs": { "description": "Alias for the affiliation", "type": "string" }, "url": { "description": "URL of the affiliation", "type": "string", "format": "uri" } }, "required": ["name"], "optional": ["sameAs", "url"] }, "name": { "description": "Name of the person", "type": "string" }, "email": { "description": "Email address of the person", "type": "string" }, "familyName": { "description": "Family name (surname) of the person", "type": "string" }, "givenName": { "description": "Given (first) name of the person", "type": "string" }, "identifier": { "description": "Unique identifier of the person, like an ORCID ID", "type": "string" }, "role": { "description": "Role the person played in creating the dataset", "type": "string" }, "title": { "description": "Title of the person", "type": "string" }, "url": { "description": "Link to the homepage or other web content describing the person", "type": "string", "format": "uri" } }, "required": ["name"], "recommended": ["familyName", "givenName ", "identifier "], "optional": ["affiliation", "email", "role", "title", "url"], "type": "object" }, "definedterm": { "@type": "DefinedTerm", "type": "object", "properties": { "name": { "description": "The name 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 for more details.", "owl:cardinality": "one", "type": "string" }, "url": { "description": "URL of the item.", "owl:cardinality": "one", "type": "string", "format": "uri" }, "curatedBy": { "description": "The person, organization, or catalog that curated this DefinedTerm for the metadata property", "anyOf": [ { "$ref": "#/definitions/person" }, { "$ref": "#/definitions/organization" }, { "$ref": "#/definitions/catalog" }, { "$ref": "#/definitions/researchproject" }, { "$ref": "#/definitions/softwareapplication" } ] }, "termCode": { "description": "A code that identifies this DefinedTerm within a DefinedTermSet.", "type": "string" }, "description": { "description": "A description of the item.", "type": "string" }, "inDefinedTermSet": { "description": "A DefinedTermSet that contains this term.", "type": "string" }, "originalName": { "description": "The original name of the item, before any metadata standardization/normalization", "type": "string" }, "isCurated": { "description": "A boolean indicator describing whether or not this DefinedTerm was curated as the value of a property.", "type": "boolean" } }, "required": [] }, "quantitativevalue": { "@type": "QuantitativeValue", "description": "A numeric value and unit for a property with potentially different units", "type": "object", "properties": { "value": { "description": "A numeric value for the property", "type": "number" }, "maxValue": { "description": "An estimated maximum numberic value if the actual value is not known. Ignore if actual numeric value is known.", "type": "number" }, "minValue": { "description": "An estimated minumum numeric value if the actual value is not known. Ignore if actual numeric value is known.", "type": "number" }, "unitText": { "description": "A unit associated with the value. E.g.- 'records' for the number of records in a database.", "type": "string" } }, "required" : ["unitText"], "recommended": ["value"], "optional": ["maxValue","minValue"] }, "softwareapplication": { "@type": "SoftwareApplication", "description": "Reusable software or algorithm definition", "properties": { "name": { "description": "name of the software, computational tool, or algorithm.", "type": "string" }, "dateModified": { "description": "date the software, computational tool, or algorithm was run", "type": "string", "format": "date" }, "url": { "description": "url of the software, computational tool, or algorithm", "type": "string", "format": "uri" } }, "required": ["name"], "recommended": ["url"], "optional": ["dateModified"], "type": "object" }, "sample": { "@type": "Sample", "description": "reusable sample object", "type": "object", "properties": { "name": { "description": "sample name", "type": "string" }, "url": { "description": "Link to sample", "type": "string", "format": "uri" }, "identifier": { "description": "an identifier for the sample", "type": "string" }, "includedInDataCatalog": { "description": "Data or resource catalog where the sample is listed", "oneOf": [ { "$ref": "#/definitions/catalog" }, { "type": "array", "items": { "$ref": "#/definitions/catalog" } } ] } }, "required": ["url", "identifier"], "recommended": ["name", "includedInDataCatalog"] }, "propertyvalue": { "@type": "PropertyValue", "description": "A property value pair", "type": "object", "properties": { "value": { "description": "A value for the property", "type": "string" }, "name": { "description": "Name of the property", "type": "string" } }, "required" : ["name"], "recommended": ["value"] } } } }, { "@id": "nde:SampleCollection", "@type": "rdfs:Class", "rdfs:comment": "Sample collections contained in the NIAID Data Ecosystem. A SampleCollection is a collection of samples with some aggregate information about the collection itself. A SampleCollection can be useful for describing sample information when only aggregated sample-level metadata is provided due to privacy issues that prevent sharing of individual sample-level metadata record.", "abstract": "Samples collections contained in the NIAID Data Ecosystem. A sample collection is an aggregate sample record.", "rdfs:label": "SampleCollection", "rdfs:subClassOf": { "@id": "schema:ItemList" }, "schema:schemaVersion":["https://schema.org/docs/releases.html#v18.0","v0.3 - 2025.12.17"], "dct:provenance":"Changes since previous version: Change the parent class of the SampleCollection schema to ItemList and reorganized the properties and expected values.", "$validation": { "$schema": "http://json-schema.org/draft-07/schema#", "type": "object", "properties": { "name": { "description": "Sample name.", "owl:cardinality": "one", "type": "string" }, "description": { "description": "A description of the sample.", "owl:cardinality": "one", "type": "string" }, "identifier": { "description": "Sample identifier or accession number, such as a digital object identifier (DOI), sequence read archive (SRA) or GenBank accession number, etc.", "abstract": "identifier or accession number", "oneOf": [ { "type": "string" }, { "items": { "type": "string" }, "type": "array" } ], "owl:cardinality": "many" }, "sameAs": { "description": "URL of additional sources for the work.", "oneOf": [ { "items": { "type": "string", "format": "uri" }, "type": "array" }, { "type": "string", "format": "uri" } ], "owl:cardinality": "many" }, "url": { "description": "URL of the work.", "type": "string", "format": "uri", "owl:cardinality": "one" }, "includedInDataCatalog": { "description": "Data or resource catalog where the sample is listed; original source of the metadata.", "abstract": "catalog containing the work", "oneOf": [ { "$ref": "#/definitions/catalog" }, { "type": "array", "items": { "$ref": "#/definitions/catalog" } } ], "owl:cardinality": "one" }, "numberOfItems": { "description": "The number of sample records in the sample collection. Min/max estimates can be used in lieu of actual number. If completely unknown, set value = 0, and unitText = 'unknown'", "anyOf": [ { "type": "array", "items": { "$ref": "#/definitions/propertyvalue" } }, { "$ref": "#/definitions/propertyvalue" }, { "type": "array", "items": { "$ref": "#/definitions/quantitativevalue" } }, { "$ref": "#/definitions/quantitativevalue" } ], "owl:cardinality": "many" }, "itemListElement": { "description": "The list of samples that are included in the sample collection", "anyOf": [ { "type": "array", "items": { "$ref": "#/definitions/minsample" } }, { "$ref": "#/definitions/minsample" }, { "type": "string", "format": "uri" }, { "type": "array", "items": { "type": "string", "format": "uri" } } ], "owl:cardinality": "many" }, "aggregateElement": { "description": "Aggregate values derived from the samples in the collection.", "anyOf": [ { "type": "array", "items": { "$ref": "#/definitions/sample" } }, { "$ref": "#/definitions/sample" } ], "owl:cardinality": "many" } }, "required": ["aggregateElement", "numberOfItems"], "recommended": ["itemListElement", "url", "identifier", "sameAs", "includedInDataCatalog"], "optional": ["name", "description"], "definitions": { "citation": { "description": "A citation object for a resource which is cited by the dataset (ie- is a derivative of the dataset) , related to the dataset, or from which the dataset was based on (ie- is derived from).", "@type": "ScholarlyArticle", "type": "object", "properties": { "author": { "description": "Author(s) of the publication", "anyOf": [ { "type": "array", "items": { "$ref": "#/definitions/person" } }, { "$ref": "#/definitions/person" }, { "type": "array", "items": { "$ref": "#/definitions/organization" } }, { "$ref": "#/definitions/organization" } ] }, "abstract": { "description": "Abstract of the publication", "type": "string" }, "datePublished": { "description": "Date the article was published", "format": "date", "type": "string" }, "description": { "description": "Description of the publication", "type": "string" }, "name": { "description": "Title of the publication", "type": "string" }, "identifier": { "description": "An identifier associated with the citation such as a digital object identifier (DOI), PubMed ID (PMID), or PubMed Central ID (PMCID)", "type": "string" }, "pmid": { "description": "A PubMed identifier (PMID) of the referenced publication", "abstract": "PubMed identifier", "type": "string" }, "doi": { "description": "A digital object identifier (DOI) of the referenced publication", "abstract": "digital object identifier", "type": "string" }, "issueNumber": { "description": "Issue number where the article appears", "type": "string" }, "journalName": { "description": "Journal where the article appears", "type": "string" }, "journalNameAbbrev": { "description": "Abbreviated journal name where the article appears", "type": "string" }, "pagination": { "description": "Page numbers in the journal where the article appears", "type": "string" }, "url": { "description": "The url of the article", "type": "string", "format": "uri" }, "volumeNumber": { "description": "Volume of the journal where the article appears", "type": "string" }, "citation": { "description": "The bibliographic citation string for the article as is provided", "type": "string" } }, "required": ["name"], "recommended": ["author", "datePublished", "doi", "identifier", "journalName", "pmid", "url"], "optional": ["abstract", "citation", "description", "issueNumber", "journalNameAbbrev", "pagination", "volumeNumber"] }, "creativework": { "description": "A resource", "@type": "CreativeWork", "type": "object", "properties": { "author": { "description": "Author(s) of the referenced work", "anyOf": [ { "type": "array", "items": { "$ref": "#/definitions/person" } }, { "$ref": "#/definitions/person" }, { "type": "array", "items": { "$ref": "#/definitions/organization" } }, { "$ref": "#/definitions/organization" } ] }, "abstract": { "description": "Abstract of the referenced work", "type": "string" }, "datePublished": { "description": "Date the referenced work was published", "format": "date", "type": "string" }, "description": { "description": "Description of the referenced work", "type": "string" }, "hasPart": { "description": "A portion of the work", "oneOf": [ { "$ref": "#/definitions/citation" } ] }, "includedInDataCatalog": { "description": "Data or tool catalog which houses the work", "oneOf": [ { "$ref": "#/definitions/catalog" } ] }, "name": { "description": "Name or title", "type": "string" }, "identifier": { "description": "An identifier associated with the work", "type": "string" }, "relationship": { "description": "How the works are related", "type": "string" }, "doi": { "description": "A digital object identifier (DOI) of the referenced work", "abstract": "digital object identifier", "type": "string" }, "url": { "description": "The url of the work", "type": "string", "format": "uri" }, "citation": { "description": "The bibliographic citation for the referenced work as is provided", "type": "string" } }, "required": ["name"], "recommended": ["author", "datePublished", "doi", "identifier", "includedInDataCatalog", "relationship", "url"], "optional": ["abstract", "citation", "description", "hasPart"] }, "topic": { "description": "Topic assigned to the work.", "type": "string", "vocabulary": { "ontology": ["edam"], "children_of": ["http://edamontology.org/topic_0003"] }, "strict": true }, "catalog": { "@type": "DataCatalog", "description": "Data or tool catalog", "type": "object", "properties": { "name": { "description": "Data or tool catalog name", "type": "string" }, "url": { "description": "Link to data or tool catalog", "type": "string", "format": "uri" }, "versionDate": { "description": "date the metadata was harvested from the catalog", "type": "string", "format": "date" }, "archivedAt": { "description": "The url(s) of one or more datasets, tools, resources or other items listed in a DataCatalog or ResourceCatalog", "oneOf": [ { "items": { "type": "string", "format": "uri" }, "type": "array" }, { "type": "string", "format": "uri" } ] } }, "required": ["name", "url"], "recommended": ["versionDate", "archivedAt"] }, "organization": { "@type": "Organization", "description": "Reusable organization definition", "properties": { "affiliation": { "type": "object", "properties": { "name": { "description": "Name of the affiliation, such as a university", "type": "string" }, "sameAs": { "description": "Alias for the affiliation", "type": "string" }, "url": { "description": "URL of the affiliation", "type": "string", "format": "uri" } }, "required": ["name"], "optional": ["sameAs", "url"] }, "alternateName": { "description": "Alias of the name", "oneOf": [ { "type": "array", "items": { "type": "string" } }, { "type": "string" } ] }, "name": { "description": "Name of the organization", "type": "string" }, "parentOrganization": { "description": "Name of the parent organization. For instance, the parentOrganization of NIAID is the National Institutes of health (NIH)", "type": "string" }, "email": { "description": "Email address of the organization", "type": "string" }, "identifier": { "description": "Unique identifier of the organization", "type": "string" }, "role": { "description": "What role the organization played in creating the dataset", "type": "string" }, "url": { "description": "Link to the organization", "type": "string", "format": "uri" } }, "required": ["name"], "recommended": ["identifier"], "optional": ["affiliation", "alternateName", "email", "parentOrganization", "role", "url"], "type": "object" }, "researchproject": { "@type": "ResearchProject", "description": "a type of organization definition", "properties": { "alternateName": { "description": "Alias of the name", "oneOf": [ { "type": "array", "items": { "type": "string" } }, { "type": "string" } ] }, "name": { "description": "Name of the organization", "type": "string" }, "parentOrganization": { "description": "Name of the parent organization. For instance, the parentOrganization of NIAID is the National Institutes of health (NIH)", "type": "string" }, "email": { "description": "Email address of the organization", "type": "string" }, "identifier": { "description": "Unique identifier of the organization", "type": "string" }, "url": { "description": "Link to the organization", "type": "string", "format": "uri" } }, "required": ["name"], "recommended": ["identifier", "url", "parentOrganization"], "optional": ["alternateName", "email", "role"], "type": "object" }, "person": { "@type": "Person", "description": "Reusable person definition", "properties": { "affiliation": { "type": "object", "properties": { "name": { "description": "Name of the affiliation, such as a university", "type": "string" }, "sameAs": { "description": "Alias for the affiliation", "type": "string" }, "url": { "description": "URL of the affiliation", "type": "string", "format": "uri" } }, "required": ["name"], "optional": ["sameAs", "url"] }, "name": { "description": "Name of the person", "type": "string" }, "email": { "description": "Email address of the person", "type": "string" }, "familyName": { "description": "Family name (surname) of the person", "type": "string" }, "givenName": { "description": "Given (first) name of the person", "type": "string" }, "identifier": { "description": "Unique identifier of the person, like an ORCID ID", "type": "string" }, "role": { "description": "Role the person played in creating the dataset", "type": "string" }, "title": { "description": "Title of the person", "type": "string" }, "url": { "description": "Link to the homepage or other web content describing the person", "type": "string", "format": "uri" } }, "required": ["name"], "recommended": ["familyName", "givenName ", "identifier "], "optional": ["affiliation", "email", "role", "title", "url"], "type": "object" }, "definedterm": { "@type": "DefinedTerm", "type": "object", "properties": { "name": { "description": "The name 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 for more details.", "owl:cardinality": "one", "type": "string" }, "url": { "description": "URL of the item.", "owl:cardinality": "one", "type": "string", "format": "uri" }, "curatedBy": { "description": "The person, organization, or catalog that curated this DefinedTerm for the metadata property", "anyOf": [ { "$ref": "#/definitions/person" }, { "$ref": "#/definitions/organization" }, { "$ref": "#/definitions/catalog" }, { "$ref": "#/definitions/researchproject" }, { "$ref": "#/definitions/softwareapplication" } ] }, "termCode": { "description": "A code that identifies this DefinedTerm within a DefinedTermSet.", "type": "string" }, "description": { "description": "A description of the item.", "type": "string" }, "inDefinedTermSet": { "description": "A DefinedTermSet that contains this term.", "type": "string" }, "originalName": { "description": "The original name of the item, before any metadata standardization/normalization", "type": "string" }, "isCurated": { "description": "A boolean indicator describing whether or not this DefinedTerm was curated as the value of a property.", "type": "boolean" } }, "required": [] }, "quantitativevalue": { "@type": "QuantitativeValue", "description": "A numeric value and unit for a property with potentially different units", "type": "object", "properties": { "value": { "description": "A numeric value for the property", "type": "number" }, "maxValue": { "description": "An estimated maximum numberic value if the actual value is not known. Ignore if actual numeric value is known.", "type": "number" }, "minValue": { "description": "An estimated minumum numeric value if the actual value is not known. Ignore if actual numeric value is known.", "type": "number" }, "unitText": { "description": "A unit associated with the value. E.g.- 'records' for the number of records in a database.", "type": "string" } }, "required" : ["unitText"], "recommended": ["value"], "optional": ["maxValue","minValue"] }, "propertyvalue": { "@type": "PropertyValue", "description": "A numeric value and unit for a property with potentially different units", "type": "object", "properties": { "value": { "description": "A numeric value for the property", "type": "number" }, "maxValue": { "description": "An estimated maximum numberic value if the actual value is not known. Ignore if actual numeric value is known.", "type": "number" }, "minValue": { "description": "An estimated minumum numeric value if the actual value is not known. Ignore if actual numeric value is known.", "type": "number" }, "unitText": { "description": "A unit associated with the value. E.g.- 'records' for the number of records in a database.", "type": "string" }, "propertyID": { "description": "A commonly used identifier for the characteristic represented by the property, e.g. a manufacturer or a standard code for a property. propertyID can be (1) a prefixed string, mainly meant to be used with standards for product properties; (2) a site-specific, non-prefixed string (e.g. the primary key of the property or the vendor-specific ID of the property), or (3) a URL indicating the type of the property, either pointing to an external vocabulary, or a Web resource that describes the property (e.g. a glossary entry). Standards bodies should promote a standard prefix for the identifiers of properties from their standards.", "oneOf": [ {"type": "string"}, { "type": "string", "format": "uri" } ] } }, "required" : ["unitText"], "recommended": ["value","propertyID"], "optional": ["maxValue","minValue"] }, "softwareapplication": { "@type": "SoftwareApplication", "description": "Reusable software or algorithm definition", "properties": { "name": { "description": "name of the software, computational tool, or algorithm.", "type": "string" }, "dateModified": { "description": "date the software, computational tool, or algorithm was run", "type": "string", "format": "date" }, "url": { "description": "url of the software, computational tool, or algorithm", "type": "string", "format": "uri" } }, "required": ["name"], "recommended": ["url"], "optional": ["dateModified"], "type": "object" }, "minsample": { "@type": "Sample", "description": "minimal sample object", "type": "object", "properties": { "name": { "description": "sample name", "type": "string" }, "url": { "description": "Link to sample", "type": "string", "format": "uri" }, "identifier": { "description": "an identifier for the sample", "type": "string" }, "includedInDataCatalog": { "description": "Data or resource catalog where the sample is listed", "oneOf": [ { "$ref": "#/definitions/catalog" }, { "type": "array", "items": { "$ref": "#/definitions/catalog" } } ] } }, "required": ["url", "identifier"], "recommended": ["name", "includedInDataCatalog"] }, "sample": { "@type": "Sample", "description": "reusable detailed sample object", "type": "object", "properties": { "usageInfo": { "description": "The terms under which the sample can be used. Note that this is related to but distinct from the license.", "abstract": "sample usage agreement", "oneOf": [ { "type": "array", "items": { "$ref": "#/definitions/creativework" } }, { "$ref": "#/definitions/creativework" } ], "owl:cardinality": "many" }, "license": { "description": "A license document that applies to this work, typically indicated by URL.", "abstract": "license for use", "format": "uri", "owl:cardinality": "one", "type": "string" }, "conditionsOfAccess": { "description": "Conditions that affect the availability of, or method(s) of access to, the sample. Options include open (freely available), restricted (may include restrictions such as on use), closed (requires registration to access), or embargoed (unpublished).", "abstract": "accessibility of the work", "type": "string", "enum": ["Closed", "Open", "Restricted", "Embargoed"], "owl:cardinality": "one" }, "isAccessibleForFree": { "description": "A flag to signal that the sample may be requested at no cost (not including shipping).", "abstract": "accessible without charge", "type": "boolean", "owl:cardinality": "one" }, "associatedPhenotype": { "description": "one or more observable traits or conditions relevant to the source of the sample.", "anyOf": [ { "description": "collection of vocabulary terms defined in ontologies", "strict": false, "type": "string", "vocabulary": { "children_of": ["http://purl.obolibrary.org/obo/UPHENO_0001001", "http://purl.obolibrary.org/obo/PATO_0000001"], "ontology": ["UPHENO","PATO"] } }, { "items": { "description": "collection of vocabulary terms defined in ontologies", "strict": false, "type": "string", "vocabulary": { "children_of": ["http://purl.obolibrary.org/obo/UPHENO_0001001", "http://purl.obolibrary.org/obo/PATO_0000001"], "ontology": ["UPHENO","PATO"] } }, "type": "array" }, { "type": "array", "items": { "$ref": "#/definitions/definedterm" } }, { "$ref": "#/definitions/definedterm" } ], "owl:cardinality": "many" }, "associatedGenotype": { "description": "One or more genetic variants or molecular features observed or inferred from the sample.", "anyOf": [ { "description": "collection of vocabulary terms defined in ontologies", "strict": false, "type": "string", "vocabulary": { "children_of": ["http://purl.obolibrary.org/obo/NCIT_C16612", "http://purl.obolibrary.org/obo/NCIT_C20181","http://purl.obolibrary.org/obo/NCIT_C17649"], "ontology": ["NCIT"] } }, { "items": { "description": "collection of vocabulary terms defined in ontologies", "strict": false, "type": "string", "vocabulary": { "children_of": ["http://purl.obolibrary.org/obo/NCIT_C16612", "http://purl.obolibrary.org/obo/NCIT_C20181","http://purl.obolibrary.org/obo/NCIT_C17649"], "ontology": ["NCIT"] } }, "type": "array" }, { "type": "array", "items": { "$ref": "#/definitions/definedterm" } }, { "$ref": "#/definitions/definedterm" } ], "owl:cardinality": "many" }, "cellType": { "description": "The type of cell represented in or derived from the biological sample, based on morphology, lineage, or molecular markers.", "anyOf": [ { "description": "collection of vocabulary terms defined in ontologies", "strict": false, "type": "string", "vocabulary": { "children_of": ["http://purl.obolibrary.org/obo/CL_0000000", "http://purl.obolibrary.org/obo/CLO_0000031"], "ontology": ["CL","CLO"] } }, { "items": { "description": "collection of vocabulary terms defined in ontologies", "strict": false, "type": "string", "vocabulary": { "children_of": ["http://purl.obolibrary.org/obo/CL_0000000", "http://purl.obolibrary.org/obo/CLO_0000031"], "ontology": ["CL","CLO"] } }, "type": "array" }, { "type": "array", "items": { "$ref": "#/definitions/definedterm" } }, { "$ref": "#/definitions/definedterm" } ], "owl:cardinality": "many" }, "infectiousAgent": { "description": "Infectious agent(s) / pathogen(s) which are the focus of the work (like SARS-CoV-2).", "abstract": "infectious agent / pathogen", "anyOf": [ { "description": "collection of vocabulary terms defined in ontologies", "strict": false, "type": "string", "vocabulary": { "children_of": ["http://purl.obolibrary.org/obo/NCBITaxon_10239", "http://purl.obolibrary.org/obo/NCBITaxon_2"], "ontology": ["ncbitaxon"] } }, { "items": { "description": "collection of vocabulary terms defined in ontologies", "strict": false, "type": "string", "vocabulary": { "children_of": ["http://purl.obolibrary.org/obo/NCBITaxon_10239", "http://purl.obolibrary.org/obo/NCBITaxon_2"], "ontology": ["ncbitaxon"] } }, "type": "array" }, { "type": "array", "items": { "$ref": "#/definitions/definedterm" } }, { "$ref": "#/definitions/definedterm" } ], "owl:cardinality": "many" }, "healthCondition": { "description": "The health condition(s) /infectious disease(s) which are the focus of the work (like COVID-19, coronavirus).", "abstract": "health condition/disease", "anyOf": [ { "description": "collection of vocabulary terms defined in ontologies", "strict": false, "type": "string", "vocabulary": { "children_of": ["http://purl.obolibrary.org/obo/MONDO_0000001", "http://purl.obolibrary.org/obo/DOID_4", "http://purl.obolibrary.org/obo/HP_0000001", "http://purl.obolibrary.org/obo/NCIT_C7057"], "ontology": ["mondo","hpo","doid","ncit"] } }, { "items": { "description": "collection of vocabulary terms defined in ontologies", "strict": false, "type": "string", "vocabulary": { "children_of": ["http://purl.obolibrary.org/obo/MONDO_0000001", "http://purl.obolibrary.org/obo/DOID_4", "http://purl.obolibrary.org/obo/HP_0000001", "http://purl.obolibrary.org/obo/NCIT_C7057"], "ontology": ["mondo","hpo","doid","ncit"] } }, "type": "array" }, { "type": "array", "items": { "$ref": "#/definitions/definedterm" } }, { "$ref": "#/definitions/definedterm" } ], "owl:cardinality": "many" }, "funding": { "description": "Funding that supports (sponsors) the collection of this dataset through some kind of financial contribution.", "abstract": "funding source (grant, contract, etc.)", "oneOf": [ { "type": "object", "@type": "MonetaryGrant", "description": "Funding that supports (sponsors) the collection of this dataset through some kind of financial contribution", "properties": { "funder": { "description": "An organization associated with a creator or funder of a dataset", "oneOf": [ { "type": "object", "@type": "Organization", "description": "Information about a single funder", "properties": { "name": { "type": "string", "description": "An organization associated with a creator or funder of a dataset" }, "parentOrganization": { "type": "string", "description": "name of the parent funding organization" } }, "required": [ "name" ] }, { "type": "array", "items": { "type": "object", "@type": "Organization", "description": "Information about a single funder", "properties": { "name": { "type": "string", "description": "An organization associated with a creator or funder of a dataset" }, "parentOrganization": { "type": "string", "description": "name of the parent funding organization" } }, "required": [ "name" ] } } ] }, "description": { "type": "string", "description": "description about the funding award / grant" }, "url": { "type": "string", "description": "award / grant URL" }, "identifier": { "type": "string", "description": "Unique identifier(s) for the grant(s) used to fund the Dataset" } }, "required": [ "funder", "identifier" ] }, { "type": "array", "items": { "type": "object", "@type": "MonetaryGrant", "description": "Funding that supports (sponsors) the collection of this dataset through some kind of financial contribution", "properties": { "funder": { "description": "An organization associated with a creator or funder of a dataset", "oneOf": [ { "type": "object", "@type": "Organization", "description": "Information about a single funder", "properties": { "name": { "type": "string", "description": "An organization associated with a creator or funder of a dataset" }, "parentOrganization": { "type": "string", "description": "name of the parent funding organization" } }, "required": [ "name" ] }, { "type": "array", "items": { "type": "object", "@type": "Organization", "description": "Information about a single funder", "properties": { "name": { "type": "string", "description": "An organization associated with a creator or funder of a dataset" }, "parentOrganization": { "type": "string", "description": "name of the parent funding organization" } }, "required": [ "name" ] } } ] }, "description": { "type": "string", "description": "description about the funding award / grant" }, "url": { "type": "string", "description": "award / grant URL" }, "identifier": { "type": "string", "description": "Unique identifier(s) for the grant(s) used to fund the Dataset" } }, "required": [ "funder", "identifier" ] } } ], "owl:cardinality": "many" }, "species": { "description": "Species / host organism from which the dataset has been collected.", "abstract": "species/host organism", "anyOf": [ { "description": "collection of vocabulary terms defined in ontologies", "strict": false, "type": "string", "vocabulary": { "children_of": ["http://purl.obolibrary.org/obo/NCBITaxon_131567", "http://purl.obolibrary.org/obo/NCBITaxon_10239"], "ontology": ["ncbitaxon"] } }, { "items": { "description": "collection of vocabulary terms defined in ontologies", "strict": false, "type": "string", "vocabulary": { "children_of": ["http://purl.obolibrary.org/obo/NCBITaxon_131567", "http://purl.obolibrary.org/obo/NCBITaxon_10239"], "ontology": ["ncbitaxon"] } }, "type": "array" }, { "type": "array", "items": { "$ref": "#/definitions/definedterm" } }, { "$ref": "#/definitions/definedterm" } ], "owl:cardinality": "many" }, "citedBy": { "description": "Publications, datasets, or computational tools that cite the sample. Examples: a dataset which reuses the sample in a secondary study.", "anyOf": [ { "type": "array", "items": { "$ref": "#/definitions/citation" } }, { "$ref": "#/definitions/citation" }, { "type": "array", "items": { "$ref": "#/definitions/creativework" } }, { "$ref": "#/definitions/creativework" } ], "owl:cardinality": "many" }, "isRelatedTo": { "description": "Datasets, resources, or samples which are related to the given sample; often sample involved in the same study. These linkages are created via human curation.", "abstract": "related resources or samples (via curation)", "anyOf": [ { "type": "array", "items": { "$ref": "#/definitions/citation" } }, { "$ref": "#/definitions/citation" }, { "type": "array", "items": { "$ref": "#/definitions/creativework" } }, { "$ref": "#/definitions/creativework" }, { "type": "array", "items": { "$ref": "#/definitions/minsample" } }, { "$ref": "#/definitions/minsample" } ], "owl:cardinality": "many" }, "isSimilarTo": { "description": "Datasets, resources, or samples which are similar to the sample, based on terms in the names, descriptions, authors, measurementTechniques, infectiousAgents, healthConditions, etc.", "abstract": "similar resources of samples (auto-assigned)", "anyOf": [ { "type": "array", "items": { "$ref": "#/definitions/citation" } }, { "$ref": "#/definitions/citation" }, { "type": "array", "items": { "$ref": "#/definitions/creativework" } }, { "$ref": "#/definitions/creativework" }, { "type": "array", "items": { "$ref": "#/definitions/minsample" } }, { "$ref": "#/definitions/minsample" } ], "owl:cardinality": "many" }, "isBasisFor": { "description": "A resource or sample which reuses the sample. For example, a sample of a cell line that was created by knocking out a gene from this cell line sample. Another example would be a sample of infected tissue that was derived from this tissue sample by infecting it with a virus.", "anyOf": [ { "type": "array", "items": { "$ref": "#/definitions/citation" } }, { "$ref": "#/definitions/citation" }, { "type": "array", "items": { "$ref": "#/definitions/creativework" } }, { "$ref": "#/definitions/creativework" }, { "type": "array", "items": { "$ref": "#/definitions/minsample" } }, { "$ref": "#/definitions/minsample" } ], "owl:cardinality": "many" }, "isBasedOn": { "description": "A resource or sample from which this sample is derived, modified, or adapted. For example a sample of a cell line, which was infected by virus sample in order to create the sample. ", "abstract": "resource or sample used to create the sample.", "owl:cardinality": "many", "anyOf": [ { "type": "array", "items": { "$ref": "#/definitions/citation" } }, { "$ref": "#/definitions/citation" }, { "type": "array", "items": { "$ref": "#/definitions/creativework" } }, { "$ref": "#/definitions/creativework" }, { "type": "array", "items": { "$ref": "#/definitions/minsample" } }, { "$ref": "#/definitions/minsample" } ] }, "hasPart": { "description": "Associated materials that constitute the sample. For example, other samples (if sample was created by pooling samples), additives, cryoprotective agents, etc. Use 'hasPart' for samples that were generated by pooling other samples. For example, a synthetic microbiome sample may use 'hasPart' to list the individual microbial samples used to generate it.", "abstract": "Associated materials or samples that constitute the sample", "anyOf": [ { "type": "array", "items": { "$ref": "#/definitions/citation" } }, { "$ref": "#/definitions/citation" }, { "type": "array", "items": { "$ref": "#/definitions/creativework" } }, { "$ref": "#/definitions/creativework" }, { "type": "array", "items": { "$ref": "#/definitions/minsample" } }, { "$ref": "#/definitions/minsample" } ], "owl:cardinality": "many" }, "isPartOf": { "description": "Associated materials the sample may help constitute. For example, the pooled sample that used this sample. Use 'isPartOf' for pooled samples generated from this sample. For example, a microbial sample that was used to generate a synthetic microbiome sample.", "abstract": "study or project including the work", "owl:cardinality": "many", "anyOf": [ { "type": "array", "items": { "$ref": "#/definitions/citation" } }, { "$ref": "#/definitions/citation" }, { "type": "array", "items": { "$ref": "#/definitions/creativework" } }, { "$ref": "#/definitions/creativework" }, { "type": "array", "items": { "$ref": "#/definitions/minsample" } }, { "$ref": "#/definitions/minsample" } ] }, "anatomicalSystem": { "description": "Indicate the anatomical system from which the sample is collect, e.g. circulatory, digestive, endocrine, immune and other systems.", "anyOf": [ { "description": "collection of vocabulary terms defined in ontologies", "strict": false, "type": "string", "vocabulary": { "children_of": ["http://purl.obolibrary.org/obo/UBERON_0000467"], "ontology": ["UBERON"] } }, { "items": { "description": "collection of vocabulary terms defined in ontologies", "strict": false, "type": "string", "vocabulary": { "children_of": ["http://purl.obolibrary.org/obo/UBERON_0000467"], "ontology": ["UBERON"] } }, "type": "array" }, { "type": "array", "items": { "$ref": "#/definitions/definedterm" } }, { "$ref": "#/definitions/definedterm" } ], "owl:cardinality": "many" }, "anatomicalStructure": { "description": "Indicate the organ, tissues the sample was collected from.", "anyOf": [ { "description": "collection of vocabulary terms defined in ontologies", "strict": false, "type": "string", "vocabulary": { "children_of": ["http://purl.obolibrary.org/obo/UBERON_0001062"], "ontology": ["UBERON"] } }, { "items": { "description": "collection of vocabulary terms defined in ontologies", "strict": false, "type": "string", "vocabulary": { "children_of": ["http://purl.obolibrary.org/obo/UBERON_0001062"], "ontology": ["UBERON"] } }, "type": "array" }, { "type": "array", "items": { "$ref": "#/definitions/definedterm" } }, { "$ref": "#/definitions/definedterm" } ], "owl:cardinality": "many" }, "sex": { "description": "The biological sex of the individual from which the sample was obtained.", "anyOf": [ { "description": "collection of vocabulary terms defined in ontologies", "strict": false, "type": "string", "vocabulary": { "children_of": ["http://purl.obolibrary.org/obo/PATO_0000047"], "ontology": ["PATO"] } }, { "items": { "description": "collection of vocabulary terms defined in ontologies", "strict": false, "type": "string", "vocabulary": { "children_of": ["http://purl.obolibrary.org/obo/PATO_0000047"], "ontology": ["PATO"] } }, "type": "array" }, { "type": "array", "items": { "$ref": "#/definitions/definedterm" } }, { "$ref": "#/definitions/definedterm" } ], "owl:cardinality": "many" }, "developmentalStage": { "description": "A temporal subdivision of a developmental process, indicating the age or stage of the object when the sample was created.", "anyOf": [ { "description": "collection of vocabulary terms defined in ontologies", "strict": false, "type": "string", "vocabulary": { "children_of": ["http://purl.obolibrary.org/obo/UBERON_0000104","http://purl.obolibrary.org/obo/NCIT_C48308"], "ontology": ["UBERON","NCIT"] } }, { "items": { "description": "collection of vocabulary terms defined in ontologies", "strict": false, "type": "string", "vocabulary": { "children_of": ["http://purl.obolibrary.org/obo/UBERON_0000104","http://purl.obolibrary.org/obo/NCIT_C48308"], "ontology": ["UBERON","NCIT"] } }, "type": "array" }, { "type": "array", "items": { "$ref": "#/definitions/definedterm" } }, { "$ref": "#/definitions/definedterm" }, { "type": "array", "items": { "$ref": "#/definitions/quantitativevalue" } }, { "$ref": "#/definitions/quantitativevalue" } ], "owl:cardinality": "many" }, "sampleAvailability": { "description": "A flag to signal that the sample is available for reuse.", "abstract": "availability of the sample", "type": "boolean", "owl:cardinality": "one" }, "sampleProcess": { "description": "The processing technique that was applied to the sample, methods used to prepare the samples.", "anyOf": [ { "description": "collection of vocabulary terms defined in ontologies", "strict": false, "type": "string", "vocabulary": { "children_of": ["http://purl.obolibrary.org/obo/OBI_0000094","http://purl.obolibrary.org/obo/NCIT_C48177","http://purl.obolibrary.org/obo/NCIT_C16680"], "ontology": ["OBI","NCIT"] } }, { "items": { "description": "collection of vocabulary terms defined in ontologies", "strict": false, "type": "string", "vocabulary": { "children_of": ["http://purl.obolibrary.org/obo/OBI_0000094","http://purl.obolibrary.org/obo/NCIT_C48177","http://purl.obolibrary.org/obo/NCIT_C16680"], "ontology": ["OBI","NCIT"] } }, "type": "array" }, { "type": "array", "items": { "$ref": "#/definitions/definedterm" } }, { "$ref": "#/definitions/definedterm" }, { "type": "array", "items": { "$ref": "#/definitions/creativework" } }, { "$ref": "#/definitions/creativework" }, { "type":"string" } ], "owl:cardinality": "many" }, "sampleQuantity": { "description": "A numeric value for a measurement of the size of a sample. If completely unknown, set value = 0, and unitText = 'unknown'", "oneOf": [ { "type": "array", "items": { "$ref": "#/definitions/quantitativevalue" } }, { "$ref": "#/definitions/quantitativevalue" } ], "owl:cardinality": "many" }, "sampleState": { "description": "Specify the condition, composition or state of the sample, for example dried, frozen, passage number.", "anyOf": [ { "type": "string" }, { "type": "array", "items": { "$ref": "#/definitions/quantitativevalue" } }, { "$ref": "#/definitions/quantitativevalue" } ], "owl:cardinality": "many" }, "sampleStorageTemperature": { "description": "The temperature at which the sample is stored.", "oneOf": [ { "type": "array", "items": { "$ref": "#/definitions/quantitativevalue" } }, { "$ref": "#/definitions/quantitativevalue" } ], "owl:cardinality": "one" }, "sampleType": { "description": "The type of sample or specimen.", "anyOf": [ { "description": "collection of vocabulary terms defined in ontologies", "strict": false, "type": "string", "vocabulary": { "children_of": ["http://purl.obolibrary.org/obo/BFO_0000040"], "ontology": ["OBI"] } }, { "items": { "description": "collection of vocabulary terms defined in ontologies", "strict": false, "type": "string", "vocabulary": { "children_of": ["http://purl.obolibrary.org/obo/BFO_0000040"], "ontology": ["OBI"] } }, "type": "array" }, { "type": "array", "items": { "$ref": "#/definitions/definedterm" } }, { "$ref": "#/definitions/definedterm" } ], "owl:cardinality": "many" }, "distribution": { "description": "A downloadable form of this dataset, at a specific location, in a specific format.", "abstract": "download link", "oneOf": [ { "items": { "@type": "DataDownload", "description": "A dataset in downloadable form.", "properties": { "contentUrl": { "format": "uri", "type": "string" }, "encodingFormat": { "description": "file type (ex: XLSX)", "type": "string" }, "dateModified": { "format": "date", "description": "date the file was modified", "type": "string" } }, "required": ["dateModified", "contentUrl"], "type": "object" }, "type": "array" }, { "@type": "DataDownload", "description": "A dataset in downloadable form.", "properties": { "contentUrl": { "format": "uri", "type": "string" }, "encodingFormat": { "description": "file type (ex: XLSX)", "type": "string" }, "dateModified": { "format": "date", "description": "date the file was modified", "type": "string" } }, "required": ["dateModified", "contentUrl"], "type": "object" } ], "owl:cardinality": "many" }, "measurementTechnique": { "description": "A technique or technology used in the collection or processing of the sample corresponding to the method used for measuring the corresponding variable(s) (described using variableMeasured). For example, if variableMeasured is cell density or cell counts, measurementTechnique could be: \"centrifugation\" or \"flow cytometry\".", "abstract": "measurement technique used to collect, process, or generate the sample", "anyOf": [ { "description": "collection of vocabulary terms defined in ontologies", "strict": false, "type": "string", "vocabulary": { "children_of": ["http://edamontology.org/topic_3361", "http://purl.obolibrary.org/obo/NCIT_C20368", "http://purl.obolibrary.org/obo/MMO_0000000", "http://www.ebi.ac.uk/efo/EFO_0000001"], "ontology": ["edam", "ncit", "mmo","efo"] } }, { "items": { "description": "collection of vocabulary terms defined in ontologies", "strict": false, "type": "string", "vocabulary": { "children_of": ["http://edamontology.org/topic_3361", "http://purl.obolibrary.org/obo/NCIT_C20368", "http://purl.obolibrary.org/obo/MMO_0000000", "http://www.ebi.ac.uk/efo/EFO_0000001"], "ontology": ["edam", "ncit", "mmo","efo"] } }, "type": "array" }, { "type": "array", "items": { "$ref": "#/definitions/definedterm" } }, { "$ref": "#/definitions/definedterm" } ], "owl:cardinality": "many" }, "variableMeasured": { "description": "Variables measured within the sample.", "oneOf": [ { "description": "collection of vocabulary terms defined in ontologies", "strict": false, "type": "string", "vocabulary": { "children_of": ["http://www.ebi.ac.uk/efo/EFO_0000001", "http://purl.obolibrary.org/obo/CMO_0000000", "http://purl.obolibrary.org/obo/NCIT_C25209"], "ontology": ["efo", "cmo","ncit"] } }, { "items": { "description": "collection of vocabulary terms defined in ontologies", "strict": false, "type": "string", "vocabulary": { "children_of": ["http://www.ebi.ac.uk/efo/EFO_0000001", "http://purl.obolibrary.org/obo/CMO_0000000", "http://purl.obolibrary.org/obo/NCIT_C25209"], "ontology": ["efo", "cmo","ncit"] } }, "type": "array" }, { "type": "array", "items": { "$ref": "#/definitions/definedterm" } }, { "$ref": "#/definitions/definedterm" } ], "owl:cardinality": "many" }, "collectionMethod": { "description": "Provide information about the conditions and methods of acquisition of samples. ", "anyOf": [ { "type": "string", "format": "uri" }, { "items": { "type": "string", "format": "uri" }, "type": "array" }, { "type": "string" }, { "items": { "type": "string" }, "type": "array" }, { "type": "array", "items": { "$ref": "#/definitions/definedterm" } }, { "$ref": "#/definitions/definedterm" } ], "owl:cardinality": "many" }, "instrument": { "description": "Provide description of instruments and devices used in collecting, processing and analysis of samples.", "anyOf": [ { "type": "string", "format": "uri" }, { "items": { "type": "string", "format": "uri" }, "type": "array" }, { "type": "string" }, { "items": { "type": "string" }, "type": "array" }, { "type": "array", "items": { "$ref": "#/definitions/definedterm" } }, { "$ref": "#/definitions/definedterm" } ], "owl:cardinality": "many" }, "environmentalSystem": { "description": "A category or description of the habitat that describes elements of an ecosystem where the sample was collected. Where possible use controlled vocabulary such as ENVO.", "anyOf": [ { "description": "collection of vocabulary terms defined in ontologies", "strict": false, "type": "string", "vocabulary": { "children_of": ["http://purl.obolibrary.org/obo/ENVO_00010483","http://purl.obolibrary.org/obo/NCIT_C62574"], "ontology": ["ENVO","NCIT"] } }, { "items": { "description": "collection of vocabulary terms defined in ontologies", "strict": false, "type": "string", "vocabulary": { "children_of": ["http://purl.obolibrary.org/obo/ENVO_00010483","http://purl.obolibrary.org/obo/NCIT_C62574"], "ontology": ["ENVO","NCIT"] } }, "type": "array" }, { "type": "array", "items": { "$ref": "#/definitions/definedterm" } }, { "$ref": "#/definitions/definedterm" } ], "owl:cardinality": "many" }, "experimentalPurpose": { "description": "Describe the planned or executed experimental procedures involving the samples.", "oneOf": [ { "type": "string" }, { "items": { "type": "string" }, "type": "array" } ], "owl:cardinality": "many" }, "aggregateRating": { "description": "The overall rating, based on a collection of reviews or ratings, of the work. These ratings can be collected based on user reviews or through Altmetric scores of web-based citations.", "abstract": "rating of the work", "oneOf": [ { "items": { "@type": "AggregateRating", "type": "object", "properties": { "ratingCount": { "description": "Total number of ratings", "type": "integer" }, "ratingValue": { "description": "Average rating", "type": "string" }, "itemReviewed": { "description": "What is being reviewed", "type": "string" } }, "required": ["ratingValue"], "recommended": ["ratingCount", "itemReviewed"] }, "type": "array" }, { "@type": "AggregateRating", "type": "object", "properties": { "ratingCount": { "description": "Total number of ratings", "type": "integer" }, "ratingValue": { "description": "Average rating", "type": "string" }, "itemReviewed": { "description": "What is being reviewed", "type": "string" } }, "required": ["ratingValue"], "recommended": ["ratingCount", "itemReviewed"] } ], "owl:cardinality": "many" }, "author": { "description": "A person or organization responsible for the collection, processing, or maintenance of the sample: Populated from collector, contributor, and maintainer.", "anyOf": [ { "type": "array", "items": { "$ref": "#/definitions/person" } }, { "$ref": "#/definitions/person" }, { "type": "array", "items": { "$ref": "#/definitions/organization" } }, { "$ref": "#/definitions/organization" } ], "owl:cardinality": "many" }, "collector": { "description": "The Person or Organization who collected the Sample.", "anyOf": [ { "type": "array", "items": { "$ref": "#/definitions/person" } }, { "$ref": "#/definitions/person" }, { "type": "array", "items": { "$ref": "#/definitions/organization" } }, { "$ref": "#/definitions/organization" } ], "owl:cardinality": "many" }, "contributor": { "description": "Person or organization that contributes to the work.", "anyOf": [ { "type": "array", "items": { "$ref": "#/definitions/person" } }, { "$ref": "#/definitions/person" }, { "type": "array", "items": { "$ref": "#/definitions/organization" } }, { "$ref": "#/definitions/organization" } ], "owl:cardinality": "many" }, "maintainer": { "description": "The Person or Organization who is responsible for the Sample.", "anyOf": [ { "type": "array", "items": { "$ref": "#/definitions/person" } }, { "$ref": "#/definitions/person" }, { "type": "array", "items": { "$ref": "#/definitions/organization" } }, { "$ref": "#/definitions/organization" } ], "owl:cardinality": "many" }, "locationOfOrigin": { "description": "The location from which the sample was originally collected.", "oneOf": [ { "items": { "@type": "AdministrativeArea", "description": "Location information", "properties": { "administrativeType": { "description": "the type of administrative area, such as country, state, county, or city", "enum": ["province", "district", "chiefdom", "village", "city", "country", "prefecture", "sub-prefecture", "clan", "Federal Capital Territory", "state", "Local Government Area", "ward"], "type": "string" }, "alternateName": { "description": "An alias for the location", "oneOf": [ { "type": "string" }, { "items": { "type": "string" }, "type": "array" } ] }, "identifier": { "description": "An identifier for the location, preferably a Wikidata ID", "type": "string" }, "locationType": { "description": "Categorization of how the location relates to the dataset", "const": "collection" }, "name": { "description": "The name of the location", "type": "string" } }, "type": "object" }, "type": "array" }, { "@type": "AdministrativeArea", "type": "object", "description": "Location information", "properties": { "administrativeType": { "description": "the type of administrative area, such as country, state, county, or city", "enum": ["province", "district", "chiefdom", "village", "city", "country", "prefecture", "sub-prefecture", "clan", "Federal Capital Territory", "state", "Local Government Area", "ward"], "type": "string" }, "alternateName": { "description": "An alias for the location", "oneOf": [ { "type": "string" }, { "items": { "type": "string" }, "type": "array" } ] }, "identifier": { "description": "An identifier for the location, preferably a Wikidata ID", "type": "string" }}, "locationType": { "description": "Categorization of how the location relates to the dataset", "const": "collection" }, "name": { "description": "The name of the location", "type": "string" } } ], "owl:cardinality": "many" }, "itemLocation": { "description": "The location where the sample is stored and/or may be ordered.", "oneOf": [ { "type": "array", "items": { "@type": "AdministrativeArea", "description": "Location information", "type": "object", "properties": { "administrativeType": { "description": "the type of administrative area, such as country, state, county, or city", "enum": ["province", "district", "chiefdom", "village", "city", "country", "prefecture", "sub-prefecture", "clan", "Federal Capital Territory", "state", "Local Government Area", "ward"], "type": "string" }, "alternateName": { "description": "An alias for the location", "oneOf": [ { "type": "string" }, { "items": { "type": "string" }, "type": "array" } ] }, "identifier": { "description": "An identifier for the location, preferably a Wikidata ID", "type": "string" }, "locationType": { "description": "Categorization of how the location relates to the dataset", "const": "storage" }, "name": { "description": "The name of the location", "type": "string" } } } }, { "@type": "AdministrativeArea", "type": "object", "description": "Location information", "properties": { "administrativeType": { "description": "the type of administrative area, such as country, state, county, or city", "enum": ["province", "district", "chiefdom", "village", "city", "country", "prefecture", "sub-prefecture", "clan", "Federal Capital Territory", "state", "Local Government Area", "ward"], "type": "string" }, "alternateName": { "description": "An alias for the location", "oneOf": [ { "type": "string" }, { "items": { "type": "string" }, "type": "array" } ] }, "identifier": { "description": "An identifier for the location, preferably a Wikidata ID", "type": "string" }}, "locationType": { "description": "Categorization of how the location relates to the dataset", "const": "storage" }, "name": { "description": "The name of the location", "type": "string" } } ], "owl:cardinality": "many" }, "citation": { "description": "The primary citation or reference to a publication, dataset, or computational tool which uses the sample. Examples: a publication which describes the creation/collection/processing of the sample. The original reference by the sample collectors/processors/maintainers that should be cited when reusing the sample. For all other references by others reusing the sample, use 'citedBy'.", "abstract": "primary citation to the work", "owl:cardinality": "many", "anyOf": [ { "type": "array", "items": { "$ref": "#/definitions/citation" } }, { "$ref": "#/definitions/citation" }, { "type": "array", "items": { "$ref": "#/definitions/creativework" } }, { "$ref": "#/definitions/creativework" } ] }, "date": { "description": "Date the sample has changed: most recent date of dateModified, dateProcessed, and dateCollected.", "abstract": "date changed", "format": "date", "type": "string", "owl:cardinality": "one" }, "dateCreated": { "description": "Date the work was created.", "format": "date", "type": "string", "owl:cardinality": "one" }, "dateModified": { "description": "Date the work was modified.", "format": "date", "type": "string", "owl:cardinality": "one" }, "datePublished": { "description": "Date the work was first published.", "format": "date", "type": "string", "owl:cardinality": "one" }, "dateCollected": { "description": "The date on which the sample was collected.", "format": "date", "type": "string", "owl:cardinality": "one" }, "dateProcessed": { "description": "The date the sample was processed or used in a method.", "format": "date", "type": "string", "owl:cardinality": "one" }, "interactionStatistic": { "description": "The number of interactions with the work, such as page views or tool downloads.", "abstract": "views or downloads", "oneOf": [ { "items": { "@type": "InteractionCounter", "type": "object", "properties": { "interactionType": { "type": "string" }, "userInteractionCount": { "type": "integer" } }, "required": ["interactionType", "userInteractionCount"] }, "type": "array" }, { "@type": "InteractionCounter", "type": "object", "properties": { "interactionType": { "type": "string" }, "userInteractionCount": { "type": "integer" } }, "required": ["interactionType", "userInteractionCount"] } ], "owl:cardinality": "many" }, "keywords": { "description": "Keywords or tags used to describe this work.", "abstract": "keywords or tags", "oneOf": [ { "type": "array", "items": { "type": "string" } }, { "type": "string" } ], "owl:cardinality": "many" }, "sdPublisher": { "description": "Original publisher of the sample metadata (like NCBI GEO, SRA, etc.).", "abstract": "original metadata source", "oneOf": [ { "$ref": "#/definitions/catalog" }, { "type": "array", "items": { "$ref": "#/definitions/catalog" } } ], "owl:cardinality": "many" }, "spatialCoverage": { "description": "The place(s) which are the focus of the sample.", "abstract": "geographic focus of the work", "oneOf": [ { "items": { "@type": "AdministrativeArea", "description": "Location information", "properties": { "administrativeType": { "description": "the type of administrative area, such as country, state, county, or city", "enum": ["province", "district", "chiefdom", "village", "city", "country", "prefecture", "sub-prefecture", "clan", "Federal Capital Territory", "state", "Local Government Area", "ward"], "type": "string" }, "alternateName": { "description": "An alias for the location", "oneOf": [ { "type": "string" }, { "items": { "type": "string" }, "type": "array" } ] }, "identifier": { "description": "An identifier for the location, preferably a Wikidata ID", "type": "string" }, "locationType": { "description": "Categorization of how the location relates to the dataset", "oneOf": [ { "enum": ["residence", "exposure", "collection", "screening", "treatment", "study location", "other", "unknown"], "type": "string" }, { "items": { "enum": ["residence", "exposure", "collection", "screening", "treatment", "study location", "other", "unknown"], "type": "string" }, "type": "array" } ] }, "name": { "description": "The name of the location", "type": "string" } }, "type": "object" }, "type": "array" }, { "@type": "AdministrativeArea", "description": "Location information", "properties": { "administrativeType": { "description": "the type of administrative area, such as country, state, county, or city", "enum": ["province", "district", "chiefdom", "village", "city", "country", "prefecture", "sub-prefecture", "clan", "Federal Capital Territory", "state", "Local Government Area", "ward"], "type": "string" }, "alternateName": { "description": "An alias for the location", "oneOf": [ { "type": "string" }, { "items": { "type": "string" }, "type": "array" } ] }, "identifier": { "description": "An identifier for the location, preferably a Wikidata ID", "type": "string" }, "locationType": { "description": "Categorization of how the location relates to the dataset", "oneOf": [ { "enum": ["residence", "exposure", "collection", "screening", "treatment", "study location", "other", "unknown"], "type": "string" }, { "items": { "enum": ["residence", "exposure", "collection", "screening", "treatment", "study location", "other", "unknown"], "type": "string" }, "type": "array" } ] }, "name": { "description": "The name of the location", "type": "string" } }, "type": "object" } ], "owl:cardinality": "many" }, "temporalCoverage": { "description": "The period of time covered during sampling.", "abstract": "time period", "oneOf": [ { "items": { "@type": "TemporalInterval", "description": "Temporal information", "properties": { "duration": { "description": "A time interval in ISO 8601 duration format", "type": "string" }, "endDate": { "description": "An end date", "format": "date", "type": "string" }, "name": { "description": "String describing the temporal interval", "type": "string" }, "startDate": { "description": "A start date", "format": "date", "type": "string" }, "temporalType": { "description": "Categorization of how the date/temporal interval relates to the dataset", "oneOf": [ { "enum": ["exposure", "collection", "screening", "treatment", "study date", "other", "unknown"], "type": "string" }, { "items": { "enum": ["exposure", "collection", "screening", "treatment", "study date", "other", "unknown"], "type": "string" }, "type": "array" } ] } }, "type": "object" }, "type": "array" }, { "@type": "TemporalInterval", "description": "Temporal information", "properties": { "duration": { "description": "A time interval in ISO 8601 duration format", "type": "string" }, "endDate": { "description": "An end date", "format": "date", "type": "string" }, "name": { "description": "String describing the temporal interval", "type": "string" }, "startDate": { "description": "A start date", "format": "date", "type": "string" }, "temporalType": { "description": "Categorization of how the date/temporal interval relates to the dataset", "oneOf": [ { "enum": ["exposure", "collection", "screening", "treatment", "study date", "other", "unknown"], "type": "string" }, { "items": { "enum": ["exposure", "collection", "screening", "treatment", "study date", "other", "unknown"], "type": "string" }, "type": "array" } ] } }, "type": "object" } ], "owl:cardinality": "many" }, "sourceOrganization": { "description": "The organization, research project, working group, or funded program on whose behalf the author/creator was working.", "anyOf": [ { "type": "array", "items": { "$ref": "#/definitions/researchproject" } }, { "$ref": "#/definitions/researchproject" }, { "type": "array", "items": { "$ref": "#/definitions/organization" } }, { "$ref": "#/definitions/organization" } ], "owl:cardinality": "many" }, "topicCategory": { "description": "Topic of the work. This topic may be assigned by a human curator or through automated algorithms.", "abstract": "topic", "anyOf": [ { "type": "array", "items": { "$ref": "#/definitions/topic" } }, { "$ref": "#/definitions/topic" }, { "type": "array", "items": { "$ref": "#/definitions/definedterm" } }, { "$ref": "#/definitions/definedterm" } ], "owl:cardinality": "many" }, "creditText": { "description": "Text that can be used to credit person(s) and/or organization(s) associated with a published Creative Work. For example, how a user should cite the sample.", "type": "string", "owl:cardinality": "one" } }, "required": [], "recommended": ["includedInDataCatalog", "author", "date", "description", "sameAs", "conditionsOfAccess", "usageInfo", "license", "cellType", "infectiousAgent", "species", "healthCondition", "funding", "creditText", "anatomicalStructure", "sex", "developmentalStage", "sampleAvailability", "sampleProcess", "sampleType", "collectionMethod", "instrument", "collector", "contributor", "locationOfOrigin", "citation", "dateModified", "dateCollected", "dateProcessed", "interactionStatistic", "keywords", "sdPublisher", "sourceOrganization", "topicCategory", "creditText"], "optional": ["associatedPhenotype", "associatedGenotype", "citedBy", "isRelatedTo", "isSimilarTo", "isBasisFor", "isBasedOn", "hasPart","isPartOf", "anatomicalSystem", "sampleQuantity", "sampleState", "sampleStorageTemperature", "distribution", "measurementTechnique", "variableMeasured", "environmentalSystem", "aggregateRating", "experimentalPurpose", "maintainer", "itemLocation", "dateCreated", "datePublished", "spatialCoverage", "temporalCoverage"] } } } }, { "@id": "nde:DataCollection", "@type": "rdfs:Class", "rdfs:comment": "Data collections contained in the NIAID Data Ecosystem. A data collection is a collection of data records from other sources that have been grouped by common search fields. The NIAID Data Ecosystem is an environment to find and access and infectious and immune-mediated disease data and resources to speed the development of diagnostics, therapeutics, and vaccines. The NIAID Data Ecosystem Discovery Portal aggregates metadata from repository of various data types and harmonizes them to this schema to enable easy cross-platform resource searching and filtering. Data collections are essentially artificial datasets that exist in the NIAID Data Ecosystem to extend the discovery of resources beyond the current scope of the data classes included in the Discovery Portal.", "abstract": "Data Collections contained in the NIAID Data Ecosystem. A data collection is a collection of data grouped by common search fields in the NIAID Data Ecosystem.", "rdfs:label": "DataCollection", "rdfs:subClassOf": { "@id": "nde:Dataset" }, "schema:schemaVersion":["https://schema.org/docs/releases.html#v18.0","v0.2 - 2026.02.04"], "dct:provenance":"Changes since previous version: Updated exampleOfWork object to include 'additionalProperty'.", "$validation": { "$schema": "http://json-schema.org/draft-07/schema#", "type": "object", "properties": { "about": { "description": "The entity type or class encapsulated by the records in this data collection. For example, if the records in this collection contain metadata about the genetic sequence, epigentic annotation, gene locus, etc.-- the entity type would be Gene, and the collection contains records 'about' Genes. These should be formatted as DefinedTerm objects (mapped to ontology terms) for easier standardization.", "oneOf": [ { "type": "array", "items": { "$ref": "#/definitions/definedterm" } }, { "$ref": "#/definitions/definedterm" } ], "owl:cardinality": "many" }, "date": { "description": "Date the work has changed: most recent date of dateModified, datePublished, and dateCreated.", "abstract": "date changed", "format": "date", "type": "string", "owl:cardinality": "one" }, "dateModified": { "description": "The date on which the data collection itself (not the underlying source records) was modified or when the item's entry was modified within a DataFeed.", "format": "date", "type": "string", "owl:cardinality": "one" }, "description": { "description": "A description of the dataset.", "owl:cardinality": "one", "type": "string" }, "includedInDataCatalog": { "description": "Repository or source which contains the records that were collected for this data collection.", "abstract": "catalog containing the source of data for the work", "oneOf": [ { "$ref": "#/definitions/catalog" }, { "type": "array", "items": { "$ref": "#/definitions/catalog" } } ], "owl:cardinality": "one" }, "name": { "description": "The name of the data collection.", "owl:cardinality": "one", "type": "string" }, "url": { "description": "URL of the source of the data collection.", "type": "string", "format": "uri", "owl:cardinality": "one" }, "collectionSize": { "description": "The number of records data collection. Min/max estimates can be used in lieu of actual number. If completely unknown, set value = 0, and unitText = 'unknown'", "anyOf": [ { "type": "array", "items": { "$ref": "#/definitions/propertyvalue" } }, { "$ref": "#/definitions/propertyvalue" }, { "type": "array", "items": { "$ref": "#/definitions/quantitativevalue" } }, { "$ref": "#/definitions/quantitativevalue" } ], "owl:cardinality": "many" }, "funding": { "description": "Funding that supports (sponsors) the creation of the records included in the data collection through some kind of financial contribution.", "abstract": "funding source (grant, contract, etc.)", "oneOf": [ { "type": "object", "@type": "MonetaryGrant", "description": "Funding that supports (sponsors) the collection of this dataset through some kind of financial contribution", "properties": { "funder": { "description": "An organization associated with a creator or funder of a dataset", "oneOf": [ { "type": "object", "@type": "Organization", "description": "Information about a single funder", "properties": { "name": { "type": "string", "description": "An organization associated with a creator or funder of a dataset" }, "parentOrganization": { "type": "string", "description": "name of the parent funding organization" } }, "required": [ "name" ] }, { "type": "array", "items": { "type": "object", "@type": "Organization", "description": "Information about a single funder", "properties": { "name": { "type": "string", "description": "An organization associated with a creator or funder of a dataset" }, "parentOrganization": { "type": "string", "description": "name of the parent funding organization" } }, "required": [ "name" ] } } ] }, "description": { "type": "string", "description": "description about the funding award / grant" }, "url": { "type": "string", "description": "award / grant URL" }, "identifier": { "type": "string", "description": "Unique identifier(s) for the grant(s) used to fund the Dataset" } }, "required": [ "funder", "identifier" ] }, { "type": "array", "items": { "type": "object", "@type": "MonetaryGrant", "description": "Funding that supports (sponsors) the collection of this dataset through some kind of financial contribution", "properties": { "funder": { "description": "An organization associated with a creator or funder of a dataset", "oneOf": [ { "type": "object", "@type": "Organization", "description": "Information about a single funder", "properties": { "name": { "type": "string", "description": "An organization associated with a creator or funder of a dataset" }, "parentOrganization": { "type": "string", "description": "name of the parent funding organization" } }, "required": [ "name" ] }, { "type": "array", "items": { "type": "object", "@type": "Organization", "description": "Information about a single funder", "properties": { "name": { "type": "string", "description": "An organization associated with a creator or funder of a dataset" }, "parentOrganization": { "type": "string", "description": "name of the parent funding organization" } }, "required": [ "name" ] } } ] }, "description": { "type": "string", "description": "description about the funding award / grant" }, "url": { "type": "string", "description": "award / grant URL" }, "identifier": { "type": "string", "description": "Unique identifier(s) for the grant(s) used to fund the Dataset" } }, "required": [ "funder", "identifier" ] } } ], "owl:cardinality": "many" }, "author": { "description": "Author or creator of the records from which the data collection was derived.", "anyOf": [ { "type": "array", "items": { "$ref": "#/definitions/person" } }, { "$ref": "#/definitions/person" }, { "type": "array", "items": { "$ref": "#/definitions/organization" } }, { "$ref": "#/definitions/organization" } ], "owl:cardinality": "many" }, "citation": { "description": "The primary citation or reference about the resource upon which the data collection was built. Examples: a publication which describes the source of the data collection. The original reference by the source of data collection by the creators/maintainers that should be cited when reusing the source of records included in the data collection. For other references to the source of the data collection, use 'citedBy'.", "abstract": "citation to the work", "owl:cardinality": "many", "anyOf": [ { "type": "array", "items": { "$ref": "#/definitions/citation" } }, { "$ref": "#/definitions/citation" }, { "type": "array", "items": { "$ref": "#/definitions/creativework" } }, { "$ref": "#/definitions/creativework" } ] }, "conditionsOfAccess": { "description": "Conditions that affect the availability of, or method(s) of access to the source records included in the data collection. Options include open (freely available), restricted (may include restrictions such as on use), closed (requires registration to access), or embargoed (unpublished).", "abstract": "accessibility of the work", "type": "string", "enum": ["Closed", "Open", "Restricted", "Embargoed"], "owl:cardinality": "one" }, "creator": { "description": "The creator/author of the data collection itself. Author and creator are generally used interchangeably (with the default being author) for most classes in the NIAID Data Ecosystem; however, for Data Collections, it is the creator of the data collection, rather than the author of the records included in the data collection.", "anyOf": [ { "type": "array", "items": { "$ref": "#/definitions/person" } }, { "$ref": "#/definitions/person" }, { "type": "array", "items": { "$ref": "#/definitions/organization" } }, { "$ref": "#/definitions/organization" } ], "owl:cardinality": "many" }, "dateCreated": { "description": "The date on which the data collection itself (not the underlying source records) was created or when the item's entry was added to a DataFeed.", "format": "date", "type": "string", "owl:cardinality": "one" }, "datePublished": { "description": "The date on which the data collection itself (not the underlying source records) was first published or when the item's entry was published within a DataFeed.", "format": "date", "type": "string", "owl:cardinality": "one" }, "exampleOfWork": { "description": "A creative work (e.g. Data record) that this work (the Data Collection) is an example/instance/realization/derivation of. For example, a Data record from which this DataCollection was derived", "abstract": "Metadata data about the record type included in the Data Collection.", "owl:cardinality": "many", "oneOf": [ { "type": "array", "items": { "$ref": "#/definitions/examplework" } }, { "$ref": "#/definitions/examplework" } ] }, "healthCondition": { "description": "The infectious disease(s) / health condition(s) which are the focus of the data collection.", "abstract": "health condition/disease", "anyOf": [ { "description": "collection of vocabulary terms defined in ontologies", "strict": false, "type": "string", "vocabulary": { "children_of": ["http://purl.obolibrary.org/obo/MONDO_0000001", "http://purl.obolibrary.org/obo/DOID_4", "http://purl.obolibrary.org/obo/HP_0000001", "http://purl.obolibrary.org/obo/NCIT_C7057"], "ontology": ["mondo","hpo","doid","ncit"] } }, { "items": { "description": "collection of vocabulary terms defined in ontologies", "strict": false, "type": "string", "vocabulary": { "children_of": ["http://purl.obolibrary.org/obo/MONDO_0000001", "http://purl.obolibrary.org/obo/DOID_4", "http://purl.obolibrary.org/obo/HP_0000001", "http://purl.obolibrary.org/obo/NCIT_C7057"], "ontology": ["mondo","hpo","doid","ncit"] } }, "type": "array" }, { "type": "array", "items": { "$ref": "#/definitions/definedterm" } }, { "$ref": "#/definitions/definedterm" } ], "owl:cardinality": "many" }, "infectiousAgent": { "description": "Infectious agent(s) / pathogen(s) which are the focus of the data collection (like SARS-CoV-2).", "abstract": "infectious agent / pathogen", "anyOf": [ { "description": "collection of vocabulary terms defined in ontologies", "strict": false, "type": "string", "vocabulary": { "children_of": ["http://purl.obolibrary.org/obo/NCBITaxon_10239", "http://purl.obolibrary.org/obo/NCBITaxon_2"], "ontology": ["ncbitaxon"] } }, { "items": { "description": "collection of vocabulary terms defined in ontologies", "strict": false, "type": "string", "vocabulary": { "children_of": ["http://purl.obolibrary.org/obo/NCBITaxon_10239", "http://purl.obolibrary.org/obo/NCBITaxon_2"], "ontology": ["ncbitaxon"] } }, "type": "array" }, { "type": "array", "items": { "$ref": "#/definitions/definedterm" } }, { "$ref": "#/definitions/definedterm" } ], "owl:cardinality": "many" }, "interactionStatistic": { "description": "The number of interactions with the work, such as page views or tool downloads.", "abstract": "views or downloads", "oneOf": [ { "items": { "@type": "InteractionCounter", "type": "object", "properties": { "interactionType": { "type": "string" }, "userInteractionCount": { "type": "integer" } }, "required": ["interactionType", "userInteractionCount"] }, "type": "array" }, { "@type": "InteractionCounter", "type": "object", "properties": { "interactionType": { "type": "string" }, "userInteractionCount": { "type": "integer" } }, "required": ["interactionType", "userInteractionCount"] } ], "owl:cardinality": "many" }, "isBasedOn": { "description": "A resource from which this data collection is derived, modified, or adapted. This can include sources of the records in the data collection if the records in the data collection were grouped by their sources.", "abstract": "resources used to create the data collection", "owl:cardinality": "many", "anyOf": [ { "type": "array", "items": { "$ref": "#/definitions/citation" } }, { "$ref": "#/definitions/citation" }, { "type": "array", "items": { "$ref": "#/definitions/creativework" } }, { "$ref": "#/definitions/creativework" }, { "type": "array", "items": { "$ref": "#/definitions/resourcecatalog" } }, { "$ref": "#/definitions/resourcecatalog" }, { "type": "array", "items": { "$ref": "#/definitions/action" } }, { "$ref": "#/definitions/action" } ] }, "license": { "description": "A license document that applies to the source of the data collection, typically indicated by URL.", "abstract": "license for use", "format": "uri", "owl:cardinality": "one", "type": "string" }, "measurementTechnique": { "description": "A technique, method or technology used in the source data for the data collection corresponding to the method used for measuring the corresponding variable(s) (for the records in the data collection, described using variableMeasured; for Observation, a StatisticalVariable). For example, if variableMeasured is: molecule concentration, measurementTechnique could be: \"mass spectrometry\" or \"nmr spectroscopy\" or \"colorimetry\" or \"immunofluorescence\". If the variableMeasured is \"depression rating\", the measurementTechnique could be \"Zung Scale\" or \"HAM-D\" or \"Beck Depression Inventory\".", "abstract": "measurement technique used to generate the records in the data collection.", "anyOf": [ { "description": "collection of vocabulary terms defined in ontologies", "strict": false, "type": "string", "vocabulary": { "children_of": ["http://edamontology.org/topic_3361", "http://purl.obolibrary.org/obo/NCIT_C20368", "http://purl.obolibrary.org/obo/MMO_0000000", "http://www.ebi.ac.uk/efo/EFO_0000001"], "ontology": ["edam", "ncit", "mmo","efo"] } }, { "items": { "description": "collection of vocabulary terms defined in ontologies", "strict": false, "type": "string", "vocabulary": { "children_of": ["http://edamontology.org/topic_3361", "http://purl.obolibrary.org/obo/NCIT_C20368", "http://purl.obolibrary.org/obo/MMO_0000000", "http://www.ebi.ac.uk/efo/EFO_0000001"], "ontology": ["edam", "ncit", "mmo","efo"] } }, "type": "array" }, { "type": "array", "items": { "$ref": "#/definitions/definedterm" } }, { "$ref": "#/definitions/definedterm" } ], "owl:cardinality": "many" }, "sameAs": { "description": "The url(s) for generating the data collection on the source website, if the source has RESTful urls", "oneOf": [ { "items": { "type": "string", "format": "uri" }, "type": "array" }, { "type": "string", "format": "uri" } ], "owl:cardinality": "many" }, "spatialCoverage": { "description": "The spatialCoverage of a CreativeWork indicates the place(s) which are the focus of the content. It is a subproperty of contentLocation intended primarily for more technical and detailed materials. For example with a Data collection, it indicates areas that the records in the collection describes or were grouped by: a data collection of New York weather would have spatialCoverage which was the place: the state of New York.", "abstract": "geographic focus of the work", "oneOf": [ { "items": { "@type": "AdministrativeArea", "description": "Location information", "properties": { "administrativeType": { "description": "the type of administrative area, such as country, state, county, or city", "enum": ["province", "district", "chiefdom", "village", "city", "country", "prefecture", "sub-prefecture", "clan", "Federal Capital Territory", "state", "Local Government Area", "ward"], "type": "string" }, "alternateName": { "description": "An alias for the location", "oneOf": [ { "type": "string" }, { "items": { "type": "string" }, "type": "array" } ] }, "identifier": { "description": "An identifier for the location, preferably a Wikidata ID", "type": "string" }, "locationType": { "description": "Categorization of how the location relates to the dataset", "oneOf": [ { "enum": ["residence", "exposure", "collection", "screening", "treatment", "study location", "other", "unknown"], "type": "string" }, { "items": { "enum": ["residence", "exposure", "collection", "screening", "treatment", "study location", "other", "unknown"], "type": "string" }, "type": "array" } ] }, "name": { "description": "The name of the location", "type": "string" } }, "type": "object" }, "type": "array" }, { "@type": "AdministrativeArea", "description": "Location information", "properties": { "administrativeType": { "description": "the type of administrative area, such as country, state, county, or city", "enum": ["province", "district", "chiefdom", "village", "city", "country", "prefecture", "sub-prefecture", "clan", "Federal Capital Territory", "state", "Local Government Area", "ward"], "type": "string" }, "alternateName": { "description": "An alias for the location", "oneOf": [ { "type": "string" }, { "items": { "type": "string" }, "type": "array" } ] }, "identifier": { "description": "An identifier for the location, preferably a Wikidata ID", "type": "string" }, "locationType": { "description": "Categorization of how the location relates to the dataset", "oneOf": [ { "enum": ["residence", "exposure", "collection", "screening", "treatment", "study location", "other", "unknown"], "type": "string" }, { "items": { "enum": ["residence", "exposure", "collection", "screening", "treatment", "study location", "other", "unknown"], "type": "string" }, "type": "array" } ] }, "name": { "description": "The name of the location", "type": "string" } }, "type": "object" } ], "owl:cardinality": "many" }, "species": { "description": "Species(es) / host organism from which records in the data collection have been collected, or is the focus of grouping of records in the data collection.", "abstract": "species/host organism", "anyOf": [ { "description": "collection of vocabulary terms defined in ontologies", "strict": false, "type": "string", "vocabulary": { "children_of": ["http://purl.obolibrary.org/obo/NCBITaxon_131567", "http://purl.obolibrary.org/obo/NCBITaxon_10239"], "ontology": ["ncbitaxon"] } }, { "items": { "description": "collection of vocabulary terms defined in ontologies", "strict": false, "type": "string", "vocabulary": { "children_of": ["http://purl.obolibrary.org/obo/NCBITaxon_131567", "http://purl.obolibrary.org/obo/NCBITaxon_10239"], "ontology": ["ncbitaxon"] } }, "type": "array" }, { "type": "array", "items": { "$ref": "#/definitions/definedterm" } }, { "$ref": "#/definitions/definedterm" } ], "owl:cardinality": "many" }, "temporalCoverage": { "description": "The period of time covered by the records grouped within the data collection.", "abstract": "time period", "oneOf": [ { "items": { "@type": "TemporalInterval", "description": "Temporal information", "properties": { "duration": { "description": "A time interval in ISO 8601 duration format", "type": "string" }, "endDate": { "description": "An end date", "format": "date", "type": "string" }, "name": { "description": "String describing the temporal interval", "type": "string" }, "startDate": { "description": "A start date", "format": "date", "type": "string" }, "temporalType": { "description": "Categorization of how the date/temporal interval relates to the dataset", "oneOf": [ { "enum": ["exposure", "collection", "screening", "treatment", "study date", "other", "unknown"], "type": "string" }, { "items": { "enum": ["exposure", "collection", "screening", "treatment", "study date", "other", "unknown"], "type": "string" }, "type": "array" } ] } }, "type": "object" }, "type": "array" }, { "@type": "TemporalInterval", "description": "Temporal information", "properties": { "duration": { "description": "A time interval in ISO 8601 duration format", "type": "string" }, "endDate": { "description": "An end date", "format": "date", "type": "string" }, "name": { "description": "String describing the temporal interval", "type": "string" }, "startDate": { "description": "A start date", "format": "date", "type": "string" }, "temporalType": { "description": "Categorization of how the date/temporal interval relates to the dataset", "oneOf": [ { "enum": ["exposure", "collection", "screening", "treatment", "study date", "other", "unknown"], "type": "string" }, { "items": { "enum": ["exposure", "collection", "screening", "treatment", "study date", "other", "unknown"], "type": "string" }, "type": "array" } ] } }, "type": "object" } ], "owl:cardinality": "many" }, "topicCategory": { "description": "Topic of the records in the data collection. This topic may be assigned by a human curator or through automated algorithms.", "abstract": "topic", "anyOf": [ { "type": "array", "items": { "$ref": "#/definitions/topic" } }, { "$ref": "#/definitions/topic" }, { "type": "array", "items": { "$ref": "#/definitions/definedterm" } }, { "$ref": "#/definitions/definedterm" } ], "owl:cardinality": "many" }, "usageInfo": { "description": "Data usage agreement for the records included in the data collection, the terms under which the underlying records in the data collection can be used. Information on how the data collection can be used. Note that this is related to but distinct from the license.", "abstract": "data usage agreement", "oneOf": [ { "type": "array", "items": { "$ref": "#/definitions/creativework" } }, { "$ref": "#/definitions/creativework" } ], "owl:cardinality": "many" }, "variableMeasured": { "description": "Variables measured within the records in the data collection. Measured variables by which the records in the data collection may have been grouped.", "oneOf": [ { "description": "collection of vocabulary terms defined in ontologies", "strict": false, "type": "string", "vocabulary": { "children_of": ["http://www.ebi.ac.uk/efo/EFO_0000001", "http://purl.obolibrary.org/obo/CMO_0000000", "http://purl.obolibrary.org/obo/NCIT_C25209"], "ontology": ["efo", "cmo","ncit"] } }, { "items": { "description": "collection of vocabulary terms defined in ontologies", "strict": false, "type": "string", "vocabulary": { "children_of": ["http://www.ebi.ac.uk/efo/EFO_0000001", "http://purl.obolibrary.org/obo/CMO_0000000", "http://purl.obolibrary.org/obo/NCIT_C25209"], "ontology": ["efo", "cmo","ncit"] } }, "type": "array" }, { "type": "array", "items": { "$ref": "#/definitions/definedterm" } }, { "$ref": "#/definitions/definedterm" } ], "owl:cardinality": "many" }, "aggregateRating": { "description": "The overall rating, based on a collection of reviews or ratings, of the work. These ratings can be collected based on user reviews or through Altmetric scores of web-based citations.", "abstract": "rating of the work", "oneOf": [ { "items": { "@type": "AggregateRating", "type": "object", "properties": { "ratingCount": { "description": "Total number of ratings", "type": "integer" }, "ratingValue": { "description": "Average rating", "type": "string" }, "itemReviewed": { "description": "What is being reviewed", "type": "string" } }, "required": ["ratingValue"], "recommended": ["ratingCount", "itemReviewed"] }, "type": "array" }, { "@type": "AggregateRating", "type": "object", "properties": { "ratingCount": { "description": "Total number of ratings", "type": "integer" }, "ratingValue": { "description": "Average rating", "type": "string" }, "itemReviewed": { "description": "What is being reviewed", "type": "string" } }, "required": ["ratingValue"], "recommended": ["ratingCount", "itemReviewed"] } ], "owl:cardinality": "many" }, "citedBy": { "description": "Publications or resources that cite the records in the data collection. Alternatively, publications or resources by which the records were grouped based on the citation of the records in the data collection. For the primary citation of the resource from which the data collection was created, use the 'citation' field.", "anyOf": [ { "type": "array", "items": { "$ref": "#/definitions/citation" } }, { "$ref": "#/definitions/citation" }, { "type": "array", "items": { "$ref": "#/definitions/creativework" } }, { "$ref": "#/definitions/creativework" } ], "owl:cardinality": "many" }, "creditText": { "description": "Text that can be used to credit person(s) and/or organization(s) associated with a published Creative Work. For example, how a user should cite the dataset.", "type": "string", "owl:cardinality": "one" }, "hasPart": { "description": "Associated materials for the records in the data collection, including data dictionaries and data limitation descriptions. This can include associated materials by which the records were grouped for having the same materials in common in the data collection.", "abstract": "data limitations or dictionaries", "anyOf": [ { "type": "array", "items": { "$ref": "#/definitions/citation" } }, { "$ref": "#/definitions/citation" }, { "type": "array", "items": { "$ref": "#/definitions/creativework" } }, { "$ref": "#/definitions/creativework" } ], "owl:cardinality": "many" }, "identifier": { "description": "identifiers for records within the data collection.", "abstract": "identifier or accession number", "oneOf": [ { "type": "string" }, { "items": { "type": "string" }, "type": "array" } ], "owl:cardinality": "many" }, "isAccessibleForFree": { "description": "A flag to signal that the items included in the data collection are accessible for free.", "abstract": "accessible without charge", "type": "boolean", "owl:cardinality": "one" }, "isBasisFor": { "description": "Dataset, resource/resource catalog or computational tool which incorporate the records included in this data collection. This can include resources by which the records were grouped (for having derivative resources in common) in the data collection.", "anyOf": [ { "type": "array", "items": { "$ref": "#/definitions/citation" } }, { "$ref": "#/definitions/citation" }, { "type": "array", "items": { "$ref": "#/definitions/creativework" } }, { "$ref": "#/definitions/creativework" } ], "owl:cardinality": "many" }, "isPartOf": { "description": "Indicates a broader study, project, or collection the records in the data collection are part of. This can include broader study, project, etc. by which the records were grouped (for being a part of) in the data collection.", "abstract": "study or project including the work", "owl:cardinality": "many", "anyOf": [ { "type": "array", "items": { "$ref": "#/definitions/citation" } }, { "$ref": "#/definitions/citation" }, { "type": "array", "items": { "$ref": "#/definitions/creativework" } }, { "$ref": "#/definitions/creativework" } ] }, "isRelatedTo": { "description": "Dataset, resource/resource catalog or computational tool which are related to the records included in the data collection. This can include resources by which the records were grouped (for being related to) in the data collection.", "abstract": "related datasets (via curation)", "anyOf": [ { "type": "array", "items": { "$ref": "#/definitions/citation" } }, { "$ref": "#/definitions/citation" }, { "type": "array", "items": { "$ref": "#/definitions/creativework" } }, { "$ref": "#/definitions/creativework" } ], "owl:cardinality": "many" }, "isSimilarTo": { "description": "Data collections which are similar to the data collection, based on terms in the names, descriptions, authors, measurementTechniques, infectiousAgents, healthConditions, etc.", "abstract": "similar datasets (auto-assigned)", "anyOf": [ { "type": "array", "items": { "$ref": "#/definitions/citation" } }, { "$ref": "#/definitions/citation" }, { "type": "array", "items": { "$ref": "#/definitions/creativework" } }, { "$ref": "#/definitions/creativework" } ], "owl:cardinality": "many" }, "keywords": { "description": "Keywords or tags used to describe this work.", "abstract": "keywords or tags", "oneOf": [ { "type": "array", "items": { "type": "string" } }, { "type": "string" } ], "owl:cardinality": "many" }, "sample": { "description": "The sample(s) which were used to generate the records in the data collection", "anyOf": [ { "type": "array", "items": { "$ref": "#/definitions/samplerecord" } }, { "$ref": "#/definitions/samplerecord" }, { "type": "string", "format": "uri" }, { "type": "array", "items": { "type": "string", "format": "uri" } }, { "type": "array", "items": { "$ref": "#/definitions/samplecollection" } }, { "$ref": "#/definitions/samplecollection" } ], "owl:cardinality": "many" }, "sdPublisher": { "description": "Original publisher of the metadata for the records included in the data collection.", "abstract": "original metadata source", "oneOf": [ { "$ref": "#/definitions/catalog" }, { "type": "array", "items": { "$ref": "#/definitions/catalog" } } ], "owl:cardinality": "many" }, "sourceOrganization": { "description": "The organization, research project, working group, or funded program on whose behalf the author/creator was working when generating the records included in the data collection. This can include organizations, programs, etc. by which the records were grouped (having the same source organization) in the data collection.", "anyOf": [ { "type": "array", "items": { "$ref": "#/definitions/researchproject" } }, { "$ref": "#/definitions/researchproject" }, { "type": "array", "items": { "$ref": "#/definitions/organization" } }, { "$ref": "#/definitions/organization" } ], "owl:cardinality": "many" }, "version": { "description": "The version of the source of the records included in the data collection.", "type": "string", "owl:cardinality": "one" } }, "required": ["about", "date", "dateModified", "description", "includedInDataCatalog", "name", "url", "collectionSize"], "recommended": ["funding", "author", "citation", "conditionsOfAccess", "creator", "dateCreated", "datePublished", "exampleOfWork", "healthCondition", "infectiousAgent", "interactionStatistic", "isBasedOn", "license", "measurementTechnique", "sameAs", "spatialCoverage", "species", "temporalCoverage", "topicCategory", "usageInfo", "variableMeasured"], "optional": ["aggregateRating", "citedBy","creditText", "hasPart", "identifier", "isAccessibleForFree", "isBasisFor", "isPartOf", "isRelatedTo", "isSimilarTo", "keywords", "sample", "sdPublisher", "sourceOrganization", "version"], "definitions": { "citation": { "description": "A citation object for a resource which is cited by the dataset (ie- is a derivative of the dataset) , related to the dataset, or from which the dataset was based on (ie- is derived from).", "@type": "ScholarlyArticle", "type": "object", "properties": { "author": { "description": "Author(s) of the publication", "anyOf": [ { "type": "array", "items": { "$ref": "#/definitions/person" } }, { "$ref": "#/definitions/person" }, { "type": "array", "items": { "$ref": "#/definitions/organization" } }, { "$ref": "#/definitions/organization" } ] }, "abstract": { "description": "Abstract of the publication", "type": "string" }, "datePublished": { "description": "Date the article was published", "format": "date", "type": "string" }, "description": { "description": "Description of the publication", "type": "string" }, "name": { "description": "Title of the publication", "type": "string" }, "identifier": { "description": "An identifier associated with the citation such as a digital object identifier (DOI), PubMed ID (PMID), or PubMed Central ID (PMCID)", "type": "string" }, "pmid": { "description": "A PubMed identifier (PMID) of the referenced publication", "abstract": "PubMed identifier", "type": "string" }, "doi": { "description": "A digital object identifier (DOI) of the referenced publication", "abstract": "digital object identifier", "type": "string" }, "issueNumber": { "description": "Issue number where the article appears", "type": "string" }, "journalName": { "description": "Journal where the article appears", "type": "string" }, "journalNameAbbrev": { "description": "Abbreviated journal name where the article appears", "type": "string" }, "pagination": { "description": "Page numbers in the journal where the article appears", "type": "string" }, "url": { "description": "The url of the article", "type": "string", "format": "uri" }, "volumeNumber": { "description": "Volume of the journal where the article appears", "type": "string" }, "citation": { "description": "The bibliographic citation string for the article as is provided", "type": "string" } }, "required": ["name"], "recommended": ["author", "datePublished", "doi", "identifier", "journalName", "pmid", "url"], "optional": ["abstract", "citation", "description", "issueNumber", "journalNameAbbrev", "pagination", "volumeNumber"] }, "creativework": { "description": "A resource", "@type": "CreativeWork", "type": "object", "properties": { "author": { "description": "Author(s) of the referenced work", "anyOf": [ { "type": "array", "items": { "$ref": "#/definitions/person" } }, { "$ref": "#/definitions/person" }, { "type": "array", "items": { "$ref": "#/definitions/organization" } }, { "$ref": "#/definitions/organization" } ] }, "abstract": { "description": "Abstract of the referenced work", "type": "string" }, "datePublished": { "description": "Date the referenced work was published", "format": "date", "type": "string" }, "description": { "description": "Description of the referenced work", "type": "string" }, "hasPart": { "description": "A portion of the work", "oneOf": [ { "$ref": "#/definitions/citation" } ] }, "includedInDataCatalog": { "description": "Data or tool catalog which houses the work", "oneOf": [ { "$ref": "#/definitions/catalog" } ] }, "name": { "description": "Name or title", "type": "string" }, "identifier": { "description": "An identifier associated with the work", "type": "string" }, "relationship": { "description": "How the works are related", "type": "string" }, "doi": { "description": "A digital object identifier (DOI) of the referenced work", "abstract": "digital object identifier", "type": "string" }, "url": { "description": "The url of the work", "type": "string", "format": "uri" }, "citation": { "description": "The bibliographic citation for the referenced work as is provided", "type": "string" } }, "required": ["name"], "recommended": ["author", "datePublished", "doi", "identifier", "includedInDataCatalog", "relationship", "url"], "optional": ["abstract", "citation", "description", "hasPart"] }, "examplework": { "description": "A creative work (e.g. Data record) that this work (the Data Collection) is an example/instance/realization/derivation of. For example, a Data record from which this DataCollection was derived.", "@type": "CreativeWork", "type": "object", "properties": { "about": { "description": "The Data type of a record included in this collection, use EDAM Data Ontology", "anyOf": [ { "type": "array", "items": { "$ref": "#/definitions/definedterm" } }, { "$ref": "#/definitions/definedterm" }, { "description": "data type of the records included in this collection.", "type": "string", "vocabulary": { "ontology": ["edam"], "children_of": ["http://edamontology.org/data_0006"] }, "strict": false }, { "type": "array", "items": { "description": "data type of the records included in this collection.", "type": "string", "vocabulary": { "ontology": ["edam"], "children_of": ["http://edamontology.org/data_0006"] }, "strict": false } } ] }, "encodingFormat": { "description": "The Formats in which a data record can be downloaded from the source, used EDAM Format ontology", "anyOf": [ { "type": "array", "items": { "$ref": "#/definitions/definedterm" } }, { "$ref": "#/definitions/definedterm" }, { "description": "data type of the records included in this collection.", "type": "string", "vocabulary": { "ontology": ["edam"], "children_of": ["http://edamontology.org/format_1915"] }, "strict": false }, { "type": "array", "items": { "description": "data type of the records included in this collection.", "type": "string", "vocabulary": { "ontology": ["edam"], "children_of": ["http://edamontology.org/format_1915"] }, "strict": false } } ] }, "potentialAction": { "description": "Potential actions, processes, or operations that could be run on this data. Whenever possible, use EDAM Operations ontology", "anyOf": [ { "type": "array", "items": { "$ref": "#/definitions/definedterm" } }, { "$ref": "#/definitions/definedterm" }, { "type": "array", "items": { "$ref": "#/definitions/action" } }, { "$ref": "#/definitions/action" } ] }, "schemaVersion": { "description": "URL(s) to the schema that was used for the data records in the data collection.", "oneOf": [ { "type": "array", "items": { "type": "string", "format": "uri" } }, { "type": "string", "format": "uri" } ] }, "additionalProperty": { "description": "Other Property/Value pairs that describe the example.", "anyOf": [ { "type": "array", "items": { "$ref": "#/definitions/propvalpair" } }, { "$ref": "#/definitions/propvalpair" } ], "owl:cardinality": "many" } }, "recommended": ["about", "encodingFormat", "schemaVersion", "potentialAction", "additionalProperty"] }, "action": { "@type": "Action", "description": "Protocols or processes that can be enacted upon a data record in the data collection. For example, the protocol or process used to generate the data collection.", "type": "object", "properties": { "name": { "description": "Protocol or process name. In the case of the data collection protocol, the name for the data collection process should follow the format 'Process for creating the {Source} {about} Data Collection in the NIAID Data Ecosystem Discovery Portal'. For example, 'Process for creating the BV-BRC Genome Data Collection in the NIAID Data Ecosystem Discovery Portal'", "type": "string" }, "description": { "description": "Protocol or process description. For example, a description of the process used to generate the data collection.", "type": "string" }, "url": { "description": "Link to protocol or process.", "type": "string", "format": "uri" }, "actionProcess": { "description": "Protocol or process description formatted as a HowTo object. For example, the description of how the Data Collection was generated formatted as a HowTo object.", "oneOf": [ { "type": "array", "items": { "$ref": "#/definitions/howto" } }, { "$ref": "#/definitions/howto" } ] } }, "required": ["name"], "recommended": ["actionProcess"], "anyOf": [ {"required":["description"]}, {"required":["url"]} ] }, "topic": { "description": "Topic assigned to the work.", "type": "string", "vocabulary": { "ontology": ["edam"], "children_of": ["http://edamontology.org/topic_0003"] }, "strict": true }, "catalog": { "@type": "DataCatalog", "description": "Data or tool catalog", "type": "object", "properties": { "name": { "description": "Data or tool catalog name", "type": "string" }, "url": { "description": "Link to data or tool catalog", "type": "string", "format": "uri" }, "versionDate": { "description": "date the metadata was harvested from the catalog", "type": "string", "format": "date" }, "archivedAt": { "description": "The url(s) of one or more datasets, tools, resources or other items listed in a DataCatalog or ResourceCatalog", "oneOf": [ { "items": { "type": "string", "format": "uri" }, "type": "array" }, { "type": "string", "format": "uri" } ] } }, "required": ["name", "url"], "recommended": ["versionDate", "archivedAt"] }, "resourcecatalog": { "@type": "ResourceCatalog", "description": "A Resource Catalog in the NIAID Data Ecosystem", "type": "object", "properties": { "name": { "description": "Resrouce catalog name", "type": "string" }, "url": { "description": "Link to the resource catalog in the Discovery Portal", "type": "string", "format": "uri" } }, "required": ["name", "url"] }, "organization": { "@type": "Organization", "description": "Reusable organization definition", "properties": { "affiliation": { "type": "object", "properties": { "name": { "description": "Name of the affiliation, such as a university", "type": "string" }, "sameAs": { "description": "Alias for the affiliation", "type": "string" }, "url": { "description": "URL of the affiliation", "type": "string", "format": "uri" } }, "required": ["name"], "optional": ["sameAs", "url"] }, "alternateName": { "description": "Alias of the name", "oneOf": [ { "type": "array", "items": { "type": "string" } }, { "type": "string" } ] }, "name": { "description": "Name of the organization", "type": "string" }, "parentOrganization": { "description": "Name of the parent organization. For instance, the parentOrganization of NIAID is the National Institutes of health (NIH)", "type": "string" }, "email": { "description": "Email address of the organization", "type": "string" }, "identifier": { "description": "Unique identifier of the organization", "type": "string" }, "role": { "description": "What role the organization played in creating the dataset", "type": "string" }, "url": { "description": "Link to the organization", "type": "string", "format": "uri" } }, "required": ["name"], "recommended": ["identifier"], "optional": ["affiliation", "alternateName", "email", "parentOrganization", "role", "url"], "type": "object" }, "researchproject": { "@type": "ResearchProject", "description": "a type of organization definition", "properties": { "alternateName": { "description": "Alias of the name", "oneOf": [ { "type": "array", "items": { "type": "string" } }, { "type": "string" } ] }, "name": { "description": "Name of the organization", "type": "string" }, "parentOrganization": { "description": "Name of the parent organization. For instance, the parentOrganization of NIAID is the National Institutes of health (NIH)", "type": "string" }, "email": { "description": "Email address of the organization", "type": "string" }, "identifier": { "description": "Unique identifier of the organization", "type": "string" }, "url": { "description": "Link to the organization", "type": "string", "format": "uri" } }, "required": ["name"], "recommended": ["identifier", "url", "parentOrganization"], "optional": ["alternateName", "email", "role"], "type": "object" }, "person": { "@type": "Person", "description": "Reusable person definition", "properties": { "affiliation": { "type": "object", "properties": { "name": { "description": "Name of the affiliation, such as a university", "type": "string" }, "sameAs": { "description": "Alias for the affiliation", "type": "string" }, "url": { "description": "URL of the affiliation", "type": "string", "format": "uri" } }, "required": ["name"], "optional": ["sameAs", "url"] }, "name": { "description": "Name of the person", "type": "string" }, "email": { "description": "Email address of the person", "type": "string" }, "familyName": { "description": "Family name (surname) of the person", "type": "string" }, "givenName": { "description": "Given (first) name of the person", "type": "string" }, "identifier": { "description": "Unique identifier of the person, like an ORCID ID", "type": "string" }, "role": { "description": "Role the person played in creating the dataset", "type": "string" }, "title": { "description": "Title of the person", "type": "string" }, "url": { "description": "Link to the homepage or other web content describing the person", "type": "string", "format": "uri" } }, "required": ["name"], "recommended": ["familyName", "givenName ", "identifier "], "optional": ["affiliation", "email", "role", "title", "url"], "type": "object" }, "definedterm": { "@type": "DefinedTerm", "type": "object", "properties": { "name": { "description": "The name 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 for more details.", "owl:cardinality": "one", "type": "string" }, "url": { "description": "URL of the item.", "owl:cardinality": "one", "type": "string", "format": "uri" }, "curatedBy": { "description": "The person, organization, or catalog that curated this DefinedTerm for the metadata property", "anyOf": [ { "$ref": "#/definitions/person" }, { "$ref": "#/definitions/organization" }, { "$ref": "#/definitions/catalog" }, { "$ref": "#/definitions/researchproject" }, { "$ref": "#/definitions/softwareapplication" } ] }, "termCode": { "description": "A code that identifies this DefinedTerm within a DefinedTermSet.", "type": "string" }, "description": { "description": "A description of the item.", "type": "string" }, "inDefinedTermSet": { "description": "A DefinedTermSet that contains this term.", "type": "string" }, "originalName": { "description": "The original name of the item, before any metadata standardization/normalization", "type": "string" }, "isCurated": { "description": "A boolean indicator describing whether or not this DefinedTerm was curated as the value of a property.", "type": "boolean" } }, "required": [] }, "howto": { "@type": "HowTo", "type": "object", "properties": { "name": { "description": "The name of the item.", "owl:cardinality": "one", "type": "string" }, "url": { "description": "URL of the item.", "owl:cardinality": "one", "type": "string", "format": "uri" }, "description": { "description": "A description of the item.", "type": "string" }, "step": { "description": "A DefinedTermSet that contains this term.", "oneOf": [ { "type": "array", "items": { "type": "string" } }, { "type": "string" } ] } }, "recommended": ["name", "url", "description", "step"] }, "softwareapplication": { "@type": "SoftwareApplication", "description": "Reusable software or algorithm definition", "properties": { "name": { "description": "name of the software, computational tool, or algorithm.", "type": "string" }, "dateModified": { "description": "date the software, computational tool, or algorithm was run", "type": "string", "format": "date" }, "url": { "description": "url of the software, computational tool, or algorithm", "type": "string", "format": "uri" } }, "required": ["name"], "recommended": ["url"], "optional": ["dateModified"], "type": "object" }, "samplerecord": { "@type": "Sample", "description": "reusable sample object", "type": "object", "properties": { "url": { "description": "Link to sample", "type": "string", "format": "uri" }, "identifier": { "description": "an identifier for the sample", "type": "string" }, "includedInDataCatalog": { "description": "Data or resource catalog where the sample is listed", "oneOf": [ { "$ref": "#/definitions/catalog" }, { "type": "array", "items": { "$ref": "#/definitions/catalog" } } ] }, "associatedPhenotype": { "description": "one or more observable traits or conditions relevant to the source of the sample.", "anyOf": [ { "description": "collection of vocabulary terms defined in ontologies", "strict": false, "type": "string", "vocabulary": { "children_of": ["http://purl.obolibrary.org/obo/UPHENO_0001001", "http://purl.obolibrary.org/obo/PATO_0000001"], "ontology": ["UPHENO","PATO"] } }, { "items": { "description": "collection of vocabulary terms defined in ontologies", "strict": false, "type": "string", "vocabulary": { "children_of": ["http://purl.obolibrary.org/obo/UPHENO_0001001", "http://purl.obolibrary.org/obo/PATO_0000001"], "ontology": ["UPHENO","PATO"] } }, "type": "array" }, { "type": "array", "items": { "$ref": "#/definitions/definedterm" } }, { "$ref": "#/definitions/definedterm" } ], "owl:cardinality": "many" }, "associatedGenotype": { "description": "One or more genetic variants or molecular features observed or inferred from the sample.", "anyOf": [ { "description": "collection of vocabulary terms defined in ontologies", "strict": false, "type": "string", "vocabulary": { "children_of": ["http://purl.obolibrary.org/obo/NCIT_C16612", "http://purl.obolibrary.org/obo/NCIT_C20181","http://purl.obolibrary.org/obo/NCIT_C17649"], "ontology": ["NCIT"] } }, { "items": { "description": "collection of vocabulary terms defined in ontologies", "strict": false, "type": "string", "vocabulary": { "children_of": ["http://purl.obolibrary.org/obo/NCIT_C16612", "http://purl.obolibrary.org/obo/NCIT_C20181","http://purl.obolibrary.org/obo/NCIT_C17649"], "ontology": ["NCIT"] } }, "type": "array" }, { "type": "array", "items": { "$ref": "#/definitions/definedterm" } }, { "$ref": "#/definitions/definedterm" } ], "owl:cardinality": "many" }, "cellType": { "description": "The type of cell represented in or derived from the biological sample, based on morphology, lineage, or molecular markers.", "anyOf": [ { "description": "collection of vocabulary terms defined in ontologies", "strict": false, "type": "string", "vocabulary": { "children_of": ["http://purl.obolibrary.org/obo/CL_0000000", "http://purl.obolibrary.org/obo/CLO_0000031"], "ontology": ["CL","CLO"] } }, { "items": { "description": "collection of vocabulary terms defined in ontologies", "strict": false, "type": "string", "vocabulary": { "children_of": ["http://purl.obolibrary.org/obo/CL_0000000", "http://purl.obolibrary.org/obo/CLO_0000031"], "ontology": ["CL","CLO"] } }, "type": "array" }, { "type": "array", "items": { "$ref": "#/definitions/definedterm" } }, { "$ref": "#/definitions/definedterm" } ], "owl:cardinality": "many" }, "anatomicalSystem": { "description": "Indicate the anatomical system from which the sample is collect, e.g. circulatory, digestive, endocrine, immune and other systems.", "anyOf": [ { "description": "collection of vocabulary terms defined in ontologies", "strict": false, "type": "string", "vocabulary": { "children_of": ["http://purl.obolibrary.org/obo/UBERON_0000467"], "ontology": ["UBERON"] } }, { "items": { "description": "collection of vocabulary terms defined in ontologies", "strict": false, "type": "string", "vocabulary": { "children_of": ["http://purl.obolibrary.org/obo/UBERON_0000467"], "ontology": ["UBERON"] } }, "type": "array" }, { "type": "array", "items": { "$ref": "#/definitions/definedterm" } }, { "$ref": "#/definitions/definedterm" } ], "owl:cardinality": "many" }, "anatomicalStructure": { "description": "Indicate the organ, tissues the sample was collected from.", "anyOf": [ { "description": "collection of vocabulary terms defined in ontologies", "strict": false, "type": "string", "vocabulary": { "children_of": ["http://purl.obolibrary.org/obo/UBERON_0001062"], "ontology": ["UBERON"] } }, { "items": { "description": "collection of vocabulary terms defined in ontologies", "strict": false, "type": "string", "vocabulary": { "children_of": ["http://purl.obolibrary.org/obo/UBERON_0001062"], "ontology": ["UBERON"] } }, "type": "array" }, { "type": "array", "items": { "$ref": "#/definitions/definedterm" } }, { "$ref": "#/definitions/definedterm" } ], "owl:cardinality": "many" }, "sex": { "description": "The biological sex of the individual from which the sample was obtained.", "anyOf": [ { "description": "collection of vocabulary terms defined in ontologies", "strict": false, "type": "string", "vocabulary": { "children_of": ["http://purl.obolibrary.org/obo/PATO_0000047"], "ontology": ["PATO"] } }, { "items": { "description": "collection of vocabulary terms defined in ontologies", "strict": false, "type": "string", "vocabulary": { "children_of": ["http://purl.obolibrary.org/obo/PATO_0000047"], "ontology": ["PATO"] } }, "type": "array" }, { "type": "array", "items": { "$ref": "#/definitions/definedterm" } }, { "$ref": "#/definitions/definedterm" } ], "owl:cardinality": "many" }, "developmentalStage": { "description": "A temporal subdivision of a developmental process, indicating the age or stage of the object when the sample was created.", "anyOf": [ { "description": "collection of vocabulary terms defined in ontologies", "strict": false, "type": "string", "vocabulary": { "children_of": ["http://purl.obolibrary.org/obo/UBERON_0000104","http://purl.obolibrary.org/obo/NCIT_C48308"], "ontology": ["UBERON","NCIT"] } }, { "items": { "description": "collection of vocabulary terms defined in ontologies", "strict": false, "type": "string", "vocabulary": { "children_of": ["http://purl.obolibrary.org/obo/UBERON_0000104","http://purl.obolibrary.org/obo/NCIT_C48308"], "ontology": ["UBERON","NCIT"] } }, "type": "array" }, { "type": "array", "items": { "$ref": "#/definitions/definedterm" } }, { "$ref": "#/definitions/definedterm" }, { "type": "array", "items": { "$ref": "#/definitions/quantitativevalue" } }, { "$ref": "#/definitions/quantitativevalue" } ], "owl:cardinality": "many" }, "sampleAvailability": { "description": "A flag to signal that the sample is available for reuse.", "abstract": "availability of the sample", "type": "boolean", "owl:cardinality": "one" }, "sampleQuantity": { "description": "A numeric value for a measurement of the size of a sample. If completely unknown, set value = 0, and unitText = 'unknown'", "oneOf": [ { "type": "array", "items": { "$ref": "#/definitions/quantitativevalue" } }, { "$ref": "#/definitions/quantitativevalue" } ], "owl:cardinality": "many" }, "sampleType": { "description": "The type of sample or specimen.", "anyOf": [ { "description": "collection of vocabulary terms defined in ontologies", "strict": false, "type": "string", "vocabulary": { "children_of": ["http://purl.obolibrary.org/obo/BFO_0000040"], "ontology": ["OBI"] } }, { "items": { "description": "collection of vocabulary terms defined in ontologies", "strict": false, "type": "string", "vocabulary": { "children_of": ["http://purl.obolibrary.org/obo/BFO_0000040"], "ontology": ["OBI"] } }, "type": "array" }, { "type": "array", "items": { "$ref": "#/definitions/definedterm" } }, { "$ref": "#/definitions/definedterm" } ], "owl:cardinality": "many" } }, "recommended": ["url", "identifier", "includedInDataCatalog", "associatedPhenotype", "associatedGenotype", "cellType", "sampleType", "anatomicalSystem", "anatomicalStructure", "sex", "developmentalStage", "sampleAvailability", "sampleQuantity"] }, "samplecollection": { "@type": "SampleCollection", "description": "reusable sampleCollection object", "type": "object", "properties": { "url": { "description": "Link to sample", "type": "string", "format": "uri" }, "identifier": { "description": "an identifier for the sample", "type": "string" }, "includedInDataCatalog": { "description": "Data or resource catalog where the sample is listed", "oneOf": [ { "$ref": "#/definitions/catalog" }, { "type": "array", "items": { "$ref": "#/definitions/catalog" } } ] }, "aggregateElement": { "description": "Aggregate information about the samples in the Sample Collection formatted as a sample object.", "oneOf": [ { "$ref": "#/definitions/samplerecord" }, { "type": "array", "items": { "$ref": "#/definitions/samplerecord" } } ] }, "itemListElement": { "description": "Samples listed in the sample collection", "oneOf": [ { "$ref": "#/definitions/minsampleinfo" }, { "type": "array", "items": { "$ref": "#/definitions/minsampleinfo" } } ] }, "numberOfItems": { "description": "The number of sample records in the sample collection. Min/max estimates can be used in lieu of actual number. If completely unknown, set value = 0, and unitText = 'unknown'", "anyOf": [ { "type": "array", "items": { "$ref": "#/definitions/propertyvalue" } }, { "$ref": "#/definitions/propertyvalue" }, { "type": "array", "items": { "$ref": "#/definitions/quantitativevalue" } }, { "$ref": "#/definitions/quantitativevalue" } ], "owl:cardinality": "many" } }, "recommended": ["url", "identifier", "includedInDataCatalog", "aggregateElement","itemListElement","numberOfItems"] }, "minsampleinfo": { "@type": "Sample", "description": "reusable sample object", "type": "object", "properties": { "url": { "description": "Link to sample", "type": "string", "format": "uri" }, "identifier": { "description": "an identifier for the sample", "type": "string" }, "includedInDataCatalog": { "description": "Data or resource catalog where the sample is listed", "oneOf": [ { "$ref": "#/definitions/catalog" }, { "type": "array", "items": { "$ref": "#/definitions/catalog" } } ] } }, "recommended": ["url", "identifier", "includedInDataCatalog"] }, "quantitativevalue": { "@type": "QuantitativeValue", "description": "A numeric value and unit for a property with potentially different units", "type": "object", "properties": { "value": { "description": "A numeric value for the property", "type": "number" }, "maxValue": { "description": "An estimated maximum numberic value if the actual value is not known. Ignore if actual numeric value is known.", "type": "number" }, "minValue": { "description": "An estimated minumum numeric value if the actual value is not known. Ignore if actual numeric value is known.", "type": "number" }, "unitText": { "description": "A unit associated with the value. E.g.- 'records' for the number of records in a database.", "type": "string" } }, "required" : ["unitText"], "recommended": ["value"], "optional": ["maxValue","minValue"] }, "propertyvalue": { "@type": "PropertyValue", "description": "A numeric value and unit for a property with potentially different units", "type": "object", "properties": { "value": { "description": "A numeric value for the property", "type": "number" }, "maxValue": { "description": "An estimated maximum numberic value if the actual value is not known. Ignore if actual numeric value is known.", "type": "number" }, "minValue": { "description": "An estimated minumum numeric value if the actual value is not known. Ignore if actual numeric value is known.", "type": "number" }, "unitText": { "description": "A unit associated with the value. E.g.- 'records' for the number of records in a database.", "type": "string" }, "propertyID": { "description": "A commonly used identifier for the characteristic represented by the property, e.g. a manufacturer or a standard code for a property. propertyID can be (1) a prefixed string, mainly meant to be used with standards for product properties; (2) a site-specific, non-prefixed string (e.g. the primary key of the property or the vendor-specific ID of the property), or (3) a URL indicating the type of the property, either pointing to an external vocabulary, or a Web resource that describes the property (e.g. a glossary entry). Standards bodies should promote a standard prefix for the identifiers of properties from their standards.", "oneOf": [ {"type": "string"}, { "type": "string", "format": "uri" } ] } }, "required" : ["unitText"], "recommended": ["value","propertyID"], "optional": ["maxValue","minValue"] }, "propvalpair": { "@type": "PropertyValue", "description": "A numeric value and unit for a property with potentially different units", "type": "object", "properties": { "value": { "description": "A numeric value for the property", "type": "number" }, "name": { "description": "The name of the property.", "type": "string" }, "unitText": { "description": "A unit associated with the value. E.g.- 'records' for the number of records in a database.", "type": "string" }, "propertyID": { "description": "A commonly used identifier for the characteristic represented by the property, e.g. a manufacturer or a standard code for a property. propertyID can be (1) a prefixed string, mainly meant to be used with standards for product properties; (2) a site-specific, non-prefixed string (e.g. the primary key of the property or the vendor-specific ID of the property), or (3) a URL indicating the type of the property, either pointing to an external vocabulary, or a Web resource that describes the property (e.g. a glossary entry). Standards bodies should promote a standard prefix for the identifiers of properties from their standards.", "oneOf": [ {"type": "string"}, { "type": "string", "format": "uri" } ] } }, "required" : ["name"], "recommended": ["value","propertyID"], "optional": ["unitText"] } } } }, { "@id": "nde:citedBy", "@type": "rdf:Property", "rdfs:comment": "Publications that cite the dataset, resource/resource catalog or computational tool. Examples: a publication which reuses the dataset in a secondary analysis, a dataset which extends the existing dataset, or a computational tool which relies on the dataset.", "rdfs:label": "citedBy", "schema:domainIncludes": [ { "@id": "nde:Dataset" }, { "@id": "nde:ComputationalTool" }, { "@id": "nde:ResourceCatalog" }, { "@id": "nde:Sample" }, { "@id": "nde:DataCollection" } ], "schema:rangeIncludes": [ { "@id": "schema:CreativeWork" }, { "@id": "niaid:ScholarlyArticle" } ] }, { "@id": "nde:date", "@type": "rdf:Property", "rdfs:comment": "Date the dataset, resource/resource catalog or computational tool has changed: most recent date of dateModified, datePublished, and dateCreated.", "rdfs:label": "date", "schema:domainIncludes": [ { "@id": "nde:Dataset" }, { "@id": "nde:ComputationalTool" }, { "@id": "nde:ResourceCatalog" }, { "@id": "nde:Sample" }, { "@id": "nde:DataCollection" } ], "schema:rangeIncludes": [ { "@id": "schema:Date" } ] }, { "@id": "nde:doi", "@type": "rdf:Property", "rdfs:comment": "Digital object identifier (DOI) for the dataset, resource/resource catalog or computational tool.", "rdfs:label": "doi", "schema:domainIncludes": [ { "@id": "nde:Dataset" }, { "@id": "nde:ComputationalTool" }, { "@id": "nde:ResourceCatalog" } ], "schema:rangeIncludes": [ { "@id": "schema:Text" } ] }, { "@id": "nde:includedInDataCatalog", "@type": "rdf:Property", "rdfs:comment": "Repository or source which contains the dataset, resource/resource catalog or computational tool.", "rdfs:label": "includedInDataCatalog", "schema:domainIncludes": [ { "@id": "nde:Dataset" }, { "@id": "nde:ComputationalTool" }, { "@id": "nde:ResourceCatalog" }, { "@id": "nde:Sample" }, { "@id": "nde:SampleCollection" }, { "@id": "nde:DataCollection" } ], "schema:rangeIncludes": [ { "@id": "schema:DataCatalog" }, { "@id": "nde:ResourceCatalog" } ] }, { "@id": "nde:isBasisFor", "@type": "rdf:Property", "rdfs:comment": "Dataset, resource/resource catalog or computational tool which incorporate this dataset, resource/resource catalog or computational tool.", "rdfs:label": "isBasisFor", "schema:domainIncludes": [ { "@id": "nde:Dataset" }, { "@id": "nde:ComputationalTool" }, { "@id": "nde:ResourceCatalog" }, { "@id": "nde:Sample" }, { "@id": "nde:DataCollection" } ], "schema:rangeIncludes": [ { "@id": "nde:Dataset" }, { "@id": "nde:ComputationalTool" }, { "@id": "nde:ResourceCatalog" }, { "@id": "nde:Sample" }, { "@id": "nde:SampleCollection" }, { "@id": "schema:CreativeWork" }, { "@id": "niaid:ScholarlyArticle" }, { "@id": "nde:DataCollection" } ] }, { "@id": "nde:isRelatedTo", "@type": "rdf:Property", "rdfs:comment": "Dataset, resource/resource catalog or computational tool which are related to the given dataset, resource/resource catalog or computational tool.", "rdfs:label": "isRelatedTo", "schema:domainIncludes": [ { "@id": "nde:Dataset" }, { "@id": "nde:ComputationalTool" }, { "@id": "nde:ResourceCatalog" }, { "@id": "nde:Sample" }, { "@id": "nde:DataCollection" } ], "schema:rangeIncludes": [ { "@id": "nde:Dataset" }, { "@id": "nde:ComputationalTool" }, { "@id": "nde:ResourceCatalog" }, { "@id": "nde:Sample" }, { "@id": "nde:SampleCollection" }, { "@id": "schema:CreativeWork" }, { "@id": "niaid:ScholarlyArticle" }, { "@id": "nde:DataCollection" } ] }, { "@id": "nde:isSimilarTo", "@type": "rdf:Property", "rdfs:comment": "Dataset, resource/resource catalog or computational tool which are similar to the dataset, resource/resource catalog or computational tool, based on terms in the names, descriptions, authors, measurementTechniques, infectiousAgents, healthConditions, etc.", "rdfs:label": "isSimilarTo", "schema:domainIncludes": [ { "@id": "nde:Dataset" }, { "@id": "nde:ComputationalTool" }, { "@id": "nde:ResourceCatalog" }, { "@id": "nde:Sample" }, { "@id": "nde:DataCollection" } ], "schema:rangeIncludes": [ { "@id": "nde:Dataset" }, { "@id": "nde:ComputationalTool" }, { "@id": "nde:ResourceCatalog" }, { "@id": "nde:Sample" }, { "@id": "nde:SampleCollection" }, { "@id": "schema:CreativeWork" }, { "@id": "niaid:ScholarlyArticle" }, { "@id": "nde:DataCollection" } ] }, { "@id": "nde:nctid", "@type": "rdf:Property", "rdfs:comment": "ClinicalTrials.gov identifier associated with the Dataset.", "rdfs:label": "nctid", "schema:domainIncludes": { "@id": "nde:Dataset" }, "schema:rangeIncludes": [ { "@id": "schema:Text" } ] }, { "@id": "nde:relationship", "@type": "rdf:Property", "rdfs:comment": "How an associated work is related to the dataset, resource/resource catalog.", "rdfs:label": "relationship", "schema:domainIncludes": [ { "@id": "nde:Dataset" }, { "@id": "nde:ResourceCatalog" } ], "schema:rangeIncludes": [ { "@id": "schema:Text" } ] }, { "@id": "nde:topicCategory", "@type": "rdf:Property", "rdfs:comment": "Topic of the dataset, resource/resource catalog or computational tool. This topic may be assigned by a human curator or through automated algorithms.", "rdfs:label": "topicCategory", "schema:domainIncludes": [ { "@id": "nde:Dataset" }, { "@id": "nde:ComputationalTool" }, { "@id": "nde:ResourceCatalog" }, { "@id": "nde:Sample" }, { "@id": "nde:DataCollection" } ], "schema:rangeIncludes": [ { "@id": "schema:Text" }, { "@id": "nde:DefinedTerm" } ] }, { "@id": "nde:collectionType", "@type": "rdf:Property", "rdfs:comment": "The type of resource/resource catalog that best describes the work.", "rdfs:label": "collectionType", "schema:domainIncludes": [ { "@id": "nde:ResourceCatalog" } ], "schema:rangeIncludes": [ { "@id": "schema:Text" }, { "@id": "nde:DefinedTerm" } ] }, { "@id": "nde:collectionSize", "@type": "rdf:Property", "rdfs:comment": "The number of records, datasets, tools, items, pages, etc. in the resource/resource catalog.", "rdfs:label": "collectionSize", "schema:domainIncludes": [ { "@id": "nde:ResourceCatalog" }, { "@id": "nde:DataCollection" } ], "schema:rangeIncludes": [ { "@id": "schema:PropertyValue" }, { "@id": "schema:QuantitativeValue" } ] }, { "@id": "nde:hasDownload", "@type": "rdf:Property", "rdfs:comment": "The resource/resource catalog provides download access to its content. Options: All content (e.g. entire data builds, tools, etc.), Partial content (just data, or just tools, etc.), Record-level (individual records, or selections of records), No downloads (information is viewable but not downloadable, users must resort to copy/paste, screenshots, etc.), Prohibited (downloading, copy/pasting, screenshotting the data is prohibited).", "rdfs:label": "hasDownload", "schema:domainIncludes": [ { "@id": "nde:ResourceCatalog" } ], "schema:rangeIncludes": [ { "@id": "schema:Text" }, { "@id": "schema:Enumeration" } ] }, { "@id": "nde:hasAPI", "@type": "rdf:Property", "rdfs:comment": "The resource/resource catalog provides API access to its content.", "rdfs:label": "hasAPI", "schema:domainIncludes": [ { "@id": "nde:ResourceCatalog" } ], "schema:rangeIncludes": [ { "@id": "schema:Boolean" } ] }, { "@id": "nde:infectiousAgent", "@type": "rdf:Property", "rdfs:comment": "Infectious agent(s) / pathogen(s) which are the focus of the dataset, resource/resource catalog or computational tool (e.g. SARS-CoV-2).", "rdfs:label": "infectiousAgent", "schema:domainIncludes": [ { "@id": "nde:Dataset" }, { "@id": "nde:ComputationalTool" }, { "@id": "nde:ResourceCatalog" }, { "@id": "nde:Sample" }, { "@id": "nde:DataCollection" } ], "schema:rangeIncludes": [ { "@id": "schema:Text" }, { "@id": "nde:DefinedTerm" } ] }, { "@id": "nde:healthCondition", "@type": "rdf:Property", "rdfs:comment": "The infectious disease(s) / health condition(s) which are the focus of the dataset, resource/resource catalog or computational tool (e.g. COVID-19, coronavirus).", "rdfs:label": "healthCondition", "schema:domainIncludes": [ { "@id": "nde:Dataset" }, { "@id": "nde:ComputationalTool" }, { "@id": "nde:ResourceCatalog" }, { "@id": "nde:Sample" }, { "@id": "nde:DataCollection" } ], "schema:rangeIncludes": [ { "@id": "schema:Text" }, { "@id": "nde:DefinedTerm" }] }, { "@id": "nde:funding", "@type": "rdf:Property", "rdfs:comment": "Funding that supports (sponsors) the collection of a dataset, resource/resource catalog or computational tool through some kind of financial contribution.", "rdfs:label": "funding", "schema:domainIncludes": [ { "@id": "nde:Dataset" }, { "@id": "nde:ComputationalTool" }, { "@id": "nde:ResourceCatalog" }, { "@id": "nde:Sample" }, { "@id": "nde:DataCollection" } ], "schema:rangeIncludes": [{ "@id": "niaid:MonetaryGrant" }], "schema:sameAs": { "@id": "schema:funding" } }, { "@id": "nde:distribution", "@type": "rdf:Property", "rdfs:comment": "A downloadable form of the dataset, resource/resource catalog, at a specific location, in a specific format.", "rdfs:label": "distribution", "schema:domainIncludes": [ { "@id": "nde:Dataset" }, { "@id": "nde:ResourceCatalog" }, { "@id": "nde:Sample" } ], "schema:rangeIncludes": [{ "@id": "niaid:DataDownload" }] }, { "@id": "nde:species", "@type": "rdf:Property", "rdfs:comment": "Species(es) from which dataset has been collected, or is the focus of a resource/resource catalog, or for which the tool was designed or applied.", "rdfs:label": "species", "schema:domainIncludes": [ { "@id": "nde:Dataset" }, { "@id": "nde:ComputationalTool" }, { "@id": "nde:ResourceCatalog" }, { "@id": "nde:Sample" }, { "@id": "nde:DataCollection" } ], "schema:rangeIncludes": [ { "@id": "schema:Text" }, { "@id": "nde:DefinedTerm" } ] }, { "@id": "nde:measurementTechnique", "@type": "rdf:Property", "rdfs:comment": "A technique, method or technology used in an Observation, StatisticalVariable or Dataset (or DataDownload, DataCatalog), corresponding to the method used for measuring the corresponding variable(s) (for datasets, described using variableMeasured; for Observation, a StatisticalVariable). For example, if variableMeasured is: molecule concentration, measurementTechnique could be: \"mass spectrometry\" or \"nmr spectroscopy\" or \"colorimetry\" or \"immunofluorescence\". If the variableMeasured is \"depression rating\", the measurementTechnique could be \"Zung Scale\" or \"HAM-D\" or \"Beck Depression Inventory\".", "rdfs:label": "measurementTechnique", "schema:domainIncludes": [ { "@id": "nde:Dataset" }, { "@id": "nde:ComputationalTool" }, { "@id": "nde:ResourceCatalog" }, { "@id": "nde:Sample" }, { "@id": "nde:DataCollection" } ], "schema:rangeIncludes": [ { "@id": "schema:Text" }, { "@id": "nde:DefinedTerm" } ] }, { "@id": "nde:variableMeasured", "@type": "rdf:Property", "rdfs:comment": "The variableMeasured property can indicate (repeated as necessary) the variables that are measured in some dataset, either described as text or as pairs of identifier and description using PropertyValue, or more explicitly as a StatisticalVariable.", "rdfs:label": "variableMeasured", "schema:domainIncludes": [ { "@id": "nde:Dataset" }, { "@id": "nde:ComputationalTool" }, { "@id": "nde:ResourceCatalog" }, { "@id": "nde:Sample" }, { "@id": "nde:DataCollection" } ], "schema:rangeIncludes": [ { "@id": "schema:Text" }, { "@id": "nde:DefinedTerm" } ] }, { "@id": "nde:curatedBy", "@type": "rdf:Property", "rdfs:comment": "The curator who generated the metadata annotation.", "rdfs:label": "curatedBy", "schema:domainIncludes": [ { "@id": "nde:DefinedTerm" } ], "schema:rangeIncludes": [ { "@id": "schema:Person" }, { "@id": "niaid:Organization" }, { "@id": "schema:DataCatalog" }, { "@id": "nde:ResourceCatalog" }, { "@id": "schema:SoftwareApplication" }, { "@id": "nde:ComputationalTool" }, { "@id": "schema:ResearchProject" } ] }, { "@id": "nde:originalName", "@type": "rdf:Property", "rdfs:comment": "The original name or term that was provided in the metadata.", "rdfs:label": "originalName", "schema:domainIncludes": [ { "@id": "nde:DefinedTerm" } ], "schema:rangeIncludes": [ { "@id": "schema:Text" } ] }, { "@id": "nde:isCurated", "@type": "rdf:Property", "rdfs:comment": "A boolean indicating whether or not a Defined Term was curated by an annotator (true) or programmatically generated (false).", "rdfs:label": "isCurated", "schema:domainIncludes": [ { "@id": "nde:DefinedTerm" } ], "schema:rangeIncludes": [ { "@id": "schema:Boolean" } ] }, { "@id": "nde:sourceOrganization", "@type": "rdf:Property", "rdfs:comment": "The organization, research project, working group, or funded program on whose behalf the author/creator was working.", "rdfs:label": "sourceOrganization", "schema:domainIncludes": [ { "@id": "nde:Dataset" }, { "@id": "nde:ComputationalTool" }, { "@id": "nde:ResourceCatalog" }, { "@id": "nde:Sample" }, { "@id": "nde:DataCollection" } ], "schema:rangeIncludes": [ { "@id": "schema:ResearchProject" }, { "@id": "niaid:Organization" } ] }, { "@id": "nde:archivedAt", "@type": "rdf:Property", "rdfs:comment": "The url of a dataset, tool, resource or other item listed in a DataCatalog or ResourceCatalog.", "rdfs:label": "archivedAt", "schema:domainIncludes": [ { "@id": "schema:DataCatalog" }, { "@id": "nde:ResourceCatalog" } ], "schema:rangeIncludes": [ { "@id": "schema:URL" } ] }, { "@id": "nde:associatedPhenotype", "@type": "rdf:Property", "rdfs:comment": "one or more observable traits or conditions relevant to the source of the sample.", "rdfs:label": "associatedPhenotype", "schema:domainIncludes": { "@id": "nde:Sample" }, "schema:rangeIncludes": [ { "@id": "schema:Text" }, { "@id": "schema:URL" }, { "@id": "schema:DefinedTerm" } ] }, { "@id": "nde:associatedGenotype", "@type": "rdf:Property", "rdfs:comment": "One or more genetic variants or molecular features observed or inferred from the sample.", "rdfs:label": "associatedGenotype", "schema:domainIncludes": { "@id": "nde:Sample" }, "schema:rangeIncludes": [ { "@id": "schema:Text" }, { "@id": "schema:URL" }, { "@id": "schema:DefinedTerm" } ] }, { "@id": "nde:cellType", "@type": "rdf:Property", "rdfs:comment": "The type of cell represented in or derived from the biological sample, based on morphology, lineage, or molecular markers.", "rdfs:label": "cellType", "schema:domainIncludes": [ { "@id": "nde:Sample" }, { "@id": "nde:SampleCollection" } ], "schema:rangeIncludes": [ { "@id": "schema:Text" }, { "@id": "schema:URL" }, { "@id": "schema:DefinedTerm" } ] }, { "@id": "nde:sample", "@type": "rdf:Property", "rdfs:comment": "The sample(s) which were used to generate the dataset or sample collection", "rdfs:label": "sample", "schema:domainIncludes": { "@id": "nde:Dataset" }, "schema:rangeIncludes": [ { "@id": "nde:Sample" }, { "@id": "nde:SampleCollection" }, { "@id": "schema:URL" } ] }, { "@id": "nde:additionalProperty", "@type": "rdf:Property", "rdfs:comment": "Other properties listed in the item metadata record.", "rdfs:label": "additionalProperty", "schema:domainIncludes": [ { "@id": "nde:Sample" }, { "@id": "schema:CreativeWork" } ], "schema:rangeIncludes": { "@id": "schema:PropertyValue" } } ] }