{ "@context": { "schema": "http://schema.org/", "rdf": "http://www.w3.org/1999/02/22-rdf-syntax-ns#", "rdfs": "http://www.w3.org/2000/01/rdf-schema#", "bioschemas": "https://discovery.biothings.io/view/bioschemas/", "niaid": "https://discovery.biothings.io/view/niaid/", "nde": "https://discovery.biothings.io/view/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. 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": "Datasets contained in the NIAID Data Ecosystem. 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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). 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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": "A citation or reference to a publication, dataset, or computational tool which uses the dataset. Examples: a publication which describes the collection/analysis of the dataset, 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.", "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" } }, "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"], "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" }, "dataset": { "description": "Link to a dataset record", "oneOf": [ { "items": { "type": "string", "format": "uri" }, "type": "array" }, { "type": "string", "format": "uri" } ] } }, "required": ["name", "url"], "recommended": ["versionDate", "dataset"] }, "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" }, { "$ref": "#/definitions/softwareapplication" } ] }, "termCode": { "description": "A code that identifies this DefinedTerm within a DefinedTermSet.", "type": "string" }, "description": { "description": "A description of the item.", "type": "string" }, "inDefinedTermSet": { "description": "A DefinedTermSet that contains this term.", "type": "string" }, "originalName": { "description": "The original name of the item, before any metadata standardization/normalization", "type": "string" }, "isCurated": { "description": "A boolean indicator describing whether or not this DefinedTerm was curated as the value of a property.", "type": "boolean" } }, "required": [] }, "softwareapplication": { "@type": "SoftwareApplication", "description": "Reusable software or algorithm definition", "properties": { "name": { "description": "name of the software, computational tool, or algorithm.", "type": "string" }, "dateModified": { "description": "date the software, computational tool, or algorithm was run", "type": "string", "format": "date" }, "url": { "description": "url of the software, computational tool, or algorithm", "type": "string", "format": "uri" } }, "required": ["name"], "recommended": ["url"], "optional": ["dateModified"], "type": "object" } } } }, { "@id": "nde:ComputationalTool", "@type": "rdfs:Class", "rdfs:comment": "ComputationalTools (software, workflows, computational tools, code) contained in the NIAID Data Ecosystem. The NIAID Data Ecosystem is a secure environment to find, access and analyze immune-mediated and infectious disease data and computational tools to speed the development of diagnostics, therapeutics, and vaccines. The NIAID Data Ecosystem Discovery Portal harvests metadata from dataset repository and harmonizes them to this schema to enable easy cross-platform dataset searching and filtering.", "rdfs:label": "ComputationalTool", "rdfs:subClassOf": { "@id": "niaid:ComputationalTool" }, "$validation": { "$schema": "http://json-schema.org/draft-07/schema#", "type": "object", "properties": { "citedBy": { "description": "Publications, datasets, or computational tools that cite the work.", "anyOf": [ { "type": "array", "items": { "$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": "A citation or reference to a publication, dataset, or computational tool which uses the computational tool. Examples: a publication which describes the development of the computational tool, a publication which describes the extension or use of the computational tool, a dataset which was processed or analyzed using the tool, or a computational tool which relies on the given tool.", "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" } }, "required": ["date", "includedInDataCatalog", "funding", "author", "description", "name"], "recommended": ["citedBy", "doi", "topicCategory", "codeRepository", "programmingLanguage", "applicationCategory", "applicationSubCategory", "softwareRequirements", "softwareVersion", "citation", "conditionsOfAccess", "dateModified", "interactionStatistic", "license", "identifier", "url"], "optional": ["isBasisFor", "isRelatedTo", "isSimilarTo", "infectiousAgent", "healthCondition", "species", "input", "output", "applicationSuite", "availableOnDevice", "downloadUrl", "featureList", "operatingSystem", "processorRequirements", "softwareAddOn", "softwareHelp", "aggregateRating", "contributor", "creator", "dateCreated", "datePublished", "discussionUrl", "hasPart", "inLanguage", "isAccessibleForFree", "isBasedOn", "isPartOf", "keywords", "provider", "sdPublisher", "thumbnailUrl", "mainEntityOfPage", "sameAs","sourceOrganization"], "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" }, "dataset": { "description": "Link to a dataset record", "oneOf": [ { "items": { "type": "string", "format": "uri" }, "type": "array" }, { "type": "string", "format": "uri" } ] } }, "required": ["name", "url"], "recommended": ["versionDate", "dataset"] }, "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" } }, { "$ref": "#/definitions/definedterm" } ] } }, "required": ["name"], "recommended": ["encodingFormat"] } } } }, { "@id": "nde:ResourceCatalog", "@type": "rdfs:Class", "rdfs:comment": "ResourceCatalogs (collections of scientific information or research outputs) contained in the NIAID Data Ecosystem. Resource catalogs include databases, repositories, knowledge bases, citation indices, software indices, browser-based data portals (web portals), etc. The NIAID Data Ecosystem is an environment to find and access and infectious and immune-mediated disease data, resources and computational tools to speed the development of diagnostics, therapeutics, and vaccines. The NIAID Data Ecosystem Discovery Portal harvests metadata from dataset repository and harmonizes them to this schema to enable easy cross-platform dataset searching and filtering.", "abstract": "ResourceCatalogs (collections of scientific information or research outputs) contained in the NIAID Data Ecosystem. Resource catalogs include databases, repositories, knowledge bases, citation indices, software indices, browser-based data portals (web portals), etc.", "rdfs:label": "ResourceCatalog", "rdfs:subClassOf": { "@id": "schema:Collection" }, "$validation": { "$schema": "http://json-schema.org/draft-07/schema#", "type": "object", "properties": { "citedBy": { "description": "Publications, datasets, or computational tools that cite the work.", "anyOf": [ { "type": "array", "items": { "$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" } }, { "$ref": "#/definitions/organization" } ], "owl:cardinality": "many" }, "citation": { "description": "A citation or reference to a publication, dataset, or computational tool which uses the resource catalog. Examples: a publication which describes the creation of the resource catalog, a publication which uses information or content of the resource catalog for secondary analysis, or a computational tool which relies on the content of the resource catalog.", "abstract": "citation to the work", "owl:cardinality": "many", "anyOf": [ { "type": "array", "items": { "$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" } }, { "$ref": "#/definitions/creativework" } ], "owl:cardinality": "many" }, "version": { "description": "Resource catalog version.", "type": "string", "owl:cardinality": "one" }, "alternateName": { "description": "An alias for the resource catalog name.", "oneOf": [ { "type": "string" }, { "type": "array", "items": { "type": "string" } } ], "owl:cardinality": "many" }, "description": { "description": "A description of the resource catalog.", "owl:cardinality": "one", "type": "string" }, "identifier": { "description": "Resource catalog identifier or accession number, such as a digital object identifier (DOI), etc.", "abstract": "identifier", "oneOf": [ { "type": "string" }, { "items": { "type": "string" }, "type": "array" } ], "owl:cardinality": "many" }, "mainEntityOfPage": { "description": "Website which describes the work and provides additional details.", "abstract": "associated webpage", "oneOf": [ { "items": { "type": "string", "format": "uri" }, "type": "array" }, { "type": "string", "format": "uri" } ], "owl:cardinality": "many" }, "name": { "description": "Resource catalog name.", "owl:cardinality": "one", "type": "string" }, "sameAs": { "description": "URL of additional sources for the work.", "oneOf": [ { "items": { "type": "string", "format": "uri" }, "type": "array" }, { "type": "string", "format": "uri" } ], "owl:cardinality": "many" }, "url": { "description": "URL of the work.", "type": "string", "format": "uri", "owl:cardinality": "one" }, "collectionSize": { "description": "The number of records, datasets, tools, items, pages, etc. in the resource catalog. Min/max estimates can be used in lieu of actual number. If completely unknown, set value = 0, and unitText = 'unknown'", "oneOf": [ { "type": "array", "items": { "$ref": "#/definitions/propertyvalue" } }, { "$ref": "#/definitions/propertyvalue" } ], "owl:cardinality": "many" }, "collectionType": { "description": "The type of resource/resource catalog that best describes the work.", "anyOf": [ { "type": "string", "enum": ["Knowledge Base", "Ontology", "Terminology", "Database", "Dataset", "Metadata Catalog", "Archive", "Cloud Ecosystem", "Corpus", "Repository", "Controlled Vocabulary", "Registry", "Data Dictionary", "Data Mart", "Data Warehouse", "Data Store", "Data Collection", "Portal"] }, { "$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" }, "dataset": { "description": "URL(s) to one or more dataset(s) contained in this resource", "oneOf": [ { "items": { "type": "string", "format": "uri" }, "type": "array" }, { "type": "string", "format": "uri" } ], "owl:cardinality": "many" } }, "required": ["date", "funding", "measurementTechnique", "description", "name", "url", "collectionType", "genre"], "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"], "optional": ["isRelatedTo", "isSimilarTo", "isBasisFor", "distribution", "includedInDataCatalog", "abstract", "aggregateRating", "creator", "hasPart", "inLanguage", "isAccessibleForFree", "isPartOf", "version", "alternateName", "mainEntityOfPage", "sameAs", "relationship", "sourceOrganization", "dataset"], "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" }, "dataset": { "description": "Link to a dataset record", "oneOf": [ { "items": { "type": "string", "format": "uri" }, "type": "array" }, { "type": "string", "format": "uri" } ] } }, "required": ["name", "url"], "recommended": ["versionDate", "dataset"] }, "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" } }, "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" }, { "$ref": "#/definitions/softwareapplication" } ] }, "termCode": { "description": "A code that identifies this DefinedTerm within a DefinedTermSet.", "type": "string" }, "description": { "description": "A description of the item.", "type": "string" }, "inDefinedTermSet": { "description": "A DefinedTermSet that contains this term.", "type": "string" }, "originalName": { "description": "The original name of the item, before any metadata standardization/normalization", "type": "string" }, "isCurated": { "description": "A boolean indicator describing whether or not this DefinedTerm was curated as the value of a property.", "type": "boolean" } }, "required": [] }, "softwareapplication": { "@type": "SoftwareApplication", "description": "Reusable software or algorithm definition", "properties": { "name": { "description": "name of the software, computational tool, or algorithm.", "type": "string" }, "dateModified": { "description": "date the software, computational tool, or algorithm was run", "type": "string", "format": "date" }, "url": { "description": "url of the software, computational tool, or algorithm", "type": "string", "format": "uri" } }, "required": ["name"], "recommended": ["url"], "optional": ["dateModified"], "type": "object" } } } }, { "@id": "nde:DefinedTerm", "@type": "rdfs:Class", "rdfs:comment": "A word, name, acronym, phrase, etc. with a formal definition. Often used in the context of category or subject classification, glossaries or dictionaries, product or creative work types, etc. Use the name property for the term being defined, use termCode if the term has an alpha-numeric code allocated, use description to provide the definition of the term.", "rdfs:label": "DefinedTerm", "rdfs:subClassOf": { "@id": "schema:DefinedTerm" }, "$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" }, "dataset": { "description": "Link to a dataset record", "oneOf": [ { "items": { "type": "string", "format": "uri" }, "type": "array" }, { "type": "string", "format": "uri" } ] } }, "required": ["name", "url"], "recommended": ["versionDate", "dataset"] }, "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:citedBy", "@type": "rdf:Property", "rdfs:comment": "Publications that cite the dataset, resource/resource catalog or computational tool.", "rdfs:label": "citedBy", "schema:domainIncludes": [ { "@id": "nde:Dataset" }, { "@id": "nde:ComputationalTool" }, { "@id": "nde:ResourceCatalog" } ], "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" } ], "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" } ], "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" } ], "schema:rangeIncludes": [ { "@id": "nde:Dataset" }, { "@id": "nde:ComputationalTool" }, { "@id": "nde:ResourceCatalog" }, { "@id": "schema:CreativeWork" }, { "@id": "niaid:ScholarlyArticle" } ] }, { "@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" } ], "schema:rangeIncludes": [ { "@id": "nde:Dataset" }, { "@id": "nde:ComputationalTool" }, { "@id": "nde:ResourceCatalog" }, { "@id": "schema:CreativeWork" }, { "@id": "niaid:ScholarlyArticle" } ] }, { "@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" } ], "schema:rangeIncludes": [ { "@id": "nde:Dataset" }, { "@id": "nde:ComputationalTool" }, { "@id": "nde:ResourceCatalog" }, { "@id": "schema:CreativeWork" }, { "@id": "niaid:ScholarlyArticle" } ] }, { "@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" } ], "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" } ], "schema:rangeIncludes": [ { "@id": "schema:PropertyValue" } ] }, { "@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" } ], "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" } ], "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" } ], "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" } ], "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" } ], "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" } ], "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" } ], "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" } ], "schema:rangeIncludes": [ { "@id": "schema:ResearchProject" }, { "@id": "niaid:Organization" } ] }, { "@id": "nde:dataset", "@type": "rdf:Property", "rdfs:comment": "A dataset contained in this catalog.", "rdfs:label": "dataset", "schema:domainIncludes": [ { "@id": "schema:DataCatalog" }, { "@id": "nde:ResourceCatalog" } ], "schema:rangeIncludes": [ { "@id": "nde:Dataset" } ] } ] }