Dataset
type: Class
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. A dataset is a collection of data of a particular experimental type.
subclass of: Dataset
schema version: https://schema.org/docs/releases.html#v18.0
schema version: v2.0 - 2025.12.12
provenance: Changes since previous version: Update the validation of the 'sample' property in the Dataset to match the changes to the SampleCollection Type.
$validation:
  $schema: http://json-schema.org/draft-07/schema#
  type: object
  properties:
    cited by:
      description: Publications, datasets, or computational tools that cite the work. Examples: a publication which reuses the dataset in a secondary analysis, a dataset which extends the existing dataset, or a computational tool which relies on the dataset. For the primary publication, use the 'citation' property.
      any of:
        type: array
      any of:
        $ref: #/definitions/citation
      any of:
        type: array
      any of:
        $ref: #/definitions/creativework
      cardinality: many
    date:
      description: Date the work has changed: most recent date of dateModified, datePublished, and dateCreated.
      abstract: date changed
      format: date
      type: string
      cardinality: one
    doi:
      description: Digital Object Identifier (DOI) for the work, not any associated publications.
      abstract: digital object identifier
      type: string
      cardinality: one
    is related to:
      description: Datasets which are related to the given dataset; often datasets involved in the same study. These linkages are created via human curation.
      abstract: related datasets (via curation)
      any of:
        type: array
      any of:
        $ref: #/definitions/citation
      any of:
        type: array
      any of:
        $ref: #/definitions/creativework
      cardinality: many
    is similar to:
      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 datasets (auto-assigned)
      any of:
        type: array
      any of:
        $ref: #/definitions/citation
      any of:
        type: array
      any of:
        $ref: #/definitions/creativework
      cardinality: many
    is basis for:
      description: A dataset which reuses the dataset.
      any of:
        type: array
      any of:
        $ref: #/definitions/citation
      any of:
        type: array
      any of:
        $ref: #/definitions/creativework
      cardinality: many
    nctid:
      description: ClinicalTrials.gov identifier associated with the dataset.
      abstract: ClinicalTrials.gov ID
      type: string
      cardinality: many
    relationship:
      description: How an associated work is related to the dataset.
      type: string
      cardinality: one
    topic category:
      description: Topic of the work. This topic may be assigned by a human curator or through automated algorithms.
      abstract: topic
      any of:
        type: array
      any of:
        $ref: #/definitions/topic
      any of:
        type: array
      any of:
        $ref: #/definitions/definedterm
      cardinality: many
    infectious agent:
      description: Infectious agent(s) / pathogen(s) which are the focus of the work (like SARS-CoV-2).
      abstract: infectious agent / pathogen
      any of:
        description: collection of vocabulary terms defined in ontologies
        strict: false
        type: string
      any of:
        type: array
      any of:
        type: array
      any of:
        $ref: #/definitions/definedterm
      cardinality: many
    health condition:
      description: The health condition(s) /infectious disease(s) which are the focus of the work (like COVID-19, coronavirus).
      abstract: health condition/disease
      any of:
        description: collection of vocabulary terms defined in ontologies
        strict: false
        type: string
      any of:
        type: array
      any of:
        type: array
      any of:
        $ref: #/definitions/definedterm
      cardinality: many
    funding:
      description: Funding that supports (sponsors) the collection of this dataset through some kind of financial contribution.
      abstract: funding source (grant, contract, etc.)
      one of: MonetaryGrant
        type: object
        description: Funding that supports (sponsors) the collection of this dataset through some kind of financial contribution
        required: funder
        required: identifier
      one of:
        type: array
        items: MonetaryGrant
      cardinality: many
    species:
      description: Species / host organism from which the dataset has been collected.
      abstract: species/host organism
      any of:
        description: collection of vocabulary terms defined in ontologies
        strict: false
        type: string
      any of:
        type: array
      any of:
        type: array
      any of:
        $ref: #/definitions/definedterm
      cardinality: many
    distribution:
      description: A downloadable form of this dataset, at a specific location, in a specific format.
      abstract: download link
      one of:
        items: DataDownload
        type: array
      one of: DataDownload
        description: A dataset in downloadable form.
        required: dateModified
        required: contentUrl
        type: object
      cardinality: many
    included in data catalog:
      description: Data or tool catalog where the work is published; original source of the metadata.
      abstract: catalog containing the work
      one of:
        $ref: #/definitions/catalog
      one of:
        type: array
      cardinality: one
    measurement technique:
      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
      any of:
        description: collection of vocabulary terms defined in ontologies
        strict: false
        type: string
      any of:
        type: array
      any of:
        type: array
      any of:
        $ref: #/definitions/definedterm
      cardinality: many
    variable measured:
      description: Variables measured within the dataset.
      one of:
        description: collection of vocabulary terms defined in ontologies
        strict: false
        type: string
      one of:
        type: array
      one of:
        type: array
      one of:
        $ref: #/definitions/definedterm
      cardinality: many
    abstract:
      description: Short description that summarizes a work.
      abstract: short description
      type: string
      cardinality: one
    aggregate rating:
      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
      one of:
        items: AggregateRating
        type: array
      one of: AggregateRating
        type: object
        required: ratingValue
        recommended: ratingCount
        recommended: itemReviewed
      cardinality: many
  required: date
  required: funding
  required: distribution
  required: includedInDataCatalog
  required: measurementTechnique
  required: author
  required: description
  required: name
  required: url
  recommended: citedBy
  recommended: doi
  recommended: infectiousAgent
  recommended: healthCondition
  recommended: species
  recommended: variableMeasured
  recommended: citation
  recommended: conditionsOfAccess
  recommended: dateCreated
  recommended: dateModified
  recommended: datePublished
  recommended: interactionStatistic
  recommended: isBasedOn
  recommended: keywords
  recommended: license
  recommended: sdPublisher
  recommended: spatialCoverage
  recommended: temporalCoverage
  recommended: usageInfo
  recommended: identifier
  recommended: topicCategory
  optional: isRelatedTo
  optional: isSimilarTo
  optional: isBasisFor
  optional: nctid
  optional: abstract
  optional: aggregateRating
  optional: creator
  optional: hasPart
  optional: inLanguage
  optional: isAccessibleForFree
  optional: isPartOf
  optional: version
  optional: alternateName
  optional: mainEntityOfPage
  optional: sameAs
  optional: relationship
  optional: sourceOrganization
  optional: sample
  optional: creditText

ComputationalTool
type: Class
comment: ComputationalTools (software, workflows, computational tools, code) contained in the NIAID Data Ecosystem. The NIAID Data Ecosystem is a secure environment to find, access and analyze immune-mediated and infectious disease data and computational tools to speed the development of diagnostics, therapeutics, and vaccines. The NIAID Data Ecosystem Discovery Portal harvests metadata from dataset repository and harmonizes them to this schema to enable easy cross-platform dataset searching and filtering.
abstract: ComputationalTools (software, workflows, computational tools, code) contained in the NIAID Data Ecosystem.
subclass of: ComputationalTool
schema version: https://schema.org/docs/releases.html#v18.0
schema version: v1.9 - 2025.09.03
provenance: Changes since previous version: Update 'citation' and 'citedBy' descriptions. Added the creditText property as optional.
$validation:
  $schema: http://json-schema.org/draft-07/schema#
  type: object
  properties:
    cited by:
      description: Publications, datasets, or computational tools that cite the work. Examples: a publication which uses the tool on a new dataset. For the primary publication, use the 'citation' property.
      any of:
        type: array
      any of:
        $ref: #/definitions/citation
      any of:
        type: array
      any of:
        $ref: #/definitions/creativework
      cardinality: many
    date:
      description: Date the work has changed: most recent date of dateModified, datePublished, and dateCreated.
      abstract: date changed
      cardinality: one
      format: date
      type: string
    doi:
      description: Digital object identifier (DOI) for the work, not any associated publications.
      abstract: digital object identifier
      cardinality: one
      type: string
    included in data catalog:
      description: Data or tool catalog where the work is published; original source of the metadata.
      abstract: catalog containing the work
      $ref: #/definitions/catalog
    is basis for:
      description: A computational tool which reuses the computational tool.
      cardinality: many
      any of:
        type: array
      any of:
        $ref: #/definitions/citation
      any of:
        type: array
      any of:
        $ref: #/definitions/creativework
    is related to:
      description: Computational tools which are related to the given computational tool. These linkages are created via human curation.
      abstract: related records (via curation)
      any of:
        type: array
      any of:
        $ref: #/definitions/citation
      any of:
        type: array
      any of:
        $ref: #/definitions/creativework
      cardinality: many
    is similar to:
      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)
      any of:
        type: array
      any of:
        $ref: #/definitions/citation
      any of:
        type: array
      any of:
        $ref: #/definitions/creativework
      cardinality: many
    topic category:
      description: Topic of the work. This topic may be assigned by a human curator or through automated algorithms.
      abstract: topic
      any of:
        type: array
      any of:
        $ref: #/definitions/topic
      any of:
        type: array
      any of:
        $ref: #/definitions/definedterm
      cardinality: many
    infectious agent:
      description: Infectious agent(s) / pathogen(s) which are the focus of the work (like SARS-CoV-2).
      abstract: infectious agent / pathogen
      any of:
        description: collection of vocabulary terms defined in ontologies
        strict: false
        type: string
      any of:
        type: array
      any of:
        type: array
      any of:
        $ref: #/definitions/definedterm
      cardinality: many
    health condition:
      description: The health condition(s) /infectious disease(s) which are the focus of the work (like COVID-19, coronavirus).
      abstract: health condition/disease
      any of:
        description: collection of vocabulary terms defined in ontologies
        strict: false
        type: string
      any of:
        type: array
      any of:
        type: array
      any of:
        $ref: #/definitions/definedterm
      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.)
      one of: MonetaryGrant
        type: object
        description: Funding that supports (sponsors) the development of this computational tool through some kind of financial contribution
        required: funder
        required: identifier
      one of:
        type: array
        items: MonetaryGrant
      cardinality: many
    species:
      description: Species / host organism from which the dataset has been collected.
      abstract: species/host organism
      any of:
        description: collection of vocabulary terms defined in ontologies
        strict: false
        type: string
      any of:
        type: array
      any of:
        type: array
      any of:
        $ref: #/definitions/definedterm
      cardinality: many
    available on device:
      description: Device or platform required to run the application, such as Bioconda, Docker, or Singularity.
      abstract: platform to run the application
      cardinality: many
      one of:
        type: array
      one of:
        type: string
    code repository:
      description: Link to the source code repository of the tool such as GitHub.
      abstract: source code link
      one of:
        format: uri
        type: string
      one of:
        type: array
      cardinality: many
    programming language:
      description: The main programming language(s) used to build or execute the tool.
      abstract: programming language
      one of:
        type: string
      one of:
        type: array
      cardinality: many
    input:
      description: software input, such as a file or parameter.
      abstract: input file/parameter
      cardinality: many
      any of:
        type: array
      any of:
        $ref: #/definitions/formalparameter
      any of:
        type: array
      any of:
        $ref: #/definitions/definedterm
    output:
      description: Output of the computational tool.
      cardinality: many
      any of:
        type: array
      any of:
        $ref: #/definitions/formalparameter
      any of:
        type: array
      any of:
        $ref: #/definitions/definedterm
    application category:
      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
      any of:
        type: string
      any of:
        type: array
      any of:
        type: array
      any of:
        $ref: #/definitions/definedterm
      cardinality: many
    application sub category:
      description: A subcategory of the computational tool, like gene regulation.
      abstract: software subcategory
      any of: DefinedTerm
        strict: false
        type: object
      cardinality: many
  required: date
  required: includedInDataCatalog
  required: funding
  required: author
  required: description
  required: name
  recommended: citedBy
  recommended: doi
  recommended: topicCategory
  recommended: codeRepository
  recommended: programmingLanguage
  recommended: applicationCategory
  recommended: applicationSubCategory
  recommended: input
  recommended: output
  recommended: featureList
  recommended: operatingSystem
  recommended: softwareRequirements
  recommended: softwareVersion
  recommended: citation
  recommended: conditionsOfAccess
  recommended: dateModified
  recommended: interactionStatistic
  recommended: license
  recommended: identifier
  recommended: url
  optional: isBasisFor
  optional: isRelatedTo
  optional: isSimilarTo
  optional: infectiousAgent
  optional: healthCondition
  optional: species
  optional: applicationSuite
  optional: availableOnDevice
  optional: downloadUrl
  optional: processorRequirements
  optional: softwareAddOn
  optional: softwareHelp
  optional: aggregateRating
  optional: contributor
  optional: creator
  optional: dateCreated
  optional: datePublished
  optional: discussionUrl
  optional: hasPart
  optional: inLanguage
  optional: isAccessibleForFree
  optional: isBasedOn
  optional: isPartOf
  optional: keywords
  optional: provider
  optional: sdPublisher
  optional: thumbnailUrl
  optional: mainEntityOfPage
  optional: sameAs
  optional: sourceOrganization
  optional: creditText

ResourceCatalog
type: Class
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.
subclass of: Collection
schema version: https://schema.org/docs/releases.html#v18.0
schema version: v2.0 - 2025.12.08
provenance: Changes since previous version: Add description for the 'about' field.
$validation:
  $schema: http://json-schema.org/draft-07/schema#
  type: object
  properties:
    about:
      description: The entity type or class encapsulated by the records in this resource. For example, if a repository has a record on CDK2, and metadata about the genetic sequence, epigentic annotation, gene locus, etc-- the entity type would be Gene, and the resource contains data 'about' Genes. These should be formatted as DefinedTerm objects (mapped to ontology terms) for easier standardization.
      one of:
        type: array
      one of:
        $ref: #/definitions/definedterm
      cardinality: many
    cited by:
      description: Publications, datasets, or computational tools that cite the work. Examples: a publication which uses information or content of the resource catalog for secondary analysis, or a computational tool which relies on the content of the resource catalog. For the primary citation, use the 'citation' field.
      any of:
        type: array
      any of:
        $ref: #/definitions/citation
      any of:
        type: array
      any of:
        $ref: #/definitions/creativework
      cardinality: many
    date:
      description: Date the work has changed: most recent date of dateModified, datePublished, and dateCreated.
      abstract: date changed
      format: date
      type: string
      cardinality: one
    doi:
      description: Digital Object Identifier (DOI) for the work, not any associated publications.
      abstract: digital object identifier
      type: string
      cardinality: one
    is related to:
      description: Resources which are related to the given resource catalog. These linkages are created via human curation.
      abstract: related datasets (via curation)
      any of:
        type: array
      any of:
        $ref: #/definitions/citation
      any of:
        type: array
      any of:
        $ref: #/definitions/creativework
      cardinality: many
    is similar to:
      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)
      any of:
        type: array
      any of:
        $ref: #/definitions/citation
      any of:
        type: array
      any of:
        $ref: #/definitions/creativework
      cardinality: many
    is basis for:
      description: A resource catalog which uses the resource catalog.
      any of:
        type: array
      any of:
        $ref: #/definitions/citation
      any of:
        type: array
      any of:
        $ref: #/definitions/creativework
      cardinality: many
    relationship:
      description: How an associated work is related to the resource catalog.
      type: string
      cardinality: one
    topic category:
      description: Topic of the work. This topic may be assigned by a human curator or through automated algorithms.
      abstract: topic
      any of:
        type: array
      any of:
        $ref: #/definitions/topic
      any of:
        type: array
      any of:
        $ref: #/definitions/definedterm
      cardinality: many
    infectious agent:
      description: Infectious agent(s) / pathogen(s) which are the focus of the work (like SARS-CoV-2).
      abstract: infectious agent / pathogen
      any of:
        description: collection of vocabulary terms defined in ontologies
        strict: false
        type: string
      any of:
        type: array
      any of:
        type: array
      any of:
        $ref: #/definitions/definedterm
      cardinality: many
    health condition:
      description: The health condition(s) /infectious disease(s) which are the focus of the work (like COVID-19, coronavirus).
      abstract: health condition/disease
      any of:
        description: collection of vocabulary terms defined in ontologies
        strict: false
        type: string
      any of:
        type: array
      any of:
        type: array
      any of:
        $ref: #/definitions/definedterm
      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.)
      one of: MonetaryGrant
        type: object
        description: Funding that supports (sponsors) the creation or maintenance of the resource catalog through some kind of financial contribution
        required: funder
        required: identifier
      one of:
        type: array
        items: MonetaryGrant
      cardinality: many
    species:
      description: Species / host organism from which the dataset has been collected.
      abstract: species/host organism
      any of:
        description: collection of vocabulary terms defined in ontologies
        strict: false
        type: string
      any of:
        type: array
      any of:
        type: array
      any of:
        $ref: #/definitions/definedterm
      cardinality: many
    distribution:
      description: A downloadable form of the resource catalog, at a specific location, in a specific format.
      abstract: download link
      one of:
        items: DataDownload
        type: array
      one of: DataDownload
        description: A downloadable form of the resource catalog.
        required: dateModified
        required: contentUrl
        type: object
      cardinality: many
    included in data catalog:
      description: A resource catalog where the resource catalog is published.
      abstract: catalog containing the work
      one of:
        $ref: #/definitions/catalog
      one of:
        type: array
      cardinality: one
    measurement technique:
      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
      any of:
        description: collection of vocabulary terms defined in ontologies
        strict: false
        type: string
      any of:
        type: array
      any of:
        type: array
      any of:
        $ref: #/definitions/definedterm
      cardinality: many
    variable measured:
      description: Variables measured within the dataset.
      one of:
        description: collection of vocabulary terms defined in ontologies
        strict: false
        type: string
      one of:
        type: array
      one of:
        type: array
      one of:
        $ref: #/definitions/definedterm
      cardinality: many
    abstract:
      description: Short description that summarizes a work.
      abstract: short description
      type: string
      cardinality: one
    aggregate rating:
      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
      one of:
        items: AggregateRating
        type: array
      one of: AggregateRating
      cardinality: many
  required: date
  required: funding
  required: measurementTechnique
  required: description
  required: name
  required: url
  required: about
  required: genre
  required: includedInDataCatalog
  recommended: author
  recommended: citedBy
  recommended: doi
  recommended: infectiousAgent
  recommended: healthCondition
  recommended: species
  recommended: variableMeasured
  recommended: citation
  recommended: conditionsOfAccess
  recommended: dateCreated
  recommended: dateModified
  recommended: datePublished
  recommended: interactionStatistic
  recommended: isBasedOn
  recommended: keywords
  recommended: license
  recommended: sdPublisher
  recommended: spatialCoverage
  recommended: temporalCoverage
  recommended: usageInfo
  recommended: identifier
  recommended: topicCategory
  recommended: collectionSize
  recommended: hasAPI
  recommended: hasDownload
  recommended: collectionType
  optional: isRelatedTo
  optional: isSimilarTo
  optional: isBasisFor
  optional: distribution
  optional: abstract
  optional: aggregateRating
  optional: creator
  optional: hasPart
  optional: inLanguage
  optional: isAccessibleForFree
  optional: isPartOf
  optional: version
  optional: alternateName
  optional: mainEntityOfPage
  optional: sameAs
  optional: relationship
  optional: sourceOrganization
  optional: archivedAt
  optional: creditText

DefinedTerm
type: Class
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.
subclass of: DefinedTerm
schema version: https://schema.org/docs/releases.html#v18.0
schema version: v1.2 - 2025.05.29
provenance: Changes since previous version: Replace includedInDataCatalog.dataset with includedInDataCatalog.archivedAt.
$validation:
  $schema: http://json-schema.org/draft-07/schema#
  type: object
  properties:
    name:
      description: The name of the item.
      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.
      cardinality: one
      type: string
    url:
      description: URL of the item.
      cardinality: one
      type: string
      format: uri
    curated by:
      description: The person, organization, or catalog that curated this DefinedTerm for the metadata property
      any of:
        $ref: #/definitions/person
      any of:
        $ref: #/definitions/organization
      any of:
        $ref: #/definitions/catalog
      any of:
        $ref: #/definitions/researchproject
      any of:
        $ref: #/definitions/softwareapplication
    term code:
      description: A code that identifies this DefinedTerm within a DefinedTermSet.
      type: string
    description:
      description: A description of the item.
      type: string
    in defined term set:
      description: A DefinedTermSet that contains this term.
      type: string
    original name:
      description: The original name of the item, before any metadata standardization/normalization
      type: string
    is curated:
      description: A boolean indicator describing whether or not this DefinedTerm was curated as the value of a property.
      type: boolean
  recommended: description
  recommended: curatedBy
  recommended: isCurated
  optional: termCode
  optional: inDefinedTermSet
  optional: originalName
  any of:
    required: name
  any of:
    required: identifier
  any of:
    required: url
  definitions:
    catalog: DataCatalog
      description: Data, resource or tool catalog
      type: object
      required: name
      required: url
      recommended: versionDate
      recommended: archivedAt
    organization: Organization
      description: Reusable organization definition
      required: name
      recommended: identifier
      optional: affiliation
      optional: alternateName
      optional: email
      optional: parentOrganization
      optional: role
      optional: url
      type: object
    researchproject: ResearchProject
      description: a type of organization definition
      required: name
      recommended: identifier
      recommended: url
      recommended: parentOrganization
      optional: alternateName
      optional: email
      optional: role
      type: object
    person: Person
      description: Reusable person definition
      required: name
      recommended: familyName
      recommended: givenName
      recommended: identifier
      optional: affiliation
      optional: email
      optional: role
      optional: title
      optional: url
      type: object
    softwareapplication: SoftwareApplication
      description: Reusable software or algorithm definition
      required: name
      recommended: url
      optional: dateModified
      type: object

Sample
type: Class
comment: Samples contained in the NIAID Data Ecosystem. A Sample is a material entity taken from a larger source, system, or environment, collected for the purpose of analysis, testing, identification, or demonstration. The NIAID Data Ecosystem Discovery Portal harvests metadata from repositories and harmonizes them to this schema to enable easy cross-platform sample searching and filtering.
abstract: Samples contained in the NIAID Data Ecosystem. A sample is a material entity taken from a larger source.
subclass of: BioSample
subclass of: CreativeWork
schema version: https://schema.org/docs/releases.html#v18.0
schema version: v0.5 - 2026.02.04
provenance: Changes since previous version: Allow DefinedTerm as an expected type for experimentalPurpose.
$validation:
  $schema: http://json-schema.org/draft-07/schema#
  type: object
  properties:
    name:
      description: Sample name.
      cardinality: one
      type: string
    description:
      description: A description of the sample.
      cardinality: one
      type: string
    identifier:
      description: Sample identifier or accession number, such as a digital object identifier (DOI), sequence read archive (SRA) or GenBank accession number, etc.
      abstract: identifier or accession number
      one of:
        type: string
      one of:
        type: array
      cardinality: many
    same as:
      description: URL of additional sources for the work.
      one of:
        type: array
      one of:
        type: string
        format: uri
      cardinality: many
    url:
      description: URL of the work.
      type: string
      format: uri
      cardinality: one
    usage info:
      description: The terms under which the sample can be used. Note that this is related to but distinct from the license.
      abstract: sample usage agreement
      one of:
        type: array
      one of:
        $ref: #/definitions/creativework
      cardinality: many
    license:
      description: A license document that applies to this work, typically indicated by URL.
      abstract: license for use
      format: uri
      cardinality: one
      type: string
    conditions of access:
      description: Conditions that affect the availability of, or method(s) of access to, the sample. Options include open (freely available), restricted (may include restrictions such as on use), closed (requires registration to access), or embargoed (unpublished).
      abstract: accessibility of the work
      type: string
      enum: Closed
      enum: Open
      enum: Restricted
      enum: Embargoed
      cardinality: one
    is accessible for free:
      description: A flag to signal that the sample may be requested at no cost (not including shipping).
      abstract: accessible without charge
      type: boolean
      cardinality: one
    included in data catalog:
      description: Data or resource catalog where the sample is listed; original source of the metadata.
      abstract: catalog containing the work
      one of:
        $ref: #/definitions/catalog
      one of:
        type: array
      cardinality: one
    associated phenotype:
      description: one or more observable traits or conditions relevant to the source of the sample.
      any of:
        description: collection of vocabulary terms defined in ontologies
        strict: false
        type: string
      any of:
        type: array
      any of:
        type: array
      any of:
        $ref: #/definitions/definedterm
      any of:
        type: array
      any of:
        $ref: #/definitions/quantitativevalue
      cardinality: many
    associated genotype:
      description: One or more genetic variants or molecular features observed or inferred from the sample.
      any of:
        description: collection of vocabulary terms defined in ontologies
        strict: false
        type: string
      any of:
        type: array
      any of:
        type: array
      any of:
        $ref: #/definitions/definedterm
      cardinality: many
    cell type:
      description: The type of cell represented in or derived from the biological sample, based on morphology, lineage, or molecular markers.
      any of:
        description: collection of vocabulary terms defined in ontologies
        strict: false
        type: string
      any of:
        type: array
      any of:
        type: array
      any of:
        $ref: #/definitions/definedterm
      cardinality: many
    infectious agent:
      description: Infectious agent(s) / pathogen(s) which are the focus of the work (like SARS-CoV-2).
      abstract: infectious agent / pathogen
      any of:
        description: collection of vocabulary terms defined in ontologies
        strict: false
        type: string
      any of:
        type: array
      any of:
        type: array
      any of:
        $ref: #/definitions/definedterm
      cardinality: many
    health condition:
      description: The health condition(s) /infectious disease(s) which are the focus of the work (like COVID-19, coronavirus).
      abstract: health condition/disease
      any of:
        description: collection of vocabulary terms defined in ontologies
        strict: false
        type: string
      any of:
        type: array
      any of:
        type: array
      any of:
        $ref: #/definitions/definedterm
      cardinality: many
    funding:
      description: Funding that supports (sponsors) the collection of this dataset through some kind of financial contribution.
      abstract: funding source (grant, contract, etc.)
      one of: MonetaryGrant
        type: object
        description: Funding that supports (sponsors) the collection of this dataset through some kind of financial contribution
        required: funder
        required: identifier
      one of:
        type: array
        items: MonetaryGrant
      cardinality: many
    species:
      description: Species / host organism from which the dataset has been collected.
      abstract: species/host organism
      any of:
        description: collection of vocabulary terms defined in ontologies
        strict: false
        type: string
      any of:
        type: array
      any of:
        type: array
      any of:
        $ref: #/definitions/definedterm
      cardinality: many
    cited by:
      description: Publications, datasets, or computational tools that cite the sample. Examples: a dataset which reuses the sample in a secondary study.
      any of:
        type: array
      any of:
        $ref: #/definitions/citation
      any of:
        type: array
      any of:
        $ref: #/definitions/creativework
      cardinality: many
    is related to:
      description: Datasets, resources, or samples which are related to the given sample; often sample involved in the same study. These linkages are created via human curation.
      abstract: related resources or samples (via curation)
      any of:
        type: array
      any of:
        $ref: #/definitions/citation
      any of:
        type: array
      any of:
        $ref: #/definitions/creativework
      any of:
        type: array
      any of:
        $ref: #/definitions/sample
      cardinality: many
    is similar to:
      description: Datasets, resources, or samples which are similar to the sample, based on terms in the names, descriptions, authors, measurementTechniques, infectiousAgents, healthConditions, etc.
      abstract: similar resources of samples (auto-assigned)
      cardinality: many
  required: name
  required: url
  required: identifier
  required: includedInDataCatalog
  required: author
  required: date
  recommended: description
  recommended: sameAs
  recommended: conditionsOfAccess
  recommended: usageInfo
  recommended: license
  recommended: cellType
  recommended: infectiousAgent
  recommended: species
  recommended: healthCondition
  recommended: funding
  recommended: creditText
  recommended: anatomicalStructure
  recommended: sex
  recommended: developmentalStage
  recommended: sampleAvailability
  recommended: sampleProcess
  recommended: sampleType
  recommended: collectionMethod
  recommended: instrument
  recommended: collector
  recommended: contributor
  recommended: locationOfOrigin
  recommended: citation
  recommended: dateModified
  recommended: dateCollected
  recommended: dateProcessed
  recommended: interactionStatistic
  recommended: keywords
  recommended: sdPublisher
  recommended: sourceOrganization
  recommended: topicCategory
  optional: associatedPhenotype
  optional: associatedGenotype
  optional: citedBy
  optional: isRelatedTo
  optional: isSimilarTo
  optional: isBasisFor
  optional: isBasedOn
  optional: hasPart
  optional: isPartOf
  optional: anatomicalSystem
  optional: sampleQuantity
  optional: sampleState
  optional: sampleStorageTemperature
  optional: distribution
  optional: measurementTechnique
  optional: variableMeasured
  optional: environmentalSystem
  optional: aggregateRating
  optional: experimentalPurpose
  optional: maintainer
  optional: itemLocation
  optional: dateCreated
  optional: datePublished
  optional: spatialCoverage
  optional: temporalCoverage
  optional: additionalProperty

SampleCollection
type: Class
comment: Sample collections contained in the NIAID Data Ecosystem. A SampleCollection is a collection of samples with some aggregate information about the collection itself. A SampleCollection can be useful for describing sample information when only aggregated sample-level metadata is provided due to privacy issues that prevent sharing of individual sample-level metadata record.
abstract: Samples collections contained in the NIAID Data Ecosystem. A sample collection is an aggregate sample record.
subclass of: ItemList
schema version: https://schema.org/docs/releases.html#v18.0
schema version: v0.3 - 2025.12.17
provenance: Changes since previous version: Change the parent class of the SampleCollection schema to ItemList and reorganized the properties and expected values.
$validation:
  $schema: http://json-schema.org/draft-07/schema#
  type: object
  properties:
    name:
      description: Sample name.
      cardinality: one
      type: string
    description:
      description: A description of the sample.
      cardinality: one
      type: string
    identifier:
      description: Sample identifier or accession number, such as a digital object identifier (DOI), sequence read archive (SRA) or GenBank accession number, etc.
      abstract: identifier or accession number
      one of:
        type: string
      one of:
        type: array
      cardinality: many
    same as:
      description: URL of additional sources for the work.
      one of:
        type: array
      one of:
        type: string
        format: uri
      cardinality: many
    url:
      description: URL of the work.
      type: string
      format: uri
      cardinality: one
    included in data catalog:
      description: Data or resource catalog where the sample is listed; original source of the metadata.
      abstract: catalog containing the work
      one of:
        $ref: #/definitions/catalog
      one of:
        type: array
      cardinality: one
    number of items:
      description: The number of sample records in the sample collection. Min/max estimates can be used in lieu of actual number. If completely unknown, set value = 0, and unitText = 'unknown'
      any of:
        type: array
      any of:
        $ref: #/definitions/propertyvalue
      any of:
        type: array
      any of:
        $ref: #/definitions/quantitativevalue
      cardinality: many
    item list element:
      description: The list of samples that are included in the sample collection
      any of:
        type: array
      any of:
        $ref: #/definitions/minsample
      any of:
        type: string
        format: uri
      any of:
        type: array
      cardinality: many
    aggregate element:
      description: Aggregate values derived from the samples in the collection.
      any of:
        type: array
      any of:
        $ref: #/definitions/sample
      cardinality: many
  required: aggregateElement
  required: numberOfItems
  recommended: itemListElement
  recommended: url
  recommended: identifier
  recommended: sameAs
  recommended: includedInDataCatalog
  optional: name
  optional: description
  definitions:
    citation: ScholarlyArticle
      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: object
      required: name
      recommended: author
      recommended: datePublished
      recommended: doi
      recommended: identifier
      recommended: journalName
      recommended: pmid
      recommended: url
      optional: abstract
      optional: citation
      optional: description
      optional: issueNumber
      optional: journalNameAbbrev
      optional: pagination
      optional: volumeNumber
    creativework: CreativeWork
      description: A resource
      type: object
      required: name
      recommended: author
      recommended: datePublished
      recommended: doi
      recommended: identifier
      recommended: includedInDataCatalog
      recommended: relationship
      recommended: url
      optional: abstract
      optional: citation
      optional: description
      optional: hasPart
    topic:
      description: Topic assigned to the work.
      type: string
      vocabulary:
        ontology: edam
        children of: http://edamontology.org/topic_0003
      strict: true
    catalog: DataCatalog
      description: Data or tool catalog
      type: object
      required: name
      required: url
      recommended: versionDate
      recommended: archivedAt
    organization: Organization
      description: Reusable organization definition
      required: name
      recommended: identifier
      optional: affiliation
      optional: alternateName
      optional: email
      optional: parentOrganization
      optional: role
      optional: url
      type: object
    researchproject: ResearchProject
      description: a type of organization definition
      required: name
      recommended: identifier
      recommended: url
      recommended: parentOrganization
      optional: alternateName
      optional: email
      optional: role
      type: object
    person: Person
      description: Reusable person definition
      required: name
      recommended: familyName
      recommended: givenName
      recommended: identifier
      optional: affiliation
      optional: email
      optional: role
      optional: title
      optional: url
      type: object
    definedterm: DefinedTerm
      type: object
    quantitativevalue: QuantitativeValue
      description: A numeric value and unit for a property with potentially different units
      type: object
      required: unitText
      recommended: value
      optional: maxValue
      optional: minValue
    propertyvalue: PropertyValue
      description: A numeric value and unit for a property with potentially different units
      type: object
      required: unitText
      recommended: value
      recommended: propertyID
      optional: maxValue
      optional: minValue
    softwareapplication: SoftwareApplication
      description: Reusable software or algorithm definition
      required: name
      recommended: url
      optional: dateModified
      type: object
    minsample: Sample
      description: minimal sample object
      type: object
      required: url
      required: identifier
      recommended: name
      recommended: includedInDataCatalog
    sample: Sample
      description: reusable detailed sample object
      type: object
      recommended: includedInDataCatalog
      recommended: author
      recommended: date
      recommended: description
      recommended: sameAs
      recommended: conditionsOfAccess
      recommended: usageInfo
      recommended: license
      recommended: cellType
      recommended: infectiousAgent
      recommended: species
      recommended: healthCondition
      recommended: funding
      recommended: creditText
      recommended: anatomicalStructure
      recommended: sex
      recommended: developmentalStage
      recommended: sampleAvailability
      recommended: sampleProcess
      recommended: sampleType
      recommended: collectionMethod
      recommended: instrument
      recommended: collector
      recommended: contributor
      recommended: locationOfOrigin
      recommended: citation
      recommended: dateModified
      recommended: dateCollected
      recommended: dateProcessed
      recommended: interactionStatistic
      recommended: keywords
      recommended: sdPublisher
      recommended: sourceOrganization
      recommended: topicCategory
      optional: associatedPhenotype
      optional: associatedGenotype
      optional: citedBy
      optional: isRelatedTo
      optional: isSimilarTo
      optional: isBasisFor
      optional: isBasedOn
      optional: hasPart
      optional: isPartOf
      optional: anatomicalSystem
      optional: sampleQuantity
      optional: sampleState
      optional: sampleStorageTemperature
      optional: distribution
      optional: measurementTechnique
      optional: variableMeasured
      optional: environmentalSystem
      optional: aggregateRating
      optional: experimentalPurpose
      optional: maintainer
      optional: itemLocation
      optional: dateCreated
      optional: datePublished
      optional: spatialCoverage
      optional: temporalCoverage

DataCollection
type: Class
comment: Data collections contained in the NIAID Data Ecosystem. A data collection is a collection of data records from other sources that have been grouped by common search fields. The NIAID Data Ecosystem is an environment to find and access and infectious and immune-mediated disease data and resources to speed the development of diagnostics, therapeutics, and vaccines. The NIAID Data Ecosystem Discovery Portal aggregates metadata from repository of various data types and harmonizes them to this schema to enable easy cross-platform resource searching and filtering. Data collections are essentially artificial datasets that exist in the NIAID Data Ecosystem to extend the discovery of resources beyond the current scope of the data classes included in the Discovery Portal.
abstract: Data Collections contained in the NIAID Data Ecosystem. A data collection is a collection of data grouped by common search fields in the NIAID Data Ecosystem.
subclass of: Dataset
schema version: https://schema.org/docs/releases.html#v18.0
schema version: v0.2 - 2026.02.04
provenance: Changes since previous version: Updated exampleOfWork object to include 'additionalProperty'.
$validation:
  $schema: http://json-schema.org/draft-07/schema#
  type: object
  properties:
    about:
      description: The entity type or class encapsulated by the records in this data collection. For example, if the records in this collection contain metadata about the genetic sequence, epigentic annotation, gene locus, etc.-- the entity type would be Gene, and the collection contains records 'about' Genes. These should be formatted as DefinedTerm objects (mapped to ontology terms) for easier standardization.
      one of:
        type: array
      one of:
        $ref: #/definitions/definedterm
      cardinality: many
    date:
      description: Date the work has changed: most recent date of dateModified, datePublished, and dateCreated.
      abstract: date changed
      format: date
      type: string
      cardinality: one
    date modified:
      description: The date on which the data collection itself (not the underlying source records) was modified or when the item's entry was modified within a DataFeed.
      format: date
      type: string
      cardinality: one
    description:
      description: A description of the dataset.
      cardinality: one
      type: string
    included in data catalog:
      description: Repository or source which contains the records that were collected for this data collection.
      abstract: catalog containing the source of data for the work
      one of:
        $ref: #/definitions/catalog
      one of:
        type: array
      cardinality: one
    name:
      description: The name of the data collection.
      cardinality: one
      type: string
    url:
      description: URL of the source of the data collection.
      type: string
      format: uri
      cardinality: one
    collection size:
      description: The number of records data collection. Min/max estimates can be used in lieu of actual number. If completely unknown, set value = 0, and unitText = 'unknown'
      any of:
        type: array
      any of:
        $ref: #/definitions/propertyvalue
      any of:
        type: array
      any of:
        $ref: #/definitions/quantitativevalue
      cardinality: many
    funding:
      description: Funding that supports (sponsors) the creation of the records included in the data collection through some kind of financial contribution.
      abstract: funding source (grant, contract, etc.)
      one of: MonetaryGrant
        type: object
        description: Funding that supports (sponsors) the collection of this dataset through some kind of financial contribution
        required: funder
        required: identifier
      one of:
        type: array
        items: MonetaryGrant
      cardinality: many
    author:
      description: Author or creator of the records from which the data collection was derived.
      any of:
        type: array
      any of:
        $ref: #/definitions/person
      any of:
        type: array
      any of:
        $ref: #/definitions/organization
      cardinality: many
    citation:
      description: The primary citation or reference about the resource upon which the data collection was built. Examples: a publication which describes the source of the data collection. The original reference by the source of data collection by the creators/maintainers that should be cited when reusing the source of records included in the data collection. For other references to the source of the data collection, use 'citedBy'.
      abstract: citation to the work
      cardinality: many
      any of:
        type: array
      any of:
        $ref: #/definitions/citation
      any of:
        type: array
      any of:
        $ref: #/definitions/creativework
    conditions of access:
      description: Conditions that affect the availability of, or method(s) of access to the source records included in the data collection. Options include open (freely available), restricted (may include restrictions such as on use), closed (requires registration to access), or embargoed (unpublished).
      abstract: accessibility of the work
      type: string
      enum: Closed
      enum: Open
      enum: Restricted
      enum: Embargoed
      cardinality: one
    creator:
      description: The creator/author of the data collection itself. Author and creator are generally used interchangeably (with the default being author) for most classes in the NIAID Data Ecosystem; however, for Data Collections, it is the creator of the data collection, rather than the author of the records included in the data collection.
      any of:
        type: array
      any of:
        $ref: #/definitions/person
      any of:
        type: array
      any of:
        $ref: #/definitions/organization
      cardinality: many
    date created:
      description: The date on which the data collection itself (not the underlying source records) was created or when the item's entry was added to a DataFeed.
      format: date
      type: string
      cardinality: one
    date published:
      description: The date on which the data collection itself (not the underlying source records) was first published or when the item's entry was published within a DataFeed.
      format: date
      type: string
      cardinality: one
    example of work:
      description: A creative work (e.g. Data record) that this work (the Data Collection) is an example/instance/realization/derivation of. For example, a Data record from which this DataCollection was derived
      abstract: Metadata data about the record type included in the Data Collection.
      cardinality: many
      one of:
        type: array
      one of:
        $ref: #/definitions/examplework
    health condition:
      description: The infectious disease(s) / health condition(s) which are the focus of the data collection.
      abstract: health condition/disease
      any of:
        description: collection of vocabulary terms defined in ontologies
        strict: false
        type: string
      any of:
        type: array
      any of:
        type: array
      any of:
        $ref: #/definitions/definedterm
      cardinality: many
    infectious agent:
      description: Infectious agent(s) / pathogen(s) which are the focus of the data collection (like SARS-CoV-2).
      abstract: infectious agent / pathogen
      any of:
        description: collection of vocabulary terms defined in ontologies
        strict: false
        type: string
      any of:
        type: array
      any of:
        type: array
      any of:
        $ref: #/definitions/definedterm
      cardinality: many
    interaction statistic:
      description: The number of interactions with the work, such as page views or tool downloads.
      abstract: views or downloads
      one of:
        items: InteractionCounter
        type: array
      one of: InteractionCounter
        type: object
        required: interactionType
        required: userInteractionCount
      cardinality: many
    is based on:
      description: A resource from which this data collection is derived, modified, or adapted. This can include sources of the records in the data collection if the records in the data collection were grouped by their sources.
      abstract: resources used to create the data collection
      cardinality: many
      any of:
        type: array
      any of:
        $ref: #/definitions/citation
      any of:
        type: array
      any of:
        $ref: #/definitions/creativework
      any of:
        type: array
      any of:
        $ref: #/definitions/resourcecatalog
      any of:
        type: array
      any of:
        $ref: #/definitions/action
    license:
      description: A license document that applies to the source of the data collection, typically indicated by URL.
      abstract: license for use
      format: uri
      cardinality: one
      type: string
    measurement technique:
      description: A technique, method or technology used in the source data for the data collection corresponding to the method used for measuring the corresponding variable(s) (for the records in the data collection, described using variableMeasured; for Observation, a StatisticalVariable). For example, if variableMeasured is: molecule concentration, measurementTechnique could be: "mass spectrometry" or "nmr spectroscopy" or "colorimetry" or "immunofluorescence". If the variableMeasured is "depression rating", the measurementTechnique could be "Zung Scale" or "HAM-D" or "Beck Depression Inventory".
      abstract: measurement technique used to generate the records in the data collection.
      any of:
        description: collection of vocabulary terms defined in ontologies
        strict: false
        type: string
      cardinality: many
  required: about
  required: date
  required: dateModified
  required: description
  required: includedInDataCatalog
  required: name
  required: url
  required: collectionSize
  recommended: funding
  recommended: author
  recommended: citation
  recommended: conditionsOfAccess
  recommended: creator
  recommended: dateCreated
  recommended: datePublished
  recommended: exampleOfWork
  recommended: healthCondition
  recommended: infectiousAgent
  recommended: interactionStatistic
  recommended: isBasedOn
  recommended: license
  recommended: measurementTechnique
  recommended: sameAs
  recommended: spatialCoverage
  recommended: species
  recommended: temporalCoverage
  recommended: topicCategory
  recommended: usageInfo
  recommended: variableMeasured
  optional: aggregateRating
  optional: citedBy
  optional: creditText
  optional: hasPart
  optional: identifier
  optional: isAccessibleForFree
  optional: isBasisFor
  optional: isPartOf
  optional: isRelatedTo
  optional: isSimilarTo
  optional: keywords
  optional: sample
  optional: sdPublisher
  optional: sourceOrganization
  optional: version

citedBy
type: Property
comment: Publications that cite the dataset, resource/resource catalog or computational tool. Examples: a publication which reuses the dataset in a secondary analysis, a dataset which extends the existing dataset, or a computational tool which relies on the dataset.
domain includes: Dataset
domain includes: ComputationalTool
domain includes: ResourceCatalog
domain includes: Sample
domain includes: DataCollection
range includes: CreativeWork
range includes: ScholarlyArticle

date
type: Property
comment: Date the dataset, resource/resource catalog or computational tool has changed: most recent date of dateModified, datePublished, and dateCreated.
domain includes: Dataset
domain includes: ComputationalTool
domain includes: ResourceCatalog
domain includes: Sample
domain includes: DataCollection
range includes: Date

doi
type: Property
comment: Digital object identifier (DOI) for the dataset, resource/resource catalog or computational tool.
domain includes: Dataset
domain includes: ComputationalTool
domain includes: ResourceCatalog
range includes: Text

includedInDataCatalog
type: Property
comment: Repository or source which contains the dataset, resource/resource catalog or computational tool.
domain includes: Dataset
domain includes: ComputationalTool
domain includes: ResourceCatalog
domain includes: Sample
domain includes: SampleCollection
domain includes: DataCollection
range includes: DataCatalog
range includes: ResourceCatalog

isBasisFor
type: Property
comment: Dataset, resource/resource catalog or computational tool which incorporate this dataset, resource/resource catalog or computational tool.
domain includes: Dataset
domain includes: ComputationalTool
domain includes: ResourceCatalog
domain includes: Sample
domain includes: DataCollection
range includes: Dataset
range includes: ComputationalTool
range includes: ResourceCatalog
range includes: Sample
range includes: SampleCollection
range includes: CreativeWork
range includes: ScholarlyArticle
range includes: DataCollection

isRelatedTo
type: Property
comment: Dataset, resource/resource catalog or computational tool which are related to the given dataset, resource/resource catalog or computational tool.
domain includes: Dataset
domain includes: ComputationalTool
domain includes: ResourceCatalog
domain includes: Sample
domain includes: DataCollection
range includes: Dataset
range includes: ComputationalTool
range includes: ResourceCatalog
range includes: Sample
range includes: SampleCollection
range includes: CreativeWork
range includes: ScholarlyArticle
range includes: DataCollection

isSimilarTo
type: Property
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.
domain includes: Dataset
domain includes: ComputationalTool
domain includes: ResourceCatalog
domain includes: Sample
domain includes: DataCollection
range includes: Dataset
range includes: ComputationalTool
range includes: ResourceCatalog
range includes: Sample
range includes: SampleCollection
range includes: CreativeWork
range includes: ScholarlyArticle
range includes: DataCollection

nctid
type: Property
comment: ClinicalTrials.gov identifier associated with the Dataset.
domain includes: Dataset
range includes: Text

relationship
type: Property
comment: How an associated work is related to the dataset, resource/resource catalog.
domain includes: Dataset
domain includes: ResourceCatalog
range includes: Text

topicCategory
type: Property
comment: Topic of the dataset, resource/resource catalog or computational tool. This topic may be assigned by a human curator or through automated algorithms.
domain includes: Dataset
domain includes: ComputationalTool
domain includes: ResourceCatalog
domain includes: Sample
domain includes: DataCollection
range includes: Text
range includes: DefinedTerm

collectionType
type: Property
comment: The type of resource/resource catalog that best describes the work.
domain includes: ResourceCatalog
range includes: Text
range includes: DefinedTerm

collectionSize
type: Property
comment: The number of records, datasets, tools, items, pages, etc. in the resource/resource catalog.
domain includes: ResourceCatalog
domain includes: DataCollection
range includes: PropertyValue
range includes: QuantitativeValue

hasDownload
type: Property
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).
domain includes: ResourceCatalog
range includes: Text
range includes: Enumeration

hasAPI
type: Property
comment: The resource/resource catalog provides API access to its content.
domain includes: ResourceCatalog
range includes: Boolean

infectiousAgent
type: Property
comment: Infectious agent(s) / pathogen(s) which are the focus of the dataset, resource/resource catalog or computational tool (e.g. SARS-CoV-2).
domain includes: Dataset
domain includes: ComputationalTool
domain includes: ResourceCatalog
domain includes: Sample
domain includes: DataCollection
range includes: Text
range includes: DefinedTerm

healthCondition
type: Property
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).
domain includes: Dataset
domain includes: ComputationalTool
domain includes: ResourceCatalog
domain includes: Sample
domain includes: DataCollection
range includes: Text
range includes: DefinedTerm

funding
type: Property
comment: Funding that supports (sponsors) the collection of a dataset, resource/resource catalog or computational tool through some kind of financial contribution.
domain includes: Dataset
domain includes: ComputationalTool
domain includes: ResourceCatalog
domain includes: Sample
domain includes: DataCollection
range includes: MonetaryGrant

distribution
type: Property
comment: A downloadable form of the dataset, resource/resource catalog, at a specific location, in a specific format.
domain includes: Dataset
domain includes: ResourceCatalog
domain includes: Sample
range includes: DataDownload

species
type: Property
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.
domain includes: Dataset
domain includes: ComputationalTool
domain includes: ResourceCatalog
domain includes: Sample
domain includes: DataCollection
range includes: Text
range includes: DefinedTerm

measurementTechnique
type: Property
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".
domain includes: Dataset
domain includes: ComputationalTool
domain includes: ResourceCatalog
domain includes: Sample
domain includes: DataCollection
range includes: Text
range includes: DefinedTerm

variableMeasured
type: Property
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.
domain includes: Dataset
domain includes: ComputationalTool
domain includes: ResourceCatalog
domain includes: Sample
domain includes: DataCollection
range includes: Text
range includes: DefinedTerm

curatedBy
type: Property
comment: The curator who generated the metadata annotation.
domain includes: DefinedTerm
range includes: Person
range includes: Organization
range includes: DataCatalog
range includes: ResourceCatalog
range includes: SoftwareApplication
range includes: ComputationalTool
range includes: ResearchProject

originalName
type: Property
comment: The original name or term that was provided in the metadata.
domain includes: DefinedTerm
range includes: Text

isCurated
type: Property
comment: A boolean indicating whether or not a Defined Term was curated by an annotator (true) or programmatically generated (false).
domain includes: DefinedTerm
range includes: Boolean

sourceOrganization
type: Property
comment: The organization, research project, working group, or funded program on whose behalf the author/creator was working.
domain includes: Dataset
domain includes: ComputationalTool
domain includes: ResourceCatalog
domain includes: Sample
domain includes: DataCollection
range includes: ResearchProject
range includes: Organization

archivedAt
type: Property
comment: The url of a dataset, tool, resource or other item listed in a DataCatalog or ResourceCatalog.
domain includes: DataCatalog
domain includes: ResourceCatalog
range includes: URL

associatedPhenotype
type: Property
comment: one or more observable traits or conditions relevant to the source of the sample.
domain includes: Sample
range includes: Text
range includes: URL
range includes: DefinedTerm

associatedGenotype
type: Property
comment: One or more genetic variants or molecular features observed or inferred from the sample.
domain includes: Sample
range includes: Text
range includes: URL
range includes: DefinedTerm

cellType
type: Property
comment: The type of cell represented in or derived from the biological sample, based on morphology, lineage, or molecular markers.
domain includes: Sample
domain includes: SampleCollection
range includes: Text
range includes: URL
range includes: DefinedTerm

sample
type: Property
comment: The sample(s) which were used to generate the dataset or sample collection
domain includes: Dataset
range includes: Sample
range includes: SampleCollection
range includes: URL

additionalProperty
type: Property
comment: Other properties listed in the item metadata record.
domain includes: Sample
domain includes: CreativeWork
range includes: PropertyValue

$ref: #/definitions/citation

$ref: #/definitions/creativework

$ref: #/definitions/citation

$ref: #/definitions/creativework

$ref: #/definitions/citation

$ref: #/definitions/creativework

$ref: #/definitions/citation

$ref: #/definitions/creativework

$ref: #/definitions/topic

$ref: #/definitions/definedterm

children of: http://purl.obolibrary.org/obo/NCBITaxon_10239
children of: http://purl.obolibrary.org/obo/NCBITaxon_2
ontology: ncbitaxon

description: collection of vocabulary terms defined in ontologies
strict: false
type: string
vocabulary:
  children of: http://purl.obolibrary.org/obo/NCBITaxon_10239
  children of: http://purl.obolibrary.org/obo/NCBITaxon_2
  ontology: ncbitaxon

$ref: #/definitions/definedterm

children of: http://purl.obolibrary.org/obo/MONDO_0000001
children of: http://purl.obolibrary.org/obo/DOID_4
children of: http://purl.obolibrary.org/obo/HP_0000001
children of: http://purl.obolibrary.org/obo/NCIT_C7057
ontology: mondo
ontology: hpo
ontology: doid
ontology: ncit

description: collection of vocabulary terms defined in ontologies
strict: false
type: string
vocabulary:
  children of: http://purl.obolibrary.org/obo/MONDO_0000001
  children of: http://purl.obolibrary.org/obo/DOID_4
  children of: http://purl.obolibrary.org/obo/HP_0000001
  children of: http://purl.obolibrary.org/obo/NCIT_C7057
  ontology: mondo
  ontology: hpo
  ontology: doid
  ontology: ncit

$ref: #/definitions/definedterm

funder:
  description: An organization associated with a creator or funder of a dataset
  one of: Organization
    type: object
    description: Information about a single funder
    properties:
      name:
        type: string
        description: An organization associated with a creator or funder of a dataset
      parent organization:
        type: string
        description: name of the parent funding organization
    required: name
  one of:
    type: array
    items: Organization
      type: object
      description: Information about a single funder
      required: name
description:
  type: string
  description: description about the funding award / grant
url:
  type: string
  description: award / grant URL
identifier:
  type: string
  description: Unique identifier(s) for the grant(s) used to fund the Dataset

type: string
description: An organization associated with a creator or funder of a dataset

type: string
description: name of the parent funding organization

MonetaryGrant
type: object
description: Funding that supports (sponsors) the collection of this dataset through some kind of financial contribution
properties:
  funder:
    description: An organization associated with a creator or funder of a dataset
    one of: Organization
      type: object
      description: Information about a single funder
      required: name
    one of:
      type: array
      items: Organization
        type: object
        description: Information about a single funder
        required: name
  description:
    type: string
    description: description about the funding award / grant
  url:
    type: string
    description: award / grant URL
  identifier:
    type: string
    description: Unique identifier(s) for the grant(s) used to fund the Dataset
required: funder
required: identifier

type: string
description: An organization associated with a creator or funder of a dataset

type: string
description: name of the parent funding organization

name:
  type: string
  description: An organization associated with a creator or funder of a dataset
parent organization:
  type: string
  description: name of the parent funding organization

children of: http://purl.obolibrary.org/obo/NCBITaxon_131567
children of: http://purl.obolibrary.org/obo/NCBITaxon_10239
ontology: ncbitaxon

description: collection of vocabulary terms defined in ontologies
strict: false
type: string
vocabulary:
  children of: http://purl.obolibrary.org/obo/NCBITaxon_131567
  children of: http://purl.obolibrary.org/obo/NCBITaxon_10239
  ontology: ncbitaxon

$ref: #/definitions/definedterm

DataDownload
description: A dataset in downloadable form.
properties:
  content url:
    format: uri
    type: string
  encoding format:
    description: file type (ex: XLSX)
    type: string
  date modified:
    format: date
    description: date the file was modified
    type: string
required: dateModified
required: contentUrl
type: object

content url:
  format: uri
  type: string
encoding format:
  description: file type (ex: XLSX)
  type: string
date modified:
  format: date
  description: date the file was modified
  type: string

$ref: #/definitions/catalog

children of: http://edamontology.org/topic_3361
children of: http://purl.obolibrary.org/obo/NCIT_C20368
children of: http://purl.obolibrary.org/obo/MMO_0000000
children of: http://www.ebi.ac.uk/efo/EFO_0000001
ontology: edam
ontology: ncit
ontology: mmo
ontology: efo

description: collection of vocabulary terms defined in ontologies
strict: false
type: string
vocabulary:
  children of: http://edamontology.org/topic_3361
  children of: http://purl.obolibrary.org/obo/NCIT_C20368
  children of: http://purl.obolibrary.org/obo/MMO_0000000
  children of: http://www.ebi.ac.uk/efo/EFO_0000001
  ontology: edam
  ontology: ncit
  ontology: mmo
  ontology: efo

$ref: #/definitions/definedterm

children of: http://www.ebi.ac.uk/efo/EFO_0000001
children of: http://purl.obolibrary.org/obo/CMO_0000000
children of: http://purl.obolibrary.org/obo/NCIT_C25209
ontology: efo
ontology: cmo
ontology: ncit

description: collection of vocabulary terms defined in ontologies
strict: false
type: string
vocabulary:
  children of: http://www.ebi.ac.uk/efo/EFO_0000001
  children of: http://purl.obolibrary.org/obo/CMO_0000000
  children of: http://purl.obolibrary.org/obo/NCIT_C25209
  ontology: efo
  ontology: cmo
  ontology: ncit

$ref: #/definitions/definedterm

AggregateRating
type: object
properties:
  rating count:
    description: Total number of ratings
    type: integer
  rating value:
    description: Average rating
    type: string
  item reviewed:
    description: What is being reviewed
    type: string
required: ratingValue
recommended: ratingCount
recommended: itemReviewed

rating count:
  description: Total number of ratings
  type: integer
rating value:
  description: Average rating
  type: string
item reviewed:
  description: What is being reviewed
  type: string

description: Author or creator of the work. The default field for the author or creator of the work.
any of:
  type: array
  items:
    $ref: #/definitions/person
any of:
  $ref: #/definitions/person
any of:
  type: array
  items:
    $ref: #/definitions/organization
any of:
  $ref: #/definitions/organization
cardinality: many

description: The primary citation or reference about the dataset. Examples: a publication which describes the creation of the dataset. The original reference by the dataset creators/maintainers that should be cited when reusing the dataset. For other references to the dataset, use 'citedBy'.
abstract: citation to the work
cardinality: many
any of:
  type: array
  items:
    $ref: #/definitions/citation
any of:
  $ref: #/definitions/citation
any of:
  type: array
  items:
    $ref: #/definitions/creativework
any of:
  $ref: #/definitions/creativework

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
enum: Open
enum: Restricted
enum: Embargoed
cardinality: one

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.
any of:
  type: array
  items:
    $ref: #/definitions/person
any of:
  $ref: #/definitions/person
any of:
  type: array
  items:
    $ref: #/definitions/organization
any of:
  $ref: #/definitions/organization
cardinality: many

description: Date the work was created.
format: date
type: string
cardinality: one

description: Date the work was modified.
format: date
type: string
cardinality: one

description: Date the work was first published.
format: date
type: string
cardinality: one

description: Associated materials for the dataset, including data dictionaries and data limitation descriptions.
abstract: data limitations or dictionaries
any of:
  type: array
  items:
    $ref: #/definitions/citation
any of:
  $ref: #/definitions/citation
any of:
  type: array
  items:
    $ref: #/definitions/creativework
any of:
  $ref: #/definitions/creativework
cardinality: many

description: The language of the content of the dataset.
cardinality: many
one of:
  items:
    type: object
    properties:
      name:
        type: string
        description: language of the work
      alternate name:
        type: string
    required: name
    recommended: alternateName
  type: array
one of:
  type: object
  properties:
    name:
      type: string
      description: language of the work
    alternate name:
      type: string
  required: name
  recommended: alternateName

description: The number of interactions with the work, such as page views or tool downloads.
abstract: views or downloads
one of:
  items: InteractionCounter
    type: object
    properties:
      interaction type:
        type: string
      user interaction count:
        type: integer
    required: interactionType
    required: userInteractionCount
  type: array
one of: InteractionCounter
  type: object
  properties:
    interaction type:
      type: string
    user interaction count:
      type: integer
  required: interactionType
  required: userInteractionCount
cardinality: many

description: A flag to signal that the work is accessible for free.
abstract: accessible without charge
type: boolean
cardinality: one

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
cardinality: many
any of:
  type: array
  items:
    $ref: #/definitions/citation
any of:
  $ref: #/definitions/citation
any of:
  type: array
  items:
    $ref: #/definitions/creativework
any of:
  $ref: #/definitions/creativework

description: Indicates a broader study, project, or collection the work is part of.
abstract: study or project including the work
cardinality: many
any of:
  type: array
  items:
    $ref: #/definitions/citation
any of:
  $ref: #/definitions/citation
any of:
  type: array
  items:
    $ref: #/definitions/creativework
any of:
  $ref: #/definitions/creativework

description: Keywords or tags used to describe this work.
abstract: keywords or tags
one of:
  type: array
  items:
    type: string
one of:
  type: string
cardinality: many

description: A license document that applies to this work, typically indicated by URL.
abstract: license for use
format: uri
cardinality: one
type: string

description: Original publisher of the dataset metadata (like GenBank, ImmPort, etc.).
abstract: original metadata source
one of:
  $ref: #/definitions/catalog
one of:
  type: array
  items:
    $ref: #/definitions/catalog
cardinality: many

description: The place(s) which are the focus of the dataset.
abstract: geographic focus of the work
one of:
  items: AdministrativeArea
    description: Location information
    properties:
      administrative type:
        description: the type of administrative area, such as country, state, county, or city
        enum: province
        enum: district
        enum: chiefdom
        enum: village
        enum: city
        enum: country
        enum: prefecture
        enum: sub-prefecture
        enum: clan
        enum: Federal Capital Territory
        enum: state
        enum: Local Government Area
        enum: ward
        type: string
      alternate name:
        description: An alias for the location
      identifier:
        description: An identifier for the location, preferably a Wikidata ID
        type: string
      location type:
        description: Categorization of how the location relates to the dataset
      name:
        description: The name of the location
        type: string
    type: object
  type: array
one of: AdministrativeArea
  description: Location information
  properties:
    administrative type:
      description: the type of administrative area, such as country, state, county, or city
      enum: province
      enum: district
      enum: chiefdom
      enum: village
      enum: city
      enum: country
      enum: prefecture
      enum: sub-prefecture
      enum: clan
      enum: Federal Capital Territory
      enum: state
      enum: Local Government Area
      enum: ward
      type: string
    alternate name:
      description: An alias for the location
      one of:
        type: string
      one of:
        type: array
    identifier:
      description: An identifier for the location, preferably a Wikidata ID
      type: string
    location type:
      description: Categorization of how the location relates to the dataset
      one of:
        enum: residence
        enum: exposure
        enum: collection
        enum: screening
        enum: treatment
        enum: study location
        enum: other
        enum: unknown
        type: string
      one of:
        type: array
    name:
      description: The name of the location
      type: string
  type: object
cardinality: many

type: string

items:
  type: string
type: array

enum: residence
enum: exposure
enum: collection
enum: screening
enum: treatment
enum: study location
enum: other
enum: unknown
type: string

items:
  enum: residence
  enum: exposure
  enum: collection
  enum: screening
  enum: treatment
  enum: study location
  enum: other
  enum: unknown
  type: string
type: array

type: string

enum: residence
enum: exposure
enum: collection
enum: screening
enum: treatment
enum: study location
enum: other
enum: unknown
type: string

description: The period of time covered within the dataset.
abstract: time period
one of:
  items: TemporalInterval
    description: Temporal information
    properties:
      duration:
        description: A time interval in ISO 8601 duration format
        type: string
      end date:
        description: An end date
        format: date
        type: string
      name:
        description: String describing the temporal interval
        type: string
      start date:
        description: A start date
        format: date
        type: string
      temporal type:
        description: Categorization of how the date/temporal interval relates to the dataset
    type: object
  type: array
one of: TemporalInterval
  description: Temporal information
  properties:
    duration:
      description: A time interval in ISO 8601 duration format
      type: string
    end date:
      description: An end date
      format: date
      type: string
    name:
      description: String describing the temporal interval
      type: string
    start date:
      description: A start date
      format: date
      type: string
    temporal type:
      description: Categorization of how the date/temporal interval relates to the dataset
      one of:
        enum: exposure
        enum: collection
        enum: screening
        enum: treatment
        enum: study date
        enum: other
        enum: unknown
        type: string
      one of:
        type: array
  type: object
cardinality: many

enum: exposure
enum: collection
enum: screening
enum: treatment
enum: study date
enum: other
enum: unknown
type: string

items:
  enum: exposure
  enum: collection
  enum: screening
  enum: treatment
  enum: study date
  enum: other
  enum: unknown
  type: string
type: array

enum: exposure
enum: collection
enum: screening
enum: treatment
enum: study date
enum: other
enum: unknown
type: string

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
one of:
  type: array
  items:
    $ref: #/definitions/creativework
one of:
  $ref: #/definitions/creativework
cardinality: many

description: Dataset version.
type: string
cardinality: one

description: An alias for the dataset name.
one of:
  type: string
one of:
  type: array
  items:
    type: string
cardinality: many

description: A description of the dataset.
cardinality: one
type: string

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
one of:
  type: string
one of:
  items:
    type: string
  type: array
cardinality: many

description: Website which describes the work and provides additional details.
abstract: associated webpage
one of:
  items:
    type: string
    format: uri
  type: array
one of:
  type: string
  format: uri
cardinality: many

description: Dataset name.
cardinality: one
type: string

description: URL of additional sources for the work.
one of:
  items:
    type: string
    format: uri
  type: array
one of:
  type: string
  format: uri
cardinality: many

description: URL of the work.
type: string
format: uri
cardinality: one

description: The organization, research project, working group, or funded program on whose behalf the author/creator was working.
any of:
  type: array
  items:
    $ref: #/definitions/researchproject
any of:
  $ref: #/definitions/researchproject
any of:
  type: array
  items:
    $ref: #/definitions/organization
any of:
  $ref: #/definitions/organization
cardinality: many

description: the samples used to generate the dataset
any of:
  type: array
  items:
    $ref: #/definitions/samplerecord
any of:
  $ref: #/definitions/samplerecord
any of:
  type: string
  format: uri
any of:
  type: array
  items:
    type: string
    format: uri
any of:
  type: array
  items:
    $ref: #/definitions/samplecollection
any of:
  $ref: #/definitions/samplecollection
cardinality: many

description: Text that can be used to credit person(s) and/or organization(s) associated with a published Creative Work. For example, how a user should cite the dataset.
type: string
cardinality: one

citation: ScholarlyArticle
  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: object
  properties:
    author:
      description: Author(s) of the publication
      any of:
        type: array
      any of:
        $ref: #/definitions/person
      any of:
        type: array
      any of:
        $ref: #/definitions/organization
    abstract:
      description: Abstract of the publication
      type: string
    date published:
      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
    issue number:
      description: Issue number where the article appears
      type: string
    journal name:
      description: Journal where the article appears
      type: string
    journal name abbrev:
      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
    volume number:
      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
  recommended: datePublished
  recommended: doi
  recommended: identifier
  recommended: journalName
  recommended: pmid
  recommended: url
  optional: abstract
  optional: citation
  optional: description
  optional: issueNumber
  optional: journalNameAbbrev
  optional: pagination
  optional: volumeNumber
creativework: CreativeWork
  description: A resource
  type: object
  properties:
    author:
      description: Author(s) of the referenced work
      any of:
        type: array
      any of:
        $ref: #/definitions/person
      any of:
        type: array
      any of:
        $ref: #/definitions/organization
    abstract:
      description: Abstract of the referenced work
      type: string
    date published:
      description: Date the referenced work was published
      format: date
      type: string
    description:
      description: Description of the referenced work
      type: string
    has part:
      description: A portion of the work
      one of:
        $ref: #/definitions/citation
    included in data catalog:
      description: Data or tool catalog which houses the work
      one of:
        $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
  recommended: datePublished
  recommended: doi
  recommended: identifier
  recommended: includedInDataCatalog
  recommended: relationship
  recommended: url
  optional: abstract
  optional: citation
  optional: description
  optional: hasPart
topic:
  description: Topic assigned to the work.
  type: string
  vocabulary:
    ontology: edam
    children of: http://edamontology.org/topic_0003
  strict: true
catalog: 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
    version date:
      description: date the metadata was harvested from the catalog
      type: string
      format: date
    archived at:
      description: The url(s) of one or more datasets, tools, resources or other items listed in a DataCatalog or ResourceCatalog
      one of:
        type: array
      one of:
        type: string
        format: uri
  required: name
  required: url
  recommended: versionDate
  recommended: archivedAt
organization: Organization
  description: Reusable organization definition
  properties:
    affiliation:
      type: object
      required: name
      optional: sameAs
      optional: url
    alternate name:
      description: Alias of the name
      one of:
        type: array
      one of:
        type: string
    name:
      description: Name of the organization
      type: string
    parent organization:
      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
  optional: alternateName
  optional: email
  optional: parentOrganization
  optional: role
  optional: url
  type: object
researchproject: ResearchProject
person: Person
definedterm: DefinedTerm
softwareapplication: SoftwareApplication
samplerecord: Sample
samplecollection: SampleCollection
minsampleinfo: Sample
quantitativevalue: QuantitativeValue
propertyvalue: PropertyValue

$ref: #/definitions/person

$ref: #/definitions/organization

$ref: #/definitions/person

$ref: #/definitions/organization

type: string
format: uri

description: Name of the affiliation, such as a university
type: string

description: Alias for the affiliation
type: string

description: URL of the affiliation
type: string
format: uri

type: string

ResearchProject
description: a type of organization definition
properties:
  alternate name:
    description: Alias of the name
    one of:
      type: array
      items:
        type: string
    one of:
      type: string
  name:
    description: Name of the organization
    type: string
  parent organization:
    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
recommended: url
recommended: parentOrganization
optional: alternateName
optional: email
optional: role
type: object

Person
description: Reusable person definition
properties:
  affiliation:
    type: object
    properties:
      name:
        description: Name of the affiliation, such as a university
        type: string
      same as:
        description: Alias for the affiliation
        type: string
      url:
        description: URL of the affiliation
        type: string
        format: uri
    required: name
    optional: sameAs
    optional: url
  name:
    description: Name of the person
    type: string
  email:
    description: Email address of the person
    type: string
  family name:
    description: Family name (surname) of the person
    type: string
  given name:
    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
recommended: givenName
recommended: identifier
optional: affiliation
optional: email
optional: role
optional: title
optional: url
type: object

DefinedTerm
type: object
properties:
  name:
    description: The name of the item.
    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.
    cardinality: one
    type: string
  url:
    description: URL of the item.
    cardinality: one
    type: string
    format: uri
  curated by:
    description: The person, organization, or catalog that curated this DefinedTerm for the metadata property
    any of:
      $ref: #/definitions/person
    any of:
      $ref: #/definitions/organization
    any of:
      $ref: #/definitions/catalog
    any of:
      $ref: #/definitions/researchproject
    any of:
      $ref: #/definitions/softwareapplication
  term code:
    description: A code that identifies this DefinedTerm within a DefinedTermSet.
    type: string
  description:
    description: A description of the item.
    type: string
  in defined term set:
    description: A DefinedTermSet that contains this term.
    type: string
  original name:
    description: The original name of the item, before any metadata standardization/normalization
    type: string
  is curated:
    description: A boolean indicator describing whether or not this DefinedTerm was curated as the value of a property.
    type: boolean

SoftwareApplication
description: Reusable software or algorithm definition
properties:
  name:
    description: name of the software, computational tool, or algorithm.
    type: string
  date modified:
    description: date the software, computational tool, or algorithm was run
    type: string
    format: date
  url:
    description: url of the software, computational tool, or algorithm
    type: string
    format: uri
required: name
recommended: url
optional: dateModified
type: object

Sample
description: reusable sample object
type: object
properties:
  url:
    description: Link to sample
    type: string
    format: uri
  identifier:
    description: an identifier for the sample
    type: string
  included in data catalog:
    description: Data or resource catalog where the sample is listed
    one of:
      $ref: #/definitions/catalog
    one of:
      type: array
      items:
        $ref: #/definitions/catalog
  associated phenotype:
    description: one or more observable traits or conditions relevant to the source of the sample.
    any of:
      description: collection of vocabulary terms defined in ontologies
      strict: false
      type: string
      vocabulary:
        children of: http://purl.obolibrary.org/obo/UPHENO_0001001
        children of: http://purl.obolibrary.org/obo/PATO_0000001
        ontology: UPHENO
        ontology: PATO
    any of:
      items:
        description: collection of vocabulary terms defined in ontologies
        strict: false
        type: string
      type: array
    any of:
      type: array
      items:
        $ref: #/definitions/definedterm
    any of:
      $ref: #/definitions/definedterm
    cardinality: many
  associated genotype:
    description: One or more genetic variants or molecular features observed or inferred from the sample.
    any of:
      description: collection of vocabulary terms defined in ontologies
      strict: false
      type: string
      vocabulary:
        children of: http://purl.obolibrary.org/obo/NCIT_C16612
        children of: http://purl.obolibrary.org/obo/NCIT_C20181
        children of: http://purl.obolibrary.org/obo/NCIT_C17649
        ontology: NCIT
    any of:
      items:
        description: collection of vocabulary terms defined in ontologies
        strict: false
        type: string
      type: array
    any of:
      type: array
      items:
        $ref: #/definitions/definedterm
    any of:
      $ref: #/definitions/definedterm
    cardinality: many
  cell type:
    description: The type of cell represented in or derived from the biological sample, based on morphology, lineage, or molecular markers.
    any of:
      description: collection of vocabulary terms defined in ontologies
      strict: false
      type: string
      vocabulary:
        children of: http://purl.obolibrary.org/obo/CL_0000000
        children of: http://purl.obolibrary.org/obo/CLO_0000031
        ontology: CL
        ontology: CLO
    any of:
      items:
        description: collection of vocabulary terms defined in ontologies
        strict: false
        type: string
      type: array
    any of:
      type: array
      items:
        $ref: #/definitions/definedterm
    any of:
      $ref: #/definitions/definedterm
    cardinality: many
  anatomical system:
    description: Indicate the anatomical system from which the sample is collect, e.g. circulatory, digestive, endocrine, immune and other systems.
    any of:
      description: collection of vocabulary terms defined in ontologies
      strict: false
      type: string
      vocabulary:
        children of: http://purl.obolibrary.org/obo/UBERON_0000467
        ontology: UBERON
    any of:
      items:
        description: collection of vocabulary terms defined in ontologies
        strict: false
        type: string
      type: array
    any of:
      type: array
      items:
        $ref: #/definitions/definedterm
    any of:
      $ref: #/definitions/definedterm
    cardinality: many
  anatomical structure:
    description: Indicate the organ, tissues the sample was collected from.
    any of:
      description: collection of vocabulary terms defined in ontologies
      strict: false
      type: string
      vocabulary:
        children of: http://purl.obolibrary.org/obo/UBERON_0001062
        ontology: UBERON
    any of:
      items:
        description: collection of vocabulary terms defined in ontologies
        strict: false
        type: string
      type: array
    any of:
      type: array
      items:
        $ref: #/definitions/definedterm
    any of:
      $ref: #/definitions/definedterm
    cardinality: many
  sex:
    description: The biological sex of the individual from which the sample was obtained.
    any of:
      description: collection of vocabulary terms defined in ontologies
      strict: false
      type: string
      vocabulary:
        children of: http://purl.obolibrary.org/obo/PATO_0000047
        ontology: PATO
    any of:
      items:
        description: collection of vocabulary terms defined in ontologies
        strict: false
        type: string
      type: array
    any of:
      type: array
      items:
        $ref: #/definitions/definedterm
    any of:
      $ref: #/definitions/definedterm
    cardinality: many
  developmental stage:
    description: A temporal subdivision of a developmental process, indicating the age or stage of the object when the sample was created.
    any of:
      description: collection of vocabulary terms defined in ontologies
      strict: false
      type: string
      vocabulary:
        children of: http://purl.obolibrary.org/obo/UBERON_0000104
        children of: http://purl.obolibrary.org/obo/NCIT_C48308
        ontology: UBERON
        ontology: NCIT
    any of:
      items:
        description: collection of vocabulary terms defined in ontologies
        strict: false
        type: string
      type: array
    any of:
      type: array
      items:
        $ref: #/definitions/definedterm
    any of:
      $ref: #/definitions/definedterm
    any of:
      type: array
      items:
        $ref: #/definitions/quantitativevalue
    any of:
      $ref: #/definitions/quantitativevalue
    cardinality: many
  sample availability:
    description: A flag to signal that the sample is available for reuse.
    abstract: availability of the sample
    type: boolean
    cardinality: one
  sample quantity:
    description: A numeric value for a measurement of the size of a sample. If completely unknown, set value = 0, and unitText = 'unknown'
    one of:
      type: array
      items:
        $ref: #/definitions/quantitativevalue
    one of:
      $ref: #/definitions/quantitativevalue
    cardinality: many
  sample type:
    description: The type of sample or specimen.
    cardinality: many
recommended: url
recommended: identifier
recommended: includedInDataCatalog
recommended: associatedPhenotype
recommended: associatedGenotype
recommended: cellType
recommended: sampleType
recommended: anatomicalSystem
recommended: anatomicalStructure
recommended: sex
recommended: developmentalStage
recommended: sampleAvailability
recommended: sampleQuantity

children of: http://purl.obolibrary.org/obo/UPHENO_0001001
children of: http://purl.obolibrary.org/obo/PATO_0000001
ontology: UPHENO
ontology: PATO

children of: http://purl.obolibrary.org/obo/NCIT_C16612
children of: http://purl.obolibrary.org/obo/NCIT_C20181
children of: http://purl.obolibrary.org/obo/NCIT_C17649
ontology: NCIT

children of: http://purl.obolibrary.org/obo/CL_0000000
children of: http://purl.obolibrary.org/obo/CLO_0000031
ontology: CL
ontology: CLO

children of: http://purl.obolibrary.org/obo/UBERON_0000467
ontology: UBERON

children of: http://purl.obolibrary.org/obo/UBERON_0001062
ontology: UBERON

children of: http://purl.obolibrary.org/obo/PATO_0000047
ontology: PATO

children of: http://purl.obolibrary.org/obo/UBERON_0000104
children of: http://purl.obolibrary.org/obo/NCIT_C48308
ontology: UBERON
ontology: NCIT

description: collection of vocabulary terms defined in ontologies
strict: false
type: string
vocabulary:
  children of: http://purl.obolibrary.org/obo/BFO_0000040
  ontology: OBI

items:
  description: collection of vocabulary terms defined in ontologies
  strict: false
  type: string
  vocabulary:
    children of: http://purl.obolibrary.org/obo/BFO_0000040
    ontology: OBI
type: array

type: array
items:
  $ref: #/definitions/definedterm

$ref: #/definitions/definedterm

SampleCollection
description: reusable sampleCollection object
type: object
properties:
  url:
    description: Link to sample
    type: string
    format: uri
  identifier:
    description: an identifier for the sample
    type: string
  included in data catalog:
    description: Data or resource catalog where the sample is listed
    one of:
      $ref: #/definitions/catalog
    one of:
      type: array
      items:
        $ref: #/definitions/catalog
  aggregate element:
    description: Aggregate information about the samples in the Sample Collection formatted as a sample object.
    one of:
      $ref: #/definitions/samplerecord
    one of:
      type: array
      items:
        $ref: #/definitions/samplerecord
  item list element:
    description: Samples listed in the sample collection
    one of:
      $ref: #/definitions/minsampleinfo
    one of:
      type: array
      items:
        $ref: #/definitions/minsampleinfo
  number of items:
    description: The number of sample records in the sample collection. Min/max estimates can be used in lieu of actual number. If completely unknown, set value = 0, and unitText = 'unknown'
    any of:
      type: array
      items:
        $ref: #/definitions/propertyvalue
    any of:
      $ref: #/definitions/propertyvalue
    any of:
      type: array
      items:
        $ref: #/definitions/quantitativevalue
    any of:
      $ref: #/definitions/quantitativevalue
    cardinality: many
recommended: url
recommended: identifier
recommended: includedInDataCatalog
recommended: aggregateElement
recommended: itemListElement
recommended: numberOfItems

Sample
description: reusable sample object
type: object
properties:
  url:
    description: Link to sample
    type: string
    format: uri
  identifier:
    description: an identifier for the sample
    type: string
  included in data catalog:
    description: Data or resource catalog where the sample is listed
    one of:
      $ref: #/definitions/catalog
    one of:
      type: array
      items:
        $ref: #/definitions/catalog
recommended: url
recommended: identifier
recommended: includedInDataCatalog

QuantitativeValue
description: A numeric value and unit for a property with potentially different units
type: object
properties:
  value:
    description: A numeric value for the property
    type: number
  max value:
    description: An estimated maximum numberic value if the actual value is not known. Ignore if actual numeric value is known.
    type: number
  min value:
    description: An estimated minumum numeric value if the actual value is not known. Ignore if actual numeric value is known.
    type: number
  unit text:
    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
optional: minValue

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
  max value:
    description: An estimated maximum numberic value if the actual value is not known. Ignore if actual numeric value is known.
    type: number
  min value:
    description: An estimated minumum numeric value if the actual value is not known. Ignore if actual numeric value is known.
    type: number
  unit text:
    description: A unit associated with the value. E.g.- 'records' for the number of records in a database.
    type: string
  property ID:
    description: A commonly used identifier for the characteristic represented by the property, e.g. a manufacturer or a standard code for a property. propertyID can be (1) a prefixed string, mainly meant to be used with standards for product properties; (2) a site-specific, non-prefixed string (e.g. the primary key of the property or the vendor-specific ID of the property), or (3) a URL indicating the type of the property, either pointing to an external vocabulary, or a Web resource that describes the property (e.g. a glossary entry). Standards bodies should promote a standard prefix for the identifiers of properties from their standards.
    one of:
      type: string
    one of:
      type: string
      format: uri
required: unitText
recommended: value
recommended: propertyID
optional: maxValue
optional: minValue

$ref: #/definitions/citation

$ref: #/definitions/creativework

$ref: #/definitions/citation

$ref: #/definitions/creativework

$ref: #/definitions/citation

$ref: #/definitions/creativework

$ref: #/definitions/citation

$ref: #/definitions/creativework

$ref: #/definitions/topic

$ref: #/definitions/definedterm

children of: http://purl.obolibrary.org/obo/NCBITaxon_10239
children of: http://purl.obolibrary.org/obo/NCBITaxon_2
ontology: ncbitaxon

description: collection of vocabulary terms defined in ontologies
strict: false
type: string
vocabulary:
  children of: http://purl.obolibrary.org/obo/NCBITaxon_10239
  children of: http://purl.obolibrary.org/obo/NCBITaxon_2
  ontology: ncbitaxon

$ref: #/definitions/definedterm

children of: http://purl.obolibrary.org/obo/MONDO_0000001
children of: http://purl.obolibrary.org/obo/DOID_4
children of: http://purl.obolibrary.org/obo/HP_0000001
children of: http://purl.obolibrary.org/obo/NCIT_C7057
ontology: mondo
ontology: hpo
ontology: doid
ontology: ncit

description: collection of vocabulary terms defined in ontologies
strict: false
type: string
vocabulary:
  children of: http://purl.obolibrary.org/obo/MONDO_0000001
  children of: http://purl.obolibrary.org/obo/DOID_4
  children of: http://purl.obolibrary.org/obo/HP_0000001
  children of: http://purl.obolibrary.org/obo/NCIT_C7057
  ontology: mondo
  ontology: hpo
  ontology: doid
  ontology: ncit

$ref: #/definitions/definedterm

funder:
  description: An organization associated with a creator or funder of a computational tool
  one of: Organization
    type: object
    description: Information about a single funder
    properties:
      name:
        type: string
        description: An organization associated with a creator or funder of a computational tool
      parent organization:
        type: string
        description: name of the parent funding organization
    required: name
  one of:
    type: array
    items: Organization
      type: object
      description: Information about a single funder
      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

type: string
description: An organization associated with a creator or funder of a computational tool

type: string
description: name of the parent funding organization

MonetaryGrant
type: object
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
    one of: Organization
      type: object
      description: Information about a single funder
      required: name
    one of:
      type: array
      items: Organization
        type: object
        description: Information about a single funder
        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
required: identifier

type: string
description: An organization associated with a creator or funder of a computational tool

type: string
description: name of the parent funding organization

name:
  type: string
  description: An organization associated with a creator or funder of a computational tool
parent organization:
  type: string
  description: name of the parent funding organization

children of: http://purl.obolibrary.org/obo/NCBITaxon_131567
children of: http://purl.obolibrary.org/obo/NCBITaxon_10239
ontology: ncbitaxon

description: collection of vocabulary terms defined in ontologies
strict: false
type: string
vocabulary:
  children of: http://purl.obolibrary.org/obo/NCBITaxon_131567
  children of: http://purl.obolibrary.org/obo/NCBITaxon_10239
  ontology: ncbitaxon

$ref: #/definitions/definedterm

type: string

format: uri
type: string

type: string

$ref: #/definitions/formalparameter

$ref: #/definitions/definedterm

$ref: #/definitions/formalparameter

$ref: #/definitions/definedterm

type: string

$ref: #/definitions/definedterm

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: 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

description: The name of the application suite to which the application belongs (e.g. Excel belongs to Office).
abstract: software suite for the tool
cardinality: many
one of:
  type: array
  items:
    type: string
one of:
  type: string

description: URL to download the computational tool.
cardinality: many
one of:
  items:
    type: string
    format: uri
  type: array
one of:
  type: string
  format: uri

description: Features or modules provided by this application (and possibly required by other applications).
abstract: features of the tool
any of: 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
any of:
  items: DefinedTerm
    strict: false
    type: object
    vocabulary:
      children of: http://edamontology.org/operation_0004
      ontology: edam
  type: array
any of:
  format: uri
  type: string
any of:
  items:
    format: uri
    type: string
  type: array
cardinality: many

type: string

type: string

format: uri
type: string

description: Operating systems supported (Windows 7, OSX 10.6, Android 1.6).
abstract: operative systems supported
cardinality: many
one of:
  type: string
one of:
  type: array
  items:
    type: string

description: Processor architecture required to run the application (e.g. IA64).
abstract: processor requirements
cardinality: many
one of:
  type: string
one of:
  type: array
  items:
    type: string

description: Additional content for a software application.
cardinality: many
one of:
  type: array
  items:
    $ref: #/definitions/creativework
one of:
  $ref: #/definitions/creativework

description: URL to access software application help.
one of: CreativeWork
  properties:
    url:
      format: uri
      type: string
  type: object
one of:
  items: CreativeWork
    properties:
      url:
        format: uri
        type: string
    type: object
  type: array
cardinality: many

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
cardinality: many
one of:
  type: array
  items:
    type: string
one of:
  type: string

description: Software version.
type: string
cardinality: one

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
one of:
  items: AggregateRating
    type: object
    properties:
      rating count:
        description: Total number of ratings
        type: integer
      rating value:
        description: Average rating
        type: string
      item reviewed:
        description: What is being reviewed
        type: string
    required: ratingValue
    recommended: ratingCount
    recommended: itemReviewed
  type: array
one of: AggregateRating
  type: object
  properties:
    rating count:
      description: Total number of ratings
      type: integer
    rating value:
      description: Average rating
      type: string
    item reviewed:
      description: What is being reviewed
      type: string
  required: ratingValue
  recommended: ratingCount
  recommended: itemReviewed
cardinality: many

description: Author or creator of the work. The default field for the author or creator of the work.
any of:
  type: array
  items:
    $ref: #/definitions/person
any of:
  $ref: #/definitions/person
any of:
  type: array
  items:
    $ref: #/definitions/organization
any of:
  $ref: #/definitions/organization
cardinality: many

description: The primary citation or reference about the computational tool. Examples: a publication which describes the development, features and/or application of the tool. The original reference by the tool developers/maintainers that should be cited when reusing the tool. For other references to the tool, use 'citedBy'.
abstract: citation to the work
any of:
  type: array
  items:
    $ref: #/definitions/citation
any of:
  $ref: #/definitions/citation
any of:
  type: array
  items:
    $ref: #/definitions/creativework
any of:
  $ref: #/definitions/creativework
cardinality: many

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
cardinality: one
type: string
enum: Closed
enum: Open
enum: Restricted
enum: Embargoed

description: A secondary contributor to the developement or maintenance of the computational tool.
abstract: contributor to development or maintenance
one of:
  type: array
  items:
    $ref: #/definitions/person
one of:
  type: array
  items:
    $ref: #/definitions/organization
cardinality: many

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.
any of:
  type: array
  items:
    $ref: #/definitions/person
any of:
  $ref: #/definitions/person
any of:
  type: array
  items:
    $ref: #/definitions/organization
any of:
  $ref: #/definitions/organization
cardinality: many

description: Date the work was created.
cardinality: one
format: date
type: string

description: Date the work was modified.
format: date
cardinality: one
type: string

description: Date the work was first published.
cardinality: one
format: date
type: string

description: A link to a webpage containing the comments about the computational tool.
abstract: link to tool discussion page
cardinality: many
type: string
format: uri

description: An item that is part of this computational tool.
any of:
  type: array
  items:
    $ref: #/definitions/citation
any of:
  $ref: #/definitions/citation
any of:
  type: array
  items:
    $ref: #/definitions/creativework
any of:
  $ref: #/definitions/creativework
cardinality: many

description: The language of the computational tool (not programming language).
cardinality: many
one of:
  items:
    type: object
    properties:
      name:
        type: string
        description: language of the work
      alternate name:
        type: string
    required: name
    recommended: alternateName
  type: array
one of:
  type: object
  properties:
    name:
      type: string
      description: language of the work
    alternate name:
      type: string
  required: name
  recommended: alternateName

description: The number of interactions with the work, such as page views or tool downloads.
abstract: views or downloads
cardinality: many
one of:
  items: InteractionCounter
    type: object
    properties:
      interaction type:
        type: string
      user interaction count:
        type: integer
    required: interactionType
    required: userInteractionCount
  type: array
one of: InteractionCounter
  type: object
  properties:
    interaction type:
      type: string
    user interaction count:
      type: integer
  required: interactionType
  required: userInteractionCount

description: A flag to signal that the work is accessible for free.
abstract: accessible without charge
cardinality: one
type: boolean

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
any of:
  type: array
  items:
    $ref: #/definitions/citation
any of:
  $ref: #/definitions/citation
any of:
  type: array
  items:
    $ref: #/definitions/creativework
any of:
  $ref: #/definitions/creativework
cardinality: many

description: Indicates a broader study, project, or collection the work is part of.
abstract: study or project including the work
any of:
  type: array
  items:
    $ref: #/definitions/citation
any of:
  $ref: #/definitions/citation
any of:
  type: array
  items:
    $ref: #/definitions/creativework
any of:
  $ref: #/definitions/creativework
cardinality: many

description: Keywords or tags used to describe this work.
abstract: keywords or tags
one of:
  type: array
  items:
    type: string
one of:
  type: string

description: A license document that applies to this work, typically indicated by URL.
abstract: license for use
format: uri
cardinality: one
type: string

description: Original publisher of the computational tool metadata (like GitHub, Dockstore, etc.).
abstract: original metadata source
one of:
  $ref: #/definitions/catalog
one of:
  type: array
  items:
    $ref: #/definitions/catalog
cardinality: many

description: A thumbnail image of the computational tool.
cardinality: many
type: string
format: uri

description: A description of the computational tool.
cardinality: one
type: string

description: Identifier for the computational tool.
cardinality: many
one of:
  type: string
one of:
  type: array
  items:
    type: string

description: Website which describes the work and provides additional details.
abstract: associated webpage
cardinality: many
one of:
  items:
    type: string
    format: uri
  type: array
one of:
  type: string
  format: uri

description: Computational tool name.
cardinality: one
type: string

description: URL of additional sources for the work.
cardinality: many
one of:
  items:
    type: string
    format: uri
  type: array
one of:
  type: string
  format: uri

description: URL of the work.
format: uri
cardinality: one
type: string

description: The organization, research project, working group, or funded program on whose behalf the author/creator was working.
any of:
  type: array
  items:
    $ref: #/definitions/researchproject
any of:
  $ref: #/definitions/researchproject
any of:
  type: array
  items:
    $ref: #/definitions/organization
any of:
  $ref: #/definitions/organization
cardinality: many

description: Text that can be used to credit person(s) and/or organization(s) associated with a published Creative Work. For example, how a user should cite the tool.
type: string
cardinality: one

citation: ScholarlyArticle
  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: object
  properties:
    author:
      description: Author(s) of the publication
      any of:
        type: array
      any of:
        $ref: #/definitions/person
      any of:
        type: array
      any of:
        $ref: #/definitions/organization
    abstract:
      description: Abstract of the publication
      type: string
    date published:
      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
    issue number:
      description: Issue number where the article appears
      type: string
    journal name:
      description: Journal where the article appears
      type: string
    journal name abbrev:
      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
    volume number:
      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
  recommended: datePublished
  recommended: doi
  recommended: identifier
  recommended: journalName
  recommended: pmid
  recommended: url
  optional: abstract
  optional: citation
  optional: description
  optional: issueNumber
  optional: journalNameAbbrev
  optional: pagination
  optional: volumeNumber
catalog: 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
    version date:
      description: date the metadata was harvested from the catalog
      type: string
      format: date
    archived at:
      description: The url(s) of one or more datasets, tools, resources or other items listed in a DataCatalog or ResourceCatalog
      one of:
        type: array
      one of:
        type: string
        format: uri
  required: name
  required: url
  recommended: versionDate
  recommended: archivedAt
creativework: CreativeWork
  description: A resource
  type: object
  properties:
    author:
      description: Author(s) of the referenced work
      any of:
        type: array
      any of:
        $ref: #/definitions/person
      any of:
        type: array
      any of:
        $ref: #/definitions/organization
    abstract:
      description: Abstract of the referenced work
      type: string
    additional type:
      description: Additional type of the referenced work, such as a Sample, Run, Experiment, or BioProject
      one of:
        type: array
    date published:
      description: Date the referenced work was published
      format: date
      type: string
    description:
      description: Description of the referenced work
      type: string
    has part:
      description: A portion of the work
      one of:
        $ref: #/definitions/citation
    included in data catalog:
      description: Data or tool catalog which houses the work
      one of:
        $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
  recommended: datePublished
  recommended: doi
  recommended: identifier
  recommended: includedInDataCatalog
  recommended: relationship
  recommended: url
  optional: abstract
  optional: citation
  optional: description
  optional: hasPart
topic:
  description: Topic assigned to the work.
  type: string
  vocabulary:
    ontology: edam
    children of: http://edamontology.org/topic_0003
  strict: true
organization: Organization
  description: Reusable organization definition
  properties:
    affiliation:
      type: object
      required: name
      optional: sameAs
      optional: url
    alternate name:
      description: Alias of the name
      one of:
        type: array
      one of:
        type: string
    name:
      description: Name of the organization
      type: string
    parent organization:
      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
  required: name
  recommended: identifier
  optional: affiliation
  optional: alternateName
  optional: email
  optional: parentOrganization
  optional: role
  optional: url
  type: object
researchproject: ResearchProject
person: Person
definedterm: DefinedTerm
softwareapplication: SoftwareApplication
formalparameter: FormalParameter

$ref: #/definitions/person

$ref: #/definitions/organization

type: string
format: uri

$ref: #/definitions/person

$ref: #/definitions/organization

properties:
  name:
    type: string
  url:
    format: uri
    type: string
required: name
recommended: url
type: object

description: Name of the affiliation, such as a university
type: string

description: Alias for the affiliation
type: string

description: URL of the affiliation
type: string
format: uri

type: string

description: What role the organization played in creating the dataset
type: string

description: Link to the organization
type: string
format: uri

ResearchProject
description: a type of organization definition
properties:
  alternate name:
    description: Alias of the name
    one of:
      type: array
      items:
        type: string
    one of:
      type: string
  name:
    description: Name of the organization
    type: string
  parent organization:
    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
recommended: url
recommended: parentOrganization
optional: alternateName
optional: email
optional: role
type: object

Person
description: Reusable person definition
properties:
  affiliation:
    type: object
    properties:
      name:
        description: Name of the affiliation, such as a university
        type: string
      same as:
        description: Alias for the affiliation
        type: string
      url:
        description: URL of the affiliation
        type: string
        format: uri
    required: name
    optional: sameAs
    optional: url
  name:
    description: Name of the person
    type: string
  email:
    description: Email address of the person
    type: string
  family name:
    description: Family name (surname) of the person
    type: string
  given name:
    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
recommended: givenName
recommended: identifier
optional: affiliation
optional: email
optional: role
optional: title
optional: url
type: object

DefinedTerm
type: object
properties:
  name:
    description: The name of the item.
    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.
    cardinality: one
    type: string
  url:
    description: URL of the item.
    cardinality: one
    type: string
    format: uri
  curated by:
    description: The person, organization, or catalog that curated this DefinedTerm for the metadata property
    any of:
      $ref: #/definitions/person
    any of:
      $ref: #/definitions/organization
    any of:
      $ref: #/definitions/catalog
    any of:
      $ref: #/definitions/researchproject
    any of:
      $ref: #/definitions/softwareapplication
  term code:
    description: A code that identifies this DefinedTerm within a DefinedTermSet.
    type: string
  description:
    description: A description of the item.
    type: string
  in defined term set:
    description: A DefinedTermSet that contains this term.
    type: string
  original name:
    description: The original name of the item, before any metadata standardization/normalization
    type: string
  is curated:
    description: A boolean indicator describing whether or not this DefinedTerm was curated as the value of a property.
    type: boolean

SoftwareApplication
description: Reusable software or algorithm definition
properties:
  name:
    description: name of the software, computational tool, or algorithm.
    type: string
  date modified:
    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
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
    any of:
      type: string
    any of:
      type: array
      items:
        type: string
    any of:
      type: string
      format: uri
    any of:
      type: array
      items:
        type: string
        format: uri
  description:
    type: string
    description: Description of the software input or output
  encoding format:
    description: File type of the software input our output
    any of:
      type: string
    any of:
      type: array
      items:
        type: string
    any of:
      type: array
      items:
        $ref: #/definitions/definedterm
    any of:
      $ref: #/definitions/definedterm
required: name
recommended: encodingFormat

$ref: #/definitions/definedterm

$ref: #/definitions/citation

$ref: #/definitions/creativework

$ref: #/definitions/citation

$ref: #/definitions/creativework

$ref: #/definitions/citation

$ref: #/definitions/creativework

$ref: #/definitions/citation

$ref: #/definitions/creativework

$ref: #/definitions/topic

$ref: #/definitions/definedterm

children of: http://purl.obolibrary.org/obo/NCBITaxon_10239
children of: http://purl.obolibrary.org/obo/NCBITaxon_2
ontology: ncbitaxon

description: collection of vocabulary terms defined in ontologies
strict: false
type: string
vocabulary:
  children of: http://purl.obolibrary.org/obo/NCBITaxon_10239
  children of: http://purl.obolibrary.org/obo/NCBITaxon_2
  ontology: ncbitaxon

$ref: #/definitions/definedterm

children of: http://purl.obolibrary.org/obo/MONDO_0000001
children of: http://purl.obolibrary.org/obo/DOID_4
children of: http://purl.obolibrary.org/obo/HP_0000001
children of: http://purl.obolibrary.org/obo/NCIT_C7057
ontology: mondo
ontology: hpo
ontology: doid
ontology: ncit

description: collection of vocabulary terms defined in ontologies
strict: false
type: string
vocabulary:
  children of: http://purl.obolibrary.org/obo/MONDO_0000001
  children of: http://purl.obolibrary.org/obo/DOID_4
  children of: http://purl.obolibrary.org/obo/HP_0000001
  children of: http://purl.obolibrary.org/obo/NCIT_C7057
  ontology: mondo
  ontology: hpo
  ontology: doid
  ontology: ncit

$ref: #/definitions/definedterm

funder:
  description: An organization associated with a creator or funder of a resource catalog
  one of: Organization
    type: object
    description: Information about a single funder
    properties:
      name:
        type: string
        description: An organization associated with a creator or funder of a resource catalog
      parent organization:
        type: string
        description: name of the parent funding organization
    required: name
  one of:
    type: array
    items: Organization
      type: object
      description: Information about a single funder
      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

type: string
description: An organization associated with a creator or funder of a dataset

type: string
description: name of the parent funding organization

MonetaryGrant
type: object
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
    one of: Organization
      type: object
      description: Information about a single funder
      required: name
    one of:
      type: array
      items: Organization
        type: object
        description: Information about a single funder
        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
required: identifier

type: string
description: An organization associated with a creator or funder of a resource catalog

type: string
description: name of the parent funding organization

name:
  type: string
  description: An organization associated with a creator or funder of a resource catalog
parent organization:
  type: string
  description: name of the parent funding organization

children of: http://purl.obolibrary.org/obo/NCBITaxon_131567
children of: http://purl.obolibrary.org/obo/NCBITaxon_10239
ontology: ncbitaxon

description: collection of vocabulary terms defined in ontologies
strict: false
type: string
vocabulary:
  children of: http://purl.obolibrary.org/obo/NCBITaxon_131567
  children of: http://purl.obolibrary.org/obo/NCBITaxon_10239
  ontology: ncbitaxon

$ref: #/definitions/definedterm

DataDownload
description: A downloadable form of the resource catalog.
properties:
  content url:
    format: uri
    type: string
  encoding format:
    description: file type (ex: XLSX)
    type: string
  date modified:
    format: date
    description: date the file was modified
    type: string
required: dateModified
required: contentUrl
type: object

content url:
  format: uri
  type: string
encoding format:
  description: file type (ex: XLSX)
  type: string
date modified:
  format: date
  description: date the file was modified
  type: string

$ref: #/definitions/catalog

children of: http://edamontology.org/topic_3361
children of: http://purl.obolibrary.org/obo/NCIT_C20368
children of: http://purl.obolibrary.org/obo/MMO_0000000
children of: http://www.ebi.ac.uk/efo/EFO_0000001
ontology: edam
ontology: ncit
ontology: mmo
ontology: efo

description: collection of vocabulary terms defined in ontologies
strict: false
type: string
vocabulary:
  children of: http://edamontology.org/topic_3361
  children of: http://purl.obolibrary.org/obo/NCIT_C20368
  children of: http://purl.obolibrary.org/obo/MMO_0000000
  children of: http://www.ebi.ac.uk/efo/EFO_0000001
  ontology: edam
  ontology: ncit
  ontology: mmo
  ontology: efo

$ref: #/definitions/definedterm

children of: http://www.ebi.ac.uk/efo/EFO_0000001
children of: http://purl.obolibrary.org/obo/CMO_0000000
children of: http://purl.obolibrary.org/obo/NCIT_C25209
ontology: efo
ontology: cmo
ontology: ncit

description: collection of vocabulary terms defined in ontologies
strict: false
type: string
vocabulary:
  children of: http://www.ebi.ac.uk/efo/EFO_0000001
  children of: http://purl.obolibrary.org/obo/CMO_0000000
  children of: http://purl.obolibrary.org/obo/NCIT_C25209
  ontology: efo
  ontology: cmo
  ontology: ncit

$ref: #/definitions/definedterm

AggregateRating
type: object
properties:
  rating count:
    description: Total number of ratings
    type: integer
  rating value:
    description: Average rating
    type: string
  item reviewed:
    description: What is being reviewed
    type: string
required: ratingValue
recommended: ratingCount
recommended: itemReviewed

AggregateRating
type: object
properties:
  rating count:
    description: Total number of ratings
    type: integer
  rating value:
    description: Average rating
    type: string
  item reviewed:
    description: What is being reviewed
    type: string
required: ratingValue
recommended: ratingCount
recommended: itemReviewed

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
any of:
  type: array
  items:
    $ref: #/definitions/person
any of:
  $ref: #/definitions/person
any of:
  type: array
  items:
    $ref: #/definitions/organization
any of:
  $ref: #/definitions/organization
cardinality: many

description: The primary citation or reference about the resource catalog. Examples: a publication which describes the development of or improvements to the resource catalog. The original reference by the resource catalog developers/maintainers that should be cited when using the resource. For all other references to the resource catalog, use 'citedBy'.
abstract: citation to the work
cardinality: many
any of:
  type: array
  items:
    $ref: #/definitions/citation
any of:
  $ref: #/definitions/citation
any of:
  type: array
  items:
    $ref: #/definitions/creativework
any of:
  $ref: #/definitions/creativework

description: Whether the resource is IID domain specific or generalist.
abstract: Whether the work is IID domain specific or generalist
type: string
enum: IID
enum: Generalist
enum: Basic science
enum: Biomedical
enum: Other
enum: Metadata
cardinality: one

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
enum: Open
enum: Restricted
enum: Embargoed
cardinality: one

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
any of:
  type: array
  items:
    $ref: #/definitions/person
any of:
  $ref: #/definitions/person
any of:
  type: array
  items:
    $ref: #/definitions/organization
any of:
  $ref: #/definitions/organization
cardinality: many

description: Date the work was created.
format: date
type: string
cardinality: one

description: Date the work was modified
format: date
type: string
cardinality: one

description: Date the work was first published
format: date
type: string
cardinality: one

description: The resource has an API through which important content may be accessed.
abstract: API availability
type: boolean
cardinality: one

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
enum: Partial content
enum: Record-level
enum: No downloads
enum: Prohibited
cardinality: one

description: Associated materials for the resource catalog, including data dictionaries and data limitation descriptions
abstract: data limitations or dictionaries
any of:
  type: array
  items:
    $ref: #/definitions/citation
any of:
  $ref: #/definitions/citation
any of:
  type: array
  items:
    $ref: #/definitions/creativework
any of:
  $ref: #/definitions/creativework
cardinality: many

description: The language of the content of the resource catalog.
one of:
  items:
    type: object
    properties:
      name:
        type: string
        description: language of the work
      alternate name:
        type: string
    required: name
    recommended: alternateName
  type: array
one of:
  type: object
  properties:
    name:
      type: string
      description: language of the work
    alternate name:
      type: string
  required: name
  recommended: alternateName
cardinality: many

description: The number of interactions with the work, such as page views or tool downloads.
abstract: views or downloads
one of:
  items: InteractionCounter
    type: object
    properties:
      interaction type:
        type: string
      user interaction count:
        type: integer
    required: interactionType
    required: userInteractionCount
  type: array
one of: InteractionCounter
  type: object
  properties:
    interaction type:
      type: string
    user interaction count:
      type: integer
  required: interactionType
  required: userInteractionCount
cardinality: many

description: A flag to signal that the work is accessible for free.
abstract: accessible without charge
type: boolean
cardinality: one

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
cardinality: many
any of:
  type: array
  items:
    $ref: #/definitions/citation
any of:
  $ref: #/definitions/citation
any of:
  type: array
  items:
    $ref: #/definitions/creativework
any of:
  $ref: #/definitions/creativework

description: Indicates a broader study, project, or collection the work is part of.
abstract: study or project including the work
cardinality: many
any of:
  type: array
  items:
    $ref: #/definitions/citation
any of:
  $ref: #/definitions/citation
any of:
  type: array
  items:
    $ref: #/definitions/creativework
any of:
  $ref: #/definitions/creativework

description: Keywords or tags used to describe this work.
abstract: keywords or tags
one of:
  type: array
  items:
    type: string
one of:
  type: string
cardinality: many

description: A license document that applies to this work, typically indicated by URL.
abstract: license for use
format: uri
cardinality: one
type: string

description: Original publisher of the resource catalog metadata (like GenBank, ImmPort, etc.).
abstract: original metadata source
one of:
  $ref: #/definitions/catalog
one of:
  type: array
  items:
    $ref: #/definitions/catalog
cardinality: many

description: The place(s) which are the focus of the resource catalog.
abstract: geographic focus of the work
one of:
  items: AdministrativeArea
    description: Location information
    properties:
      administrative type:
        description: the type of administrative area, such as country, state, county, or city
        enum: province
        enum: district
        enum: chiefdom
        enum: village
        enum: city
        enum: country
        enum: prefecture
        enum: sub-prefecture
        enum: clan
        enum: Federal Capital Territory
        enum: state
        enum: Local Government Area
        enum: ward
        type: string
      alternate name:
        description: An alias for the location
      identifier:
        description: An identifier for the location, preferably a Wikidata ID
        type: string
      location type:
        description: Categorization of how the location relates to the dataset
      name:
        description: The name of the location
        type: string
    type: object
  type: array
one of: AdministrativeArea
  description: Location information
  properties:
    administrative type:
      description: the type of administrative area, such as country, state, county, or city
      enum: province
      enum: district
      enum: chiefdom
      enum: village
      enum: city
      enum: country
      enum: prefecture
      enum: sub-prefecture
      enum: clan
      enum: Federal Capital Territory
      enum: state
      enum: Local Government Area
      enum: ward
      type: string
    alternate name:
      description: An alias for the location
      one of:
        type: string
      one of:
        type: array
    identifier:
      description: An identifier for the location, preferably a Wikidata ID
      type: string
    location type:
      description: Categorization of how the location relates to the dataset
      one of:
        enum: residence
        enum: exposure
        enum: collection
        enum: screening
        enum: treatment
        enum: study location
        enum: other
        enum: unknown
        type: string
      one of:
        type: array
    name:
      description: The name of the location
      type: string
  type: object
cardinality: many

type: string

items:
  type: string
type: array

enum: residence
enum: exposure
enum: collection
enum: screening
enum: treatment
enum: study location
enum: other
enum: unknown
type: string

items:
  enum: residence
  enum: exposure
  enum: collection
  enum: screening
  enum: treatment
  enum: study location
  enum: other
  enum: unknown
  type: string
type: array

type: string

enum: residence
enum: exposure
enum: collection
enum: screening
enum: treatment
enum: study location
enum: other
enum: unknown
type: string

description: The period of time covered within the resource catalog.
abstract: time period
one of:
  items: TemporalInterval
    description: Temporal information
    properties:
      duration:
        description: A time interval in ISO 8601 duration format
        type: string
      end date:
        description: An end date
        format: date
        type: string
      name:
        description: String describing the temporal interval
        type: string
      start date:
        description: A start date
        format: date
        type: string
      temporal type:
        description: Categorization of how the date/temporal interval relates to the dataset
    type: object
  type: array
one of: TemporalInterval
  description: Temporal information
  properties:
    duration:
      description: A time interval in ISO 8601 duration format
      type: string
    end date:
      description: An end date
      format: date
      type: string
    name:
      description: String describing the temporal interval
      type: string
    start date:
      description: A start date
      format: date
      type: string
    temporal type:
      description: Categorization of how the date/temporal interval relates to the dataset
      one of:
        enum: exposure
        enum: collection
        enum: screening
        enum: treatment
        enum: study date
        enum: other
        enum: unknown
        type: string
      one of:
        type: array
  type: object
cardinality: many

enum: exposure
enum: collection
enum: screening
enum: treatment
enum: study date
enum: other
enum: unknown
type: string

items:
  enum: exposure
  enum: collection
  enum: screening
  enum: treatment
  enum: study date
  enum: other
  enum: unknown
  type: string
type: array

enum: exposure
enum: collection
enum: screening
enum: treatment
enum: study date
enum: other
enum: unknown
type: string

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
one of:
  type: array
  items:
    $ref: #/definitions/creativework
one of:
  $ref: #/definitions/creativework
cardinality: many

description: Resource catalog version.
type: string
cardinality: one

description: An alias for the resource catalog name.
one of:
  type: string
one of:
  type: array
  items:
    type: string
cardinality: many

description: A description of the resource catalog.
cardinality: one
type: string

description: Resource catalog identifier or accession number, such as a digital object identifier (DOI), etc.
abstract: identifier
one of:
  type: string
one of:
  items:
    type: string
  type: array
cardinality: many

description: Website which describes the work and provides additional details.
abstract: associated webpage
one of:
  items:
    type: string
    format: uri
  type: array
one of:
  type: string
  format: uri
cardinality: many

description: Resource catalog name.
cardinality: one
type: string

description: URL of additional sources for the work.
one of:
  items:
    type: string
    format: uri
  type: array
one of:
  type: string
  format: uri
cardinality: many

description: URL of the work.
type: string
format: uri
cardinality: one

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'
any of:
  type: array
  items:
    $ref: #/definitions/propertyvalue
any of:
  $ref: #/definitions/propertyvalue
any of:
  type: array
  items:
    $ref: #/definitions/quantitativevalue
any of:
  $ref: #/definitions/quantitativevalue
cardinality: many

description: The type of resource/resource catalog that best describes the work.
any of:
  type: string
  enum: Knowledge Base
  enum: Ontology
  enum: Terminology
  enum: Database
  enum: Dataset
  enum: Metadata Catalog
  enum: Archive
  enum: Cloud Ecosystem
  enum: Corpus
  enum: Repository
  enum: Controlled Vocabulary
  enum: Registry
  enum: Data Dictionary
  enum: Data Mart
  enum: Data Warehouse
  enum: Data Store
  enum: Data Collection
  enum: Portal
any of:
  $ref: #/definitions/collectiontypes
cardinality: one

description: The organization, research project, working group, or funded program on whose behalf the author/creator was working.
any of:
  type: array
  items:
    $ref: #/definitions/researchproject
any of:
  $ref: #/definitions/researchproject
any of:
  type: array
  items:
    $ref: #/definitions/organization
any of:
  $ref: #/definitions/organization
cardinality: many

description: The url(s) of one or more datasets, tools, resources or other items listed in a DataCatalog or ResourceCatalog
one of:
  items:
    type: string
    format: uri
  type: array
one of:
  type: string
  format: uri
cardinality: many

description: Text that can be used to credit person(s) and/or organization(s) associated with a published Creative Work. For example, how a user should cite the resource.
type: string
cardinality: one

citation: ScholarlyArticle
  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: object
  properties:
    author:
      description: Author(s) of the publication
      any of:
        type: array
      any of:
        $ref: #/definitions/person
      any of:
        type: array
      any of:
        $ref: #/definitions/organization
    abstract:
      description: Abstract of the publication
      type: string
    date published:
      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
    issue number:
      description: Issue number where the article appears
      type: string
    journal name:
      description: Journal where the article appears
      type: string
    journal name abbrev:
      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
    volume number:
      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
  recommended: datePublished
  recommended: doi
  recommended: identifier
  recommended: journalName
  recommended: pmid
  recommended: url
  optional: abstract
  optional: citation
  optional: description
  optional: issueNumber
  optional: journalNameAbbrev
  optional: pagination
  optional: volumeNumber
creativework: CreativeWork
  description: A resource
  type: object
  properties:
    author:
      description: Author(s) of the referenced work
      any of:
        type: array
      any of:
        $ref: #/definitions/person
      any of:
        type: array
      any of:
        $ref: #/definitions/organization
    abstract:
      description: Abstract of the referenced work
      type: string
    date published:
      description: Date the referenced work was published
      format: date
      type: string
    description:
      description: Description of the referenced work
      type: string
    has part:
      description: A portion of the work
      one of:
        $ref: #/definitions/citation
    included in data catalog:
      description: Data, resource or tool catalog which houses the work
      one of:
        $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
  recommended: datePublished
  recommended: doi
  recommended: identifier
  recommended: includedInDataCatalog
  recommended: relationship
  recommended: url
  optional: abstract
  optional: citation
  optional: description
  optional: hasPart
topic:
  description: Topic assigned to the work.
  type: string
  vocabulary:
    ontology: edam
    children of: http://edamontology.org/topic_0003
  strict: true
catalog: 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
    version date:
      description: date the metadata was harvested from the catalog
      type: string
      format: date
    archived at:
      description: The url(s) of one or more datasets, tools, resources or other items listed in a DataCatalog or ResourceCatalog
      one of:
        type: array
      one of:
        type: string
        format: uri
  required: name
  required: url
  recommended: versionDate
  recommended: archivedAt
organization: Organization
  description: Reusable organization definition
  properties:
    affiliation:
      type: object
      required: name
      optional: sameAs
      optional: url
    alternate name:
      description: Alias of the name
      one of:
        type: array
      one of:
        type: string
    name:
      description: Name of the organization
      type: string
    parent organization:
      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
  optional: alternateName
  optional: email
  optional: parentOrganization
  optional: role
  optional: url
  type: object
researchproject: ResearchProject
person: Person
propertyvalue: PropertyValue
quantitativevalue: QuantitativeValue
collectiontypes: DefinedTerm
definedterm: DefinedTerm
softwareapplication: SoftwareApplication

$ref: #/definitions/person

$ref: #/definitions/organization

$ref: #/definitions/person

$ref: #/definitions/organization

type: string
format: uri

description: Name of the affiliation, such as a university
type: string

description: Alias for the affiliation
type: string

description: URL of the affiliation
type: string
format: uri

type: string

ResearchProject
description: a type of organization definition
properties:
  alternate name:
    description: Alias of the name
    one of:
      type: array
      items:
        type: string
    one of:
      type: string
  name:
    description: Name of the organization
    type: string
  parent organization:
    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
recommended: url
recommended: parentOrganization
optional: alternateName
optional: email
optional: role
type: object

Person
description: Reusable person definition
properties:
  affiliation:
    type: object
    properties:
      name:
        description: Name of the affiliation, such as a university
        type: string
      same as:
        description: Alias for the affiliation
        type: string
      url:
        description: URL of the affiliation
        type: string
        format: uri
    required: name
    optional: sameAs
    optional: url
  name:
    description: Name of the person
    type: string
  email:
    description: Email address of the person
    type: string
  family name:
    description: Family name (surname) of the person
    type: string
  given name:
    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
recommended: givenName
recommended: identifier
optional: affiliation
optional: email
optional: role
optional: title
optional: url
type: object

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
  max value:
    description: An estimated maximum numberic value if the actual value is not known. Ignore if actual numeric value is known.
    type: number
  min value:
    description: An estimated minumum numeric value if the actual value is not known. Ignore if actual numeric value is known.
    type: number
  unit text:
    description: A unit associated with the value. E.g.- 'records' for the number of records in a database.
    type: string
  property ID:
    description: A commonly used identifier for the characteristic represented by the property, e.g. a manufacturer or a standard code for a property. propertyID can be (1) a prefixed string, mainly meant to be used with standards for product properties; (2) a site-specific, non-prefixed string (e.g. the primary key of the property or the vendor-specific ID of the property), or (3) a URL indicating the type of the property, either pointing to an external vocabulary, or a Web resource that describes the property (e.g. a glossary entry). Standards bodies should promote a standard prefix for the identifiers of properties from their standards.
    one of:
      type: string
    one of:
      type: string
      format: uri
required: unitText
recommended: value
recommended: propertyID
optional: maxValue
optional: minValue

QuantitativeValue
description: A numeric value and unit for a property with potentially different units
type: object
properties:
  value:
    description: A numeric value for the property
    type: number
  max value:
    description: An estimated maximum numberic value if the actual value is not known. Ignore if actual numeric value is known.
    type: number
  min value:
    description: An estimated minumum numeric value if the actual value is not known. Ignore if actual numeric value is known.
    type: number
  unit text:
    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
optional: minValue

DefinedTerm
description: potential ontology-linked resource types
type: string
vocabulary:
  ontology: ncit
  children of: http://purl.obolibrary.org/obo/NCIT_C16048
strict: false

DefinedTerm
type: object
properties:
  name:
    description: The name of the item.
    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.
    cardinality: one
    type: string
  url:
    description: URL of the item.
    cardinality: one
    type: string
    format: uri
  curated by:
    description: The person, organization, or catalog that curated this DefinedTerm for the metadata property
    any of:
      $ref: #/definitions/person
    any of:
      $ref: #/definitions/organization
    any of:
      $ref: #/definitions/catalog
    any of:
      $ref: #/definitions/researchproject
    any of:
      $ref: #/definitions/softwareapplication
  term code:
    description: A code that identifies this DefinedTerm within a DefinedTermSet.
    type: string
  description:
    description: A description of the item.
    type: string
  in defined term set:
    description: A DefinedTermSet that contains this term.
    type: string
  original name:
    description: The original name of the item, before any metadata standardization/normalization
    type: string
  is curated:
    description: A boolean indicator describing whether or not this DefinedTerm was curated as the value of a property.
    type: boolean

SoftwareApplication
description: Reusable software or algorithm definition
properties:
  name:
    description: name of the software, computational tool, or algorithm.
    type: string
  date modified:
    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

description: Data, resource or tool catalog name
type: string

description: Link to data, resource or tool catalog
type: string
format: uri

description: date the metadata was harvested from the catalog
type: string
format: date

description: The url(s) of one or more datasets, tools, resources or other items listed in a DataCatalog or ResourceCatalog
one of:
  items:
    type: string
    format: uri
  type: array
one of:
  type: string
  format: uri

type: object
properties:
  name:
    description: Name of the affiliation, such as a university
    type: string
  same as:
    description: Alias for the affiliation
    type: string
  url:
    description: URL of the affiliation
    type: string
    format: uri
required: name
optional: sameAs
optional: url

description: Alias of the name
one of:
  type: array
  items:
    type: string
one of:
  type: string

description: Name of the organization
type: string

description: Name of the parent organization. For instance, the parentOrganization of NIAID is the National Institutes of health (NIH)
type: string

description: Email address of the organization
type: string

description: Unique identifier of the organization
type: string

description: What role the organization played in creating the dataset
type: string

description: Link to the organization
type: string
format: uri

description: Alias of the name
one of:
  type: array
  items:
    type: string
one of:
  type: string

description: Name of the organization
type: string

description: Name of the parent organization. For instance, the parentOrganization of NIAID is the National Institutes of health (NIH)
type: string

description: Email address of the organization
type: string

description: Unique identifier of the organization
type: string

description: Link to the organization
type: string
format: uri

type: object
properties:
  name:
    description: Name of the affiliation, such as a university
    type: string
  same as:
    description: Alias for the affiliation
    type: string
  url:
    description: URL of the affiliation
    type: string
    format: uri
required: name
optional: sameAs
optional: url

description: Name of the person
type: string

description: Email address of the person
type: string

description: Family name (surname) of the person
type: string

description: Given (first) name of the person
type: string

description: Unique identifier of the person, like an ORCID ID
type: string

description: Role the person played in creating the resource catalog
type: string

description: Title of the person
type: string

description: Link to the homepage or other web content describing the person
type: string
format: uri

description: name of the software, computational tool, or algorithm.
type: string

description: date the software, computational tool, or algorithm was run
type: string
format: date

description: url of the software, computational tool, or algorithm
type: string
format: uri

type: string

type: string
format: uri

$ref: #/definitions/creativework

$ref: #/definitions/catalog

children of: http://purl.obolibrary.org/obo/UPHENO_0001001
children of: http://purl.obolibrary.org/obo/PATO_0000001
ontology: UPHENO
ontology: PATO

description: collection of vocabulary terms defined in ontologies
strict: false
type: string
vocabulary:
  children of: http://purl.obolibrary.org/obo/UPHENO_0001001
  children of: http://purl.obolibrary.org/obo/PATO_0000001
  ontology: UPHENO
  ontology: PATO

$ref: #/definitions/definedterm

$ref: #/definitions/quantitativevalue

children of: http://purl.obolibrary.org/obo/NCIT_C16612
children of: http://purl.obolibrary.org/obo/NCIT_C20181
children of: http://purl.obolibrary.org/obo/NCIT_C17649
ontology: NCIT

description: collection of vocabulary terms defined in ontologies
strict: false
type: string
vocabulary:
  children of: http://purl.obolibrary.org/obo/NCIT_C16612
  children of: http://purl.obolibrary.org/obo/NCIT_C20181
  children of: http://purl.obolibrary.org/obo/NCIT_C17649
  ontology: NCIT

$ref: #/definitions/definedterm

children of: http://purl.obolibrary.org/obo/CL_0000000
children of: http://purl.obolibrary.org/obo/CLO_0000031
ontology: CL
ontology: CLO

description: collection of vocabulary terms defined in ontologies
strict: false
type: string
vocabulary:
  children of: http://purl.obolibrary.org/obo/CL_0000000
  children of: http://purl.obolibrary.org/obo/CLO_0000031
  ontology: CL
  ontology: CLO

$ref: #/definitions/definedterm

children of: http://purl.obolibrary.org/obo/NCBITaxon_10239
children of: http://purl.obolibrary.org/obo/NCBITaxon_2
ontology: ncbitaxon

description: collection of vocabulary terms defined in ontologies
strict: false
type: string
vocabulary:
  children of: http://purl.obolibrary.org/obo/NCBITaxon_10239
  children of: http://purl.obolibrary.org/obo/NCBITaxon_2
  ontology: ncbitaxon

$ref: #/definitions/definedterm

children of: http://purl.obolibrary.org/obo/MONDO_0000001
children of: http://purl.obolibrary.org/obo/DOID_4
children of: http://purl.obolibrary.org/obo/HP_0000001
children of: http://purl.obolibrary.org/obo/NCIT_C7057
ontology: mondo
ontology: hpo
ontology: doid
ontology: ncit

description: collection of vocabulary terms defined in ontologies
strict: false
type: string
vocabulary:
  children of: http://purl.obolibrary.org/obo/MONDO_0000001
  children of: http://purl.obolibrary.org/obo/DOID_4
  children of: http://purl.obolibrary.org/obo/HP_0000001
  children of: http://purl.obolibrary.org/obo/NCIT_C7057
  ontology: mondo
  ontology: hpo
  ontology: doid
  ontology: ncit

$ref: #/definitions/definedterm

funder:
  description: An organization associated with a creator or funder of a dataset
  one of: Organization
    type: object
    description: Information about a single funder
    properties:
      name:
        type: string
        description: An organization associated with a creator or funder of a dataset
      parent organization:
        type: string
        description: name of the parent funding organization
    required: name
  one of:
    type: array
    items: Organization
      type: object
      description: Information about a single funder
      required: name
description:
  type: string
  description: description about the funding award / grant
url:
  type: string
  description: award / grant URL
identifier:
  type: string
  description: Unique identifier(s) for the grant(s) used to fund the Dataset

type: string
description: An organization associated with a creator or funder of a dataset

type: string
description: name of the parent funding organization

MonetaryGrant
type: object
description: Funding that supports (sponsors) the collection of this dataset through some kind of financial contribution
properties:
  funder:
    description: An organization associated with a creator or funder of a dataset
    one of: Organization
      type: object
      description: Information about a single funder
      required: name
    one of:
      type: array
      items: Organization
        type: object
        description: Information about a single funder
        required: name
  description:
    type: string
    description: description about the funding award / grant
  url:
    type: string
    description: award / grant URL
  identifier:
    type: string
    description: Unique identifier(s) for the grant(s) used to fund the Dataset
required: funder
required: identifier

type: string
description: An organization associated with a creator or funder of a dataset

type: string
description: name of the parent funding organization

name:
  type: string
  description: An organization associated with a creator or funder of a dataset
parent organization:
  type: string
  description: name of the parent funding organization

children of: http://purl.obolibrary.org/obo/NCBITaxon_131567
children of: http://purl.obolibrary.org/obo/NCBITaxon_10239
ontology: ncbitaxon

description: collection of vocabulary terms defined in ontologies
strict: false
type: string
vocabulary:
  children of: http://purl.obolibrary.org/obo/NCBITaxon_131567
  children of: http://purl.obolibrary.org/obo/NCBITaxon_10239
  ontology: ncbitaxon

$ref: #/definitions/definedterm

$ref: #/definitions/citation

$ref: #/definitions/creativework

$ref: #/definitions/citation

$ref: #/definitions/creativework

$ref: #/definitions/sample

type: array
items:
  $ref: #/definitions/citation

$ref: #/definitions/citation

type: array
items:
  $ref: #/definitions/creativework

$ref: #/definitions/creativework

type: array
items:
  $ref: #/definitions/sample

$ref: #/definitions/sample

description: A resource or sample which reuses the sample. For example, a sample of a cell line that was created by knocking out a gene from this cell line sample. Another example would be a sample of infected tissue that was derived from this tissue sample by infecting it with a virus.
any of:
  type: array
  items:
    $ref: #/definitions/citation
any of:
  $ref: #/definitions/citation
any of:
  type: array
  items:
    $ref: #/definitions/creativework
any of:
  $ref: #/definitions/creativework
any of:
  type: array
  items:
    $ref: #/definitions/sample
any of:
  $ref: #/definitions/sample
cardinality: many

description: A resource or sample from which this sample is derived, modified, or adapted. For example a sample of a cell line, which was infected by virus sample in order to create the sample.
abstract: resource or sample used to create the sample.
cardinality: many
any of:
  type: array
  items:
    $ref: #/definitions/citation
any of:
  $ref: #/definitions/citation
any of:
  type: array
  items:
    $ref: #/definitions/creativework
any of:
  $ref: #/definitions/creativework
any of:
  type: array
  items:
    $ref: #/definitions/sample
any of:
  $ref: #/definitions/sample

description: Associated materials that constitute the sample. For example, other samples (if sample was created by pooling samples), additives, cryoprotective agents, etc. Use 'hasPart' for samples that were generated by pooling other samples. For example, a synthetic microbiome sample may use 'hasPart' to list the individual microbial samples used to generate it.
abstract: Associated materials or samples that constitute the sample
any of:
  type: array
  items:
    $ref: #/definitions/citation
any of:
  $ref: #/definitions/citation
any of:
  type: array
  items:
    $ref: #/definitions/creativework
any of:
  $ref: #/definitions/creativework
any of:
  type: array
  items:
    $ref: #/definitions/sample
any of:
  $ref: #/definitions/sample
cardinality: many

description: Associated materials the sample may help constitute. For example, the pooled sample that used this sample. Use 'isPartOf' for pooled samples generated from this sample. For example, a microbial sample that was used to generate a synthetic microbiome sample.
abstract: study or project including the work
cardinality: many
any of:
  type: array
  items:
    $ref: #/definitions/citation
any of:
  $ref: #/definitions/citation
any of:
  type: array
  items:
    $ref: #/definitions/creativework
any of:
  $ref: #/definitions/creativework
any of:
  type: array
  items:
    $ref: #/definitions/sample
any of:
  $ref: #/definitions/sample

description: Indicate the anatomical system from which the sample is collect, e.g. circulatory, digestive, endocrine, immune and other systems.
any of:
  description: collection of vocabulary terms defined in ontologies
  strict: false
  type: string
  vocabulary:
    children of: http://purl.obolibrary.org/obo/UBERON_0000467
    ontology: UBERON
any of:
  items:
    description: collection of vocabulary terms defined in ontologies
    strict: false
    type: string
    vocabulary:
      children of: http://purl.obolibrary.org/obo/UBERON_0000467
      ontology: UBERON
  type: array
any of:
  type: array
  items:
    $ref: #/definitions/definedterm
any of:
  $ref: #/definitions/definedterm
cardinality: many

description: Indicate the organ, tissues the sample was collected from.
any of:
  description: collection of vocabulary terms defined in ontologies
  strict: false
  type: string
  vocabulary:
    children of: http://purl.obolibrary.org/obo/UBERON_0001062
    ontology: UBERON
any of:
  items:
    description: collection of vocabulary terms defined in ontologies
    strict: false
    type: string
    vocabulary:
      children of: http://purl.obolibrary.org/obo/UBERON_0001062
      ontology: UBERON
  type: array
any of:
  type: array
  items:
    $ref: #/definitions/definedterm
any of:
  $ref: #/definitions/definedterm
cardinality: many

description: The biological sex of the individual from which the sample was obtained.
any of:
  description: collection of vocabulary terms defined in ontologies
  strict: false
  type: string
  vocabulary:
    children of: http://purl.obolibrary.org/obo/PATO_0000047
    ontology: PATO
any of:
  items:
    description: collection of vocabulary terms defined in ontologies
    strict: false
    type: string
    vocabulary:
      children of: http://purl.obolibrary.org/obo/PATO_0000047
      ontology: PATO
  type: array
any of:
  type: array
  items:
    $ref: #/definitions/definedterm
any of:
  $ref: #/definitions/definedterm
cardinality: many

description: A temporal subdivision of a developmental process, indicating the age or stage of the object when the sample was created.
any of:
  description: collection of vocabulary terms defined in ontologies
  strict: false
  type: string
  vocabulary:
    children of: http://purl.obolibrary.org/obo/UBERON_0000104
    children of: http://purl.obolibrary.org/obo/NCIT_C48308
    ontology: UBERON
    ontology: NCIT
any of:
  items:
    description: collection of vocabulary terms defined in ontologies
    strict: false
    type: string
    vocabulary:
      children of: http://purl.obolibrary.org/obo/UBERON_0000104
      children of: http://purl.obolibrary.org/obo/NCIT_C48308
      ontology: UBERON
      ontology: NCIT
  type: array
any of:
  type: array
  items:
    $ref: #/definitions/definedterm
any of:
  $ref: #/definitions/definedterm
any of:
  type: array
  items:
    $ref: #/definitions/quantitativevalue
any of:
  $ref: #/definitions/quantitativevalue
cardinality: many

description: A flag to signal that the sample is available for reuse.
abstract: availability of the sample
type: boolean
cardinality: one

description: The processing technique that was applied to the sample, methods used to prepare the samples.
any of:
  description: collection of vocabulary terms defined in ontologies
  strict: false
  type: string
  vocabulary:
    children of: http://purl.obolibrary.org/obo/OBI_0000094
    children of: http://purl.obolibrary.org/obo/NCIT_C48177
    children of: http://purl.obolibrary.org/obo/NCIT_C16680
    ontology: OBI
    ontology: NCIT
any of:
  items:
    description: collection of vocabulary terms defined in ontologies
    strict: false
    type: string
    vocabulary:
      children of: http://purl.obolibrary.org/obo/OBI_0000094
      children of: http://purl.obolibrary.org/obo/NCIT_C48177
      children of: http://purl.obolibrary.org/obo/NCIT_C16680
      ontology: OBI
      ontology: NCIT
  type: array
any of:
  type: array
  items:
    $ref: #/definitions/definedterm
any of:
  $ref: #/definitions/definedterm
any of:
  type: array
  items:
    $ref: #/definitions/creativework
any of:
  $ref: #/definitions/creativework
any of:
  type: string
cardinality: many

description: A numeric value for a measurement of the size of a sample. If completely unknown, set value = 0, and unitText = 'unknown'
one of:
  type: array
  items:
    $ref: #/definitions/quantitativevalue
one of:
  $ref: #/definitions/quantitativevalue
cardinality: many

description: Specify the condition, composition or state of the sample, for example dried, frozen, passage number.
any of:
  type: string
any of:
  type: array
  items:
    $ref: #/definitions/quantitativevalue
any of:
  $ref: #/definitions/quantitativevalue
cardinality: many

description: The temperature at which the sample is stored.
one of:
  type: array
  items:
    $ref: #/definitions/quantitativevalue
one of:
  $ref: #/definitions/quantitativevalue
cardinality: one

description: The type of sample or specimen.
any of:
  description: collection of vocabulary terms defined in ontologies
  strict: false
  type: string
  vocabulary:
    children of: http://purl.obolibrary.org/obo/BFO_0000040
    ontology: OBI
any of:
  items:
    description: collection of vocabulary terms defined in ontologies
    strict: false
    type: string
    vocabulary:
      children of: http://purl.obolibrary.org/obo/BFO_0000040
      ontology: OBI
  type: array
any of:
  type: array
  items:
    $ref: #/definitions/definedterm
any of:
  $ref: #/definitions/definedterm
cardinality: many

description: A downloadable form of this dataset, at a specific location, in a specific format.
abstract: download link
one of:
  items: DataDownload
    description: A dataset in downloadable form.
    properties:
      content url:
        format: uri
        type: string
      encoding format:
        description: file type (ex: XLSX)
        type: string
      date modified:
        format: date
        description: date the file was modified
        type: string
    required: dateModified
    required: contentUrl
    type: object
  type: array
one of: DataDownload
  description: A dataset in downloadable form.
  properties:
    content url:
      format: uri
      type: string
    encoding format:
      description: file type (ex: XLSX)
      type: string
    date modified:
      format: date
      description: date the file was modified
      type: string
  required: dateModified
  required: contentUrl
  type: object
cardinality: many

description: A technique or technology used in the collection or processing of the sample corresponding to the method used for measuring the corresponding variable(s) (described using variableMeasured). For example, if variableMeasured is cell density or cell counts, measurementTechnique could be: "centrifugation" or "flow cytometry".
abstract: measurement technique used to collect, process, or generate the sample
any of:
  description: collection of vocabulary terms defined in ontologies
  strict: false
  type: string
  vocabulary:
    children of: http://edamontology.org/topic_3361
    children of: http://purl.obolibrary.org/obo/NCIT_C20368
    children of: http://purl.obolibrary.org/obo/MMO_0000000
    children of: http://www.ebi.ac.uk/efo/EFO_0000001
    ontology: edam
    ontology: ncit
    ontology: mmo
    ontology: efo
any of:
  items:
    description: collection of vocabulary terms defined in ontologies
    strict: false
    type: string
    vocabulary:
      children of: http://edamontology.org/topic_3361
      children of: http://purl.obolibrary.org/obo/NCIT_C20368
      children of: http://purl.obolibrary.org/obo/MMO_0000000
      children of: http://www.ebi.ac.uk/efo/EFO_0000001
      ontology: edam
      ontology: ncit
      ontology: mmo
      ontology: efo
  type: array
any of:
  type: array
  items:
    $ref: #/definitions/definedterm
any of:
  $ref: #/definitions/definedterm
cardinality: many

description: Variables measured within the sample.
one of:
  description: collection of vocabulary terms defined in ontologies
  strict: false
  type: string
  vocabulary:
    children of: http://www.ebi.ac.uk/efo/EFO_0000001
    children of: http://purl.obolibrary.org/obo/CMO_0000000
    children of: http://purl.obolibrary.org/obo/NCIT_C25209
    ontology: efo
    ontology: cmo
    ontology: ncit
one of:
  items:
    description: collection of vocabulary terms defined in ontologies
    strict: false
    type: string
    vocabulary:
      children of: http://www.ebi.ac.uk/efo/EFO_0000001
      children of: http://purl.obolibrary.org/obo/CMO_0000000
      children of: http://purl.obolibrary.org/obo/NCIT_C25209
      ontology: efo
      ontology: cmo
      ontology: ncit
  type: array
one of:
  type: array
  items:
    $ref: #/definitions/definedterm
one of:
  $ref: #/definitions/definedterm
cardinality: many

description: Provide information about the conditions and methods of acquisition of samples.
any of:
  type: string
  format: uri
any of:
  items:
    type: string
    format: uri
  type: array
any of:
  type: string
any of:
  items:
    type: string
  type: array
any of:
  type: array
  items:
    $ref: #/definitions/definedterm
any of:
  $ref: #/definitions/definedterm
cardinality: many

description: Provide description of instruments and devices used in collecting, processing and analysis of samples.
any of:
  type: string
  format: uri
any of:
  items:
    type: string
    format: uri
  type: array
any of:
  type: string
any of:
  items:
    type: string
  type: array
any of:
  type: array
  items:
    $ref: #/definitions/definedterm
any of:
  $ref: #/definitions/definedterm
cardinality: many

description: A category or description of the habitat that describes elements of an ecosystem where the sample was collected. Where possible use controlled vocabulary such as ENVO.
any of:
  description: collection of vocabulary terms defined in ontologies
  strict: false
  type: string
  vocabulary:
    children of: http://purl.obolibrary.org/obo/ENVO_00010483
    children of: http://purl.obolibrary.org/obo/NCIT_C62574
    ontology: ENVO
    ontology: NCIT
any of:
  items:
    description: collection of vocabulary terms defined in ontologies
    strict: false
    type: string
    vocabulary:
      children of: http://purl.obolibrary.org/obo/ENVO_00010483
      children of: http://purl.obolibrary.org/obo/NCIT_C62574
      ontology: ENVO
      ontology: NCIT
  type: array
any of:
  type: array
  items:
    $ref: #/definitions/definedterm
any of:
  $ref: #/definitions/definedterm
cardinality: many

description: Describe the planned or executed experimental procedures involving the samples.
any of:
  type: string
any of:
  items:
    type: string
  type: array
any of:
  type: array
  items:
    $ref: #/definitions/definedterm
any of:
  $ref: #/definitions/definedterm
cardinality: many

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
one of:
  items: AggregateRating
    type: object
    properties:
      rating count:
        description: Total number of ratings
        type: integer
      rating value:
        description: Average rating
        type: string
      item reviewed:
        description: What is being reviewed
        type: string
    required: ratingValue
    recommended: ratingCount
    recommended: itemReviewed
  type: array
one of: AggregateRating
  type: object
  properties:
    rating count:
      description: Total number of ratings
      type: integer
    rating value:
      description: Average rating
      type: string
    item reviewed:
      description: What is being reviewed
      type: string
  required: ratingValue
  recommended: ratingCount
  recommended: itemReviewed
cardinality: many

description: A person or organization responsible for the collection, processing, or maintenance of the sample: Populated from collector, contributor, and maintainer.
any of:
  type: array
  items:
    $ref: #/definitions/person
any of:
  $ref: #/definitions/person
any of:
  type: array
  items:
    $ref: #/definitions/organization
any of:
  $ref: #/definitions/organization
cardinality: many

description: The Person or Organization who collected the Sample.
any of:
  type: array
  items:
    $ref: #/definitions/person
any of:
  $ref: #/definitions/person
any of:
  type: array
  items:
    $ref: #/definitions/organization
any of:
  $ref: #/definitions/organization
cardinality: many

description: Person or organization that contributes to the work.
any of:
  type: array
  items:
    $ref: #/definitions/person
any of:
  $ref: #/definitions/person
any of:
  type: array
  items:
    $ref: #/definitions/organization
any of:
  $ref: #/definitions/organization
cardinality: many

description: The Person or Organization who is responsible for the Sample.
any of:
  type: array
  items:
    $ref: #/definitions/person
any of:
  $ref: #/definitions/person
any of:
  type: array
  items:
    $ref: #/definitions/organization
any of:
  $ref: #/definitions/organization
cardinality: many

description: The location from which the sample was originally collected.
one of:
  items: AdministrativeArea
    description: Location information
    properties:
      administrative type:
        description: the type of administrative area, such as country, state, county, or city
        enum: province
        enum: district
        enum: chiefdom
        enum: village
        enum: city
        enum: country
        enum: prefecture
        enum: sub-prefecture
        enum: clan
        enum: Federal Capital Territory
        enum: state
        enum: Local Government Area
        enum: ward
        type: string
      alternate name:
        description: An alias for the location
      identifier:
        description: An identifier for the location, preferably a Wikidata ID
        type: string
      location type:
        description: Categorization of how the location relates to the dataset
        const: collection
      name:
        description: The name of the location
        type: string
    type: object
  type: array
one of: AdministrativeArea
  type: object
  description: Location information
  properties:
    administrative type:
      description: the type of administrative area, such as country, state, county, or city
      enum: province
      enum: district
      enum: chiefdom
      enum: village
      enum: city
      enum: country
      enum: prefecture
      enum: sub-prefecture
      enum: clan
      enum: Federal Capital Territory
      enum: state
      enum: Local Government Area
      enum: ward
      type: string
    alternate name:
      description: An alias for the location
      one of:
        type: string
      one of:
        type: array
    identifier:
      description: An identifier for the location, preferably a Wikidata ID
      type: string
  location type:
    description: Categorization of how the location relates to the dataset
    const: collection
  name:
    description: The name of the location
    type: string
cardinality: many

type: string

items:
  type: string
type: array

type: string

description: The location where the sample is stored and/or may be ordered.
one of:
  type: array
  items: AdministrativeArea
    description: Location information
    type: object
    properties:
      administrative type:
        description: the type of administrative area, such as country, state, county, or city
        enum: province
        enum: district
        enum: chiefdom
        enum: village
        enum: city
        enum: country
        enum: prefecture
        enum: sub-prefecture
        enum: clan
        enum: Federal Capital Territory
        enum: state
        enum: Local Government Area
        enum: ward
        type: string
      alternate name:
        description: An alias for the location
      identifier:
        description: An identifier for the location, preferably a Wikidata ID
        type: string
      location type:
        description: Categorization of how the location relates to the dataset
        const: storage
      name:
        description: The name of the location
        type: string
one of: AdministrativeArea
  type: object
  description: Location information
  properties:
    administrative type:
      description: the type of administrative area, such as country, state, county, or city
      enum: province
      enum: district
      enum: chiefdom
      enum: village
      enum: city
      enum: country
      enum: prefecture
      enum: sub-prefecture
      enum: clan
      enum: Federal Capital Territory
      enum: state
      enum: Local Government Area
      enum: ward
      type: string
    alternate name:
      description: An alias for the location
      one of:
        type: string
      one of:
        type: array
    identifier:
      description: An identifier for the location, preferably a Wikidata ID
      type: string
  location type:
    description: Categorization of how the location relates to the dataset
    const: storage
  name:
    description: The name of the location
    type: string
cardinality: many

type: string

items:
  type: string
type: array

type: string

description: The primary citation or reference to a publication, dataset, or computational tool which uses the sample. Examples: a publication which describes the creation/collection/processing of the sample. The original reference by the sample collectors/processors/maintainers that should be cited when reusing the sample. For all other references by others reusing the sample, use 'citedBy'.
abstract: primary citation to the work
cardinality: many
any of:
  type: array
  items:
    $ref: #/definitions/citation
any of:
  $ref: #/definitions/citation
any of:
  type: array
  items:
    $ref: #/definitions/creativework
any of:
  $ref: #/definitions/creativework

description: Date the sample has changed: most recent date of dateModified, dateProcessed, and dateCollected.
abstract: date changed
format: date
type: string
cardinality: one

description: Date the work was created.
format: date
type: string
cardinality: one

description: Date the work was modified.
format: date
type: string
cardinality: one

description: Date the work was first published.
format: date
type: string
cardinality: one

description: The date on which the sample was collected.
format: date
type: string
cardinality: one

description: The date the sample was processed or used in a method.
format: date
type: string
cardinality: one

description: The number of interactions with the work, such as page views or tool downloads.
abstract: views or downloads
one of:
  items: InteractionCounter
    type: object
    properties:
      interaction type:
        type: string
      user interaction count:
        type: integer
    required: interactionType
    required: userInteractionCount
  type: array
one of: InteractionCounter
  type: object
  properties:
    interaction type:
      type: string
    user interaction count:
      type: integer
  required: interactionType
  required: userInteractionCount
cardinality: many

description: Keywords or tags used to describe this work.
abstract: keywords or tags
one of:
  type: array
  items:
    type: string
one of:
  type: string
cardinality: many

description: Original publisher of the sample metadata (like NCBI GEO, SRA, etc.).
abstract: original metadata source
one of:
  $ref: #/definitions/catalog
one of:
  type: array
  items:
    $ref: #/definitions/catalog
cardinality: many

description: The place(s) which are the focus of the sample.
abstract: geographic focus of the work
one of:
  items: AdministrativeArea
    description: Location information
    properties:
      administrative type:
        description: the type of administrative area, such as country, state, county, or city
        enum: province
        enum: district
        enum: chiefdom
        enum: village
        enum: city
        enum: country
        enum: prefecture
        enum: sub-prefecture
        enum: clan
        enum: Federal Capital Territory
        enum: state
        enum: Local Government Area
        enum: ward
        type: string
      alternate name:
        description: An alias for the location
      identifier:
        description: An identifier for the location, preferably a Wikidata ID
        type: string
      location type:
        description: Categorization of how the location relates to the dataset
      name:
        description: The name of the location
        type: string
    type: object
  type: array
one of: AdministrativeArea
  description: Location information
  properties:
    administrative type:
      description: the type of administrative area, such as country, state, county, or city
      enum: province
      enum: district
      enum: chiefdom
      enum: village
      enum: city
      enum: country
      enum: prefecture
      enum: sub-prefecture
      enum: clan
      enum: Federal Capital Territory
      enum: state
      enum: Local Government Area
      enum: ward
      type: string
    alternate name:
      description: An alias for the location
      one of:
        type: string
      one of:
        type: array
    identifier:
      description: An identifier for the location, preferably a Wikidata ID
      type: string
    location type:
      description: Categorization of how the location relates to the dataset
      one of:
        enum: residence
        enum: exposure
        enum: collection
        enum: screening
        enum: treatment
        enum: study location
        enum: other
        enum: unknown
        type: string
      one of:
        type: array
    name:
      description: The name of the location
      type: string
  type: object
cardinality: many

type: string

items:
  type: string
type: array

enum: residence
enum: exposure
enum: collection
enum: screening
enum: treatment
enum: study location
enum: other
enum: unknown
type: string

items:
  enum: residence
  enum: exposure
  enum: collection
  enum: screening
  enum: treatment
  enum: study location
  enum: other
  enum: unknown
  type: string
type: array

type: string

enum: residence
enum: exposure
enum: collection
enum: screening
enum: treatment
enum: study location
enum: other
enum: unknown
type: string

description: The period of time covered during sampling.
abstract: time period
one of:
  items: TemporalInterval
    description: Temporal information
    properties:
      duration:
        description: A time interval in ISO 8601 duration format
        type: string
      end date:
        description: An end date
        format: date
        type: string
      name:
        description: String describing the temporal interval
        type: string
      start date:
        description: A start date
        format: date
        type: string
      temporal type:
        description: Categorization of how the date/temporal interval relates to the dataset
    type: object
  type: array
one of: TemporalInterval
  description: Temporal information
  properties:
    duration:
      description: A time interval in ISO 8601 duration format
      type: string
    end date:
      description: An end date
      format: date
      type: string
    name:
      description: String describing the temporal interval
      type: string
    start date:
      description: A start date
      format: date
      type: string
    temporal type:
      description: Categorization of how the date/temporal interval relates to the dataset
      one of:
        enum: exposure
        enum: collection
        enum: screening
        enum: treatment
        enum: study date
        enum: other
        enum: unknown
        type: string
      one of:
        type: array
  type: object
cardinality: many

enum: exposure
enum: collection
enum: screening
enum: treatment
enum: study date
enum: other
enum: unknown
type: string

items:
  enum: exposure
  enum: collection
  enum: screening
  enum: treatment
  enum: study date
  enum: other
  enum: unknown
  type: string
type: array

enum: exposure
enum: collection
enum: screening
enum: treatment
enum: study date
enum: other
enum: unknown
type: string

description: The organization, research project, working group, or funded program on whose behalf the author/creator was working.
any of:
  type: array
  items:
    $ref: #/definitions/researchproject
any of:
  $ref: #/definitions/researchproject
any of:
  type: array
  items:
    $ref: #/definitions/organization
any of:
  $ref: #/definitions/organization
cardinality: many

description: Topic of the work. This topic may be assigned by a human curator or through automated algorithms.
abstract: topic
any of:
  type: array
  items:
    $ref: #/definitions/topic
any of:
  $ref: #/definitions/topic
any of:
  type: array
  items:
    $ref: #/definitions/definedterm
any of:
  $ref: #/definitions/definedterm
cardinality: many

description: Text that can be used to credit person(s) and/or organization(s) associated with a published Creative Work. For example, how a user should cite the sample.
type: string
cardinality: one

description: Other Property/Value pairs that describe the sample.
any of:
  type: array
  items:
    $ref: #/definitions/propertyvalue
any of:
  $ref: #/definitions/propertyvalue
cardinality: many

citation: ScholarlyArticle
  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: object
  properties:
    author:
      description: Author(s) of the publication
      any of:
        type: array
      any of:
        $ref: #/definitions/person
      any of:
        type: array
      any of:
        $ref: #/definitions/organization
    abstract:
      description: Abstract of the publication
      type: string
    date published:
      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
    issue number:
      description: Issue number where the article appears
      type: string
    journal name:
      description: Journal where the article appears
      type: string
    journal name abbrev:
      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
    volume number:
      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
  recommended: datePublished
  recommended: doi
  recommended: identifier
  recommended: journalName
  recommended: pmid
  recommended: url
  optional: abstract
  optional: citation
  optional: description
  optional: issueNumber
  optional: journalNameAbbrev
  optional: pagination
  optional: volumeNumber
creativework: CreativeWork
  description: A resource
  type: object
  properties:
    author:
      description: Author(s) of the referenced work
      any of:
        type: array
      any of:
        $ref: #/definitions/person
      any of:
        type: array
      any of:
        $ref: #/definitions/organization
    abstract:
      description: Abstract of the referenced work
      type: string
    date published:
      description: Date the referenced work was published
      format: date
      type: string
    description:
      description: Description of the referenced work
      type: string
    has part:
      description: A portion of the work
      one of:
        $ref: #/definitions/citation
    included in data catalog:
      description: Data or tool catalog which houses the work
      one of:
        $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
  recommended: datePublished
  recommended: doi
  recommended: identifier
  recommended: includedInDataCatalog
  recommended: relationship
  recommended: url
  optional: abstract
  optional: citation
  optional: description
  optional: hasPart
topic:
  description: Topic assigned to the work.
  type: string
  vocabulary:
    ontology: edam
    children of: http://edamontology.org/topic_0003
  strict: true
catalog: 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
    version date:
      description: date the metadata was harvested from the catalog
      type: string
      format: date
    archived at:
      description: The url(s) of one or more datasets, tools, resources or other items listed in a DataCatalog or ResourceCatalog
      one of:
        type: array
      one of:
        type: string
        format: uri
  required: name
  required: url
  recommended: versionDate
  recommended: archivedAt
organization: Organization
  description: Reusable organization definition
  properties:
    affiliation:
      type: object
      required: name
      optional: sameAs
      optional: url
    alternate name:
      description: Alias of the name
      one of:
        type: array
      one of:
        type: string
    name:
      description: Name of the organization
      type: string
    parent organization:
      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
  optional: alternateName
  optional: email
  optional: parentOrganization
  optional: role
  optional: url
  type: object
researchproject: ResearchProject
person: Person
definedterm: DefinedTerm
quantitativevalue: QuantitativeValue
softwareapplication: SoftwareApplication
sample: Sample
propertyvalue: PropertyValue

$ref: #/definitions/person

$ref: #/definitions/organization

$ref: #/definitions/person

$ref: #/definitions/organization

type: string
format: uri

description: Name of the affiliation, such as a university
type: string

description: Alias for the affiliation
type: string

description: URL of the affiliation
type: string
format: uri

type: string

ResearchProject
description: a type of organization definition
properties:
  alternate name:
    description: Alias of the name
    one of:
      type: array
      items:
        type: string
    one of:
      type: string
  name:
    description: Name of the organization
    type: string
  parent organization:
    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
recommended: url
recommended: parentOrganization
optional: alternateName
optional: email
optional: role
type: object

Person
description: Reusable person definition
properties:
  affiliation:
    type: object
    properties:
      name:
        description: Name of the affiliation, such as a university
        type: string
      same as:
        description: Alias for the affiliation
        type: string
      url:
        description: URL of the affiliation
        type: string
        format: uri
    required: name
    optional: sameAs
    optional: url
  name:
    description: Name of the person
    type: string
  email:
    description: Email address of the person
    type: string
  family name:
    description: Family name (surname) of the person
    type: string
  given name:
    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
recommended: givenName
recommended: identifier
optional: affiliation
optional: email
optional: role
optional: title
optional: url
type: object

DefinedTerm
type: object
properties:
  name:
    description: The name of the item.
    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.
    cardinality: one
    type: string
  url:
    description: URL of the item.
    cardinality: one
    type: string
    format: uri
  curated by:
    description: The person, organization, or catalog that curated this DefinedTerm for the metadata property
    any of:
      $ref: #/definitions/person
    any of:
      $ref: #/definitions/organization
    any of:
      $ref: #/definitions/catalog
    any of:
      $ref: #/definitions/researchproject
    any of:
      $ref: #/definitions/softwareapplication
  term code:
    description: A code that identifies this DefinedTerm within a DefinedTermSet.
    type: string
  description:
    description: A description of the item.
    type: string
  in defined term set:
    description: A DefinedTermSet that contains this term.
    type: string
  original name:
    description: The original name of the item, before any metadata standardization/normalization
    type: string
  is curated:
    description: A boolean indicator describing whether or not this DefinedTerm was curated as the value of a property.
    type: boolean

QuantitativeValue
description: A numeric value and unit for a property with potentially different units
type: object
properties:
  value:
    description: A numeric value for the property
    type: number
  max value:
    description: An estimated maximum numberic value if the actual value is not known. Ignore if actual numeric value is known.
    type: number
  min value:
    description: An estimated minumum numeric value if the actual value is not known. Ignore if actual numeric value is known.
    type: number
  unit text:
    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
optional: minValue

SoftwareApplication
description: Reusable software or algorithm definition
properties:
  name:
    description: name of the software, computational tool, or algorithm.
    type: string
  date modified:
    description: date the software, computational tool, or algorithm was run
    type: string
    format: date
  url:
    description: url of the software, computational tool, or algorithm
    type: string
    format: uri
required: name
recommended: url
optional: dateModified
type: object

Sample
description: reusable sample object
type: object
properties:
  name:
    description: sample name
    type: string
  url:
    description: Link to sample
    type: string
    format: uri
  identifier:
    description: an identifier for the sample
    type: string
  included in data catalog:
    description: Data or resource catalog where the sample is listed
    one of:
      $ref: #/definitions/catalog
    one of:
      type: array
      items:
        $ref: #/definitions/catalog
required: url
required: identifier
recommended: name
recommended: includedInDataCatalog

PropertyValue
description: A property value pair
type: object
properties:
  value:
    description: A value for the property
    type: string
  name:
    description: Name of the property
    type: string
required: name
recommended: value

type: string

type: string
format: uri

$ref: #/definitions/catalog

$ref: #/definitions/propertyvalue

$ref: #/definitions/quantitativevalue

$ref: #/definitions/minsample

type: string
format: uri

$ref: #/definitions/sample

description: Author(s) of the publication
any of:
  type: array
  items:
    $ref: #/definitions/person
any of:
  $ref: #/definitions/person
any of:
  type: array
  items:
    $ref: #/definitions/organization
any of:
  $ref: #/definitions/organization

description: Abstract of the publication
type: string

description: Date the article was published
format: date
type: string

description: Description of the publication
type: string

description: Title of the publication
type: string

description: An identifier associated with the citation such as a digital object identifier (DOI), PubMed ID (PMID), or PubMed Central ID (PMCID)
type: string

description: A PubMed identifier (PMID) of the referenced publication
abstract: PubMed identifier
type: string

description: A digital object identifier (DOI) of the referenced publication
abstract: digital object identifier
type: string

description: Issue number where the article appears
type: string

description: Journal where the article appears
type: string

description: Abbreviated journal name where the article appears
type: string

description: Page numbers in the journal where the article appears
type: string

description: The url of the article
type: string
format: uri

description: Volume of the journal where the article appears
type: string

description: The bibliographic citation string for the article as is provided
type: string

description: Author(s) of the referenced work
any of:
  type: array
  items:
    $ref: #/definitions/person
any of:
  $ref: #/definitions/person
any of:
  type: array
  items:
    $ref: #/definitions/organization
any of:
  $ref: #/definitions/organization

description: Abstract of the referenced work
type: string

description: Date the referenced work was published
format: date
type: string

description: Description of the referenced work
type: string

description: A portion of the work
one of:
  $ref: #/definitions/citation

description: Data or tool catalog which houses the work
one of:
  $ref: #/definitions/catalog

description: Name or title
type: string

description: An identifier associated with the work
type: string

description: How the works are related
type: string

description: A digital object identifier (DOI) of the referenced work
abstract: digital object identifier
type: string

description: The url of the work
type: string
format: uri

description: The bibliographic citation for the referenced work as is provided
type: string

description: Data or tool catalog name
type: string

description: Link to data or tool catalog
type: string
format: uri

description: date the metadata was harvested from the catalog
type: string
format: date

description: The url(s) of one or more datasets, tools, resources or other items listed in a DataCatalog or ResourceCatalog
one of:
  items:
    type: string
    format: uri
  type: array
one of:
  type: string
  format: uri

type: object
properties:
  name:
    description: Name of the affiliation, such as a university
    type: string
  same as:
    description: Alias for the affiliation
    type: string
  url:
    description: URL of the affiliation
    type: string
    format: uri
required: name
optional: sameAs
optional: url

description: Alias of the name
one of:
  type: array
  items:
    type: string
one of:
  type: string

description: Name of the organization
type: string

description: Name of the parent organization. For instance, the parentOrganization of NIAID is the National Institutes of health (NIH)
type: string

description: Email address of the organization
type: string

description: Unique identifier of the organization
type: string

description: What role the organization played in creating the dataset
type: string

description: Link to the organization
type: string
format: uri

description: Alias of the name
one of:
  type: array
  items:
    type: string
one of:
  type: string

description: Name of the organization
type: string

description: Name of the parent organization. For instance, the parentOrganization of NIAID is the National Institutes of health (NIH)
type: string

description: Email address of the organization
type: string

description: Unique identifier of the organization
type: string

description: Link to the organization
type: string
format: uri

type: object
properties:
  name:
    description: Name of the affiliation, such as a university
    type: string
  same as:
    description: Alias for the affiliation
    type: string
  url:
    description: URL of the affiliation
    type: string
    format: uri
required: name
optional: sameAs
optional: url

description: Name of the person
type: string

description: Email address of the person
type: string

description: Family name (surname) of the person
type: string

description: Given (first) name of the person
type: string

description: Unique identifier of the person, like an ORCID ID
type: string

description: Role the person played in creating the dataset
type: string

description: Title of the person
type: string

description: Link to the homepage or other web content describing the person
type: string
format: uri

description: The name of the item.
cardinality: one
type: string

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.
cardinality: one
type: string

description: URL of the item.
cardinality: one
type: string
format: uri

description: The person, organization, or catalog that curated this DefinedTerm for the metadata property
any of:
  $ref: #/definitions/person
any of:
  $ref: #/definitions/organization
any of:
  $ref: #/definitions/catalog
any of:
  $ref: #/definitions/researchproject
any of:
  $ref: #/definitions/softwareapplication

description: A code that identifies this DefinedTerm within a DefinedTermSet.
type: string

description: A description of the item.
type: string

description: A DefinedTermSet that contains this term.
type: string

description: The original name of the item, before any metadata standardization/normalization
type: string

description: A boolean indicator describing whether or not this DefinedTerm was curated as the value of a property.
type: boolean

description: A numeric value for the property
type: number

description: An estimated maximum numberic value if the actual value is not known. Ignore if actual numeric value is known.
type: number

description: An estimated minumum numeric value if the actual value is not known. Ignore if actual numeric value is known.
type: number

description: A unit associated with the value. E.g.- 'records' for the number of records in a database.
type: string

description: A numeric value for the property
type: number

description: An estimated maximum numberic value if the actual value is not known. Ignore if actual numeric value is known.
type: number

description: An estimated minumum numeric value if the actual value is not known. Ignore if actual numeric value is known.
type: number

description: A unit associated with the value. E.g.- 'records' for the number of records in a database.
type: string

description: A commonly used identifier for the characteristic represented by the property, e.g. a manufacturer or a standard code for a property. propertyID can be (1) a prefixed string, mainly meant to be used with standards for product properties; (2) a site-specific, non-prefixed string (e.g. the primary key of the property or the vendor-specific ID of the property), or (3) a URL indicating the type of the property, either pointing to an external vocabulary, or a Web resource that describes the property (e.g. a glossary entry). Standards bodies should promote a standard prefix for the identifiers of properties from their standards.
one of:
  type: string
one of:
  type: string
  format: uri

description: name of the software, computational tool, or algorithm.
type: string

description: date the software, computational tool, or algorithm was run
type: string
format: date

description: url of the software, computational tool, or algorithm
type: string
format: uri

description: sample name
type: string

description: Link to sample
type: string
format: uri

description: an identifier for the sample
type: string

description: Data or resource catalog where the sample is listed
one of:
  $ref: #/definitions/catalog
one of:
  type: array
  items:
    $ref: #/definitions/catalog

description: The terms under which the sample can be used. Note that this is related to but distinct from the license.
abstract: sample usage agreement
one of:
  type: array
  items:
    $ref: #/definitions/creativework
one of:
  $ref: #/definitions/creativework
cardinality: many

description: A license document that applies to this work, typically indicated by URL.
abstract: license for use
format: uri
cardinality: one
type: string

description: Conditions that affect the availability of, or method(s) of access to, the sample. Options include open (freely available), restricted (may include restrictions such as on use), closed (requires registration to access), or embargoed (unpublished).
abstract: accessibility of the work
type: string
enum: Closed
enum: Open
enum: Restricted
enum: Embargoed
cardinality: one

description: A flag to signal that the sample may be requested at no cost (not including shipping).
abstract: accessible without charge
type: boolean
cardinality: one

description: one or more observable traits or conditions relevant to the source of the sample.
any of:
  description: collection of vocabulary terms defined in ontologies
  strict: false
  type: string
  vocabulary:
    children of: http://purl.obolibrary.org/obo/UPHENO_0001001
    children of: http://purl.obolibrary.org/obo/PATO_0000001
    ontology: UPHENO
    ontology: PATO
any of:
  items:
    description: collection of vocabulary terms defined in ontologies
    strict: false
    type: string
    vocabulary:
      children of: http://purl.obolibrary.org/obo/UPHENO_0001001
      children of: http://purl.obolibrary.org/obo/PATO_0000001
      ontology: UPHENO
      ontology: PATO
  type: array
any of:
  type: array
  items:
    $ref: #/definitions/definedterm
any of:
  $ref: #/definitions/definedterm
cardinality: many

description: One or more genetic variants or molecular features observed or inferred from the sample.
any of:
  description: collection of vocabulary terms defined in ontologies
  strict: false
  type: string
  vocabulary:
    children of: http://purl.obolibrary.org/obo/NCIT_C16612
    children of: http://purl.obolibrary.org/obo/NCIT_C20181
    children of: http://purl.obolibrary.org/obo/NCIT_C17649
    ontology: NCIT
any of:
  items:
    description: collection of vocabulary terms defined in ontologies
    strict: false
    type: string
    vocabulary:
      children of: http://purl.obolibrary.org/obo/NCIT_C16612
      children of: http://purl.obolibrary.org/obo/NCIT_C20181
      children of: http://purl.obolibrary.org/obo/NCIT_C17649
      ontology: NCIT
  type: array
any of:
  type: array
  items:
    $ref: #/definitions/definedterm
any of:
  $ref: #/definitions/definedterm
cardinality: many

description: The type of cell represented in or derived from the biological sample, based on morphology, lineage, or molecular markers.
any of:
  description: collection of vocabulary terms defined in ontologies
  strict: false
  type: string
  vocabulary:
    children of: http://purl.obolibrary.org/obo/CL_0000000
    children of: http://purl.obolibrary.org/obo/CLO_0000031
    ontology: CL
    ontology: CLO
any of:
  items:
    description: collection of vocabulary terms defined in ontologies
    strict: false
    type: string
    vocabulary:
      children of: http://purl.obolibrary.org/obo/CL_0000000
      children of: http://purl.obolibrary.org/obo/CLO_0000031
      ontology: CL
      ontology: CLO
  type: array
any of:
  type: array
  items:
    $ref: #/definitions/definedterm
any of:
  $ref: #/definitions/definedterm
cardinality: many

description: Infectious agent(s) / pathogen(s) which are the focus of the work (like SARS-CoV-2).
abstract: infectious agent / pathogen
any of:
  description: collection of vocabulary terms defined in ontologies
  strict: false
  type: string
  vocabulary:
    children of: http://purl.obolibrary.org/obo/NCBITaxon_10239
    children of: http://purl.obolibrary.org/obo/NCBITaxon_2
    ontology: ncbitaxon
any of:
  items:
    description: collection of vocabulary terms defined in ontologies
    strict: false
    type: string
    vocabulary:
      children of: http://purl.obolibrary.org/obo/NCBITaxon_10239
      children of: http://purl.obolibrary.org/obo/NCBITaxon_2
      ontology: ncbitaxon
  type: array
any of:
  type: array
  items:
    $ref: #/definitions/definedterm
any of:
  $ref: #/definitions/definedterm
cardinality: many

description: The health condition(s) /infectious disease(s) which are the focus of the work (like COVID-19, coronavirus).
abstract: health condition/disease
any of:
  description: collection of vocabulary terms defined in ontologies
  strict: false
  type: string
  vocabulary:
    children of: http://purl.obolibrary.org/obo/MONDO_0000001
    children of: http://purl.obolibrary.org/obo/DOID_4
    children of: http://purl.obolibrary.org/obo/HP_0000001
    children of: http://purl.obolibrary.org/obo/NCIT_C7057
    ontology: mondo
    ontology: hpo
    ontology: doid
    ontology: ncit
any of:
  items:
    description: collection of vocabulary terms defined in ontologies
    strict: false
    type: string
    vocabulary:
      children of: http://purl.obolibrary.org/obo/MONDO_0000001
      children of: http://purl.obolibrary.org/obo/DOID_4
      children of: http://purl.obolibrary.org/obo/HP_0000001
      children of: http://purl.obolibrary.org/obo/NCIT_C7057
      ontology: mondo
      ontology: hpo
      ontology: doid
      ontology: ncit
  type: array
any of:
  type: array
  items:
    $ref: #/definitions/definedterm
any of:
  $ref: #/definitions/definedterm
cardinality: many

description: Funding that supports (sponsors) the collection of this dataset through some kind of financial contribution.
abstract: funding source (grant, contract, etc.)
one of: MonetaryGrant
  type: object
  description: Funding that supports (sponsors) the collection of this dataset through some kind of financial contribution
  properties:
    funder:
      description: An organization associated with a creator or funder of a dataset
      one of: Organization
        type: object
        description: Information about a single funder
        required: name
      one of:
        type: array
        items: Organization
    description:
      type: string
      description: description about the funding award / grant
    url:
      type: string
      description: award / grant URL
    identifier:
      type: string
      description: Unique identifier(s) for the grant(s) used to fund the Dataset
  required: funder
  required: identifier
one of:
  type: array
  items: MonetaryGrant
    type: object
    description: Funding that supports (sponsors) the collection of this dataset through some kind of financial contribution
    properties:
      funder:
        description: An organization associated with a creator or funder of a dataset
        one of: Organization
      description:
        type: string
        description: description about the funding award / grant
      url:
        type: string
        description: award / grant URL
      identifier:
        type: string
        description: Unique identifier(s) for the grant(s) used to fund the Dataset
    required: funder
    required: identifier
cardinality: many

name:
  type: string
  description: An organization associated with a creator or funder of a dataset
parent organization:
  type: string
  description: name of the parent funding organization

Organization
type: object
description: Information about a single funder
properties:
  name:
    type: string
    description: An organization associated with a creator or funder of a dataset
  parent organization:
    type: string
    description: name of the parent funding organization
required: name

Organization
type: object
description: Information about a single funder
properties:
  name:
    type: string
    description: An organization associated with a creator or funder of a dataset
  parent organization:
    type: string
    description: name of the parent funding organization
required: name

type: array
items: Organization
  type: object
  description: Information about a single funder
  properties:
    name:
      type: string
      description: An organization associated with a creator or funder of a dataset
    parent organization:
      type: string
      description: name of the parent funding organization
  required: name

description: Species / host organism from which the dataset has been collected.
abstract: species/host organism
any of:
  description: collection of vocabulary terms defined in ontologies
  strict: false
  type: string
  vocabulary:
    children of: http://purl.obolibrary.org/obo/NCBITaxon_131567
    children of: http://purl.obolibrary.org/obo/NCBITaxon_10239
    ontology: ncbitaxon
any of:
  items:
    description: collection of vocabulary terms defined in ontologies
    strict: false
    type: string
    vocabulary:
      children of: http://purl.obolibrary.org/obo/NCBITaxon_131567
      children of: http://purl.obolibrary.org/obo/NCBITaxon_10239
      ontology: ncbitaxon
  type: array
any of:
  type: array
  items:
    $ref: #/definitions/definedterm
any of:
  $ref: #/definitions/definedterm
cardinality: many

description: Publications, datasets, or computational tools that cite the sample. Examples: a dataset which reuses the sample in a secondary study.
any of:
  type: array
  items:
    $ref: #/definitions/citation
any of:
  $ref: #/definitions/citation
any of:
  type: array
  items:
    $ref: #/definitions/creativework
any of:
  $ref: #/definitions/creativework
cardinality: many

description: Datasets, resources, or samples which are related to the given sample; often sample involved in the same study. These linkages are created via human curation.
abstract: related resources or samples (via curation)
any of:
  type: array
  items:
    $ref: #/definitions/citation
any of:
  $ref: #/definitions/citation
any of:
  type: array
  items:
    $ref: #/definitions/creativework
any of:
  $ref: #/definitions/creativework
any of:
  type: array
  items:
    $ref: #/definitions/minsample
any of:
  $ref: #/definitions/minsample
cardinality: many

description: Datasets, resources, or samples which are similar to the sample, based on terms in the names, descriptions, authors, measurementTechniques, infectiousAgents, healthConditions, etc.
abstract: similar resources of samples (auto-assigned)
any of:
  type: array
  items:
    $ref: #/definitions/citation
any of:
  $ref: #/definitions/citation
any of:
  type: array
  items:
    $ref: #/definitions/creativework
any of:
  $ref: #/definitions/creativework
any of:
  type: array
  items:
    $ref: #/definitions/minsample
any of:
  $ref: #/definitions/minsample
cardinality: many

description: A resource or sample which reuses the sample. For example, a sample of a cell line that was created by knocking out a gene from this cell line sample. Another example would be a sample of infected tissue that was derived from this tissue sample by infecting it with a virus.
any of:
  type: array
  items:
    $ref: #/definitions/citation
any of:
  $ref: #/definitions/citation
any of:
  type: array
  items:
    $ref: #/definitions/creativework
any of:
  $ref: #/definitions/creativework
any of:
  type: array
  items:
    $ref: #/definitions/minsample
any of:
  $ref: #/definitions/minsample
cardinality: many

description: A resource or sample from which this sample is derived, modified, or adapted. For example a sample of a cell line, which was infected by virus sample in order to create the sample.
abstract: resource or sample used to create the sample.
cardinality: many
any of:
  type: array
  items:
    $ref: #/definitions/citation
any of:
  $ref: #/definitions/citation
any of:
  type: array
  items:
    $ref: #/definitions/creativework
any of:
  $ref: #/definitions/creativework
any of:
  type: array
  items:
    $ref: #/definitions/minsample
any of:
  $ref: #/definitions/minsample

description: Associated materials that constitute the sample. For example, other samples (if sample was created by pooling samples), additives, cryoprotective agents, etc. Use 'hasPart' for samples that were generated by pooling other samples. For example, a synthetic microbiome sample may use 'hasPart' to list the individual microbial samples used to generate it.
abstract: Associated materials or samples that constitute the sample
any of:
  type: array
  items:
    $ref: #/definitions/citation
any of:
  $ref: #/definitions/citation
any of:
  type: array
  items:
    $ref: #/definitions/creativework
any of:
  $ref: #/definitions/creativework
any of:
  type: array
  items:
    $ref: #/definitions/minsample
any of:
  $ref: #/definitions/minsample
cardinality: many

description: Associated materials the sample may help constitute. For example, the pooled sample that used this sample. Use 'isPartOf' for pooled samples generated from this sample. For example, a microbial sample that was used to generate a synthetic microbiome sample.
abstract: study or project including the work
cardinality: many
any of:
  type: array
  items:
    $ref: #/definitions/citation
any of:
  $ref: #/definitions/citation
any of:
  type: array
  items:
    $ref: #/definitions/creativework
any of:
  $ref: #/definitions/creativework
any of:
  type: array
  items:
    $ref: #/definitions/minsample
any of:
  $ref: #/definitions/minsample

description: Indicate the anatomical system from which the sample is collect, e.g. circulatory, digestive, endocrine, immune and other systems.
any of:
  description: collection of vocabulary terms defined in ontologies
  strict: false
  type: string
  vocabulary:
    children of: http://purl.obolibrary.org/obo/UBERON_0000467
    ontology: UBERON
any of:
  items:
    description: collection of vocabulary terms defined in ontologies
    strict: false
    type: string
    vocabulary:
      children of: http://purl.obolibrary.org/obo/UBERON_0000467
      ontology: UBERON
  type: array
any of:
  type: array
  items:
    $ref: #/definitions/definedterm
any of:
  $ref: #/definitions/definedterm
cardinality: many

description: Indicate the organ, tissues the sample was collected from.
any of:
  description: collection of vocabulary terms defined in ontologies
  strict: false
  type: string
  vocabulary:
    children of: http://purl.obolibrary.org/obo/UBERON_0001062
    ontology: UBERON
any of:
  items:
    description: collection of vocabulary terms defined in ontologies
    strict: false
    type: string
    vocabulary:
      children of: http://purl.obolibrary.org/obo/UBERON_0001062
      ontology: UBERON
  type: array
any of:
  type: array
  items:
    $ref: #/definitions/definedterm
any of:
  $ref: #/definitions/definedterm
cardinality: many

description: The biological sex of the individual from which the sample was obtained.
any of:
  description: collection of vocabulary terms defined in ontologies
  strict: false
  type: string
  vocabulary:
    children of: http://purl.obolibrary.org/obo/PATO_0000047
    ontology: PATO
any of:
  items:
    description: collection of vocabulary terms defined in ontologies
    strict: false
    type: string
    vocabulary:
      children of: http://purl.obolibrary.org/obo/PATO_0000047
      ontology: PATO
  type: array
any of:
  type: array
  items:
    $ref: #/definitions/definedterm
any of:
  $ref: #/definitions/definedterm
cardinality: many

description: A temporal subdivision of a developmental process, indicating the age or stage of the object when the sample was created.
any of:
  description: collection of vocabulary terms defined in ontologies
  strict: false
  type: string
  vocabulary:
    children of: http://purl.obolibrary.org/obo/UBERON_0000104
    children of: http://purl.obolibrary.org/obo/NCIT_C48308
    ontology: UBERON
    ontology: NCIT
any of:
  items:
    description: collection of vocabulary terms defined in ontologies
    strict: false
    type: string
    vocabulary:
      children of: http://purl.obolibrary.org/obo/UBERON_0000104
      children of: http://purl.obolibrary.org/obo/NCIT_C48308
      ontology: UBERON
      ontology: NCIT
  type: array
any of:
  type: array
  items:
    $ref: #/definitions/definedterm
any of:
  $ref: #/definitions/definedterm
any of:
  type: array
  items:
    $ref: #/definitions/quantitativevalue
any of:
  $ref: #/definitions/quantitativevalue
cardinality: many

description: A flag to signal that the sample is available for reuse.
abstract: availability of the sample
type: boolean
cardinality: one

description: The processing technique that was applied to the sample, methods used to prepare the samples.
any of:
  description: collection of vocabulary terms defined in ontologies
  strict: false
  type: string
  vocabulary:
    children of: http://purl.obolibrary.org/obo/OBI_0000094
    children of: http://purl.obolibrary.org/obo/NCIT_C48177
    children of: http://purl.obolibrary.org/obo/NCIT_C16680
    ontology: OBI
    ontology: NCIT
any of:
  items:
    description: collection of vocabulary terms defined in ontologies
    strict: false
    type: string
    vocabulary:
      children of: http://purl.obolibrary.org/obo/OBI_0000094
      children of: http://purl.obolibrary.org/obo/NCIT_C48177
      children of: http://purl.obolibrary.org/obo/NCIT_C16680
      ontology: OBI
      ontology: NCIT
  type: array
any of:
  type: array
  items:
    $ref: #/definitions/definedterm
any of:
  $ref: #/definitions/definedterm
any of:
  type: array
  items:
    $ref: #/definitions/creativework
any of:
  $ref: #/definitions/creativework
any of:
  type: string
cardinality: many

description: A numeric value for a measurement of the size of a sample. If completely unknown, set value = 0, and unitText = 'unknown'
one of:
  type: array
  items:
    $ref: #/definitions/quantitativevalue
one of:
  $ref: #/definitions/quantitativevalue
cardinality: many

description: Specify the condition, composition or state of the sample, for example dried, frozen, passage number.
any of:
  type: string
any of:
  type: array
  items:
    $ref: #/definitions/quantitativevalue
any of:
  $ref: #/definitions/quantitativevalue
cardinality: many

description: The temperature at which the sample is stored.
one of:
  type: array
  items:
    $ref: #/definitions/quantitativevalue
one of:
  $ref: #/definitions/quantitativevalue
cardinality: one

description: The type of sample or specimen.
any of:
  description: collection of vocabulary terms defined in ontologies
  strict: false
  type: string
  vocabulary:
    children of: http://purl.obolibrary.org/obo/BFO_0000040
    ontology: OBI
any of:
  items:
    description: collection of vocabulary terms defined in ontologies
    strict: false
    type: string
    vocabulary:
      children of: http://purl.obolibrary.org/obo/BFO_0000040
      ontology: OBI
  type: array
any of:
  type: array
  items:
    $ref: #/definitions/definedterm
any of:
  $ref: #/definitions/definedterm
cardinality: many

description: A downloadable form of this dataset, at a specific location, in a specific format.
abstract: download link
one of:
  items: DataDownload
    description: A dataset in downloadable form.
    properties:
      content url:
        format: uri
        type: string
      encoding format:
        description: file type (ex: XLSX)
        type: string
      date modified:
        format: date
        description: date the file was modified
        type: string
    required: dateModified
    required: contentUrl
    type: object
  type: array
one of: DataDownload
  description: A dataset in downloadable form.
  properties:
    content url:
      format: uri
      type: string
    encoding format:
      description: file type (ex: XLSX)
      type: string
    date modified:
      format: date
      description: date the file was modified
      type: string
  required: dateModified
  required: contentUrl
  type: object
cardinality: many

description: A technique or technology used in the collection or processing of the sample corresponding to the method used for measuring the corresponding variable(s) (described using variableMeasured). For example, if variableMeasured is cell density or cell counts, measurementTechnique could be: "centrifugation" or "flow cytometry".
abstract: measurement technique used to collect, process, or generate the sample
any of:
  description: collection of vocabulary terms defined in ontologies
  strict: false
  type: string
  vocabulary:
    children of: http://edamontology.org/topic_3361
    children of: http://purl.obolibrary.org/obo/NCIT_C20368
    children of: http://purl.obolibrary.org/obo/MMO_0000000
    children of: http://www.ebi.ac.uk/efo/EFO_0000001
    ontology: edam
    ontology: ncit
    ontology: mmo
    ontology: efo
any of:
  items:
    description: collection of vocabulary terms defined in ontologies
    strict: false
    type: string
    vocabulary:
      children of: http://edamontology.org/topic_3361
      children of: http://purl.obolibrary.org/obo/NCIT_C20368
      children of: http://purl.obolibrary.org/obo/MMO_0000000
      children of: http://www.ebi.ac.uk/efo/EFO_0000001
      ontology: edam
      ontology: ncit
      ontology: mmo
      ontology: efo
  type: array
any of:
  type: array
  items:
    $ref: #/definitions/definedterm
any of:
  $ref: #/definitions/definedterm
cardinality: many

description: Variables measured within the sample.
one of:
  description: collection of vocabulary terms defined in ontologies
  strict: false
  type: string
  vocabulary:
    children of: http://www.ebi.ac.uk/efo/EFO_0000001
    children of: http://purl.obolibrary.org/obo/CMO_0000000
    children of: http://purl.obolibrary.org/obo/NCIT_C25209
    ontology: efo
    ontology: cmo
    ontology: ncit
one of:
  items:
    description: collection of vocabulary terms defined in ontologies
    strict: false
    type: string
    vocabulary:
      children of: http://www.ebi.ac.uk/efo/EFO_0000001
      children of: http://purl.obolibrary.org/obo/CMO_0000000
      children of: http://purl.obolibrary.org/obo/NCIT_C25209
      ontology: efo
      ontology: cmo
      ontology: ncit
  type: array
one of:
  type: array
  items:
    $ref: #/definitions/definedterm
one of:
  $ref: #/definitions/definedterm
cardinality: many

description: Provide information about the conditions and methods of acquisition of samples.
any of:
  type: string
  format: uri
any of:
  items:
    type: string
    format: uri
  type: array
any of:
  type: string
any of:
  items:
    type: string
  type: array
any of:
  type: array
  items:
    $ref: #/definitions/definedterm
any of:
  $ref: #/definitions/definedterm
cardinality: many

description: Provide description of instruments and devices used in collecting, processing and analysis of samples.
any of:
  type: string
  format: uri
any of:
  items:
    type: string
    format: uri
  type: array
any of:
  type: string
any of:
  items:
    type: string
  type: array
any of:
  type: array
  items:
    $ref: #/definitions/definedterm
any of:
  $ref: #/definitions/definedterm
cardinality: many

description: A category or description of the habitat that describes elements of an ecosystem where the sample was collected. Where possible use controlled vocabulary such as ENVO.
any of:
  description: collection of vocabulary terms defined in ontologies
  strict: false
  type: string
  vocabulary:
    children of: http://purl.obolibrary.org/obo/ENVO_00010483
    children of: http://purl.obolibrary.org/obo/NCIT_C62574
    ontology: ENVO
    ontology: NCIT
any of:
  items:
    description: collection of vocabulary terms defined in ontologies
    strict: false
    type: string
    vocabulary:
      children of: http://purl.obolibrary.org/obo/ENVO_00010483
      children of: http://purl.obolibrary.org/obo/NCIT_C62574
      ontology: ENVO
      ontology: NCIT
  type: array
any of:
  type: array
  items:
    $ref: #/definitions/definedterm
any of:
  $ref: #/definitions/definedterm
cardinality: many

description: Describe the planned or executed experimental procedures involving the samples.
one of:
  type: string
one of:
  items:
    type: string
  type: array
cardinality: many

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
one of:
  items: AggregateRating
    type: object
    properties:
      rating count:
        description: Total number of ratings
        type: integer
      rating value:
        description: Average rating
        type: string
      item reviewed:
        description: What is being reviewed
        type: string
    required: ratingValue
    recommended: ratingCount
    recommended: itemReviewed
  type: array
one of: AggregateRating
  type: object
  properties:
    rating count:
      description: Total number of ratings
      type: integer
    rating value:
      description: Average rating
      type: string
    item reviewed:
      description: What is being reviewed
      type: string
  required: ratingValue
  recommended: ratingCount
  recommended: itemReviewed
cardinality: many

description: A person or organization responsible for the collection, processing, or maintenance of the sample: Populated from collector, contributor, and maintainer.
any of:
  type: array
  items:
    $ref: #/definitions/person
any of:
  $ref: #/definitions/person
any of:
  type: array
  items:
    $ref: #/definitions/organization
any of:
  $ref: #/definitions/organization
cardinality: many

description: The Person or Organization who collected the Sample.
any of:
  type: array
  items:
    $ref: #/definitions/person
any of:
  $ref: #/definitions/person
any of:
  type: array
  items:
    $ref: #/definitions/organization
any of:
  $ref: #/definitions/organization
cardinality: many

description: Person or organization that contributes to the work.
any of:
  type: array
  items:
    $ref: #/definitions/person
any of:
  $ref: #/definitions/person
any of:
  type: array
  items:
    $ref: #/definitions/organization
any of:
  $ref: #/definitions/organization
cardinality: many

description: The Person or Organization who is responsible for the Sample.
any of:
  type: array
  items:
    $ref: #/definitions/person
any of:
  $ref: #/definitions/person
any of:
  type: array
  items:
    $ref: #/definitions/organization
any of:
  $ref: #/definitions/organization
cardinality: many

description: The location from which the sample was originally collected.
one of:
  items: AdministrativeArea
    description: Location information
    properties:
      administrative type:
        description: the type of administrative area, such as country, state, county, or city
        enum: province
        enum: district
        enum: chiefdom
        enum: village
        enum: city
        enum: country
        enum: prefecture
        enum: sub-prefecture
        enum: clan
        enum: Federal Capital Territory
        enum: state
        enum: Local Government Area
        enum: ward
        type: string
      alternate name:
        description: An alias for the location
      identifier:
        description: An identifier for the location, preferably a Wikidata ID
        type: string
      location type:
        description: Categorization of how the location relates to the dataset
        const: collection
      name:
        description: The name of the location
        type: string
    type: object
  type: array
one of: AdministrativeArea
  type: object
  description: Location information
  properties:
    administrative type:
      description: the type of administrative area, such as country, state, county, or city
      enum: province
      enum: district
      enum: chiefdom
      enum: village
      enum: city
      enum: country
      enum: prefecture
      enum: sub-prefecture
      enum: clan
      enum: Federal Capital Territory
      enum: state
      enum: Local Government Area
      enum: ward
      type: string
    alternate name:
      description: An alias for the location
      one of:
        type: string
      one of:
        type: array
    identifier:
      description: An identifier for the location, preferably a Wikidata ID
      type: string
  location type:
    description: Categorization of how the location relates to the dataset
    const: collection
  name:
    description: The name of the location
    type: string
cardinality: many

type: string

items:
  type: string
type: array

type: string

description: The location where the sample is stored and/or may be ordered.
one of:
  type: array
  items: AdministrativeArea
    description: Location information
    type: object
    properties:
      administrative type:
        description: the type of administrative area, such as country, state, county, or city
        enum: province
        enum: district
        enum: chiefdom
        enum: village
        enum: city
        enum: country
        enum: prefecture
        enum: sub-prefecture
        enum: clan
        enum: Federal Capital Territory
        enum: state
        enum: Local Government Area
        enum: ward
        type: string
      alternate name:
        description: An alias for the location
      identifier:
        description: An identifier for the location, preferably a Wikidata ID
        type: string
      location type:
        description: Categorization of how the location relates to the dataset
        const: storage
      name:
        description: The name of the location
        type: string
one of: AdministrativeArea
  type: object
  description: Location information
  properties:
    administrative type:
      description: the type of administrative area, such as country, state, county, or city
      enum: province
      enum: district
      enum: chiefdom
      enum: village
      enum: city
      enum: country
      enum: prefecture
      enum: sub-prefecture
      enum: clan
      enum: Federal Capital Territory
      enum: state
      enum: Local Government Area
      enum: ward
      type: string
    alternate name:
      description: An alias for the location
      one of:
        type: string
      one of:
        type: array
    identifier:
      description: An identifier for the location, preferably a Wikidata ID
      type: string
  location type:
    description: Categorization of how the location relates to the dataset
    const: storage
  name:
    description: The name of the location
    type: string
cardinality: many

type: string

items:
  type: string
type: array

type: string

description: The primary citation or reference to a publication, dataset, or computational tool which uses the sample. Examples: a publication which describes the creation/collection/processing of the sample. The original reference by the sample collectors/processors/maintainers that should be cited when reusing the sample. For all other references by others reusing the sample, use 'citedBy'.
abstract: primary citation to the work
cardinality: many
any of:
  type: array
  items:
    $ref: #/definitions/citation
any of:
  $ref: #/definitions/citation
any of:
  type: array
  items:
    $ref: #/definitions/creativework
any of:
  $ref: #/definitions/creativework

description: Date the sample has changed: most recent date of dateModified, dateProcessed, and dateCollected.
abstract: date changed
format: date
type: string
cardinality: one

description: Date the work was created.
format: date
type: string
cardinality: one

description: Date the work was modified.
format: date
type: string
cardinality: one

description: Date the work was first published.
format: date
type: string
cardinality: one

description: The date on which the sample was collected.
format: date
type: string
cardinality: one

description: The date the sample was processed or used in a method.
format: date
type: string
cardinality: one

description: The number of interactions with the work, such as page views or tool downloads.
abstract: views or downloads
one of:
  items: InteractionCounter
    type: object
    properties:
      interaction type:
        type: string
      user interaction count:
        type: integer
    required: interactionType
    required: userInteractionCount
  type: array
one of: InteractionCounter
  type: object
  properties:
    interaction type:
      type: string
    user interaction count:
      type: integer
  required: interactionType
  required: userInteractionCount
cardinality: many

description: Keywords or tags used to describe this work.
abstract: keywords or tags
one of:
  type: array
  items:
    type: string
one of:
  type: string
cardinality: many

description: Original publisher of the sample metadata (like NCBI GEO, SRA, etc.).
abstract: original metadata source
one of:
  $ref: #/definitions/catalog
one of:
  type: array
  items:
    $ref: #/definitions/catalog
cardinality: many

description: The place(s) which are the focus of the sample.
abstract: geographic focus of the work
one of:
  items: AdministrativeArea
    description: Location information
    properties:
      administrative type:
        description: the type of administrative area, such as country, state, county, or city
        enum: province
        enum: district
        enum: chiefdom
        enum: village
        enum: city
        enum: country
        enum: prefecture
        enum: sub-prefecture
        enum: clan
        enum: Federal Capital Territory
        enum: state
        enum: Local Government Area
        enum: ward
        type: string
      alternate name:
        description: An alias for the location
      identifier:
        description: An identifier for the location, preferably a Wikidata ID
        type: string
      location type:
        description: Categorization of how the location relates to the dataset
      name:
        description: The name of the location
        type: string
    type: object
  type: array
one of: AdministrativeArea
  description: Location information
  properties:
    administrative type:
      description: the type of administrative area, such as country, state, county, or city
      enum: province
      enum: district
      enum: chiefdom
      enum: village
      enum: city
      enum: country
      enum: prefecture
      enum: sub-prefecture
      enum: clan
      enum: Federal Capital Territory
      enum: state
      enum: Local Government Area
      enum: ward
      type: string
    alternate name:
      description: An alias for the location
      one of:
        type: string
      one of:
        type: array
    identifier:
      description: An identifier for the location, preferably a Wikidata ID
      type: string
    location type:
      description: Categorization of how the location relates to the dataset
      one of:
        enum: residence
        enum: exposure
        enum: collection
        enum: screening
        enum: treatment
        enum: study location
        enum: other
        enum: unknown
        type: string
      one of:
        type: array
    name:
      description: The name of the location
      type: string
  type: object
cardinality: many

type: string

items:
  type: string
type: array

enum: residence
enum: exposure
enum: collection
enum: screening
enum: treatment
enum: study location
enum: other
enum: unknown
type: string

items:
  enum: residence
  enum: exposure
  enum: collection
  enum: screening
  enum: treatment
  enum: study location
  enum: other
  enum: unknown
  type: string
type: array

type: string

enum: residence
enum: exposure
enum: collection
enum: screening
enum: treatment
enum: study location
enum: other
enum: unknown
type: string

description: The period of time covered during sampling.
abstract: time period
one of:
  items: TemporalInterval
    description: Temporal information
    properties:
      duration:
        description: A time interval in ISO 8601 duration format
        type: string
      end date:
        description: An end date
        format: date
        type: string
      name:
        description: String describing the temporal interval
        type: string
      start date:
        description: A start date
        format: date
        type: string
      temporal type:
        description: Categorization of how the date/temporal interval relates to the dataset
    type: object
  type: array
one of: TemporalInterval
  description: Temporal information
  properties:
    duration:
      description: A time interval in ISO 8601 duration format
      type: string
    end date:
      description: An end date
      format: date
      type: string
    name:
      description: String describing the temporal interval
      type: string
    start date:
      description: A start date
      format: date
      type: string
    temporal type:
      description: Categorization of how the date/temporal interval relates to the dataset
      one of:
        enum: exposure
        enum: collection
        enum: screening
        enum: treatment
        enum: study date
        enum: other
        enum: unknown
        type: string
      one of:
        type: array
  type: object
cardinality: many

enum: exposure
enum: collection
enum: screening
enum: treatment
enum: study date
enum: other
enum: unknown
type: string

items:
  enum: exposure
  enum: collection
  enum: screening
  enum: treatment
  enum: study date
  enum: other
  enum: unknown
  type: string
type: array

enum: exposure
enum: collection
enum: screening
enum: treatment
enum: study date
enum: other
enum: unknown
type: string

description: The organization, research project, working group, or funded program on whose behalf the author/creator was working.
any of:
  type: array
  items:
    $ref: #/definitions/researchproject
any of:
  $ref: #/definitions/researchproject
any of:
  type: array
  items:
    $ref: #/definitions/organization
any of:
  $ref: #/definitions/organization
cardinality: many

description: Topic of the work. This topic may be assigned by a human curator or through automated algorithms.
abstract: topic
any of:
  type: array
  items:
    $ref: #/definitions/topic
any of:
  $ref: #/definitions/topic
any of:
  type: array
  items:
    $ref: #/definitions/definedterm
any of:
  $ref: #/definitions/definedterm
cardinality: many

description: Text that can be used to credit person(s) and/or organization(s) associated with a published Creative Work. For example, how a user should cite the sample.
type: string
cardinality: one

$ref: #/definitions/definedterm

$ref: #/definitions/catalog

$ref: #/definitions/propertyvalue

$ref: #/definitions/quantitativevalue

funder:
  description: An organization associated with a creator or funder of a dataset
  one of: Organization
    type: object
    description: Information about a single funder
    properties:
      name:
        type: string
        description: An organization associated with a creator or funder of a dataset
      parent organization:
        type: string
        description: name of the parent funding organization
    required: name
  one of:
    type: array
    items: Organization
      type: object
      description: Information about a single funder
      required: name
description:
  type: string
  description: description about the funding award / grant
url:
  type: string
  description: award / grant URL
identifier:
  type: string
  description: Unique identifier(s) for the grant(s) used to fund the Dataset

type: string
description: An organization associated with a creator or funder of a dataset

type: string
description: name of the parent funding organization

MonetaryGrant
type: object
description: Funding that supports (sponsors) the collection of this dataset through some kind of financial contribution
properties:
  funder:
    description: An organization associated with a creator or funder of a dataset
    one of: Organization
      type: object
      description: Information about a single funder
      required: name
    one of:
      type: array
      items: Organization
        type: object
        description: Information about a single funder
        required: name
  description:
    type: string
    description: description about the funding award / grant
  url:
    type: string
    description: award / grant URL
  identifier:
    type: string
    description: Unique identifier(s) for the grant(s) used to fund the Dataset
required: funder
required: identifier

type: string
description: An organization associated with a creator or funder of a dataset

type: string
description: name of the parent funding organization

name:
  type: string
  description: An organization associated with a creator or funder of a dataset
parent organization:
  type: string
  description: name of the parent funding organization

$ref: #/definitions/person

$ref: #/definitions/organization

$ref: #/definitions/citation

$ref: #/definitions/creativework

$ref: #/definitions/person

$ref: #/definitions/organization

$ref: #/definitions/examplework

children of: http://purl.obolibrary.org/obo/MONDO_0000001
children of: http://purl.obolibrary.org/obo/DOID_4
children of: http://purl.obolibrary.org/obo/HP_0000001
children of: http://purl.obolibrary.org/obo/NCIT_C7057
ontology: mondo
ontology: hpo
ontology: doid
ontology: ncit

description: collection of vocabulary terms defined in ontologies
strict: false
type: string
vocabulary:
  children of: http://purl.obolibrary.org/obo/MONDO_0000001
  children of: http://purl.obolibrary.org/obo/DOID_4
  children of: http://purl.obolibrary.org/obo/HP_0000001
  children of: http://purl.obolibrary.org/obo/NCIT_C7057
  ontology: mondo
  ontology: hpo
  ontology: doid
  ontology: ncit

$ref: #/definitions/definedterm

children of: http://purl.obolibrary.org/obo/NCBITaxon_10239
children of: http://purl.obolibrary.org/obo/NCBITaxon_2
ontology: ncbitaxon

description: collection of vocabulary terms defined in ontologies
strict: false
type: string
vocabulary:
  children of: http://purl.obolibrary.org/obo/NCBITaxon_10239
  children of: http://purl.obolibrary.org/obo/NCBITaxon_2
  ontology: ncbitaxon

$ref: #/definitions/definedterm

InteractionCounter
type: object
properties:
  interaction type:
    type: string
  user interaction count:
    type: integer
required: interactionType
required: userInteractionCount

interaction type:
  type: string
user interaction count:
  type: integer

$ref: #/definitions/citation

$ref: #/definitions/creativework

$ref: #/definitions/resourcecatalog

$ref: #/definitions/action

children of: http://edamontology.org/topic_3361
children of: http://purl.obolibrary.org/obo/NCIT_C20368
children of: http://purl.obolibrary.org/obo/MMO_0000000
children of: http://www.ebi.ac.uk/efo/EFO_0000001
ontology: edam
ontology: ncit
ontology: mmo
ontology: efo

items:
  description: collection of vocabulary terms defined in ontologies
  strict: false
  type: string
  vocabulary:
    children of: http://edamontology.org/topic_3361
    children of: http://purl.obolibrary.org/obo/NCIT_C20368
    children of: http://purl.obolibrary.org/obo/MMO_0000000
    children of: http://www.ebi.ac.uk/efo/EFO_0000001
    ontology: edam
    ontology: ncit
    ontology: mmo
    ontology: efo
type: array

type: array
items:
  $ref: #/definitions/definedterm

$ref: #/definitions/definedterm

description: The url(s) for generating the data collection on the source website, if the source has RESTful urls
one of:
  items:
    type: string
    format: uri
  type: array
one of:
  type: string
  format: uri
cardinality: many

description: The spatialCoverage of a CreativeWork indicates the place(s) which are the focus of the content. It is a subproperty of contentLocation intended primarily for more technical and detailed materials. For example with a Data collection, it indicates areas that the records in the collection describes or were grouped by: a data collection of New York weather would have spatialCoverage which was the place: the state of New York.
abstract: geographic focus of the work
one of:
  items: AdministrativeArea
    description: Location information
    properties:
      administrative type:
        description: the type of administrative area, such as country, state, county, or city
        enum: province
        enum: district
        enum: chiefdom
        enum: village
        enum: city
        enum: country
        enum: prefecture
        enum: sub-prefecture
        enum: clan
        enum: Federal Capital Territory
        enum: state
        enum: Local Government Area
        enum: ward
        type: string
      alternate name:
        description: An alias for the location
      identifier:
        description: An identifier for the location, preferably a Wikidata ID
        type: string
      location type:
        description: Categorization of how the location relates to the dataset
      name:
        description: The name of the location
        type: string
    type: object
  type: array
one of: AdministrativeArea
  description: Location information
  properties:
    administrative type:
      description: the type of administrative area, such as country, state, county, or city
      enum: province
      enum: district
      enum: chiefdom
      enum: village
      enum: city
      enum: country
      enum: prefecture
      enum: sub-prefecture
      enum: clan
      enum: Federal Capital Territory
      enum: state
      enum: Local Government Area
      enum: ward
      type: string
    alternate name:
      description: An alias for the location
      one of:
        type: string
      one of:
        type: array
    identifier:
      description: An identifier for the location, preferably a Wikidata ID
      type: string
    location type:
      description: Categorization of how the location relates to the dataset
      one of:
        enum: residence
        enum: exposure
        enum: collection
        enum: screening
        enum: treatment
        enum: study location
        enum: other
        enum: unknown
        type: string
      one of:
        type: array
    name:
      description: The name of the location
      type: string
  type: object
cardinality: many

type: string

items:
  type: string
type: array

enum: residence
enum: exposure
enum: collection
enum: screening
enum: treatment
enum: study location
enum: other
enum: unknown
type: string

items:
  enum: residence
  enum: exposure
  enum: collection
  enum: screening
  enum: treatment
  enum: study location
  enum: other
  enum: unknown
  type: string
type: array

type: string

enum: residence
enum: exposure
enum: collection
enum: screening
enum: treatment
enum: study location
enum: other
enum: unknown
type: string

description: Species(es) / host organism from which records in the data collection have been collected, or is the focus of grouping of records in the data collection.
abstract: species/host organism
any of:
  description: collection of vocabulary terms defined in ontologies
  strict: false
  type: string
  vocabulary:
    children of: http://purl.obolibrary.org/obo/NCBITaxon_131567
    children of: http://purl.obolibrary.org/obo/NCBITaxon_10239
    ontology: ncbitaxon
any of:
  items:
    description: collection of vocabulary terms defined in ontologies
    strict: false
    type: string
    vocabulary:
      children of: http://purl.obolibrary.org/obo/NCBITaxon_131567
      children of: http://purl.obolibrary.org/obo/NCBITaxon_10239
      ontology: ncbitaxon
  type: array
any of:
  type: array
  items:
    $ref: #/definitions/definedterm
any of:
  $ref: #/definitions/definedterm
cardinality: many

description: The period of time covered by the records grouped within the data collection.
abstract: time period
one of:
  items: TemporalInterval
    description: Temporal information
    properties:
      duration:
        description: A time interval in ISO 8601 duration format
        type: string
      end date:
        description: An end date
        format: date
        type: string
      name:
        description: String describing the temporal interval
        type: string
      start date:
        description: A start date
        format: date
        type: string
      temporal type:
        description: Categorization of how the date/temporal interval relates to the dataset
    type: object
  type: array
one of: TemporalInterval
  description: Temporal information
  properties:
    duration:
      description: A time interval in ISO 8601 duration format
      type: string
    end date:
      description: An end date
      format: date
      type: string
    name:
      description: String describing the temporal interval
      type: string
    start date:
      description: A start date
      format: date
      type: string
    temporal type:
      description: Categorization of how the date/temporal interval relates to the dataset
      one of:
        enum: exposure
        enum: collection
        enum: screening
        enum: treatment
        enum: study date
        enum: other
        enum: unknown
        type: string
      one of:
        type: array
  type: object
cardinality: many

enum: exposure
enum: collection
enum: screening
enum: treatment
enum: study date
enum: other
enum: unknown
type: string

items:
  enum: exposure
  enum: collection
  enum: screening
  enum: treatment
  enum: study date
  enum: other
  enum: unknown
  type: string
type: array

enum: exposure
enum: collection
enum: screening
enum: treatment
enum: study date
enum: other
enum: unknown
type: string

description: Topic of the records in the data collection. This topic may be assigned by a human curator or through automated algorithms.
abstract: topic
any of:
  type: array
  items:
    $ref: #/definitions/topic
any of:
  $ref: #/definitions/topic
any of:
  type: array
  items:
    $ref: #/definitions/definedterm
any of:
  $ref: #/definitions/definedterm
cardinality: many

description: Data usage agreement for the records included in the data collection, the terms under which the underlying records in the data collection can be used. Information on how the data collection can be used. Note that this is related to but distinct from the license.
abstract: data usage agreement
one of:
  type: array
  items:
    $ref: #/definitions/creativework
one of:
  $ref: #/definitions/creativework
cardinality: many

description: Variables measured within the records in the data collection. Measured variables by which the records in the data collection may have been grouped.
one of:
  description: collection of vocabulary terms defined in ontologies
  strict: false
  type: string
  vocabulary:
    children of: http://www.ebi.ac.uk/efo/EFO_0000001
    children of: http://purl.obolibrary.org/obo/CMO_0000000
    children of: http://purl.obolibrary.org/obo/NCIT_C25209
    ontology: efo
    ontology: cmo
    ontology: ncit
one of:
  items:
    description: collection of vocabulary terms defined in ontologies
    strict: false
    type: string
    vocabulary:
      children of: http://www.ebi.ac.uk/efo/EFO_0000001
      children of: http://purl.obolibrary.org/obo/CMO_0000000
      children of: http://purl.obolibrary.org/obo/NCIT_C25209
      ontology: efo
      ontology: cmo
      ontology: ncit
  type: array
one of:
  type: array
  items:
    $ref: #/definitions/definedterm
one of:
  $ref: #/definitions/definedterm
cardinality: many

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
one of:
  items: AggregateRating
    type: object
    properties:
      rating count:
        description: Total number of ratings
        type: integer
      rating value:
        description: Average rating
        type: string
      item reviewed:
        description: What is being reviewed
        type: string
    required: ratingValue
    recommended: ratingCount
    recommended: itemReviewed
  type: array
one of: AggregateRating
  type: object
  properties:
    rating count:
      description: Total number of ratings
      type: integer
    rating value:
      description: Average rating
      type: string
    item reviewed:
      description: What is being reviewed
      type: string
  required: ratingValue
  recommended: ratingCount
  recommended: itemReviewed
cardinality: many

description: Publications or resources that cite the records in the data collection. Alternatively, publications or resources by which the records were grouped based on the citation of the records in the data collection. For the primary citation of the resource from which the data collection was created, use the 'citation' field.
any of:
  type: array
  items:
    $ref: #/definitions/citation
any of:
  $ref: #/definitions/citation
any of:
  type: array
  items:
    $ref: #/definitions/creativework
any of:
  $ref: #/definitions/creativework
cardinality: many

description: Text that can be used to credit person(s) and/or organization(s) associated with a published Creative Work. For example, how a user should cite the dataset.
type: string
cardinality: one

description: Associated materials for the records in the data collection, including data dictionaries and data limitation descriptions. This can include associated materials by which the records were grouped for having the same materials in common in the data collection.
abstract: data limitations or dictionaries
any of:
  type: array
  items:
    $ref: #/definitions/citation
any of:
  $ref: #/definitions/citation
any of:
  type: array
  items:
    $ref: #/definitions/creativework
any of:
  $ref: #/definitions/creativework
cardinality: many

description: identifiers for records within the data collection.
abstract: identifier or accession number
one of:
  type: string
one of:
  items:
    type: string
  type: array
cardinality: many

description: A flag to signal that the items included in the data collection are accessible for free.
abstract: accessible without charge
type: boolean
cardinality: one

description: Dataset, resource/resource catalog or computational tool which incorporate the records included in this data collection. This can include resources by which the records were grouped (for having derivative resources in common) in the data collection.
any of:
  type: array
  items:
    $ref: #/definitions/citation
any of:
  $ref: #/definitions/citation
any of:
  type: array
  items:
    $ref: #/definitions/creativework
any of:
  $ref: #/definitions/creativework
cardinality: many

description: Indicates a broader study, project, or collection the records in the data collection are part of. This can include broader study, project, etc. by which the records were grouped (for being a part of) in the data collection.
abstract: study or project including the work
cardinality: many
any of:
  type: array
  items:
    $ref: #/definitions/citation
any of:
  $ref: #/definitions/citation
any of:
  type: array
  items:
    $ref: #/definitions/creativework
any of:
  $ref: #/definitions/creativework

description: Dataset, resource/resource catalog or computational tool which are related to the records included in the data collection. This can include resources by which the records were grouped (for being related to) in the data collection.
abstract: related datasets (via curation)
any of:
  type: array
  items:
    $ref: #/definitions/citation
any of:
  $ref: #/definitions/citation
any of:
  type: array
  items:
    $ref: #/definitions/creativework
any of:
  $ref: #/definitions/creativework
cardinality: many

description: Data collections which are similar to the data collection, based on terms in the names, descriptions, authors, measurementTechniques, infectiousAgents, healthConditions, etc.
abstract: similar datasets (auto-assigned)
any of:
  type: array
  items:
    $ref: #/definitions/citation
any of:
  $ref: #/definitions/citation
any of:
  type: array
  items:
    $ref: #/definitions/creativework
any of:
  $ref: #/definitions/creativework
cardinality: many

description: Keywords or tags used to describe this work.
abstract: keywords or tags
one of:
  type: array
  items:
    type: string
one of:
  type: string
cardinality: many

description: The sample(s) which were used to generate the records in the data collection
any of:
  type: array
  items:
    $ref: #/definitions/samplerecord
any of:
  $ref: #/definitions/samplerecord
any of:
  type: string
  format: uri
any of:
  type: array
  items:
    type: string
    format: uri
any of:
  type: array
  items:
    $ref: #/definitions/samplecollection
any of:
  $ref: #/definitions/samplecollection
cardinality: many

description: Original publisher of the metadata for the records included in the data collection.
abstract: original metadata source
one of:
  $ref: #/definitions/catalog
one of:
  type: array
  items:
    $ref: #/definitions/catalog
cardinality: many

description: The organization, research project, working group, or funded program on whose behalf the author/creator was working when generating the records included in the data collection. This can include organizations, programs, etc. by which the records were grouped (having the same source organization) in the data collection.
any of:
  type: array
  items:
    $ref: #/definitions/researchproject
any of:
  $ref: #/definitions/researchproject
any of:
  type: array
  items:
    $ref: #/definitions/organization
any of:
  $ref: #/definitions/organization
cardinality: many

description: The version of the source of the records included in the data collection.
type: string
cardinality: one

citation: ScholarlyArticle
  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: object
  properties:
    author:
      description: Author(s) of the publication
      any of:
        type: array
      any of:
        $ref: #/definitions/person
      any of:
        type: array
      any of:
        $ref: #/definitions/organization
    abstract:
      description: Abstract of the publication
      type: string
    date published:
      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
    issue number:
      description: Issue number where the article appears
      type: string
    journal name:
      description: Journal where the article appears
      type: string
    journal name abbrev:
      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
    volume number:
      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
  recommended: datePublished
  recommended: doi
  recommended: identifier
  recommended: journalName
  recommended: pmid
  recommended: url
  optional: abstract
  optional: citation
  optional: description
  optional: issueNumber
  optional: journalNameAbbrev
  optional: pagination
  optional: volumeNumber
creativework: CreativeWork
  description: A resource
  type: object
  properties:
    author:
      description: Author(s) of the referenced work
      any of:
        type: array
      any of:
        $ref: #/definitions/person
      any of:
        type: array
      any of:
        $ref: #/definitions/organization
    abstract:
      description: Abstract of the referenced work
      type: string
    date published:
      description: Date the referenced work was published
      format: date
      type: string
    description:
      description: Description of the referenced work
      type: string
    has part:
      description: A portion of the work
      one of:
        $ref: #/definitions/citation
    included in data catalog:
      description: Data or tool catalog which houses the work
      one of:
        $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
  recommended: datePublished
  recommended: doi
  recommended: identifier
  recommended: includedInDataCatalog
  recommended: relationship
  recommended: url
  optional: abstract
  optional: citation
  optional: description
  optional: hasPart
examplework: CreativeWork
  description: A creative work (e.g. Data record) that this work (the Data Collection) is an example/instance/realization/derivation of. For example, a Data record from which this DataCollection was derived.
  type: object
  properties:
    about:
      description: The Data type of a record included in this collection, use EDAM Data Ontology
      any of:
        type: array
      any of:
        $ref: #/definitions/definedterm
      any of:
        description: data type of the records included in this collection.
        type: string
        strict: false
      any of:
        type: array
    encoding format:
      description: The Formats in which a data record can be downloaded from the source, used EDAM Format ontology
      any of:
        type: array
      any of:
        $ref: #/definitions/definedterm
      any of:
        description: data type of the records included in this collection.
        type: string
        strict: false
      any of:
        type: array
    potential action:
      description: Potential actions, processes, or operations that could be run on this data. Whenever possible, use EDAM Operations ontology
      any of:
        type: array
      any of:
        $ref: #/definitions/definedterm
      any of:
        type: array
      any of:
        $ref: #/definitions/action
    schema version:
      description: URL(s) to the schema that was used for the data records in the data collection.
      one of:
        type: array
      one of:
        type: string
        format: uri
    additional property:
      description: Other Property/Value pairs that describe the example.
      any of:
        type: array
      any of:
        $ref: #/definitions/propvalpair
      cardinality: many
  recommended: about
  recommended: encodingFormat
  recommended: schemaVersion
  recommended: potentialAction
  recommended: additionalProperty
action: Action
  description: Protocols or processes that can be enacted upon a data record in the data collection. For example, the protocol or process used to generate the data collection.
  type: object
  properties:
    name:
      description: Protocol or process name. In the case of the data collection protocol, the name for the data collection process should follow the format 'Process for creating the {Source} {about} Data Collection in the NIAID Data Ecosystem Discovery Portal'. For example, 'Process for creating the BV-BRC Genome Data Collection in the NIAID Data Ecosystem Discovery Portal'
      type: string
  required: name
  recommended: actionProcess
catalog: DataCatalog
resourcecatalog: ResourceCatalog
organization: Organization
researchproject: ResearchProject
person: Person
definedterm: DefinedTerm
howto: HowTo
softwareapplication: SoftwareApplication
samplerecord: Sample
samplecollection: SampleCollection
minsampleinfo: Sample
quantitativevalue: QuantitativeValue
propertyvalue: PropertyValue
propvalpair: PropertyValue

$ref: #/definitions/person

$ref: #/definitions/organization

$ref: #/definitions/person

$ref: #/definitions/organization

$ref: #/definitions/definedterm

ontology: edam
children of: http://edamontology.org/data_0006

description: data type of the records included in this collection.
type: string
vocabulary:
  ontology: edam
  children of: http://edamontology.org/data_0006
strict: false

$ref: #/definitions/definedterm

ontology: edam
children of: http://edamontology.org/format_1915

description: data type of the records included in this collection.
type: string
vocabulary:
  ontology: edam
  children of: http://edamontology.org/format_1915
strict: false

$ref: #/definitions/definedterm

$ref: #/definitions/action

type: string
format: uri

$ref: #/definitions/propvalpair

description: Protocol or process description. For example, a description of the process used to generate the data collection.
type: string

description: Link to protocol or process.
type: string
format: uri

description: Protocol or process description formatted as a HowTo object. For example, the description of how the Data Collection was generated formatted as a HowTo object.
one of:
  type: array
  items:
    $ref: #/definitions/howto
one of:
  $ref: #/definitions/howto

required: description

required: url

description: Topic assigned to the work.
type: string
vocabulary:
  ontology: edam
  children of: http://edamontology.org/topic_0003
strict: true

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
  version date:
    description: date the metadata was harvested from the catalog
    type: string
    format: date
  archived at:
    description: The url(s) of one or more datasets, tools, resources or other items listed in a DataCatalog or ResourceCatalog
    one of:
      items:
        type: string
        format: uri
      type: array
    one of:
      type: string
      format: uri
required: name
required: url
recommended: versionDate
recommended: archivedAt

ResourceCatalog
description: A Resource Catalog in the NIAID Data Ecosystem
type: object
properties:
  name:
    description: Resrouce catalog name
    type: string
  url:
    description: Link to the resource catalog in the Discovery Portal
    type: string
    format: uri
required: name
required: url

Organization
description: Reusable organization definition
properties:
  affiliation:
    type: object
    properties:
      name:
        description: Name of the affiliation, such as a university
        type: string
      same as:
        description: Alias for the affiliation
        type: string
      url:
        description: URL of the affiliation
        type: string
        format: uri
    required: name
    optional: sameAs
    optional: url
  alternate name:
    description: Alias of the name
    one of:
      type: array
      items:
        type: string
    one of:
      type: string
  name:
    description: Name of the organization
    type: string
  parent organization:
    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
optional: alternateName
optional: email
optional: parentOrganization
optional: role
optional: url
type: object

ResearchProject
description: a type of organization definition
properties:
  alternate name:
    description: Alias of the name
    one of:
      type: array
      items:
        type: string
    one of:
      type: string
  name:
    description: Name of the organization
    type: string
  parent organization:
    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
recommended: url
recommended: parentOrganization
optional: alternateName
optional: email
optional: role
type: object

Person
description: Reusable person definition
properties:
  affiliation:
    type: object
    properties:
      name:
        description: Name of the affiliation, such as a university
        type: string
      same as:
        description: Alias for the affiliation
        type: string
      url:
        description: URL of the affiliation
        type: string
        format: uri
    required: name
    optional: sameAs
    optional: url
  name:
    description: Name of the person
    type: string
  email:
    description: Email address of the person
    type: string
  family name:
    description: Family name (surname) of the person
    type: string
  given name:
    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
recommended: givenName
recommended: identifier
optional: affiliation
optional: email
optional: role
optional: title
optional: url
type: object

DefinedTerm
type: object
properties:
  name:
    description: The name of the item.
    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.
    cardinality: one
    type: string
  url:
    description: URL of the item.
    cardinality: one
    type: string
    format: uri
  curated by:
    description: The person, organization, or catalog that curated this DefinedTerm for the metadata property
    any of:
      $ref: #/definitions/person
    any of:
      $ref: #/definitions/organization
    any of:
      $ref: #/definitions/catalog
    any of:
      $ref: #/definitions/researchproject
    any of:
      $ref: #/definitions/softwareapplication
  term code:
    description: A code that identifies this DefinedTerm within a DefinedTermSet.
    type: string
  description:
    description: A description of the item.
    type: string
  in defined term set:
    description: A DefinedTermSet that contains this term.
    type: string
  original name:
    description: The original name of the item, before any metadata standardization/normalization
    type: string
  is curated:
    description: A boolean indicator describing whether or not this DefinedTerm was curated as the value of a property.
    type: boolean

HowTo
type: object
properties:
  name:
    description: The name of the item.
    cardinality: one
    type: string
  url:
    description: URL of the item.
    cardinality: one
    type: string
    format: uri
  description:
    description: A description of the item.
    type: string
  step:
    description: A DefinedTermSet that contains this term.
    one of:
      type: array
      items:
        type: string
    one of:
      type: string
recommended: name
recommended: url
recommended: description
recommended: step

SoftwareApplication
description: Reusable software or algorithm definition
properties:
  name:
    description: name of the software, computational tool, or algorithm.
    type: string
  date modified:
    description: date the software, computational tool, or algorithm was run
    type: string
    format: date
  url:
    description: url of the software, computational tool, or algorithm
    type: string
    format: uri
required: name
recommended: url
optional: dateModified
type: object

Sample
description: reusable sample object
type: object
properties:
  url:
    description: Link to sample
    type: string
    format: uri
  identifier:
    description: an identifier for the sample
    type: string
  included in data catalog:
    description: Data or resource catalog where the sample is listed
    one of:
      $ref: #/definitions/catalog
    one of:
      type: array
      items:
        $ref: #/definitions/catalog
  associated phenotype:
    description: one or more observable traits or conditions relevant to the source of the sample.
    any of:
      description: collection of vocabulary terms defined in ontologies
      strict: false
      type: string
      vocabulary:
        children of: http://purl.obolibrary.org/obo/UPHENO_0001001
        children of: http://purl.obolibrary.org/obo/PATO_0000001
        ontology: UPHENO
        ontology: PATO
    any of:
      items:
        description: collection of vocabulary terms defined in ontologies
        strict: false
        type: string
      type: array
    any of:
      type: array
      items:
        $ref: #/definitions/definedterm
    any of:
      $ref: #/definitions/definedterm
    cardinality: many
  associated genotype:
    description: One or more genetic variants or molecular features observed or inferred from the sample.
    any of:
      description: collection of vocabulary terms defined in ontologies
      strict: false
      type: string
      vocabulary:
        children of: http://purl.obolibrary.org/obo/NCIT_C16612
        children of: http://purl.obolibrary.org/obo/NCIT_C20181
        children of: http://purl.obolibrary.org/obo/NCIT_C17649
        ontology: NCIT
    any of:
      items:
        description: collection of vocabulary terms defined in ontologies
        strict: false
        type: string
      type: array
    any of:
      type: array
      items:
        $ref: #/definitions/definedterm
    any of:
      $ref: #/definitions/definedterm
    cardinality: many
  cell type:
    description: The type of cell represented in or derived from the biological sample, based on morphology, lineage, or molecular markers.
    any of:
      description: collection of vocabulary terms defined in ontologies
      strict: false
      type: string
      vocabulary:
        children of: http://purl.obolibrary.org/obo/CL_0000000
        children of: http://purl.obolibrary.org/obo/CLO_0000031
        ontology: CL
        ontology: CLO
    any of:
      items:
        description: collection of vocabulary terms defined in ontologies
        strict: false
        type: string
      type: array
    any of:
      type: array
      items:
        $ref: #/definitions/definedterm
    any of:
      $ref: #/definitions/definedterm
    cardinality: many
  anatomical system:
    description: Indicate the anatomical system from which the sample is collect, e.g. circulatory, digestive, endocrine, immune and other systems.
    any of:
      description: collection of vocabulary terms defined in ontologies
      strict: false
      type: string
      vocabulary:
        children of: http://purl.obolibrary.org/obo/UBERON_0000467
        ontology: UBERON
    any of:
      items:
        description: collection of vocabulary terms defined in ontologies
        strict: false
        type: string
      type: array
    any of:
      type: array
      items:
        $ref: #/definitions/definedterm
    any of:
      $ref: #/definitions/definedterm
    cardinality: many
  anatomical structure:
    description: Indicate the organ, tissues the sample was collected from.
    any of:
      description: collection of vocabulary terms defined in ontologies
      strict: false
      type: string
      vocabulary:
        children of: http://purl.obolibrary.org/obo/UBERON_0001062
        ontology: UBERON
    any of:
      items:
        description: collection of vocabulary terms defined in ontologies
        strict: false
        type: string
      type: array
    any of:
      type: array
      items:
        $ref: #/definitions/definedterm
    any of:
      $ref: #/definitions/definedterm
    cardinality: many
  sex:
    description: The biological sex of the individual from which the sample was obtained.
    any of:
      description: collection of vocabulary terms defined in ontologies
      strict: false
      type: string
      vocabulary:
        children of: http://purl.obolibrary.org/obo/PATO_0000047
        ontology: PATO
    any of:
      items:
        description: collection of vocabulary terms defined in ontologies
        strict: false
        type: string
      type: array
    any of:
      type: array
      items:
        $ref: #/definitions/definedterm
    any of:
      $ref: #/definitions/definedterm
    cardinality: many
  developmental stage:
    description: A temporal subdivision of a developmental process, indicating the age or stage of the object when the sample was created.
    any of:
      description: collection of vocabulary terms defined in ontologies
      strict: false
      type: string
      vocabulary:
        children of: http://purl.obolibrary.org/obo/UBERON_0000104
        children of: http://purl.obolibrary.org/obo/NCIT_C48308
        ontology: UBERON
        ontology: NCIT
    any of:
      items:
        description: collection of vocabulary terms defined in ontologies
        strict: false
        type: string
      type: array
    any of:
      type: array
      items:
        $ref: #/definitions/definedterm
    any of:
      $ref: #/definitions/definedterm
    any of:
      type: array
      items:
        $ref: #/definitions/quantitativevalue
    any of:
      $ref: #/definitions/quantitativevalue
    cardinality: many
  sample availability:
    description: A flag to signal that the sample is available for reuse.
    abstract: availability of the sample
    type: boolean
    cardinality: one
  sample quantity:
    description: A numeric value for a measurement of the size of a sample. If completely unknown, set value = 0, and unitText = 'unknown'
    one of:
      type: array
      items:
        $ref: #/definitions/quantitativevalue
    one of:
      $ref: #/definitions/quantitativevalue
    cardinality: many
  sample type:
    description: The type of sample or specimen.
    cardinality: many
recommended: url
recommended: identifier
recommended: includedInDataCatalog
recommended: associatedPhenotype
recommended: associatedGenotype
recommended: cellType
recommended: sampleType
recommended: anatomicalSystem
recommended: anatomicalStructure
recommended: sex
recommended: developmentalStage
recommended: sampleAvailability
recommended: sampleQuantity

children of: http://purl.obolibrary.org/obo/UPHENO_0001001
children of: http://purl.obolibrary.org/obo/PATO_0000001
ontology: UPHENO
ontology: PATO

children of: http://purl.obolibrary.org/obo/NCIT_C16612
children of: http://purl.obolibrary.org/obo/NCIT_C20181
children of: http://purl.obolibrary.org/obo/NCIT_C17649
ontology: NCIT

children of: http://purl.obolibrary.org/obo/CL_0000000
children of: http://purl.obolibrary.org/obo/CLO_0000031
ontology: CL
ontology: CLO

children of: http://purl.obolibrary.org/obo/UBERON_0000467
ontology: UBERON

children of: http://purl.obolibrary.org/obo/UBERON_0001062
ontology: UBERON

children of: http://purl.obolibrary.org/obo/PATO_0000047
ontology: PATO

children of: http://purl.obolibrary.org/obo/UBERON_0000104
children of: http://purl.obolibrary.org/obo/NCIT_C48308
ontology: UBERON
ontology: NCIT

description: collection of vocabulary terms defined in ontologies
strict: false
type: string
vocabulary:
  children of: http://purl.obolibrary.org/obo/BFO_0000040
  ontology: OBI

items:
  description: collection of vocabulary terms defined in ontologies
  strict: false
  type: string
  vocabulary:
    children of: http://purl.obolibrary.org/obo/BFO_0000040
    ontology: OBI
type: array

type: array
items:
  $ref: #/definitions/definedterm

$ref: #/definitions/definedterm

SampleCollection
description: reusable sampleCollection object
type: object
properties:
  url:
    description: Link to sample
    type: string
    format: uri
  identifier:
    description: an identifier for the sample
    type: string
  included in data catalog:
    description: Data or resource catalog where the sample is listed
    one of:
      $ref: #/definitions/catalog
    one of:
      type: array
      items:
        $ref: #/definitions/catalog
  aggregate element:
    description: Aggregate information about the samples in the Sample Collection formatted as a sample object.
    one of:
      $ref: #/definitions/samplerecord
    one of:
      type: array
      items:
        $ref: #/definitions/samplerecord
  item list element:
    description: Samples listed in the sample collection
    one of:
      $ref: #/definitions/minsampleinfo
    one of:
      type: array
      items:
        $ref: #/definitions/minsampleinfo
  number of items:
    description: The number of sample records in the sample collection. Min/max estimates can be used in lieu of actual number. If completely unknown, set value = 0, and unitText = 'unknown'
    any of:
      type: array
      items:
        $ref: #/definitions/propertyvalue
    any of:
      $ref: #/definitions/propertyvalue
    any of:
      type: array
      items:
        $ref: #/definitions/quantitativevalue
    any of:
      $ref: #/definitions/quantitativevalue
    cardinality: many
recommended: url
recommended: identifier
recommended: includedInDataCatalog
recommended: aggregateElement
recommended: itemListElement
recommended: numberOfItems

Sample
description: reusable sample object
type: object
properties:
  url:
    description: Link to sample
    type: string
    format: uri
  identifier:
    description: an identifier for the sample
    type: string
  included in data catalog:
    description: Data or resource catalog where the sample is listed
    one of:
      $ref: #/definitions/catalog
    one of:
      type: array
      items:
        $ref: #/definitions/catalog
recommended: url
recommended: identifier
recommended: includedInDataCatalog

QuantitativeValue
description: A numeric value and unit for a property with potentially different units
type: object
properties:
  value:
    description: A numeric value for the property
    type: number
  max value:
    description: An estimated maximum numberic value if the actual value is not known. Ignore if actual numeric value is known.
    type: number
  min value:
    description: An estimated minumum numeric value if the actual value is not known. Ignore if actual numeric value is known.
    type: number
  unit text:
    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
optional: minValue

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
  max value:
    description: An estimated maximum numberic value if the actual value is not known. Ignore if actual numeric value is known.
    type: number
  min value:
    description: An estimated minumum numeric value if the actual value is not known. Ignore if actual numeric value is known.
    type: number
  unit text:
    description: A unit associated with the value. E.g.- 'records' for the number of records in a database.
    type: string
  property ID:
    description: A commonly used identifier for the characteristic represented by the property, e.g. a manufacturer or a standard code for a property. propertyID can be (1) a prefixed string, mainly meant to be used with standards for product properties; (2) a site-specific, non-prefixed string (e.g. the primary key of the property or the vendor-specific ID of the property), or (3) a URL indicating the type of the property, either pointing to an external vocabulary, or a Web resource that describes the property (e.g. a glossary entry). Standards bodies should promote a standard prefix for the identifiers of properties from their standards.
    one of:
      type: string
    one of:
      type: string
      format: uri
required: unitText
recommended: value
recommended: propertyID
optional: maxValue
optional: minValue

PropertyValue
description: A numeric value and unit for a property with potentially different units
type: object
properties:
  value:
    description: A numeric value for the property
    type: number
  name:
    description: The name of the property.
    type: string
  unit text:
    description: A unit associated with the value. E.g.- 'records' for the number of records in a database.
    type: string
  property ID:
    description: A commonly used identifier for the characteristic represented by the property, e.g. a manufacturer or a standard code for a property. propertyID can be (1) a prefixed string, mainly meant to be used with standards for product properties; (2) a site-specific, non-prefixed string (e.g. the primary key of the property or the vendor-specific ID of the property), or (3) a URL indicating the type of the property, either pointing to an external vocabulary, or a Web resource that describes the property (e.g. a glossary entry). Standards bodies should promote a standard prefix for the identifiers of properties from their standards.
    one of:
      type: string
    one of:
      type: string
      format: uri
required: name
recommended: value
recommended: propertyID
optional: unitText