Dataset.json

{
  "@context": {
    "owl": "http://www.w3.org/2002/07/owl#",
    "rdf": "http://www.w3.org/1999/02/22-rdf-syntax-ns#",
    "rdfs": "http://www.w3.org/2000/01/rdf-schema#",
    "schema": "http://schema.org/",
    "niaid": "https://discovery.biothings.io/view/niaid/"
  },
  "@id": "https://discovery.biothings.io/view/niaid/",
  "@graph": [{
      "@id": "niaid:Dataset",
      "@type": "rdfs:Class",
      "rdfs:comment": "A schema describing a minimal Dataset for the National Institute of Allergy and Infectious Disease (NIAID). A dataset is a collection of data of a particular experimental type. Additional schema.org and/or custom properties could be added.",
      "rdfs:label": "Dataset",
      "rdfs:subClassOf": {
        "@id": "schema:Dataset"
      },
      "schema:isPartOf": {
        "@id": "https://discovery.biothings.io/view/niaid/"
      },
      "$validation": {
        "$schema": "http://json-schema.org/draft-07/schema#",
        "type": "object",
        "properties": {
          "name": {
            "description": "Descriptive name of the dataset",
            "owl:cardinality": "one",
            "type": "string"
          },
          "description": {
            "description": "Longer description of what is contained in the dataset",
            "owl:cardinality": "one",
            "type": "string"
          },
          "measurementTechnique": {
            "description": "A technique or technology used in a Dataset, corresponding to the method used for measuring the corresponding variable(s).",
            "owl:cardinality": "many",
            "oneOf": [{
                "$ref": "#/definitions/controlledVocabulary"
              },
              {
                "type": "array",
                "items": {
                  "$ref": "#/definitions/controlledVocabulary"
                }
              }
            ]
          },
          "identifier": {
            "description": "Identifiers for the dataset (ideally less than 15 characters)",
            "owl:cardinality": "many",
            "oneOf": [{
                "type": "string"
              },
              {
                "type": "array",
                "items": {
                  "type": "string"
                }
              }
            ]
          },
          "creator": {
            "description": "Name of the author or organization that created the dataset.  Note: schema.org/creator and schema.org/organization have additional fields that can provide more information about the author/organization, if desired.",
            "owl:cardinality": "many",
            "anyOf": [{
                "$ref": "#/definitions/person"
              },
              {
                "type": "array",
                "items": {
                  "$ref": "#/definitions/person"
                }
              },
              {
                "$ref": "#/definitions/organization"
              },
              {
                "type": "array",
                "items": {
                  "$ref": "#/definitions/organization"
                }
              }
            ]
          },
          "sdPublisher": {
            "description": "Original publisher of the Dataset metadata (like GenBank, ImmPort, etc.). Indicates the party responsible for generating and publishing the current structured data markup, typically in cases where the structured data is derived automatically from existing published content but published on a different site. For example, student projects and open data initiatives often re-publish existing content with more explicitly structured metadata. The sdPublisher property helps make such practices more explicit.",
            "owl:cardinality": "many",
            "anyOf": [{
                "$ref": "#/definitions/person"
              },
              {
                "type": "array",
                "items": {
                  "$ref": "#/definitions/person"
                }
              },
              {
                "$ref": "#/definitions/organization"
              },
              {
                "type": "array",
                "items": {
                  "$ref": "#/definitions/organization"
                }
              }
            ]
          },
          "distribution": {
            "description": "DataDownload objects, which contain the URL link to download the raw, analyzed, and summary data associated with the dataset as well as associated metadata for the file.",
            "owl:cardinality": "many",
            "oneOf": [{
                "$ref": "#/definitions/dataDownload"
              },
              {
                "type": "array",
                "items": {
                  "$ref": "#/definitions/dataDownload"
                }
              }
            ]
          },
          "citation": {
            "description": "Journal article or other publication associated with the dataset (stored as an object, not a string)",
            "owl:cardinality": "many",
            "oneOf": [{
                "$ref": "#/definitions/article"
              },
              {
                "type": "array",
                "items": {
                  "$ref": "#/definitions/article"
                }
              }
            ]
          },
          "funding": {
            "description": "Funding that supports (sponsors) the collection of this dataset through some kind of financial contribution",
            "owl:cardinality": "many",
            "oneOf": [{
                "$ref": "#/definitions/monetaryGrant"
              },
              {
                "type": "array",
                "items": {
                  "$ref": "#/definitions/monetaryGrant"
                }
              }
            ]
          },
          "license": {
            "description": "A license document that applies to this content, typically indicated by URL.",
            "type": "string",
            "owl:cardinality": "one",
            "format": "uri"
          },
          "species": {
            "description": "Species(es) from which dataset has been collected",
            "owl:cardinality": "many",
            "oneOf": [{
                "$ref": "#/definitions/speciesControlledVocabulary"
              },
              {
                "type": "array",
                "items": {
                  "$ref": "#/definitions/speciesControlledVocabulary"
                }
              }
            ]
          },
          "infectiousAgent": {
            "description": "Infectious agent(s) / pathogen(s) which are the focus of the dataset (e.g. SARS-CoV-2)",
            "owl:cardinality": "many",
            "oneOf": [{
                "$ref": "#/definitions/pathogenControlledVocabulary"
              },
              {
                "type": "array",
                "items": {
                  "$ref": "#/definitions/pathogenControlledVocabulary"
                }
              }
            ]
          },
          "healthCondition": {
            "description": "The Infectious disease(s) / health condition(s) which are the focus of the dataset (e.g. COVID-19, pneumonia, etc.)",
            "owl:cardinality": "many",
            "oneOf": [{
                "$ref": "#/definitions/diseaseControlledVocabulary"
              },
              {
                "type": "array",
                "items": {
                  "$ref": "#/definitions/diseaseControlledVocabulary"
                }
              }
            ]
          },
          "spatialCoverage": {
            "description": "spatial information related to the dataset",
            "owl:cardinality": "many",
            "oneOf": [{
                "$ref": "#/definitions/place"
              },
              {
                "type": "array",
                "items": {
                  "$ref": "#/definitions/place"
                }
              }
            ]
          },
          "temporalCoverage": {
            "description": "temporal information related to the dataset. For dates pertaining to the dataset record, use datePublished, dateCreated, dateModified, etc.",
            "owl:cardinality": "many",
            "oneOf": [{
                "$ref": "#/definitions/temporalInterval"
              },
              {
                "type": "array",
                "items": {
                  "$ref": "#/definitions/temporalInterval"
                }
              }
            ]
          }
        },
        "required": [
          "name",
          "description",
          "measurementTechnique",
          "creator",
          "distribution",
          "funding",
          "identifier"
        ],
        "recommended": [
          "citation",
          "license",
          "species",
          "infectiousAgent",
          "healthCondition",
          "spatialCoverage",
          "temporalCoverage"
        ],
        "optional": [
          "sdPublisher"
        ],
        "definitions": {
          "person": {
            "description": "Reusable person definition",
            "@type": "Person",
            "type": "object",
            "properties": {
              "name": {
                "type": "string"
              }
            },
            "required": [
              "name"
            ]
          },
          "organization": {
            "description": "Reusable organization definition",
            "@type": "Organization",
            "type": "object",
            "properties": {
              "name": {
                "type": "string"
              }
            },
            "required": [
              "name"
            ]
          },
          "controlledVocabulary": {
            "description": "collection of vocabulary terms defined in ontologies",
            "@type": "DefinedTerm",
            "type": "string",
            "vocabulary": {
              "ontology": ["edam", "ncit"],
              "children_of": ["http://edamontology.org/topic_3361", "http://purl.obolibrary.org/obo/NCIT_C20368"]
            },
            "strict": false
          },
          "pathogenControlledVocabulary": {
            "description": "collection of vocabulary terms defined in ontologies",
            "@type": "DefinedTerm",
            "type": "string",
            "vocabulary": {
              "ontology": ["ncbitaxon"],
              "children_of": ["http://purl.obolibrary.org/obo/NCBITaxon_10239", "http://purl.obolibrary.org/obo/NCBITaxon_2"]
            },
            "strict": false
          },
          "speciesControlledVocabulary": {
            "description": "collection of vocabulary terms defined in ontologies",
            "@type": "DefinedTerm",
            "type": "string",
            "vocabulary": {
              "ontology": ["ncbitaxon"],
              "children_of": ["http://purl.obolibrary.org/obo/NCBITaxon_131567", "http://purl.obolibrary.org/obo/NCBITaxon_10239"]
            },
            "strict": false
          },
          "diseaseControlledVocabulary": {
            "description": "collection of vocabulary terms defined in ontologies",
            "@type": "DefinedTerm",
            "type": "string",
            "vocabulary": {
              "ontology": ["mondo"],
              "children_of": ["http://purl.obolibrary.org/obo/MONDO_0000001"]
            },
            "strict": false
          },
          "monetaryGrant": {
            "type": "object",
            "@type": "MonetaryGrant",
            "description": "Funding that supports (sponsors) the collection of this dataset through some kind of financial contribution",
            "properties": {
              "funder": {
                "description": "An organization associated with a creator or funder of a dataset",
                "oneOf": [{
                    "$ref": "#/definitions/funder"
                  },
                  {
                    "type": "array",
                    "items": {
                      "$ref": "#/definitions/funder"
                    }
                  }
                ]
              },
              "description": {
                "type": "string",
                "description": "description about the funding award / grant"
              },
              "url": {
                "type": "string",
                "description": "award / grant URL"
              },
              "identifier": {
                "type": "string",
                "description": "Unique identifier(s) for the grant(s) used to fund the Dataset"
              }
            },
            "required": [
              "funder",
              "identifier"
            ]
          },
          "funder": {
            "type": "object",
            "@type": "Organization",
            "description": "Information about a single funder",
            "properties": {
              "name": {
                "type": "string",
                "description": "An organization associated with a creator or funder of a dataset"
              },
              "parentOrganization": {
                "type": "string",
                "description": "name of the parent funding organization"
              }
            },
            "required": [
              "name"
            ]
          },
          "dataDownload": {
            "description": "A dataset in downloadable form.",
            "@type": "DataDownload",
            "type": "object",
            "properties": {
              "dateModified": {
                "type": "string",
                "format": "date"
              },
              "contentUrl": {
                "type": "string",
                "format": "uri"
              }
            },
            "required": [
              "dateModified",
              "contentUrl"
            ]
          },
          "article": {
            "description": "A scholarly article in which the dataset is cited.",
            "@type": "ScholarlyArticle",
            "type": "object",
            "properties": {
              "name": {
                "type": "string"
              },
              "url": {
                "type": "string",
                "format": "uri"
              }
            },
            "required": [
              "url"
            ]
          },
          "place": {
            "description": "Location information",
            "@type": "AdministrativeArea",
            "type": "object",
            "properties": {
              "locationType": {
                "description": "Categorization of how the location relates to the dataset or computational tool",
                "oneOf": [{
                    "type": "string",
                    "enum": [
                      "residence",
                      "exposure",
                      "collection",
                      "screening",
                      "treatment",
                      "study location",
                      "other",
                      "unknown"
                    ]
                  },
                  {
                    "type": "array",
                    "items": {
                      "type": "string",
                      "enum": [
                        "residence",
                        "exposure",
                        "collection",
                        "screening",
                        "treatment",
                        "study location",
                        "other",
                        "unknown"
                      ]
                    }
                  }
                ]
              },
              "administrativeType": {
                "description": "the type of administrative area",
                "type": "string",
                "enum": [
                  "province",
                  "district",
                  "chiefdom",
                  "village",
                  "city",
                  "country",
                  "prefecture",
                  "sub-prefecture",
                  "clan",
                  "Federal Capital Territory",
                  "state",
                  "Local Government Area",
                  "ward"
                ]
              },
              "alternateName": {
                "description": "An alias for the location.",
                "oneOf": [{
                    "type": "string"
                  },
                  {
                    "type": "array",
                    "items": {
                      "type": "string"
                    }
                  }
                ]
              },
              "identifier": {
                "description": "An identifier for the location, preferably a Wikidata ID.",
                "type": "string"
              },
              "name": {
                "description": "The name of the item.",
                "type": "string"
              }
            }
          },
          "temporalInterval": {
            "description": "Temporal information",
            "@type": "TemporalInterval",
            "type": "object",
            "properties": {
              "temporalType": {
                "description": "Categorization of how the date/temporal interval relates to the dataset or computational tool",
                "oneOf": [{
                    "type": "string",
                    "enum": [
                      "exposure",
                      "collection",
                      "screening",
                      "treatment",
                      "study date",
                      "other",
                      "unknown"
                    ]
                  },
                  {
                    "type": "array",
                    "items": {
                      "type": "string",
                      "enum": [
                        "exposure",
                        "collection",
                        "screening",
                        "treatment",
                        "study date",
                        "other",
                        "unknown"
                      ]
                    }
                  }
                ]
              },
              "startDate": {
                "description": "A start date. ",
                "type": "string",
                "format": "date"
              },
              "name": {
                "description": "String describing the temporal interval",
                "type": "string"
              },
              "endDate": {
                "description": "An end date.",
                "type": "string",
                "format": "date"
              },
              "duration": {
                "description": "A time interval in ISO 8601 duration format.",
                "type": "string"
              }
            }
          }
        }
      }
    }
  ]
}