ComputationalTool.json

{
  "@context": {
    "schema": "http://schema.org/",
    "rdf": "http://www.w3.org/1999/02/22-rdf-syntax-ns#",
    "rdfs": "http://www.w3.org/2000/01/rdf-schema#",
    "bioschemas": "https://discovery.biothings.io/view/bioschemas/",
    "niaid": "http://discovery.biothings.io/view/niaid/"
  },
  "@graph": [
    {
      "@id": "niaid:ComputationalTool",
      "@type": "rdfs:Class",
      "rdfs:comment": "A schema describing a minimal ComputationalTool for the National Institute of Allergy and Infectious Disease (NIAID). A ComputationalTool is a software used for the collection, processing, distribution, analysis, visualization, interpretation, etc. of data. Additional schema.org and/or custom properties could be added.",
      "rdfs:label": "ComputationalTool",
      "rdfs:subClassOf": {
        "@id": "bioschemas:ComputationalTool"
      },
      "$validation": {
        "$schema": "http://json-schema.org/draft-07/schema#",
        "type": "object",
        "properties": {
          "name": {
            "description": "Descriptive name of the computational tool",
            "owl:cardinality": "one",
            "type": "string"
          },
          "description": {
            "description": "Longer description of what is contained in the computational tool",
            "owl:cardinality": "one",
            "type": "string"
          },
          "identifier": {
            "description": "Identifiers for the computational tool (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 computational tool.  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 ComputationalTool metadata (like GitHub). 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"
                }
              }
            ]
          },
          "url": {
            "description": "software/code location.",
            "owl:cardinality": "one",
            "type": "string",
            "format": "uri"
          },
          "dateModified": {
            "description": "date when the computational tool has been modified",
            "owl:cardinality": "one",
            "owl:cardinality": "one",
            "type": "string",
            "format": "date"
          },
          "license": {
            "description": "A license document that applies to this content, typically indicated by URL.",
            "owl:cardinality": "one",
            "type": "string",
            "format": "uri"
          },
          "citation": {
            "description": "Journal article or other publication associated with the computational tool (stored as an object, not a string)",
            "owl:cardinality": "many",
            "oneOf": [{
                "$ref": "#/definitions/article"
              },
              {
                "type": "array",
                "items": {
                  "$ref": "#/definitions/article"
                }
              }
            ]
          },
          "applicationCategory": {
            "description": "Type of software application, e.g. 'Game, Multimedia'. Please use terms from the 'Tool type' table in the biotools documentation.",
            "owl:cardinality": "many",
            "anyOf": [
              {
                "type": "string"
              },
              {
                "type": "array",
                "items": {
                  "type": "string"
                }
              },
              {
                "type": "string",
                "format": "uri"
              },
              {
                "type": "array",
                "items": {
                  "type": "string",
                  "format": "uri"
                }
              }
            ]
          },
          "applicationSubCategory": {
            "description": "Subcategory of the application, e.g. 'Arcade Game'. Use an EDAM:Topic to describe the category of application",
            "owl:cardinality": "many",
            "oneOf": [
              {
                "$ref": "#/definitions/edamTopic"
              },
              {
                "type": "array",
                "items": {
                  "$ref": "#/definitions/edamTopic"
                }
              }
            ]
          },
          "codeRepository": {
            "description": "Link to the source code repository of the tool.",
            "owl:cardinality": "many",
            "oneOf": [
              {
                "type": "string",
                "format": "uri"
              },
              {
                "type": "array",
                "items": {
                  "type": "string",
                  "format": "uri"
                }
              }
            ]
          },
          "programmingLanguage": {
            "description": "The main programming language(s) used to build or execute the tool. Please use terms from the ‘Programming language’ table in the Bio.Tools documentation",
            "owl:cardinality": "many",
            "oneOf": [
              {
                "type": "string"
              },
              {
                "type": "array",
                "items": {
                  "type": "string"
                }
              }
            ]
          },
          "softwareVersion": {
            "description": "Version(s) of the tool, which this information is valid for. Can also be a comma-delimited list and include hyphen-separated ranges of versions.",
            "owl:cardinality": "many",
            "oneOf": [
              {
                "type": "string"
              },
              {
                "type": "array",
                "items": {
                  "type": "string"
                }
              }
            ]
          },
          "featureList": {
            "description": "Features or modules provided by this application (and possibly required by other applications). Functionality provided by the tool. This is similar to measurementTechnique in Dataset.",
            "owl:cardinality": "many",
            "anyOf": [
              {
                "$ref": "#/definitions/edamOperation"
              },
              {
                "type": "array",
                "items": {
                  "$ref": "#/definitions/edamOperation"
                }
              },
              {
                "type": "string",
                "format": "uri"
              },
              {
                "type": "array",
                "items": {
                  "type": "string",
                  "format": "uri"
                }
              }
            ]
          },
          "species": {
            "description": "Species(es) from which the computation tool is based",
            "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 computational tool (e.g. SARS-CoV-2)",
            "owl:cardinality": "many",
            "oneOf": [{
                "$ref": "#/definitions/pathogenControlledVocabulary"
              },
              {
                "type": "array",
                "items": {
                  "$ref": "#/definitions/pathogenControlledVocabulary"
                }
              }
            ]
          },
          "healthCondition": {
            "description": "The infectious disease(s) or health condition(s) which are the focus of the computational tool (e.g. COVID-19, pneumonia, etc.)",
            "owl:cardinality": "many",
            "oneOf": [{
                "$ref": "#/definitions/diseaseControlledVocabulary"
              },
              {
                "type": "array",
                "items": {
                  "$ref": "#/definitions/diseaseControlledVocabulary"
                }
              }
            ]
          },
          "funding": {
            "description": "Funding that supports (sponsors) the collection of this computational tool through some kind of financial contribution",
            "owl:cardinality": "many",
            "oneOf": [{
                "$ref": "#/definitions/monetaryGrant"
              },
              {
                "type": "array",
                "items": {
                  "$ref": "#/definitions/monetaryGrant"
                }
              }
            ]
          },
          "softwareHelp": {
            "description": "A documentation of the tool.",
            "owl:cardinality": "many",
            "oneOf": [
              {
                "$ref": "#/definitions/documentation"
              },
              {
                "type": "array",
                "items": {
                  "$ref": "#/definitions/documentation"
                }
              }
            ]
          }
        },
        "required": [
          "name",
          "description",
          "identifier",
          "creator",
          "url",
          "funding"
        ],
        "recommended": [
          "dateModified",
          "license",
          "citation",
          "applicationCategory",
          "applicationSubCategory",
          "codeRepository",
          "programmingLanguage",
          "softwareVersion",
          "featureList",
          "softwareHelp"
        ],
        "optional": [
          "sdPublisher",
          "species",
          "infectiousAgent",
          "healthCondition"
        ],
        "definitions": {
          "edamTopic": {
            "@type": "DefinedTerm",
            "type": "object",
            "strict": false,
            "vocabulary": {
              "ontology": [
                "edam"
              ],
              "children_of": [
                "http://edamontology.org/topic_0003"
              ],
              "property": {
                "name": {
                  "type": "string"
                },
                "url": {
                  "type": "string",
                  "format": "uri"
                },
                "identifier": {
                  "type": "string"
                }
              }
            }
          },
          "edamOperation": {
            "@type": "DefinedTerm",
            "type": "object",
            "strict": false,
            "vocabulary": {
              "ontology": [
                "edam"
              ],
              "children_of": [
                "http://edamontology.org/operation_0004"
              ],
              "property": {
                "name": {
                  "type": "string"
                },
                "url": {
                  "type": "string",
                  "format": "uri"
                },
                "identifier": {
                  "type": "string"
                }
              }
            }
          },
          "article": {
            "description": "A scholarly article in which the computational tool is cited.",
            "@type": "ScholarlyArticle",
            "type": "object",
            "properties": {
              "name": {
                "type": "string"
              },
              "url": {
                "type": "string",
                "format": "uri"
              }
            },
            "required": [
              "url"
            ]
          },
          "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"
            ]
          },
          "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 computational tool through some kind of financial contribution",
            "properties": {
              "funder": {
                "description": "An organization associated with a creator or funder of a computational tool",
                "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 computational tool"
              },
              "parentOrganization": {
                "type": "string",
                "description": "name of the parent funding organization"
              }
            },
            "required": [
              "name"
            ]
          },
          "documentation": {
            "@type": "CreativeWork",
            "type": "object",
            "properties": {
              "url": {
                  "type": "string",
                  "format": "uri"
                }
            }
          }
        }
      }
    },
    {
      "@id": "niaid:codeRepository",
      "@type": "rdf:Property",
      "rdfs:comment": "Link to the source code repository of the tool.",
      "rdfs:label": "codeRepository",
      "schema:domainIncludes": {
        "@id": "niaid:ComputationalTool"
      },
      "schema:rangeIncludes": [
        {
          "@id": "schema:URL"
        }
      ]
    },
    {
      "@id": "niaid:programmingLanguage",
      "@type": "rdf:Property",
      "rdfs:comment": "The main programming language(s) used to build or execute the tool. Please use terms from the ‘Programming language’ table in the Bio.Tools documentation",
      "rdfs:label": "programmingLanguage",
      "schema:domainIncludes": {
        "@id": "niaid:ComputationalTool"
      },
      "schema:rangeIncludes": [
        {
          "@id": "schema:Text"
        },
        {
          "@id": "schema:ComputerLanguage"
        }
      ]
    },
    {
      "@id": "niaid:funder",
      "@type": "rdf:Property",
      "rdfs:comment": "An organization that supports (sponsors) the development or maintenance of this computational tool through some kind of financial contribution.",
      "rdfs:label": "funder",
      "schema:domainIncludes": [{
        "@id": "niaid:MonetaryGrant"
      }],
      "schema:rangeIncludes": {
        "@id": "niaid:Organization"
      },
      "schema:sameAs": {
        "@id": "schema:funder"
      }
    }
  ]
}