nanopub_graphdati-0.9.0.yaml

$schema: http://json-schema.org/draft-04/schema#
description: |
  NOTE: This schema is NOT an official Nanopub JSON Schema by the
  [Nanopub Organization](http://nanopub.org/). It is conceptually derived
  from their fine work for the needs of GraphDati.

  The purpose of this schema is to manage assertions (labeled as edges in
  the schema) and associated metadata such as assertion citation, context and
  general metadata.  This format is designed for use with GraphDati.
  It differs from the nanopub_bel schema due to a stricter specification
  of the nanopub.context object in nanobpub_bel.

  Please provide feedback as github issues or pull requests at
  https://github.com/belbio/schemas.

  The master version of this JSON Schema is managed at:
  https://github.com/belbio/schemas/blob/master/schemas/nanopub_graphdati-0.9.0.yaml

  A nanopub file is either a single nanopub, an array of nanopubs or uses
  the JSON Lines (http://jsonlines.org/) format with a nanopub (or schema_uri,
  metadata object) per line.

  Note: This JSON schema is designed to work with the Swagger Specification as a
  schema object which does not allow 'type' to be an array so not able to specify
  optional elements as "type": ["string", "null"] for example.

  Nanopubs can be stored as either individual JSON files with a single optional
  metadata JSON file OR as collection using an array of JSON Nanopubs or a JSONLines
  version where each line is a nanopub JSON object.  In an array or JSONLines
  version, the metadata and schema_uri objects need to be at the top.

  Obviously some combinations of the following objects in the anyOf below
  are not compatible.  It doesn't make sense to use the nanopub object and
  array of nanopub objects at the same time.

anyOf:
  - $ref: '#/definitions/nanopub'
  - $ref: "#/definitions/schema_uri"
  - $ref: "#/definitions/metadata"
  - type: array
    items:
      anyOf:
        - $ref: '#/definitions/nanopub'
        - $ref: "#/definitions/schema_uri"
        - $ref: '#/definitions/metadata'

definitions:
  schema_uri:
    type: object
    additionalProperties: false
    required:
      - schema_uri
    properties:
      schema_uri:
        type: object
        additionalProperties: false
        required:
          - uri
        properties:
          uri:
            type: string
            format: uri
            description: JSON Schema definition URI
  metadata:
    description: Nanopub collection metadata used to document and validate nanopub collection
    type: object
    required:
      - metadata
    description: suggested but not required properties are listed below
    properties:
      metadata:
        type: object
        additionalProperties: true
        properties:
          copyright:
            type: string
          collection_name:
            type: string
          description:
            type: string
            description: |
              add any additional information here on why this collection was
              created, what is consists of, additional contact instructions, etc
          version:
            type: string
          license:
            type: string
          contact:
            type: string
            description: email address to contact for details on this nanopub collection
          namespaces:
            type: array
            description: |
              If using a namespace:value entity in your edge or context objects, this provides a
              way of providing an abbreviated namespace to support an unambiguous
              namespace value.
            items:
              type: object
              properties:
                name:
                  type: string
                uri:
                  type: string
                  format: uri

  nanopub:
    description: Smallest unit of relational knowledge with context (see http://nanopub.org/)
    type: object
    additionalProperties: false
    required:
      - nanopub
    properties:
      nanopub:
        type: object
        additionalProperties: false
        required:
          - type
          - citation
          - edges
        properties:
          schema_uri:
            type: string
            format: uri
          id:
            oneOf:
              - type: string
              - type: "null"
            description: ID of nanopub
          type:
            description: 'Type of nanopub: BEL version 2.0.0, PEL, LegEL, etc'
            type: object
            additionalProperties: false
            required:
              - name
              - version
            properties:
              name:
                type: string
                description: Name of Nanopub type, e.g. BEL, PEL, LegEL, etc
              version:
                type: string
                description: Version of Nanopub type, e.g. 2.0.0
          context:
            description: Context of the edge[s] (e.g for BEL nanopubs, the species, tissue, disease)
              state, ...
            type: array
            items:
              type: object
          citation:
            description: |
              Reference to the source. The specific type of nanopub may have
              specific objects required for citations.
              The following properties are optional.
            type: object
            additionalProperties: true
            anyOf:
              - required:
                - uri
              - required:
                - database
              - required:
                - reference

            properties:
              uri:
                type: string
                format: uri
                description: URL of this citation, e.g. a website cited should have this field

              database:
                type: object
                required:
                  - name
                  - id
                properties:
                  name:
                    type: string
                    description: name of database, e.g. Pubmed, DOI, etc
                  id:
                    description: Source ID of citation, e.g. Pubmed ID for Pubmed citations
                    oneOf:
                     - type: string
                     - type: number

              reference:
                oneOf:
                  - type: string
                    description: |
                      Citation as single unparsed string, e.g.
                      Edmunds W, Pebody R, et al. 2000. The sero-epidemiology of
                      diptheria in Western Europe. Epidemiol Infect 125(1):113-25.
                  - type: object
                    description: reference object

              authors:
                type: array
                items:
                  type: string
              source_name:
                type: string
                description: name of journal, book, website, database
              source_type:
                type: string
                description: type of citation, journal, book, website, database
              title:
                type: string
                description: Title of citation (journal article title, web page title, book chapter title)
              date_published:
                type: string
                description: ISO Date format, e.g. 2016-12-31 for December 31, 2016
              comments:
                type: string
                description: Comments about the citation by Nanopub creator(s)
          edges:
            description: List of edges, minimum of 1 edge required, all edges must match context
            type: array
            minItems: 1
            items:
              type: object
              additionalProperties: false
              required:
                - subject
              properties:
                subject:
                  type: string
                relation:
                  oneOf:
                    - type: string
                    - type: "null"
                object:
                  oneOf:
                    - type: string
                    - type: "null"
          evidence:
            description: Any specific summary text that serves as a basis for this edge and context.
            type: string
          metadata:
            description: |
              Optional metadata elements - Creator information, creation date, additional notes, etc
              Any additional metadata elements can be added as needed.
            type: object
            additionalProperties: true
            properties:
              creation_date:
                type: string
                format: date
              modification_date:
                type: string
                format: date
              nanopub_collection:
                type: string
                description: Name of a set of nanopubs if applicable, used to group nanopubs into sets
              author_name:
                type: string
              author_email:
                type: string
                format: email
              notes:
                type: string
                description: General notes about Nanopub created by author or editors.