beacon-common.yaml

# Information about the organisation hosting the GA4GH Beacon service:
organisation:
  id: org.example
  name: GDI Example Organisation
  welcomeUrl: https://gdi.example.org

  # The following are all OPTIONAL:
  description: >-
    This is the default description of the Beacon.
    Please update your Beacon info via configuration files.
  address: Local street 1, 50709 City, COUNTRY
  contactUrl: mailto:no-reply@example.org
  logoUrl: https://gdi.onemilliongenomes.eu/images/gdi-logo-no-text.svg


# This section defines the GA4GH Beacon entity-schemas and displayed texts.
# Full paths are constructed as: "${schemaBaseUrl}${schemaVersionTag}${path}".
# This info is used to construct schema references and details of entry-types.
# Although this stuff is pretty much static and could be hard-coded into code,
# hopefully the YAML-formatted representation is more friendly when something
# needs to be changed.
compliance:
  specification: GA4GH Beacon v2
  schemaBaseUrl: https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/
  schemaVersionTag: v2.2.0
  schemas:

    - id: info
      name: Beacon Info
      description: Metadata describing a Beacon instance.
      path: /framework/json/responses/sections/beaconInfoResults.json

    - id: configuration
      name: Beacon Configuration
      description: >-
        The Beacon configuration reports several attributes of the beacon
        instance related to security, maturity and available entry types. Where
        appropriate the details returned in `service-info` should mirror the
        ones in this configuration.
      path: /framework/json/configuration/beaconConfigurationSchema.json

    - id: entryTypes
      name: Entry Types
      description: >-
        This is a dictionary of the entry types implemented in this Beacon
        instance.
      path: /framework/json/configuration/entryTypesSchema.json

    - id: map
      name: Beacon Map
      description: >-
        Map of a Beacon, its entry types and endpoints. It is conceptually
        similar to a website sitemap.
      path: /framework/json/configuration/beaconMapSchema.json

    - id: filteringTerm
      name: Filtering Terms
      description: >-
        Schema for the Filtering Terms list related to the hosting entry type.
        It is kept separated to allow updating it independently.
      path: /framework/json/configuration/filteringTermsSchema.json

    - id: genomicVariant
      name: Genomic variation
      description: Default schema for a genomic variant entry.
      path: /models/json/beacon-v2-default-model/genomicVariations/defaultSchema.json

    - id: dataset
      name: Dataset
      description: Default schema for a genomic dataset.
      path: /models/json/beacon-v2-default-model/datasets/defaultSchema.json

    - id: individual
      name: Individual
      description: Default schema for an individual entry.
      path: /models/json/beacon-v2-default-model/individuals/defaultSchema.json


# These items are displayed at /configuration, /entry_types, and /map:
# Configure the properties to fine-tune how they appear in these endpoints.
# "schemaId" is a reference to "compliance.schemas[].id" in this file.
entryTypes:
  - id: genomicVariant
    name: Genomic Variants
    description: The location of a sequence.
    openapi: /models/src/beacon-v2-default-model/genomicVariations/endpoints.yaml
    schemaId: genomicVariant
    mainPath: /g_variants
    ontologyTerm:
      id: ENSGLOSSARY:0000092
      label: variant

  - id: dataset
    name: Dataset
    description: A Dataset is a collection of records, like rows in a database or cards in a cardholder.
    openapi: /models/src/beacon-v2-default-model/datasets/endpoints.yaml
    schemaId: dataset
    mainPath: /datasets
    ontologyTerm:
      id: NCIT:C47824
      label: Data set

  - id: individual
    name: Individual
    description: A human being. It could be a Patient, a Tissue Donor, a Participant, a Human Study Subject, etc.
    openapi: /models/src/beacon-v2-default-model/individuals/endpoints.yaml
    schemaId: individual
    mainPath: /individuals
    ontologyTerm:
      id: NCIT:C25190
      label: Person