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Enum: GeneDiseaseValiditySourceEnum

The curation body that assigned a gene-disease validity classification. Values are GenCC submitters; each carries a gencc_submitter annotation with its GenCC submitter CURIE, read from the GenCC submissions export. Only the submitters whose classifications dismech entries cite are enumerated; any other GenCC submitter is OTHER_GENCC_SUBMITTER with its name in notes.

URI: dismech:enum/GeneDiseaseValiditySourceEnum

Permissible Values

Value Meaning Description Additional Info
CLINGEN None ClinGen Gene-Disease Validity, assigned by a Gene Curation Expert Panel under... Title: ClinGen
G2P None Gene2Phenotype (EMBL-EBI), which curates gene-disease pairs for specific clin... Title: Gene2Phenotype
ORPHANET None Orphanet Title: Orphanet
GENOMICS_ENGLAND_PANELAPP None Genomics England PanelApp, whose green/amber/red gene ratings on diagnostic p... Title: Genomics England PanelApp
PANELAPP_AUSTRALIA None PanelApp Australia (Australian Genomics), which rates genes on diagnostic pan... Title: PanelApp Australia
OTHER_GENCC_SUBMITTER None Any other GenCC submitter (for example a diagnostic laboratory) Title: Other GenCC submitter

Slots

Name Description
classified_by The external curation body that assigned the classification

Comments

  • There is deliberately no value for dismech or a curator. A validity tier is a classification made under a published framework; when no external body has made one, leave gene_disease_validity absent and say so in Genetic.notes rather than minting a tier (#10179).

Identifier and Mapping Information

Schema Source

  • from schema: https://w3id.org/monarch-initiative/dismech

LinkML Source

name: GeneDiseaseValiditySourceEnum
description: The curation body that assigned a gene-disease validity classification.
  Values are GenCC submitters; each carries a `gencc_submitter` annotation with its
  GenCC submitter CURIE, read from the GenCC submissions export. Only the submitters
  whose classifications dismech entries cite are enumerated; any other GenCC submitter
  is OTHER_GENCC_SUBMITTER with its name in `notes`.
comments:
- There is deliberately no value for dismech or a curator. A validity tier is a classification
  made under a published framework; when no external body has made one, leave `gene_disease_validity`
  absent and say so in `Genetic.notes` rather than minting a tier (#10179).
from_schema: https://w3id.org/monarch-initiative/dismech
rank: 1000
permissible_values:
  CLINGEN:
    text: CLINGEN
    description: ClinGen Gene-Disease Validity, assigned by a Gene Curation Expert
      Panel under the ClinGen SOP. Cite the assertion as a `CGGV:` reference.
    annotations:
      gencc_submitter:
        tag: gencc_submitter
        value: GENCC:000102
    title: ClinGen
  G2P:
    text: G2P
    description: Gene2Phenotype (EMBL-EBI), which curates gene-disease pairs for specific
      clinical panels on its own confidence scale.
    annotations:
      gencc_submitter:
        tag: gencc_submitter
        value: GENCC:000112
    title: Gene2Phenotype
  ORPHANET:
    text: ORPHANET
    description: Orphanet. Every Orphanet submission to GenCC is SUPPORTIVE, so the
      tier records that Orphanet lists the pair, not that it graded it.
    annotations:
      gencc_submitter:
        tag: gencc_submitter
        value: GENCC:000110
    title: Orphanet
  GENOMICS_ENGLAND_PANELAPP:
    text: GENOMICS_ENGLAND_PANELAPP
    description: Genomics England PanelApp, whose green/amber/red gene ratings on
      diagnostic panels are mapped onto the GenCC tiers.
    annotations:
      gencc_submitter:
        tag: gencc_submitter
        value: GENCC:000104
    title: Genomics England PanelApp
  PANELAPP_AUSTRALIA:
    text: PANELAPP_AUSTRALIA
    description: PanelApp Australia (Australian Genomics), which rates genes on diagnostic
      panels on the same green/amber/red scale.
    annotations:
      gencc_submitter:
        tag: gencc_submitter
        value: GENCC:000111
    title: PanelApp Australia
  OTHER_GENCC_SUBMITTER:
    text: OTHER_GENCC_SUBMITTER
    description: Any other GenCC submitter (for example a diagnostic laboratory).
      Name it in `notes`.
    title: Other GenCC submitter