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Enum: GeneSetRelationshipEnum

How an external gene set (e.g. an MSigDB/KEGG pathway, a cell-type signature, or an expression-perturbation signature) relates to a disease entry. Records the semantics of a curated disease<->gene-set link so the link is auditable and the right kind of alignment can be applied.

URI: dismech:enum/GeneSetRelationshipEnum

Permissible Values

Value Meaning Description
CANONICAL_PATHWAY None A curated pathway gene set representing the disease's canonical mechanism (e
CELL_TYPE_SIGNATURE None A marker gene set for a cell type relevant to the disease
PERTURBATION_SIGNATURE None An up/down expression signature from a perturbation or contrast (e
DISEASE_SIGNATURE None A differential-expression signature derived from the disease itself
OTHER None A related gene set that does not fit the categories above

Identifier and Mapping Information

Schema Source

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

LinkML Source

name: GeneSetRelationshipEnum
description: How an external gene set (e.g. an MSigDB/KEGG pathway, a cell-type signature,
  or an expression-perturbation signature) relates to a disease entry. Records the
  semantics of a curated disease<->gene-set link so the link is auditable and the
  right kind of alignment can be applied.
from_schema: https://w3id.org/monarch-initiative/dismech
rank: 1000
permissible_values:
  CANONICAL_PATHWAY:
    text: CANONICAL_PATHWAY
    description: A curated pathway gene set representing the disease's canonical mechanism
      (e.g. KEGG_ASTHMA for asthma). The primary target for BP alignment against the
      pathograph.
  CELL_TYPE_SIGNATURE:
    text: CELL_TYPE_SIGNATURE
    description: A marker gene set for a cell type relevant to the disease.
  PERTURBATION_SIGNATURE:
    text: PERTURBATION_SIGNATURE
    description: An up/down expression signature from a perturbation or contrast (e.g.
      drug response, knockout) relevant to the disease.
  DISEASE_SIGNATURE:
    text: DISEASE_SIGNATURE
    description: A differential-expression signature derived from the disease itself.
  OTHER:
    text: OTHER
    description: A related gene set that does not fit the categories above.