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Class: GeneSetAssociation

A curated link between this disease and an external gene set, referenced by its structured-source id (MYGENESET:, resolving to references_cache/MYGENESET.md). The gene set's membership and curated GO interpretation live upstream / in the cache file; this object records only the precise disease<->set link and its semantics, avoiding re-duplication of genes in the KB. It is the anchor for BP alignment (just genesets-align): the set's curated biological processes are scored against this disease's pathograph._

URI: dismech:class/GeneSetAssociation

 classDiagram
    class GeneSetAssociation
    click GeneSetAssociation href "../../classes/GeneSetAssociation/"
      GeneSetAssociation : gene_set

      GeneSetAssociation : note

      GeneSetAssociation : relationship





        GeneSetAssociation --> "0..1" GeneSetRelationshipEnum : relationship
        click GeneSetRelationshipEnum href "../../enums/GeneSetRelationshipEnum/"

Slots

Name Cardinality and Range Description Inheritance
gene_set 1
Uriorcurie		 Structured-source id of the gene set, e direct
relationship 0..1
GeneSetRelationshipEnum		 How the gene set relates to this disease direct
note 0..1
String		 Free-text curator note on the link (e direct

Usages

used by used in type used
Disease gene_sets range GeneSetAssociation

Identifier and Mapping Information

Schema Source

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

Mappings

Mapping Type Mapped Value
self dismech:GeneSetAssociation
native dismech:GeneSetAssociation

LinkML Source

Direct

name: GeneSetAssociation
description: 'A curated link between this disease and an external gene set, referenced
  by its structured-source id (MYGENESET:<id>, resolving to references_cache/MYGENESET_<id>.md).
  The gene set''s membership and curated GO interpretation live upstream / in the
  cache file; this object records only the precise disease<->set link and its semantics,
  avoiding re-duplication of genes in the KB. It is the anchor for BP alignment (`just
  genesets-align`): the set''s curated biological processes are scored against this
  disease''s pathograph.'
from_schema: https://w3id.org/monarch-initiative/dismech
attributes:
  gene_set:
    name: gene_set
    description: Structured-source id of the gene set, e.g. MYGENESET:KEGG_ASTHMA.
      Resolves to references_cache/MYGENESET_<id>.md.
    from_schema: https://w3id.org/monarch-initiative/dismech
    rank: 1000
    domain_of:
    - GeneSetAssociation
    range: uriorcurie
    required: true
  relationship:
    name: relationship
    description: How the gene set relates to this disease.
    from_schema: https://w3id.org/monarch-initiative/dismech
    domain_of:
    - GeneSetAssociation
    - BiomarkerReadout
    - PhenotypeReadout
    range: GeneSetRelationshipEnum
  note:
    name: note
    description: Free-text curator note on the link (e.g. which arms overlap).
    from_schema: https://w3id.org/monarch-initiative/dismech
    rank: 1000
    domain_of:
    - GeneSetAssociation
    range: string

Induced

name: GeneSetAssociation
description: 'A curated link between this disease and an external gene set, referenced
  by its structured-source id (MYGENESET:<id>, resolving to references_cache/MYGENESET_<id>.md).
  The gene set''s membership and curated GO interpretation live upstream / in the
  cache file; this object records only the precise disease<->set link and its semantics,
  avoiding re-duplication of genes in the KB. It is the anchor for BP alignment (`just
  genesets-align`): the set''s curated biological processes are scored against this
  disease''s pathograph.'
from_schema: https://w3id.org/monarch-initiative/dismech
attributes:
  gene_set:
    name: gene_set
    description: Structured-source id of the gene set, e.g. MYGENESET:KEGG_ASTHMA.
      Resolves to references_cache/MYGENESET_<id>.md.
    from_schema: https://w3id.org/monarch-initiative/dismech
    rank: 1000
    alias: gene_set
    owner: GeneSetAssociation
    domain_of:
    - GeneSetAssociation
    range: uriorcurie
    required: true
  relationship:
    name: relationship
    description: How the gene set relates to this disease.
    from_schema: https://w3id.org/monarch-initiative/dismech
    alias: relationship
    owner: GeneSetAssociation
    domain_of:
    - GeneSetAssociation
    - BiomarkerReadout
    - PhenotypeReadout
    range: GeneSetRelationshipEnum
  note:
    name: note
    description: Free-text curator note on the link (e.g. which arms overlap).
    from_schema: https://w3id.org/monarch-initiative/dismech
    rank: 1000
    alias: note
    owner: GeneSetAssociation
    domain_of:
    - GeneSetAssociation
    range: string