GeneDescriptor

This element represents an identifier for a gene, using the Gene Descriptor from the VRSATILE Framework. Gene Descriptors can be used to transmit the information that the gene is thought to play a causative role in the disease phenotypes being described in cases where the exact variant cannot be transmitted, either for privacy reasons or because it is unknown.

Gene Descriptors may also be used to contextualize variants described in a VariationDescriptor.

Data model

Definition of the GeneDescriptor element

Field	Type	Multiplicity	Description
value_id	string	1..1	Official identifier of the gene. REQUIRED.
symbol	string	1..1	Official gene symbol. REQUIRED.
description	string	0..1	A free-text description of the gene
alternate_ids	list of string	0..*	Alternative identifier(s) of the gene
xrefs	list of string	0..*	Related concept IDs (e.g. gene ortholog IDs) may be placed in xrefs
alternate_symbols	list of string	0..*	Alternative symbol(s) of the gene

Example

geneDescriptor:
  valueId: "HGNC:3477"
  symbol: "ETF1"

Optionally, with alternative identifiers:

geneDescriptor:
  valueId: "HGNC:3477"
  symbol: "ETF1"
  alternateIds:
  - "ensembl:ENSG00000120705"
  - "ncbigene:2107"
  - "ucsc:uc003ldc.6"
  - "OMIM:600285"

Using the gene descriptor to convey alternate identifiers, symbols and orthologs:

geneDescriptor:
  valueId: "HGNC:3477"
  symbol: "ETF1"
  alternateIds:
  - "ensembl:ENSG00000120705"
  - "ncbigene:2107"
  - "ucsc:uc003ldc.6"
  - "OMIM:600285"
  alternateSymbols:
  - "SUP45L1"
  - "ERF1"
  - "ERF"
  - "eRF1"
  - "TB3-1"
  - "RF1"
  xrefs:
  - "VGNC:97422"
  - "MGI:2385071"
  - "RGD:1305712"
  - "ensembl:ENSRNOG00000019450"
  - "ncbigene:307503"

Explanations

value_id

The id represents the accession number of comparable identifier for the gene.

It SHOULD be a CURIE identifier with a prefix that is used by the official organism gene nomenclature committee. In the case of Humans, this is the HGNC, e.g. HGNC:347

symbol

This SHOULD use official gene symbol as designated by the organism gene nomenclature committee. In the case of human this is the HUGO Gene Nomenclature Committee e.g. ETF1.

description

A free-text description of the value object. This should be only used to convey information which is otherwise not possible to encode using the schema.

alternate_ids

This field can be used to provide identifiers to alternative resources where this gene is used or catalogued. For example, the NCBI and Ensemble both provide alternative identifiers for genes where they catalogue the transcripts for a gene e.g. ncbigene:2107, ensembl:ENSG00000120705 These identifiers SHOULD be represented in CURIE form with a corresponding Resource.

alternate_symbols

This field can be used to list the alternate symbols used to refer to the gene. These include the previously approved gene symbols and those used in the literature or other databases to refer to the gene.

xrefs

This field can be used to provide identifiers to alternative resources representing related, but not equivalent concepts, for example gene ortholog ids