Guidelines for 'database cross references' and 'definition database cross references'

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  DRAFT - see also http://wiki.geneontology.org/index.php/Curator_Guide:_Enzymes_and_Reactions and http://wiki.geneontology.org/index.php/Enzymes_and_EC_mappings



We have two types of cross-references in the ontology: (1) Definition database cross-references and (2) General database cross-references.

Definition database cross-references

Definition database cross-references are citable references that have helped generate the term and term's definition. Includes

  • PMIDs (ideally all terms should have a PMID, but we have many terms not having them yet)
  • RHEA for enzymes*

Can also include (if nothing else is available)

  • ISBN
  • Wikipedia
  • EC*
  • KEGG*
  • MetaCyc*
  • TCDB*
  • GOC:(curator initials)
  • *Only relevant for MF terms.
  • Definition database cross-references also need to be added as General database cross-references.

General database cross-references

General database cross-references are links to external resources.

  • EC
  • KEGG
  • MetaCyc
  • Reactome
  • RHEA
  • TCDB for transporters (abbreviated as 'TC')

General cross-reference types

  • GO is now adding a type for database cross-references (still optional until we populate all values). Note that these do not apply to definition cross-references.
  • The db xref types are derived from the W3.org standards. The types of skos:mappingRelation used by GO are:
  • skos:exactMatch: GO term meaning is exactly the same as the cross-referenced term; single EXACT or RELATED match allowed per term for any xref type
  • skos:broadMatch: GO term meaning is narrower than that of the cross-referenced term. More than one BROAD xref is allowed per term, and BROAD xref can be mapped to multiple terms
  • skos:narrowMatch: GO term meaning is more general than that of the cross-referenced term. More than one NARROW xref is allowed per term, but a given NARROW xref can only be mapped to a single term
  • skos:relatedMatch: GO term meaning is not exactly the same as the cross-referenced term, but the best match; single EXACT or RELATED match allowed per term for any xref type
  • Rhea cross-references are skos:exactMatch (since only 1:1 mappings are allowed)
  • EC and MetaCyc cross-references are skos:narrowMatch by default but can be upgraded to skos:exactMatch if there is a 1:1 correspondence.
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Review Status

Last reviewed: January 8, 2021

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