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

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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*. Note that RHEAs IDs that are not yet public cannot be used in definition xrefs.

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: GO editors can use provisional ECs. Preliminary ECs have a letter in the last section of the EC number, for e.g., 3.5.1.n3. Preliminary EC numbers can be sued as cross references and definition cross references, since they are unique like the complete ones. When they are turned into real EC numbers they are "transferred", so the new ID is traceable.
  • KEGG
  • MetaCyc
  • Reactome
  • RHEA: GO editors can use new (not yet public) RHEA IDs as database cross-references. These are filtered out from the public version of the ontology until they are available. Note that they cannot be used as definition xrefs.
  • TCDB for transporters (abbreviated as 'TC')

Adding database cross-reference types

Database cross-references may have a type (optional). 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:
  • To edit a cross-reference type:
    • Click on the @ sign next to the cross-reference.
    • Click on the + sign on the right to add an annotation.
    • Select source in the left-hand menu, and Literal in the right-hand menu. Add the cross-reference type:
      • 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
  • Most Rhea cross-references are skos:exactMatch; but exceptions are allowed
  • Most EC and MetaCyc cross-references are skos:narrowMatch by default but can be upgraded to skos:exactMatch if there is a 1:1 correspondence.
  • Only one skos:exactMatch for each cross-reference source is allowed.
 See Ontology_Editors_Daily_Workflow for commit, push and merge instructions.

Review Status

Last reviewed: August 4, 2021

Back to: Editing the Ontology