Guidelines for 'database cross references' and 'definition database cross references'
See Ontology_Editors_Daily_Workflow for creating branches and basic Protégé instructions.
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)
- 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.
- TCDB for transporters (abbreviated as 'TC')
General cross-reference types
- GO is now adding a
typefor 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:mappingRelationused 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:narrowMatchby default but can be upgraded to
skos:exactMatchif there is a 1:1 correspondence.
See Ontology_Editors_Daily_Workflow for commit, push and merge instructions.
Last reviewed: January 8, 2021