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)
- *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.
GO is now adding a
type for each database cross-reference. These 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 xreferenced term; single EXACT or RELATED match allowed per term for any xref type
- skos:broadMatch: GO term meaning is narrower than that of the xreferenced 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 xreferenced 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 xreferenced term, but the best match; single EXACT or RELATED match allowed per term for any xref type
See Ontology_Editors_Daily_Workflow for commit, push and merge instructions.
Last reviewed: January 8, 2021