Guidelines for database cross references: Difference between revisions
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GO is now adding a <code>type</code> for each database cross-reference. These are derived from the [https://www.w3.org/TR/skos-reference/#mapping W3.org standards]. The types of <code>skos:mappingRelation</code> used by GO are: | GO is now adding a <code>type</code> for each database cross-reference. These are derived from the [https://www.w3.org/TR/skos-reference/#mapping W3.org standards]. The types of <code>skos:mappingRelation</code> 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 | * <code>skos:exactMatch</code>: 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 | * <code>skos:broadMatch</code>: 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 | * <code>skos:narrowMatch</code>: 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 | * <code>skos:relatedMatch</code>: 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 | ||
Revision as of 03:27, 8 January 2021
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)
- ISBN
- Wikipedia
- EC*
- KEGG*
- MetaCyc*
- TCDB*
- *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
Cross-reference types
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 typeskos: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 termsskos: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 termskos: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.
Review Status
Last reviewed: January 8, 2021