Guidelines for 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)

• 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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