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

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')

==Adding cross-reference types==
GO is now adding a <code>type</code> 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 [https://www.w3.org/TR/skos-reference/#mapping W3.org standards]. The types of <code>skos:mappingRelation</code> used by GO are: 
* To edit a cross-reference type:
** Click on the <code>@</code> sign next to the cross-reference. 
** Click on the <code>+</code> sign on the right to add an annotation.
** Select <code>source</code> in the left-hand menu, and <code>Literal</code> in the right-hand menu. Add the cross-reference type:
*** <code>skos:exactMatch</code>: GO term meaning is exactly the same as the cross-referenced term; single EXACT or RELATED match allowed per term for any xref type
*** <code>skos:broadMatch</code>: 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
*** <code>skos:narrowMatch</code>: 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
*** <code>skos:relatedMatch</code>: 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 <code>skos:exactMatch</code>; but exceptions are allowed
* Most EC and MetaCyc cross-references are <code>skos:narrowMatch</code> by default but can be upgraded to <code>skos:exactMatch</code> if there is a 1:1 correspondence. 
* Only one <code>skos:exactMatch</code> 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

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