Guidelines for database cross references: Difference between revisions

Revision as of 04:53, 4 August 2021

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 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:
To edit a cross-reference type:
- Click on the @ sign next to the cross-reference.
- Click on the + sign on the right to add an annotation.
- Select source in the left-hand menu, and Literal in the right-hand menu. Add the cross-reference type:
  - 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

Most Rhea cross-references are skos:exactMatch; but exceptions are allowed
Most EC and MetaCyc cross-references are skos:narrowMatch by default but can be upgraded to skos:exactMatch if there is a 1:1 correspondence.
Only one skos:exactMatch 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

Back to: Editing the Ontology

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-  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.
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 * MetaCyc
 * Reactome
-* Rhea
+* RHEA
-* TCDB
+* TCDB for transporters (abbreviated as 'TC')
-==General cross-reference types==
+==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.
+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
-* <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
+* Most Rhea cross-references are <code>skos:exactMatch</code>; but exceptions are allowed
-* <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
+* 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.
-* <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
+* Only one <code>skos:exactMatch</code> for each cross-reference source is allowed.
-* <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
-* Rhea cross-references are <code>skos:exactMatch</code> (since only 1:1 mappings are allowed)
-* 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.
    See [[Ontology_Editors_Daily_Workflow]] for commit, push and merge instructions.
 == Review Status ==
-Last reviewed: January 8, 2021
+Last reviewed: August 4, 2021
 [[Ontology_Development#Editing_the_Ontology |Back to: Editing the Ontology]]
 [[Category:GO Editors]][[Category:Ontology]][[Category:Editor_Guide_2018]]