Guidelines for database cross references: Difference between revisions

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  See [[Ontology_Editors_Daily_Workflow]] for creating branches and basic Protégé instructions.
  DRAFT
We have two types of cross-references in the ontology: (1) Definition database cross-references and (2) General database cross-references.  
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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Includes
Includes
* PMIDs (ideally all terms should have a PMID, but we have many terms not having them yet)
* PMIDs (ideally all terms should have a PMID, but we have many terms not having them yet)
* Rhea for enzymes
* RHEA for enzymes*


Can also include (if nothing else is available)
Can also include (if nothing else is available)
* ISBN
* ISBN
* Wikipedia
* Wikipedia
* EC
* EC*
* MetaCyc
* KEGG*
* 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==
General database cross-references are links to external resources.  
General database cross-references are links to external resources.  
* Rhea
 
* EC
* EC
* KEGG
* MetaCyc
* MetaCyc
* KEGG
* 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.
   See [[Ontology_Editors_Daily_Workflow]] for commit, push and merge instructions.


== Review Status ==
== Review Status ==
Last reviewed: February 26, 2020
Last reviewed: August 4, 2021


[[Ontology_Development#Editing_the_Ontology |Back to: Editing the Ontology]]
[[Ontology_Development#Editing_the_Ontology |Back to: Editing the Ontology]]


[[Category:GO Editors]][[Category:Ontology]][[Category:Editor_Guide_2018]]
[[Category:GO Editors]][[Category:Ontology]][[Category:Editor_Guide_2018]]

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