Guidelines for database cross references

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 TO BE COMPLETED

We have two types of cross-references in the ontology: (1) Definition database cross-references and (2) General/term database cross-references, also known as 'Mappings' (for example in AmiGO). Guidelines for definition database cross-references can be found in the Guidelines for GO textual definitions page. The present page describes guidelines for general/term database cross-references.

Database cross-references

General database cross-references, or general dbxrefs, are links to external resources. They should be used where a GO term is identical to an object in another database. The following table lists the main resources to which GO makes cross-references.

Aspect Database Prefix in GO (case-sensitive)  Example mapping Notes
 All  Wikipedia  Wikipedia:  Wikipedia:Barr_body  
 Molecular Function  EC  EC:  EC:2.7.7.27  
  • Partial ECs should only be used for grouping classes, for example GO:0016491 oxidoreductase activity maps to EC:1.-.-.-'. Dashes are mandatory.
  • Provisional ECs (#.#.#.n#; for e.g., 3.5.1.n3) are allowed.
 KEGG reactions  KEGG_REACTION:  KEGG_REACTION:R00948  
 MetaCyc  MetaCyc:  MetaCyc:GLUC1PADENYLTRANS-RXN  
 Rhea  RHEA:  RHEA:12120  
  • GO maps to the non-directional reaction.
  • GO editors can use new (not yet public) RHEA IDs as database cross-references. These are filtered out from the public version of the ontology until they are available.
 TCDB TC:  TC:3.A.1.115.1  
 MEROPS      
 University of Minnesota Biocatalysis/Biodegradation Database (UM-BBD) reaction    UM-BBD_reactionID:r0920
 Biological Process  KEGG_PATHWAY    
 MetaCyc pathway    
 University of Minnesota Biocatalysis/Biodegradation Database (UM-BBD) pathway    UM-BBD_pathwayID:tbz   
     


Exact, broad, narrow general cross references

  • If the term in GO and in the external database have the same meaning, the scope of the cross reference is exactMatch. ** Note that a database cross reference can be an exactMatch to a single GO term, and that a GO term may only have a single exactMatch cross reference to any given external database.
  • If the term in the external database represents a more specific concept than the GO term, for example if an external database has different entries for specific substrates, then it is added to the GO term as narrowMatch.
    • Note that a GO term may have multiple exactMatch cross reference to a given external database, and the same narrowMatch may be present on more than one GO term.
  • If the term is the external database represents a broader concept than the GO term, then it is added to the GO term as broadMatch.

Examples

PROPOSE TO CHANGE THIS PRACTICE

  • If a GO term is obsoleted has a cross-reference to a valid external database entry, then the cross-reference is kept on the obsolete GO term. This situation arises when a term is out of scope for GO but correct in the external database.

TO

  • Valid EC numbers that are exact matches of an obsolete GO term should be made 'narrow match' of the appropriate GO term.

When to not to add database cross-references

  • Obsolete GO terms should not have any database cross references, even in the definition cross-reference. If there is no other definition cross reference available, use GOC:curators.
  • Cross references deprecated in the source database should not be included in GO.


Step-by-step instructions

Adding a database cross-reference

  1.  In Protege, navigate to the term to which you wish to add to a database cross references'.
  2.  In the Annotation window on the right, click on the + to the right of Annotations at the very top of the window.
  3.  In the pop-up window that appears, select 'database_cross_reference' in the left hand window, and 'Literal' tab on the right side.
  4. Add cross reference ID and select 'xsd:string' as Datatype.
  5. Click on OK to save your edits.
  6. See Ontology_Editors_Daily_Workflow for commit, push and merge instructions.

Adding a database cross-reference types

Database cross-references may have a type (optional).

  • If the same cross-reference is used on multiple GO terms, then reference type is mandatory. In this case, it is a broadMatch.
  • If a term has more than one cross reference from a source (for example, 2 RHEA database cross references), then reference type is mandatory. In this case, it is a narrowMatch.
  • The db xref types are derived from the W3.org standards. The types of skos:mappingRelation used by GO are: exactMatch, broadMatch, narrowMatch and relatedMatch.
  • 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; need to add this to have multiple RHEA cross refs
      • 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 implicitly skos:exactMatch by default. This can be changed by an editor if it is not the case.
  • EC and MetaCyc cross-references have no default type but are not considered exact; if they are exact, type skos:exactMatch should be added for clarity.
  • 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: March 13, 2024

Reviewed by: Pascale Gaudet


Back to: Ontology editors' manual