Guidelines for database cross references: Difference between revisions
Jump to navigation
Jump to search
| (12 intermediate revisions by the same user not shown) | |||
| Line 3: | Line 3: | ||
DRAFT | 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 | ||
| Line 13: | Line 14: | ||
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* | ||
Can also include (if nothing else is available) | Can also include (if nothing else is available) | ||
* ISBN | * ISBN | ||
* Wikipedia | * Wikipedia | ||
* EC | * EC* | ||
* MetaCyc | * 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. | ||
* EC | * EC | ||
* KEGG | |||
* MetaCyc | * MetaCyc | ||
* | * Reactome | ||
* RHEA | |||
* TCDB for transporters (abbreviated as 'TC') | |||
==General 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: | |||
* <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 | |||
* 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. | See [[Ontology_Editors_Daily_Workflow]] for commit, push and merge instructions. | ||
== Review Status == | == Review Status == | ||
Last reviewed: | Last reviewed: January 8, 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 04:02, 8 January 2021
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
typefor 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:mappingRelationused 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 typeskos: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 termsskos: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 termskos: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:narrowMatchby default but can be upgraded toskos:exactMatchif there is a 1:1 correspondence.
See Ontology_Editors_Daily_Workflow for commit, push and merge instructions.
Review Status
Last reviewed: January 8, 2021