Changes between Version 55 and Version 56 of GOAnnotationGuidelines


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Timestamp:
Feb 25, 2015, 4:26:19 PM (6 years ago)
Author:
vw253
Comment:

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  • GOAnnotationGuidelines

    v55 v56  
    3333GO annotation extensions capture specificity that would be undesirable in the ontology. See the [http://wiki.geneontology.org/index.php/Annotation_Extension GOC annotation extension documentation]
    3434
    35   * Format The basic format is relation(Database prefix:database_ID). Additional format/syntax documentation [AnnotationExtensionSyntax PomBase documentation for Annotation Extension Syntax]
     35  * Basic Format: relation(Database prefix:database_ID). Additional format/syntax documentation [AnnotationExtensionSyntax PomBase documentation for Annotation Extension Syntax]
    3636 
    37 * When to use an extension versus requesting a new term? See  [wiki:PrePostComposeGO PomBase "Precompose or postcompose?" wiki]
     37  * When to use an extension versus requesting a new term? See  [wiki:PrePostComposeGO PomBase "Precompose or postcompose?" wiki]
    3838
    39 An exception to this rule is when a signalling pathway is activated by a number of different stresses. In this case the stress will be added as a "during..." extension. The rationale for this exception is that the specific annotations do not offer any obvious benefits to users (for enrichments etc). This would change if  2 distinct pathways were observed with  distinct gene products annotated for each pathway (this test can be used to make  decisions about further proposed exceptions). Note that you should continue to make a concurrent "response to x stress" for these gene products.
    4039
    4140  * [http://wiki.geneontology.org/index.php/Annotation_Extension#The_basic_format GO annotation extension wiki]