Changes between Version 54 and Version 55 of GOAnnotationGuidelines


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Timestamp:
Feb 25, 2015, 4:25:24 PM (6 years ago)
Author:
vw253
Comment:

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  • GOAnnotationGuidelines

    v54 v55  
    3232
    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]
    34   * When to use an extension versus requesting a new term? See  [wiki:PrePostComposeGO PomBase "Precompose or postcompose?" wiki]
    35  
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    37 
     35  * Format The basic format is relation(Database prefix:database_ID). Additional format/syntax documentation [AnnotationExtensionSyntax PomBase documentation for Annotation Extension Syntax]
     36 
     37* When to use an extension versus requesting a new term? See  [wiki:PrePostComposeGO PomBase "Precompose or postcompose?" wiki]
    3838
    3939An 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.
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    42  * The basic format is relation(Database prefix:database_ID). Additional format/syntax documentation is available:
    43   * [AnnotationExtensionSyntax PomBase documentation for Annotation Extension Syntax]
    4441  * [http://wiki.geneontology.org/index.php/Annotation_Extension#The_basic_format GO annotation extension wiki]
    4542 * Relations in use: