Changes between Version 50 and Version 51 of GOAnnotationGuidelines


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Timestamp:
Feb 25, 2015, 4:18:56 PM (6 years ago)
Author:
vw253
Comment:

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  • GOAnnotationGuidelines

    v50 v51  
    1818   * Or request your term(s) on the [https://sourceforge.net/p/geneontology/ontology-requests/ GO Ontology Requests tracker] at !SourceForge  include -- name, text definition, parent(s), synonyms, reference, etc.
    1919
     20  * when should I request a new GO term   
     21 A general rule is that when a GO process term is representing a single process, a single GO term should be required.
     22   * For example, request a more speciifc term which links 2 parents negative regulation of SREBP signaling pathway by transcription factor catabolism with parents: GO:2000639 negative regulation of SREBP signaling pathway
     23    GO:0010620 negative regulation of transcription by transcription factor catabolism
     24
    2025== Reporting errors  to GO ==
    2126
     
    2732GO 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]
    2833 * When to use an extension versus requesting a new term?
     34 
     35 
    2936  * [wiki:PrePostComposeGO PomBase "Precompose or postcompose?" wiki]
    30   * [http://wiki.geneontology.org/index.php/Annotation_Extension#When_should_a_curator_use_the_Annotation_Extension_field_instead_of_requesting_a_new_GO_term.3F GO "when to use extensions" wiki] and [http://wiki.geneontology.org/index.php/Annotation_Extension#Annotation_Examples annotation examples]
     37 
    3138
    32 A general rule is that when a GO process term is representing a single process, a single GO term should be requested.
    33 For example,
    34 negative regulation of SREBP signaling pathway by transcription factor catabolism
    35 with parents:
    36 GO:2000639 negative regulation of SREBP signaling pathway
    37 GO:0010620
    38 negative regulation of transcription by transcription factor catabolism
     39
    3940
    4041An 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.