Changes between Version 29 and Version 30 of GOAnnotationGuidelines


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Timestamp:
Feb 25, 2015, 9:56:58 AM (6 years ago)
Author:
vw253
Comment:

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  • GOAnnotationGuidelines

    v29 v30  
    6666=== Annotation Specificity ===
    6767
     68  At PomBase  we have tagged some terms  as 'not to be used for direct annotation' because it should always or usually)  be possible to make a more specific annotation.
     69  Examples include:
     70  * DNA replication (meiotic or mitotic?)
     71  * cell cycle/regulation of cell cycle (meiotic or mitotic? which transition?)
     72  * splicing via the spliceosome -> nuclear mRNA cis splicing, via spliceosome  (no trans splicing in pombe)
     73  * cytokinesis (should use terms under the appropriate cell cycle mitotic (usually) or meiotic)
     74  * cell wall organization  -> fungal-type cell wall organization or biogenesis or one of its descendants
     75  * transport (vesicle-meidated? transmembrane? etc)
    6876
    6977==== Biological Process ====
     
    8391Regulation of transcription and signalling pathways Consists of four components: a signal transduction cascade, a transcription factor, the process of transcription and a downstream process. The signal transduction cascade regulates the downstream process ONLY. The transcription factor regulates transcription AND the downstream process. For instance, the transcription factor ste11 should be annotated to positive regulation of transcription involved in sporulation AND signal transduction involved in positive regulation of sporulation. Mam2 in contrast is only annotated to signal transduction involved in positive regulation of sporulation.
    8492
    85  * Translation
    86   * For annotations to translation, it should always be possible to specify [http://www.ebi.ac.uk/QuickGO/GTerm?id=GO:0002181 cytoplasmic translation (GO:0002181)] or [http://www.ebi.ac.uk/QuickGO/GTerm?id=GO:0032543 mitochondrial translation (GO:0032543)]
    87 
    88  * Splicing
    89   * Annotations for GT-AG type splicing via the spliceosome should always be to [http://www.ebi.ac.uk/QuickGO/GTerm?id=GO:0045292 nuclear mRNA cis splicing, via spliceosome (GO:0045292)]
    90 
    91  * Cytokinesis
    92   * Annotations for cytokinesis in fission yeast should always be to [http://www.ebi.ac.uk/QuickGO/GTerm?id=GO:0033205 GO:cell cycle cytokinesis (GO:0033205)] or one of its descendants
    93   * Cytokinesis terms are in the "mapping to specific terms" file
    94 
    95  * Cell wall organization
    96   * Annotations to cell wall organization should always be to [http://www.ebi.ac.uk/QuickGO/GTerm?id=GO:0071852 Fungal-type cell wall organization or biogenesis (GO:0071852)] or one of its descendants
    97   * Cell wall organization terms are in the "mapping to specific terms" file
    98 
    9993 * Transport/Localization
    100   * Always check that transport and localization terms have "cellular" ancestry, usually to [http://www.ebi.ac.uk/QuickGO/GTerm?id=GO:0046907 intracellular transport (GO:0046907)] or [http://www.ebi.ac.uk/QuickGO/GTerm?id=GO:0051641 cellular localization (GO:0051641)]
    10194  * Check that the appropriate "intracellular" term is used, e.g, [http://www.ebi.ac.uk/QuickGO/GTerm?id=GO:0006886 intracellular protein transport (GO:0006886)]
    10295  * Note the distinction between "transport" and "localization" and always use the appropriate branch. Localization is more general and can involve establishment or maintenance at a specific location, whereas transport involves directed movement
    103   * Note that all transmembrane transporters should have an annotation to the process of [http://www.ebi.ac.uk/QuickGO/GTerm?id=GO:0055085 transmembrane transport (GO:0055085)]. In some cases, GO will have a function-process link that allows the transport process annotation to be inferred; in other cases, you may want to request an MF-BP link.
     96  * Note that all transmembrane transporters should have an annotation to the process of [http://www.ebi.ac.uk/QuickGO/GTerm?id=GO:0055085 transmembrane transport (GO:0055085)].
    10497  * Note that [http://www.ebi.ac.uk/QuickGO/GTerm?id=GO:0006913 nucleocytoplasmic transport (GO:0006913)] is NOT "transmembrane transport", as the lipid bilayer is not traversed.
    105 
    106  * DNA replication
    107   * Annotations to "canonical DNA replication" should be to [http://www.ebi.ac.uk/QuickGO/GTerm?id=GO:0006261 DNA-dependent DNA replication (GO:0006261)] or one of its descendants. Nuclear DNA replication in pombe is 'nuclear cell cycle DNA replication' [http://www.ebi.ac.uk/QuickGO/GTerm?id=GO:0033260 GO:0033260].
    108   * DNA replication terms are in the "mapping to specific terms" file
    10998
    11099 * Metabolic processes