Changes between Version 92 and Version 93 of GOAnnotationGuidelines


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Timestamp:
Jun 27, 2017, 4:48:45 PM (3 years ago)
Author:
mah79
Comment:

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  • GOAnnotationGuidelines

    v92 v93  
    1212== Requesting New GO Terms ==
    1313
    14  * [http://go.termgenie.org/ TermGenie main page] If the term you need follows one of the patterns supported by !TermGenie, you can use it and get a stable ID immediately
    15  * [http://go.termgenie.org/help/index.html TermGenie GO help] (includes how to set up user access)
     14 * (Info on !TermGenie successor will go here)
    1615 * Or request your term(s) on the [https://github.com/geneontology/go-annotation/issues GO Ontology Requests tracker] at !GitHub -- include name, text definition, parent(s), synonyms, reference, etc.
    1716
     
    2524 * Ontology
    2625 * Annotation [https://github.com/geneontology/go-annotation/issues GO Annotation Issues tracker] at !GitHub - use this to raise questions for the GO group, or to report mapping problems (see below)
    27  * Protein2GO
    2826
    2927== GO Annotation Extensions ==
     
    3129 * GO 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]
    3230 * Basic Format: relation(Database prefix:database_ID). Additional format/syntax documentation [AnnotationExtensionSyntax PomBase Annotation Extension Syntax documentation]  [http://wiki.geneontology.org/index.php/Annotation_Extension#The_basic_format GOC Annotation Extension Syntax documentation]
    33  * Which relations can be used in GO extensions?  [wiki:ListOfRelationsForGO List of relations used by PomBase for GO] Graphical View of Relations [http://www.ebi.ac.uk/QuickGO/AnnotationExtensionRelations.html}
     31 * Which relations can be used in GO extensions?  [wiki:ListOfRelationsForGO List of relations used by PomBase for GO] (warning: some parts likely out of date as of 2017)
     32 * Graphical View of Relations [http://www.ebi.ac.uk/QuickGO/AnnotationExtensionRelations.html}
    3433 * [OntologiesInUse Ontologies used in col 16 and examples of uses]
    3534 * When to use an extension versus requesting a new term? See [wiki:PrePostComposeGO PomBase "Precompose or postcompose?" wiki]
     
    4746  * cytokinesis (should use terms under the appropriate cell cycle mitotic (usually) or meiotic)
    4847  * cell wall organization -> fungal-type cell wall organization or biogenesis or one of its descendants
    49   * transport (vesicle-meidated? transmembrane? etc)
    50   * sporulation ->ascospore formation or children
     48  * transport (vesicle-mediated? transmembrane? etc)
     49  * sporulation -> ascospore formation or children
    5150
    5251=== GO annotation and Redundancy ===
    5352
    54  If you are annotating a newer paper, and it repeats older well annotated experiments, you do not need to capture the annotation.
     53 If you are annotating a newer paper, and it repeats older, well-annotated experiments, you do not need to capture the annotation again.
    5554
    5655
     
    6261  * GO or phenotype?
    6362   * We use GO annotations to describe direct involvement in a process, or its regulation (see below for more detail on regulation). We don't  annotate indirect upstream effects. Caution must therefore be used when using IMP to make process annotation, as it often isn't clear whether the effect is directly involved, regulation, or only affecting a process indirectly. Often a number of phenotypes are used to make a GO annotation.
    64     * Example 1 dil1 in /curs/c7fac5251ee4f493/ro/ where annotation to dynein-driven meiotic oscillatory nuclear movement with IMP is based on a combination of phenotypes:
     63    * Example 1: dil1 in /curs/c7fac5251ee4f493/ro/ where annotation to dynein-driven meiotic oscillatory nuclear movement with IMP is based on a combination of phenotypes:
    6564     * decreased meiotic recombination
    6665     * horsetail movement abolished
    6766     * unequal meiotic chromosome segregation
    6867     * decreased protein localization to microtubule cytoskeleton
    69     * Example 2 nda3 and mug164 annotations to intracellular distribution of mitochondria with IMP is based on
     68    * Example 2: nda3 and mug164 annotations to intracellular distribution of mitochondria with IMP is based on
    7069     * abolished mitochondrion inheritance
    7170     * mitochondrial aggregation at cell tip
     
    7675   * Lots of ongoing discussion among !PomBase curators and with other GO annotators, about when to annotate to regulation terms and when not.
    7776   * This is also connected with filling in start and end details for the process terms that still need them.
     77   * To do: when !PomBase deploys qualifiers (e.g. "causally upstream of or within" add documentation (2017-06-27)
    7878 * Transcription
    7979  * [http://wiki.geneontology.org/index.php/Transcription Transcription Overhaul details]