Changes between Version 89 and Version 90 of GOAnnotationGuidelines


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Timestamp:
Aug 5, 2015, 4:29:35 PM (5 years ago)
Author:
mah79
Comment:

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  • GOAnnotationGuidelines

    v89 v90  
    33== Background Reading ==
    44
    5  * [http://www.geneontology.org/GO.contents.doc.shtml#annotation General GOC documentation]
     5 * [http://geneontology.org/page/documentation General GOC documentation]
    66 * [http://geneontology.org/page/annotation GOC annotation documentation]
    7   * [http://www.geneontology.org/GO.evidence.shtml GOC evidence code documentation]
    8   * [http://www.geneontology.org/GO.format.annotation.shtml GO Annotation File formats]
    9  * [http://www.geneontology.org/GO.annotation.conventions.shtml GOC annotation conventions]   
     7  * [http://geneontology.org/page/guide-go-evidence-codes GOC evidence code documentation]
     8  * [http://geneontology.org/page/go-annotation-file-formats GO Annotation File formats]
     9 * GOC annotation [http://geneontology.org/page/go-annotation-conventions conventions] and [http://geneontology.org/page/go-annotation-standard-operating-procedures standard operating procedures]
    1010 
    1111
     
    1414 * [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
    1515 * [http://go.termgenie.org/help/index.html TermGenie GO help] (includes how to set up user access)
    16  * 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.
     16 * 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.
    1717
    1818 * When should I request a new GO term?
     
    2424
    2525 * Ontology
    26  * Annotation [https://sourceforge.net/p/geneontology/annotation-issues/ GO Annotation Issues tracker] at !SourceForge - use this to raise questions for the GO group, or to report mapping problems (see below)
     26 * 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)
    2727 * Protein2GO
    2828
     
    3333 * 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}
    3434 * [OntologiesInUse Ontologies used in col 16 and examples of uses]
    35  * When to use an extension versus requesting a new term? See [wiki:PrePostComposeGO PomBase "Precompose or postcompose?" wiki]
     35 * When to use an extension versus requesting a new term? See [wiki:PrePostComposeGO PomBase "Precompose or postcompose?" wiki]
     36 * There's also a tracker specifically for [https://github.com/geneontology/annotation_extensions/issues GO annotation extension issues]
    3637
    3738 
     
    4748  * cell wall organization -> fungal-type cell wall organization or biogenesis or one of its descendants
    4849  * transport (vesicle-meidated? transmembrane? etc)
    49   * sporulation ->ascospore formation  or children
     50  * sporulation ->ascospore formation or children
    5051
    5152=== GO annotation and Redundancy ===
     
    101102 * DNA binding - for sequence-specific DNA binding, use an annotation extension with 'occurs_at' and a SO ID (also see [#GOAnnotationExtensions] above). The rationale is that the bound substrate is the whole DNA molecule, and the SO extension indicates the region where binding takes place.
    102103  * If you don't know whether a gene product is binding to DNA or protein (or both) in chromatin, you can use "chromatin binding" again with 'occurs_at(SO:nnn)' extensions ... BUT:
    103   * Don't use "promoter binding" terms if the only evidence is chromatin immunoprecipitation (ChIP). In fact, it's safer not to use a binding term at all; use a "chromatin" cellular component term instead. See the [http://wiki.geneontology.org/index.php/Annotation_consistency_:_ChIP_experiments GO wiki page on ChIP experiments]. Specify where with 'coincident_with(SO:nnn)' extensions.
     104  * Don't use "promoter binding" terms if the only evidence is chromatin immunoprecipitation (ChIP). In fact, it's safer not to use a binding term at all; use a "chromatin" cellular component term instead. See the [http://wiki.geneontology.org/index.php/Annotation_consistency_:_ChIP_experiments GO wiki page on ChIP experiments]. Specify where with 'coincident_with(SO:nnn)' or ''coincident_with(PomBase:id)' extensions.
    104105 * Transcription factors - wherever possible make annotation to both:
    105106  * 1. a transcription factor activity term (sequence-specific DNA binding transcription factor activity (GO:0003700) or a descendant) with any target genes as has_regulation_target extensions, and optionally a promoter in an occurs_at(SO:nnn) extension; and a
     
    115116 
    116117 * Identifier for the specific form of a gene product, for example to describe if a particular cellular location is observed with a specific modification of a protein.
    117   * For modified forms of proteins (e.g. phosphorylated, methylated) use Protein Ontology entries (PR:[id]) request from [https://sourceforge.net/p/pro-obo/term-requests/ PRO tracker ] or [http://pir.georgetown.edu/cgi-bin/pro/race_pro Race Pro]
     118  * For modified forms of proteins (e.g. phosphorylated, methylated) use Protein Ontology entries (PR:[id]) request from [https://sourceforge.net/p/pro-obo/term-requests/ PRO tracker ] or [http://pir.georgetown.edu/cgi-bin/pro/race_pro RACE-PRO]
    118119  * splice variants can use !PomBase splice variant IDs (no examples curated yet)
    119120
     
    130131
    131132----
    132 [WikiStart Return to main page] or [CurationGuidelines Curation Guidelines]
     133[WikiStart Return to main page]