Changes between Version 89 and Version 90 of GOAnnotationGuidelines
- Timestamp:
- Aug 5, 2015, 4:29:35 PM (5 years ago)
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GOAnnotationGuidelines
v89 v90 3 3 == Background Reading == 4 4 5 * [http:// www.geneontology.org/GO.contents.doc.shtml#annotation General GOC documentation]5 * [http://geneontology.org/page/documentation General GOC documentation] 6 6 * [http://geneontology.org/page/annotation GOC annotation documentation] 7 * [http:// www.geneontology.org/GO.evidence.shtmlGOC evidence code documentation]8 * [http:// www.geneontology.org/GO.format.annotation.shtmlGO 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] 10 10 11 11 … … 14 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 15 * [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. 17 17 18 18 * When should I request a new GO term? … … 24 24 25 25 * 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) 27 27 * Protein2GO 28 28 … … 33 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} 34 34 * [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] 36 37 37 38 … … 47 48 * cell wall organization -> fungal-type cell wall organization or biogenesis or one of its descendants 48 49 * transport (vesicle-meidated? transmembrane? etc) 49 * sporulation ->ascospore formation 50 * sporulation ->ascospore formation or children 50 51 51 52 === GO annotation and Redundancy === … … 101 102 * 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. 102 103 * 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. 104 105 * Transcription factors - wherever possible make annotation to both: 105 106 * 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 … … 115 116 116 117 * 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 R ace 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] 118 119 * splice variants can use !PomBase splice variant IDs (no examples curated yet) 119 120 … … 130 131 131 132 ---- 132 [WikiStart Return to main page] or [CurationGuidelines Curation Guidelines]133 [WikiStart Return to main page]
