wiki:GOAnnotationGuidelines

Version 7 (modified by gomidori, 8 years ago) (diff)

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PomBase GO Annotation Guidelines

GO Consortium Documentation - Ontology

These pages describe the overall structure of GO and scope of each main branch:

GO Consortium Documentation - Annotation

All of the general annotation documentation and recommendations on GO web and wiki pages are applicable. Links to some of the most useful:

Finding and Requesting GO Terms

  • Ways to search for GO terms:
    • directly in the curation tool
    • online GO browsers - QuickGO or AmiGO
    • install OBO-Edit (the least convenient option, but the most sophisticated search interface)
  • If you have trouble finding an existing term, request synonyms from GO (SF tracker) to make the search easier in future
  • If you have a problem locating a term in the curation tool using a string which was *already* a synonym in GO, make a note in Problems identifying ontology terms. Kim can use this to configure the search to give improved results.
  • Requesting new terms
    • If the term you need follows one of the patterns supported by TermGenie, you can use it and get a stable ID immediately
    • Otherwise, request your term(s) on the GO Ontology Requests tracker at SourceForge
      • Any information you can include -- name, text definition, parent(s), synonyms, reference, etc. -- will be much appreciated by the GO editors

GO Annotation Extensions

GO annotation extensions capture specificity that would be undesirable in the ontology.

A general rule is that when a GO process term is representing a single process, a single GO term should be requested. For example, negative regulation of SREBP signaling pathway by transcription factor catabolism with parents: GO:2000639 negative regulation of SREBP signaling pathway GO:0010620 negative regulation of transcription by transcription factor catabolism

An 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.

Specific GO Annotation Guidelines for PomBase

Recommended Terms

In many cases, the best GO term to use for a process or component in pombe is more specific than the term that mot closely matches wordings we typically find in papers. For example, see "DNA replication" or "sporulation" below. Where possible, we map more general GO terms to more specific ones that can always be substituted for pombe annotations. The mapping file is in the dropbox at Dropbox/pombase/ontologies/GO/mappings/GO_mapping_to_specific_terms.txt

Biological Process

  • Regulation
    • Lots of discussion going on among PomBase curators and with other GO annotators, about when to annotate to regulation terms and when not. It's also connected with filling in start and end details for the process terms that still need them. Conclusions will be posted or linked here. (2012-06-07)
  • Cytokinesis
  • DNA replication
  • Metabolic processes
    • Always check that "metabolic process" terms used have "cellular metabolic/biosynthetic/catabolic process" parentage; if not, request a change in GO
  • Sporulation
    • use ascospore formation (GO:0030437) or children
    • Sporulation terms are in the "mapping to specific terms" file

Cellular Component

  • You can usually use the specific "nuclear x" or "cytoplasmic x" macromolecular complex terms.
    • In particular, because fission yeast has no nuclear envelope breakdown during mitosis, you can always annotate to the "nuclear" versions of terms for chromosomes, chromatin regions, etc., e.g.
    • These terms are in the "mapping to specific terms" file

Molecular Function

  • Protein binding - annotate to GO:0005515 (or an allowable descendant) if there is enough information to conclude that there is a direct physical interaction. Otherwise just make BioGRID interaction annotation(s).
    • use IPI evidence; a 'with' entry is mandatory
    • note that GO:0019899 'enzyme binding' is in the do-not-annotate subset
    • we haven't (yet) tried to systematically delete older protein binding annotations that may not fit the direct interaction criterion
    • some protein binding annotations could presumably be inferred automatically from enzyme activity + input annotations (e.g. a protein kinase and a substrate identified in an extension)

GO annotation and Redundancy

You don't need to make every GO annotation in a paper, if an annotation is already present (or well known) from a previous annotated experiment(s)/papers. For example, you don't need to annotate every demonstrated occurrence of Cdc2 to protein kinase activity.

  • Some guidelines -- make an additional annotation if:
    • There is any new information, for instance an additional annotation extension or qualifier
    • Two (or more) papers containing new experimental information were published within a few months of each other, in which case curate both
    • It lends extra support to a term/annotation which may be considered not well-supported
    • You don't need to make every IGI annotation to support a GO process (usually you should be able to make a single IMP annotation). However, make sure the individual genetic interactions are curated in BioGRID (note: some older IGI annotations that over-interpret the available evidence will gradually be removed if the interactions are represented in BioGRID).

Gene Product Forms, or "Column 17"

GO supplementary IC (inferred from curator) annotation

Updating Existing/Legacy? Annotations

  • Check all existing ISS, IEA, TAS and NAS annotations to see if any are no longer required, or are incorrect
    • Remove any TAS/NAS/ISS which are now covered by experiment
    • Automated mappings (IEA) will be suppressed by experimental data. Are any IEA annotations not covered by your manual annotation? It should be possible to make a manual annotation to cover all automated mappings (if no experimentally supported annotation can be made, a manually evaluated ISS should be possible)
    • Mappings that can't be replaced by manual ISS or experimental annotations may be incorrect and need to be removed. Report incorrect mappings on the GO annotation issues tracker
      • Swiss-Prot keyword (SPKW, SP_KW, UniProtKB-KW) mappings: choose category "UniProt KW2GO mapping", group "GOA", and assign to "goa-ebi"
      • Swiss-Prot Subcellular Location (SP_SL, UniProtKB-SubCell) mappings: category "UniProt subcell2GO mapping", group "GOA", assign to "goa-ebi"
      • InterPro mappings: category "InterPro mapping", group "InterPro", assign to "interhelp"
      • For UniProt keyword and subcellular location mappings, you can also go to the UniProt entry from a PomBase gene page and send a message to UniProt. Ivo Pedruzzi will fix it quickly.
    • Some "pombe kw mappings" have NAS evidence code (you will know these are mappings because they will not be visible in the Artemis curation tool. These will need to be deleted from the mapping file.
    • If a mapping doesn't seem to be the problem, the ontology may need to be revised; contact GO editors via the ontology tracker
  • Check for consistency with other annotations and other resources
  • Make sure all remaining ISS are made to an experimentally characterised ortholog.
    • If the gene has an S. cerevisiae ortholog, check the annotations to the ortholog in SGD.
      • If the gene in SGD is not annotated to a term, and you think it clearly should be, mail them (sgd-helpdesk at lists.stanford.edu) to add it so that the ISS is supported. This is frequently required when annotation gene products which are not published.
    • Can you make any further annotations based on what SGD has? (Note reasons why annotations cannot be transferred; 1:1 is easiest)

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