wiki:AnnotationCompleteChecklist

Version 5 (modified by mah79, 5 years ago) (diff)

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Annotation Complete Checklist ( page in progress)

The point when a gene product (or complex) is considered "annotation complete" is a good time to do some basic consistency checks:

This should include:

Gene specific

  • refine localisation screen based on low throughput (expand)
  • refine ISS (expand)
  • refine ISA (expand)
  • refine existing annotations to normalize phenotypes

Complex specific

  • look at enrichment for process /component /function IC to fill in gaps

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)
  • Ask experts to give feedback on lists