Curation Status

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Public Notes describing Curation Status

Unannotated genes have the note '[This gene has not been manually annotated]'. When curating a gene, add one of the following notes:

  1. <curation_status>Basic annotations have been added to this gene, 24-MAR-2008 PF</curation_status>
  2. <curation_status>Gene has been comprehensively annotated, 10-NOV-2007 PF</curation_status>
  3. (not yet implemented!) <curation_status>Curation Status: Reviewed by Rex Chisholm, 15-NOV-2007</curation_status>

Description of curation status notes

Basic annotation: the gene has partial annotations: a curated model, and/or and/or gene product annotation, description, and/or manual GO annotations.

Comprehensively annotated: Gene that is as completely annotated as possible. This excludes the 'Summary'. Otherwise, it includes:

  • Curated model
  • Functional annotations (gene product, description)
  • Gene ontology annotations
  • Literature (if applicable). This one is subject to curators judgment; if there is a very large body of literature but the important papers have been annotators, a gene can still be considered comprehensively annotated.
    • A gene with limited information can be marked 'comprehensively annotated' (for example, GO annotations to the root; gene product = 'unknown') if the search for annotations (GO and potential gene product names) has been exhaustive.
    • Pseudogenes are marked 'comprehensively annotated' (NO GO).

These statements go below the summary after a line break. We use 'comprehensive annotation' even when there is no summary. In this case, the curation status alone goes into the summary field: <summary><curation_status>Gene has been comprehensively annotated, 10-NOV-2007 PF</curation_status></summary>.

Updating gene annotations

  • Whenever you update annotations to a gene, update the date and the initials (whether they are 'Basic' or 'Comprehensive'. The other notes should be pasted as 'private notes'.

For discussion

Pascale Examples:

  • DDB0238773: (IEP from a paper) [Curation Status: Basic annotations added, Nov 19, 2007 PG]
  • DDB0233426: ISS and summary: [Curation Status: Gene has been comprehensively annotated, Dec 18, 2007 PG]
  • DDB0238780 one ISS: [Curation Status: Basic annotations added, Nov 20, 2007 PG]
  • DDB0191146: did GO, papers: [Curation Status: Gene has been comprehensively annotated, Dec 18, 2007 PG]
  • I am also wondering whether we should put 'comprehensively curated' for genes we dont intend to go back to (genes with no ortholog, or where the ortholog is not characterized...) ie, something annotated to all 'unknown' because it doesn't have domains or sequence similarity, in a way is comprehensively annotated??

Petra Examples:

  • In general, I think if we have a good gene product other than unknown (and most often this is also followed by a description (if sometimes short), we should use 'basic'. If the gene product is 'unknown' then rather just 'verified'. Consequentially, the completely unknown I would rather keep just 'verified', I think.
    • geneDDB0252622 [Basic annotations]

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