Difference between revisions of "Concise Descriptions"

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*Curator History
*Curator History
*Description (toggles between different kinds of description)
*Description (toggles between different types of description)
*Accession Evidence
*Accession Evidence

Revision as of 22:44, 22 July 2011

Concise Description Curation

Genes with Recent Publications and No Concise Description

The list below contains genes for which a paper has recently been published but for which we do not yet have a concise description. The paper in parentheses after the gene name is the recent paper that prompted adding the gene to the list, but may not be the only relevant publication, so we may need to check other papers for writing a complete description.

If you'd like to work on one of these genes, feel free to check it out on the concise description check-out form and remove it from the list here.


Please also feel free to add genes to the list if you come across them in the context of other curation, but can't write a concise description right away. Someone else may be able to pick up that gene and write the description in the mean time.

  • pix-1 (see WBPaper00038193)
  • git-1 (see WBPaper00038193)
  • sepa-1 (see WBPaper00033110)
  • maco-1 (see WBPaper00038258)
  • tfg-1 (see WBPaper00038310)
  • sec-13 and other sec- secretion pathway genes (see WBPaper00038310)
  • gcy-28 (see WBPaper00038243)
  • pptr-1 (see WBPaper00032946)
  • alr-1 (see WBPaper00038207)
  • crtc-1 (see WBPaper00038172)
  • snf-12 (see WBPaper00038424)
  • lin-54 (see WBPaper00028753)
  • lin-53 (see WBPaper00028573)
  • cnt-2 (see WBPaper00038432)
  • orai-1 (see WBPaper00028994)

Keeping Gene Names Up-to-Date

Concise descriptions typically begin with the name of the gene, either its CGC name, e.g. unc-7, or its sequence name, e.g. Y24F12A.2. Sometimes the CGC name changes, but more frequently, the gene with a sequence name acquires a CGC name due to more intensive study or characterization.

  • To keep the names up-to-date in the concise descriptions, there are two emails to check:
    • Check each email from the webserver@sanger.ac.uk and pay particular attention to the emails with subject heading NAMEDB: CGC added to WBGenennnnnnnn. These are typically the cases where a CGC name is added to a gene that previously was known only by its sequence name. If we've written a concise description for this gene using the sequence name, then I update the description to now use the CGC name using the concise_description_new_cgi.
    • Mary Ann Tuli and Jonathan Hodgkin send an email, on which they cc Cecilia Nakamura and me, confirming all of the updated persons, labs, and gene names as recorded by the CGC. In the body of the email is a list of new gene names and assignments that I also check. Note that there is some redundancy here: any new gene name mentioned in the updates email should also be added to the name server and thus come through as a NAMEDB email. In my experience, though, a little redundancy is not always a bad thing and helps to keep things from falling through the cracks. As above, I make any necessary gene name changes using the concise_description_new_cgi.

Building an Ontology Annotator interface for concise description curation

  • Curation starts by querying for a gene, this is an autocomplete dropdown, that is populated from the OBO file for genes.
  • Querying for a gene either brings up data in Postgres or brings up a session populated with gene information, curator name, date, and new pgid.
  • Order and description of fields for the Concise Description OA:
  • WBGene
  • Curator
  • Curator History
  • Description (toggles between different types of description)
  • Paper
  • Accession Evidence
  • Last Updated
  • PGID
  • No dump

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