Difference between revisions of "Concise Descriptions"

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*Field 5: '''Description Text''' : ''' This field is a big text box, it expands when selected.'''
*Field 5: '''Description Text''' : ''' This field is a big text box, it expands when selected.'''
*Field 6: Paper ''cdc_paper'': This is an multi-ontology, has limited values, works off the paper tables in postgres, has term information.
*Field 6: Paper ''cdc_paper'': This is an multi-ontology, has limited values, works off the paper tables in postgres, has term information.
*Field 7: Accession Evidence ''cdc_accession''
*Field 7: Accession Evidence ''cdc_accession'': This is a text field, values are separated by commas.
*Field 8: Last Updated ''cdc_lastupdate''
*Field 8: Last Updated ''cdc_lastupdate''
*Field 9: PGID ''no table''
*Field 9: PGID ''no table''

Revision as of 18:50, 26 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, wbgene is an autocomplete (not a dropdown), the term info is populated from the gene info from the gin_ tables, not an OBO file.
  • Querying for a gene brings up data from postgres or tells you there are no matches. To make a new annotation, click the New button to generate curator, date, pgid, and curator history.
  • Order and description of fields for the Concise Description OA (name of postgres table in italics):
  • Field 1: WBGene cdc_wbgene: This is an ontology with finite values, has term information
  • Field 2: Curator cdc_curator: This is a drop-down, can have only a single value, has no term information. Since these have linited values, they are hard-coded into psotgres.
  • Field 3: Curator History cdc_curhistory: This is an ontology, does not have its own obo tables, uses the history table for the curator field (cdc_curator_hst)in postgres, has term information, stores the PGID of the annotation. Allows editing, but should not be edited, because then you would change the value and if someone else were to click on term information they would see a different value.
  • Field 4: Description cdc_description : This is a dropdown, has limited values, so hard-coded in postgres, has no term information, values are:
    • Concise Description --> Concise_description
    • Human Disease Relevance --> Human_disease_relevance
    • Provisional Description --> Provisional_description,
    • Sequence Features --> Sequence_features
    • Functional Pathway --> Functional_pathway
    • Functional Physical Interaction --> Functional_physical_interaction
    • Biological Process --> Biological_process
    • Molecular Function --> Molecular_function
    • Expression --> Expression
    • Other Description --> Other_description.
  • Field 5: Description Text : This field is a big text box, it expands when selected.
  • Field 6: Paper cdc_paper: This is an multi-ontology, has limited values, works off the paper tables in postgres, has term information.
  • Field 7: Accession Evidence cdc_accession: This is a text field, values are separated by commas.
  • Field 8: Last Updated cdc_lastupdate
  • Field 9: PGID no table
  • Field 10: No dump cdc_nodump

Checking Results of find_evidence.pl

From the results of the find_evidence.pl script, these are the types of evidences used for concise descriptions and some thoughts on what to do with them in the future and in the new OA:

  • WBPaper - keep, convert all paper evidence to WBPaper evidence in the form, wherever possible remove meeting abstracts
  • WBPerson
  • Expr_pattern
  • WBRNAi
  • Microarray_results
  • Gene_regulation

I queried WS to see if there were cases where there was an Expr_pattern that was not connected to a paper; there are 453 cases.

Originally I was thinking we could just do away with this, but there may be cases where we want to cite an object in WB for which there isn't a paper reference.

Could we keep these types of evidences available to us, but perhaps collapse them in a drop-down so that they don't take up a lot of room if we're not using them, but they're not gone, either?

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