NOV 30 2009

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Dicty 2010

  • Dicty 2010 meeting: setting up registration site
    • Warren sent 'prototype' page to Sidd & Yulia
    • Sidd and Yulia are planning to finish for preview for Emma and us on Friday, Dec. 4th

D pur database

  • Discuss D. pur database issues
    • Plan to have testing version around Dec. 16th. Also dictyBase new release testing.
    • Add JGI protein IDs because they are being used in genome paper. Petra send email reminder to Adam - done Nov 30. pm
    • Generate mapping as soon as we receive updated tables.

Not talked about:

    • What about the long ugly gene IDs? Also in db? Or simple mapping file? : -> Mapping file.
    • Writing a D. pur database paper?

Pseudogene feature bug

  • When we normally split genes, we create two new Gene IDs and map the old one
  • When one of the split genes is a pseudogene, we cannot associate this feature to a new gene.
  • Just briefly described, Sidd will look into this when updating curation interface.

Bob curation update

  • Computer has been fixed and is back in business
  • Curation goal of 25 gene models / week

Not talked about the following items


  • The GOC would like the MODs to be able to load and display GAF files by January or so.
  1. You name and database: Pascale, dictyBase
  2. Do you currently upload GAF files from external sources, such as from GOA? No
  3. What is the frequency of incorporation of external GAF files? ad hoc
  4. Do you expect your your database to run manual and/or automated verifications (redundancies, quality of annotations) before integrating the GAFs that will be provided by ref genome? Yes - We will want to put a script that removes redundant annotations, and have the possibility to verify the PAINT annotations (the current visualization tools such as GO-nuts should be enough)
  5. How are the accepted annotations from GOA loaded into your database ? Do you have a script that loads these annotations into your MOD? No - not yet applicable.
  6. Are those external annotations displayed on your web pages for GO annotations? No
  7. Do you display the original source of the annotation (column 15)? Yes - We would/will do !
  8. Does the annotations from the external GAFs appear in your GAF file that gets submitted to the GO database? No
  9. What appears in your GAF file as the annotation source for annotations originally coming from external sources? The original contributor

GenBank loader bug


Protein Domain info

  • Discuss deletion of domains from Protein Information after creating a curated gene model. When there has been no change to the sequence the domain evidence is still valid and it would be useful to retain the information.

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