FEB 16 2009

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Genbank update

[Review items]

  1. Look at validation output after the previous fixes.
    • Need to fix minor errors to treat these kind of CDS as partial

DDB0219202 DDB0252579


[Action items]

  1. delete old C2 record from GenBank: [1] No answer from karen yet
  2. insert Gernot's floatigs http://bugs.dictybase.org/issuetrackers/dictyBase%20Enhancements/0727: The C2 floatig Gernot sent corresponds to contig DDB0215037. What to do now? (1) remove from floatigs (2) contact Gernot to see if we can remove more of the C2 floatig?

D. purpureum

  • Update Feb 2: Sidd needs to re-run patches from dictybase, including uploading all gene models.

Making a 'Protein' page and/or adding tabs or collapsible sections

  • Yulia will try to make the tabs more visible/ done, but she will make one more change, increase size of active tab about 20%.
  • We'll send the prototype to a few usrs for feedback: Bill Loomis, Robert Insall, Thierry Soldati, Jeff Williams, Chris Thompson, Robin Williams, Gareth Bloomfield, Silvia Jimenez

DDB_G - DDB-UniProt mapping file

  • Remove promoter elements DDB IDs
  • add links to DDB_G if can be found

Scripts for the Update Downloads page


Updating electronic InterPro2GO mappings

  • Current ones date from April 2007

DDB_G_ID_SOPs

No progress....


Topics carried over from previous meetings

  • Issues with dicty database import (updates)


  • BioMart: status: Sidd will work on that once he's done with purpureum


  • InterMine: having problems loading out GFF3 file


  • Physarum site: looking for related species: working on Gene Predictions and Blast server (Sidd and Yulia);

Nov 24-2008: [ON HOLD] problem with script for loading and testing being overlapping (???) Cannot afford to spend a lot of time on this until the next release.


  • Modware paper


  • [ACTION ITEM]: Yulia to change links to external resources to include Identifier (for eg: EC:4.3.2.1.; UniProt: Q12345)



  • Other Ensemblized Genomes: Rex to pursue with the EBI

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