FEB 23 2009

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Genbank update

  • Majority of the errors/warnings/suspicious product names fixed. Waiting for karen's response to send final submission.
  • All clean code, notes, all new now! Sidd and Yulia rock!!
  • Sidd will call Karen if she doesn't respond this week.
  • From next GenBank update it's only gonna be the 'changed' genes. Everything that's on gene curation page (all that gets exported to GenBank).

[Action items]

  1. delete old C2 record from GenBank: [1] No answer from karen yet On hold until after update.
  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

  • Needs to rerun the patches from start along with software testing.

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%.
  • Splice variants discussion. One tab for each, sequences and proteins, with the ability to toggle between the variants.
  • 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
  • Need to draft letter to these users. Petra started letter, will send to Pascale.

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


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
  • GO curation tool: Protein2GO
    • One consideration is that the old file format will be retired on 1st Aug 2009.
  • 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:; UniProt: Q12345)
  • Other Ensemblized Genomes: Rex to pursue with the EBI

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