FEB 2 2009

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Genbank update

[Action items]

    • Sidd: tell Karen we have fixed all gene products as much as we could. We feel the remaining gene products are useful, even though they trigger warnings at NCBI
    • Sidd: Karen asked to include transcript_id and protein_id qualifiers on corresponding mRNA/CDS features, as described in the Eukaryotic Submission Guide, http://www.ncbi.nlm.nih.gov/Genbank/eukaryotic_genome_submission.html. In addition, be sure to include product qualifiers on all the mRNAs; these should match the corresponding CDS product.


    • Genes with internal stops? Sidd and Yulia to provide curators a list so P&P look at them.

(not done?)

    • tRNA names: add gene products as Genbank wants them (histidine transfer RNA -> tRNA-His) (not done? not in the database)
  1. delete old C2 record from GenBank: [1]


  1. 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?

DDB_G - DDB-UniProt mapping file

  • When will the promoter elements IDs be removed from the file?

D. purpureum

  • Last week: Sidd was to ask Dong to get a copy of vm that is running on test site and use that as a dev vm, and started writing a script for fixing JGI data, using DPU_G as prefix. DONE.
  • Update Feb 2: Sidd needs to re-run patches from dictybase, including uploading all gene models.

Gene page design

see [[2]]

Conversion tool from DDB-> DDB_G IDs

  • Anup said he'll maintain it for a couple of months and then will move out of the lab.
  • Sidd is making a tool

DDB_G - DDB-UniProt mapping file


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:; UniProt: Q12345)

  • Scripts for the Update Downloads page : status? Pascale notes to make downloads: Update_Downloads_Page

  • Other Ensemblized Genomes: Rex to pursue with the EBI

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