JAN 6 2009

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Contents

Updates on current projects

GenBank update

Incorporating sequence data (C2 floatigs)

Steps involved

See also [http://bugs.dictybase.org/issuetrackers/dictyBase%20Enhancements/0727]

Stock Center Update

  • Received all materials ?
  • Plan for bar coding, etc


D. purpureum update

ID mapping problem

People are having a hard time with list containing obsolete (or non-primary) IDs and primary IDs; or mapping our DDB IDs with our new DDB_G IDs (which are now part of our GO gene association file).

(Pascale): I see two possibilities:

  1. Provide a small tool where people can enter a list and would be returned a 3 column file with DDB_G ID - current dictybase ID - former dictybase ID(s)
  2. Have dictyMart handle that.

Do we change the Gene ID if a gene model changes completely?

See example of a corrected gene model that was flipped but is in the same location [1].

  • If we change the ID, how dramatically does a gene model have to change before we do? Strand changes only? Non-overlapping coordinate changes (shifts)?
  • ESTs and Regulatory elements: Will those be on the new gene page?
  • If we do not change the ID, the links such as expression, Gene DB, Inparanoid etc will disappear, which is ok as they are useless.
  • DECISION and DISCUSSION: We do keep the Gene ID, as it is a locus identifier. Pascale raised that it's still a problem that people cannot see from any ID if the sequence (the gene model) has changed. Eric said that as long as we keep the gene predictions when we curate a model, we cannot show by ID that a gene model has changed, meaning, we could only retain a DDB ID in an unchanged model, if the gene prediction would go away. The protein ID that's coming also doesn't solve the problem because it is essentially the same as the DDB ID.

Establishing Priorities

New GO tool

  • Probably the most efficient way to do this would be to use EBI's Protein2GO file
  • Pro's: oracle-based
  • Con's : java
  • Estimated time to implement: Very rough first pass, just a ballpark.

Modware

  • Would like to have this ready for use (1) for implementing new genomes into dictyBase (2) for publication and (3) for re-applying for funding
  • Estimated time to implement: Very rough estimate, just a ballpark.

Update BioMart or switch to InterMine

  • See http://gmod.org/wiki/InterMine and emails from Warren pasted here
  • The reason to push this is to use dictyMart to convert our IDs, which is problematic for our users.
  • Estimated time to implement:
  • Current status: Guys from flymine are trying to setup a dictyMine prototype using our GFF file. We are trying to work with them get the first version up and running for a test drive.
  • One important point here is which one to choose and what are the factors that we should consider for that choice ?
  • RESOLUTION: Focus on updating dictyMart because it's what people are used to (even though it will change) and because functionalities are not exactly the same. Let the guys from flymine do what they can, and we see what happens with dictymine and probably eventually have this too.

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

  • The gene page is getting pretty huge!
  • We'd like to add more information from the Swiss-Prot annotations (to ensure they dont have more data than we do), which will lengthen the gene page even more
  • Estimated time to implement:
  • Show and tell of first prototype

Stock Center software improvements


ACTION ITEMS

  1. Other Ensemblized Genomes: Rex to pursue with the EBI


See also Sidd's [2] and Yulia's [3] projects



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