DEC 20 2010

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Contents

Work/Project schedule as discussed in this meeting

  1. Curators finish first pass end of January.
  2. This Release: on test 12/29, testing and bug fixing week of Jan 3-7.
  3. Fix Chr2 RNAseq (about 2 days)
  4. Start on Biomart overhaul
  5. GenBank update starting on or about February 1st
  6. Work on Gene Page to include expression section and start with Harry's data, plus fix caching.


Next release 2.19 (Dec. 29th)

Migrating reference tables and GO to Chado
  • New reference curation interface by yulia.

[Working on]

  • Gene page display software.
  • GAF dumper.

[Leftover]

  • Adding user audit feature to the new reference curation interface.
  • GO update for dictyMart
wait for biomart update


  • After new OBO file upgrade, curators (with help of Sidd) need to check where terms don't map and map manually. [Reported by GOA QC script]
  • Additional taxon checks as a part of GO parser module
Automate curation stats -Excel (Yulia)
references/go curation stats after migration to chado:
how to keep track of curation on GO (if all we will get is a file with annotations)
the way referenceas are stored will change, need to figure out how to keep track of curation
create audit table to keep track
Multigenomes update
Bug in BLAST reported by Petra requires library update
Above project requires upgrade of our web app library(after 1 year) and three pieces of web applications. (~Approx 3 weeks). This need to be done at some point to get in sync with current dictybase release(GO and reference migrations).

DONE

Interpro domains for all dicty genes (Yulia)
Run whole pipeline couple of times to test


Link to ENSEMBL [Yulia]
Our links from the genome browse don't work anymore (at least for me - Petra), e.g. [1]. And it would be nice to link to the EnsemblProtists from our gene pages. Example link, [2]

working link for EmsemblProtists for GBrowse http://protists.ensembl.org/Dictyostelium_discoideum/Location/View?db=core;r=1:1000-30000

Action: wrote patch that adds Ensembl linkouts for genes. Used the same gff3 as they used for import (10-14-2009)

Fix Pseudogene - Gene association bug [Yulia]
Pseudogene features cannot be associated with another gene, which needs fixing. See issue [3] [Petra]
Link outs to GenBank [Yulia]

The GenBank links on the Gene pages (see for example sadA gene) we link out to our own version of the sequence (for example sadA AY178767). This is misleading and also unnecessary. We should link to GenBank directly and remove the tab for the GenBank sequence.

Action: fixed gene page and gbrowse links, removed genbank features from sequence dropdown in BLAST

Stock Center User requests (Yulia) [Done]
  • Add shopping cart to each strain and plasmid page.
    • SC search pages
    • strain catalog
    • strain page
  • Make shopping cart 'sticky' so it remembers what's in it.

Action: extended cookies lifespan to 3 month (was set to expire with session end), Added shopping card to all SC pages

GBrowse2 update

  • Chr 2 gene curation: We are not doing Chr2 genes now but focus on all others as Chr2 was run later by Sidd in comparison to Garteh's sequence and is in a separate list. In order to curate the about 600 Chr2 genes without changes we need GBrowse2 fixed so the alignement of RNAseq is correct. See snapshot below of misaligned RNAseq that is rendered not only useless but even irritating by the shift .
  • There is now a aper by Adam and Gadi that mentions in the abstract the RNAseq is available at dictyBase.
  • Sidd says it takes about 2 days to update chr2 data.


Image:CHr2-RNAseq.png

GO Annotations

  • Once GO is in Chado (after the next release to the public - early January??)), we cannot use the old tool anymore, and thus, cannot edit GO. A major thing we do right now is deleting GO from newly annotated pseudogenes. we need to discuss if we can find an interim solution how to do this until we move to the EBI tool, or if we let everything slack and curators have to make notes/lists of what to delete and change once we have a tool again.
  • Emily also send me 6 annotations we have that don't pass the new taxon restriction script, which I'll have to check into these days. There are sometimes other user requests that involve GO annotations, that I won't be able to access for a while.
  • I told Emily that we have now decided to use their tool. We agreed on talking about things (tentatively 2nd week of January), and Sidd/Yulia should be part and if possible Pascale (and everyone else who wants to). We'll schedule this before the end of year. (Petra)
Issues to solve
Syncing new DDB_G ids between genbank updates.
Syncing our literature references.

Expression Data from Harry

  • WE NEED TO DECIDE IF WE CAN ADD HIS DATA AND IN WHICH FORM AND WHEN.
  • Harry sent expression, spatial and temporal, plus cell cycle regulation data, in an Excel sheet with Macros. User request
  • We should have a look at the data table and make a plan when and how we can use it.
  • I can visualize the graphs (not so elegantly because I can't have Macros on the Mac) and it would be great to have those linked to genes. Here is a screenshot of what the graphs look like Image:Harry_graphs.png
We could either show it on a new tab or section in a gene page.
Specs
Will not be searchable.
Rough ballpark 2 and half weeks.
Have to go through a release at least.

Conclusion: Discuss again when would be right time to do this. Sidd and Warren said we also need to update the gene page caching and these two things could well be done together. This would then take ~3 weeks. Pascale mentioned that adding Harry's data might set a precedent and 'inspire' other people (Gadi) to submit much more (in not such a neat format).

New Genomes (from Joan Strassmann)

  • We need Rex to give update where we stand.

Gene page caching

  • Have decided to leave the 7 day expiration in place
  • we will be reverting to originally planned solution of running a weekly script to refresh all gene pages ?
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