WBConfCall 2012.02.16-Agenda and Minutes

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Agenda and Minutes for the Conference Call 2nd February 2012


ACeDB WS231 models sign-off

Unified Interaction model - Chris & Kimberly

  • PaulD: The model is OK but is the web capable of displaying it?
  • Todd: there are changes we will need to make.
  • PaulD: it is being included in WS231.
  • PaulD: there are some things emailed about like XREFS in the interactor_info hash.
  • PaulD: has the data been uploaded?
  • Chris: Yes - it has all been tested and works fine now.

Legacy data incorporation (Variation Phenotype_info) - Karen

  • PaulD: the model is integrated but some tags need to be double checked.

New Homology type nemNOG - Michael

  • PaulD: this is a single tag addition. It is not a problem.

Re-homing of Rescued_by_Transgene from Variation -> Phenotype_info - Karen

  • PaulD: There are no issues for this one and no implications for the web site.

Removal of Accession_number XREF from the Homology_group - Michael

  • PaulD: There are no problems.

?Transposon, Corresponding_CDS and Corresponding_Pseudogene - Paul

  • PaulD: the Transposon object needs to be connected to the Corresponding_CDS and Corresponding_Pseudogene.
  • PaulD: Will have to think some more about whether to have gene objects associated with Transposons to display them better.

John Spieth - Priapulus caudatus

A short discussion regarding hosting Priapulus caudatus and helping the small research community call genes on the assembly?

  • John: Priapulus caudatus is a an organism near the root of the nematode taxonomic tree. It has a small community studying it. The question is: should we host it? The community wants help in annotating the genome.
  • MichaelP: hosting is no problem, geneset prediction is possible, but how much post-processing is required?
  • Is there any RNASEq?
  • PaulK: we need RNASeq if we are to spend any effort on this.
  • John: maybe we should table this until we know better what the situation is. They are doing some work on it already.

Mary Ann - Nemagenetag

The Nemagenetag consortium have asked that I remove the two existing references attached to their ttTi- alleles (WBPaper00028894& WBPaper00033043) and replace with the just published http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0030482

I explained that it's not our normal practice to remove existing references, and reassured them that the most recent paper will appear at the top of the bibliography. They have replied saying they understand but the existing two refs were interim papers.

Do you think I've done the right thing in not removing the older two refs or would it actually be OK to remove them? Both of the older references are cited in the new paper.

Does someone have a better explanation than "it's not normal WormBase practice" I could send?

  • PaulK: Why do they want it removed?
  • Mary Ann: they are just interim references cited in the main publication. I said it was not our policy to removed references, but I would like to be able to say why it is not our policy.
  • PaulK: would you have cited them all if you were curating them from scratch?
  • Mary Ann: yes.
  • PaulD: having all three is not a bad thing, maybe they just want to emphasise their new one.
  • Todd: we put new ones at the top already.
  • Mary Ann: OK

Michael Paulini - Metaanalysis of orthology

There is a paper that tried to find to find orthologs of human genes. They have a list of genes they believe are real orthologs. They say the worm genes have a human ortholog but don't say which one. Should we put the paper into wormbase? We have all the components of the metaanalysis in wormbase already. This is very circular. Should we put the paper into wormbase as an orthology? Should we put their results in as an additional result in wormbase?

  • MichaelP: should we treat metaanalysis as the same as main publications?
  • MichaelP: Instead of putting them in as orthologs, put them in as regular papers, so we can go to the paper and get all connected genes.
  • MichaelP: the paper should appear and we can pull out the genes easily.
  • PaulS: can we engage the effort in the future

Todd/Abby - Web development status

  • Abby: we are splitting out CDS as a separate page. We are going through the pages checking their functionality. We should be ready in time to WS230. Could people please test the beta pages
  • Todd: we currently have two sites. This is a lot of work.
  • Todd: we have the beta site and the staging site where things are prepared.
  • Todd: I will clarify what the sites do by email in the next couple of days.
  • Can we report errors through the site or should we go through GitHub?
  • Todd: go through GitHub.

Outstanding Helpdesk Issues

None ... so far

handing over to Daniel Wang