WBConfCall 2014.01.23-Agenda and Minutes

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Revision as of 17:12, 23 January 2014 by Pdavis (talk | contribs) (→‎Discussion)
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New Starters

Sanger WormBase/ParaSite

Models Sign Off

  • New model/class: Rnaseq_library - Gary W.
 Status: Withdrawn
  • New model/class: GO annotation model - Kimberly VA.
 Status: Under development (Post WS242)
  • Additional Func: Strain - Kimberly VA.
 Status: Incorporated for WS242
 Change: NCBITaxonomyID UNIQUE Int // Allows for finer grade attachment of NCBItaxon IDs
  • Additional Func: Gene_cluster - Karen Y.
 Status: Tested HX and Curator, any tweaks?.
 Change: http://wiki.wormbase.org/index.php/WormBase_Model:Gene_cluster#WS242_for_phylogenetic-based_clusters
  • Additional Func: ?Expr_pattern simple model addition - Daniela
 Status: Incorporated for WS242
 Change: Type  EPIC	  ?Text

GO::Species Annotation

In our annotation file, we currently have (or will have) annotations that reference these taxon IDs:

   taxon:273526 Serratia marcescens subsp. marcescens Db11
   taxon:652611 Pseudomonas aeruginosa PA14
   taxon:474186 Enterococcus faecalis OG1RF

The taxon IDs refer to specific strains of the bacteria used for testing host-pathogen interactions in C. elegans. They are included in GO annotations for terms like "response to Gram negative/positive bacterium".

It looks like we have ?Species objects for each of these bacteria, but corresponding taxon IDs are to the more general 'parent'.

It also looks like we have a ?Strain object, IGX2, for the Serratia strain, but not for the other two bacteria.

How would you like to reference these other taxon IDs? Should we create new ?Species objects that include the strain in the name?

Topic Curation

Status for WS242 and ideas for the next one.

Comments: Multi Species topics are a little problematic in terms of build

  • WS241 - all core species were rebuilt in their entirity as the Topic included Protein coding genes
  • WS242 - C. elegans is being rebuilt from scratch with ncRNA build patches applied to the remaining core species.

Species considered for inclusion

  • Necator americanus <= WS242
  • Romanomermis culicivorax <= ParaSite


Helpdesk/Chair - Paul Davis

Apologies for Absence



  • HelpDesk - noting unanswered, but a couple of issues users might get back to me about.
  • Models - Paul will tag the models as soon as the call ends so that Caltech and Hinxton can start preparing uploads by the end of next week.
Could Karen check her model in the final file....should be ok.
  • GO curation - Issue with connecting to species objects as the taxon I'd in the file is different to that in the species object in WormBase.
Option a) create additional species/strain hybrid species objects to allow the correct attribution and taxonomic representation.

Option b) add taxonomy ids to the ?Strain class.  - proposed and added above.
  • topics for next release
Caltech, pathways that feed into/out of topics that they have already covered.
Or push novel info from elegans out to other species
Additional topics could be chosen from the topic browser on the sit [Resources -> topics]

could work on a number of topics before pushing them out
Or spread the topic over a number of releases.
  • species for inclusion
Giving everyone a heads up as requested on a previous call.

Necator americanus from Makedonka - WS242 
Second Clade 1 species with a large genome - being used as an out group by the 50 Helminth project.
Tricinella is the only other Clade 1 and is probably more significant.
Will work with the species to polish the data, but postpone, and might push to ParaSite? Or could show in some way on WormBase.

Web team is also a bit light on manpower at the moment and so best to stage in worms over a few releases.
  • gitHub issues that are flagged as under_testing should be looked at and closed as Abby wants to merging staging to master tomorrow.

  • fair well to Joachim who is leaving OICR.