Difference between revisions of "WBConfCall 2014.01.23-Agenda and Minutes"

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   Status: Tested HX and Curator, any tweaks?.
   Status: Tested HX and Curator, any tweaks?.
* If it is not too late Hi I would like to request a simple model change for the ?Expr_pattern model
* Additional Func: ?Expr_pattern simple model addition - Daniela
Add:Type  EPIC   ?Text  
EPIC   ?Text  
Under Type so it will look like:
Type Reporter_gene ?Text
Type Reporter_gene ?Text
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Tiling_array ?Analysis  
Tiling_array ?Analysis  
EPIC   ?Text  
EPIC   ?Text  
== GO::Species Annotation ==
== GO::Species Annotation ==

Revision as of 11:54, 23 January 2014


New Starters

Sanger WormBase

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Status: Withdrawn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: Gene_cluster - Karen Y.
 Status: Tested HX and Curator, any tweaks?.
  • Additional Func: ?Expr_pattern simple model addition - Daniela
Add:Type  EPIC	  ?Text 

Type	Reporter_gene ?Text
	In_situ Text
	Antibody ?Text
	Northern Text 
	Western Text  
	RT_PCR Text   
	Localizome ?Text 
	Microarray ?Microarray_experiment 
	Tiling_array ?Analysis 
	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.

Species considered for inclusion

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


first ParaSite group member started 20th of January ... or so


Helpdesk/Chair - Paul Davis

Apologies for Absence

Help issues