WBConfCall 2015.06.18-Agenda and Minutes

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It's the one before the meeting!!!

Please submit your agenda items here


  • Posters - are they ready?
  • Talks - are they ready?
  • Freebies - are they ready?
  • Help Desk during the meeting - time table needed.
    • List your poster time here:
      • Mary Ann's 955C = Sat 4.30pm - 6.00pm
      • Gary Williams: 956A = Thurs 19:30 - 21:00
      • Bruce Bolt/Michael Paulini: 952C = Saturday 15:00 - 18:00
      • Paul Davis: 1243C = Sat 16:30 - 18:00
  • Survey: Todd and Sibyl started a user survey in a Google form. I am still working on the survey. Please do not edit. https://docs.google.com/a/wormbase.org/forms/d/1BkZCX1hZ3b-vDdWB4KjIvieALc_GLnYqYCTqnMaJ7Rg/edit (Need to be logged in with WormBase google account to edit it).
  • Todd and Sibyl will be at CalTech 22nd-24th, along with the remote workers.

WormBase Workshop roll call

  • Tools & Resources (first hour)
    • Intermine/WormMine - Chris Grove
    • JBrowse - Scott Cain
    • WormBase Ontology Browser - Raymond Lee
    • ParaSite, Ensembl Genomes & UCSC Assembly Hub for C. elegans - Kevin Howe
    • Gene Ontology annotations and enrichment tools - Kimberly Van Auken
  • Community Annotation (last 30 minutes)
    • Contributing variation data to WormBase - Mary Ann Tuli
    • Micropublications - Daniela Raciti
    • Contributing & editing gene concise descriptions - Ranjana Kishore
  • Workshops will be next Thursday (one week from conference call) and Saturday, 1pm - 2:30pm
  • Workshops will be held in UCLA's Northwest Auditorium

Help Desk

Models for WS250

The following Models have been proposaed and are in a pretty good state to go in for WS250.

Plan is to incorporate changes into CVS today.......I will email out a link once done. If curators could take a look to make sure they are happy with the incorporation. WS250 models will then be tagged Friday afternoon (HX) Friday AM (CA).

GO_term Model change - Kimberly

1) Remove the Term tag.  The name of the GO_term would be populated in the
Name tag.  This change will have downstream effects for the build and web

2) Add an Alt_id tag to populate secondary IDs as listed in the GO obo
file.  This would allow anyone searching WB with a secondary, or
alternate, GO ID to still arrive at the correct GO_term page.

3) Although this doesn't affect any tags in the model, starting with WS250
we will populate the Version tag with the information in the
'data-version:' tag in the obo file, not the 'remark' tag that holds the
SVN revision number.  All terms have the Version tag populated, so we
should remove the comment in the ?GO_term model about version only being
stored on the 3 parent terms.

4) Version
Version UNIQUE Text UNIQUE Text // Lincoln, to store version number of GO


Version UNIQUE Text // store "Gene Ontology releases/2015-06-13" as single value.

GO_annotation mods - Thomas.
Thomas input suggests: UNIQUE for single value (most notable Gene, GO_Term, and GO_Code)
Kimberly: I agree that we could add UNIQUE constraints to Gene, GO_term, and
GO_code.  We could probably also add the UNIQUE constraint to Reference
and GO_reference as well as Contributed_by and Date_last_updated.

Request for phenotype_info tag name changes - Karen

Variation_effect 	Gain_of_function_undetermined_type    #Evidence
			Antimorph_gain_of_function    #Evidence
			Dominant_negative_gain_of_function    #Evidence
			Hypermorph_gain_of_function    #Evidence
			Neomorph_gain_of_function    #Evidence
			Loss_of_function_undetermined_extent    #Evidence    
			Null    #Evidence
			Predicted_null_via_sequence #Evidence
			Probable_null_via_phenotype #Evidence
			Hypomorph_reduction_of_function #Evidence
			Predicted_hypomorph_via_sequence    #Evidence
			Probable_hypomorph_via_phenotype  #Evidence
			Wild_allele    #Evidence

Expr_pattern model change - Daniela

Remove Cell and Cell_group

Expression_data Life_stage ?Life_stage XREF Expr_pattern #Qualifier
                Anatomy_term ?Anatomy_term XREF Expr_pattern #Qualifier
                GO_term ?GO_term XREF Expr_pattern #GR_condition
                Not_in_Life_stage ?Life_stage #Qualifier
                Not_in_Anatomy_term ?Anatomy_term #Qualifier
                Not_in_GO_term ?GO_term #GR_condition 

WBProcess class - Karen/Thomas

?WBProcess      Public_name UNIQUE ?Text
                Summary UNIQUE ?Text #Evidence
                Other_name ?Text
                Related_topic ....
                // Everything else unchanged.

Name' is not needed. 

Summary UNIQUE ?Text #Evidence in ?Construct and Remark in ?Phenotype_info (Remark should actually be Summary). 

Yes, Process_term can be deleted.

Gene - Biotype - Michael
?Gene Gene_info Biotype UNIQUE ?SO_term

UNIQUE Quest continued - Thomas

?Strain Genotype Text
                Properties Outcrossed Text

?Rearrangement Isolation Date DateType
                                Source_rearrangement ?Rearrangement


SO_name and SO_definition should be UNIQUE

Track Hub

can I solicit some feedback on that one: http://forums.wormbase.org/index.php?topic=2550.msg6408;topicseen#msg6408 Mh6 (talk)