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

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 display.

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.

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)