WBConfCall 2015.06.18-Agenda and Minutes

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Agenda

It's the one before the meeting!!!

Please submit your agenda items here

IWM

  • 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
      • Scott Cain: 953A = Thursday 9:00-10:30 (21:00-22:30)
  • 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.
  • Hinxton crew arriving afternoon/evening Tues 23rd

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
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

to

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_term

SO_name and SO_definition should be UNIQUE

Track Hub

Minutes

IWM

  • CalTech have one poster, Hinxton have 3 posters and OICR have one.
  • MA to send Scott slide master - DONE
  • Freebie bags are ready and boxes have been assigned to cars to be transported to UCLA.
  • Talks are in progress. PS to send his slides round soon.
  • Raymond will video workshops to put online at later date. Blog hilights with summary and slides. Could also just record audio and add slides. Could also put on youtube.

WormBase IWM event schedule

  • Wed Jun 24
    • 20:45 - 20:50 (8:45-8:50pm) Plenary 1 - Paul S - Royce Hall
  • Thu Jun 25
    • 13:00 - 14:30 (1.00-2.30pm) WB Tutorial: Tools & Resource, Community Annotation - Chris, Scott, Raymond, Kevin, Kimberly, Mary Ann, Daniela, Ranjana - Northwest Auditorium
    • 19:30 - 22:30 (7.30-10.30pm) WB Table - Pauley Pavilion
    • 19:30-21:00 (7.30-9pm) Even "A" Posters (Gary) - Pauley Pavilion
    • 21:00 -22:30 (9:00-10:30pm) Odd "A" Posters (Scott) - Pauley Pavilion
  • Fri Jun 26
    • 19:30 - 22:30 (7.30-10.30pm) WB Table - Pauley Pavilion
  • Sat Jun 27
    • 13:00 - 14:30 (1.00-2.30pm) WB Tutorial: Tools & Resource, Community Annotation - Chris, Scott, Raymond, Kevin, Kimberly, Mary Ann, Daniela, Ranjana - Northwest Auditorium
    • 15:00-18:00 (3:00-6pm) WB Table - Pauley Pavilion
    • 15:00-16:30 (3:00-4:30pm) Even "C" Posters (Bruce/Michael)
    • 16:30-18:00 (4.30-6:00pm) Odd "C" Posters (Mary Ann, Paul D)

Sign up for table duty

There should be one person from each site available at each session

  • Thursday 19:30-21:00 - Mary Ann, Chris, Paul, Daniela
  • Thursday 21:00-22:30 - Karen, Paul, Wen
  • Friday 19:30-21:00 - Chris, Gary, Raymond
  • Friday 21:00-22:30 - Karen, Wen
  • Saturday 15:00-16:30 - Mary Ann, Chris, Raymond
  • Saturday 16:30-18:00 - Chris, Michael, Bruce, Daniela

Survey

  • Will be launched at meeting and run through the summer (to end of Aug?). PS to mention in plenary talk.
  • Todd requests that staff look at survey and add new questions. Staff should not move things around too much, as reorganisation will be done once the survey is nearly completed.
  • Survey has pages - the website, biographical info (level of position, location, research interests, how often site used), asks what our curation priorities should be. Curators from each data type should look at "their" sections. TH working on website and outreach sections. Useful to know e.g. do people know how often we release data.
  • We will not be embracing a subscription model for WB so survey should not have questions about funding.
  • Make questions about species higher profile.
  • Community curation will be added to raise awareness.
  • Website questions - speed, ease of finding info, how to do difficult tasks, proposed new features
  • Which MOD has best features (analysis, browsers).
  • Will will display link in workshop
  • Karen has a GSA markup survey. Should be possible to add to Todd's survey. 6 questions. Karen to send link to Todd. Will be promoted from GSA booth

Models

  • Let Paul know if OK.
  • Problems with antibody class.
  • Changes committed after call and tagged 19-June

AOB

  • Next upload 10th July

Track Hub

  • we got an UCSC assembly / track hub ready for testing at: http://ftp.ebi.ac.uk/pub/databases/wormbase/releases/current-productionrelease/COMPARATIVE_ANALYSIS/hub/hub.txt
  • It contains WS245 and WS248 gene models, as well as cDNA alignments and repeats. In addition is shows 29-way multiple alignments between the genomes of WormBase (WS248) based on progressive cactus. And for demonstration purposes additional tracks showing the depth of alignment from the raw output, evolutionary pressure from phyloP and conservation probabilities from phastCons.
  • It would be great, if there would be some people testing it, as we found quite a few problems attaching it to Ensembl sites (with our changes/improvements going into the next E! code release). We managed to get the latest EG release to use them, so you can try the EG metazoa site for testing.
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