WormBase-Caltech Weekly Calls

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Revision as of 18:04, 24 July 2014 by Matuli (talk | contribs) (→‎Agenda)
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Previous Years

2009 Meetings

2011 Meetings

2012 Meetings

2013 Meetings

2014 Meetings







July 3, 2014

WS245 Upload

  • Tuesday, July 29th local citace upload (to Wen)
  • Friday, August 1st citace upload to Hinxton

Data models freeze

  • Next Friday July 11th

Automated Concise Descriptions

  • James and Ranjana making progress
  • Several examples of automated descriptions, proof of concept
  • Based on 3 GO categories and homology
  • Add tissue-specific expression, and go live
  • Should add 1000s of descriptions (automated)
  • Next, pick terms of higher granularity
  • We should ask users what they want: e.g. Is an Ascaris suum gene ortholog in C. elegans essential?
  • Manual annotations in future? How can edits be tracked? Gets a new tag?
  • Automated descriptions for all objects?
  • We will likely separate manual from automated descriptions to ease editing and tracking
  • GO terms can be added as IDs and be converted (automatically) to the term name with hyperlink on the web site

New Tazendra machine

  • Up and running at dhcp-52-226.caltech.edu; IP address:
  • Juancarlos will sync the current Tazendra data to the new machine after meeting
  • Curators will test forms and dumpers; compare dump outputs from new and old machine
  • We can make the new machine live later in the month

July 10, 2014


Construct model/annotation

  • Need to add "Construct" under list of "Detection methods" in the ?Interaction model
  • Chris will send corrected models.wrm file to Karen
  • Karen will send models.wrm to Paul Davis by tomorrow
  • Interaction OA dumper will need to be updated to accommodate constructs and transgene changes (Chris will work on with Juancarlos)

BioGRID data

  • Mike Tyers agreed to release physical interaction data for C. elegans
  • We will import data into the Interaction OA and WormBase
  • Attribution? Reference to an ?Analysis object? Would need an additional field for Analysis objects? Could reference as Database accession number
  • Chris will discuss with Kimberly

July 17, 2014


  • Travel Arrangements for the October SAB in England and GO Meeting in Spain
  • Have advisory board members been contacted? Are they all available?


  • Model and OA are now live
  • Transgenes have been replaced with appropriate construct objects


  • Pushing code to the live web site soon

July 24, 2014



  • Travel arrangements

Nomenclature pages on the website

  • See email from Mary Ann sent 18th July

July 31, 2014


  • Topic 1
  • Topic 2