WormBase-Caltech Weekly Calls July 2014

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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


  • Happening on Oct 7 and 8th, 2014, with advisors
    • Monday whole day
    • Tuesday till 1pm
  • Pre-meeting on Oct 6, Sunday afternoon

Nomenclature pages on the website

  • See email from Mary Ann sent 18th July.
  • Will still use single link under 'Nomenclature' in black banner in bottom of wormbase.org page, but add a link in widget to redirect to different link for 'other nematode'

WormBook chapter on wormbase

  • to replace NAR article
  • to show users what are data and the means to access these data
    • gene function view, eg, gene expression, anatomy
    • GBrowse
    • WormMine
    • Process/Topic page


  • canonical net works can be pre-constracted and display in Topic page
  • dynamic display issue

Expression data

  • data from Waterston group, 130 diagrams
  • topo maps, mountain views data

Misc issues

  • 'curated_by' tag is going to be retired. -D file is generated
  • construct OA works well.

July 31, 2014


  • Suggestion for dealing with supplemental materials (ky)

Can we start collecting links to the online version of a paper, for easy access in the OA term info?

    • It is often the case that I have to chase down information in supplemental materials, unfortunately, it is not obvious that supplemental materials exist for a paper that needs to be retrieved during PDF download, or where to get it example WBPaper00045251, making the capture of supplemental materials onerous.
    • use of supplemental or online data storage is becoming the norm, our need for it during curation will be increased