WormBase-Caltech Weekly Calls

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June 2, 2016


  • Wen will create ticket to create wormbase.org URL
  • Will go under Tools menu
  • Ranjana will make blog post once it is live

Postgres Timestamps

  • Wen, Chris, and Juancarlos have been working on updating older timestamps for OA entries in Postgres
  • For OA entries generated upon creation of some OA's, the Postgres timestamp is the data of OA creation, not the original data of the object
  • Chris identified all objects from various OAs that had the same initial import timestamp, Wen determined the original ACEDB timestamps for those objects, and Juancarlos is updating the OA entries (curator timestamps) to reflect the object's original timestamp
  • This will be good for consistency going forward and for tracking history of object generation over time

Transgenome project

  • Daniela spoke to developer on project
  • They're fixing/cleaning up data on their end
  • Working on mapping fosmids to latest release of WormBase
  • Probably will import data in a month

UMOD phenotype call yesterday

  • Discussed phenotype data associations
  • Many MODs curate phenotypes to genotype; cannot always make direct, unambiguous associations to a single gene
  • SGD curate to gene, using controlled vocabulary
  • Monarch phenotype data exchange format; can include many levels of detail
  • Common challenge: identifying the single causative agent/mutation

June 9, 2016


  • Wen will make it work off current (live) release of WormBase
  • Do we want to make it more versatile? Add features to specify information to retrieve (specify columns)?
  • Maybe later, but is sufficient for now
  • WormBase official [URL| <http://www.wormbase.org/tools/mine/simplemine.cgi>]

Flagging papers for species

  • Going forward, Kimberly, Jane, and Michael will manually flag papers for species
  • Retroactively, papers will be flagged by scripts
  • ~1000 papers not flagged as C. elegans, but likely mentioned in body of paper; Kimberly reviewing
  • These papers often don't have curatable data