WormBase-Caltech Weekly Calls

From WormBaseWiki
Revision as of 09:04, 11 March 2016 by Matuli (talk | contribs)
Jump to navigationJump to search

Previous Years

2009 Meetings

2011 Meetings

2012 Meetings

2013 Meetings

2014 Meetings

2015 Meetings

2016 Meetings



March 3, 2016

Sentence-level indexing

  • Chris playing around with flagging sentences as positive/negative for phenotype and flagging keywords as true or false positives
  • It may be helpful to objectify sentences and generate unambiguous, unique IDs for sentences
  • There will likely be difficulty in unambiguously pulling out sentences from re-processed papers
  • Best identifier would be the sentence itself
  • Sentence 'objects' could be connected to annotations in WB

Proteomic datasets

  • Wen wants to systematically collect proteomic datasets
  • Many are scattered across different resources
  • Would also help ParaSite to index similar datasets for parasites
  • MESH terms may help identify proteomic papers

MOD-human disease collaboration

  • FlyBase working on a shared template for curating human disease
  • SGD, ZFIN, MGI, FlyBase, and WormBase meeting at Caltech to discuss
  • One priority is minimizing redundancy of effort
  • There is a common portal for human diseases in progress
  • Should consider Monarch initiative approach

AddGene & WB constructs

  • Karen working with AddGene to pull in worm reagents (plasmids/constructs)
  • AddGene does want to have better linking to WormBase

Metabolomic data

  • Can we show chemical structures for metabolites?
  • User (M. Witting) says metabolism people will want monoisotopic masses - these masses aren't available through ChEBI at the moment and it will be a while for them to provide them. Will find a formula and sources files for Juancarlos to implement a calculator in the OA.
  • We already use, sync and collaborate with ChEBI

March 10, 2016

Adding WormBase-Parasite Paper to the Curation Pipeline (Kimberly)

  • Developing new paper editor for Jane and Michael P. to approve parasite papers
  • Adding species information to ALL papers; can be one or more species per paper
  • Would like to then incorporate parasite papers into downstream SVM flagging pipeline and curation status form
  • Species information could be used to keep curation stats clear
  • We should discuss the curation and tracking of non-elegans species on the next site-wide call
  • Might be best to have a separate ParaSite-specific curation status form; depends on use-case
  • We may be able to just add new columns to the curation status form, Caltech vs EBI
  • Michael and Jane want to curate gene function, e.g. GO; not sure what else

Dynamo-DB backend for Datomic

  • REST-API now switched to dynamodb backend.
  • Juancarlos could set up a form to try Datomic queries

WB FAQ page

  • Need to request write access from Todd
  • We should find out whether this page is used much. It needs updating considerably.