WormBase-Caltech Weekly Calls

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Previous Years

2009 Meetings

2011 Meetings

2012 Meetings

2013 Meetings

2014 Meetings









September 4, 2014

I need to leave at 5.30pm (ermm, 9.30am CA time?) Mary Ann

Concise Descriptions

  • Automated descriptions to go in for WS245

New Upload Schedule

  • Delayed a couple weeks compared to original schedule
  • Official citace upload to Hinxton on October 10th
  • We can/should upload our data Wednesday before SAB trip (October 1st) to Hinxton
  • Wen needs queries to include in Citace Upload summary by October 1st
  • Upload contingent on models freeze

Data submission as part of publication process

  • eLife considering micro-publication, addendums to papers (individual add-on experimental results)
  • Can certain data be required to publish? Sequence info, etc. ?
  • Could there be a pilot with a specific publisher (like GSA markup)?


  • http://www.elixir-europe.org/
  • Use RDF (Resource Description Framework) triples
  • Checking individual statements/sentences from literature for data presence/absence in database

New tags in Qualifier Hash

  • Life_stage and Anatomy_term
  • Adding to enable annotation of EPIC data
  • Couples (or attempts to) time-and-space (life_stage-and-anatomy) annotation of expression pattern
  • Can ambiguities be captured?
  • This approach (bit of a kludge) introduces some denormalization (normalization can be automated later)

LEGO Curation

  • Setting up connection to Minerva
  • Juancarlos working with Seth, Chris, Heiko to debug setup
  • Would be good (necessary?) to establish a working protocol for collaboration
  • Raymond's LEGO-like approach to curating anatomy function
    • Annotate a phenotype by annotating relevant DB objects, e.g. anatomy term, GO term, etc. as well as context/condition
    • Use minimal relationships (relationship ontologies complicated and difficult to use)

September 11, 2014

SAB Meeting

  • Can we start putting together a more detailed agenda, at least for Caltech?
  • Would be good to decide on our talk topics so we can begin putting our presentation(s) together.
  • Curation Stats numbers spreadsheet
    • Good to capture amount of time (FTEs) on curation, but also software development, curation tools, pipelines, data modeling, help desk, fixing old data
  • Would be good to have a rough breakdown of every curator's FTE breakdown
  • Allocation of resources
  • Ontology development; how much time is spent? Is it worth it?
  • What tools do we have, or could we develop, that could substantially improve efficiency/effectiveness of curation? Example: sequence generation tool
  • What are considerations for future database migration? We should account for migration delays to curation, etc.
  • The curation database (like Postgres now) may or may not be the same database that drives the website
  • Are our curation pipelines capturing sufficient detail (or too much, unnecessary detail)?
  • Is it worth capturing negative data?

SAB Talk Proposals

  • Nomenclature - not stats, but what we do, how it's done, communication etc Mary Ann
  • Physical Interaction Curation - a relatively new data type for us, discuss existing data, strategies for going forward, what groups we could/do collaborate with, what files we could provide
  • Community-Assisted Curation - what we currently do (author first pass, data submission forms), what more we could do (CANTO)
  • Topic-Based Curation

September 18, 2014