WormBase-Caltech Weekly Calls

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Previous Years

2009 Meetings

2011 Meetings

2012 Meetings

2013 Meetings

2014 Meetings

2015 Meetings

2016 Meetings

2017 Meetings

GoToMeeting link: https://www.gotomeet.me/wormbase1

2018 Meetings












December 6, 2018

SObA for disease (& other ontology?) annotations

  • Next Alliance all-hands call in February, present SObA for Skunkworks (innovation talks)?
  • SObA top-slicing (summary view) gets tricky; Raymond looking into better solutions, if available
  • SObA summary could be redundant with ribbon? SObA would provide dynamic, trimmed nodes

Worm phenotype ontology

  • Meeting today at 12pm Pacific, 3pm Eastern
  • In process of adding back obsolete terms to the ontology
  • Question about "has_obo_namespace" attribute; not required for ODK process; used by WB pipelines?

ISB Meeting, Cambridge, UK, April 2019

  • Abstracts from WB?
    • New Author First Pass - Daniela, Valerio, Kimberly, et al.
    • Automated gene descriptions - Ranjana, gene description working group

GO expression data using Uberon anatomy terms

  • Some GO curators curating C. elegans expression annotations (from synapse annotation project) to Uberon anatomy terms, not WBbt terms
  • Kimberly will look into enforcing Noctua editor to use C. elegans anatomy ontology when creating C. elegans annotations
  • Can possibly perform automated mapping if appropriate cross-references exist
  • Kimberly has already found annotations to inappropriate Uberon terms

December 13, 2018

Protege Tutorial

Updates to Gene Regulation OA

  • Removed two unused fields/tables: Trans-regulator Seq and Trans-regulated Seq
  • (In progress) Now a single field for anatomy, life stage, and subcellular localization (SCL) (as opposed to a set of each for each type of regulation result)
  • May require ?Interaction model change if anatomy, lifestage, and/or SCL to be annotated without a result type

Micropublication workshop IWM 2019

  • Micropublication group will apply for a workshop
  • If they get it they will need a tiny (~5 min) slot in the general WB

RNAi uniquely_mapped tags

  • User pointed out that an RNAi object in WormMine was not flagged as "Uniquely mapped"
  • Turns out that the current RNAi mapping pipeline does not add a "Uniquely_mapped" tag
  • All existing tags are coming from older RNAi objects in CitaceMinus
  • Chris working on .ACE file to delete all of these tags from CitaceMinus
  • Chris will upload the .ACE file to citpub@spica in the Data_for_midbuild directory for Wen

Worm wiring & Worm Atlas

  • Todd and Raymond meeting this afternoon
  • Chris will join
  • 2pm Pacific time

WS270 upload

  • Jan 11th upload to Hinxton
  • Tuesday, January 8th citace upload 10am

Alliance grant renewal

  • Send Paul drafts for working group updates before next Thursday Dec 20, just to give him a heads up on content
  • Paul currently working off All-Hands meeting presentations

Alliance vs. MODs efficiencies

  • Compare user pipelines for getting info like:
    • for a human disease gene, what are the phenotypes in model organisms?
  • What are the best work products of the Alliance so far?
    • Expression ribbon
    • Orthology
    • Molecular interactions? Good to have nicer interface, consolidation of data; no automated comparative tools yet, but can get equivalent results with some clicking
    • How to best measure impact?

Noctua imports

  • Can we export/duplicate a Noctua model to apply to a different gene?
  • Can export in GPAD or GAF
  • Want to seed Noctua models with MOD data; efficient, large scale import

December 20, 2018

Authors, Papers, Meeting Abstracts

  • https://github.com/WormBase/website/issues/6802
  • Authors on older (i.e. 2000) meeting abstracts don't always have associated WBPerson objects
    • Anything we can/should do about this?
  • Author on some older abstracts are also listed First Name Last Name as opposed to Last Name, First Name
    • This results in display errors - Todd and Sibyl will try to fix this
    • Any way to fix the source data via script?
  • Can meeting abstracts be added to TPC?
  • Some WB users are still using the old Textpresso. Put a message on that site that it will soon be retired?
    • The old Textpresso site is what comes up first in a Google search for 'textpresso'.
  • Other suggestions from Jonathan:
    • Having the possibility to restrict a search to a given field (e.g. title) and being able to rank the different columns in the results (i.e. by journal or year, etc, not just Doc score) would be welcome.