Difference between revisions of "WormBase-Caltech Weekly Calls"

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* Could have phenotype graphs from particular perspective, e.g. via anatomy, via life stage, via GO, etc.
 
* Could have phenotype graphs from particular perspective, e.g. via anatomy, via life stage, via GO, etc.
 
* Would be great to have a comparative view mechanism
 
* Would be great to have a comparative view mechanism
 +
 +
== January 12, 2017 ==
 +
=== Caltech LEGO Call ===
 +
*Confirm time: Mondays, 11am PST (2pm EST/7pm GMT)
 +
*Start January 23rd
 +
*Format?
 +
**Start with curation of one paper together?
 +
**Curators then select individual topics?

Revision as of 15:46, 12 January 2017

Previous Years

2009 Meetings

2011 Meetings

2012 Meetings

2013 Meetings

2014 Meetings

2015 Meetings

2016 Meetings

2017 Meetings

January 5, 2017

BioCurator meeting

  • Who from WormBase will go?
    • Raymond (SObA), Chris (Community curation), Mary Ann, Wen would like to go
    • Daniela maybe for micropublication

International C. elegans Meeting

  • June 2017
  • Whether all WB staff go depends on whether we have an all hands meeting before/after
  • Plenty of things to present; AGR stuff etc.

Citace upload

  • Prepare files by 10am on Tuesday, Jan 10

LEGO curation

  • Kimberly working on different C. elegans models
  • Working on several pathways simultaneously
  • Should be in production soon (this year), fully evidenced
  • Full benefit may not be apparent until AGR has LEGO fully integrated
  • Working out how inferred annotations propagate from Noctua/LEGO model to GAF
  • MGI creating many LEGO models
  • How are curators, that went to training, using LEGO?
  • Curation level view may not be amenable to general biologist/user viewing
  • What is the best existing pathway display? WikiPathways? Protege?
  • GO people (Seth, Chris M., Suzi etc.) are working on display, but have limited resources for this
  • Maybe we could work with WikiPathways team?
  • Pathway studio at RGD? Manually generated
  • Should WB have a LEGO call? Yes, probably
  • Curators may need access to Protein2GO for full curation/inference by sequence similarity
  • How do we/should we resolve parallel pipelines for curating cellular component data (Go versus Expression pattern)?
  • How do we accommodate specific versus general processes? E.g. specific versus general cell division
  • We would like a mechanism for a LEGO curator to pull relevant data from GAF
  • We would like curators to focus on pathway perspective of curation, where authors can submit experimental details with a potential automated or semi-automated mechanism to bridge the gap

Expression widget

  • Daniela and Sibyl working on a more compact display of the expression data widget on gene pages
  • Should we keep subcellular localization in the expression widget? Yes

SObA for Gene Ontology

  • Raymond and Juancarlos working on
  • First for WormBase, eventually want for AGR
  • For GO data, will have three different roots (for each branch of GO); One DAG for each
  • Could have phenotype graphs from particular perspective, e.g. via anatomy, via life stage, via GO, etc.
  • Would be great to have a comparative view mechanism

January 12, 2017

Caltech LEGO Call

  • Confirm time: Mondays, 11am PST (2pm EST/7pm GMT)
  • Start January 23rd
  • Format?
    • Start with curation of one paper together?
    • Curators then select individual topics?