Difference between revisions of "WormBase-Caltech Weekly Calls"

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=== Datomic ===
=== Datomic ===
* Juancarlos discussing with Adam, Sibyl, Matt, Kevin
* Juancarlos discussing with Adam, Sibyl, Matt, Kevin
* People are working on URL widgets: person widgets are done, except for lineage graph
* People are working on URL widgets: person widgets updated and ready for production, except for lineage widget.
* Other URL widgets have also been completed
* Some other URL widgets have also been completed
=== ACEDB dependencies ===
=== ACEDB dependencies ===

Revision as of 20:24, 9 February 2017

Previous Years

2009 Meetings

2011 Meetings

2012 Meetings

2013 Meetings

2014 Meetings

2015 Meetings

2016 Meetings

2017 Meetings


February 2, 2017

Methods in Molecular Biology chapter

  • Chris and Mary Ann will be in touch with individuals about section writing
  • Karen: FlyBase chapter has small sections rather than long articles about their pages; should we keep our sections small; a few paragraphs each?
    • As long as we stick to the "how to" focus, we can write as much as needed
  • Raymond: We should try to write so that the content remains pertinent for a while

Pharyngeal phenotype terms

  • Karen has made pharyngeal pumping phenotype terms for NemaMetrix micropublications
  • It is common for many groups to involve serotonin-induced pharyngeal pumping to analyze strains; we do have a serotonin-induced pharyngeal pumping variant term- should I use this for all pumping phenotypes? In addition we have an EPG variant term and again, people tend to use EPGs to record pumping activity - should all reported pharyngeal pumping phenotypes that were measured by EPGs be annotated with this term? These questions highlight a need to revisit the pharyngeal phenotype branch and clarify how we should be focused on annotating these reported annotations.
  • Karen asked Raymond/Gary and any other person interested in the group to help with pharyngeal phenotype term organization
  • Raymond: Not very familiar with the existing usage of the terms and phenotype ontology structure wrt pharyngeal terms
  • Authors submit phenotype data as part of the micropublication process
  • Proposal for phenotype ontology going forward: create terms with logical definitions (OWL statements)
  • We will start exploring more usage of logical definitions for phenotypes
  • Will start meeting Thursday afternoons, starting next week (Feb 9), 1:30pm Pacific
  • Karen will prepare the terms to be looked through.....

SObA graph for GO

  • Juancarlos & Raymond making progress
  • Added toggling for different roots of GO
  • Difficult to navigate graph when lots of terms (e.g. tax-4)
  • What can be done to improve the display?
  • Filtering out IEA annotations; currently only for phenotype annotations; will expand to all IEA annotations
  • Kimberly generating GO slim, 15-20 terms for each branch of GO, possible to use in ribbon display
  • Could we distinguish between is_a, part_of, and regulates relationships?
  • To simplify graph, could we further minimize the display of higher level/indirect nodes?
  • Would we want parallel paths to root to be trimmed?

February 9, 2017

AGR Disease working group

  • disease association file (DAF) pretty much worked out; data quartermasters are creating DAF files for each DB
  • Have a simple mockup for the display of disease data on a gene report page: https://docs.google.com/presentation/d/1YuD4_-mPS2AhIfaX41M8IIhiS63iiSy9ebcOQEZxoJQ/edit#slide=id.p4
  • We should remove underscores from "is_model_of" and translate to "is a model of"
  • Should spell out evidence codes
  • Kevin, WB data quartermaster, working on developing the disease association file (DAF) from the WormBase build
  • Ranjana working on a new ?Disease_model_annotation class and model
  • Disease working group has handed off mockup to AGR UI working group to start development

C3 working group

  • Proposing ontology working group to handle ontology data and display


  • Juancarlos discussing with Adam, Sibyl, Matt, Kevin
  • People are working on URL widgets: person widgets updated and ready for production, except for lineage widget.
  • Some other URL widgets have also been completed

ACEDB dependencies

  • Raymond was asked to collect all CIT curator uses of ACEDB, e.g. programmatic access via ACE Perl
  • Send Raymond list of any CIT ACEDB-dependent processes
  • Going forward, how are model changes made/proposed?
  • Are we still proposing models in ACEDB and having them be converted? Not sure
  • We need to establish a models migration plan
  • Curators should review cronjobs that may need access to ACEDB
  • Juancarlos can collect list of cronjobs using ACEDB; will send email of list
  • Karen: WB Wiki page for OA forms, tables, scripts, etc. : http://wiki.wormbase.org/index.php/OA_forms,_tables,_scripts,_etc


  • CIT upload February 28th? Need to check with Hinxton


  • Sent two micropublications
  • In review and given DOI's

Methods in Molecular Biology chapter

  • Submission deadline April 1
  • Mary Ann and Chris are organizing, will contact authors of older WormBook chapters
  • We want to co-opt text from WormBook chapters that are specifically how-to guide with troubleshooting tips
  • Everyone that has contributed this type of text, now or in this process, will be given authorship
  • In future, could have small methods descriptions as micropublications; e.g. how to navigate the phenotype widget
  • Content in older WormBook chapters that doesn't make it into the MIMB chapter could be micropublished
  • We can review help desk inquiries to inform us as to what content should be included