WormBase-Caltech Weekly Calls

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Previous Years

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2011 Meetings

2012 Meetings

2013 Meetings

2014 Meetings

2015 Meetings

2016 Meetings

2017 Meetings




April 6, 2017

AGR time spent

  • Paul S asking about %time spent on AGR project
  • Time spent on working groups, conference calls, AGR development
  • Send estimates to Paul


  • Two tables added to SimpleMine for human orthology
  • Now SimpleMine output has many columns (30+)
  • We may want to give users the option to specify which output they want
  • Users could specify groups of data (with checkboxes): gene IDs/names, phenotypes, orthology, etc.
  • All checkboxes can be checked by default

Enrichment tools

  • Raymond working on display for paper

Gene Ontology SObA graph

  • Raymond, Juancarlos working on
  • Working on paper

WormMine updates

  • WS258 adding gene class
  • WS259 adding more info (almost all meta data) on variations, laboratory and strains, RNAi phenotypes (hopefully)
  • Expression data in WormMine is problematic
  • Many genes being annotated to the same ~6 tissues or so
  • Resulting in erroneous data for some genes
  • Chris will send GitHub ticket to Todd
  • Todd will discuss with Paulo today

Gene Ontology

  • Some very complex terms becoming immediate children of root terms (e.g. "biological process")
  • May be result of attempt to create logical definitions/equivalence axioms
  • Raymond will discuss with Kimberly

April 13, 2017

Methods in Molecular Biology chapter

  • Chapter draft sent out Monday night
  • Will send to Martin at MiMB by late next week
  • Please take a look and send comments
  • Authors check their sections and send figure legends to Chris

Progress report

  • If someone finds the 2016 report, send around to group
  • May 1st deadline (need to verify)

2017 IWM

  • Early registration Deadline May 18th

Models for citace

  • Wen will fit models to local citace, should be ready by tomorrow

Citace Upload

  • Tuesday, April 25th, 10am

Enrichment tool

  • Now available for gene ontology and phenotype on live site
  • Paper being submitted soon
  • Need to change "Tissue Enrichment Analysis" link title under WormBase Tools menu

SObA for Gene Ontology

  • Data source was server on Berkeley BOP; thought it was public but were discouraged to use
  • Seth Carbon said we could use it but might not always be working; now it seems to be down or dysfunctional
  • SObA for GO will be broken until we install our own local server (Raymond working on)

Dumping data for upload, taking over for Karen

  • Karen will take care of dumping and uploading the data for this upload
  • Karen will review the molecule curation with other curators at the IWM

Datomic meeting

  • Matt, Sibyl, Adam, Todd, Juancarlos, Raymond sat in
  • Raymond: thought Datomic would take over from ACEDB completely, but it seems we will still use ACEDB for some time for e.g. FMap
  • Seems there should be an executive meeting about Datomic to make clear what it will be used for and what it won't be used for
  • Several web pages and widgets are now being served by Datomic
  • There's a question about how we now handle model changes going forward
  • Juancarlos will send around link for newest Datomic querying tool; may require access for specific IP addresses

April 20, 2017

Gene Ontology data for SObA

  • Use of GO server; hasn't been reliable
  • Raymond working on establishing our own server to host all GO data
  • Raymond and Juancarlos will keep working on SObA representation of GO annotations

Progress Report

  • WS259 can be used as the current reference
  • Paul will send around last year's progress report
  • What was the last release that we referenced in last year's progress report? We'll say WS254
  • Wen will generate numbers for WS254 (resurrect WS254 ACEDB)
  • Opportunity to specify/narrow scope of project
  • Want to push community/automated curation, with curators laying foundation of data models, forms
  • Promote LEGO curation; need to learn what needs to be said about plan going forward/what we want to accomplish

LEGO curation

  • Phenotype curation in LEGO? Need to review phenotype-to-GO pipeline
  • Want/need a mapping of phenotype terms to GO process terms; may require context-dependent mapping (e.g. "dumpy" phenotype)
  • We don't make direct associations of phenotypes to LEGO models, although we do have "inferred from mutant phenotype" evidence code
  • Want a mechanism to automate conversion of WB annotations into LEGO models
  • Want a display mechanism that is user friendly, convert hairball into pathway
  • We could focus on a particular topic/disease and collectively contribute
  • Do we want to write a proposal to take existing, granular annotations (e.g. at level of mutation details) and map to LEGO model?
  • Can we integrate the micropublication pipeline into LEGO model generation?
  • How to assess the confidence of assertions?

Follow up on transgene question from user

  • Karen will contact authors of paper

Citace upload

  • Tuesday, Apr 25th, 10am

April 27, 2017

Gene Ontology data for SObA