WormBase-Caltech Weekly Calls

Previous Years

2009 Meetings

2011 Meetings

2012 Meetings

2013 Meetings

2014 Meetings

2015 Meetings

2016 Meetings

2017 Meetings

January

February

March

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

SimpleMine

• 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)

Follow up on transgene question from user

• Karen will contact authors of paper

Citace upload

• Tuesday, Apr 25th, 10am