WormBase-Caltech Weekly Calls
From WormBaseWiki
Previous Years
2016 Meetings
May 5, 2015
Tissue enrichment tool
- Some slight modifications have been made
- Raymond/Juancarlos request testing
- Made adjustments to gene name handling
- Tool could go live for the next release
- Data will remain frozen at WS252
Gene summaries
- Paul asked Norbert about gene descriptions
- FB has been getting good community response for contributing gene descriptions
- Automation still sounds like the right way to go
- Ranjana will look at summaries at other MOD sites
Phenotype display
- MGI/MGD had a graph display of phenotype ontology (Paul S.)
- Made phenotype ontology slim for the summary heatmaps
- How do all of the MODs display phenotypes?
Progress reports
- Curators can write a paragraph on innovation
- Community curation (report numbers)
- WOBr
- SObA
- Automated descriptions
- Micropublications
Curation pipeline comparisons
- Would be nice to compare how MODs prioritize curation, triage papers, etc.
- How many MODs curate paper-by-paper (for all datatypes at once) vs. our method, by datatype?
- WB & MGI curate by datatype, most others by paper (for all datatypes)
- How are all MODs doing in terms of paper coverage?
- Do we need more manual effort, more automation? How much, given cost of each?
SPELL
- SGD uses SPELL but does not develop
May 12, 2016
Communication tools for umod teams
- Mike Cherry set up Stanford umod-project- email lists for the different umod groups, PIs, software developers, and curators
- umod-project-curation@lists.stanford.edu
- https://mailman.stanford.edu/mailman/listinfo/umod-project-curation
- note: if you signup for a digest, you will receive e-mails from the list on a different time scale than people who didn't choose 'digest'
- Slack is back, download the app and look umod-project. You can also visit https://umod-project.slack.com/.
- Browse the channels and join the ones that you want.
- Suzi Lewis will be setting up a github account for project tracking and wiki pages
Human Disease working group meeting
- Next Monday and Tuesday, in Kerckhoff 024
- Curators will review data models for human disease at each site
- Brainstorming session for future plans
- Possibility of molecule-disease interactions ("exacerbated by", "ameliorated by")
Metabolomics
- Wen came across metabolic profiling papers while looking for proteomics papers
- Wen will send to Karen, who is managing metabolites as part of molecule class
- BIGG database, a new metabolite database (http://bigg.ucsd.edu/)
Progress Report
- Send Paul progress report blurbs in next week (by Thursday)
Cross MOD call
- Reviewed FlyBase and Rat Genome Database this week
- Will review SGD and MGI next week
- Suzi Lewis asking about Intermine instances; what can Mine do that the Base cannot, and vice versa?
- Other MODs have more fully functional and fully populated InterMine instances
FraqMine/SimpleMine
- http://tazendra.caltech.edu/~azurebrd/cgi-bin/forms/fraqmine.cgi
- We want to make the tool available to users, maybe under Tools menu
- Will need to discuss with Todd (Paul sending email)
Micropublications
BioCADDIE developers are currently working on indexing datasets requested by the NIH for inclusion in a June 30 Prototype test. After then they will reach out to us to look into the WormData (micropublication) indexing.
