Difference between revisions of "WormBase-Caltech Weekly Calls"
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* Karen will take care of dumping and uploading the data for this upload | * 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 | * 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 | ||
Revision as of 18:33, 13 April 2017
Previous Years
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
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
