WormBase-Caltech Weekly Calls
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Contents
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
- 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
- All GO annotation data loaded at Caltech (bigGO solr database, 54GB)
- 100 species, 922296 bioentity (protein, gene product ...)
- Testing site, try
let-23, KRas (human) eat-4, SLC17A7 (human)
- Heavy querying may cause the server to go down; need to check why
- ~7 hours to load
- Can there be an option to specify a GO term and zoom in to that portion of the graph?
- Implement a GO-Slim browsing functionality?
AGR lexica
- Karen's SBIR, trying to get gene names from each AGR database
- Non-trivial, in some cases, to query out curated papers list