Difference between revisions of "WormBase-Caltech Weekly Calls"
From WormBaseWiki
Jump to navigationJump to searchm (→June 12, 2014) |
m (→Agenda) |
||
Line 80: | Line 80: | ||
=== Agenda === | === Agenda === | ||
* Topic 1 | * Topic 1 | ||
− | * | + | * Reactome tutorial |
+ | ** review event | ||
+ | ** hear thoughts from attending curators |
Revision as of 22:01, 11 June 2014
Contents
Previous Years
2014 Meetings
June 5, 2014
Agenda
- GAF vs GPAD/GPI file formats
- GO still uses both, but is moving towards using GPAD/GPI as their preferred format.
- We will always need GAF for WOBr?
- LEGO Curation/Noctua Development
- Tool is still under significant development at Berkeley.
- What are our plans/goals at Caltech? How best to align this with Berkeley development?
WormBase Ontology Browser (WOBr) for WS244 release
- User interface: would be good if curators could have a look and review again
- Latest GAFs added were for Life Stage and Disease
- GitHub WOBr tracker: https://github.com/azurebrd/wobr
GAF vs GPAD/GPI file formats
- GO traditionally uses GAF format
- May be migrating to GPAD/GPI [Gene Product Annotation Data / Gene Product Information] format in future
- Backend of Amigo2/WOBr uses owltools
- Kimberly discussing with GO team
- We already have scripts to convert GPAD to ACE format
LEGO curation / Noctua Development
- (Too?) much flexibility in what can be curated into Noctua
- Final data model may still need refinement?
- Need to wait for final word on data model before finalizing curation pipeline
- We may be able to develop curation tools ahead of final LEGO data model
- Would be good to have discussions about complex biological scenarios and how to best capture
Construct OA
- Karen and Juancarlos working on ?Construct OA
- Other OA's may need to be updated accordingly
- Wen will set up a local database with the proposed ?Construct model
Reactome tutorial
- 10am PDT tomorrow (Friday)
- WebEx conference
- Initial talk of curating chromosome segregation, may be too complex
- Paper sent around to summarize Reactome model and curation pipeline
New Topic for WS245
- Many possible topics; would be good to choose a topic that has some new papers and would be amenable to drawing a pathway
- We discussed: aging, apoptosis, defecation, feeding, ascarosides...
- We will try apoptosis
- Chris will look into and send around findings
Mapping of promoters
- We have annotated many promoters for expression patterns, for example, but have not been mapped to genome
- Ultimately want to map constructs (or components of constructs) to the genome
- Construct components should be converted to sequence feature objects (?Feature)
June 12, 2014
Agenda
- Topic 1
- Reactome tutorial
- review event
- hear thoughts from attending curators