WormBase-Caltech Weekly Calls
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Previous Years
GoToMeeting link: https://www.gotomeet.me/wormbase1
2018 Meetings
December 6, 2018
SObA for disease (& other ontology?) annotations
- Next Alliance all-hands call in February, present SObA for Skunkworks (innovation talks)?
- SObA top-slicing (summary view) gets tricky; Raymond looking into better solutions, if available
- SObA summary could be redundant with ribbon? SObA would provide dynamic, trimmed nodes
Worm phenotype ontology
- Meeting today at 12pm Pacific, 3pm Eastern
- In process of adding back obsolete terms to the ontology
- Question about "has_obo_namespace" attribute; not required for ODK process; used by WB pipelines?
ISB Meeting, Cambridge, UK, April 2019
- Abstracts from WB?
- New Author First Pass - Daniela, Valerio, Kimberly, et al.
- Automated gene descriptions - Ranjana, gene description working group
GO expression data using Uberon anatomy terms
- Some GO curators curating C. elegans expression annotations (from synapse annotation project) to Uberon anatomy terms, not WBbt terms
- Kimberly will look into enforcing Noctua editor to use C. elegans anatomy ontology when creating C. elegans annotations
- Can possibly perform automated mapping if appropriate cross-references exist
- Kimberly has already found annotations to inappropriate Uberon terms
December 13, 2018
Protege Tutorial
- Doodle poll open: https://doodle.com/poll/kn49rd3rggymn68g
- Please fill out poll if you are interested in attending
- Resources available
- here (right-click and Save As): https://www.dropbox.com/s/6fygtby4x6d2t0r/ProtegeShortCourse.zip?dl=0
- and here: https://protege.stanford.edu/shortcourse/201810/resources.html
Updates to Gene Regulation OA
- Removed two unused fields/tables: Trans-regulator Seq and Trans-regulated Seq
- (In progress) Now a single field for anatomy, life stage, and subcellular localization (SCL) (as opposed to a set of each for each type of regulation result)
- May require ?Interaction model change if anatomy, lifestage, and/or SCL to be annotated without a result type
Micropublication workshop IWM 2019
- Micropublication group will apply for a workshop
- If they get it they won't need a slot in the general WB
RNAi uniquely_mapped tags
- User pointed out that an RNAi object in WormMine was not flagged as "Uniquely mapped"
- Turns out that the current RNAi mapping pipeline does not add a "Uniquely_mapped" tag
- All existing tags are coming from older RNAi objects in CitaceMinus
- Chris working on .ACE file to delete all of these tags from CitaceMinus
Worm wiring & Worm Atlas
- Todd and Raymond meeting this afternoon
- Chris will join
- 2pm Pacific time
WS270 upload
- Jan 11th upload to Hinxton
- Tuesday, January 8th citace upload 10am
Alliance grant renewal
- Send Paul drafts for working group updates before next Thursday Dec 20, just to give him a heads up on content
- Paul currently working off All-Hands meeting presentations
Alliance vs. MODs efficiencies
- Compare user pipelines for getting info like:
- for a human disease gene, what are the phenotypes in model organisms?
- What are the best work products of the Alliance so far?
- Expression ribbon
- Orthology
- Molecular interactions? Good to have nicer interface, consolidation of data; no automated comparative tools yet, but can get equivalent results with some clicking
- How to best measure impact?