WormBase-Caltech Weekly Calls
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Contents
Previous Years
2015 Meetings
February 2015
February 5, 2015
Community Annotation
- Mary Ann discussed with Paul S.
- Mary Ann would like to develop a prototype curation form (for variations/molecular lesions) for the international meeting
- Test version in 6 weeks?
- Juancarlos would need a list of required fields, field types, data connections, etc.
- Could take advantage of existing forms
- Ranjana and Juancarlos working on the concise description form
Changing GAF format
- What implications does this have for the WormBase Ontology Browser?
- What testing of generation of the GAF could be done (and sent to Raymond)?
- Kimberly will discuss with Kevin
Automated descriptions with updated release schedule
- WS247 database will not be ready with enough time for Ranjana and James to incorporate into the automated description generation
- They can make do with older files
Citace upload for WS248
- Tuesday March 3rd
February 12, 2015
Physical Interaction Curation
- We have begun physical interaction in Interaction OA
- We are establishing a pipeline to share all physical and genetic interactions with BioGRID
- It would be good to clarify which curators can/will curate physical interactions
- Would be good if phenotype curators could curate genetic AND physical interactions in the same paper
- Something that John DeModena could do?
- Xiaodong capturing protein-DNA interactions
- We still need to decide what level of detail we would like to capture
- We could try to capture specific protein sequences used in experiments
- We don't have individual protein/peptide sequence objects, maybe we want them? IDs for domain instances?
- We have an SVM pipeline "geneprodgo"
- A lot of GO protein interaction data to extract; might use ?Analysis objects to track attribution of curation
BioGRID interaction sharing
- Provenance and attribution issues
- ?Analysis object can be created for BioGRID attribution
- WormBase has imported all worm (C. elegans) physical (protein-protein) interactions from BioGRID
- Working on importing BioGRID genetic interactions, or at least resolving overlap
- WormBase will send physical and genetic interaction data to BioGRID at every upload
- Rose et al are considering regulatory interaction data, currently discussing
WormBook WormBase Chapter
- Feb 28 deadline coming up
- Can be about 3 pages per chapter
- Sections can be written as stand alone and merged as necessary
- Putatively 8 - 10 chapters being written
User submitted Phenotype (RNAi) data
- A user recently requested addition of RNAi data for a handful of papers
- I (Chris) directed them to our trial RNAi data submission table
- Would be good to embed community annotation forms into WormBase website so that users could log in and add data without having to re-enter personal information
- Can we map user login info to WBPerson ID? Is that already the case? Would be good.
Clone Mapper Software
- We will adopt Clone Mapper for RNAi clone mapping
- Chris and Kevin working with Jonathan Ewbank
- Important issue remains: what cutoff for the Clone Mapper tool do we choose?
- We are working on creating RNAi reagent objects in WormBase to capture targets (and off targets) independently of any RNAi experiments
WormBase PI meeting for database migration
- Next week to discuss current new database considerations
- Datomic, MongoDB, etc. front runners
Virtual Fly Brain
- Paul S will talk to group
- 8:30am meeting next Monday
- Coordination with fly and fish groups
- Working out applicable ontologies
February 19, 2015
Citace Upload
- 10am March 3rd
International Meeting Workshop
- Raymond will cover WormBase Ontology Browser
- Ranjana will cover concise description submission/correction
- Paul S. will present at plenary session to make a call for community annotation
- Kevin will present Parasite and sequence repositories/submission
Int. Mtg. Booth and Posters?
- Would be good to have a projector at booth like last time; show people how to get data, etc.
- Keep the poster for advertisement/outreach and displaying the most current WB poster (Xiaodong's SeqFeat)
- Could have prepared presentation/slides displayed on projector at booth by default as a background; change to live demo as needed
- Could demonstrate community annotation?
- Advertisement & Outreach
- Community annotation poster?
WS247 WormBase Ontology Browser built
- Number of genes with Gene Ontology annotations dropped
- May be explained by lack of Phenotype-to-GO annotations
- Raymond can send numbers to Kimberly
