WormBase-Caltech Weekly Calls

Previous Years

2009 Meetings

2011 Meetings

2012 Meetings

2013 Meetings

2014 Meetings

2015 Meetings

January

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