WormBase-Caltech Weekly Calls
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Revision as of 19:50, 26 February 2015 by Kyook (talk | contribs) (→Model change errors for WS248 upload)
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
February 26, 2015
WormBook chapter(s)
- We'll do a round of reviews and edits on Google Docs
- Eventually we'll transition to Word Docs
- We can hand in next week sometime
- WRT community annotation, we can discuss what we already have
2015 International C. elegans meeting
- Posters
- Could submit abstracts for 1-2 posters
- Could project slides/posters projected at Help Desk booth
- Self explanatory slides projected?
- Workshop
- Volunteers:
- Raymond : WOBr
- Mary Ann : Community annotation (for variation)
- Ranjana : Concise descriptions
- Kevin : Parasite, sequence repositories & submission
- Chris : WormMine
- Kimberly : Finding and using GO annotations
- Scott Cain : JBrowse
- Volunteers:
- WormBase staff could have distinctive outfits (shirts or hats)
- Paul S could wear it at opening plenary talk
- Maybe Kevin Howe could request a booth for ParaSite?
Model change errors for WS248 upload
- Main problem is fixing a model after it has been tagged. We want to avoid having to do this because once a model has been tagged it is employed at different centers, fixing a tagged model would required extra work at all these centers.
- Historical_gene tag accidentally removed from ?Construct model
- Would be good for all curators to see an explicit diff output to confirm all changes made
- Before tagging the models, would be good for Paul Davis to send a formal diff of all changes made to confirm; Paul summarizes the changes in CVS. All curators should look at the CVS summary of changes to make sure only the requested changes had been made.
Automated concise descriptions
- Orthology pipeline needed to be reworked
- Find best match by multiple orthology searching methods
- 120,000+ total automated descriptions
- 5 Caenorhabditis species
- Pristionchus pacificus
- Brugia malayi
- Onchocerca volvulus
- One-to-many orthologies start to become unwieldy
- Because of upload time crunches, we may want to fall back on older files if necessary
Database infrastructure
- Narrowed down to Datomic and MongoDB
- Thomas, Lincoln thought Datomic was better
- Datomic *could* possibly be bought out
- Could still be changed over; would require work, but would have technology in place, worth it
- Will have timestamps
- Still planning to have a single all-encompassing database
BioGRID data sharing pipeline
- Juancarlos developed a BioGRID TAB2 dump file from the Interaction OA
- Eventually will send all worm genetic and physical interactions to BioGRID
- Will omit genetic no_interactions
- Will omit interactions with no PubMed ID: reviews or person evidence only
- Will omit interactions with uncloned genes (no Entrez ID)
- As of Feb 25, 2015, we have ~8220 total novel* genetic interactions to submit to BioGRID (*novel to BioGRID)
Species for genes in Postgres
- We will talk to Michael Paulini about getting species info for genes
- Need to get from GeneACE or some place else
- Added after meeting - yes, all Species are in Geneace. (Mary Ann)
