WormBase-Caltech Weekly Calls February 2015

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
• 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)