WormBase-Caltech Weekly Calls February 2015

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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)