WormBase SAB Meeting

WormBase_Consortium Scientific Advisory Board Meeting

California Institute of Technology, January 27-29, 2013

Sunday 27th Jan – Pre-Meeting (WormBase central)

(Advisory Board not required to attend this session)

Monday 28th Jan

9:00 - 12:00: Overview, Website / UI

• Introduction: Where we are, grant status, etc - (Paul Sternberg; 15 min)

Monday morning Website: status, plans, and how much we can accomplish. (60) WormMine (20) Many Genomes (50) Transcriptome data (30) Monday afternoon Literature curation workflow and tools (50) Towards Integrated Phenotype Curation (30) Interactions (20) GO (20) Cell Function (10) Processes and pathways (20) ??Transcriptional Networks: Revisiting tools with respect to Community Annotation (40) Acedb migration (20)

• • Website introduction; usage; web team accomplishments; objectives and milestones. (Todd; 20 minutes)
  • Tour of the new website (Abby; 20 minutes)
  • Intermine introduction, status, and goals (JD; 15 minutes)

BELOW IS OLD STUFF:

Wednesday 2nd Feb – Pre-Meeting (WormBase central)

(Advisory Board not required to attend this session)

9:00 - 9:15 delegates arrive

9:15 - 9:30 pre-pre-meeting coffee

9:30 – 18:00 Put right the World

Potential Discussion topics

• Release cycle
  • Implications of less frequent releases
  • Strategies for "as live" display of certain data types
• Gene-structure curation
  • Manual versus automatic-RNASeq-guided (and how we might do the latter)
  • Which genomes should be manually curated?
  • Community annotation of tier III genomes
  • Should we invest resources into "semi-automatic" annotation of 3rd party genomes?
• New species
  • Minimal requirements for integration into WormBase
    • Submission to ENA/Genbank? Gene-set?
    • Ownership of genome assemblies? Tier IIs required to be owned by Wormbase for re-submission
  • Support for "tier IV" (transcriptome-only) / "tier V" (genome-only) worms
  • Support for "in-progress" genome projects (See also Ensembl pre-sites)
• (Re-)sequencing
  • What should the elegans reference sequence be?
    • We have RNASeq evidence from at least four labs for about 500 to 1000 genomic errors in the reference sequence compared to 'their' N2. However each lab has a different set of errors.
    • Re-sequencing a standard N2 isolate and make available from CGC.
      • This has been discussed and proposed a number of times, but has never progressed from "That's a really good idea" :(
      • Requires willing lab to prep large number of samples
      • Requires money for new tech seq run
  • Handling 1000s of elegans mutant and wild isolate strain genomes?
    • Representation of non-reference variants of genes/features etc.
  • Chip-seq and other large datasets - where should the be stored to maximise usage but cut overhead?
• (Re-)distribution of tasks within the consortium
  • Array probe mapping
  • RNAi target identification
  • C.elegans monthly clone submission
• Visualisation
  • GBrowse: making it -seq friendly
  • Interaction browser: what shall we use?
• website development
  • implications of freeze on current website development - should we make this public?
  • will existing developments be incorporated into new website at start?

Thursday 3rd Feb – Millikan Board Room

9:00 - 12:00: Overview, Website / UI

• Introduction: Where we are; Hinxton Reorganization - (Paul Sternberg; 15 min)

• Slot for new Hinxton PIs (Paul Kersey and Matt Berriman; 30 mins)
• User interface
  • Site usage; introduction to the new site (Todd; 30 minutes) (Presentation on Prezi.com)
  • Tour of the new website (Abby; 30 minutes)

• Process and pathway curation and display (Karen; 10 minutes)

• Data Integration/Data Mining - WormMart & Future Perspectives (Ruihua; 10 minutes)

13:00 – 15:00 Build, Genetic data, Sequence curation and analysis, other nematodes

• Build update - Kevin H. (20 mins)
• Genetic data - Mary Ann (presented by Kevin; 20 mins)
• C. elegans + Tier II Manual curation and projects - Paul D. (20 mins)
• Non-elegans species - an update - Michael P. (20 mins)
• Large scale datasets (curation/modENCODE) - Gary W. (30 mins)
  • microarray and SPELL -Wen C. (5 min)

15:30 - 17:00: Literature Curation

• Literature curation introducton : Gary Schindelman (update on stats) - 7-10 minutes

• Ontology Annotator
  • Juancarlos Chan - general introduction of OA (15 min)
  • Xiaodong Wang - developing interaction OA; BioGRID (5-10 min)

• Picture curation : Daniela Raciti - 10 minutes
• Virtual Worm Overview : Chris Grove - 3 minutes

• Collaboration with other Databases/Projects - automation (ARRA), GO
  • journal article processing (GSA markup) Arun, Karen (15 min)
  • Automatic Triage - Using Support Vector Machine (SVM) (Ruihua; 10 minutes)
  • Semi-Automated GO Curation - Exporting our Cellular Component Curation Pipeline to other MODs, Progress on Molecular Function Pipeline (Kimberly; 10 minutes)

• WormBook (Jane Mendel, 10 minutes)

17:00 - 17:30: General Discussion

• to be determined during talks

Friday 4th Feb – Millikan Board Room

13:00 – 15:00 Post ABM Discussion

(Advisory Board not required to attend this session)

Arrivals/Departures

Arrive

• Hinxton Crew - Pasadena Tuesday afternoon/evening?
• Kimberly - Pasadena, Monday 1/31 evening
• Ranjana - Tuesday, 2/1 evening

Depart

• Hinxton Crew minus Michael - Pasadena Sunday before lunch?
• Michael P. - Pasadena Saturday morning
• Kimberly - Friday, 2/4 evening
• Ranjana - Saturday afternoon