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 - 10:30: Overview, Website / UI

• Introduction: Where we are, grant status, etc - (Paul Sternberg; 15 min)
• Website: status, plans, and how much we can accomplish. (60)
  • Site 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)

• Many Genomes (50)
• Transcriptome data (30)

10:30 - 10:40 -- COFFEE

• • 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 Kevin and Todd)

Monday morning Website: status, plans, and how much we can accomplish. (60) Todd, Abby WormMine (30) JD Many Genomes (60) Hinxton Many Transcriptomes (30) [incl. Wen on SPELL]

Monday afternoon Literature curation workflow and tools (30). Towards Integrated phenotype curation: (alleles, RNAi, transgenes, interactions, GO (40). Gene expression and regulation: Transcriptional Networks (Xioadong, Daniela) Community Annotation (30): Concise descriptions [Kimberly, Ranjana]; Human disease Processes and pathways (30). Karen Community Annotation wikiPathways [Karen]; Community Annotation: by webforms with focus on specific types Community Annotation gene models?; Acedb migration (20) Websites pages for other species

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