WormBase-Caltech Weekly Calls

2009 Meetings

2011 Meetings

February

March

April

May

June

July

August

September

October 6, 2011

SVM

• SVM Manuscript in process of resubmission
• Messy procedures in place; needs to be cleaned up
• Yuling able to get pipeline running from beginning to the end
• May take longer than previously expected to get up and running
• FlyBase has code running for SVM
• Yuling should contact FlyBase to make sure they're OK, once he has WormBase SVM working
• SGD would like to incorporate SVM into they're database
• Yuri would work on SGD SVM, ultimately

Physical interaction model

• Close to done
• Once model approved, work on:
  • Converting BioGRID file to the ACE model
  • Convert existing YH data into new model

Image curation

• Need to establish legal process for acquiring images
• Contact Caltech Office of the General Counsel for approval

WORM Paper

• Karen working on it
• Need a clearer/new plan

Expression pattern display

• Showing composite images with the option to see greater detail
• Separate out detail images according to Qualifier tags (Certain, Uncertain, Partial)
• Render oblique angles of cells/tissues to show 3D features/morphology of anatomy objects and, possibly, animations
• "Real" images should always take precedence to "virtual" images
• May talk to John Murray or Bill Mohler for confocal images of embryos

Worm Method (Worm Book)

• Any new web pages for C. elegans researchers, send to Raymond
• URL-finder for neuroscience (Yuling)

Textpresso

• Working on Fly Textpresso site (and others)
• Rose Oughtred would like Wnt Textpresso tools
• PDF tools (URL extractor)
• SVM re-working
• Arun working on GSA editor

Grants

• Need to think about next grant in a couple of months (winter); due in October 2012? 30 pages, short?
• Focus on writing papers (anatomy function, WORM, virtual worm, etc.)
• Focus on human-relevance
• Need Gantt charts and quarterly statements of progress
• Stats
  • Where are we with each data type
  • Status of website
  • Automation
  • What is different in the field?
  • How is data changing?

October 13, 2011

WORM Publiction

• Looks good overall
• Change "library" of papers to "index"
• Putative deadline of November 15th
• Put in more details about the new website?
• Figures? Screenshots from new website? Gene page features?
• Save other (detailed) content for future papers

Paper pipeline

• Need to fix some PubMed IDs
• Over 900 articles in Postgres do not have a PubMed ID; Why? How to fix?
• Could some aspects of the pipeline be accomplished by a non-PhD?
• Supplemental hires? Students?
• What tasks would need to be done?
• Can these tasks be scripted/automated? Community input?

SVM

• Almost all scripts working
• Output of SVM slightly different from Ruihua's results
• Need to resolve the differences
• Data inconsistencies
• Need to spot check the papers to see what the major problems might be
• Yuling ~90% confident in his results
• Get feedback from relevant/interested curator(s)
• One-day CPU/computation time (~30 hours for 70 papers with 9 models)

NAR Publication Accepted

Genetic Interaction Curation

• Sharing curated genetic interactions with BioGRID
• What tools will each database use and how will we share data?
  • Both BioGRID and WormBase will use the IMS tool at BioGRID for physical interactions
  • WormBase will use the Ontology Annotator for genetic interactions
  • BioGRID may still use IMS for genetic interactions, but the format will have to be parsed to populate Postgres
• BioGRID-curated genetic interactions can be flagged as such for later review

Physical Interaction model

• Kimberly and Paul Davis discussing
• XREF questions
  • Paul would like to minimize the number of XREFs in the model
  • Which XREFs can we remove?

Elsevier Linking

• Establishing pipeline for linking Science Direct papers to Wormbase and viceversa

October 20, 2011

Data Submission Working Group

• One representative from each site
• Raymond from Caltech
• Have a discussion for every type
  • How are we doing?
  • Are we up to date?
  • Do we want unpublished data?
  • Quality control
  • Data type priority?
• Groups/people that have a lot of data of a particular type; acquire their data
  • How can we facilitate data submission from these groups/individuals?
  • Ultimately like to train these users/submitters to use curator tools
• Form-filling as part of publication process?
• What data types are we missing? Wiki Pages
  • qPCR?
  • Nanostring?
  • Single molecule studies, absolute quantities?
  • SAGE?
  • 3C (Chromosome Conformation Capture), 4C, 5C
  • Metabalome?
  • Pathways/Processes?
  • Drug/disease interactions?
  • Infections?
  • Examples of C. elegans as a model?
• Expression data
  • How do annotate a presence/absence call on expression of a given gene?
  • rpkm cutoff?
  • Number of molecules?
  • Case-by-case thresholds