Difference between revisions of "WormBase-Caltech Weekly Calls"
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**Which XREFs can we remove? | **Which XREFs can we remove? | ||
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− | *Establishing |
Revision as of 23:29, 13 October 2011
2011 Meetings
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