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| | [[WormBase-Caltech_Weekly_Calls_September_2011|September]] | | [[WormBase-Caltech_Weekly_Calls_September_2011|September]] |
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| | + | [[WormBase-Caltech_Weekly_Calls_October_2011|October]] |
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| − |
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| − | == October 6, 2011 ==
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| − |
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| − | SVM
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| − | *SVM Manuscript in process of resubmission
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| − | *Messy procedures in place; needs to be cleaned up
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| − | *Yuling able to get pipeline running from beginning to the end
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| − | *May take longer than previously expected to get up and running
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| − | *FlyBase has code running for SVM
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| − | *Yuling should contact FlyBase to make sure they're OK, once he has WormBase SVM working
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| − | *SGD would like to incorporate SVM into they're database
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| − | *Yuri would work on SGD SVM, ultimately
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| − |
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| − |
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| − | Physical interaction model
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| − | *Close to done
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| − | *Once model approved, work on:
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| − | **Converting BioGRID file to the ACE model
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| − | **Convert existing YH data into new model
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| − |
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| − |
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| − | Image curation
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| − | *Need to establish legal process for acquiring images
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| − | *Contact Caltech Office of the General Counsel for approval
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| − |
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| − |
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| − | WORM Paper
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| − | *Karen working on it
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| − | *Need a clearer/new plan
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| − |
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| − |
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| − | Expression pattern display
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| − | * Showing composite images with the option to see greater detail
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| − | * Separate out detail images according to Qualifier tags (Certain, Uncertain, Partial)
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| − | * Render oblique angles of cells/tissues to show 3D features/morphology of anatomy objects and, possibly, animations
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| − | * "Real" images should always take precedence to "virtual" images
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| − | * May talk to John Murray or Bill Mohler for confocal images of embryos
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| − |
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| − |
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| − | Worm Method (Worm Book)
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| − | *Any new web pages for C. elegans researchers, send to Raymond
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| − | *URL-finder for neuroscience (Yuling)
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| − |
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| − |
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| − | Textpresso
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| − | *Working on Fly Textpresso site (and others)
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| − | *Rose Oughtred would like Wnt Textpresso tools
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| − | *PDF tools (URL extractor)
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| − | *SVM re-working
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| − | *Arun working on GSA editor
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| − |
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| − |
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| − | Grants
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| − | * Need to think about next grant in a couple of months (winter); due in October 2012? 30 pages, short?
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| − | * Focus on writing papers (anatomy function, WORM, virtual worm, etc.)
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| − | * Focus on human-relevance
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| − | * Need Gantt charts and quarterly statements of progress
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| − | * Stats
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| − | ** Where are we with each data type
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| − | ** Status of website
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| − | ** Automation
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| − | ** What is different in the field?
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| − | ** How is data changing?
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| − |
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| − |
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| − | == October 13, 2011 ==
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| − |
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| − | WORM Publiction
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| − | *Looks good overall
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| − | *Change "library" of papers to "index"
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| − | *Putative deadline of November 15th
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| − | *Put in more details about the new website?
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| − | *Figures? Screenshots from new website? Gene page features?
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| − | *Save other (detailed) content for future papers
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| − |
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| − |
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| − | Paper pipeline
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| − | *Need to fix some PubMed IDs
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| − | *Over 900 articles in Postgres do not have a PubMed ID; Why? How to fix?
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| − | *Could some aspects of the pipeline be accomplished by a non-PhD?
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| − | *Supplemental hires? Students?
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| − | *What tasks would need to be done?
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| − | *Can these tasks be scripted/automated? Community input?
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| − |
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| − |
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| − | SVM
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| − | *Almost all scripts working
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| − | *Output of SVM slightly different from Ruihua's results
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| − | *Need to resolve the differences
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| − | *Data inconsistencies
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| − | *Need to spot check the papers to see what the major problems might be
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| − | *Yuling ~90% confident in his results
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| − | *Get feedback from relevant/interested curator(s)
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| − | *One-day CPU/computation time (~30 hours for 70 papers with 9 models)
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| − |
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| − |
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| − | NAR Publication Accepted
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| − |
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| − |
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| − | Genetic Interaction Curation
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| − | *Sharing curated genetic interactions with BioGRID
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| − | *What tools will each database use and how will we share data?
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| − | **Both BioGRID and WormBase will use the IMS tool at BioGRID for physical interactions
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| − | **WormBase will use the Ontology Annotator for genetic interactions
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| − | **BioGRID may still use IMS for genetic interactions, but the format will have to be parsed to populate Postgres
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| − | *BioGRID-curated genetic interactions can be flagged as such for later review
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| − |
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| − |
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| − | Physical Interaction model
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| − | *Kimberly and Paul Davis discussing
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| − | *XREF questions
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| − | **Paul would like to minimize the number of XREFs in the model
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| − | **Which XREFs can we remove?
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| − |
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| − | Elsevier Linking
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| − | *Establishing pipeline for linking Science Direct papers to Wormbase and viceversa
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| − |
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| − |
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| − |
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| − | == October 20, 2011 ==
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| − |
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| − | Data Submission Working Group
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| − | *One representative from each site
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| − | *Raymond from Caltech, with Juancarlos
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| − | *Have a discussion for every type
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| − | **How are we doing?
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| − | **Are we up to date?
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| − | **Do we want unpublished data?
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| − | **Quality control
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| − | **Data type priority?
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| − | *Groups/people that have a lot of data of a particular type; acquire their data
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| − | **How can we facilitate data submission from these groups/individuals?
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| − | **Ultimately like to train these users/submitters to use curator tools
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| − | *Form-filling as part of publication process?
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| − | *What data types are we missing? Wiki Pages
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| − | **qPCR?
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| − | **Nanostring?
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| − | **Single molecule studies, absolute quantities?
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| − | **SAGE?
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| − | **3C (Chromosome Conformation Capture), 4C, 5C
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| − | **Metabalome?
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| − | **Pathways/Processes?
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| − | **Drug/disease interactions?
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| − | **Infections?
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| − | **Examples of C. elegans as a model?
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| − | *Expression data
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| − | **How do annotate a presence/absence call on expression of a given gene?
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| − | **rpkm cutoff?
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| − | **Number of molecules?
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| − | **Case-by-case thresholds
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| − | *Disease vs Process pages?
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| − | **100 diseases modeled in ''C. elegans''?
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| − | **Flat-file capture and display of disease-relevance information (as opposed to ontology-based)
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| − | *"Subject" vs. "Process" vs. "Disease"
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| − | **Examples of "Subject": Sewage treatment, Biofilm formation, etc.
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| − | **Examples of "Disease": Alzheimer's, Huntington's, Cancer, etc.
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| − | **Examples of "Process": Development, Innate immunity, Organ formation, etc.
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| − | **User experience?
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| − | *User-submitted data inconsistency/discrepancy flag?
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| − |
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| − |
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| − | WORM Paper
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| − | *Still requesting any major comments or content changes
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| − | *"Final" version available next week
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| − |
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| − |
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| − | ''C. elegans'' Research Resources Chapter (WormBook)
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| − | *Yahoo-like Yellow pages of useful URLs with brief descriptions of each site
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| − | *URLs being pulled from papers by Yuling
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| − |
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| − |
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| − |
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| − | == October 27, 2011 ==
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| − |
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| − |
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| − | NAR Proofs are in
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| − | *Karen will send around
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| − | *Going back out tomorrow; everyone check
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| − | *Add Arun as author
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| − |
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| − |
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| − | Predicted Gene Interactions
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| − | *Wei wei contacted Paul
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| − | *Who is the contact person? Xiaodong can be point person
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| − | *Add URLs to Gene Orienteer and Interolog database on gene pages
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| − | *Issue is with syncing the databases and updating
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| − |
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| − |
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| − | SVM
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| − | *Yuling finsished running SVM pipeline; can make run every two weeks
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| − | *Need to learn how to best train the models; do we need to retrain?
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| − | *Gary Williams sent e-mail; incorrect paper IDs on some SVM results
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| − | **Gene structure correction papers have been incorrect
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| − | **May need to retrain the gene structure correction SVM
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| − | **Need someone at Caltech to work with Yuling to retrain the model
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| − | *Kimberly will look through e-mail archive about the issue
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| − | *We could really improve the training set, as original set may have been inadequate
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| − | *What data types do we retrain: Expression pattern? Phenotype?
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| − | *Improve training by including verified positive papers from last two years (since last training)
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| − | *In past, needed 400 papers to train; would be best to lower requirement
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| − | *Antibody and transgene SVM works well; maybe incorporate for Expression pattern SVM?
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| − | *Use pattern matching to correct SVM results or vice versa?
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| − | *Good to make progress on Gene Structure correction papers
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| − | *Keeping track of sentences/paragraphs; performing SVM on paragraphs (vs papers)?
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| − |
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| − |
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| − | Collecting URLs from papers (Raymond)
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| − | *For interesting/relevant URLs for C. elegans
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| − | *Journal URLs are problematic
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| − | *Yuling runs scripts on Textpresso corpus to collect URLs
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| − | *PubMed XML of journals (Kimberly)
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| − |
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| − |
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| − | WORM Publication
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| − | *Final version available
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| − | *Review for corrections
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| − | *To submit early next week (before Wednesday)
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