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| [[WormBase-Caltech_Weekly_Calls_June_2013|June]] | | [[WormBase-Caltech_Weekly_Calls_June_2013|June]] |
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| + | [[WormBase-Caltech_Weekly_Calls_July_2013|July]] |
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− | = July 11, 2013 =
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− | | + | = August 1, 2013 = |
− | Geneace daily dump
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− | *EBI is moving nameserver location
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− | *Getting real-time updates of gene list for genes in OA
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− | *Michael Paulini set up nightly geneace dumps to FTP site
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− | *We have gene file from nameserver: cgc name, public names, sequence name, live/dead status, gene IDs
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− | *What data do we want additionally? Synonyms?
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− | Spica has officially been moved to new machine
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− | *Let Raymond know of any problems
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− | *Would be good to track all accounts on Spica (and any other machine)
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− | **Can use log of all user logins
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− | AMIGO 2 still moving forward
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− | *AMIGO 2 might go live July 17th
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− | *We should be able to start configuring for WormBase at that point
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− | Process Pages/WikiPathways
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− | *iFrame window doesn't work/load on Firefox; they are working on it
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− | *iFrame window interactive display somewhat problematic
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− | *Discussing Cytoscape as alternative?
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− | *Using Cytoscape to display pathways would require significant development
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− | *Some app available to load GPML from WikiPathways into Cytoscape, but JD couldn't get it working (yet)
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− | *Having all process-related interactions in an Interactions widget on Process Pages
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− | **Users need a clearer legend explaining what the different edges mean
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− | **We need to modify some edges (e.g. flat ends do not mean repression; maybe they should)
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− | Author First Pass Forms
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− | *Currently we collect data from authors that we may not have intention of curating (at least right away)
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− | *We can provide a disclaimer on the letter to authors explaining that some data may not be curated immediately
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− | *All data is catalogued
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− | Sequence Feature curation
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− | *Xiaodong met with Gary Williams and Mary Ann Tuli at IWM
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− | *Enhancer curation?
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− | *Significant backlog on sequence feature curation
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− | *Margie Ho asking about curated enhancers, regulatory regions
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− | *Margie has 30 papers with highly annotated regulatory regions
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− | *Gary W. is prioritizing curation of these now
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− | *Gary will propose appropriate model changes (e.g. Add "silencer" and "enhancer" to method for GBrowse display)
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− | User use case: All G-protein coupled receptors expressed in AWC neurons
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− | *Quantitative expression data is not effectively linked to anatomy terms
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− | *Wen will propose model fix to accommodate this association
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− | *Genes expressed above some pre-defined threshold will be associated with a cell
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− | *For example, Ping (in Paul's lab) will be performing AWC single cell profling
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− | *AWA and BAG neurons has been profiled by tiling arrays
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− | *Male linker cell by RNA-Seq (Erich and Mihoko)
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− | Curation strategies
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− | *Change our paper-by-paper curation
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− | *We may be able to make use of a Textpresso categorization program to tag papers
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− | *Caltech curators can then prioritize their curation based on a particular category or topic
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− | *We can look at the [http://www.biomedcentral.com/1471-2105/7/370 Textpresso paper] and reconvene next week to discuss
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− | = July 18, 2013 = | |
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− | Textpresso Paper categorization
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− | *Prioritization of papers based on: 1) SVM-Textpresso script categorization, and 2) Ideal prioritization scheme according to curation status
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− | *How does this tie into our grant quarterly progress report?
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− | *Can we create a putative milestone to achieve for the WS240 upload?
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− | *How do we consider backlog size wrt priorities and categorization?
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− | *Even if a data-type backlog is small, it would be worth going back to older curation to check for accuracy and consistency
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− | *Will this pipeline be more efficient? We should define metrics to measure curation effectiveness/efficiency
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− | **Compare curation statistics of new pipeline to last year or two of curation statistics
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− | *Yuling can run existing SVM pipeline on corpus (supervised learning); unsupervised learning will require more human effort
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− | *We can provide lists of keywords to improve the categorization
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− | *There are 1750 papers with author first pass responses, Juancarlos emailed the paperIDs with timestamp of response
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− | Upload
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− | *Next upload (WS240) deadline will be last Friday in September (Sept 27th, 2013)
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− | ACEDB, Citace Minus
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− | *We will remove write-access from citace, moving personal files to citpub for write-access
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− | *Wen will send out a summary e-mail
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− | *Raymond can/will create individual user accounts (for those who want it) with access to personal versions of CitaceMinus and WS
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− | **Personal versions of CitaceMinus and WS will be write-accessible
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− | **Write e-mail to Raymond to request an account on Spica
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− | Nightly GeneAce dumps
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− | *What data from nameserver do we want to pull nightly?
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− | *We need schema and existing data from Michael Paulini
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− | *Until curators (Kimberly ?) tell Juancarlos what we want to extract, we're keeping the scripts that get data from the nameserver.
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− | = July 25, 2013 =
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− | Ontology Browsers
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− | * We are currently testing and developing AMIGO2 for integration into WormBase
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− | ** most recent version at http://mangolassi.caltech.edu/~azurebrd/cgi-bin/testing/amigo/wobr/amigo.cgi
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− | * Example Browsers:
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− | ** [http://www.ebi.ac.uk/ontology-lookup/ Ontology Lookup Service (OLS)] from EBI
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− | ** [http://www.sequenceontology.org/browser/obob.cgi MISO] (Sequence Ontology Browser from www.sequenceontology.org)
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− | ** OBO-Edit
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− | ** Protege
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− | * We are trying to decide on what would be an optimal ontology browsing experience
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− | * Browser experience features to consider:
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− | ** Directed Acyclic Graph (DAG) view
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− | *** Good for visualizing "Path to Root" relationships of an ontology term
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− | ** Viewing children, parents, and/or siblings
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− | *** Interactive expanding/collapsing of terms
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− | *** Static tree or table views
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− | *** "Inferred Tree View" - a compressed path to root tree view (in text format)
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− | ** Clicking to open a new web page versus interactive browsing without reloads
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− | * Consensus is that interactive expandable and collapsible nodes would be ideal
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− | * We will use the Gene Ontology as a pilot ontology to first introduce/integrate into the WormBase site; other ontologies can come later
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− | * We will provide link outs to AMIGO and related sites/services to take advantage of their data and tools
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− | Sequence features related to expression patterns and gene regulation interactions
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− | * Add a "Transcription factor binding" tag to Expr_pattern model? Not necessary?
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− | * Already captured in gene regulation interactions?
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− | * We need to discuss (site-wide) what model changes (if any) would be required to adequately capture this information
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− | * Gary Williams working on curating sequence features to link appropriately to Expr_pattern, Interaction (regulatory), and (maybe) Transgenes
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− | Author First Pass paper word frequency analysis
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− | * Yuling performed word frequency analysis of whole papers and now sections
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− | * Karen took the "Titles" analysis, filtered out words with less than 10 hits, highlighted potential keywords
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− | * How should we go about choosing a topic?
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− | * We will choose AFP papers with "stress" in the title and assess curation status of each paper for our individual data types
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− | ** WBPaper00031692
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− | ** WBPaper00031694
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− | ** WBPaper00031842
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− | ** WBPaper00031873
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− | ** WBPaper00032236
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− | ** WBPaper00032241
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− | ** WBPaper00033114
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− | ** WBPaper00032321
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− | ** WBPaper00034757
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− | ** WBPaper00035114
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− | ** WBPaper00036083
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− | ** WBPaper00036413
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− | ** WBPaper00036090
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− | ** WBPaper00036135
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− | ** WBPaper00035965
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− | ** WBPaper00037147
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− | ** WBPaper00037595
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− | ** WBPaper00037886
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− | ** WBPaper00038233
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− | ** WBPaper00039783
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− | ** WBPaper00039990
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− | ** WBPaper00038093
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− | ** WBPaper00040006
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− | ** WBPaper00039878
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− | ** WBPaper00039835
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− | ** WBPaper00040166
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− | ** WBPaper00039788
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− | ** WBPaper00040384
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− | ** WBPaper00038464
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− | ** WBPaper00040697
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− | ** WBPaper00040849
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− | ** WBPaper00041075
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− | ** WBPaper00040133
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− | ** WBPaper00040902
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− | ** WBPaper00041277
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− | ** WBPaper00041295
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− | ** WBPaper00041568
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− | ** WBPaper00041528
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− | ** WBPaper00041150
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− | ** WBPaper00041610
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− | ** WBPaper00041663
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− | ** WBPaper00041866
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− | ** WBPaper00042148
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− | ** WBPaper00042067
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− | ** WBPaper00042178
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