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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]] |
| | | | |
| − | = 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
| |
| − | *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
| |
| − | *Quantitative expression data is not effectively linked to anatomy terms
| |
| − | *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
| |
| − | *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
| |
| − | *Change our paper-by-paper curation
| |
| − | *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
| |
| − | *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 = | |
| − | | |
| − | | |
| − | Textpresso Paper categorization
| |
| − | *Prioritization of papers based on: 1) SVM-Textpresso script categorization, and 2) Ideal prioritization scheme according to curation status
| |
| − | *How does this tie into our grant quarterly progress report?
| |
| − | *Can we create a putative milestone to achieve for the WS240 upload?
| |
| − | *How do we consider backlog size wrt priorities and categorization?
| |
| − | *Even if a data-type backlog is small, it would be worth going back to older curation to check for accuracy and consistency
| |
| − | *Will this pipeline be more efficient? We should define metrics to measure curation effectiveness/efficiency
| |
| − | **Compare curation statistics of new pipeline to last year or two of curation statistics
| |
| − | *Yuling can run existing SVM pipeline on corpus (supervised learning); unsupervised learning will require more human effort
| |
| − | *We can provide lists of keywords to improve the categorization
| |
| − | *There are 1750 papers with author first pass responses, Juancarlos emailed the paperIDs with timestamp of response
| |
| − | | |
| − | | |
| − | Upload
| |
| − | *Next upload (WS240) deadline will be last Friday in September (Sept 27th, 2013)
| |
| − | | |
| − | | |
| − | ACEDB, Citace Minus
| |
| − | *We will remove write-access from citace, moving personal files to citpub for write-access
| |
| − | *Wen will send out a summary e-mail
| |
| − | *Raymond can/will create individual user accounts (for those who want it) with access to personal versions of CitaceMinus and WS
| |
| − | **Personal versions of CitaceMinus and WS will be write-accessible
| |
| − | **Write e-mail to Raymond to request an account on Spica
| |
| − | | |
| − | | |
| − | Nightly GeneAce dumps
| |
| − | *What data from nameserver do we want to pull nightly?
| |
| − | *We need schema and existing data from Michael Paulini
| |
| − | *Until curators (Kimberly ?) tell Juancarlos what we want to extract, we're keeping the scripts that get data from the nameserver.
| |
| − | | |
| − | | |
| − | = July 25, 2013 =
| |
| − | | |
| − | Ontology Browsers
| |
| − | * We are currently testing and developing AMIGO2 for integration into WormBase
| |
| − | ** most recent version at http://mangolassi.caltech.edu/~azurebrd/cgi-bin/testing/amigo/wobr/amigo.cgi
| |
| − | * Example Browsers:
| |
| − | ** [http://www.ebi.ac.uk/ontology-lookup/ Ontology Lookup Service (OLS)] from EBI
| |
| − | ** [http://www.sequenceontology.org/browser/obob.cgi MISO] (Sequence Ontology Browser from www.sequenceontology.org)
| |
| − | ** OBO-Edit
| |
| − | ** Protege
| |
| − | * We are trying to decide on what would be an optimal ontology browsing experience
| |
| − | * Browser experience features to consider:
| |
| − | ** Directed Acyclic Graph (DAG) view
| |
| − | *** Good for visualizing "Path to Root" relationships of an ontology term
| |
| − | ** Viewing children, parents, and/or siblings
| |
| − | *** Interactive expanding/collapsing of terms
| |
| − | *** Static tree or table views
| |
| − | *** "Inferred Tree View" - a compressed path to root tree view (in text format)
| |
| − | ** Clicking to open a new web page versus interactive browsing without reloads
| |
| − | * Consensus is that interactive expandable and collapsible nodes would be ideal
| |
| − | * We will use the Gene Ontology as a pilot ontology to first introduce/integrate into the WormBase site; other ontologies can come later
| |
| − | * We will provide link outs to AMIGO and related sites/services to take advantage of their data and tools
| |
| − | | |
| − | | |
| − | Sequence features related to expression patterns and gene regulation interactions
| |
| − | * Add a "Transcription factor binding" tag to Expr_pattern model? Not necessary?
| |
| − | * Already captured in gene regulation interactions?
| |
| − | * We need to discuss (site-wide) what model changes (if any) would be required to adequately capture this information
| |
| − | * Gary Williams working on curating sequence features to link appropriately to Expr_pattern, Interaction (regulatory), and (maybe) Transgenes
| |
| − | | |
| − | | |
| − | Author First Pass paper word frequency analysis
| |
| − | * Yuling performed word frequency analysis of whole papers and now sections
| |
| − | * Karen took the "Titles" analysis, filtered out words with less than 10 hits, highlighted potential keywords
| |
| − | * How should we go about choosing a topic?
| |
| − | * We will choose AFP papers with "stress" in the title and assess curation status of each paper for our individual data types
| |
| − | ** WBPaper00031692
| |
| − | ** WBPaper00031694
| |
| − | ** WBPaper00031842
| |
| − | ** WBPaper00031873
| |
| − | ** WBPaper00032236
| |
| − | ** WBPaper00032241
| |
| − | ** WBPaper00033114
| |
| − | ** WBPaper00032321
| |
| − | ** WBPaper00034757
| |
| − | ** WBPaper00035114
| |
| − | ** WBPaper00036083
| |
| − | ** WBPaper00036413
| |
| − | ** WBPaper00036090
| |
| − | ** WBPaper00036135
| |
| − | ** WBPaper00035965
| |
| − | ** WBPaper00037147
| |
| − | ** WBPaper00037595
| |
| − | ** WBPaper00037886
| |
| − | ** WBPaper00038233
| |
| − | ** WBPaper00039783
| |
| − | ** WBPaper00039990
| |
| − | ** WBPaper00038093
| |
| − | ** WBPaper00040006
| |
| − | ** WBPaper00039878
| |
| − | ** WBPaper00039835
| |
| − | ** WBPaper00040166
| |
| − | ** WBPaper00039788
| |
| − | ** WBPaper00040384
| |
| − | ** WBPaper00038464
| |
| − | ** WBPaper00040697
| |
| − | ** WBPaper00040849
| |
| − | ** WBPaper00041075
| |
| − | ** WBPaper00040133
| |
| − | ** WBPaper00040902
| |
| − | ** WBPaper00041277
| |
| − | ** WBPaper00041295
| |
| − | ** WBPaper00041568
| |
| − | ** WBPaper00041528
| |
| − | ** WBPaper00041150
| |
| − | ** WBPaper00041610
| |
| − | ** WBPaper00041663
| |
| − | ** WBPaper00041866
| |
| − | ** WBPaper00042148
| |
| − | ** WBPaper00042067
| |
| − | ** WBPaper00042178
| |
