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| | = 2016 Meetings = | | = 2016 Meetings = |
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| − | == January 7, 2016 ==
| + | [[WormBase-Caltech_Weekly_Calls_January_2016|January]] |
| − | | |
| − | === SAB 2016 ===
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| − | * Schedule for Caltech talks:
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| − | ** SAB wiki: http://wiki.wormbase.org/index.php/2016_Advisory_Board_Meeting#Organisation_of_SAB_talks
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| − | ** Mary Ann, Chris, and Ranjana will discuss how to condense and streamline a presentation on community curation
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| − | ** We should have a talk about LEGO curation and pathways; Kimberly happy to present
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| − | *** LEGO adoption can be made cross-MOD and encourage collaboration
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| − | ** Maybe move micropublication talk to the end of the day; it will generate a lot of discussion; will try earlier in the day, 5 min talk, 5 min discussion before longer discussion
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| − | ** Maybe include discussion of expression summary description in Gary Williams talk about large scale expression data and visualization
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| − | | |
| − | === Expression summaries ===
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| − | * We want to consolidate large-scale expression data into a human-readable summary
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| − | * Would be good to consolidate large-scale and small-scale expression data
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| − | * We will adapt anatomical expression data for the SObA graph in future
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| − | | |
| − | === Phenotype form ===
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| − | * Now on sandbox, allows for RNAi transgene data
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| − | * Will finish up, write documentation and make live
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| − | * Will continue to send out e-mail requests
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| − | | |
| − | === E-Merge Tech outsourcing ===
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| − | * Company called Chris asking if we would want them to curate for us
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| − | * Website: http://www.e-mergeglobal.com/
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| − | * Will send them some phenotype curation for some papers and ask them to curate new papers, as a pilot
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| − | * They will give us a cost estimate after a free pilot
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| − | * Will see if it is cost-effective; good to know what they charge
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| − | | |
| − | == January 14, 2016 ==
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| − | | |
| − | ===LEGO===
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| − | *Sent out slides for an overview talk of LEGO and the Noctua curation tool. (Kimberly)
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| − | | |
| − | === Collecting info for SAB ===
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| − | * Chris would like to collect summaries of curation progress over last year in a Google Doc
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| − | * Google doc: https://docs.google.com/document/d/1S8EjL20owW07RH9kIi8HbnTAtP5JierliBuyOo2oDVc/edit
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| − | * Would be good to include progress on various projects or curation efforts (or curation changes)
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| − | * Next week at group meeting we can review and decide what should be presented as the overview for curation to the SAB
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| − | | |
| − | | |
| − | == January 21, 2016 ==
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| − | | |
| − | === SAB ===
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| − | * Agenda items for literature curation overview
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| − | * Todd will discuss outreach; Chris will talk to Todd about Caltech plans for outreach
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| − | * Cataloging web usage on WB site, SPELL, etc.
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| − | * We can discuss hosting all WB services and tools under the same web domain
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| − | | |
| − | === Phenotype form ===
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| − | * New phenotype form is live: http://tazendra.caltech.edu/~azurebrd/cgi-bin/forms/allele_phenotype.cgi
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| − | * We should point out response rate and paper coverage for community curation
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| − | * How long can we expect to complete curation for phenotype with current pipelines
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| − | * Can request PIs to check coverage of their allele phenotypes
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| − | * We want this to lead to development of pathways
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| − | | |
| − | === The Allied Genetics Conference, Orlando, July 2016 ===
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| − | * WB needs to decide who will go
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| − | * Intermine project will have their own room
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| − | * MODs will present together
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| − | | |
| − | | |
| − | == January 28, 2016 ==
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| − | | |
| − | === SAB talks ===
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| − | * Literature curation overview
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| − | ** General publication trends for C. elegans and data types
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| − | ** Our coverage, backlogs, outreach and curation efforts
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| − | * Automated paper flagging and data identification (Karen)
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| − | ** SVM pipeline, keyword/string matching, data extraction
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| − | * Automated gene descriptions (Ranjana)
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| − | ** Manual writing doesn't scale (currently ~5000 descriptions)
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| − | ** Amenable to automation (pulling together primary data for descriptions)
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| − | ** Mention gene description form
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| − | * Community annnotation numbers (Mary Ann & Chris)
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| − | ** Other MODs efforts
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| − | ** WB submission forms and pilot response rates
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| − | * Micropublications
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| − | ** Incentivizing community contributions
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| − | ** Micropublication form
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| − | ** How data is displayed on WormBase
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| − | * LEGO
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| − | ** What it is, how it's different, why it's important
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| − | ** Priorities for LEGO models: signaling pathways, development, human disease biology (signal transduction, cilia pathology, etc.)
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| − | * SObA
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| − | ** WB uses ontologies extensively, many annotations
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| − | ** Need an easy-to-consume data display
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| − | ** Have WOBr
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| − | ** Convention is to provide list format of data display, e.g. mouse expression summary
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| − | ** SObA: intuitive summary view of ontology annotations from gene perspective
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| − | ** Ontology trimmed to display only relevant ontology terms
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| − | * What do we not have a talk about:
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| − | ** Human disease curation
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| − | ** SPELL/modSeek
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| − | ** Metabolite curation
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| − | * Google Doc: https://docs.google.com/document/d/1uvSIIecWTmVjhUPA8f4FHIECSTJhloy8Z2ocujx96Uw/edit
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