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| | [[WormBase-Caltech_Weekly_Calls_October_2016|October]] | | [[WormBase-Caltech_Weekly_Calls_October_2016|October]] |
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| | + | [[WormBase-Caltech_Weekly_Calls_November_2016|November]] |
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| − | == November 3, 2016 ==
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| − | === Micropublication update === | + | == December 1, 2016 == |
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| − | * First Nemametrix micro in for WS257
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| − | * Two lined up for WS258
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| − | * Karen and Daniela in touch with e-publishing platforms (HighWire [http://home.highwire.org], Collaborative knowledge foundation[http://coko.foundation]), to set up collaborations for the Micropublication: biology e-journal [http://www.micropublicationbiology.org]
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| − | * Discussing putting worm breeder's gazette articles into micropublications
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| − | * Collaborative knowledge foundation is a non-profit publisher, some former member of Highwire
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| − | * Would be good to have a faster way to display micropublications (standard WB pipeline needs at least 4 months)
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| − | ** Could use content management systems (CMSs)
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| − | * Maybe will propose a workshop for the 2017 international ''C. elegans'' meeting
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| − | | |
| − | === Intellectual (Person) Lineage ===
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| − | * Example page: http://tazendra.caltech.edu/~azurebrd/cgi-bin/forms/worm_lineage.cgi?action=lineage&twonumber=two363
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| − | * Example: http://tazendra.caltech.edu/~azurebrd/cgi-bin/forms/worm_lineage.cgi?action=lineage&twonumber=two625
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| − | * Still a stand alone page
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| − | * Will make live once incorporated feedback
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| − | * Will display as widget on a WBPerson page
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| − | * May want to display or point to the lineage display on WB homepage
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| − | * Data relies on self-reporting connections
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| − | * Not entirely clear what the direction of the arrows means
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| − | * Can click and hold on a node to open up the graph for that person
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| − | * Help documentation still needs to be written up
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| − | | |
| − | === Tim Schedl visiting WB tomorrow ===
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| − | * Will come to WB CIT around 11:30am
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| − | | |
| − | == November 10, 2016 ==
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| − | | |
| − | === Update from AGR portal use case working group ===
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| − | * Preparing document for the Dec. 6th leadership meeting
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| − | * Need to address several questions about prototype development process
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| − | * Communication has been insufficient, leading to a lag in use case implementation and possibly off-target expectations
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| − | * Working group would like to know:
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| − | ** What are the boundaries of responsibility for the use case working group?
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| − | ** Will there be a data integration working group to collect data as required for a use case?
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| − | ** What group or groups does the use case working group need to hand off tasks to?
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| − | ** What overall decisions about technologies need to be made about AGR before implementing use cases?
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| − | * Working on an idea to show comparisons between transcript and protein isoforms
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| − | * Would be great to be able to have a common display of phenotypes, using a ribbon-style and a standard ontology slim
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| − | | |
| − | === Person Lineage graph ===
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| − | * current view [http://juancarlos.wormbase.org/resources/person/WBPerson363#02--10 Low complexity person], [http://juancarlos.wormbase.org/resources/person/WBPerson625#02--10 High complexity person]
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| − | * ~31,000 orphans in DB; ~14,000 orphans with an email address
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| − | * Do we need to distinguish between "real" WB people and those simply created as a co-author?
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| − | * Will email ~14,000 people to ask them to provide person connections
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| − | | |
| − | === Micropublications ===
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| − | * Karen and Daniela spoke to person at HighWire
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| − | * Working on publication platform, getting cost estimates
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| − | * Met with people at Collaborative Knowledge Foundation
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| − | * Similar in scope to HighWire, but have more modern software
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| − | * Will probably write a grant together with Collaborative Knowledge Foundation
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| − | * Also planning to apply for a Big Data to Knowledge grant
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| − | * Added two pubications from nemametrix, adding one more today
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| − | * Need a window of time to handle submissions given the turn around time for reviewers
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| − | * "Data not shown" references could be handled as micropublication
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| − | * Tim Schedl suggested doing a workshop at the 2017 IWM for micropublications
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| − | ** The Future of Scholarly Communication
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| − | ** Who else would be involved? GSA (WormBook, G3)? JoVE?
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| − | | |
| − | === Wild isolate library (Erik Anderson) ===
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| − | * CeNDR (C. elegans Natural Diversity Resource)
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| − | * https://elegansvariation.org/
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| − | * Want to have links out to their database from WormBase
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| − | * WormBase already has 250 strains; many more that are not in WB
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| − | * Has 342 strains in total
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| − | * They would like to have integrated views of their database in WB; may be too difficult to have an integrated view
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| − | * WB will take in all of their strains
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| − | * CGC has most but not all of their strains
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| − | * Can discuss on next WB site-wide call
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| − | | |
| − | === WormBase IWM Workshop ===
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| − | * Ranjana will send in a workshop proposal
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| − | | |
| − | === 2017 IWM ===
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| − | * What do we want to communicate/emphasize about WormBase at the 2017 IWM?
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| − | * Maybe explain and discuss AGR; what it means to our users
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| − | * What do we want to ask our user community for?
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| − | | |
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| − | == November 17, 2016 ==
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| − | *lineage tool good for featuring in AGR
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| − | *AGR curator call - SGD simpler, fewer datatype, impressed with triaging and organization of paper curation prioritization, curation is paper-by-paper, author response form is minimal - no specific author comments captured, just check boxes
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| − | *SGD moving spell to the cloud, and will give us an amazon image, into which we will be able to load WB data
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| − | *Caltech has an amazon cloud already for use for SPELL, but not enough for all our data
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| − | *SPELL built locally on textpresso, once built, data loaded up; users download a lot
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| − | | |
| − | *Post GO meeting
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| − | Pascal, David Hill and Kimberly piloting a pathway annotation - looking at PAINT annotations to create templates for curation of the signaling pathway in NOCTUA and look for ontology and other issues that need to be addressed - using the TOR pathway, will be useful in the AGR
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| − | | |
| − | *Strain requests will be sent from disease OA to Mary Ann
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| − | *Strains included in nightly_genace.pl
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| − | | |
| − | *Next Thursday = Thanksgiving
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| − | *AGR meeting Dec 6, Paul S.
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