WormBase-Caltech Weekly Calls
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Contents
Previous Years
2016 Meetings
November 17, 2016
- lineage tool good for featuring in AGR
- 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
- SGD moving spell to the cloud, and will give us an amazon image, into which we will be able to load WB data
- Caltech has an amazon cloud already for use for SPELL, but not enough for all our data
- SPELL built locally on textpresso, once built, data loaded up; users download a lot
- Post GO meeting
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
- Strain requests will be sent from disease OA to Mary Ann
- Strains included in nightly_genace.pl
- Next Thursday = Thanksgiving
- AGR meeting Dec 6, Paul S.
November 3, 2016
Micropublication update
- First Nemametrix micro in for WS257
- Two lined up for WS258
- Karen and Daniela in touch with e-publishing platforms (HighWire [1], Collaborative knowledge foundation[2]), to set up collaborations for the Micropublication: biology e-journal [3]
- Discussing putting worm breeder's gazette articles into micropublications
- Collaborative knowledge foundation is a non-profit publisher, some former member of Highwire
- Would be good to have a faster way to display micropublications (standard WB pipeline needs at least 4 months)
- Could use content management systems (CMSs)
- Maybe will propose a workshop for the 2017 international C. elegans meeting
Intellectual (Person) Lineage
- Example page: http://tazendra.caltech.edu/~azurebrd/cgi-bin/forms/worm_lineage.cgi?action=lineage&twonumber=two363
- Example: http://tazendra.caltech.edu/~azurebrd/cgi-bin/forms/worm_lineage.cgi?action=lineage&twonumber=two625
- Still a stand alone page
- Will make live once incorporated feedback
- Will display as widget on a WBPerson page
- May want to display or point to the lineage display on WB homepage
- Data relies on self-reporting connections
- Not entirely clear what the direction of the arrows means
- Can click and hold on a node to open up the graph for that person
- Help documentation still needs to be written up
Tim Schedl visiting WB tomorrow
- Will come to WB CIT around 11:30am
November 10, 2016
Update from AGR portal use case working group
- Preparing document for the Dec. 6th leadership meeting
- Need to address several questions about prototype development process
- Communication has been insufficient, leading to a lag in use case implementation and possibly off-target expectations
- Working group would like to know:
- What are the boundaries of responsibility for the use case working group?
- Will there be a data integration working group to collect data as required for a use case?
- What group or groups does the use case working group need to hand off tasks to?
- What overall decisions about technologies need to be made about AGR before implementing use cases?
- Working on an idea to show comparisons between transcript and protein isoforms
- Would be great to be able to have a common display of phenotypes, using a ribbon-style and a standard ontology slim
Person Lineage graph
- current view Low complexity person, High complexity person
- ~31,000 orphans in DB; ~14,000 orphans with an email address
- Do we need to distinguish between "real" WB people and those simply created as a co-author?
- Will email ~14,000 people to ask them to provide person connections
Micropublications
- Karen and Daniela spoke to person at HighWire
- Working on publication platform, getting cost estimates
- Met with people at Collaborative Knowledge Foundation
- Similar in scope to HighWire, but have more modern software
- Will probably write a grant together with Collaborative Knowledge Foundation
- Also planning to apply for a Big Data to Knowledge grant
- Added two pubications from nemametrix, adding one more today
- Need a window of time to handle submissions given the turn around time for reviewers
- "Data not shown" references could be handled as micropublication
- Tim Schedl suggested doing a workshop at the 2017 IWM for micropublications
- The Future of Scholarly Communication
- Who else would be involved? GSA (WormBook, G3)? JoVE?
Wild isolate library (Erik Anderson)
- CeNDR (C. elegans Natural Diversity Resource)
- https://elegansvariation.org/
- Want to have links out to their database from WormBase
- WormBase already has 250 strains; many more that are not in WB
- Has 342 strains in total
- They would like to have integrated views of their database in WB; may be too difficult to have an integrated view
- WB will take in all of their strains
- CGC has most but not all of their strains
- Can discuss on next WB site-wide call
WormBase IWM Workshop
- Ranjana will send in a workshop proposal
2017 IWM
- What do we want to communicate/emphasize about WormBase at the 2017 IWM?
- Maybe explain and discuss AGR; what it means to our users
- What do we want to ask our user community for?