Previous Years

2016 Meetings

January

February

March

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?

WormBase-Caltech Weekly Calls

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