Difference between revisions of "WormBase-Caltech Weekly Calls"
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* Stickers, screen cloths? | * Stickers, screen cloths? | ||
* Jessie's design(s)? | * Jessie's design(s)? | ||
− | * Daniel reaching out to Caltech security | + | * Daniel reaching out to Caltech security who has nice screen cloths |
+ | * Print list of WormBase tools or user guide on cloth (one side; logo on the other?)? | ||
+ | * Will get quote | ||
=== Life stage and anatomy ontologies === | === Life stage and anatomy ontologies === |
Revision as of 16:11, 18 April 2019
Previous Years
GoToMeeting link: https://www.gotomeet.me/wormbase1
2019 Meetings
April 4, 2019
Paul's Biocuration Keynote
- At Biocuration keynote, Paul S. will talk about web forms, including Author First Pass form
- Can someone send Paul the latest AFP form location and documentation
- Will also discuss the future of micropublications
IWM Swag
- Stickers vs. screen cloths
- Daniela had contacted Jessie to make new graphic; she's interested, but do we still need a new graphic?
- Plan was to make ~2,000 screen cloths (4x4 inch or 6x6 inch?)
- As for design would be nice to have new design
- Gary had made cartoon for community curation (proposal might be offensive to some)
- Include water bottles for special contributors? In addition to shot glasses?
- Turn around time? ~ 1 month; designs done in April; submit request by mid-May at latest
- Worm in apple graphic? Dragon worm cartooon? Maybe some variation on it?
- We can ask Jessie if she can draw up a couple quick sketch ideas
Collaborators tool
- Juancarlos worked on a tool to extract WBPerson collaborators
- WB staff generally had ~100 collaborators, Paul S has 670
- Distinguish between collaborators and coauthors? Manual (self reported) vs. automatic associations?
- Make modification to ACEDB model?
- Maybe 'collaborators' should be restricted to the laboratory level?
April 11, 2019
Canadian C. elegans meeting
the "Canadian C. elegans meeting” that will follow the 2019 annual conference of the Canadian Society for Molecular Biosciences. The CSMB conference is held at Université de Montréal on June 2-5, 2019 and will focus on Model systems in cancer research (https://www.fourwav.es/view/1174/info/). The C. elegans conference will be held at the CHUM Research Center in downtown Montréal on Thursday June 6, 2019, and will offer opportunities for both oral and poster presentations. The schedule is not finalized yet but it should start around 8:30am and end around 6pm, followed by an apero in a nearby pub. The costs of registrations will depend on the number of participants but will be between 35 and 50 $ per person (it will cover the costs of lunch, coffee break and logistics).
- Karen may be able to go; she will contact Kimberly for any pertinent information
Feedback from small RNA meeting April 3-5, 2019
- Future meeting invitations and summer workshop?
- Dustin Updike - in Maine - interested in running a summer workshop for students
- Maybe one or two week-long (5-10 days); unconfirmed
- Wen followed up with him: WormBase curator could attend and present on JBrowse, scientific writing, micropublications
- Hopefully they can cover travel costs of WB curators
- Dustin will get back to us about details as they emerge
- Julie Claycomb interested in having WB curator at Toronto's worm meeting
New SVM approach
- Michael will send around paper list with new and old results in the same file
- Raymond looked at his data types; at first glance thinks there may be quite a few false positives and false negatives
- Can represent new SVM scores as histograms, presumably produce Gaussian curves, can we accept the overlap in distribution tails?
- Old thresholds were not necessarily gold standards, probably somewhat arbitrarily chosen initially; we can use the old metrics to roughly choose a new set of corresponding thresholds for the new SVM scores
IWM workshop
- On Saturday of meeting
NIH workshop on Trustworthiness
- Chris attended on Monday and Tuesday
- Not quite clear that there is or will be any mandate from funders; just encouragement
- FAIR data and TRUST-worthy repositories
- FAIR = Findable, Accessible, Interoperable, Reusable
- TRUST = Transparency, Responsibility, User community, Sustainability, Technology
- Chris will review briefly at next site-wide call
- Karen: This is something the data commons really wants
- Maybe just need to make sure that the Alliance meets these requirements going forward, not so much for WormBase (?)
April 18, 2019
IWM swag
- Stickers, screen cloths?
- Jessie's design(s)?
- Daniel reaching out to Caltech security who has nice screen cloths
- Print list of WormBase tools or user guide on cloth (one side; logo on the other?)?
- Will get quote
Life stage and anatomy ontologies
- Each ontology now has an ODK GitHub repository (thanks Nico!):
- Anatomy ontology: https://github.com/obophenotype/c-elegans-gross-anatomy-ontology
- Life stage ontology: https://github.com/obophenotype/c-elegans-development-ontology
- We will perform a round of comparisons between the original OBO files and the ODK-generated OBO files
- Will follow up with quality control fixes (e.g. duplicate or missing definitions)