WormBase-Caltech Weekly Calls March 2019
- 1 March 7, 2019
- 2 March 21, 2019
- 3 March 28, 2019
March 7, 2019
- Still haven't heard back from organizers yet
- Think of ideas for the meeting
- Local upload to Spica is Tuesday, March 12th, 10am Pacific
Trustworthy data repositories workshop
- Chris will go to NIH, April 8 and 9
- To discuss trustworthiness standards for data repositories
March 21, 2019
IWM 2019 workshop
- Start with gene page, that's when you have a single gene --Kimberly
- Then go on to data mining, for multiple genes--SimpleMine, WormMine, Parasite BioMart etc --Wen and Chris
- Then you can also visualize data with these tools-WoBR, SoBA, etc
- If you are interested in other species, find cross-species data at the Alliance --Ranjana
- Help us curate your data! End with community curation-New Author First pass form, community curation forms--Daniela
I think we have a good flow here, can keep thinking about this. Ranjana will shorten abstract and submit final list first week of April.
IWM 2019 swag ideas
- WormBase sticker
- Micropub folks have done stickers, in Paul's office, take a look
- Daniela will look into this, pricing and time
- Gary's ideas:
- Screen cleaning cloths with community curation theme on them, he will send around the picture
- Water bottles for the top community curators
- Fidget spinners, with the WB picture in the middle
- Gary will talk to Daniel to see if he can help with finding sellers/prices
We could do them all , a mixture, depending on the budget, need to ask Paul S. what the budget is for IWM swag
March 28, 2019
Textpresso Central vs Old Textpresso site
- A search for "SimpleMine" got 1 paper in TPC, 5 papers in the old site.
- A search for "alg-5" in TPC got 6 hits but the first two were redundant. The result missed pmid29927939 that was found by the old site.
- A search for allele "ev673" in TPC returns no results, but expected paper (PMID:24004945 / WBPaper00044133) returned in old site.
- TPC is undergoing an update to the paper pipeline
- Individual issues should be entered in GitHub tracker
- Duplicates result from XML vs PDF documents (should probably be merged somehow), as well as supplementals
Protein-protein interactions up-to-date
- We should post an announcement to the community
- Could ask for feedback if any authors are aware of anything missing
- Can Wen mention (at small RNA meeting) that micropub representatives can do site visits to discuss micropubs?
Allele display on gene pages
- Some have expressed that the display could be better
- We will need some specific feedback
- We had made several changes to isolate phenotypic alleles from non-phenotypic alleles
- Screen cloths/cleaners? preferred option; order ~2,000
- Stickers also? maybe not
- Shot glasses (40-50 remaining)? Specific prizes for top community curators?
- Left over WB bags (not high quality; maybe don't bother)
Help desk enrichment analysis
- David (now postdoc at MIT) helped respond to user question; will eventually need to maintain without David
- Should migrate enrichment analysis to Alliance (although ontologies not aligned yet)
- Design requires decisions for tuning; some may not be obvious to users
- Could allow curator or user to tune parameters? What are the statistical arguments?
- We could try to simplify the current maintenance to make it easier to manage parameters in-house
- Would be good to take advantage of WB person/author data to pull out list of collaborators for a given person/author
- Should that be time/data interval restricted/specified? Just be inclusive and user/author can edit/trim as needed
- Pedigree vs. collaborators analysis?