Difference between revisions of "WormBase-Caltech Weekly Calls"

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== July 5, 2018 ==
=== Community Curation Mass Email update ===
* Emails (1 per paper) sent (most batches 75 at a time): 3,227 total
** June 11: 5
** June 20: 15
** June 21: 82
** June 22: 6
** June 25: 75
** June 26: 80
** June 28: 363
** June 29: 600
** June 30: 300
** July 1: 450
** July 2: 1,251
** Email success rate:
*** 482 emails bounced (15%)
**** 74 bounced emails had a backup email (2%)
**** 292 bounced emails had no backup (12%)
**** 88% of emails were successfully sent
*** 52 out of office replies (2%)
* Total community annotations received since June 11: 718 (115 papers)
** June 13: 24 (3 papers)
** June 14: 8 (3 papers)
** June 17: 1 (1 paper)
** June 20: 13 (3 papers)
** June 21: 13 (4 papers)
** June 25: 13 (4 papers)
** June 26: 20 (7 papers)
** June 28: 17 (8 papers)
** June 29: 131 (8 papers)
** June 30: 4 (2 papers)
** July 1: 24 (5 papers)
** July 2: 184 (36 papers)
** July 3: 179 (20 papers)
** July 4: 27 (9 papers)
** July 5: 62 (pre-meeting) (4 papers)
* We may want to give people the option to "opt-out" either for a paper or for all emails or both
* May be good to ask SAB and users at meetings how they feel about these email requests
* Is it worthwhile to send requests about same paper to same people after a wait period?
=== SAB Literature Curation overview ===
* Outline: https://docs.google.com/document/d/1OUHoFYC3deEmZvgzmOtmxpt5iBrVio9sAZG66kRHwsE/edit?usp=sharing
* Want to ask about:
** Data type history, current types, priorities going forward?
** Community curation? Pilot results, should we expand?
** Data type vs. topic-based curation?
** Val Wood and PomBase have found topic-based curation to be more efficient
* Alliance working groups:
** data type focused
** Has affected our curation approach
=== WS267 Citace upload ===
* July 20th, upload to Hinxton
* July 17th, local CIT upload
=== Model changes ===
* Some minor tag name changes
* Changes to GO_annotation to accommodate RO terms
=== Curation Status Form: flagged vs. validated papers ===
* Papers validated by curators are not necessarily considered flagged
* Author first pass forms: prepopulated with SVM, string-matches
* Curation First Pass: are forms still used?
* TFP (Textpresso first pass) not currently used?
== July 19, 2018 ==
=== PomBase SObA ===
* Val Wood would be interested in using SObA for PomBase
* Some immediate action items to deal with for expanding SObA to other ontologies and databases
* Maybe highlight leaf nodes with more granular information? Already available in unweighted view
=== Outreach ===
* SAB suggested continuing site visits for WormBase tutorials
* SAB suggested host institution provide funds; we can at least ask
== July 26th, 2018 ==
=== Temporarily Withdrawn Paper (WBPaper00054672) ===
*A recently epublished Genetics paper (2018 Jun 26)  "...has been temporarily removed at the authors' request, to allow review of a companion article. The article 301078 will appear in a future issue of GENETICS."
*We already have the PDF in postgres (as of 2018-07-10), but I don't see the paper in TPC or the curation status form.
*Is there anything we should do here? Temporarily remove the PDF from postgres?
** Remove entirely and get new paper from scratch? OK
=== Expression display on the anatomy page ===
* Suggested last week to have a way to display genes and associated evidences on the anatomy page. Rank order by number of evidences.
* Mock here: https://docs.google.com/presentation/d/1HE_QhJrs5oScmORdiAAdTxfavAnF6NUQhtJGWvcC7EQ/edit#slide=id.p2
* Consider grouping evidence per gene (Expr_pattern objects)
* Should we apply a weight to each piece of evidence, type of evidence?
** Apply less weight to large scale, e.g. RNAseq data?
* Users likely want to know confidence of presence/absence call as well as degree of specificity
* Need to consider methods used: Single-cell RNAseq of pool of cell types IDed by sequencing may not be as reliable an annotation to a specific cell, cell type or tissue; but single-cell RNAseq from physically isolated cells based on marker/reporter expression may be more reliable
* We will first rank-order the list based on genes with a higher number of Expr_pattern objects
=== SAB Follow Up ===
*SAB Report (Paul sent around a Word doc)
=== Noctua ===
* Can import annotations, but can't edit them and resubmit them; essentially read-only
* Possibility of micropublishing a Noctua model
=== Picture curation ===
* Marie-Claire started picture curation with Daniela
* Jae reported that Simon James at Florey Institute of Neuroscience and Mental Health, Australia wants to submit many images (some published, some not)
=== Asian-Pacific Worm Meeting ===
* 200+ attendees, mostly grad students, post docs, PIs
* Complaining about connection speed; wondering when is the busiest time/highest traffic time, so they can avoid traffic? Will talk to Todd
** Is this mostly users from China? Could it be a firewall issue? Seems to be all people from China, Japan, Korea, Australia, etc.
** Can we set up a VPN to do remote response testing?
** Can we login to a remote network (with permission) and test the WB site?
* Some widgets, e.g. Location or Interactions, often throwing time-out errors; possibly due to too much data
** What pages in particular? How frequently?
* Some people feel that JBrowse is slower than GBrowse
* People asking about essential genes in N2? Other strains? Other species? Junho Lee asked
** Have a Postgres query to get a table of most considerations, but have to perform locally and send out table to users
** Long term solution is implementation of ?Phenotype_experiment/?Phenotype_annotation class to query out a table
* Gene descriptions sometimes inaccurate and/or public gene names in description inconsistent with current website display of public name
* GO terms seem confusing or possibly redundant with other terms; good to get this feedback to GO
* Micropublications:
** What is the minimum requirement for micropublication? Each submission reviewed manually now; range of submission types
** Can the data be reusable in other publications? Can be cited, but not republished as novel finding
** Index by PubMed; working on it now; have ISSN from Library of Congress; working towards PubMed indexing
** Impact factor? Cannot know until it's in PubMed and citations are accumulated
** Plan is to expand to other species; store data in a repository, especially for species without an existing repository; could create a generic repository at AGR
** People in other fields/working in other species, encourage reaching out to micropub team
* Questions about WB/AGR interactions:
** Will WormBase still be around after AGR? Yes, but perhaps integrated into the AGR portal/site eventually
* Will WB be free forever? People know that FlyBase is asking for donations
** Current funding mechanism does not allow WB to charge
* Suggestions:
** People find WormMine difficult to use; would like step-by-step tutorial, possibly video tutorials
*** Pointed users to WormBase YouTube channel
** Data submission:
*** Junho Lee: de-novo genome assembly of Hawaiian strain; found interesting data, would like to submit (should discuss with Kevin Howe)
*** Image set to submit (Simon James, see above)
* People were happy to see a WormBase curator at the meeting; would like to see WB curator at next meeting again
** Next Asia meeting in Hong Kong in 2 years

Revision as of 14:41, 2 August 2018