Difference between revisions of "WormBase-Caltech Weekly Calls"
From WormBaseWiki
Jump to navigationJump to searchLine 162: | Line 162: | ||
** Index by PubMed; working on it now; have ISSN from Library of Congress; working towards PubMed indexing | ** 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 | ** 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 |
Revision as of 18:49, 26 July 2018
Previous Years
GoToMeeting link: https://www.gotomeet.me/wormbase1
2018 Meetings
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%)
- 482 emails bounced (15%)
- 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)
Asia 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