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| | [[WormBase-Caltech_Weekly_Calls_June_2018|June]] | | [[WormBase-Caltech_Weekly_Calls_June_2018|June]] |
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| − | | + | [[WormBase-Caltech_Weekly_Calls_July_2018|July]] |
| − | == July 5, 2018 ==
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| − | | |
| − | === Community Curation Mass Email update ===
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| − | * Emails (1 per paper) sent (most batches 75 at a time): 3,227 total
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| − | ** June 11: 5
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| − | ** June 20: 15
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| − | ** June 21: 82
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| − | ** June 22: 6
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| − | ** June 25: 75
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| − | ** June 26: 80
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| − | ** June 28: 363
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| − | ** June 29: 600
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| − | ** June 30: 300
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| − | ** July 1: 450
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| − | ** July 2: 1,251
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| − | ** Email success rate:
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| − | *** 482 emails bounced (15%)
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| − | **** 74 bounced emails had a backup email (2%)
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| − | **** 292 bounced emails had no backup (12%)
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| − | **** 88% of emails were successfully sent
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| − | *** 52 out of office replies (2%)
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| − | * Total community annotations received since June 11: 718 (115 papers)
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| − | ** June 13: 24 (3 papers)
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| − | ** June 14: 8 (3 papers)
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| − | ** June 17: 1 (1 paper)
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| − | ** June 20: 13 (3 papers)
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| − | ** June 21: 13 (4 papers)
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| − | ** June 25: 13 (4 papers)
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| − | ** June 26: 20 (7 papers)
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| − | ** June 28: 17 (8 papers)
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| − | ** June 29: 131 (8 papers)
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| − | ** June 30: 4 (2 papers)
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| − | ** July 1: 24 (5 papers)
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| − | ** July 2: 184 (36 papers)
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| − | ** July 3: 179 (20 papers)
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| − | ** July 4: 27 (9 papers)
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| − | ** July 5: 62 (pre-meeting) (4 papers)
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| − | * We may want to give people the option to "opt-out" either for a paper or for all emails or both
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| − | * May be good to ask SAB and users at meetings how they feel about these email requests
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| − | * Is it worthwhile to send requests about same paper to same people after a wait period?
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| − | | |
| − | === SAB Literature Curation overview ===
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| − | * Outline: https://docs.google.com/document/d/1OUHoFYC3deEmZvgzmOtmxpt5iBrVio9sAZG66kRHwsE/edit?usp=sharing
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| − | * Want to ask about:
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| − | ** Data type history, current types, priorities going forward?
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| − | ** Community curation? Pilot results, should we expand?
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| − | ** Data type vs. topic-based curation?
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| − | ** Val Wood and PomBase have found topic-based curation to be more efficient
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| − | * Alliance working groups:
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| − | ** data type focused
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| − | ** Has affected our curation approach
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| − | | |
| − | === WS267 Citace upload ===
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| − | * July 20th, upload to Hinxton
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| − | * July 17th, local CIT upload
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| − | | |
| − | === Model changes ===
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| − | * Some minor tag name changes
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| − | * Changes to GO_annotation to accommodate RO terms
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| − | | |
| − | === Curation Status Form: flagged vs. validated papers ===
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| − | * Papers validated by curators are not necessarily considered flagged
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| − | * Author first pass forms: prepopulated with SVM, string-matches
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| − | * Curation First Pass: are forms still used?
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| − | * TFP (Textpresso first pass) not currently used?
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| − | | |
| − | | |
| − | == July 19, 2018 ==
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| − | | |
| − | === PomBase SObA ===
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| − | * Val Wood would be interested in using SObA for PomBase
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| − | * Some immediate action items to deal with for expanding SObA to other ontologies and databases
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| − | * Maybe highlight leaf nodes with more granular information? Already available in unweighted view
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| − | | |
| − | === Outreach ===
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| − | * SAB suggested continuing site visits for WormBase tutorials
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| − | * SAB suggested host institution provide funds; we can at least ask
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| − | | |
| − | == July 26th, 2018 ==
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| − | | |
| − | === Temporarily Withdrawn Paper (WBPaper00054672) ===
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| − | *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."
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| − | *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.
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| − | *Is there anything we should do here? Temporarily remove the PDF from postgres?
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| − | ** Remove entirely and get new paper from scratch? OK
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| − | | |
| − | === Expression display on the anatomy page ===
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| − | * Suggested last week to have a way to display genes and associated evidences on the anatomy page. Rank order by number of evidences.
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| − | * Mock here: https://docs.google.com/presentation/d/1HE_QhJrs5oScmORdiAAdTxfavAnF6NUQhtJGWvcC7EQ/edit#slide=id.p2
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| − | * Consider grouping evidence per gene (Expr_pattern objects)
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| − | * Should we apply a weight to each piece of evidence, type of evidence?
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| − | ** Apply less weight to large scale, e.g. RNAseq data?
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| − | * Users likely want to know confidence of presence/absence call as well as degree of specificity
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| − | * 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
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| − | * We will first rank-order the list based on genes with a higher number of Expr_pattern objects
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| − | | |
| − | === SAB Follow Up ===
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| − | *SAB Report (Paul sent around a Word doc)
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| − | | |
| − | === Noctua ===
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| − | * Can import annotations, but can't edit them and resubmit them; essentially read-only
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| − | * Possibility of micropublishing a Noctua model
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| − | | |
| − | === Picture curation ===
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| − | * Marie-Claire started picture curation with Daniela
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| − | * Jae reported that Simon James at Florey Institute of Neuroscience and Mental Health, Australia wants to submit many images (some published, some not)
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| − | | |
| − | === Asian-Pacific Worm Meeting ===
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| − | * 200+ attendees, mostly grad students, post docs, PIs
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| − | * Complaining about connection speed; wondering when is the busiest time/highest traffic time, so they can avoid traffic? Will talk to Todd
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| − | ** Is this mostly users from China? Could it be a firewall issue? Seems to be all people from China, Japan, Korea, Australia, etc.
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| − | ** Can we set up a VPN to do remote response testing?
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| − | ** Can we login to a remote network (with permission) and test the WB site?
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| − | * Some widgets, e.g. Location or Interactions, often throwing time-out errors; possibly due to too much data
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| − | ** What pages in particular? How frequently?
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| − | * Some people feel that JBrowse is slower than GBrowse
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| − | * People asking about essential genes in N2? Other strains? Other species? Junho Lee asked
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| − | ** Have a Postgres query to get a table of most considerations, but have to perform locally and send out table to users
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| − | ** Long term solution is implementation of ?Phenotype_experiment/?Phenotype_annotation class to query out a table
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| − | * Gene descriptions sometimes inaccurate and/or public gene names in description inconsistent with current website display of public name
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| − | * GO terms seem confusing or possibly redundant with other terms; good to get this feedback to GO
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| − | * Micropublications:
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| − | ** What is the minimum requirement for micropublication? Each submission reviewed manually now; range of submission types
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| − | ** Can the data be reusable in other publications? Can be cited, but not republished as novel finding
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| − | ** Index by PubMed; working on it now; have ISSN from Library of Congress; working towards PubMed indexing
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| − | ** Impact factor? Cannot know until it's in PubMed and citations are accumulated
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| − | ** 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
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| − | ** People in other fields/working in other species, encourage reaching out to micropub team
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| − | * Questions about WB/AGR interactions:
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| − | ** Will WormBase still be around after AGR? Yes, but perhaps integrated into the AGR portal/site eventually
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| − | * Will WB be free forever? People know that FlyBase is asking for donations
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| − | ** Current funding mechanism does not allow WB to charge
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| − | * Suggestions:
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| − | ** People find WormMine difficult to use; would like step-by-step tutorial, possibly video tutorials
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| − | *** Pointed users to WormBase YouTube channel
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| − | ** Data submission:
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| − | *** Junho Lee: de-novo genome assembly of Hawaiian strain; found interesting data, would like to submit (should discuss with Kevin Howe)
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| − | *** Image set to submit (Simon James, see above)
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| − | * People were happy to see a WormBase curator at the meeting; would like to see WB curator at next meeting again
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| − | ** Next Asia meeting in Hong Kong in 2 years
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