Difference between revisions of "WormBase-Caltech Weekly Calls"

From WormBaseWiki
Jump to navigationJump to search
 
(225 intermediate revisions by 8 users not shown)
Line 18: Line 18:
  
 
[[WormBase-Caltech_Weekly_Calls_2018|2018 Meetings]]
 
[[WormBase-Caltech_Weekly_Calls_2018|2018 Meetings]]
 +
 +
[[WormBase-Caltech_Weekly_Calls_2019|2019 Meetings]]
  
  
 
GoToMeeting link: https://www.gotomeet.me/wormbase1
 
GoToMeeting link: https://www.gotomeet.me/wormbase1
  
 +
= 2020 Meetings =
  
= 2019 Meetings =
+
== January 9, 2020 ==
 
 
[[WormBase-Caltech_Weekly_Calls_January_2019|January]]
 
 
 
[[WormBase-Caltech_Weekly_Calls_February_2019|February]]
 
 
 
[[WormBase-Caltech_Weekly_Calls_March_2019|March]]
 
 
 
[[WormBase-Caltech_Weekly_Calls_April_2019|April]]
 
  
[[WormBase-Caltech_Weekly_Calls_May_2019|May]]
+
=== Phenotype Curation Requests ===
 +
* 1,229 emails sent Dec 3-6, 2019
 +
* Received 194 annotations from 40 papers and from 37 distinct community curators
 +
** 37 papers requested, 3 additional papers annotated
 +
** 104 Phenotype OA annotations (from 27 papers; 25 distinct curators)
 +
** 90 RNAi OA annotations (from 20 papers; 19 distinct curators)
 +
* 43 bounced emails
 +
** 2 resent to new addresses
 +
** 5 have backup email addresses (also sent)
  
 +
=== Worm Area Meetings ===
 +
* Chris has (re)requested slots for WormBase for the Worcester Area Worm Meeting and the Boston Area Worm Meeting
 +
* Will update group if/when a slot is assigned (probably not until Fall 2020 at the earliest)
  
== June 6, 2019 ==
+
=== Reference widget Textpresso linkouts ===
 +
* Now live on WormBase, WS274
 +
* [https://github.com/WormBase/website/issues/7347 GitHub ticket]
 +
* Applies to the following classes: genes, strains, variations, transgenes, constructs, anatomy terms, clones, life stages, rearrangements, molecules, processes
 +
* Gene example: https://wormbase.org/species/c_elegans/gene/WBGene00022861#0d--10
 +
* Strain example: https://wormbase.org/species/c_elegans/strain/WBStrain00004309#05--10
 +
* Variation example: https://wormbase.org/species/c_elegans/variation/WBVar00248884#08--10
 +
* Transgene example: https://wormbase.org/species/all/transgene/WBTransgene00004654#04--10
 +
** Known issue: searching on synonyms in addition to public name; Sibyl will fix
 +
* Construct example: https://wormbase.org/species/all/construct/WBCnstr00023113#03--10
 +
** Known issue: not working now; need to only search on public name when available, not on summary; Sibyl will fix
 +
* Anatomy term example: https://wormbase.org/species/all/anatomy_term/WBbt:0005772#05--10
 +
** Known challenge: "Psub1" will essentially never match the intended target and "P1" may find the embryonic cell or the postembryonic cell
 +
* Clone example: https://wormbase.org/species/c_elegans/clone/W02C12#03--10
 +
* Life stage example: https://wormbase.org/species/all/life_stage/WBls:0000038#03--10
 +
** Known challenge: "L4 larva Ce" will never match; "L4 larva" maybe; but "L4" alone will not unless a synonym
 +
* Rearrangement example: https://wormbase.org/species/all/rearrangement/sDp3#03--10
 +
* Molecule example: https://wormbase.org/resources/molecule/WBMol:00003650#03--10
 +
* Process examples:
 +
** https://wormbase.org/resources/wbprocess/WBbiopr:00000001#09--10
 +
** https://wormbase.org/resources/wbprocess/WBbiopr:00000079#09--10
 +
* Michael has improved phrase search and combined supplemental documents with main paper documents; should roll out soon
  
=== New SObA graphs ===
+
=== WS276 Citace upload ===
* May put graphs within existing widgets, but don't need to rush to get that ready for IWM
+
* Hinxton upload Jan 31, 2020
 +
* Citace upload on Tuesday, Jan 28, 2020
  
=== Phenotype association file format ===
+
=== Author First Pass paper ===
* May be best to leave the format as is
+
* AFP resent to Database
* There are problems; paper IDs keep switching columns
+
* Automated descriptions about to be sent
* Would need to revisit the reasoning for why we do it that way
+
* SObA, write for micropub? One micropub on SObA and another on comparative SObA
* When will the Alliance produce a similar/replacement file? Not sure
 
  
=== Phenotype requests ===
+
=== Noctua/GO-CAM ===
* Sent out 1140 emails on May 30
+
* New version of the Noctua form released next week
* Since have received 374 annotations from 54 papers (42 requested, 12 additional)
+
* Imports from WormBase?
* 21 papers flagged as not having phenotypes
+
** Big push in coming months will be to pull in all manual annotations from WB into Noctua (on track)
* Of 1140 papers emailed about, 35 emails bounced, and have received some flagging or curation on 63 (63/1105 = ~6% response rate), in first week
+
** Need to work on annotation history on back end
 +
** May have face-to-face meeting in Pasadena
  
 +
=== Variation curation ===
 +
* Have a backlog; Paul D is assigned but has been overwhelmed
 +
* Have asserted this as a priority
 +
* We have the allele-sequence form; where does it go? Hinxton
 +
* Need to get allele/variation data in an Alliance-submission friendly form and pull it into the Alliance
 +
* Need to integrate curation with the Variant Effect Predictor (VEP) pipeline
  
== June 13, 2019 ==
+
=== Topic meetings ===
 +
* Asia (Taipei) meeting, Paul S going
 +
* Aging meeting, Wen could go? (Wen: I can ask if they provide a timeslot for oral presentation.)
 +
* TAGC in April, Chris going
  
=== IWM ===
 
* Coordinating transportation of swag boxes to Pauley Pavilion
 
* Workshop on Saturday June 22, from 1pm to 2:30pm
 
* Saturday morning micropublication breakfast 7:30 - 8:30am
 
* Workshop
 
** Presenters: it may be best to present as use cases rather than a research project
 
** Chris will cover SimpleMine for Wen
 
** Chris: won't do live demo; only screenshots, maybe some video
 
* Paul's lab will do marathon bibs to show lab affiliation and graphical abstract
 
* Paul's talk
 
** Cover Alliance
 
** New features
 
*** SObA (for new data)
 
*** Complete for protein-protein interactions
 
*** RNASeq tools
 
*** Updated automated gene concise descriptions?
 
** Phenotype community curation
 
*** Chris will send Paul numbers on: top community curators, overall stats (number of annotations, papers, curators)
 
** Author First Pass
 
** Micropublication
 
  
=== SGD SAB ===
+
== January 16, 2020 ==
* Paul attended
 
* Alliance publicity was discussed
 
* SAB likes the Alliance orthology features
 
* Working on topics: displaying papers and data
 
* Pathways: discussion about best approach
 
* Metabolic engineering
 
* Meta data about RNASeq data
 
** SPELL tool, basically only tool of its kind available; need new tools
 
* Species-specific proteins: how best to find them? HMMs (Jackhammer)?
 
  
=== Concise descriptions ===
+
=== Variation names ===
* Progress being made within the Alliance to update the automated concise gene descriptions
+
* Daniela entered a new allele name (tkTi1) in the temporary allele form CGI but it prompted an error: tkTi1 does not match 1 or 2 sets of 1-3 letters and 1-6 digits
.
* We will still accept manually written descriptions and display them in parallel with automated descriptions
+
* Daniela asked Juancarlos to modify the temporary variation ID form to allow up to 4 letters instead of 3.
 +
* Form here: http://tazendra.caltech.edu/~azurebrd/cgi-bin/forms/generic.cgi?action=TempVariationObo
 +
* From the nomenclature guidelines: Newly generated Transposon insertions, especially those located in apparently intergenic regions, may also be given Ti (transposon insertion) names. These consist of the designation identifying the laboratory of origin, the two letters Ti, and a number, all italicized. Example: eTi13 is an insertion of a Mos transposon into an intergenic region on LGIII.
 +
* We will wait for Paul D/Tim response and act accordingly
 +
* for now the CGI has been changed to allow 4 letters, we will revert if need be
  
=== Micropubs ===
+
=== Webinars ===
* If people are requesting manually written gene descriptions, they could submit a microreview
+
* During an AFP call we discussed the possibility to have webinars for authors to guide them through the form.
* Concern was expressed about how to handle a really high throughput of submissions:
+
* Is having a webinar series something WB is interested in doing?
** Daniela: Working towards automating as much of the processing pipeline as possible
+
** we will start with an AFP/micropub webinar and will take it from there based on interest and attendance
** Raymond: The throughput will be handled appropriately depending on demand; priority scheme will help
 
** Not getting lots of submissions yet, probably won't be inundated in the near future
 
** Karen: tools are still being developed; the platform is not being advertised as much as it could be; will ramp up outreach and communication once tools are in place to handle more submissions
 
* Karen: micropub team will reach out to curators to help build submission forms for respective data types
 

Latest revision as of 20:05, 16 January 2020

Previous Years

2009 Meetings

2011 Meetings

2012 Meetings

2013 Meetings

2014 Meetings

2015 Meetings

2016 Meetings

2017 Meetings

2018 Meetings

2019 Meetings


GoToMeeting link: https://www.gotomeet.me/wormbase1

2020 Meetings

January 9, 2020

Phenotype Curation Requests

  • 1,229 emails sent Dec 3-6, 2019
  • Received 194 annotations from 40 papers and from 37 distinct community curators
    • 37 papers requested, 3 additional papers annotated
    • 104 Phenotype OA annotations (from 27 papers; 25 distinct curators)
    • 90 RNAi OA annotations (from 20 papers; 19 distinct curators)
  • 43 bounced emails
    • 2 resent to new addresses
    • 5 have backup email addresses (also sent)

Worm Area Meetings

  • Chris has (re)requested slots for WormBase for the Worcester Area Worm Meeting and the Boston Area Worm Meeting
  • Will update group if/when a slot is assigned (probably not until Fall 2020 at the earliest)

Reference widget Textpresso linkouts

WS276 Citace upload

  • Hinxton upload Jan 31, 2020
  • Citace upload on Tuesday, Jan 28, 2020

Author First Pass paper

  • AFP resent to Database
  • Automated descriptions about to be sent
  • SObA, write for micropub? One micropub on SObA and another on comparative SObA

Noctua/GO-CAM

  • New version of the Noctua form released next week
  • Imports from WormBase?
    • Big push in coming months will be to pull in all manual annotations from WB into Noctua (on track)
    • Need to work on annotation history on back end
    • May have face-to-face meeting in Pasadena

Variation curation

  • Have a backlog; Paul D is assigned but has been overwhelmed
  • Have asserted this as a priority
  • We have the allele-sequence form; where does it go? Hinxton
  • Need to get allele/variation data in an Alliance-submission friendly form and pull it into the Alliance
  • Need to integrate curation with the Variant Effect Predictor (VEP) pipeline

Topic meetings

  • Asia (Taipei) meeting, Paul S going
  • Aging meeting, Wen could go? (Wen: I can ask if they provide a timeslot for oral presentation.)
  • TAGC in April, Chris going


January 16, 2020

Variation names

  • Daniela entered a new allele name (tkTi1) in the temporary allele form CGI but it prompted an error: tkTi1 does not match 1 or 2 sets of 1-3 letters and 1-6 digits
.
  • Daniela asked Juancarlos to modify the temporary variation ID form to allow up to 4 letters instead of 3.
  • Form here: http://tazendra.caltech.edu/~azurebrd/cgi-bin/forms/generic.cgi?action=TempVariationObo
  • From the nomenclature guidelines: Newly generated Transposon insertions, especially those located in apparently intergenic regions, may also be given Ti (transposon insertion) names. These consist of the designation identifying the laboratory of origin, the two letters Ti, and a number, all italicized. Example: eTi13 is an insertion of a Mos transposon into an intergenic region on LGIII.
  • We will wait for Paul D/Tim response and act accordingly
  • for now the CGI has been changed to allow 4 letters, we will revert if need be

Webinars

  • During an AFP call we discussed the possibility to have webinars for authors to guide them through the form.
  • Is having a webinar series something WB is interested in doing?
    • we will start with an AFP/micropub webinar and will take it from there based on interest and attendance