Difference between revisions of "WormBase-Caltech Weekly Calls"

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= 2020 Meetings =
 
= 2020 Meetings =
  
== January 9, 2020 ==
+
[[WormBase-Caltech_Weekly_Calls_January_2020|January]]
  
=== Phenotype Curation Requests ===
+
[[WormBase-Caltech_Weekly_Calls_February_2020|February]]
* 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 ===
+
[[WormBase-Caltech_Weekly_Calls_March_2020|March]]
* 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 ===
+
[[WormBase-Caltech_Weekly_Calls_April_2020|April]]
* 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
 
  
=== WS276 Citace upload ===
+
[[WormBase-Caltech_Weekly_Calls_May_2020|May]]
* 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 ===
+
== June 4, 2020 ==
* 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 ===
+
=== Citace (tentative) upload ===
* Have a backlog; Paul D is assigned but has been overwhelmed
+
* CIT curators upload to citace on Tuesday, July 7th, 10am Pacific
* Have asserted this as a priority
+
* Citace upload to Hinxton on Friday, July 10th
* 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 ===
+
=== Caltech reopening ===
* Asia (Taipei) meeting, Paul S going
+
* Paul looking to get plan approved
* Aging meeting, Wen could go? (Wen: I can ask if they provide a timeslot for oral presentation.)
+
* People that want to come to campus need to watch training video
* TAGC in April, Chris going
+
* Masks available in Paul's lab
 +
* Can have maximum of 3 people in WormBase rooms at a time; probably best to only allow one person per WB room
 +
** Could possibly have 2 people in big room (Church 64) as long as they stay at least 10 feet apart
 +
* Need to coordinate, maybe make a Google calendar to do so (also Slack)
 +
* Before and after you go to campus, you need to take your temperature and assess your symptoms (if any) and submit info on form
 +
* Also, need to submit who you were in contact with for contact tracing
 +
* Form is used all week, and hold on to it until asked to be submitted
 +
* If someone goes in to the office, they could print several forms for people to pick up in WB offices
  
 +
=== Nameserver ===
 +
* Nameserver was down
 +
* CIT curators would still like to have a single form to interact with
 +
* Is it possible to create objects at Caltech and let a cronjob assign IDs via the nameserver? May not be a good idea
 +
* Still putting genotype and all info for a strain in the reason/why field in the nameserver
 +
* We plan to eventually connect strains to genotypes, but need model changes and curation effort to sort out
 +
* Hinxton is pulling in CGC strains, how often?
 +
* Caltech could possibly get a block of IDs
  
== January 16, 2020 ==
+
=== Alliance SimpleMine ===
 
+
* Any updates? 3.1 feature freeze is tomorrow
=== Variation names ===
+
* Pending on PI decision; Paul S. will bring it up tomorrow on the Alliance PI call
* 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
 
 
 
 
 
 
 
== January 23, 2020 ==
 
 
 
=== WS276 Citace upload ===
 
* Next Tuesday, Jan 28 10am Pacific
 
 
 
=== Extracellular/secreted proteins list ===
 
* Peter Roy looking for a list of C. elegans genes whose protein products are secreted
 
* Chris pointed him to BioMart search for SignalP and transmembrane proteins, and to the GO term page for "extracellular region" but Peter doesn't think that's exhaustive enough
 
* Does anyone have any other suggestions or know of an empirical data set?
 
https://www.ncbi.nlm.nih.gov/pubmed/22823938
 

Revision as of 00:09, 5 June 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

February

March

April

May


June 4, 2020

Citace (tentative) upload

  • CIT curators upload to citace on Tuesday, July 7th, 10am Pacific
  • Citace upload to Hinxton on Friday, July 10th

Caltech reopening

  • Paul looking to get plan approved
  • People that want to come to campus need to watch training video
  • Masks available in Paul's lab
  • Can have maximum of 3 people in WormBase rooms at a time; probably best to only allow one person per WB room
    • Could possibly have 2 people in big room (Church 64) as long as they stay at least 10 feet apart
  • Need to coordinate, maybe make a Google calendar to do so (also Slack)
  • Before and after you go to campus, you need to take your temperature and assess your symptoms (if any) and submit info on form
  • Also, need to submit who you were in contact with for contact tracing
  • Form is used all week, and hold on to it until asked to be submitted
  • If someone goes in to the office, they could print several forms for people to pick up in WB offices

Nameserver

  • Nameserver was down
  • CIT curators would still like to have a single form to interact with
  • Is it possible to create objects at Caltech and let a cronjob assign IDs via the nameserver? May not be a good idea
  • Still putting genotype and all info for a strain in the reason/why field in the nameserver
  • We plan to eventually connect strains to genotypes, but need model changes and curation effort to sort out
  • Hinxton is pulling in CGC strains, how often?
  • Caltech could possibly get a block of IDs

Alliance SimpleMine

  • Any updates? 3.1 feature freeze is tomorrow
  • Pending on PI decision; Paul S. will bring it up tomorrow on the Alliance PI call