Difference between revisions of "WormBase-Caltech Weekly Calls"

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* Will mention data submission pipelines
 
* Will mention data submission pipelines
 
* [https://www.umassmed.edu/ambroslab/meetings/bawm/BAWM-PIs/ BAWM PIs list]
 
* [https://www.umassmed.edu/ambroslab/meetings/bawm/BAWM-PIs/ BAWM PIs list]
 
  
 
=== BioGRID protein-protein interaction sharing ===
 
=== BioGRID protein-protein interaction sharing ===
 
* Chris just sent BioGRID (Rose) WS275 worm PPIs
 
* Chris just sent BioGRID (Rose) WS275 worm PPIs

Revision as of 19:27, 30 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


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?
  • A survey of putative secreted and transmembrane proteins encoded in the C. elegans genome: https://www.ncbi.nlm.nih.gov/pubmed/22823938
  • PF00188 Cysteine-rich secretory protein family Pfam
    • This is a large family of cysteine-rich secretory proteins, antigen 5, and pathogenesis-related 1 proteins (CAP) that are found in a wide range of organisms, including prokaryotes [PMID:12625841]


January 30, 2020

WormBase sponsorship of TAGC C. elegans community mixer?

  • Anne Marie Mahoney has asked if WormBase is interested in sponsoring the TAGC meeting's C. elegans community mixer
  • For reference, someone just sponsored the Yeast Mixer for $2,500
  • In order to be listed as a sponsor in the meeting book, they need our response by next Friday (Feb 7th); if we agree after that, the mixer will display us as sponsor but we won't be in the book

Boston Area Worm Meeting talk confirmed

  • We will get a BAWM slot for September 23rd, 2020
  • Chris will plan on presenting
  • Can focus on topics pertaining to attendees; likely to be Boston labs and presenting labs
  • Can split time to discuss general topics and more specific topics
  • Will mention data submission pipelines
  • BAWM PIs list

BioGRID protein-protein interaction sharing

  • Chris just sent BioGRID (Rose) WS275 worm PPIs