Difference between revisions of "WormBase-Caltech Weekly Calls"

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[[WormBase-Caltech_Weekly_Calls_2019|2019 Meetings]]
 
[[WormBase-Caltech_Weekly_Calls_2019|2019 Meetings]]
  
 +
[[WormBase-Caltech_Weekly_Calls_2020|2020 Meetings]]
  
GoToMeeting link: https://www.gotomeet.me/wormbase1
+
= 2021 Meetings =
  
= 2020 Meetings =
+
[[WormBase-Caltech_Weekly_Calls_January_2021|January]]
  
== January 9, 2020 ==
+
[[WormBase-Caltech_Weekly_Calls_February_2021|February]]
  
=== Phenotype Curation Requests ===
+
[[WormBase-Caltech_Weekly_Calls_March_2021|March]]
* 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_April_2021|April]]
* 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_May_2021|May]]
* 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 ===
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[[WormBase-Caltech_Weekly_Calls_June_2021|June]]
* Hinxton upload Jan 31, 2020
 
* Citace upload on Tuesday, Jan 28, 2020
 
  
=== Author First Pass paper ===
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[[WormBase-Caltech_Weekly_Calls_July_2021|July]]
* 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 ===
+
[[WormBase-Caltech_Weekly_Calls_August_2021|August]]
* 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 ===
+
[[WormBase-Caltech_Weekly_Calls_September_2021|September]]
* 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 ===
+
[[WormBase-Caltech_Weekly_Calls_October_2021|October]]
* 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 ===
+
== November 4 2021 ==
* 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 ===
+
=== Migrating Paper Pipeline to Alliance ===
* During an AFP call we discussed the possibility to have webinars for authors to guide them through the form.
+
*Meeting abstracts
* Is having a webinar series something WB is interested in doing?
+
**Continuing to review what we have and standardize bibliographic info before we migrate
** we will start with an AFP/micropub webinar and will take it from there based on interest and attendance
+
**QC checks highlight some older abstracts with little-to-no data - propose to invalidate these so we don't migrate poor quality paper data to the Alliance
 +
**We can always respond to individual requests to add old meeting abstracts if they arise
  
  
 +
== November 11 2021 ==
  
== January 23, 2020 ==
+
=== WS284 upload dates for Caltech ===
 +
* When are files due for the Caltech group?
  
=== Extracellular/secreted proteins list ===
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===Minutes===
* Peter Roy looking for a list of C. elegans genes whose protein products are secreted
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*WS284 upload-Better to upload before the holidays or in Jan 2022
* 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
+
*Wen will contact Paul D/Hinxton to find out when the WS284 models will be released
* Does anyone have any other suggestions or know of an empirical data set?
+
 
 +
 
 +
== November 18 2021 ==
 +
Proposal for upgrading tanzendra/mangolassi computing resources
 +
1. Move them to Chen. (done)
 +
  monitor stability of network
 +
 
 +
Old hardware and out of support OS (Ubuntu 14.04)
 +
 
 +
2. Establish a development environment for Dockerizing services (curation OA, other web forms, postgres DB)
 +
  (use Valerio's local server/desktop)
 +
 
 +
3. Establish a local file server for storage and download access (PDFs, dump files)
 +
 
 +
4. Run dockerized services from AWS
 +
 
 +
5. Continuous development and integration locally -> AWS
 +
 
 +
===Commercial antibodies===
 +
* Daniela contacted ZFIN and FlyBase. ZFIN does curate commercial antibodies only if found in publications. Waiting for FlyBase feedback (Sian out).
 +
* TODO: Contact TAIR and see if they including commercial antibodies and if  they charge companies  (Daniela sent a message on slack). Tanya: We have not charged for placing the links but have strongly encouraged a corporate subscription for the two companies.
 +
* This can be an  Alliance project. Need to contact companies and see who is interested (need to have a  price in mind for that).
 +
* Can pilot text mining for commercial antibodies
 +
* GeneCards charges for inclusion of commercial reagents on their website: "Companies that wish to provide deep links to their products (e.g. reagents, assays, antibodies, clones, etc) in the Services and other relevant sections of GeneCards, should contact sales@lifemapsc.com." From https://www.genecards.org/Guide/FAQ

Latest revision as of 17:51, 18 November 2021

Previous Years

2009 Meetings

2011 Meetings

2012 Meetings

2013 Meetings

2014 Meetings

2015 Meetings

2016 Meetings

2017 Meetings

2018 Meetings

2019 Meetings

2020 Meetings

2021 Meetings

January

February

March

April

May

June

July

August

September

October


November 4 2021

Migrating Paper Pipeline to Alliance

  • Meeting abstracts
    • Continuing to review what we have and standardize bibliographic info before we migrate
    • QC checks highlight some older abstracts with little-to-no data - propose to invalidate these so we don't migrate poor quality paper data to the Alliance
    • We can always respond to individual requests to add old meeting abstracts if they arise


November 11 2021

WS284 upload dates for Caltech

  • When are files due for the Caltech group?

Minutes

  • WS284 upload-Better to upload before the holidays or in Jan 2022
  • Wen will contact Paul D/Hinxton to find out when the WS284 models will be released


November 18 2021

Proposal for upgrading tanzendra/mangolassi computing resources

1. Move them to Chen. (done)
  monitor stability of network
Old hardware and out of support OS (Ubuntu 14.04)
2. Establish a development environment for Dockerizing services (curation OA, other web forms, postgres DB)
  (use Valerio's local server/desktop)
3. Establish a local file server for storage and download access (PDFs, dump files)
4. Run dockerized services from AWS
5. Continuous development and integration locally -> AWS

Commercial antibodies

  • Daniela contacted ZFIN and FlyBase. ZFIN does curate commercial antibodies only if found in publications. Waiting for FlyBase feedback (Sian out).
  • TODO: Contact TAIR and see if they including commercial antibodies and if they charge companies (Daniela sent a message on slack). Tanya: We have not charged for placing the links but have strongly encouraged a corporate subscription for the two companies.
  • This can be an Alliance project. Need to contact companies and see who is interested (need to have a price in mind for that).
  • Can pilot text mining for commercial antibodies
  • GeneCards charges for inclusion of commercial reagents on their website: "Companies that wish to provide deep links to their products (e.g. reagents, assays, antibodies, clones, etc) in the Services and other relevant sections of GeneCards, should contact sales@lifemapsc.com." From https://www.genecards.org/Guide/FAQ