Difference between revisions of "WormBase-Caltech Weekly Calls"

From WormBaseWiki
Jump to navigationJump to search
m
 
(701 intermediate revisions by 11 users not shown)
Line 21: Line 21:
 
[[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 ===
+
[[WormBase-Caltech_Weekly_Calls_June_2021|June]]
* Hinxton upload Jan 31, 2020
 
* Citace upload on Tuesday, Jan 28, 2020
 
  
=== Author First Pass paper ===
+
[[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 ===
 
* 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 ===
+
== September 2, 2021 ==
* 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
 
  
 +
1. Moving forward with Alliance-friendly Person pages for community curation/authorship tracking<br>
 +
Needed for
 +
*AFP community curation
 +
*microPublication author tracking for all species
 +
*stub of person Alliance model already exists made by Adam http://dev.alliancegenome.org:11223/redoc#tag/Person
  
== January 16, 2020 ==
+
Problems:
 +
*this is not an Alliance-wide interest for tracking their communities person; however, Alliance is not against person pages, just not supportive of developing this class into the many ways it will be useful for us and our communities
 +
*need to do this outside of Alliance
  
=== Variation names ===
+
Action
* 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
.
+
*Paul talks to zfin about interest in person pages
* Daniela asked Juancarlos to modify the temporary variation ID form to allow up to 4 letters instead of 3.
+
*Juancarlos talks to Cecilia -need to know important elements to make author to person connection for biolink schema
* Form here: http://tazendra.caltech.edu/~azurebrd/cgi-bin/forms/generic.cgi?action=TempVariationObo
+
*Daniela and Karen invite PomBase to start harmonizing a person model, will send all Alliance an invite
* 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 ===
+
Will do
* During an AFP call we discussed the possibility to have webinars for authors to guide them through the form.
+
*create biolink model based on current WB postgres/Caltech model
* Is having a webinar series something WB is interested in doing?
+
*Adam will add tables when we have them
** we will start with an AFP/micropub webinar and will take it from there based on interest and attendance
 
  
 +
2. Need to make sure CenGen stuff is included in this next release - need to request Todd to delay release until Adam returns from vacation to deal with it.
  
 +
== September 16, 2021 ==
  
== January 16, 2020 ==
+
1. CeNGEN enriched genes per cell type data targeted for WS283.
  
=== Extracellular/secreted proteins list ===
+
2. some non-WB objects were present in the Strains and Variations lists coming from the nightly geneace dump.  Juancarlos changed the OA population script script to exclude those.
* 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
+
== September 23, 2021 ==
* Does anyone have any other suggestions or know of an empirical data set?
+
 
 +
1. Help desk ticket on citing the bar graph / FPKM expression data from selected modENCODE libraries - okay to just cite WormBase or should the user cite additional, or other, resources/publications?
 +
* Okay to cite WormBase, but also ask user to cite the WormBase paper (for now NAR, but in the future, Genetics)
 +
* Update the WB page on citing WormBase
 +
 
 +
2. CeNGEN data on Gene page for WS282. A short blog to highlight.
 +
 
 +
3. Server room in Braun power down for no apparent reason. Reset.

Latest revision as of 18:17, 23 September 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 2, 2021

1. Moving forward with Alliance-friendly Person pages for community curation/authorship tracking
Needed for

Problems:

  • this is not an Alliance-wide interest for tracking their communities person; however, Alliance is not against person pages, just not supportive of developing this class into the many ways it will be useful for us and our communities
  • need to do this outside of Alliance

Action

  • Paul talks to zfin about interest in person pages
  • Juancarlos talks to Cecilia -need to know important elements to make author to person connection for biolink schema
  • Daniela and Karen invite PomBase to start harmonizing a person model, will send all Alliance an invite

Will do

  • create biolink model based on current WB postgres/Caltech model
  • Adam will add tables when we have them

2. Need to make sure CenGen stuff is included in this next release - need to request Todd to delay release until Adam returns from vacation to deal with it.

September 16, 2021

1. CeNGEN enriched genes per cell type data targeted for WS283.

2. some non-WB objects were present in the Strains and Variations lists coming from the nightly geneace dump. Juancarlos changed the OA population script script to exclude those.

September 23, 2021

1. Help desk ticket on citing the bar graph / FPKM expression data from selected modENCODE libraries - okay to just cite WormBase or should the user cite additional, or other, resources/publications?

  • Okay to cite WormBase, but also ask user to cite the WormBase paper (for now NAR, but in the future, Genetics)
  • Update the WB page on citing WormBase

2. CeNGEN data on Gene page for WS282. A short blog to highlight.

3. Server room in Braun power down for no apparent reason. Reset.