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
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[[WormBase-Caltech_Weekly_Calls_2021|2021 Meetings]]
  
= 2020 Meetings =
+
= 2022 Meetings =
  
== January 9, 2020 ==
+
[[WormBase-Caltech_Weekly_Calls_January_2018|January]]
  
=== Phenotype Curation Requests ===
+
= January 13th, 2022 =
* 1,229 emails sent Dec 3-6, 2019
+
== tm variation - gene associations ==
* Received 194 annotations from 40 papers and from 37 distinct community curators
+
*Update on progress and some questions for the Caltech curators
** 37 papers requested, 3 additional papers annotated
+
*Background: not all variations were being associated with genes in the OA table because some of those associations are in WS but not in geneace, so weren't coming through in the nightly geneace dump.  Some variation-gene associations are made as part of the VEP pipeline during the build.
** 104 Phenotype OA annotations (from 27 papers; 25 distinct curators)
+
**https://github.com/WormBase/website/issues/8262
** 90 RNAi OA annotations (from 20 papers; 19 distinct curators)
+
**https://wiki.wormbase.org/index.php/WBGene_information_and_status_pipeline
* 43 bounced emails
+
**https://wiki.wormbase.org/index.php/Source_and_maintenance_of_non-WBGene_info
** 2 resent to new addresses
+
**https://wiki.wormbase.org/index.php/Updating_Postgres_with_New_WS_Information
** 5 have backup email addresses (also sent)
+
*Wen now downloads several full ACeDB classes from the latest WS release in the form of .ace files so we can also have whatever information is in WS.  Raymond wrote a script to sync those files to tazendra for further processing/use.
 +
*A few questions that we want to confirm before going forward:
 +
**In the WS variations file, there are 2,130,801 total variations (1,911,339 total Live) while in postgres there are currently 106,080.
 +
***Only include Status = Live variations?
 +
***Include regardless of whether there is an associated gene (this seems to be the current practice?).
 +
***Currently, some variations with a given Method, e.g. Million_mutation, are NOT included.  We would continue this filtering.
 +
****SNP
 +
****WGS_Hawaiian_Waterston
 +
****WGS_Pasadena_Quinlan
 +
****WGS_Hobert
 +
****Million_mutation
 +
****WGS_Yanai
 +
****WGS_De_Bono
 +
****WGS_Andersen
 +
****WGS_Flibotte
 +
****WGS_Rose
 +
***Do we want other filters?
 +
**For genes, the ace file contains ALL the gene objects in WB regardless of species.
 +
***We've recently had an author request, via the Acknowledge pipeline, to associate genes of other, less well studied Caenorhabditis species, e.g. C. inopinata, to [https://academic.oup.com/g3journal/article/11/3/jkab022/6121926 their paper].
 +
***Do we want all Caenorhabditis (and other nematode) species genes in our various gene tables, e.g. obo, paper? Any other species?
 +
***The effect on the autocomplete, if we include all, probably won't be a problem 1,018,332 vs 306116)
 +
***Some of the gene ids from other species don't have 'WBGene' prefixes, e.g. Sp34_10109610.  Should we keep this in a separate table from genes with 'WBGene' prefixes?
  
=== Worm Area Meetings ===
+
= January 20th, 2022 =
* 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 ===
+
== Proposal for updating gene and variation information from WS releases ==
* Now live on WormBase, WS274
+
=== Genes ===
* [https://github.com/WormBase/website/issues/7347 GitHub ticket]
+
*Have two tables:
* Applies to the following classes: genes, strains, variations, transgenes, constructs, anatomy terms, clones, life stages, rearrangements, molecules, processes
+
**One continues as is - contains only ids for the [https://wormbase.org/species/all core nematode species] (all have WBGene ids)
* Gene example: https://wormbase.org/species/c_elegans/gene/WBGene00022861#0d--10
+
**Second, new table - contains non-WGene ids for [https://wormbase.org/species/al comparator nematode genomes]
* Strain example: https://wormbase.org/species/c_elegans/strain/WBStrain00004309#05--10
+
***Include other elegans and remanei strains?
* Variation example: https://wormbase.org/species/c_elegans/variation/WBVar00248884#08--10
+
**Would not include ids for non-WB (and WBParaSite) genomes, e.g. Drosophila or budding yeast
* Transgene example: https://wormbase.org/species/all/transgene/WBTransgene00004654#04--10
+
=== Variations ===
** Known issue: searching on synonyms in addition to public name; Sibyl will fix
+
*Include all variations that have a value for:
* Construct example: https://wormbase.org/species/all/construct/WBCnstr00023113#03--10
+
**Method - current filters applied (filter SNP, Million_mutation, WGS's)
** Known issue: not working now; need to only search on public name when available, not on summary; Sibyl will fix
+
**Species - all
* Anatomy term example: https://wormbase.org/species/all/anatomy_term/WBbt:0005772#05--10
+
**Status - include all three status values (Live, Dead, Suppressed)
** Known challenge: "Psub1" will essentially never match the intended target and "P1" may find the embryonic cell or the postembryonic cell
+
*Whether a variation has a gene association doesn't matter (not a filter criteria for postgres)
* Clone example: https://wormbase.org/species/c_elegans/clone/W02C12#03--10
+
*From Paul D. - a number of variations in geneace were not making their way as individual objects to WS during the build and so were only created in WS via xref (hence the lack of other information). He's updated geneace with Species and other information wherever possible for the next build.
* Life stage example: https://wormbase.org/species/all/life_stage/WBls:0000038#03--10
+
*Variation merges are infrequent; previous ones may have been due to nameserver issues
** Known challenge: "L4 larva Ce" will never match; "L4 larva" maybe; but "L4" alone will not unless a synonym
+
*New Methods arise infrequently, but we could check our parsing script against the list of Methods in each release to make sure we're up-to-date. Would need an inclusion and exclusion list.
* 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 ===
 
* 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?
 
https://www.ncbi.nlm.nih.gov/pubmed/22823938
 

Latest revision as of 15:24, 20 January 2022

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January

January 13th, 2022

tm variation - gene associations

  • Update on progress and some questions for the Caltech curators
  • Background: not all variations were being associated with genes in the OA table because some of those associations are in WS but not in geneace, so weren't coming through in the nightly geneace dump. Some variation-gene associations are made as part of the VEP pipeline during the build.
  • Wen now downloads several full ACeDB classes from the latest WS release in the form of .ace files so we can also have whatever information is in WS. Raymond wrote a script to sync those files to tazendra for further processing/use.
  • A few questions that we want to confirm before going forward:
    • In the WS variations file, there are 2,130,801 total variations (1,911,339 total Live) while in postgres there are currently 106,080.
      • Only include Status = Live variations?
      • Include regardless of whether there is an associated gene (this seems to be the current practice?).
      • Currently, some variations with a given Method, e.g. Million_mutation, are NOT included. We would continue this filtering.
        • SNP
        • WGS_Hawaiian_Waterston
        • WGS_Pasadena_Quinlan
        • WGS_Hobert
        • Million_mutation
        • WGS_Yanai
        • WGS_De_Bono
        • WGS_Andersen
        • WGS_Flibotte
        • WGS_Rose
      • Do we want other filters?
    • For genes, the ace file contains ALL the gene objects in WB regardless of species.
      • We've recently had an author request, via the Acknowledge pipeline, to associate genes of other, less well studied Caenorhabditis species, e.g. C. inopinata, to their paper.
      • Do we want all Caenorhabditis (and other nematode) species genes in our various gene tables, e.g. obo, paper? Any other species?
      • The effect on the autocomplete, if we include all, probably won't be a problem 1,018,332 vs 306116)
      • Some of the gene ids from other species don't have 'WBGene' prefixes, e.g. Sp34_10109610. Should we keep this in a separate table from genes with 'WBGene' prefixes?

January 20th, 2022

Proposal for updating gene and variation information from WS releases

Genes

  • Have two tables:
    • One continues as is - contains only ids for the core nematode species (all have WBGene ids)
    • Second, new table - contains non-WGene ids for comparator nematode genomes
      • Include other elegans and remanei strains?
    • Would not include ids for non-WB (and WBParaSite) genomes, e.g. Drosophila or budding yeast

Variations

  • Include all variations that have a value for:
    • Method - current filters applied (filter SNP, Million_mutation, WGS's)
    • Species - all
    • Status - include all three status values (Live, Dead, Suppressed)
  • Whether a variation has a gene association doesn't matter (not a filter criteria for postgres)
  • From Paul D. - a number of variations in geneace were not making their way as individual objects to WS during the build and so were only created in WS via xref (hence the lack of other information). He's updated geneace with Species and other information wherever possible for the next build.
  • Variation merges are infrequent; previous ones may have been due to nameserver issues
  • New Methods arise infrequently, but we could check our parsing script against the list of Methods in each release to make sure we're up-to-date. Would need an inclusion and exclusion list.