Difference between revisions of "WormBase-Caltech Weekly Calls"

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[[WormBase-Caltech_Weekly_Calls_2020|2020 Meetings]]
 
[[WormBase-Caltech_Weekly_Calls_2020|2020 Meetings]]
  
= 2021 Meetings =
+
[[WormBase-Caltech_Weekly_Calls_2021|2021 Meetings]]
  
[[WormBase-Caltech_Weekly_Calls_January_2021|January]]
+
= 2022 Meetings =
  
[[WormBase-Caltech_Weekly_Calls_February_2021|February]]
+
[[WormBase-Caltech_Weekly_Calls_January_2018|January]]
  
[[WormBase-Caltech_Weekly_Calls_March_2021|March]]
+
= 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.
 +
**https://github.com/WormBase/website/issues/8262
 +
**https://wiki.wormbase.org/index.php/WBGene_information_and_status_pipeline
 +
**https://wiki.wormbase.org/index.php/Source_and_maintenance_of_non-WBGene_info
 +
**https://wiki.wormbase.org/index.php/Updating_Postgres_with_New_WS_Information
 +
*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?
  
[[WormBase-Caltech_Weekly_Calls_April_2021|April]]
+
= January 20th, 2022 =
  
[[WormBase-Caltech_Weekly_Calls_May_2021|May]]
+
== Proposal for updating gene and variation information from WS releases ==
 
+
=== Genes ===
[[WormBase-Caltech_Weekly_Calls_June_2021|June]]
+
*Have two tables:
 
+
**One continues as is - contains only ids for the [https://wormbase.org/species/all core nematode species] (all have WBGene ids)
[[WormBase-Caltech_Weekly_Calls_July_2021|July]]
+
**Second, new table - contains non-WGene ids for [https://wormbase.org/species/al comparator nematode genomes]
 
+
***Include other elegans and remanei strains?
[[WormBase-Caltech_Weekly_Calls_August_2021|August]]
+
**Would not include ids for non-WB (and WBParaSite) genomes, e.g. Drosophila or budding yeast
 
+
=== Variations ===
[[WormBase-Caltech_Weekly_Calls_September_2021|September]]
+
*Include all variations that have a value for:
 
+
**Method - current filters applied (filter SNP, Million_mutation, WGS's)
[[WormBase-Caltech_Weekly_Calls_October_2021|October]]
+
**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.
== November 4 2021 ==
+
*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.
=== 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 the 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 15:24, 20 January 2022

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

2022 Meetings

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.