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]]
  
 +
[[WormBase-Caltech_Weekly_Calls_2021|2021 Meetings]]
  
 +
= 2022 Meetings =
  
= 2020 Meetings =
+
[[WormBase-Caltech_Weekly_Calls_January_2018|January]]
  
[[WormBase-Caltech_Weekly_Calls_January_2020|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.
 +
**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_February_2020|February]]
+
= January 20th, 2022 =
  
[[WormBase-Caltech_Weekly_Calls_March_2020|March]]
+
== Proposal for updating gene and variation information from WS releases ==
 
+
=== Genes ===
[[WormBase-Caltech_Weekly_Calls_April_2020|April]]
+
*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_May_2020|May]]
+
**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_June_2020|June]]
+
**Would not include ids for non-WB (and WBParaSite) genomes, e.g. Drosophila or budding yeast
 
+
=== Variations ===
[[WormBase-Caltech_Weekly_Calls_July_2020|July]]
+
*Include all variations that have a value for:
 
+
**Method - current filters applied (filter SNP, Million_mutation, WGS's)
[[WormBase-Caltech_Weekly_Calls_August_2020|August]]
+
**Species - all
 
+
**Status - include all three status values (Live, Dead, Suppressed)
[[WormBase-Caltech_Weekly_Calls_September_2020|September]]
+
*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.
[[WormBase-Caltech_Weekly_Calls_October_2020|October]]
+
*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.
 
 
==Nov 5th, 2020==
 
 
 
===WS279 GAF 2.0 and disease files===
 
*Valerio and Ranjana still working with the GAF 2.0 files to generate gene descriptions
 
*Valerio and Ranjana will probably have a meeting with Magdalena to sort out the FTP file issues for gene descriptions
 
*Will let Raymond know if the disease GAFs are okay after they test these for gene descriptions
 
*Raymond needs the GAFs for WoBR
 
 
 
===Experimenting with addeding new citace data to the current WS release ===
 
*Wen will take the newest expression, physical interaction, and paper class from postgres, add them to WS279 to create a "WS279.1" version of ACeDB database. Then compare WS279.1 to WS279 by comparing the SimpleMine results generated from these two versions of ACeDB. The goal is to explore the possibility of notifying users some of the new curation since the data freeze for the WS build.
 
 
 
===MicroPub user webinar on Nov 9th===
 
*Ranjana and Kimberly have conflicts--Alliance call and GO call. Anyway microPub team is running the show and they have other WormBasers to help as well.
 
 
 
===WS280 deadlines===
 
*Caltech files due for citace: Dec 15th, 2020
 
 
 
 
 
==Nov 12th, 2020==
 
=== Cynthia Kenyon tool ===
 
* developed a new tool for the worm, complete with very nice tutorials, for analyzing gene expression data using Gene Module analysis.
 
* tool at http://genemodules.org
 
* add link outs from the gene expression widget or add in general WB tools?
 
 
 
=== Graphical curation tool update===
 
* We will show a live demo on the current state of the graphical curation tool
 
 
 
=== Curating to human genes in ACEDB ===
 
* Karen requested option to curate constructs with human genes
 
* Would we need to change our human genes in ACEDB? For example, migrate from Ensembl IDs to HGNC IDs as primary keys?
 
 
 
=== GAF (and GAF-like) file headers ===
 
* GO GAF files (on FTP, WS279) for WormBase now in 2.2 format with header like
 
!gaf-version: 2.2
 
!generated-by: WormBase
 
!date-generated: 2020-10-30
 
! WB annotations 00015014
 
* For files that can migrate to 2.2 format (e.g. always require column 4 qualifier) we could adopt a similar header
 
* For other files (that cannot always have a qualifier in column 4), we could stick to 2.0 format with a header like:
 
!gaf-version: 2.0
 
!generated-by: WormBase
 
!date-generated: 2020-10-30
 
* Current need is to include information about format specification, possibly in addition to other extra header content.
 
* New proposed headers:
 
  !project-URL: https://wormbase.org
 
!specification-URL: https://github.com/geneontology/geneontology.github.io/blob/issue-go-annotation-2917-gaf-2_2-doc/_docs/go-annotation-file-gaf-format-22.md
 
OR
 
!specification-URL: https://wiki.wormbase.org/index.php/WormBase_gene_association_file
 
!project-release: WS279
 
* Could repurpose the Wiki page: https://wiki.wormbase.org/index.php/WormBase_gene_association_file from internal docs only to include user guide info, including how our GAF-like files deviate in format from standard GAF
 

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.