Difference between revisions of "WormBase-Caltech Weekly Calls"

From WormBaseWiki
Jump to navigationJump to search
m
 
(423 intermediate revisions by 9 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]]
  
 +
[[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 ===
 +
*Have two tables:
 +
**One continues as is - contains only ids for the [https://wormbase.org/species/all core nematode species] (all have WBGene ids)
 +
**Second, new table - contains non-WGene ids for [https://wormbase.org/species/al 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.
  
[[WormBase-Caltech_Weekly_Calls_April_2020|April]]
+
= January 27th, 2022 =
  
[[WormBase-Caltech_Weekly_Calls_May_2020|May]]
+
== C. elegans BioCyc ==
 
+
*Schedule a demo session with Peter Karp
[[WormBase-Caltech_Weekly_Calls_June_2020|June]]
+
*Monday, Thursday, Friday mornings work for him and his team
 
+
*Caltech preference?
[[WormBase-Caltech_Weekly_Calls_July_2020|July]]
 
 
 
[[WormBase-Caltech_Weekly_Calls_August_2020|August]]
 
 
 
[[WormBase-Caltech_Weekly_Calls_September_2020|September]]
 
 
 
 
 
 
 
== October 1, 2020 ==
 
 
 
=== Gene association file formats on FTP ===
 
* For example, current production release ONTOLOGY directory: ftp://ftp.wormbase.org/pub/wormbase/releases/current-production-release/ONTOLOGY/
 
* Our association files have format "*.wb"; is this useful or necessary?
 
* Other than referring to GAF in the header, it isn't clear to users what the columns refer to or what the column headers should be
 
* We could add a README file and/or convert to the new [https://github.com/geneontology/geneontology.github.io/blob/issue-go-annotation-2917-gaf-2_2-doc/_docs/go-annotation-file-gaf-format-22.md GAF 2.2 format] which would have a more expressive file header and possibly column headers(?)
 
** File headers could possibly link to the format specification page
 
 
 
=== Phenotype association file idiosyncrasy ===
 
* As we've discussed previously, there is an oddity to how the phenotype association file we provide lists, or doesn't, references
 
* According to the GAF spec, column 6 is for reference and is required, whereas column 8 is "With (or) From" and is optional
 
* When we have a reference, the WBPaper ID is provided in column 6 and the WBVar ID or RNAi ID is provided in column 8
 
* However, when we have no reference (personal communication, e.g. from NBP allele submissions), the WBVar ID is instead put in column 6 (because we need something there), and column 8 is blank.
 
** This results in (1) column 6 having a mix of paper/reference IDs (good) and WBVar IDs (not good) and (2) WBVar IDs split between column 6 and 8; thus making it tedious to parse this file
 
* Proposed solution: Can we come up with some type of reference object ID to associate to the personal communications (or any annotations currently lacking a formal reference)?
 
* With the proposed solution, we can always have a reference ID in column 6 (the intended purpose of the column) and WBVar IDs for alleles can always remain consistently in column 8
 

Latest revision as of 14:52, 27 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.

January 27th, 2022

C. elegans BioCyc

  • Schedule a demo session with Peter Karp
  • Monday, Thursday, Friday mornings work for him and his team
  • Caltech preference?