Difference between revisions of "WormBase-Caltech Weekly Calls"

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[[WormBase-Caltech_Weekly_Calls_2016|2016 Meetings]]
 
[[WormBase-Caltech_Weekly_Calls_2016|2016 Meetings]]
  
= 2017 Meetings =
+
[[WormBase-Caltech_Weekly_Calls_2017|2017 Meetings]]
  
[[WormBase-Caltech_Weekly_Calls_January_2017|January]]
+
[[WormBase-Caltech_Weekly_Calls_2018|2018 Meetings]]
  
 +
[[WormBase-Caltech_Weekly_Calls_2019|2019 Meetings]]
  
== February 2, 2017 ==
+
[[WormBase-Caltech_Weekly_Calls_2020|2020 Meetings]]
  
=== Methods in Molecular Biology chapter ===
+
[[WormBase-Caltech_Weekly_Calls_2021|2021 Meetings]]
* Chris and Mary Ann will be in touch with individuals about section writing
 
* Karen: FlyBase chapter has small sections rather than long articles about their pages; should we keep our sections small; a few paragraphs each?
 
** As long as we stick to the "how to" focus, we can write as much as needed
 
* Raymond: We should try to write so that the content remains pertinent for a while
 
  
=== Pharyngeal phenotype terms ===
+
= 2022 Meetings =
* Karen has made pharyngeal pumping phenotype terms for NemaMetrix micropublications
 
* It is common for many groups to involve serotonin-induced pharyngeal pumping to analyze strains; we do have a serotonin-induced pharyngeal pumping variant term- should I use this for all pumping phenotypes? In addition we have an EPG variant term and again, people tend to use EPGs to record pumping activity - should all reported pharyngeal pumping phenotypes that were measured  by EPGs be annotated with this term?  These questions highlight a need to revisit the pharyngeal phenotype branch and clarify how we should be focused on annotating these reported annotations.
 
* Karen asked Raymond/Gary and any other person interested in the group to help with pharyngeal phenotype term organization
 
* Raymond: Not very familiar with the existing usage of the terms and phenotype ontology structure wrt pharyngeal terms
 
* Authors submit phenotype data as part of the micropublication process
 
* Proposal for phenotype ontology going forward: create terms with logical definitions (OWL statements)
 
* We will start exploring more usage of logical definitions for phenotypes
 
* Will start meeting Thursday afternoons, starting next week (Feb 9), 1:30pm Pacific
 
* Karen will prepare the terms to be looked through.....
 
  
=== SObA graph for GO ===
+
[[WormBase-Caltech_Weekly_Calls_January_2018|January]]
* Juancarlos & Raymond making progress
 
* Added toggling for different roots of GO
 
* Difficult to navigate graph when lots of terms (e.g. tax-4)
 
* What can be done to improve the display?
 
* Filtering out IEA annotations; currently only for phenotype annotations; will expand to all IEA annotations
 
* Kimberly generating GO slim, 15-20 terms for each branch of GO, possible to use in ribbon display
 
* Could we distinguish between is_a, part_of, and regulates relationships?
 
* To simplify graph, could we further minimize the display of higher level/indirect nodes?
 
* Would we want parallel paths to root to be trimmed?
 
  
 +
= 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?
  
== February 9, 2017 ==
+
= January 20th, 2022 =
  
=== AGR Disease working group ===
+
== Proposal for updating gene and variation information from WS releases ==
* disease association file (DAF) pretty much worked out; data quartermasters are creating DAF files for each DB
+
=== Genes ===
* Have a simple mockup for the display of disease data on a gene report page: https://docs.google.com/presentation/d/1YuD4_-mPS2AhIfaX41M8IIhiS63iiSy9ebcOQEZxoJQ/edit#slide=id.p4
+
*Have two tables:
* We should remove underscores from "is_model_of" and translate to "is a model of"
+
**One continues as is - contains only ids for the [https://wormbase.org/species/all core nematode species] (all have WBGene ids)
* Should spell out evidence codes
+
**Second, new table - contains non-WGene ids for [https://wormbase.org/species/al comparator nematode genomes]
* Kevin, WB data quartermaster, working on developing the disease association file (DAF) from the WormBase build
+
***Include other elegans and remanei strains?
* Ranjana working on a new ?Disease_model_annotation class and model
+
**Would not include ids for non-WB (and WBParaSite) genomes, e.g. Drosophila or budding yeast
* Disease working group has handed off mockup to AGR UI working group to start development
+
=== 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.
  
=== C3 working group ===
+
= January 27th, 2022 =
* Proposing ontology working group to handle ontology data and display
 
  
=== Datomic ===
+
== C. elegans BioCyc ==
* Juancarlos discussing with Adam, Sibyl, Matt, Kevin
+
*Schedule a demo session with Peter Karp
* People are working on URL widgets: person widgets updated and ready for production, except for lineage widget.
+
*Monday, Thursday, Friday mornings work for him and his team
* Some other URL widgets have also been completed
+
*Caltech preference?
 
 
=== ACEDB dependencies ===
 
* Raymond was asked to collect all CIT curator uses of ACEDB, e.g. programmatic access via ACE Perl
 
* Send Raymond list of any CIT ACEDB-dependent processes
 
* Going forward, how are model changes made/proposed?
 
* Are we still proposing models in ACEDB and having them be converted? Not sure
 
* We need to establish a models migration plan
 
* Curators should review cronjobs that may need access to ACEDB
 
* Juancarlos can collect list of cronjobs using ACEDB; will send email of list
 
* Karen: WB Wiki page for OA forms, tables, scripts, etc. : http://wiki.wormbase.org/index.php/OA_forms,_tables,_scripts,_etc
 
 
 
=== Upload ===
 
* CIT upload February 28th? Need to check with Hinxton
 
 
 
=== Nemametrix ===
 
* Sent two micropublications
 
* In review and given DOI's
 
 
 
=== Methods in Molecular Biology chapter ===
 
* Submission deadline April 1
 
* Mary Ann and Chris are organizing, will contact authors of older WormBook chapters
 
* We want to co-opt text from WormBook chapters that are specifically how-to guide with troubleshooting tips
 
* Everyone that has contributed this type of text, now or in this process, will be given authorship
 
* In future, could have small methods descriptions as micropublications; e.g. how to navigate the phenotype widget
 
* Content in older WormBook chapters that doesn't make it into the MIMB chapter could be micropublished
 
* We can review help desk inquiries to inform us as to what content should be included
 
 
 
 
 
 
 
== February 16, 2017 ==
 
 
 
=== SObA graph for GO annotations ===
 
* May be able to download a single image that can be browsed offline
 
* Phantom.js screenshot?
 
* Maybe download an SVG?
 
* May need to use the unweighted view for downloadable images
 
* Will want to create SObA graphs for expression soon
 
 
 
=== Phenotype and GO enrichment tools ===
 
* David (Angeles) has built the tools
 
* Raymond will send around links to the tools when ready
 
* Something to consider for GO enrichment: consider three branches separately or together?
 
 
 
=== Biocuration abstract deadline ===
 
* Tomorrow (Feb 17) deadline for poster abstracts
 
* AGR Disease working group submitted an abstract
 
 
 
=== LEGO curation call ===
 
* Regular Monday calls
 
* Lots of good discussion; much about using proper relations
 
* GO group this week discussed possibly establishing standards or recommendations
 
* May be good to divide up biological topics among curators
 
* Concern about over-proliferation of relations
 
 
 
== February 23, 2017 ==
 
 
 
=== SObA graph for GO annotations ===
 
* Added the ability to download a single image that can be browsed offline
 
Go to a graph for say, [http://tazendra.caltech.edu/~azurebrd/cgi-bin/testing/amigo/soba_go.cgi?action=annotSummaryCytoscape&focusTermId=WBGene00002335&fakeRootFlag=1&filterLongestFlag=1 let-60]
 
Zoom in to a level where labels are visible for all the nodes you want to show (Don' worry if some are off canvas).
 
Click "export png", right mouse button (YMMV) to "Save Image As"
 
Saved image is 8000 dpi wide, sufficient to show all text clearly.
 
 
 
=== Modeling and curation future in Datomic ===
 
* Will modeling take place directly in Datomic, or through ACEDB and the converter software?
 
* Test trial of modeling some change in Datomic and ACEDB?
 
* How much curator involvement in model changes?
 
* Will there be a board to approve model changes?
 
 
 
=== MIMB chapter ===
 
* Thank you to those who have already submitted their contribution to the google drive.
 
* Polite reminder to those who haven't to do so as soon as possible.
 
 
 
=== OA cosmetic changes ===
 
* Section heading for categories?
 
* Tab labels changing from number to a name?
 
* Field name font color configurable?
 

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?