Difference between revisions of "WormBase-Caltech Weekly Calls"

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[[WormBase-Caltech_Weekly_Calls_August_2020|August]]
 
[[WormBase-Caltech_Weekly_Calls_August_2020|August]]
  
 +
[[WormBase-Caltech_Weekly_Calls_September_2020|September]]
  
== September 3, 2020 ==
 
  
=== WS279 Citace upload ===
+
== October 1, 2020 ==
* September 25
 
* Local CIT upload (to Wen) Tuesday September 22 by 10am Pacific
 
  
=== New AFP datatype for curation status form (CSF)? ===
+
=== Gene association file formats on FTP ===
* afp_othergenefunc (to capture gene function other than enzymatic activity)
+
* For example, current production release ONTOLOGY directory: ftp://ftp.wormbase.org/pub/wormbase/releases/current-production-release/ONTOLOGY/
* Can wait a bit before adding to CSF; if there will be dedicated curation for that data type we may add later
+
* 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
  
=== GO annotation for description ===
+
=== Phenotype association file idiosyncrasy ===
* Kimberly will look into 'male tail tip developement' terms for description
+
* 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
 +
* Proposal is to put WBPerson IDs in column 6 for personal communications. Chris & Karen will check if this will work.
  
=== Migrate wobr1 server to AWS ===
+
=== Server space in Chen Building ===
* SOLR, WOBr, SObA, Enrichment analysis
+
* It looks like that we will not have a specific space for server computers.
* Working with Sibyl on the process
 
* Will try migrating wobr1 first, as a test case
 
* May eventually move, for example, Tazendra
 
** Will there be drawbacks to doing this?
 
** Can we regularly ssh into Tazendra on AWS without issue? Costs for transferring large files
 
* Don't yet know the details of the costs, but we can try and keep track
 
* We should move into WB or Alliance AWS instances (or Stanford)
 
  
=== WormBase talk at Boston Area Worm Meeting ===
 
* https://www.umassmed.edu/ambroslab/meetings/bawm/
 
* Meeting will be virtual on Zoom
 
* Chris will give a talk September 23rd, 6pm Eastern, 3pm Pacific (probably first speaker but not sure)
 
* Send topic requests to Chris for the talk
 
* Current topics:
 
** Micropublications
 
** Author First Pass
 
** Automated Gene Descriptions
 
** Community Curation
 
** WB Query Tools
 
* Chris will ask organizers if others can join: post on WormBase blog? May draw too large an audience for the zoom channel;
 
* If the organizers record the talk, we can post it on the blog and WB YouTube channel
 
  
 +
== October 8, 2020 ==
  
== September 10, 2020 ==
+
=== Webinar Announcement ===
 +
* Here is the live registration site: http://tazendra.caltech.edu/~azurebrd/cgi-bin/forms/webinar.cgi
 +
* Caltech zoom allows 300 attendees.
  
=== GO GAF Files ===
+
=== Descriptions from GO-CAM models ===
* WS278 GO GAF is using the new 2.2 file format
+
* One suggestion for the Alliance is to create a description based on a GO-CAM model
* [https://github.com/geneontology/geneontology.github.io/blob/issue-go-annotation-2917-gaf-2_2-doc/_docs/go-annotation-file-gaf-format-22.md Specifications]
+
* Could also micropublish some descriptions (semi-automated?)
* GO will not be emitting GAF 2.2 until the end of the year (will try to get a fixed date)
+
* Can make curators authors of micropublications for GO-CAM models/pathways
* Implications for gene descriptions, but what about other tools, applications at WB?
 
* Some errors in the current WS278 GAF, but will get fixed soon
 
** Impacts gene descriptions for WS278, so using WS277 for now; will be OK once source GAF is fixed
 
  
===Disease files on FTP===
+
=== Transcription Factors in WormBase ===
*No changes for WS278 FTP files, except an extra custom file that Hinxton is producing mostly for gene descriptions so that we don't get the wrong human diseases via poor orthology calls (see GitHub issue https://github.com/WormBase/website/issues/7839)
+
* WormBase has a ?Transcription_factor class that is currently underutilized
*Will be some consolidation of disease data possibly for WS279 FTP files, implications for downstream tools--gene descriptions, WOBR, ??
+
* Chris spoke with Gary Williams about the status as he has done much of the work on the class
 +
* Because transcription factors can often be complexes, it was decided to create the ?Transcription_factor class rather than simply an extension of tags to the existing ?Gene class
 +
* The class seems reasonably complete; it's important to note that some TFs are general transcription factors, not necessarily gene-specific or sequence-specific DNA-binding TFs; it will be good to make that distinction clear to users
 +
* Chris has compiled a [https://docs.google.com/spreadsheets/d/1KdmvybWDWHXdlJwZgfleL4xHDoyPoYR13WAUcERF82g/edit?usp=sharing Google sheet] to assess the class before Gary W. leaves WB in the next couple of weeks
 +
* The Google sheet has several tabs/worksheets, including one for the ACEDB data model (and notes about usage of tags), a summary table of associated genes, bound sequence features, existence of other protein-DNA binding data, etc.
 +
* It would be good to make TF binding info (per gene and globally) more accessibly to our users, maybe via a new widget on gene pages (e.g. list incoming, regulating TFs and, for TF genes themselves, list potential target genes)
  
=== WormBase talk at Worcester Area Worm Meeting ===
+
== October 15, 2020 ==
* Chris set to give talk on December 1st, 2020, via Zoom, 4pm (or 4:30pm) EST / 1pm Pacific
 
* 30 minute slot; complementary to BAWM talk?
 
* WormBase members can attend
 
  
=== WormBase talk at Boston Area Worm Meeting ===
+
=== BioGRID data sharing ===
* https://www.umassmed.edu/ambroslab/meetings/bawm/
+
* Rose from BioGRID proposed that BioGRID curate high-throughput C. elegans interaction datasets, capturing confidence scores when available, and making those annotations available to WormBase for regular ingest
* Chris will give a talk September 23rd (< 2 weeks), 6pm Eastern, 3pm Pacific (probably first speaker but not sure)
+
* Will need to consider a few points:
* WormBase members can attend; Zoom link will be sent next Monday
+
** BioGRID doesn't curate protein-DNA interactions
 +
** We don't yet know the turn-around timeline for BioGRID curation of worm datasets; WB may be able to curate them much sooner
 +
* Chris and Jae will work with Rose et al. to coordinate HTP curation
  
=== Worm Anatomy Ontology Fixes ===
+
=== Enriched genes ===
* Raymond working on addressing warnings and errors (missing definitions, duplicate labels, duplicate definitions)
+
* Some genes are considered "enriched" for an expression cluster data set even if the enrichment was in comparison to another cell or tissue (not whole animal)
* Assessing the best way to address them
+
* We should reconsider the ?Expression_cluster model to make sure we can appropriately model and communicate enrichment or subtypes thereof
* Would be good to be able to automate some edits; options:
 
** Use OWL API (need someone proficient in coding with OWL API)
 
** Convert to OBO, programmatically edit, convert back to OWL?
 
** Use Cellfie plugin for Protege?
 
** Should discuss with Nico once we have a sense as to what changes need to be made
 
  
=== Dead Variations in Postgres ===
 
* Currently pulling in variations/alleles from Postgres to populate "allele" and "genetic perturbation" categories in Textpresso
 
* Noticed that many transgene names were being included, which can result in false positives for the categories
 
* Looking at Postgres table "obo_data_variation", there are ~100,000 entries, ~40,000 with status "Dead" and ~60,000 with status "Live"
 
* Trying to determine the history of the "Dead" variations, where most of the transgene names are coming from
 
* May still want to include "Dead" variations/alleles in Textpresso category for historical reasons
 
* We could use pattern matching to filter out transgene names
 
* Possible to search C. elegans corpus for all "real" allele public names in the "Dead" set to see if they should still be included in categories
 
  
=== WS279 Citace Upload ===
+
== October 22, 2020 ==
* Local Caltech upload to Spica, Tuesday September 22, 10am Pacific
 
  
 +
=== CHEBI ===
 +
* Karen spoke to CHEBI personnel on Tuesday
 +
* CHEBI only has ~2 curators to create new entities
 +
* CHEBI had submitted a proposal to establish pipelines to process requests from MODs
 +
* Chemical Translation Service (CTS)
 +
* OxO = https://www.ebi.ac.uk/spot/oxo/search
  
== September 17, 2020 ==
+
=== Training Webinar ===
 
+
* Scheduled for tomorrow at 1pm Pacific/4pm Eastern
=== Species errors in CITace ===
 
* Wen is reviewing species coming from CIT and will send individual curators lists of species that need correction
 
 
 
=== Webinars ===
 
* We could perform a general WormBase webinar to cover all of WormBase
 
* Follow up with more specific webinars in following months: JBrowse, WormMine, Micropublication, AFP
 
* Chris and Wen can discuss how to setup
 

Latest revision as of 18:40, 22 October 2020

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January

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May

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August

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 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
  • Proposal is to put WBPerson IDs in column 6 for personal communications. Chris & Karen will check if this will work.

Server space in Chen Building

  • It looks like that we will not have a specific space for server computers.


October 8, 2020

Webinar Announcement

Descriptions from GO-CAM models

  • One suggestion for the Alliance is to create a description based on a GO-CAM model
  • Could also micropublish some descriptions (semi-automated?)
  • Can make curators authors of micropublications for GO-CAM models/pathways

Transcription Factors in WormBase

  • WormBase has a ?Transcription_factor class that is currently underutilized
  • Chris spoke with Gary Williams about the status as he has done much of the work on the class
  • Because transcription factors can often be complexes, it was decided to create the ?Transcription_factor class rather than simply an extension of tags to the existing ?Gene class
  • The class seems reasonably complete; it's important to note that some TFs are general transcription factors, not necessarily gene-specific or sequence-specific DNA-binding TFs; it will be good to make that distinction clear to users
  • Chris has compiled a Google sheet to assess the class before Gary W. leaves WB in the next couple of weeks
  • The Google sheet has several tabs/worksheets, including one for the ACEDB data model (and notes about usage of tags), a summary table of associated genes, bound sequence features, existence of other protein-DNA binding data, etc.
  • It would be good to make TF binding info (per gene and globally) more accessibly to our users, maybe via a new widget on gene pages (e.g. list incoming, regulating TFs and, for TF genes themselves, list potential target genes)

October 15, 2020

BioGRID data sharing

  • Rose from BioGRID proposed that BioGRID curate high-throughput C. elegans interaction datasets, capturing confidence scores when available, and making those annotations available to WormBase for regular ingest
  • Will need to consider a few points:
    • BioGRID doesn't curate protein-DNA interactions
    • We don't yet know the turn-around timeline for BioGRID curation of worm datasets; WB may be able to curate them much sooner
  • Chris and Jae will work with Rose et al. to coordinate HTP curation

Enriched genes

  • Some genes are considered "enriched" for an expression cluster data set even if the enrichment was in comparison to another cell or tissue (not whole animal)
  • We should reconsider the ?Expression_cluster model to make sure we can appropriately model and communicate enrichment or subtypes thereof


October 22, 2020

CHEBI

  • Karen spoke to CHEBI personnel on Tuesday
  • CHEBI only has ~2 curators to create new entities
  • CHEBI had submitted a proposal to establish pipelines to process requests from MODs
  • Chemical Translation Service (CTS)
  • OxO = https://www.ebi.ac.uk/spot/oxo/search

Training Webinar

  • Scheduled for tomorrow at 1pm Pacific/4pm Eastern