Difference between revisions of "WormBase-Caltech Weekly Calls"

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[[WormBase-Caltech_Weekly_Calls_2018|2018 Meetings]]
 
[[WormBase-Caltech_Weekly_Calls_2018|2018 Meetings]]
  
 +
[[WormBase-Caltech_Weekly_Calls_2019|2019 Meetings]]
  
GoToMeeting link: https://www.gotomeet.me/wormbase1
 
  
  
= 2019 Meetings =
 
  
[[WormBase-Caltech_Weekly_Calls_January_2019|January]]
+
= 2020 Meetings =
  
[[WormBase-Caltech_Weekly_Calls_February_2019|February]]
+
[[WormBase-Caltech_Weekly_Calls_January_2020|January]]
  
[[WormBase-Caltech_Weekly_Calls_March_2019|March]]
+
[[WormBase-Caltech_Weekly_Calls_February_2020|February]]
  
[[WormBase-Caltech_Weekly_Calls_April_2019|April]]
+
[[WormBase-Caltech_Weekly_Calls_March_2020|March]]
  
[[WormBase-Caltech_Weekly_Calls_May_2019|May]]
+
[[WormBase-Caltech_Weekly_Calls_April_2020|April]]
  
 +
[[WormBase-Caltech_Weekly_Calls_May_2020|May]]
  
== June 6, 2019 ==
+
[[WormBase-Caltech_Weekly_Calls_June_2020|June]]
  
=== New SObA graphs ===
+
[[WormBase-Caltech_Weekly_Calls_July_2020|July]]
* May put graphs within existing widgets, but don't need to rush to get that ready for IWM
 
  
=== Phenotype association file format ===
+
[[WormBase-Caltech_Weekly_Calls_August_2020|August]]
* May be best to leave the format as is
 
* There are problems; paper IDs keep switching columns
 
* Would need to revisit the reasoning for why we do it that way
 
* When will the Alliance produce a similar/replacement file? Not sure
 
  
=== Phenotype requests ===
+
[[WormBase-Caltech_Weekly_Calls_September_2020|September]]
* Sent out 1140 emails on May 30
 
* Since have received 374 annotations from 54 papers (42 requested, 12 additional)
 
* 21 papers flagged as not having phenotypes
 
* Of 1140 papers emailed about, 35 emails bounced, and have received some flagging or curation on 63 (63/1105 = ~6% response rate), in first week
 
  
  
== June 13, 2019 ==
+
== October 1, 2020 ==
  
=== IWM ===
+
=== Gene association file formats on FTP ===
* Coordinating transportation of swag boxes to Pauley Pavilion
+
* For example, current production release ONTOLOGY directory: ftp://ftp.wormbase.org/pub/wormbase/releases/current-production-release/ONTOLOGY/
* Workshop on Saturday June 22, from 1pm to 2:30pm
+
* Our association files have format "*.wb"; is this useful or necessary?
* Saturday morning micropublication breakfast 7:30 - 8:30am
+
* 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
* Workshop
+
* 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(?)
** Presenters: it may be best to present as use cases rather than a research project
+
** File headers could possibly link to the format specification page
** Chris will cover SimpleMine for Wen
 
** Chris: won't do live demo; only screenshots, maybe some video
 
* Paul's lab will do marathon bibs to show lab affiliation and graphical abstract
 
* Paul's talk
 
** Cover Alliance
 
** New features
 
*** SObA (for new data)
 
*** Complete for protein-protein interactions
 
*** RNASeq tools
 
*** Updated automated gene concise descriptions?
 
** Phenotype community curation
 
*** Chris will send Paul numbers on: top community curators, overall stats (number of annotations, papers, curators)
 
** Author First Pass
 
** Micropublication
 
  
=== SGD SAB ===
+
=== Phenotype association file idiosyncrasy ===
* Paul attended
+
* As we've discussed previously, there is an oddity to how the phenotype association file we provide lists, or doesn't, references
* Alliance publicity was discussed
+
* According to the GAF spec, column 6 is for reference and is required, whereas column 8 is "With (or) From" and is optional
* SAB likes the Alliance orthology features
+
* 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
* Working on topics: displaying papers and data
+
* 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.
* Pathways: discussion about best approach
+
** 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
* Metabolic engineering
+
* 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)?
* Meta data about RNASeq data
+
* 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
** SPELL tool, basically only tool of its kind available; need new tools
+
* Proposal is to put WBPerson IDs in column 6 for personal communications. Chris & Karen will check if this will work.
* Species-specific proteins: how best to find them? HMMs (Jackhammer)?
 
  
=== Concise descriptions ===
+
=== Server space in Chen Building ===
* Progress being made within the Alliance to update the automated concise gene descriptions
+
* It looks like that we will not have a specific space for server computers.
* We will still accept manually written descriptions and display them in parallel with automated descriptions
 
  
=== Micropublications ===
 
* If people are requesting manually written gene descriptions, they could submit a microreview
 
* Concern was expressed about how to handle a really high throughput of submissions:
 
** Daniela: Working towards automating as much of the processing pipeline as possible
 
** Raymond: The throughput will be handled appropriately depending on demand; priority scheme will help
 
** Not getting lots of submissions yet, probably won't be inundated in the near future
 
** Karen: tools are still being developed; the platform is not being advertised as much as it could be; will ramp up outreach and communication once tools are in place to handle more submissions
 
* Karen: Micropublications team will reach out to curators to help build submission forms for respective data types
 
  
=== Undiagnosed Disease Network data ===
+
== October 8, 2020 ==
* Andy Golden will meet with Ranjana and Chris at IWM to discuss
 
* Andy asked about protocol pages at WormBase?
 
* Paul: Bioprotocols and Protocols IO
 
* Maybe we could interface with those existing resources to link to relevant protocols from WormBase (and WormBook)
 
  
==June 27th, 2019==
+
=== Webinar Announcement ===
===IWM 2019===
+
* Here is the live registration site: http://tazendra.caltech.edu/~azurebrd/cgi-bin/forms/webinar.cgi
*Impressions, analysis, feedback from Users etc etc
+
* Caltech zoom allows 300 attendees.
  
===Giving disease model annotations a stable identifier===
+
=== Descriptions from GO-CAM models ===
*Currently disease model annotations get a temporary ID at the time of dump,  
+
* One suggestion for the Alliance is to create a description based on a GO-CAM model
<pre style="white-space: pre-wrap;  
+
* Could also micropublish some descriptions (semi-automated?)
white-space: -moz-pre-wrap;
+
* Can make curators authors of micropublications for GO-CAM models/pathways
white-space: -pre-wrap;
+
 
white-space: -o-pre-wrap;
+
=== Transcription Factors in WormBase ===
word-wrap: break-word">
+
* WormBase has a ?Transcription_factor class that is currently underutilized
Disease_model_annotation : "00000004"
+
* Chris spoke with Gary Williams about the status as he has done much of the work on the class
Disease_term "DOID:0050833"
+
* 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
Disease_of_species "Homo sapiens"
+
* 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
Variation "WBVar00275555"
+
* 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
Disease_relevant_gene "WBGene00011559"
+
* 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.
Inferred_gene "WBGene00011559"
+
* 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)
Association_type "is_implicated_in"
+
 
Evidence_code "IMP"
+
== October 15, 2020 ==
Genetic_sex "hermaphrodite"
+
 
Paper_evidence "WBPaper00035924"
+
=== BioGRID data sharing ===
Database "OMIM" "gene" "613891 "
+
* 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
Database "OMIM" "disease" "258900"
+
* Will need to consider a few points:
Curator_confirmed "WBPerson324"
+
** BioGRID doesn't curate protein-DNA interactions
Date_last_updated "2017-04-24"
+
** We don't yet know the turn-around timeline for BioGRID curation of worm datasets; WB may be able to curate them much sooner
</pre>
+
* Chris and Jae will work with Rose et al. to coordinate HTP curation
*Would like to institute stable identifiers across releases, so the plan is to call these objects, 'WBDisease_annotation:<number>' so then the above identifier would become ''WBDisease_annotation:00000004"
+
 
*ID convention--is underscore allowed?
+
=== Enriched genes ===
*Is 'WBDisease_annotation:00000004' too long for acedb?
+
* 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

Latest revision as of 16:33, 15 October 2020

Previous Years

2009 Meetings

2011 Meetings

2012 Meetings

2013 Meetings

2014 Meetings

2015 Meetings

2016 Meetings

2017 Meetings

2018 Meetings

2019 Meetings



2020 Meetings

January

February

March

April

May

June

July

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