Difference between revisions of "WormBase-Caltech Weekly Calls"

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GoToMeeting link: https://www.gotomeet.me/wormbase1
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= 2020 Meetings =
 
= 2020 Meetings =
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[[WormBase-Caltech_Weekly_Calls_January_2020|January]]
 
[[WormBase-Caltech_Weekly_Calls_January_2020|January]]
  
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[[WormBase-Caltech_Weekly_Calls_February_2020|February]]
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[[WormBase-Caltech_Weekly_Calls_March_2020|March]]
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[[WormBase-Caltech_Weekly_Calls_April_2020|April]]
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[[WormBase-Caltech_Weekly_Calls_May_2020|May]]
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[[WormBase-Caltech_Weekly_Calls_June_2020|June]]
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[[WormBase-Caltech_Weekly_Calls_July_2020|July]]
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[[WormBase-Caltech_Weekly_Calls_August_2020|August]]
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[[WormBase-Caltech_Weekly_Calls_September_2020|September]]
  
== February 6, 2020 ==
 
  
=== Worcester Area Worm Meeting talk ===
+
== October 1, 2020 ==
* Confirmed for December 2020 or February 2021
 
  
=== Alaska software ===
+
=== Gene association file formats on FTP ===
* Code developed and maintained by Joseph, but not long term solution
+
* For example, current production release ONTOLOGY directory: ftp://ftp.wormbase.org/pub/wormbase/releases/current-production-release/ONTOLOGY/
* Raymond and Eduardo talked about taking it over
+
* Our association files have format "*.wb"; is this useful or necessary?
* Why have a web application vs. a command-line application?
+
* 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
** Wanted to make it easy, but also to capture meta data for WB
+
* 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(?)
* Should/will find out from Joseph about how hard it is to maintain the software
+
** File headers could possibly link to the format specification page
* Maybe it could be taken over by Alliance, as RNA-Seq/Microarray meta data are getting harmonized
 
* Expression working group working with Brian Oliver to have GEO take in more structured meta data
 
* Array Express tried requiring more structured meta data, but authors stopped submitting
 
* May be possible to build a form that collects meta data while simultaneously submitting to GEO in parallel
 
  
 +
=== 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.
  
== February 13, 2020 ==
+
=== Server space in Chen Building ===
 +
* It looks like that we will not have a specific space for server computers.
  
=== Alliance Literature Group ===
 
* Held first meeting on Monday, February 10th
 
* Regular meetings will be on Tuesdays at 10am/1pm/6pm
 
* Representatives from each group will give a brief overview of their literature pipelines before the group gets into details about deliverables
 
* Question about centralized paper repository; group needs guidance from Alliance PIs on how to proceed
 
  
=== ?Genotype class model ===
+
== October 8, 2020 ==
* [https://docs.google.com/document/d/19hP9r6BpPW3FSAeC_67FNyNq58NGp4eaXBT42Ch3gDE/edit?pli=1#bookmark=id.7r3e8pg19rd8 Proposal]
 
* Can aim to implement for WS277 but may have to wait until WS278
 
  
=== Genotype OA ===
+
=== Webinar Announcement ===
* Will put documentation [[Genotype|here]]
+
* Here is the live registration site: http://tazendra.caltech.edu/~azurebrd/cgi-bin/forms/webinar.cgi
 +
* Caltech zoom allows 300 attendees.
  
=== WB All-Hands Meeting ===
+
=== Descriptions from GO-CAM models ===
* [https://doodle.com/poll/7f65p4ba6d88ztzt Doodle poll]
+
* One suggestion for the Alliance is to create a description based on a GO-CAM model
* Any thoughts at this point? Still need to discuss with Hinxton, Toronto.
+
* 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 [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)
  
== February 20, 2020 ==
+
== October 15, 2020 ==
  
=== Genotype ===
+
=== BioGRID data sharing ===
* We will equate superficially similar/identical genotypes for now
+
* 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
* What if labs sequence strains later and find out more?
+
* Will need to consider a few points:
* Labs will have to report strains and their sequence and we back-curate accordingly
+
** 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
  
=== VC2010 assembly genes ===
+
=== Enriched genes ===
* WormMine now returning double the gene count for C. elegans genes because of incorporation of newest VC2010 assembly
+
* 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)
* How to best handle these "extra" genes?
+
* We should reconsider the ?Expression_cluster model to make sure we can appropriately model and communicate enrichment or subtypes thereof
* We could make different species entries that specify the assembly version
 
  
  
== February 27, 2020 ==
+
== October 22, 2020 ==
  
=== Genotype ===
+
=== CHEBI ===
* [[Genotype|Genotype Wiki page]] updated
+
* Karen spoke to CHEBI personnel on Tuesday
* Will start building Genotype OA
+
* 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
  
=== Outreach inbox ===
+
=== Training Webinar ===
* 65 unread messages pertaining to AFP, some dating back to June. Can we clean these up?
+
* Scheduled for tomorrow at 1pm Pacific/4pm Eastern
* Many are bounced emails messages
 
* Do we want a common place to track bad/bouncing email addresses? We need to distinguish addresses that bounce for policy/SPAM reasons versus those that are likely outdated or no longer in use.
 

Latest revision as of 18:40, 22 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


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