Difference between revisions of "WormBase-Caltech Weekly Calls"

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[[WormBase-Caltech_Weekly_Calls_September_2020|September]]
 
[[WormBase-Caltech_Weekly_Calls_September_2020|September]]
  
 +
[[WormBase-Caltech_Weekly_Calls_October_2020|October]]
  
== October 1, 2020 ==
 
  
=== Gene association file formats on FTP ===
+
==Nov 5th, 2020==
* 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 ===
+
===WS279 GAF 2.0 and disease files===
* As we've discussed previously, there is an oddity to how the phenotype association file we provide lists, or doesn't, references
+
*Valerio and Ranjana still working with the GAF 2.0 files to generate gene descriptions
* According to the GAF spec, column 6 is for reference and is required, whereas column 8 is "With (or) From" and is optional
+
*Valerio and Ranjana will probably have a meeting with Magdalena to sort out the FTP file issues for gene descriptions
* 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
+
*Will let Raymond know if the disease GAFs are okay after they test these for gene descriptions
* 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.
+
*Raymond needs the GAFs for WoBR
** 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 ===
+
===Experimenting with addeding new citace data to the current WS release ===
* It looks like that we will not have a specific space for server computers.
+
*Wen will take the newest expression, physical interaction, and paper class from postgres, add them to WS279 to create a "WS279.1" version of ACeDB database. Then compare WS279.1 to WS279 by comparing the SimpleMine results generated from these two versions of ACeDB. The goal is to explore the possibility of notifying users some of the new curation since the data freeze for the WS build.
  
 +
===MicroPub user webinar on Nov 9th===
 +
*Ranjana and Kimberly have conflicts--Alliance call and GO call. Anyway microPub team is running the show and they have other WormBasers to help as well.
  
== October 8, 2020 ==
+
===WS280 deadlines===
 +
*Caltech files due for citace: Dec 15th, 2020
  
=== Webinar Announcement ===
 
* Here is the live registration site: http://tazendra.caltech.edu/~azurebrd/cgi-bin/forms/webinar.cgi
 
* Caltech zoom allows 300 attendees.
 
  
=== Descriptions from GO-CAM models ===
+
==Nov 12th, 2020==
* One suggestion for the Alliance is to create a description based on a GO-CAM model
+
=== Cynthia Kenyon tool ===
* Could also micropublish some descriptions (semi-automated?)
+
* developed a new tool for the worm, complete with tutorials, for analyzing gene expression data using Gene Module analysis.
* Can make curators authors of micropublications for GO-CAM models/pathways
+
* tool at http://genemodules.org
 +
* add link outs from the gene expression widget or add in general WB tools?
 +
* if we want to incorporate we need to have it updated.
 +
* are they maintaining it?
 +
* there's no RNAseq, can be outdated
 +
* maybe good to add a blog post
  
=== Transcription Factors in WormBase ===
+
=== Graphical curation tool update===
* WormBase has a ?Transcription_factor class that is currently underutilized
+
* We will show a live demo on the current state of the graphical curation tool
* 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)
 
  
== October 15, 2020 ==
+
=== Curating to human genes in ACEDB ===
 +
* Karen requested option to curate constructs with human genes
 +
* Would we need to change our human genes in ACEDB? For example, migrate from Ensembl IDs to HGNC IDs as primary keys?
 +
* Will discuss on next site-wide call
  
=== BioGRID data sharing ===
+
=== GAF (and GAF-like) file headers ===
* 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
+
* GO GAF files (on FTP, WS279) for WormBase now in 2.2 format with header like
* Will need to consider a few points:
+
!gaf-version: 2.2
** BioGRID doesn't curate protein-DNA interactions
+
!generated-by: WormBase
** We don't yet know the turn-around timeline for BioGRID curation of worm datasets; WB may be able to curate them much sooner
+
!date-generated: 2020-10-30
* Chris and Jae will work with Rose et al. to coordinate HTP curation
+
! WB annotations 00015014
 +
* For files that can migrate to 2.2 format (e.g. always require column 4 qualifier) we could adopt a similar header
 +
* For other files (that cannot always have a qualifier in column 4), we could stick to 2.0 format with a header like:
 +
!gaf-version: 2.0
 +
!generated-by: WormBase
 +
!date-generated: 2020-10-30
 +
* Current need is to include information about format specification, possibly in addition to other extra header content.
 +
* New proposed headers:
 +
!project-URL: https://wormbase.org
 +
!specification-URL: https://github.com/geneontology/geneontology.github.io/blob/issue-go-annotation-2917-gaf-2_2-doc/_docs/go-annotation-file-gaf-format-22.md
 +
OR
 +
!specification-URL: https://wiki.wormbase.org/index.php/WormBase_gene_association_file
 +
!project-release: WS279
 +
* Could repurpose the Wiki page: https://wiki.wormbase.org/index.php/WormBase_gene_association_file from internal docs only to include user guide info, including how our GAF-like files deviate in format from standard GAF
  
=== 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
 
  
 +
== Nov 19, 2020 ==
  
== October 22, 2020 ==
+
=== Webinars ===
 +
* JBrowse webinar tomorrow (Friday)
 +
** Ranjana will host; Wen will provide tech support; Daniela will collect user questions from chat in Google Doc; Chris will write staff answers to questions in Google Doc
 +
* Background slides put together for when audience is waiting
 +
* Wen will start the meeting at 9:30am Pacific; can run a test poll
 +
* Questions will be collected in Google Doc; answers can be written into the Google Doc in real time; we can use the Google Doc as a reference to assemble FAQs later
  
=== CHEBI ===
+
=== Alaska ===
* Karen spoke to CHEBI personnel on Tuesday
+
* Is Eduardo still working on it?
* CHEBI only has ~2 curators to create new entities
+
* He replied to a user asking about Alaska
* CHEBI had submitted a proposal to establish pipelines to process requests from MODs
+
* Is it still running? Maintained?
* Chemical Translation Service (CTS)
+
* Can we tell what usage it gets?
* OxO = https://www.ebi.ac.uk/spot/oxo/search
+
* Is it useful for the Alliance? Maybe can write it into grant?
 +
* Is it commercially viable? Maybe someone can write an SBIR grant proposal?
  
=== Training Webinar ===
+
=== Server space ===
* Scheduled for tomorrow at 1pm Pacific/4pm Eastern
+
* No new space in Chen building
 
+
* Many servers will stay in a server room where they are currently
 
+
* Other servers we will need to see if they can be moved to Chen
== October 29, 2020 ==
+
* Paul may have some space for servers in his lab designated space (or his own office)
 
+
* It may be possible to move some machines over to the WB space in Chen as soon as we can get a key, but may have to wait until the official move in late January
=== Overview Webinar debriefing ===
 
* What's Good
 
* What needs improvement
 
* Participant requests:
 
  A place to look for Worm methods (a public {moderated} wiki page?)
 

Latest revision as of 17:52, 19 November 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


Nov 5th, 2020

WS279 GAF 2.0 and disease files

  • Valerio and Ranjana still working with the GAF 2.0 files to generate gene descriptions
  • Valerio and Ranjana will probably have a meeting with Magdalena to sort out the FTP file issues for gene descriptions
  • Will let Raymond know if the disease GAFs are okay after they test these for gene descriptions
  • Raymond needs the GAFs for WoBR

Experimenting with addeding new citace data to the current WS release

  • Wen will take the newest expression, physical interaction, and paper class from postgres, add them to WS279 to create a "WS279.1" version of ACeDB database. Then compare WS279.1 to WS279 by comparing the SimpleMine results generated from these two versions of ACeDB. The goal is to explore the possibility of notifying users some of the new curation since the data freeze for the WS build.

MicroPub user webinar on Nov 9th

  • Ranjana and Kimberly have conflicts--Alliance call and GO call. Anyway microPub team is running the show and they have other WormBasers to help as well.

WS280 deadlines

  • Caltech files due for citace: Dec 15th, 2020


Nov 12th, 2020

Cynthia Kenyon tool

  • developed a new tool for the worm, complete with tutorials, for analyzing gene expression data using Gene Module analysis.
  • tool at http://genemodules.org
  • add link outs from the gene expression widget or add in general WB tools?
  • if we want to incorporate we need to have it updated.
  • are they maintaining it?
  • there's no RNAseq, can be outdated
  • maybe good to add a blog post

Graphical curation tool update

  • We will show a live demo on the current state of the graphical curation tool

Curating to human genes in ACEDB

  • Karen requested option to curate constructs with human genes
  • Would we need to change our human genes in ACEDB? For example, migrate from Ensembl IDs to HGNC IDs as primary keys?
  • Will discuss on next site-wide call

GAF (and GAF-like) file headers

  • GO GAF files (on FTP, WS279) for WormBase now in 2.2 format with header like
!gaf-version: 2.2
!generated-by: WormBase
!date-generated: 2020-10-30
! WB annotations 00015014
  • For files that can migrate to 2.2 format (e.g. always require column 4 qualifier) we could adopt a similar header
  • For other files (that cannot always have a qualifier in column 4), we could stick to 2.0 format with a header like:
!gaf-version: 2.0
!generated-by: WormBase
!date-generated: 2020-10-30
  • Current need is to include information about format specification, possibly in addition to other extra header content.
  • New proposed headers:
!project-URL: https://wormbase.org
!specification-URL: https://github.com/geneontology/geneontology.github.io/blob/issue-go-annotation-2917-gaf-2_2-doc/_docs/go-annotation-file-gaf-format-22.md

OR

!specification-URL: https://wiki.wormbase.org/index.php/WormBase_gene_association_file
!project-release: WS279


Nov 19, 2020

Webinars

  • JBrowse webinar tomorrow (Friday)
    • Ranjana will host; Wen will provide tech support; Daniela will collect user questions from chat in Google Doc; Chris will write staff answers to questions in Google Doc
  • Background slides put together for when audience is waiting
  • Wen will start the meeting at 9:30am Pacific; can run a test poll
  • Questions will be collected in Google Doc; answers can be written into the Google Doc in real time; we can use the Google Doc as a reference to assemble FAQs later

Alaska

  • Is Eduardo still working on it?
  • He replied to a user asking about Alaska
  • Is it still running? Maintained?
  • Can we tell what usage it gets?
  • Is it useful for the Alliance? Maybe can write it into grant?
  • Is it commercially viable? Maybe someone can write an SBIR grant proposal?

Server space

  • No new space in Chen building
  • Many servers will stay in a server room where they are currently
  • Other servers we will need to see if they can be moved to Chen
  • Paul may have some space for servers in his lab designated space (or his own office)
  • It may be possible to move some machines over to the WB space in Chen as soon as we can get a key, but may have to wait until the official move in late January