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_February_2020|February]]
 
[[WormBase-Caltech_Weekly_Calls_February_2020|February]]
  
 +
[[WormBase-Caltech_Weekly_Calls_March_2020|March]]
  
== March 5, 2020 ==
+
[[WormBase-Caltech_Weekly_Calls_April_2020|April]]
 
 
=== WormBase curation ===
 
* Tim Schedl: WB needs to do more curation for phenotype and variation
 
* Doing community curation, but not fast enough
 
* Would like to work on more automation; e.g. having Textpresso return all sentences mentioning an allele in papers that are predicted to have phenotype data
 
 
 
=== Alaksa ===
 
* Joesph may be able to meet with Raymond
 
* How can the tool be maintained? If it can't it needs to be pulled
 
  
=== Single cell expression tool ===
+
[[WormBase-Caltech_Weekly_Calls_May_2020|May]]
* Tool is here: http://de.wormcells.com/
 
* What do we need to consider for pulling into WormBase?
 
* Where does the data sit and how does the tool access it? Can we integrate the data more into WormBase (e.g. local curation databases)?
 
** Would want it to be in sync with WormBase releases
 
** May not need to reprocess with every release with current (small-ish) data set
 
* Fully integrated tool versus an embedded tool?
 
  
=== Name service updates ===
+
[[WormBase-Caltech_Weekly_Calls_June_2020|June]]
* For now we will stick to the CGIs that Juancarlos has built for variations and strains
 
* Juancarlos can discuss with Matt R. and Sibyl the possibility of integrating API requests to the Name service into a CGI form for the OA
 
  
 +
[[WormBase-Caltech_Weekly_Calls_July_2020|July]]
  
== March 12, 2020 ==
+
[[WormBase-Caltech_Weekly_Calls_August_2020|August]]
  
=== Cancelled meetings ===
+
[[WormBase-Caltech_Weekly_Calls_September_2020|September]]
* Meetings are being cancelled, including Biocuration 2020. Ranjana will update our Wormbase meeting page with a note to users (done)
 
* We should start doing online advertisement for micropublications with webinars
 
  
=== Storing invalid/avoided WBPersons and email addresses in Postgres ===
 
* Currently Chris has been maintaining ([https://docs.google.com/spreadsheets/d/1FHhQk_IZIBLYkOUdVf9Kfh5zx66rkHOEVFQQ6wzT2ks/edit?usp=sharing on Google sheets]) a list of papers, people, and email addresses to omit from future WormBase outreach requests
 
* Valerio would like to add these to Postgres to keep a more central repository of them
 
* Chris would still like to be able to readily update/edit the content of those lists
 
  
* Proposed solutions: Keep the list in a flat file and have a cron job to sync the data to postgres daily or create a simple form to create/modify entries directly in postgres
+
== October 1, 2020 ==
  
=== Updates on Alaska ===
+
=== 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 [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
  
Raymond and Eduardo met with Joseph and decided to have the tool running as is for now even though maintaining it can be hard
+
=== Phenotype association file idiosyncrasy ===
The future plan is to move the platform to Google colab to reduce maintainance work.
+
* 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.
  
==Nameservice discussion==
+
=== Server space in Chen Building ===
*Getting a token has worked for Chris and Ranjana
+
* It looks like that we will not have a specific space for server computers.
*Karen and Daniela need to get tokens
 
  
==Noctua GO-CAM updates==
 
*Noctua is a production tool available for annotations right now
 
*Create as many interconnected models and make available for curators is the ongoing goal
 
*Reactome models are in the process of being imported
 
*Real time validation messages as curation is being done, is being worked on
 
*Kimberly will send out the details for logging into Noctua and make sure all curators are on the login list
 
  
 +
== October 8, 2020 ==
  
== March 19, 2020 ==
+
=== Webinar Announcement ===
 +
* Here is the live registration site: http://tazendra.caltech.edu/~azurebrd/cgi-bin/forms/webinar.cgi
 +
* Caltech zoom allows 300 attendees.
  
=== Citace Upload ===
+
=== Descriptions from GO-CAM models ===
* Tuesday, March 31st
+
* 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
  
=== Latest ACEDB ===
+
=== Transcription Factors in WormBase ===
* Getting latest ACEDB build from staging FTP (for descriptions, etc.)
+
* 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)
  
=== Storing email addresses/persons to omit from requests ===
+
== October 15, 2020 ==
* Chris and Juancarlos will work on a form to submit email addresses and WBPerson IDs to Postgres
 
  
=== Mailing lists ===
+
=== BioGRID data sharing ===
* Let Todd know if you want to keep your caltech.edu account on the mailing lists
+
* 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
  
==March 26th==
 
===Community curation===
 
*Do we need to publicize any data form and urge Users to contribute? The AFP and phenotype forms already send targeted e-mail
 
* Paul S. is getting people from the lab to do phenotype curation; Chris G will run a tutorial for interested people
 
* Blog about phenotype form to make people generally aware
 
* Could the phenotype form be adapted for other species? Possibly but depends on:
 
** Whether genotypes could be loaded and recognized
 
  
=== AFP for older papers ===
+
== October 22, 2020 ==
* Discussed recently
 
* Many (all?) Old papers have already gone through the old AFP pipeline
 
* Need to check what has already been curated
 
  
=== Omit form ===
+
=== CHEBI ===
* http://tazendra.caltech.edu/~postgres/cgi-bin/omit_form.cgi
+
* Karen spoke to CHEBI personnel on Tuesday
* Can view, add, or edit persons, email addresses, and IP addresses to omit from email requests and IP address to block
+
* 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

Latest revision as of 18:06, 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