Difference between revisions of "WormBase-Caltech Weekly Calls"

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[[WormBase-Caltech_Weekly_Calls_July_2020|July]]
 
[[WormBase-Caltech_Weekly_Calls_July_2020|July]]
  
 +
[[WormBase-Caltech_Weekly_Calls_August_2020|August]]
  
==July 9th, 2020==
+
[[WormBase-Caltech_Weekly_Calls_September_2020|September]]
===Gene names issue in SimpleMine and other mining tools===
 
*Wen: Last week, Jonathan Ewbank raised the issue of gene names that may refer to multiple objects.
 
*this can be an issue for multiple data mining tools including WormMine, BioMart, and Gene Set Enrichment.
 
*Perhaps have a standalone approach to check if any gene name among a list may refer to multiple objects (users check their name lists before submitting them to any data mining tool).
 
*Jae: The public name issue has heterogeneous natures. That means there may be no single solution to solve all those problems.
 
*Gene list curation from high-throughput studies, confusing usage of public names probably less than 2% (still cannot be ignored). See examples below--
 
**single public name is assigned to multiple WBgene ID, Wen has a list of these genes
 
**overlapped or dicistronic genes, ex. mrpl-44 and F02A9.10
 
**overlapped or dicistronic, but has a single sequence name, examples:
 
    exos-4.1 and tin-9.2 (B0564.1)
 
    eat-18 and lev-10 (Y105E8A.7)
 
    cha-1 and unc-17 (ZC416.8)
 
  
**simple confusion from authors, ex. mdh-1 and mdh-2
+
[[WormBase-Caltech_Weekly_Calls_October_2020|October]]
*One of the most significant problems is a propagation to other DB and papers of  these gene name issues.
 
*We can make a special note for each gene page, but the people using batch analysis could not catch that easily.
 
*Conclusion: Jae and Wen will work on a tool that lets Users "sanitize" their gene lists before submission to data mining tools.  They will also write a microPub explaining this issue to the community.
 
  
===Wormicloud===
 
*Please test and leave any feedback on the word cloud tool (Wormicloud), https://wormicloud.textpressolab.com/
 
*Valerio and Jae have worked on a tool that uses data in Textpresso; given a keyword, eg. "transposon", the tool generates a word cloud and word trend.
 
*Any keyword can generate a graph that plots trends of occurence across the years in publication abstracts.
 
  
===Noctua 2.0 form ready to use===
+
==Nov 5th, 2020==
*Caltech summer student will try using Noctua initially for dauer (neuronal signaling) pathways
 
  
===Nightly names service updates to postgres===
+
===WS279 GAF 2.0 and disease files===
*Nightly using Matt's wb-names-export.jar to get full output of genes from datomic/names service, and updating postgres based on that.
+
*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.
  
==July 16th, 2020==
+
===MicroPub user webinar on Nov 9th===
===Citing ontologies and their versions===
+
*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.
*Came up in the context of the Alliance: It would be best practice to provide users with the list of ontologies used and their versions/date.
+
 
*If WB ontology developers could make sure their ontology file headers (WB anatomy ontology, WB life stage, etc.) conformed to obo file header specifications, then it would be easy to pull in version and date information into the Alliance.
+
===WS280 deadlines===
*Some useful links
+
*Caltech files due for citace: Dec 15th, 2020
**http://www.obofoundry.org/principles/fp-004-versioning.html
+
 
**http://obo-dashboard-test.ontodev.com/ (you can see that wbbt, wbls version metadata attribute is generating a warning).
+
 
**Note: OBO-foundry may not have been updated, but good practice to check your headers, anyway.
+
==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
 +
* 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
 +
 
 +
 
 +
== 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

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

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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