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]]
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[[WormBase-Caltech_Weekly_Calls_February_2020|February]]
  
[[WormBase-Caltech_Weekly_Calls_April_2019|April]]
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[[WormBase-Caltech_Weekly_Calls_March_2020|March]]
  
[[WormBase-Caltech_Weekly_Calls_May_2019|May]]
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[[WormBase-Caltech_Weekly_Calls_April_2020|April]]
  
[[WormBase-Caltech_Weekly_Calls_June_2019|June]]
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[[WormBase-Caltech_Weekly_Calls_May_2020|May]]
  
[[WormBase-Caltech_Weekly_Calls_July_2019|July]]
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[[WormBase-Caltech_Weekly_Calls_June_2020|June]]
  
[[WormBase-Caltech_Weekly_Calls_August_2019|August]]
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[[WormBase-Caltech_Weekly_Calls_July_2020|July]]
  
[[WormBase-Caltech_Weekly_Calls_September_2019|September]]
 
  
[[WormBase-Caltech_Weekly_Calls_October_2019|October]]
+
==July 9th, 2020==
 +
===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)
  
[[WormBase-Caltech_Weekly_Calls_November_2019|November]]
+
**simple confusion from authors, ex. mdh-1 and mdh-2
 +
*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.
  
== December 5, 2019 ==
+
===Noctua 2.0 form ready to use===
 +
*Caltech summer student will try using Noctua initially for dauer (neuronal signaling) pathways
  
=== New interaction Venn diagram tool ===
+
===Nightly names service updates to postgres===
* [https://staging.wormbase.org/species/c_elegans/gene/WBGene00000912#08--10 daf-16 interactions]
+
*Nightly using Matt's wb-names-export.jar to get full output of genes from datomic/names service, and updating postgres based on that.
* Venn diagram shows how various interactors have multiple interaction types with a common focus gene
 
* For a given selected gene set, you can copy to clipboard, download CSV, TSV, and link to enrichment analysis or WormMine
 
* Very nice! It would be great to have the gene list options here available wherever lists are provided in WormBase (Sibyl working on it)
 
* Request: add SimpleMine as another link out (go to SimpleMine with the gene list prepopulated)
 
* Request: could there be a toggle to include/exclude high-throughput interactions?
 
* Request: The Venn circle labels sometimes get in the way of seeing the diagram; can they be moved to the side or possibly replace simply with single letters like "P", "G" and "R" for "physical", "genetic" and "regulatory" respectively? Might still need a legend?
 
* Request: Change the wording "Browse selection" to something like "View/analyze gene list"
 
* Where else could we implement a similar type of Venn diagram tool? Disease or phenotype annotations?
 
  
=== New round of phenotype requests ===
 
* GMail really throttling email sending
 
* Chris will reach out to Google/GMail to see if we can:
 
** A) get a clear explanation about what their restrictions are and how they work and
 
** B) see if we can get a paid plan to help expedite the email process (see how much cost)
 
  
=== Aligning interaction data with GO and GO-CAM ===
+
==July 16th, 2020==
* The Alliance interactions working group is considering proposing a greater alignment between GO interaction annotations (like "binding" annotations with IPI evidence codes, for example) and Alliance molecular interaction annotations
+
===Citing ontologies and their versions===
* Also, would like to propose a pipeline for possibly automatically generating GO-CAM annotations/networks based on inferences made from phenotype annotations, genetic interactions, regulatory interactions, and molecular interactions
+
*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.
* Much of this depends on genetic perturbation (e.g. allele/variant) annotation to effects, like loss-of-function or gain-of-function annotations
+
*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.
** Would be good to get a sense from other Alliance members the extent to which we could rely on the presence of such annotations
+
*Some useful links
* Chris and Kimberly will meet to discuss further
+
**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).
=== Short SObA talk at Alliance meeting ===
+
**Note: OBO-foundry may not have been updated, but good practice to check your headers, anyway.
* Raymond prepared to give short talk on SObA to the Alliance group
 
 
 
=== Single cell data visualization tool ===
 
* Eduardo will present to Paul's lab meeting tomorrow
 
* Will discuss at Alliance expression working group pre-meeting
 

Latest revision as of 00:03, 16 July 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


July 9th, 2020

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
  • 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

  • Caltech summer student will try using Noctua initially for dauer (neuronal signaling) pathways

Nightly names service updates to postgres

  • Nightly using Matt's wb-names-export.jar to get full output of genes from datomic/names service, and updating postgres based on that.


July 16th, 2020

Citing ontologies and their versions

  • 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.
  • Some useful links