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]]
  
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[[WormBase-Caltech_Weekly_Calls_2019|2019 Meetings]]
  
GoToMeeting link: https://www.gotomeet.me/wormbase1
 
  
  
= 2019 Meetings =
 
  
[[WormBase-Caltech_Weekly_Calls_January_2019|January]]
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= 2020 Meetings =
  
[[WormBase-Caltech_Weekly_Calls_February_2019|February]]
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[[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]]
 
  
[[WormBase-Caltech_Weekly_Calls_September_2019|September]]
 
  
[[WormBase-Caltech_Weekly_Calls_October_2019|October]]
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==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]]
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**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===
 +
*Nightly using Matt's wb-names-export.jar to get full output of genes from datomic/names service, and updating postgres based on that.

Latest revision as of 20:57, 14 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 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.