Difference between revisions of "WormBase-Caltech Weekly Calls"

From WormBaseWiki
Jump to navigationJump to search
 
(465 intermediate revisions by 9 users not shown)
Line 21: Line 21:
 
[[WormBase-Caltech_Weekly_Calls_2019|2019 Meetings]]
 
[[WormBase-Caltech_Weekly_Calls_2019|2019 Meetings]]
  
 +
[[WormBase-Caltech_Weekly_Calls_2020|2020 Meetings]]
  
 +
= 2021 Meetings =
  
 +
[[WormBase-Caltech_Weekly_Calls_January_2021|January]]
  
= 2020 Meetings =
+
[[WormBase-Caltech_Weekly_Calls_February_2021|February]]
  
[[WormBase-Caltech_Weekly_Calls_January_2020|January]]
+
[[WormBase-Caltech_Weekly_Calls_March_2021|March]]
  
[[WormBase-Caltech_Weekly_Calls_February_2020|February]]
+
[[WormBase-Caltech_Weekly_Calls_April_2021|April]]
  
[[WormBase-Caltech_Weekly_Calls_March_2020|March]]
+
[[WormBase-Caltech_Weekly_Calls_May_2021|May]]
  
[[WormBase-Caltech_Weekly_Calls_April_2020|April]]
+
[[WormBase-Caltech_Weekly_Calls_June_2021|June]]
  
[[WormBase-Caltech_Weekly_Calls_May_2020|May]]
+
[[WormBase-Caltech_Weekly_Calls_July_2021|July]]
  
[[WormBase-Caltech_Weekly_Calls_June_2020|June]]
+
[[WormBase-Caltech_Weekly_Calls_August_2021|August]]
  
[[WormBase-Caltech_Weekly_Calls_July_2020|July]]
 
  
 +
== September 2, 2021 ==
  
==July 9th, 2020==
+
1. Moving forward with Alliance-friendly Person pages for community curation/authorship tracking<br>
===Gene names issue in SimpleMine and other mining tools===
+
Needed for  
*Wen: Last week, Jonathan Ewbank raised the issue of gene names that may refer to multiple objects.  
+
*AFP community curation
*this can be an issue for multiple data mining tools including WormMine, BioMart, and Gene Set Enrichment.
+
*microPublication author tracking for all species
*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).
+
*stub of person Alliance model already exists made by Adam http://dev.alliancegenome.org:11223/redoc#tag/Person
*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
+
Problems:
*One of the most significant problems is a propagation to other DB and papers of  these gene name issues.
+
*this is not an Alliance-wide interest for tracking their communities person; however, Alliance is not against person pages, just not supportive of developing this class into the many ways it will be useful for us and our communities
*We can make a special note for each gene page, but the people using batch analysis could not catch that easily.
+
*need to do this outside of Alliance
*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===
+
Action
*Please test and leave any feedback on the word cloud tool (Wormicloud), https://wormicloud.textpressolab.com/
+
*Paul talks to zfin about interest in person pages
*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.
+
*Juancarlos talks to Cecilia -need to know important elements to make author to person connection for biolink schema
*Any keyword can generate a graph that plots trends of occurence across the years in publication abstracts.
+
*Daniela and Karen invite PomBase to start harmonizing a person model, will send all Alliance an invite
  
===Noctua 2.0 form ready to use===
+
Will do
*Caltech summer student will try using Noctua initially for dauer (neuronal signaling) pathways
+
*create biolink model based on current WB postgres/Caltech model
 +
*Adam will add tables when we have them
  
===Nightly names service updates to postgres===
+
2. Need to make sure CenGen stuff is included in this next release - need to request Todd to delay release until Adam returns from vacation to deal with it.
*Nightly using Matt's wb-names-export.jar to get full output of genes from datomic/names service, and updating postgres based on that.
 
  
 +
== September 16, 2021 ==
  
==July 16th, 2020==
+
1. CeNGEN enriched genes per cell type data targeted for WS283.
===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
 
**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.
 
* Chris worked with Nico yesterday to update the ODK version for WBbt and WBls; versioning should be fine now (once the OBO dashboard runs again (hasn't run since February))
 
* Important point: the GitHub release version date tag (e.g. "v2020-06-30") needs to match the ODK release date (as stored in the OBO and OWL file headers)
 
** There are some existing mismatches, Chris is cataloging them now
 
  
=== Gene Name Sanitizer ===
+
2. some non-WB objects were present in the Strains and Variations lists coming from the nightly geneace dump.  Juancarlos changed the OA population script script to exclude those.
* Would be good to always (when possible) make users aware of name ambiguities
 
* Wen will keep the "Multiple Output" section at the bottom of SimpleMine output
 
* The gene name sanitizer will be built as a stand alone tool
 
* Important to include history of gene names
 
  
=== Tools linking to SimpleMine ===
+
== September 23, 2021 ==
* Vennter and other tools link to SimpleMine with hard coded field/column names; we should have more dynamic/robust linking without relying on hard coded field names
+
 
 +
1. Help desk ticket on citing the bar graph / FPKM expression data from selected modENCODE libraries - okay to just cite WormBase or should the user cite additional, or other, resources/publications?
 +
* Okay to cite WormBase, but also ask user to cite the WormBase paper (for now NAR, but in the future, Genetics)
 +
* Update the WB page on citing WormBase
 +
 
 +
2. CeNGEN data on Gene page for WS282. A short blog to highlight.
 +
 
 +
3. Server room in Braun power down for no apparent reason. Reset.

Latest revision as of 18:17, 23 September 2021

Previous Years

2009 Meetings

2011 Meetings

2012 Meetings

2013 Meetings

2014 Meetings

2015 Meetings

2016 Meetings

2017 Meetings

2018 Meetings

2019 Meetings

2020 Meetings

2021 Meetings

January

February

March

April

May

June

July

August


September 2, 2021

1. Moving forward with Alliance-friendly Person pages for community curation/authorship tracking
Needed for

Problems:

  • this is not an Alliance-wide interest for tracking their communities person; however, Alliance is not against person pages, just not supportive of developing this class into the many ways it will be useful for us and our communities
  • need to do this outside of Alliance

Action

  • Paul talks to zfin about interest in person pages
  • Juancarlos talks to Cecilia -need to know important elements to make author to person connection for biolink schema
  • Daniela and Karen invite PomBase to start harmonizing a person model, will send all Alliance an invite

Will do

  • create biolink model based on current WB postgres/Caltech model
  • Adam will add tables when we have them

2. Need to make sure CenGen stuff is included in this next release - need to request Todd to delay release until Adam returns from vacation to deal with it.

September 16, 2021

1. CeNGEN enriched genes per cell type data targeted for WS283.

2. some non-WB objects were present in the Strains and Variations lists coming from the nightly geneace dump. Juancarlos changed the OA population script script to exclude those.

September 23, 2021

1. Help desk ticket on citing the bar graph / FPKM expression data from selected modENCODE libraries - okay to just cite WormBase or should the user cite additional, or other, resources/publications?

  • Okay to cite WormBase, but also ask user to cite the WormBase paper (for now NAR, but in the future, Genetics)
  • Update the WB page on citing WormBase

2. CeNGEN data on Gene page for WS282. A short blog to highlight.

3. Server room in Braun power down for no apparent reason. Reset.