Difference between revisions of "WormBase-Caltech Weekly Calls"

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[[WormBase-Caltech_Weekly_Calls_2020|2020 Meetings]]
 
[[WormBase-Caltech_Weekly_Calls_2020|2020 Meetings]]
  
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= 2021 Meetings =
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[[WormBase-Caltech_Weekly_Calls_January_2021|January]]
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[[WormBase-Caltech_Weekly_Calls_February_2021|February]]
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[[WormBase-Caltech_Weekly_Calls_March_2021|March]]
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[[WormBase-Caltech_Weekly_Calls_April_2021|April]]
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[[WormBase-Caltech_Weekly_Calls_May_2021|May]]
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[[WormBase-Caltech_Weekly_Calls_June_2021|June]]
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[[WormBase-Caltech_Weekly_Calls_July_2021|July]]
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[[WormBase-Caltech_Weekly_Calls_August_2021|August]]
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== September 2, 2021 ==
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1. Moving forward with Alliance-friendly Person pages for community curation/authorship tracking<br>
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Needed for
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*AFP community curation
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*microPublication author tracking for all species
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*stub of person Alliance model already exists made by Adam http://dev.alliancegenome.org:11223/redoc#tag/Person
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Problems:
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*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
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*need to do this outside of Alliance
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Action
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*Paul talks to zfin about interest in person pages
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*Juancarlos talks to Cecilia -need to know important elements to make author to person connection for biolink schema
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*Daniela and Karen invite PomBase to start harmonizing a person model, will send all Alliance an invite
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Will do
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*create biolink model based on current WB postgres/Caltech model
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*Adam will add tables when we have them
  
= 2021 Meetings =
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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.
== January 14th, 2021 ==
 
  
===PubMed LinkOut to WormBase Paper Pages (Kimberly) ===
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== September 16, 2021 ==
* Other databases [https://www.ncbi.nlm.nih.gov/projects/linkout/doc/nonbiblinkout.html link out from PubMed] to their respective paper pages
 
* For example, https://pubmed.ncbi.nlm.nih.gov/20864032/ links out to GO and MGI paper pages
 
* Would like to set this up for WormBase and ultimately for the Alliance, but this will require some developer help
 
* Work on this next month (after AFP and GO grant submissions)?
 
  
===Update cycle for HGNC data in the OA (Ranjana) ===
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1. CeNGEN enriched genes per cell type data targeted for WS283.
*Juancarlos had these questions for us:
 
<pre style="white-space: pre-wrap;
 
white-space: -moz-pre-wrap;
 
white-space: -pre-wrap;
 
white-space: -o-pre-wrap;
 
word-wrap: break-word">
 
  
There's a script here that repopulates the postgres obo_*_hgnc tables
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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.
based off of Chris and Wen's data
 
/home/postgres/work/pgpopulation/obo_oa_ontologies/populate_obo_hgnc.pl
 
  
It's not on a cronjob, because I think the files are not updated that
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== September 23, 2021 ==
often.  Do we want to run this every night, or run it manually when
 
the files get re-generated ?  Or run every night, and check if the
 
files's timestamps have changed, then repopulate postgres ?
 
  
</pre>
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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?
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* Okay to cite WormBase, but also ask user to cite the WormBase paper (for now NAR, but in the future, Genetics)
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* Update the WB page on citing WormBase
  
===Minutes===
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2. CeNGEN data on Gene page for WS282. A short blog to highlight.
===PubMed LinkOut to WormBase Paper Pages (Kimberly) ===
 
  
===Update cycle for HGNC data in the OA (Ranjana) ===
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3. Server room in Braun power down for no apparent reason. Reset.
*We will update when Alliance updates the data
 
*Juancarlos will set it to check the timestamps and if they change will do an update for the OAs
 

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.