Difference between revisions of "WormBase-Caltech Weekly Calls"

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[[WormBase-Caltech_Weekly_Calls_2019|2019 Meetings]]
 
[[WormBase-Caltech_Weekly_Calls_2019|2019 Meetings]]
  
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[[WormBase-Caltech_Weekly_Calls_2020|2020 Meetings]]
  
  
 +
= 2021 Meetings =
 +
== January 14th, 2021 ==
  
= 2020 Meetings =
+
===PubMed LinkOut to WormBase Paper Pages (Kimberly) ===
 +
* 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)?
  
[[WormBase-Caltech_Weekly_Calls_January_2020|January]]
+
===Update cycle for HGNC data in the OA (Ranjana) ===
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*Juancarlos had these questions for us:
 +
<pre style="white-space: pre-wrap;
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[[WormBase-Caltech_Weekly_Calls_February_2020|February]]
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There's a script here that repopulates the postgres obo_*_hgnc tables
 +
based off of Chris and Wen's data
 +
/home/postgres/work/pgpopulation/obo_oa_ontologies/populate_obo_hgnc.pl
  
[[WormBase-Caltech_Weekly_Calls_March_2020|March]]
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It's not on a cronjob, because I think the files are not updated that
 +
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 ?
  
[[WormBase-Caltech_Weekly_Calls_April_2020|April]]
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</pre>
  
[[WormBase-Caltech_Weekly_Calls_May_2020|May]]
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===Minutes===
 +
====PubMed LinkOut to WormBase Paper Pages====
  
[[WormBase-Caltech_Weekly_Calls_June_2020|June]]
+
====Update cycle for HGNC data in the OA====
 +
*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
  
[[WormBase-Caltech_Weekly_Calls_July_2020|July]]
+
====CENGEN====
 
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*Wen, Daniela, and Raymond will look at the datasets to work out how to incorporate. Start simple.
 
+
*We will make links to pages on their site.
==August 6th, 2020==
 
===Experimental conditions data flow into Alliance===
 
*Experimental conditions in disease annotations: WB has inducers (used to recapitulate the disease condition) and modifiers (a modifier can ameliorate, exacerbate, or have no effect, on the disease condition)
 
*We use the WB Molecule CV for Inducers and Modifiers in disease annotation
 
*Experimental conditions in phenotype annotations: are free text (captured in remarks); will probably need to formalize later on
 
*So for data flow into Alliance:
 
**In the short term we will load the Molecule CV into the Alliance (Ranjana and Michael P. will work on this)
 
**Groups will switch to using common data model that works for all and common ontology/ontologies in the near future.
 

Latest revision as of 20:03, 14 January 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 14th, 2021

PubMed LinkOut to WormBase Paper Pages (Kimberly)

  • Other databases 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)

  • Juancarlos had these questions for us:

There's a script here that repopulates the postgres obo_*_hgnc tables
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
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 ?

Minutes

PubMed LinkOut to WormBase Paper Pages

Update cycle for HGNC data in the OA

  • 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

CENGEN

  • Wen, Daniela, and Raymond will look at the datasets to work out how to incorporate. Start simple.
  • We will make links to pages on their site.