Difference between revisions of "WormBase-Caltech Weekly Calls"

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= 2021 Meetings =
 
= 2021 Meetings =
== January 14th, 2021 ==
 
  
===PubMed LinkOut to WormBase Paper Pages (Kimberly) ===
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[[WormBase-Caltech_Weekly_Calls_January_2021|January]]
* 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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[[WormBase-Caltech_Weekly_Calls_February_2021|February]]
*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
 
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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== March 4, 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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=== Webinar Monday ===
 +
* Juancarlos can send a reminder email; he just needs the text for the body of the email message
 +
* Can we send the webinar reminder to WB staff? Cannot use staff@wormbase.org to register
 +
* Raymond will try to remember to forward to staff
  
==Minutes==
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=== Neural Network (NN) evaluation ===
 +
* Kimberly (and other curators) looking through NN results
 +
* Had previously prevented LOW scoring SVMs(?) from being sent to authors
 +
* We need an agreed upon protocol for evaluation
 +
* To avoid bias, we should randomly sample papers; usually will find negatives; how do we represent high, medium and low-scoring papers in the set without making curators review >> 100 papers?
 +
* Michael will come up with protocol and send around list of papers for each data type (in Google Doc)
 +
* Perhaps evaluation should happen on non-curated, newer papers

Latest revision as of 18:42, 4 March 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 4, 2021

Webinar Monday

  • Juancarlos can send a reminder email; he just needs the text for the body of the email message
  • Can we send the webinar reminder to WB staff? Cannot use staff@wormbase.org to register
  • Raymond will try to remember to forward to staff

Neural Network (NN) evaluation

  • Kimberly (and other curators) looking through NN results
  • Had previously prevented LOW scoring SVMs(?) from being sent to authors
  • We need an agreed upon protocol for evaluation
  • To avoid bias, we should randomly sample papers; usually will find negatives; how do we represent high, medium and low-scoring papers in the set without making curators review >> 100 papers?
  • Michael will come up with protocol and send around list of papers for each data type (in Google Doc)
  • Perhaps evaluation should happen on non-curated, newer papers