0cb3ed51ec356e4ace67ffd13690994fa022719e
lrnassar
  Mon Feb 10 09:34:27 2020 -0800
Tweaking AVADA desc page in response to PI email no RM

diff --git src/hg/makeDb/trackDb/human/avada.html src/hg/makeDb/trackDb/human/avada.html
index 71cd293..fefee63 100644
--- src/hg/makeDb/trackDb/human/avada.html
+++ src/hg/makeDb/trackDb/human/avada.html
@@ -1,24 +1,24 @@
 <h2>Description</h2>
 
 <p>
 This track shows the genomic positions of variants in the
 <a href="http://bejerano.stanford.edu/AVADA/" target="_blank">AVADA database</a>. 
 AVADA is a database of variants built by a machine learning software
 that analyzes full text research articles to find the gene mentions in the text that 
-look like they are most relevant for genetic diagnosis, finds variant descriptions
-and uses the genes to map the variants to the genome. For details see the 
+look like they are most relevant for monogenic (non-cancer) genetic diagnosis, finds variant 
+descriptions and uses the genes to map the variants to the genome. For details see the 
 <a target=_blank href="https://doi.org/10.1038/s41436-019-0643-6">AVADA paper</a>.
 </p>
 <p>As the data is automatically extracted from full-text publications, it includes 
 some false positives. In the original study, out of 200 randomly selected articles,
 only 99 were considered relevant after manual curation. Ideally, the track is used
 in combination with variants found in human patients, to find relevant literature, 
 or with Genome Browser tracks of variant databases that curated a single study 
 for each variant, like our tracks for HGMD or LOVD.
 <p>
 
 <h2>Display Conventions and Configuration</h2>
 
 <p>
 Genomic locations of a variants are labeled with the variant description
 in the original next. This is not a normalized HGVS string, but the original
@@ -59,22 +59,21 @@
 The AVADA VCF file was reformatted at UCSC to the <a href="../goldenPath/help/bigBed.html">bigBed</a> format.
 The program that performs the conversion is available on
 <a href="https://github.com/ucscGenomeBrowser/kent/blob/master/src/hg/makeDb/avada"
 target="_blank">Github</a>. The paper reference information was added from
 MEDLINE and is used Courtesy of the U.S. National Library of Medicine, according 
 to its <a href="https://www.nlm.nih.gov/databases/download/terms_and_conditions_pubmed.html" target=_blank>
 Terms and Conditions</a>.</p>
 
 <h2>Credits</h2>
 <p>
 Thanks to Gill Bejerano and Johannes Birgmeier for making the data available.
 </p>
 
 <h2>References</h2>
 <p>
-Johannes Birgmeier, Cole A. Deisseroth, Laura E. Hayward, Luisa M. T. Galhardo, Andrew P. Tierno, Karthik A. Jagadeesh, Peter D. Stenson, David N. Cooper, Jonathan A. Bernstein, Maximilian Haeussler, and Gill Bejerano:
-<em>et al</em>.
+Johannes Birgmeier, Cole A. Deisseroth, Laura E. Hayward, Luisa M. T. Galhardo, Andrew P. Tierno, Karthik A. Jagadeesh, Peter D. Stenson, David N. Cooper, Jonathan A. Bernstein, Maximilian Haeussler, and Gill Bejerano.
 <a href="https://doi.org/10.1038/s41436-019-0643-6" target="_blank">
 AVADA: Towards Automated Pathogenic Variant Evidence Retrieval Directly from the Full Text Literature. </a>.
 <em>Genetics in Medicine</em>. 2019.
 PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/31467448" target="_blank">31467448</a>
 </p>