18470eb8d3875f90afe85196e3582c394eaf2716
lrnassar
  Wed Mar 20 17:07:49 2024 -0700
Updating the chromosome band description page to clarify that we do not generate these data anymore, instead we download it from NCBI, refs #31551

diff --git src/hg/makeDb/trackDb/human/cytoBand.html src/hg/makeDb/trackDb/human/cytoBand.html
index af3e6d2..a4d73ac 100644
--- src/hg/makeDb/trackDb/human/cytoBand.html
+++ src/hg/makeDb/trackDb/human/cytoBand.html
@@ -3,33 +3,43 @@
 The chromosome band track represents the approximate 
 location of bands seen on Giemsa-stained chromosomes.
 Chromosomes are displayed in the browser with the short arm first.  
 Cytologically identified bands on the chromosome are numbered outward 
 from the centromere on the short (p) and long (q) arms.  At low resolution, 
 bands are classified using the nomenclature 
 [<em>chromosome</em>][<em>arm</em>][<em>band</em>], where <em>band</em> is a 
 single digit. Examples of bands on chromosome 3 include 3p2, 3p1, cen, 3q1, 
 and 3q2.  At a finer resolution, some of the bands are subdivided into 
 sub-bands, adding a second digit to the <em>band</em> number, e.g. 3p26. This 
 resolution produces about 500 bands. A final subdivision into a 
 total of 862 sub-bands is made by adding a period and another digit to the 
 <em>band</em>, resulting in 3p26.3, 3p26.2, etc. </P>
 
 <H2>Methods</H2>
-<P>
-A full description of the method by which the chromosome band locations are 
-estimated can be found in Furey and Haussler, 2003.
+<p>
+Chromosome band information was <a target="_blank"
+href="https://ftp.ncbi.nlm.nih.gov/pub/gdp/">downloaded from NCBI</a>
+using the ideogram.gz file for the respective assembly. These data were then 
+transformed into our visualization format. See our <a target="_blank"
+href="https://github.com/ucscGenomeBrowser/kent/tree/master/src/hg/makeDb/doc">
+assembly creation documentation</a> for the organism of interest
+to see the specific steps taken to transform these data.
+Band lengths are typically estimated based on FISH or other
+molecular markers interpreted via microscopy.</p>
+<p>
+For some of our older assemblies, greater than 10 years old, the tracks were
+created as detailed below and in Furey and Haussler, 2003.</p>
 <P>
 Barbara Trask, Vivian Cheung, Norma Nowak and others in the BAC Resource
 Consortium used fluorescent in-situ hybridization (FISH) to determine a 
 cytogenetic location for large genomic clones on the chromosomes.
 The results from these experiments are the primary source of information used
 in estimating the chromosome band locations.
 For more information about the process, see the paper, Cheung,
 <EM>et al.</EM>, 2001.  and the accompanying web site,
 <A HREF="https://www.ncbi.nlm.nih.gov/genome/cyto/hbrc.shtml" 
 TARGET=_blank>Human BAC Resource</A>.</P>
 <P>
 BAC clone placements in the human sequence are determined at UCSC using a 
 combination of full BAC clone sequence, BAC end sequence, and STS marker 
 information.</P>