| | | | Displaying Your Own Columns in the UCSC Gene Sorter | 
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 |  | The Gene Sorter provides dozens of columns containing information on genes 
computed at UCSC or provided by outside collaborators. In addition to these 
standard columns, users may also upload their own columns for
temporary display in the browser. Custom columns are viewable only on the 
machine from which they were uploaded and are kept only for 8 hours after the 
last time they were accessed. Optionally, users can make custom columns viewable 
by others as well. 
 Gene Sorter custom columns are based on files in line-oriented format. 
Each column is described by an initial column line followed by one or 
more data lines. The column line describes the 
name, hyperlinks, and other overall characteristics of the column. Each data line
contains specific information about a gene annotated by the column. Lines 
starting with # are ignored.
Only one column file may be loaded at a time; however, multiple column 
descriptions may be included in the same custom file, separated by blank lines.  
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Each column description must begin with a column line containing the keyword
column followed by an optional set of one or more attribute pairs:
 
Attribute values must be enclosed in quotes if they contain spaces or tabs. 
Attribute names and data values are case-sensitive.
The following attributes may be defined:
column [attribute1]=[value1] [attribute2]=[value2]...
 
  name - Symbolic name of the custom column (not displayed to user). 
  shortLabel - Label displayed at the top of the column in the Gene
	Sorter display. The default value is User Column.
  longLabel - Short description of the column
       	displayed after the name on the configuration and filter pages.
       	The default value is User custom column.
  visibility - Controls whether column is displayed by default: 
	on = display column, off = hide column. 
       	The default is on.
  priority - Specifies the display order of the column relative to 
	others. Columns with lower priority values appear toward the lefthand side
	of the display. The standard browser columns have priorities between 	
	0 and 20.  The default priority is 2.01.
  itemUrl - URL used to construct hyperlinks accessed by clicking on 
	column data values. 
       	If the URL contains %s, the column value will be inserted at
	that position in the hyperlink string. For example, if 
	itemUrl for a column is defined as 
	http://genome.ucsc.edu/cgi-bin/hgTracks?db=hg16& position=%s
	(the UCSC Genome Browser URL), clicking on the data value NM_024014 will
	open the Human Jul. 2003 Genome Browser to the position occupied by
	RefSeq accession NM_024014. There is no default for this attribute.
  labelUrl - URL of the hyperlink accessed by clicking on the column 
	label.	No default.
  search - When the atribute is set to one of the following values, 
	column data may be searched using the Gene Sorter search 
	text box. Rows containing matches will be moved to the top of the 
	display. 
    
     By default, no search criterion is set.exact - matches only if the text entered in the
	position search box exactly matches the column data text.
     prefix - matches if search text exactly matches the initial part of the 
	column data text.
     fuzzy - matches if search text matches any portion of the 
	column data text.
    idLookup - When set, this attribute specifies the standard column 
	that should be used to link key values to the Gene Sorter 
	display.
	For example, if idLookup is set 
	to refSeq, a custom column data row containing the key  
	NM_024014 will display on the same row as the RefSeq row 
	containing NM_024014. The idLookup values are case-sensitive.
	By default,
	idLookup is set to the acc (GenBank) column. To 
	determine the idLookup value that corresponds to a specific 
	standard column, click the column's title in the
	Gene Sorter display (use the configure button to turn on the column 
	display if it is currently hidden). The near.do.colInfo parameter
	in the URL linked to the column title is set to the 
	idLookup value that corresponds to that column.
  isNumber - When this attribute is set to on, the filter 
	page displays numerical max/min controls for this column. Default is 
	off.
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 |  |  Data lines are of the format: 
[key] [value] 
 
key - links the custom column data value to a data value in the column specified by the 
idLookup attribute. If idLookup is unset, the browser looks
for a match in the acc (GenBank) column.
value - data value to be displayed in the custom column row that 
matches the specified key. It is permissible to have more than one 
key/value pair per key.  In this case, the column displays a comma-separated
list of values. 
 
Data line keys and values are case-sensitive.
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Example 1
 
This example defines a custom column for the Jul. 2003 Gene Sorter. The 
column's key values are linked to data in the refSeq column. Column rows can be 
filtered by numerical range by setting the max/min values for the column on the 
filter page. 
 
Example 2
#Custom column file for MyLab Trial 3
#
#Column line:
#
column name="MyLab Data" shortLabel="MyLab" longLabel="MyLab Trial 3" 
visibility=on priority=2.05 idLookup=refSeq isNumber=on
#
#Data lines (key links to refSeq column):
#
NM_005523    1.2
NM_005522    4.5
NM_018951    5.1
NM_000522    5.7
NM_030661    9.4
NM_002141    5.2
NM_024014    4.3
NM_006896    6.0
 
This example defines a custom column for the Oct. 2003 mouse Gene Sorter. The 
column's key values are linked by default to the acc (GenBank) column. 
Clicking on the column's title (UCSCLab) displays the web page
http://genome.ucsc.edu/. Clicking on a specific data value displays the web page 
http://genome.ucsc.edu/cgi-bin/hgTracks?db=mm4 (the UCSC Genome Browser) at the 
position specified by the data value. A search on the word MOUSE will
display a list of all UCSC BioLab data that contains the string 
"MOUSE".   
#Custom column file for UCSC BioLab Test Data 
#
#Column line:
#
column name="UCSCLab Data" shortLabel="UCSCLab" longLabel="UCSC BioLab Test Data 4/4/04" 
visibility=on priority=2.05 
itemUrl=http://genome.ucsc.edu/cgi-bin/hgTracks?db=mm4&position=%s 
labelUrl=http://genome.ucsc.edu search=fuzzy 
#
#Data lines (key links to refSeq column):
#
U20370      HXAB_MOUSE
L08757      HXAA_MOUSE
NM_008264   HXAD_MOUSE
# The following 2 lines demonstrate multiple data values for 1 key:
AK083575    NM_010449
AK083575    Q8BNI8
M95599      NM_010451
M28021      HXA5_MOUSE
NM_010454   HXA6_MOUSE
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