Scriptable Interface

Overview

GeneNetwork (GN) provides a scriptable interface that allows other services and web users to retrieve data, map QTLs, generate lists of covariates, or to link to the most appropriate page of data for a particular tissue or transcript. This page documents the GN scriptable interface. GN functions are invoked using commands, which usually takes the form of a URL beginning
http://robot.genenetwork.org/webqtl/main.py?...

At the end of this type of command, after the question mark, you need to add a set of keywords and values separated by the = character, for example, cmd=get or probeset=100011_at. Keywords and values that GN will recognize are listed and explained in the table below.

The keyword-value pairs should be separated by the & character. A complete query might look like
cmd=get&probeset=100011_at&probe=all&format=column
The order of the keyword-value pairs in the list is unimportant. However, the cmd keyword is required and its value determines what other keywords are required or allowed. In examples, we always use the cmd keyword first.

Putting the whole query together results in a string that looks like http://robot.genenetwork.org/webqtl/main.py?cmd=get&probeset=100011_at&probe=all&format=column
Although this command is shown on two lines of text, it is really just one line, and there should be no carriage return or line break.

Specific commands

cmd=genotype retrieves genotype data for any of the supported sets of recombinant inbred lines.

cmd=get or cmd=trait retrieves trait data from databases of published phenotypes or gene expression data. It can also retrieve marker genotypes as numerical codes for correlation searches.

cmd=map retrieves trait data and searches for associations among BXD marker genotypes, returning marker names, regression coefficients and likelihood ratio statistics.

cmd=interval retrieves trait data and performs interval mappng, returning map positions of peak likelihood ratio statistic.

cmd=correlation retrieves trait data and searches for correlations with traits in another (or the same) trait database. cmd=correlation and cmd=pearson use Pearson product-moment correlation. cmd=spearman uses Spearman rank-sum correlation.

Commands and Keywords

Function	Command keyword-value	Other keywords (bold keywords are required)	Allowed values [Comments or descriptions in square brackets]
Retrieve genotype data	cmd=genotype cmd=gen	riset	axb, bxa, bxd, bxh, cxb
		chr ⁽³⁾	1, 2, 3, ..., 19, X
		format ⁽⁴⁾	row, column
Example: http://robot.genenetwork.org/webqtl/main.py?cmd=genotype&riset=BXD&chr=1&format=column

Retrieve trait data	cmd=get cmd=trait cmd=tra	probeset ⁽¹⁾	[Probe or probeset identifier, trait record number (for db=3), or marker name (for db=4)]
		db	Each database stored in GN is assigned a short code required to identify the particular database from which you would like to retrieve data.
		probe ⁽¹⁾	all pm mm OR [Affymetrix cell location code] ⁽³⁾
		format ⁽⁴⁾	row, column
Example: http://robot.genenetwork.org/webqtl/main.py?cmd=get&probeset=98332_at&db=bra08-03MAS5&probe=119637&format=col

Single-marker regression	cmd=map	probeset ⁽¹⁾	[Probe or probeset identifier, trait record number (for db=3) or marker name (for db=4)]
		db	Each database stored in GN is assigned a short code required to identify the particular database from which you would like to retrieve data.
		probe ⁽¹⁾	all [Affymetrix cell location code] ⁽²⁾
		return	number of LRS values to be reported; all LRS are reported if omitted
		sort	lrs [sorts by descending pvalue] [sorts by ascending position by default]
Example: http://robot.genenetwork.org/webqtl/main.py?cmd=map&probeset=98332_at&db=bra08-03MAS5&sort=lrs&return=20

QTL interval mapping	cmd=interval cmd=int	probeset ⁽¹⁾	[Probe or probeset identifier, trait record number (for db=3), or marker name (for db=4)]
		db	Each database stored in GN is assigned a short code required to identify the particular database from which you would like to retrieve data.
		probe ⁽¹⁾	[Affymetrix cell location code] ⁽²⁾
		chr	1, 2, 3, ..., 19, X
		sort	lrs [sorts by descending pvalue] [sorts by ascending position by default]
Example: http://robot.genenetwork.org/webqtl/main.py?cmd=interval&probeset=98332_at&db=bra08-03MAS5&chr=1

Trait correlation search	cmd=correlation cmd=cor cmd=pearson cmd=pea cmd=spearman cmd=spe	probeset ⁽¹⁾	[Affymetrix probeset identifier, trait record number (for db=3) or marker name (for db=4)]
		db	Each database stored in GN is assigned a short code required to identify the particular database from which you would like to retrieve data.
		searchdb	Each database stored in GN is assigned a short code required to identify the particular database from which you would like to retrieve data.
		probe ⁽¹⁾	[Affymetrix cell location code] ⁽²⁾
		return	[Maximum number of correlations to be reported]
		sort	pvalue [sorts by ascending pvalue] [sorts by descending correlation by default]
		id	yes [Includes NCBI Entrez Gene ID for each transcript in the output (for expression data only).] only [Returns only NCBI Entrez Gene ID for each transcript (for expression data only).]
Example: http://robot.genenetwork.org/webqtl/main.py?cmd=cor&probeset=100001_at&probe=136415&db=bra08-03MAS5&searchdb=BXDPublish&return=500&sort=pvalue

Open Trait Data and Analysis Form	cmd=show cmd=shw	probeset ⁽¹⁾	[Affymetrix probeset identifier, trait record number (for db=3) or marker name (for db=4)]
		db	Each database stored in GN is assigned a short code required to identify the particular database from which you would like to retrieve data.
		probe ⁽¹⁾	[Affymetrix cell location code] ⁽²⁾
Example: http://gn1.genenetwork.org/webqtl/main.py?cmd=show&db=HC_M2_0606_M&probeset=1415670_at&probe=269753

The script below is used to filter a list of probes or probe sets that target the same gene or transcript to find the single probe or probe set with highest expression and to then display the Statistics Page for that particular data. This script does not use the cgi-bin format.
Show Best Trait Data Statistics Page	parameters	examples	Notes
	gene= refseq= geneid= database= searchAlias=	gene=Rho refseq=NM_145383 geneid=212541 database=Eye_M2_0906_R searchAlias=1	There are three supported search term types: 1. Gene symbol, 2. RefSeq identifier, 3. Entrez gene identifier. Although not recommended, the string "&searchAlias=1" can be added at the end of the command to retrieve data using the alias of a proper gene symbol when the original does not work. Thus "gene=RP4" will resolve to "gene=Rho" only if you add "&searchAlias=1" at the end of the command. Each database stored in GN is assigned a short code required to identify the particular database from which you would like to retrieve data.
Example 1: http://gn1.genenetwork.org/webqtl/main.py?FormID=showBest&gene=Rho&database=HC_M2_0606_P
Example 2: http://gn1.genenetwork.org/webqtl/main.py?FormID=showBest&refseq=NM_145383&database=HC_M2_0606_P
Example 3: http://gn1.genenetwork.org/webqtl/main.py?FormID=showBest&geneid=212541&database=HC_M2_0606_P
Example 4: http://gn1.genenetwork.org/webqtl/main.py?FormID=showBest&gene=RP4&database=HC_M2_0606_P&searchAlias=1
This script was originally written to allow connections from the NEIBank to GeneNetwork by H. Li and R. Williams (see News of April 25, 2007).

Search for gene data	cmd=search cmd=sch	gene refseq genbankid	The name or ID of the gene or protein to be searched, choose one and only one type of identifier
		alias	[0 or 1] Whether to search for possible aliases (only when a gene name is supplied), optional, disabled by default (0)
		species	Optional, only human, mouse and rat are supported now. Default is mouse if not specified.
		tissue	Optional, if not specified, display traits from all available tissues. For tissue abbreviations, please check http://gn1.genenetwork.org/webqtl/main.py?cmd=help&topic=tissue
		format	[html or text], Optional, if not specified, return result in HTML format
Example 1 : http://gn1.genenetwork.org/webqtl/main.py?cmd=sch&gene=ddx25 Example 2 : http://gn1.genenetwork.org/webqtl/main.py?cmd=sch&refseq=NM_133594&species=rat Example 3 : http://gn1.genenetwork.org/webqtl/main.py?cmd=sch&genbankid=AW047046 Example 4 : http://gn1.genenetwork.org/webqtl/main.py?cmd=sch&gene=GRTH&alias=1&species=rat&tissue=fat Example 5 : http://gn1.genenetwork.org/webqtl/main.py?cmd=sch&gene=Grin2b&tissue=hip&format=text

Notes

A value is required for the probeset but not for probe keyword. With only probeset, commands will retrieve the average for the probeset from different average method. With probeset and probe=all, commands will retrieve data for all probes of that probeset; with probe, data for a single probe. If the specified probeset and probe are inconsistent, no data is returned.
The Affymetrix cell location code is six characters. The first three characters are the column or x location, and the last three the row or y location; for example, 237198. If the column has less than three digits, it should be preceded by one or two X characters to make three characters. Similarly, the row should be prefixed with one or two Y characters, if necessary; for example, X24YY9 or XX8Y34.
If chr is omitted, command will retrieve information for all chromosomes.
If format is omitted, row formatting is the default.