latest news

1.Feb.2012

Added circular bacterial genome map

21.Sep.2010

Added new pathway map "Biosynthesis of secondary metabolites"

11.Nov.2009

Pathway Projector paper published.

19.Sep.2009

Documentation is added.

19.Jul.2009

Reference map and webpage renewal

27.Nov.2008

Beta

• Pathway Projector overview

• Zoomable User Interface

» Google Maps API

» Ext JS 2.0

• Pathway map

» KEGG Atlas

» Re-creation

• Search

• Meta word search

• Molecular mass search

» Results

• Route search

» Results

• Sequence-based search (BLAST)

» Results

• Pathway prediction (GEM System)

• Output

• Annotation

• Data mapping

• Mapping format

» Organism

» Genes

» Proteins

» Metabolites

» Time series data

» Pathway

» Organism comparison

• SOAP service

» Perl

» Python

» Ruby

• Manual editing

» XML data export

» XML data import

• Data

• Information window

» Click mode

» Mouse over mode

• Organism

• Databases

• Installation

Annotation

• Data mapping

example graphic example graphic

Users can reflect experimental data, such as transcriptomics, proteomics or metabolomics. Specify the color or scale of the lines or circles freely, a customized map overlays on the pathway map. Furthermore, users can put original pictures on map.





1st step : Open a Data Mapping tab window in the Tools and input own data. Or else, users can upload data file following data format.

route


2nd step : Click a "Generate Overlay Map" button.



Finish : A browser backs to main page and shows the mapped pathway. Users can switch to reference pathway map from the top-right buttons.

• Mapping format

» Organism

To set organism, users should use KEGG organism IDs (e.g. E. coli is eco, Human is hsa). Default is reference pathway map.

Organism:eco

» Genes

When the "organism" is set, users can change this gene parameters. 1st column is "gene name", 2nd column is color (e.g. #FF0000, red), 3rd column is stroke width (default: 8).

// when the organism is eco
pgk,#FF0000,12
tpiA,blue
eco:b2926,red

» Proteins

1st column is EC number (e.g. 1.1.1.1) or reaction ID (e.g. R00010), 2nd column is color, 3rd column is stroke width (default: 8).

Set ALL reactions to black with 10px stroke width

reaction,black,10

Enzyme: EC Number, stroke-width=10px

1.1.1.-,black,10

Reaction: KEGG ID

R01512,blue

» Metabolites

1st column is compound ID, 2nd column is color, 3rd column is circle size, 4th colum is label, 5th column is label size.

Set all compounds/glycans to gray with r = 13px.

compound,#cccccc,13

KEGG ID, color, size, label="Coenzyme A", label size.

C00010,red,13,Coenzyme A,20

» Time series data

1st line is target components' ID with chart type (line or bar). 2nd line or later, plese input own data by CSV format. At the end, it should be remembered that "//".

>C00158,line
1,10
2,20
3,30
4,40
5,60
6,90
7,109
8,200
9,80
10,9
//

Or alternatively, please upload the 【Tab-delimited data】 file. The format is following:
the first rows are components name, and the first column is time point. And the columns are experimental data.
For example;


C00111 C00118 C00236 C00197
1 45 53 53 23
2 98 79 79 69
3 45 53 53 23
4 79 34 69 43
5 32 79 67 0
6 11 20 44 20
7 20 30 55 30
8 31 40 64 40
9 71 10 74 70
10 87 45 10 52
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» Pathway

1st column is pathway name e.g. glycolysis (or pathway id e.g. rn00010), 2nd column is color

glycolysis,red
rn00020,blue

» Organism comparison

example graphic
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• SOAP service

Pathway Projector provides web-service as SOAP service. Users can get the data mapped pathway maps URLs by service.
This service is Perl, Ruby and Phthon compliant.
The sample codes for each language are as follows;

» SOAP

This SOAP service is SOAP1.1 (Latest version is SOAP1.2).

» Perl

require SOAP::Lite ver0.60.

#!/usr/bin/perl
use SOAP::Lite;
use warnings;
use strict;

# WSDL file
my $WSDL = "http://www.g-language.org/PathwayProjector/PathwayProjector.wsdl";

# create SOAP driver
my $soap = SOAP::Lite->service($WSDL)->proxy('http://localhost/', timeout=>600);

# input data
my $input = SOAP::Data->type(array => ['Organism:eco', 'pgk,red']);

# run your job
my ($pngFile, $pathway) = $soap->mapping( $input );

print "PNG file : " . $pngFile . "\n";
print "Pathway URL : " . $pathway . "\n";

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» Python

require SOAPpy and related library.

#!/usr/bin/python

from SOAPpy import WSDL

# create WSDL driver
wsdl = 'http://www.g-language.org/PathwayProjector/PathwayProjector.wsdl'
serv = WSDL.Proxy(wsdl)

# input data
input = ['Organism:eco', 'pgk,red']

# run your job
(pngFile, pathway) = serv.mapping(input)

# polling your job
print "PNG file : " + pngFile + "\n"
print "Pathway URL : " + pathway + "\n"

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» Ruby

require Ruby1.8.1 or later, or install SOAP library for Ruby.

#!/usr/bin/ruby

require 'soap/wsdlDriver'

# create WSDL driver
wsdl = "http://www.g-language.org/PathwayProjector/PathwayProjector.wsdl"
serv = SOAP::WSDLDriverFactory.new(wsdl).create_rpc_driver
serv.generate_explicit_type = true

# input data
input = ['Organism:eco', 'pgk,red']

# run your job
(pngFile, pathway) = serv.mapping(input)

# polling your job
print "PNG file : " + pngFile + "\n"
print "Pathway URL : " + pathway + "\n"

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• Manual editing

example graphic example graphic

Users can easily annotate and edit the maps by placing custom markers, scribing lines. Moreover, users can share these added custom comments or annotations among researchers as XML.

example graphic

» XML export

Output XML format file by "GetXML" button.


After clicking the "GetXML" button, a new window will open with XML data.


» XML import

If you input the XML data in this text area and click "Import" button, your previous edited picture is reproduced.


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