This workflow uses one or more services that
are deprecated as of 31st December 2012
(over 12 years ago), and may no longer function.
Show details...
Affected service WSDL:
- http://soap.genome.jp/KEGG.wsdl
Details:
KEGG will be moving from a WSDL/SOAP interface to REST. Details of the new REST services can be found here.
Working examples that use the new REST service can be viewed here, here and here.
Kegg pathway diagrams
Created: 2010-03-19 12:41:27
Last updated: 2010-03-19 12:41:28
Find pathways in which all the genes in the list are involved. For each pathway draw the pathway diagram. Colour all enzyme boxes with colours specified. This workflow still has one problem. The list of colours have to be specified. I would like ideally to only except one background and one foreground colour and expand that to a list with length equivalent to the number of enzymes found - just duplicating the specified colours. However with almost no Taverna documentation to speak of, none of my efforts wanted to work so far.
Find pathways in which all the genes in the list are involved. For each pathway draw the pathway diagram.
for each protein draw a diagram of the Kegg pathway that its protein is involved in and where available visualise the structures
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Workflow Components
|
Authors (1)
|  |
|
Titles (2)
| |
| Kegg pathway diagrams |
| Kegg pathway diagrams with enzymes coloured on path diagram |
|
Descriptions (3)
| |
| Find pathways in which all the genes in the list are involved. For each pathway draw the pathway diagram. Colour all enzyme boxes with colours specified. This workflow still has one problem. The list of colours have to be specified. I would like ideally to only except one background and one foreground colour and expand that to a list with length equivalent to the number of enzymes found - just duplicating the specified colours. However with almost no Taverna documentation to speak of, none of my efforts wanted to work so far. |
| Find pathways in which all the genes in the list are involved. For each pathway draw the pathway diagram. |
| for each protein draw a diagram of the Kegg pathway that its protein is involved in and where available visualise the structures |
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Dependencies (0)
| |
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Inputs (4)
| |
| Name |
Description |
| gene_ids |
A list of KEGG gene ids
|
| Species |
The three letter species code
The three letter species code used by KEGG
KEGG
|
| bg_color |
The background colour for the boxes containing enzymes. Values can be given as strings or hexadecimal RGB colour codes.
The background colour for the boxes containing enzymes.
|
| fg_color |
The text colour for the boxes containing enzymes. Values can be given as strings or hexadecimal RGB colour codes.
|
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Processors (12)
| |
| Name |
Type |
Description |
| Workflow89 |
workflow |
|
| Get_Image_From_URL_2 |
localworker |
ScriptURL inputURL = null;
if (base != void) {
inputURL = new URL(new URL(base), url);
} else {
inputURL = new URL(url);
}
byte[] contents;
if (inputURL.openConnection().getContentLength() == -1) {
// Content size unknown, must read first...
byte[] buffer = new byte[1024];
int bytesRead = 0;
int totalBytesRead = 0;
InputStream is = inputURL.openStream();
while (bytesRead != -1) {
totalBytesRead += bytesRead;
bytesRead = is.read(buffer, 0, 1024);
}
contents = new byte[totalBytesRead];
} else {
contents = new byte[inputURL.openConnection().getContentLength()];
}
int bytesRead = 0;
int totalBytesRead = 0;
InputStream is = inputURL.openStream();
while (bytesRead != -1) {
bytesRead = is.read(contents, totalBytesRead, contents.length - totalBytesRead);
totalBytesRead += bytesRead;
if (contents.length==totalBytesRead) break;
}
image = contents;
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| color_pathway_by_objects |
wsdl |
Wsdlhttp://soap.genome.jp/KEGG.wsdlWsdl Operationcolor_pathway_by_objects |
| get_enzymes_by_gene |
wsdl |
Wsdlhttp://soap.genome.jp/KEGG.wsdlWsdl Operationget_enzymes_by_gene |
| get_genes_by_enzyme |
wsdl |
Wsdlhttp://soap.genome.jp/KEGG.wsdlWsdl Operationget_genes_by_enzyme |
| get_pathways_by_genes |
wsdl |
Wsdlhttp://soap.genome.jp/KEGG.wsdlWsdl Operationget_pathways_by_genes |
| Flatten_List |
localworker |
Scriptflatten(inputs, outputs, depth) {
for (i = inputs.iterator(); i.hasNext();) {
element = i.next();
if (element instanceof Collection && depth > 0) {
flatten(element, outputs, depth - 1);
} else {
outputs.add(element);
}
}
}
outputlist = new ArrayList();
flatten(inputlist, outputlist, 1); |
| Flatten_List_2 |
localworker |
Scriptflatten(inputs, outputs, depth) {
for (i = inputs.iterator(); i.hasNext();) {
element = i.next();
if (element instanceof Collection && depth > 0) {
flatten(element, outputs, depth - 1);
} else {
outputs.add(element);
}
}
}
outputlist = new ArrayList();
flatten(inputlist, outputlist, 1); |
| Remove_String_Duplicates |
localworker |
ScriptList strippedlist = new ArrayList();
for (Iterator i = stringlist.iterator(); i.hasNext();) {
String item = (String) i.next();
if (strippedlist.contains(item) == false) {
strippedlist.add(item);
}
}
|
| Beanshell |
beanshell |
ScriptList bg_colors = new ArrayList();
List fg_colors = new ArrayList();
for (int i = 0; i < genes_list.size(); i++) {
fg_colors.add(fg_color);
bg_colors.add(bg_color);
}
|
| Flatten_List_3 |
localworker |
Scriptflatten(inputs, outputs, depth) {
for (i = inputs.iterator(); i.hasNext();) {
element = i.next();
if (element instanceof Collection && depth > 0) {
flatten(element, outputs, depth - 1);
} else {
outputs.add(element);
}
}
}
outputlist = new ArrayList();
flatten(inputlist, outputlist, 1); |
| Flatten_List_4 |
localworker |
Scriptflatten(inputs, outputs, depth) {
for (i = inputs.iterator(); i.hasNext();) {
element = i.next();
if (element instanceof Collection && depth > 0) {
flatten(element, outputs, depth - 1);
} else {
outputs.add(element);
}
}
}
outputlist = new ArrayList();
flatten(inputlist, outputlist, 1); |
|
Beanshells (1)
| |
| Name |
Description |
Inputs |
Outputs |
| Beanshell |
|
bg_color
fg_color
genes_list
|
bg_colors
fg_colors
|
|
Outputs (6)
| |
| Name |
Description |
| KeggPathwayIDs |
A list of the pathways found.
|
| keggimageurl |
The URLs of the images produced for the KeggImage output
The URLs of the images produced for the KeggImage output.
|
| keggGeneNames |
A list of the gene ids, that was given as input with the species code concatenated.
|
| coloured_images |
List of pathway diagram with enzyme boxes coloured in specified colours
|
| enzyme_list |
List of enzyme id retrieve from Kegg using get_enzymes_by_gene
|
| genes_list |
List of ids that are enzymes
|
|
Datalinks (25)
| |
| Source |
Sink |
| Species |
Workflow89:part1 |
| gene_ids |
Workflow89:part2 |
| color_pathway_by_objects:return |
Get_Image_From_URL_2:url |
| get_pathways_by_genes:return |
color_pathway_by_objects:pathway_id |
| Remove_String_Duplicates:strippedlist |
color_pathway_by_objects:object_id_list |
| Flatten_List_3:outputlist |
color_pathway_by_objects:bg_color_list |
| Flatten_List_4:outputlist |
color_pathway_by_objects:fg_color_list |
| Workflow89:string |
get_enzymes_by_gene:genes_id |
| Species |
get_genes_by_enzyme:org |
| Flatten_List:outputlist |
get_genes_by_enzyme:enzyme_id |
| Workflow89:string |
get_pathways_by_genes:genes_id_list |
| get_enzymes_by_gene:return |
Flatten_List:inputlist |
| get_genes_by_enzyme:return |
Flatten_List_2:inputlist |
| Flatten_List_2:outputlist |
Remove_String_Duplicates:stringlist |
| Remove_String_Duplicates:strippedlist |
Beanshell:genes_list |
| bg_color |
Beanshell:bg_color |
| fg_color |
Beanshell:fg_color |
| Beanshell:bg_colors |
Flatten_List_3:inputlist |
| Beanshell:fg_colors |
Flatten_List_4:inputlist |
| get_pathways_by_genes:return |
KeggPathwayIDs |
| color_pathway_by_objects:return |
keggimageurl |
| Workflow89:string |
keggGeneNames |
| Get_Image_From_URL_2:image |
coloured_images |
| Flatten_List:outputlist |
enzyme_list |
| Remove_String_Duplicates:strippedlist |
genes_list |
|
Coordinations (0)
| |
Uploader
License
All versions of this Workflow are
licensed under:
Version 2
(of 3)
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Francois Belleau
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