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.
Get Pathway-Genes and gene description by Entrez gene id
Created: 2012-03-27 10:52:31
Last updated: 2012-04-03 09:20:02
Given a specific entrez gene id, returns the pathways that this gene participates in and for each of those pathways which genes (including their description) are associated with.
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Workflow Components
|
Authors (1)
|  |
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Titles (1)
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| Get Pathway-Genes and gene description by Entrez gene id |
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Descriptions (1)
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| Given a specific entrez gene id, returns the pathways that this gene participates in and for each of those pathways which genes (including their description) are associated with. |
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Dependencies (0)
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Inputs (1)
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| Name |
Description |
| entrez_gene_id |
Give an entrez gene id
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Processors (13)
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| Name |
Type |
Description |
| get_pathways_by_genes |
wsdl |
Wsdlhttp://soap.genome.jp/KEGG.wsdlWsdl Operationget_pathways_by_genes |
| get_genes_by_pathway |
wsdl |
Wsdlhttp://soap.genome.jp/KEGG.wsdlWsdl Operationget_genes_by_pathway |
| getPathwayDescription |
wsdl |
Wsdlhttp://soap.genome.jp/KEGG.wsdlWsdl Operationbtit |
| add_ncbi_to_string |
beanshell |
ScriptString[] split = input.split("\n");
Vector nonEmpty = new Vector();
for (int i = 0; i < split.length; i++)
{
String trimmed = split[i].trim();
nonEmpty.add(trimmed);
}
String output = "";
for (int i = 0; i < nonEmpty.size(); i++)
{
output = output + "ncbi-geneid:" + (String) (nonEmpty.elementAt(i) + "\n");
} |
| convertToKEGGid |
wsdl |
Wsdlhttp://soap.genome.jp/KEGG.wsdlWsdl Operationbconv |
| splitAndSendOnlyKEGGgeneID |
localworker |
ScriptList split = new ArrayList();
if (!string.equals("")) {
String regexString = ",";
if (regex != void) {
regexString = regex;
}
String[] result = string.split(regexString);
for (int i = 1; i < result.length; i=i+3) {
split.add(result[i]);
}
}
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| lister |
localworker |
ScriptList split = new ArrayList();
if (!string.equals("")) {
String regexString = ",";
if (regex != void) {
regexString = regex;
}
String[] result = string.split(regexString);
for (int i = 0; i < result.length; i++) {
split.add(result[i]);
}
} |
| splitOnTab |
stringconstant |
Value\t |
| SplitOnNewLine |
stringconstant |
Value\n |
| Clean_List_of_Strings_by_separator |
localworker |
Scriptfilteredlist = new ArrayList();
for (Iterator i = stringlist.iterator(); i.hasNext();) {
String item = (String) i.next();
String[] tokens = item.split(separators);
filteredlist.add(tokens[1]);
}
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| separators_value |
stringconstant |
Value[:] |
| getGeneDescription |
wsdl |
Wsdlhttp://soap.genome.jp/KEGG.wsdlWsdl Operationbtit |
| Clean_List_of_Strings_by_separator_2 |
beanshell |
Scriptfilteredlist = new ArrayList();
for (Iterator i = stringlist.iterator(); i.hasNext();) {
String item = (String) i.next();
String[] tokens = item.split(separators);
filteredlist.add(tokens[1]);
}
|
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Beanshells (2)
| |
| Name |
Description |
Inputs |
Outputs |
| add_ncbi_to_string |
|
input
|
output
|
| Clean_List_of_Strings_by_separator_2 |
|
stringlist
separators
|
filteredlist
|
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Outputs (3)
| |
| Name |
Description |
| Pathway |
|
| geneList |
|
| gene_description |
|
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Datalinks (17)
| |
| Source |
Sink |
| lister:split |
get_pathways_by_genes:genes_id_list |
| get_pathways_by_genes:return |
get_genes_by_pathway:pathway_id |
| get_pathways_by_genes:return |
getPathwayDescription:string |
| entrez_gene_id |
add_ncbi_to_string:input |
| add_ncbi_to_string:output |
convertToKEGGid:string |
| convertToKEGGid:return |
splitAndSendOnlyKEGGgeneID:string |
| splitOnTab:value |
splitAndSendOnlyKEGGgeneID:regex |
| splitAndSendOnlyKEGGgeneID:split |
lister:string |
| SplitOnNewLine:value |
lister:regex |
| get_genes_by_pathway:return |
Clean_List_of_Strings_by_separator:stringlist |
| separators_value:value |
Clean_List_of_Strings_by_separator:separators |
| get_genes_by_pathway:return |
getGeneDescription:string |
| getGeneDescription:return |
Clean_List_of_Strings_by_separator_2:stringlist |
| separators_value:value |
Clean_List_of_Strings_by_separator_2:separators |
| getPathwayDescription:return |
Pathway |
| Clean_List_of_Strings_by_separator:filteredlist |
geneList |
| Clean_List_of_Strings_by_separator_2:filteredlist |
gene_description |
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Coordinations (0)
| |
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License
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