AllPW2CHEBI
Created: 2015-09-01 14:58:14
Last updated: 2015-10-12 12:39:19
This workflow uses the WikiPathways Webservice/API to query to retrieve all Chemical Entities of Biological Interest (ChEBI) identifers for all pathways and merge them to one, unique list.
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Authors (1)
Titles (1)
Descriptions (1)
This workflow uses the WikiPathways Webservice/API to query to retrieve all Chemical Entities of Biological Interest (ChEBI) identifers for all pathways and merge them to one, unique list. |
Dependencies (0)
Inputs (1)
Name |
Description |
wp_id |
A WikiPathway identifier
|
Processors (6)
Name |
Type |
Description |
getChEBIXrefList |
rest |
The WikiPathways Webservice/API is queried for Chemical Entities of Biological Interest (ChEBI) identifiers in the given pathway. |
Parse_chebi_id |
xpath |
The ChEBI identifiers are parsed from the WikiPathways XML file output. Xpath Expression/ns1:getXrefListResponse/ns1:xrefs |
Split_string_into_string_list_by_regular_expression |
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]);
}
}
|
regex_value |
stringconstant |
Value\n |
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); |
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);
}
}
|
Outputs (1)
Name |
Description |
chebi_id_list |
Chemical Entities of Biological Interest (ChEBI) identifer
|
Datalinks (7)
Source |
Sink |
Split_string_into_string_list_by_regular_expression:split |
getChEBIXrefList: |
getChEBIXrefList:responseBody |
Parse_chebi_id:xml_text |
regex_value:value |
Split_string_into_string_list_by_regular_expression:regex |
wp_id |
Split_string_into_string_list_by_regular_expression:string |
Parse_chebi_id:nodelist |
Flatten_List:inputlist |
Flatten_List:outputlist |
Remove_String_Duplicates:stringlist |
Remove_String_Duplicates:strippedlist |
chebi_id_list |
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Version 2 (latest)
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