GetWikiPWByENS
Created: 2015-10-02 09:36:00
Last updated: 2015-10-12 12:41:56
This workflow uses the WikiPathways Webservice/API to query for pathways containing a specific ENSEMBL identifier. The mapping service behind WikiPathways takes care of the identifier mapping, making sure that all relevant results are found even if they were originally reported using a different identifier scheme.
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Descriptions (1)
This workflow uses the WikiPathways Webservice/API to query for pathways containing a specific ENSEMBL identifier. The mapping service behind WikiPathways takes care of the identifier mapping, making sure that all relevant results are found even if they were originally reported using a different identifier scheme. |
Dependencies (0)
Inputs (1)
Name |
Description |
ens_id |
ENSEMBL identifer
|
Processors (9)
Name |
Type |
Description |
findPathwaysByENSXref |
rest |
The WikiPathways Webservice/API is queried for pathways with a specific ENSEMBL identifier. |
Parse_pathway_URIs |
xpath |
The unique resource identifiers are parsed from the WikiPathways XML file output. Xpath Expression/ns1:findPathwaysByXrefResponse/ns1:result/ns2:url |
Split_string_into_string_list_by_regular_expression |
localworker |
If an input file is used, this service will split the file on the newline character, making sure that the file is parsed correctly. 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 |
The character to split the input string (or text in file) on. Currently newline character (\n). Value\n |
Parse_species |
xpath |
The species are parsed from the WikiPathways XML file output. Xpath Expression/ns1:findPathwaysByXrefResponse/ns1:result/ns2:species |
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); |
Merge_String_List_to_a_String_2 |
localworker |
ScriptString seperatorString = "\n";
if (seperator != void) {
seperatorString = seperator;
}
StringBuffer sb = new StringBuffer();
for (Iterator i = stringlist.iterator(); i.hasNext();) {
String item = (String) i.next();
sb.append(item);
if (i.hasNext()) {
sb.append(seperatorString);
}
}
concatenated = sb.toString();
|
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); |
Merge_String_List_to_a_String_2_2 |
localworker |
ScriptString seperatorString = "\n";
if (seperator != void) {
seperatorString = seperator;
}
StringBuffer sb = new StringBuffer();
for (Iterator i = stringlist.iterator(); i.hasNext();) {
String item = (String) i.next();
sb.append(item);
if (i.hasNext()) {
sb.append(seperatorString);
}
}
concatenated = sb.toString();
|
Outputs (3)
Name |
Description |
pathway_URI_list |
Pathway unique resource identifer, usually a resovable link.
|
ens_id |
ENSEMBL identifer
|
species_list |
The species for which the pathway is annotated.
|
Datalinks (12)
Source |
Sink |
Split_string_into_string_list_by_regular_expression:split |
findPathwaysByENSXref: |
findPathwaysByENSXref:responseBody |
Parse_pathway_URIs:xml_text |
regex_value:value |
Split_string_into_string_list_by_regular_expression:regex |
ens_id |
Split_string_into_string_list_by_regular_expression:string |
findPathwaysByENSXref:responseBody |
Parse_species:xml_text |
Parse_pathway_URIs:nodelist |
Flatten_List:inputlist |
Flatten_List:outputlist |
Merge_String_List_to_a_String_2:stringlist |
Parse_species:nodelist |
Flatten_List_2:inputlist |
Flatten_List_2:outputlist |
Merge_String_List_to_a_String_2_2:stringlist |
Merge_String_List_to_a_String_2:concatenated |
pathway_URI_list |
Split_string_into_string_list_by_regular_expression:split |
ens_id |
Merge_String_List_to_a_String_2_2:concatenated |
species_list |
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Version 2 (latest)
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