Triplify UniProt text search results [myexperiments:uniprotkb_search2rdf]
Created: 2009-11-30 19:55:35
Last updated: 2009-11-30 19:56:33
TAG: knowledgescope, uniprotkb, bio2rdf, search, rdf
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Authors (1)
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Titles (1)
Triplify UniProt text search results [myexperiments:uniprotkb_search2rdf] |
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Descriptions (7)
test values:
uniprot
hk1 |
TAG: knowledgescope, uniprotkb, bio2rdf, search, rdf |
test values:
namespace=uniprot
query=hk1
query=pdb4
query=paget disease |
TAG: knowledgescope, uniprotkb, bio2rdf, search |
test values:
namespace=uniprot
search=hk1 |
test values:
namespace=uniprot
query=hk1
query=pdb4 |
|
![header=[] body=[These are the listed dependencies of the workflow] cssheader=[boxoverTooltipHeader] cssbody=[boxoverTooltipBody] delay=[200] Information](/images/famfamfam_silk/information.png?1680607579)
Dependencies (0)
Inputs (2)
Name |
Description |
query |
hk1
hexokinase
pdb4
paget disease
|
uniprotkb_namespace |
uniprot
uniref
uniparc
citations
keywords
locations
taxonomy
uniprot
uniref
citations
|
Processors (6)
Name |
Type |
Description |
build_uniprot_search_url |
beanshell |
Scriptoutput = "http://www.uniprot.org/" + string1 + "/?query=" + string2.replace(" ","+") + "&limit=100000&format=list"; |
Get_Web_Page_from_URL |
localworker |
ScriptURL inputURL = null;
if (base != void) {
inputURL = new URL(new URL(base), url);
}
else {
inputURL = new URL(url);
}
URLConnection con = inputURL.openConnection();
InputStream in = con.getInputStream();
InputStreamReader isr = new InputStreamReader(in);
Reader inReader = new BufferedReader(isr);
StringBuffer buf = new StringBuffer();
int ch;
while ((ch = inReader.read()) > -1) {
buf.append((char)ch);
}
inReader.close();
contents = buf.toString();
//String NEWLINE = System.getProperty("line.separator");
//
//URL inputURL = null;
//if (base != void) {
// inputURL = new URL(new URL(base), url);
//} else {
// inputURL = new URL(url);
//}
//StringBuffer result = new StringBuffer();
//BufferedReader reader = new BufferedReader(new InputStreamReader(inputURL.openStream()));
//String line = null;
//while ((line = reader.readLine()) != null) {
// result.append(line);
// result.append(NEWLINE);
//}
//
//contents = result.toString();
|
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]);
}
}
|
eol |
stringconstant |
Value\n |
build_bmuri |
beanshell |
Scriptoutput = "http://bio2rdf.org/" + string1 + ":" + string2; |
build_ntriples |
beanshell |
Scriptsearch = search.replace(" ","_");
Integer count = 0;
search_ntriples = "";
count_ntriples = "";
for (Iterator i = stringlist.iterator(); i.hasNext();) {
String id = (String) i.next();
count = count + 1;
search_ntriples = search_ntriples + "\n .";
}
if (count != 0) {
count_ntriples = "\n \""+count+"\" .";
count_ntriples = count_ntriples + "\n .";
count_ntriples = count_ntriples + "\n .";
} |
Beanshells (3)
Name |
Description |
Inputs |
Outputs |
build_uniprot_search_url |
|
string1
string2
|
output
|
build_bmuri |
|
string1
string2
|
output
|
build_ntriples |
|
stringlist
namespace
search
|
count_ntriples
search_ntriples
|
Outputs (4)
Name |
Description |
bmuris |
|
search_count_ntriples |
|
uniprotkb_search_ntriples |
|
url |
|
Datalinks (14)
Source |
Sink |
query |
build_uniprot_search_url:string2 |
uniprotkb_namespace |
build_uniprot_search_url:string1 |
build_uniprot_search_url:output |
Get_Web_Page_from_URL:url |
Get_Web_Page_from_URL:contents |
Split_string_into_string_list_by_regular_expression:string |
eol:value |
Split_string_into_string_list_by_regular_expression:regex |
uniprotkb_namespace |
build_bmuri:string1 |
Split_string_into_string_list_by_regular_expression:split |
build_bmuri:string2 |
Split_string_into_string_list_by_regular_expression:split |
build_ntriples:stringlist |
query |
build_ntriples:search |
uniprotkb_namespace |
build_ntriples:namespace |
build_bmuri:output |
bmuris |
build_ntriples:count_ntriples |
search_count_ntriples |
build_ntriples:search_ntriples |
uniprotkb_search_ntriples |
build_uniprot_search_url:output |
url |
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