Triplify UniProt database list [myexperiments:uniprotkb_namespace2rdf]
Created: 2009-11-30 19:35:17
Last updated: 2009-11-30 19:43:03
TAG: knowledgescope, uniprotkb, bio2rdf, banff_manifesto
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Authors (1)
![header=[] body=[These are the descriptive titles embedded within the workflow version] cssheader=[boxoverTooltipHeader] cssbody=[boxoverTooltipBody] delay=[200] Information](/images/famfamfam_silk/information.png?1680607579)
Titles (3)
[myexperiments:uniprot_namespace2rdf] |
Triplify UniProt database list [myexperiments:uniprot_namespace2rdf] |
Triplify UniProt database list [myexperiments:uniprotkb_namespace2rdf] |
![header=[] body=[These are the descriptions embedded within the workflow version] cssheader=[boxoverTooltipHeader] cssbody=[boxoverTooltipBody] delay=[200] Information](/images/famfamfam_silk/information.png?1680607579)
Descriptions (4)
TAG: knowledgescope, uniprotkb, bio2rdf, banff_manifesto |
TAG: knowledgescope, uniprot, bio2rdf, banff_manifesto |
TAG: knowledgescope, uniprotkb, bio2rdf, banff_manifesto |
TAG: knowledgescope, uniprotkb, bio2rdf, banff manifesto |
![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)
Processors (6)
Name |
Type |
Description |
uniprotkb_namespaces |
stringconstant |
Valueuniprot,uniref,uniparc,citations,keywords,locations,taxonomy |
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]);
}
}
|
Merge_String_List_to_a_String |
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();
|
build_uniprot_namespace_ntriple |
beanshell |
ScriptString desc, uri, nsid, title;
title = "";
if (namespace.equals("uniprot")) title = "Protein knowledgebase";
if (namespace.equals("uniref")) title = "Sequence clusters";
if (namespace.equals("uniparc")) title = "Sequence archive";
if (namespace.equals("citations")) title = "Publications cited in or computationally mapped to UniProtKB";
if (namespace.equals("taxonomy")) title = "Organisms are classified in a hierarchical tree structure";
if (namespace.equals("keywords")) title = "UniProtKB entries are tagged with keywords";
if (namespace.equals("locations")) title = "Subcellular location";
uri = "";
nsid = "bm:ns:" + namespace;
ntriples = "\n" + uri + " .";
ntriples = ntriples + "\n" + uri + " \"" + nsid + "\" .";
ntriples = ntriples + "\n" + uri + " .";
ntriples = ntriples + "\n" + uri + " \"http://www.uniprot.org/" + namespace +"\" .";
ntriples = ntriples + "\n" + uri + " \"" + namespace +"\" .";
ntriples = ntriples + "\n" + uri + " \""+ title +"\" .";
ntriples = ntriples + "\n" + uri + " \""+ title +" ["+nsid+"]\" .";
|
UniProt_provider |
beanshell |
Script
ntriples = "\n .";
ntriples = ntriples + "\n \"bm:ns:uniprotkb\" .";
ntriples = ntriples + "\n \"http://www.uniprot.org\" .";
ntriples = ntriples + "\n \"uniprotkb\" .";
ntriples = ntriples + "\n \"Universal Protein Resource\" .";
ntriples = ntriples + "\n \"Universal Protein Resource [ns:uniprotkb]\" .";
|
Concatenate_two_strings |
localworker |
Scriptoutput = string1 + string2; |
Beanshells (2)
Name |
Description |
Inputs |
Outputs |
build_uniprot_namespace_ntriple |
|
namespace
|
ntriples
|
UniProt_provider |
|
|
ntriples
|
Outputs (2)
Name |
Description |
uniprotkb_namespace_ntriples |
|
namespace_list |
|
Datalinks (7)
Source |
Sink |
uniprotkb_namespaces:value |
Split_string_into_string_list_by_regular_expression:string |
build_uniprot_namespace_ntriple:ntriples |
Merge_String_List_to_a_String:stringlist |
Split_string_into_string_list_by_regular_expression:split |
build_uniprot_namespace_ntriple:namespace |
UniProt_provider:ntriples |
Concatenate_two_strings:string1 |
Merge_String_List_to_a_String:concatenated |
Concatenate_two_strings:string2 |
Concatenate_two_strings:output |
uniprotkb_namespace_ntriples |
Split_string_into_string_list_by_regular_expression:split |
namespace_list |
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