Triplify NCBI databases external reference list [myexperiment:ncbi_xref_namespace2rdf]

Value

Value

Script

import java.util.regex.*;

String line, id, desc, url, urlPattern, category, example;

line = "";
namespace = "";

Pattern thePat = Pattern.compile("(?m)/db_xref="(.*?):(.*?)"");
Matcher matcher = thePat.matcher(in);
if (matcher.find()) {
	id = matcher.group(1);
	example = id + ":" + matcher.group(2);

	id = id.toLowerCase();
	id = id.replace(" ", "");
	namespace = id;

	line = line + "\n   .";
	line = line + "\n   .";
	line = line + "\n  \"bm:ns:"+id+"\" .";
	line = line + "\n  \""+id+"\" .";
	line = line + "\n  \""+example+"\" .";
}

thePat = Pattern.compile("(?m)^    

Script

String 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();

Script

List 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]);
	}
}

Script

URL 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();

Script

String id = "ncbi";
String title = "National Center for Biotechnology Information";
 
ntriples =            "\n   .";
ntriples = ntriples + "\n  \"bm:ns:"+id+"\" .";
ntriples = ntriples + "\n  \"" + title + " [bm:ns:"+id+"]\" .";
ntriples = ntriples + "\n  \"" + title + "\" .";
ntriples = ntriples + "\n  \""+id+"\" .";
ntriples = ntriples + "\n";

Script

output = string1 + string2;

Script

List strippedlist = new ArrayList();
for (Iterator i = stringlist.iterator(); i.hasNext();) {
	String item = (String) i.next();
	if (strippedlist.contains(item) == false) {
		strippedlist.add(item);
	}
}