Get the list of GeneID for all pathways of a specified taxon

Value

Script

output = "http://kegg.bio2rdf.org/sparql?default-graph-uri=&query=SELECT+%3FPathway+%0D%0AWHERE+{%0D%0A++%3FPathway+a+%3Chttp%3A%2F%2Fbio2rdf.org%2Fns%2Fkegg%23Pathway%3E+.%0D%0A++FILTER(regex(%3FPathway+%2C+%22"+string1+"%22))+.%0D%0A}&format=text%2Fhtml&debug=on";

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

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

List split = new ArrayList();
if (!html.equals("")) {
	String regexString = "\n";
	if (regex != void) {
		regexString = regex;
	}
	String[] result = html.split(regexString);
	for (int i = 0; i < result.length; i++) {
		split.add(result[i]);
	}
}

import java.util.regex.*;

uris = new ArrayList();
Pattern thePat = Pattern.compile("

Script

import java.net.*; 
import java.io.*;


            // Construct data
            String data = "query=" + URLEncoder.encode("insert in graph <"+graph+"> { "+n3+" }", "UTF-8");
            
            // Create a socket to the host
            String hostname = "localhost";
            int port = 8890;
            InetAddress addr = InetAddress.getByName(hostname);
            Socket socket = new Socket(addr, port);
        
            // Send header
            String path = "/sparql";
            BufferedWriter wr = new BufferedWriter(new OutputStreamWriter(socket.getOutputStream(), "UTF8"));
            wr.write("POST "+path+" HTTP/1.0\r\n");
            wr.write("Content-Length: "+data.length()+"\r\n");
            wr.write("Content-Type: application/x-www-form-urlencoded\r\n");
            wr.write("\r\n");
        
            // Send data
            wr.write(data);
            wr.flush();
        
            // Get response
            BufferedReader rd = new BufferedReader(new InputStreamReader(socket.getInputStream()));

	StringBuffer buf = new StringBuffer();
            String line;
            while ((line = rd.readLine()) != null) {
		buf.append(line);
            }
            wr.close();
            rd.close();
	
	html = buf.toString();

Value

Script

output = "http://kegg.bio2rdf.org/sparql?default-graph-uri=&query=CONSTRUCT+{%0D%0A%3FPathway+%3Chttp%3A%2F%2Fbio2rdf.org%2Fns%2Fbio2rdf%23xGeneID%3E+%3Fgeneid+.%0D%0A}%0D%0AWHERE+{%0D%0A++%3FPathway+%3Chttp%3A%2F%2Fbio2rdf.org%2Fns%2Fkegg%23xRelation%3E+%3FxRelation+.%0D%0A++FILTER(%3FPathway+%3D+%3C"+string1+"%3E)+.%0D%0A++%3FxRelation+%3Fp1+%3Fs1+.%0D%0A++FILTER(%3Fp1+%3D+%3Chttp%3A%2F%2Fbio2rdf.org%2Fns%2Fkegg%23xEntry1%3E+OR+%3Fp1+%3D+%3Chttp%3A%2F%2Fbio2rdf.org%2Fns%2Fkegg%23xEntry2%3E+)+.%0D%0A++%3Fs1+%3Chttp%3A%2F%2Fbio2rdf.org%2Fns%2Fkegg%23xRef%3E+%3FxRef+.%0D%0A++%3FxRef+%3Chttp%3A%2F%2Fwww.w3.org%2F2002%2F07%2Fowl%23sameAs%3E+%3Fgeneid+.%0D%0A}&format=text%2Frdf%2Bn3&debug=on";

Value

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

output = "DELETE FROM GRAPH <"+string1+"> { ?s ?p ?o } WHERE { GRAPH  ?g { ?s ?p ?o }} ";

Value

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();