bioDBnet - Biological Database Network

bioDBnet: Web Services: REST - Sample Code

Sample code for bioDBnet REST APIs

Sample code in different languagues is provided. If you would like to share your code with other bioDBnet users, please contact us.

PHP: Convert JSON results from bioDBnet's db2db call to a PHP array

$biodbnetRestApiCall = "https://biodbnet-abcc.ncifcrf.gov/webServices/rest.php/biodbnetRestApi.json?method=db2db&format=row&input=genesymbol&inputValues=MYC,MTOR&outputs=geneid,affyid&taxonId=9606";

$response = file_get_contents($biodbnetRestApiCall);

$formattedResponse = json_decode($response, true);

Python: Call to get XML formatted results from bioDBnet's db2db

import urllib

url = 'https://biodbnet-abcc.ncifcrf.gov/webServices/rest.php/biodbnetRestApi.xml?method=db2db&format=row&input=genesymbol&inputValues=MYC,MTOR&outputs=geneid,affyid&taxonId=9606'

u = urllib.urlopen(url)

response = u.read()

Java: Call to get JSON results as a Java String object from bioDBnet's db2db. (http://rest.elkstein.org/2008/02/using-rest-in-java.html)

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

public class RestCalls {

public static void main(String[] args) throws Exception {

String urlStr = "https://biodbnet-abcc.ncifcrf.gov/webServices/rest.php/biodbnetRestApi.json?method=db2db&format=row&input=genesymbol&inputValues=MYC,MTOR&outputs=geneid,affyid&taxonId=9606";

URL url = new URL(urlStr);

HttpURLConnection conn = (HttpURLConnection)url.openConnection();

BufferedReader rd = new BufferedReader(new InputStreamReader(conn.getInputStream()));
StringBuilder sb = new StringBuilder();
String line;

while ((line = rd.readLine()) != null) {
sb.append(line);
}
rd.close();

conn.disconnect();
System.out.println(sb.toString());

}

}

R: Sample code using the RCurl library.

library('RCurl')

response = getURL("https://biodbnet-abcc.ncifcrf.gov/webServices/rest.php/biodbnetRestApi.json?method=db2db&format=row&input=genesymbol&inputValues=MYC,MTOR&outputs=geneid,affyid&taxonId=9606")

cat(response)