SnomedClient.java

import org.json.*

/**
 * Class that provides a static method for querying SNOMED class descendants from BioPortal.
 */
public class SnomedClient {
  static String API_ROOT = "https://data.bioontology.org/ontologies/SNOMEDCT/classes/";
  static String API_KEY = "";
  static String PAGE_SIZE = "500";

  /**
   * Query Bioportal to retrieve list of descendants for a given SNOMED code.
   *
   * @Param String snomedCode A string identifying a concept in SNOMED-CT. For example: 44054006
   * @Return HashMap<String,String> A hashmap that contains all descendants of the given SNOMED term. Keys are the snomed codes, while values is the preferred label of the term.
   */
  static HashMap<String,String> queryDescendants(String snomedCode) {
    // Set up variables for query ..
    URL url;
    HttpURLConnection conn;
    BufferedReader rd;
    String line;
    String result = "";
    String qString = API_ROOT + snomedCode + "/descendants?apikey="+API_KEY+"&expand_class_hierarchy=true&pagesize=" + PAGE_SIZE

    // Perform query to retrieve SNOMED code descendants
    url = new URL(qString);
    conn = (HttpURLConnection) url.openConnection();
    conn.setRequestMethod("GET");
    conn.setRequestProperty("Authorization", "apikey token=" + API_KEY);
    conn.setRequestProperty("Accept", "application/json");
    rd = new BufferedReader(
                                    new InputStreamReader(conn.getInputStream()));
    while ((line = rd.readLine()) != null) {
                    result += line;
    }
    rd.close();

    // Convert results to JSON
    JSONTokener tokener = new JSONTokener(result);
    JSONObject root = new JSONObject(tokener);

    // Extract a map of SNOMED code -> label
    HashMap<String, String> descendants = new HashMap<String, String>();
    Map<String,Object> outerMap = root.toMap();
    for(obj in outerMap["collection"]) {
      String code = obj["@id"].tokenize('/').last();
      descendants[code] = obj["prefLabel"];
    }

    return descendants;
  }
}