Metacat

package edu.ucsb.nceas.metacat.annotation;

import java.io.InputStream;

import java.io.InputStreamReader;

import java.net.URL;

import java.net.URLEncoder;

import org.apache.log4j.Logger;

import org.w3c.dom.Document;

import org.w3c.dom.NodeList;

import com.hp.hpl.jena.ontology.ConversionException;

import com.hp.hpl.jena.ontology.OntClass;

import com.hp.hpl.jena.rdf.model.Resource;

import edu.ucsb.nceas.utilities.XMLUtilities;

public class BioPortalService {

	private static Logger logMetacat = Logger.getLogger(BioPortalService.class);

    // for looking up concepts in BioPortal

    private static final String REST_URL = "http://data.bioontology.org";

    private static final String API_KEY = "24e4775e-54e0-11e0-9d7b-005056aa3316";

    /**

	 * Look up possible concept from BioPortal annotation service.

	 * @see "http://data.bioontology.org/documentation"

	 * @param superClass

	 * @param text

	 * @return

	 */

	public static Resource lookupAnnotationClass(OntClass superClass, String text, String ontologies) {

		// no point calling the service

		if (text == null || text.length() == 0) {

			return null;

		}

		try {

			String urlParameters = "apikey=" + API_KEY;

			urlParameters += "&format=xml";

			if (ontologies != null) {

				urlParameters += "&ontologies=" + ontologies;

			}

			urlParameters += "&text=" + URLEncoder.encode(text, "UTF-8");

			String url = REST_URL + "/annotator?" + urlParameters ;

			URL restURL = new URL(url);

			InputStream is = restURL.openStream();

			Document doc = XMLUtilities.getXMLReaderAsDOMDocument(new InputStreamReader(is, "UTF-8"));

			NodeList classNodeList = XMLUtilities.getNodeListWithXPath(doc, "//annotation/annotatedClass/id");

			if (classNodeList != null && classNodeList.getLength() > 0) {

				for (int i = 0; i < classNodeList.getLength(); i++) {

					String classURI = classNodeList.item(i).getFirstChild().getNodeValue();

					logMetacat.info("annotator suggested: " + classURI);

					Resource subclass = superClass.getModel().getResource(classURI);

					// check that it is a subclass of superClass

					boolean isSubclass = false;

					try {

						isSubclass = superClass.hasSubClass(subclass);

					} catch (ConversionException ce) {

						logMetacat.warn("Skipping unknown subclass: " + classURI, ce);

						// try the next one

						continue;

					}

					if (isSubclass) {

						return subclass;

					}

				}

			}

		} catch (Exception e) {

			logMetacat.error("Could not lookup BioPortal annotation for text=" + text, e);

		}

		return null;

	}

}