A Java program writted to query multiple data sources - Coexpress, Corum, Gene Ontology (Biological Processes, Cellular Compartments, Molecular Functions), Gene Co-occurrence (Publications, KEGG Pathways, OMIM Diseases), Protein Domain-domain interactions and Gene Ideogram-Ideogram Interactions, which are stored as RDF in a Virtuoso triple store…

Interactors.java

package org.deri.ppi;

import java.io.BufferedReader;
import java.io.BufferedWriter;
import java.io.DataInputStream;
import java.io.FileInputStream;
import java.io.FileWriter;
import java.io.IOException;
import java.io.InputStreamReader;
import java.net.HttpURLConnection;
import java.net.URL;
import java.net.URLEncoder;
import java.util.HashMap;

/**
 * Retrieves information from multiple data sources stored in Virtuoso as RDF
 */
 
public class Interactors {

	static final HashMap<String, String> geneList = new HashMap<String, String>();
	static final HashMap<String, String> goBPList = new HashMap<String, String>();
	static final HashMap<String, String> goCCList = new HashMap<String, String>();
	static final HashMap<String, String> goMFList = new HashMap<String, String>();
	/**
	 * @param args
	 */
	public static void main(String[] args) throws IOException{
		//----- HGNC file which provides EntrezGene-HGNC ID conversion
		FileInputStream hgncstream = new FileInputStream("hgncConvertor.tsv");
		DataInputStream hgncin = new DataInputStream(hgncstream);
		BufferedReader hgncbr = new BufferedReader(new InputStreamReader(hgncin));
		
		String hgncIdline;
		int genecount = 0;
		while ((hgncIdline = hgncbr.readLine()) != null)   {
			String [] hgncParts = hgncIdline.split("\t");
			if(genecount++ > 0) {
				if(hgncParts.length > 1)
					geneList.put(hgncParts[1], hgncParts[0]);
			}
		}
		
		// ---- Custom GO File generated which removes the parent nodes 
		FileInputStream gostream = new FileInputStream("constrictedGo_rel.tsv");
		DataInputStream goin = new DataInputStream(gostream);
		BufferedReader gobr = new BufferedReader(new InputStreamReader(goin));
		
		String goline;
		while ((goline = gobr.readLine()) != null)   {
			String [] goParts = goline.split("\t");
			if(goParts.length > 2)
				goBPList.put(goParts[0], goParts[2]);
			if(goParts.length > 3)
				goCCList.put(goParts[0], goParts[3]);
			if(goParts.length > 4)
				goMFList.put(goParts[0], goParts[4]);
			
		}
		
		//- Test data for pairs of proteins of the format - EntrezID_A | UniprotID_A | EnsemblID_A | ChrStart_A | CHrStop_A | ChrLength_A | ChrNumber_A | ChrStrand_A | ... Repeat for B ... | Ideogram_A | Ideogram_B | Domains_A | Domains_B
		FileInputStream stream = new FileInputStream("interactorsIdeogramDomainRef.tsv");
		DataInputStream in = new DataInputStream(stream);
		BufferedReader br = new BufferedReader(new InputStreamReader(in));
		
		FileWriter foutstream = new FileWriter("interactorsIdeogramDomainRef_scores.tsv");
		BufferedWriter out = new BufferedWriter(foutstream);
		
		String pathLine;
		int count = 0;
		while ((pathLine = br.readLine()) != null)   {
			String [] strParts = pathLine.split("\t");
			if(strParts.length < 20)
				continue;
			double ddScore = 0.0; 
			double ideoScore = 0.0;
			double coExpressScore = 0.0;
			int corumScore = 0, cooccurPub = 0, cooccurPath = 0, cooccurDis = 0;
			int goBPScore = 0, goCCScore = 0, goMFScore = 0;
			
			//--------------- Coexpress Processing here ------------------ //
			/*PREFIX ppi: <http://data.bioinfo.deri.ie/>
				PREFIX ns1: <http://coxpresdb.jp/rdf/def/0.1/>
				PREFIX geneid: <http://bio2rdf.org/geneid:>

				SELECT * WHERE {{
				?coexpressInt ns1:gene_id_1 geneid:24147;
				ns1:gene_id_2 geneid:23556;
				ns1:mutual_rank ?rank
				} UNION {
				?coexpressInt ns1:gene_id_2 geneid:3280;
				ns1:gene_id_1 geneid:23556;
				ns1:mutual_rank ?rank
				}
				}*/
			
			String coexpressQuery = "PREFIX ppi: <http://data.bioinfo.deri.ie/>" +
					"PREFIX ns1: <http://coxpresdb.jp/rdf/def/0.1/>" +
					"PREFIX geneid: <http://bio2rdf.org/geneid:>" +
					"SELECT DISTINCT * WHERE {{" +
						"?coexpressInt ns1:gene_id_1 geneid:"+strParts[0]+";ns1:gene_id_2 geneid:"+strParts[8]+";ns1:pcc ?pcc" +
					"} UNION {" +
						"?coexpressInt ns1:gene_id_2 geneid:"+strParts[8]+";ns1:gene_id_1 geneid:"+strParts[0]+";ns1:pcc ?pcc" +
					"}}";
			String coexpressQueryStr = "http://srvgal78.deri.ie/sparql/?default-graph-uri=&query="+URLEncoder.encode(coexpressQuery, "UTF-8")+ "&format=text%2Ftab-separated-values&timeout=0&debug=on";
			String coexpressResult = httpGet(coexpressQueryStr);
			String [] ceresultParts = coexpressResult.split("\t");
			if(ceresultParts.length > 2) {
				coExpressScore = Double.parseDouble(ceresultParts[3]);
			}
			
			// -------------------------- Corum Complexes processing ------- //
			//<http://data.bioinfo.deri.ie/CORUM/1> <http://data.bioinfo.deri.ie/componets> <http://purl.uniprot.org/uniprot/P41182> , <http://purl.uniprot.org/uniprot/P56524> 
			String corumQuery = "SELECT (COUNT (DISTINCT ?s) AS ?complexes) WHERE {" +
					"?s <http://data.bioinfo.deri.ie/componets> <http://purl.uniprot.org/uniprot/" + strParts[1] + "> , <http://purl.uniprot.org/uniprot/" + strParts[9] + "> ." +
					"}";
			String corumQueryStr = "http://srvgal78.deri.ie/sparql/?default-graph-uri=&query="+URLEncoder.encode(corumQuery, "UTF-8")+ "&format=text%2Ftab-separated-values&timeout=0&debug=on";
			String corumResult = httpGet(corumQueryStr);
			String [] corumParts = corumResult.split("\t");
			corumScore = Integer.parseInt(corumParts[1]);
			
			// -------------------------- GO processing includes only leaves ------- //
			String goCC1 = goCCList.containsKey(strParts[1]) ? goCCList.get(strParts[1]) : "";
			String goCC2 = goCCList.containsKey(strParts[9]) ? goCCList.get(strParts[9]) : "";
			if(!(goCC1.isEmpty() || goCC2.isEmpty())) {
				String [] goCC1parts = goCC1.split(";");
				String [] goCC2parts = goCC2.split(";");
				for(int cc1 = 0; cc1< goCC1parts.length; cc1++){
					for(int cc2 = 0; cc2<goCC2parts.length; cc2++ ){
						goCCScore += ((goCC1parts[cc1].matches(goCC2parts[cc2])) ? 1 : 0);
					}
				}
			}				
			
			String goBP1 = goBPList.containsKey(strParts[1]) ? goBPList.get(strParts[1]) : "";
			String goBP2 = goBPList.containsKey(strParts[9]) ? goBPList.get(strParts[9]) : "";
			if(!(goBP1.isEmpty() || goBP2.isEmpty())) {
				String [] goBP1parts = goBP1.split(";");
				String [] goBP2parts = goBP2.split(";");
				for(int bp1 = 0; bp1< goBP1parts.length; bp1++){
					for(int bp2 = 0; bp2<goBP2parts.length; bp2++ ){
						goBPScore += ((goBP1parts[bp1].matches(goBP2parts[bp2])) ? 1 : 0);
					}
				}
			}	
			
			String goMF1 = goMFList.containsKey(strParts[1]) ? goMFList.get(strParts[1]) : "";
			String goMF2 = goMFList.containsKey(strParts[9]) ? goMFList.get(strParts[9]) : "";
			if(!(goMF1.isEmpty() || goMF2.isEmpty())) {
				String [] goMF1parts = goMF1.split(";");
				String [] goMF2parts = goMF2.split(";");
				for(int mf1 = 0; mf1< goMF1parts.length; mf1++){
					for(int mf2 = 0; mf2<goMF2parts.length; mf2++ ){
						goMFScore += ((goMF1parts[mf1].matches(goMF2parts[mf2])) ? 1 : 0);
					}
				}
			}	
			
			// ---------------------- Cooccurrence processing here  ------------------------- //
			if(geneList.containsKey(strParts[0]) && geneList.containsKey(strParts[8])) {
				String connector = (geneList.get(strParts[0]) + "_" + geneList.get(strParts[8])).toLowerCase();
				String connector1 = (geneList.get(strParts[8]) + "_" + geneList.get(strParts[0])).toLowerCase();
				
				String coPathQuery = "SELECT * WHERE {" +
								"GRAPH <http://tcga.deri.ie/pathwayconnectors/> { {" +
									"<http://tcga.deri.ie/con:"+connector+"> a <http://tcga.deri.ie/schema/keggCon> ;" +
									"<http://tcga.deri.ie/schema/weight> ?weight" +
								"} UNION { " +
									"<http://tcga.deri.ie/con:"+connector1+"> a <http://tcga.deri.ie/schema/keggCon> ;" +
									"<http://tcga.deri.ie/schema/weight> ?weight" +
								"}}}";
				String coPathQueryURL = "http://srvgal78.deri.ie/sparql/?default-graph-uri=&query="+URLEncoder.encode(coPathQuery, "UTF-8")+ "&format=text%2Ftab-separated-values&timeout=0&debug=on";
				String coPathResults = httpGet(coPathQueryURL);
				String [] coPathResultsParts = coPathResults.split("\t");
				if(coPathResultsParts.length > 1)
					cooccurPath = Integer.parseInt(coPathResultsParts[1].substring(1,coPathResultsParts[1].length()-1));
				
				String coPubQuery = "SELECT * WHERE {" +
						"GRAPH <http://tcga.deri.ie/pubmedconnectors/> { {" +
							"<http://tcga.deri.ie/con:"+connector+"> a <http://tcga.deri.ie/schema/pubmedCon> ;" +
							"<http://tcga.deri.ie/schema/weight> ?weight" +
						"} UNION { " +
							"<http://tcga.deri.ie/con:"+connector1+"> a <http://tcga.deri.ie/schema/pubmedCon> ;" +
							"<http://tcga.deri.ie/schema/weight> ?weight" +
						"}}}";
				String coPubQueryURL = "http://srvgal78.deri.ie/sparql/?default-graph-uri=&query="+URLEncoder.encode(coPubQuery, "UTF-8")+ "&format=text%2Ftab-separated-values&timeout=0&debug=on";
				String coPubResults = httpGet(coPubQueryURL);
				String [] coPubResultsParts = coPubResults.split("\t");
				if(coPubResultsParts.length > 1)
					cooccurPub = Integer.parseInt(coPubResultsParts[1].substring(1,coPubResultsParts[1].length()-1));
				
				String coDisQuery = "SELECT * WHERE {" +
						"GRAPH <http://tcga.deri.ie/diseaseconnectors/> { {" +
							"<http://tcga.deri.ie/con:"+connector+"> a <http://tcga.deri.ie/schema/omimCon> ;" +
							"<http://tcga.deri.ie/schema/weight> ?weight" +
						"} UNION { " +
							"<http://tcga.deri.ie/con:"+connector1+"> a <http://tcga.deri.ie/schema/omimCon> ;" +
							"<http://tcga.deri.ie/schema/weight> ?weight" +
						"}}}";
				String coDisQueryURL = "http://srvgal78.deri.ie/sparql/?default-graph-uri=&query="+URLEncoder.encode(coDisQuery, "UTF-8")+ "&format=text%2Ftab-separated-values&timeout=0&debug=on";
				String coDisResults = httpGet(coDisQueryURL);
				String [] coDisResultsParts = coDisResults.split("\t");
				if(coDisResultsParts.length > 1)
					cooccurDis = Integer.parseInt(coDisResultsParts[1].substring(1,coDisResultsParts[1].length()-1));
			}
			
			//------- Ideogram Interaction processing here ---- //
			if(! (strParts[16].isEmpty() || strParts[17].isEmpty())) {
				/*
				 * SELECT * WHERE {{<http://data.bioinfo.deri.ie/IIinter:chr1_p13.3-chr11_q22.3> <http://data.bioinfo.deri.ie/inferredScore> ?inferredScore} UNION {<http://data.bioinfo.deri.ie/IIinter:chr11_q22.3-chr1_p13.3> <http://data.bioinfo.deri.ie/inferredScore> ?inferredScore
					}}
				 */
				String ideogramInter = "chr" + strParts[6] + "_" +strParts[16] + "-chr" + strParts[14] + "_" + strParts[17];
				String ideogramInter2 = "chr" + strParts[14] + "_" + strParts[17] + "-chr" + strParts[6] + "_" +strParts[16];
				String query = "SELECT * WHERE {{ <http://data.bioinfo.deri.ie/IIinter:"+ideogramInter+"> <http://data.bioinfo.deri.ie/inferredScore> ?inferredScore " +
						"} UNION { <http://data.bioinfo.deri.ie/IIinter:"+ideogramInter2+"> <http://data.bioinfo.deri.ie/inferredScore> ?inferredScore" +
						"}}";
				String urlStr = "http://srvgal78.deri.ie/sparql/?default-graph-uri=&query="+URLEncoder.encode(query, "UTF-8")+ "&format=text%2Ftab-separated-values&timeout=0&debug=on";
				String result = httpGet(urlStr);
				String [] resultParts = result.split("\t");
				if(resultParts.length > 1) {
					if(!resultParts[1].isEmpty()) {
						ideoScore = Double.parseDouble(resultParts[1].substring(1,resultParts[1].length()-1));
					}
				}
			}
			
			//-------- Domain-Domain Interaction processing here -----/
			if(! (strParts[18].matches("NA") || strParts[19].matches("NA")) ) {
				String [] domain1Parts = strParts[18].split(";");
				String [] domain2Parts = strParts[19].split(";");
				
				
				for(int i = 0; i < domain1Parts.length ; i++){
					for(int j = 0; j < domain2Parts.length ; j++){
						/*
						 * SELECT ?inferredScore ?score WHERE { {<http://data.bioinfo.deri.ie/DDinter:PF04487_PF03299> a <http://data.bioinfo.deri.ie/DDinter> .
							OPTIONAL {<http://data.bioinfo.deri.ie/DDinter:PF04487_PF03299> <http://data.bioinfo.deri.ie/score> ?score} .
							OPTIONAL {<http://data.bioinfo.deri.ie/DDinter:PF04487_PF03299> <http://data.bioinfo.deri.ie/inferredScore> ?inferredScore } }
							UNION {<http://data.bioinfo.deri.ie/DDinter:PF03299_PF04487> a <http://data.bioinfo.deri.ie/DDinter> .
							OPTIONAL {<http://data.bioinfo.deri.ie/DDinter:PF03299_PF04487> <http://data.bioinfo.deri.ie/score> ?score} .
							OPTIONAL {<http://data.bioinfo.deri.ie/DDinter:PF03299_PF04487> <http://data.bioinfo.deri.ie/inferredScore> ?inferredScore } }
							}
						 */
						String query = "SELECT * WHERE { { <http://data.bioinfo.deri.ie/DDinter:"+domain1Parts[i]+"_"+domain2Parts[j]+"> a <http://data.bioinfo.deri.ie/DDinter> ."+
									"OPTIONAL {<http://data.bioinfo.deri.ie/DDinter:"+domain1Parts[i]+"_"+domain2Parts[j]+"> <http://data.bioinfo.deri.ie/score> ?score} ."+
									"OPTIONAL {<http://data.bioinfo.deri.ie/DDinter:"+domain1Parts[i]+"_"+domain2Parts[j]+"> <http://data.bioinfo.deri.ie/inferredScore> ?inferredScore }"+
								"} UNION { " +
									"<http://data.bioinfo.deri.ie/DDinter:"+domain2Parts[j]+"_"+domain1Parts[i]+"> a <http://data.bioinfo.deri.ie/DDinter> ."+
									"OPTIONAL {<http://data.bioinfo.deri.ie/DDinter:"+domain2Parts[j]+"_"+domain1Parts[i]+"> <http://data.bioinfo.deri.ie/score> ?score} ." +
									"OPTIONAL {<http://data.bioinfo.deri.ie/DDinter:"+domain2Parts[j]+"_"+domain1Parts[i]+"> <http://data.bioinfo.deri.ie/inferredScore> ?inferredScore}"+
								"}}";
						// query = http://srvgal78.deri.ie/sparql/?default-graph-uri=&query=+SELECT+*+WHERE+%7B%0D%0A%3Fs+a+%3Chttp%3A%2F%2Fdata.bioinfo.deri.ie%2FDDinter%3E+.%0D%0A%3Fs+%3Chttp%3A%2F%2Fdata.bioinfo.deri.ie%2FinferredScore%3E+%3Fo%0D%0A%7D&format=text%2Ftab-separated-values&timeout=0&debug=on
						String urlStr = "http://srvgal78.deri.ie/sparql/?default-graph-uri=&query="+URLEncoder.encode(query, "UTF-8")+ "&format=text%2Ftab-separated-values&timeout=0&debug=on";
						String result = httpGet(urlStr);
						String [] resultParts = result.split("\t");
						double ddMaxScore = 0.0;
						for(int k = 2; k < resultParts.length; k++) {
							double ddCurrentScore = 0.0;
							if(!resultParts[k].isEmpty()) {
								ddCurrentScore = Double.parseDouble(resultParts[k].substring(1,resultParts[k].length()-1));
							}
							if(ddCurrentScore > ddMaxScore)
								ddMaxScore = ddCurrentScore;
						}
						ddScore += ddMaxScore;
					}
				}
			}
			
			/// ---- Write the scores to output file ----//
			out.write(strParts[1] + "\t" + strParts[9] + "\t" + ddScore + "\t" + ideoScore + "\t" + coExpressScore + "\t" + corumScore + "\t" + 
					cooccurPub + "\t" + cooccurPath + "\t" + cooccurDis + "\t" + goBPScore + "\t" + goCCScore + "\t" + goMFScore + "\n");
			
			System.out.println(count++);
		//	if(count > 5000)
		//		break;
		}
		in.close();
		out.close();
	}

	public static String httpGet(String urlStr) {
		try {  
		  URL url = new URL(urlStr);
		  HttpURLConnection conn =
		      (HttpURLConnection) url.openConnection();
		//  conn.addRequestProperty("Accept", "application/xml");
		  if (conn.getResponseCode() != 200) {
			  return null;
		//    throw new IOException(conn.getResponseMessage());
		  }

		  // Buffer the result into a string
		  BufferedReader rd = new BufferedReader(
		      new InputStreamReader(conn.getInputStream()));
		  StringBuilder sb = new StringBuilder();
		  String line;
		  while ((line = rd.readLine()) != null) {
		    sb.append(line + "\t");
		  }
		  rd.close();

		  conn.disconnect();
		  return sb.toString();
		} catch (IOException e) {
			e.printStackTrace();
		}
		return "";
	}
}