BioDataSource.java

// BridgeDb,
// An abstraction layer for identifier mapping services, both local and online.
// Copyright 2006-2009 BridgeDb developers
//
// Licensed under the Apache License, Version 2.0 (the "License");
// you may not use this file except in compliance with the License.
// You may obtain a copy of the License at
//
// http://www.apache.org/licenses/LICENSE-2.0
//
// Unless required by applicable law or agreed to in writing, software
// distributed under the License is distributed on an "AS IS" BASIS,
// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
// See the License for the specific language governing permissions and
// limitations under the License.
//
package org.bridgedb.bio;

import java.io.BufferedReader;
import java.io.IOException;
import java.io.InputStream;
import java.io.InputStreamReader;
import java.util.HashMap;
import java.util.Map;
import java.util.logging.Level;
import java.util.logging.Logger;
import java.util.regex.Pattern;

import javax.xml.parsers.ParserConfigurationException;

import org.bridgedb.DataSource;
import org.bridgedb.DataSourcePatterns;
import org.bridgedb.impl.InternalUtils;
import org.xml.sax.InputSource;
import org.xml.sax.SAXException;

/**
 * @deprecated use resources.org.bridgedb.bio.datasources.txt instead 
 *
 * Definition of many common biological DataSources.
 * Meta data about these Data Sources, such as URL templates,
 * are read from a bundled text file. Call the init() method
 * at the start of your program to initialize all meta data.  
 */
public class BioDataSource 
{
	public static final DataSource TAIR = DataSource.register (
		 "A", "TAIR").asDataSource();
	public static final DataSource AGILENT = DataSource.register (
		"Ag", "Agilent").asDataSource();
	public static final DataSource BIOGRID = DataSource.register (
		"Bg", "BioGrid").asDataSource();
	public static final DataSource BIOCYC = DataSource.register (
		"Bc", "BioCyc").asDataSource();
	public static final DataSource CCDS = DataSource.register (
		"Cc", "CCDS").asDataSource();
	public static final DataSource CAS = DataSource.register (
		"Ca", "CAS").asDataSource();
	public static final DataSource CHEBI = DataSource.register (
		"Ce", "ChEBI").asDataSource();
	public static final DataSource HMDB = DataSource.register (
		"Ch", "HMDB").asDataSource();
	public static final DataSource KEGG_COMPOUND = DataSource.register (
		"Ck", "KEGG Compound").asDataSource();
    /** @deprecated use one of the organism-specific system codes instead */ 
    //Oct 29 2013 Christian: Had to add this back in for Examples/ChebiPubchemExample.java to work!
	public static final DataSource PUBCHEM = DataSource.register (
		"Cp", "PubChem").asDataSource();
	public static final DataSource PUBCHEM_SUBSTANCE = DataSource.register (
		"Cps", "PubChem-substance").asDataSource();
	public static final DataSource PUBCHEM_COMPOUND = DataSource.register (
		"Cpc", "PubChem-compound").asDataSource();
	public static final DataSource CHEMSPIDER = DataSource.register (
		"Cs", "Chemspider").asDataSource();
	public static final DataSource SGD = DataSource.register (
		"D", "SGD").asDataSource();
	public static final DataSource ENZYME_CODE = DataSource.register (
		"E", "Enzyme Nomenclature").asDataSource();
	public static final DataSource ECOLI = DataSource.register (
		"Ec", "EcoGene").asDataSource();
	public static final DataSource EMBL = DataSource.register (
		"Em", "EMBL").asDataSource();
	public static final DataSource ENSEMBL = DataSource.register (
		"En", "Ensembl").asDataSource();
	/** @deprecated use ENSEMBL instead */
	public static final DataSource ENSEMBL_MOSQUITO = DataSource.register (
		"EnAg", "Ensembl Mosquito").asDataSource();
	/** @deprecated use ENSEMBL instead */
	public static final DataSource GRAMENE_ARABIDOPSIS = DataSource.register (
		"EnAt", "Gramene Arabidopsis").asDataSource();
	/** @deprecated use ENSEMBL instead */
	public static final DataSource ENSEMBL_BSUBTILIS = DataSource.register (
		"EnBs", "Ensembl B. subtilis").asDataSource();
	/** @deprecated use ENSEMBL instead */
	public static final DataSource ENSEMBL_COW = DataSource.register (
		"EnBt", "Ensembl Cow").asDataSource();
	/** @deprecated use ENSEMBL instead */
	public static final DataSource ENSEMBL_CELEGANS = DataSource.register (
		"EnCe", "Ensembl C. elegans").asDataSource();
	/** @deprecated use ENSEMBL instead */
	public static final DataSource ENSEMBL_DOG = DataSource.register (
		"EnCf", "Ensembl Dog").asDataSource();
	/** @deprecated use ENSEMBL instead */
	public static final DataSource ENSEMBL_FRUITFLY = DataSource.register (
		"EnDm", "Ensembl Fruitfly").asDataSource();
	/** @deprecated use ENSEMBL instead */
	public static final DataSource ENSEMBL_ZEBRAFISH = DataSource.register (
		"EnDr", "Ensembl Zebrafish").asDataSource();
	/** @deprecated use ENSEMBL instead */
	public static final DataSource ENSEMBL_ECOLI = DataSource.register (
		"EnEc", "Ensembl E. coli").asDataSource();
	/** @deprecated use ENSEMBL instead */
	public static final DataSource ENSEMBL_CHICKEN = DataSource.register (
		"EnGg", "Ensembl Chicken").asDataSource(); 
	/** @deprecated use ENSEMBL instead */
	public static final DataSource ENSEMBL_HUMAN = DataSource.register (
		"EnHs", "Ensembl Human").asDataSource();
	/** @deprecated use ENSEMBL instead */
	public static final DataSource ENSEMBL_MOUSE = DataSource.register (
		"EnMm", "Ensembl Mouse").asDataSource();
	/** @deprecated use ENSEMBL instead */
	public static final DataSource ENSEMBL_MTUBERCULOSIS = DataSource.register (
		"EnMx", "Ensembl M. tuberculosis").asDataSource();
	/** @deprecated use ENSEMBL instead */
	public static final DataSource GRAMENE_RICE = DataSource.register (
		"EnOj", "Gramene Rice").asDataSource();
	/** @deprecated use ENSEMBL instead */
	public static final DataSource ENSEMBL_CHIMP = DataSource.register (
		"EnPt", "Ensembl Chimp").asDataSource();
	/** @deprecated use ENSEMBL instead */
	public static final DataSource ENSEMBL_HORSE = DataSource.register (
		"EnQc", "Ensembl Horse").asDataSource();
	/** @deprecated use ENSEMBL instead */
	public static final DataSource ENSEMBL_RAT = DataSource.register (
		"EnRn", "Ensembl Rat").asDataSource();
	/** @deprecated use ENSEMBL instead */
	public static final DataSource ENSEMBL_SCEREVISIAE = DataSource.register (
		"EnSc", "Ensembl Yeast").asDataSource();
	/** @deprecated use ENSEMBL instead */
	public static final DataSource ENSEMBL_XENOPUS = DataSource.register (
		"EnXt", "Ensembl Xenopus").asDataSource();
	public static final DataSource FLYBASE = DataSource.register (
		"F", "FlyBase").asDataSource();
	public static final DataSource GENBANK = DataSource.register (
		"G", "GenBank").asDataSource(); 
	public static final DataSource CODELINK = DataSource.register (
		"Ge", "CodeLink").asDataSource(); 
	public static final DataSource GRAMENE_GENES_DB = DataSource.register (
		"Gg", "Gramene Genes DB").asDataSource(); 
	public static final DataSource GRAMENE_LITERATURE = DataSource.register (
		"Gl", "Gramene Literature").asDataSource();
	public static final DataSource GRAMENE_PATHWAY = DataSource.register (
		"Gp", "Gramene Pathway").asDataSource();
	public static final DataSource GENE_WIKI = DataSource.register (
		"Gw", "Gene Wiki").asDataSource(); 
	public static final DataSource HUGO = DataSource.register (
		"H", "HGNC").asDataSource();
	public static final DataSource HSGENE = DataSource.register (
		"Hs", "HsGene").asDataSource();
	public static final DataSource INTERPRO = DataSource.register (
		"I", "InterPro").asDataSource();
	public static final DataSource ILLUMINA = DataSource.register (
		"Il", "Illumina").asDataSource(); 
	public static final DataSource IPI = DataSource.register (
		"Ip", "IPI").asDataSource(); 
	public static final DataSource IRGSP_GENE = DataSource.register (
		"Ir", "IRGSP Gene").asDataSource();
	public static final DataSource KEGG_GENES = DataSource.register (
		"Kg", "KEGG Genes").asDataSource();
	public static final DataSource ENTREZ_GENE = DataSource.register (
		"L", "Entrez Gene").asDataSource();
	public static final DataSource MGI = DataSource.register (
		"M", "MGI").asDataSource();
	public static final DataSource MIRBASE = DataSource.register (
		"Mb", "miRBase Sequence").asDataSource();
	public static final DataSource MIRBASE_MATURE = DataSource.register (
		"Mbm", "miRBase mature sequence").asDataSource();
	public static final DataSource MAIZE_GDB = DataSource.register (
		"Mg", "MaizeGDB").asDataSource();
	public static final DataSource NASC_GENE = DataSource.register (
		"N", "NASC Gene").asDataSource(); 
	public static final DataSource NUGOWIKI = DataSource.register (
		"Nw", "NuGO wiki").asDataSource();
	public static final DataSource OTHER = DataSource.register (
		"O", "Other").asDataSource();
	public static final DataSource ORYZA_BASE = DataSource.register (
		"Ob", "Oryzabase").asDataSource();
	public static final DataSource OMIM = DataSource.register (
		"Om", "OMIM").asDataSource();
	public static final DataSource RICE_ENSEMBL_GENE = DataSource.register (
		"Os", "Rice Ensembl Gene").asDataSource();
	public static final DataSource PDB = DataSource.register (
		"Pd", "PDB").asDataSource();
	public static final DataSource PFAM = DataSource.register (
		"Pf", "Pfam").asDataSource();
	public static final DataSource PLANTGDB = DataSource.register (
		"Pl", "PlantGDB").asDataSource(); 
	public static final DataSource REFSEQ = DataSource.register (
		"Q", "RefSeq").asDataSource();
	public static final DataSource RGD = DataSource.register (
		"R", "RGD").asDataSource(); 
	public static final DataSource REACTOME = DataSource.register (
		"Re", "Reactome").asDataSource();
	public static final DataSource KEGG_REACTION = DataSource.register (
		"Rk", "KEGG Reaction").asDataSource();
	public static final DataSource RFAM = DataSource.register (
		"Rf", "Rfam").asDataSource();
	/** NB the UNIPROT datasource is for Uniprot accession numbers like P12345 */
	public static final DataSource UNIPROT = DataSource.register (
		"S", "Uniprot-TrEMBL").asDataSource(); 
	/** THE UNIPROT_SWISSPROT datasource is for id's like P53_HUMAN */
	public static final DataSource UNIPROT_SWISSPROT = DataSource.register (
		"Sp", "Uniprot-SwissProt").asDataSource();
	public static final DataSource SNP = DataSource.register (
		"Sn", "dbSNP").asDataSource();
	public static final DataSource GENE_ONTOLOGY = DataSource.register (
		"T", "GeneOntology").asDataSource();
	public static final DataSource TAXONOMY_NCBI = DataSource.register (
		"Tn", "NCBI Taxonomy Database").asDataSource(); 
	public static final DataSource TIGR = DataSource.register (
		"Ti", "TIGR").asDataSource(); 
	public static final DataSource TUBERCULIST = DataSource.register (
		"Tb", "TubercuList").asDataSource(); 
	public static final DataSource UNIGENE = DataSource.register (
		"U", "UniGene").asDataSource();
	public static final DataSource UCSC = DataSource.register (
		"Uc", "UCSC Genome Browser").asDataSource();
	public static final DataSource WORMBASE = DataSource.register (
		"W", "WormBase").asDataSource();
	public static final DataSource WIKIGENE = DataSource.register (
		"Wg", "WikiGenes").asDataSource();
	public static final DataSource WIKIPEDIA = DataSource.register (
		"Wi", "Wikipedia").asDataSource();
	public static final DataSource WIKIPATHWAYS = DataSource.register (
		"Wp", "WikiPathways").asDataSource();
	public static final DataSource WHEAT_GENE_NAMES = DataSource.register (
		"Wn", "Wheat gene names").asDataSource();
	public static final DataSource WHEAT_GENE_REFERENCES= DataSource.register (
		"Wr", "Wheat gene refs").asDataSource();
	public static final DataSource AFFY = DataSource.register (
		"X", "Affy").asDataSource();
	public static final DataSource ZFIN = DataSource.register (
		"Z", "ZFIN").asDataSource();
	public static final DataSource RHEA = DataSource.register (
			"Rh", "Rhea").asDataSource();
	public static final DataSource MACIE = DataSource.register (
			"Ma", "MACiE").asDataSource();
	public static final DataSource UNIPATHWAY = DataSource.register (
			"Up", "Unipathway").asDataSource();

	/* 
	 * Make patterns of regular expressions for matching 
	 * the gene identifiers with specific gene databases.
	 * (see, 
	 * http://www.childrens-mercy.org/stats/model/arrayDataManagement.htm ) 
	 */	
	private static final Map<Organism, DataSource> ensemblBySpecies = new HashMap<Organism, DataSource>();

	/**
	 *  @deprecated use datasources.txt instead
	 */
	static {
		//sgd
		DataSourcePatterns.registerPattern(
			BioDataSource.TAXONOMY_NCBI, 
			Pattern.compile("\\d+"));

		//sgd
		DataSourcePatterns.registerPattern(
			BioDataSource.SGD, 
			Pattern.compile("S\\d{9}"));
		
		//flybase
		DataSourcePatterns.registerPattern(
			BioDataSource.FLYBASE, 
			Pattern.compile("(C[RG]\\d{4,5}|FBgn\\d{7})")
		);		
		//genbank (http://www.ncbi.nlm.nih.gov/Sequin/acc.html)		
		DataSourcePatterns.registerPattern(
				BioDataSource.GENBANK, 
				Pattern.compile("(\\w\\d{5})|(\\w{2}\\d{6})|(\\w{3}\\d{5})")
		);
		//interpro
		DataSourcePatterns.registerPattern(
				BioDataSource.INTERPRO, 				
				Pattern.compile("IPR\\d{6}")
			);
		//entrez gene
		DataSourcePatterns.registerPattern(
				BioDataSource.ENTREZ_GENE, 
				Pattern.compile("\\d+")
		);
		//gene wiki (using entrez gene ids)
		DataSourcePatterns.registerPattern(
				BioDataSource.GENE_WIKI, 
				Pattern.compile("\\d+")
		);

		//MGI
		DataSourcePatterns.registerPattern(
				BioDataSource.MGI, 
				Pattern.compile("MGI:\\d+")
		);

		DataSourcePatterns.registerPattern (
				BioDataSource.RFAM,
				Pattern.compile ("RF\\d+")
		);
		DataSourcePatterns.registerPattern (
				BioDataSource.IPI,
				Pattern.compile ("IPI\\d+")
		);
		DataSourcePatterns.registerPattern (
				BioDataSource.UCSC,
				Pattern.compile ("uc\\d{3}[a-z]{3}\\.\\d")
		);
		DataSourcePatterns.registerPattern (
				BioDataSource.ILLUMINA,
				Pattern.compile ("ILMN_\\d+")
		);
		DataSourcePatterns.registerPattern (
				BioDataSource.MIRBASE,
				Pattern.compile ("MI\\d+")
		);
		//refseq
		DataSourcePatterns.registerPattern(
				BioDataSource.REFSEQ, 
				Pattern.compile("\\w{2}_\\d+")
		);

		//RGD
		DataSourcePatterns.registerPattern(
				BioDataSource.RGD, 
				Pattern.compile("RGD:\\d+")
		);

		//UniProtKB/TrEMBL
		DataSourcePatterns.registerPattern(
				BioDataSource.UNIPROT, 
				Pattern.compile("([A-N,R-][0-9][A-Z][A-Z,0-9][A-Z,0-9][0-9])|([O,P,Q][0-9][A-Z,0-9][A-Z,0-9][A-Z,0-9][0-9])")
		);

		//UniProtKB/Swiss-Prot
		DataSourcePatterns.registerPattern(
				BioDataSource.UNIPROT_SWISSPROT, 
				Pattern.compile("[A-Z0-9]+_[A-Z]+")
		);

		//gene ontology
		DataSourcePatterns.registerPattern(
				BioDataSource.GENE_ONTOLOGY, 
				Pattern.compile("GO:\\d+")
		);

		//unigene
		DataSourcePatterns.registerPattern(
				BioDataSource.UNIGENE, 
				Pattern.compile("[A-Z][a-z][a-z]?\\.\\d+")
		);

		//Wormbase
		DataSourcePatterns.registerPattern(
				BioDataSource.WORMBASE, 
				Pattern.compile("WBGene\\d{8}")
		);

		//affymetrix
		DataSourcePatterns.registerPattern(
				BioDataSource.AFFY, 
				Pattern.compile(".+_at")
		);

		//Ensemble
		DataSourcePatterns.registerPattern(
				BioDataSource.ENSEMBL_HUMAN, 
				Pattern.compile("ENSG\\d{11}")
		);
		DataSourcePatterns.registerPattern(
				BioDataSource.ENSEMBL_MOUSE, 
				Pattern.compile("ENSMUSG\\d{11}")
		);
		DataSourcePatterns.registerPattern(
				BioDataSource.ENSEMBL_RAT, 
				Pattern.compile("ENSRNOG\\d{11}")
		);
		DataSourcePatterns.registerPattern(
				BioDataSource.ENSEMBL_MOSQUITO, 
				Pattern.compile("AGAP\\d{6}")
		);
		DataSourcePatterns.registerPattern(
				BioDataSource.ENSEMBL_BSUBTILIS, 
				Pattern.compile("EBBACG\\d{11}")
		);
		DataSourcePatterns.registerPattern(
				BioDataSource.ENSEMBL_ECOLI, 
				Pattern.compile("EBESCG\\d{11}")
		);
		DataSourcePatterns.registerPattern(
				BioDataSource.ENSEMBL_CHICKEN, 
				Pattern.compile("ENSGALG\\d{11}")
		);
		DataSourcePatterns.registerPattern(
				BioDataSource.ENSEMBL_HORSE, 
				Pattern.compile("ENSECAG\\d{11}")
		);
		DataSourcePatterns.registerPattern(
				BioDataSource.ENSEMBL_XENOPUS, 
				Pattern.compile("ENSXETG\\d{11}")
		);
		DataSourcePatterns.registerPattern(
				BioDataSource.ENSEMBL_CHIMP, 
				Pattern.compile("ENSPTRG\\d{11}")
		);
		DataSourcePatterns.registerPattern(
				BioDataSource.ENSEMBL_COW, 
				Pattern.compile("ENSBTAG\\d{11}")
		);
		DataSourcePatterns.registerPattern(
				BioDataSource.ENSEMBL_DOG, 
				Pattern.compile("ENSCAFG\\d{11}")
		);
		DataSourcePatterns.registerPattern(
				BioDataSource.ENSEMBL_ZEBRAFISH, 
				Pattern.compile("ENSDARG\\d{11}")
		);
		DataSourcePatterns.registerPattern(
				BioDataSource.ENSEMBL_MTUBERCULOSIS,
				Pattern.compile("EBMYCG\\d{11}")
		);
		DataSourcePatterns.registerPattern(
				BioDataSource.ENSEMBL_FRUITFLY, 
				Pattern.compile("FBgn\\d{7}")
		);
		DataSourcePatterns.registerPattern(
				BioDataSource.ENSEMBL_SCEREVISIAE, 
				Pattern.compile("Y[A-Z][RL]\\d{3}[WC](?:\\-[A-Z])?")
		);
		DataSourcePatterns.registerPattern(
				BioDataSource.TAIR,
				Pattern.compile("AT[\\dCM]G\\d{5}")
				);
		DataSourcePatterns.registerPattern(
				BioDataSource.GRAMENE_ARABIDOPSIS,
				Pattern.compile("AT[\\dCM]G\\d{5}\\-TAIR\\-G")
		);
		DataSourcePatterns.registerPattern(
				BioDataSource.IRGSP_GENE,
				Pattern.compile("Os\\d{2}g\\d+")
		);
		DataSourcePatterns.registerPattern(
				BioDataSource.GRAMENE_GENES_DB,
				Pattern.compile("GR:\\d+")
		);
		DataSourcePatterns.registerPattern(
				BioDataSource.BIOGRID,
				Pattern.compile("\\d+")
		);
		DataSourcePatterns.registerPattern(
				BioDataSource.NASC_GENE,
				Pattern.compile("AT[\\dCM]G\\d{5}\\-TAIR\\-G")
		);
		DataSourcePatterns.registerPattern(
				BioDataSource.PLANTGDB,
				Pattern.compile("PUT-[\\w\\d-]+")
		);
		//EMBL		
		DataSourcePatterns.registerPattern(
				BioDataSource.EMBL,
				Pattern.compile("\\w{2}\\d{6}")
		);
		
		//HUGO
		DataSourcePatterns.registerPattern(
				BioDataSource.HUGO,
				Pattern.compile("[A-Z][A-Z,0-9]+")
		);
		
		//OMIM (http://www.ncbi.nlm.nih.gov/Omim/omimfaq.html#numbering_system)		
		DataSourcePatterns.registerPattern(
				BioDataSource.OMIM,		
				Pattern.compile("\\d{6}(\\.\\d{4})?")
		);

		//PDB ( http://www.rcsb.org/robohelp_f/#search_database/query_results.htm )
		DataSourcePatterns.registerPattern(
				BioDataSource.PDB, 
				Pattern.compile("\\d[A-Z\\d]{3}")
		);

		//Pfam (http://pfam.sanger.ac.uk/help)
		DataSourcePatterns.registerPattern(
			BioDataSource.PFAM,		
			Pattern.compile("(PF\\d{5})|(PB\\d{6})")
		);

		//Zfin (http://zfin.org/zf_info/dbase/PAPERS/ZFIN_DataModel/sectioniv_1.html)
		DataSourcePatterns.registerPattern(
				BioDataSource.ZFIN, 
				Pattern.compile("ZDB.+")
		);
		
		DataSourcePatterns.registerPattern(
				BioDataSource.AGILENT,
				Pattern.compile("A_\\d+_.+")
		);

		DataSourcePatterns.registerPattern(
				BioDataSource.HMDB,
				Pattern.compile("HMDB\\d{5}")
		);

		DataSourcePatterns.registerPattern(
				BioDataSource.CAS,
				Pattern.compile("\\d+-\\d{2}-\\d{1}")
		);
		
		DataSourcePatterns.registerPattern(
				BioDataSource.ENZYME_CODE,
				Pattern.compile("(\\d+\\.){3}\\d+")
		);

		DataSourcePatterns.registerPattern(
				BioDataSource.CHEBI,
				Pattern.compile("CHEBI\\:\\d+")
		);

		DataSourcePatterns.registerPattern(
				BioDataSource.KEGG_COMPOUND,
				Pattern.compile("C\\d+")
		);
		
		DataSourcePatterns.registerPattern(
				BioDataSource.KEGG_GENES,
				Pattern.compile("[a-z]{3}:.+")
		);
		DataSourcePatterns.registerPattern(
				BioDataSource.BIOCYC,
				Pattern.compile("^\\w+\\:[A-Za-z0-9-]+$")
		);		
		DataSourcePatterns.registerPattern(
				BioDataSource.TUBERCULIST,
				Pattern.compile("Rv\\d{4}(A|B|c|\\.\\d)?")
		);	
		DataSourcePatterns.registerPattern(
				BioDataSource.RHEA, 
				Pattern.compile("^\\d{5}$")
		);
		DataSourcePatterns.registerPattern(
				BioDataSource.MACIE, 
				Pattern.compile("^M\\d{4}$")
		);
		DataSourcePatterns.registerPattern(
				BioDataSource.UNIPATHWAY, 
				Pattern.compile("^UPA\\d{5}$")
		);
		
		ensemblBySpecies.put (Organism.BacillusSubtilis, ENSEMBL_BSUBTILIS);
		ensemblBySpecies.put (Organism.CaenorhabditisElegans, ENSEMBL_CELEGANS);
		ensemblBySpecies.put (Organism.GallusGallus, ENSEMBL_CHICKEN);
		ensemblBySpecies.put (Organism.PanTroglodytes, ENSEMBL_CHIMP);
		ensemblBySpecies.put (Organism.BosTaurus, ENSEMBL_COW);
		ensemblBySpecies.put (Organism.CanisFamiliaris, ENSEMBL_DOG);
		ensemblBySpecies.put (Organism.EscherichiaColi, ENSEMBL_ECOLI);
		ensemblBySpecies.put (Organism.DrosophilaMelanogaster, ENSEMBL_FRUITFLY);
		ensemblBySpecies.put (Organism.EquusCaballus, ENSEMBL_HORSE);
		ensemblBySpecies.put (Organism.HomoSapiens, ENSEMBL_HUMAN);
		ensemblBySpecies.put (Organism.AnophelesGambiae, ENSEMBL_MOSQUITO);
		ensemblBySpecies.put (Organism.MusMusculus, ENSEMBL_MOUSE);
		ensemblBySpecies.put (Organism.RattusNorvegicus, ENSEMBL_RAT);
		ensemblBySpecies.put (Organism.SaccharomycesCerevisiae, ENSEMBL_SCEREVISIAE);
		ensemblBySpecies.put (Organism.XenopusTropicalis, ENSEMBL_XENOPUS);
		ensemblBySpecies.put (Organism.DanioRerio, ENSEMBL_ZEBRAFISH);		
		ensemblBySpecies.put (Organism.MycobacteriumTuberculosis, ENSEMBL_MTUBERCULOSIS);
		
		//Reactions
		DataSourcePatterns.registerPattern(
				BioDataSource.KEGG_REACTION,
				Pattern.compile("^R\\d+$")
		);
		DataSourcePatterns.registerPattern(
				BioDataSource.REACTOME,
				Pattern.compile("^REACT_\\d+(\\.\\d+)?$")
		);
	}
	
	/**
	 * @return the species-specific Ensembl DataSource corresponding to a given organism, or null if there isn't one known.
	 * @param org an organism
	 * @deprecated
	 */
	public static DataSource getSpeciesSpecificEnsembl(Organism org)
	{
		return ensemblBySpecies.get(org);
	}
	
	/** Call this to initialize the BioDataSource.XXX constants. 
	 * 	You should call this before using any of these constants, 
	 * 	or they may be undefined.
	 */
	public static void init() 
	{
		InputStream is = BioDataSource.class.getClassLoader().getResourceAsStream("org/bridgedb/bio/datasources.txt");
		try
		{
            DataSourceTxt.loadInputStream(is);
			InternalUtils.readXmlConfig(
					new InputSource(
							BioDataSource.class.getClassLoader().getResourceAsStream(
									"org/bridgedb/bio/datasources.xml")));
			
		}
		catch (IOException ex)
		{
			throw new Error(ex);
		}
		catch (ParserConfigurationException e)
		{
			throw new Error(e);
		}
		catch (SAXException e)
		{
			throw new Error(e);
		}
		
	}
}