org.bridgedb.bio.BioDataSource Maven / Gradle / Ivy
// 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 ensemblBySpecies = new HashMap();
/**
* @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);
}
}
}
© 2015 - 2025 Weber Informatics LLC | Privacy Policy