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VoidCreator.java
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import java.io.FileNotFoundException;
import java.net.URLEncoder;
import java.util.Calendar;
import com.hp.hpl.jena.rdf.model.Literal;
import com.hp.hpl.jena.rdf.model.Model;
import com.hp.hpl.jena.rdf.model.ModelFactory;
import com.hp.hpl.jena.rdf.model.Property;
import com.hp.hpl.jena.rdf.model.Resource;
import com.hp.hpl.jena.sparql.vocabulary.FOAF;
import com.hp.hpl.jena.vocabulary.DCTerms;
import com.hp.hpl.jena.vocabulary.DCTypes;
import com.hp.hpl.jena.vocabulary.RDF;
import com.hp.hpl.jena.vocabulary.VCARD;
import java.io.FileOutputStream;
import java.io.IOException;
import java.io.UnsupportedEncodingException;
import java.util.HashMap;
public class VoidCreator {
private static final String BASE_URI = "https://raw.github.com/andrawaag/EnsemblLinksetExtractor/master/data/";
public static final Property linkPredicate = Skos.relatedMatch;
private final Model model;
private final Resource andra;
private final Resource bridgeDB;
private final Resource christian;
private final Resource ensembl;
private final Resource ensemblDataset;
private final Resource ensemblLinkset;
private final Resource ensemblLicense;
private final Resource script;
public static final HashMap<String,String> identifiersOrg = getIdentifiersOrg();
public VoidCreator(){
model = ModelFactory.createDefaultModel();
andra = model.createResource("http://orcid.org/0000-0002-5711-4872");
bridgeDB = model.createResource("http://www.bridgedb.org/");
christian = model.createResource("https://wiki.openphacts.org/index.php/User:Christian");
ensembl = model.createResource("http://www.ensembl.org/");
ensemblDataset = model.createResource(BASE_URI + "ensemblDataset");
ensemblLinkset = model.createResource(BASE_URI + "ensemblLinksetDataset");
ensemblLicense = model.createResource("http://apr2013.archive.ensembl.org/info/about/legal/index.html");
script = model.createResource("https://raw.github.com/andrawaag/EnsemblLinksetExtractor/master/createLinkSets.java");
//TODO These don't appear to work.
model.setNsPrefix("", BASE_URI);
model.setNsPrefix("dcterms", DCTerms.NS);
model.setNsPrefix("dctypes", DCTypes.NS);
model.setNsPrefix("dul", Dul.NS);
model.setNsPrefix("pac", Pav.NS);
model.setNsPrefix("rdf", RDF.getURI());
model.setNsPrefix("skos", Skos.NS);
model.setNsPrefix("void", Void.NS);
model.setNsPrefix("xsd", "http://www.w3.org/2001/XMLSchema#");
}
//Here I am being lazy as all species so far appear to be name_name_name_majorVersiob_minorVersion
//TODO add a nice lookup table here
private String extractSpeciesName (String species){
String[] parts = species.split("_");
return parts[0] + " " + parts[1];
}
//TODO add a nice lookup table here
private String extractSpeciesOneWord (String species){
String[] parts = species.split("_");
return parts[0] + "_" + parts[1];
}
private String extractMajorVersion (String species){
String[] parts = species.split("_");
return parts[3];
}
private String extractMinorVersion (String species){
String[] parts = species.split("_");
return parts[3] + "_" + parts[4];
}
private Resource createSpeciesLinkset(String species){
return model.createResource(BASE_URI + extractSpeciesOneWord(species) + "-linkset");
}
private Resource createSpeciesDataSetLinkset(String species, String dataSetName){
return model.createResource(BASE_URI + extractSpeciesOneWord(species) + "-" + dataSetName + "-linkset");
}
private Resource createSpeciesDataset(String species){
return model.createResource(BASE_URI + extractSpeciesOneWord(species) + "-dataset");
}
private Resource createDulResource(String species){
return model.createResource(BASE_URI + "EnsemblMapsFor_" + extractSpeciesOneWord(species));
}
private Resource getFtp (String version){
return model.createResource("ftp://ftp.ensembl.org/pub/release-" + version);
}
private Resource getFtp (String version, String species){
return model.createResource("ftp://ftp.ensembl.org/pub/release-" + version + "/mysql/" + species);
}
private void createDatasetDescription() {
Resource voidHeaderResource = model.createResource();
voidHeaderResource.addProperty(RDF.type, Void.DatasetDescription);
voidHeaderResource.addProperty(DCTerms.title, model.createLiteral("Ensembl Genome VoID Description"));
voidHeaderResource.addProperty(Pav.createdBy, andra);
voidHeaderResource.addProperty(Pav.createdBy, christian);
voidHeaderResource.addProperty(Pav.createdWith, script);
Calendar now = Calendar.getInstance();
Literal nowLiteral = model.createTypedLiteral(now);
voidHeaderResource.addProperty(Pav.createdOn, nowLiteral);
voidHeaderResource.addProperty(FOAF.primaryTopic, ensemblLinkset);
}
public void createGeneralVoid(String version, Calendar issuedOn){
createDatasetDescription();
createEnsemblLinksetDataset(version);
createEnsemblDataset(version, issuedOn);
}
private void createEnsemblLinksetDataset(String version) {
ensemblLinkset.addProperty(RDF.type, Void.Dataset);
ensemblLinkset.addLiteral(DCTerms.title, "Ensembl Genome Linksets");
ensemblLinkset.addLiteral(DCTerms.description, "Linksets extracted from the Ensembl Genome Database that link genes by species across several datasets");
ensemblLinkset.addProperty(DCTerms.publisher, bridgeDB);
ensemblLinkset.addProperty(Dcat.landingPage, ensembl);
ensemblLinkset.addProperty(DCTerms.license, ensemblLicense);
//TODO add Andra's Lisence here
ensemblLinkset.addProperty(Pav.createdBy, andra);
Calendar now = Calendar.getInstance();
Literal nowLiteral = model.createTypedLiteral(now);
ensemblLinkset.addProperty(Pav.createdOn, nowLiteral);
ensemblLinkset.addProperty(Pav.createdWith, script);
ensemblLinkset.addProperty(DCTerms.issued, nowLiteral);
ensemblLinkset.addLiteral(Pav.version, version);
ensemblLinkset.addProperty(Pav.importedOn, nowLiteral);
ensemblLinkset.addProperty(Pav.importedBy, andra);
ensemblLinkset.addProperty(Pav.importedOn, nowLiteral);
ensemblLinkset.addProperty(Pav.importedFrom, getFtp(version));
ensemblLinkset.addProperty(Void.linkPredicate, linkPredicate);
}
private void createEnsemblDataset(String version, Calendar issuedOn) {
ensemblDataset.addProperty(RDF.type, DCTypes.Dataset);
ensemblDataset.addLiteral(DCTerms.title, "Ensembl Genome Database");
ensemblDataset.addLiteral(DCTerms.description, "The Ensembl project produces genome databases for vertebrates and other eukaryotic species, and makes this information freely available online.");
ensemblDataset.addProperty(DCTerms.publisher, ensembl);
ensemblDataset.addProperty(Dcat.landingPage, ensembl);
ensemblDataset.addProperty(DCTerms.license, ensemblLicense);
ensemblDataset.addProperty(Pav.createdBy, ensembl);
Literal issuedLieteral = model.createTypedLiteral(issuedOn);
ensemblDataset.addProperty(DCTerms.issued, issuedLieteral);
ensemblDataset.addLiteral(Pav.version, version);
ensemblDataset.addProperty(Dcat.downloadURL, getFtp(version));
}
public void createSpecies(String species, Calendar issuedOn) throws FileNotFoundException {
createDulExpresses(species);
Resource speciesLinkset = createSpeciesLinkset(species);
Resource speciesDataset = createSpeciesDataset(species);
ensemblLinkset.addProperty(Void.subset, speciesLinkset);
ensemblDataset.addProperty(Void.subset, speciesDataset);
String speciesName = extractSpeciesName(species);
speciesLinkset.addProperty(RDF.type, Void.Dataset);
speciesLinkset.addLiteral(DCTerms.title, "Ensembl " + speciesName + " Linksets");
speciesLinkset.addLiteral(DCTerms.description, "Linksets extracted from the Ensembl Genome Database that link genes for "
+ speciesName + " across several datasets");
speciesLinkset.addProperty(Pav.importedFrom, speciesDataset);
speciesLinkset.addLiteral(Pav.version, this.extractMinorVersion(species));
speciesLinkset.addProperty(Dul.expresses, createDulResource(species));
speciesDataset.addProperty(RDF.type, DCTypes.Dataset);
speciesDataset.addLiteral(DCTerms.title, "Ensembl " + speciesName);
speciesDataset.addLiteral(DCTerms.description, "The subset of Ensembl that relates to " + speciesName);
speciesDataset.addLiteral(Dcat.mediaType, "text/csv");
speciesDataset.addLiteral(Pav.version, this.extractMinorVersion(species));
Literal issuedLieteral = model.createTypedLiteral(issuedOn);
speciesDataset.addProperty(DCTerms.issued, issuedLieteral);
speciesDataset.addProperty(Pav.importedFrom, getFtp(this.extractMajorVersion(species), species));
}
/**
* This is under review see https://openphacts2011.atlassian.net/browse/IMS-281
*
* @param model
* @param species
* @throws FileNotFoundException
*/
private void createDulExpresses(String species) throws FileNotFoundException {
Resource dulResource = createDulResource(species);
dulResource.addProperty(RDF.type, FOAF.Organization);
Resource geneResource = model.createResource("ftp://ftp.ensembl.org/pub/release-71/mysql/"+species+"/gene.txt.gz");
geneResource.addLiteral(Rr.column, "stable_id");
geneResource.addLiteral(Rr.column, "gene_id");
geneResource.addProperty(DCTerms.description, model.createResource("http://www.ensembl.org/info/docs/api/core/core_schema.html#gene"));
Resource externalDbResource = model.createResource("ftp://ftp.ensembl.org/pub/release-71/mysql/"+species+"/external_db.txt.gz");
externalDbResource.addLiteral(Rr.column, "external_db_id");
externalDbResource.addLiteral(Rr.column, "db_name");
externalDbResource.addProperty(DCTerms.description, model.createResource("http://www.ensembl.org/info/docs/api/core/core_schema.html#external_db"));
Resource xrefResource = model.createResource("ftp://ftp.ensembl.org/pub/release-71/mysql/"+species+"/xref.txt.gz");
xrefResource.addLiteral(Rr.tableName, "xref_id");
xrefResource.addLiteral(Rr.tableName, "external_db_id");
xrefResource.addLiteral(Rr.tableName, "dbprimary_acc");
xrefResource.addLiteral(Rr.tableName, "display_label");
xrefResource.addProperty(DCTerms.description, model.createResource("http://www.ensembl.org/info/docs/api/core/core_schema.html#external_db"));
Resource objectXrefResource = model.createResource("ftp://ftp.ensembl.org/pub/release-71/mysql/"+species+"/object_xref.txt.gz");
objectXrefResource.addLiteral(Rr.tableName, "object_xref_id");
objectXrefResource.addLiteral(Rr.tableName, "ensembl_id");
objectXrefResource.addProperty(DCTerms.description, model.createResource("http://www.ensembl.org/info/docs/api/core/core_schema.html#external_db"));
dulResource.addProperty(VCARD.Orgname, model.createResource("http://www.ensembl.org"));
dulResource.addProperty(Rr.tableName, geneResource);
dulResource.addProperty(Rr.tableName, externalDbResource);
dulResource.addProperty(Rr.tableName, xrefResource);
dulResource.addProperty(Rr.tableName, model.createResource("ftp://ftp.ensembl.org/pub/release-71/mysql/"+species+"/object_xref.txt.gz"));
}
public Resource createSpecificVoid(String species, String dataSource, long size) throws UnsupportedEncodingException {
String dataSourceName = URLEncoder.encode(dataSource.split("#")[1], "UTF-8");
String speciesName = extractSpeciesName(species);
Resource specificResource = createSpeciesDataSetLinkset(species, dataSourceName);
specificResource.addProperty(RDF.type, Void.Linkset);
specificResource.addProperty(DCTerms.title,
model.createLiteral("Ensembl-" + dataSourceName + " Linkset for " + speciesName,"en"));
specificResource.addProperty(DCTerms.description,
model.createLiteral("A linkset which links Ensembl with "+dataSourceName+ " for the species " + speciesName,"en"));
String object = identifiersOrg.get(dataSource);
specificResource.addProperty(Void.objectsTarget, model.createResource(object));
if (size > 0){
specificResource.addLiteral(Void.triples, size);
}
//Subset back to the species linkset and indirectly the rest
Resource speciesLinkset = createSpeciesLinkset(species);
speciesLinkset.addProperty(Void.subset, specificResource);
return specificResource;
}
public void write(String path) throws IOException{
FileOutputStream fout;
fout = new FileOutputStream(path);
model.write(fout, "TURTLE");
fout.close();
}
private static HashMap getIdentifiersOrg() {
HashMap<String,String> identifiersOrg = new HashMap<String,String>();
identifiersOrg.put("http://dbName#AGD", "http://identifiers.org/agd/");
identifiersOrg.put("http://dbName#AGD_GENE", "http://identifiers.org/agd/");
identifiersOrg.put("http://dbName#AGD_TRANSCRIPT", "http://identifiers.org/agd/");
identifiersOrg.put("http://dbName#ArrayExpress", "http://identifiers.org/arrayexpress/");
identifiersOrg.put("http://dbName#BRENDA", "http://identifiers.org/brenda/");
identifiersOrg.put("http://dbName#BioCyc", "http://identifiers.org/biocyc/");
identifiersOrg.put("http://dbName#BioGRID", "http://identifiers.org/biogrid/");
identifiersOrg.put("http://dbName#CCDS", "http://identifiers.org/ccds/");
identifiersOrg.put("http://dbName#CGD", "http://identifiers.org/cgd/");
identifiersOrg.put("http://dbName#COG", "http://identifiers.org/cogs/");
// identifiersOrg.put("http://dbName#Clone_based_vega_gene", "http://identifiers.org/vega/"); // TODO CHECK!!!!!!
identifiersOrg.put("http://dbName#DIP", "http://identifiers.org/dip/");
identifiersOrg.put("http://dbName#DisProt", "http://identifiers.org/disprot/");
identifiersOrg.put("http://dbName#DrugBank", "http://identifiers.org/drugbank/");
identifiersOrg.put("http://dbName#EC_NUMBER", "http://identifiers.org/ec-code/");
identifiersOrg.put("http://dbName#EMBL", "http://identifiers.org/ena.embl/");
identifiersOrg.put("http://dbName#EMBLBANK_GENE", "http://identifiers.org/ena.embl/");
identifiersOrg.put("http://dbName#EMBLBANK_TRANSCRIPT", "http://identifiers.org/ena.embl/");
identifiersOrg.put("http://dbName#ENS_LRG_gene", "http://identifiers.org/lrg/");
//TODO check this identifiersOrg.put("http://dbName#EPD", "http://identifiers.org/epd/");
identifiersOrg.put("http://dbName#EchoBASE", "http://identifiers.org/echobase/");
identifiersOrg.put("http://dbName#EcoGene", "http://identifiers.org/ecogene/");
identifiersOrg.put("http://dbName#EntrezGene", "http://identifiers.org/ncbigene/");
identifiersOrg.put("http://dbName#GO", "http://identifiers.org/go/");
identifiersOrg.put("http://dbName#GOA", "http://identifiers.org/goa/");
identifiersOrg.put("http://dbName#GO_to_gene", "http://identifiers.org/go/");
identifiersOrg.put("http://dbName#GO_to_transcript", "http://identifiers.org/go/");
identifiersOrg.put("http://dbName#GPCR", "http://identifiers.org/gpcrdb/");
identifiersOrg.put("http://dbName#GeneDB", "http://identifiers.org/genedb/");
identifiersOrg.put("http://dbName#Gramene_GenesDB", "http://identifiers.org/gramene.gene/");
identifiersOrg.put("http://dbName#HAMAP", "http://identifiers.org/hamap/");
identifiersOrg.put("http://dbName#HGNC", "http://identifiers.org/hgnc/");
identifiersOrg.put("http://dbName#HOGENOM", "http://identifiers.org/hogenom/");
identifiersOrg.put("http://dbName#HPA", "http://identifiers.org/hpa/");
identifiersOrg.put("http://dbName#HSSP", "http://identifiers.org/hssp/");
identifiersOrg.put("http://dbName#INSDC", "http://identifiers.org/insdc/");
identifiersOrg.put("http://dbName#IPI", "http://identifiers.org/ipi/");
identifiersOrg.put("http://dbName#IntAct", "http://identifiers.org/intact/");
identifiersOrg.put("http://dbName#IntEnz", "http://identifiers.org/ec-code/");
identifiersOrg.put("http://dbName#Interpro", "http://identifiers.org/interpro/");
identifiersOrg.put("http://dbName#LRG", "http://identifiers.org/lrg/");
identifiersOrg.put("http://dbName#Leproma", "http://identifiers.org/myco.lepra/");
identifiersOrg.put("http://dbName#MEROPS", "http://identifiers.org/merops/");
identifiersOrg.put("http://dbName#MGI", "http://identifiers.org/mgd/");
//TOD check this identifiersOrg.put("http://dbName#MGI_transcript_name", "http://identifiers.org/mgi/");
identifiersOrg.put("http://dbName#MIM", "http://identifiers.org/omim/");
identifiersOrg.put("http://dbName#MIM_GENE", "http://identifiers.org/omim/");
identifiersOrg.put("http://dbName#MIM_MORBID", "http://identifiers.org/omim/");
identifiersOrg.put("http://dbName#MOD", "http://identifiers.org/obo.psi-mod/");
identifiersOrg.put("http://dbName#OTTG", "http://identifiers.org/ensembl/");
identifiersOrg.put("http://dbName#Orphanet", "http://identifiers.org/orphanet/");
identifiersOrg.put("http://dbName#PBO", "http://identifiers.org/pombase/");
identifiersOrg.put("http://dbName#PDB", "http://identifiers.org/pdb/");
identifiersOrg.put("http://dbName#PDBsum", "http://identifiers.org/pdb/");
identifiersOrg.put("http://dbName#PFAM", "http://identifiers.org/pfam/");
identifiersOrg.put("http://dbName#PGD", "http://identifiers.org/pseudomonas/");
identifiersOrg.put("http://dbName#PIR", "http://identifiers.org/pirsf/");
identifiersOrg.put("http://dbName#PO", "http://identifiers.org/obo.po/");
identifiersOrg.put("http://dbName#PRF", "http://identifiers.org/ncbiprotein/");
identifiersOrg.put("http://dbName#PUBMED", "http://identifiers.org/pubmed/");
identifiersOrg.put("http://dbName#PeroxiBase", "http://identifiers.org/peroxibase/");
identifiersOrg.put("http://dbName#PomBase", "http://identifiers.org/pombase/");
identifiersOrg.put("http://dbName#ProSite", "http://identifiers.org/prosite/");
identifiersOrg.put("http://dbName#REBASE", "http://identifiers.org/rebase/");
identifiersOrg.put("http://dbName#RFAM", "http://identifiers.org/rfam/");
identifiersOrg.put("http://dbName#RGD", "http://identifiers.org/rgd/");
identifiersOrg.put("http://dbName#Reactome", "http://identifiers.org/reactome/");
identifiersOrg.put("http://dbName#RefSeq_mRNA", "http://identifiers.org/refseq/");
identifiersOrg.put("http://dbName#RefSeq_mRNA_predicted", "http://identifiers.org/refseq/");
identifiersOrg.put("http://dbName#RefSeq_ncRNA", "http://identifiers.org/refseq/");
identifiersOrg.put("http://dbName#RefSeq_ncRNA_predicted", "http://identifiers.org/refseq/");
identifiersOrg.put("http://dbName#RefSeq_peptide", "http://identifiers.org/refseq/");
identifiersOrg.put("http://dbName#RefSeq_peptide_predicted", "http://identifiers.org/refseq/");
identifiersOrg.put("http://dbName#Rhea", "http://identifiers.org/rhea/");
identifiersOrg.put("http://dbName#SGD", "http://identifiers.org/sgd/");
identifiersOrg.put("http://dbName#SGN", "http://identifiers.org/sgn/");
identifiersOrg.put("http://dbName#SMART", "http://identifiers.org/smart/");
identifiersOrg.put("http://dbName#SO", "http://identifiers.org/obo.so/");
identifiersOrg.put("http://dbName#SubtiList", "http://identifiers.org/subtilist/");
identifiersOrg.put("http://dbName#Superfamily", "http://identifiers.org/supfam/");
identifiersOrg.put("http://dbName#TAIR_LOCUS", "http://identifiers.org/tair.locus/");
identifiersOrg.put("http://dbName#TAIR_LOCUS_MODEL", "http://identifiers.org/tair.locus/");
identifiersOrg.put("http://dbName#TIGR", "http://identifiers.org/tigrfam/");
identifiersOrg.put("http://dbName#TIGR_GeneIndex", "http://identifiers.org/tigrfam/");
identifiersOrg.put("http://dbName#TIGR_ID", "http://identifiers.org/tigrfam/");
identifiersOrg.put("http://dbName#TIGR_LOCUS", "http://identifiers.org/tigrfam/");
identifiersOrg.put("http://dbName#TIGR_LOCUS_MODEL", "http://identifiers.org/tigrfam/");
identifiersOrg.put("http://dbName#TIGR_TRANSCRIPT_ID", "http://identifiers.org/tigrfam/");
identifiersOrg.put("http://dbName#ToxoDB", "http://identifiers.org/toxoplasma/");
identifiersOrg.put("http://dbName#TubercuList", "http://identifiers.org/myco.tuber/");
identifiersOrg.put("http://dbName#UniGene", "http://identifiers.org/unigene/");
identifiersOrg.put("http://dbName#UniParc", "http://identifiers.org/uniparc/");
identifiersOrg.put("http://dbName#UniProtKB_all", "http://identifiers.org/uniprot/");
identifiersOrg.put("http://dbName#Uniprot/SPTREMBL", "http://identifiers.org/uniprot/");
identifiersOrg.put("http://dbName#Uniprot/SWISSPROT", "http://identifiers.org/uniprot/");
identifiersOrg.put("http://dbName#WikiGene", "http://identifiers.org/wikigene/");
identifiersOrg.put("http://dbName#ZFIN_ID", "http://identifiers.org/zfin/");
identifiersOrg.put("http://dbName#ZFIN_xpat", "http://identifiers.org/zfin.expression/");
identifiersOrg.put("http://dbName#flybase_annotation_id", "http://identifiers.org/flybase/");
identifiersOrg.put("http://dbName#flybase_gene_id", "http://identifiers.org/flybase/");
identifiersOrg.put("http://dbName#flybase_polypeptide_id", "http://identifiers.org/flybase/");
identifiersOrg.put("http://dbName#flybase_transcript_id", "http://identifiers.org/flybase/");
identifiersOrg.put("http://dbName#flybase_translation_id", "http://identifiers.org/flybase/");
identifiersOrg.put("http://dbName#goslim_goa", "http://identifiers.org/goa/");
identifiersOrg.put("http://dbName#miRBase", "http://identifiers.org/mirbase/");
identifiersOrg.put("http://dbName#protein_id", "http://identifiers.org/insdc/");
identifiersOrg.put("http://dbName#wormbase_id", "http://identifiers.org/wormbase/");
return identifiersOrg;
}
}