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Merge pull request #10 from phenopackets/hpo-annotations
HPO Phenote annotations import
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131 changes: 131 additions & 0 deletions
131
src/main/scala/org/phenopackets/pxftools/util/HPOAnnotations.scala
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| package org.phenopackets.pxftools.util | ||
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| import java.util.UUID | ||
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| import scala.collection.JavaConverters._ | ||
| import scala.collection.mutable | ||
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| import org.phenopackets.api.PhenoPacket | ||
| import org.phenopackets.api.io.RDFReader | ||
| import org.phenopackets.api.util.ContextUtil | ||
| import org.phenopackets.pxftools.util.PhenoPacketVocabulary._ | ||
| import org.phenoscape.scowl._ | ||
| import org.semanticweb.owlapi.apibinding.OWLManager | ||
| import org.semanticweb.owlapi.model.AxiomType | ||
| import org.semanticweb.owlapi.model.IRI | ||
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| import com.github.jsonldjava.core.Context | ||
| import com.github.tototoshi.csv.CSVReader | ||
| import com.hp.hpl.jena.rdf.model.ModelFactory | ||
| import com.hp.hpl.jena.rdf.model.Resource | ||
| import com.hp.hpl.jena.rdf.model.ResourceFactory | ||
| import com.hp.hpl.jena.rdf.model.Statement | ||
| import com.hp.hpl.jena.vocabulary.RDF | ||
| import com.hp.hpl.jena.vocabulary.RDFS | ||
| import com.typesafe.scalalogging.LazyLogging | ||
| import com.github.tototoshi.csv.TSVFormat | ||
| import java.io.InputStream | ||
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| object HPOAnnotations extends LazyLogging { | ||
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| def read(stream: InputStream): PhenoPacket = importFromTable(CSVReader.open(scala.io.Source.fromInputStream(stream, "utf-8"))(new TSVFormat {})) | ||
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| def importFromTable(table: CSVReader): PhenoPacket = { | ||
| val packetURI = s"urn:uuid:${UUID.randomUUID.toString}" | ||
| val packet = ResourceFactory.createResource(packetURI) | ||
| val triples = table.iteratorWithHeaders.flatMap(rowToTriples(_, packet)).toSeq | ||
| val model = ModelFactory.createDefaultModel() | ||
| model.add(triples.asJava) | ||
| RDFReader.readModel(model, packetURI) | ||
| } | ||
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| private def rowToTriples(row: Map[String, String], packet: Resource): Set[Statement] = { | ||
| val statements = mutable.Set.empty[Statement] | ||
| row.getOpt("Disease ID").foreach { diseaseID => | ||
| val disease = ResourceFactory.createResource(ContextUtil.expandIdentifierAsValue(diseaseID.trim, HPOContext)) | ||
| statements += ResourceFactory.createStatement(packet, Diseases, disease) | ||
| row.getOpt("Disease Name").foreach { diseaseLabel => | ||
| statements += ResourceFactory.createStatement(disease, RDFS.label, ResourceFactory.createTypedLiteral(diseaseLabel.trim)) | ||
| } | ||
| val association = ResourceFactory.createResource() | ||
| statements += ResourceFactory.createStatement(packet, PhenotypeProfile, association) | ||
| statements += ResourceFactory.createStatement(association, Entity, disease) | ||
| val phenotype = ResourceFactory.createResource() | ||
| statements += ResourceFactory.createStatement(association, Phenotype, phenotype) | ||
| row.getOpt("Phenotype ID").foreach { phenotypeID => | ||
| val phenotypeType = ResourceFactory.createResource(ContextUtil.expandIdentifierAsValue(phenotypeID.trim, HPOContext)) | ||
| val phenoRelation = if (row.getOpt("Negation ID").exists(_.trim.toUpperCase == "NOT")) { | ||
| OWLComplementOf | ||
| } else RDF.`type` | ||
| statements += ResourceFactory.createStatement(phenotype, phenoRelation, phenotypeType) | ||
| row.getOpt("Phenotype Name").foreach { phenotypeLabel => | ||
| statements += ResourceFactory.createStatement(phenotypeType, RDFS.label, ResourceFactory.createTypedLiteral(phenotypeLabel.trim)) | ||
| } | ||
| } | ||
| row.getOpt("Age of Onset ID").foreach { onsetID => | ||
| val onsetType = ResourceFactory.createResource(ContextUtil.expandIdentifierAsValue(onsetID.trim, HPOContext)) | ||
| val onset = ResourceFactory.createResource() | ||
| statements += ResourceFactory.createStatement(phenotype, Onset, onset) | ||
| statements += ResourceFactory.createStatement(onset, RDF.`type`, onsetType) | ||
| row.getOpt("Age of Onset Name").foreach { onsetLabel => | ||
| statements += ResourceFactory.createStatement(onsetType, RDFS.label, ResourceFactory.createTypedLiteral(onsetLabel.trim)) | ||
| } | ||
| } | ||
| row.getOpt("Frequency").foreach { frequencyDesc => | ||
| val frequency = ResourceFactory.createResource() | ||
| statements += ResourceFactory.createStatement(phenotype, Frequency, frequency) | ||
| statements += ResourceFactory.createStatement(frequency, Description, ResourceFactory.createTypedLiteral(frequencyDesc.trim)) | ||
| } | ||
| row.getOpt("Description").foreach { description => | ||
| statements += ResourceFactory.createStatement(phenotype, Description, ResourceFactory.createTypedLiteral(description.trim)) | ||
| } | ||
| if (row.getOpt("Evidence ID").nonEmpty || row.getOpt("Pub").nonEmpty) { | ||
| val evidence = ResourceFactory.createResource() | ||
| statements += ResourceFactory.createStatement(association, Evidence, evidence) | ||
| row.getOpt("Evidence ID").foreach { evidenceID => | ||
| val evidenceTypeOpt = evidenceCodesToURI.get(evidenceID.trim) | ||
| val evidenceType = evidenceTypeOpt.getOrElse { | ||
| logger.warn(s"No IRI found for evidence code $evidenceID") | ||
| ResourceFactory.createResource(evidenceID.trim) | ||
| } | ||
| statements += ResourceFactory.createStatement(evidence, RDF.`type`, evidenceType) | ||
| row.getOpt("Evidence Name").foreach { evidenceName => | ||
| statements += ResourceFactory.createStatement(evidenceType, RDFS.label, ResourceFactory.createTypedLiteral(evidenceName.trim)) | ||
| } | ||
| } | ||
| row.getOpt("Pub").foreach { pubID => | ||
| val pub = ResourceFactory.createResource(ContextUtil.expandIdentifierAsValue(pubID.trim, HPOContext)) | ||
| statements += ResourceFactory.createStatement(evidence, Source, pub) | ||
| } | ||
| } | ||
| } | ||
| statements.toSet | ||
| } | ||
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| private val HPOContext: Context = new Context().parse(Map[String, Object]( | ||
| "obo" -> "http://purl.obolibrary.org/obo/", | ||
| "HP" -> "obo:HP_", | ||
| "OMIM" -> "obo:OMIM_").asJava) | ||
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| /** | ||
| * HPO annotations use shorthand labels as evidence IDs | ||
| */ | ||
| private lazy val evidenceCodesToURI: Map[String, Resource] = { | ||
| val manager = OWLManager.createOWLOntologyManager() | ||
| val eco = manager.loadOntology(IRI.create("http://purl.obolibrary.org/obo/eco.owl")) | ||
| val HasExactSynonym = AnnotationProperty("http://www.geneontology.org/formats/oboInOwl#hasExactSynonym") | ||
| (for { | ||
| AnnotationAssertion(_, HasExactSynonym, term: IRI, synonym ^^ dt) <- eco.getAxioms(AxiomType.ANNOTATION_ASSERTION).asScala | ||
| } yield { | ||
| synonym -> ResourceFactory.createResource(term.toString) | ||
| }).toMap | ||
| } | ||
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| private implicit class NullEmptyStringMap(val self: Map[String, String]) extends AnyVal { | ||
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| //scala-csv puts empty strings in the result map; convert to None instead | ||
| def getOpt(key: String): Option[String] = self.get(key).filter(_.nonEmpty) | ||
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| } | ||
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| } |
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23 changes: 23 additions & 0 deletions
23
src/main/scala/org/phenopackets/pxftools/util/PhenoPacketVocabulary.scala
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| Original file line number | Diff line number | Diff line change |
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| @@ -0,0 +1,23 @@ | ||
| package org.phenopackets.pxftools.util | ||
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| import com.hp.hpl.jena.rdf.model.ResourceFactory | ||
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| object PhenoPacketVocabulary { | ||
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| private val Pheno = "http://phenopackets.org" | ||
| private val DC = "http://purl.org/dc/terms" | ||
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| private def p = ResourceFactory.createProperty(_: String) | ||
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| val Diseases = p(s"$Pheno/diseases") | ||
| val PhenotypeProfile = p(s"$Pheno/phenotype_profile") | ||
| val Entity = p(s"$Pheno/entity") | ||
| val Phenotype = p(s"$Pheno/phenotype") | ||
| val Onset = p(s"$Pheno/onset") | ||
| val Frequency = p(s"$Pheno/frequency") | ||
| val Evidence = p(s"$Pheno/evidence") | ||
| val Description = p(s"$DC/description") | ||
| val Source = p(s"$DC/source") | ||
| val OWLComplementOf = p("http://www.w3.org/2002/07/owl#complementOf") | ||
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| } |