This repository has been archived by the owner on Sep 25, 2018. It is now read-only.
-
Notifications
You must be signed in to change notification settings - Fork 1
Commit
This commit does not belong to any branch on this repository, and may belong to a fork outside of the repository.
Initial implementation of Noctua model reader for disease-phenotype m…
…odels.
- Loading branch information
Showing
3 changed files
with
218 additions
and
22 deletions.
There are no files selected for viewing
186 changes: 186 additions & 0 deletions
186
src/main/scala/org/phenopackets/pxftools/util/NoctuaDiseasePhenotypeModelReader.scala
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,186 @@ | ||
| package org.phenopackets.pxftools.util | ||
|
|
||
| import java.io.InputStream | ||
|
|
||
| import scala.collection.JavaConverters._ | ||
|
|
||
| import org.phenopackets.api.PhenoPacket | ||
| import org.phenopackets.api.model.association.PhenotypeAssociation | ||
| import org.phenopackets.api.model.condition.Phenotype | ||
| import org.phenopackets.api.model.entity.Disease | ||
| import org.phenopackets.api.model.evidence.Evidence | ||
| import org.phenopackets.api.model.evidence.Publication | ||
| import org.phenopackets.api.model.ontology.OntologyClass | ||
| import org.phenopackets.pxftools.util.NoctuaModelVocabulary._ | ||
| import org.phenoscape.scowl._ | ||
| import org.semanticweb.owlapi.apibinding.OWLManager | ||
| import org.semanticweb.owlapi.model.AxiomType | ||
| import org.semanticweb.owlapi.model.IRI | ||
| import org.semanticweb.owlapi.model.OWLClass | ||
| import org.semanticweb.owlapi.model.OWLEntity | ||
| import org.semanticweb.owlapi.model.OWLNamedIndividual | ||
| import org.semanticweb.owlapi.model.OWLOntology | ||
|
|
||
| import com.google.common.base.Optional | ||
| import com.typesafe.scalalogging.LazyLogging | ||
|
|
||
| import scalaz._ | ||
| import scalaz.Scalaz._ | ||
| import org.phenopackets.api.model.condition.ConditionFrequency | ||
| import org.phenopackets.api.model.ontology.ClassInstance | ||
| import org.phenopackets.api.model.condition.ConditionSeverity | ||
| import org.phenopackets.api.model.condition.TemporalRegion | ||
|
|
||
| object NoctuaDiseasePhenotypeModelReader extends LazyLogging { | ||
|
|
||
| def read(stream: InputStream): PhenoPacket = { | ||
| val manager = OWLManager.createOWLOntologyManager() | ||
| val ont = manager.loadOntologyFromOntologyDocument(stream) | ||
| stream.close() | ||
| createPhenoPacket(ont) | ||
| } | ||
|
|
||
| def createPhenoPacket(ont: OWLOntology): PhenoPacket = { | ||
| val builder = PhenoPacket.newBuilder() | ||
| ont.getOntologyID.getOntologyIRI.asScala.foreach(iri => builder.id(iri.toString)) | ||
| val associationsAndAnnotations = (for { | ||
| ObjectPropertyAssertion(annotations, HasPart, subj: OWLNamedIndividual, obj: OWLNamedIndividual) <- ont.getAxioms(AxiomType.OBJECT_PROPERTY_ASSERTION).asScala | ||
| } yield Map(Association(subj, obj) -> annotations)).reduce(_ |+| _) | ||
| var diseases = Set.empty[Disease] | ||
| for { | ||
| (Association(diseaseInd, phenotypeInd), annotations) <- associationsAndAnnotations | ||
| } { | ||
| val allDiseaseTypes = findOWLTypes(diseaseInd, ont) | ||
| if (allDiseaseTypes.size > 1) { | ||
| logger.warn(s"More than one type found for disease $diseaseInd; keeping only one to use as the entity ID.") | ||
| } | ||
| allDiseaseTypes.headOption.foreach { diseaseClass => | ||
| val disease = new Disease() | ||
| disease.setId(diseaseClass.getIRI.toString) | ||
| findLabel(diseaseClass, ont).foreach(disease.setLabel) | ||
| findDescription(diseaseInd, ont).foreach(disease.setLabel) | ||
| diseases += disease | ||
| val phenotype = new Phenotype() | ||
| updateAsClassInstance(phenotype, phenotypeInd, ont) | ||
| findFrequency(phenotypeInd, ont).foreach(phenotype.setFrequency) | ||
| findSeverity(phenotypeInd, ont).foreach(phenotype.setSeverity) | ||
| findTimeOfOnset(phenotypeInd, ont).foreach(phenotype.setTimeOfOnset) | ||
| findTimeOfOffset(phenotypeInd, ont).foreach(phenotype.setTimeOfFinishing) | ||
| val associationBuilder = new PhenotypeAssociation.Builder(phenotype) | ||
| associationBuilder.setEntity(disease) | ||
| annotations.foreach { | ||
| case Annotation(AxiomHasEvidence, evidence: IRI) => associationBuilder.addEvidence(toEvidence(Individual(evidence), ont)) | ||
| case Annotation(DCContributor, contributor ^^ _) => associationBuilder.setContributorId(contributor) | ||
| case Annotation(DCDate, date ^^ _) => associationBuilder.setDate(date) | ||
| case _ => | ||
| } | ||
| builder.addPhenotypeAssociation(associationBuilder.build()) | ||
| } | ||
| } | ||
| builder.setDiseases(diseases.toSeq.asJava) | ||
| builder.build() | ||
| } | ||
|
|
||
| private def toEvidence(ind: OWLNamedIndividual, ont: OWLOntology): Evidence = { | ||
| val evidence = new Evidence() | ||
| updateAsClassInstance(evidence, ind, ont) | ||
| val publications = for { | ||
| ObjectPropertyAssertion(_, HasSupportingReference, _, reference: IRI) <- ont.getObjectPropertyAssertionAxioms(ind).asScala | ||
| } yield { | ||
| val pubBuilder = new Publication.Builder() | ||
| pubBuilder.setId(reference.toString) | ||
| findLabel(Individual(reference), ont).foreach(pubBuilder.setTitle) | ||
| pubBuilder.build() | ||
| } | ||
| evidence.setSupportingPublications(publications.toSeq.asJava) | ||
| evidence | ||
| } | ||
|
|
||
| private def toOntologyClass(term: OWLClass, ont: OWLOntology): OntologyClass = { | ||
| val classBuilder = new OntologyClass.Builder(term.getIRI.toString) | ||
| findLabel(term, ont).foreach(classBuilder.setLabel) | ||
| classBuilder.build() | ||
| } | ||
|
|
||
| private def findLabel(item: OWLEntity, ont: OWLOntology): Option[String] = (for { | ||
| AnnotationAssertion(_, RDFSLabel, _, label ^^ _) <- ont.getAnnotationAssertionAxioms(item.getIRI).asScala | ||
| } yield label).headOption | ||
|
|
||
| private def findDescription(item: OWLEntity, ont: OWLOntology): Option[String] = (for { | ||
| AnnotationAssertion(_, DCDescription, _, desc ^^ _) <- ont.getAnnotationAssertionAxioms(item.getIRI).asScala | ||
| } yield desc).headOption | ||
|
|
||
| private def findFrequency(phenotypeInd: OWLNamedIndividual, ont: OWLOntology): Option[ConditionFrequency] = (for { | ||
| ObjectPropertyAssertion(_, ConditionToFrequency, _, frequencyInd: OWLNamedIndividual) <- ont.getObjectPropertyAssertionAxioms(phenotypeInd).asScala | ||
| } yield { | ||
| val frequency = new ConditionFrequency() | ||
| updateAsClassInstance(frequency, frequencyInd, ont) | ||
| frequency | ||
| }).headOption | ||
|
|
||
| private def findSeverity(phenotypeInd: OWLNamedIndividual, ont: OWLOntology): Option[ConditionSeverity] = (for { | ||
| ObjectPropertyAssertion(_, ConditionToSeverity, _, severityInd: OWLNamedIndividual) <- ont.getObjectPropertyAssertionAxioms(phenotypeInd).asScala | ||
| } yield { | ||
| val severity = new ConditionSeverity() | ||
| updateAsClassInstance(severity, severityInd, ont) | ||
| severity | ||
| }).headOption | ||
|
|
||
| private def findTimeOfOnset(phenotypeInd: OWLNamedIndividual, ont: OWLOntology): Option[TemporalRegion] = (for { | ||
| ObjectPropertyAssertion(_, ExistenceStartsDuring, _, onsetInd: OWLNamedIndividual) <- ont.getObjectPropertyAssertionAxioms(phenotypeInd).asScala | ||
| } yield { | ||
| toTemporalRegion(onsetInd, ont) | ||
| }).headOption | ||
|
|
||
| private def findTimeOfOffset(phenotypeInd: OWLNamedIndividual, ont: OWLOntology): Option[TemporalRegion] = (for { | ||
| ObjectPropertyAssertion(_, ExistenceEndsDuring, _, offsetInd: OWLNamedIndividual) <- ont.getObjectPropertyAssertionAxioms(phenotypeInd).asScala | ||
| } yield { | ||
| toTemporalRegion(offsetInd, ont) | ||
| }).headOption | ||
|
|
||
| private def toTemporalRegion(regionInd: OWLNamedIndividual, ont: OWLOntology): TemporalRegion = { | ||
| val region = new TemporalRegion() | ||
| updateAsClassInstance(region, regionInd, ont) | ||
| for { | ||
| ObjectPropertyAssertion(_, TemporalRegionToStart, _, start ^^ _) <- ont.getObjectPropertyAssertionAxioms(regionInd).asScala | ||
| } { | ||
| region.setStartTime(start) | ||
| } | ||
| for { | ||
| ObjectPropertyAssertion(_, TemporalRegionToEnd, _, end ^^ _) <- ont.getObjectPropertyAssertionAxioms(regionInd).asScala | ||
| } { | ||
| region.setEndTime(end) | ||
| } | ||
| region | ||
|
|
||
| } | ||
|
|
||
| private def updateAsClassInstance(instance: ClassInstance, ind: OWLNamedIndividual, ont: OWLOntology): Unit = { | ||
| findDescription(ind, ont).foreach(instance.setDescription) | ||
| instance.setTypes(findTypes(ind, ont).toSeq.asJava) | ||
| instance.setNegatedTypes(findNegatedTypes(ind, ont).toSeq.asJava) | ||
| } | ||
|
|
||
| private def findTypes(individual: OWLNamedIndividual, ont: OWLOntology): Set[OntologyClass] = | ||
| findOWLTypes(individual, ont).map(toOntologyClass(_, ont)) | ||
|
|
||
| private def findOWLTypes(individual: OWLNamedIndividual, ont: OWLOntology): Set[OWLClass] = for { | ||
| ClassAssertion(_, owlClass: OWLClass, subj) <- ont.getClassAssertionAxioms(individual).asScala.toSet | ||
| } yield owlClass | ||
|
|
||
| private def findNegatedTypes(individual: OWLNamedIndividual, ont: OWLOntology): Set[OntologyClass] = | ||
| findNegatedOWLTypes(individual, ont).map(toOntologyClass(_, ont)) | ||
|
|
||
| private def findNegatedOWLTypes(individual: OWLNamedIndividual, ont: OWLOntology): Set[OWLClass] = for { | ||
| ClassAssertion(_, ObjectComplementOf(owlClass: OWLClass), subj) <- ont.getClassAssertionAxioms(individual).asScala.toSet | ||
| } yield owlClass | ||
|
|
||
| private case class Association(subj: OWLNamedIndividual, obj: OWLNamedIndividual) | ||
|
|
||
| private implicit class OptionalOption[T](val self: Optional[T]) extends AnyVal { | ||
|
|
||
| def asScala: Option[T] = if (self.isPresent) Some(self.get) else None | ||
|
|
||
| } | ||
|
|
||
| } |
29 changes: 29 additions & 0 deletions
29
src/main/scala/org/phenopackets/pxftools/util/NoctuaModelVocabulary.scala
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,29 @@ | ||
| package org.phenopackets.pxftools.util | ||
|
|
||
| import org.phenoscape.scowl._ | ||
| import org.semanticweb.owlapi.apibinding.OWLManager | ||
|
|
||
| import com.hp.hpl.jena.vocabulary.DC_11 | ||
|
|
||
| object NoctuaModelVocabulary { | ||
|
|
||
| private val factory = OWLManager.getOWLDataFactory | ||
|
|
||
| val DCTitle = AnnotationProperty(DC_11.title.getURI) | ||
| val DCDescription = AnnotationProperty(DC_11.description.getURI) | ||
| val DCSource = AnnotationProperty(DC_11.source.getURI) | ||
| val DCDate = AnnotationProperty(DC_11.date.getURI) | ||
| val DCContributor = AnnotationProperty(DC_11.contributor.getURI) | ||
| val RDFSComment = factory.getRDFSComment | ||
| val HasPart = ObjectProperty("http://purl.obolibrary.org/obo/BFO_0000051") | ||
| val ConditionToFrequency = ObjectProperty("http://example.org/condition_to_frequency") //FIXME | ||
| val ConditionToSeverity = ObjectProperty("http://example.org/condition_to_severity") //FIXME | ||
| val TemporalRegionToStart = DataProperty("http://example.org/temporal_region_start_at") //FIXME | ||
| val TemporalRegionToEnd = DataProperty("http://example.org/temporal_region_end_at") //FIXME | ||
| val ExistenceStartsDuring = ObjectProperty("http://purl.obolibrary.org/obo/RO_0002488") | ||
| val ExistenceEndsDuring = ObjectProperty("http://purl.obolibrary.org/obo/RO_0002492") | ||
| val AxiomHasEvidence = AnnotationProperty("http://purl.obolibrary.org/obo/RO_0002612") | ||
| val HasSupportingReference = ObjectProperty("http://purl.obolibrary.org/obo/SEPIO_0000124") | ||
| val Publication = Class("http://purl.obolibrary.org/obo/IAO_0000311") | ||
|
|
||
| } |
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters