Check if provided taxon constraints are implied by those already in an ontology

compare-taxon-constraints.sc

// scala 2.13.3
// ammonite 2.3.8

import $ivy.`net.sourceforge.owlapi:owlapi-distribution:4.5.20`
import $ivy.`org.semanticweb.elk:elk-owlapi:0.4.3`
import $ivy.`org.phenoscape::scowl:1.3.4`
import $ivy.`com.outr::scribe-slf4j:2.7.12`

import scala.io.Source
import org.phenoscape.scowl._
import org.semanticweb.owlapi.apibinding.OWLManager
import org.semanticweb.elk.owlapi.ElkReasonerFactory
import org.semanticweb.owlapi.reasoner.InferenceType
import org.semanticweb.owlapi.model.OWLClass
import org.semanticweb.owlapi.model.OWLClassExpression

val InTaxon = ObjectProperty("http://purl.obolibrary.org/obo/RO_0002162")

final case class Constraint(goTerm: OWLClass, goLabel: String, taxonTerm: OWLClass, taxonLabel: String) {

  def expression: OWLClassExpression = goTerm and (InTaxon some taxonTerm)

}

def readConstraintsFile(file: os.Path): List[Constraint] = {
  Source
    .fromFile(file.toIO, "utf-8")
    .getLines()
    .drop(1)
    .map { line =>
      val columns = line.split("\t", -1)
      val goTerm = Class(columns(0).trim().replaceFirst("GO:", "http://purl.obolibrary.org/obo/GO_"))
      val goLabel = columns(1).trim()
      val taxonTerm = Class(
        columns(2)
          .trim()
          .replaceFirst("NCBITaxon:", "http://purl.obolibrary.org/obo/NCBITaxon_")
          .replaceFirst("NCBITaxon_Union:", "http://purl.obolibrary.org/obo/NCBITaxon_Union_")
      )
      val taxonLabel = columns(3).trim()
      Constraint(goTerm, goLabel, taxonTerm, taxonLabel)
    }
    .to(List)
}

@main
def main(onlyConstraintsFile: os.Path, neverConstraintsFile: os.Path, ontologyFile: os.Path) = {
  val manager = OWLManager.createOWLOntologyManager()
  val ontology = OWLManager.createOWLOntologyManager().loadOntologyFromOntologyDocument(ontologyFile.toIO)
  val reasoner = new ElkReasonerFactory().createReasoner(ontology)
  reasoner.precomputeInferences(InferenceType.CLASS_HIERARCHY)
  for {
    constraint @ Constraint(goTerm, goLabel, taxonTerm, taxonLabel) <- readConstraintsFile(onlyConstraintsFile)
  } {
    val equivalents = reasoner.getEquivalentClasses(constraint.expression)
    if (equivalents.contains(OWLNothing))
      println(s"$goLabel\t${goTerm.getIRI()}\t$taxonLabel\t${taxonTerm.getIRI()}\tonly in taxon\tno longer compatible")
    else if (!equivalents.contains(goTerm))
      println(s"$goLabel\t${goTerm.getIRI()}\t$taxonLabel\t${taxonTerm.getIRI()}\tonly in taxon\tno longer constrained")
  }
  for {
    constraint @ Constraint(goTerm, goLabel, taxonTerm, taxonLabel) <- readConstraintsFile(neverConstraintsFile)
  } {
    val equivalents = reasoner.getEquivalentClasses(constraint.expression)
    if (!equivalents.contains(OWLNothing))
      println(
        s"$goLabel\t${goTerm.getIRI()}\t$taxonLabel\t${taxonTerm.getIRI()}\tnever in taxon\tno longer constrained"
      )
    else if (equivalents.contains(goTerm))
      println(s"$goLabel\t${goTerm.getIRI()}\t$taxonLabel\t${taxonTerm.getIRI()}\tnever in taxon\tno longer compatible")
  }
}