MouseAnnotations.groovy

@Grapes([
    @Grab(group='org.semanticweb.elk', module='elk-owlapi', version='0.4.2'),
    @Grab(group='net.sourceforge.owlapi', module='owlapi-api', version='4.1.0'),
    @Grab(group='net.sourceforge.owlapi', module='owlapi-apibinding', version='4.1.0'),
    @Grab(group='net.sourceforge.owlapi', module='owlapi-impl', version='4.1.0'),
    @Grab(group='net.sourceforge.owlapi', module='owlapi-parsers', version='4.1.0'),
    @Grab(group='org.codehaus.gpars', module='gpars', version='1.1.0'),
    @GrabConfig(systemClassLoader=true)
])

import org.semanticweb.owlapi.model.parameters.*;
import org.semanticweb.elk.owlapi.ElkReasonerFactory;
import org.semanticweb.elk.owlapi.ElkReasonerConfiguration;
import org.semanticweb.elk.reasoner.config.*;
import org.semanticweb.owlapi.apibinding.OWLManager;
import org.semanticweb.owlapi.reasoner.*;
import org.semanticweb.owlapi.reasoner.structural.StructuralReasoner
import org.semanticweb.owlapi.vocab.OWLRDFVocabulary;
import org.semanticweb.owlapi.model.*;
import org.semanticweb.owlapi.io.*;
import org.semanticweb.owlapi.owllink.*;
import org.semanticweb.owlapi.util.*;
import org.semanticweb.owlapi.search.*;
import org.semanticweb.owlapi.manchestersyntax.renderer.*;
import org.semanticweb.owlapi.reasoner.structural.*;

import groovyx.gpars.GParsPool;

OWLOntologyManager manager = OWLManager.createOWLOntologyManager()
OWLOntology phenomenet = manager.loadOntologyFromOntologyDocument(
    new File("data/a.owl"))

OWLDataFactory fac = manager.getOWLDataFactory()
ConsoleProgressMonitor progressMonitor = new ConsoleProgressMonitor()
OWLReasonerConfiguration config = new SimpleConfiguration(progressMonitor)
OWLDataFactory dataFactory = manager.getOWLDataFactory()
ElkReasonerFactory reasonerFactory = new ElkReasonerFactory()
OWLReasoner phenomeReasoner = reasonerFactory.createReasoner(
    phenomenet, config)

def getLabel = { term_id ->
    IRI iri = IRI.create("http://purl.obolibrary.org/obo/$term_id")
    OWLClass cl = dataFactory.getOWLClass(iri)
    for(OWLAnnotation a : EntitySearcher.getAnnotations(cl, phenomenet, dataFactory.getRDFSLabel())) {
        OWLAnnotationValue value = a.getValue();
        if(value instanceof OWLLiteral) {
            return ((OWLLiteral) value).getLiteral();
        }
    }
    return "";
}

def getAnchestors = { reasoner, term_id ->
    IRI iri = IRI.create("http://purl.obolibrary.org/obo/$term_id")
    OWLClass cl = dataFactory.getOWLClass(iri)
    def res = reasoner.getSuperClasses(cl, false).getFlattened()
    return res
}

def getChildren = { reasoner, term_id ->
    IRI iri = IRI.create("http://purl.obolibrary.org/obo/$term_id")
    OWLClass cl = dataFactory.getOWLClass(iri)
    def res = reasoner.getSubClasses(cl, false).getFlattened()
    return res
}

def getName = { cl ->
  def iri = cl.toString()
  def name = iri
  if (iri.startsWith("<http://purl.obolibrary.org/obo/")) {
    name = iri.substring(32, iri.length() - 1)
  } else if (iri.startsWith("<http://aber-owl.net/")) {
    name = iri.substring(21, iri.length() - 1)
  }
  return name
}

def phenos = new HashSet<String>();

new File("data/phenos.tab").eachLine { line ->
    def pheno = line.trim()
    phenos.add(pheno)
}

def mgiAnnots = [:].withDefault {new HashSet<String>()}
def omimAnnots = [:].withDefault {new HashSet<String>()}


new File("data/phenotype_annotation.tab").splitEachLine("\t") { items ->
    if (items[0] != "OMIM") return;
    def omim = items[0] + ":" + items[1];
    pheno = items[4].replaceAll(":", "_")
    if (pheno in phenos) {
	omimAnnots[omim].add(pheno)
    }
}

new File("data/MGI_GenePheno.rpt").splitEachLine("\t") { items ->
    pheno = items[4].replaceAll(":", "_")
    if (pheno in phenos) {
	def mgis = items[6].split(",")
	mgis.each { mgi ->
	    mgiAnnots[mgi].add(pheno)
	}
    }
}

def omims = new HashSet<String>();
def mgis = new HashSet<String>();
new File("data/mgi_omim.tab").eachLine { line ->
  if (line.startsWith("#")) return;
    def items = line.split("\t")
    for (def omim: items[2].split("\\|")) { 
	if (omim != "") omims.add(omim)
    }
    mgis.add(items[8])
}


// Add predicted annotations
// mgiAnnots = [:].withDefault {new HashSet<String>()}

// new File("data/predictions_filtered.txt").splitEachLine("\t") { items ->
//   pheno = items[2]
//   if (pheno in phenos) {
//     def gene = items[0]
//     if (gene in mgis) {	
//       mgiAnnots[gene].add(pheno)
//     }
//   }
// }

// new File("data/inferred-phenos.txt").splitEachLine("\t") { items ->
//   pheno = items[2]
//   if (pheno in phenos) {
//     def gene = items[0]
//     if (gene in mgis) {	
//       mgiAnnots[gene].add(pheno)
//     }
//   }
// }

// Remove general terms and leave only specific

// mgiAnnots.keySet().each { mgi ->
//   def annots = mgiAnnots[mgi].collect()
//   annots.each { pheno ->
//     getAnchestors(phenomeReasoner, pheno).each { anch ->
//       anch = getName(anch)
//       if (anch in mgiAnnots[mgi]) {
//         mgiAnnots[mgi].remove(anch)
//       }
//     }
//   }
// }


// def out = new PrintWriter(new BufferedWriter(new FileWriter("data/mgi_annotations_gd.tab")))
// mgiAnnots.each { mgi, annots ->
//   if (mgi in mgis) {
//     out.print(mgi)
//     annots.each { pheno ->
//       out.print("\t" + pheno)
//     }
//     out.println()
//   }
// }
// out.close()


out = new PrintWriter(new BufferedWriter(new FileWriter("data/omim_annotations.tab")))
omimAnnots.each { omim, annots ->
  if (omim in omims) {
    out.print(omim)
    annots.each { pheno ->
      out.print("\t" + pheno)
    }
    out.println()
  }
}
out.close()