How to query go-plus

[davidbio]

Hi,

I want to find all "never in" and "only in" relations between GOs and NCBITaxon or NCBITaxon_Union.
They are in the go-plus.owl but I don't know anything about the owl format and how to query it.

This code using owlapi 5.5 helped me finding all "only in" relations, but I am still missing "never in".

IRI iri = IRI.create("http://current.geneontology.org/ontology/extensions/go-plus.owl");
OWLOntology ontology = manager.loadOntologyFromOntologyDocument(iri);
for (OWLAxiom axiom : ontology.getAxioms()) {
	if (axiom.isOfType(AxiomType.SUBCLASS_OF)) {
		String ax = axiom.toString();
		Set<OWLEntity> signature = axiom.getSignature();
		if ((ax.contains("RO_0002160") || ax.contains("RO_0002161")) && ax.contains("GO_") && ax.contains("NCBITaxon_")) {
			StringBuilder sb = new StringBuilder();
			for (OWLEntity owlEntity : signature) {
				if (sb.length() > 0) {
					sb.append(" -> ");
				}
				sb.append(owlEntity.getIRI()
						      .getRemainder()
						      .get());
			}
			System.out.println(sb.toString());
		}
	}
}

Can anyone help to extract this information in a reliable way?

[kltm]

Tagging @balhoff

[balhoff]

@davidbio I finally completed this ticket (geneontology/go-ontology#19759), which makes it much easier to see "complete" taxon constraints (e.g., including those that are logically inferred from use of particular anatomical terms or cell types). So that may affect your code for querying them. After the precomputation, all relevant taxon constraints for a term should be findable by looking at its own axioms or else traversing up the "is_a" class hierarchy. No need to to traverse any other relations. The precomputed taxon constraints are merged into go-plus, and have an annotation source "computed".

Here is one way to get them, loosely based on your code above. I included the SNAPSHOT URL, since these precomputed results aren't in a release yet. But they should be included in the November official release.

public static void main(String[] args) throws OWLOntologyCreationException {
        IRI iri = IRI.create("http://purl.obolibrary.org/obo/go/snapshot/extensions/go-plus.owl");
        OWLOntologyManager manager = OWLManager.createOWLOntologyManager();
        OWLDataFactory factory = manager.getOWLDataFactory();
        OWLObjectProperty inTaxon = factory.getOWLObjectProperty(IRI.create("http://purl.obolibrary.org/obo/RO_0002162"));
        OWLAnnotationProperty source = factory.getOWLAnnotationProperty(IRI.create("http://www.geneontology.org/formats/oboInOwl#source"));
        OWLLiteral computed = factory.getOWLLiteral("computed");
        OWLAnnotation isComputed = factory.getOWLAnnotation(source, computed);
        OWLOntology ontology = manager.loadOntologyFromOntologyDocument(iri);
        for (OWLSubClassOfAxiom axiom : ontology.getAxioms(AxiomType.SUBCLASS_OF)) {
            if (axiom.getAnnotations().contains(isComputed) && axiom.getSubClass().isNamed()
                    && axiom.getSubClass().asOWLClass().getIRI().toString().startsWith("http://purl.obolibrary.org/obo/GO_")) {
                OWLClass subclass = axiom.getSubClass().asOWLClass();
                OWLClassExpression superclass = axiom.getSuperClass();
                if ((superclass instanceof OWLObjectSomeValuesFrom)
                        && ((OWLObjectSomeValuesFrom) superclass).getProperty().equals(inTaxon)
                        && ((OWLObjectSomeValuesFrom) superclass).getFiller().isNamed()) {
                    System.out.println(
                            subclass.getIRI() +
                                    " always_in_taxon " +
                                    ((OWLObjectSomeValuesFrom) superclass).getFiller().asOWLClass().getIRI());
                } else if ((superclass instanceof OWLObjectComplementOf)
                        && (((OWLObjectComplementOf) superclass).getOperand() instanceof OWLObjectSomeValuesFrom)) {
                    OWLObjectSomeValuesFrom svf = (OWLObjectSomeValuesFrom) ((OWLObjectComplementOf) superclass).getOperand();
                    if (svf.getProperty().equals(inTaxon)
                            && svf.getFiller().isNamed()) {
                        System.out.println(
                                subclass.getIRI() +
                                        " never_in_taxon " +
                                        svf.getFiller().asOWLClass().getIRI());
                    }
                }
            }
        }
    }

[balhoff]

Another approach that may be simpler would be to use this file: http://snapshot.geneontology.org/ontology/imports/go-computed-taxon-constraints.obo (but preferably from an official release rather than snapshot; it should be out in the November release).

[davidbio]

@balhoff
Thank you for this thorough answer and effort.

[davidbio]

@balhoff
Sorry to bother you again with this but I am not able to resolve the NCBITaxon_Union entities from the go-plus.owl with owlapi.
I can see that unions can contain taxa or union (composite-like pattern) but I am not able to resolve the relations to get a proper union2taxon mapping.

Honestly, I feel like this data structure is "over-engineered" and people are/will not be able to use it. They will always depend on intermediate mapping files or partial extractions like go-computed-taxon-constraints.obo. My point is that this feels too complicated for the people who want to make use of this resource.

[balhoff]

@davidbio yes it is complicated; it's set up that way so that we can use the OWL reasoner for QC. Outside of that use case it is not a user-friendly way to provide this info. That's why we're now generating the computed taxon constraints file—otherwise you need to query an OWL reasoner to know the actual constraints applying to a term. If there is a particular format that you think would be broadly useful, please let us know and we can look at adding it as a product. OWL is probably not right for most consumers.

For getting the taxa within each union, I can provide the OWL API code if that would be useful to you, or else see if this file works: http://release.geneontology.org/2023-10-09/ontology/imports/go-taxon-groupings.obo

Here is the OWL API code:

package uk.ac.manchester.owl.owlapi;

import org.semanticweb.owlapi.apibinding.OWLManager;
import org.semanticweb.owlapi.model.*;
import org.semanticweb.owlapi.search.EntitySearcher;

import java.util.HashSet;
import java.util.Set;
import java.util.stream.Collectors;

public class Example {

    public static Set<OWLClass> expandUnion(OWLClass term, OWLOntology ontology) {
        return EntitySearcher.getEquivalentClasses(term, ontology).stream()
                .filter(cls -> cls instanceof OWLObjectUnionOf)
                .map(cls -> ((OWLObjectUnionOf) cls).getOperands().stream()
                        .filter(OWLClassExpression::isNamed)
                        .map(OWLClassExpression::asOWLClass).collect(Collectors.toSet()))
                .findFirst().orElse(new HashSet<>());
    }

    public static String taxonString(OWLClass taxon, OWLOntology ontology) {
        if (taxon.getIRI().toString().startsWith("http://purl.obolibrary.org/obo/NCBITaxon_Union")) {
            return expandUnion(taxon, ontology).stream().map(t -> t.getIRI().toString()).collect(Collectors.joining("|"));
        } else {
            return taxon.getIRI().toString();
        }
    }

    public static void main(String[] args) throws OWLOntologyCreationException {
        IRI iri = IRI.create("http://purl.obolibrary.org/obo/go/snapshot/extensions/go-plus.owl");
        OWLOntologyManager manager = OWLManager.createOWLOntologyManager();
        OWLDataFactory factory = manager.getOWLDataFactory();
        OWLObjectProperty inTaxon = factory.getOWLObjectProperty(IRI.create("http://purl.obolibrary.org/obo/RO_0002162"));
        OWLAnnotationProperty source = factory.getOWLAnnotationProperty(IRI.create("http://www.geneontology.org/formats/oboInOwl#source"));
        OWLLiteral computed = factory.getOWLLiteral("computed");
        OWLAnnotation isComputed = factory.getOWLAnnotation(source, computed);
        OWLOntology ontology = manager.loadOntologyFromOntologyDocument(iri);
        for (OWLSubClassOfAxiom axiom : ontology.getAxioms(AxiomType.SUBCLASS_OF)) {
            if (axiom.getAnnotations().contains(isComputed) && axiom.getSubClass().isNamed()
                    && axiom.getSubClass().asOWLClass().getIRI().toString().startsWith("http://purl.obolibrary.org/obo/GO_")) {
                OWLClass subclass = axiom.getSubClass().asOWLClass();
                OWLClassExpression superclass = axiom.getSuperClass();
                if ((superclass instanceof OWLObjectSomeValuesFrom)
                        && ((OWLObjectSomeValuesFrom) superclass).getProperty().equals(inTaxon)
                        && ((OWLObjectSomeValuesFrom) superclass).getFiller().isNamed()) {
                    OWLClass taxon = ((OWLObjectSomeValuesFrom) superclass).getFiller().asOWLClass();
                    System.out.println(subclass.getIRI() + " always_in_taxon " + taxonString(taxon, ontology));
                } else if ((superclass instanceof OWLObjectComplementOf)
                        && (((OWLObjectComplementOf) superclass).getOperand() instanceof OWLObjectSomeValuesFrom)) {
                    OWLObjectSomeValuesFrom svf = (OWLObjectSomeValuesFrom) ((OWLObjectComplementOf) superclass).getOperand();
                    if (svf.getProperty().equals(inTaxon)
                            && svf.getFiller().isNamed()) {
                        OWLClass taxon = svf.getFiller().asOWLClass();
                        System.out.println(subclass.getIRI() + " never_in_taxon " + taxonString(taxon, ontology));
                    }
                }
            }
        }
    }

}

[davidbio]

@balhoff
I appreciate your commitment and understanding in this matter.

I also like the idea of being able to extract the information with the help of your code from the original source directly.
This is very useful to me and I am convinced that other ppl will also benefit from these code snippets.