Package org.incenp.obofoundry.sssom.owl

Class XrefExtractor

  • public class XrefExtractor
extends Object
    Extract mappings from cross-references (oboInOwl:hasDbXref annotations) in a ontology.

    • Constructor Detail

      • XrefExtractor

        public XrefExtractor()

    • Method Detail

      • setPrefixMap

        public void setPrefixMap​(Map<String,​String> map)
        Sets the prefix map to be used when processing cross-reference annotations. By default, only cross-references using a known prefix name will be derived into mappings.
        Parameters:
        map - A map of prefix names to URL prefixes.

      • addPrefixToPredicateMapping

        public void addPrefixToPredicateMapping​(String prefixName,
                                        String predicate)
        Maps a prefix name to a predicate. By default, mappings derived from cross-references have a oboInOwl:hasDbXref predicate. Use this method to force the use of another predicate for cross-references that use a specific prefix name.
        Parameters:
        prefixName - The prefix name, as used in cross-references.
        predicate - The mapping predicate to use.

      • fillPrefixToPredicateMap

        public void fillPrefixToPredicateMap​(org.semanticweb.owlapi.model.OWLOntology ontology)
        Gets the mappings between prefix names and predicates from annotations in the given ontology.

        This method recognises the following annotations:

        • oboInOwl#treat-xrefs-as-equivalent: map a prefix name to the skos:exactMatch predicate;
        • oboInOwl#treat-xrefs-as-is_a: map a prefix name to the skos:broadMatch predicate;
        • oboInOwl#treat-xrefs-as-has-subclass: map a prefix name to the skos:narrowMatch predicate;
        • oboInOwl#treat-xrefs-as-genus-differentia: map a prefix name to the semapv:crossSpeciesExactMatch predicate;
        • oboInOwl#treat-xrefs-as-reverse-genus-differentia: likewise.
        Parameters:
        ontology - The ontology to extract the prefix-to-predicate mappings from.

      • includeObsoletes

        public void includeObsoletes​(boolean value)
        Indicates whether cross-references on obsoleted terms should be extracted. The default behaviour is to ignore obsoleted terms.
        Parameters:
        value - true to extract cross-references on obsoleted terms.

      • extract

        public MappingSet extract​(org.semanticweb.owlapi.model.OWLOntology ontology)
        Extract mappings from cross-references in the specified ontology. Only cross-references with prefixes that are (1) known, and (2) associated with a predicate (through either addPrefixToPredicateMapping(String, String) or fillPrefixToPredicateMap(OWLOntology)) are taken into account.
        Parameters:
        ontology - The ontology to extract mappings from.
        Returns:
        The set of mappings extracted from the ontology.

      • extract

        public MappingSet extract​(org.semanticweb.owlapi.model.OWLOntology ontology,
                          boolean permissive,
                          boolean includeGeneric)
        Extract mappings from cross-references in the specified ontology.
        Parameters:
        ontology - The ontology to extract mappings from.
        permissive - If true, cross-references using an non-resolvable prefix name will not be ignored.
        includeGeneric - If true, cross-references using a prefix name that has not been associated to a mapping predicate will not be ignored, and will yield mappings with the oboInOwl:hasDbXref predicate.
        Returns:
        The set of mappings extracted from the ontology.

      • getUnknownPrefixNames

        public Set<String> getUnknownPrefixNames()
        Gets any prefix names encountered in cross-references that could not be resolved.
        Returns:
        The list of unknown prefix names.