<?xml version="1.0"?>
<rdf:RDF
    xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"
    xmlns:xsd="http://www.w3.org/2001/XMLSchema#"
    xmlns:rdfs="http://www.w3.org/2000/01/rdf-schema#"
    xmlns:owl="http://www.w3.org/2002/07/owl#"
    xmlns:biomanta="http://biomanta.sourceforge.net/2007/07/biomanta_extension_02.owl#"
    xmlns:psimi="http://biomanta.sourceforge.net/2007/07/psimi_instance_edit.owl#"
    xmlns:bp="http://www.biopax.org/release/biopax-level2.owl#"
    xmlns:ncbi_taxo="http://biomanta.sourceforge.net/2007/10/ncbi_taxo_2759_dataset.owl"
    xmlns:cc="http://biomanta.sourceforge.net/2008/04/cellular_component.owl"
    xmlns:oboinowl="http://www.geneontology.org/formats/oboInOwl#"
  xml:base="http://biomanta.sourceforge.net/2007/07/biomanta_extension_02.owl">
  <owl:Ontology rdf:about="">
    <rdfs:comment rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
    >This is version 1.0 of the BioMANTA Extension Ontology, currently under development by the BioMANTA research group</rdfs:comment>
    <owl:imports rdf:resource="http://www.biopax.org/release/biopax-level2.owl" />
    <owl:imports rdf:resource="http://biomanta.sourceforge.net/2007/07/psimi_instance_edit.owl" />
    <owl:imports rdf:resource="http://biomanta.sourceforge.net/2008/04/cellular_component.owl" />
    <owl:imports rdf:resource="http://biomanta.sourceforge.net/2008/04/ncbi_taxo_2759_dataset.owl" />
    <owl:imports rdf:resource="http://www.geneontology.org/formats/oboInOwl" />
  </owl:Ontology>

  <owl:Class rdf:ID="ExperimentalObservation">
    <owl:disjointWith>
      <owl:Class rdf:ID="UnspecifiedObservation"/>
    </owl:disjointWith>
    <owl:disjointWith>
      <owl:Class rdf:ID="PredictedObservation"/>
    </owl:disjointWith>
    <owl:disjointWith>
      <owl:Class rdf:ID="InferedObservation"/>
    </owl:disjointWith>
    <rdfs:subClassOf>
      <owl:Class rdf:ID="Observation"/>
    </rdfs:subClassOf>
  </owl:Class>

  <owl:Class rdf:about="#UnspecifiedObservation">
    <owl:disjointWith>
      <owl:Class rdf:about="#PredictedObservation"/>
    </owl:disjointWith>
    <owl:disjointWith>
      <owl:Class rdf:about="#InferedObservation"/>
    </owl:disjointWith>
    <owl:disjointWith rdf:resource="#ExperimentalObservation"/>
    <rdfs:subClassOf rdf:resource="#Observation"/>
  </owl:Class>

  <owl:Class rdf:about="#InferedObservation">
    <rdfs:subClassOf rdf:resource="#Observation"/>
    <owl:disjointWith rdf:resource="#UnspecifiedObservation"/>
    <owl:disjointWith>
      <owl:Class rdf:about="#PredictedObservation"/>
    </owl:disjointWith>
    <owl:disjointWith rdf:resource="#ExperimentalObservation"/>
  </owl:Class>

  <owl:Class rdf:about="#PredictedObservation">
    <rdfs:subClassOf rdf:resource="#Observation"/>
    <owl:disjointWith rdf:resource="#UnspecifiedObservation"/>
    <owl:disjointWith rdf:resource="#InferedObservation"/>
    <owl:disjointWith rdf:resource="#ExperimentalObservation"/>
  </owl:Class>

  <owl:ObjectProperty rdf:ID="sourceOfData">
    <rdfs:comment rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
    >this is used to indicate the source of the data, for example, the identity of the data in a third party resource. The rage of this property is bp:unificationXref</rdfs:comment>
    <rdfs:domain rdf:resource="#Observation"/>
    <rdfs:range rdf:resource="http://www.biopax.org/release/biopax-level2.owl#unificationXref"/>
  </owl:ObjectProperty>

  <owl:ObjectProperty rdf:ID="observedInteraction">
    <rdfs:comment rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
    >Indicates what interaction was observed in this observation (experiment)The range of biomanta:observedInteraction is a value from bp:interaction</rdfs:comment>
    <rdfs:domain rdf:resource="#Observation"/>
    <rdfs:range rdf:resource="http://www.biopax.org/release/biopax-level2.owl#interaction"/>
  </owl:ObjectProperty>

  <owl:ObjectProperty rdf:ID="inferencingMethod">
    <rdfs:comment rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
    >the range of biomanta:inferencingMethod is a value from psi-mi:inference_MI_0362</rdfs:comment>
    <rdfs:domain rdf:resource="#InferedObservation"/>
    <rdfs:range rdf:resource="http://biomanta.sourceforge.net/2007/07/psi-mi_instance_edit.owl#inference_MI_0362"/>
  </owl:ObjectProperty>

  <owl:ObjectProperty rdf:ID="experimentalMethod">
    <rdfs:comment rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
    >the range of biomanta:experimentalMethod is a value from  psi-mi:experimental_interaction_detection_MI_0045</rdfs:comment>
    <rdfs:domain rdf:resource="#ExperimentalObservation"/>
    <rdfs:range rdf:resource="http://biomanta.sourceforge.net/2007/07/psi-mi_instance_edit.owl#experimental_interaction_detection_MI_0045"/>
  </owl:ObjectProperty>

  <owl:ObjectProperty rdf:ID="referenceForObservation">
    <rdfs:comment rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
    >The range of biomanta:referenceForObservation is bp:publicationXref</rdfs:comment>
    <rdfs:domain rdf:resource="#Observation"/>
    <rdfs:range rdf:resource="http://www.biopax.org/release/biopax-level2.owl#publicationXref"/>
  </owl:ObjectProperty>

  <owl:ObjectProperty rdf:ID="predictionMethod">
    <rdfs:domain rdf:resource="#PredictedObservation"/>
    <rdfs:range rdf:resource="http://biomanta.sourceforge.net/2007/07/psi-mi_instance_edit.owl#interaction_prediction_MI_0063"/>
    <rdfs:comment rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
    >the range of biomanta:predictionMethod is a value from psi-mi:interaction_prediction_MI_0063</rdfs:comment>
  </owl:ObjectProperty>

  <owl:ObjectProperty rdf:ID="unspecifiedMethod">
    <rdfs:domain rdf:resource="#UnspecifiedObservation"/>
    <rdfs:range rdf:resource="http://biomanta.sourceforge.net/2007/07/psi-mi_instance_edit.owl#unspecified_method_MI_0686"/>
    <rdfs:comment rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
    >the range of biomanta:unspecifiedMethod is a value from psi-mi:unspecified_method_MI_0686</rdfs:comment>
  </owl:ObjectProperty>

  <owl:ObjectProperty rdf:ID="subcellularLocation">
    <rdfs:domain rdf:resource="http://www.biopax.org/release/biopax-level2.owl#entity"/>
    <rdfs:range rdf:resource="http://biomanta.sourceforge.net/2008/04/cellular_component.owl#GO_0005575"/>
    <rdfs:comment rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
    >the domain of biomanta:subcellularLocation is bp:entity, while the range is an instance from Gene Ontology's cellular component hierarchy</rdfs:comment>
  </owl:ObjectProperty>

  <owl:DatatypeProperty rdf:ID="URL">
    <rdfs:range rdf:resource="http://www.w3.org/2001/XMLSchema#anyURI"/>
    <rdfs:comment rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
    >The domain of the property biomanta:URL is any owl:Thing; the datatype range is http://www.w3.org/2001/XMLSchema#anyURI, where anyURI has a value which is the URL for the interaction in the source database</rdfs:comment>
  </owl:DatatypeProperty>

  <owl:ObjectProperty rdf:ID="fromNCBISpecies">
    <rdfs:range rdf:resource="http://biomanta.sourceforge.net/2007/10/ncbi_taxo.owl#ncbi_taxo_2759"/>
    <rdfs:domain rdf:resource="http://www.biopax.org/release/biopax-level2.owl#physicalEntity"/>
    <rdfs:comment rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
    >The range is the class corresponding to eukaryote in the NCBI ontology. Everything is a sub class of this class.</rdfs:comment>
  </owl:ObjectProperty>
  
  <owl:ObjectProperty rdf:ID="hasPrimaryRef">
      <rdfs:domain rdf:resource="http://www.biopax.org/release/biopax-level2.owl#physicalEntity"/>
      <rdfs:range rdf:resource="http://www.geneontology.org/formats/oboInOwl#DbXref"/>
      <rdfs:comment rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
      >Used to point to the primary reference of the given physical entity.</rdfs:comment>
  </owl:ObjectProperty>

  <owl:ObjectProperty rdf:ID="hasSecondaryRef">
      <rdfs:domain rdf:resource="http://www.biopax.org/release/biopax-level2.owl#physicalEntity"/>
      <rdfs:range rdf:resource="http://www.geneontology.org/formats/oboInOwl#DbXref"/>
      <rdfs:comment rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
      >Used to point to the secondary reference(s) of the given physical entity.</rdfs:comment>
  </owl:ObjectProperty>
  
  <owl:DatatypeProperty rdf:ID="fromKB">
      <rdfs:domain rdf:resource="http://www.geneontology.org/formats/oboInOwl#DbXref"/>
      <rdfs:range rdf:resource="http://www.w3.org/2001/XMLSchema#string"/>
      <rdfs:comment rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Denotes the name of the DB of this reference.</rdfs:comment>
  </owl:DatatypeProperty>

  <owl:DatatypeProperty rdf:ID="hasID">
      <rdfs:domain rdf:resource="http://www.geneontology.org/formats/oboInOwl#DbXref"/>
      <rdfs:range rdf:resource="http://www.w3.org/2001/XMLSchema#string"/>
      <rdfs:comment rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Denotes the ID of this reference.</rdfs:comment>
  </owl:DatatypeProperty>
  
  <owl:DatatypeProperty rdf:ID="hasRefType">
        <rdfs:domain rdf:resource="http://www.geneontology.org/formats/oboInOwl#DbXref"/>
        <rdfs:range rdf:resource="http://www.w3.org/2001/XMLSchema#string"/>
        <rdfs:comment rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Denotes the type of this reference,
        either "identity", "secondary-cc" or others.</rdfs:comment>
  </owl:DatatypeProperty>

  <owl:DatatypeProperty rdf:ID="hasSequence">
    <rdfs:domain rdf:resource="http://www.biopax.org/release/biopax-level2.owl#physicalEntity"/>
    <rdfs:range rdf:resource="http://www.w3.org/2001/XMLSchema#string"/>
    <rdfs:comment rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
    >Points to the genetic sequence of the physical eneity.</rdfs:comment>
  </owl:DatatypeProperty>
  
  <owl:DatatypeProperty rdf:ID="hasFullName">
      <rdfs:domain rdf:resource="http://www.biopax.org/release/biopax-level2.owl#physicalEntity"/>
      <rdfs:range rdf:resource="http://www.w3.org/2001/XMLSchema#string"/>
      <rdfs:comment rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
      >Points to the full name of the physical eneity.</rdfs:comment>
  </owl:DatatypeProperty>

  <owl:DatatypeProperty rdf:ID="hasShortLabel">
      <rdfs:domain rdf:resource="http://www.biopax.org/release/biopax-level2.owl#physicalEntity"/>
      <rdfs:range rdf:resource="http://www.w3.org/2001/XMLSchema#string"/>
      <rdfs:comment rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
      >Points to the short label of the physical eneity.</rdfs:comment>
  </owl:DatatypeProperty>

  <owl:ObjectProperty rdf:ID="maps_to_psimi_participant">
      <rdfs:domain rdf:resource="http://www.biopax.org/release/biopax-level2.owl#physicalEntity"/>
      <rdfs:domain rdf:resource="http://www.biopax.org/release/biopax-level2.owl#physicalEntity"/>
      <rdfs:comment rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
      >Points from the merged physical entity to the entity in an individual dataset, such as DIP or IntACT.</rdfs:comment>
  </owl:ObjectProperty>

</rdf:RDF>

<!-- Created with Protege (with OWL Plugin 3.2.1, Build 365)  http://protege.stanford.edu AND modified by Melissa Davis m.davis@imb.uq.edu.au -->
