Example #1
0
  @Test
  public final void testNormalizeInoh() {
    // there're two Protein objects that have entityReference
    // rdf:ID="IMR_0100366_G_alpha_s_Canonical" (in fact a generic ProteinReference inproperly
    // defined);
    // and that PR has two UniProt UnificationXref: P63092 (human), P63095 (rat).
    // Identifiers.org URI for the PR should NOT be generated.
    //
    // Also, there was a bug when replacing the PR's URI (warning: IllegalBioPAXArgumentException:
    // Incompatible type!..)
    // The cause is that there was a (weird, invalid) PublicationXref having db:id as UniProt:P63092
    // that gets the same URI!
    // To avoid such issues altogether (despite illegal pub. xrefs), the Normalizer won't use
    // Identifiers.org for PublicationXrefs anymore.

    Model model = simpleIO.convertFromOWL(getClass().getResourceAsStream("/test-inoh.owl"));
    Normalizer normalizer = new Normalizer();
    normalizer.setXmlBase("");
    normalizer.normalize(model);

    // A weird PublicationXref that uses a UniProt ID won't be normalized:
    assertFalse(model.containsID("http://identifiers.org/uniprot/P63092"));

    // A PR with two UniProt IDs/unif.xrefs - human, rat - won't be normalized!
    assertTrue(model.containsID(model.getXmlBase() + "IMR_0100366_G_alpha_s_Canonical"));
    assertEquals(
        "ProteinReference",
        model
            .getByID(model.getXmlBase() + "IMR_0100366_G_alpha_s_Canonical")
            .getModelInterface()
            .getSimpleName());
  }
Example #2
0
  @Test
  public final void testNormalize2() {
    Model model = BioPAXLevel.L3.getDefaultFactory().createModel();
    Xref ref = model.addNew(UnificationXref.class, "Xref1");
    ref.setDb("uniprotkb"); // will be converted to 'uniprot'
    ref.setId("Q0VCL1");
    Xref uniprotX = ref;
    ProteinReference pr = model.addNew(ProteinReference.class, "ProteinReference");
    pr.setDisplayName("ProteinReference");
    pr.addXref(uniprotX);
    ref = model.addNew(RelationshipXref.class, "Xref2");
    ref.setDb("refseq");
    ref.setId("NP_001734");
    pr.addXref(ref);
    // normalizer won't merge diff. types of xref with the same db:id
    ref = model.addNew(PublicationXref.class, "Xref3");
    ref.setDb("pubmed");
    ref.setId("2549346"); // the same id
    pr.addXref(ref);
    ref = model.addNew(RelationshipXref.class, "Xref4");
    ref.setDb("pubmed");
    ref.setId("2549346"); // the same id
    pr.addXref(ref);

    Normalizer normalizer = new Normalizer();
    normalizer.normalize(model);

    ProteinReference e = (ProteinReference) model.getByID("http://identifiers.org/uniprot/Q0VCL1");
    assertNotNull(e);

    assertEquals(4, e.getXref().size());
    //		print(e, model);
  }
Example #3
0
 @Test
 public final void testAutoName() {
   Model model = BioPAXLevel.L3.getDefaultFactory().createModel();
   Provenance pro = model.addNew(Provenance.class, "http://identifiers.org/pid.pathway/");
   pro.setStandardName("foo");
   Normalizer.autoName(pro);
   assertNotNull(pro.getStandardName());
   assertTrue(pro.getName().contains("PID"));
   assertTrue(pro.getName().contains("NCI_Nature curated"));
   assertFalse(pro.getStandardName().equals("foo"));
 }
Example #4
0
  @Test
  public final void testNormalize3() {
    Model model = BioPAXLevel.L3.getDefaultFactory().createModel();
    Xref ref = model.addNew(UnificationXref.class, "Xref1");
    ref.setDb("uniprotkb"); // will be converted to 'uniprot'
    ref.setId("Q0VCL1");
    ProteinReference pr = model.addNew(ProteinReference.class, "ProteinReference1");
    pr.setDisplayName("A ProteinReference");
    pr.addXref(ref);
    assertEquals(1, ref.getXrefOf().size());

    //    	System.out.println("Before the model is normalized - ");
    //    	print(pr, model);

    // go normalize!
    Normalizer normalizer = new Normalizer();
    normalizer.normalize(model);

    //		System.out.println("After the model is normalized - ");
    //		print(pr, model);

    assertFalse(model.contains(pr)); // replaced by new norm. PR in the model
    assertFalse(model.contains(ref)); // replaced by new norm. xref in the model
    // now xrefOf is consistent with xref for all objects inn the model (since after some paxtools
    // 4.1.3 snapshot)
    assertEquals(0, pr.getXref().size()); // old PR has xref removed!
    assertEquals(
        0, ref.getXrefOf().size()); // because the old xref was replaced in all parent elements!

    ProteinReference e = (ProteinReference) model.getByID("http://identifiers.org/uniprot/Q0VCL1");
    assertNotNull(e);
    assertEquals(1, e.getXref().size());

    String normUri = Normalizer.uri(model.getXmlBase(), "UNIPROT", "Q0VCL1", UnificationXref.class);
    ref = (UnificationXref) model.getByID(normUri);
    assertNotNull(ref);
    assertEquals(1, ref.getXrefOf().size());

    //		print(e, model);
  }
Example #5
0
  @Test
  public final void testUri() {
    // using null or non-standard db
    assertEquals(
        Normalizer.uri("test/", "foo", "bar", UnificationXref.class),
        Normalizer.uri("test/", "FOo", "bar", UnificationXref.class));
    // 'pubchem' is a ambigous synonym (correct ones are: pubchem-substance, pubchem-compound, etc.)
    assertEquals(
        Normalizer.uri("", "pubchem", "bar", UnificationXref.class),
        Normalizer.uri("", "PubChem", "bar", UnificationXref.class));
    assertEquals(
        Normalizer.uri("", null, "bar", UnificationXref.class),
        Normalizer.uri(null, null, "bar", UnificationXref.class));
    assertFalse(
        Normalizer.uri(null, "foo", "bar", UnificationXref.class)
            .equals(Normalizer.uri(null, "foo", "BAR", UnificationXref.class)));
    assertFalse(
        Normalizer.uri(null, "foo", "bar", UnificationXref.class)
            .equals(Normalizer.uri(null, "foo", "bar", PublicationXref.class)));

    // using standard db names (Miriam is used to normalize name and/or get identifiers.org URI) -
    assertEquals(
        Normalizer.uri("test/", "pubmed", "12345", PublicationXref.class),
        Normalizer.uri("test/", "PubMED", "12345", PublicationXref.class));
    assertEquals(
        "http://identifiers.org/pubmed/12345",
        Normalizer.uri("test/", "PubMED", "12345", PublicationXref.class));
    assertFalse(
        "http://identifiers.org/pubmed/12345"
            .equals(
                Normalizer.uri(
                    null, "PubMED", "12345", RelationshipXref.class))); // - not PublicationXref

    assertEquals(
        "http://identifiers.org/chebi/CHEBI:12345",
        Normalizer.uri("", "chebi", "CHEBI:12345", SmallMoleculeReference.class));
    assertEquals(
        "http://identifiers.org/pubchem.substance/12345",
        Normalizer.uri("", "pubchem-substance", "12345", SmallMoleculeReference.class));

    System.setProperty(
        "biopax.normalizer.uri.strategy", Normalizer.VALUE_NORMALIZER_URI_STRATEGY_SIMPLE);
    assertEquals(
        "SequenceModificationVocabulary_protein_modification_ontology_MOD_12345",
        Normalizer.uri("", "PSI-mod", "MOD:12345", SequenceModificationVocabulary.class));
    assertEquals(
        "ControlledVocabulary_protein_modification_ontology_MOD_12345",
        Normalizer.uri("", "MOD", "MOD:12345", ControlledVocabulary.class));
    System.setProperty(
        "biopax.normalizer.uri.strategy", Normalizer.VALUE_NORMALIZER_URI_STRATEGY_MD5);
    // wrong id (case-sens.)
    assertFalse(
        "http://identifiers.org/chebi/CHEBI:12345"
            .equals(Normalizer.uri("", "chebi", "chebi:12345", SmallMoleculeReference.class)));
    // no 'pubchem' namespace there
    assertFalse(
        "http://identifiers.org/pubchem/12345"
            .equals(Normalizer.uri("", "pubchem-substance", "12345", UnificationXref.class)));

    // when there're special symbols, spaces in the 'id' part
    assertEquals(
        "UnificationXref_foo_bar", Normalizer.uri(null, null, "foo bar", UnificationXref.class));

    assertEquals(
        "http://identifiers.org/taxonomy/9606",
        Normalizer.uri(null, "taxonomy", "9606", BioSource.class));
    assertEquals(
        "http://identifiers.org/taxonomy/9606",
        Normalizer.uri(null, "NCBI Taxonomy", "9606", BioSource.class));
    assertEquals(
        "http://identifiers.org/taxonomy/9606",
        Normalizer.uri(null, "NEWT", "9606", BioSource.class));
    // when organism's id is not taxID (e.g., if the BioSource has tissue, cellType CVs...)
    assertNotSame(
        "http://identifiers.org/taxonomy/9606",
        Normalizer.uri(null, "taxonomy", "9606_blah_blah", BioSource.class));

    String uri = Normalizer.uri("", "UniProt", "W0C7J9", UnificationXref.class);
    assertEquals("UnificationXref_uniprot_knowledgebase_W0C7J9", uri);
  }
Example #6
0
  @Test
  public final void testNormalize() throws UnsupportedEncodingException {
    // Note: a UniProt AC version (e.g. P68250.1 .. P68250.94) is not the same thing as isoform ID!

    Model model = BioPAXLevel.L3.getDefaultFactory().createModel();
    Xref ref = model.addNew(UnificationXref.class, "Xref1");
    ref.setDb("uniprotkb");
    ref.setId("P68250");
    ProteinReference pr = model.addNew(ProteinReference.class, "ProteinReference1");
    pr.setDisplayName("ProteinReference1");
    pr.addXref(ref);
    ref = model.addNew(RelationshipXref.class, "Xref2");
    ref.setDb("refseq");
    ref.setId("NP_001734");
    ref.setIdVersion(
        "1"); // this xref won't be removed by norm. (version matters in xrefs comparing!)
    pr.addXref(ref);
    ref = model.addNew(UnificationXref.class, "Xref3");
    ref.setDb("uniprotkb"); // will be converted to 'uniprot knowledgebase'
    /* The following ID is the secondary accession of P68250,
     * but Normalizer won't complain (it's Validator's and - later - Merger's job)!
     * However, if it were P68250, the normalize(model) would throw exception
     * (because ProteinReference1 becomes ProteinReference2, both get RDFId= urn:miriam:uniprot:P68250!)
     */
    ref.setId("Q0VCL1");
    Xref uniprotX = ref;

    pr = model.addNew(ProteinReference.class, "ProteinReference2");
    pr.setDisplayName("ProteinReference2");
    pr.addXref(uniprotX);
    ref = model.addNew(RelationshipXref.class, "Xref4");
    ref.setDb("refseq");
    ref.setId("NP_001734");
    pr.addXref(ref);

    // this ER is duplicate (same uniprot xref as ProteinReference2's) and must be removed by
    // normalizer
    pr = model.addNew(ProteinReference.class, "ProteinReference3");
    pr.setDisplayName("ProteinReference3");
    pr.addXref(uniprotX);
    ref = model.addNew(RelationshipXref.class, "Xref5");
    ref.setDb("refseq");
    ref.setId("NP_001734");
    pr.addXref(ref);

    // normalizer won't merge diff. types of xref with the same db:id
    ref = model.addNew(PublicationXref.class, "Xref6");
    ref.setDb("pubmed");
    ref.setId("2549346"); // the same id
    pr.addXref(ref);
    ref = model.addNew(RelationshipXref.class, "Xref7");
    ref.setDb("pubmed");
    ref.setId("2549346"); // the same id
    pr.addXref(ref);

    // add biosource
    ref = model.addNew(UnificationXref.class, "Xref8");
    ref.setDb("taxonomy");
    ref.setId("10090"); // the same id
    BioSource bioSource = model.addNew(BioSource.class, "BioSource_Mouse_Tissue");
    bioSource.addXref((UnificationXref) ref);

    // Provenance (must set ID and standard names from a name)
    Provenance pro1 = model.addNew(Provenance.class, "pid");
    pro1.addName("nci_nature"); // must be case insensitive (recognized)
    pro1.setStandardName("foo"); // must be replaced
    // Provenance (must create names from urn)
    Provenance pro2 = model.addNew(Provenance.class, "http://identifiers.org/signaling-gateway/");

    // add some entities with props
    Pathway pw1 = model.addNew(Pathway.class, "pathway");
    pw1.addDataSource(pro1);
    pw1.setStandardName("Pathway");
    Pathway pw2 = model.addNew(Pathway.class, "sub_pathway");
    pw2.setStandardName("Sub-Pathway");
    pw2.addDataSource(pro2);
    pw1.addPathwayComponent(pw2);

    // add data to test uniprot isoform xref and PR normalization
    ref = model.addNew(UnificationXref.class, "Xref9");
    ref.setDb("UniProt"); // normalizer will change it to "uniprot isoform"
    ref.setId("P68250-2");
    pr = model.addNew(ProteinReference.class, "ProteinReference4");
    pr.setDisplayName("ProteinReference1isoformA");
    pr.addXref(ref);

    // next ones are to test normalizer can auto-fix 'uniprot' to 'uniprot isoform' xref,
    // and also merge xrefs #9,#10 and PRs #4,#5 into one PR with one xref
    // below, uniprot xref's idVersion='2' will be moved back to the id value, and db set to
    // "UniProt Isoform" -
    ref = model.addNew(UnificationXref.class, "Xref10");
    ref.setDb(
        "UniProtKb"); // NOT to be replaced with "UniProt Isoform" (version and isoform # are not
    // the same thing)
    ref.setId("P68250");
    ref.setIdVersion("2"); // may be lost after merging with two other P68250 xrefs
    // (version is not the same as isoform, unless db name is 'uniprot isoform')
    pr = model.addNew(ProteinReference.class, "ProteinReference5");
    pr.setDisplayName("ProteinReference1isoformB");
    pr.addXref(ref);

    // Following three Xrefs and PRs will be normalized to uniprot.isoform:P68250-1 and merged into
    // one
    ref = model.addNew(UnificationXref.class, "Xref11");
    ref.setDb("UniProtKb"); // will be replaced with "uniprot isoform"
    ref.setId("P68250-1");
    pr = model.addNew(ProteinReference.class, "ProteinReference6");
    pr.addXref(ref);
    ref = model.addNew(UnificationXref.class, "Xref12");
    ref.setDb("UniProt Isoform"); // because this is standard (isoform) db name (special case) ->
    ref.setId("P68250"); // - this id will set to "P68250-1",
    ref.setIdVersion("1"); // - and idVersion will be cleared!
    pr = model.addNew(ProteinReference.class, "ProteinReference7");
    pr.addXref(ref);
    ref = model.addNew(UnificationXref.class, "Xref13");
    ref.setDb("UniProt Isoform");
    ref.setId("P68250-1");
    pr = model.addNew(ProteinReference.class, "ProteinReference8");
    pr.addXref(ref);

    // special dangling UXs to test/catch a weird bug that accidentally makes db='uniprot
    // isoform'...
    UnificationXref ux = model.addNew(UnificationXref.class, "UniprotUX1");
    ux.setDb("uniprot");
    ux.setId("W0C7J9");
    ux = model.addNew(UnificationXref.class, "UniprotUX2");
    ux.setDb("uniprot");
    ux.setId("W0C7J9.1"); // NOT to be changed to 'uniprot isoform'
    ux = model.addNew(UnificationXref.class, "UniprotUX3");
    ux.setDb("uniprot");
    ux.setId("W0C7J9"); // NOT to be changed to 'uniprot isoform'
    ux.setIdVersion("1");
    ux = model.addNew(UnificationXref.class, "UniprotUX4");
    ux.setDb("uniprot"); // will be changed to 'uniprot isoform'
    ux.setId("W0C7J9-1");
    ux = model.addNew(UnificationXref.class, "UniprotUX5");
    ux.setDb("uniprot"); // will be changed to 'uniprot isoform'
    ux.setId("P68250-3");

    // go normalize!
    Normalizer normalizer = new Normalizer();
    normalizer.normalize(model);

    //		//tmp test print
    //		ByteArrayOutputStream out = new ByteArrayOutputStream();
    //		simpleIO.convertToOWL(model, out);
    //		System.out.println(out.toString());

    // test for a bug that causes db='uniprot' become 'uniprot isoform' (the id matches both
    // patterns)
    assertTrue(model.containsID("UnificationXref_uniprot_knowledgebase_W0C7J9"));
    assertFalse(model.containsID("UnificationXref_uniprot_isoform_W0C7J9"));
    assertTrue(model.containsID("UnificationXref_uniprot_knowledgebase_W0C7J9_1"));
    assertTrue(model.containsID("UnificationXref_uniprot_isoform_W0C7J9-1"));
    assertTrue(model.containsID("UnificationXref_uniprot_isoform_P68250-3"));
    assertTrue(model.containsID("UnificationXref_uniprot_knowledgebase_W0C7J9"));

    // check Xref
    String normUri = Normalizer.uri(model.getXmlBase(), "uniprot", "P68250", UnificationXref.class);
    BioPAXElement bpe = model.getByID(normUri);
    assertTrue(bpe instanceof UnificationXref);

    // check PR
    bpe = model.getByID("http://identifiers.org/uniprot/Q0VCL1");
    assertTrue(bpe instanceof ProteinReference);
    assertTrue(
        model.containsID(
            "Xref7")); // RX is not normalized unless (by mistake) it has identifiers.org uri

    // test BioSource
    assertFalse(model.containsID("BioSource_Mouse_Tissue"));
    bpe =
        model.getByID(
            Normalizer.uri(
                model.getXmlBase(),
                "taxonomy",
                "10090",
                BioSource.class)); // "taxonomy" - capitalization can be any
    assertTrue(bpe instanceof BioSource);
    normUri = Normalizer.uri(model.getXmlBase(), "taxonomy", "10090", UnificationXref.class);
    bpe = model.getByID(normUri);
    assertTrue(bpe instanceof UnificationXref);

    // test that one of each pair ProteinReference, 2nd,3rd and 4th,5th is removed/merged:
    assertEquals(4, model.getObjects(ProteinReference.class).size());

    // Provenance is no more normalized (Miriam is not enough for this task)!
    assertEquals(2, model.getObjects(Provenance.class).size());

    // dataSource property is not inferred/inherited from pw1 anymore (prop. inference feature was
    // removed)
    pw2 = (Pathway) model.getByID("sub_pathway");
    assertEquals(1, pw2.getDataSource().size());
    pw1 = (Pathway) model.getByID("pathway");
    assertEquals(1, pw1.getDataSource().size());

    // test uniprot isoform xrefs are detected and normalized the same way
    // get the expected xref URI first
    normUri =
        Normalizer.uri(model.getXmlBase(), "uniprot isoform", "P68250-2", UnificationXref.class);
    bpe = model.getByID(normUri);
    assertNotNull(bpe);
    assertEquals(1, ((Xref) bpe).getXrefOf().size());
  }