Package org.openbel.framework.common.model

Examples of org.openbel.framework.common.model.Term

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        // proteinAbundance(PFH:"RAF Family") hasMembers list(
        //         proteinAbundance(HGNC:ARAF),
        //         proteinAbundance(HGNC:BRAF),
        //         proteinAbundance(HGNC:RAF1))

        Term subject1 = new Term(FunctionEnum.PROTEIN_ABUNDANCE,
                asBelObjs(new Parameter(pfh, "RAF Family")));

        Statement.Object object1 =
                new Statement.Object(new Term(FunctionEnum.LIST, asBelObjs(
                        new Term(FunctionEnum.PROTEIN_ABUNDANCE,
                                asBelObjs(new Parameter(hgnc, "ARAF"))),
                        new Term(FunctionEnum.PROTEIN_ABUNDANCE,
                                asBelObjs(new Parameter(hgnc, "BRAF"))),
                        new Term(FunctionEnum.PROTEIN_ABUNDANCE,
                                asBelObjs(new Parameter(hgnc, "RAF1")))
                        )));

        Statement s1 =
                new Statement(subject1, null, null, object1,
                        RelationshipType.HAS_MEMBERS);

        // Example 2:
        // complexAbundance(NCH:"NADPH Oxidase Complex") hasComponents list(
        //         proteinAbundance(HGNC:NCF1),
        //         proteinAbundance(HGNC:CYBB))

        Term subject2 = new Term(FunctionEnum.COMPLEX_ABUNDANCE,
                asBelObjs(new Parameter(nch, "NADPH Oxidase Complex")));

        Statement.Object object2 =
                new Statement.Object(new Term(FunctionEnum.LIST, asBelObjs(
                        new Term(FunctionEnum.PROTEIN_ABUNDANCE,
                                asBelObjs(new Parameter(hgnc, "NCF1"))),
                        new Term(FunctionEnum.PROTEIN_ABUNDANCE,
                                asBelObjs(new Parameter(hgnc, "CYBB"))))));

        Statement s2 =
                new Statement(subject2, null, null, object2,
                        RelationshipType.HAS_COMPONENTS);
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        // The example:
        // pathology(MESHD:"Atherosclerosis") positiveCorrelation list(
        //         biologicalProcess(GO:"lipid oxidation"),
        //         biologicalProcess(GO:"protein oxidation"))

        Term stmtSubject = new Term(FunctionEnum.PATHOLOGY,
                asBelObjs(new Parameter(meshd, "Atherosclerosis")));

        Statement.Object stmtObject =
                new Statement.Object(new Term(FunctionEnum.LIST,
                        asBelObjs(
                                new Term(FunctionEnum.BIOLOGICAL_PROCESS,
                                        asBelObjs(new Parameter(go,
                                                "lipid oxidation"))),
                                new Term(FunctionEnum.BIOLOGICAL_PROCESS,
                                        asBelObjs(new Parameter(go,
                                                "protein oxidation"))))));

        Statement s = new Statement(stmtSubject, null, null, stmtObject,
                RelationshipType.POSITIVE_CORRELATION);
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    @Test
    public void testModificationExpansions()
            throws RecognitionException {
        final ModificationExpansionRule rule = new ModificationExpansionRule();

        Term term;
        List<Statement> stmts;

        // valid substitution
        term = BELParser.parseTerm("p(HGNC:TNF,sub(V,599,E))");
        assertThat(rule.match(term), is(true));
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    /**
     * Test that a definitional statement doesn't match the rule.
     */
    @Test
    public void testMatchDefinitionalStatement() {
        Term a = new Term(PROTEIN_ABUNDANCE,
                Arrays.asList((BELObject) CommonModelFactory.getInstance()
                        .createParameter(null, "A")));
        Statement defStmt = new Statement(a);

        assertFalse(new DistributeStatementExpansionRule().match(defStmt));
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    /**
     * Test that a simple statement doesn't match the rule.
     */
    @Test
    public void testMatchSimpleStatement() {
        Term a = new Term(PROTEIN_ABUNDANCE,
                Arrays.asList((BELObject) CommonModelFactory.getInstance()
                        .createParameter(null, "A")));
        Term b = new Term(PROTEIN_ABUNDANCE,
                Arrays.asList((BELObject) CommonModelFactory.getInstance()
                        .createParameter(null, "B")));
        Statement simpleStmt = new Statement(a, null, null,
                new Statement.Object(b), INCREASES);

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    /**
     * Test that a nested statement does match the rule.
     */
    @Test
    public void testMatchNestedStatement() {
        Term a = new Term(PROTEIN_ABUNDANCE,
                Arrays.asList((BELObject) CommonModelFactory.getInstance()
                        .createParameter(null, "A")));
        Term b = new Term(GENE_ABUNDANCE,
                Arrays.asList((BELObject) CommonModelFactory.getInstance()
                        .createParameter(null, "B")));
        Term c = new Term(RNA_ABUNDANCE,
                Arrays.asList((BELObject) CommonModelFactory.getInstance()
                        .createParameter(null, "C")));

        Statement bc = new Statement(b, null, null, new Statement.Object(c),
                INCREASES);
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     * Test that a deeply-nested statement does not match the statement
     * expansion rule.
     */
    @Test
    public void testDeeplyNestedExpansion() {
        Term a = new Term(PROTEIN_ABUNDANCE,
                Arrays.asList((BELObject) CommonModelFactory.getInstance()
                        .createParameter(null, "A")));
        Term b = new Term(GENE_ABUNDANCE,
                Arrays.asList((BELObject) CommonModelFactory.getInstance()
                        .createParameter(null, "B")));
        Term c = new Term(RNA_ABUNDANCE,
                Arrays.asList((BELObject) CommonModelFactory.getInstance()
                        .createParameter(null, "C")));
        Term d = new Term(ABUNDANCE,
                Arrays.asList((BELObject) CommonModelFactory.getInstance()
                        .createParameter(null, "D")));
        Term e = new Term(CATALYTIC_ACTIVITY,
                Arrays.asList((BELObject) CommonModelFactory.getInstance()
                        .createParameter(null, "E")));

        Statement de = new Statement(d, null, null, new Statement.Object(e),
                INCREASES);
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    /**
     * Test the correct statement expansion for a singularly-nested statement.
     */
    @Test
    public void testSimpleNestedExpansion() {
        Term a = new Term(PROTEIN_ABUNDANCE,
                Arrays.asList((BELObject) CommonModelFactory.getInstance()
                        .createParameter(null, "A")));
        Term b = new Term(GENE_ABUNDANCE,
                Arrays.asList((BELObject) CommonModelFactory.getInstance()
                        .createParameter(null, "B")));
        Term c = new Term(RNA_ABUNDANCE,
                Arrays.asList((BELObject) CommonModelFactory.getInstance()
                        .createParameter(null, "C")));

        Statement bc = new Statement(b, null, null, new Statement.Object(c),
                INCREASES);
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        // Set term function
        Function f = source.getFunction();
        FunctionEnum funcEnum = fromString(f.value());

        // Destination type
        Term dest = new Term(funcEnum);

        // Schema defines either a list of arg values or terms
        List<JAXBElement> prmtrms = source.getParameterOrTerm();
        final List<BELObject> args = new ArrayList<BELObject>();

        final ParameterConverter pConverter = new ParameterConverter();
        for (final JAXBElement el : prmtrms) {
            if (el instanceof XBELParameter) {
                // Defer to ParameterConverter
                args.add(pConverter.convert((XBELParameter) el));
            } else if (el instanceof XBELTerm) {
                args.add(convert((XBELTerm) el));
            }
        }

        dest.setFunctionArguments(args);

        return dest;
    }
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    public XBELStatement convert(Statement source) {
        if (source == null) return null;

        XBELStatement xstmt = new XBELStatement();

        Term subject = source.getSubject();
        TermConverter tConverter = new TermConverter();
        XBELSubject xs = new XBELSubject();
        // Defer to TermConverter
        xs.setTerm(tConverter.convert(subject));
        xstmt.setSubject(xs);
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Related Classes of org.openbel.framework.common.model.Term

  • org.openbel.framework.api.DefaultDialect
  • org.openbel.framework.api.DefaultSpeciesDialect
  • org.openbel.framework.api.internal.KAMStoreDaoImpl
  • org.openbel.framework.api.KamBuilder
  • org.openbel.framework.api.Resolver
  • org.openbel.framework.common.bel.parser.BELStatementParser
  • org.openbel.framework.common.bel.parser.BELStatementParserTest
  • org.openbel.framework.common.enums.FunctionEnum
  • org.openbel.framework.common.InvalidArgument
  • org.openbel.framework.common.protonetwork.model.StatementTable
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