Package org.openbel.framework.common.model

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

97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
        final List<TableStatement> stmts = st.getStatements();
        final Map<Integer, Statement> si = st.getIndexedStatements();

        final List<Statement> expansions = new ArrayList<Statement>();
        for (int i = 0, n = stmts.size(); i < n; i++) {
            final Statement stmt = si.get(i);

            // expand subject term
            expandTerm(stmt.getSubject(), expansions);

            if (stmt.getObject() != null) {
                if (stmt.getObject().getTerm() != null) {
                    // expand the rest of simple statement
                    expandTerm(stmt.getObject().getTerm(), expansions);
                } else {
                    // expand the rest of nested statement
                    final Term nsub = stmt.getObject().getStatement()
                            .getSubject();
                    final Term nobj = stmt.getObject().getStatement()
                            .getObject().getTerm();

                    expandTerm(nsub, expansions);
                    expandTerm(nobj, expansions);
                }
View Full Code Here
146
147
148
149
150
151
152
153
154
155
156
        final StatementTable st = pn.getStatementTable();
        final List<TableStatement> ts = st.getStatements();
        final Map<Integer, Statement> index = st.getIndexedStatements();

        for (int i = 0, n = ts.size(); i < n; i++) {
            final Statement stmt = index.get(i);

            if (stmt == null) {
                continue;
            }
View Full Code Here
97
98
99
100
101
102
103
104
105
106
107
108
        Term abundance = (Term) firstArgument; // only argument of a moleculary
                                               // activity term is the abundance
        // Molecular activities connect to its abundance term with ACTS_IN
        // relationship
        final Object obj = new Object(activity);
        Statement statement =
                new Statement(abundance, null, null, obj, ACTS_IN);
        attachExpansionRuleCitation(statement);
        statements.add(statement);

        return statements;
    }
View Full Code Here
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
    @Override
    public List<Statement> expand(Statement statement) {
        List<Statement> statements = new ArrayList<Statement>();

        // A -> (B -> C) implies A
        Statement definitional = new Statement(statement.getSubject());
        attachExpansionRuleCitation(definitional);
        statements.add(definitional);

        // A -> (B -> C) implies B -> C
        Statement object = statement.getObject().getStatement();
        Statement extracted = new Statement(object.getSubject());
        extracted.setRelationshipType(object.getRelationshipType());
        extracted.setObject(new Statement.Object(object.getObject().getTerm()));
        attachExpansionRuleCitation(extracted);
        statements.add(extracted);

        return statements;
    }
View Full Code Here
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
        // all reactants connect to reaction with REACTANT_IN relationship
        for (BELObject reactant : reactants.getFunctionArguments()) {
            Term sub = (Term) reactant;
            Object obj = new Object(reaction);
            Statement stmt = new Statement(sub, null, null, obj, REACTANT_IN);
            attachExpansionRuleCitation(stmt);
            statements.add(stmt);
        }

        // a reaction connects to its products with HAS_PRODUCT relationship
        for (BELObject product : products.getFunctionArguments()) {
            Term sub = (Term) product;
            Object obj = new Object(sub);
            Statement stmt =
                    new Statement(reaction, null, null, obj, HAS_PRODUCT);
            attachExpansionRuleCitation(stmt);
            statements.add(stmt);
        }

        return statements;
View Full Code Here
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
    @Override
    public List<Statement> expand(Statement statement) {
        List<Statement> statements = new ArrayList<Statement>();

        // A -> (B -> C) implies B -> C
        Statement object = statement.getObject().getStatement();
        Statement s1 = new Statement(object.getSubject());
        s1.setRelationshipType(object.getRelationshipType());
        s1.setObject(new Statement.Object(object.getObject().getTerm()));
        attachExpansionRuleCitation(s1);
        statements.add(s1);

        // A -> (B -> C) implies A -> C
        Statement s2 = new Statement(statement.getSubject());
        s2.setRelationshipType(resolveMediatedRelationship(
                statement.getRelationshipType(), object.getRelationshipType()));
        s2.setObject(new Statement.Object(object.getObject().getTerm()));
        attachExpansionRuleCitation(s2);
        statements.add(s2);

        return statements;
    }
View Full Code Here
99
100
101
102
103
104
105
106
107
108
109
110
                                             // degradation term is the protein

        // Protein degradation term connects to its protein with
        // DIRECTLY_DECREASES relationship
        final Object obj = new Object(protein);
        Statement statement =
                new Statement(degradation, null, null, obj, DIRECTLY_DECREASES);
        attachExpansionRuleCitation(statement);
        statements.add(statement);

        return statements;
    }
View Full Code Here
98
99
100
101
102
103
104
105
106
107
108
        // compositeAbundance connects to its abundance terms with INCLUDES
        // relationship
        for (BELObject o : term.getFunctionArguments()) {
            Term t = (Term) o; // component of the composite term
            final Object obj = new Object(t);
            Statement s = new Statement(term, null, null, obj, INCLUDES);
            attachExpansionRuleCitation(s);
            statements.add(s);
        }
        return statements;
    }
View Full Code Here
308
309
310
311
312
313
314
315
316
317
318
319
320
321
322
323
324
325
326
327
328
329
330
331
332
333
334
335
336
337
338
                                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);

        try {
            subject.checkListUsage(s1, null);
            subject.checkListUsage(s2, null);
View Full Code Here
374
375
376
377
378
379
380
381
382
383
384
                                                "lipid oxidation"))),
                                new Term(FunctionEnum.BIOLOGICAL_PROCESS,
                                        asBelObjs(new Parameter(go,
                                                "protein oxidation"))))));

        Statement s = new Statement(stmtSubject, null, null, stmtObject,
                RelationshipType.POSITIVE_CORRELATION);

        subject.checkListUsage(s, null);
        fail("expected semantic failure");
    }
View Full Code Here
TOP

Related Classes of org.openbel.framework.common.model.Statement

  • org.openbel.framework.common.bel.converters.BELStatementConverter
  • org.openbel.framework.common.bel.parser.BELStatementParser
  • org.openbel.framework.common.InvalidArgument
  • org.openbel.framework.common.protonetwork.model.StatementTable
  • org.openbel.framework.common.xbel.converters.StatementConverter
  • org.openbel.framework.compiler.PhaseThreeImpl
  • org.openbel.framework.core.compiler.expansion.ComplexAbundanceExpansionRule
  • org.openbel.framework.core.compiler.expansion.CompositeAbundanceExpansionRule
  • org.openbel.framework.core.compiler.expansion.DegradationExpansionRule
  • org.openbel.framework.core.compiler.expansion.DistributeStatementExpansionRule
    • Copyright © 2018 www.massapicom. All rights reserved.
    All source code are property of their respective owners. Java is a trademark of Sun Microsystems, Inc and owned by ORACLE Inc. Contact coftware#gmail.com.