Adds evidence codes to a species in a model.
46 """usage: addingEvidenceCodes_2 <input-filename> <output-filename>
47 Adds controlled vocabulary term to a species
54 errors = d.getNumErrors();
57 print(
"Read Error(s):\n");
60 print(
"Correct the above and re-run.\n");
62 n = d.getModel().getNumSpecies();
64 print(
"Model has no species.\n Cannot add CV terms\n");
66 s = d.getModel().getSpecies(0);
71 if (
not s.isSetMetaId()):
72 s.setMetaId(
"metaid_0000052");
74 cv1 = CVTerm(BIOLOGICAL_QUALIFIER);
75 cv1.setBiologicalQualifierType(BQB_OCCURS_IN);
76 cv1.addResource(
"urn:miriam:obo.go:GO%3A0005764");
95 blank_att = XMLAttributes();
97 resource_att = XMLAttributes();
100 statement_triple = XMLTriple(
"Statement",
101 "http://www.w3.org/1999/02/22-rdf-syntax-ns#",
104 statement_token = XMLToken(statement_triple, blank_att);
106 statement = XMLNode(statement_token);
109 subject_triple = XMLTriple(
"subject",
110 "http://www.w3.org/1999/02/22-rdf-syntax-ns#",
113 resource_att.clear();
114 resource_att.add(
"rdf:resource",
"#" + s.getMetaId());
116 subject_token = XMLToken(subject_triple, resource_att);
118 subject = XMLNode(subject_token);
122 predicate_triple = XMLTriple(
"predicate",
123 "http://www.w3.org/1999/02/22-rdf-syntax-ns#",
126 resource_att.clear();
127 resource_att.add(
"rdf:resource",
128 "http://biomodels.net/biology-qualifiers/occursIn");
130 predicate_token = XMLToken(predicate_triple, resource_att);
132 predicate = XMLNode(predicate_token);
135 object_triple = XMLTriple(
"object",
136 "http://www.w3.org/1999/02/22-rdf-syntax-ns#",
139 resource_att.clear();
140 resource_att.add(
"rdf:resource",
"urn:miriam:obo.go:GO%3A0005764");
142 object_token = XMLToken(object_triple, resource_att);
144 object_ = XMLNode(object_token);
147 bqbiol_triple = XMLTriple(
"isDescribedBy",
148 "http://biomodels.net/biology-qualifiers/",
151 bqbiol_token = XMLToken(bqbiol_triple, blank_att);
153 bqbiol = XMLNode(bqbiol_token);
156 bag_triple = XMLTriple(
"Bag",
157 "http://www.w3.org/1999/02/22-rdf-syntax-ns#",
160 bag_token = XMLToken(bag_triple, blank_att);
162 bag = XMLNode(bag_token);
165 li_triple = XMLTriple(
"li",
166 "http://www.w3.org/1999/02/22-rdf-syntax-ns#",
169 resource_att.clear();
170 resource_att.add(
"rdf:resource",
"urn:miriam:obo.eco:ECO%3A0000004");
172 li_token = XMLToken(li_triple, resource_att);
175 li = XMLNode(li_token);
179 resource_att.clear();
180 resource_att.add(
"rdf:resource",
"urn:miriam:pubmed:7017716");
181 li_token = XMLToken(li_triple, resource_att);
183 li = XMLNode(li_token);
188 bqbiol.addChild(bag);
191 statement.addChild(subject);
192 statement.addChild(predicate);
193 statement.addChild(object_);
194 statement.addChild(bqbiol);
201 xmlns = XMLNamespaces();
202 xmlns.add(
"http://www.w3.org/1999/02/22-rdf-syntax-ns#",
"rdf");
203 xmlns.add(
"http://purl.org/dc/elements/1.1/",
"dc");
204 xmlns.add(
"http://purl.org/dc/terms/",
"dcterms");
205 xmlns.add(
"http://www.w3.org/2001/vcard-rdf/3.0#",
"vCard");
206 xmlns.add(
"http://biomodels.net/biology-qualifiers/",
"bqbiol");
207 xmlns.add(
"http://biomodels.net/model-qualifiers/",
"bqmodel");
209 RDF_triple = XMLTriple(
"RDF",
210 "http://www.w3.org/1999/02/22-rdf-syntax-ns#",
213 RDF_token = XMLToken(RDF_triple, blank_att, xmlns);
215 annotation = XMLNode(RDF_token);
218 annotation.addChild(statement);
220 s.appendAnnotation(annotation);
226 if __name__ ==
'__main__':