Running this code:
import owlready2 as or2
or2.onto_path.append("../../data/ontologies/")
mondo_ontology = or2.get_ontology("../../data/ontologies/mondo.owl").load()
icd10cm_ontology = or2.get_ontology("../../data/ontologies/icd10cm_rdfxml.owl").load()
query = """
PREFIX MONDO: <
http://purl.obolibrary.org/obo/MONDO_>
PREFIX ICD10CM: <
http://purl.bioontology.org/ontology/ICD10CM/>
PREFIX skos: <
http://www.w3.org/2004/02/skos/core#>
INSERT {
MONDO:0000088 skos:exactMatch ICD10CM:E30.1 .
}
"""
or2.default_world.sparql(query)
I get:
{
"name": "ParsingError",
"message": "('Error at $end', None)",
"stack": "---------------------------------------------------------------------------
ParsingError Traceback (most recent call last)
Cell In[32], line 15
5 for index, row in df.iterrows():
6 query = \"\"\"
7 PREFIX MONDO: <
http://purl.obolibrary.org/obo/MONDO_>
8 PREFIX ICD10CM: <
http://purl.bioontology.org/ontology/ICD10CM/>
(...)
13 }
14 \"\"\"
---> 15 or2.default_world.sparql(query)
File /usr/local/lib/python3.11/site-packages/owlready2/namespace.py:466, in World.sparql(self, sparql, params, error_on_undefined_entities, spawn)
465 def sparql(self, sparql, params = (), error_on_undefined_entities = True, spawn = False):
--> 466 return self._prepare_sparql(sparql, error_on_undefined_entities).execute(params, None, spawn)
File /usr/local/lib/python3.11/site-packages/owlready2/namespace.py:471, in World._prepare_sparql(self, sparql, error_on_undefined_entities)
468 @lru_cache(maxsize = 1024)
469 def _prepare_sparql(self, sparql, error_on_undefined_entities):
470 import owlready2.sparql.main
--> 471 return owlready2.sparql.main.Translator(self, error_on_undefined_entities).parse(sparql)
File /usr/local/lib/python3.11/site-packages/owlready2/sparql/main.py:61, in Translator.parse(self, sparql)
59 self.escape_mark += \"รง\"
60 CURRENT_TRANSLATOR.set(self)
---> 61 self.main_query = PARSER.parse(LEXER.lex(sparql))
62 return self.finalize()
File /usr/local/lib/python3.11/site-packages/owlready2/rply.py:451, in LRParser.parse(self, tokenizer, state)
449 raise AssertionError(\"For now, error_handler must raise.\")
450 else:
--> 451 raise ParsingError(\"Error at %s\" % lookahead, lookahead.source_pos)
ParsingError: ('Error at $end', None)"
}
What am I doing wrong? Any help would be appreciated. Thank you.
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