From fe7f7b928a5bed0548cfa8e8afa5a03953c037cd Mon Sep 17 00:00:00 2001
From: Carlos Vega <carlos.vega@uni.lu>
Date: Tue, 19 Nov 2019 14:48:01 +0100
Subject: [PATCH] added possibility to filteer by type
---
biokb/biokb.py | 13 +++++++++++--
1 file changed, 11 insertions(+), 2 deletions(-)
diff --git a/biokb/biokb.py b/biokb/biokb.py
index db7ea41..11c65bb 100644
--- a/biokb/biokb.py
+++ b/biokb/biokb.py
@@ -58,7 +58,13 @@ class BioKBservice(TextMiningService):
return values
- def get_co_occurrences(self, entity: str, limit: int = 20) -> List[CoOccurrence]:
+ def get_co_occurrences(self, entity: str, limit: int = 20, types: List[str] = []) -> List[CoOccurrence]:
+
+ entity_types_filter = ''
+ if len(types) > 0:
+ types_str = ', '.join((f'<{t}>' for t in types))
+ entity_types_filter = f'FILTER (?e_type IN ({types_str}) )'
+
entity = standarise_underscored_entity_code(entity)
query = """
select * where {
@@ -68,6 +74,8 @@ class BioKBservice(TextMiningService):
?s <http://lcsb.uni.lu/biokb#containsEntity> <http://lcsb.uni.lu/biokb/entities/%ENTITY%> .
?s a <http://lcsb.uni.lu/biokb#Publication> .
?s <http://lcsb.uni.lu/biokb#containsEntity> ?other_entity .
+ ?other_entity a ?e_type .
+ %ENTITY_TYPE_FILTER%
OPTIONAL {?ss rdfs:subClassOf ?other_entity} .
@@ -88,7 +96,8 @@ class BioKBservice(TextMiningService):
GROUP BY ?other_entity
} ORDER BY DESC(?count) LIMIT %LIMIT%
- """.replace('%ENTITY%', entity).replace('%LIMIT%', str(limit))
+ """.replace('%ENTITY%', entity).replace('%LIMIT%', str(limit)).replace('%ENTITY_TYPE_FILTER%', entity_types_filter)
+ print(query)
results = self._run_sparql_query(query)
values = []
values = []
--
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