sparql

Helpers to construct and execute SPARQL queries against the UniProtKB SPARQL endpoint.

build_sparql_generic_by_uniprot_accessions_query(uniprot_accs, select_clause, where_clause, limit=10000, groupby_clause='')

Builds a generic SPARQL query and filters by the given UniProt accessions.

Parameters:

Name	Type	Description	Default
uniprot_accs	Iterable[str]	An iterable of UniProt accessions to filter by.	required
select_clause	str	The SELECT clause of the SPARQL query, without the "SELECT" keyword.	required
where_clause	str	The WHERE clause of the SPARQL query, without the "WHERE" keyword.	required
limit	int	The maximum number of results to return. Default is 10,000.	10000
groupby_clause		The GROUP BY clause of the SPARQL query, without the "GROUP BY" keyword.	''

Returns:

Type	Description
str	A string containing the complete SPARQL query.

build_sparql_generic_query(select_clause, where_clause, limit=10000, groupby_clause='')

Builds a generic SPARQL query with the given select and where clauses.

Parameters:

Name	Type	Description	Default
select_clause	str	The SELECT clause body of the SPARQL query, without the "SELECT" keyword.	required
where_clause	str	The WHERE clause body of the SPARQL query, without the "WHERE" keyword.	required
limit	int	The maximum number of results to return. Default is 10,000.	10000
groupby_clause		The GROUP BY clause of the SPARQL query, without the "GROUP BY" keyword.	''

Returns:

Type	Description
str	A string containing the complete SPARQL query.

execute_sparql_search(sparql_query, timeout)

Execute a SPARQL query.

Parameters:

Name	Type	Description	Default
sparql_query	str	The SPARQL query to execute.	required
timeout	int	Timeout for the SPARQL query in seconds. Must be less than 2700 seconds (45 minutes).	required

Returns:

Type	Description
list	A list of bindings returned by the SPARQL query.