biocypher.BioCypher

class biocypher.BioCypher(dbms: str = None, offline: bool = None, strict_mode: bool = None, biocypher_config_path: str = None, schema_config_path: str = None, head_ontology: dict = None, tail_ontologies: dict = None, output_directory: str = None, cache_directory: str = None, db_name: str = None)

Orchestration of BioCypher operations.

Instantiate this class to interact with BioCypher.

Args:

dbms (str): The database management system to use. For supported

systems see SUPPORTED_DBMS.

offline (bool): Whether to run in offline mode. In offline mode

the Knowledge Graph is written to files. In online mode, it is written to a database or hold in memory.

strict_mode (bool): Whether to run in strict mode. If True, the

translator will raise an error if a node or edge does not provide source, version, and licence information.

biocypher_config_path (str): Path to the BioCypher config file.

schema_config_path (str): Path to the user schema config

file.

head_ontology (dict): The head ontology defined by URL (‘url’) and root

node (‘root_node’).

tail_ontologies (dict): The tail ontologies defined by URL and

join nodes for both head and tail ontology.

output_directory (str): Path to the output directory. If not

provided, the default value ‘biocypher-out’ will be used.

cache_directory (str): Path to the cache directory.

__init__(dbms: str = None, offline: bool = None, strict_mode: bool = None, biocypher_config_path: str = None, schema_config_path: str = None, head_ontology: dict = None, tail_ontologies: dict = None, output_directory: str = None, cache_directory: str = None, db_name: str = None)

Methods

__init__([dbms, offline, strict_mode, ...])
add(entities)	Add entities to the in-memory database.
add_edges(edges)	Add new edges to the internal representation.
add_nodes(nodes)	Add new nodes to the internal representation.
download(*resources)	Download or load from cache the resources given by the adapter.
get_kg()	Get the in-memory KG instance.
log_duplicates()	Log duplicate nodes and edges.
log_missing_input_labels()	Log missing input labels.
merge_edges(edges)	Merge edges into database.
merge_nodes(nodes)	Merge nodes into database.
reverse_translate_query(query)	Reverse translate a query from its BioCypher equivalent.
reverse_translate_term(term)	Reverse translate a term from its BioCypher equivalent.
show_ontology_structure(**kwargs)	Show the ontology structure using treelib or write to GRAPHML file.
summary()	Call convenience and reporting methods.
to_df()	Create DataFrame using internal representation.
to_networkx()	Create networkx using internal representation.
translate_query(query)	Translate a query to its BioCypher equivalent.
translate_term(term)	Translate a term to its BioCypher equivalent.
write_edges(edges[, batch_size])	Write edges to database.
write_import_call()	Write a shell script to import the database.
write_nodes(nodes[, batch_size, force])	Write nodes to database.
write_schema_info([as_node])	Write an extended schema info to file or node.