Output

BioCypher development was initially centred around a Neo4j graph database output due to the migration of OmniPath to a Neo4j backend. Importantly, we understand BioCypher as an abstraction of the build process of a biomedical knowledge graph, and thus are open towards any output format for the knowledge representation. We are currently working on other output formats, such as RDF, SQL, and ArangoDB, and will update the documentation accordingly.

The used output format is specified via the dbms parameter in the biocypher_config.yaml (see the Configuration for an example). Currently supported are neo4j, arangodb, rdf, csv, postgres, sqlite, and networkx.

Furthermore, you can specify whether to use the offline or online mode.

• For the online mode set offline: false. You need a running database instance and BioCypher will connect to this instance and directly writes the output to the database.

• For the offline mode set offline: true. BioCypher will output.write the knowledge graph to files in a designated output folder (standard being biocypher-out/ and the current datetime). Furthermore you can generate a bash script to insert the knowledge graph files into the specified dbms by running bc.write_import_call().

Caution

The online mode is currently only supported for the neo4j database.

Details about the usage of the online and offline mode and the different supported output formats are described on the following pages:

• Neo4j
  • Install Neo4j
  • Neo4j settings
  • Offline mode
  • Online mode
• ArangoDB
• CSV
  • CSV settings
  • Offline mode
• RDF
  • RDF settings
• PostgreSQL
  • Install PostgreSQL
  • PostgreSQL settings
  • Offline mode
• SQLite
  • SQLite settings
  • Offline mode
• NetworkX
  • NetworkX settings
  • Offline mode