KGX

Knowledge Graph eXchange (KGX) is a Python tool for working with and sharing Biolink Model compliant knowledge graphs. KGX is capable of reading and transforming a knowledge graph (KG) from a Neo4j instance or from various serialization formats like TSV, JSON, JSON Lines, OBOGraph JSON, TRAPI JSON, and RDF N-Triples. KGX can be run in two distinct modes: Streaming, where a graph is streamed from one form to another, and No streaming, where the entire graph is loaded into memory first, before continuing with other operations. In addition to transformations, KGX provides a suite of graph operations that can be applied to a KG: for example, clique merge, graph merge, and identifier remapping. KGX can be also used to generate graph summary reports which describe the composition of a given KG. For the purpose of schema validation, KGX provides a validator that can be used to validate your knowledge graph for Biolink Model compliance.

The codebase can be found at https://github.com/biolink/kgx and latest releases are available on https://pypi.org/project/kgx. KGX is also available as a Docker container at https://hub.docker.com/repository/docker/biolink/kgx. The complete documentation on KGX is available at https://kgx.readthedocs.io/. KGX designates both a standard text format for the Biolink Model compliant knowledge graph (KG) data in between different implementation of that KG data (of which there are several). In addition, KGX also stands for the software program that interconverts KG data in between the different implementations and the KGX file format (either way) while also performing basic validation of the KG data. In fact, KGX also uses BMT to access the Biolink Model.