RTX KG2

Description: RTX-KG2 (Reasoning Tool X, Knowledge Graph Generation Two) is the second-generation knowledge graph for the ARAX biomedical reasoning system. Knowledge sources: A list of knowledge sources, including descriptions of each, can be found here.

Technical details: This Github repository contains all of the code for building KG2 as well as all of the documentation about how to build, host, access, and use KG2. The KG2 build system produces knowledge graphs in a Biolink model standard-compliant JSON format and in a tab-separated value (TSV) format that can be imported into a Neo4j graph database system. Through additional scripts in the ARAX kg2c subdirectory, the build system can produce a "canonicalized" knowledge graph where synonym concepts (nodes) are identified. Through additional scripts in the mediKanren subdirectory, the build system can produce an export of the KG2 knowledge graph that is suitable for importing into the mediKanren biomedical reasoning system.

Example edge:

Additional Links:

• Expander Agent wiki page
• Issue Tracker
• Wood, E.C., Glen, A.K., Kvarfordt, L.G. et al. RTX-KG2: a system for building a semantically standardized knowledge graph for translational biomedicine. BMC Bioinformatics 23, 400 (2022). https://doi.org/10.1186/s12859-022-04932-3
• The preprint can be found at: doi:10.1101/2021.10.17.464747