BioThings Explorer (BTE)

Homepage URL: https://explorer.biothings.io

Description

BioThings Explorer (BTE) is an application supported by Exploring Agent. The service queries a virtual, federated knowledge graph derived from the aggregated information in a network of biomedical web services. BTE leverages semantically precise annotations of the inputs and outputs for each resource (captured in the SmartAPI registry) and automates the chaining of web service calls to execute multi-step graph queries. Because there is no large, centralized knowledge graph to maintain, BTE is distributed as a lightweight application that dynamically retrieves information at query time. More information about BioThings Explorer can be found at https://explorer.biothings.io.

BTE's "creative mode" (which is called by the Tranlator UI to generate inferred relationships) is based on a series of explicitly-defined query templates, available here.

The scoring/ranking of results in BTE incorporates a number of factors, including:

• the number of paths connecting the query node to the answer node
• the length of each path
• the number of redundant paths/edges
• the provenance of the edges (e.g., text-mined versus curated)
• the Normalized Google Distance between nodes in the path

Team Contacts

• Andrew Su
• Chunlei Wu

Source Code

• https://github.com/biothings/biothings_explorer - Primary code repository for BioThings Explorer

Additional Links

• Exploring Agent
• Preprint: BioThings Explorer: a query engine for a federated knowledge graph of biomedical APIs
• BioThings Explorer Home Page