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BioThings Explorer Autonomous Relay Agent Page

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.

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

BTE is registered on SmartAPI here. If you would like to deploy your own instance, see the installation documentation.

Use Cases

echo '{
  "message": {
    "query_graph": {
      "nodes": {
        "n02": {
          "categories": [
            "biolink:Disease"
          ],
          "ids": [
            "MONDO:0005148"
          ]
        },
        "n01": {
          "categories": [
            "biolink:ChemicalEntity"
          ]
        }
      },
      "edges": {
        "e01": {
          "subject": "n01",
          "object": "n02",
          "predicates": [
            "biolink:treats"
          ],
          "knowledge_type": "inferred"
        }
      }
    }
  }
}
' > creative.json

# An inferred-mode query
curl -X POST \
"https://bte.transltr.io/v1/query" \
-H "Content-Type: application/json" \
-H "accept: application/json" \
-d @creative.json

Knowledge Providers Accessed

BioThings Explorer maintains an allow-list of Knowledge Providers, see here.

Source Code

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