GrEBI
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Overview
Integrative querying across multiple biomedical knowledge graphs, utilizing ontologies and LLM embeddings, accessible via a web API and UI.
Installation
docker-compose upEnvironment Variables
- GREBI_NEO_DATA_PATH
- GREBI_SOLR_PATH
- GREBI_SQLITE_SEARCH_PATH
- GREBI_METADATA_JSON_SEARCH_PATH
- GREBI_PREFIX_MAP_PATH
- GREBI_CONTEXT_PATH
- PUBLIC_URL
- REACT_APP_APIURL
- REACT_APP_ENV
Security Notes
The application generally employs good security practices, such as parameterized queries for Neo4j and Solr, and input validation against query templates, which mitigates common injection risks. Solr queries use `ClientUtils.escapeQueryChars` for user-provided strings. However, Neo4j is configured with `NEO4J_AUTH=none` in deployments, making the database inherently unsecured and relying entirely on external network isolation for protection. The `GrebiNeoRepo.rawQuery` method directly executes Cypher queries, which could be a risk if used with unsanitized user input, though its current visible uses appear to be with trusted internal queries.
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