is a Knowledge Graph.
BioBTree is a unified biomedical knowledge graph that integrates more than 70 primary data sources, including Ensembl, UniProt, PDB, ChEMBL, Reactome, and ClinVar, into a single queryable graph of cross-reference edges spanning genes, proteins, compounds, diseases, pathways, and clinical data. It lets users search, map, and traverse identifiers across databases with a chain-query syntax (for example, mapping a gene in Ensembl to UniProt proteins and on to PDB structures), and exposes the graph through a REST API, a Model Context Protocol (MCP) server, and a question-answering web interface for grounding LLM responses in structured biomedical data.
biomedical, genomics, proteomics, pathways, drug discovery, clinical
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Tamer Gur
Github: tamerh
| ID | Name | URL | Category | Format | Description |
|---|---|---|---|---|---|
| biobtree.graph.human-subgraph | BioBTree Knowledge Graph - Human Subgraph (KGX) | 20816742 | Graph | kgx | Human-scoped, Neo4j-ready subgraph of... |
| biobtree.api | BioBTree REST API | api | Programming Interface | http | REST API for searching identifiers an... |
| biobtree.mcp | BioBTree MCP Server | mcp | Programming Interface | http | Model Context Protocol (MCP) server e... |
| biobtree.qa | BioBTree Q&A Interface | biobtree | Graphical Interface | http | Web-based question-and-answer interfa... |
| biobtree.docs | BioBTree Repository and Documentation | biobtree | Documentation | http | Source code, dataset documentation, a... |
| ID | Name | URL | Category | Format | Relation | Description |
|---|---|---|---|---|---|---|
| sugi-atlas.portal | Sugi Atlas Web Site | atlas | Graphical Interface | http | was derived from | Sugi Atlas web site with search and o... |
| sugi-atlas.manifest | Sugi Atlas Manifest | manifest.json (12.2 MB) | Product | json | was derived from | JSON manifest of the atlas corpus, ma... |
BioBTree is a unified biomedical knowledge graph that integrates more than 70 primary data sources into a single queryable graph of cross-reference edges. It spans genes, proteins, compounds, diseases, pathways, and clinical data from resources such as Ensembl, UniProt, PDB, ChEMBL, Reactome, and ClinVar.
Users can search identifiers and special keywords, map between databases using a chain-query syntax, and traverse connections across resources in a single query. BioBTree is accessible through a REST API, a Model Context Protocol (MCP) server for AI and LLM integration, and a question-answering web interface designed to ground LLM responses in authoritative, identifier-anchored biomedical data.
Created: June 15, 2026 | Last modified: June 24, 2026