Web of Biological Data

A queryable layer connecting biomedical knowledge graphs and dataset metadata.

WOBD links biomedical knowledge graphs so a single query can move across them. One member — the NIAID Data Ecosystem (NDE) — is unusual in that it indexes datasets rather than biology directly. That lets a query start from a mechanistic finding in one graph and end at the datasets you could analyze to investigate it further.

Other members supply the biology. The Gene Expression Atlas (GXA), for example, contributes differential-expression results across many diseases and tissues. WOBD is part of the wider Proto-OKN federation; today's templated queries cover NDE and GXA, while the unified MCP server reaches all 27 Proto-OKN graphs. Learn more

Two ways to query WOBD

Templated queries

Pick a template and fill in your search terms — genes, diseases, datasets, contrasts. The app assembles and executes the SPARQL for you. Currently covers NDE and GXA. Good for focused, reproducible workflows; no SPARQL required.

Browse templates

Unified MCP server

Connect an AI assistant — Claude, ChatGPT, VS Code — to a single Model Context Protocol server spanning all 27 Proto-OKN graphs. The assistant discovers graphs, inspects schemas, runs SPARQL, bridges identifiers, and combines results in conversation. Good for open-ended, cross-graph questions.

How to connect