Enables alignment of world-reference entities (Taxon, ChemicalEntityTerm, Country) to Wikidata via SPARQL search, resolving wikidataId / skos:exactMatch keys through the wikidata_alignment_search tool.
Click on "Deploy Server".
Wait a few minutes for the server to deploy. Once ready, it will show a "Started" state.
In the chat, type @ followed by the MCP server name and your instructions, e.g., "@world-reference-mcp look up the NCBI taxonomy entry for the red fox"
That's it! The server will respond to your query, and you can continue using it as needed.
Here is a step-by-step guide with screenshots.
Version: 0.1.0
World-reference data — organism taxonomy, OBO reference terms, food/nutrition
composition, organism and weather observations, and Wikidata alignment — as an
MCP tool surface and, through agent-connector-sdk's declarative mcp_tool
source adapter, as bounded, checkpointed ingestion streams onto the
epistemic-graph world_model ontology (feat/world-model-ontology).
Ledger row | Sources | Target class |
EH-358 (taxonomy) | NCBI Taxonomy (E-utilities), GBIF backbone |
|
EH-359 (reference terms) | EBI OLS4 (GO, UBERON, ENVO, PATO, ChEBI, FoodOn) |
|
EH-360 (nutrition) | USDA FoodData Central |
|
EH-361 (observations) | GBIF occurrences, iNaturalist, Open-Meteo, NOAA GHCND |
|
EH-362 (alignment) | Wikidata SPARQL |
|
Related MCP server: BioMCP
Nine MCP tools, one FastMCP server (world-reference-mcp console script):
taxonomy_ncbi_search, taxonomy_gbif_search, reference_term_list,
fdc_food_search, gbif_occurrence_search, inaturalist_observation_search,
open_meteo_weather_observation, noaa_ghcnd_daily, wikidata_alignment_search.
Every tool is keyless except fdc_food_search and noaa_ghcnd_daily, whose
credentials are resolved server-side through agent_connector_sdk.credentials
(WORLD_REFERENCE_FDC_API_KEY, WORLD_REFERENCE_NOAA_TOKEN) — never accepted
as a tool argument.
See AGENTS.md for architecture, the ontology-mapping
authority, rate limits, and commands.
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