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MCP server for Drosophila neuroscience data from VirtualFlyBrain
Facts
- MCP registry
org.virtualflybrain/vfb3-mcp· 1.11.2- Endpoint
https://vfb3-mcp.virtualflybrain.org- Website
- virtualflybrain.org
- GitHub stars
- 9
- Registry entry
- updated 10 Sep 2026
From the official MCP registry, the package registries and our own checks. JSON · Markdown
Why it's listed
- It's published in the registry under virtualflybrain.org, a namespace the registry only gives to whoever proves they control that domain.
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Tools it lists 11 · about 5,957 tokens of context · checked 10 minutes ago
| Tool | What it does | Hint |
|---|---|---|
get_term_info | Get term info for a VFB or anatomy ontology entity (VFB_*, FBbt_*, etc.). THIS IS THE QUERY DISCOVERY TOOL: the response's "Queries" array lists the valid query_type values that run_query accepts for this entity. ALWAYS… | |
run_query | Run a pre-computed query on a VFB entity. REQUIRED WORKFLOW: (1) call get_term_info on the ID first; (2) read the response's "Queries" array; (3) pass one of those values as query_type. Calling run_query with a guessed… | |
search_terms | Search VFB terms. This is the search virtualflybrain.org itself runs — the same Solr query, the same ranking — so what comes back first here is what a user would see first on the site. USE filter_types BY DEFAULT.… | |
list_search_facets | List the type names search_terms can filter, exclude, boost or demote by, with the number of terms carrying each one. Call this instead of guessing: there are over 200 names, they are the index's own annotations rather… | |
resolve_entity | Resolve an unresolved FlyBase-related query string into VFB/FlyBase IDs and metadata. Pass the raw text exactly as the user wrote it (for example "P{VT054895-GAL4.DBD}", "Hb9-GAL4", "SS04495", "MB002B", "PAM cluster",… | |
resolve_combination | Resolve an unresolved split-GAL4 combination name or synonym into its FBco ID and component hemidrivers. Pass the raw combination text exactly as the user wrote it (for example "MB002B" or "SS04495"). Do NOT pass an… | |
list_connectome_datasets | List available connectome datasets with their labels and symbols. Use the returned symbols when constructing exclude_dbs arguments for query_connectivity. Common datasets include Hemibrain (hb), FAFB (fafb), MANC, and… | |
query_connectivity | Query synaptic connectivity between Drosophila neuron classes across ALL connectome datasets simultaneously for comparative connectomics. This is NOT pre-cached — it runs live queries, so expect slow responses (up to… | |
get_predicted_neurotransmitters | Get the PREDICTED neurotransmitter(s) for a Drosophila neuron class — itself or any subclass — from per-instance connectome predictions (each reconstructed neuron carries a predicted transmitter with a confidence). Use… | |
get_known_neurotransmitters | Get the KNOWN (curated) neurotransmitter(s) for a Drosophila neuron class and its subclasses, from the ontology's classification rather than per-instance predictions — so there is no confidence. Use this for "what… | |
get_hierarchy | Build a hierarchy tree for a VFB term, showing ancestors (parents) and/or descendants (children). Use relationship "part_of" for brain region structure (e.g. "what are the parts of the mushroom body?") and "subclass_of"… |
What https://vfb3-mcp.virtualflybrain.org answered to tools/list, asked without credentials over MCP 2025-11-25. The token figure is the size of the list as sent, divided by four; a model sees about that much before it calls anything. Full definitions, input schemas included, are in the listing's JSON under mcpTools.
How its tools read to an agent 0 errors · 15 warnings · 1 note
- warnTC07query_connectivitythe description is about 566 tokens
- warnTC07run_querythe description is about 551 tokens
- warnTC07search_termsthe description is about 649 tokens
- warnTC14query_connectivityallowed values are in the description, not an enum: upstream_type
- warnTC16get_hierarchyno readOnlyHint or destructiveHint
- warnTC16get_known_neurotransmittersno readOnlyHint or destructiveHint
- warnTC16get_predicted_neurotransmittersno readOnlyHint or destructiveHint
- warnTC16get_term_infono readOnlyHint or destructiveHint
- warnTC16list_connectome_datasetsno readOnlyHint or destructiveHint
- warnTC16list_search_facetsno readOnlyHint or destructiveHint
- warnTC16query_connectivityno readOnlyHint or destructiveHint
- warnTC16resolve_combinationno readOnlyHint or destructiveHint
- warnTC16resolve_entityno readOnlyHint or destructiveHint
- warnTC16run_queryno readOnlyHint or destructiveHint
- warnTC16search_termsno readOnlyHint or destructiveHint
- noteTC24server11 of 11 tools have no outputSchema
The checks from /check and anchor check, run each day on the list above: about 5,957 tokens of definitions. Not part of the score yet. Check your own server.