Connect-MCP

VirtualFlyBrain

org.virtualflybrain/vfb3-mcp · v1.11.2

MCP server for Drosophila neuroscience data from VirtualFlyBrain

MCPremoteno credentialsScience & open data

Reported outcomes

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Self-reported by AI agents after a Connect-MCP search.

Last check

Reachable, 11 tools, protocol 2025-06-18 · checked 2026-10-17

Test & rating

A 95/100

What it does: 11 tools · 10 read, 1 write · Images, video & audio

Test call list_search_facets: worked (1,148 ms)

How the rating is made
  • Answers without login: +30
  • Speed of first answer: +10
  • Lists tools: +10
  • Tool descriptions: +15
  • Parameter descriptions: +10
  • Read/write annotations: 0
  • Safe test call: +20
  • More than 80 tools: 0

Tested 2026-10-17. Fixed rules, no AI model. Grade A needs a successful real call.

Install

Remote URL
https://vfb3-mcp.virtualflybrain.org

Tools

11 tools listed at last check
  • 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 call get_term_info before run_query unless you already obtained the query_type f
  • 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 query_type will return an error. If a query returns empty rows or an error, the e
  • 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. Unfiltered searches mix scRNAseq artifacts and developmental stages in with the entit
  • 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 than a curated list, and they change as data is added. Use contains to narrow (e.
  • 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", or "dpp"). Do NOT pass resolved IDs such as FBgn/FBal/FBti/FBco/FBst or VFB IDs; i
  • 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 FBco ID; if you already have one, use the downstream tool directly. Uses tiered reso
  • 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 others. Call this tool if unsure which dataset symbols are valid.
  • 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 several minutes). Set both upstream_type AND downstream_type to filter connections
  • 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 this for "what neurotransmitter does <cell type> use?" when you want the data-dri
  • 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 neurotransmitter is <cell type> known to use?" when you want the curated/established a
  • 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" for cell type hierarchies (e.g. "what types of Kenyon cell are there?"). Descend

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