VirtualFlyBrain

Connect Remote server

claude mcp add --transport http vfb3-mcp https://vfb3-mcp.virtualflybrain.org

{
  "mcpServers": {
    "vfb3-mcp": {
      "url": "https://vfb3-mcp.virtualflybrain.org"
    }
  }
}

{
  "servers": {
    "vfb3-mcp": {
      "type": "http",
      "url": "https://vfb3-mcp.virtualflybrain.org"
    }
  }
}

Settings > Connectors > Add custom connector
URL: https://vfb3-mcp.virtualflybrain.org

Tools 11 found in our 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 obta…

• 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 ro…

• 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 stag…

• 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 c…

• 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/FB…

• 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 direc…

• 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 va…

• 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 t…

• 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…

• 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…

• 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…

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