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verified live · 26h ago
vfb3-mcp
MCP server for Drosophila neuroscience data from VirtualFlyBrain
Tools
9
GitHub stars
2
Installs / wk
—
Licence
MIT
Transport
streamable-http
Last checked
26h ago
Tools & capabilities
9 toolsRead from the running server on 26h ago.
get_hierarchy
id*directionmax_depthrelationship*
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… 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?"). Descendants are returned as a nested tree for both relationship types. Ancestors are returned as a nested chain, filtered to nervous system terms for part_of. Start with max_depth=1 for direct parents/children, and offer to go deeper if the user wants more detail.
get_term_info
id*force_refresh
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 ru… 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 from a previous get_term_info call in this conversation. Returns: SuperTypes (classification), Tags (data flags like has_image, has_neuron_connectivity), Queries (valid query_types for run_query), RelatedTools (other MCP tools applicable to this entity, with default_args ready to copy — e.g. get_hierarchy with subclass_of for cell types or part_of for nervous-system regions), Images (keyed by template brain ID), Publications, Synonyms. Supports batch — pass an array of IDs to fetch in parallel; batch results are returned as a JSON object keyed by ID. To build VFB browser URLs from the Images field: https://v2.virtualflybrain.org/org.geppetto.frontend/geppetto?id=<VFB_ID>&i=<TEMPLATE_ID>,<IMAGE_ID1>,<IMAGE_ID2> — id= sets the focus term and i= lists images for the 3D viewer (template ID must be first in i= to set the coordinate space).
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 H… 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.
list_search_facets
contains
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… 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.g. contains="lineage" for the ~120 lineage clones, contains="connectivity" to find the connectome facets). The counts tell you whether a name is broad or niche — "entity" covers everything, a single lineage covers a handful.
query_connectivity
limitoffsetweightexclude_dbsupstream_typegroup_by_class
+1
Query synaptic connectivity between Drosophila neuron classes across ALL connectome datasets simultaneously for comparative connectomics. This is NOT pre-cached — it runs live quer… 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 between two specific neuron classes (e.g., "What Tm1→T3 connections exist across all datasets?"). At least one of upstream_type or downstream_type is required. CONSTRAINTS: Only accepts neuron class terms (OWL IDs like FBbt_00003789 or labels like "transmedullary neuron Tm1") — anatomical regions or neuropils (e.g., "lobula", "medulla") are NOT accepted. NOT suitable for individual neuron-to-neuron connections — for pre-computed connections of a single individual neuron, use run_query with NeuronNeuronConnectivityQuery instead. NOT for muscle/sense organ connections. RECOMMENDED DEFAULTS: weight=5, exclude_dbs=["hb","fafb"] unless user specifies otherwise. For both-ends queries, start with weight≥50 to avoid timeouts. RESULT SIZE: a broad query is enormous (a single class at weight=5 can be over 50,000 connections), so results are ranked strongest-first and paged — you get limit rows (default 50) plus a summary computed over ALL of them: totals, per-dataset counts, distinct neuron counts, and the top class pairs. Answer from the summary and quote a handful of rows; only page with offset if the user asks for specific further rows. WORKFLOW: Confirm parameters with user before querying. Use search_terms with filter_types ["neuron","class"] to validate/canonicalize neuron type labels. If zero results, try relaxation: lower weight to 1, then remove exclude_dbs filter, then try group_by_class=true — report what worked and let user decide. group_by_class=true is usually the better first call on a broad query: it aggregates to class pairs instead of returning every neuron pair.
resolve_combination
name*
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 "MB… 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 resolution: exact name → synonym → broad pattern match. Returns FBco ID, combination name, matched synonym (if applicable), and component allele IDs/names. IMPORTANT: When match is via synonym, confirm the resolved combination with the user before proceeding (e.g., "Your search for 'MB002B' matched [formal name] (FBco...) via synonym. Shall I proceed?"). If multiple matches, show disambiguation list and ask user to choose.
resolve_entity
name*
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"… 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; if you already have an ID, use the downstream tool directly. Uses tiered resolution: exact name → synonym → broad pattern match. Returns match_type (EXACT/SYNONYM/BROAD), feature ID, name, type, and synonyms. IMPORTANT: When match_type is SYNONYM or BROAD, always confirm the resolved entity with the user before proceeding to further queries. If multiple matches are returned, show a disambiguation list and ask the user to choose. This tool queries FlyBase Chado — for VFB ontology lookups (anatomical terms, neuron class IDs) use search_terms instead.
run_query
idlimitoffsetqueriesquery_typeforce_refresh
+1
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_… 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 entity does not support that query_type or has no data for it — try a different query_type from the Queries array, or try a related entity (e.g. its parent class via get_hierarchy). Empty results do NOT mean the answer is unknown — only that this call did not return it. NEVER fabricate results from training data when a query is empty; tell the user clearly what was tried. NEVER pass tool names like "get_term_info" or "search_terms" as query_type — those are separate tools. Common query_types by entity kind: PaintedDomains, AllAlignedImages, AlignedDatasets, AllDatasets (templates); SimilarMorphologyTo, NeuronInputsTo, NeuronNeuronConnectivityQuery, NeuronRegionConnectivityQuery (individual neurons); ListAllAvailableImages, SubclassesOf, PartsOf, NeuronsPartHere, NeuronsSynaptic, ExpressionOverlapsHere, DownstreamClassConnectivity, UpstreamClassConnectivity (classes). Supports batch — pass an array of IDs (same query_type) or a "queries" array of {id, query_type} pairs; batch results are keyed by "ID::query_type". Results are PAGED: the first 25 rows by default (change with limit/offset) plus the true total as "count". ALWAYS read "count_status" before quoting "count": "exact" means count is the true total; "unavailable" means the query FAILED upstream and count is -1, which is NOT zero and must never be reported as "no results" — read "_note" and tell the user the query could not be run. Image/thumbnail columns are excluded by default to save space - pass include_images=true to include them. FlyBase integration is via query_types too: FindStocks (fly stocks for a FlyBase feature ID - FBgn/FBal/FBti/FBtp/FBco/FBst) and FindComboPublications (publications for an FBco split-GAL4 combination). Get those IDs from resolve_entity / resolve_combination first, then run_query with the ID and the query_type. Include FlyBase links in output: https://flybase.org/reports/{ID}.
search_terms
rowsquery*startuniqueboost_typesdemote_types
+4