VirtualFlyBrain

Reviewed Jan 1, 2000.

• tools: 11 tools scanned
• metadata: scanned

No findings.

Tools (11)

• 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 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>,<IMAG

• 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 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 ne

• 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 entity the user wants. Common filter_types recipes: - Neuron classes: ["neuron", "class"] - Individual neurons with images: ["neuron", "has_image"] - Neurons with connectome data: ["neuron", "has_neuron_connectivity"] - Brain regions / neuropils: ["anatomy"] - Genes: ["gene"] - Driver lines / expression patterns: ["expression_pattern"] - Datasets: ["dataset"] There are over 200 type names and they change as data is added, so do NOT guess them: call list_search_facets to see the current vocabulary (optionally filtered, e.g. contains="lineage"). Names are matched case- and separator-insensitively, and a name that does not exist is an error with suggestions rather than a silently empty result. De

• 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.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.

• 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; 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.

• 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 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.

• 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 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 w

• 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-driven prediction and its confidence. By default results are aggregated to flat per-class rows (one per cell type × neurotransmitter) with instance counts, percent_of_class and mean_confidence; set aggregate=false for one row per individual neuron. Set split_by_dataset=true to get one row per (cell type, neurotransmitter, dataset) so you can see agreement across connectomes. The neurotransmitter is reported as a GO secretion term (nt_id/nt_label), the same id space as get_known_neurotransmitters. This is distinct from get_known_neurotransmitters, which returns the ontology-curated classification without confidence. CONSTRAINTS: neuron class terms only (FBbt id or label); use search_terms with f

• 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 answer. Returns one row per (cell type, neurotransmitter): {cell_type_id, cell_type, nt_id, nt_label}, where the neurotransmitter is a GO secretion term (same id space as get_predicted_neurotransmitters). Empty when the ontology asserts none — in that case try get_predicted_neurotransmitters for the data-driven prediction. CONSTRAINTS: neuron class terms only (FBbt id or label); use search_terms with filter_types ["neuron","class"] to canonicalize.

• 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?"). 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.