diff --git a/app/privacy/page.js b/app/privacy/page.js index 10bde75..7da27ed 100644 --- a/app/privacy/page.js +++ b/app/privacy/page.js @@ -32,7 +32,8 @@ export default function PrivacyPage() {

What We Do Not Collect By Default

@@ -49,11 +50,42 @@ export default function PrivacyPage() {
-

Data Sharing

- +

Where your question goes

+

+ To answer you, we send your question and the data we retrieved from Virtual Fly Brain to ELM, the + University of Edinburgh’s own AI platform. We do not store your question or the answer. ELM does log + prompts and interactions, for a maximum of two years, and its privacy notice explains that:{' '} + + elm.edina.ac.uk/site/privacy-policy + . +

+

+ Because this service has no accounts and no login, ELM holds no information that identifies you — the + request reaches it under Virtual Fly Brain’s own credentials. Your question is held on University of + Edinburgh infrastructure, is not shared with any third party, and is not used to train anyone’s AI + models. Individual prompts are not routinely read; ELM examines them only in exceptional circumstances, + for safeguarding or legal compliance. +

+

+ Please still avoid typing personal information into your question. We ask this because it is good practice, + not because we can see it. +

+
+ +
+

Analytics

+

+ We use Google Analytics to count how the service is used: how long answers take, which broad topic a + question fell into, which tools ran, and whether the answer succeeded. These measurements are sent from our + server, not from your browser, so we set no cookies and store nothing on your device, and Google does not + receive your IP address — only ours. Each measurement carries a one-off random identifier that is + never reused, so your requests cannot be linked to one another. No question text and no answer text is ever + included. +

+

+ Google Analytics is operated by Google LLC in the United States, under the UK Extension to the EU–US + Data Privacy Framework. +

diff --git a/test-results/task-battery/latest.json b/test-results/task-battery/latest.json index cd27699..f7acbf4 100644 --- a/test-results/task-battery/latest.json +++ b/test-results/task-battery/latest.json @@ -1,29 +1,59 @@ { "metadata": { - "run_id": "task-battery-2026-08-10T12-33-40-726Z", - "started_at": "2026-08-10T12:33:40.726Z", - "completed_at": "2026-08-10T12:49:04.084Z", - "git_sha": "68d4d426c1a48de20a983e13d9dc67ac045442ea", + "run_id": "task-battery-2026-08-10T17-16-49-499Z", + "started_at": "2026-08-10T17:16:49.499Z", + "completed_at": "2026-08-10T17:24:55.948Z", + "git_sha": "457fc5653f05a943560c0d085f9ca154ce742b26", "task_file": "/home/runner/work/VFBchat/VFBchat/VFBchat/tests/task-battery/tasks.json", "base_url": "http://127.0.0.1:3210", "started_server": true, "server_command": "start", - "repetitions": 3, - "concurrency": 1, - "timeout_ms": 360000 + "repetitions": 1, + "concurrency": 4, + "timeout_ms": 240000 }, "prompt": { "provenance_instruction": "Answer the following question about Drosophila neuroscience. For every claim you make, state where the information comes from - for example: the specific database, dataset, or tool query you used; the publication (with full citation); or your general training knowledge. If you are uncertain or do not have a source, say so explicitly rather than guessing." }, "summary": { - "total": 3, - "ok": 1, - "errors": 2, + "total": 64, + "ok": 63, + "errors": 1, "by_tier": { + "T1": { + "total": 8, + "ok": 8, + "errors": 0 + }, + "T2": { + "total": 8, + "ok": 8, + "errors": 0 + }, "T3": { - "total": 3, + "total": 8, + "ok": 7, + "errors": 1 + }, + "T4": { + "total": 6, + "ok": 6, + "errors": 0 + }, + "T5": { + "total": 1, "ok": 1, - "errors": 2 + "errors": 0 + }, + "T6": { + "total": 21, + "ok": 21, + "errors": 0 + }, + "T7": { + "total": 12, + "ok": 12, + "errors": 0 } }, "quality": { @@ -76,31 +106,41 @@ "task_ids": [] }, "slow_followup_turn": { - "count": 0, - "task_ids": [] + "count": 1, + "task_ids": [ + "C7" + ] } }, - "mean_duration_ms": 67421 + "conversation": { + "total": 12, + "ok": 12, + "turns": 27, + "followup_turns": 15, + "followup_median_ms": 11309, + "followup_max_ms": 130947 + }, + "mean_duration_ms": 22273 }, "results": [ { "attempt_index": 0, "task_index": 0, - "task_id": "T3.8", - "tier": 3, - "title": "Dataset coverage", - "question": "For the DNa02 descending neuron type, what data is available in VFB? Is it in the Hemibrain, FAFB, or both? Are there light microscopy images and driver lines?", + "task_id": "T1.1", + "tier": 1, + "title": "Brain region identification", + "question": "What are the major subdivisions of the Drosophila mushroom body?", "requires_graph": false, "min_graphs": 0, "repetition": 1, - "duration_ms": 202263, + "duration_ms": 31465, "status_messages": [ { "message": "Thinking...", "phase": "llm" }, { - "message": "Planning the answer", + "message": "Planning (direct lookup)", "phase": "llm" }, { @@ -112,13 +152,121 @@ "phase": "mcp" }, { - "message": "Finding genetic tools", + "message": "Checking the answer is covered", + "phase": "llm" + }, + { + "message": "Writing the answer", + "phase": "llm" + } + ], + "event_count": 59, + "ok": true, + "request_id": "6755c564-84c8-4116-aabe-e411e0c7eb50", + "response_id": "chatcmpl-9dc74f1c82461aa5e8ee7d5700b41012", + "images_count": 8, + "graphs_count": 0, + "response": "The major subdivisions of the Drosophila [mushroom body](https://www.virtualflybrain.org/reports/FBbt_00005801 \"Open mushroom body in Virtual Fly Brain\") are the calyx, pedunculus, and mushroom body lobe system. The mushroom body lobe system consists of a vertical branch and a medial branch, which have different structures at different life stages.", + "quality_flags": { + "has_tool_status": true, + "no_tool_factual_answer": false, + "tool_claim_without_tool": false, + "disambiguation_only_answer": false, + "investigation_plan_answer": false, + "not_verified_or_no_results_answer": false, + "graph_failure_mentioned": false, + "missing_required_graph": false, + "used_data_resource": false, + "response_chars": 350, + "status_count": 6 + } + }, + { + "attempt_index": 1, + "task_index": 1, + "task_id": "T1.2", + "tier": 1, + "title": "Neuron type classification", + "question": "What types of Kenyon cells exist in the adult Drosophila brain?", + "requires_graph": false, + "min_graphs": 0, + "repetition": 1, + "duration_ms": 32142, + "status_messages": [ + { + "message": "Thinking...", + "phase": "llm" + }, + { + "message": "Planning the answer", + "phase": "llm" + }, + { + "message": "Resolving 1 term in VFB", + "phase": "mcp" + }, + { + "message": "Summarising neuron taxonomy", "phase": "mcp" }, { "message": "Checking the answer is covered", "phase": "llm" }, + { + "message": "Writing the answer", + "phase": "llm" + } + ], + "event_count": 83, + "ok": true, + "request_id": "827efe7e-47fa-449c-97f7-3a26563e58a9", + "response_id": "chatcmpl-fefc87b1c305ea58fe4bce2199295579", + "images_count": 8, + "graphs_count": 0, + "response": "There are several types of Kenyon cells in the adult Drosophila brain, including alpha/beta, alpha'/beta', and gamma Kenyon cells, which can be further subdivided into core/surface/posterior, anterior-posterior/middle, dorsal/main/gamma-s/gamma-t, and claw-count classes. VFB holds [37](https://v2.virtualflybrain.org/org.geppetto.frontend/geppetto?q=FBbt_00003686,SubclassesOf \"Run in VFB: Subclasses of Kenyon cell\") subclasses of [Kenyon cell](https://www.virtualflybrain.org/reports/FBbt_00003686 \"Open Kenyon cell in Virtual Fly Brain\").", + "quality_flags": { + "has_tool_status": true, + "no_tool_factual_answer": false, + "tool_claim_without_tool": false, + "disambiguation_only_answer": false, + "investigation_plan_answer": false, + "not_verified_or_no_results_answer": false, + "graph_failure_mentioned": false, + "missing_required_graph": false, + "used_data_resource": false, + "response_chars": 542, + "status_count": 6 + } + }, + { + "attempt_index": 2, + "task_index": 2, + "task_id": "T1.3", + "tier": 1, + "title": "Basic connectivity", + "question": "What are the main input neurons to the mushroom body?", + "requires_graph": false, + "min_graphs": 0, + "repetition": 1, + "duration_ms": 31506, + "status_messages": [ + { + "message": "Thinking...", + "phase": "llm" + }, + { + "message": "Planning the answer", + "phase": "llm" + }, + { + "message": "Resolving 1 term in VFB", + "phase": "mcp" + }, + { + "message": "Querying VFB connectivity", + "phase": "mcp" + }, { "message": "Querying VFB", "phase": "mcp" @@ -127,6 +275,10 @@ "message": "Querying VFB", "phase": "mcp" }, + { + "message": "Checking the answer is covered", + "phase": "llm" + }, { "message": "Querying VFB", "phase": "mcp" @@ -140,13 +292,221 @@ "phase": "llm" } ], - "event_count": 184, + "event_count": 92, "ok": true, - "request_id": "9a4ad432-6780-4bfb-95a3-4943eac04744", - "response_id": "chatcmpl-a1e11b4cd73228545dce813e4cf75518", + "request_id": "0923e6ad-4fea-455e-875f-e2d8c7d0d6a9", + "response_id": "chatcmpl-e54222ff2c5724ceabc30608e9b63753", "images_count": 8, + "graphs_count": 1, + "response": "The main input neurons to the [mushroom body](https://www.virtualflybrain.org/reports/FBbt_00005801 \"Open mushroom body in Virtual Fly Brain\") are sensory interneuron afferents to the calyx. VFB records show that there are [366](https://v2.virtualflybrain.org/org.geppetto.frontend/geppetto?q=FBbt_00005801,NeuronsPresynapticHere \"Run in VFB: Neurons with presynaptic terminals in mushroom body\") neurons with presynaptic terminals in the mushroom body, including larval uniglomerular projection neurons and larval antennal lobe multiglomerular projection neurons. The connectome data indicates that these neurons provide input to the mushroom body.", + "graphs": [ + { + "type": "basic_graph", + "version": 1, + "title": "mushroom body region connectivity preview", + "directed": true, + "layout": "radial", + "nodes": [ + { + "id": "FBbt_00005801", + "label": "mushroom body", + "group": "queried region", + "color": null, + "size": 2.4 + }, + { + "id": "FBbt_00111716", + "label": "larval antennal lobe multiglomerular projection neuron C2", + "group": "presynaptic neuron", + "color": null, + "size": 1.15 + }, + { + "id": "FBbt_00111717", + "label": "larval antennal lobe multiglomerular projection neuron bilateral lower", + "group": "presynaptic neuron", + "color": null, + "size": 1.15 + }, + { + "id": "FBbt_00111675", + "label": "larval uniglomerular projection neuron 63a", + "group": "presynaptic neuron", + "color": null, + "size": 1.15 + }, + { + "id": "FBbt_00111684", + "label": "larval uniglomerular projection neuron 67b", + "group": "presynaptic neuron", + "color": null, + "size": 1.15 + }, + { + "id": "FBbt_00111685", + "label": "larval uniglomerular projection neuron 74a", + "group": "presynaptic neuron", + "color": null, + "size": 1.15 + }, + { + "id": "FBbt_20000069", + "label": "ATL005", + "group": "postsynaptic neuron", + "color": null, + "size": 1.15 + }, + { + "id": "FBbt_20000071", + "label": "ATL007", + "group": "postsynaptic neuron", + "color": null, + "size": 1.15 + }, + { + "id": "FBbt_20000083", + "label": "ATL019", + "group": "postsynaptic neuron", + "color": null, + "size": 1.15 + }, + { + "id": "FBbt_20000084", + "label": "ATL020", + "group": "postsynaptic neuron", + "color": null, + "size": 1.15 + }, + { + "id": "FBbt_00111628", + "label": "adult odd neuron of the calyx", + "group": "postsynaptic neuron", + "color": null, + "size": 1.15 + } + ], + "edges": [ + { + "source": "FBbt_00111716", + "target": "FBbt_00005801", + "label": "presynaptic sites in mushroom body", + "weight": 0 + }, + { + "source": "FBbt_00111717", + "target": "FBbt_00005801", + "label": "presynaptic sites in mushroom body", + "weight": 0 + }, + { + "source": "FBbt_00111675", + "target": "FBbt_00005801", + "label": "presynaptic sites in mushroom body", + "weight": 0 + }, + { + "source": "FBbt_00111684", + "target": "FBbt_00005801", + "label": "presynaptic sites in mushroom body", + "weight": 0 + }, + { + "source": "FBbt_00111685", + "target": "FBbt_00005801", + "label": "presynaptic sites in mushroom body", + "weight": 0 + }, + { + "source": "FBbt_00005801", + "target": "FBbt_20000069", + "label": "postsynaptic sites in mushroom body", + "weight": 0 + }, + { + "source": "FBbt_00005801", + "target": "FBbt_20000071", + "label": "postsynaptic sites in mushroom body", + "weight": 0 + }, + { + "source": "FBbt_00005801", + "target": "FBbt_20000083", + "label": "postsynaptic sites in mushroom body", + "weight": 0 + }, + { + "source": "FBbt_00005801", + "target": "FBbt_20000084", + "label": "postsynaptic sites in mushroom body", + "weight": 0 + }, + { + "source": "FBbt_00005801", + "target": "FBbt_00111628", + "label": "postsynaptic sites in mushroom body", + "weight": 0 + } + ] + } + ], + "quality_flags": { + "has_tool_status": true, + "no_tool_factual_answer": false, + "tool_claim_without_tool": false, + "disambiguation_only_answer": false, + "investigation_plan_answer": false, + "not_verified_or_no_results_answer": false, + "graph_failure_mentioned": false, + "missing_required_graph": false, + "used_data_resource": false, + "response_chars": 649, + "status_count": 10 + } + }, + { + "attempt_index": 3, + "task_index": 3, + "task_id": "T1.4", + "tier": 1, + "title": "Gene expression", + "question": "What neurotransmitter do mushroom body Kenyon cells use?", + "requires_graph": false, + "min_graphs": 0, + "repetition": 1, + "duration_ms": 29186, + "status_messages": [ + { + "message": "Thinking...", + "phase": "llm" + }, + { + "message": "Planning the answer", + "phase": "llm" + }, + { + "message": "Resolving 1 term in VFB", + "phase": "mcp" + }, + { + "message": "Looking up neurotransmitter data", + "phase": "mcp" + }, + { + "message": "Checking the answer is covered", + "phase": "llm" + }, + { + "message": "Writing the answer", + "phase": "llm" + } + ], + "event_count": 25, + "ok": true, + "request_id": "c86ebe3d-1cf4-478f-b82d-d98e95832621", + "response_id": "chatcmpl-bfea29541f1246b2ceddd45757fd3d87", + "images_count": 6, "graphs_count": 0, - "response": "For the [descending neuron of the anterior dorsal brain DNa02](https://www.virtualflybrain.org/reports/FBbt_00047573 \"Open descending neuron of the anterior dorsal brain DNa02 in Virtual Fly Brain\"), VFB holds various data, including images, splits targeting DNa02, and transgene expression reports. There are [18](https://v2.virtualflybrain.org/org.geppetto.frontend/geppetto?q=FBbt_00047573,ListAllAvailableImages \"Run in VFB: List all available images of DNa02\") available images of DNa02. Two genetic tools are available to label DNa02 descending neurons, which are [P{R87D07-GAL4.DBD} ∩ P{R75C10-p65.AD} expression pattern](https://www.virtualflybrain.org/reports/VFBexp_FBtp0122422FBtp0119138 \"Open P{R87D07-GAL4.DBD} ∩ P{R75C10-p65.AD} expression pattern in Virtual Fly Brain\") and [P{VT025718-GAL4.DBD} ∩ P{R22C05-p65.AD} expression pattern](https://www.virtualflybrain.org/reports/VFBexp_FBtp0123634FBtp0118395 \"Open P{VT025718-GAL4.DBD} ∩ P{R22C05-p65.AD} expression pattern in Virtual Fly Brain\"). These tools are also reported to show transgene expression in DNa02. The images of DNa02 are available from both MaleCNS and FlyEM-HB datasets, indicating that DNa02 is present in both the Hemibrain and potentially FAFB, given the diversity of image sources.", + "response": "Mushroom body Kenyon cells use acetylcholine as their primary neurotransmitter.", "quality_flags": { "has_tool_status": true, "no_tool_factual_answer": false, @@ -157,25 +517,64 @@ "graph_failure_mentioned": false, "missing_required_graph": false, "used_data_resource": false, - "response_chars": 1267, - "status_count": 11 + "response_chars": 79, + "status_count": 6 } }, { - "attempt_index": 1, - "task_index": 0, - "task_id": "T3.8", - "tier": 3, - "title": "Dataset coverage", - "question": "For the DNa02 descending neuron type, what data is available in VFB? Is it in the Hemibrain, FAFB, or both? Are there light microscopy images and driver lines?", + "attempt_index": 4, + "task_index": 4, + "task_id": "T1.5", + "tier": 1, + "title": "Neuroanatomy", + "question": "What brain regions does the antennal lobe connect to?", "requires_graph": false, "min_graphs": 0, - "repetition": 2, - "ok": false, - "duration_ms": null, - "error": "Timed out after 360000 ms", + "repetition": 1, + "duration_ms": 13440, + "status_messages": [ + { + "message": "Thinking...", + "phase": "llm" + }, + { + "message": "Planning the answer", + "phase": "llm" + }, + { + "message": "Resolving 1 term in VFB", + "phase": "mcp" + }, + { + "message": "Reading VFB term info", + "phase": "mcp" + }, + { + "message": "Querying VFB", + "phase": "mcp" + }, + { + "message": "Querying VFB", + "phase": "mcp" + }, + { + "message": "Checking the answer is covered", + "phase": "llm" + }, + { + "message": "Writing the answer", + "phase": "llm" + } + ], + "event_count": 141, + "ok": true, + "request_id": "41a6355e-9c0c-4864-9d7e-b9dead88054b", + "response_id": "chatcmpl-aa1986746dd8e6ebb78859b65bec1aee", + "images_count": 6, + "graphs_count": 0, + "response": "The [antennal lobe](https://www.virtualflybrain.org/reports/FBbt_00003924 \"Open antennal lobe in Virtual Fly Brain\") connects to various brain regions through neurons with presynaptic and postsynaptic terminals. Neurons with presynaptic terminals in the antennal lobe include [larval antennal lobe picky local neuron](https://www.virtualflybrain.org/reports/FBbt_00111694 \"Open larval antennal lobe picky local neuron in Virtual Fly Brain\"), [larval antennal lobe broad local neuron](https://www.virtualflybrain.org/reports/FBbt_00111700 \"Open larval antennal lobe broad local neuron in Virtual Fly Brain\"), and adult olfactory receptor neurons. Neurons with postsynaptic terminals in the antennal lobe include adult antennal lobe projection neurons, such as DL5, DM4, VA1d, VL1, VL2a, VM2, and VM4, as well as multiglomerular antennal lobe projection neurons like L1 adPN.", "quality_flags": { - "has_tool_status": false, + "has_tool_status": true, "no_tool_factual_answer": false, "tool_claim_without_tool": false, "disambiguation_only_answer": false, @@ -184,25 +583,56 @@ "graph_failure_mentioned": false, "missing_required_graph": false, "used_data_resource": false, - "response_chars": 25, - "status_count": 0 + "response_chars": 873, + "status_count": 8 } }, { - "attempt_index": 2, - "task_index": 0, - "task_id": "T3.8", - "tier": 3, - "title": "Dataset coverage", - "question": "For the DNa02 descending neuron type, what data is available in VFB? Is it in the Hemibrain, FAFB, or both? Are there light microscopy images and driver lines?", + "attempt_index": 5, + "task_index": 5, + "task_id": "T1.6", + "tier": 1, + "title": "Cell count", + "question": "Approximately how many neurons are in the adult Drosophila central brain?", "requires_graph": false, "min_graphs": 0, - "repetition": 3, - "ok": false, - "duration_ms": null, - "error": "Timed out after 360000 ms", + "repetition": 1, + "duration_ms": 17051, + "status_messages": [ + { + "message": "Thinking...", + "phase": "llm" + }, + { + "message": "Planning the answer", + "phase": "llm" + }, + { + "message": "Resolving 1 term in VFB", + "phase": "mcp" + }, + { + "message": "Counting neurons", + "phase": "mcp" + }, + { + "message": "Checking the answer is covered", + "phase": "llm" + }, + { + "message": "Writing the answer", + "phase": "llm" + } + ], + "event_count": 49, + "ok": true, + "request_id": "d1c5e0a4-b713-4193-a252-0c588f9856e4", + "response_id": "chatcmpl-476256daa911c93b56bec8141f73e2c5", + "images_count": 0, + "graphs_count": 0, + "response": "The adult Drosophila central brain could not be matched to a VFB record. However, there is information available that approximately more than 125,000 neurons are in the Drosophila brain.\n\n**Published neuron-count estimates — adult central brain** (from the literature):\n\n- more than 125,000 neurons (adult Drosophila central brain connectome/model) — A Drosophila computational brain model reveals sensorimotor processing. — PMID 39358519\n- ~139,255 neurons (whole adult Drosophila brain) — Neuronal wiring diagram of an adult brain. — PMID 39358518\n\n_VFB has annotated 9,413 neuron types with some part in adult central brain — a curated annotation count, not the biological total._", "quality_flags": { - "has_tool_status": false, + "has_tool_status": true, "no_tool_factual_answer": false, "tool_claim_without_tool": false, "disambiguation_only_answer": false, @@ -211,8 +641,7431 @@ "graph_failure_mentioned": false, "missing_required_graph": false, "used_data_resource": false, - "response_chars": 25, - "status_count": 0 + "response_chars": 683, + "status_count": 6 + } + }, + { + "attempt_index": 6, + "task_index": 6, + "task_id": "T1.7", + "tier": 1, + "title": "Central complex structure", + "question": "What are the main components of the Drosophila central complex and what functions are they associated with?", + "requires_graph": false, + "min_graphs": 0, + "repetition": 1, + "duration_ms": 19363, + "status_messages": [ + { + "message": "Thinking...", + "phase": "llm" + }, + { + "message": "Planning the answer", + "phase": "llm" + }, + { + "message": "Resolving 1 term in VFB", + "phase": "mcp" + }, + { + "message": "Querying VFB connectivity", + "phase": "mcp" + }, + { + "message": "Checking the answer is covered", + "phase": "llm" + }, + { + "message": "Writing the answer", + "phase": "llm" + } + ], + "event_count": 64, + "ok": true, + "request_id": "30df6ba2-de57-4fbd-bc5d-5bb1d05d0ab1", + "response_id": "chatcmpl-0292635a9f61195d7f77826a511d7824", + "images_count": 0, + "graphs_count": 1, + "response": "The main components of the central complex are the ellipsoid body, fan-shaped body, paired noduli, asymmetrical bodies, and protocerebral bridge. These components are associated with functions including navigation and orientation, locomotor control, and sleep/arousal and memory-related behaviours.", + "graphs": [ + { + "type": "basic_graph", + "version": 1, + "title": "adult central complex region connectivity preview", + "directed": true, + "layout": "radial", + "nodes": [ + { + "id": "FBbt_00003632", + "label": "adult central complex", + "group": "queried region", + "color": null, + "size": 2.4 + }, + { + "id": "FBbt_00111369", + "label": "PEN_PB2", + "group": "presynaptic and postsynaptic neuron", + "color": null, + "size": 1.15 + }, + { + "id": "FBbt_00111370", + "label": "PEN_PB3", + "group": "presynaptic and postsynaptic neuron", + "color": null, + "size": 1.15 + }, + { + "id": "FBbt_00111373", + "label": "PEN_PB7", + "group": "presynaptic and postsynaptic neuron", + "color": null, + "size": 1.15 + }, + { + "id": "FBbt_00111374", + "label": "PEN_PB8", + "group": "presynaptic and postsynaptic neuron", + "color": null, + "size": 1.15 + }, + { + "id": "FBbt_00111376", + "label": "adult protocerebral bridge glomerulus 1-ellipsoid body canal-dorsal gall neuron", + "group": "presynaptic and postsynaptic neuron", + "color": null, + "size": 1.15 + } + ], + "edges": [ + { + "source": "FBbt_00111369", + "target": "FBbt_00003632", + "label": "presynaptic sites in adult central complex", + "weight": 0 + }, + { + "source": "FBbt_00111370", + "target": "FBbt_00003632", + "label": "presynaptic sites in adult central complex", + "weight": 0 + }, + { + "source": "FBbt_00111373", + "target": "FBbt_00003632", + "label": "presynaptic sites in adult central complex", + "weight": 0 + }, + { + "source": "FBbt_00111374", + "target": "FBbt_00003632", + "label": "presynaptic sites in adult central complex", + "weight": 0 + }, + { + "source": "FBbt_00111376", + "target": "FBbt_00003632", + "label": "presynaptic sites in adult central complex", + "weight": 0 + }, + { + "source": "FBbt_00003632", + "target": "FBbt_00111369", + "label": "postsynaptic sites in adult central complex", + "weight": 0 + }, + { + "source": "FBbt_00003632", + "target": "FBbt_00111370", + "label": "postsynaptic sites in adult central complex", + "weight": 0 + }, + { + "source": "FBbt_00003632", + "target": "FBbt_00111373", + "label": "postsynaptic sites in adult central complex", + "weight": 0 + }, + { + "source": "FBbt_00003632", + "target": "FBbt_00111374", + "label": "postsynaptic sites in adult central complex", + "weight": 0 + }, + { + "source": "FBbt_00003632", + "target": "FBbt_00111376", + "label": "postsynaptic sites in adult central complex", + "weight": 0 + } + ] + } + ], + "quality_flags": { + "has_tool_status": true, + "no_tool_factual_answer": false, + "tool_claim_without_tool": false, + "disambiguation_only_answer": false, + "investigation_plan_answer": false, + "not_verified_or_no_results_answer": false, + "graph_failure_mentioned": false, + "missing_required_graph": false, + "used_data_resource": false, + "response_chars": 298, + "status_count": 6 + } + }, + { + "attempt_index": 7, + "task_index": 7, + "task_id": "T1.8", + "tier": 1, + "title": "Genetic tools", + "question": "What genetic tools are commonly used to label mushroom body neurons in Drosophila?", + "requires_graph": false, + "min_graphs": 0, + "repetition": 1, + "duration_ms": 21988, + "status_messages": [ + { + "message": "Thinking...", + "phase": "llm" + }, + { + "message": "Planning the answer", + "phase": "llm" + }, + { + "message": "Resolving 1 term in VFB", + "phase": "mcp" + }, + { + "message": "Finding genetic tools", + "phase": "mcp" + }, + { + "message": "Checking the answer is covered", + "phase": "llm" + }, + { + "message": "Writing the answer", + "phase": "llm" + } + ], + "event_count": 267, + "ok": true, + "request_id": "e175bccd-8db0-4b7f-91e4-1424af055fa1", + "response_id": "chatcmpl-7861945329a6783af91007d8fcb507be", + "images_count": 8, + "graphs_count": 0, + "response": "Genetic tools such as PBac{544.SVS-1}Bsg[CPTI100062] and PBac{602.P.SVS-1}Fas2[CPTI000483] are used to label neurons. VFB records show multiple transgene expression patterns, including PBac{566.P.SVS-1}Bsg[CPTI100005], PBac{566.P.SVS-1}IA-2[CPTI100013], PBac{566.P.SVS-1}sgg[CPTI100027], PBac{602.P.SVS-1}HDAC4[CPTI000077], PBac{602.P.SVS-1}Pax[CPTI000161], PBac{602.P.SVS-1}Sema1a[CPTI000505], PBac{602.P.SVS-1}Tm1[CPTI000760], PBac{602.P.SVS-1}dlg1[CPTI000207], PBac{602.P.SVS-1}dlp[CPTI000445], and PBac{602.P.SVS-1}hzg[CPTI000737]. For [Kenyon cell](https://www.virtualflybrain.org/reports/FBbt_00003686 \"Open Kenyon cell in Virtual Fly Brain\"), VFB holds [92](https://v2.virtualflybrain.org/org.geppetto.frontend/geppetto?q=FBbt_00003686,TransgeneExpressionHere \"Run in VFB: Transgene expression in Kenyon cell\") transgene expression reports.", + "quality_flags": { + "has_tool_status": true, + "no_tool_factual_answer": false, + "tool_claim_without_tool": false, + "disambiguation_only_answer": false, + "investigation_plan_answer": false, + "not_verified_or_no_results_answer": false, + "graph_failure_mentioned": false, + "missing_required_graph": false, + "used_data_resource": false, + "response_chars": 847, + "status_count": 6 + } + }, + { + "attempt_index": 8, + "task_index": 8, + "task_id": "T2.1", + "tier": 2, + "title": "Circuit motif", + "question": "Describe the dopaminergic input to mushroom body output neurons (MBONs). Which DAN types connect to which MBON types?", + "requires_graph": false, + "min_graphs": 0, + "repetition": 1, + "duration_ms": 27596, + "status_messages": [ + { + "message": "Thinking...", + "phase": "llm" + }, + { + "message": "Planning the answer", + "phase": "llm" + }, + { + "message": "Resolving 4 terms in VFB", + "phase": "mcp" + }, + { + "message": "Querying VFB connectivity", + "phase": "mcp" + }, + { + "message": "Checking the answer is covered", + "phase": "llm" + }, + { + "message": "Querying VFB", + "phase": "mcp" + }, + { + "message": "Querying VFB", + "phase": "mcp" + }, + { + "message": "Checking the answer is covered", + "phase": "llm" + }, + { + "message": "Writing the answer", + "phase": "llm" + } + ], + "event_count": 87, + "ok": true, + "request_id": "3d9bae69-f166-4dbf-ae36-4129f61df37e", + "response_id": "chatcmpl-03332f60ce2f4dffb8f62fde0e0a9ed2", + "images_count": 8, + "graphs_count": 1, + "response": "Dopaminergic input to mushroom body output neurons comes from specific dopaminergic neuron types, including dopaminergic PPL1 neurons and dopaminergic PAM neurons. The strongest specific input to [mushroom body output neuron](https://www.virtualflybrain.org/reports/FBbt_00047953 \"Open mushroom body output neuron in Virtual Fly Brain\"), ranked by mean synaptic weight per connected pair, are [adult cholinergic neuron](https://www.virtualflybrain.org/reports/FBbt_00058205 \"Open adult cholinergic neuron in Virtual Fly Brain\") and [Kenyon cell](https://www.virtualflybrain.org/reports/FBbt_00003686 \"Open Kenyon cell in Virtual Fly Brain\"). VFB holds [69](https://v2.virtualflybrain.org/org.geppetto.frontend/geppetto?q=FBbt_00047953,SubclassesOf \"Run in VFB: Subclasses of MBON\") subclasses of mushroom body output neuron.", + "graphs": [ + { + "type": "basic_graph", + "version": 1, + "title": "Upstream partners of MBON", + "directed": true, + "layout": "circle", + "nodes": [ + { + "id": "FBbt_00005131", + "label": "dopaminergic neuron", + "group": null, + "color": null, + "size": 1.93 + }, + { + "id": "FBbt_00047953", + "label": "MBON", + "group": null, + "color": null, + "size": 4 + }, + { + "id": "FBbt_00058206", + "label": "adult dopaminergic neuron", + "group": null, + "color": null, + "size": 1.92 + }, + { + "id": "FBbt_00048138", + "label": "mushroom body dopaminergic neuron", + "group": null, + "color": null, + "size": 1.91 + }, + { + "id": "FBbt_00049839", + "label": "adult dopaminergic mushroom body input neuron", + "group": null, + "color": null, + "size": 1.07 + }, + { + "id": "FBbt_00100214", + "label": "adult dopaminergic PAM neuron", + "group": null, + "color": null, + "size": 1.07 + }, + { + "id": "FBbt_00100219", + "label": "dopaminergic PPL1 neuron", + "group": null, + "color": null, + "size": 1.02 + }, + { + "id": "FBbt_00049840", + "label": "mushroom body PPL1 neuron", + "group": null, + "color": null, + "size": 1.02 + }, + { + "id": "FBbt_00111020", + "label": "dopaminergic PAM neuron 8", + "group": null, + "color": null, + "size": 1.01 + }, + { + "id": "FBbt_00111018", + "label": "dopaminergic PAM neuron 6", + "group": null, + "color": null, + "size": 1.01 + }, + { + "id": "FBbt_00111017", + "label": "dopaminergic PAM neuron 5", + "group": null, + "color": null, + "size": 1.01 + }, + { + "id": "FBbt_00110994", + "label": "dopaminergic PAM neuron 10", + "group": null, + "color": null, + "size": 1.01 + }, + { + "id": "FBbt_00110993", + "label": "dopaminergic PAM neuron 4", + "group": null, + "color": null, + "size": 1.01 + }, + { + "id": "FBbt_00111022", + "label": "dopaminergic PAM neuron 11", + "group": null, + "color": null, + "size": 1.01 + }, + { + "id": "FBbt_00007364", + "label": "octopaminergic neuron", + "group": null, + "color": null, + "size": 1.01 + }, + { + "id": "FBbt_00058203", + "label": "adult octopaminergic neuron", + "group": null, + "color": null, + "size": 1.01 + } + ], + "edges": [ + { + "source": "FBbt_00005131", + "target": "FBbt_00047953", + "label": "651367", + "weight": 651367 + }, + { + "source": "FBbt_00058206", + "target": "FBbt_00047953", + "label": "650172", + "weight": 650172 + }, + { + "source": "FBbt_00048138", + "target": "FBbt_00047953", + "label": "641765", + "weight": 641765 + }, + { + "source": "FBbt_00049839", + "target": "FBbt_00047953", + "label": "47142", + "weight": 47142 + }, + { + "source": "FBbt_00100214", + "target": "FBbt_00047953", + "label": "47139", + "weight": 47139 + }, + { + "source": "FBbt_00100219", + "target": "FBbt_00047953", + "label": "17270", + "weight": 17270 + }, + { + "source": "FBbt_00049840", + "target": "FBbt_00047953", + "label": "16097", + "weight": 16097 + }, + { + "source": "FBbt_00111020", + "target": "FBbt_00047953", + "label": "7988", + "weight": 7988 + }, + { + "source": "FBbt_00111018", + "target": "FBbt_00047953", + "label": "7650", + "weight": 7650 + }, + { + "source": "FBbt_00111017", + "target": "FBbt_00047953", + "label": "5433", + "weight": 5433 + }, + { + "source": "FBbt_00110994", + "target": "FBbt_00047953", + "label": "4482", + "weight": 4482 + }, + { + "source": "FBbt_00110993", + "target": "FBbt_00047953", + "label": "4248", + "weight": 4248 + }, + { + "source": "FBbt_00111022", + "target": "FBbt_00047953", + "label": "4033", + "weight": 4033 + }, + { + "source": "FBbt_00007364", + "target": "FBbt_00047953", + "label": "3790", + "weight": 3790 + }, + { + "source": "FBbt_00058203", + "target": "FBbt_00047953", + "label": "3547", + "weight": 3547 + } + ] + } + ], + "quality_flags": { + "has_tool_status": true, + "no_tool_factual_answer": false, + "tool_claim_without_tool": false, + "disambiguation_only_answer": false, + "investigation_plan_answer": false, + "not_verified_or_no_results_answer": false, + "graph_failure_mentioned": false, + "missing_required_graph": false, + "used_data_resource": false, + "response_chars": 824, + "status_count": 9 + } + }, + { + "attempt_index": 9, + "task_index": 9, + "task_id": "T2.2", + "tier": 2, + "title": "Cross-dataset comparison", + "question": "Is the connectivity of olfactory projection neurons consistent between the Hemibrain and FAFB connectome datasets?", + "requires_graph": false, + "min_graphs": 0, + "repetition": 1, + "duration_ms": 19364, + "status_messages": [ + { + "message": "Thinking...", + "phase": "llm" + }, + { + "message": "Planning the answer", + "phase": "llm" + }, + { + "message": "Resolving 3 terms in VFB", + "phase": "mcp" + }, + { + "message": "Querying VFB connectivity", + "phase": "mcp" + }, + { + "message": "Querying VFB", + "phase": "mcp" + }, + { + "message": "Querying VFB", + "phase": "mcp" + }, + { + "message": "Checking the answer is covered", + "phase": "llm" + }, + { + "message": "Querying VFB", + "phase": "mcp" + }, + { + "message": "Querying VFB", + "phase": "mcp" + }, + { + "message": "Checking the answer is covered", + "phase": "llm" + }, + { + "message": "Writing the answer", + "phase": "llm" + } + ], + "event_count": 61, + "ok": true, + "request_id": "eaaec351-5fa2-45c5-904c-b277fe774d25", + "response_id": "chatcmpl-64eec5d28dd2c0f5ca7d10ee88279e94", + "images_count": 8, + "graphs_count": 0, + "response": "The connectivity of olfactory projection neurons is not directly compared between the Hemibrain and FAFB connectome datasets in VFB evidence. VFB does not currently hold data on the consistency of [olfactory projection neuron](https://www.virtualflybrain.org/reports/FBbt_00051298 \"Open olfactory projection neuron in Virtual Fly Brain\") connectivity between these two datasets.", + "quality_flags": { + "has_tool_status": true, + "no_tool_factual_answer": false, + "tool_claim_without_tool": false, + "disambiguation_only_answer": false, + "investigation_plan_answer": false, + "not_verified_or_no_results_answer": false, + "graph_failure_mentioned": false, + "missing_required_graph": false, + "used_data_resource": false, + "response_chars": 378, + "status_count": 11 + } + }, + { + "attempt_index": 10, + "task_index": 10, + "task_id": "T2.3", + "tier": 2, + "title": "Reagent identification", + "question": "I want to image neurons in the lateral horn. What split-GAL4 driver lines are available that target lateral horn neuron types?", + "requires_graph": false, + "min_graphs": 0, + "repetition": 1, + "duration_ms": 23662, + "status_messages": [ + { + "message": "Thinking...", + "phase": "llm" + }, + { + "message": "Planning the answer", + "phase": "llm" + }, + { + "message": "Resolving 1 term in VFB", + "phase": "mcp" + }, + { + "message": "Reading VFB term info", + "phase": "mcp" + }, + { + "message": "Finding genetic tools", + "phase": "mcp" + }, + { + "message": "Checking the answer is covered", + "phase": "llm" + }, + { + "message": "Querying VFB", + "phase": "mcp" + }, + { + "message": "Checking the answer is covered", + "phase": "llm" + }, + { + "message": "Writing the answer", + "phase": "llm" + }, + { + "message": "Checking before saying VFB has no data", + "phase": "mcp" + }, + { + "message": "Querying VFB", + "phase": "mcp" + }, + { + "message": "Querying VFB", + "phase": "mcp" + }, + { + "message": "Querying VFB", + "phase": "mcp" + }, + { + "message": "Checking the answer is covered", + "phase": "llm" + }, + { + "message": "Writing the answer", + "phase": "llm" + } + ], + "event_count": 218, + "ok": true, + "request_id": "54a04339-3fec-49c2-abc7-035f8bc1848c", + "response_id": "chatcmpl-71e1de4c71a4c3eabe48699fcd318a8f", + "images_count": 8, + "graphs_count": 0, + "response": "VFB holds [1934](https://v2.virtualflybrain.org/org.geppetto.frontend/geppetto?q=FBbt_00007053,TransgeneExpressionHere \"Run in VFB: Transgene expression in adult lateral horn\") transgene expression reports for [adult lateral horn](https://www.virtualflybrain.org/reports/FBbt_00007053 \"Open adult lateral horn in Virtual Fly Brain\"), including driver lines such as P{GMR11B09-GAL4} and PBac{566.P.SVS-1}IA-2[CPTI100013]. The documentation mentions FlyLight split-GAL4 lines for Lateral Horn from Dolan et al.", + "quality_flags": { + "has_tool_status": true, + "no_tool_factual_answer": false, + "tool_claim_without_tool": false, + "disambiguation_only_answer": false, + "investigation_plan_answer": false, + "not_verified_or_no_results_answer": false, + "graph_failure_mentioned": false, + "missing_required_graph": false, + "used_data_resource": false, + "response_chars": 508, + "status_count": 15 + } + }, + { + "attempt_index": 11, + "task_index": 11, + "task_id": "T2.4", + "tier": 2, + "title": "Neuron characterisation", + "question": "What is known about the LPLC2 visual neuron type? Where is it, what does it connect to, and what is its function?", + "requires_graph": false, + "min_graphs": 0, + "repetition": 1, + "duration_ms": 24695, + "status_messages": [ + { + "message": "Thinking...", + "phase": "llm" + }, + { + "message": "Planning the answer", + "phase": "llm" + }, + { + "message": "Resolving 1 term in VFB", + "phase": "mcp" + }, + { + "message": "Querying VFB", + "phase": "mcp" + }, + { + "message": "Querying VFB connectivity", + "phase": "mcp" + }, + { + "message": "Checking the answer is covered", + "phase": "llm" + }, + { + "message": "Writing the answer", + "phase": "llm" + }, + { + "message": "Checking before saying VFB has no data", + "phase": "mcp" + }, + { + "message": "Querying VFB", + "phase": "mcp" + }, + { + "message": "Querying VFB", + "phase": "mcp" + }, + { + "message": "Querying VFB", + "phase": "mcp" + }, + { + "message": "Checking the answer is covered", + "phase": "llm" + }, + { + "message": "Writing the answer", + "phase": "llm" + } + ], + "event_count": 176, + "ok": true, + "request_id": "646eca10-7e2a-42ac-a0ce-eb98858c51be", + "response_id": "chatcmpl-0c7281d7d12d83f11492a2ea9957c643", + "images_count": 7, + "graphs_count": 0, + "response": "The [lobula plate-lobula columnar neuron LPLC2](https://www.virtualflybrain.org/reports/FBbt_00111763 \"Open lobula plate-lobula columnar neuron LPLC2 in Virtual Fly Brain\") is located in the dorsal area of the lateral cell body rind, has distinct dendritic arbors in each lobula plate layer, and detects looming stimuli, eliciting a jump escape response. VFB holds [723](https://v2.virtualflybrain.org/org.geppetto.frontend/geppetto?q=FBbt_00111763,ListAllAvailableImages \"Run in VFB: List all available images of LPLC2\") images of LPLC2. There are [2](https://v2.virtualflybrain.org/org.geppetto.frontend/geppetto?q=FBbt_00111763,SplitsTargeting \"Run in VFB: Splits targeting LPLC2\") splits targeting LPLC2 and 2 scRNAseq data results for LPLC2.", + "quality_flags": { + "has_tool_status": true, + "no_tool_factual_answer": false, + "tool_claim_without_tool": false, + "disambiguation_only_answer": false, + "investigation_plan_answer": false, + "not_verified_or_no_results_answer": false, + "graph_failure_mentioned": false, + "missing_required_graph": false, + "used_data_resource": false, + "response_chars": 746, + "status_count": 13 + } + }, + { + "attempt_index": 12, + "task_index": 12, + "task_id": "T2.5", + "tier": 2, + "title": "Comparative anatomy", + "question": "How does the organisation of the antennal lobe compare between adult and larval Drosophila?", + "requires_graph": false, + "min_graphs": 0, + "repetition": 1, + "duration_ms": 7968, + "status_messages": [ + { + "message": "Thinking...", + "phase": "llm" + }, + { + "message": "Planning the answer", + "phase": "llm" + }, + { + "message": "Resolving 1 term in VFB", + "phase": "mcp" + }, + { + "message": "Querying VFB", + "phase": "mcp" + }, + { + "message": "Checking the answer is covered", + "phase": "llm" + }, + { + "message": "Writing the answer", + "phase": "llm" + } + ], + "event_count": 37, + "ok": true, + "request_id": "23ed5537-39e7-45f9-9a51-47982da28977", + "response_id": "chatcmpl-ea11ff7e568ddef63c49e39cd8eb9cb4", + "images_count": 6, + "graphs_count": 0, + "response": "The adult [antennal lobe](https://www.virtualflybrain.org/reports/FBbt_00003924 \"Open antennal lobe in Virtual Fly Brain\") has approximately 50 glomeruli, while the larval antennal lobe has around 22 glomeruli.", + "quality_flags": { + "has_tool_status": true, + "no_tool_factual_answer": false, + "tool_claim_without_tool": false, + "disambiguation_only_answer": false, + "investigation_plan_answer": false, + "not_verified_or_no_results_answer": false, + "graph_failure_mentioned": false, + "missing_required_graph": false, + "used_data_resource": false, + "response_chars": 210, + "status_count": 6 + } + }, + { + "attempt_index": 13, + "task_index": 13, + "task_id": "T2.6", + "tier": 2, + "title": "Publications for a circuit", + "question": "What publications describe the PPL1 dopaminergic neurons and their role in aversive memory?", + "requires_graph": false, + "min_graphs": 0, + "repetition": 1, + "duration_ms": 20773, + "status_messages": [ + { + "message": "Thinking...", + "phase": "llm" + }, + { + "message": "Planning the answer", + "phase": "llm" + }, + { + "phase": "plan", + "message": "The plan is contested — sampling again before committing." + }, + { + "message": "Resolving 1 term in VFB", + "phase": "mcp" + }, + { + "message": "Querying VFB", + "phase": "mcp" + }, + { + "message": "Reading VFB term info", + "phase": "mcp" + }, + { + "message": "Reading the literature", + "phase": "mcp" + }, + { + "message": "Checking the literature", + "phase": "mcp" + }, + { + "message": "Checking the answer is covered", + "phase": "llm" + }, + { + "message": "Writing the answer", + "phase": "llm" + } + ], + "event_count": 67, + "ok": true, + "request_id": "f30796cb-cbf9-4e20-b5ff-22db87da326a", + "response_id": "chatcmpl-9e3fac6af1ba91bbfc64978bc3749196", + "images_count": 8, + "graphs_count": 0, + "response": "Publications describing the dopaminergic PPL1 neurons and their role in aversive memory include Claridge-Chang et al., 2009, Mao and Davis, 2009, Budnik and White, 1988, and Ren et al., 2016.", + "quality_flags": { + "has_tool_status": true, + "no_tool_factual_answer": false, + "tool_claim_without_tool": false, + "disambiguation_only_answer": false, + "investigation_plan_answer": false, + "not_verified_or_no_results_answer": false, + "graph_failure_mentioned": false, + "missing_required_graph": false, + "used_data_resource": false, + "response_chars": 191, + "status_count": 10 + } + }, + { + "attempt_index": 14, + "task_index": 14, + "task_id": "T2.7", + "tier": 2, + "title": "Morphological similarity", + "question": "Are there neurons in the Hemibrain dataset that are morphologically similar to the fru+ mAL neurons described in light microscopy studies?", + "requires_graph": false, + "min_graphs": 0, + "repetition": 1, + "duration_ms": 9793, + "status_messages": [ + { + "message": "Thinking...", + "phase": "llm" + }, + { + "message": "Planning the answer", + "phase": "llm" + }, + { + "message": "Resolving 2 terms in VFB", + "phase": "mcp" + }, + { + "message": "Querying VFB", + "phase": "mcp" + }, + { + "message": "Checking the answer is covered", + "phase": "llm" + }, + { + "message": "Writing the answer", + "phase": "llm" + } + ], + "event_count": 31, + "ok": true, + "request_id": "5865b839-0fbb-4ac7-993c-99df867a3edd", + "response_id": "chatcmpl-8c1fffded1ed9ae0e253fbe71029a538", + "images_count": 5, + "graphs_count": 0, + "response": "The Hemibrain dataset contains neurons morphologically similar to the fru+ mAL neurons described in light microscopy studies.", + "quality_flags": { + "has_tool_status": true, + "no_tool_factual_answer": false, + "tool_claim_without_tool": false, + "disambiguation_only_answer": false, + "investigation_plan_answer": false, + "not_verified_or_no_results_answer": false, + "graph_failure_mentioned": false, + "missing_required_graph": false, + "used_data_resource": false, + "response_chars": 125, + "status_count": 6 + } + }, + { + "attempt_index": 15, + "task_index": 15, + "task_id": "T2.8", + "tier": 2, + "title": "Upstream circuit", + "question": "What sensory neurons provide input to the fan-shaped body, and through how many synaptic steps?", + "requires_graph": false, + "min_graphs": 0, + "repetition": 1, + "duration_ms": 23402, + "status_messages": [ + { + "message": "Thinking...", + "phase": "llm" + }, + { + "message": "Planning the answer", + "phase": "llm" + }, + { + "phase": "plan", + "message": "The plan is contested — sampling again before committing." + }, + { + "message": "Resolving 1 term in VFB", + "phase": "mcp" + }, + { + "message": "Reading VFB term info", + "phase": "mcp" + }, + { + "message": "Tracing the pathway", + "phase": "mcp" + }, + { + "message": "Querying VFB", + "phase": "mcp" + }, + { + "message": "Checking the answer is covered", + "phase": "llm" + }, + { + "message": "Querying VFB", + "phase": "mcp" + }, + { + "message": "Checking the answer is covered", + "phase": "llm" + }, + { + "message": "Writing the answer", + "phase": "llm" + }, + { + "message": "Checking before saying VFB has no data", + "phase": "mcp" + }, + { + "message": "Querying VFB", + "phase": "mcp" + }, + { + "message": "Querying VFB", + "phase": "mcp" + }, + { + "message": "Querying VFB", + "phase": "mcp" + }, + { + "message": "Checking the answer is covered", + "phase": "llm" + }, + { + "message": "Writing the answer", + "phase": "llm" + } + ], + "event_count": 337, + "ok": true, + "request_id": "ea19e709-32a7-4ea7-9473-d8e14d25510a", + "response_id": "chatcmpl-3a67634c46b27ec7469358f4488fcaa5", + "images_count": 8, + "graphs_count": 0, + "response": "The [fan-shaped body](https://www.virtualflybrain.org/reports/FBbt_00003679 \"Open fan-shaped body in Virtual Fly Brain\") receives input from various sensory neurons. VFB records show [102](https://v2.virtualflybrain.org/org.geppetto.frontend/geppetto?q=FBbt_00003679,NeuronsPresynapticHere \"Run in VFB: Neurons with presynaptic terminals in fan-shaped body\") neurons with presynaptic terminals in the fan-shaped body. The first 12 of these include [PFNd_PB2](https://www.virtualflybrain.org/reports/FBbt_00111391 \"Open PFNd_PB2 in Virtual Fly Brain\"), [PFNd_PB3](https://www.virtualflybrain.org/reports/FBbt_00111392 \"Open PFNd_PB3 in Virtual Fly Brain\"), [PFNd_PB5](https://www.virtualflybrain.org/reports/FBbt_00111394 \"Open PFNd_PB5 in Virtual Fly Brain\"), [PFNa_PB4](https://www.virtualflybrain.org/reports/FBbt_00111398 \"Open PFNa_PB4 in Virtual Fly Brain\"), [PFNa_PB5](https://www.virtualflybrain.org/reports/FBbt_00111399 \"Open PFNa_PB5 in Virtual Fly Brain\"), PFNa_PB6, PFNa_PB7, PFNa_PB9, PFNp_PB7, [protocerebral bridge glomerulus 8-fan-shaped body-ipsilateral ventral gall surround neuron](https://www.virtualflybrain.org/reports/FBbt_00111463 \"Open protocerebral bridge glomerulus 8-fan-shaped body-ipsilateral ventral gall surround neuron in Virtual Fly Brain\"), [adult ExR1 neuron of DM3 lineage](https://www.virtualflybrain.org/reports/FBbt_00053034 \"Open adult ExR1 neuron of DM3 lineage in Virtual Fly Brain\"), and adult ExR1 neuron of DM4 lineage. However, the exact number of synaptic steps between these sensory neurons and the fan-shaped body is not specified.", + "quality_flags": { + "has_tool_status": true, + "no_tool_factual_answer": false, + "tool_claim_without_tool": false, + "disambiguation_only_answer": false, + "investigation_plan_answer": false, + "not_verified_or_no_results_answer": false, + "graph_failure_mentioned": false, + "missing_required_graph": false, + "used_data_resource": false, + "response_chars": 1581, + "status_count": 17 + } + }, + { + "attempt_index": 16, + "task_index": 16, + "task_id": "T3.1", + "tier": 3, + "title": "Bidirectional connectivity", + "question": "Are there reciprocal connections between mushroom body output neurons (MBONs) and dopaminergic neurons (DANs)? Which pairs have the strongest mutual connectivity?", + "requires_graph": false, + "min_graphs": 0, + "repetition": 1, + "duration_ms": 19526, + "status_messages": [ + { + "message": "Thinking...", + "phase": "llm" + }, + { + "message": "Planning the answer", + "phase": "llm" + }, + { + "message": "Resolving 2 terms in VFB", + "phase": "mcp" + }, + { + "message": "Querying VFB connectivity", + "phase": "mcp" + }, + { + "message": "Checking the answer is covered", + "phase": "llm" + }, + { + "message": "Querying VFB", + "phase": "mcp" + }, + { + "message": "Querying VFB", + "phase": "mcp" + }, + { + "message": "Checking the answer is covered", + "phase": "llm" + }, + { + "message": "Writing the answer", + "phase": "llm" + } + ], + "event_count": 122, + "ok": true, + "request_id": "c38b2f58-3cc2-43a0-ad1a-0cea29df145b", + "response_id": "chatcmpl-3078d23a1603d309890ae3f949ae221b", + "images_count": 8, + "graphs_count": 0, + "response": "There are reciprocal connections between mushroom body output neurons and dopaminergic neurons. VFB found 5 reciprocal class-level pairs between [mushroom body output neuron](https://www.virtualflybrain.org/reports/FBbt_00047953 \"Open mushroom body output neuron in Virtual Fly Brain\") and [dopaminergic neuron](https://www.virtualflybrain.org/reports/FBbt_00005131 \"Open dopaminergic neuron in Virtual Fly Brain\"). The strongest specific targets of mushroom body output neuron include [primary interneuron](https://www.virtualflybrain.org/reports/FBbt_00052517 \"Open primary interneuron in Virtual Fly Brain\"), [primary neuron](https://www.virtualflybrain.org/reports/FBbt_00047097 \"Open primary neuron in Virtual Fly Brain\"), [adult GABAergic neuron](https://www.virtualflybrain.org/reports/FBbt_00058207 \"Open adult GABAergic neuron in Virtual Fly Brain\"), [GABAergic neuron](https://www.virtualflybrain.org/reports/FBbt_00007228 \"Open GABAergic neuron in Virtual Fly Brain\"), [adult glutamatergic neuron](https://www.virtualflybrain.org/reports/FBbt_00058208 \"Open adult glutamatergic neuron in Virtual Fly Brain\"), [glutamatergic neuron](https://www.virtualflybrain.org/reports/FBbt_00100291 \"Open glutamatergic neuron in Virtual Fly Brain\"), [adult lateral horn neuron](https://www.virtualflybrain.org/reports/FBbt_00048293 \"Open adult lateral horn neuron in Virtual Fly Brain\"), and [adult cholinergic neuron](https://www.virtualflybrain.org/reports/FBbt_00058205 \"Open adult cholinergic neuron in Virtual Fly Brain\"). The strongest specific targets of dopaminergic neuron include adult cholinergic neuron and [adult Kenyon cell](https://www.virtualflybrain.org/reports/FBbt_00049825 \"Open adult Kenyon cell in Virtual Fly Brain\").", + "quality_flags": { + "has_tool_status": true, + "no_tool_factual_answer": false, + "tool_claim_without_tool": false, + "disambiguation_only_answer": false, + "investigation_plan_answer": false, + "not_verified_or_no_results_answer": false, + "graph_failure_mentioned": false, + "missing_required_graph": false, + "used_data_resource": false, + "response_chars": 1738, + "status_count": 9 + } + }, + { + "attempt_index": 17, + "task_index": 17, + "task_id": "T3.2", + "tier": 3, + "title": "Pathway tracing", + "question": "Trace a pathway from olfactory receptor neurons to the lateral horn. What are the intermediate neuron types and their connections?", + "requires_graph": false, + "min_graphs": 0, + "repetition": 1, + "duration_ms": 16998, + "status_messages": [ + { + "message": "Thinking...", + "phase": "llm" + }, + { + "message": "Planning the answer", + "phase": "llm" + }, + { + "message": "Resolving 2 terms in VFB", + "phase": "mcp" + }, + { + "message": "Tracing the pathway", + "phase": "mcp" + }, + { + "message": "Checking the answer is covered", + "phase": "llm" + }, + { + "message": "Querying VFB", + "phase": "mcp" + }, + { + "message": "Querying VFB", + "phase": "mcp" + }, + { + "message": "Checking the answer is covered", + "phase": "llm" + }, + { + "message": "Writing the answer", + "phase": "llm" + } + ], + "event_count": 129, + "ok": true, + "request_id": "506616aa-cde2-44ad-9641-6f1a163b9e98", + "response_id": "chatcmpl-5f1540765d7ed2c7ba9f18a6d1ee3bbe", + "images_count": 8, + "graphs_count": 0, + "response": "The pathway from olfactory receptor neurons to the lateral horn involves intermediate neurons. Antennal lobe projection neurons are intermediate neurons that connect olfactory receptor neurons to the lateral horn. The strongest specific inputs to [olfactory receptor neuron](https://www.virtualflybrain.org/reports/FBbt_00005926 \"Open olfactory receptor neuron in Virtual Fly Brain\") are from [adult antennal lobe local neuron lLN](https://www.virtualflybrain.org/reports/FBbt_00051502 \"Open adult antennal lobe local neuron lLN in Virtual Fly Brain\"), [adult local interneuron of the lateral ALl1 neuroblast](https://www.virtualflybrain.org/reports/FBbt_00007394 \"Open adult local interneuron of the lateral ALl1 neuroblast in Virtual Fly Brain\"), [antennal lobe local neuron](https://www.virtualflybrain.org/reports/FBbt_00052874 \"Open antennal lobe local neuron in Virtual Fly Brain\"), [adult antennal lobe local neuron](https://www.virtualflybrain.org/reports/FBbt_00007390 \"Open adult antennal lobe local neuron in Virtual Fly Brain\"), and [olfactory system neuron](https://www.virtualflybrain.org/reports/FBbt_00007697 \"Open olfactory system neuron in Virtual Fly Brain\"). VFB holds [1661](https://v2.virtualflybrain.org/org.geppetto.frontend/geppetto?q=FBbt_00007053,NeuronsPartHere \"Run in VFB: Neurons with some part in adult lateral horn\") neurons with some part in [adult lateral horn](https://www.virtualflybrain.org/reports/FBbt_00007053 \"Open adult lateral horn in Virtual Fly Brain\") and [1658](https://v2.virtualflybrain.org/org.geppetto.frontend/geppetto?q=FBbt_00007053,NeuronsSynaptic \"Run in VFB: Neurons with synaptic terminals in adult lateral horn\") neurons with synaptic terminals in adult lateral horn.", + "quality_flags": { + "has_tool_status": true, + "no_tool_factual_answer": false, + "tool_claim_without_tool": false, + "disambiguation_only_answer": false, + "investigation_plan_answer": false, + "not_verified_or_no_results_answer": false, + "graph_failure_mentioned": false, + "missing_required_graph": false, + "used_data_resource": false, + "response_chars": 1727, + "status_count": 9 + } + }, + { + "attempt_index": 18, + "task_index": 18, + "task_id": "T3.3", + "tier": 3, + "title": "Cell type taxonomy depth", + "question": "How many distinct neuron types are currently classified within the adult Drosophila visual system, and how are they organised hierarchically?", + "requires_graph": false, + "min_graphs": 0, + "repetition": 1, + "duration_ms": 7685, + "status_messages": [ + { + "message": "Thinking...", + "phase": "llm" + }, + { + "message": "Planning the answer", + "phase": "llm" + }, + { + "message": "Resolving 1 term in VFB", + "phase": "mcp" + }, + { + "message": "Reading VFB term info", + "phase": "mcp" + }, + { + "message": "Summarising neuron taxonomy", + "phase": "mcp" + }, + { + "message": "Checking the answer is covered", + "phase": "llm" + }, + { + "message": "Writing the answer", + "phase": "llm" + } + ], + "event_count": 53, + "ok": true, + "request_id": "6c1ecfd1-2740-4980-9eb6-0283ec67ce7a", + "response_id": "chatcmpl-b3e0d632c38ceec65fad53aecdcb3645", + "images_count": 0, + "graphs_count": 0, + "response": "The question about the number of distinct neuron types in the adult Drosophila visual system and their hierarchical organization cannot be fully answered from VFB evidence. However, it is known that there are subclasses of visual system neuron.", + "quality_flags": { + "has_tool_status": true, + "no_tool_factual_answer": false, + "tool_claim_without_tool": false, + "disambiguation_only_answer": false, + "investigation_plan_answer": false, + "not_verified_or_no_results_answer": false, + "graph_failure_mentioned": false, + "missing_required_graph": false, + "used_data_resource": false, + "response_chars": 244, + "status_count": 7 + } + }, + { + "attempt_index": 19, + "task_index": 19, + "task_id": "T3.4", + "tier": 3, + "title": "Connectivity strength comparison", + "question": "Which neuron type provides the strongest synaptic input to the MBON-gamma1pedc>a/b neuron, and how does this compare to the next strongest inputs?", + "requires_graph": false, + "min_graphs": 0, + "repetition": 1, + "duration_ms": 10747, + "status_messages": [ + { + "message": "Thinking...", + "phase": "llm" + }, + { + "message": "Planning the answer", + "phase": "llm" + }, + { + "message": "Resolving 1 term in VFB", + "phase": "mcp" + }, + { + "message": "Querying VFB connectivity", + "phase": "mcp" + }, + { + "message": "Checking the literature", + "phase": "mcp" + }, + { + "message": "Checking the answer is covered", + "phase": "llm" + }, + { + "message": "Querying VFB", + "phase": "mcp" + }, + { + "message": "Checking the answer is covered", + "phase": "llm" + }, + { + "message": "Writing the answer", + "phase": "llm" + } + ], + "event_count": 51, + "ok": true, + "request_id": "29df1b22-259f-411e-861f-02ed981c9f56", + "response_id": "chatcmpl-e88ba1b4e2b65b76c8790ba59bf33c66", + "images_count": 8, + "graphs_count": 0, + "response": "The strongest synaptic input to the MBON-gamma1pedc>a/b neuron is not specified. VFB holds upstream connectivity classes for [mushroom body output neuron 11](https://www.virtualflybrain.org/reports/FBbt_00100246 \"Open mushroom body output neuron 11 in Virtual Fly Brain\"), but the lookup did not complete.", + "quality_flags": { + "has_tool_status": true, + "no_tool_factual_answer": false, + "tool_claim_without_tool": false, + "disambiguation_only_answer": false, + "investigation_plan_answer": false, + "not_verified_or_no_results_answer": false, + "graph_failure_mentioned": false, + "missing_required_graph": false, + "used_data_resource": false, + "response_chars": 305, + "status_count": 9 + } + }, + { + "attempt_index": 20, + "task_index": 20, + "task_id": "T3.5", + "tier": 3, + "title": "Shared connectivity", + "question": "Do the alpha/beta and gamma Kenyon cells converge on any of the same downstream MBON types? Which MBONs receive input from both?", + "requires_graph": false, + "min_graphs": 0, + "repetition": 1, + "duration_ms": 13869, + "status_messages": [ + { + "message": "Thinking...", + "phase": "llm" + }, + { + "message": "Planning the answer", + "phase": "llm" + }, + { + "message": "Resolving 3 terms in VFB", + "phase": "mcp" + }, + { + "message": "Querying VFB connectivity", + "phase": "mcp" + }, + { + "message": "Checking the answer is covered", + "phase": "llm" + }, + { + "message": "Querying VFB", + "phase": "mcp" + }, + { + "message": "Querying VFB", + "phase": "mcp" + }, + { + "message": "Checking the answer is covered", + "phase": "llm" + }, + { + "message": "Writing the answer", + "phase": "llm" + } + ], + "event_count": 79, + "ok": true, + "request_id": "3ed0d5a4-2483-4153-adc0-6e7807339e47", + "response_id": "chatcmpl-5b7a312d7d1c63e9aff6fb30cf0b760e", + "images_count": 8, + "graphs_count": 0, + "response": "The evidence does not provide information on whether the alpha/beta and gamma Kenyon cells converge on the same downstream [mushroom body output neuron](https://www.virtualflybrain.org/reports/FBbt_00047953 \"Open mushroom body output neuron in Virtual Fly Brain\") types. VFB does not currently hold data on the downstream connectivity classes for gamma Kenyon cells. VFB holds [69](https://v2.virtualflybrain.org/org.geppetto.frontend/geppetto?q=FBbt_00047953,SubclassesOf \"Run in VFB: Subclasses of MBON\") subclasses of mushroom body output neuron and [6](https://v2.virtualflybrain.org/org.geppetto.frontend/geppetto?q=FBbt_00100248,SubclassesOf \"Run in VFB: Subclasses of KCab\") subclasses of [alpha/beta Kenyon cell](https://www.virtualflybrain.org/reports/FBbt_00100248 \"Open alpha/beta Kenyon cell in Virtual Fly Brain\").", + "quality_flags": { + "has_tool_status": true, + "no_tool_factual_answer": false, + "tool_claim_without_tool": false, + "disambiguation_only_answer": false, + "investigation_plan_answer": false, + "not_verified_or_no_results_answer": false, + "graph_failure_mentioned": false, + "missing_required_graph": false, + "used_data_resource": false, + "response_chars": 827, + "status_count": 9 + } + }, + { + "attempt_index": 21, + "task_index": 21, + "task_id": "T3.6", + "tier": 3, + "title": "Anatomical containment chain", + "question": "Trace the anatomical containment hierarchy from the DA1 glomerulus up to the top-level brain structure. What is each level in the hierarchy?", + "requires_graph": false, + "min_graphs": 0, + "repetition": 1, + "duration_ms": 10780, + "status_messages": [ + { + "message": "Thinking...", + "phase": "llm" + }, + { + "message": "Planning the answer", + "phase": "llm" + }, + { + "message": "Resolving 1 term in VFB", + "phase": "mcp" + }, + { + "message": "Tracing the pathway", + "phase": "mcp" + }, + { + "message": "Querying VFB", + "phase": "mcp" + }, + { + "message": "Checking the answer is covered", + "phase": "llm" + }, + { + "message": "Writing the answer", + "phase": "llm" + } + ], + "event_count": 92, + "ok": true, + "request_id": "eb74e3ea-d13d-43cc-8b4c-c7507452e827", + "response_id": "chatcmpl-7855b42a02d885879ec9b398f4db0bbf", + "images_count": 0, + "graphs_count": 0, + "response": "The anatomical containment hierarchy from the DA1 glomerulus up to the top-level brain structure is: DA1 glomerulus -> adult olfactory antennal lobe glomerulus -> adult antennal lobe -> adult deutocerebrum -> adult cerebrum -> adult central brain -> adult brain. VFB does not currently hold data on parts of the [antennal lobe glomerulus DA1](https://www.virtualflybrain.org/reports/FBbt_00003932 \"Open antennal lobe glomerulus DA1 in Virtual Fly Brain\").", + "quality_flags": { + "has_tool_status": true, + "no_tool_factual_answer": false, + "tool_claim_without_tool": false, + "disambiguation_only_answer": false, + "investigation_plan_answer": false, + "not_verified_or_no_results_answer": false, + "graph_failure_mentioned": false, + "missing_required_graph": false, + "used_data_resource": false, + "response_chars": 455, + "status_count": 7 + } + }, + { + "attempt_index": 22, + "task_index": 22, + "task_id": "T3.7", + "tier": 3, + "title": "Cross-region connectivity", + "question": "What neuron types connect the central complex to the lateral accessory lobe, and how strong are these connections?", + "requires_graph": false, + "min_graphs": 0, + "repetition": 1, + "duration_ms": 16915, + "status_messages": [ + { + "message": "Thinking...", + "phase": "llm" + }, + { + "message": "Planning the answer", + "phase": "llm" + }, + { + "message": "Resolving 2 terms in VFB", + "phase": "mcp" + }, + { + "message": "Tracing the pathway", + "phase": "mcp" + }, + { + "message": "Querying VFB", + "phase": "mcp" + }, + { + "message": "Querying VFB", + "phase": "mcp" + }, + { + "message": "Checking the answer is covered", + "phase": "llm" + }, + { + "message": "Querying VFB", + "phase": "mcp" + }, + { + "message": "Querying VFB", + "phase": "mcp" + }, + { + "message": "Checking the answer is covered", + "phase": "llm" + }, + { + "message": "Writing the answer", + "phase": "llm" + } + ], + "event_count": 134, + "ok": true, + "request_id": "2dacdca2-d66d-4cce-a71d-695c3876df95", + "response_id": "chatcmpl-4209df9056541f6172d6da592f9b4fb0", + "images_count": 8, + "graphs_count": 0, + "response": "PFL classes are central-complex-related neuron classes connecting the [adult central complex](https://www.virtualflybrain.org/reports/FBbt_00003632 \"Open adult central complex in Virtual Fly Brain\") to the [lateral accessory lobe on L3 CNS template, Wood2018](https://www.virtualflybrain.org/reports/VFB_00050314 \"Open lateral accessory lobe on L3 CNS template, Wood2018 in Virtual Fly Brain\"). VFB records show that neurons such as [PEN_PB2](https://www.virtualflybrain.org/reports/FBbt_00111369 \"Open PEN_PB2 in Virtual Fly Brain\"), [PEN_PB3](https://www.virtualflybrain.org/reports/FBbt_00111370 \"Open PEN_PB3 in Virtual Fly Brain\"), [PEN_PB7](https://www.virtualflybrain.org/reports/FBbt_00111373 \"Open PEN_PB7 in Virtual Fly Brain\"), [PEN_PB8](https://www.virtualflybrain.org/reports/FBbt_00111374 \"Open PEN_PB8 in Virtual Fly Brain\"), and several adult protocerebral bridge glomerulus neurons have some part in the adult central complex and have synaptic terminals there. However, the strength of these connections is not specified. VFB does not currently hold data on neurons with presynaptic or postsynaptic terminals in the embryonic/larval lateral accessory lobe.", + "quality_flags": { + "has_tool_status": true, + "no_tool_factual_answer": false, + "tool_claim_without_tool": false, + "disambiguation_only_answer": false, + "investigation_plan_answer": false, + "not_verified_or_no_results_answer": false, + "graph_failure_mentioned": false, + "missing_required_graph": false, + "used_data_resource": false, + "response_chars": 1173, + "status_count": 11 + } + }, + { + "attempt_index": 23, + "task_index": 23, + "task_id": "T3.8", + "tier": 3, + "title": "Dataset coverage", + "question": "For the DNa02 descending neuron type, what data is available in VFB? Is it in the Hemibrain, FAFB, or both? Are there light microscopy images and driver lines?", + "requires_graph": false, + "min_graphs": 0, + "repetition": 1, + "ok": false, + "duration_ms": null, + "error": "Timed out after 240000 ms", + "quality_flags": { + "has_tool_status": false, + "no_tool_factual_answer": false, + "tool_claim_without_tool": false, + "disambiguation_only_answer": false, + "investigation_plan_answer": false, + "not_verified_or_no_results_answer": false, + "graph_failure_mentioned": false, + "missing_required_graph": false, + "used_data_resource": false, + "response_chars": 25, + "status_count": 0 + } + }, + { + "attempt_index": 24, + "task_index": 24, + "task_id": "T4.1", + "tier": 4, + "title": "Experimental planning", + "question": "I want to study the neural circuit underlying CO2 avoidance in Drosophila. What neurons are involved, how are they connected, and what genetic tools can I use to access them?", + "requires_graph": false, + "min_graphs": 0, + "repetition": 1, + "duration_ms": 9429, + "status_messages": [ + { + "message": "Thinking...", + "phase": "llm" + }, + { + "message": "Planning the answer", + "phase": "llm" + }, + { + "message": "Resolving 1 term in VFB", + "phase": "mcp" + }, + { + "message": "Querying VFB", + "phase": "mcp" + }, + { + "message": "Checking the answer is covered", + "phase": "llm" + }, + { + "message": "Writing the answer", + "phase": "llm" + } + ], + "event_count": 92, + "ok": true, + "request_id": "aebf3410-a0d5-46f2-a4ae-1b8beb87cb61", + "response_id": "chatcmpl-40349a259b65ebbb5f5699c7d8d173ff", + "images_count": 0, + "graphs_count": 0, + "response": "The neurons involved in the detection of carbon dioxide include carbon dioxide sensitive neurons. These neurons have downstream connections to GABAergic local interneuron of the adult antennal lobe, adult antennal lobe local neuron lLN2P, and cholinergic local interneuron of the adult antennal lobe. Genetic tools for accessing these neurons include Gr21a, Gr63a, and E409 expression patterns.", + "quality_flags": { + "has_tool_status": true, + "no_tool_factual_answer": false, + "tool_claim_without_tool": false, + "disambiguation_only_answer": false, + "investigation_plan_answer": false, + "not_verified_or_no_results_answer": false, + "graph_failure_mentioned": false, + "missing_required_graph": false, + "used_data_resource": false, + "response_chars": 394, + "status_count": 6 + } + }, + { + "attempt_index": 25, + "task_index": 25, + "task_id": "T4.2", + "tier": 4, + "title": "Complete neuron profile", + "question": "Give me a comprehensive profile of the giant fiber neuron: its anatomy, connectivity, available driver lines, and relevant publications.", + "requires_graph": false, + "min_graphs": 0, + "repetition": 1, + "duration_ms": 19842, + "status_messages": [ + { + "message": "Thinking...", + "phase": "llm" + }, + { + "message": "Planning the answer", + "phase": "llm" + }, + { + "message": "Resolving 1 term in VFB", + "phase": "mcp" + }, + { + "message": "Querying VFB", + "phase": "mcp" + }, + { + "message": "Querying VFB connectivity", + "phase": "mcp" + }, + { + "message": "Querying VFB", + "phase": "mcp" + }, + { + "message": "Checking the literature", + "phase": "mcp" + }, + { + "message": "Checking the answer is covered", + "phase": "llm" + }, + { + "message": "Writing the answer", + "phase": "llm" + } + ], + "event_count": 363, + "ok": true, + "request_id": "9034886c-39cb-4790-ad56-c809f112cad0", + "response_id": "chatcmpl-38979a4c7f39098899c629a476ca2cae", + "images_count": 8, + "graphs_count": 1, + "response": "The [giant fiber neuron](https://www.virtualflybrain.org/reports/FBbt_00004020 \"Open giant fiber neuron in Virtual Fly Brain\") is a large adult descending neuron that controls jump escape behavior. Its downstream connectivity classes for DNp01 include [389](https://v2.virtualflybrain.org/org.geppetto.frontend/geppetto?q=FBbt_00004020,DownstreamClassConnectivity \"Run in VFB: Downstream connectivity classes for DNp01\") entries, and its upstream connectivity classes for DNp01 include [472](https://v2.virtualflybrain.org/org.geppetto.frontend/geppetto?q=FBbt_00004020,UpstreamClassConnectivity \"Run in VFB: Upstream connectivity classes for DNp01\") entries. The giant fiber neuron connects to various neuron types, including [adult VNC neuron](https://www.virtualflybrain.org/reports/FBbt_00059289 \"Open adult VNC neuron in Virtual Fly Brain\"), [thoracic neuron](https://www.virtualflybrain.org/reports/FBbt_00001983 \"Open thoracic neuron in Virtual Fly Brain\"), [mesothoracic neuron](https://www.virtualflybrain.org/reports/FBbt_00001985 \"Open mesothoracic neuron in Virtual Fly Brain\"), [primary neuron](https://www.virtualflybrain.org/reports/FBbt_00047097 \"Open primary neuron in Virtual Fly Brain\"), [Notch OFF hemilineage secondary neuron](https://www.virtualflybrain.org/reports/FBbt_00049542 \"Open Notch OFF hemilineage secondary neuron in Virtual Fly Brain\"), [prothoracic neuron](https://www.virtualflybrain.org/reports/FBbt_00001984 \"Open prothoracic neuron in Virtual Fly Brain\"), [Notch ON hemilineage secondary neuron](https://www.virtualflybrain.org/reports/FBbt_00049541 \"Open Notch ON hemilineage secondary neuron in Virtual Fly Brain\"), [adult ascending neuron](https://www.virtualflybrain.org/reports/FBbt_00048301 \"Open adult ascending neuron in Virtual Fly Brain\"), [sensory system neuron](https://www.virtualflybrain.org/reports/FBbt_00007693 \"Open sensory system neuron in Virtual Fly Brain\"), [projection neuron](https://www.virtualflybrain.org/reports/FBbt_00007392 \"Open projection neuron in Virtual Fly Brain\"), [Notch OFF hemilineage primary neuron](https://www.virtualflybrain.org/reports/FBbt_00047105 \"Open Notch OFF hemilineage primary neuron in Virtual Fly Brain\"), and [adult visual projection neuron](https://www.virtualflybrain.org/reports/FBbt_00048286 \"Open adult visual projection neuron in Virtual Fly Brain\").\n\nThere are [10](https://v2.virtualflybrain.org/org.geppetto.frontend/geppetto?q=FBbt_00004020,TransgeneExpressionHere \"Run in VFB: Transgene expression in DNp01\") transgene expression patterns available for DNp01, including [P{GMR78G07-GAL4} expression pattern](https://www.virtualflybrain.org/reports/VFBexp_FBtp0062972 \"Open P{GMR78G07-GAL4} expression pattern in Virtual Fly Brain\"), [P{GMR79D08-GAL4} expression pattern](https://www.virtualflybrain.org/reports/VFBexp_FBtp0063022 \"Open P{GMR79D08-GAL4} expression pattern in Virtual Fly Brain\"), [P{GMR91H05-GAL4} expression pattern](https://www.virtualflybrain.org/reports/VFBexp_FBtp0064022 \"Open P{GMR91H05-GAL4} expression pattern in Virtual Fly Brain\"), [P{R48A11-GAL4.DBD} ∩ P{R30C01-p65.AD} expression pattern](https://www.virtualflybrain.org/reports/VFBexp_FBtp0121835FBtp0118557 \"Open P{R48A11-GAL4.DBD} ∩ P{R30C01-p65.AD} expression pattern in Virtual Fly Brain\"), [P{R68A06-GAL4.DBD} ∩ P{R25C08-p65.AD} expression pattern](https://www.virtualflybrain.org/reports/VFBexp_FBtp0116198FBtp0118471 \"Open P{R68A06-GAL4.DBD} ∩ P{R25C08-p65.AD} expression pattern in Virtual Fly Brain\"), [P{R79H02-GAL4.DBD} ∩ P{R14A01-p65.AD} expression pattern](https://www.virtualflybrain.org/reports/VFBexp_FBtp0122311FBtp0118233 \"Open P{R79H02-GAL4.DBD} ∩ P{R14A01-p65.AD} expression pattern in Virtual Fly Brain\"), [P{R79H02-GAL4.DBD} ∩ P{R25C08-p65.AD} expression pattern](https://www.virtualflybrain.org/reports/VFBexp_FBtp0122311FBtp0118471 \"Open P{R79H02-GAL4.DBD} ∩ P{R25C08-p65.AD} expression pattern in Virtual Fly Brain\"), [P{VT004455-GAL4.DBD} ∩ P{R10A12-p65.AD} expression pattern](https://www.virtualflybrain.org/reports/VFBexp_FBtp0122730FBtp0118153 \"Open P{VT004455-GAL4.DBD} ∩ P{R10A12-p65.AD} expression pattern in Virtual Fly Brain\"), P{VT014708-GAL4} expression pattern, and P{VT046265-GAL4} expression pattern.\n\nThe giant fiber neuron is described in the publication by Thomas and Wyman (1984).", + "graphs": [ + { + "type": "basic_graph", + "version": 1, + "title": "Downstream partners of DNp01", + "directed": true, + "layout": "circle", + "nodes": [ + { + "id": "FBbt_00004020", + "label": "DNp01", + "group": null, + "color": null, + "size": 4 + }, + { + "id": "FBbt_00047095", + "label": "adult neuron", + "group": null, + "color": null, + "size": 1.48 + }, + { + "id": "FBbt_00005106", + "label": "neuron", + "group": null, + "color": null, + "size": 1.48 + }, + { + "id": "FBbt_00059271", + "label": "CNS neuron", + "group": null, + "color": null, + "size": 1.47 + }, + { + "id": "FBbt_00059289", + "label": "adult VNC neuron", + "group": null, + "color": null, + "size": 1.31 + }, + { + "id": "FBbt_00001983", + "label": "thoracic neuron", + "group": null, + "color": null, + "size": 1.31 + }, + { + "id": "FBbt_00001985", + "label": "mesothoracic neuron", + "group": null, + "color": null, + "size": 1.19 + }, + { + "id": "FBbt_00047097", + "label": "primary neuron", + "group": null, + "color": null, + "size": 1.13 + }, + { + "id": "FBbt_00049542", + "label": "Notch OFF hemilineage secondary neuron", + "group": null, + "color": null, + "size": 1.13 + }, + { + "id": "FBbt_00001984", + "label": "prothoracic neuron", + "group": null, + "color": null, + "size": 1.12 + }, + { + "id": "FBbt_00049541", + "label": "Notch ON hemilineage secondary neuron", + "group": null, + "color": null, + "size": 1.08 + }, + { + "id": "FBbt_00048301", + "label": "adult ascending neuron", + "group": null, + "color": null, + "size": 1.07 + }, + { + "id": "FBbt_00007693", + "label": "sensory system neuron", + "group": null, + "color": null, + "size": 1.06 + }, + { + "id": "FBbt_00007392", + "label": "projection neuron", + "group": null, + "color": null, + "size": 1.06 + }, + { + "id": "FBbt_00047105", + "label": "Notch OFF hemilineage primary neuron", + "group": null, + "color": null, + "size": 1.06 + }, + { + "id": "FBbt_00048286", + "label": "adult visual projection neuron", + "group": null, + "color": null, + "size": 1.06 + } + ], + "edges": [ + { + "source": "FBbt_00004020", + "target": "FBbt_00047095", + "label": "4235", + "weight": 4235 + }, + { + "source": "FBbt_00004020", + "target": "FBbt_00005106", + "label": "4235", + "weight": 4235 + }, + { + "source": "FBbt_00004020", + "target": "FBbt_00059271", + "label": "4193", + "weight": 4193 + }, + { + "source": "FBbt_00004020", + "target": "FBbt_00059289", + "label": "2779", + "weight": 2779 + }, + { + "source": "FBbt_00004020", + "target": "FBbt_00001983", + "label": "2758", + "weight": 2758 + }, + { + "source": "FBbt_00004020", + "target": "FBbt_00001985", + "label": "1651", + "weight": 1651 + }, + { + "source": "FBbt_00004020", + "target": "FBbt_00047097", + "label": "1197", + "weight": 1197 + }, + { + "source": "FBbt_00004020", + "target": "FBbt_00049542", + "label": "1152", + "weight": 1152 + }, + { + "source": "FBbt_00004020", + "target": "FBbt_00001984", + "label": "1098", + "weight": 1098 + }, + { + "source": "FBbt_00004020", + "target": "FBbt_00049541", + "label": "674", + "weight": 674 + }, + { + "source": "FBbt_00004020", + "target": "FBbt_00048301", + "label": "641", + "weight": 641 + }, + { + "source": "FBbt_00004020", + "target": "FBbt_00007693", + "label": "556", + "weight": 556 + }, + { + "source": "FBbt_00004020", + "target": "FBbt_00007392", + "label": "505", + "weight": 505 + }, + { + "source": "FBbt_00004020", + "target": "FBbt_00047105", + "label": "495", + "weight": 495 + }, + { + "source": "FBbt_00004020", + "target": "FBbt_00048286", + "label": "494", + "weight": 494 + } + ] + } + ], + "quality_flags": { + "has_tool_status": true, + "no_tool_factual_answer": false, + "tool_claim_without_tool": false, + "disambiguation_only_answer": false, + "investigation_plan_answer": false, + "not_verified_or_no_results_answer": false, + "graph_failure_mentioned": false, + "missing_required_graph": false, + "used_data_resource": false, + "response_chars": 4311, + "status_count": 9 + } + }, + { + "attempt_index": 26, + "task_index": 26, + "task_id": "T4.3", + "tier": 4, + "title": "Hypothesis generation", + "question": "Based on connectivity data, what neuron types might mediate a connection between the visual system and the mushroom body? Could visual information reach the memory circuit?", + "requires_graph": false, + "min_graphs": 0, + "repetition": 1, + "duration_ms": 17548, + "status_messages": [ + { + "message": "Thinking...", + "phase": "llm" + }, + { + "message": "Planning the answer", + "phase": "llm" + }, + { + "message": "Resolving 2 terms in VFB", + "phase": "mcp" + }, + { + "message": "Tracing the pathway", + "phase": "mcp" + }, + { + "message": "Querying VFB connectivity", + "phase": "mcp" + }, + { + "message": "Checking the answer is covered", + "phase": "llm" + }, + { + "message": "Querying VFB", + "phase": "mcp" + }, + { + "message": "Querying VFB", + "phase": "mcp" + }, + { + "message": "Checking the answer is covered", + "phase": "llm" + }, + { + "message": "Writing the answer", + "phase": "llm" + } + ], + "event_count": 178, + "ok": true, + "request_id": "274deef7-044d-4499-8ae1-48ebdc17526d", + "response_id": "chatcmpl-be3a1ce126d973dc05a873bd90752385", + "images_count": 8, + "graphs_count": 1, + "response": "Based on connectivity data, adult visual projection neurons might mediate the connection between the visual system and the [mushroom body](https://www.virtualflybrain.org/reports/FBbt_00005801 \"Open mushroom body in Virtual Fly Brain\"), as they have presynaptic terminals in the mushroom body. Projection neurons are also suggested to mediate this connection. The strongest specific inputs to [visual system neuron](https://www.virtualflybrain.org/reports/FBbt_00047736 \"Open visual system neuron in Virtual Fly Brain\") include [optic lobe narrow field columnar neuron](https://www.virtualflybrain.org/reports/FBbt_00110136 \"Open optic lobe narrow field columnar neuron in Virtual Fly Brain\"), [optic lobe intrinsic columnar neuron](https://www.virtualflybrain.org/reports/FBbt_00007578 \"Open optic lobe intrinsic columnar neuron in Virtual Fly Brain\"), [adult optic lobe neuron](https://www.virtualflybrain.org/reports/FBbt_00003702 \"Open adult optic lobe neuron in Virtual Fly Brain\"), and [adult optic lobe columnar neuron](https://www.virtualflybrain.org/reports/FBbt_00005129 \"Open adult optic lobe columnar neuron in Virtual Fly Brain\"). The strongest specific targets of visual system neuron include adult optic lobe neuron, [optic lobe wide-field columnar neuron](https://www.virtualflybrain.org/reports/FBbt_00110137 \"Open optic lobe wide-field columnar neuron in Virtual Fly Brain\"), adult optic lobe columnar neuron, optic lobe intrinsic columnar neuron, and [adult visual projection neuron](https://www.virtualflybrain.org/reports/FBbt_00048286 \"Open adult visual projection neuron in Virtual Fly Brain\"). Visual information could reach the memory circuit through these connections. VFB holds [602](https://v2.virtualflybrain.org/org.geppetto.frontend/geppetto?q=FBbt_00005801,NeuronsPartHere \"Run in VFB: Neurons with some part in mushroom body\") neurons with some part in mushroom body and [601](https://v2.virtualflybrain.org/org.geppetto.frontend/geppetto?q=FBbt_00005801,NeuronsSynaptic \"Run in VFB: Neurons with synaptic terminals in mushroom body\") neurons with synaptic terminals in mushroom body.", + "graphs": [ + { + "type": "basic_graph", + "version": 1, + "title": "Downstream partners of visual system neuron", + "directed": true, + "layout": "circle", + "nodes": [ + { + "id": "FBbt_00047736", + "label": "visual system neuron", + "group": null, + "color": null, + "size": 4 + }, + { + "id": "FBbt_00005106", + "label": "neuron", + "group": null, + "color": null, + "size": 1.33 + }, + { + "id": "FBbt_00047095", + "label": "adult neuron", + "group": null, + "color": null, + "size": 1.33 + }, + { + "id": "FBbt_00059271", + "label": "CNS neuron", + "group": null, + "color": null, + "size": 1.33 + }, + { + "id": "FBbt_00007693", + "label": "sensory system neuron", + "group": null, + "color": null, + "size": 1.31 + }, + { + "id": "FBbt_00005129", + "label": "adult optic lobe columnar neuron", + "group": null, + "color": null, + "size": 1.22 + }, + { + "id": "FBbt_00003702", + "label": "adult optic lobe neuron", + "group": null, + "color": null, + "size": 1.22 + }, + { + "id": "FBbt_00007578", + "label": "optic lobe intrinsic columnar neuron", + "group": null, + "color": null, + "size": 1.16 + }, + { + "id": "FBbt_00110137", + "label": "optic lobe wide-field columnar neuron", + "group": null, + "color": null, + "size": 1.08 + }, + { + "id": "FBbt_00007392", + "label": "projection neuron", + "group": null, + "color": null, + "size": 1.08 + }, + { + "id": "FBbt_00048287", + "label": "visual projection neuron", + "group": null, + "color": null, + "size": 1.08 + }, + { + "id": "FBbt_00048286", + "label": "adult visual projection neuron", + "group": null, + "color": null, + "size": 1.08 + }, + { + "id": "FBbt_00003788", + "label": "transmedullary neuron", + "group": null, + "color": null, + "size": 1.07 + }, + { + "id": "FBbt_00110136", + "label": "optic lobe narrow field columnar neuron", + "group": null, + "color": null, + "size": 1.06 + }, + { + "id": "FBbt_00049542", + "label": "Notch OFF hemilineage secondary neuron", + "group": null, + "color": null, + "size": 1.05 + } + ], + "edges": [ + { + "source": "FBbt_00047736", + "target": "FBbt_00005106", + "label": "52519700", + "weight": 1000000 + }, + { + "source": "FBbt_00047736", + "target": "FBbt_00047095", + "label": "52515264", + "weight": 1000000 + }, + { + "source": "FBbt_00047736", + "target": "FBbt_00059271", + "label": "52026280", + "weight": 1000000 + }, + { + "source": "FBbt_00047736", + "target": "FBbt_00007693", + "label": "49149406", + "weight": 1000000 + }, + { + "source": "FBbt_00047736", + "target": "FBbt_00047736", + "label": "49133005", + "weight": 1000000 + }, + { + "source": "FBbt_00047736", + "target": "FBbt_00005129", + "label": "34860032", + "weight": 1000000 + }, + { + "source": "FBbt_00047736", + "target": "FBbt_00003702", + "label": "34548245", + "weight": 1000000 + }, + { + "source": "FBbt_00047736", + "target": "FBbt_00007578", + "label": "24889906", + "weight": 1000000 + }, + { + "source": "FBbt_00047736", + "target": "FBbt_00110137", + "label": "12826675", + "weight": 1000000 + }, + { + "source": "FBbt_00047736", + "target": "FBbt_00007392", + "label": "12324568", + "weight": 1000000 + }, + { + "source": "FBbt_00047736", + "target": "FBbt_00048287", + "label": "12309806", + "weight": 1000000 + }, + { + "source": "FBbt_00047736", + "target": "FBbt_00048286", + "label": "12308357", + "weight": 1000000 + }, + { + "source": "FBbt_00047736", + "target": "FBbt_00003788", + "label": "11821502", + "weight": 1000000 + }, + { + "source": "FBbt_00047736", + "target": "FBbt_00110136", + "label": "8919227", + "weight": 1000000 + }, + { + "source": "FBbt_00047736", + "target": "FBbt_00049542", + "label": "8358929", + "weight": 1000000 + } + ] + } + ], + "quality_flags": { + "has_tool_status": true, + "no_tool_factual_answer": false, + "tool_claim_without_tool": false, + "disambiguation_only_answer": false, + "investigation_plan_answer": false, + "not_verified_or_no_results_answer": false, + "graph_failure_mentioned": false, + "missing_required_graph": false, + "used_data_resource": false, + "response_chars": 2117, + "status_count": 10 + } + }, + { + "attempt_index": 27, + "task_index": 27, + "task_id": "T4.4", + "tier": 4, + "title": "Comparative analysis", + "question": "Compare the downstream targets of the two main types of clock neurons (s-LNv and l-LNv). Do they converge on any common target neuron types?", + "requires_graph": false, + "min_graphs": 0, + "repetition": 1, + "duration_ms": 12275, + "status_messages": [ + { + "message": "Thinking...", + "phase": "llm" + }, + { + "message": "Planning the answer", + "phase": "llm" + }, + { + "message": "Resolving 2 terms in VFB", + "phase": "mcp" + }, + { + "message": "Querying VFB connectivity", + "phase": "mcp" + }, + { + "message": "Checking the answer is covered", + "phase": "llm" + }, + { + "message": "Querying VFB", + "phase": "mcp" + }, + { + "message": "Querying VFB", + "phase": "mcp" + }, + { + "message": "Checking the answer is covered", + "phase": "llm" + }, + { + "message": "Writing the answer", + "phase": "llm" + } + ], + "event_count": 90, + "ok": true, + "request_id": "48c7133c-c0b9-4ad1-b9f8-ca959f38df43", + "response_id": "chatcmpl-2409d82373b95e2d1ebd6b5ec616acd9", + "images_count": 8, + "graphs_count": 1, + "response": "The downstream targets of [l-LNv neuron](https://www.virtualflybrain.org/reports/FBbt_00003763 \"Open l-LNv neuron in Virtual Fly Brain\") include [adult visual projection neuron](https://www.virtualflybrain.org/reports/FBbt_00048286 \"Open adult visual projection neuron in Virtual Fly Brain\"), [sensory system neuron](https://www.virtualflybrain.org/reports/FBbt_00007693 \"Open sensory system neuron in Virtual Fly Brain\"), [Notch ON hemilineage secondary neuron](https://www.virtualflybrain.org/reports/FBbt_00049541 \"Open Notch ON hemilineage secondary neuron in Virtual Fly Brain\"), [optic lobe narrow field columnar neuron](https://www.virtualflybrain.org/reports/FBbt_00110136 \"Open optic lobe narrow field columnar neuron in Virtual Fly Brain\"), [optic lobe intrinsic columnar neuron](https://www.virtualflybrain.org/reports/FBbt_00007578 \"Open optic lobe intrinsic columnar neuron in Virtual Fly Brain\"), [adult optic lobe neuron](https://www.virtualflybrain.org/reports/FBbt_00003702 \"Open adult optic lobe neuron in Virtual Fly Brain\"), and [adult optic lobe columnar neuron](https://www.virtualflybrain.org/reports/FBbt_00005129 \"Open adult optic lobe columnar neuron in Virtual Fly Brain\"). VFB does not currently hold data on the downstream connectivity classes for [adult s-LNv neuron](https://www.virtualflybrain.org/reports/FBbt_00007428 \"Open adult s-LNv neuron in Virtual Fly Brain\").", + "graphs": [ + { + "type": "basic_graph", + "version": 1, + "title": "Downstream targets by source class", + "directed": true, + "layout": "circle", + "nodes": [ + { + "id": "FBbt_00003763", + "label": "l-LNv", + "group": null, + "color": null, + "size": 4 + }, + { + "id": "FBbt_00005106", + "label": "neuron", + "group": null, + "color": null, + "size": 1.17 + }, + { + "id": "FBbt_00047095", + "label": "adult neuron", + "group": null, + "color": null, + "size": 1.17 + }, + { + "id": "FBbt_00059271", + "label": "CNS neuron", + "group": null, + "color": null, + "size": 1.17 + }, + { + "id": "FBbt_00059274", + "label": "adult CNS neuron", + "group": null, + "color": null, + "size": 1.17 + }, + { + "id": "FBbt_00007693", + "label": "sensory system neuron", + "group": null, + "color": null, + "size": 1.17 + }, + { + "id": "FBbt_00047736", + "label": "visual system neuron", + "group": null, + "color": null, + "size": 1.17 + }, + { + "id": "FBbt_00005125", + "label": "interneuron", + "group": null, + "color": null, + "size": 1.16 + }, + { + "id": "FBbt_00052046", + "label": "adult interneuron", + "group": null, + "color": null, + "size": 1.16 + }, + { + "id": "FBbt_00001366", + "label": "supraesophageal ganglion neuron", + "group": null, + "color": null, + "size": 1.16 + }, + { + "id": "FBbt_00003702", + "label": "adult optic lobe neuron", + "group": null, + "color": null, + "size": 1.15 + }, + { + "id": "FBbt_00059247", + "label": "adult visual neuropil intrinsic neuron", + "group": null, + "color": null, + "size": 1.15 + }, + { + "id": "FBbt_00007577", + "label": "adult optic lobe intrinsic neuron", + "group": null, + "color": null, + "size": 1.15 + }, + { + "id": "FBbt_00007173", + "label": "cholinergic neuron", + "group": null, + "color": null, + "size": 1.14 + }, + { + "id": "FBbt_00058205", + "label": "adult cholinergic neuron", + "group": null, + "color": null, + "size": 1.14 + }, + { + "id": "FBbt_00005129", + "label": "adult optic lobe columnar neuron", + "group": null, + "color": null, + "size": 1.14 + }, + { + "id": "FBbt_00007578", + "label": "optic lobe intrinsic columnar neuron", + "group": null, + "color": null, + "size": 1.14 + }, + { + "id": "FBbt_00047096", + "label": "secondary neuron", + "group": null, + "color": null, + "size": 1.13 + }, + { + "id": "FBbt_00110136", + "label": "optic lobe narrow field columnar neuron", + "group": null, + "color": null, + "size": 1.13 + }, + { + "id": "FBbt_00049539", + "label": "Notch ON hemilineage neuron", + "group": null, + "color": null, + "size": 1.13 + }, + { + "id": "FBbt_00049541", + "label": "Notch ON hemilineage secondary neuron", + "group": null, + "color": null, + "size": 1.13 + } + ], + "edges": [ + { + "source": "FBbt_00003763", + "target": "FBbt_00005106", + "label": "6184", + 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"quality_flags": { + "has_tool_status": true, + "no_tool_factual_answer": false, + "tool_claim_without_tool": false, + "disambiguation_only_answer": false, + "investigation_plan_answer": false, + "not_verified_or_no_results_answer": false, + "graph_failure_mentioned": false, + "missing_required_graph": false, + "used_data_resource": false, + "response_chars": 1400, + "status_count": 9 + } + }, + { + "attempt_index": 28, + "task_index": 28, + "task_id": "T4.5", + "tier": 4, + "title": "Novel circuit exploration", + "question": "What is the connectivity between thermosensory neurons and the mushroom body? Could temperature information influence memory formation?", + "requires_graph": false, + "min_graphs": 0, + "repetition": 1, + "duration_ms": 76749, + "status_messages": [ + { + "message": "Thinking...", + "phase": "llm" + }, + { + "message": "Planning the answer", + "phase": "llm" + }, + { + "message": "Resolving 2 terms in VFB", + "phase": "mcp" + }, + { + "message": "Tracing the pathway", + "phase": "mcp" + }, + { + "message": "Querying VFB connectivity", + "phase": "mcp" + }, + { + "message": "Querying VFB", + "phase": "mcp" + }, + { + "message": "Querying VFB", + "phase": "mcp" + }, + { + "message": "Checking the answer is covered", + "phase": "llm" + }, + { + "message": "Querying VFB", + "phase": "mcp" + }, + { + "message": "Querying VFB", + "phase": "mcp" + }, + { + "message": "Checking the answer is covered", + "phase": "llm" + }, + { + "message": "Writing the answer", + "phase": "llm" + } + ], + "event_count": 159, + "ok": true, + "request_id": "2d7694e9-77e6-4ee1-912d-42d7b4fd0620", + "response_id": "chatcmpl-92f6788bd5fdbf2cb566737e799fbf9e", + "images_count": 8, + "graphs_count": 1, + "response": "Thermosensory neurons connect to the [mushroom body](https://www.virtualflybrain.org/reports/FBbt_00005801 \"Open mushroom body in Virtual Fly Brain\"). The strongest specific targets of [thermosensory neuron](https://www.virtualflybrain.org/reports/FBbt_00005918 \"Open thermosensory neuron in Virtual Fly Brain\") include [projection neuron](https://www.virtualflybrain.org/reports/FBbt_00007392 \"Open projection neuron in Virtual Fly Brain\"), [adult antennal lobe projection neuron](https://www.virtualflybrain.org/reports/FBbt_00067123 \"Open adult antennal lobe projection neuron in Virtual Fly Brain\"), and [antennal lobe projection neuron](https://www.virtualflybrain.org/reports/FBbt_00007422 \"Open antennal lobe projection neuron in Virtual Fly Brain\"). Thermosensory neurons also receive input from [adult antennal lobe local neuron lLN2](https://www.virtualflybrain.org/reports/FBbt_00007396 \"Open adult antennal lobe local neuron lLN2 in Virtual Fly Brain\"), [unilateral local interneuron of the adult antennal lobe](https://www.virtualflybrain.org/reports/FBbt_00051503 \"Open unilateral local interneuron of the adult antennal lobe in Virtual Fly Brain\"), and [adult antennal lobe local neuron](https://www.virtualflybrain.org/reports/FBbt_00007390 \"Open adult antennal lobe local neuron in Virtual Fly Brain\").\n\nVFB records show [366](https://v2.virtualflybrain.org/org.geppetto.frontend/geppetto?q=FBbt_00005801,NeuronsPresynapticHere \"Run in VFB: Neurons with presynaptic terminals in mushroom body\") neurons with presynaptic terminals in mushroom body and [304](https://v2.virtualflybrain.org/org.geppetto.frontend/geppetto?q=FBbt_00005801,NeuronsPostsynapticHere \"Run in VFB: Neurons with postsynaptic terminals in mushroom body\") neurons with postsynaptic terminals in mushroom body. The connectivity between thermosensory neurons and the mushroom body could allow temperature information to influence memory formation, given the role of the mushroom body in memory and learning.", + "graphs": [ + { + "type": "basic_graph", + "version": 1, + "title": "Downstream partners of thermosensory neuron", + "directed": true, + "layout": "circle", + "nodes": [ + { + "id": "FBbt_00005918", + "label": "thermosensory neuron", + "group": null, + "color": null, + "size": 4 + }, + { + "id": "FBbt_00005106", + "label": "neuron", + "group": null, + "color": null, + "size": 1.4 + }, + { + "id": "FBbt_00047095", + "label": "adult neuron", + "group": null, + "color": null, + "size": 1.39 + }, + { + "id": "FBbt_00059271", + "label": "CNS neuron", + "group": null, + "color": null, + "size": 1.38 + }, + { + "id": "FBbt_00007392", + "label": "projection neuron", + "group": null, + "color": null, + "size": 1.22 + }, + { + "id": "FBbt_00007422", + "label": "antennal lobe projection neuron", + "group": null, + "color": null, + "size": 1.21 + }, + { + "id": "FBbt_00067123", + "label": "adult antennal lobe projection neuron", + "group": null, + "color": null, + "size": 1.21 + }, + { + "id": "FBbt_00051493", + "label": "local neuron", + "group": null, + "color": null, + "size": 1.15 + }, + { + "id": "FBbt_00052874", + "label": "antennal lobe local neuron", + "group": null, + "color": null, + "size": 1.15 + }, + { + "id": "FBbt_00007390", + "label": "adult antennal lobe local neuron", + "group": null, + "color": null, + "size": 1.15 + }, + { + "id": "FBbt_00007384", + "label": "multiglomerular antennal lobe projection neuron", + "group": null, + "color": null, + "size": 1.14 + }, + { + "id": "FBbt_00007441", + "label": "adult multiglomerular antennal lobe projection neuron", + "group": null, + "color": null, + "size": 1.14 + }, + { + "id": "FBbt_00049427", + "label": "adult lateral horn input neuron", + "group": null, + "color": null, + "size": 1.12 + }, + { + "id": "FBbt_00053398", + "label": "adult antennal lobe projection neuron to lateral horn", + "group": null, + "color": null, + "size": 1.12 + }, + { + "id": "FBbt_00053397", + "label": "antennal lobe projection neuron to mushroom body", + "group": null, + "color": null, + "size": 1.11 + }, + { + "id": "FBbt_00007394", + "label": "adult local interneuron of the lateral ALl1 neuroblast", + "group": null, + "color": null, + "size": 1.11 + } + ], + "edges": [ + { + "source": "FBbt_00005918", + "target": "FBbt_00005106", + "label": "78601", + "weight": 78601 + }, + { + "source": "FBbt_00005918", + "target": "FBbt_00047095", + "label": "77005", + "weight": 77005 + }, + { + "source": "FBbt_00005918", + "target": "FBbt_00059271", + "label": "75663", + "weight": 75663 + }, + { + "source": "FBbt_00005918", + "target": "FBbt_00007392", + "label": "42907", + "weight": 42907 + }, + { + "source": "FBbt_00005918", + "target": "FBbt_00007422", + "label": "41794", + "weight": 41794 + }, + { + "source": "FBbt_00005918", + "target": "FBbt_00067123", + "label": "41646", + "weight": 41646 + }, + { + "source": "FBbt_00005918", + "target": "FBbt_00051493", + "label": "30596", + "weight": 30596 + }, + { + "source": "FBbt_00005918", + "target": "FBbt_00052874", + "label": "30596", + "weight": 30596 + }, + { + "source": "FBbt_00005918", + "target": "FBbt_00007390", + "label": "30271", + "weight": 30271 + }, + { + "source": "FBbt_00005918", + "target": "FBbt_00007384", + "label": "27881", + "weight": 27881 + }, + { + "source": "FBbt_00005918", + "target": "FBbt_00007441", + "label": "27735", + "weight": 27735 + }, + { + "source": "FBbt_00005918", + "target": "FBbt_00049427", + "label": "24184", + "weight": 24184 + }, + { + "source": "FBbt_00005918", + "target": "FBbt_00053398", + "label": "24184", + "weight": 24184 + }, + { + "source": "FBbt_00005918", + "target": "FBbt_00053397", + "label": "22043", + "weight": 22043 + }, + { + "source": "FBbt_00005918", + "target": "FBbt_00007394", + "label": "21470", + "weight": 21470 + } + ] + } + ], + "quality_flags": { + "has_tool_status": true, + "no_tool_factual_answer": false, + "tool_claim_without_tool": false, + "disambiguation_only_answer": false, + "investigation_plan_answer": false, + "not_verified_or_no_results_answer": false, + "graph_failure_mentioned": false, + "missing_required_graph": false, + "used_data_resource": false, + "response_chars": 1993, + "status_count": 12 + } + }, + { + "attempt_index": 29, + "task_index": 29, + "task_id": "T4.6", + "tier": 4, + "title": "Data availability survey", + "question": "I'm interested in studying the subesophageal zone (SEZ). How well-characterised is this region in VFB? What neuron types are annotated, what connectomics data is available, and what genetic tools exist for SEZ neurons?", + "requires_graph": false, + "min_graphs": 0, + "repetition": 1, + "duration_ms": 203516, + "status_messages": [ + { + "message": "Thinking...", + "phase": "llm" + }, + { + "message": "Planning the answer", + "phase": "llm" + }, + { + "message": "Resolving 1 term in VFB", + "phase": "mcp" + }, + { + "message": "Reading VFB term info", + "phase": "mcp" + }, + { + "message": "Finding genetic tools", + "phase": "mcp" + }, + { + "message": "Querying VFB", + "phase": "mcp" + }, + { + "message": "Querying VFB", + "phase": "mcp" + }, + { + "message": "Checking the answer is covered", + "phase": "llm" + }, + { + "message": "Querying VFB", + "phase": "mcp" + }, + { + "message": "Querying VFB", + "phase": "mcp" + }, + { + "message": "Querying VFB", + "phase": "mcp" + }, + { + "message": "Checking the answer is covered", + "phase": "llm" + }, + { + "message": "Writing the answer", + "phase": "llm" + } + ], + "event_count": 245, + "ok": true, + "request_id": "80a3bd6d-3b2b-44f8-a205-fe553822f2e9", + "response_id": "chatcmpl-fe2b19e856859e1da09f8dc125a96634", + "images_count": 1, + "graphs_count": 0, + "response": "The [subesophageal zone](https://www.virtualflybrain.org/reports/FBbt_00051068 \"Open subesophageal zone in Virtual Fly Brain\") is a well-characterised region in VFB, with various neuron types annotated. VFB records show [2,698](https://v2.virtualflybrain.org/org.geppetto.frontend/geppetto?q=FBbt_00051068,NeuronsPartHere \"Run in VFB: Neurons with some part in subesophageal zone\") neurons with some part in the subesophageal zone, including [serotonergic SE1 neuron](https://www.virtualflybrain.org/reports/FBbt_00001980 \"Open serotonergic SE1 neuron in Virtual Fly Brain\") and [intrinsic antennal mechanosensory and motor center neuron](https://www.virtualflybrain.org/reports/FBbt_00111352 \"Open intrinsic antennal mechanosensory and motor center neuron in Virtual Fly Brain\"). There are also [2,598](https://v2.virtualflybrain.org/org.geppetto.frontend/geppetto?q=FBbt_00051068,NeuronsSynaptic \"Run in VFB: Neurons with synaptic terminals in subesophageal zone\") neurons with synaptic terminals in the subesophageal zone, such as [AMMC-VLP](https://www.virtualflybrain.org/reports/FBbt_00111354 \"Open AMMC-VLP in Virtual Fly Brain\") and [AMMC-Bi1](https://www.virtualflybrain.org/reports/FBbt_00111465 \"Open AMMC-Bi1 in Virtual Fly Brain\"), and [1,813](https://v2.virtualflybrain.org/org.geppetto.frontend/geppetto?q=FBbt_00051068,NeuronsPresynapticHere \"Run in VFB: Neurons with presynaptic terminals in subesophageal zone\") neurons with presynaptic terminals in the subesophageal zone, including AMMC-Bi1 and AVLP391.\n\nConnectomics data is available for the subesophageal zone, with the connectome data indicating synaptic connections between neurons in this region.\n\nGenetic tools exist for SEZ neurons, including GAL4 drivers and binary/intersectional drivers, with VFB holding 4,205 genetic tool/expression pattern rows for the subesophageal zone. The first 12 transgene expression patterns include [P{GMR12D05-GAL4} expression pattern](https://www.virtualflybrain.org/reports/VFBexp_FBtp0057511 \"Open P{GMR12D05-GAL4} expression pattern in Virtual Fly Brain\") and [P{GMR16C05-GAL4} expression pattern](https://www.virtualflybrain.org/reports/VFBexp_FBtp0057869 \"Open P{GMR16C05-GAL4} expression pattern in Virtual Fly Brain\").", + "quality_flags": { + "has_tool_status": true, + "no_tool_factual_answer": false, + "tool_claim_without_tool": false, + "disambiguation_only_answer": false, + "investigation_plan_answer": false, + "not_verified_or_no_results_answer": false, + "graph_failure_mentioned": false, + "missing_required_graph": false, + "used_data_resource": false, + "response_chars": 2236, + "status_count": 13 + } + }, + { + "attempt_index": 30, + "task_index": 30, + "task_id": "G1", + "tier": 5, + "title": "Graph view regression - medulla region connectivity", + "question": "what are the class summarised connectivity from the medulla in graph form", + "requires_graph": true, + "min_graphs": 1, + "repetition": 1, + "duration_ms": 17862, + "status_messages": [ + { + "message": "Thinking...", + "phase": "llm" + }, + { + "message": "Planning the answer", + "phase": "llm" + }, + { + "phase": "plan", + "message": "The plan is contested — sampling again before committing." + }, + { + "message": "Resolving 1 term in VFB", + "phase": "mcp" + }, + { + "message": "Reading VFB term info", + "phase": "mcp" + }, + { + "message": "Querying VFB", + "phase": "mcp" + }, + { + "message": "Querying VFB", + "phase": "mcp" + }, + { + "message": "Querying VFB connectivity", + "phase": "mcp" + }, + { + "message": "Querying VFB", + "phase": "mcp" + }, + { + "message": "Querying VFB", + "phase": "mcp" + }, + { + "message": "Checking the answer is covered", + "phase": "llm" + }, + { + "message": "Writing the answer", + "phase": "llm" + } + ], + "event_count": 110, + "ok": true, + "request_id": "a5e5f867-4e09-4b85-bf46-f7021e6ca1fc", + "response_id": "chatcmpl-295c10dfde4d0d53754ff930de52e34e", + "images_count": 8, + "graphs_count": 1, + "response": "The [medulla](https://www.virtualflybrain.org/reports/FBbt_00003748 \"Open medulla in Virtual Fly Brain\") has various connections, including neurons with presynaptic and postsynaptic terminals. There are [262](https://v2.virtualflybrain.org/org.geppetto.frontend/geppetto?q=FBbt_00003748,NeuronsPresynapticHere \"Run in VFB: Neurons with presynaptic terminals in medulla\") neuron types with presynaptic terminals in the medulla and [333](https://v2.virtualflybrain.org/org.geppetto.frontend/geppetto?q=FBbt_00003748,NeuronsPostsynapticHere \"Run in VFB: Neurons with postsynaptic terminals in medulla\") neuron types with postsynaptic terminals. The first 12 neuron types with presynaptic terminals include [Dm8b](https://www.virtualflybrain.org/reports/FBbt_00110069 \"Open Dm8b in Virtual Fly Brain\"), [PS128](https://www.virtualflybrain.org/reports/FBbt_20001883 \"Open PS128 in Virtual Fly Brain\"), and [Mi10b](https://www.virtualflybrain.org/reports/FBbt_00110070 \"Open Mi10b in Virtual Fly Brain\"), while the first 12 neuron types with postsynaptic terminals include [CB3849](https://www.virtualflybrain.org/reports/FBbt_20007264 \"Open CB3849 in Virtual Fly Brain\"), [TmY-ds](https://www.virtualflybrain.org/reports/FBbt_00052643 \"Open TmY-ds in Virtual Fly Brain\"), and [Y6](https://www.virtualflybrain.org/reports/FBbt_00007580 \"Open Y6 in Virtual Fly Brain\").", + "graphs": [ + { + "type": "basic_graph", + "version": 1, + "title": "medulla region connectivity preview", + "directed": true, + "layout": "radial", + "nodes": [ + { + "id": "FBbt_00003748", + "label": "medulla", + "group": "queried region", + "color": null, + "size": 2.4 + }, + { + "id": "FBbt_20007264", + "label": "CB3849", + "group": "presynaptic and postsynaptic neuron", + "color": null, + "size": 1.15 + }, + { + "id": "FBbt_00110069", + "label": "Dm8b", + "group": "presynaptic neuron", + "color": null, + "size": 1.15 + }, + { + "id": "FBbt_00110070", + "label": "Mi10b", + "group": "presynaptic neuron", + "color": null, + "size": 1.15 + }, + { + "id": "FBbt_20001883", + "label": "PS128", + "group": "presynaptic neuron", + "color": null, + "size": 1.15 + }, + { + "id": "FBbt_00052643", + "label": "TmY-ds", + "group": "presynaptic and postsynaptic neuron", + "color": null, + "size": 1.15 + }, + { + "id": "FBbt_00003774", + "label": "Dm7", + "group": "postsynaptic neuron", + "color": null, + "size": 1.15 + }, + { + "id": "FBbt_00007580", + "label": "Y6", + "group": "postsynaptic neuron", + "color": null, + "size": 1.15 + }, + { + "id": "FBbt_00047183", + "label": "extra l-LNv neuron", + "group": "postsynaptic neuron", + "color": null, + 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If you use Virtual Fly Brain data, tools, or resources in your research, please cite their work using the citation formats below, which include a reference to Court et al., 2023, Virtual Fly Brain—An interactive atlas of the Drosophila nervous system, Frontiers in Physiology, https://doi.org/10.3389/fphys.2023.1076533.", + "quality_flags": { + "has_tool_status": true, + "no_tool_factual_answer": false, + "tool_claim_without_tool": false, + "disambiguation_only_answer": false, + "investigation_plan_answer": false, + "not_verified_or_no_results_answer": false, + "graph_failure_mentioned": false, + "missing_required_graph": false, + "used_data_resource": false, + "response_chars": 461, + "status_count": 6 + } + }, + { + "attempt_index": 33, + "task_index": 33, + "task_id": "D3", + "tier": 6, + "title": "Funding", + "question": "Who funds Virtual Fly Brain and since when?", + "requires_graph": false, + "min_graphs": 0, + "repetition": 1, + "duration_ms": 5376, + "status_messages": [ + { + "message": "Thinking...", + "phase": "llm" + }, + { + "message": "Planning the answer", + "phase": "llm" + }, + { + "message": "Reading VFB documentation", + "phase": "mcp" + }, + { + "message": "Checking VFB documentation", + "phase": "mcp" + }, + { + "message": "Checking the answer is covered", + "phase": "llm" + }, + { + "message": "Writing the answer", + "phase": "llm" + } + ], + "event_count": 25, + "ok": true, + "request_id": "7ef0693d-b3b1-459e-842b-d065385f992c", + "response_id": "chatcmpl-abfa35240e40687826834503d5b2644c", + "images_count": 0, + "graphs_count": 0, + "response": "Virtual Fly Brain is funded by multiple UK research councils and charitable foundations since 2009.", + "quality_flags": { + "has_tool_status": true, + "no_tool_factual_answer": false, + "tool_claim_without_tool": false, + "disambiguation_only_answer": false, + "investigation_plan_answer": false, + "not_verified_or_no_results_answer": false, + "graph_failure_mentioned": false, + "missing_required_graph": false, + "used_data_resource": false, + "response_chars": 99, + "status_count": 6 + } + }, + { + "attempt_index": 34, + "task_index": 34, + "task_id": "D4", + "tier": 6, + "title": "Policies / accessibility", + "question": "What is Virtual Fly Brain's accessibility statement?", + "requires_graph": false, + "min_graphs": 0, + "repetition": 1, + "duration_ms": 6960, + "status_messages": [ + { + "message": "Thinking...", + "phase": "llm" + }, + { + "message": "Planning (direct lookup)", + "phase": "llm" + }, + { + "message": "Resolving 1 term in VFB", + "phase": "mcp" + }, + { + "message": "Reading VFB term info", + "phase": "mcp" + }, + { + "message": "Checking the literature", + "phase": "mcp" + }, + { + "message": "Checking the answer is covered", + "phase": "llm" + }, + { + "message": "Writing the answer", + "phase": "llm" + } + ], + "event_count": 65, + "ok": true, + "request_id": "707ba3dd-9a44-44e8-b020-e06ee0df5ca2", + "response_id": "chatcmpl-83705a1172293060d341b054907e2219", + "images_count": 0, + "graphs_count": 0, + "response": "Virtual Fly Brain's accessibility statement is that the website is partially compliant with the Web Content Accessibility Guidelines (WCAG) 2.2 AA standard, with non-compliances listed, and the University of Edinburgh is committed to making its websites and applications accessible in line with the regulations.", + "quality_flags": { + "has_tool_status": true, + "no_tool_factual_answer": false, + "tool_claim_without_tool": false, + "disambiguation_only_answer": false, + "investigation_plan_answer": false, + "not_verified_or_no_results_answer": false, + "graph_failure_mentioned": false, + "missing_required_graph": false, + "used_data_resource": false, + "response_chars": 311, + "status_count": 7 + } + }, + { + "attempt_index": 35, + "task_index": 35, + "task_id": "D5", + "tier": 6, + "title": "Contact / contribute", + "question": "How do I report a problem or contribute data to Virtual Fly Brain?", + "requires_graph": false, + "min_graphs": 0, + "repetition": 1, + "duration_ms": 9819, + "status_messages": [ + { + "message": "Thinking...", + "phase": "llm" + }, + { + "message": "Planning the answer", + "phase": "llm" + }, + { + "message": "Reading VFB documentation", + "phase": "mcp" + }, + { + "message": "Checking VFB documentation", + "phase": "mcp" + }, + { + "message": "Checking the answer is covered", + "phase": "llm" + }, + { + "message": "Writing the answer", + "phase": "llm" + } + ], + "event_count": 107, + "ok": true, + "request_id": "b3ae3f58-f136-403d-8134-70945f945f37", + "response_id": "chatcmpl-58c0ad5681189ec6b3df543b6026197c", + "images_count": 0, + "graphs_count": 0, + "response": "To report a problem or contribute data to Virtual Fly Brain, you can get in touch with the team through the contact page. For help with using Virtual Fly Brain, you can email support@virtualflybrain.org, which goes to the public support forum where questions and responses are visible to the community. To report technical issues, bugs, or request new features, you can use GitHub Issues. For data inclusion discussions, collaboration proposals, or confidential matters, you can email data@virtualflybrain.org.", + "quality_flags": { + "has_tool_status": true, + "no_tool_factual_answer": false, + "tool_claim_without_tool": false, + "disambiguation_only_answer": false, + "investigation_plan_answer": false, + "not_verified_or_no_results_answer": false, + "graph_failure_mentioned": false, + "missing_required_graph": false, + "used_data_resource": false, + "response_chars": 510, + "status_count": 6 + } + }, + { + "attempt_index": 36, + "task_index": 36, + "task_id": "D6", + "tier": 6, + "title": "Website how-to: 3D Viewer", + "question": "How do I use the 3D Viewer on the VFB website?", + "requires_graph": false, + "min_graphs": 0, + "repetition": 1, + "duration_ms": 7521, + "status_messages": [ + { + "message": "Thinking...", + "phase": "llm" + }, + { + "message": "Planning the answer", + "phase": "llm" + }, + { + "message": "Reading VFB documentation", + "phase": "mcp" + }, + { + "message": "Checking the literature", + "phase": "mcp" + }, + { + "message": "Checking the answer is covered", + "phase": "llm" + }, + { + "message": "Writing the answer", + "phase": "llm" + } + ], + "event_count": 85, + "ok": true, + "request_id": "9a3994bf-c73b-4f7f-bbe9-933badbb215d", + "response_id": "chatcmpl-d26ed7a643645777f66d923dde7c1173", + "images_count": 0, + "graphs_count": 0, + "response": "To use the 3D Viewer on the VFB website, point and click to select neurons or expression. Click and drag with the mouse or use the directional icons to rotate or move. Use the zoom icons or scroll with the mouse to zoom in or out. The camera icon starts or stops a rotation animation of the scene, and the sphere icon toggles wireframes on or off.", + "quality_flags": { + "has_tool_status": true, + "no_tool_factual_answer": false, + "tool_claim_without_tool": false, + "disambiguation_only_answer": false, + "investigation_plan_answer": false, + "not_verified_or_no_results_answer": false, + "graph_failure_mentioned": false, + "missing_required_graph": false, + "used_data_resource": false, + "response_chars": 347, + "status_count": 6 + } + }, + { + "attempt_index": 37, + "task_index": 37, + "task_id": "D7", + "tier": 6, + "title": "Website how-to: Circuit Browser", + "question": "What is the Circuit Browser tab on VFB and how do I use it?", + "requires_graph": false, + "min_graphs": 0, + "repetition": 1, + "duration_ms": 13162, + "status_messages": [ + { + "message": "Thinking...", + "phase": "llm" + }, + { + "message": "Planning the answer", + "phase": "llm" + }, + { + "message": "Resolving 1 term in VFB", + "phase": "mcp" + }, + { + "message": "Reading VFB documentation", + "phase": "mcp" + }, + { + "message": "Reading VFB documentation", + "phase": "mcp" + }, + { + "message": "Checking VFB documentation", + "phase": "mcp" + }, + { + "message": "Checking the answer is covered", + "phase": "llm" + }, + { + "message": "Writing the answer", + "phase": "llm" + } + ], + "event_count": 45, + "ok": true, + "request_id": "a85f413b-68bb-47fb-a588-8a1e52342452", + "response_id": "chatcmpl-8d250165e0f947d8e51f6d93cbd77c99", + "images_count": 0, + "graphs_count": 0, + "response": "The Circuit Browser tab on VFB allows you to find the strongest paths from one neuron to another. To use it, you would typically specify a source neuron and a target neuron.", + "quality_flags": { + "has_tool_status": true, + "no_tool_factual_answer": false, + "tool_claim_without_tool": false, + "disambiguation_only_answer": false, + "investigation_plan_answer": false, + "not_verified_or_no_results_answer": false, + "graph_failure_mentioned": false, + "missing_required_graph": false, + "used_data_resource": false, + "response_chars": 173, + "status_count": 8 + } + }, + { + "attempt_index": 38, + "task_index": 38, + "task_id": "D8", + "tier": 6, + "title": "Concepts: NBLAST", + "question": "What is NBLAST and what does an NBLAST similarity score mean?", + "requires_graph": false, + "min_graphs": 0, + "repetition": 1, + "duration_ms": 9414, + "status_messages": [ + { + "message": "Thinking...", + "phase": "llm" + }, + { + "message": "Planning the answer", + "phase": "llm" + }, + { + "message": "Resolving 1 term in VFB", + "phase": "mcp" + }, + { + "message": "Reading VFB term info", + "phase": "mcp" + }, + { + "message": "Checking the literature", + "phase": "mcp" + }, + { + "message": "Checking the answer is covered", + "phase": "llm" + }, + { + "message": "Writing the answer", + "phase": "llm" + } + ], + "event_count": 56, + "ok": true, + "request_id": "b7bb1d3c-0843-4a7c-95e9-634d82ce1153", + "response_id": "chatcmpl-daa4ebf7055c67532d5b5b73178a9313", + "images_count": 0, + "graphs_count": 0, + "response": "NBLAST is a method used to calculate similarity scores, which represent the morphological similarity between neurons or expression patterns. An NBLAST similarity score is a measure of how similar two neurons or expression patterns are in terms of their morphology.", + "quality_flags": { + "has_tool_status": true, + "no_tool_factual_answer": false, + "tool_claim_without_tool": false, + "disambiguation_only_answer": false, + "investigation_plan_answer": false, + "not_verified_or_no_results_answer": false, + "graph_failure_mentioned": false, + "missing_required_graph": false, + "used_data_resource": false, + "response_chars": 264, + "status_count": 7 + } + }, + { + "attempt_index": 39, + "task_index": 39, + "task_id": "D9", + "tier": 6, + "title": "Concepts: confidence values", + "question": "What do confidence values mean on Virtual Fly Brain?", + "requires_graph": false, + "min_graphs": 0, + "repetition": 1, + "duration_ms": 7533, + "status_messages": [ + { + "message": "Thinking...", + "phase": "llm" + }, + { + "message": "Planning the answer", + "phase": "llm" + }, + { + "message": "Resolving 1 term in VFB", + "phase": "mcp" + }, + { + "message": "Reading VFB documentation", + "phase": "mcp" + }, + { + "message": "Checking the literature", + "phase": "mcp" + }, + { + "message": "Checking the answer is covered", + "phase": "llm" + }, + { + "message": "Writing the answer", + "phase": "llm" + } + ], + "event_count": 26, + "ok": true, + "request_id": "d0b724e0-86ff-4d1c-954a-f284a5b9793b", + "response_id": "chatcmpl-002a2f2e979257bf6fd1e498c2eea6f0", + "images_count": 1, + "graphs_count": 0, + "response": "Confidence values are represented by the property key \"confidence_value\" in the PDB.", + "quality_flags": { + "has_tool_status": true, + "no_tool_factual_answer": false, + "tool_claim_without_tool": false, + "disambiguation_only_answer": false, + "investigation_plan_answer": false, + "not_verified_or_no_results_answer": false, + "graph_failure_mentioned": false, + "missing_required_graph": false, + "used_data_resource": false, + "response_chars": 84, + "status_count": 7 + } + }, + { + "attempt_index": 40, + "task_index": 40, + "task_id": "D10", + "tier": 6, + "title": "Concepts: bridging registrations", + "question": "What are bridging registrations between brain templates in VFB?", + "requires_graph": false, + "min_graphs": 0, + "repetition": 1, + "duration_ms": 9050, + "status_messages": [ + { + "message": "Thinking...", + "phase": "llm" + }, + { + "message": "Planning the answer", + "phase": "llm" + }, + { + "message": "Resolving 1 term in VFB", + "phase": "mcp" + }, + { + "message": "Reading VFB term info", + "phase": "mcp" + }, + { + "message": "Checking VFB documentation", + "phase": "mcp" + }, + { + "message": "Checking the answer is covered", + "phase": "llm" + }, + { + "message": "Writing the answer", + "phase": "llm" + } + ], + "event_count": 44, + "ok": true, + "request_id": "238bb633-44e3-4836-8b1b-9ed929cc0da0", + "response_id": "chatcmpl-ac3b8e4e9acb9416791cd74ca000c0cf", + "images_count": 8, + "graphs_count": 0, + "response": "Bridging registrations between brain templates in VFB are transformations to map between different canonical Drosophila templates. VFB's documentation does not appear to cover bridging registrations.", + "quality_flags": { + "has_tool_status": true, + "no_tool_factual_answer": false, + "tool_claim_without_tool": false, + "disambiguation_only_answer": false, + "investigation_plan_answer": false, + "not_verified_or_no_results_answer": false, + "graph_failure_mentioned": false, + "missing_required_graph": false, + "used_data_resource": false, + "response_chars": 199, + "status_count": 7 + } + }, + { + "attempt_index": 41, + "task_index": 41, + "task_id": "D11", + "tier": 6, + "title": "Data coverage & templates", + "question": "What imaging data types and brain templates does Virtual Fly Brain hold?", + "requires_graph": false, + "min_graphs": 0, + "repetition": 1, + "duration_ms": 6132, + "status_messages": [ + { + "message": "Thinking...", + "phase": "llm" + }, + { + "message": "Planning the answer", + "phase": "llm" + }, + { + "message": "Reading VFB documentation", + "phase": "mcp" + }, + { + "message": "Checking VFB documentation", + "phase": "mcp" + }, + { + "message": "Checking the answer is covered", + "phase": "llm" + }, + { + "message": "Writing the answer", + "phase": "llm" + } + ], + "event_count": 55, + "ok": true, + "request_id": "34d5660e-816f-467a-9685-cdd956809f35", + "response_id": "chatcmpl-d896bc7b75470a48f2e045c397f871a8", + "images_count": 0, + "graphs_count": 0, + "response": "Virtual Fly Brain holds various imaging data types, including skeleton, mesh, and volume, and brain templates with painted domains/regions. The retrieved neuron object can provide different representations of neuron data, such as its skeleton, mesh, and volume.", + "quality_flags": { + "has_tool_status": true, + "no_tool_factual_answer": false, + "tool_claim_without_tool": false, + "disambiguation_only_answer": false, + "investigation_plan_answer": false, + "not_verified_or_no_results_answer": false, + "graph_failure_mentioned": false, + "missing_required_graph": false, + "used_data_resource": false, + "response_chars": 261, + "status_count": 6 + } + }, + { + "attempt_index": 42, + "task_index": 42, + "task_id": "D12", + "tier": 6, + "title": "Release changelog", + "question": "What was included in the latest Virtual Fly Brain release?", + "requires_graph": false, + "min_graphs": 0, + "repetition": 1, + "duration_ms": 7099, + "status_messages": [ + { + "message": "Thinking...", + "phase": "llm" + }, + { + "message": "Planning the answer", + "phase": "llm" + }, + { + "message": "Reading VFB term info", + "phase": "mcp" + }, + { + "message": "Checking the literature", + "phase": "mcp" + }, + { + "message": "Checking the answer is covered", + "phase": "llm" + }, + { + "message": "Writing the answer", + "phase": "llm" + } + ], + "event_count": 91, + "ok": true, + "request_id": "eeb00379-3a56-4826-a2ec-cab1ce568299", + "response_id": "chatcmpl-432afb8aa26c92ffe77a7e58ede09cdc", + "images_count": 0, + "graphs_count": 0, + "response": "The latest Virtual Fly Brain release includes various data and software improvements, such as new images and annotations, including but not limited to: Adult Brain fru clones, Adult VNC neuropils, Adult VNS neuropils, AMMC local and projection neurons, Biomechanical origins of proprioceptive maps in the Drosophila leg, BrainName neuropils and tracts, BrainTrap lines, and many others.", + "quality_flags": { + "has_tool_status": true, + "no_tool_factual_answer": false, + "tool_claim_without_tool": false, + "disambiguation_only_answer": false, + "investigation_plan_answer": false, + "not_verified_or_no_results_answer": false, + "graph_failure_mentioned": false, + "missing_required_graph": false, + "used_data_resource": false, + "response_chars": 386, + "status_count": 6 + } + }, + { + "attempt_index": 43, + "task_index": 43, + "task_id": "D13", + "tier": 6, + "title": "API: VFB-connect (Python)", + "question": "How do I install and get started with VFB-connect in Python?", + "requires_graph": false, + "min_graphs": 0, + "repetition": 1, + "duration_ms": 8570, + "status_messages": [ + { + "message": "Thinking...", + "phase": "llm" + }, + { + "message": "Planning the answer", + "phase": "llm" + }, + { + "message": "Reading VFB documentation", + "phase": "mcp" + }, + { + "message": "Checking the literature", + "phase": "mcp" + }, + { + "message": "Checking the answer is covered", + "phase": "llm" + }, + { + "message": "Writing the answer", + "phase": "llm" + } + ], + "event_count": 58, + "ok": true, + "request_id": "a2641fc1-380f-4dd3-afdc-e38d8b9ad043", + "response_id": "chatcmpl-b9c2df2e6a0fbffb0b5f62865a385918", + "images_count": 0, + "graphs_count": 0, + "response": "To install and get started with VFB-connect in Python, ensure you have the VFBConnect library installed using the recommended Python version 3.10.14. Install the library by running\n```\npip install vfb-connect\n```\nThen, import the VFBConnect library using\n```\nfrom import vfb\n```", + "quality_flags": { + "has_tool_status": true, + "no_tool_factual_answer": false, + "tool_claim_without_tool": false, + "disambiguation_only_answer": false, + "investigation_plan_answer": false, + "not_verified_or_no_results_answer": false, + "graph_failure_mentioned": false, + "missing_required_graph": false, + "used_data_resource": false, + "response_chars": 278, + "status_count": 6 + } + }, + { + "attempt_index": 44, + "task_index": 44, + "task_id": "D14", + "tier": 6, + "title": "API: REST endpoints", + "question": "How can I query Virtual Fly Brain programmatically using the SOLR or Owlery API?", + "requires_graph": false, + "min_graphs": 0, + "repetition": 1, + "duration_ms": 10777, + "status_messages": [ + { + "message": "Thinking...", + "phase": "llm" + }, + { + "message": "Planning the answer", + "phase": "llm" + }, + { + "message": "Reading VFB documentation", + "phase": "mcp" + }, + { + "message": "Checking VFB documentation", + "phase": "mcp" + }, + { + "message": "Checking the answer is covered", + "phase": "llm" + }, + { + "message": "Writing the answer", + "phase": "llm" + } + ], + "event_count": 91, + "ok": true, + "request_id": "35314934-9a85-4d86-a092-6fdb14bf1686", + "response_id": "chatcmpl-f24ed53392e1e6f7c59644f9041ab555", + "images_count": 0, + "graphs_count": 0, + "response": "To query Virtual Fly Brain programmatically, you can use the Owlery API, which provides OWL reasoning services for VFB's ontologies. The API endpoint is https://owl.virtualflybrain.org/, and it supports various query operations, including DL queries, SPARQL queries, and knowledgebase operations. The SOLR Search API provides fast text search and autocomplete functionality for VFB entities, datasets, and publications.", + "quality_flags": { + "has_tool_status": true, + "no_tool_factual_answer": false, + "tool_claim_without_tool": false, + "disambiguation_only_answer": false, + "investigation_plan_answer": false, + "not_verified_or_no_results_answer": false, + "graph_failure_mentioned": false, + "missing_required_graph": false, + "used_data_resource": false, + "response_chars": 419, + "status_count": 6 + } + }, + { + "attempt_index": 45, + "task_index": 45, + "task_id": "D15", + "tier": 6, + "title": "API: integrations", + "question": "How do I explore Virtual Fly Brain neurons using Navis or pymaid?", + "requires_graph": false, + "min_graphs": 0, + "repetition": 1, + "duration_ms": 9954, + "status_messages": [ + { + "message": "Thinking...", + "phase": "llm" + }, + { + "message": "Planning the answer", + "phase": "llm" + }, + { + "message": "Resolving 2 terms in VFB", + "phase": "mcp" + }, + { + "message": "Reading VFB documentation", + "phase": "mcp" + }, + { + "message": "Checking VFB documentation", + "phase": "mcp" + }, + { + "message": "Checking the answer is covered", + "phase": "llm" + }, + { + "message": "Writing the answer", + "phase": "llm" + } + ], + "event_count": 108, + "ok": true, + "request_id": "1c8583e0-a716-47f2-9891-9bee7b96c9d5", + "response_id": "chatcmpl-18b24def0e57babd6ae3fcb32df4d7e3", + "images_count": 0, + "graphs_count": 0, + "response": "To explore Virtual Fly Brain neurons, you can use the pymaid library, which lets you interface with a CATMAID server such as those provided by Virtual Fly Brain. You can connect to the Virtual Fly Brain CATMAID server, retrieve neurons, and plot them using navis. Virtual Fly Brain provides tutorials on how to explore neurons using navis or pymaid.\n\nVFB's documentation does not appear to cover Navis.\nVFB's documentation does not appear to cover pymaid.", + "quality_flags": { + "has_tool_status": true, + "no_tool_factual_answer": false, + "tool_claim_without_tool": false, + "disambiguation_only_answer": false, + "investigation_plan_answer": false, + "not_verified_or_no_results_answer": false, + "graph_failure_mentioned": false, + "missing_required_graph": false, + "used_data_resource": false, + "response_chars": 455, + "status_count": 7 + } + }, + { + "attempt_index": 46, + "task_index": 46, + "task_id": "D16", + "tier": 6, + "title": "MCP tool usage", + "question": "How do I use the Virtual Fly Brain Model Context Protocol (MCP) tool?", + "requires_graph": false, + "min_graphs": 0, + "repetition": 1, + "duration_ms": 14964, + "status_messages": [ + { + "message": "Thinking...", + "phase": "llm" + }, + { + "message": "Planning the answer", + "phase": "llm" + }, + { + "phase": "plan", + "message": "The plan is contested — sampling again before committing." + }, + { + "message": "Reading VFB documentation", + "phase": "mcp" + }, + { + "message": "Reading VFB documentation", + "phase": "mcp" + }, + { + "message": "Checking VFB documentation", + "phase": "mcp" + }, + { + "message": "Checking the answer is covered", + "phase": "llm" + }, + { + "message": "Writing the answer", + "phase": "llm" + } + ], + "event_count": 99, + "ok": true, + "request_id": "ca139303-4fa2-4d21-8e49-6bd010fe0527", + "response_id": "chatcmpl-b812aeab849cbea86d018b2c4ac81586", + "images_count": 0, + "graphs_count": 0, + "response": "To use the Virtual Fly Brain Model Context Protocol (MCP) tool, follow these steps:\nOpen Claude Desktop, navigate to Settings, and add a new MCP server with the settings:\nServer Name: virtual-fly-brain,\nType: HTTP,\nServer URL: https://vfb3-mcp.virtualflybrain.org.\nAlternatively, use the Configuration JSON method or set up the tool with GitHub Copilot or VS Code.\n\n```\n{\n\"mcpServers\": {\n\"virtual-fly-brain\": {\n\"type\": \"http\",\n\"url\": \"https://vfb3-mcp.virtualflybrain.org\",\n\"tools\": [\"*\"]\n}\n}\n}\n```", + "quality_flags": { + "has_tool_status": true, + "no_tool_factual_answer": false, + "tool_claim_without_tool": false, + "disambiguation_only_answer": false, + "investigation_plan_answer": false, + "not_verified_or_no_results_answer": false, + "graph_failure_mentioned": false, + "missing_required_graph": false, + "used_data_resource": false, + "response_chars": 498, + "status_count": 8 + } + }, + { + "attempt_index": 47, + "task_index": 47, + "task_id": "D17", + "tier": 6, + "title": "News / operational", + "question": "When did predicted neurotransmitters for EM data become available on VFB?", + "requires_graph": false, + "min_graphs": 0, + "repetition": 1, + "duration_ms": 7780, + "status_messages": [ + { + "message": "Thinking...", + "phase": "llm" + }, + { + "message": "Planning the answer", + "phase": "llm" + }, + { + "phase": "plan", + "message": "The plan is contested — sampling again before committing." + }, + { + "message": "Resolving 1 term in VFB", + "phase": "mcp" + }, + { + "message": "Reading VFB term info", + "phase": "mcp" + }, + { + "message": "Checking the literature", + "phase": "mcp" + }, + { + "message": "Checking the answer is covered", + "phase": "llm" + }, + { + "message": "Writing the answer", + "phase": "llm" + } + ], + "event_count": 41, + "ok": true, + "request_id": "ff5929cf-cf48-4839-9352-a3e89925a9ee", + "response_id": "chatcmpl-c45275e255d55d3e242d67cd2d534edf", + "images_count": 0, + "graphs_count": 0, + "response": "VFB's documentation does not appear to cover when predicted neurotransmitters for EM data became available. For more information, searching virtualflybrain.org may be helpful.", + "quality_flags": { + "has_tool_status": true, + "no_tool_factual_answer": false, + "tool_claim_without_tool": false, + "disambiguation_only_answer": false, + "investigation_plan_answer": false, + "not_verified_or_no_results_answer": false, + "graph_failure_mentioned": false, + "missing_required_graph": false, + "used_data_resource": false, + "response_chars": 175, + "status_count": 8 + } + }, + { + "attempt_index": 48, + "task_index": 48, + "task_id": "D18", + "tier": 6, + "title": "Community events", + "question": "When and where is the NeuroFly 2026 conference?", + "requires_graph": false, + "min_graphs": 0, + "repetition": 1, + "duration_ms": 8975, + "status_messages": [ + { + "message": "Thinking...", + "phase": "llm" + }, + { + "message": "Planning the answer", + "phase": "llm" + }, + { + "message": "Resolving 1 term in VFB", + "phase": "mcp" + }, + { + "message": "Reading VFB documentation", + "phase": "mcp" + }, + { + "message": "Checking VFB documentation", + "phase": "mcp" + }, + { + "message": "Checking the answer is covered", + "phase": "llm" + }, + { + "message": "Writing the answer", + "phase": "llm" + } + ], + "event_count": 40, + "ok": true, + "request_id": "27ef4631-8457-40fc-a5cc-a2963b3a545a", + "response_id": "chatcmpl-e449fd3316629dc3a973827b37cc2cc8", + "images_count": 0, + "graphs_count": 0, + "response": "The NeuroFly 2026 conference will be held at the University of Cologne, Germany, from September 7th to 11th, 2026.", + "quality_flags": { + "has_tool_status": true, + "no_tool_factual_answer": false, + "tool_claim_without_tool": false, + "disambiguation_only_answer": false, + "investigation_plan_answer": false, + "not_verified_or_no_results_answer": false, + "graph_failure_mentioned": false, + "missing_required_graph": false, + "used_data_resource": false, + "response_chars": 114, + "status_count": 7 + } + }, + { + "attempt_index": 49, + "task_index": 49, + "task_id": "D19", + "tier": 6, + "title": "Workshops / training", + "question": "What materials are available from the VFB 'Hacking the connectome' workshop?", + "requires_graph": false, + "min_graphs": 0, + "repetition": 1, + "duration_ms": 10471, + "status_messages": [ + { + "message": "Thinking...", + "phase": "llm" + }, + { + "message": "Planning the answer", + "phase": "llm" + }, + { + "message": "Resolving 1 term in VFB", + "phase": "mcp" + }, + { + "message": "Reading VFB documentation", + "phase": "mcp" + }, + { + "message": "Checking VFB documentation", + "phase": "mcp" + }, + { + "message": "Checking the answer is covered", + "phase": "llm" + }, + { + "message": "Writing the answer", + "phase": "llm" + } + ], + "event_count": 88, + "ok": true, + "request_id": "0ed9ec78-a3c0-4f2d-9f75-b6425336d603", + "response_id": "chatcmpl-072f08ab2ef72c7df44ff578d98e1afc", + "images_count": 0, + "graphs_count": 0, + "response": "Materials from the VFB 'Hacking the connectome' workshop are available. The workshop materials include a recorded introduction session and workshop notebooks that demonstrate how to use available tools to explore and analyse published connectomes on VFB.\n\nTo access these materials, you can visit the VFB website and follow the link to the workshop page. The page includes a recorded introduction session and workshop notebooks.\n\n```\n{\n \"intro\": \"https://www.virtualflybrain.org/docs/past-workshops/connectome\"\n}\n```", + "quality_flags": { + "has_tool_status": true, + "no_tool_factual_answer": false, + "tool_claim_without_tool": false, + "disambiguation_only_answer": false, + "investigation_plan_answer": false, + "not_verified_or_no_results_answer": false, + "graph_failure_mentioned": false, + "missing_required_graph": false, + "used_data_resource": false, + "response_chars": 516, + "status_count": 7 + } + }, + { + "attempt_index": 50, + "task_index": 50, + "task_id": "D20", + "tier": 6, + "title": "Hosted / archived sites", + "question": "Where can I access the FAFB or FANC CATMAID datasets via Virtual Fly Brain?", + "requires_graph": false, + "min_graphs": 0, + "repetition": 1, + "duration_ms": 17513, + "status_messages": [ + { + "message": "Thinking...", + "phase": "llm" + }, + { + "message": "Planning the answer", + "phase": "llm" + }, + { + "message": "Resolving 3 terms in VFB", + "phase": "mcp" + }, + { + "message": "Querying VFB", + "phase": "mcp" + }, + { + "message": "Reading VFB term info", + "phase": "mcp" + }, + { + "message": "Checking VFB documentation", + "phase": "mcp" + }, + { + "message": "Checking the answer is covered", + "phase": "llm" + }, + { + "message": "Writing the answer", + "phase": "llm" + } + ], + "event_count": 64, + "ok": true, + "request_id": "db8d5b57-ba21-4d8c-9246-313a976feb5d", + "response_id": "chatcmpl-d0ab561186e37f8eb676ceb9ff46dfac", + "images_count": 8, + "graphs_count": 0, + "response": "The FAFB CATMAID dataset can be accessed via https://fafb.catmaid.virtualflybrain.org. Virtual Fly Brain hosts several CATMAID instances for exploring connectomic reconstruction data, including FAFB. The name \"FANC\" could not be matched.", + "quality_flags": { + "has_tool_status": true, + "no_tool_factual_answer": false, + "tool_claim_without_tool": false, + "disambiguation_only_answer": false, + "investigation_plan_answer": false, + "not_verified_or_no_results_answer": false, + "graph_failure_mentioned": false, + "missing_required_graph": false, + "used_data_resource": false, + "response_chars": 237, + "status_count": 8 + } + }, + { + "attempt_index": 51, + "task_index": 51, + "task_id": "D21", + "tier": 6, + "title": "Anatomy teaching diagrams", + "question": "Is there a circuit diagram of the mushroom body available on Virtual Fly Brain?", + "requires_graph": false, + "min_graphs": 0, + "repetition": 1, + "duration_ms": 7908, + "status_messages": [ + { + "message": "Thinking...", + "phase": "llm" + }, + { + "message": "Planning the answer", + "phase": "llm" + }, + { + "message": "Resolving 1 term in VFB", + "phase": "mcp" + }, + { + "message": "Reading VFB term info", + "phase": "mcp" + }, + { + "message": "Checking VFB documentation", + "phase": "mcp" + }, + { + "message": "Checking the answer is covered", + "phase": "llm" + }, + { + "message": "Writing the answer", + "phase": "llm" + } + ], + "event_count": 23, + "ok": true, + "request_id": "63e82a06-b11f-48ad-b8ed-474f7f93a928", + "response_id": "chatcmpl-3bad5257cddace7fe2ef4ce230b324e3", + "images_count": 8, + "graphs_count": 0, + "response": "There is a circuit diagram of the [mushroom body](https://www.virtualflybrain.org/reports/FBbt_00005801 \"Open mushroom body in Virtual Fly Brain\") available on Virtual Fly Brain.", + "quality_flags": { + "has_tool_status": true, + "no_tool_factual_answer": false, + "tool_claim_without_tool": false, + "disambiguation_only_answer": false, + "investigation_plan_answer": false, + "not_verified_or_no_results_answer": false, + "graph_failure_mentioned": false, + "missing_required_graph": false, + "used_data_resource": false, + "response_chars": 178, + "status_count": 7 + } + }, + { + "attempt_index": 52, + "task_index": 52, + "task_id": "C1", + "tier": 7, + "title": "Pronoun follow-up on a region", + "question": "What is the medulla?", + "requires_graph": false, + "min_graphs": 0, + "repetition": 1, + "duration_ms": 13290, + "status_messages": [ + { + "message": "Thinking...", + "phase": "llm" + }, + { + "message": "Running the query behind that suggestion", + "phase": "mcp" + }, + { + "message": "Resolving 1 term in VFB", + "phase": "mcp" + }, + { + "message": "Querying VFB", + "phase": "mcp" + }, + { + "message": "Querying VFB", + "phase": "mcp" + }, + { + "message": "Checking the answer is covered", + "phase": "llm" + }, + { + "message": "Writing the answer", + "phase": "llm" + } + ], + "event_count": 86, + "conversation": true, + "turns": [ + { + "turn": 1, + "question": "What is the medulla?", + "focus": null, + "clicked": null, + "duration_ms": 6944, + "ok": true, + "response": "The [medulla](https://www.virtualflybrain.org/reports/FBbt_00003748 \"Open medulla in Virtual Fly Brain\") is the second optic neuropil, sandwiched between the lamina and the lobula complex. It is divided into 10 layers: 1-6 make up the outer medulla, the seventh layer exhibits a distinct architecture and layers 8-10 make up the inner medulla.", + "followons": [ + { + "id": "FBbt_00003748", + "query_type": "ImagesNeurons", + "query": "Which neuron images have a part in the medulla?" + }, + { + "id": "FBbt_00003748", + "query_type": "TransgeneExpressionHere", + "query": "Which driver lines label the medulla?" + }, + { + "id": "FBbt_00003748", + "query_type": "NeuronsPartHere", + "query": "Which neurons have part of their arbour in the medulla?" + }, + { + "id": "FBbt_00003748", + "query_type": "NeuronsSynaptic", + "query": "Which neurons have synaptic terminals in the medulla?" + }, + { + "id": "FBbt_00003748", + "query_type": "NeuronsPostsynapticHere", + "query": "Which neurons receive output from the medulla?" + }, + { + "id": "FBbt_00003748", + "query_type": "NeuronsPresynapticHere", + "query": "Which neurons provide input to the medulla?" + } + ], + "context_terms": [ + { + "id": "FBbt_00003748", + "label": "medulla" + } + ], + "reproduction": { + "ids": [ + { + "id": "FBbt_00003748", + "label": "medulla" + } + ], + "calls": [], + "unmapped": [] + }, + "status_count": 6, + "problems": [] + }, + { + "turn": 2, + "question": "Which neurons receive output from it?", + "focus": null, + "clicked": null, + "duration_ms": 6346, + "ok": true, + "response": "Neurons that receive output from the [medulla](https://www.virtualflybrain.org/reports/FBbt_00003748 \"Open medulla in Virtual Fly Brain\") include [CB3849](https://www.virtualflybrain.org/reports/FBbt_20007264 \"Open CB3849 in Virtual Fly Brain\"), [TmY-ds](https://www.virtualflybrain.org/reports/FBbt_00052643 \"Open TmY-ds in Virtual Fly Brain\"), [Y6](https://www.virtualflybrain.org/reports/FBbt_00007580 \"Open Y6 in Virtual Fly Brain\"), [extra l-LNv neuron](https://www.virtualflybrain.org/reports/FBbt_00047183 \"Open extra l-LNv neuron in Virtual Fly Brain\"), [Dm7](https://www.virtualflybrain.org/reports/FBbt_00003774 \"Open Dm7 in Virtual Fly Brain\"), Mi6, Mi8, Tm10, Tm13, Tm14, Tm18, and Tm19. VFB records show [333](https://v2.virtualflybrain.org/org.geppetto.frontend/geppetto?q=FBbt_00003748,NeuronsPostsynapticHere \"Run in VFB: Neurons with postsynaptic terminals in medulla\") neurons with postsynaptic terminals in the medulla.", + "followons": [ + { + "id": "FBbt_00003748", + "query_type": "ImagesNeurons", + "query": "Which neuron images have a part in the medulla?" + }, + { + "id": "FBbt_00003748", + "query_type": "TransgeneExpressionHere", + "query": "Which driver lines label the medulla?" + }, + { + "id": "FBbt_00003748", + "query_type": "NeuronsPartHere", + "query": "Which neurons have part of their arbour in the medulla?" + }, + { + "id": "FBbt_00003748", + "query_type": "NeuronsSynaptic", + "query": "Which neurons have synaptic terminals in the medulla?" + }, + { + "id": "FBbt_00003748", + "query_type": "PartsOf", + "query": "What are the anatomical parts of the medulla?" + }, + { + "id": "FBbt_00003748", + "query_type": "LineageClonesIn", + "query": "Which lineage clones are found in the medulla?" + } + ], + "context_terms": [ + { + "id": "FBbt_00003748", + "label": "medulla" + } + ], + "reproduction": { + "ids": [ + { + "id": "FBbt_00003748", + "label": "medulla" + } + ], + "calls": [ + { + "id": "FBbt_00003748", + "query_type": "NeuronsPostsynapticHere", + "fn": "get_neurons_with_postsynaptic_terminals_in" + }, + { + "id": "FBbt_00003748", + "query_type": "NeuronsPresynapticHere", + "fn": "get_neurons_with_presynaptic_terminals_in" + } + ], + "unmapped": [] + }, + "status_count": 7, + "problems": [] + } + ], + "ok": true, + "request_id": "f2d88acd-a64e-4ed6-a147-795705dbaf38", + "response_id": "chatcmpl-d635cd19270149d6142ee9ec38408de4", + "images_count": 8, + "graphs_count": 0, + "response": "Neurons that receive output from the [medulla](https://www.virtualflybrain.org/reports/FBbt_00003748 \"Open medulla in Virtual Fly Brain\") include [CB3849](https://www.virtualflybrain.org/reports/FBbt_20007264 \"Open CB3849 in Virtual Fly Brain\"), [TmY-ds](https://www.virtualflybrain.org/reports/FBbt_00052643 \"Open TmY-ds in Virtual Fly Brain\"), [Y6](https://www.virtualflybrain.org/reports/FBbt_00007580 \"Open Y6 in Virtual Fly Brain\"), [extra l-LNv neuron](https://www.virtualflybrain.org/reports/FBbt_00047183 \"Open extra l-LNv neuron in Virtual Fly Brain\"), [Dm7](https://www.virtualflybrain.org/reports/FBbt_00003774 \"Open Dm7 in Virtual Fly Brain\"), Mi6, Mi8, Tm10, Tm13, Tm14, Tm18, and Tm19. VFB records show [333](https://v2.virtualflybrain.org/org.geppetto.frontend/geppetto?q=FBbt_00003748,NeuronsPostsynapticHere \"Run in VFB: Neurons with postsynaptic terminals in medulla\") neurons with postsynaptic terminals in the medulla.", + "quality_flags": { + "has_tool_status": true, + "no_tool_factual_answer": false, + "tool_claim_without_tool": false, + "disambiguation_only_answer": false, + "investigation_plan_answer": false, + "not_verified_or_no_results_answer": false, + "graph_failure_mentioned": false, + "missing_required_graph": false, + "used_data_resource": false, + "response_chars": 938, + "status_count": 7, + "addressless_followon": false, + "context_lost_across_turn": false, + "unmatched_claim_after_resolve": false, + "repeats_answered_question": false, + "slow_followup_turn": false, + "slowest_followup_ms": 6346 + } + }, + { + "attempt_index": 53, + "task_index": 53, + "task_id": "C2", + "tier": 7, + "title": "A clicked chip keeps its address", + "question": "What is the mushroom body?", + "requires_graph": false, + "min_graphs": 0, + "repetition": 1, + "duration_ms": 18549, + "status_messages": [ + { + "message": "Thinking...", + "phase": "llm" + }, + { + "message": "Running the query behind that suggestion", + "phase": "mcp" + }, + { + "message": "Resolving 1 term in VFB", + "phase": "mcp" + }, + { + "message": "Querying VFB", + "phase": "mcp" + }, + { + "message": "Checking the answer is covered", + "phase": "llm" + }, + { + "message": "Querying VFB", + "phase": "mcp" + }, + { + "message": "Checking the answer is covered", + "phase": "llm" + }, + { + "message": "Writing the answer", + "phase": "llm" + } + ], + "event_count": 351, + "conversation": true, + "turns": [ + { + "turn": 1, + "question": "What is the mushroom body?", + "focus": null, + "clicked": null, + "duration_ms": 8071, + "ok": true, + "response": "The [mushroom body](https://www.virtualflybrain.org/reports/FBbt_00005801 \"Open mushroom body in Virtual Fly Brain\") is a bilaterally paired neuropil structure situated postero-dorsally in the protocerebrum that functions in olfactory associative learning and memory. It is divided into the calyx, which receives sensory interneuron afferents, the pedunculus, a thick axon bundle, and the mushroom body lobe system, which consists of a vertical branch and a medial branch and has different structures at different life stages.", + "followons": [ + { + "id": "FBbt_00005801", + "query_type": "ImagesNeurons", + "query": "Which neuron images have a part in the mushroom body?" + }, + { + "id": "FBbt_00005801", + "query_type": "TransgeneExpressionHere", + "query": "Which driver lines label the mushroom body?" + }, + { + "id": "FBbt_00005801", + "query_type": "NeuronsPartHere", + "query": "Which neurons have part of their arbour in the mushroom body?" + }, + { + "id": "FBbt_00005801", + "query_type": "NeuronsSynaptic", + "query": "Which neurons have synaptic terminals in the mushroom body?" + }, + { + "id": "FBbt_00005801", + "query_type": "NeuronsPresynapticHere", + "query": "Which neurons provide input to the mushroom body?" + }, + { + "id": "FBbt_00005801", + "query_type": "NeuronsPostsynapticHere", + "query": "Which neurons receive output from the mushroom body?" + } + ], + "context_terms": [ + { + "id": "FBbt_00005801", + "label": "mushroom body" + } + ], + "reproduction": { + "ids": [ + { + "id": "FBbt_00005801", + "label": "mushroom body" + } + ], + "calls": [], + "unmapped": [] + }, + "status_count": 6, + "problems": [] + }, + { + "turn": 2, + "question": "Which neuron images have a part in the mushroom body?", + "focus": { + "id": "FBbt_00005801", + "query_type": "ImagesNeurons" + }, + "clicked": 0, + "duration_ms": 10478, + "ok": true, + "response": "Images of neurons with some part in [mushroom body](https://www.virtualflybrain.org/reports/FBbt_00005801 \"Open mushroom body in Virtual Fly Brain\") are available, with [27,619](https://v2.virtualflybrain.org/org.geppetto.frontend/geppetto?q=FBbt_00005801,ImagesNeurons \"Run in VFB: Images of neurons with some part in mushroom body\") images. The first 12 images, along with their VFB ids, are: VT020731 FLP 14-3; GMR 24E06 FLP 6-1; GMR 75F01 FLP 9-2; GMR 21G01 FLP 9-1; GMR 24E06 FLP 6-2; GMR 127E09 FLP 9-5; GMR 67E07 FLP 30-1; GMR 29D11 FLP 45-3; GMR 74C11 FLP 9-1; GMR 40D06 FLP 2-1; GMR 12G07 FLP 7-2; GMR 93G04 FLP 12-1. Additionally, there are [602](https://v2.virtualflybrain.org/org.geppetto.frontend/geppetto?q=FBbt_00005801,NeuronsPartHere \"Run in VFB: Neurons with some part in mushroom body\") neurons with some part in mushroom body, including [adult odd neuron of the calyx](https://www.virtualflybrain.org/reports/FBbt_00111628 \"Open adult odd neuron of the calyx in Virtual Fly Brain\"), [larval uniglomerular projection neuron 63a](https://www.virtualflybrain.org/reports/FBbt_00111675 \"Open larval uniglomerular projection neuron 63a in Virtual Fly Brain\"), [larval uniglomerular projection neuron 67b](https://www.virtualflybrain.org/reports/FBbt_00111684 \"Open larval uniglomerular projection neuron 67b in Virtual Fly Brain\"), [larval uniglomerular projection neuron 74a](https://www.virtualflybrain.org/reports/FBbt_00111685 \"Open larval uniglomerular projection neuron 74a in Virtual Fly Brain\"), [larval antennal lobe multiglomerular projection neuron C2](https://www.virtualflybrain.org/reports/FBbt_00111716 \"Open larval antennal lobe multiglomerular projection neuron C2 in Virtual Fly Brain\"), [larval antennal lobe multiglomerular projection neuron bilateral lower](https://www.virtualflybrain.org/reports/FBbt_00111717 \"Open larval antennal lobe multiglomerular projection neuron bilateral lower in Virtual Fly Brain\"), larval antennal lobe multiglomerular projection neuron bilateral upper, larval antennal lobe multiglomerular projection neuron D, larval antennal lobe multiglomerular projection neuron cobra, AOTU021, AOTU022, and [ATL005](https://www.virtualflybrain.org/reports/FBbt_20000069 \"Open ATL005 in Virtual Fly Brain\").", + "followons": [ + { + "id": "FBbt_00005801", + "query_type": "TransgeneExpressionHere", + "query": "Which driver lines label the mushroom body?" + }, + { + "id": "FBbt_00005801", + "query_type": "NeuronsSynaptic", + "query": "Which neurons have synaptic terminals in the mushroom body?" + }, + { + "id": "FBbt_00005801", + "query_type": "NeuronsPresynapticHere", + "query": "Which neurons provide input to the mushroom body?" + }, + { + "id": "FBbt_00005801", + "query_type": "NeuronsPostsynapticHere", + "query": "Which neurons receive output from the mushroom body?" + }, + { + "id": "FBbt_00005801", + "query_type": "PartsOf", + "query": "What are the anatomical parts of the mushroom body?" + }, + { + "id": "FBbt_00005801", + "query_type": "LineageClonesIn", + "query": "Which lineage clones are found in the mushroom body?" + } + ], + "context_terms": [ + { + "id": "FBbt_00005801", + "label": "mushroom body" + } + ], + "reproduction": { + "ids": [ + { + "id": "FBbt_00005801", + "label": "mushroom body" + } + ], + "calls": [ + { + "id": "FBbt_00005801", + "query_type": "ImagesNeurons", + "fn": "get_images_neurons" + }, + { + "id": "FBbt_00005801", + "query_type": "NeuronsPartHere", + "fn": "get_neurons_with_part_in" + } + ], + "unmapped": [] + }, + "status_count": 8, + "problems": [] + } + ], + "ok": true, + "request_id": "e8c70e75-887c-4264-851b-f04eb0289ba9", + "response_id": "chatcmpl-1099c9f71a10164c6c2f03fd0e0d741b", + "images_count": 8, + "graphs_count": 0, + "response": "Images of neurons with some part in [mushroom body](https://www.virtualflybrain.org/reports/FBbt_00005801 \"Open mushroom body in Virtual Fly Brain\") are available, with [27,619](https://v2.virtualflybrain.org/org.geppetto.frontend/geppetto?q=FBbt_00005801,ImagesNeurons \"Run in VFB: Images of neurons with some part in mushroom body\") images. The first 12 images, along with their VFB ids, are: VT020731 FLP 14-3; GMR 24E06 FLP 6-1; GMR 75F01 FLP 9-2; GMR 21G01 FLP 9-1; GMR 24E06 FLP 6-2; GMR 127E09 FLP 9-5; GMR 67E07 FLP 30-1; GMR 29D11 FLP 45-3; GMR 74C11 FLP 9-1; GMR 40D06 FLP 2-1; GMR 12G07 FLP 7-2; GMR 93G04 FLP 12-1. Additionally, there are [602](https://v2.virtualflybrain.org/org.geppetto.frontend/geppetto?q=FBbt_00005801,NeuronsPartHere \"Run in VFB: Neurons with some part in mushroom body\") neurons with some part in mushroom body, including [adult odd neuron of the calyx](https://www.virtualflybrain.org/reports/FBbt_00111628 \"Open adult odd neuron of the calyx in Virtual Fly Brain\"), [larval uniglomerular projection neuron 63a](https://www.virtualflybrain.org/reports/FBbt_00111675 \"Open larval uniglomerular projection neuron 63a in Virtual Fly Brain\"), [larval uniglomerular projection neuron 67b](https://www.virtualflybrain.org/reports/FBbt_00111684 \"Open larval uniglomerular projection neuron 67b in Virtual Fly Brain\"), [larval uniglomerular projection neuron 74a](https://www.virtualflybrain.org/reports/FBbt_00111685 \"Open larval uniglomerular projection neuron 74a in Virtual Fly Brain\"), [larval antennal lobe multiglomerular projection neuron C2](https://www.virtualflybrain.org/reports/FBbt_00111716 \"Open larval antennal lobe multiglomerular projection neuron C2 in Virtual Fly Brain\"), [larval antennal lobe multiglomerular projection neuron bilateral lower](https://www.virtualflybrain.org/reports/FBbt_00111717 \"Open larval antennal lobe multiglomerular projection neuron bilateral lower in Virtual Fly Brain\"), larval antennal lobe multiglomerular projection neuron bilateral upper, larval antennal lobe multiglomerular projection neuron D, larval antennal lobe multiglomerular projection neuron cobra, AOTU021, AOTU022, and [ATL005](https://www.virtualflybrain.org/reports/FBbt_20000069 \"Open ATL005 in Virtual Fly Brain\").", + "quality_flags": { + "has_tool_status": true, + "no_tool_factual_answer": false, + "tool_claim_without_tool": false, + "disambiguation_only_answer": false, + "investigation_plan_answer": false, + "not_verified_or_no_results_answer": false, + "graph_failure_mentioned": false, + "missing_required_graph": false, + "used_data_resource": false, + "response_chars": 2262, + "status_count": 8, + "addressless_followon": false, + "context_lost_across_turn": false, + "unmatched_claim_after_resolve": false, + "repeats_answered_question": false, + "slow_followup_turn": false, + "slowest_followup_ms": 10478 + } + }, + { + "attempt_index": 54, + "task_index": 54, + "task_id": "C3", + "tier": 7, + "title": "Topic switch and back", + "question": "What is the fan-shaped body?", + "requires_graph": false, + "min_graphs": 0, + "repetition": 1, + "duration_ms": 25172, + "status_messages": [ + { + "message": "Thinking...", + "phase": "llm" + }, + { + "message": "Running the query behind that suggestion", + "phase": "mcp" + }, + { + "message": "Resolving 1 term in VFB", + "phase": "mcp" + }, + { + "message": "Querying VFB", + "phase": "mcp" + }, + { + "message": "Checking the answer is covered", + "phase": "llm" + }, + { + "message": "Writing the answer", + "phase": "llm" + } + ], + "event_count": 125, + "conversation": true, + "turns": [ + { + "turn": 1, + "question": "What is the fan-shaped body?", + "focus": null, + "clicked": null, + "duration_ms": 7133, + "ok": true, + "response": "The [fan-shaped body](https://www.virtualflybrain.org/reports/FBbt_00003679 \"Open fan-shaped body in Virtual Fly Brain\") is the largest synaptic neuropil domain of the adult central complex, located posterior to the ellipsoid body and anterior to the protocerebral bridge. It is composed of a rough 2-dimensional grid of layers and columns. Eight horizontal layers, numbered bottom to top, form a fan shape and can be divided into vertical columns. An additional, much narrower, 9th layer, which lacks a columnar organization, sits dorsal to layer 8. The number of columns varies for different neuronal types.", + "followons": [ + { + "id": "FBbt_00003679", + "query_type": "ImagesNeurons", + "query": "Which neuron images have a part in the fan-shaped body?" + }, + { + "id": "FBbt_00003679", + "query_type": "TransgeneExpressionHere", + "query": "Which driver lines label the fan-shaped body?" + }, + { + "id": "FBbt_00003679", + "query_type": "NeuronsPartHere", + "query": "Which neurons have part of their arbour in the fan-shaped body?" + }, + { + "id": "FBbt_00003679", + "query_type": "NeuronsSynaptic", + "query": "Which neurons have synaptic terminals in the fan-shaped body?" + }, + { + "id": "FBbt_00003679", + "query_type": "NeuronsPresynapticHere", + "query": "Which neurons provide input to the fan-shaped body?" + }, + { + "id": "FBbt_00003679", + "query_type": "NeuronsPostsynapticHere", + "query": "Which neurons receive output from the fan-shaped body?" + } + ], + "context_terms": [ + { + "id": "FBbt_00003679", + "label": "fan-shaped body" + } + ], + "reproduction": { + "ids": [ + { + "id": "FBbt_00003679", + "label": "fan-shaped body" + } + ], + "calls": [], + "unmapped": [] + }, + "status_count": 6, + "problems": [] + }, + { + "turn": 2, + "question": "What about the ellipsoid body?", + "focus": null, + "clicked": null, + "duration_ms": 8888, + "ok": true, + "response": "The [ellipsoid body](https://www.virtualflybrain.org/reports/FBbt_00003678 \"Open ellipsoid body in Virtual Fly Brain\") is a doughnut-shaped synaptic neuropil domain of the central complex of the adult brain that lies just anterior to the [fan-shaped body](https://www.virtualflybrain.org/reports/FBbt_00003679 \"Open fan-shaped body in Virtual Fly Brain\"). Its hole, the ellipsoid body canal, points anteriorly and has an axon tract, the anterior bundle, running through it.", + "followons": [ + { + "id": "FBbt_00003678", + "query_type": "ImagesNeurons", + "query": "Which neuron images have a part in the ellipsoid body?" + }, + { + "id": "FBbt_00003678", + "query_type": "TransgeneExpressionHere", + "query": "Which driver lines label the ellipsoid body?" + }, + { + "id": "FBbt_00003678", + "query_type": "NeuronsPartHere", + "query": "Which neurons have part of their arbour in the ellipsoid body?" + }, + { + "id": "FBbt_00003678", + "query_type": "NeuronsSynaptic", + "query": "Which neurons have synaptic terminals in the ellipsoid body?" + }, + { + "id": "FBbt_00003678", + "query_type": "NeuronsPresynapticHere", + "query": "Which neurons provide input to the ellipsoid body?" + }, + { + "id": "FBbt_00003678", + "query_type": "NeuronsPostsynapticHere", + "query": "Which neurons receive output from the ellipsoid body?" + } + ], + "context_terms": [ + { + "id": "FBbt_00003678", + "label": "ellipsoid body" + }, + { + "id": "FBbt_00003679", + "label": "fan-shaped body" + } + ], + "reproduction": { + "ids": [ + { + "id": "FBbt_00003678", + "label": "ellipsoid body" + }, + { + "id": "FBbt_00003679", + "label": "fan-shaped body" + } + ], + "calls": [], + "unmapped": [] + }, + "status_count": 6, + "problems": [] + }, + { + "turn": 3, + "question": "Which neurons have synaptic terminals in the fan-shaped body?", + "focus": null, + "clicked": null, + "duration_ms": 9151, + "ok": true, + "response": "Neurons with synaptic terminals in the [fan-shaped body](https://www.virtualflybrain.org/reports/FBbt_00003679 \"Open fan-shaped body in Virtual Fly Brain\") include [229](https://v2.virtualflybrain.org/org.geppetto.frontend/geppetto?q=FBbt_00003679,NeuronsPartHere \"Run in VFB: Neurons with some part in fan-shaped body\") neuron types, such as [PFNa_PB4](https://www.virtualflybrain.org/reports/FBbt_00111398 \"Open PFNa_PB4 in Virtual Fly Brain\"), [PFNa_PB5](https://www.virtualflybrain.org/reports/FBbt_00111399 \"Open PFNa_PB5 in Virtual Fly Brain\"), [PFNd_PB2](https://www.virtualflybrain.org/reports/FBbt_00111391 \"Open PFNd_PB2 in Virtual Fly Brain\"), [PFNd_PB3](https://www.virtualflybrain.org/reports/FBbt_00111392 \"Open PFNd_PB3 in Virtual Fly Brain\"), [PFNd_PB5](https://www.virtualflybrain.org/reports/FBbt_00111394 \"Open PFNd_PB5 in Virtual Fly Brain\"). The first 12 of these, with their VFB ids, are: PFNd_PB2; PFNd_PB3; PFNd_PB5; PFNa_PB4; PFNa_PB5; PFNa_PB6; PFNa_PB7; PFNa_PB9; PFNp_PB7; [PFL1_PB5](https://www.virtualflybrain.org/reports/FBbt_00111438 \"Open PFL1_PB5 in Virtual Fly Brain\"); [PFL3](https://www.virtualflybrain.org/reports/FBbt_00111443 \"Open PFL3 in Virtual Fly Brain\"); [PFL2](https://www.virtualflybrain.org/reports/FBbt_00111451 \"Open PFL2 in Virtual Fly Brain\").", + "followons": [ + { + "id": "FBbt_00003679", + "query_type": "ImagesNeurons", + "query": "Which neuron images have a part in the fan-shaped body?" + }, + { + "id": "FBbt_00003679", + "query_type": "TransgeneExpressionHere", + "query": "Which driver lines label the fan-shaped body?" + }, + { + "id": "FBbt_00003679", + "query_type": "NeuronsPartHere", + "query": "Which neurons have part of their arbour in the fan-shaped body?" + }, + { + "id": "FBbt_00003679", + "query_type": "NeuronsPresynapticHere", + "query": "Which neurons provide input to the fan-shaped body?" + }, + { + "id": "FBbt_00003679", + "query_type": "NeuronsPostsynapticHere", + "query": "Which neurons receive output from the fan-shaped body?" + }, + { + "id": "FBbt_00003679", + "query_type": "PartsOf", + "query": "What are the anatomical parts of the fan-shaped body?" + } + ], + "context_terms": [ + { + "id": "FBbt_00003679", + "label": "fan-shaped body" + }, + { + "id": "FBbt_00003678", + "label": "ellipsoid body" + } + ], + "reproduction": { + "ids": [ + { + "id": "FBbt_00003679", + "label": "fan-shaped body" + }, + { + "id": "FBbt_00003678", + "label": "ellipsoid body" + } + ], + "calls": [ + { + "id": "FBbt_00003679", + "query_type": "NeuronsSynaptic", + "fn": "get_neurons_with_synapses_in" + } + ], + "unmapped": [] + }, + "status_count": 6, + "problems": [] + } + ], + "ok": true, + "request_id": "2a4f541b-f111-444c-b3f2-c88fd9667866", + "response_id": "chatcmpl-3cfc31dd86f45a4f7b5473409f231e0b", + "images_count": 8, + "graphs_count": 0, + "response": "Neurons with synaptic terminals in the [fan-shaped body](https://www.virtualflybrain.org/reports/FBbt_00003679 \"Open fan-shaped body in Virtual Fly Brain\") include [229](https://v2.virtualflybrain.org/org.geppetto.frontend/geppetto?q=FBbt_00003679,NeuronsPartHere \"Run in VFB: Neurons with some part in fan-shaped body\") neuron types, such as [PFNa_PB4](https://www.virtualflybrain.org/reports/FBbt_00111398 \"Open PFNa_PB4 in Virtual Fly Brain\"), [PFNa_PB5](https://www.virtualflybrain.org/reports/FBbt_00111399 \"Open PFNa_PB5 in Virtual Fly Brain\"), [PFNd_PB2](https://www.virtualflybrain.org/reports/FBbt_00111391 \"Open PFNd_PB2 in Virtual Fly Brain\"), [PFNd_PB3](https://www.virtualflybrain.org/reports/FBbt_00111392 \"Open PFNd_PB3 in Virtual Fly Brain\"), [PFNd_PB5](https://www.virtualflybrain.org/reports/FBbt_00111394 \"Open PFNd_PB5 in Virtual Fly Brain\"). The first 12 of these, with their VFB ids, are: PFNd_PB2; PFNd_PB3; PFNd_PB5; PFNa_PB4; PFNa_PB5; PFNa_PB6; PFNa_PB7; PFNa_PB9; PFNp_PB7; [PFL1_PB5](https://www.virtualflybrain.org/reports/FBbt_00111438 \"Open PFL1_PB5 in Virtual Fly Brain\"); [PFL3](https://www.virtualflybrain.org/reports/FBbt_00111443 \"Open PFL3 in Virtual Fly Brain\"); [PFL2](https://www.virtualflybrain.org/reports/FBbt_00111451 \"Open PFL2 in Virtual Fly Brain\").", + "quality_flags": { + "has_tool_status": true, + "no_tool_factual_answer": false, + "tool_claim_without_tool": false, + "disambiguation_only_answer": false, + "investigation_plan_answer": false, + "not_verified_or_no_results_answer": false, + "graph_failure_mentioned": false, + "missing_required_graph": false, + "used_data_resource": false, + "response_chars": 1296, + "status_count": 6, + "addressless_followon": false, + "context_lost_across_turn": false, + "unmatched_claim_after_resolve": false, + "repeats_answered_question": false, + "slow_followup_turn": false, + "slowest_followup_ms": 9151 + } + }, + { + "attempt_index": 55, + "task_index": 55, + "task_id": "C4", + "tier": 7, + "title": "Refinement onto a cell type", + "question": "What is a Kenyon cell?", + "requires_graph": false, + "min_graphs": 0, + "repetition": 1, + "duration_ms": 14682, + "status_messages": [ + { + "message": "Thinking...", + "phase": "llm" + }, + { + "message": "Running the query behind that suggestion", + "phase": "mcp" + }, + { + "message": "Resolving 1 term in VFB", + "phase": "mcp" + }, + { + "message": "Querying VFB", + "phase": "mcp" + }, + { + "message": "Checking the answer is covered", + "phase": "llm" + }, + { + "message": "Writing the answer", + "phase": "llm" + } + ], + "event_count": 143, + "conversation": true, + "turns": [ + { + "turn": 1, + "question": "What is a Kenyon cell?", + "focus": null, + "clicked": null, + "duration_ms": 7173, + "ok": true, + "response": "A [Kenyon cell](https://www.virtualflybrain.org/reports/FBbt_00003686 \"Open Kenyon cell in Virtual Fly Brain\") is an intrinsic neuron of the mushroom body. Kenyon cells are part of the olfactory pathway in Drosophila.", + "followons": [ + { + "id": "FBbt_00003686", + "query_type": "ListAllAvailableImages", + "query": "Which images of Kenyon cell does VFB have?" + }, + { + "id": "FBbt_00003686", + "query_type": "UpstreamClassConnectivity", + "query": "What connects to the Kenyon cell upstream?" + }, + { + "id": "FBbt_00003686", + "query_type": "DownstreamClassConnectivity", + "query": "What does the Kenyon cell connect to downstream?" + }, + { + "id": "FBbt_00003686", + "query_type": "TransgeneExpressionHere", + "query": "Which driver lines label the Kenyon cell?" + }, + { + "id": "FBbt_00003686", + "query_type": "anatScRNAseqQuery", + "query": "What single-cell transcriptomic clusters are there for Kenyon cell?" + }, + { + "id": "FBbt_00003686", + "query_type": "SubclassesOf", + "query": "What are the subtypes of the Kenyon cell?" + } + ], + "context_terms": [ + { + "id": "FBbt_00003686", + "label": "Kenyon cell" + } + ], + "reproduction": { + "ids": [ + { + "id": "FBbt_00003686", + "label": "Kenyon cell" + } + ], + "calls": [], + "unmapped": [] + }, + "status_count": 7, + "problems": [] + }, + { + "turn": 2, + "question": "What are its subtypes?", + "focus": null, + "clicked": null, + "duration_ms": 7509, + "ok": true, + "response": "The subtypes of [Kenyon cell](https://www.virtualflybrain.org/reports/FBbt_00003686 \"Open Kenyon cell in Virtual Fly Brain\") are [37](https://v2.virtualflybrain.org/org.geppetto.frontend/geppetto?q=FBbt_00003686,SubclassesOf \"Run in VFB: Subclasses of Kenyon cell\") subclasses, including [KCab-c(i)](https://www.virtualflybrain.org/reports/FBbt_00049111 \"Open KCab-c(i) in Virtual Fly Brain\"), [KCab-c](https://www.virtualflybrain.org/reports/FBbt_00110929 \"Open KCab-c in Virtual Fly Brain\"), [KCg-m](https://www.virtualflybrain.org/reports/FBbt_00111061 \"Open KCg-m in Virtual Fly Brain\"), [Kenyon cell of main calyx](https://www.virtualflybrain.org/reports/FBbt_00047926 \"Open Kenyon cell of main calyx in Virtual Fly Brain\"), and [gamma Kenyon cell](https://www.virtualflybrain.org/reports/FBbt_00100247 \"Open gamma Kenyon cell in Virtual Fly Brain\"). The first 12 subclasses, with their identifiers, are: KCab-c(i); KCab-c(o); larval gamma Kenyon cell; KCg-s; KCg-s4; KCg-t; larval alpha'/beta' Kenyon cell; KCab-sc; alpha'/beta' anterior-posterior type 1 Kenyon cell of lACA; Kenyon cell of main calyx; single-claw Kenyon cell; and multi-claw Kenyon cell.", + "followons": [ + { + "id": "FBbt_00003686", + "query_type": "ListAllAvailableImages", + "query": "Which images of Kenyon cell does VFB have?" + }, + { + "id": "FBbt_00003686", + "query_type": "UpstreamClassConnectivity", + "query": "What connects to the Kenyon cell upstream?" + }, + { + "id": "FBbt_00003686", + "query_type": "DownstreamClassConnectivity", + "query": "What does the Kenyon cell connect to downstream?" + }, + { + "id": "FBbt_00003686", + "query_type": "TransgeneExpressionHere", + "query": "Which driver lines label the Kenyon cell?" + }, + { + "id": "FBbt_00003686", + "query_type": "anatScRNAseqQuery", + "query": "What single-cell transcriptomic clusters are there for Kenyon cell?" + } + ], + "context_terms": [ + { + "id": "FBbt_00003686", + "label": "Kenyon cell" + } + ], + "reproduction": { + "ids": [ + { + "id": "FBbt_00003686", + "label": "Kenyon cell" + } + ], + "calls": [ + { + "id": "FBbt_00003686", + "query_type": "SubclassesOf", + "fn": "get_subclasses_of" + } + ], + "unmapped": [] + }, + "status_count": 6, + "problems": [] + } + ], + "ok": true, + "request_id": "c721665f-c27a-48da-9407-9693542525b8", + "response_id": "chatcmpl-6be21b0f54c7e0e8bcb3586935a58e44", + "images_count": 8, + "graphs_count": 0, + "response": "The subtypes of [Kenyon cell](https://www.virtualflybrain.org/reports/FBbt_00003686 \"Open Kenyon cell in Virtual Fly Brain\") are [37](https://v2.virtualflybrain.org/org.geppetto.frontend/geppetto?q=FBbt_00003686,SubclassesOf \"Run in VFB: Subclasses of Kenyon cell\") subclasses, including [KCab-c(i)](https://www.virtualflybrain.org/reports/FBbt_00049111 \"Open KCab-c(i) in Virtual Fly Brain\"), [KCab-c](https://www.virtualflybrain.org/reports/FBbt_00110929 \"Open KCab-c in Virtual Fly Brain\"), [KCg-m](https://www.virtualflybrain.org/reports/FBbt_00111061 \"Open KCg-m in Virtual Fly Brain\"), [Kenyon cell of main calyx](https://www.virtualflybrain.org/reports/FBbt_00047926 \"Open Kenyon cell of main calyx in Virtual Fly Brain\"), and [gamma Kenyon cell](https://www.virtualflybrain.org/reports/FBbt_00100247 \"Open gamma Kenyon cell in Virtual Fly Brain\"). The first 12 subclasses, with their identifiers, are: KCab-c(i); KCab-c(o); larval gamma Kenyon cell; KCg-s; KCg-s4; KCg-t; larval alpha'/beta' Kenyon cell; KCab-sc; alpha'/beta' anterior-posterior type 1 Kenyon cell of lACA; Kenyon cell of main calyx; single-claw Kenyon cell; and multi-claw Kenyon cell.", + "quality_flags": { + "has_tool_status": true, + "no_tool_factual_answer": false, + "tool_claim_without_tool": false, + "disambiguation_only_answer": false, + "investigation_plan_answer": false, + "not_verified_or_no_results_answer": false, + "graph_failure_mentioned": false, + "missing_required_graph": false, + "used_data_resource": false, + "response_chars": 1161, + "status_count": 6, + "addressless_followon": false, + "context_lost_across_turn": false, + "unmatched_claim_after_resolve": false, + "repeats_answered_question": false, + "slow_followup_turn": false, + "slowest_followup_ms": 7509 + } + }, + { + "attempt_index": 56, + "task_index": 56, + "task_id": "C5", + "tier": 7, + "title": "A presentation directive is not part of the term name", + "question": "What are the anatomical parts of the medulla? List them.", + "requires_graph": false, + "min_graphs": 0, + "repetition": 1, + "duration_ms": 31760, + "status_messages": [ + { + "message": "Thinking...", + "phase": "llm" + }, + { + "message": "Planning the answer", + "phase": "llm" + }, + { + "message": "Resolving 1 term in VFB", + "phase": "mcp" + }, + { + "message": "Reading VFB term info", + "phase": "mcp" + }, + { + "message": "Querying VFB", + "phase": "mcp" + }, + { + "message": "Querying VFB", + "phase": "mcp" + }, + { + "message": "Checking the answer is covered", + "phase": "llm" + }, + { + "message": "Querying VFB", + "phase": "mcp" + }, + { + "message": "Querying VFB", + "phase": "mcp" + }, + { + "message": "Querying VFB", + "phase": "mcp" + }, + { + "message": "Checking the answer is covered", + "phase": "llm" + }, + { + "message": "Writing the answer", + "phase": "llm" + } + ], + "event_count": 114, + "conversation": true, + "turns": [ + { + "turn": 1, + "question": "What are the anatomical parts of the medulla? List them.", + "focus": null, + "clicked": null, + "duration_ms": 9726, + "ok": true, + "response": "The [medulla](https://www.virtualflybrain.org/reports/FBbt_00003748 \"Open medulla in Virtual Fly Brain\") is divided into 10 layers: 1-6 make up the outer (distal) medulla, the seventh (or serpentine) layer exhibits a distinct architecture and layers 8-10 make up the inner (proximal) medulla. Anatomical parts of the medulla include adult chandelier glial cell, adult distal medulla astrocyte-like glial cell, [distal medulla glial cell](https://www.virtualflybrain.org/reports/FBbt_00100528 \"Open distal medulla glial cell in Virtual Fly Brain\"), medulla layer, adult distal medulla ensheathing glial cell, [plexiform medulla](https://www.virtualflybrain.org/reports/FBbt_00045001 \"Open plexiform medulla in Virtual Fly Brain\"), [medulla dorsal rim area](https://www.virtualflybrain.org/reports/FBbt_00045002 \"Open medulla dorsal rim area in Virtual Fly Brain\"), medulla layer M1, medulla layer M5, inner medulla, medulla layer M8, and medulla layer M9.", + "followons": [ + { + "id": "FBbt_00003748", + "query_type": "ImagesNeurons", + "query": "Which neuron images have a part in the medulla?" + }, + { + "id": "FBbt_00003748", + "query_type": "TransgeneExpressionHere", + "query": "Which driver lines label the medulla?" + }, + { + "id": "FBbt_00003748", + "query_type": "NeuronsPartHere", + "query": "Which neurons have part of their arbour in the medulla?" + }, + { + "id": "FBbt_00003748", + "query_type": "NeuronsSynaptic", + "query": "Which neurons have synaptic terminals in the medulla?" + }, + { + "id": "FBbt_00003748", + "query_type": "NeuronsPostsynapticHere", + "query": "Which neurons receive output from the medulla?" + }, + { + "id": "FBbt_00003748", + "query_type": "NeuronsPresynapticHere", + "query": "Which neurons provide input to the medulla?" + } + ], + "context_terms": [ + { + "id": "FBbt_00003748", + "label": "medulla" + } + ], + "reproduction": { + "ids": [ + { + "id": "FBbt_00003748", + "label": "medulla" + } + ], + "calls": [ + { + "id": "FBbt_00003748", + "query_type": "PartsOf", + "fn": "get_parts_of" + } + ], + "unmapped": [] + }, + "status_count": 8, + "problems": [] + }, + { + "turn": 2, + "question": "And which neurons have part of their arbour there?", + "focus": null, + "clicked": null, + "duration_ms": 22034, + "ok": true, + "response": "Neurons with some part in the [medulla](https://www.virtualflybrain.org/reports/FBbt_00003748 \"Open medulla in Virtual Fly Brain\") include [Dm8b](https://www.virtualflybrain.org/reports/FBbt_00110069 \"Open Dm8b in Virtual Fly Brain\"), [MC](https://www.virtualflybrain.org/reports/FBbt_00111640 \"Open MC in Virtual Fly Brain\"), [PS128](https://www.virtualflybrain.org/reports/FBbt_20001883 \"Open PS128 in Virtual Fly Brain\"), [medulla intrinsic neuron vGlutMinew1a](https://www.virtualflybrain.org/reports/FBbt_00110033 \"Open medulla intrinsic neuron vGlutMinew1a in Virtual Fly Brain\"), [TmY27](https://www.virtualflybrain.org/reports/FBbt_00110067 \"Open TmY27 in Virtual Fly Brain\"), and others, with a total of [471](https://v2.virtualflybrain.org/org.geppetto.frontend/geppetto?q=FBbt_00003748,NeuronsPartHere \"Run in VFB: Neurons with some part in medulla\") neuron types. The medulla also contains neurons with synaptic terminals, presynaptic terminals, and postsynaptic terminals, with [464](https://v2.virtualflybrain.org/org.geppetto.frontend/geppetto?q=FBbt_00003748,NeuronsSynaptic \"Run in VFB: Neurons with synaptic terminals in medulla\"), [262](https://v2.virtualflybrain.org/org.geppetto.frontend/geppetto?q=FBbt_00003748,NeuronsPresynapticHere \"Run in VFB: Neurons with presynaptic terminals in medulla\"), and [333](https://v2.virtualflybrain.org/org.geppetto.frontend/geppetto?q=FBbt_00003748,NeuronsPostsynapticHere \"Run in VFB: Neurons with postsynaptic terminals in medulla\") results, respectively. VFB holds [226524](https://v2.virtualflybrain.org/org.geppetto.frontend/geppetto?q=FBbt_00003748,ImagesNeurons \"Run in VFB: Images of neurons with some part in medulla\") images of neurons with some part in the medulla.", + "followons": [ + { + "id": "FBbt_00003748", + "query_type": "ImagesNeurons", + "query": "Which neuron images have a part in the medulla?" + }, + { + "id": "FBbt_00003748", + "query_type": "TransgeneExpressionHere", + "query": "Which driver lines label the medulla?" + }, + { + "id": "FBbt_00003748", + "query_type": "PartsOf", + "query": "What are the anatomical parts of the medulla?" + }, + { + "id": "FBbt_00003748", + "query_type": "LineageClonesIn", + "query": "Which lineage clones are found in the medulla?" + }, + { + "id": "FBbt_00003748", + "query_type": "ListAllAvailableImages", + "query": "Which images of medulla does VFB have?" + }, + { + "id": "FBbt_00003748", + "query_type": "TractsNervesInnervatingHere", + "query": "Which tracts and nerves innervate the medulla?" + } + ], + "context_terms": [ + { + "id": "FBbt_00003748", + "label": "medulla" + } + ], + "reproduction": { + "ids": [ + { + "id": "FBbt_00003748", + "label": "medulla" + } + ], + "calls": [ + { + "id": "FBbt_00003748", + "query_type": "NeuronsPartHere", + "fn": "get_neurons_with_part_in" + }, + { + "id": "FBbt_00003748", + "query_type": "NeuronsSynaptic", + "fn": "get_neurons_with_synapses_in" + }, + { + "id": "FBbt_00003748", + "query_type": "NeuronsPresynapticHere", + "fn": "get_neurons_with_presynaptic_terminals_in" + }, + { + "id": "FBbt_00003748", + "query_type": "NeuronsPostsynapticHere", + "fn": "get_neurons_with_postsynaptic_terminals_in" + }, + { + "id": "FBbt_00003748", + "query_type": "PartsOf", + "fn": "get_parts_of" + } + ], + "unmapped": [] + }, + "status_count": 12, + "problems": [] + } + ], + "ok": true, + "request_id": "df17217a-0aff-4baa-951f-cf673f7d1dda", + "response_id": "chatcmpl-9ed32e477cce4d3f2d372f233a17586f", + "images_count": 8, + "graphs_count": 0, + "response": "Neurons with some part in the [medulla](https://www.virtualflybrain.org/reports/FBbt_00003748 \"Open medulla in Virtual Fly Brain\") include [Dm8b](https://www.virtualflybrain.org/reports/FBbt_00110069 \"Open Dm8b in Virtual Fly Brain\"), [MC](https://www.virtualflybrain.org/reports/FBbt_00111640 \"Open MC in Virtual Fly Brain\"), [PS128](https://www.virtualflybrain.org/reports/FBbt_20001883 \"Open PS128 in Virtual Fly Brain\"), [medulla intrinsic neuron vGlutMinew1a](https://www.virtualflybrain.org/reports/FBbt_00110033 \"Open medulla intrinsic neuron vGlutMinew1a in Virtual Fly Brain\"), [TmY27](https://www.virtualflybrain.org/reports/FBbt_00110067 \"Open TmY27 in Virtual Fly Brain\"), and others, with a total of [471](https://v2.virtualflybrain.org/org.geppetto.frontend/geppetto?q=FBbt_00003748,NeuronsPartHere \"Run in VFB: Neurons with some part in medulla\") neuron types. The medulla also contains neurons with synaptic terminals, presynaptic terminals, and postsynaptic terminals, with [464](https://v2.virtualflybrain.org/org.geppetto.frontend/geppetto?q=FBbt_00003748,NeuronsSynaptic \"Run in VFB: Neurons with synaptic terminals in medulla\"), [262](https://v2.virtualflybrain.org/org.geppetto.frontend/geppetto?q=FBbt_00003748,NeuronsPresynapticHere \"Run in VFB: Neurons with presynaptic terminals in medulla\"), and [333](https://v2.virtualflybrain.org/org.geppetto.frontend/geppetto?q=FBbt_00003748,NeuronsPostsynapticHere \"Run in VFB: Neurons with postsynaptic terminals in medulla\") results, respectively. VFB holds [226524](https://v2.virtualflybrain.org/org.geppetto.frontend/geppetto?q=FBbt_00003748,ImagesNeurons \"Run in VFB: Images of neurons with some part in medulla\") images of neurons with some part in the medulla.", + "quality_flags": { + "has_tool_status": true, + "no_tool_factual_answer": false, + "tool_claim_without_tool": false, + "disambiguation_only_answer": false, + "investigation_plan_answer": false, + "not_verified_or_no_results_answer": false, + "graph_failure_mentioned": false, + "missing_required_graph": false, + "used_data_resource": false, + "response_chars": 1734, + "status_count": 12, + "addressless_followon": false, + "context_lost_across_turn": false, + "unmatched_claim_after_resolve": false, + "repeats_answered_question": false, + "slow_followup_turn": false, + "slowest_followup_ms": 22034 + } + }, + { + "attempt_index": 57, + "task_index": 57, + "task_id": "C6", + "tier": 7, + "title": "Innervation asked of a pronoun", + "question": "Tell me about the antennal lobe.", + "requires_graph": false, + "min_graphs": 0, + "repetition": 1, + "duration_ms": 19680, + "status_messages": [ + { + "message": "Thinking...", + "phase": "llm" + }, + { + "message": "Running the query behind that suggestion", + "phase": "mcp" + }, + { + "message": "Resolving 1 term in VFB", + "phase": "mcp" + }, + { + "message": "Querying VFB", + "phase": "mcp" + }, + { + "message": "Checking the answer is covered", + "phase": "llm" + }, + { + "message": "Querying VFB", + "phase": "mcp" + }, + { + "message": "Checking the answer is covered", + "phase": "llm" + }, + { + "message": "Writing the answer", + "phase": "llm" + } + ], + "event_count": 162, + "conversation": true, + "turns": [ + { + "turn": 1, + "question": "Tell me about the antennal lobe.", + "focus": null, + "clicked": null, + "duration_ms": 11629, + "ok": true, + "response": "The [antennal lobe](https://www.virtualflybrain.org/reports/FBbt_00003924 \"Open antennal lobe in Virtual Fly Brain\") is a synaptic neuropil domain of the deutocerebrum that is the main target for innervation from the antennal nerve. VFB holds records including transgene expression in antennal lobe commissural pioneer interneuron, downstream connectivity classes for antennal lobe commissural pioneer interneuron, and upstream connectivity classes for antennal lobe commissural pioneer interneuron. The antennal lobe is a region in the Drosophila nervous system where users can search for synaptic input.", + "followons": [ + { + "id": "FBbt_00003924", + "query_type": "ListAllAvailableImages", + "query": "Which images of antennal lobe does VFB have?" + }, + { + "id": "FBbt_00003924", + "query_type": "NeuronsPartHere", + "query": "Which neurons have part of their arbour in the antennal lobe?" + }, + { + "id": "FBbt_00003924", + "query_type": "NeuronsSynaptic", + "query": "Which neurons have synaptic terminals in the antennal lobe?" + }, + { + "id": "FBbt_00003924", + "query_type": "NeuronsPresynapticHere", + "query": "Which neurons provide input to the antennal lobe?" + }, + { + "id": "FBbt_00003924", + "query_type": "NeuronsPostsynapticHere", + "query": "Which neurons receive output from the antennal lobe?" + }, + { + "id": "FBbt_00003924", + "query_type": "PartsOf", + "query": "What are the anatomical parts of the antennal lobe?" + } + ], + "context_terms": [ + { + "id": "FBbt_00003924", + "label": "antennal lobe" + } + ], + "reproduction": { + "ids": [ + { + "id": "FBbt_00003924", + "label": "antennal lobe" + } + ], + "calls": [], + "unmapped": [] + }, + "status_count": 6, + "problems": [] + }, + { + "turn": 2, + "question": "Which neurons innervate it?", + "focus": null, + "clicked": null, + "duration_ms": 8051, + "ok": true, + "response": "The [antennal lobe](https://www.virtualflybrain.org/reports/FBbt_00003924 \"Open antennal lobe in Virtual Fly Brain\") is innervated by several types of neurons, including [larval antennal lobe picky local neuron](https://www.virtualflybrain.org/reports/FBbt_00111694 \"Open larval antennal lobe picky local neuron in Virtual Fly Brain\"), [larval antennal lobe broad local neuron](https://www.virtualflybrain.org/reports/FBbt_00111700 \"Open larval antennal lobe broad local neuron in Virtual Fly Brain\"), and various adult olfactory receptor neurons such as [adult olfactory receptor neuron Ir75d ac1](https://www.virtualflybrain.org/reports/FBbt_00110011 \"Open adult olfactory receptor neuron Ir75d ac1 in Virtual Fly Brain\") and adult olfactory receptor neuron Or35a ac3I. Additionally, neurons like [PLP077](https://www.virtualflybrain.org/reports/FBbt_20001577 \"Open PLP077 in Virtual Fly Brain\"), pharyngeal VL1 neuron, and ORN_VM6 also innervate the antennal lobe. Furthermore, adult antennal lobe projection neurons, including [adult antennal lobe projection neuron DL5](https://www.virtualflybrain.org/reports/FBbt_00059280 \"Open adult antennal lobe projection neuron DL5 in Virtual Fly Brain\"), adult antennal lobe projection neuron DM4, and adult antennal lobe projection neuron VA1d, have synaptic terminals in the antennal lobe.", + "followons": [ + { + "id": "FBbt_00003924", + "query_type": "ListAllAvailableImages", + "query": "Which images of antennal lobe does VFB have?" + }, + { + "id": "FBbt_00003924", + "query_type": "NeuronsPartHere", + "query": "Which neurons have part of their arbour in the antennal lobe?" + }, + { + "id": "FBbt_00003924", + "query_type": "NeuronsPostsynapticHere", + "query": "Which neurons receive output from the antennal lobe?" + }, + { + "id": "FBbt_00003924", + "query_type": "PartsOf", + "query": "What are the anatomical parts of the antennal lobe?" + }, + { + "id": "FBbt_00003924", + "query_type": "SubclassesOf", + "query": "What are the subtypes of the antennal lobe?" + }, + { + "id": "FBbt_00003924", + "query_type": "TractsNervesInnervatingHere", + "query": "Which tracts and nerves innervate the antennal lobe?" + } + ], + "context_terms": [ + { + "id": "FBbt_00003924", + "label": "antennal lobe" + } + ], + "reproduction": { + "ids": [ + { + "id": "FBbt_00003924", + "label": "antennal lobe" + } + ], + "calls": [ + { + "id": "FBbt_00003924", + "query_type": "NeuronsPresynapticHere", + "fn": "get_neurons_with_presynaptic_terminals_in" + }, + { + "id": "FBbt_00003924", + "query_type": "NeuronsSynaptic", + "fn": "get_neurons_with_synapses_in" + } + ], + "unmapped": [] + }, + "status_count": 8, + "problems": [] + } + ], + "ok": true, + "request_id": "b84273a9-7584-46e9-b3d5-3140508d700e", + "response_id": "chatcmpl-315ad8788287d29f3c6f8328c5293519", + "images_count": 6, + "graphs_count": 0, + "response": "The [antennal lobe](https://www.virtualflybrain.org/reports/FBbt_00003924 \"Open antennal lobe in Virtual Fly Brain\") is innervated by several types of neurons, including [larval antennal lobe picky local neuron](https://www.virtualflybrain.org/reports/FBbt_00111694 \"Open larval antennal lobe picky local neuron in Virtual Fly Brain\"), [larval antennal lobe broad local neuron](https://www.virtualflybrain.org/reports/FBbt_00111700 \"Open larval antennal lobe broad local neuron in Virtual Fly Brain\"), and various adult olfactory receptor neurons such as [adult olfactory receptor neuron Ir75d ac1](https://www.virtualflybrain.org/reports/FBbt_00110011 \"Open adult olfactory receptor neuron Ir75d ac1 in Virtual Fly Brain\") and adult olfactory receptor neuron Or35a ac3I. Additionally, neurons like [PLP077](https://www.virtualflybrain.org/reports/FBbt_20001577 \"Open PLP077 in Virtual Fly Brain\"), pharyngeal VL1 neuron, and ORN_VM6 also innervate the antennal lobe. Furthermore, adult antennal lobe projection neurons, including [adult antennal lobe projection neuron DL5](https://www.virtualflybrain.org/reports/FBbt_00059280 \"Open adult antennal lobe projection neuron DL5 in Virtual Fly Brain\"), adult antennal lobe projection neuron DM4, and adult antennal lobe projection neuron VA1d, have synaptic terminals in the antennal lobe.", + "quality_flags": { + "has_tool_status": true, + "no_tool_factual_answer": false, + "tool_claim_without_tool": false, + "disambiguation_only_answer": false, + "investigation_plan_answer": false, + "not_verified_or_no_results_answer": false, + "graph_failure_mentioned": false, + "missing_required_graph": false, + "used_data_resource": false, + "response_chars": 1337, + "status_count": 8, + "addressless_followon": false, + "context_lost_across_turn": false, + "unmatched_claim_after_resolve": false, + "repeats_answered_question": false, + "slow_followup_turn": false, + "slowest_followup_ms": 8051 + } + }, + { + "attempt_index": 58, + "task_index": 58, + "task_id": "C7", + "tier": 7, + "title": "Two chip clicks in a row", + "question": "What is the medulla?", + "requires_graph": false, + "min_graphs": 0, + "repetition": 1, + "duration_ms": 150455, + "status_messages": [ + { + "message": "Thinking...", + "phase": "llm" + }, + { + "message": "Running the query behind that suggestion", + "phase": "mcp" + }, + { + "message": "Resolving 1 term in VFB", + "phase": "mcp" + }, + { + "message": "Querying VFB", + "phase": "mcp" + }, + { + "message": "Checking the answer is covered", + "phase": "llm" + }, + { + "message": "Writing the answer", + "phase": "llm" + } + ], + "event_count": 299, + "conversation": true, + "turns": [ + { + "turn": 1, + "question": "What is the medulla?", + "focus": null, + "clicked": null, + "duration_ms": 10691, + "ok": true, + "response": "The [medulla](https://www.virtualflybrain.org/reports/FBbt_00003748 \"Open medulla in Virtual Fly Brain\") is the second optic neuropil, sandwiched between the lamina and the lobula complex. It is divided into 10 layers: layers 1-6 make up the outer medulla, the seventh layer exhibits a distinct architecture, and layers 8-10 make up the inner medulla.", + "followons": [ + { + "id": "FBbt_00003748", + "query_type": "ImagesNeurons", + "query": "Which neuron images have a part in the medulla?" + }, + { + "id": "FBbt_00003748", + "query_type": "TransgeneExpressionHere", + "query": "Which driver lines label the medulla?" + }, + { + "id": "FBbt_00003748", + "query_type": "NeuronsPartHere", + "query": "Which neurons have part of their arbour in the medulla?" + }, + { + "id": "FBbt_00003748", + "query_type": "NeuronsSynaptic", + "query": "Which neurons have synaptic terminals in the medulla?" + }, + { + "id": "FBbt_00003748", + "query_type": "NeuronsPostsynapticHere", + "query": "Which neurons receive output from the medulla?" + }, + { + "id": "FBbt_00003748", + "query_type": "NeuronsPresynapticHere", + "query": "Which neurons provide input to the medulla?" + } + ], + "context_terms": [ + { + "id": "FBbt_00003748", + "label": "medulla" + } + ], + "reproduction": { + "ids": [ + { + "id": "FBbt_00003748", + "label": "medulla" + } + ], + "calls": [], + "unmapped": [] + }, + "status_count": 6, + "problems": [] + }, + { + "turn": 2, + "question": "Which neuron images have a part in the medulla?", + "focus": { + "id": "FBbt_00003748", + "query_type": "ImagesNeurons" + }, + "clicked": 0, + "duration_ms": 8817, + "ok": true, + "response": "There are images of neurons with parts in the [medulla](https://www.virtualflybrain.org/reports/FBbt_00003748 \"Open medulla in Virtual Fly Brain\"). The first 12 images, with their VFB ids, are: OA-AL2i2 (VFB_fw042336); MC64 (VFB_fw043756); MC64 (VFB_fw043755); aMe5 (VFB_fw043590); MeTu3 (VFB_fw043751); MeTu3 (VFB_fw043750); MeTu3 (VFB_fw043744); aMe5 (VFB_fw043591); MeTu-DRA (VFB_fw043752); MeVP6 (VFB_fw043593); MeTu3 (VFB_fw043746); MeTu3 (VFB_fw043745). VFB holds [226,524](https://v2.virtualflybrain.org/org.geppetto.frontend/geppetto?q=FBbt_00003748,ImagesNeurons \"Run in VFB: Images of neurons with some part in medulla\") such images.", + "followons": [ + { + "id": "FBbt_00003748", + "query_type": "TransgeneExpressionHere", + "query": "Which driver lines label the medulla?" + }, + { + "id": "FBbt_00003748", + "query_type": "NeuronsSynaptic", + "query": "Which neurons have synaptic terminals in the medulla?" + }, + { + "id": "FBbt_00003748", + "query_type": "NeuronsPostsynapticHere", + "query": "Which neurons receive output from the medulla?" + }, + { + "id": "FBbt_00003748", + "query_type": "NeuronsPresynapticHere", + "query": "Which neurons provide input to the medulla?" + }, + { + "id": "FBbt_00003748", + "query_type": "PartsOf", + "query": "What are the anatomical parts of the medulla?" + }, + { + "id": "FBbt_00003748", + "query_type": "LineageClonesIn", + "query": "Which lineage clones are found in the medulla?" + } + ], + "context_terms": [ + { + "id": "FBbt_00003748", + "label": "medulla" + } + ], + "reproduction": { + "ids": [ + { + "id": "FBbt_00003748", + "label": "medulla" + } + ], + "calls": [ + { + "id": "FBbt_00003748", + "query_type": "ImagesNeurons", + "fn": "get_images_neurons" + }, + { + "id": "FBbt_00003748", + "query_type": "NeuronsPartHere", + "fn": "get_neurons_with_part_in" + } + ], + "unmapped": [] + }, + "status_count": 8, + "problems": [] + }, + { + "turn": 3, + "question": "Which driver lines label the medulla?", + "focus": { + "id": "FBbt_00003748", + "query_type": "TransgeneExpressionHere" + }, + "clicked": 0, + "duration_ms": 130947, + "ok": true, + "response": "The first 12 driver lines that label the [medulla](https://www.virtualflybrain.org/reports/FBbt_00003748 \"Open medulla in Virtual Fly Brain\") are: [PBac{544.SVS-1}B4[CPTI100035] expression pattern](https://www.virtualflybrain.org/reports/VFBexp_FBti0143533 \"Open PBac{544.SVS-1}B4[CPTI100035] expression pattern in Virtual Fly Brain\"); [PBac{544.SVS-1}Fer2LCH[CPTI100064] expression pattern](https://www.virtualflybrain.org/reports/VFBexp_FBti0143547 \"Open PBac{544.SVS-1}Fer2LCH[CPTI100064] expression pattern in Virtual Fly Brain\"); [PBac{566.P.SVS-1}IA-2[CPTI100013] expression pattern](https://www.virtualflybrain.org/reports/VFBexp_FBti0143524 \"Open PBac{566.P.SVS-1}IA-2[CPTI100013] expression pattern in Virtual Fly Brain\"); [PBac{602.P.SVS-1}CG7675[CPTI000703] expression pattern](https://www.virtualflybrain.org/reports/VFBexp_FBti0144033 \"Open PBac{602.P.SVS-1}CG7675[CPTI000703] expression pattern in Virtual Fly Brain\"); [PBac{602.P.SVS-1}dlg1[CPTI000207] expression pattern](https://www.virtualflybrain.org/reports/VFBexp_FBti0144076 \"Open PBac{602.P.SVS-1}dlg1[CPTI000207] expression pattern in Virtual Fly Brain\"); PBac{681.P.FSVS-1}CG11138[CPTI001659] expression pattern; PBac{681.P.FSVS-1}CG6983[CPTI001802] expression pattern; PBac{681.P.FSVS-1}CG7920[CPTI002166] expression pattern; PBac{681.P.FSVS-1}CG9336[CPTI001654] expression pattern; PBac{681.P.FSVS-1}Pka-R2[CPTI001580] expression pattern; PBac{681.P.FSVS-1}cpx[CPTI001473] expression pattern; PBac{681.P.FSVS-1}larp[CPTI002498] expression pattern. VFB holds [2,342](https://v2.virtualflybrain.org/org.geppetto.frontend/geppetto?q=FBbt_00003748,TransgeneExpressionHere \"Run in VFB: Transgene expression in medulla\") such driver lines.", + "followons": [ + { + "id": "FBbt_00003748", + "query_type": "ImagesNeurons", + "query": "Which neuron images have a part in the medulla?" + }, + { + "id": "FBbt_00003748", + "query_type": "NeuronsPartHere", + "query": "Which neurons have part of their arbour in the medulla?" + }, + { + "id": "FBbt_00003748", + "query_type": "NeuronsSynaptic", + "query": "Which neurons have synaptic terminals in the medulla?" + }, + { + "id": "FBbt_00003748", + "query_type": "NeuronsPostsynapticHere", + "query": "Which neurons receive output from the medulla?" + }, + { + "id": "FBbt_00003748", + "query_type": "NeuronsPresynapticHere", + "query": "Which neurons provide input to the medulla?" + }, + { + "id": "FBbt_00003748", + "query_type": "PartsOf", + "query": "What are the anatomical parts of the medulla?" + } + ], + "context_terms": [ + { + "id": "FBbt_00003748", + "label": "medulla" + } + ], + "reproduction": { + "ids": [ + { + "id": "FBbt_00003748", + "label": "medulla" + } + ], + "calls": [ + { + "id": "FBbt_00003748", + "query_type": "TransgeneExpressionHere", + "fn": "get_transgene_expression_here" + }, + { + "id": "FBbt_00003748", + "query_type": "NeuronsPartHere", + "fn": "get_neurons_with_part_in" + }, + { + "id": "FBbt_00003748", + "query_type": "ImagesNeurons", + "fn": "get_images_neurons" + } + ], + "unmapped": [] + }, + "status_count": 6, + "problems": [] + } + ], + "ok": true, + "request_id": "c031a8f0-d8e8-49d6-976d-8567a0b3854d", + "response_id": "chatcmpl-2abfd2f45f86ffd56587dc06d1cf349b", + "images_count": 8, + "graphs_count": 0, + "response": "The first 12 driver lines that label the [medulla](https://www.virtualflybrain.org/reports/FBbt_00003748 \"Open medulla in Virtual Fly Brain\") are: [PBac{544.SVS-1}B4[CPTI100035] expression pattern](https://www.virtualflybrain.org/reports/VFBexp_FBti0143533 \"Open PBac{544.SVS-1}B4[CPTI100035] expression pattern in Virtual Fly Brain\"); [PBac{544.SVS-1}Fer2LCH[CPTI100064] expression pattern](https://www.virtualflybrain.org/reports/VFBexp_FBti0143547 \"Open PBac{544.SVS-1}Fer2LCH[CPTI100064] expression pattern in Virtual Fly Brain\"); [PBac{566.P.SVS-1}IA-2[CPTI100013] expression pattern](https://www.virtualflybrain.org/reports/VFBexp_FBti0143524 \"Open PBac{566.P.SVS-1}IA-2[CPTI100013] expression pattern in Virtual Fly Brain\"); [PBac{602.P.SVS-1}CG7675[CPTI000703] expression pattern](https://www.virtualflybrain.org/reports/VFBexp_FBti0144033 \"Open PBac{602.P.SVS-1}CG7675[CPTI000703] expression pattern in Virtual Fly Brain\"); [PBac{602.P.SVS-1}dlg1[CPTI000207] expression pattern](https://www.virtualflybrain.org/reports/VFBexp_FBti0144076 \"Open PBac{602.P.SVS-1}dlg1[CPTI000207] expression pattern in Virtual Fly Brain\"); PBac{681.P.FSVS-1}CG11138[CPTI001659] expression pattern; PBac{681.P.FSVS-1}CG6983[CPTI001802] expression pattern; PBac{681.P.FSVS-1}CG7920[CPTI002166] expression pattern; PBac{681.P.FSVS-1}CG9336[CPTI001654] expression pattern; PBac{681.P.FSVS-1}Pka-R2[CPTI001580] expression pattern; PBac{681.P.FSVS-1}cpx[CPTI001473] expression pattern; PBac{681.P.FSVS-1}larp[CPTI002498] expression pattern. VFB holds [2,342](https://v2.virtualflybrain.org/org.geppetto.frontend/geppetto?q=FBbt_00003748,TransgeneExpressionHere \"Run in VFB: Transgene expression in medulla\") such driver lines.", + "quality_flags": { + "has_tool_status": true, + "no_tool_factual_answer": false, + "tool_claim_without_tool": false, + "disambiguation_only_answer": false, + "investigation_plan_answer": false, + "not_verified_or_no_results_answer": false, + "graph_failure_mentioned": false, + "missing_required_graph": false, + "used_data_resource": false, + "response_chars": 1710, + "status_count": 6, + "addressless_followon": false, + "context_lost_across_turn": false, + "unmatched_claim_after_resolve": false, + "repeats_answered_question": false, + "slow_followup_turn": true, + "slowest_followup_ms": 130947 + } + }, + { + "attempt_index": 59, + "task_index": 59, + "task_id": "C8", + "tier": 7, + "title": "Driver lines asked warm", + "question": "What is the mushroom body?", + "requires_graph": false, + "min_graphs": 0, + "repetition": 1, + "duration_ms": 22053, + "status_messages": [ + { + "message": "Thinking...", + "phase": "llm" + }, + { + "message": "Running the query behind that suggestion", + "phase": "mcp" + }, + { + "message": "Resolving 1 term in VFB", + "phase": "mcp" + }, + { + "message": "Querying VFB", + "phase": "mcp" + }, + { + "message": "Checking the answer is covered", + "phase": "llm" + }, + { + "message": "Writing the answer", + "phase": "llm" + } + ], + "event_count": 318, + "conversation": true, + "turns": [ + { + "turn": 1, + "question": "What is the mushroom body?", + "focus": null, + "clicked": null, + "duration_ms": 10744, + "ok": true, + "response": "The [mushroom body](https://www.virtualflybrain.org/reports/FBbt_00005801 \"Open mushroom body in Virtual Fly Brain\") is a bilaterally paired neuropil structure situated postero-dorsally in the protocerebrum that functions in olfactory associative learning and memory. It is divided into the calyx, which receives sensory interneuron afferents, the pedunculus, a thick axon bundle extending from the calyx to the base of the lobes, and the mushroom body lobe system, which consists of a vertical branch and a medial branch, and has different structures at different life stages.", + "followons": [ + { + "id": "FBbt_00005801", + "query_type": "ImagesNeurons", + "query": "Which neuron images have a part in the mushroom body?" + }, + { + "id": "FBbt_00005801", + "query_type": "TransgeneExpressionHere", + "query": "Which driver lines label the mushroom body?" + }, + { + "id": "FBbt_00005801", + "query_type": "NeuronsPartHere", + "query": "Which neurons have part of their arbour in the mushroom body?" + }, + { + "id": "FBbt_00005801", + "query_type": "NeuronsSynaptic", + "query": "Which neurons have synaptic terminals in the mushroom body?" + }, + { + "id": "FBbt_00005801", + "query_type": "NeuronsPresynapticHere", + "query": "Which neurons provide input to the mushroom body?" + }, + { + "id": "FBbt_00005801", + "query_type": "NeuronsPostsynapticHere", + "query": "Which neurons receive output from the mushroom body?" + } + ], + "context_terms": [ + { + "id": "FBbt_00005801", + "label": "mushroom body" + } + ], + "reproduction": { + "ids": [ + { + "id": "FBbt_00005801", + "label": "mushroom body" + } + ], + "calls": [], + "unmapped": [] + }, + "status_count": 6, + "problems": [] + }, + { + "turn": 2, + "question": "Which driver lines label it?", + "focus": null, + "clicked": null, + "duration_ms": 11309, + "ok": true, + "response": "The [mushroom body](https://www.virtualflybrain.org/reports/FBbt_00005801 \"Open mushroom body in Virtual Fly Brain\") is labeled by multiple driver lines, including those whose expression patterns are recorded in VFB as [PBac{544.SVS-1}Bsg[CPTI100062] expression pattern](https://www.virtualflybrain.org/reports/VFBexp_FBti0143545 \"Open PBac{544.SVS-1}Bsg[CPTI100062] expression pattern in Virtual Fly Brain\"), [PBac{566.P.SVS-1}Bsg[CPTI100005] expression pattern](https://www.virtualflybrain.org/reports/VFBexp_FBti0143520 \"Open PBac{566.P.SVS-1}Bsg[CPTI100005] expression pattern in Virtual Fly Brain\"), [PBac{566.P.SVS-1}IA-2[CPTI100013] expression pattern](https://www.virtualflybrain.org/reports/VFBexp_FBti0143524 \"Open PBac{566.P.SVS-1}IA-2[CPTI100013] expression pattern in Virtual Fly Brain\"), [PBac{566.P.SVS-1}sgg[CPTI100027] expression pattern](https://www.virtualflybrain.org/reports/VFBexp_FBti0143529 \"Open PBac{566.P.SVS-1}sgg[CPTI100027] expression pattern in Virtual Fly Brain\"), [PBac{602.P.SVS-1}Fas2[CPTI000483] expression pattern](https://www.virtualflybrain.org/reports/VFBexp_FBti0144014 \"Open PBac{602.P.SVS-1}Fas2[CPTI000483] expression pattern in Virtual Fly Brain\"), PBac{602.P.SVS-1}HDAC4[CPTI000077] expression pattern, PBac{602.P.SVS-1}Pax[CPTI000161] expression pattern, PBac{602.P.SVS-1}Sema1a[CPTI000505] expression pattern, PBac{602.P.SVS-1}Tm1[CPTI000760] expression pattern, PBac{602.P.SVS-1}dlg1[CPTI000207] expression pattern, PBac{602.P.SVS-1}dlp[CPTI000445] expression pattern, and PBac{602.P.SVS-1}hzg[CPTI000737] expression pattern. Hemidrivers, such as P{VT017411-GAL4.DBD} ∩ P{VT019018-p65.AD}, are also used.", + "followons": [ + { + "id": "FBbt_00005801", + "query_type": "ImagesNeurons", + "query": "Which neuron images have a part in the mushroom body?" + }, + { + "id": "FBbt_00005801", + "query_type": "NeuronsPartHere", + "query": "Which neurons have part of their arbour in the mushroom body?" + }, + { + "id": "FBbt_00005801", + "query_type": "NeuronsSynaptic", + "query": "Which neurons have synaptic terminals in the mushroom body?" + }, + { + "id": "FBbt_00005801", + "query_type": "NeuronsPresynapticHere", + "query": "Which neurons provide input to the mushroom body?" + }, + { + "id": "FBbt_00005801", + "query_type": "NeuronsPostsynapticHere", + "query": "Which neurons receive output from the mushroom body?" + }, + { + "id": "FBbt_00005801", + "query_type": "PartsOf", + "query": "What are the anatomical parts of the mushroom body?" + } + ], + "context_terms": [ + { + "id": "FBbt_00005801", + "label": "mushroom body" + } + ], + "reproduction": { + "ids": [ + { + "id": "FBbt_00005801", + "label": "mushroom body" + } + ], + "calls": [ + { + "id": "FBbt_00005801", + "query_type": "TransgeneExpressionHere", + "fn": "get_transgene_expression_here" + } + ], + "unmapped": [] + }, + "status_count": 6, + "problems": [] + } + ], + "ok": true, + "request_id": "52ad4d69-b77f-4daf-b24a-937420edc3eb", + "response_id": "chatcmpl-73e12f129124acd031b1762bf6ad9626", + "images_count": 8, + "graphs_count": 0, + "response": "The [mushroom body](https://www.virtualflybrain.org/reports/FBbt_00005801 \"Open mushroom body in Virtual Fly Brain\") is labeled by multiple driver lines, including those whose expression patterns are recorded in VFB as [PBac{544.SVS-1}Bsg[CPTI100062] expression pattern](https://www.virtualflybrain.org/reports/VFBexp_FBti0143545 \"Open PBac{544.SVS-1}Bsg[CPTI100062] expression pattern in Virtual Fly Brain\"), [PBac{566.P.SVS-1}Bsg[CPTI100005] expression pattern](https://www.virtualflybrain.org/reports/VFBexp_FBti0143520 \"Open PBac{566.P.SVS-1}Bsg[CPTI100005] expression pattern in Virtual Fly Brain\"), [PBac{566.P.SVS-1}IA-2[CPTI100013] expression pattern](https://www.virtualflybrain.org/reports/VFBexp_FBti0143524 \"Open PBac{566.P.SVS-1}IA-2[CPTI100013] expression pattern in Virtual Fly Brain\"), [PBac{566.P.SVS-1}sgg[CPTI100027] expression pattern](https://www.virtualflybrain.org/reports/VFBexp_FBti0143529 \"Open PBac{566.P.SVS-1}sgg[CPTI100027] expression pattern in Virtual Fly Brain\"), [PBac{602.P.SVS-1}Fas2[CPTI000483] expression pattern](https://www.virtualflybrain.org/reports/VFBexp_FBti0144014 \"Open PBac{602.P.SVS-1}Fas2[CPTI000483] expression pattern in Virtual Fly Brain\"), PBac{602.P.SVS-1}HDAC4[CPTI000077] expression pattern, PBac{602.P.SVS-1}Pax[CPTI000161] expression pattern, PBac{602.P.SVS-1}Sema1a[CPTI000505] expression pattern, PBac{602.P.SVS-1}Tm1[CPTI000760] expression pattern, PBac{602.P.SVS-1}dlg1[CPTI000207] expression pattern, PBac{602.P.SVS-1}dlp[CPTI000445] expression pattern, and PBac{602.P.SVS-1}hzg[CPTI000737] expression pattern. Hemidrivers, such as P{VT017411-GAL4.DBD} ∩ P{VT019018-p65.AD}, are also used.", + "quality_flags": { + "has_tool_status": true, + "no_tool_factual_answer": false, + "tool_claim_without_tool": false, + "disambiguation_only_answer": false, + "investigation_plan_answer": false, + "not_verified_or_no_results_answer": false, + "graph_failure_mentioned": false, + "missing_required_graph": false, + "used_data_resource": false, + "response_chars": 1653, + "status_count": 6, + "addressless_followon": false, + "context_lost_across_turn": false, + "unmatched_claim_after_resolve": false, + "repeats_answered_question": false, + "slow_followup_turn": false, + "slowest_followup_ms": 11309 + } + }, + { + "attempt_index": 60, + "task_index": 60, + "task_id": "C9", + "tier": 7, + "title": "A follow-up that changes the term, not the query", + "question": "Which neurons provide input to the medulla?", + "requires_graph": false, + "min_graphs": 0, + "repetition": 1, + "duration_ms": 22780, + "status_messages": [ + { + "message": "Thinking...", + "phase": "llm" + }, + { + "message": "Planning the answer", + "phase": "llm" + }, + { + "message": "Resolving 1 term in VFB", + "phase": "mcp" + }, + { + "message": "Reading VFB term info", + "phase": "mcp" + }, + { + "message": "Querying VFB", + "phase": "mcp" + }, + { + "message": "Checking the answer is covered", + "phase": "llm" + }, + { + "message": "Writing the answer", + "phase": "llm" + }, + { + "message": "Checking before saying VFB has no data", + "phase": "mcp" + }, + { + "message": "Querying VFB", + "phase": "mcp" + }, + { + "message": "Querying VFB", + "phase": "mcp" + }, + { + "message": "Querying VFB", + "phase": "mcp" + }, + { + "message": "Checking the answer is covered", + "phase": "llm" + }, + { + "message": "Writing the answer", + "phase": "llm" + } + ], + "event_count": 146, + "conversation": true, + "turns": [ + { + "turn": 1, + "question": "Which neurons provide input to the medulla?", + "focus": null, + "clicked": null, + "duration_ms": 8559, + "ok": true, + "response": "Neurons with presynaptic terminals in [medulla](https://www.virtualflybrain.org/reports/FBbt_00003748 \"Open medulla in Virtual Fly Brain\") provide input to the medulla. VFB records show [262](https://v2.virtualflybrain.org/org.geppetto.frontend/geppetto?q=FBbt_00003748,NeuronsPresynapticHere \"Run in VFB: Neurons with presynaptic terminals in medulla\") neuron types with presynaptic terminals in medulla, including [Dm8b](https://www.virtualflybrain.org/reports/FBbt_00110069 \"Open Dm8b in Virtual Fly Brain\"), [PS128](https://www.virtualflybrain.org/reports/FBbt_20001883 \"Open PS128 in Virtual Fly Brain\"), [Mi10b](https://www.virtualflybrain.org/reports/FBbt_00110070 \"Open Mi10b in Virtual Fly Brain\"), [CB3849](https://www.virtualflybrain.org/reports/FBbt_20007264 \"Open CB3849 in Virtual Fly Brain\"), [TmY-ds](https://www.virtualflybrain.org/reports/FBbt_00052643 \"Open TmY-ds in Virtual Fly Brain\"), [Dm7](https://www.virtualflybrain.org/reports/FBbt_00003774 \"Open Dm7 in Virtual Fly Brain\"), Mi6, Mi8, Tm10, Tm13, Tm14, and Tm18.", + "followons": [ + { + "id": "FBbt_00003748", + "query_type": "ImagesNeurons", + "query": "Which neuron images have a part in the medulla?" + }, + { + "id": "FBbt_00003748", + "query_type": "TransgeneExpressionHere", + "query": "Which driver lines label the medulla?" + }, + { + "id": "FBbt_00003748", + "query_type": "NeuronsPartHere", + "query": "Which neurons have part of their arbour in the medulla?" + }, + { + "id": "FBbt_00003748", + "query_type": "NeuronsSynaptic", + "query": "Which neurons have synaptic terminals in the medulla?" + }, + { + "id": "FBbt_00003748", + "query_type": "PartsOf", + "query": "What are the anatomical parts of the medulla?" + }, + { + "id": "FBbt_00003748", + "query_type": "LineageClonesIn", + "query": "Which lineage clones are found in the medulla?" + } + ], + "context_terms": [ + { + "id": "FBbt_00003748", + "label": "medulla" + } + ], + "reproduction": { + "ids": [ + { + "id": "FBbt_00003748", + "label": "medulla" + } + ], + "calls": [ + { + "id": "FBbt_00003748", + "query_type": "NeuronsPresynapticHere", + "fn": "get_neurons_with_presynaptic_terminals_in" + }, + { + "id": "FBbt_00003748", + "query_type": "NeuronsPostsynapticHere", + "fn": "get_neurons_with_postsynaptic_terminals_in" + } + ], + "unmapped": [] + }, + "status_count": 9, + "problems": [] + }, + { + "turn": 2, + "question": "And the lobula?", + "focus": null, + "clicked": null, + "duration_ms": 14221, + "ok": true, + "response": "Neurons with synaptic terminals in [lobula](https://www.virtualflybrain.org/reports/FBbt_00003852 \"Open lobula in Virtual Fly Brain\") provide input to the lobula. VFB records show [528](https://v2.virtualflybrain.org/org.geppetto.frontend/geppetto?q=FBbt_00003852,NeuronsPartHere \"Run in VFB: Neurons with some part in lobula\") neuron types with synaptic terminals in lobula, including [AVLP391](https://www.virtualflybrain.org/reports/FBbt_20000500 \"Open AVLP391 in Virtual Fly Brain\"), [PLP031](https://www.virtualflybrain.org/reports/FBbt_20001531 \"Open PLP031 in Virtual Fly Brain\"), [TmY27](https://www.virtualflybrain.org/reports/FBbt_00110067 \"Open TmY27 in Virtual Fly Brain\"), [lobula columnar neuron vGlutLcnnew2](https://www.virtualflybrain.org/reports/FBbt_00110100 \"Open lobula columnar neuron vGlutLcnnew2 in Virtual Fly Brain\"), [OA-AL2b](https://www.virtualflybrain.org/reports/FBbt_00110145 \"Open OA-AL2b in Virtual Fly Brain\"), adult histaminergic HP3 neuron, translobula neuron, Tl1, Tl2, Tm1a, SIP063, and SLP339.", + "followons": [ + { + "id": "FBbt_00003852", + "query_type": "NeuronsPresynapticHere", + "query": "Which neurons provide input to the lobula?" + }, + { + "id": "FBbt_00003852", + "query_type": "NeuronsPostsynapticHere", + "query": "Which neurons receive output from the lobula?" + }, + { + "id": "FBbt_00003852", + "query_type": "PartsOf", + "query": "What are the anatomical parts of the lobula?" + }, + { + "id": "FBbt_00003852", + "query_type": "TractsNervesInnervatingHere", + "query": "Which tracts and nerves innervate the lobula?" + }, + { + "id": "FBbt_00003852", + "query_type": "LineageClonesIn", + "query": "Which lineage clones are found in the lobula?" + }, + { + "id": "FBbt_00003852", + "query_type": "ImagesNeurons", + "query": "Which neuron images have a part in the lobula?" + } + ], + "context_terms": [ + { + "id": "FBbt_00003852", + "label": "lobula" + }, + { + "id": "FBbt_00003748", + "label": "medulla" + } + ], + "reproduction": { + "ids": [ + { + "id": "FBbt_00003852", + "label": "lobula" + }, + { + "id": "FBbt_00003748", + "label": "medulla" + } + ], + "calls": [ + { + "id": "FBbt_00003852", + "query_type": "ListAllAvailableImages", + "fn": "get_instances" + }, + { + "id": "FBbt_00003852", + "query_type": "NeuronsPartHere", + "fn": "get_neurons_with_part_in" + }, + { + "id": "FBbt_00003852", + "query_type": "NeuronsSynaptic", + "fn": "get_neurons_with_synapses_in" + }, + { + "id": "FBbt_00003748", + "query_type": "NeuronsPresynapticHere", + "fn": "get_neurons_with_presynaptic_terminals_in" + }, + { + "id": "FBbt_00003748", + "query_type": "NeuronsPostsynapticHere", + "fn": "get_neurons_with_postsynaptic_terminals_in" + } + ], + "unmapped": [] + }, + "status_count": 13, + "problems": [] + } + ], + "ok": true, + "request_id": "177a5ce9-1ac0-43da-b478-e9fe922984c3", + "response_id": "chatcmpl-9dc30652a2f2e2cad090741ed3240309", + "images_count": 4, + "graphs_count": 0, + "response": "Neurons with synaptic terminals in [lobula](https://www.virtualflybrain.org/reports/FBbt_00003852 \"Open lobula in Virtual Fly Brain\") provide input to the lobula. VFB records show [528](https://v2.virtualflybrain.org/org.geppetto.frontend/geppetto?q=FBbt_00003852,NeuronsPartHere \"Run in VFB: Neurons with some part in lobula\") neuron types with synaptic terminals in lobula, including [AVLP391](https://www.virtualflybrain.org/reports/FBbt_20000500 \"Open AVLP391 in Virtual Fly Brain\"), [PLP031](https://www.virtualflybrain.org/reports/FBbt_20001531 \"Open PLP031 in Virtual Fly Brain\"), [TmY27](https://www.virtualflybrain.org/reports/FBbt_00110067 \"Open TmY27 in Virtual Fly Brain\"), [lobula columnar neuron vGlutLcnnew2](https://www.virtualflybrain.org/reports/FBbt_00110100 \"Open lobula columnar neuron vGlutLcnnew2 in Virtual Fly Brain\"), [OA-AL2b](https://www.virtualflybrain.org/reports/FBbt_00110145 \"Open OA-AL2b in Virtual Fly Brain\"), adult histaminergic HP3 neuron, translobula neuron, Tl1, Tl2, Tm1a, SIP063, and SLP339.", + "quality_flags": { + "has_tool_status": true, + "no_tool_factual_answer": false, + "tool_claim_without_tool": false, + "disambiguation_only_answer": false, + "investigation_plan_answer": false, + "not_verified_or_no_results_answer": false, + "graph_failure_mentioned": false, + "missing_required_graph": false, + "used_data_resource": false, + "response_chars": 1033, + "status_count": 13, + "addressless_followon": false, + "context_lost_across_turn": false, + "unmatched_claim_after_resolve": false, + "repeats_answered_question": false, + "slow_followup_turn": false, + "slowest_followup_ms": 14221 + } + }, + { + "attempt_index": 61, + "task_index": 61, + "task_id": "C10", + "tier": 7, + "title": "A term the session already resolved is never called unmatched", + "question": "What is the protocerebral bridge?", + "requires_graph": false, + "min_graphs": 0, + "repetition": 1, + "duration_ms": 51590, + "status_messages": [ + { + "message": "Thinking...", + "phase": "llm" + }, + { + "message": "Planning the answer", + "phase": "llm" + }, + { + "message": "Resolving 2 terms in VFB", + "phase": "mcp" + }, + { + "message": "Querying VFB connectivity", + "phase": "mcp" + }, + { + "message": "Querying VFB", + "phase": "mcp" + }, + { + "message": "Querying VFB", + "phase": "mcp" + }, + { + "message": "Querying VFB", + "phase": "mcp" + }, + { + "message": "Querying VFB", + "phase": "mcp" + }, + { + "message": "Checking the answer is covered", + "phase": "llm" + }, + { + "message": "Querying VFB", + "phase": "mcp" + }, + { + "message": "Checking the answer is covered", + "phase": "llm" + }, + { + "message": "Writing the answer", + "phase": "llm" + } + ], + "event_count": 190, + "conversation": true, + "turns": [ + { + "turn": 1, + "question": "What is the protocerebral bridge?", + "focus": null, + "clicked": null, + "duration_ms": 6597, + "ok": true, + "response": "The [protocerebral bridge](https://www.virtualflybrain.org/reports/FBbt_00003668 \"Open protocerebral bridge in Virtual Fly Brain\") is a handle bar-shaped synaptic neuropil located just posterior to the fan-shaped body. Its lateral edge ends at the posterior end of the inferior clamp near the medial equatorial fascicle. A row of 18 connected slices, 9 on each side of the midline, forms a dorso-posteriorly located part of the central complex embedded in the cortex between the calyces of the two mushroom bodies.", + "followons": [ + { + "id": "FBbt_00003668", + "query_type": "ListAllAvailableImages", + "query": "Which images of protocerebral bridge does VFB have?" + }, + { + "id": "FBbt_00003668", + "query_type": "NeuronsPartHere", + "query": "Which neurons have part of their arbour in the protocerebral bridge?" + }, + { + "id": "FBbt_00003668", + "query_type": "NeuronsSynaptic", + "query": "Which neurons have synaptic terminals in the protocerebral bridge?" + }, + { + "id": "FBbt_00003668", + "query_type": "NeuronsPresynapticHere", + "query": "Which neurons provide input to the protocerebral bridge?" + }, + { + "id": "FBbt_00003668", + "query_type": "NeuronsPostsynapticHere", + "query": "Which neurons receive output from the protocerebral bridge?" + }, + { + "id": "FBbt_00003668", + "query_type": "PartsOf", + "query": "What are the anatomical parts of the protocerebral bridge?" + } + ], + "context_terms": [ + { + "id": "FBbt_00003668", + "label": "protocerebral bridge" + } + ], + "reproduction": { + "ids": [ + { + "id": "FBbt_00003668", + "label": "protocerebral bridge" + } + ], + "calls": [], + "unmapped": [] + }, + "status_count": 6, + "problems": [] + }, + { + "turn": 2, + "question": "How does it relate to the ellipsoid body?", + "focus": null, + "clicked": null, + "duration_ms": 14847, + "ok": true, + "response": "The [protocerebral bridge](https://www.virtualflybrain.org/reports/FBbt_00003668 \"Open protocerebral bridge in Virtual Fly Brain\") and the [ellipsoid body](https://www.virtualflybrain.org/reports/FBbt_00003678 \"Open ellipsoid body in Virtual Fly Brain\") are connected by neurons. VFB records show that there are neurons with some part in the ellipsoid body, including [adult protocerebral bridge glomerulus 1-ellipsoid body canal-dorsal gall neuron](https://www.virtualflybrain.org/reports/FBbt_00111376 \"Open adult protocerebral bridge glomerulus 1-ellipsoid body canal-dorsal gall neuron in Virtual Fly Brain\"), and adult protocerebral bridge glomerulus 4-ellipsoid body canal-ventral gall neuron, among others. These neurons also have synaptic terminals in the ellipsoid body.", + "followons": [ + { + "id": "FBbt_00003668", + "query_type": "ListAllAvailableImages", + "query": "Which images of protocerebral bridge does VFB have?" + }, + { + "id": "FBbt_00003668", + "query_type": "NeuronsPartHere", + "query": "Which neurons have part of their arbour in the protocerebral bridge?" + }, + { + "id": "FBbt_00003668", + "query_type": "NeuronsSynaptic", + "query": "Which neurons have synaptic terminals in the protocerebral bridge?" + }, + { + "id": "FBbt_00003668", + "query_type": "NeuronsPresynapticHere", + "query": "Which neurons provide input to the protocerebral bridge?" + }, + { + "id": "FBbt_00003668", + "query_type": "NeuronsPostsynapticHere", + "query": "Which neurons receive output from the protocerebral bridge?" + }, + { + "id": "FBbt_00003668", + "query_type": "PartsOf", + "query": "What are the anatomical parts of the protocerebral bridge?" + } + ], + "context_terms": [ + { + "id": "FBbt_00003668", + "label": "protocerebral bridge" + }, + { + "id": "FBbt_00003678", + "label": "ellipsoid body" + } + ], + "reproduction": { + "ids": [ + { + "id": "FBbt_00003668", + "label": "protocerebral bridge" + }, + { + "id": "FBbt_00003678", + "label": "ellipsoid body" + } + ], + "calls": [ + { + "id": "FBbt_00003678", + "query_type": "ListAllAvailableImages", + "fn": "get_instances" + }, + { + "id": "FBbt_00003678", + "query_type": "NeuronsPartHere", + "fn": "get_neurons_with_part_in" + }, + { + "id": "FBbt_00003678", + "query_type": "NeuronsSynaptic", + "fn": "get_neurons_with_synapses_in" + } + ], + "unmapped": [] + }, + "status_count": 13, + "problems": [] + }, + { + "turn": 3, + "question": "Which neurons connect them?", + "focus": null, + "clicked": null, + "duration_ms": 30146, + "ok": true, + "response": "The neurons that connect the [protocerebral bridge](https://www.virtualflybrain.org/reports/FBbt_00003668 \"Open protocerebral bridge in Virtual Fly Brain\") and the [ellipsoid body](https://www.virtualflybrain.org/reports/FBbt_00003678 \"Open ellipsoid body in Virtual Fly Brain\") include the [adult protocerebral bridge glomerulus 1-ellipsoid body canal-dorsal gall neuron](https://www.virtualflybrain.org/reports/FBbt_00111376 \"Open adult protocerebral bridge glomerulus 1-ellipsoid body canal-dorsal gall neuron in Virtual Fly Brain\") and the adult protocerebral bridge glomerulus 4-ellipsoid body canal-ventral gall neuron. VFB records show that there are neurons with some part in the ellipsoid body, including these, and also the adult protocerebral bridge glomerulus 5-ellipsoid body canal-dorsal gall neuron, the adult protocerebral bridge glomerulus 6-ellipsoid body canal-ventral gall neuron, the adult protocerebral bridge glomerulus 7-ellipsoid body canal-dorsal gall neuron, and the adult protocerebral bridge glomerulus 8-ellipsoid body canal-ventral gall neuron.", + "followons": [ + { + "id": "FBbt_00003668", + "query_type": "ListAllAvailableImages", + "query": "Which images of protocerebral bridge does VFB have?" + }, + { + "id": "FBbt_00003668", + "query_type": "NeuronsPartHere", + "query": "Which neurons have part of their arbour in the protocerebral bridge?" + }, + { + "id": "FBbt_00003668", + "query_type": "PartsOf", + "query": "What are the anatomical parts of the protocerebral bridge?" + }, + { + "id": "FBbt_00003668", + "query_type": "TractsNervesInnervatingHere", + "query": "Which tracts and nerves innervate the protocerebral bridge?" + }, + { + "id": "FBbt_00003668", + "query_type": "LineageClonesIn", + "query": "Which lineage clones are found in the protocerebral bridge?" + }, + { + "id": "FBbt_00003668", + "query_type": "ImagesNeurons", + "query": "Which neuron images have a part in the protocerebral bridge?" + } + ], + "context_terms": [ + { + "id": "FBbt_00003668", + "label": "protocerebral bridge" + }, + { + "id": "FBbt_00003678", + "label": "ellipsoid body" + } + ], + "reproduction": { + "ids": [ + { + "id": "FBbt_00003668", + "label": "protocerebral bridge" + }, + { + "id": "FBbt_00003678", + "label": "ellipsoid body" + } + ], + "calls": [ + { + "id": "FBbt_00003668", + "query_type": "NeuronsPresynapticHere", + "fn": "get_neurons_with_presynaptic_terminals_in" + }, + { + "id": "FBbt_00003668", + "query_type": "NeuronsPostsynapticHere", + "fn": "get_neurons_with_postsynaptic_terminals_in" + }, + { + "id": "FBbt_00003678", + "query_type": "NeuronsPresynapticHere", + "fn": "get_neurons_with_presynaptic_terminals_in" + }, + { + "id": "FBbt_00003678", + "query_type": "NeuronsPostsynapticHere", + "fn": "get_neurons_with_postsynaptic_terminals_in" + }, + { + "id": "FBbt_00003668", + "query_type": "NeuronsSynaptic", + "fn": "get_neurons_with_synapses_in" + }, + { + "id": "FBbt_00003678", + "query_type": "ListAllAvailableImages", + "fn": "get_instances" + }, + { + "id": "FBbt_00003678", + "query_type": "NeuronsPartHere", + "fn": "get_neurons_with_part_in" + }, + { + "id": "FBbt_00003678", + "query_type": "NeuronsSynaptic", + "fn": "get_neurons_with_synapses_in" + } + ], + "unmapped": [] + }, + "status_count": 12, + "problems": [] + } + ], + "ok": true, + "request_id": "947da328-b6c9-466b-ab74-e4c3db67dfad", + "response_id": "chatcmpl-9dfa7a62255919bfd6fd02edf9c6380e", + "images_count": 8, + "graphs_count": 1, + "response": "The neurons that connect the [protocerebral bridge](https://www.virtualflybrain.org/reports/FBbt_00003668 \"Open protocerebral bridge in Virtual Fly Brain\") and the [ellipsoid body](https://www.virtualflybrain.org/reports/FBbt_00003678 \"Open ellipsoid body in Virtual Fly Brain\") include the [adult protocerebral bridge glomerulus 1-ellipsoid body canal-dorsal gall neuron](https://www.virtualflybrain.org/reports/FBbt_00111376 \"Open adult protocerebral bridge glomerulus 1-ellipsoid body canal-dorsal gall neuron in Virtual Fly Brain\") and the adult protocerebral bridge glomerulus 4-ellipsoid body canal-ventral gall neuron. VFB records show that there are neurons with some part in the ellipsoid body, including these, and also the adult protocerebral bridge glomerulus 5-ellipsoid body canal-dorsal gall neuron, the adult protocerebral bridge glomerulus 6-ellipsoid body canal-ventral gall neuron, the adult protocerebral bridge glomerulus 7-ellipsoid body canal-dorsal gall neuron, and the adult protocerebral bridge glomerulus 8-ellipsoid body canal-ventral gall neuron.", + "graphs": [ + { + "type": "basic_graph", + "version": 1, + "title": "Upstream partners of P6-8P9", + "directed": true, + "layout": "circle", + "nodes": [ + { + "id": "FBbt_00047095", + "label": "adult neuron", + "group": null, + "color": null, + "size": 1.37 + }, + { + "id": "FBbt_00111056", + "label": "P6-8P9", + "group": null, + "color": null, + "size": 4 + }, + { + "id": "FBbt_00005106", + "label": "neuron", + "group": null, + "color": null, + "size": 1.37 + }, + { + "id": "FBbt_00049819", + "label": "adult central complex neuron", + "group": null, + "color": null, + "size": 1.37 + }, + { + "id": "FBbt_00059271", + "label": "CNS neuron", + "group": null, + "color": null, + "size": 1.37 + }, + { + "id": "FBbt_00053387", + "label": "intrinsic neuron of the central complex", + "group": null, + "color": null, + "size": 1.21 + }, + { + "id": "FBbt_00007515", + "label": "large field neuron of the central complex", + "group": null, + "color": null, + "size": 1.2 + }, + { + "id": "FBbt_00003648", + "label": "large field neuron", + "group": null, + "color": null, + "size": 1.2 + }, + { + "id": "FBbt_00003666", + "label": "adult intrinsic protocerebral bridge neuron", + "group": null, + "color": null, + "size": 1.19 + }, + { + "id": "FBbt_00049807", + "label": "adult intrinsic protocerebral bridge 18 glomeruli-delta7 neuron", + "group": null, + "color": null, + "size": 1.17 + }, + { + "id": "FBbt_00007514", + "label": "small field neuron of the central complex", + "group": null, + "color": null, + "size": 1.14 + }, + { + "id": "FBbt_00003633", + "label": "small field neuron", + "group": null, + "color": null, + "size": 1.14 + }, + { + "id": "FBbt_00003637", + "label": "adult ellipsoid body-protocerebral bridge-gall neuron", + "group": null, + "color": null, + "size": 1.12 + }, + { + "id": "FBbt_00047030", + "label": "adult ellipsoid body-protocerebral bridge 1 glomerulus-dorsal/ventral gall neuron", + "group": null, + "color": null, + "size": 1.11 + }, + { + "id": "FBbt_00049822", + "label": "fan-shaped body extrinsic columnar neuron", + "group": null, + "color": null, + "size": 1.02 + } + ], + "edges": [ + { + "source": "FBbt_00047095", + "target": "FBbt_00111056", + "label": "3201", + "weight": 3201 + }, + { + "source": "FBbt_00005106", + "target": "FBbt_00111056", + "label": "3201", + "weight": 3201 + }, + { + "source": "FBbt_00049819", + "target": "FBbt_00111056", + "label": "3197", + "weight": 3197 + }, + { + "source": "FBbt_00059271", + "target": "FBbt_00111056", + "label": "3197", + "weight": 3197 + }, + { + "source": "FBbt_00053387", + "target": "FBbt_00111056", + "label": "1817", + "weight": 1817 + }, + { + "source": "FBbt_00007515", + "target": "FBbt_00111056", + "label": "1740", + "weight": 1740 + }, + { + "source": "FBbt_00003648", + "target": "FBbt_00111056", + "label": "1740", + "weight": 1740 + }, + { + "source": "FBbt_00003666", + "target": "FBbt_00111056", + "label": "1662", + "weight": 1662 + }, + { + "source": "FBbt_00049807", + "target": "FBbt_00111056", + "label": "1469", + "weight": 1469 + }, + { + "source": "FBbt_00007514", + "target": "FBbt_00111056", + "label": "1191", + "weight": 1191 + }, + { + "source": "FBbt_00003633", + "target": "FBbt_00111056", + "label": "1191", + "weight": 1191 + }, + { + "source": "FBbt_00003637", + "target": "FBbt_00111056", + "label": "1020", + "weight": 1020 + }, + { + "source": "FBbt_00047030", + "target": "FBbt_00111056", + "label": "935", + "weight": 935 + }, + { + "source": "FBbt_00111056", + "target": "FBbt_00111056", + "label": "193", + "weight": 193 + }, + { + "source": "FBbt_00049822", + "target": "FBbt_00111056", + "label": "166", + "weight": 166 + } + ] + } + ], + "quality_flags": { + "has_tool_status": true, + "no_tool_factual_answer": false, + "tool_claim_without_tool": false, + "disambiguation_only_answer": false, + "investigation_plan_answer": false, + "not_verified_or_no_results_answer": false, + "graph_failure_mentioned": false, + "missing_required_graph": false, + "used_data_resource": false, + "response_chars": 1075, + "status_count": 12, + "addressless_followon": false, + "context_lost_across_turn": false, + "unmatched_claim_after_resolve": false, + "repeats_answered_question": false, + "slow_followup_turn": false, + "slowest_followup_ms": 30146 + } + }, + { + "attempt_index": 62, + "task_index": 62, + "task_id": "C11", + "tier": 7, + "title": "The answer hands over its own working", + "question": "Which neurons have part of them in the medulla?", + "requires_graph": false, + "min_graphs": 0, + "repetition": 1, + "duration_ms": 22927, + "status_messages": [ + { + "message": "Thinking...", + "phase": "llm" + }, + { + "message": "Planning the answer", + "phase": "llm" + }, + { + "message": "Resolving 1 term in VFB", + "phase": "mcp" + }, + { + "message": "Querying VFB", + "phase": "mcp" + }, + { + "message": "Checking VFB documentation", + "phase": "mcp" + }, + { + "message": "Checking the answer is covered", + "phase": "llm" + }, + { + "message": "Writing the answer", + "phase": "llm" + } + ], + "event_count": 31, + "conversation": true, + "turns": [ + { + "turn": 1, + "question": "Which neurons have part of them in the medulla?", + "focus": null, + "clicked": null, + "duration_ms": 11065, + "ok": true, + "response": "Neurons with some part in the [medulla](https://www.virtualflybrain.org/reports/FBbt_00003748 \"Open medulla in Virtual Fly Brain\") include [Dm8b](https://www.virtualflybrain.org/reports/FBbt_00110069 \"Open Dm8b in Virtual Fly Brain\"), [MC](https://www.virtualflybrain.org/reports/FBbt_00111640 \"Open MC in Virtual Fly Brain\"), [PS128](https://www.virtualflybrain.org/reports/FBbt_20001883 \"Open PS128 in Virtual Fly Brain\"), [TmY27](https://www.virtualflybrain.org/reports/FBbt_00110067 \"Open TmY27 in Virtual Fly Brain\"), and [medulla intrinsic neuron vGlutMinew1a](https://www.virtualflybrain.org/reports/FBbt_00110033 \"Open medulla intrinsic neuron vGlutMinew1a in Virtual Fly Brain\"). VFB records show [471](https://v2.virtualflybrain.org/org.geppetto.frontend/geppetto?q=FBbt_00003748,NeuronsPartHere \"Run in VFB: Neurons with some part in medulla\") neuron types have some part in the medulla.", + "followons": [ + { + "id": "FBbt_00003748", + "query_type": "TransgeneExpressionHere", + "query": "Which driver lines label the medulla?" + }, + { + "id": "FBbt_00003748", + "query_type": "NeuronsSynaptic", + "query": "Which neurons have synaptic terminals in the medulla?" + }, + { + "id": "FBbt_00003748", + "query_type": "NeuronsPostsynapticHere", + "query": "Which neurons receive output from the medulla?" + }, + { + "id": "FBbt_00003748", + "query_type": "NeuronsPresynapticHere", + "query": "Which neurons provide input to the medulla?" + }, + { + "id": "FBbt_00003748", + "query_type": "PartsOf", + "query": "What are the anatomical parts of the medulla?" + }, + { + "id": "FBbt_00003748", + "query_type": "LineageClonesIn", + "query": "Which lineage clones are found in the medulla?" + } + ], + "context_terms": [ + { + "id": "FBbt_00003748", + "label": "medulla" + } + ], + "reproduction": { + "ids": [ + { + "id": "FBbt_00003748", + "label": "medulla" + } + ], + "calls": [ + { + "id": "FBbt_00003748", + "query_type": "NeuronsPartHere", + "fn": "get_neurons_with_part_in" + }, + { + "id": "FBbt_00003748", + "query_type": "ImagesNeurons", + "fn": "get_images_neurons" + } + ], + "unmapped": [] + }, + "status_count": 9, + "problems": [] + }, + { + "turn": 2, + "question": "How would I get that same result in Python with vfbquery?", + "focus": null, + "clicked": null, + "duration_ms": 11862, + "ok": true, + "response": "The code below returns the [471](https://v2.virtualflybrain.org/org.geppetto.frontend/geppetto?q=FBbt_00003748,NeuronsPartHere \"Run in VFB: Neurons with some part in medulla\") neuron types VFB has annotated for [medulla](https://www.virtualflybrain.org/reports/FBbt_00003748 \"Open medulla in Virtual Fly Brain\"), as a table.\n```python\n# Reproduce this answer in Python — pip install vfbquery\n#\n# These are the exact ids this conversation resolved and the exact catalogue\n# queries it ran, so this returns the same rows the answer was written from\n# rather than a fresh search that might land on a different term.\nimport vfbquery\n\nMEDULLA = 'FBbt_00003748' # medulla\n\n# NeuronsPartHere for medulla\nneurons_part_here = vfbquery.get_neurons_with_part_in(MEDULLA)\n# ImagesNeurons for medulla\nimages_neurons = vfbquery.get_images_neurons(MEDULLA)\n```", + "followons": [ + { + "id": "FBbt_00003748", + "query_type": "ImagesNeurons", + "query": "Which neuron images have a part in the medulla?" + }, + { + "id": "FBbt_00003748", + "query_type": "TransgeneExpressionHere", + "query": "Which driver lines label the medulla?" + }, + { + "id": "FBbt_00003748", + "query_type": "NeuronsPartHere", + "query": "Which neurons have part of their arbour in the medulla?" + }, + { + "id": "FBbt_00003748", + "query_type": "NeuronsSynaptic", + "query": "Which neurons have synaptic terminals in the medulla?" + }, + { + "id": "FBbt_00003748", + "query_type": "NeuronsPostsynapticHere", + "query": "Which neurons receive output from the medulla?" + }, + { + "id": "FBbt_00003748", + "query_type": "NeuronsPresynapticHere", + "query": "Which neurons provide input to the medulla?" + } + ], + "context_terms": [ + { + "id": "FBbt_00003748", + "label": "medulla" + } + ], + "reproduction": { + "ids": [ + { + "id": "FBbt_00003748", + "label": "medulla" + } + ], + "calls": [ + { + "id": "FBbt_00003748", + "query_type": "NeuronsPartHere", + "fn": "get_neurons_with_part_in" + }, + { + "id": "FBbt_00003748", + "query_type": "ImagesNeurons", + "fn": "get_images_neurons" + } + ], + "unmapped": [] + }, + "status_count": 7, + "problems": [] + } + ], + "ok": true, + "request_id": "5c85f200-ed05-4a79-9b8e-959837f1e3ec", + "response_id": "chatcmpl-3d16517a4e71f82054194bdc39189b38", + "images_count": 8, + "graphs_count": 0, + "response": "The code below returns the [471](https://v2.virtualflybrain.org/org.geppetto.frontend/geppetto?q=FBbt_00003748,NeuronsPartHere \"Run in VFB: Neurons with some part in medulla\") neuron types VFB has annotated for [medulla](https://www.virtualflybrain.org/reports/FBbt_00003748 \"Open medulla in Virtual Fly Brain\"), as a table.\n```python\n# Reproduce this answer in Python — pip install vfbquery\n#\n# These are the exact ids this conversation resolved and the exact catalogue\n# queries it ran, so this returns the same rows the answer was written from\n# rather than a fresh search that might land on a different term.\nimport vfbquery\n\nMEDULLA = 'FBbt_00003748' # medulla\n\n# NeuronsPartHere for medulla\nneurons_part_here = vfbquery.get_neurons_with_part_in(MEDULLA)\n# ImagesNeurons for medulla\nimages_neurons = vfbquery.get_images_neurons(MEDULLA)\n```", + "quality_flags": { + "has_tool_status": true, + "no_tool_factual_answer": false, + "tool_claim_without_tool": false, + "disambiguation_only_answer": false, + "investigation_plan_answer": false, + "not_verified_or_no_results_answer": false, + "graph_failure_mentioned": false, + "missing_required_graph": false, + "used_data_resource": false, + "response_chars": 845, + "status_count": 7, + "addressless_followon": false, + "context_lost_across_turn": false, + "unmatched_claim_after_resolve": false, + "repeats_answered_question": false, + "slow_followup_turn": false, + "slowest_followup_ms": 11862 + } + }, + { + "attempt_index": 63, + "task_index": 63, + "task_id": "C12", + "tier": 7, + "title": "Asking for the ids afterwards gets the ids, not a promise of them", + "question": "What are the subclasses of Kenyon cell?", + "requires_graph": false, + "min_graphs": 0, + "repetition": 1, + "duration_ms": 31131, + "status_messages": [ + { + "message": "Thinking...", + "phase": "llm" + }, + { + "message": "Planning the answer", + "phase": "llm" + }, + { + "message": "Resolving 1 term in VFB", + "phase": "mcp" + }, + { + "message": "Reading VFB term info", + "phase": "mcp" + }, + { + "message": "Querying VFB", + "phase": "mcp" + }, + { + "message": "Checking the answer is covered", + "phase": "llm" + }, + { + "message": "Writing the answer", + "phase": "llm" + } + ], + "event_count": 107, + "conversation": true, + "turns": [ + { + "turn": 1, + "question": "What are the subclasses of Kenyon cell?", + "focus": null, + "clicked": null, + "duration_ms": 7874, + "ok": true, + "response": "The subclasses of [Kenyon cell](https://www.virtualflybrain.org/reports/FBbt_00003686 \"Open Kenyon cell in Virtual Fly Brain\") include [KCab-c(i)](https://www.virtualflybrain.org/reports/FBbt_00049111 \"Open KCab-c(i) in Virtual Fly Brain\"), [KCab-c](https://www.virtualflybrain.org/reports/FBbt_00110929 \"Open KCab-c in Virtual Fly Brain\"), [KCg-m](https://www.virtualflybrain.org/reports/FBbt_00111061 \"Open KCg-m in Virtual Fly Brain\"), [Kenyon cell of main calyx](https://www.virtualflybrain.org/reports/FBbt_00047926 \"Open Kenyon cell of main calyx in Virtual Fly Brain\"), and [gamma Kenyon cell](https://www.virtualflybrain.org/reports/FBbt_00100247 \"Open gamma Kenyon cell in Virtual Fly Brain\"), among [37](https://v2.virtualflybrain.org/org.geppetto.frontend/geppetto?q=FBbt_00003686,SubclassesOf \"Run in VFB: Subclasses of Kenyon cell\") subclasses. VFB holds 37 subclasses of Kenyon cell.", + "followons": [ + { + "id": "FBbt_00003686", + "query_type": "ListAllAvailableImages", + "query": "Which images of Kenyon cell does VFB have?" + }, + { + "id": "FBbt_00003686", + "query_type": "UpstreamClassConnectivity", + "query": "What connects to the Kenyon cell upstream?" + }, + { + "id": "FBbt_00003686", + "query_type": "DownstreamClassConnectivity", + "query": "What does the Kenyon cell connect to downstream?" + }, + { + "id": "FBbt_00003686", + "query_type": "TransgeneExpressionHere", + "query": "Which driver lines label the Kenyon cell?" + }, + { + "id": "FBbt_00003686", + "query_type": "anatScRNAseqQuery", + "query": "What single-cell transcriptomic clusters are there for Kenyon cell?" + }, + { + "id": "FBbt_00003686", + "query_type": "SubclassesOf", + "query": "What are the subtypes of the Kenyon cell?" + } + ], + "context_terms": [ + { + "id": "FBbt_00003686", + "label": "Kenyon cell" + } + ], + "reproduction": { + "ids": [ + { + "id": "FBbt_00003686", + "label": "Kenyon cell" + } + ], + "calls": [ + { + "id": "FBbt_00003686", + "query_type": "SubclassesOf", + "fn": "get_subclasses_of" + } + ], + "unmapped": [] + }, + "status_count": 6, + "problems": [] + }, + { + "turn": 2, + "question": "Can you list the VFB IDs so I can reproduce this myself?", + "focus": null, + "clicked": null, + "duration_ms": 23257, + "ok": true, + "response": "The code below returns the [37](https://v2.virtualflybrain.org/org.geppetto.frontend/geppetto?q=FBbt_00003686,SubclassesOf \"Run in VFB: Subclasses of Kenyon cell\") subclasses of [Kenyon cell](https://www.virtualflybrain.org/reports/FBbt_00003686 \"Open Kenyon cell in Virtual Fly Brain\") that VFB has annotated, as a table. The first 12 subclasses, with their VFB ids, are provided in the evidence, including [KCab-c(i)](https://www.virtualflybrain.org/reports/FBbt_00049111 \"Open KCab-c(i) in Virtual Fly Brain\") (FBbt_00049111), [KCab-c](https://www.virtualflybrain.org/reports/FBbt_00110929 \"Open KCab-c in Virtual Fly Brain\")(o) (FBbt_00049112), larval [gamma Kenyon cell](https://www.virtualflybrain.org/reports/FBbt_00100247 \"Open gamma Kenyon cell in Virtual Fly Brain\") (FBbt_00049827), and [Kenyon cell of main calyx](https://www.virtualflybrain.org/reports/FBbt_00047926 \"Open Kenyon cell of main calyx in Virtual Fly Brain\") (FBbt_00047926).\n\n```python\n# Reproduce this answer in Python — pip install vfbquery\n#\n# These are the exact ids this conversation resolved and the exact catalogue\n# queries it ran, so this returns the same rows the answer was written from\n# rather than a fresh search that might land on a different term.\nimport vfbquery\n\nKENYON_CELL = 'FBbt_00003686' # Kenyon cell\n\n# SubclassesOf for Kenyon cell\nsubclasses_of = vfbquery.get_subclasses_of(KENYON_CELL)\n```", + "followons": [ + { + "id": "FBbt_00003686", + "query_type": "ListAllAvailableImages", + "query": "Which images of Kenyon cell does VFB have?" + }, + { + "id": "FBbt_00003686", + "query_type": "UpstreamClassConnectivity", + "query": "What connects to the Kenyon cell upstream?" + }, + { + "id": "FBbt_00003686", + "query_type": "DownstreamClassConnectivity", + "query": "What does the Kenyon cell connect to downstream?" + }, + { + "id": "FBbt_00003686", + "query_type": "TransgeneExpressionHere", + "query": "Which driver lines label the Kenyon cell?" + }, + { + "id": "FBbt_00003686", + "query_type": "anatScRNAseqQuery", + "query": "What single-cell transcriptomic clusters are there for Kenyon cell?" + } + ], + "context_terms": [ + { + "id": "FBbt_00003686", + "label": "Kenyon cell" + } + ], + "reproduction": { + "ids": [ + { + "id": "FBbt_00003686", + "label": "Kenyon cell" + } + ], + "calls": [ + { + "id": "FBbt_00003686", + "query_type": "SubclassesOf", + "fn": "get_subclasses_of" + } + ], + "unmapped": [] + }, + "status_count": 7, + "problems": [] + } + ], + "ok": true, + "request_id": "af3628a6-cf2f-4857-be0e-8d1f96cd7bef", + "response_id": "chatcmpl-1ff7ae199c30c5f2933276cbc2495cdf", + "images_count": 8, + "graphs_count": 0, + "response": "The code below returns the [37](https://v2.virtualflybrain.org/org.geppetto.frontend/geppetto?q=FBbt_00003686,SubclassesOf \"Run in VFB: Subclasses of Kenyon cell\") subclasses of [Kenyon cell](https://www.virtualflybrain.org/reports/FBbt_00003686 \"Open Kenyon cell in Virtual Fly Brain\") that VFB has annotated, as a table. The first 12 subclasses, with their VFB ids, are provided in the evidence, including [KCab-c(i)](https://www.virtualflybrain.org/reports/FBbt_00049111 \"Open KCab-c(i) in Virtual Fly Brain\") (FBbt_00049111), [KCab-c](https://www.virtualflybrain.org/reports/FBbt_00110929 \"Open KCab-c in Virtual Fly Brain\")(o) (FBbt_00049112), larval [gamma Kenyon cell](https://www.virtualflybrain.org/reports/FBbt_00100247 \"Open gamma Kenyon cell in Virtual Fly Brain\") (FBbt_00049827), and [Kenyon cell of main calyx](https://www.virtualflybrain.org/reports/FBbt_00047926 \"Open Kenyon cell of main calyx in Virtual Fly Brain\") (FBbt_00047926).\n\n```python\n# Reproduce this answer in Python — pip install vfbquery\n#\n# These are the exact ids this conversation resolved and the exact catalogue\n# queries it ran, so this returns the same rows the answer was written from\n# rather than a fresh search that might land on a different term.\nimport vfbquery\n\nKENYON_CELL = 'FBbt_00003686' # Kenyon cell\n\n# SubclassesOf for Kenyon cell\nsubclasses_of = vfbquery.get_subclasses_of(KENYON_CELL)\n```", + "quality_flags": { + "has_tool_status": true, + "no_tool_factual_answer": false, + "tool_claim_without_tool": false, + "disambiguation_only_answer": false, + "investigation_plan_answer": false, + "not_verified_or_no_results_answer": false, + "graph_failure_mentioned": false, + "missing_required_graph": false, + "used_data_resource": false, + "response_chars": 1393, + "status_count": 7, + "addressless_followon": false, + "context_lost_across_turn": false, + "unmatched_claim_after_resolve": false, + "repeats_answered_question": false, + "slow_followup_turn": false, + "slowest_followup_ms": 23257 } } ] diff --git a/test-results/task-battery/task-battery-2026-08-10T17-16-49-499Z.json b/test-results/task-battery/task-battery-2026-08-10T17-16-49-499Z.json new file mode 100644 index 0000000..f7acbf4 --- /dev/null +++ b/test-results/task-battery/task-battery-2026-08-10T17-16-49-499Z.json @@ -0,0 +1,8072 @@ +{ + "metadata": { + "run_id": "task-battery-2026-08-10T17-16-49-499Z", + "started_at": "2026-08-10T17:16:49.499Z", + "completed_at": "2026-08-10T17:24:55.948Z", + "git_sha": "457fc5653f05a943560c0d085f9ca154ce742b26", + "task_file": "/home/runner/work/VFBchat/VFBchat/VFBchat/tests/task-battery/tasks.json", + "base_url": "http://127.0.0.1:3210", + "started_server": true, + "server_command": "start", + "repetitions": 1, + "concurrency": 4, + "timeout_ms": 240000 + }, + "prompt": { + "provenance_instruction": "Answer the following question about Drosophila neuroscience. For every claim you make, state where the information comes from - for example: the specific database, dataset, or tool query you used; the publication (with full citation); or your general training knowledge. If you are uncertain or do not have a source, say so explicitly rather than guessing." + }, + "summary": { + "total": 64, + "ok": 63, + "errors": 1, + "by_tier": { + "T1": { + "total": 8, + "ok": 8, + "errors": 0 + }, + "T2": { + "total": 8, + "ok": 8, + "errors": 0 + }, + "T3": { + "total": 8, + "ok": 7, + "errors": 1 + }, + "T4": { + "total": 6, + "ok": 6, + "errors": 0 + }, + "T5": { + "total": 1, + "ok": 1, + "errors": 0 + }, + "T6": { + "total": 21, + "ok": 21, + "errors": 0 + }, + "T7": { + "total": 12, + "ok": 12, + "errors": 0 + } + }, + "quality": { + "no_tool_factual_answer": { + "count": 0, + "task_ids": [] + }, + "tool_claim_without_tool": { + "count": 0, + "task_ids": [] + }, + "disambiguation_only_answer": { + "count": 0, + "task_ids": [] + }, + "investigation_plan_answer": { + "count": 0, + "task_ids": [] + }, + "not_verified_or_no_results_answer": { + "count": 0, + "task_ids": [] + }, + "graph_failure_mentioned": { + "count": 0, + "task_ids": [] + }, + "missing_required_graph": { + "count": 0, + "task_ids": [] + }, + "used_data_resource": { + "count": 0, + "task_ids": [] + }, + "addressless_followon": { + "count": 0, + "task_ids": [] + }, + "context_lost_across_turn": { + "count": 0, + "task_ids": [] + }, + "unmatched_claim_after_resolve": { + "count": 0, + "task_ids": [] + }, + "repeats_answered_question": { + "count": 0, + "task_ids": [] + }, + "slow_followup_turn": { + "count": 1, + "task_ids": [ + "C7" + ] + } + }, + "conversation": { + "total": 12, + "ok": 12, + "turns": 27, + "followup_turns": 15, + "followup_median_ms": 11309, + "followup_max_ms": 130947 + }, + "mean_duration_ms": 22273 + }, + "results": [ + { + "attempt_index": 0, + "task_index": 0, + "task_id": "T1.1", + "tier": 1, + "title": "Brain region identification", + "question": "What are the major subdivisions of the Drosophila mushroom body?", + "requires_graph": false, + "min_graphs": 0, + "repetition": 1, + "duration_ms": 31465, + "status_messages": [ + { + "message": "Thinking...", + "phase": "llm" + }, + { + "message": "Planning (direct lookup)", + "phase": "llm" + }, + { + "message": "Resolving 1 term in VFB", + "phase": "mcp" + }, + { + "message": "Reading VFB term info", + "phase": "mcp" + }, + { + "message": "Checking the answer is covered", + "phase": "llm" + }, + { + "message": "Writing the answer", + "phase": "llm" + } + ], + "event_count": 59, + "ok": true, + "request_id": "6755c564-84c8-4116-aabe-e411e0c7eb50", + "response_id": "chatcmpl-9dc74f1c82461aa5e8ee7d5700b41012", + "images_count": 8, + "graphs_count": 0, + "response": "The major subdivisions of the Drosophila [mushroom body](https://www.virtualflybrain.org/reports/FBbt_00005801 \"Open mushroom body in Virtual Fly Brain\") are the calyx, pedunculus, and mushroom body lobe system. The mushroom body lobe system consists of a vertical branch and a medial branch, which have different structures at different life stages.", + "quality_flags": { + "has_tool_status": true, + "no_tool_factual_answer": false, + "tool_claim_without_tool": false, + "disambiguation_only_answer": false, + "investigation_plan_answer": false, + "not_verified_or_no_results_answer": false, + "graph_failure_mentioned": false, + "missing_required_graph": false, + "used_data_resource": false, + "response_chars": 350, + "status_count": 6 + } + }, + { + "attempt_index": 1, + "task_index": 1, + "task_id": "T1.2", + "tier": 1, + "title": "Neuron type classification", + "question": "What types of Kenyon cells exist in the adult Drosophila brain?", + "requires_graph": false, + "min_graphs": 0, + "repetition": 1, + "duration_ms": 32142, + "status_messages": [ + { + "message": "Thinking...", + "phase": "llm" + }, + { + "message": "Planning the answer", + "phase": "llm" + }, + { + "message": "Resolving 1 term in VFB", + "phase": "mcp" + }, + { + "message": "Summarising neuron taxonomy", + "phase": "mcp" + }, + { + "message": "Checking the answer is covered", + "phase": "llm" + }, + { + "message": "Writing the answer", + "phase": "llm" + } + ], + "event_count": 83, + "ok": true, + "request_id": "827efe7e-47fa-449c-97f7-3a26563e58a9", + "response_id": "chatcmpl-fefc87b1c305ea58fe4bce2199295579", + "images_count": 8, + "graphs_count": 0, + "response": "There are several types of Kenyon cells in the adult Drosophila brain, including alpha/beta, alpha'/beta', and gamma Kenyon cells, which can be further subdivided into core/surface/posterior, anterior-posterior/middle, dorsal/main/gamma-s/gamma-t, and claw-count classes. VFB holds [37](https://v2.virtualflybrain.org/org.geppetto.frontend/geppetto?q=FBbt_00003686,SubclassesOf \"Run in VFB: Subclasses of Kenyon cell\") subclasses of [Kenyon cell](https://www.virtualflybrain.org/reports/FBbt_00003686 \"Open Kenyon cell in Virtual Fly Brain\").", + "quality_flags": { + "has_tool_status": true, + "no_tool_factual_answer": false, + "tool_claim_without_tool": false, + "disambiguation_only_answer": false, + "investigation_plan_answer": false, + "not_verified_or_no_results_answer": false, + "graph_failure_mentioned": false, + "missing_required_graph": false, + "used_data_resource": false, + "response_chars": 542, + "status_count": 6 + } + }, + { + "attempt_index": 2, + "task_index": 2, + "task_id": "T1.3", + "tier": 1, + "title": "Basic connectivity", + "question": "What are the main input neurons to the mushroom body?", + "requires_graph": false, + "min_graphs": 0, + "repetition": 1, + "duration_ms": 31506, + "status_messages": [ + { + "message": "Thinking...", + "phase": "llm" + }, + { + "message": "Planning the answer", + "phase": "llm" + }, + { + "message": "Resolving 1 term in VFB", + "phase": "mcp" + }, + { + "message": "Querying VFB connectivity", + "phase": "mcp" + }, + { + "message": "Querying VFB", + "phase": "mcp" + }, + { + "message": "Querying VFB", + "phase": "mcp" + }, + { + "message": "Checking the answer is covered", + "phase": "llm" + }, + { + "message": "Querying VFB", + "phase": "mcp" + }, + { + "message": "Checking the answer is covered", + "phase": "llm" + }, + { + "message": "Writing the answer", + "phase": "llm" + } + ], + "event_count": 92, + "ok": true, + "request_id": "0923e6ad-4fea-455e-875f-e2d8c7d0d6a9", + "response_id": "chatcmpl-e54222ff2c5724ceabc30608e9b63753", + "images_count": 8, + "graphs_count": 1, + "response": "The main input neurons to the [mushroom body](https://www.virtualflybrain.org/reports/FBbt_00005801 \"Open mushroom body in Virtual Fly Brain\") are sensory interneuron afferents to the calyx. VFB records show that there are [366](https://v2.virtualflybrain.org/org.geppetto.frontend/geppetto?q=FBbt_00005801,NeuronsPresynapticHere \"Run in VFB: Neurons with presynaptic terminals in mushroom body\") neurons with presynaptic terminals in the mushroom body, including larval uniglomerular projection neurons and larval antennal lobe multiglomerular projection neurons. The connectome data indicates that these neurons provide input to the mushroom body.", + "graphs": [ + { + "type": "basic_graph", + "version": 1, + "title": "mushroom body region connectivity preview", + "directed": true, + "layout": "radial", + "nodes": [ + { + "id": "FBbt_00005801", + "label": "mushroom body", + "group": "queried region", + "color": null, + "size": 2.4 + }, + { + "id": "FBbt_00111716", + "label": "larval antennal lobe multiglomerular projection neuron C2", + "group": "presynaptic neuron", + "color": null, + "size": 1.15 + }, + { + "id": "FBbt_00111717", + "label": "larval antennal lobe multiglomerular projection neuron bilateral lower", + "group": "presynaptic neuron", + "color": null, + "size": 1.15 + }, + { + "id": "FBbt_00111675", + "label": "larval uniglomerular projection neuron 63a", + "group": "presynaptic neuron", + "color": null, + "size": 1.15 + }, + { + "id": "FBbt_00111684", + "label": "larval uniglomerular projection neuron 67b", + "group": "presynaptic neuron", + "color": null, + "size": 1.15 + }, + { + "id": "FBbt_00111685", + "label": "larval uniglomerular projection neuron 74a", + "group": "presynaptic neuron", + "color": null, + "size": 1.15 + }, + { + "id": "FBbt_20000069", + "label": "ATL005", + "group": "postsynaptic neuron", + "color": null, + "size": 1.15 + }, + { + "id": "FBbt_20000071", + "label": "ATL007", + "group": "postsynaptic neuron", + "color": null, + "size": 1.15 + }, + { + "id": "FBbt_20000083", + "label": "ATL019", + "group": "postsynaptic neuron", + "color": null, + "size": 1.15 + }, + { + "id": "FBbt_20000084", + "label": "ATL020", + "group": "postsynaptic neuron", + "color": null, + "size": 1.15 + }, + { + "id": "FBbt_00111628", + "label": "adult odd neuron of the calyx", + "group": "postsynaptic neuron", + "color": null, + "size": 1.15 + } + ], + "edges": [ + { + "source": "FBbt_00111716", + "target": "FBbt_00005801", + "label": "presynaptic sites in mushroom body", + "weight": 0 + }, + { + "source": 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"task_index": 4, + "task_id": "T1.5", + "tier": 1, + "title": "Neuroanatomy", + "question": "What brain regions does the antennal lobe connect to?", + "requires_graph": false, + "min_graphs": 0, + "repetition": 1, + "duration_ms": 13440, + "status_messages": [ + { + "message": "Thinking...", + "phase": "llm" + }, + { + "message": "Planning the answer", + "phase": "llm" + }, + { + "message": "Resolving 1 term in VFB", + "phase": "mcp" + }, + { + "message": "Reading VFB term info", + "phase": "mcp" + }, + { + "message": "Querying VFB", + "phase": "mcp" + }, + { + "message": "Querying VFB", + "phase": "mcp" + }, + { + "message": "Checking the answer is covered", + "phase": "llm" + }, + { + "message": "Writing the answer", + "phase": "llm" + } + ], + "event_count": 141, + "ok": true, + "request_id": "41a6355e-9c0c-4864-9d7e-b9dead88054b", + "response_id": "chatcmpl-aa1986746dd8e6ebb78859b65bec1aee", + "images_count": 6, + "graphs_count": 0, + "response": "The [antennal 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Neurons with presynaptic terminals in the antennal lobe include [larval antennal lobe picky local neuron](https://www.virtualflybrain.org/reports/FBbt_00111694 \"Open larval antennal lobe picky local neuron in Virtual Fly Brain\"), [larval antennal lobe broad local neuron](https://www.virtualflybrain.org/reports/FBbt_00111700 \"Open larval antennal lobe broad local neuron in Virtual Fly Brain\"), and adult olfactory receptor neurons. Neurons with postsynaptic terminals in the antennal lobe include adult antennal lobe projection neurons, such as DL5, DM4, VA1d, VL1, VL2a, VM2, and VM4, as well as multiglomerular antennal lobe projection neurons like L1 adPN.", + "quality_flags": { + "has_tool_status": true, + "no_tool_factual_answer": false, + "tool_claim_without_tool": false, + "disambiguation_only_answer": false, + "investigation_plan_answer": false, + "not_verified_or_no_results_answer": false, + "graph_failure_mentioned": false, + "missing_required_graph": false, + "used_data_resource": false, + "response_chars": 873, + "status_count": 8 + } + }, + { + "attempt_index": 5, + "task_index": 5, + "task_id": "T1.6", + "tier": 1, + "title": "Cell count", + "question": "Approximately how many neurons are in the adult Drosophila central brain?", + "requires_graph": false, + "min_graphs": 0, + "repetition": 1, + "duration_ms": 17051, + "status_messages": [ + { + "message": "Thinking...", + "phase": "llm" + }, + { + "message": "Planning the answer", + "phase": "llm" + }, + { + "message": "Resolving 1 term in VFB", + "phase": "mcp" + }, + { + "message": "Counting neurons", + "phase": "mcp" + }, + { + "message": "Checking the answer is covered", + "phase": "llm" + }, + { + "message": "Writing the answer", + "phase": "llm" + } + ], + "event_count": 49, + "ok": true, + "request_id": "d1c5e0a4-b713-4193-a252-0c588f9856e4", + "response_id": "chatcmpl-476256daa911c93b56bec8141f73e2c5", + "images_count": 0, + "graphs_count": 0, + "response": "The adult Drosophila central brain could not be matched to a VFB record. However, there is information available that approximately more than 125,000 neurons are in the Drosophila brain.\n\n**Published neuron-count estimates — adult central brain** (from the literature):\n\n- more than 125,000 neurons (adult Drosophila central brain connectome/model) — A Drosophila computational brain model reveals sensorimotor processing. — PMID 39358519\n- ~139,255 neurons (whole adult Drosophila brain) — Neuronal wiring diagram of an adult brain. — PMID 39358518\n\n_VFB has annotated 9,413 neuron types with some part in adult central brain — a curated annotation count, not the biological total._", + "quality_flags": { + "has_tool_status": true, + "no_tool_factual_answer": false, + "tool_claim_without_tool": false, + "disambiguation_only_answer": false, + "investigation_plan_answer": false, + "not_verified_or_no_results_answer": false, + "graph_failure_mentioned": false, + "missing_required_graph": false, + "used_data_resource": false, + "response_chars": 683, + "status_count": 6 + } + }, + { + "attempt_index": 6, + "task_index": 6, + "task_id": "T1.7", + "tier": 1, + "title": "Central complex structure", + "question": "What are the main components of the Drosophila central complex and what functions are they associated with?", + "requires_graph": false, + "min_graphs": 0, + "repetition": 1, + "duration_ms": 19363, + "status_messages": [ + { + "message": "Thinking...", + "phase": "llm" + }, + { + "message": "Planning the answer", + "phase": "llm" + }, + { + "message": "Resolving 1 term in VFB", + "phase": "mcp" + }, + { + "message": "Querying VFB connectivity", + "phase": "mcp" + }, + { + "message": "Checking the answer is covered", + "phase": "llm" + }, + { + "message": "Writing the answer", + "phase": "llm" + } + ], + "event_count": 64, + "ok": true, + "request_id": "30df6ba2-de57-4fbd-bc5d-5bb1d05d0ab1", + "response_id": "chatcmpl-0292635a9f61195d7f77826a511d7824", + "images_count": 0, + "graphs_count": 1, + "response": "The main components of the central complex are the ellipsoid body, fan-shaped body, paired noduli, asymmetrical bodies, and protocerebral bridge. These components are associated with functions including navigation and orientation, locomotor control, and sleep/arousal and memory-related behaviours.", + "graphs": [ + { + "type": "basic_graph", + "version": 1, + "title": "adult central complex region connectivity preview", + "directed": true, + "layout": "radial", + "nodes": [ + { + "id": "FBbt_00003632", + "label": "adult central complex", + "group": "queried region", + "color": null, + "size": 2.4 + }, + { + "id": "FBbt_00111369", + "label": "PEN_PB2", + "group": "presynaptic and postsynaptic neuron", + "color": null, + "size": 1.15 + }, + { + "id": "FBbt_00111370", + "label": "PEN_PB3", + "group": "presynaptic and postsynaptic neuron", + "color": null, + "size": 1.15 + }, + { + "id": "FBbt_00111373", + "label": "PEN_PB7", + "group": "presynaptic and postsynaptic neuron", + "color": null, + "size": 1.15 + }, + { + "id": "FBbt_00111374", + "label": "PEN_PB8", + "group": "presynaptic and postsynaptic neuron", + "color": null, + "size": 1.15 + }, + { + "id": "FBbt_00111376", + "label": "adult protocerebral bridge glomerulus 1-ellipsoid body canal-dorsal gall neuron", + "group": "presynaptic and postsynaptic neuron", + "color": null, + "size": 1.15 + } + ], + "edges": [ + { + "source": "FBbt_00111369", + "target": "FBbt_00003632", + "label": "presynaptic sites in adult central complex", + "weight": 0 + }, + { + "source": "FBbt_00111370", + "target": "FBbt_00003632", + "label": "presynaptic sites in adult central complex", + "weight": 0 + }, + { + "source": "FBbt_00111373", + "target": "FBbt_00003632", + "label": "presynaptic sites in adult central complex", + "weight": 0 + }, + { + "source": "FBbt_00111374", + "target": "FBbt_00003632", + "label": "presynaptic sites in adult central complex", + "weight": 0 + }, + { + "source": "FBbt_00111376", + "target": "FBbt_00003632", + "label": "presynaptic sites in adult central complex", + "weight": 0 + }, + { + "source": "FBbt_00003632", + "target": "FBbt_00111369", + "label": "postsynaptic sites in adult central complex", + "weight": 0 + }, + { + "source": "FBbt_00003632", + "target": "FBbt_00111370", + "label": "postsynaptic sites in adult central complex", + "weight": 0 + }, + { + "source": "FBbt_00003632", + "target": "FBbt_00111373", + "label": "postsynaptic sites in adult central complex", + "weight": 0 + }, + { + "source": "FBbt_00003632", + "target": "FBbt_00111374", + "label": "postsynaptic sites in adult central complex", + "weight": 0 + }, + { + "source": "FBbt_00003632", + "target": "FBbt_00111376", + "label": "postsynaptic sites in adult central complex", + "weight": 0 + } + ] + } + ], + "quality_flags": { + "has_tool_status": true, + "no_tool_factual_answer": false, + "tool_claim_without_tool": false, + "disambiguation_only_answer": false, + "investigation_plan_answer": false, + "not_verified_or_no_results_answer": false, + "graph_failure_mentioned": false, + "missing_required_graph": false, + "used_data_resource": false, + "response_chars": 298, + "status_count": 6 + } + }, + { + "attempt_index": 7, + "task_index": 7, + "task_id": "T1.8", + "tier": 1, + "title": "Genetic tools", + "question": "What genetic tools are commonly used to label mushroom body neurons in Drosophila?", + "requires_graph": false, + "min_graphs": 0, + "repetition": 1, + "duration_ms": 21988, + "status_messages": [ + { + "message": "Thinking...", + "phase": "llm" + }, + { + "message": "Planning the answer", + "phase": "llm" + }, + { + "message": "Resolving 1 term in VFB", + "phase": "mcp" + }, + { + "message": "Finding genetic tools", + "phase": "mcp" + }, + { + "message": "Checking the answer is covered", + "phase": "llm" + }, + { + "message": "Writing the answer", + "phase": "llm" + } + ], + "event_count": 267, + "ok": true, + "request_id": "e175bccd-8db0-4b7f-91e4-1424af055fa1", + "response_id": "chatcmpl-7861945329a6783af91007d8fcb507be", + "images_count": 8, + "graphs_count": 0, + "response": "Genetic tools such as PBac{544.SVS-1}Bsg[CPTI100062] and PBac{602.P.SVS-1}Fas2[CPTI000483] are used to label neurons. VFB records show multiple transgene expression patterns, including PBac{566.P.SVS-1}Bsg[CPTI100005], PBac{566.P.SVS-1}IA-2[CPTI100013], PBac{566.P.SVS-1}sgg[CPTI100027], PBac{602.P.SVS-1}HDAC4[CPTI000077], PBac{602.P.SVS-1}Pax[CPTI000161], PBac{602.P.SVS-1}Sema1a[CPTI000505], PBac{602.P.SVS-1}Tm1[CPTI000760], PBac{602.P.SVS-1}dlg1[CPTI000207], PBac{602.P.SVS-1}dlp[CPTI000445], and PBac{602.P.SVS-1}hzg[CPTI000737]. For [Kenyon cell](https://www.virtualflybrain.org/reports/FBbt_00003686 \"Open Kenyon cell in Virtual Fly Brain\"), VFB holds [92](https://v2.virtualflybrain.org/org.geppetto.frontend/geppetto?q=FBbt_00003686,TransgeneExpressionHere \"Run in VFB: Transgene expression in Kenyon cell\") transgene expression reports.", + "quality_flags": { + "has_tool_status": true, + "no_tool_factual_answer": false, + "tool_claim_without_tool": false, + "disambiguation_only_answer": false, + "investigation_plan_answer": false, + "not_verified_or_no_results_answer": false, + "graph_failure_mentioned": false, + "missing_required_graph": false, + "used_data_resource": false, + "response_chars": 847, + "status_count": 6 + } + }, + { + "attempt_index": 8, + "task_index": 8, + "task_id": "T2.1", + "tier": 2, + "title": "Circuit motif", + "question": "Describe the dopaminergic input to mushroom body output neurons (MBONs). Which DAN types connect to which MBON types?", + "requires_graph": false, + "min_graphs": 0, + "repetition": 1, + "duration_ms": 27596, + "status_messages": [ + { + "message": "Thinking...", + "phase": "llm" + }, + { + "message": "Planning the answer", + "phase": "llm" + }, + { + "message": "Resolving 4 terms in VFB", + "phase": "mcp" + }, + { + "message": "Querying VFB connectivity", + "phase": "mcp" + }, + { + "message": "Checking the answer is covered", + "phase": "llm" + }, + { + "message": "Querying VFB", + "phase": "mcp" + }, + { + "message": "Querying VFB", + "phase": "mcp" + }, + { + "message": "Checking the answer is covered", + "phase": "llm" + }, + { + "message": "Writing the answer", + "phase": "llm" + } + ], + "event_count": 87, + "ok": true, + "request_id": "3d9bae69-f166-4dbf-ae36-4129f61df37e", + "response_id": "chatcmpl-03332f60ce2f4dffb8f62fde0e0a9ed2", + "images_count": 8, + "graphs_count": 1, + "response": "Dopaminergic input to mushroom body output neurons comes from specific dopaminergic neuron types, including dopaminergic PPL1 neurons and dopaminergic PAM neurons. The strongest specific input to [mushroom body output neuron](https://www.virtualflybrain.org/reports/FBbt_00047953 \"Open mushroom body output neuron in Virtual Fly Brain\"), ranked by mean synaptic weight per connected pair, are [adult cholinergic neuron](https://www.virtualflybrain.org/reports/FBbt_00058205 \"Open adult cholinergic neuron in Virtual Fly Brain\") and [Kenyon cell](https://www.virtualflybrain.org/reports/FBbt_00003686 \"Open Kenyon cell in Virtual Fly Brain\"). VFB holds [69](https://v2.virtualflybrain.org/org.geppetto.frontend/geppetto?q=FBbt_00047953,SubclassesOf \"Run in VFB: Subclasses of MBON\") subclasses of mushroom body output neuron.", + "graphs": [ + { + "type": "basic_graph", + "version": 1, + "title": "Upstream partners of MBON", + "directed": true, + "layout": "circle", + "nodes": [ + { + "id": "FBbt_00005131", + "label": "dopaminergic neuron", + "group": null, + "color": null, + "size": 1.93 + }, + { + "id": "FBbt_00047953", + "label": "MBON", + "group": null, + "color": null, + "size": 4 + }, + { + "id": "FBbt_00058206", + "label": "adult dopaminergic neuron", + "group": null, + "color": null, + "size": 1.92 + }, + { + "id": "FBbt_00048138", + "label": "mushroom body dopaminergic neuron", + "group": null, + "color": null, + "size": 1.91 + }, + { + "id": "FBbt_00049839", + "label": "adult dopaminergic mushroom body input neuron", + "group": null, + "color": null, + "size": 1.07 + }, + { + "id": "FBbt_00100214", + "label": "adult 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"Querying VFB", + "phase": "mcp" + }, + { + "message": "Checking the answer is covered", + "phase": "llm" + }, + { + "message": "Querying VFB", + "phase": "mcp" + }, + { + "message": "Querying VFB", + "phase": "mcp" + }, + { + "message": "Checking the answer is covered", + "phase": "llm" + }, + { + "message": "Writing the answer", + "phase": "llm" + } + ], + "event_count": 61, + "ok": true, + "request_id": "eaaec351-5fa2-45c5-904c-b277fe774d25", + "response_id": "chatcmpl-64eec5d28dd2c0f5ca7d10ee88279e94", + "images_count": 8, + "graphs_count": 0, + "response": "The connectivity of olfactory projection neurons is not directly compared between the Hemibrain and FAFB connectome datasets in VFB evidence. VFB does not currently hold data on the consistency of [olfactory projection neuron](https://www.virtualflybrain.org/reports/FBbt_00051298 \"Open olfactory projection neuron in Virtual Fly Brain\") connectivity between these two datasets.", + "quality_flags": { + "has_tool_status": true, + "no_tool_factual_answer": false, + "tool_claim_without_tool": false, + "disambiguation_only_answer": false, + "investigation_plan_answer": false, + "not_verified_or_no_results_answer": false, + "graph_failure_mentioned": false, + "missing_required_graph": false, + "used_data_resource": false, + "response_chars": 378, + "status_count": 11 + } + }, + { + "attempt_index": 10, + "task_index": 10, + "task_id": "T2.3", + "tier": 2, + "title": "Reagent identification", + "question": "I want to image neurons in the lateral horn. What split-GAL4 driver lines are available that target lateral horn neuron types?", + "requires_graph": false, + "min_graphs": 0, + "repetition": 1, + "duration_ms": 23662, + "status_messages": [ + { + "message": "Thinking...", + "phase": "llm" + }, + { + "message": "Planning the answer", + "phase": "llm" + }, + { + "message": "Resolving 1 term in VFB", + "phase": "mcp" + }, + { + "message": "Reading VFB term info", + "phase": "mcp" + }, + { + "message": "Finding genetic tools", + "phase": "mcp" + }, + { + "message": "Checking the answer is covered", + "phase": "llm" + }, + { + "message": "Querying VFB", + "phase": "mcp" + }, + { + "message": "Checking the answer is covered", + "phase": "llm" + }, + { + "message": "Writing the answer", + "phase": "llm" + }, + { + "message": "Checking before saying VFB has no data", + "phase": "mcp" + }, + { + "message": "Querying VFB", + "phase": "mcp" + }, + { + "message": "Querying VFB", + "phase": "mcp" + }, + { + "message": "Querying VFB", + "phase": "mcp" + }, + { + "message": "Checking the answer is covered", + "phase": "llm" + }, + { + "message": "Writing the answer", + "phase": "llm" + } + ], + "event_count": 218, + "ok": true, + "request_id": "54a04339-3fec-49c2-abc7-035f8bc1848c", + "response_id": "chatcmpl-71e1de4c71a4c3eabe48699fcd318a8f", + "images_count": 8, + "graphs_count": 0, + "response": "VFB holds [1934](https://v2.virtualflybrain.org/org.geppetto.frontend/geppetto?q=FBbt_00007053,TransgeneExpressionHere \"Run in VFB: Transgene expression in adult lateral horn\") transgene expression reports for [adult lateral horn](https://www.virtualflybrain.org/reports/FBbt_00007053 \"Open adult lateral horn in Virtual Fly Brain\"), including driver lines such as P{GMR11B09-GAL4} and PBac{566.P.SVS-1}IA-2[CPTI100013]. The documentation mentions FlyLight split-GAL4 lines for Lateral Horn from Dolan et al.", + "quality_flags": { + "has_tool_status": true, + "no_tool_factual_answer": false, + "tool_claim_without_tool": false, + "disambiguation_only_answer": false, + "investigation_plan_answer": false, + "not_verified_or_no_results_answer": false, + "graph_failure_mentioned": false, + "missing_required_graph": false, + "used_data_resource": false, + "response_chars": 508, + "status_count": 15 + } + }, + { + "attempt_index": 11, + "task_index": 11, + "task_id": "T2.4", + "tier": 2, + "title": "Neuron characterisation", + "question": "What is known about the LPLC2 visual neuron type? Where is it, what does it connect to, and what is its function?", + "requires_graph": false, + "min_graphs": 0, + "repetition": 1, + "duration_ms": 24695, + "status_messages": [ + { + "message": "Thinking...", + "phase": "llm" + }, + { + "message": "Planning the answer", + "phase": "llm" + }, + { + "message": "Resolving 1 term in VFB", + "phase": "mcp" + }, + { + "message": "Querying VFB", + "phase": "mcp" + }, + { + "message": "Querying VFB connectivity", + "phase": "mcp" + }, + { + "message": "Checking the answer is covered", + "phase": "llm" + }, + { + "message": "Writing the answer", + "phase": "llm" + }, + { + "message": "Checking before saying VFB has no data", + "phase": "mcp" + }, + { + "message": "Querying VFB", + "phase": "mcp" + }, + { + "message": "Querying VFB", + "phase": "mcp" + }, + { + "message": "Querying VFB", + "phase": "mcp" + }, + { + "message": "Checking the answer is covered", + "phase": "llm" + }, + { + "message": "Writing the answer", + "phase": "llm" + } + ], + "event_count": 176, + "ok": true, + "request_id": "646eca10-7e2a-42ac-a0ce-eb98858c51be", + "response_id": "chatcmpl-0c7281d7d12d83f11492a2ea9957c643", + "images_count": 7, + "graphs_count": 0, + "response": "The [lobula plate-lobula columnar neuron LPLC2](https://www.virtualflybrain.org/reports/FBbt_00111763 \"Open lobula plate-lobula columnar neuron LPLC2 in Virtual Fly Brain\") is located in the dorsal area of the lateral cell body rind, has distinct dendritic arbors in each lobula plate layer, and detects looming stimuli, eliciting a jump escape response. VFB holds [723](https://v2.virtualflybrain.org/org.geppetto.frontend/geppetto?q=FBbt_00111763,ListAllAvailableImages \"Run in VFB: List all available images of LPLC2\") images of LPLC2. There are [2](https://v2.virtualflybrain.org/org.geppetto.frontend/geppetto?q=FBbt_00111763,SplitsTargeting \"Run in VFB: Splits targeting LPLC2\") splits targeting LPLC2 and 2 scRNAseq data results for LPLC2.", + "quality_flags": { + "has_tool_status": true, + "no_tool_factual_answer": false, + "tool_claim_without_tool": false, + "disambiguation_only_answer": false, + "investigation_plan_answer": false, + "not_verified_or_no_results_answer": false, + "graph_failure_mentioned": false, + "missing_required_graph": false, + "used_data_resource": false, + "response_chars": 746, + "status_count": 13 + } + }, + { + "attempt_index": 12, + "task_index": 12, + "task_id": "T2.5", + "tier": 2, + "title": "Comparative anatomy", + "question": "How does the organisation of the antennal lobe compare between adult and larval Drosophila?", + "requires_graph": false, + "min_graphs": 0, + "repetition": 1, + "duration_ms": 7968, + "status_messages": [ + { + "message": "Thinking...", + "phase": "llm" + }, + { + "message": "Planning the answer", + "phase": "llm" + }, + { + "message": "Resolving 1 term in VFB", + "phase": "mcp" + }, + { + "message": "Querying VFB", + "phase": "mcp" + }, + { + "message": "Checking the answer is covered", + "phase": "llm" + }, + { + "message": "Writing the answer", + "phase": "llm" + } + ], + "event_count": 37, + "ok": true, + "request_id": "23ed5537-39e7-45f9-9a51-47982da28977", + "response_id": "chatcmpl-ea11ff7e568ddef63c49e39cd8eb9cb4", + "images_count": 6, + "graphs_count": 0, + "response": "The adult [antennal lobe](https://www.virtualflybrain.org/reports/FBbt_00003924 \"Open antennal lobe in Virtual Fly Brain\") has approximately 50 glomeruli, while the larval antennal lobe has around 22 glomeruli.", + "quality_flags": { + "has_tool_status": true, + "no_tool_factual_answer": false, + "tool_claim_without_tool": false, + "disambiguation_only_answer": false, + "investigation_plan_answer": false, + "not_verified_or_no_results_answer": false, + 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14, + "task_index": 14, + "task_id": "T2.7", + "tier": 2, + "title": "Morphological similarity", + "question": "Are there neurons in the Hemibrain dataset that are morphologically similar to the fru+ mAL neurons described in light microscopy studies?", + "requires_graph": false, + "min_graphs": 0, + "repetition": 1, + "duration_ms": 9793, + "status_messages": [ + { + "message": "Thinking...", + "phase": "llm" + }, + { + "message": "Planning the answer", + "phase": "llm" + }, + { + "message": "Resolving 2 terms in VFB", + "phase": "mcp" + }, + { + "message": "Querying VFB", + "phase": "mcp" + }, + { + "message": "Checking the answer is covered", + "phase": "llm" + }, + { + "message": "Writing the answer", + "phase": "llm" + } + ], + "event_count": 31, + "ok": true, + "request_id": "5865b839-0fbb-4ac7-993c-99df867a3edd", + "response_id": "chatcmpl-8c1fffded1ed9ae0e253fbe71029a538", + "images_count": 5, + "graphs_count": 0, + "response": "The Hemibrain dataset contains neurons morphologically similar to the fru+ mAL neurons described in light microscopy studies.", + "quality_flags": { + "has_tool_status": true, + "no_tool_factual_answer": false, + "tool_claim_without_tool": false, + "disambiguation_only_answer": false, + "investigation_plan_answer": false, + "not_verified_or_no_results_answer": false, + "graph_failure_mentioned": false, + "missing_required_graph": false, + "used_data_resource": false, + "response_chars": 125, + "status_count": 6 + } + }, + { + "attempt_index": 15, + "task_index": 15, + "task_id": "T2.8", + "tier": 2, + "title": "Upstream circuit", + "question": "What sensory neurons provide input to the fan-shaped body, and through how many synaptic steps?", + "requires_graph": false, + "min_graphs": 0, + "repetition": 1, + "duration_ms": 23402, + "status_messages": [ + { + "message": "Thinking...", + "phase": "llm" + }, + { + "message": "Planning the answer", + "phase": "llm" + }, + { + "phase": "plan", + "message": "The plan is contested — sampling again before committing." + }, + { + "message": "Resolving 1 term in VFB", + "phase": "mcp" + }, + { + "message": "Reading VFB term info", + "phase": "mcp" + }, + { + "message": "Tracing the pathway", + "phase": "mcp" + }, + { + "message": "Querying VFB", + "phase": "mcp" + }, + { + "message": "Checking the answer is covered", + "phase": "llm" + }, + { + "message": "Querying VFB", + "phase": "mcp" + }, + { + "message": "Checking the answer is covered", + "phase": "llm" + }, + { + "message": "Writing the answer", + "phase": "llm" + }, + { + "message": "Checking before saying VFB has no data", + "phase": "mcp" + }, + { + "message": "Querying VFB", + "phase": "mcp" + }, + { + "message": "Querying VFB", + "phase": "mcp" + }, + { + "message": "Querying VFB", + "phase": "mcp" + }, + { + "message": "Checking the answer is covered", + "phase": "llm" + }, + { + "message": "Writing the answer", + "phase": "llm" + } + ], + "event_count": 337, + "ok": true, + "request_id": "ea19e709-32a7-4ea7-9473-d8e14d25510a", + "response_id": "chatcmpl-3a67634c46b27ec7469358f4488fcaa5", + "images_count": 8, + "graphs_count": 0, + "response": "The [fan-shaped body](https://www.virtualflybrain.org/reports/FBbt_00003679 \"Open fan-shaped body in Virtual Fly Brain\") receives input from various sensory neurons. VFB records show [102](https://v2.virtualflybrain.org/org.geppetto.frontend/geppetto?q=FBbt_00003679,NeuronsPresynapticHere \"Run in VFB: Neurons with presynaptic terminals in fan-shaped body\") neurons with presynaptic terminals in the fan-shaped body. The first 12 of these include [PFNd_PB2](https://www.virtualflybrain.org/reports/FBbt_00111391 \"Open PFNd_PB2 in Virtual Fly Brain\"), [PFNd_PB3](https://www.virtualflybrain.org/reports/FBbt_00111392 \"Open PFNd_PB3 in Virtual Fly Brain\"), [PFNd_PB5](https://www.virtualflybrain.org/reports/FBbt_00111394 \"Open PFNd_PB5 in Virtual Fly Brain\"), [PFNa_PB4](https://www.virtualflybrain.org/reports/FBbt_00111398 \"Open PFNa_PB4 in Virtual Fly Brain\"), [PFNa_PB5](https://www.virtualflybrain.org/reports/FBbt_00111399 \"Open PFNa_PB5 in Virtual Fly Brain\"), PFNa_PB6, PFNa_PB7, PFNa_PB9, PFNp_PB7, [protocerebral bridge glomerulus 8-fan-shaped body-ipsilateral ventral gall surround neuron](https://www.virtualflybrain.org/reports/FBbt_00111463 \"Open protocerebral bridge glomerulus 8-fan-shaped body-ipsilateral ventral gall surround neuron in Virtual Fly Brain\"), [adult ExR1 neuron of DM3 lineage](https://www.virtualflybrain.org/reports/FBbt_00053034 \"Open adult ExR1 neuron of DM3 lineage in Virtual Fly Brain\"), and adult ExR1 neuron of DM4 lineage. However, the exact number of synaptic steps between these sensory neurons and the fan-shaped body is not specified.", + "quality_flags": { + "has_tool_status": true, + "no_tool_factual_answer": false, + "tool_claim_without_tool": false, + "disambiguation_only_answer": false, + "investigation_plan_answer": false, + "not_verified_or_no_results_answer": false, + "graph_failure_mentioned": false, + "missing_required_graph": false, + "used_data_resource": false, + "response_chars": 1581, + "status_count": 17 + } + }, + { + "attempt_index": 16, + "task_index": 16, + "task_id": "T3.1", + "tier": 3, + "title": "Bidirectional connectivity", + "question": "Are there reciprocal connections between mushroom body output neurons (MBONs) and dopaminergic neurons (DANs)? Which pairs have the strongest mutual connectivity?", + "requires_graph": false, + "min_graphs": 0, + "repetition": 1, + "duration_ms": 19526, + "status_messages": [ + { + "message": "Thinking...", + "phase": "llm" + }, + { + "message": "Planning the answer", + "phase": "llm" + }, + { + "message": "Resolving 2 terms in VFB", + "phase": "mcp" + }, + { + "message": "Querying VFB connectivity", + "phase": "mcp" + }, + { + "message": "Checking the answer is covered", + "phase": "llm" + }, + { + "message": "Querying VFB", + "phase": "mcp" + }, + { + "message": "Querying VFB", + "phase": "mcp" + }, + { + "message": "Checking the answer is covered", + "phase": "llm" + }, + { + "message": "Writing the answer", + "phase": "llm" + } + ], + "event_count": 122, + "ok": true, + "request_id": "c38b2f58-3cc2-43a0-ad1a-0cea29df145b", + "response_id": "chatcmpl-3078d23a1603d309890ae3f949ae221b", + "images_count": 8, + "graphs_count": 0, + "response": "There are reciprocal connections between mushroom body output neurons and dopaminergic neurons. VFB found 5 reciprocal class-level pairs between [mushroom body output neuron](https://www.virtualflybrain.org/reports/FBbt_00047953 \"Open mushroom body output neuron in Virtual Fly Brain\") and [dopaminergic neuron](https://www.virtualflybrain.org/reports/FBbt_00005131 \"Open dopaminergic neuron in Virtual Fly Brain\"). The strongest specific targets of mushroom body output neuron include [primary interneuron](https://www.virtualflybrain.org/reports/FBbt_00052517 \"Open primary interneuron in Virtual Fly Brain\"), [primary neuron](https://www.virtualflybrain.org/reports/FBbt_00047097 \"Open primary neuron in Virtual Fly Brain\"), [adult GABAergic neuron](https://www.virtualflybrain.org/reports/FBbt_00058207 \"Open adult GABAergic neuron in Virtual Fly Brain\"), [GABAergic neuron](https://www.virtualflybrain.org/reports/FBbt_00007228 \"Open GABAergic neuron in Virtual Fly Brain\"), [adult glutamatergic neuron](https://www.virtualflybrain.org/reports/FBbt_00058208 \"Open adult glutamatergic neuron in Virtual Fly Brain\"), [glutamatergic neuron](https://www.virtualflybrain.org/reports/FBbt_00100291 \"Open glutamatergic neuron in Virtual Fly Brain\"), [adult lateral horn neuron](https://www.virtualflybrain.org/reports/FBbt_00048293 \"Open adult lateral horn neuron in Virtual Fly Brain\"), and [adult cholinergic neuron](https://www.virtualflybrain.org/reports/FBbt_00058205 \"Open adult cholinergic neuron in Virtual Fly Brain\"). The strongest specific targets of dopaminergic neuron include adult cholinergic neuron and [adult Kenyon cell](https://www.virtualflybrain.org/reports/FBbt_00049825 \"Open adult Kenyon cell in Virtual Fly Brain\").", + "quality_flags": { + "has_tool_status": true, + "no_tool_factual_answer": false, + "tool_claim_without_tool": false, + "disambiguation_only_answer": false, + "investigation_plan_answer": false, + "not_verified_or_no_results_answer": false, + "graph_failure_mentioned": false, + "missing_required_graph": false, + "used_data_resource": false, + "response_chars": 1738, + "status_count": 9 + } + }, + { + "attempt_index": 17, + "task_index": 17, + "task_id": "T3.2", + "tier": 3, + "title": "Pathway tracing", + "question": "Trace a pathway from olfactory receptor neurons to the lateral horn. What are the intermediate neuron types and their connections?", + "requires_graph": false, + "min_graphs": 0, + "repetition": 1, + "duration_ms": 16998, + "status_messages": [ + { + "message": "Thinking...", + "phase": "llm" + }, + { + "message": "Planning the answer", + "phase": "llm" + }, + { + "message": "Resolving 2 terms in VFB", + "phase": "mcp" + }, + { + "message": "Tracing the pathway", + "phase": "mcp" + }, + { + "message": "Checking the answer is covered", + "phase": "llm" + }, + { + "message": "Querying VFB", + "phase": "mcp" + }, + { + "message": "Querying VFB", + "phase": "mcp" + }, + { + "message": "Checking the answer is covered", + "phase": "llm" + }, + { + "message": "Writing the answer", + "phase": "llm" + } + ], + "event_count": 129, + "ok": true, + "request_id": "506616aa-cde2-44ad-9641-6f1a163b9e98", + "response_id": "chatcmpl-5f1540765d7ed2c7ba9f18a6d1ee3bbe", + "images_count": 8, + "graphs_count": 0, + "response": "The pathway from olfactory receptor neurons to the lateral horn involves intermediate neurons. Antennal lobe projection neurons are intermediate neurons that connect olfactory receptor neurons to the lateral horn. The strongest specific inputs to [olfactory receptor neuron](https://www.virtualflybrain.org/reports/FBbt_00005926 \"Open olfactory receptor neuron in Virtual Fly Brain\") are from [adult antennal lobe local neuron lLN](https://www.virtualflybrain.org/reports/FBbt_00051502 \"Open adult antennal lobe local neuron lLN in Virtual Fly Brain\"), [adult local interneuron of the lateral ALl1 neuroblast](https://www.virtualflybrain.org/reports/FBbt_00007394 \"Open adult local interneuron of the lateral ALl1 neuroblast in Virtual Fly Brain\"), [antennal lobe local neuron](https://www.virtualflybrain.org/reports/FBbt_00052874 \"Open antennal lobe local neuron in Virtual Fly Brain\"), [adult antennal lobe local neuron](https://www.virtualflybrain.org/reports/FBbt_00007390 \"Open adult antennal lobe local neuron in Virtual Fly Brain\"), and [olfactory system neuron](https://www.virtualflybrain.org/reports/FBbt_00007697 \"Open olfactory system neuron in Virtual Fly Brain\"). VFB holds [1661](https://v2.virtualflybrain.org/org.geppetto.frontend/geppetto?q=FBbt_00007053,NeuronsPartHere \"Run in VFB: Neurons with some part in adult lateral horn\") neurons with some part in [adult lateral horn](https://www.virtualflybrain.org/reports/FBbt_00007053 \"Open adult lateral horn in Virtual Fly Brain\") and [1658](https://v2.virtualflybrain.org/org.geppetto.frontend/geppetto?q=FBbt_00007053,NeuronsSynaptic \"Run in VFB: Neurons with synaptic terminals in adult lateral horn\") neurons with synaptic terminals in adult lateral horn.", + "quality_flags": { + "has_tool_status": true, + "no_tool_factual_answer": false, + "tool_claim_without_tool": false, + "disambiguation_only_answer": false, + "investigation_plan_answer": false, + "not_verified_or_no_results_answer": false, + "graph_failure_mentioned": false, + "missing_required_graph": false, + "used_data_resource": false, + "response_chars": 1727, + "status_count": 9 + } + }, + { + "attempt_index": 18, + "task_index": 18, + "task_id": "T3.3", + "tier": 3, + "title": "Cell type taxonomy depth", + "question": "How many distinct neuron types are currently classified within the adult Drosophila visual system, and how are they organised hierarchically?", + "requires_graph": false, + "min_graphs": 0, + "repetition": 1, + "duration_ms": 7685, + "status_messages": [ + { + "message": "Thinking...", + "phase": "llm" + }, + { + "message": "Planning the answer", + "phase": "llm" + }, + { + "message": "Resolving 1 term in VFB", + "phase": "mcp" + }, + { + "message": "Reading VFB term info", + "phase": "mcp" + }, + { + "message": "Summarising neuron taxonomy", + "phase": "mcp" + }, + { + "message": "Checking the answer is covered", + "phase": "llm" + }, + { + "message": "Writing the answer", + "phase": "llm" + } + ], + "event_count": 53, + "ok": true, + "request_id": "6c1ecfd1-2740-4980-9eb6-0283ec67ce7a", + "response_id": "chatcmpl-b3e0d632c38ceec65fad53aecdcb3645", + "images_count": 0, + "graphs_count": 0, + "response": "The question about the number of distinct neuron types in the adult Drosophila visual system and their hierarchical organization cannot be fully answered from VFB evidence. However, it is known that there are subclasses of visual system neuron.", + "quality_flags": { + "has_tool_status": true, + "no_tool_factual_answer": false, + "tool_claim_without_tool": false, + "disambiguation_only_answer": false, + "investigation_plan_answer": false, + "not_verified_or_no_results_answer": false, + "graph_failure_mentioned": false, + "missing_required_graph": false, + "used_data_resource": false, + "response_chars": 244, + "status_count": 7 + } + }, + { + "attempt_index": 19, + "task_index": 19, + "task_id": "T3.4", + "tier": 3, + "title": "Connectivity strength comparison", + "question": "Which neuron type provides the strongest synaptic input to the MBON-gamma1pedc>a/b neuron, and how does this compare to the next strongest inputs?", + "requires_graph": false, + "min_graphs": 0, + "repetition": 1, + "duration_ms": 10747, + "status_messages": [ + { + "message": "Thinking...", + "phase": "llm" + }, + { + "message": "Planning the answer", + "phase": "llm" + }, + { + "message": "Resolving 1 term in VFB", + "phase": "mcp" + }, + { + "message": "Querying VFB connectivity", + "phase": "mcp" + }, + { + "message": "Checking the literature", + "phase": "mcp" + }, + { + "message": "Checking the answer is covered", + "phase": "llm" + }, + { + "message": "Querying VFB", + "phase": "mcp" + }, + { + "message": "Checking the answer is covered", + "phase": "llm" + }, + { + "message": "Writing the answer", + "phase": "llm" + } + ], + "event_count": 51, + "ok": true, + "request_id": "29df1b22-259f-411e-861f-02ed981c9f56", + "response_id": "chatcmpl-e88ba1b4e2b65b76c8790ba59bf33c66", + "images_count": 8, + "graphs_count": 0, + "response": "The strongest synaptic input to the MBON-gamma1pedc>a/b neuron is not specified. VFB holds upstream connectivity classes for [mushroom body output neuron 11](https://www.virtualflybrain.org/reports/FBbt_00100246 \"Open mushroom body output neuron 11 in Virtual Fly Brain\"), but the lookup did not complete.", + "quality_flags": { + "has_tool_status": true, + "no_tool_factual_answer": false, + "tool_claim_without_tool": false, + "disambiguation_only_answer": false, + "investigation_plan_answer": false, + "not_verified_or_no_results_answer": false, + "graph_failure_mentioned": false, + "missing_required_graph": false, + "used_data_resource": false, + "response_chars": 305, + "status_count": 9 + } + }, + { + "attempt_index": 20, + "task_index": 20, + "task_id": "T3.5", + "tier": 3, + "title": "Shared connectivity", + "question": "Do the alpha/beta and gamma Kenyon cells converge on any of the same downstream MBON types? Which MBONs receive input from both?", + "requires_graph": false, + "min_graphs": 0, + "repetition": 1, + "duration_ms": 13869, + "status_messages": [ + { + "message": "Thinking...", + "phase": "llm" + }, + { + "message": "Planning the answer", + "phase": "llm" + }, + { + "message": "Resolving 3 terms in VFB", + "phase": "mcp" + }, + { + "message": "Querying VFB connectivity", + "phase": "mcp" + }, + { + "message": "Checking the answer is covered", + "phase": "llm" + }, + { + "message": "Querying VFB", + "phase": "mcp" + }, + { + "message": "Querying VFB", + "phase": "mcp" + }, + { + "message": "Checking the answer is covered", + "phase": "llm" + }, + { + "message": "Writing the answer", + "phase": "llm" + } + ], + "event_count": 79, + "ok": true, + "request_id": "3ed0d5a4-2483-4153-adc0-6e7807339e47", + "response_id": "chatcmpl-5b7a312d7d1c63e9aff6fb30cf0b760e", + "images_count": 8, + "graphs_count": 0, + "response": "The evidence does not provide information on whether the alpha/beta and gamma Kenyon cells converge on the same downstream [mushroom body output neuron](https://www.virtualflybrain.org/reports/FBbt_00047953 \"Open mushroom body output neuron in Virtual Fly Brain\") types. VFB does not currently hold data on the downstream connectivity classes for gamma Kenyon cells. VFB holds [69](https://v2.virtualflybrain.org/org.geppetto.frontend/geppetto?q=FBbt_00047953,SubclassesOf \"Run in VFB: Subclasses of MBON\") subclasses of mushroom body output neuron and [6](https://v2.virtualflybrain.org/org.geppetto.frontend/geppetto?q=FBbt_00100248,SubclassesOf \"Run in VFB: Subclasses of KCab\") subclasses of [alpha/beta Kenyon cell](https://www.virtualflybrain.org/reports/FBbt_00100248 \"Open alpha/beta Kenyon cell in Virtual Fly Brain\").", + "quality_flags": { + "has_tool_status": true, + "no_tool_factual_answer": false, + "tool_claim_without_tool": false, + "disambiguation_only_answer": false, + "investigation_plan_answer": false, + "not_verified_or_no_results_answer": false, + "graph_failure_mentioned": false, + "missing_required_graph": false, + "used_data_resource": false, + "response_chars": 827, + "status_count": 9 + } + }, + { + "attempt_index": 21, + "task_index": 21, + "task_id": "T3.6", + "tier": 3, + "title": "Anatomical containment chain", + "question": "Trace the anatomical containment hierarchy from the DA1 glomerulus up to the top-level brain structure. What is each level in the hierarchy?", + "requires_graph": false, + "min_graphs": 0, + "repetition": 1, + "duration_ms": 10780, + "status_messages": [ + { + "message": "Thinking...", + "phase": "llm" + }, + { + "message": "Planning the answer", + "phase": "llm" + }, + { + "message": "Resolving 1 term in VFB", + "phase": "mcp" + }, + { + "message": "Tracing the pathway", + "phase": "mcp" + }, + { + "message": "Querying VFB", + "phase": "mcp" + }, + { + "message": "Checking the answer is covered", + "phase": "llm" + }, + { + "message": "Writing the answer", + "phase": "llm" + } + ], + "event_count": 92, + "ok": true, + "request_id": "eb74e3ea-d13d-43cc-8b4c-c7507452e827", + "response_id": "chatcmpl-7855b42a02d885879ec9b398f4db0bbf", + "images_count": 0, + "graphs_count": 0, + "response": "The anatomical containment hierarchy from the DA1 glomerulus up to the top-level brain structure is: DA1 glomerulus -> adult olfactory antennal lobe glomerulus -> adult antennal lobe -> adult deutocerebrum -> adult cerebrum -> adult central brain -> adult brain. VFB does not currently hold data on parts of the [antennal lobe glomerulus DA1](https://www.virtualflybrain.org/reports/FBbt_00003932 \"Open antennal lobe glomerulus DA1 in Virtual Fly Brain\").", + "quality_flags": { + "has_tool_status": true, + "no_tool_factual_answer": false, + "tool_claim_without_tool": false, + "disambiguation_only_answer": false, + "investigation_plan_answer": false, + "not_verified_or_no_results_answer": false, + "graph_failure_mentioned": false, + "missing_required_graph": false, + "used_data_resource": false, + "response_chars": 455, + "status_count": 7 + } + }, + { + "attempt_index": 22, + "task_index": 22, + "task_id": "T3.7", + "tier": 3, + "title": "Cross-region connectivity", + "question": "What neuron types connect the central complex to the lateral accessory lobe, and how strong are these connections?", + "requires_graph": false, + "min_graphs": 0, + "repetition": 1, + "duration_ms": 16915, + "status_messages": [ + { + "message": "Thinking...", + "phase": "llm" + }, + { + "message": "Planning the answer", + "phase": "llm" + }, + { + "message": "Resolving 2 terms in VFB", + "phase": "mcp" + }, + { + "message": "Tracing the pathway", + "phase": "mcp" + }, + { + "message": "Querying VFB", + "phase": "mcp" + }, + { + "message": "Querying VFB", + "phase": "mcp" + }, + { + "message": "Checking the answer is covered", + "phase": "llm" + }, + { + "message": "Querying VFB", + "phase": "mcp" + }, + { + "message": "Querying VFB", + "phase": "mcp" + }, + { + "message": "Checking the answer is covered", + "phase": "llm" + }, + { + "message": "Writing the answer", + "phase": "llm" + } + ], + "event_count": 134, + "ok": true, + "request_id": "2dacdca2-d66d-4cce-a71d-695c3876df95", + "response_id": "chatcmpl-4209df9056541f6172d6da592f9b4fb0", + "images_count": 8, + "graphs_count": 0, + "response": "PFL classes are central-complex-related neuron classes connecting the [adult central complex](https://www.virtualflybrain.org/reports/FBbt_00003632 \"Open adult central complex in Virtual Fly Brain\") to the [lateral accessory lobe on L3 CNS template, Wood2018](https://www.virtualflybrain.org/reports/VFB_00050314 \"Open lateral accessory lobe on L3 CNS template, Wood2018 in Virtual Fly Brain\"). VFB records show that neurons such as [PEN_PB2](https://www.virtualflybrain.org/reports/FBbt_00111369 \"Open PEN_PB2 in Virtual Fly Brain\"), [PEN_PB3](https://www.virtualflybrain.org/reports/FBbt_00111370 \"Open PEN_PB3 in Virtual Fly Brain\"), [PEN_PB7](https://www.virtualflybrain.org/reports/FBbt_00111373 \"Open PEN_PB7 in Virtual Fly Brain\"), [PEN_PB8](https://www.virtualflybrain.org/reports/FBbt_00111374 \"Open PEN_PB8 in Virtual Fly Brain\"), and several adult protocerebral bridge glomerulus neurons have some part in the adult central complex and have synaptic terminals there. However, the strength of these connections is not specified. VFB does not currently hold data on neurons with presynaptic or postsynaptic terminals in the embryonic/larval lateral accessory lobe.", + "quality_flags": { + "has_tool_status": true, + "no_tool_factual_answer": false, + "tool_claim_without_tool": false, + "disambiguation_only_answer": false, + "investigation_plan_answer": false, + "not_verified_or_no_results_answer": false, + "graph_failure_mentioned": false, + "missing_required_graph": false, + "used_data_resource": false, + "response_chars": 1173, + "status_count": 11 + } + }, + { + "attempt_index": 23, + "task_index": 23, + "task_id": "T3.8", + "tier": 3, + "title": "Dataset coverage", + "question": "For the DNa02 descending neuron type, what data is available in VFB? Is it in the Hemibrain, FAFB, or both? Are there light microscopy images and driver lines?", + "requires_graph": false, + "min_graphs": 0, + "repetition": 1, + "ok": false, + "duration_ms": null, + "error": "Timed out after 240000 ms", + "quality_flags": { + "has_tool_status": false, + "no_tool_factual_answer": false, + "tool_claim_without_tool": false, + "disambiguation_only_answer": false, + "investigation_plan_answer": false, + "not_verified_or_no_results_answer": false, + "graph_failure_mentioned": false, + "missing_required_graph": false, + "used_data_resource": false, + "response_chars": 25, + "status_count": 0 + } + }, + { + "attempt_index": 24, + "task_index": 24, + "task_id": "T4.1", + "tier": 4, + "title": "Experimental planning", + "question": "I want to study the neural circuit underlying CO2 avoidance in Drosophila. What neurons are involved, how are they connected, and what genetic tools can I use to access them?", + "requires_graph": false, + "min_graphs": 0, + "repetition": 1, + "duration_ms": 9429, + "status_messages": [ + { + "message": "Thinking...", + "phase": "llm" + }, + { + "message": "Planning the answer", + "phase": "llm" + }, + { + "message": "Resolving 1 term in VFB", + "phase": "mcp" + }, + { + "message": "Querying VFB", + "phase": "mcp" + }, + { + "message": "Checking the answer is covered", + "phase": "llm" + }, + { + "message": "Writing the answer", + "phase": "llm" + } + ], + "event_count": 92, + "ok": true, + "request_id": "aebf3410-a0d5-46f2-a4ae-1b8beb87cb61", + "response_id": "chatcmpl-40349a259b65ebbb5f5699c7d8d173ff", + "images_count": 0, + "graphs_count": 0, + "response": "The neurons involved in the detection of carbon dioxide include carbon dioxide sensitive neurons. These neurons have downstream connections to GABAergic local interneuron of the adult antennal lobe, adult antennal lobe local neuron lLN2P, and cholinergic local interneuron of the adult antennal lobe. Genetic tools for accessing these neurons include Gr21a, Gr63a, and E409 expression patterns.", + "quality_flags": { + "has_tool_status": true, + "no_tool_factual_answer": false, + "tool_claim_without_tool": false, + "disambiguation_only_answer": false, + "investigation_plan_answer": false, + "not_verified_or_no_results_answer": false, + "graph_failure_mentioned": false, + "missing_required_graph": false, + "used_data_resource": false, + "response_chars": 394, + "status_count": 6 + } + }, + { + "attempt_index": 25, + "task_index": 25, + "task_id": "T4.2", + "tier": 4, + "title": "Complete neuron profile", + "question": "Give me a comprehensive profile of the giant fiber neuron: its anatomy, connectivity, available driver lines, and relevant publications.", + "requires_graph": false, + "min_graphs": 0, + "repetition": 1, + "duration_ms": 19842, + "status_messages": [ + { + "message": "Thinking...", + "phase": "llm" + }, + { + "message": "Planning the answer", + "phase": "llm" + }, + { + "message": "Resolving 1 term in VFB", + "phase": "mcp" + }, + { + "message": "Querying VFB", + "phase": "mcp" + }, + { + "message": "Querying VFB connectivity", + "phase": "mcp" + }, + { + "message": "Querying VFB", + "phase": "mcp" + }, + { + "message": "Checking the literature", + "phase": "mcp" + }, + { + "message": "Checking the answer is covered", + "phase": "llm" + }, + { + "message": "Writing the answer", + "phase": "llm" + } + ], + "event_count": 363, + "ok": true, + "request_id": "9034886c-39cb-4790-ad56-c809f112cad0", + "response_id": "chatcmpl-38979a4c7f39098899c629a476ca2cae", + "images_count": 8, + "graphs_count": 1, + "response": "The [giant fiber neuron](https://www.virtualflybrain.org/reports/FBbt_00004020 \"Open giant fiber neuron in Virtual Fly Brain\") is a large adult descending neuron that controls jump escape behavior. Its downstream connectivity classes for DNp01 include [389](https://v2.virtualflybrain.org/org.geppetto.frontend/geppetto?q=FBbt_00004020,DownstreamClassConnectivity \"Run in VFB: Downstream connectivity classes for DNp01\") entries, and its upstream connectivity classes for DNp01 include [472](https://v2.virtualflybrain.org/org.geppetto.frontend/geppetto?q=FBbt_00004020,UpstreamClassConnectivity \"Run in VFB: Upstream connectivity classes for DNp01\") entries. The giant fiber neuron connects to various neuron types, including [adult VNC neuron](https://www.virtualflybrain.org/reports/FBbt_00059289 \"Open adult VNC neuron in Virtual Fly Brain\"), [thoracic neuron](https://www.virtualflybrain.org/reports/FBbt_00001983 \"Open thoracic neuron in Virtual Fly Brain\"), [mesothoracic neuron](https://www.virtualflybrain.org/reports/FBbt_00001985 \"Open mesothoracic neuron in Virtual Fly Brain\"), [primary neuron](https://www.virtualflybrain.org/reports/FBbt_00047097 \"Open primary neuron in Virtual Fly Brain\"), [Notch OFF hemilineage secondary neuron](https://www.virtualflybrain.org/reports/FBbt_00049542 \"Open Notch OFF hemilineage secondary neuron in Virtual Fly Brain\"), [prothoracic neuron](https://www.virtualflybrain.org/reports/FBbt_00001984 \"Open prothoracic neuron in Virtual Fly Brain\"), [Notch ON hemilineage secondary neuron](https://www.virtualflybrain.org/reports/FBbt_00049541 \"Open Notch ON hemilineage secondary neuron in Virtual Fly Brain\"), [adult ascending neuron](https://www.virtualflybrain.org/reports/FBbt_00048301 \"Open adult ascending neuron in Virtual Fly Brain\"), [sensory system neuron](https://www.virtualflybrain.org/reports/FBbt_00007693 \"Open sensory system neuron in Virtual Fly Brain\"), [projection neuron](https://www.virtualflybrain.org/reports/FBbt_00007392 \"Open projection neuron in Virtual Fly Brain\"), [Notch OFF hemilineage primary neuron](https://www.virtualflybrain.org/reports/FBbt_00047105 \"Open Notch OFF hemilineage primary neuron in Virtual Fly Brain\"), and [adult visual projection neuron](https://www.virtualflybrain.org/reports/FBbt_00048286 \"Open adult visual projection neuron in Virtual Fly Brain\").\n\nThere are [10](https://v2.virtualflybrain.org/org.geppetto.frontend/geppetto?q=FBbt_00004020,TransgeneExpressionHere \"Run in VFB: Transgene expression in DNp01\") transgene expression patterns available for DNp01, including [P{GMR78G07-GAL4} expression pattern](https://www.virtualflybrain.org/reports/VFBexp_FBtp0062972 \"Open P{GMR78G07-GAL4} expression pattern in Virtual Fly Brain\"), [P{GMR79D08-GAL4} expression pattern](https://www.virtualflybrain.org/reports/VFBexp_FBtp0063022 \"Open P{GMR79D08-GAL4} expression pattern in Virtual Fly Brain\"), [P{GMR91H05-GAL4} expression pattern](https://www.virtualflybrain.org/reports/VFBexp_FBtp0064022 \"Open P{GMR91H05-GAL4} expression pattern in Virtual Fly Brain\"), [P{R48A11-GAL4.DBD} ∩ P{R30C01-p65.AD} expression pattern](https://www.virtualflybrain.org/reports/VFBexp_FBtp0121835FBtp0118557 \"Open P{R48A11-GAL4.DBD} ∩ P{R30C01-p65.AD} expression pattern in Virtual Fly Brain\"), [P{R68A06-GAL4.DBD} ∩ P{R25C08-p65.AD} expression pattern](https://www.virtualflybrain.org/reports/VFBexp_FBtp0116198FBtp0118471 \"Open P{R68A06-GAL4.DBD} ∩ P{R25C08-p65.AD} expression pattern in Virtual Fly Brain\"), [P{R79H02-GAL4.DBD} ∩ P{R14A01-p65.AD} expression pattern](https://www.virtualflybrain.org/reports/VFBexp_FBtp0122311FBtp0118233 \"Open P{R79H02-GAL4.DBD} ∩ P{R14A01-p65.AD} expression pattern in Virtual Fly Brain\"), [P{R79H02-GAL4.DBD} ∩ P{R25C08-p65.AD} expression pattern](https://www.virtualflybrain.org/reports/VFBexp_FBtp0122311FBtp0118471 \"Open P{R79H02-GAL4.DBD} ∩ P{R25C08-p65.AD} expression pattern in Virtual Fly Brain\"), [P{VT004455-GAL4.DBD} ∩ P{R10A12-p65.AD} expression pattern](https://www.virtualflybrain.org/reports/VFBexp_FBtp0122730FBtp0118153 \"Open P{VT004455-GAL4.DBD} ∩ P{R10A12-p65.AD} expression pattern in Virtual Fly Brain\"), P{VT014708-GAL4} expression pattern, and P{VT046265-GAL4} expression pattern.\n\nThe giant fiber neuron is described in the publication by Thomas and Wyman (1984).", + "graphs": [ + { + "type": "basic_graph", + "version": 1, + "title": "Downstream partners of DNp01", + "directed": true, + "layout": "circle", + "nodes": [ + { + "id": "FBbt_00004020", + "label": "DNp01", + "group": null, + "color": null, + "size": 4 + }, + { + "id": "FBbt_00047095", + "label": "adult neuron", + "group": null, + "color": null, + "size": 1.48 + }, + { + "id": "FBbt_00005106", + "label": "neuron", + "group": null, + "color": null, + "size": 1.48 + }, + { + "id": "FBbt_00059271", + "label": "CNS neuron", + "group": null, + "color": null, + "size": 1.47 + }, + { + "id": "FBbt_00059289", + "label": "adult VNC neuron", + "group": null, + "color": null, + "size": 1.31 + }, + { + "id": "FBbt_00001983", + "label": "thoracic neuron", + "group": null, + "color": null, + "size": 1.31 + }, + { + "id": "FBbt_00001985", + "label": "mesothoracic neuron", + "group": null, + "color": null, + "size": 1.19 + }, + { + "id": "FBbt_00047097", + "label": "primary neuron", + "group": null, + "color": null, + "size": 1.13 + }, + { + "id": "FBbt_00049542", + "label": "Notch OFF hemilineage secondary neuron", + "group": null, + "color": null, + "size": 1.13 + }, + { + "id": "FBbt_00001984", + "label": "prothoracic 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visual system and the mushroom body? Could visual information reach the memory circuit?", + "requires_graph": false, + "min_graphs": 0, + "repetition": 1, + "duration_ms": 17548, + "status_messages": [ + { + "message": "Thinking...", + "phase": "llm" + }, + { + "message": "Planning the answer", + "phase": "llm" + }, + { + "message": "Resolving 2 terms in VFB", + "phase": "mcp" + }, + { + "message": "Tracing the pathway", + "phase": "mcp" + }, + { + "message": "Querying VFB connectivity", + "phase": "mcp" + }, + { + "message": "Checking the answer is covered", + "phase": "llm" + }, + { + "message": "Querying VFB", + "phase": "mcp" + }, + { + "message": "Querying VFB", + "phase": "mcp" + }, + { + "message": "Checking the answer is covered", + "phase": "llm" + }, + { + "message": "Writing the answer", + "phase": "llm" + } + ], + "event_count": 178, + "ok": true, + "request_id": "274deef7-044d-4499-8ae1-48ebdc17526d", + "response_id": "chatcmpl-be3a1ce126d973dc05a873bd90752385", + "images_count": 8, + "graphs_count": 1, + "response": "Based on connectivity data, adult visual projection neurons might mediate the connection between the visual system and the [mushroom body](https://www.virtualflybrain.org/reports/FBbt_00005801 \"Open mushroom body in Virtual Fly Brain\"), as they have presynaptic terminals in the mushroom body. Projection neurons are also suggested to mediate this connection. The strongest specific inputs to [visual system neuron](https://www.virtualflybrain.org/reports/FBbt_00047736 \"Open visual system neuron in Virtual Fly Brain\") include [optic lobe narrow field columnar neuron](https://www.virtualflybrain.org/reports/FBbt_00110136 \"Open optic lobe narrow field columnar neuron in Virtual Fly Brain\"), [optic lobe intrinsic columnar neuron](https://www.virtualflybrain.org/reports/FBbt_00007578 \"Open optic lobe intrinsic columnar neuron in Virtual Fly Brain\"), [adult optic lobe neuron](https://www.virtualflybrain.org/reports/FBbt_00003702 \"Open adult optic lobe neuron in Virtual Fly Brain\"), and [adult optic lobe columnar neuron](https://www.virtualflybrain.org/reports/FBbt_00005129 \"Open adult optic lobe columnar neuron in Virtual Fly Brain\"). The strongest specific targets of visual system neuron include adult optic lobe neuron, [optic lobe wide-field columnar neuron](https://www.virtualflybrain.org/reports/FBbt_00110137 \"Open optic lobe wide-field columnar neuron in Virtual Fly Brain\"), adult optic lobe columnar neuron, optic lobe intrinsic columnar neuron, and [adult visual projection neuron](https://www.virtualflybrain.org/reports/FBbt_00048286 \"Open adult visual projection neuron in Virtual Fly Brain\"). Visual information could reach the memory circuit through these connections. VFB holds [602](https://v2.virtualflybrain.org/org.geppetto.frontend/geppetto?q=FBbt_00005801,NeuronsPartHere \"Run in VFB: Neurons with some part in mushroom body\") neurons with some part in mushroom body and [601](https://v2.virtualflybrain.org/org.geppetto.frontend/geppetto?q=FBbt_00005801,NeuronsSynaptic \"Run in VFB: Neurons with synaptic terminals in mushroom body\") neurons with synaptic terminals in mushroom body.", + "graphs": [ + { + "type": "basic_graph", + "version": 1, + "title": "Downstream partners of visual system neuron", + "directed": true, + "layout": "circle", + "nodes": [ + { + "id": "FBbt_00047736", + "label": "visual system neuron", + "group": null, + "color": null, + "size": 4 + }, + { + "id": "FBbt_00005106", + "label": "neuron", + "group": null, + "color": null, + "size": 1.33 + }, + { + "id": "FBbt_00047095", + "label": "adult neuron", + "group": null, + "color": null, + "size": 1.33 + }, + { + "id": "FBbt_00059271", + "label": "CNS neuron", + "group": null, + "color": null, + "size": 1.33 + }, + { + "id": "FBbt_00007693", + "label": "sensory system neuron", + "group": null, + "color": null, + "size": 1.31 + }, + { + "id": "FBbt_00005129", + "label": "adult optic lobe columnar neuron", + "group": null, + "color": null, + "size": 1.22 + }, + { + "id": "FBbt_00003702", + "label": "adult optic lobe neuron", + "group": null, + "color": null, + "size": 1.22 + }, + { + "id": "FBbt_00007578", + "label": "optic lobe intrinsic columnar neuron", + "group": null, + "color": null, + "size": 1.16 + }, + { + "id": "FBbt_00110137", + "label": "optic lobe wide-field columnar neuron", + "group": null, + "color": null, + "size": 1.08 + }, + { + "id": "FBbt_00007392", + "label": "projection neuron", + "group": null, + "color": null, + "size": 1.08 + }, + { + "id": "FBbt_00048287", + "label": "visual projection neuron", + "group": null, + "color": null, + "size": 1.08 + }, + { + "id": "FBbt_00048286", + "label": "adult visual projection neuron", + "group": null, + "color": null, + "size": 1.08 + }, + { + "id": "FBbt_00003788", + "label": "transmedullary neuron", + "group": null, + "color": null, + "size": 1.07 + }, + { + "id": "FBbt_00110136", + "label": "optic lobe narrow field columnar neuron", + "group": null, + "color": null, + "size": 1.06 + }, + { + "id": "FBbt_00049542", + "label": "Notch OFF hemilineage secondary neuron", + "group": null, + "color": null, + "size": 1.05 + } + ], + "edges": [ + { + "source": "FBbt_00047736", + "target": "FBbt_00005106", + "label": "52519700", + "weight": 1000000 + }, + { + "source": "FBbt_00047736", + "target": "FBbt_00047095", + "label": "52515264", + "weight": 1000000 + }, + { + "source": "FBbt_00047736", + "target": "FBbt_00059271", + "label": "52026280", + "weight": 1000000 + }, + { + "source": "FBbt_00047736", + "target": "FBbt_00007693", + "label": "49149406", + "weight": 1000000 + }, + { + "source": "FBbt_00047736", + "target": "FBbt_00047736", + "label": "49133005", + "weight": 1000000 + }, + { + "source": "FBbt_00047736", + "target": "FBbt_00005129", + "label": "34860032", + "weight": 1000000 + }, + { + "source": "FBbt_00047736", + "target": "FBbt_00003702", + "label": "34548245", + "weight": 1000000 + }, + { + "source": "FBbt_00047736", + "target": "FBbt_00007578", + "label": "24889906", + "weight": 1000000 + }, + { + "source": "FBbt_00047736", + "target": "FBbt_00110137", + "label": "12826675", + "weight": 1000000 + }, + { + "source": "FBbt_00047736", + "target": "FBbt_00007392", + "label": "12324568", + "weight": 1000000 + }, + { + "source": "FBbt_00047736", + "target": "FBbt_00048287", + "label": "12309806", + "weight": 1000000 + }, + { + "source": "FBbt_00047736", + "target": "FBbt_00048286", + "label": "12308357", + "weight": 1000000 + }, + { + "source": "FBbt_00047736", + "target": "FBbt_00003788", + "label": "11821502", + "weight": 1000000 + }, + { + "source": "FBbt_00047736", + "target": "FBbt_00110136", + "label": "8919227", + "weight": 1000000 + }, + { + "source": "FBbt_00047736", + "target": "FBbt_00049542", + "label": "8358929", + "weight": 1000000 + } + ] + } + ], + "quality_flags": { + "has_tool_status": true, + "no_tool_factual_answer": false, + "tool_claim_without_tool": false, + "disambiguation_only_answer": false, + "investigation_plan_answer": false, + "not_verified_or_no_results_answer": false, + "graph_failure_mentioned": false, + "missing_required_graph": false, + "used_data_resource": false, + "response_chars": 2117, + "status_count": 10 + } + }, + { + "attempt_index": 27, + "task_index": 27, + "task_id": "T4.4", + "tier": 4, + "title": "Comparative analysis", + "question": "Compare the downstream targets of the two main types of clock neurons (s-LNv and l-LNv). Do they converge on any common target neuron types?", + "requires_graph": false, + "min_graphs": 0, + "repetition": 1, + "duration_ms": 12275, + "status_messages": [ + { + "message": "Thinking...", + "phase": "llm" + }, + { + "message": "Planning the answer", + "phase": "llm" + }, + { + "message": "Resolving 2 terms in VFB", + "phase": "mcp" + }, + { + "message": "Querying VFB connectivity", + "phase": "mcp" + }, + { + "message": "Checking the answer is covered", + "phase": "llm" + }, + { + "message": "Querying VFB", + "phase": "mcp" + }, + { + "message": "Querying VFB", + "phase": "mcp" + }, + { + "message": "Checking the answer is covered", + "phase": "llm" + }, + { + "message": "Writing the answer", + "phase": "llm" + } + ], + "event_count": 90, + "ok": true, + "request_id": "48c7133c-c0b9-4ad1-b9f8-ca959f38df43", + "response_id": "chatcmpl-2409d82373b95e2d1ebd6b5ec616acd9", + "images_count": 8, + "graphs_count": 1, + "response": "The downstream targets of [l-LNv neuron](https://www.virtualflybrain.org/reports/FBbt_00003763 \"Open l-LNv neuron in Virtual Fly Brain\") include [adult visual projection neuron](https://www.virtualflybrain.org/reports/FBbt_00048286 \"Open adult visual projection neuron in Virtual Fly Brain\"), [sensory system neuron](https://www.virtualflybrain.org/reports/FBbt_00007693 \"Open sensory system neuron in Virtual Fly Brain\"), [Notch ON hemilineage secondary neuron](https://www.virtualflybrain.org/reports/FBbt_00049541 \"Open Notch ON hemilineage secondary neuron in Virtual Fly Brain\"), [optic lobe narrow field columnar neuron](https://www.virtualflybrain.org/reports/FBbt_00110136 \"Open optic lobe narrow field columnar neuron in Virtual Fly Brain\"), [optic lobe intrinsic columnar neuron](https://www.virtualflybrain.org/reports/FBbt_00007578 \"Open optic lobe intrinsic columnar neuron in Virtual Fly Brain\"), [adult optic lobe neuron](https://www.virtualflybrain.org/reports/FBbt_00003702 \"Open adult optic lobe neuron in Virtual Fly Brain\"), and [adult optic lobe columnar neuron](https://www.virtualflybrain.org/reports/FBbt_00005129 \"Open adult optic lobe columnar neuron in Virtual Fly Brain\"). VFB does not currently hold data on the downstream connectivity classes for [adult s-LNv neuron](https://www.virtualflybrain.org/reports/FBbt_00007428 \"Open adult s-LNv neuron in Virtual Fly Brain\").", + "graphs": [ + { + "type": "basic_graph", + "version": 1, + "title": "Downstream targets by source class", + "directed": true, + "layout": "circle", + "nodes": [ + { + "id": "FBbt_00003763", + "label": "l-LNv", + "group": null, + "color": null, + "size": 4 + }, + { + "id": "FBbt_00005106", + "label": "neuron", + "group": null, + "color": null, + "size": 1.17 + }, + { + "id": "FBbt_00047095", + "label": "adult neuron", + "group": null, + "color": null, + "size": 1.17 + }, + { + "id": "FBbt_00059271", + "label": "CNS neuron", + "group": null, + "color": null, + "size": 1.17 + }, + { + "id": "FBbt_00059274", + "label": "adult CNS neuron", + "group": null, + "color": null, + "size": 1.17 + }, + { + "id": "FBbt_00007693", + "label": "sensory system neuron", + "group": null, + "color": null, + "size": 1.17 + }, + { + "id": "FBbt_00047736", + "label": "visual system neuron", + "group": null, + "color": null, + "size": 1.17 + }, + { + "id": "FBbt_00005125", + "label": "interneuron", + "group": null, + "color": null, + "size": 1.16 + }, + { + "id": "FBbt_00052046", + "label": "adult interneuron", + "group": null, + "color": null, + "size": 1.16 + }, + { + "id": "FBbt_00001366", + "label": "supraesophageal ganglion neuron", + "group": null, + "color": null, + "size": 1.16 + }, + { + "id": "FBbt_00003702", + "label": "adult optic lobe neuron", + "group": null, + "color": null, + "size": 1.15 + }, + { + "id": "FBbt_00059247", + "label": "adult visual neuropil intrinsic neuron", + "group": null, + "color": null, + "size": 1.15 + }, + { + "id": "FBbt_00007577", + "label": "adult optic lobe intrinsic neuron", + "group": null, + "color": null, + "size": 1.15 + }, + { + "id": "FBbt_00007173", + "label": "cholinergic neuron", + "group": null, + "color": null, + "size": 1.14 + }, + { + "id": "FBbt_00058205", + "label": "adult cholinergic neuron", + "group": null, + "color": null, + "size": 1.14 + }, + { + "id": "FBbt_00005129", + "label": "adult optic lobe columnar neuron", + "group": null, + "color": null, + "size": 1.14 + }, + { + "id": "FBbt_00007578", + "label": "optic lobe intrinsic columnar neuron", + "group": null, + "color": null, + "size": 1.14 + }, + { + "id": "FBbt_00047096", + "label": "secondary neuron", + "group": null, + "color": null, + "size": 1.13 + }, + { + "id": "FBbt_00110136", + "label": "optic lobe narrow field columnar neuron", + "group": null, + "color": null, + "size": 1.13 + }, + { + "id": "FBbt_00049539", + "label": "Notch ON hemilineage neuron", + "group": null, + "color": null, + "size": 1.13 + }, + { + "id": "FBbt_00049541", + "label": "Notch ON hemilineage secondary neuron", + "group": null, + "color": null, + "size": 1.13 + } + ], + "edges": [ + { + "source": "FBbt_00003763", + "target": "FBbt_00005106", + "label": "6184", + 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"quality_flags": { + "has_tool_status": true, + "no_tool_factual_answer": false, + "tool_claim_without_tool": false, + "disambiguation_only_answer": false, + "investigation_plan_answer": false, + "not_verified_or_no_results_answer": false, + "graph_failure_mentioned": false, + "missing_required_graph": false, + "used_data_resource": false, + "response_chars": 1400, + "status_count": 9 + } + }, + { + "attempt_index": 28, + "task_index": 28, + "task_id": "T4.5", + "tier": 4, + "title": "Novel circuit exploration", + "question": "What is the connectivity between thermosensory neurons and the mushroom body? Could temperature information influence memory formation?", + "requires_graph": false, + "min_graphs": 0, + "repetition": 1, + "duration_ms": 76749, + "status_messages": [ + { + "message": "Thinking...", + "phase": "llm" + }, + { + "message": "Planning the answer", + "phase": "llm" + }, + { + "message": "Resolving 2 terms in VFB", + "phase": "mcp" + }, + { + "message": "Tracing the pathway", + "phase": "mcp" + }, + { + "message": "Querying VFB connectivity", + "phase": "mcp" + }, + { + "message": "Querying VFB", + "phase": "mcp" + }, + { + "message": "Querying VFB", + "phase": "mcp" + }, + { + "message": "Checking the answer is covered", + "phase": "llm" + }, + { + "message": "Querying VFB", + "phase": "mcp" + }, + { + "message": "Querying VFB", + "phase": "mcp" + }, + { + "message": "Checking the answer is covered", + "phase": "llm" + }, + { + "message": "Writing the answer", + "phase": "llm" + } + ], + "event_count": 159, + "ok": true, + "request_id": "2d7694e9-77e6-4ee1-912d-42d7b4fd0620", + "response_id": "chatcmpl-92f6788bd5fdbf2cb566737e799fbf9e", + "images_count": 8, + "graphs_count": 1, + "response": "Thermosensory neurons connect to the [mushroom body](https://www.virtualflybrain.org/reports/FBbt_00005801 \"Open mushroom body in Virtual Fly Brain\"). The strongest specific targets of [thermosensory neuron](https://www.virtualflybrain.org/reports/FBbt_00005918 \"Open thermosensory neuron in Virtual Fly Brain\") include [projection neuron](https://www.virtualflybrain.org/reports/FBbt_00007392 \"Open projection neuron in Virtual Fly Brain\"), [adult antennal lobe projection neuron](https://www.virtualflybrain.org/reports/FBbt_00067123 \"Open adult antennal lobe projection neuron in Virtual Fly Brain\"), and [antennal lobe projection neuron](https://www.virtualflybrain.org/reports/FBbt_00007422 \"Open antennal lobe projection neuron in Virtual Fly Brain\"). Thermosensory neurons also receive input from [adult antennal lobe local neuron lLN2](https://www.virtualflybrain.org/reports/FBbt_00007396 \"Open adult antennal lobe local neuron lLN2 in Virtual Fly Brain\"), [unilateral local interneuron of the adult antennal lobe](https://www.virtualflybrain.org/reports/FBbt_00051503 \"Open unilateral local interneuron of the adult antennal lobe in Virtual Fly Brain\"), and [adult antennal lobe local neuron](https://www.virtualflybrain.org/reports/FBbt_00007390 \"Open adult antennal lobe local neuron in Virtual Fly Brain\").\n\nVFB records show [366](https://v2.virtualflybrain.org/org.geppetto.frontend/geppetto?q=FBbt_00005801,NeuronsPresynapticHere \"Run in VFB: Neurons with presynaptic terminals in mushroom body\") neurons with presynaptic terminals in mushroom body and [304](https://v2.virtualflybrain.org/org.geppetto.frontend/geppetto?q=FBbt_00005801,NeuronsPostsynapticHere \"Run in VFB: Neurons with postsynaptic terminals in mushroom body\") neurons with postsynaptic terminals in mushroom body. The connectivity between thermosensory neurons and the mushroom body could allow temperature information to influence memory formation, given the role of the mushroom body in memory and learning.", + "graphs": [ + { + "type": "basic_graph", + "version": 1, + "title": "Downstream partners of thermosensory neuron", + "directed": true, + "layout": "circle", + "nodes": [ + { + "id": "FBbt_00005918", + "label": "thermosensory neuron", + "group": null, + "color": null, + "size": 4 + }, + { + "id": "FBbt_00005106", + "label": "neuron", + "group": null, + "color": null, + "size": 1.4 + }, + { + "id": "FBbt_00047095", + "label": "adult neuron", + "group": null, + "color": null, + "size": 1.39 + }, + { + "id": "FBbt_00059271", + "label": "CNS neuron", + "group": null, + "color": null, + "size": 1.38 + }, + { + "id": "FBbt_00007392", + "label": "projection neuron", + "group": null, + "color": null, + "size": 1.22 + }, + { + "id": "FBbt_00007422", + "label": "antennal lobe projection neuron", + "group": null, + "color": null, + "size": 1.21 + }, + { + "id": "FBbt_00067123", + "label": "adult antennal lobe projection neuron", + "group": null, + "color": null, + "size": 1.21 + }, + { + "id": "FBbt_00051493", + "label": "local neuron", + "group": null, + "color": null, + "size": 1.15 + }, + { + "id": "FBbt_00052874", + "label": "antennal lobe local neuron", + "group": null, + "color": null, + "size": 1.15 + }, + { + "id": "FBbt_00007390", + "label": "adult antennal lobe local neuron", + "group": null, + "color": null, + "size": 1.15 + }, + { + "id": "FBbt_00007384", + "label": "multiglomerular antennal lobe projection neuron", + "group": null, + "color": null, + "size": 1.14 + }, + { + "id": "FBbt_00007441", + "label": "adult multiglomerular antennal lobe projection neuron", + "group": null, + "color": null, + "size": 1.14 + }, + { + "id": "FBbt_00049427", + "label": "adult lateral horn input neuron", + "group": null, + "color": null, + "size": 1.12 + }, + { + "id": "FBbt_00053398", + "label": "adult antennal lobe projection neuron to lateral horn", + "group": null, + "color": null, + "size": 1.12 + }, + { + "id": "FBbt_00053397", + "label": "antennal lobe projection neuron to mushroom body", + "group": null, + "color": null, + "size": 1.11 + }, + { + "id": "FBbt_00007394", + "label": "adult local interneuron of the lateral ALl1 neuroblast", + "group": null, + "color": null, + "size": 1.11 + } + ], + "edges": [ + { + "source": "FBbt_00005918", + "target": "FBbt_00005106", + "label": "78601", + "weight": 78601 + }, + { + "source": "FBbt_00005918", + "target": "FBbt_00047095", + "label": "77005", + "weight": 77005 + }, + { + "source": "FBbt_00005918", + "target": "FBbt_00059271", + "label": "75663", + "weight": 75663 + }, + { + "source": "FBbt_00005918", + "target": "FBbt_00007392", + "label": "42907", + "weight": 42907 + }, + { + "source": "FBbt_00005918", + "target": "FBbt_00007422", + "label": "41794", + "weight": 41794 + }, + { + "source": "FBbt_00005918", + "target": "FBbt_00067123", + "label": "41646", + "weight": 41646 + }, + { + "source": "FBbt_00005918", + "target": "FBbt_00051493", + "label": "30596", + "weight": 30596 + }, + { + "source": "FBbt_00005918", + "target": "FBbt_00052874", + "label": "30596", + "weight": 30596 + }, + { + "source": "FBbt_00005918", + "target": "FBbt_00007390", + "label": "30271", + "weight": 30271 + }, + { + "source": "FBbt_00005918", + "target": "FBbt_00007384", + "label": "27881", + "weight": 27881 + }, + { + "source": "FBbt_00005918", + "target": "FBbt_00007441", + "label": "27735", + "weight": 27735 + }, + { + "source": "FBbt_00005918", + "target": "FBbt_00049427", + "label": "24184", + "weight": 24184 + }, + { + "source": "FBbt_00005918", + "target": "FBbt_00053398", + "label": "24184", + "weight": 24184 + }, + { + "source": "FBbt_00005918", + "target": "FBbt_00053397", + "label": "22043", + "weight": 22043 + }, + { + "source": "FBbt_00005918", + "target": "FBbt_00007394", + "label": "21470", + "weight": 21470 + } + ] + } + ], + "quality_flags": { + "has_tool_status": true, + "no_tool_factual_answer": false, + "tool_claim_without_tool": false, + "disambiguation_only_answer": false, + "investigation_plan_answer": false, + "not_verified_or_no_results_answer": false, + "graph_failure_mentioned": false, + "missing_required_graph": false, + "used_data_resource": false, + "response_chars": 1993, + "status_count": 12 + } + }, + { + "attempt_index": 29, + "task_index": 29, + "task_id": "T4.6", + "tier": 4, + "title": "Data availability survey", + "question": "I'm interested in studying the subesophageal zone (SEZ). How well-characterised is this region in VFB? What neuron types are annotated, what connectomics data is available, and what genetic tools exist for SEZ neurons?", + "requires_graph": false, + "min_graphs": 0, + "repetition": 1, + "duration_ms": 203516, + "status_messages": [ + { + "message": "Thinking...", + "phase": "llm" + }, + { + "message": "Planning the answer", + "phase": "llm" + }, + { + "message": "Resolving 1 term in VFB", + "phase": "mcp" + }, + { + "message": "Reading VFB term info", + "phase": "mcp" + }, + { + "message": "Finding genetic tools", + "phase": "mcp" + }, + { + "message": "Querying VFB", + "phase": "mcp" + }, + { + "message": "Querying VFB", + "phase": "mcp" + }, + { + "message": "Checking the answer is covered", + "phase": "llm" + }, + { + "message": "Querying VFB", + "phase": "mcp" + }, + { + "message": "Querying VFB", + "phase": "mcp" + }, + { + "message": "Querying VFB", + "phase": "mcp" + }, + { + "message": "Checking the answer is covered", + "phase": "llm" + }, + { + "message": "Writing the answer", + "phase": "llm" + } + ], + "event_count": 245, + "ok": true, + "request_id": "80a3bd6d-3b2b-44f8-a205-fe553822f2e9", + "response_id": "chatcmpl-fe2b19e856859e1da09f8dc125a96634", + "images_count": 1, + "graphs_count": 0, + "response": "The [subesophageal zone](https://www.virtualflybrain.org/reports/FBbt_00051068 \"Open subesophageal zone in Virtual Fly Brain\") is a well-characterised region in VFB, with various neuron types annotated. VFB records show [2,698](https://v2.virtualflybrain.org/org.geppetto.frontend/geppetto?q=FBbt_00051068,NeuronsPartHere \"Run in VFB: Neurons with some part in subesophageal zone\") neurons with some part in the subesophageal zone, including [serotonergic SE1 neuron](https://www.virtualflybrain.org/reports/FBbt_00001980 \"Open serotonergic SE1 neuron in Virtual Fly Brain\") and [intrinsic antennal mechanosensory and motor center neuron](https://www.virtualflybrain.org/reports/FBbt_00111352 \"Open intrinsic antennal mechanosensory and motor center neuron in Virtual Fly Brain\"). There are also [2,598](https://v2.virtualflybrain.org/org.geppetto.frontend/geppetto?q=FBbt_00051068,NeuronsSynaptic \"Run in VFB: Neurons with synaptic terminals in subesophageal zone\") neurons with synaptic terminals in the subesophageal zone, such as [AMMC-VLP](https://www.virtualflybrain.org/reports/FBbt_00111354 \"Open AMMC-VLP in Virtual Fly Brain\") and [AMMC-Bi1](https://www.virtualflybrain.org/reports/FBbt_00111465 \"Open AMMC-Bi1 in Virtual Fly Brain\"), and [1,813](https://v2.virtualflybrain.org/org.geppetto.frontend/geppetto?q=FBbt_00051068,NeuronsPresynapticHere \"Run in VFB: Neurons with presynaptic terminals in subesophageal zone\") neurons with presynaptic terminals in the subesophageal zone, including AMMC-Bi1 and AVLP391.\n\nConnectomics data is available for the subesophageal zone, with the connectome data indicating synaptic connections between neurons in this region.\n\nGenetic tools exist for SEZ neurons, including GAL4 drivers and binary/intersectional drivers, with VFB holding 4,205 genetic tool/expression pattern rows for the subesophageal zone. The first 12 transgene expression patterns include [P{GMR12D05-GAL4} expression pattern](https://www.virtualflybrain.org/reports/VFBexp_FBtp0057511 \"Open P{GMR12D05-GAL4} expression pattern in Virtual Fly Brain\") and [P{GMR16C05-GAL4} expression pattern](https://www.virtualflybrain.org/reports/VFBexp_FBtp0057869 \"Open P{GMR16C05-GAL4} expression pattern in Virtual Fly Brain\").", + "quality_flags": { + "has_tool_status": true, + "no_tool_factual_answer": false, + "tool_claim_without_tool": false, + "disambiguation_only_answer": false, + "investigation_plan_answer": false, + "not_verified_or_no_results_answer": false, + "graph_failure_mentioned": false, + "missing_required_graph": false, + "used_data_resource": false, + "response_chars": 2236, + "status_count": 13 + } + }, + { + "attempt_index": 30, + "task_index": 30, + "task_id": "G1", + "tier": 5, + "title": "Graph view regression - medulla region connectivity", + "question": "what are the class summarised connectivity from the medulla in graph form", + "requires_graph": true, + "min_graphs": 1, + "repetition": 1, + "duration_ms": 17862, + "status_messages": [ + { + "message": "Thinking...", + "phase": "llm" + }, + { + "message": "Planning the answer", + "phase": "llm" + }, + { + "phase": "plan", + "message": "The plan is contested — sampling again before committing." + }, + { + "message": "Resolving 1 term in VFB", + "phase": "mcp" + }, + { + "message": "Reading VFB term info", + "phase": "mcp" + }, + { + "message": "Querying VFB", + "phase": "mcp" + }, + { + "message": "Querying VFB", + "phase": "mcp" + }, + { + "message": "Querying VFB connectivity", + "phase": "mcp" + }, + { + "message": "Querying VFB", + "phase": "mcp" + }, + { + "message": "Querying VFB", + "phase": "mcp" + }, + { + "message": "Checking the answer is covered", + "phase": "llm" + }, + { + "message": "Writing the answer", + "phase": "llm" + } + ], + "event_count": 110, + "ok": true, + "request_id": "a5e5f867-4e09-4b85-bf46-f7021e6ca1fc", + "response_id": "chatcmpl-295c10dfde4d0d53754ff930de52e34e", + "images_count": 8, + "graphs_count": 1, + "response": "The [medulla](https://www.virtualflybrain.org/reports/FBbt_00003748 \"Open medulla in Virtual Fly Brain\") has various connections, including neurons with presynaptic and postsynaptic terminals. There are [262](https://v2.virtualflybrain.org/org.geppetto.frontend/geppetto?q=FBbt_00003748,NeuronsPresynapticHere \"Run in VFB: Neurons with presynaptic terminals in medulla\") neuron types with presynaptic terminals in the medulla and [333](https://v2.virtualflybrain.org/org.geppetto.frontend/geppetto?q=FBbt_00003748,NeuronsPostsynapticHere \"Run in VFB: Neurons with postsynaptic terminals in medulla\") neuron types with postsynaptic terminals. The first 12 neuron types with presynaptic terminals include [Dm8b](https://www.virtualflybrain.org/reports/FBbt_00110069 \"Open Dm8b in Virtual Fly Brain\"), [PS128](https://www.virtualflybrain.org/reports/FBbt_20001883 \"Open PS128 in Virtual Fly Brain\"), and [Mi10b](https://www.virtualflybrain.org/reports/FBbt_00110070 \"Open Mi10b in Virtual Fly Brain\"), while the first 12 neuron types with postsynaptic terminals include [CB3849](https://www.virtualflybrain.org/reports/FBbt_20007264 \"Open CB3849 in Virtual Fly Brain\"), [TmY-ds](https://www.virtualflybrain.org/reports/FBbt_00052643 \"Open TmY-ds in Virtual Fly Brain\"), and [Y6](https://www.virtualflybrain.org/reports/FBbt_00007580 \"Open Y6 in Virtual Fly Brain\").", + "graphs": [ + { + "type": "basic_graph", + "version": 1, + "title": "medulla region connectivity preview", + "directed": true, + "layout": "radial", + "nodes": [ + { + "id": "FBbt_00003748", + "label": "medulla", + "group": "queried region", + "color": null, + "size": 2.4 + }, + { + "id": "FBbt_20007264", + "label": "CB3849", + "group": "presynaptic and postsynaptic neuron", + "color": null, + "size": 1.15 + }, + { + "id": "FBbt_00110069", + "label": "Dm8b", + "group": "presynaptic neuron", + "color": null, + "size": 1.15 + }, + { + "id": "FBbt_00110070", + "label": "Mi10b", + "group": "presynaptic neuron", + "color": null, + "size": 1.15 + }, + { + "id": "FBbt_20001883", + "label": "PS128", + "group": "presynaptic neuron", + "color": null, + "size": 1.15 + }, + { + "id": "FBbt_00052643", + "label": "TmY-ds", + "group": "presynaptic and postsynaptic neuron", + "color": null, + "size": 1.15 + }, + { + "id": "FBbt_00003774", + "label": "Dm7", + "group": "postsynaptic neuron", + "color": null, + "size": 1.15 + }, + { + "id": "FBbt_00007580", + "label": "Y6", + "group": "postsynaptic neuron", + "color": null, + "size": 1.15 + }, + { + "id": "FBbt_00047183", + "label": "extra l-LNv neuron", + "group": "postsynaptic neuron", + "color": null, + "size": 1.15 + } + ], + "edges": [ + { + "source": "FBbt_20007264", + "target": "FBbt_00003748", + "label": "presynaptic sites in medulla", + "weight": 0 + }, + { + "source": "FBbt_00110069", + "target": "FBbt_00003748", + "label": "presynaptic sites in medulla", + "weight": 0 + }, + { + "source": "FBbt_00110070", + "target": "FBbt_00003748", + "label": "presynaptic sites in medulla", + "weight": 0 + }, + { + "source": "FBbt_20001883", + "target": "FBbt_00003748", + "label": "presynaptic sites in medulla", + "weight": 0 + }, + { + "source": "FBbt_00052643", + "target": "FBbt_00003748", + "label": "presynaptic sites in medulla", + "weight": 0 + }, + { + "source": "FBbt_00003748", + "target": "FBbt_20007264", + "label": "postsynaptic sites in medulla", + "weight": 0 + }, + { + "source": "FBbt_00003748", + "target": "FBbt_00003774", + "label": "postsynaptic sites in medulla", + "weight": 0 + }, + { + "source": "FBbt_00003748", + "target": "FBbt_00052643", + "label": "postsynaptic sites in medulla", + "weight": 0 + }, + { + "source": "FBbt_00003748", + "target": "FBbt_00007580", + "label": "postsynaptic sites in medulla", + "weight": 0 + }, + { + "source": "FBbt_00003748", + "target": "FBbt_00047183", + "label": "postsynaptic sites in medulla", + "weight": 0 + } + ] + } + ], + "quality_flags": { + "has_tool_status": true, + "no_tool_factual_answer": false, + "tool_claim_without_tool": false, + "disambiguation_only_answer": false, + "investigation_plan_answer": false, + "not_verified_or_no_results_answer": false, + "graph_failure_mentioned": false, + "missing_required_graph": false, + "used_data_resource": false, + "response_chars": 1362, + "status_count": 12 + } + }, + { + "attempt_index": 31, + "task_index": 31, + "task_id": "D1", + "tier": 6, + "title": "Project identity", + "question": "What is Virtual Fly Brain and who is it for?", + "requires_graph": false, + "min_graphs": 0, + "repetition": 1, + "duration_ms": 5917, + "status_messages": [ + { + "message": "Thinking...", + "phase": "llm" + }, + { + "message": "Planning (direct lookup)", + "phase": "llm" + }, + { + "message": "Resolving 1 term in VFB", + "phase": "mcp" + }, + { + "message": "Reading VFB term info", + "phase": "mcp" + }, + { + "message": "Checking the literature", + "phase": "mcp" + }, + { + "message": "Checking the answer is covered", + "phase": "llm" + }, + { + "message": "Writing the answer", + "phase": "llm" + } + ], + "event_count": 42, + "ok": true, + "request_id": "b99d2993-cc2f-4a7b-aca6-a4c0b01e7c7f", + "response_id": "chatcmpl-67ec02a90155c51c59d0255470f0a751", + "images_count": 0, + "graphs_count": 0, + "response": "Virtual Fly Brain is an interactive tool for neurobiologists to explore the detailed neuroanatomy, neuron connectivity, and gene expression of Drosophila melanogaster.", + "quality_flags": { + "has_tool_status": true, + "no_tool_factual_answer": false, + "tool_claim_without_tool": false, + "disambiguation_only_answer": false, + "investigation_plan_answer": false, + "not_verified_or_no_results_answer": false, + "graph_failure_mentioned": false, + "missing_required_graph": false, + "used_data_resource": false, + "response_chars": 167, + "status_count": 7 + } + }, + { + "attempt_index": 32, + "task_index": 32, + "task_id": "D2", + "tier": 6, + "title": "Citation", + "question": "How should I cite Virtual Fly Brain in a publication?", + "requires_graph": false, + "min_graphs": 0, + "repetition": 1, + "duration_ms": 9366, + "status_messages": [ + { + "message": "Thinking...", + "phase": "llm" + }, + { + "message": "Planning the answer", + "phase": "llm" + }, + { + "message": "Reading VFB documentation", + "phase": "mcp" + }, + { + "message": "Checking the literature", + "phase": "mcp" + }, + { + "message": "Checking the answer is covered", + "phase": "llm" + }, + { + "message": "Writing the answer", + "phase": "llm" + } + ], + "event_count": 116, + "ok": true, + "request_id": "39495c08-d487-46f2-8c16-95f582df7d25", + "response_id": "chatcmpl-77ec913b73d3af1d818797e7206bdc6f", + "images_count": 0, + "graphs_count": 0, + "response": "To cite Virtual Fly Brain in a publication, use the citation VFB evidence on their website, including APA, MLA, Chicago, and BibTeX formats. If you use Virtual Fly Brain data, tools, or resources in your research, please cite their work using the citation formats below, which include a reference to Court et al., 2023, Virtual Fly Brain—An interactive atlas of the Drosophila nervous system, Frontiers in Physiology, https://doi.org/10.3389/fphys.2023.1076533.", + "quality_flags": { + "has_tool_status": true, + "no_tool_factual_answer": false, + "tool_claim_without_tool": false, + "disambiguation_only_answer": false, + "investigation_plan_answer": false, + "not_verified_or_no_results_answer": false, + "graph_failure_mentioned": false, + "missing_required_graph": false, + "used_data_resource": false, + "response_chars": 461, + "status_count": 6 + } + }, + { + "attempt_index": 33, + "task_index": 33, + "task_id": "D3", + "tier": 6, + "title": "Funding", + "question": "Who funds Virtual Fly Brain and since when?", + "requires_graph": false, + "min_graphs": 0, + "repetition": 1, + "duration_ms": 5376, + "status_messages": [ + { + "message": "Thinking...", + "phase": "llm" + }, + { + "message": "Planning the answer", + "phase": "llm" + }, + { + "message": "Reading VFB documentation", + "phase": "mcp" + }, + { + "message": "Checking VFB documentation", + "phase": "mcp" + }, + { + "message": "Checking the answer is covered", + "phase": "llm" + }, + { + "message": "Writing the answer", + "phase": "llm" + } + ], + "event_count": 25, + "ok": true, + "request_id": "7ef0693d-b3b1-459e-842b-d065385f992c", + "response_id": "chatcmpl-abfa35240e40687826834503d5b2644c", + "images_count": 0, + "graphs_count": 0, + "response": "Virtual Fly Brain is funded by multiple UK research councils and charitable foundations since 2009.", + "quality_flags": { + "has_tool_status": true, + "no_tool_factual_answer": false, + "tool_claim_without_tool": false, + "disambiguation_only_answer": false, + "investigation_plan_answer": false, + "not_verified_or_no_results_answer": false, + "graph_failure_mentioned": false, + "missing_required_graph": false, + "used_data_resource": false, + "response_chars": 99, + "status_count": 6 + } + }, + { + "attempt_index": 34, + "task_index": 34, + "task_id": "D4", + "tier": 6, + "title": "Policies / accessibility", + "question": "What is Virtual Fly Brain's accessibility statement?", + "requires_graph": false, + "min_graphs": 0, + "repetition": 1, + "duration_ms": 6960, + "status_messages": [ + { + "message": "Thinking...", + "phase": "llm" + }, + { + "message": "Planning (direct lookup)", + "phase": "llm" + }, + { + "message": "Resolving 1 term in VFB", + "phase": "mcp" + }, + { + "message": "Reading VFB term info", + "phase": "mcp" + }, + { + "message": "Checking the literature", + "phase": "mcp" + }, + { + "message": "Checking the answer is covered", + "phase": "llm" + }, + { + "message": "Writing the answer", + "phase": "llm" + } + ], + "event_count": 65, + "ok": true, + "request_id": "707ba3dd-9a44-44e8-b020-e06ee0df5ca2", + "response_id": "chatcmpl-83705a1172293060d341b054907e2219", + "images_count": 0, + "graphs_count": 0, + "response": "Virtual Fly Brain's accessibility statement is that the website is partially compliant with the Web Content Accessibility Guidelines (WCAG) 2.2 AA standard, with non-compliances listed, and the University of Edinburgh is committed to making its websites and applications accessible in line with the regulations.", + "quality_flags": { + "has_tool_status": true, + "no_tool_factual_answer": false, + "tool_claim_without_tool": false, + "disambiguation_only_answer": false, + "investigation_plan_answer": false, + "not_verified_or_no_results_answer": false, + "graph_failure_mentioned": false, + "missing_required_graph": false, + "used_data_resource": false, + "response_chars": 311, + "status_count": 7 + } + }, + { + "attempt_index": 35, + "task_index": 35, + "task_id": "D5", + "tier": 6, + "title": "Contact / contribute", + "question": "How do I report a problem or contribute data to Virtual Fly Brain?", + "requires_graph": false, + "min_graphs": 0, + "repetition": 1, + "duration_ms": 9819, + "status_messages": [ + { + "message": "Thinking...", + "phase": "llm" + }, + { + "message": "Planning the answer", + "phase": "llm" + }, + { + "message": "Reading VFB documentation", + "phase": "mcp" + }, + { + "message": "Checking VFB documentation", + "phase": "mcp" + }, + { + "message": "Checking the answer is covered", + "phase": "llm" + }, + { + "message": "Writing the answer", + "phase": "llm" + } + ], + "event_count": 107, + "ok": true, + "request_id": "b3ae3f58-f136-403d-8134-70945f945f37", + "response_id": "chatcmpl-58c0ad5681189ec6b3df543b6026197c", + "images_count": 0, + "graphs_count": 0, + "response": "To report a problem or contribute data to Virtual Fly Brain, you can get in touch with the team through the contact page. For help with using Virtual Fly Brain, you can email support@virtualflybrain.org, which goes to the public support forum where questions and responses are visible to the community. To report technical issues, bugs, or request new features, you can use GitHub Issues. For data inclusion discussions, collaboration proposals, or confidential matters, you can email data@virtualflybrain.org.", + "quality_flags": { + "has_tool_status": true, + "no_tool_factual_answer": false, + "tool_claim_without_tool": false, + "disambiguation_only_answer": false, + "investigation_plan_answer": false, + "not_verified_or_no_results_answer": false, + "graph_failure_mentioned": false, + "missing_required_graph": false, + "used_data_resource": false, + "response_chars": 510, + "status_count": 6 + } + }, + { + "attempt_index": 36, + "task_index": 36, + "task_id": "D6", + "tier": 6, + "title": "Website how-to: 3D Viewer", + "question": "How do I use the 3D Viewer on the VFB website?", + "requires_graph": false, + "min_graphs": 0, + "repetition": 1, + "duration_ms": 7521, + "status_messages": [ + { + "message": "Thinking...", + "phase": "llm" + }, + { + "message": "Planning the answer", + "phase": "llm" + }, + { + "message": "Reading VFB documentation", + "phase": "mcp" + }, + { + "message": "Checking the literature", + "phase": "mcp" + }, + { + "message": "Checking the answer is covered", + "phase": "llm" + }, + { + "message": "Writing the answer", + "phase": "llm" + } + ], + "event_count": 85, + "ok": true, + "request_id": "9a3994bf-c73b-4f7f-bbe9-933badbb215d", + "response_id": "chatcmpl-d26ed7a643645777f66d923dde7c1173", + "images_count": 0, + "graphs_count": 0, + "response": "To use the 3D Viewer on the VFB website, point and click to select neurons or expression. Click and drag with the mouse or use the directional icons to rotate or move. Use the zoom icons or scroll with the mouse to zoom in or out. The camera icon starts or stops a rotation animation of the scene, and the sphere icon toggles wireframes on or off.", + "quality_flags": { + "has_tool_status": true, + "no_tool_factual_answer": false, + "tool_claim_without_tool": false, + "disambiguation_only_answer": false, + "investigation_plan_answer": false, + "not_verified_or_no_results_answer": false, + "graph_failure_mentioned": false, + "missing_required_graph": false, + "used_data_resource": false, + "response_chars": 347, + "status_count": 6 + } + }, + { + "attempt_index": 37, + "task_index": 37, + "task_id": "D7", + "tier": 6, + "title": "Website how-to: Circuit Browser", + "question": "What is the Circuit Browser tab on VFB and how do I use it?", + "requires_graph": false, + "min_graphs": 0, + "repetition": 1, + "duration_ms": 13162, + "status_messages": [ + { + "message": "Thinking...", + "phase": "llm" + }, + { + "message": "Planning the answer", + "phase": "llm" + }, + { + "message": "Resolving 1 term in VFB", + "phase": "mcp" + }, + { + "message": "Reading VFB documentation", + "phase": "mcp" + }, + { + "message": "Reading VFB documentation", + "phase": "mcp" + }, + { + "message": "Checking VFB documentation", + "phase": "mcp" + }, + { + "message": "Checking the answer is covered", + "phase": "llm" + }, + { + "message": "Writing the answer", + "phase": "llm" + } + ], + "event_count": 45, + "ok": true, + "request_id": "a85f413b-68bb-47fb-a588-8a1e52342452", + "response_id": "chatcmpl-8d250165e0f947d8e51f6d93cbd77c99", + "images_count": 0, + "graphs_count": 0, + "response": "The Circuit Browser tab on VFB allows you to find the strongest paths from one neuron to another. To use it, you would typically specify a source neuron and a target neuron.", + "quality_flags": { + "has_tool_status": true, + "no_tool_factual_answer": false, + "tool_claim_without_tool": false, + "disambiguation_only_answer": false, + "investigation_plan_answer": false, + "not_verified_or_no_results_answer": false, + "graph_failure_mentioned": false, + "missing_required_graph": false, + "used_data_resource": false, + "response_chars": 173, + "status_count": 8 + } + }, + { + "attempt_index": 38, + "task_index": 38, + "task_id": "D8", + "tier": 6, + "title": "Concepts: NBLAST", + "question": "What is NBLAST and what does an NBLAST similarity score mean?", + "requires_graph": false, + "min_graphs": 0, + "repetition": 1, + "duration_ms": 9414, + "status_messages": [ + { + "message": "Thinking...", + "phase": "llm" + }, + { + "message": "Planning the answer", + "phase": "llm" + }, + { + "message": "Resolving 1 term in VFB", + "phase": "mcp" + }, + { + "message": "Reading VFB term info", + "phase": "mcp" + }, + { + "message": "Checking the literature", + "phase": "mcp" + }, + { + "message": "Checking the answer is covered", + "phase": "llm" + }, + { + "message": "Writing the answer", + "phase": "llm" + } + ], + "event_count": 56, + "ok": true, + "request_id": "b7bb1d3c-0843-4a7c-95e9-634d82ce1153", + "response_id": "chatcmpl-daa4ebf7055c67532d5b5b73178a9313", + "images_count": 0, + "graphs_count": 0, + "response": "NBLAST is a method used to calculate similarity scores, which represent the morphological similarity between neurons or expression patterns. An NBLAST similarity score is a measure of how similar two neurons or expression patterns are in terms of their morphology.", + "quality_flags": { + "has_tool_status": true, + "no_tool_factual_answer": false, + "tool_claim_without_tool": false, + "disambiguation_only_answer": false, + "investigation_plan_answer": false, + "not_verified_or_no_results_answer": false, + "graph_failure_mentioned": false, + "missing_required_graph": false, + "used_data_resource": false, + "response_chars": 264, + "status_count": 7 + } + }, + { + "attempt_index": 39, + "task_index": 39, + "task_id": "D9", + "tier": 6, + "title": "Concepts: confidence values", + "question": "What do confidence values mean on Virtual Fly Brain?", + "requires_graph": false, + "min_graphs": 0, + "repetition": 1, + "duration_ms": 7533, + "status_messages": [ + { + "message": "Thinking...", + "phase": "llm" + }, + { + "message": "Planning the answer", + "phase": "llm" + }, + { + "message": "Resolving 1 term in VFB", + "phase": "mcp" + }, + { + "message": "Reading VFB documentation", + "phase": "mcp" + }, + { + "message": "Checking the literature", + "phase": "mcp" + }, + { + "message": "Checking the answer is covered", + "phase": "llm" + }, + { + "message": "Writing the answer", + "phase": "llm" + } + ], + "event_count": 26, + "ok": true, + "request_id": "d0b724e0-86ff-4d1c-954a-f284a5b9793b", + "response_id": "chatcmpl-002a2f2e979257bf6fd1e498c2eea6f0", + "images_count": 1, + "graphs_count": 0, + "response": "Confidence values are represented by the property key \"confidence_value\" in the PDB.", + "quality_flags": { + "has_tool_status": true, + "no_tool_factual_answer": false, + "tool_claim_without_tool": false, + "disambiguation_only_answer": false, + "investigation_plan_answer": false, + "not_verified_or_no_results_answer": false, + "graph_failure_mentioned": false, + "missing_required_graph": false, + "used_data_resource": false, + "response_chars": 84, + "status_count": 7 + } + }, + { + "attempt_index": 40, + "task_index": 40, + "task_id": "D10", + "tier": 6, + "title": "Concepts: bridging registrations", + "question": "What are bridging registrations between brain templates in VFB?", + "requires_graph": false, + "min_graphs": 0, + "repetition": 1, + "duration_ms": 9050, + "status_messages": [ + { + "message": "Thinking...", + "phase": "llm" + }, + { + "message": "Planning the answer", + "phase": "llm" + }, + { + "message": "Resolving 1 term in VFB", + "phase": "mcp" + }, + { + "message": "Reading VFB term info", + "phase": "mcp" + }, + { + "message": "Checking VFB documentation", + "phase": "mcp" + }, + { + "message": "Checking the answer is covered", + "phase": "llm" + }, + { + "message": "Writing the answer", + "phase": "llm" + } + ], + "event_count": 44, + "ok": true, + "request_id": "238bb633-44e3-4836-8b1b-9ed929cc0da0", + "response_id": "chatcmpl-ac3b8e4e9acb9416791cd74ca000c0cf", + "images_count": 8, + "graphs_count": 0, + "response": "Bridging registrations between brain templates in VFB are transformations to map between different canonical Drosophila templates. VFB's documentation does not appear to cover bridging registrations.", + "quality_flags": { + "has_tool_status": true, + "no_tool_factual_answer": false, + "tool_claim_without_tool": false, + "disambiguation_only_answer": false, + "investigation_plan_answer": false, + "not_verified_or_no_results_answer": false, + "graph_failure_mentioned": false, + "missing_required_graph": false, + "used_data_resource": false, + "response_chars": 199, + "status_count": 7 + } + }, + { + "attempt_index": 41, + "task_index": 41, + "task_id": "D11", + "tier": 6, + "title": "Data coverage & templates", + "question": "What imaging data types and brain templates does Virtual Fly Brain hold?", + "requires_graph": false, + "min_graphs": 0, + "repetition": 1, + "duration_ms": 6132, + "status_messages": [ + { + "message": "Thinking...", + "phase": "llm" + }, + { + "message": "Planning the answer", + "phase": "llm" + }, + { + "message": "Reading VFB documentation", + "phase": "mcp" + }, + { + "message": "Checking VFB documentation", + "phase": "mcp" + }, + { + "message": "Checking the answer is covered", + "phase": "llm" + }, + { + "message": "Writing the answer", + "phase": "llm" + } + ], + "event_count": 55, + "ok": true, + "request_id": "34d5660e-816f-467a-9685-cdd956809f35", + "response_id": "chatcmpl-d896bc7b75470a48f2e045c397f871a8", + "images_count": 0, + "graphs_count": 0, + "response": "Virtual Fly Brain holds various imaging data types, including skeleton, mesh, and volume, and brain templates with painted domains/regions. The retrieved neuron object can provide different representations of neuron data, such as its skeleton, mesh, and volume.", + "quality_flags": { + "has_tool_status": true, + "no_tool_factual_answer": false, + "tool_claim_without_tool": false, + "disambiguation_only_answer": false, + "investigation_plan_answer": false, + "not_verified_or_no_results_answer": false, + "graph_failure_mentioned": false, + "missing_required_graph": false, + "used_data_resource": false, + "response_chars": 261, + "status_count": 6 + } + }, + { + "attempt_index": 42, + "task_index": 42, + "task_id": "D12", + "tier": 6, + "title": "Release changelog", + "question": "What was included in the latest Virtual Fly Brain release?", + "requires_graph": false, + "min_graphs": 0, + "repetition": 1, + "duration_ms": 7099, + "status_messages": [ + { + "message": "Thinking...", + "phase": "llm" + }, + { + "message": "Planning the answer", + "phase": "llm" + }, + { + "message": "Reading VFB term info", + "phase": "mcp" + }, + { + "message": "Checking the literature", + "phase": "mcp" + }, + { + "message": "Checking the answer is covered", + "phase": "llm" + }, + { + "message": "Writing the answer", + "phase": "llm" + } + ], + "event_count": 91, + "ok": true, + "request_id": "eeb00379-3a56-4826-a2ec-cab1ce568299", + "response_id": "chatcmpl-432afb8aa26c92ffe77a7e58ede09cdc", + "images_count": 0, + "graphs_count": 0, + "response": "The latest Virtual Fly Brain release includes various data and software improvements, such as new images and annotations, including but not limited to: Adult Brain fru clones, Adult VNC neuropils, Adult VNS neuropils, AMMC local and projection neurons, Biomechanical origins of proprioceptive maps in the Drosophila leg, BrainName neuropils and tracts, BrainTrap lines, and many others.", + "quality_flags": { + "has_tool_status": true, + "no_tool_factual_answer": false, + "tool_claim_without_tool": false, + "disambiguation_only_answer": false, + "investigation_plan_answer": false, + "not_verified_or_no_results_answer": false, + "graph_failure_mentioned": false, + "missing_required_graph": false, + "used_data_resource": false, + "response_chars": 386, + "status_count": 6 + } + }, + { + "attempt_index": 43, + "task_index": 43, + "task_id": "D13", + "tier": 6, + "title": "API: VFB-connect (Python)", + "question": "How do I install and get started with VFB-connect in Python?", + "requires_graph": false, + "min_graphs": 0, + "repetition": 1, + "duration_ms": 8570, + "status_messages": [ + { + "message": "Thinking...", + "phase": "llm" + }, + { + "message": "Planning the answer", + "phase": "llm" + }, + { + "message": "Reading VFB documentation", + "phase": "mcp" + }, + { + "message": "Checking the literature", + "phase": "mcp" + }, + { + "message": "Checking the answer is covered", + "phase": "llm" + }, + { + "message": "Writing the answer", + "phase": "llm" + } + ], + "event_count": 58, + "ok": true, + "request_id": "a2641fc1-380f-4dd3-afdc-e38d8b9ad043", + "response_id": "chatcmpl-b9c2df2e6a0fbffb0b5f62865a385918", + "images_count": 0, + "graphs_count": 0, + "response": "To install and get started with VFB-connect in Python, ensure you have the VFBConnect library installed using the recommended Python version 3.10.14. Install the library by running\n```\npip install vfb-connect\n```\nThen, import the VFBConnect library using\n```\nfrom import vfb\n```", + "quality_flags": { + "has_tool_status": true, + "no_tool_factual_answer": false, + "tool_claim_without_tool": false, + "disambiguation_only_answer": false, + "investigation_plan_answer": false, + "not_verified_or_no_results_answer": false, + "graph_failure_mentioned": false, + "missing_required_graph": false, + "used_data_resource": false, + "response_chars": 278, + "status_count": 6 + } + }, + { + "attempt_index": 44, + "task_index": 44, + "task_id": "D14", + "tier": 6, + "title": "API: REST endpoints", + "question": "How can I query Virtual Fly Brain programmatically using the SOLR or Owlery API?", + "requires_graph": false, + "min_graphs": 0, + "repetition": 1, + "duration_ms": 10777, + "status_messages": [ + { + "message": "Thinking...", + "phase": "llm" + }, + { + "message": "Planning the answer", + "phase": "llm" + }, + { + "message": "Reading VFB documentation", + "phase": "mcp" + }, + { + "message": "Checking VFB documentation", + "phase": "mcp" + }, + { + "message": "Checking the answer is covered", + "phase": "llm" + }, + { + "message": "Writing the answer", + "phase": "llm" + } + ], + "event_count": 91, + "ok": true, + "request_id": "35314934-9a85-4d86-a092-6fdb14bf1686", + "response_id": "chatcmpl-f24ed53392e1e6f7c59644f9041ab555", + "images_count": 0, + "graphs_count": 0, + "response": "To query Virtual Fly Brain programmatically, you can use the Owlery API, which provides OWL reasoning services for VFB's ontologies. The API endpoint is https://owl.virtualflybrain.org/, and it supports various query operations, including DL queries, SPARQL queries, and knowledgebase operations. The SOLR Search API provides fast text search and autocomplete functionality for VFB entities, datasets, and publications.", + "quality_flags": { + "has_tool_status": true, + "no_tool_factual_answer": false, + "tool_claim_without_tool": false, + "disambiguation_only_answer": false, + "investigation_plan_answer": false, + "not_verified_or_no_results_answer": false, + "graph_failure_mentioned": false, + "missing_required_graph": false, + "used_data_resource": false, + "response_chars": 419, + "status_count": 6 + } + }, + { + "attempt_index": 45, + "task_index": 45, + "task_id": "D15", + "tier": 6, + "title": "API: integrations", + "question": "How do I explore Virtual Fly Brain neurons using Navis or pymaid?", + "requires_graph": false, + "min_graphs": 0, + "repetition": 1, + "duration_ms": 9954, + "status_messages": [ + { + "message": "Thinking...", + "phase": "llm" + }, + { + "message": "Planning the answer", + "phase": "llm" + }, + { + "message": "Resolving 2 terms in VFB", + "phase": "mcp" + }, + { + "message": "Reading VFB documentation", + "phase": "mcp" + }, + { + "message": "Checking VFB documentation", + "phase": "mcp" + }, + { + "message": "Checking the answer is covered", + "phase": "llm" + }, + { + "message": "Writing the answer", + "phase": "llm" + } + ], + "event_count": 108, + "ok": true, + "request_id": "1c8583e0-a716-47f2-9891-9bee7b96c9d5", + "response_id": "chatcmpl-18b24def0e57babd6ae3fcb32df4d7e3", + "images_count": 0, + "graphs_count": 0, + "response": "To explore Virtual Fly Brain neurons, you can use the pymaid library, which lets you interface with a CATMAID server such as those provided by Virtual Fly Brain. You can connect to the Virtual Fly Brain CATMAID server, retrieve neurons, and plot them using navis. Virtual Fly Brain provides tutorials on how to explore neurons using navis or pymaid.\n\nVFB's documentation does not appear to cover Navis.\nVFB's documentation does not appear to cover pymaid.", + "quality_flags": { + "has_tool_status": true, + "no_tool_factual_answer": false, + "tool_claim_without_tool": false, + "disambiguation_only_answer": false, + "investigation_plan_answer": false, + "not_verified_or_no_results_answer": false, + "graph_failure_mentioned": false, + "missing_required_graph": false, + "used_data_resource": false, + "response_chars": 455, + "status_count": 7 + } + }, + { + "attempt_index": 46, + "task_index": 46, + "task_id": "D16", + "tier": 6, + "title": "MCP tool usage", + "question": "How do I use the Virtual Fly Brain Model Context Protocol (MCP) tool?", + "requires_graph": false, + "min_graphs": 0, + "repetition": 1, + "duration_ms": 14964, + "status_messages": [ + { + "message": "Thinking...", + "phase": "llm" + }, + { + "message": "Planning the answer", + "phase": "llm" + }, + { + "phase": "plan", + "message": "The plan is contested — sampling again before committing." + }, + { + "message": "Reading VFB documentation", + "phase": "mcp" + }, + { + "message": "Reading VFB documentation", + "phase": "mcp" + }, + { + "message": "Checking VFB documentation", + "phase": "mcp" + }, + { + "message": "Checking the answer is covered", + "phase": "llm" + }, + { + "message": "Writing the answer", + "phase": "llm" + } + ], + "event_count": 99, + "ok": true, + "request_id": "ca139303-4fa2-4d21-8e49-6bd010fe0527", + "response_id": "chatcmpl-b812aeab849cbea86d018b2c4ac81586", + "images_count": 0, + "graphs_count": 0, + "response": "To use the Virtual Fly Brain Model Context Protocol (MCP) tool, follow these steps:\nOpen Claude Desktop, navigate to Settings, and add a new MCP server with the settings:\nServer Name: virtual-fly-brain,\nType: HTTP,\nServer URL: https://vfb3-mcp.virtualflybrain.org.\nAlternatively, use the Configuration JSON method or set up the tool with GitHub Copilot or VS Code.\n\n```\n{\n\"mcpServers\": {\n\"virtual-fly-brain\": {\n\"type\": \"http\",\n\"url\": \"https://vfb3-mcp.virtualflybrain.org\",\n\"tools\": [\"*\"]\n}\n}\n}\n```", + "quality_flags": { + "has_tool_status": true, + "no_tool_factual_answer": false, + "tool_claim_without_tool": false, + "disambiguation_only_answer": false, + "investigation_plan_answer": false, + "not_verified_or_no_results_answer": false, + "graph_failure_mentioned": false, + "missing_required_graph": false, + "used_data_resource": false, + "response_chars": 498, + "status_count": 8 + } + }, + { + "attempt_index": 47, + "task_index": 47, + "task_id": "D17", + "tier": 6, + "title": "News / operational", + "question": "When did predicted neurotransmitters for EM data become available on VFB?", + "requires_graph": false, + "min_graphs": 0, + "repetition": 1, + "duration_ms": 7780, + "status_messages": [ + { + "message": "Thinking...", + "phase": "llm" + }, + { + "message": "Planning the answer", + "phase": "llm" + }, + { + "phase": "plan", + "message": "The plan is contested — sampling again before committing." + }, + { + "message": "Resolving 1 term in VFB", + "phase": "mcp" + }, + { + "message": "Reading VFB term info", + "phase": "mcp" + }, + { + "message": "Checking the literature", + "phase": "mcp" + }, + { + "message": "Checking the answer is covered", + "phase": "llm" + }, + { + "message": "Writing the answer", + "phase": "llm" + } + ], + "event_count": 41, + "ok": true, + "request_id": "ff5929cf-cf48-4839-9352-a3e89925a9ee", + "response_id": "chatcmpl-c45275e255d55d3e242d67cd2d534edf", + "images_count": 0, + "graphs_count": 0, + "response": "VFB's documentation does not appear to cover when predicted neurotransmitters for EM data became available. For more information, searching virtualflybrain.org may be helpful.", + "quality_flags": { + "has_tool_status": true, + "no_tool_factual_answer": false, + "tool_claim_without_tool": false, + "disambiguation_only_answer": false, + "investigation_plan_answer": false, + "not_verified_or_no_results_answer": false, + "graph_failure_mentioned": false, + "missing_required_graph": false, + "used_data_resource": false, + "response_chars": 175, + "status_count": 8 + } + }, + { + "attempt_index": 48, + "task_index": 48, + "task_id": "D18", + "tier": 6, + "title": "Community events", + "question": "When and where is the NeuroFly 2026 conference?", + "requires_graph": false, + "min_graphs": 0, + "repetition": 1, + "duration_ms": 8975, + "status_messages": [ + { + "message": "Thinking...", + "phase": "llm" + }, + { + "message": "Planning the answer", + "phase": "llm" + }, + { + "message": "Resolving 1 term in VFB", + "phase": "mcp" + }, + { + "message": "Reading VFB documentation", + "phase": "mcp" + }, + { + "message": "Checking VFB documentation", + "phase": "mcp" + }, + { + "message": "Checking the answer is covered", + "phase": "llm" + }, + { + "message": "Writing the answer", + "phase": "llm" + } + ], + "event_count": 40, + "ok": true, + "request_id": "27ef4631-8457-40fc-a5cc-a2963b3a545a", + "response_id": "chatcmpl-e449fd3316629dc3a973827b37cc2cc8", + "images_count": 0, + "graphs_count": 0, + "response": "The NeuroFly 2026 conference will be held at the University of Cologne, Germany, from September 7th to 11th, 2026.", + "quality_flags": { + "has_tool_status": true, + "no_tool_factual_answer": false, + "tool_claim_without_tool": false, + "disambiguation_only_answer": false, + "investigation_plan_answer": false, + "not_verified_or_no_results_answer": false, + "graph_failure_mentioned": false, + "missing_required_graph": false, + "used_data_resource": false, + "response_chars": 114, + "status_count": 7 + } + }, + { + "attempt_index": 49, + "task_index": 49, + "task_id": "D19", + "tier": 6, + "title": "Workshops / training", + "question": "What materials are available from the VFB 'Hacking the connectome' workshop?", + "requires_graph": false, + "min_graphs": 0, + "repetition": 1, + "duration_ms": 10471, + "status_messages": [ + { + "message": "Thinking...", + "phase": "llm" + }, + { + "message": "Planning the answer", + "phase": "llm" + }, + { + "message": "Resolving 1 term in VFB", + "phase": "mcp" + }, + { + "message": "Reading VFB documentation", + "phase": "mcp" + }, + { + "message": "Checking VFB documentation", + "phase": "mcp" + }, + { + "message": "Checking the answer is covered", + "phase": "llm" + }, + { + "message": "Writing the answer", + "phase": "llm" + } + ], + "event_count": 88, + "ok": true, + "request_id": "0ed9ec78-a3c0-4f2d-9f75-b6425336d603", + "response_id": "chatcmpl-072f08ab2ef72c7df44ff578d98e1afc", + "images_count": 0, + "graphs_count": 0, + "response": "Materials from the VFB 'Hacking the connectome' workshop are available. The workshop materials include a recorded introduction session and workshop notebooks that demonstrate how to use available tools to explore and analyse published connectomes on VFB.\n\nTo access these materials, you can visit the VFB website and follow the link to the workshop page. The page includes a recorded introduction session and workshop notebooks.\n\n```\n{\n \"intro\": \"https://www.virtualflybrain.org/docs/past-workshops/connectome\"\n}\n```", + "quality_flags": { + "has_tool_status": true, + "no_tool_factual_answer": false, + "tool_claim_without_tool": false, + "disambiguation_only_answer": false, + "investigation_plan_answer": false, + "not_verified_or_no_results_answer": false, + "graph_failure_mentioned": false, + "missing_required_graph": false, + "used_data_resource": false, + "response_chars": 516, + "status_count": 7 + } + }, + { + "attempt_index": 50, + "task_index": 50, + "task_id": "D20", + "tier": 6, + "title": "Hosted / archived sites", + "question": "Where can I access the FAFB or FANC CATMAID datasets via Virtual Fly Brain?", + "requires_graph": false, + "min_graphs": 0, + "repetition": 1, + "duration_ms": 17513, + "status_messages": [ + { + "message": "Thinking...", + "phase": "llm" + }, + { + "message": "Planning the answer", + "phase": "llm" + }, + { + "message": "Resolving 3 terms in VFB", + "phase": "mcp" + }, + { + "message": "Querying VFB", + "phase": "mcp" + }, + { + "message": "Reading VFB term info", + "phase": "mcp" + }, + { + "message": "Checking VFB documentation", + "phase": "mcp" + }, + { + "message": "Checking the answer is covered", + "phase": "llm" + }, + { + "message": "Writing the answer", + "phase": "llm" + } + ], + "event_count": 64, + "ok": true, + "request_id": "db8d5b57-ba21-4d8c-9246-313a976feb5d", + "response_id": "chatcmpl-d0ab561186e37f8eb676ceb9ff46dfac", + "images_count": 8, + "graphs_count": 0, + "response": "The FAFB CATMAID dataset can be accessed via https://fafb.catmaid.virtualflybrain.org. Virtual Fly Brain hosts several CATMAID instances for exploring connectomic reconstruction data, including FAFB. The name \"FANC\" could not be matched.", + "quality_flags": { + "has_tool_status": true, + "no_tool_factual_answer": false, + "tool_claim_without_tool": false, + "disambiguation_only_answer": false, + "investigation_plan_answer": false, + "not_verified_or_no_results_answer": false, + "graph_failure_mentioned": false, + "missing_required_graph": false, + "used_data_resource": false, + "response_chars": 237, + "status_count": 8 + } + }, + { + "attempt_index": 51, + "task_index": 51, + "task_id": "D21", + "tier": 6, + "title": "Anatomy teaching diagrams", + "question": "Is there a circuit diagram of the mushroom body available on Virtual Fly Brain?", + "requires_graph": false, + "min_graphs": 0, + "repetition": 1, + "duration_ms": 7908, + "status_messages": [ + { + "message": "Thinking...", + "phase": "llm" + }, + { + "message": "Planning the answer", + "phase": "llm" + }, + { + "message": "Resolving 1 term in VFB", + "phase": "mcp" + }, + { + "message": "Reading VFB term info", + "phase": "mcp" + }, + { + "message": "Checking VFB documentation", + "phase": "mcp" + }, + { + "message": "Checking the answer is covered", + "phase": "llm" + }, + { + "message": "Writing the answer", + "phase": "llm" + } + ], + "event_count": 23, + "ok": true, + "request_id": "63e82a06-b11f-48ad-b8ed-474f7f93a928", + "response_id": "chatcmpl-3bad5257cddace7fe2ef4ce230b324e3", + "images_count": 8, + "graphs_count": 0, + "response": "There is a circuit diagram of the [mushroom body](https://www.virtualflybrain.org/reports/FBbt_00005801 \"Open mushroom body in Virtual Fly Brain\") available on Virtual Fly Brain.", + "quality_flags": { + "has_tool_status": true, + "no_tool_factual_answer": false, + "tool_claim_without_tool": false, + "disambiguation_only_answer": false, + "investigation_plan_answer": false, + "not_verified_or_no_results_answer": false, + "graph_failure_mentioned": false, + "missing_required_graph": false, + "used_data_resource": false, + "response_chars": 178, + "status_count": 7 + } + }, + { + "attempt_index": 52, + "task_index": 52, + "task_id": "C1", + "tier": 7, + "title": "Pronoun follow-up on a region", + "question": "What is the medulla?", + "requires_graph": false, + "min_graphs": 0, + "repetition": 1, + "duration_ms": 13290, + "status_messages": [ + { + "message": "Thinking...", + "phase": "llm" + }, + { + "message": "Running the query behind that suggestion", + "phase": "mcp" + }, + { + "message": "Resolving 1 term in VFB", + "phase": "mcp" + }, + { + "message": "Querying VFB", + "phase": "mcp" + }, + { + "message": "Querying VFB", + "phase": "mcp" + }, + { + "message": "Checking the answer is covered", + "phase": "llm" + }, + { + "message": "Writing the answer", + "phase": "llm" + } + ], + "event_count": 86, + "conversation": true, + "turns": [ + { + "turn": 1, + "question": "What is the medulla?", + "focus": null, + "clicked": null, + "duration_ms": 6944, + "ok": true, + "response": "The [medulla](https://www.virtualflybrain.org/reports/FBbt_00003748 \"Open medulla in Virtual Fly Brain\") is the second optic neuropil, sandwiched between the lamina and the lobula complex. It is divided into 10 layers: 1-6 make up the outer medulla, the seventh layer exhibits a distinct architecture and layers 8-10 make up the inner medulla.", + "followons": [ + { + "id": "FBbt_00003748", + "query_type": "ImagesNeurons", + "query": "Which neuron images have a part in the medulla?" + }, + { + "id": "FBbt_00003748", + "query_type": "TransgeneExpressionHere", + "query": "Which driver lines label the medulla?" + }, + { + "id": "FBbt_00003748", + "query_type": "NeuronsPartHere", + "query": "Which neurons have part of their arbour in the medulla?" + }, + { + "id": "FBbt_00003748", + "query_type": "NeuronsSynaptic", + "query": "Which neurons have synaptic terminals in the medulla?" + }, + { + "id": "FBbt_00003748", + "query_type": "NeuronsPostsynapticHere", + "query": "Which neurons receive output from the medulla?" + }, + { + "id": "FBbt_00003748", + "query_type": "NeuronsPresynapticHere", + "query": "Which neurons provide input to the medulla?" + } + ], + "context_terms": [ + { + "id": "FBbt_00003748", + "label": "medulla" + } + ], + "reproduction": { + "ids": [ + { + "id": "FBbt_00003748", + "label": "medulla" + } + ], + "calls": [], + "unmapped": [] + }, + "status_count": 6, + "problems": [] + }, + { + "turn": 2, + "question": "Which neurons receive output from it?", + "focus": null, + "clicked": null, + "duration_ms": 6346, + "ok": true, + "response": "Neurons that receive output from the [medulla](https://www.virtualflybrain.org/reports/FBbt_00003748 \"Open medulla in Virtual Fly Brain\") include [CB3849](https://www.virtualflybrain.org/reports/FBbt_20007264 \"Open CB3849 in Virtual Fly Brain\"), [TmY-ds](https://www.virtualflybrain.org/reports/FBbt_00052643 \"Open TmY-ds in Virtual Fly Brain\"), [Y6](https://www.virtualflybrain.org/reports/FBbt_00007580 \"Open Y6 in Virtual Fly Brain\"), [extra l-LNv neuron](https://www.virtualflybrain.org/reports/FBbt_00047183 \"Open extra l-LNv neuron in Virtual Fly Brain\"), [Dm7](https://www.virtualflybrain.org/reports/FBbt_00003774 \"Open Dm7 in Virtual Fly Brain\"), Mi6, Mi8, Tm10, Tm13, Tm14, Tm18, and Tm19. VFB records show [333](https://v2.virtualflybrain.org/org.geppetto.frontend/geppetto?q=FBbt_00003748,NeuronsPostsynapticHere \"Run in VFB: Neurons with postsynaptic terminals in medulla\") neurons with postsynaptic terminals in the medulla.", + "followons": [ + { + "id": "FBbt_00003748", + "query_type": "ImagesNeurons", + "query": "Which neuron images have a part in the medulla?" + }, + { + "id": "FBbt_00003748", + "query_type": "TransgeneExpressionHere", + "query": "Which driver lines label the medulla?" + }, + { + "id": "FBbt_00003748", + "query_type": "NeuronsPartHere", + "query": "Which neurons have part of their arbour in the medulla?" + }, + { + "id": "FBbt_00003748", + "query_type": "NeuronsSynaptic", + "query": "Which neurons have synaptic terminals in the medulla?" + }, + { + "id": "FBbt_00003748", + "query_type": "PartsOf", + "query": "What are the anatomical parts of the medulla?" + }, + { + "id": "FBbt_00003748", + "query_type": "LineageClonesIn", + "query": "Which lineage clones are found in the medulla?" + } + ], + "context_terms": [ + { + "id": "FBbt_00003748", + "label": "medulla" + } + ], + "reproduction": { + "ids": [ + { + "id": "FBbt_00003748", + "label": "medulla" + } + ], + "calls": [ + { + "id": "FBbt_00003748", + "query_type": "NeuronsPostsynapticHere", + "fn": "get_neurons_with_postsynaptic_terminals_in" + }, + { + "id": "FBbt_00003748", + "query_type": "NeuronsPresynapticHere", + "fn": "get_neurons_with_presynaptic_terminals_in" + } + ], + "unmapped": [] + }, + "status_count": 7, + "problems": [] + } + ], + "ok": true, + "request_id": "f2d88acd-a64e-4ed6-a147-795705dbaf38", + "response_id": "chatcmpl-d635cd19270149d6142ee9ec38408de4", + "images_count": 8, + "graphs_count": 0, + "response": "Neurons that receive output from the [medulla](https://www.virtualflybrain.org/reports/FBbt_00003748 \"Open medulla in Virtual Fly Brain\") include [CB3849](https://www.virtualflybrain.org/reports/FBbt_20007264 \"Open CB3849 in Virtual Fly Brain\"), [TmY-ds](https://www.virtualflybrain.org/reports/FBbt_00052643 \"Open TmY-ds in Virtual Fly Brain\"), [Y6](https://www.virtualflybrain.org/reports/FBbt_00007580 \"Open Y6 in Virtual Fly Brain\"), [extra l-LNv neuron](https://www.virtualflybrain.org/reports/FBbt_00047183 \"Open extra l-LNv neuron in Virtual Fly Brain\"), [Dm7](https://www.virtualflybrain.org/reports/FBbt_00003774 \"Open Dm7 in Virtual Fly Brain\"), Mi6, Mi8, Tm10, Tm13, Tm14, Tm18, and Tm19. VFB records show [333](https://v2.virtualflybrain.org/org.geppetto.frontend/geppetto?q=FBbt_00003748,NeuronsPostsynapticHere \"Run in VFB: Neurons with postsynaptic terminals in medulla\") neurons with postsynaptic terminals in the medulla.", + "quality_flags": { + "has_tool_status": true, + "no_tool_factual_answer": false, + "tool_claim_without_tool": false, + "disambiguation_only_answer": false, + "investigation_plan_answer": false, + "not_verified_or_no_results_answer": false, + "graph_failure_mentioned": false, + "missing_required_graph": false, + "used_data_resource": false, + "response_chars": 938, + "status_count": 7, + "addressless_followon": false, + "context_lost_across_turn": false, + "unmatched_claim_after_resolve": false, + "repeats_answered_question": false, + "slow_followup_turn": false, + "slowest_followup_ms": 6346 + } + }, + { + "attempt_index": 53, + "task_index": 53, + "task_id": "C2", + "tier": 7, + "title": "A clicked chip keeps its address", + "question": "What is the mushroom body?", + "requires_graph": false, + "min_graphs": 0, + "repetition": 1, + "duration_ms": 18549, + "status_messages": [ + { + "message": "Thinking...", + "phase": "llm" + }, + { + "message": "Running the query behind that suggestion", + "phase": "mcp" + }, + { + "message": "Resolving 1 term in VFB", + "phase": "mcp" + }, + { + "message": "Querying VFB", + "phase": "mcp" + }, + { + "message": "Checking the answer is covered", + "phase": "llm" + }, + { + "message": "Querying VFB", + "phase": "mcp" + }, + { + "message": "Checking the answer is covered", + "phase": "llm" + }, + { + "message": "Writing the answer", + "phase": "llm" + } + ], + "event_count": 351, + "conversation": true, + "turns": [ + { + "turn": 1, + "question": "What is the mushroom body?", + "focus": null, + "clicked": null, + "duration_ms": 8071, + "ok": true, + "response": "The [mushroom body](https://www.virtualflybrain.org/reports/FBbt_00005801 \"Open mushroom body in Virtual Fly Brain\") is a bilaterally paired neuropil structure situated postero-dorsally in the protocerebrum that functions in olfactory associative learning and memory. It is divided into the calyx, which receives sensory interneuron afferents, the pedunculus, a thick axon bundle, and the mushroom body lobe system, which consists of a vertical branch and a medial branch and has different structures at different life stages.", + "followons": [ + { + "id": "FBbt_00005801", + "query_type": "ImagesNeurons", + "query": "Which neuron images have a part in the mushroom body?" + }, + { + "id": "FBbt_00005801", + "query_type": "TransgeneExpressionHere", + "query": "Which driver lines label the mushroom body?" + }, + { + "id": "FBbt_00005801", + "query_type": "NeuronsPartHere", + "query": "Which neurons have part of their arbour in the mushroom body?" + }, + { + "id": "FBbt_00005801", + "query_type": "NeuronsSynaptic", + "query": "Which neurons have synaptic terminals in the mushroom body?" + }, + { + "id": "FBbt_00005801", + "query_type": "NeuronsPresynapticHere", + "query": "Which neurons provide input to the mushroom body?" + }, + { + "id": "FBbt_00005801", + "query_type": "NeuronsPostsynapticHere", + "query": "Which neurons receive output from the mushroom body?" + } + ], + "context_terms": [ + { + "id": "FBbt_00005801", + "label": "mushroom body" + } + ], + "reproduction": { + "ids": [ + { + "id": "FBbt_00005801", + "label": "mushroom body" + } + ], + "calls": [], + "unmapped": [] + }, + "status_count": 6, + "problems": [] + }, + { + "turn": 2, + "question": "Which neuron images have a part in the mushroom body?", + "focus": { + "id": "FBbt_00005801", + "query_type": "ImagesNeurons" + }, + "clicked": 0, + "duration_ms": 10478, + "ok": true, + "response": "Images of neurons with some part in [mushroom body](https://www.virtualflybrain.org/reports/FBbt_00005801 \"Open mushroom body in Virtual Fly Brain\") are available, with [27,619](https://v2.virtualflybrain.org/org.geppetto.frontend/geppetto?q=FBbt_00005801,ImagesNeurons \"Run in VFB: Images of neurons with some part in mushroom body\") images. The first 12 images, along with their VFB ids, are: VT020731 FLP 14-3; GMR 24E06 FLP 6-1; GMR 75F01 FLP 9-2; GMR 21G01 FLP 9-1; GMR 24E06 FLP 6-2; GMR 127E09 FLP 9-5; GMR 67E07 FLP 30-1; GMR 29D11 FLP 45-3; GMR 74C11 FLP 9-1; GMR 40D06 FLP 2-1; GMR 12G07 FLP 7-2; GMR 93G04 FLP 12-1. Additionally, there are [602](https://v2.virtualflybrain.org/org.geppetto.frontend/geppetto?q=FBbt_00005801,NeuronsPartHere \"Run in VFB: Neurons with some part in mushroom body\") neurons with some part in mushroom body, including [adult odd neuron of the calyx](https://www.virtualflybrain.org/reports/FBbt_00111628 \"Open adult odd neuron of the calyx in Virtual Fly Brain\"), [larval uniglomerular projection neuron 63a](https://www.virtualflybrain.org/reports/FBbt_00111675 \"Open larval uniglomerular projection neuron 63a in Virtual Fly Brain\"), [larval uniglomerular projection neuron 67b](https://www.virtualflybrain.org/reports/FBbt_00111684 \"Open larval uniglomerular projection neuron 67b in Virtual Fly Brain\"), [larval uniglomerular projection neuron 74a](https://www.virtualflybrain.org/reports/FBbt_00111685 \"Open larval uniglomerular projection neuron 74a in Virtual Fly Brain\"), [larval antennal lobe multiglomerular projection neuron C2](https://www.virtualflybrain.org/reports/FBbt_00111716 \"Open larval antennal lobe multiglomerular projection neuron C2 in Virtual Fly Brain\"), [larval antennal lobe multiglomerular projection neuron bilateral lower](https://www.virtualflybrain.org/reports/FBbt_00111717 \"Open larval antennal lobe multiglomerular projection neuron bilateral lower in Virtual Fly Brain\"), larval antennal lobe multiglomerular projection neuron bilateral upper, larval antennal lobe multiglomerular projection neuron D, larval antennal lobe multiglomerular projection neuron cobra, AOTU021, AOTU022, and [ATL005](https://www.virtualflybrain.org/reports/FBbt_20000069 \"Open ATL005 in Virtual Fly Brain\").", + "followons": [ + { + "id": "FBbt_00005801", + "query_type": "TransgeneExpressionHere", + "query": "Which driver lines label the mushroom body?" + }, + { + "id": "FBbt_00005801", + "query_type": "NeuronsSynaptic", + "query": "Which neurons have synaptic terminals in the mushroom body?" + }, + { + "id": "FBbt_00005801", + "query_type": "NeuronsPresynapticHere", + "query": "Which neurons provide input to the mushroom body?" + }, + { + "id": "FBbt_00005801", + "query_type": "NeuronsPostsynapticHere", + "query": "Which neurons receive output from the mushroom body?" + }, + { + "id": "FBbt_00005801", + "query_type": "PartsOf", + "query": "What are the anatomical parts of the mushroom body?" + }, + { + "id": "FBbt_00005801", + "query_type": "LineageClonesIn", + "query": "Which lineage clones are found in the mushroom body?" + } + ], + "context_terms": [ + { + "id": "FBbt_00005801", + "label": "mushroom body" + } + ], + "reproduction": { + "ids": [ + { + "id": "FBbt_00005801", + "label": "mushroom body" + } + ], + "calls": [ + { + "id": "FBbt_00005801", + "query_type": "ImagesNeurons", + "fn": "get_images_neurons" + }, + { + "id": "FBbt_00005801", + "query_type": "NeuronsPartHere", + "fn": "get_neurons_with_part_in" + } + ], + "unmapped": [] + }, + "status_count": 8, + "problems": [] + } + ], + "ok": true, + "request_id": "e8c70e75-887c-4264-851b-f04eb0289ba9", + "response_id": "chatcmpl-1099c9f71a10164c6c2f03fd0e0d741b", + "images_count": 8, + "graphs_count": 0, + "response": "Images of neurons with some part in [mushroom body](https://www.virtualflybrain.org/reports/FBbt_00005801 \"Open mushroom body in Virtual Fly Brain\") are available, with [27,619](https://v2.virtualflybrain.org/org.geppetto.frontend/geppetto?q=FBbt_00005801,ImagesNeurons \"Run in VFB: Images of neurons with some part in mushroom body\") images. The first 12 images, along with their VFB ids, are: VT020731 FLP 14-3; GMR 24E06 FLP 6-1; GMR 75F01 FLP 9-2; GMR 21G01 FLP 9-1; GMR 24E06 FLP 6-2; GMR 127E09 FLP 9-5; GMR 67E07 FLP 30-1; GMR 29D11 FLP 45-3; GMR 74C11 FLP 9-1; GMR 40D06 FLP 2-1; GMR 12G07 FLP 7-2; GMR 93G04 FLP 12-1. Additionally, there are [602](https://v2.virtualflybrain.org/org.geppetto.frontend/geppetto?q=FBbt_00005801,NeuronsPartHere \"Run in VFB: Neurons with some part in mushroom body\") neurons with some part in mushroom body, including [adult odd neuron of the calyx](https://www.virtualflybrain.org/reports/FBbt_00111628 \"Open adult odd neuron of the calyx in Virtual Fly Brain\"), [larval uniglomerular projection neuron 63a](https://www.virtualflybrain.org/reports/FBbt_00111675 \"Open larval uniglomerular projection neuron 63a in Virtual Fly Brain\"), [larval uniglomerular projection neuron 67b](https://www.virtualflybrain.org/reports/FBbt_00111684 \"Open larval uniglomerular projection neuron 67b in Virtual Fly Brain\"), [larval uniglomerular projection neuron 74a](https://www.virtualflybrain.org/reports/FBbt_00111685 \"Open larval uniglomerular projection neuron 74a in Virtual Fly Brain\"), [larval antennal lobe multiglomerular projection neuron C2](https://www.virtualflybrain.org/reports/FBbt_00111716 \"Open larval antennal lobe multiglomerular projection neuron C2 in Virtual Fly Brain\"), [larval antennal lobe multiglomerular projection neuron bilateral lower](https://www.virtualflybrain.org/reports/FBbt_00111717 \"Open larval antennal lobe multiglomerular projection neuron bilateral lower in Virtual Fly Brain\"), larval antennal lobe multiglomerular projection neuron bilateral upper, larval antennal lobe multiglomerular projection neuron D, larval antennal lobe multiglomerular projection neuron cobra, AOTU021, AOTU022, and [ATL005](https://www.virtualflybrain.org/reports/FBbt_20000069 \"Open ATL005 in Virtual Fly Brain\").", + "quality_flags": { + "has_tool_status": true, + "no_tool_factual_answer": false, + "tool_claim_without_tool": false, + "disambiguation_only_answer": false, + "investigation_plan_answer": false, + "not_verified_or_no_results_answer": false, + "graph_failure_mentioned": false, + "missing_required_graph": false, + "used_data_resource": false, + "response_chars": 2262, + "status_count": 8, + "addressless_followon": false, + "context_lost_across_turn": false, + "unmatched_claim_after_resolve": false, + "repeats_answered_question": false, + "slow_followup_turn": false, + "slowest_followup_ms": 10478 + } + }, + { + "attempt_index": 54, + "task_index": 54, + "task_id": "C3", + "tier": 7, + "title": "Topic switch and back", + "question": "What is the fan-shaped body?", + "requires_graph": false, + "min_graphs": 0, + "repetition": 1, + "duration_ms": 25172, + "status_messages": [ + { + "message": "Thinking...", + "phase": "llm" + }, + { + "message": "Running the query behind that suggestion", + "phase": "mcp" + }, + { + "message": "Resolving 1 term in VFB", + "phase": "mcp" + }, + { + "message": "Querying VFB", + "phase": "mcp" + }, + { + "message": "Checking the answer is covered", + "phase": "llm" + }, + { + "message": "Writing the answer", + "phase": "llm" + } + ], + "event_count": 125, + "conversation": true, + "turns": [ + { + "turn": 1, + "question": "What is the fan-shaped body?", + "focus": null, + "clicked": null, + "duration_ms": 7133, + "ok": true, + "response": "The [fan-shaped body](https://www.virtualflybrain.org/reports/FBbt_00003679 \"Open fan-shaped body in Virtual Fly Brain\") is the largest synaptic neuropil domain of the adult central complex, located posterior to the ellipsoid body and anterior to the protocerebral bridge. It is composed of a rough 2-dimensional grid of layers and columns. Eight horizontal layers, numbered bottom to top, form a fan shape and can be divided into vertical columns. An additional, much narrower, 9th layer, which lacks a columnar organization, sits dorsal to layer 8. The number of columns varies for different neuronal types.", + "followons": [ + { + "id": "FBbt_00003679", + "query_type": "ImagesNeurons", + "query": "Which neuron images have a part in the fan-shaped body?" + }, + { + "id": "FBbt_00003679", + "query_type": "TransgeneExpressionHere", + "query": "Which driver lines label the fan-shaped body?" + }, + { + "id": "FBbt_00003679", + "query_type": "NeuronsPartHere", + "query": "Which neurons have part of their arbour in the fan-shaped body?" + }, + { + "id": "FBbt_00003679", + "query_type": "NeuronsSynaptic", + "query": "Which neurons have synaptic terminals in the fan-shaped body?" + }, + { + "id": "FBbt_00003679", + "query_type": "NeuronsPresynapticHere", + "query": "Which neurons provide input to the fan-shaped body?" + }, + { + "id": "FBbt_00003679", + "query_type": "NeuronsPostsynapticHere", + "query": "Which neurons receive output from the fan-shaped body?" + } + ], + "context_terms": [ + { + "id": "FBbt_00003679", + "label": "fan-shaped body" + } + ], + "reproduction": { + "ids": [ + { + "id": "FBbt_00003679", + "label": "fan-shaped body" + } + ], + "calls": [], + "unmapped": [] + }, + "status_count": 6, + "problems": [] + }, + { + "turn": 2, + "question": "What about the ellipsoid body?", + "focus": null, + "clicked": null, + "duration_ms": 8888, + "ok": true, + "response": "The [ellipsoid body](https://www.virtualflybrain.org/reports/FBbt_00003678 \"Open ellipsoid body in Virtual Fly Brain\") is a doughnut-shaped synaptic neuropil domain of the central complex of the adult brain that lies just anterior to the [fan-shaped body](https://www.virtualflybrain.org/reports/FBbt_00003679 \"Open fan-shaped body in Virtual Fly Brain\"). Its hole, the ellipsoid body canal, points anteriorly and has an axon tract, the anterior bundle, running through it.", + "followons": [ + { + "id": "FBbt_00003678", + "query_type": "ImagesNeurons", + "query": "Which neuron images have a part in the ellipsoid body?" + }, + { + "id": "FBbt_00003678", + "query_type": "TransgeneExpressionHere", + "query": "Which driver lines label the ellipsoid body?" + }, + { + "id": "FBbt_00003678", + "query_type": "NeuronsPartHere", + "query": "Which neurons have part of their arbour in the ellipsoid body?" + }, + { + "id": "FBbt_00003678", + "query_type": "NeuronsSynaptic", + "query": "Which neurons have synaptic terminals in the ellipsoid body?" + }, + { + "id": "FBbt_00003678", + "query_type": "NeuronsPresynapticHere", + "query": "Which neurons provide input to the ellipsoid body?" + }, + { + "id": "FBbt_00003678", + "query_type": "NeuronsPostsynapticHere", + "query": "Which neurons receive output from the ellipsoid body?" + } + ], + "context_terms": [ + { + "id": "FBbt_00003678", + "label": "ellipsoid body" + }, + { + "id": "FBbt_00003679", + "label": "fan-shaped body" + } + ], + "reproduction": { + "ids": [ + { + "id": "FBbt_00003678", + "label": "ellipsoid body" + }, + { + "id": "FBbt_00003679", + "label": "fan-shaped body" + } + ], + "calls": [], + "unmapped": [] + }, + "status_count": 6, + "problems": [] + }, + { + "turn": 3, + "question": "Which neurons have synaptic terminals in the fan-shaped body?", + "focus": null, + "clicked": null, + "duration_ms": 9151, + "ok": true, + "response": "Neurons with synaptic terminals in the [fan-shaped body](https://www.virtualflybrain.org/reports/FBbt_00003679 \"Open fan-shaped body in Virtual Fly Brain\") include [229](https://v2.virtualflybrain.org/org.geppetto.frontend/geppetto?q=FBbt_00003679,NeuronsPartHere \"Run in VFB: Neurons with some part in fan-shaped body\") neuron types, such as [PFNa_PB4](https://www.virtualflybrain.org/reports/FBbt_00111398 \"Open PFNa_PB4 in Virtual Fly Brain\"), [PFNa_PB5](https://www.virtualflybrain.org/reports/FBbt_00111399 \"Open PFNa_PB5 in Virtual Fly Brain\"), [PFNd_PB2](https://www.virtualflybrain.org/reports/FBbt_00111391 \"Open PFNd_PB2 in Virtual Fly Brain\"), [PFNd_PB3](https://www.virtualflybrain.org/reports/FBbt_00111392 \"Open PFNd_PB3 in Virtual Fly Brain\"), [PFNd_PB5](https://www.virtualflybrain.org/reports/FBbt_00111394 \"Open PFNd_PB5 in Virtual Fly Brain\"). The first 12 of these, with their VFB ids, are: PFNd_PB2; PFNd_PB3; PFNd_PB5; PFNa_PB4; PFNa_PB5; PFNa_PB6; PFNa_PB7; PFNa_PB9; PFNp_PB7; [PFL1_PB5](https://www.virtualflybrain.org/reports/FBbt_00111438 \"Open PFL1_PB5 in Virtual Fly Brain\"); [PFL3](https://www.virtualflybrain.org/reports/FBbt_00111443 \"Open PFL3 in Virtual Fly Brain\"); [PFL2](https://www.virtualflybrain.org/reports/FBbt_00111451 \"Open PFL2 in Virtual Fly Brain\").", + "followons": [ + { + "id": "FBbt_00003679", + "query_type": "ImagesNeurons", + "query": "Which neuron images have a part in the fan-shaped body?" + }, + { + "id": "FBbt_00003679", + "query_type": "TransgeneExpressionHere", + "query": "Which driver lines label the fan-shaped body?" + }, + { + "id": "FBbt_00003679", + "query_type": "NeuronsPartHere", + "query": "Which neurons have part of their arbour in the fan-shaped body?" + }, + { + "id": "FBbt_00003679", + "query_type": "NeuronsPresynapticHere", + "query": "Which neurons provide input to the fan-shaped body?" + }, + { + "id": "FBbt_00003679", + "query_type": "NeuronsPostsynapticHere", + "query": "Which neurons receive output from the fan-shaped body?" + }, + { + "id": "FBbt_00003679", + "query_type": "PartsOf", + "query": "What are the anatomical parts of the fan-shaped body?" + } + ], + "context_terms": [ + { + "id": "FBbt_00003679", + "label": "fan-shaped body" + }, + { + "id": "FBbt_00003678", + "label": "ellipsoid body" + } + ], + "reproduction": { + "ids": [ + { + "id": "FBbt_00003679", + "label": "fan-shaped body" + }, + { + "id": "FBbt_00003678", + "label": "ellipsoid body" + } + ], + "calls": [ + { + "id": "FBbt_00003679", + "query_type": "NeuronsSynaptic", + "fn": "get_neurons_with_synapses_in" + } + ], + "unmapped": [] + }, + "status_count": 6, + "problems": [] + } + ], + "ok": true, + "request_id": "2a4f541b-f111-444c-b3f2-c88fd9667866", + "response_id": "chatcmpl-3cfc31dd86f45a4f7b5473409f231e0b", + "images_count": 8, + "graphs_count": 0, + "response": "Neurons with synaptic terminals in the [fan-shaped body](https://www.virtualflybrain.org/reports/FBbt_00003679 \"Open fan-shaped body in Virtual Fly Brain\") include [229](https://v2.virtualflybrain.org/org.geppetto.frontend/geppetto?q=FBbt_00003679,NeuronsPartHere \"Run in VFB: Neurons with some part in fan-shaped body\") neuron types, such as [PFNa_PB4](https://www.virtualflybrain.org/reports/FBbt_00111398 \"Open PFNa_PB4 in Virtual Fly Brain\"), [PFNa_PB5](https://www.virtualflybrain.org/reports/FBbt_00111399 \"Open PFNa_PB5 in Virtual Fly Brain\"), [PFNd_PB2](https://www.virtualflybrain.org/reports/FBbt_00111391 \"Open PFNd_PB2 in Virtual Fly Brain\"), [PFNd_PB3](https://www.virtualflybrain.org/reports/FBbt_00111392 \"Open PFNd_PB3 in Virtual Fly Brain\"), [PFNd_PB5](https://www.virtualflybrain.org/reports/FBbt_00111394 \"Open PFNd_PB5 in Virtual Fly Brain\"). The first 12 of these, with their VFB ids, are: PFNd_PB2; PFNd_PB3; PFNd_PB5; PFNa_PB4; PFNa_PB5; PFNa_PB6; PFNa_PB7; PFNa_PB9; PFNp_PB7; [PFL1_PB5](https://www.virtualflybrain.org/reports/FBbt_00111438 \"Open PFL1_PB5 in Virtual Fly Brain\"); [PFL3](https://www.virtualflybrain.org/reports/FBbt_00111443 \"Open PFL3 in Virtual Fly Brain\"); [PFL2](https://www.virtualflybrain.org/reports/FBbt_00111451 \"Open PFL2 in Virtual Fly Brain\").", + "quality_flags": { + "has_tool_status": true, + "no_tool_factual_answer": false, + "tool_claim_without_tool": false, + "disambiguation_only_answer": false, + "investigation_plan_answer": false, + "not_verified_or_no_results_answer": false, + "graph_failure_mentioned": false, + "missing_required_graph": false, + "used_data_resource": false, + "response_chars": 1296, + "status_count": 6, + "addressless_followon": false, + "context_lost_across_turn": false, + "unmatched_claim_after_resolve": false, + "repeats_answered_question": false, + "slow_followup_turn": false, + "slowest_followup_ms": 9151 + } + }, + { + "attempt_index": 55, + "task_index": 55, + "task_id": "C4", + "tier": 7, + "title": "Refinement onto a cell type", + "question": "What is a Kenyon cell?", + "requires_graph": false, + "min_graphs": 0, + "repetition": 1, + "duration_ms": 14682, + "status_messages": [ + { + "message": "Thinking...", + "phase": "llm" + }, + { + "message": "Running the query behind that suggestion", + "phase": "mcp" + }, + { + "message": "Resolving 1 term in VFB", + "phase": "mcp" + }, + { + "message": "Querying VFB", + "phase": "mcp" + }, + { + "message": "Checking the answer is covered", + "phase": "llm" + }, + { + "message": "Writing the answer", + "phase": "llm" + } + ], + "event_count": 143, + "conversation": true, + "turns": [ + { + "turn": 1, + "question": "What is a Kenyon cell?", + "focus": null, + "clicked": null, + "duration_ms": 7173, + "ok": true, + "response": "A [Kenyon cell](https://www.virtualflybrain.org/reports/FBbt_00003686 \"Open Kenyon cell in Virtual Fly Brain\") is an intrinsic neuron of the mushroom body. Kenyon cells are part of the olfactory pathway in Drosophila.", + "followons": [ + { + "id": "FBbt_00003686", + "query_type": "ListAllAvailableImages", + "query": "Which images of Kenyon cell does VFB have?" + }, + { + "id": "FBbt_00003686", + "query_type": "UpstreamClassConnectivity", + "query": "What connects to the Kenyon cell upstream?" + }, + { + "id": "FBbt_00003686", + "query_type": "DownstreamClassConnectivity", + "query": "What does the Kenyon cell connect to downstream?" + }, + { + "id": "FBbt_00003686", + "query_type": "TransgeneExpressionHere", + "query": "Which driver lines label the Kenyon cell?" + }, + { + "id": "FBbt_00003686", + "query_type": "anatScRNAseqQuery", + "query": "What single-cell transcriptomic clusters are there for Kenyon cell?" + }, + { + "id": "FBbt_00003686", + "query_type": "SubclassesOf", + "query": "What are the subtypes of the Kenyon cell?" + } + ], + "context_terms": [ + { + "id": "FBbt_00003686", + "label": "Kenyon cell" + } + ], + "reproduction": { + "ids": [ + { + "id": "FBbt_00003686", + "label": "Kenyon cell" + } + ], + "calls": [], + "unmapped": [] + }, + "status_count": 7, + "problems": [] + }, + { + "turn": 2, + "question": "What are its subtypes?", + "focus": null, + "clicked": null, + "duration_ms": 7509, + "ok": true, + "response": "The subtypes of [Kenyon cell](https://www.virtualflybrain.org/reports/FBbt_00003686 \"Open Kenyon cell in Virtual Fly Brain\") are [37](https://v2.virtualflybrain.org/org.geppetto.frontend/geppetto?q=FBbt_00003686,SubclassesOf \"Run in VFB: Subclasses of Kenyon cell\") subclasses, including [KCab-c(i)](https://www.virtualflybrain.org/reports/FBbt_00049111 \"Open KCab-c(i) in Virtual Fly Brain\"), [KCab-c](https://www.virtualflybrain.org/reports/FBbt_00110929 \"Open KCab-c in Virtual Fly Brain\"), [KCg-m](https://www.virtualflybrain.org/reports/FBbt_00111061 \"Open KCg-m in Virtual Fly Brain\"), [Kenyon cell of main calyx](https://www.virtualflybrain.org/reports/FBbt_00047926 \"Open Kenyon cell of main calyx in Virtual Fly Brain\"), and [gamma Kenyon cell](https://www.virtualflybrain.org/reports/FBbt_00100247 \"Open gamma Kenyon cell in Virtual Fly Brain\"). The first 12 subclasses, with their identifiers, are: KCab-c(i); KCab-c(o); larval gamma Kenyon cell; KCg-s; KCg-s4; KCg-t; larval alpha'/beta' Kenyon cell; KCab-sc; alpha'/beta' anterior-posterior type 1 Kenyon cell of lACA; Kenyon cell of main calyx; single-claw Kenyon cell; and multi-claw Kenyon cell.", + "followons": [ + { + "id": "FBbt_00003686", + "query_type": "ListAllAvailableImages", + "query": "Which images of Kenyon cell does VFB have?" + }, + { + "id": "FBbt_00003686", + "query_type": "UpstreamClassConnectivity", + "query": "What connects to the Kenyon cell upstream?" + }, + { + "id": "FBbt_00003686", + "query_type": "DownstreamClassConnectivity", + "query": "What does the Kenyon cell connect to downstream?" + }, + { + "id": "FBbt_00003686", + "query_type": "TransgeneExpressionHere", + "query": "Which driver lines label the Kenyon cell?" + }, + { + "id": "FBbt_00003686", + "query_type": "anatScRNAseqQuery", + "query": "What single-cell transcriptomic clusters are there for Kenyon cell?" + } + ], + "context_terms": [ + { + "id": "FBbt_00003686", + "label": "Kenyon cell" + } + ], + "reproduction": { + "ids": [ + { + "id": "FBbt_00003686", + "label": "Kenyon cell" + } + ], + "calls": [ + { + "id": "FBbt_00003686", + "query_type": "SubclassesOf", + "fn": "get_subclasses_of" + } + ], + "unmapped": [] + }, + "status_count": 6, + "problems": [] + } + ], + "ok": true, + "request_id": "c721665f-c27a-48da-9407-9693542525b8", + "response_id": "chatcmpl-6be21b0f54c7e0e8bcb3586935a58e44", + "images_count": 8, + "graphs_count": 0, + "response": "The subtypes of [Kenyon cell](https://www.virtualflybrain.org/reports/FBbt_00003686 \"Open Kenyon cell in Virtual Fly Brain\") are [37](https://v2.virtualflybrain.org/org.geppetto.frontend/geppetto?q=FBbt_00003686,SubclassesOf \"Run in VFB: Subclasses of Kenyon cell\") subclasses, including [KCab-c(i)](https://www.virtualflybrain.org/reports/FBbt_00049111 \"Open KCab-c(i) in Virtual Fly Brain\"), [KCab-c](https://www.virtualflybrain.org/reports/FBbt_00110929 \"Open KCab-c in Virtual Fly Brain\"), [KCg-m](https://www.virtualflybrain.org/reports/FBbt_00111061 \"Open KCg-m in Virtual Fly Brain\"), [Kenyon cell of main calyx](https://www.virtualflybrain.org/reports/FBbt_00047926 \"Open Kenyon cell of main calyx in Virtual Fly Brain\"), and [gamma Kenyon cell](https://www.virtualflybrain.org/reports/FBbt_00100247 \"Open gamma Kenyon cell in Virtual Fly Brain\"). The first 12 subclasses, with their identifiers, are: KCab-c(i); KCab-c(o); larval gamma Kenyon cell; KCg-s; KCg-s4; KCg-t; larval alpha'/beta' Kenyon cell; KCab-sc; alpha'/beta' anterior-posterior type 1 Kenyon cell of lACA; Kenyon cell of main calyx; single-claw Kenyon cell; and multi-claw Kenyon cell.", + "quality_flags": { + "has_tool_status": true, + "no_tool_factual_answer": false, + "tool_claim_without_tool": false, + "disambiguation_only_answer": false, + "investigation_plan_answer": false, + "not_verified_or_no_results_answer": false, + "graph_failure_mentioned": false, + "missing_required_graph": false, + "used_data_resource": false, + "response_chars": 1161, + "status_count": 6, + "addressless_followon": false, + "context_lost_across_turn": false, + "unmatched_claim_after_resolve": false, + "repeats_answered_question": false, + "slow_followup_turn": false, + "slowest_followup_ms": 7509 + } + }, + { + "attempt_index": 56, + "task_index": 56, + "task_id": "C5", + "tier": 7, + "title": "A presentation directive is not part of the term name", + "question": "What are the anatomical parts of the medulla? List them.", + "requires_graph": false, + "min_graphs": 0, + "repetition": 1, + "duration_ms": 31760, + "status_messages": [ + { + "message": "Thinking...", + "phase": "llm" + }, + { + "message": "Planning the answer", + "phase": "llm" + }, + { + "message": "Resolving 1 term in VFB", + "phase": "mcp" + }, + { + "message": "Reading VFB term info", + "phase": "mcp" + }, + { + "message": "Querying VFB", + "phase": "mcp" + }, + { + "message": "Querying VFB", + "phase": "mcp" + }, + { + "message": "Checking the answer is covered", + "phase": "llm" + }, + { + "message": "Querying VFB", + "phase": "mcp" + }, + { + "message": "Querying VFB", + "phase": "mcp" + }, + { + "message": "Querying VFB", + "phase": "mcp" + }, + { + "message": "Checking the answer is covered", + "phase": "llm" + }, + { + "message": "Writing the answer", + "phase": "llm" + } + ], + "event_count": 114, + "conversation": true, + "turns": [ + { + "turn": 1, + "question": "What are the anatomical parts of the medulla? List them.", + "focus": null, + "clicked": null, + "duration_ms": 9726, + "ok": true, + "response": "The [medulla](https://www.virtualflybrain.org/reports/FBbt_00003748 \"Open medulla in Virtual Fly Brain\") is divided into 10 layers: 1-6 make up the outer (distal) medulla, the seventh (or serpentine) layer exhibits a distinct architecture and layers 8-10 make up the inner (proximal) medulla. Anatomical parts of the medulla include adult chandelier glial cell, adult distal medulla astrocyte-like glial cell, [distal medulla glial cell](https://www.virtualflybrain.org/reports/FBbt_00100528 \"Open distal medulla glial cell in Virtual Fly Brain\"), medulla layer, adult distal medulla ensheathing glial cell, [plexiform medulla](https://www.virtualflybrain.org/reports/FBbt_00045001 \"Open plexiform medulla in Virtual Fly Brain\"), [medulla dorsal rim area](https://www.virtualflybrain.org/reports/FBbt_00045002 \"Open medulla dorsal rim area in Virtual Fly Brain\"), medulla layer M1, medulla layer M5, inner medulla, medulla layer M8, and medulla layer M9.", + "followons": [ + { + "id": "FBbt_00003748", + "query_type": "ImagesNeurons", + "query": "Which neuron images have a part in the medulla?" + }, + { + "id": "FBbt_00003748", + "query_type": "TransgeneExpressionHere", + "query": "Which driver lines label the medulla?" + }, + { + "id": "FBbt_00003748", + "query_type": "NeuronsPartHere", + "query": "Which neurons have part of their arbour in the medulla?" + }, + { + "id": "FBbt_00003748", + "query_type": "NeuronsSynaptic", + "query": "Which neurons have synaptic terminals in the medulla?" + }, + { + "id": "FBbt_00003748", + "query_type": "NeuronsPostsynapticHere", + "query": "Which neurons receive output from the medulla?" + }, + { + "id": "FBbt_00003748", + "query_type": "NeuronsPresynapticHere", + "query": "Which neurons provide input to the medulla?" + } + ], + "context_terms": [ + { + "id": "FBbt_00003748", + "label": "medulla" + } + ], + "reproduction": { + "ids": [ + { + "id": "FBbt_00003748", + "label": "medulla" + } + ], + "calls": [ + { + "id": "FBbt_00003748", + "query_type": "PartsOf", + "fn": "get_parts_of" + } + ], + "unmapped": [] + }, + "status_count": 8, + "problems": [] + }, + { + "turn": 2, + "question": "And which neurons have part of their arbour there?", + "focus": null, + "clicked": null, + "duration_ms": 22034, + "ok": true, + "response": "Neurons with some part in the [medulla](https://www.virtualflybrain.org/reports/FBbt_00003748 \"Open medulla in Virtual Fly Brain\") include [Dm8b](https://www.virtualflybrain.org/reports/FBbt_00110069 \"Open Dm8b in Virtual Fly Brain\"), [MC](https://www.virtualflybrain.org/reports/FBbt_00111640 \"Open MC in Virtual Fly Brain\"), [PS128](https://www.virtualflybrain.org/reports/FBbt_20001883 \"Open PS128 in Virtual Fly Brain\"), [medulla intrinsic neuron vGlutMinew1a](https://www.virtualflybrain.org/reports/FBbt_00110033 \"Open medulla intrinsic neuron vGlutMinew1a in Virtual Fly Brain\"), [TmY27](https://www.virtualflybrain.org/reports/FBbt_00110067 \"Open TmY27 in Virtual Fly Brain\"), and others, with a total of [471](https://v2.virtualflybrain.org/org.geppetto.frontend/geppetto?q=FBbt_00003748,NeuronsPartHere \"Run in VFB: Neurons with some part in medulla\") neuron types. The medulla also contains neurons with synaptic terminals, presynaptic terminals, and postsynaptic terminals, with [464](https://v2.virtualflybrain.org/org.geppetto.frontend/geppetto?q=FBbt_00003748,NeuronsSynaptic \"Run in VFB: Neurons with synaptic terminals in medulla\"), [262](https://v2.virtualflybrain.org/org.geppetto.frontend/geppetto?q=FBbt_00003748,NeuronsPresynapticHere \"Run in VFB: Neurons with presynaptic terminals in medulla\"), and [333](https://v2.virtualflybrain.org/org.geppetto.frontend/geppetto?q=FBbt_00003748,NeuronsPostsynapticHere \"Run in VFB: Neurons with postsynaptic terminals in medulla\") results, respectively. VFB holds [226524](https://v2.virtualflybrain.org/org.geppetto.frontend/geppetto?q=FBbt_00003748,ImagesNeurons \"Run in VFB: Images of neurons with some part in medulla\") images of neurons with some part in the medulla.", + "followons": [ + { + "id": "FBbt_00003748", + "query_type": "ImagesNeurons", + "query": "Which neuron images have a part in the medulla?" + }, + { + "id": "FBbt_00003748", + "query_type": "TransgeneExpressionHere", + "query": "Which driver lines label the medulla?" + }, + { + "id": "FBbt_00003748", + "query_type": "PartsOf", + "query": "What are the anatomical parts of the medulla?" + }, + { + "id": "FBbt_00003748", + "query_type": "LineageClonesIn", + "query": "Which lineage clones are found in the medulla?" + }, + { + "id": "FBbt_00003748", + "query_type": "ListAllAvailableImages", + "query": "Which images of medulla does VFB have?" + }, + { + "id": "FBbt_00003748", + "query_type": "TractsNervesInnervatingHere", + "query": "Which tracts and nerves innervate the medulla?" + } + ], + "context_terms": [ + { + "id": "FBbt_00003748", + "label": "medulla" + } + ], + "reproduction": { + "ids": [ + { + "id": "FBbt_00003748", + "label": "medulla" + } + ], + "calls": [ + { + "id": "FBbt_00003748", + "query_type": "NeuronsPartHere", + "fn": "get_neurons_with_part_in" + }, + { + "id": "FBbt_00003748", + "query_type": "NeuronsSynaptic", + "fn": "get_neurons_with_synapses_in" + }, + { + "id": "FBbt_00003748", + "query_type": "NeuronsPresynapticHere", + "fn": "get_neurons_with_presynaptic_terminals_in" + }, + { + "id": "FBbt_00003748", + "query_type": "NeuronsPostsynapticHere", + "fn": "get_neurons_with_postsynaptic_terminals_in" + }, + { + "id": "FBbt_00003748", + "query_type": "PartsOf", + "fn": "get_parts_of" + } + ], + "unmapped": [] + }, + "status_count": 12, + "problems": [] + } + ], + "ok": true, + "request_id": "df17217a-0aff-4baa-951f-cf673f7d1dda", + "response_id": "chatcmpl-9ed32e477cce4d3f2d372f233a17586f", + "images_count": 8, + "graphs_count": 0, + "response": "Neurons with some part in the [medulla](https://www.virtualflybrain.org/reports/FBbt_00003748 \"Open medulla in Virtual Fly Brain\") include [Dm8b](https://www.virtualflybrain.org/reports/FBbt_00110069 \"Open Dm8b in Virtual Fly Brain\"), [MC](https://www.virtualflybrain.org/reports/FBbt_00111640 \"Open MC in Virtual Fly Brain\"), [PS128](https://www.virtualflybrain.org/reports/FBbt_20001883 \"Open PS128 in Virtual Fly Brain\"), [medulla intrinsic neuron vGlutMinew1a](https://www.virtualflybrain.org/reports/FBbt_00110033 \"Open medulla intrinsic neuron vGlutMinew1a in Virtual Fly Brain\"), [TmY27](https://www.virtualflybrain.org/reports/FBbt_00110067 \"Open TmY27 in Virtual Fly Brain\"), and others, with a total of [471](https://v2.virtualflybrain.org/org.geppetto.frontend/geppetto?q=FBbt_00003748,NeuronsPartHere \"Run in VFB: Neurons with some part in medulla\") neuron types. The medulla also contains neurons with synaptic terminals, presynaptic terminals, and postsynaptic terminals, with [464](https://v2.virtualflybrain.org/org.geppetto.frontend/geppetto?q=FBbt_00003748,NeuronsSynaptic \"Run in VFB: Neurons with synaptic terminals in medulla\"), [262](https://v2.virtualflybrain.org/org.geppetto.frontend/geppetto?q=FBbt_00003748,NeuronsPresynapticHere \"Run in VFB: Neurons with presynaptic terminals in medulla\"), and [333](https://v2.virtualflybrain.org/org.geppetto.frontend/geppetto?q=FBbt_00003748,NeuronsPostsynapticHere \"Run in VFB: Neurons with postsynaptic terminals in medulla\") results, respectively. VFB holds [226524](https://v2.virtualflybrain.org/org.geppetto.frontend/geppetto?q=FBbt_00003748,ImagesNeurons \"Run in VFB: Images of neurons with some part in medulla\") images of neurons with some part in the medulla.", + "quality_flags": { + "has_tool_status": true, + "no_tool_factual_answer": false, + "tool_claim_without_tool": false, + "disambiguation_only_answer": false, + "investigation_plan_answer": false, + "not_verified_or_no_results_answer": false, + "graph_failure_mentioned": false, + "missing_required_graph": false, + "used_data_resource": false, + "response_chars": 1734, + "status_count": 12, + "addressless_followon": false, + "context_lost_across_turn": false, + "unmatched_claim_after_resolve": false, + "repeats_answered_question": false, + "slow_followup_turn": false, + "slowest_followup_ms": 22034 + } + }, + { + "attempt_index": 57, + "task_index": 57, + "task_id": "C6", + "tier": 7, + "title": "Innervation asked of a pronoun", + "question": "Tell me about the antennal lobe.", + "requires_graph": false, + "min_graphs": 0, + "repetition": 1, + "duration_ms": 19680, + "status_messages": [ + { + "message": "Thinking...", + "phase": "llm" + }, + { + "message": "Running the query behind that suggestion", + "phase": "mcp" + }, + { + "message": "Resolving 1 term in VFB", + "phase": "mcp" + }, + { + "message": "Querying VFB", + "phase": "mcp" + }, + { + "message": "Checking the answer is covered", + "phase": "llm" + }, + { + "message": "Querying VFB", + "phase": "mcp" + }, + { + "message": "Checking the answer is covered", + "phase": "llm" + }, + { + "message": "Writing the answer", + "phase": "llm" + } + ], + "event_count": 162, + "conversation": true, + "turns": [ + { + "turn": 1, + "question": "Tell me about the antennal lobe.", + "focus": null, + "clicked": null, + "duration_ms": 11629, + "ok": true, + "response": "The [antennal lobe](https://www.virtualflybrain.org/reports/FBbt_00003924 \"Open antennal lobe in Virtual Fly Brain\") is a synaptic neuropil domain of the deutocerebrum that is the main target for innervation from the antennal nerve. VFB holds records including transgene expression in antennal lobe commissural pioneer interneuron, downstream connectivity classes for antennal lobe commissural pioneer interneuron, and upstream connectivity classes for antennal lobe commissural pioneer interneuron. The antennal lobe is a region in the Drosophila nervous system where users can search for synaptic input.", + "followons": [ + { + "id": "FBbt_00003924", + "query_type": "ListAllAvailableImages", + "query": "Which images of antennal lobe does VFB have?" + }, + { + "id": "FBbt_00003924", + "query_type": "NeuronsPartHere", + "query": "Which neurons have part of their arbour in the antennal lobe?" + }, + { + "id": "FBbt_00003924", + "query_type": "NeuronsSynaptic", + "query": "Which neurons have synaptic terminals in the antennal lobe?" + }, + { + "id": "FBbt_00003924", + "query_type": "NeuronsPresynapticHere", + "query": "Which neurons provide input to the antennal lobe?" + }, + { + "id": "FBbt_00003924", + "query_type": "NeuronsPostsynapticHere", + "query": "Which neurons receive output from the antennal lobe?" + }, + { + "id": "FBbt_00003924", + "query_type": "PartsOf", + "query": "What are the anatomical parts of the antennal lobe?" + } + ], + "context_terms": [ + { + "id": "FBbt_00003924", + "label": "antennal lobe" + } + ], + "reproduction": { + "ids": [ + { + "id": "FBbt_00003924", + "label": "antennal lobe" + } + ], + "calls": [], + "unmapped": [] + }, + "status_count": 6, + "problems": [] + }, + { + "turn": 2, + "question": "Which neurons innervate it?", + "focus": null, + "clicked": null, + "duration_ms": 8051, + "ok": true, + "response": "The [antennal lobe](https://www.virtualflybrain.org/reports/FBbt_00003924 \"Open antennal lobe in Virtual Fly Brain\") is innervated by several types of neurons, including [larval antennal lobe picky local neuron](https://www.virtualflybrain.org/reports/FBbt_00111694 \"Open larval antennal lobe picky local neuron in Virtual Fly Brain\"), [larval antennal lobe broad local neuron](https://www.virtualflybrain.org/reports/FBbt_00111700 \"Open larval antennal lobe broad local neuron in Virtual Fly Brain\"), and various adult olfactory receptor neurons such as [adult olfactory receptor neuron Ir75d ac1](https://www.virtualflybrain.org/reports/FBbt_00110011 \"Open adult olfactory receptor neuron Ir75d ac1 in Virtual Fly Brain\") and adult olfactory receptor neuron Or35a ac3I. Additionally, neurons like [PLP077](https://www.virtualflybrain.org/reports/FBbt_20001577 \"Open PLP077 in Virtual Fly Brain\"), pharyngeal VL1 neuron, and ORN_VM6 also innervate the antennal lobe. Furthermore, adult antennal lobe projection neurons, including [adult antennal lobe projection neuron DL5](https://www.virtualflybrain.org/reports/FBbt_00059280 \"Open adult antennal lobe projection neuron DL5 in Virtual Fly Brain\"), adult antennal lobe projection neuron DM4, and adult antennal lobe projection neuron VA1d, have synaptic terminals in the antennal lobe.", + "followons": [ + { + "id": "FBbt_00003924", + "query_type": "ListAllAvailableImages", + "query": "Which images of antennal lobe does VFB have?" + }, + { + "id": "FBbt_00003924", + "query_type": "NeuronsPartHere", + "query": "Which neurons have part of their arbour in the antennal lobe?" + }, + { + "id": "FBbt_00003924", + "query_type": "NeuronsPostsynapticHere", + "query": "Which neurons receive output from the antennal lobe?" + }, + { + "id": "FBbt_00003924", + "query_type": "PartsOf", + "query": "What are the anatomical parts of the antennal lobe?" + }, + { + "id": "FBbt_00003924", + "query_type": "SubclassesOf", + "query": "What are the subtypes of the antennal lobe?" + }, + { + "id": "FBbt_00003924", + "query_type": "TractsNervesInnervatingHere", + "query": "Which tracts and nerves innervate the antennal lobe?" + } + ], + "context_terms": [ + { + "id": "FBbt_00003924", + "label": "antennal lobe" + } + ], + "reproduction": { + "ids": [ + { + "id": "FBbt_00003924", + "label": "antennal lobe" + } + ], + "calls": [ + { + "id": "FBbt_00003924", + "query_type": "NeuronsPresynapticHere", + "fn": "get_neurons_with_presynaptic_terminals_in" + }, + { + "id": "FBbt_00003924", + "query_type": "NeuronsSynaptic", + "fn": "get_neurons_with_synapses_in" + } + ], + "unmapped": [] + }, + "status_count": 8, + "problems": [] + } + ], + "ok": true, + "request_id": "b84273a9-7584-46e9-b3d5-3140508d700e", + "response_id": "chatcmpl-315ad8788287d29f3c6f8328c5293519", + "images_count": 6, + "graphs_count": 0, + "response": "The [antennal lobe](https://www.virtualflybrain.org/reports/FBbt_00003924 \"Open antennal lobe in Virtual Fly Brain\") is innervated by several types of neurons, including [larval antennal lobe picky local neuron](https://www.virtualflybrain.org/reports/FBbt_00111694 \"Open larval antennal lobe picky local neuron in Virtual Fly Brain\"), [larval antennal lobe broad local neuron](https://www.virtualflybrain.org/reports/FBbt_00111700 \"Open larval antennal lobe broad local neuron in Virtual Fly Brain\"), and various adult olfactory receptor neurons such as [adult olfactory receptor neuron Ir75d ac1](https://www.virtualflybrain.org/reports/FBbt_00110011 \"Open adult olfactory receptor neuron Ir75d ac1 in Virtual Fly Brain\") and adult olfactory receptor neuron Or35a ac3I. Additionally, neurons like [PLP077](https://www.virtualflybrain.org/reports/FBbt_20001577 \"Open PLP077 in Virtual Fly Brain\"), pharyngeal VL1 neuron, and ORN_VM6 also innervate the antennal lobe. Furthermore, adult antennal lobe projection neurons, including [adult antennal lobe projection neuron DL5](https://www.virtualflybrain.org/reports/FBbt_00059280 \"Open adult antennal lobe projection neuron DL5 in Virtual Fly Brain\"), adult antennal lobe projection neuron DM4, and adult antennal lobe projection neuron VA1d, have synaptic terminals in the antennal lobe.", + "quality_flags": { + "has_tool_status": true, + "no_tool_factual_answer": false, + "tool_claim_without_tool": false, + "disambiguation_only_answer": false, + "investigation_plan_answer": false, + "not_verified_or_no_results_answer": false, + "graph_failure_mentioned": false, + "missing_required_graph": false, + "used_data_resource": false, + "response_chars": 1337, + "status_count": 8, + "addressless_followon": false, + "context_lost_across_turn": false, + "unmatched_claim_after_resolve": false, + "repeats_answered_question": false, + "slow_followup_turn": false, + "slowest_followup_ms": 8051 + } + }, + { + "attempt_index": 58, + "task_index": 58, + "task_id": "C7", + "tier": 7, + "title": "Two chip clicks in a row", + "question": "What is the medulla?", + "requires_graph": false, + "min_graphs": 0, + "repetition": 1, + "duration_ms": 150455, + "status_messages": [ + { + "message": "Thinking...", + "phase": "llm" + }, + { + "message": "Running the query behind that suggestion", + "phase": "mcp" + }, + { + "message": "Resolving 1 term in VFB", + "phase": "mcp" + }, + { + "message": "Querying VFB", + "phase": "mcp" + }, + { + "message": "Checking the answer is covered", + "phase": "llm" + }, + { + "message": "Writing the answer", + "phase": "llm" + } + ], + "event_count": 299, + "conversation": true, + "turns": [ + { + "turn": 1, + "question": "What is the medulla?", + "focus": null, + "clicked": null, + "duration_ms": 10691, + "ok": true, + "response": "The [medulla](https://www.virtualflybrain.org/reports/FBbt_00003748 \"Open medulla in Virtual Fly Brain\") is the second optic neuropil, sandwiched between the lamina and the lobula complex. It is divided into 10 layers: layers 1-6 make up the outer medulla, the seventh layer exhibits a distinct architecture, and layers 8-10 make up the inner medulla.", + "followons": [ + { + "id": "FBbt_00003748", + "query_type": "ImagesNeurons", + "query": "Which neuron images have a part in the medulla?" + }, + { + "id": "FBbt_00003748", + "query_type": "TransgeneExpressionHere", + "query": "Which driver lines label the medulla?" + }, + { + "id": "FBbt_00003748", + "query_type": "NeuronsPartHere", + "query": "Which neurons have part of their arbour in the medulla?" + }, + { + "id": "FBbt_00003748", + "query_type": "NeuronsSynaptic", + "query": "Which neurons have synaptic terminals in the medulla?" + }, + { + "id": "FBbt_00003748", + "query_type": "NeuronsPostsynapticHere", + "query": "Which neurons receive output from the medulla?" + }, + { + "id": "FBbt_00003748", + "query_type": "NeuronsPresynapticHere", + "query": "Which neurons provide input to the medulla?" + } + ], + "context_terms": [ + { + "id": "FBbt_00003748", + "label": "medulla" + } + ], + "reproduction": { + "ids": [ + { + "id": "FBbt_00003748", + "label": "medulla" + } + ], + "calls": [], + "unmapped": [] + }, + "status_count": 6, + "problems": [] + }, + { + "turn": 2, + "question": "Which neuron images have a part in the medulla?", + "focus": { + "id": "FBbt_00003748", + "query_type": "ImagesNeurons" + }, + "clicked": 0, + "duration_ms": 8817, + "ok": true, + "response": "There are images of neurons with parts in the [medulla](https://www.virtualflybrain.org/reports/FBbt_00003748 \"Open medulla in Virtual Fly Brain\"). The first 12 images, with their VFB ids, are: OA-AL2i2 (VFB_fw042336); MC64 (VFB_fw043756); MC64 (VFB_fw043755); aMe5 (VFB_fw043590); MeTu3 (VFB_fw043751); MeTu3 (VFB_fw043750); MeTu3 (VFB_fw043744); aMe5 (VFB_fw043591); MeTu-DRA (VFB_fw043752); MeVP6 (VFB_fw043593); MeTu3 (VFB_fw043746); MeTu3 (VFB_fw043745). VFB holds [226,524](https://v2.virtualflybrain.org/org.geppetto.frontend/geppetto?q=FBbt_00003748,ImagesNeurons \"Run in VFB: Images of neurons with some part in medulla\") such images.", + "followons": [ + { + "id": "FBbt_00003748", + "query_type": "TransgeneExpressionHere", + "query": "Which driver lines label the medulla?" + }, + { + "id": "FBbt_00003748", + "query_type": "NeuronsSynaptic", + "query": "Which neurons have synaptic terminals in the medulla?" + }, + { + "id": "FBbt_00003748", + "query_type": "NeuronsPostsynapticHere", + "query": "Which neurons receive output from the medulla?" + }, + { + "id": "FBbt_00003748", + "query_type": "NeuronsPresynapticHere", + "query": "Which neurons provide input to the medulla?" + }, + { + "id": "FBbt_00003748", + "query_type": "PartsOf", + "query": "What are the anatomical parts of the medulla?" + }, + { + "id": "FBbt_00003748", + "query_type": "LineageClonesIn", + "query": "Which lineage clones are found in the medulla?" + } + ], + "context_terms": [ + { + "id": "FBbt_00003748", + "label": "medulla" + } + ], + "reproduction": { + "ids": [ + { + "id": "FBbt_00003748", + "label": "medulla" + } + ], + "calls": [ + { + "id": "FBbt_00003748", + "query_type": "ImagesNeurons", + "fn": "get_images_neurons" + }, + { + "id": "FBbt_00003748", + "query_type": "NeuronsPartHere", + "fn": "get_neurons_with_part_in" + } + ], + "unmapped": [] + }, + "status_count": 8, + "problems": [] + }, + { + "turn": 3, + "question": "Which driver lines label the medulla?", + "focus": { + "id": "FBbt_00003748", + "query_type": "TransgeneExpressionHere" + }, + "clicked": 0, + "duration_ms": 130947, + "ok": true, + "response": "The first 12 driver lines that label the [medulla](https://www.virtualflybrain.org/reports/FBbt_00003748 \"Open medulla in Virtual Fly Brain\") are: [PBac{544.SVS-1}B4[CPTI100035] expression pattern](https://www.virtualflybrain.org/reports/VFBexp_FBti0143533 \"Open PBac{544.SVS-1}B4[CPTI100035] expression pattern in Virtual Fly Brain\"); [PBac{544.SVS-1}Fer2LCH[CPTI100064] expression pattern](https://www.virtualflybrain.org/reports/VFBexp_FBti0143547 \"Open PBac{544.SVS-1}Fer2LCH[CPTI100064] expression pattern in Virtual Fly Brain\"); [PBac{566.P.SVS-1}IA-2[CPTI100013] expression pattern](https://www.virtualflybrain.org/reports/VFBexp_FBti0143524 \"Open PBac{566.P.SVS-1}IA-2[CPTI100013] expression pattern in Virtual Fly Brain\"); [PBac{602.P.SVS-1}CG7675[CPTI000703] expression pattern](https://www.virtualflybrain.org/reports/VFBexp_FBti0144033 \"Open PBac{602.P.SVS-1}CG7675[CPTI000703] expression pattern in Virtual Fly Brain\"); [PBac{602.P.SVS-1}dlg1[CPTI000207] expression pattern](https://www.virtualflybrain.org/reports/VFBexp_FBti0144076 \"Open PBac{602.P.SVS-1}dlg1[CPTI000207] expression pattern in Virtual Fly Brain\"); PBac{681.P.FSVS-1}CG11138[CPTI001659] expression pattern; PBac{681.P.FSVS-1}CG6983[CPTI001802] expression pattern; PBac{681.P.FSVS-1}CG7920[CPTI002166] expression pattern; PBac{681.P.FSVS-1}CG9336[CPTI001654] expression pattern; PBac{681.P.FSVS-1}Pka-R2[CPTI001580] expression pattern; PBac{681.P.FSVS-1}cpx[CPTI001473] expression pattern; PBac{681.P.FSVS-1}larp[CPTI002498] expression pattern. VFB holds [2,342](https://v2.virtualflybrain.org/org.geppetto.frontend/geppetto?q=FBbt_00003748,TransgeneExpressionHere \"Run in VFB: Transgene expression in medulla\") such driver lines.", + "followons": [ + { + "id": "FBbt_00003748", + "query_type": "ImagesNeurons", + "query": "Which neuron images have a part in the medulla?" + }, + { + "id": "FBbt_00003748", + "query_type": "NeuronsPartHere", + "query": "Which neurons have part of their arbour in the medulla?" + }, + { + "id": "FBbt_00003748", + "query_type": "NeuronsSynaptic", + "query": "Which neurons have synaptic terminals in the medulla?" + }, + { + "id": "FBbt_00003748", + "query_type": "NeuronsPostsynapticHere", + "query": "Which neurons receive output from the medulla?" + }, + { + "id": "FBbt_00003748", + "query_type": "NeuronsPresynapticHere", + "query": "Which neurons provide input to the medulla?" + }, + { + "id": "FBbt_00003748", + "query_type": "PartsOf", + "query": "What are the anatomical parts of the medulla?" + } + ], + "context_terms": [ + { + "id": "FBbt_00003748", + "label": "medulla" + } + ], + "reproduction": { + "ids": [ + { + "id": "FBbt_00003748", + "label": "medulla" + } + ], + "calls": [ + { + "id": "FBbt_00003748", + "query_type": "TransgeneExpressionHere", + "fn": "get_transgene_expression_here" + }, + { + "id": "FBbt_00003748", + "query_type": "NeuronsPartHere", + "fn": "get_neurons_with_part_in" + }, + { + "id": "FBbt_00003748", + "query_type": "ImagesNeurons", + "fn": "get_images_neurons" + } + ], + "unmapped": [] + }, + "status_count": 6, + "problems": [] + } + ], + "ok": true, + "request_id": "c031a8f0-d8e8-49d6-976d-8567a0b3854d", + "response_id": "chatcmpl-2abfd2f45f86ffd56587dc06d1cf349b", + "images_count": 8, + "graphs_count": 0, + "response": "The first 12 driver lines that label the [medulla](https://www.virtualflybrain.org/reports/FBbt_00003748 \"Open medulla in Virtual Fly Brain\") are: [PBac{544.SVS-1}B4[CPTI100035] expression pattern](https://www.virtualflybrain.org/reports/VFBexp_FBti0143533 \"Open PBac{544.SVS-1}B4[CPTI100035] expression pattern in Virtual Fly Brain\"); [PBac{544.SVS-1}Fer2LCH[CPTI100064] expression pattern](https://www.virtualflybrain.org/reports/VFBexp_FBti0143547 \"Open PBac{544.SVS-1}Fer2LCH[CPTI100064] expression pattern in Virtual Fly Brain\"); [PBac{566.P.SVS-1}IA-2[CPTI100013] expression pattern](https://www.virtualflybrain.org/reports/VFBexp_FBti0143524 \"Open PBac{566.P.SVS-1}IA-2[CPTI100013] expression pattern in Virtual Fly Brain\"); [PBac{602.P.SVS-1}CG7675[CPTI000703] expression pattern](https://www.virtualflybrain.org/reports/VFBexp_FBti0144033 \"Open PBac{602.P.SVS-1}CG7675[CPTI000703] expression pattern in Virtual Fly Brain\"); [PBac{602.P.SVS-1}dlg1[CPTI000207] expression pattern](https://www.virtualflybrain.org/reports/VFBexp_FBti0144076 \"Open PBac{602.P.SVS-1}dlg1[CPTI000207] expression pattern in Virtual Fly Brain\"); PBac{681.P.FSVS-1}CG11138[CPTI001659] expression pattern; PBac{681.P.FSVS-1}CG6983[CPTI001802] expression pattern; PBac{681.P.FSVS-1}CG7920[CPTI002166] expression pattern; PBac{681.P.FSVS-1}CG9336[CPTI001654] expression pattern; PBac{681.P.FSVS-1}Pka-R2[CPTI001580] expression pattern; PBac{681.P.FSVS-1}cpx[CPTI001473] expression pattern; PBac{681.P.FSVS-1}larp[CPTI002498] expression pattern. VFB holds [2,342](https://v2.virtualflybrain.org/org.geppetto.frontend/geppetto?q=FBbt_00003748,TransgeneExpressionHere \"Run in VFB: Transgene expression in medulla\") such driver lines.", + "quality_flags": { + "has_tool_status": true, + "no_tool_factual_answer": false, + "tool_claim_without_tool": false, + "disambiguation_only_answer": false, + "investigation_plan_answer": false, + "not_verified_or_no_results_answer": false, + "graph_failure_mentioned": false, + "missing_required_graph": false, + "used_data_resource": false, + "response_chars": 1710, + "status_count": 6, + "addressless_followon": false, + "context_lost_across_turn": false, + "unmatched_claim_after_resolve": false, + "repeats_answered_question": false, + "slow_followup_turn": true, + "slowest_followup_ms": 130947 + } + }, + { + "attempt_index": 59, + "task_index": 59, + "task_id": "C8", + "tier": 7, + "title": "Driver lines asked warm", + "question": "What is the mushroom body?", + "requires_graph": false, + "min_graphs": 0, + "repetition": 1, + "duration_ms": 22053, + "status_messages": [ + { + "message": "Thinking...", + "phase": "llm" + }, + { + "message": "Running the query behind that suggestion", + "phase": "mcp" + }, + { + "message": "Resolving 1 term in VFB", + "phase": "mcp" + }, + { + "message": "Querying VFB", + "phase": "mcp" + }, + { + "message": "Checking the answer is covered", + "phase": "llm" + }, + { + "message": "Writing the answer", + "phase": "llm" + } + ], + "event_count": 318, + "conversation": true, + "turns": [ + { + "turn": 1, + "question": "What is the mushroom body?", + "focus": null, + "clicked": null, + "duration_ms": 10744, + "ok": true, + "response": "The [mushroom body](https://www.virtualflybrain.org/reports/FBbt_00005801 \"Open mushroom body in Virtual Fly Brain\") is a bilaterally paired neuropil structure situated postero-dorsally in the protocerebrum that functions in olfactory associative learning and memory. It is divided into the calyx, which receives sensory interneuron afferents, the pedunculus, a thick axon bundle extending from the calyx to the base of the lobes, and the mushroom body lobe system, which consists of a vertical branch and a medial branch, and has different structures at different life stages.", + "followons": [ + { + "id": "FBbt_00005801", + "query_type": "ImagesNeurons", + "query": "Which neuron images have a part in the mushroom body?" + }, + { + "id": "FBbt_00005801", + "query_type": "TransgeneExpressionHere", + "query": "Which driver lines label the mushroom body?" + }, + { + "id": "FBbt_00005801", + "query_type": "NeuronsPartHere", + "query": "Which neurons have part of their arbour in the mushroom body?" + }, + { + "id": "FBbt_00005801", + "query_type": "NeuronsSynaptic", + "query": "Which neurons have synaptic terminals in the mushroom body?" + }, + { + "id": "FBbt_00005801", + "query_type": "NeuronsPresynapticHere", + "query": "Which neurons provide input to the mushroom body?" + }, + { + "id": "FBbt_00005801", + "query_type": "NeuronsPostsynapticHere", + "query": "Which neurons receive output from the mushroom body?" + } + ], + "context_terms": [ + { + "id": "FBbt_00005801", + "label": "mushroom body" + } + ], + "reproduction": { + "ids": [ + { + "id": "FBbt_00005801", + "label": "mushroom body" + } + ], + "calls": [], + "unmapped": [] + }, + "status_count": 6, + "problems": [] + }, + { + "turn": 2, + "question": "Which driver lines label it?", + "focus": null, + "clicked": null, + "duration_ms": 11309, + "ok": true, + "response": "The [mushroom body](https://www.virtualflybrain.org/reports/FBbt_00005801 \"Open mushroom body in Virtual Fly Brain\") is labeled by multiple driver lines, including those whose expression patterns are recorded in VFB as [PBac{544.SVS-1}Bsg[CPTI100062] expression pattern](https://www.virtualflybrain.org/reports/VFBexp_FBti0143545 \"Open PBac{544.SVS-1}Bsg[CPTI100062] expression pattern in Virtual Fly Brain\"), [PBac{566.P.SVS-1}Bsg[CPTI100005] expression pattern](https://www.virtualflybrain.org/reports/VFBexp_FBti0143520 \"Open PBac{566.P.SVS-1}Bsg[CPTI100005] expression pattern in Virtual Fly Brain\"), [PBac{566.P.SVS-1}IA-2[CPTI100013] expression pattern](https://www.virtualflybrain.org/reports/VFBexp_FBti0143524 \"Open PBac{566.P.SVS-1}IA-2[CPTI100013] expression pattern in Virtual Fly Brain\"), [PBac{566.P.SVS-1}sgg[CPTI100027] expression pattern](https://www.virtualflybrain.org/reports/VFBexp_FBti0143529 \"Open PBac{566.P.SVS-1}sgg[CPTI100027] expression pattern in Virtual Fly Brain\"), [PBac{602.P.SVS-1}Fas2[CPTI000483] expression pattern](https://www.virtualflybrain.org/reports/VFBexp_FBti0144014 \"Open PBac{602.P.SVS-1}Fas2[CPTI000483] expression pattern in Virtual Fly Brain\"), PBac{602.P.SVS-1}HDAC4[CPTI000077] expression pattern, PBac{602.P.SVS-1}Pax[CPTI000161] expression pattern, PBac{602.P.SVS-1}Sema1a[CPTI000505] expression pattern, PBac{602.P.SVS-1}Tm1[CPTI000760] expression pattern, PBac{602.P.SVS-1}dlg1[CPTI000207] expression pattern, PBac{602.P.SVS-1}dlp[CPTI000445] expression pattern, and PBac{602.P.SVS-1}hzg[CPTI000737] expression pattern. Hemidrivers, such as P{VT017411-GAL4.DBD} ∩ P{VT019018-p65.AD}, are also used.", + "followons": [ + { + "id": "FBbt_00005801", + "query_type": "ImagesNeurons", + "query": "Which neuron images have a part in the mushroom body?" + }, + { + "id": "FBbt_00005801", + "query_type": "NeuronsPartHere", + "query": "Which neurons have part of their arbour in the mushroom body?" + }, + { + "id": "FBbt_00005801", + "query_type": "NeuronsSynaptic", + "query": "Which neurons have synaptic terminals in the mushroom body?" + }, + { + "id": "FBbt_00005801", + "query_type": "NeuronsPresynapticHere", + "query": "Which neurons provide input to the mushroom body?" + }, + { + "id": "FBbt_00005801", + "query_type": "NeuronsPostsynapticHere", + "query": "Which neurons receive output from the mushroom body?" + }, + { + "id": "FBbt_00005801", + "query_type": "PartsOf", + "query": "What are the anatomical parts of the mushroom body?" + } + ], + "context_terms": [ + { + "id": "FBbt_00005801", + "label": "mushroom body" + } + ], + "reproduction": { + "ids": [ + { + "id": "FBbt_00005801", + "label": "mushroom body" + } + ], + "calls": [ + { + "id": "FBbt_00005801", + "query_type": "TransgeneExpressionHere", + "fn": "get_transgene_expression_here" + } + ], + "unmapped": [] + }, + "status_count": 6, + "problems": [] + } + ], + "ok": true, + "request_id": "52ad4d69-b77f-4daf-b24a-937420edc3eb", + "response_id": "chatcmpl-73e12f129124acd031b1762bf6ad9626", + "images_count": 8, + "graphs_count": 0, + "response": "The [mushroom body](https://www.virtualflybrain.org/reports/FBbt_00005801 \"Open mushroom body in Virtual Fly Brain\") is labeled by multiple driver lines, including those whose expression patterns are recorded in VFB as [PBac{544.SVS-1}Bsg[CPTI100062] expression pattern](https://www.virtualflybrain.org/reports/VFBexp_FBti0143545 \"Open PBac{544.SVS-1}Bsg[CPTI100062] expression pattern in Virtual Fly Brain\"), [PBac{566.P.SVS-1}Bsg[CPTI100005] expression pattern](https://www.virtualflybrain.org/reports/VFBexp_FBti0143520 \"Open PBac{566.P.SVS-1}Bsg[CPTI100005] expression pattern in Virtual Fly Brain\"), [PBac{566.P.SVS-1}IA-2[CPTI100013] expression pattern](https://www.virtualflybrain.org/reports/VFBexp_FBti0143524 \"Open PBac{566.P.SVS-1}IA-2[CPTI100013] expression pattern in Virtual Fly Brain\"), [PBac{566.P.SVS-1}sgg[CPTI100027] expression pattern](https://www.virtualflybrain.org/reports/VFBexp_FBti0143529 \"Open PBac{566.P.SVS-1}sgg[CPTI100027] expression pattern in Virtual Fly Brain\"), [PBac{602.P.SVS-1}Fas2[CPTI000483] expression pattern](https://www.virtualflybrain.org/reports/VFBexp_FBti0144014 \"Open PBac{602.P.SVS-1}Fas2[CPTI000483] expression pattern in Virtual Fly Brain\"), PBac{602.P.SVS-1}HDAC4[CPTI000077] expression pattern, PBac{602.P.SVS-1}Pax[CPTI000161] expression pattern, PBac{602.P.SVS-1}Sema1a[CPTI000505] expression pattern, PBac{602.P.SVS-1}Tm1[CPTI000760] expression pattern, PBac{602.P.SVS-1}dlg1[CPTI000207] expression pattern, PBac{602.P.SVS-1}dlp[CPTI000445] expression pattern, and PBac{602.P.SVS-1}hzg[CPTI000737] expression pattern. Hemidrivers, such as P{VT017411-GAL4.DBD} ∩ P{VT019018-p65.AD}, are also used.", + "quality_flags": { + "has_tool_status": true, + "no_tool_factual_answer": false, + "tool_claim_without_tool": false, + "disambiguation_only_answer": false, + "investigation_plan_answer": false, + "not_verified_or_no_results_answer": false, + "graph_failure_mentioned": false, + "missing_required_graph": false, + "used_data_resource": false, + "response_chars": 1653, + "status_count": 6, + "addressless_followon": false, + "context_lost_across_turn": false, + "unmatched_claim_after_resolve": false, + "repeats_answered_question": false, + "slow_followup_turn": false, + "slowest_followup_ms": 11309 + } + }, + { + "attempt_index": 60, + "task_index": 60, + "task_id": "C9", + "tier": 7, + "title": "A follow-up that changes the term, not the query", + "question": "Which neurons provide input to the medulla?", + "requires_graph": false, + "min_graphs": 0, + "repetition": 1, + "duration_ms": 22780, + "status_messages": [ + { + "message": "Thinking...", + "phase": "llm" + }, + { + "message": "Planning the answer", + "phase": "llm" + }, + { + "message": "Resolving 1 term in VFB", + "phase": "mcp" + }, + { + "message": "Reading VFB term info", + "phase": "mcp" + }, + { + "message": "Querying VFB", + "phase": "mcp" + }, + { + "message": "Checking the answer is covered", + "phase": "llm" + }, + { + "message": "Writing the answer", + "phase": "llm" + }, + { + "message": "Checking before saying VFB has no data", + "phase": "mcp" + }, + { + "message": "Querying VFB", + "phase": "mcp" + }, + { + "message": "Querying VFB", + "phase": "mcp" + }, + { + "message": "Querying VFB", + "phase": "mcp" + }, + { + "message": "Checking the answer is covered", + "phase": "llm" + }, + { + "message": "Writing the answer", + "phase": "llm" + } + ], + "event_count": 146, + "conversation": true, + "turns": [ + { + "turn": 1, + "question": "Which neurons provide input to the medulla?", + "focus": null, + "clicked": null, + "duration_ms": 8559, + "ok": true, + "response": "Neurons with presynaptic terminals in [medulla](https://www.virtualflybrain.org/reports/FBbt_00003748 \"Open medulla in Virtual Fly Brain\") provide input to the medulla. VFB records show [262](https://v2.virtualflybrain.org/org.geppetto.frontend/geppetto?q=FBbt_00003748,NeuronsPresynapticHere \"Run in VFB: Neurons with presynaptic terminals in medulla\") neuron types with presynaptic terminals in medulla, including [Dm8b](https://www.virtualflybrain.org/reports/FBbt_00110069 \"Open Dm8b in Virtual Fly Brain\"), [PS128](https://www.virtualflybrain.org/reports/FBbt_20001883 \"Open PS128 in Virtual Fly Brain\"), [Mi10b](https://www.virtualflybrain.org/reports/FBbt_00110070 \"Open Mi10b in Virtual Fly Brain\"), [CB3849](https://www.virtualflybrain.org/reports/FBbt_20007264 \"Open CB3849 in Virtual Fly Brain\"), [TmY-ds](https://www.virtualflybrain.org/reports/FBbt_00052643 \"Open TmY-ds in Virtual Fly Brain\"), [Dm7](https://www.virtualflybrain.org/reports/FBbt_00003774 \"Open Dm7 in Virtual Fly Brain\"), Mi6, Mi8, Tm10, Tm13, Tm14, and Tm18.", + "followons": [ + { + "id": "FBbt_00003748", + "query_type": "ImagesNeurons", + "query": "Which neuron images have a part in the medulla?" + }, + { + "id": "FBbt_00003748", + "query_type": "TransgeneExpressionHere", + "query": "Which driver lines label the medulla?" + }, + { + "id": "FBbt_00003748", + "query_type": "NeuronsPartHere", + "query": "Which neurons have part of their arbour in the medulla?" + }, + { + "id": "FBbt_00003748", + "query_type": "NeuronsSynaptic", + "query": "Which neurons have synaptic terminals in the medulla?" + }, + { + "id": "FBbt_00003748", + "query_type": "PartsOf", + "query": "What are the anatomical parts of the medulla?" + }, + { + "id": "FBbt_00003748", + "query_type": "LineageClonesIn", + "query": "Which lineage clones are found in the medulla?" + } + ], + "context_terms": [ + { + "id": "FBbt_00003748", + "label": "medulla" + } + ], + "reproduction": { + "ids": [ + { + "id": "FBbt_00003748", + "label": "medulla" + } + ], + "calls": [ + { + "id": "FBbt_00003748", + "query_type": "NeuronsPresynapticHere", + "fn": "get_neurons_with_presynaptic_terminals_in" + }, + { + "id": "FBbt_00003748", + "query_type": "NeuronsPostsynapticHere", + "fn": "get_neurons_with_postsynaptic_terminals_in" + } + ], + "unmapped": [] + }, + "status_count": 9, + "problems": [] + }, + { + "turn": 2, + "question": "And the lobula?", + "focus": null, + "clicked": null, + "duration_ms": 14221, + "ok": true, + "response": "Neurons with synaptic terminals in [lobula](https://www.virtualflybrain.org/reports/FBbt_00003852 \"Open lobula in Virtual Fly Brain\") provide input to the lobula. VFB records show [528](https://v2.virtualflybrain.org/org.geppetto.frontend/geppetto?q=FBbt_00003852,NeuronsPartHere \"Run in VFB: Neurons with some part in lobula\") neuron types with synaptic terminals in lobula, including [AVLP391](https://www.virtualflybrain.org/reports/FBbt_20000500 \"Open AVLP391 in Virtual Fly Brain\"), [PLP031](https://www.virtualflybrain.org/reports/FBbt_20001531 \"Open PLP031 in Virtual Fly Brain\"), [TmY27](https://www.virtualflybrain.org/reports/FBbt_00110067 \"Open TmY27 in Virtual Fly Brain\"), [lobula columnar neuron vGlutLcnnew2](https://www.virtualflybrain.org/reports/FBbt_00110100 \"Open lobula columnar neuron vGlutLcnnew2 in Virtual Fly Brain\"), [OA-AL2b](https://www.virtualflybrain.org/reports/FBbt_00110145 \"Open OA-AL2b in Virtual Fly Brain\"), adult histaminergic HP3 neuron, translobula neuron, Tl1, Tl2, Tm1a, SIP063, and SLP339.", + "followons": [ + { + "id": "FBbt_00003852", + "query_type": "NeuronsPresynapticHere", + "query": "Which neurons provide input to the lobula?" + }, + { + "id": "FBbt_00003852", + "query_type": "NeuronsPostsynapticHere", + "query": "Which neurons receive output from the lobula?" + }, + { + "id": "FBbt_00003852", + "query_type": "PartsOf", + "query": "What are the anatomical parts of the lobula?" + }, + { + "id": "FBbt_00003852", + "query_type": "TractsNervesInnervatingHere", + "query": "Which tracts and nerves innervate the lobula?" + }, + { + "id": "FBbt_00003852", + "query_type": "LineageClonesIn", + "query": "Which lineage clones are found in the lobula?" + }, + { + "id": "FBbt_00003852", + "query_type": "ImagesNeurons", + "query": "Which neuron images have a part in the lobula?" + } + ], + "context_terms": [ + { + "id": "FBbt_00003852", + "label": "lobula" + }, + { + "id": "FBbt_00003748", + "label": "medulla" + } + ], + "reproduction": { + "ids": [ + { + "id": "FBbt_00003852", + "label": "lobula" + }, + { + "id": "FBbt_00003748", + "label": "medulla" + } + ], + "calls": [ + { + "id": "FBbt_00003852", + "query_type": "ListAllAvailableImages", + "fn": "get_instances" + }, + { + "id": "FBbt_00003852", + "query_type": "NeuronsPartHere", + "fn": "get_neurons_with_part_in" + }, + { + "id": "FBbt_00003852", + "query_type": "NeuronsSynaptic", + "fn": "get_neurons_with_synapses_in" + }, + { + "id": "FBbt_00003748", + "query_type": "NeuronsPresynapticHere", + "fn": "get_neurons_with_presynaptic_terminals_in" + }, + { + "id": "FBbt_00003748", + "query_type": "NeuronsPostsynapticHere", + "fn": "get_neurons_with_postsynaptic_terminals_in" + } + ], + "unmapped": [] + }, + "status_count": 13, + "problems": [] + } + ], + "ok": true, + "request_id": "177a5ce9-1ac0-43da-b478-e9fe922984c3", + "response_id": "chatcmpl-9dc30652a2f2e2cad090741ed3240309", + "images_count": 4, + "graphs_count": 0, + "response": "Neurons with synaptic terminals in [lobula](https://www.virtualflybrain.org/reports/FBbt_00003852 \"Open lobula in Virtual Fly Brain\") provide input to the lobula. VFB records show [528](https://v2.virtualflybrain.org/org.geppetto.frontend/geppetto?q=FBbt_00003852,NeuronsPartHere \"Run in VFB: Neurons with some part in lobula\") neuron types with synaptic terminals in lobula, including [AVLP391](https://www.virtualflybrain.org/reports/FBbt_20000500 \"Open AVLP391 in Virtual Fly Brain\"), [PLP031](https://www.virtualflybrain.org/reports/FBbt_20001531 \"Open PLP031 in Virtual Fly Brain\"), [TmY27](https://www.virtualflybrain.org/reports/FBbt_00110067 \"Open TmY27 in Virtual Fly Brain\"), [lobula columnar neuron vGlutLcnnew2](https://www.virtualflybrain.org/reports/FBbt_00110100 \"Open lobula columnar neuron vGlutLcnnew2 in Virtual Fly Brain\"), [OA-AL2b](https://www.virtualflybrain.org/reports/FBbt_00110145 \"Open OA-AL2b in Virtual Fly Brain\"), adult histaminergic HP3 neuron, translobula neuron, Tl1, Tl2, Tm1a, SIP063, and SLP339.", + "quality_flags": { + "has_tool_status": true, + "no_tool_factual_answer": false, + "tool_claim_without_tool": false, + "disambiguation_only_answer": false, + "investigation_plan_answer": false, + "not_verified_or_no_results_answer": false, + "graph_failure_mentioned": false, + "missing_required_graph": false, + "used_data_resource": false, + "response_chars": 1033, + "status_count": 13, + "addressless_followon": false, + "context_lost_across_turn": false, + "unmatched_claim_after_resolve": false, + "repeats_answered_question": false, + "slow_followup_turn": false, + "slowest_followup_ms": 14221 + } + }, + { + "attempt_index": 61, + "task_index": 61, + "task_id": "C10", + "tier": 7, + "title": "A term the session already resolved is never called unmatched", + "question": "What is the protocerebral bridge?", + "requires_graph": false, + "min_graphs": 0, + "repetition": 1, + "duration_ms": 51590, + "status_messages": [ + { + "message": "Thinking...", + "phase": "llm" + }, + { + "message": "Planning the answer", + "phase": "llm" + }, + { + "message": "Resolving 2 terms in VFB", + "phase": "mcp" + }, + { + "message": "Querying VFB connectivity", + "phase": "mcp" + }, + { + "message": "Querying VFB", + "phase": "mcp" + }, + { + "message": "Querying VFB", + "phase": "mcp" + }, + { + "message": "Querying VFB", + "phase": "mcp" + }, + { + "message": "Querying VFB", + "phase": "mcp" + }, + { + "message": "Checking the answer is covered", + "phase": "llm" + }, + { + "message": "Querying VFB", + "phase": "mcp" + }, + { + "message": "Checking the answer is covered", + "phase": "llm" + }, + { + "message": "Writing the answer", + "phase": "llm" + } + ], + "event_count": 190, + "conversation": true, + "turns": [ + { + "turn": 1, + "question": "What is the protocerebral bridge?", + "focus": null, + "clicked": null, + "duration_ms": 6597, + "ok": true, + "response": "The [protocerebral bridge](https://www.virtualflybrain.org/reports/FBbt_00003668 \"Open protocerebral bridge in Virtual Fly Brain\") is a handle bar-shaped synaptic neuropil located just posterior to the fan-shaped body. Its lateral edge ends at the posterior end of the inferior clamp near the medial equatorial fascicle. A row of 18 connected slices, 9 on each side of the midline, forms a dorso-posteriorly located part of the central complex embedded in the cortex between the calyces of the two mushroom bodies.", + "followons": [ + { + "id": "FBbt_00003668", + "query_type": "ListAllAvailableImages", + "query": "Which images of protocerebral bridge does VFB have?" + }, + { + "id": "FBbt_00003668", + "query_type": "NeuronsPartHere", + "query": "Which neurons have part of their arbour in the protocerebral bridge?" + }, + { + "id": "FBbt_00003668", + "query_type": "NeuronsSynaptic", + "query": "Which neurons have synaptic terminals in the protocerebral bridge?" + }, + { + "id": "FBbt_00003668", + "query_type": "NeuronsPresynapticHere", + "query": "Which neurons provide input to the protocerebral bridge?" + }, + { + "id": "FBbt_00003668", + "query_type": "NeuronsPostsynapticHere", + "query": "Which neurons receive output from the protocerebral bridge?" + }, + { + "id": "FBbt_00003668", + "query_type": "PartsOf", + "query": "What are the anatomical parts of the protocerebral bridge?" + } + ], + "context_terms": [ + { + "id": "FBbt_00003668", + "label": "protocerebral bridge" + } + ], + "reproduction": { + "ids": [ + { + "id": "FBbt_00003668", + "label": "protocerebral bridge" + } + ], + "calls": [], + "unmapped": [] + }, + "status_count": 6, + "problems": [] + }, + { + "turn": 2, + "question": "How does it relate to the ellipsoid body?", + "focus": null, + "clicked": null, + "duration_ms": 14847, + "ok": true, + "response": "The [protocerebral bridge](https://www.virtualflybrain.org/reports/FBbt_00003668 \"Open protocerebral bridge in Virtual Fly Brain\") and the [ellipsoid body](https://www.virtualflybrain.org/reports/FBbt_00003678 \"Open ellipsoid body in Virtual Fly Brain\") are connected by neurons. VFB records show that there are neurons with some part in the ellipsoid body, including [adult protocerebral bridge glomerulus 1-ellipsoid body canal-dorsal gall neuron](https://www.virtualflybrain.org/reports/FBbt_00111376 \"Open adult protocerebral bridge glomerulus 1-ellipsoid body canal-dorsal gall neuron in Virtual Fly Brain\"), and adult protocerebral bridge glomerulus 4-ellipsoid body canal-ventral gall neuron, among others. These neurons also have synaptic terminals in the ellipsoid body.", + "followons": [ + { + "id": "FBbt_00003668", + "query_type": "ListAllAvailableImages", + "query": "Which images of protocerebral bridge does VFB have?" + }, + { + "id": "FBbt_00003668", + "query_type": "NeuronsPartHere", + "query": "Which neurons have part of their arbour in the protocerebral bridge?" + }, + { + "id": "FBbt_00003668", + "query_type": "NeuronsSynaptic", + "query": "Which neurons have synaptic terminals in the protocerebral bridge?" + }, + { + "id": "FBbt_00003668", + "query_type": "NeuronsPresynapticHere", + "query": "Which neurons provide input to the protocerebral bridge?" + }, + { + "id": "FBbt_00003668", + "query_type": "NeuronsPostsynapticHere", + "query": "Which neurons receive output from the protocerebral bridge?" + }, + { + "id": "FBbt_00003668", + "query_type": "PartsOf", + "query": "What are the anatomical parts of the protocerebral bridge?" + } + ], + "context_terms": [ + { + "id": "FBbt_00003668", + "label": "protocerebral bridge" + }, + { + "id": "FBbt_00003678", + "label": "ellipsoid body" + } + ], + "reproduction": { + "ids": [ + { + "id": "FBbt_00003668", + "label": "protocerebral bridge" + }, + { + "id": "FBbt_00003678", + "label": "ellipsoid body" + } + ], + "calls": [ + { + "id": "FBbt_00003678", + "query_type": "ListAllAvailableImages", + "fn": "get_instances" + }, + { + "id": "FBbt_00003678", + "query_type": "NeuronsPartHere", + "fn": "get_neurons_with_part_in" + }, + { + "id": "FBbt_00003678", + "query_type": "NeuronsSynaptic", + "fn": "get_neurons_with_synapses_in" + } + ], + "unmapped": [] + }, + "status_count": 13, + "problems": [] + }, + { + "turn": 3, + "question": "Which neurons connect them?", + "focus": null, + "clicked": null, + "duration_ms": 30146, + "ok": true, + "response": "The neurons that connect the [protocerebral bridge](https://www.virtualflybrain.org/reports/FBbt_00003668 \"Open protocerebral bridge in Virtual Fly Brain\") and the [ellipsoid body](https://www.virtualflybrain.org/reports/FBbt_00003678 \"Open ellipsoid body in Virtual Fly Brain\") include the [adult protocerebral bridge glomerulus 1-ellipsoid body canal-dorsal gall neuron](https://www.virtualflybrain.org/reports/FBbt_00111376 \"Open adult protocerebral bridge glomerulus 1-ellipsoid body canal-dorsal gall neuron in Virtual Fly Brain\") and the adult protocerebral bridge glomerulus 4-ellipsoid body canal-ventral gall neuron. VFB records show that there are neurons with some part in the ellipsoid body, including these, and also the adult protocerebral bridge glomerulus 5-ellipsoid body canal-dorsal gall neuron, the adult protocerebral bridge glomerulus 6-ellipsoid body canal-ventral gall neuron, the adult protocerebral bridge glomerulus 7-ellipsoid body canal-dorsal gall neuron, and the adult protocerebral bridge glomerulus 8-ellipsoid body canal-ventral gall neuron.", + "followons": [ + { + "id": "FBbt_00003668", + "query_type": "ListAllAvailableImages", + "query": "Which images of protocerebral bridge does VFB have?" + }, + { + "id": "FBbt_00003668", + "query_type": "NeuronsPartHere", + "query": "Which neurons have part of their arbour in the protocerebral bridge?" + }, + { + "id": "FBbt_00003668", + "query_type": "PartsOf", + "query": "What are the anatomical parts of the protocerebral bridge?" + }, + { + "id": "FBbt_00003668", + "query_type": "TractsNervesInnervatingHere", + "query": "Which tracts and nerves innervate the protocerebral bridge?" + }, + { + "id": "FBbt_00003668", + "query_type": "LineageClonesIn", + "query": "Which lineage clones are found in the protocerebral bridge?" + }, + { + "id": "FBbt_00003668", + "query_type": "ImagesNeurons", + "query": "Which neuron images have a part in the protocerebral bridge?" + } + ], + "context_terms": [ + { + "id": "FBbt_00003668", + "label": "protocerebral bridge" + }, + { + "id": "FBbt_00003678", + "label": "ellipsoid body" + } + ], + "reproduction": { + "ids": [ + { + "id": "FBbt_00003668", + "label": "protocerebral bridge" + }, + { + "id": "FBbt_00003678", + "label": "ellipsoid body" + } + ], + "calls": [ + { + "id": "FBbt_00003668", + "query_type": "NeuronsPresynapticHere", + "fn": "get_neurons_with_presynaptic_terminals_in" + }, + { + "id": "FBbt_00003668", + "query_type": "NeuronsPostsynapticHere", + "fn": "get_neurons_with_postsynaptic_terminals_in" + }, + { + "id": "FBbt_00003678", + "query_type": "NeuronsPresynapticHere", + "fn": "get_neurons_with_presynaptic_terminals_in" + }, + { + "id": "FBbt_00003678", + "query_type": "NeuronsPostsynapticHere", + "fn": "get_neurons_with_postsynaptic_terminals_in" + }, + { + "id": "FBbt_00003668", + "query_type": "NeuronsSynaptic", + "fn": "get_neurons_with_synapses_in" + }, + { + "id": "FBbt_00003678", + "query_type": "ListAllAvailableImages", + "fn": "get_instances" + }, + { + "id": "FBbt_00003678", + "query_type": "NeuronsPartHere", + "fn": "get_neurons_with_part_in" + }, + { + "id": "FBbt_00003678", + "query_type": "NeuronsSynaptic", + "fn": "get_neurons_with_synapses_in" + } + ], + "unmapped": [] + }, + "status_count": 12, + "problems": [] + } + ], + "ok": true, + "request_id": "947da328-b6c9-466b-ab74-e4c3db67dfad", + "response_id": "chatcmpl-9dfa7a62255919bfd6fd02edf9c6380e", + "images_count": 8, + "graphs_count": 1, + "response": "The neurons that connect the [protocerebral bridge](https://www.virtualflybrain.org/reports/FBbt_00003668 \"Open protocerebral bridge in Virtual Fly Brain\") and the [ellipsoid body](https://www.virtualflybrain.org/reports/FBbt_00003678 \"Open ellipsoid body in Virtual Fly Brain\") include the [adult protocerebral bridge glomerulus 1-ellipsoid body canal-dorsal gall neuron](https://www.virtualflybrain.org/reports/FBbt_00111376 \"Open adult protocerebral bridge glomerulus 1-ellipsoid body canal-dorsal gall neuron in Virtual Fly Brain\") and the adult protocerebral bridge glomerulus 4-ellipsoid body canal-ventral gall neuron. VFB records show that there are neurons with some part in the ellipsoid body, including these, and also the adult protocerebral bridge glomerulus 5-ellipsoid body canal-dorsal gall neuron, the adult protocerebral bridge glomerulus 6-ellipsoid body canal-ventral gall neuron, the adult protocerebral bridge glomerulus 7-ellipsoid body canal-dorsal gall neuron, and the adult protocerebral bridge glomerulus 8-ellipsoid body canal-ventral gall neuron.", + "graphs": [ + { + "type": "basic_graph", + "version": 1, + "title": "Upstream partners of P6-8P9", + "directed": true, + "layout": "circle", + "nodes": [ + { + "id": "FBbt_00047095", + "label": "adult neuron", + "group": null, + "color": null, + "size": 1.37 + }, + { + "id": "FBbt_00111056", + "label": "P6-8P9", + "group": null, + "color": null, + "size": 4 + }, + { + "id": "FBbt_00005106", + "label": "neuron", + "group": null, + "color": null, + "size": 1.37 + }, + { + "id": "FBbt_00049819", + "label": "adult central complex neuron", + "group": null, + "color": null, + "size": 1.37 + }, + { + "id": "FBbt_00059271", + "label": "CNS neuron", + "group": null, + "color": null, + "size": 1.37 + }, + { + "id": "FBbt_00053387", + "label": "intrinsic neuron of the central complex", + "group": null, + "color": null, + "size": 1.21 + }, + { + "id": "FBbt_00007515", + "label": "large field neuron of the central complex", + "group": null, + "color": null, + "size": 1.2 + }, + { + "id": "FBbt_00003648", + "label": "large field neuron", + "group": null, + "color": null, + "size": 1.2 + }, + { + "id": "FBbt_00003666", + "label": "adult intrinsic protocerebral bridge neuron", + "group": null, + "color": null, + "size": 1.19 + }, + { + "id": "FBbt_00049807", + "label": "adult intrinsic protocerebral bridge 18 glomeruli-delta7 neuron", + "group": null, + "color": null, + "size": 1.17 + }, + { + "id": "FBbt_00007514", + "label": "small field neuron of the central complex", + "group": null, + "color": null, + "size": 1.14 + }, + { + "id": "FBbt_00003633", + "label": "small field neuron", + "group": null, + "color": null, + "size": 1.14 + }, + { + "id": "FBbt_00003637", + "label": "adult ellipsoid body-protocerebral bridge-gall neuron", + "group": null, + "color": null, + "size": 1.12 + }, + { + "id": "FBbt_00047030", + "label": "adult ellipsoid body-protocerebral bridge 1 glomerulus-dorsal/ventral gall neuron", + "group": null, + "color": null, + "size": 1.11 + }, + { + "id": "FBbt_00049822", + "label": "fan-shaped body extrinsic columnar neuron", + "group": null, + "color": null, + "size": 1.02 + } + ], + "edges": [ + { + "source": "FBbt_00047095", + "target": "FBbt_00111056", + "label": "3201", + "weight": 3201 + }, + { + "source": "FBbt_00005106", + "target": "FBbt_00111056", + "label": "3201", + "weight": 3201 + }, + { + "source": "FBbt_00049819", + "target": "FBbt_00111056", + "label": "3197", + "weight": 3197 + }, + { + "source": "FBbt_00059271", + "target": "FBbt_00111056", + "label": "3197", + "weight": 3197 + }, + { + "source": "FBbt_00053387", + "target": "FBbt_00111056", + "label": "1817", + "weight": 1817 + }, + { + "source": "FBbt_00007515", + "target": "FBbt_00111056", + "label": "1740", + "weight": 1740 + }, + { + "source": "FBbt_00003648", + "target": "FBbt_00111056", + "label": "1740", + "weight": 1740 + }, + { + "source": "FBbt_00003666", + "target": "FBbt_00111056", + "label": "1662", + "weight": 1662 + }, + { + "source": "FBbt_00049807", + "target": "FBbt_00111056", + "label": "1469", + "weight": 1469 + }, + { + "source": "FBbt_00007514", + "target": "FBbt_00111056", + "label": "1191", + "weight": 1191 + }, + { + "source": "FBbt_00003633", + "target": "FBbt_00111056", + "label": "1191", + "weight": 1191 + }, + { + "source": "FBbt_00003637", + "target": "FBbt_00111056", + "label": "1020", + "weight": 1020 + }, + { + "source": "FBbt_00047030", + "target": "FBbt_00111056", + "label": "935", + "weight": 935 + }, + { + "source": "FBbt_00111056", + "target": "FBbt_00111056", + "label": "193", + "weight": 193 + }, + { + "source": "FBbt_00049822", + "target": "FBbt_00111056", + "label": "166", + "weight": 166 + } + ] + } + ], + "quality_flags": { + "has_tool_status": true, + "no_tool_factual_answer": false, + "tool_claim_without_tool": false, + "disambiguation_only_answer": false, + "investigation_plan_answer": false, + "not_verified_or_no_results_answer": false, + "graph_failure_mentioned": false, + "missing_required_graph": false, + "used_data_resource": false, + "response_chars": 1075, + "status_count": 12, + "addressless_followon": false, + "context_lost_across_turn": false, + "unmatched_claim_after_resolve": false, + "repeats_answered_question": false, + "slow_followup_turn": false, + "slowest_followup_ms": 30146 + } + }, + { + "attempt_index": 62, + "task_index": 62, + "task_id": "C11", + "tier": 7, + "title": "The answer hands over its own working", + "question": "Which neurons have part of them in the medulla?", + "requires_graph": false, + "min_graphs": 0, + "repetition": 1, + "duration_ms": 22927, + "status_messages": [ + { + "message": "Thinking...", + "phase": "llm" + }, + { + "message": "Planning the answer", + "phase": "llm" + }, + { + "message": "Resolving 1 term in VFB", + "phase": "mcp" + }, + { + "message": "Querying VFB", + "phase": "mcp" + }, + { + "message": "Checking VFB documentation", + "phase": "mcp" + }, + { + "message": "Checking the answer is covered", + "phase": "llm" + }, + { + "message": "Writing the answer", + "phase": "llm" + } + ], + "event_count": 31, + "conversation": true, + "turns": [ + { + "turn": 1, + "question": "Which neurons have part of them in the medulla?", + "focus": null, + "clicked": null, + "duration_ms": 11065, + "ok": true, + "response": "Neurons with some part in the [medulla](https://www.virtualflybrain.org/reports/FBbt_00003748 \"Open medulla in Virtual Fly Brain\") include [Dm8b](https://www.virtualflybrain.org/reports/FBbt_00110069 \"Open Dm8b in Virtual Fly Brain\"), [MC](https://www.virtualflybrain.org/reports/FBbt_00111640 \"Open MC in Virtual Fly Brain\"), [PS128](https://www.virtualflybrain.org/reports/FBbt_20001883 \"Open PS128 in Virtual Fly Brain\"), [TmY27](https://www.virtualflybrain.org/reports/FBbt_00110067 \"Open TmY27 in Virtual Fly Brain\"), and [medulla intrinsic neuron vGlutMinew1a](https://www.virtualflybrain.org/reports/FBbt_00110033 \"Open medulla intrinsic neuron vGlutMinew1a in Virtual Fly Brain\"). VFB records show [471](https://v2.virtualflybrain.org/org.geppetto.frontend/geppetto?q=FBbt_00003748,NeuronsPartHere \"Run in VFB: Neurons with some part in medulla\") neuron types have some part in the medulla.", + "followons": [ + { + "id": "FBbt_00003748", + "query_type": "TransgeneExpressionHere", + "query": "Which driver lines label the medulla?" + }, + { + "id": "FBbt_00003748", + "query_type": "NeuronsSynaptic", + "query": "Which neurons have synaptic terminals in the medulla?" + }, + { + "id": "FBbt_00003748", + "query_type": "NeuronsPostsynapticHere", + "query": "Which neurons receive output from the medulla?" + }, + { + "id": "FBbt_00003748", + "query_type": "NeuronsPresynapticHere", + "query": "Which neurons provide input to the medulla?" + }, + { + "id": "FBbt_00003748", + "query_type": "PartsOf", + "query": "What are the anatomical parts of the medulla?" + }, + { + "id": "FBbt_00003748", + "query_type": "LineageClonesIn", + "query": "Which lineage clones are found in the medulla?" + } + ], + "context_terms": [ + { + "id": "FBbt_00003748", + "label": "medulla" + } + ], + "reproduction": { + "ids": [ + { + "id": "FBbt_00003748", + "label": "medulla" + } + ], + "calls": [ + { + "id": "FBbt_00003748", + "query_type": "NeuronsPartHere", + "fn": "get_neurons_with_part_in" + }, + { + "id": "FBbt_00003748", + "query_type": "ImagesNeurons", + "fn": "get_images_neurons" + } + ], + "unmapped": [] + }, + "status_count": 9, + "problems": [] + }, + { + "turn": 2, + "question": "How would I get that same result in Python with vfbquery?", + "focus": null, + "clicked": null, + "duration_ms": 11862, + "ok": true, + "response": "The code below returns the [471](https://v2.virtualflybrain.org/org.geppetto.frontend/geppetto?q=FBbt_00003748,NeuronsPartHere \"Run in VFB: Neurons with some part in medulla\") neuron types VFB has annotated for [medulla](https://www.virtualflybrain.org/reports/FBbt_00003748 \"Open medulla in Virtual Fly Brain\"), as a table.\n```python\n# Reproduce this answer in Python — pip install vfbquery\n#\n# These are the exact ids this conversation resolved and the exact catalogue\n# queries it ran, so this returns the same rows the answer was written from\n# rather than a fresh search that might land on a different term.\nimport vfbquery\n\nMEDULLA = 'FBbt_00003748' # medulla\n\n# NeuronsPartHere for medulla\nneurons_part_here = vfbquery.get_neurons_with_part_in(MEDULLA)\n# ImagesNeurons for medulla\nimages_neurons = vfbquery.get_images_neurons(MEDULLA)\n```", + "followons": [ + { + "id": "FBbt_00003748", + "query_type": "ImagesNeurons", + "query": "Which neuron images have a part in the medulla?" + }, + { + "id": "FBbt_00003748", + "query_type": "TransgeneExpressionHere", + "query": "Which driver lines label the medulla?" + }, + { + "id": "FBbt_00003748", + "query_type": "NeuronsPartHere", + "query": "Which neurons have part of their arbour in the medulla?" + }, + { + "id": "FBbt_00003748", + "query_type": "NeuronsSynaptic", + "query": "Which neurons have synaptic terminals in the medulla?" + }, + { + "id": "FBbt_00003748", + "query_type": "NeuronsPostsynapticHere", + "query": "Which neurons receive output from the medulla?" + }, + { + "id": "FBbt_00003748", + "query_type": "NeuronsPresynapticHere", + "query": "Which neurons provide input to the medulla?" + } + ], + "context_terms": [ + { + "id": "FBbt_00003748", + "label": "medulla" + } + ], + "reproduction": { + "ids": [ + { + "id": "FBbt_00003748", + "label": "medulla" + } + ], + "calls": [ + { + "id": "FBbt_00003748", + "query_type": "NeuronsPartHere", + "fn": "get_neurons_with_part_in" + }, + { + "id": "FBbt_00003748", + "query_type": "ImagesNeurons", + "fn": "get_images_neurons" + } + ], + "unmapped": [] + }, + "status_count": 7, + "problems": [] + } + ], + "ok": true, + "request_id": "5c85f200-ed05-4a79-9b8e-959837f1e3ec", + "response_id": "chatcmpl-3d16517a4e71f82054194bdc39189b38", + "images_count": 8, + "graphs_count": 0, + "response": "The code below returns the [471](https://v2.virtualflybrain.org/org.geppetto.frontend/geppetto?q=FBbt_00003748,NeuronsPartHere \"Run in VFB: Neurons with some part in medulla\") neuron types VFB has annotated for [medulla](https://www.virtualflybrain.org/reports/FBbt_00003748 \"Open medulla in Virtual Fly Brain\"), as a table.\n```python\n# Reproduce this answer in Python — pip install vfbquery\n#\n# These are the exact ids this conversation resolved and the exact catalogue\n# queries it ran, so this returns the same rows the answer was written from\n# rather than a fresh search that might land on a different term.\nimport vfbquery\n\nMEDULLA = 'FBbt_00003748' # medulla\n\n# NeuronsPartHere for medulla\nneurons_part_here = vfbquery.get_neurons_with_part_in(MEDULLA)\n# ImagesNeurons for medulla\nimages_neurons = vfbquery.get_images_neurons(MEDULLA)\n```", + "quality_flags": { + "has_tool_status": true, + "no_tool_factual_answer": false, + "tool_claim_without_tool": false, + "disambiguation_only_answer": false, + "investigation_plan_answer": false, + "not_verified_or_no_results_answer": false, + "graph_failure_mentioned": false, + "missing_required_graph": false, + "used_data_resource": false, + "response_chars": 845, + "status_count": 7, + "addressless_followon": false, + "context_lost_across_turn": false, + "unmatched_claim_after_resolve": false, + "repeats_answered_question": false, + "slow_followup_turn": false, + "slowest_followup_ms": 11862 + } + }, + { + "attempt_index": 63, + "task_index": 63, + "task_id": "C12", + "tier": 7, + "title": "Asking for the ids afterwards gets the ids, not a promise of them", + "question": "What are the subclasses of Kenyon cell?", + "requires_graph": false, + "min_graphs": 0, + "repetition": 1, + "duration_ms": 31131, + "status_messages": [ + { + "message": "Thinking...", + "phase": "llm" + }, + { + "message": "Planning the answer", + "phase": "llm" + }, + { + "message": "Resolving 1 term in VFB", + "phase": "mcp" + }, + { + "message": "Reading VFB term info", + "phase": "mcp" + }, + { + "message": "Querying VFB", + "phase": "mcp" + }, + { + "message": "Checking the answer is covered", + "phase": "llm" + }, + { + "message": "Writing the answer", + "phase": "llm" + } + ], + "event_count": 107, + "conversation": true, + "turns": [ + { + "turn": 1, + "question": "What are the subclasses of Kenyon cell?", + "focus": null, + "clicked": null, + "duration_ms": 7874, + "ok": true, + "response": "The subclasses of [Kenyon cell](https://www.virtualflybrain.org/reports/FBbt_00003686 \"Open Kenyon cell in Virtual Fly Brain\") include [KCab-c(i)](https://www.virtualflybrain.org/reports/FBbt_00049111 \"Open KCab-c(i) in Virtual Fly Brain\"), [KCab-c](https://www.virtualflybrain.org/reports/FBbt_00110929 \"Open KCab-c in Virtual Fly Brain\"), [KCg-m](https://www.virtualflybrain.org/reports/FBbt_00111061 \"Open KCg-m in Virtual Fly Brain\"), [Kenyon cell of main calyx](https://www.virtualflybrain.org/reports/FBbt_00047926 \"Open Kenyon cell of main calyx in Virtual Fly Brain\"), and [gamma Kenyon cell](https://www.virtualflybrain.org/reports/FBbt_00100247 \"Open gamma Kenyon cell in Virtual Fly Brain\"), among [37](https://v2.virtualflybrain.org/org.geppetto.frontend/geppetto?q=FBbt_00003686,SubclassesOf \"Run in VFB: Subclasses of Kenyon cell\") subclasses. VFB holds 37 subclasses of Kenyon cell.", + "followons": [ + { + "id": "FBbt_00003686", + "query_type": "ListAllAvailableImages", + "query": "Which images of Kenyon cell does VFB have?" + }, + { + "id": "FBbt_00003686", + "query_type": "UpstreamClassConnectivity", + "query": "What connects to the Kenyon cell upstream?" + }, + { + "id": "FBbt_00003686", + "query_type": "DownstreamClassConnectivity", + "query": "What does the Kenyon cell connect to downstream?" + }, + { + "id": "FBbt_00003686", + "query_type": "TransgeneExpressionHere", + "query": "Which driver lines label the Kenyon cell?" + }, + { + "id": "FBbt_00003686", + "query_type": "anatScRNAseqQuery", + "query": "What single-cell transcriptomic clusters are there for Kenyon cell?" + }, + { + "id": "FBbt_00003686", + "query_type": "SubclassesOf", + "query": "What are the subtypes of the Kenyon cell?" + } + ], + "context_terms": [ + { + "id": "FBbt_00003686", + "label": "Kenyon cell" + } + ], + "reproduction": { + "ids": [ + { + "id": "FBbt_00003686", + "label": "Kenyon cell" + } + ], + "calls": [ + { + "id": "FBbt_00003686", + "query_type": "SubclassesOf", + "fn": "get_subclasses_of" + } + ], + "unmapped": [] + }, + "status_count": 6, + "problems": [] + }, + { + "turn": 2, + "question": "Can you list the VFB IDs so I can reproduce this myself?", + "focus": null, + "clicked": null, + "duration_ms": 23257, + "ok": true, + "response": "The code below returns the [37](https://v2.virtualflybrain.org/org.geppetto.frontend/geppetto?q=FBbt_00003686,SubclassesOf \"Run in VFB: Subclasses of Kenyon cell\") subclasses of [Kenyon cell](https://www.virtualflybrain.org/reports/FBbt_00003686 \"Open Kenyon cell in Virtual Fly Brain\") that VFB has annotated, as a table. The first 12 subclasses, with their VFB ids, are provided in the evidence, including [KCab-c(i)](https://www.virtualflybrain.org/reports/FBbt_00049111 \"Open KCab-c(i) in Virtual Fly Brain\") (FBbt_00049111), [KCab-c](https://www.virtualflybrain.org/reports/FBbt_00110929 \"Open KCab-c in Virtual Fly Brain\")(o) (FBbt_00049112), larval [gamma Kenyon cell](https://www.virtualflybrain.org/reports/FBbt_00100247 \"Open gamma Kenyon cell in Virtual Fly Brain\") (FBbt_00049827), and [Kenyon cell of main calyx](https://www.virtualflybrain.org/reports/FBbt_00047926 \"Open Kenyon cell of main calyx in Virtual Fly Brain\") (FBbt_00047926).\n\n```python\n# Reproduce this answer in Python — pip install vfbquery\n#\n# These are the exact ids this conversation resolved and the exact catalogue\n# queries it ran, so this returns the same rows the answer was written from\n# rather than a fresh search that might land on a different term.\nimport vfbquery\n\nKENYON_CELL = 'FBbt_00003686' # Kenyon cell\n\n# SubclassesOf for Kenyon cell\nsubclasses_of = vfbquery.get_subclasses_of(KENYON_CELL)\n```", + "followons": [ + { + "id": "FBbt_00003686", + "query_type": "ListAllAvailableImages", + "query": "Which images of Kenyon cell does VFB have?" + }, + { + "id": "FBbt_00003686", + "query_type": "UpstreamClassConnectivity", + "query": "What connects to the Kenyon cell upstream?" + }, + { + "id": "FBbt_00003686", + "query_type": "DownstreamClassConnectivity", + "query": "What does the Kenyon cell connect to downstream?" + }, + { + "id": "FBbt_00003686", + "query_type": "TransgeneExpressionHere", + "query": "Which driver lines label the Kenyon cell?" + }, + { + "id": "FBbt_00003686", + "query_type": "anatScRNAseqQuery", + "query": "What single-cell transcriptomic clusters are there for Kenyon cell?" + } + ], + "context_terms": [ + { + "id": "FBbt_00003686", + "label": "Kenyon cell" + } + ], + "reproduction": { + "ids": [ + { + "id": "FBbt_00003686", + "label": "Kenyon cell" + } + ], + "calls": [ + { + "id": "FBbt_00003686", + "query_type": "SubclassesOf", + "fn": "get_subclasses_of" + } + ], + "unmapped": [] + }, + "status_count": 7, + "problems": [] + } + ], + "ok": true, + "request_id": "af3628a6-cf2f-4857-be0e-8d1f96cd7bef", + "response_id": "chatcmpl-1ff7ae199c30c5f2933276cbc2495cdf", + "images_count": 8, + "graphs_count": 0, + "response": "The code below returns the [37](https://v2.virtualflybrain.org/org.geppetto.frontend/geppetto?q=FBbt_00003686,SubclassesOf \"Run in VFB: Subclasses of Kenyon cell\") subclasses of [Kenyon cell](https://www.virtualflybrain.org/reports/FBbt_00003686 \"Open Kenyon cell in Virtual Fly Brain\") that VFB has annotated, as a table. The first 12 subclasses, with their VFB ids, are provided in the evidence, including [KCab-c(i)](https://www.virtualflybrain.org/reports/FBbt_00049111 \"Open KCab-c(i) in Virtual Fly Brain\") (FBbt_00049111), [KCab-c](https://www.virtualflybrain.org/reports/FBbt_00110929 \"Open KCab-c in Virtual Fly Brain\")(o) (FBbt_00049112), larval [gamma Kenyon cell](https://www.virtualflybrain.org/reports/FBbt_00100247 \"Open gamma Kenyon cell in Virtual Fly Brain\") (FBbt_00049827), and [Kenyon cell of main calyx](https://www.virtualflybrain.org/reports/FBbt_00047926 \"Open Kenyon cell of main calyx in Virtual Fly Brain\") (FBbt_00047926).\n\n```python\n# Reproduce this answer in Python — pip install vfbquery\n#\n# These are the exact ids this conversation resolved and the exact catalogue\n# queries it ran, so this returns the same rows the answer was written from\n# rather than a fresh search that might land on a different term.\nimport vfbquery\n\nKENYON_CELL = 'FBbt_00003686' # Kenyon cell\n\n# SubclassesOf for Kenyon cell\nsubclasses_of = vfbquery.get_subclasses_of(KENYON_CELL)\n```", + "quality_flags": { + "has_tool_status": true, + "no_tool_factual_answer": false, + "tool_claim_without_tool": false, + "disambiguation_only_answer": false, + "investigation_plan_answer": false, + "not_verified_or_no_results_answer": false, + "graph_failure_mentioned": false, + "missing_required_graph": false, + "used_data_resource": false, + "response_chars": 1393, + "status_count": 7, + "addressless_followon": false, + "context_lost_across_turn": false, + "unmatched_claim_after_resolve": false, + "repeats_answered_question": false, + "slow_followup_turn": false, + "slowest_followup_ms": 23257 + } + } + ] +}