From 37b9fb8e6b531fa39870a02edaff2c111e68bfc0 Mon Sep 17 00:00:00 2001 From: Claude Date: Tue, 11 Aug 2026 17:42:47 +0000 Subject: [PATCH 1/2] Bump to 4.2.7 for release The release-tag assertion added in #23 fails a v* build when package.json disagrees with the tag, so the bump has to land before the tag is cut. That is the guard working as intended: v4.2.3 shipped reading 4.2.2 and reported itself as 4.2.2 while being entirely correct, which is indistinguishable from a failed rollout. Co-Authored-By: Claude Opus 5 --- package-lock.json | 4 ++-- package.json | 2 +- 2 files changed, 3 insertions(+), 3 deletions(-) diff --git a/package-lock.json b/package-lock.json index 2e6d949..7399ecd 100644 --- a/package-lock.json +++ b/package-lock.json @@ -1,12 +1,12 @@ { "name": "vfb-chat-client", - "version": "4.2.6", + "version": "4.2.7", "lockfileVersion": 3, "requires": true, "packages": { "": { "name": "vfb-chat-client", - "version": "4.2.6", + "version": "4.2.7", "dependencies": { "@modelcontextprotocol/sdk": "^1.26.0", "axios": "^1.13.5", diff --git a/package.json b/package.json index 6c513d7..0e2333d 100644 --- a/package.json +++ b/package.json @@ -1,6 +1,6 @@ { "name": "vfb-chat-client", - "version": "4.2.6", + "version": "4.2.7", "private": true, "scripts": { "dev": "next dev", From 0d5910e9ee22c20a3360c46330eb2acb200cddb2 Mon Sep 17 00:00:00 2001 From: "github-actions[bot]" <41898282+github-actions[bot]@users.noreply.github.com> Date: Tue, 11 Aug 2026 17:51:25 +0000 Subject: [PATCH 2/2] Add task battery results for 37b9fb8 [skip ci] --- test-results/task-battery/latest.json | 1845 ++-- ...task-battery-2026-08-11T17-44-06-563Z.json | 7951 +++++++++++++++++ 2 files changed, 9180 insertions(+), 616 deletions(-) create mode 100644 test-results/task-battery/task-battery-2026-08-11T17-44-06-563Z.json diff --git a/test-results/task-battery/latest.json b/test-results/task-battery/latest.json index a87714f..1fad7c4 100644 --- a/test-results/task-battery/latest.json +++ b/test-results/task-battery/latest.json @@ -1,9 +1,9 @@ { "metadata": { - "run_id": "task-battery-2026-08-11T16-13-45-873Z", - "started_at": "2026-08-11T16:13:45.873Z", - "completed_at": "2026-08-11T16:22:43.027Z", - "git_sha": "4bfe66abb06bfe54881cc48b4d77670edf1cfad3", + "run_id": "task-battery-2026-08-11T17-44-06-563Z", + "started_at": "2026-08-11T17:44:06.563Z", + "completed_at": "2026-08-11T17:51:24.675Z", + "git_sha": "37b9fb8e6b531fa39870a02edaff2c111e68bfc0", "task_file": "/home/runner/work/VFBchat/VFBchat/VFBchat/tests/task-battery/tasks.json", "base_url": "http://127.0.0.1:3210", "started_server": true, @@ -17,8 +17,8 @@ }, "summary": { "total": 64, - "ok": 64, - "errors": 0, + "ok": 63, + "errors": 1, "by_tier": { "T1": { "total": 8, @@ -32,8 +32,8 @@ }, "T3": { "total": 8, - "ok": 8, - "errors": 0 + "ok": 7, + "errors": 1 }, "T4": { "total": 6, @@ -106,10 +106,8 @@ "task_ids": [] }, "slow_followup_turn": { - "count": 1, - "task_ids": [ - "C7" - ] + "count": 0, + "task_ids": [] } }, "conversation": { @@ -117,10 +115,10 @@ "ok": 12, "turns": 27, "followup_turns": 15, - "followup_median_ms": 9600, - "followup_max_ms": 185370 + "followup_median_ms": 10070, + "followup_max_ms": 69118 }, - "mean_duration_ms": 26444 + "mean_duration_ms": 23273 }, "results": [ { @@ -133,7 +131,7 @@ "requires_graph": false, "min_graphs": 0, "repetition": 1, - "duration_ms": 37972, + "duration_ms": 14783, "status_messages": [ { "message": "Thinking...", @@ -160,13 +158,13 @@ "phase": "llm" } ], - "event_count": 59, + "event_count": 101, "ok": true, - "request_id": "1d9c571b-8bbc-4443-a28d-4705922080f7", - "response_id": "chatcmpl-dcbbbcdcfc371d55d311d169d2d81c5e", + "request_id": "fd726da7-d540-425b-92c1-db12ad9cfac9", + "response_id": "chatcmpl-0a09cceb4a1498506afc20f7a99c47ac", "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.", + "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 calyx is closest to the cortex and receives sensory interneuron afferents, the pedunculus is a thick axon bundle extending from the calyx to the base of the lobes, and 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, @@ -177,7 +175,7 @@ "graph_failure_mentioned": false, "missing_required_graph": false, "used_data_resource": false, - "response_chars": 350, + "response_chars": 522, "status_count": 6 } }, @@ -191,7 +189,7 @@ "requires_graph": false, "min_graphs": 0, "repetition": 1, - "duration_ms": 40434, + "duration_ms": 14872, "status_messages": [ { "message": "Thinking...", @@ -213,26 +211,18 @@ "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": 166, + "event_count": 83, "ok": true, - "request_id": "8acbbc91-21e1-4252-ad42-fc5fb7fe27bc", - "response_id": "chatcmpl-483ea4511366c218279bc8d02f8ffdcc", + "request_id": "73740e7e-aa94-4a64-9341-f20d39b7ba53", + "response_id": "chatcmpl-c3fe3c7de371b99d74497ec268721442", "images_count": 8, "graphs_count": 0, - "response": "There are several types of Kenyon cells in the adult Drosophila brain. The types of Kenyon cells 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 others. VFB records show [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\"). The first 12 subclasses 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.", + "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, @@ -243,8 +233,8 @@ "graph_failure_mentioned": false, "missing_required_graph": false, "used_data_resource": false, - "response_chars": 1245, - "status_count": 8 + "response_chars": 542, + "status_count": 6 } }, { @@ -257,7 +247,7 @@ "requires_graph": false, "min_graphs": 0, "repetition": 1, - "duration_ms": 39031, + "duration_ms": 18887, "status_messages": [ { "message": "Thinking...", @@ -287,18 +277,180 @@ "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": 85, + "event_count": 124, "ok": true, - "request_id": "9b4c94ad-db98-4b19-b4a1-5a6a49d30c3d", - "response_id": "chatcmpl-cb8bbe7bc596b996358119c406deb0ac", + "request_id": "3c295087-bf10-4a87-9254-630b0f8a8966", + "response_id": "chatcmpl-4544a7d911dfd8f7f43f70644f162e52", "images_count": 8, - "graphs_count": 0, - "response": "The main input neurons to the [mushroom body](https://www.virtualflybrain.org/reports/FBbt_00005801 \"Open mushroom body in Virtual Fly Brain\") are the ones with presynaptic terminals in the mushroom body. VFB 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 this characteristic, including [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\"), and [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\").", + "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 mushroom body, including larval uniglomerular projection neurons and larval antennal lobe multiglomerular projection neurons. Additionally, VFB holds records of neurons with postsynaptic terminals in mushroom body, totaling [304](https://v2.virtualflybrain.org/org.geppetto.frontend/geppetto?q=FBbt_00005801,NeuronsPostsynapticHere \"Run in VFB: Neurons with postsynaptic terminals in mushroom body\") results, which include adult odd neurons of the calyx and other types. The calyx receives sensory interneuron afferents.", + "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, @@ -309,8 +461,8 @@ "graph_failure_mentioned": false, "missing_required_graph": false, "used_data_resource": false, - "response_chars": 989, - "status_count": 8 + "response_chars": 955, + "status_count": 11 } }, { @@ -323,7 +475,7 @@ "requires_graph": false, "min_graphs": 0, "repetition": 1, - "duration_ms": 35902, + "duration_ms": 12191, "status_messages": [ { "message": "Thinking...", @@ -341,10 +493,6 @@ "message": "Looking up neurotransmitter data", "phase": "mcp" }, - { - "message": "Checking the literature", - "phase": "mcp" - }, { "message": "Checking the answer is covered", "phase": "llm" @@ -354,13 +502,13 @@ "phase": "llm" } ], - "event_count": 22, + "event_count": 25, "ok": true, - "request_id": "c687e975-120a-4791-96dc-a8446c5016d7", - "response_id": "chatcmpl-e89aa1613393e92af4132763b38c6f99", + "request_id": "131b2986-98bd-42c9-b5bc-de253816c78b", + "response_id": "chatcmpl-96e7f024b350797863f21cd16f273515", "images_count": 6, "graphs_count": 0, - "response": "The neurotransmitter used by mushroom body Kenyon cells is not specified.", + "response": "Mushroom body Kenyon cells use acetylcholine as their primary neurotransmitter.", "quality_flags": { "has_tool_status": true, "no_tool_factual_answer": false, @@ -371,8 +519,8 @@ "graph_failure_mentioned": false, "missing_required_graph": false, "used_data_resource": false, - "response_chars": 73, - "status_count": 7 + "response_chars": 79, + "status_count": 6 } }, { @@ -385,7 +533,7 @@ "requires_graph": false, "min_graphs": 0, "repetition": 1, - "duration_ms": 21632, + "duration_ms": 24185, "status_messages": [ { "message": "Thinking...", @@ -420,13 +568,13 @@ "phase": "llm" } ], - "event_count": 122, + "event_count": 140, "ok": true, - "request_id": "f9c8ec64-9a02-412a-a402-c769a1873758", - "response_id": "chatcmpl-52f4c3ef628e620bd5f56b2562f59e2b", + "request_id": "d2c6e8b0-96d3-4cb4-b066-e52450324ba2", + "response_id": "chatcmpl-5b18ca4fdb0594556997de36d7e80bdc", "images_count": 6, "graphs_count": 1, - "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. VFB records show [266](https://v2.virtualflybrain.org/org.geppetto.frontend/geppetto?q=FBbt_00003924,NeuronsPresynapticHere \"Run in VFB: Neurons with presynaptic terminals in antennal lobe\") neurons with presynaptic terminals in the antennal lobe, 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\") and [adult olfactory receptor neuron Ir75d ac1](https://www.virtualflybrain.org/reports/FBbt_00110011 \"Open adult olfactory receptor neuron Ir75d ac1 in Virtual Fly Brain\"). Additionally, there are [518](https://v2.virtualflybrain.org/org.geppetto.frontend/geppetto?q=FBbt_00003924,NeuronsPostsynapticHere \"Run in VFB: Neurons with postsynaptic terminals in antennal lobe\") neurons with postsynaptic terminals in the antennal lobe, such as [AMMC-Bi16](https://www.virtualflybrain.org/reports/FBbt_00111480 \"Open AMMC-Bi16 in Virtual Fly Brain\") and [adult antennal lobe projection neuron DL5](https://www.virtualflybrain.org/reports/FBbt_00059280 \"Open adult antennal lobe projection neuron DL5 in Virtual Fly Brain\"). These neurons likely play a role in processing olfactory information.", + "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 such as Ir75d ac1 and Or35a ac3I. Neurons with postsynaptic terminals in the antennal lobe include adult antennal lobe projection neurons like DL5, DM4, and VA1d, as well as multiglomerular antennal lobe projection neurons like L1 adPN.", "graphs": [ { "type": "basic_graph", @@ -592,7 +740,7 @@ "graph_failure_mentioned": false, "missing_required_graph": false, "used_data_resource": false, - "response_chars": 1423, + "response_chars": 881, "status_count": 8 } }, @@ -606,7 +754,7 @@ "requires_graph": false, "min_graphs": 0, "repetition": 1, - "duration_ms": 19405, + "duration_ms": 18666, "status_messages": [ { "message": "Thinking...", @@ -635,8 +783,8 @@ ], "event_count": 39, "ok": true, - "request_id": "5c78bd33-418b-462a-bb07-a7f94ad35526", - "response_id": "chatcmpl-d78bd0f3c82abb224a8cc5a922215031", + "request_id": "8587dee9-b68d-4aad-9334-4ac909c46c70", + "response_id": "chatcmpl-50e58cbed9e24804efef68ec8fa4e5b1", "images_count": 8, "graphs_count": 0, "response": "Approximately 32,388 neurons are in the [adult central brain](https://www.virtualflybrain.org/reports/FBbt_00047887 \"Open adult central brain in Virtual Fly Brain\"). VFB has annotated [9413](https://v2.virtualflybrain.org/org.geppetto.frontend/geppetto?q=FBbt_00047887,NeuronsPartHere \"Run in VFB: Neurons with some part in adult central brain\") neuron types with some part in the adult central brain.\n\n**Published neuron-count estimates — adult central brain** (from the literature):\n\n- ~32,388 neurons (Whole adult brain, both optic lobes and ocellar ganglia included. Ventral nerve cord NOT included; neurons crossing the neck connective are truncated at the brain boundary. Subcount: fully in central brain. One female adult. Dataset: FlyWire connectome neurons, v783.) — Dorkenwald S et al. (2024) Nature 634(8032):124-138 — 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._", @@ -664,7 +812,7 @@ "requires_graph": false, "min_graphs": 0, "repetition": 1, - "duration_ms": 22385, + "duration_ms": 26763, "status_messages": [ { "message": "Thinking...", @@ -693,8 +841,8 @@ ], "event_count": 103, "ok": true, - "request_id": "d3ccfab7-677c-42cf-aac4-c839e0ba1eb0", - "response_id": "chatcmpl-4772e789a99ccf6c8a64b8bc96ae0a05", + "request_id": "6a7b8ad9-11ee-4863-8c2a-a167083948e8", + "response_id": "chatcmpl-74b1f688e5963bb9e242cd8ecfa8b5fb", "images_count": 8, "graphs_count": 1, "response": "The main components of the Drosophila central complex include the ellipsoid body, the fan-shaped body, the three paired noduli, the asymmetrical bodies, and the protocerebral bridge. These components are associated with functions such as navigation and orientation, locomotor control, and sleep/arousal and memory-related behaviors. VFB holds [363](https://v2.virtualflybrain.org/org.geppetto.frontend/geppetto?q=FBbt_00003632,NeuronsPartHere \"Run in VFB: Neurons with some part in adult central complex\") records of neurons with some part in [adult central complex](https://www.virtualflybrain.org/reports/FBbt_00003632 \"Open adult central complex in Virtual Fly Brain\") and [362](https://v2.virtualflybrain.org/org.geppetto.frontend/geppetto?q=FBbt_00003632,NeuronsSynaptic \"Run in VFB: Neurons with synaptic terminals in adult central complex\") records of neurons with synaptic terminals in adult central complex.", @@ -837,7 +985,7 @@ "requires_graph": false, "min_graphs": 0, "repetition": 1, - "duration_ms": 20619, + "duration_ms": 21328, "status_messages": [ { "message": "Thinking...", @@ -864,13 +1012,13 @@ "phase": "llm" } ], - "event_count": 69, + "event_count": 132, "ok": true, - "request_id": "7454ee73-8abf-4e79-b723-4b39d79d3411", - "response_id": "chatcmpl-33469970679aa04b2d2f79648e6321ab", + "request_id": "be9b3e68-2af6-4b71-8efc-2c1b8fcdb489", + "response_id": "chatcmpl-26a2b89197fd27f4d2c819cc0ce402c3", "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 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 for [Kenyon cell](https://www.virtualflybrain.org/reports/FBbt_00003686 \"Open Kenyon cell in Virtual Fly Brain\").", + "response": "Genetic tools commonly used to label mushroom body neurons, such as [Kenyon cell](https://www.virtualflybrain.org/reports/FBbt_00003686 \"Open Kenyon cell in Virtual Fly Brain\"), include PBac{544.SVS-1}Bsg[CPTI100062] and PBac{566.P.SVS-1}Bsg[CPTI100005] expression patterns. VFB records show multiple transgene expression patterns, including PBac{602.P.SVS-1}Fas2[CPTI000483], PBac{602.P.SVS-1}HDAC4[CPTI000077], and PBac{602.P.SVS-1}Pax[CPTI000161].", "quality_flags": { "has_tool_status": true, "no_tool_factual_answer": false, @@ -881,7 +1029,7 @@ "graph_failure_mentioned": false, "missing_required_graph": false, "used_data_resource": false, - "response_chars": 428, + "response_chars": 450, "status_count": 6 } }, @@ -895,7 +1043,7 @@ "requires_graph": false, "min_graphs": 0, "repetition": 1, - "duration_ms": 23200, + "duration_ms": 26150, "status_messages": [ { "message": "Thinking...", @@ -934,13 +1082,13 @@ "phase": "llm" } ], - "event_count": 80, + "event_count": 97, "ok": true, - "request_id": "81938c61-6066-46de-b44d-e664e053a622", - "response_id": "chatcmpl-6d9757f10667960bad8230445012fb14", + "request_id": "da38e537-bd00-4bc7-8af3-b8f5f7588231", + "response_id": "chatcmpl-97731e223245325dc6bf27d117493872", "images_count": 8, "graphs_count": 1, - "response": "Dopaminergic input to mushroom body output neurons (MBONs) comes from specific dopaminergic neuron types, including dopaminergic PPL1 neurons and dopaminergic PAM neurons. The strongest specific inputs to MBONs are from adult cholinergic neurons and 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 MBON.", + "response": "Dopaminergic input to mushroom body output neurons comes from specific types of dopaminergic neurons, including dopaminergic PPL1 neurons and dopaminergic PAM neurons. The strongest specific inputs to mushroom body output neurons are from adult cholinergic neurons and Kenyon cells, with 7.22 and 7.09 synapses per connected pair, respectively. 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](https://www.virtualflybrain.org/reports/FBbt_00047953 \"Open mushroom body output neuron in Virtual Fly Brain\").", "graphs": [ { "type": "basic_graph", @@ -1166,7 +1314,7 @@ "graph_failure_mentioned": false, "missing_required_graph": false, "used_data_resource": false, - "response_chars": 423, + "response_chars": 640, "status_count": 9 } }, @@ -1180,7 +1328,7 @@ "requires_graph": false, "min_graphs": 0, "repetition": 1, - "duration_ms": 19712, + "duration_ms": 89557, "status_messages": [ { "message": "Thinking...", @@ -1191,7 +1339,7 @@ "phase": "llm" }, { - "message": "Resolving 1 term in VFB", + "message": "Resolving 3 terms in VFB", "phase": "mcp" }, { @@ -1243,13 +1391,13 @@ "phase": "llm" } ], - "event_count": 153, + "event_count": 396, "ok": true, - "request_id": "f1dff33e-8e81-4545-a562-38c22c476648", - "response_id": "chatcmpl-b71a622cbedf938fa677f9de69b2d716", - "images_count": 5, + "request_id": "90918f4e-4fdc-4d87-93a0-f6c7d58bc3c1", + "response_id": "chatcmpl-8a5755bd6c5455e25f260e6feb4b15ac", + "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.", + "response": "The connectivity of olfactory projection neurons is not directly compared between the Hemibrain and FAFB connectome datasets in VFB evidence. VFB records show that [olfactory projection neuron](https://www.virtualflybrain.org/reports/FBbt_00051298 \"Open olfactory projection neuron in Virtual Fly Brain\") has 60,114 downstream classes and 37,427 upstream classes, with the strongest specific targets and inputs including [sNPF neuron](https://www.virtualflybrain.org/reports/FBbt_00048378 \"Open sNPF neuron in Virtual Fly Brain\"), [adult Kenyon cell](https://www.virtualflybrain.org/reports/FBbt_00049825 \"Open adult Kenyon cell in Virtual Fly Brain\"), [local neuron](https://www.virtualflybrain.org/reports/FBbt_00051493 \"Open local neuron 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\").", "quality_flags": { "has_tool_status": true, "no_tool_factual_answer": false, @@ -1260,7 +1408,7 @@ "graph_failure_mentioned": false, "missing_required_graph": false, "used_data_resource": false, - "response_chars": 141, + "response_chars": 920, "status_count": 15 } }, @@ -1274,7 +1422,7 @@ "requires_graph": false, "min_graphs": 0, "repetition": 1, - "duration_ms": 16661, + "duration_ms": 17349, "status_messages": [ { "message": "Thinking...", @@ -1315,8 +1463,8 @@ ], "event_count": 169, "ok": true, - "request_id": "06caa2ab-823a-4f0b-84a2-9d417dd9efe5", - "response_id": "chatcmpl-a9f8e457a0a1f3f06175d45fbc5f1ce9", + "request_id": "7bea7c15-ade0-4cf8-a8a5-434188cb7698", + "response_id": "chatcmpl-c5dd36bb0c5d04a0696a08ee606ec061", "images_count": 8, "graphs_count": 0, "response": "There are split-GAL4 driver lines available that target lateral horn neuron types. VFB records show [4](https://v2.virtualflybrain.org/org.geppetto.frontend/geppetto?q=FBbt_00048293,SplitsTargeting \"Run in VFB: Splits targeting LHN\") split-GAL4 combinations that target lateral horn neurons, which are: [P{R23C06-GAL4.DBD} ∩ P{VT004984-p65.AD} expression pattern](https://www.virtualflybrain.org/reports/VFBexp_FBtp0099468FBtp0119463 \"Open P{R23C06-GAL4.DBD} ∩ P{VT004984-p65.AD} expression pattern in Virtual Fly Brain\"); [P{VT008489-GAL4.DBD} ∩ P{VT006486-p65.AD} expression pattern](https://www.virtualflybrain.org/reports/VFBexp_FBtp0122916FBtp0119497 \"Open P{VT008489-GAL4.DBD} ∩ P{VT006486-p65.AD} expression pattern in Virtual Fly Brain\"); [P{VT026953-GAL4.DBD} ∩ P{R45B08-p65.AD} expression pattern](https://www.virtualflybrain.org/reports/VFBexp_FBtp0123770FBtp0118765 \"Open P{VT026953-GAL4.DBD} ∩ P{R45B08-p65.AD} expression pattern in Virtual Fly Brain\"); and [P{VT033629-GAL4.DBD} ∩ P{VT037488-p65.AD} expression pattern](https://www.virtualflybrain.org/reports/VFBexp_FBtp0124008FBtp0149648 \"Open P{VT033629-GAL4.DBD} ∩ P{VT037488-p65.AD} expression pattern in Virtual Fly Brain\"). VFB holds [24022](https://v2.virtualflybrain.org/org.geppetto.frontend/geppetto?q=FBbt_00048293,ListAllAvailableImages \"Run in VFB: List all available images of LHN\") available images of [adult lateral horn neuron](https://www.virtualflybrain.org/reports/FBbt_00048293 \"Open adult lateral horn neuron in Virtual Fly Brain\") and [1374](https://v2.virtualflybrain.org/org.geppetto.frontend/geppetto?q=FBbt_00048293,SubclassesOf \"Run in VFB: Subclasses of LHN\") subclasses of adult lateral horn neuron.", @@ -1344,7 +1492,7 @@ "requires_graph": false, "min_graphs": 0, "repetition": 1, - "duration_ms": 26093, + "duration_ms": 22419, "status_messages": [ { "message": "Thinking...", @@ -1370,18 +1518,42 @@ "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": 152, + "event_count": 215, "ok": true, - "request_id": "e13b74f6-ab3a-4265-b5cc-58d1df0acadb", - "response_id": "chatcmpl-376c4408819ea31e54aaeb271e5a8d83", + "request_id": "e39b7e82-b22a-4b3c-ab34-fa7ca7ff6c6b", + "response_id": "chatcmpl-0e9ff1ca326d29360191a882f0844daf", "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 and has distinct dendritic arbors in each lobula plate layer. It detects looming stimuli, which elicits a jump escape response. The LPLC2 neuron has its main dendritic arbors in layers 4 and 5B of the lobula, with minor processes in layer 5A, and presynaptic sites in layer 4. It projects to an optic glomerulus of the PVLP, anterior to LPLC1 and dorsal to LC4. There are approximately 80 of these cells per optic lobe, and they are cholinergic.", + "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 a type of neuron with a distinct dendritic arbor in each lobula plate layer, extending outwards from the main fiber in the direction of motion detection for the layer. It is involved in detecting looming stimuli and 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 datasets available for this neuron type.", "quality_flags": { "has_tool_status": true, "no_tool_factual_answer": false, @@ -1392,8 +1564,8 @@ "graph_failure_mentioned": false, "missing_required_graph": false, "used_data_resource": false, - "response_chars": 678, - "status_count": 7 + "response_chars": 834, + "status_count": 13 } }, { @@ -1406,7 +1578,7 @@ "requires_graph": false, "min_graphs": 0, "repetition": 1, - "duration_ms": 10552, + "duration_ms": 9231, "status_messages": [ { "message": "Thinking...", @@ -1435,8 +1607,8 @@ ], "event_count": 37, "ok": true, - "request_id": "1edf010b-cfa7-437f-aed3-48bc83b54574", - "response_id": "chatcmpl-fe20c8ea4895d33a02ddb26087ca44e5", + "request_id": "a58f70e9-78f4-4907-89af-6f18bd94e5bb", + "response_id": "chatcmpl-c5e2ed955eeca79d5ec35061e61d5129", "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.", @@ -1464,7 +1636,7 @@ "requires_graph": false, "min_graphs": 0, "repetition": 1, - "duration_ms": 15968, + "duration_ms": 21005, "status_messages": [ { "message": "Thinking...", @@ -1474,12 +1646,16 @@ "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", + "message": "Querying VFB", "phase": "mcp" }, { @@ -1501,11 +1677,11 @@ ], "event_count": 108, "ok": true, - "request_id": "a3475a6b-20d5-481a-832c-192b5dbf416c", - "response_id": "chatcmpl-c6043496c38da0fd177fb501528246a0", + "request_id": "1327b937-5753-4bd7-902c-f1f751a9a084", + "response_id": "chatcmpl-43b6cd1e6a4e09f8280d5cf4c955982b", "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. The dopaminergic PPL1 neurons are located in the posterior inferior lateral protocerebrum of the adult brain and project to various parts of the mushroom body. These neurons are involved in aversive memory.", + "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. Additionally, Mao and Davis, 2009, and Claridge-Chang et al., 2009, are also mentioned as describing PPL1 dopaminergic neurons and their role in aversive memory.", "quality_flags": { "has_tool_status": true, "no_tool_factual_answer": false, @@ -1516,8 +1692,8 @@ "graph_failure_mentioned": false, "missing_required_graph": false, "used_data_resource": false, - "response_chars": 398, - "status_count": 8 + "response_chars": 353, + "status_count": 9 } }, { @@ -1530,7 +1706,7 @@ "requires_graph": false, "min_graphs": 0, "repetition": 1, - "duration_ms": 11816, + "duration_ms": 14988, "status_messages": [ { "message": "Thinking...", @@ -1552,15 +1728,27 @@ "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": 31, + "event_count": 34, "ok": true, - "request_id": "88f2c69e-bdcb-4061-bace-550248f77ec2", - "response_id": "chatcmpl-e37ada7ef231f3c91eed49b17e75342f", + "request_id": "44a14dbb-ecd6-4721-8816-8b4188f22c7a", + "response_id": "chatcmpl-5787e5c8788405df7fa19d38e8a411a5", "images_count": 5, "graphs_count": 0, "response": "The Hemibrain dataset contains neurons morphologically similar to the fru+ mAL neurons described in light microscopy studies.", @@ -1575,7 +1763,7 @@ "missing_required_graph": false, "used_data_resource": false, "response_chars": 125, - "status_count": 6 + "status_count": 9 } }, { @@ -1588,7 +1776,7 @@ "requires_graph": false, "min_graphs": 0, "repetition": 1, - "duration_ms": 16729, + "duration_ms": 13882, "status_messages": [ { "message": "Thinking...", @@ -1633,8 +1821,8 @@ ], "event_count": 159, "ok": true, - "request_id": "7409df18-8232-430f-b367-e09d29a17946", - "response_id": "chatcmpl-425b7e069f2941cc1d26d81005e728bb", + "request_id": "22c684d1-f306-4c78-9d6e-0bd3a29a0469", + "response_id": "chatcmpl-bde3f2d931b8eea0a96b54a8f7d32e94", "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\") neuron types with presynaptic terminals in the fan-shaped body, including [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. The connectome data indicates that these neurons provide input to the fan-shaped body, but the exact number of synaptic steps is not specified.", @@ -1662,7 +1850,7 @@ "requires_graph": false, "min_graphs": 0, "repetition": 1, - "duration_ms": 24890, + "duration_ms": 20485, "status_messages": [ { "message": "Thinking...", @@ -1701,13 +1889,13 @@ "phase": "llm" } ], - "event_count": 146, + "event_count": 126, "ok": true, - "request_id": "9c0e7b5a-a3d7-4b54-8d5a-2f25cb067c91", - "response_id": "chatcmpl-a59f24ecd14290a75a959815df9d11ff", + "request_id": "6ba9ee2d-e05d-487b-b5bf-882dabe978b7", + "response_id": "chatcmpl-4777ea620fa250ef91e5211fad730bb5", "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 these two neuron types. The strongest specific targets of [mushroom body output neuron](https://www.virtualflybrain.org/reports/FBbt_00047953 \"Open mushroom body output neuron in Virtual Fly Brain\") 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\"). For [dopaminergic neuron](https://www.virtualflybrain.org/reports/FBbt_00005131 \"Open dopaminergic neuron in Virtual Fly Brain\"), the strongest specific targets are adult cholinergic neuron and [adult Kenyon cell](https://www.virtualflybrain.org/reports/FBbt_00049825 \"Open adult Kenyon cell in Virtual Fly Brain\"). However, the specific pairs with the strongest mutual connectivity between mushroom body output neurons and dopaminergic neurons are not detailed in VFB evidence.", + "response": "There are reciprocal connections between mushroom body output neurons and dopaminergic neurons. VFB found 5 reciprocal class-level pairs between these two neuron types. The strongest specific inputs to mushroom body output neurons are adult cholinergic neurons and Kenyon cells, with mean synaptic weights of 7.22 and 7.09 synapses per connected pair, respectively. For dopaminergic neurons, the strongest specific targets are adult cholinergic neurons and adult Kenyon cells, with mean synaptic weights of 2.68 and 2.04 synapses per connected pair, respectively.", "quality_flags": { "has_tool_status": true, "no_tool_factual_answer": false, @@ -1718,7 +1906,7 @@ "graph_failure_mentioned": false, "missing_required_graph": false, "used_data_resource": false, - "response_chars": 1870, + "response_chars": 563, "status_count": 9 } }, @@ -1732,7 +1920,7 @@ "requires_graph": false, "min_graphs": 0, "repetition": 1, - "duration_ms": 11603, + "duration_ms": 16241, "status_messages": [ { "message": "Thinking...", @@ -1754,18 +1942,30 @@ "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": 7, + "event_count": 140, "ok": true, - "request_id": "fc8204fb-f853-4f39-80e5-f744323e1cd2", - "response_id": "local-fc8204fb-f853-4f39-80e5-f744323e1cd2", + "request_id": "39d72f55-f3bb-4a10-921b-dadfd7997642", + "response_id": "chatcmpl-a677d442f29054f6477dd62faacf3606", "images_count": 8, "graphs_count": 0, - "response": "I could not complete the answer just now (the language service did not respond). Please try again in a moment.", + "response": "The pathway from olfactory receptor neurons to the [adult lateral horn](https://www.virtualflybrain.org/reports/FBbt_00007053 \"Open adult lateral horn in Virtual Fly Brain\") involves intermediate neuron types. Antennal lobe projection neurons are intermediate neuron types between olfactory receptor neurons and the lateral horn. The strongest specific inputs to olfactory receptor neurons include [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\"), [olfactory system neuron](https://www.virtualflybrain.org/reports/FBbt_00007697 \"Open olfactory system neuron in Virtual Fly Brain\"), and [adult antennal sensory neuron](https://www.virtualflybrain.org/reports/FBbt_00051173 \"Open adult antennal sensory 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\") records of neurons with some part in adult lateral horn 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\") records of neurons with synaptic terminals in adult lateral horn.", "quality_flags": { "has_tool_status": true, "no_tool_factual_answer": false, @@ -1776,8 +1976,8 @@ "graph_failure_mentioned": false, "missing_required_graph": false, "used_data_resource": false, - "response_chars": 110, - "status_count": 6 + "response_chars": 1796, + "status_count": 9 } }, { @@ -1790,7 +1990,7 @@ "requires_graph": false, "min_graphs": 0, "repetition": 1, - "duration_ms": 8984, + "duration_ms": 10051, "status_messages": [ { "message": "Thinking...", @@ -1829,13 +2029,13 @@ "phase": "llm" } ], - "event_count": 10, + "event_count": 102, "ok": true, - "request_id": "1116dad7-a436-4916-abf1-78e3a88bf66b", - "response_id": "local-1116dad7-a436-4916-abf1-78e3a88bf66b", + "request_id": "bf7dff9b-6270-455a-acce-0d1e26b08e1d", + "response_id": "chatcmpl-90f23b17ad3e7e038558cc10325566d9", "images_count": 5, "graphs_count": 0, - "response": "I could not complete the answer just now (the language service did not respond). Please try again in a moment.", + "response": "The adult Drosophila visual system contains [950](https://v2.virtualflybrain.org/org.geppetto.frontend/geppetto?q=FBbt_00047736,SubclassesOf \"Run in VFB: Subclasses of visual system neuron\") distinct neuron types that are classified as subclasses of [visual system neuron](https://www.virtualflybrain.org/reports/FBbt_00047736 \"Open visual system neuron in Virtual Fly Brain\"). These include, but are not limited to, [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\"), [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\"), [PS070](https://www.virtualflybrain.org/reports/FBbt_20001825 \"Open PS070 in Virtual Fly Brain\"), PS071, PS073, adult visual neuropil intrinsic neuron, lamina wide-field neuron, medulla intrinsic neuron vGlutMinew1a, TmY27, and Mi10b.", "quality_flags": { "has_tool_status": true, "no_tool_factual_answer": false, @@ -1846,7 +2046,7 @@ "graph_failure_mentioned": false, "missing_required_graph": false, "used_data_resource": false, - "response_chars": 110, + "response_chars": 1041, "status_count": 9 } }, @@ -1860,7 +2060,7 @@ "requires_graph": false, "min_graphs": 0, "repetition": 1, - "duration_ms": 10846, + "duration_ms": 16294, "status_messages": [ { "message": "Thinking...", @@ -1894,18 +2094,42 @@ "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": 10, + "event_count": 110, "ok": true, - "request_id": "35eaa4f6-b131-4e18-93f7-a5b30a05df4f", - "response_id": "local-35eaa4f6-b131-4e18-93f7-a5b30a05df4f", + "request_id": "d0d2e0a2-4dc0-4ed7-a773-416116e6f13d", + "response_id": "chatcmpl-8b1e678228ef92d93ba818fd80b3184c", "images_count": 8, "graphs_count": 0, - "response": "I could not complete the answer just now (the language service did not respond). Please try again in a moment.", + "response": "VFB holds downstream and 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 for these queries.", "quality_flags": { "has_tool_status": true, "no_tool_factual_answer": false, @@ -1916,8 +2140,8 @@ "graph_failure_mentioned": false, "missing_required_graph": false, "used_data_resource": false, - "response_chars": 110, - "status_count": 9 + "response_chars": 257, + "status_count": 15 } }, { @@ -1930,7 +2154,7 @@ "requires_graph": false, "min_graphs": 0, "repetition": 1, - "duration_ms": 2259, + "duration_ms": 14166, "status_messages": [ { "message": "Thinking...", @@ -1941,7 +2165,23 @@ "phase": "llm" }, { - "message": "Checking the literature", + "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" }, { @@ -1953,13 +2193,13 @@ "phase": "llm" } ], - "event_count": 25, + "event_count": 91, "ok": true, - "request_id": "5a8daf28-0137-404b-b025-257cdff23464", - "response_id": "chatcmpl-2b261fc55a6bd1d57d29c80f021644ab", - "images_count": 0, + "request_id": "30d0e7e8-179d-4b04-a482-405e400c04cd", + "response_id": "chatcmpl-0a94df9caa19276aac0c7fef686c41c2", + "images_count": 8, "graphs_count": 0, - "response": "The alpha/beta and gamma Kenyon cells could not be matched to a VFB record.", + "response": "The connectome data indicates that [alpha/beta Kenyon cell](https://www.virtualflybrain.org/reports/FBbt_00100248 \"Open alpha/beta Kenyon cell in Virtual Fly Brain\") and [gamma Kenyon cell](https://www.virtualflybrain.org/reports/FBbt_00100247 \"Open gamma Kenyon cell in Virtual Fly Brain\") have some downstream targets in common, but the specific [mushroom body output neuron](https://www.virtualflybrain.org/reports/FBbt_00047953 \"Open mushroom body output neuron in Virtual Fly Brain\") VFB does not currently hold downstream connectivity classes for gamma Kenyon cell. 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.", "quality_flags": { "has_tool_status": true, "no_tool_factual_answer": false, @@ -1970,8 +2210,8 @@ "graph_failure_mentioned": false, "missing_required_graph": false, "used_data_resource": false, - "response_chars": 75, - "status_count": 5 + "response_chars": 924, + "status_count": 9 } }, { @@ -1984,7 +2224,7 @@ "requires_graph": false, "min_graphs": 0, "repetition": 1, - "duration_ms": 8824, + "duration_ms": 11337, "status_messages": [ { "message": "Thinking...", @@ -2006,10 +2246,6 @@ "message": "Querying VFB", "phase": "mcp" }, - { - "message": "Checking the literature", - "phase": "mcp" - }, { "message": "Checking the answer is covered", "phase": "llm" @@ -2019,13 +2255,13 @@ "phase": "llm" } ], - "event_count": 9, + "event_count": 91, "ok": true, - "request_id": "e8983ff4-b939-47d5-93dd-538730713350", - "response_id": "local-e8983ff4-b939-47d5-93dd-538730713350", + "request_id": "508ecf0e-953c-45cf-91cb-bc60d0930964", + "response_id": "chatcmpl-23f03f56d8e030a52e9557cce869bafc", "images_count": 0, "graphs_count": 0, - "response": "I could not complete the answer just now (the language service did not respond). Please try again in a moment.", + "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 [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, @@ -2036,8 +2272,8 @@ "graph_failure_mentioned": false, "missing_required_graph": false, "used_data_resource": false, - "response_chars": 110, - "status_count": 8 + "response_chars": 451, + "status_count": 7 } }, { @@ -2050,7 +2286,7 @@ "requires_graph": false, "min_graphs": 0, "repetition": 1, - "duration_ms": 1419, + "duration_ms": 21426, "status_messages": [ { "message": "Thinking...", @@ -2061,69 +2297,19 @@ "phase": "llm" }, { - "message": "Checking the literature", + "message": "Resolving 2 terms in VFB", "phase": "mcp" }, { - "message": "Checking the answer is covered", - "phase": "llm" - }, - { - "message": "Writing the answer", - "phase": "llm" - } - ], - "event_count": 6, - "ok": true, - "request_id": "5a8f0ade-f604-4bd4-bd37-447b6da062ad", - "response_id": "local-5a8f0ade-f604-4bd4-bd37-447b6da062ad", - "images_count": 0, - "graphs_count": 0, - "response": "I could not complete the answer just now (the language service did not respond). Please try again in a moment.", - "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": 110, - "status_count": 5 - } - }, - { - "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, - "duration_ms": 205623, - "status_messages": [ - { - "message": "Thinking...", - "phase": "llm" - }, - { - "message": "Planning the answer", - "phase": "llm" - }, - { - "message": "Resolving 1 term in VFB", + "message": "Tracing the pathway", "phase": "mcp" }, { - "message": "Reading VFB term info", + "message": "Querying VFB", "phase": "mcp" }, { - "message": "Querying VFB connectivity", + "message": "Querying VFB", "phase": "mcp" }, { @@ -2138,10 +2324,6 @@ "message": "Querying VFB", "phase": "mcp" }, - { - "message": "Querying VFB", - "phase": "mcp" - }, { "message": "Checking the answer is covered", "phase": "llm" @@ -2151,13 +2333,13 @@ "phase": "llm" } ], - "event_count": 129, + "event_count": 151, "ok": true, - "request_id": "7210d828-d5c9-4ad2-a809-cc9649276f8d", - "response_id": "chatcmpl-47e4533118ee336e2c7e5e7cc0ab1711", + "request_id": "4a1f0ab8-d6b3-4544-ba2e-fe1bafef465a", + "response_id": "chatcmpl-17798be498d9fcd723f33c77f02d5d93", "images_count": 8, "graphs_count": 0, - "response": "Data for [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\") is available in VFB, including light microscopy images and driver lines. VFB holds [18](https://v2.virtualflybrain.org/org.geppetto.frontend/geppetto?q=FBbt_00047573,ListAllAvailableImages \"Run in VFB: List all available images of DNa02\") images of descending neuron of the anterior dorsal brain DNa02. There are [2](https://v2.virtualflybrain.org/org.geppetto.frontend/geppetto?q=FBbt_00047573,SplitsTargeting \"Run in VFB: Splits targeting DNa02\") split-GAL4 combinations that target descending neuron of the anterior dorsal brain DNa02. VFB also has 2 transgene expression reports for descending neuron of the anterior dorsal brain DNa02.\n\nData for descending neuron of the anterior dorsal brain DNa02 is available in several datasets, including the Hemibrain and FAFB.", + "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. VFB records show [363](https://v2.virtualflybrain.org/org.geppetto.frontend/geppetto?q=FBbt_00003632,NeuronsPartHere \"Run in VFB: Neurons with some part in adult central complex\") neurons with some part in the adult central complex, including [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. However, VFB does not currently hold data on neurons with some part in the embryonic/larval lateral accessory lobe, or neurons with presynaptic or postsynaptic terminals in the embryonic/larval lateral accessory lobe.", "quality_flags": { "has_tool_status": true, "no_tool_factual_answer": false, @@ -2168,10 +2350,37 @@ "graph_failure_mentioned": false, "missing_required_graph": false, "used_data_resource": false, - "response_chars": 971, + "response_chars": 1157, "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, @@ -2182,7 +2391,7 @@ "requires_graph": false, "min_graphs": 0, "repetition": 1, - "duration_ms": 8034, + "duration_ms": 10966, "status_messages": [ { "message": "Thinking...", @@ -2192,6 +2401,10 @@ "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" @@ -2209,10 +2422,10 @@ "phase": "llm" } ], - "event_count": 53, + "event_count": 54, "ok": true, - "request_id": "3f020a1b-3b30-40e0-831b-b8d7df258295", - "response_id": "chatcmpl-82415949494b074a5ecf84409627029d", + "request_id": "11ee07aa-8ea0-4c0f-9c6e-695192d06692", + "response_id": "chatcmpl-fc100344b836941f08fee5614f6a99e6", "images_count": 0, "graphs_count": 0, "response": "The carbon dioxide sensitive neuron is involved in CO2 avoidance and is connected to downstream classes such as GABAergic local interneuron of the adult antennal lobe and adult antennal lobe local neuron lLN2P.", @@ -2227,7 +2440,7 @@ "missing_required_graph": false, "used_data_resource": false, "response_chars": 210, - "status_count": 6 + "status_count": 7 } }, { @@ -2240,7 +2453,7 @@ "requires_graph": false, "min_graphs": 0, "repetition": 1, - "duration_ms": 26498, + "duration_ms": 31352, "status_messages": [ { "message": "Thinking...", @@ -2279,13 +2492,13 @@ "phase": "llm" } ], - "event_count": 208, + "event_count": 301, "ok": true, - "request_id": "b4b9680f-26fe-46cb-8c02-53b747d9855a", - "response_id": "chatcmpl-707ce2b3180270b9af37c70d917a9c9e", + "request_id": "1a116368-b4d1-4a55-8cc4-42e3140300e0", + "response_id": "chatcmpl-2ceba0e384bff5ae0340273c7cb360bc", "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. It has a large cell body located posterior to the lower protocerebrum and a large descending axon, several times larger than any other axon in the cervical connective. There is one of these cells per hemisphere.\n\nThe giant fiber neuron has downstream connectivity classes for DNp01, with [389](https://v2.virtualflybrain.org/org.geppetto.frontend/geppetto?q=FBbt_00004020,DownstreamClassConnectivity \"Run in VFB: Downstream connectivity classes for DNp01\") classes, and upstream connectivity classes for DNp01, with [472](https://v2.virtualflybrain.org/org.geppetto.frontend/geppetto?q=FBbt_00004020,UpstreamClassConnectivity \"Run in VFB: Upstream connectivity classes for DNp01\") classes.\n\nVFB records show that the giant fiber neuron is connected 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\"), and [projection neuron](https://www.virtualflybrain.org/reports/FBbt_00007392 \"Open projection neuron in Virtual Fly Brain\"), among others.\n\nThere are [10](https://v2.virtualflybrain.org/org.geppetto.frontend/geppetto?q=FBbt_00004020,TransgeneExpressionHere \"Run in VFB: Transgene expression in DNp01\") available transgene expression patterns for the giant fiber neuron, 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\"), and P{VT014708-GAL4} expression pattern, among others.", + "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. It has a large cell body located posterior to the lower protocerebrum and a large descending axon that enters the cervical connective via the posterior cerebro-cervical fascicle and descends on the ipsilateral side in the dorsal cervical fasciculus. The giant fiber neuron has dendritic arborization in the ipsilateral zones A and B of the antennal mechanosensory and motor center, where it receives substantial input from zone A and B Johnston organ neurons. It also arborizes in the posterior ventrolateral protocerebrum and gorget. In the ventral nerve cord, it forms electrical synapses with downstream motor and premotor neurons at the inframedial bridge and at the axonal lateral bend.\n\nThe giant fiber neuron has downstream connectivity classes ([389](https://v2.virtualflybrain.org/org.geppetto.frontend/geppetto?q=FBbt_00004020,DownstreamClassConnectivity \"Run in VFB: Downstream connectivity classes for DNp01\")) and upstream connectivity classes ([472](https://v2.virtualflybrain.org/org.geppetto.frontend/geppetto?q=FBbt_00004020,UpstreamClassConnectivity \"Run in VFB: Upstream connectivity classes for DNp01\")). Available driver lines include [5](https://v2.virtualflybrain.org/org.geppetto.frontend/geppetto?q=FBbt_00004020,SplitsTargeting \"Run in VFB: Splits targeting DNp01\") split-GAL4 combinations. There are also [10](https://v2.virtualflybrain.org/org.geppetto.frontend/geppetto?q=FBbt_00004020,TransgeneExpressionHere \"Run in VFB: Transgene expression in DNp01\") transgene expression reports available for the giant fiber neuron, including expression patterns for P{GMR78G07-GAL4}, P{GMR79D08-GAL4}, and P{GMR91H05-GAL4}, as well as several split-GAL4 combinations.\n\nRelevant publications include Thomas and Wyman (1984), Koto et al. (1981), Power (1948), and many others.", "graphs": [ { "type": "basic_graph", @@ -2511,7 +2724,7 @@ "graph_failure_mentioned": false, "missing_required_graph": false, "used_data_resource": false, - "response_chars": 2223, + "response_chars": 1991, "status_count": 9 } }, @@ -2525,7 +2738,7 @@ "requires_graph": false, "min_graphs": 0, "repetition": 1, - "duration_ms": 2673, + "duration_ms": 14480, "status_messages": [ { "message": "Thinking...", @@ -2536,7 +2749,27 @@ "phase": "llm" }, { - "message": "Checking the literature", + "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" }, { @@ -2548,13 +2781,221 @@ "phase": "llm" } ], - "event_count": 59, + "event_count": 113, "ok": true, - "request_id": "cda9d9ee-5c02-4528-85a0-e4b2ee9973e9", - "response_id": "chatcmpl-0e6a269d1ea8ffb388240be7e69da11b", - "images_count": 0, - "graphs_count": 0, - "response": "The question of which neuron types might mediate a connection between the visual system and the mushroom body, and whether visual information could reach the memory circuit, cannot be answered with VFB evidence, as the subject could not be matched to a VFB record at all.", + "request_id": "e47aa4bc-4456-4f54-a398-25d4433493cf", + "response_id": "chatcmpl-a29a4d9233d4dfb3b5ed0224a3ec35ef", + "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. The connectome data indicates that [visual system neuron](https://www.virtualflybrain.org/reports/FBbt_00047736 \"Open visual system neuron in Virtual Fly Brain\") connects to several neuron types, including [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\"), and [adult optic lobe neuron](https://www.virtualflybrain.org/reports/FBbt_00003702 \"Open adult optic lobe neuron in Virtual Fly Brain\"). Visual information could potentially reach the mushroom body via 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\") records of neurons with some part 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, @@ -2565,8 +3006,8 @@ "graph_failure_mentioned": false, "missing_required_graph": false, "used_data_resource": false, - "response_chars": 271, - "status_count": 5 + "response_chars": 1264, + "status_count": 10 } }, { @@ -2579,7 +3020,7 @@ "requires_graph": false, "min_graphs": 0, "repetition": 1, - "duration_ms": 19636, + "duration_ms": 75434, "status_messages": [ { "message": "Thinking...", @@ -2620,8 +3061,8 @@ ], "event_count": 90, "ok": true, - "request_id": "98c7f8d5-f1e5-4aa3-9c61-5b002a6d821a", - "response_id": "chatcmpl-c998e64409d50e47590228f0c4988a84", + "request_id": "57c53753-ac6a-4c65-9def-96f353bc4455", + "response_id": "chatcmpl-a6d55af2a65a6768d45f5abcc07d9df7", "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\").", @@ -2929,7 +3370,7 @@ "requires_graph": false, "min_graphs": 0, "repetition": 1, - "duration_ms": 93381, + "duration_ms": 82814, "status_messages": [ { "message": "Thinking...", @@ -2948,21 +3389,13 @@ "phase": "mcp" }, { - "message": "Querying VFB connectivity", - "phase": "mcp" - }, - { - "message": "Querying VFB", + "message": "Tracing the pathway", "phase": "mcp" }, { - "message": "Querying VFB", + "message": "Querying VFB connectivity", "phase": "mcp" }, - { - "message": "Checking the answer is covered", - "phase": "llm" - }, { "message": "Querying VFB", "phase": "mcp" @@ -2975,18 +3408,6 @@ "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" @@ -3004,13 +3425,228 @@ "phase": "llm" } ], - "event_count": 336, - "ok": true, - "request_id": "a5ca5d9e-ad97-4836-9e89-ee8bb33e1ab3", - "response_id": "chatcmpl-e0643431a3ce7d463e2cdb8ab0f64eab", - "images_count": 8, - "graphs_count": 0, - "response": "The connectivity between thermosensory neurons and the [mushroom body](https://www.virtualflybrain.org/reports/FBbt_00005801 \"Open mushroom body in Virtual Fly Brain\") is not directly described in VFB evidence. However, VFB's class-level connectivity table for [thermosensory neuron](https://www.virtualflybrain.org/reports/FBbt_00005918 \"Open thermosensory neuron in Virtual Fly Brain\") lists 2,400 downstream classes and 1,538 upstream classes. The strongest specific targets of thermosensory neuron 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\"), while the strongest specific inputs to thermosensory neuron include [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\nRegarding the mushroom body, VFB holds data on neurons with some part in mushroom body, neurons with synaptic terminals in mushroom body, neurons with presynaptic terminals in mushroom body, and neurons with postsynaptic terminals in mushroom body, with [602](https://v2.virtualflybrain.org/org.geppetto.frontend/geppetto?q=FBbt_00005801,NeuronsPartHere \"Run in VFB: Neurons with some part in mushroom body\"), [601](https://v2.virtualflybrain.org/org.geppetto.frontend/geppetto?q=FBbt_00005801,NeuronsSynaptic \"Run in VFB: Neurons with synaptic terminals in mushroom body\"), [366](https://v2.virtualflybrain.org/org.geppetto.frontend/geppetto?q=FBbt_00005801,NeuronsPresynapticHere \"Run in VFB: 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\") results, respectively.\n\nWhether temperature information could influence memory formation via the connectivity between thermosensory neurons and the mushroom body is not explicitly stated in VFB evidence.", + "event_count": 263, + "ok": true, + "request_id": "b45d6487-f999-4721-bcdd-40b53c20a653", + "response_id": "chatcmpl-2f5d1a5b67c2c73689a1e91224c9f41b", + "images_count": 8, + "graphs_count": 1, + "response": "The connectivity between thermosensory neurons and the [mushroom body](https://www.virtualflybrain.org/reports/FBbt_00005801 \"Open mushroom body in Virtual Fly Brain\") is supported by evidence from VFB. Thermosensory neurons are connected to the mushroom body, with antennal lobe projection neurons acting as a connection point. VFB's class-level connectivity table for [thermosensory neuron](https://www.virtualflybrain.org/reports/FBbt_00005918 \"Open thermosensory neuron in Virtual Fly Brain\") lists downstream classes, including [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\"), with mean synaptic weights per connected pair ranging from 18.7 to 18.9 synapses.\n\nVFB also lists upstream classes for thermosensory neuron, including [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\"), with mean synaptic weights per connected pair ranging from 8.34 to 10.1 synapses.\n\nAdditionally, VFB holds records of neurons with presynaptic and postsynaptic terminals in the mushroom body, with [366](https://v2.virtualflybrain.org/org.geppetto.frontend/geppetto?q=FBbt_00005801,NeuronsPresynapticHere \"Run in VFB: 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\") results, respectively.\n\nTemperature information could potentially influence memory formation, as thermosensory neurons influence mushroom body memory formation through thermosensory projection neurons, with downstream evidence to mushroom body dopaminergic neurons and Kenyon cell classes.", + "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, @@ -3021,8 +3657,8 @@ "graph_failure_mentioned": false, "missing_required_graph": false, "used_data_resource": false, - "response_chars": 2666, - "status_count": 18 + "response_chars": 2478, + "status_count": 13 } }, { @@ -3035,7 +3671,7 @@ "requires_graph": false, "min_graphs": 0, "repetition": 1, - "duration_ms": 226523, + "duration_ms": 206606, "status_messages": [ { "message": "Thinking...", @@ -3078,13 +3714,13 @@ "phase": "llm" } ], - "event_count": 193, + "event_count": 144, "ok": true, - "request_id": "2d1453d7-b1db-4df9-b0a5-79204a26ba03", - "response_id": "chatcmpl-3b7cb926fe54d4f58381894d058c2332", + "request_id": "f88491ff-8fc9-438b-b881-9d9f8f20f3cd", + "response_id": "chatcmpl-c6fba330c4ae0656c076a568821ce991", "images_count": 0, "graphs_count": 0, - "response": "The subesophageal zone (SEZ) is a well-characterised region, with annotated neuron types, available connectomics data, and existing genetic tools for SEZ neurons. The [larval subesophageal zone descending SEZ DN neuron](https://www.virtualflybrain.org/reports/FBbt_00111241 \"Open larval subesophageal zone descending SEZ DN neuron in Virtual Fly Brain\") is one of the annotated neuron types. This neuron has its soma location in the cell body rind of the larval gnathal ganglion, and has synaptic input/output in the larval central nervous system, receiving synaptic input from and sending synaptic output to the larval A00c neuron and the larval Basin neuron. Genetic tools exist for SEZ neurons, including GAL4 drivers and binary/intersectional drivers, with 4205 genetic tool/expression pattern rows available for the subesophageal zone. Connectomics data available for the SEZ includes downstream and upstream connectivity classes, as well as transgene expression reports and split-GAL4 combinations.", + "response": "The subesophageal zone (SEZ) is characterised in VFB with annotated neuron types, including the [larval subesophageal zone descending SEZ DN neuron](https://www.virtualflybrain.org/reports/FBbt_00111241 \"Open larval subesophageal zone descending SEZ DN neuron in Virtual Fly Brain\"). There are genetic tools for SEZ neurons, including GAL4 drivers and binary/intersectional drivers, with VFB returning 4205 genetic tool/expression pattern rows for subesophageal zone. VFB holds data on transgene expression in larval subesophageal zone descending SEZ DN neuron, downstream connectivity classes for larval subesophageal zone descending SEZ DN neuron, and upstream connectivity classes for larval subesophageal zone descending SEZ DN neuron.", "quality_flags": { "has_tool_status": true, "no_tool_factual_answer": false, @@ -3095,7 +3731,7 @@ "graph_failure_mentioned": false, "missing_required_graph": false, "used_data_resource": false, - "response_chars": 1004, + "response_chars": 739, "status_count": 10 } }, @@ -3109,7 +3745,7 @@ "requires_graph": true, "min_graphs": 1, "repetition": 1, - "duration_ms": 36072, + "duration_ms": 19795, "status_messages": [ { "message": "Thinking...", @@ -3156,13 +3792,13 @@ "phase": "llm" } ], - "event_count": 197, + "event_count": 193, "ok": true, - "request_id": "a9a101df-ce7e-4434-a32a-3b1d883febff", - "response_id": "chatcmpl-fea2980b7e377ca0e7ce8c522a9a1173", + "request_id": "25b3ebd8-8be2-4ea7-8971-aa16c262407d", + "response_id": "chatcmpl-09c3de1528eb5d390ee504d18424d083", "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 [471](https://v2.virtualflybrain.org/org.geppetto.frontend/geppetto?q=FBbt_00003748,NeuronsPartHere \"Run in VFB: Neurons with some part in medulla\") neuron types with some part in it, [464](https://v2.virtualflybrain.org/org.geppetto.frontend/geppetto?q=FBbt_00003748,NeuronsSynaptic \"Run in VFB: Neurons with synaptic terminals in medulla\") neuron types with synaptic terminals in it, [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 it, 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 in it. The first 12 neuron types with presynaptic terminals in the medulla are [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. The first 12 neuron types with postsynaptic terminals in the medulla are CB3849, TmY-ds, [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, Mi6, Mi8, Tm10, Tm13, Tm14, Tm18, and Tm19.", + "response": "The [medulla](https://www.virtualflybrain.org/reports/FBbt_00003748 \"Open medulla in Virtual Fly Brain\") has various connections, including [471](https://v2.virtualflybrain.org/org.geppetto.frontend/geppetto?q=FBbt_00003748,NeuronsPartHere \"Run in VFB: Neurons with some part in medulla\") neuron types with some part in it, [464](https://v2.virtualflybrain.org/org.geppetto.frontend/geppetto?q=FBbt_00003748,NeuronsSynaptic \"Run in VFB: Neurons with synaptic terminals in medulla\") neuron types with synaptic terminals in it, [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 it, 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 in it. Some of the neurons with presynaptic terminals in the medulla 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\"), [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. Some of the neurons with postsynaptic terminals in the medulla include CB3849, TmY-ds, [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, Mi6, Mi8, Tm10, Tm13, Tm14, Tm18, and Tm19.", "graphs": [ { "type": "basic_graph", @@ -3309,7 +3945,7 @@ "graph_failure_mentioned": false, "missing_required_graph": false, "used_data_resource": false, - "response_chars": 2012, + "response_chars": 2008, "status_count": 11 } }, @@ -3323,7 +3959,7 @@ "requires_graph": false, "min_graphs": 0, "repetition": 1, - "duration_ms": 7098, + "duration_ms": 7349, "status_messages": [ { "message": "Thinking...", @@ -3354,13 +3990,13 @@ "phase": "llm" } ], - "event_count": 49, + "event_count": 42, "ok": true, - "request_id": "8dd08513-6a48-4b4c-b2f5-877f466418bb", - "response_id": "chatcmpl-fab7ec61b1adfe733c0caab5d09117cd", + "request_id": "ccc54125-4e28-4a12-a381-07e43b21f416", + "response_id": "chatcmpl-2631ef95dedba9e0f70fb8f2b9393e18", "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. It is for neurobiologists.", + "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, @@ -3371,7 +4007,7 @@ "graph_failure_mentioned": false, "missing_required_graph": false, "used_data_resource": false, - "response_chars": 194, + "response_chars": 167, "status_count": 7 } }, @@ -3385,7 +4021,7 @@ "requires_graph": false, "min_graphs": 0, "repetition": 1, - "duration_ms": 34685, + "duration_ms": 41972, "status_messages": [ { "message": "Thinking...", @@ -3414,8 +4050,8 @@ ], "event_count": 23, "ok": true, - "request_id": "89c27540-ace1-4e40-b1fe-70e12842412a", - "response_id": "chatcmpl-930111456a4ea75cb8bc2ee102803057", + "request_id": "4da7b3ef-2b21-458a-9bfd-c4554d5792fe", + "response_id": "chatcmpl-e0e2008819988b463ce258c13079510d", "images_count": 0, "graphs_count": 0, "response": "To cite Virtual Fly Brain in a publication, use the following citation formats:\n\n```\nAPA\nCourt, R., Costa, M., Pilgrim, C., Millburn, G., Holmes, A., McLachlan, A., Larkin, A., Matentzoglu, N., Kir, H., Parkinson, H., Brown, N. H., O’Kane, C. J., Armstrong, J. D., Jefferis, G. S. X. E., & Osumi-Sutherland, D. (2023). Virtual Fly Brain—An interactive atlas of the Drosophila nervous system. Frontiers in Physiology, 14. https://doi.org/10.3389/fphys.2023.1076533\n\nMLA\nCourt, Robert, et al. “Virtual Fly Brain—An Interactive Atlas of the Drosophila Nervous System.” Frontiers in Physiology, vol. 14, 2023, https://doi.org/10.3389/fphys.2023.1076533.\n\nChicago\nCourt, Robert, Costa, Marta, Pilgrim, Clare, Millburn, Gillian, Holmes, Alex, McLachlan, Alex, Larkin, Aoife et al. “Virtual Fly Brain—An interactive atlas of the Drosophila nervous system.” Frontiers in Physiology 14, (2023). https://doi.org/10.3389/fphys.2023.1076533.\n\nBibTeX\n@article{Court_2023,\nauthor = {Robert Court and Marta Costa and Clare Pilgrim and Gillian Millburn and Alex Holmes and Alex McLachlan and Aoife Larkin and Nicolas Matentzoglu and Huseyin Kir and Helen Parkinson and Nicolas H. Brown and Cahir J. O'Kane and J. Douglas Armstrong and Gregory S. X. E. Jefferis and David Osumi-Sutherland},\ntitle = \"{Virtual Fly Brain—An interactive atlas of the Drosophila nervous system}\",\njournal = {Frontiers in Physiology},\nvolume = {14},\npublisher = {Frontiers Media {SA}},\nyear = {2023},\nmonth = {jan},\nabstract = \"{As a model organism, Drosophila is uniquely placed to contribute to our understanding of how brains control complex behavior. Not only does it have complex adaptive behaviors, but also a uniquely powerful genetic toolkit, increasingly complete dense connectomic maps of the central nervous system and a rapidly growing set of transcriptomic profiles of cell types. But this also poses a challenge: Given the massive amounts of VFB evidence, how are researchers to Find, Access, Integrate and Reuse (FAIR) relevant data in order to develop an integrated anatomical and molecular picture of circuits, inform hypothesis generation, and find reagents for experiments to test these hypotheses? The Virtual Fly Brain (virtualflybrain.org) web application & API provide a solution to this problem, using FAIR principles to integrate 3D images of neurons and brain regions, connectomics, transcriptomics and reagent expression data covering the whole CNS in both larva and adult. Users can search for neurons, neuroanatomy and reagents by name, location, or connectivity, via text search, clicking on 3D images, search-by-image, and queries by type (e.g., dopaminergic neuron) or properties (e.g., synaptic input in the antennal lobe). Returned results include cross-registered 3D images that can be explored in linked 2D and 3D browsers or downloaded under open licenses, and extensive descriptions of cell types and regions curated from the literature. These solutions are potentially extensible to cover similar atlasing and data integration challenges in vertebrates.}\",\nissn = {1664-042X},\ndoi = {10.3389/fphys.2023.1076533},\nurl = {https://doi.org/10.3389/fphys.2023.1076533},\n}\n```", @@ -3443,7 +4079,7 @@ "requires_graph": false, "min_graphs": 0, "repetition": 1, - "duration_ms": 5368, + "duration_ms": 5681, "status_messages": [ { "message": "Thinking...", @@ -3470,13 +4106,13 @@ "phase": "llm" } ], - "event_count": 25, + "event_count": 28, "ok": true, - "request_id": "205331c7-4eee-4afd-b631-5aec3fb40efb", - "response_id": "chatcmpl-1a89418d5fd9e0fc715fcd839c6e1533", + "request_id": "0c2faff4-5c23-4847-84f4-75e2c2ac79c0", + "response_id": "chatcmpl-3caf83930ab40bb2c87e22bb560e3c19", "images_count": 0, "graphs_count": 0, - "response": "Virtual Fly Brain is funded by multiple UK research councils and charitable foundations since 2009.", + "response": "Virtual Fly Brain has been supported by grants from multiple UK research councils and charitable foundations since 2009.", "quality_flags": { "has_tool_status": true, "no_tool_factual_answer": false, @@ -3487,7 +4123,7 @@ "graph_failure_mentioned": false, "missing_required_graph": false, "used_data_resource": false, - "response_chars": 99, + "response_chars": 120, "status_count": 6 } }, @@ -3501,7 +4137,7 @@ "requires_graph": false, "min_graphs": 0, "repetition": 1, - "duration_ms": 5482, + "duration_ms": 4712, "status_messages": [ { "message": "Thinking...", @@ -3534,8 +4170,8 @@ ], "event_count": 42, "ok": true, - "request_id": "8f33aafb-a56d-4202-aac7-04d59ba7e96d", - "response_id": "chatcmpl-5baaf7fd253ea7ab29e31b6705d3981e", + "request_id": "898b9d72-0830-4e66-a26c-902d92349b12", + "response_id": "chatcmpl-5315ebf299744b475287be3eea1b8ab2", "images_count": 0, "graphs_count": 0, "response": "Virtual Fly Brain is partially compliant with the Web Content Accessibility Guidelines (WCAG) 2.2 AA standard, with known accessibility limitations and non-compliances listed.", @@ -3563,7 +4199,7 @@ "requires_graph": false, "min_graphs": 0, "repetition": 1, - "duration_ms": 7849, + "duration_ms": 9087, "status_messages": [ { "message": "Thinking...", @@ -3590,13 +4226,13 @@ "phase": "llm" } ], - "event_count": 105, + "event_count": 126, "ok": true, - "request_id": "2f233ca0-7c0a-47db-a368-54b52b4b008f", - "response_id": "chatcmpl-858ed20c9767a4230eef1e4b20fcc060", + "request_id": "45a031e8-ecc8-4468-8f29-268ee644c368", + "response_id": "chatcmpl-b881483a1a5bba66774effe089afeb27", "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 for technical support, bug reports, data contributions, or questions about using VFB software and data. For help, comments, suggestions, or general questions, use the public support forum at support@virtualflybrain.org. Bug reports and feature requests can be submitted through GitHub Issues. For data contributions and private inquiries, contact Virtual Fly Brain via private email at data@virtualflybrain.org.", + "response": "To report a problem or contribute data to Virtual Fly Brain, you can get in touch with the team for technical support, bug reports, data contributions, or questions about using VFB software and data. You can contact Virtual Fly Brain through their public support forum, GitHub issues, or private email. For help with using Virtual Fly Brain, comments, suggestions, or general questions, use the public support forum at support@virtualflybrain.org. Bug reports and feature requests can be submitted through GitHub Issues. For data contributions or private inquiries, use the private email at data@virtualflybrain.org.", "quality_flags": { "has_tool_status": true, "no_tool_factual_answer": false, @@ -3607,7 +4243,7 @@ "graph_failure_mentioned": false, "missing_required_graph": false, "used_data_resource": false, - "response_chars": 507, + "response_chars": 616, "status_count": 6 } }, @@ -3621,7 +4257,7 @@ "requires_graph": false, "min_graphs": 0, "repetition": 1, - "duration_ms": 7402, + "duration_ms": 10220, "status_messages": [ { "message": "Thinking...", @@ -3650,8 +4286,8 @@ ], "event_count": 85, "ok": true, - "request_id": "6c4f4630-ab1c-4898-8ec5-b975d231edb7", - "response_id": "chatcmpl-ccca0bae2a6c1847861e68b699647a7a", + "request_id": "36f8e60d-93f5-497a-b30d-f1f6f410393a", + "response_id": "chatcmpl-68ab9bb3019849e3f550660193a9c856", "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.", @@ -3679,7 +4315,7 @@ "requires_graph": false, "min_graphs": 0, "repetition": 1, - "duration_ms": 11018, + "duration_ms": 13928, "status_messages": [ { "message": "Thinking...", @@ -3690,11 +4326,11 @@ "phase": "llm" }, { - "message": "Resolving 1 term in VFB", - "phase": "mcp" + "phase": "plan", + "message": "The plan is contested — sampling again before committing." }, { - "message": "Reading VFB documentation", + "message": "Resolving 1 term in VFB", "phase": "mcp" }, { @@ -3714,13 +4350,13 @@ "phase": "llm" } ], - "event_count": 58, + "event_count": 84, "ok": true, - "request_id": "754ca24b-a762-4a21-a144-a7dab6ab27aa", - "response_id": "chatcmpl-da5987a6d914faf682ba5604bee00ba0", + "request_id": "94e5a64d-d18a-404d-a778-25898bc43468", + "response_id": "chatcmpl-fe1a8dc87f41106eb9edb34df1b74294", "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 select a source neuron and a target neuron, and the Circuit Browser would then display the strongest paths between them.", + "response": "The Circuit Browser tab on VFB allows you to find the strongest paths from one neuron to another. The strongest paths are the shortest or highest weighted paths, and they are arranged from strongest at the bottom to weakest at the top. To use it, you would typically select a source neuron and a target neuron, and the Circuit Browser would then display the strongest paths between them.", "quality_flags": { "has_tool_status": true, "no_tool_factual_answer": false, @@ -3731,7 +4367,7 @@ "graph_failure_mentioned": false, "missing_required_graph": false, "used_data_resource": false, - "response_chars": 249, + "response_chars": 387, "status_count": 8 } }, @@ -3745,7 +4381,7 @@ "requires_graph": false, "min_graphs": 0, "repetition": 1, - "duration_ms": 7842, + "duration_ms": 9830, "status_messages": [ { "message": "Thinking...", @@ -3776,13 +4412,13 @@ "phase": "llm" } ], - "event_count": 116, + "event_count": 56, "ok": true, - "request_id": "b32c9140-9fa0-4248-93d2-8403533b978a", - "response_id": "chatcmpl-86f9dbcc7c9d6c46c154632a3cf79147", + "request_id": "35b36c61-241e-4abc-8610-61aeb864b82d", + "response_id": "chatcmpl-e45999662d934ee4cff7f473c9490120", "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. The similarity scores are calculated using NBLAST or other third-party scores.\n\nThe NBLAST similarity score is a measure of how similar the morphology of one neuron is to another. It is computed per registered neuron, allowing for a scored comparison of individual neurons.\n\nThe meaning of an NBLAST similarity score is that it quantifies the degree of morphological similarity between neurons, with higher scores indicating greater similarity.", + "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, @@ -3793,7 +4429,7 @@ "graph_failure_mentioned": false, "missing_required_graph": false, "used_data_resource": false, - "response_chars": 585, + "response_chars": 264, "status_count": 7 } }, @@ -3807,7 +4443,7 @@ "requires_graph": false, "min_graphs": 0, "repetition": 1, - "duration_ms": 7124, + "duration_ms": 10438, "status_messages": [ { "message": "Thinking...", @@ -3840,8 +4476,8 @@ ], "event_count": 26, "ok": true, - "request_id": "d84aafd0-51a4-499d-9ad0-1b56d94955eb", - "response_id": "chatcmpl-9ebb3700db4ef0c485c5fb9a28f2f472", + "request_id": "56882c48-0f8e-42cc-a981-d7d4fec81bb2", + "response_id": "chatcmpl-d0a050085d337747c785eda1ea73c0d7", "images_count": 1, "graphs_count": 0, "response": "Confidence values are represented by the property key \"confidence_value\" in the PDB.", @@ -3869,7 +4505,7 @@ "requires_graph": false, "min_graphs": 0, "repetition": 1, - "duration_ms": 8396, + "duration_ms": 10784, "status_messages": [ { "message": "Thinking...", @@ -3900,13 +4536,13 @@ "phase": "llm" } ], - "event_count": 40, + "event_count": 53, "ok": true, - "request_id": "51644171-8ed5-46c2-9673-cf99c4e0bc07", - "response_id": "chatcmpl-c68b6365d28823167ce04fe87bacbc7a", + "request_id": "c064221d-b9a9-4f92-a432-fafc6df0a00d", + "response_id": "chatcmpl-30dbeff2cff63ce4ccf157f46dfe00e8", "images_count": 8, "graphs_count": 0, - "response": "The term \"bridging registrations\" could not be matched. Transformations to map between different canonical Drosophila templates are described in VFB's documentation.", + "response": "Bridging registrations between brain templates in VFB could not be matched, and the name \"bridging registrations\" returned zero any near matches. The documentation mentions transformations to map between different canonical Drosophila templates.", "quality_flags": { "has_tool_status": true, "no_tool_factual_answer": false, @@ -3917,7 +4553,7 @@ "graph_failure_mentioned": false, "missing_required_graph": false, "used_data_resource": false, - "response_chars": 165, + "response_chars": 245, "status_count": 7 } }, @@ -3931,7 +4567,7 @@ "requires_graph": false, "min_graphs": 0, "repetition": 1, - "duration_ms": 4078, + "duration_ms": 10288, "status_messages": [ { "message": "Thinking...", @@ -3941,6 +4577,10 @@ "message": "Planning the answer", "phase": "llm" }, + { + "phase": "plan", + "message": "The plan is contested — sampling again before committing." + }, { "message": "Reading VFB term info", "phase": "mcp" @@ -3958,10 +4598,10 @@ "phase": "llm" } ], - "event_count": 22, + "event_count": 23, "ok": true, - "request_id": "41cd7224-b891-4975-b1c1-1887f2575a83", - "response_id": "chatcmpl-ea848bf376664eb2184c1f91f32d06ec", + "request_id": "e6740a16-7352-4a3d-881a-c0c6f499b1f6", + "response_id": "chatcmpl-7aee01cc3e301811c2e65d2af499ce3d", "images_count": 0, "graphs_count": 0, "response": "Virtual Fly Brain holds imaging data types including skeleton, mesh, and volume.", @@ -3976,7 +4616,7 @@ "missing_required_graph": false, "used_data_resource": false, "response_chars": 80, - "status_count": 6 + "status_count": 7 } }, { @@ -3989,7 +4629,7 @@ "requires_graph": false, "min_graphs": 0, "repetition": 1, - "duration_ms": 5067, + "duration_ms": 6791, "status_messages": [ { "message": "Thinking...", @@ -4018,8 +4658,8 @@ ], "event_count": 46, "ok": true, - "request_id": "1c4e09fd-441b-4a73-843e-1bc41a78b847", - "response_id": "chatcmpl-3abeae0712a57fc032bfa19e36de10fc", + "request_id": "d6e8c9fa-3e3e-4ddd-b522-ee70f13c7975", + "response_id": "chatcmpl-f0af832a2cc1419397189acf39f60e42", "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 confocal microscopy images, EM reconstructed neurons, and other datasets from different researchers and labs.", @@ -4047,7 +4687,7 @@ "requires_graph": false, "min_graphs": 0, "repetition": 1, - "duration_ms": 7197, + "duration_ms": 8555, "status_messages": [ { "message": "Thinking...", @@ -4062,7 +4702,7 @@ "phase": "mcp" }, { - "message": "Checking VFB documentation", + "message": "Checking the literature", "phase": "mcp" }, { @@ -4074,13 +4714,13 @@ "phase": "llm" } ], - "event_count": 58, + "event_count": 53, "ok": true, - "request_id": "05df5539-bc7a-4bee-b664-eda2101c5ef2", - "response_id": "chatcmpl-f19992d9b2caa9a7c9d84a7c3d8c7abe", + "request_id": "a25e6098-2417-4d4a-a3bb-829cf5d7e479", + "response_id": "chatcmpl-3dbe6a0e754c1d55bc116ade0bf770c3", "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```", + "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 it using\n```\nfrom import vfb\n```", "quality_flags": { "has_tool_status": true, "no_tool_factual_answer": false, @@ -4091,7 +4731,7 @@ "graph_failure_mentioned": false, "missing_required_graph": false, "used_data_resource": false, - "response_chars": 278, + "response_chars": 257, "status_count": 6 } }, @@ -4105,7 +4745,7 @@ "requires_graph": false, "min_graphs": 0, "repetition": 1, - "duration_ms": 9456, + "duration_ms": 12357, "status_messages": [ { "message": "Thinking...", @@ -4132,13 +4772,13 @@ "phase": "llm" } ], - "event_count": 101, + "event_count": 91, "ok": true, - "request_id": "40dbf3e7-beac-46e3-8416-9a4c62a24c73", - "response_id": "chatcmpl-d61845cc5fbded37b2d11b861ca0e0e7", + "request_id": "2be935fa-b125-4f53-9518-6c22136f2ed3", + "response_id": "chatcmpl-66a298e972b2e4958d75961bc1905fc4", "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 Description Logic (DL) queries, SPARQL queries with OWL reasoning, and access to multiple knowledgebases. The SOLR Search API provides fast text search and autocomplete functionality for VFB entities, datasets, and publications.", + "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 such as 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, @@ -4149,7 +4789,7 @@ "graph_failure_mentioned": false, "missing_required_graph": false, "used_data_resource": false, - "response_chars": 467, + "response_chars": 415, "status_count": 6 } }, @@ -4163,7 +4803,7 @@ "requires_graph": false, "min_graphs": 0, "repetition": 1, - "duration_ms": 10559, + "duration_ms": 13810, "status_messages": [ { "message": "Thinking...", @@ -4194,13 +4834,13 @@ "phase": "llm" } ], - "event_count": 87, + "event_count": 116, "ok": true, - "request_id": "e3fe2d00-ddf0-4a7f-8cd0-9e8a64c64000", - "response_id": "chatcmpl-ff9b75daa9d97d49a24c998caa3b20ac", + "request_id": "e63c3a46-a4b1-4312-8fa2-6e699c1551bc", + "response_id": "chatcmpl-88f273b00ae67d6c51b9d48250111b2c", "images_count": 0, "graphs_count": 0, - "response": "To explore Virtual Fly Brain neurons, you can refer to the tutorials provided on the Virtual Fly Brain website. Additionally, you can use the pymaid library to interface with a CATMAID server and retrieve neuron data, and then use navis to plot and analyze the neurons. VFB's documentation does not appear to cover Navis. VFB's documentation does not appear to cover pymaid.", + "response": "To explore Virtual Fly Brain neurons, you can use the following steps:\n1. Connect to the VFB CATMAID server using pymaid.connect_catmaid()\n2. Retrieve neurons using pymaid.get_neurons() or pymaid.find_neurons()\n3. Plot the neurons using navis.plot3d()\n4. Access the connectors of a neuron using the.connectors attribute\n5. Use pymaid.get_volume() to retrieve neuropil volumes and plot them with the neurons.\nVFB's documentation does not appear to cover pymaid.", "quality_flags": { "has_tool_status": true, "no_tool_factual_answer": false, @@ -4211,7 +4851,7 @@ "graph_failure_mentioned": false, "missing_required_graph": false, "used_data_resource": false, - "response_chars": 374, + "response_chars": 460, "status_count": 7 } }, @@ -4225,7 +4865,7 @@ "requires_graph": false, "min_graphs": 0, "repetition": 1, - "duration_ms": 10366, + "duration_ms": 14378, "status_messages": [ { "message": "Thinking...", @@ -4252,13 +4892,13 @@ "phase": "llm" } ], - "event_count": 124, + "event_count": 140, "ok": true, - "request_id": "3a84c0f6-2f0d-4ffd-99d2-bfd3afa7b8a6", - "response_id": "chatcmpl-af592df837945fe5da0d28e70a4b4de2", + "request_id": "9aff2e42-0cef-41c6-905b-9ca72fd04a16", + "response_id": "chatcmpl-9b8ed993299ad10de7f09eb45afd25ae", "images_count": 0, "graphs_count": 0, - "response": "To use the Virtual Fly Brain Model Context Protocol (MCP) tool, follow these steps:\n1. Open Claude Desktop,\n2. go to Settings,\n3. navigate to the MCP section, and\n4. add a new MCP server with the settings:\n - Server Name: virtual-fly-brain,\n - Type: HTTP,\n - Server URL: https://vfb3-mcp.virtualflybrain.org.\n\nAlternatively, you can use the Configuration JSON method or set up the tool with GitHub Copilot or other MCP-compatible clients.\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```", + "response": "To use the Virtual Fly Brain Model Context Protocol (MCP) tool, follow these steps: Open Claude Desktop, go to Settings, navigate to the MCP section, and add a new MCP server with the provided settings. Alternatively, use the Configuration JSON or Claude Code setup methods. For GitHub Copilot, open VS Code, search for \"MCP\" in the settings, and add the server URL. For other MCP-compatible clients, use the provided JSON configuration. Test the connection by asking your AI assistant questions like \"Get information about the neuron \" or \"Search for terms related to medulla in the fly brain\".\n\n```json\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, @@ -4269,7 +4909,7 @@ "graph_failure_mentioned": false, "missing_required_graph": false, "used_data_resource": false, - "response_chars": 577, + "response_chars": 733, "status_count": 6 } }, @@ -4283,7 +4923,7 @@ "requires_graph": false, "min_graphs": 0, "repetition": 1, - "duration_ms": 9227, + "duration_ms": 6433, "status_messages": [ { "message": "Thinking...", @@ -4316,11 +4956,11 @@ ], "event_count": 40, "ok": true, - "request_id": "eaad02f0-f3d2-4e5d-a093-eb0f42856a1f", - "response_id": "chatcmpl-b750c9a017465e8251a5557cb2eb0daf", + "request_id": "b4564cf1-f496-4a37-a324-7883eceb1ef7", + "response_id": "chatcmpl-960e892ed313d8f8cc38f0343ea853c1", "images_count": 0, "graphs_count": 0, - "response": "VFB's documentation does not appear to cover when predicted neurotransmitters for EM data became available on VFB. Searching virtualflybrain.org may provide more information.", + "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, @@ -4331,7 +4971,7 @@ "graph_failure_mentioned": false, "missing_required_graph": false, "used_data_resource": false, - "response_chars": 174, + "response_chars": 175, "status_count": 7 } }, @@ -4345,7 +4985,7 @@ "requires_graph": false, "min_graphs": 0, "repetition": 1, - "duration_ms": 19751, + "duration_ms": 9549, "status_messages": [ { "message": "Thinking...", @@ -4355,10 +4995,6 @@ "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" @@ -4380,10 +5016,10 @@ "phase": "llm" } ], - "event_count": 41, + "event_count": 40, "ok": true, - "request_id": "34c6f3c3-02c0-4bd1-9bc2-2bb30c07d4e9", - "response_id": "chatcmpl-a8550ec42f5341fdf9d5c8a25c6d5774", + "request_id": "1f3d46ca-41e3-496e-81eb-5632f62cddda", + "response_id": "chatcmpl-ac6b589730a8f8ae4423f15fc83f53c3", "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.", @@ -4398,7 +5034,7 @@ "missing_required_graph": false, "used_data_resource": false, "response_chars": 114, - "status_count": 8 + "status_count": 7 } }, { @@ -4411,7 +5047,7 @@ "requires_graph": false, "min_graphs": 0, "repetition": 1, - "duration_ms": 8025, + "duration_ms": 11283, "status_messages": [ { "message": "Thinking...", @@ -4444,11 +5080,11 @@ ], "event_count": 55, "ok": true, - "request_id": "c8ac5303-4080-47d4-8673-86f6c7248821", - "response_id": "chatcmpl-32298dd946c1afce6f4e29a079a33fd2", + "request_id": "03d6d10c-0175-4c70-bb2b-d103bbd17c07", + "response_id": "chatcmpl-e738863c5b292ea25db012c5c4aa42c1", "images_count": 0, "graphs_count": 0, - "response": "Materials from the Virtual Fly Brain \"Hacking the connectome\" workshop are available. These include a recorded introduction session and workshop notebooks that demonstrate how to use available tools to explore and analyse published connectomes on Virtual Fly Brain.\n\n```\nhttps://www.virtualflybrain.org/docs/past-workshops/connectome\n```", + "response": "Materials from the Virtual Fly Brain \"Hacking the connectome\" workshop are available. These include a recorded introduction session and workshop notebooks that demonstrate how to use available tools to explore and analyze published connectomes on Virtual Fly Brain.\n\n```\nhttps://www.virtualflybrain.org/docs/past-workshops/connectome\n```", "quality_flags": { "has_tool_status": true, "no_tool_factual_answer": false, @@ -4473,7 +5109,7 @@ "requires_graph": false, "min_graphs": 0, "repetition": 1, - "duration_ms": 12995, + "duration_ms": 19539, "status_messages": [ { "message": "Thinking...", @@ -4483,10 +5119,6 @@ "message": "Planning the answer", "phase": "llm" }, - { - "phase": "plan", - "message": "The plan is contested — sampling again before committing." - }, { "message": "Resolving 3 terms in VFB", "phase": "mcp" @@ -4495,6 +5127,10 @@ "message": "Querying VFB", "phase": "mcp" }, + { + "message": "Reading VFB term info", + "phase": "mcp" + }, { "message": "Checking VFB documentation", "phase": "mcp" @@ -4508,13 +5144,13 @@ "phase": "llm" } ], - "event_count": 64, + "event_count": 93, "ok": true, - "request_id": "e564bb75-cb40-4c51-9791-a4aff7454b1c", - "response_id": "chatcmpl-189f4d752de407d361fe9f3ec7bd6579", + "request_id": "efc35e66-1103-4045-89b5-6ae70a089f07", + "response_id": "chatcmpl-87d9bd33146b34f9a1b950cc0177d08d", "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.", + "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, with closest records found including Fancl, FANCI, and Fancm. The name \"CATMAID\" could not be matched.", "quality_flags": { "has_tool_status": true, "no_tool_factual_answer": false, @@ -4525,7 +5161,7 @@ "graph_failure_mentioned": false, "missing_required_graph": false, "used_data_resource": false, - "response_chars": 237, + "response_chars": 340, "status_count": 8 } }, @@ -4539,7 +5175,7 @@ "requires_graph": false, "min_graphs": 0, "repetition": 1, - "duration_ms": 6676, + "duration_ms": 7303, "status_messages": [ { "message": "Thinking...", @@ -4570,13 +5206,13 @@ "phase": "llm" } ], - "event_count": 22, + "event_count": 25, "ok": true, - "request_id": "5a53041d-74ea-4dce-8321-f37a434845c9", - "response_id": "chatcmpl-88146c94845db07f20db72439db6f408", + "request_id": "394f4b6e-c064-42c4-aaab-e759a4718243", + "response_id": "chatcmpl-b12e2ae6a82d94117aa76039c7a27200", "images_count": 8, "graphs_count": 0, - "response": "A circuit diagram of the [mushroom body](https://www.virtualflybrain.org/reports/FBbt_00005801 \"Open mushroom body in Virtual Fly Brain\") is available on Virtual Fly Brain.", + "response": "Yes, 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, @@ -4587,7 +5223,7 @@ "graph_failure_mentioned": false, "missing_required_graph": false, "used_data_resource": false, - "response_chars": 172, + "response_chars": 183, "status_count": 7 } }, @@ -4601,7 +5237,7 @@ "requires_graph": false, "min_graphs": 0, "repetition": 1, - "duration_ms": 14046, + "duration_ms": 11712, "status_messages": [ { "message": "Thinking...", @@ -4640,7 +5276,7 @@ "question": "What is the medulla?", "focus": null, "clicked": null, - "duration_ms": 6596, + "duration_ms": 5369, "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": [ @@ -4699,7 +5335,7 @@ "question": "Which neurons receive output from it?", "focus": null, "clicked": null, - "duration_ms": 7450, + "duration_ms": 6343, "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": [ @@ -4766,8 +5402,8 @@ } ], "ok": true, - "request_id": "726925bc-7ec3-4482-b10d-de8575375375", - "response_id": "chatcmpl-08318c47bed9774ad8125cfc2baad919", + "request_id": "0fed7818-58f1-4c8c-9a38-dea15cd9cc9c", + "response_id": "chatcmpl-7fd7f6802e40a8f870357f8f2cdae772", "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.", @@ -4788,7 +5424,7 @@ "unmatched_claim_after_resolve": false, "repeats_answered_question": false, "slow_followup_turn": false, - "slowest_followup_ms": 7450 + "slowest_followup_ms": 6343 } }, { @@ -4801,7 +5437,7 @@ "requires_graph": false, "min_graphs": 0, "repetition": 1, - "duration_ms": 15343, + "duration_ms": 16766, "status_messages": [ { "message": "Thinking...", @@ -4836,7 +5472,7 @@ "phase": "llm" } ], - "event_count": 199, + "event_count": 201, "conversation": true, "turns": [ { @@ -4844,9 +5480,9 @@ "question": "What is the mushroom body?", "focus": null, "clicked": null, - "duration_ms": 7153, + "duration_ms": 8139, "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.", + "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", @@ -4906,9 +5542,9 @@ "query_type": "ImagesNeurons" }, "clicked": 0, - "duration_ms": 8190, + "duration_ms": 8627, "ok": true, - "response": "There are images of neurons with parts in the [mushroom body](https://www.virtualflybrain.org/reports/FBbt_00005801 \"Open mushroom body in Virtual Fly Brain\"). VFB records show [27619](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 of neurons. The first 12 images, 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.", + "response": "There are images of neurons with parts in the [mushroom body](https://www.virtualflybrain.org/reports/FBbt_00005801 \"Open mushroom body in Virtual Fly Brain\"). VFB holds [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 of neurons with some part in the mushroom body. The first 12 images are of neurons 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, and GMR 93G04 FLP 12-1.", "followons": [ { "id": "FBbt_00005801", @@ -4973,11 +5609,11 @@ } ], "ok": true, - "request_id": "32b18a18-bf54-44b6-91aa-48b6fc3c02ed", - "response_id": "chatcmpl-b5d7743fad9207ca4e76fd2b1bc8b37c", + "request_id": "017ce329-fcf1-41d3-a82b-19b32d2b1b91", + "response_id": "chatcmpl-eed69962625e9be7893ecba73ccda366", "images_count": 8, "graphs_count": 0, - "response": "There are images of neurons with parts in the [mushroom body](https://www.virtualflybrain.org/reports/FBbt_00005801 \"Open mushroom body in Virtual Fly Brain\"). VFB records show [27619](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 of neurons. The first 12 images, 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.", + "response": "There are images of neurons with parts in the [mushroom body](https://www.virtualflybrain.org/reports/FBbt_00005801 \"Open mushroom body in Virtual Fly Brain\"). VFB holds [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 of neurons with some part in the mushroom body. The first 12 images are of neurons 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, and GMR 93G04 FLP 12-1.", "quality_flags": { "has_tool_status": true, "no_tool_factual_answer": false, @@ -4988,14 +5624,14 @@ "graph_failure_mentioned": false, "missing_required_graph": false, "used_data_resource": false, - "response_chars": 638, + "response_chars": 661, "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": 8190 + "slowest_followup_ms": 8627 } }, { @@ -5008,7 +5644,7 @@ "requires_graph": false, "min_graphs": 0, "repetition": 1, - "duration_ms": 22219, + "duration_ms": 86137, "status_messages": [ { "message": "Thinking...", @@ -5035,7 +5671,7 @@ "phase": "llm" } ], - "event_count": 126, + "event_count": 125, "conversation": true, "turns": [ { @@ -5043,7 +5679,7 @@ "question": "What is the fan-shaped body?", "focus": null, "clicked": null, - "duration_ms": 6233, + "duration_ms": 6949, "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": [ @@ -5102,9 +5738,9 @@ "question": "What about the ellipsoid body?", "focus": null, "clicked": null, - "duration_ms": 7841, + "duration_ms": 10070, "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\").", + "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, located just anterior to the [fan-shaped body](https://www.virtualflybrain.org/reports/FBbt_00003679 \"Open fan-shaped body in Virtual Fly Brain\"), with a hole (the ellipsoid body canal) pointing anteriorly.", "followons": [ { "id": "FBbt_00003678", @@ -5169,9 +5805,9 @@ "question": "Which neurons have synaptic terminals in the fan-shaped body?", "focus": null, "clicked": null, - "duration_ms": 8145, + "duration_ms": 69118, "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\"), and [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\").", + "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", @@ -5239,11 +5875,11 @@ } ], "ok": true, - "request_id": "2dc0c7cb-f095-441d-871c-687fc2a07f68", - "response_id": "chatcmpl-3d77772c22bbc1d935bc7484b511f85b", + "request_id": "0a710e79-a2f6-4cb0-9676-61e871044dcd", + "response_id": "chatcmpl-02a0467b7846c49812abe318d1032bd1", "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\"), and [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\").", + "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, @@ -5254,14 +5890,14 @@ "graph_failure_mentioned": false, "missing_required_graph": false, "used_data_resource": false, - "response_chars": 1300, + "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": 8145 + "slowest_followup_ms": 69118 } }, { @@ -5274,7 +5910,7 @@ "requires_graph": false, "min_graphs": 0, "repetition": 1, - "duration_ms": 12633, + "duration_ms": 14081, "status_messages": [ { "message": "Thinking...", @@ -5301,7 +5937,7 @@ "phase": "llm" } ], - "event_count": 137, + "event_count": 146, "conversation": true, "turns": [ { @@ -5309,7 +5945,7 @@ "question": "What is a Kenyon cell?", "focus": null, "clicked": null, - "duration_ms": 5767, + "duration_ms": 6083, "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": [ @@ -5368,9 +6004,9 @@ "question": "What are its subtypes?", "focus": null, "clicked": null, - "duration_ms": 6866, + "duration_ms": 7998, "ok": true, - "response": "The subtypes of [Kenyon cell](https://www.virtualflybrain.org/reports/FBbt_00003686 \"Open Kenyon cell in Virtual Fly Brain\") include [37](https://v2.virtualflybrain.org/org.geppetto.frontend/geppetto?q=FBbt_00003686,SubclassesOf \"Run in VFB: Subclasses of Kenyon cell\") subclasses, such as [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\"). Some specific subtypes 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.", + "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 subtypes, with their VFB ids, 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", @@ -5425,11 +6061,11 @@ } ], "ok": true, - "request_id": "724c5e24-ad88-4bc4-9133-eb03676cbc2c", - "response_id": "chatcmpl-61dac7b2014cd2e837574807f2541bea", + "request_id": "b074e6c3-2b53-4ec2-98df-925d8a44761d", + "response_id": "chatcmpl-817e9b4e3b3537c807f40879e898d05f", "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\") include [37](https://v2.virtualflybrain.org/org.geppetto.frontend/geppetto?q=FBbt_00003686,SubclassesOf \"Run in VFB: Subclasses of Kenyon cell\") subclasses, such as [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\"). Some specific subtypes 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.", + "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 subtypes, with their VFB ids, 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, @@ -5440,14 +6076,14 @@ "graph_failure_mentioned": false, "missing_required_graph": false, "used_data_resource": false, - "response_chars": 1136, + "response_chars": 1155, "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": 6866 + "slowest_followup_ms": 7998 } }, { @@ -5460,7 +6096,7 @@ "requires_graph": false, "min_graphs": 0, "repetition": 1, - "duration_ms": 21059, + "duration_ms": 20569, "status_messages": [ { "message": "Thinking...", @@ -5494,6 +6130,14 @@ "message": "Querying VFB", "phase": "mcp" }, + { + "message": "Querying VFB", + "phase": "mcp" + }, + { + "message": "Querying VFB", + "phase": "mcp" + }, { "message": "Checking the answer is covered", "phase": "llm" @@ -5503,7 +6147,7 @@ "phase": "llm" } ], - "event_count": 112, + "event_count": 114, "conversation": true, "turns": [ { @@ -5511,9 +6155,9 @@ "question": "What are the anatomical parts of the medulla? List them.", "focus": null, "clicked": null, - "duration_ms": 8908, + "duration_ms": 8430, "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.", + "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 medulla, the seventh layer exhibits a distinct architecture, and layers 8-10 make up the inner medulla. Some of the 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", @@ -5576,39 +6220,39 @@ "question": "And which neurons have part of their arbour there?", "focus": null, "clicked": null, - "duration_ms": 12151, + "duration_ms": 12139, "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\"), [Mi10b](https://www.virtualflybrain.org/reports/FBbt_00110070 \"Open Mi10b in Virtual Fly Brain\"), medulla tangential neuron vGlutMtnew1, medulla tangential neuron vGlutMtnew2, Tm1a, [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 MeSps. 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 with some part in the medulla.", + "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\"), [Mi10b](https://www.virtualflybrain.org/reports/FBbt_00110070 \"Open Mi10b in Virtual Fly Brain\"), medulla tangential neuron vGlutMtnew1, medulla tangential neuron vGlutMtnew2, Tm1a, [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 MeSps. 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 medulla.", "followons": [ { "id": "FBbt_00003748", - "query_type": "TransgeneExpressionHere", - "query": "Which driver lines label the medulla?" + "query_type": "ImagesNeurons", + "query": "Which neuron images have a part in the medulla?" }, { "id": "FBbt_00003748", - "query_type": "NeuronsSynaptic", - "query": "Which neurons have synaptic terminals in the medulla?" + "query_type": "TransgeneExpressionHere", + "query": "Which driver lines label the medulla?" }, { "id": "FBbt_00003748", - "query_type": "NeuronsPostsynapticHere", - "query": "Which neurons receive output from the medulla?" + "query_type": "PartsOf", + "query": "What are the anatomical parts of the medulla?" }, { "id": "FBbt_00003748", - "query_type": "NeuronsPresynapticHere", - "query": "Which neurons provide input to the medulla?" + "query_type": "LineageClonesIn", + "query": "Which lineage clones are found in the medulla?" }, { "id": "FBbt_00003748", - "query_type": "PartsOf", - "query": "What are the anatomical parts of the medulla?" + "query_type": "ListAllAvailableImages", + "query": "Which images of medulla does VFB have?" }, { "id": "FBbt_00003748", - "query_type": "LineageClonesIn", - "query": "Which lineage clones are found in the medulla?" + "query_type": "TractsNervesInnervatingHere", + "query": "Which tracts and nerves innervate the medulla?" } ], "context_terms": [ @@ -5632,8 +6276,18 @@ }, { "id": "FBbt_00003748", - "query_type": "ImagesNeurons", - "fn": "get_images_neurons" + "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", @@ -5643,16 +6297,16 @@ ], "unmapped": [] }, - "status_count": 10, + "status_count": 12, "problems": [] } ], "ok": true, - "request_id": "e619ba1a-2283-4413-b816-5dcf64e55fd5", - "response_id": "chatcmpl-52bba2abd0f6d49a63d8f73792d1cfb9", + "request_id": "3684752f-3357-490b-8990-c6cef2688f15", + "response_id": "chatcmpl-e14907594a130d4b38485ef8d31d80e2", "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\"), [Mi10b](https://www.virtualflybrain.org/reports/FBbt_00110070 \"Open Mi10b in Virtual Fly Brain\"), medulla tangential neuron vGlutMtnew1, medulla tangential neuron vGlutMtnew2, Tm1a, [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 MeSps. 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 with some part in the medulla.", + "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\"), [Mi10b](https://www.virtualflybrain.org/reports/FBbt_00110070 \"Open Mi10b in Virtual Fly Brain\"), medulla tangential neuron vGlutMtnew1, medulla tangential neuron vGlutMtnew2, Tm1a, [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 MeSps. 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 medulla.", "quality_flags": { "has_tool_status": true, "no_tool_factual_answer": false, @@ -5663,14 +6317,14 @@ "graph_failure_mentioned": false, "missing_required_graph": false, "used_data_resource": false, - "response_chars": 1287, - "status_count": 10, + "response_chars": 1292, + "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": 12151 + "slowest_followup_ms": 12139 } }, { @@ -5683,7 +6337,7 @@ "requires_graph": false, "min_graphs": 0, "repetition": 1, - "duration_ms": 16342, + "duration_ms": 19196, "status_messages": [ { "message": "Thinking...", @@ -5718,9 +6372,9 @@ "question": "Tell me about the antennal lobe.", "focus": null, "clicked": null, - "duration_ms": 10417, + "duration_ms": 13435, "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 various records related to the antennal lobe, 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 via the Virtual Fly Brain web application.", + "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. It is a region in the Drosophila nervous system. VFB holds various data related to the antennal lobe, 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. Users can search for synaptic input in the antennal lobe via the Virtual Fly Brain web application.", "followons": [ { "id": "FBbt_00003924", @@ -5777,7 +6431,7 @@ "question": "Which neurons innervate it?", "focus": null, "clicked": null, - "duration_ms": 5925, + "duration_ms": 5761, "ok": true, "response": "The [antennal lobe](https://www.virtualflybrain.org/reports/FBbt_00003924 \"Open antennal lobe in Virtual Fly Brain\") is innervated by various 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\"), [PLP077](https://www.virtualflybrain.org/reports/FBbt_20001577 \"Open PLP077 in Virtual Fly Brain\"), [adult olfactory receptor neuron Ir75d ac1](https://www.virtualflybrain.org/reports/FBbt_00110011 \"Open adult olfactory receptor neuron Ir75d ac1 in Virtual Fly Brain\"), [adult olfactory receptor neuron Ir75d ac2](https://www.virtualflybrain.org/reports/FBbt_00110014 \"Open adult olfactory receptor neuron Ir75d ac2 in Virtual Fly Brain\"), adult olfactory receptor neuron Ir75d ac4, pharyngeal VL1 neuron, ORN_VM6, adult olfactory receptor neuron Or35a ac3I, adult olfactory receptor neuron Or35a ac3II, adult olfactory receptor neuron Or85b ab3, and adult olfactory receptor neuron Or85b ab11. VFB records show [266](https://v2.virtualflybrain.org/org.geppetto.frontend/geppetto?q=FBbt_00003924,NeuronsPresynapticHere \"Run in VFB: Neurons with presynaptic terminals in antennal lobe\") neurons with presynaptic terminals in the antennal lobe.", "followons": [ @@ -5839,8 +6493,8 @@ } ], "ok": true, - "request_id": "1195cd56-871f-402f-b5f0-479da3225fef", - "response_id": "chatcmpl-2bd86f31950fde642925ac68880e7c69", + "request_id": "3554877d-41a5-4d6e-a91c-a9f9ef3e9456", + "response_id": "chatcmpl-fb1458e67de769ec8b0c4ff66dff7dd3", "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 various 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\"), [PLP077](https://www.virtualflybrain.org/reports/FBbt_20001577 \"Open PLP077 in Virtual Fly Brain\"), [adult olfactory receptor neuron Ir75d ac1](https://www.virtualflybrain.org/reports/FBbt_00110011 \"Open adult olfactory receptor neuron Ir75d ac1 in Virtual Fly Brain\"), [adult olfactory receptor neuron Ir75d ac2](https://www.virtualflybrain.org/reports/FBbt_00110014 \"Open adult olfactory receptor neuron Ir75d ac2 in Virtual Fly Brain\"), adult olfactory receptor neuron Ir75d ac4, pharyngeal VL1 neuron, ORN_VM6, adult olfactory receptor neuron Or35a ac3I, adult olfactory receptor neuron Or35a ac3II, adult olfactory receptor neuron Or85b ab3, and adult olfactory receptor neuron Or85b ab11. VFB records show [266](https://v2.virtualflybrain.org/org.geppetto.frontend/geppetto?q=FBbt_00003924,NeuronsPresynapticHere \"Run in VFB: Neurons with presynaptic terminals in antennal lobe\") neurons with presynaptic terminals in the antennal lobe.", @@ -5861,7 +6515,7 @@ "unmatched_claim_after_resolve": false, "repeats_answered_question": false, "slow_followup_turn": false, - "slowest_followup_ms": 5925 + "slowest_followup_ms": 5761 } }, { @@ -5874,7 +6528,7 @@ "requires_graph": false, "min_graphs": 0, "repetition": 1, - "duration_ms": 202381, + "duration_ms": 22928, "status_messages": [ { "message": "Thinking...", @@ -5909,7 +6563,7 @@ "question": "What is the medulla?", "focus": null, "clicked": null, - "duration_ms": 7411, + "duration_ms": 5631, "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": [ @@ -5971,9 +6625,9 @@ "query_type": "ImagesNeurons" }, "clicked": 0, - "duration_ms": 185370, + "duration_ms": 7448, "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 neuron images returned by the query are: OA-AL2i2; MC64; MC64; aMe5; MeTu3; MeTu3; MeTu3; aMe5; MeTu-DRA; MeVP6; MeTu3; MeTu3.", + "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 neuron 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).", "followons": [ { "id": "FBbt_00003748", @@ -6044,7 +6698,7 @@ "query_type": "TransgeneExpressionHere" }, "clicked": 0, - "duration_ms": 9600, + "duration_ms": 9848, "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 [2342](https://v2.virtualflybrain.org/org.geppetto.frontend/geppetto?q=FBbt_00003748,TransgeneExpressionHere \"Run in VFB: Transgene expression in medulla\") transgene expression reports for medulla.", "followons": [ @@ -6116,8 +6770,8 @@ } ], "ok": true, - "request_id": "7c13b44f-5380-4cf9-9e19-57bc000d170c", - "response_id": "chatcmpl-ddcb9fda34e0b991eaa7085b3f78f434", + "request_id": "9e0b725a-5570-4aee-b100-b64050f9990b", + "response_id": "chatcmpl-cdd7af281384c4c59d4cb36387aa4dfc", "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 [2342](https://v2.virtualflybrain.org/org.geppetto.frontend/geppetto?q=FBbt_00003748,TransgeneExpressionHere \"Run in VFB: Transgene expression in medulla\") transgene expression reports for medulla.", @@ -6137,8 +6791,8 @@ "context_lost_across_turn": false, "unmatched_claim_after_resolve": false, "repeats_answered_question": false, - "slow_followup_turn": true, - "slowest_followup_ms": 185370 + "slow_followup_turn": false, + "slowest_followup_ms": 9848 } }, { @@ -6151,7 +6805,7 @@ "requires_graph": false, "min_graphs": 0, "repetition": 1, - "duration_ms": 12747, + "duration_ms": 11929, "status_messages": [ { "message": "Thinking...", @@ -6178,7 +6832,7 @@ "phase": "llm" } ], - "event_count": 62, + "event_count": 34, "conversation": true, "turns": [ { @@ -6186,7 +6840,7 @@ "question": "What is the mushroom body?", "focus": null, "clicked": null, - "duration_ms": 8065, + "duration_ms": 7847, "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": [ @@ -6245,9 +6899,9 @@ "question": "Which driver lines label it?", "focus": null, "clicked": null, - "duration_ms": 4682, + "duration_ms": 4082, "ok": true, - "response": "The driver lines that label the [mushroom body](https://www.virtualflybrain.org/reports/FBbt_00005801 \"Open mushroom body in Virtual Fly Brain\") include P{VT017411-GAL4.DBD} and P{VT019018-p65.AD}, which are used as hemidrivers. VFB records show [4130](https://v2.virtualflybrain.org/org.geppetto.frontend/geppetto?q=FBbt_00005801,TransgeneExpressionHere \"Run in VFB: Transgene expression in mushroom body\") instances of transgene expression in mushroom body.", + "response": "The TransgeneExpressionHere query returns 3,996 results. VFB holds [4130](https://v2.virtualflybrain.org/org.geppetto.frontend/geppetto?q=FBbt_00005801,TransgeneExpressionHere \"Run in VFB: Transgene expression in mushroom body\") transgene expression reports for [mushroom body](https://www.virtualflybrain.org/reports/FBbt_00005801 \"Open mushroom body in Virtual Fly Brain\").", "followons": [ { "id": "FBbt_00005801", @@ -6307,11 +6961,11 @@ } ], "ok": true, - "request_id": "8da6f851-4bf4-40dc-a3c4-cb66294f28b0", - "response_id": "chatcmpl-76e88de9cf5a5eddb624b413a1d7c924", + "request_id": "f2ba7c98-e03a-45e8-ab3e-5284e6377def", + "response_id": "chatcmpl-50f551519ea1f823b86b96c7d948b60c", "images_count": 8, "graphs_count": 0, - "response": "The driver lines that label the [mushroom body](https://www.virtualflybrain.org/reports/FBbt_00005801 \"Open mushroom body in Virtual Fly Brain\") include P{VT017411-GAL4.DBD} and P{VT019018-p65.AD}, which are used as hemidrivers. VFB records show [4130](https://v2.virtualflybrain.org/org.geppetto.frontend/geppetto?q=FBbt_00005801,TransgeneExpressionHere \"Run in VFB: Transgene expression in mushroom body\") instances of transgene expression in mushroom body.", + "response": "The TransgeneExpressionHere query returns 3,996 results. VFB holds [4130](https://v2.virtualflybrain.org/org.geppetto.frontend/geppetto?q=FBbt_00005801,TransgeneExpressionHere \"Run in VFB: Transgene expression in mushroom body\") transgene expression reports for [mushroom body](https://www.virtualflybrain.org/reports/FBbt_00005801 \"Open mushroom body in Virtual Fly Brain\").", "quality_flags": { "has_tool_status": true, "no_tool_factual_answer": false, @@ -6322,14 +6976,14 @@ "graph_failure_mentioned": false, "missing_required_graph": false, "used_data_resource": false, - "response_chars": 459, + "response_chars": 375, "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": 4682 + "slowest_followup_ms": 4082 } }, { @@ -6342,7 +6996,7 @@ "requires_graph": false, "min_graphs": 0, "repetition": 1, - "duration_ms": 20365, + "duration_ms": 19124, "status_messages": [ { "message": "Thinking...", @@ -6360,26 +7014,6 @@ "message": "Reading VFB term info", "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" @@ -6393,7 +7027,7 @@ "phase": "llm" } ], - "event_count": 152, + "event_count": 63, "conversation": true, "turns": [ { @@ -6401,9 +7035,9 @@ "question": "Which neurons provide input to the medulla?", "focus": null, "clicked": null, - "duration_ms": 6787, + "duration_ms": 5641, "ok": true, - "response": "Neurons that provide input to 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\"), [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. VFB records show that there are [262](https://v2.virtualflybrain.org/org.geppetto.frontend/geppetto?q=FBbt_00003748,NeuronsPresynapticHere \"Run in VFB: Neurons with presynaptic terminals in medulla\") neurons with presynaptic terminals in the medulla.", + "response": "Neurons that provide input to 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\"), [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. 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\") neurons with presynaptic terminals in medulla.", "followons": [ { "id": "FBbt_00003748", @@ -6471,39 +7105,39 @@ "question": "And the lobula?", "focus": null, "clicked": null, - "duration_ms": 13578, + "duration_ms": 13483, "ok": true, - "response": "Neurons that provide input to the [lobula](https://www.virtualflybrain.org/reports/FBbt_00003852 \"Open lobula in Virtual Fly Brain\") include [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. VFB records show that there are [528](https://v2.virtualflybrain.org/org.geppetto.frontend/geppetto?q=FBbt_00003852,NeuronsPartHere \"Run in VFB: Neurons with some part in lobula\") neurons with synaptic terminals in the lobula.", + "response": "Neurons that provide input to the [lobula](https://www.virtualflybrain.org/reports/FBbt_00003852 \"Open lobula in Virtual Fly Brain\") include those with presynaptic terminals in lobula. VFB holds various records related to lobula, including neurons with some part in lobula, neurons with synaptic terminals in lobula, and transgene expression in lobula.", "followons": [ { "id": "FBbt_00003852", - "query_type": "NeuronsPresynapticHere", - "query": "Which neurons provide input to the lobula?" + "query_type": "ListAllAvailableImages", + "query": "Which images of lobula does VFB have?" }, { "id": "FBbt_00003852", - "query_type": "NeuronsPostsynapticHere", - "query": "Which neurons receive output from the lobula?" + "query_type": "NeuronsPartHere", + "query": "Which neurons have part of their arbour in the lobula?" }, { "id": "FBbt_00003852", - "query_type": "PartsOf", - "query": "What are the anatomical parts of the lobula?" + "query_type": "NeuronsSynaptic", + "query": "Which neurons have synaptic terminals in the lobula?" }, { "id": "FBbt_00003852", - "query_type": "TractsNervesInnervatingHere", - "query": "Which tracts and nerves innervate the lobula?" + "query_type": "NeuronsPresynapticHere", + "query": "Which neurons provide input to the lobula?" }, { "id": "FBbt_00003852", - "query_type": "LineageClonesIn", - "query": "Which lineage clones are found in the lobula?" + "query_type": "NeuronsPostsynapticHere", + "query": "Which neurons receive output from the lobula?" }, { "id": "FBbt_00003852", - "query_type": "ImagesNeurons", - "query": "Which neuron images have a part in the lobula?" + "query_type": "PartsOf", + "query": "What are the anatomical parts of the lobula?" } ], "context_terms": [ @@ -6528,21 +7162,6 @@ } ], "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", @@ -6556,16 +7175,16 @@ ], "unmapped": [] }, - "status_count": 12, + "status_count": 7, "problems": [] } ], "ok": true, - "request_id": "f97a7a7a-ec4c-47cb-bcf1-215dbbb188e2", - "response_id": "chatcmpl-023c01d9eb992405fa14e336b67d2a18", + "request_id": "a61bf34b-cf57-40a5-9351-0988bcfcaf3d", + "response_id": "chatcmpl-4ffd68c5071ceb8290bb643ab251f89e", "images_count": 4, "graphs_count": 0, - "response": "Neurons that provide input to the [lobula](https://www.virtualflybrain.org/reports/FBbt_00003852 \"Open lobula in Virtual Fly Brain\") include [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. VFB records show that there are [528](https://v2.virtualflybrain.org/org.geppetto.frontend/geppetto?q=FBbt_00003852,NeuronsPartHere \"Run in VFB: Neurons with some part in lobula\") neurons with synaptic terminals in the lobula.", + "response": "Neurons that provide input to the [lobula](https://www.virtualflybrain.org/reports/FBbt_00003852 \"Open lobula in Virtual Fly Brain\") include those with presynaptic terminals in lobula. VFB holds various records related to lobula, including neurons with some part in lobula, neurons with synaptic terminals in lobula, and transgene expression in lobula.", "quality_flags": { "has_tool_status": true, "no_tool_factual_answer": false, @@ -6576,14 +7195,14 @@ "graph_failure_mentioned": false, "missing_required_graph": false, "used_data_resource": false, - "response_chars": 1015, - "status_count": 12, + "response_chars": 352, + "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": 13578 + "slowest_followup_ms": 13483 } }, { @@ -6596,7 +7215,7 @@ "requires_graph": false, "min_graphs": 0, "repetition": 1, - "duration_ms": 40186, + "duration_ms": 45470, "status_messages": [ { "message": "Thinking...", @@ -6655,7 +7274,7 @@ "question": "What is the protocerebral bridge?", "focus": null, "clicked": null, - "duration_ms": 6555, + "duration_ms": 6912, "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": [ @@ -6714,9 +7333,9 @@ "question": "How does it relate to the ellipsoid body?", "focus": null, "clicked": null, - "duration_ms": 14982, + "duration_ms": 17718, "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 synaptic terminals in the ellipsoid body that include adult protocerebral bridge glomerulus neurons, indicating a connection between the two structures.", + "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 others with similar names, indicating a connection between the two. The connectome data indicates that there are [103](https://v2.virtualflybrain.org/org.geppetto.frontend/geppetto?q=FBbt_00003678,NeuronsPartHere \"Run in VFB: Neurons with some part in ellipsoid body\") neurons with some part in the ellipsoid body and [102](https://v2.virtualflybrain.org/org.geppetto.frontend/geppetto?q=FBbt_00003678,NeuronsSynaptic \"Run in VFB: Neurons with synaptic terminals in ellipsoid body\") neurons with synaptic terminals in the ellipsoid body, with some of these neurons having names that suggest a connection to the protocerebral bridge.", "followons": [ { "id": "FBbt_00003668", @@ -6789,7 +7408,7 @@ ], "unmapped": [] }, - "status_count": 14, + "status_count": 13, "problems": [] }, { @@ -6797,9 +7416,9 @@ "question": "Which neurons connect them?", "focus": null, "clicked": null, - "duration_ms": 18649, + "duration_ms": 20840, "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 [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\"), adult protocerebral bridge glomerulus 4-ellipsoid body canal-ventral gall neuron, adult protocerebral bridge glomerulus 5-ellipsoid body canal-dorsal gall neuron, adult protocerebral bridge glomerulus 6-ellipsoid body canal-ventral gall neuron, adult protocerebral bridge glomerulus 7-ellipsoid body canal-dorsal gall neuron, and adult protocerebral bridge glomerulus 8-ellipsoid body canal-ventral gall neuron. [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\"), and [PEN_PB8](https://www.virtualflybrain.org/reports/FBbt_00111374 \"Open PEN_PB8 in Virtual Fly Brain\") neurons also have synaptic terminals in both the protocerebral bridge and the ellipsoid body.", + "response": "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 [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\"), adult protocerebral bridge glomerulus 4-ellipsoid body canal-ventral gall neuron, adult protocerebral bridge glomerulus 5-ellipsoid body canal-dorsal gall neuron, adult protocerebral bridge glomerulus 6-ellipsoid body canal-ventral gall neuron, adult protocerebral bridge glomerulus 7-ellipsoid body canal-dorsal gall neuron, and adult protocerebral bridge glomerulus 8-ellipsoid body canal-ventral gall neuron. [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\"), and [PEN_PB8](https://www.virtualflybrain.org/reports/FBbt_00111374 \"Open PEN_PB8 in Virtual Fly Brain\") neurons also have synaptic terminals in both the protocerebral bridge and the ellipsoid body.", "followons": [ { "id": "FBbt_00003668", @@ -6902,11 +7521,11 @@ } ], "ok": true, - "request_id": "5617da07-15ee-40c6-9f64-645aeeff0ff6", - "response_id": "chatcmpl-5b216e6ffbf06847a49f8bba4844e119", + "request_id": "a085bc76-c285-4645-98ac-9be7f5fed228", + "response_id": "chatcmpl-732d8ced3c218ee2726024480aeb8f7b", "images_count": 8, "graphs_count": 0, - "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 [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\"), adult protocerebral bridge glomerulus 4-ellipsoid body canal-ventral gall neuron, adult protocerebral bridge glomerulus 5-ellipsoid body canal-dorsal gall neuron, adult protocerebral bridge glomerulus 6-ellipsoid body canal-ventral gall neuron, adult protocerebral bridge glomerulus 7-ellipsoid body canal-dorsal gall neuron, and adult protocerebral bridge glomerulus 8-ellipsoid body canal-ventral gall neuron. [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\"), and [PEN_PB8](https://www.virtualflybrain.org/reports/FBbt_00111374 \"Open PEN_PB8 in Virtual Fly Brain\") neurons also have synaptic terminals in both the protocerebral bridge and the ellipsoid body.", + "response": "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 [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\"), adult protocerebral bridge glomerulus 4-ellipsoid body canal-ventral gall neuron, adult protocerebral bridge glomerulus 5-ellipsoid body canal-dorsal gall neuron, adult protocerebral bridge glomerulus 6-ellipsoid body canal-ventral gall neuron, adult protocerebral bridge glomerulus 7-ellipsoid body canal-dorsal gall neuron, and adult protocerebral bridge glomerulus 8-ellipsoid body canal-ventral gall neuron. [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\"), and [PEN_PB8](https://www.virtualflybrain.org/reports/FBbt_00111374 \"Open PEN_PB8 in Virtual Fly Brain\") neurons also have synaptic terminals in both the protocerebral bridge and the ellipsoid body.", "quality_flags": { "has_tool_status": true, "no_tool_factual_answer": false, @@ -6917,14 +7536,14 @@ "graph_failure_mentioned": false, "missing_required_graph": false, "used_data_resource": false, - "response_chars": 1449, + "response_chars": 1445, "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": 18649 + "slowest_followup_ms": 20840 } }, { @@ -6937,7 +7556,7 @@ "requires_graph": false, "min_graphs": 0, "repetition": 1, - "duration_ms": 24447, + "duration_ms": 27814, "status_messages": [ { "message": "Thinking...", @@ -6956,7 +7575,7 @@ "phase": "mcp" }, { - "message": "Checking the literature", + "message": "Checking VFB documentation", "phase": "mcp" }, { @@ -6968,7 +7587,7 @@ "phase": "llm" } ], - "event_count": 31, + "event_count": 42, "conversation": true, "turns": [ { @@ -6976,10 +7595,15 @@ "question": "Which neurons have part of them in the medulla?", "focus": null, "clicked": null, - "duration_ms": 13309, + "duration_ms": 14385, "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.", + "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\"), [Mi10b](https://www.virtualflybrain.org/reports/FBbt_00110070 \"Open Mi10b in Virtual Fly Brain\"), medulla tangential neuron vGlutMtnew1, medulla tangential neuron vGlutMtnew2, Tm1a, [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 MeSps. 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 medulla.", "followons": [ + { + "id": "FBbt_00003748", + "query_type": "ImagesNeurons", + "query": "Which neuron images have a part in the medulla?" + }, { "id": "FBbt_00003748", "query_type": "TransgeneExpressionHere", @@ -7004,11 +7628,6 @@ "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": [ @@ -7029,16 +7648,11 @@ "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": 11, + "status_count": 8, "problems": [] }, { @@ -7046,9 +7660,9 @@ "question": "How would I get that same result in Python with vfbquery?", "focus": null, "clicked": null, - "duration_ms": 11138, + "duration_ms": 13429, "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```", + "response": "The code below returns the neurons with some part in the [medulla](https://www.virtualflybrain.org/reports/FBbt_00003748 \"Open medulla in Virtual Fly Brain\"), as a table. VFB holds [471](https://v2.virtualflybrain.org/org.geppetto.frontend/geppetto?q=FBbt_00003748,NeuronsPartHere \"Run in VFB: Neurons with some part in medulla\") neuron types with some part in medulla.\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```", "followons": [ { "id": "FBbt_00003748", @@ -7099,11 +7713,6 @@ "id": "FBbt_00003748", "query_type": "NeuronsPartHere", "fn": "get_neurons_with_part_in" - }, - { - "id": "FBbt_00003748", - "query_type": "ImagesNeurons", - "fn": "get_images_neurons" } ], "unmapped": [] @@ -7113,11 +7722,11 @@ } ], "ok": true, - "request_id": "ba7dfddb-bff3-4bb3-b6fb-c2cc0d405ebf", - "response_id": "chatcmpl-d3c82dc974b240369660f4e131ee36b1", + "request_id": "c78af163-0a26-49b7-ae9e-48f0de0f53d7", + "response_id": "chatcmpl-98872b9949811c4020cd793347c80397", "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```", + "response": "The code below returns the neurons with some part in the [medulla](https://www.virtualflybrain.org/reports/FBbt_00003748 \"Open medulla in Virtual Fly Brain\"), as a table. VFB holds [471](https://v2.virtualflybrain.org/org.geppetto.frontend/geppetto?q=FBbt_00003748,NeuronsPartHere \"Run in VFB: Neurons with some part in medulla\") neuron types with some part in medulla.\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```", "quality_flags": { "has_tool_status": true, "no_tool_factual_answer": false, @@ -7128,14 +7737,14 @@ "graph_failure_mentioned": false, "missing_required_graph": false, "used_data_resource": false, - "response_chars": 845, + "response_chars": 808, "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": 11138 + "slowest_followup_ms": 13429 } }, { @@ -7148,7 +7757,7 @@ "requires_graph": false, "min_graphs": 0, "repetition": 1, - "duration_ms": 19592, + "duration_ms": 31727, "status_messages": [ { "message": "Thinking...", @@ -7170,6 +7779,10 @@ "message": "Querying VFB", "phase": "mcp" }, + { + "message": "Querying VFB", + "phase": "mcp" + }, { "message": "Checking the answer is covered", "phase": "llm" @@ -7179,7 +7792,7 @@ "phase": "llm" } ], - "event_count": 47, + "event_count": 214, "conversation": true, "turns": [ { @@ -7187,9 +7800,9 @@ "question": "What are the subclasses of Kenyon cell?", "focus": null, "clicked": null, - "duration_ms": 6335, + "duration_ms": 11924, "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\"). 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.", + "response": "The subclasses of [Kenyon cell](https://www.virtualflybrain.org/reports/FBbt_00003686 \"Open Kenyon cell in Virtual Fly Brain\") are 37 in number, 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 VFB ids, 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. 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.", "followons": [ { "id": "FBbt_00003686", @@ -7252,9 +7865,9 @@ "question": "Can you list the VFB IDs so I can reproduce this myself?", "focus": null, "clicked": null, - "duration_ms": 13257, + "duration_ms": 19803, "ok": true, - "response": "The code below returns the 12 VFB IDs of [Kenyon cell](https://www.virtualflybrain.org/reports/FBbt_00003686 \"Open Kenyon cell in Virtual Fly Brain\") subclasses that were retrieved, as a table. VFB holds a total of [37](https://v2.virtualflybrain.org/org.geppetto.frontend/geppetto?q=FBbt_00003686,SubclassesOf \"Run in VFB: Subclasses of Kenyon cell\") subclasses of Kenyon cell.\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```", + "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: [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); KCg-s (FBbt_00049830); KCg-s4 (FBbt_00049832); KCg-t (FBbt_00049833); larval alpha'/beta' Kenyon cell (FBbt_00049835); KCab-sc (FBbt_00049838); alpha'/beta' anterior-posterior type 1 Kenyon cell of lACA (FBbt_00049859); [Kenyon cell of main calyx](https://www.virtualflybrain.org/reports/FBbt_00047926 \"Open Kenyon cell of main calyx in Virtual Fly Brain\") (FBbt_00047926); single-claw Kenyon cell (FBbt_00047993); multi-claw Kenyon cell (FBbt_00047994).\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", @@ -7304,16 +7917,16 @@ ], "unmapped": [] }, - "status_count": 7, + "status_count": 8, "problems": [] } ], "ok": true, - "request_id": "0c5ffda9-037d-46ff-8f3f-8ab10f35084f", - "response_id": "chatcmpl-5d9b9b4e907cdd09dcd1dc26e0f630ef", + "request_id": "4ec32e17-7bcc-4550-8e73-bca69e981d74", + "response_id": "chatcmpl-4e73a761f62e5da8e7010b1775134517", "images_count": 8, "graphs_count": 0, - "response": "The code below returns the 12 VFB IDs of [Kenyon cell](https://www.virtualflybrain.org/reports/FBbt_00003686 \"Open Kenyon cell in Virtual Fly Brain\") subclasses that were retrieved, as a table. VFB holds a total of [37](https://v2.virtualflybrain.org/org.geppetto.frontend/geppetto?q=FBbt_00003686,SubclassesOf \"Run in VFB: Subclasses of Kenyon cell\") subclasses of Kenyon cell.\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```", + "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: [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); KCg-s (FBbt_00049830); KCg-s4 (FBbt_00049832); KCg-t (FBbt_00049833); larval alpha'/beta' Kenyon cell (FBbt_00049835); KCab-sc (FBbt_00049838); alpha'/beta' anterior-posterior type 1 Kenyon cell of lACA (FBbt_00049859); [Kenyon cell of main calyx](https://www.virtualflybrain.org/reports/FBbt_00047926 \"Open Kenyon cell of main calyx in Virtual Fly Brain\") (FBbt_00047926); single-claw Kenyon cell (FBbt_00047993); multi-claw Kenyon cell (FBbt_00047994).\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, @@ -7324,14 +7937,14 @@ "graph_failure_mentioned": false, "missing_required_graph": false, "used_data_resource": false, - "response_chars": 819, - "status_count": 7, + "response_chars": 1655, + "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": 13257 + "slowest_followup_ms": 19803 } } ] diff --git a/test-results/task-battery/task-battery-2026-08-11T17-44-06-563Z.json b/test-results/task-battery/task-battery-2026-08-11T17-44-06-563Z.json new file mode 100644 index 0000000..1fad7c4 --- /dev/null +++ b/test-results/task-battery/task-battery-2026-08-11T17-44-06-563Z.json @@ -0,0 +1,7951 @@ +{ + "metadata": { + "run_id": "task-battery-2026-08-11T17-44-06-563Z", + "started_at": "2026-08-11T17:44:06.563Z", + "completed_at": "2026-08-11T17:51:24.675Z", + "git_sha": "37b9fb8e6b531fa39870a02edaff2c111e68bfc0", + "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": 0, + "task_ids": [] + } + }, + "conversation": { + "total": 12, + "ok": 12, + "turns": 27, + "followup_turns": 15, + "followup_median_ms": 10070, + "followup_max_ms": 69118 + }, + "mean_duration_ms": 23273 + }, + "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": 14783, + "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": 101, + "ok": true, + "request_id": "fd726da7-d540-425b-92c1-db12ad9cfac9", + "response_id": "chatcmpl-0a09cceb4a1498506afc20f7a99c47ac", + "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 calyx is closest to the cortex and receives sensory interneuron afferents, the pedunculus is a thick axon bundle extending from the calyx to the base of the lobes, and 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": 522, + "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": 14872, + "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": "73740e7e-aa94-4a64-9341-f20d39b7ba53", + "response_id": "chatcmpl-c3fe3c7de371b99d74497ec268721442", + "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": 18887, + "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": "Querying VFB", + "phase": "mcp" + }, + { + "message": "Checking the answer is covered", + "phase": "llm" + }, + { + "message": "Writing the answer", + "phase": "llm" + } + ], + "event_count": 124, + "ok": true, + "request_id": "3c295087-bf10-4a87-9254-630b0f8a8966", + "response_id": "chatcmpl-4544a7d911dfd8f7f43f70644f162e52", + "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 mushroom body, including larval uniglomerular projection neurons and larval antennal lobe multiglomerular projection neurons. Additionally, VFB holds records of neurons with postsynaptic terminals in mushroom body, totaling [304](https://v2.virtualflybrain.org/org.geppetto.frontend/geppetto?q=FBbt_00005801,NeuronsPostsynapticHere \"Run in VFB: Neurons with postsynaptic terminals in mushroom body\") results, which include adult odd neurons of the calyx and other types. The calyx receives sensory interneuron afferents.", + "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": 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{ + "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": 955, + "status_count": 11 + } + }, + { + "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": 12191, + "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": "131b2986-98bd-42c9-b5bc-de253816c78b", + "response_id": "chatcmpl-96e7f024b350797863f21cd16f273515", + "images_count": 6, + "graphs_count": 0, + "response": "Mushroom body Kenyon cells use acetylcholine as their primary neurotransmitter.", + "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": 79, + "status_count": 6 + } + }, + { + "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": 1, + "duration_ms": 24185, + "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": "Writing the answer", + "phase": "llm" + } + ], + "event_count": 140, + "ok": true, + "request_id": "d2c6e8b0-96d3-4cb4-b066-e52450324ba2", + "response_id": "chatcmpl-5b18ca4fdb0594556997de36d7e80bdc", + "images_count": 6, + "graphs_count": 1, + "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 such as Ir75d ac1 and Or35a ac3I. Neurons with postsynaptic terminals in the antennal lobe include adult antennal lobe projection neurons like DL5, DM4, and VA1d, as well as multiglomerular antennal lobe projection neurons like L1 adPN.", + "graphs": [ + { + "type": "basic_graph", + "version": 1, + "title": "antennal lobe region connectivity preview", + "directed": true, + "layout": "radial", + "nodes": [ + { + "id": "FBbt_00003924", + "label": "antennal lobe", + "group": "queried region", + "color": null, + "size": 2.4 + }, + { + "id": "FBbt_00111694", + "label": "larval antennal lobe picky local neuron", + "group": "presynaptic and postsynaptic neuron", + "color": null, + "size": 1.15 + }, + { + "id": "FBbt_00111700", + "label": "larval antennal lobe broad local neuron", + "group": "presynaptic and postsynaptic neuron", + "color": null, + "size": 1.15 + }, + { + "id": "FBbt_20001577", + "label": "PLP077", + "group": "presynaptic and postsynaptic neuron", + "color": null, + "size": 1.15 + }, + { + "id": "FBbt_00110011", + "label": "adult olfactory receptor neuron Ir75d ac1", + "group": "presynaptic neuron", + "color": null, + "size": 1.15 + }, + { + "id": "FBbt_00110014", + "label": "adult olfactory receptor neuron Ir75d ac2", + "group": "presynaptic neuron", + "color": null, + "size": 1.15 + }, + { + "id": "FBbt_00110017", + "label": "adult olfactory receptor neuron Ir75d ac4", + "group": "presynaptic neuron", + "color": null, + "size": 1.15 + }, + { + "id": "FBbt_00111480", + "label": "AMMC-Bi16", + "group": "postsynaptic neuron", + "color": null, + "size": 1.15 + }, + { + "id": "FBbt_00059280", + "label": "adult antennal lobe projection neuron DL5", + "group": "postsynaptic neuron", + "color": null, + "size": 1.15 + }, + { + "id": "FBbt_00059281", + "label": "adult antennal lobe projection neuron DM4", + "group": "postsynaptic neuron", + "color": null, + "size": 1.15 + } + ], + "edges": [ + { + "source": "FBbt_00111694", + "target": "FBbt_00003924", + "label": "presynaptic sites in antennal lobe", + "weight": 0 + }, + { + "source": "FBbt_00111700", + "target": "FBbt_00003924", + "label": "presynaptic sites in antennal lobe", + "weight": 0 + }, + { + "source": "FBbt_20001577", + "target": "FBbt_00003924", + "label": "presynaptic sites in antennal lobe", + "weight": 0 + }, + { + "source": "FBbt_00110011", + "target": "FBbt_00003924", + "label": "presynaptic sites in antennal lobe", + "weight": 0 + }, + { + "source": "FBbt_00110014", + "target": "FBbt_00003924", + "label": "presynaptic sites in antennal lobe", + "weight": 0 + }, + { + "source": "FBbt_00110017", + "target": "FBbt_00003924", + "label": "presynaptic sites in antennal lobe", + "weight": 0 + }, + { + "source": "FBbt_00003924", + "target": "FBbt_00111480", + "label": "postsynaptic sites in antennal lobe", + "weight": 0 + }, + { + "source": "FBbt_00003924", + "target": "FBbt_00111694", + "label": "postsynaptic sites in antennal lobe", + "weight": 0 + }, + { + "source": "FBbt_00003924", + "target": "FBbt_00111700", + "label": "postsynaptic sites in antennal lobe", + "weight": 0 + }, + { + "source": "FBbt_00003924", + "target": "FBbt_20001577", + "label": "postsynaptic sites in antennal lobe", + "weight": 0 + }, + { + "source": "FBbt_00003924", + "target": "FBbt_00059280", + "label": "postsynaptic sites in antennal lobe", + "weight": 0 + }, + { + "source": "FBbt_00003924", + "target": "FBbt_00059281", + "label": "postsynaptic sites in antennal lobe", + "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": 881, + "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": 18666, + "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": 39, + "ok": true, + "request_id": "8587dee9-b68d-4aad-9334-4ac909c46c70", + "response_id": "chatcmpl-50e58cbed9e24804efef68ec8fa4e5b1", + "images_count": 8, + "graphs_count": 0, + "response": "Approximately 32,388 neurons are in the [adult central brain](https://www.virtualflybrain.org/reports/FBbt_00047887 \"Open adult central brain in Virtual Fly Brain\"). VFB has annotated [9413](https://v2.virtualflybrain.org/org.geppetto.frontend/geppetto?q=FBbt_00047887,NeuronsPartHere \"Run in VFB: Neurons with some part in adult central brain\") neuron types with some part in the adult central brain.\n\n**Published neuron-count estimates — adult central brain** (from the literature):\n\n- ~32,388 neurons (Whole adult brain, both optic lobes and ocellar ganglia included. Ventral nerve cord NOT included; neurons crossing the neck connective are truncated at the brain boundary. Subcount: fully in central brain. One female adult. Dataset: FlyWire connectome neurons, v783.) — Dorkenwald S et al. (2024) Nature 634(8032):124-138 — 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": 977, + "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": 26763, + "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": 103, + "ok": true, + "request_id": "6a7b8ad9-11ee-4863-8c2a-a167083948e8", + "response_id": "chatcmpl-74b1f688e5963bb9e242cd8ecfa8b5fb", + "images_count": 8, + "graphs_count": 1, + "response": "The main components of the Drosophila central complex include the ellipsoid body, the fan-shaped body, the three paired noduli, the asymmetrical bodies, and the protocerebral bridge. These components are associated with functions such as navigation and orientation, locomotor control, and sleep/arousal and memory-related behaviors. VFB holds [363](https://v2.virtualflybrain.org/org.geppetto.frontend/geppetto?q=FBbt_00003632,NeuronsPartHere \"Run in VFB: Neurons with some part in adult central complex\") records of neurons with some part in [adult central complex](https://www.virtualflybrain.org/reports/FBbt_00003632 \"Open adult central complex in Virtual Fly Brain\") and [362](https://v2.virtualflybrain.org/org.geppetto.frontend/geppetto?q=FBbt_00003632,NeuronsSynaptic \"Run in VFB: Neurons with synaptic terminals in adult central complex\") records of neurons with synaptic terminals in adult central complex.", + "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": 916, + "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": 21328, + "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": 132, + "ok": true, + "request_id": "be9b3e68-2af6-4b71-8efc-2c1b8fcdb489", + "response_id": "chatcmpl-26a2b89197fd27f4d2c819cc0ce402c3", + "images_count": 8, + "graphs_count": 0, + "response": "Genetic tools commonly used to label mushroom body neurons, such as [Kenyon cell](https://www.virtualflybrain.org/reports/FBbt_00003686 \"Open Kenyon cell in Virtual Fly Brain\"), include PBac{544.SVS-1}Bsg[CPTI100062] and PBac{566.P.SVS-1}Bsg[CPTI100005] expression patterns. VFB records show multiple transgene expression patterns, including PBac{602.P.SVS-1}Fas2[CPTI000483], PBac{602.P.SVS-1}HDAC4[CPTI000077], and PBac{602.P.SVS-1}Pax[CPTI000161].", + "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": 450, + "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": 26150, + "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": 97, + "ok": true, + "request_id": "da38e537-bd00-4bc7-8af3-b8f5f7588231", + "response_id": "chatcmpl-97731e223245325dc6bf27d117493872", + "images_count": 8, + "graphs_count": 1, + "response": "Dopaminergic input to mushroom body output neurons comes from specific types of dopaminergic neurons, including dopaminergic PPL1 neurons and dopaminergic PAM neurons. The strongest specific inputs to mushroom body output neurons are from adult cholinergic neurons and Kenyon cells, with 7.22 and 7.09 synapses per connected pair, respectively. 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](https://www.virtualflybrain.org/reports/FBbt_00047953 \"Open mushroom body output neuron in Virtual Fly Brain\").", + "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": 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"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": 640, + "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": 89557, + "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" + }, + { + "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": 396, + "ok": true, + "request_id": "90918f4e-4fdc-4d87-93a0-f6c7d58bc3c1", + "response_id": "chatcmpl-8a5755bd6c5455e25f260e6feb4b15ac", + "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 records show that [olfactory projection neuron](https://www.virtualflybrain.org/reports/FBbt_00051298 \"Open olfactory projection neuron in Virtual Fly Brain\") has 60,114 downstream classes and 37,427 upstream classes, with the strongest specific targets and inputs including [sNPF neuron](https://www.virtualflybrain.org/reports/FBbt_00048378 \"Open sNPF neuron in Virtual Fly Brain\"), [adult Kenyon cell](https://www.virtualflybrain.org/reports/FBbt_00049825 \"Open adult Kenyon cell in Virtual Fly Brain\"), [local neuron](https://www.virtualflybrain.org/reports/FBbt_00051493 \"Open local neuron 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\").", + "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": 920, + "status_count": 15 + } + }, + { + "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": 17349, + "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" + } + ], + "event_count": 169, + "ok": true, + "request_id": "7bea7c15-ade0-4cf8-a8a5-434188cb7698", + "response_id": "chatcmpl-c5dd36bb0c5d04a0696a08ee606ec061", + "images_count": 8, + "graphs_count": 0, + "response": "There are split-GAL4 driver lines available that target lateral horn neuron types. VFB records show [4](https://v2.virtualflybrain.org/org.geppetto.frontend/geppetto?q=FBbt_00048293,SplitsTargeting \"Run in VFB: Splits targeting LHN\") split-GAL4 combinations that target lateral horn neurons, which are: [P{R23C06-GAL4.DBD} ∩ P{VT004984-p65.AD} expression pattern](https://www.virtualflybrain.org/reports/VFBexp_FBtp0099468FBtp0119463 \"Open P{R23C06-GAL4.DBD} ∩ P{VT004984-p65.AD} expression pattern in Virtual Fly Brain\"); [P{VT008489-GAL4.DBD} ∩ P{VT006486-p65.AD} expression pattern](https://www.virtualflybrain.org/reports/VFBexp_FBtp0122916FBtp0119497 \"Open P{VT008489-GAL4.DBD} ∩ P{VT006486-p65.AD} expression pattern in Virtual Fly Brain\"); [P{VT026953-GAL4.DBD} ∩ P{R45B08-p65.AD} expression pattern](https://www.virtualflybrain.org/reports/VFBexp_FBtp0123770FBtp0118765 \"Open P{VT026953-GAL4.DBD} ∩ P{R45B08-p65.AD} expression pattern in Virtual Fly Brain\"); and [P{VT033629-GAL4.DBD} ∩ P{VT037488-p65.AD} expression pattern](https://www.virtualflybrain.org/reports/VFBexp_FBtp0124008FBtp0149648 \"Open P{VT033629-GAL4.DBD} ∩ P{VT037488-p65.AD} expression pattern in Virtual Fly Brain\"). VFB holds [24022](https://v2.virtualflybrain.org/org.geppetto.frontend/geppetto?q=FBbt_00048293,ListAllAvailableImages \"Run in VFB: List all available images of LHN\") available images of [adult lateral horn neuron](https://www.virtualflybrain.org/reports/FBbt_00048293 \"Open adult lateral horn neuron in Virtual Fly Brain\") and [1374](https://v2.virtualflybrain.org/org.geppetto.frontend/geppetto?q=FBbt_00048293,SubclassesOf \"Run in VFB: Subclasses of LHN\") subclasses of adult lateral horn 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": 1694, + "status_count": 9 + } + }, + { + "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": 22419, + "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": 215, + "ok": true, + "request_id": "e39b7e82-b22a-4b3c-ab34-fa7ca7ff6c6b", + "response_id": "chatcmpl-0e9ff1ca326d29360191a882f0844daf", + "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 a type of neuron with a distinct dendritic arbor in each lobula plate layer, extending outwards from the main fiber in the direction of motion detection for the layer. It is involved in detecting looming stimuli and 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 datasets available for this neuron type.", + "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": 834, + "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": 9231, + "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": "a58f70e9-78f4-4907-89af-6f18bd94e5bb", + "response_id": "chatcmpl-c5e2ed955eeca79d5ec35061e61d5129", + "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": 21005, + "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 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": 108, + "ok": true, + "request_id": "1327b937-5753-4bd7-902c-f1f751a9a084", + "response_id": "chatcmpl-43b6cd1e6a4e09f8280d5cf4c955982b", + "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. Additionally, Mao and Davis, 2009, and Claridge-Chang et al., 2009, are also mentioned as describing PPL1 dopaminergic neurons and their role in aversive memory.", + "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": 353, + "status_count": 9 + } + }, + { + "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": 14988, + "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": "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": 34, + "ok": true, + "request_id": "44a14dbb-ecd6-4721-8816-8b4188f22c7a", + "response_id": "chatcmpl-5787e5c8788405df7fa19d38e8a411a5", + "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": 9 + } + }, + { + "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": 13882, + "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": "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" + } + ], + "event_count": 159, + "ok": true, + "request_id": "22c684d1-f306-4c78-9d6e-0bd3a29a0469", + "response_id": "chatcmpl-bde3f2d931b8eea0a96b54a8f7d32e94", + "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\") neuron types with presynaptic terminals in the fan-shaped body, including [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. The connectome data indicates that these neurons provide input to the fan-shaped body, but the exact number of synaptic steps 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": 1594, + "status_count": 10 + } + }, + { + "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": 20485, + "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": 126, + "ok": true, + "request_id": "6ba9ee2d-e05d-487b-b5bf-882dabe978b7", + "response_id": "chatcmpl-4777ea620fa250ef91e5211fad730bb5", + "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 these two neuron types. The strongest specific inputs to mushroom body output neurons are adult cholinergic neurons and Kenyon cells, with mean synaptic weights of 7.22 and 7.09 synapses per connected pair, respectively. For dopaminergic neurons, the strongest specific targets are adult cholinergic neurons and adult Kenyon cells, with mean synaptic weights of 2.68 and 2.04 synapses per connected pair, respectively.", + "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": 563, + "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": 16241, + "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": 140, + "ok": true, + "request_id": "39d72f55-f3bb-4a10-921b-dadfd7997642", + "response_id": "chatcmpl-a677d442f29054f6477dd62faacf3606", + "images_count": 8, + "graphs_count": 0, + "response": "The pathway from olfactory receptor neurons to the [adult lateral horn](https://www.virtualflybrain.org/reports/FBbt_00007053 \"Open adult lateral horn in Virtual Fly Brain\") involves intermediate neuron types. Antennal lobe projection neurons are intermediate neuron types between olfactory receptor neurons and the lateral horn. The strongest specific inputs to olfactory receptor neurons include [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\"), [olfactory system neuron](https://www.virtualflybrain.org/reports/FBbt_00007697 \"Open olfactory system neuron in Virtual Fly Brain\"), and [adult antennal sensory neuron](https://www.virtualflybrain.org/reports/FBbt_00051173 \"Open adult antennal sensory 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\") records of neurons with some part in adult lateral horn 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\") records of 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": 1796, + "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": 10051, + "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": "Querying VFB", + "phase": "mcp" + }, + { + "message": "Checking the answer is covered", + "phase": "llm" + }, + { + "message": "Writing the answer", + "phase": "llm" + } + ], + "event_count": 102, + "ok": true, + "request_id": "bf7dff9b-6270-455a-acce-0d1e26b08e1d", + "response_id": "chatcmpl-90f23b17ad3e7e038558cc10325566d9", + "images_count": 5, + "graphs_count": 0, + "response": "The adult Drosophila visual system contains [950](https://v2.virtualflybrain.org/org.geppetto.frontend/geppetto?q=FBbt_00047736,SubclassesOf \"Run in VFB: Subclasses of visual system neuron\") distinct neuron types that are classified as subclasses of [visual system neuron](https://www.virtualflybrain.org/reports/FBbt_00047736 \"Open visual system neuron in Virtual Fly Brain\"). These include, but are not limited to, [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\"), [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\"), [PS070](https://www.virtualflybrain.org/reports/FBbt_20001825 \"Open PS070 in Virtual Fly Brain\"), PS071, PS073, adult visual neuropil intrinsic neuron, lamina wide-field neuron, medulla intrinsic neuron vGlutMinew1a, TmY27, and Mi10b.", + "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": 1041, + "status_count": 9 + } + }, + { + "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": 16294, + "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" + }, + { + "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": 110, + "ok": true, + "request_id": "d0d2e0a2-4dc0-4ed7-a773-416116e6f13d", + "response_id": "chatcmpl-8b1e678228ef92d93ba818fd80b3184c", + "images_count": 8, + "graphs_count": 0, + "response": "VFB holds downstream and 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 for these queries.", + "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": 257, + "status_count": 15 + } + }, + { + "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": 14166, + "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": 91, + "ok": true, + "request_id": "30d0e7e8-179d-4b04-a482-405e400c04cd", + "response_id": "chatcmpl-0a94df9caa19276aac0c7fef686c41c2", + "images_count": 8, + "graphs_count": 0, + "response": "The connectome data indicates that [alpha/beta Kenyon cell](https://www.virtualflybrain.org/reports/FBbt_00100248 \"Open alpha/beta Kenyon cell in Virtual Fly Brain\") and [gamma Kenyon cell](https://www.virtualflybrain.org/reports/FBbt_00100247 \"Open gamma Kenyon cell in Virtual Fly Brain\") have some downstream targets in common, but the specific [mushroom body output neuron](https://www.virtualflybrain.org/reports/FBbt_00047953 \"Open mushroom body output neuron in Virtual Fly Brain\") VFB does not currently hold downstream connectivity classes for gamma Kenyon cell. 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.", + "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": 924, + "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": 11337, + "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": 91, + "ok": true, + "request_id": "508ecf0e-953c-45cf-91cb-bc60d0930964", + "response_id": "chatcmpl-23f03f56d8e030a52e9557cce869bafc", + "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 [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": 451, + "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": 21426, + "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": 151, + "ok": true, + "request_id": "4a1f0ab8-d6b3-4544-ba2e-fe1bafef465a", + "response_id": "chatcmpl-17798be498d9fcd723f33c77f02d5d93", + "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. VFB records show [363](https://v2.virtualflybrain.org/org.geppetto.frontend/geppetto?q=FBbt_00003632,NeuronsPartHere \"Run in VFB: Neurons with some part in adult central complex\") neurons with some part in the adult central complex, including [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. However, VFB does not currently hold data on neurons with some part in the embryonic/larval lateral accessory lobe, or 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": 1157, + "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": 10966, + "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": "Checking the answer is covered", + "phase": "llm" + }, + { + "message": "Writing the answer", + "phase": "llm" + } + ], + "event_count": 54, + "ok": true, + "request_id": "11ee07aa-8ea0-4c0f-9c6e-695192d06692", + "response_id": "chatcmpl-fc100344b836941f08fee5614f6a99e6", + "images_count": 0, + "graphs_count": 0, + "response": "The carbon dioxide sensitive neuron is involved in CO2 avoidance and is connected to downstream classes such as GABAergic local interneuron of the adult antennal lobe and adult antennal lobe local neuron lLN2P.", + "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": 7 + } + }, + { + "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": 31352, + "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": 301, + "ok": true, + "request_id": "1a116368-b4d1-4a55-8cc4-42e3140300e0", + "response_id": "chatcmpl-2ceba0e384bff5ae0340273c7cb360bc", + "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. It has a large cell body located posterior to the lower protocerebrum and a large descending axon that enters the cervical connective via the posterior cerebro-cervical fascicle and descends on the ipsilateral side in the dorsal cervical fasciculus. The giant fiber neuron has dendritic arborization in the ipsilateral zones A and B of the antennal mechanosensory and motor center, where it receives substantial input from zone A and B Johnston organ neurons. It also arborizes in the posterior ventrolateral protocerebrum and gorget. In the ventral nerve cord, it forms electrical synapses with downstream motor and premotor neurons at the inframedial bridge and at the axonal lateral bend.\n\nThe giant fiber neuron has downstream connectivity classes ([389](https://v2.virtualflybrain.org/org.geppetto.frontend/geppetto?q=FBbt_00004020,DownstreamClassConnectivity \"Run in VFB: Downstream connectivity classes for DNp01\")) and upstream connectivity classes ([472](https://v2.virtualflybrain.org/org.geppetto.frontend/geppetto?q=FBbt_00004020,UpstreamClassConnectivity \"Run in VFB: Upstream connectivity classes for DNp01\")). Available driver lines include [5](https://v2.virtualflybrain.org/org.geppetto.frontend/geppetto?q=FBbt_00004020,SplitsTargeting \"Run in VFB: Splits targeting DNp01\") split-GAL4 combinations. There are also [10](https://v2.virtualflybrain.org/org.geppetto.frontend/geppetto?q=FBbt_00004020,TransgeneExpressionHere \"Run in VFB: Transgene expression in DNp01\") transgene expression reports available for the giant fiber neuron, including expression patterns for P{GMR78G07-GAL4}, P{GMR79D08-GAL4}, and P{GMR91H05-GAL4}, as well as several split-GAL4 combinations.\n\nRelevant publications include Thomas and Wyman (1984), Koto et al. (1981), Power (1948), and many others.", + "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": 1991, + "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": 14480, + "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": 113, + "ok": true, + "request_id": "e47aa4bc-4456-4f54-a398-25d4433493cf", + "response_id": "chatcmpl-a29a4d9233d4dfb3b5ed0224a3ec35ef", + "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. The connectome data indicates that [visual system neuron](https://www.virtualflybrain.org/reports/FBbt_00047736 \"Open visual system neuron in Virtual Fly Brain\") connects to several neuron types, including [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\"), and [adult optic lobe neuron](https://www.virtualflybrain.org/reports/FBbt_00003702 \"Open adult optic lobe neuron in Virtual Fly Brain\"). Visual information could potentially reach the mushroom body via 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\") records of neurons with some part 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": 1264, + "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": 75434, + "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": "57c53753-ac6a-4c65-9def-96f353bc4455", + "response_id": "chatcmpl-a6d55af2a65a6768d45f5abcc07d9df7", + "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": 82814, + "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 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": 263, + "ok": true, + "request_id": "b45d6487-f999-4721-bcdd-40b53c20a653", + "response_id": "chatcmpl-2f5d1a5b67c2c73689a1e91224c9f41b", + "images_count": 8, + "graphs_count": 1, + "response": "The connectivity between thermosensory neurons and the [mushroom body](https://www.virtualflybrain.org/reports/FBbt_00005801 \"Open mushroom body in Virtual Fly Brain\") is supported by evidence from VFB. Thermosensory neurons are connected to the mushroom body, with antennal lobe projection neurons acting as a connection point. VFB's class-level connectivity table for [thermosensory neuron](https://www.virtualflybrain.org/reports/FBbt_00005918 \"Open thermosensory neuron in Virtual Fly Brain\") lists downstream classes, including [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\"), with mean synaptic weights per connected pair ranging from 18.7 to 18.9 synapses.\n\nVFB also lists upstream classes for thermosensory neuron, including [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\"), with mean synaptic weights per connected pair ranging from 8.34 to 10.1 synapses.\n\nAdditionally, VFB holds records of neurons with presynaptic and postsynaptic terminals in the mushroom body, with [366](https://v2.virtualflybrain.org/org.geppetto.frontend/geppetto?q=FBbt_00005801,NeuronsPresynapticHere \"Run in VFB: 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\") results, respectively.\n\nTemperature information could potentially influence memory formation, as thermosensory neurons influence mushroom body memory formation through thermosensory projection neurons, with downstream evidence to mushroom body dopaminergic neurons and Kenyon cell classes.", + "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": 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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": 2478, + "status_count": 13 + } + }, + { + "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": 206606, + "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 connectivity", + "phase": "mcp" + }, + { + "message": "Querying VFB", + "phase": "mcp" + }, + { + "message": "Checking the answer is covered", + "phase": "llm" + }, + { + "message": "Writing the answer", + "phase": "llm" + } + ], + "event_count": 144, + "ok": true, + "request_id": "f88491ff-8fc9-438b-b881-9d9f8f20f3cd", + "response_id": "chatcmpl-c6fba330c4ae0656c076a568821ce991", + "images_count": 0, + "graphs_count": 0, + "response": "The subesophageal zone (SEZ) is characterised in VFB with annotated neuron types, including the [larval subesophageal zone descending SEZ DN neuron](https://www.virtualflybrain.org/reports/FBbt_00111241 \"Open larval subesophageal zone descending SEZ DN neuron in Virtual Fly Brain\"). There are genetic tools for SEZ neurons, including GAL4 drivers and binary/intersectional drivers, with VFB returning 4205 genetic tool/expression pattern rows for subesophageal zone. VFB holds data on transgene expression in larval subesophageal zone descending SEZ DN neuron, downstream connectivity classes for larval subesophageal zone descending SEZ DN neuron, and upstream connectivity classes for larval subesophageal zone descending SEZ DN 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": 739, + "status_count": 10 + } + }, + { + "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": 19795, + "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 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": 193, + "ok": true, + "request_id": "25b3ebd8-8be2-4ea7-8971-aa16c262407d", + "response_id": "chatcmpl-09c3de1528eb5d390ee504d18424d083", + "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 [471](https://v2.virtualflybrain.org/org.geppetto.frontend/geppetto?q=FBbt_00003748,NeuronsPartHere \"Run in VFB: Neurons with some part in medulla\") neuron types with some part in it, [464](https://v2.virtualflybrain.org/org.geppetto.frontend/geppetto?q=FBbt_00003748,NeuronsSynaptic \"Run in VFB: Neurons with synaptic terminals in medulla\") neuron types with synaptic terminals in it, [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 it, 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 in it. Some of the neurons with presynaptic terminals in the medulla 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\"), [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. Some of the neurons with postsynaptic terminals in the medulla include CB3849, TmY-ds, [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, Mi6, Mi8, Tm10, Tm13, Tm14, Tm18, and Tm19.", + "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": 2008, + "status_count": 11 + } + }, + { + "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": 7349, + "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": "ccc54125-4e28-4a12-a381-07e43b21f416", + "response_id": "chatcmpl-2631ef95dedba9e0f70fb8f2b9393e18", + "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": 41972, + "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": 23, + "ok": true, + "request_id": "4da7b3ef-2b21-458a-9bfd-c4554d5792fe", + "response_id": "chatcmpl-e0e2008819988b463ce258c13079510d", + "images_count": 0, + "graphs_count": 0, + "response": "To cite Virtual Fly Brain in a publication, use the following citation formats:\n\n```\nAPA\nCourt, R., Costa, M., Pilgrim, C., Millburn, G., Holmes, A., McLachlan, A., Larkin, A., Matentzoglu, N., Kir, H., Parkinson, H., Brown, N. H., O’Kane, C. J., Armstrong, J. D., Jefferis, G. S. X. E., & Osumi-Sutherland, D. (2023). Virtual Fly Brain—An interactive atlas of the Drosophila nervous system. Frontiers in Physiology, 14. https://doi.org/10.3389/fphys.2023.1076533\n\nMLA\nCourt, Robert, et al. “Virtual Fly Brain—An Interactive Atlas of the Drosophila Nervous System.” Frontiers in Physiology, vol. 14, 2023, https://doi.org/10.3389/fphys.2023.1076533.\n\nChicago\nCourt, Robert, Costa, Marta, Pilgrim, Clare, Millburn, Gillian, Holmes, Alex, McLachlan, Alex, Larkin, Aoife et al. “Virtual Fly Brain—An interactive atlas of the Drosophila nervous system.” Frontiers in Physiology 14, (2023). https://doi.org/10.3389/fphys.2023.1076533.\n\nBibTeX\n@article{Court_2023,\nauthor = {Robert Court and Marta Costa and Clare Pilgrim and Gillian Millburn and Alex Holmes and Alex McLachlan and Aoife Larkin and Nicolas Matentzoglu and Huseyin Kir and Helen Parkinson and Nicolas H. Brown and Cahir J. O'Kane and J. Douglas Armstrong and Gregory S. X. E. Jefferis and David Osumi-Sutherland},\ntitle = \"{Virtual Fly Brain—An interactive atlas of the Drosophila nervous system}\",\njournal = {Frontiers in Physiology},\nvolume = {14},\npublisher = {Frontiers Media {SA}},\nyear = {2023},\nmonth = {jan},\nabstract = \"{As a model organism, Drosophila is uniquely placed to contribute to our understanding of how brains control complex behavior. Not only does it have complex adaptive behaviors, but also a uniquely powerful genetic toolkit, increasingly complete dense connectomic maps of the central nervous system and a rapidly growing set of transcriptomic profiles of cell types. But this also poses a challenge: Given the massive amounts of VFB evidence, how are researchers to Find, Access, Integrate and Reuse (FAIR) relevant data in order to develop an integrated anatomical and molecular picture of circuits, inform hypothesis generation, and find reagents for experiments to test these hypotheses? The Virtual Fly Brain (virtualflybrain.org) web application & API provide a solution to this problem, using FAIR principles to integrate 3D images of neurons and brain regions, connectomics, transcriptomics and reagent expression data covering the whole CNS in both larva and adult. Users can search for neurons, neuroanatomy and reagents by name, location, or connectivity, via text search, clicking on 3D images, search-by-image, and queries by type (e.g., dopaminergic neuron) or properties (e.g., synaptic input in the antennal lobe). Returned results include cross-registered 3D images that can be explored in linked 2D and 3D browsers or downloaded under open licenses, and extensive descriptions of cell types and regions curated from the literature. These solutions are potentially extensible to cover similar atlasing and data integration challenges in vertebrates.}\",\nissn = {1664-042X},\ndoi = {10.3389/fphys.2023.1076533},\nurl = {https://doi.org/10.3389/fphys.2023.1076533},\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": 3170, + "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": 5681, + "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": 28, + "ok": true, + "request_id": "0c2faff4-5c23-4847-84f4-75e2c2ac79c0", + "response_id": "chatcmpl-3caf83930ab40bb2c87e22bb560e3c19", + "images_count": 0, + "graphs_count": 0, + "response": "Virtual Fly Brain has been supported by grants from 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": 120, + "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": 4712, + "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": "898b9d72-0830-4e66-a26c-902d92349b12", + "response_id": "chatcmpl-5315ebf299744b475287be3eea1b8ab2", + "images_count": 0, + "graphs_count": 0, + "response": "Virtual Fly Brain is partially compliant with the Web Content Accessibility Guidelines (WCAG) 2.2 AA standard, with known accessibility limitations and non-compliances listed.", + "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": 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": 9087, + "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": 126, + "ok": true, + "request_id": "45a031e8-ecc8-4468-8f29-268ee644c368", + "response_id": "chatcmpl-b881483a1a5bba66774effe089afeb27", + "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 for technical support, bug reports, data contributions, or questions about using VFB software and data. You can contact Virtual Fly Brain through their public support forum, GitHub issues, or private email. For help with using Virtual Fly Brain, comments, suggestions, or general questions, use the public support forum at support@virtualflybrain.org. Bug reports and feature requests can be submitted through GitHub Issues. For data contributions or private inquiries, use the private email at 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": 616, + "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": 10220, + "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": "36f8e60d-93f5-497a-b30d-f1f6f410393a", + "response_id": "chatcmpl-68ab9bb3019849e3f550660193a9c856", + "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": 13928, + "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 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": 84, + "ok": true, + "request_id": "94e5a64d-d18a-404d-a778-25898bc43468", + "response_id": "chatcmpl-fe1a8dc87f41106eb9edb34df1b74294", + "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. The strongest paths are the shortest or highest weighted paths, and they are arranged from strongest at the bottom to weakest at the top. To use it, you would typically select a source neuron and a target neuron, and the Circuit Browser would then display the strongest paths between them.", + "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": 387, + "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": 9830, + "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": "35b36c61-241e-4abc-8610-61aeb864b82d", + "response_id": "chatcmpl-e45999662d934ee4cff7f473c9490120", + "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": 10438, + "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": "56882c48-0f8e-42cc-a981-d7d4fec81bb2", + "response_id": "chatcmpl-d0a050085d337747c785eda1ea73c0d7", + "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": 10784, + "status_messages": [ + { + "message": "Thinking...", + "phase": "llm" + }, + { + "message": "Planning the answer", + "phase": "llm" + }, + { + "message": "Resolving 2 terms 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": 53, + "ok": true, + "request_id": "c064221d-b9a9-4f92-a432-fafc6df0a00d", + "response_id": "chatcmpl-30dbeff2cff63ce4ccf157f46dfe00e8", + "images_count": 8, + "graphs_count": 0, + "response": "Bridging registrations between brain templates in VFB could not be matched, and the name \"bridging registrations\" returned zero any near matches. The documentation mentions transformations to map between different canonical Drosophila templates.", + "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": 245, + "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": 10288, + "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 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": 23, + "ok": true, + "request_id": "e6740a16-7352-4a3d-881a-c0c6f499b1f6", + "response_id": "chatcmpl-7aee01cc3e301811c2e65d2af499ce3d", + "images_count": 0, + "graphs_count": 0, + "response": "Virtual Fly Brain holds imaging data types including 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": 80, + "status_count": 7 + } + }, + { + "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": 6791, + "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": 46, + "ok": true, + "request_id": "d6e8c9fa-3e3e-4ddd-b522-ee70f13c7975", + "response_id": "chatcmpl-f0af832a2cc1419397189acf39f60e42", + "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 confocal microscopy images, EM reconstructed neurons, and other datasets from different researchers and labs.", + "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": 241, + "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": 8555, + "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": 53, + "ok": true, + "request_id": "a25e6098-2417-4d4a-a3bb-829cf5d7e479", + "response_id": "chatcmpl-3dbe6a0e754c1d55bc116ade0bf770c3", + "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 it 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": 257, + "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": 12357, + "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": "2be935fa-b125-4f53-9518-6c22136f2ed3", + "response_id": "chatcmpl-66a298e972b2e4958d75961bc1905fc4", + "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 such as 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": 415, + "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": 13810, + "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": 116, + "ok": true, + "request_id": "e63c3a46-a4b1-4312-8fa2-6e699c1551bc", + "response_id": "chatcmpl-88f273b00ae67d6c51b9d48250111b2c", + "images_count": 0, + "graphs_count": 0, + "response": "To explore Virtual Fly Brain neurons, you can use the following steps:\n1. Connect to the VFB CATMAID server using pymaid.connect_catmaid()\n2. Retrieve neurons using pymaid.get_neurons() or pymaid.find_neurons()\n3. Plot the neurons using navis.plot3d()\n4. Access the connectors of a neuron using the.connectors attribute\n5. Use pymaid.get_volume() to retrieve neuropil volumes and plot them with the neurons.\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": 460, + "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": 14378, + "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": 140, + "ok": true, + "request_id": "9aff2e42-0cef-41c6-905b-9ca72fd04a16", + "response_id": "chatcmpl-9b8ed993299ad10de7f09eb45afd25ae", + "images_count": 0, + "graphs_count": 0, + "response": "To use the Virtual Fly Brain Model Context Protocol (MCP) tool, follow these steps: Open Claude Desktop, go to Settings, navigate to the MCP section, and add a new MCP server with the provided settings. Alternatively, use the Configuration JSON or Claude Code setup methods. For GitHub Copilot, open VS Code, search for \"MCP\" in the settings, and add the server URL. For other MCP-compatible clients, use the provided JSON configuration. Test the connection by asking your AI assistant questions like \"Get information about the neuron \" or \"Search for terms related to medulla in the fly brain\".\n\n```json\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": 733, + "status_count": 6 + } + }, + { + "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": 6433, + "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": 40, + "ok": true, + "request_id": "b4564cf1-f496-4a37-a324-7883eceb1ef7", + "response_id": "chatcmpl-960e892ed313d8f8cc38f0343ea853c1", + "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": 7 + } + }, + { + "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": 9549, + "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": "1f3d46ca-41e3-496e-81eb-5632f62cddda", + "response_id": "chatcmpl-ac6b589730a8f8ae4423f15fc83f53c3", + "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": 11283, + "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": 55, + "ok": true, + "request_id": "03d6d10c-0175-4c70-bb2b-d103bbd17c07", + "response_id": "chatcmpl-e738863c5b292ea25db012c5c4aa42c1", + "images_count": 0, + "graphs_count": 0, + "response": "Materials from the Virtual Fly Brain \"Hacking the connectome\" workshop are available. These include a recorded introduction session and workshop notebooks that demonstrate how to use available tools to explore and analyze published connectomes on Virtual Fly Brain.\n\n```\nhttps://www.virtualflybrain.org/docs/past-workshops/connectome\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": 337, + "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": 19539, + "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": 93, + "ok": true, + "request_id": "efc35e66-1103-4045-89b5-6ae70a089f07", + "response_id": "chatcmpl-87d9bd33146b34f9a1b950cc0177d08d", + "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, with closest records found including Fancl, FANCI, and Fancm. The name \"CATMAID\" 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": 340, + "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": 7303, + "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": 25, + "ok": true, + "request_id": "394f4b6e-c064-42c4-aaab-e759a4718243", + "response_id": "chatcmpl-b12e2ae6a82d94117aa76039c7a27200", + "images_count": 8, + "graphs_count": 0, + "response": "Yes, 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": 183, + "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": 11712, + "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": 5369, + "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": 6343, + "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": "0fed7818-58f1-4c8c-9a38-dea15cd9cc9c", + "response_id": "chatcmpl-7fd7f6802e40a8f870357f8f2cdae772", + "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": 6343 + } + }, + { + "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": 16766, + "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": 201, + "conversation": true, + "turns": [ + { + "turn": 1, + "question": "What is the mushroom body?", + "focus": null, + "clicked": null, + "duration_ms": 8139, + "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": 8627, + "ok": true, + "response": "There are images of neurons with parts in the [mushroom body](https://www.virtualflybrain.org/reports/FBbt_00005801 \"Open mushroom body in Virtual Fly Brain\"). VFB holds [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 of neurons with some part in the mushroom body. The first 12 images are of neurons 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, and GMR 93G04 FLP 12-1.", + "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": "017ce329-fcf1-41d3-a82b-19b32d2b1b91", + "response_id": "chatcmpl-eed69962625e9be7893ecba73ccda366", + "images_count": 8, + "graphs_count": 0, + "response": "There are images of neurons with parts in the [mushroom body](https://www.virtualflybrain.org/reports/FBbt_00005801 \"Open mushroom body in Virtual Fly Brain\"). VFB holds [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 of neurons with some part in the mushroom body. The first 12 images are of neurons 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, and GMR 93G04 FLP 12-1.", + "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": 661, + "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": 8627 + } + }, + { + "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": 86137, + "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": 6949, + "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": 10070, + "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, located just anterior to the [fan-shaped body](https://www.virtualflybrain.org/reports/FBbt_00003679 \"Open fan-shaped body in Virtual Fly Brain\"), with a hole (the ellipsoid body canal) pointing anteriorly.", + "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": 69118, + "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": "0a710e79-a2f6-4cb0-9676-61e871044dcd", + "response_id": "chatcmpl-02a0467b7846c49812abe318d1032bd1", + "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": 69118 + } + }, + { + "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": 14081, + "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": 146, + "conversation": true, + "turns": [ + { + "turn": 1, + "question": "What is a Kenyon cell?", + "focus": null, + "clicked": null, + "duration_ms": 6083, + "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": 7998, + "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 subtypes, with their VFB ids, 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": "b074e6c3-2b53-4ec2-98df-925d8a44761d", + "response_id": "chatcmpl-817e9b4e3b3537c807f40879e898d05f", + "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 subtypes, with their VFB ids, 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": 1155, + "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": 7998 + } + }, + { + "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": 20569, + "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": 8430, + "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 medulla, the seventh layer exhibits a distinct architecture, and layers 8-10 make up the inner medulla. Some of the 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": 12139, + "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\"), [Mi10b](https://www.virtualflybrain.org/reports/FBbt_00110070 \"Open Mi10b in Virtual Fly Brain\"), medulla tangential neuron vGlutMtnew1, medulla tangential neuron vGlutMtnew2, Tm1a, [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 MeSps. 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 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": "3684752f-3357-490b-8990-c6cef2688f15", + "response_id": "chatcmpl-e14907594a130d4b38485ef8d31d80e2", + "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\"), [Mi10b](https://www.virtualflybrain.org/reports/FBbt_00110070 \"Open Mi10b in Virtual Fly Brain\"), medulla tangential neuron vGlutMtnew1, medulla tangential neuron vGlutMtnew2, Tm1a, [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 MeSps. 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 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": 1292, + "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": 12139 + } + }, + { + "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": 19196, + "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": 158, + "conversation": true, + "turns": [ + { + "turn": 1, + "question": "Tell me about the antennal lobe.", + "focus": null, + "clicked": null, + "duration_ms": 13435, + "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. It is a region in the Drosophila nervous system. VFB holds various data related to the antennal lobe, 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. Users can search for synaptic input in the antennal lobe via the Virtual Fly Brain web application.", + "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": 5761, + "ok": true, + "response": "The [antennal lobe](https://www.virtualflybrain.org/reports/FBbt_00003924 \"Open antennal lobe in Virtual Fly Brain\") is innervated by various 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\"), [PLP077](https://www.virtualflybrain.org/reports/FBbt_20001577 \"Open PLP077 in Virtual Fly Brain\"), [adult olfactory receptor neuron Ir75d ac1](https://www.virtualflybrain.org/reports/FBbt_00110011 \"Open adult olfactory receptor neuron Ir75d ac1 in Virtual Fly Brain\"), [adult olfactory receptor neuron Ir75d ac2](https://www.virtualflybrain.org/reports/FBbt_00110014 \"Open adult olfactory receptor neuron Ir75d ac2 in Virtual Fly Brain\"), adult olfactory receptor neuron Ir75d ac4, pharyngeal VL1 neuron, ORN_VM6, adult olfactory receptor neuron Or35a ac3I, adult olfactory receptor neuron Or35a ac3II, adult olfactory receptor neuron Or85b ab3, and adult olfactory receptor neuron Or85b ab11. VFB records show [266](https://v2.virtualflybrain.org/org.geppetto.frontend/geppetto?q=FBbt_00003924,NeuronsPresynapticHere \"Run in VFB: Neurons with presynaptic terminals in antennal lobe\") neurons with presynaptic 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": "NeuronsSynaptic", + "query": "Which neurons have synaptic terminals 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?" + } + ], + "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" + } + ], + "unmapped": [] + }, + "status_count": 6, + "problems": [] + } + ], + "ok": true, + "request_id": "3554877d-41a5-4d6e-a91c-a9f9ef3e9456", + "response_id": "chatcmpl-fb1458e67de769ec8b0c4ff66dff7dd3", + "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 various 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\"), [PLP077](https://www.virtualflybrain.org/reports/FBbt_20001577 \"Open PLP077 in Virtual Fly Brain\"), [adult olfactory receptor neuron Ir75d ac1](https://www.virtualflybrain.org/reports/FBbt_00110011 \"Open adult olfactory receptor neuron Ir75d ac1 in Virtual Fly Brain\"), [adult olfactory receptor neuron Ir75d ac2](https://www.virtualflybrain.org/reports/FBbt_00110014 \"Open adult olfactory receptor neuron Ir75d ac2 in Virtual Fly Brain\"), adult olfactory receptor neuron Ir75d ac4, pharyngeal VL1 neuron, ORN_VM6, adult olfactory receptor neuron Or35a ac3I, adult olfactory receptor neuron Or35a ac3II, adult olfactory receptor neuron Or85b ab3, and adult olfactory receptor neuron Or85b ab11. VFB records show [266](https://v2.virtualflybrain.org/org.geppetto.frontend/geppetto?q=FBbt_00003924,NeuronsPresynapticHere \"Run in VFB: Neurons with presynaptic terminals in antennal lobe\") neurons with presynaptic 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": 1435, + "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": 5761 + } + }, + { + "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": 22928, + "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": 302, + "conversation": true, + "turns": [ + { + "turn": 1, + "question": "What is the medulla?", + "focus": null, + "clicked": null, + "duration_ms": 5631, + "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 neuron images have a part in the medulla?", + "focus": { + "id": "FBbt_00003748", + "query_type": "ImagesNeurons" + }, + "clicked": 0, + "duration_ms": 7448, + "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 neuron 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).", + "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": 9848, + "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 [2342](https://v2.virtualflybrain.org/org.geppetto.frontend/geppetto?q=FBbt_00003748,TransgeneExpressionHere \"Run in VFB: Transgene expression in medulla\") transgene expression reports for medulla.", + "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": "9e0b725a-5570-4aee-b100-b64050f9990b", + "response_id": "chatcmpl-cdd7af281384c4c59d4cb36387aa4dfc", + "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 [2342](https://v2.virtualflybrain.org/org.geppetto.frontend/geppetto?q=FBbt_00003748,TransgeneExpressionHere \"Run in VFB: Transgene expression in medulla\") transgene expression reports for 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": 1732, + "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": 9848 + } + }, + { + "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": 11929, + "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": 34, + "conversation": true, + "turns": [ + { + "turn": 1, + "question": "What is the mushroom body?", + "focus": null, + "clicked": null, + "duration_ms": 7847, + "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": 4082, + "ok": true, + "response": "The TransgeneExpressionHere query returns 3,996 results. VFB holds [4130](https://v2.virtualflybrain.org/org.geppetto.frontend/geppetto?q=FBbt_00005801,TransgeneExpressionHere \"Run in VFB: Transgene expression in mushroom body\") transgene expression reports for [mushroom body](https://www.virtualflybrain.org/reports/FBbt_00005801 \"Open mushroom body in Virtual Fly Brain\").", + "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": "f2ba7c98-e03a-45e8-ab3e-5284e6377def", + "response_id": "chatcmpl-50f551519ea1f823b86b96c7d948b60c", + "images_count": 8, + "graphs_count": 0, + "response": "The TransgeneExpressionHere query returns 3,996 results. VFB holds [4130](https://v2.virtualflybrain.org/org.geppetto.frontend/geppetto?q=FBbt_00005801,TransgeneExpressionHere \"Run in VFB: Transgene expression in mushroom body\") transgene expression reports for [mushroom body](https://www.virtualflybrain.org/reports/FBbt_00005801 \"Open mushroom body 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": 375, + "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": 4082 + } + }, + { + "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": 19124, + "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": 63, + "conversation": true, + "turns": [ + { + "turn": 1, + "question": "Which neurons provide input to the medulla?", + "focus": null, + "clicked": null, + "duration_ms": 5641, + "ok": true, + "response": "Neurons that provide input to 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\"), [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. 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\") neurons with presynaptic terminals in 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": "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": 13483, + "ok": true, + "response": "Neurons that provide input to the [lobula](https://www.virtualflybrain.org/reports/FBbt_00003852 \"Open lobula in Virtual Fly Brain\") include those with presynaptic terminals in lobula. VFB holds various records related to lobula, including neurons with some part in lobula, neurons with synaptic terminals in lobula, and transgene expression in lobula.", + "followons": [ + { + "id": "FBbt_00003852", + "query_type": "ListAllAvailableImages", + "query": "Which images of lobula does VFB have?" + }, + { + "id": "FBbt_00003852", + "query_type": "NeuronsPartHere", + "query": "Which neurons have part of their arbour in the lobula?" + }, + { + "id": "FBbt_00003852", + "query_type": "NeuronsSynaptic", + "query": "Which neurons have synaptic terminals in the lobula?" + }, + { + "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?" + } + ], + "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_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": 7, + "problems": [] + } + ], + "ok": true, + "request_id": "a61bf34b-cf57-40a5-9351-0988bcfcaf3d", + "response_id": "chatcmpl-4ffd68c5071ceb8290bb643ab251f89e", + "images_count": 4, + "graphs_count": 0, + "response": "Neurons that provide input to the [lobula](https://www.virtualflybrain.org/reports/FBbt_00003852 \"Open lobula in Virtual Fly Brain\") include those with presynaptic terminals in lobula. VFB holds various records related to lobula, including neurons with some part in lobula, neurons with synaptic terminals in lobula, and transgene expression in lobula.", + "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": 352, + "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": 13483 + } + }, + { + "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": 45470, + "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": 197, + "conversation": true, + "turns": [ + { + "turn": 1, + "question": "What is the protocerebral bridge?", + "focus": null, + "clicked": null, + "duration_ms": 6912, + "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": 17718, + "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 others with similar names, indicating a connection between the two. The connectome data indicates that there are [103](https://v2.virtualflybrain.org/org.geppetto.frontend/geppetto?q=FBbt_00003678,NeuronsPartHere \"Run in VFB: Neurons with some part in ellipsoid body\") neurons with some part in the ellipsoid body and [102](https://v2.virtualflybrain.org/org.geppetto.frontend/geppetto?q=FBbt_00003678,NeuronsSynaptic \"Run in VFB: Neurons with synaptic terminals in ellipsoid body\") neurons with synaptic terminals in the ellipsoid body, with some of these neurons having names that suggest a connection to the protocerebral bridge.", + "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": 20840, + "ok": true, + "response": "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 [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\"), adult protocerebral bridge glomerulus 4-ellipsoid body canal-ventral gall neuron, adult protocerebral bridge glomerulus 5-ellipsoid body canal-dorsal gall neuron, adult protocerebral bridge glomerulus 6-ellipsoid body canal-ventral gall neuron, adult protocerebral bridge glomerulus 7-ellipsoid body canal-dorsal gall neuron, and adult protocerebral bridge glomerulus 8-ellipsoid body canal-ventral gall neuron. [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\"), and [PEN_PB8](https://www.virtualflybrain.org/reports/FBbt_00111374 \"Open PEN_PB8 in Virtual Fly Brain\") neurons also have synaptic terminals in both the protocerebral bridge and 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": "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": "a085bc76-c285-4645-98ac-9be7f5fed228", + "response_id": "chatcmpl-732d8ced3c218ee2726024480aeb8f7b", + "images_count": 8, + "graphs_count": 0, + "response": "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 [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\"), adult protocerebral bridge glomerulus 4-ellipsoid body canal-ventral gall neuron, adult protocerebral bridge glomerulus 5-ellipsoid body canal-dorsal gall neuron, adult protocerebral bridge glomerulus 6-ellipsoid body canal-ventral gall neuron, adult protocerebral bridge glomerulus 7-ellipsoid body canal-dorsal gall neuron, and adult protocerebral bridge glomerulus 8-ellipsoid body canal-ventral gall neuron. [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\"), and [PEN_PB8](https://www.virtualflybrain.org/reports/FBbt_00111374 \"Open PEN_PB8 in Virtual Fly Brain\") neurons also have synaptic terminals in both the protocerebral bridge and the ellipsoid body.", + "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": 1445, + "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": 20840 + } + }, + { + "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": 27814, + "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": 42, + "conversation": true, + "turns": [ + { + "turn": 1, + "question": "Which neurons have part of them in the medulla?", + "focus": null, + "clicked": null, + "duration_ms": 14385, + "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\"), [Mi10b](https://www.virtualflybrain.org/reports/FBbt_00110070 \"Open Mi10b in Virtual Fly Brain\"), medulla tangential neuron vGlutMtnew1, medulla tangential neuron vGlutMtnew2, Tm1a, [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 MeSps. 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 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": "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": "NeuronsPartHere", + "fn": "get_neurons_with_part_in" + } + ], + "unmapped": [] + }, + "status_count": 8, + "problems": [] + }, + { + "turn": 2, + "question": "How would I get that same result in Python with vfbquery?", + "focus": null, + "clicked": null, + "duration_ms": 13429, + "ok": true, + "response": "The code below returns the neurons with some part in the [medulla](https://www.virtualflybrain.org/reports/FBbt_00003748 \"Open medulla in Virtual Fly Brain\"), as a table. VFB holds [471](https://v2.virtualflybrain.org/org.geppetto.frontend/geppetto?q=FBbt_00003748,NeuronsPartHere \"Run in VFB: Neurons with some part in medulla\") neuron types with some part in medulla.\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```", + "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" + } + ], + "unmapped": [] + }, + "status_count": 7, + "problems": [] + } + ], + "ok": true, + "request_id": "c78af163-0a26-49b7-ae9e-48f0de0f53d7", + "response_id": "chatcmpl-98872b9949811c4020cd793347c80397", + "images_count": 8, + "graphs_count": 0, + "response": "The code below returns the neurons with some part in the [medulla](https://www.virtualflybrain.org/reports/FBbt_00003748 \"Open medulla in Virtual Fly Brain\"), as a table. VFB holds [471](https://v2.virtualflybrain.org/org.geppetto.frontend/geppetto?q=FBbt_00003748,NeuronsPartHere \"Run in VFB: Neurons with some part in medulla\") neuron types with some part in medulla.\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```", + "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": 808, + "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": 13429 + } + }, + { + "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": 31727, + "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": 214, + "conversation": true, + "turns": [ + { + "turn": 1, + "question": "What are the subclasses of Kenyon cell?", + "focus": null, + "clicked": null, + "duration_ms": 11924, + "ok": true, + "response": "The subclasses of [Kenyon cell](https://www.virtualflybrain.org/reports/FBbt_00003686 \"Open Kenyon cell in Virtual Fly Brain\") are 37 in number, 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 VFB ids, 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. 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.", + "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": 19803, + "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: [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); KCg-s (FBbt_00049830); KCg-s4 (FBbt_00049832); KCg-t (FBbt_00049833); larval alpha'/beta' Kenyon cell (FBbt_00049835); KCab-sc (FBbt_00049838); alpha'/beta' anterior-posterior type 1 Kenyon cell of lACA (FBbt_00049859); [Kenyon cell of main calyx](https://www.virtualflybrain.org/reports/FBbt_00047926 \"Open Kenyon cell of main calyx in Virtual Fly Brain\") (FBbt_00047926); single-claw Kenyon cell (FBbt_00047993); multi-claw Kenyon cell (FBbt_00047994).\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": 8, + "problems": [] + } + ], + "ok": true, + "request_id": "4ec32e17-7bcc-4550-8e73-bca69e981d74", + "response_id": "chatcmpl-4e73a761f62e5da8e7010b1775134517", + "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: [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); KCg-s (FBbt_00049830); KCg-s4 (FBbt_00049832); KCg-t (FBbt_00049833); larval alpha'/beta' Kenyon cell (FBbt_00049835); KCab-sc (FBbt_00049838); alpha'/beta' anterior-posterior type 1 Kenyon cell of lACA (FBbt_00049859); [Kenyon cell of main calyx](https://www.virtualflybrain.org/reports/FBbt_00047926 \"Open Kenyon cell of main calyx in Virtual Fly Brain\") (FBbt_00047926); single-claw Kenyon cell (FBbt_00047993); multi-claw Kenyon cell (FBbt_00047994).\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": 1655, + "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": 19803 + } + } + ] +}