diff --git a/app/api/chat/route.js b/app/api/chat/route.js index df9f31b..412a940 100644 --- a/app/api/chat/route.js +++ b/app/api/chat/route.js @@ -33,7 +33,7 @@ import { stripSupersededFigures } from '../../../lib/countProvenance.mjs' import { isAggregateClassPartner } from '../../../lib/classPartners.mjs' import { planNextAttempt } from '../../../lib/callBudget.mjs' import { detectJailbreakRule } from '../../../lib/jailbreak.mjs' -import { safeToolArgs } from '../../../lib/safeToolArgs.mjs' +import { safeToolArgs, safeText } from '../../../lib/safeToolArgs.mjs' import { createRunSignal, throwIfAborted, isRunAbortedWith, NOBODY_WAITING } from '../../../lib/runSignal.mjs' import { parseScrnaseqClusters, parseClusterExpression, extractRequestedGenes, buildExpressionMatrix, renderExpressionMarkdown } from '../../../lib/scrnaseq.mjs' import { pickSeedIndividuals, parseSimilarityHits, groupSimilarByClass } from '../../../lib/similarNeurons.mjs' @@ -1203,7 +1203,7 @@ async function callMcpToolWithRetry(client, name, args, { retries = VFB_MCP_MAX_ // `spent` and `next` are the two facts that were missing when this was // diagnosed from logs alone: a stall looks exactly like a server refusing // three times unless the line says which budget ran out. - console.error(`[VFBchat] MCP CALL FAILED | tool=${name} | attempt=${attempt + 1}/${retries + 1} | transient=${transient} | spent=${elapsedMs}ms/${budgetMs}ms | next=${next.reason} | args=${safeToolArgs(args)} | error=${error?.message || error}`) + console.error(`[VFBchat] MCP CALL FAILED | tool=${name} | attempt=${attempt + 1}/${retries + 1} | transient=${transient} | spent=${elapsedMs}ms/${budgetMs}ms | next=${next.reason} | args=${safeToolArgs(args)} | error=${safeText(error?.message || error)}`) if (!next.retry) throw error attemptTimeoutMs = next.timeoutMs if (next.waitMs > 0) await new Promise(resolve => setTimeout(resolve, next.waitMs)) @@ -1277,7 +1277,7 @@ async function callMcpToolTextWithForceRefresh(client, name, args, { budget } = if (!isFailedRunQueryPayload(retryText)) return retryText return annotateFailedRunQuery(retryText) } catch (error) { - console.error(`[VFBchat] force_refresh retry for ${name} failed: ${error?.message || error}`) + console.error(`[VFBchat] force_refresh retry for ${name} failed: ${safeText(error?.message || error)}`) return annotateFailedRunQuery(text) } } diff --git a/app/page.js b/app/page.js index 8a3d0e3..92b2ff8 100644 --- a/app/page.js +++ b/app/page.js @@ -1031,7 +1031,7 @@ export default function Home() { - Raw security logs are retained for up to 30 days - We do not store full chat content for routine analytics - If you report a problem, you can optionally attach the visible chat for investigation for up to 30 days -- Do not share confidential or sensitive information +- Do not share personal, confidential or sensitive information - Use this tool to enhance your understanding of neuroscience concepts - See the [Privacy Notice](/privacy) for more information diff --git a/app/privacy/page.js b/app/privacy/page.js index e2aa589..3a10d1e 100644 --- a/app/privacy/page.js +++ b/app/privacy/page.js @@ -19,6 +19,36 @@ export default function PrivacyPage() { VFB Chat is a public-facing AI-assisted interface to Virtual Fly Brain data.
++ The University of Edinburgh is the data controller for the personal data + described in this notice. The University is registered with the Information + Commissioner’s Office under registration number Z6426984. VFB Chat is operated by the + Virtual Fly Brain project in the School of Informatics. +
++ We process this data in the performance of a task carried out in the public + interest (UK GDPR Article 6(1)(e)). The University’s constitution is + statutory — the Universities (Scotland) Acts 1858 to 1966 — and the Further and + Higher Education (Scotland) Act 2005 provides for the undertaking of research among + fundable bodies, of which the University is one. Operating Virtual Fly Brain as an open + research resource, and making its data reachable, falls within those functions. We process + only the minimum technical data needed to run the service securely and to show how much it + is used; the IP address held for abuse prevention is processed on the same basis, because + it exists solely to keep that service available. +
++ Where you choose to attach a conversation to a problem report, we rely on your{' '} + consent for that transcript. You do not have to attach one, and you can + ask us to delete it at any time. +
++ To find published papers, the service may also search PubMed (US National Library of + Medicine) and bioRxiv. What is sent to them is a search term built from the Virtual Fly + Brain terms your question resolved to — not your question, and nothing that + identifies you. +
Please still avoid typing personal information into your question. We ask this because it is good practice,
not because we can see it.
@@ -101,9 +137,36 @@ export default function PrivacyPage() {
- Every answer carries a response ID, shown beneath it. We hold no account and no name for you,
- so that ID is the only way we can find the records relating to a particular exchange. Quote it
- when you ask what we hold about one, or ask for it to be deleted.
+ Under data protection law you have the right to:
+
+ How to exercise them. Every answer carries a response ID, shown beneath it.
+ We hold no account and no name for you, so that ID is the only way we can find the records
+ relating to a particular exchange — quote it when you ask what we hold, or ask for it
+ to be deleted. Because we hold nothing that identifies you, there will be cases where we
+ cannot locate any data for a request; where that happens we will say so.
+
+ If you are unhappy with how we have handled your data, please contact the
+ University’s Data Protection Officer using the details below. You also have the right
+ to complain to the UK supervisory authority, the{' '}
+
+ Information Commissioner’s Office
+ , at any time.
For the main Virtual Fly Brain website privacy notice and broader policy information, see{' '}
diff --git a/docker-compose.yml b/docker-compose.yml
index 2d43b90..75c0f51 100644
--- a/docker-compose.yml
+++ b/docker-compose.yml
@@ -20,6 +20,7 @@ services:
- SEARCH_ALLOWLIST=${SEARCH_ALLOWLIST:-virtualflybrain.org,*.virtualflybrain.org,flybase.org,neurofly.org,*.neurofly.org,vfb-connect.readthedocs.io}
- OUTBOUND_ALLOWLIST=${OUTBOUND_ALLOWLIST:-virtualflybrain.org,*.virtualflybrain.org,flybase.org,neurofly.org,*.neurofly.org,vfb-connect.readthedocs.io,doi.org,pubmed.ncbi.nlm.nih.gov,biorxiv.org,medrxiv.org}
- REVIEWED_DOCS_INDEX_FILE=${REVIEWED_DOCS_INDEX_FILE:-/app/config/reviewed-docs-index.json}
+ - NCBI_EMAIL=${NCBI_EMAIL:-vfb@virtualflybrain.org}
- GA_MEASUREMENT_ID=${GA_MEASUREMENT_ID}
- GA_API_SECRET=${GA_API_SECRET}
volumes:
diff --git a/lib/governance.js b/lib/governance.js
index fd9230f..6af4752 100644
--- a/lib/governance.js
+++ b/lib/governance.js
@@ -289,8 +289,15 @@ export function recordAnalyticsEvent(event) {
total_images: 0,
total_citations: 0,
tool_usage: {},
- blocked_requested_domains: {},
- blocked_response_domains: {},
+ // Counts only. The hostnames themselves are NOT kept here.
+ //
+ // A blocked "requested" domain is a hostname the user typed into a question,
+ // extracted by regex before any outbound call is made. This store is the
+ // 26-month tier, and a fragment of what someone wrote does not belong in it —
+ // the 30-day security and blocked-search logs already hold the names, which
+ // is where an abuse investigation would look anyway.
+ blocked_requested_domain_count: 0,
+ blocked_response_domain_count: 0,
vfb_term_ids: {}
}
@@ -311,21 +318,14 @@ export function recordAnalyticsEvent(event) {
incrementMap(bucket.tool_usage, toolName, Number(count) || 0)
}
- for (const hostname of blockedRequested) {
- incrementMap(bucket.blocked_requested_domains, hostname, 1)
- }
-
- for (const hostname of blockedResponse) {
- incrementMap(bucket.blocked_response_domains, hostname, 1)
- }
+ bucket.blocked_requested_domain_count += blockedRequested.length
+ bucket.blocked_response_domain_count += blockedResponse.length
for (const termId of event.vfbTermIds || []) {
incrementMap(bucket.vfb_term_ids, termId, 1)
}
bucket.tool_usage = normalizeCountMap(bucket.tool_usage)
- bucket.blocked_requested_domains = normalizeCountMap(bucket.blocked_requested_domains)
- bucket.blocked_response_domains = normalizeCountMap(bucket.blocked_response_domains)
bucket.vfb_term_ids = normalizeCountMap(bucket.vfb_term_ids)
data.buckets[bucketKey] = bucket
@@ -373,6 +373,16 @@ export async function sendStructuredTelemetry(event) {
const gaConfig = getGoogleAnalyticsConfig()
if (!gaConfig.enabled) return
+ // Everything here is generalised or drawn from VFB's own published vocabulary.
+ // Nothing a user typed reaches this payload.
+ //
+ // Two fields are worth being explicit about, because they look like content
+ // and are not. `topic_category` is a classification into one of six fixed
+ // values — anatomy, connectivity, gene expression, images, publications,
+ // how-to — so no text can travel through it. `vfb_term_ids` is matched out of
+ // the ANSWER, not the question, by /\b(?:VFB|FBbt)_\d{8}\b/: VFB and FlyBase
+ // ontology identifiers from VFB's own public data, and structurally incapable
+ // of carrying anything else.
const payload = {
client_id: event.requestId || createRequestId(),
events: [{
diff --git a/lib/liveHarness.mjs b/lib/liveHarness.mjs
index 228f32b..8ed1fd4 100644
--- a/lib/liveHarness.mjs
+++ b/lib/liveHarness.mjs
@@ -15,7 +15,7 @@
// See outputs/reports/vfbchat-harness-design.md §4, §8, §9.
import { runHarness } from './orchestrator.mjs'
-import { safeToolArgs } from './safeToolArgs.mjs'
+import { safeToolArgs, safeText } from './safeToolArgs.mjs'
import { throwIfAborted, isRunAbortedWith } from './runSignal.mjs'
// The largest MCP result this process will turn into a JavaScript object graph.
@@ -162,8 +162,14 @@ export function buildLiveDeps(p) {
// shape-only: search_reviewed_docs is called with the whole user question as
// its `query` on every turn, so JSON.stringify(args) here put the question
// verbatim into the cluster log on any doc-search blip.
+ //
+ // The ERROR needs the same treatment, and did not have it. An upstream
+ // message quotes what it was given: get_reviewed_page takes a URL whose
+ // path is unconstrained — only the host must be allow-listed — and the
+ // fetcher throws that URL back. So a redacted `args` sat next to an
+ // unredacted `error` carrying the same value. Seen in a public CI log.
try {
- console.error(`[VFBchat] TOOL FAILED | tool=${name} | args=${safeToolArgs(args)} | error=${msg}`)
+ console.error(`[VFBchat] TOOL FAILED | tool=${name} | args=${safeToolArgs(args)} | error=${safeText(msg)}`)
} catch { /* logging best-effort */ }
return { error: msg, tool: name }
}
diff --git a/lib/safeToolArgs.mjs b/lib/safeToolArgs.mjs
index c5351be..32017e2 100644
--- a/lib/safeToolArgs.mjs
+++ b/lib/safeToolArgs.mjs
@@ -27,7 +27,15 @@ const SAFE_KEYS = new Set([
// No whitespace. An id, a query type and a template name have none; a sentence
// does. A safe KEY carrying a sentence is still a sentence — "the neuron I was
// looking at earlier" arriving as `id` is the user's prose, not an identifier.
-const SAFE_VALUE_RE = /^[\w.,:/-]{0,80}$/
+//
+// Absence of whitespace was the ONLY test here, and it is not enough: a URL, a
+// filesystem path, or a 70-character lab-internal string all pass it, and all of
+// them are something the user typed. So the rule is identifier-SHAPED rather
+// than merely space-free — no `/` or `:`, which is what excludes URLs and paths,
+// and 40 characters rather than 80, comfortably longer than any VFB id, query
+// type, template or gene symbol and shorter than a phrase worth logging.
+// Anything outside that is rendered as its length, exactly as before.
+const SAFE_VALUE_RE = /^[\w.,+-]{0,40}$/
/**
* A free-text value rendered for a container log: its length, not its content.
diff --git a/test-results/task-battery/latest.json b/test-results/task-battery/latest.json
index 38f240f..e70d7b2 100644
--- a/test-results/task-battery/latest.json
+++ b/test-results/task-battery/latest.json
@@ -1,9 +1,9 @@
{
"metadata": {
- "run_id": "task-battery-2026-08-19T14-38-31-533Z",
- "started_at": "2026-08-19T14:38:31.533Z",
- "completed_at": "2026-08-19T14:53:24.106Z",
- "git_sha": "cdf7d5e0f9faaeda112e855f6bc2530ba3d80fee",
+ "run_id": "task-battery-2026-08-19T19-09-12-796Z",
+ "started_at": "2026-08-19T19:09:12.796Z",
+ "completed_at": "2026-08-19T19:24:00.168Z",
+ "git_sha": "a2a31973ab572d5b3b7762ba92283f874943f763",
"task_file": "/home/runner/work/VFBchat/VFBchat/VFBchat/tests/task-battery/tasks.json",
"base_url": "http://127.0.0.1:3210",
"started_server": true,
@@ -27,13 +27,13 @@
},
"T2": {
"total": 8,
- "ok": 8,
- "errors": 0
+ "ok": 7,
+ "errors": 1
},
"T3": {
"total": 8,
- "ok": 7,
- "errors": 1
+ "ok": 8,
+ "errors": 0
},
"T4": {
"total": 6,
@@ -108,7 +108,7 @@
"slow_followup_turn": {
"count": 1,
"task_ids": [
- "C2"
+ "C3"
]
}
},
@@ -117,10 +117,10 @@
"ok": 12,
"turns": 27,
"followup_turns": 15,
- "followup_median_ms": 15605,
- "followup_max_ms": 193442
+ "followup_median_ms": 10228,
+ "followup_max_ms": 190201
},
- "mean_duration_ms": 46910
+ "mean_duration_ms": 37129
},
"results": [
{
@@ -133,7 +133,7 @@
"requires_graph": false,
"min_graphs": 0,
"repetition": 1,
- "duration_ms": 19169,
+ "duration_ms": 15102,
"status_messages": [
{
"message": "Thinking...",
@@ -160,13 +160,13 @@
"phase": "llm"
}
],
- "event_count": 78,
+ "event_count": 76,
"ok": true,
- "request_id": "f3d5178d-838e-4e8a-a703-ce7780daf7eb",
- "response_id": "chatcmpl-83981bfc77bb1be0f067e477d922de86",
+ "request_id": "9184afb8-09a9-4718-99b6-8f03783fd816",
+ "response_id": "chatcmpl-195bc36bc75ef2e0f4d6636e0f15f9ca",
"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. Additionally, the lobes are further divided into compartments such as α, β, and γ.",
+ "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. The lobes are further divided into compartments such as α, β, and γ.",
"quality_flags": {
"has_tool_status": true,
"no_tool_factual_answer": false,
@@ -177,7 +177,7 @@
"graph_failure_mentioned": false,
"missing_required_graph": false,
"used_data_resource": false,
- "response_chars": 433,
+ "response_chars": 419,
"status_count": 6
}
},
@@ -191,7 +191,7 @@
"requires_graph": false,
"min_graphs": 0,
"repetition": 1,
- "duration_ms": 22456,
+ "duration_ms": 75487,
"status_messages": [
{
"message": "Thinking...",
@@ -220,11 +220,11 @@
],
"event_count": 83,
"ok": true,
- "request_id": "1c2fd961-43e2-42b8-8468-9afb020fe49b",
- "response_id": "chatcmpl-a93ab3f21fb02fdceffb9c35d96ab60d",
+ "request_id": "b7e5ac85-fa78-47ae-8062-2009ba2f9b7d",
+ "response_id": "chatcmpl-274ec20f3bb35a51eddf7a98f01e3040",
"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\").",
+ "response": "There are several types of Kenyon cells in the adult Drosophila brain, including alpha/beta, alpha'/beta', and gamma Kenyon cells. These 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,
@@ -249,7 +249,7 @@
"requires_graph": false,
"min_graphs": 0,
"repetition": 1,
- "duration_ms": 83060,
+ "duration_ms": 14809,
"status_messages": [
{
"message": "Thinking...",
@@ -292,13 +292,13 @@
"phase": "llm"
}
],
- "event_count": 73,
+ "event_count": 100,
"ok": true,
- "request_id": "606294b8-e098-4186-9e41-700984529ef0",
- "response_id": "chatcmpl-85cc96717dba7b8ba068a4e27629a1c0",
+ "request_id": "715b559c-3502-47b7-9d04-4c97e8ac6613",
+ "response_id": "chatcmpl-c7a8e2c4e10de26e6ec16e55e01cfe46",
"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 [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.",
+ "response": "The main input neurons to the [mushroom body](https://www.virtualflybrain.org/reports/FBbt_00005801 \"Open mushroom body in Virtual Fly Brain\") include sensory interneuron afferents to the calyx. VFB records show that there are [366](https://v2.virtualflybrain.org/org.geppetto.frontend/geppetto?q=FBbt_00005801,NeuronsPresynapticHere \"Run in VFB: Neurons with presynaptic terminals in mushroom body\") neurons with presynaptic terminals in the mushroom body, including larval uniglomerular projection neurons and larval antennal lobe multiglomerular projection neurons. Additionally, the connectome data indicates that there are [304](https://v2.virtualflybrain.org/org.geppetto.frontend/geppetto?q=FBbt_00005801,NeuronsPostsynapticHere \"Run in VFB: Neurons with postsynaptic terminals in mushroom body\") neurons with postsynaptic terminals in the mushroom body.",
"graphs": [
{
"type": "basic_graph",
@@ -459,7 +459,7 @@
"graph_failure_mentioned": false,
"missing_required_graph": false,
"used_data_resource": false,
- "response_chars": 545,
+ "response_chars": 861,
"status_count": 10
}
},
@@ -473,7 +473,7 @@
"requires_graph": false,
"min_graphs": 0,
"repetition": 1,
- "duration_ms": 16968,
+ "duration_ms": 14119,
"status_messages": [
{
"message": "Thinking...",
@@ -502,8 +502,8 @@
],
"event_count": 25,
"ok": true,
- "request_id": "52ff6fc2-c761-4b33-971a-d2e4e0e8b4e1",
- "response_id": "chatcmpl-65d02b6bdd4db0e0f6083fca81dfaafb",
+ "request_id": "f6c1a43d-7b3e-4189-bcae-6943a0f5e83a",
+ "response_id": "chatcmpl-90a1d260a096ed4bacdd7ebf7e5dc9ba",
"images_count": 6,
"graphs_count": 0,
"response": "Mushroom body Kenyon cells use acetylcholine as their primary neurotransmitter.",
@@ -531,7 +531,7 @@
"requires_graph": false,
"min_graphs": 0,
"repetition": 1,
- "duration_ms": 14219,
+ "duration_ms": 16100,
"status_messages": [
{
"message": "Thinking...",
@@ -566,13 +566,13 @@
"phase": "llm"
}
],
- "event_count": 140,
+ "event_count": 176,
"ok": true,
- "request_id": "f05c27a0-b164-49b1-8d21-a9c68d4ab0d7",
- "response_id": "chatcmpl-0fa38d449d5ed0749ad6efbb9d87ba45",
+ "request_id": "f56eb0a4-f366-49bb-930f-786394706adf",
+ "response_id": "chatcmpl-40eeea66acd7085a383e38b11df5fd47",
"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 [AMMC-Bi16](https://www.virtualflybrain.org/reports/FBbt_00111480 \"Open AMMC-Bi16 in Virtual Fly Brain\"), adult antennal lobe projection neurons like DL5 and VA1d, and adult multiglomerular antennal lobe projection neuron L1 adPN.",
+ "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 Or35a ac3I and Or85b ab3. Neurons with postsynaptic terminals in the antennal lobe include adult antennal lobe projection neurons like DL5, DM4, and VL1, as well as multiglomerular antennal lobe projection neurons like L1 adPN. VFB holds [266](https://v2.virtualflybrain.org/org.geppetto.frontend/geppetto?q=FBbt_00003924,NeuronsPresynapticHere \"Run in VFB: Neurons with presynaptic terminals in antennal lobe\") records of neurons with presynaptic terminals in the antennal lobe and [518](https://v2.virtualflybrain.org/org.geppetto.frontend/geppetto?q=FBbt_00003924,NeuronsPostsynapticHere \"Run in VFB: Neurons with postsynaptic terminals in antennal lobe\") records of neurons with postsynaptic terminals in the antennal lobe.",
"graphs": [
{
"type": "basic_graph",
@@ -738,7 +738,7 @@
"graph_failure_mentioned": false,
"missing_required_graph": false,
"used_data_resource": false,
- "response_chars": 974,
+ "response_chars": 1380,
"status_count": 8
}
},
@@ -752,7 +752,7 @@
"requires_graph": false,
"min_graphs": 0,
"repetition": 1,
- "duration_ms": 13611,
+ "duration_ms": 13744,
"status_messages": [
{
"message": "Thinking...",
@@ -779,13 +779,13 @@
"phase": "llm"
}
],
- "event_count": 57,
+ "event_count": 37,
"ok": true,
- "request_id": "e2cb70c3-8b2f-40bf-9353-129fc3395257",
- "response_id": "chatcmpl-2952f792c1c93ce8842db25dfe3b6124",
+ "request_id": "942b5a40-6985-4bc7-82dd-496d040374ed",
+ "response_id": "chatcmpl-0116ff21b5a7f0df3c865bf019e36d93",
"images_count": 8,
"graphs_count": 0,
- "response": "Approximately 139,255 neurons are in the adult Drosophila central brain, according to Dorkenwald et al. 2024. VFB has annotated [9,413](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](https://www.virtualflybrain.org/reports/FBbt_00047887 \"Open adult central brain in Virtual Fly 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](https://doi.org/10.1038/s41586-024-07558-y \"Open Dorkenwald S et al. (2024) Nature 634(8032):124-138 — PMID 39358518 via DOI (new tab)\")\n\n_FlyWire reports 32,388 neurons FULLY CONTAINED in the central brain out of 139,255 in the whole brain. Neurons that arborise in the central brain but also elsewhere are not in that subcount, so it is a lower bound on 'neurons in the central brain', not a census of them._\n\n_VFB has annotated 9,413 neuron types with some part in adult central brain — a curated annotation count, not the biological total._\n\nReference: [How many neurons are in the fly brain?](https://www.virtualflybrain.org/docs/concepts/neuron-counts/ \"Open “How many neurons are in the fly brain?” — Virtual Fly Brain documentation (new tab)\")",
+ "response": "The [adult central brain](https://www.virtualflybrain.org/reports/FBbt_00047887 \"Open adult central brain in Virtual Fly Brain\") contains approximately 32,388 neurons, according to the neuron count reported by FlyWire for neurons fully contained in the 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](https://doi.org/10.1038/s41586-024-07558-y \"Open Dorkenwald S et al. (2024) Nature 634(8032):124-138 — PMID 39358518 via DOI (new tab)\")\n\n_FlyWire reports 32,388 neurons FULLY CONTAINED in the central brain out of 139,255 in the whole brain. Neurons that arborise in the central brain but also elsewhere are not in that subcount, so it is a lower bound on 'neurons in the central brain', not a census of them._\n\n_VFB has annotated 9,413 neuron types with some part in adult central brain — a curated annotation count, not the biological total._\n\nReference: [How many neurons are in the fly brain?](https://www.virtualflybrain.org/docs/concepts/neuron-counts/ \"Open “How many neurons are in the fly brain?” — Virtual Fly Brain documentation (new tab)\")",
"quality_flags": {
"has_tool_status": true,
"no_tool_factual_answer": false,
@@ -796,7 +796,7 @@
"graph_failure_mentioned": false,
"missing_required_graph": false,
"used_data_resource": false,
- "response_chars": 1647,
+ "response_chars": 1463,
"status_count": 6
}
},
@@ -810,7 +810,7 @@
"requires_graph": false,
"min_graphs": 0,
"repetition": 1,
- "duration_ms": 21348,
+ "duration_ms": 18856,
"status_messages": [
{
"message": "Thinking...",
@@ -837,13 +837,13 @@
"phase": "llm"
}
],
- "event_count": 141,
+ "event_count": 102,
"ok": true,
- "request_id": "ed4401fe-c618-4908-898c-1f719530581d",
- "response_id": "chatcmpl-daeacdb872bf76277d894d541570530d",
+ "request_id": "3a6cf58e-9f3c-4516-8e16-e6bd93601a52",
+ "response_id": "chatcmpl-aedc6153c2365b1713c420f21eec4649",
"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 behaviours. The ellipsoid body, fan-shaped body, protocerebral bridge, paired noduli, and asymmetric body are also referred to as the five core structures of the central complex. 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 the [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 the adult central complex.",
+ "response": "The main components of the Drosophila central complex are the ellipsoid body, the fan-shaped body, the three paired noduli, the asymmetrical bodies, and the protocerebral bridge. These components are associated with functions including navigation and orientation, locomotor control, and sleep/arousal and memory-related behaviours. 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",
@@ -969,7 +969,7 @@
"graph_failure_mentioned": false,
"missing_required_graph": false,
"used_data_resource": false,
- "response_chars": 1092,
+ "response_chars": 915,
"status_count": 6
}
},
@@ -983,7 +983,7 @@
"requires_graph": false,
"min_graphs": 0,
"repetition": 1,
- "duration_ms": 24897,
+ "duration_ms": 73039,
"status_messages": [
{
"message": "Thinking...",
@@ -1010,13 +1010,13 @@
"phase": "llm"
}
],
- "event_count": 69,
+ "event_count": 91,
"ok": true,
- "request_id": "d78e1ccd-c297-4304-982c-d232858c8563",
- "response_id": "chatcmpl-8a62b322c810a097d6604f69c6c2ac40",
+ "request_id": "c09fca3a-dfac-4f7e-aae8-48429d9237f7",
+ "response_id": "chatcmpl-d96a013bc0dd2de563dd4683fee5295f",
"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.",
"quality_flags": {
"has_tool_status": true,
"no_tool_factual_answer": false,
@@ -1027,7 +1027,7 @@
"graph_failure_mentioned": false,
"missing_required_graph": false,
"used_data_resource": false,
- "response_chars": 428,
+ "response_chars": 274,
"status_count": 6
}
},
@@ -1041,7 +1041,7 @@
"requires_graph": false,
"min_graphs": 0,
"repetition": 1,
- "duration_ms": 27646,
+ "duration_ms": 79139,
"status_messages": [
{
"message": "Thinking...",
@@ -1080,13 +1080,13 @@
"phase": "llm"
}
],
- "event_count": 125,
+ "event_count": 94,
"ok": true,
- "request_id": "214570d9-ff8a-4542-b5f8-1c21fdb5317e",
- "response_id": "chatcmpl-08b1dadb2be944a698551e587e6f8c4e",
+ "request_id": "1496b28a-bf7a-4dae-a981-b47b74a81d8d",
+ "response_id": "chatcmpl-2031e0bf6095440c7766d0cbe0fde30b",
"images_count": 8,
"graphs_count": 1,
- "response": "Dopaminergic input to mushroom body output neurons (MBONs) comes from specific dopaminergic neuron types. VFB found 84 upstream class-connectivity partners matching \"dopaminergic neuron\" for MBON, with top mapped pairs including dopaminergic PPL1 neuron and dopaminergic PAM neuron. However, the strongest specific inputs to MBON 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 MBON.",
+ "response": "Dopaminergic input to mushroom body output neurons (MBONs) comes from specific dopaminergic neuron types. VFB records that dopaminergic PPL1 neurons and dopaminergic PAM neurons provide input to MBONs. However, the specific connections between different types of dopaminergic neurons and MBONs are not detailed in VFB evidence. VFB holds [69](https://v2.virtualflybrain.org/org.geppetto.frontend/geppetto?q=FBbt_00047953,SubclassesOf \"Run in VFB: Subclasses of MBON\") subclasses of MBON.",
"graphs": [
{
"type": "basic_graph",
@@ -1312,7 +1312,7 @@
"graph_failure_mentioned": false,
"missing_required_graph": false,
"used_data_resource": false,
- "response_chars": 604,
+ "response_chars": 487,
"status_count": 9
}
},
@@ -1326,7 +1326,7 @@
"requires_graph": false,
"min_graphs": 0,
"repetition": 1,
- "duration_ms": 201497,
+ "duration_ms": 26678,
"status_messages": [
{
"message": "Thinking...",
@@ -1373,13 +1373,13 @@
"phase": "llm"
}
],
- "event_count": 155,
+ "event_count": 145,
"ok": true,
- "request_id": "fa83d343-431f-40cd-aafa-3b90c2e2696c",
- "response_id": "chatcmpl-bf7694ea72b5750ad7f9d3055ff514ae",
+ "request_id": "165efb83-ea45-455f-bc7b-00196c0f9cec",
+ "response_id": "chatcmpl-19a48d3ae479dd633e70a725f9a7304c",
"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's class-level connectivity tables for [olfactory projection neuron](https://www.virtualflybrain.org/reports/FBbt_00051298 \"Open olfactory projection neuron in Virtual Fly Brain\") list downstream and upstream classes, ranked by total synaptic weight and mean synaptic weight per connected pair. The strongest specific targets of olfactory projection neuron include [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 lateral horn neuron](https://www.virtualflybrain.org/reports/FBbt_00048293 \"Open adult lateral horn neuron in Virtual Fly Brain\"). The strongest specific inputs to olfactory projection neuron include [PNS neuron](https://www.virtualflybrain.org/reports/FBbt_00059272 \"Open PNS neuron in Virtual Fly Brain\"), [sensory neuron](https://www.virtualflybrain.org/reports/FBbt_00005124 \"Open sensory neuron in Virtual Fly Brain\"), [olfactory system neuron](https://www.virtualflybrain.org/reports/FBbt_00007697 \"Open olfactory system neuron in Virtual Fly Brain\"), and [chemosensory system neuron](https://www.virtualflybrain.org/reports/FBbt_00007696 \"Open chemosensory system neuron in Virtual Fly Brain\"). VFB does not currently hold direct comparisons of olfactory projection neuron connectivity between the Hemibrain and FAFB datasets.",
+ "response": "The connectivity of olfactory projection neurons is listed in VFB's class-level connectivity tables. Downstream classes for [olfactory projection neuron](https://www.virtualflybrain.org/reports/FBbt_00051298 \"Open olfactory projection neuron in Virtual Fly Brain\") include [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 lateral horn neuron](https://www.virtualflybrain.org/reports/FBbt_00048293 \"Open adult lateral horn neuron in Virtual Fly Brain\"), with mean synaptic weights per connected pair ranging from 7.24 to 13.8. Upstream classes include [PNS neuron](https://www.virtualflybrain.org/reports/FBbt_00059272 \"Open PNS neuron in Virtual Fly Brain\"), [sensory neuron](https://www.virtualflybrain.org/reports/FBbt_00005124 \"Open sensory neuron in Virtual Fly Brain\"), [olfactory system neuron](https://www.virtualflybrain.org/reports/FBbt_00007697 \"Open olfactory system neuron in Virtual Fly Brain\"), and [chemosensory system neuron](https://www.virtualflybrain.org/reports/FBbt_00007696 \"Open chemosensory system neuron in Virtual Fly Brain\"), with mean synaptic weights per connected pair ranging from 10 to 15. VFB does not currently hold direct comparisons of the connectivity of olfactory projection neurons between the Hemibrain and FAFB connectome datasets.",
"quality_flags": {
"has_tool_status": true,
"no_tool_factual_answer": false,
@@ -1390,7 +1390,7 @@
"graph_failure_mentioned": false,
"missing_required_graph": false,
"used_data_resource": false,
- "response_chars": 1698,
+ "response_chars": 1578,
"status_count": 11
}
},
@@ -1404,7 +1404,7 @@
"requires_graph": false,
"min_graphs": 0,
"repetition": 1,
- "duration_ms": 21068,
+ "duration_ms": 15628,
"status_messages": [
{
"message": "Thinking...",
@@ -1438,18 +1438,42 @@
"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": 159,
+ "event_count": 205,
"ok": true,
- "request_id": "c9e95ba4-62ed-4238-9d8a-73eee049011c",
- "response_id": "chatcmpl-f30bba53318a5cdab57132aa301c382d",
+ "request_id": "dee783c9-2358-41bb-ad03-7ab26a2be537",
+ "response_id": "chatcmpl-910f4d7f5e0a505842a5b58fc0eb7d52",
"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\"); [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 [175](https://v2.virtualflybrain.org/org.geppetto.frontend/geppetto?q=FBbt_00048293,TransgeneExpressionHere \"Run in VFB: Transgene expression in LHN\") transgene expression reports for [adult lateral horn neuron](https://www.virtualflybrain.org/reports/FBbt_00048293 \"Open adult lateral horn neuron in Virtual Fly Brain\").",
+ "response": "VFB holds 1924 transgene expression reports for [adult lateral horn](https://www.virtualflybrain.org/reports/FBbt_00007053 \"Open adult lateral horn in Virtual Fly Brain\"), including driver lines such as P{GMR11B09-GAL4} and PBac{566.P.SVS-1}IA-2[CPTI100013].",
"quality_flags": {
"has_tool_status": true,
"no_tool_factual_answer": false,
@@ -1460,8 +1484,8 @@
"graph_failure_mentioned": false,
"missing_required_graph": false,
"used_data_resource": false,
- "response_chars": 1522,
- "status_count": 9
+ "response_chars": 258,
+ "status_count": 15
}
},
{
@@ -1474,7 +1498,7 @@
"requires_graph": false,
"min_graphs": 0,
"repetition": 1,
- "duration_ms": 204926,
+ "duration_ms": 28633,
"status_messages": [
{
"message": "Thinking...",
@@ -1505,13 +1529,13 @@
"phase": "llm"
}
],
- "event_count": 93,
+ "event_count": 205,
"ok": true,
- "request_id": "f6c1c443-9c3a-4b0b-9540-e3be3171af08",
- "response_id": "chatcmpl-e338ae3c58d51256e9dfdc7ee5cbd8ff",
+ "request_id": "60c87ed1-7f43-4339-a441-f7a135901188",
+ "response_id": "chatcmpl-80540f99b1c906d02cbd90b28dad33fa",
"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 and projects to an optic glomerulus of the PVLP, eliciting a jump escape response. VFB holds various records related to LPLC2, including its neuron profile and term information.",
+ "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 specific characteristics and functions. It is located in the dorsal area of the lateral cell body rind and has distinct dendritic arbors in each lobula plate layer, extending outwards from the main fiber in the direction of motion detection for the layer. This arrangement allows it to detect looming stimuli and elicit a jump escape response. In the lobula, it has its main dendritic arbors in layers 4 and 5B, with minor processes in layer 5A, and presynaptic sites in layer 4. Its arbors span approximately 25 lobula optic columns, overlapping with other LPLC2 cells. The LPLC2 neuron 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.",
"quality_flags": {
"has_tool_status": true,
"no_tool_factual_answer": false,
@@ -1522,7 +1546,7 @@
"graph_failure_mentioned": false,
"missing_required_graph": false,
"used_data_resource": false,
- "response_chars": 499,
+ "response_chars": 950,
"status_count": 7
}
},
@@ -1536,7 +1560,7 @@
"requires_graph": false,
"min_graphs": 0,
"repetition": 1,
- "duration_ms": 12996,
+ "duration_ms": 8545,
"status_messages": [
{
"message": "Thinking...",
@@ -1565,8 +1589,8 @@
],
"event_count": 37,
"ok": true,
- "request_id": "d1596745-2a45-4fe0-b98a-d511d91bd6a1",
- "response_id": "chatcmpl-4e4eff804ee0e98f7d96f2c07efa584b",
+ "request_id": "8da808d6-0650-46d4-bf99-bb5a78fc10c5",
+ "response_id": "chatcmpl-cb18854cc1e780ccce14928fb674c72b",
"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.",
@@ -1594,50 +1618,11 @@
"requires_graph": false,
"min_graphs": 0,
"repetition": 1,
- "duration_ms": 19555,
- "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": "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": 65,
- "ok": true,
- "request_id": "53e35c0d-9c5b-487a-b86b-6601547cfd17",
- "response_id": "chatcmpl-acfd21740befc858eaa991d0f0de71e7",
- "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.",
+ "ok": false,
+ "duration_ms": null,
+ "error": "Timed out after 240000 ms",
"quality_flags": {
- "has_tool_status": true,
+ "has_tool_status": false,
"no_tool_factual_answer": false,
"tool_claim_without_tool": false,
"disambiguation_only_answer": false,
@@ -1646,8 +1631,8 @@
"graph_failure_mentioned": false,
"missing_required_graph": false,
"used_data_resource": false,
- "response_chars": 191,
- "status_count": 8
+ "response_chars": 25,
+ "status_count": 0
}
},
{
@@ -1660,7 +1645,7 @@
"requires_graph": false,
"min_graphs": 0,
"repetition": 1,
- "duration_ms": 24621,
+ "duration_ms": 131202,
"status_messages": [
{
"message": "Thinking...",
@@ -1671,19 +1656,7 @@
"phase": "llm"
},
{
- "message": "Resolving 1 term in VFB",
- "phase": "mcp"
- },
- {
- "message": "Querying VFB",
- "phase": "mcp"
- },
- {
- "message": "Checking the answer is covered",
- "phase": "llm"
- },
- {
- "message": "Querying VFB",
+ "message": "Resolving 2 terms in VFB",
"phase": "mcp"
},
{
@@ -1699,13 +1672,13 @@
"phase": "llm"
}
],
- "event_count": 71,
+ "event_count": 31,
"ok": true,
- "request_id": "991ae305-c005-4ae3-aa7c-aa2dda48caaf",
- "response_id": "chatcmpl-b898c1b14b118aaef094f411fbc409ca",
+ "request_id": "8bb54007-3dc2-4ae1-9aa7-1e3e75b0b022",
+ "response_id": "chatcmpl-d5ce9afb869ddedfabbaf73b9c00305d",
"images_count": 5,
"graphs_count": 0,
- "response": "The Hemibrain dataset contains neurons morphologically similar to the fru+ mAL neurons described in light microscopy studies. VFB records show that these include the adult fruitless mAL neuron, adult fru-mAL neuron, fru-aDT-b, and adult fruitless aDT2 neuron.",
+ "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,
@@ -1716,8 +1689,8 @@
"graph_failure_mentioned": false,
"missing_required_graph": false,
"used_data_resource": false,
- "response_chars": 259,
- "status_count": 9
+ "response_chars": 125,
+ "status_count": 6
}
},
{
@@ -1730,7 +1703,7 @@
"requires_graph": false,
"min_graphs": 0,
"repetition": 1,
- "duration_ms": 84087,
+ "duration_ms": 194541,
"status_messages": [
{
"message": "Thinking...",
@@ -1775,11 +1748,11 @@
],
"event_count": 159,
"ok": true,
- "request_id": "ca1af736-c09f-48f2-b75c-e253ba942f91",
- "response_id": "chatcmpl-8b77f263574bf593d2c88748dc564802",
+ "request_id": "7a968141-2c05-479a-a30c-e6847174bcee",
+ "response_id": "chatcmpl-4c9a8e77a6887f35580f00513091acaf",
"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. The first 12 of these include [PFNd_PB2](https://www.virtualflybrain.org/reports/FBbt_00111391 \"Open PFNd_PB2 in Virtual Fly Brain\"), [PFNd_PB3](https://www.virtualflybrain.org/reports/FBbt_00111392 \"Open PFNd_PB3 in Virtual Fly Brain\"), [PFNd_PB5](https://www.virtualflybrain.org/reports/FBbt_00111394 \"Open PFNd_PB5 in Virtual Fly Brain\"), [PFNa_PB4](https://www.virtualflybrain.org/reports/FBbt_00111398 \"Open PFNa_PB4 in Virtual Fly Brain\"), [PFNa_PB5](https://www.virtualflybrain.org/reports/FBbt_00111399 \"Open PFNa_PB5 in Virtual Fly Brain\"), PFNa_PB6, PFNa_PB7, PFNa_PB9, PFNp_PB7, [protocerebral bridge glomerulus 8-fan-shaped body-ipsilateral ventral gall surround neuron](https://www.virtualflybrain.org/reports/FBbt_00111463 \"Open protocerebral bridge glomerulus 8-fan-shaped body-ipsilateral ventral gall surround neuron in Virtual Fly Brain\"), [adult ExR1 neuron of DM3 lineage](https://www.virtualflybrain.org/reports/FBbt_00053034 \"Open adult ExR1 neuron of DM3 lineage in Virtual Fly Brain\"), and adult ExR1 neuron of DM4 lineage. However, the exact number of synaptic steps between these sensory neurons and the fan-shaped body is not specified.",
+ "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,
@@ -1790,7 +1763,7 @@
"graph_failure_mentioned": false,
"missing_required_graph": false,
"used_data_resource": false,
- "response_chars": 1586,
+ "response_chars": 1594,
"status_count": 10
}
},
@@ -1804,7 +1777,7 @@
"requires_graph": false,
"min_graphs": 0,
"repetition": 1,
- "duration_ms": 27951,
+ "duration_ms": 18314,
"status_messages": [
{
"message": "Thinking...",
@@ -1843,13 +1816,13 @@
"phase": "llm"
}
],
- "event_count": 132,
+ "event_count": 123,
"ok": true,
- "request_id": "7e843662-4215-44c1-a87b-cad4fa8b61e2",
- "response_id": "chatcmpl-a1b952fc692ea779d256cc04096748c2",
+ "request_id": "e3b99b00-4062-43cf-a60f-54ebb3a46858",
+ "response_id": "chatcmpl-8227164834b52eb33aa8f3ad30cee57a",
"images_count": 8,
"graphs_count": 0,
- "response": "There are reciprocal connections between mushroom body output neurons and dopaminergic neurons. VFB found 5 reciprocal class-level pairs between [mushroom body output neuron](https://www.virtualflybrain.org/reports/FBbt_00047953 \"Open mushroom body output neuron in Virtual Fly Brain\") and [dopaminergic neuron](https://www.virtualflybrain.org/reports/FBbt_00005131 \"Open dopaminergic neuron in Virtual Fly Brain\"). The strongest specific inputs to mushroom body output neuron are [adult cholinergic neuron](https://www.virtualflybrain.org/reports/FBbt_00058205 \"Open adult cholinergic neuron in Virtual Fly Brain\"), with 7.22 synapses per connected pair, and [Kenyon cell](https://www.virtualflybrain.org/reports/FBbt_00003686 \"Open Kenyon cell in Virtual Fly Brain\"), with 7.09 synapses per connected pair. The strongest specific targets of dopaminergic neuron are adult cholinergic neuron, with 2.68 synapses per connected pair, and [adult Kenyon cell](https://www.virtualflybrain.org/reports/FBbt_00049825 \"Open adult Kenyon cell in Virtual Fly Brain\"), with 2.04 synapses per connected pair.",
+ "response": "There are reciprocal connections between mushroom body output neurons and dopaminergic neurons. VFB found 5 reciprocal class-level pairs between [mushroom body output neuron](https://www.virtualflybrain.org/reports/FBbt_00047953 \"Open mushroom body output neuron in Virtual Fly Brain\") and [dopaminergic neuron](https://www.virtualflybrain.org/reports/FBbt_00005131 \"Open dopaminergic neuron in Virtual Fly Brain\"). The strongest specific targets of mushroom body output neuron include [primary interneuron](https://www.virtualflybrain.org/reports/FBbt_00052517 \"Open primary interneuron in Virtual Fly Brain\"), [primary neuron](https://www.virtualflybrain.org/reports/FBbt_00047097 \"Open primary neuron in Virtual Fly Brain\"), [adult GABAergic neuron](https://www.virtualflybrain.org/reports/FBbt_00058207 \"Open adult GABAergic neuron in Virtual Fly Brain\"), [GABAergic neuron](https://www.virtualflybrain.org/reports/FBbt_00007228 \"Open GABAergic neuron in Virtual Fly Brain\"), [adult glutamatergic neuron](https://www.virtualflybrain.org/reports/FBbt_00058208 \"Open adult glutamatergic neuron in Virtual Fly Brain\"), [glutamatergic neuron](https://www.virtualflybrain.org/reports/FBbt_00100291 \"Open glutamatergic neuron in Virtual Fly Brain\"), [adult lateral horn neuron](https://www.virtualflybrain.org/reports/FBbt_00048293 \"Open adult lateral horn neuron in Virtual Fly Brain\"), and [adult cholinergic neuron](https://www.virtualflybrain.org/reports/FBbt_00058205 \"Open adult cholinergic neuron in Virtual Fly Brain\"). For dopaminergic neuron, 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\").",
"quality_flags": {
"has_tool_status": true,
"no_tool_factual_answer": false,
@@ -1860,7 +1833,7 @@
"graph_failure_mentioned": false,
"missing_required_graph": false,
"used_data_resource": false,
- "response_chars": 1096,
+ "response_chars": 1736,
"status_count": 9
}
},
@@ -1874,7 +1847,7 @@
"requires_graph": false,
"min_graphs": 0,
"repetition": 1,
- "duration_ms": 28618,
+ "duration_ms": 22026,
"status_messages": [
{
"message": "Thinking...",
@@ -1913,13 +1886,13 @@
"phase": "llm"
}
],
- "event_count": 159,
+ "event_count": 142,
"ok": true,
- "request_id": "8ef7a0e8-e336-4595-96bd-4106fbb1754d",
- "response_id": "chatcmpl-9c7728ed8b4ed94db81475871240b029",
+ "request_id": "0396edbf-4049-4494-8fbb-8839f834e873",
+ "response_id": "chatcmpl-4c3a4ee477809cfffd76ac21644a1833",
"images_count": 8,
"graphs_count": 0,
- "response": "The pathway from olfactory receptor neurons to the lateral horn involves projection neurons that reach the lateral horn through four antennal-lobe tracts. Antennal lobe projection neurons are intermediate neurons 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\"), and [olfactory system neuron](https://www.virtualflybrain.org/reports/FBbt_00007697 \"Open olfactory system neuron in Virtual Fly Brain\"). VFB does not currently hold downstream connectivity classes for [olfactory receptor neuron](https://www.virtualflybrain.org/reports/FBbt_00005926 \"Open olfactory receptor 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](https://www.virtualflybrain.org/reports/FBbt_00007053 \"Open adult lateral horn in Virtual Fly Brain\") and [1658](https://v2.virtualflybrain.org/org.geppetto.frontend/geppetto?q=FBbt_00007053,NeuronsSynaptic \"Run in VFB: Neurons with synaptic terminals in adult lateral horn\") records of neurons with synaptic terminals in adult lateral horn.",
+ "response": "The pathway from olfactory receptor neurons to the lateral horn involves projection neurons that reach the lateral horn through four antennal-lobe tracts. Antennal lobe projection neurons are intermediate neuron types and they connect olfactory receptor neurons to 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\"), and [adult antennal lobe local neuron](https://www.virtualflybrain.org/reports/FBbt_00007390 \"Open adult antennal lobe local 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](https://www.virtualflybrain.org/reports/FBbt_00007053 \"Open adult lateral horn in Virtual Fly Brain\") and [1658](https://v2.virtualflybrain.org/org.geppetto.frontend/geppetto?q=FBbt_00007053,NeuronsSynaptic \"Run in VFB: Neurons with synaptic terminals in adult lateral horn\") records of neurons with synaptic terminals in adult lateral horn.",
"quality_flags": {
"has_tool_status": true,
"no_tool_factual_answer": false,
@@ -1930,7 +1903,7 @@
"graph_failure_mentioned": false,
"missing_required_graph": false,
"used_data_resource": false,
- "response_chars": 1896,
+ "response_chars": 1573,
"status_count": 9
}
},
@@ -1944,7 +1917,7 @@
"requires_graph": false,
"min_graphs": 0,
"repetition": 1,
- "duration_ms": 196830,
+ "duration_ms": 191486,
"status_messages": [
{
"message": "Thinking...",
@@ -1983,13 +1956,13 @@
"phase": "llm"
}
],
- "event_count": 131,
+ "event_count": 103,
"ok": true,
- "request_id": "6305f4ef-10e7-40d3-aaec-84c2ad5f7a87",
- "response_id": "chatcmpl-39a0e3885cf7aa3d1c11793b5cf8c57b",
+ "request_id": "89945cf2-9a57-4b71-99c0-e7ec5d79cc20",
+ "response_id": "chatcmpl-339e4d911760dfabc850aaca4d85a5a2",
"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 [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. VFB holds various other data related to visual system neuron, including available images, splits targeting it, scRNAseq data, transgene expression, and downstream and upstream connectivity classes.",
+ "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 currently 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,
@@ -2000,7 +1973,7 @@
"graph_failure_mentioned": false,
"missing_required_graph": false,
"used_data_resource": false,
- "response_chars": 1214,
+ "response_chars": 1051,
"status_count": 9
}
},
@@ -2014,7 +1987,7 @@
"requires_graph": false,
"min_graphs": 0,
"repetition": 1,
- "duration_ms": 25261,
+ "duration_ms": 12577,
"status_messages": [
{
"message": "Thinking...",
@@ -2048,42 +2021,18 @@
"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": 109,
+ "event_count": 51,
"ok": true,
- "request_id": "791ea879-0e36-4f62-aafd-c9f85960475c",
- "response_id": "chatcmpl-1b0f2698d67baf059d5fe831c61115b1",
+ "request_id": "63cbeb21-753c-4d53-99b0-ba5b71fb313d",
+ "response_id": "chatcmpl-4a8ad4459e3f457bc9dfa68a37364a76",
"images_count": 8,
"graphs_count": 0,
- "response": "The strongest synaptic input to the MBON-gamma1pedc>a/b neuron is not specified in VFB evidence.",
+ "response": "The strongest synaptic input to the MBON-gamma1pedc>a/b neuron is not specified. VFB holds upstream connectivity classes for [mushroom body output neuron 11](https://www.virtualflybrain.org/reports/FBbt_00100246 \"Open mushroom body output neuron 11 in Virtual Fly Brain\"), but the lookup did not complete.",
"quality_flags": {
"has_tool_status": true,
"no_tool_factual_answer": false,
@@ -2094,8 +2043,8 @@
"graph_failure_mentioned": false,
"missing_required_graph": false,
"used_data_resource": false,
- "response_chars": 96,
- "status_count": 15
+ "response_chars": 305,
+ "status_count": 9
}
},
{
@@ -2108,7 +2057,7 @@
"requires_graph": false,
"min_graphs": 0,
"repetition": 1,
- "duration_ms": 19172,
+ "duration_ms": 12164,
"status_messages": [
{
"message": "Thinking...",
@@ -2147,13 +2096,13 @@
"phase": "llm"
}
],
- "event_count": 134,
+ "event_count": 69,
"ok": true,
- "request_id": "071e4b5a-0793-4090-88d5-c7142a987753",
- "response_id": "chatcmpl-1b1cfd065070253db0f6b9f71e50fe7a",
+ "request_id": "6131ec63-bee8-461b-9409-0dc75fe07c6d",
+ "response_id": "chatcmpl-32672f1a4aaa4eaa45fb2c39069f9ba2",
"images_count": 8,
"graphs_count": 0,
- "response": "The connectome data indicates that Kenyon cells, including both alpha/beta Kenyon cells and gamma Kenyon cells, provide input to mushroom body output neurons. VFB records show that Kenyon cells have a mean synaptic weight of 7.09 per connected pair with mushroom body output neurons, with 59% of individuals connected. However, the specific downstream [mushroom body output neuron](https://www.virtualflybrain.org/reports/FBbt_00047953 \"Open mushroom body output neuron in Virtual Fly Brain\") VFB holds [69](https://v2.virtualflybrain.org/org.geppetto.frontend/geppetto?q=FBbt_00047953,SubclassesOf \"Run in VFB: Subclasses of MBON\") subclasses of mushroom body output neuron and [6](https://v2.virtualflybrain.org/org.geppetto.frontend/geppetto?q=FBbt_00100248,SubclassesOf \"Run in VFB: Subclasses of KCab\") subclasses of [alpha/beta Kenyon cell](https://www.virtualflybrain.org/reports/FBbt_00100248 \"Open alpha/beta Kenyon cell in Virtual Fly Brain\").",
+ "response": "The connectome data indicates that [mushroom body output neuron](https://www.virtualflybrain.org/reports/FBbt_00047953 \"Open mushroom body output neuron in Virtual Fly Brain\") receives input from [Kenyon cell](https://www.virtualflybrain.org/reports/FBbt_00003686 \"Open Kenyon cell in Virtual Fly Brain\"), with 7.09 synapses per connected pair, and 59% of individuals connected. VFB holds [69](https://v2.virtualflybrain.org/org.geppetto.frontend/geppetto?q=FBbt_00047953,SubclassesOf \"Run in VFB: Subclasses of MBON\") subclasses of mushroom body output neuron and [6](https://v2.virtualflybrain.org/org.geppetto.frontend/geppetto?q=FBbt_00100248,SubclassesOf \"Run in VFB: Subclasses of KCab\") subclasses of [alpha/beta Kenyon cell](https://www.virtualflybrain.org/reports/FBbt_00100248 \"Open alpha/beta Kenyon cell in Virtual Fly Brain\").",
"quality_flags": {
"has_tool_status": true,
"no_tool_factual_answer": false,
@@ -2164,7 +2113,7 @@
"graph_failure_mentioned": false,
"missing_required_graph": false,
"used_data_resource": false,
- "response_chars": 953,
+ "response_chars": 839,
"status_count": 9
}
},
@@ -2178,7 +2127,7 @@
"requires_graph": false,
"min_graphs": 0,
"repetition": 1,
- "duration_ms": 19642,
+ "duration_ms": 13716,
"status_messages": [
{
"message": "Thinking...",
@@ -2209,13 +2158,13 @@
"phase": "llm"
}
],
- "event_count": 91,
+ "event_count": 89,
"ok": true,
- "request_id": "87925d38-7818-4c01-87bc-3e0818c3ab8a",
- "response_id": "chatcmpl-cac9830cd95bfad139783c86c5c8fc32",
+ "request_id": "b2ebfa98-074f-4174-917a-e5e6514b17b3",
+ "response_id": "chatcmpl-41d1dd86119d19e10b16a668378b2ff6",
"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\").",
+ "response": "The 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,
@@ -2226,7 +2175,7 @@
"graph_failure_mentioned": false,
"missing_required_graph": false,
"used_data_resource": false,
- "response_chars": 451,
+ "response_chars": 440,
"status_count": 7
}
},
@@ -2240,7 +2189,7 @@
"requires_graph": false,
"min_graphs": 0,
"repetition": 1,
- "duration_ms": 29102,
+ "duration_ms": 21165,
"status_messages": [
{
"message": "Thinking...",
@@ -2287,13 +2236,13 @@
"phase": "llm"
}
],
- "event_count": 133,
+ "event_count": 147,
"ok": true,
- "request_id": "eb4b14ec-5a02-490d-b0f6-85f270f08ffb",
- "response_id": "chatcmpl-0613ddc9d1f79399c60452f72490329e",
+ "request_id": "5d1d423a-0bfa-4abb-b967-e2cd47033510",
+ "response_id": "chatcmpl-a080a2e9064fddf14f39072154632a52",
"images_count": 8,
"graphs_count": 0,
- "response": "Neurons that connect the [adult central complex](https://www.virtualflybrain.org/reports/FBbt_00003632 \"Open adult central complex in Virtual Fly Brain\") to the lateral accessory lobe include [PFL1](https://www.virtualflybrain.org/reports/FBbt_00111433 \"Open PFL1 in Virtual Fly Brain\"), [PFL2_PB4](https://www.virtualflybrain.org/reports/FBbt_00111453 \"Open PFL2_PB4 in Virtual Fly Brain\"), [PFL3_PB7](https://www.virtualflybrain.org/reports/FBbt_00111450 \"Open PFL3_PB7 in Virtual Fly Brain\"), [PFL1_PB1](https://www.virtualflybrain.org/reports/FBbt_00111434 \"Open PFL1_PB1 in Virtual Fly Brain\"), [PFL1_PB7](https://www.virtualflybrain.org/reports/FBbt_00111440 \"Open PFL1_PB7 in Virtual Fly Brain\"), and [PFL1_PB2](https://www.virtualflybrain.org/reports/FBbt_00111435 \"Open PFL1_PB2 in Virtual Fly Brain\"). VFB does not currently hold data on neurons with some part in embryonic/larval lateral accessory lobe, neurons with presynaptic terminals in embryonic/larval lateral accessory lobe, or neurons with postsynaptic terminals in embryonic/larval lateral accessory lobe.",
+ "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. The strength of connections between the central complex and the lateral accessory lobe is not specified.",
"quality_flags": {
"has_tool_status": true,
"no_tool_factual_answer": false,
@@ -2304,7 +2253,7 @@
"graph_failure_mentioned": false,
"missing_required_graph": false,
"used_data_resource": false,
- "response_chars": 1076,
+ "response_chars": 1262,
"status_count": 11
}
},
@@ -2318,11 +2267,62 @@
"requires_graph": false,
"min_graphs": 0,
"repetition": 1,
- "ok": false,
- "duration_ms": null,
- "error": "Timed out after 240000 ms",
+ "duration_ms": 82579,
+ "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": "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": 155,
+ "ok": true,
+ "request_id": "985aacc3-a308-414a-90e0-69a8f4bf528e",
+ "response_id": "chatcmpl-2d5a1bcfa73c5491a40e2abe2a7d08b5",
+ "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. There are [18](https://v2.virtualflybrain.org/org.geppetto.frontend/geppetto?q=FBbt_00047573,ListAllAvailableImages \"Run in VFB: List all available images of DNa02\") images available, as well as [2](https://v2.virtualflybrain.org/org.geppetto.frontend/geppetto?q=FBbt_00047573,SplitsTargeting \"Run in VFB: Splits targeting DNa02\") split-GAL4 combinations that target DNa02, and 2 transgene expression reports. The available images include those from MaleCNS and FlyEM-HB datasets. Additionally, there are 2 genetic tools available to label DNa02 descending neurons, which are [P{R87D07-GAL4.DBD} ∩ P{R75C10-p65.AD} expression pattern](https://www.virtualflybrain.org/reports/VFBexp_FBtp0122422FBtp0119138 \"Open P{R87D07-GAL4.DBD} ∩ P{R75C10-p65.AD} expression pattern in Virtual Fly Brain\") and [P{VT025718-GAL4.DBD} ∩ P{R22C05-p65.AD} expression pattern](https://www.virtualflybrain.org/reports/VFBexp_FBtp0123634FBtp0118395 \"Open P{VT025718-GAL4.DBD} ∩ P{R22C05-p65.AD} expression pattern in Virtual Fly Brain\").",
"quality_flags": {
- "has_tool_status": false,
+ "has_tool_status": true,
"no_tool_factual_answer": false,
"tool_claim_without_tool": false,
"disambiguation_only_answer": false,
@@ -2331,8 +2331,8 @@
"graph_failure_mentioned": false,
"missing_required_graph": false,
"used_data_resource": false,
- "response_chars": 25,
- "status_count": 0
+ "response_chars": 1287,
+ "status_count": 11
}
},
{
@@ -2345,7 +2345,7 @@
"requires_graph": false,
"min_graphs": 0,
"repetition": 1,
- "duration_ms": 74317,
+ "duration_ms": 9277,
"status_messages": [
{
"message": "Thinking...",
@@ -2374,8 +2374,8 @@
],
"event_count": 53,
"ok": true,
- "request_id": "c661fa5c-1a1d-4e8b-8e82-5cdc729a8515",
- "response_id": "chatcmpl-016e4ec08a5713a6e11fd89792a2afa9",
+ "request_id": "bcf28c7f-51ca-498f-9862-e5fa5555f651",
+ "response_id": "chatcmpl-c1ebc74883fdbdadc3bdaeff0d6f74da",
"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.",
@@ -2403,7 +2403,7 @@
"requires_graph": false,
"min_graphs": 0,
"repetition": 1,
- "duration_ms": 98725,
+ "duration_ms": 220304,
"status_messages": [
{
"message": "Thinking...",
@@ -2442,13 +2442,13 @@
"phase": "llm"
}
],
- "event_count": 231,
+ "event_count": 331,
"ok": true,
- "request_id": "e91a74d2-ff6d-490f-a0b3-bcc54db6eb10",
- "response_id": "chatcmpl-b11ff76c7fdbff30fd6dca0b4043842a",
+ "request_id": "0a97bfce-bade-47ea-a2e2-88333c1fa80e",
+ "response_id": "chatcmpl-deabc04cf13dc8adc089cf4acd47cb8d",
"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 distinct anatomy and connectivity, with a large cell body located posterior to the lower protocerebrum and a large descending axon that is several times larger than any other axon in the cervical connective. There is one giant fiber neuron per hemisphere.\n\nAvailable driver lines for the giant fiber neuron include [5](https://v2.virtualflybrain.org/org.geppetto.frontend/geppetto?q=FBbt_00004020,SplitsTargeting \"Run in VFB: Splits targeting DNp01\") split-GAL4 combinations. VFB records show 14 transgene expression reports for the giant fiber neuron, but the query returned [10](https://v2.virtualflybrain.org/org.geppetto.frontend/geppetto?q=FBbt_00004020,TransgeneExpressionHere \"Run in VFB: Transgene expression in DNp01\") results, including expression patterns for P{GMR78G07-GAL4}, P{GMR79D08-GAL4}, and P{GMR91H05-GAL4}, as well as several split-GAL4 combinations.\n\nRelevant publications for the giant fiber neuron include Thomas and Wyman (1984), Koto et al. (1981), and Namiki et al. (2018). The giant fiber neuron's downstream connectivity classes and upstream connectivity classes are numerous, with [389](https://v2.virtualflybrain.org/org.geppetto.frontend/geppetto?q=FBbt_00004020,DownstreamClassConnectivity \"Run in VFB: Downstream connectivity classes for DNp01\") and [472](https://v2.virtualflybrain.org/org.geppetto.frontend/geppetto?q=FBbt_00004020,UpstreamClassConnectivity \"Run in VFB: Upstream connectivity classes for DNp01\") classes, respectively.",
+ "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 can be identified by its large descending axon, which is several times larger than any other axon in the cervical connective. There is one giant fiber neuron per hemisphere.\n\nThe giant fiber neuron, also known as DNp01, has specific connectivity, with [389](https://v2.virtualflybrain.org/org.geppetto.frontend/geppetto?q=FBbt_00004020,DownstreamClassConnectivity \"Run in VFB: Downstream connectivity classes for DNp01\") downstream and [472](https://v2.virtualflybrain.org/org.geppetto.frontend/geppetto?q=FBbt_00004020,UpstreamClassConnectivity \"Run in VFB: Upstream connectivity classes for DNp01\") upstream connectivity classes.\n\nVFB holds [10](https://v2.virtualflybrain.org/org.geppetto.frontend/geppetto?q=FBbt_00004020,TransgeneExpressionHere \"Run in VFB: Transgene expression in DNp01\") transgene expression reports for the giant fiber neuron, including expression patterns for P{GMR78G07-GAL4}, P{GMR79D08-GAL4}, P{GMR91H05-GAL4}, P{R48A11-GAL4.DBD} ∩ P{R30C01-p65.AD}, P{R68A06-GAL4.DBD} ∩ P{R25C08-p65.AD}, P{R79H02-GAL4.DBD} ∩ P{R14A01-p65.AD}, P{R79H02-GAL4.DBD} ∩ P{R25C08-p65.AD}, P{VT004455-GAL4.DBD} ∩ P{R10A12-p65.AD}, P{VT014708-GAL4}, and P{VT046265-GAL4}.\n\nRelevant publications include those by Thomas and Wyman (1984), Koto et al. (1981), Namiki et al. (2018), and Power (1948).",
"graphs": [
{
"type": "basic_graph",
@@ -2674,7 +2674,7 @@
"graph_failure_mentioned": false,
"missing_required_graph": false,
"used_data_resource": false,
- "response_chars": 1679,
+ "response_chars": 1573,
"status_count": 9
}
},
@@ -2688,7 +2688,7 @@
"requires_graph": false,
"min_graphs": 0,
"repetition": 1,
- "duration_ms": 28424,
+ "duration_ms": 23691,
"status_messages": [
{
"message": "Thinking...",
@@ -2722,6 +2722,10 @@
"message": "Querying VFB",
"phase": "mcp"
},
+ {
+ "message": "Querying VFB",
+ "phase": "mcp"
+ },
{
"message": "Checking the answer is covered",
"phase": "llm"
@@ -2731,13 +2735,13 @@
"phase": "llm"
}
],
- "event_count": 129,
+ "event_count": 148,
"ok": true,
- "request_id": "38c62c1a-6a2d-4934-9a96-22ecc8664d49",
- "response_id": "chatcmpl-27d9837549c1635607b186c99c3b1b79",
+ "request_id": "dde8850c-1890-424c-ae80-b582ab8ac1dc",
+ "response_id": "chatcmpl-7eb658b2038b7089e78e5f999b7b234c",
"images_count": 8,
"graphs_count": 1,
- "response": "Based on connectivity data, adult visual projection neurons and 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\"). The connectome data indicates that adult visual projection neurons have presynaptic terminals in the mushroom body. VFB records show that the strongest specific targets of [visual system neuron](https://www.virtualflybrain.org/reports/FBbt_00047736 \"Open visual system neuron in Virtual Fly Brain\") include [adult optic lobe neuron](https://www.virtualflybrain.org/reports/FBbt_00003702 \"Open adult optic lobe neuron in Virtual Fly Brain\"), [optic lobe wide-field columnar neuron](https://www.virtualflybrain.org/reports/FBbt_00110137 \"Open optic lobe wide-field columnar 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\"), and that visual system neuron also connects to itself.\n\nVFB holds [602](https://v2.virtualflybrain.org/org.geppetto.frontend/geppetto?q=FBbt_00005801,NeuronsPartHere \"Run in VFB: Neurons with some part in mushroom body\") neurons with some part in mushroom body and [601](https://v2.virtualflybrain.org/org.geppetto.frontend/geppetto?q=FBbt_00005801,NeuronsSynaptic \"Run in VFB: Neurons with synaptic terminals in mushroom body\") neurons with synaptic terminals in mushroom body.",
+ "response": "Based on connectivity data, adult visual projection neurons and projection neurons might mediate a connection between the visual system and the [mushroom body](https://www.virtualflybrain.org/reports/FBbt_00005801 \"Open mushroom body in Virtual Fly Brain\"). The connectome data indicates that [visual system neuron](https://www.virtualflybrain.org/reports/FBbt_00047736 \"Open visual system neuron in Virtual Fly Brain\") has synaptic connections with several neuron types, including [adult optic lobe neuron](https://www.virtualflybrain.org/reports/FBbt_00003702 \"Open adult optic lobe neuron in Virtual Fly Brain\"), [optic lobe wide-field columnar neuron](https://www.virtualflybrain.org/reports/FBbt_00110137 \"Open optic lobe wide-field columnar neuron in Virtual Fly Brain\"), [adult optic lobe columnar neuron](https://www.virtualflybrain.org/reports/FBbt_00005129 \"Open adult optic lobe 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 [transmedullary neuron](https://www.virtualflybrain.org/reports/FBbt_00003788 \"Open transmedullary neuron in Virtual Fly Brain\"). Additionally, VFB's \"Neurons with some part in mushroom body\" query returns [602](https://v2.virtualflybrain.org/org.geppetto.frontend/geppetto?q=FBbt_00005801,NeuronsPartHere \"Run in VFB: Neurons with some part in mushroom body\") results, which may include neuron types that could facilitate the connection between the visual system and the mushroom body. This suggests that visual information could reach the memory circuit via these connections.",
"graphs": [
{
"type": "basic_graph",
@@ -2956,8 +2960,8 @@
"graph_failure_mentioned": false,
"missing_required_graph": false,
"used_data_resource": false,
- "response_chars": 1497,
- "status_count": 10
+ "response_chars": 1672,
+ "status_count": 11
}
},
{
@@ -2970,7 +2974,7 @@
"requires_graph": false,
"min_graphs": 0,
"repetition": 1,
- "duration_ms": 206341,
+ "duration_ms": 73239,
"status_messages": [
{
"message": "Thinking...",
@@ -3011,8 +3015,8 @@
],
"event_count": 90,
"ok": true,
- "request_id": "5e25c1a7-6ff9-4704-b82c-200b5226e239",
- "response_id": "chatcmpl-49c649daf522a581fea9f9a2c0a1e8a1",
+ "request_id": "6c2b23cb-3640-42e0-805b-503c69a8180f",
+ "response_id": "chatcmpl-82cd3f5b28d7f7a0342339b51bb11aa1",
"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\").",
@@ -3320,7 +3324,7 @@
"requires_graph": false,
"min_graphs": 0,
"repetition": 1,
- "duration_ms": 26720,
+ "duration_ms": 18502,
"status_messages": [
{
"message": "Thinking...",
@@ -3330,6 +3334,10 @@
"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"
@@ -3367,13 +3375,13 @@
"phase": "llm"
}
],
- "event_count": 224,
+ "event_count": 251,
"ok": true,
- "request_id": "ae2d14ec-2cb9-4f60-9167-d28ae221cb68",
- "response_id": "chatcmpl-1843ce52d2f59e0f0d32ed594ccbc930",
+ "request_id": "0ee0950a-5449-4d94-836a-be4bbf67aa5e",
+ "response_id": "chatcmpl-2049fa496ec9aca2308833295ddadaa2",
"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, the strongest specific targets of [thermosensory neuron](https://www.virtualflybrain.org/reports/FBbt_00005918 \"Open thermosensory neuron in Virtual Fly Brain\") include [projection neuron](https://www.virtualflybrain.org/reports/FBbt_00007392 \"Open projection neuron in Virtual Fly Brain\"), [adult antennal lobe projection neuron](https://www.virtualflybrain.org/reports/FBbt_00067123 \"Open adult antennal lobe projection neuron in Virtual Fly Brain\"), and [antennal lobe projection neuron](https://www.virtualflybrain.org/reports/FBbt_00007422 \"Open antennal lobe projection neuron in Virtual Fly Brain\"), with 18.9, 18.8, and 18.7 synapses per connected pair, respectively. Additionally, 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\"), with 10.1, 10, and 9.06 synapses per connected pair, respectively. VFB holds [366](https://v2.virtualflybrain.org/org.geppetto.frontend/geppetto?q=FBbt_00005801,NeuronsPresynapticHere \"Run in VFB: Neurons with presynaptic terminals in mushroom body\") records of 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\") records of neurons with postsynaptic terminals in mushroom body. Temperature information could potentially influence memory formation through the connections between thermosensory neurons and the mushroom body, but the exact nature of this influence is not specified in VFB evidence.",
+ "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, thermosensory neurons have downstream connections to several classes of neurons, including projection neurons and antennal lobe projection neurons, which may have connections to the mushroom body. The mushroom body itself has presynaptic and postsynaptic connections to various neurons, including larval uniglomerular projection neurons and adult odd neurons of the calyx.\n\nThermosensory neurons have strong specific targets, 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. They also receive input from adult antennal lobe local neurons and unilateral local interneurons of the adult antennal lobe, with mean synaptic weights per connected pair ranging from 8.34 to 10.1 synapses.\n\nWhile VFB evidence does not directly describe the connectivity between thermosensory neurons and the mushroom body, it suggests that thermosensory information could influence memory formation through connections to neurons that project to the mushroom body.",
"quality_flags": {
"has_tool_status": true,
"no_tool_factual_answer": false,
@@ -3384,8 +3392,8 @@
"graph_failure_mentioned": false,
"missing_required_graph": false,
"used_data_resource": false,
- "response_chars": 2265,
- "status_count": 11
+ "response_chars": 1641,
+ "status_count": 12
}
},
{
@@ -3398,7 +3406,7 @@
"requires_graph": false,
"min_graphs": 0,
"repetition": 1,
- "duration_ms": 219780,
+ "duration_ms": 27497,
"status_messages": [
{
"message": "Thinking...",
@@ -3428,10 +3436,6 @@
"message": "Querying VFB",
"phase": "mcp"
},
- {
- "message": "Querying VFB",
- "phase": "mcp"
- },
{
"message": "Checking the answer is covered",
"phase": "llm"
@@ -3457,13 +3461,13 @@
"phase": "llm"
}
],
- "event_count": 239,
+ "event_count": 271,
"ok": true,
- "request_id": "c78675ad-fbf7-4688-946c-1c7f9a05cfeb",
- "response_id": "chatcmpl-f5ff5e49e8da7de1f87ea86d18577eee",
+ "request_id": "d6d9241e-8c94-4d07-a28f-783b4e9ad780",
+ "response_id": "chatcmpl-786a116b3e98b85ab21e7e5e4c53ba8b",
"images_count": 1,
"graphs_count": 0,
- "response": "The [subesophageal zone](https://www.virtualflybrain.org/reports/FBbt_00051068 \"Open subesophageal zone in Virtual Fly Brain\") is a well-characterised region in VFB, with various neuron types annotated. VFB records show [2,698](https://v2.virtualflybrain.org/org.geppetto.frontend/geppetto?q=FBbt_00051068,NeuronsPartHere \"Run in VFB: Neurons with some part in subesophageal zone\") neurons with some part in the subesophageal zone, including serotonergic SE1 and SE3 neurons, and larval CCAP subesophageal IN-1 and IN-2 neurons. The connectome data indicates [2,598](https://v2.virtualflybrain.org/org.geppetto.frontend/geppetto?q=FBbt_00051068,NeuronsSynaptic \"Run in VFB: Neurons with synaptic terminals in subesophageal zone\") neurons with synaptic terminals in the subesophageal zone, and [1,813](https://v2.virtualflybrain.org/org.geppetto.frontend/geppetto?q=FBbt_00051068,NeuronsPresynapticHere \"Run in VFB: Neurons with presynaptic terminals in subesophageal zone\") neurons with presynaptic terminals in the subesophageal zone.\n\nGenetic tools for subesophageal zone neurons are available, including GAL4 drivers and binary/intersectional drivers. VFB holds 4,205 transgene expression reports for the subesophageal zone, with examples including P{GMR12D05-GAL4} and P{VT000003-GAL4} expression patterns.\n\nThe subesophageal zone has been characterised in both larvae and adults, with VFB returning two results for the term: larval subesophageal zone and adult subesophageal zone.",
+ "response": "The [subesophageal zone](https://www.virtualflybrain.org/reports/FBbt_00051068 \"Open subesophageal zone in Virtual Fly Brain\") is well-characterised in VFB, with available imagery and various queries for neuron types and connectomics data. VFB records show [2,698](https://v2.virtualflybrain.org/org.geppetto.frontend/geppetto?q=FBbt_00051068,NeuronsPartHere \"Run in VFB: Neurons with some part in subesophageal zone\") neurons with some part in the subesophageal zone, including [serotonergic SE1 neuron](https://www.virtualflybrain.org/reports/FBbt_00001980 \"Open serotonergic SE1 neuron in Virtual Fly Brain\") and [larval CCAP subesophageal IN-1 neuron](https://www.virtualflybrain.org/reports/FBbt_00111345 \"Open larval CCAP subesophageal IN-1 neuron in Virtual Fly Brain\"). There are also [2,598](https://v2.virtualflybrain.org/org.geppetto.frontend/geppetto?q=FBbt_00051068,NeuronsSynaptic \"Run in VFB: Neurons with synaptic terminals in subesophageal zone\") neurons with synaptic terminals in the subesophageal zone, such as [intrinsic antennal mechanosensory and motor center neuron](https://www.virtualflybrain.org/reports/FBbt_00111352 \"Open intrinsic antennal mechanosensory and motor center neuron in Virtual Fly Brain\") and [AMMC-VLP](https://www.virtualflybrain.org/reports/FBbt_00111354 \"Open AMMC-VLP in Virtual Fly Brain\").\n\nVFB holds 4,205 genetic tool/expression pattern rows for the subesophageal zone, including GAL4 drivers and binary/intersectional drivers like [P{GMR12D05-GAL4} expression pattern](https://www.virtualflybrain.org/reports/VFBexp_FBtp0057511 \"Open P{GMR12D05-GAL4} expression pattern in Virtual Fly Brain\") and [P{GMR16C05-GAL4} expression pattern](https://www.virtualflybrain.org/reports/VFBexp_FBtp0057869 \"Open P{GMR16C05-GAL4} expression pattern in Virtual Fly Brain\").\n\nThe connectome data indicates that there are neurons with presynaptic and postsynaptic terminals in the subesophageal zone, but the exact numbers are not provided in the current results.\n\nVFB has annotated [29,765](https://v2.virtualflybrain.org/org.geppetto.frontend/geppetto?q=FBbt_00051068,ImagesNeurons \"Run in VFB: Images of neurons with some part in subesophageal zone\") images of neurons with some part in the subesophageal zone, including [GMR 21B06 FLP 10-2](https://www.virtualflybrain.org/reports/VFB_00051256 \"Open GMR 21B06 FLP 10-2 in Virtual Fly Brain\") and [GMR 39C03 FLP 7-1](https://www.virtualflybrain.org/reports/VFB_00051225 \"Open GMR 39C03 FLP 7-1 in Virtual Fly Brain\").",
"quality_flags": {
"has_tool_status": true,
"no_tool_factual_answer": false,
@@ -3474,8 +3478,8 @@
"graph_failure_mentioned": false,
"missing_required_graph": false,
"used_data_resource": false,
- "response_chars": 1485,
- "status_count": 14
+ "response_chars": 2507,
+ "status_count": 13
}
},
{
@@ -3488,7 +3492,7 @@
"requires_graph": true,
"min_graphs": 1,
"repetition": 1,
- "duration_ms": 210798,
+ "duration_ms": 78618,
"status_messages": [
{
"message": "Thinking...",
@@ -3514,10 +3518,6 @@
"message": "Querying VFB",
"phase": "mcp"
},
- {
- "message": "Querying VFB",
- "phase": "mcp"
- },
{
"message": "Querying VFB connectivity",
"phase": "mcp"
@@ -3539,13 +3539,13 @@
"phase": "llm"
}
],
- "event_count": 223,
+ "event_count": 191,
"ok": true,
- "request_id": "72a97ec5-e321-402e-ba35-e4b4b288b72f",
- "response_id": "chatcmpl-cdb51e1c8742d9e40509e53e38cdafc6",
+ "request_id": "0051a721-2a3f-4513-9917-8c8600ae9fc3",
+ "response_id": "chatcmpl-83e89a150dc222d64ef858cd80fc718c",
"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, [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, 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. Specifically, the presynaptic terminals in the medulla are connected to 262 neuron types, and the postsynaptic terminals are connected to 333 neuron types. Some of the neuron types 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 neuron types 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.",
+ "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, [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, and [333](https://v2.virtualflybrain.org/org.geppetto.frontend/geppetto?q=FBbt_00003748,NeuronsPostsynapticHere \"Run in VFB: Neurons with postsynaptic terminals in medulla\") neuron types with postsynaptic terminals. The first 12 neuron types with presynaptic terminals 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.",
"graphs": [
{
"type": "basic_graph",
@@ -3692,8 +3692,8 @@
"graph_failure_mentioned": false,
"missing_required_graph": false,
"used_data_resource": false,
- "response_chars": 2156,
- "status_count": 12
+ "response_chars": 1994,
+ "status_count": 11
}
},
{
@@ -3706,7 +3706,7 @@
"requires_graph": false,
"min_graphs": 0,
"repetition": 1,
- "duration_ms": 127834,
+ "duration_ms": 5232,
"status_messages": [
{
"message": "Thinking...",
@@ -3739,8 +3739,8 @@
],
"event_count": 21,
"ok": true,
- "request_id": "956c98e7-5192-4c87-8348-d2ca20088095",
- "response_id": "chatcmpl-a2b3d985b04c644487086f1b0499f413",
+ "request_id": "62e97c16-c441-43a6-86e7-a6fc73b53478",
+ "response_id": "chatcmpl-346f1177aaf1af5c0da208c5c4cd231d",
"images_count": 0,
"graphs_count": 0,
"response": "Virtual Fly Brain is for the Drosophila research community.",
@@ -3768,7 +3768,7 @@
"requires_graph": false,
"min_graphs": 0,
"repetition": 1,
- "duration_ms": 15572,
+ "duration_ms": 7975,
"status_messages": [
{
"message": "Thinking...",
@@ -3795,13 +3795,13 @@
"phase": "llm"
}
],
- "event_count": 118,
+ "event_count": 63,
"ok": true,
- "request_id": "10768a00-fc58-4ddb-a822-ac6f64d98ccb",
- "response_id": "chatcmpl-d6d13c696aa61dbc00edd58710999ee7",
+ "request_id": "070820a9-1499-4ece-b073-7784c29d85a8",
+ "response_id": "chatcmpl-139ae0570a44709011ea0b63a5040bb6",
"images_count": 0,
"graphs_count": 0,
- "response": "To cite Virtual Fly Brain in a publication, use the citation VFB evidence on their website, including APA, MLA, Chicago, and BibTeX formats. If you use Virtual Fly Brain data, tools, or resources in your research, please cite their work using the citation formats below, which include a reference to Court et al., 2023, Virtual Fly Brain—An interactive atlas of the Drosophila nervous system, published in Frontiers in Physiology, https://doi.org/10.3389/fphys.2023.1076533.",
+ "response": "To cite Virtual Fly Brain in a publication, use the citation VFB evidence on the website, including APA, MLA, Chicago, and BibTeX formats. If you use Virtual Fly Brain data, tools, or resources in your research, please cite their work using the citation formats below.",
"quality_flags": {
"has_tool_status": true,
"no_tool_factual_answer": false,
@@ -3812,7 +3812,7 @@
"graph_failure_mentioned": false,
"missing_required_graph": false,
"used_data_resource": false,
- "response_chars": 474,
+ "response_chars": 268,
"status_count": 6
}
},
@@ -3826,7 +3826,7 @@
"requires_graph": false,
"min_graphs": 0,
"repetition": 1,
- "duration_ms": 15370,
+ "duration_ms": 6405,
"status_messages": [
{
"message": "Thinking...",
@@ -3853,13 +3853,13 @@
"phase": "llm"
}
],
- "event_count": 28,
+ "event_count": 25,
"ok": true,
- "request_id": "1f5bfe40-5ff6-42d7-913e-bdf18ab58e4f",
- "response_id": "chatcmpl-19e32ee44c08cbc30d2905e9769ce1ea",
+ "request_id": "06c94bea-cc50-4c3a-8129-a8bf7d2fd864",
+ "response_id": "chatcmpl-516da8e60aa6b8b967f90fd13e2ac444",
"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.",
+ "response": "Virtual Fly Brain is funded by multiple UK research councils and charitable foundations since 2009.",
"quality_flags": {
"has_tool_status": true,
"no_tool_factual_answer": false,
@@ -3870,7 +3870,7 @@
"graph_failure_mentioned": false,
"missing_required_graph": false,
"used_data_resource": false,
- "response_chars": 120,
+ "response_chars": 99,
"status_count": 6
}
},
@@ -3884,7 +3884,7 @@
"requires_graph": false,
"min_graphs": 0,
"repetition": 1,
- "duration_ms": 18245,
+ "duration_ms": 9670,
"status_messages": [
{
"message": "Thinking...",
@@ -3915,13 +3915,13 @@
"phase": "llm"
}
],
- "event_count": 113,
+ "event_count": 122,
"ok": true,
- "request_id": "b2fde9bb-1e53-4044-b8cd-fb9cec4a6743",
- "response_id": "chatcmpl-83de9a6979b53647c840cd3491fbb751",
+ "request_id": "68edab54-8503-408d-9f6f-7e97bdeed192",
+ "response_id": "chatcmpl-8cc57e022c446ef96efad85a24238165",
"images_count": 0,
"graphs_count": 0,
- "response": "Virtual Fly Brain's accessibility statement is in line with the Public Sector Bodies (Websites and Mobile Applications) (No. 2) Accessibility Regulations 2018. The University of Edinburgh is committed to making its websites and applications accessible, and Virtual Fly Brain is partially compliant with the Web Content Accessibility Guidelines (WCAG) 2.2 AA standard. Some features, such as 3D image stacks, neuron skeletons, and connectivity diagrams, cannot be made fully accessible without losing scientific meaning, and the limitations are documented.",
+ "response": "Virtual Fly Brain's accessibility statement is in line with the Public Sector Bodies (Websites and Mobile Applications) (No. 2) Accessibility Regulations 2018. The University of Edinburgh is committed to making its websites and applications accessible, and Virtual Fly Brain is partially compliant with the Web Content Accessibility Guidelines (WCAG) 2.2 AA standard. The website is designed to be accessible to as many people as possible, but some features, such as 3D image stacks, neuron skeletons, and connectivity diagrams, cannot be made fully accessible without losing scientific meaning.",
"quality_flags": {
"has_tool_status": true,
"no_tool_factual_answer": false,
@@ -3932,7 +3932,7 @@
"graph_failure_mentioned": false,
"missing_required_graph": false,
"used_data_resource": false,
- "response_chars": 555,
+ "response_chars": 595,
"status_count": 7
}
},
@@ -3946,7 +3946,7 @@
"requires_graph": false,
"min_graphs": 0,
"repetition": 1,
- "duration_ms": 18158,
+ "duration_ms": 9019,
"status_messages": [
{
"message": "Thinking...",
@@ -3973,13 +3973,13 @@
"phase": "llm"
}
],
- "event_count": 121,
+ "event_count": 101,
"ok": true,
- "request_id": "aaef7a60-dc1b-4ca3-a84f-c2e33d2dfa74",
- "response_id": "chatcmpl-049bd82d20818bf6b9b7faa94b88f6b2",
+ "request_id": "06922c9c-138a-459c-b64c-06749268e520",
+ "response_id": "chatcmpl-94fab8e7dde505a8321b1a36911587b9",
"images_count": 0,
"graphs_count": 0,
- "response": "To report a problem or contribute data to Virtual Fly Brain, users can get in touch with the team through the contact page. For help with using Virtual Fly Brain, comments, suggestions, or general questions, users can email support@virtualflybrain.org, which goes to the public support forum where questions and responses are visible to the community. Bug reports and feature requests can be made through GitHub Issues, allowing the development team to track and address technical problems efficiently. For data inclusion discussions, collaboration proposals, or confidential matters, users can email data@virtualflybrain.org.",
+ "response": "To report a problem or contribute data to Virtual Fly Brain, you can get in touch with the team through the contact page. For help with using Virtual Fly Brain, you can use the public support forum at support@virtualflybrain.org. To report technical issues, bugs, or request new features, you can use GitHub Issues. For data inclusion discussions, collaboration proposals, or confidential matters, you can contact the team via private email at data@virtualflybrain.org.",
"quality_flags": {
"has_tool_status": true,
"no_tool_factual_answer": false,
@@ -3990,7 +3990,7 @@
"graph_failure_mentioned": false,
"missing_required_graph": false,
"used_data_resource": false,
- "response_chars": 626,
+ "response_chars": 469,
"status_count": 6
}
},
@@ -4004,7 +4004,7 @@
"requires_graph": false,
"min_graphs": 0,
"repetition": 1,
- "duration_ms": 14708,
+ "duration_ms": 9805,
"status_messages": [
{
"message": "Thinking...",
@@ -4031,13 +4031,13 @@
"phase": "llm"
}
],
- "event_count": 94,
+ "event_count": 96,
"ok": true,
- "request_id": "28db3bab-d05b-4678-bec1-67489d927b2f",
- "response_id": "chatcmpl-f6ab8b1bef90887ec8b2f5fa1c99f88d",
+ "request_id": "1f833ae3-cca4-4532-9742-25623927ad02",
+ "response_id": "chatcmpl-67dc842723dba1e822cd2116e650f2bb",
"images_count": 0,
"graphs_count": 0,
- "response": "To use the 3D Viewer on the VFB website, select neurons or expression by point and click, rotate or move by click and drag with the mouse or use the directional icons, zoom in or out using the zoom icons or scroll with the mouse, and use the home icon to reset the view. The camera icon starts or stops a rotation animation of the scene, and the sphere icon toggles wireframes on or off.",
+ "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 the view. Use the zoom icons or scroll with the mouse to zoom in or out. The home button resets the view. Additionally, 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,
@@ -4048,7 +4048,7 @@
"graph_failure_mentioned": false,
"missing_required_graph": false,
"used_data_resource": false,
- "response_chars": 387,
+ "response_chars": 403,
"status_count": 6
}
},
@@ -4062,7 +4062,7 @@
"requires_graph": false,
"min_graphs": 0,
"repetition": 1,
- "duration_ms": 21570,
+ "duration_ms": 11274,
"status_messages": [
{
"message": "Thinking...",
@@ -4072,10 +4072,6 @@
"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"
@@ -4101,10 +4097,10 @@
"phase": "llm"
}
],
- "event_count": 59,
+ "event_count": 58,
"ok": true,
- "request_id": "bff80a03-cae9-4822-84ec-c18c22969dc5",
- "response_id": "chatcmpl-a4eb48cdc5c02675b47c8a3e31fea16e",
+ "request_id": "2736d90b-f27e-42da-98aa-0e80c16b59a5",
+ "response_id": "chatcmpl-af9ce4c3d9fa9e3466f04f0b9fd3364c",
"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.",
@@ -4119,7 +4115,7 @@
"missing_required_graph": false,
"used_data_resource": false,
"response_chars": 249,
- "status_count": 9
+ "status_count": 8
}
},
{
@@ -4132,7 +4128,7 @@
"requires_graph": false,
"min_graphs": 0,
"repetition": 1,
- "duration_ms": 26741,
+ "duration_ms": 12267,
"status_messages": [
{
"message": "Thinking...",
@@ -4163,13 +4159,13 @@
"phase": "llm"
}
],
- "event_count": 133,
+ "event_count": 132,
"ok": true,
- "request_id": "c9de49bd-a3dd-4826-bbb0-d015f4238e11",
- "response_id": "chatcmpl-4d943a73abc512cec57d6eca5f504f28",
+ "request_id": "d0f9f625-410f-4388-806a-a2bd70a85539",
+ "response_id": "chatcmpl-8d0ede4db875808955c0234f5ed83a25",
"images_count": 0,
"graphs_count": 0,
- "response": "NBLAST is a method to quantify morphological similarity. It works on \"dotprops\" which represent neurons as tangent vectors. For each tangent vector in the query neuron, NBLAST finds the closest tangent vector in the target neuron and calculates a score from the distance between and the dotproduct of the two vectors. The final NBLAST score is the sum over all query-target vector pairs. Typically, this score is normalized to a self-self comparison, with a perfect match scoring 1.\n\nAn NBLAST similarity score represents the degree of morphological similarity between two neurons, with higher scores indicating greater similarity.",
+ "response": "NBLAST is a method to quantify morphological similarity. It works on \"dotprops\" which represent neurons as tangent vectors. For each tangent vector in the query neuron, NBLAST finds the closest tangent vector in the target neuron and calculates a score from the distance between and the dotproduct of the two vectors. The final NBLAST score is the sum over all query-target vector pairs. Typically, this score is normalized to a self-self comparison, with a perfect match scoring 1. An NBLAST similarity score therefore measures how similar the morphology of two neurons is, with higher scores indicating greater similarity.",
"quality_flags": {
"has_tool_status": true,
"no_tool_factual_answer": false,
@@ -4180,7 +4176,7 @@
"graph_failure_mentioned": false,
"missing_required_graph": false,
"used_data_resource": false,
- "response_chars": 631,
+ "response_chars": 624,
"status_count": 7
}
},
@@ -4194,7 +4190,7 @@
"requires_graph": false,
"min_graphs": 0,
"repetition": 1,
- "duration_ms": 17732,
+ "duration_ms": 14221,
"status_messages": [
{
"message": "Thinking...",
@@ -4204,10 +4200,6 @@
"message": "Planning the answer",
"phase": "llm"
},
- {
- "message": "Resolving 1 term in VFB",
- "phase": "mcp"
- },
{
"message": "Reading VFB documentation",
"phase": "mcp"
@@ -4225,13 +4217,13 @@
"phase": "llm"
}
],
- "event_count": 78,
+ "event_count": 63,
"ok": true,
- "request_id": "acf31592-521a-4323-aed0-a5f18280ef7d",
- "response_id": "chatcmpl-835b6e947f5f37d3a44834d3f6c86223",
+ "request_id": "2bd6efa0-3d86-425c-a777-b9deea19b026",
+ "response_id": "chatcmpl-efdfbbb1286750218b8abd5055bf71af",
"images_count": 0,
"graphs_count": 0,
- "response": "Confidence values on Virtual Fly Brain represent the source study's own confidence score for predictions, such as predicted neurotransmitters, and should be read against the publication it came from rather than compared across datasets. The value shown is the source study’s own confidence score, carried through unchanged, with each study defining its own scale and threshold for calling a prediction.",
+ "response": "Confidence values on Virtual Fly Brain represent the source study's own confidence score for predictions, such as predicted neurotransmitters. These values should be read against the publication they came from, rather than compared across datasets, as each study defines its own scale and threshold for calling a prediction.",
"quality_flags": {
"has_tool_status": true,
"no_tool_factual_answer": false,
@@ -4242,8 +4234,8 @@
"graph_failure_mentioned": false,
"missing_required_graph": false,
"used_data_resource": false,
- "response_chars": 402,
- "status_count": 7
+ "response_chars": 324,
+ "status_count": 6
}
},
{
@@ -4256,7 +4248,7 @@
"requires_graph": false,
"min_graphs": 0,
"repetition": 1,
- "duration_ms": 14714,
+ "duration_ms": 8648,
"status_messages": [
{
"message": "Thinking...",
@@ -4287,13 +4279,13 @@
"phase": "llm"
}
],
- "event_count": 35,
+ "event_count": 50,
"ok": true,
- "request_id": "948ed702-5ebd-4c09-9f1d-6d5e56c8ceed",
- "response_id": "chatcmpl-38b10891261d346470ad377b358a1951",
+ "request_id": "39ed2342-4d07-4763-9353-4b28e93bed33",
+ "response_id": "chatcmpl-fdaddd1a011ce8700358316fdc1d1c87",
"images_count": 8,
"graphs_count": 0,
- "response": "Bridging registrations are transformations that map one template onto another, allowing data registered to different templates to be compared in a common space.",
+ "response": "Bridging registrations are transformations that map one template onto another, allowing data registered to different templates to be compared in a common space. The name \"bridging registrations\" could not be matched in VFB.",
"quality_flags": {
"has_tool_status": true,
"no_tool_factual_answer": false,
@@ -4304,7 +4296,7 @@
"graph_failure_mentioned": false,
"missing_required_graph": false,
"used_data_resource": false,
- "response_chars": 160,
+ "response_chars": 223,
"status_count": 7
}
},
@@ -4318,7 +4310,7 @@
"requires_graph": false,
"min_graphs": 0,
"repetition": 1,
- "duration_ms": 14592,
+ "duration_ms": 8087,
"status_messages": [
{
"message": "Thinking...",
@@ -4345,13 +4337,13 @@
"phase": "llm"
}
],
- "event_count": 96,
+ "event_count": 94,
"ok": true,
- "request_id": "901ada14-a46e-4323-a0be-36775acbb357",
- "response_id": "chatcmpl-3c89c1424e25ac8e536eecfb4c0aaba7",
+ "request_id": "c9376840-558e-4ede-a4ce-4e1d4086b397",
+ "response_id": "chatcmpl-59a9088f0427df9300a79a0e94a89ec0",
"images_count": 0,
"graphs_count": 0,
- "response": "Virtual Fly Brain holds light microscopy data, including confocal image stacks from over a hundred studies, which are registered onto standard templates. The data types include driver expression patterns, split-GAL4 combinations, expression pattern fragments, single neurons, clones or lineages, and painted domains. The brain templates used are JRC2018Unisex, JRC2018UnisexVNC, JFRC2, and Court2018 VNS.",
+ "response": "Virtual Fly Brain holds light microscopy data, including confocal image stacks from over a hundred studies, registered onto standard templates. The data types include driver expression patterns, split-GAL4 combinations, expression pattern fragments, single neurons, clones or lineages, and painted domains. The brain templates used are JRC2018Unisex, JRC2018UnisexVNC, JFRC2, and Court2018 VNS.",
"quality_flags": {
"has_tool_status": true,
"no_tool_factual_answer": false,
@@ -4362,7 +4354,7 @@
"graph_failure_mentioned": false,
"missing_required_graph": false,
"used_data_resource": false,
- "response_chars": 404,
+ "response_chars": 394,
"status_count": 6
}
},
@@ -4403,7 +4395,7 @@
"requires_graph": false,
"min_graphs": 0,
"repetition": 1,
- "duration_ms": 12374,
+ "duration_ms": 6341,
"status_messages": [
{
"message": "Thinking...",
@@ -4432,8 +4424,8 @@
],
"event_count": 31,
"ok": true,
- "request_id": "8638d7df-58f1-4303-9a4e-4847cf693d99",
- "response_id": "chatcmpl-5fa74d0031e7c5e881bcd553caf28bdd",
+ "request_id": "bd3ca570-ca5a-4cf8-b335-a37556e69fb1",
+ "response_id": "chatcmpl-354def3e417ea15d1fd60351e6d519e5",
"images_count": 0,
"graphs_count": 0,
"response": "To install and get started with VFB-connect in Python, you can install it via PyPi using the command\n```\npip install vfb-connect\n```",
@@ -4461,7 +4453,7 @@
"requires_graph": false,
"min_graphs": 0,
"repetition": 1,
- "duration_ms": 15178,
+ "duration_ms": 9945,
"status_messages": [
{
"message": "Thinking...",
@@ -4488,13 +4480,13 @@
"phase": "llm"
}
],
- "event_count": 69,
+ "event_count": 120,
"ok": true,
- "request_id": "67f2f06c-2150-4a5f-965f-2d381d9693f3",
- "response_id": "chatcmpl-1028cecd21a1993303bada6058dfb61a",
+ "request_id": "3fd0404c-d504-4d5e-851b-d44f52218e7e",
+ "response_id": "chatcmpl-20b90b2d64c8f5826171d9e038126c34",
"images_count": 0,
"graphs_count": 0,
- "response": "To query Virtual Fly Brain programmatically, you can use the SOLR Search API or the Owlery API. The Owlery API provides OWL reasoning services, including Description Logic (DL) queries and SPARQL queries with OWL reasoning, and its base URL is https://owl.virtualflybrain.org/.",
+ "response": "To query Virtual Fly Brain programmatically, you can use the Owlery API or the SOLR API. The Owlery API provides OWL reasoning services, including Description Logic (DL) queries and SPARQL queries with OWL reasoning. The base URL for the Owlery API is https://owl.virtualflybrain.org/. You can use the API to perform various queries, such as getting subclasses, superclasses, equivalent classes, and instances of a class. You can also use the SPARQL query endpoint to perform SPARQL queries with OWL reasoning.",
"quality_flags": {
"has_tool_status": true,
"no_tool_factual_answer": false,
@@ -4505,7 +4497,7 @@
"graph_failure_mentioned": false,
"missing_required_graph": false,
"used_data_resource": false,
- "response_chars": 277,
+ "response_chars": 510,
"status_count": 6
}
},
@@ -4519,7 +4511,7 @@
"requires_graph": false,
"min_graphs": 0,
"repetition": 1,
- "duration_ms": 15853,
+ "duration_ms": 10869,
"status_messages": [
{
"message": "Thinking...",
@@ -4550,13 +4542,13 @@
"phase": "llm"
}
],
- "event_count": 102,
+ "event_count": 117,
"ok": true,
- "request_id": "d3e87903-7625-4d90-8584-2cfe94367e88",
- "response_id": "chatcmpl-9bc4946ac589b1eacc073cd886e0e7c6",
+ "request_id": "d2877537-4ff9-41b6-994a-139750c1c09e",
+ "response_id": "chatcmpl-177cb456855a746ca0018986908b8766",
"images_count": 0,
"graphs_count": 0,
- "response": "To explore Virtual Fly Brain neurons, you can use the navis Python package, which provides functions for analyzing, manipulating, and visualizing neurons. You can load example neurons using `navis.example_neurons()` and access their properties, such as `id`, `nodes`, `cable_length`, and `soma`. You can also create a `NeuronList` to work with multiple neurons at a time. VFB's documentation does not appear to cover pymaid.",
+ "response": "To explore Virtual Fly Brain neurons, you can use the tutorials provided on the Virtual Fly Brain website. Additionally, you can use the navis Python package, which provides functions for analyzing, manipulating, and visualizing neurons. You can load example neurons using `navis.example_neurons()` and access their properties, such as `id`, `nodes`, `cable_length`, and `soma`. You can also create a `NeuronList` to work with multiple neurons at a time. VFB's documentation does not appear to cover pymaid.",
"quality_flags": {
"has_tool_status": true,
"no_tool_factual_answer": false,
@@ -4567,7 +4559,7 @@
"graph_failure_mentioned": false,
"missing_required_graph": false,
"used_data_resource": false,
- "response_chars": 424,
+ "response_chars": 507,
"status_count": 7
}
},
@@ -4581,7 +4573,7 @@
"requires_graph": false,
"min_graphs": 0,
"repetition": 1,
- "duration_ms": 12506,
+ "duration_ms": 7856,
"status_messages": [
{
"message": "Thinking...",
@@ -4608,13 +4600,13 @@
"phase": "llm"
}
],
- "event_count": 95,
+ "event_count": 92,
"ok": true,
- "request_id": "033b17b3-ead7-484c-b801-d0c6fa5a3d9d",
- "response_id": "chatcmpl-2d9a3a9bed10ba0c48e43bbb60a6ead1",
+ "request_id": "b5c30fc3-ca6e-4dfe-b37c-0ab60f5dbf5c",
+ "response_id": "chatcmpl-16dca0316bd645bae8aec43620f3f96e",
"images_count": 0,
"graphs_count": 0,
- "response": "To use the Virtual Fly Brain Model Context Protocol (MCP) tool, access it at https://vfb3-mcp.virtualflybrain.org, and configure your client to connect to this URL. You can then ask your AI assistant questions like \"Get information about the neuron \" or \"Search for terms related to medulla in the fly brain\" to query VFB data through Large Language Models.",
+ "response": "To use the Virtual Fly Brain Model Context Protocol (MCP) tool, access it at https://vfb3-mcp.virtualflybrain.org. Configure your client to connect to this URL, then ask your AI assistant questions like \"Get information about the neuron \" or \"Search for terms related to medulla in the fly brain\" to query VFB data through Large Language Models.",
"quality_flags": {
"has_tool_status": true,
"no_tool_factual_answer": false,
@@ -4625,7 +4617,7 @@
"graph_failure_mentioned": false,
"missing_required_graph": false,
"used_data_resource": false,
- "response_chars": 357,
+ "response_chars": 345,
"status_count": 6
}
},
@@ -4639,7 +4631,7 @@
"requires_graph": false,
"min_graphs": 0,
"repetition": 1,
- "duration_ms": 5698,
+ "duration_ms": 5226,
"status_messages": [
{
"message": "Thinking...",
@@ -4649,6 +4641,10 @@
"message": "Planning the answer",
"phase": "llm"
},
+ {
+ "message": "Resolving 1 term in VFB",
+ "phase": "mcp"
+ },
{
"message": "Reading VFB term info",
"phase": "mcp"
@@ -4666,13 +4662,13 @@
"phase": "llm"
}
],
- "event_count": 29,
+ "event_count": 43,
"ok": true,
- "request_id": "d69488b3-badd-423f-b9b1-0543795f84e9",
- "response_id": "chatcmpl-3f4fb58811b83a3ca1d47832ee452e36",
+ "request_id": "fc5798a1-17da-4f93-9a71-f9e913237ecc",
+ "response_id": "chatcmpl-12713c19c1068f3d89447507644205f0",
"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.",
+ "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 on this topic.",
"quality_flags": {
"has_tool_status": true,
"no_tool_factual_answer": false,
@@ -4683,8 +4679,8 @@
"graph_failure_mentioned": false,
"missing_required_graph": false,
"used_data_resource": false,
- "response_chars": 114,
- "status_count": 6
+ "response_chars": 188,
+ "status_count": 7
}
},
{
@@ -4697,7 +4693,7 @@
"requires_graph": false,
"min_graphs": 0,
"repetition": 1,
- "duration_ms": 10871,
+ "duration_ms": 6783,
"status_messages": [
{
"message": "Thinking...",
@@ -4730,8 +4726,8 @@
],
"event_count": 40,
"ok": true,
- "request_id": "67065dc9-56c2-49c4-b9cf-e3ca106d777c",
- "response_id": "chatcmpl-8342406c4cce562e477aa93a5e6cd98e",
+ "request_id": "e08b496e-2129-4705-b3a5-228f3ea83b2b",
+ "response_id": "chatcmpl-6a4cf7ce453599391733d7405476b295",
"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.",
@@ -4759,7 +4755,7 @@
"requires_graph": false,
"min_graphs": 0,
"repetition": 1,
- "duration_ms": 12306,
+ "duration_ms": 7646,
"status_messages": [
{
"message": "Thinking...",
@@ -4790,13 +4786,13 @@
"phase": "llm"
}
],
- "event_count": 74,
+ "event_count": 64,
"ok": true,
- "request_id": "b689233b-8314-47df-909e-d03bdf6625cc",
- "response_id": "chatcmpl-4f74d6d5e028b95e7c103c2d8d98ad1a",
+ "request_id": "e20dcef1-09b2-4048-b477-c4153d2690b5",
+ "response_id": "chatcmpl-e02df58d96a959dc31642c786bd1ed04",
"images_count": 0,
"graphs_count": 0,
- "response": "Materials from the Virtual Fly Brain \"Hacking the connectome\" workshop include tutorials, workshop notebooks, recorded introduction sessions, and tools such as NBLAST, VFBconnect, and Navis. The workshop covered topics including introduction to connectomic data and tools, tool landscape, discovery, mapping, visualization, and connectomics.",
+ "response": "Materials from the VFB 'Hacking the connectome' workshop are available. The workshop materials include tutorials, workshop notebooks, and recorded introduction sessions, covering topics such as introduction to connectomic data and tools, tool landscape, discovery, mapping, visualisation, and connectomics.",
"quality_flags": {
"has_tool_status": true,
"no_tool_factual_answer": false,
@@ -4807,7 +4803,7 @@
"graph_failure_mentioned": false,
"missing_required_graph": false,
"used_data_resource": false,
- "response_chars": 341,
+ "response_chars": 306,
"status_count": 7
}
},
@@ -4821,7 +4817,7 @@
"requires_graph": false,
"min_graphs": 0,
"repetition": 1,
- "duration_ms": 23657,
+ "duration_ms": 18705,
"status_messages": [
{
"message": "Thinking...",
@@ -4831,6 +4827,10 @@
"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"
@@ -4856,13 +4856,13 @@
"phase": "llm"
}
],
- "event_count": 91,
+ "event_count": 86,
"ok": true,
- "request_id": "c59360e1-d9b2-4007-891f-673ae6ef1365",
- "response_id": "chatcmpl-d9228628c8e78bb78b10e67420631684",
+ "request_id": "ae2ce7c5-1c56-438a-b9ed-78a6aa2506a7",
+ "response_id": "chatcmpl-f9bf4497995bf4e2cdf36a4109b22196",
"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 the FAFB dataset. The FAFB CATMAID dataset is hosted at https://fafb.catmaid.virtualflybrain.org and contains EM reconstructed neurons from Dolan et al., 2019.",
+ "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 and FANC datasets. The name \"FANC\" could not be matched, with closest records found including Fancl, FANCI, and Fancm.",
"quality_flags": {
"has_tool_status": true,
"no_tool_factual_answer": false,
@@ -4873,8 +4873,8 @@
"graph_failure_mentioned": false,
"missing_required_graph": false,
"used_data_resource": false,
- "response_chars": 353,
- "status_count": 8
+ "response_chars": 317,
+ "status_count": 9
}
},
{
@@ -4887,7 +4887,7 @@
"requires_graph": false,
"min_graphs": 0,
"repetition": 1,
- "duration_ms": 7848,
+ "duration_ms": 5751,
"status_messages": [
{
"message": "Thinking...",
@@ -4920,8 +4920,8 @@
],
"event_count": 22,
"ok": true,
- "request_id": "aa3dcadb-a14c-48d7-9076-c3546f0c279e",
- "response_id": "chatcmpl-5723f662acc4b40e7d23b4bf221b8cfa",
+ "request_id": "09ded804-45dd-4a9e-99ff-f6a8dd5afd42",
+ "response_id": "chatcmpl-51da78de1c54142150e068e9b8823c7a",
"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.",
@@ -4949,7 +4949,7 @@
"requires_graph": false,
"min_graphs": 0,
"repetition": 1,
- "duration_ms": 16150,
+ "duration_ms": 10739,
"status_messages": [
{
"message": "Thinking...",
@@ -4988,7 +4988,7 @@
"question": "What is the medulla?",
"focus": null,
"clicked": null,
- "duration_ms": 7793,
+ "duration_ms": 5179,
"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": [
@@ -5047,7 +5047,7 @@
"question": "Which neurons receive output from it?",
"focus": null,
"clicked": null,
- "duration_ms": 8357,
+ "duration_ms": 5560,
"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": [
@@ -5114,8 +5114,8 @@
}
],
"ok": true,
- "request_id": "ce9527e3-f61d-4500-b5d9-ac2072e2a50c",
- "response_id": "chatcmpl-2a4c52ad1c76eb21f13529a186af5bed",
+ "request_id": "193423c0-8df4-4536-8cd4-f0a21eef6736",
+ "response_id": "chatcmpl-0e278ca7d56857d5e63b83755e7d5cd7",
"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.",
@@ -5136,7 +5136,7 @@
"unmatched_claim_after_resolve": false,
"repeats_answered_question": false,
"slow_followup_turn": false,
- "slowest_followup_ms": 8357
+ "slowest_followup_ms": 5560
}
},
{
@@ -5149,7 +5149,7 @@
"requires_graph": false,
"min_graphs": 0,
"repetition": 1,
- "duration_ms": 209602,
+ "duration_ms": 21839,
"status_messages": [
{
"message": "Thinking...",
@@ -5184,7 +5184,7 @@
"phase": "llm"
}
],
- "event_count": 252,
+ "event_count": 201,
"conversation": true,
"turns": [
{
@@ -5192,7 +5192,7 @@
"question": "What is the mushroom body?",
"focus": null,
"clicked": null,
- "duration_ms": 16160,
+ "duration_ms": 12095,
"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. The mushroom body also has a compartmental organisation, with the dendrites of mushroom body output neurons and the axon terminals of dopaminergic neurons tiling the lobes into a stereotyped grid of 15 compartments.",
"followons": [
@@ -5254,9 +5254,9 @@
"query_type": "ImagesNeurons"
},
"clicked": 0,
- "duration_ms": 193442,
+ "duration_ms": 9743,
"ok": true,
- "response": "Images of neurons with some part in the [mushroom body](https://www.virtualflybrain.org/reports/FBbt_00005801 \"Open mushroom body in Virtual Fly Brain\") are available, with [27,619](https://v2.virtualflybrain.org/org.geppetto.frontend/geppetto?q=FBbt_00005801,ImagesNeurons \"Run in VFB: Images of neurons with some part in mushroom body\") images of neurons. The first 12 images, along with their VFB ids, include 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. Additionally, there are [602](https://v2.virtualflybrain.org/org.geppetto.frontend/geppetto?q=FBbt_00005801,NeuronsPartHere \"Run in VFB: Neurons with some part in mushroom body\") neurons with some part in the mushroom body, including [adult odd neuron of the calyx](https://www.virtualflybrain.org/reports/FBbt_00111628 \"Open adult odd neuron of the calyx in Virtual Fly Brain\"), [larval uniglomerular projection neuron 63a](https://www.virtualflybrain.org/reports/FBbt_00111675 \"Open larval uniglomerular projection neuron 63a in Virtual Fly Brain\"), [larval uniglomerular projection neuron 67b](https://www.virtualflybrain.org/reports/FBbt_00111684 \"Open larval uniglomerular projection neuron 67b in Virtual Fly Brain\"), and others.",
+ "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",
@@ -5321,11 +5321,11 @@
}
],
"ok": true,
- "request_id": "229267ad-b129-44b0-8e57-195215ed5bc0",
- "response_id": "chatcmpl-d41115ba92e17c49bf344b44abffd6c3",
+ "request_id": "4e4bcbf2-9f6a-46c5-a25a-d5b22ea47c5e",
+ "response_id": "chatcmpl-f7e5fbf32548e6e0f1f1457a0fb2cd94",
"images_count": 8,
"graphs_count": 0,
- "response": "Images of neurons with some part in the [mushroom body](https://www.virtualflybrain.org/reports/FBbt_00005801 \"Open mushroom body in Virtual Fly Brain\") are available, with [27,619](https://v2.virtualflybrain.org/org.geppetto.frontend/geppetto?q=FBbt_00005801,ImagesNeurons \"Run in VFB: Images of neurons with some part in mushroom body\") images of neurons. The first 12 images, along with their VFB ids, include 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. Additionally, there are [602](https://v2.virtualflybrain.org/org.geppetto.frontend/geppetto?q=FBbt_00005801,NeuronsPartHere \"Run in VFB: Neurons with some part in mushroom body\") neurons with some part in the mushroom body, including [adult odd neuron of the calyx](https://www.virtualflybrain.org/reports/FBbt_00111628 \"Open adult odd neuron of the calyx in Virtual Fly Brain\"), [larval uniglomerular projection neuron 63a](https://www.virtualflybrain.org/reports/FBbt_00111675 \"Open larval uniglomerular projection neuron 63a in Virtual Fly Brain\"), [larval uniglomerular projection neuron 67b](https://www.virtualflybrain.org/reports/FBbt_00111684 \"Open larval uniglomerular projection neuron 67b in Virtual Fly Brain\"), and others.",
+ "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,
@@ -5336,14 +5336,14 @@
"graph_failure_mentioned": false,
"missing_required_graph": false,
"used_data_resource": false,
- "response_chars": 1384,
+ "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": true,
- "slowest_followup_ms": 193442
+ "slow_followup_turn": false,
+ "slowest_followup_ms": 9743
}
},
{
@@ -5356,7 +5356,7 @@
"requires_graph": false,
"min_graphs": 0,
"repetition": 1,
- "duration_ms": 36869,
+ "duration_ms": 385480,
"status_messages": [
{
"message": "Thinking...",
@@ -5378,12 +5378,20 @@
"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": 130,
+ "event_count": 247,
"conversation": true,
"turns": [
{
@@ -5391,9 +5399,9 @@
"question": "What is the fan-shaped body?",
"focus": null,
"clicked": null,
- "duration_ms": 9394,
+ "duration_ms": 6817,
"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.",
+ "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 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",
@@ -5450,9 +5458,9 @@
"question": "What about the ellipsoid body?",
"focus": null,
"clicked": null,
- "duration_ms": 15605,
+ "duration_ms": 188462,
"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.",
+ "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\").",
"followons": [
{
"id": "FBbt_00003678",
@@ -5517,9 +5525,9 @@
"question": "Which neurons have synaptic terminals in the fan-shaped body?",
"focus": null,
"clicked": null,
- "duration_ms": 11870,
+ "duration_ms": 190201,
"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 results from the VFB \"NeuronsSynaptic\" query 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\"); and [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\"), and [PFNd_PB5](https://www.virtualflybrain.org/reports/FBbt_00111394 \"Open PFNd_PB5 in Virtual Fly Brain\"). The first 12 results from VFB's \"NeuronsSynaptic\" query 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\"), and [PFL2](https://www.virtualflybrain.org/reports/FBbt_00111451 \"Open PFL2 in Virtual Fly Brain\"). Additionally, VFB's \"Neurons with presynaptic terminals in fan-shaped body\" query returns [102](https://v2.virtualflybrain.org/org.geppetto.frontend/geppetto?q=FBbt_00003679,NeuronsPresynapticHere \"Run in VFB: Neurons with presynaptic terminals in fan-shaped body\") results, including PFNd_PB2, PFNd_PB3, PFNd_PB5, PFNa_PB4, PFNa_PB5, 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.",
"followons": [
{
"id": "FBbt_00003679",
@@ -5536,11 +5544,6 @@
"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",
@@ -5550,6 +5553,11 @@
"id": "FBbt_00003679",
"query_type": "PartsOf",
"query": "What are the anatomical parts of the fan-shaped body?"
+ },
+ {
+ "id": "FBbt_00003679",
+ "query_type": "LineageClonesIn",
+ "query": "Which lineage clones are found in the fan-shaped body?"
}
],
"context_terms": [
@@ -5578,20 +5586,25 @@
"id": "FBbt_00003679",
"query_type": "NeuronsSynaptic",
"fn": "get_neurons_with_synapses_in"
+ },
+ {
+ "id": "FBbt_00003679",
+ "query_type": "NeuronsPresynapticHere",
+ "fn": "get_neurons_with_presynaptic_terminals_in"
}
],
"unmapped": []
},
- "status_count": 6,
+ "status_count": 8,
"problems": []
}
],
"ok": true,
- "request_id": "b77fed79-1df2-4b21-8595-1873668bde82",
- "response_id": "chatcmpl-4961cdc1ffb55c86061e0bc522ab18d4",
+ "request_id": "1cd1410a-6853-4ab5-8533-eb51206c919e",
+ "response_id": "chatcmpl-37656374d84a60607045f57ffb030b47",
"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 results from the VFB \"NeuronsSynaptic\" query 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\"); and [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\"), and [PFNd_PB5](https://www.virtualflybrain.org/reports/FBbt_00111394 \"Open PFNd_PB5 in Virtual Fly Brain\"). The first 12 results from VFB's \"NeuronsSynaptic\" query 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\"), and [PFL2](https://www.virtualflybrain.org/reports/FBbt_00111451 \"Open PFL2 in Virtual Fly Brain\"). Additionally, VFB's \"Neurons with presynaptic terminals in fan-shaped body\" query returns [102](https://v2.virtualflybrain.org/org.geppetto.frontend/geppetto?q=FBbt_00003679,NeuronsPresynapticHere \"Run in VFB: Neurons with presynaptic terminals in fan-shaped body\") results, including PFNd_PB2, PFNd_PB3, PFNd_PB5, PFNa_PB4, PFNa_PB5, 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.",
"quality_flags": {
"has_tool_status": true,
"no_tool_factual_answer": false,
@@ -5602,14 +5615,14 @@
"graph_failure_mentioned": false,
"missing_required_graph": false,
"used_data_resource": false,
- "response_chars": 1319,
- "status_count": 6,
+ "response_chars": 2150,
+ "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": 15605
+ "slow_followup_turn": true,
+ "slowest_followup_ms": 190201
}
},
{
@@ -5622,7 +5635,7 @@
"requires_graph": false,
"min_graphs": 0,
"repetition": 1,
- "duration_ms": 17166,
+ "duration_ms": 11871,
"status_messages": [
{
"message": "Thinking...",
@@ -5657,9 +5670,9 @@
"question": "What is a Kenyon cell?",
"focus": null,
"clicked": null,
- "duration_ms": 6424,
+ "duration_ms": 4820,
"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 and a type of neuron in the olfactory pathway of Drosophila.",
+ "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.",
"followons": [
{
"id": "FBbt_00003686",
@@ -5716,7 +5729,7 @@
"question": "What are its subtypes?",
"focus": null,
"clicked": null,
- "duration_ms": 10742,
+ "duration_ms": 7051,
"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": [
@@ -5773,8 +5786,8 @@
}
],
"ok": true,
- "request_id": "5a186034-51fd-439d-a6a0-be0f4f27d9c1",
- "response_id": "chatcmpl-f5266772c6b3b0c2e66024ea9a832793",
+ "request_id": "8a1b55da-26c0-4ced-aa57-21f4bd2095cd",
+ "response_id": "chatcmpl-ca680219e702fe57e990f57a743eb0e3",
"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.",
@@ -5795,7 +5808,7 @@
"unmatched_claim_after_resolve": false,
"repeats_answered_question": false,
"slow_followup_turn": false,
- "slowest_followup_ms": 10742
+ "slowest_followup_ms": 7051
}
},
{
@@ -5808,7 +5821,7 @@
"requires_graph": false,
"min_graphs": 0,
"repetition": 1,
- "duration_ms": 35130,
+ "duration_ms": 33633,
"status_messages": [
{
"message": "Thinking...",
@@ -5851,7 +5864,7 @@
"phase": "llm"
}
],
- "event_count": 112,
+ "event_count": 60,
"conversation": true,
"turns": [
{
@@ -5859,9 +5872,9 @@
"question": "What are the anatomical parts of the medulla? List them.",
"focus": null,
"clicked": null,
- "duration_ms": 13968,
+ "duration_ms": 8426,
"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. 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.",
+ "response": "The [medulla](https://www.virtualflybrain.org/reports/FBbt_00003748 \"Open medulla in Virtual Fly Brain\") is divided into 10 layers: 1-6 make up the outer (distal) medulla, the seventh (or serpentine) layer exhibits a distinct architecture and layers 8-10 make up the inner (proximal) medulla. Anatomical parts of the medulla include adult chandelier glial cell, adult distal medulla astrocyte-like glial cell, [distal medulla glial cell](https://www.virtualflybrain.org/reports/FBbt_00100528 \"Open distal medulla glial cell in Virtual Fly Brain\"), medulla layer, adult distal medulla ensheathing glial cell, [plexiform medulla](https://www.virtualflybrain.org/reports/FBbt_00045001 \"Open plexiform medulla in Virtual Fly Brain\"), [medulla dorsal rim area](https://www.virtualflybrain.org/reports/FBbt_00045002 \"Open medulla dorsal rim area in Virtual Fly Brain\"), medulla layer M1, medulla layer M5, inner medulla, medulla layer M8, and medulla layer M9.",
"followons": [
{
"id": "FBbt_00003748",
@@ -5924,9 +5937,9 @@
"question": "And which neurons have part of their arbour there?",
"focus": null,
"clicked": null,
- "duration_ms": 21162,
+ "duration_ms": 25207,
"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\"), and others, with a total of [471](https://v2.virtualflybrain.org/org.geppetto.frontend/geppetto?q=FBbt_00003748,NeuronsPartHere \"Run in VFB: Neurons with some part in medulla\") neuron types.",
"followons": [
{
"id": "FBbt_00003748",
@@ -5996,11 +6009,11 @@
}
],
"ok": true,
- "request_id": "a6fa73d0-ec1d-42e9-bb8a-746c841375ba",
- "response_id": "chatcmpl-872942ed75e7411960fcb52272702f62",
+ "request_id": "1eeeefac-7f95-4f0f-9e01-5601cb8480ff",
+ "response_id": "chatcmpl-6654660f687bfe15120568e52dee87d8",
"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\"), and others, with a total of [471](https://v2.virtualflybrain.org/org.geppetto.frontend/geppetto?q=FBbt_00003748,NeuronsPartHere \"Run in VFB: Neurons with some part in medulla\") neuron types.",
"quality_flags": {
"has_tool_status": true,
"no_tool_factual_answer": false,
@@ -6011,14 +6024,14 @@
"graph_failure_mentioned": false,
"missing_required_graph": false,
"used_data_resource": false,
- "response_chars": 1287,
+ "response_chars": 875,
"status_count": 10,
"addressless_followon": false,
"context_lost_across_turn": false,
"unmatched_claim_after_resolve": false,
"repeats_answered_question": false,
"slow_followup_turn": false,
- "slowest_followup_ms": 21162
+ "slowest_followup_ms": 25207
}
},
{
@@ -6031,7 +6044,7 @@
"requires_graph": false,
"min_graphs": 0,
"repetition": 1,
- "duration_ms": 34530,
+ "duration_ms": 31710,
"status_messages": [
{
"message": "Thinking...",
@@ -6066,7 +6079,7 @@
"phase": "llm"
}
],
- "event_count": 277,
+ "event_count": 276,
"conversation": true,
"turns": [
{
@@ -6074,9 +6087,9 @@
"question": "Tell me about the antennal lobe.",
"focus": null,
"clicked": null,
- "duration_ms": 16471,
+ "duration_ms": 23785,
"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 and 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.",
+ "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 and is the main target for innervation from the antennal nerve. 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. The Virtual Fly Brain web application allows users to search for synaptic input in the antennal lobe.",
"followons": [
{
"id": "FBbt_00003924",
@@ -6133,9 +6146,9 @@
"question": "Which neurons innervate it?",
"focus": null,
"clicked": null,
- "duration_ms": 18059,
+ "duration_ms": 7925,
"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. These 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\"), [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, which are among the [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. Additionally, neurons such as [AMMC-Bi16](https://www.virtualflybrain.org/reports/FBbt_00111480 \"Open AMMC-Bi16 in Virtual Fly Brain\"), [adult antennal lobe projection neuron DL5](https://www.virtualflybrain.org/reports/FBbt_00059280 \"Open adult antennal lobe projection neuron DL5 in Virtual Fly Brain\"), adult antennal lobe projection neuron DM4, adult antennal lobe projection neuron VA1d, adult antennal lobe projection neuron VL1, adult antennal lobe projection neuron VL2a, adult antennal lobe projection neuron VM2, adult antennal lobe projection neuron VM4, and adult multiglomerular antennal lobe projection neuron L1 adPN are among the [673](https://v2.virtualflybrain.org/org.geppetto.frontend/geppetto?q=FBbt_00003924,NeuronsSynaptic \"Run in VFB: Neurons with synaptic terminals in antennal lobe\") neurons with synaptic terminals in the antennal lobe.",
+ "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, which are among the [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. Additionally, neurons such as [AMMC-Bi16](https://www.virtualflybrain.org/reports/FBbt_00111480 \"Open AMMC-Bi16 in Virtual Fly Brain\"), [adult antennal lobe projection neuron DL5](https://www.virtualflybrain.org/reports/FBbt_00059280 \"Open adult antennal lobe projection neuron DL5 in Virtual Fly Brain\"), adult antennal lobe projection neuron DM4, adult antennal lobe projection neuron VA1d, adult antennal lobe projection neuron VL1, adult antennal lobe projection neuron VL2a, adult antennal lobe projection neuron VM2, adult antennal lobe projection neuron VM4, and adult multiglomerular antennal lobe projection neuron L1 adPN are among the [673](https://v2.virtualflybrain.org/org.geppetto.frontend/geppetto?q=FBbt_00003924,NeuronsSynaptic \"Run in VFB: Neurons with synaptic terminals in antennal lobe\") neurons with synaptic terminals in the antennal lobe.",
"followons": [
{
"id": "FBbt_00003924",
@@ -6200,11 +6213,11 @@
}
],
"ok": true,
- "request_id": "ee61afde-2225-4023-bdc5-255745ac5741",
- "response_id": "chatcmpl-19b94d3833e93edb1d7be68d7bba1474",
+ "request_id": "ad994574-d91f-4200-9031-33680b113322",
+ "response_id": "chatcmpl-ecd1d20c39406d82bcb891a9df5f07a6",
"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. These 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\"), [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, which are among the [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. Additionally, neurons such as [AMMC-Bi16](https://www.virtualflybrain.org/reports/FBbt_00111480 \"Open AMMC-Bi16 in Virtual Fly Brain\"), [adult antennal lobe projection neuron DL5](https://www.virtualflybrain.org/reports/FBbt_00059280 \"Open adult antennal lobe projection neuron DL5 in Virtual Fly Brain\"), adult antennal lobe projection neuron DM4, adult antennal lobe projection neuron VA1d, adult antennal lobe projection neuron VL1, adult antennal lobe projection neuron VL2a, adult antennal lobe projection neuron VM2, adult antennal lobe projection neuron VM4, and adult multiglomerular antennal lobe projection neuron L1 adPN are among the [673](https://v2.virtualflybrain.org/org.geppetto.frontend/geppetto?q=FBbt_00003924,NeuronsSynaptic \"Run in VFB: Neurons with synaptic terminals in antennal lobe\") neurons with synaptic terminals in the antennal lobe.",
+ "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, which are among the [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. Additionally, neurons such as [AMMC-Bi16](https://www.virtualflybrain.org/reports/FBbt_00111480 \"Open AMMC-Bi16 in Virtual Fly Brain\"), [adult antennal lobe projection neuron DL5](https://www.virtualflybrain.org/reports/FBbt_00059280 \"Open adult antennal lobe projection neuron DL5 in Virtual Fly Brain\"), adult antennal lobe projection neuron DM4, adult antennal lobe projection neuron VA1d, adult antennal lobe projection neuron VL1, adult antennal lobe projection neuron VL2a, adult antennal lobe projection neuron VM2, adult antennal lobe projection neuron VM4, and adult multiglomerular antennal lobe projection neuron L1 adPN are among the [673](https://v2.virtualflybrain.org/org.geppetto.frontend/geppetto?q=FBbt_00003924,NeuronsSynaptic \"Run in VFB: Neurons with synaptic terminals in antennal lobe\") neurons with synaptic terminals in the antennal lobe.",
"quality_flags": {
"has_tool_status": true,
"no_tool_factual_answer": false,
@@ -6215,14 +6228,14 @@
"graph_failure_mentioned": false,
"missing_required_graph": false,
"used_data_resource": false,
- "response_chars": 2306,
+ "response_chars": 2302,
"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": 18059
+ "slowest_followup_ms": 7925
}
},
{
@@ -6235,7 +6248,7 @@
"requires_graph": false,
"min_graphs": 0,
"repetition": 1,
- "duration_ms": 28498,
+ "duration_ms": 17236,
"status_messages": [
{
"message": "Thinking...",
@@ -6270,9 +6283,9 @@
"question": "What is the medulla?",
"focus": null,
"clicked": null,
- "duration_ms": 14267,
+ "duration_ms": 4735,
"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.",
+ "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",
@@ -6332,9 +6345,9 @@
"query_type": "ImagesNeurons"
},
"clicked": 0,
- "duration_ms": 7808,
+ "duration_ms": 8318,
"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\"). VFB holds [226,524](https://v2.virtualflybrain.org/org.geppetto.frontend/geppetto?q=FBbt_00003748,ImagesNeurons \"Run in VFB: Images of neurons with some part in medulla\") images of neurons with some part in the medulla. The first 12 images are of neurons including T4a_R, T4a_L, with VFB ids such as VFB_jrmc10ep and VFB_jrmc10g2. Additionally, there are [471](https://v2.virtualflybrain.org/org.geppetto.frontend/geppetto?q=FBbt_00003748,NeuronsPartHere \"Run in VFB: Neurons with some part in medulla\") neurons with some part in the medulla, including [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\"), and [medulla intrinsic neuron vGlutMinew1a](https://www.virtualflybrain.org/reports/FBbt_00110033 \"Open medulla intrinsic neuron vGlutMinew1a in Virtual Fly Brain\").",
+ "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 neurons with some part in the medulla are: T4a_R (MaleCNS:113529); T4a_L (MaleCNS:74469); T4a_L (MaleCNS:107619); T4a_R (MaleCNS:153494); T4a_L (MaleCNS:90547); T4a_R (MaleCNS:95926); T4a_L (MaleCNS:207048); [T4a_L (MaleCNS:97069)](https://www.virtualflybrain.org/reports/VFB_jrmc10fb \"Open T4a_L (MaleCNS:97069) in Virtual Fly Brain\"); T4a_L (MaleCNS:166703); T4a_R (MaleCNS:113836); [T4a_L (MaleCNS:543841)](https://www.virtualflybrain.org/reports/VFB_jrmc10fd \"Open T4a_L (MaleCNS:543841) in Virtual Fly Brain\"); [T4a_L (MaleCNS:150592)](https://www.virtualflybrain.org/reports/VFB_jrmc10fa \"Open T4a_L (MaleCNS:150592) in Virtual Fly Brain\"). Additionally, there are [471](https://v2.virtualflybrain.org/org.geppetto.frontend/geppetto?q=FBbt_00003748,NeuronsPartHere \"Run in VFB: Neurons with some part in medulla\") neurons with some part in the medulla, including [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. In total, there are [226,524](https://v2.virtualflybrain.org/org.geppetto.frontend/geppetto?q=FBbt_00003748,ImagesNeurons \"Run in VFB: Images of neurons with some part in medulla\") images of neurons with some part in the medulla.",
"followons": [
{
"id": "FBbt_00003748",
@@ -6405,7 +6418,7 @@
"query_type": "TransgeneExpressionHere"
},
"clicked": 0,
- "duration_ms": 6423,
+ "duration_ms": 4183,
"ok": true,
"response": "The [medulla](https://www.virtualflybrain.org/reports/FBbt_00003748 \"Open medulla in Virtual Fly Brain\") is labeled by [2,342](https://v2.virtualflybrain.org/org.geppetto.frontend/geppetto?q=FBbt_00003748,TransgeneExpressionHere \"Run in VFB: Transgene expression in medulla\") driver lines, including [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\"), and [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\").",
"followons": [
@@ -6477,8 +6490,8 @@
}
],
"ok": true,
- "request_id": "0f224a73-9235-42a2-a0ed-73032f1f8fc3",
- "response_id": "chatcmpl-2c08edc5dce63b2f140c528a5eaf956f",
+ "request_id": "74decb41-7892-4983-b602-4e34aa596f0f",
+ "response_id": "chatcmpl-12824a7523a6ebaa90fa3260f089deca",
"images_count": 8,
"graphs_count": 0,
"response": "The [medulla](https://www.virtualflybrain.org/reports/FBbt_00003748 \"Open medulla in Virtual Fly Brain\") is labeled by [2,342](https://v2.virtualflybrain.org/org.geppetto.frontend/geppetto?q=FBbt_00003748,TransgeneExpressionHere \"Run in VFB: Transgene expression in medulla\") driver lines, including [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\"), and [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\").",
@@ -6499,7 +6512,7 @@
"unmatched_claim_after_resolve": false,
"repeats_answered_question": false,
"slow_followup_turn": false,
- "slowest_followup_ms": 7808
+ "slowest_followup_ms": 8318
}
},
{
@@ -6512,7 +6525,7 @@
"requires_graph": false,
"min_graphs": 0,
"repetition": 1,
- "duration_ms": 21173,
+ "duration_ms": 18793,
"status_messages": [
{
"message": "Thinking...",
@@ -6539,7 +6552,7 @@
"phase": "llm"
}
],
- "event_count": 72,
+ "event_count": 259,
"conversation": true,
"turns": [
{
@@ -6547,9 +6560,9 @@
"question": "What is the mushroom body?",
"focus": null,
"clicked": null,
- "duration_ms": 13101,
+ "duration_ms": 8565,
"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 is closest to the cortex and receives sensory interneuron afferents; the pedunculus, which is 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. The mushroom body also has a compartmental organisation, with the dendrites of mushroom body output neurons and the axon terminals of dopaminergic neurons tiling the lobes into a stereotyped grid of 15 compartments.",
+ "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",
@@ -6606,9 +6619,9 @@
"question": "Which driver lines label it?",
"focus": null,
"clicked": null,
- "duration_ms": 8071,
+ "duration_ms": 10228,
"ok": true,
- "response": "The [mushroom body](https://www.virtualflybrain.org/reports/FBbt_00005801 \"Open mushroom body in Virtual Fly Brain\") is labelled by various driver lines. VFB records show that there are transgene expression patterns for the mushroom body, with [4130](https://v2.virtualflybrain.org/org.geppetto.frontend/geppetto?q=FBbt_00005801,TransgeneExpressionHere \"Run in VFB: Transgene expression in mushroom body\") results. Split-GAL4 lines are also reported, with 3060 cell-type-specific lines for the adult CNS and 1373 characterised in third-instar larvae.",
+ "response": "The [mushroom body](https://www.virtualflybrain.org/reports/FBbt_00005801 \"Open mushroom body in Virtual Fly Brain\") is labeled by several driver lines, including PBac{544.SVS-1}Bsg[CPTI100062], PBac{566.P.SVS-1}Bsg[CPTI100005], PBac{566.P.SVS-1}IA-2[CPTI100013], PBac{566.P.SVS-1}sgg[CPTI100027], PBac{602.P.SVS-1}Fas2[CPTI000483], PBac{602.P.SVS-1}HDAC4[CPTI000077], PBac{602.P.SVS-1}Pax[CPTI000161], PBac{602.P.SVS-1}Sema1a[CPTI000505], PBac{602.P.SVS-1}Tm1[CPTI000760], PBac{602.P.SVS-1}dlg1[CPTI000207], PBac{602.P.SVS-1}dlp[CPTI000445], and PBac{602.P.SVS-1}hzg[CPTI000737]. Additionally, Split-GAL4 lines are available for labeling specific cell types in the mushroom body.",
"followons": [
{
"id": "FBbt_00005801",
@@ -6668,11 +6681,11 @@
}
],
"ok": true,
- "request_id": "08bf354f-becb-49ad-8c18-82e6cee214a5",
- "response_id": "chatcmpl-ca3262f1935b0fd8563dd1e8a6ec9dfb",
+ "request_id": "e79f7e85-432f-43ae-9e23-0bf53a06caf4",
+ "response_id": "chatcmpl-1455ce905db1e888e8ac1fd6ff236aec",
"images_count": 8,
"graphs_count": 0,
- "response": "The [mushroom body](https://www.virtualflybrain.org/reports/FBbt_00005801 \"Open mushroom body in Virtual Fly Brain\") is labelled by various driver lines. VFB records show that there are transgene expression patterns for the mushroom body, with [4130](https://v2.virtualflybrain.org/org.geppetto.frontend/geppetto?q=FBbt_00005801,TransgeneExpressionHere \"Run in VFB: Transgene expression in mushroom body\") results. Split-GAL4 lines are also reported, with 3060 cell-type-specific lines for the adult CNS and 1373 characterised in third-instar larvae.",
+ "response": "The [mushroom body](https://www.virtualflybrain.org/reports/FBbt_00005801 \"Open mushroom body in Virtual Fly Brain\") is labeled by several driver lines, including PBac{544.SVS-1}Bsg[CPTI100062], PBac{566.P.SVS-1}Bsg[CPTI100005], PBac{566.P.SVS-1}IA-2[CPTI100013], PBac{566.P.SVS-1}sgg[CPTI100027], PBac{602.P.SVS-1}Fas2[CPTI000483], PBac{602.P.SVS-1}HDAC4[CPTI000077], PBac{602.P.SVS-1}Pax[CPTI000161], PBac{602.P.SVS-1}Sema1a[CPTI000505], PBac{602.P.SVS-1}Tm1[CPTI000760], PBac{602.P.SVS-1}dlg1[CPTI000207], PBac{602.P.SVS-1}dlp[CPTI000445], and PBac{602.P.SVS-1}hzg[CPTI000737]. Additionally, Split-GAL4 lines are available for labeling specific cell types in the mushroom body.",
"quality_flags": {
"has_tool_status": true,
"no_tool_factual_answer": false,
@@ -6683,14 +6696,14 @@
"graph_failure_mentioned": false,
"missing_required_graph": false,
"used_data_resource": false,
- "response_chars": 550,
+ "response_chars": 680,
"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": 8071
+ "slowest_followup_ms": 10228
}
},
{
@@ -6703,7 +6716,7 @@
"requires_graph": false,
"min_graphs": 0,
"repetition": 1,
- "duration_ms": 28421,
+ "duration_ms": 21434,
"status_messages": [
{
"message": "Thinking...",
@@ -6718,11 +6731,11 @@
"phase": "mcp"
},
{
- "message": "Reading VFB term info",
+ "message": "Querying VFB",
"phase": "mcp"
},
{
- "message": "Querying VFB",
+ "message": "Reading VFB term info",
"phase": "mcp"
},
{
@@ -6758,7 +6771,7 @@
"phase": "llm"
}
],
- "event_count": 173,
+ "event_count": 162,
"conversation": true,
"turns": [
{
@@ -6766,9 +6779,9 @@
"question": "Which neurons provide input to the medulla?",
"focus": null,
"clicked": null,
- "duration_ms": 8366,
+ "duration_ms": 6196,
"ok": true,
- "response": "The 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.",
+ "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. These neurons have presynaptic terminals in the medulla. Additionally, neurons such as 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 have postsynaptic terminals in the medulla, indicating that they receive input from other neurons, but may also provide output to the medulla.",
"followons": [
{
"id": "FBbt_00003748",
@@ -6836,9 +6849,9 @@
"question": "And the lobula?",
"focus": null,
"clicked": null,
- "duration_ms": 20055,
+ "duration_ms": 15237,
"ok": true,
- "response": "The [lobula](https://www.virtualflybrain.org/reports/FBbt_00003852 \"Open lobula in Virtual Fly Brain\") is the anterior domain of the adult lobula complex. It can be divided into six layers and houses many columnar neurons. 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 some part in the lobula, and 528 neurons with synaptic terminals in the lobula. Some of these neurons 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.",
+ "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. These neurons have synaptic terminals in the lobula. VFB holds [528](https://v2.virtualflybrain.org/org.geppetto.frontend/geppetto?q=FBbt_00003852,NeuronsPartHere \"Run in VFB: Neurons with some part in lobula\") records of neurons with some part in the lobula and 528 records of neurons with synaptic terminals in the lobula.",
"followons": [
{
"id": "FBbt_00003852",
@@ -6926,11 +6939,11 @@
}
],
"ok": true,
- "request_id": "dabe5a5c-d4b0-44e5-b1c5-b9dc74ffc9b0",
- "response_id": "chatcmpl-5c30632e9242c9e6b846b12f79307a82",
+ "request_id": "b7847bf5-8474-4db7-a847-b7616e0a66c7",
+ "response_id": "chatcmpl-eb0b33f2cc955576c1670f5278a16c2d",
"images_count": 4,
"graphs_count": 0,
- "response": "The [lobula](https://www.virtualflybrain.org/reports/FBbt_00003852 \"Open lobula in Virtual Fly Brain\") is the anterior domain of the adult lobula complex. It can be divided into six layers and houses many columnar neurons. 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 some part in the lobula, and 528 neurons with synaptic terminals in the lobula. Some of these neurons 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.",
+ "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. These neurons have synaptic terminals in the lobula. VFB holds [528](https://v2.virtualflybrain.org/org.geppetto.frontend/geppetto?q=FBbt_00003852,NeuronsPartHere \"Run in VFB: Neurons with some part in lobula\") records of neurons with some part in the lobula and 528 records of neurons with synaptic terminals in the lobula.",
"quality_flags": {
"has_tool_status": true,
"no_tool_factual_answer": false,
@@ -6941,14 +6954,14 @@
"graph_failure_mentioned": false,
"missing_required_graph": false,
"used_data_resource": false,
- "response_chars": 1173,
+ "response_chars": 1113,
"status_count": 13,
"addressless_followon": false,
"context_lost_across_turn": false,
"unmatched_claim_after_resolve": false,
"repeats_answered_question": false,
"slow_followup_turn": false,
- "slowest_followup_ms": 20055
+ "slowest_followup_ms": 15237
}
},
{
@@ -6961,7 +6974,7 @@
"requires_graph": false,
"min_graphs": 0,
"repetition": 1,
- "duration_ms": 53861,
+ "duration_ms": 35883,
"status_messages": [
{
"message": "Thinking...",
@@ -7012,7 +7025,7 @@
"phase": "llm"
}
],
- "event_count": 182,
+ "event_count": 284,
"conversation": true,
"turns": [
{
@@ -7020,7 +7033,7 @@
"question": "What is the protocerebral bridge?",
"focus": null,
"clicked": null,
- "duration_ms": 8813,
+ "duration_ms": 6232,
"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. It forms a dorso-posteriorly located part of the central complex embedded in the cortex between the calyces of the two mushroom bodies, and is composed of a row of 18 connected slices, 9 on each side of the midline, numbered 1-9 from medial to lateral.",
"followons": [
@@ -7079,9 +7092,9 @@
"question": "How does it relate to the ellipsoid body?",
"focus": null,
"clicked": null,
- "duration_ms": 15451,
+ "duration_ms": 9329,
"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 neurons with some part in the ellipsoid body, including [adult protocerebral bridge glomerulus 1-ellipsoid body canal-dorsal gall neuron](https://www.virtualflybrain.org/reports/FBbt_00111376 \"Open adult protocerebral bridge glomerulus 1-ellipsoid body canal-dorsal gall neuron in Virtual Fly Brain\") and adult protocerebral bridge glomerulus 4-ellipsoid body canal-ventral gall neuron, indicating a relationship 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 some neurons have synaptic terminals in both the protocerebral bridge and the ellipsoid body, such as the [adult protocerebral bridge glomerulus 1-ellipsoid body canal-dorsal gall neuron](https://www.virtualflybrain.org/reports/FBbt_00111376 \"Open adult protocerebral bridge glomerulus 1-ellipsoid body canal-dorsal gall neuron in Virtual Fly Brain\").",
"followons": [
{
"id": "FBbt_00003668",
@@ -7162,9 +7175,9 @@
"question": "Which neurons connect them?",
"focus": null,
"clicked": null,
- "duration_ms": 29597,
+ "duration_ms": 20322,
"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\") and adult protocerebral bridge glomerulus 4-ellipsoid body canal-ventral gall neuron. VFB records show neurons with some part in the ellipsoid body, such as [PEN_PB2](https://www.virtualflybrain.org/reports/FBbt_00111369 \"Open PEN_PB2 in Virtual Fly Brain\"), [PEN_PB3](https://www.virtualflybrain.org/reports/FBbt_00111370 \"Open PEN_PB3 in Virtual Fly Brain\"), [PEN_PB7](https://www.virtualflybrain.org/reports/FBbt_00111373 \"Open PEN_PB7 in Virtual Fly Brain\"), and [PEN_PB8](https://www.virtualflybrain.org/reports/FBbt_00111374 \"Open PEN_PB8 in Virtual Fly Brain\"), indicating a relationship between the two structures. Additionally, VFB's query results show that there are neurons with presynaptic and postsynaptic terminals in both the protocerebral bridge and the ellipsoid body, including [EPG_PB5](https://www.virtualflybrain.org/reports/FBbt_00111416 \"Open EPG_PB5 in Virtual Fly Brain\"), [EPG_PB2](https://www.virtualflybrain.org/reports/FBbt_00111419 \"Open EPG_PB2 in Virtual Fly Brain\"), [EPG_PB6](https://www.virtualflybrain.org/reports/FBbt_00111421 \"Open EPG_PB6 in Virtual Fly Brain\"), PEN_PB2, PEN_PB3, PEN_PB7, and PEN_PB8.",
+ "response": "The [adult protocerebral bridge glomerulus 1-ellipsoid body canal-dorsal gall neuron](https://www.virtualflybrain.org/reports/FBbt_00111376 \"Open adult protocerebral bridge glomerulus 1-ellipsoid body canal-dorsal gall neuron in Virtual Fly Brain\") is one example of a neuron that connects 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\"). VFB records show that some neurons have synaptic terminals in both the protocerebral bridge and the ellipsoid body. These include the adult protocerebral bridge glomerulus 1-ellipsoid body canal-dorsal gall neuron, the adult protocerebral bridge glomerulus 4-ellipsoid body canal-ventral gall neuron, the adult protocerebral bridge glomerulus 5-ellipsoid body canal-dorsal gall neuron, the adult protocerebral bridge glomerulus 6-ellipsoid body canal-ventral gall neuron, the adult protocerebral bridge glomerulus 7-ellipsoid body canal-dorsal gall neuron, and the adult protocerebral bridge glomerulus 8-ellipsoid body canal-ventral gall neuron. Other neurons that have synaptic terminals in the protocerebral bridge include [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 that have synaptic terminals in the ellipsoid body include PEN_PB2, PEN_PB3, PEN_PB5, PEN_PB7, and PEN_PB8.",
"followons": [
{
"id": "FBbt_00003668",
@@ -7267,11 +7280,11 @@
}
],
"ok": true,
- "request_id": "8e104cc7-70fd-4d92-be2a-e469986f2864",
- "response_id": "chatcmpl-bd91b6f1ba101bef42bfdd6ee0297791",
+ "request_id": "731fd71a-50a1-45f3-b555-8dff26f7fde6",
+ "response_id": "chatcmpl-9e188c24cd1eb91895154be14c2f553d",
"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\") and adult protocerebral bridge glomerulus 4-ellipsoid body canal-ventral gall neuron. VFB records show neurons with some part in the ellipsoid body, such as [PEN_PB2](https://www.virtualflybrain.org/reports/FBbt_00111369 \"Open PEN_PB2 in Virtual Fly Brain\"), [PEN_PB3](https://www.virtualflybrain.org/reports/FBbt_00111370 \"Open PEN_PB3 in Virtual Fly Brain\"), [PEN_PB7](https://www.virtualflybrain.org/reports/FBbt_00111373 \"Open PEN_PB7 in Virtual Fly Brain\"), and [PEN_PB8](https://www.virtualflybrain.org/reports/FBbt_00111374 \"Open PEN_PB8 in Virtual Fly Brain\"), indicating a relationship between the two structures. Additionally, VFB's query results show that there are neurons with presynaptic and postsynaptic terminals in both the protocerebral bridge and the ellipsoid body, including [EPG_PB5](https://www.virtualflybrain.org/reports/FBbt_00111416 \"Open EPG_PB5 in Virtual Fly Brain\"), [EPG_PB2](https://www.virtualflybrain.org/reports/FBbt_00111419 \"Open EPG_PB2 in Virtual Fly Brain\"), [EPG_PB6](https://www.virtualflybrain.org/reports/FBbt_00111421 \"Open EPG_PB6 in Virtual Fly Brain\"), PEN_PB2, PEN_PB3, PEN_PB7, and PEN_PB8.",
+ "response": "The [adult protocerebral bridge glomerulus 1-ellipsoid body canal-dorsal gall neuron](https://www.virtualflybrain.org/reports/FBbt_00111376 \"Open adult protocerebral bridge glomerulus 1-ellipsoid body canal-dorsal gall neuron in Virtual Fly Brain\") is one example of a neuron that connects 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\"). VFB records show that some neurons have synaptic terminals in both the protocerebral bridge and the ellipsoid body. These include the adult protocerebral bridge glomerulus 1-ellipsoid body canal-dorsal gall neuron, the adult protocerebral bridge glomerulus 4-ellipsoid body canal-ventral gall neuron, the adult protocerebral bridge glomerulus 5-ellipsoid body canal-dorsal gall neuron, the adult protocerebral bridge glomerulus 6-ellipsoid body canal-ventral gall neuron, the adult protocerebral bridge glomerulus 7-ellipsoid body canal-dorsal gall neuron, and the adult protocerebral bridge glomerulus 8-ellipsoid body canal-ventral gall neuron. Other neurons that have synaptic terminals in the protocerebral bridge include [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 that have synaptic terminals in the ellipsoid body include PEN_PB2, PEN_PB3, PEN_PB5, PEN_PB7, and PEN_PB8.",
"quality_flags": {
"has_tool_status": true,
"no_tool_factual_answer": false,
@@ -7282,14 +7295,14 @@
"graph_failure_mentioned": false,
"missing_required_graph": false,
"used_data_resource": false,
- "response_chars": 1673,
+ "response_chars": 1798,
"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": 29597
+ "slowest_followup_ms": 20322
}
},
{
@@ -7302,7 +7315,7 @@
"requires_graph": false,
"min_graphs": 0,
"repetition": 1,
- "duration_ms": 37902,
+ "duration_ms": 25254,
"status_messages": [
{
"message": "Thinking...",
@@ -7333,7 +7346,7 @@
"phase": "llm"
}
],
- "event_count": 47,
+ "event_count": 51,
"conversation": true,
"turns": [
{
@@ -7341,9 +7354,9 @@
"question": "Which neurons have part of them in the medulla?",
"focus": null,
"clicked": null,
- "duration_ms": 17694,
+ "duration_ms": 11952,
"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\"), and [TmY27](https://www.virtualflybrain.org/reports/FBbt_00110067 \"Open TmY27 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. VFB holds [226524](https://v2.virtualflybrain.org/org.geppetto.frontend/geppetto?q=FBbt_00003748,ImagesNeurons \"Run in VFB: Images of neurons with some part in medulla\") images of neurons with some part in the medulla.",
+ "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\"), and [TmY27](https://www.virtualflybrain.org/reports/FBbt_00110067 \"Open TmY27 in Virtual Fly Brain\"). 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",
@@ -7406,9 +7419,9 @@
"question": "How would I get that same result in Python with vfbquery?",
"focus": null,
"clicked": null,
- "duration_ms": 20208,
+ "duration_ms": 13302,
"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. VFB holds [226524](https://v2.virtualflybrain.org/org.geppetto.frontend/geppetto?q=FBbt_00003748,ImagesNeurons \"Run in VFB: Images of neurons with some part in medulla\") images of neurons with some part in the medulla.\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```",
+ "response": "The code below returns the neurons with some part in [medulla](https://www.virtualflybrain.org/reports/FBbt_00003748 \"Open medulla in Virtual Fly Brain\"), as a table, using vfbquery to interface with VFB. 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",
@@ -7468,11 +7481,11 @@
}
],
"ok": true,
- "request_id": "b1232b2d-936c-44b8-aadb-1131f4f477bf",
- "response_id": "chatcmpl-14a4ae5f658c060b111d08e96e6c58bb",
+ "request_id": "a3f47263-6617-4e4f-81c9-e8d2093d9a31",
+ "response_id": "chatcmpl-2f900735c424ffa9bee3dd79e06896eb",
"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. VFB holds [226524](https://v2.virtualflybrain.org/org.geppetto.frontend/geppetto?q=FBbt_00003748,ImagesNeurons \"Run in VFB: Images of neurons with some part in medulla\") images of neurons with some part in the medulla.\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```",
+ "response": "The code below returns the neurons with some part in [medulla](https://www.virtualflybrain.org/reports/FBbt_00003748 \"Open medulla in Virtual Fly Brain\"), as a table, using vfbquery to interface with VFB. 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,
@@ -7483,14 +7496,14 @@
"graph_failure_mentioned": false,
"missing_required_graph": false,
"used_data_resource": false,
- "response_chars": 982,
+ "response_chars": 842,
"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": 20208
+ "slowest_followup_ms": 13302
}
},
{
@@ -7503,7 +7516,7 @@
"requires_graph": false,
"min_graphs": 0,
"repetition": 1,
- "duration_ms": 37625,
+ "duration_ms": 29886,
"status_messages": [
{
"message": "Thinking...",
@@ -7538,7 +7551,7 @@
"phase": "llm"
}
],
- "event_count": 215,
+ "event_count": 158,
"conversation": true,
"turns": [
{
@@ -7546,9 +7559,9 @@
"question": "What are the subclasses of Kenyon cell?",
"focus": null,
"clicked": null,
- "duration_ms": 12619,
+ "duration_ms": 9647,
"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.",
+ "response": "The subclasses 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\"). 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 subclasses of Kenyon cell.",
"followons": [
{
"id": "FBbt_00003686",
@@ -7611,9 +7624,9 @@
"question": "Can you list the VFB IDs so I can reproduce this myself?",
"focus": null,
"clicked": null,
- "duration_ms": 25006,
+ "duration_ms": 20238,
"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); and 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```",
+ "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. VFB holds these 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\"), with their respective VFB ids such as FBbt_00049111, FBbt_00049112, FBbt_00049827, FBbt_00049830, FBbt_00049832, FBbt_00049833, FBbt_00049835, FBbt_00049838, FBbt_00049859, FBbt_00047926, FBbt_00047993, and 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",
@@ -7668,11 +7681,11 @@
}
],
"ok": true,
- "request_id": "f3a3a13c-caeb-4be7-85a2-6beb7e54117b",
- "response_id": "chatcmpl-d1da22bd2cb83d6914d782acf14da6b1",
+ "request_id": "80793a51-4b0d-4910-abfa-f4c82ca022eb",
+ "response_id": "chatcmpl-2508fc98fb7146e87c77ffa0f6762832",
"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); and 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```",
+ "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. VFB holds these 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\"), with their respective VFB ids such as FBbt_00049111, FBbt_00049112, FBbt_00049827, FBbt_00049830, FBbt_00049832, FBbt_00049833, FBbt_00049835, FBbt_00049838, FBbt_00049859, FBbt_00047926, FBbt_00047993, and 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,
@@ -7683,14 +7696,14 @@
"graph_failure_mentioned": false,
"missing_required_graph": false,
"used_data_resource": false,
- "response_chars": 1659,
+ "response_chars": 1592,
"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": 25006
+ "slowest_followup_ms": 20238
}
}
]
diff --git a/test-results/task-battery/task-battery-2026-08-19T19-09-12-796Z.json b/test-results/task-battery/task-battery-2026-08-19T19-09-12-796Z.json
new file mode 100644
index 0000000..e70d7b2
--- /dev/null
+++ b/test-results/task-battery/task-battery-2026-08-19T19-09-12-796Z.json
@@ -0,0 +1,7710 @@
+{
+ "metadata": {
+ "run_id": "task-battery-2026-08-19T19-09-12-796Z",
+ "started_at": "2026-08-19T19:09:12.796Z",
+ "completed_at": "2026-08-19T19:24:00.168Z",
+ "git_sha": "a2a31973ab572d5b3b7762ba92283f874943f763",
+ "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": 62,
+ "errors": 2,
+ "by_tier": {
+ "T1": {
+ "total": 8,
+ "ok": 8,
+ "errors": 0
+ },
+ "T2": {
+ "total": 8,
+ "ok": 7,
+ "errors": 1
+ },
+ "T3": {
+ "total": 8,
+ "ok": 8,
+ "errors": 0
+ },
+ "T4": {
+ "total": 6,
+ "ok": 6,
+ "errors": 0
+ },
+ "T5": {
+ "total": 1,
+ "ok": 1,
+ "errors": 0
+ },
+ "T6": {
+ "total": 21,
+ "ok": 20,
+ "errors": 1
+ },
+ "T7": {
+ "total": 12,
+ "ok": 12,
+ "errors": 0
+ }
+ },
+ "quality": {
+ "no_tool_factual_answer": {
+ "count": 0,
+ "task_ids": []
+ },
+ "tool_claim_without_tool": {
+ "count": 0,
+ "task_ids": []
+ },
+ "disambiguation_only_answer": {
+ "count": 0,
+ "task_ids": []
+ },
+ "investigation_plan_answer": {
+ "count": 0,
+ "task_ids": []
+ },
+ "not_verified_or_no_results_answer": {
+ "count": 0,
+ "task_ids": []
+ },
+ "graph_failure_mentioned": {
+ "count": 0,
+ "task_ids": []
+ },
+ "missing_required_graph": {
+ "count": 0,
+ "task_ids": []
+ },
+ "used_data_resource": {
+ "count": 0,
+ "task_ids": []
+ },
+ "addressless_followon": {
+ "count": 0,
+ "task_ids": []
+ },
+ "context_lost_across_turn": {
+ "count": 0,
+ "task_ids": []
+ },
+ "unmatched_claim_after_resolve": {
+ "count": 0,
+ "task_ids": []
+ },
+ "repeats_answered_question": {
+ "count": 0,
+ "task_ids": []
+ },
+ "slow_followup_turn": {
+ "count": 1,
+ "task_ids": [
+ "C3"
+ ]
+ }
+ },
+ "conversation": {
+ "total": 12,
+ "ok": 12,
+ "turns": 27,
+ "followup_turns": 15,
+ "followup_median_ms": 10228,
+ "followup_max_ms": 190201
+ },
+ "mean_duration_ms": 37129
+ },
+ "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": 15102,
+ "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": 76,
+ "ok": true,
+ "request_id": "9184afb8-09a9-4718-99b6-8f03783fd816",
+ "response_id": "chatcmpl-195bc36bc75ef2e0f4d6636e0f15f9ca",
+ "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. The lobes are further divided into compartments such as α, β, and γ.",
+ "quality_flags": {
+ "has_tool_status": true,
+ "no_tool_factual_answer": false,
+ "tool_claim_without_tool": false,
+ "disambiguation_only_answer": false,
+ "investigation_plan_answer": false,
+ "not_verified_or_no_results_answer": false,
+ "graph_failure_mentioned": false,
+ "missing_required_graph": false,
+ "used_data_resource": false,
+ "response_chars": 419,
+ "status_count": 6
+ }
+ },
+ {
+ "attempt_index": 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": 75487,
+ "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": "b7e5ac85-fa78-47ae-8062-2009ba2f9b7d",
+ "response_id": "chatcmpl-274ec20f3bb35a51eddf7a98f01e3040",
+ "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. These 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": 14809,
+ "status_messages": [
+ {
+ "message": "Thinking...",
+ "phase": "llm"
+ },
+ {
+ "message": "Planning the answer",
+ "phase": "llm"
+ },
+ {
+ "message": "Resolving 1 term in VFB",
+ "phase": "mcp"
+ },
+ {
+ "message": "Querying VFB connectivity",
+ "phase": "mcp"
+ },
+ {
+ "message": "Querying VFB",
+ "phase": "mcp"
+ },
+ {
+ "message": "Querying VFB",
+ "phase": "mcp"
+ },
+ {
+ "message": "Checking the answer is covered",
+ "phase": "llm"
+ },
+ {
+ "message": "Querying VFB",
+ "phase": "mcp"
+ },
+ {
+ "message": "Checking the answer is covered",
+ "phase": "llm"
+ },
+ {
+ "message": "Writing the answer",
+ "phase": "llm"
+ }
+ ],
+ "event_count": 100,
+ "ok": true,
+ "request_id": "715b559c-3502-47b7-9d04-4c97e8ac6613",
+ "response_id": "chatcmpl-c7a8e2c4e10de26e6ec16e55e01cfe46",
+ "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\") include sensory interneuron afferents to the calyx. VFB records show that there are [366](https://v2.virtualflybrain.org/org.geppetto.frontend/geppetto?q=FBbt_00005801,NeuronsPresynapticHere \"Run in VFB: Neurons with presynaptic terminals in mushroom body\") neurons with presynaptic terminals in the mushroom body, including larval uniglomerular projection neurons and larval antennal lobe multiglomerular projection neurons. Additionally, the connectome data indicates that there are [304](https://v2.virtualflybrain.org/org.geppetto.frontend/geppetto?q=FBbt_00005801,NeuronsPostsynapticHere \"Run in VFB: Neurons with postsynaptic terminals in mushroom body\") neurons with postsynaptic terminals in the mushroom body.",
+ "graphs": [
+ {
+ "type": "basic_graph",
+ "version": 1,
+ "title": "mushroom body region connectivity preview",
+ "directed": true,
+ "layout": "radial",
+ "nodes": [
+ {
+ "id": "FBbt_00005801",
+ "label": "mushroom body",
+ "group": "queried region",
+ "color": null,
+ "size": 2.4
+ },
+ {
+ "id": "FBbt_00111716",
+ "label": "larval antennal lobe multiglomerular projection neuron C2",
+ "group": "presynaptic neuron",
+ "color": null,
+ "size": 1.15
+ },
+ {
+ "id": "FBbt_00111717",
+ "label": "larval antennal lobe multiglomerular projection neuron bilateral lower",
+ "group": "presynaptic neuron",
+ "color": null,
+ "size": 1.15
+ },
+ {
+ "id": "FBbt_00111675",
+ "label": "larval uniglomerular projection neuron 63a",
+ "group": "presynaptic neuron",
+ "color": null,
+ "size": 1.15
+ },
+ {
+ "id": "FBbt_00111684",
+ "label": "larval uniglomerular projection neuron 67b",
+ "group": "presynaptic neuron",
+ "color": null,
+ "size": 1.15
+ },
+ {
+ "id": "FBbt_00111685",
+ "label": "larval uniglomerular projection neuron 74a",
+ "group": "presynaptic neuron",
+ "color": null,
+ "size": 1.15
+ },
+ {
+ "id": "FBbt_20000069",
+ "label": "ATL005",
+ "group": "postsynaptic neuron",
+ "color": null,
+ "size": 1.15
+ },
+ {
+ "id": "FBbt_20000071",
+ "label": "ATL007",
+ "group": "postsynaptic neuron",
+ "color": null,
+ "size": 1.15
+ },
+ {
+ "id": "FBbt_20000083",
+ "label": "ATL019",
+ "group": "postsynaptic neuron",
+ "color": null,
+ "size": 1.15
+ },
+ {
+ "id": "FBbt_20000084",
+ "label": "ATL020",
+ "group": "postsynaptic neuron",
+ "color": null,
+ "size": 1.15
+ },
+ {
+ "id": "FBbt_00111628",
+ "label": "adult odd neuron of the calyx",
+ "group": "postsynaptic neuron",
+ "color": null,
+ "size": 1.15
+ }
+ ],
+ "edges": [
+ {
+ "source": "FBbt_00111716",
+ "target": "FBbt_00005801",
+ "label": "presynaptic sites in mushroom body",
+ "weight": 0
+ },
+ {
+ "source": "FBbt_00111717",
+ "target": "FBbt_00005801",
+ "label": "presynaptic sites in mushroom body",
+ "weight": 0
+ },
+ {
+ "source": "FBbt_00111675",
+ "target": "FBbt_00005801",
+ "label": "presynaptic sites in mushroom body",
+ "weight": 0
+ },
+ {
+ "source": "FBbt_00111684",
+ "target": "FBbt_00005801",
+ "label": "presynaptic sites in mushroom body",
+ "weight": 0
+ },
+ {
+ "source": "FBbt_00111685",
+ "target": "FBbt_00005801",
+ "label": "presynaptic sites in mushroom body",
+ "weight": 0
+ },
+ {
+ "source": "FBbt_00005801",
+ "target": "FBbt_20000069",
+ "label": "postsynaptic sites in mushroom body",
+ "weight": 0
+ },
+ {
+ "source": "FBbt_00005801",
+ "target": "FBbt_20000071",
+ "label": "postsynaptic sites in mushroom body",
+ "weight": 0
+ },
+ {
+ "source": "FBbt_00005801",
+ "target": "FBbt_20000083",
+ "label": "postsynaptic sites in mushroom body",
+ "weight": 0
+ },
+ {
+ "source": "FBbt_00005801",
+ "target": "FBbt_20000084",
+ "label": "postsynaptic sites in mushroom body",
+ "weight": 0
+ },
+ {
+ "source": "FBbt_00005801",
+ "target": "FBbt_00111628",
+ "label": "postsynaptic sites in mushroom body",
+ "weight": 0
+ }
+ ]
+ }
+ ],
+ "quality_flags": {
+ "has_tool_status": true,
+ "no_tool_factual_answer": false,
+ "tool_claim_without_tool": false,
+ "disambiguation_only_answer": false,
+ "investigation_plan_answer": false,
+ "not_verified_or_no_results_answer": false,
+ "graph_failure_mentioned": false,
+ "missing_required_graph": false,
+ "used_data_resource": false,
+ "response_chars": 861,
+ "status_count": 10
+ }
+ },
+ {
+ "attempt_index": 3,
+ "task_index": 3,
+ "task_id": "T1.4",
+ "tier": 1,
+ "title": "Gene expression",
+ "question": "What neurotransmitter do mushroom body Kenyon cells use?",
+ "requires_graph": false,
+ "min_graphs": 0,
+ "repetition": 1,
+ "duration_ms": 14119,
+ "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": "f6c1a43d-7b3e-4189-bcae-6943a0f5e83a",
+ "response_id": "chatcmpl-90a1d260a096ed4bacdd7ebf7e5dc9ba",
+ "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": 16100,
+ "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": 176,
+ "ok": true,
+ "request_id": "f56eb0a4-f366-49bb-930f-786394706adf",
+ "response_id": "chatcmpl-40eeea66acd7085a383e38b11df5fd47",
+ "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 Or35a ac3I and Or85b ab3. Neurons with postsynaptic terminals in the antennal lobe include adult antennal lobe projection neurons like DL5, DM4, and VL1, as well as multiglomerular antennal lobe projection neurons like L1 adPN. VFB holds [266](https://v2.virtualflybrain.org/org.geppetto.frontend/geppetto?q=FBbt_00003924,NeuronsPresynapticHere \"Run in VFB: Neurons with presynaptic terminals in antennal lobe\") records of neurons with presynaptic terminals in the antennal lobe and [518](https://v2.virtualflybrain.org/org.geppetto.frontend/geppetto?q=FBbt_00003924,NeuronsPostsynapticHere \"Run in VFB: Neurons with postsynaptic terminals in antennal lobe\") records of neurons with postsynaptic terminals in the antennal lobe.",
+ "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": 1380,
+ "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": 13744,
+ "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": 37,
+ "ok": true,
+ "request_id": "942b5a40-6985-4bc7-82dd-496d040374ed",
+ "response_id": "chatcmpl-0116ff21b5a7f0df3c865bf019e36d93",
+ "images_count": 8,
+ "graphs_count": 0,
+ "response": "The [adult central brain](https://www.virtualflybrain.org/reports/FBbt_00047887 \"Open adult central brain in Virtual Fly Brain\") contains approximately 32,388 neurons, according to the neuron count reported by FlyWire for neurons fully contained in the 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](https://doi.org/10.1038/s41586-024-07558-y \"Open Dorkenwald S et al. (2024) Nature 634(8032):124-138 — PMID 39358518 via DOI (new tab)\")\n\n_FlyWire reports 32,388 neurons FULLY CONTAINED in the central brain out of 139,255 in the whole brain. Neurons that arborise in the central brain but also elsewhere are not in that subcount, so it is a lower bound on 'neurons in the central brain', not a census of them._\n\n_VFB has annotated 9,413 neuron types with some part in adult central brain — a curated annotation count, not the biological total._\n\nReference: [How many neurons are in the fly brain?](https://www.virtualflybrain.org/docs/concepts/neuron-counts/ \"Open “How many neurons are in the fly brain?” — Virtual Fly Brain documentation (new tab)\")",
+ "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": 1463,
+ "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": 18856,
+ "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": 102,
+ "ok": true,
+ "request_id": "3a6cf58e-9f3c-4516-8e16-e6bd93601a52",
+ "response_id": "chatcmpl-aedc6153c2365b1713c420f21eec4649",
+ "images_count": 8,
+ "graphs_count": 1,
+ "response": "The main components of the Drosophila central complex are the ellipsoid body, the fan-shaped body, the three paired noduli, the asymmetrical bodies, and the protocerebral bridge. These components are associated with functions including navigation and orientation, locomotor control, and sleep/arousal and memory-related behaviours. 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": 915,
+ "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": 73039,
+ "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": 91,
+ "ok": true,
+ "request_id": "c09fca3a-dfac-4f7e-aae8-48429d9237f7",
+ "response_id": "chatcmpl-d96a013bc0dd2de563dd4683fee5295f",
+ "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.",
+ "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": 274,
+ "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": 79139,
+ "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": 94,
+ "ok": true,
+ "request_id": "1496b28a-bf7a-4dae-a981-b47b74a81d8d",
+ "response_id": "chatcmpl-2031e0bf6095440c7766d0cbe0fde30b",
+ "images_count": 8,
+ "graphs_count": 1,
+ "response": "Dopaminergic input to mushroom body output neurons (MBONs) comes from specific dopaminergic neuron types. VFB records that dopaminergic PPL1 neurons and dopaminergic PAM neurons provide input to MBONs. However, the specific connections between different types of dopaminergic neurons and MBONs are not detailed in VFB evidence. VFB holds [69](https://v2.virtualflybrain.org/org.geppetto.frontend/geppetto?q=FBbt_00047953,SubclassesOf \"Run in VFB: Subclasses of MBON\") subclasses of MBON.",
+ "graphs": [
+ {
+ "type": "basic_graph",
+ "version": 1,
+ "title": "Upstream partners of MBON",
+ "directed": true,
+ "layout": "circle",
+ "nodes": [
+ {
+ "id": "FBbt_00005131",
+ "label": "dopaminergic neuron",
+ "group": null,
+ "color": null,
+ "size": 1.93
+ },
+ {
+ "id": "FBbt_00047953",
+ "label": "MBON",
+ "group": null,
+ "color": null,
+ "size": 4
+ },
+ {
+ "id": "FBbt_00058206",
+ "label": "adult dopaminergic neuron",
+ "group": null,
+ "color": null,
+ "size": 1.92
+ },
+ {
+ "id": "FBbt_00048138",
+ "label": "mushroom body dopaminergic neuron",
+ "group": null,
+ "color": null,
+ "size": 1.91
+ },
+ {
+ "id": "FBbt_00049839",
+ "label": "adult dopaminergic mushroom body input neuron",
+ "group": null,
+ "color": null,
+ "size": 1.07
+ },
+ {
+ "id": "FBbt_00100214",
+ "label": "adult dopaminergic PAM neuron",
+ "group": null,
+ "color": null,
+ "size": 1.07
+ },
+ {
+ "id": "FBbt_00100219",
+ "label": "dopaminergic PPL1 neuron",
+ "group": null,
+ "color": null,
+ "size": 1.02
+ },
+ {
+ "id": "FBbt_00049840",
+ "label": "mushroom body PPL1 neuron",
+ "group": null,
+ "color": null,
+ "size": 1.02
+ },
+ {
+ "id": "FBbt_00111020",
+ "label": "dopaminergic PAM neuron 8",
+ "group": null,
+ "color": null,
+ "size": 1.01
+ },
+ {
+ "id": "FBbt_00111018",
+ "label": "dopaminergic PAM neuron 6",
+ "group": null,
+ "color": null,
+ "size": 1.01
+ },
+ {
+ "id": "FBbt_00111017",
+ "label": "dopaminergic PAM neuron 5",
+ "group": null,
+ "color": null,
+ "size": 1.01
+ },
+ {
+ "id": "FBbt_00110994",
+ "label": "dopaminergic PAM neuron 10",
+ "group": null,
+ "color": null,
+ "size": 1.01
+ },
+ {
+ "id": "FBbt_00110993",
+ "label": "dopaminergic PAM neuron 4",
+ "group": null,
+ "color": null,
+ "size": 1.01
+ },
+ {
+ "id": "FBbt_00111022",
+ "label": "dopaminergic PAM neuron 11",
+ "group": null,
+ "color": null,
+ "size": 1.01
+ },
+ {
+ "id": "FBbt_00007364",
+ "label": "octopaminergic neuron",
+ "group": null,
+ "color": null,
+ "size": 1.01
+ },
+ {
+ "id": "FBbt_00058203",
+ "label": "adult octopaminergic neuron",
+ "group": null,
+ "color": null,
+ "size": 1.01
+ }
+ ],
+ "edges": [
+ {
+ "source": "FBbt_00005131",
+ "target": "FBbt_00047953",
+ "label": "651367",
+ "weight": 651367
+ },
+ {
+ "source": "FBbt_00058206",
+ "target": "FBbt_00047953",
+ "label": "650172",
+ "weight": 650172
+ },
+ {
+ "source": "FBbt_00048138",
+ "target": "FBbt_00047953",
+ "label": "641765",
+ "weight": 641765
+ },
+ {
+ "source": "FBbt_00049839",
+ "target": "FBbt_00047953",
+ "label": "47142",
+ "weight": 47142
+ },
+ {
+ "source": "FBbt_00100214",
+ "target": "FBbt_00047953",
+ "label": "47139",
+ "weight": 47139
+ },
+ {
+ "source": "FBbt_00100219",
+ "target": "FBbt_00047953",
+ "label": "17270",
+ "weight": 17270
+ },
+ {
+ "source": "FBbt_00049840",
+ "target": "FBbt_00047953",
+ "label": "16097",
+ "weight": 16097
+ },
+ {
+ "source": "FBbt_00111020",
+ "target": "FBbt_00047953",
+ "label": "7988",
+ "weight": 7988
+ },
+ {
+ "source": "FBbt_00111018",
+ "target": "FBbt_00047953",
+ "label": "7650",
+ "weight": 7650
+ },
+ {
+ "source": "FBbt_00111017",
+ "target": "FBbt_00047953",
+ "label": "5433",
+ "weight": 5433
+ },
+ {
+ "source": "FBbt_00110994",
+ "target": "FBbt_00047953",
+ "label": "4482",
+ "weight": 4482
+ },
+ {
+ "source": "FBbt_00110993",
+ "target": "FBbt_00047953",
+ "label": "4248",
+ "weight": 4248
+ },
+ {
+ "source": "FBbt_00111022",
+ "target": "FBbt_00047953",
+ "label": "4033",
+ "weight": 4033
+ },
+ {
+ "source": "FBbt_00007364",
+ "target": "FBbt_00047953",
+ "label": "3790",
+ "weight": 3790
+ },
+ {
+ "source": "FBbt_00058203",
+ "target": "FBbt_00047953",
+ "label": "3547",
+ "weight": 3547
+ }
+ ]
+ }
+ ],
+ "quality_flags": {
+ "has_tool_status": true,
+ "no_tool_factual_answer": false,
+ "tool_claim_without_tool": false,
+ "disambiguation_only_answer": false,
+ "investigation_plan_answer": false,
+ "not_verified_or_no_results_answer": false,
+ "graph_failure_mentioned": false,
+ "missing_required_graph": false,
+ "used_data_resource": false,
+ "response_chars": 487,
+ "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": 26678,
+ "status_messages": [
+ {
+ "message": "Thinking...",
+ "phase": "llm"
+ },
+ {
+ "message": "Planning the answer",
+ "phase": "llm"
+ },
+ {
+ "message": "Resolving 3 terms in VFB",
+ "phase": "mcp"
+ },
+ {
+ "message": "Querying VFB connectivity",
+ "phase": "mcp"
+ },
+ {
+ "message": "Querying VFB",
+ "phase": "mcp"
+ },
+ {
+ "message": "Querying VFB",
+ "phase": "mcp"
+ },
+ {
+ "message": "Checking the answer is covered",
+ "phase": "llm"
+ },
+ {
+ "message": "Querying VFB",
+ "phase": "mcp"
+ },
+ {
+ "message": "Querying VFB",
+ "phase": "mcp"
+ },
+ {
+ "message": "Checking the answer is covered",
+ "phase": "llm"
+ },
+ {
+ "message": "Writing the answer",
+ "phase": "llm"
+ }
+ ],
+ "event_count": 145,
+ "ok": true,
+ "request_id": "165efb83-ea45-455f-bc7b-00196c0f9cec",
+ "response_id": "chatcmpl-19a48d3ae479dd633e70a725f9a7304c",
+ "images_count": 8,
+ "graphs_count": 0,
+ "response": "The connectivity of olfactory projection neurons is listed in VFB's class-level connectivity tables. Downstream classes for [olfactory projection neuron](https://www.virtualflybrain.org/reports/FBbt_00051298 \"Open olfactory projection neuron in Virtual Fly Brain\") include [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 lateral horn neuron](https://www.virtualflybrain.org/reports/FBbt_00048293 \"Open adult lateral horn neuron in Virtual Fly Brain\"), with mean synaptic weights per connected pair ranging from 7.24 to 13.8. Upstream classes include [PNS neuron](https://www.virtualflybrain.org/reports/FBbt_00059272 \"Open PNS neuron in Virtual Fly Brain\"), [sensory neuron](https://www.virtualflybrain.org/reports/FBbt_00005124 \"Open sensory neuron in Virtual Fly Brain\"), [olfactory system neuron](https://www.virtualflybrain.org/reports/FBbt_00007697 \"Open olfactory system neuron in Virtual Fly Brain\"), and [chemosensory system neuron](https://www.virtualflybrain.org/reports/FBbt_00007696 \"Open chemosensory system neuron in Virtual Fly Brain\"), with mean synaptic weights per connected pair ranging from 10 to 15. VFB does not currently hold direct comparisons of the connectivity of olfactory projection neurons between the Hemibrain and FAFB connectome datasets.",
+ "quality_flags": {
+ "has_tool_status": true,
+ "no_tool_factual_answer": false,
+ "tool_claim_without_tool": false,
+ "disambiguation_only_answer": false,
+ "investigation_plan_answer": false,
+ "not_verified_or_no_results_answer": false,
+ "graph_failure_mentioned": false,
+ "missing_required_graph": false,
+ "used_data_resource": false,
+ "response_chars": 1578,
+ "status_count": 11
+ }
+ },
+ {
+ "attempt_index": 10,
+ "task_index": 10,
+ "task_id": "T2.3",
+ "tier": 2,
+ "title": "Reagent identification",
+ "question": "I want to image neurons in the lateral horn. What split-GAL4 driver lines are available that target lateral horn neuron types?",
+ "requires_graph": false,
+ "min_graphs": 0,
+ "repetition": 1,
+ "duration_ms": 15628,
+ "status_messages": [
+ {
+ "message": "Thinking...",
+ "phase": "llm"
+ },
+ {
+ "message": "Planning the answer",
+ "phase": "llm"
+ },
+ {
+ "message": "Resolving 1 term in VFB",
+ "phase": "mcp"
+ },
+ {
+ "message": "Reading VFB term info",
+ "phase": "mcp"
+ },
+ {
+ "message": "Finding genetic tools",
+ "phase": "mcp"
+ },
+ {
+ "message": "Checking the answer is covered",
+ "phase": "llm"
+ },
+ {
+ "message": "Querying VFB",
+ "phase": "mcp"
+ },
+ {
+ "message": "Checking the answer is covered",
+ "phase": "llm"
+ },
+ {
+ "message": "Writing the answer",
+ "phase": "llm"
+ },
+ {
+ "message": "Checking before saying VFB has no data",
+ "phase": "mcp"
+ },
+ {
+ "message": "Querying VFB",
+ "phase": "mcp"
+ },
+ {
+ "message": "Querying VFB",
+ "phase": "mcp"
+ },
+ {
+ "message": "Querying VFB",
+ "phase": "mcp"
+ },
+ {
+ "message": "Checking the answer is covered",
+ "phase": "llm"
+ },
+ {
+ "message": "Writing the answer",
+ "phase": "llm"
+ }
+ ],
+ "event_count": 205,
+ "ok": true,
+ "request_id": "dee783c9-2358-41bb-ad03-7ab26a2be537",
+ "response_id": "chatcmpl-910f4d7f5e0a505842a5b58fc0eb7d52",
+ "images_count": 8,
+ "graphs_count": 0,
+ "response": "VFB holds 1924 transgene expression reports for [adult lateral horn](https://www.virtualflybrain.org/reports/FBbt_00007053 \"Open adult lateral horn in Virtual Fly Brain\"), including driver lines such as P{GMR11B09-GAL4} and PBac{566.P.SVS-1}IA-2[CPTI100013].",
+ "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": 258,
+ "status_count": 15
+ }
+ },
+ {
+ "attempt_index": 11,
+ "task_index": 11,
+ "task_id": "T2.4",
+ "tier": 2,
+ "title": "Neuron characterisation",
+ "question": "What is known about the LPLC2 visual neuron type? Where is it, what does it connect to, and what is its function?",
+ "requires_graph": false,
+ "min_graphs": 0,
+ "repetition": 1,
+ "duration_ms": 28633,
+ "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"
+ }
+ ],
+ "event_count": 205,
+ "ok": true,
+ "request_id": "60c87ed1-7f43-4339-a441-f7a135901188",
+ "response_id": "chatcmpl-80540f99b1c906d02cbd90b28dad33fa",
+ "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 specific characteristics and functions. It is located in the dorsal area of the lateral cell body rind and has distinct dendritic arbors in each lobula plate layer, extending outwards from the main fiber in the direction of motion detection for the layer. This arrangement allows it to detect looming stimuli and elicit a jump escape response. In the lobula, it has its main dendritic arbors in layers 4 and 5B, with minor processes in layer 5A, and presynaptic sites in layer 4. Its arbors span approximately 25 lobula optic columns, overlapping with other LPLC2 cells. The LPLC2 neuron 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.",
+ "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": 950,
+ "status_count": 7
+ }
+ },
+ {
+ "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": 8545,
+ "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": "8da808d6-0650-46d4-bf99-bb5a78fc10c5",
+ "response_id": "chatcmpl-cb18854cc1e780ccce14928fb674c72b",
+ "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,
+ "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": 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": 131202,
+ "status_messages": [
+ {
+ "message": "Thinking...",
+ "phase": "llm"
+ },
+ {
+ "message": "Planning the answer",
+ "phase": "llm"
+ },
+ {
+ "message": "Resolving 2 terms in VFB",
+ "phase": "mcp"
+ },
+ {
+ "message": "Querying VFB",
+ "phase": "mcp"
+ },
+ {
+ "message": "Checking the answer is covered",
+ "phase": "llm"
+ },
+ {
+ "message": "Writing the answer",
+ "phase": "llm"
+ }
+ ],
+ "event_count": 31,
+ "ok": true,
+ "request_id": "8bb54007-3dc2-4ae1-9aa7-1e3e75b0b022",
+ "response_id": "chatcmpl-d5ce9afb869ddedfabbaf73b9c00305d",
+ "images_count": 5,
+ "graphs_count": 0,
+ "response": "The Hemibrain dataset contains neurons morphologically similar to the fru+ mAL neurons described in light microscopy studies.",
+ "quality_flags": {
+ "has_tool_status": true,
+ "no_tool_factual_answer": false,
+ "tool_claim_without_tool": false,
+ "disambiguation_only_answer": false,
+ "investigation_plan_answer": false,
+ "not_verified_or_no_results_answer": false,
+ "graph_failure_mentioned": false,
+ "missing_required_graph": false,
+ "used_data_resource": false,
+ "response_chars": 125,
+ "status_count": 6
+ }
+ },
+ {
+ "attempt_index": 15,
+ "task_index": 15,
+ "task_id": "T2.8",
+ "tier": 2,
+ "title": "Upstream circuit",
+ "question": "What sensory neurons provide input to the fan-shaped body, and through how many synaptic steps?",
+ "requires_graph": false,
+ "min_graphs": 0,
+ "repetition": 1,
+ "duration_ms": 194541,
+ "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": "7a968141-2c05-479a-a30c-e6847174bcee",
+ "response_id": "chatcmpl-4c9a8e77a6887f35580f00513091acaf",
+ "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": 18314,
+ "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": 123,
+ "ok": true,
+ "request_id": "e3b99b00-4062-43cf-a60f-54ebb3a46858",
+ "response_id": "chatcmpl-8227164834b52eb33aa8f3ad30cee57a",
+ "images_count": 8,
+ "graphs_count": 0,
+ "response": "There are reciprocal connections between mushroom body output neurons and dopaminergic neurons. VFB found 5 reciprocal class-level pairs between [mushroom body output neuron](https://www.virtualflybrain.org/reports/FBbt_00047953 \"Open mushroom body output neuron in Virtual Fly Brain\") and [dopaminergic neuron](https://www.virtualflybrain.org/reports/FBbt_00005131 \"Open dopaminergic neuron in Virtual Fly Brain\"). The strongest specific targets of mushroom body output neuron include [primary interneuron](https://www.virtualflybrain.org/reports/FBbt_00052517 \"Open primary interneuron in Virtual Fly Brain\"), [primary neuron](https://www.virtualflybrain.org/reports/FBbt_00047097 \"Open primary neuron in Virtual Fly Brain\"), [adult GABAergic neuron](https://www.virtualflybrain.org/reports/FBbt_00058207 \"Open adult GABAergic neuron in Virtual Fly Brain\"), [GABAergic neuron](https://www.virtualflybrain.org/reports/FBbt_00007228 \"Open GABAergic neuron in Virtual Fly Brain\"), [adult glutamatergic neuron](https://www.virtualflybrain.org/reports/FBbt_00058208 \"Open adult glutamatergic neuron in Virtual Fly Brain\"), [glutamatergic neuron](https://www.virtualflybrain.org/reports/FBbt_00100291 \"Open glutamatergic neuron in Virtual Fly Brain\"), [adult lateral horn neuron](https://www.virtualflybrain.org/reports/FBbt_00048293 \"Open adult lateral horn neuron in Virtual Fly Brain\"), and [adult cholinergic neuron](https://www.virtualflybrain.org/reports/FBbt_00058205 \"Open adult cholinergic neuron in Virtual Fly Brain\"). For dopaminergic neuron, 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\").",
+ "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": 1736,
+ "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": 22026,
+ "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": 142,
+ "ok": true,
+ "request_id": "0396edbf-4049-4494-8fbb-8839f834e873",
+ "response_id": "chatcmpl-4c3a4ee477809cfffd76ac21644a1833",
+ "images_count": 8,
+ "graphs_count": 0,
+ "response": "The pathway from olfactory receptor neurons to the lateral horn involves projection neurons that reach the lateral horn through four antennal-lobe tracts. Antennal lobe projection neurons are intermediate neuron types and they connect olfactory receptor neurons to 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\"), and [adult antennal lobe local neuron](https://www.virtualflybrain.org/reports/FBbt_00007390 \"Open adult antennal lobe local 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](https://www.virtualflybrain.org/reports/FBbt_00007053 \"Open adult lateral horn in Virtual Fly Brain\") and [1658](https://v2.virtualflybrain.org/org.geppetto.frontend/geppetto?q=FBbt_00007053,NeuronsSynaptic \"Run in VFB: Neurons with synaptic terminals in adult lateral horn\") 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": 1573,
+ "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": 191486,
+ "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": 103,
+ "ok": true,
+ "request_id": "89945cf2-9a57-4b71-99c0-e7ec5d79cc20",
+ "response_id": "chatcmpl-339e4d911760dfabc850aaca4d85a5a2",
+ "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 currently 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": 1051,
+ "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": 12577,
+ "status_messages": [
+ {
+ "message": "Thinking...",
+ "phase": "llm"
+ },
+ {
+ "message": "Planning the answer",
+ "phase": "llm"
+ },
+ {
+ "message": "Resolving 1 term in VFB",
+ "phase": "mcp"
+ },
+ {
+ "message": "Querying VFB connectivity",
+ "phase": "mcp"
+ },
+ {
+ "message": "Checking the literature",
+ "phase": "mcp"
+ },
+ {
+ "message": "Checking the answer is covered",
+ "phase": "llm"
+ },
+ {
+ "message": "Querying VFB",
+ "phase": "mcp"
+ },
+ {
+ "message": "Checking the answer is covered",
+ "phase": "llm"
+ },
+ {
+ "message": "Writing the answer",
+ "phase": "llm"
+ }
+ ],
+ "event_count": 51,
+ "ok": true,
+ "request_id": "63cbeb21-753c-4d53-99b0-ba5b71fb313d",
+ "response_id": "chatcmpl-4a8ad4459e3f457bc9dfa68a37364a76",
+ "images_count": 8,
+ "graphs_count": 0,
+ "response": "The strongest synaptic input to the MBON-gamma1pedc>a/b neuron is not specified. VFB holds upstream connectivity classes for [mushroom body output neuron 11](https://www.virtualflybrain.org/reports/FBbt_00100246 \"Open mushroom body output neuron 11 in Virtual Fly Brain\"), but the lookup did not complete.",
+ "quality_flags": {
+ "has_tool_status": true,
+ "no_tool_factual_answer": false,
+ "tool_claim_without_tool": false,
+ "disambiguation_only_answer": false,
+ "investigation_plan_answer": false,
+ "not_verified_or_no_results_answer": false,
+ "graph_failure_mentioned": false,
+ "missing_required_graph": false,
+ "used_data_resource": false,
+ "response_chars": 305,
+ "status_count": 9
+ }
+ },
+ {
+ "attempt_index": 20,
+ "task_index": 20,
+ "task_id": "T3.5",
+ "tier": 3,
+ "title": "Shared connectivity",
+ "question": "Do the alpha/beta and gamma Kenyon cells converge on any of the same downstream MBON types? Which MBONs receive input from both?",
+ "requires_graph": false,
+ "min_graphs": 0,
+ "repetition": 1,
+ "duration_ms": 12164,
+ "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": 69,
+ "ok": true,
+ "request_id": "6131ec63-bee8-461b-9409-0dc75fe07c6d",
+ "response_id": "chatcmpl-32672f1a4aaa4eaa45fb2c39069f9ba2",
+ "images_count": 8,
+ "graphs_count": 0,
+ "response": "The connectome data indicates that [mushroom body output neuron](https://www.virtualflybrain.org/reports/FBbt_00047953 \"Open mushroom body output neuron in Virtual Fly Brain\") receives input from [Kenyon cell](https://www.virtualflybrain.org/reports/FBbt_00003686 \"Open Kenyon cell in Virtual Fly Brain\"), with 7.09 synapses per connected pair, and 59% of individuals connected. VFB holds [69](https://v2.virtualflybrain.org/org.geppetto.frontend/geppetto?q=FBbt_00047953,SubclassesOf \"Run in VFB: Subclasses of MBON\") subclasses of mushroom body output neuron and [6](https://v2.virtualflybrain.org/org.geppetto.frontend/geppetto?q=FBbt_00100248,SubclassesOf \"Run in VFB: Subclasses of KCab\") subclasses of [alpha/beta Kenyon cell](https://www.virtualflybrain.org/reports/FBbt_00100248 \"Open alpha/beta Kenyon cell in Virtual Fly Brain\").",
+ "quality_flags": {
+ "has_tool_status": true,
+ "no_tool_factual_answer": false,
+ "tool_claim_without_tool": false,
+ "disambiguation_only_answer": false,
+ "investigation_plan_answer": false,
+ "not_verified_or_no_results_answer": false,
+ "graph_failure_mentioned": false,
+ "missing_required_graph": false,
+ "used_data_resource": false,
+ "response_chars": 839,
+ "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": 13716,
+ "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": 89,
+ "ok": true,
+ "request_id": "b2ebfa98-074f-4174-917a-e5e6514b17b3",
+ "response_id": "chatcmpl-41d1dd86119d19e10b16a668378b2ff6",
+ "images_count": 0,
+ "graphs_count": 0,
+ "response": "The 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": 440,
+ "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": 21165,
+ "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": 147,
+ "ok": true,
+ "request_id": "5d1d423a-0bfa-4abb-b967-e2cd47033510",
+ "response_id": "chatcmpl-a080a2e9064fddf14f39072154632a52",
+ "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. The strength of connections between the central complex and the lateral accessory lobe 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": 1262,
+ "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,
+ "duration_ms": 82579,
+ "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": "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": 155,
+ "ok": true,
+ "request_id": "985aacc3-a308-414a-90e0-69a8f4bf528e",
+ "response_id": "chatcmpl-2d5a1bcfa73c5491a40e2abe2a7d08b5",
+ "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. There are [18](https://v2.virtualflybrain.org/org.geppetto.frontend/geppetto?q=FBbt_00047573,ListAllAvailableImages \"Run in VFB: List all available images of DNa02\") images available, as well as [2](https://v2.virtualflybrain.org/org.geppetto.frontend/geppetto?q=FBbt_00047573,SplitsTargeting \"Run in VFB: Splits targeting DNa02\") split-GAL4 combinations that target DNa02, and 2 transgene expression reports. The available images include those from MaleCNS and FlyEM-HB datasets. Additionally, there are 2 genetic tools available to label DNa02 descending neurons, which are [P{R87D07-GAL4.DBD} ∩ P{R75C10-p65.AD} expression pattern](https://www.virtualflybrain.org/reports/VFBexp_FBtp0122422FBtp0119138 \"Open P{R87D07-GAL4.DBD} ∩ P{R75C10-p65.AD} expression pattern in Virtual Fly Brain\") and [P{VT025718-GAL4.DBD} ∩ P{R22C05-p65.AD} expression pattern](https://www.virtualflybrain.org/reports/VFBexp_FBtp0123634FBtp0118395 \"Open P{VT025718-GAL4.DBD} ∩ P{R22C05-p65.AD} expression pattern in Virtual Fly Brain\").",
+ "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": 1287,
+ "status_count": 11
+ }
+ },
+ {
+ "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": 9277,
+ "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": 53,
+ "ok": true,
+ "request_id": "bcf28c7f-51ca-498f-9862-e5fa5555f651",
+ "response_id": "chatcmpl-c1ebc74883fdbdadc3bdaeff0d6f74da",
+ "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": 6
+ }
+ },
+ {
+ "attempt_index": 25,
+ "task_index": 25,
+ "task_id": "T4.2",
+ "tier": 4,
+ "title": "Complete neuron profile",
+ "question": "Give me a comprehensive profile of the giant fiber neuron: its anatomy, connectivity, available driver lines, and relevant publications.",
+ "requires_graph": false,
+ "min_graphs": 0,
+ "repetition": 1,
+ "duration_ms": 220304,
+ "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": 331,
+ "ok": true,
+ "request_id": "0a97bfce-bade-47ea-a2e2-88333c1fa80e",
+ "response_id": "chatcmpl-deabc04cf13dc8adc089cf4acd47cb8d",
+ "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 can be identified by its large descending axon, which is several times larger than any other axon in the cervical connective. There is one giant fiber neuron per hemisphere.\n\nThe giant fiber neuron, also known as DNp01, has specific connectivity, with [389](https://v2.virtualflybrain.org/org.geppetto.frontend/geppetto?q=FBbt_00004020,DownstreamClassConnectivity \"Run in VFB: Downstream connectivity classes for DNp01\") downstream and [472](https://v2.virtualflybrain.org/org.geppetto.frontend/geppetto?q=FBbt_00004020,UpstreamClassConnectivity \"Run in VFB: Upstream connectivity classes for DNp01\") upstream connectivity classes.\n\nVFB holds [10](https://v2.virtualflybrain.org/org.geppetto.frontend/geppetto?q=FBbt_00004020,TransgeneExpressionHere \"Run in VFB: Transgene expression in DNp01\") transgene expression reports for the giant fiber neuron, including expression patterns for P{GMR78G07-GAL4}, P{GMR79D08-GAL4}, P{GMR91H05-GAL4}, P{R48A11-GAL4.DBD} ∩ P{R30C01-p65.AD}, P{R68A06-GAL4.DBD} ∩ P{R25C08-p65.AD}, P{R79H02-GAL4.DBD} ∩ P{R14A01-p65.AD}, P{R79H02-GAL4.DBD} ∩ P{R25C08-p65.AD}, P{VT004455-GAL4.DBD} ∩ P{R10A12-p65.AD}, P{VT014708-GAL4}, and P{VT046265-GAL4}.\n\nRelevant publications include those by Thomas and Wyman (1984), Koto et al. (1981), Namiki et al. (2018), and Power (1948).",
+ "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": 1573,
+ "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": 23691,
+ "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": "Querying VFB",
+ "phase": "mcp"
+ },
+ {
+ "message": "Checking the answer is covered",
+ "phase": "llm"
+ },
+ {
+ "message": "Writing the answer",
+ "phase": "llm"
+ }
+ ],
+ "event_count": 148,
+ "ok": true,
+ "request_id": "dde8850c-1890-424c-ae80-b582ab8ac1dc",
+ "response_id": "chatcmpl-7eb658b2038b7089e78e5f999b7b234c",
+ "images_count": 8,
+ "graphs_count": 1,
+ "response": "Based on connectivity data, adult visual projection neurons and projection neurons might mediate a connection between the visual system and the [mushroom body](https://www.virtualflybrain.org/reports/FBbt_00005801 \"Open mushroom body in Virtual Fly Brain\"). The connectome data indicates that [visual system neuron](https://www.virtualflybrain.org/reports/FBbt_00047736 \"Open visual system neuron in Virtual Fly Brain\") has synaptic connections with several neuron types, including [adult optic lobe neuron](https://www.virtualflybrain.org/reports/FBbt_00003702 \"Open adult optic lobe neuron in Virtual Fly Brain\"), [optic lobe wide-field columnar neuron](https://www.virtualflybrain.org/reports/FBbt_00110137 \"Open optic lobe wide-field columnar neuron in Virtual Fly Brain\"), [adult optic lobe columnar neuron](https://www.virtualflybrain.org/reports/FBbt_00005129 \"Open adult optic lobe 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 [transmedullary neuron](https://www.virtualflybrain.org/reports/FBbt_00003788 \"Open transmedullary neuron in Virtual Fly Brain\"). Additionally, VFB's \"Neurons with some part in mushroom body\" query returns [602](https://v2.virtualflybrain.org/org.geppetto.frontend/geppetto?q=FBbt_00005801,NeuronsPartHere \"Run in VFB: Neurons with some part in mushroom body\") results, which may include neuron types that could facilitate the connection between the visual system and the mushroom body. This suggests that visual information could reach the memory circuit via these connections.",
+ "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": 1672,
+ "status_count": 11
+ }
+ },
+ {
+ "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": 73239,
+ "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": "6c2b23cb-3640-42e0-805b-503c69a8180f",
+ "response_id": "chatcmpl-82cd3f5b28d7f7a0342339b51bb11aa1",
+ "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",
+ "weight": 6184
+ },
+ {
+ "source": "FBbt_00003763",
+ "target": "FBbt_00047095",
+ "label": "6184",
+ "weight": 6184
+ },
+ {
+ "source": "FBbt_00003763",
+ "target": "FBbt_00059271",
+ "label": "6052",
+ "weight": 6052
+ },
+ {
+ "source": "FBbt_00003763",
+ "target": "FBbt_00059274",
+ "label": "6052",
+ "weight": 6052
+ },
+ {
+ "source": "FBbt_00003763",
+ "target": "FBbt_00007693",
+ "label": "6017",
+ "weight": 6017
+ },
+ {
+ "source": "FBbt_00003763",
+ "target": "FBbt_00047736",
+ "label": "6017",
+ "weight": 6017
+ },
+ {
+ "source": "FBbt_00003763",
+ "target": "FBbt_00005125",
+ "label": "5780",
+ "weight": 5780
+ },
+ {
+ "source": "FBbt_00003763",
+ "target": "FBbt_00052046",
+ "label": "5780",
+ "weight": 5780
+ },
+ {
+ "source": "FBbt_00003763",
+ "target": "FBbt_00001366",
+ "label": "5693",
+ "weight": 5693
+ },
+ {
+ "source": "FBbt_00003763",
+ "target": "FBbt_00003702",
+ "label": "5399",
+ "weight": 5399
+ },
+ {
+ "source": "FBbt_00003763",
+ "target": "FBbt_00059247",
+ "label": "5377",
+ "weight": 5377
+ },
+ {
+ "source": "FBbt_00003763",
+ "target": "FBbt_00007577",
+ "label": "5377",
+ "weight": 5377
+ },
+ {
+ "source": "FBbt_00003763",
+ "target": "FBbt_00007173",
+ "label": "5198",
+ "weight": 5198
+ },
+ {
+ "source": "FBbt_00003763",
+ "target": "FBbt_00058205",
+ "label": "5198",
+ "weight": 5198
+ },
+ {
+ "source": "FBbt_00003763",
+ "target": "FBbt_00005129",
+ "label": "5106",
+ "weight": 5106
+ },
+ {
+ "source": "FBbt_00003763",
+ "target": "FBbt_00007578",
+ "label": "5052",
+ "weight": 5052
+ },
+ {
+ "source": "FBbt_00003763",
+ "target": "FBbt_00047096",
+ "label": "4721",
+ "weight": 4721
+ },
+ {
+ "source": "FBbt_00003763",
+ "target": "FBbt_00110136",
+ "label": "4654",
+ "weight": 4654
+ },
+ {
+ "source": "FBbt_00003763",
+ "target": "FBbt_00049539",
+ "label": "4548",
+ "weight": 4548
+ },
+ {
+ "source": "FBbt_00003763",
+ "target": "FBbt_00049541",
+ "label": "4548",
+ "weight": 4548
+ }
+ ]
+ }
+ ],
+ "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": 18502,
+ "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": "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": 251,
+ "ok": true,
+ "request_id": "0ee0950a-5449-4d94-836a-be4bbf67aa5e",
+ "response_id": "chatcmpl-2049fa496ec9aca2308833295ddadaa2",
+ "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, thermosensory neurons have downstream connections to several classes of neurons, including projection neurons and antennal lobe projection neurons, which may have connections to the mushroom body. The mushroom body itself has presynaptic and postsynaptic connections to various neurons, including larval uniglomerular projection neurons and adult odd neurons of the calyx.\n\nThermosensory neurons have strong specific targets, 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. They also receive input from adult antennal lobe local neurons and unilateral local interneurons of the adult antennal lobe, with mean synaptic weights per connected pair ranging from 8.34 to 10.1 synapses.\n\nWhile VFB evidence does not directly describe the connectivity between thermosensory neurons and the mushroom body, it suggests that thermosensory information could influence memory formation through connections to neurons that project to the mushroom 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": 1641,
+ "status_count": 12
+ }
+ },
+ {
+ "attempt_index": 29,
+ "task_index": 29,
+ "task_id": "T4.6",
+ "tier": 4,
+ "title": "Data availability survey",
+ "question": "I'm interested in studying the subesophageal zone (SEZ). How well-characterised is this region in VFB? What neuron types are annotated, what connectomics data is available, and what genetic tools exist for SEZ neurons?",
+ "requires_graph": false,
+ "min_graphs": 0,
+ "repetition": 1,
+ "duration_ms": 27497,
+ "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": "Finding genetic tools",
+ "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": 271,
+ "ok": true,
+ "request_id": "d6d9241e-8c94-4d07-a28f-783b4e9ad780",
+ "response_id": "chatcmpl-786a116b3e98b85ab21e7e5e4c53ba8b",
+ "images_count": 1,
+ "graphs_count": 0,
+ "response": "The [subesophageal zone](https://www.virtualflybrain.org/reports/FBbt_00051068 \"Open subesophageal zone in Virtual Fly Brain\") is well-characterised in VFB, with available imagery and various queries for neuron types and connectomics data. VFB records show [2,698](https://v2.virtualflybrain.org/org.geppetto.frontend/geppetto?q=FBbt_00051068,NeuronsPartHere \"Run in VFB: Neurons with some part in subesophageal zone\") neurons with some part in the subesophageal zone, including [serotonergic SE1 neuron](https://www.virtualflybrain.org/reports/FBbt_00001980 \"Open serotonergic SE1 neuron in Virtual Fly Brain\") and [larval CCAP subesophageal IN-1 neuron](https://www.virtualflybrain.org/reports/FBbt_00111345 \"Open larval CCAP subesophageal IN-1 neuron in Virtual Fly Brain\"). There are also [2,598](https://v2.virtualflybrain.org/org.geppetto.frontend/geppetto?q=FBbt_00051068,NeuronsSynaptic \"Run in VFB: Neurons with synaptic terminals in subesophageal zone\") neurons with synaptic terminals in the subesophageal zone, such as [intrinsic antennal mechanosensory and motor center neuron](https://www.virtualflybrain.org/reports/FBbt_00111352 \"Open intrinsic antennal mechanosensory and motor center neuron in Virtual Fly Brain\") and [AMMC-VLP](https://www.virtualflybrain.org/reports/FBbt_00111354 \"Open AMMC-VLP in Virtual Fly Brain\").\n\nVFB holds 4,205 genetic tool/expression pattern rows for the subesophageal zone, including GAL4 drivers and binary/intersectional drivers like [P{GMR12D05-GAL4} expression pattern](https://www.virtualflybrain.org/reports/VFBexp_FBtp0057511 \"Open P{GMR12D05-GAL4} expression pattern in Virtual Fly Brain\") and [P{GMR16C05-GAL4} expression pattern](https://www.virtualflybrain.org/reports/VFBexp_FBtp0057869 \"Open P{GMR16C05-GAL4} expression pattern in Virtual Fly Brain\").\n\nThe connectome data indicates that there are neurons with presynaptic and postsynaptic terminals in the subesophageal zone, but the exact numbers are not provided in the current results.\n\nVFB has annotated [29,765](https://v2.virtualflybrain.org/org.geppetto.frontend/geppetto?q=FBbt_00051068,ImagesNeurons \"Run in VFB: Images of neurons with some part in subesophageal zone\") images of neurons with some part in the subesophageal zone, including [GMR 21B06 FLP 10-2](https://www.virtualflybrain.org/reports/VFB_00051256 \"Open GMR 21B06 FLP 10-2 in Virtual Fly Brain\") and [GMR 39C03 FLP 7-1](https://www.virtualflybrain.org/reports/VFB_00051225 \"Open GMR 39C03 FLP 7-1 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": 2507,
+ "status_count": 13
+ }
+ },
+ {
+ "attempt_index": 30,
+ "task_index": 30,
+ "task_id": "G1",
+ "tier": 5,
+ "title": "Graph view regression - medulla region connectivity",
+ "question": "what are the class summarised connectivity from the medulla in graph form",
+ "requires_graph": true,
+ "min_graphs": 1,
+ "repetition": 1,
+ "duration_ms": 78618,
+ "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": 191,
+ "ok": true,
+ "request_id": "0051a721-2a3f-4513-9917-8c8600ae9fc3",
+ "response_id": "chatcmpl-83e89a150dc222d64ef858cd80fc718c",
+ "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, [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, and [333](https://v2.virtualflybrain.org/org.geppetto.frontend/geppetto?q=FBbt_00003748,NeuronsPostsynapticHere \"Run in VFB: Neurons with postsynaptic terminals in medulla\") neuron types with postsynaptic terminals. The first 12 neuron types with presynaptic terminals 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.",
+ "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": 1994,
+ "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": 5232,
+ "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": 21,
+ "ok": true,
+ "request_id": "62e97c16-c441-43a6-86e7-a6fc73b53478",
+ "response_id": "chatcmpl-346f1177aaf1af5c0da208c5c4cd231d",
+ "images_count": 0,
+ "graphs_count": 0,
+ "response": "Virtual Fly Brain is for the Drosophila research community.",
+ "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": 59,
+ "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": 7975,
+ "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": 63,
+ "ok": true,
+ "request_id": "070820a9-1499-4ece-b073-7784c29d85a8",
+ "response_id": "chatcmpl-139ae0570a44709011ea0b63a5040bb6",
+ "images_count": 0,
+ "graphs_count": 0,
+ "response": "To cite Virtual Fly Brain in a publication, use the citation VFB evidence on the website, including APA, MLA, Chicago, and BibTeX formats. If you use Virtual Fly Brain data, tools, or resources in your research, please cite their work using the citation formats below.",
+ "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": 268,
+ "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": 6405,
+ "status_messages": [
+ {
+ "message": "Thinking...",
+ "phase": "llm"
+ },
+ {
+ "message": "Planning the answer",
+ "phase": "llm"
+ },
+ {
+ "message": "Reading VFB documentation",
+ "phase": "mcp"
+ },
+ {
+ "message": "Checking VFB documentation",
+ "phase": "mcp"
+ },
+ {
+ "message": "Checking the answer is covered",
+ "phase": "llm"
+ },
+ {
+ "message": "Writing the answer",
+ "phase": "llm"
+ }
+ ],
+ "event_count": 25,
+ "ok": true,
+ "request_id": "06c94bea-cc50-4c3a-8129-a8bf7d2fd864",
+ "response_id": "chatcmpl-516da8e60aa6b8b967f90fd13e2ac444",
+ "images_count": 0,
+ "graphs_count": 0,
+ "response": "Virtual Fly Brain is funded by multiple UK research councils and charitable foundations since 2009.",
+ "quality_flags": {
+ "has_tool_status": true,
+ "no_tool_factual_answer": false,
+ "tool_claim_without_tool": false,
+ "disambiguation_only_answer": false,
+ "investigation_plan_answer": false,
+ "not_verified_or_no_results_answer": false,
+ "graph_failure_mentioned": false,
+ "missing_required_graph": false,
+ "used_data_resource": false,
+ "response_chars": 99,
+ "status_count": 6
+ }
+ },
+ {
+ "attempt_index": 34,
+ "task_index": 34,
+ "task_id": "D4",
+ "tier": 6,
+ "title": "Policies / accessibility",
+ "question": "What is Virtual Fly Brain's accessibility statement?",
+ "requires_graph": false,
+ "min_graphs": 0,
+ "repetition": 1,
+ "duration_ms": 9670,
+ "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": 122,
+ "ok": true,
+ "request_id": "68edab54-8503-408d-9f6f-7e97bdeed192",
+ "response_id": "chatcmpl-8cc57e022c446ef96efad85a24238165",
+ "images_count": 0,
+ "graphs_count": 0,
+ "response": "Virtual Fly Brain's accessibility statement is in line with the Public Sector Bodies (Websites and Mobile Applications) (No. 2) Accessibility Regulations 2018. The University of Edinburgh is committed to making its websites and applications accessible, and Virtual Fly Brain is partially compliant with the Web Content Accessibility Guidelines (WCAG) 2.2 AA standard. The website is designed to be accessible to as many people as possible, but some features, such as 3D image stacks, neuron skeletons, and connectivity diagrams, cannot be made fully accessible without losing scientific meaning.",
+ "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": 595,
+ "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": 9019,
+ "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": 101,
+ "ok": true,
+ "request_id": "06922c9c-138a-459c-b64c-06749268e520",
+ "response_id": "chatcmpl-94fab8e7dde505a8321b1a36911587b9",
+ "images_count": 0,
+ "graphs_count": 0,
+ "response": "To report a problem or contribute data to Virtual Fly Brain, you can get in touch with the team through the contact page. For help with using Virtual Fly Brain, you can use the public support forum at support@virtualflybrain.org. To report technical issues, bugs, or request new features, you can use GitHub Issues. For data inclusion discussions, collaboration proposals, or confidential matters, you can contact the team via 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": 469,
+ "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": 9805,
+ "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": 96,
+ "ok": true,
+ "request_id": "1f833ae3-cca4-4532-9742-25623927ad02",
+ "response_id": "chatcmpl-67dc842723dba1e822cd2116e650f2bb",
+ "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 the view. Use the zoom icons or scroll with the mouse to zoom in or out. The home button resets the view. Additionally, 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": 403,
+ "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": 11274,
+ "status_messages": [
+ {
+ "message": "Thinking...",
+ "phase": "llm"
+ },
+ {
+ "message": "Planning the answer",
+ "phase": "llm"
+ },
+ {
+ "message": "Resolving 1 term in VFB",
+ "phase": "mcp"
+ },
+ {
+ "message": "Reading VFB documentation",
+ "phase": "mcp"
+ },
+ {
+ "message": "Reading VFB documentation",
+ "phase": "mcp"
+ },
+ {
+ "message": "Checking VFB documentation",
+ "phase": "mcp"
+ },
+ {
+ "message": "Checking the answer is covered",
+ "phase": "llm"
+ },
+ {
+ "message": "Writing the answer",
+ "phase": "llm"
+ }
+ ],
+ "event_count": 58,
+ "ok": true,
+ "request_id": "2736d90b-f27e-42da-98aa-0e80c16b59a5",
+ "response_id": "chatcmpl-af9ce4c3d9fa9e3466f04f0b9fd3364c",
+ "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.",
+ "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": 249,
+ "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": 12267,
+ "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": 132,
+ "ok": true,
+ "request_id": "d0f9f625-410f-4388-806a-a2bd70a85539",
+ "response_id": "chatcmpl-8d0ede4db875808955c0234f5ed83a25",
+ "images_count": 0,
+ "graphs_count": 0,
+ "response": "NBLAST is a method to quantify morphological similarity. It works on \"dotprops\" which represent neurons as tangent vectors. For each tangent vector in the query neuron, NBLAST finds the closest tangent vector in the target neuron and calculates a score from the distance between and the dotproduct of the two vectors. The final NBLAST score is the sum over all query-target vector pairs. Typically, this score is normalized to a self-self comparison, with a perfect match scoring 1. An NBLAST similarity score therefore measures how similar the morphology of two neurons is, with higher scores indicating greater similarity.",
+ "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": 624,
+ "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": 14221,
+ "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": 63,
+ "ok": true,
+ "request_id": "2bd6efa0-3d86-425c-a777-b9deea19b026",
+ "response_id": "chatcmpl-efdfbbb1286750218b8abd5055bf71af",
+ "images_count": 0,
+ "graphs_count": 0,
+ "response": "Confidence values on Virtual Fly Brain represent the source study's own confidence score for predictions, such as predicted neurotransmitters. These values should be read against the publication they came from, rather than compared across datasets, as each study defines its own scale and threshold for calling a prediction.",
+ "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": 324,
+ "status_count": 6
+ }
+ },
+ {
+ "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": 8648,
+ "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": 50,
+ "ok": true,
+ "request_id": "39ed2342-4d07-4763-9353-4b28e93bed33",
+ "response_id": "chatcmpl-fdaddd1a011ce8700358316fdc1d1c87",
+ "images_count": 8,
+ "graphs_count": 0,
+ "response": "Bridging registrations are transformations that map one template onto another, allowing data registered to different templates to be compared in a common space. The name \"bridging registrations\" could not be matched in VFB.",
+ "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": 223,
+ "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": 8087,
+ "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": 94,
+ "ok": true,
+ "request_id": "c9376840-558e-4ede-a4ce-4e1d4086b397",
+ "response_id": "chatcmpl-59a9088f0427df9300a79a0e94a89ec0",
+ "images_count": 0,
+ "graphs_count": 0,
+ "response": "Virtual Fly Brain holds light microscopy data, including confocal image stacks from over a hundred studies, registered onto standard templates. The data types include driver expression patterns, split-GAL4 combinations, expression pattern fragments, single neurons, clones or lineages, and painted domains. The brain templates used are JRC2018Unisex, JRC2018UnisexVNC, JFRC2, and Court2018 VNS.",
+ "quality_flags": {
+ "has_tool_status": true,
+ "no_tool_factual_answer": false,
+ "tool_claim_without_tool": false,
+ "disambiguation_only_answer": false,
+ "investigation_plan_answer": false,
+ "not_verified_or_no_results_answer": false,
+ "graph_failure_mentioned": false,
+ "missing_required_graph": false,
+ "used_data_resource": false,
+ "response_chars": 394,
+ "status_count": 6
+ }
+ },
+ {
+ "attempt_index": 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,
+ "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": 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": 6341,
+ "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": 31,
+ "ok": true,
+ "request_id": "bd3ca570-ca5a-4cf8-b335-a37556e69fb1",
+ "response_id": "chatcmpl-354def3e417ea15d1fd60351e6d519e5",
+ "images_count": 0,
+ "graphs_count": 0,
+ "response": "To install and get started with VFB-connect in Python, you can install it via PyPi using the command\n```\npip install vfb-connect\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": 132,
+ "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": 9945,
+ "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": 120,
+ "ok": true,
+ "request_id": "3fd0404c-d504-4d5e-851b-d44f52218e7e",
+ "response_id": "chatcmpl-20b90b2d64c8f5826171d9e038126c34",
+ "images_count": 0,
+ "graphs_count": 0,
+ "response": "To query Virtual Fly Brain programmatically, you can use the Owlery API or the SOLR API. The Owlery API provides OWL reasoning services, including Description Logic (DL) queries and SPARQL queries with OWL reasoning. The base URL for the Owlery API is https://owl.virtualflybrain.org/. You can use the API to perform various queries, such as getting subclasses, superclasses, equivalent classes, and instances of a class. You can also use the SPARQL query endpoint to perform SPARQL queries with OWL reasoning.",
+ "quality_flags": {
+ "has_tool_status": true,
+ "no_tool_factual_answer": false,
+ "tool_claim_without_tool": false,
+ "disambiguation_only_answer": false,
+ "investigation_plan_answer": false,
+ "not_verified_or_no_results_answer": false,
+ "graph_failure_mentioned": false,
+ "missing_required_graph": false,
+ "used_data_resource": false,
+ "response_chars": 510,
+ "status_count": 6
+ }
+ },
+ {
+ "attempt_index": 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": 10869,
+ "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": 117,
+ "ok": true,
+ "request_id": "d2877537-4ff9-41b6-994a-139750c1c09e",
+ "response_id": "chatcmpl-177cb456855a746ca0018986908b8766",
+ "images_count": 0,
+ "graphs_count": 0,
+ "response": "To explore Virtual Fly Brain neurons, you can use the tutorials provided on the Virtual Fly Brain website. Additionally, you can use the navis Python package, which provides functions for analyzing, manipulating, and visualizing neurons. You can load example neurons using `navis.example_neurons()` and access their properties, such as `id`, `nodes`, `cable_length`, and `soma`. You can also create a `NeuronList` to work with multiple neurons at a time. VFB'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": 507,
+ "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": 7856,
+ "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": 92,
+ "ok": true,
+ "request_id": "b5c30fc3-ca6e-4dfe-b37c-0ab60f5dbf5c",
+ "response_id": "chatcmpl-16dca0316bd645bae8aec43620f3f96e",
+ "images_count": 0,
+ "graphs_count": 0,
+ "response": "To use the Virtual Fly Brain Model Context Protocol (MCP) tool, access it at https://vfb3-mcp.virtualflybrain.org. Configure your client to connect to this URL, then ask your AI assistant questions like \"Get information about the neuron \" or \"Search for terms related to medulla in the fly brain\" to query VFB data through Large Language Models.",
+ "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": 345,
+ "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": 5226,
+ "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": 43,
+ "ok": true,
+ "request_id": "fc5798a1-17da-4f93-9a71-f9e913237ecc",
+ "response_id": "chatcmpl-12713c19c1068f3d89447507644205f0",
+ "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 on this topic.",
+ "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": 188,
+ "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": 6783,
+ "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": 40,
+ "ok": true,
+ "request_id": "e08b496e-2129-4705-b3a5-228f3ea83b2b",
+ "response_id": "chatcmpl-6a4cf7ce453599391733d7405476b295",
+ "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": 7646,
+ "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": 64,
+ "ok": true,
+ "request_id": "e20dcef1-09b2-4048-b477-c4153d2690b5",
+ "response_id": "chatcmpl-e02df58d96a959dc31642c786bd1ed04",
+ "images_count": 0,
+ "graphs_count": 0,
+ "response": "Materials from the VFB 'Hacking the connectome' workshop are available. The workshop materials include tutorials, workshop notebooks, and recorded introduction sessions, covering topics such as introduction to connectomic data and tools, tool landscape, discovery, mapping, visualisation, and connectomics.",
+ "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": 306,
+ "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": 18705,
+ "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 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": 86,
+ "ok": true,
+ "request_id": "ae2ce7c5-1c56-438a-b9ed-78a6aa2506a7",
+ "response_id": "chatcmpl-f9bf4497995bf4e2cdf36a4109b22196",
+ "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 and FANC datasets. The name \"FANC\" could not be matched, with closest records found including Fancl, FANCI, and Fancm.",
+ "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": 317,
+ "status_count": 9
+ }
+ },
+ {
+ "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": 5751,
+ "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": 22,
+ "ok": true,
+ "request_id": "09ded804-45dd-4a9e-99ff-f6a8dd5afd42",
+ "response_id": "chatcmpl-51da78de1c54142150e068e9b8823c7a",
+ "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.",
+ "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": 172,
+ "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": 10739,
+ "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": 5179,
+ "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": 5560,
+ "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": "193423c0-8df4-4536-8cd4-f0a21eef6736",
+ "response_id": "chatcmpl-0e278ca7d56857d5e63b83755e7d5cd7",
+ "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": 5560
+ }
+ },
+ {
+ "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": 21839,
+ "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": 12095,
+ "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. The mushroom body also has a compartmental organisation, with the dendrites of mushroom body output neurons and the axon terminals of dopaminergic neurons tiling the lobes into a stereotyped grid of 15 compartments.",
+ "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": 9743,
+ "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": "4e4bcbf2-9f6a-46c5-a25a-d5b22ea47c5e",
+ "response_id": "chatcmpl-f7e5fbf32548e6e0f1f1457a0fb2cd94",
+ "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": 9743
+ }
+ },
+ {
+ "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": 385480,
+ "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": 247,
+ "conversation": true,
+ "turns": [
+ {
+ "turn": 1,
+ "question": "What is the fan-shaped body?",
+ "focus": null,
+ "clicked": null,
+ "duration_ms": 6817,
+ "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 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": 188462,
+ "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\").",
+ "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": 190201,
+ "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 results from VFB's \"NeuronsSynaptic\" query 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\"), and [PFL2](https://www.virtualflybrain.org/reports/FBbt_00111451 \"Open PFL2 in Virtual Fly Brain\"). Additionally, VFB's \"Neurons with presynaptic terminals in fan-shaped body\" query returns [102](https://v2.virtualflybrain.org/org.geppetto.frontend/geppetto?q=FBbt_00003679,NeuronsPresynapticHere \"Run in VFB: Neurons with presynaptic terminals in fan-shaped body\") results, including PFNd_PB2, PFNd_PB3, PFNd_PB5, PFNa_PB4, PFNa_PB5, 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.",
+ "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": "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?"
+ },
+ {
+ "id": "FBbt_00003679",
+ "query_type": "LineageClonesIn",
+ "query": "Which lineage clones are found in 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"
+ },
+ {
+ "id": "FBbt_00003679",
+ "query_type": "NeuronsPresynapticHere",
+ "fn": "get_neurons_with_presynaptic_terminals_in"
+ }
+ ],
+ "unmapped": []
+ },
+ "status_count": 8,
+ "problems": []
+ }
+ ],
+ "ok": true,
+ "request_id": "1cd1410a-6853-4ab5-8533-eb51206c919e",
+ "response_id": "chatcmpl-37656374d84a60607045f57ffb030b47",
+ "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 results from VFB's \"NeuronsSynaptic\" query 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\"), and [PFL2](https://www.virtualflybrain.org/reports/FBbt_00111451 \"Open PFL2 in Virtual Fly Brain\"). Additionally, VFB's \"Neurons with presynaptic terminals in fan-shaped body\" query returns [102](https://v2.virtualflybrain.org/org.geppetto.frontend/geppetto?q=FBbt_00003679,NeuronsPresynapticHere \"Run in VFB: Neurons with presynaptic terminals in fan-shaped body\") results, including PFNd_PB2, PFNd_PB3, PFNd_PB5, PFNa_PB4, PFNa_PB5, 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.",
+ "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": 2150,
+ "status_count": 8,
+ "addressless_followon": false,
+ "context_lost_across_turn": false,
+ "unmatched_claim_after_resolve": false,
+ "repeats_answered_question": false,
+ "slow_followup_turn": true,
+ "slowest_followup_ms": 190201
+ }
+ },
+ {
+ "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": 11871,
+ "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": 4820,
+ "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.",
+ "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": 7051,
+ "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": "8a1b55da-26c0-4ced-aa57-21f4bd2095cd",
+ "response_id": "chatcmpl-ca680219e702fe57e990f57a743eb0e3",
+ "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": 7051
+ }
+ },
+ {
+ "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": 33633,
+ "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": "Checking the answer is covered",
+ "phase": "llm"
+ },
+ {
+ "message": "Writing the answer",
+ "phase": "llm"
+ }
+ ],
+ "event_count": 60,
+ "conversation": true,
+ "turns": [
+ {
+ "turn": 1,
+ "question": "What are the anatomical parts of the medulla? List them.",
+ "focus": null,
+ "clicked": null,
+ "duration_ms": 8426,
+ "ok": true,
+ "response": "The [medulla](https://www.virtualflybrain.org/reports/FBbt_00003748 \"Open medulla in Virtual Fly Brain\") is divided into 10 layers: 1-6 make up the outer (distal) medulla, the seventh (or serpentine) layer exhibits a distinct architecture and layers 8-10 make up the inner (proximal) medulla. Anatomical parts of the medulla include adult chandelier glial cell, adult distal medulla astrocyte-like glial cell, [distal medulla glial cell](https://www.virtualflybrain.org/reports/FBbt_00100528 \"Open distal medulla glial cell in Virtual Fly Brain\"), medulla layer, adult distal medulla ensheathing glial cell, [plexiform medulla](https://www.virtualflybrain.org/reports/FBbt_00045001 \"Open plexiform medulla in Virtual Fly Brain\"), [medulla dorsal rim area](https://www.virtualflybrain.org/reports/FBbt_00045002 \"Open medulla dorsal rim area in Virtual Fly Brain\"), medulla layer M1, medulla layer M5, inner medulla, medulla layer M8, and medulla layer M9.",
+ "followons": [
+ {
+ "id": "FBbt_00003748",
+ "query_type": "ImagesNeurons",
+ "query": "Which neuron images have a part in the medulla?"
+ },
+ {
+ "id": "FBbt_00003748",
+ "query_type": "TransgeneExpressionHere",
+ "query": "Which driver lines label the medulla?"
+ },
+ {
+ "id": "FBbt_00003748",
+ "query_type": "NeuronsPartHere",
+ "query": "Which neurons have part of their arbour in the medulla?"
+ },
+ {
+ "id": "FBbt_00003748",
+ "query_type": "NeuronsSynaptic",
+ "query": "Which neurons have synaptic terminals in the medulla?"
+ },
+ {
+ "id": "FBbt_00003748",
+ "query_type": "NeuronsPostsynapticHere",
+ "query": "Which neurons receive output from the medulla?"
+ },
+ {
+ "id": "FBbt_00003748",
+ "query_type": "NeuronsPresynapticHere",
+ "query": "Which neurons provide input to the medulla?"
+ }
+ ],
+ "context_terms": [
+ {
+ "id": "FBbt_00003748",
+ "label": "medulla"
+ }
+ ],
+ "reproduction": {
+ "ids": [
+ {
+ "id": "FBbt_00003748",
+ "label": "medulla"
+ }
+ ],
+ "calls": [
+ {
+ "id": "FBbt_00003748",
+ "query_type": "PartsOf",
+ "fn": "get_parts_of"
+ }
+ ],
+ "unmapped": []
+ },
+ "status_count": 8,
+ "problems": []
+ },
+ {
+ "turn": 2,
+ "question": "And which neurons have part of their arbour there?",
+ "focus": null,
+ "clicked": null,
+ "duration_ms": 25207,
+ "ok": true,
+ "response": "Neurons with some part in the [medulla](https://www.virtualflybrain.org/reports/FBbt_00003748 \"Open medulla in Virtual Fly Brain\") include [Dm8b](https://www.virtualflybrain.org/reports/FBbt_00110069 \"Open Dm8b in Virtual Fly Brain\"), [MC](https://www.virtualflybrain.org/reports/FBbt_00111640 \"Open MC in Virtual Fly Brain\"), [PS128](https://www.virtualflybrain.org/reports/FBbt_20001883 \"Open PS128 in Virtual Fly Brain\"), [medulla intrinsic neuron vGlutMinew1a](https://www.virtualflybrain.org/reports/FBbt_00110033 \"Open medulla intrinsic neuron vGlutMinew1a in Virtual Fly Brain\"), [TmY27](https://www.virtualflybrain.org/reports/FBbt_00110067 \"Open TmY27 in Virtual Fly Brain\"), and others, with a total of [471](https://v2.virtualflybrain.org/org.geppetto.frontend/geppetto?q=FBbt_00003748,NeuronsPartHere \"Run in VFB: Neurons with some part in medulla\") neuron types.",
+ "followons": [
+ {
+ "id": "FBbt_00003748",
+ "query_type": "TransgeneExpressionHere",
+ "query": "Which driver lines label the medulla?"
+ },
+ {
+ "id": "FBbt_00003748",
+ "query_type": "NeuronsSynaptic",
+ "query": "Which neurons have synaptic terminals in the medulla?"
+ },
+ {
+ "id": "FBbt_00003748",
+ "query_type": "NeuronsPostsynapticHere",
+ "query": "Which neurons receive output from the medulla?"
+ },
+ {
+ "id": "FBbt_00003748",
+ "query_type": "NeuronsPresynapticHere",
+ "query": "Which neurons provide input to the medulla?"
+ },
+ {
+ "id": "FBbt_00003748",
+ "query_type": "PartsOf",
+ "query": "What are the anatomical parts of the medulla?"
+ },
+ {
+ "id": "FBbt_00003748",
+ "query_type": "LineageClonesIn",
+ "query": "Which lineage clones are found in the medulla?"
+ }
+ ],
+ "context_terms": [
+ {
+ "id": "FBbt_00003748",
+ "label": "medulla"
+ }
+ ],
+ "reproduction": {
+ "ids": [
+ {
+ "id": "FBbt_00003748",
+ "label": "medulla"
+ }
+ ],
+ "calls": [
+ {
+ "id": "FBbt_00003748",
+ "query_type": "NeuronsPartHere",
+ "fn": "get_neurons_with_part_in"
+ },
+ {
+ "id": "FBbt_00003748",
+ "query_type": "ImagesNeurons",
+ "fn": "get_images_neurons"
+ },
+ {
+ "id": "FBbt_00003748",
+ "query_type": "PartsOf",
+ "fn": "get_parts_of"
+ }
+ ],
+ "unmapped": []
+ },
+ "status_count": 10,
+ "problems": []
+ }
+ ],
+ "ok": true,
+ "request_id": "1eeeefac-7f95-4f0f-9e01-5601cb8480ff",
+ "response_id": "chatcmpl-6654660f687bfe15120568e52dee87d8",
+ "images_count": 8,
+ "graphs_count": 0,
+ "response": "Neurons with some part in the [medulla](https://www.virtualflybrain.org/reports/FBbt_00003748 \"Open medulla in Virtual Fly Brain\") include [Dm8b](https://www.virtualflybrain.org/reports/FBbt_00110069 \"Open Dm8b in Virtual Fly Brain\"), [MC](https://www.virtualflybrain.org/reports/FBbt_00111640 \"Open MC in Virtual Fly Brain\"), [PS128](https://www.virtualflybrain.org/reports/FBbt_20001883 \"Open PS128 in Virtual Fly Brain\"), [medulla intrinsic neuron vGlutMinew1a](https://www.virtualflybrain.org/reports/FBbt_00110033 \"Open medulla intrinsic neuron vGlutMinew1a in Virtual Fly Brain\"), [TmY27](https://www.virtualflybrain.org/reports/FBbt_00110067 \"Open TmY27 in Virtual Fly Brain\"), and others, with a total of [471](https://v2.virtualflybrain.org/org.geppetto.frontend/geppetto?q=FBbt_00003748,NeuronsPartHere \"Run in VFB: Neurons with some part in medulla\") neuron types.",
+ "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": 875,
+ "status_count": 10,
+ "addressless_followon": false,
+ "context_lost_across_turn": false,
+ "unmatched_claim_after_resolve": false,
+ "repeats_answered_question": false,
+ "slow_followup_turn": false,
+ "slowest_followup_ms": 25207
+ }
+ },
+ {
+ "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": 31710,
+ "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": 276,
+ "conversation": true,
+ "turns": [
+ {
+ "turn": 1,
+ "question": "Tell me about the antennal lobe.",
+ "focus": null,
+ "clicked": null,
+ "duration_ms": 23785,
+ "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 and is the main target for innervation from the antennal nerve. 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. The Virtual Fly Brain web application allows users to search for synaptic input 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": "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": 7925,
+ "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, which are among the [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. Additionally, neurons such as [AMMC-Bi16](https://www.virtualflybrain.org/reports/FBbt_00111480 \"Open AMMC-Bi16 in Virtual Fly Brain\"), [adult antennal lobe projection neuron DL5](https://www.virtualflybrain.org/reports/FBbt_00059280 \"Open adult antennal lobe projection neuron DL5 in Virtual Fly Brain\"), adult antennal lobe projection neuron DM4, adult antennal lobe projection neuron VA1d, adult antennal lobe projection neuron VL1, adult antennal lobe projection neuron VL2a, adult antennal lobe projection neuron VM2, adult antennal lobe projection neuron VM4, and adult multiglomerular antennal lobe projection neuron L1 adPN are among the [673](https://v2.virtualflybrain.org/org.geppetto.frontend/geppetto?q=FBbt_00003924,NeuronsSynaptic \"Run in VFB: Neurons with synaptic terminals in antennal lobe\") neurons with synaptic terminals in the antennal lobe.",
+ "followons": [
+ {
+ "id": "FBbt_00003924",
+ "query_type": "ListAllAvailableImages",
+ "query": "Which images of antennal lobe does VFB have?"
+ },
+ {
+ "id": "FBbt_00003924",
+ "query_type": "NeuronsPartHere",
+ "query": "Which neurons have part of their arbour in the antennal lobe?"
+ },
+ {
+ "id": "FBbt_00003924",
+ "query_type": "NeuronsPostsynapticHere",
+ "query": "Which neurons receive output from the antennal lobe?"
+ },
+ {
+ "id": "FBbt_00003924",
+ "query_type": "PartsOf",
+ "query": "What are the anatomical parts of the antennal lobe?"
+ },
+ {
+ "id": "FBbt_00003924",
+ "query_type": "SubclassesOf",
+ "query": "What are the subtypes of the antennal lobe?"
+ },
+ {
+ "id": "FBbt_00003924",
+ "query_type": "TractsNervesInnervatingHere",
+ "query": "Which tracts and nerves innervate the antennal lobe?"
+ }
+ ],
+ "context_terms": [
+ {
+ "id": "FBbt_00003924",
+ "label": "antennal lobe"
+ }
+ ],
+ "reproduction": {
+ "ids": [
+ {
+ "id": "FBbt_00003924",
+ "label": "antennal lobe"
+ }
+ ],
+ "calls": [
+ {
+ "id": "FBbt_00003924",
+ "query_type": "NeuronsPresynapticHere",
+ "fn": "get_neurons_with_presynaptic_terminals_in"
+ },
+ {
+ "id": "FBbt_00003924",
+ "query_type": "NeuronsSynaptic",
+ "fn": "get_neurons_with_synapses_in"
+ }
+ ],
+ "unmapped": []
+ },
+ "status_count": 8,
+ "problems": []
+ }
+ ],
+ "ok": true,
+ "request_id": "ad994574-d91f-4200-9031-33680b113322",
+ "response_id": "chatcmpl-ecd1d20c39406d82bcb891a9df5f07a6",
+ "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, which are among the [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. Additionally, neurons such as [AMMC-Bi16](https://www.virtualflybrain.org/reports/FBbt_00111480 \"Open AMMC-Bi16 in Virtual Fly Brain\"), [adult antennal lobe projection neuron DL5](https://www.virtualflybrain.org/reports/FBbt_00059280 \"Open adult antennal lobe projection neuron DL5 in Virtual Fly Brain\"), adult antennal lobe projection neuron DM4, adult antennal lobe projection neuron VA1d, adult antennal lobe projection neuron VL1, adult antennal lobe projection neuron VL2a, adult antennal lobe projection neuron VM2, adult antennal lobe projection neuron VM4, and adult multiglomerular antennal lobe projection neuron L1 adPN are among the [673](https://v2.virtualflybrain.org/org.geppetto.frontend/geppetto?q=FBbt_00003924,NeuronsSynaptic \"Run in VFB: Neurons with synaptic terminals in antennal lobe\") neurons with synaptic terminals in the antennal lobe.",
+ "quality_flags": {
+ "has_tool_status": true,
+ "no_tool_factual_answer": false,
+ "tool_claim_without_tool": false,
+ "disambiguation_only_answer": false,
+ "investigation_plan_answer": false,
+ "not_verified_or_no_results_answer": false,
+ "graph_failure_mentioned": false,
+ "missing_required_graph": false,
+ "used_data_resource": false,
+ "response_chars": 2302,
+ "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": 7925
+ }
+ },
+ {
+ "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": 17236,
+ "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": 87,
+ "conversation": true,
+ "turns": [
+ {
+ "turn": 1,
+ "question": "What is the medulla?",
+ "focus": null,
+ "clicked": null,
+ "duration_ms": 4735,
+ "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": 8318,
+ "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 neurons with some part in the medulla are: T4a_R (MaleCNS:113529); T4a_L (MaleCNS:74469); T4a_L (MaleCNS:107619); T4a_R (MaleCNS:153494); T4a_L (MaleCNS:90547); T4a_R (MaleCNS:95926); T4a_L (MaleCNS:207048); [T4a_L (MaleCNS:97069)](https://www.virtualflybrain.org/reports/VFB_jrmc10fb \"Open T4a_L (MaleCNS:97069) in Virtual Fly Brain\"); T4a_L (MaleCNS:166703); T4a_R (MaleCNS:113836); [T4a_L (MaleCNS:543841)](https://www.virtualflybrain.org/reports/VFB_jrmc10fd \"Open T4a_L (MaleCNS:543841) in Virtual Fly Brain\"); [T4a_L (MaleCNS:150592)](https://www.virtualflybrain.org/reports/VFB_jrmc10fa \"Open T4a_L (MaleCNS:150592) in Virtual Fly Brain\"). Additionally, there are [471](https://v2.virtualflybrain.org/org.geppetto.frontend/geppetto?q=FBbt_00003748,NeuronsPartHere \"Run in VFB: Neurons with some part in medulla\") neurons with some part in the medulla, including [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. In total, there are [226,524](https://v2.virtualflybrain.org/org.geppetto.frontend/geppetto?q=FBbt_00003748,ImagesNeurons \"Run in VFB: Images of neurons with some part in medulla\") images of neurons with some part in the medulla.",
+ "followons": [
+ {
+ "id": "FBbt_00003748",
+ "query_type": "TransgeneExpressionHere",
+ "query": "Which driver lines label the medulla?"
+ },
+ {
+ "id": "FBbt_00003748",
+ "query_type": "NeuronsSynaptic",
+ "query": "Which neurons have synaptic terminals in the medulla?"
+ },
+ {
+ "id": "FBbt_00003748",
+ "query_type": "NeuronsPostsynapticHere",
+ "query": "Which neurons receive output from the medulla?"
+ },
+ {
+ "id": "FBbt_00003748",
+ "query_type": "NeuronsPresynapticHere",
+ "query": "Which neurons provide input to the medulla?"
+ },
+ {
+ "id": "FBbt_00003748",
+ "query_type": "PartsOf",
+ "query": "What are the anatomical parts of the medulla?"
+ },
+ {
+ "id": "FBbt_00003748",
+ "query_type": "LineageClonesIn",
+ "query": "Which lineage clones are found in the medulla?"
+ }
+ ],
+ "context_terms": [
+ {
+ "id": "FBbt_00003748",
+ "label": "medulla"
+ }
+ ],
+ "reproduction": {
+ "ids": [
+ {
+ "id": "FBbt_00003748",
+ "label": "medulla"
+ }
+ ],
+ "calls": [
+ {
+ "id": "FBbt_00003748",
+ "query_type": "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": 4183,
+ "ok": true,
+ "response": "The [medulla](https://www.virtualflybrain.org/reports/FBbt_00003748 \"Open medulla in Virtual Fly Brain\") is labeled by [2,342](https://v2.virtualflybrain.org/org.geppetto.frontend/geppetto?q=FBbt_00003748,TransgeneExpressionHere \"Run in VFB: Transgene expression in medulla\") driver lines, including [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\"), and [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\").",
+ "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": "74decb41-7892-4983-b602-4e34aa596f0f",
+ "response_id": "chatcmpl-12824a7523a6ebaa90fa3260f089deca",
+ "images_count": 8,
+ "graphs_count": 0,
+ "response": "The [medulla](https://www.virtualflybrain.org/reports/FBbt_00003748 \"Open medulla in Virtual Fly Brain\") is labeled by [2,342](https://v2.virtualflybrain.org/org.geppetto.frontend/geppetto?q=FBbt_00003748,TransgeneExpressionHere \"Run in VFB: Transgene expression in medulla\") driver lines, including [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\"), and [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\").",
+ "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": 888,
+ "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": 8318
+ }
+ },
+ {
+ "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": 18793,
+ "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": 259,
+ "conversation": true,
+ "turns": [
+ {
+ "turn": 1,
+ "question": "What is the mushroom body?",
+ "focus": null,
+ "clicked": null,
+ "duration_ms": 8565,
+ "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": 10228,
+ "ok": true,
+ "response": "The [mushroom body](https://www.virtualflybrain.org/reports/FBbt_00005801 \"Open mushroom body in Virtual Fly Brain\") is labeled by several driver lines, including PBac{544.SVS-1}Bsg[CPTI100062], PBac{566.P.SVS-1}Bsg[CPTI100005], PBac{566.P.SVS-1}IA-2[CPTI100013], PBac{566.P.SVS-1}sgg[CPTI100027], PBac{602.P.SVS-1}Fas2[CPTI000483], PBac{602.P.SVS-1}HDAC4[CPTI000077], PBac{602.P.SVS-1}Pax[CPTI000161], PBac{602.P.SVS-1}Sema1a[CPTI000505], PBac{602.P.SVS-1}Tm1[CPTI000760], PBac{602.P.SVS-1}dlg1[CPTI000207], PBac{602.P.SVS-1}dlp[CPTI000445], and PBac{602.P.SVS-1}hzg[CPTI000737]. Additionally, Split-GAL4 lines are available for labeling specific cell types in the mushroom body.",
+ "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": "e79f7e85-432f-43ae-9e23-0bf53a06caf4",
+ "response_id": "chatcmpl-1455ce905db1e888e8ac1fd6ff236aec",
+ "images_count": 8,
+ "graphs_count": 0,
+ "response": "The [mushroom body](https://www.virtualflybrain.org/reports/FBbt_00005801 \"Open mushroom body in Virtual Fly Brain\") is labeled by several driver lines, including PBac{544.SVS-1}Bsg[CPTI100062], PBac{566.P.SVS-1}Bsg[CPTI100005], PBac{566.P.SVS-1}IA-2[CPTI100013], PBac{566.P.SVS-1}sgg[CPTI100027], PBac{602.P.SVS-1}Fas2[CPTI000483], PBac{602.P.SVS-1}HDAC4[CPTI000077], PBac{602.P.SVS-1}Pax[CPTI000161], PBac{602.P.SVS-1}Sema1a[CPTI000505], PBac{602.P.SVS-1}Tm1[CPTI000760], PBac{602.P.SVS-1}dlg1[CPTI000207], PBac{602.P.SVS-1}dlp[CPTI000445], and PBac{602.P.SVS-1}hzg[CPTI000737]. Additionally, Split-GAL4 lines are available for labeling specific cell types in the mushroom 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": 680,
+ "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": 10228
+ }
+ },
+ {
+ "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": 21434,
+ "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": "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"
+ },
+ {
+ "message": "Checking the answer is covered",
+ "phase": "llm"
+ },
+ {
+ "message": "Writing the answer",
+ "phase": "llm"
+ }
+ ],
+ "event_count": 162,
+ "conversation": true,
+ "turns": [
+ {
+ "turn": 1,
+ "question": "Which neurons provide input to the medulla?",
+ "focus": null,
+ "clicked": null,
+ "duration_ms": 6196,
+ "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. These neurons have presynaptic terminals in the medulla. Additionally, neurons such as 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 have postsynaptic terminals in the medulla, indicating that they receive input from other neurons, but may also provide output to 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": "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": 15237,
+ "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. These neurons have synaptic terminals in the lobula. VFB holds [528](https://v2.virtualflybrain.org/org.geppetto.frontend/geppetto?q=FBbt_00003852,NeuronsPartHere \"Run in VFB: Neurons with some part in lobula\") records of neurons with some part in the lobula and 528 records of neurons with synaptic terminals in the lobula.",
+ "followons": [
+ {
+ "id": "FBbt_00003852",
+ "query_type": "NeuronsPresynapticHere",
+ "query": "Which neurons provide input to the lobula?"
+ },
+ {
+ "id": "FBbt_00003852",
+ "query_type": "NeuronsPostsynapticHere",
+ "query": "Which neurons receive output from the lobula?"
+ },
+ {
+ "id": "FBbt_00003852",
+ "query_type": "PartsOf",
+ "query": "What are the anatomical parts of the lobula?"
+ },
+ {
+ "id": "FBbt_00003852",
+ "query_type": "TractsNervesInnervatingHere",
+ "query": "Which tracts and nerves innervate the lobula?"
+ },
+ {
+ "id": "FBbt_00003852",
+ "query_type": "LineageClonesIn",
+ "query": "Which lineage clones are found in the lobula?"
+ },
+ {
+ "id": "FBbt_00003852",
+ "query_type": "ImagesNeurons",
+ "query": "Which neuron images have a part in the lobula?"
+ }
+ ],
+ "context_terms": [
+ {
+ "id": "FBbt_00003852",
+ "label": "lobula"
+ },
+ {
+ "id": "FBbt_00003748",
+ "label": "medulla"
+ }
+ ],
+ "reproduction": {
+ "ids": [
+ {
+ "id": "FBbt_00003852",
+ "label": "lobula"
+ },
+ {
+ "id": "FBbt_00003748",
+ "label": "medulla"
+ }
+ ],
+ "calls": [
+ {
+ "id": "FBbt_00003852",
+ "query_type": "ListAllAvailableImages",
+ "fn": "get_instances"
+ },
+ {
+ "id": "FBbt_00003852",
+ "query_type": "NeuronsPartHere",
+ "fn": "get_neurons_with_part_in"
+ },
+ {
+ "id": "FBbt_00003852",
+ "query_type": "NeuronsSynaptic",
+ "fn": "get_neurons_with_synapses_in"
+ },
+ {
+ "id": "FBbt_00003748",
+ "query_type": "NeuronsPresynapticHere",
+ "fn": "get_neurons_with_presynaptic_terminals_in"
+ },
+ {
+ "id": "FBbt_00003748",
+ "query_type": "NeuronsPostsynapticHere",
+ "fn": "get_neurons_with_postsynaptic_terminals_in"
+ }
+ ],
+ "unmapped": []
+ },
+ "status_count": 13,
+ "problems": []
+ }
+ ],
+ "ok": true,
+ "request_id": "b7847bf5-8474-4db7-a847-b7616e0a66c7",
+ "response_id": "chatcmpl-eb0b33f2cc955576c1670f5278a16c2d",
+ "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. These neurons have synaptic terminals in the lobula. VFB holds [528](https://v2.virtualflybrain.org/org.geppetto.frontend/geppetto?q=FBbt_00003852,NeuronsPartHere \"Run in VFB: Neurons with some part in lobula\") records of neurons with some part in the lobula and 528 records of neurons with synaptic terminals in the 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": 1113,
+ "status_count": 13,
+ "addressless_followon": false,
+ "context_lost_across_turn": false,
+ "unmatched_claim_after_resolve": false,
+ "repeats_answered_question": false,
+ "slow_followup_turn": false,
+ "slowest_followup_ms": 15237
+ }
+ },
+ {
+ "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": 35883,
+ "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": 284,
+ "conversation": true,
+ "turns": [
+ {
+ "turn": 1,
+ "question": "What is the protocerebral bridge?",
+ "focus": null,
+ "clicked": null,
+ "duration_ms": 6232,
+ "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. It forms a dorso-posteriorly located part of the central complex embedded in the cortex between the calyces of the two mushroom bodies, and is composed of a row of 18 connected slices, 9 on each side of the midline, numbered 1-9 from medial to lateral.",
+ "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": 9329,
+ "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 some neurons have synaptic terminals in both the protocerebral bridge and the ellipsoid body, such as the [adult protocerebral bridge glomerulus 1-ellipsoid body canal-dorsal gall neuron](https://www.virtualflybrain.org/reports/FBbt_00111376 \"Open adult protocerebral bridge glomerulus 1-ellipsoid body canal-dorsal gall neuron in Virtual Fly Brain\").",
+ "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": 12,
+ "problems": []
+ },
+ {
+ "turn": 3,
+ "question": "Which neurons connect them?",
+ "focus": null,
+ "clicked": null,
+ "duration_ms": 20322,
+ "ok": true,
+ "response": "The [adult protocerebral bridge glomerulus 1-ellipsoid body canal-dorsal gall neuron](https://www.virtualflybrain.org/reports/FBbt_00111376 \"Open adult protocerebral bridge glomerulus 1-ellipsoid body canal-dorsal gall neuron in Virtual Fly Brain\") is one example of a neuron that connects 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\"). VFB records show that some neurons have synaptic terminals in both the protocerebral bridge and the ellipsoid body. These include the adult protocerebral bridge glomerulus 1-ellipsoid body canal-dorsal gall neuron, the adult protocerebral bridge glomerulus 4-ellipsoid body canal-ventral gall neuron, the adult protocerebral bridge glomerulus 5-ellipsoid body canal-dorsal gall neuron, the adult protocerebral bridge glomerulus 6-ellipsoid body canal-ventral gall neuron, the adult protocerebral bridge glomerulus 7-ellipsoid body canal-dorsal gall neuron, and the adult protocerebral bridge glomerulus 8-ellipsoid body canal-ventral gall neuron. Other neurons that have synaptic terminals in the protocerebral bridge include [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 that have synaptic terminals in the ellipsoid body include PEN_PB2, PEN_PB3, PEN_PB5, PEN_PB7, and PEN_PB8.",
+ "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": "731fd71a-50a1-45f3-b555-8dff26f7fde6",
+ "response_id": "chatcmpl-9e188c24cd1eb91895154be14c2f553d",
+ "images_count": 8,
+ "graphs_count": 0,
+ "response": "The [adult protocerebral bridge glomerulus 1-ellipsoid body canal-dorsal gall neuron](https://www.virtualflybrain.org/reports/FBbt_00111376 \"Open adult protocerebral bridge glomerulus 1-ellipsoid body canal-dorsal gall neuron in Virtual Fly Brain\") is one example of a neuron that connects 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\"). VFB records show that some neurons have synaptic terminals in both the protocerebral bridge and the ellipsoid body. These include the adult protocerebral bridge glomerulus 1-ellipsoid body canal-dorsal gall neuron, the adult protocerebral bridge glomerulus 4-ellipsoid body canal-ventral gall neuron, the adult protocerebral bridge glomerulus 5-ellipsoid body canal-dorsal gall neuron, the adult protocerebral bridge glomerulus 6-ellipsoid body canal-ventral gall neuron, the adult protocerebral bridge glomerulus 7-ellipsoid body canal-dorsal gall neuron, and the adult protocerebral bridge glomerulus 8-ellipsoid body canal-ventral gall neuron. Other neurons that have synaptic terminals in the protocerebral bridge include [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 that have synaptic terminals in the ellipsoid body include PEN_PB2, PEN_PB3, PEN_PB5, PEN_PB7, and PEN_PB8.",
+ "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": 1798,
+ "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": 20322
+ }
+ },
+ {
+ "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": 25254,
+ "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": 51,
+ "conversation": true,
+ "turns": [
+ {
+ "turn": 1,
+ "question": "Which neurons have part of them in the medulla?",
+ "focus": null,
+ "clicked": null,
+ "duration_ms": 11952,
+ "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\"), and [TmY27](https://www.virtualflybrain.org/reports/FBbt_00110067 \"Open TmY27 in Virtual Fly Brain\"). 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": 9,
+ "problems": []
+ },
+ {
+ "turn": 2,
+ "question": "How would I get that same result in Python with vfbquery?",
+ "focus": null,
+ "clicked": null,
+ "duration_ms": 13302,
+ "ok": true,
+ "response": "The code below returns the neurons with some part in [medulla](https://www.virtualflybrain.org/reports/FBbt_00003748 \"Open medulla in Virtual Fly Brain\"), as a table, using vfbquery to interface with VFB. 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": "a3f47263-6617-4e4f-81c9-e8d2093d9a31",
+ "response_id": "chatcmpl-2f900735c424ffa9bee3dd79e06896eb",
+ "images_count": 8,
+ "graphs_count": 0,
+ "response": "The code below returns the neurons with some part in [medulla](https://www.virtualflybrain.org/reports/FBbt_00003748 \"Open medulla in Virtual Fly Brain\"), as a table, using vfbquery to interface with VFB. 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": 842,
+ "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": 13302
+ }
+ },
+ {
+ "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": 29886,
+ "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": 158,
+ "conversation": true,
+ "turns": [
+ {
+ "turn": 1,
+ "question": "What are the subclasses of Kenyon cell?",
+ "focus": null,
+ "clicked": null,
+ "duration_ms": 9647,
+ "ok": true,
+ "response": "The subclasses 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\"). 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 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": 20238,
+ "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. VFB holds these 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\"), with their respective VFB ids such as FBbt_00049111, FBbt_00049112, FBbt_00049827, FBbt_00049830, FBbt_00049832, FBbt_00049833, FBbt_00049835, FBbt_00049838, FBbt_00049859, FBbt_00047926, FBbt_00047993, and 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": "80793a51-4b0d-4910-abfa-f4c82ca022eb",
+ "response_id": "chatcmpl-2508fc98fb7146e87c77ffa0f6762832",
+ "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. VFB holds these 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\"), with their respective VFB ids such as FBbt_00049111, FBbt_00049112, FBbt_00049827, FBbt_00049830, FBbt_00049832, FBbt_00049833, FBbt_00049835, FBbt_00049838, FBbt_00049859, FBbt_00047926, FBbt_00047993, and 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": 1592,
+ "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": 20238
+ }
+ }
+ ]
+}
diff --git a/tests/unit/consoleLeakGuard.test.mjs b/tests/unit/consoleLeakGuard.test.mjs
index 9c0f6a3..01fc8ce 100644
--- a/tests/unit/consoleLeakGuard.test.mjs
+++ b/tests/unit/consoleLeakGuard.test.mjs
@@ -183,6 +183,43 @@ test('a failing tool reports its arguments by shape', async () => {
assert.match(output, /max_results:5/, 'the safe arguments are still legible')
})
+test('a failing tool reports the upstream error by shape, not verbatim', async () => {
+ // The gap this closes: `args` was rendered shape-only while `error` beside it
+ // was not, and an upstream message quotes what it was given. get_reviewed_page
+ // takes a URL whose PATH is unconstrained — only the host is allow-listed —
+ // and the fetcher throws that URL back in its message. So a redacted `args`
+ // sat next to an unredacted copy of the same user-supplied value.
+ const url = `https://virtualflybrain.org/${CANARY}-unpublished-notes`
+ const { deps } = buildLiveDeps({
+ toolDefs: TOOL_DEFS,
+ apiBaseUrl: 'https://elm.example/api/v1',
+ apiKey: 'k',
+ defaultModel: 'm',
+ streamText: async () => 'x',
+ collectGraphs: () => [],
+ executeTool: async () => { throw new Error(`Fetch failed for ${url}: HTTP 404`) }
+ })
+ const output = await captureConsole(() => deps.runTool('get_reviewed_page', { url }))
+ assertNoLeak(output, 'the tool-failure error message')
+ assert.match(output, /error=Your Rights and Contact
+
+