diff --git a/app/page.js b/app/page.js index 523ebf5..59ab57f 100644 --- a/app/page.js +++ b/app/page.js @@ -656,6 +656,53 @@ function FeedbackPrompt({ msg, feedbackState, onSubmitHelpful, onSelectNeedsWork ) } +/** + * The identifier for one answer, shown so it can be quoted. + * + * The DPIA describes a data-subject-rights route in which someone asks about + * the data held on a particular exchange by quoting its response identifier. + * The identifier was generated and stored from the beginning and never shown, + * so the route could not be exercised and an assessor could disprove it in a + * browser in under a minute. + * + * On EVERY answer, not only the latest. The feedback prompt is deliberately + * rendered once at the foot of the conversation, but the response someone wants + * to ask about is often not the last one, and an identifier that is only + * available for the newest answer does not support the route the DPIA sets out. + * + * Quiet by design — 0.68em, muted, below the sources line — and selectable, with + * a copy button for the common case. The clipboard API is unavailable over plain + * HTTP and in some embedded browsers, so the text itself is always selectable + * and the button degrades to saying so rather than to nothing. + */ +function ResponseIdentifier({ responseId }) { + const [copied, setCopied] = useState('') + const copy = useCallback(() => { + const write = globalThis.navigator?.clipboard?.writeText + if (typeof write !== 'function') { setCopied('select and copy'); return } + globalThis.navigator.clipboard.writeText(responseId) + .then(() => setCopied('copied')) + .catch(() => setCopied('select and copy')) + }, [responseId]) + return ( +
+ Response ID: + + {responseId} + + + {copied ? {copied} : null} +
+ ) +} + // Only re-renders when its own props change, NOT when sibling messages // are added or the thinking indicator ticks. const ChatMessage = memo(function ChatMessage({ @@ -816,6 +863,7 @@ const ChatMessage = memo(function ChatMessage({ ))} )} + {msg.role === 'assistant' && msg.responseId ? : null} ) }) diff --git a/app/privacy/page.js b/app/privacy/page.js index c43f8a5..e2aa589 100644 --- a/app/privacy/page.js +++ b/app/privacy/page.js @@ -100,6 +100,11 @@ export default function PrivacyPage() {

Your Rights and Contact

+

+ 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. +

For the main Virtual Fly Brain website privacy notice and broader policy information, see{' '} ({ slug, re }) + +// EACH PATTERN CARRIES A SLUG, AND THE SLUG IS WHAT GETS LOGGED. +// +// The escalation and gate lines used to print the matched sentence itself. That +// sentence is prose the model wrote, and the model writes an absence by +// restating the question — so the user's wording came back out of it and into +// the cluster log aggregator, outside governance.js's file mode and outside +// pruneRetention. Logging the sentence's LENGTH would have closed that and left +// nothing behind; logging which pattern matched keeps the more useful half. The +// rate at which each SHAPE of denial fires is a property of the deployment, it +// is countable across runs in a way a free-text sentence never was, and it +// contains nothing of the user's. const ABSENCE_PATTERNS = [ // VFB does not (currently) hold / have / contain / include / provide / list … - new RegExp(`${DB}${GAP}\\b(?:does not|doesn't|do not|don't)\\b[^.!?\\n]{0,20}\\b(?:hold|have|contain|include|provide|list|store|offer|record)s?\\b`, 'i'), + entry('does-not-hold', new RegExp(`${DB}${GAP}\\b(?:does not|doesn't|do not|don't)\\b[^.!?\\n]{0,20}\\b(?:hold|have|contain|include|provide|list|store|offer|record)s?\\b`, 'i')), // VFB has no … / there are no records in VFB … / no data is available in VFB - new RegExp(`${DB}${GAP}\\b(?:has|have|holds?|contains?)\\s+no\\b`, 'i'), - new RegExp(`\\bno\\s+(?:data|records?|information|images?|entries|annotations?)\\b${GAP}\\b(?:in|for|from|within)\\s+${DB}`, 'i'), - new RegExp(`${DB}${GAP}\\b(?:lacks|is missing|are missing)\\b`, 'i'), + entry('has-no', new RegExp(`${DB}${GAP}\\b(?:has|have|holds?|contains?)\\s+no\\b`, 'i')), + entry('no-data-in', new RegExp(`\\bno\\s+(?:data|records?|information|images?|entries|annotations?)\\b${GAP}\\b(?:in|for|from|within)\\s+${DB}`, 'i')), + entry('lacks', new RegExp(`${DB}${GAP}\\b(?:lacks|is missing|are missing)\\b`, 'i')), // … are not present in / not available in / not provided in the current data. // // "provided", "listed" and "given" were not in this list and a live run walked @@ -173,9 +187,9 @@ const ABSENCE_PATTERNS = [ // number of lineage clones, are not provided in the current data" — every one // of which VFB holds and advertises a query for. The verb a model reaches for // is not fixed, so the list has to cover the family rather than the instance. - new RegExp(`\\b(?:is|are|were|was)\\s+not\\s+(?:present|available|found|included|recorded|annotated|provided|listed|given|shown|reported|captured|specified|detailed)\\b${GAP}\\b(?:in|for|within|by)\\s+${DB}`, 'i'), + entry('is-not-present-in', new RegExp(`\\b(?:is|are|were|was)\\s+not\\s+(?:present|available|found|included|recorded|annotated|provided|listed|given|shown|reported|captured|specified|detailed)\\b${GAP}\\b(?:in|for|within|by)\\s+${DB}`, 'i')), // "no such records exist" / "there is no record of X" with VFB nearby - new RegExp(`\\bthere (?:is|are) no\\b${GAP}\\b(?:record|data|entry|entries|image)s?\\b`, 'i'), + entry('there-is-no', new RegExp(`\\bthere (?:is|are) no\\b${GAP}\\b(?:record|data|entry|entries|image)s?\\b`, 'i')), // THE EVIDENCE BLOCK, TALKING ABOUT ITSELF, IN VFB'S NAME. // // harnessFraming rewrites "the provided evidence" to "VFB evidence", which @@ -193,7 +207,7 @@ const ABSENCE_PATTERNS = [ // working set, and the gap between subject and negation is long here — the // sentence recites a whole catalogue first — so this pattern gets a long window // that the specificity of its subject pays for. - new RegExp('\\b(?:VFB|the|this)\\s+evidence\\b[^.!?\\n]{0,160}?\\b(?:does not|doesn\'t|do not)\\s+(?:include|contain|provide|list|show|specify|report)\\b', 'i') + entry('evidence-does-not', new RegExp('\\b(?:VFB|the|this)\\s+evidence\\b[^.!?\\n]{0,160}?\\b(?:does not|doesn\'t|do not)\\s+(?:include|contain|provide|list|show|specify|report)\\b', 'i')) ] /** Split into sentences, keeping each sentence's offset so a repair can be spliced back. */ @@ -219,8 +233,12 @@ export function findAbsenceClaims(text = '') { const src = String(text) const masked = src.replace(/\[([^\]]*)\]\([^)]*\)/g, (m, label) => label + ' '.repeat(m.length - label.length)) return sentences(masked) - .filter(s => ABSENCE_PATTERNS.some(re => re.test(s.text))) - .map(s => ({ ...s, text: src.slice(s.start, s.end) })) + .map(s => ({ s, hit: ABSENCE_PATTERNS.find(p => p.re.test(s.text)) })) + .filter(({ hit }) => Boolean(hit)) + // `pattern` is the slug of the FIRST pattern that matched. First rather than + // all of them: the patterns overlap by design and a list of three slugs says + // less than the most specific one that fired. + .map(({ s, hit }) => ({ ...s, text: src.slice(s.start, s.end), pattern: hit.slug })) } // --- saying something true instead ------------------------------------------- @@ -331,7 +349,11 @@ export function repairUnlicensedAbsences(answerText = '', licence) { return { text: cleaned.trim() ? cleaned : replacement, - repairs: claims.map(c => c.text.trim()) + repairs: claims.map(c => c.text.trim()), + // The same repairs named by pattern rather than quoted. Callers that write + // to the container log use these; the strings above are for the trace, which + // is off unless VFB_HARNESS_TRACE is set. + patterns: claims.map(c => c.pattern) } } diff --git a/lib/orchestrator.mjs b/lib/orchestrator.mjs index 7598725..48ef961 100644 --- a/lib/orchestrator.mjs +++ b/lib/orchestrator.mjs @@ -37,6 +37,7 @@ import { splitMarkdownCell, stripMarkdownLinks } from './markdownLinks.mjs' import { summariseSimilarity } from './similarNeurons.mjs' import { summariseDatasetBreakdown, isDatasetBreakdownQuestion, withoutDatasetSenseConnectome } from './datasetAxis.mjs' import { recordObservedCount } from './countProvenance.mjs' +import { safeText } from './safeToolArgs.mjs' import { summariseClassPartners, isClassConnectivityPayload } from './classPartners.mjs' import { synthGuidance } from './guidanceCards.mjs' import { isIndividualImageQuery, querySemantics, isGeneExpressionQuestion, isDriverLineQuestion, isSplitGal4Question, isAboutVfbItself, asksIntrinsic, INTRINSIC_RE } from './queryTypes.mjs' @@ -554,8 +555,13 @@ export async function maybeEscalateBeforeAbsence(ledger, answer, deps, log = () // On stderr as well as the trace. The trace is per-request and only reachable // from a debug flag; the rate at which answers try to deny data is a property // of the deployment, and it belongs where the grounding audit already is. + // The QUERIES are VFB's own vocabulary. The claimed SENTENCE is prose the + // model wrote by restating the question, so what goes to the log is which + // absence pattern it matched and how long it was — countable across runs, + // and carrying none of the user's wording. The sentence itself is in the + // trace, which is off unless VFB_HARNESS_TRACE is set. console.error(`[VFBchat] ABSENCE ESCALATION | queries=${picks.map(p => `${p.query_type}@${p.id}`).join(',')}` - + ` | claimed="${claims[0].text.trim().slice(0, 120)}"`) + + ` | claimed=absence:${claims[0].pattern} | len=${claims[0].text.trim().length}`) // The draft that denied the data has already been streamed. It is about to be // rewritten, so take it off the screen first — otherwise the replacement is // appended to it and the reader gets both. @@ -581,10 +587,10 @@ export function gateAbsence(ledger, answer, log = () => {}) { if (!text.trim()) return answer try { const licence = absenceLicence(ledger) - const { text: repaired, repairs } = repairUnlicensedAbsences(text, licence) + const { text: repaired, repairs, patterns } = repairUnlicensedAbsences(text, licence) if (!repairs.length) return answer log({ step: 'absence-gate', removed: repairs.length, first: repairs[0].slice(0, 140) }) - console.error(`[VFBchat] ABSENCE GATE | removed=${repairs.length} | licensed=false | ${repairs[0].slice(0, 160)}`) + console.error(`[VFBchat] ABSENCE GATE | removed=${repairs.length} | licensed=false | absence:${patterns.join(',')}`) return repaired } catch (e) { // A guard that throws must not cost the answer. @@ -944,7 +950,7 @@ async function resolveTerms(ledger, names, deps, models, log, speculative = new record = repRecord effectiveId = rep.id publications = extractPublicationRefs(repFetched || {}) - console.error(`[VFBchat] deprecated term redirected | term="${name}" ${id} -> ${rep.id}`) + console.error(`[VFBchat] deprecated term redirected | term=${safeText(name)} ${id} -> ${rep.id}`) } } } @@ -989,7 +995,9 @@ async function resolveTerms(ledger, names, deps, models, log, speculative = new const fid = String(fetchedId || '') const mismatched = /^(FBbt|VFB|FBgn|FBal|FBti|FBtp|FBco)_/.test(fid) && shortId(fid) !== shortId(effectiveId) if (/^(error|threw|null)/.test(fid) || mismatched) { - console.error(`[VFBchat] get_term_info FAILED | term="${name}" requested_id=${effectiveId} returned=${fid} | digest=${digest ? 'kept' : 'discarded'}`) + // The ids identify the term precisely and are VFB's own; the requested NAME + // is often the user's phrase, so it is rendered by shape. + console.error(`[VFBchat] get_term_info FAILED | term=${safeText(name)} requested_id=${effectiveId} returned=${fid} | digest=${digest ? 'kept' : 'discarded'}`) } // Registry: the term-info Name (canonical) and every query-result row label diff --git a/lib/safeToolArgs.mjs b/lib/safeToolArgs.mjs index a57b046..c5351be 100644 --- a/lib/safeToolArgs.mjs +++ b/lib/safeToolArgs.mjs @@ -29,6 +29,28 @@ const SAFE_KEYS = new Set([ // looking at earlier" arriving as `id` is the user's prose, not an identifier. const SAFE_VALUE_RE = /^[\w.,:/-]{0,80}$/ +/** + * A free-text value rendered for a container log: its length, not its content. + * + * safeToolArgs solved this for tool ARGUMENTS. The same rule applies to every + * other free-text value a diagnostic wants to print, and those arrived + * separately and were not covered: the term name in the term-info failure + * report, and the verbatim absence sentence in the escalation and gate lines. + * A term name is often the user's own phrase, and an absence sentence is prose + * the model wrote by restating the question — "VFB does not currently hold data + * on the line from Kyoto that labels PAM neurons" puts the question in the + * cluster log aggregator, outside governance.js's 0600 file mode and outside + * the 30-day pruneRetention. + * + * Under VFB_HARNESS_TRACE the value is printed in full, exactly as safeToolArgs + * does, so the diagnostic loses nothing when someone is actually debugging. + */ +export function safeText(value, { trace = process.env.VFB_HARNESS_TRACE === 'true', max = 200 } = {}) { + const s = value === null || value === undefined ? '' : String(value) + if (trace) return s.slice(0, max) + return `` +} + /** * A one-line, log-safe rendering of a tool's arguments. * `{ query: 'does the mutant line from Kyoto label PAM neurons?', max_results: 5 }` diff --git a/test-results/task-battery/latest.json b/test-results/task-battery/latest.json index 6c0a9df..73c2a6b 100644 --- a/test-results/task-battery/latest.json +++ b/test-results/task-battery/latest.json @@ -1,9 +1,9 @@ { "metadata": { - "run_id": "task-battery-2026-08-13T12-25-21-397Z", - "started_at": "2026-08-13T12:25:21.397Z", - "completed_at": "2026-08-13T12:35:04.442Z", - "git_sha": "943f5a8a7e8aac967b0e297cb84324a5c393c889", + "run_id": "task-battery-2026-08-13T14-27-45-264Z", + "started_at": "2026-08-13T14:27:45.264Z", + "completed_at": "2026-08-13T14:33:51.826Z", + "git_sha": "17a1644227dd4dfec5b7b7dfe9bb54a25b098bcc", "task_file": "/home/runner/work/VFBchat/VFBchat/VFBchat/tests/task-battery/tasks.json", "base_url": "http://127.0.0.1:3210", "started_server": true, @@ -17,8 +17,8 @@ }, "summary": { "total": 64, - "ok": 64, - "errors": 0, + "ok": 63, + "errors": 1, "by_tier": { "T1": { "total": 8, @@ -32,8 +32,8 @@ }, "T3": { "total": 8, - "ok": 8, - "errors": 0 + "ok": 7, + "errors": 1 }, "T4": { "total": 6, @@ -106,10 +106,8 @@ "task_ids": [] }, "slow_followup_turn": { - "count": 1, - "task_ids": [ - "C3" - ] + "count": 0, + "task_ids": [] } }, "conversation": { @@ -117,10 +115,10 @@ "ok": 12, "turns": 27, "followup_turns": 15, - "followup_median_ms": 14119, - "followup_max_ms": 194217 + "followup_median_ms": 7712, + "followup_max_ms": 22924 }, - "mean_duration_ms": 31489 + "mean_duration_ms": 18648 }, "results": [ { @@ -133,7 +131,7 @@ "requires_graph": false, "min_graphs": 0, "repetition": 1, - "duration_ms": 55016, + "duration_ms": 13826, "status_messages": [ { "message": "Thinking...", @@ -162,8 +160,8 @@ ], "event_count": 101, "ok": true, - "request_id": "58f87000-66c5-4172-a44f-4a2f0bb86b99", - "response_id": "chatcmpl-50b579a61c278d219b2ce5b3947d3540", + "request_id": "9a088aa0-69c5-488b-8a6d-eacefb8ab1c7", + "response_id": "chatcmpl-a4329381d1808d7022ebcb0319b58732", "images_count": 8, "graphs_count": 0, "response": "The major subdivisions of the Drosophila [mushroom body](https://www.virtualflybrain.org/reports/FBbt_00005801 \"Open mushroom body in Virtual Fly Brain\") are the calyx, pedunculus, and mushroom body lobe system. The calyx is closest to the cortex and receives sensory interneuron afferents, the pedunculus is a thick axon bundle extending from the calyx to the base of the lobes, and the mushroom body lobe system consists of a vertical branch and a medial branch, which have different structures at different life stages.", @@ -191,7 +189,7 @@ "requires_graph": false, "min_graphs": 0, "repetition": 1, - "duration_ms": 90466, + "duration_ms": 13537, "status_messages": [ { "message": "Thinking...", @@ -220,8 +218,8 @@ ], "event_count": 83, "ok": true, - "request_id": "e428c142-49b4-4f3c-b9d7-93a8487f9e7d", - "response_id": "chatcmpl-0887640e0c51d789f173b3a1c00d23ca", + "request_id": "48cd19eb-0c70-434e-94af-e9dc99f4bfdd", + "response_id": "chatcmpl-24c80354a746e3da302da18d71eef55d", "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\").", @@ -249,7 +247,7 @@ "requires_graph": false, "min_graphs": 0, "repetition": 1, - "duration_ms": 62388, + "duration_ms": 12084, "status_messages": [ { "message": "Thinking...", @@ -296,13 +294,13 @@ "phase": "llm" } ], - "event_count": 77, + "event_count": 94, "ok": true, - "request_id": "5223324b-cc06-4333-8890-b62bb79a8d6b", - "response_id": "chatcmpl-963d07321c27595d4cc0241e48d8a47c", + "request_id": "536f5c15-84e1-4166-83f0-3592dba32b17", + "response_id": "chatcmpl-65b0bb28aaa940aff7ef0dfc8710707f", "images_count": 8, "graphs_count": 1, - "response": "The main input neurons to the [mushroom body](https://www.virtualflybrain.org/reports/FBbt_00005801 \"Open mushroom body in Virtual Fly Brain\") are sensory interneuron afferents to the calyx. VFB records show that there are [366](https://v2.virtualflybrain.org/org.geppetto.frontend/geppetto?q=FBbt_00005801,NeuronsPresynapticHere \"Run in VFB: Neurons with presynaptic terminals in mushroom body\") neurons with presynaptic terminals in mushroom body, including larval uniglomerular projection neurons and larval antennal lobe multiglomerular projection neurons.", + "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 [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, such as [larval uniglomerular projection neuron 63a](https://www.virtualflybrain.org/reports/FBbt_00111675 \"Open larval uniglomerular projection neuron 63a in Virtual Fly Brain\"), [larval uniglomerular projection neuron 67b](https://www.virtualflybrain.org/reports/FBbt_00111684 \"Open larval uniglomerular projection neuron 67b in Virtual Fly Brain\"), and [larval antennal lobe multiglomerular projection neuron C2](https://www.virtualflybrain.org/reports/FBbt_00111716 \"Open larval antennal lobe multiglomerular projection neuron C2 in Virtual Fly Brain\").", "graphs": [ { "type": "basic_graph", @@ -463,7 +461,7 @@ "graph_failure_mentioned": false, "missing_required_graph": false, "used_data_resource": false, - "response_chars": 560, + "response_chars": 996, "status_count": 11 } }, @@ -477,7 +475,7 @@ "requires_graph": false, "min_graphs": 0, "repetition": 1, - "duration_ms": 60115, + "duration_ms": 10543, "status_messages": [ { "message": "Thinking...", @@ -506,8 +504,8 @@ ], "event_count": 24, "ok": true, - "request_id": "4a3e7906-de6a-47fd-b450-2b1b82fe7486", - "response_id": "chatcmpl-ffd6214ae62e086fd8d4f5868a74d12b", + "request_id": "d3462821-fd35-4b17-bccf-5b6fb818898f", + "response_id": "chatcmpl-25b0b6016cf424369cc5ac29c2bc932e", "images_count": 6, "graphs_count": 0, "response": "The primary neurotransmitter used by mushroom body Kenyon cells is acetylcholine.", @@ -535,7 +533,7 @@ "requires_graph": false, "min_graphs": 0, "repetition": 1, - "duration_ms": 32626, + "duration_ms": 18840, "status_messages": [ { "message": "Thinking...", @@ -545,12 +543,16 @@ "message": "Planning the answer", "phase": "llm" }, + { + "phase": "plan", + "message": "The plan is contested — sampling again before committing." + }, { "message": "Resolving 1 term in VFB", "phase": "mcp" }, { - "message": "Querying VFB connectivity", + "message": "Reading VFB term info", "phase": "mcp" }, { @@ -570,168 +572,13 @@ "phase": "llm" } ], - "event_count": 140, + "event_count": 171, "ok": true, - "request_id": "868be79c-3dc2-4f79-8848-e006b3b26592", - "response_id": "chatcmpl-5246e2cc62c3168a2c5f1efab11b82d3", + "request_id": "a31bb0fa-68d1-488b-8859-9f8d3bbf2047", + "response_id": "chatcmpl-5b6b9f5f5c2989290b0d5ad547f79869", "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.", - "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 - } - ] - } - ], + "graphs_count": 0, + "response": "The [antennal lobe](https://www.virtualflybrain.org/reports/FBbt_00003924 \"Open antennal lobe in Virtual Fly Brain\") connects to various brain regions through neurons with presynaptic and postsynaptic terminals. Neurons with presynaptic terminals in the antennal lobe include adult olfactory receptor neurons, such as [adult olfactory receptor neuron Ir75d ac1](https://www.virtualflybrain.org/reports/FBbt_00110011 \"Open adult olfactory receptor neuron Ir75d ac1 in Virtual Fly Brain\") and adult olfactory receptor neuron Or35a ac3I, as well as other neurons like [larval antennal lobe picky local neuron](https://www.virtualflybrain.org/reports/FBbt_00111694 \"Open larval antennal lobe picky local neuron in Virtual Fly Brain\") and [PLP077](https://www.virtualflybrain.org/reports/FBbt_20001577 \"Open PLP077 in Virtual Fly Brain\"). Neurons with postsynaptic terminals in the antennal lobe include adult antennal lobe projection neurons, such as [adult antennal lobe projection neuron DL5](https://www.virtualflybrain.org/reports/FBbt_00059280 \"Open adult antennal lobe projection neuron DL5 in Virtual Fly Brain\") and adult antennal lobe projection neuron VM4, as well as other neurons like [AMMC-Bi16](https://www.virtualflybrain.org/reports/FBbt_00111480 \"Open AMMC-Bi16 in Virtual Fly Brain\") and adult multiglomerular antennal lobe projection neuron L1 adPN.", "quality_flags": { "has_tool_status": true, "no_tool_factual_answer": false, @@ -742,8 +589,8 @@ "graph_failure_mentioned": false, "missing_required_graph": false, "used_data_resource": false, - "response_chars": 974, - "status_count": 8 + "response_chars": 1364, + "status_count": 9 } }, { @@ -756,7 +603,7 @@ "requires_graph": false, "min_graphs": 0, "repetition": 1, - "duration_ms": 22427, + "duration_ms": 13762, "status_messages": [ { "message": "Thinking...", @@ -785,8 +632,8 @@ ], "event_count": 39, "ok": true, - "request_id": "579a0bde-e046-4f82-8344-92359a73675d", - "response_id": "chatcmpl-fa7542b4f423f9b62cb8e149452e40cb", + "request_id": "70058ca4-6f47-4557-830c-446b6d7dd5c2", + "response_id": "chatcmpl-cbc0b026d668a625e24ea1b6716a1f9f", "images_count": 8, "graphs_count": 0, "response": "Approximately 32,388 neurons are in the [adult central brain](https://www.virtualflybrain.org/reports/FBbt_00047887 \"Open adult central brain in Virtual Fly Brain\"). VFB has annotated [9413](https://v2.virtualflybrain.org/org.geppetto.frontend/geppetto?q=FBbt_00047887,NeuronsPartHere \"Run in VFB: Neurons with some part in adult central brain\") neuron types with some part in the adult central brain.\n\n**Published neuron-count estimates — adult central brain** (from the literature):\n\n- ~32,388 neurons (Whole adult brain, both optic lobes and ocellar ganglia included. Ventral nerve cord NOT included; neurons crossing the neck connective are truncated at the brain boundary. Subcount: fully in central brain. One female adult. Dataset: FlyWire connectome neurons, v783.) — Dorkenwald S et al. (2024) Nature 634(8032):124-138 — PMID 39358518\n\n_VFB has annotated 9,413 neuron types with some part in adult central brain — a curated annotation count, not the biological total._", @@ -814,7 +661,7 @@ "requires_graph": false, "min_graphs": 0, "repetition": 1, - "duration_ms": 30464, + "duration_ms": 18100, "status_messages": [ { "message": "Thinking...", @@ -841,13 +688,13 @@ "phase": "llm" } ], - "event_count": 103, + "event_count": 105, "ok": true, - "request_id": "9ba26678-9b96-487a-a481-df57d664f1a2", - "response_id": "chatcmpl-fd6d12d50e1d253ac971d6f8e96c7be5", + "request_id": "30e424f0-f65e-40c9-98c9-4bf099f2589d", + "response_id": "chatcmpl-908c9e5e5c9e4e1e2d80a076e400309b", "images_count": 8, "graphs_count": 1, - "response": "The main components of the Drosophila central complex include the ellipsoid body, the fan-shaped body, the three paired noduli, the asymmetrical bodies, and the protocerebral bridge. These components are associated with functions such as navigation and orientation, locomotor control, and sleep/arousal and memory-related behaviors. VFB holds [363](https://v2.virtualflybrain.org/org.geppetto.frontend/geppetto?q=FBbt_00003632,NeuronsPartHere \"Run in VFB: Neurons with some part in adult central complex\") records of neurons with some part in [adult central complex](https://www.virtualflybrain.org/reports/FBbt_00003632 \"Open adult central complex in Virtual Fly Brain\") and [362](https://v2.virtualflybrain.org/org.geppetto.frontend/geppetto?q=FBbt_00003632,NeuronsSynaptic \"Run in VFB: Neurons with synaptic terminals in adult central complex\") records of neurons with synaptic terminals in adult central complex.", + "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. 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.", "graphs": [ { "type": "basic_graph", @@ -973,7 +820,7 @@ "graph_failure_mentioned": false, "missing_required_graph": false, "used_data_resource": false, - "response_chars": 916, + "response_chars": 925, "status_count": 6 } }, @@ -987,7 +834,7 @@ "requires_graph": false, "min_graphs": 0, "repetition": 1, - "duration_ms": 15893, + "duration_ms": 18557, "status_messages": [ { "message": "Thinking...", @@ -1014,13 +861,13 @@ "phase": "llm" } ], - "event_count": 81, + "event_count": 73, "ok": true, - "request_id": "e82b51ed-40b9-4bd3-9c46-acfdd8fc589c", - "response_id": "chatcmpl-1e68b1fc829dc1c22353a38a2c6617d6", + "request_id": "eff98100-f5ac-46dd-8e66-62a37d2b4ee9", + "response_id": "chatcmpl-2d9b0326363543b0df8f9dd36af3072c", "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, among others. 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.", + "response": "Genetic tools such as PBac{544.SVS-1}Bsg[CPTI100062] and PBac{566.P.SVS-1}Bsg[CPTI100005] are used to label neurons in Drosophila. 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\").", "quality_flags": { "has_tool_status": true, "no_tool_factual_answer": false, @@ -1031,7 +878,7 @@ "graph_failure_mentioned": false, "missing_required_graph": false, "used_data_resource": false, - "response_chars": 502, + "response_chars": 441, "status_count": 6 } }, @@ -1045,7 +892,7 @@ "requires_graph": false, "min_graphs": 0, "repetition": 1, - "duration_ms": 26341, + "duration_ms": 21055, "status_messages": [ { "message": "Thinking...", @@ -1084,13 +931,13 @@ "phase": "llm" } ], - "event_count": 97, + "event_count": 104, "ok": true, - "request_id": "5a6caf02-edcc-410c-b9e4-804ba91da841", - "response_id": "chatcmpl-ec151a8e4fd535ad29a47602c22c91ce", + "request_id": "a77c3c27-e236-423d-97cc-bce910a2c333", + "response_id": "chatcmpl-13fec087eabb07dc85b9f7cb635587dd", "images_count": 8, "graphs_count": 1, - "response": "Dopaminergic input to mushroom body output neurons (MBONs) comes from specific dopaminergic neuron types, including dopaminergic PPL1 neurons and dopaminergic PAM neurons. The strongest specific inputs to MBONs are 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 found that dopaminergic PPL1 neurons and dopaminergic PAM neurons are among the upstream class-connectivity partners of MBONs. The strongest specific inputs to MBONs, ranked by mean synaptic weight per connected pair, are adult cholinergic neurons and Kenyon cells. VFB holds [69](https://v2.virtualflybrain.org/org.geppetto.frontend/geppetto?q=FBbt_00047953,SubclassesOf \"Run in VFB: Subclasses of MBON\") subclasses of MBON.", "graphs": [ { "type": "basic_graph", @@ -1316,7 +1163,7 @@ "graph_failure_mentioned": false, "missing_required_graph": false, "used_data_resource": false, - "response_chars": 480, + "response_chars": 535, "status_count": 9 } }, @@ -1330,7 +1177,7 @@ "requires_graph": false, "min_graphs": 0, "repetition": 1, - "duration_ms": 25985, + "duration_ms": 15236, "status_messages": [ { "message": "Thinking...", @@ -1377,13 +1224,13 @@ "phase": "llm" } ], - "event_count": 191, + "event_count": 155, "ok": true, - "request_id": "e8320728-0014-4087-9021-0d20578f7010", - "response_id": "chatcmpl-7a0934696aacebe9945315f1227cc1fb", + "request_id": "536eecfa-4abe-43f6-9757-1d7b4babe710", + "response_id": "chatcmpl-6f4558f0664ac481827350bcd3c5a099", "images_count": 8, "graphs_count": 0, - "response": "The connectivity of olfactory projection neurons is recorded 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 of 13.8, 13.3, 11.5, and 7.24, respectively. Upstream classes for 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\"), [chemosensory system neuron](https://www.virtualflybrain.org/reports/FBbt_00007696 \"Open chemosensory system neuron in Virtual Fly Brain\"), [sensory system neuron](https://www.virtualflybrain.org/reports/FBbt_00007693 \"Open sensory system 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\"), [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 lLN](https://www.virtualflybrain.org/reports/FBbt_00051502 \"Open adult antennal lobe local neuron lLN in Virtual Fly Brain\"), with mean synaptic weights per connected pair ranging from 15 to 10. VFB does not currently hold data on the consistency of olfactory projection neuron connectivity between the Hemibrain and FAFB connectome datasets.", + "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.", "quality_flags": { "has_tool_status": true, "no_tool_factual_answer": false, @@ -1394,7 +1241,7 @@ "graph_failure_mentioned": false, "missing_required_graph": false, "used_data_resource": false, - "response_chars": 2209, + "response_chars": 1698, "status_count": 11 } }, @@ -1408,7 +1255,7 @@ "requires_graph": false, "min_graphs": 0, "repetition": 1, - "duration_ms": 28026, + "duration_ms": 15819, "status_messages": [ { "message": "Thinking...", @@ -1442,42 +1289,18 @@ "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": 178, + "event_count": 183, "ok": true, - "request_id": "227dfbd1-bd9f-4c09-8d77-e1eb3dea0cf3", - "response_id": "chatcmpl-4c13735c9b58840c0e9163e01b1491ee", + "request_id": "c29c0b1a-6c7d-40aa-8648-26d4c3bd3f84", + "response_id": "chatcmpl-a2cd36af124083d67b85bbc5c3203eb9", "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].", + "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, specifically: [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\"). VFB also holds [24022](https://v2.virtualflybrain.org/org.geppetto.frontend/geppetto?q=FBbt_00048293,ListAllAvailableImages \"Run in VFB: List all available images of LHN\") available images of adult lateral horn neuron and [1374](https://v2.virtualflybrain.org/org.geppetto.frontend/geppetto?q=FBbt_00048293,SubclassesOf \"Run in VFB: Subclasses of LHN\") subclasses of adult lateral horn neuron.", "quality_flags": { "has_tool_status": true, "no_tool_factual_answer": false, @@ -1488,8 +1311,8 @@ "graph_failure_mentioned": false, "missing_required_graph": false, "used_data_resource": false, - "response_chars": 258, - "status_count": 15 + "response_chars": 1919, + "status_count": 9 } }, { @@ -1502,7 +1325,7 @@ "requires_graph": false, "min_graphs": 0, "repetition": 1, - "duration_ms": 27816, + "duration_ms": 15835, "status_messages": [ { "message": "Thinking...", @@ -1533,13 +1356,13 @@ "phase": "llm" } ], - "event_count": 145, + "event_count": 112, "ok": true, - "request_id": "2631a53e-2f8c-4d8f-b84f-279b3c9e2a19", - "response_id": "chatcmpl-1c7552952adbcd5c729ef5846795360e", + "request_id": "cc057a32-e2ed-4365-8911-41166d5cf2b3", + "response_id": "chatcmpl-db208e4834909f594831e8680106678f", "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. The LPLC2 neuron projects to an optic glomerulus of the PVLP, anterior to LPLC1 and dorsal to LC4. Its activity elicits a jump escape response. There are approximately 80 of these cells per optic lobe and they are cholinergic.", + "response": "The [lobula plate-lobula columnar neuron LPLC2](https://www.virtualflybrain.org/reports/FBbt_00111763 \"Open lobula plate-lobula columnar neuron LPLC2 in Virtual Fly Brain\") is a type of neuron with a distinct dendritic arbor in each lobula plate layer, extending outwards from the main fiber in the direction of motion detection for the layer. It is located in the dorsal area of the lateral cell body rind and is involved in detecting looming stimuli, eliciting a jump escape response. VFB records show that the lobula plate-lobula columnar neuron LPLC2 has specific characteristics and functions.", "quality_flags": { "has_tool_status": true, "no_tool_factual_answer": false, @@ -1550,7 +1373,7 @@ "graph_failure_mentioned": false, "missing_required_graph": false, "used_data_resource": false, - "response_chars": 734, + "response_chars": 598, "status_count": 7 } }, @@ -1564,7 +1387,7 @@ "requires_graph": false, "min_graphs": 0, "repetition": 1, - "duration_ms": 10272, + "duration_ms": 8038, "status_messages": [ { "message": "Thinking...", @@ -1593,8 +1416,8 @@ ], "event_count": 37, "ok": true, - "request_id": "28303cff-666c-4e55-8ff9-2ca67ceef927", - "response_id": "chatcmpl-9e76aca37f68e55927f6ed8d0f4b0a43", + "request_id": "68f9e55e-a3a6-4622-9724-a1ea75681b38", + "response_id": "chatcmpl-90887dd29bf6698101f9483d50e5d801", "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.", @@ -1622,7 +1445,7 @@ "requires_graph": false, "min_graphs": 0, "repetition": 1, - "duration_ms": 25514, + "duration_ms": 136161, "status_messages": [ { "message": "Thinking...", @@ -1641,7 +1464,7 @@ "phase": "mcp" }, { - "message": "Querying VFB", + "message": "Reading VFB term info", "phase": "mcp" }, { @@ -1663,11 +1486,11 @@ ], "event_count": 114, "ok": true, - "request_id": "00ccf72d-9ab7-4fa4-b9e5-1669c9445ddb", - "response_id": "chatcmpl-a8ff816b7e7a59f418ea0250f9687a13", + "request_id": "3d8c082c-52a9-4877-ae1a-90d98584397a", + "response_id": "chatcmpl-f06d55efde913320edbb7c4660db68cb", "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. Other sources also mention Mao and Davis (2009), Claridge-Chang et al. (2009), and Ren et al. (2016) as describing PPL1 dopaminergic neurons and their role in aversive memory.", + "response": "Publications describing the dopaminergic PPL1 neurons and their role in aversive memory include Claridge-Chang et al., 2009, Mao and Davis, 2009, Budnik and White, 1988, and Ren et al., 2016. The dopaminergic PPL1 neurons are described as having cell bodies located in the posterior inferior lateral protocerebrum of the adult brain and project to various parts of the mushroom body. These neurons are involved in aversive memory.", "quality_flags": { "has_tool_status": true, "no_tool_factual_answer": false, @@ -1678,7 +1501,7 @@ "graph_failure_mentioned": false, "missing_required_graph": false, "used_data_resource": false, - "response_chars": 367, + "response_chars": 430, "status_count": 9 } }, @@ -1692,7 +1515,7 @@ "requires_graph": false, "min_graphs": 0, "repetition": 1, - "duration_ms": 20960, + "duration_ms": 8740, "status_messages": [ { "message": "Thinking...", @@ -1714,27 +1537,15 @@ "message": "Checking the answer is covered", "phase": "llm" }, - { - "message": "Querying VFB", - "phase": "mcp" - }, - { - "message": "Querying VFB", - "phase": "mcp" - }, - { - "message": "Checking the answer is covered", - "phase": "llm" - }, { "message": "Writing the answer", "phase": "llm" } ], - "event_count": 34, + "event_count": 31, "ok": true, - "request_id": "a13f87e9-9c6e-437d-8eac-89e44809405a", - "response_id": "chatcmpl-4015949b74e30f3e05f1ad4c0c43d153", + "request_id": "d252352c-67dd-4575-ad46-b481ddf25b19", + "response_id": "chatcmpl-3a4992a61d2b2054b4b24ca26d33dca3", "images_count": 5, "graphs_count": 0, "response": "The Hemibrain dataset contains neurons morphologically similar to the fru+ mAL neurons described in light microscopy studies.", @@ -1749,7 +1560,7 @@ "missing_required_graph": false, "used_data_resource": false, "response_chars": 125, - "status_count": 9 + "status_count": 6 } }, { @@ -1762,7 +1573,7 @@ "requires_graph": false, "min_graphs": 0, "repetition": 1, - "duration_ms": 17427, + "duration_ms": 13285, "status_messages": [ { "message": "Thinking...", @@ -1805,13 +1616,13 @@ "phase": "llm" } ], - "event_count": 152, + "event_count": 156, "ok": true, - "request_id": "f9d3737d-3d81-4e6b-817b-448566b38752", - "response_id": "chatcmpl-47d6861af8fbdfe37ebb0c579df16838", + "request_id": "70b972b3-fde7-4258-a0dc-7a853c2c8846", + "response_id": "chatcmpl-14eb69b256e2a1bcd66151b71f09fbc0", "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.", + "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.", "quality_flags": { "has_tool_status": true, "no_tool_factual_answer": false, @@ -1822,7 +1633,7 @@ "graph_failure_mentioned": false, "missing_required_graph": false, "used_data_resource": false, - "response_chars": 1470, + "response_chars": 1450, "status_count": 10 } }, @@ -1836,7 +1647,7 @@ "requires_graph": false, "min_graphs": 0, "repetition": 1, - "duration_ms": 22032, + "duration_ms": 16050, "status_messages": [ { "message": "Thinking...", @@ -1875,13 +1686,13 @@ "phase": "llm" } ], - "event_count": 144, + "event_count": 135, "ok": true, - "request_id": "c111b569-22f4-49f5-afc8-53ae150a1e4a", - "response_id": "chatcmpl-9ec12b5ad8414962b1926187dfd54bd2", + "request_id": "833a0fe2-ab75-4111-b31a-40bf2cf8fc87", + "response_id": "chatcmpl-a46c43b3689cb8f09047bfdd661357a0", "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\") in the inspected partner breakdowns. 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\").", + "response": "There are reciprocal connections between mushroom body output neurons and dopaminergic neurons. VFB found 5 reciprocal class-level pairs between [mushroom body output neuron](https://www.virtualflybrain.org/reports/FBbt_00047953 \"Open mushroom body output neuron in Virtual Fly Brain\") and [dopaminergic neuron](https://www.virtualflybrain.org/reports/FBbt_00005131 \"Open dopaminergic neuron in Virtual Fly Brain\"). The strongest specific targets of mushroom body output neuron include [primary interneuron](https://www.virtualflybrain.org/reports/FBbt_00052517 \"Open primary interneuron in Virtual Fly Brain\"), [primary neuron](https://www.virtualflybrain.org/reports/FBbt_00047097 \"Open primary neuron in Virtual Fly Brain\"), [adult GABAergic neuron](https://www.virtualflybrain.org/reports/FBbt_00058207 \"Open adult GABAergic neuron in Virtual Fly Brain\"), [GABAergic neuron](https://www.virtualflybrain.org/reports/FBbt_00007228 \"Open GABAergic neuron in Virtual Fly Brain\"), [adult glutamatergic neuron](https://www.virtualflybrain.org/reports/FBbt_00058208 \"Open adult glutamatergic neuron in Virtual Fly Brain\"), [glutamatergic neuron](https://www.virtualflybrain.org/reports/FBbt_00100291 \"Open glutamatergic neuron in Virtual Fly Brain\"), [adult lateral horn neuron](https://www.virtualflybrain.org/reports/FBbt_00048293 \"Open adult lateral horn neuron in Virtual Fly Brain\"), and [adult cholinergic neuron](https://www.virtualflybrain.org/reports/FBbt_00058205 \"Open adult cholinergic neuron in Virtual Fly Brain\"). The strongest specific targets of dopaminergic neuron include adult cholinergic neuron and [adult Kenyon cell](https://www.virtualflybrain.org/reports/FBbt_00049825 \"Open adult Kenyon cell in Virtual Fly Brain\").", "quality_flags": { "has_tool_status": true, "no_tool_factual_answer": false, @@ -1892,7 +1703,7 @@ "graph_failure_mentioned": false, "missing_required_graph": false, "used_data_resource": false, - "response_chars": 1772, + "response_chars": 1738, "status_count": 9 } }, @@ -1906,7 +1717,7 @@ "requires_graph": false, "min_graphs": 0, "repetition": 1, - "duration_ms": 18895, + "duration_ms": 14555, "status_messages": [ { "message": "Thinking...", @@ -1945,13 +1756,13 @@ "phase": "llm" } ], - "event_count": 138, + "event_count": 156, "ok": true, - "request_id": "0651a857-22c4-4218-b18e-0fcea5f8b5ab", - "response_id": "chatcmpl-3129652526ade1eab5aab76c65e975a3", + "request_id": "b276a2a4-0e1a-42d0-9449-318b44dbde6e", + "response_id": "chatcmpl-7765c6917284fad38baa4a9c88c9ee7d", "images_count": 8, "graphs_count": 0, - "response": "The pathway from olfactory receptor neurons to the lateral horn involves intermediate neurons. Antennal lobe projection neurons are intermediate neurons that connect olfactory receptor neurons to the lateral horn. The strongest specific inputs to olfactory receptor neurons include [adult antennal lobe local neuron lLN](https://www.virtualflybrain.org/reports/FBbt_00051502 \"Open adult antennal lobe local neuron lLN in Virtual Fly Brain\"), [adult local interneuron of the lateral ALl1 neuroblast](https://www.virtualflybrain.org/reports/FBbt_00007394 \"Open adult local interneuron of the lateral ALl1 neuroblast in Virtual Fly Brain\"), [antennal lobe local neuron](https://www.virtualflybrain.org/reports/FBbt_00052874 \"Open antennal lobe local neuron in Virtual Fly Brain\"), [adult antennal lobe local neuron](https://www.virtualflybrain.org/reports/FBbt_00007390 \"Open adult antennal lobe local neuron in Virtual Fly Brain\"), [olfactory system neuron](https://www.virtualflybrain.org/reports/FBbt_00007697 \"Open olfactory system neuron in Virtual Fly Brain\"), and [adult antennal sensory neuron](https://www.virtualflybrain.org/reports/FBbt_00051173 \"Open adult antennal sensory neuron in Virtual Fly Brain\"). VFB holds [1661](https://v2.virtualflybrain.org/org.geppetto.frontend/geppetto?q=FBbt_00007053,NeuronsPartHere \"Run in VFB: Neurons with some part in adult lateral horn\") records of neurons with some part in [adult lateral horn](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 intermediate neuron types. Antennal lobe projection neurons are interneurons whose dendrites innervate the antennal lobe and whose axons innervate higher brain centers, including the lateral horn. The strongest specific inputs to olfactory receptor neurons include [adult antennal lobe local neuron lLN](https://www.virtualflybrain.org/reports/FBbt_00051502 \"Open adult antennal lobe local neuron lLN in Virtual Fly Brain\"), [adult local interneuron of the lateral ALl1 neuroblast](https://www.virtualflybrain.org/reports/FBbt_00007394 \"Open adult local interneuron of the lateral ALl1 neuroblast in Virtual Fly Brain\"), [antennal lobe local neuron](https://www.virtualflybrain.org/reports/FBbt_00052874 \"Open antennal lobe local neuron in Virtual Fly Brain\"), [adult antennal lobe local neuron](https://www.virtualflybrain.org/reports/FBbt_00007390 \"Open adult antennal lobe local neuron in Virtual Fly Brain\"), [olfactory system neuron](https://www.virtualflybrain.org/reports/FBbt_00007697 \"Open olfactory system neuron in Virtual Fly Brain\"), and [adult antennal sensory neuron](https://www.virtualflybrain.org/reports/FBbt_00051173 \"Open adult antennal sensory neuron in Virtual Fly Brain\"). VFB holds [1661](https://v2.virtualflybrain.org/org.geppetto.frontend/geppetto?q=FBbt_00007053,NeuronsPartHere \"Run in VFB: Neurons with some part in adult lateral horn\") records of neurons with some part in [adult lateral horn](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, @@ -1962,7 +1773,7 @@ "graph_failure_mentioned": false, "missing_required_graph": false, "used_data_resource": false, - "response_chars": 1784, + "response_chars": 1840, "status_count": 9 } }, @@ -1976,7 +1787,7 @@ "requires_graph": false, "min_graphs": 0, "repetition": 1, - "duration_ms": 13288, + "duration_ms": 9456, "status_messages": [ { "message": "Thinking...", @@ -2015,13 +1826,13 @@ "phase": "llm" } ], - "event_count": 102, + "event_count": 103, "ok": true, - "request_id": "a9a05afc-5654-42c8-ac46-8b74d9ee12a4", - "response_id": "chatcmpl-2bc198edaf1eb99b36c60887895b4b68", + "request_id": "5ac3c618-585e-459f-b2b9-5133ba208eda", + "response_id": "chatcmpl-a423b7e62777ecf67160aa7e3dd5c739", "images_count": 5, "graphs_count": 0, - "response": "The adult Drosophila visual system contains [950](https://v2.virtualflybrain.org/org.geppetto.frontend/geppetto?q=FBbt_00047736,SubclassesOf \"Run in VFB: Subclasses of visual system neuron\") distinct neuron types that are classified as subclasses of [visual system neuron](https://www.virtualflybrain.org/reports/FBbt_00047736 \"Open visual system neuron in Virtual Fly Brain\"). These include, but are not limited to, [Dm8b](https://www.virtualflybrain.org/reports/FBbt_00110069 \"Open Dm8b in Virtual Fly Brain\"), [MC](https://www.virtualflybrain.org/reports/FBbt_00111640 \"Open MC in Virtual Fly Brain\"), [AVLP391](https://www.virtualflybrain.org/reports/FBbt_20000500 \"Open AVLP391 in Virtual Fly Brain\"), [PLP031](https://www.virtualflybrain.org/reports/FBbt_20001531 \"Open PLP031 in Virtual Fly Brain\"), [PS070](https://www.virtualflybrain.org/reports/FBbt_20001825 \"Open PS070 in Virtual Fly Brain\"), PS071, PS073, adult visual neuropil intrinsic neuron, lamina wide-field neuron, medulla intrinsic neuron vGlutMinew1a, TmY27, and Mi10b.", + "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, @@ -2032,7 +1843,7 @@ "graph_failure_mentioned": false, "missing_required_graph": false, "used_data_resource": false, - "response_chars": 1041, + "response_chars": 1051, "status_count": 9 } }, @@ -2046,7 +1857,7 @@ "requires_graph": false, "min_graphs": 0, "repetition": 1, - "duration_ms": 23135, + "duration_ms": 15322, "status_messages": [ { "message": "Thinking...", @@ -2109,13 +1920,13 @@ "phase": "llm" } ], - "event_count": 120, + "event_count": 106, "ok": true, - "request_id": "de86994b-f2df-4b60-bb33-5952a782abf0", - "response_id": "chatcmpl-757d07f1fc82294ee257b65657db32ab", + "request_id": "23bca8a9-b597-4b5c-982d-7f3ff682c79b", + "response_id": "chatcmpl-730a429c63a1c7d95e7573881a775461", "images_count": 8, "graphs_count": 0, - "response": "The neuron type referred to in the question, MBON-gamma1pedc>a/b, is not the same as the resolved entity [mushroom body output neuron 11](https://www.virtualflybrain.org/reports/FBbt_00100246 \"Open mushroom body output neuron 11 in Virtual Fly Brain\").", + "response": "That lookup did not complete, so this answer cannot say what VFB holds there.", "quality_flags": { "has_tool_status": true, "no_tool_factual_answer": false, @@ -2126,7 +1937,7 @@ "graph_failure_mentioned": false, "missing_required_graph": false, "used_data_resource": false, - "response_chars": 252, + "response_chars": 77, "status_count": 15 } }, @@ -2140,7 +1951,7 @@ "requires_graph": false, "min_graphs": 0, "repetition": 1, - "duration_ms": 16882, + "duration_ms": 11277, "status_messages": [ { "message": "Thinking...", @@ -2179,13 +1990,13 @@ "phase": "llm" } ], - "event_count": 108, + "event_count": 103, "ok": true, - "request_id": "e19feb59-e564-43d6-8a13-0545f49c290d", - "response_id": "chatcmpl-7d5a393e341d36b341be6000b3a8d223", + "request_id": "889cfd3c-6f01-4583-befc-fe7512c6581b", + "response_id": "chatcmpl-0b854481c0a5194c878fba9e237d5efa", "images_count": 8, "graphs_count": 0, - "response": "The literature does not provide a clear answer to whether alpha/beta and gamma Kenyon cells converge on the same downstream [mushroom body output neuron](https://www.virtualflybrain.org/reports/FBbt_00047953 \"Open mushroom body output neuron in Virtual Fly Brain\") types. VFB returned matching entries including [KCab-c](https://www.virtualflybrain.org/reports/FBbt_00110929 \"Open KCab-c in Virtual Fly Brain\") and [gamma Kenyon cell](https://www.virtualflybrain.org/reports/FBbt_00100247 \"Open gamma Kenyon cell in Virtual Fly Brain\"), but the evidence does not specify which mushroom body output neurons receive input from both. VFB does not currently hold downstream connectivity classes for gamma Kenyon cell. VFB holds [69](https://v2.virtualflybrain.org/org.geppetto.frontend/geppetto?q=FBbt_00047953,SubclassesOf \"Run in VFB: Subclasses of MBON\") subclasses of mushroom body output neuron and [6](https://v2.virtualflybrain.org/org.geppetto.frontend/geppetto?q=FBbt_00100248,SubclassesOf \"Run in VFB: Subclasses of KCab\") subclasses of [alpha/beta Kenyon cell](https://www.virtualflybrain.org/reports/FBbt_00100248 \"Open alpha/beta Kenyon cell in Virtual Fly Brain\").", + "response": "The connectome data indicates that alpha/beta Kenyon cells and gamma Kenyon cells have distinct downstream targets. VFB returned matching entries including [KCab-c](https://www.virtualflybrain.org/reports/FBbt_00110929 \"Open KCab-c in Virtual Fly Brain\") and [gamma Kenyon cell](https://www.virtualflybrain.org/reports/FBbt_00100247 \"Open gamma Kenyon cell in Virtual Fly Brain\"), but the evidence does not specify which mushroom body output neurons receive input from both. VFB does not currently hold data on downstream connectivity classes for gamma Kenyon cells. VFB holds [69](https://v2.virtualflybrain.org/org.geppetto.frontend/geppetto?q=FBbt_00047953,SubclassesOf \"Run in VFB: Subclasses of MBON\") subclasses of [mushroom body output neuron](https://www.virtualflybrain.org/reports/FBbt_00047953 \"Open mushroom body output neuron in Virtual Fly Brain\") 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, @@ -2196,7 +2007,7 @@ "graph_failure_mentioned": false, "missing_required_graph": false, "used_data_resource": false, - "response_chars": 1174, + "response_chars": 1140, "status_count": 9 } }, @@ -2210,7 +2021,7 @@ "requires_graph": false, "min_graphs": 0, "repetition": 1, - "duration_ms": 16724, + "duration_ms": 10995, "status_messages": [ { "message": "Thinking...", @@ -2241,13 +2052,13 @@ "phase": "llm" } ], - "event_count": 91, + "event_count": 92, "ok": true, - "request_id": "55b9d76b-db73-41ef-997e-c9a1d3c2c06f", - "response_id": "chatcmpl-f6e00a35aec3abb4d1e3547e239247a0", + "request_id": "b53459a8-b192-4c14-9bd1-60ca27d4efc0", + "response_id": "chatcmpl-b5bca8d5b94528434617957dcdcadbbd", "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 anatomical containment hierarchy from the DA1 glomerulus up to the top-level brain structure is: DA1 glomerulus -> adult olfactory antennal lobe glomerulus -> adult antennal lobe -> adult deutocerebrum -> adult cerebrum -> adult central brain -> adult brain. VFB does not currently hold data on parts of the [antennal lobe glomerulus DA1](https://www.virtualflybrain.org/reports/FBbt_00003932 \"Open antennal lobe glomerulus DA1 in Virtual Fly Brain\").", "quality_flags": { "has_tool_status": true, "no_tool_factual_answer": false, @@ -2258,7 +2069,7 @@ "graph_failure_mentioned": false, "missing_required_graph": false, "used_data_resource": false, - "response_chars": 451, + "response_chars": 455, "status_count": 7 } }, @@ -2272,7 +2083,7 @@ "requires_graph": false, "min_graphs": 0, "repetition": 1, - "duration_ms": 23932, + "duration_ms": 13873, "status_messages": [ { "message": "Thinking...", @@ -2319,13 +2130,13 @@ "phase": "llm" } ], - "event_count": 140, + "event_count": 149, "ok": true, - "request_id": "78d7c55c-f07c-424d-9a5e-465ae52d63d5", - "response_id": "chatcmpl-99398420a7cb15ebf8020fd16baa7d05", + "request_id": "ff5a0b3b-9ca7-4274-bb69-e785c12c7d5a", + "response_id": "chatcmpl-c51c32f2870a5a1fe3a5ec8fcf0a492c", "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. 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.", + "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 that neurons with some part in the adult central complex 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\"), [PEN_PB8](https://www.virtualflybrain.org/reports/FBbt_00111374 \"Open PEN_PB8 in Virtual Fly Brain\"), and several adult protocerebral bridge glomerulus neurons. The same neurons are also found among those with synaptic terminals in the adult central complex. However, VFB does not currently hold data on neurons with presynaptic or postsynaptic terminals in the embryonic/larval lateral accessory lobe.", "quality_flags": { "has_tool_status": true, "no_tool_factual_answer": false, @@ -2336,7 +2147,7 @@ "graph_failure_mentioned": false, "missing_required_graph": false, "used_data_resource": false, - "response_chars": 1148, + "response_chars": 1020, "status_count": 11 } }, @@ -2350,62 +2161,11 @@ "requires_graph": false, "min_graphs": 0, "repetition": 1, - "duration_ms": 204266, - "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": 166, - "ok": true, - "request_id": "36843366-07cf-445e-ae87-d9d9fdb787d6", - "response_id": "chatcmpl-3a0e2e36465a8f9d761716382c4c7469", - "images_count": 8, - "graphs_count": 0, - "response": "Data for [descending neuron of the anterior dorsal brain DNa02](https://www.virtualflybrain.org/reports/FBbt_00047573 \"Open descending neuron of the anterior dorsal brain DNa02 in Virtual Fly Brain\") is available in VFB, including light microscopy images and driver lines. VFB holds [18](https://v2.virtualflybrain.org/org.geppetto.frontend/geppetto?q=FBbt_00047573,ListAllAvailableImages \"Run in VFB: List all available images of DNa02\") images of DNa02. There are [2](https://v2.virtualflybrain.org/org.geppetto.frontend/geppetto?q=FBbt_00047573,SplitsTargeting \"Run in VFB: Splits targeting DNa02\") split-GAL4 combinations that target DNa02, and 2 transgene expression reports for DNa02. VFB evidence includes images, splits targeting DNa02, transgene expression reports, downstream connectivity classes, and upstream connectivity classes. Genetic tools are available to label descending neuron of the anterior dorsal brain DNa02. The images of DNa02 are from various sources, including MaleCNS and FlyEM-HB.", + "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, @@ -2414,8 +2174,8 @@ "graph_failure_mentioned": false, "missing_required_graph": false, "used_data_resource": false, - "response_chars": 1011, - "status_count": 11 + "response_chars": 25, + "status_count": 0 } }, { @@ -2428,7 +2188,7 @@ "requires_graph": false, "min_graphs": 0, "repetition": 1, - "duration_ms": 11136, + "duration_ms": 5744, "status_messages": [ { "message": "Thinking...", @@ -2455,13 +2215,13 @@ "phase": "llm" } ], - "event_count": 53, + "event_count": 55, "ok": true, - "request_id": "1d26581d-32a1-4c82-8cd0-9b8ff841d06e", - "response_id": "chatcmpl-35a6855b463a4b64ee45e3dfa9909b43", + "request_id": "10c4866d-574c-418f-acb2-5e51e54e6db5", + "response_id": "chatcmpl-125419b73f7caad177aac6100efa5a5a", "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.", + "response": "The neurons involved in the detection of carbon dioxide are carbon dioxide sensitive neurons. These neurons are involved in the detection of carbon dioxide.\n\nThe question of how these neurons are connected and what genetic tools can be used to access them remains unanswered.", "quality_flags": { "has_tool_status": true, "no_tool_factual_answer": false, @@ -2472,7 +2232,7 @@ "graph_failure_mentioned": false, "missing_required_graph": false, "used_data_resource": false, - "response_chars": 210, + "response_chars": 275, "status_count": 6 } }, @@ -2486,7 +2246,7 @@ "requires_graph": false, "min_graphs": 0, "repetition": 1, - "duration_ms": 20619, + "duration_ms": 43801, "status_messages": [ { "message": "Thinking...", @@ -2525,13 +2285,13 @@ "phase": "llm" } ], - "event_count": 173, + "event_count": 383, "ok": true, - "request_id": "f488555c-9c4b-4dd2-8801-adad835c8a43", - "response_id": "chatcmpl-9c50cadba7b26f2e7e0b1cfcd7e75251", + "request_id": "a1963153-aa29-4e53-8ecf-7d644655c88f", + "response_id": "chatcmpl-a48824c6de192b76eb5c44156a65cdff", "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 there is one of these cells 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\nFor genetic manipulation, there are [10](https://v2.virtualflybrain.org/org.geppetto.frontend/geppetto?q=FBbt_00004020,TransgeneExpressionHere \"Run in VFB: Transgene expression in DNp01\") available transgene expression patterns in DNp01, including P{GMR78G07-GAL4}, P{GMR79D08-GAL4}, and P{VT014708-GAL4}.\n\nPublications by Thomas and Wyman (1984), Koto et al. (1981), and Namiki et al. (2018) provide further information on the giant fiber neuron.", + "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. The giant fiber neuron enters the cervical connective via the posterior cerebro-cervical fascicle and descends on the ipsilateral side, in the dorsal cervical fasciculus. In the brain, it has dendritic arborization in the ipsilateral zones A and B of the antennal mechanosensory and motor center, where it receives substantial input from zone A and B Johnston organ neurons. It also arborizes in the posterior ventrolateral protocerebrum and gorget. The giant fiber neuron enters the VNC near the dorsal midline and extends posteroventrally to the mesothoracic neuromere, where it turns ventrolaterally, and ends abruptly without branching. In the mesothoracic neuromere, it forms electrical synapses with downstream motor and premotor neurons at the inframedial bridge, where the two giant fiber neurons connect across the midline, and at the axonal lateral bend.\n\nThe giant fiber neuron has [389](https://v2.virtualflybrain.org/org.geppetto.frontend/geppetto?q=FBbt_00004020,DownstreamClassConnectivity \"Run in VFB: Downstream connectivity classes for DNp01\") downstream connectivity classes 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. Available driver lines include [5](https://v2.virtualflybrain.org/org.geppetto.frontend/geppetto?q=FBbt_00004020,SplitsTargeting \"Run in VFB: Splits targeting DNp01\") split-GAL4 combinations. VFB records show [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}, and P{GMR91H05-GAL4}, among others.\n\nRelevant publications for the giant fiber neuron include Thomas and Wyman (1984), Koto et al. (1981), Power (1948), and others.", "graphs": [ { "type": "basic_graph", @@ -2757,7 +2517,7 @@ "graph_failure_mentioned": false, "missing_required_graph": false, "used_data_resource": false, - "response_chars": 1223, + "response_chars": 2344, "status_count": 9 } }, @@ -2771,7 +2531,7 @@ "requires_graph": false, "min_graphs": 0, "repetition": 1, - "duration_ms": 19713, + "duration_ms": 14880, "status_messages": [ { "message": "Thinking...", @@ -2814,13 +2574,13 @@ "phase": "llm" } ], - "event_count": 179, + "event_count": 142, "ok": true, - "request_id": "c66e0129-a3fd-4879-935d-e9d1e4341351", - "response_id": "chatcmpl-dcb6c46fc198dbc2250166a40df4b031", + "request_id": "b6c16bb8-e2b7-4d77-98f3-392120d0b885", + "response_id": "chatcmpl-4940aa73d0cff86cf9f51b247d9ec28a", "images_count": 8, "graphs_count": 1, - "response": "Based on connectivity data, adult visual projection neurons might mediate the connection between the visual system and the [mushroom body](https://www.virtualflybrain.org/reports/FBbt_00005801 \"Open mushroom body in Virtual Fly Brain\"), as they have presynaptic terminals in the mushroom body. Projection neurons are also suggested to mediate this connection. The strongest specific inputs to [visual system neuron](https://www.virtualflybrain.org/reports/FBbt_00047736 \"Open visual system neuron in Virtual Fly Brain\") include [optic lobe narrow field columnar neuron](https://www.virtualflybrain.org/reports/FBbt_00110136 \"Open optic lobe narrow field columnar neuron in Virtual Fly Brain\"), [optic lobe intrinsic columnar neuron](https://www.virtualflybrain.org/reports/FBbt_00007578 \"Open optic lobe intrinsic columnar neuron in Virtual Fly Brain\"), [adult optic lobe neuron](https://www.virtualflybrain.org/reports/FBbt_00003702 \"Open adult optic lobe neuron in Virtual Fly Brain\"), and [adult optic lobe columnar neuron](https://www.virtualflybrain.org/reports/FBbt_00005129 \"Open adult optic lobe columnar neuron in Virtual Fly Brain\"). The strongest specific targets of visual system neuron are adult optic lobe neuron, [optic lobe wide-field columnar neuron](https://www.virtualflybrain.org/reports/FBbt_00110137 \"Open optic lobe wide-field columnar neuron in Virtual Fly Brain\"), adult optic lobe columnar neuron, optic lobe intrinsic columnar neuron, and [adult visual projection neuron](https://www.virtualflybrain.org/reports/FBbt_00048286 \"Open adult visual projection neuron in Virtual Fly Brain\"). Visual information could potentially reach the memory circuit through these connections. VFB holds [602](https://v2.virtualflybrain.org/org.geppetto.frontend/geppetto?q=FBbt_00005801,NeuronsPartHere \"Run in VFB: Neurons with some part in mushroom body\") neurons with some part in mushroom body and [601](https://v2.virtualflybrain.org/org.geppetto.frontend/geppetto?q=FBbt_00005801,NeuronsSynaptic \"Run in VFB: Neurons with synaptic terminals in mushroom body\") neurons with synaptic terminals in mushroom body.", + "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 adult visual projection neurons have presynaptic terminals in the mushroom body. VFB records show that projection neurons are also potential mediators of this connection.\n\nVisual information could reach the memory circuit via these neurons. 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 visual projection neuron](https://www.virtualflybrain.org/reports/FBbt_00048286 \"Open adult visual projection neuron in Virtual Fly Brain\"), among others.\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.", "graphs": [ { "type": "basic_graph", @@ -3039,7 +2799,7 @@ "graph_failure_mentioned": false, "missing_required_graph": false, "used_data_resource": false, - "response_chars": 2125, + "response_chars": 1588, "status_count": 10 } }, @@ -3053,7 +2813,7 @@ "requires_graph": false, "min_graphs": 0, "repetition": 1, - "duration_ms": 18556, + "duration_ms": 14621, "status_messages": [ { "message": "Thinking...", @@ -3094,8 +2854,8 @@ ], "event_count": 90, "ok": true, - "request_id": "15fac114-7507-4e03-8ee4-bbe1c016b76f", - "response_id": "chatcmpl-e959575d6405faec993ebe262374d5ca", + "request_id": "d94993b2-6219-4f85-9b9f-29de6ee3e178", + "response_id": "chatcmpl-24669aa07cb10b21731aaecac53cffae", "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\").", @@ -3403,7 +3163,7 @@ "requires_graph": false, "min_graphs": 0, "repetition": 1, - "duration_ms": 82578, + "duration_ms": 20209, "status_messages": [ { "message": "Thinking...", @@ -3413,6 +3173,10 @@ "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" @@ -3454,13 +3218,13 @@ "phase": "llm" } ], - "event_count": 139, + "event_count": 175, "ok": true, - "request_id": "becc5404-5927-426c-980d-726fb686f977", - "response_id": "chatcmpl-df3e41de607e3807476877fee292b464", + "request_id": "ebd0297e-8bca-4e06-9add-9da54592e8af", + "response_id": "chatcmpl-120f6a712b7036296df6bdab9466236e", "images_count": 8, "graphs_count": 1, - "response": "Thermosensory neurons are connected to the [mushroom body](https://www.virtualflybrain.org/reports/FBbt_00005801 \"Open mushroom body in Virtual Fly Brain\"). The strongest specific targets of [thermosensory neuron](https://www.virtualflybrain.org/reports/FBbt_00005918 \"Open thermosensory neuron in Virtual Fly Brain\") include [projection neuron](https://www.virtualflybrain.org/reports/FBbt_00007392 \"Open projection neuron in Virtual Fly Brain\"), [adult antennal lobe projection neuron](https://www.virtualflybrain.org/reports/FBbt_00067123 \"Open adult antennal lobe projection neuron in Virtual Fly Brain\"), and [antennal lobe projection neuron](https://www.virtualflybrain.org/reports/FBbt_00007422 \"Open antennal lobe projection neuron in Virtual Fly Brain\"). Thermosensory neurons influence mushroom body memory formation through thermosensory projection neurons, with downstream evidence to mushroom body dopaminergic neurons and Kenyon cell classes. 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 and [304](https://v2.virtualflybrain.org/org.geppetto.frontend/geppetto?q=FBbt_00005801,NeuronsPostsynapticHere \"Run in VFB: Neurons with postsynaptic terminals in mushroom body\") neurons with postsynaptic terminals in mushroom body. Temperature information could influence memory formation due to the connectivity between thermosensory neurons and the mushroom body.", + "response": "The connectivity between thermosensory neurons and the [mushroom body](https://www.virtualflybrain.org/reports/FBbt_00005801 \"Open mushroom body in Virtual Fly Brain\") is supported by evidence from VFB, which suggests that thermosensory neurons influence mushroom body memory formation through thermosensory projection neurons. VFB's class-level connectivity table for [thermosensory neuron](https://www.virtualflybrain.org/reports/FBbt_00005918 \"Open thermosensory neuron in Virtual Fly Brain\") lists downstream classes, including [projection neuron](https://www.virtualflybrain.org/reports/FBbt_00007392 \"Open projection neuron in Virtual Fly Brain\"), [adult antennal lobe projection neuron](https://www.virtualflybrain.org/reports/FBbt_00067123 \"Open adult antennal lobe projection neuron in Virtual Fly Brain\"), and [antennal lobe projection neuron](https://www.virtualflybrain.org/reports/FBbt_00007422 \"Open antennal lobe projection neuron in Virtual Fly Brain\"), with the strongest specific targets having 18.9, 18.8, and 18.7 synapses per connected pair, respectively. Additionally, VFB's query for neurons with presynaptic terminals in mushroom body returns [366](https://v2.virtualflybrain.org/org.geppetto.frontend/geppetto?q=FBbt_00005801,NeuronsPresynapticHere \"Run in VFB: Neurons with presynaptic terminals in mushroom body\") results, and the query for neurons with postsynaptic terminals in mushroom body returns [304](https://v2.virtualflybrain.org/org.geppetto.frontend/geppetto?q=FBbt_00005801,NeuronsPostsynapticHere \"Run in VFB: Neurons with postsynaptic terminals in mushroom body\") results. This suggests that temperature information could indeed influence memory formation in the mushroom body.", "graphs": [ { "type": "basic_graph", @@ -3686,8 +3450,8 @@ "graph_failure_mentioned": false, "missing_required_graph": false, "used_data_resource": false, - "response_chars": 1567, - "status_count": 12 + "response_chars": 1718, + "status_count": 13 } }, { @@ -3700,7 +3464,7 @@ "requires_graph": false, "min_graphs": 0, "repetition": 1, - "duration_ms": 213596, + "duration_ms": 200594, "status_messages": [ { "message": "Thinking...", @@ -3710,10 +3474,6 @@ "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" @@ -3727,7 +3487,23 @@ "phase": "mcp" }, { - "message": "Querying VFB connectivity", + "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" }, { @@ -3743,13 +3519,13 @@ "phase": "llm" } ], - "event_count": 193, + "event_count": 227, "ok": true, - "request_id": "6c2ed8c0-0f12-4ab8-a80c-eb261c570cc4", - "response_id": "chatcmpl-be80c1ec463352ad9f5a59c360338134", - "images_count": 0, + "request_id": "08f9b5d3-ee47-412f-919a-91c37e970279", + "response_id": "chatcmpl-cd3acb0aead0ff3b9d2488131bbbe2a0", + "images_count": 1, "graphs_count": 0, - "response": "The subesophageal zone is characterised in VFB with annotated neuron types, including the [larval subesophageal zone descending SEZ DN neuron](https://www.virtualflybrain.org/reports/FBbt_00111241 \"Open larval subesophageal zone descending SEZ DN neuron in Virtual Fly Brain\"). This neuron has its soma location in the cell body rind of the larval gnathal ganglion and has synaptic input/output in the larval central nervous system, receiving synaptic input from neurons such as the larval A00c neuron and the larval Basin neuron, and sending synaptic output to these cells. Genetic tools exist for SEZ neurons, including GAL4 drivers and binary/intersectional drivers, with VFB returning 4205 genetic tool/expression pattern rows for the subesophageal zone. The larval subesophageal zone descending SEZ DN neuron has available connectomics data. VFB holds transgene expression reports and downstream and upstream connectivity classes for the larval subesophageal zone descending SEZ DN neuron.", + "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 and genetic tools 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 have synaptic terminals in the subesophageal zone, such as intrinsic antennal mechanosensory and motor center neurons and [AMMC-VLP](https://www.virtualflybrain.org/reports/FBbt_00111354 \"Open AMMC-VLP in Virtual Fly Brain\") neurons. Additionally, [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 have presynaptic terminals in the subesophageal zone, including [AMMC-Bi1](https://www.virtualflybrain.org/reports/FBbt_00111465 \"Open AMMC-Bi1 in Virtual Fly Brain\"), [AMMC-Bi4](https://www.virtualflybrain.org/reports/FBbt_00111468 \"Open AMMC-Bi4 in Virtual Fly Brain\"), and [AMMC-Bi8](https://www.virtualflybrain.org/reports/FBbt_00111472 \"Open AMMC-Bi8 in Virtual Fly Brain\") neurons. There are also genetic tools available for subesophageal zone neurons, including 4,205 GAL4 drivers and binary/intersectional drivers, such as P{GMR12D05-GAL4} and P{GMR16C05-GAL4} expression patterns.", "quality_flags": { "has_tool_status": true, "no_tool_factual_answer": false, @@ -3760,8 +3536,8 @@ "graph_failure_mentioned": false, "missing_required_graph": false, "used_data_resource": false, - "response_chars": 994, - "status_count": 10 + "response_chars": 1782, + "status_count": 13 } }, { @@ -3774,7 +3550,7 @@ "requires_graph": true, "min_graphs": 1, "repetition": 1, - "duration_ms": 16002, + "duration_ms": 15750, "status_messages": [ { "message": "Thinking...", @@ -3817,13 +3593,13 @@ "phase": "llm" } ], - "event_count": 192, + "event_count": 188, "ok": true, - "request_id": "e7dcab91-a96a-4935-925c-7d6ee9b24502", - "response_id": "chatcmpl-fee636be5ead800816598014850cf9c9", + "request_id": "baa96a24-0660-46db-af32-9b7bfc313514", + "response_id": "chatcmpl-5fb9eed861935601e114d026a35b78d9", "images_count": 8, "graphs_count": 1, - "response": "The [medulla](https://www.virtualflybrain.org/reports/FBbt_00003748 \"Open medulla in Virtual Fly Brain\") has various connections, including [471](https://v2.virtualflybrain.org/org.geppetto.frontend/geppetto?q=FBbt_00003748,NeuronsPartHere \"Run in VFB: Neurons with some part in medulla\") neuron types with some part in it, [464](https://v2.virtualflybrain.org/org.geppetto.frontend/geppetto?q=FBbt_00003748,NeuronsSynaptic \"Run in VFB: Neurons with synaptic terminals in medulla\") neuron types with synaptic terminals in it, [262](https://v2.virtualflybrain.org/org.geppetto.frontend/geppetto?q=FBbt_00003748,NeuronsPresynapticHere \"Run in VFB: Neurons with presynaptic terminals in medulla\") neuron types with presynaptic terminals in it, and [333](https://v2.virtualflybrain.org/org.geppetto.frontend/geppetto?q=FBbt_00003748,NeuronsPostsynapticHere \"Run in VFB: Neurons with postsynaptic terminals in medulla\") neuron types with postsynaptic terminals in it. Some of the neurons with presynaptic terminals in the medulla 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. Some of the neurons with postsynaptic terminals in the medulla are CB3849, TmY-ds, [Y6](https://www.virtualflybrain.org/reports/FBbt_00007580 \"Open Y6 in Virtual Fly Brain\"), [extra l-LNv neuron](https://www.virtualflybrain.org/reports/FBbt_00047183 \"Open extra l-LNv neuron in Virtual Fly Brain\"), Dm7, Mi6, Mi8, Tm10, Tm13, Tm14, Tm18, and Tm19.", + "response": "The [medulla](https://www.virtualflybrain.org/reports/FBbt_00003748 \"Open medulla in Virtual Fly Brain\") has various connections, including [471](https://v2.virtualflybrain.org/org.geppetto.frontend/geppetto?q=FBbt_00003748,NeuronsPartHere \"Run in VFB: Neurons with some part in medulla\") neuron types with some part in it, [464](https://v2.virtualflybrain.org/org.geppetto.frontend/geppetto?q=FBbt_00003748,NeuronsSynaptic \"Run in VFB: Neurons with synaptic terminals in medulla\") neuron types with synaptic terminals in it, [262](https://v2.virtualflybrain.org/org.geppetto.frontend/geppetto?q=FBbt_00003748,NeuronsPresynapticHere \"Run in VFB: Neurons with presynaptic terminals in medulla\") neuron types with presynaptic terminals in it, and [333](https://v2.virtualflybrain.org/org.geppetto.frontend/geppetto?q=FBbt_00003748,NeuronsPostsynapticHere \"Run in VFB: Neurons with postsynaptic terminals in medulla\") neuron types with postsynaptic terminals in it. Neurons with presynaptic terminals in the medulla include [Dm8b](https://www.virtualflybrain.org/reports/FBbt_00110069 \"Open Dm8b in Virtual Fly Brain\"), [PS128](https://www.virtualflybrain.org/reports/FBbt_20001883 \"Open PS128 in Virtual Fly Brain\"), [Mi10b](https://www.virtualflybrain.org/reports/FBbt_00110070 \"Open Mi10b in Virtual Fly Brain\"), [CB3849](https://www.virtualflybrain.org/reports/FBbt_20007264 \"Open CB3849 in Virtual Fly Brain\"), [TmY-ds](https://www.virtualflybrain.org/reports/FBbt_00052643 \"Open TmY-ds in Virtual Fly Brain\"), [Dm7](https://www.virtualflybrain.org/reports/FBbt_00003774 \"Open Dm7 in Virtual Fly Brain\"), Mi6, Mi8, Tm10, Tm13, Tm14, and Tm18. Neurons with postsynaptic terminals in the medulla include CB3849, TmY-ds, [Y6](https://www.virtualflybrain.org/reports/FBbt_00007580 \"Open Y6 in Virtual Fly Brain\"), [extra l-LNv neuron](https://www.virtualflybrain.org/reports/FBbt_00047183 \"Open extra l-LNv neuron in Virtual Fly Brain\"), Dm7, Mi6, Mi8, Tm10, Tm13, Tm14, Tm18, and Tm19.", "graphs": [ { "type": "basic_graph", @@ -3970,7 +3746,7 @@ "graph_failure_mentioned": false, "missing_required_graph": false, "used_data_resource": false, - "response_chars": 2000, + "response_chars": 1984, "status_count": 10 } }, @@ -3984,7 +3760,7 @@ "requires_graph": false, "min_graphs": 0, "repetition": 1, - "duration_ms": 6574, + "duration_ms": 5779, "status_messages": [ { "message": "Thinking...", @@ -4017,8 +3793,8 @@ ], "event_count": 42, "ok": true, - "request_id": "b6b7bb14-3f16-40ad-992b-456f680a55a2", - "response_id": "chatcmpl-da75fdd5e3a7ec9af801670df5dc7d29", + "request_id": "c222703d-ee80-4563-8ab9-4f79429d8137", + "response_id": "chatcmpl-73bef331360ddcca5446898ced704c22", "images_count": 0, "graphs_count": 0, "response": "Virtual Fly Brain is an interactive tool for neurobiologists to explore the detailed neuroanatomy, neuron connectivity, and gene expression of Drosophila melanogaster.", @@ -4046,7 +3822,7 @@ "requires_graph": false, "min_graphs": 0, "repetition": 1, - "duration_ms": 36967, + "duration_ms": 38559, "status_messages": [ { "message": "Thinking...", @@ -4075,8 +3851,8 @@ ], "event_count": 23, "ok": true, - "request_id": "27ac97fd-9957-4f32-8318-f2411f52a303", - "response_id": "chatcmpl-4fe1ed15a3d4691be387f1d40d7fa4fe", + "request_id": "cfa5410f-736e-4d97-851b-176d7e95193a", + "response_id": "chatcmpl-44938f342d32253639bd1e4a9c0c8107", "images_count": 0, "graphs_count": 0, "response": "To cite Virtual Fly Brain in a publication, use the following citation formats:\n\n```\nAPA\nCourt, R., Costa, M., Pilgrim, C., Millburn, G., Holmes, A., McLachlan, A., Larkin, A., Matentzoglu, N., Kir, H., Parkinson, H., Brown, N. H., O’Kane, C. J., Armstrong, J. D., Jefferis, G. S. X. E., & Osumi-Sutherland, D. (2023). Virtual Fly Brain—An interactive atlas of the Drosophila nervous system. Frontiers in Physiology, 14. https://doi.org/10.3389/fphys.2023.1076533\n\nMLA\nCourt, Robert, et al. “Virtual Fly Brain—An Interactive Atlas of the Drosophila Nervous System.” Frontiers in Physiology, vol. 14, 2023, https://doi.org/10.3389/fphys.2023.1076533.\n\nChicago\nCourt, Robert, Costa, Marta, Pilgrim, Clare, Millburn, Gillian, Holmes, Alex, McLachlan, Alex, Larkin, Aoife et al. “Virtual Fly Brain—An interactive atlas of the Drosophila nervous system.” Frontiers in Physiology 14, (2023). https://doi.org/10.3389/fphys.2023.1076533.\n\nBibTeX\n@article{Court_2023,\nauthor = {Robert Court and Marta Costa and Clare Pilgrim and Gillian Millburn and Alex Holmes and Alex McLachlan and Aoife Larkin and Nicolas Matentzoglu and Huseyin Kir and Helen Parkinson and Nicolas H. Brown and Cahir J. O'Kane and J. Douglas Armstrong and Gregory S. X. E. Jefferis and David Osumi-Sutherland},\ntitle = \"{Virtual Fly Brain—An interactive atlas of the Drosophila nervous system}\",\njournal = {Frontiers in Physiology},\nvolume = {14},\npublisher = {Frontiers Media {SA}},\nyear = {2023},\nmonth = {jan},\nabstract = \"{As a model organism, Drosophila is uniquely placed to contribute to our understanding of how brains control complex behavior. Not only does it have complex adaptive behaviors, but also a uniquely powerful genetic toolkit, increasingly complete dense connectomic maps of the central nervous system and a rapidly growing set of transcriptomic profiles of cell types. But this also poses a challenge: Given the massive amounts of VFB evidence, how are researchers to Find, Access, Integrate and Reuse (FAIR) relevant data in order to develop an integrated anatomical and molecular picture of circuits, inform hypothesis generation, and find reagents for experiments to test these hypotheses? The Virtual Fly Brain (virtualflybrain.org) web application & API provide a solution to this problem, using FAIR principles to integrate 3D images of neurons and brain regions, connectomics, transcriptomics and reagent expression data covering the whole CNS in both larva and adult. Users can search for neurons, neuroanatomy and reagents by name, location, or connectivity, via text search, clicking on 3D images, search-by-image, and queries by type (e.g., dopaminergic neuron) or properties (e.g., synaptic input in the antennal lobe). Returned results include cross-registered 3D images that can be explored in linked 2D and 3D browsers or downloaded under open licenses, and extensive descriptions of cell types and regions curated from the literature. These solutions are potentially extensible to cover similar atlasing and data integration challenges in vertebrates.}\",\nissn = {1664-042X},\ndoi = {10.3389/fphys.2023.1076533},\nurl = {https://doi.org/10.3389/fphys.2023.1076533},\n}\n```", @@ -4104,7 +3880,7 @@ "requires_graph": false, "min_graphs": 0, "repetition": 1, - "duration_ms": 6446, + "duration_ms": 5381, "status_messages": [ { "message": "Thinking...", @@ -4133,8 +3909,8 @@ ], "event_count": 28, "ok": true, - "request_id": "accbe23f-f291-44a3-8ac7-358a28fb94ca", - "response_id": "chatcmpl-1ff2d46deab787f56044f5990ea7c077", + "request_id": "0ec22e1a-bd6e-439a-a201-5196a2d28281", + "response_id": "chatcmpl-2e57b858351c29e3e366f60eaf2af986", "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.", @@ -4162,7 +3938,7 @@ "requires_graph": false, "min_graphs": 0, "repetition": 1, - "duration_ms": 7159, + "duration_ms": 4759, "status_messages": [ { "message": "Thinking...", @@ -4193,13 +3969,13 @@ "phase": "llm" } ], - "event_count": 65, + "event_count": 42, "ok": true, - "request_id": "da3e79c8-e86f-43f1-817e-a4fcb0cdd900", - "response_id": "chatcmpl-b5d601f3b083c957448bd6c7ebc7f982", + "request_id": "be25e75d-3641-4866-83c2-142ac8a5e515", + "response_id": "chatcmpl-96e54583ecaa645e9d8e192d8d3ae846", "images_count": 0, "graphs_count": 0, - "response": "Virtual Fly Brain's accessibility statement is that the website is partially compliant with the Web Content Accessibility Guidelines (WCAG) 2.2 AA standard, with non-compliances listed, and the University of Edinburgh is committed to making its websites and applications accessible in line with the regulations.", + "response": "Virtual Fly Brain is partially compliant with the Web Content Accessibility Guidelines (WCAG) 2.2 AA standard, with known accessibility limitations and non-compliances listed.", "quality_flags": { "has_tool_status": true, "no_tool_factual_answer": false, @@ -4210,7 +3986,7 @@ "graph_failure_mentioned": false, "missing_required_graph": false, "used_data_resource": false, - "response_chars": 311, + "response_chars": 175, "status_count": 7 } }, @@ -4224,7 +4000,7 @@ "requires_graph": false, "min_graphs": 0, "repetition": 1, - "duration_ms": 9503, + "duration_ms": 7768, "status_messages": [ { "message": "Thinking...", @@ -4251,13 +4027,13 @@ "phase": "llm" } ], - "event_count": 88, + "event_count": 85, "ok": true, - "request_id": "caf27f09-60c9-4c7e-a53b-6b06611148f9", - "response_id": "chatcmpl-3b58cd79e26adf6fee2286abcff66eda", + "request_id": "791d0f94-82e3-42da-b552-1f417b65f9ee", + "response_id": "chatcmpl-1231ca939d2b4d503d8fe21e03bfef83", "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. Bug reports and feature requests can be submitted through GitHub Issues. For data contributions and private inquiries, you can use the private email at data@virtualflybrain.org.", + "response": "To report a problem or contribute data to Virtual Fly Brain, you can get in touch with the team through the contact us page. For help with using Virtual Fly Brain, you can use the public support forum at support@virtualflybrain.org. Bug reports and feature requests can be submitted through GitHub Issues. For data contributions or private inquiries, you can email data@virtualflybrain.org.", "quality_flags": { "has_tool_status": true, "no_tool_factual_answer": false, @@ -4268,7 +4044,7 @@ "graph_failure_mentioned": false, "missing_required_graph": false, "used_data_resource": false, - "response_chars": 407, + "response_chars": 390, "status_count": 6 } }, @@ -4282,7 +4058,7 @@ "requires_graph": false, "min_graphs": 0, "repetition": 1, - "duration_ms": 9345, + "duration_ms": 7600, "status_messages": [ { "message": "Thinking...", @@ -4309,13 +4085,13 @@ "phase": "llm" } ], - "event_count": 85, + "event_count": 87, "ok": true, - "request_id": "667fbdaa-95a5-4126-9756-eec32d36d344", - "response_id": "chatcmpl-36121676fb0403362848860bf50dadef", + "request_id": "b9d31d3d-d7bf-439c-9241-e51c91d3b92c", + "response_id": "chatcmpl-13f4581d5802a21c01f0526725f680a4", "images_count": 0, "graphs_count": 0, - "response": "To use the 3D Viewer on the VFB website, point and click to select neurons or expression. Click and drag with the mouse or use the directional icons to rotate or move. Use the zoom icons or scroll with the mouse to zoom in or out. The camera icon starts or stops a rotation animation of the scene, and the sphere icon toggles wireframes on or off.", + "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 scene. Use the zoom icons or scroll with the mouse to zoom in or out. The camera icon starts or stops a rotation animation of the scene, and the sphere icon toggles wireframes on or off.", "quality_flags": { "has_tool_status": true, "no_tool_factual_answer": false, @@ -4326,7 +4102,7 @@ "graph_failure_mentioned": false, "missing_required_graph": false, "used_data_resource": false, - "response_chars": 347, + "response_chars": 357, "status_count": 6 } }, @@ -4340,7 +4116,7 @@ "requires_graph": false, "min_graphs": 0, "repetition": 1, - "duration_ms": 12401, + "duration_ms": 10175, "status_messages": [ { "message": "Thinking...", @@ -4377,8 +4153,8 @@ ], "event_count": 58, "ok": true, - "request_id": "e5486d3a-03ff-42ab-a3db-23200a78b359", - "response_id": "chatcmpl-d920495154bb2d01dad8b2a86ecf3d59", + "request_id": "eec71746-93cb-4c5b-ad50-759e48829558", + "response_id": "chatcmpl-a7c3af23535e4d99ed61cc6f04b65763", "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.", @@ -4406,7 +4182,7 @@ "requires_graph": false, "min_graphs": 0, "repetition": 1, - "duration_ms": 8448, + "duration_ms": 6658, "status_messages": [ { "message": "Thinking...", @@ -4437,13 +4213,13 @@ "phase": "llm" } ], - "event_count": 71, + "event_count": 62, "ok": true, - "request_id": "1c8fe17f-708d-4a0a-b840-c3e38e0df3ff", - "response_id": "chatcmpl-1deca54f0e382155fbf565bf8c714c09", + "request_id": "e37f7ed7-36cc-42b9-9a6c-224e1ee6fae1", + "response_id": "chatcmpl-0dc695b143b2f169a9c1beb0112393fe", "images_count": 0, "graphs_count": 0, - "response": "NBLAST is a method used to calculate similarity scores, which represent the morphological similarity between neurons or expression patterns. The similarity scores are calculated using NBLAST or other third-party scores. An NBLAST similarity score is a measure of how similar the morphology of one neuron or expression pattern is to another.", + "response": "NBLAST is a method used to calculate similarity scores, which represent the morphological similarity between neurons or expression patterns. The similarity scores are calculated using NBLAST. An NBLAST similarity score means a measure of the morphological similarity between neurons or expression patterns.", "quality_flags": { "has_tool_status": true, "no_tool_factual_answer": false, @@ -4454,7 +4230,7 @@ "graph_failure_mentioned": false, "missing_required_graph": false, "used_data_resource": false, - "response_chars": 340, + "response_chars": 306, "status_count": 7 } }, @@ -4468,7 +4244,7 @@ "requires_graph": false, "min_graphs": 0, "repetition": 1, - "duration_ms": 8614, + "duration_ms": 6488, "status_messages": [ { "message": "Thinking...", @@ -4501,8 +4277,8 @@ ], "event_count": 26, "ok": true, - "request_id": "6b4a12d1-87d1-43b4-a82a-d2bae45debf9", - "response_id": "chatcmpl-003edecd3d3cffc94f7c4e448bf1253f", + "request_id": "d6ebd064-6c54-4350-9058-5340eb82cb14", + "response_id": "chatcmpl-5111d67563b791723c1280fd9fc9e100", "images_count": 1, "graphs_count": 0, "response": "Confidence values are represented by the property key \"confidence_value\" in the PDB.", @@ -4530,7 +4306,7 @@ "requires_graph": false, "min_graphs": 0, "repetition": 1, - "duration_ms": 9445, + "duration_ms": 7610, "status_messages": [ { "message": "Thinking...", @@ -4563,11 +4339,11 @@ ], "event_count": 38, "ok": true, - "request_id": "36e42b86-8a7a-4fd9-8e74-5f24da4dc385", - "response_id": "chatcmpl-928b669e098b172caaf924dae67380de", + "request_id": "695868cf-541f-427a-a945-b0d83993943b", + "response_id": "chatcmpl-b66e022ab14bed35d05aa1c62263c592", "images_count": 8, "graphs_count": 0, - "response": "Bridging registrations between brain templates in VFB could not be matched. The documentation mentions transformations to map between different canonical Drosophila templates.", + "response": "Bridging registrations between brain templates in VFB could not be matched. The documentation describes transformations to map between different canonical Drosophila templates.", "quality_flags": { "has_tool_status": true, "no_tool_factual_answer": false, @@ -4578,7 +4354,7 @@ "graph_failure_mentioned": false, "missing_required_graph": false, "used_data_resource": false, - "response_chars": 175, + "response_chars": 176, "status_count": 7 } }, @@ -4592,7 +4368,7 @@ "requires_graph": false, "min_graphs": 0, "repetition": 1, - "duration_ms": 6019, + "duration_ms": 4141, "status_messages": [ { "message": "Thinking...", @@ -4621,8 +4397,8 @@ ], "event_count": 22, "ok": true, - "request_id": "3f1d9a11-0313-4fb7-addf-5392ad47c6a1", - "response_id": "chatcmpl-cbb51f4ae3d517926f07bd68b3319cc4", + "request_id": "75846814-39dd-4e5a-997c-a587dc782a0d", + "response_id": "chatcmpl-259c16f5f82cae8b21eaa2c0f3d8c68f", "images_count": 0, "graphs_count": 0, "response": "Virtual Fly Brain holds imaging data types including skeleton, mesh, and volume.", @@ -4650,7 +4426,7 @@ "requires_graph": false, "min_graphs": 0, "repetition": 1, - "duration_ms": 7523, + "duration_ms": 5472, "status_messages": [ { "message": "Thinking...", @@ -4679,8 +4455,8 @@ ], "event_count": 46, "ok": true, - "request_id": "11d50801-03c2-47a1-a5a6-0b1adaa4a8f4", - "response_id": "chatcmpl-47c64746baa2be14780d4a6366924925", + "request_id": "75a96c23-c408-494b-ab86-3b79a2326fad", + "response_id": "chatcmpl-6014f7992aea61d9c536653edee3478c", "images_count": 0, "graphs_count": 0, "response": "The latest Virtual Fly Brain release includes various data and software improvements, such as new images and annotations, including confocal microscopy images, EM reconstructed neurons, and other datasets from different researchers and labs.", @@ -4708,7 +4484,7 @@ "requires_graph": false, "min_graphs": 0, "repetition": 1, - "duration_ms": 9228, + "duration_ms": 7238, "status_messages": [ { "message": "Thinking...", @@ -4735,13 +4511,13 @@ "phase": "llm" } ], - "event_count": 30, + "event_count": 58, "ok": true, - "request_id": "cecab799-cbb1-41a2-8489-cdb34c94622f", - "response_id": "chatcmpl-7ef12eaa1366b20cc9ecc0da89451f4c", + "request_id": "c02cb76f-cc5f-432a-a579-42d041ab4e4f", + "response_id": "chatcmpl-16efc1b88c2c38565bc33e467c0c841d", "images_count": 0, "graphs_count": 0, - "response": "To install VFB-connect, use the command:\n```\npip install vfb-connect\n```\nThen, import the library in Python with:\n```\nfrom import vfb\n```", + "response": "To install and get started with VFB-connect in Python, ensure you have the VFBConnect library installed using the recommended Python version 3.10.14. Install the library by running\n```\npip install vfb-connect\n```\nThen, import the VFBConnect library using\n```\nfrom import vfb\n```", "quality_flags": { "has_tool_status": true, "no_tool_factual_answer": false, @@ -4752,7 +4528,7 @@ "graph_failure_mentioned": false, "missing_required_graph": false, "used_data_resource": false, - "response_chars": 137, + "response_chars": 278, "status_count": 6 } }, @@ -4766,7 +4542,7 @@ "requires_graph": false, "min_graphs": 0, "repetition": 1, - "duration_ms": 12400, + "duration_ms": 9668, "status_messages": [ { "message": "Thinking...", @@ -4793,13 +4569,13 @@ "phase": "llm" } ], - "event_count": 124, + "event_count": 103, "ok": true, - "request_id": "addb1dd5-3ce3-4edd-bbb5-7e9eecb9d974", - "response_id": "chatcmpl-b2d9d7ed8c101eea78560e0c4dc627dd", + "request_id": "82eacb76-b11f-49e1-a805-808b7e416d5c", + "response_id": "chatcmpl-752cbe927c99546656e710f11b9f318c", "images_count": 0, "graphs_count": 0, - "response": "To query Virtual Fly Brain programmatically, you can use the SOLR Search API for fast text search and autocomplete functionality, or the Owlery API for OWL reasoning services and complex queries over class hierarchies and relationships. The Owlery API provides OWL reasoning services for Virtual Fly Brain's ontologies, enabling complex queries over class hierarchies and relationships, and supports various query operations, including Description Logic queries, SPARQL queries with OWL reasoning, and access to multiple knowledgebases. The API endpoint for the Owlery API is https://owl.virtualflybrain.org/.", + "response": "To query Virtual Fly Brain programmatically, you can use the Owlery API, which provides OWL reasoning services for VFB's ontologies. The API endpoint is https://owl.virtualflybrain.org/, and it supports various query operations, including Description Logic (DL) queries, SPARQL queries with OWL reasoning, and access to multiple knowledgebases. Alternatively, the SOLR Search API provides fast text search and autocomplete functionality for VFB entities, datasets, and publications.", "quality_flags": { "has_tool_status": true, "no_tool_factual_answer": false, @@ -4810,7 +4586,7 @@ "graph_failure_mentioned": false, "missing_required_graph": false, "used_data_resource": false, - "response_chars": 609, + "response_chars": 482, "status_count": 6 } }, @@ -4824,7 +4600,7 @@ "requires_graph": false, "min_graphs": 0, "repetition": 1, - "duration_ms": 12907, + "duration_ms": 12547, "status_messages": [ { "message": "Thinking...", @@ -4855,13 +4631,13 @@ "phase": "llm" } ], - "event_count": 130, + "event_count": 47, "ok": true, - "request_id": "ec66d54f-bfa3-45c1-9f36-378e8ac14c5f", - "response_id": "chatcmpl-ffd8acf01347f5947ab92717f92174b4", + "request_id": "b7a9d6fd-38bd-4fab-a2be-2587c32015df", + "response_id": "chatcmpl-359cef998dd57591b8af7bbe50c5ae64", "images_count": 0, "graphs_count": 0, - "response": "To explore Virtual Fly Brain neurons, you can use the pymaid library to interface with a CATMAID server and retrieve neuron data. You can then use Navis to plot and analyze the neurons. The pymaid library is built on top of Navis and returns data in a way that you can plug them straight into Navis to use features such as plotting. VFB's documentation does not appear to cover Navis or pymaid directly, in the sense that a search for \"pymaid\" returned nothing, and \"Navis\" was not matched automatically, although candidates were offered for the latter.", + "response": "To explore Virtual Fly Brain neurons, you can use the following steps:\n```\nimport pymaid\nimport navis\n\nnavis.set_pbars(jupyter=False)\npymaid.set_pbars(jupyter=False)\n\n# Connect to the VFB CATMAID server hosting the FAFB data\nrm = pymaid.connect_catmaid(server=\"https://fafb.catmaid.virtualflybrain.org/\", api_token=None, max_threads=10)\n\n# Test call to see if connection works\nprint(f'Server is running CATMAID version {rm.catmaid_version}')\n```\nVFB's documentation does not appear to cover Navis. VFB's documentation does not appear to cover pymaid.", "quality_flags": { "has_tool_status": true, "no_tool_factual_answer": false, @@ -4872,7 +4648,7 @@ "graph_failure_mentioned": false, "missing_required_graph": false, "used_data_resource": false, - "response_chars": 553, + "response_chars": 550, "status_count": 7 } }, @@ -4886,7 +4662,7 @@ "requires_graph": false, "min_graphs": 0, "repetition": 1, - "duration_ms": 10287, + "duration_ms": 13017, "status_messages": [ { "message": "Thinking...", @@ -4901,7 +4677,7 @@ "phase": "mcp" }, { - "message": "Checking the literature", + "message": "Checking VFB documentation", "phase": "mcp" }, { @@ -4913,13 +4689,13 @@ "phase": "llm" } ], - "event_count": 104, + "event_count": 142, "ok": true, - "request_id": "f5d8a605-d1cb-4799-a28e-7ef954d95deb", - "response_id": "chatcmpl-a06a83fe92441cba36a02657d430f832", + "request_id": "c589b194-3841-4a71-92c3-3f4e6276cdbe", + "response_id": "chatcmpl-f143a138b6559a3ebc5e159c0ba1ae37", "images_count": 0, "graphs_count": 0, - "response": "To use the Virtual Fly Brain Model Context Protocol (MCP) tool, follow these steps:\nOpen Claude Desktop, navigate to Settings, and add a new MCP server with the provided settings.\nAlternatively, use the Configuration JSON or Claude Code setup methods.\nFor GitHub Copilot, open VS Code, install the MCP extension, and add the server URL.\nFor other MCP-compatible clients, use the provided JSON configuration.\nTest the connection by asking AI assistant questions.\n\n```\n{\n\"mcpServers\": {\n\"virtual-fly-brain\": {\n\"type\": \"http\",\n\"url\": \"https://vfb3-mcp.virtualflybrain.org\",\n\"tools\": [\"*\"]\n}\n}\n}\n```", + "response": "To use the Virtual Fly Brain Model Context Protocol (MCP) tool, follow these steps: Open Claude Desktop, go to Settings, navigate to the MCP section, and add a new MCP server with the provided settings. Alternatively, use the Configuration JSON or Claude Code setup methods. For GitHub Copilot setup, open VS Code, search for \"MCP\" in the settings, and add the server URL. For other MCP-compatible clients, use the provided JSON configuration. To test the connection, ask your AI assistant questions like \"Get information about the neuron \" or \"Search for terms related to medulla in the fly brain\".\n\n```json\n{\n\"mcpServers\": {\n \"virtual-fly-brain\": {\n \"type\": \"http\",\n \"url\": \"https://vfb3-mcp.virtualflybrain.org\",\n \"tools\": [\"*\"]\n }\n}\n}\n```", "quality_flags": { "has_tool_status": true, "no_tool_factual_answer": false, @@ -4930,7 +4706,7 @@ "graph_failure_mentioned": false, "missing_required_graph": false, "used_data_resource": false, - "response_chars": 595, + "response_chars": 742, "status_count": 6 } }, @@ -4944,7 +4720,7 @@ "requires_graph": false, "min_graphs": 0, "repetition": 1, - "duration_ms": 8587, + "duration_ms": 5380, "status_messages": [ { "message": "Thinking...", @@ -4977,11 +4753,11 @@ ], "event_count": 43, "ok": true, - "request_id": "0c37adbe-010d-4734-97e7-ef4fed92c512", - "response_id": "chatcmpl-ebc41ba537139bc51d88e5d48f92541c", + "request_id": "415a3f24-421e-4b89-8b19-ece9a2589384", + "response_id": "chatcmpl-9147aba576cff359bb9c7aa883155f2b", "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.", + "response": "VFB's documentation does not appear to cover when predicted neurotransmitters for EM data became available on VFB. For more information, searching virtualflybrain.org may be helpful.", "quality_flags": { "has_tool_status": true, "no_tool_factual_answer": false, @@ -4992,7 +4768,7 @@ "graph_failure_mentioned": false, "missing_required_graph": false, "used_data_resource": false, - "response_chars": 188, + "response_chars": 182, "status_count": 7 } }, @@ -5006,7 +4782,7 @@ "requires_graph": false, "min_graphs": 0, "repetition": 1, - "duration_ms": 21600, + "duration_ms": 7382, "status_messages": [ { "message": "Thinking...", @@ -5039,8 +4815,8 @@ ], "event_count": 40, "ok": true, - "request_id": "5ea2473f-a78c-40b4-bce9-9b31b8d233e8", - "response_id": "chatcmpl-6cb8d207becbd1dc676918ee16817a16", + "request_id": "335a19bf-4c4c-4fc4-97e6-f4a987a7d9c9", + "response_id": "chatcmpl-93bc5bd92c779d18ab25aa299c878fbf", "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.", @@ -5068,7 +4844,7 @@ "requires_graph": false, "min_graphs": 0, "repetition": 1, - "duration_ms": 9631, + "duration_ms": 7169, "status_messages": [ { "message": "Thinking...", @@ -5099,13 +4875,13 @@ "phase": "llm" } ], - "event_count": 85, + "event_count": 48, "ok": true, - "request_id": "20830153-f9e4-4976-bd1b-b715b1b1e18b", - "response_id": "chatcmpl-6bf014cfacbfb82b0fbef3e3a718ce4c", + "request_id": "128d4a6c-8971-456b-bf3f-0e2a853bb99a", + "response_id": "chatcmpl-32fe93f64693d45a66d5d58ab3aaef27", "images_count": 0, "graphs_count": 0, - "response": "Materials from the Virtual Fly Brain \"Hacking the connectome\" workshop are available, including a recorded introduction session and workshop notebooks that demonstrate how to use available tools to explore and analyse published connectomes on VFB. The workshop notebooks can be followed along with to show examples of how you can use the available tools to explore and analyse the published connectomes available on VFB.\n\n```\nhttps://www.virtualflybrain.org/docs/past-workshops/connectome\n```", + "response": "Materials from the Virtual Fly Brain \"Hacking the connectome\" workshop include a recorded introduction session and workshop notebooks that demonstrate how to use available tools to explore and analyze published connectomes on VFB.", "quality_flags": { "has_tool_status": true, "no_tool_factual_answer": false, @@ -5116,7 +4892,7 @@ "graph_failure_mentioned": false, "missing_required_graph": false, "used_data_resource": false, - "response_chars": 492, + "response_chars": 230, "status_count": 7 } }, @@ -5130,7 +4906,7 @@ "requires_graph": false, "min_graphs": 0, "repetition": 1, - "duration_ms": 14261, + "duration_ms": 10798, "status_messages": [ { "message": "Thinking...", @@ -5140,12 +4916,16 @@ "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": "Reading VFB documentation", + "message": "Querying VFB", "phase": "mcp" }, { @@ -5161,13 +4941,13 @@ "phase": "llm" } ], - "event_count": 56, + "event_count": 85, "ok": true, - "request_id": "683c4810-350a-4d96-bfb6-52b2e31df050", - "response_id": "chatcmpl-c3a6f252928e12f21fb329b2051d366b", + "request_id": "503b033f-7eba-4ae3-9298-d800003ac274", + "response_id": "chatcmpl-66cae95be1a0acfe3f5a534958febfad", "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.", + "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 being Fancl, FANCI, and Fancm.", "quality_flags": { "has_tool_status": true, "no_tool_factual_answer": false, @@ -5178,8 +4958,8 @@ "graph_failure_mentioned": false, "missing_required_graph": false, "used_data_resource": false, - "response_chars": 217, - "status_count": 7 + "response_chars": 313, + "status_count": 8 } }, { @@ -5192,7 +4972,7 @@ "requires_graph": false, "min_graphs": 0, "repetition": 1, - "duration_ms": 9165, + "duration_ms": 7144, "status_messages": [ { "message": "Thinking...", @@ -5225,8 +5005,8 @@ ], "event_count": 22, "ok": true, - "request_id": "09d10261-0ec6-4f3f-9d05-2abb1850b768", - "response_id": "chatcmpl-5414cbe1d7e84b40f5052bfaca7ec7bc", + "request_id": "19ac5531-042b-467b-90b9-d6453edde63a", + "response_id": "chatcmpl-7e82d996feb840909156ac781a584735", "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.", @@ -5254,7 +5034,7 @@ "requires_graph": false, "min_graphs": 0, "repetition": 1, - "duration_ms": 16465, + "duration_ms": 11007, "status_messages": [ { "message": "Thinking...", @@ -5293,9 +5073,9 @@ "question": "What is the medulla?", "focus": null, "clicked": null, - "duration_ms": 5852, + "duration_ms": 5384, "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: 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", @@ -5352,7 +5132,7 @@ "question": "Which neurons receive output from it?", "focus": null, "clicked": null, - "duration_ms": 10613, + "duration_ms": 5623, "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": [ @@ -5419,8 +5199,8 @@ } ], "ok": true, - "request_id": "8de5fcfa-16b0-42e2-a291-107f6f16f5d3", - "response_id": "chatcmpl-5ab26d68303064a0457655f1cbb00dd4", + "request_id": "5f982228-cc05-4505-b089-ac1a4e665f4e", + "response_id": "chatcmpl-479452e10a34dadccb3fdea6cc05cf1f", "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.", @@ -5441,7 +5221,7 @@ "unmatched_claim_after_resolve": false, "repeats_answered_question": false, "slow_followup_turn": false, - "slowest_followup_ms": 10613 + "slowest_followup_ms": 5623 } }, { @@ -5454,7 +5234,7 @@ "requires_graph": false, "min_graphs": 0, "repetition": 1, - "duration_ms": 21756, + "duration_ms": 13581, "status_messages": [ { "message": "Thinking...", @@ -5489,7 +5269,7 @@ "phase": "llm" } ], - "event_count": 201, + "event_count": 188, "conversation": true, "turns": [ { @@ -5497,9 +5277,9 @@ "question": "What is the mushroom body?", "focus": null, "clicked": null, - "duration_ms": 7637, + "duration_ms": 5869, "ok": true, - "response": "The [mushroom body](https://www.virtualflybrain.org/reports/FBbt_00005801 \"Open mushroom body in Virtual Fly Brain\") is a bilaterally paired neuropil structure situated postero-dorsally in the protocerebrum that functions in olfactory associative learning and memory. It is divided into the calyx, which receives sensory interneuron afferents, the pedunculus, a thick axon bundle, and the mushroom body lobe system, which consists of a vertical branch and a medial branch, and has different structures at different life stages.", + "response": "The [mushroom body](https://www.virtualflybrain.org/reports/FBbt_00005801 \"Open mushroom body in Virtual Fly Brain\") is a bilaterally paired neuropil structure situated postero-dorsally in the protocerebrum that functions in olfactory associative learning and memory. It is divided into the calyx, which receives sensory interneuron afferents, the pedunculus, a thick axon bundle, and the mushroom body lobe system, which consists of a vertical branch and a medial branch and has different structures at different life stages.", "followons": [ { "id": "FBbt_00005801", @@ -5559,9 +5339,9 @@ "query_type": "ImagesNeurons" }, "clicked": 0, - "duration_ms": 14119, + "duration_ms": 7712, "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.", + "response": "There are images of neurons with parts in the [mushroom body](https://www.virtualflybrain.org/reports/FBbt_00005801 \"Open mushroom body in Virtual Fly Brain\"). VFB records show [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, including 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", @@ -5626,11 +5406,11 @@ } ], "ok": true, - "request_id": "20ded381-d443-477a-b5f3-1f1ef1680c8d", - "response_id": "chatcmpl-8f42ae4bf4c619c7d5f08f6fc066226a", + "request_id": "633a63a6-49d3-44e1-9a71-a80edb97da67", + "response_id": "chatcmpl-a41b76fa334a09b9f03cc62f30a70d45", "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.", + "response": "There are images of neurons with parts in the [mushroom body](https://www.virtualflybrain.org/reports/FBbt_00005801 \"Open mushroom body in Virtual Fly Brain\"). VFB records show [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, including 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, @@ -5641,14 +5421,14 @@ "graph_failure_mentioned": false, "missing_required_graph": false, "used_data_resource": false, - "response_chars": 661, + "response_chars": 607, "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": 14119 + "slowest_followup_ms": 7712 } }, { @@ -5661,7 +5441,7 @@ "requires_graph": false, "min_graphs": 0, "repetition": 1, - "duration_ms": 212559, + "duration_ms": 21640, "status_messages": [ { "message": "Thinking...", @@ -5683,20 +5463,12 @@ "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": 234, + "event_count": 129, "conversation": true, "turns": [ { @@ -5704,7 +5476,7 @@ "question": "What is the fan-shaped body?", "focus": null, "clicked": null, - "duration_ms": 7358, + "duration_ms": 6863, "ok": true, "response": "The [fan-shaped body](https://www.virtualflybrain.org/reports/FBbt_00003679 \"Open fan-shaped body in Virtual Fly Brain\") is the largest synaptic neuropil domain of the adult central complex, located posterior to the ellipsoid body and anterior to the protocerebral bridge. It is composed of a rough 2-dimensional grid of layers and columns. Eight horizontal layers, numbered bottom to top, form a fan shape and can be divided into vertical columns. An additional, much narrower, 9th layer, which lacks a columnar organization, sits dorsal to layer 8. The number of columns varies for different neuronal types.", "followons": [ @@ -5763,9 +5535,9 @@ "question": "What about the ellipsoid body?", "focus": null, "clicked": null, - "duration_ms": 10984, + "duration_ms": 6953, "ok": true, - "response": "The [ellipsoid body](https://www.virtualflybrain.org/reports/FBbt_00003678 \"Open ellipsoid body in Virtual Fly Brain\") is a doughnut-shaped synaptic neuropil domain of the central complex of the adult brain that lies just anterior to the [fan-shaped body](https://www.virtualflybrain.org/reports/FBbt_00003679 \"Open fan-shaped body in Virtual Fly Brain\").", + "response": "The [ellipsoid body](https://www.virtualflybrain.org/reports/FBbt_00003678 \"Open ellipsoid body in Virtual Fly Brain\") is a doughnut shaped synaptic neuropil domain of the central complex of the adult brain 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", @@ -5830,9 +5602,9 @@ "question": "Which neurons have synaptic terminals in the fan-shaped body?", "focus": null, "clicked": null, - "duration_ms": 194217, + "duration_ms": 7824, "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 neuron types with their VFB ids are: PFNd_PB2, PFNd_PB3, PFNd_PB5, PFNa_PB4, PFNa_PB5, PFNa_PB6, PFNa_PB7, PFNa_PB9, PFNp_PB7, [PFL1_PB5](https://www.virtualflybrain.org/reports/FBbt_00111438 \"Open PFL1_PB5 in Virtual Fly Brain\"), [PFL3](https://www.virtualflybrain.org/reports/FBbt_00111443 \"Open PFL3 in Virtual Fly Brain\"), and [PFL2](https://www.virtualflybrain.org/reports/FBbt_00111451 \"Open PFL2 in Virtual Fly Brain\"). Additionally, [102](https://v2.virtualflybrain.org/org.geppetto.frontend/geppetto?q=FBbt_00003679,NeuronsPresynapticHere \"Run in VFB: Neurons with presynaptic terminals in fan-shaped body\") neurons have presynaptic terminals in the fan-shaped body, 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.", + "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\"); [PFL2](https://www.virtualflybrain.org/reports/FBbt_00111451 \"Open PFL2 in Virtual Fly Brain\").", "followons": [ { "id": "FBbt_00003679", @@ -5849,6 +5621,11 @@ "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", @@ -5858,11 +5635,6 @@ "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": [ @@ -5891,25 +5663,20 @@ "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, + "status_count": 6, "problems": [] } ], "ok": true, - "request_id": "fcf65f20-bb92-4b70-8b0b-57e7123fc68a", - "response_id": "chatcmpl-0eb8adf1705ce42b23331e8e5d69204f", + "request_id": "f794d583-b672-4d03-808c-144d20685354", + "response_id": "chatcmpl-645ba501d88e173338f4ec4ba4ead57d", "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 neuron types with their VFB ids are: PFNd_PB2, PFNd_PB3, PFNd_PB5, PFNa_PB4, PFNa_PB5, PFNa_PB6, PFNa_PB7, PFNa_PB9, PFNp_PB7, [PFL1_PB5](https://www.virtualflybrain.org/reports/FBbt_00111438 \"Open PFL1_PB5 in Virtual Fly Brain\"), [PFL3](https://www.virtualflybrain.org/reports/FBbt_00111443 \"Open PFL3 in Virtual Fly Brain\"), and [PFL2](https://www.virtualflybrain.org/reports/FBbt_00111451 \"Open PFL2 in Virtual Fly Brain\"). Additionally, [102](https://v2.virtualflybrain.org/org.geppetto.frontend/geppetto?q=FBbt_00003679,NeuronsPresynapticHere \"Run in VFB: Neurons with presynaptic terminals in fan-shaped body\") neurons have presynaptic terminals in the fan-shaped body, 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.", + "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\"); [PFL2](https://www.virtualflybrain.org/reports/FBbt_00111451 \"Open PFL2 in Virtual Fly Brain\").", "quality_flags": { "has_tool_status": true, "no_tool_factual_answer": false, @@ -5920,14 +5687,14 @@ "graph_failure_mentioned": false, "missing_required_graph": false, "used_data_resource": false, - "response_chars": 2113, - "status_count": 8, + "response_chars": 1313, + "status_count": 6, "addressless_followon": false, "context_lost_across_turn": false, "unmatched_claim_after_resolve": false, "repeats_answered_question": false, - "slow_followup_turn": true, - "slowest_followup_ms": 194217 + "slow_followup_turn": false, + "slowest_followup_ms": 7824 } }, { @@ -5940,7 +5707,7 @@ "requires_graph": false, "min_graphs": 0, "repetition": 1, - "duration_ms": 18843, + "duration_ms": 13035, "status_messages": [ { "message": "Thinking...", @@ -5967,7 +5734,7 @@ "phase": "llm" } ], - "event_count": 146, + "event_count": 137, "conversation": true, "turns": [ { @@ -5975,7 +5742,7 @@ "question": "What is a Kenyon cell?", "focus": null, "clicked": null, - "duration_ms": 9741, + "duration_ms": 6547, "ok": true, "response": "A [Kenyon cell](https://www.virtualflybrain.org/reports/FBbt_00003686 \"Open Kenyon cell in Virtual Fly Brain\") is an intrinsic neuron of the mushroom body. Kenyon cells are part of the olfactory pathway in Drosophila.", "followons": [ @@ -6034,9 +5801,9 @@ "question": "What are its subtypes?", "focus": null, "clicked": null, - "duration_ms": 9102, + "duration_ms": 6487, "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.", + "response": "The subtypes of [Kenyon cell](https://www.virtualflybrain.org/reports/FBbt_00003686 \"Open Kenyon cell in Virtual Fly Brain\") include [37](https://v2.virtualflybrain.org/org.geppetto.frontend/geppetto?q=FBbt_00003686,SubclassesOf \"Run in VFB: Subclasses of Kenyon cell\") subclasses, such as [KCab-c(i)](https://www.virtualflybrain.org/reports/FBbt_00049111 \"Open KCab-c(i) in Virtual Fly Brain\"), [KCab-c](https://www.virtualflybrain.org/reports/FBbt_00110929 \"Open KCab-c in Virtual Fly Brain\"), [KCg-m](https://www.virtualflybrain.org/reports/FBbt_00111061 \"Open KCg-m in Virtual Fly Brain\"), [Kenyon cell of main calyx](https://www.virtualflybrain.org/reports/FBbt_00047926 \"Open Kenyon cell of main calyx in Virtual Fly Brain\"), and [gamma Kenyon cell](https://www.virtualflybrain.org/reports/FBbt_00100247 \"Open gamma Kenyon cell in Virtual Fly Brain\"). Some specific subtypes are KCab-c(i), KCab-c(o), larval gamma Kenyon cell, KCg-s, KCg-s4, KCg-t, larval alpha'/beta' Kenyon cell, KCab-sc, alpha'/beta' anterior-posterior type 1 Kenyon cell of lACA, Kenyon cell of main calyx, single-claw Kenyon cell, and multi-claw Kenyon cell.", "followons": [ { "id": "FBbt_00003686", @@ -6091,11 +5858,11 @@ } ], "ok": true, - "request_id": "25688b0c-ae4d-43ee-9306-431c494bf896", - "response_id": "chatcmpl-bbac6dc5db03498bbce160af0694abb8", + "request_id": "5b3d7031-4978-4cc0-8955-dd5d5a202375", + "response_id": "chatcmpl-a25573e236b4fcab0f85a73c54659475", "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.", + "response": "The subtypes of [Kenyon cell](https://www.virtualflybrain.org/reports/FBbt_00003686 \"Open Kenyon cell in Virtual Fly Brain\") include [37](https://v2.virtualflybrain.org/org.geppetto.frontend/geppetto?q=FBbt_00003686,SubclassesOf \"Run in VFB: Subclasses of Kenyon cell\") subclasses, such as [KCab-c(i)](https://www.virtualflybrain.org/reports/FBbt_00049111 \"Open KCab-c(i) in Virtual Fly Brain\"), [KCab-c](https://www.virtualflybrain.org/reports/FBbt_00110929 \"Open KCab-c in Virtual Fly Brain\"), [KCg-m](https://www.virtualflybrain.org/reports/FBbt_00111061 \"Open KCg-m in Virtual Fly Brain\"), [Kenyon cell of main calyx](https://www.virtualflybrain.org/reports/FBbt_00047926 \"Open Kenyon cell of main calyx in Virtual Fly Brain\"), and [gamma Kenyon cell](https://www.virtualflybrain.org/reports/FBbt_00100247 \"Open gamma Kenyon cell in Virtual Fly Brain\"). Some specific subtypes are KCab-c(i), KCab-c(o), larval gamma Kenyon cell, KCg-s, KCg-s4, KCg-t, larval alpha'/beta' Kenyon cell, KCab-sc, alpha'/beta' anterior-posterior type 1 Kenyon cell of lACA, Kenyon cell of main calyx, single-claw Kenyon cell, and multi-claw Kenyon cell.", "quality_flags": { "has_tool_status": true, "no_tool_factual_answer": false, @@ -6106,14 +5873,14 @@ "graph_failure_mentioned": false, "missing_required_graph": false, "used_data_resource": false, - "response_chars": 1155, + "response_chars": 1136, "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": 9102 + "slowest_followup_ms": 6487 } }, { @@ -6126,7 +5893,7 @@ "requires_graph": false, "min_graphs": 0, "repetition": 1, - "duration_ms": 31518, + "duration_ms": 20308, "status_messages": [ { "message": "Thinking...", @@ -6169,7 +5936,7 @@ "phase": "llm" } ], - "event_count": 56, + "event_count": 112, "conversation": true, "turns": [ { @@ -6177,7 +5944,7 @@ "question": "What are the anatomical parts of the medulla? List them.", "focus": null, "clicked": null, - "duration_ms": 13085, + "duration_ms": 8739, "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.", "followons": [ @@ -6242,9 +6009,9 @@ "question": "And which neurons have part of their arbour there?", "focus": null, "clicked": null, - "duration_ms": 18433, + "duration_ms": 11569, "ok": true, - "response": "Neurons with some part in the [medulla](https://www.virtualflybrain.org/reports/FBbt_00003748 \"Open medulla in Virtual Fly Brain\") include [471](https://v2.virtualflybrain.org/org.geppetto.frontend/geppetto?q=FBbt_00003748,NeuronsPartHere \"Run in VFB: Neurons with some part in medulla\") neuron types, such as [Dm8b](https://www.virtualflybrain.org/reports/FBbt_00110069 \"Open Dm8b in Virtual Fly Brain\"), [MC](https://www.virtualflybrain.org/reports/FBbt_00111640 \"Open MC in Virtual Fly Brain\"), [PS128](https://www.virtualflybrain.org/reports/FBbt_20001883 \"Open PS128 in Virtual Fly Brain\"), [TmY27](https://www.virtualflybrain.org/reports/FBbt_00110067 \"Open TmY27 in Virtual Fly Brain\"), and [medulla intrinsic neuron vGlutMinew1a](https://www.virtualflybrain.org/reports/FBbt_00110033 \"Open medulla intrinsic neuron vGlutMinew1a in Virtual Fly Brain\").", + "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.", "followons": [ { "id": "FBbt_00003748", @@ -6314,11 +6081,11 @@ } ], "ok": true, - "request_id": "af3db551-b368-40d4-b0d6-841211b2fa0e", - "response_id": "chatcmpl-9e4e553983f814947c9b6684c902d3d6", + "request_id": "f8147c80-e7b9-4a29-b9b6-ae5a6aa5c779", + "response_id": "chatcmpl-68004ef633c2a7d6e2e1d9c1c4d535e2", "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 [471](https://v2.virtualflybrain.org/org.geppetto.frontend/geppetto?q=FBbt_00003748,NeuronsPartHere \"Run in VFB: Neurons with some part in medulla\") neuron types, such as [Dm8b](https://www.virtualflybrain.org/reports/FBbt_00110069 \"Open Dm8b in Virtual Fly Brain\"), [MC](https://www.virtualflybrain.org/reports/FBbt_00111640 \"Open MC in Virtual Fly Brain\"), [PS128](https://www.virtualflybrain.org/reports/FBbt_20001883 \"Open PS128 in Virtual Fly Brain\"), [TmY27](https://www.virtualflybrain.org/reports/FBbt_00110067 \"Open TmY27 in Virtual Fly Brain\"), and [medulla intrinsic neuron vGlutMinew1a](https://www.virtualflybrain.org/reports/FBbt_00110033 \"Open medulla intrinsic neuron vGlutMinew1a in Virtual Fly Brain\").", + "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.", "quality_flags": { "has_tool_status": true, "no_tool_factual_answer": false, @@ -6329,14 +6096,14 @@ "graph_failure_mentioned": false, "missing_required_graph": false, "used_data_resource": false, - "response_chars": 859, + "response_chars": 1287, "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": 18433 + "slowest_followup_ms": 11569 } }, { @@ -6349,7 +6116,7 @@ "requires_graph": false, "min_graphs": 0, "repetition": 1, - "duration_ms": 19757, + "duration_ms": 15546, "status_messages": [ { "message": "Thinking...", @@ -6376,7 +6143,7 @@ "phase": "llm" } ], - "event_count": 7, + "event_count": 160, "conversation": true, "turns": [ { @@ -6384,9 +6151,9 @@ "question": "Tell me about the antennal lobe.", "focus": null, "clicked": null, - "duration_ms": 15590, + "duration_ms": 9674, "ok": true, - "response": "The [antennal lobe](https://www.virtualflybrain.org/reports/FBbt_00003924 \"Open antennal lobe in Virtual Fly Brain\") is a synaptic neuropil domain of the deutocerebrum that is the main target for innervation from the antennal nerve. It is a region in the Drosophila nervous system where synaptic input can be searched for via the Virtual Fly Brain web application. 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.", + "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 where synaptic input can be searched via the Virtual Fly Brain web application. VFB holds various data related to the antennal lobe, including transgene expression in antennal lobe commissural pioneer interneuron, as well as downstream and upstream connectivity classes for antennal lobe commissural pioneer interneuron.", "followons": [ { "id": "FBbt_00003924", @@ -6443,9 +6210,9 @@ "question": "Which neurons innervate it?", "focus": null, "clicked": null, - "duration_ms": 4167, + "duration_ms": 5872, "ok": true, - "response": "I could not complete the answer just now (the language service did not respond). Please try again in a moment.", + "response": "The [antennal lobe](https://www.virtualflybrain.org/reports/FBbt_00003924 \"Open antennal lobe in Virtual Fly Brain\") is innervated by several types of neurons, including [larval antennal lobe picky local neuron](https://www.virtualflybrain.org/reports/FBbt_00111694 \"Open larval antennal lobe picky local neuron in Virtual Fly Brain\"), [larval antennal lobe broad local neuron](https://www.virtualflybrain.org/reports/FBbt_00111700 \"Open larval antennal lobe broad local neuron in Virtual Fly Brain\"), [PLP077](https://www.virtualflybrain.org/reports/FBbt_20001577 \"Open PLP077 in Virtual Fly Brain\"), [adult olfactory receptor neuron Ir75d ac1](https://www.virtualflybrain.org/reports/FBbt_00110011 \"Open adult olfactory receptor neuron Ir75d ac1 in Virtual Fly Brain\"), [adult olfactory receptor neuron Ir75d ac2](https://www.virtualflybrain.org/reports/FBbt_00110014 \"Open adult olfactory receptor neuron Ir75d ac2 in Virtual Fly Brain\"), adult olfactory receptor neuron Ir75d ac4, pharyngeal VL1 neuron, ORN_VM6, adult olfactory receptor neuron Or35a ac3I, adult olfactory receptor neuron Or35a ac3II, adult olfactory receptor neuron Or85b ab3, and adult olfactory receptor neuron Or85b ab11. VFB records show [266](https://v2.virtualflybrain.org/org.geppetto.frontend/geppetto?q=FBbt_00003924,NeuronsPresynapticHere \"Run in VFB: Neurons with presynaptic terminals in antennal lobe\") neurons with presynaptic terminals in the antennal lobe.", "followons": [ { "id": "FBbt_00003924", @@ -6505,11 +6272,11 @@ } ], "ok": true, - "request_id": "43917d9f-0c8d-435f-a6f5-aefdf5376b85", - "response_id": "local-43917d9f-0c8d-435f-a6f5-aefdf5376b85", + "request_id": "ee849716-6f03-4848-b90f-4bd7d1f9b58e", + "response_id": "chatcmpl-c10e2cd90873c68560587f9f2c1feaf5", "images_count": 6, "graphs_count": 0, - "response": "I could not complete the answer just now (the language service did not respond). Please try again in a moment.", + "response": "The [antennal lobe](https://www.virtualflybrain.org/reports/FBbt_00003924 \"Open antennal lobe in Virtual Fly Brain\") is innervated by several types of neurons, including [larval antennal lobe picky local neuron](https://www.virtualflybrain.org/reports/FBbt_00111694 \"Open larval antennal lobe picky local neuron in Virtual Fly Brain\"), [larval antennal lobe broad local neuron](https://www.virtualflybrain.org/reports/FBbt_00111700 \"Open larval antennal lobe broad local neuron in Virtual Fly Brain\"), [PLP077](https://www.virtualflybrain.org/reports/FBbt_20001577 \"Open PLP077 in Virtual Fly Brain\"), [adult olfactory receptor neuron Ir75d ac1](https://www.virtualflybrain.org/reports/FBbt_00110011 \"Open adult olfactory receptor neuron Ir75d ac1 in Virtual Fly Brain\"), [adult olfactory receptor neuron Ir75d ac2](https://www.virtualflybrain.org/reports/FBbt_00110014 \"Open adult olfactory receptor neuron Ir75d ac2 in Virtual Fly Brain\"), adult olfactory receptor neuron Ir75d ac4, pharyngeal VL1 neuron, ORN_VM6, adult olfactory receptor neuron Or35a ac3I, adult olfactory receptor neuron Or35a ac3II, adult olfactory receptor neuron Or85b ab3, and adult olfactory receptor neuron Or85b ab11. VFB records show [266](https://v2.virtualflybrain.org/org.geppetto.frontend/geppetto?q=FBbt_00003924,NeuronsPresynapticHere \"Run in VFB: Neurons with presynaptic terminals in antennal lobe\") neurons with presynaptic terminals in the antennal lobe.", "quality_flags": { "has_tool_status": true, "no_tool_factual_answer": false, @@ -6520,14 +6287,14 @@ "graph_failure_mentioned": false, "missing_required_graph": false, "used_data_resource": false, - "response_chars": 110, + "response_chars": 1444, "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": 4167 + "slowest_followup_ms": 5872 } }, { @@ -6540,7 +6307,7 @@ "requires_graph": false, "min_graphs": 0, "repetition": 1, - "duration_ms": 28267, + "duration_ms": 15795, "status_messages": [ { "message": "Thinking...", @@ -6567,7 +6334,7 @@ "phase": "llm" } ], - "event_count": 302, + "event_count": 91, "conversation": true, "turns": [ { @@ -6575,9 +6342,9 @@ "question": "What is the medulla?", "focus": null, "clicked": null, - "duration_ms": 6038, + "duration_ms": 4858, "ok": true, - "response": "The [medulla](https://www.virtualflybrain.org/reports/FBbt_00003748 \"Open medulla in Virtual Fly Brain\") is the second optic neuropil, sandwiched between the lamina and the lobula complex. It is divided into 10 layers: layers 1-6 make up the outer medulla, the seventh layer exhibits a distinct architecture, and layers 8-10 make up the inner medulla.", + "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", @@ -6637,9 +6404,9 @@ "query_type": "ImagesNeurons" }, "clicked": 0, - "duration_ms": 10631, + "duration_ms": 5138, "ok": true, - "response": "There are images of neurons with parts in the [medulla](https://www.virtualflybrain.org/reports/FBbt_00003748 \"Open medulla in Virtual Fly Brain\"). The first 12 neuron images, with their VFB ids, are: OA-AL2i2 (VFB_fw042336); MC64 (VFB_fw043756); MC64 (VFB_fw043755); aMe5 (VFB_fw043590); MeTu3 (VFB_fw043751); MeTu3 (VFB_fw043750); MeTu3 (VFB_fw043744); aMe5 (VFB_fw043591); MeTu-DRA (VFB_fw043752); MeVP6 (VFB_fw043593); MeTu3 (VFB_fw043746); MeTu3 (VFB_fw043745).", + "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 records show [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, including images of OA-AL2i2, MC64, aMe5, MeTu3, MeTu-DRA, and MeVP6.", "followons": [ { "id": "FBbt_00003748", @@ -6710,9 +6477,9 @@ "query_type": "TransgeneExpressionHere" }, "clicked": 0, - "duration_ms": 11598, + "duration_ms": 5799, "ok": true, - "response": "The first 12 driver lines that label the [medulla](https://www.virtualflybrain.org/reports/FBbt_00003748 \"Open medulla in Virtual Fly Brain\") are: [PBac{544.SVS-1}B4[CPTI100035] expression pattern](https://www.virtualflybrain.org/reports/VFBexp_FBti0143533 \"Open PBac{544.SVS-1}B4[CPTI100035] expression pattern in Virtual Fly Brain\"); [PBac{544.SVS-1}Fer2LCH[CPTI100064] expression pattern](https://www.virtualflybrain.org/reports/VFBexp_FBti0143547 \"Open PBac{544.SVS-1}Fer2LCH[CPTI100064] expression pattern in Virtual Fly Brain\"); [PBac{566.P.SVS-1}IA-2[CPTI100013] expression pattern](https://www.virtualflybrain.org/reports/VFBexp_FBti0143524 \"Open PBac{566.P.SVS-1}IA-2[CPTI100013] expression pattern in Virtual Fly Brain\"); [PBac{602.P.SVS-1}CG7675[CPTI000703] expression pattern](https://www.virtualflybrain.org/reports/VFBexp_FBti0144033 \"Open PBac{602.P.SVS-1}CG7675[CPTI000703] expression pattern in Virtual Fly Brain\"); [PBac{602.P.SVS-1}dlg1[CPTI000207] expression pattern](https://www.virtualflybrain.org/reports/VFBexp_FBti0144076 \"Open PBac{602.P.SVS-1}dlg1[CPTI000207] expression pattern in Virtual Fly Brain\"); PBac{681.P.FSVS-1}CG11138[CPTI001659] expression pattern; PBac{681.P.FSVS-1}CG6983[CPTI001802] expression pattern; PBac{681.P.FSVS-1}CG7920[CPTI002166] expression pattern; PBac{681.P.FSVS-1}CG9336[CPTI001654] expression pattern; PBac{681.P.FSVS-1}Pka-R2[CPTI001580] expression pattern; PBac{681.P.FSVS-1}cpx[CPTI001473] expression pattern; PBac{681.P.FSVS-1}larp[CPTI002498] expression pattern. VFB holds [2342](https://v2.virtualflybrain.org/org.geppetto.frontend/geppetto?q=FBbt_00003748,TransgeneExpressionHere \"Run in VFB: Transgene expression in medulla\") transgene expression reports for medulla.", + "response": "VFB records show [2,342](https://v2.virtualflybrain.org/org.geppetto.frontend/geppetto?q=FBbt_00003748,TransgeneExpressionHere \"Run in VFB: Transgene expression in medulla\") transgene expression patterns in the [medulla](https://www.virtualflybrain.org/reports/FBbt_00003748 \"Open medulla in Virtual Fly Brain\"), 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", @@ -6782,11 +6549,11 @@ } ], "ok": true, - "request_id": "722ffb23-0851-4bf0-a6cb-fa68b032cd07", - "response_id": "chatcmpl-c5ec5b88683f8f81e40fd477cf284c57", + "request_id": "9ac495ff-69a8-4366-919d-4f6b53ffcb48", + "response_id": "chatcmpl-33a885c3de47687076e3ef69f029351e", "images_count": 8, "graphs_count": 0, - "response": "The first 12 driver lines that label the [medulla](https://www.virtualflybrain.org/reports/FBbt_00003748 \"Open medulla in Virtual Fly Brain\") are: [PBac{544.SVS-1}B4[CPTI100035] expression pattern](https://www.virtualflybrain.org/reports/VFBexp_FBti0143533 \"Open PBac{544.SVS-1}B4[CPTI100035] expression pattern in Virtual Fly Brain\"); [PBac{544.SVS-1}Fer2LCH[CPTI100064] expression pattern](https://www.virtualflybrain.org/reports/VFBexp_FBti0143547 \"Open PBac{544.SVS-1}Fer2LCH[CPTI100064] expression pattern in Virtual Fly Brain\"); [PBac{566.P.SVS-1}IA-2[CPTI100013] expression pattern](https://www.virtualflybrain.org/reports/VFBexp_FBti0143524 \"Open PBac{566.P.SVS-1}IA-2[CPTI100013] expression pattern in Virtual Fly Brain\"); [PBac{602.P.SVS-1}CG7675[CPTI000703] expression pattern](https://www.virtualflybrain.org/reports/VFBexp_FBti0144033 \"Open PBac{602.P.SVS-1}CG7675[CPTI000703] expression pattern in Virtual Fly Brain\"); [PBac{602.P.SVS-1}dlg1[CPTI000207] expression pattern](https://www.virtualflybrain.org/reports/VFBexp_FBti0144076 \"Open PBac{602.P.SVS-1}dlg1[CPTI000207] expression pattern in Virtual Fly Brain\"); PBac{681.P.FSVS-1}CG11138[CPTI001659] expression pattern; PBac{681.P.FSVS-1}CG6983[CPTI001802] expression pattern; PBac{681.P.FSVS-1}CG7920[CPTI002166] expression pattern; PBac{681.P.FSVS-1}CG9336[CPTI001654] expression pattern; PBac{681.P.FSVS-1}Pka-R2[CPTI001580] expression pattern; PBac{681.P.FSVS-1}cpx[CPTI001473] expression pattern; PBac{681.P.FSVS-1}larp[CPTI002498] expression pattern. VFB holds [2342](https://v2.virtualflybrain.org/org.geppetto.frontend/geppetto?q=FBbt_00003748,TransgeneExpressionHere \"Run in VFB: Transgene expression in medulla\") transgene expression reports for medulla.", + "response": "VFB records show [2,342](https://v2.virtualflybrain.org/org.geppetto.frontend/geppetto?q=FBbt_00003748,TransgeneExpressionHere \"Run in VFB: Transgene expression in medulla\") transgene expression patterns in the [medulla](https://www.virtualflybrain.org/reports/FBbt_00003748 \"Open medulla in Virtual Fly Brain\"), 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, @@ -6797,14 +6564,14 @@ "graph_failure_mentioned": false, "missing_required_graph": false, "used_data_resource": false, - "response_chars": 1732, + "response_chars": 911, "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": 11598 + "slowest_followup_ms": 5799 } }, { @@ -6817,7 +6584,7 @@ "requires_graph": false, "min_graphs": 0, "repetition": 1, - "duration_ms": 13876, + "duration_ms": 9283, "status_messages": [ { "message": "Thinking...", @@ -6844,7 +6611,7 @@ "phase": "llm" } ], - "event_count": 76, + "event_count": 34, "conversation": true, "turns": [ { @@ -6852,7 +6619,7 @@ "question": "What is the mushroom body?", "focus": null, "clicked": null, - "duration_ms": 7916, + "duration_ms": 6372, "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": [ @@ -6911,9 +6678,9 @@ "question": "Which driver lines label it?", "focus": null, "clicked": null, - "duration_ms": 5960, + "duration_ms": 2911, "ok": true, - "response": "The [mushroom body](https://www.virtualflybrain.org/reports/FBbt_00005801 \"Open mushroom body in Virtual Fly Brain\") is labeled by multiple driver lines, but specific lines are not identified in VFB evidence. However, the documentation mentions Hemidrivers, which are P{VT017411-GAL4.DBD} ∩ P{VT019018-p65.AD}. VFB holds [4130](https://v2.virtualflybrain.org/org.geppetto.frontend/geppetto?q=FBbt_00005801,TransgeneExpressionHere \"Run in VFB: Transgene expression in mushroom body\") records of transgene expression in mushroom body.", + "response": "The [mushroom body](https://www.virtualflybrain.org/reports/FBbt_00005801 \"Open mushroom body in Virtual Fly Brain\") is labeled by multiple driver lines, with VFB recording [4130](https://v2.virtualflybrain.org/org.geppetto.frontend/geppetto?q=FBbt_00005801,TransgeneExpressionHere \"Run in VFB: Transgene expression in mushroom body\") instances of transgene expression in the mushroom body.", "followons": [ { "id": "FBbt_00005801", @@ -6973,11 +6740,11 @@ } ], "ok": true, - "request_id": "d5c5868f-14a1-4743-a302-df850b66ff16", - "response_id": "chatcmpl-087a562df72c30d775236c3b16b747e0", + "request_id": "a68d6581-2ce6-4570-a8e1-b715a08b075e", + "response_id": "chatcmpl-cf4a3e7a5966ccdf5ae5e04ed1c658c5", "images_count": 8, "graphs_count": 0, - "response": "The [mushroom body](https://www.virtualflybrain.org/reports/FBbt_00005801 \"Open mushroom body in Virtual Fly Brain\") is labeled by multiple driver lines, but specific lines are not identified in VFB evidence. However, the documentation mentions Hemidrivers, which are P{VT017411-GAL4.DBD} ∩ P{VT019018-p65.AD}. VFB holds [4130](https://v2.virtualflybrain.org/org.geppetto.frontend/geppetto?q=FBbt_00005801,TransgeneExpressionHere \"Run in VFB: Transgene expression in mushroom body\") records of transgene expression in mushroom body.", + "response": "The [mushroom body](https://www.virtualflybrain.org/reports/FBbt_00005801 \"Open mushroom body in Virtual Fly Brain\") is labeled by multiple driver lines, with VFB recording [4130](https://v2.virtualflybrain.org/org.geppetto.frontend/geppetto?q=FBbt_00005801,TransgeneExpressionHere \"Run in VFB: Transgene expression in mushroom body\") instances of transgene expression in the mushroom body.", "quality_flags": { "has_tool_status": true, "no_tool_factual_answer": false, @@ -6988,14 +6755,14 @@ "graph_failure_mentioned": false, "missing_required_graph": false, "used_data_resource": false, - "response_chars": 532, + "response_chars": 390, "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": 5960 + "slowest_followup_ms": 2911 } }, { @@ -7008,7 +6775,7 @@ "requires_graph": false, "min_graphs": 0, "repetition": 1, - "duration_ms": 27742, + "duration_ms": 27431, "status_messages": [ { "message": "Thinking...", @@ -7018,6 +6785,10 @@ "message": "Planning the answer", "phase": "llm" }, + { + "phase": "plan", + "message": "The plan is contested — sampling again before committing." + }, { "message": "Resolving 1 term in VFB", "phase": "mcp" @@ -7063,7 +6834,7 @@ "phase": "llm" } ], - "event_count": 136, + "event_count": 213, "conversation": true, "turns": [ { @@ -7071,9 +6842,9 @@ "question": "Which neurons provide input to the medulla?", "focus": null, "clicked": null, - "duration_ms": 6847, + "duration_ms": 4507, "ok": true, - "response": "Neurons that provide input to the [medulla](https://www.virtualflybrain.org/reports/FBbt_00003748 \"Open medulla in Virtual Fly Brain\") include [Dm8b](https://www.virtualflybrain.org/reports/FBbt_00110069 \"Open Dm8b in Virtual Fly Brain\"), [PS128](https://www.virtualflybrain.org/reports/FBbt_20001883 \"Open PS128 in Virtual Fly Brain\"), [Mi10b](https://www.virtualflybrain.org/reports/FBbt_00110070 \"Open Mi10b in Virtual Fly Brain\"), [CB3849](https://www.virtualflybrain.org/reports/FBbt_20007264 \"Open CB3849 in Virtual Fly Brain\"), [TmY-ds](https://www.virtualflybrain.org/reports/FBbt_00052643 \"Open TmY-ds in Virtual Fly Brain\"), [Dm7](https://www.virtualflybrain.org/reports/FBbt_00003774 \"Open Dm7 in Virtual Fly Brain\"), Mi6, Mi8, Tm10, Tm13, Tm14, and Tm18. VFB records show [262](https://v2.virtualflybrain.org/org.geppetto.frontend/geppetto?q=FBbt_00003748,NeuronsPresynapticHere \"Run in VFB: Neurons with presynaptic terminals in medulla\") neurons with presynaptic terminals in medulla.", + "response": "The neurons that provide input to the [medulla](https://www.virtualflybrain.org/reports/FBbt_00003748 \"Open medulla in Virtual Fly Brain\") are those with presynaptic terminals in the medulla. VFB records show [262](https://v2.virtualflybrain.org/org.geppetto.frontend/geppetto?q=FBbt_00003748,NeuronsPresynapticHere \"Run in VFB: Neurons with presynaptic terminals in medulla\") such neurons. The first 12 of these, with their VFB ids, 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; Tm18.", "followons": [ { "id": "FBbt_00003748", @@ -7141,9 +6912,9 @@ "question": "And the lobula?", "focus": null, "clicked": null, - "duration_ms": 20895, + "duration_ms": 22924, "ok": true, - "response": "Neurons that provide input to the [lobula](https://www.virtualflybrain.org/reports/FBbt_00003852 \"Open lobula in Virtual Fly Brain\") include [AVLP391](https://www.virtualflybrain.org/reports/FBbt_20000500 \"Open AVLP391 in Virtual Fly Brain\"), [PLP031](https://www.virtualflybrain.org/reports/FBbt_20001531 \"Open PLP031 in Virtual Fly Brain\"), [TmY27](https://www.virtualflybrain.org/reports/FBbt_00110067 \"Open TmY27 in Virtual Fly Brain\"), [lobula columnar neuron vGlutLcnnew2](https://www.virtualflybrain.org/reports/FBbt_00110100 \"Open lobula columnar neuron vGlutLcnnew2 in Virtual Fly Brain\"), [OA-AL2b](https://www.virtualflybrain.org/reports/FBbt_00110145 \"Open OA-AL2b in Virtual Fly Brain\"), adult histaminergic HP3 neuron, translobula neuron, Tl1, Tl2, Tm1a, SIP063, and SLP339. VFB records show [528](https://v2.virtualflybrain.org/org.geppetto.frontend/geppetto?q=FBbt_00003852,NeuronsPartHere \"Run in VFB: Neurons with some part in lobula\") neurons with synaptic terminals in lobula.", + "response": "The neurons that provide input to the [lobula](https://www.virtualflybrain.org/reports/FBbt_00003852 \"Open lobula in Virtual Fly Brain\") are those with presynaptic terminals in the lobula. VFB holds records of such neurons in this session.\n\nNeurons with some part in the lobula 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, among [528](https://v2.virtualflybrain.org/org.geppetto.frontend/geppetto?q=FBbt_00003852,NeuronsPartHere \"Run in VFB: Neurons with some part in lobula\") total.\n\nSimilarly, 528 neurons have synaptic terminals in the lobula, including the same first 12 as those with some part in the lobula.\n\nThere are [4](https://v2.virtualflybrain.org/org.geppetto.frontend/geppetto?q=FBbt_00003852,ListAllAvailableImages \"Run in VFB: List all available images of lobula\") available images of the lobula.", "followons": [ { "id": "FBbt_00003852", @@ -7226,16 +6997,16 @@ ], "unmapped": [] }, - "status_count": 13, + "status_count": 14, "problems": [] } ], "ok": true, - "request_id": "818c8e17-c09c-4fd8-b43e-9fa48c5e105f", - "response_id": "chatcmpl-6195bb12ffe3270edbea2be05b1791a2", + "request_id": "6d822681-6d9a-4a7c-ad89-e0420efbffef", + "response_id": "chatcmpl-7129544fab100a36d1a66d9620cccb25", "images_count": 4, "graphs_count": 0, - "response": "Neurons that provide input to the [lobula](https://www.virtualflybrain.org/reports/FBbt_00003852 \"Open lobula in Virtual Fly Brain\") include [AVLP391](https://www.virtualflybrain.org/reports/FBbt_20000500 \"Open AVLP391 in Virtual Fly Brain\"), [PLP031](https://www.virtualflybrain.org/reports/FBbt_20001531 \"Open PLP031 in Virtual Fly Brain\"), [TmY27](https://www.virtualflybrain.org/reports/FBbt_00110067 \"Open TmY27 in Virtual Fly Brain\"), [lobula columnar neuron vGlutLcnnew2](https://www.virtualflybrain.org/reports/FBbt_00110100 \"Open lobula columnar neuron vGlutLcnnew2 in Virtual Fly Brain\"), [OA-AL2b](https://www.virtualflybrain.org/reports/FBbt_00110145 \"Open OA-AL2b in Virtual Fly Brain\"), adult histaminergic HP3 neuron, translobula neuron, Tl1, Tl2, Tm1a, SIP063, and SLP339. VFB records show [528](https://v2.virtualflybrain.org/org.geppetto.frontend/geppetto?q=FBbt_00003852,NeuronsPartHere \"Run in VFB: Neurons with some part in lobula\") neurons with synaptic terminals in lobula.", + "response": "The neurons that provide input to the [lobula](https://www.virtualflybrain.org/reports/FBbt_00003852 \"Open lobula in Virtual Fly Brain\") are those with presynaptic terminals in the lobula. VFB holds records of such neurons in this session.\n\nNeurons with some part in the lobula 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, among [528](https://v2.virtualflybrain.org/org.geppetto.frontend/geppetto?q=FBbt_00003852,NeuronsPartHere \"Run in VFB: Neurons with some part in lobula\") total.\n\nSimilarly, 528 neurons have synaptic terminals in the lobula, including the same first 12 as those with some part in the lobula.\n\nThere are [4](https://v2.virtualflybrain.org/org.geppetto.frontend/geppetto?q=FBbt_00003852,ListAllAvailableImages \"Run in VFB: List all available images of lobula\") available images of the lobula.", "quality_flags": { "has_tool_status": true, "no_tool_factual_answer": false, @@ -7246,14 +7017,14 @@ "graph_failure_mentioned": false, "missing_required_graph": false, "used_data_resource": false, - "response_chars": 996, - "status_count": 13, + "response_chars": 1423, + "status_count": 14, "addressless_followon": false, "context_lost_across_turn": false, "unmatched_claim_after_resolve": false, "repeats_answered_question": false, "slow_followup_turn": false, - "slowest_followup_ms": 20895 + "slowest_followup_ms": 22924 } }, { @@ -7266,7 +7037,7 @@ "requires_graph": false, "min_graphs": 0, "repetition": 1, - "duration_ms": 48715, + "duration_ms": 39991, "status_messages": [ { "message": "Thinking...", @@ -7285,7 +7056,7 @@ "phase": "mcp" }, { - "message": "Querying VFB", + "message": "Querying VFB connectivity", "phase": "mcp" }, { @@ -7321,7 +7092,7 @@ "phase": "llm" } ], - "event_count": 203, + "event_count": 100, "conversation": true, "turns": [ { @@ -7329,9 +7100,9 @@ "question": "What is the protocerebral bridge?", "focus": null, "clicked": null, - "duration_ms": 7321, + "duration_ms": 6844, "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.", + "response": "The [protocerebral bridge](https://www.virtualflybrain.org/reports/FBbt_00003668 \"Open protocerebral bridge in Virtual Fly Brain\") is a handle bar-shaped synaptic neuropil located just posterior to the fan-shaped body. Its lateral edge ends at the posterior end of the inferior clamp near the medial equatorial fascicle. A row of 18 connected slices, 9 on each side of the midline, numbered 1-9 from medial to lateral, forms a dorso-posteriorly located part of the central complex embedded in the cortex between the calyces of the two mushroom bodies.", "followons": [ { "id": "FBbt_00003668", @@ -7388,9 +7159,9 @@ "question": "How does it relate to the ellipsoid body?", "focus": null, "clicked": null, - "duration_ms": 15094, + "duration_ms": 14072, "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. For example, 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\") has synaptic terminals in the ellipsoid body. VFB records show that there are [102](https://v2.virtualflybrain.org/org.geppetto.frontend/geppetto?q=FBbt_00003678,NeuronsSynaptic \"Run in VFB: Neurons with synaptic terminals in ellipsoid body\") neurons with synaptic terminals in the ellipsoid body, and some of these neurons have names that indicate a connection to the protocerebral bridge, such as the adult protocerebral bridge glomerulus 1-ellipsoid body canal-dorsal gall neuron.", + "response": "The [protocerebral bridge](https://www.virtualflybrain.org/reports/FBbt_00003668 \"Open protocerebral bridge in Virtual Fly Brain\") and the [ellipsoid body](https://www.virtualflybrain.org/reports/FBbt_00003678 \"Open ellipsoid body in Virtual Fly Brain\") are connected by neurons. VFB records show that there are neurons with some part in the ellipsoid body, including [adult protocerebral bridge glomerulus 1-ellipsoid body canal-dorsal gall neuron](https://www.virtualflybrain.org/reports/FBbt_00111376 \"Open adult protocerebral bridge glomerulus 1-ellipsoid body canal-dorsal gall neuron in Virtual Fly Brain\"), and adult protocerebral bridge glomerulus 4-ellipsoid body canal-ventral gall neuron, among others. These neurons also have synaptic terminals in the ellipsoid body.", "followons": [ { "id": "FBbt_00003668", @@ -7463,7 +7234,7 @@ ], "unmapped": [] }, - "status_count": 12, + "status_count": 13, "problems": [] }, { @@ -7471,9 +7242,9 @@ "question": "Which neurons connect them?", "focus": null, "clicked": null, - "duration_ms": 26300, + "duration_ms": 19075, "ok": true, - "response": "Neurons that connect the [protocerebral bridge](https://www.virtualflybrain.org/reports/FBbt_00003668 \"Open protocerebral bridge in Virtual Fly Brain\") and the [ellipsoid body](https://www.virtualflybrain.org/reports/FBbt_00003678 \"Open ellipsoid body in Virtual Fly Brain\") include 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\"), 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. VFB records show that there are [103](https://v2.virtualflybrain.org/org.geppetto.frontend/geppetto?q=FBbt_00003678,NeuronsPartHere \"Run in VFB: Neurons with some part in ellipsoid body\") neuron types with some part in the ellipsoid body and [193](https://v2.virtualflybrain.org/org.geppetto.frontend/geppetto?q=FBbt_00003668,NeuronsSynaptic \"Run in VFB: Neurons with synaptic terminals in protocerebral bridge\") neurons with synaptic terminals in the protocerebral bridge.", + "response": "Neurons that connect the [protocerebral bridge](https://www.virtualflybrain.org/reports/FBbt_00003668 \"Open protocerebral bridge in Virtual Fly Brain\") and the [ellipsoid body](https://www.virtualflybrain.org/reports/FBbt_00003678 \"Open ellipsoid body in Virtual Fly Brain\") include the [adult protocerebral bridge glomerulus 1-ellipsoid body canal-dorsal gall neuron](https://www.virtualflybrain.org/reports/FBbt_00111376 \"Open adult protocerebral bridge glomerulus 1-ellipsoid body canal-dorsal gall neuron in Virtual Fly Brain\") and the adult protocerebral bridge glomerulus 4-ellipsoid body canal-ventral gall neuron. VFB records show that there are neurons with some part in the ellipsoid body, including these neurons, among others.", "followons": [ { "id": "FBbt_00003668", @@ -7576,11 +7347,219 @@ } ], "ok": true, - "request_id": "adae4d30-cdd1-4317-acb7-612cb9854b8f", - "response_id": "chatcmpl-bc2ef58c153b08e086f65e1a4e5d571c", + "request_id": "6197cd96-afc0-40bb-931a-021923f445a1", + "response_id": "chatcmpl-60c5013e3d8b754918e844cdfd5740ff", "images_count": 8, - "graphs_count": 0, - "response": "Neurons that connect the [protocerebral bridge](https://www.virtualflybrain.org/reports/FBbt_00003668 \"Open protocerebral bridge in Virtual Fly Brain\") and the [ellipsoid body](https://www.virtualflybrain.org/reports/FBbt_00003678 \"Open ellipsoid body in Virtual Fly Brain\") include 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\"), 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. VFB records show that there are [103](https://v2.virtualflybrain.org/org.geppetto.frontend/geppetto?q=FBbt_00003678,NeuronsPartHere \"Run in VFB: Neurons with some part in ellipsoid body\") neuron types with some part in the ellipsoid body and [193](https://v2.virtualflybrain.org/org.geppetto.frontend/geppetto?q=FBbt_00003668,NeuronsSynaptic \"Run in VFB: Neurons with synaptic terminals in protocerebral bridge\") neurons with synaptic terminals in the protocerebral bridge.", + "graphs_count": 1, + "response": "Neurons that connect the [protocerebral bridge](https://www.virtualflybrain.org/reports/FBbt_00003668 \"Open protocerebral bridge in Virtual Fly Brain\") and the [ellipsoid body](https://www.virtualflybrain.org/reports/FBbt_00003678 \"Open ellipsoid body in Virtual Fly Brain\") include the [adult protocerebral bridge glomerulus 1-ellipsoid body canal-dorsal gall neuron](https://www.virtualflybrain.org/reports/FBbt_00111376 \"Open adult protocerebral bridge glomerulus 1-ellipsoid body canal-dorsal gall neuron in Virtual Fly Brain\") and the adult protocerebral bridge glomerulus 4-ellipsoid body canal-ventral gall neuron. VFB records show that there are neurons with some part in the ellipsoid body, including these neurons, among others.", + "graphs": [ + { + "type": "basic_graph", + "version": 1, + "title": "Upstream partners of P6-8P9", + "directed": true, + "layout": "circle", + "nodes": [ + { + "id": "FBbt_00047095", + "label": "adult neuron", + "group": null, + "color": null, + "size": 1.37 + }, + { + "id": "FBbt_00111056", + "label": "P6-8P9", + "group": null, + "color": null, + "size": 4 + }, + { + "id": "FBbt_00005106", + "label": "neuron", + "group": null, + "color": null, + "size": 1.37 + }, + { + "id": "FBbt_00049819", + "label": "adult central complex neuron", + "group": null, + "color": null, + "size": 1.37 + }, + { + "id": "FBbt_00059271", + "label": "CNS neuron", + "group": null, + "color": null, + "size": 1.37 + }, + { + "id": "FBbt_00053387", + "label": "intrinsic neuron of the central complex", + "group": null, + "color": null, + "size": 1.21 + }, + { + "id": "FBbt_00007515", + "label": "large field neuron of the central complex", + "group": null, + "color": null, + "size": 1.2 + }, + { + "id": "FBbt_00003648", + "label": "large field neuron", + "group": null, + "color": null, + "size": 1.2 + }, + { + "id": "FBbt_00003666", + "label": "adult intrinsic protocerebral bridge neuron", + "group": null, + "color": null, + "size": 1.19 + }, + { + "id": "FBbt_00049807", + "label": "adult intrinsic protocerebral bridge 18 glomeruli-delta7 neuron", + "group": null, + "color": null, + "size": 1.17 + }, + { + "id": "FBbt_00007514", + "label": "small field neuron of the central complex", + "group": null, + "color": null, + "size": 1.14 + }, + { + "id": "FBbt_00003633", + "label": "small field neuron", + "group": null, + "color": null, + "size": 1.14 + }, + { + "id": "FBbt_00003637", + "label": "adult ellipsoid body-protocerebral bridge-gall neuron", + "group": null, + "color": null, + "size": 1.12 + }, + { + "id": "FBbt_00047030", + "label": "adult ellipsoid body-protocerebral bridge 1 glomerulus-dorsal/ventral gall neuron", + "group": null, + "color": null, + "size": 1.11 + }, + { + "id": "FBbt_00049822", + "label": "fan-shaped body extrinsic columnar neuron", + "group": null, + "color": null, + "size": 1.02 + } + ], + "edges": [ + { + "source": "FBbt_00047095", + "target": "FBbt_00111056", + "label": "3201", + "weight": 3201 + }, + { + "source": "FBbt_00005106", + "target": "FBbt_00111056", + "label": "3201", + "weight": 3201 + }, + { + "source": "FBbt_00049819", + "target": "FBbt_00111056", + "label": "3197", + "weight": 3197 + }, + { + "source": "FBbt_00059271", + "target": "FBbt_00111056", + "label": "3197", + "weight": 3197 + }, + { + "source": "FBbt_00053387", + "target": "FBbt_00111056", + "label": "1817", + "weight": 1817 + }, + { + "source": "FBbt_00007515", + "target": "FBbt_00111056", + "label": "1740", + "weight": 1740 + }, + { + "source": "FBbt_00003648", + "target": "FBbt_00111056", + "label": "1740", + "weight": 1740 + }, + { + "source": "FBbt_00003666", + "target": "FBbt_00111056", + "label": "1662", + "weight": 1662 + }, + { + "source": "FBbt_00049807", + "target": "FBbt_00111056", + "label": "1469", + "weight": 1469 + }, + { + "source": "FBbt_00007514", + "target": "FBbt_00111056", + "label": "1191", + "weight": 1191 + }, + { + "source": "FBbt_00003633", + "target": "FBbt_00111056", + "label": "1191", + "weight": 1191 + }, + { + "source": "FBbt_00003637", + "target": "FBbt_00111056", + "label": "1020", + "weight": 1020 + }, + { + "source": "FBbt_00047030", + "target": "FBbt_00111056", + "label": "935", + "weight": 935 + }, + { + "source": "FBbt_00111056", + "target": "FBbt_00111056", + "label": "193", + "weight": 193 + }, + { + "source": "FBbt_00049822", + "target": "FBbt_00111056", + "label": "166", + "weight": 166 + } + ] + } + ], "quality_flags": { "has_tool_status": true, "no_tool_factual_answer": false, @@ -7591,14 +7570,14 @@ "graph_failure_mentioned": false, "missing_required_graph": false, "used_data_resource": false, - "response_chars": 1438, + "response_chars": 738, "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": 26300 + "slowest_followup_ms": 19075 } }, { @@ -7611,7 +7590,7 @@ "requires_graph": false, "min_graphs": 0, "repetition": 1, - "duration_ms": 30973, + "duration_ms": 25323, "status_messages": [ { "message": "Thinking...", @@ -7642,7 +7621,7 @@ "phase": "llm" } ], - "event_count": 62, + "event_count": 43, "conversation": true, "turns": [ { @@ -7650,7 +7629,7 @@ "question": "Which neurons have part of them in the medulla?", "focus": null, "clicked": null, - "duration_ms": 14161, + "duration_ms": 13285, "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.", "followons": [ @@ -7707,7 +7686,7 @@ ], "unmapped": [] }, - "status_count": 8, + "status_count": 9, "problems": [] }, { @@ -7715,9 +7694,9 @@ "question": "How would I get that same result in Python with vfbquery?", "focus": null, "clicked": null, - "duration_ms": 16811, + "duration_ms": 12038, "ok": true, - "response": "The code below returns the neurons with some part in the [medulla](https://www.virtualflybrain.org/reports/FBbt_00003748 \"Open medulla in Virtual Fly Brain\"), as a table, along with other related data such as images of neurons with some part in the medulla. 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.\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. 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.\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", @@ -7777,11 +7756,11 @@ } ], "ok": true, - "request_id": "dd0e856e-d43e-4ffa-b2d9-68a4824f7822", - "response_id": "chatcmpl-508bda0507667a61741d92ac54b599e6", + "request_id": "d37cc8d6-0d82-4d24-9cba-335011c62c9c", + "response_id": "chatcmpl-5807e3e04ad72fd6c318b67dac51c538", "images_count": 8, "graphs_count": 0, - "response": "The code below returns the neurons with some part in the [medulla](https://www.virtualflybrain.org/reports/FBbt_00003748 \"Open medulla in Virtual Fly Brain\"), as a table, along with other related data such as images of neurons with some part in the medulla. 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.\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. 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.\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, @@ -7792,14 +7771,14 @@ "graph_failure_mentioned": false, "missing_required_graph": false, "used_data_resource": false, - "response_chars": 906, + "response_chars": 815, "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": 16811 + "slowest_followup_ms": 12038 } }, { @@ -7812,7 +7791,7 @@ "requires_graph": false, "min_graphs": 0, "repetition": 1, - "duration_ms": 35235, + "duration_ms": 29238, "status_messages": [ { "message": "Thinking...", @@ -7847,7 +7826,7 @@ "phase": "llm" } ], - "event_count": 67, + "event_count": 100, "conversation": true, "turns": [ { @@ -7855,9 +7834,9 @@ "question": "What are the subclasses of Kenyon cell?", "focus": null, "clicked": null, - "duration_ms": 14873, + "duration_ms": 9449, "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", @@ -7920,9 +7899,9 @@ "question": "Can you list the VFB IDs so I can reproduce this myself?", "focus": null, "clicked": null, - "duration_ms": 20362, + "duration_ms": 19789, "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\").\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 records for the subclasses of Kenyon cell, including their VFB ids, such as FBbt_00049111 for [KCab-c(i)](https://www.virtualflybrain.org/reports/FBbt_00049111 \"Open KCab-c(i) in Virtual Fly Brain\") and FBbt_00049112 for [KCab-c](https://www.virtualflybrain.org/reports/FBbt_00110929 \"Open KCab-c in Virtual Fly Brain\")(o).\n\n(query=\"SubclassesOf\", id=\"\", format=\"table\")\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", @@ -7977,11 +7956,11 @@ } ], "ok": true, - "request_id": "f567740b-f8aa-4248-b238-98fee4f0dd31", - "response_id": "chatcmpl-225d1466f56f5fc8e835d08c33db0611", + "request_id": "379e917b-2874-49e6-9b24-15f7bc578826", + "response_id": "chatcmpl-a121381a9200119acb7c23c2e38afe3f", "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\").\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 records for the subclasses of Kenyon cell, including their VFB ids, such as FBbt_00049111 for [KCab-c(i)](https://www.virtualflybrain.org/reports/FBbt_00049111 \"Open KCab-c(i) in Virtual Fly Brain\") and FBbt_00049112 for [KCab-c](https://www.virtualflybrain.org/reports/FBbt_00110929 \"Open KCab-c in Virtual Fly Brain\")(o).\n\n(query=\"SubclassesOf\", id=\"\", format=\"table\")\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, @@ -7992,14 +7971,14 @@ "graph_failure_mentioned": false, "missing_required_graph": false, "used_data_resource": false, - "response_chars": 1369, + "response_chars": 1151, "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": 20362 + "slowest_followup_ms": 19789 } } ] diff --git a/test-results/task-battery/task-battery-2026-08-13T12-36-49-371Z.json b/test-results/task-battery/task-battery-2026-08-13T12-36-49-371Z.json new file mode 100644 index 0000000..e25b15d --- /dev/null +++ b/test-results/task-battery/task-battery-2026-08-13T12-36-49-371Z.json @@ -0,0 +1,8032 @@ +{ + "metadata": { + "run_id": "task-battery-2026-08-13T12-36-49-371Z", + "started_at": "2026-08-13T12:36:49.371Z", + "completed_at": "2026-08-13T12:43:31.935Z", + "git_sha": "effe08700d55ca239a990a4a3816a5d0100c9b73", + "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": 64, + "errors": 0, + "by_tier": { + "T1": { + "total": 8, + "ok": 8, + "errors": 0 + }, + "T2": { + "total": 8, + "ok": 8, + "errors": 0 + }, + "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": 21, + "errors": 0 + }, + "T7": { + "total": 12, + "ok": 12, + "errors": 0 + } + }, + "quality": { + "no_tool_factual_answer": { + "count": 0, + "task_ids": [] + }, + "tool_claim_without_tool": { + "count": 0, + "task_ids": [] + }, + "disambiguation_only_answer": { + "count": 0, + "task_ids": [] + }, + "investigation_plan_answer": { + "count": 0, + "task_ids": [] + }, + "not_verified_or_no_results_answer": { + "count": 0, + "task_ids": [] + }, + "graph_failure_mentioned": { + "count": 0, + "task_ids": [] + }, + "missing_required_graph": { + "count": 0, + "task_ids": [] + }, + "used_data_resource": { + "count": 0, + "task_ids": [] + }, + "addressless_followon": { + "count": 0, + "task_ids": [] + }, + "context_lost_across_turn": { + "count": 0, + "task_ids": [] + }, + "unmatched_claim_after_resolve": { + "count": 0, + "task_ids": [] + }, + "repeats_answered_question": { + "count": 0, + "task_ids": [] + }, + "slow_followup_turn": { + "count": 0, + "task_ids": [] + } + }, + "conversation": { + "total": 12, + "ok": 12, + "turns": 27, + "followup_turns": 15, + "followup_median_ms": 9901, + "followup_max_ms": 71565 + }, + "mean_duration_ms": 24282 + }, + "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": 18167, + "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": 100, + "ok": true, + "request_id": "2baefb79-c07d-4f9d-9569-aba4ddcb60b5", + "response_id": "chatcmpl-d3857820752ac418aceda3a8b7e66364", + "images_count": 8, + "graphs_count": 0, + "response": "The major subdivisions of the Drosophila [mushroom body](https://www.virtualflybrain.org/reports/FBbt_00005801 \"Open mushroom body in Virtual Fly Brain\") are the calyx, pedunculus, and mushroom body lobe system. The calyx is closest to the cortex and receives sensory interneuron afferents. The pedunculus is a thick axon bundle extending from the calyx to the base of the lobes. The mushroom body lobe system consists of a vertical branch and a medial branch, which have different structures at different life stages.", + "quality_flags": { + "has_tool_status": true, + "no_tool_factual_answer": false, + "tool_claim_without_tool": false, + "disambiguation_only_answer": false, + "investigation_plan_answer": false, + "not_verified_or_no_results_answer": false, + "graph_failure_mentioned": false, + "missing_required_graph": false, + "used_data_resource": false, + "response_chars": 518, + "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": 17847, + "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": "db66fd94-f95d-4e60-8458-a53cb5a04f50", + "response_id": "chatcmpl-95ae0d71d1bebc6e6b495f6a005969e4", + "images_count": 8, + "graphs_count": 0, + "response": "There are several types of Kenyon cells in the adult Drosophila brain, including alpha/beta, alpha'/beta', and gamma Kenyon cells, which can be further subdivided into core/surface/posterior, anterior-posterior/middle, dorsal/main/gamma-s/gamma-t, and claw-count classes. VFB holds [37](https://v2.virtualflybrain.org/org.geppetto.frontend/geppetto?q=FBbt_00003686,SubclassesOf \"Run in VFB: Subclasses of Kenyon cell\") subclasses of [Kenyon cell](https://www.virtualflybrain.org/reports/FBbt_00003686 \"Open Kenyon cell in Virtual Fly Brain\").", + "quality_flags": { + "has_tool_status": true, + "no_tool_factual_answer": false, + "tool_claim_without_tool": false, + "disambiguation_only_answer": false, + "investigation_plan_answer": false, + "not_verified_or_no_results_answer": false, + "graph_failure_mentioned": false, + "missing_required_graph": false, + "used_data_resource": false, + "response_chars": 542, + "status_count": 6 + } + }, + { + "attempt_index": 2, + "task_index": 2, + "task_id": "T1.3", + "tier": 1, + "title": "Basic connectivity", + "question": "What are the main input neurons to the mushroom body?", + "requires_graph": false, + "min_graphs": 0, + "repetition": 1, + "duration_ms": 17577, + "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": 74, + "ok": true, + "request_id": "51aa4a5e-3aa8-4dc4-9900-59175690c7a0", + "response_id": "chatcmpl-3051eb10d1ab6ffae5eac21872a77545", + "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 the mushroom body, including larval uniglomerular projection neurons and larval antennal lobe multiglomerular projection neurons.", + "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": 549, + "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": 15563, + "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": "e0f6442e-f8eb-4437-a615-7615c04648f6", + "response_id": "chatcmpl-33c94be9f3a3a29062f037e71124f137", + "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": 23983, + "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": 165, + "ok": true, + "request_id": "0bb0c634-6e7e-4b95-98a2-769e8818ad6d", + "response_id": "chatcmpl-06060d2b12cc549eea12c8db28a53337", + "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. These neurons likely connect the antennal lobe to other parts of the brain, although the specific regions are not detailed here.", + "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": 1103, + "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": 17010, + "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": "6fc47188-8568-4248-8711-d9c0533d482e", + "response_id": "chatcmpl-24397e3cdc27e53ec7e1018dd875f581", + "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. VFB has annotated [9413](https://v2.virtualflybrain.org/org.geppetto.frontend/geppetto?q=FBbt_00047887,NeuronsPartHere \"Run in VFB: Neurons with some part in adult central brain\") neuron types with some part in the adult central brain.\n\n**Published neuron-count estimates — adult central brain** (from the literature):\n\n- ~32,388 neurons (Whole adult brain, both optic lobes and ocellar ganglia included. Ventral nerve cord NOT included; neurons crossing the neck connective are truncated at the brain boundary. Subcount: fully in central brain. One female adult. Dataset: FlyWire connectome neurons, v783.) — Dorkenwald S et al. (2024) Nature 634(8032):124-138 — PMID 39358518\n\n_VFB has annotated 9,413 neuron types with some part in adult central brain — a curated annotation count, not the biological total._", + "quality_flags": { + "has_tool_status": true, + "no_tool_factual_answer": false, + "tool_claim_without_tool": false, + "disambiguation_only_answer": false, + "investigation_plan_answer": false, + "not_verified_or_no_results_answer": false, + "graph_failure_mentioned": false, + "missing_required_graph": false, + "used_data_resource": false, + "response_chars": 979, + "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": 20200, + "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": 105, + "ok": true, + "request_id": "9ae0f904-f3fd-4e9c-8003-6f195bad790c", + "response_id": "chatcmpl-0391c4232cbf52ea1c02ebafa7e4da63", + "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. 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.", + "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": 925, + "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": 23556, + "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": 97, + "ok": true, + "request_id": "5a503756-a009-4f35-8e0e-a2523ba39309", + "response_id": "chatcmpl-d1dafc7c9fe3bddc6e7cf5216c172ad1", + "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, among others. VFB records show multiple transgene expression patterns, but the specific genetic tools used for labeling Kenyon cell are not fully detailed in VFB evidence.", + "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": 446, + "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": 26450, + "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": 77, + "ok": true, + "request_id": "6a884b9e-3bb4-4641-8466-55a2991d303d", + "response_id": "chatcmpl-0e93a829b2a749a3eb854c8eb5681ad4", + "images_count": 8, + "graphs_count": 1, + "response": "Dopaminergic input to mushroom body output neurons comes from specific dopaminergic neuron types, including dopaminergic PPL1 neurons and dopaminergic PAM neurons. The strongest specific inputs to [mushroom body output neuron](https://www.virtualflybrain.org/reports/FBbt_00047953 \"Open mushroom body output neuron in Virtual Fly Brain\") are [adult cholinergic neuron](https://www.virtualflybrain.org/reports/FBbt_00058205 \"Open adult cholinergic neuron in Virtual Fly Brain\") and [Kenyon cell](https://www.virtualflybrain.org/reports/FBbt_00003686 \"Open Kenyon cell in Virtual Fly Brain\"). VFB holds [69](https://v2.virtualflybrain.org/org.geppetto.frontend/geppetto?q=FBbt_00047953,SubclassesOf \"Run in VFB: Subclasses of MBON\") subclasses of mushroom body output neuron.", + "graphs": [ + { + "type": "basic_graph", + "version": 1, + "title": "Upstream partners of MBON", + "directed": true, + "layout": "circle", + "nodes": [ + { + "id": "FBbt_00005131", + "label": "dopaminergic neuron", + "group": null, + "color": null, + "size": 1.93 + }, + { + "id": "FBbt_00047953", + "label": "MBON", + "group": null, + "color": null, + "size": 4 + }, + { + "id": "FBbt_00058206", + "label": "adult dopaminergic neuron", + "group": null, + "color": null, + "size": 1.92 + }, + { + "id": "FBbt_00048138", + "label": "mushroom body dopaminergic neuron", + "group": null, + "color": null, + "size": 1.91 + }, + { + "id": "FBbt_00049839", + "label": "adult dopaminergic mushroom body input neuron", + "group": null, + "color": null, + "size": 1.07 + }, + { + "id": "FBbt_00100214", + "label": "adult dopaminergic PAM neuron", + "group": null, + "color": null, + "size": 1.07 + }, + { + "id": "FBbt_00100219", + "label": "dopaminergic PPL1 neuron", + "group": null, + "color": null, + "size": 1.02 + }, + { + "id": "FBbt_00049840", + "label": "mushroom body PPL1 neuron", + "group": null, + "color": null, + "size": 1.02 + }, + { + "id": "FBbt_00111020", + "label": "dopaminergic PAM neuron 8", + "group": null, + "color": null, + "size": 1.01 + }, + { + "id": "FBbt_00111018", + "label": "dopaminergic PAM neuron 6", + "group": null, + "color": null, + "size": 1.01 + }, + { + "id": "FBbt_00111017", + "label": "dopaminergic PAM neuron 5", + "group": null, + "color": null, + "size": 1.01 + }, + { + "id": "FBbt_00110994", + "label": "dopaminergic PAM neuron 10", + "group": null, + "color": null, + "size": 1.01 + }, + { + "id": "FBbt_00110993", + "label": "dopaminergic PAM neuron 4", + "group": null, + "color": null, + "size": 1.01 + }, + { + "id": "FBbt_00111022", + "label": "dopaminergic PAM neuron 11", + "group": null, + "color": null, + "size": 1.01 + }, + { + "id": "FBbt_00007364", + "label": "octopaminergic neuron", + "group": null, + "color": null, + "size": 1.01 + }, + { + "id": "FBbt_00058203", + "label": "adult octopaminergic neuron", + "group": null, + "color": null, + "size": 1.01 + } + ], + "edges": [ + { + "source": "FBbt_00005131", + "target": "FBbt_00047953", + "label": "651367", + "weight": 651367 + }, + { + "source": "FBbt_00058206", + "target": "FBbt_00047953", + "label": "650172", + "weight": 650172 + }, + { + "source": "FBbt_00048138", + "target": "FBbt_00047953", + "label": "641765", + "weight": 641765 + }, + { + "source": "FBbt_00049839", + "target": "FBbt_00047953", + "label": "47142", + "weight": 47142 + }, + { + "source": "FBbt_00100214", + "target": "FBbt_00047953", + "label": "47139", + "weight": 47139 + }, + { + "source": "FBbt_00100219", + "target": "FBbt_00047953", + "label": "17270", + "weight": 17270 + }, + { + "source": "FBbt_00049840", + "target": "FBbt_00047953", + "label": "16097", + "weight": 16097 + }, + { + "source": "FBbt_00111020", + "target": "FBbt_00047953", + "label": "7988", + "weight": 7988 + }, + { + "source": "FBbt_00111018", + "target": "FBbt_00047953", + "label": "7650", + "weight": 7650 + }, + { + "source": "FBbt_00111017", + "target": "FBbt_00047953", + "label": "5433", + "weight": 5433 + }, + { + "source": "FBbt_00110994", + "target": "FBbt_00047953", + "label": "4482", + "weight": 4482 + }, + { + "source": "FBbt_00110993", + "target": "FBbt_00047953", + "label": "4248", + "weight": 4248 + }, + { + "source": "FBbt_00111022", + "target": "FBbt_00047953", + "label": "4033", + "weight": 4033 + }, + { + "source": "FBbt_00007364", + "target": "FBbt_00047953", + "label": "3790", + "weight": 3790 + }, + { + "source": "FBbt_00058203", + "target": "FBbt_00047953", + "label": "3547", + "weight": 3547 + } + ] + } + ], + "quality_flags": { + "has_tool_status": true, + "no_tool_factual_answer": false, + "tool_claim_without_tool": false, + "disambiguation_only_answer": false, + "investigation_plan_answer": false, + "not_verified_or_no_results_answer": false, + "graph_failure_mentioned": false, + "missing_required_graph": false, + "used_data_resource": false, + "response_chars": 773, + "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": 14854, + "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": "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": "4ebf8498-d0ef-4a43-aa3e-fca4ef94eda2", + "response_id": "chatcmpl-72feada4a788df2c60a07ed408e9b255", + "images_count": 5, + "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, but do not specify the consistency of connectivity between these datasets. 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\"), while the strongest specific inputs 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\").", + "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": 1539, + "status_count": 9 + } + }, + { + "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": 21224, + "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": 202, + "ok": true, + "request_id": "c6f56eef-a45a-4732-980e-67d94137031c", + "response_id": "chatcmpl-7ab5a097356c9a110f72345cc02483a9", + "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]. FlyLight split-GAL4 lines for Lateral Horn are mentioned in the documentation, referencing Dolan et al., 2019.", + "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": 369, + "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": 24373, + "status_messages": [ + { + "message": "Thinking...", + "phase": "llm" + }, + { + "message": "Planning the answer", + "phase": "llm" + }, + { + "message": "Resolving 1 term in VFB", + "phase": "mcp" + }, + { + "message": "Querying VFB", + "phase": "mcp" + }, + { + "message": "Querying VFB connectivity", + "phase": "mcp" + }, + { + "message": "Checking the answer is covered", + "phase": "llm" + }, + { + "message": "Writing the answer", + "phase": "llm" + }, + { + "message": "Checking before saying VFB has no data", + "phase": "mcp" + }, + { + "message": "Querying VFB", + "phase": "mcp" + }, + { + "message": "Querying VFB", + "phase": "mcp" + }, + { + "message": "Querying VFB", + "phase": "mcp" + }, + { + "message": "Checking the answer is covered", + "phase": "llm" + }, + { + "message": "Writing the answer", + "phase": "llm" + } + ], + "event_count": 187, + "ok": true, + "request_id": "a4b14c25-e582-47c8-8967-d34cea6ac199", + "response_id": "chatcmpl-f65d8c9d5accfd159352c6b4dafd39f3", + "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 elicits a jump escape response. VFB holds [723](https://v2.virtualflybrain.org/org.geppetto.frontend/geppetto?q=FBbt_00111763,ListAllAvailableImages \"Run in VFB: List all available images of LPLC2\") images of LPLC2. There are [2](https://v2.virtualflybrain.org/org.geppetto.frontend/geppetto?q=FBbt_00111763,SplitsTargeting \"Run in VFB: Splits targeting LPLC2\") splits targeting LPLC2 and 2 scRNAseq datasets available for this neuron type.", + "quality_flags": { + "has_tool_status": true, + "no_tool_factual_answer": false, + "tool_claim_without_tool": false, + "disambiguation_only_answer": false, + "investigation_plan_answer": false, + "not_verified_or_no_results_answer": false, + "graph_failure_mentioned": false, + "missing_required_graph": false, + "used_data_resource": false, + "response_chars": 766, + "status_count": 13 + } + }, + { + "attempt_index": 12, + "task_index": 12, + "task_id": "T2.5", + "tier": 2, + "title": "Comparative anatomy", + "question": "How does the organisation of the antennal lobe compare between adult and larval Drosophila?", + "requires_graph": false, + "min_graphs": 0, + "repetition": 1, + "duration_ms": 11927, + "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": "f9558587-b939-40a4-b0ea-8057fc583afa", + "response_id": "chatcmpl-339591faabd8702a5edaa5f6a3a2be20", + "images_count": 6, + "graphs_count": 0, + "response": "The adult [antennal lobe](https://www.virtualflybrain.org/reports/FBbt_00003924 \"Open antennal lobe in Virtual Fly Brain\") has approximately 50 glomeruli, while the larval antennal lobe has around 22 glomeruli.", + "quality_flags": { + "has_tool_status": true, + "no_tool_factual_answer": false, + "tool_claim_without_tool": false, + "disambiguation_only_answer": false, + "investigation_plan_answer": false, + "not_verified_or_no_results_answer": false, + "graph_failure_mentioned": false, + "missing_required_graph": false, + "used_data_resource": false, + "response_chars": 210, + "status_count": 6 + } + }, + { + "attempt_index": 13, + "task_index": 13, + "task_id": "T2.6", + "tier": 2, + "title": "Publications for a circuit", + "question": "What publications describe the PPL1 dopaminergic neurons and their role in aversive memory?", + "requires_graph": false, + "min_graphs": 0, + "repetition": 1, + "duration_ms": 15210, + "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": "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": "33eb47d2-9f13-492f-8f84-d528fa976ded", + "response_id": "chatcmpl-3cdd758c6f62ac532008c66ad2d73e5a", + "images_count": 8, + "graphs_count": 0, + "response": "Publications describing the dopaminergic PPL1 neurons and their role in aversive memory include Claridge-Chang et al., 2009, Mao and Davis, 2009, Budnik and White, 1988, and Ren et al., 2016.", + "quality_flags": { + "has_tool_status": true, + "no_tool_factual_answer": false, + "tool_claim_without_tool": false, + "disambiguation_only_answer": false, + "investigation_plan_answer": false, + "not_verified_or_no_results_answer": false, + "graph_failure_mentioned": false, + "missing_required_graph": false, + "used_data_resource": false, + "response_chars": 191, + "status_count": 8 + } + }, + { + "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": 10737, + "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": "77faa0e8-2318-430a-9c81-3317c2b9c784", + "response_id": "chatcmpl-4af4ed4ce499894f12406156f711244a", + "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": 15928, + "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": 146, + "ok": true, + "request_id": "3ec90467-1674-4bd1-a8e9-444942a334c7", + "response_id": "chatcmpl-1f3cb3726d18405b161a3d81680da6b1", + "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.", + "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": 1450, + "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": 19437, + "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": 103, + "ok": true, + "request_id": "59a17b01-d393-4770-82b0-069a6ae57bab", + "response_id": "chatcmpl-506935195cd975633ef2d54a1099c001", + "images_count": 8, + "graphs_count": 0, + "response": "There are reciprocal connections between mushroom body output neurons and dopaminergic neurons. The strongest specific targets of [mushroom body output neuron](https://www.virtualflybrain.org/reports/FBbt_00047953 \"Open mushroom body output neuron in Virtual Fly Brain\") include [primary interneuron](https://www.virtualflybrain.org/reports/FBbt_00052517 \"Open primary interneuron in Virtual Fly Brain\"), [primary neuron](https://www.virtualflybrain.org/reports/FBbt_00047097 \"Open primary neuron in Virtual Fly Brain\"), [adult GABAergic neuron](https://www.virtualflybrain.org/reports/FBbt_00058207 \"Open adult GABAergic neuron in Virtual Fly Brain\"), [GABAergic neuron](https://www.virtualflybrain.org/reports/FBbt_00007228 \"Open GABAergic neuron in Virtual Fly Brain\"), [adult glutamatergic neuron](https://www.virtualflybrain.org/reports/FBbt_00058208 \"Open adult glutamatergic neuron in Virtual Fly Brain\"), [glutamatergic neuron](https://www.virtualflybrain.org/reports/FBbt_00100291 \"Open glutamatergic neuron in Virtual Fly Brain\"), [adult lateral horn neuron](https://www.virtualflybrain.org/reports/FBbt_00048293 \"Open adult lateral horn neuron in Virtual Fly Brain\"), and [adult cholinergic neuron](https://www.virtualflybrain.org/reports/FBbt_00058205 \"Open adult cholinergic neuron in Virtual Fly Brain\"). For [dopaminergic neuron](https://www.virtualflybrain.org/reports/FBbt_00005131 \"Open dopaminergic neuron in Virtual Fly Brain\"), the strongest specific targets are adult cholinergic neuron and [adult Kenyon cell](https://www.virtualflybrain.org/reports/FBbt_00049825 \"Open adult Kenyon cell in Virtual Fly Brain\").", + "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": 1634, + "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": 17039, + "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": 132, + "ok": true, + "request_id": "6170a2e2-cb5e-4d67-aef3-d2cf9f3d7d11", + "response_id": "chatcmpl-7e399d47a31e6649fa48f0310e0a8052", + "images_count": 8, + "graphs_count": 0, + "response": "The pathway from olfactory receptor neurons to the lateral horn involves intermediate neuron types. Antennal lobe projection neurons are one such intermediate type 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\"), [adult antennal lobe local neuron](https://www.virtualflybrain.org/reports/FBbt_00007390 \"Open adult antennal lobe local neuron in Virtual Fly Brain\"), and [olfactory system neuron](https://www.virtualflybrain.org/reports/FBbt_00007697 \"Open olfactory system neuron in Virtual Fly Brain\"). VFB holds [1661](https://v2.virtualflybrain.org/org.geppetto.frontend/geppetto?q=FBbt_00007053,NeuronsPartHere \"Run in VFB: Neurons with some part in adult lateral horn\") neurons with some part in [adult lateral horn](https://www.virtualflybrain.org/reports/FBbt_00007053 \"Open adult lateral horn in Virtual Fly Brain\") and [1658](https://v2.virtualflybrain.org/org.geppetto.frontend/geppetto?q=FBbt_00007053,NeuronsSynaptic \"Run in VFB: Neurons with synaptic terminals in adult lateral horn\") neurons with synaptic terminals in adult lateral horn.", + "quality_flags": { + "has_tool_status": true, + "no_tool_factual_answer": false, + "tool_claim_without_tool": false, + "disambiguation_only_answer": false, + "investigation_plan_answer": false, + "not_verified_or_no_results_answer": false, + "graph_failure_mentioned": false, + "missing_required_graph": false, + "used_data_resource": false, + "response_chars": 1631, + "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": 15112, + "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": 134, + "ok": true, + "request_id": "a35f498a-8472-46f2-b6fc-e6683fced511", + "response_id": "chatcmpl-4712411eb27a05de945142aca6434a93", + "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, among others. VFB holds various other records related to visual system neuron, including available images, splits targeting it, scRNAseq data, transgene expression, and downstream and upstream connectivity classes.", + "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": 1231, + "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": 20249, + "status_messages": [ + { + "message": "Thinking...", + "phase": "llm" + }, + { + "message": "Planning the answer", + "phase": "llm" + }, + { + "message": "Resolving 1 term in VFB", + "phase": "mcp" + }, + { + "message": "Querying VFB connectivity", + "phase": "mcp" + }, + { + "message": "Checking the literature", + "phase": "mcp" + }, + { + "message": "Checking the answer is covered", + "phase": "llm" + }, + { + "message": "Querying VFB", + "phase": "mcp" + }, + { + "message": "Checking the answer is covered", + "phase": "llm" + }, + { + "message": "Writing the answer", + "phase": "llm" + }, + { + "message": "Checking before saying VFB has no data", + "phase": "mcp" + }, + { + "message": "Querying VFB", + "phase": "mcp" + }, + { + "message": "Querying VFB", + "phase": "mcp" + }, + { + "message": "Querying VFB", + "phase": "mcp" + }, + { + "message": "Checking the answer is covered", + "phase": "llm" + }, + { + "message": "Writing the answer", + "phase": "llm" + } + ], + "event_count": 96, + "ok": true, + "request_id": "97353228-105c-4eb8-b744-2d6e223fb690", + "response_id": "chatcmpl-a1d1ead8bc19cac13e0d04988cb04a86", + "images_count": 8, + "graphs_count": 0, + "response": "That lookup did not complete, so this answer cannot say what VFB holds there.", + "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": 77, + "status_count": 15 + } + }, + { + "attempt_index": 20, + "task_index": 20, + "task_id": "T3.5", + "tier": 3, + "title": "Shared connectivity", + "question": "Do the alpha/beta and gamma Kenyon cells converge on any of the same downstream MBON types? Which MBONs receive input from both?", + "requires_graph": false, + "min_graphs": 0, + "repetition": 1, + "duration_ms": 16046, + "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": 130, + "ok": true, + "request_id": "e5181e46-c696-4a66-b422-a0b164e47be9", + "response_id": "chatcmpl-c9443bf67645ddf89709b12e5a06253d", + "images_count": 8, + "graphs_count": 0, + "response": "The [alpha/beta Kenyon cell](https://www.virtualflybrain.org/reports/FBbt_00100248 \"Open alpha/beta Kenyon cell in Virtual Fly Brain\") and [gamma Kenyon cell](https://www.virtualflybrain.org/reports/FBbt_00100247 \"Open gamma Kenyon cell in Virtual Fly Brain\") are types of Kenyon cells, which are upstream of [mushroom body output neuron](https://www.virtualflybrain.org/reports/FBbt_00047953 \"Open mushroom body output neuron in Virtual Fly Brain\"). VFB records show that [Kenyon cell](https://www.virtualflybrain.org/reports/FBbt_00003686 \"Open Kenyon cell in Virtual Fly Brain\") connects to mushroom body output neuron with 7.09 synapses per connected pair, and 59% of individuals are connected. However, the specific downstream mushroom body output neuron types that receive input from both alpha/beta Kenyon cell and gamma Kenyon cell are not specified in the available connectivity data. VFB holds [69](https://v2.virtualflybrain.org/org.geppetto.frontend/geppetto?q=FBbt_00047953,SubclassesOf \"Run in VFB: Subclasses of MBON\") subclasses of mushroom body output neuron and [6](https://v2.virtualflybrain.org/org.geppetto.frontend/geppetto?q=FBbt_00100248,SubclassesOf \"Run in VFB: Subclasses of KCab\") subclasses of alpha/beta Kenyon cell.", + "quality_flags": { + "has_tool_status": true, + "no_tool_factual_answer": false, + "tool_claim_without_tool": false, + "disambiguation_only_answer": false, + "investigation_plan_answer": false, + "not_verified_or_no_results_answer": false, + "graph_failure_mentioned": false, + "missing_required_graph": false, + "used_data_resource": false, + "response_chars": 1246, + "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": 13257, + "status_messages": [ + { + "message": "Thinking...", + "phase": "llm" + }, + { + "message": "Planning the answer", + "phase": "llm" + }, + { + "message": "Resolving 1 term in VFB", + "phase": "mcp" + }, + { + "message": "Tracing the pathway", + "phase": "mcp" + }, + { + "message": "Querying VFB", + "phase": "mcp" + }, + { + "message": "Checking the answer is covered", + "phase": "llm" + }, + { + "message": "Writing the answer", + "phase": "llm" + } + ], + "event_count": 92, + "ok": true, + "request_id": "460e1691-d589-4f6f-8194-81985dc16121", + "response_id": "chatcmpl-90be8ad9ac22a06cac8a53dacb6071a6", + "images_count": 0, + "graphs_count": 0, + "response": "The anatomical containment hierarchy from the DA1 glomerulus up to the top-level brain structure is: DA1 glomerulus -> adult olfactory antennal lobe glomerulus -> adult antennal lobe -> adult deutocerebrum -> adult cerebrum -> adult central brain -> adult brain. VFB does not currently hold data on parts of the [antennal lobe glomerulus DA1](https://www.virtualflybrain.org/reports/FBbt_00003932 \"Open antennal lobe glomerulus DA1 in Virtual Fly Brain\").", + "quality_flags": { + "has_tool_status": true, + "no_tool_factual_answer": false, + "tool_claim_without_tool": false, + "disambiguation_only_answer": false, + "investigation_plan_answer": false, + "not_verified_or_no_results_answer": false, + "graph_failure_mentioned": false, + "missing_required_graph": false, + "used_data_resource": false, + "response_chars": 455, + "status_count": 7 + } + }, + { + "attempt_index": 22, + "task_index": 22, + "task_id": "T3.7", + "tier": 3, + "title": "Cross-region connectivity", + "question": "What neuron types connect the central complex to the lateral accessory lobe, and how strong are these connections?", + "requires_graph": false, + "min_graphs": 0, + "repetition": 1, + "duration_ms": 20258, + "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": 148, + "ok": true, + "request_id": "185b7f92-b7ca-4a0a-8014-725dcc3b5dd0", + "response_id": "chatcmpl-d2dbc8ad2efe36fae1067e48acbd1d6e", + "images_count": 8, + "graphs_count": 0, + "response": "PFL classes are central-complex-related neuron classes connecting the central complex to the lateral accessory lobe. VFB records show that neurons with some part in the [adult central complex](https://www.virtualflybrain.org/reports/FBbt_00003632 \"Open adult central complex in Virtual Fly Brain\") 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\"), [PEN_PB8](https://www.virtualflybrain.org/reports/FBbt_00111374 \"Open PEN_PB8 in Virtual Fly Brain\"), and several adult protocerebral bridge glomerulus neurons. The same neurons are also found among those with synaptic terminals in the adult central complex. However, VFB does not currently hold data on neurons with presynaptic or postsynaptic terminals in the embryonic/larval lateral accessory lobe.", + "quality_flags": { + "has_tool_status": true, + "no_tool_factual_answer": false, + "tool_claim_without_tool": false, + "disambiguation_only_answer": false, + "investigation_plan_answer": false, + "not_verified_or_no_results_answer": false, + "graph_failure_mentioned": false, + "missing_required_graph": false, + "used_data_resource": false, + "response_chars": 1014, + "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": 215855, + "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": 88, + "ok": true, + "request_id": "824b4cb5-1a2d-4e02-81f5-aacaca60bc36", + "response_id": "chatcmpl-d17c07e7f9f980ce91863ef927d245a6", + "images_count": 8, + "graphs_count": 0, + "response": "Data for [descending neuron of the anterior dorsal brain DNa02](https://www.virtualflybrain.org/reports/FBbt_00047573 \"Open descending neuron of the anterior dorsal brain DNa02 in Virtual Fly Brain\") is available in VFB, including light microscopy images and driver lines. VFB holds [18](https://v2.virtualflybrain.org/org.geppetto.frontend/geppetto?q=FBbt_00047573,ListAllAvailableImages \"Run in VFB: List all available images of DNa02\") images of DNa02 and [2](https://v2.virtualflybrain.org/org.geppetto.frontend/geppetto?q=FBbt_00047573,SplitsTargeting \"Run in VFB: Splits targeting DNa02\") transgene expression reports. There are also 2 split-GAL4 combinations that target DNa02. The images include those from the FlyEM-HB and MaleCNS 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": 749, + "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": 34605, + "status_messages": [ + { + "message": "Thinking...", + "phase": "llm" + }, + { + "message": "Planning the answer", + "phase": "llm" + }, + { + "phase": "plan", + "message": "The plan is contested — sampling again before committing." + }, + { + "message": "Resolving 1 term in VFB", + "phase": "mcp" + }, + { + "message": "Querying VFB", + "phase": "mcp" + }, + { + "message": "Checking the answer is covered", + "phase": "llm" + }, + { + "message": "Writing the answer", + "phase": "llm" + } + ], + "event_count": 71, + "ok": true, + "request_id": "a61a5030-8f5d-4ffd-ae51-93f1a0035013", + "response_id": "chatcmpl-3fac6f6dee2a21d24daf799d63ace708", + "images_count": 0, + "graphs_count": 0, + "response": "Neurons involved in the detection of carbon dioxide include carbon dioxide sensitive neurons. These neurons are connected to downstream classes such as GABAergic local interneuron of the adult antennal lobe and adult antennal lobe local neuron lLN2P. The question of genetic tools to access these neurons remains unanswered.", + "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": 7 + } + }, + { + "attempt_index": 25, + "task_index": 25, + "task_id": "T4.2", + "tier": 4, + "title": "Complete neuron profile", + "question": "Give me a comprehensive profile of the giant fiber neuron: its anatomy, connectivity, available driver lines, and relevant publications.", + "requires_graph": false, + "min_graphs": 0, + "repetition": 1, + "duration_ms": 56696, + "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": 405, + "ok": true, + "request_id": "59883650-6bb7-444f-a540-313b25139804", + "response_id": "chatcmpl-b2de858858b1e00125a0be49839b3243", + "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, with its 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. The axon enters the cervical connective via the posterior cerebro-cervical fascicle and descends on the ipsilateral side, in the dorsal cervical fasciculus. In the brain, the giant fiber neuron has dendritic arborization in the ipsilateral zones A and B of the antennal mechanosensory and motor center, where it receives substantial input from zone A and B Johnston organ neurons. It also arborizes in the posterior ventrolateral protocerebrum and gorget. The neuron enters the ventral nerve cord near the dorsal midline and extends posteroventrally to the mesothoracic neuromere, where it turns ventrolaterally and ends abruptly without branching. In the mesothoracic neuromere, it forms electrical synapses with downstream motor and premotor neurons at the inframedial bridge and at the axonal lateral bend.\n\nThe giant fiber neuron has downstream connectivity classes for DNp01, with [389](https://v2.virtualflybrain.org/org.geppetto.frontend/geppetto?q=FBbt_00004020,DownstreamClassConnectivity \"Run in VFB: Downstream connectivity classes for DNp01\") results, and upstream connectivity classes for DNp01, with [472](https://v2.virtualflybrain.org/org.geppetto.frontend/geppetto?q=FBbt_00004020,UpstreamClassConnectivity \"Run in VFB: Upstream connectivity classes for DNp01\") results. Relevant publications include Thomas and Wyman (1984), Koto et al. (1981), and Namiki et al. (2018).\n\nTransgene expression in DNp01 includes expression patterns from [10](https://v2.virtualflybrain.org/org.geppetto.frontend/geppetto?q=FBbt_00004020,TransgeneExpressionHere \"Run in VFB: Transgene expression in DNp01\") different transgenes, such as P{GMR78G07-GAL4}, P{GMR79D08-GAL4}, and P{GMR91H05-GAL4}, as well as several split-GAL4 combinations.", + "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": 2138, + "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": 34971, + "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": 159, + "ok": true, + "request_id": "75db7f4e-f4da-4b61-80b8-6914132e76db", + "response_id": "chatcmpl-a1ba0ae0721c1eff0f4d0e9c7ff5071f", + "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 inputs to [visual system neuron](https://www.virtualflybrain.org/reports/FBbt_00047736 \"Open visual system neuron in Virtual Fly Brain\") include [optic lobe narrow field columnar neuron](https://www.virtualflybrain.org/reports/FBbt_00110136 \"Open optic lobe narrow field columnar neuron in Virtual Fly Brain\"), [optic lobe intrinsic columnar neuron](https://www.virtualflybrain.org/reports/FBbt_00007578 \"Open optic lobe intrinsic columnar neuron in Virtual Fly Brain\"), and [adult optic lobe neuron](https://www.virtualflybrain.org/reports/FBbt_00003702 \"Open adult optic lobe neuron in Virtual Fly Brain\"), while the strongest specific targets of visual system neuron include adult optic lobe neuron, [optic lobe wide-field columnar neuron](https://www.virtualflybrain.org/reports/FBbt_00110137 \"Open optic lobe wide-field columnar neuron in Virtual Fly Brain\"), and [adult optic lobe columnar neuron](https://www.virtualflybrain.org/reports/FBbt_00005129 \"Open adult optic lobe columnar neuron in Virtual Fly Brain\"). VFB also lists [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 the mushroom body. This suggests that visual information could reach the memory circuit via these neurons.", + "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": 1762, + "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": 15883, + "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": "c53d96a7-1c7b-48ee-ad1b-2cf2f8ee328b", + "response_id": "chatcmpl-cfe9f76209734053b6b23e7fd29e858b", + "images_count": 8, + "graphs_count": 1, + "response": "The downstream targets of [l-LNv neuron](https://www.virtualflybrain.org/reports/FBbt_00003763 \"Open l-LNv neuron in Virtual Fly Brain\") include [adult visual projection neuron](https://www.virtualflybrain.org/reports/FBbt_00048286 \"Open adult visual projection neuron in Virtual Fly Brain\"), [sensory system neuron](https://www.virtualflybrain.org/reports/FBbt_00007693 \"Open sensory system neuron in Virtual Fly Brain\"), [Notch ON hemilineage secondary neuron](https://www.virtualflybrain.org/reports/FBbt_00049541 \"Open Notch ON hemilineage secondary neuron in Virtual Fly Brain\"), [optic lobe narrow field columnar neuron](https://www.virtualflybrain.org/reports/FBbt_00110136 \"Open optic lobe narrow field columnar neuron in Virtual Fly Brain\"), [optic lobe intrinsic columnar neuron](https://www.virtualflybrain.org/reports/FBbt_00007578 \"Open optic lobe intrinsic columnar neuron in Virtual Fly Brain\"), [adult optic lobe neuron](https://www.virtualflybrain.org/reports/FBbt_00003702 \"Open adult optic lobe neuron in Virtual Fly Brain\"), and [adult optic lobe columnar neuron](https://www.virtualflybrain.org/reports/FBbt_00005129 \"Open adult optic lobe columnar neuron in Virtual Fly Brain\"). VFB does not currently hold data on the downstream connectivity classes for [adult s-LNv neuron](https://www.virtualflybrain.org/reports/FBbt_00007428 \"Open adult s-LNv neuron in Virtual Fly Brain\").", + "graphs": [ + { + "type": "basic_graph", + "version": 1, + "title": "Downstream targets by source class", + "directed": true, + "layout": "circle", + "nodes": [ + { + "id": "FBbt_00003763", + "label": "l-LNv", + "group": null, + "color": null, + "size": 4 + }, + { + "id": "FBbt_00005106", + "label": "neuron", + "group": null, + "color": null, + "size": 1.17 + }, + { + "id": "FBbt_00047095", + "label": "adult neuron", + "group": null, + "color": null, + "size": 1.17 + }, + { + "id": "FBbt_00059271", + "label": "CNS neuron", + "group": null, + "color": null, + "size": 1.17 + }, + { + "id": "FBbt_00059274", + "label": "adult CNS neuron", + "group": null, + "color": null, + "size": 1.17 + }, + { + "id": "FBbt_00007693", + "label": "sensory system neuron", + "group": null, + "color": null, + "size": 1.17 + }, + { + "id": "FBbt_00047736", + "label": "visual system neuron", + "group": null, + "color": null, + "size": 1.17 + }, + { + "id": "FBbt_00005125", + "label": "interneuron", + "group": null, + "color": null, + "size": 1.16 + }, + { + "id": "FBbt_00052046", + "label": "adult interneuron", + "group": null, + "color": null, + "size": 1.16 + }, + { + "id": "FBbt_00001366", + "label": "supraesophageal ganglion neuron", + "group": null, + "color": null, + "size": 1.16 + }, + { + "id": "FBbt_00003702", + "label": "adult optic lobe neuron", + "group": null, + "color": null, + "size": 1.15 + }, + { + "id": "FBbt_00059247", + "label": "adult visual neuropil intrinsic neuron", + "group": null, + "color": null, + "size": 1.15 + }, + { + "id": "FBbt_00007577", + "label": "adult optic lobe intrinsic neuron", + "group": null, + "color": null, + "size": 1.15 + }, + { + "id": "FBbt_00007173", + "label": "cholinergic neuron", + "group": null, + "color": null, + "size": 1.14 + }, + { + "id": "FBbt_00058205", + "label": "adult cholinergic neuron", + "group": null, + "color": null, + "size": 1.14 + }, + { + "id": "FBbt_00005129", + "label": "adult optic lobe columnar neuron", + "group": null, + "color": null, + "size": 1.14 + }, + { + "id": "FBbt_00007578", + "label": "optic lobe intrinsic columnar neuron", + "group": null, + "color": null, + "size": 1.14 + }, + { + "id": "FBbt_00047096", + "label": "secondary neuron", + "group": null, + "color": null, + "size": 1.13 + }, + { + "id": "FBbt_00110136", + "label": "optic lobe narrow field columnar neuron", + "group": null, + "color": null, + "size": 1.13 + }, + { + "id": "FBbt_00049539", + "label": "Notch ON hemilineage neuron", + "group": null, + "color": null, + "size": 1.13 + }, + { + "id": "FBbt_00049541", + "label": "Notch ON hemilineage secondary neuron", + "group": null, + "color": null, + "size": 1.13 + } + ], + "edges": [ + { + "source": "FBbt_00003763", + "target": "FBbt_00005106", + "label": "6184", + 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"quality_flags": { + "has_tool_status": true, + "no_tool_factual_answer": false, + "tool_claim_without_tool": false, + "disambiguation_only_answer": false, + "investigation_plan_answer": false, + "not_verified_or_no_results_answer": false, + "graph_failure_mentioned": false, + "missing_required_graph": false, + "used_data_resource": false, + "response_chars": 1400, + "status_count": 9 + } + }, + { + "attempt_index": 28, + "task_index": 28, + "task_id": "T4.5", + "tier": 4, + "title": "Novel circuit exploration", + "question": "What is the connectivity between thermosensory neurons and the mushroom body? Could temperature information influence memory formation?", + "requires_graph": false, + "min_graphs": 0, + "repetition": 1, + "duration_ms": 19371, + "status_messages": [ + { + "message": "Thinking...", + "phase": "llm" + }, + { + "message": "Planning the answer", + "phase": "llm" + }, + { + "message": "Resolving 2 terms in VFB", + "phase": "mcp" + }, + { + "message": "Tracing the pathway", + "phase": "mcp" + }, + { + "message": "Querying VFB connectivity", + "phase": "mcp" + }, + { + "message": "Querying VFB", + "phase": "mcp" + }, + { + "message": "Querying VFB", + "phase": "mcp" + }, + { + "message": "Checking the answer is covered", + "phase": "llm" + }, + { + "message": "Querying VFB", + "phase": "mcp" + }, + { + "message": "Querying VFB", + "phase": "mcp" + }, + { + "message": "Checking the answer is covered", + "phase": "llm" + }, + { + "message": "Writing the answer", + "phase": "llm" + } + ], + "event_count": 200, + "ok": true, + "request_id": "a60bbe97-50c7-4964-b761-00588e32fbec", + "response_id": "chatcmpl-37fbe7bbf447570b442f4503e06d8e06", + "images_count": 8, + "graphs_count": 1, + "response": "The connectivity between thermosensory neurons and the [mushroom body](https://www.virtualflybrain.org/reports/FBbt_00005801 \"Open mushroom body in Virtual Fly Brain\") is supported by evidence that thermosensory neurons influence mushroom body memory formation. Thermosensory neurons are connected to the mushroom body, with antennal lobe projection neurons acting as a connection point. The strongest specific targets of thermosensory neurons include projection neurons, adult antennal lobe projection neurons, and antennal lobe projection neurons, with 18.9, 18.8, and 18.7 synapses per connected pair, respectively. The mushroom body receives presynaptic input from [366](https://v2.virtualflybrain.org/org.geppetto.frontend/geppetto?q=FBbt_00005801,NeuronsPresynapticHere \"Run in VFB: Neurons with presynaptic terminals in mushroom body\") neurons and postsynaptic input from [304](https://v2.virtualflybrain.org/org.geppetto.frontend/geppetto?q=FBbt_00005801,NeuronsPostsynapticHere \"Run in VFB: Neurons with postsynaptic terminals in mushroom body\") neurons. VFB records show that thermosensory neurons have downstream connectivity classes and upstream connectivity classes, with the strongest specific inputs including [adult antennal lobe local neuron lLN2](https://www.virtualflybrain.org/reports/FBbt_00007396 \"Open adult antennal lobe local neuron lLN2 in Virtual Fly Brain\"), [unilateral local interneuron of the adult antennal lobe](https://www.virtualflybrain.org/reports/FBbt_00051503 \"Open unilateral local interneuron of the adult antennal lobe in Virtual Fly Brain\"), and [adult antennal lobe local neuron](https://www.virtualflybrain.org/reports/FBbt_00007390 \"Open adult antennal lobe local neuron in Virtual Fly Brain\").", + "graphs": [ + { + "type": "basic_graph", + "version": 1, + "title": "Downstream partners of thermosensory neuron", + "directed": true, + "layout": "circle", + "nodes": [ + { + "id": "FBbt_00005918", + "label": "thermosensory neuron", + "group": null, + "color": null, + "size": 4 + }, + { + "id": "FBbt_00005106", + "label": "neuron", + "group": null, + "color": null, + "size": 1.4 + }, + { + "id": "FBbt_00047095", + "label": "adult neuron", + "group": null, + "color": null, + "size": 1.39 + }, + { + "id": "FBbt_00059271", + "label": "CNS neuron", + "group": null, + "color": null, + "size": 1.38 + }, + { + "id": "FBbt_00007392", + "label": "projection neuron", + "group": null, + "color": null, + "size": 1.22 + }, + { + "id": "FBbt_00007422", + "label": "antennal lobe projection neuron", + "group": null, + "color": null, + "size": 1.21 + }, + { + "id": "FBbt_00067123", + "label": "adult antennal lobe projection neuron", + "group": null, + "color": null, + "size": 1.21 + }, + { + "id": "FBbt_00051493", + "label": "local neuron", + "group": null, + "color": null, + "size": 1.15 + }, + { + "id": "FBbt_00052874", + "label": "antennal lobe local neuron", + "group": null, + "color": null, + "size": 1.15 + }, + { + "id": "FBbt_00007390", + "label": "adult antennal lobe local neuron", + "group": null, + "color": null, + "size": 1.15 + }, + { + "id": "FBbt_00007384", + "label": "multiglomerular antennal lobe projection neuron", + "group": null, + "color": null, + "size": 1.14 + }, + { + "id": "FBbt_00007441", + "label": "adult multiglomerular antennal lobe projection neuron", + "group": null, + "color": null, + "size": 1.14 + }, + { + "id": "FBbt_00049427", + "label": "adult lateral horn input neuron", + "group": null, + "color": null, + "size": 1.12 + }, + { + "id": "FBbt_00053398", + "label": "adult antennal lobe projection neuron to lateral horn", + "group": null, + "color": null, + "size": 1.12 + }, + { + "id": "FBbt_00053397", + "label": "antennal lobe projection neuron to mushroom body", + "group": null, + "color": null, + "size": 1.11 + }, + { + "id": "FBbt_00007394", + "label": "adult local interneuron of the lateral ALl1 neuroblast", + "group": null, + "color": null, + "size": 1.11 + } + ], + "edges": [ + { + "source": "FBbt_00005918", + "target": "FBbt_00005106", + "label": 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"FBbt_00005918", + "target": "FBbt_00007441", + "label": "27735", + "weight": 27735 + }, + { + "source": "FBbt_00005918", + "target": "FBbt_00049427", + "label": "24184", + "weight": 24184 + }, + { + "source": "FBbt_00005918", + "target": "FBbt_00053398", + "label": "24184", + "weight": 24184 + }, + { + "source": "FBbt_00005918", + "target": "FBbt_00053397", + "label": "22043", + "weight": 22043 + }, + { + "source": "FBbt_00005918", + "target": "FBbt_00007394", + "label": "21470", + "weight": 21470 + } + ] + } + ], + "quality_flags": { + "has_tool_status": true, + "no_tool_factual_answer": false, + "tool_claim_without_tool": false, + "disambiguation_only_answer": false, + "investigation_plan_answer": false, + "not_verified_or_no_results_answer": false, + "graph_failure_mentioned": false, + "missing_required_graph": false, + "used_data_resource": false, + "response_chars": 1740, + "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": 206859, + "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": 204, + "ok": true, + "request_id": "72db4741-6cb4-483f-b62e-62f7944aab4f", + "response_id": "chatcmpl-2081450533b92c16583844017ea98458", + "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 holds [2698](https://v2.virtualflybrain.org/org.geppetto.frontend/geppetto?q=FBbt_00051068,NeuronsPartHere \"Run in VFB: Neurons with some part in subesophageal zone\") records of 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\"), [serotonergic SE3 neuron](https://www.virtualflybrain.org/reports/FBbt_00001982 \"Open serotonergic SE3 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 4205 genetic tool/expression pattern rows for the subesophageal zone, including GAL4 drivers and binary/intersectional drivers such as [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\"). Additionally, VFB has [29765](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, and [1](https://v2.virtualflybrain.org/org.geppetto.frontend/geppetto?q=FBbt_00051068,ListAllAvailableImages \"Run in VFB: List all available images of subesophageal zone\") image of the subesophageal zone itself, which is the [adult subesophageal zone on adult brain template JFRC2](https://www.virtualflybrain.org/reports/VFB_00030856 \"Open adult subesophageal zone on adult brain template JFRC2 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": 2066, + "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": 17231, + "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 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": 190, + "ok": true, + "request_id": "9e48311b-9831-490c-810b-7b40b8a58ae5", + "response_id": "chatcmpl-00acf077bf3e5f3f6d9f7556b10a4b71", + "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": 10 + } + }, + { + "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": 7979, + "status_messages": [ + { + "message": "Thinking...", + "phase": "llm" + }, + { + "message": "Planning (direct lookup)", + "phase": "llm" + }, + { + "message": "Resolving 1 term in VFB", + "phase": "mcp" + }, + { + "message": "Reading VFB term info", + "phase": "mcp" + }, + { + "message": "Checking the literature", + "phase": "mcp" + }, + { + "message": "Checking the answer is covered", + "phase": "llm" + }, + { + "message": "Writing the answer", + "phase": "llm" + } + ], + "event_count": 42, + "ok": true, + "request_id": "ddedbd4a-c099-4c78-8a23-1e2c4055eb13", + "response_id": "chatcmpl-e559b3a6e80804c809a05a66031b2670", + "images_count": 0, + "graphs_count": 0, + "response": "Virtual Fly Brain is an interactive tool for neurobiologists to explore the detailed neuroanatomy, neuron connectivity, and gene expression of Drosophila melanogaster.", + "quality_flags": { + "has_tool_status": true, + "no_tool_factual_answer": false, + "tool_claim_without_tool": false, + "disambiguation_only_answer": false, + "investigation_plan_answer": false, + "not_verified_or_no_results_answer": false, + "graph_failure_mentioned": false, + "missing_required_graph": false, + "used_data_resource": false, + "response_chars": 167, + "status_count": 7 + } + }, + { + "attempt_index": 32, + "task_index": 32, + "task_id": "D2", + "tier": 6, + "title": "Citation", + "question": "How should I cite Virtual Fly Brain in a publication?", + "requires_graph": false, + "min_graphs": 0, + "repetition": 1, + "duration_ms": 35603, + "status_messages": [ + { + "message": "Thinking...", + "phase": "llm" + }, + { + "message": "Planning the answer", + "phase": "llm" + }, + { + "message": "Reading VFB documentation", + "phase": "mcp" + }, + { + "message": "Checking the literature", + "phase": "mcp" + }, + { + "message": "Checking the answer is covered", + "phase": "llm" + }, + { + "message": "Writing the answer", + "phase": "llm" + } + ], + "event_count": 23, + "ok": true, + "request_id": "783b2af7-cff9-482d-83c3-bef2c9b440e9", + "response_id": "chatcmpl-b435c8711a91ad6ff6194bbef1a1f332", + "images_count": 0, + "graphs_count": 0, + "response": "To cite Virtual Fly Brain in a publication, use the following citation formats:\n\n```\nAPA\nCourt, R., Costa, M., Pilgrim, C., Millburn, G., Holmes, A., McLachlan, A., Larkin, A., Matentzoglu, N., Kir, H., Parkinson, H., Brown, N. H., O’Kane, C. J., Armstrong, J. D., Jefferis, G. S. X. E., & Osumi-Sutherland, D. (2023). Virtual Fly Brain—An interactive atlas of the Drosophila nervous system. Frontiers in Physiology, 14. https://doi.org/10.3389/fphys.2023.1076533\n\nMLA\nCourt, Robert, et al. “Virtual Fly Brain—An Interactive Atlas of the Drosophila Nervous System.” Frontiers in Physiology, vol. 14, 2023, https://doi.org/10.3389/fphys.2023.1076533.\n\nChicago\nCourt, Robert, Costa, Marta, Pilgrim, Clare, Millburn, Gillian, Holmes, Alex, McLachlan, Alex, Larkin, Aoife et al. “Virtual Fly Brain—An interactive atlas of the Drosophila nervous system.” Frontiers in Physiology 14, (2023). https://doi.org/10.3389/fphys.2023.1076533.\n\nBibTeX\n@article{Court_2023,\nauthor = {Robert Court and Marta Costa and Clare Pilgrim and Gillian Millburn and Alex Holmes and Alex McLachlan and Aoife Larkin and Nicolas Matentzoglu and Huseyin Kir and Helen Parkinson and Nicolas H. Brown and Cahir J. O'Kane and J. Douglas Armstrong and Gregory S. X. E. Jefferis and David Osumi-Sutherland},\ntitle = \"{Virtual Fly Brain—An interactive atlas of the Drosophila nervous system}\",\njournal = {Frontiers in Physiology},\nvolume = {14},\npublisher = {Frontiers Media {SA}},\nyear = {2023},\nmonth = {jan},\nabstract = \"{As a model organism, Drosophila is uniquely placed to contribute to our understanding of how brains control complex behavior. Not only does it have complex adaptive behaviors, but also a uniquely powerful genetic toolkit, increasingly complete dense connectomic maps of the central nervous system and a rapidly growing set of transcriptomic profiles of cell types. But this also poses a challenge: Given the massive amounts of VFB evidence, how are researchers to Find, Access, Integrate and Reuse (FAIR) relevant data in order to develop an integrated anatomical and molecular picture of circuits, inform hypothesis generation, and find reagents for experiments to test these hypotheses? The Virtual Fly Brain (virtualflybrain.org) web application & API provide a solution to this problem, using FAIR principles to integrate 3D images of neurons and brain regions, connectomics, transcriptomics and reagent expression data covering the whole CNS in both larva and adult. Users can search for neurons, neuroanatomy and reagents by name, location, or connectivity, via text search, clicking on 3D images, search-by-image, and queries by type (e.g., dopaminergic neuron) or properties (e.g., synaptic input in the antennal lobe). Returned results include cross-registered 3D images that can be explored in linked 2D and 3D browsers or downloaded under open licenses, and extensive descriptions of cell types and regions curated from the literature. These solutions are potentially extensible to cover similar atlasing and data integration challenges in vertebrates.}\",\nissn = {1664-042X},\ndoi = {10.3389/fphys.2023.1076533},\nurl = {https://doi.org/10.3389/fphys.2023.1076533},\n}\n```", + "quality_flags": { + "has_tool_status": true, + "no_tool_factual_answer": false, + "tool_claim_without_tool": false, + "disambiguation_only_answer": false, + "investigation_plan_answer": false, + "not_verified_or_no_results_answer": false, + "graph_failure_mentioned": false, + "missing_required_graph": false, + "used_data_resource": false, + "response_chars": 3170, + "status_count": 6 + } + }, + { + "attempt_index": 33, + "task_index": 33, + "task_id": "D3", + "tier": 6, + "title": "Funding", + "question": "Who funds Virtual Fly Brain and since when?", + "requires_graph": false, + "min_graphs": 0, + "repetition": 1, + "duration_ms": 5868, + "status_messages": [ + { + "message": "Thinking...", + "phase": "llm" + }, + { + "message": "Planning the answer", + "phase": "llm" + }, + { + "message": "Reading VFB documentation", + "phase": "mcp" + }, + { + "message": "Checking VFB documentation", + "phase": "mcp" + }, + { + "message": "Checking the answer is covered", + "phase": "llm" + }, + { + "message": "Writing the answer", + "phase": "llm" + } + ], + "event_count": 28, + "ok": true, + "request_id": "2b80ccaf-06ad-4532-b46a-b14d7a7c1700", + "response_id": "chatcmpl-710597e45f580c5c572ef09c5e44ad5f", + "images_count": 0, + "graphs_count": 0, + "response": "Virtual Fly Brain has been supported by grants from multiple UK research councils and charitable foundations since 2009.", + "quality_flags": { + "has_tool_status": true, + "no_tool_factual_answer": false, + "tool_claim_without_tool": false, + "disambiguation_only_answer": false, + "investigation_plan_answer": false, + "not_verified_or_no_results_answer": false, + "graph_failure_mentioned": false, + "missing_required_graph": false, + "used_data_resource": false, + "response_chars": 120, + "status_count": 6 + } + }, + { + "attempt_index": 34, + "task_index": 34, + "task_id": "D4", + "tier": 6, + "title": "Policies / accessibility", + "question": "What is Virtual Fly Brain's accessibility statement?", + "requires_graph": false, + "min_graphs": 0, + "repetition": 1, + "duration_ms": 5415, + "status_messages": [ + { + "message": "Thinking...", + "phase": "llm" + }, + { + "message": "Planning (direct lookup)", + "phase": "llm" + }, + { + "message": "Resolving 1 term in VFB", + "phase": "mcp" + }, + { + "message": "Reading VFB term info", + "phase": "mcp" + }, + { + "message": "Checking the literature", + "phase": "mcp" + }, + { + "message": "Checking the answer is covered", + "phase": "llm" + }, + { + "message": "Writing the answer", + "phase": "llm" + } + ], + "event_count": 42, + "ok": true, + "request_id": "4b8fbb56-9387-4253-ad00-692ab231e35b", + "response_id": "chatcmpl-de4427e1eb62650479ab3ee0889e6736", + "images_count": 0, + "graphs_count": 0, + "response": "Virtual Fly Brain is partially compliant with the Web Content Accessibility Guidelines (WCAG) 2.2 AA standard, with known accessibility limitations and non-compliances listed.", + "quality_flags": { + "has_tool_status": true, + "no_tool_factual_answer": false, + "tool_claim_without_tool": false, + "disambiguation_only_answer": false, + "investigation_plan_answer": false, + "not_verified_or_no_results_answer": false, + "graph_failure_mentioned": false, + "missing_required_graph": false, + "used_data_resource": false, + "response_chars": 175, + "status_count": 7 + } + }, + { + "attempt_index": 35, + "task_index": 35, + "task_id": "D5", + "tier": 6, + "title": "Contact / contribute", + "question": "How do I report a problem or contribute data to Virtual Fly Brain?", + "requires_graph": false, + "min_graphs": 0, + "repetition": 1, + "duration_ms": 8169, + "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": 90, + "ok": true, + "request_id": "99f9f73f-1ed9-4a37-90a7-314794b7d1bd", + "response_id": "chatcmpl-1774503d48108776961c0d1e0c373d69", + "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. Bug reports and feature requests can be submitted through GitHub issues. For data contributions or private inquiries, 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": 419, + "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": 7618, + "status_messages": [ + { + "message": "Thinking...", + "phase": "llm" + }, + { + "message": "Planning the answer", + "phase": "llm" + }, + { + "message": "Reading VFB documentation", + "phase": "mcp" + }, + { + "message": "Checking the literature", + "phase": "mcp" + }, + { + "message": "Checking the answer is covered", + "phase": "llm" + }, + { + "message": "Writing the answer", + "phase": "llm" + } + ], + "event_count": 85, + "ok": true, + "request_id": "e537055d-f1e1-49de-8e0a-7dccb88b81e9", + "response_id": "chatcmpl-db4c8b45118fa10a1f424c7734ee6dea", + "images_count": 0, + "graphs_count": 0, + "response": "To use the 3D Viewer on the VFB website, point and click to select neurons or expression. Click and drag with the mouse or use the directional icons to rotate or move. Use the zoom icons or scroll with the mouse to zoom in or out. The camera icon starts or stops a rotation animation of the scene, and the sphere icon toggles wireframes on or off.", + "quality_flags": { + "has_tool_status": true, + "no_tool_factual_answer": false, + "tool_claim_without_tool": false, + "disambiguation_only_answer": false, + "investigation_plan_answer": false, + "not_verified_or_no_results_answer": false, + "graph_failure_mentioned": false, + "missing_required_graph": false, + "used_data_resource": false, + "response_chars": 347, + "status_count": 6 + } + }, + { + "attempt_index": 37, + "task_index": 37, + "task_id": "D7", + "tier": 6, + "title": "Website how-to: Circuit Browser", + "question": "What is the Circuit Browser tab on VFB and how do I use it?", + "requires_graph": false, + "min_graphs": 0, + "repetition": 1, + "duration_ms": 11416, + "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": "8f6ebe32-5b5d-47b8-a8f5-013d4d74580d", + "response_id": "chatcmpl-ebe3e79ae74081539c5526996d813f52", + "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": 9574, + "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": 67, + "ok": true, + "request_id": "1fce32ab-3b63-4ce2-aeec-35bf34fee59b", + "response_id": "chatcmpl-fe136a9413a3ad07701540a1a50965ff", + "images_count": 0, + "graphs_count": 0, + "response": "NBLAST is a method used to calculate similarity scores, which represent the morphological similarity between neurons or expression patterns. The similarity scores are calculated using NBLAST or other third-party scores. An NBLAST similarity score means a measure of the morphological similarity between neurons or 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": 334, + "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": 7898, + "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": 42, + "ok": true, + "request_id": "542a2cee-9387-4157-b1d3-8c6e935cbf8e", + "response_id": "chatcmpl-c184f1ca6a221f4e7b0133010acf2893", + "images_count": 1, + "graphs_count": 0, + "response": "Confidence values provide a measure of the confidence or reliability of a particular piece of data, and are represented by the property key \"confidence_value\" in the PDB.", + "quality_flags": { + "has_tool_status": true, + "no_tool_factual_answer": false, + "tool_claim_without_tool": false, + "disambiguation_only_answer": false, + "investigation_plan_answer": false, + "not_verified_or_no_results_answer": false, + "graph_failure_mentioned": false, + "missing_required_graph": false, + "used_data_resource": false, + "response_chars": 170, + "status_count": 7 + } + }, + { + "attempt_index": 40, + "task_index": 40, + "task_id": "D10", + "tier": 6, + "title": "Concepts: bridging registrations", + "question": "What are bridging registrations between brain templates in VFB?", + "requires_graph": false, + "min_graphs": 0, + "repetition": 1, + "duration_ms": 8803, + "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": 38, + "ok": true, + "request_id": "0ec1e2cf-06c6-4e58-b29c-51d78ed4831f", + "response_id": "chatcmpl-9bd10e164cd291aa71d70369a60ddb6a", + "images_count": 8, + "graphs_count": 0, + "response": "Bridging registrations between brain templates in VFB could not be matched. The documentation mentions transformations to map between different canonical Drosophila templates.", + "quality_flags": { + "has_tool_status": true, + "no_tool_factual_answer": false, + "tool_claim_without_tool": false, + "disambiguation_only_answer": false, + "investigation_plan_answer": false, + "not_verified_or_no_results_answer": false, + "graph_failure_mentioned": false, + "missing_required_graph": false, + "used_data_resource": false, + "response_chars": 175, + "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": 4681, + "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": 25, + "ok": true, + "request_id": "c722d311-c0ed-435d-86d1-99b2bf14f3cb", + "response_id": "chatcmpl-0fe2758d1ae829f7c1a50a88bf2f27a2", + "images_count": 0, + "graphs_count": 0, + "response": "Virtual Fly Brain holds imaging data types including skeleton, mesh, and volume representations of neurons.", + "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": 107, + "status_count": 6 + } + }, + { + "attempt_index": 42, + "task_index": 42, + "task_id": "D12", + "tier": 6, + "title": "Release changelog", + "question": "What was included in the latest Virtual Fly Brain release?", + "requires_graph": false, + "min_graphs": 0, + "repetition": 1, + "duration_ms": 5286, + "status_messages": [ + { + "message": "Thinking...", + "phase": "llm" + }, + { + "message": "Planning the answer", + "phase": "llm" + }, + { + "message": "Reading VFB term info", + "phase": "mcp" + }, + { + "message": "Checking the literature", + "phase": "mcp" + }, + { + "message": "Checking the answer is covered", + "phase": "llm" + }, + { + "message": "Writing the answer", + "phase": "llm" + } + ], + "event_count": 46, + "ok": true, + "request_id": "15455b16-bb99-413f-af17-633f858a3306", + "response_id": "chatcmpl-c2e569161460f123c8c447d2d12adc6d", + "images_count": 0, + "graphs_count": 0, + "response": "The latest Virtual Fly Brain release includes various data and software improvements, such as new images and annotations, including confocal microscopy images, EM reconstructed neurons, and other datasets from different researchers and labs.", + "quality_flags": { + "has_tool_status": true, + "no_tool_factual_answer": false, + "tool_claim_without_tool": false, + "disambiguation_only_answer": false, + "investigation_plan_answer": false, + "not_verified_or_no_results_answer": false, + "graph_failure_mentioned": false, + "missing_required_graph": false, + "used_data_resource": false, + "response_chars": 241, + "status_count": 6 + } + }, + { + "attempt_index": 43, + "task_index": 43, + "task_id": "D13", + "tier": 6, + "title": "API: VFB-connect (Python)", + "question": "How do I install and get started with VFB-connect in Python?", + "requires_graph": false, + "min_graphs": 0, + "repetition": 1, + "duration_ms": 7830, + "status_messages": [ + { + "message": "Thinking...", + "phase": "llm" + }, + { + "message": "Planning the answer", + "phase": "llm" + }, + { + "message": "Reading VFB documentation", + "phase": "mcp" + }, + { + "message": "Checking the literature", + "phase": "mcp" + }, + { + "message": "Checking the answer is covered", + "phase": "llm" + }, + { + "message": "Writing the answer", + "phase": "llm" + } + ], + "event_count": 58, + "ok": true, + "request_id": "593b88ce-4946-471b-a3ac-24aa87f2d2ea", + "response_id": "chatcmpl-f43153a3e3a04a94fb4d71e356fcc4b8", + "images_count": 0, + "graphs_count": 0, + "response": "To install and get started with VFB-connect in Python, ensure you have the VFBConnect library installed using the recommended Python version 3.10.14. Install the library by running\n```\npip install vfb-connect\n```\nThen, import the VFBConnect library using\n```\nfrom import vfb\n```", + "quality_flags": { + "has_tool_status": true, + "no_tool_factual_answer": false, + "tool_claim_without_tool": false, + "disambiguation_only_answer": false, + "investigation_plan_answer": false, + "not_verified_or_no_results_answer": false, + "graph_failure_mentioned": false, + "missing_required_graph": false, + "used_data_resource": false, + "response_chars": 278, + "status_count": 6 + } + }, + { + "attempt_index": 44, + "task_index": 44, + "task_id": "D14", + "tier": 6, + "title": "API: REST endpoints", + "question": "How can I query Virtual Fly Brain programmatically using the SOLR or Owlery API?", + "requires_graph": false, + "min_graphs": 0, + "repetition": 1, + "duration_ms": 9869, + "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": 103, + "ok": true, + "request_id": "805c390e-8768-4f3b-a457-1c66f7c84564", + "response_id": "chatcmpl-35f24b545b4648c0cbe93ff284d71cfc", + "images_count": 0, + "graphs_count": 0, + "response": "To query Virtual Fly Brain programmatically, you can use the Owlery API, which provides OWL reasoning services for VFB's ontologies. The API endpoint is https://owl.virtualflybrain.org/, and it supports various query operations, including Description Logic (DL) queries, SPARQL queries with OWL reasoning, and access to multiple knowledgebases. Alternatively, the SOLR Search API provides fast text search and autocomplete functionality for VFB entities, datasets, and publications.", + "quality_flags": { + "has_tool_status": true, + "no_tool_factual_answer": false, + "tool_claim_without_tool": false, + "disambiguation_only_answer": false, + "investigation_plan_answer": false, + "not_verified_or_no_results_answer": false, + "graph_failure_mentioned": false, + "missing_required_graph": false, + "used_data_resource": false, + "response_chars": 482, + "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": 9829, + "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": 91, + "ok": true, + "request_id": "01a2956d-0969-4695-9c32-a8c8f9c5ee58", + "response_id": "chatcmpl-4dbc8d845cfc3459e6d166dbc35ed3f8", + "images_count": 0, + "graphs_count": 0, + "response": "To explore Virtual Fly Brain neurons, you can use the pymaid library, which lets you interface with a CATMAID server such as those provided by Virtual Fly Brain. You can connect to the Virtual Fly Brain CATMAID server, retrieve neurons, and plot them using navis.\n\nVFB's documentation does not appear to cover Navis.\nVFB's documentation does not appear to cover pymaid.", + "quality_flags": { + "has_tool_status": true, + "no_tool_factual_answer": false, + "tool_claim_without_tool": false, + "disambiguation_only_answer": false, + "investigation_plan_answer": false, + "not_verified_or_no_results_answer": false, + "graph_failure_mentioned": false, + "missing_required_graph": false, + "used_data_resource": false, + "response_chars": 369, + "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": 13635, + "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": 152, + "ok": true, + "request_id": "c8a163ac-0bec-49cc-9562-5e719f6b307d", + "response_id": "chatcmpl-0c07ceb09511c852d3978762e28afebd", + "images_count": 0, + "graphs_count": 0, + "response": "To use the Virtual Fly Brain Model Context Protocol (MCP) tool, follow these steps:\nOpen Claude Desktop and go to Settings, navigate to the MCP section, add a new MCP server with the specified settings, and restart Claude Code for changes to take effect.\nAlternatively, use the Configuration JSON or Claude Code Setup methods.\nFor GitHub Copilot Setup, open VS Code with GitHub Copilot installed, open Settings, search for \"MCP\" in the settings search, find the MCP Servers setting, add the server URL, and give it a name.\nFor other MCP-compatible clients, use the provided JSON configuration.\nFor Gemini Setup, connect through custom Python/Node.js clients that support MCP.\n\n```json\n{\n\"mcpServers\": {\n\"virtual-fly-brain\": {\n\"type\": \"http\",\n\"url\": \"https://vfb3-mcp.virtualflybrain.org\",\n\"tools\": [\"*\"]\n}\n}\n}\n```", + "quality_flags": { + "has_tool_status": true, + "no_tool_factual_answer": false, + "tool_claim_without_tool": false, + "disambiguation_only_answer": false, + "investigation_plan_answer": false, + "not_verified_or_no_results_answer": false, + "graph_failure_mentioned": false, + "missing_required_graph": false, + "used_data_resource": false, + "response_chars": 813, + "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": 7060, + "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": "ba2a4a73-fa53-471a-b2a2-b8e4e4f30849", + "response_id": "chatcmpl-9409e71af11da56a1380ed1dfccc36b7", + "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": 9813, + "status_messages": [ + { + "message": "Thinking...", + "phase": "llm" + }, + { + "message": "Planning the answer", + "phase": "llm" + }, + { + "phase": "plan", + "message": "The plan is contested — sampling again before committing." + }, + { + "message": "Resolving 1 term in VFB", + "phase": "mcp" + }, + { + "message": "Reading VFB documentation", + "phase": "mcp" + }, + { + "message": "Checking VFB documentation", + "phase": "mcp" + }, + { + "message": "Checking the answer is covered", + "phase": "llm" + }, + { + "message": "Writing the answer", + "phase": "llm" + } + ], + "event_count": 41, + "ok": true, + "request_id": "231e0777-3311-477b-b97d-7bff7d029661", + "response_id": "chatcmpl-558d5bea298a1c9f4e82658faa0e280c", + "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": 8 + } + }, + { + "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": 7994, + "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": 53, + "ok": true, + "request_id": "61221616-99bc-4813-9365-76e629890799", + "response_id": "chatcmpl-6edf0dc31b31fcb99347005afb8c15e2", + "images_count": 0, + "graphs_count": 0, + "response": "Materials from the Virtual Fly Brain \"Hacking the connectome\" workshop are available. These include a recorded introduction session and workshop notebooks that demonstrate how to use available tools to explore and analyze published connectomes on Virtual Fly Brain.", + "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": 265, + "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": 19006, + "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": 65, + "ok": true, + "request_id": "5761eaa3-9bf3-423d-a249-0497a9e5eb76", + "response_id": "chatcmpl-a2e649605bb38d6e05de635139324ad5", + "images_count": 8, + "graphs_count": 0, + "response": "The FAFB CATMAID dataset can be accessed via https://fafb.catmaid.virtualflybrain.org. Virtual Fly Brain hosts several CATMAID instances for exploring connectomic reconstruction data, including FAFB. The name \"FANC\" could not be matched.", + "quality_flags": { + "has_tool_status": true, + "no_tool_factual_answer": false, + "tool_claim_without_tool": false, + "disambiguation_only_answer": false, + "investigation_plan_answer": false, + "not_verified_or_no_results_answer": false, + "graph_failure_mentioned": false, + "missing_required_graph": false, + "used_data_resource": false, + "response_chars": 237, + "status_count": 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": 9203, + "status_messages": [ + { + "message": "Thinking...", + "phase": "llm" + }, + { + "message": "Planning the answer", + "phase": "llm" + }, + { + "message": "Resolving 1 term in VFB", + "phase": "mcp" + }, + { + "message": "Reading VFB term info", + "phase": "mcp" + }, + { + "message": "Checking VFB documentation", + "phase": "mcp" + }, + { + "message": "Checking the answer is covered", + "phase": "llm" + }, + { + "message": "Writing the answer", + "phase": "llm" + } + ], + "event_count": 23, + "ok": true, + "request_id": "0112d719-4056-4371-95bf-bc88543349c3", + "response_id": "chatcmpl-0bbda16a21d78ebcbc311671b435f291", + "images_count": 8, + "graphs_count": 0, + "response": "There is a circuit diagram of the [mushroom body](https://www.virtualflybrain.org/reports/FBbt_00005801 \"Open mushroom body in Virtual Fly Brain\") available on Virtual Fly Brain.", + "quality_flags": { + "has_tool_status": true, + "no_tool_factual_answer": false, + "tool_claim_without_tool": false, + "disambiguation_only_answer": false, + "investigation_plan_answer": false, + "not_verified_or_no_results_answer": false, + "graph_failure_mentioned": false, + "missing_required_graph": false, + "used_data_resource": false, + "response_chars": 178, + "status_count": 7 + } + }, + { + "attempt_index": 52, + "task_index": 52, + "task_id": "C1", + "tier": 7, + "title": "Pronoun follow-up on a region", + "question": "What is the medulla?", + "requires_graph": false, + "min_graphs": 0, + "repetition": 1, + "duration_ms": 13388, + "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": 5983, + "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": 7405, + "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": "364cf698-61cc-497e-9f37-2754fa6e16ae", + "response_id": "chatcmpl-0a9951f3b004be90fc0fe0af84410559", + "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": 7405 + } + }, + { + "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": 15212, + "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": 7121, + "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 neuron images have a part in the mushroom body?", + "focus": { + "id": "FBbt_00005801", + "query_type": "ImagesNeurons" + }, + "clicked": 0, + "duration_ms": 8091, + "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": "b9af9748-0180-4d25-852e-b881f533b1f1", + "response_id": "chatcmpl-16c6e4183a40e23e278ef0bb2f7c1e41", + "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": 8091 + } + }, + { + "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": 87802, + "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": 250, + "conversation": true, + "turns": [ + { + "turn": 1, + "question": "What is the fan-shaped body?", + "focus": null, + "clicked": null, + "duration_ms": 7497, + "ok": true, + "response": "The [fan-shaped body](https://www.virtualflybrain.org/reports/FBbt_00003679 \"Open fan-shaped body in Virtual Fly Brain\") is the largest synaptic neuropil domain of the adult central complex, located posterior to the ellipsoid body and anterior to the protocerebral bridge. It is composed of a rough 2-dimensional grid of layers and columns. Eight horizontal layers, numbered bottom to top, form a fan shape and can be divided into vertical columns. An additional, much narrower, 9th layer, which lacks a columnar organization, sits dorsal to layer 8. The number of columns varies for different neuronal types.", + "followons": [ + { + "id": "FBbt_00003679", + "query_type": "ImagesNeurons", + "query": "Which neuron images have a part in the fan-shaped body?" + }, + { + "id": "FBbt_00003679", + "query_type": "TransgeneExpressionHere", + "query": "Which driver lines label the fan-shaped body?" + }, + { + "id": "FBbt_00003679", + "query_type": "NeuronsPartHere", + "query": "Which neurons have part of their arbour in the fan-shaped body?" + }, + { + "id": "FBbt_00003679", + "query_type": "NeuronsSynaptic", + "query": "Which neurons have synaptic terminals in the fan-shaped body?" + }, + { + "id": "FBbt_00003679", + "query_type": "NeuronsPresynapticHere", + "query": "Which neurons provide input to the fan-shaped body?" + }, + { + "id": "FBbt_00003679", + "query_type": "NeuronsPostsynapticHere", + "query": "Which neurons receive output from the fan-shaped body?" + } + ], + "context_terms": [ + { + "id": "FBbt_00003679", + "label": "fan-shaped body" + } + ], + "reproduction": { + "ids": [ + { + "id": "FBbt_00003679", + "label": "fan-shaped body" + } + ], + "calls": [], + "unmapped": [] + }, + "status_count": 6, + "problems": [] + }, + { + "turn": 2, + "question": "What about the ellipsoid body?", + "focus": null, + "clicked": null, + "duration_ms": 8740, + "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": 71565, + "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 for the fan-shaped body 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\"). 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": "97390dc5-7a63-4103-82b2-35303e77f874", + "response_id": "chatcmpl-d6dfde75009847d16a251e3c66cf5a85", + "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 for the fan-shaped body 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\"). 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": 2160, + "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": 71565 + } + }, + { + "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": 13294, + "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": 147, + "conversation": true, + "turns": [ + { + "turn": 1, + "question": "What is a Kenyon cell?", + "focus": null, + "clicked": null, + "duration_ms": 6624, + "ok": true, + "response": "A [Kenyon cell](https://www.virtualflybrain.org/reports/FBbt_00003686 \"Open Kenyon cell in Virtual Fly Brain\") is an intrinsic neuron of the mushroom body. Kenyon cells are part of the olfactory pathway in Drosophila.", + "followons": [ + { + "id": "FBbt_00003686", + "query_type": "ListAllAvailableImages", + "query": "Which images of Kenyon cell does VFB have?" + }, + { + "id": "FBbt_00003686", + "query_type": "UpstreamClassConnectivity", + "query": "What connects to the Kenyon cell upstream?" + }, + { + "id": "FBbt_00003686", + "query_type": "DownstreamClassConnectivity", + "query": "What does the Kenyon cell connect to downstream?" + }, + { + "id": "FBbt_00003686", + "query_type": "TransgeneExpressionHere", + "query": "Which driver lines label the Kenyon cell?" + }, + { + "id": "FBbt_00003686", + "query_type": "anatScRNAseqQuery", + "query": "What single-cell transcriptomic clusters are there for Kenyon cell?" + }, + { + "id": "FBbt_00003686", + "query_type": "SubclassesOf", + "query": "What are the subtypes of the Kenyon cell?" + } + ], + "context_terms": [ + { + "id": "FBbt_00003686", + "label": "Kenyon cell" + } + ], + "reproduction": { + "ids": [ + { + "id": "FBbt_00003686", + "label": "Kenyon cell" + } + ], + "calls": [], + "unmapped": [] + }, + "status_count": 7, + "problems": [] + }, + { + "turn": 2, + "question": "What are its subtypes?", + "focus": null, + "clicked": null, + "duration_ms": 6670, + "ok": true, + "response": "The subtypes of [Kenyon cell](https://www.virtualflybrain.org/reports/FBbt_00003686 \"Open Kenyon cell in Virtual Fly Brain\") include [37](https://v2.virtualflybrain.org/org.geppetto.frontend/geppetto?q=FBbt_00003686,SubclassesOf \"Run in VFB: Subclasses of Kenyon cell\") subclasses, such as [KCab-c(i)](https://www.virtualflybrain.org/reports/FBbt_00049111 \"Open KCab-c(i) in Virtual Fly Brain\"), [KCab-c](https://www.virtualflybrain.org/reports/FBbt_00110929 \"Open KCab-c in Virtual Fly Brain\"), [KCg-m](https://www.virtualflybrain.org/reports/FBbt_00111061 \"Open KCg-m in Virtual Fly Brain\"), [Kenyon cell of main calyx](https://www.virtualflybrain.org/reports/FBbt_00047926 \"Open Kenyon cell of main calyx in Virtual Fly Brain\"), and [gamma Kenyon cell](https://www.virtualflybrain.org/reports/FBbt_00100247 \"Open gamma Kenyon cell in Virtual Fly Brain\"). The first 12 subclasses, along 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": "74ea3300-f3f9-4ebd-9355-0789d473e36e", + "response_id": "chatcmpl-97042b88dd80f17588f5872368450b3f", + "images_count": 8, + "graphs_count": 0, + "response": "The subtypes of [Kenyon cell](https://www.virtualflybrain.org/reports/FBbt_00003686 \"Open Kenyon cell in Virtual Fly Brain\") include [37](https://v2.virtualflybrain.org/org.geppetto.frontend/geppetto?q=FBbt_00003686,SubclassesOf \"Run in VFB: Subclasses of Kenyon cell\") subclasses, such as [KCab-c(i)](https://www.virtualflybrain.org/reports/FBbt_00049111 \"Open KCab-c(i) in Virtual Fly Brain\"), [KCab-c](https://www.virtualflybrain.org/reports/FBbt_00110929 \"Open KCab-c in Virtual Fly Brain\"), [KCg-m](https://www.virtualflybrain.org/reports/FBbt_00111061 \"Open KCg-m in Virtual Fly Brain\"), [Kenyon cell of main calyx](https://www.virtualflybrain.org/reports/FBbt_00047926 \"Open Kenyon cell of main calyx in Virtual Fly Brain\"), and [gamma Kenyon cell](https://www.virtualflybrain.org/reports/FBbt_00100247 \"Open gamma Kenyon cell in Virtual Fly Brain\"). The first 12 subclasses, along 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": 1165, + "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": 6670 + } + }, + { + "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": 24197, + "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": 113, + "conversation": true, + "turns": [ + { + "turn": 1, + "question": "What are the anatomical parts of the medulla? List them.", + "focus": null, + "clicked": null, + "duration_ms": 9624, + "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.", + "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": 14573, + "ok": true, + "response": "Neurons with some part in the [medulla](https://www.virtualflybrain.org/reports/FBbt_00003748 \"Open medulla in Virtual Fly Brain\") include [Dm8b](https://www.virtualflybrain.org/reports/FBbt_00110069 \"Open Dm8b in Virtual Fly Brain\"), [MC](https://www.virtualflybrain.org/reports/FBbt_00111640 \"Open MC in Virtual Fly Brain\"), [PS128](https://www.virtualflybrain.org/reports/FBbt_20001883 \"Open PS128 in Virtual Fly Brain\"), [medulla intrinsic neuron vGlutMinew1a](https://www.virtualflybrain.org/reports/FBbt_00110033 \"Open medulla intrinsic neuron vGlutMinew1a in Virtual Fly Brain\"), [TmY27](https://www.virtualflybrain.org/reports/FBbt_00110067 \"Open TmY27 in Virtual Fly Brain\"), [Mi10b](https://www.virtualflybrain.org/reports/FBbt_00110070 \"Open Mi10b in Virtual Fly Brain\"), medulla tangential neuron vGlutMtnew1, medulla tangential neuron vGlutMtnew2, Tm1a, [CB3849](https://www.virtualflybrain.org/reports/FBbt_20007264 \"Open CB3849 in Virtual Fly Brain\"), [TmY-ds](https://www.virtualflybrain.org/reports/FBbt_00052643 \"Open TmY-ds in Virtual Fly Brain\"), and MeSps. VFB holds [471](https://v2.virtualflybrain.org/org.geppetto.frontend/geppetto?q=FBbt_00003748,NeuronsPartHere \"Run in VFB: Neurons with some part in medulla\") records of neuron types 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": "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": "86345100-e6eb-4c93-8527-ce2f27abed96", + "response_id": "chatcmpl-4d47f93027e11dc9e007063a25a62ea1", + "images_count": 8, + "graphs_count": 0, + "response": "Neurons with some part in the [medulla](https://www.virtualflybrain.org/reports/FBbt_00003748 \"Open medulla in Virtual Fly Brain\") include [Dm8b](https://www.virtualflybrain.org/reports/FBbt_00110069 \"Open Dm8b in Virtual Fly Brain\"), [MC](https://www.virtualflybrain.org/reports/FBbt_00111640 \"Open MC in Virtual Fly Brain\"), [PS128](https://www.virtualflybrain.org/reports/FBbt_20001883 \"Open PS128 in Virtual Fly Brain\"), [medulla intrinsic neuron vGlutMinew1a](https://www.virtualflybrain.org/reports/FBbt_00110033 \"Open medulla intrinsic neuron vGlutMinew1a in Virtual Fly Brain\"), [TmY27](https://www.virtualflybrain.org/reports/FBbt_00110067 \"Open TmY27 in Virtual Fly Brain\"), [Mi10b](https://www.virtualflybrain.org/reports/FBbt_00110070 \"Open Mi10b in Virtual Fly Brain\"), medulla tangential neuron vGlutMtnew1, medulla tangential neuron vGlutMtnew2, Tm1a, [CB3849](https://www.virtualflybrain.org/reports/FBbt_20007264 \"Open CB3849 in Virtual Fly Brain\"), [TmY-ds](https://www.virtualflybrain.org/reports/FBbt_00052643 \"Open TmY-ds in Virtual Fly Brain\"), and MeSps. VFB holds [471](https://v2.virtualflybrain.org/org.geppetto.frontend/geppetto?q=FBbt_00003748,NeuronsPartHere \"Run in VFB: Neurons with some part in medulla\") records of neuron types with some part in the medulla.", + "quality_flags": { + "has_tool_status": true, + "no_tool_factual_answer": false, + "tool_claim_without_tool": false, + "disambiguation_only_answer": false, + "investigation_plan_answer": false, + "not_verified_or_no_results_answer": false, + "graph_failure_mentioned": false, + "missing_required_graph": false, + "used_data_resource": false, + "response_chars": 1291, + "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": 14573 + } + }, + { + "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": 17947, + "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": 161, + "conversation": true, + "turns": [ + { + "turn": 1, + "question": "Tell me about the antennal lobe.", + "focus": null, + "clicked": null, + "duration_ms": 10856, + "ok": true, + "response": "The [antennal lobe](https://www.virtualflybrain.org/reports/FBbt_00003924 \"Open antennal lobe in Virtual Fly Brain\") is a synaptic neuropil domain of the deutocerebrum that is the main target for innervation from the antennal nerve. VFB holds records including transgene expression in antennal lobe commissural pioneer interneuron, downstream connectivity classes for antennal lobe commissural pioneer interneuron, and upstream connectivity classes for antennal lobe commissural pioneer interneuron. The antennal lobe is a region in the Drosophila nervous system where users can search for synaptic input via the Virtual Fly Brain web application.", + "followons": [ + { + "id": "FBbt_00003924", + "query_type": "ListAllAvailableImages", + "query": "Which images of antennal lobe does VFB have?" + }, + { + "id": "FBbt_00003924", + "query_type": "NeuronsPartHere", + "query": "Which neurons have part of their arbour in the antennal lobe?" + }, + { + "id": "FBbt_00003924", + "query_type": "NeuronsSynaptic", + "query": "Which neurons have synaptic terminals in the antennal lobe?" + }, + { + "id": "FBbt_00003924", + "query_type": "NeuronsPresynapticHere", + "query": "Which neurons provide input to the antennal lobe?" + }, + { + "id": "FBbt_00003924", + "query_type": "NeuronsPostsynapticHere", + "query": "Which neurons receive output from the antennal lobe?" + }, + { + "id": "FBbt_00003924", + "query_type": "PartsOf", + "query": "What are the anatomical parts of the antennal lobe?" + } + ], + "context_terms": [ + { + "id": "FBbt_00003924", + "label": "antennal lobe" + } + ], + "reproduction": { + "ids": [ + { + "id": "FBbt_00003924", + "label": "antennal lobe" + } + ], + "calls": [], + "unmapped": [] + }, + "status_count": 6, + "problems": [] + }, + { + "turn": 2, + "question": "Which neurons innervate it?", + "focus": null, + "clicked": null, + "duration_ms": 7091, + "ok": true, + "response": "The [antennal lobe](https://www.virtualflybrain.org/reports/FBbt_00003924 \"Open antennal lobe in Virtual Fly Brain\") is innervated by several types of neurons, including [larval antennal lobe picky local neuron](https://www.virtualflybrain.org/reports/FBbt_00111694 \"Open larval antennal lobe picky local neuron in Virtual Fly Brain\"), [larval antennal lobe broad local neuron](https://www.virtualflybrain.org/reports/FBbt_00111700 \"Open larval antennal lobe broad local neuron in Virtual Fly Brain\"), [PLP077](https://www.virtualflybrain.org/reports/FBbt_20001577 \"Open PLP077 in Virtual Fly Brain\"), [adult olfactory receptor neuron Ir75d ac1](https://www.virtualflybrain.org/reports/FBbt_00110011 \"Open adult olfactory receptor neuron Ir75d ac1 in Virtual Fly Brain\"), [adult olfactory receptor neuron Ir75d ac2](https://www.virtualflybrain.org/reports/FBbt_00110014 \"Open adult olfactory receptor neuron Ir75d ac2 in Virtual Fly Brain\"), adult olfactory receptor neuron Ir75d ac4, pharyngeal VL1 neuron, ORN_VM6, adult olfactory receptor neuron Or35a ac3I, adult olfactory receptor neuron Or35a ac3II, adult olfactory receptor neuron Or85b ab3, and adult olfactory receptor neuron Or85b ab11. VFB holds records of [266](https://v2.virtualflybrain.org/org.geppetto.frontend/geppetto?q=FBbt_00003924,NeuronsPresynapticHere \"Run in VFB: Neurons with presynaptic terminals in antennal lobe\") neurons with presynaptic terminals in the antennal lobe.", + "followons": [ + { + "id": "FBbt_00003924", + "query_type": "ListAllAvailableImages", + "query": "Which images of antennal lobe does VFB have?" + }, + { + "id": "FBbt_00003924", + "query_type": "NeuronsPartHere", + "query": "Which neurons have part of their arbour in the antennal lobe?" + }, + { + "id": "FBbt_00003924", + "query_type": "NeuronsSynaptic", + "query": "Which neurons have synaptic terminals in the antennal lobe?" + }, + { + "id": "FBbt_00003924", + "query_type": "NeuronsPostsynapticHere", + "query": "Which neurons receive output from the antennal lobe?" + }, + { + "id": "FBbt_00003924", + "query_type": "PartsOf", + "query": "What are the anatomical parts of the antennal lobe?" + }, + { + "id": "FBbt_00003924", + "query_type": "SubclassesOf", + "query": "What are the subtypes of the antennal lobe?" + } + ], + "context_terms": [ + { + "id": "FBbt_00003924", + "label": "antennal lobe" + } + ], + "reproduction": { + "ids": [ + { + "id": "FBbt_00003924", + "label": "antennal lobe" + } + ], + "calls": [ + { + "id": "FBbt_00003924", + "query_type": "NeuronsPresynapticHere", + "fn": "get_neurons_with_presynaptic_terminals_in" + } + ], + "unmapped": [] + }, + "status_count": 6, + "problems": [] + } + ], + "ok": true, + "request_id": "15507585-6b5e-402e-b432-1463bbeb7b26", + "response_id": "chatcmpl-8833c5523702cc7135434ee34ceb4199", + "images_count": 6, + "graphs_count": 0, + "response": "The [antennal lobe](https://www.virtualflybrain.org/reports/FBbt_00003924 \"Open antennal lobe in Virtual Fly Brain\") is innervated by several types of neurons, including [larval antennal lobe picky local neuron](https://www.virtualflybrain.org/reports/FBbt_00111694 \"Open larval antennal lobe picky local neuron in Virtual Fly Brain\"), [larval antennal lobe broad local neuron](https://www.virtualflybrain.org/reports/FBbt_00111700 \"Open larval antennal lobe broad local neuron in Virtual Fly Brain\"), [PLP077](https://www.virtualflybrain.org/reports/FBbt_20001577 \"Open PLP077 in Virtual Fly Brain\"), [adult olfactory receptor neuron Ir75d ac1](https://www.virtualflybrain.org/reports/FBbt_00110011 \"Open adult olfactory receptor neuron Ir75d ac1 in Virtual Fly Brain\"), [adult olfactory receptor neuron Ir75d ac2](https://www.virtualflybrain.org/reports/FBbt_00110014 \"Open adult olfactory receptor neuron Ir75d ac2 in Virtual Fly Brain\"), adult olfactory receptor neuron Ir75d ac4, pharyngeal VL1 neuron, ORN_VM6, adult olfactory receptor neuron Or35a ac3I, adult olfactory receptor neuron Or35a ac3II, adult olfactory receptor neuron Or85b ab3, and adult olfactory receptor neuron Or85b ab11. VFB holds records of [266](https://v2.virtualflybrain.org/org.geppetto.frontend/geppetto?q=FBbt_00003924,NeuronsPresynapticHere \"Run in VFB: Neurons with presynaptic terminals in antennal lobe\") neurons with presynaptic terminals in the antennal lobe.", + "quality_flags": { + "has_tool_status": true, + "no_tool_factual_answer": false, + "tool_claim_without_tool": false, + "disambiguation_only_answer": false, + "investigation_plan_answer": false, + "not_verified_or_no_results_answer": false, + "graph_failure_mentioned": false, + "missing_required_graph": false, + "used_data_resource": false, + "response_chars": 1448, + "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": 7091 + } + }, + { + "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": 24324, + "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": 264, + "conversation": true, + "turns": [ + { + "turn": 1, + "question": "What is the medulla?", + "focus": null, + "clicked": null, + "duration_ms": 6634, + "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": 7789, + "ok": true, + "response": "There are images of neurons with parts in the [medulla](https://www.virtualflybrain.org/reports/FBbt_00003748 \"Open medulla in Virtual Fly Brain\"). The first 12 neuron images returned by the query are: OA-AL2i2; MC64; aMe5; MeTu3; MeTu-DRA; MeVP6. 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 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": 9901, + "ok": true, + "response": "The driver lines that label the [medulla](https://www.virtualflybrain.org/reports/FBbt_00003748 \"Open medulla in Virtual Fly Brain\") include PBac{544.SVS-1}B4[CPTI100035], PBac{544.SVS-1}Fer2LCH[CPTI100064], PBac{566.P.SVS-1}IA-2[CPTI100013], PBac{602.P.SVS-1}CG7675[CPTI000703], PBac{602.P.SVS-1}dlg1[CPTI000207], PBac{681.P.FSVS-1}CG11138[CPTI001659], PBac{681.P.FSVS-1}CG6983[CPTI001802], PBac{681.P.FSVS-1}CG7920[CPTI002166], PBac{681.P.FSVS-1}CG9336[CPTI001654], PBac{681.P.FSVS-1}Pka-R2[CPTI001580], PBac{681.P.FSVS-1}cpx[CPTI001473], and PBac{681.P.FSVS-1}larp[CPTI002498]. VFB holds [2,342](https://v2.virtualflybrain.org/org.geppetto.frontend/geppetto?q=FBbt_00003748,TransgeneExpressionHere \"Run in VFB: Transgene expression in medulla\") transgene expression reports for medulla.", + "followons": [ + { + "id": "FBbt_00003748", + "query_type": "ImagesNeurons", + "query": "Which neuron images have a part in the medulla?" + }, + { + "id": "FBbt_00003748", + "query_type": "NeuronsPartHere", + "query": "Which neurons have part of their arbour in the medulla?" + }, + { + "id": "FBbt_00003748", + "query_type": "NeuronsSynaptic", + "query": "Which neurons have synaptic terminals in the medulla?" + }, + { + "id": "FBbt_00003748", + "query_type": "NeuronsPostsynapticHere", + "query": "Which neurons receive output from the medulla?" + }, + { + "id": "FBbt_00003748", + "query_type": "NeuronsPresynapticHere", + "query": "Which neurons provide input to the medulla?" + }, + { + "id": "FBbt_00003748", + "query_type": "PartsOf", + "query": "What are the anatomical parts of the medulla?" + } + ], + "context_terms": [ + { + "id": "FBbt_00003748", + "label": "medulla" + } + ], + "reproduction": { + "ids": [ + { + "id": "FBbt_00003748", + "label": "medulla" + } + ], + "calls": [ + { + "id": "FBbt_00003748", + "query_type": "TransgeneExpressionHere", + "fn": "get_transgene_expression_here" + }, + { + "id": "FBbt_00003748", + "query_type": "NeuronsPartHere", + "fn": "get_neurons_with_part_in" + }, + { + "id": "FBbt_00003748", + "query_type": "ImagesNeurons", + "fn": "get_images_neurons" + } + ], + "unmapped": [] + }, + "status_count": 6, + "problems": [] + } + ], + "ok": true, + "request_id": "5695e5bc-181a-4f26-80be-861d4f450007", + "response_id": "chatcmpl-f3475f9f247d376f437663c7e94f9c38", + "images_count": 8, + "graphs_count": 0, + "response": "The driver lines that label the [medulla](https://www.virtualflybrain.org/reports/FBbt_00003748 \"Open medulla in Virtual Fly Brain\") include PBac{544.SVS-1}B4[CPTI100035], PBac{544.SVS-1}Fer2LCH[CPTI100064], PBac{566.P.SVS-1}IA-2[CPTI100013], PBac{602.P.SVS-1}CG7675[CPTI000703], PBac{602.P.SVS-1}dlg1[CPTI000207], PBac{681.P.FSVS-1}CG11138[CPTI001659], PBac{681.P.FSVS-1}CG6983[CPTI001802], PBac{681.P.FSVS-1}CG7920[CPTI002166], PBac{681.P.FSVS-1}CG9336[CPTI001654], PBac{681.P.FSVS-1}Pka-R2[CPTI001580], PBac{681.P.FSVS-1}cpx[CPTI001473], and PBac{681.P.FSVS-1}larp[CPTI002498]. VFB holds [2,342](https://v2.virtualflybrain.org/org.geppetto.frontend/geppetto?q=FBbt_00003748,TransgeneExpressionHere \"Run in VFB: Transgene expression in medulla\") transgene expression reports for medulla.", + "quality_flags": { + "has_tool_status": true, + "no_tool_factual_answer": false, + "tool_claim_without_tool": false, + "disambiguation_only_answer": false, + "investigation_plan_answer": false, + "not_verified_or_no_results_answer": false, + "graph_failure_mentioned": false, + "missing_required_graph": false, + "used_data_resource": false, + "response_chars": 789, + "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": 9901 + } + }, + { + "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": 11467, + "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": 25, + "conversation": true, + "turns": [ + { + "turn": 1, + "question": "What is the mushroom body?", + "focus": null, + "clicked": null, + "duration_ms": 7055, + "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": 4412, + "ok": true, + "response": "VFB records show that there are [4130](https://v2.virtualflybrain.org/org.geppetto.frontend/geppetto?q=FBbt_00005801,TransgeneExpressionHere \"Run in VFB: Transgene expression in mushroom body\") transgene expression reports for [mushroom body](https://www.virtualflybrain.org/reports/FBbt_00005801 \"Open mushroom body in Virtual Fly Brain\").", + "followons": [ + { + "id": "FBbt_00005801", + "query_type": "ImagesNeurons", + "query": "Which neuron images have a part in the mushroom body?" + }, + { + "id": "FBbt_00005801", + "query_type": "NeuronsPartHere", + "query": "Which neurons have part of their arbour in the mushroom body?" + }, + { + "id": "FBbt_00005801", + "query_type": "NeuronsSynaptic", + "query": "Which neurons have synaptic terminals in the mushroom body?" + }, + { + "id": "FBbt_00005801", + "query_type": "NeuronsPresynapticHere", + "query": "Which neurons provide input to the mushroom body?" + }, + { + "id": "FBbt_00005801", + "query_type": "NeuronsPostsynapticHere", + "query": "Which neurons receive output from the mushroom body?" + }, + { + "id": "FBbt_00005801", + "query_type": "PartsOf", + "query": "What are the anatomical parts of the mushroom body?" + } + ], + "context_terms": [ + { + "id": "FBbt_00005801", + "label": "mushroom body" + } + ], + "reproduction": { + "ids": [ + { + "id": "FBbt_00005801", + "label": "mushroom body" + } + ], + "calls": [ + { + "id": "FBbt_00005801", + "query_type": "TransgeneExpressionHere", + "fn": "get_transgene_expression_here" + } + ], + "unmapped": [] + }, + "status_count": 6, + "problems": [] + } + ], + "ok": true, + "request_id": "faf3b18a-992d-4ceb-8f7f-bae76f02bd5c", + "response_id": "chatcmpl-383373e9c92df4e4673f31abc628f6e8", + "images_count": 8, + "graphs_count": 0, + "response": "VFB records show that there are [4130](https://v2.virtualflybrain.org/org.geppetto.frontend/geppetto?q=FBbt_00005801,TransgeneExpressionHere \"Run in VFB: Transgene expression in mushroom body\") transgene expression reports for [mushroom body](https://www.virtualflybrain.org/reports/FBbt_00005801 \"Open mushroom body in Virtual Fly Brain\").", + "quality_flags": { + "has_tool_status": true, + "no_tool_factual_answer": false, + "tool_claim_without_tool": false, + "disambiguation_only_answer": false, + "investigation_plan_answer": false, + "not_verified_or_no_results_answer": false, + "graph_failure_mentioned": false, + "missing_required_graph": false, + "used_data_resource": false, + "response_chars": 340, + "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": 4412 + } + }, + { + "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": 25041, + "status_messages": [ + { + "message": "Thinking...", + "phase": "llm" + }, + { + "message": "Planning the answer", + "phase": "llm" + }, + { + "message": "Resolving 1 term in VFB", + "phase": "mcp" + }, + { + "message": "Reading VFB term info", + "phase": "mcp" + }, + { + "message": "Querying VFB", + "phase": "mcp" + }, + { + "message": "Checking the answer is covered", + "phase": "llm" + }, + { + "message": "Writing the answer", + "phase": "llm" + }, + { + "message": "Checking before saying VFB has no data", + "phase": "mcp" + }, + { + "message": "Querying VFB", + "phase": "mcp" + }, + { + "message": "Querying VFB", + "phase": "mcp" + }, + { + "message": "Querying VFB", + "phase": "mcp" + }, + { + "message": "Checking the answer is covered", + "phase": "llm" + }, + { + "message": "Writing the answer", + "phase": "llm" + } + ], + "event_count": 163, + "conversation": true, + "turns": [ + { + "turn": 1, + "question": "Which neurons provide input to the medulla?", + "focus": null, + "clicked": null, + "duration_ms": 7426, + "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 they receive input from other neurons within 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": 17615, + "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 lobula and 528 records of neurons with synaptic terminals in 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": "ab8acf49-9736-4916-9b4c-8153aba1f597", + "response_id": "chatcmpl-37169e072acde097bf2f9a26acace33b", + "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 lobula and 528 records of neurons with synaptic terminals in lobula.", + "quality_flags": { + "has_tool_status": true, + "no_tool_factual_answer": false, + "tool_claim_without_tool": false, + "disambiguation_only_answer": false, + "investigation_plan_answer": false, + "not_verified_or_no_results_answer": false, + "graph_failure_mentioned": false, + "missing_required_graph": false, + "used_data_resource": false, + "response_chars": 1105, + "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": 17615 + } + }, + { + "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": 43173, + "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": 137, + "conversation": true, + "turns": [ + { + "turn": 1, + "question": "What is the protocerebral bridge?", + "focus": null, + "clicked": null, + "duration_ms": 6960, + "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": 18137, + "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 both part of the central complex in the Drosophila brain. Neurons with some part in the ellipsoid body include [adult protocerebral bridge glomerulus 1-ellipsoid body canal-dorsal gall neuron](https://www.virtualflybrain.org/reports/FBbt_00111376 \"Open adult protocerebral bridge glomerulus 1-ellipsoid body canal-dorsal gall neuron in Virtual Fly Brain\"), adult protocerebral bridge glomerulus 4-ellipsoid body canal-ventral gall neuron, and other similar neurons, indicating a connection between the two structures. VFB records show that there are [103](https://v2.virtualflybrain.org/org.geppetto.frontend/geppetto?q=FBbt_00003678,NeuronsPartHere \"Run in VFB: Neurons with some part in ellipsoid body\") neurons with some part in the ellipsoid body and [102](https://v2.virtualflybrain.org/org.geppetto.frontend/geppetto?q=FBbt_00003678,NeuronsSynaptic \"Run in VFB: Neurons with synaptic terminals in ellipsoid body\") neurons with synaptic terminals in the ellipsoid body, some of which are associated with the protocerebral bridge.", + "followons": [ + { + "id": "FBbt_00003668", + "query_type": "ListAllAvailableImages", + "query": "Which images of protocerebral bridge does VFB have?" + }, + { + "id": "FBbt_00003668", + "query_type": "NeuronsPartHere", + "query": "Which neurons have part of their arbour in the protocerebral bridge?" + }, + { + "id": "FBbt_00003668", + "query_type": "NeuronsSynaptic", + "query": "Which neurons have synaptic terminals in the protocerebral bridge?" + }, + { + "id": "FBbt_00003668", + "query_type": "NeuronsPresynapticHere", + "query": "Which neurons provide input to the protocerebral bridge?" + }, + { + "id": "FBbt_00003668", + "query_type": "NeuronsPostsynapticHere", + "query": "Which neurons receive output from the protocerebral bridge?" + }, + { + "id": "FBbt_00003668", + "query_type": "PartsOf", + "query": "What are the anatomical parts of the protocerebral bridge?" + } + ], + "context_terms": [ + { + "id": "FBbt_00003668", + "label": "protocerebral bridge" + }, + { + "id": "FBbt_00003678", + "label": "ellipsoid body" + } + ], + "reproduction": { + "ids": [ + { + "id": "FBbt_00003668", + "label": "protocerebral bridge" + }, + { + "id": "FBbt_00003678", + "label": "ellipsoid body" + } + ], + "calls": [ + { + "id": "FBbt_00003678", + "query_type": "ListAllAvailableImages", + "fn": "get_instances" + }, + { + "id": "FBbt_00003678", + "query_type": "NeuronsPartHere", + "fn": "get_neurons_with_part_in" + }, + { + "id": "FBbt_00003678", + "query_type": "NeuronsSynaptic", + "fn": "get_neurons_with_synapses_in" + } + ], + "unmapped": [] + }, + "status_count": 14, + "problems": [] + }, + { + "turn": 3, + "question": "Which neurons connect them?", + "focus": null, + "clicked": null, + "duration_ms": 18076, + "ok": true, + "response": "Neurons that connect the [protocerebral bridge](https://www.virtualflybrain.org/reports/FBbt_00003668 \"Open protocerebral bridge in Virtual Fly Brain\") and the [ellipsoid body](https://www.virtualflybrain.org/reports/FBbt_00003678 \"Open ellipsoid body in Virtual Fly Brain\") include [adult protocerebral bridge glomerulus 1-ellipsoid body canal-dorsal gall neuron](https://www.virtualflybrain.org/reports/FBbt_00111376 \"Open adult protocerebral bridge glomerulus 1-ellipsoid body canal-dorsal gall neuron in Virtual Fly Brain\"), adult protocerebral bridge glomerulus 4-ellipsoid body canal-ventral gall neuron, and other similar neurons. VFB records show that there are neurons with presynaptic terminals in both the protocerebral bridge and 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\"), as well as neurons with postsynaptic terminals in both structures.", + "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": "e6be5c6d-8688-4b26-a6f2-9296aa29b5de", + "response_id": "chatcmpl-3f46e065329d4eeba3ced1415c91610b", + "images_count": 8, + "graphs_count": 0, + "response": "Neurons that connect the [protocerebral bridge](https://www.virtualflybrain.org/reports/FBbt_00003668 \"Open protocerebral bridge in Virtual Fly Brain\") and the [ellipsoid body](https://www.virtualflybrain.org/reports/FBbt_00003678 \"Open ellipsoid body in Virtual Fly Brain\") include [adult protocerebral bridge glomerulus 1-ellipsoid body canal-dorsal gall neuron](https://www.virtualflybrain.org/reports/FBbt_00111376 \"Open adult protocerebral bridge glomerulus 1-ellipsoid body canal-dorsal gall neuron in Virtual Fly Brain\"), adult protocerebral bridge glomerulus 4-ellipsoid body canal-ventral gall neuron, and other similar neurons. VFB records show that there are neurons with presynaptic terminals in both the protocerebral bridge and 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\"), as well as neurons with postsynaptic terminals in both structures.", + "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": 1248, + "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": 18137 + } + }, + { + "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": 22467, + "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 literature", + "phase": "mcp" + }, + { + "message": "Checking the answer is covered", + "phase": "llm" + }, + { + "message": "Writing the answer", + "phase": "llm" + } + ], + "event_count": 44, + "conversation": true, + "turns": [ + { + "turn": 1, + "question": "Which neurons have part of them in the medulla?", + "focus": null, + "clicked": null, + "duration_ms": 11012, + "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.", + "followons": [ + { + "id": "FBbt_00003748", + "query_type": "ImagesNeurons", + "query": "Which neuron images have a part in the medulla?" + }, + { + "id": "FBbt_00003748", + "query_type": "TransgeneExpressionHere", + "query": "Which driver lines label the medulla?" + }, + { + "id": "FBbt_00003748", + "query_type": "NeuronsSynaptic", + "query": "Which neurons have synaptic terminals in the medulla?" + }, + { + "id": "FBbt_00003748", + "query_type": "NeuronsPostsynapticHere", + "query": "Which neurons receive output from the medulla?" + }, + { + "id": "FBbt_00003748", + "query_type": "NeuronsPresynapticHere", + "query": "Which neurons provide input to the medulla?" + }, + { + "id": "FBbt_00003748", + "query_type": "PartsOf", + "query": "What are the anatomical parts of the medulla?" + } + ], + "context_terms": [ + { + "id": "FBbt_00003748", + "label": "medulla" + } + ], + "reproduction": { + "ids": [ + { + "id": "FBbt_00003748", + "label": "medulla" + } + ], + "calls": [ + { + "id": "FBbt_00003748", + "query_type": "NeuronsPartHere", + "fn": "get_neurons_with_part_in" + } + ], + "unmapped": [] + }, + "status_count": 8, + "problems": [] + }, + { + "turn": 2, + "question": "How would I get that same result in Python with vfbquery?", + "focus": null, + "clicked": null, + "duration_ms": 11455, + "ok": true, + "response": "The code below returns the neurons with some part in the [medulla](https://www.virtualflybrain.org/reports/FBbt_00003748 \"Open medulla in Virtual Fly Brain\"), as a table. VFB 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.\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": "38287140-83bd-4fb7-b97b-84682d70ea5c", + "response_id": "chatcmpl-531a142e07d998ef1bf79823fd5d39b1", + "images_count": 8, + "graphs_count": 0, + "response": "The code below returns the neurons with some part in the [medulla](https://www.virtualflybrain.org/reports/FBbt_00003748 \"Open medulla in Virtual Fly Brain\"), as a table. VFB 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.\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": 819, + "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": 11455 + } + }, + { + "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": 25687, + "status_messages": [ + { + "message": "Thinking...", + "phase": "llm" + }, + { + "message": "Planning the answer", + "phase": "llm" + }, + { + "phase": "plan", + "message": "The plan is contested — sampling again before committing." + }, + { + "message": "Resolving 1 term in VFB", + "phase": "mcp" + }, + { + "message": "Reading VFB term info", + "phase": "mcp" + }, + { + "message": "Querying VFB", + "phase": "mcp" + }, + { + "message": "Querying VFB", + "phase": "mcp" + }, + { + "message": "Checking the answer is covered", + "phase": "llm" + }, + { + "message": "Writing the answer", + "phase": "llm" + } + ], + "event_count": 76, + "conversation": true, + "turns": [ + { + "turn": 1, + "question": "What are the subclasses of Kenyon cell?", + "focus": null, + "clicked": null, + "duration_ms": 8730, + "ok": true, + "response": "The subclasses of [Kenyon cell](https://www.virtualflybrain.org/reports/FBbt_00003686 \"Open Kenyon cell in Virtual Fly Brain\") are 37 in number, including [KCab-c(i)](https://www.virtualflybrain.org/reports/FBbt_00049111 \"Open KCab-c(i) in Virtual Fly Brain\"), [KCab-c](https://www.virtualflybrain.org/reports/FBbt_00110929 \"Open KCab-c in Virtual Fly Brain\"), [KCg-m](https://www.virtualflybrain.org/reports/FBbt_00111061 \"Open KCg-m in Virtual Fly Brain\"), [Kenyon cell of main calyx](https://www.virtualflybrain.org/reports/FBbt_00047926 \"Open Kenyon cell of main calyx in Virtual Fly Brain\"), and [gamma Kenyon cell](https://www.virtualflybrain.org/reports/FBbt_00100247 \"Open gamma Kenyon cell in Virtual Fly Brain\"). The first 12 subclasses, with their VFB ids, are: KCab-c(i); KCab-c(o); larval gamma Kenyon cell; KCg-s; KCg-s4; KCg-t; larval alpha'/beta' Kenyon cell; KCab-sc; alpha'/beta' anterior-posterior type 1 Kenyon cell of lACA; Kenyon cell of main calyx; single-claw Kenyon cell; and multi-claw Kenyon cell. VFB holds [37](https://v2.virtualflybrain.org/org.geppetto.frontend/geppetto?q=FBbt_00003686,SubclassesOf \"Run in VFB: Subclasses of Kenyon cell\") subclasses of Kenyon cell.", + "followons": [ + { + "id": "FBbt_00003686", + "query_type": "ListAllAvailableImages", + "query": "Which images of Kenyon cell does VFB have?" + }, + { + "id": "FBbt_00003686", + "query_type": "UpstreamClassConnectivity", + "query": "What connects to the Kenyon cell upstream?" + }, + { + "id": "FBbt_00003686", + "query_type": "DownstreamClassConnectivity", + "query": "What does the Kenyon cell connect to downstream?" + }, + { + "id": "FBbt_00003686", + "query_type": "TransgeneExpressionHere", + "query": "Which driver lines label the Kenyon cell?" + }, + { + "id": "FBbt_00003686", + "query_type": "anatScRNAseqQuery", + "query": "What single-cell transcriptomic clusters are there for Kenyon cell?" + }, + { + "id": "FBbt_00003686", + "query_type": "SubclassesOf", + "query": "What are the subtypes of the Kenyon cell?" + } + ], + "context_terms": [ + { + "id": "FBbt_00003686", + "label": "Kenyon cell" + } + ], + "reproduction": { + "ids": [ + { + "id": "FBbt_00003686", + "label": "Kenyon cell" + } + ], + "calls": [ + { + "id": "FBbt_00003686", + "query_type": "SubclassesOf", + "fn": "get_subclasses_of" + } + ], + "unmapped": [] + }, + "status_count": 6, + "problems": [] + }, + { + "turn": 2, + "question": "Can you list the VFB IDs so I can reproduce this myself?", + "focus": null, + "clicked": null, + "duration_ms": 16957, + "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 records show 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.\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": 9, + "problems": [] + } + ], + "ok": true, + "request_id": "916b5e4e-01d0-4e83-912c-a44a112f9cfe", + "response_id": "chatcmpl-bffeb44a771ad94f10453d5a87499603", + "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 records show 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.\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": 1407, + "status_count": 9, + "addressless_followon": false, + "context_lost_across_turn": false, + "unmatched_claim_after_resolve": false, + "repeats_answered_question": false, + "slow_followup_turn": false, + "slowest_followup_ms": 16957 + } + } + ] +} diff --git a/test-results/task-battery/task-battery-2026-08-13T14-27-45-264Z.json b/test-results/task-battery/task-battery-2026-08-13T14-27-45-264Z.json new file mode 100644 index 0000000..73c2a6b --- /dev/null +++ b/test-results/task-battery/task-battery-2026-08-13T14-27-45-264Z.json @@ -0,0 +1,7985 @@ +{ + "metadata": { + "run_id": "task-battery-2026-08-13T14-27-45-264Z", + "started_at": "2026-08-13T14:27:45.264Z", + "completed_at": "2026-08-13T14:33:51.826Z", + "git_sha": "17a1644227dd4dfec5b7b7dfe9bb54a25b098bcc", + "task_file": "/home/runner/work/VFBchat/VFBchat/VFBchat/tests/task-battery/tasks.json", + "base_url": "http://127.0.0.1:3210", + "started_server": true, + "server_command": "start", + "repetitions": 1, + "concurrency": 4, + "timeout_ms": 240000 + }, + "prompt": { + "provenance_instruction": "Answer the following question about Drosophila neuroscience. For every claim you make, state where the information comes from - for example: the specific database, dataset, or tool query you used; the publication (with full citation); or your general training knowledge. If you are uncertain or do not have a source, say so explicitly rather than guessing." + }, + "summary": { + "total": 64, + "ok": 63, + "errors": 1, + "by_tier": { + "T1": { + "total": 8, + "ok": 8, + "errors": 0 + }, + "T2": { + "total": 8, + "ok": 8, + "errors": 0 + }, + "T3": { + "total": 8, + "ok": 7, + "errors": 1 + }, + "T4": { + "total": 6, + "ok": 6, + "errors": 0 + }, + "T5": { + "total": 1, + "ok": 1, + "errors": 0 + }, + "T6": { + "total": 21, + "ok": 21, + "errors": 0 + }, + "T7": { + "total": 12, + "ok": 12, + "errors": 0 + } + }, + "quality": { + "no_tool_factual_answer": { + "count": 0, + "task_ids": [] + }, + "tool_claim_without_tool": { + "count": 0, + "task_ids": [] + }, + "disambiguation_only_answer": { + "count": 0, + "task_ids": [] + }, + "investigation_plan_answer": { + "count": 0, + "task_ids": [] + }, + "not_verified_or_no_results_answer": { + "count": 0, + "task_ids": [] + }, + "graph_failure_mentioned": { + "count": 0, + "task_ids": [] + }, + "missing_required_graph": { + "count": 0, + "task_ids": [] + }, + "used_data_resource": { + "count": 0, + "task_ids": [] + }, + "addressless_followon": { + "count": 0, + "task_ids": [] + }, + "context_lost_across_turn": { + "count": 0, + "task_ids": [] + }, + "unmatched_claim_after_resolve": { + "count": 0, + "task_ids": [] + }, + "repeats_answered_question": { + "count": 0, + "task_ids": [] + }, + "slow_followup_turn": { + "count": 0, + "task_ids": [] + } + }, + "conversation": { + "total": 12, + "ok": 12, + "turns": 27, + "followup_turns": 15, + "followup_median_ms": 7712, + "followup_max_ms": 22924 + }, + "mean_duration_ms": 18648 + }, + "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": 13826, + "status_messages": [ + { + "message": "Thinking...", + "phase": "llm" + }, + { + "message": "Planning (direct lookup)", + "phase": "llm" + }, + { + "message": "Resolving 1 term in VFB", + "phase": "mcp" + }, + { + "message": "Reading VFB term info", + "phase": "mcp" + }, + { + "message": "Checking the answer is covered", + "phase": "llm" + }, + { + "message": "Writing the answer", + "phase": "llm" + } + ], + "event_count": 101, + "ok": true, + "request_id": "9a088aa0-69c5-488b-8a6d-eacefb8ab1c7", + "response_id": "chatcmpl-a4329381d1808d7022ebcb0319b58732", + "images_count": 8, + "graphs_count": 0, + "response": "The major subdivisions of the Drosophila [mushroom body](https://www.virtualflybrain.org/reports/FBbt_00005801 \"Open mushroom body in Virtual Fly Brain\") are the calyx, pedunculus, and mushroom body lobe system. The calyx is closest to the cortex and receives sensory interneuron afferents, the pedunculus is a thick axon bundle extending from the calyx to the base of the lobes, and the mushroom body lobe system consists of a vertical branch and a medial branch, which have different structures at different life stages.", + "quality_flags": { + "has_tool_status": true, + "no_tool_factual_answer": false, + "tool_claim_without_tool": false, + "disambiguation_only_answer": false, + "investigation_plan_answer": false, + "not_verified_or_no_results_answer": false, + "graph_failure_mentioned": false, + "missing_required_graph": false, + "used_data_resource": false, + "response_chars": 522, + "status_count": 6 + } + }, + { + "attempt_index": 1, + "task_index": 1, + "task_id": "T1.2", + "tier": 1, + "title": "Neuron type classification", + "question": "What types of Kenyon cells exist in the adult Drosophila brain?", + "requires_graph": false, + "min_graphs": 0, + "repetition": 1, + "duration_ms": 13537, + "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": "48cd19eb-0c70-434e-94af-e9dc99f4bfdd", + "response_id": "chatcmpl-24c80354a746e3da302da18d71eef55d", + "images_count": 8, + "graphs_count": 0, + "response": "There are several types of Kenyon cells in the adult Drosophila brain, including alpha/beta, alpha'/beta', and gamma Kenyon cells, which can be further subdivided into core/surface/posterior, anterior-posterior/middle, dorsal/main/gamma-s/gamma-t, and claw-count classes. VFB holds [37](https://v2.virtualflybrain.org/org.geppetto.frontend/geppetto?q=FBbt_00003686,SubclassesOf \"Run in VFB: Subclasses of Kenyon cell\") subclasses of [Kenyon cell](https://www.virtualflybrain.org/reports/FBbt_00003686 \"Open Kenyon cell in Virtual Fly Brain\").", + "quality_flags": { + "has_tool_status": true, + "no_tool_factual_answer": false, + "tool_claim_without_tool": false, + "disambiguation_only_answer": false, + "investigation_plan_answer": false, + "not_verified_or_no_results_answer": false, + "graph_failure_mentioned": false, + "missing_required_graph": false, + "used_data_resource": false, + "response_chars": 542, + "status_count": 6 + } + }, + { + "attempt_index": 2, + "task_index": 2, + "task_id": "T1.3", + "tier": 1, + "title": "Basic connectivity", + "question": "What are the main input neurons to the mushroom body?", + "requires_graph": false, + "min_graphs": 0, + "repetition": 1, + "duration_ms": 12084, + "status_messages": [ + { + "message": "Thinking...", + "phase": "llm" + }, + { + "message": "Planning the answer", + "phase": "llm" + }, + { + "message": "Resolving 1 term in VFB", + "phase": "mcp" + }, + { + "message": "Querying VFB connectivity", + "phase": "mcp" + }, + { + "message": "Querying VFB", + "phase": "mcp" + }, + { + "message": "Querying VFB", + "phase": "mcp" + }, + { + "message": "Checking the answer is covered", + "phase": "llm" + }, + { + "message": "Querying VFB", + "phase": "mcp" + }, + { + "message": "Querying VFB", + "phase": "mcp" + }, + { + "message": "Checking the answer is covered", + "phase": "llm" + }, + { + "message": "Writing the answer", + "phase": "llm" + } + ], + "event_count": 94, + "ok": true, + "request_id": "536f5c15-84e1-4166-83f0-3592dba32b17", + "response_id": "chatcmpl-65b0bb28aaa940aff7ef0dfc8710707f", + "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 [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, such as [larval uniglomerular projection neuron 63a](https://www.virtualflybrain.org/reports/FBbt_00111675 \"Open larval uniglomerular projection neuron 63a in Virtual Fly Brain\"), [larval uniglomerular projection neuron 67b](https://www.virtualflybrain.org/reports/FBbt_00111684 \"Open larval uniglomerular projection neuron 67b in Virtual Fly Brain\"), and [larval antennal lobe multiglomerular projection neuron C2](https://www.virtualflybrain.org/reports/FBbt_00111716 \"Open larval antennal lobe multiglomerular projection neuron C2 in Virtual Fly Brain\").", + "graphs": [ + { + "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": 996, + "status_count": 11 + } + }, + { + "attempt_index": 3, + "task_index": 3, + "task_id": "T1.4", + "tier": 1, + "title": "Gene expression", + "question": "What neurotransmitter do mushroom body Kenyon cells use?", + "requires_graph": false, + "min_graphs": 0, + "repetition": 1, + "duration_ms": 10543, + "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": 24, + "ok": true, + "request_id": "d3462821-fd35-4b17-bccf-5b6fb818898f", + "response_id": "chatcmpl-25b0b6016cf424369cc5ac29c2bc932e", + "images_count": 6, + "graphs_count": 0, + "response": "The primary neurotransmitter used by mushroom body Kenyon cells is acetylcholine.", + "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": 81, + "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": 18840, + "status_messages": [ + { + "message": "Thinking...", + "phase": "llm" + }, + { + "message": "Planning the answer", + "phase": "llm" + }, + { + "phase": "plan", + "message": "The plan is contested — sampling again before committing." + }, + { + "message": "Resolving 1 term in VFB", + "phase": "mcp" + }, + { + "message": "Reading VFB term info", + "phase": "mcp" + }, + { + "message": "Querying VFB", + "phase": "mcp" + }, + { + "message": "Querying VFB", + "phase": "mcp" + }, + { + "message": "Checking the answer is covered", + "phase": "llm" + }, + { + "message": "Writing the answer", + "phase": "llm" + } + ], + "event_count": 171, + "ok": true, + "request_id": "a31bb0fa-68d1-488b-8859-9f8d3bbf2047", + "response_id": "chatcmpl-5b6b9f5f5c2989290b0d5ad547f79869", + "images_count": 6, + "graphs_count": 0, + "response": "The [antennal lobe](https://www.virtualflybrain.org/reports/FBbt_00003924 \"Open antennal lobe in Virtual Fly Brain\") connects to various brain regions through neurons with presynaptic and postsynaptic terminals. Neurons with presynaptic terminals in the antennal lobe include adult olfactory receptor neurons, such as [adult olfactory receptor neuron Ir75d ac1](https://www.virtualflybrain.org/reports/FBbt_00110011 \"Open adult olfactory receptor neuron Ir75d ac1 in Virtual Fly Brain\") and adult olfactory receptor neuron Or35a ac3I, as well as other neurons like [larval antennal lobe picky local neuron](https://www.virtualflybrain.org/reports/FBbt_00111694 \"Open larval antennal lobe picky local neuron in Virtual Fly Brain\") and [PLP077](https://www.virtualflybrain.org/reports/FBbt_20001577 \"Open PLP077 in Virtual Fly Brain\"). Neurons with postsynaptic terminals in the antennal lobe include adult antennal lobe projection neurons, such as [adult antennal lobe projection neuron DL5](https://www.virtualflybrain.org/reports/FBbt_00059280 \"Open adult antennal lobe projection neuron DL5 in Virtual Fly Brain\") and adult antennal lobe projection neuron VM4, as well as other neurons like [AMMC-Bi16](https://www.virtualflybrain.org/reports/FBbt_00111480 \"Open AMMC-Bi16 in Virtual Fly Brain\") and adult multiglomerular antennal lobe projection neuron L1 adPN.", + "quality_flags": { + "has_tool_status": true, + "no_tool_factual_answer": false, + "tool_claim_without_tool": false, + "disambiguation_only_answer": false, + "investigation_plan_answer": false, + "not_verified_or_no_results_answer": false, + "graph_failure_mentioned": false, + "missing_required_graph": false, + "used_data_resource": false, + "response_chars": 1364, + "status_count": 9 + } + }, + { + "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": 13762, + "status_messages": [ + { + "message": "Thinking...", + "phase": "llm" + }, + { + "message": "Planning the answer", + "phase": "llm" + }, + { + "message": "Resolving 1 term in VFB", + "phase": "mcp" + }, + { + "message": "Counting neurons", + "phase": "mcp" + }, + { + "message": "Checking the answer is covered", + "phase": "llm" + }, + { + "message": "Writing the answer", + "phase": "llm" + } + ], + "event_count": 39, + "ok": true, + "request_id": "70058ca4-6f47-4557-830c-446b6d7dd5c2", + "response_id": "chatcmpl-cbc0b026d668a625e24ea1b6716a1f9f", + "images_count": 8, + "graphs_count": 0, + "response": "Approximately 32,388 neurons are in the [adult central brain](https://www.virtualflybrain.org/reports/FBbt_00047887 \"Open adult central brain in Virtual Fly Brain\"). VFB has annotated [9413](https://v2.virtualflybrain.org/org.geppetto.frontend/geppetto?q=FBbt_00047887,NeuronsPartHere \"Run in VFB: Neurons with some part in adult central brain\") neuron types with some part in the adult central brain.\n\n**Published neuron-count estimates — adult central brain** (from the literature):\n\n- ~32,388 neurons (Whole adult brain, both optic lobes and ocellar ganglia included. Ventral nerve cord NOT included; neurons crossing the neck connective are truncated at the brain boundary. Subcount: fully in central brain. One female adult. Dataset: FlyWire connectome neurons, v783.) — Dorkenwald S et al. (2024) Nature 634(8032):124-138 — PMID 39358518\n\n_VFB has annotated 9,413 neuron types with some part in adult central brain — a curated annotation count, not the biological total._", + "quality_flags": { + "has_tool_status": true, + "no_tool_factual_answer": false, + "tool_claim_without_tool": false, + "disambiguation_only_answer": false, + "investigation_plan_answer": false, + "not_verified_or_no_results_answer": false, + "graph_failure_mentioned": false, + "missing_required_graph": false, + "used_data_resource": false, + "response_chars": 977, + "status_count": 6 + } + }, + { + "attempt_index": 6, + "task_index": 6, + "task_id": "T1.7", + "tier": 1, + "title": "Central complex structure", + "question": "What are the main components of the Drosophila central complex and what functions are they associated with?", + "requires_graph": false, + "min_graphs": 0, + "repetition": 1, + "duration_ms": 18100, + "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": 105, + "ok": true, + "request_id": "30e424f0-f65e-40c9-98c9-4bf099f2589d", + "response_id": "chatcmpl-908c9e5e5c9e4e1e2d80a076e400309b", + "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. 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.", + "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": 925, + "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": 18557, + "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": 73, + "ok": true, + "request_id": "eff98100-f5ac-46dd-8e66-62a37d2b4ee9", + "response_id": "chatcmpl-2d9b0326363543b0df8f9dd36af3072c", + "images_count": 8, + "graphs_count": 0, + "response": "Genetic tools such as PBac{544.SVS-1}Bsg[CPTI100062] and PBac{566.P.SVS-1}Bsg[CPTI100005] are used to label neurons in Drosophila. 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\").", + "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": 441, + "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": 21055, + "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": 104, + "ok": true, + "request_id": "a77c3c27-e236-423d-97cc-bce910a2c333", + "response_id": "chatcmpl-13fec087eabb07dc85b9f7cb635587dd", + "images_count": 8, + "graphs_count": 1, + "response": "Dopaminergic input to mushroom body output neurons (MBONs) comes from specific dopaminergic neuron types. VFB found that dopaminergic PPL1 neurons and dopaminergic PAM neurons are among the upstream class-connectivity partners of MBONs. The strongest specific inputs to MBONs, ranked by mean synaptic weight per connected pair, are adult cholinergic neurons and Kenyon cells. VFB holds [69](https://v2.virtualflybrain.org/org.geppetto.frontend/geppetto?q=FBbt_00047953,SubclassesOf \"Run in VFB: Subclasses of MBON\") subclasses of MBON.", + "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": 535, + "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": 15236, + "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": 155, + "ok": true, + "request_id": "536eecfa-4abe-43f6-9757-1d7b4babe710", + "response_id": "chatcmpl-6f4558f0664ac481827350bcd3c5a099", + "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.", + "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": 1698, + "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": 15819, + "status_messages": [ + { + "message": "Thinking...", + "phase": "llm" + }, + { + "message": "Planning the answer", + "phase": "llm" + }, + { + "message": "Resolving 1 term in VFB", + "phase": "mcp" + }, + { + "message": "Reading VFB term info", + "phase": "mcp" + }, + { + "message": "Finding genetic tools", + "phase": "mcp" + }, + { + "message": "Checking the answer is covered", + "phase": "llm" + }, + { + "message": "Querying VFB", + "phase": "mcp" + }, + { + "message": "Checking the answer is covered", + "phase": "llm" + }, + { + "message": "Writing the answer", + "phase": "llm" + } + ], + "event_count": 183, + "ok": true, + "request_id": "c29c0b1a-6c7d-40aa-8648-26d4c3bd3f84", + "response_id": "chatcmpl-a2cd36af124083d67b85bbc5c3203eb9", + "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, specifically: [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\"). VFB also holds [24022](https://v2.virtualflybrain.org/org.geppetto.frontend/geppetto?q=FBbt_00048293,ListAllAvailableImages \"Run in VFB: List all available images of LHN\") available images of adult lateral horn neuron and [1374](https://v2.virtualflybrain.org/org.geppetto.frontend/geppetto?q=FBbt_00048293,SubclassesOf \"Run in VFB: Subclasses of LHN\") subclasses of adult lateral horn neuron.", + "quality_flags": { + "has_tool_status": true, + "no_tool_factual_answer": false, + "tool_claim_without_tool": false, + "disambiguation_only_answer": false, + "investigation_plan_answer": false, + "not_verified_or_no_results_answer": false, + "graph_failure_mentioned": false, + "missing_required_graph": false, + "used_data_resource": false, + "response_chars": 1919, + "status_count": 9 + } + }, + { + "attempt_index": 11, + "task_index": 11, + "task_id": "T2.4", + "tier": 2, + "title": "Neuron characterisation", + "question": "What is known about the LPLC2 visual neuron type? Where is it, what does it connect to, and what is its function?", + "requires_graph": false, + "min_graphs": 0, + "repetition": 1, + "duration_ms": 15835, + "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": 112, + "ok": true, + "request_id": "cc057a32-e2ed-4365-8911-41166d5cf2b3", + "response_id": "chatcmpl-db208e4834909f594831e8680106678f", + "images_count": 7, + "graphs_count": 0, + "response": "The [lobula plate-lobula columnar neuron LPLC2](https://www.virtualflybrain.org/reports/FBbt_00111763 \"Open lobula plate-lobula columnar neuron LPLC2 in Virtual Fly Brain\") is a type of neuron with a distinct dendritic arbor in each lobula plate layer, extending outwards from the main fiber in the direction of motion detection for the layer. It is located in the dorsal area of the lateral cell body rind and is involved in detecting looming stimuli, eliciting a jump escape response. VFB records show that the lobula plate-lobula columnar neuron LPLC2 has specific characteristics and functions.", + "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": 598, + "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": 8038, + "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": "68f9e55e-a3a6-4622-9724-a1ea75681b38", + "response_id": "chatcmpl-90887dd29bf6698101f9483d50e5d801", + "images_count": 6, + "graphs_count": 0, + "response": "The adult [antennal lobe](https://www.virtualflybrain.org/reports/FBbt_00003924 \"Open antennal lobe in Virtual Fly Brain\") has approximately 50 glomeruli, while the larval antennal lobe has around 22 glomeruli.", + "quality_flags": { + "has_tool_status": true, + "no_tool_factual_answer": false, + "tool_claim_without_tool": false, + "disambiguation_only_answer": false, + "investigation_plan_answer": false, + "not_verified_or_no_results_answer": false, + "graph_failure_mentioned": false, + "missing_required_graph": false, + "used_data_resource": false, + "response_chars": 210, + "status_count": 6 + } + }, + { + "attempt_index": 13, + "task_index": 13, + "task_id": "T2.6", + "tier": 2, + "title": "Publications for a circuit", + "question": "What publications describe the PPL1 dopaminergic neurons and their role in aversive memory?", + "requires_graph": false, + "min_graphs": 0, + "repetition": 1, + "duration_ms": 136161, + "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": "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": 114, + "ok": true, + "request_id": "3d8c082c-52a9-4877-ae1a-90d98584397a", + "response_id": "chatcmpl-f06d55efde913320edbb7c4660db68cb", + "images_count": 8, + "graphs_count": 0, + "response": "Publications describing the dopaminergic PPL1 neurons and their role in aversive memory include Claridge-Chang et al., 2009, Mao and Davis, 2009, Budnik and White, 1988, and Ren et al., 2016. The dopaminergic PPL1 neurons are described as having cell bodies located in the posterior inferior lateral protocerebrum of the adult brain and project to various parts of the mushroom body. These neurons are involved in aversive memory.", + "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": 430, + "status_count": 9 + } + }, + { + "attempt_index": 14, + "task_index": 14, + "task_id": "T2.7", + "tier": 2, + "title": "Morphological similarity", + "question": "Are there neurons in the Hemibrain dataset that are morphologically similar to the fru+ mAL neurons described in light microscopy studies?", + "requires_graph": false, + "min_graphs": 0, + "repetition": 1, + "duration_ms": 8740, + "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": 31, + "ok": true, + "request_id": "d252352c-67dd-4575-ad46-b481ddf25b19", + "response_id": "chatcmpl-3a4992a61d2b2054b4b24ca26d33dca3", + "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": 13285, + "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": 156, + "ok": true, + "request_id": "70b972b3-fde7-4258-a0dc-7a853c2c8846", + "response_id": "chatcmpl-14eb69b256e2a1bcd66151b71f09fbc0", + "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.", + "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": 1450, + "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": 16050, + "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": 135, + "ok": true, + "request_id": "833a0fe2-ab75-4111-b31a-40bf2cf8fc87", + "response_id": "chatcmpl-a46c43b3689cb8f09047bfdd661357a0", + "images_count": 8, + "graphs_count": 0, + "response": "There are reciprocal connections between mushroom body output neurons and dopaminergic neurons. VFB found 5 reciprocal class-level pairs between [mushroom body output neuron](https://www.virtualflybrain.org/reports/FBbt_00047953 \"Open mushroom body output neuron in Virtual Fly Brain\") and [dopaminergic neuron](https://www.virtualflybrain.org/reports/FBbt_00005131 \"Open dopaminergic neuron in Virtual Fly Brain\"). The strongest specific targets of mushroom body output neuron include [primary interneuron](https://www.virtualflybrain.org/reports/FBbt_00052517 \"Open primary interneuron in Virtual Fly Brain\"), [primary neuron](https://www.virtualflybrain.org/reports/FBbt_00047097 \"Open primary neuron in Virtual Fly Brain\"), [adult GABAergic neuron](https://www.virtualflybrain.org/reports/FBbt_00058207 \"Open adult GABAergic neuron in Virtual Fly Brain\"), [GABAergic neuron](https://www.virtualflybrain.org/reports/FBbt_00007228 \"Open GABAergic neuron in Virtual Fly Brain\"), [adult glutamatergic neuron](https://www.virtualflybrain.org/reports/FBbt_00058208 \"Open adult glutamatergic neuron in Virtual Fly Brain\"), [glutamatergic neuron](https://www.virtualflybrain.org/reports/FBbt_00100291 \"Open glutamatergic neuron in Virtual Fly Brain\"), [adult lateral horn neuron](https://www.virtualflybrain.org/reports/FBbt_00048293 \"Open adult lateral horn neuron in Virtual Fly Brain\"), and [adult cholinergic neuron](https://www.virtualflybrain.org/reports/FBbt_00058205 \"Open adult cholinergic neuron in Virtual Fly Brain\"). The strongest specific targets of dopaminergic neuron include adult cholinergic neuron and [adult Kenyon cell](https://www.virtualflybrain.org/reports/FBbt_00049825 \"Open adult Kenyon cell in Virtual Fly Brain\").", + "quality_flags": { + "has_tool_status": true, + "no_tool_factual_answer": false, + "tool_claim_without_tool": false, + "disambiguation_only_answer": false, + "investigation_plan_answer": false, + "not_verified_or_no_results_answer": false, + "graph_failure_mentioned": false, + "missing_required_graph": false, + "used_data_resource": false, + "response_chars": 1738, + "status_count": 9 + } + }, + { + "attempt_index": 17, + "task_index": 17, + "task_id": "T3.2", + "tier": 3, + "title": "Pathway tracing", + "question": "Trace a pathway from olfactory receptor neurons to the lateral horn. What are the intermediate neuron types and their connections?", + "requires_graph": false, + "min_graphs": 0, + "repetition": 1, + "duration_ms": 14555, + "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": 156, + "ok": true, + "request_id": "b276a2a4-0e1a-42d0-9449-318b44dbde6e", + "response_id": "chatcmpl-7765c6917284fad38baa4a9c88c9ee7d", + "images_count": 8, + "graphs_count": 0, + "response": "The pathway from olfactory receptor neurons to the lateral horn involves intermediate neuron types. Antennal lobe projection neurons are interneurons whose dendrites innervate the antennal lobe and whose axons innervate higher brain centers, including the lateral horn. The strongest specific inputs to olfactory receptor neurons include [adult antennal lobe local neuron lLN](https://www.virtualflybrain.org/reports/FBbt_00051502 \"Open adult antennal lobe local neuron lLN in Virtual Fly Brain\"), [adult local interneuron of the lateral ALl1 neuroblast](https://www.virtualflybrain.org/reports/FBbt_00007394 \"Open adult local interneuron of the lateral ALl1 neuroblast in Virtual Fly Brain\"), [antennal lobe local neuron](https://www.virtualflybrain.org/reports/FBbt_00052874 \"Open antennal lobe local neuron in Virtual Fly Brain\"), [adult antennal lobe local neuron](https://www.virtualflybrain.org/reports/FBbt_00007390 \"Open adult antennal lobe local neuron in Virtual Fly Brain\"), [olfactory system neuron](https://www.virtualflybrain.org/reports/FBbt_00007697 \"Open olfactory system neuron in Virtual Fly Brain\"), and [adult antennal sensory neuron](https://www.virtualflybrain.org/reports/FBbt_00051173 \"Open adult antennal sensory neuron in Virtual Fly Brain\"). VFB holds [1661](https://v2.virtualflybrain.org/org.geppetto.frontend/geppetto?q=FBbt_00007053,NeuronsPartHere \"Run in VFB: Neurons with some part in adult lateral horn\") records of neurons with some part in [adult lateral horn](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": 1840, + "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": 9456, + "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": "5ac3c618-585e-459f-b2b9-5133ba208eda", + "response_id": "chatcmpl-a423b7e62777ecf67160aa7e3dd5c739", + "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": 15322, + "status_messages": [ + { + "message": "Thinking...", + "phase": "llm" + }, + { + "message": "Planning the answer", + "phase": "llm" + }, + { + "message": "Resolving 1 term in VFB", + "phase": "mcp" + }, + { + "message": "Querying VFB connectivity", + "phase": "mcp" + }, + { + "message": "Checking the literature", + "phase": "mcp" + }, + { + "message": "Checking the answer is covered", + "phase": "llm" + }, + { + "message": "Querying VFB", + "phase": "mcp" + }, + { + "message": "Checking the answer is covered", + "phase": "llm" + }, + { + "message": "Writing the answer", + "phase": "llm" + }, + { + "message": "Checking before saying VFB has no data", + "phase": "mcp" + }, + { + "message": "Querying VFB", + "phase": "mcp" + }, + { + "message": "Querying VFB", + "phase": "mcp" + }, + { + "message": "Querying VFB", + "phase": "mcp" + }, + { + "message": "Checking the answer is covered", + "phase": "llm" + }, + { + "message": "Writing the answer", + "phase": "llm" + } + ], + "event_count": 106, + "ok": true, + "request_id": "23bca8a9-b597-4b5c-982d-7f3ff682c79b", + "response_id": "chatcmpl-730a429c63a1c7d95e7573881a775461", + "images_count": 8, + "graphs_count": 0, + "response": "That lookup did not complete, so this answer cannot say what VFB holds there.", + "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": 77, + "status_count": 15 + } + }, + { + "attempt_index": 20, + "task_index": 20, + "task_id": "T3.5", + "tier": 3, + "title": "Shared connectivity", + "question": "Do the alpha/beta and gamma Kenyon cells converge on any of the same downstream MBON types? Which MBONs receive input from both?", + "requires_graph": false, + "min_graphs": 0, + "repetition": 1, + "duration_ms": 11277, + "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": 103, + "ok": true, + "request_id": "889cfd3c-6f01-4583-befc-fe7512c6581b", + "response_id": "chatcmpl-0b854481c0a5194c878fba9e237d5efa", + "images_count": 8, + "graphs_count": 0, + "response": "The connectome data indicates that alpha/beta Kenyon cells and gamma Kenyon cells have distinct downstream targets. VFB returned matching entries including [KCab-c](https://www.virtualflybrain.org/reports/FBbt_00110929 \"Open KCab-c in Virtual Fly Brain\") and [gamma Kenyon cell](https://www.virtualflybrain.org/reports/FBbt_00100247 \"Open gamma Kenyon cell in Virtual Fly Brain\"), but the evidence does not specify which mushroom body output neurons receive input from both. VFB does not currently hold data on downstream connectivity classes for gamma Kenyon cells. VFB holds [69](https://v2.virtualflybrain.org/org.geppetto.frontend/geppetto?q=FBbt_00047953,SubclassesOf \"Run in VFB: Subclasses of MBON\") subclasses of [mushroom body output neuron](https://www.virtualflybrain.org/reports/FBbt_00047953 \"Open mushroom body output neuron in Virtual Fly Brain\") 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": 1140, + "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": 10995, + "status_messages": [ + { + "message": "Thinking...", + "phase": "llm" + }, + { + "message": "Planning the answer", + "phase": "llm" + }, + { + "message": "Resolving 1 term in VFB", + "phase": "mcp" + }, + { + "message": "Tracing the pathway", + "phase": "mcp" + }, + { + "message": "Querying VFB", + "phase": "mcp" + }, + { + "message": "Checking the answer is covered", + "phase": "llm" + }, + { + "message": "Writing the answer", + "phase": "llm" + } + ], + "event_count": 92, + "ok": true, + "request_id": "b53459a8-b192-4c14-9bd1-60ca27d4efc0", + "response_id": "chatcmpl-b5bca8d5b94528434617957dcdcadbbd", + "images_count": 0, + "graphs_count": 0, + "response": "The anatomical containment hierarchy from the DA1 glomerulus up to the top-level brain structure is: DA1 glomerulus -> adult olfactory antennal lobe glomerulus -> adult antennal lobe -> adult deutocerebrum -> adult cerebrum -> adult central brain -> adult brain. VFB does not currently hold data on parts of the [antennal lobe glomerulus DA1](https://www.virtualflybrain.org/reports/FBbt_00003932 \"Open antennal lobe glomerulus DA1 in Virtual Fly Brain\").", + "quality_flags": { + "has_tool_status": true, + "no_tool_factual_answer": false, + "tool_claim_without_tool": false, + "disambiguation_only_answer": false, + "investigation_plan_answer": false, + "not_verified_or_no_results_answer": false, + "graph_failure_mentioned": false, + "missing_required_graph": false, + "used_data_resource": false, + "response_chars": 455, + "status_count": 7 + } + }, + { + "attempt_index": 22, + "task_index": 22, + "task_id": "T3.7", + "tier": 3, + "title": "Cross-region connectivity", + "question": "What neuron types connect the central complex to the lateral accessory lobe, and how strong are these connections?", + "requires_graph": false, + "min_graphs": 0, + "repetition": 1, + "duration_ms": 13873, + "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": 149, + "ok": true, + "request_id": "ff5a0b3b-9ca7-4274-bb69-e785c12c7d5a", + "response_id": "chatcmpl-c51c32f2870a5a1fe3a5ec8fcf0a492c", + "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 that neurons with some part in the adult central complex 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\"), [PEN_PB8](https://www.virtualflybrain.org/reports/FBbt_00111374 \"Open PEN_PB8 in Virtual Fly Brain\"), and several adult protocerebral bridge glomerulus neurons. The same neurons are also found among those with synaptic terminals in the adult central complex. However, VFB does not currently hold data on neurons with presynaptic or postsynaptic terminals in the embryonic/larval lateral accessory lobe.", + "quality_flags": { + "has_tool_status": true, + "no_tool_factual_answer": false, + "tool_claim_without_tool": false, + "disambiguation_only_answer": false, + "investigation_plan_answer": false, + "not_verified_or_no_results_answer": false, + "graph_failure_mentioned": false, + "missing_required_graph": false, + "used_data_resource": false, + "response_chars": 1020, + "status_count": 11 + } + }, + { + "attempt_index": 23, + "task_index": 23, + "task_id": "T3.8", + "tier": 3, + "title": "Dataset coverage", + "question": "For the DNa02 descending neuron type, what data is available in VFB? Is it in the Hemibrain, FAFB, or both? Are there light microscopy images and driver lines?", + "requires_graph": false, + "min_graphs": 0, + "repetition": 1, + "ok": false, + "duration_ms": null, + "error": "Timed out after 240000 ms", + "quality_flags": { + "has_tool_status": false, + "no_tool_factual_answer": false, + "tool_claim_without_tool": false, + "disambiguation_only_answer": false, + "investigation_plan_answer": false, + "not_verified_or_no_results_answer": false, + "graph_failure_mentioned": false, + "missing_required_graph": false, + "used_data_resource": false, + "response_chars": 25, + "status_count": 0 + } + }, + { + "attempt_index": 24, + "task_index": 24, + "task_id": "T4.1", + "tier": 4, + "title": "Experimental planning", + "question": "I want to study the neural circuit underlying CO2 avoidance in Drosophila. What neurons are involved, how are they connected, and what genetic tools can I use to access them?", + "requires_graph": false, + "min_graphs": 0, + "repetition": 1, + "duration_ms": 5744, + "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": 55, + "ok": true, + "request_id": "10c4866d-574c-418f-acb2-5e51e54e6db5", + "response_id": "chatcmpl-125419b73f7caad177aac6100efa5a5a", + "images_count": 0, + "graphs_count": 0, + "response": "The neurons involved in the detection of carbon dioxide are carbon dioxide sensitive neurons. These neurons are involved in the detection of carbon dioxide.\n\nThe question of how these neurons are connected and what genetic tools can be used to access them remains unanswered.", + "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": 275, + "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": 43801, + "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": 383, + "ok": true, + "request_id": "a1963153-aa29-4e53-8ecf-7d644655c88f", + "response_id": "chatcmpl-a48824c6de192b76eb5c44156a65cdff", + "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. The giant fiber neuron enters the cervical connective via the posterior cerebro-cervical fascicle and descends on the ipsilateral side, in the dorsal cervical fasciculus. In the brain, it has dendritic arborization in the ipsilateral zones A and B of the antennal mechanosensory and motor center, where it receives substantial input from zone A and B Johnston organ neurons. It also arborizes in the posterior ventrolateral protocerebrum and gorget. The giant fiber neuron enters the VNC near the dorsal midline and extends posteroventrally to the mesothoracic neuromere, where it turns ventrolaterally, and ends abruptly without branching. In the mesothoracic neuromere, it forms electrical synapses with downstream motor and premotor neurons at the inframedial bridge, where the two giant fiber neurons connect across the midline, and at the axonal lateral bend.\n\nThe giant fiber neuron has [389](https://v2.virtualflybrain.org/org.geppetto.frontend/geppetto?q=FBbt_00004020,DownstreamClassConnectivity \"Run in VFB: Downstream connectivity classes for DNp01\") downstream connectivity classes 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. Available driver lines include [5](https://v2.virtualflybrain.org/org.geppetto.frontend/geppetto?q=FBbt_00004020,SplitsTargeting \"Run in VFB: Splits targeting DNp01\") split-GAL4 combinations. VFB records show [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}, and P{GMR91H05-GAL4}, among others.\n\nRelevant publications for the giant fiber neuron include Thomas and Wyman (1984), Koto et al. (1981), Power (1948), and others.", + "graphs": [ + { + "type": "basic_graph", + "version": 1, + "title": "Downstream partners of DNp01", + "directed": true, + "layout": "circle", + "nodes": [ + { + "id": "FBbt_00004020", + "label": "DNp01", + "group": null, + "color": null, + "size": 4 + }, + { + "id": "FBbt_00047095", + "label": "adult neuron", + "group": null, + "color": null, + "size": 1.48 + }, + { + "id": "FBbt_00005106", + "label": "neuron", + "group": null, + "color": null, + "size": 1.48 + }, + { + "id": "FBbt_00059271", + "label": "CNS neuron", + "group": null, + "color": null, + "size": 1.47 + }, + { + "id": "FBbt_00059289", + "label": "adult VNC neuron", + "group": null, + "color": null, + "size": 1.31 + }, + { + "id": "FBbt_00001983", + "label": "thoracic neuron", + "group": null, + "color": null, + "size": 1.31 + }, + { + "id": "FBbt_00001985", + "label": "mesothoracic neuron", + "group": null, + "color": null, + "size": 1.19 + }, + { + "id": "FBbt_00047097", + "label": "primary neuron", + "group": null, + "color": null, + "size": 1.13 + }, + { + "id": "FBbt_00049542", + "label": "Notch OFF hemilineage secondary neuron", + "group": null, + "color": null, + "size": 1.13 + }, + { + "id": "FBbt_00001984", + "label": "prothoracic neuron", + "group": null, + "color": null, + "size": 1.12 + }, + { + "id": "FBbt_00049541", + "label": "Notch ON hemilineage secondary neuron", + "group": null, + "color": null, + "size": 1.08 + }, + { + "id": "FBbt_00048301", + "label": "adult ascending neuron", + "group": null, + "color": null, + "size": 1.07 + }, + { + "id": "FBbt_00007693", + "label": "sensory system neuron", + "group": null, + "color": null, + "size": 1.06 + }, + { + "id": "FBbt_00007392", + "label": "projection neuron", + "group": null, + "color": null, + "size": 1.06 + }, + { + "id": "FBbt_00047105", + "label": "Notch OFF hemilineage primary neuron", + "group": null, + "color": null, + "size": 1.06 + }, + { + "id": "FBbt_00048286", + "label": "adult visual projection neuron", + "group": null, + "color": null, + "size": 1.06 + } + ], + "edges": [ + { + "source": "FBbt_00004020", + "target": "FBbt_00047095", + "label": "4235", + "weight": 4235 + }, + { + "source": "FBbt_00004020", + "target": "FBbt_00005106", + "label": "4235", + "weight": 4235 + }, + { + "source": "FBbt_00004020", + "target": "FBbt_00059271", + "label": "4193", + "weight": 4193 + }, + { + "source": "FBbt_00004020", + "target": "FBbt_00059289", + "label": "2779", + "weight": 2779 + }, + { + "source": "FBbt_00004020", + "target": "FBbt_00001983", + "label": "2758", + "weight": 2758 + }, + { + "source": "FBbt_00004020", + "target": "FBbt_00001985", + "label": "1651", + "weight": 1651 + }, + { + "source": "FBbt_00004020", + "target": "FBbt_00047097", + "label": "1197", + "weight": 1197 + }, + { + "source": "FBbt_00004020", + "target": "FBbt_00049542", + "label": "1152", + "weight": 1152 + }, + { + "source": "FBbt_00004020", + "target": "FBbt_00001984", + "label": "1098", + "weight": 1098 + }, + { + "source": "FBbt_00004020", + "target": "FBbt_00049541", + "label": "674", + "weight": 674 + }, + { + "source": "FBbt_00004020", + "target": "FBbt_00048301", + "label": "641", + "weight": 641 + }, + { + "source": "FBbt_00004020", + "target": "FBbt_00007693", + "label": "556", + "weight": 556 + }, + { + "source": "FBbt_00004020", + "target": "FBbt_00007392", + "label": "505", + "weight": 505 + }, + { + "source": "FBbt_00004020", + "target": "FBbt_00047105", + "label": "495", + "weight": 495 + }, + { + "source": "FBbt_00004020", + "target": "FBbt_00048286", + "label": "494", + "weight": 494 + } + ] + } + ], + "quality_flags": { + "has_tool_status": true, + "no_tool_factual_answer": false, + "tool_claim_without_tool": false, + "disambiguation_only_answer": false, + "investigation_plan_answer": false, + "not_verified_or_no_results_answer": false, + "graph_failure_mentioned": false, + "missing_required_graph": false, + "used_data_resource": false, + "response_chars": 2344, + "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": 14880, + "status_messages": [ + { + "message": "Thinking...", + "phase": "llm" + }, + { + "message": "Planning the answer", + "phase": "llm" + }, + { + "message": "Resolving 2 terms in VFB", + "phase": "mcp" + }, + { + "message": "Tracing the pathway", + "phase": "mcp" + }, + { + "message": "Querying VFB connectivity", + "phase": "mcp" + }, + { + "message": "Checking the answer is covered", + "phase": "llm" + }, + { + "message": "Querying VFB", + "phase": "mcp" + }, + { + "message": "Querying VFB", + "phase": "mcp" + }, + { + "message": "Checking the answer is covered", + "phase": "llm" + }, + { + "message": "Writing the answer", + "phase": "llm" + } + ], + "event_count": 142, + "ok": true, + "request_id": "b6c16bb8-e2b7-4d77-98f3-392120d0b885", + "response_id": "chatcmpl-4940aa73d0cff86cf9f51b247d9ec28a", + "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 adult visual projection neurons have presynaptic terminals in the mushroom body. VFB records show that projection neurons are also potential mediators of this connection.\n\nVisual information could reach the memory circuit via these neurons. 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 visual projection neuron](https://www.virtualflybrain.org/reports/FBbt_00048286 \"Open adult visual projection neuron in Virtual Fly Brain\"), among others.\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.", + "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": 1588, + "status_count": 10 + } + }, + { + "attempt_index": 27, + "task_index": 27, + "task_id": "T4.4", + "tier": 4, + "title": "Comparative analysis", + "question": "Compare the downstream targets of the two main types of clock neurons (s-LNv and l-LNv). Do they converge on any common target neuron types?", + "requires_graph": false, + "min_graphs": 0, + "repetition": 1, + "duration_ms": 14621, + "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": "d94993b2-6219-4f85-9b9f-29de6ee3e178", + "response_id": "chatcmpl-24669aa07cb10b21731aaecac53cffae", + "images_count": 8, + "graphs_count": 1, + "response": "The downstream targets of [l-LNv neuron](https://www.virtualflybrain.org/reports/FBbt_00003763 \"Open l-LNv neuron in Virtual Fly Brain\") include [adult visual projection neuron](https://www.virtualflybrain.org/reports/FBbt_00048286 \"Open adult visual projection neuron in Virtual Fly Brain\"), [sensory system neuron](https://www.virtualflybrain.org/reports/FBbt_00007693 \"Open sensory system neuron in Virtual Fly Brain\"), [Notch ON hemilineage secondary neuron](https://www.virtualflybrain.org/reports/FBbt_00049541 \"Open Notch ON hemilineage secondary neuron in Virtual Fly Brain\"), [optic lobe narrow field columnar neuron](https://www.virtualflybrain.org/reports/FBbt_00110136 \"Open optic lobe narrow field columnar neuron in Virtual Fly Brain\"), [optic lobe intrinsic columnar neuron](https://www.virtualflybrain.org/reports/FBbt_00007578 \"Open optic lobe intrinsic columnar neuron in Virtual Fly Brain\"), [adult optic lobe neuron](https://www.virtualflybrain.org/reports/FBbt_00003702 \"Open adult optic lobe neuron in Virtual Fly Brain\"), and [adult optic lobe columnar neuron](https://www.virtualflybrain.org/reports/FBbt_00005129 \"Open adult optic lobe columnar neuron in Virtual Fly Brain\"). VFB does not currently hold data on the downstream connectivity classes for [adult s-LNv neuron](https://www.virtualflybrain.org/reports/FBbt_00007428 \"Open adult s-LNv neuron in Virtual Fly Brain\").", + "graphs": [ + { + "type": "basic_graph", + "version": 1, + "title": "Downstream targets by source class", + "directed": true, + "layout": "circle", + "nodes": [ + { + "id": "FBbt_00003763", + "label": "l-LNv", + "group": null, + "color": null, + "size": 4 + }, + { + "id": "FBbt_00005106", + "label": "neuron", + "group": null, + "color": null, + "size": 1.17 + }, + { + "id": "FBbt_00047095", + "label": "adult neuron", + "group": null, + "color": null, + "size": 1.17 + }, + { + "id": "FBbt_00059271", + "label": "CNS neuron", + "group": null, + "color": null, + "size": 1.17 + }, + { + "id": "FBbt_00059274", + "label": "adult CNS neuron", + "group": null, + "color": null, + "size": 1.17 + }, + { + "id": "FBbt_00007693", + "label": "sensory system neuron", + "group": null, + "color": null, + "size": 1.17 + }, + { + "id": "FBbt_00047736", + "label": "visual system neuron", + "group": null, + "color": null, + "size": 1.17 + }, + { + "id": "FBbt_00005125", + "label": "interneuron", + "group": null, + "color": null, + "size": 1.16 + }, + { + "id": "FBbt_00052046", + "label": "adult interneuron", + "group": null, + "color": null, + "size": 1.16 + }, + { + "id": "FBbt_00001366", + "label": "supraesophageal ganglion neuron", + "group": null, + "color": null, + "size": 1.16 + }, + { + "id": "FBbt_00003702", + "label": "adult optic lobe neuron", + "group": null, + "color": null, + "size": 1.15 + }, + { + "id": "FBbt_00059247", + "label": "adult visual neuropil intrinsic neuron", + "group": null, + "color": null, + "size": 1.15 + }, + { + "id": "FBbt_00007577", + "label": "adult optic lobe intrinsic neuron", + "group": null, + "color": null, + "size": 1.15 + }, + { + "id": "FBbt_00007173", + "label": "cholinergic neuron", + "group": null, + "color": null, + "size": 1.14 + }, + { + "id": "FBbt_00058205", + "label": "adult cholinergic neuron", + "group": null, + "color": null, + "size": 1.14 + }, + { + "id": "FBbt_00005129", + "label": "adult optic lobe columnar neuron", + "group": null, + "color": null, + "size": 1.14 + }, + { + "id": "FBbt_00007578", + "label": "optic lobe intrinsic columnar neuron", + "group": null, + "color": null, + "size": 1.14 + }, + { + "id": "FBbt_00047096", + "label": "secondary neuron", + "group": null, + "color": null, + "size": 1.13 + }, + { + "id": "FBbt_00110136", + "label": "optic lobe narrow field columnar neuron", + "group": null, + "color": null, + "size": 1.13 + }, + { + "id": "FBbt_00049539", + "label": "Notch ON hemilineage neuron", + "group": null, + "color": null, + "size": 1.13 + }, + { + "id": "FBbt_00049541", + "label": "Notch ON hemilineage secondary neuron", + "group": null, + "color": null, + "size": 1.13 + } + ], + "edges": [ + { + "source": "FBbt_00003763", + "target": "FBbt_00005106", + "label": "6184", + 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"quality_flags": { + "has_tool_status": true, + "no_tool_factual_answer": false, + "tool_claim_without_tool": false, + "disambiguation_only_answer": false, + "investigation_plan_answer": false, + "not_verified_or_no_results_answer": false, + "graph_failure_mentioned": false, + "missing_required_graph": false, + "used_data_resource": false, + "response_chars": 1400, + "status_count": 9 + } + }, + { + "attempt_index": 28, + "task_index": 28, + "task_id": "T4.5", + "tier": 4, + "title": "Novel circuit exploration", + "question": "What is the connectivity between thermosensory neurons and the mushroom body? Could temperature information influence memory formation?", + "requires_graph": false, + "min_graphs": 0, + "repetition": 1, + "duration_ms": 20209, + "status_messages": [ + { + "message": "Thinking...", + "phase": "llm" + }, + { + "message": "Planning the answer", + "phase": "llm" + }, + { + "phase": "plan", + "message": "The plan is contested — sampling again before committing." + }, + { + "message": "Resolving 2 terms in VFB", + "phase": "mcp" + }, + { + "message": "Tracing the pathway", + "phase": "mcp" + }, + { + "message": "Querying VFB connectivity", + "phase": "mcp" + }, + { + "message": "Querying VFB", + "phase": "mcp" + }, + { + "message": "Querying VFB", + "phase": "mcp" + }, + { + "message": "Checking the answer is covered", + "phase": "llm" + }, + { + "message": "Querying VFB", + "phase": "mcp" + }, + { + "message": "Querying VFB", + "phase": "mcp" + }, + { + "message": "Checking the answer is covered", + "phase": "llm" + }, + { + "message": "Writing the answer", + "phase": "llm" + } + ], + "event_count": 175, + "ok": true, + "request_id": "ebd0297e-8bca-4e06-9add-9da54592e8af", + "response_id": "chatcmpl-120f6a712b7036296df6bdab9466236e", + "images_count": 8, + "graphs_count": 1, + "response": "The connectivity between thermosensory neurons and the [mushroom body](https://www.virtualflybrain.org/reports/FBbt_00005801 \"Open mushroom body in Virtual Fly Brain\") is supported by evidence from VFB, which suggests that thermosensory neurons influence mushroom body memory formation through thermosensory projection neurons. VFB's class-level connectivity table for [thermosensory neuron](https://www.virtualflybrain.org/reports/FBbt_00005918 \"Open thermosensory neuron in Virtual Fly Brain\") lists downstream classes, including [projection neuron](https://www.virtualflybrain.org/reports/FBbt_00007392 \"Open projection neuron in Virtual Fly Brain\"), [adult antennal lobe projection neuron](https://www.virtualflybrain.org/reports/FBbt_00067123 \"Open adult antennal lobe projection neuron in Virtual Fly Brain\"), and [antennal lobe projection neuron](https://www.virtualflybrain.org/reports/FBbt_00007422 \"Open antennal lobe projection neuron in Virtual Fly Brain\"), with the strongest specific targets having 18.9, 18.8, and 18.7 synapses per connected pair, respectively. Additionally, VFB's query for neurons with presynaptic terminals in mushroom body returns [366](https://v2.virtualflybrain.org/org.geppetto.frontend/geppetto?q=FBbt_00005801,NeuronsPresynapticHere \"Run in VFB: Neurons with presynaptic terminals in mushroom body\") results, and the query for neurons with postsynaptic terminals in mushroom body returns [304](https://v2.virtualflybrain.org/org.geppetto.frontend/geppetto?q=FBbt_00005801,NeuronsPostsynapticHere \"Run in VFB: Neurons with postsynaptic terminals in mushroom body\") results. This suggests that temperature information could indeed influence memory formation in the mushroom body.", + "graphs": [ + { + "type": "basic_graph", + "version": 1, + "title": "Downstream partners of thermosensory neuron", + "directed": true, + "layout": "circle", + "nodes": [ + { + "id": "FBbt_00005918", + "label": "thermosensory neuron", + "group": null, + "color": null, + "size": 4 + }, + { + "id": "FBbt_00005106", + "label": "neuron", + "group": null, + "color": null, + "size": 1.4 + }, + { + "id": "FBbt_00047095", + "label": "adult neuron", + "group": null, + "color": null, + "size": 1.39 + }, + { + "id": "FBbt_00059271", + "label": "CNS neuron", + "group": null, + "color": null, + "size": 1.38 + }, + { + "id": "FBbt_00007392", + "label": "projection neuron", + "group": null, + "color": null, + "size": 1.22 + }, + { + "id": "FBbt_00007422", + "label": "antennal lobe projection neuron", + "group": null, + "color": null, + "size": 1.21 + }, + { + "id": "FBbt_00067123", + "label": "adult antennal lobe projection neuron", + "group": null, + "color": null, + "size": 1.21 + }, + { + "id": "FBbt_00051493", + "label": "local neuron", + "group": null, + "color": null, + "size": 1.15 + }, + { + "id": "FBbt_00052874", + "label": "antennal lobe local neuron", + "group": null, + "color": null, + "size": 1.15 + }, + { + "id": "FBbt_00007390", + "label": "adult antennal lobe local neuron", + "group": null, + "color": null, + "size": 1.15 + }, + { + "id": "FBbt_00007384", + "label": "multiglomerular antennal lobe projection neuron", + "group": null, + "color": null, + "size": 1.14 + }, + { + "id": "FBbt_00007441", + "label": "adult multiglomerular antennal lobe projection neuron", + "group": null, + "color": null, + "size": 1.14 + }, + { + "id": "FBbt_00049427", + "label": "adult lateral horn input neuron", + "group": null, + "color": null, + "size": 1.12 + }, + { + "id": "FBbt_00053398", + "label": "adult antennal lobe projection neuron to lateral horn", + "group": null, + "color": null, + "size": 1.12 + }, + { + "id": "FBbt_00053397", + "label": "antennal lobe projection neuron to mushroom body", + "group": null, + "color": null, + "size": 1.11 + }, + { + "id": "FBbt_00007394", + "label": "adult local interneuron of the lateral ALl1 neuroblast", + "group": null, + "color": null, + "size": 1.11 + } + ], + "edges": [ + { + "source": "FBbt_00005918", + "target": "FBbt_00005106", + "label": "78601", + "weight": 78601 + }, + { + "source": "FBbt_00005918", + "target": "FBbt_00047095", + "label": "77005", + "weight": 77005 + }, + { + "source": "FBbt_00005918", + "target": "FBbt_00059271", + "label": "75663", + "weight": 75663 + }, + { + "source": "FBbt_00005918", + "target": "FBbt_00007392", + "label": "42907", + "weight": 42907 + }, + { + "source": "FBbt_00005918", + "target": "FBbt_00007422", + "label": "41794", + "weight": 41794 + }, + { + "source": "FBbt_00005918", + "target": "FBbt_00067123", + "label": "41646", + "weight": 41646 + }, + { + "source": "FBbt_00005918", + "target": "FBbt_00051493", + "label": "30596", + "weight": 30596 + }, + { + "source": "FBbt_00005918", + "target": "FBbt_00052874", + "label": "30596", + "weight": 30596 + }, + { + "source": "FBbt_00005918", + "target": "FBbt_00007390", + "label": "30271", + "weight": 30271 + }, + { + "source": "FBbt_00005918", + "target": "FBbt_00007384", + "label": "27881", + "weight": 27881 + }, + { + "source": "FBbt_00005918", + "target": "FBbt_00007441", + "label": "27735", + "weight": 27735 + }, + { + "source": "FBbt_00005918", + "target": "FBbt_00049427", + "label": "24184", + "weight": 24184 + }, + { + "source": "FBbt_00005918", + "target": "FBbt_00053398", + "label": "24184", + "weight": 24184 + }, + { + "source": "FBbt_00005918", + "target": "FBbt_00053397", + "label": "22043", + "weight": 22043 + }, + { + "source": "FBbt_00005918", + "target": "FBbt_00007394", + "label": "21470", + "weight": 21470 + } + ] + } + ], + "quality_flags": { + "has_tool_status": true, + "no_tool_factual_answer": false, + "tool_claim_without_tool": false, + "disambiguation_only_answer": false, + "investigation_plan_answer": false, + "not_verified_or_no_results_answer": false, + "graph_failure_mentioned": false, + "missing_required_graph": false, + "used_data_resource": false, + "response_chars": 1718, + "status_count": 13 + } + }, + { + "attempt_index": 29, + "task_index": 29, + "task_id": "T4.6", + "tier": 4, + "title": "Data availability survey", + "question": "I'm interested in studying the subesophageal zone (SEZ). How well-characterised is this region in VFB? What neuron types are annotated, what connectomics data is available, and what genetic tools exist for SEZ neurons?", + "requires_graph": false, + "min_graphs": 0, + "repetition": 1, + "duration_ms": 200594, + "status_messages": [ + { + "message": "Thinking...", + "phase": "llm" + }, + { + "message": "Planning the answer", + "phase": "llm" + }, + { + "message": "Resolving 1 term in VFB", + "phase": "mcp" + }, + { + "message": "Reading VFB term info", + "phase": "mcp" + }, + { + "message": "Finding genetic tools", + "phase": "mcp" + }, + { + "message": "Querying VFB", + "phase": "mcp" + }, + { + "message": "Querying VFB", + "phase": "mcp" + }, + { + "message": "Checking the answer is covered", + "phase": "llm" + }, + { + "message": "Querying VFB", + "phase": "mcp" + }, + { + "message": "Querying VFB", + "phase": "mcp" + }, + { + "message": "Querying VFB", + "phase": "mcp" + }, + { + "message": "Checking the answer is covered", + "phase": "llm" + }, + { + "message": "Writing the answer", + "phase": "llm" + } + ], + "event_count": 227, + "ok": true, + "request_id": "08f9b5d3-ee47-412f-919a-91c37e970279", + "response_id": "chatcmpl-cd3acb0aead0ff3b9d2488131bbbe2a0", + "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 and genetic tools 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 have synaptic terminals in the subesophageal zone, such as intrinsic antennal mechanosensory and motor center neurons and [AMMC-VLP](https://www.virtualflybrain.org/reports/FBbt_00111354 \"Open AMMC-VLP in Virtual Fly Brain\") neurons. Additionally, [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 have presynaptic terminals in the subesophageal zone, including [AMMC-Bi1](https://www.virtualflybrain.org/reports/FBbt_00111465 \"Open AMMC-Bi1 in Virtual Fly Brain\"), [AMMC-Bi4](https://www.virtualflybrain.org/reports/FBbt_00111468 \"Open AMMC-Bi4 in Virtual Fly Brain\"), and [AMMC-Bi8](https://www.virtualflybrain.org/reports/FBbt_00111472 \"Open AMMC-Bi8 in Virtual Fly Brain\") neurons. There are also genetic tools available for subesophageal zone neurons, including 4,205 GAL4 drivers and binary/intersectional drivers, such as P{GMR12D05-GAL4} and P{GMR16C05-GAL4} 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": 1782, + "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": 15750, + "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 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": 188, + "ok": true, + "request_id": "baa96a24-0660-46db-af32-9b7bfc313514", + "response_id": "chatcmpl-5fb9eed861935601e114d026a35b78d9", + "images_count": 8, + "graphs_count": 1, + "response": "The [medulla](https://www.virtualflybrain.org/reports/FBbt_00003748 \"Open medulla in Virtual Fly Brain\") has various connections, including [471](https://v2.virtualflybrain.org/org.geppetto.frontend/geppetto?q=FBbt_00003748,NeuronsPartHere \"Run in VFB: Neurons with some part in medulla\") neuron types with some part in it, [464](https://v2.virtualflybrain.org/org.geppetto.frontend/geppetto?q=FBbt_00003748,NeuronsSynaptic \"Run in VFB: Neurons with synaptic terminals in medulla\") neuron types with synaptic terminals in it, [262](https://v2.virtualflybrain.org/org.geppetto.frontend/geppetto?q=FBbt_00003748,NeuronsPresynapticHere \"Run in VFB: Neurons with presynaptic terminals in medulla\") neuron types with presynaptic terminals in it, and [333](https://v2.virtualflybrain.org/org.geppetto.frontend/geppetto?q=FBbt_00003748,NeuronsPostsynapticHere \"Run in VFB: Neurons with postsynaptic terminals in medulla\") neuron types with postsynaptic terminals in it. Neurons with presynaptic terminals in the medulla include [Dm8b](https://www.virtualflybrain.org/reports/FBbt_00110069 \"Open Dm8b in Virtual Fly Brain\"), [PS128](https://www.virtualflybrain.org/reports/FBbt_20001883 \"Open PS128 in Virtual Fly Brain\"), [Mi10b](https://www.virtualflybrain.org/reports/FBbt_00110070 \"Open Mi10b in Virtual Fly Brain\"), [CB3849](https://www.virtualflybrain.org/reports/FBbt_20007264 \"Open CB3849 in Virtual Fly Brain\"), [TmY-ds](https://www.virtualflybrain.org/reports/FBbt_00052643 \"Open TmY-ds in Virtual Fly Brain\"), [Dm7](https://www.virtualflybrain.org/reports/FBbt_00003774 \"Open Dm7 in Virtual Fly Brain\"), Mi6, Mi8, Tm10, Tm13, Tm14, and Tm18. Neurons with postsynaptic terminals in the medulla include CB3849, TmY-ds, [Y6](https://www.virtualflybrain.org/reports/FBbt_00007580 \"Open Y6 in Virtual Fly Brain\"), [extra l-LNv neuron](https://www.virtualflybrain.org/reports/FBbt_00047183 \"Open extra l-LNv neuron in Virtual Fly Brain\"), Dm7, Mi6, Mi8, Tm10, Tm13, Tm14, Tm18, and Tm19.", + "graphs": [ + { + "type": "basic_graph", + "version": 1, + "title": "medulla region connectivity preview", + "directed": true, + "layout": "radial", + "nodes": [ + { + "id": "FBbt_00003748", + "label": "medulla", + "group": "queried region", + "color": null, + "size": 2.4 + }, + { + "id": "FBbt_20007264", + "label": "CB3849", + "group": "presynaptic and postsynaptic neuron", + "color": null, + "size": 1.15 + }, + { + "id": "FBbt_00110069", + "label": "Dm8b", + "group": "presynaptic neuron", + "color": null, + "size": 1.15 + }, + { + "id": "FBbt_00110070", + "label": "Mi10b", + "group": "presynaptic neuron", + "color": null, + "size": 1.15 + }, + { + "id": "FBbt_20001883", + "label": "PS128", + "group": "presynaptic neuron", + "color": null, + "size": 1.15 + }, + { + "id": "FBbt_00052643", + "label": "TmY-ds", + "group": "presynaptic and postsynaptic neuron", + "color": null, + "size": 1.15 + }, + { + "id": "FBbt_00003774", + "label": "Dm7", + "group": "postsynaptic neuron", + "color": null, + "size": 1.15 + }, + { + "id": "FBbt_00007580", + "label": "Y6", + "group": "postsynaptic neuron", + "color": null, + "size": 1.15 + }, + { + "id": "FBbt_00047183", + "label": "extra l-LNv neuron", + "group": "postsynaptic neuron", + "color": null, + "size": 1.15 + } + ], + "edges": [ + { + "source": "FBbt_20007264", + "target": "FBbt_00003748", + "label": "presynaptic sites in medulla", + "weight": 0 + }, + { + "source": "FBbt_00110069", + "target": "FBbt_00003748", + "label": "presynaptic sites in medulla", + "weight": 0 + }, + { + "source": "FBbt_00110070", + "target": "FBbt_00003748", + "label": "presynaptic sites in medulla", + "weight": 0 + }, + { + "source": "FBbt_20001883", + "target": "FBbt_00003748", + "label": "presynaptic sites in medulla", + "weight": 0 + }, + { + "source": "FBbt_00052643", + "target": "FBbt_00003748", + "label": "presynaptic sites in medulla", + "weight": 0 + }, + { + "source": "FBbt_00003748", + "target": "FBbt_20007264", + "label": "postsynaptic sites in medulla", + "weight": 0 + }, + { + "source": "FBbt_00003748", + "target": "FBbt_00003774", + "label": "postsynaptic sites in medulla", + "weight": 0 + }, + { + "source": "FBbt_00003748", + "target": "FBbt_00052643", + "label": "postsynaptic sites in medulla", + "weight": 0 + }, + { + "source": "FBbt_00003748", + "target": "FBbt_00007580", + "label": "postsynaptic sites in medulla", + "weight": 0 + }, + { + "source": "FBbt_00003748", + "target": "FBbt_00047183", + "label": "postsynaptic sites in medulla", + "weight": 0 + } + ] + } + ], + "quality_flags": { + "has_tool_status": true, + "no_tool_factual_answer": false, + "tool_claim_without_tool": false, + "disambiguation_only_answer": false, + "investigation_plan_answer": false, + "not_verified_or_no_results_answer": false, + "graph_failure_mentioned": false, + "missing_required_graph": false, + "used_data_resource": false, + "response_chars": 1984, + "status_count": 10 + } + }, + { + "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": 5779, + "status_messages": [ + { + "message": "Thinking...", + "phase": "llm" + }, + { + "message": "Planning (direct lookup)", + "phase": "llm" + }, + { + "message": "Resolving 1 term in VFB", + "phase": "mcp" + }, + { + "message": "Reading VFB term info", + "phase": "mcp" + }, + { + "message": "Checking the literature", + "phase": "mcp" + }, + { + "message": "Checking the answer is covered", + "phase": "llm" + }, + { + "message": "Writing the answer", + "phase": "llm" + } + ], + "event_count": 42, + "ok": true, + "request_id": "c222703d-ee80-4563-8ab9-4f79429d8137", + "response_id": "chatcmpl-73bef331360ddcca5446898ced704c22", + "images_count": 0, + "graphs_count": 0, + "response": "Virtual Fly Brain is an interactive tool for neurobiologists to explore the detailed neuroanatomy, neuron connectivity, and gene expression of Drosophila melanogaster.", + "quality_flags": { + "has_tool_status": true, + "no_tool_factual_answer": false, + "tool_claim_without_tool": false, + "disambiguation_only_answer": false, + "investigation_plan_answer": false, + "not_verified_or_no_results_answer": false, + "graph_failure_mentioned": false, + "missing_required_graph": false, + "used_data_resource": false, + "response_chars": 167, + "status_count": 7 + } + }, + { + "attempt_index": 32, + "task_index": 32, + "task_id": "D2", + "tier": 6, + "title": "Citation", + "question": "How should I cite Virtual Fly Brain in a publication?", + "requires_graph": false, + "min_graphs": 0, + "repetition": 1, + "duration_ms": 38559, + "status_messages": [ + { + "message": "Thinking...", + "phase": "llm" + }, + { + "message": "Planning the answer", + "phase": "llm" + }, + { + "message": "Reading VFB documentation", + "phase": "mcp" + }, + { + "message": "Checking the literature", + "phase": "mcp" + }, + { + "message": "Checking the answer is covered", + "phase": "llm" + }, + { + "message": "Writing the answer", + "phase": "llm" + } + ], + "event_count": 23, + "ok": true, + "request_id": "cfa5410f-736e-4d97-851b-176d7e95193a", + "response_id": "chatcmpl-44938f342d32253639bd1e4a9c0c8107", + "images_count": 0, + "graphs_count": 0, + "response": "To cite Virtual Fly Brain in a publication, use the following citation formats:\n\n```\nAPA\nCourt, R., Costa, M., Pilgrim, C., Millburn, G., Holmes, A., McLachlan, A., Larkin, A., Matentzoglu, N., Kir, H., Parkinson, H., Brown, N. H., O’Kane, C. J., Armstrong, J. D., Jefferis, G. S. X. E., & Osumi-Sutherland, D. (2023). Virtual Fly Brain—An interactive atlas of the Drosophila nervous system. Frontiers in Physiology, 14. https://doi.org/10.3389/fphys.2023.1076533\n\nMLA\nCourt, Robert, et al. “Virtual Fly Brain—An Interactive Atlas of the Drosophila Nervous System.” Frontiers in Physiology, vol. 14, 2023, https://doi.org/10.3389/fphys.2023.1076533.\n\nChicago\nCourt, Robert, Costa, Marta, Pilgrim, Clare, Millburn, Gillian, Holmes, Alex, McLachlan, Alex, Larkin, Aoife et al. “Virtual Fly Brain—An interactive atlas of the Drosophila nervous system.” Frontiers in Physiology 14, (2023). https://doi.org/10.3389/fphys.2023.1076533.\n\nBibTeX\n@article{Court_2023,\nauthor = {Robert Court and Marta Costa and Clare Pilgrim and Gillian Millburn and Alex Holmes and Alex McLachlan and Aoife Larkin and Nicolas Matentzoglu and Huseyin Kir and Helen Parkinson and Nicolas H. Brown and Cahir J. O'Kane and J. Douglas Armstrong and Gregory S. X. E. Jefferis and David Osumi-Sutherland},\ntitle = \"{Virtual Fly Brain—An interactive atlas of the Drosophila nervous system}\",\njournal = {Frontiers in Physiology},\nvolume = {14},\npublisher = {Frontiers Media {SA}},\nyear = {2023},\nmonth = {jan},\nabstract = \"{As a model organism, Drosophila is uniquely placed to contribute to our understanding of how brains control complex behavior. Not only does it have complex adaptive behaviors, but also a uniquely powerful genetic toolkit, increasingly complete dense connectomic maps of the central nervous system and a rapidly growing set of transcriptomic profiles of cell types. But this also poses a challenge: Given the massive amounts of VFB evidence, how are researchers to Find, Access, Integrate and Reuse (FAIR) relevant data in order to develop an integrated anatomical and molecular picture of circuits, inform hypothesis generation, and find reagents for experiments to test these hypotheses? The Virtual Fly Brain (virtualflybrain.org) web application & API provide a solution to this problem, using FAIR principles to integrate 3D images of neurons and brain regions, connectomics, transcriptomics and reagent expression data covering the whole CNS in both larva and adult. Users can search for neurons, neuroanatomy and reagents by name, location, or connectivity, via text search, clicking on 3D images, search-by-image, and queries by type (e.g., dopaminergic neuron) or properties (e.g., synaptic input in the antennal lobe). Returned results include cross-registered 3D images that can be explored in linked 2D and 3D browsers or downloaded under open licenses, and extensive descriptions of cell types and regions curated from the literature. These solutions are potentially extensible to cover similar atlasing and data integration challenges in vertebrates.}\",\nissn = {1664-042X},\ndoi = {10.3389/fphys.2023.1076533},\nurl = {https://doi.org/10.3389/fphys.2023.1076533},\n}\n```", + "quality_flags": { + "has_tool_status": true, + "no_tool_factual_answer": false, + "tool_claim_without_tool": false, + "disambiguation_only_answer": false, + "investigation_plan_answer": false, + "not_verified_or_no_results_answer": false, + "graph_failure_mentioned": false, + "missing_required_graph": false, + "used_data_resource": false, + "response_chars": 3170, + "status_count": 6 + } + }, + { + "attempt_index": 33, + "task_index": 33, + "task_id": "D3", + "tier": 6, + "title": "Funding", + "question": "Who funds Virtual Fly Brain and since when?", + "requires_graph": false, + "min_graphs": 0, + "repetition": 1, + "duration_ms": 5381, + "status_messages": [ + { + "message": "Thinking...", + "phase": "llm" + }, + { + "message": "Planning the answer", + "phase": "llm" + }, + { + "message": "Reading VFB documentation", + "phase": "mcp" + }, + { + "message": "Checking VFB documentation", + "phase": "mcp" + }, + { + "message": "Checking the answer is covered", + "phase": "llm" + }, + { + "message": "Writing the answer", + "phase": "llm" + } + ], + "event_count": 28, + "ok": true, + "request_id": "0ec22e1a-bd6e-439a-a201-5196a2d28281", + "response_id": "chatcmpl-2e57b858351c29e3e366f60eaf2af986", + "images_count": 0, + "graphs_count": 0, + "response": "Virtual Fly Brain has been supported by grants from multiple UK research councils and charitable foundations since 2009.", + "quality_flags": { + "has_tool_status": true, + "no_tool_factual_answer": false, + "tool_claim_without_tool": false, + "disambiguation_only_answer": false, + "investigation_plan_answer": false, + "not_verified_or_no_results_answer": false, + "graph_failure_mentioned": false, + "missing_required_graph": false, + "used_data_resource": false, + "response_chars": 120, + "status_count": 6 + } + }, + { + "attempt_index": 34, + "task_index": 34, + "task_id": "D4", + "tier": 6, + "title": "Policies / accessibility", + "question": "What is Virtual Fly Brain's accessibility statement?", + "requires_graph": false, + "min_graphs": 0, + "repetition": 1, + "duration_ms": 4759, + "status_messages": [ + { + "message": "Thinking...", + "phase": "llm" + }, + { + "message": "Planning (direct lookup)", + "phase": "llm" + }, + { + "message": "Resolving 1 term in VFB", + "phase": "mcp" + }, + { + "message": "Reading VFB term info", + "phase": "mcp" + }, + { + "message": "Checking the literature", + "phase": "mcp" + }, + { + "message": "Checking the answer is covered", + "phase": "llm" + }, + { + "message": "Writing the answer", + "phase": "llm" + } + ], + "event_count": 42, + "ok": true, + "request_id": "be25e75d-3641-4866-83c2-142ac8a5e515", + "response_id": "chatcmpl-96e54583ecaa645e9d8e192d8d3ae846", + "images_count": 0, + "graphs_count": 0, + "response": "Virtual Fly Brain is partially compliant with the Web Content Accessibility Guidelines (WCAG) 2.2 AA standard, with known accessibility limitations and non-compliances listed.", + "quality_flags": { + "has_tool_status": true, + "no_tool_factual_answer": false, + "tool_claim_without_tool": false, + "disambiguation_only_answer": false, + "investigation_plan_answer": false, + "not_verified_or_no_results_answer": false, + "graph_failure_mentioned": false, + "missing_required_graph": false, + "used_data_resource": false, + "response_chars": 175, + "status_count": 7 + } + }, + { + "attempt_index": 35, + "task_index": 35, + "task_id": "D5", + "tier": 6, + "title": "Contact / contribute", + "question": "How do I report a problem or contribute data to Virtual Fly Brain?", + "requires_graph": false, + "min_graphs": 0, + "repetition": 1, + "duration_ms": 7768, + "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": 85, + "ok": true, + "request_id": "791d0f94-82e3-42da-b552-1f417b65f9ee", + "response_id": "chatcmpl-1231ca939d2b4d503d8fe21e03bfef83", + "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 us page. For help with using Virtual Fly Brain, you can use the public support forum at support@virtualflybrain.org. Bug reports and feature requests can be submitted through GitHub Issues. For data contributions or private inquiries, you can email data@virtualflybrain.org.", + "quality_flags": { + "has_tool_status": true, + "no_tool_factual_answer": false, + "tool_claim_without_tool": false, + "disambiguation_only_answer": false, + "investigation_plan_answer": false, + "not_verified_or_no_results_answer": false, + "graph_failure_mentioned": false, + "missing_required_graph": false, + "used_data_resource": false, + "response_chars": 390, + "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": 7600, + "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": 87, + "ok": true, + "request_id": "b9d31d3d-d7bf-439c-9241-e51c91d3b92c", + "response_id": "chatcmpl-13f4581d5802a21c01f0526725f680a4", + "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 scene. Use the zoom icons or scroll with the mouse to zoom in or out. The camera icon starts or stops a rotation animation of the scene, and the sphere icon toggles wireframes on or off.", + "quality_flags": { + "has_tool_status": true, + "no_tool_factual_answer": false, + "tool_claim_without_tool": false, + "disambiguation_only_answer": false, + "investigation_plan_answer": false, + "not_verified_or_no_results_answer": false, + "graph_failure_mentioned": false, + "missing_required_graph": false, + "used_data_resource": false, + "response_chars": 357, + "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": 10175, + "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": "eec71746-93cb-4c5b-ad50-759e48829558", + "response_id": "chatcmpl-a7c3af23535e4d99ed61cc6f04b65763", + "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": 6658, + "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": 62, + "ok": true, + "request_id": "e37f7ed7-36cc-42b9-9a6c-224e1ee6fae1", + "response_id": "chatcmpl-0dc695b143b2f169a9c1beb0112393fe", + "images_count": 0, + "graphs_count": 0, + "response": "NBLAST is a method used to calculate similarity scores, which represent the morphological similarity between neurons or expression patterns. The similarity scores are calculated using NBLAST. An NBLAST similarity score means a measure of the morphological similarity between neurons or 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": 306, + "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": 6488, + "status_messages": [ + { + "message": "Thinking...", + "phase": "llm" + }, + { + "message": "Planning the answer", + "phase": "llm" + }, + { + "message": "Resolving 1 term in VFB", + "phase": "mcp" + }, + { + "message": "Reading VFB documentation", + "phase": "mcp" + }, + { + "message": "Checking the literature", + "phase": "mcp" + }, + { + "message": "Checking the answer is covered", + "phase": "llm" + }, + { + "message": "Writing the answer", + "phase": "llm" + } + ], + "event_count": 26, + "ok": true, + "request_id": "d6ebd064-6c54-4350-9058-5340eb82cb14", + "response_id": "chatcmpl-5111d67563b791723c1280fd9fc9e100", + "images_count": 1, + "graphs_count": 0, + "response": "Confidence values are represented by the property key \"confidence_value\" in the PDB.", + "quality_flags": { + "has_tool_status": true, + "no_tool_factual_answer": false, + "tool_claim_without_tool": false, + "disambiguation_only_answer": false, + "investigation_plan_answer": false, + "not_verified_or_no_results_answer": false, + "graph_failure_mentioned": false, + "missing_required_graph": false, + "used_data_resource": false, + "response_chars": 84, + "status_count": 7 + } + }, + { + "attempt_index": 40, + "task_index": 40, + "task_id": "D10", + "tier": 6, + "title": "Concepts: bridging registrations", + "question": "What are bridging registrations between brain templates in VFB?", + "requires_graph": false, + "min_graphs": 0, + "repetition": 1, + "duration_ms": 7610, + "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": 38, + "ok": true, + "request_id": "695868cf-541f-427a-a945-b0d83993943b", + "response_id": "chatcmpl-b66e022ab14bed35d05aa1c62263c592", + "images_count": 8, + "graphs_count": 0, + "response": "Bridging registrations between brain templates in VFB could not be matched. The documentation describes transformations to map between different canonical Drosophila templates.", + "quality_flags": { + "has_tool_status": true, + "no_tool_factual_answer": false, + "tool_claim_without_tool": false, + "disambiguation_only_answer": false, + "investigation_plan_answer": false, + "not_verified_or_no_results_answer": false, + "graph_failure_mentioned": false, + "missing_required_graph": false, + "used_data_resource": false, + "response_chars": 176, + "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": 4141, + "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": 22, + "ok": true, + "request_id": "75846814-39dd-4e5a-997c-a587dc782a0d", + "response_id": "chatcmpl-259c16f5f82cae8b21eaa2c0f3d8c68f", + "images_count": 0, + "graphs_count": 0, + "response": "Virtual Fly Brain holds imaging data types including skeleton, mesh, and volume.", + "quality_flags": { + "has_tool_status": true, + "no_tool_factual_answer": false, + "tool_claim_without_tool": false, + "disambiguation_only_answer": false, + "investigation_plan_answer": false, + "not_verified_or_no_results_answer": false, + "graph_failure_mentioned": false, + "missing_required_graph": false, + "used_data_resource": false, + "response_chars": 80, + "status_count": 6 + } + }, + { + "attempt_index": 42, + "task_index": 42, + "task_id": "D12", + "tier": 6, + "title": "Release changelog", + "question": "What was included in the latest Virtual Fly Brain release?", + "requires_graph": false, + "min_graphs": 0, + "repetition": 1, + "duration_ms": 5472, + "status_messages": [ + { + "message": "Thinking...", + "phase": "llm" + }, + { + "message": "Planning the answer", + "phase": "llm" + }, + { + "message": "Reading VFB term info", + "phase": "mcp" + }, + { + "message": "Checking the literature", + "phase": "mcp" + }, + { + "message": "Checking the answer is covered", + "phase": "llm" + }, + { + "message": "Writing the answer", + "phase": "llm" + } + ], + "event_count": 46, + "ok": true, + "request_id": "75a96c23-c408-494b-ab86-3b79a2326fad", + "response_id": "chatcmpl-6014f7992aea61d9c536653edee3478c", + "images_count": 0, + "graphs_count": 0, + "response": "The latest Virtual Fly Brain release includes various data and software improvements, such as new images and annotations, including confocal microscopy images, EM reconstructed neurons, and other datasets from different researchers and labs.", + "quality_flags": { + "has_tool_status": true, + "no_tool_factual_answer": false, + "tool_claim_without_tool": false, + "disambiguation_only_answer": false, + "investigation_plan_answer": false, + "not_verified_or_no_results_answer": false, + "graph_failure_mentioned": false, + "missing_required_graph": false, + "used_data_resource": false, + "response_chars": 241, + "status_count": 6 + } + }, + { + "attempt_index": 43, + "task_index": 43, + "task_id": "D13", + "tier": 6, + "title": "API: VFB-connect (Python)", + "question": "How do I install and get started with VFB-connect in Python?", + "requires_graph": false, + "min_graphs": 0, + "repetition": 1, + "duration_ms": 7238, + "status_messages": [ + { + "message": "Thinking...", + "phase": "llm" + }, + { + "message": "Planning the answer", + "phase": "llm" + }, + { + "message": "Reading VFB documentation", + "phase": "mcp" + }, + { + "message": "Checking the literature", + "phase": "mcp" + }, + { + "message": "Checking the answer is covered", + "phase": "llm" + }, + { + "message": "Writing the answer", + "phase": "llm" + } + ], + "event_count": 58, + "ok": true, + "request_id": "c02cb76f-cc5f-432a-a579-42d041ab4e4f", + "response_id": "chatcmpl-16efc1b88c2c38565bc33e467c0c841d", + "images_count": 0, + "graphs_count": 0, + "response": "To install and get started with VFB-connect in Python, ensure you have the VFBConnect library installed using the recommended Python version 3.10.14. Install the library by running\n```\npip install vfb-connect\n```\nThen, import the VFBConnect library using\n```\nfrom import vfb\n```", + "quality_flags": { + "has_tool_status": true, + "no_tool_factual_answer": false, + "tool_claim_without_tool": false, + "disambiguation_only_answer": false, + "investigation_plan_answer": false, + "not_verified_or_no_results_answer": false, + "graph_failure_mentioned": false, + "missing_required_graph": false, + "used_data_resource": false, + "response_chars": 278, + "status_count": 6 + } + }, + { + "attempt_index": 44, + "task_index": 44, + "task_id": "D14", + "tier": 6, + "title": "API: REST endpoints", + "question": "How can I query Virtual Fly Brain programmatically using the SOLR or Owlery API?", + "requires_graph": false, + "min_graphs": 0, + "repetition": 1, + "duration_ms": 9668, + "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": 103, + "ok": true, + "request_id": "82eacb76-b11f-49e1-a805-808b7e416d5c", + "response_id": "chatcmpl-752cbe927c99546656e710f11b9f318c", + "images_count": 0, + "graphs_count": 0, + "response": "To query Virtual Fly Brain programmatically, you can use the Owlery API, which provides OWL reasoning services for VFB's ontologies. The API endpoint is https://owl.virtualflybrain.org/, and it supports various query operations, including Description Logic (DL) queries, SPARQL queries with OWL reasoning, and access to multiple knowledgebases. Alternatively, the SOLR Search API provides fast text search and autocomplete functionality for VFB entities, datasets, and publications.", + "quality_flags": { + "has_tool_status": true, + "no_tool_factual_answer": false, + "tool_claim_without_tool": false, + "disambiguation_only_answer": false, + "investigation_plan_answer": false, + "not_verified_or_no_results_answer": false, + "graph_failure_mentioned": false, + "missing_required_graph": false, + "used_data_resource": false, + "response_chars": 482, + "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": 12547, + "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": 47, + "ok": true, + "request_id": "b7a9d6fd-38bd-4fab-a2be-2587c32015df", + "response_id": "chatcmpl-359cef998dd57591b8af7bbe50c5ae64", + "images_count": 0, + "graphs_count": 0, + "response": "To explore Virtual Fly Brain neurons, you can use the following steps:\n```\nimport pymaid\nimport navis\n\nnavis.set_pbars(jupyter=False)\npymaid.set_pbars(jupyter=False)\n\n# Connect to the VFB CATMAID server hosting the FAFB data\nrm = pymaid.connect_catmaid(server=\"https://fafb.catmaid.virtualflybrain.org/\", api_token=None, max_threads=10)\n\n# Test call to see if connection works\nprint(f'Server is running CATMAID version {rm.catmaid_version}')\n```\nVFB's documentation does not appear to cover Navis. 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": 550, + "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": 13017, + "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": 142, + "ok": true, + "request_id": "c589b194-3841-4a71-92c3-3f4e6276cdbe", + "response_id": "chatcmpl-f143a138b6559a3ebc5e159c0ba1ae37", + "images_count": 0, + "graphs_count": 0, + "response": "To use the Virtual Fly Brain Model Context Protocol (MCP) tool, follow these steps: Open Claude Desktop, go to Settings, navigate to the MCP section, and add a new MCP server with the provided settings. Alternatively, use the Configuration JSON or Claude Code setup methods. For GitHub Copilot setup, open VS Code, search for \"MCP\" in the settings, and add the server URL. For other MCP-compatible clients, use the provided JSON configuration. To test the connection, ask your AI assistant questions like \"Get information about the neuron \" or \"Search for terms related to medulla in the fly brain\".\n\n```json\n{\n\"mcpServers\": {\n \"virtual-fly-brain\": {\n \"type\": \"http\",\n \"url\": \"https://vfb3-mcp.virtualflybrain.org\",\n \"tools\": [\"*\"]\n }\n}\n}\n```", + "quality_flags": { + "has_tool_status": true, + "no_tool_factual_answer": false, + "tool_claim_without_tool": false, + "disambiguation_only_answer": false, + "investigation_plan_answer": false, + "not_verified_or_no_results_answer": false, + "graph_failure_mentioned": false, + "missing_required_graph": false, + "used_data_resource": false, + "response_chars": 742, + "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": 5380, + "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": "415a3f24-421e-4b89-8b19-ece9a2589384", + "response_id": "chatcmpl-9147aba576cff359bb9c7aa883155f2b", + "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. For more information, searching virtualflybrain.org may be helpful.", + "quality_flags": { + "has_tool_status": true, + "no_tool_factual_answer": false, + "tool_claim_without_tool": false, + "disambiguation_only_answer": false, + "investigation_plan_answer": false, + "not_verified_or_no_results_answer": false, + "graph_failure_mentioned": false, + "missing_required_graph": false, + "used_data_resource": false, + "response_chars": 182, + "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": 7382, + "status_messages": [ + { + "message": "Thinking...", + "phase": "llm" + }, + { + "message": "Planning the answer", + "phase": "llm" + }, + { + "message": "Resolving 1 term in VFB", + "phase": "mcp" + }, + { + "message": "Reading VFB documentation", + "phase": "mcp" + }, + { + "message": "Checking VFB documentation", + "phase": "mcp" + }, + { + "message": "Checking the answer is covered", + "phase": "llm" + }, + { + "message": "Writing the answer", + "phase": "llm" + } + ], + "event_count": 40, + "ok": true, + "request_id": "335a19bf-4c4c-4fc4-97e6-f4a987a7d9c9", + "response_id": "chatcmpl-93bc5bd92c779d18ab25aa299c878fbf", + "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": 7169, + "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": 48, + "ok": true, + "request_id": "128d4a6c-8971-456b-bf3f-0e2a853bb99a", + "response_id": "chatcmpl-32fe93f64693d45a66d5d58ab3aaef27", + "images_count": 0, + "graphs_count": 0, + "response": "Materials from the Virtual Fly Brain \"Hacking the connectome\" workshop include a recorded introduction session and workshop notebooks that demonstrate how to use available tools to explore and analyze published connectomes on 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": 230, + "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": 10798, + "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": "Checking VFB documentation", + "phase": "mcp" + }, + { + "message": "Checking the answer is covered", + "phase": "llm" + }, + { + "message": "Writing the answer", + "phase": "llm" + } + ], + "event_count": 85, + "ok": true, + "request_id": "503b033f-7eba-4ae3-9298-d800003ac274", + "response_id": "chatcmpl-66cae95be1a0acfe3f5a534958febfad", + "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 being 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": 313, + "status_count": 8 + } + }, + { + "attempt_index": 51, + "task_index": 51, + "task_id": "D21", + "tier": 6, + "title": "Anatomy teaching diagrams", + "question": "Is there a circuit diagram of the mushroom body available on Virtual Fly Brain?", + "requires_graph": false, + "min_graphs": 0, + "repetition": 1, + "duration_ms": 7144, + "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": "19ac5531-042b-467b-90b9-d6453edde63a", + "response_id": "chatcmpl-7e82d996feb840909156ac781a584735", + "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": 11007, + "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": 5384, + "ok": true, + "response": "The [medulla](https://www.virtualflybrain.org/reports/FBbt_00003748 \"Open medulla in Virtual Fly Brain\") is the second optic neuropil, sandwiched between the lamina and the lobula complex. It is divided into 10 layers: layers 1-6 make up the outer medulla, the seventh layer exhibits a distinct architecture, and layers 8-10 make up the inner medulla.", + "followons": [ + { + "id": "FBbt_00003748", + "query_type": "ImagesNeurons", + "query": "Which neuron images have a part in the medulla?" + }, + { + "id": "FBbt_00003748", + "query_type": "TransgeneExpressionHere", + "query": "Which driver lines label the medulla?" + }, + { + "id": "FBbt_00003748", + "query_type": "NeuronsPartHere", + "query": "Which neurons have part of their arbour in the medulla?" + }, + { + "id": "FBbt_00003748", + "query_type": "NeuronsSynaptic", + "query": "Which neurons have synaptic terminals in the medulla?" + }, + { + "id": "FBbt_00003748", + "query_type": "NeuronsPostsynapticHere", + "query": "Which neurons receive output from the medulla?" + }, + { + "id": "FBbt_00003748", + "query_type": "NeuronsPresynapticHere", + "query": "Which neurons provide input to the medulla?" + } + ], + "context_terms": [ + { + "id": "FBbt_00003748", + "label": "medulla" + } + ], + "reproduction": { + "ids": [ + { + "id": "FBbt_00003748", + "label": "medulla" + } + ], + "calls": [], + "unmapped": [] + }, + "status_count": 6, + "problems": [] + }, + { + "turn": 2, + "question": "Which neurons receive output from it?", + "focus": null, + "clicked": null, + "duration_ms": 5623, + "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": "5f982228-cc05-4505-b089-ac1a4e665f4e", + "response_id": "chatcmpl-479452e10a34dadccb3fdea6cc05cf1f", + "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": 5623 + } + }, + { + "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": 13581, + "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": 188, + "conversation": true, + "turns": [ + { + "turn": 1, + "question": "What is the mushroom body?", + "focus": null, + "clicked": null, + "duration_ms": 5869, + "ok": true, + "response": "The [mushroom body](https://www.virtualflybrain.org/reports/FBbt_00005801 \"Open mushroom body in Virtual Fly Brain\") is a bilaterally paired neuropil structure situated postero-dorsally in the protocerebrum that functions in olfactory associative learning and memory. It is divided into the calyx, which receives sensory interneuron afferents, the pedunculus, a thick axon bundle, and the mushroom body lobe system, which consists of a vertical branch and a medial branch and has different structures at different life stages.", + "followons": [ + { + "id": "FBbt_00005801", + "query_type": "ImagesNeurons", + "query": "Which neuron images have a part in the mushroom body?" + }, + { + "id": "FBbt_00005801", + "query_type": "TransgeneExpressionHere", + "query": "Which driver lines label the mushroom body?" + }, + { + "id": "FBbt_00005801", + "query_type": "NeuronsPartHere", + "query": "Which neurons have part of their arbour in the mushroom body?" + }, + { + "id": "FBbt_00005801", + "query_type": "NeuronsSynaptic", + "query": "Which neurons have synaptic terminals in the mushroom body?" + }, + { + "id": "FBbt_00005801", + "query_type": "NeuronsPresynapticHere", + "query": "Which neurons provide input to the mushroom body?" + }, + { + "id": "FBbt_00005801", + "query_type": "NeuronsPostsynapticHere", + "query": "Which neurons receive output from the mushroom body?" + } + ], + "context_terms": [ + { + "id": "FBbt_00005801", + "label": "mushroom body" + } + ], + "reproduction": { + "ids": [ + { + "id": "FBbt_00005801", + "label": "mushroom body" + } + ], + "calls": [], + "unmapped": [] + }, + "status_count": 6, + "problems": [] + }, + { + "turn": 2, + "question": "Which neuron images have a part in the mushroom body?", + "focus": { + "id": "FBbt_00005801", + "query_type": "ImagesNeurons" + }, + "clicked": 0, + "duration_ms": 7712, + "ok": true, + "response": "There are images of neurons with parts in the [mushroom body](https://www.virtualflybrain.org/reports/FBbt_00005801 \"Open mushroom body in Virtual Fly Brain\"). VFB records show [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, including 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": "633a63a6-49d3-44e1-9a71-a80edb97da67", + "response_id": "chatcmpl-a41b76fa334a09b9f03cc62f30a70d45", + "images_count": 8, + "graphs_count": 0, + "response": "There are images of neurons with parts in the [mushroom body](https://www.virtualflybrain.org/reports/FBbt_00005801 \"Open mushroom body in Virtual Fly Brain\"). VFB records show [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, including 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": 607, + "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": 7712 + } + }, + { + "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": 21640, + "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": 129, + "conversation": true, + "turns": [ + { + "turn": 1, + "question": "What is the fan-shaped body?", + "focus": null, + "clicked": null, + "duration_ms": 6863, + "ok": true, + "response": "The [fan-shaped body](https://www.virtualflybrain.org/reports/FBbt_00003679 \"Open fan-shaped body in Virtual Fly Brain\") is the largest synaptic neuropil domain of the adult central complex, located posterior to the ellipsoid body and anterior to the protocerebral bridge. It is composed of a rough 2-dimensional grid of layers and columns. Eight horizontal layers, numbered bottom to top, form a fan shape and can be divided into vertical columns. An additional, much narrower, 9th layer, which lacks a columnar organization, sits dorsal to layer 8. The number of columns varies for different neuronal types.", + "followons": [ + { + "id": "FBbt_00003679", + "query_type": "ImagesNeurons", + "query": "Which neuron images have a part in the fan-shaped body?" + }, + { + "id": "FBbt_00003679", + "query_type": "TransgeneExpressionHere", + "query": "Which driver lines label the fan-shaped body?" + }, + { + "id": "FBbt_00003679", + "query_type": "NeuronsPartHere", + "query": "Which neurons have part of their arbour in the fan-shaped body?" + }, + { + "id": "FBbt_00003679", + "query_type": "NeuronsSynaptic", + "query": "Which neurons have synaptic terminals in the fan-shaped body?" + }, + { + "id": "FBbt_00003679", + "query_type": "NeuronsPresynapticHere", + "query": "Which neurons provide input to the fan-shaped body?" + }, + { + "id": "FBbt_00003679", + "query_type": "NeuronsPostsynapticHere", + "query": "Which neurons receive output from the fan-shaped body?" + } + ], + "context_terms": [ + { + "id": "FBbt_00003679", + "label": "fan-shaped body" + } + ], + "reproduction": { + "ids": [ + { + "id": "FBbt_00003679", + "label": "fan-shaped body" + } + ], + "calls": [], + "unmapped": [] + }, + "status_count": 6, + "problems": [] + }, + { + "turn": 2, + "question": "What about the ellipsoid body?", + "focus": null, + "clicked": null, + "duration_ms": 6953, + "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": 7824, + "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\"); [PFL2](https://www.virtualflybrain.org/reports/FBbt_00111451 \"Open PFL2 in Virtual Fly Brain\").", + "followons": [ + { + "id": "FBbt_00003679", + "query_type": "ImagesNeurons", + "query": "Which neuron images have a part in the fan-shaped body?" + }, + { + "id": "FBbt_00003679", + "query_type": "TransgeneExpressionHere", + "query": "Which driver lines label the fan-shaped body?" + }, + { + "id": "FBbt_00003679", + "query_type": "NeuronsPartHere", + "query": "Which neurons have part of their arbour in the fan-shaped body?" + }, + { + "id": "FBbt_00003679", + "query_type": "NeuronsPresynapticHere", + "query": "Which neurons provide input to the fan-shaped body?" + }, + { + "id": "FBbt_00003679", + "query_type": "NeuronsPostsynapticHere", + "query": "Which neurons receive output from the fan-shaped body?" + }, + { + "id": "FBbt_00003679", + "query_type": "PartsOf", + "query": "What are the anatomical parts of the fan-shaped body?" + } + ], + "context_terms": [ + { + "id": "FBbt_00003679", + "label": "fan-shaped body" + }, + { + "id": "FBbt_00003678", + "label": "ellipsoid body" + } + ], + "reproduction": { + "ids": [ + { + "id": "FBbt_00003679", + "label": "fan-shaped body" + }, + { + "id": "FBbt_00003678", + "label": "ellipsoid body" + } + ], + "calls": [ + { + "id": "FBbt_00003679", + "query_type": "NeuronsSynaptic", + "fn": "get_neurons_with_synapses_in" + } + ], + "unmapped": [] + }, + "status_count": 6, + "problems": [] + } + ], + "ok": true, + "request_id": "f794d583-b672-4d03-808c-144d20685354", + "response_id": "chatcmpl-645ba501d88e173338f4ec4ba4ead57d", + "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\"); [PFL2](https://www.virtualflybrain.org/reports/FBbt_00111451 \"Open PFL2 in Virtual Fly Brain\").", + "quality_flags": { + "has_tool_status": true, + "no_tool_factual_answer": false, + "tool_claim_without_tool": false, + "disambiguation_only_answer": false, + "investigation_plan_answer": false, + "not_verified_or_no_results_answer": false, + "graph_failure_mentioned": false, + "missing_required_graph": false, + "used_data_resource": false, + "response_chars": 1313, + "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": 7824 + } + }, + { + "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": 13035, + "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": 137, + "conversation": true, + "turns": [ + { + "turn": 1, + "question": "What is a Kenyon cell?", + "focus": null, + "clicked": null, + "duration_ms": 6547, + "ok": true, + "response": "A [Kenyon cell](https://www.virtualflybrain.org/reports/FBbt_00003686 \"Open Kenyon cell in Virtual Fly Brain\") is an intrinsic neuron of the mushroom body. Kenyon cells are part of the olfactory pathway in Drosophila.", + "followons": [ + { + "id": "FBbt_00003686", + "query_type": "ListAllAvailableImages", + "query": "Which images of Kenyon cell does VFB have?" + }, + { + "id": "FBbt_00003686", + "query_type": "UpstreamClassConnectivity", + "query": "What connects to the Kenyon cell upstream?" + }, + { + "id": "FBbt_00003686", + "query_type": "DownstreamClassConnectivity", + "query": "What does the Kenyon cell connect to downstream?" + }, + { + "id": "FBbt_00003686", + "query_type": "TransgeneExpressionHere", + "query": "Which driver lines label the Kenyon cell?" + }, + { + "id": "FBbt_00003686", + "query_type": "anatScRNAseqQuery", + "query": "What single-cell transcriptomic clusters are there for Kenyon cell?" + }, + { + "id": "FBbt_00003686", + "query_type": "SubclassesOf", + "query": "What are the subtypes of the Kenyon cell?" + } + ], + "context_terms": [ + { + "id": "FBbt_00003686", + "label": "Kenyon cell" + } + ], + "reproduction": { + "ids": [ + { + "id": "FBbt_00003686", + "label": "Kenyon cell" + } + ], + "calls": [], + "unmapped": [] + }, + "status_count": 7, + "problems": [] + }, + { + "turn": 2, + "question": "What are its subtypes?", + "focus": null, + "clicked": null, + "duration_ms": 6487, + "ok": true, + "response": "The subtypes of [Kenyon cell](https://www.virtualflybrain.org/reports/FBbt_00003686 \"Open Kenyon cell in Virtual Fly Brain\") include [37](https://v2.virtualflybrain.org/org.geppetto.frontend/geppetto?q=FBbt_00003686,SubclassesOf \"Run in VFB: Subclasses of Kenyon cell\") subclasses, such as [KCab-c(i)](https://www.virtualflybrain.org/reports/FBbt_00049111 \"Open KCab-c(i) in Virtual Fly Brain\"), [KCab-c](https://www.virtualflybrain.org/reports/FBbt_00110929 \"Open KCab-c in Virtual Fly Brain\"), [KCg-m](https://www.virtualflybrain.org/reports/FBbt_00111061 \"Open KCg-m in Virtual Fly Brain\"), [Kenyon cell of main calyx](https://www.virtualflybrain.org/reports/FBbt_00047926 \"Open Kenyon cell of main calyx in Virtual Fly Brain\"), and [gamma Kenyon cell](https://www.virtualflybrain.org/reports/FBbt_00100247 \"Open gamma Kenyon cell in Virtual Fly Brain\"). Some specific subtypes are KCab-c(i), KCab-c(o), larval gamma Kenyon cell, KCg-s, KCg-s4, KCg-t, larval alpha'/beta' Kenyon cell, KCab-sc, alpha'/beta' anterior-posterior type 1 Kenyon cell of lACA, Kenyon cell of main calyx, single-claw Kenyon cell, and multi-claw Kenyon cell.", + "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": "5b3d7031-4978-4cc0-8955-dd5d5a202375", + "response_id": "chatcmpl-a25573e236b4fcab0f85a73c54659475", + "images_count": 8, + "graphs_count": 0, + "response": "The subtypes of [Kenyon cell](https://www.virtualflybrain.org/reports/FBbt_00003686 \"Open Kenyon cell in Virtual Fly Brain\") include [37](https://v2.virtualflybrain.org/org.geppetto.frontend/geppetto?q=FBbt_00003686,SubclassesOf \"Run in VFB: Subclasses of Kenyon cell\") subclasses, such as [KCab-c(i)](https://www.virtualflybrain.org/reports/FBbt_00049111 \"Open KCab-c(i) in Virtual Fly Brain\"), [KCab-c](https://www.virtualflybrain.org/reports/FBbt_00110929 \"Open KCab-c in Virtual Fly Brain\"), [KCg-m](https://www.virtualflybrain.org/reports/FBbt_00111061 \"Open KCg-m in Virtual Fly Brain\"), [Kenyon cell of main calyx](https://www.virtualflybrain.org/reports/FBbt_00047926 \"Open Kenyon cell of main calyx in Virtual Fly Brain\"), and [gamma Kenyon cell](https://www.virtualflybrain.org/reports/FBbt_00100247 \"Open gamma Kenyon cell in Virtual Fly Brain\"). Some specific subtypes are KCab-c(i), KCab-c(o), larval gamma Kenyon cell, KCg-s, KCg-s4, KCg-t, larval alpha'/beta' Kenyon cell, KCab-sc, alpha'/beta' anterior-posterior type 1 Kenyon cell of lACA, Kenyon cell of main calyx, single-claw Kenyon cell, and multi-claw Kenyon cell.", + "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": 1136, + "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": 6487 + } + }, + { + "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": 20308, + "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": 112, + "conversation": true, + "turns": [ + { + "turn": 1, + "question": "What are the anatomical parts of the medulla? List them.", + "focus": null, + "clicked": null, + "duration_ms": 8739, + "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.", + "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": 11569, + "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.", + "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": "f8147c80-e7b9-4a29-b9b6-ae5a6aa5c779", + "response_id": "chatcmpl-68004ef633c2a7d6e2e1d9c1c4d535e2", + "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.", + "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": 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": 11569 + } + }, + { + "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": 15546, + "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": 160, + "conversation": true, + "turns": [ + { + "turn": 1, + "question": "Tell me about the antennal lobe.", + "focus": null, + "clicked": null, + "duration_ms": 9674, + "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 where synaptic input can be searched via the Virtual Fly Brain web application. VFB holds various data related to the antennal lobe, including transgene expression in antennal lobe commissural pioneer interneuron, as well as downstream and upstream connectivity classes for antennal lobe commissural pioneer interneuron.", + "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": 5872, + "ok": true, + "response": "The [antennal lobe](https://www.virtualflybrain.org/reports/FBbt_00003924 \"Open antennal lobe in Virtual Fly Brain\") is innervated by several types of neurons, including [larval antennal lobe picky local neuron](https://www.virtualflybrain.org/reports/FBbt_00111694 \"Open larval antennal lobe picky local neuron in Virtual Fly Brain\"), [larval antennal lobe broad local neuron](https://www.virtualflybrain.org/reports/FBbt_00111700 \"Open larval antennal lobe broad local neuron in Virtual Fly Brain\"), [PLP077](https://www.virtualflybrain.org/reports/FBbt_20001577 \"Open PLP077 in Virtual Fly Brain\"), [adult olfactory receptor neuron Ir75d ac1](https://www.virtualflybrain.org/reports/FBbt_00110011 \"Open adult olfactory receptor neuron Ir75d ac1 in Virtual Fly Brain\"), [adult olfactory receptor neuron Ir75d ac2](https://www.virtualflybrain.org/reports/FBbt_00110014 \"Open adult olfactory receptor neuron Ir75d ac2 in Virtual Fly Brain\"), adult olfactory receptor neuron Ir75d ac4, pharyngeal VL1 neuron, ORN_VM6, adult olfactory receptor neuron Or35a ac3I, adult olfactory receptor neuron Or35a ac3II, adult olfactory receptor neuron Or85b ab3, and adult olfactory receptor neuron Or85b ab11. VFB records show [266](https://v2.virtualflybrain.org/org.geppetto.frontend/geppetto?q=FBbt_00003924,NeuronsPresynapticHere \"Run in VFB: Neurons with presynaptic terminals in antennal lobe\") neurons with presynaptic terminals in the antennal lobe.", + "followons": [ + { + "id": "FBbt_00003924", + "query_type": "ListAllAvailableImages", + "query": "Which images of antennal lobe does VFB have?" + }, + { + "id": "FBbt_00003924", + "query_type": "NeuronsPartHere", + "query": "Which neurons have part of their arbour in the antennal lobe?" + }, + { + "id": "FBbt_00003924", + "query_type": "NeuronsSynaptic", + "query": "Which neurons have synaptic terminals in the antennal lobe?" + }, + { + "id": "FBbt_00003924", + "query_type": "NeuronsPostsynapticHere", + "query": "Which neurons receive output from the antennal lobe?" + }, + { + "id": "FBbt_00003924", + "query_type": "PartsOf", + "query": "What are the anatomical parts of the antennal lobe?" + }, + { + "id": "FBbt_00003924", + "query_type": "SubclassesOf", + "query": "What are the subtypes of the antennal lobe?" + } + ], + "context_terms": [ + { + "id": "FBbt_00003924", + "label": "antennal lobe" + } + ], + "reproduction": { + "ids": [ + { + "id": "FBbt_00003924", + "label": "antennal lobe" + } + ], + "calls": [ + { + "id": "FBbt_00003924", + "query_type": "NeuronsPresynapticHere", + "fn": "get_neurons_with_presynaptic_terminals_in" + } + ], + "unmapped": [] + }, + "status_count": 6, + "problems": [] + } + ], + "ok": true, + "request_id": "ee849716-6f03-4848-b90f-4bd7d1f9b58e", + "response_id": "chatcmpl-c10e2cd90873c68560587f9f2c1feaf5", + "images_count": 6, + "graphs_count": 0, + "response": "The [antennal lobe](https://www.virtualflybrain.org/reports/FBbt_00003924 \"Open antennal lobe in Virtual Fly Brain\") is innervated by several types of neurons, including [larval antennal lobe picky local neuron](https://www.virtualflybrain.org/reports/FBbt_00111694 \"Open larval antennal lobe picky local neuron in Virtual Fly Brain\"), [larval antennal lobe broad local neuron](https://www.virtualflybrain.org/reports/FBbt_00111700 \"Open larval antennal lobe broad local neuron in Virtual Fly Brain\"), [PLP077](https://www.virtualflybrain.org/reports/FBbt_20001577 \"Open PLP077 in Virtual Fly Brain\"), [adult olfactory receptor neuron Ir75d ac1](https://www.virtualflybrain.org/reports/FBbt_00110011 \"Open adult olfactory receptor neuron Ir75d ac1 in Virtual Fly Brain\"), [adult olfactory receptor neuron Ir75d ac2](https://www.virtualflybrain.org/reports/FBbt_00110014 \"Open adult olfactory receptor neuron Ir75d ac2 in Virtual Fly Brain\"), adult olfactory receptor neuron Ir75d ac4, pharyngeal VL1 neuron, ORN_VM6, adult olfactory receptor neuron Or35a ac3I, adult olfactory receptor neuron Or35a ac3II, adult olfactory receptor neuron Or85b ab3, and adult olfactory receptor neuron Or85b ab11. VFB records show [266](https://v2.virtualflybrain.org/org.geppetto.frontend/geppetto?q=FBbt_00003924,NeuronsPresynapticHere \"Run in VFB: Neurons with presynaptic terminals in antennal lobe\") neurons with presynaptic terminals in the antennal lobe.", + "quality_flags": { + "has_tool_status": true, + "no_tool_factual_answer": false, + "tool_claim_without_tool": false, + "disambiguation_only_answer": false, + "investigation_plan_answer": false, + "not_verified_or_no_results_answer": false, + "graph_failure_mentioned": false, + "missing_required_graph": false, + "used_data_resource": false, + "response_chars": 1444, + "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": 5872 + } + }, + { + "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": 15795, + "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": 91, + "conversation": true, + "turns": [ + { + "turn": 1, + "question": "What is the medulla?", + "focus": null, + "clicked": null, + "duration_ms": 4858, + "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": 5138, + "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 records show [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, including images of OA-AL2i2, MC64, aMe5, MeTu3, MeTu-DRA, and MeVP6.", + "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": 5799, + "ok": true, + "response": "VFB records show [2,342](https://v2.virtualflybrain.org/org.geppetto.frontend/geppetto?q=FBbt_00003748,TransgeneExpressionHere \"Run in VFB: Transgene expression in medulla\") transgene expression patterns in the [medulla](https://www.virtualflybrain.org/reports/FBbt_00003748 \"Open medulla in Virtual Fly Brain\"), 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": "9ac495ff-69a8-4366-919d-4f6b53ffcb48", + "response_id": "chatcmpl-33a885c3de47687076e3ef69f029351e", + "images_count": 8, + "graphs_count": 0, + "response": "VFB records show [2,342](https://v2.virtualflybrain.org/org.geppetto.frontend/geppetto?q=FBbt_00003748,TransgeneExpressionHere \"Run in VFB: Transgene expression in medulla\") transgene expression patterns in the [medulla](https://www.virtualflybrain.org/reports/FBbt_00003748 \"Open medulla in Virtual Fly Brain\"), 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": 911, + "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": 5799 + } + }, + { + "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": 9283, + "status_messages": [ + { + "message": "Thinking...", + "phase": "llm" + }, + { + "message": "Running the query behind that suggestion", + "phase": "mcp" + }, + { + "message": "Resolving 1 term in VFB", + "phase": "mcp" + }, + { + "message": "Querying VFB", + "phase": "mcp" + }, + { + "message": "Checking the answer is covered", + "phase": "llm" + }, + { + "message": "Writing the answer", + "phase": "llm" + } + ], + "event_count": 34, + "conversation": true, + "turns": [ + { + "turn": 1, + "question": "What is the mushroom body?", + "focus": null, + "clicked": null, + "duration_ms": 6372, + "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": 2911, + "ok": true, + "response": "The [mushroom body](https://www.virtualflybrain.org/reports/FBbt_00005801 \"Open mushroom body in Virtual Fly Brain\") is labeled by multiple driver lines, with VFB recording [4130](https://v2.virtualflybrain.org/org.geppetto.frontend/geppetto?q=FBbt_00005801,TransgeneExpressionHere \"Run in VFB: Transgene expression in mushroom body\") instances of transgene expression in 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": "a68d6581-2ce6-4570-a8e1-b715a08b075e", + "response_id": "chatcmpl-cf4a3e7a5966ccdf5ae5e04ed1c658c5", + "images_count": 8, + "graphs_count": 0, + "response": "The [mushroom body](https://www.virtualflybrain.org/reports/FBbt_00005801 \"Open mushroom body in Virtual Fly Brain\") is labeled by multiple driver lines, with VFB recording [4130](https://v2.virtualflybrain.org/org.geppetto.frontend/geppetto?q=FBbt_00005801,TransgeneExpressionHere \"Run in VFB: Transgene expression in mushroom body\") instances of transgene expression in 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": 390, + "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": 2911 + } + }, + { + "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": 27431, + "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": "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": 213, + "conversation": true, + "turns": [ + { + "turn": 1, + "question": "Which neurons provide input to the medulla?", + "focus": null, + "clicked": null, + "duration_ms": 4507, + "ok": true, + "response": "The neurons that provide input to the [medulla](https://www.virtualflybrain.org/reports/FBbt_00003748 \"Open medulla in Virtual Fly Brain\") are those with presynaptic terminals in the medulla. VFB records show [262](https://v2.virtualflybrain.org/org.geppetto.frontend/geppetto?q=FBbt_00003748,NeuronsPresynapticHere \"Run in VFB: Neurons with presynaptic terminals in medulla\") such neurons. The first 12 of these, with their VFB ids, 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; Tm18.", + "followons": [ + { + "id": "FBbt_00003748", + "query_type": "ImagesNeurons", + "query": "Which neuron images have a part in the medulla?" + }, + { + "id": "FBbt_00003748", + "query_type": "TransgeneExpressionHere", + "query": "Which driver lines label the medulla?" + }, + { + "id": "FBbt_00003748", + "query_type": "NeuronsPartHere", + "query": "Which neurons have part of their arbour in the medulla?" + }, + { + "id": "FBbt_00003748", + "query_type": "NeuronsSynaptic", + "query": "Which neurons have synaptic terminals in the medulla?" + }, + { + "id": "FBbt_00003748", + "query_type": "PartsOf", + "query": "What are the anatomical parts of the medulla?" + }, + { + "id": "FBbt_00003748", + "query_type": "LineageClonesIn", + "query": "Which lineage clones are found in the medulla?" + } + ], + "context_terms": [ + { + "id": "FBbt_00003748", + "label": "medulla" + } + ], + "reproduction": { + "ids": [ + { + "id": "FBbt_00003748", + "label": "medulla" + } + ], + "calls": [ + { + "id": "FBbt_00003748", + "query_type": "NeuronsPresynapticHere", + "fn": "get_neurons_with_presynaptic_terminals_in" + }, + { + "id": "FBbt_00003748", + "query_type": "NeuronsPostsynapticHere", + "fn": "get_neurons_with_postsynaptic_terminals_in" + } + ], + "unmapped": [] + }, + "status_count": 9, + "problems": [] + }, + { + "turn": 2, + "question": "And the lobula?", + "focus": null, + "clicked": null, + "duration_ms": 22924, + "ok": true, + "response": "The neurons that provide input to the [lobula](https://www.virtualflybrain.org/reports/FBbt_00003852 \"Open lobula in Virtual Fly Brain\") are those with presynaptic terminals in the lobula. VFB holds records of such neurons in this session.\n\nNeurons with some part in the lobula 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, among [528](https://v2.virtualflybrain.org/org.geppetto.frontend/geppetto?q=FBbt_00003852,NeuronsPartHere \"Run in VFB: Neurons with some part in lobula\") total.\n\nSimilarly, 528 neurons have synaptic terminals in the lobula, including the same first 12 as those with some part in the lobula.\n\nThere are [4](https://v2.virtualflybrain.org/org.geppetto.frontend/geppetto?q=FBbt_00003852,ListAllAvailableImages \"Run in VFB: List all available images of lobula\") available images of 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": 14, + "problems": [] + } + ], + "ok": true, + "request_id": "6d822681-6d9a-4a7c-ad89-e0420efbffef", + "response_id": "chatcmpl-7129544fab100a36d1a66d9620cccb25", + "images_count": 4, + "graphs_count": 0, + "response": "The neurons that provide input to the [lobula](https://www.virtualflybrain.org/reports/FBbt_00003852 \"Open lobula in Virtual Fly Brain\") are those with presynaptic terminals in the lobula. VFB holds records of such neurons in this session.\n\nNeurons with some part in the lobula 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, among [528](https://v2.virtualflybrain.org/org.geppetto.frontend/geppetto?q=FBbt_00003852,NeuronsPartHere \"Run in VFB: Neurons with some part in lobula\") total.\n\nSimilarly, 528 neurons have synaptic terminals in the lobula, including the same first 12 as those with some part in the lobula.\n\nThere are [4](https://v2.virtualflybrain.org/org.geppetto.frontend/geppetto?q=FBbt_00003852,ListAllAvailableImages \"Run in VFB: List all available images of lobula\") available images of 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": 1423, + "status_count": 14, + "addressless_followon": false, + "context_lost_across_turn": false, + "unmatched_claim_after_resolve": false, + "repeats_answered_question": false, + "slow_followup_turn": false, + "slowest_followup_ms": 22924 + } + }, + { + "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": 39991, + "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": "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, + "conversation": true, + "turns": [ + { + "turn": 1, + "question": "What is the protocerebral bridge?", + "focus": null, + "clicked": null, + "duration_ms": 6844, + "ok": true, + "response": "The [protocerebral bridge](https://www.virtualflybrain.org/reports/FBbt_00003668 \"Open protocerebral bridge in Virtual Fly Brain\") is a handle bar-shaped synaptic neuropil located just posterior to the fan-shaped body. Its lateral edge ends at the posterior end of the inferior clamp near the medial equatorial fascicle. A row of 18 connected slices, 9 on each side of the midline, numbered 1-9 from medial to lateral, forms a dorso-posteriorly located part of the central complex embedded in the cortex between the calyces of the two mushroom bodies.", + "followons": [ + { + "id": "FBbt_00003668", + "query_type": "ListAllAvailableImages", + "query": "Which images of protocerebral bridge does VFB have?" + }, + { + "id": "FBbt_00003668", + "query_type": "NeuronsPartHere", + "query": "Which neurons have part of their arbour in the protocerebral bridge?" + }, + { + "id": "FBbt_00003668", + "query_type": "NeuronsSynaptic", + "query": "Which neurons have synaptic terminals in the protocerebral bridge?" + }, + { + "id": "FBbt_00003668", + "query_type": "NeuronsPresynapticHere", + "query": "Which neurons provide input to the protocerebral bridge?" + }, + { + "id": "FBbt_00003668", + "query_type": "NeuronsPostsynapticHere", + "query": "Which neurons receive output from the protocerebral bridge?" + }, + { + "id": "FBbt_00003668", + "query_type": "PartsOf", + "query": "What are the anatomical parts of the protocerebral bridge?" + } + ], + "context_terms": [ + { + "id": "FBbt_00003668", + "label": "protocerebral bridge" + } + ], + "reproduction": { + "ids": [ + { + "id": "FBbt_00003668", + "label": "protocerebral bridge" + } + ], + "calls": [], + "unmapped": [] + }, + "status_count": 6, + "problems": [] + }, + { + "turn": 2, + "question": "How does it relate to the ellipsoid body?", + "focus": null, + "clicked": null, + "duration_ms": 14072, + "ok": true, + "response": "The [protocerebral bridge](https://www.virtualflybrain.org/reports/FBbt_00003668 \"Open protocerebral bridge in Virtual Fly Brain\") and the [ellipsoid body](https://www.virtualflybrain.org/reports/FBbt_00003678 \"Open ellipsoid body in Virtual Fly Brain\") are connected by neurons. VFB records show that there are neurons with some part in the ellipsoid body, including [adult protocerebral bridge glomerulus 1-ellipsoid body canal-dorsal gall neuron](https://www.virtualflybrain.org/reports/FBbt_00111376 \"Open adult protocerebral bridge glomerulus 1-ellipsoid body canal-dorsal gall neuron in Virtual Fly Brain\"), and adult protocerebral bridge glomerulus 4-ellipsoid body canal-ventral gall neuron, among others. These neurons also have synaptic terminals in the ellipsoid body.", + "followons": [ + { + "id": "FBbt_00003668", + "query_type": "ListAllAvailableImages", + "query": "Which images of protocerebral bridge does VFB have?" + }, + { + "id": "FBbt_00003668", + "query_type": "NeuronsPartHere", + "query": "Which neurons have part of their arbour in the protocerebral bridge?" + }, + { + "id": "FBbt_00003668", + "query_type": "NeuronsSynaptic", + "query": "Which neurons have synaptic terminals in the protocerebral bridge?" + }, + { + "id": "FBbt_00003668", + "query_type": "NeuronsPresynapticHere", + "query": "Which neurons provide input to the protocerebral bridge?" + }, + { + "id": "FBbt_00003668", + "query_type": "NeuronsPostsynapticHere", + "query": "Which neurons receive output from the protocerebral bridge?" + }, + { + "id": "FBbt_00003668", + "query_type": "PartsOf", + "query": "What are the anatomical parts of the protocerebral bridge?" + } + ], + "context_terms": [ + { + "id": "FBbt_00003668", + "label": "protocerebral bridge" + }, + { + "id": "FBbt_00003678", + "label": "ellipsoid body" + } + ], + "reproduction": { + "ids": [ + { + "id": "FBbt_00003668", + "label": "protocerebral bridge" + }, + { + "id": "FBbt_00003678", + "label": "ellipsoid body" + } + ], + "calls": [ + { + "id": "FBbt_00003678", + "query_type": "ListAllAvailableImages", + "fn": "get_instances" + }, + { + "id": "FBbt_00003678", + "query_type": "NeuronsPartHere", + "fn": "get_neurons_with_part_in" + }, + { + "id": "FBbt_00003678", + "query_type": "NeuronsSynaptic", + "fn": "get_neurons_with_synapses_in" + } + ], + "unmapped": [] + }, + "status_count": 13, + "problems": [] + }, + { + "turn": 3, + "question": "Which neurons connect them?", + "focus": null, + "clicked": null, + "duration_ms": 19075, + "ok": true, + "response": "Neurons that connect the [protocerebral bridge](https://www.virtualflybrain.org/reports/FBbt_00003668 \"Open protocerebral bridge in Virtual Fly Brain\") and the [ellipsoid body](https://www.virtualflybrain.org/reports/FBbt_00003678 \"Open ellipsoid body in Virtual Fly Brain\") include the [adult protocerebral bridge glomerulus 1-ellipsoid body canal-dorsal gall neuron](https://www.virtualflybrain.org/reports/FBbt_00111376 \"Open adult protocerebral bridge glomerulus 1-ellipsoid body canal-dorsal gall neuron in Virtual Fly Brain\") and the adult protocerebral bridge glomerulus 4-ellipsoid body canal-ventral gall neuron. VFB records show that there are neurons with some part in the ellipsoid body, including these neurons, among others.", + "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": 13, + "problems": [] + } + ], + "ok": true, + "request_id": "6197cd96-afc0-40bb-931a-021923f445a1", + "response_id": "chatcmpl-60c5013e3d8b754918e844cdfd5740ff", + "images_count": 8, + "graphs_count": 1, + "response": "Neurons that connect the [protocerebral bridge](https://www.virtualflybrain.org/reports/FBbt_00003668 \"Open protocerebral bridge in Virtual Fly Brain\") and the [ellipsoid body](https://www.virtualflybrain.org/reports/FBbt_00003678 \"Open ellipsoid body in Virtual Fly Brain\") include the [adult protocerebral bridge glomerulus 1-ellipsoid body canal-dorsal gall neuron](https://www.virtualflybrain.org/reports/FBbt_00111376 \"Open adult protocerebral bridge glomerulus 1-ellipsoid body canal-dorsal gall neuron in Virtual Fly Brain\") and the adult protocerebral bridge glomerulus 4-ellipsoid body canal-ventral gall neuron. VFB records show that there are neurons with some part in the ellipsoid body, including these neurons, among others.", + "graphs": [ + { + "type": "basic_graph", + "version": 1, + "title": "Upstream partners of P6-8P9", + "directed": true, + "layout": "circle", + "nodes": [ + { + "id": "FBbt_00047095", + "label": "adult neuron", + "group": null, + "color": null, + "size": 1.37 + }, + { + "id": "FBbt_00111056", + "label": "P6-8P9", + "group": null, + "color": null, + "size": 4 + }, + { + "id": "FBbt_00005106", + "label": "neuron", + "group": null, + "color": null, + "size": 1.37 + }, + { + "id": "FBbt_00049819", + "label": "adult central complex neuron", + "group": null, + "color": null, + "size": 1.37 + }, + { + "id": "FBbt_00059271", + "label": "CNS neuron", + "group": null, + "color": null, + "size": 1.37 + }, + { + "id": "FBbt_00053387", + "label": "intrinsic neuron of the central complex", + "group": null, + "color": null, + "size": 1.21 + }, + { + "id": "FBbt_00007515", + "label": "large field neuron of the central complex", + "group": null, + "color": null, + "size": 1.2 + }, + { + "id": "FBbt_00003648", + "label": "large field neuron", + "group": null, + "color": null, + "size": 1.2 + }, + { + "id": "FBbt_00003666", + "label": "adult intrinsic protocerebral bridge neuron", + "group": null, + "color": null, + "size": 1.19 + }, + { + "id": "FBbt_00049807", + "label": "adult intrinsic protocerebral bridge 18 glomeruli-delta7 neuron", + "group": null, + "color": null, + "size": 1.17 + }, + { + "id": "FBbt_00007514", + "label": "small field neuron of the central complex", + "group": null, + "color": null, + "size": 1.14 + }, + { + "id": "FBbt_00003633", + "label": "small field neuron", + "group": null, + "color": null, + "size": 1.14 + }, + { + "id": "FBbt_00003637", + "label": "adult ellipsoid body-protocerebral bridge-gall neuron", + "group": null, + "color": null, + "size": 1.12 + }, + { + "id": "FBbt_00047030", + "label": "adult ellipsoid body-protocerebral bridge 1 glomerulus-dorsal/ventral gall neuron", + "group": null, + "color": null, + "size": 1.11 + }, + { + "id": "FBbt_00049822", + "label": "fan-shaped body extrinsic columnar neuron", + "group": null, + "color": null, + "size": 1.02 + } + ], + "edges": [ + { + "source": "FBbt_00047095", + "target": "FBbt_00111056", + "label": "3201", + "weight": 3201 + }, + { + "source": "FBbt_00005106", + "target": "FBbt_00111056", + "label": "3201", + "weight": 3201 + }, + { + "source": "FBbt_00049819", + "target": "FBbt_00111056", + "label": "3197", + "weight": 3197 + }, + { + "source": "FBbt_00059271", + "target": "FBbt_00111056", + "label": "3197", + "weight": 3197 + }, + { + "source": "FBbt_00053387", + "target": "FBbt_00111056", + "label": "1817", + "weight": 1817 + }, + { + "source": "FBbt_00007515", + "target": "FBbt_00111056", + "label": "1740", + "weight": 1740 + }, + { + "source": "FBbt_00003648", + "target": "FBbt_00111056", + "label": "1740", + "weight": 1740 + }, + { + "source": "FBbt_00003666", + "target": "FBbt_00111056", + "label": "1662", + "weight": 1662 + }, + { + "source": "FBbt_00049807", + "target": "FBbt_00111056", + "label": "1469", + "weight": 1469 + }, + { + "source": "FBbt_00007514", + "target": "FBbt_00111056", + "label": "1191", + "weight": 1191 + }, + { + "source": "FBbt_00003633", + "target": "FBbt_00111056", + "label": "1191", + "weight": 1191 + }, + { + "source": "FBbt_00003637", + "target": "FBbt_00111056", + "label": "1020", + "weight": 1020 + }, + { + "source": "FBbt_00047030", + "target": "FBbt_00111056", + "label": "935", + "weight": 935 + }, + { + "source": "FBbt_00111056", + "target": "FBbt_00111056", + "label": "193", + "weight": 193 + }, + { + "source": "FBbt_00049822", + "target": "FBbt_00111056", + "label": "166", + "weight": 166 + } + ] + } + ], + "quality_flags": { + "has_tool_status": true, + "no_tool_factual_answer": false, + "tool_claim_without_tool": false, + "disambiguation_only_answer": false, + "investigation_plan_answer": false, + "not_verified_or_no_results_answer": false, + "graph_failure_mentioned": false, + "missing_required_graph": false, + "used_data_resource": false, + "response_chars": 738, + "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": 19075 + } + }, + { + "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": 25323, + "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 literature", + "phase": "mcp" + }, + { + "message": "Checking the answer is covered", + "phase": "llm" + }, + { + "message": "Writing the answer", + "phase": "llm" + } + ], + "event_count": 43, + "conversation": true, + "turns": [ + { + "turn": 1, + "question": "Which neurons have part of them in the medulla?", + "focus": null, + "clicked": null, + "duration_ms": 13285, + "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.", + "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": 12038, + "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. 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.\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": "d37cc8d6-0d82-4d24-9cba-335011c62c9c", + "response_id": "chatcmpl-5807e3e04ad72fd6c318b67dac51c538", + "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. 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.\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": 815, + "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": 12038 + } + }, + { + "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": 29238, + "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": 100, + "conversation": true, + "turns": [ + { + "turn": 1, + "question": "What are the subclasses of Kenyon cell?", + "focus": null, + "clicked": null, + "duration_ms": 9449, + "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": 19789, + "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 records for the subclasses of Kenyon cell, including their VFB ids, such as FBbt_00049111 for [KCab-c(i)](https://www.virtualflybrain.org/reports/FBbt_00049111 \"Open KCab-c(i) in Virtual Fly Brain\") and FBbt_00049112 for [KCab-c](https://www.virtualflybrain.org/reports/FBbt_00110929 \"Open KCab-c in Virtual Fly Brain\")(o).\n\n(query=\"SubclassesOf\", id=\"\", format=\"table\")\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": "379e917b-2874-49e6-9b24-15f7bc578826", + "response_id": "chatcmpl-a121381a9200119acb7c23c2e38afe3f", + "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 records for the subclasses of Kenyon cell, including their VFB ids, such as FBbt_00049111 for [KCab-c(i)](https://www.virtualflybrain.org/reports/FBbt_00049111 \"Open KCab-c(i) in Virtual Fly Brain\") and FBbt_00049112 for [KCab-c](https://www.virtualflybrain.org/reports/FBbt_00110929 \"Open KCab-c in Virtual Fly Brain\")(o).\n\n(query=\"SubclassesOf\", id=\"\", format=\"table\")\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": 1151, + "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": 19789 + } + } + ] +} diff --git a/tests/unit/absence.test.mjs b/tests/unit/absence.test.mjs index 671bbdb..040ef72 100644 --- a/tests/unit/absence.test.mjs +++ b/tests/unit/absence.test.mjs @@ -464,3 +464,42 @@ test('the unmatched block is absent when every name resolved', () => { assert.ok(!renderCoverageBlock(ledger).includes('NAMES THAT DID NOT MATCH')) assert.ok(!renderShelf(buildShelf(ledger)).includes('NAMES THAT DID NOT MATCH'), 'and the default is still no block') }) + +// --- naming a denial without quoting it -------------------------------------- +// +// The escalation and gate lines print to the container log, which is outside +// governance.js's file mode and outside pruneRetention. They used to print the +// matched sentence, and a model writes an absence by restating the question, so +// the user's wording went with it. The slug is what replaced it. + +test('every absence pattern reports a stable slug', () => { + const cases = [ + ['VFB does not currently hold data on that line.', 'does-not-hold'], + ['VFB has no images of that neuron.', 'has-no'], + ['There are no records in VFB for that driver.', 'no-data-in'], + ['VFB lacks connectivity for that class.', 'lacks'], + ['The layer subdivisions are not annotated in the current data.', 'is-not-present-in'], + ['There is no record of that stock.', 'there-is-no'] + ] + for (const [sentence, slug] of cases) { + const claims = findAbsenceClaims(sentence) + assert.equal(claims.length, 1, `missed: ${sentence}`) + assert.equal(claims[0].pattern, slug, sentence) + } +}) + +test('the repairs come back named as well as quoted', () => { + const answer = 'VFB does not currently hold data on that. There is no record of it either.' + const { repairs, patterns } = repairUnlicensedAbsences(answer, absenceLicence(ledgerWith(Q))) + assert.equal(repairs.length, patterns.length, 'one slug per repair, in the same order') + assert.deepEqual(patterns, ['does-not-hold', 'there-is-no']) + // The strings are still there for the trace; only the log line changed. + assert.ok(repairs[0].includes('does not currently hold')) +}) + +test('a slug is a slug — no user wording can reach the log through it', () => { + const claims = findAbsenceClaims('VFB does not currently hold data on the SECRETLINE from Kyoto.') + assert.equal(claims.length, 1) + assert.ok(!claims[0].pattern.includes('SECRETLINE')) + assert.match(claims[0].pattern, /^[a-z-]+$/) +}) diff --git a/tests/unit/consoleLeakGuard.test.mjs b/tests/unit/consoleLeakGuard.test.mjs new file mode 100644 index 0000000..9c0f6a3 --- /dev/null +++ b/tests/unit/consoleLeakGuard.test.mjs @@ -0,0 +1,206 @@ +// The container log must not contain the user's text. Asserted, not reviewed. +// +// Finding A1b was closed by lib/safeToolArgs.mjs, which renders tool arguments +// by shape rather than by value. Nothing asserted it stayed closed, and the +// surface had already been widened three times by diagnostics added for good +// reasons — each one caught by somebody reading the code rather than by a +// failing test. A guard nobody can regress past is worth more than a guard that +// was correct on the day it was written. +// +// WHAT THIS ACTUALLY TESTS +// +// Every path below is driven for real — runHarness with mocked ELM and MCP, the +// absence escalation, the absence gate, the tool-failure reporter — with a +// canary string planted where the user's text enters. The assertion is that the +// canary never reaches console.log/warn/error. It is a behavioural test, not a +// grep over the source, so a NEW diagnostic that interpolates user text fails it +// without anyone having to remember this file exists. +// +// The second half asserts the other direction: under VFB_HARNESS_TRACE the same +// values ARE printed. A privacy guard that cannot be switched off for debugging +// gets switched off by deleting it. + +import test from 'node:test' +import assert from 'node:assert/strict' +import { runHarness, maybeEscalateBeforeAbsence, gateAbsence } from '../../lib/orchestrator.mjs' +import { createLedger, addTerm } from '../../lib/ledger.mjs' +import { buildLiveDeps } from '../../lib/liveHarness.mjs' +import { safeText, safeToolArgs } from '../../lib/safeToolArgs.mjs' + +// Distinctive enough that no legitimate diagnostic could produce it by accident, +// and shaped like the things users actually type: a phrase with spaces in it. +const CANARY = 'CANARY7Q' +const QUESTION = `does the ${CANARY} line from Kyoto label PAM neurons?` +const TERM_NAME = `${CANARY} expression pattern` + +/** Run fn with all three console writers captured. Returns everything written. */ +async function captureConsole(fn) { + const written = [] + const originals = { log: console.log, warn: console.warn, error: console.error } + const grab = (...args) => { + written.push(args.map(a => { + if (typeof a === 'string') return a + try { return JSON.stringify(a) } catch { return String(a) } + }).join(' ')) + } + console.log = grab; console.warn = grab; console.error = grab + try { await fn() } finally { Object.assign(console, originals) } + return written.join('\n') +} + +/** Assert the canary is nowhere in what was written, quoting the log if it is. */ +function assertNoLeak(output, what) { + assert.ok(!output.includes(CANARY), `${what} wrote user text to the console:\n${output}`) +} + +const TOOL_DEFS = [ + { name: 'vfb_search_terms', purpose: 'search terms', parameters: { type: 'object', required: ['query'], properties: { query: { type: 'string' } } } }, + { name: 'vfb_get_term_info', purpose: 'term info', parameters: { type: 'object', required: ['id'], properties: { id: { type: 'string' } } } } +] + +function harnessDeps({ termInfo }) { + return { + toolDefs: TOOL_DEFS, + models: { planner: 'm', extract: 'm', synth: 'm' }, + maxToolRounds: 6, + async callStructured({ schemaName }) { + if (schemaName === 'plan') { + return { + ok: true, + value: { + intent: 'term_info', underspecified: false, clarifying_question: '', + terms_to_resolve: [TERM_NAME], + steps: [{ id: 's1', tool: 'vfb_get_term_info', answers: [QUESTION] }] + } + } + } + if (schemaName === 'extract') return { ok: true, value: { relevant: true, answered: true, claim: 'c', verbatim: 'v' } } + if (schemaName && schemaName.endsWith('_args')) return { ok: true, value: { id: 'FBbt_00000001' } } + return { ok: false } + }, + async callText() { return 'An answer.' }, + async runTool(name, args) { + if (name === 'vfb_search_terms') return { response: { docs: [{ short_form: 'FBbt_00000001', label: args.query }] } } + if (name === 'vfb_get_term_info') return termInfo(args) + return { ok: true } + } + } +} + +// --- the request path ------------------------------------------------------ + +test('a term-info failure names the id, never the name the user typed', async () => { + // The report exists to say WHICH lookup failed, and the ontology id says that + // precisely. The requested name is often the user's own phrase. + const output = await captureConsole(() => runHarness(QUESTION, harnessDeps({ + termInfo: () => ({ error: 'upstream 502' }) + }))) + assertNoLeak(output, 'the term-info failure report') + assert.match(output, /get_term_info FAILED/, 'the diagnostic still fires') + assert.match(output, /requested_id=FBbt_00000001/, 'and still says which lookup it was') +}) + +test('a deprecated-term redirect names both ids, never the name', async () => { + const output = await captureConsole(() => runHarness(QUESTION, harnessDeps({ + termInfo: (args) => args.id === 'FBbt_00000001' + ? { Id: args.id, Name: 'obsolete thing', SuperTypes: ['Class'], replaced_by: 'FBbt_00009999', Publications: [] } + : { Id: args.id, Name: 'current thing', SuperTypes: ['Class', 'Anatomy'], Publications: [] } + }))) + assertNoLeak(output, 'the deprecated-term redirect') + assert.match(output, /deprecated term redirected \| term= FBbt_00000001 -> FBbt_00009999/) +}) + +test('a whole harness run leaks nothing, on the ordinary path', async () => { + const output = await captureConsole(() => runHarness(QUESTION, harnessDeps({ + termInfo: (args) => ({ Id: args.id, Name: 'medulla', SuperTypes: ['Class', 'Anatomy'], Publications: [] }) + }))) + assertNoLeak(output, 'an ordinary run') +}) + +// --- the absence pair ------------------------------------------------------ +// +// Both of these print a sentence the MODEL wrote. That is not the user's typed +// text, which is exactly why it was not treated as one — but the model writes an +// absence by restating the question, so the question comes back out in it. + +function absenceLedger() { + const ledger = createLedger(QUESTION) + // Queries the term advertises and nothing ran: the commonest way to arrive at + // a denial, and the state the escalation exists for. + addTerm(ledger, TERM_NAME, { + id: 'FBbt_00000001', label: TERM_NAME, + digest: { + id: 'FBbt_00000001', + name: 'expression pattern', + queries: [ + { query_type: 'SubClasses', label: 'Subclasses of expression pattern', count: 34 }, + { query_type: 'TransgeneExpressionHere', label: 'Transgene expression here', count: 88 } + ] + }, + attempted: true + }) + ledger.budget.toolRoundsLeft = 0 + return ledger +} + +const DENIAL = `VFB does not currently hold data on the ${CANARY} line from Kyoto.` + +test('the absence escalation reports its queries, not the sentence it read', async () => { + const output = await captureConsole(() => maybeEscalateBeforeAbsence(absenceLedger(), DENIAL, {}, () => {})) + assertNoLeak(output, 'the absence escalation') + assert.match(output, /ABSENCE ESCALATION \| queries=/, 'the useful half survives') + // The denial is named, not quoted: which SHAPE of absence fired is countable + // across runs and contains nothing the user wrote. + assert.match(output, /claimed=absence:does-not-hold \| len=\d+/) +}) + +test('the absence gate reports how many it removed, not what they said', async () => { + const ledger = absenceLedger() + const output = await captureConsole(() => { gateAbsence(ledger, DENIAL, () => {}) }) + assertNoLeak(output, 'the absence gate') + assert.match(output, /ABSENCE GATE \| removed=1 \| licensed=false \| absence:does-not-hold/) +}) + +// --- tool failures --------------------------------------------------------- + +test('a failing tool reports its arguments by shape', async () => { + // startDocSearch passes the WHOLE user question as search_reviewed_docs' + // `query`, on every non-underspecified turn. This is the path that broke the + // promise the third time. + 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('reviewed docs unreachable') } + }) + const output = await captureConsole(() => deps.runTool('search_reviewed_docs', { query: QUESTION, max_results: 5 })) + assertNoLeak(output, 'the tool-failure report') + assert.match(output, /TOOL FAILED \| tool=search_reviewed_docs/) + assert.match(output, /query:/) + assert.match(output, /max_results:5/, 'the safe arguments are still legible') +}) + +// --- the escape hatch ------------------------------------------------------ + +test('VFB_HARNESS_TRACE prints the values in full, so the guard survives debugging', () => { + // A privacy guard that cannot be switched off for debugging gets switched off + // by deleting it. Both renderers take the flag the same way. + assert.equal(safeText(QUESTION, { trace: true }), QUESTION) + assert.equal(safeText(QUESTION, { trace: false }), ``) + assert.match(safeToolArgs({ query: QUESTION }, { trace: true }), /Kyoto/) + assert.ok(!safeToolArgs({ query: QUESTION }, { trace: false }).includes('Kyoto')) +}) + +test('safeText reports a length for every shape of nothing', () => { + assert.equal(safeText('', { trace: false }), '') + assert.equal(safeText(null, { trace: false }), '') + assert.equal(safeText(undefined, { trace: false }), '') + // The length is the WHOLE length, so a truncated preview cannot be mistaken + // for the whole value when the flag is on. + const long = 'x'.repeat(500) + assert.equal(safeText(long, { trace: false }), '') + assert.equal(safeText(long, { trace: true, max: 10 }).length, 10) +})