diff --git a/docs/adr/absence-requires-evidence.md b/docs/adr/absence-requires-evidence.md new file mode 100644 index 0000000..3ae0154 --- /dev/null +++ b/docs/adr/absence-requires-evidence.md @@ -0,0 +1,88 @@ +# Absence requires evidence + +Status: accepted +Date: 2026-08-10 + +## Context + +`lib/coverage.mjs` has stated the rule since the four-state model was +introduced: of RUN, EMPTY, FAILED and UNRUN, only EMPTY licenses an absence. +The synthesis prompt repeats it three times in capitals. + +Measured against production v4.2.1 — thirteen questions, three repetitions each, +answers judged blind — **fourteen of thirty-nine answers asserted that VFB holds +nothing, and not one of them had a query behind it that had run and come back +empty.** Three of those denials were about `γ Kenyon cells`, `α/β Kenyon cells` +and `MBON-γ1pedc>α/β`, which are FBbt_00100247, FBbt_00100248 and +FBbt_00100246 — classes the ontology has held for years. + +An instruction violated at that rate is not a control. This is the same lesson +the project already learned for counts, where the answer was not a firmer +instruction but `repairMistranscribedCounts`: state the rule, then enforce it +deterministically after the model has had its say. + +## Decision + +Three layers, in the order they should bite. + +**1. Make the name findable.** `lib/nameNormalise.mjs` transliterates Greek +letters to the spellings FlyBase and FBbt actually store, and normalises primes, +arrows, dashes and non-breaking spaces. It is the first rung of `nameVariants`, +and only when there is something to transliterate — an ASCII name still pays +exactly one extra search for its plural, as before. + +**2. Go and look before conceding.** If the drafted answer claims an absence and +nothing came back empty, `maybeEscalateBeforeAbsence` injects the failed and the +most relevant unrun queries and writes the answer again. Failed queries go +first: a lookup that fell over is the one case with positive evidence that the +absence is an artefact. + +**3. Do not ship what was not earned.** `gateAbsence` removes absence claims the +ledger does not license. It is the floor, not the fix — by the time it fires, +escalation has already had its chance. + +`renderShelf` also gained a NAMES THAT DID NOT MATCH block, for the +half-resolved question: one term matches, another does not, the shelf is +non-empty so the no-coverage floor never fires, and nothing in the prompt +distinguished "never looked at" from "checked and found wanting". + +## Consequences + +The absence rate went from 14/39 to 1/39 on the same questions, with no errors +and a median cost of 66 s → 77 s. The full 64-task battery stays at 64/64. + +Three deliberate costs, recorded because each one is a place a future reader may +reasonably disagree: + +- **Relevance orders escalation attempts; it does not veto them.** "Are any + mushroom body output neurons cholinergic?" scores every query the class + advertises at zero, because no label contains the word "cholinergic" — while + `SubClasses`, scoring zero, is the query that answers it. Filtering here would + escalate nothing in the case the guard exists for. + +- **A query the escalation chose cannot license the claim it was chosen to + check.** An early version ran `ListAllAvailableImages` for a question about + hemisphere symmetry, got an empty, and licensed the symmetry denial with it. + The guard was manufacturing its own permission, which is worse than the bug it + replaces. So a run where escalation genuinely proves an absence now hedges it + rather than stating it flatly. Hedging a true absence is a worse answer; + asserting a false one is a wrong answer. + +- **Escalation stops at `ABSENCE_ESCALATION_DEADLINE_MS` (120 s, env-tunable).** + It buys a second synthesis costing 60–90 s, and one started too late takes the + first answer down with it — which it did, once, on the first CI run of this + branch. A false absence is worse than a hedge; it is not worse than no answer. + +## Known limits + +- A licence is per-RUN, not per-claim: one genuinely empty query entitles every + absence sentence in that answer. Narrowing it to the subject of each sentence + needs claim-to-query matching, which is not reliably decidable from the text. +- The detector is a pattern list built from sentences production actually wrote. + It will miss constructions nobody has written yet. Add them from observed + output rather than by imagination, and keep a negative case beside each one — + "serotonin is not present in these neurons" is a claim about the world and + must survive. +- `T3.8` runs at 190–205 s against the workflow's `TASK_BATTERY_TIMEOUT_MS` of + 240 s and has been marginal for several releases. It is unrelated to this + change and wants that ceiling raised to 360000. diff --git a/lib/absence.mjs b/lib/absence.mjs index 0a9dead..1fbeb0c 100644 --- a/lib/absence.mjs +++ b/lib/absence.mjs @@ -175,7 +175,25 @@ const ABSENCE_PATTERNS = [ // 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'), // "no such records exist" / "there is no record of X" with VFB nearby - new RegExp(`\\bthere (?:is|are) no\\b${GAP}\\b(?:record|data|entry|entries|image)s?\\b`, 'i') + new RegExp(`\\bthere (?:is|are) no\\b${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 + // reads to a user as a statement about the database. Its author deliberately + // declined to rewrite the NEGATIVE forms — turning "the evidence does not + // provide X" into "VFB does not record X" would upgrade a limit of this answer + // into a claim about VFB, which is the invention that module exists to stop. + // Correct, and it leaves the sentence in place: + // + // "VFB evidence lists queries for subclasses ... but it does not include a + // completed query or result set identifying specific types lacking images." + // + // Deleting it is the move neither module was making. It is not a claim about + // fly anatomy that a reader loses, it is a description of this program's + // 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') ] /** Split into sentences, keeping each sentence's offset so a repair can be spliced back. */ diff --git a/lib/harnessFraming.mjs b/lib/harnessFraming.mjs index 3b9fc9b..118ea42 100644 --- a/lib/harnessFraming.mjs +++ b/lib/harnessFraming.mjs @@ -106,7 +106,25 @@ const INPUT_NOUN_RULES = [ // X" is an admission of a gap, and rewriting it to "VFB does not record X" // would upgrade a statement about this answer's reach into a claim about the // database — exactly the invention the INPUT_SENTENCE rule exists to avoid. -const EVIDENCE_SUBJECT = '(?:the|this|that)\\s+(?:VFB\\s+)?evidence' +// +// THE DETERMINER IS OPTIONAL, AND THAT IS A BUG FIX RATHER THAN A LOOSENING. +// +// INPUT_NOUN matches "(the )?provided evidence" INCLUDING the article, so by the +// time these rules run the text no longer says "the evidence" — it says "VFB +// evidence", with nothing in front of it. Every rule below then failed to match +// this module's own output. Production, S46: +// +// "VFB evidence lists queries for subclasses, scRNAseq data, transgene +// expression, and connectivity for mushroom body output neuron, but it does +// not include a completed query or result set identifying specific types +// lacking images." +// +// That began life as "the provided evidence lists …", should have become "VFB +// records …", and instead shipped a sentence about this program's working set +// wearing VFB's name. It is the exact failure this module exists to prevent, +// produced by this module, because two of its passes disagreed about whether the +// article was part of the noun. +const EVIDENCE_SUBJECT = '(?:(?:the|this|that)\\s+(?:VFB\\s+)?|VFB\\s+)evidence' const EVIDENCE_SUBJECT_RULES = [ // "the evidence does provide information on X" -> "VFB records X" @@ -184,6 +202,22 @@ export function stripHarnessFraming(text = '') { for (const re of CLAUSE_RULES) out = out.replace(re, '') for (const [re, to] of EVIDENCE_SUBJECT_RULES) out = out.replace(re, to) for (const [re, to] of INPUT_NOUN_RULES) out = out.replace(re, to) + // AND AGAIN, BECAUSE THE PASS ABOVE CREATES WORK FOR THE PASS BEFORE IT. + // + // EVIDENCE_SUBJECT needs "the evidence"; INPUT_NOUN matches "the provided + // evidence" as a unit and rewrites it to "VFB evidence". So a sentence written + // as "the provided evidence lists queries for …" is invisible to the subject + // rules on the first pass — the word "provided" is in the way — and by the + // time it has been normalised into the shape those rules recognise, they have + // already run. It shipped as "VFB evidence lists queries for subclasses, + // scRNAseq data, transgene expression … but it does not include a completed + // query", which is this program's working set wearing VFB's name. + // + // Two passes, not a merged rule: the rules are correct, their ORDER was wrong, + // and re-running them is cheaper to read and to verify than teaching every + // subject rule to also spell out INPUT_NOUN. It terminates because the second + // pass has no output the first pass has not already seen. + for (const [re, to] of EVIDENCE_SUBJECT_RULES) out = out.replace(re, to) // Only after something was actually removed or rewritten. An answer that // opens with "However," of its own accord is the model's prose, not our diff --git a/lib/ledger.mjs b/lib/ledger.mjs index 96fbb33..275c8c8 100644 --- a/lib/ledger.mjs +++ b/lib/ledger.mjs @@ -21,6 +21,12 @@ export function createLedger(question, { maxToolRounds = 24 } = {}) { resources: [], // data_resource handles (lightweight) retrieval: [], // [{ kind:'doc'|'literature', reasons:[], ... }] budget: { toolRoundsLeft: maxToolRounds, tokenEstimate: 0 }, + // Wall clock, not rounds. The round budget bounds how much WORK a question + // may do and says nothing about how long that work has taken — and the two + // come apart badly when the backends are slow. Anything deciding whether to + // buy one more model call late in a run has to know how much of the run + // deadline is already gone. + startedAt: Date.now(), openQuestions: [], // sub-questions still uncovered (derived from plan) registry: {} // authoritative normalised-label -> id, from VFB data only } diff --git a/lib/orchestrator.mjs b/lib/orchestrator.mjs index ac31231..2fb283b 100644 --- a/lib/orchestrator.mjs +++ b/lib/orchestrator.mjs @@ -396,6 +396,39 @@ export async function runHarness(question, deps) { return { answer: gateAbsence(ledger, answer, log), ledger, trace, guardTripped: true } } +/** + * How far into a run the escalation may still buy a second synthesis. + * + * THE NUMBER IS DERIVED, NOT PICKED. + * + * The escalation costs up to three MCP rounds plus a full synthesis, and the + * measured cost of that second pass is 60-90 s. So the only question is what it + * has to finish inside of, and there are two ceilings, of which the tighter one + * governs: + * + * 600 s DEFAULT_RUN_DEADLINE_MS, the product's real ceiling. + * 240 s TASK_BATTERY_TIMEOUT_MS, which is this project's own recorded opinion + * about when an answer has taken too long to be worth having. + * + * Half the run deadline was the first attempt, and it is wrong against the + * second: an escalation starting at 290 s cannot possibly finish before 240 s, + * so the guard was guaranteed to turn the slowest answers into no answer at all. + * It did precisely that on the first CI run of this branch — 63 of 64 tasks + * passed and the 64th was "Timed out after 240000 ms". + * + * 120 s + 90 s = 210 s leaves real margin under the tighter ceiling. Measured + * across the 39-rep tranche, the first synthesis lands inside 120 s on the large + * majority of questions (median 63 s), so this trims the tail rather than the + * guard. + * + * Env-overridable because how fast the backends are on the day is a deployment + * fact rather than a code one. + */ +export const ABSENCE_ESCALATION_DEADLINE_MS = Math.max( + 10000, + Number(process.env.ABSENCE_ESCALATION_DEADLINE_MS) || 120000 +) + /** * Go back and look, rather than tell the reader there is nothing to find. * @@ -426,6 +459,25 @@ export async function runHarness(question, deps) { */ export async function maybeEscalateBeforeAbsence(ledger, answer, deps, log = () => {}) { if (!ledger || ledger._absenceEscalated) return false + // TIME, WHICH IS NOT THE SAME THING AS ROUNDS. + // + // The escalation buys a second synthesis, and a synthesis is the most + // expensive call in the pipeline. Measured on the first full run of this + // branch: S14 escalated at around three minutes, went round again, and the + // second synthesis timed out — so a question that had produced a usable if + // hedged answer produced "the language service did not respond" instead. One + // rep in thirty-nine, and entirely self-inflicted. + // + // A false absence is worse than a hedge, which is why this guard exists. It is + // NOT worse than no answer at all, so the guard has to stop wanting a second + // opinion once there is no longer time to form one. The gate below still runs + // — it costs nothing — so a run that skips escalation still cannot ship a + // denial it did not earn. It simply has to hedge instead of going and looking. + const elapsed = Date.now() - (ledger.startedAt || Date.now()) + if (elapsed > ABSENCE_ESCALATION_DEADLINE_MS) { + log({ step: 'absence-escalation', injected: 0, reason: 'too-late', elapsed }) + return false + } const licence = absenceLicence(ledger) // A run holding a genuine empty result is entitled to its absence. So is an // answer that never made one. @@ -921,6 +973,43 @@ async function resolveTerms(ledger, names, deps, models, log, speculative = new } log({ resolve: name, id: effectiveId, refs: publications.length, queries: digest?.queries?.length || 0, superseded: superseded ? superseded.fromId : undefined }) + // A DEFINITION IS ALREADY WRITTEN. DO NOT ASK A MODEL TO WRITE IT AGAIN. + // + // "What is the ellipsoid body?" returned the same 254 characters on all + // three reps: "a doughnut shaped synaptic neuropil domain of the central + // complex of the adult brain that lies just anterior to the fan-shaped + // body." VFB's own Description does not stop there: + // + // "… Its hole (the ellipsoid body canal) points anteriorly and has an axon + // tract (the anterior bundle) running through it. It is divided into + // concentric layers and into 16 radial segments, 8 per hemisphere, + // numbered 1-8 from superior medial to inferior medial (Ito et al., + // 2014)." + // + // Two thirds of a curated, cited definition, gone — and not to a truncation + // bug. The extractor below is a weak model summarising the whole term-info + // record into one `claim`, so a definitional question sends authoritative + // prose through two paraphrase hops, extract and then synthesise, before it + // reaches the reader. Summarising a summary is what costs the last two + // sentences, and it costs them identically every time, which is why three + // reps agreed to the character. + // + // So for a definitional question the description is carried VERBATIM as its + // own evidence row. This is the same principle the rest of the pipeline + // already runs on — the model narrates, the deterministic layer carries what + // is already exact — applied to text rather than to counts. The extractor + // still runs, because it finds things the description does not say; this row + // only guarantees the definition itself survives the trip. + if (info && digest?.description && isDefinitionalQuestion(ledger.question)) { + addEvidence(ledger, buildEvidenceRow({ + source: 'vfb', + claim: `VFB's full definition of ${digest.name || name}: ${digest.description}`, + verbatim: digest.description, + locator: { term: name, id: effectiveId, field: 'description' } + })) + log({ definition_verbatim: name, id: effectiveId, chars: digest.description.length }) + } + // VFB-first: let the extractor decide what in the FULL term-info answers the // question (Description, Relationships, Queries, counts, …) — no field is // pre-selected. Skip only when there is no term-info at all. diff --git a/test-results/task-battery/latest.json b/test-results/task-battery/latest.json index 2d2c63d..36b6b0b 100644 --- a/test-results/task-battery/latest.json +++ b/test-results/task-battery/latest.json @@ -1,9 +1,9 @@ { "metadata": { - "run_id": "task-battery-2026-08-10T07-54-44-874Z", - "started_at": "2026-08-10T07:54:44.874Z", - "completed_at": "2026-08-10T08:02:26.346Z", - "git_sha": "c8becb3aa130397c880119aef649129f00b19198", + "run_id": "task-battery-2026-08-10T09-57-21-415Z", + "started_at": "2026-08-10T09:57:21.415Z", + "completed_at": "2026-08-10T10:08:37.186Z", + "git_sha": "e02f5421f2741f0b6946c6de4aeafa6fd3643d1e", "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, @@ -106,9 +106,10 @@ "task_ids": [] }, "slow_followup_turn": { - "count": 1, + "count": 2, "task_ids": [ - "C1" + "C3", + "C7" ] } }, @@ -117,10 +118,10 @@ "ok": 12, "turns": 27, "followup_turns": 15, - "followup_median_ms": 10560, - "followup_max_ms": 125468 + "followup_median_ms": 10600, + "followup_max_ms": 188171 }, - "mean_duration_ms": 28302 + "mean_duration_ms": 32891 }, "results": [ { @@ -133,7 +134,7 @@ "requires_graph": false, "min_graphs": 0, "repetition": 1, - "duration_ms": 33247, + "duration_ms": 40298, "status_messages": [ { "message": "Thinking...", @@ -160,13 +161,13 @@ "phase": "llm" } ], - "event_count": 100, + "event_count": 59, "ok": true, - "request_id": "1c74d4d9-e2e2-414d-be5a-6943d732319a", - "response_id": "chatcmpl-b7b3d234a6f0aa6cb69c6edecd7bfcf3", + "request_id": "79ecd216-5c0d-4a49-88b9-6e39c96ba39c", + "response_id": "chatcmpl-207be5ea6116c1f9a5d75eb6a6749583", "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.", + "response": "The major subdivisions of the Drosophila [mushroom body](https://www.virtualflybrain.org/reports/FBbt_00005801 \"Open mushroom body in Virtual Fly Brain\") are the calyx, pedunculus, and mushroom body lobe system. The mushroom body lobe system consists of a vertical branch and a medial branch, which have different structures at different life stages.", "quality_flags": { "has_tool_status": true, "no_tool_factual_answer": false, @@ -177,7 +178,7 @@ "graph_failure_mentioned": false, "missing_required_graph": false, "used_data_resource": false, - "response_chars": 518, + "response_chars": 350, "status_count": 6 } }, @@ -191,7 +192,7 @@ "requires_graph": false, "min_graphs": 0, "repetition": 1, - "duration_ms": 32815, + "duration_ms": 42956, "status_messages": [ { "message": "Thinking...", @@ -220,11 +221,11 @@ ], "event_count": 83, "ok": true, - "request_id": "3a4ce8c7-68e9-488e-9818-f6d59f5a6f40", - "response_id": "chatcmpl-b8c76a242bd8add0aa527b92be29c8d7", + "request_id": "1635ce40-cfd5-443d-8c7a-96e2bf275734", + "response_id": "chatcmpl-8aed3bd14b6ce9fa827b10db2f15fc08", "images_count": 8, "graphs_count": 0, - "response": "There are several types of Kenyon cells in the adult Drosophila brain, including alpha/beta, alpha'/beta', and gamma Kenyon cells. These can be further subdivided into core/surface/posterior, anterior-posterior/middle, dorsal/main/gamma-s/gamma-t, and claw-count classes. VFB holds [37](https://v2.virtualflybrain.org/org.geppetto.frontend/geppetto?q=FBbt_00003686,SubclassesOf \"Run in VFB: Subclasses of Kenyon cell\") subclasses of [Kenyon cell](https://www.virtualflybrain.org/reports/FBbt_00003686 \"Open Kenyon cell in Virtual Fly Brain\").", + "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, @@ -249,7 +250,7 @@ "requires_graph": false, "min_graphs": 0, "repetition": 1, - "duration_ms": 32267, + "duration_ms": 42051, "status_messages": [ { "message": "Thinking...", @@ -283,6 +284,10 @@ "message": "Querying VFB", "phase": "mcp" }, + { + "message": "Querying VFB", + "phase": "mcp" + }, { "message": "Checking the answer is covered", "phase": "llm" @@ -292,13 +297,13 @@ "phase": "llm" } ], - "event_count": 102, + "event_count": 92, "ok": true, - "request_id": "62555deb-c149-42e0-8c91-4225dfab4421", - "response_id": "chatcmpl-8aa5c02a902b16287ae6dfbbbb75bf44", + "request_id": "827294a6-115e-4519-9528-578de389e504", + "response_id": "chatcmpl-0479691c99f56b50e562a5bdbd139d00", "images_count": 8, "graphs_count": 1, - "response": "The main input neurons to the [mushroom body](https://www.virtualflybrain.org/reports/FBbt_00005801 \"Open mushroom body in Virtual Fly Brain\") include sensory interneuron afferents to the calyx. VFB records show that there are [366](https://v2.virtualflybrain.org/org.geppetto.frontend/geppetto?q=FBbt_00005801,NeuronsPresynapticHere \"Run in VFB: Neurons with presynaptic terminals in mushroom body\") neurons with presynaptic terminals in the mushroom body, with examples including larval uniglomerular projection neurons and larval antennal lobe multiglomerular projection neurons. Additionally, the connectome data indicates that there are [304](https://v2.virtualflybrain.org/org.geppetto.frontend/geppetto?q=FBbt_00005801,NeuronsPostsynapticHere \"Run in VFB: Neurons with postsynaptic terminals in mushroom body\") neurons with postsynaptic terminals in the mushroom body.", + "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. The connectome data indicates that these neurons provide input to the mushroom body.", "graphs": [ { "type": "basic_graph", @@ -459,8 +464,8 @@ "graph_failure_mentioned": false, "missing_required_graph": false, "used_data_resource": false, - "response_chars": 875, - "status_count": 10 + "response_chars": 645, + "status_count": 11 } }, { @@ -473,7 +478,7 @@ "requires_graph": false, "min_graphs": 0, "repetition": 1, - "duration_ms": 30720, + "duration_ms": 40738, "status_messages": [ { "message": "Thinking...", @@ -502,8 +507,8 @@ ], "event_count": 24, "ok": true, - "request_id": "e15157d5-088e-4d66-bdf8-fd50ddc09f63", - "response_id": "chatcmpl-6a3a3354fe9bd1f0641c184a2400798b", + "request_id": "87526c30-d0fc-46e0-b0fd-b6f327dffa20", + "response_id": "chatcmpl-e2e3392d80a2fe2f94f2ecf694e8f950", "images_count": 6, "graphs_count": 0, "response": "Mushroom body Kenyon cells use acetylcholine as a neurotransmitter.", @@ -531,7 +536,7 @@ "requires_graph": false, "min_graphs": 0, "repetition": 1, - "duration_ms": 23939, + "duration_ms": 22154, "status_messages": [ { "message": "Thinking...", @@ -553,6 +558,10 @@ "message": "Reading VFB term info", "phase": "mcp" }, + { + "message": "Querying VFB connectivity", + "phase": "mcp" + }, { "message": "Querying VFB", "phase": "mcp" @@ -570,13 +579,168 @@ "phase": "llm" } ], - "event_count": 149, + "event_count": 122, "ok": true, - "request_id": "36ff6b99-fda7-4312-bc17-19f75d10a9ce", - "response_id": "chatcmpl-26865db3b3944016e998c695ca313e0d", + "request_id": "b598d362-53c9-47f4-a6ec-02db7fde026f", + "response_id": "chatcmpl-bf0767c7934b1f69f5c76a71f286688f", "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 and local neurons such as [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 [larval antennal lobe broad local neuron](https://www.virtualflybrain.org/reports/FBbt_00111700 \"Open larval antennal lobe broad local neuron 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 VA1d, as well as local neurons like larval antennal lobe picky local neuron and larval antennal lobe broad local neuron.", + "graphs_count": 1, + "response": "The [antennal lobe](https://www.virtualflybrain.org/reports/FBbt_00003924 \"Open antennal lobe in Virtual Fly Brain\") connects to various brain regions through neurons with presynaptic and postsynaptic terminals. VFB records show [266](https://v2.virtualflybrain.org/org.geppetto.frontend/geppetto?q=FBbt_00003924,NeuronsPresynapticHere \"Run in VFB: Neurons with presynaptic terminals in antennal lobe\") neurons with presynaptic terminals in the antennal lobe, including [larval antennal lobe picky local neuron](https://www.virtualflybrain.org/reports/FBbt_00111694 \"Open larval antennal lobe picky local neuron in Virtual Fly Brain\") and [adult olfactory receptor neuron Ir75d ac1](https://www.virtualflybrain.org/reports/FBbt_00110011 \"Open adult olfactory receptor neuron Ir75d ac1 in Virtual Fly Brain\"). Additionally, [518](https://v2.virtualflybrain.org/org.geppetto.frontend/geppetto?q=FBbt_00003924,NeuronsPostsynapticHere \"Run in VFB: Neurons with postsynaptic terminals in antennal lobe\") neurons have postsynaptic terminals in the antennal lobe, such as [AMMC-Bi16](https://www.virtualflybrain.org/reports/FBbt_00111480 \"Open AMMC-Bi16 in Virtual Fly Brain\") and [adult antennal lobe projection neuron DL5](https://www.virtualflybrain.org/reports/FBbt_00059280 \"Open adult antennal lobe projection neuron DL5 in Virtual Fly Brain\"). These neurons likely play a role in processing olfactory information.", + "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, @@ -587,8 +751,8 @@ "graph_failure_mentioned": false, "missing_required_graph": false, "used_data_resource": false, - "response_chars": 1114, - "status_count": 9 + "response_chars": 1413, + "status_count": 10 } }, { @@ -601,7 +765,7 @@ "requires_graph": false, "min_graphs": 0, "repetition": 1, - "duration_ms": 22420, + "duration_ms": 10729, "status_messages": [ { "message": "Thinking...", @@ -628,13 +792,13 @@ "phase": "llm" } ], - "event_count": 26, + "event_count": 44, "ok": true, - "request_id": "72dee274-a42a-4ef1-99f9-7029c775268f", - "response_id": "chatcmpl-370c031329812789e51eed410a222f01", + "request_id": "21dbcd23-abb7-4708-a1f2-db7fa840da86", + "response_id": "chatcmpl-d1cf09ec31f55c8bc901b88233eaa5d4", "images_count": 0, "graphs_count": 0, - "response": "The central brain of the adult Drosophila contains more than 125,000 neurons.\n\n**Published neuron-count estimates — adult central brain** (from the literature):\n\n- more than 125,000 neurons (adult Drosophila central brain connectome/model) — A Drosophila computational brain model reveals sensorimotor processing. — PMID 39358519\n\n_VFB has annotated 9,413 neuron types with some part in adult central brain — a curated annotation count, not the biological total._", + "response": "The adult Drosophila central brain could not be matched to a VFB record. However, approximately more than 125,000 neurons are in the Drosophila brain.\n\n**Published neuron-count estimates — adult central brain** (from the literature):\n\n- more than 125,000 neurons (adult Drosophila central brain connectome/model) — A Drosophila computational brain model reveals sensorimotor processing. — PMID 39358519\n- ~139,255 neurons (whole adult Drosophila brain) — Neuronal wiring diagram of an adult brain. — PMID 39358518\n\n_VFB has annotated 9,413 neuron types with some part in adult central brain — a curated annotation count, not the biological total._", "quality_flags": { "has_tool_status": true, "no_tool_factual_answer": false, @@ -645,7 +809,7 @@ "graph_failure_mentioned": false, "missing_required_graph": false, "used_data_resource": false, - "response_chars": 463, + "response_chars": 647, "status_count": 6 } }, @@ -659,7 +823,7 @@ "requires_graph": false, "min_graphs": 0, "repetition": 1, - "duration_ms": 29715, + "duration_ms": 9398, "status_messages": [ { "message": "Thinking...", @@ -688,8 +852,8 @@ ], "event_count": 64, "ok": true, - "request_id": "df31ee6d-3443-4c27-a9bc-9631701cbd0b", - "response_id": "chatcmpl-c076bd004ef7627ac40e010d2def409c", + "request_id": "cc17de83-e53f-403f-aee2-ad65506dec98", + "response_id": "chatcmpl-8eaa46120dc8d035e3f4943079d3b6c3", "images_count": 0, "graphs_count": 1, "response": "The main components of the central complex are the ellipsoid body, fan-shaped body, paired noduli, asymmetrical bodies, and protocerebral bridge. These components are associated with functions including navigation and orientation, locomotor control, and sleep/arousal and memory-related behaviours.", @@ -832,7 +996,7 @@ "requires_graph": false, "min_graphs": 0, "repetition": 1, - "duration_ms": 30068, + "duration_ms": 18643, "status_messages": [ { "message": "Thinking...", @@ -859,13 +1023,13 @@ "phase": "llm" } ], - "event_count": 81, + "event_count": 80, "ok": true, - "request_id": "8391cee1-338c-4f8c-8879-6ee825fd7315", - "response_id": "chatcmpl-e69b4da5f3179ccb8b050fd5749dd07a", + "request_id": "3d6ecd42-d3ee-4eae-9b2d-d2398add5d93", + "response_id": "chatcmpl-2e1296a99b63ee29b6b9fd3971cc0cdc", "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 commonly used to label mushroom body neurons, specifically [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.", "quality_flags": { "has_tool_status": true, "no_tool_factual_answer": false, @@ -876,7 +1040,7 @@ "graph_failure_mentioned": false, "missing_required_graph": false, "used_data_resource": false, - "response_chars": 502, + "response_chars": 507, "status_count": 6 } }, @@ -890,7 +1054,7 @@ "requires_graph": false, "min_graphs": 0, "repetition": 1, - "duration_ms": 26771, + "duration_ms": 24149, "status_messages": [ { "message": "Thinking...", @@ -929,13 +1093,13 @@ "phase": "llm" } ], - "event_count": 73, + "event_count": 102, "ok": true, - "request_id": "4a0304f5-bd78-4554-8f5a-fbbf8f72009f", - "response_id": "chatcmpl-d7e841557fb240b413cf4d9b51d27c79", + "request_id": "8738b277-5e69-4a51-8e19-24be5492ef63", + "response_id": "chatcmpl-024216c1079f96e79cd0a7356840760d", "images_count": 8, "graphs_count": 1, - "response": "Dopaminergic input to mushroom body output neurons comes from specific DAN types, including dopaminergic PPL1 neurons and dopaminergic PAM neurons. VFB records that dopaminergic PPL1 neuron connects to adult [mushroom body output neuron](https://www.virtualflybrain.org/reports/FBbt_00047953 \"Open mushroom body output neuron in Virtual Fly Brain\"). VFB holds [69](https://v2.virtualflybrain.org/org.geppetto.frontend/geppetto?q=FBbt_00047953,SubclassesOf \"Run in VFB: Subclasses of MBON\") subclasses of mushroom body output neuron.", + "response": "Dopaminergic input to mushroom body output neurons (MBONs) comes from specific dopaminergic neuron types, including dopaminergic PPL1 neurons and dopaminergic PAM neurons. The connectome data indicates that [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\") are among the strongest inputs to MBON, 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.", "graphs": [ { "type": "basic_graph", @@ -1161,7 +1325,7 @@ "graph_failure_mentioned": false, "missing_required_graph": false, "used_data_resource": false, - "response_chars": 532, + "response_chars": 716, "status_count": 9 } }, @@ -1175,7 +1339,7 @@ "requires_graph": false, "min_graphs": 0, "repetition": 1, - "duration_ms": 79171, + "duration_ms": 17794, "status_messages": [ { "message": "Thinking...", @@ -1186,13 +1350,21 @@ "phase": "llm" }, { - "message": "Resolving 1 term in VFB", + "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" @@ -1214,13 +1386,13 @@ "phase": "llm" } ], - "event_count": 127, + "event_count": 60, "ok": true, - "request_id": "b0454d14-8b85-4b1f-bcee-71875b382e00", - "response_id": "chatcmpl-db79355b7c92e4637240ec077680f43c", - "images_count": 5, + "request_id": "76a1fa03-42ec-41d8-88e2-085d4e48a2a7", + "response_id": "chatcmpl-458150795a9139983e22cce9641cd49d", + "images_count": 8, "graphs_count": 0, - "response": "The connectivity of olfactory projection neurons is not directly compared between the Hemibrain and FAFB connectome datasets in VFB evidence. VFB records show that [olfactory projection neuron](https://www.virtualflybrain.org/reports/FBbt_00051298 \"Open olfactory projection neuron in Virtual Fly Brain\") has 60,114 downstream classes and 37,427 upstream classes, ranked by total synaptic weight. 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\").", + "response": "The connectivity of olfactory projection neurons is not directly compared between the Hemibrain and FAFB connectome datasets in VFB evidence. VFB does not currently hold data on the consistency of [olfactory projection neuron](https://www.virtualflybrain.org/reports/FBbt_00051298 \"Open olfactory projection neuron in Virtual Fly Brain\") connectivity between these datasets.", "quality_flags": { "has_tool_status": true, "no_tool_factual_answer": false, @@ -1231,8 +1403,8 @@ "graph_failure_mentioned": false, "missing_required_graph": false, "used_data_resource": false, - "response_chars": 1523, - "status_count": 9 + "response_chars": 374, + "status_count": 11 } }, { @@ -1245,7 +1417,7 @@ "requires_graph": false, "min_graphs": 0, "repetition": 1, - "duration_ms": 82172, + "duration_ms": 17011, "status_messages": [ { "message": "Thinking...", @@ -1308,10 +1480,10 @@ "phase": "llm" } ], - "event_count": 197, + "event_count": 190, "ok": true, - "request_id": "f8af1967-6223-4c3f-8c1f-21475d842e13", - "response_id": "chatcmpl-168687f13b676fcb6af275c3dedfc1fa", + "request_id": "a1df35d9-c095-4d20-9168-d57703853b18", + "response_id": "chatcmpl-15a61c62df3671d73849c93cce6a197f", "images_count": 8, "graphs_count": 0, "response": "VFB holds [1934](https://v2.virtualflybrain.org/org.geppetto.frontend/geppetto?q=FBbt_00007053,TransgeneExpressionHere \"Run in VFB: Transgene expression in adult lateral horn\") transgene expression reports for [adult lateral horn](https://www.virtualflybrain.org/reports/FBbt_00007053 \"Open adult lateral horn in Virtual Fly Brain\"), including driver lines such as P{GMR11B09-GAL4} and PBac{566.P.SVS-1}IA-2[CPTI100013].", @@ -1339,7 +1511,7 @@ "requires_graph": false, "min_graphs": 0, "repetition": 1, - "duration_ms": 24373, + "duration_ms": 88055, "status_messages": [ { "message": "Thinking...", @@ -1349,6 +1521,10 @@ "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" @@ -1370,13 +1546,13 @@ "phase": "llm" } ], - "event_count": 126, + "event_count": 153, "ok": true, - "request_id": "4c5c433e-ea00-47c0-bf62-a9155d27598b", - "response_id": "chatcmpl-0c49737a15ede45d34781e43c9bf5e03", + "request_id": "bdffa560-09fa-46bf-936a-a8dd4c74bbce", + "response_id": "chatcmpl-c35b9009bfedb0579bdb02c022995370", "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 visual neuron type 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, allowing it to detect looming (expansion) stimuli. Its activity elicits a jump escape response. The LPLC2 projects to an optic glomerulus of the PVLP, anterior to LPLC1 and dorsal to LC4. There are approximately 80 of these cells per optic lobe and they are cholinergic.", + "response": "The [lobula plate-lobula columnar neuron LPLC2](https://www.virtualflybrain.org/reports/FBbt_00111763 \"Open lobula plate-lobula columnar neuron LPLC2 in Virtual Fly Brain\") is located in the dorsal area of the lateral cell body rind and has distinct dendritic arbors in each lobula plate layer. It detects looming stimuli, which elicits a jump escape response. The LPLC2 neuron has its main dendritic arbors in layers 4 and 5B of the lobula, with minor processes in layer 5A, and presynaptic sites in layer 4. It projects to an optic glomerulus of the PVLP, anterior to LPLC1 and dorsal to LC4. There are approximately 80 of these cells per optic lobe, and they are cholinergic.", "quality_flags": { "has_tool_status": true, "no_tool_factual_answer": false, @@ -1387,8 +1563,8 @@ "graph_failure_mentioned": false, "missing_required_graph": false, "used_data_resource": false, - "response_chars": 618, - "status_count": 7 + "response_chars": 678, + "status_count": 8 } }, { @@ -1401,7 +1577,7 @@ "requires_graph": false, "min_graphs": 0, "repetition": 1, - "duration_ms": 9917, + "duration_ms": 7037, "status_messages": [ { "message": "Thinking...", @@ -1430,8 +1606,8 @@ ], "event_count": 37, "ok": true, - "request_id": "ed879115-744e-4c08-a3d5-f78c572514e7", - "response_id": "chatcmpl-65f6a1abce1f82b2c95349ab9e04aed9", + "request_id": "8076f7bc-d5aa-4150-9175-ace90cf2c82a", + "response_id": "chatcmpl-c8433392e4a9d9c5c540a6ea5508feca", "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.", @@ -1459,7 +1635,7 @@ "requires_graph": false, "min_graphs": 0, "repetition": 1, - "duration_ms": 15243, + "duration_ms": 203247, "status_messages": [ { "message": "Thinking...", @@ -1469,6 +1645,10 @@ "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" @@ -1478,7 +1658,7 @@ "phase": "mcp" }, { - "message": "Reading VFB term info", + "message": "Querying VFB", "phase": "mcp" }, { @@ -1498,13 +1678,13 @@ "phase": "llm" } ], - "event_count": 66, + "event_count": 101, "ok": true, - "request_id": "0eceabcf-3f47-4c72-871c-64d26c87aac9", - "response_id": "chatcmpl-ff68c50eaa126bbb07dafa918a7bef7b", + "request_id": "9eae37c6-44c1-4e00-abff-263ce8572569", + "response_id": "chatcmpl-2d2ff3d8aeb8b8e697c03ca10686781a", "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.", + "response": "Publications describing the dopaminergic PPL1 neurons and their role in aversive memory include Claridge-Chang et al., 2009, Mao and Davis, 2009, Budnik and White, 1988, and Ren et al., 2016. The dopaminergic PPL1 neurons are located in the posterior inferior lateral protocerebrum of the adult brain and project to various parts of the mushroom body.", "quality_flags": { "has_tool_status": true, "no_tool_factual_answer": false, @@ -1515,8 +1695,8 @@ "graph_failure_mentioned": false, "missing_required_graph": false, "used_data_resource": false, - "response_chars": 191, - "status_count": 9 + "response_chars": 351, + "status_count": 10 } }, { @@ -1529,7 +1709,7 @@ "requires_graph": false, "min_graphs": 0, "repetition": 1, - "duration_ms": 7870, + "duration_ms": 11638, "status_messages": [ { "message": "Thinking...", @@ -1539,6 +1719,10 @@ "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" @@ -1556,10 +1740,10 @@ "phase": "llm" } ], - "event_count": 31, + "event_count": 32, "ok": true, - "request_id": "f27aa2cb-df3e-4573-8b69-2e6c24fd2da5", - "response_id": "chatcmpl-f3ee8f48968a59ded4aa1a35940cbcef", + "request_id": "8cb19b49-fc10-49ab-b930-010be58e3444", + "response_id": "chatcmpl-48ee13b413fe99e3fc5ecef5ec786d7d", "images_count": 5, "graphs_count": 0, "response": "The Hemibrain dataset contains neurons morphologically similar to the fru+ mAL neurons described in light microscopy studies.", @@ -1574,7 +1758,7 @@ "missing_required_graph": false, "used_data_resource": false, "response_chars": 125, - "status_count": 6 + "status_count": 7 } }, { @@ -1587,7 +1771,7 @@ "requires_graph": false, "min_graphs": 0, "repetition": 1, - "duration_ms": 17213, + "duration_ms": 16482, "status_messages": [ { "message": "Thinking...", @@ -1634,13 +1818,13 @@ "phase": "llm" } ], - "event_count": 158, + "event_count": 152, "ok": true, - "request_id": "f971b1b5-dccb-4776-9ac6-fea625a530bb", - "response_id": "chatcmpl-bc050ef89ed046fd57428174ef479df2", + "request_id": "57769663-817e-4961-9f70-e001af6f3b26", + "response_id": "chatcmpl-4da4d3de47a08902daf4fff60d14c4bd", "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 that there are [102](https://v2.virtualflybrain.org/org.geppetto.frontend/geppetto?q=FBbt_00003679,NeuronsPresynapticHere \"Run in VFB: Neurons with presynaptic terminals in fan-shaped body\") neurons with presynaptic terminals in the fan-shaped body. The first 12 of these include [PFNd_PB2](https://www.virtualflybrain.org/reports/FBbt_00111391 \"Open PFNd_PB2 in Virtual Fly Brain\"), [PFNd_PB3](https://www.virtualflybrain.org/reports/FBbt_00111392 \"Open PFNd_PB3 in Virtual Fly Brain\"), [PFNd_PB5](https://www.virtualflybrain.org/reports/FBbt_00111394 \"Open PFNd_PB5 in Virtual Fly Brain\"), [PFNa_PB4](https://www.virtualflybrain.org/reports/FBbt_00111398 \"Open PFNa_PB4 in Virtual Fly Brain\"), [PFNa_PB5](https://www.virtualflybrain.org/reports/FBbt_00111399 \"Open PFNa_PB5 in Virtual Fly Brain\"), PFNa_PB6, PFNa_PB7, PFNa_PB9, PFNp_PB7, [protocerebral bridge glomerulus 8-fan-shaped body-ipsilateral ventral gall surround neuron](https://www.virtualflybrain.org/reports/FBbt_00111463 \"Open protocerebral bridge glomerulus 8-fan-shaped body-ipsilateral ventral gall surround neuron in Virtual Fly Brain\"), [adult ExR1 neuron of DM3 lineage](https://www.virtualflybrain.org/reports/FBbt_00053034 \"Open adult ExR1 neuron of DM3 lineage in Virtual Fly Brain\"), and adult ExR1 neuron of DM4 lineage. The number of synaptic steps between these neurons and the fan-shaped body is not specified.", + "response": "The [fan-shaped body](https://www.virtualflybrain.org/reports/FBbt_00003679 \"Open fan-shaped body in Virtual Fly Brain\") receives input from various sensory neurons. VFB records show that there are [102](https://v2.virtualflybrain.org/org.geppetto.frontend/geppetto?q=FBbt_00003679,NeuronsPresynapticHere \"Run in VFB: Neurons with presynaptic terminals in fan-shaped body\") neurons with presynaptic terminals in the fan-shaped body, including [PFNd_PB2](https://www.virtualflybrain.org/reports/FBbt_00111391 \"Open PFNd_PB2 in Virtual Fly Brain\"), [PFNd_PB3](https://www.virtualflybrain.org/reports/FBbt_00111392 \"Open PFNd_PB3 in Virtual Fly Brain\"), [PFNd_PB5](https://www.virtualflybrain.org/reports/FBbt_00111394 \"Open PFNd_PB5 in Virtual Fly Brain\"), [PFNa_PB4](https://www.virtualflybrain.org/reports/FBbt_00111398 \"Open PFNa_PB4 in Virtual Fly Brain\"), [PFNa_PB5](https://www.virtualflybrain.org/reports/FBbt_00111399 \"Open PFNa_PB5 in Virtual Fly Brain\"), PFNa_PB6, PFNa_PB7, PFNa_PB9, PFNp_PB7, [protocerebral bridge glomerulus 8-fan-shaped body-ipsilateral ventral gall surround neuron](https://www.virtualflybrain.org/reports/FBbt_00111463 \"Open protocerebral bridge glomerulus 8-fan-shaped body-ipsilateral ventral gall surround neuron in Virtual Fly Brain\"), [adult ExR1 neuron of DM3 lineage](https://www.virtualflybrain.org/reports/FBbt_00053034 \"Open adult ExR1 neuron of DM3 lineage in Virtual Fly Brain\"), and adult ExR1 neuron of DM4 lineage. The number of synaptic steps between these neurons and the fan-shaped body is not specified.", "quality_flags": { "has_tool_status": true, "no_tool_factual_answer": false, @@ -1651,7 +1835,7 @@ "graph_failure_mentioned": false, "missing_required_graph": false, "used_data_resource": false, - "response_chars": 1573, + "response_chars": 1553, "status_count": 11 } }, @@ -1665,7 +1849,7 @@ "requires_graph": false, "min_graphs": 0, "repetition": 1, - "duration_ms": 18103, + "duration_ms": 35013, "status_messages": [ { "message": "Thinking...", @@ -1699,18 +1883,42 @@ "message": "Checking the answer is covered", "phase": "llm" }, + { + "message": "Writing the answer", + "phase": "llm" + }, + { + "message": "Checking before saying VFB has no data", + "phase": "mcp" + }, + { + "message": "Querying VFB", + "phase": "mcp" + }, + { + "message": "Querying VFB", + "phase": "mcp" + }, + { + "message": "Querying VFB", + "phase": "mcp" + }, + { + "message": "Checking the answer is covered", + "phase": "llm" + }, { "message": "Writing the answer", "phase": "llm" } ], - "event_count": 139, + "event_count": 278, "ok": true, - "request_id": "409fa6f0-0f7e-4bb6-93bf-ab6275acb2a6", - "response_id": "chatcmpl-7463af57fdd47fa3dc342e0a4fc88535", + "request_id": "344df32e-7b87-45d3-a499-ac18b895320d", + "response_id": "chatcmpl-c1a426c89a0b1f8dfba7a03490111904", "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.\n\nThe strongest specific targets of mushroom body output neuron are [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\").\n\nThe strongest specific targets of dopaminergic neuron are adult cholinergic neuron and [adult Kenyon cell](https://www.virtualflybrain.org/reports/FBbt_00049825 \"Open adult Kenyon cell in Virtual Fly Brain\"). Dopaminergic neuron also connects to itself.", + "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 connectome data indicates that the strongest specific inputs to mushroom body output neuron are [adult cholinergic neuron](https://www.virtualflybrain.org/reports/FBbt_00058205 \"Open adult cholinergic neuron in Virtual Fly Brain\") and [Kenyon cell](https://www.virtualflybrain.org/reports/FBbt_00003686 \"Open Kenyon cell in Virtual Fly Brain\"), while the strongest specific targets of dopaminergic neuron 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, @@ -1721,8 +1929,8 @@ "graph_failure_mentioned": false, "missing_required_graph": false, "used_data_resource": false, - "response_chars": 1813, - "status_count": 9 + "response_chars": 1015, + "status_count": 15 } }, { @@ -1735,7 +1943,7 @@ "requires_graph": false, "min_graphs": 0, "repetition": 1, - "duration_ms": 16072, + "duration_ms": 24416, "status_messages": [ { "message": "Thinking...", @@ -1774,13 +1982,13 @@ "phase": "llm" } ], - "event_count": 113, + "event_count": 139, "ok": true, - "request_id": "9d6bac95-1e09-4407-af7e-a2cd3cb60840", - "response_id": "chatcmpl-82e3b48613b38f7579b4684edff5c857", + "request_id": "b0b4fb8e-a14a-44a9-83c9-9004cb0848d0", + "response_id": "chatcmpl-9c07cea5c601173253dac06882981401", "images_count": 8, "graphs_count": 0, - "response": "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\"), 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.", + "response": "The pathway from olfactory receptor neurons to the lateral horn involves intermediate neurons. Antennal lobe projection neurons are intermediate neurons between olfactory receptor neurons and lateral horn. The connectome data indicates that the strongest specific inputs to [olfactory receptor neuron](https://www.virtualflybrain.org/reports/FBbt_00005926 \"Open olfactory receptor neuron in Virtual Fly Brain\") are from various types of local neurons, including [adult antennal lobe local neuron lLN](https://www.virtualflybrain.org/reports/FBbt_00051502 \"Open adult antennal lobe local neuron lLN in Virtual Fly Brain\"), [adult local interneuron of the lateral ALl1 neuroblast](https://www.virtualflybrain.org/reports/FBbt_00007394 \"Open adult local interneuron of the lateral ALl1 neuroblast in Virtual Fly Brain\"), [antennal lobe local neuron](https://www.virtualflybrain.org/reports/FBbt_00052874 \"Open antennal lobe local neuron in Virtual Fly Brain\"), and [adult antennal lobe local neuron](https://www.virtualflybrain.org/reports/FBbt_00007390 \"Open adult antennal lobe local neuron in Virtual Fly Brain\"). VFB holds [1661](https://v2.virtualflybrain.org/org.geppetto.frontend/geppetto?q=FBbt_00007053,NeuronsPartHere \"Run in VFB: Neurons with some part in adult lateral horn\") records of neurons with some part in [adult lateral horn](https://www.virtualflybrain.org/reports/FBbt_00007053 \"Open adult lateral horn in Virtual Fly Brain\") and [1658](https://v2.virtualflybrain.org/org.geppetto.frontend/geppetto?q=FBbt_00007053,NeuronsSynaptic \"Run in VFB: Neurons with synaptic terminals in adult lateral horn\") records of neurons with synaptic terminals in adult lateral horn.", "quality_flags": { "has_tool_status": true, "no_tool_factual_answer": false, @@ -1791,7 +1999,7 @@ "graph_failure_mentioned": false, "missing_required_graph": false, "used_data_resource": false, - "response_chars": 1521, + "response_chars": 1684, "status_count": 9 } }, @@ -1805,7 +2013,7 @@ "requires_graph": false, "min_graphs": 0, "repetition": 1, - "duration_ms": 6663, + "duration_ms": 8267, "status_messages": [ { "message": "Thinking...", @@ -1836,13 +2044,13 @@ "phase": "llm" } ], - "event_count": 24, + "event_count": 53, "ok": true, - "request_id": "9ef88995-f509-4060-b039-8a112a44b252", - "response_id": "chatcmpl-d86a34f6a730da27c5d64c6975e3b00e", + "request_id": "95594d77-1fd4-460a-a87f-0a2fe497b95c", + "response_id": "chatcmpl-56e214e7b0b3d06edb13afd51f2fb774", "images_count": 0, "graphs_count": 0, - "response": "The classification of neuron types within the visual system includes subclasses of visual system neuron.", + "response": "The question about the number of distinct neuron types in the adult Drosophila visual system and their hierarchical organization cannot be fully answered from VFB evidence. However, it is known that there are subclasses of visual system neuron.", "quality_flags": { "has_tool_status": true, "no_tool_factual_answer": false, @@ -1853,7 +2061,7 @@ "graph_failure_mentioned": false, "missing_required_graph": false, "used_data_resource": false, - "response_chars": 104, + "response_chars": 244, "status_count": 7 } }, @@ -1867,7 +2075,7 @@ "requires_graph": false, "min_graphs": 0, "repetition": 1, - "duration_ms": 17554, + "duration_ms": 10361, "status_messages": [ { "message": "Thinking...", @@ -1901,42 +2109,18 @@ "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": 136, + "event_count": 51, "ok": true, - "request_id": "7a9524ba-fe75-4995-bb9b-0e2c619a620a", - "response_id": "chatcmpl-119c6362929cf8881f4b0dc270643bf8", + "request_id": "40c412db-7a7a-451e-81c9-f4b84cd0ba0d", + "response_id": "chatcmpl-c31d63118f5956fd8e5da6769be56e60", "images_count": 8, "graphs_count": 0, - "response": "The strongest synaptic input to the MBON-gamma1pedc>a/b neuron is not specified in VFB evidence.", + "response": "The strongest synaptic input to the MBON-gamma1pedc>a/b neuron is not specified. VFB holds upstream connectivity classes for [mushroom body output neuron 11](https://www.virtualflybrain.org/reports/FBbt_00100246 \"Open mushroom body output neuron 11 in Virtual Fly Brain\"), but the lookup did not complete.", "quality_flags": { "has_tool_status": true, "no_tool_factual_answer": false, @@ -1947,8 +2131,8 @@ "graph_failure_mentioned": false, "missing_required_graph": false, "used_data_resource": false, - "response_chars": 96, - "status_count": 15 + "response_chars": 305, + "status_count": 9 } }, { @@ -1961,7 +2145,7 @@ "requires_graph": false, "min_graphs": 0, "repetition": 1, - "duration_ms": 13493, + "duration_ms": 12914, "status_messages": [ { "message": "Thinking...", @@ -1991,10 +2175,6 @@ "message": "Querying VFB", "phase": "mcp" }, - { - "message": "Querying VFB", - "phase": "mcp" - }, { "message": "Checking the answer is covered", "phase": "llm" @@ -2004,13 +2184,13 @@ "phase": "llm" } ], - "event_count": 89, + "event_count": 77, "ok": true, - "request_id": "f6f74f38-28df-4a38-bbf7-a4196522b75e", - "response_id": "chatcmpl-4cf164da6462f87e3978395cd1cf2ee1", + "request_id": "d4b052c0-c4af-4ac6-bbfa-20ea38ce48f3", + "response_id": "chatcmpl-4fdf1679ee0b2268ed75ac166063d47f", "images_count": 8, "graphs_count": 0, - "response": "The connectome data indicates that [Kenyon cell](https://www.virtualflybrain.org/reports/FBbt_00003686 \"Open Kenyon cell in Virtual Fly Brain\") provides a strong input to [mushroom body output neuron](https://www.virtualflybrain.org/reports/FBbt_00047953 \"Open mushroom body output neuron in Virtual Fly Brain\"), with 7.09 synapses per connected pair and 59% of individuals connected. VFB does not currently hold data on the downstream connectivity classes for [gamma Kenyon cell](https://www.virtualflybrain.org/reports/FBbt_00100247 \"Open gamma 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 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 evidence does not specify which mushroom body output neurons receive input from both alpha/beta Kenyon cells and gamma Kenyon cells. VFB does not currently hold data on the downstream connectivity classes for gamma Kenyon cells. VFB holds [69](https://v2.virtualflybrain.org/org.geppetto.frontend/geppetto?q=FBbt_00047953,SubclassesOf \"Run in VFB: Subclasses of MBON\") subclasses of [mushroom body output neuron](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, @@ -2021,8 +2201,8 @@ "graph_failure_mentioned": false, "missing_required_graph": false, "used_data_resource": false, - "response_chars": 1043, - "status_count": 10 + "response_chars": 806, + "status_count": 9 } }, { @@ -2035,7 +2215,7 @@ "requires_graph": false, "min_graphs": 0, "repetition": 1, - "duration_ms": 13002, + "duration_ms": 11700, "status_messages": [ { "message": "Thinking...", @@ -2068,11 +2248,11 @@ ], "event_count": 92, "ok": true, - "request_id": "e840dce5-3476-4ca0-822e-debaf8c27f29", - "response_id": "chatcmpl-e99fa282980a7d61487def1447e754cb", + "request_id": "0d1f6876-0531-4243-9399-308c01dbca7e", + "response_id": "chatcmpl-8fcd9fa12949b6f3cc1337a4548e6e4a", "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.\nVFB 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, @@ -2083,7 +2263,7 @@ "graph_failure_mentioned": false, "missing_required_graph": false, "used_data_resource": false, - "response_chars": 451, + "response_chars": 455, "status_count": 7 } }, @@ -2097,7 +2277,7 @@ "requires_graph": false, "min_graphs": 0, "repetition": 1, - "duration_ms": 16525, + "duration_ms": 18512, "status_messages": [ { "message": "Thinking...", @@ -2135,6 +2315,10 @@ "message": "Querying VFB", "phase": "mcp" }, + { + "message": "Querying VFB", + "phase": "mcp" + }, { "message": "Checking the answer is covered", "phase": "llm" @@ -2144,13 +2328,13 @@ "phase": "llm" } ], - "event_count": 142, + "event_count": 134, "ok": true, - "request_id": "fb4d2c23-3ca8-4b34-9b0b-46bff4abd1cf", - "response_id": "chatcmpl-3c032f91299eef36710761cf8e8d409b", + "request_id": "ec4451ee-d3b7-46fd-8dc2-cca37011c1e4", + "response_id": "chatcmpl-0e0d419477e5227201373be6e057d57f", "images_count": 8, "graphs_count": 0, - "response": "Neurons that connect the [adult central complex](https://www.virtualflybrain.org/reports/FBbt_00003632 \"Open adult central complex in Virtual Fly Brain\") to the [lateral accessory lobe on L3 CNS template, Wood2018](https://www.virtualflybrain.org/reports/VFB_00050314 \"Open lateral accessory lobe on L3 CNS template, Wood2018 in Virtual Fly Brain\") include [PFL1](https://www.virtualflybrain.org/reports/FBbt_00111433 \"Open PFL1 in Virtual Fly Brain\"), [PFL2_PB4](https://www.virtualflybrain.org/reports/FBbt_00111453 \"Open PFL2_PB4 in Virtual Fly Brain\"), [PFL3_PB7](https://www.virtualflybrain.org/reports/FBbt_00111450 \"Open PFL3_PB7 in Virtual Fly Brain\"), [PFL1_PB1](https://www.virtualflybrain.org/reports/FBbt_00111434 \"Open PFL1_PB1 in Virtual Fly Brain\"), [PFL1_PB7](https://www.virtualflybrain.org/reports/FBbt_00111440 \"Open PFL1_PB7 in Virtual Fly Brain\"), and [PFL1_PB2](https://www.virtualflybrain.org/reports/FBbt_00111435 \"Open PFL1_PB2 in Virtual Fly Brain\"). VFB does not currently hold data on neurons with some part in embryonic/larval lateral accessory lobe, neurons with presynaptic terminals in embryonic/larval lateral accessory lobe, or neurons with postsynaptic terminals in embryonic/larval lateral accessory lobe.", + "response": "Neurons that connect the [adult central complex](https://www.virtualflybrain.org/reports/FBbt_00003632 \"Open adult central complex in Virtual Fly Brain\") to the lateral accessory lobe include [PFL1](https://www.virtualflybrain.org/reports/FBbt_00111433 \"Open PFL1 in Virtual Fly Brain\"), [PFL2_PB4](https://www.virtualflybrain.org/reports/FBbt_00111453 \"Open PFL2_PB4 in Virtual Fly Brain\"), [PFL3_PB7](https://www.virtualflybrain.org/reports/FBbt_00111450 \"Open PFL3_PB7 in Virtual Fly Brain\"), [PFL1_PB1](https://www.virtualflybrain.org/reports/FBbt_00111434 \"Open PFL1_PB1 in Virtual Fly Brain\"), [PFL1_PB7](https://www.virtualflybrain.org/reports/FBbt_00111440 \"Open PFL1_PB7 in Virtual Fly Brain\"), and [PFL1_PB2](https://www.virtualflybrain.org/reports/FBbt_00111435 \"Open PFL1_PB2 in Virtual Fly Brain\"). VFB does not currently hold data on neurons with some part in embryonic/larval lateral accessory lobe, neurons with presynaptic terminals in embryonic/larval lateral accessory lobe, or neurons with postsynaptic terminals in embryonic/larval lateral accessory lobe.", "quality_flags": { "has_tool_status": true, "no_tool_factual_answer": false, @@ -2161,8 +2345,8 @@ "graph_failure_mentioned": false, "missing_required_graph": false, "used_data_resource": false, - "response_chars": 1241, - "status_count": 11 + "response_chars": 1076, + "status_count": 12 } }, { @@ -2175,66 +2359,11 @@ "requires_graph": false, "min_graphs": 0, "repetition": 1, - "duration_ms": 201012, - "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": "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": 93, - "ok": true, - "request_id": "f201c005-2690-4b85-b5d2-fd784c45b152", - "response_id": "chatcmpl-bd40e8dcff30282cd5b289b6ac8659e4", - "images_count": 8, - "graphs_count": 0, - "response": "Data for [descending neuron of the anterior dorsal brain DNa02](https://www.virtualflybrain.org/reports/FBbt_00047573 \"Open descending neuron of the anterior dorsal brain DNa02 in Virtual Fly Brain\") is available in VFB, including light microscopy images and driver lines. There are [18](https://v2.virtualflybrain.org/org.geppetto.frontend/geppetto?q=FBbt_00047573,ListAllAvailableImages \"Run in VFB: List all available images of DNa02\") available images of DNa02 and [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. Additionally, there are 2 transgene expression reports for DNa02. The images are from both MaleCNS and FlyEM-HB datasets.", + "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, @@ -2243,8 +2372,8 @@ "graph_failure_mentioned": false, "missing_required_graph": false, "used_data_resource": false, - "response_chars": 769, - "status_count": 12 + "response_chars": 25, + "status_count": 0 } }, { @@ -2257,7 +2386,7 @@ "requires_graph": false, "min_graphs": 0, "repetition": 1, - "duration_ms": 6858, + "duration_ms": 6837, "status_messages": [ { "message": "Thinking...", @@ -2284,13 +2413,13 @@ "phase": "llm" } ], - "event_count": 55, + "event_count": 53, "ok": true, - "request_id": "14b6f1b1-5b43-4805-9729-31741d5974b9", - "response_id": "chatcmpl-f6e4842dc3e83c5e6e56199340838744", + "request_id": "20331d40-14fe-4eb5-97af-1e403858e5bd", + "response_id": "chatcmpl-521e17b751640a3bbe59736171029a94", "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 evidence does not specify how these neurons are connected or what genetic tools can be used to access them.", + "response": "The carbon dioxide sensitive neuron is involved in CO2 avoidance and is connected to downstream classes such as GABAergic local interneuron of the adult antennal lobe and adult antennal lobe local neuron lLN2P.", "quality_flags": { "has_tool_status": true, "no_tool_factual_answer": false, @@ -2301,7 +2430,7 @@ "graph_failure_mentioned": false, "missing_required_graph": false, "used_data_resource": false, - "response_chars": 269, + "response_chars": 210, "status_count": 6 } }, @@ -2315,7 +2444,7 @@ "requires_graph": false, "min_graphs": 0, "repetition": 1, - "duration_ms": 27702, + "duration_ms": 26363, "status_messages": [ { "message": "Thinking...", @@ -2354,13 +2483,13 @@ "phase": "llm" } ], - "event_count": 353, + "event_count": 300, "ok": true, - "request_id": "84b801a9-3ad8-452e-8273-d57043a3faa3", - "response_id": "chatcmpl-7f1e0de15b3ad1326a33423f52269e74", + "request_id": "bde75b10-1205-49d3-949d-395f919f4bb4", + "response_id": "chatcmpl-d14d815b291dbee12979b31c24cbbfb7", "images_count": 8, "graphs_count": 1, - "response": "The [giant fiber neuron](https://www.virtualflybrain.org/reports/FBbt_00004020 \"Open giant fiber neuron in Virtual Fly Brain\") is a large adult descending neuron that controls jump escape behavior. It has a large cell body located posterior to the lower protocerebrum and a large descending axon that enters the cervical connective via the posterior cerebro-cervical fascicle and descends on the ipsilateral side in the dorsal cervical fasciculus. The giant fiber neuron has dendritic arborization in the ipsilateral zones A and B of the antennal mechanosensory and motor center, where it receives substantial input from zone A and B Johnston organ neurons. It also arborizes in the posterior ventrolateral protocerebrum and gorget. In the 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 is connected to various neuron types, including [adult VNC neuron](https://www.virtualflybrain.org/reports/FBbt_00059289 \"Open adult VNC neuron in Virtual Fly Brain\"), [thoracic neuron](https://www.virtualflybrain.org/reports/FBbt_00001983 \"Open thoracic neuron in Virtual Fly Brain\"), [mesothoracic neuron](https://www.virtualflybrain.org/reports/FBbt_00001985 \"Open mesothoracic neuron in Virtual Fly Brain\"), [primary neuron](https://www.virtualflybrain.org/reports/FBbt_00047097 \"Open primary neuron in Virtual Fly Brain\"), and [sensory system neuron](https://www.virtualflybrain.org/reports/FBbt_00007693 \"Open sensory system neuron in Virtual Fly Brain\"). Available driver lines include [5](https://v2.virtualflybrain.org/org.geppetto.frontend/geppetto?q=FBbt_00004020,SplitsTargeting \"Run in VFB: Splits targeting DNp01\") split-GAL4 combinations. There are [10](https://v2.virtualflybrain.org/org.geppetto.frontend/geppetto?q=FBbt_00004020,TransgeneExpressionHere \"Run in VFB: Transgene expression in DNp01\") transgene expression reports available for the giant fiber neuron, including expression patterns for P{GMR78G07-GAL4}, P{GMR79D08-GAL4}, and P{R48A11-GAL4.DBD} ∩ P{R30C01-p65.AD}.\n\nRelevant publications on the giant fiber neuron include Thomas and Wyman (1984), Koto et al. (1981), Power (1948), Ito et al. (2014), Kamikouchi et al. (2009), and Kennedy and Broadie (2018).", + "response": "The [giant fiber neuron](https://www.virtualflybrain.org/reports/FBbt_00004020 \"Open giant fiber neuron in Virtual Fly Brain\") is a large adult descending neuron that controls jump escape behavior. It has a large cell body located posterior to the lower protocerebrum and a large descending axon that enters the cervical connective via the posterior cerebro-cervical fascicle and descends on the ipsilateral side in the dorsal cervical fasciculus. The giant fiber neuron has dendritic arborization in the ipsilateral zones A and B of the antennal mechanosensory and motor center, where it receives substantial input from zone A and B Johnston organ neurons. It also arborizes in the posterior ventrolateral protocerebrum and gorget. In the 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 is connected to various other neurons, including adult VNC neurons, thoracic neurons, mesothoracic neurons, primary neurons, and sensory system neurons. 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 and [10](https://v2.virtualflybrain.org/org.geppetto.frontend/geppetto?q=FBbt_00004020,TransgeneExpressionHere \"Run in VFB: Transgene expression in DNp01\") transgene expression reports, such as P{GMR78G07-GAL4} and P{R48A11-GAL4.DBD} ∩ P{R30C01-p65.AD}. Relevant publications include Thomas and Wyman (1984), Koto et al. (1981), Power (1948), and others.", "graphs": [ { "type": "basic_graph", @@ -2586,7 +2715,7 @@ "graph_failure_mentioned": false, "missing_required_graph": false, "used_data_resource": false, - "response_chars": 2306, + "response_chars": 1616, "status_count": 9 } }, @@ -2600,7 +2729,7 @@ "requires_graph": false, "min_graphs": 0, "repetition": 1, - "duration_ms": 16356, + "duration_ms": 23222, "status_messages": [ { "message": "Thinking...", @@ -2642,18 +2771,42 @@ "message": "Checking the answer is covered", "phase": "llm" }, + { + "message": "Writing the answer", + "phase": "llm" + }, + { + "message": "Checking before saying VFB has no data", + "phase": "mcp" + }, + { + "message": "Querying VFB", + "phase": "mcp" + }, + { + "message": "Querying VFB", + "phase": "mcp" + }, + { + "message": "Querying VFB", + "phase": "mcp" + }, + { + "message": "Checking the answer is covered", + "phase": "llm" + }, { "message": "Writing the answer", "phase": "llm" } ], - "event_count": 175, + "event_count": 442, "ok": true, - "request_id": "7652dd55-01ae-47f9-b5f9-2ecb26f53edb", - "response_id": "chatcmpl-aa856a9aa6d0b332799554811a19f56d", + "request_id": "f4ad8b05-9f8c-421a-8352-ea98657b24c9", + "response_id": "chatcmpl-9b9e15aeea6278a5917eaf088ea8c5c3", "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 also might 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\") are [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\"), [adult optic lobe columnar neuron](https://www.virtualflybrain.org/reports/FBbt_00005129 \"Open adult optic lobe columnar neuron in Virtual Fly Brain\"), [transmedullary neuron](https://www.virtualflybrain.org/reports/FBbt_00003788 \"Open transmedullary neuron in Virtual Fly Brain\"), and [optic lobe wide-field columnar neuron](https://www.virtualflybrain.org/reports/FBbt_00110137 \"Open optic lobe wide-field 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, adult optic lobe columnar neuron, optic lobe intrinsic columnar neuron, [adult visual projection neuron](https://www.virtualflybrain.org/reports/FBbt_00048286 \"Open adult visual projection neuron in Virtual Fly Brain\"), and transmedullary neuron. Visual information could reach the memory circuit via these connections.", + "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.\n\nThe 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\"), [adult optic lobe columnar neuron](https://www.virtualflybrain.org/reports/FBbt_00005129 \"Open adult optic lobe columnar neuron in Virtual Fly Brain\"), [transmedullary neuron](https://www.virtualflybrain.org/reports/FBbt_00003788 \"Open transmedullary neuron in Virtual Fly Brain\"), and [optic lobe wide-field columnar neuron](https://www.virtualflybrain.org/reports/FBbt_00110137 \"Open optic lobe wide-field columnar neuron in Virtual Fly Brain\"). The strongest specific targets of visual system neuron include adult optic lobe neuron, optic lobe wide-field columnar neuron, adult optic lobe columnar neuron, optic lobe intrinsic columnar neuron, [adult visual projection neuron](https://www.virtualflybrain.org/reports/FBbt_00048286 \"Open adult visual projection neuron in Virtual Fly Brain\"), and transmedullary neuron.\n\nVFB lists neurons with some part in mushroom body, neurons with synaptic terminals in mushroom body, neurons with presynaptic terminals in mushroom body, and neurons with postsynaptic terminals in mushroom body. These include various types of projection neurons and other neuron types.\n\nVisual information could reach the memory circuit via these connections, as the mushroom body is involved in memory and learning.", "graphs": [ { "type": "basic_graph", @@ -2872,8 +3025,8 @@ "graph_failure_mentioned": false, "missing_required_graph": false, "used_data_resource": false, - "response_chars": 1863, - "status_count": 11 + "response_chars": 2228, + "status_count": 17 } }, { @@ -2886,7 +3039,7 @@ "requires_graph": false, "min_graphs": 0, "repetition": 1, - "duration_ms": 71798, + "duration_ms": 133850, "status_messages": [ { "message": "Thinking...", @@ -2927,8 +3080,8 @@ ], "event_count": 90, "ok": true, - "request_id": "f7d0c752-7309-4f69-9c2b-6a4da3d1ef59", - "response_id": "chatcmpl-7e6840a139cc2ad64a56cd5ee395097d", + "request_id": "740869a2-0d49-4be2-be97-e040753133c5", + "response_id": "chatcmpl-e926aea640ce5368f6072c8b856ab4ab", "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\").", @@ -3236,7 +3389,7 @@ "requires_graph": false, "min_graphs": 0, "repetition": 1, - "duration_ms": 14085, + "duration_ms": 196137, "status_messages": [ { "message": "Thinking...", @@ -3287,13 +3440,13 @@ "phase": "llm" } ], - "event_count": 179, + "event_count": 183, "ok": true, - "request_id": "ca409a2b-fa5b-4feb-9193-64507455ad87", - "response_id": "chatcmpl-e3aa9a2c72703f3986803b473091f8a0", + "request_id": "6935d415-3129-4b57-b042-f3f66dc15d49", + "response_id": "chatcmpl-4b28f3f8cde3d61bf74875e889d12d4e", "images_count": 8, "graphs_count": 1, - "response": "Thermosensory neurons connect to the [mushroom body](https://www.virtualflybrain.org/reports/FBbt_00005801 \"Open mushroom body in Virtual Fly Brain\"). The downstream class-connectivity previews for adult thermosensory projection neurons include mushroom-body-associated dopaminergic neurons and gamma main Kenyon cells. VFB's class-level connectivity table for [thermosensory neuron](https://www.virtualflybrain.org/reports/FBbt_00005918 \"Open thermosensory neuron in Virtual Fly Brain\") lists [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\") as strong targets, with 18.9, 18.8, and 18.7 synapses per connected pair, respectively.\n\nVFB holds [366](https://v2.virtualflybrain.org/org.geppetto.frontend/geppetto?q=FBbt_00005801,NeuronsPresynapticHere \"Run in VFB: Neurons with presynaptic terminals in mushroom body\") records of neurons with presynaptic terminals in mushroom body and [304](https://v2.virtualflybrain.org/org.geppetto.frontend/geppetto?q=FBbt_00005801,NeuronsPostsynapticHere \"Run in VFB: Neurons with postsynaptic terminals in mushroom body\") records of neurons with postsynaptic terminals in mushroom body.\n\nThe connectivity between thermosensory neurons and the mushroom body may allow temperature information to influence memory formation, as the mushroom body is involved in learning and memory.", + "response": "Thermosensory neurons connect to the [mushroom body](https://www.virtualflybrain.org/reports/FBbt_00005801 \"Open mushroom body in Virtual Fly Brain\") via projection neurons. The downstream class-connectivity previews for adult thermosensory projection neurons include mushroom-body-associated dopaminergic neurons and gamma main Kenyon cells. VFB's class-level connectivity table for [thermosensory neuron](https://www.virtualflybrain.org/reports/FBbt_00005918 \"Open thermosensory neuron in Virtual Fly Brain\") lists [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\") as strong targets, with 18.9, 18.8, and 18.7 synapses per connected pair, respectively.\n\nVFB holds [366](https://v2.virtualflybrain.org/org.geppetto.frontend/geppetto?q=FBbt_00005801,NeuronsPresynapticHere \"Run in VFB: Neurons with presynaptic terminals in mushroom body\") records of neurons with presynaptic terminals in mushroom body and [304](https://v2.virtualflybrain.org/org.geppetto.frontend/geppetto?q=FBbt_00005801,NeuronsPostsynapticHere \"Run in VFB: Neurons with postsynaptic terminals in mushroom body\") records of neurons with postsynaptic terminals in mushroom body.\n\nTemperature information could potentially influence memory formation through the connectivity between thermosensory neurons and the mushroom body, given that the mushroom body is involved in learning and memory.", "graphs": [ { "type": "basic_graph", @@ -3519,7 +3672,7 @@ "graph_failure_mentioned": false, "missing_required_graph": false, "used_data_resource": false, - "response_chars": 1703, + "response_chars": 1747, "status_count": 12 } }, @@ -3533,7 +3686,7 @@ "requires_graph": false, "min_graphs": 0, "repetition": 1, - "duration_ms": 200191, + "duration_ms": 205871, "status_messages": [ { "message": "Thinking...", @@ -3543,6 +3696,10 @@ "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" @@ -3588,13 +3745,13 @@ "phase": "llm" } ], - "event_count": 243, + "event_count": 230, "ok": true, - "request_id": "a4e13041-58cb-4c99-ac20-ff8e14bb4f00", - "response_id": "chatcmpl-b9331a25c88b5ac53dcb48247bb6026f", + "request_id": "3312bdd7-2ac6-46b8-be75-5e30a4d350a4", + "response_id": "chatcmpl-4e1a0a0e93321fdc71392a20e400e059", "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 types of data available. There are [2,698](https://v2.virtualflybrain.org/org.geppetto.frontend/geppetto?q=FBbt_00051068,NeuronsPartHere \"Run in VFB: Neurons with some part in subesophageal zone\") neurons with some part in the subesophageal zone, including [serotonergic SE1 neuron](https://www.virtualflybrain.org/reports/FBbt_00001980 \"Open serotonergic SE1 neuron in Virtual Fly Brain\"), [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\"). Additionally, [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 neuron](https://www.virtualflybrain.org/reports/FBbt_00111352 \"Open intrinsic antennal mechanosensory and motor center neuron in Virtual Fly Brain\") and [AMMC-VLP](https://www.virtualflybrain.org/reports/FBbt_00111354 \"Open AMMC-VLP in Virtual Fly Brain\").\n\nVFB also holds connectomics data for the subesophageal zone, including neurons with presynaptic and postsynaptic terminals, although the exact counts for these are not provided in the current results.\n\nFor genetic tools, there are 4,205 transgene expression patterns in the subesophageal zone, including GAL4 drivers such as P{GMR12D05-GAL4} and binary/intersectional drivers.\n\nThere is one available image of the subesophageal zone, which is the adult subesophageal zone on the adult brain template JFRC2.", + "response": "The [subesophageal zone](https://www.virtualflybrain.org/reports/FBbt_00051068 \"Open subesophageal zone in Virtual Fly Brain\") is well-characterised, with available imagery and various queries for neuron types and connectomics data. VFB records show [2,698](https://v2.virtualflybrain.org/org.geppetto.frontend/geppetto?q=FBbt_00051068,NeuronsPartHere \"Run in VFB: Neurons with some part in subesophageal zone\") neurons with some part in the subesophageal zone, including [serotonergic SE1 neuron](https://www.virtualflybrain.org/reports/FBbt_00001980 \"Open serotonergic SE1 neuron in Virtual Fly Brain\") and [larval CCAP subesophageal IN-1 neuron](https://www.virtualflybrain.org/reports/FBbt_00111345 \"Open larval CCAP subesophageal IN-1 neuron in Virtual Fly Brain\"). There are also [2,598](https://v2.virtualflybrain.org/org.geppetto.frontend/geppetto?q=FBbt_00051068,NeuronsSynaptic \"Run in VFB: Neurons with synaptic terminals in subesophageal zone\") neurons with synaptic terminals in the subesophageal zone, such as [intrinsic antennal mechanosensory and motor center neuron](https://www.virtualflybrain.org/reports/FBbt_00111352 \"Open intrinsic antennal mechanosensory and motor center neuron in Virtual Fly Brain\") and [AMMC-VLP](https://www.virtualflybrain.org/reports/FBbt_00111354 \"Open AMMC-VLP in Virtual Fly Brain\").\n\nFor genetic tools, VFB holds 4,205 transgene expression reports for the subesophageal zone, including [P{GMR12D05-GAL4} expression pattern](https://www.virtualflybrain.org/reports/VFBexp_FBtp0057511 \"Open P{GMR12D05-GAL4} expression pattern in Virtual Fly Brain\") and P{VT000003-GAL4} expression pattern.\n\nConnectivity data indicates that there are neurons with presynaptic and postsynaptic terminals in the subesophageal zone, but the exact details of these connections are not specified here.\n\nVFB holds [29,765](https://v2.virtualflybrain.org/org.geppetto.frontend/geppetto?q=FBbt_00051068,ImagesNeurons \"Run in VFB: Images of neurons with some part in subesophageal zone\") images of neurons with some part in the subesophageal zone.", "quality_flags": { "has_tool_status": true, "no_tool_factual_answer": false, @@ -3605,8 +3762,8 @@ "graph_failure_mentioned": false, "missing_required_graph": false, "used_data_resource": false, - "response_chars": 1938, - "status_count": 13 + "response_chars": 2070, + "status_count": 14 } }, { @@ -3619,7 +3776,7 @@ "requires_graph": true, "min_graphs": 1, "repetition": 1, - "duration_ms": 15077, + "duration_ms": 17434, "status_messages": [ { "message": "Thinking...", @@ -3645,6 +3802,10 @@ "message": "Querying VFB", "phase": "mcp" }, + { + "message": "Querying VFB", + "phase": "mcp" + }, { "message": "Querying VFB connectivity", "phase": "mcp" @@ -3666,13 +3827,13 @@ "phase": "llm" } ], - "event_count": 172, + "event_count": 146, "ok": true, - "request_id": "2a39fb07-a57f-4d53-9624-a4f7e4c65d63", - "response_id": "chatcmpl-0ec1b1d90477b85463d9da9d9ad1b666", + "request_id": "69b522dd-5eca-4698-aad4-4481ffef4307", + "response_id": "chatcmpl-1eb6ffb1bf93fd93cf3b18c722aa6527", "images_count": 8, "graphs_count": 1, - "response": "The [medulla](https://www.virtualflybrain.org/reports/FBbt_00003748 \"Open medulla in Virtual Fly Brain\") has neurons with presynaptic terminals, with [262](https://v2.virtualflybrain.org/org.geppetto.frontend/geppetto?q=FBbt_00003748,NeuronsPresynapticHere \"Run in VFB: Neurons with presynaptic terminals in medulla\") results, and neurons with postsynaptic terminals, with [333](https://v2.virtualflybrain.org/org.geppetto.frontend/geppetto?q=FBbt_00003748,NeuronsPostsynapticHere \"Run in VFB: Neurons with postsynaptic terminals in medulla\") results. These include neurons such as [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, which have presynaptic terminals in the medulla, and 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, which have postsynaptic terminals in the medulla.", + "response": "The [medulla](https://www.virtualflybrain.org/reports/FBbt_00003748 \"Open medulla in Virtual Fly Brain\") has neurons with presynaptic terminals, with [262](https://v2.virtualflybrain.org/org.geppetto.frontend/geppetto?q=FBbt_00003748,NeuronsPresynapticHere \"Run in VFB: Neurons with presynaptic terminals in medulla\") results, including [Dm8b](https://www.virtualflybrain.org/reports/FBbt_00110069 \"Open Dm8b in Virtual Fly Brain\"), [PS128](https://www.virtualflybrain.org/reports/FBbt_20001883 \"Open PS128 in Virtual Fly Brain\"), [Mi10b](https://www.virtualflybrain.org/reports/FBbt_00110070 \"Open Mi10b in Virtual Fly Brain\"), [CB3849](https://www.virtualflybrain.org/reports/FBbt_20007264 \"Open CB3849 in Virtual Fly Brain\"), [TmY-ds](https://www.virtualflybrain.org/reports/FBbt_00052643 \"Open TmY-ds in Virtual Fly Brain\"), [Dm7](https://www.virtualflybrain.org/reports/FBbt_00003774 \"Open Dm7 in Virtual Fly Brain\"), Mi6, Mi8, Tm10, Tm13, Tm14, and Tm18. It also has neurons with postsynaptic terminals, with [333](https://v2.virtualflybrain.org/org.geppetto.frontend/geppetto?q=FBbt_00003748,NeuronsPostsynapticHere \"Run in VFB: Neurons with postsynaptic terminals in medulla\") results, including 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", @@ -3819,8 +3980,8 @@ "graph_failure_mentioned": false, "missing_required_graph": false, "used_data_resource": false, - "response_chars": 1605, - "status_count": 11 + "response_chars": 1484, + "status_count": 12 } }, { @@ -3833,7 +3994,7 @@ "requires_graph": false, "min_graphs": 0, "repetition": 1, - "duration_ms": 6083, + "duration_ms": 5612, "status_messages": [ { "message": "Thinking...", @@ -3866,8 +4027,8 @@ ], "event_count": 42, "ok": true, - "request_id": "df45b880-bf9f-4bdf-95f2-f6bd69abf663", - "response_id": "chatcmpl-f393253724cf118054328db11a807a11", + "request_id": "d07ff3de-25f6-403a-9f1f-e7d51ccab58a", + "response_id": "chatcmpl-d2e7784e33e1c4439dd1838bde60868d", "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.", @@ -3895,7 +4056,7 @@ "requires_graph": false, "min_graphs": 0, "repetition": 1, - "duration_ms": 9056, + "duration_ms": 35056, "status_messages": [ { "message": "Thinking...", @@ -3922,13 +4083,13 @@ "phase": "llm" } ], - "event_count": 118, + "event_count": 23, "ok": true, - "request_id": "13c3b758-8aa1-4e0e-a6de-99d13a33afb2", - "response_id": "chatcmpl-6d4605e8ad09fa49fabd0a5badc09926", + "request_id": "f0d18c63-f5de-4bee-8962-1e5ff42113cd", + "response_id": "chatcmpl-438509c077c4f051ff7ccae2caea30e2", "images_count": 0, "graphs_count": 0, - "response": "To cite Virtual Fly Brain in a publication, use the citation VFB evidence on their website, including APA, MLA, Chicago, and BibTeX formats. If you use Virtual Fly Brain data, tools, or resources in your research, please cite their work using the citation formats below, which include a reference to Court et al., 2023, Virtual Fly Brain—An interactive atlas of the Drosophila nervous system, published in Frontiers in Physiology, https://doi.org/10.3389/fphys.2023.1076533.", + "response": "To cite Virtual Fly Brain in a publication, use the 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, @@ -3939,7 +4100,7 @@ "graph_failure_mentioned": false, "missing_required_graph": false, "used_data_resource": false, - "response_chars": 474, + "response_chars": 3170, "status_count": 6 } }, @@ -3953,7 +4114,7 @@ "requires_graph": false, "min_graphs": 0, "repetition": 1, - "duration_ms": 5374, + "duration_ms": 7090, "status_messages": [ { "message": "Thinking...", @@ -3982,8 +4143,8 @@ ], "event_count": 25, "ok": true, - "request_id": "a3520da8-838e-461f-8734-07190072d4cb", - "response_id": "chatcmpl-7a33c24eaadcb8a37e045388ccef70b0", + "request_id": "a0dbd65b-69f1-47ba-92a5-28ea59583682", + "response_id": "chatcmpl-a9659abb35f13414b4096dbc0d996867", "images_count": 0, "graphs_count": 0, "response": "Virtual Fly Brain is funded by multiple UK research councils and charitable foundations since 2009.", @@ -4011,7 +4172,7 @@ "requires_graph": false, "min_graphs": 0, "repetition": 1, - "duration_ms": 6081, + "duration_ms": 6424, "status_messages": [ { "message": "Thinking...", @@ -4044,8 +4205,8 @@ ], "event_count": 65, "ok": true, - "request_id": "db0dd4f0-153b-42c5-aefa-632d8167b8e8", - "response_id": "chatcmpl-2123b2595683e3c6b86abe21418cb98b", + "request_id": "7259ce48-336f-4287-8165-54398698699d", + "response_id": "chatcmpl-5bc3cbde8c8c670f526d7a9dc259df73", "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.", @@ -4073,7 +4234,7 @@ "requires_graph": false, "min_graphs": 0, "repetition": 1, - "duration_ms": 10459, + "duration_ms": 9379, "status_messages": [ { "message": "Thinking...", @@ -4100,13 +4261,13 @@ "phase": "llm" } ], - "event_count": 119, + "event_count": 136, "ok": true, - "request_id": "81e30426-bd0c-4151-ab45-6dbd12dc8fba", - "response_id": "chatcmpl-40b5f44719f9c04341071b7210b30e71", + "request_id": "db5674af-c9ea-4fc4-bfdc-d684fc931d33", + "response_id": "chatcmpl-ed6a2c3382dc8709ba8634aafb076ca0", "images_count": 0, "graphs_count": 0, - "response": "To report a problem or contribute data to Virtual Fly Brain, you can get in touch with the team through the contact page. For help with using Virtual Fly Brain, you can email the public support forum at support@virtualflybrain.org, where questions and responses are visible to the community. Before emailing, check the support forum archives to see if your question has already been answered. To report technical issues, bugs, or request new features, use GitHub Issues. For data inclusion discussions, collaboration proposals, or confidential matters, email data@virtualflybrain.org.", + "response": "To report a problem or contribute data to Virtual Fly Brain, you can get in touch with the Virtual Fly Brain team for technical support, bug reports, data contributions, collaboration opportunities, or questions about using VFB software and data. You can contact Virtual Fly Brain through their public support forum, GitHub issues, or private email. For help with using Virtual Fly Brain, comments, suggestions, or general questions, 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.", "quality_flags": { "has_tool_status": true, "no_tool_factual_answer": false, @@ -4117,7 +4278,7 @@ "graph_failure_mentioned": false, "missing_required_graph": false, "used_data_resource": false, - "response_chars": 584, + "response_chars": 680, "status_count": 6 } }, @@ -4131,7 +4292,7 @@ "requires_graph": false, "min_graphs": 0, "repetition": 1, - "duration_ms": 7842, + "duration_ms": 8487, "status_messages": [ { "message": "Thinking...", @@ -4160,11 +4321,11 @@ ], "event_count": 85, "ok": true, - "request_id": "481b8067-cd7e-4acc-9e21-619e030edf95", - "response_id": "chatcmpl-d1c5d13dd8444de85a1b1facf56da88c", + "request_id": "03400182-6810-4ca1-ae6e-b2e275165da0", + "response_id": "chatcmpl-31215a551a7af2f38207c7651ad2c044", "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. Use the zoom icons or scroll with the mouse to zoom in or out. The camera icon starts and 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, @@ -4175,7 +4336,7 @@ "graph_failure_mentioned": false, "missing_required_graph": false, "used_data_resource": false, - "response_chars": 347, + "response_chars": 348, "status_count": 6 } }, @@ -4189,7 +4350,7 @@ "requires_graph": false, "min_graphs": 0, "repetition": 1, - "duration_ms": 12234, + "duration_ms": 12803, "status_messages": [ { "message": "Thinking...", @@ -4226,11 +4387,11 @@ ], "event_count": 83, "ok": true, - "request_id": "215169f1-f092-4781-b2b0-2788bae8eb19", - "response_id": "chatcmpl-26c2769b68a843caa51783683b40c139", + "request_id": "3603dcf1-9ac7-459a-acf7-adaeae6c52f8", + "response_id": "chatcmpl-80afea218f847f4fcfc301dfebddbb91", "images_count": 0, "graphs_count": 0, - "response": "The Circuit Browser tab allows you to find the strongest paths from one neuron to another. The strongest paths are the shortest/highest weighted paths, arranged from strongest at the bottom to weakest at the top. To use it, search for the source neuron to start from, noting that the query is directional. A detailed explanation for the algorithm used to determine path strengths is available.", + "response": "The Circuit Browser tab allows you to find the strongest paths from one neuron to another. To use it, search for the source neuron to start from, noting that the query is directional. The strongest paths are the shortest or highest weighted paths, arranged from strongest at the bottom to weakest at the top. A detailed explanation for the algorithm used to determine path strengths is available.", "quality_flags": { "has_tool_status": true, "no_tool_factual_answer": false, @@ -4241,7 +4402,7 @@ "graph_failure_mentioned": false, "missing_required_graph": false, "used_data_resource": false, - "response_chars": 393, + "response_chars": 396, "status_count": 8 } }, @@ -4255,7 +4416,7 @@ "requires_graph": false, "min_graphs": 0, "repetition": 1, - "duration_ms": 7329, + "duration_ms": 18013, "status_messages": [ { "message": "Thinking...", @@ -4286,13 +4447,13 @@ "phase": "llm" } ], - "event_count": 56, + "event_count": 178, "ok": true, - "request_id": "ba7aafa6-ed47-41e2-abd6-88bfe18ab1aa", - "response_id": "chatcmpl-4663cae6bceb75ce0708ad9bc6d6d664", + "request_id": "f7b20840-c423-4d01-9b8f-6cfaec6da867", + "response_id": "chatcmpl-4ddbd218d85f88bbb97c4ec44542135b", "images_count": 0, "graphs_count": 0, - "response": "NBLAST is a method used to calculate similarity scores, which represent the morphological similarity between neurons or expression patterns. An NBLAST similarity score is a measure of how similar two neurons or expression patterns are in terms of their morphology.", + "response": "NBLAST is a method to quantify morphological similarity. It works on \"dotprops\" which represent neurons as tangent vectors. For each tangent vector in the query neuron, NBLAST finds the closest tangent vector in the target neuron and calculates a score from the distance between and the dotproduct of the two vectors. The final NBLAST score is the sum over all query-target vector pairs. Typically, this score is normalized to a self-self comparison, where a perfect match would be 1.\n\nAn NBLAST similarity score is a measure of how similar the morphology of two neurons is, with higher scores indicating greater similarity. The score is computed per registered neuron, making it a scored comparison of individual neurons rather than a property of the cell type.\n\nI could not match \"NBLAST\" to a VFB term, so I cannot speak to what VFB holds for it.", "quality_flags": { "has_tool_status": true, "no_tool_factual_answer": false, @@ -4303,7 +4464,7 @@ "graph_failure_mentioned": false, "missing_required_graph": false, "used_data_resource": false, - "response_chars": 264, + "response_chars": 849, "status_count": 7 } }, @@ -4317,7 +4478,7 @@ "requires_graph": false, "min_graphs": 0, "repetition": 1, - "duration_ms": 6017, + "duration_ms": 9396, "status_messages": [ { "message": "Thinking...", @@ -4350,8 +4511,8 @@ ], "event_count": 26, "ok": true, - "request_id": "b975a851-3722-473f-91fa-8ea1f615de55", - "response_id": "chatcmpl-f066f59fc020d66a3988e62a736cb568", + "request_id": "fe2c6363-d7e4-4f72-8022-57b7928bcc43", + "response_id": "chatcmpl-bdce8ac35689a285b6a41e19beb3431d", "images_count": 1, "graphs_count": 0, "response": "Confidence values are represented by the property key \"confidence_value\" in the PDB.", @@ -4379,7 +4540,7 @@ "requires_graph": false, "min_graphs": 0, "repetition": 1, - "duration_ms": 10094, + "duration_ms": 10677, "status_messages": [ { "message": "Thinking...", @@ -4434,10 +4595,10 @@ "phase": "llm" } ], - "event_count": 73, + "event_count": 76, "ok": true, - "request_id": "e5834fea-4bbe-4e53-bae0-328476c239e0", - "response_id": "chatcmpl-359030c7b24dcafad65bdfa869a47043", + "request_id": "c2916940-fea5-4105-9347-5f47d7d2bef5", + "response_id": "chatcmpl-4f3cdeae8217767dbbc137c536b312b8", "images_count": 8, "graphs_count": 0, "response": "Bridging registrations between brain templates in VFB are transformations to map between different canonical Drosophila templates.", @@ -4465,7 +4626,7 @@ "requires_graph": false, "min_graphs": 0, "repetition": 1, - "duration_ms": 5186, + "duration_ms": 6585, "status_messages": [ { "message": "Thinking...", @@ -4492,13 +4653,13 @@ "phase": "llm" } ], - "event_count": 33, + "event_count": 55, "ok": true, - "request_id": "e7249067-fdfd-421e-8da1-037a27e4b388", - "response_id": "chatcmpl-200ea81ebab0fc7bdd37ea5ec0289274", + "request_id": "d132494e-047e-4638-b1c1-06a9373208a0", + "response_id": "chatcmpl-324123b5f6e4c6b51e7a1aa3e85b0390", "images_count": 0, "graphs_count": 0, - "response": "Virtual Fly Brain holds various imaging data types, including skeleton, mesh, and volume, and brain templates with painted domains/regions.", + "response": "Virtual Fly Brain holds various imaging data types, including skeleton, mesh, and volume, and brain templates with painted domains/regions. The retrieved neuron object can provide different representations of neuron data, such as its skeleton, mesh, and volume.", "quality_flags": { "has_tool_status": true, "no_tool_factual_answer": false, @@ -4509,7 +4670,7 @@ "graph_failure_mentioned": false, "missing_required_graph": false, "used_data_resource": false, - "response_chars": 139, + "response_chars": 261, "status_count": 6 } }, @@ -4523,7 +4684,7 @@ "requires_graph": false, "min_graphs": 0, "repetition": 1, - "duration_ms": 10584, + "duration_ms": 5103, "status_messages": [ { "message": "Thinking...", @@ -4550,13 +4711,13 @@ "phase": "llm" } ], - "event_count": 147, + "event_count": 46, "ok": true, - "request_id": "ba90ec69-fa5c-4669-99a8-ab14ad73c160", - "response_id": "chatcmpl-247bb8b004459451187e00cbf346fea8", + "request_id": "5ad69095-00ff-4a07-b662-b26c9d0303e4", + "response_id": "chatcmpl-3de8b46381b072d2f135591eca97f10c", "images_count": 0, "graphs_count": 0, - "response": "The latest Virtual Fly Brain release includes the following ontologies and vocabularies: Drosophila Anatomy Ontology, FlyBase, FlyBase Developmental Ontology, FlyBase Controlled Vocabulary, Gene Ontology, Sequence types and features ontology, GENO ontology, Information Artifact Ontology, Phenotype And Trait Ontology, Basic Formal Ontology, Common Anatomy Reference Ontology, Ontology for Biomedical Investigations, Population and Community Ontology, OBO Relations Ontology, Uber-anatomy Ontology, NCBI organismal classification, Biological Imaging Methods Ontology, Drosophila Phenotype Ontology, C elegans Phenotype Ontology, and Zebrafish Phenotype Ontology.", + "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, @@ -4567,7 +4728,7 @@ "graph_failure_mentioned": false, "missing_required_graph": false, "used_data_resource": false, - "response_chars": 662, + "response_chars": 241, "status_count": 6 } }, @@ -4581,7 +4742,7 @@ "requires_graph": false, "min_graphs": 0, "repetition": 1, - "duration_ms": 7062, + "duration_ms": 5496, "status_messages": [ { "message": "Thinking...", @@ -4596,7 +4757,7 @@ "phase": "mcp" }, { - "message": "Checking the literature", + "message": "Checking VFB documentation", "phase": "mcp" }, { @@ -4608,13 +4769,13 @@ "phase": "llm" } ], - "event_count": 58, + "event_count": 31, "ok": true, - "request_id": "39a247ad-0e4d-4177-9f6d-9b8d09f4410c", - "response_id": "chatcmpl-6b1af732fb5c5cf31603abf9eecb3cef", + "request_id": "23c48ced-f0fc-45d0-87f3-8f99eae948aa", + "response_id": "chatcmpl-72bd330b0d91b63a3855c7938a1d2506", "images_count": 0, "graphs_count": 0, - "response": "To install and get started with VFB-connect in Python, ensure you have the VFBConnect library installed using the recommended Python version 3.10.14. Install the library by running\n```\npip install vfb-connect\n```\nThen, import the VFBConnect library using\n```\nfrom import vfb\n```", + "response": "To install and get started with VFB-connect in Python, you can install it via PyPi using the command\n```\npip install vfb-connect\n```", "quality_flags": { "has_tool_status": true, "no_tool_factual_answer": false, @@ -4625,7 +4786,7 @@ "graph_failure_mentioned": false, "missing_required_graph": false, "used_data_resource": false, - "response_chars": 278, + "response_chars": 132, "status_count": 6 } }, @@ -4639,7 +4800,7 @@ "requires_graph": false, "min_graphs": 0, "repetition": 1, - "duration_ms": 9830, + "duration_ms": 10991, "status_messages": [ { "message": "Thinking...", @@ -4666,13 +4827,13 @@ "phase": "llm" } ], - "event_count": 107, + "event_count": 153, "ok": true, - "request_id": "4b069148-077d-41b3-a7c1-1772c3ddcb45", - "response_id": "chatcmpl-139766efda378a5657a4fd8e0f1b172c", + "request_id": "c88a2af8-2655-423b-964c-c732f971c4c1", + "response_id": "chatcmpl-45ddc706ef0ce8ed7eb52fdfc0fca307", "images_count": 0, "graphs_count": 0, - "response": "To query Virtual Fly Brain programmatically, you can use the Owlery API, which provides OWL reasoning services for VFB's ontologies. The API endpoint is https://owl.virtualflybrain.org/ and it supports various query operations such as subclasses, superclasses, equivalent classes, satisfiability, and instances. You can also use SPARQL queries with OWL reasoning. Additionally, the SOLR Search API provides fast text search and autocomplete functionality for VFB entities, datasets, and publications.", + "response": "To query Virtual Fly Brain programmatically, you can use the SOLR Search API or the Owlery API. The SOLR Search API provides fast text search and autocomplete functionality for VFB entities, datasets, and publications. The Owlery API provides OWL reasoning services for VFB's ontologies, enabling complex queries over class hierarchies and relationships.\n\nThe Owlery API endpoint is https://owl.virtualflybrain.org/ and it supports various query operations such as subclasses, superclasses, equivalent classes, satisfiability, and instances. You can also use SPARQL queries with OWL reasoning.\n\nYou can access the Owlery API at its base URL https://owl.virtualflybrain.org/ to perform these queries.", "quality_flags": { "has_tool_status": true, "no_tool_factual_answer": false, @@ -4683,7 +4844,7 @@ "graph_failure_mentioned": false, "missing_required_graph": false, "used_data_resource": false, - "response_chars": 500, + "response_chars": 699, "status_count": 6 } }, @@ -4697,7 +4858,7 @@ "requires_graph": false, "min_graphs": 0, "repetition": 1, - "duration_ms": 8466, + "duration_ms": 10289, "status_messages": [ { "message": "Thinking...", @@ -4728,13 +4889,13 @@ "phase": "llm" } ], - "event_count": 88, + "event_count": 105, "ok": true, - "request_id": "4c75ccba-e757-41f7-a1c0-6ee4c3ef15f2", - "response_id": "chatcmpl-536310e557fb8f052823d3eea586e6a6", + "request_id": "8d029709-0e23-496b-8535-404a430bff36", + "response_id": "chatcmpl-237eaba536a0c182b863c77fa6366755", "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.\n\nVFB's documentation does not appear to cover Navis.\nVFB's documentation does not appear to cover pymaid.", + "response": "To explore Virtual Fly Brain neurons, you can refer to the tutorials provided. The pymaid library lets you interface with a CATMAID server, such as those provided by Virtual Fly Brain, and returns data in a way that you can use features such as plotting. You can connect to the Virtual Fly Brain CATMAID server, retrieve neurons, and plot them. VFB'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, @@ -4745,7 +4906,7 @@ "graph_failure_mentioned": false, "missing_required_graph": false, "used_data_resource": false, - "response_chars": 357, + "response_chars": 449, "status_count": 7 } }, @@ -4759,7 +4920,7 @@ "requires_graph": false, "min_graphs": 0, "repetition": 1, - "duration_ms": 9493, + "duration_ms": 13018, "status_messages": [ { "message": "Thinking...", @@ -4773,6 +4934,10 @@ "message": "Reading VFB documentation", "phase": "mcp" }, + { + "message": "Reading VFB documentation", + "phase": "mcp" + }, { "message": "Checking VFB documentation", "phase": "mcp" @@ -4786,13 +4951,13 @@ "phase": "llm" } ], - "event_count": 103, + "event_count": 104, "ok": true, - "request_id": "43db3a71-cdd4-4f31-8434-f20358c09573", - "response_id": "chatcmpl-950abccc0f7a508fa85af63a069dd864", + "request_id": "7083dd5f-f27f-45df-a0c3-600475acdf2f", + "response_id": "chatcmpl-4c83842a91c95966c816fd8b045c4c7d", "images_count": 0, "graphs_count": 0, - "response": "To use the Virtual Fly Brain Model Context Protocol (MCP) tool, follow these steps:\nOpen Claude Desktop, go to Settings, navigate to the MCP section, and add a new MCP server with the settings:\nServer Name: virtual-fly-brain,\nType: HTTP,\nServer URL: https://vfb3-mcp.virtualflybrain.org.\nAlternatively, use the Configuration JSON method or set up the tool with GitHub Copilot or VS Code.\n\n```\n{\n\"mcpServers\": {\n\"virtual-fly-brain\": {\n\"type\": \"http\",\n\"url\": \"https://vfb3-mcp.virtualflybrain.org\",\n\"tools\": [\"*\"]\n}\n}\n}\n```", + "response": "To use the Virtual Fly Brain Model Context Protocol (MCP) tool, access it at vfb3-mcp.virtualflybrain.org and follow the setup instructions for your preferred client, such as Claude Desktop or GitHub Copilot. Configure the MCP server settings, restart your client if necessary, and test the connection by asking questions like \"Get information about the neuron \" or \"Search for terms related to medulla in the fly brain\".\n\n```\n{\n\"mcpServers\": {\n\"virtual-fly-brain\": {\n\"type\": \"http\",\n\"url\": \"https://vfb3-mcp.virtualflybrain.org\",\n\"tools\": [\"*\"]\n}\n}\n}\n```", "quality_flags": { "has_tool_status": true, "no_tool_factual_answer": false, @@ -4803,8 +4968,8 @@ "graph_failure_mentioned": false, "missing_required_graph": false, "used_data_resource": false, - "response_chars": 521, - "status_count": 6 + "response_chars": 555, + "status_count": 7 } }, { @@ -4817,7 +4982,7 @@ "requires_graph": false, "min_graphs": 0, "repetition": 1, - "duration_ms": 4889, + "duration_ms": 8022, "status_messages": [ { "message": "Thinking...", @@ -4827,6 +4992,10 @@ "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" @@ -4848,13 +5017,13 @@ "phase": "llm" } ], - "event_count": 40, + "event_count": 42, "ok": true, - "request_id": "e64f4339-fb3f-460e-a30c-e9feeacc7c2f", - "response_id": "chatcmpl-017a9609d77a75a43f1f2055273469f2", + "request_id": "44e8feb4-6de3-404b-8207-93adf3a3b3b5", + "response_id": "chatcmpl-3e30dfddf86cc69425ed45e11af7fbde", "images_count": 0, "graphs_count": 0, - "response": "VFB's documentation does not appear to cover when predicted neurotransmitters for EM data became available. For more information, searching virtualflybrain.org may be helpful.", + "response": "VFB's documentation does not appear to cover when predicted neurotransmitters for EM data became available on VFB. For more information, try searching virtualflybrain.org.", "quality_flags": { "has_tool_status": true, "no_tool_factual_answer": false, @@ -4865,8 +5034,8 @@ "graph_failure_mentioned": false, "missing_required_graph": false, "used_data_resource": false, - "response_chars": 175, - "status_count": 7 + "response_chars": 171, + "status_count": 8 } }, { @@ -4879,7 +5048,7 @@ "requires_graph": false, "min_graphs": 0, "repetition": 1, - "duration_ms": 17804, + "duration_ms": 7909, "status_messages": [ { "message": "Thinking...", @@ -4898,7 +5067,7 @@ "phase": "mcp" }, { - "message": "Checking the literature", + "message": "Checking VFB documentation", "phase": "mcp" }, { @@ -4912,8 +5081,8 @@ ], "event_count": 40, "ok": true, - "request_id": "aab529bb-34a3-477e-9037-3ddbf272b208", - "response_id": "chatcmpl-9d89b7bb153e80564103e16a5431b313", + "request_id": "0d0d2207-54b4-4c66-8785-59b0664b2e38", + "response_id": "chatcmpl-371b3fa100c02c3fabffcaa74f50fe2e", "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.", @@ -4941,7 +5110,7 @@ "requires_graph": false, "min_graphs": 0, "repetition": 1, - "duration_ms": 8874, + "duration_ms": 10274, "status_messages": [ { "message": "Thinking...", @@ -4972,13 +5141,13 @@ "phase": "llm" } ], - "event_count": 75, + "event_count": 52, "ok": true, - "request_id": "98993b86-1b53-46a2-b7e7-168d37d22e3e", - "response_id": "chatcmpl-2c23b22328e1244cda40c75c4a618433", + "request_id": "58436467-47c4-4351-91e1-35281e94ed0f", + "response_id": "chatcmpl-e62288e422f63ec871f036895c93479f", "images_count": 0, "graphs_count": 0, - "response": "Materials from the VFB 'Hacking the connectome' workshop are available. The materials include a recorded introduction session and workshop notebooks that demonstrate how to use available tools to explore and analyze published connectomes on VFB.\n\nTo access these materials, you can watch the recorded introduction session and follow along with the workshop notebooks.\n\n```\nhttps://www.virtualflybrain.org/docs/past-workshops/connectome\n```", + "response": "Materials from the VFB 'Hacking the connectome' workshop are available. The materials include a recorded introduction session and workshop notebooks that demonstrate how to use available tools to explore and analyse published connectomes on VFB.", "quality_flags": { "has_tool_status": true, "no_tool_factual_answer": false, @@ -4989,7 +5158,7 @@ "graph_failure_mentioned": false, "missing_required_graph": false, "used_data_resource": false, - "response_chars": 439, + "response_chars": 245, "status_count": 7 } }, @@ -5003,7 +5172,7 @@ "requires_graph": false, "min_graphs": 0, "repetition": 1, - "duration_ms": 19731, + "duration_ms": 20635, "status_messages": [ { "message": "Thinking...", @@ -5044,8 +5213,8 @@ ], "event_count": 82, "ok": true, - "request_id": "9320305c-beef-4e9d-89c9-deaaf29e2a8e", - "response_id": "chatcmpl-ea77d4120930d0076806485bc97c0ace", + "request_id": "1735f25f-531e-473f-9102-b87431479a4f", + "response_id": "chatcmpl-25e1986acf18074048da2953ad63ada6", "images_count": 8, "graphs_count": 0, "response": "The FAFB CATMAID dataset can be accessed via https://fafb.catmaid.virtualflybrain.org. Virtual Fly Brain hosts several CATMAID instances for exploring connectomic reconstruction data, including FAFB. The name \"FANC\" could not be matched, with closest records found including Fancl, FANCI, and Fancm.", @@ -5073,7 +5242,7 @@ "requires_graph": false, "min_graphs": 0, "repetition": 1, - "duration_ms": 5391, + "duration_ms": 6073, "status_messages": [ { "message": "Thinking...", @@ -5104,13 +5273,13 @@ "phase": "llm" } ], - "event_count": 22, + "event_count": 23, "ok": true, - "request_id": "e8f9606e-e356-4bed-89c4-f2079ad1b33d", - "response_id": "chatcmpl-ad5070e63c3cc2181e5e6f236ec083fc", + "request_id": "81e88695-8a02-4291-b79c-733891ce4238", + "response_id": "chatcmpl-ba60c5d933e332294ed7e5f72eac2ce7", "images_count": 8, "graphs_count": 0, - "response": "A circuit diagram of the [mushroom body](https://www.virtualflybrain.org/reports/FBbt_00005801 \"Open mushroom body in Virtual Fly Brain\") is available on Virtual Fly Brain.", + "response": "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, @@ -5121,7 +5290,7 @@ "graph_failure_mentioned": false, "missing_required_graph": false, "used_data_resource": false, - "response_chars": 172, + "response_chars": 178, "status_count": 7 } }, @@ -5135,7 +5304,7 @@ "requires_graph": false, "min_graphs": 0, "repetition": 1, - "duration_ms": 129958, + "duration_ms": 11071, "status_messages": [ { "message": "Thinking...", @@ -5166,7 +5335,7 @@ "phase": "llm" } ], - "event_count": 84, + "event_count": 86, "conversation": true, "turns": [ { @@ -5174,9 +5343,9 @@ "question": "What is the medulla?", "focus": null, "clicked": null, - "duration_ms": 4490, + "duration_ms": 5054, "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.", + "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 (distal) medulla, the seventh (or serpentine) layer exhibits a distinct architecture and layers 8-10 make up the inner (proximal) medulla.", "followons": [ { "id": "FBbt_00003748", @@ -5233,9 +5402,9 @@ "question": "Which neurons receive output from it?", "focus": null, "clicked": null, - "duration_ms": 125468, + "duration_ms": 6017, "ok": true, - "response": "The [medulla](https://www.virtualflybrain.org/reports/FBbt_00003748 \"Open medulla in Virtual Fly Brain\") sends output to several neurons, including [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 that receive output from the medulla.", + "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", @@ -5300,11 +5469,11 @@ } ], "ok": true, - "request_id": "0e67346b-915e-4e8f-a237-a5cb5d1a1bee", - "response_id": "chatcmpl-bc6ca4a4295e6c5a0fcaf8e1a4c7bc14", + "request_id": "01d915c8-21c4-4379-804a-7bb88ab2b6a5", + "response_id": "chatcmpl-1dfd5c1e71524a889c408f4ac6b18743", "images_count": 8, "graphs_count": 0, - "response": "The [medulla](https://www.virtualflybrain.org/reports/FBbt_00003748 \"Open medulla in Virtual Fly Brain\") sends output to several neurons, including [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 that receive output from the medulla.", + "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, @@ -5315,14 +5484,14 @@ "graph_failure_mentioned": false, "missing_required_graph": false, "used_data_resource": false, - "response_chars": 934, + "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": true, - "slowest_followup_ms": 125468 + "slow_followup_turn": false, + "slowest_followup_ms": 6017 } }, { @@ -5335,7 +5504,7 @@ "requires_graph": false, "min_graphs": 0, "repetition": 1, - "duration_ms": 14783, + "duration_ms": 16709, "status_messages": [ { "message": "Thinking...", @@ -5370,7 +5539,7 @@ "phase": "llm" } ], - "event_count": 358, + "event_count": 353, "conversation": true, "turns": [ { @@ -5378,9 +5547,9 @@ "question": "What is the mushroom body?", "focus": null, "clicked": null, - "duration_ms": 5054, + "duration_ms": 6109, "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.", + "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", @@ -5440,9 +5609,9 @@ "query_type": "ImagesNeurons" }, "clicked": 0, - "duration_ms": 9729, + "duration_ms": 10600, "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\"). These include VT020731 FLP 14-3, GMR 24E06 FLP 6-1, GMR 75F01 FLP 9-2, GMR 21G01 FLP 9-1, GMR 24E06 FLP 6-2, GMR 127E09 FLP 9-5, GMR 67E07 FLP 30-1, GMR 29D11 FLP 45-3, GMR 74C11 FLP 9-1, GMR 40D06 FLP 2-1, GMR 12G07 FLP 7-2, and GMR 93G04 FLP 12-1. 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 neurons with some part in the mushroom body include [adult odd neuron of the calyx](https://www.virtualflybrain.org/reports/FBbt_00111628 \"Open adult odd neuron of the calyx in Virtual Fly Brain\"), [larval uniglomerular projection neuron 63a](https://www.virtualflybrain.org/reports/FBbt_00111675 \"Open larval uniglomerular projection neuron 63a in Virtual Fly Brain\"), [larval uniglomerular projection neuron 67b](https://www.virtualflybrain.org/reports/FBbt_00111684 \"Open larval uniglomerular projection neuron 67b in Virtual Fly Brain\"), [larval uniglomerular projection neuron 74a](https://www.virtualflybrain.org/reports/FBbt_00111685 \"Open larval uniglomerular projection neuron 74a in Virtual Fly Brain\"), [larval antennal lobe multiglomerular projection neuron C2](https://www.virtualflybrain.org/reports/FBbt_00111716 \"Open larval antennal lobe multiglomerular projection neuron C2 in Virtual Fly Brain\"), [larval antennal lobe multiglomerular projection neuron bilateral lower](https://www.virtualflybrain.org/reports/FBbt_00111717 \"Open larval antennal lobe multiglomerular projection neuron bilateral lower in Virtual Fly Brain\"), larval antennal lobe multiglomerular projection neuron bilateral upper, larval antennal lobe multiglomerular projection neuron D, larval antennal lobe multiglomerular projection neuron cobra, AOTU021, AOTU022, and [ATL005](https://www.virtualflybrain.org/reports/FBbt_20000069 \"Open ATL005 in Virtual Fly Brain\"). There are [602](https://v2.virtualflybrain.org/org.geppetto.frontend/geppetto?q=FBbt_00005801,NeuronsPartHere \"Run in VFB: Neurons with some part in mushroom body\") neurons with some part in the mushroom body.", + "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, with the first 12 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. The connectome data indicates that there are [602](https://v2.virtualflybrain.org/org.geppetto.frontend/geppetto?q=FBbt_00005801,NeuronsPartHere \"Run in VFB: Neurons with some part in mushroom body\") neurons with some part in the mushroom body, including [adult odd neuron of the calyx](https://www.virtualflybrain.org/reports/FBbt_00111628 \"Open adult odd neuron of the calyx in Virtual Fly Brain\"), [larval uniglomerular projection neuron 63a](https://www.virtualflybrain.org/reports/FBbt_00111675 \"Open larval uniglomerular projection neuron 63a in Virtual Fly Brain\"), [larval uniglomerular projection neuron 67b](https://www.virtualflybrain.org/reports/FBbt_00111684 \"Open larval uniglomerular projection neuron 67b in Virtual Fly Brain\"), [larval uniglomerular projection neuron 74a](https://www.virtualflybrain.org/reports/FBbt_00111685 \"Open larval uniglomerular projection neuron 74a in Virtual Fly Brain\"), [larval antennal lobe multiglomerular projection neuron C2](https://www.virtualflybrain.org/reports/FBbt_00111716 \"Open larval antennal lobe multiglomerular projection neuron C2 in Virtual Fly Brain\"), [larval antennal lobe multiglomerular projection neuron bilateral lower](https://www.virtualflybrain.org/reports/FBbt_00111717 \"Open larval antennal lobe multiglomerular projection neuron bilateral lower in Virtual Fly Brain\"), larval antennal lobe multiglomerular projection neuron bilateral upper, larval antennal lobe multiglomerular projection neuron D, larval antennal lobe multiglomerular projection neuron cobra, AOTU021, AOTU022, and [ATL005](https://www.virtualflybrain.org/reports/FBbt_20000069 \"Open ATL005 in Virtual Fly Brain\").", "followons": [ { "id": "FBbt_00005801", @@ -5507,11 +5676,11 @@ } ], "ok": true, - "request_id": "a6bed3fe-a91f-4f3d-8371-c765a4628d8d", - "response_id": "chatcmpl-73fa84ddf2753187145f47d6de021021", + "request_id": "90cb6b3a-3121-47ce-997b-2272e5513232", + "response_id": "chatcmpl-6cc4afd710422bb908da4fe02b04978b", "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\"). These include VT020731 FLP 14-3, GMR 24E06 FLP 6-1, GMR 75F01 FLP 9-2, GMR 21G01 FLP 9-1, GMR 24E06 FLP 6-2, GMR 127E09 FLP 9-5, GMR 67E07 FLP 30-1, GMR 29D11 FLP 45-3, GMR 74C11 FLP 9-1, GMR 40D06 FLP 2-1, GMR 12G07 FLP 7-2, and GMR 93G04 FLP 12-1. 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 neurons with some part in the mushroom body include [adult odd neuron of the calyx](https://www.virtualflybrain.org/reports/FBbt_00111628 \"Open adult odd neuron of the calyx in Virtual Fly Brain\"), [larval uniglomerular projection neuron 63a](https://www.virtualflybrain.org/reports/FBbt_00111675 \"Open larval uniglomerular projection neuron 63a in Virtual Fly Brain\"), [larval uniglomerular projection neuron 67b](https://www.virtualflybrain.org/reports/FBbt_00111684 \"Open larval uniglomerular projection neuron 67b in Virtual Fly Brain\"), [larval uniglomerular projection neuron 74a](https://www.virtualflybrain.org/reports/FBbt_00111685 \"Open larval uniglomerular projection neuron 74a in Virtual Fly Brain\"), [larval antennal lobe multiglomerular projection neuron C2](https://www.virtualflybrain.org/reports/FBbt_00111716 \"Open larval antennal lobe multiglomerular projection neuron C2 in Virtual Fly Brain\"), [larval antennal lobe multiglomerular projection neuron bilateral lower](https://www.virtualflybrain.org/reports/FBbt_00111717 \"Open larval antennal lobe multiglomerular projection neuron bilateral lower in Virtual Fly Brain\"), larval antennal lobe multiglomerular projection neuron bilateral upper, larval antennal lobe multiglomerular projection neuron D, larval antennal lobe multiglomerular projection neuron cobra, AOTU021, AOTU022, and [ATL005](https://www.virtualflybrain.org/reports/FBbt_20000069 \"Open ATL005 in Virtual Fly Brain\"). There are [602](https://v2.virtualflybrain.org/org.geppetto.frontend/geppetto?q=FBbt_00005801,NeuronsPartHere \"Run in VFB: Neurons with some part in mushroom body\") neurons with some part in the mushroom body.", + "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, with the first 12 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. The connectome data indicates that there are [602](https://v2.virtualflybrain.org/org.geppetto.frontend/geppetto?q=FBbt_00005801,NeuronsPartHere \"Run in VFB: Neurons with some part in mushroom body\") neurons with some part in the mushroom body, including [adult odd neuron of the calyx](https://www.virtualflybrain.org/reports/FBbt_00111628 \"Open adult odd neuron of the calyx in Virtual Fly Brain\"), [larval uniglomerular projection neuron 63a](https://www.virtualflybrain.org/reports/FBbt_00111675 \"Open larval uniglomerular projection neuron 63a in Virtual Fly Brain\"), [larval uniglomerular projection neuron 67b](https://www.virtualflybrain.org/reports/FBbt_00111684 \"Open larval uniglomerular projection neuron 67b in Virtual Fly Brain\"), [larval uniglomerular projection neuron 74a](https://www.virtualflybrain.org/reports/FBbt_00111685 \"Open larval uniglomerular projection neuron 74a in Virtual Fly Brain\"), [larval antennal lobe multiglomerular projection neuron C2](https://www.virtualflybrain.org/reports/FBbt_00111716 \"Open larval antennal lobe multiglomerular projection neuron C2 in Virtual Fly Brain\"), [larval antennal lobe multiglomerular projection neuron bilateral lower](https://www.virtualflybrain.org/reports/FBbt_00111717 \"Open larval antennal lobe multiglomerular projection neuron bilateral lower in Virtual Fly Brain\"), larval antennal lobe multiglomerular projection neuron bilateral upper, larval antennal lobe multiglomerular projection neuron D, larval antennal lobe multiglomerular projection neuron cobra, AOTU021, AOTU022, and [ATL005](https://www.virtualflybrain.org/reports/FBbt_20000069 \"Open ATL005 in Virtual Fly Brain\").", "quality_flags": { "has_tool_status": true, "no_tool_factual_answer": false, @@ -5522,14 +5691,14 @@ "graph_failure_mentioned": false, "missing_required_graph": false, "used_data_resource": false, - "response_chars": 2312, + "response_chars": 2286, "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": 9729 + "slowest_followup_ms": 10600 } }, { @@ -5542,7 +5711,7 @@ "requires_graph": false, "min_graphs": 0, "repetition": 1, - "duration_ms": 80271, + "duration_ms": 142204, "status_messages": [ { "message": "Thinking...", @@ -5577,9 +5746,9 @@ "question": "What is the fan-shaped body?", "focus": null, "clicked": null, - "duration_ms": 5050, + "duration_ms": 5894, "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.", + "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", @@ -5636,9 +5805,9 @@ "question": "What about the ellipsoid body?", "focus": null, "clicked": null, - "duration_ms": 6619, + "duration_ms": 9350, "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", @@ -5703,9 +5872,9 @@ "question": "Which neurons have synaptic terminals in the fan-shaped body?", "focus": null, "clicked": null, - "duration_ms": 68602, + "duration_ms": 126960, "ok": true, - "response": "Neurons with synaptic terminals in the [fan-shaped body](https://www.virtualflybrain.org/reports/FBbt_00003679 \"Open fan-shaped body in Virtual Fly Brain\") include [229](https://v2.virtualflybrain.org/org.geppetto.frontend/geppetto?q=FBbt_00003679,NeuronsPartHere \"Run in VFB: Neurons with some part in fan-shaped body\") neuron types, such as [PFNa_PB4](https://www.virtualflybrain.org/reports/FBbt_00111398 \"Open PFNa_PB4 in Virtual Fly Brain\"), [PFNa_PB5](https://www.virtualflybrain.org/reports/FBbt_00111399 \"Open PFNa_PB5 in Virtual Fly Brain\"), [PFNd_PB2](https://www.virtualflybrain.org/reports/FBbt_00111391 \"Open PFNd_PB2 in Virtual Fly Brain\"), [PFNd_PB3](https://www.virtualflybrain.org/reports/FBbt_00111392 \"Open PFNd_PB3 in Virtual Fly Brain\"), [PFNd_PB5](https://www.virtualflybrain.org/reports/FBbt_00111394 \"Open PFNd_PB5 in Virtual Fly Brain\"). The first 12 of these, with their VFB ids, are: PFNd_PB2; PFNd_PB3; PFNd_PB5; PFNa_PB4; PFNa_PB5; PFNa_PB6; PFNa_PB7; PFNa_PB9; PFnP_PB7; [PFL1_PB5](https://www.virtualflybrain.org/reports/FBbt_00111438 \"Open PFL1_PB5 in Virtual Fly Brain\"); [PFL3](https://www.virtualflybrain.org/reports/FBbt_00111443 \"Open PFL3 in Virtual Fly Brain\"); [PFL2](https://www.virtualflybrain.org/reports/FBbt_00111451 \"Open PFL2 in Virtual Fly Brain\").", + "response": "Neurons with synaptic terminals in the [fan-shaped body](https://www.virtualflybrain.org/reports/FBbt_00003679 \"Open fan-shaped body in Virtual Fly Brain\") include [229](https://v2.virtualflybrain.org/org.geppetto.frontend/geppetto?q=FBbt_00003679,NeuronsPartHere \"Run in VFB: Neurons with some part in fan-shaped body\") neuron types, such as [PFNa_PB4](https://www.virtualflybrain.org/reports/FBbt_00111398 \"Open PFNa_PB4 in Virtual Fly Brain\"), [PFNa_PB5](https://www.virtualflybrain.org/reports/FBbt_00111399 \"Open PFNa_PB5 in Virtual Fly Brain\"), [PFNd_PB2](https://www.virtualflybrain.org/reports/FBbt_00111391 \"Open PFNd_PB2 in Virtual Fly Brain\"), [PFNd_PB3](https://www.virtualflybrain.org/reports/FBbt_00111392 \"Open PFNd_PB3 in Virtual Fly Brain\"), [PFNd_PB5](https://www.virtualflybrain.org/reports/FBbt_00111394 \"Open PFNd_PB5 in Virtual Fly Brain\"). The first 12 of these, with their VFB ids, are: PFNd_PB2; PFNd_PB3; PFNd_PB5; PFNa_PB4; PFNa_PB5; PFNa_PB6; PFNa_PB7; PFNa_PB9; PFNp_PB7; [PFL1_PB5](https://www.virtualflybrain.org/reports/FBbt_00111438 \"Open PFL1_PB5 in Virtual Fly Brain\"); [PFL3](https://www.virtualflybrain.org/reports/FBbt_00111443 \"Open PFL3 in Virtual Fly Brain\"); [PFL2](https://www.virtualflybrain.org/reports/FBbt_00111451 \"Open PFL2 in Virtual Fly Brain\").", "followons": [ { "id": "FBbt_00003679", @@ -5773,11 +5942,11 @@ } ], "ok": true, - "request_id": "d157eeba-e9f6-485f-bebf-c6c01b485626", - "response_id": "chatcmpl-50b25e32f75937abcd71780c3555a696", + "request_id": "bc77fbff-a911-417c-b758-d70f666ba5c4", + "response_id": "chatcmpl-757e4f11d1a0ef9a26c83f70bec4927c", "images_count": 8, "graphs_count": 0, - "response": "Neurons with synaptic terminals in the [fan-shaped body](https://www.virtualflybrain.org/reports/FBbt_00003679 \"Open fan-shaped body in Virtual Fly Brain\") include [229](https://v2.virtualflybrain.org/org.geppetto.frontend/geppetto?q=FBbt_00003679,NeuronsPartHere \"Run in VFB: Neurons with some part in fan-shaped body\") neuron types, such as [PFNa_PB4](https://www.virtualflybrain.org/reports/FBbt_00111398 \"Open PFNa_PB4 in Virtual Fly Brain\"), [PFNa_PB5](https://www.virtualflybrain.org/reports/FBbt_00111399 \"Open PFNa_PB5 in Virtual Fly Brain\"), [PFNd_PB2](https://www.virtualflybrain.org/reports/FBbt_00111391 \"Open PFNd_PB2 in Virtual Fly Brain\"), [PFNd_PB3](https://www.virtualflybrain.org/reports/FBbt_00111392 \"Open PFNd_PB3 in Virtual Fly Brain\"), [PFNd_PB5](https://www.virtualflybrain.org/reports/FBbt_00111394 \"Open PFNd_PB5 in Virtual Fly Brain\"). The first 12 of these, with their VFB ids, are: PFNd_PB2; PFNd_PB3; PFNd_PB5; PFNa_PB4; PFNa_PB5; PFNa_PB6; PFNa_PB7; PFNa_PB9; PFnP_PB7; [PFL1_PB5](https://www.virtualflybrain.org/reports/FBbt_00111438 \"Open PFL1_PB5 in Virtual Fly Brain\"); [PFL3](https://www.virtualflybrain.org/reports/FBbt_00111443 \"Open PFL3 in Virtual Fly Brain\"); [PFL2](https://www.virtualflybrain.org/reports/FBbt_00111451 \"Open PFL2 in Virtual Fly Brain\").", + "response": "Neurons with synaptic terminals in the [fan-shaped body](https://www.virtualflybrain.org/reports/FBbt_00003679 \"Open fan-shaped body in Virtual Fly Brain\") include [229](https://v2.virtualflybrain.org/org.geppetto.frontend/geppetto?q=FBbt_00003679,NeuronsPartHere \"Run in VFB: Neurons with some part in fan-shaped body\") neuron types, such as [PFNa_PB4](https://www.virtualflybrain.org/reports/FBbt_00111398 \"Open PFNa_PB4 in Virtual Fly Brain\"), [PFNa_PB5](https://www.virtualflybrain.org/reports/FBbt_00111399 \"Open PFNa_PB5 in Virtual Fly Brain\"), [PFNd_PB2](https://www.virtualflybrain.org/reports/FBbt_00111391 \"Open PFNd_PB2 in Virtual Fly Brain\"), [PFNd_PB3](https://www.virtualflybrain.org/reports/FBbt_00111392 \"Open PFNd_PB3 in Virtual Fly Brain\"), [PFNd_PB5](https://www.virtualflybrain.org/reports/FBbt_00111394 \"Open PFNd_PB5 in Virtual Fly Brain\"). The first 12 of these, with their VFB ids, are: PFNd_PB2; PFNd_PB3; PFNd_PB5; PFNa_PB4; PFNa_PB5; PFNa_PB6; PFNa_PB7; PFNa_PB9; PFNp_PB7; [PFL1_PB5](https://www.virtualflybrain.org/reports/FBbt_00111438 \"Open PFL1_PB5 in Virtual Fly Brain\"); [PFL3](https://www.virtualflybrain.org/reports/FBbt_00111443 \"Open PFL3 in Virtual Fly Brain\"); [PFL2](https://www.virtualflybrain.org/reports/FBbt_00111451 \"Open PFL2 in Virtual Fly Brain\").", "quality_flags": { "has_tool_status": true, "no_tool_factual_answer": false, @@ -5794,8 +5963,8 @@ "context_lost_across_turn": false, "unmatched_claim_after_resolve": false, "repeats_answered_question": false, - "slow_followup_turn": false, - "slowest_followup_ms": 68602 + "slow_followup_turn": true, + "slowest_followup_ms": 126960 } }, { @@ -5808,7 +5977,7 @@ "requires_graph": false, "min_graphs": 0, "repetition": 1, - "duration_ms": 12398, + "duration_ms": 11389, "status_messages": [ { "message": "Thinking...", @@ -5835,7 +6004,7 @@ "phase": "llm" } ], - "event_count": 145, + "event_count": 138, "conversation": true, "turns": [ { @@ -5843,7 +6012,7 @@ "question": "What is a Kenyon cell?", "focus": null, "clicked": null, - "duration_ms": 5662, + "duration_ms": 5589, "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": [ @@ -5902,9 +6071,9 @@ "question": "What are its subtypes?", "focus": null, "clicked": null, - "duration_ms": 6736, + "duration_ms": 5800, "ok": true, - "response": "The subtypes of [Kenyon cell](https://www.virtualflybrain.org/reports/FBbt_00003686 \"Open Kenyon cell in Virtual Fly Brain\") are [37](https://v2.virtualflybrain.org/org.geppetto.frontend/geppetto?q=FBbt_00003686,SubclassesOf \"Run in VFB: Subclasses of Kenyon cell\") subclasses, including [KCab-c(i)](https://www.virtualflybrain.org/reports/FBbt_00049111 \"Open KCab-c(i) in Virtual Fly Brain\"), [KCab-c](https://www.virtualflybrain.org/reports/FBbt_00110929 \"Open KCab-c in Virtual Fly Brain\"), [KCg-m](https://www.virtualflybrain.org/reports/FBbt_00111061 \"Open KCg-m in Virtual Fly Brain\"), [Kenyon cell of main calyx](https://www.virtualflybrain.org/reports/FBbt_00047926 \"Open Kenyon cell of main calyx in Virtual Fly Brain\"), and [gamma Kenyon cell](https://www.virtualflybrain.org/reports/FBbt_00100247 \"Open gamma Kenyon cell in Virtual Fly Brain\"). The first 12 subclasses, with their 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\") 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\"). Some of the 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", @@ -5959,11 +6128,11 @@ } ], "ok": true, - "request_id": "6ef8faf4-2511-4a74-aaff-08064c0f1627", - "response_id": "chatcmpl-db108d979fd10b8bde37ea291a6be3d2", + "request_id": "8e316b01-08d7-4030-bfed-74609fff22b9", + "response_id": "chatcmpl-28cd40d0495ac0db8b86657f5235ece3", "images_count": 8, "graphs_count": 0, - "response": "The subtypes of [Kenyon cell](https://www.virtualflybrain.org/reports/FBbt_00003686 \"Open Kenyon cell in Virtual Fly Brain\") are [37](https://v2.virtualflybrain.org/org.geppetto.frontend/geppetto?q=FBbt_00003686,SubclassesOf \"Run in VFB: Subclasses of Kenyon cell\") subclasses, including [KCab-c(i)](https://www.virtualflybrain.org/reports/FBbt_00049111 \"Open KCab-c(i) in Virtual Fly Brain\"), [KCab-c](https://www.virtualflybrain.org/reports/FBbt_00110929 \"Open KCab-c in Virtual Fly Brain\"), [KCg-m](https://www.virtualflybrain.org/reports/FBbt_00111061 \"Open KCg-m in Virtual Fly Brain\"), [Kenyon cell of main calyx](https://www.virtualflybrain.org/reports/FBbt_00047926 \"Open Kenyon cell of main calyx in Virtual Fly Brain\"), and [gamma Kenyon cell](https://www.virtualflybrain.org/reports/FBbt_00100247 \"Open gamma Kenyon cell in Virtual Fly Brain\"). The first 12 subclasses, with their 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\") 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\"). Some of the 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, @@ -5974,14 +6143,14 @@ "graph_failure_mentioned": false, "missing_required_graph": false, "used_data_resource": false, - "response_chars": 1157, + "response_chars": 1141, "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": 6736 + "slowest_followup_ms": 5800 } }, { @@ -5994,7 +6163,7 @@ "requires_graph": false, "min_graphs": 0, "repetition": 1, - "duration_ms": 20698, + "duration_ms": 16869, "status_messages": [ { "message": "Thinking...", @@ -6008,10 +6177,6 @@ "message": "Resolving 1 term in VFB", "phase": "mcp" }, - { - "message": "Reading VFB term info", - "phase": "mcp" - }, { "message": "Querying VFB", "phase": "mcp" @@ -6045,9 +6210,9 @@ "question": "What are the anatomical parts of the medulla? List them.", "focus": null, "clicked": null, - "duration_ms": 8288, + "duration_ms": 8457, "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 anatomical parts of the medulla include adult chandelier glial cell, adult distal medulla astrocyte-like glial cell, [distal medulla glial cell](https://www.virtualflybrain.org/reports/FBbt_00100528 \"Open distal medulla glial cell in Virtual Fly Brain\"), medulla layer, adult distal medulla ensheathing glial cell, [plexiform medulla](https://www.virtualflybrain.org/reports/FBbt_00045001 \"Open plexiform medulla in Virtual Fly Brain\"), [medulla dorsal rim area](https://www.virtualflybrain.org/reports/FBbt_00045002 \"Open medulla dorsal rim area in Virtual Fly Brain\"), medulla layer M1, medulla layer M5, inner medulla, medulla layer M8, and medulla layer M9.", + "response": "The [medulla](https://www.virtualflybrain.org/reports/FBbt_00003748 \"Open medulla in Virtual Fly Brain\") is divided into 10 layers: 1-6 make up the outer medulla, the seventh layer exhibits a distinct architecture and layers 8-10 make up the inner medulla. 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", @@ -6110,9 +6275,9 @@ "question": "And which neurons have part of their arbour there?", "focus": null, "clicked": null, - "duration_ms": 12410, + "duration_ms": 8412, "ok": true, - "response": "Neurons with some part in the [medulla](https://www.virtualflybrain.org/reports/FBbt_00003748 \"Open medulla in Virtual Fly Brain\") include [Dm8b](https://www.virtualflybrain.org/reports/FBbt_00110069 \"Open Dm8b in Virtual Fly Brain\"), [MC](https://www.virtualflybrain.org/reports/FBbt_00111640 \"Open MC in Virtual Fly Brain\"), [PS128](https://www.virtualflybrain.org/reports/FBbt_20001883 \"Open PS128 in Virtual Fly Brain\"), [medulla intrinsic neuron vGlutMinew1a](https://www.virtualflybrain.org/reports/FBbt_00110033 \"Open medulla intrinsic neuron vGlutMinew1a in Virtual Fly Brain\"), [TmY27](https://www.virtualflybrain.org/reports/FBbt_00110067 \"Open TmY27 in Virtual Fly Brain\"), [Mi10b](https://www.virtualflybrain.org/reports/FBbt_00110070 \"Open Mi10b in Virtual Fly Brain\"), medulla tangential neuron vGlutMtnew1, medulla tangential neuron vGlutMtnew2, Tm1a, [CB3849](https://www.virtualflybrain.org/reports/FBbt_20007264 \"Open CB3849 in Virtual Fly Brain\"), [TmY-ds](https://www.virtualflybrain.org/reports/FBbt_00052643 \"Open TmY-ds in Virtual Fly Brain\"), and MeSps. VFB records show [471](https://v2.virtualflybrain.org/org.geppetto.frontend/geppetto?q=FBbt_00003748,NeuronsPartHere \"Run in VFB: Neurons with some part in medulla\") neuron types with some part in the medulla.", + "response": "Neurons with some part in the [medulla](https://www.virtualflybrain.org/reports/FBbt_00003748 \"Open medulla in Virtual Fly Brain\") include [Dm8b](https://www.virtualflybrain.org/reports/FBbt_00110069 \"Open Dm8b in Virtual Fly Brain\"), [MC](https://www.virtualflybrain.org/reports/FBbt_00111640 \"Open MC in Virtual Fly Brain\"), [PS128](https://www.virtualflybrain.org/reports/FBbt_20001883 \"Open PS128 in Virtual Fly Brain\"), [medulla intrinsic neuron vGlutMinew1a](https://www.virtualflybrain.org/reports/FBbt_00110033 \"Open medulla intrinsic neuron vGlutMinew1a in Virtual Fly Brain\"), [TmY27](https://www.virtualflybrain.org/reports/FBbt_00110067 \"Open TmY27 in Virtual Fly Brain\"), [Mi10b](https://www.virtualflybrain.org/reports/FBbt_00110070 \"Open Mi10b in Virtual Fly Brain\"), medulla tangential neuron vGlutMtnew1, medulla tangential neuron vGlutMtnew2, Tm1a, [CB3849](https://www.virtualflybrain.org/reports/FBbt_20007264 \"Open CB3849 in Virtual Fly Brain\"), [TmY-ds](https://www.virtualflybrain.org/reports/FBbt_00052643 \"Open TmY-ds in Virtual Fly Brain\"), and MeSps. VFB holds [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", @@ -6177,16 +6342,16 @@ ], "unmapped": [] }, - "status_count": 10, + "status_count": 9, "problems": [] } ], "ok": true, - "request_id": "0672ce5b-bc82-43cd-9e2a-980cc8e1e42b", - "response_id": "chatcmpl-2956afabf6ab6b7f61e9a283bea8ef63", + "request_id": "78c9553c-6d2d-4afa-8b7d-54868780100e", + "response_id": "chatcmpl-3618082e41422e5dd230b1a0cbafa6e3", "images_count": 8, "graphs_count": 0, - "response": "Neurons with some part in the [medulla](https://www.virtualflybrain.org/reports/FBbt_00003748 \"Open medulla in Virtual Fly Brain\") include [Dm8b](https://www.virtualflybrain.org/reports/FBbt_00110069 \"Open Dm8b in Virtual Fly Brain\"), [MC](https://www.virtualflybrain.org/reports/FBbt_00111640 \"Open MC in Virtual Fly Brain\"), [PS128](https://www.virtualflybrain.org/reports/FBbt_20001883 \"Open PS128 in Virtual Fly Brain\"), [medulla intrinsic neuron vGlutMinew1a](https://www.virtualflybrain.org/reports/FBbt_00110033 \"Open medulla intrinsic neuron vGlutMinew1a in Virtual Fly Brain\"), [TmY27](https://www.virtualflybrain.org/reports/FBbt_00110067 \"Open TmY27 in Virtual Fly Brain\"), [Mi10b](https://www.virtualflybrain.org/reports/FBbt_00110070 \"Open Mi10b in Virtual Fly Brain\"), medulla tangential neuron vGlutMtnew1, medulla tangential neuron vGlutMtnew2, Tm1a, [CB3849](https://www.virtualflybrain.org/reports/FBbt_20007264 \"Open CB3849 in Virtual Fly Brain\"), [TmY-ds](https://www.virtualflybrain.org/reports/FBbt_00052643 \"Open TmY-ds in Virtual Fly Brain\"), and MeSps. VFB records show [471](https://v2.virtualflybrain.org/org.geppetto.frontend/geppetto?q=FBbt_00003748,NeuronsPartHere \"Run in VFB: Neurons with some part in medulla\") neuron types with some part in the medulla.", + "response": "Neurons with some part in the [medulla](https://www.virtualflybrain.org/reports/FBbt_00003748 \"Open medulla in Virtual Fly Brain\") include [Dm8b](https://www.virtualflybrain.org/reports/FBbt_00110069 \"Open Dm8b in Virtual Fly Brain\"), [MC](https://www.virtualflybrain.org/reports/FBbt_00111640 \"Open MC in Virtual Fly Brain\"), [PS128](https://www.virtualflybrain.org/reports/FBbt_20001883 \"Open PS128 in Virtual Fly Brain\"), [medulla intrinsic neuron vGlutMinew1a](https://www.virtualflybrain.org/reports/FBbt_00110033 \"Open medulla intrinsic neuron vGlutMinew1a in Virtual Fly Brain\"), [TmY27](https://www.virtualflybrain.org/reports/FBbt_00110067 \"Open TmY27 in Virtual Fly Brain\"), [Mi10b](https://www.virtualflybrain.org/reports/FBbt_00110070 \"Open Mi10b in Virtual Fly Brain\"), medulla tangential neuron vGlutMtnew1, medulla tangential neuron vGlutMtnew2, Tm1a, [CB3849](https://www.virtualflybrain.org/reports/FBbt_20007264 \"Open CB3849 in Virtual Fly Brain\"), [TmY-ds](https://www.virtualflybrain.org/reports/FBbt_00052643 \"Open TmY-ds in Virtual Fly Brain\"), and MeSps. VFB holds [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, @@ -6197,14 +6362,14 @@ "graph_failure_mentioned": false, "missing_required_graph": false, "used_data_resource": false, - "response_chars": 1287, - "status_count": 10, + "response_chars": 1291, + "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": 12410 + "slowest_followup_ms": 8412 } }, { @@ -6217,7 +6382,7 @@ "requires_graph": false, "min_graphs": 0, "repetition": 1, - "duration_ms": 14774, + "duration_ms": 18452, "status_messages": [ { "message": "Thinking...", @@ -6239,12 +6404,20 @@ "message": "Checking the answer is covered", "phase": "llm" }, + { + "message": "Querying VFB", + "phase": "mcp" + }, + { + "message": "Checking the answer is covered", + "phase": "llm" + }, { "message": "Writing the answer", "phase": "llm" } ], - "event_count": 163, + "event_count": 264, "conversation": true, "turns": [ { @@ -6252,9 +6425,9 @@ "question": "Tell me about the antennal lobe.", "focus": null, "clicked": null, - "duration_ms": 9735, + "duration_ms": 10490, "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 for. 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.", + "response": "The [antennal lobe](https://www.virtualflybrain.org/reports/FBbt_00003924 \"Open antennal lobe in Virtual Fly Brain\") is a synaptic neuropil domain of the deutocerebrum that is the main target for innervation from the antennal nerve. VFB holds various records related to the antennal lobe, including transgene expression in antennal lobe commissural pioneer interneuron, downstream connectivity classes for antennal lobe commissural pioneer interneuron, and upstream connectivity classes for antennal lobe commissural pioneer interneuron. The antennal lobe is a region in the Drosophila nervous system where users can search for synaptic input.", "followons": [ { "id": "FBbt_00003924", @@ -6311,9 +6484,9 @@ "question": "Which neurons innervate it?", "focus": null, "clicked": null, - "duration_ms": 5039, + "duration_ms": 7962, "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 that there are [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.", + "response": "The [antennal lobe](https://www.virtualflybrain.org/reports/FBbt_00003924 \"Open antennal lobe in Virtual Fly Brain\") is innervated by various neurons, including [larval antennal lobe picky local neuron](https://www.virtualflybrain.org/reports/FBbt_00111694 \"Open larval antennal lobe picky local neuron in Virtual Fly Brain\"), [larval antennal lobe broad local neuron](https://www.virtualflybrain.org/reports/FBbt_00111700 \"Open larval antennal lobe broad local neuron in Virtual Fly Brain\"), [PLP077](https://www.virtualflybrain.org/reports/FBbt_20001577 \"Open PLP077 in Virtual Fly Brain\"), [adult olfactory receptor neuron Ir75d ac1](https://www.virtualflybrain.org/reports/FBbt_00110011 \"Open adult olfactory receptor neuron Ir75d ac1 in Virtual Fly Brain\"), [adult olfactory receptor neuron Ir75d ac2](https://www.virtualflybrain.org/reports/FBbt_00110014 \"Open adult olfactory receptor neuron Ir75d ac2 in Virtual Fly Brain\"), adult olfactory receptor neuron Ir75d ac4, pharyngeal VL1 neuron, ORN_VM6, adult olfactory receptor neuron Or35a ac3I, adult olfactory receptor neuron Or35a ac3II, adult olfactory receptor neuron Or85b ab3, and adult olfactory receptor neuron Or85b ab11, which have presynaptic terminals in the antennal lobe. Additionally, neurons such as [AMMC-Bi16](https://www.virtualflybrain.org/reports/FBbt_00111480 \"Open AMMC-Bi16 in Virtual Fly Brain\"), [adult antennal lobe projection neuron DL5](https://www.virtualflybrain.org/reports/FBbt_00059280 \"Open adult antennal lobe projection neuron DL5 in Virtual Fly Brain\"), adult antennal lobe projection neuron DM4, adult antennal lobe projection neuron VA1d, adult antennal lobe projection neuron VL1, adult antennal lobe projection neuron VL2a, adult antennal lobe projection neuron VM2, adult antennal lobe projection neuron VM4, and adult multiglomerular antennal lobe projection neuron L1 adPN have synaptic terminals in the antennal lobe.", "followons": [ { "id": "FBbt_00003924", @@ -6325,11 +6498,6 @@ "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", @@ -6344,6 +6512,11 @@ "id": "FBbt_00003924", "query_type": "SubclassesOf", "query": "What are the subtypes of the antennal lobe?" + }, + { + "id": "FBbt_00003924", + "query_type": "TractsNervesInnervatingHere", + "query": "Which tracts and nerves innervate the antennal lobe?" } ], "context_terms": [ @@ -6364,20 +6537,25 @@ "id": "FBbt_00003924", "query_type": "NeuronsPresynapticHere", "fn": "get_neurons_with_presynaptic_terminals_in" + }, + { + "id": "FBbt_00003924", + "query_type": "NeuronsSynaptic", + "fn": "get_neurons_with_synapses_in" } ], "unmapped": [] }, - "status_count": 6, + "status_count": 8, "problems": [] } ], "ok": true, - "request_id": "391e02d0-94e4-4d28-894d-8195ba4c3c62", - "response_id": "chatcmpl-773d27a49b16e0d81209809f9f317785", + "request_id": "e7e804d2-7a02-4a28-b112-6e7cfb4cca56", + "response_id": "chatcmpl-c1f4e973865dc1ff2aa31e0a20db6c30", "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 that there are [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.", + "response": "The [antennal lobe](https://www.virtualflybrain.org/reports/FBbt_00003924 \"Open antennal lobe in Virtual Fly Brain\") is innervated by various neurons, including [larval antennal lobe picky local neuron](https://www.virtualflybrain.org/reports/FBbt_00111694 \"Open larval antennal lobe picky local neuron in Virtual Fly Brain\"), [larval antennal lobe broad local neuron](https://www.virtualflybrain.org/reports/FBbt_00111700 \"Open larval antennal lobe broad local neuron in Virtual Fly Brain\"), [PLP077](https://www.virtualflybrain.org/reports/FBbt_20001577 \"Open PLP077 in Virtual Fly Brain\"), [adult olfactory receptor neuron Ir75d ac1](https://www.virtualflybrain.org/reports/FBbt_00110011 \"Open adult olfactory receptor neuron Ir75d ac1 in Virtual Fly Brain\"), [adult olfactory receptor neuron Ir75d ac2](https://www.virtualflybrain.org/reports/FBbt_00110014 \"Open adult olfactory receptor neuron Ir75d ac2 in Virtual Fly Brain\"), adult olfactory receptor neuron Ir75d ac4, pharyngeal VL1 neuron, ORN_VM6, adult olfactory receptor neuron Or35a ac3I, adult olfactory receptor neuron Or35a ac3II, adult olfactory receptor neuron Or85b ab3, and adult olfactory receptor neuron Or85b ab11, which have presynaptic terminals in the antennal lobe. Additionally, neurons such as [AMMC-Bi16](https://www.virtualflybrain.org/reports/FBbt_00111480 \"Open AMMC-Bi16 in Virtual Fly Brain\"), [adult antennal lobe projection neuron DL5](https://www.virtualflybrain.org/reports/FBbt_00059280 \"Open adult antennal lobe projection neuron DL5 in Virtual Fly Brain\"), adult antennal lobe projection neuron DM4, adult antennal lobe projection neuron VA1d, adult antennal lobe projection neuron VL1, adult antennal lobe projection neuron VL2a, adult antennal lobe projection neuron VM2, adult antennal lobe projection neuron VM4, and adult multiglomerular antennal lobe projection neuron L1 adPN have synaptic terminals in the antennal lobe.", "quality_flags": { "has_tool_status": true, "no_tool_factual_answer": false, @@ -6388,14 +6566,14 @@ "graph_failure_mentioned": false, "missing_required_graph": false, "used_data_resource": false, - "response_chars": 1459, - "status_count": 6, + "response_chars": 1920, + "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": 5039 + "slowest_followup_ms": 7962 } }, { @@ -6408,7 +6586,7 @@ "requires_graph": false, "min_graphs": 0, "repetition": 1, - "duration_ms": 80975, + "duration_ms": 202781, "status_messages": [ { "message": "Thinking...", @@ -6435,7 +6613,7 @@ "phase": "llm" } ], - "event_count": 404, + "event_count": 303, "conversation": true, "turns": [ { @@ -6443,9 +6621,9 @@ "question": "What is the medulla?", "focus": null, "clicked": null, - "duration_ms": 3912, + "duration_ms": 4960, "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.", + "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 (distal) medulla, the seventh (or serpentine) layer exhibits a distinct architecture and layers 8-10 make up the inner (proximal) medulla.", "followons": [ { "id": "FBbt_00003748", @@ -6505,9 +6683,9 @@ "query_type": "ImagesNeurons" }, "clicked": 0, - "duration_ms": 7117, + "duration_ms": 9650, "ok": true, - "response": "There are images of neurons with parts in the [medulla](https://www.virtualflybrain.org/reports/FBbt_00003748 \"Open medulla in Virtual Fly Brain\"). The first 12 neurons with images, along 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 medulla. The first 12 images, with their VFB ids, are: OA-AL2i2 (VFB_fw042336); MC64 (VFB_fw043756); MC64 (VFB_fw043755); aMe5 (VFB_fw043590); MeTu3 (VFB_fw043751); MeTu3 (VFB_fw043750); MeTu3 (VFB_fw043744); aMe5 (VFB_fw043591); MeTu-DRA (VFB_fw043752); MeVP6 (VFB_fw043593); MeTu3 (VFB_fw043746); MeTu3 (VFB_fw043745).", "followons": [ { "id": "FBbt_00003748", @@ -6578,9 +6756,9 @@ "query_type": "TransgeneExpressionHere" }, "clicked": 0, - "duration_ms": 69946, + "duration_ms": 188171, "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\"), along with their VFB ids, 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\") (VFBexp_FBti0143533); [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\") (VFBexp_FBti0143547); [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\") (VFBexp_FBti0143524); [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\") (VFBexp_FBti0144033); [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\") (VFBexp_FBti0144076); PBac{681.P.FSVS-1}CG11138[CPTI001659] expression pattern (VFBexp_FBti0143873); PBac{681.P.FSVS-1}CG6983[CPTI001802] expression pattern (VFBexp_FBti0143897); PBac{681.P.FSVS-1}CG7920[CPTI002166] expression pattern (VFBexp_FBti0143839); PBac{681.P.FSVS-1}CG9336[CPTI001654] expression pattern (VFBexp_FBti0143870); PBac{681.P.FSVS-1}Pka-R2[CPTI001580] expression pattern (VFBexp_FBti0143863); PBac{681.P.FSVS-1}cpx[CPTI001473] expression pattern (VFBexp_FBti0143853); PBac{681.P.FSVS-1}larp[CPTI002498] expression pattern (VFBexp_FBti0143781).", + "response": "The [medulla](https://www.virtualflybrain.org/reports/FBbt_00003748 \"Open medulla in Virtual Fly Brain\") is labeled by [2,342](https://v2.virtualflybrain.org/org.geppetto.frontend/geppetto?q=FBbt_00003748,TransgeneExpressionHere \"Run in VFB: Transgene expression in medulla\") driver lines. The first 12 driver lines, with their VFB ids, 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.", "followons": [ { "id": "FBbt_00003748", @@ -6650,11 +6828,11 @@ } ], "ok": true, - "request_id": "f28638dd-f8e6-4003-bf93-2415746466c8", - "response_id": "chatcmpl-722852d5e9c470303cce1d772c02b902", + "request_id": "334027ee-4b59-43c0-8134-32f634fb65c4", + "response_id": "chatcmpl-93feb07c91de53dc1656451e91f40c50", "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\"), along with their VFB ids, 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\") (VFBexp_FBti0143533); [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\") (VFBexp_FBti0143547); [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\") (VFBexp_FBti0143524); [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\") (VFBexp_FBti0144033); [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\") (VFBexp_FBti0144076); PBac{681.P.FSVS-1}CG11138[CPTI001659] expression pattern (VFBexp_FBti0143873); PBac{681.P.FSVS-1}CG6983[CPTI001802] expression pattern (VFBexp_FBti0143897); PBac{681.P.FSVS-1}CG7920[CPTI002166] expression pattern (VFBexp_FBti0143839); PBac{681.P.FSVS-1}CG9336[CPTI001654] expression pattern (VFBexp_FBti0143870); PBac{681.P.FSVS-1}Pka-R2[CPTI001580] expression pattern (VFBexp_FBti0143863); PBac{681.P.FSVS-1}cpx[CPTI001473] expression pattern (VFBexp_FBti0143853); PBac{681.P.FSVS-1}larp[CPTI002498] expression pattern (VFBexp_FBti0143781).", + "response": "The [medulla](https://www.virtualflybrain.org/reports/FBbt_00003748 \"Open medulla in Virtual Fly Brain\") is labeled by [2,342](https://v2.virtualflybrain.org/org.geppetto.frontend/geppetto?q=FBbt_00003748,TransgeneExpressionHere \"Run in VFB: Transgene expression in medulla\") driver lines. The first 12 driver lines, with their VFB ids, 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.", "quality_flags": { "has_tool_status": true, "no_tool_factual_answer": false, @@ -6665,14 +6843,14 @@ "graph_failure_mentioned": false, "missing_required_graph": false, "used_data_resource": false, - "response_chars": 1803, + "response_chars": 1719, "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": 69946 + "slow_followup_turn": true, + "slowest_followup_ms": 188171 } }, { @@ -6685,7 +6863,7 @@ "requires_graph": false, "min_graphs": 0, "repetition": 1, - "duration_ms": 9632, + "duration_ms": 10375, "status_messages": [ { "message": "Thinking...", @@ -6712,7 +6890,7 @@ "phase": "llm" } ], - "event_count": 48, + "event_count": 64, "conversation": true, "turns": [ { @@ -6720,9 +6898,9 @@ "question": "What is the mushroom body?", "focus": null, "clicked": null, - "duration_ms": 5152, + "duration_ms": 6126, "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.", + "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", @@ -6779,9 +6957,9 @@ "question": "Which driver lines label it?", "focus": null, "clicked": null, - "duration_ms": 4480, + "duration_ms": 4249, "ok": true, - "response": "The [mushroom body](https://www.virtualflybrain.org/reports/FBbt_00005801 \"Open mushroom body in Virtual Fly Brain\") is labeled by several driver lines, including P{VT017411-GAL4.DBD} and P{VT019018-p65.AD}, which are used as hemidrivers.", + "response": "The [mushroom body](https://www.virtualflybrain.org/reports/FBbt_00005801 \"Open mushroom body in Virtual Fly Brain\") is labeled by several driver lines, including P{VT017411-GAL4.DBD} and P{VT019018-p65.AD}, which are used as hemidrivers. VFB records show [4130](https://v2.virtualflybrain.org/org.geppetto.frontend/geppetto?q=FBbt_00005801,TransgeneExpressionHere \"Run in VFB: Transgene expression in mushroom body\") instances of transgene expression in mushroom body.", "followons": [ { "id": "FBbt_00005801", @@ -6841,11 +7019,11 @@ } ], "ok": true, - "request_id": "dd00a094-d507-4a38-b3ea-ac5de7f39581", - "response_id": "chatcmpl-5ed36cf198602331752496a9b60a5dc4", + "request_id": "af887580-1ff0-4bf8-b8d3-0491bca1156f", + "response_id": "chatcmpl-1bdcbdfd1ef7ac39d2be218a2cf9e63f", "images_count": 8, "graphs_count": 0, - "response": "The [mushroom body](https://www.virtualflybrain.org/reports/FBbt_00005801 \"Open mushroom body in Virtual Fly Brain\") is labeled by several driver lines, including P{VT017411-GAL4.DBD} and P{VT019018-p65.AD}, which are used as hemidrivers.", + "response": "The [mushroom body](https://www.virtualflybrain.org/reports/FBbt_00005801 \"Open mushroom body in Virtual Fly Brain\") is labeled by several driver lines, including P{VT017411-GAL4.DBD} and P{VT019018-p65.AD}, which are used as hemidrivers. VFB records show [4130](https://v2.virtualflybrain.org/org.geppetto.frontend/geppetto?q=FBbt_00005801,TransgeneExpressionHere \"Run in VFB: Transgene expression in mushroom body\") instances of transgene expression in mushroom body.", "quality_flags": { "has_tool_status": true, "no_tool_factual_answer": false, @@ -6856,14 +7034,14 @@ "graph_failure_mentioned": false, "missing_required_graph": false, "used_data_resource": false, - "response_chars": 238, + "response_chars": 469, "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": 4480 + "slowest_followup_ms": 4249 } }, { @@ -6876,7 +7054,7 @@ "requires_graph": false, "min_graphs": 0, "repetition": 1, - "duration_ms": 32501, + "duration_ms": 20236, "status_messages": [ { "message": "Thinking...", @@ -6890,10 +7068,6 @@ "message": "Resolving 1 term in VFB", "phase": "mcp" }, - { - "message": "Searching VFB terms", - "phase": "mcp" - }, { "message": "Reading VFB term info", "phase": "mcp" @@ -6935,7 +7109,7 @@ "phase": "llm" } ], - "event_count": 158, + "event_count": 149, "conversation": true, "turns": [ { @@ -6943,9 +7117,9 @@ "question": "Which neurons provide input to the medulla?", "focus": null, "clicked": null, - "duration_ms": 15590, + "duration_ms": 6270, "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.", + "response": "Neurons with presynaptic terminals in [medulla](https://www.virtualflybrain.org/reports/FBbt_00003748 \"Open medulla in Virtual Fly Brain\") provide input to the medulla. VFB records show [262](https://v2.virtualflybrain.org/org.geppetto.frontend/geppetto?q=FBbt_00003748,NeuronsPresynapticHere \"Run in VFB: Neurons with presynaptic terminals in medulla\") neuron types with presynaptic terminals in medulla, including [Dm8b](https://www.virtualflybrain.org/reports/FBbt_00110069 \"Open Dm8b in Virtual Fly Brain\"), [PS128](https://www.virtualflybrain.org/reports/FBbt_20001883 \"Open PS128 in Virtual Fly Brain\"), [Mi10b](https://www.virtualflybrain.org/reports/FBbt_00110070 \"Open Mi10b in Virtual Fly Brain\"), [CB3849](https://www.virtualflybrain.org/reports/FBbt_20007264 \"Open CB3849 in Virtual Fly Brain\"), [TmY-ds](https://www.virtualflybrain.org/reports/FBbt_00052643 \"Open TmY-ds in Virtual Fly Brain\"), [Dm7](https://www.virtualflybrain.org/reports/FBbt_00003774 \"Open Dm7 in Virtual Fly Brain\"), Mi6, Mi8, Tm10, Tm13, Tm14, and Tm18.", "followons": [ { "id": "FBbt_00003748", @@ -7013,9 +7187,9 @@ "question": "And the lobula?", "focus": null, "clicked": null, - "duration_ms": 16910, + "duration_ms": 13965, "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.", + "response": "Neurons with synaptic terminals in [lobula](https://www.virtualflybrain.org/reports/FBbt_00003852 \"Open lobula in Virtual Fly Brain\") provide input to the lobula. VFB records show [528](https://v2.virtualflybrain.org/org.geppetto.frontend/geppetto?q=FBbt_00003852,NeuronsPartHere \"Run in VFB: Neurons with some part in lobula\") neuron types with synaptic terminals in lobula, including [AVLP391](https://www.virtualflybrain.org/reports/FBbt_20000500 \"Open AVLP391 in Virtual Fly Brain\"), [PLP031](https://www.virtualflybrain.org/reports/FBbt_20001531 \"Open PLP031 in Virtual Fly Brain\"), [TmY27](https://www.virtualflybrain.org/reports/FBbt_00110067 \"Open TmY27 in Virtual Fly Brain\"), [lobula columnar neuron vGlutLcnnew2](https://www.virtualflybrain.org/reports/FBbt_00110100 \"Open lobula columnar neuron vGlutLcnnew2 in Virtual Fly Brain\"), [OA-AL2b](https://www.virtualflybrain.org/reports/FBbt_00110145 \"Open OA-AL2b in Virtual Fly Brain\"), adult histaminergic HP3 neuron, translobula neuron, Tl1, Tl2, Tm1a, SIP063, and SLP339.", "followons": [ { "id": "FBbt_00003852", @@ -7098,16 +7272,16 @@ ], "unmapped": [] }, - "status_count": 14, + "status_count": 13, "problems": [] } ], "ok": true, - "request_id": "9c1fad4e-2c63-4c0f-9434-d44253a57838", - "response_id": "chatcmpl-c4ac73174c4cc567936b869009979b3f", + "request_id": "a338284f-5c9a-4528-8440-20caac36b83d", + "response_id": "chatcmpl-90d3574b47476f373a6ffccb33b365ff", "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.", + "response": "Neurons with synaptic terminals in [lobula](https://www.virtualflybrain.org/reports/FBbt_00003852 \"Open lobula in Virtual Fly Brain\") provide input to the lobula. VFB records show [528](https://v2.virtualflybrain.org/org.geppetto.frontend/geppetto?q=FBbt_00003852,NeuronsPartHere \"Run in VFB: Neurons with some part in lobula\") neuron types with synaptic terminals in lobula, including [AVLP391](https://www.virtualflybrain.org/reports/FBbt_20000500 \"Open AVLP391 in Virtual Fly Brain\"), [PLP031](https://www.virtualflybrain.org/reports/FBbt_20001531 \"Open PLP031 in Virtual Fly Brain\"), [TmY27](https://www.virtualflybrain.org/reports/FBbt_00110067 \"Open TmY27 in Virtual Fly Brain\"), [lobula columnar neuron vGlutLcnnew2](https://www.virtualflybrain.org/reports/FBbt_00110100 \"Open lobula columnar neuron vGlutLcnnew2 in Virtual Fly Brain\"), [OA-AL2b](https://www.virtualflybrain.org/reports/FBbt_00110145 \"Open OA-AL2b in Virtual Fly Brain\"), adult histaminergic HP3 neuron, translobula neuron, Tl1, Tl2, Tm1a, SIP063, and SLP339.", "quality_flags": { "has_tool_status": true, "no_tool_factual_answer": false, @@ -7118,14 +7292,14 @@ "graph_failure_mentioned": false, "missing_required_graph": false, "used_data_resource": false, - "response_chars": 1105, - "status_count": 14, + "response_chars": 1033, + "status_count": 13, "addressless_followon": false, "context_lost_across_turn": false, "unmatched_claim_after_resolve": false, "repeats_answered_question": false, "slow_followup_turn": false, - "slowest_followup_ms": 16910 + "slowest_followup_ms": 13965 } }, { @@ -7138,7 +7312,7 @@ "requires_graph": false, "min_graphs": 0, "repetition": 1, - "duration_ms": 36636, + "duration_ms": 40600, "status_messages": [ { "message": "Thinking...", @@ -7148,6 +7322,10 @@ "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" @@ -7189,7 +7367,7 @@ "phase": "llm" } ], - "event_count": 163, + "event_count": 155, "conversation": true, "turns": [ { @@ -7197,9 +7375,9 @@ "question": "What is the protocerebral bridge?", "focus": null, "clicked": null, - "duration_ms": 5216, + "duration_ms": 5126, "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.", + "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 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", @@ -7256,9 +7434,9 @@ "question": "How does it relate to the ellipsoid body?", "focus": null, "clicked": null, - "duration_ms": 11497, + "duration_ms": 16567, "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 related in that some neurons have synaptic terminals in both. For example, neurons such as the [adult protocerebral bridge glomerulus 1-ellipsoid body canal-dorsal gall neuron](https://www.virtualflybrain.org/reports/FBbt_00111376 \"Open adult protocerebral bridge glomerulus 1-ellipsoid body canal-dorsal gall neuron in Virtual Fly Brain\") and the adult protocerebral bridge glomerulus 4-ellipsoid body canal-ventral gall neuron have synaptic terminals in the ellipsoid body. VFB records show [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 are also associated with the protocerebral bridge.", + "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 related in that some neurons have parts in both. 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\") and other similar neurons have synaptic terminals in the ellipsoid body.", "followons": [ { "id": "FBbt_00003668", @@ -7331,7 +7509,7 @@ ], "unmapped": [] }, - "status_count": 12, + "status_count": 14, "problems": [] }, { @@ -7339,9 +7517,9 @@ "question": "Which neurons connect them?", "focus": null, "clicked": null, - "duration_ms": 19923, + "duration_ms": 18907, "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 some neurons have synaptic terminals in both the protocerebral bridge and the ellipsoid body. For example, [PEN_PB2](https://www.virtualflybrain.org/reports/FBbt_00111369 \"Open PEN_PB2 in Virtual Fly Brain\"), [PEN_PB3](https://www.virtualflybrain.org/reports/FBbt_00111370 \"Open PEN_PB3 in Virtual Fly Brain\"), [PEN_PB7](https://www.virtualflybrain.org/reports/FBbt_00111373 \"Open PEN_PB7 in Virtual Fly Brain\"), and [PEN_PB8](https://www.virtualflybrain.org/reports/FBbt_00111374 \"Open PEN_PB8 in Virtual Fly Brain\") neurons have synaptic terminals in the ellipsoid body. Additionally, VFB's query results show that there are neurons with presynaptic and postsynaptic terminals in both the protocerebral bridge and the ellipsoid body.", + "response": "The [adult protocerebral bridge glomerulus 1-ellipsoid body canal-dorsal gall neuron](https://www.virtualflybrain.org/reports/FBbt_00111376 \"Open adult protocerebral bridge glomerulus 1-ellipsoid body canal-dorsal gall neuron in Virtual Fly Brain\") and other similar neurons have synaptic terminals in the [ellipsoid body](https://www.virtualflybrain.org/reports/FBbt_00003678 \"Open ellipsoid body in Virtual Fly Brain\") and are among the neurons that connect the [protocerebral bridge](https://www.virtualflybrain.org/reports/FBbt_00003668 \"Open protocerebral bridge in Virtual Fly Brain\") and the ellipsoid body. VFB records show that [PEN_PB2](https://www.virtualflybrain.org/reports/FBbt_00111369 \"Open PEN_PB2 in Virtual Fly Brain\"), [PEN_PB3](https://www.virtualflybrain.org/reports/FBbt_00111370 \"Open PEN_PB3 in Virtual Fly Brain\"), [PEN_PB7](https://www.virtualflybrain.org/reports/FBbt_00111373 \"Open PEN_PB7 in Virtual Fly Brain\"), and [PEN_PB8](https://www.virtualflybrain.org/reports/FBbt_00111374 \"Open PEN_PB8 in Virtual Fly Brain\") neurons have postsynaptic terminals in the protocerebral bridge and presynaptic terminals in the ellipsoid body. Additionally, [EPG_PB5](https://www.virtualflybrain.org/reports/FBbt_00111416 \"Open EPG_PB5 in Virtual Fly Brain\"), [EPG_PB2](https://www.virtualflybrain.org/reports/FBbt_00111419 \"Open EPG_PB2 in Virtual Fly Brain\"), [EPG_PB6](https://www.virtualflybrain.org/reports/FBbt_00111421 \"Open EPG_PB6 in Virtual Fly Brain\"), and other neurons have presynaptic terminals in the protocerebral bridge and postsynaptic terminals in the ellipsoid body.", "followons": [ { "id": "FBbt_00003668", @@ -7439,16 +7617,16 @@ ], "unmapped": [] }, - "status_count": 12, + "status_count": 13, "problems": [] } ], "ok": true, - "request_id": "d8ab3f62-f12d-44a2-9ec5-fdc27e5c107a", - "response_id": "chatcmpl-9023864278ee1d0d9563fa68ce58117e", + "request_id": "6edb575a-d88d-45ce-a955-20fdd8c25a2b", + "response_id": "chatcmpl-25033cb3479fae6de7b59b0e66d2d60d", "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\") and the adult protocerebral bridge glomerulus 4-ellipsoid body canal-ventral gall neuron. VFB records show that some neurons have synaptic terminals in both the protocerebral bridge and the ellipsoid body. For example, [PEN_PB2](https://www.virtualflybrain.org/reports/FBbt_00111369 \"Open PEN_PB2 in Virtual Fly Brain\"), [PEN_PB3](https://www.virtualflybrain.org/reports/FBbt_00111370 \"Open PEN_PB3 in Virtual Fly Brain\"), [PEN_PB7](https://www.virtualflybrain.org/reports/FBbt_00111373 \"Open PEN_PB7 in Virtual Fly Brain\"), and [PEN_PB8](https://www.virtualflybrain.org/reports/FBbt_00111374 \"Open PEN_PB8 in Virtual Fly Brain\") neurons have synaptic terminals in the ellipsoid body. Additionally, VFB's query results show that there are neurons with presynaptic and postsynaptic terminals in both the protocerebral bridge and the ellipsoid body.", + "response": "The [adult protocerebral bridge glomerulus 1-ellipsoid body canal-dorsal gall neuron](https://www.virtualflybrain.org/reports/FBbt_00111376 \"Open adult protocerebral bridge glomerulus 1-ellipsoid body canal-dorsal gall neuron in Virtual Fly Brain\") and other similar neurons have synaptic terminals in the [ellipsoid body](https://www.virtualflybrain.org/reports/FBbt_00003678 \"Open ellipsoid body in Virtual Fly Brain\") and are among the neurons that connect the [protocerebral bridge](https://www.virtualflybrain.org/reports/FBbt_00003668 \"Open protocerebral bridge in Virtual Fly Brain\") and the ellipsoid body. VFB records show that [PEN_PB2](https://www.virtualflybrain.org/reports/FBbt_00111369 \"Open PEN_PB2 in Virtual Fly Brain\"), [PEN_PB3](https://www.virtualflybrain.org/reports/FBbt_00111370 \"Open PEN_PB3 in Virtual Fly Brain\"), [PEN_PB7](https://www.virtualflybrain.org/reports/FBbt_00111373 \"Open PEN_PB7 in Virtual Fly Brain\"), and [PEN_PB8](https://www.virtualflybrain.org/reports/FBbt_00111374 \"Open PEN_PB8 in Virtual Fly Brain\") neurons have postsynaptic terminals in the protocerebral bridge and presynaptic terminals in the ellipsoid body. Additionally, [EPG_PB5](https://www.virtualflybrain.org/reports/FBbt_00111416 \"Open EPG_PB5 in Virtual Fly Brain\"), [EPG_PB2](https://www.virtualflybrain.org/reports/FBbt_00111419 \"Open EPG_PB2 in Virtual Fly Brain\"), [EPG_PB6](https://www.virtualflybrain.org/reports/FBbt_00111421 \"Open EPG_PB6 in Virtual Fly Brain\"), and other neurons have presynaptic terminals in the protocerebral bridge and postsynaptic terminals in the ellipsoid body.", "quality_flags": { "has_tool_status": true, "no_tool_factual_answer": false, @@ -7459,14 +7637,14 @@ "graph_failure_mentioned": false, "missing_required_graph": false, "used_data_resource": false, - "response_chars": 1379, - "status_count": 12, + "response_chars": 1603, + "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": 19923 + "slowest_followup_ms": 18907 } }, { @@ -7479,7 +7657,7 @@ "requires_graph": false, "min_graphs": 0, "repetition": 1, - "duration_ms": 21912, + "duration_ms": 22908, "status_messages": [ { "message": "Thinking...", @@ -7510,7 +7688,7 @@ "phase": "llm" } ], - "event_count": 31, + "event_count": 45, "conversation": true, "turns": [ { @@ -7518,9 +7696,9 @@ "question": "Which neurons have part of them in the medulla?", "focus": null, "clicked": null, - "duration_ms": 12339, + "duration_ms": 9384, "ok": true, - "response": "Neurons with some part in the [medulla](https://www.virtualflybrain.org/reports/FBbt_00003748 \"Open medulla in Virtual Fly Brain\") include [Dm8b](https://www.virtualflybrain.org/reports/FBbt_00110069 \"Open Dm8b in Virtual Fly Brain\"), [MC](https://www.virtualflybrain.org/reports/FBbt_00111640 \"Open MC in Virtual Fly Brain\"), [PS128](https://www.virtualflybrain.org/reports/FBbt_20001883 \"Open PS128 in Virtual Fly Brain\"), [TmY27](https://www.virtualflybrain.org/reports/FBbt_00110067 \"Open TmY27 in Virtual Fly Brain\"), and [medulla intrinsic neuron vGlutMinew1a](https://www.virtualflybrain.org/reports/FBbt_00110033 \"Open medulla intrinsic neuron vGlutMinew1a in Virtual Fly Brain\"). VFB records show [471](https://v2.virtualflybrain.org/org.geppetto.frontend/geppetto?q=FBbt_00003748,NeuronsPartHere \"Run in VFB: Neurons with some part in medulla\") neuron types have some part in the medulla.", + "response": "Neurons with some part in the [medulla](https://www.virtualflybrain.org/reports/FBbt_00003748 \"Open medulla in Virtual Fly Brain\") include [Dm8b](https://www.virtualflybrain.org/reports/FBbt_00110069 \"Open Dm8b in Virtual Fly Brain\"), [MC](https://www.virtualflybrain.org/reports/FBbt_00111640 \"Open MC in Virtual Fly Brain\"), [PS128](https://www.virtualflybrain.org/reports/FBbt_20001883 \"Open PS128 in Virtual Fly Brain\"), [medulla intrinsic neuron vGlutMinew1a](https://www.virtualflybrain.org/reports/FBbt_00110033 \"Open medulla intrinsic neuron vGlutMinew1a in Virtual Fly Brain\"), 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.", "followons": [ { "id": "FBbt_00003748", @@ -7588,9 +7766,9 @@ "question": "How would I get that same result in Python with vfbquery?", "focus": null, "clicked": null, - "duration_ms": 9573, + "duration_ms": 13524, "ok": true, - "response": "The code below returns the [471](https://v2.virtualflybrain.org/org.geppetto.frontend/geppetto?q=FBbt_00003748,NeuronsPartHere \"Run in VFB: Neurons with some part in medulla\") neuron types VFB has annotated for [medulla](https://www.virtualflybrain.org/reports/FBbt_00003748 \"Open medulla in Virtual Fly Brain\"), as a table.\n```python\n# Reproduce this answer in Python — pip install vfbquery\n#\n# These are the exact ids this conversation resolved and the exact catalogue\n# queries it ran, so this returns the same rows the answer was written from\n# rather than a fresh search that might land on a different term.\nimport vfbquery\n\nMEDULLA = 'FBbt_00003748' # medulla\n\n# NeuronsPartHere for medulla\nneurons_part_here = vfbquery.get_neurons_with_part_in(MEDULLA)\n# ImagesNeurons for medulla\nimages_neurons = vfbquery.get_images_neurons(MEDULLA)\n```", + "response": "The code below returns the neurons with some part in the [medulla](https://www.virtualflybrain.org/reports/FBbt_00003748 \"Open medulla in Virtual Fly Brain\"), as annotated by VFB. 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# ImagesNeurons for medulla\nimages_neurons = vfbquery.get_images_neurons(MEDULLA)\n```", "followons": [ { "id": "FBbt_00003748", @@ -7655,11 +7833,11 @@ } ], "ok": true, - "request_id": "00d2c35a-10b7-4ae6-9f13-92f610c14c2b", - "response_id": "chatcmpl-f77281fad207c1afb8f633bbfdd85ee1", + "request_id": "1b85b4df-2ba8-4534-8421-f743aa2631f5", + "response_id": "chatcmpl-aaeb2ecef2281c0c75871444e567cc97", "images_count": 8, "graphs_count": 0, - "response": "The code below returns the [471](https://v2.virtualflybrain.org/org.geppetto.frontend/geppetto?q=FBbt_00003748,NeuronsPartHere \"Run in VFB: Neurons with some part in medulla\") neuron types VFB has annotated for [medulla](https://www.virtualflybrain.org/reports/FBbt_00003748 \"Open medulla in Virtual Fly Brain\"), as a table.\n```python\n# Reproduce this answer in Python — pip install vfbquery\n#\n# These are the exact ids this conversation resolved and the exact catalogue\n# queries it ran, so this returns the same rows the answer was written from\n# rather than a fresh search that might land on a different term.\nimport vfbquery\n\nMEDULLA = 'FBbt_00003748' # medulla\n\n# NeuronsPartHere for medulla\nneurons_part_here = vfbquery.get_neurons_with_part_in(MEDULLA)\n# ImagesNeurons for medulla\nimages_neurons = vfbquery.get_images_neurons(MEDULLA)\n```", + "response": "The code below returns the neurons with some part in the [medulla](https://www.virtualflybrain.org/reports/FBbt_00003748 \"Open medulla in Virtual Fly Brain\"), as annotated by VFB. 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# ImagesNeurons for medulla\nimages_neurons = vfbquery.get_images_neurons(MEDULLA)\n```", "quality_flags": { "has_tool_status": true, "no_tool_factual_answer": false, @@ -7670,14 +7848,14 @@ "graph_failure_mentioned": false, "missing_required_graph": false, "used_data_resource": false, - "response_chars": 845, + "response_chars": 910, "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": 9573 + "slowest_followup_ms": 13524 } }, { @@ -7690,7 +7868,7 @@ "requires_graph": false, "min_graphs": 0, "repetition": 1, - "duration_ms": 16528, + "duration_ms": 20837, "status_messages": [ { "message": "Thinking...", @@ -7701,21 +7879,17 @@ "phase": "llm" }, { - "message": "Resolving 1 term in VFB", - "phase": "mcp" + "phase": "plan", + "message": "The plan is contested — sampling again before committing." }, { - "message": "Reading VFB term info", + "message": "Resolving 1 term in VFB", "phase": "mcp" }, { - "message": "Querying VFB", + "message": "Reading VFB term info", "phase": "mcp" }, - { - "message": "Checking the answer is covered", - "phase": "llm" - }, { "message": "Querying VFB", "phase": "mcp" @@ -7729,7 +7903,7 @@ "phase": "llm" } ], - "event_count": 48, + "event_count": 81, "conversation": true, "turns": [ { @@ -7737,9 +7911,9 @@ "question": "What are the subclasses of Kenyon cell?", "focus": null, "clicked": null, - "duration_ms": 5968, + "duration_ms": 5159, "ok": true, - "response": "The subclasses of [Kenyon cell](https://www.virtualflybrain.org/reports/FBbt_00003686 \"Open Kenyon cell in Virtual Fly Brain\") include [KCab-c(i)](https://www.virtualflybrain.org/reports/FBbt_00049111 \"Open KCab-c(i) in Virtual Fly Brain\"), [KCab-c](https://www.virtualflybrain.org/reports/FBbt_00110929 \"Open KCab-c in Virtual Fly Brain\"), [KCg-m](https://www.virtualflybrain.org/reports/FBbt_00111061 \"Open KCg-m in Virtual Fly Brain\"), [Kenyon cell of main calyx](https://www.virtualflybrain.org/reports/FBbt_00047926 \"Open Kenyon cell of main calyx in Virtual Fly Brain\"), and [gamma Kenyon cell](https://www.virtualflybrain.org/reports/FBbt_00100247 \"Open gamma Kenyon cell in Virtual Fly Brain\"), among [37](https://v2.virtualflybrain.org/org.geppetto.frontend/geppetto?q=FBbt_00003686,SubclassesOf \"Run in VFB: Subclasses of Kenyon cell\") subclasses. VFB holds 37 subclasses of Kenyon cell.", + "response": "The subclasses of [Kenyon cell](https://www.virtualflybrain.org/reports/FBbt_00003686 \"Open Kenyon cell in Virtual Fly Brain\") include [KCab-c(i)](https://www.virtualflybrain.org/reports/FBbt_00049111 \"Open KCab-c(i) in Virtual Fly Brain\"), [KCab-c](https://www.virtualflybrain.org/reports/FBbt_00110929 \"Open KCab-c in Virtual Fly Brain\"), [KCg-m](https://www.virtualflybrain.org/reports/FBbt_00111061 \"Open KCg-m in Virtual Fly Brain\"), [Kenyon cell of main calyx](https://www.virtualflybrain.org/reports/FBbt_00047926 \"Open Kenyon cell of main calyx in Virtual Fly Brain\"), and [gamma Kenyon cell](https://www.virtualflybrain.org/reports/FBbt_00100247 \"Open gamma Kenyon cell in Virtual Fly Brain\"), among [37](https://v2.virtualflybrain.org/org.geppetto.frontend/geppetto?q=FBbt_00003686,SubclassesOf \"Run in VFB: Subclasses of Kenyon cell\") total subclasses. VFB holds 37 subclasses of Kenyon cell.", "followons": [ { "id": "FBbt_00003686", @@ -7802,10 +7976,15 @@ "question": "Can you list the VFB IDs so I can reproduce this myself?", "focus": null, "clicked": null, - "duration_ms": 10560, + "duration_ms": 15678, "ok": true, - "response": "The code below returns the 12 VFB IDs of subclasses of [Kenyon cell](https://www.virtualflybrain.org/reports/FBbt_00003686 \"Open Kenyon cell in Virtual Fly Brain\") that were retrieved, as a table. VFB holds a total of [37](https://v2.virtualflybrain.org/org.geppetto.frontend/geppetto?q=FBbt_00003686,SubclassesOf \"Run in VFB: Subclasses of Kenyon cell\") subclasses of Kenyon cell.\n\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# ListAllAvailableImages for Kenyon cell\nlist_all_available_images = vfbquery.get_instances(KENYON_CELL)\n```", + "response": "The code below returns the VFB IDs for [Kenyon cell](https://www.virtualflybrain.org/reports/FBbt_00003686 \"Open Kenyon cell in Virtual Fly Brain\"), as listed. VFB holds several IDs for Kenyon cell, including VFB_00100451, VFB_00100431, VFB_00100417, VFB_00100395, VFB_00100335, and VFB_00050000.\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", @@ -7845,25 +8024,20 @@ "id": "FBbt_00003686", "query_type": "SubclassesOf", "fn": "get_subclasses_of" - }, - { - "id": "FBbt_00003686", - "query_type": "ListAllAvailableImages", - "fn": "get_instances" } ], "unmapped": [] }, - "status_count": 9, + "status_count": 8, "problems": [] } ], "ok": true, - "request_id": "d66c3aa3-6bec-4047-84cd-ca4653d9c259", - "response_id": "chatcmpl-716d9747949644eb4df1f01bd433a56f", + "request_id": "88688782-11f4-45d9-8b8d-0bd7e3e09e7c", + "response_id": "chatcmpl-e49f23a1641586ccc2e8da9b07ec4e83", "images_count": 8, "graphs_count": 0, - "response": "The code below returns the 12 VFB IDs of subclasses of [Kenyon cell](https://www.virtualflybrain.org/reports/FBbt_00003686 \"Open Kenyon cell in Virtual Fly Brain\") that were retrieved, as a table. VFB holds a total of [37](https://v2.virtualflybrain.org/org.geppetto.frontend/geppetto?q=FBbt_00003686,SubclassesOf \"Run in VFB: Subclasses of Kenyon cell\") subclasses of Kenyon cell.\n\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# ListAllAvailableImages for Kenyon cell\nlist_all_available_images = vfbquery.get_instances(KENYON_CELL)\n```", + "response": "The code below returns the VFB IDs for [Kenyon cell](https://www.virtualflybrain.org/reports/FBbt_00003686 \"Open Kenyon cell in Virtual Fly Brain\"), as listed. VFB holds several IDs for Kenyon cell, including VFB_00100451, VFB_00100431, VFB_00100417, VFB_00100395, VFB_00100335, and VFB_00050000.\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, @@ -7874,14 +8048,14 @@ "graph_failure_mentioned": false, "missing_required_graph": false, "used_data_resource": false, - "response_chars": 928, - "status_count": 9, + "response_chars": 738, + "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": 10560 + "slowest_followup_ms": 15678 } } ] diff --git a/test-results/task-battery/task-battery-2026-08-10T09-57-21-415Z.json b/test-results/task-battery/task-battery-2026-08-10T09-57-21-415Z.json new file mode 100644 index 0000000..36b6b0b --- /dev/null +++ b/test-results/task-battery/task-battery-2026-08-10T09-57-21-415Z.json @@ -0,0 +1,8062 @@ +{ + "metadata": { + "run_id": "task-battery-2026-08-10T09-57-21-415Z", + "started_at": "2026-08-10T09:57:21.415Z", + "completed_at": "2026-08-10T10:08:37.186Z", + "git_sha": "e02f5421f2741f0b6946c6de4aeafa6fd3643d1e", + "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": 2, + "task_ids": [ + "C3", + "C7" + ] + } + }, + "conversation": { + "total": 12, + "ok": 12, + "turns": 27, + "followup_turns": 15, + "followup_median_ms": 10600, + "followup_max_ms": 188171 + }, + "mean_duration_ms": 32891 + }, + "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": 40298, + "status_messages": [ + { + "message": "Thinking...", + "phase": "llm" + }, + { + "message": "Planning (direct lookup)", + "phase": "llm" + }, + { + "message": "Resolving 1 term in VFB", + "phase": "mcp" + }, + { + "message": "Reading VFB term info", + "phase": "mcp" + }, + { + "message": "Checking the answer is covered", + "phase": "llm" + }, + { + "message": "Writing the answer", + "phase": "llm" + } + ], + "event_count": 59, + "ok": true, + "request_id": "79ecd216-5c0d-4a49-88b9-6e39c96ba39c", + "response_id": "chatcmpl-207be5ea6116c1f9a5d75eb6a6749583", + "images_count": 8, + "graphs_count": 0, + "response": "The major subdivisions of the Drosophila [mushroom body](https://www.virtualflybrain.org/reports/FBbt_00005801 \"Open mushroom body in Virtual Fly Brain\") are the calyx, pedunculus, and mushroom body lobe system. The mushroom body lobe system consists of a vertical branch and a medial branch, which have different structures at different life stages.", + "quality_flags": { + "has_tool_status": true, + "no_tool_factual_answer": false, + "tool_claim_without_tool": false, + "disambiguation_only_answer": false, + "investigation_plan_answer": false, + "not_verified_or_no_results_answer": false, + "graph_failure_mentioned": false, + "missing_required_graph": false, + "used_data_resource": false, + "response_chars": 350, + "status_count": 6 + } + }, + { + "attempt_index": 1, + "task_index": 1, + "task_id": "T1.2", + "tier": 1, + "title": "Neuron type classification", + "question": "What types of Kenyon cells exist in the adult Drosophila brain?", + "requires_graph": false, + "min_graphs": 0, + "repetition": 1, + "duration_ms": 42956, + "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": "1635ce40-cfd5-443d-8c7a-96e2bf275734", + "response_id": "chatcmpl-8aed3bd14b6ce9fa827b10db2f15fc08", + "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": 42051, + "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": 92, + "ok": true, + "request_id": "827294a6-115e-4519-9528-578de389e504", + "response_id": "chatcmpl-0479691c99f56b50e562a5bdbd139d00", + "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. The connectome data indicates that these neurons provide input to the mushroom body.", + "graphs": [ + { + "type": "basic_graph", + "version": 1, + "title": "mushroom body region connectivity preview", + "directed": true, + "layout": "radial", + "nodes": [ + { + "id": "FBbt_00005801", + "label": "mushroom body", + "group": "queried region", + "color": null, + "size": 2.4 + }, + { + "id": "FBbt_00111716", + "label": "larval antennal lobe multiglomerular projection neuron C2", + "group": "presynaptic neuron", + "color": null, + "size": 1.15 + }, + { + "id": "FBbt_00111717", + "label": "larval antennal lobe multiglomerular projection neuron bilateral lower", + "group": "presynaptic neuron", + "color": null, + "size": 1.15 + }, + { + "id": "FBbt_00111675", + "label": "larval uniglomerular projection neuron 63a", + "group": "presynaptic neuron", + "color": null, + "size": 1.15 + }, + { + "id": "FBbt_00111684", + "label": "larval uniglomerular projection neuron 67b", + "group": "presynaptic 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"response_id": "chatcmpl-bf0767c7934b1f69f5c76a71f286688f", + "images_count": 6, + "graphs_count": 1, + "response": "The [antennal lobe](https://www.virtualflybrain.org/reports/FBbt_00003924 \"Open antennal lobe in Virtual Fly Brain\") connects to various brain regions through neurons with presynaptic and postsynaptic terminals. VFB records show [266](https://v2.virtualflybrain.org/org.geppetto.frontend/geppetto?q=FBbt_00003924,NeuronsPresynapticHere \"Run in VFB: Neurons with presynaptic terminals in antennal lobe\") neurons with presynaptic terminals in the antennal lobe, including [larval antennal lobe picky local neuron](https://www.virtualflybrain.org/reports/FBbt_00111694 \"Open larval antennal lobe picky local neuron in Virtual Fly Brain\") and [adult olfactory receptor neuron Ir75d ac1](https://www.virtualflybrain.org/reports/FBbt_00110011 \"Open adult olfactory receptor neuron Ir75d ac1 in Virtual Fly Brain\"). Additionally, [518](https://v2.virtualflybrain.org/org.geppetto.frontend/geppetto?q=FBbt_00003924,NeuronsPostsynapticHere \"Run in VFB: Neurons with postsynaptic terminals in antennal lobe\") neurons have postsynaptic terminals in the antennal lobe, such as [AMMC-Bi16](https://www.virtualflybrain.org/reports/FBbt_00111480 \"Open AMMC-Bi16 in Virtual Fly Brain\") and [adult antennal lobe projection neuron DL5](https://www.virtualflybrain.org/reports/FBbt_00059280 \"Open adult antennal lobe projection neuron DL5 in Virtual Fly Brain\"). These neurons likely play a role in processing olfactory information.", + "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": 1413, + "status_count": 10 + } + }, + { + "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": 10729, + "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": 44, + "ok": true, + "request_id": "21dbcd23-abb7-4708-a1f2-db7fa840da86", + "response_id": "chatcmpl-d1cf09ec31f55c8bc901b88233eaa5d4", + "images_count": 0, + "graphs_count": 0, + "response": "The adult Drosophila central brain could not be matched to a VFB record. 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It detects looming stimuli, which elicits a jump escape response. The LPLC2 neuron has its main dendritic arbors in layers 4 and 5B of the lobula, with minor processes in layer 5A, and presynaptic sites in layer 4. It projects to an optic glomerulus of the PVLP, anterior to LPLC1 and dorsal to LC4. There are approximately 80 of these cells per optic lobe, and they are cholinergic.", + "quality_flags": { + "has_tool_status": true, + "no_tool_factual_answer": false, + "tool_claim_without_tool": false, + "disambiguation_only_answer": false, + "investigation_plan_answer": false, + "not_verified_or_no_results_answer": false, + "graph_failure_mentioned": false, + "missing_required_graph": false, + "used_data_resource": false, + "response_chars": 678, + "status_count": 8 + } + }, + { + "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": 7037, + "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": "8076f7bc-d5aa-4150-9175-ace90cf2c82a", + "response_id": "chatcmpl-c8433392e4a9d9c5c540a6ea5508feca", + "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": 203247, + "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": "Querying VFB", + "phase": "mcp" + }, + { + "message": "Reading the literature", + "phase": "mcp" + }, + { + "message": "Checking the literature", + "phase": "mcp" + }, + { + "message": "Checking the answer is covered", + "phase": "llm" + }, + { + "message": "Writing the answer", + "phase": "llm" + } + ], + "event_count": 101, + "ok": true, + "request_id": "9eae37c6-44c1-4e00-abff-263ce8572569", + "response_id": "chatcmpl-2d2ff3d8aeb8b8e697c03ca10686781a", + "images_count": 8, + "graphs_count": 0, + "response": "Publications describing the dopaminergic PPL1 neurons and their role in aversive memory include Claridge-Chang et al., 2009, Mao and Davis, 2009, Budnik and White, 1988, and Ren et al., 2016. The dopaminergic PPL1 neurons are located in the posterior inferior lateral protocerebrum of the adult brain and project to various parts of the mushroom body.", + "quality_flags": { + "has_tool_status": true, + "no_tool_factual_answer": false, + "tool_claim_without_tool": false, + "disambiguation_only_answer": false, + "investigation_plan_answer": false, + "not_verified_or_no_results_answer": false, + "graph_failure_mentioned": false, + "missing_required_graph": false, + "used_data_resource": false, + "response_chars": 351, + "status_count": 10 + } + }, + { + "attempt_index": 14, + "task_index": 14, + "task_id": "T2.7", + "tier": 2, + "title": "Morphological similarity", + "question": "Are there neurons in the Hemibrain dataset that are morphologically similar to the fru+ mAL neurons described in light microscopy studies?", + "requires_graph": false, + "min_graphs": 0, + "repetition": 1, + "duration_ms": 11638, + "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", + "phase": "mcp" + }, + { + "message": "Checking the answer is covered", + "phase": "llm" + }, + { + "message": "Writing the answer", + "phase": "llm" + } + ], + "event_count": 32, + "ok": true, + "request_id": "8cb19b49-fc10-49ab-b930-010be58e3444", + "response_id": "chatcmpl-48ee13b413fe99e3fc5ecef5ec786d7d", + "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": 7 + } + }, + { + "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": 16482, + "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": "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": 152, + "ok": true, + "request_id": "57769663-817e-4961-9f70-e001af6f3b26", + "response_id": "chatcmpl-4da4d3de47a08902daf4fff60d14c4bd", + "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 that there are [102](https://v2.virtualflybrain.org/org.geppetto.frontend/geppetto?q=FBbt_00003679,NeuronsPresynapticHere \"Run in VFB: Neurons with presynaptic terminals in fan-shaped body\") neurons with presynaptic terminals in the fan-shaped body, including [PFNd_PB2](https://www.virtualflybrain.org/reports/FBbt_00111391 \"Open PFNd_PB2 in Virtual Fly Brain\"), [PFNd_PB3](https://www.virtualflybrain.org/reports/FBbt_00111392 \"Open PFNd_PB3 in Virtual Fly Brain\"), [PFNd_PB5](https://www.virtualflybrain.org/reports/FBbt_00111394 \"Open PFNd_PB5 in Virtual Fly Brain\"), [PFNa_PB4](https://www.virtualflybrain.org/reports/FBbt_00111398 \"Open PFNa_PB4 in Virtual Fly Brain\"), [PFNa_PB5](https://www.virtualflybrain.org/reports/FBbt_00111399 \"Open PFNa_PB5 in Virtual Fly Brain\"), PFNa_PB6, PFNa_PB7, PFNa_PB9, PFNp_PB7, [protocerebral bridge glomerulus 8-fan-shaped body-ipsilateral ventral gall surround neuron](https://www.virtualflybrain.org/reports/FBbt_00111463 \"Open protocerebral bridge glomerulus 8-fan-shaped body-ipsilateral ventral gall surround neuron in Virtual Fly Brain\"), [adult ExR1 neuron of DM3 lineage](https://www.virtualflybrain.org/reports/FBbt_00053034 \"Open adult ExR1 neuron of DM3 lineage in Virtual Fly Brain\"), and adult ExR1 neuron of DM4 lineage. The number of synaptic steps between these neurons and the fan-shaped body is not specified.", + "quality_flags": { + "has_tool_status": true, + "no_tool_factual_answer": false, + "tool_claim_without_tool": false, + "disambiguation_only_answer": false, + "investigation_plan_answer": false, + "not_verified_or_no_results_answer": false, + "graph_failure_mentioned": false, + "missing_required_graph": false, + "used_data_resource": false, + "response_chars": 1553, + "status_count": 11 + } + }, + { + "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": 35013, + "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" + }, + { + "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": 278, + "ok": true, + "request_id": "344df32e-7b87-45d3-a499-ac18b895320d", + "response_id": "chatcmpl-c1a426c89a0b1f8dfba7a03490111904", + "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 connectome data indicates that the strongest specific inputs to mushroom body output neuron are [adult cholinergic neuron](https://www.virtualflybrain.org/reports/FBbt_00058205 \"Open adult cholinergic neuron in Virtual Fly Brain\") and [Kenyon cell](https://www.virtualflybrain.org/reports/FBbt_00003686 \"Open Kenyon cell in Virtual Fly Brain\"), while the strongest specific targets of dopaminergic neuron 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": 1015, + "status_count": 15 + } + }, + { + "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": 24416, + "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": 139, + "ok": true, + "request_id": "b0b4fb8e-a14a-44a9-83c9-9004cb0848d0", + "response_id": "chatcmpl-9c07cea5c601173253dac06882981401", + "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 between olfactory receptor neurons and lateral horn. The connectome data indicates that the strongest specific inputs to [olfactory receptor neuron](https://www.virtualflybrain.org/reports/FBbt_00005926 \"Open olfactory receptor neuron in Virtual Fly Brain\") are from various types of local neurons, including [adult antennal lobe local neuron lLN](https://www.virtualflybrain.org/reports/FBbt_00051502 \"Open adult antennal lobe local neuron lLN in Virtual Fly Brain\"), [adult local interneuron of the lateral ALl1 neuroblast](https://www.virtualflybrain.org/reports/FBbt_00007394 \"Open adult local interneuron of the lateral ALl1 neuroblast in Virtual Fly Brain\"), [antennal lobe local neuron](https://www.virtualflybrain.org/reports/FBbt_00052874 \"Open antennal lobe local neuron in Virtual Fly Brain\"), and [adult antennal lobe local neuron](https://www.virtualflybrain.org/reports/FBbt_00007390 \"Open adult antennal lobe local neuron in Virtual Fly Brain\"). VFB holds [1661](https://v2.virtualflybrain.org/org.geppetto.frontend/geppetto?q=FBbt_00007053,NeuronsPartHere \"Run in VFB: Neurons with some part in adult lateral horn\") records of neurons with some part in [adult lateral horn](https://www.virtualflybrain.org/reports/FBbt_00007053 \"Open adult lateral horn in Virtual Fly Brain\") and [1658](https://v2.virtualflybrain.org/org.geppetto.frontend/geppetto?q=FBbt_00007053,NeuronsSynaptic \"Run in VFB: Neurons with synaptic terminals in adult lateral horn\") records of neurons with synaptic terminals in adult lateral horn.", + "quality_flags": { + "has_tool_status": true, + "no_tool_factual_answer": false, + "tool_claim_without_tool": false, + "disambiguation_only_answer": false, + "investigation_plan_answer": false, + "not_verified_or_no_results_answer": false, + "graph_failure_mentioned": false, + "missing_required_graph": false, + "used_data_resource": false, + "response_chars": 1684, + "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": 8267, + "status_messages": [ + { + "message": "Thinking...", + "phase": "llm" + }, + { + "message": "Planning the answer", + "phase": "llm" + }, + { + "message": "Resolving 1 term in VFB", + "phase": "mcp" + }, + { + "message": "Reading VFB term info", + "phase": "mcp" + }, + { + "message": "Summarising neuron taxonomy", + "phase": "mcp" + }, + { + "message": "Checking the answer is covered", + "phase": "llm" + }, + { + "message": "Writing the answer", + "phase": "llm" + } + ], + "event_count": 53, + "ok": true, + "request_id": "95594d77-1fd4-460a-a87f-0a2fe497b95c", + "response_id": "chatcmpl-56e214e7b0b3d06edb13afd51f2fb774", + "images_count": 0, + "graphs_count": 0, + "response": "The question about the number of distinct neuron types in the adult Drosophila visual system and their hierarchical organization cannot be fully answered from VFB evidence. However, it is known that there are subclasses of visual system neuron.", + "quality_flags": { + "has_tool_status": true, + "no_tool_factual_answer": false, + "tool_claim_without_tool": false, + "disambiguation_only_answer": false, + "investigation_plan_answer": false, + "not_verified_or_no_results_answer": false, + "graph_failure_mentioned": false, + "missing_required_graph": false, + "used_data_resource": false, + "response_chars": 244, + "status_count": 7 + } + }, + { + "attempt_index": 19, + "task_index": 19, + "task_id": "T3.4", + "tier": 3, + "title": "Connectivity strength comparison", + "question": "Which neuron type provides the strongest synaptic input to the MBON-gamma1pedc>a/b neuron, and how does this compare to the next strongest inputs?", + "requires_graph": false, + "min_graphs": 0, + "repetition": 1, + "duration_ms": 10361, + "status_messages": [ + { + "message": "Thinking...", + "phase": "llm" + }, + { + "message": "Planning the answer", + "phase": "llm" + }, + { + "message": "Resolving 1 term in VFB", + "phase": "mcp" + }, + { + "message": "Querying VFB connectivity", + "phase": "mcp" + }, + { + "message": "Checking the literature", + "phase": "mcp" + }, + { + "message": "Checking the answer is covered", + "phase": "llm" + }, + { + "message": "Querying VFB", + "phase": "mcp" + }, + { + "message": "Checking the answer is covered", + "phase": "llm" + }, + { + "message": "Writing the answer", + "phase": "llm" + } + ], + "event_count": 51, + "ok": true, + "request_id": "40c412db-7a7a-451e-81c9-f4b84cd0ba0d", + "response_id": "chatcmpl-c31d63118f5956fd8e5da6769be56e60", + "images_count": 8, + "graphs_count": 0, + "response": "The strongest synaptic input to the MBON-gamma1pedc>a/b neuron is not specified. VFB holds upstream connectivity classes for [mushroom body output neuron 11](https://www.virtualflybrain.org/reports/FBbt_00100246 \"Open mushroom body output neuron 11 in Virtual Fly Brain\"), but the lookup did not complete.", + "quality_flags": { + "has_tool_status": true, + "no_tool_factual_answer": false, + "tool_claim_without_tool": false, + "disambiguation_only_answer": false, + "investigation_plan_answer": false, + "not_verified_or_no_results_answer": false, + "graph_failure_mentioned": false, + "missing_required_graph": false, + "used_data_resource": false, + "response_chars": 305, + "status_count": 9 + } + }, + { + "attempt_index": 20, + "task_index": 20, + "task_id": "T3.5", + "tier": 3, + "title": "Shared connectivity", + "question": "Do the alpha/beta and gamma Kenyon cells converge on any of the same downstream MBON types? Which MBONs receive input from both?", + "requires_graph": false, + "min_graphs": 0, + "repetition": 1, + "duration_ms": 12914, + "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": 77, + "ok": true, + "request_id": "d4b052c0-c4af-4ac6-bbfa-20ea38ce48f3", + "response_id": "chatcmpl-4fdf1679ee0b2268ed75ac166063d47f", + "images_count": 8, + "graphs_count": 0, + "response": "The evidence does not specify which mushroom body output neurons receive input from both alpha/beta Kenyon cells and gamma Kenyon cells. VFB does not currently hold data on the downstream connectivity classes for gamma Kenyon cells. VFB holds [69](https://v2.virtualflybrain.org/org.geppetto.frontend/geppetto?q=FBbt_00047953,SubclassesOf \"Run in VFB: Subclasses of MBON\") subclasses of [mushroom body output neuron](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": 806, + "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": 11700, + "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": "0d1f6876-0531-4243-9399-308c01dbca7e", + "response_id": "chatcmpl-8fcd9fa12949b6f3cc1337a4548e6e4a", + "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": 18512, + "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": "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": "ec4451ee-d3b7-46fd-8dc2-cca37011c1e4", + "response_id": "chatcmpl-0e0d419477e5227201373be6e057d57f", + "images_count": 8, + "graphs_count": 0, + "response": "Neurons that connect the [adult central complex](https://www.virtualflybrain.org/reports/FBbt_00003632 \"Open adult central complex in Virtual Fly Brain\") to the lateral accessory lobe include [PFL1](https://www.virtualflybrain.org/reports/FBbt_00111433 \"Open PFL1 in Virtual Fly Brain\"), [PFL2_PB4](https://www.virtualflybrain.org/reports/FBbt_00111453 \"Open PFL2_PB4 in Virtual Fly Brain\"), [PFL3_PB7](https://www.virtualflybrain.org/reports/FBbt_00111450 \"Open PFL3_PB7 in Virtual Fly Brain\"), [PFL1_PB1](https://www.virtualflybrain.org/reports/FBbt_00111434 \"Open PFL1_PB1 in Virtual Fly Brain\"), [PFL1_PB7](https://www.virtualflybrain.org/reports/FBbt_00111440 \"Open PFL1_PB7 in Virtual Fly Brain\"), and [PFL1_PB2](https://www.virtualflybrain.org/reports/FBbt_00111435 \"Open PFL1_PB2 in Virtual Fly Brain\"). VFB does not currently hold data on neurons with some part in embryonic/larval lateral accessory lobe, neurons with presynaptic terminals in embryonic/larval lateral accessory lobe, or neurons with postsynaptic terminals in embryonic/larval lateral accessory lobe.", + "quality_flags": { + "has_tool_status": true, + "no_tool_factual_answer": false, + "tool_claim_without_tool": false, + "disambiguation_only_answer": false, + "investigation_plan_answer": false, + "not_verified_or_no_results_answer": false, + "graph_failure_mentioned": false, + "missing_required_graph": false, + "used_data_resource": false, + "response_chars": 1076, + "status_count": 12 + } + }, + { + "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": 6837, + "status_messages": [ + { + "message": "Thinking...", + "phase": "llm" + }, + { + "message": "Planning the answer", + "phase": "llm" + }, + { + "message": "Resolving 1 term in VFB", + "phase": "mcp" + }, + { + "message": "Querying VFB", + "phase": "mcp" + }, + { + "message": "Checking the answer is covered", + "phase": "llm" + }, + { + "message": "Writing the answer", + "phase": "llm" + } + ], + "event_count": 53, + "ok": true, + "request_id": "20331d40-14fe-4eb5-97af-1e403858e5bd", + "response_id": "chatcmpl-521e17b751640a3bbe59736171029a94", + "images_count": 0, + "graphs_count": 0, + "response": "The carbon dioxide sensitive neuron is involved in CO2 avoidance and is connected to downstream classes such as GABAergic local interneuron of the adult antennal lobe and adult antennal lobe local neuron lLN2P.", + "quality_flags": { + "has_tool_status": true, + "no_tool_factual_answer": false, + "tool_claim_without_tool": false, + "disambiguation_only_answer": false, + "investigation_plan_answer": false, + "not_verified_or_no_results_answer": false, + "graph_failure_mentioned": false, + "missing_required_graph": false, + "used_data_resource": false, + "response_chars": 210, + "status_count": 6 + } + }, + { + "attempt_index": 25, + "task_index": 25, + "task_id": "T4.2", + "tier": 4, + "title": "Complete neuron profile", + "question": "Give me a comprehensive profile of the giant fiber neuron: its anatomy, connectivity, available driver lines, and relevant publications.", + "requires_graph": false, + "min_graphs": 0, + "repetition": 1, + "duration_ms": 26363, + "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": 300, + "ok": true, + "request_id": "bde75b10-1205-49d3-949d-395f919f4bb4", + "response_id": "chatcmpl-d14d815b291dbee12979b31c24cbbfb7", + "images_count": 8, + "graphs_count": 1, + "response": "The [giant fiber neuron](https://www.virtualflybrain.org/reports/FBbt_00004020 \"Open giant fiber neuron in Virtual Fly Brain\") is a large adult descending neuron that controls jump escape behavior. It has a large cell body located posterior to the lower protocerebrum and a large descending axon that enters the cervical connective via the posterior cerebro-cervical fascicle and descends on the ipsilateral side in the dorsal cervical fasciculus. The giant fiber neuron has dendritic arborization in the ipsilateral zones A and B of the antennal mechanosensory and motor center, where it receives substantial input from zone A and B Johnston organ neurons. It also arborizes in the posterior ventrolateral protocerebrum and gorget. In the 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 is connected to various other neurons, including adult VNC neurons, thoracic neurons, mesothoracic neurons, primary neurons, and sensory system neurons. 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 and [10](https://v2.virtualflybrain.org/org.geppetto.frontend/geppetto?q=FBbt_00004020,TransgeneExpressionHere \"Run in VFB: Transgene expression in DNp01\") transgene expression reports, such as P{GMR78G07-GAL4} and P{R48A11-GAL4.DBD} ∩ P{R30C01-p65.AD}. Relevant publications 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": 1616, + "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": 23222, + "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" + }, + { + "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": 442, + "ok": true, + "request_id": "f4ad8b05-9f8c-421a-8352-ea98657b24c9", + "response_id": "chatcmpl-9b9e15aeea6278a5917eaf088ea8c5c3", + "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.\n\nThe 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\"), [adult optic lobe columnar neuron](https://www.virtualflybrain.org/reports/FBbt_00005129 \"Open adult optic lobe columnar neuron in Virtual Fly Brain\"), [transmedullary neuron](https://www.virtualflybrain.org/reports/FBbt_00003788 \"Open transmedullary neuron in Virtual Fly Brain\"), and [optic lobe wide-field columnar neuron](https://www.virtualflybrain.org/reports/FBbt_00110137 \"Open optic lobe wide-field columnar neuron in Virtual Fly Brain\"). The strongest specific targets of visual system neuron include adult optic lobe neuron, optic lobe wide-field columnar neuron, adult optic lobe columnar neuron, optic lobe intrinsic columnar neuron, [adult visual projection neuron](https://www.virtualflybrain.org/reports/FBbt_00048286 \"Open adult visual projection neuron in Virtual Fly Brain\"), and transmedullary neuron.\n\nVFB lists neurons with some part in mushroom body, neurons with synaptic terminals in mushroom body, neurons with presynaptic terminals in mushroom body, and neurons with postsynaptic terminals in mushroom body. These include various types of projection neurons and other neuron types.\n\nVisual information could reach the memory circuit via these connections, as the mushroom body is involved in memory and learning.", + "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": 2228, + "status_count": 17 + } + }, + { + "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": 133850, + "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": "740869a2-0d49-4be2-be97-e040753133c5", + "response_id": "chatcmpl-e926aea640ce5368f6072c8b856ab4ab", + "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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"FBbt_00059247", + "label": "5377", + "weight": 5377 + }, + { + "source": "FBbt_00003763", + "target": "FBbt_00007577", + "label": "5377", + "weight": 5377 + }, + { + "source": "FBbt_00003763", + "target": "FBbt_00007173", + "label": "5198", + "weight": 5198 + }, + { + "source": "FBbt_00003763", + "target": "FBbt_00058205", + "label": "5198", + "weight": 5198 + }, + { + "source": "FBbt_00003763", + "target": "FBbt_00005129", + "label": "5106", + "weight": 5106 + }, + { + "source": "FBbt_00003763", + "target": "FBbt_00007578", + "label": "5052", + "weight": 5052 + }, + { + "source": "FBbt_00003763", + "target": "FBbt_00047096", + "label": "4721", + "weight": 4721 + }, + { + "source": "FBbt_00003763", + "target": "FBbt_00110136", + "label": "4654", + "weight": 4654 + }, + { + "source": "FBbt_00003763", + "target": "FBbt_00049539", + "label": "4548", + "weight": 4548 + }, + { + "source": "FBbt_00003763", + "target": "FBbt_00049541", + "label": "4548", + "weight": 4548 + } + ] + } + ], + "quality_flags": { + "has_tool_status": true, + "no_tool_factual_answer": false, + "tool_claim_without_tool": false, + "disambiguation_only_answer": false, + "investigation_plan_answer": false, + "not_verified_or_no_results_answer": false, + "graph_failure_mentioned": false, + "missing_required_graph": false, + "used_data_resource": false, + "response_chars": 1400, + "status_count": 9 + } + }, + { + "attempt_index": 28, + "task_index": 28, + "task_id": "T4.5", + "tier": 4, + "title": "Novel circuit exploration", + "question": "What is the connectivity between thermosensory neurons and the mushroom body? Could temperature information influence memory formation?", + "requires_graph": false, + "min_graphs": 0, + "repetition": 1, + "duration_ms": 196137, + "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": 183, + "ok": true, + "request_id": "6935d415-3129-4b57-b042-f3f66dc15d49", + "response_id": "chatcmpl-4b28f3f8cde3d61bf74875e889d12d4e", + "images_count": 8, + "graphs_count": 1, + "response": "Thermosensory neurons connect to the [mushroom body](https://www.virtualflybrain.org/reports/FBbt_00005801 \"Open mushroom body in Virtual Fly Brain\") via projection neurons. The downstream class-connectivity previews for adult thermosensory projection neurons include mushroom-body-associated dopaminergic neurons and gamma main Kenyon cells. VFB's class-level connectivity table for [thermosensory neuron](https://www.virtualflybrain.org/reports/FBbt_00005918 \"Open thermosensory neuron in Virtual Fly Brain\") lists [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\") as strong targets, with 18.9, 18.8, and 18.7 synapses per connected pair, respectively.\n\nVFB holds [366](https://v2.virtualflybrain.org/org.geppetto.frontend/geppetto?q=FBbt_00005801,NeuronsPresynapticHere \"Run in VFB: Neurons with presynaptic terminals in mushroom body\") records of neurons with presynaptic terminals in mushroom body and [304](https://v2.virtualflybrain.org/org.geppetto.frontend/geppetto?q=FBbt_00005801,NeuronsPostsynapticHere \"Run in VFB: Neurons with postsynaptic terminals in mushroom body\") records of neurons with postsynaptic terminals in mushroom body.\n\nTemperature information could potentially influence memory formation through the connectivity between thermosensory neurons and the mushroom body, given that the mushroom body is involved in learning and memory.", + "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": 1747, + "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": 205871, + "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": "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": 230, + "ok": true, + "request_id": "3312bdd7-2ac6-46b8-be75-5e30a4d350a4", + "response_id": "chatcmpl-4e1a0a0e93321fdc71392a20e400e059", + "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, with available imagery and various queries for neuron types and connectomics data. VFB records show [2,698](https://v2.virtualflybrain.org/org.geppetto.frontend/geppetto?q=FBbt_00051068,NeuronsPartHere \"Run in VFB: Neurons with some part in subesophageal zone\") neurons with some part in the subesophageal zone, including [serotonergic SE1 neuron](https://www.virtualflybrain.org/reports/FBbt_00001980 \"Open serotonergic SE1 neuron in Virtual Fly Brain\") and [larval CCAP subesophageal IN-1 neuron](https://www.virtualflybrain.org/reports/FBbt_00111345 \"Open larval CCAP subesophageal IN-1 neuron in Virtual Fly Brain\"). There are also [2,598](https://v2.virtualflybrain.org/org.geppetto.frontend/geppetto?q=FBbt_00051068,NeuronsSynaptic \"Run in VFB: Neurons with synaptic terminals in subesophageal zone\") neurons with synaptic terminals in the subesophageal zone, such as [intrinsic antennal mechanosensory and motor center neuron](https://www.virtualflybrain.org/reports/FBbt_00111352 \"Open intrinsic antennal mechanosensory and motor center neuron in Virtual Fly Brain\") and [AMMC-VLP](https://www.virtualflybrain.org/reports/FBbt_00111354 \"Open AMMC-VLP in Virtual Fly Brain\").\n\nFor genetic tools, VFB holds 4,205 transgene expression reports for the subesophageal zone, including [P{GMR12D05-GAL4} expression pattern](https://www.virtualflybrain.org/reports/VFBexp_FBtp0057511 \"Open P{GMR12D05-GAL4} expression pattern in Virtual Fly Brain\") and P{VT000003-GAL4} expression pattern.\n\nConnectivity data indicates that there are neurons with presynaptic and postsynaptic terminals in the subesophageal zone, but the exact details of these connections are not specified here.\n\nVFB holds [29,765](https://v2.virtualflybrain.org/org.geppetto.frontend/geppetto?q=FBbt_00051068,ImagesNeurons \"Run in VFB: Images of neurons with some part in subesophageal zone\") images of neurons with some part in the subesophageal zone.", + "quality_flags": { + "has_tool_status": true, + "no_tool_factual_answer": false, + "tool_claim_without_tool": false, + "disambiguation_only_answer": false, + "investigation_plan_answer": false, + "not_verified_or_no_results_answer": false, + "graph_failure_mentioned": false, + "missing_required_graph": false, + "used_data_resource": false, + "response_chars": 2070, + "status_count": 14 + } + }, + { + "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": 17434, + "status_messages": [ + { + "message": "Thinking...", + "phase": "llm" + }, + { + "message": "Planning the answer", + "phase": "llm" + }, + { + "phase": "plan", + "message": "The plan is contested — sampling again before committing." + }, + { + "message": "Resolving 1 term in VFB", + "phase": "mcp" + }, + { + "message": "Reading VFB term info", + "phase": "mcp" + }, + { + "message": "Querying VFB", + "phase": "mcp" + }, + { + "message": "Querying VFB", + "phase": "mcp" + }, + { + "message": "Querying VFB connectivity", + "phase": "mcp" + }, + { + "message": "Querying VFB", + "phase": "mcp" + }, + { + "message": "Querying VFB", + "phase": "mcp" + }, + { + "message": "Checking the answer is covered", + "phase": "llm" + }, + { + "message": "Writing the answer", + "phase": "llm" + } + ], + "event_count": 146, + "ok": true, + "request_id": "69b522dd-5eca-4698-aad4-4481ffef4307", + "response_id": "chatcmpl-1eb6ffb1bf93fd93cf3b18c722aa6527", + "images_count": 8, + "graphs_count": 1, + "response": "The [medulla](https://www.virtualflybrain.org/reports/FBbt_00003748 \"Open medulla in Virtual Fly Brain\") has neurons with presynaptic terminals, with [262](https://v2.virtualflybrain.org/org.geppetto.frontend/geppetto?q=FBbt_00003748,NeuronsPresynapticHere \"Run in VFB: Neurons with presynaptic terminals in medulla\") results, including [Dm8b](https://www.virtualflybrain.org/reports/FBbt_00110069 \"Open Dm8b in Virtual Fly Brain\"), [PS128](https://www.virtualflybrain.org/reports/FBbt_20001883 \"Open PS128 in Virtual Fly Brain\"), [Mi10b](https://www.virtualflybrain.org/reports/FBbt_00110070 \"Open Mi10b in Virtual Fly Brain\"), [CB3849](https://www.virtualflybrain.org/reports/FBbt_20007264 \"Open CB3849 in Virtual Fly Brain\"), [TmY-ds](https://www.virtualflybrain.org/reports/FBbt_00052643 \"Open TmY-ds in Virtual Fly Brain\"), [Dm7](https://www.virtualflybrain.org/reports/FBbt_00003774 \"Open Dm7 in Virtual Fly Brain\"), Mi6, Mi8, Tm10, Tm13, Tm14, and Tm18. It also has neurons with postsynaptic terminals, with [333](https://v2.virtualflybrain.org/org.geppetto.frontend/geppetto?q=FBbt_00003748,NeuronsPostsynapticHere \"Run in VFB: Neurons with postsynaptic terminals in medulla\") results, including 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": 1484, + "status_count": 12 + } + }, + { + "attempt_index": 31, + "task_index": 31, + "task_id": "D1", + "tier": 6, + "title": "Project identity", + "question": "What is Virtual Fly Brain and who is it for?", + "requires_graph": false, + "min_graphs": 0, + "repetition": 1, + "duration_ms": 5612, + "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": "d07ff3de-25f6-403a-9f1f-e7d51ccab58a", + "response_id": "chatcmpl-d2e7784e33e1c4439dd1838bde60868d", + "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": 35056, + "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": "f0d18c63-f5de-4bee-8962-1e5ff42113cd", + "response_id": "chatcmpl-438509c077c4f051ff7ccae2caea30e2", + "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": 7090, + "status_messages": [ + { + "message": "Thinking...", + "phase": "llm" + }, + { + "message": "Planning the answer", + "phase": "llm" + }, + { + "message": "Reading VFB documentation", + "phase": "mcp" + }, + { + "message": "Checking VFB documentation", + "phase": "mcp" + }, + { + "message": "Checking the answer is covered", + "phase": "llm" + }, + { + "message": "Writing the answer", + "phase": "llm" + } + ], + "event_count": 25, + "ok": true, + "request_id": "a0dbd65b-69f1-47ba-92a5-28ea59583682", + "response_id": "chatcmpl-a9659abb35f13414b4096dbc0d996867", + "images_count": 0, + "graphs_count": 0, + "response": "Virtual Fly Brain is funded by multiple UK research councils and charitable foundations since 2009.", + "quality_flags": { + "has_tool_status": true, + "no_tool_factual_answer": false, + "tool_claim_without_tool": false, + "disambiguation_only_answer": false, + "investigation_plan_answer": false, + "not_verified_or_no_results_answer": false, + "graph_failure_mentioned": false, + "missing_required_graph": false, + "used_data_resource": false, + "response_chars": 99, + "status_count": 6 + } + }, + { + "attempt_index": 34, + "task_index": 34, + "task_id": "D4", + "tier": 6, + "title": "Policies / accessibility", + "question": "What is Virtual Fly Brain's accessibility statement?", + "requires_graph": false, + "min_graphs": 0, + "repetition": 1, + "duration_ms": 6424, + "status_messages": [ + { + "message": "Thinking...", + "phase": "llm" + }, + { + "message": "Planning (direct lookup)", + "phase": "llm" + }, + { + "message": "Resolving 1 term in VFB", + "phase": "mcp" + }, + { + "message": "Reading VFB term info", + "phase": "mcp" + }, + { + "message": "Checking the literature", + "phase": "mcp" + }, + { + "message": "Checking the answer is covered", + "phase": "llm" + }, + { + "message": "Writing the answer", + "phase": "llm" + } + ], + "event_count": 65, + "ok": true, + "request_id": "7259ce48-336f-4287-8165-54398698699d", + "response_id": "chatcmpl-5bc3cbde8c8c670f526d7a9dc259df73", + "images_count": 0, + "graphs_count": 0, + "response": "Virtual Fly Brain's accessibility statement is that the website is partially compliant with the Web Content Accessibility Guidelines (WCAG) 2.2 AA standard, with non-compliances listed, and the University of Edinburgh is committed to making its websites and applications accessible in line with the regulations.", + "quality_flags": { + "has_tool_status": true, + "no_tool_factual_answer": false, + "tool_claim_without_tool": false, + "disambiguation_only_answer": false, + "investigation_plan_answer": false, + "not_verified_or_no_results_answer": false, + "graph_failure_mentioned": false, + "missing_required_graph": false, + "used_data_resource": false, + "response_chars": 311, + "status_count": 7 + } + }, + { + "attempt_index": 35, + "task_index": 35, + "task_id": "D5", + "tier": 6, + "title": "Contact / contribute", + "question": "How do I report a problem or contribute data to Virtual Fly Brain?", + "requires_graph": false, + "min_graphs": 0, + "repetition": 1, + "duration_ms": 9379, + "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": 136, + "ok": true, + "request_id": "db5674af-c9ea-4fc4-bfdc-d684fc931d33", + "response_id": "chatcmpl-ed6a2c3382dc8709ba8634aafb076ca0", + "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 Virtual Fly Brain team for technical support, bug reports, data contributions, collaboration opportunities, or questions about using VFB software and data. You can contact Virtual Fly Brain through their public support forum, GitHub issues, or private email. For help with using Virtual Fly Brain, comments, suggestions, or general questions, 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.", + "quality_flags": { + "has_tool_status": true, + "no_tool_factual_answer": false, + "tool_claim_without_tool": false, + "disambiguation_only_answer": false, + "investigation_plan_answer": false, + "not_verified_or_no_results_answer": false, + "graph_failure_mentioned": false, + "missing_required_graph": false, + "used_data_resource": false, + "response_chars": 680, + "status_count": 6 + } + }, + { + "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": 8487, + "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": "03400182-6810-4ca1-ae6e-b2e275165da0", + "response_id": "chatcmpl-31215a551a7af2f38207c7651ad2c044", + "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 and 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": 348, + "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": 12803, + "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": 83, + "ok": true, + "request_id": "3603dcf1-9ac7-459a-acf7-adaeae6c52f8", + "response_id": "chatcmpl-80afea218f847f4fcfc301dfebddbb91", + "images_count": 0, + "graphs_count": 0, + "response": "The Circuit Browser tab allows you to find the strongest paths from one neuron to another. To use it, search for the source neuron to start from, noting that the query is directional. The strongest paths are the shortest or highest weighted paths, arranged from strongest at the bottom to weakest at the top. A detailed explanation for the algorithm used to determine path strengths is available.", + "quality_flags": { + "has_tool_status": true, + "no_tool_factual_answer": false, + "tool_claim_without_tool": false, + "disambiguation_only_answer": false, + "investigation_plan_answer": false, + "not_verified_or_no_results_answer": false, + "graph_failure_mentioned": false, + "missing_required_graph": false, + "used_data_resource": false, + "response_chars": 396, + "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": 18013, + "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": 178, + "ok": true, + "request_id": "f7b20840-c423-4d01-9b8f-6cfaec6da867", + "response_id": "chatcmpl-4ddbd218d85f88bbb97c4ec44542135b", + "images_count": 0, + "graphs_count": 0, + "response": "NBLAST is a method to quantify morphological similarity. It works on \"dotprops\" which represent neurons as tangent vectors. For each tangent vector in the query neuron, NBLAST finds the closest tangent vector in the target neuron and calculates a score from the distance between and the dotproduct of the two vectors. The final NBLAST score is the sum over all query-target vector pairs. Typically, this score is normalized to a self-self comparison, where a perfect match would be 1.\n\nAn NBLAST similarity score is a measure of how similar the morphology of two neurons is, with higher scores indicating greater similarity. The score is computed per registered neuron, making it a scored comparison of individual neurons rather than a property of the cell type.\n\nI could not match \"NBLAST\" to a VFB term, so I cannot speak to what VFB holds for it.", + "quality_flags": { + "has_tool_status": true, + "no_tool_factual_answer": false, + "tool_claim_without_tool": false, + "disambiguation_only_answer": false, + "investigation_plan_answer": false, + "not_verified_or_no_results_answer": false, + "graph_failure_mentioned": false, + "missing_required_graph": false, + "used_data_resource": false, + "response_chars": 849, + "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": 9396, + "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": "fe2c6363-d7e4-4f72-8022-57b7928bcc43", + "response_id": "chatcmpl-bdce8ac35689a285b6a41e19beb3431d", + "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": 10677, + "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" + }, + { + "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": 76, + "ok": true, + "request_id": "c2916940-fea5-4105-9347-5f47d7d2bef5", + "response_id": "chatcmpl-4f3cdeae8217767dbbc137c536b312b8", + "images_count": 8, + "graphs_count": 0, + "response": "Bridging registrations between brain templates in VFB are 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": 130, + "status_count": 13 + } + }, + { + "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": 6585, + "status_messages": [ + { + "message": "Thinking...", + "phase": "llm" + }, + { + "message": "Planning the answer", + "phase": "llm" + }, + { + "message": "Reading VFB documentation", + "phase": "mcp" + }, + { + "message": "Checking VFB documentation", + "phase": "mcp" + }, + { + "message": "Checking the answer is covered", + "phase": "llm" + }, + { + "message": "Writing the answer", + "phase": "llm" + } + ], + "event_count": 55, + "ok": true, + "request_id": "d132494e-047e-4638-b1c1-06a9373208a0", + "response_id": "chatcmpl-324123b5f6e4c6b51e7a1aa3e85b0390", + "images_count": 0, + "graphs_count": 0, + "response": "Virtual Fly Brain holds various imaging data types, including skeleton, mesh, and volume, and brain templates with painted domains/regions. The retrieved neuron object can provide different representations of neuron data, such as its skeleton, mesh, and volume.", + "quality_flags": { + "has_tool_status": true, + "no_tool_factual_answer": false, + "tool_claim_without_tool": false, + "disambiguation_only_answer": false, + "investigation_plan_answer": false, + "not_verified_or_no_results_answer": false, + "graph_failure_mentioned": false, + "missing_required_graph": false, + "used_data_resource": false, + "response_chars": 261, + "status_count": 6 + } + }, + { + "attempt_index": 42, + "task_index": 42, + "task_id": "D12", + "tier": 6, + "title": "Release changelog", + "question": "What was included in the latest Virtual Fly Brain release?", + "requires_graph": false, + "min_graphs": 0, + "repetition": 1, + "duration_ms": 5103, + "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": "5ad69095-00ff-4a07-b662-b26c9d0303e4", + "response_id": "chatcmpl-3de8b46381b072d2f135591eca97f10c", + "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": 5496, + "status_messages": [ + { + "message": "Thinking...", + "phase": "llm" + }, + { + "message": "Planning the answer", + "phase": "llm" + }, + { + "message": "Reading VFB documentation", + "phase": "mcp" + }, + { + "message": "Checking VFB documentation", + "phase": "mcp" + }, + { + "message": "Checking the answer is covered", + "phase": "llm" + }, + { + "message": "Writing the answer", + "phase": "llm" + } + ], + "event_count": 31, + "ok": true, + "request_id": "23c48ced-f0fc-45d0-87f3-8f99eae948aa", + "response_id": "chatcmpl-72bd330b0d91b63a3855c7938a1d2506", + "images_count": 0, + "graphs_count": 0, + "response": "To install and get started with VFB-connect in Python, you can install it via PyPi using the command\n```\npip install vfb-connect\n```", + "quality_flags": { + "has_tool_status": true, + "no_tool_factual_answer": false, + "tool_claim_without_tool": false, + "disambiguation_only_answer": false, + "investigation_plan_answer": false, + "not_verified_or_no_results_answer": false, + "graph_failure_mentioned": false, + "missing_required_graph": false, + "used_data_resource": false, + "response_chars": 132, + "status_count": 6 + } + }, + { + "attempt_index": 44, + "task_index": 44, + "task_id": "D14", + "tier": 6, + "title": "API: REST endpoints", + "question": "How can I query Virtual Fly Brain programmatically using the SOLR or Owlery API?", + "requires_graph": false, + "min_graphs": 0, + "repetition": 1, + "duration_ms": 10991, + "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": 153, + "ok": true, + "request_id": "c88a2af8-2655-423b-964c-c732f971c4c1", + "response_id": "chatcmpl-45ddc706ef0ce8ed7eb52fdfc0fca307", + "images_count": 0, + "graphs_count": 0, + "response": "To query Virtual Fly Brain programmatically, you can use the SOLR Search API or the Owlery API. The SOLR Search API provides fast text search and autocomplete functionality for VFB entities, datasets, and publications. The Owlery API provides OWL reasoning services for VFB's ontologies, enabling complex queries over class hierarchies and relationships.\n\nThe Owlery API endpoint is https://owl.virtualflybrain.org/ and it supports various query operations such as subclasses, superclasses, equivalent classes, satisfiability, and instances. You can also use SPARQL queries with OWL reasoning.\n\nYou can access the Owlery API at its base URL https://owl.virtualflybrain.org/ to perform these queries.", + "quality_flags": { + "has_tool_status": true, + "no_tool_factual_answer": false, + "tool_claim_without_tool": false, + "disambiguation_only_answer": false, + "investigation_plan_answer": false, + "not_verified_or_no_results_answer": false, + "graph_failure_mentioned": false, + "missing_required_graph": false, + "used_data_resource": false, + "response_chars": 699, + "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": 10289, + "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": 105, + "ok": true, + "request_id": "8d029709-0e23-496b-8535-404a430bff36", + "response_id": "chatcmpl-237eaba536a0c182b863c77fa6366755", + "images_count": 0, + "graphs_count": 0, + "response": "To explore Virtual Fly Brain neurons, you can refer to the tutorials provided. The pymaid library lets you interface with a CATMAID server, such as those provided by Virtual Fly Brain, and returns data in a way that you can use features such as plotting. You can connect to the Virtual Fly Brain CATMAID server, retrieve neurons, and plot them. VFB'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": 449, + "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": 13018, + "status_messages": [ + { + "message": "Thinking...", + "phase": "llm" + }, + { + "message": "Planning the answer", + "phase": "llm" + }, + { + "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": 104, + "ok": true, + "request_id": "7083dd5f-f27f-45df-a0c3-600475acdf2f", + "response_id": "chatcmpl-4c83842a91c95966c816fd8b045c4c7d", + "images_count": 0, + "graphs_count": 0, + "response": "To use the Virtual Fly Brain Model Context Protocol (MCP) tool, access it at vfb3-mcp.virtualflybrain.org and follow the setup instructions for your preferred client, such as Claude Desktop or GitHub Copilot. Configure the MCP server settings, restart your client if necessary, and test the connection by asking questions like \"Get information about the neuron \" or \"Search for terms related to medulla in the fly brain\".\n\n```\n{\n\"mcpServers\": {\n\"virtual-fly-brain\": {\n\"type\": \"http\",\n\"url\": \"https://vfb3-mcp.virtualflybrain.org\",\n\"tools\": [\"*\"]\n}\n}\n}\n```", + "quality_flags": { + "has_tool_status": true, + "no_tool_factual_answer": false, + "tool_claim_without_tool": false, + "disambiguation_only_answer": false, + "investigation_plan_answer": false, + "not_verified_or_no_results_answer": false, + "graph_failure_mentioned": false, + "missing_required_graph": false, + "used_data_resource": false, + "response_chars": 555, + "status_count": 7 + } + }, + { + "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": 8022, + "status_messages": [ + { + "message": "Thinking...", + "phase": "llm" + }, + { + "message": "Planning the answer", + "phase": "llm" + }, + { + "phase": "plan", + "message": "The plan is contested — sampling again before committing." + }, + { + "message": "Resolving 1 term in VFB", + "phase": "mcp" + }, + { + "message": "Reading VFB term info", + "phase": "mcp" + }, + { + "message": "Checking the literature", + "phase": "mcp" + }, + { + "message": "Checking the answer is covered", + "phase": "llm" + }, + { + "message": "Writing the answer", + "phase": "llm" + } + ], + "event_count": 42, + "ok": true, + "request_id": "44e8feb4-6de3-404b-8207-93adf3a3b3b5", + "response_id": "chatcmpl-3e30dfddf86cc69425ed45e11af7fbde", + "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, try searching 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": 171, + "status_count": 8 + } + }, + { + "attempt_index": 48, + "task_index": 48, + "task_id": "D18", + "tier": 6, + "title": "Community events", + "question": "When and where is the NeuroFly 2026 conference?", + "requires_graph": false, + "min_graphs": 0, + "repetition": 1, + "duration_ms": 7909, + "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": "0d0d2207-54b4-4c66-8785-59b0664b2e38", + "response_id": "chatcmpl-371b3fa100c02c3fabffcaa74f50fe2e", + "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": 10274, + "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": 52, + "ok": true, + "request_id": "58436467-47c4-4351-91e1-35281e94ed0f", + "response_id": "chatcmpl-e62288e422f63ec871f036895c93479f", + "images_count": 0, + "graphs_count": 0, + "response": "Materials from the VFB 'Hacking the connectome' workshop are available. The materials include a recorded introduction session and workshop notebooks that demonstrate how to use available tools to explore and analyse 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": 245, + "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": 20635, + "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": 82, + "ok": true, + "request_id": "1735f25f-531e-473f-9102-b87431479a4f", + "response_id": "chatcmpl-25e1986acf18074048da2953ad63ada6", + "images_count": 8, + "graphs_count": 0, + "response": "The FAFB CATMAID dataset can be accessed via https://fafb.catmaid.virtualflybrain.org. Virtual Fly Brain hosts several CATMAID instances for exploring connectomic reconstruction data, including FAFB. The name \"FANC\" could not be matched, with closest records found including Fancl, FANCI, and Fancm.", + "quality_flags": { + "has_tool_status": true, + "no_tool_factual_answer": false, + "tool_claim_without_tool": false, + "disambiguation_only_answer": false, + "investigation_plan_answer": false, + "not_verified_or_no_results_answer": false, + "graph_failure_mentioned": false, + "missing_required_graph": false, + "used_data_resource": false, + "response_chars": 299, + "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": 6073, + "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": "81e88695-8a02-4291-b79c-733891ce4238", + "response_id": "chatcmpl-ba60c5d933e332294ed7e5f72eac2ce7", + "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": 11071, + "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": 5054, + "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 (distal) medulla, the seventh (or serpentine) layer exhibits a distinct architecture and layers 8-10 make up the inner (proximal) 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": 6017, + "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": "01d915c8-21c4-4379-804a-7bb88ab2b6a5", + "response_id": "chatcmpl-1dfd5c1e71524a889c408f4ac6b18743", + "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": 6017 + } + }, + { + "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": 16709, + "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": 353, + "conversation": true, + "turns": [ + { + "turn": 1, + "question": "What is the mushroom body?", + "focus": null, + "clicked": null, + "duration_ms": 6109, + "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": 10600, + "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, with the first 12 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. The connectome data indicates that there are [602](https://v2.virtualflybrain.org/org.geppetto.frontend/geppetto?q=FBbt_00005801,NeuronsPartHere \"Run in VFB: Neurons with some part in mushroom body\") neurons with some part in the mushroom body, including [adult odd neuron of the calyx](https://www.virtualflybrain.org/reports/FBbt_00111628 \"Open adult odd neuron of the calyx in Virtual Fly Brain\"), [larval uniglomerular projection neuron 63a](https://www.virtualflybrain.org/reports/FBbt_00111675 \"Open larval uniglomerular projection neuron 63a in Virtual Fly Brain\"), [larval uniglomerular projection neuron 67b](https://www.virtualflybrain.org/reports/FBbt_00111684 \"Open larval uniglomerular projection neuron 67b in Virtual Fly Brain\"), [larval uniglomerular projection neuron 74a](https://www.virtualflybrain.org/reports/FBbt_00111685 \"Open larval uniglomerular projection neuron 74a in Virtual Fly Brain\"), [larval antennal lobe multiglomerular projection neuron C2](https://www.virtualflybrain.org/reports/FBbt_00111716 \"Open larval antennal lobe multiglomerular projection neuron C2 in Virtual Fly Brain\"), [larval antennal lobe multiglomerular projection neuron bilateral lower](https://www.virtualflybrain.org/reports/FBbt_00111717 \"Open larval antennal lobe multiglomerular projection neuron bilateral lower in Virtual Fly Brain\"), larval antennal lobe multiglomerular projection neuron bilateral upper, larval antennal lobe multiglomerular projection neuron D, larval antennal lobe multiglomerular projection neuron cobra, AOTU021, AOTU022, and [ATL005](https://www.virtualflybrain.org/reports/FBbt_20000069 \"Open ATL005 in Virtual Fly Brain\").", + "followons": [ + { + "id": "FBbt_00005801", + "query_type": "TransgeneExpressionHere", + "query": "Which driver lines label the mushroom body?" + }, + { + "id": "FBbt_00005801", + "query_type": "NeuronsSynaptic", + "query": "Which neurons have synaptic terminals in the mushroom body?" + }, + { + "id": "FBbt_00005801", + "query_type": "NeuronsPresynapticHere", + "query": "Which neurons provide input to the mushroom body?" + }, + { + "id": "FBbt_00005801", + "query_type": "NeuronsPostsynapticHere", + "query": "Which neurons receive output from the mushroom body?" + }, + { + "id": "FBbt_00005801", + "query_type": "PartsOf", + "query": "What are the anatomical parts of the mushroom body?" + }, + { + "id": "FBbt_00005801", + "query_type": "LineageClonesIn", + "query": "Which lineage clones are found in the mushroom body?" + } + ], + "context_terms": [ + { + "id": "FBbt_00005801", + "label": "mushroom body" + } + ], + "reproduction": { + "ids": [ + { + "id": "FBbt_00005801", + "label": "mushroom body" + } + ], + "calls": [ + { + "id": "FBbt_00005801", + "query_type": "ImagesNeurons", + "fn": "get_images_neurons" + }, + { + "id": "FBbt_00005801", + "query_type": "NeuronsPartHere", + "fn": "get_neurons_with_part_in" + } + ], + "unmapped": [] + }, + "status_count": 8, + "problems": [] + } + ], + "ok": true, + "request_id": "90cb6b3a-3121-47ce-997b-2272e5513232", + "response_id": "chatcmpl-6cc4afd710422bb908da4fe02b04978b", + "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, with the first 12 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. The connectome data indicates that there are [602](https://v2.virtualflybrain.org/org.geppetto.frontend/geppetto?q=FBbt_00005801,NeuronsPartHere \"Run in VFB: Neurons with some part in mushroom body\") neurons with some part in the mushroom body, including [adult odd neuron of the calyx](https://www.virtualflybrain.org/reports/FBbt_00111628 \"Open adult odd neuron of the calyx in Virtual Fly Brain\"), [larval uniglomerular projection neuron 63a](https://www.virtualflybrain.org/reports/FBbt_00111675 \"Open larval uniglomerular projection neuron 63a in Virtual Fly Brain\"), [larval uniglomerular projection neuron 67b](https://www.virtualflybrain.org/reports/FBbt_00111684 \"Open larval uniglomerular projection neuron 67b in Virtual Fly Brain\"), [larval uniglomerular projection neuron 74a](https://www.virtualflybrain.org/reports/FBbt_00111685 \"Open larval uniglomerular projection neuron 74a in Virtual Fly Brain\"), [larval antennal lobe multiglomerular projection neuron C2](https://www.virtualflybrain.org/reports/FBbt_00111716 \"Open larval antennal lobe multiglomerular projection neuron C2 in Virtual Fly Brain\"), [larval antennal lobe multiglomerular projection neuron bilateral lower](https://www.virtualflybrain.org/reports/FBbt_00111717 \"Open larval antennal lobe multiglomerular projection neuron bilateral lower in Virtual Fly Brain\"), larval antennal lobe multiglomerular projection neuron bilateral upper, larval antennal lobe multiglomerular projection neuron D, larval antennal lobe multiglomerular projection neuron cobra, AOTU021, AOTU022, and [ATL005](https://www.virtualflybrain.org/reports/FBbt_20000069 \"Open ATL005 in Virtual Fly Brain\").", + "quality_flags": { + "has_tool_status": true, + "no_tool_factual_answer": false, + "tool_claim_without_tool": false, + "disambiguation_only_answer": false, + "investigation_plan_answer": false, + "not_verified_or_no_results_answer": false, + "graph_failure_mentioned": false, + "missing_required_graph": false, + "used_data_resource": false, + "response_chars": 2286, + "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": 10600 + } + }, + { + "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": 142204, + "status_messages": [ + { + "message": "Thinking...", + "phase": "llm" + }, + { + "message": "Running the query behind that suggestion", + "phase": "mcp" + }, + { + "message": "Resolving 1 term in VFB", + "phase": "mcp" + }, + { + "message": "Querying VFB", + "phase": "mcp" + }, + { + "message": "Checking the answer is covered", + "phase": "llm" + }, + { + "message": "Writing the answer", + "phase": "llm" + } + ], + "event_count": 125, + "conversation": true, + "turns": [ + { + "turn": 1, + "question": "What is the fan-shaped body?", + "focus": null, + "clicked": null, + "duration_ms": 5894, + "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": 9350, + "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": 126960, + "ok": true, + "response": "Neurons with synaptic terminals in the [fan-shaped body](https://www.virtualflybrain.org/reports/FBbt_00003679 \"Open fan-shaped body in Virtual Fly Brain\") include [229](https://v2.virtualflybrain.org/org.geppetto.frontend/geppetto?q=FBbt_00003679,NeuronsPartHere \"Run in VFB: Neurons with some part in fan-shaped body\") neuron types, such as [PFNa_PB4](https://www.virtualflybrain.org/reports/FBbt_00111398 \"Open PFNa_PB4 in Virtual Fly Brain\"), [PFNa_PB5](https://www.virtualflybrain.org/reports/FBbt_00111399 \"Open PFNa_PB5 in Virtual Fly Brain\"), [PFNd_PB2](https://www.virtualflybrain.org/reports/FBbt_00111391 \"Open PFNd_PB2 in Virtual Fly Brain\"), [PFNd_PB3](https://www.virtualflybrain.org/reports/FBbt_00111392 \"Open PFNd_PB3 in Virtual Fly Brain\"), [PFNd_PB5](https://www.virtualflybrain.org/reports/FBbt_00111394 \"Open PFNd_PB5 in Virtual Fly Brain\"). The first 12 of these, with their VFB ids, are: PFNd_PB2; PFNd_PB3; PFNd_PB5; PFNa_PB4; PFNa_PB5; PFNa_PB6; PFNa_PB7; PFNa_PB9; PFNp_PB7; [PFL1_PB5](https://www.virtualflybrain.org/reports/FBbt_00111438 \"Open PFL1_PB5 in Virtual Fly Brain\"); [PFL3](https://www.virtualflybrain.org/reports/FBbt_00111443 \"Open PFL3 in Virtual Fly Brain\"); [PFL2](https://www.virtualflybrain.org/reports/FBbt_00111451 \"Open PFL2 in Virtual Fly Brain\").", + "followons": [ + { + "id": "FBbt_00003679", + "query_type": "ImagesNeurons", + "query": "Which neuron images have a part in the fan-shaped body?" + }, + { + "id": "FBbt_00003679", + "query_type": "TransgeneExpressionHere", + "query": "Which driver lines label the fan-shaped body?" + }, + { + "id": "FBbt_00003679", + "query_type": "NeuronsPartHere", + "query": "Which neurons have part of their arbour in the fan-shaped body?" + }, + { + "id": "FBbt_00003679", + "query_type": "NeuronsPresynapticHere", + "query": "Which neurons provide input to the fan-shaped body?" + }, + { + "id": "FBbt_00003679", + "query_type": "NeuronsPostsynapticHere", + "query": "Which neurons receive output from the fan-shaped body?" + }, + { + "id": "FBbt_00003679", + "query_type": "PartsOf", + "query": "What are the anatomical parts of the fan-shaped body?" + } + ], + "context_terms": [ + { + "id": "FBbt_00003679", + "label": "fan-shaped body" + }, + { + "id": "FBbt_00003678", + "label": "ellipsoid body" + } + ], + "reproduction": { + "ids": [ + { + "id": "FBbt_00003679", + "label": "fan-shaped body" + }, + { + "id": "FBbt_00003678", + "label": "ellipsoid body" + } + ], + "calls": [ + { + "id": "FBbt_00003679", + "query_type": "NeuronsSynaptic", + "fn": "get_neurons_with_synapses_in" + } + ], + "unmapped": [] + }, + "status_count": 6, + "problems": [] + } + ], + "ok": true, + "request_id": "bc77fbff-a911-417c-b758-d70f666ba5c4", + "response_id": "chatcmpl-757e4f11d1a0ef9a26c83f70bec4927c", + "images_count": 8, + "graphs_count": 0, + "response": "Neurons with synaptic terminals in the [fan-shaped body](https://www.virtualflybrain.org/reports/FBbt_00003679 \"Open fan-shaped body in Virtual Fly Brain\") include [229](https://v2.virtualflybrain.org/org.geppetto.frontend/geppetto?q=FBbt_00003679,NeuronsPartHere \"Run in VFB: Neurons with some part in fan-shaped body\") neuron types, such as [PFNa_PB4](https://www.virtualflybrain.org/reports/FBbt_00111398 \"Open PFNa_PB4 in Virtual Fly Brain\"), [PFNa_PB5](https://www.virtualflybrain.org/reports/FBbt_00111399 \"Open PFNa_PB5 in Virtual Fly Brain\"), [PFNd_PB2](https://www.virtualflybrain.org/reports/FBbt_00111391 \"Open PFNd_PB2 in Virtual Fly Brain\"), [PFNd_PB3](https://www.virtualflybrain.org/reports/FBbt_00111392 \"Open PFNd_PB3 in Virtual Fly Brain\"), [PFNd_PB5](https://www.virtualflybrain.org/reports/FBbt_00111394 \"Open PFNd_PB5 in Virtual Fly Brain\"). The first 12 of these, with their VFB ids, are: PFNd_PB2; PFNd_PB3; PFNd_PB5; PFNa_PB4; PFNa_PB5; PFNa_PB6; PFNa_PB7; PFNa_PB9; PFNp_PB7; [PFL1_PB5](https://www.virtualflybrain.org/reports/FBbt_00111438 \"Open PFL1_PB5 in Virtual Fly Brain\"); [PFL3](https://www.virtualflybrain.org/reports/FBbt_00111443 \"Open PFL3 in Virtual Fly Brain\"); [PFL2](https://www.virtualflybrain.org/reports/FBbt_00111451 \"Open PFL2 in Virtual Fly Brain\").", + "quality_flags": { + "has_tool_status": true, + "no_tool_factual_answer": false, + "tool_claim_without_tool": false, + "disambiguation_only_answer": false, + "investigation_plan_answer": false, + "not_verified_or_no_results_answer": false, + "graph_failure_mentioned": false, + "missing_required_graph": false, + "used_data_resource": false, + "response_chars": 1296, + "status_count": 6, + "addressless_followon": false, + "context_lost_across_turn": false, + "unmatched_claim_after_resolve": false, + "repeats_answered_question": false, + "slow_followup_turn": true, + "slowest_followup_ms": 126960 + } + }, + { + "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": 11389, + "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": 138, + "conversation": true, + "turns": [ + { + "turn": 1, + "question": "What is a Kenyon cell?", + "focus": null, + "clicked": null, + "duration_ms": 5589, + "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": 5800, + "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\"). Some of the 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": "8e316b01-08d7-4030-bfed-74609fff22b9", + "response_id": "chatcmpl-28cd40d0495ac0db8b86657f5235ece3", + "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\"). Some of the 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": 1141, + "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": 5800 + } + }, + { + "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": 16869, + "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", + "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": 8457, + "ok": true, + "response": "The [medulla](https://www.virtualflybrain.org/reports/FBbt_00003748 \"Open medulla in Virtual Fly Brain\") is divided into 10 layers: 1-6 make up the outer medulla, the seventh layer exhibits a distinct architecture and layers 8-10 make up the inner medulla. 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": 8412, + "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": 9, + "problems": [] + } + ], + "ok": true, + "request_id": "78c9553c-6d2d-4afa-8b7d-54868780100e", + "response_id": "chatcmpl-3618082e41422e5dd230b1a0cbafa6e3", + "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": 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": 8412 + } + }, + { + "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": 18452, + "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": 264, + "conversation": true, + "turns": [ + { + "turn": 1, + "question": "Tell me about the antennal lobe.", + "focus": null, + "clicked": null, + "duration_ms": 10490, + "ok": true, + "response": "The [antennal lobe](https://www.virtualflybrain.org/reports/FBbt_00003924 \"Open antennal lobe in Virtual Fly Brain\") is a synaptic neuropil domain of the deutocerebrum that is the main target for innervation from the antennal nerve. VFB holds various records related to the antennal lobe, including transgene expression in antennal lobe commissural pioneer interneuron, downstream connectivity classes for antennal lobe commissural pioneer interneuron, and upstream connectivity classes for antennal lobe commissural pioneer interneuron. The antennal lobe is a region in the Drosophila nervous system where users can search for synaptic input.", + "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": 7962, + "ok": true, + "response": "The [antennal lobe](https://www.virtualflybrain.org/reports/FBbt_00003924 \"Open antennal lobe in Virtual Fly Brain\") is innervated by various neurons, including [larval antennal lobe picky local neuron](https://www.virtualflybrain.org/reports/FBbt_00111694 \"Open larval antennal lobe picky local neuron in Virtual Fly Brain\"), [larval antennal lobe broad local neuron](https://www.virtualflybrain.org/reports/FBbt_00111700 \"Open larval antennal lobe broad local neuron in Virtual Fly Brain\"), [PLP077](https://www.virtualflybrain.org/reports/FBbt_20001577 \"Open PLP077 in Virtual Fly Brain\"), [adult olfactory receptor neuron Ir75d ac1](https://www.virtualflybrain.org/reports/FBbt_00110011 \"Open adult olfactory receptor neuron Ir75d ac1 in Virtual Fly Brain\"), [adult olfactory receptor neuron Ir75d ac2](https://www.virtualflybrain.org/reports/FBbt_00110014 \"Open adult olfactory receptor neuron Ir75d ac2 in Virtual Fly Brain\"), adult olfactory receptor neuron Ir75d ac4, pharyngeal VL1 neuron, ORN_VM6, adult olfactory receptor neuron Or35a ac3I, adult olfactory receptor neuron Or35a ac3II, adult olfactory receptor neuron Or85b ab3, and adult olfactory receptor neuron Or85b ab11, which have presynaptic terminals in the antennal lobe. Additionally, neurons such as [AMMC-Bi16](https://www.virtualflybrain.org/reports/FBbt_00111480 \"Open AMMC-Bi16 in Virtual Fly Brain\"), [adult antennal lobe projection neuron DL5](https://www.virtualflybrain.org/reports/FBbt_00059280 \"Open adult antennal lobe projection neuron DL5 in Virtual Fly Brain\"), adult antennal lobe projection neuron DM4, adult antennal lobe projection neuron VA1d, adult antennal lobe projection neuron VL1, adult antennal lobe projection neuron VL2a, adult antennal lobe projection neuron VM2, adult antennal lobe projection neuron VM4, and adult multiglomerular antennal lobe projection neuron L1 adPN have synaptic terminals in the antennal lobe.", + "followons": [ + { + "id": "FBbt_00003924", + "query_type": "ListAllAvailableImages", + "query": "Which images of antennal lobe does VFB have?" + }, + { + "id": "FBbt_00003924", + "query_type": "NeuronsPartHere", + "query": "Which neurons have part of their arbour in the antennal lobe?" + }, + { + "id": "FBbt_00003924", + "query_type": "NeuronsPostsynapticHere", + "query": "Which neurons receive output from the antennal lobe?" + }, + { + "id": "FBbt_00003924", + "query_type": "PartsOf", + "query": "What are the anatomical parts of the antennal lobe?" + }, + { + "id": "FBbt_00003924", + "query_type": "SubclassesOf", + "query": "What are the subtypes of the antennal lobe?" + }, + { + "id": "FBbt_00003924", + "query_type": "TractsNervesInnervatingHere", + "query": "Which tracts and nerves innervate the antennal lobe?" + } + ], + "context_terms": [ + { + "id": "FBbt_00003924", + "label": "antennal lobe" + } + ], + "reproduction": { + "ids": [ + { + "id": "FBbt_00003924", + "label": "antennal lobe" + } + ], + "calls": [ + { + "id": "FBbt_00003924", + "query_type": "NeuronsPresynapticHere", + "fn": "get_neurons_with_presynaptic_terminals_in" + }, + { + "id": "FBbt_00003924", + "query_type": "NeuronsSynaptic", + "fn": "get_neurons_with_synapses_in" + } + ], + "unmapped": [] + }, + "status_count": 8, + "problems": [] + } + ], + "ok": true, + "request_id": "e7e804d2-7a02-4a28-b112-6e7cfb4cca56", + "response_id": "chatcmpl-c1f4e973865dc1ff2aa31e0a20db6c30", + "images_count": 6, + "graphs_count": 0, + "response": "The [antennal lobe](https://www.virtualflybrain.org/reports/FBbt_00003924 \"Open antennal lobe in Virtual Fly Brain\") is innervated by various neurons, including [larval antennal lobe picky local neuron](https://www.virtualflybrain.org/reports/FBbt_00111694 \"Open larval antennal lobe picky local neuron in Virtual Fly Brain\"), [larval antennal lobe broad local neuron](https://www.virtualflybrain.org/reports/FBbt_00111700 \"Open larval antennal lobe broad local neuron in Virtual Fly Brain\"), [PLP077](https://www.virtualflybrain.org/reports/FBbt_20001577 \"Open PLP077 in Virtual Fly Brain\"), [adult olfactory receptor neuron Ir75d ac1](https://www.virtualflybrain.org/reports/FBbt_00110011 \"Open adult olfactory receptor neuron Ir75d ac1 in Virtual Fly Brain\"), [adult olfactory receptor neuron Ir75d ac2](https://www.virtualflybrain.org/reports/FBbt_00110014 \"Open adult olfactory receptor neuron Ir75d ac2 in Virtual Fly Brain\"), adult olfactory receptor neuron Ir75d ac4, pharyngeal VL1 neuron, ORN_VM6, adult olfactory receptor neuron Or35a ac3I, adult olfactory receptor neuron Or35a ac3II, adult olfactory receptor neuron Or85b ab3, and adult olfactory receptor neuron Or85b ab11, which have presynaptic terminals in the antennal lobe. Additionally, neurons such as [AMMC-Bi16](https://www.virtualflybrain.org/reports/FBbt_00111480 \"Open AMMC-Bi16 in Virtual Fly Brain\"), [adult antennal lobe projection neuron DL5](https://www.virtualflybrain.org/reports/FBbt_00059280 \"Open adult antennal lobe projection neuron DL5 in Virtual Fly Brain\"), adult antennal lobe projection neuron DM4, adult antennal lobe projection neuron VA1d, adult antennal lobe projection neuron VL1, adult antennal lobe projection neuron VL2a, adult antennal lobe projection neuron VM2, adult antennal lobe projection neuron VM4, and adult multiglomerular antennal lobe projection neuron L1 adPN have synaptic terminals in the antennal lobe.", + "quality_flags": { + "has_tool_status": true, + "no_tool_factual_answer": false, + "tool_claim_without_tool": false, + "disambiguation_only_answer": false, + "investigation_plan_answer": false, + "not_verified_or_no_results_answer": false, + "graph_failure_mentioned": false, + "missing_required_graph": false, + "used_data_resource": false, + "response_chars": 1920, + "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": 7962 + } + }, + { + "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": 202781, + "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": 303, + "conversation": true, + "turns": [ + { + "turn": 1, + "question": "What is the medulla?", + "focus": null, + "clicked": null, + "duration_ms": 4960, + "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 (distal) medulla, the seventh (or serpentine) layer exhibits a distinct architecture and layers 8-10 make up the inner (proximal) 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": 9650, + "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 medulla. The first 12 images, with their VFB ids, are: OA-AL2i2 (VFB_fw042336); MC64 (VFB_fw043756); MC64 (VFB_fw043755); aMe5 (VFB_fw043590); MeTu3 (VFB_fw043751); MeTu3 (VFB_fw043750); MeTu3 (VFB_fw043744); aMe5 (VFB_fw043591); MeTu-DRA (VFB_fw043752); MeVP6 (VFB_fw043593); MeTu3 (VFB_fw043746); MeTu3 (VFB_fw043745).", + "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": 188171, + "ok": true, + "response": "The [medulla](https://www.virtualflybrain.org/reports/FBbt_00003748 \"Open medulla in Virtual Fly Brain\") is labeled by [2,342](https://v2.virtualflybrain.org/org.geppetto.frontend/geppetto?q=FBbt_00003748,TransgeneExpressionHere \"Run in VFB: Transgene expression in medulla\") driver lines. The first 12 driver lines, with their VFB ids, 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.", + "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": "334027ee-4b59-43c0-8134-32f634fb65c4", + "response_id": "chatcmpl-93feb07c91de53dc1656451e91f40c50", + "images_count": 8, + "graphs_count": 0, + "response": "The [medulla](https://www.virtualflybrain.org/reports/FBbt_00003748 \"Open medulla in Virtual Fly Brain\") is labeled by [2,342](https://v2.virtualflybrain.org/org.geppetto.frontend/geppetto?q=FBbt_00003748,TransgeneExpressionHere \"Run in VFB: Transgene expression in medulla\") driver lines. The first 12 driver lines, with their VFB ids, 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.", + "quality_flags": { + "has_tool_status": true, + "no_tool_factual_answer": false, + "tool_claim_without_tool": false, + "disambiguation_only_answer": false, + "investigation_plan_answer": false, + "not_verified_or_no_results_answer": false, + "graph_failure_mentioned": false, + "missing_required_graph": false, + "used_data_resource": false, + "response_chars": 1719, + "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": 188171 + } + }, + { + "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": 10375, + "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": 64, + "conversation": true, + "turns": [ + { + "turn": 1, + "question": "What is the mushroom body?", + "focus": null, + "clicked": null, + "duration_ms": 6126, + "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 driver lines label it?", + "focus": null, + "clicked": null, + "duration_ms": 4249, + "ok": true, + "response": "The [mushroom body](https://www.virtualflybrain.org/reports/FBbt_00005801 \"Open mushroom body in Virtual Fly Brain\") is labeled by several driver lines, including P{VT017411-GAL4.DBD} and P{VT019018-p65.AD}, which are used as hemidrivers. VFB records show [4130](https://v2.virtualflybrain.org/org.geppetto.frontend/geppetto?q=FBbt_00005801,TransgeneExpressionHere \"Run in VFB: Transgene expression in mushroom body\") instances of transgene expression in mushroom body.", + "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": "af887580-1ff0-4bf8-b8d3-0491bca1156f", + "response_id": "chatcmpl-1bdcbdfd1ef7ac39d2be218a2cf9e63f", + "images_count": 8, + "graphs_count": 0, + "response": "The [mushroom body](https://www.virtualflybrain.org/reports/FBbt_00005801 \"Open mushroom body in Virtual Fly Brain\") is labeled by several driver lines, including P{VT017411-GAL4.DBD} and P{VT019018-p65.AD}, which are used as hemidrivers. VFB records show [4130](https://v2.virtualflybrain.org/org.geppetto.frontend/geppetto?q=FBbt_00005801,TransgeneExpressionHere \"Run in VFB: Transgene expression in mushroom body\") instances of transgene expression in mushroom body.", + "quality_flags": { + "has_tool_status": true, + "no_tool_factual_answer": false, + "tool_claim_without_tool": false, + "disambiguation_only_answer": false, + "investigation_plan_answer": false, + "not_verified_or_no_results_answer": false, + "graph_failure_mentioned": false, + "missing_required_graph": false, + "used_data_resource": false, + "response_chars": 469, + "status_count": 6, + "addressless_followon": false, + "context_lost_across_turn": false, + "unmatched_claim_after_resolve": false, + "repeats_answered_question": false, + "slow_followup_turn": false, + "slowest_followup_ms": 4249 + } + }, + { + "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": 20236, + "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": 149, + "conversation": true, + "turns": [ + { + "turn": 1, + "question": "Which neurons provide input to the medulla?", + "focus": null, + "clicked": null, + "duration_ms": 6270, + "ok": true, + "response": "Neurons with presynaptic terminals in [medulla](https://www.virtualflybrain.org/reports/FBbt_00003748 \"Open medulla in Virtual Fly Brain\") provide input to the medulla. VFB records show [262](https://v2.virtualflybrain.org/org.geppetto.frontend/geppetto?q=FBbt_00003748,NeuronsPresynapticHere \"Run in VFB: Neurons with presynaptic terminals in medulla\") neuron types with presynaptic terminals in medulla, including [Dm8b](https://www.virtualflybrain.org/reports/FBbt_00110069 \"Open Dm8b in Virtual Fly Brain\"), [PS128](https://www.virtualflybrain.org/reports/FBbt_20001883 \"Open PS128 in Virtual Fly Brain\"), [Mi10b](https://www.virtualflybrain.org/reports/FBbt_00110070 \"Open Mi10b in Virtual Fly Brain\"), [CB3849](https://www.virtualflybrain.org/reports/FBbt_20007264 \"Open CB3849 in Virtual Fly Brain\"), [TmY-ds](https://www.virtualflybrain.org/reports/FBbt_00052643 \"Open TmY-ds in Virtual Fly Brain\"), [Dm7](https://www.virtualflybrain.org/reports/FBbt_00003774 \"Open Dm7 in Virtual Fly Brain\"), Mi6, Mi8, Tm10, Tm13, Tm14, and Tm18.", + "followons": [ + { + "id": "FBbt_00003748", + "query_type": "ImagesNeurons", + "query": "Which neuron images have a part in the medulla?" + }, + { + "id": "FBbt_00003748", + "query_type": "TransgeneExpressionHere", + "query": "Which driver lines label the medulla?" + }, + { + "id": "FBbt_00003748", + "query_type": "NeuronsPartHere", + "query": "Which neurons have part of their arbour in the medulla?" + }, + { + "id": "FBbt_00003748", + "query_type": "NeuronsSynaptic", + "query": "Which neurons have synaptic terminals in the medulla?" + }, + { + "id": "FBbt_00003748", + "query_type": "PartsOf", + "query": "What are the anatomical parts of the medulla?" + }, + { + "id": "FBbt_00003748", + "query_type": "LineageClonesIn", + "query": "Which lineage clones are found in the medulla?" + } + ], + "context_terms": [ + { + "id": "FBbt_00003748", + "label": "medulla" + } + ], + "reproduction": { + "ids": [ + { + "id": "FBbt_00003748", + "label": "medulla" + } + ], + "calls": [ + { + "id": "FBbt_00003748", + "query_type": "NeuronsPresynapticHere", + "fn": "get_neurons_with_presynaptic_terminals_in" + }, + { + "id": "FBbt_00003748", + "query_type": "NeuronsPostsynapticHere", + "fn": "get_neurons_with_postsynaptic_terminals_in" + } + ], + "unmapped": [] + }, + "status_count": 9, + "problems": [] + }, + { + "turn": 2, + "question": "And the lobula?", + "focus": null, + "clicked": null, + "duration_ms": 13965, + "ok": true, + "response": "Neurons with synaptic terminals in [lobula](https://www.virtualflybrain.org/reports/FBbt_00003852 \"Open lobula in Virtual Fly Brain\") provide input to the lobula. VFB records show [528](https://v2.virtualflybrain.org/org.geppetto.frontend/geppetto?q=FBbt_00003852,NeuronsPartHere \"Run in VFB: Neurons with some part in lobula\") neuron types with synaptic terminals in lobula, including [AVLP391](https://www.virtualflybrain.org/reports/FBbt_20000500 \"Open AVLP391 in Virtual Fly Brain\"), [PLP031](https://www.virtualflybrain.org/reports/FBbt_20001531 \"Open PLP031 in Virtual Fly Brain\"), [TmY27](https://www.virtualflybrain.org/reports/FBbt_00110067 \"Open TmY27 in Virtual Fly Brain\"), [lobula columnar neuron vGlutLcnnew2](https://www.virtualflybrain.org/reports/FBbt_00110100 \"Open lobula columnar neuron vGlutLcnnew2 in Virtual Fly Brain\"), [OA-AL2b](https://www.virtualflybrain.org/reports/FBbt_00110145 \"Open OA-AL2b in Virtual Fly Brain\"), adult histaminergic HP3 neuron, translobula neuron, Tl1, Tl2, Tm1a, SIP063, and SLP339.", + "followons": [ + { + "id": "FBbt_00003852", + "query_type": "NeuronsPresynapticHere", + "query": "Which neurons provide input to the lobula?" + }, + { + "id": "FBbt_00003852", + "query_type": "NeuronsPostsynapticHere", + "query": "Which neurons receive output from the lobula?" + }, + { + "id": "FBbt_00003852", + "query_type": "PartsOf", + "query": "What are the anatomical parts of the lobula?" + }, + { + "id": "FBbt_00003852", + "query_type": "TractsNervesInnervatingHere", + "query": "Which tracts and nerves innervate the lobula?" + }, + { + "id": "FBbt_00003852", + "query_type": "LineageClonesIn", + "query": "Which lineage clones are found in the lobula?" + }, + { + "id": "FBbt_00003852", + "query_type": "ImagesNeurons", + "query": "Which neuron images have a part in the lobula?" + } + ], + "context_terms": [ + { + "id": "FBbt_00003852", + "label": "lobula" + }, + { + "id": "FBbt_00003748", + "label": "medulla" + } + ], + "reproduction": { + "ids": [ + { + "id": "FBbt_00003852", + "label": "lobula" + }, + { + "id": "FBbt_00003748", + "label": "medulla" + } + ], + "calls": [ + { + "id": "FBbt_00003852", + "query_type": "ListAllAvailableImages", + "fn": "get_instances" + }, + { + "id": "FBbt_00003852", + "query_type": "NeuronsPartHere", + "fn": "get_neurons_with_part_in" + }, + { + "id": "FBbt_00003852", + "query_type": "NeuronsSynaptic", + "fn": "get_neurons_with_synapses_in" + }, + { + "id": "FBbt_00003748", + "query_type": "NeuronsPresynapticHere", + "fn": "get_neurons_with_presynaptic_terminals_in" + }, + { + "id": "FBbt_00003748", + "query_type": "NeuronsPostsynapticHere", + "fn": "get_neurons_with_postsynaptic_terminals_in" + } + ], + "unmapped": [] + }, + "status_count": 13, + "problems": [] + } + ], + "ok": true, + "request_id": "a338284f-5c9a-4528-8440-20caac36b83d", + "response_id": "chatcmpl-90d3574b47476f373a6ffccb33b365ff", + "images_count": 4, + "graphs_count": 0, + "response": "Neurons with synaptic terminals in [lobula](https://www.virtualflybrain.org/reports/FBbt_00003852 \"Open lobula in Virtual Fly Brain\") provide input to the lobula. VFB records show [528](https://v2.virtualflybrain.org/org.geppetto.frontend/geppetto?q=FBbt_00003852,NeuronsPartHere \"Run in VFB: Neurons with some part in lobula\") neuron types with synaptic terminals in lobula, including [AVLP391](https://www.virtualflybrain.org/reports/FBbt_20000500 \"Open AVLP391 in Virtual Fly Brain\"), [PLP031](https://www.virtualflybrain.org/reports/FBbt_20001531 \"Open PLP031 in Virtual Fly Brain\"), [TmY27](https://www.virtualflybrain.org/reports/FBbt_00110067 \"Open TmY27 in Virtual Fly Brain\"), [lobula columnar neuron vGlutLcnnew2](https://www.virtualflybrain.org/reports/FBbt_00110100 \"Open lobula columnar neuron vGlutLcnnew2 in Virtual Fly Brain\"), [OA-AL2b](https://www.virtualflybrain.org/reports/FBbt_00110145 \"Open OA-AL2b in Virtual Fly Brain\"), adult histaminergic HP3 neuron, translobula neuron, Tl1, Tl2, Tm1a, SIP063, and SLP339.", + "quality_flags": { + "has_tool_status": true, + "no_tool_factual_answer": false, + "tool_claim_without_tool": false, + "disambiguation_only_answer": false, + "investigation_plan_answer": false, + "not_verified_or_no_results_answer": false, + "graph_failure_mentioned": false, + "missing_required_graph": false, + "used_data_resource": false, + "response_chars": 1033, + "status_count": 13, + "addressless_followon": false, + "context_lost_across_turn": false, + "unmatched_claim_after_resolve": false, + "repeats_answered_question": false, + "slow_followup_turn": false, + "slowest_followup_ms": 13965 + } + }, + { + "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": 40600, + "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": 155, + "conversation": true, + "turns": [ + { + "turn": 1, + "question": "What is the protocerebral bridge?", + "focus": null, + "clicked": null, + "duration_ms": 5126, + "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 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": 16567, + "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 related in that some neurons have parts in both. 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\") and other similar neurons 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": 14, + "problems": [] + }, + { + "turn": 3, + "question": "Which neurons connect them?", + "focus": null, + "clicked": null, + "duration_ms": 18907, + "ok": true, + "response": "The [adult protocerebral bridge glomerulus 1-ellipsoid body canal-dorsal gall neuron](https://www.virtualflybrain.org/reports/FBbt_00111376 \"Open adult protocerebral bridge glomerulus 1-ellipsoid body canal-dorsal gall neuron in Virtual Fly Brain\") and other similar neurons have synaptic terminals in the [ellipsoid body](https://www.virtualflybrain.org/reports/FBbt_00003678 \"Open ellipsoid body in Virtual Fly Brain\") and are among the neurons that connect the [protocerebral bridge](https://www.virtualflybrain.org/reports/FBbt_00003668 \"Open protocerebral bridge in Virtual Fly Brain\") and the ellipsoid body. VFB records show that [PEN_PB2](https://www.virtualflybrain.org/reports/FBbt_00111369 \"Open PEN_PB2 in Virtual Fly Brain\"), [PEN_PB3](https://www.virtualflybrain.org/reports/FBbt_00111370 \"Open PEN_PB3 in Virtual Fly Brain\"), [PEN_PB7](https://www.virtualflybrain.org/reports/FBbt_00111373 \"Open PEN_PB7 in Virtual Fly Brain\"), and [PEN_PB8](https://www.virtualflybrain.org/reports/FBbt_00111374 \"Open PEN_PB8 in Virtual Fly Brain\") neurons have postsynaptic terminals in the protocerebral bridge and presynaptic terminals in the ellipsoid body. Additionally, [EPG_PB5](https://www.virtualflybrain.org/reports/FBbt_00111416 \"Open EPG_PB5 in Virtual Fly Brain\"), [EPG_PB2](https://www.virtualflybrain.org/reports/FBbt_00111419 \"Open EPG_PB2 in Virtual Fly Brain\"), [EPG_PB6](https://www.virtualflybrain.org/reports/FBbt_00111421 \"Open EPG_PB6 in Virtual Fly Brain\"), and other neurons have presynaptic terminals in the protocerebral bridge and postsynaptic 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": "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": "6edb575a-d88d-45ce-a955-20fdd8c25a2b", + "response_id": "chatcmpl-25033cb3479fae6de7b59b0e66d2d60d", + "images_count": 8, + "graphs_count": 0, + "response": "The [adult protocerebral bridge glomerulus 1-ellipsoid body canal-dorsal gall neuron](https://www.virtualflybrain.org/reports/FBbt_00111376 \"Open adult protocerebral bridge glomerulus 1-ellipsoid body canal-dorsal gall neuron in Virtual Fly Brain\") and other similar neurons have synaptic terminals in the [ellipsoid body](https://www.virtualflybrain.org/reports/FBbt_00003678 \"Open ellipsoid body in Virtual Fly Brain\") and are among the neurons that connect the [protocerebral bridge](https://www.virtualflybrain.org/reports/FBbt_00003668 \"Open protocerebral bridge in Virtual Fly Brain\") and the ellipsoid body. VFB records show that [PEN_PB2](https://www.virtualflybrain.org/reports/FBbt_00111369 \"Open PEN_PB2 in Virtual Fly Brain\"), [PEN_PB3](https://www.virtualflybrain.org/reports/FBbt_00111370 \"Open PEN_PB3 in Virtual Fly Brain\"), [PEN_PB7](https://www.virtualflybrain.org/reports/FBbt_00111373 \"Open PEN_PB7 in Virtual Fly Brain\"), and [PEN_PB8](https://www.virtualflybrain.org/reports/FBbt_00111374 \"Open PEN_PB8 in Virtual Fly Brain\") neurons have postsynaptic terminals in the protocerebral bridge and presynaptic terminals in the ellipsoid body. Additionally, [EPG_PB5](https://www.virtualflybrain.org/reports/FBbt_00111416 \"Open EPG_PB5 in Virtual Fly Brain\"), [EPG_PB2](https://www.virtualflybrain.org/reports/FBbt_00111419 \"Open EPG_PB2 in Virtual Fly Brain\"), [EPG_PB6](https://www.virtualflybrain.org/reports/FBbt_00111421 \"Open EPG_PB6 in Virtual Fly Brain\"), and other neurons have presynaptic terminals in the protocerebral bridge and postsynaptic terminals in the ellipsoid body.", + "quality_flags": { + "has_tool_status": true, + "no_tool_factual_answer": false, + "tool_claim_without_tool": false, + "disambiguation_only_answer": false, + "investigation_plan_answer": false, + "not_verified_or_no_results_answer": false, + "graph_failure_mentioned": false, + "missing_required_graph": false, + "used_data_resource": false, + "response_chars": 1603, + "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": 18907 + } + }, + { + "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": 22908, + "status_messages": [ + { + "message": "Thinking...", + "phase": "llm" + }, + { + "message": "Planning the answer", + "phase": "llm" + }, + { + "message": "Resolving 1 term in VFB", + "phase": "mcp" + }, + { + "message": "Querying VFB", + "phase": "mcp" + }, + { + "message": "Checking VFB documentation", + "phase": "mcp" + }, + { + "message": "Checking the answer is covered", + "phase": "llm" + }, + { + "message": "Writing the answer", + "phase": "llm" + } + ], + "event_count": 45, + "conversation": true, + "turns": [ + { + "turn": 1, + "question": "Which neurons have part of them in the medulla?", + "focus": null, + "clicked": null, + "duration_ms": 9384, + "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.", + "followons": [ + { + "id": "FBbt_00003748", + "query_type": "TransgeneExpressionHere", + "query": "Which driver lines label the medulla?" + }, + { + "id": "FBbt_00003748", + "query_type": "NeuronsSynaptic", + "query": "Which neurons have synaptic terminals in the medulla?" + }, + { + "id": "FBbt_00003748", + "query_type": "NeuronsPostsynapticHere", + "query": "Which neurons receive output from the medulla?" + }, + { + "id": "FBbt_00003748", + "query_type": "NeuronsPresynapticHere", + "query": "Which neurons provide input to the medulla?" + }, + { + "id": "FBbt_00003748", + "query_type": "PartsOf", + "query": "What are the anatomical parts of the medulla?" + }, + { + "id": "FBbt_00003748", + "query_type": "LineageClonesIn", + "query": "Which lineage clones are found in the medulla?" + } + ], + "context_terms": [ + { + "id": "FBbt_00003748", + "label": "medulla" + } + ], + "reproduction": { + "ids": [ + { + "id": "FBbt_00003748", + "label": "medulla" + } + ], + "calls": [ + { + "id": "FBbt_00003748", + "query_type": "NeuronsPartHere", + "fn": "get_neurons_with_part_in" + }, + { + "id": "FBbt_00003748", + "query_type": "ImagesNeurons", + "fn": "get_images_neurons" + } + ], + "unmapped": [] + }, + "status_count": 10, + "problems": [] + }, + { + "turn": 2, + "question": "How would I get that same result in Python with vfbquery?", + "focus": null, + "clicked": null, + "duration_ms": 13524, + "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 annotated by VFB. 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# ImagesNeurons for medulla\nimages_neurons = vfbquery.get_images_neurons(MEDULLA)\n```", + "followons": [ + { + "id": "FBbt_00003748", + "query_type": "ImagesNeurons", + "query": "Which neuron images have a part in the medulla?" + }, + { + "id": "FBbt_00003748", + "query_type": "TransgeneExpressionHere", + "query": "Which driver lines label the medulla?" + }, + { + "id": "FBbt_00003748", + "query_type": "NeuronsPartHere", + "query": "Which neurons have part of their arbour in the medulla?" + }, + { + "id": "FBbt_00003748", + "query_type": "NeuronsSynaptic", + "query": "Which neurons have synaptic terminals in the medulla?" + }, + { + "id": "FBbt_00003748", + "query_type": "NeuronsPostsynapticHere", + "query": "Which neurons receive output from the medulla?" + }, + { + "id": "FBbt_00003748", + "query_type": "NeuronsPresynapticHere", + "query": "Which neurons provide input to the medulla?" + } + ], + "context_terms": [ + { + "id": "FBbt_00003748", + "label": "medulla" + } + ], + "reproduction": { + "ids": [ + { + "id": "FBbt_00003748", + "label": "medulla" + } + ], + "calls": [ + { + "id": "FBbt_00003748", + "query_type": "NeuronsPartHere", + "fn": "get_neurons_with_part_in" + }, + { + "id": "FBbt_00003748", + "query_type": "ImagesNeurons", + "fn": "get_images_neurons" + } + ], + "unmapped": [] + }, + "status_count": 7, + "problems": [] + } + ], + "ok": true, + "request_id": "1b85b4df-2ba8-4534-8421-f743aa2631f5", + "response_id": "chatcmpl-aaeb2ecef2281c0c75871444e567cc97", + "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 annotated by VFB. 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# ImagesNeurons for medulla\nimages_neurons = vfbquery.get_images_neurons(MEDULLA)\n```", + "quality_flags": { + "has_tool_status": true, + "no_tool_factual_answer": false, + "tool_claim_without_tool": false, + "disambiguation_only_answer": false, + "investigation_plan_answer": false, + "not_verified_or_no_results_answer": false, + "graph_failure_mentioned": false, + "missing_required_graph": false, + "used_data_resource": false, + "response_chars": 910, + "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": 13524 + } + }, + { + "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": 20837, + "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" + } + ], + "event_count": 81, + "conversation": true, + "turns": [ + { + "turn": 1, + "question": "What are the subclasses of Kenyon cell?", + "focus": null, + "clicked": null, + "duration_ms": 5159, + "ok": true, + "response": "The subclasses of [Kenyon cell](https://www.virtualflybrain.org/reports/FBbt_00003686 \"Open Kenyon cell in Virtual Fly Brain\") include [KCab-c(i)](https://www.virtualflybrain.org/reports/FBbt_00049111 \"Open KCab-c(i) in Virtual Fly Brain\"), [KCab-c](https://www.virtualflybrain.org/reports/FBbt_00110929 \"Open KCab-c in Virtual Fly Brain\"), [KCg-m](https://www.virtualflybrain.org/reports/FBbt_00111061 \"Open KCg-m in Virtual Fly Brain\"), [Kenyon cell of main calyx](https://www.virtualflybrain.org/reports/FBbt_00047926 \"Open Kenyon cell of main calyx in Virtual Fly Brain\"), and [gamma Kenyon cell](https://www.virtualflybrain.org/reports/FBbt_00100247 \"Open gamma Kenyon cell in Virtual Fly Brain\"), among [37](https://v2.virtualflybrain.org/org.geppetto.frontend/geppetto?q=FBbt_00003686,SubclassesOf \"Run in VFB: Subclasses of Kenyon cell\") total subclasses. VFB holds 37 subclasses of Kenyon cell.", + "followons": [ + { + "id": "FBbt_00003686", + "query_type": "ListAllAvailableImages", + "query": "Which images of Kenyon cell does VFB have?" + }, + { + "id": "FBbt_00003686", + "query_type": "UpstreamClassConnectivity", + "query": "What connects to the Kenyon cell upstream?" + }, + { + "id": "FBbt_00003686", + "query_type": "DownstreamClassConnectivity", + "query": "What does the Kenyon cell connect to downstream?" + }, + { + "id": "FBbt_00003686", + "query_type": "TransgeneExpressionHere", + "query": "Which driver lines label the Kenyon cell?" + }, + { + "id": "FBbt_00003686", + "query_type": "anatScRNAseqQuery", + "query": "What single-cell transcriptomic clusters are there for Kenyon cell?" + }, + { + "id": "FBbt_00003686", + "query_type": "SubclassesOf", + "query": "What are the subtypes of the Kenyon cell?" + } + ], + "context_terms": [ + { + "id": "FBbt_00003686", + "label": "Kenyon cell" + } + ], + "reproduction": { + "ids": [ + { + "id": "FBbt_00003686", + "label": "Kenyon cell" + } + ], + "calls": [ + { + "id": "FBbt_00003686", + "query_type": "SubclassesOf", + "fn": "get_subclasses_of" + } + ], + "unmapped": [] + }, + "status_count": 6, + "problems": [] + }, + { + "turn": 2, + "question": "Can you list the VFB IDs so I can reproduce this myself?", + "focus": null, + "clicked": null, + "duration_ms": 15678, + "ok": true, + "response": "The code below returns the VFB IDs for [Kenyon cell](https://www.virtualflybrain.org/reports/FBbt_00003686 \"Open Kenyon cell in Virtual Fly Brain\"), as listed. VFB holds several IDs for Kenyon cell, including VFB_00100451, VFB_00100431, VFB_00100417, VFB_00100395, VFB_00100335, and VFB_00050000.\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": "88688782-11f4-45d9-8b8d-0bd7e3e09e7c", + "response_id": "chatcmpl-e49f23a1641586ccc2e8da9b07ec4e83", + "images_count": 8, + "graphs_count": 0, + "response": "The code below returns the VFB IDs for [Kenyon cell](https://www.virtualflybrain.org/reports/FBbt_00003686 \"Open Kenyon cell in Virtual Fly Brain\"), as listed. VFB holds several IDs for Kenyon cell, including VFB_00100451, VFB_00100431, VFB_00100417, VFB_00100395, VFB_00100335, and VFB_00050000.\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": 738, + "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": 15678 + } + } + ] +} diff --git a/tests/unit/absence.test.mjs b/tests/unit/absence.test.mjs index 5961088..db68f31 100644 --- a/tests/unit/absence.test.mjs +++ b/tests/unit/absence.test.mjs @@ -18,7 +18,7 @@ import test from 'node:test' import assert from 'node:assert/strict' import { asciiSpelling, transliterateGreek, normaliseTypography, hasGreek } from '../../lib/nameNormalise.mjs' -import { nameVariants, maybeEscalateBeforeAbsence, gateAbsence } from '../../lib/orchestrator.mjs' +import { nameVariants, maybeEscalateBeforeAbsence, gateAbsence, ABSENCE_ESCALATION_DEADLINE_MS } from '../../lib/orchestrator.mjs' import { nextAction } from '../../lib/controller.mjs' import { absenceLicence, findAbsenceClaims, repairUnlicensedAbsences, @@ -340,6 +340,28 @@ test('a draft that denies data sends the loop round again, with rounds to do it' assert.equal(nextAction(ledger).action, 'run_step') }) +test('a run with no time left hedges instead of turning slow into nothing', async () => { + // The first CI run of this branch: 63 of 64 tasks passed and the 64th was + // "Timed out after 240000 ms". The escalation buys a second synthesis costing + // 60-90 s, so one started late cannot finish — and it takes the first answer + // down with it. A false absence is worse than a hedge; it is not worse than no + // answer. + const ledger = ledgerWith(Q) + ledger.startedAt = Date.now() - (ABSENCE_ESCALATION_DEADLINE_MS + 1000) + const went = await maybeEscalateBeforeAbsence(ledger, 'VFB does not currently hold data on that.', {}, () => {}) + assert.equal(went, false) + assert.equal(ledger.plan.filter(s => s.absence_query).length, 0) + // The gate costs no model call, so it still runs and the denial still cannot ship. + assert.ok(!/does not currently hold/.test(gateAbsence(ledger, 'VFB does not currently hold data on that.', () => {}))) +}) + +test('the escalation window fits under the tighter of the two ceilings', () => { + // 600 s is the run deadline; 240 s is TASK_BATTERY_TIMEOUT_MS, the project's + // own recorded opinion about when an answer has taken too long. The second + // pass costs up to 90 s, so starting it must leave that much margin under 240. + assert.ok(ABSENCE_ESCALATION_DEADLINE_MS + 90000 < 240000) +}) + test('a draft that claims nothing is left alone, however thin the ledger', async () => { const ledger = ledgerWith(Q) const went = await maybeEscalateBeforeAbsence(ledger, 'The medulla has 10 layers, M1 to M10.', {}, () => {}) diff --git a/tests/unit/harnessFraming.test.mjs b/tests/unit/harnessFraming.test.mjs index b4c611f..984c18a 100644 --- a/tests/unit/harnessFraming.test.mjs +++ b/tests/unit/harnessFraming.test.mjs @@ -62,7 +62,21 @@ test('a sentence reporting what the input contained is dropped, not rewritten', test('input nouns that survive in a longer sentence are renamed, not left', () => { const out = stripHarnessFraming('The provided evidence lists three connectome datasets.') assert.ok(!/provided evidence/i.test(out), out) - assert.ok(/VFB evidence/i.test(out), out) + // This used to assert "VFB evidence", which was the weaker outcome the module + // settled for rather than the one it is aiming at. EVIDENCE_SUBJECT needs "the + // evidence"; INPUT_NOUN matches "the provided evidence" as a unit. So the + // subject rules ran first, found the word "provided" in the way, and did + // nothing — and the noun rule then produced exactly the subject they would + // have handled, one pass too late. Production shipped the consequence: "VFB + // evidence lists queries for subclasses, scRNAseq data … but it does not + // include a completed query", which is this program's working set wearing + // VFB's name. + // + // With the subject rules re-run after the noun rules, the sentence lands where + // the module was always pointed: about VFB, not about a document. "VFB + // evidence" remains the floor for constructions the subject rules do not + // cover, so what is asserted here is that the sentence got past the floor. + assert.match(out, /^VFB records three connectome datasets\.$/, out) }) // --- what must NOT be touched ----------------------------------------------