An MCP server and CLI built on the FIBER decision-context compiler: a typed decision query is
compiled into the smallest decision-sufficient evidence region, delivered with a Context
Certificate stating exactly what was omitted.
The preclinical glioma engine now compiles a complete bounded research workflow, adapts its next
stage from typed outcomes, and admits only capability-matched institution-local workers before
dispatch. Worker routing is deterministic and fail-closed; the engine never turns an unimplemented
stage into a generic action and never makes clinical decisions.
The route can also drive the autonomous engine end to end through the typed stage/action adapter;
MCP exposes this as a simulation-only rehearsal, while production hosts supply their own local
workers.
Evidence is an execution gate, not a passive report: P01 cross-family triangulation must qualify
before the P07 stage router can admit a worker. The evidence-gated stage engine returns an explicit
evidence hold or capability hold with next actions, and only then runs bounded evidence,
multimodal, mechanism, experiment, computation, replication, release, and federation stages.
Implementation of the AURORA BioPRISM / OncoWorld / FIBER blueprint (v0.6, 935 registered spec
modules). A Rust workspace whose central idea is that context assembly is a compiler pass:
instead of retrieval plus summarisation plus vibes-based compaction, a typed decision query is
compiled into the smallest decision-sufficient evidence region, delivered as a Decision
Section, and accompanied by a Context Certificate that states exactly what was omitted and
whether the omission could have changed the decision.
Compile the smallest decision-sufficient evidence region. Never traverse the whole knowledge
structure by default.
What the measurements actually say
The reference world ships 761 facts, 750 of them exploratory distractors that all consume the same
protected cohort_id hub. FIBER compiles the query down to 11 facts (1.45% of the world) and
the deterministic oracle still returns the correct verdict with all four leakage witnesses.
It is not alone in doing so. Under equal tuning, a 5-hop incidence walk and a BM25 retriever at
k=11 select exactly the same eleven facts. The distribution's own compare_baselines.py measures
the graph baseline only at depth 7 and unbounded — the two settings where it returns everything —
and reports a 69× advantage that vanishes under equal tuning. That is a strawman comparison, and
correcting it is what 43.38 and 43.41 require.
So the reference world cannot tell these methods apart. crates/worldgen makes
the structure a parameter and builds one that can — distractors attached near the target instead of
at a hub leaf, decisive facts behind a relay chain, and distractor tags camouflaged to tokenise into
the protected vocabulary:
Strategy
Facts
Sound?
Closure
Admissible
full-context
762
yes
100%
yes
graph-5-hop
750
no
0%
no
graph-7-hop
750
no
0%
no
graph-11-hop
761
yes
100%
yes
lexical-top-11 (BM25)
11
yes
91%
no
fiber
11
yes
100%
yes
Three distinct failure modes appear. The graph walk has no usable depth: 5–10 pull in 98% of the
world and still miss every decisive witness; 11 is the first sound setting and by then it has
taken everything. BM25 reaches the right verdict from a 91% protected closure — right by luck,
having dropped a protected fact that happened not to matter, and raising k to 50 never recovers it.
FIBER is the only admissible strategy: right verdict and full closure, at 11 facts.
That last failure is why the harness ranks on admissibility rather than verdict alone — ranking on
verdict would have crowned the strategy that violated the mandatory closure and got away with it.
This does not show FIBER wins generally: the discriminating world was built to expose these modes,
just as the reference world was built to expose hub expansion. The full structural family sweep has
now been run — 36 cells over attachment x relay depth x tag style x distractor count — and the two
formerly missing baselines are in the panel. The sweep's headline is a negative result for FIBER: a
plain backward walk over the directed factor edges, closure first, is admissible in all 36 cells
at exactly FIBER's fact count, so on this family admissibility and cost cannot distinguish the
compiler from that walk; the fixed-basis embedding retriever, by contrast, fails every camouflaged
cell at the tight budget. Full analysis: docs/FINDINGS.md. How much of the blueprint the
workspace actually covers, and which sections have nothing standing in for them:
docs/COVERAGE.md. The crate layout and the blueprint path:
docs/ARCHITECTURE.md.
The Rust glioma research engine tracks executable capabilities in
docs/glioma/PROGRAM_PLAN.md. P10 F32 adds longitudinal replication
transport through analyze_glioma_longitudinal_transport and the MCP tool
glioma_longitudinal_transport_analyze: studies must bind the same estimand and effect unit and
cover one shared time grid, with incomplete studies excluded rather than imputed. Different model
systems incur the maximum transport gap and are included only when the request explicitly allows
that maximum; signature similarity weights admitted sources. Effects are bounded to ±1,000,000,000
milli-units before fixed-point pooling. Its gate and threshold policy is
explicitly repository-defined because this checkout has no configured detailed source blueprint
for that slot.
P10 F03 plans prospective resolvers for conflicting preclinical claims through
analyze_glioma_prospective_contradiction and MCP glioma_prospective_contradiction_plan. Rival
statements, evidence reports, design reports, and local artifacts remain digest-bound. Evidence is
counted by independent group, shared support across rivals cannot establish exclusive support, and
low-quality, null, and unresolved findings remain visible. Resolver prediction intervals must
separate a rival pair and pass feasibility, risk, and budget gates. A plan_ready result means the
bounded portfolio covers all declared rival pairs; it does not mean an experiment ran or a claim
was resolved. Its contract is repository-defined because this checkout has no detailed P10-F03
blueprint configured.
P10 F02 compares independent study effects through analyze_glioma_multistudy_concordance and
MCP glioma_multistudy_concordance_analyze. It binds an exact estimand and unit, reports every
eligible same-model pair by interval overlap and confident direction, and keeps cross-model pairs
incomparable. It retains null, unresolved, and low-quality studies without imputation or pooling.
The contract is repository-defined because this checkout has no configured detailed P10-F02
blueprint.
P10 F04 audits registered-outcome reporting through
audit_glioma_registered_outcome_reporting and MCP
glioma_registered_outcome_reporting_audit. It compares local registry protocols with reviewed
result-report metadata, marks overdue missing primary outcomes, and separates incomplete,
ambiguous, unregistered, and not-yet-due outcomes. It accepts no effect values and treats reporting
differences as review signals rather than proof of publication bias or misconduct. Its contract is
repository-defined because this checkout has no detailed P10-F04 blueprint.
P10 F05 adds build_glioma_registered_outcome_record and MCP
glioma_registered_outcome_record_build for a single digest-bound study outcome. P10 F06 adds
build_glioma_registered_outcome_evidence_panel and MCP
glioma_registered_outcome_evidence_panel to combine compatible records across independent studies
without pooling effects. The companion glioma_registered_outcome_sensitivity_analyze route
evaluates caller-declared missing-result ranges as separate scenarios. These contracts are
repository-defined because this checkout has no detailed P10-F05/F06 blueprints.
Autonomous agent process boundary
The Rust runtime also exposes an opt-in Docker-backed command boundary for callers that need an
explicit Linux process boundary. It is not connected to agent tool dispatch or the trial provider;
its limits and integration boundary are documented in docs/OCI_SANDBOX.md.
The Python SDK includes a secret-safe operator entry point for the autonomous brain:
For keyless local development, the same boundary supports an explicit credentialless fixture:
python -m prism_sdk provider-status --provider local and run --provider local --model local-model
use the runtime's bounded in-memory transport; no key or network provider is contacted.
For actual local-model inference without an OpenAI key, use the first-class Ollama preset:
python -m prism_sdk provider-status --provider ollama (default endpoint
http://127.0.0.1:11434/v1), then run with --provider ollama --model <installed-model> and
--approve-provider-call. The Ollama path is explicit, credentialless, OpenAI-compatible, and
loopback-by-default; it fails closed when the local server is unavailable rather than falling
back to a synthetic response.
For a grounded research pass, LocalNeurosurgicalAgent.grounded_real_data_research() /
grounded_public_literature_research() (Python) or groundedRealDataResearch() /
groundedPublicLiteratureResearch() (TypeScript) composes a bounded real-data or six-specialty
PubMed context, an explicitly approved credentialless local-model call, and the matching
authoritative draft-claim audit. It accepts Ollama or another caller-registered local provider,
returns context/bundle digests and structured claims, and remains grounded_for_human_review; a
provider outage fails closed and never produces synthetic evidence.
Before the authoritative draft audit, the bridge requires every model citation to be present in
the exact bounded context it received; unseen-but-valid snapshot records are rejected rather than
treated as grounded.
Set tool_loop=True (Python) or toolLoop: true (TypeScript) to expose bounded, read-only,
credentialless snapshot tools to the local model: row search, a ClinicalTrials.gov trial-landscape
view (neurosurgery_real_data_trial_landscape_view), and a cBioPortal/GDC molecular-coverage view
(neurosurgery_real_data_molecular_coverage_view). Calls are capped by explicit turn and call
budgets, recorded as a sanitized tool_trace, and their returned citation identities are added to
the closure check; the final audit widens only to the same source facets, never to a network or
patient-data tool. The trial and molecular views, plus the comparative
neurosurgery_real_data_cohort_landscape_view, return descriptive aggregates plus exact rows for
citation, not eligibility, efficacy, safety, treatment, or patient inference. A third review-queue view
(neurosurgery_real_data_review_queue_view) exposes only explicit missing-link, abstract, date,
or sample-count obligations for qualified human review; its bounded task rows are citation
closed and never treated as clinical findings.
The loop also exposes neurosurgery_real_data_reconciliation_view, which returns the canonical
PMID/normalized-DOI crosswalk ledger (missing or shared identifiers, counts, and exact metadata
rows) for human review. It never repairs or merges identifiers, fetches a source, or treats an
identifier relationship as biological or clinical evidence; returned rows are citation-closed.
It also exposes neurosurgery_real_data_research_brief_view, a deterministic glioma topic-lane
extractor covering integrated molecular identity, genomics, imaging, pathology, trials, outcomes,
tumor microenvironment, and treatment-effect metadata. Topic membership is lexical and
reviewer-facing—not relevance, evidence quality, biology, or clinical advice—and each returned
record is citation-closed to the supplied real snapshot.
The public-literature tool loop also exposes neurosurgery_public_literature_review_queue_view,
which projects the real PubMed snapshot's missing DOI/abstract/MeSH/publication-type and duplicate-
identifier obligations into citation-closed reviewer tasks. It is specialty-scoped, read-only,
and never treats missing metadata as negative evidence.
It also exposes neurosurgery_public_literature_integrity_view, which returns bounded PubMed
source-completeness and identifier-hygiene counts, review reasons, and exact metadata issues for
the caller's fixed lane. Issues remain citation-closed reviewer work; they are never evidence
rankings, negative findings, or clinical conclusions.
The glioma loop also exposes neurosurgery_real_data_evidence_graph_view, a bounded traversal of
explicit study/profile/PMID crosswalks. Graph edges are identifier/provenance metadata—not causal
or biological links—and every returned node is added to the citation closure set.
It also exposes neurosurgery_real_data_evidence_acquisition_view, which turns the validated
snapshot and the fixed glioma request into a bounded next-evidence worklist. The worklist carries
only local replay queries, source-linked metadata references, match counts, and explicit reviewer
obligations; it never fetches a source, opens a patient asset, or authorizes a clinical action.
The public-literature loop exposes the parallel
neurosurgery_public_literature_evidence_acquisition_view for a fixed specialty lane. It compiles
the checked-in PubMed snapshot into the same bounded, reviewer-owned local worklist while keeping
PMID references and the human_review_required boundary explicit; it never treats a planned query
as proof that evidence exists.
The glioma loop also exposes neurosurgery_real_data_coverage_view, a digest-bound inventory of
source, record-kind, temporal, assay, and explicit linkage coverage plus bounded gaps. It preserves
caller scope and omissions, but never converts coverage into a quality score or clinical claim.
Both loops also expose neurosurgery_specialty_evidence_map_view, which projects the fixed lane's
identity, spatial, functional, and temporal coverage states, missingness counters, and reviewer
questions. It returns planning metadata only (never observation values or clinical inference), is
provider-free/read-only, and rejects reports that drift from the caller's specialty lane.
When the caller supplies an explicit UTC freshness clock, the loops also expose a freshness view
(neurosurgery_real_data_freshness_view or neurosurgery_public_literature_freshness_view) that
returns bounded source-age states and digest metadata. No host clock, fetch, quality inference, or
synthetic fallback is used.
The function accepts structured real-data facets (record kind, trial status/phase/study type and
date bounds, molecular/genomic selectors, linked publication/MeSH selectors, and source IDs) or
PubMed facets (publication type, MeSH term, and date bounds). A model may add a narrower facet or
change lexical text, but cannot override a caller facet or increase its result limit; the specialty
lane is never model-selectable.
The lexical field is optional for facet-only searches; when omitted it uses the current bounded
question (or caller text) as the selector.
Tool results retain bounded source metadata such as trial status/phase/study type, molecular and
genomic datatype labels, publication/MeSH labels, aggregate enrollment/sample counts, and abstract
excerpts when present; recognized related_records edges preserve the source crosswalk, while
patient-level values are never projected.
The glioma tool loop also offers a digest-bound identifier-reconciliation view for canonical
PMID/normalized-DOI missing/shared rows; it is metadata-only human-review work and never repairs,
merges, fetches, or clinically interprets identifiers.
The operator commands expose the same mode with --tool-loop, --max-tool-turns 1..8, and
--max-tool-calls 1..32; persisted traces retain only search-text digests and structured facets.
For these grounded helpers, an HTTP provider must resolve to loopback (localhost, 127.0.0.1,
or ::1); remote credentialless gateways are rejected before any evidence tool or network call.
The bounded groundedRealDataResearchLoop() / groundedPublicLiteratureResearchLoop() helpers
extend this into a finite autonomous fan-out: each pass re-renders the source context, audits its
claims, and turns only model-reported unknowns into deduplicated metadata queries. The returned
pass ledger, pending queries, termination reason, and loop digest are caller-owned and remain held
for human review.
The real-data loop also accepts the same structured registry, molecular, genomic, and PubMed
facets as neurosurgery_real_data_query; the normalized facet set is retained in the ledger and
bound into its loop digest, so a restart cannot silently switch evidence slices.
When a caller supplies an explicit lexical text facet, it is used for the first pass; subsequent
unknown-derived passes replace only that lexical selector while preserving every structured facet,
so autonomous follow-up work changes the searched slice without widening its source boundary.
Each persisted pass also carries a canonical digest of its claim payload; resume rejects missing or
altered claims before another local-model call.
The public-literature loop also accepts structured public_literature_query facets (specialty,
publication type, MeSH term, inclusive date bounds, and limit); follow-up passes change only the
lexical text selector, and the complete facet set is retained and resume-fenced.
Pass a prior ledger as resume_from (Python) or resumeFrom (TypeScript) with a larger total
pass budget to continue pending queries after a process restart; schema, provider/model, source
bundle, and loop digest are revalidated before another local-model call.
The provider-free capability router now maps the complete neurosurgical tool surface into both
biomedical and neuroscience profiles: sanitized FHIR/DICOM imports, evidence programs and
autonomous review waves, trial landscapes, molecular coverage, and the public-literature
refresh/link/integrity queue, workbench, and portfolio tools. Natural-language routing remains
lexical and abstaining; it only selects a reviewed capability and never authorizes a provider,
patient-file access, clinical action, or external effect.
grounded_research_portfolio() / groundedResearchPortfolio() coordinates both planes in one
source-separated digest: real glioma population evidence and specialty PubMed evidence retain
independent loop/audit identities while their counts and pending work are aggregated for review.
When both snapshots are supplied, the portfolio also runs the existing provider-free
neurosurgery_literature_link_audit automatically. Its bounded exact PMID/normalized-DOI links,
unmatched identifiers, and metadata mismatches remain a separate reviewer artifact and never
imply cohort overlap, causality, or clinical applicability.
The portfolio and grounded-autopilot CLI also accept an optional real, de-identified
case_asset_manifest plus bounded query. The authoritative manifest projection contributes only
asset-kind coverage, digests, and reviewer obligations; asset bytes, identifiers, and clinical
values never enter the local-model context. The attachment is specialty-bound and remains a
separate case-provenance plane from population and PMID evidence.
The Python process boundary now exposes the same workflow as aurora-agent grounded-portfolio:
it reads bounded, checked-in non-synthetic snapshots, runs Ollama on loopback (or an explicit
in-memory fixture), and atomically persists a digest-bound answer/claim ledger. --resume only
continues a store whose question, provider/model, source selection, and child loop digests verify;
no API-key argument or prompt exists on this command, and it remains research-only and
human-review gated.
When current public evidence is needed, add --refresh-real-data and/or
--refresh-public-literature together with --approve-network. The refreshers use only the
allow-listed credentialless public endpoints, validate each candidate snapshot, and atomically
replace the selected files before the first model call. Refresh cannot be combined with --resume
because changing a source digest would invalidate the persisted loop; receipts are returned in
source_refresh and the run remains human-review gated.
The same receipt is retained in the digest-bound output store and replayed on --resume without
re-fetching sources.
Use --real-data-query-file query.json (also supported by grounded-autopilot) to apply a
bounded JSON facet object to the glioma plane; the selected facet set is retained and resume-fenced.
Use --public-literature-query-file query.json with either command to apply publication-type,
MeSH, date-range, specialty, and limit facets to the PubMed plane; that slice is also retained and
resume-fenced.
For free-text routing, aurora-agent grounded-autopilot first runs the provider-free six-specialty
intake, stops with needs_evidence when the routed snapshot is absent, and only then invokes the
approved local model. Glioma requires the real glioma snapshot; the other specialties require the
PubMed snapshot. The envelope preserves source-plane separation and an explicit human-review hold;
it never falls back to synthetic evidence or emits clinical advice. Its --intake-output is an
atomic, digest-bound restart checkpoint: --resume rechecks the question, route, source paths,
provider/model, and bounded controls (only a larger pass budget is allowed), then hands verified
child ledgers back to the worker. Checkpoints retain caller-owned research claims only—never keys,
patient data, or hidden model state.
To refresh that PubMed plane on any supported platform, use the credentialless NCBI boundary:
aurora-agent refresh-public-literature --approve-network. It retrieves six bounded specialty
lanes, computes the Rust-compatible source and bundle digests, validates synthetic_data=false,
and atomically replaces the snapshot only after every lane is linked and hash-checked. No API key,
provider, patient data, or synthetic fallback is accepted.
The grounded commands can perform that refresh inline with
--refresh-public-literature --approve-network (and, for glioma, add
--refresh-real-data). Inline refresh is opt-in, refuses --resume, and returns source digests
and retrieval metadata in source_refresh so the model never runs against an unreported corpus.
For the complete glioma population plane, aurora-agent refresh-real-glioma --approve-network
retrieves only aggregate metadata from ClinicalTrials.gov, NCI GDC, cBioPortal, NCI PDQ, and
PubMed. It validates the Rust-compatible source hashes and required registry/genomic/portal/
guideline planes, then atomically installs a last-known-good snapshot; no patient rows, assay
values, imaging, credentials, or synthetic fallback are fetched or retained.
The real-data context also serializes each bounded reviewer obligation (task ID, source identity,
and rationale), so an autonomous worker cannot mistake an unresolved metadata queue for a clean
corpus.
Resumable evidence-backed provider calls in both SDKs now capture authoritative request, wire,
credential, provider configuration, and transport identities before awaited caller callbacks.
Observers and rehydrators receive detached projections; credential/provider graph checks repeat
after callbacks and after the caller-owned dispatch transaction. That transaction must durably
commit the private idempotency receipt with the provider_in_flight checkpoint before any
transport call, and the graph is checked again before terminal settlement. This is a guarded
same-process boundary, not an exactly-once claim: deployments still own authenticated durable
receipt storage, provider-side idempotency, and uncertain-outcome reconciliation.
The Rust workspace also ships a dedicated, provider-neutral neurosurgical research agent in
bioprism-neurosurgery. It routes de-identified glioma, cranial-base,
craniofacial, encephalocele, spina-bifida and Chiari requests through deterministic read-only
tools, emits explicit evidence gaps and a reproducible request digest, and always holds the
result for human review. Each response carries a specialty-specific research profile covering
identity, anatomy, time, evidence questions, confounders, and reviewer roles. It uses no OpenAI API or credential; see
docs/NEUROSURGICAL_AGENT.md. A synthetic fixture exists only for
offline contract tests; it is not used by the real-data path.
The neurosurgery_evidence_audit tool adds per-specialty intake coverage for measured,
unmeasured, uninterpretable, conflicting, and missing-provenance observation classes before the
route executes.
The neurosurgery_specialty_evidence_map tool expands that audit into four explicit dimensions
for each lane—identity, spatial/anatomic, functional/intervention, and longitudinal context—so
glioma, cranial-base, craniosynostosis, encephalocele, spina-bifida, and Chiari review cannot hide
which domain inputs are absent, uninterpretable, conflicting, or provenance-incomplete. It is
available through the Rust CLI (--specialty-evidence-map), MCP, Python
specialty_evidence_map(), and TypeScript specialtyEvidenceMap(); it inventories supplied
metadata only and never interprets imaging, pathology, genomics, or operative text.
The map self-validates its digest and canonical source rows; mission audits rebuild typed glioma
maps against the exact request and supplied snapshots before handoff.
The neurosurgery_evidence_synthesis tool is the cross-plane handoff: it composes the redacted
case audit with caller evidence, the validated real glioma population snapshot, and/or the
validated six-specialty PubMed snapshot. Each plane stays separate, exact source identifiers and
URIs remain inspectable, optional freshness reports are attached to the supplied bundle digests,
and cross-bundle PMID correspondences are reported only as links (never as cohort or patient
claims). Reference/query bounds, truncation, missing snapshots, and incomplete case coverage
become explicit review items. The Rust CLI (--evidence-synthesis), Python
evidence_synthesis(), TypeScript evidenceSynthesis(), and MCP expose the same no-key,
network-free, read-only contract; raw case labels and values are never echoed.
The same report is now included automatically by mission helpers: one-bundle missions expose the
corresponding evidence plane, while dual glioma missions expose both planes and exact links in a
single digest-bound handoff.
Persisted synthesis reports self-validate their plane separation, lane counts, freshness bindings,
asset/disposition projections, and provider boundary; mission audits also replay the report against
the exact request and supplied snapshots so a structurally valid report cannot be rebound silently.
The neurosurgery_research_plan tool turns those explicit gaps into a bounded, source-linked
caller handoff. It can query only a supplied local real-glioma or six-specialty PubMed snapshot,
attaches stable source IDs/URIs for reviewer inspection, and keeps population/citation context
separate from patient observations. It never fetches, invokes a model, writes state, or emits
diagnosis, prognosis, treatment, triage, or procedural instructions; every plan remains held for
human review. Rust, MCP, Python, TypeScript, and the offline CLI expose the same digest-bound
contract with task/reference bounds.
Every persisted plan now carries a plan_digest and validates its task/source projections; mission
audits replay the recorded bounds and local queries against the exact request and snapshot before
handoff.
The neurosurgery_research_brief tool adds a deterministic, source-linked reconnaissance pass
over the same validated snapshots: it groups exact lexical matches into specialty topic lanes,
returns stable record IDs/URIs, preserves abstract availability and truncation, reports
cross-topic overlap and explicit unknowns, and emits reviewer prompts. It does not rank evidence,
summarize unsupported claims, call a model, or turn population literature into patient evidence;
human_review_required remains true. The Rust CLI (--research-brief), Python
research_brief(), and TypeScript researchBrief() facades are parity surfaces for this report.
Persisted briefs expose validate_integrity() and validate_for_inputs(...); mission audits replay
the brief against the exact request and source snapshot, including topic counts, truncation, and
source-link projections.
The standalone neurosurgery_evidence_graph projection is likewise digest- and topology-checked;
its validate_for_inputs(...) replay confirms every emitted node/edge came from the exact local
glioma snapshot and persisted bounds.
The shared neurosurgery_evidence_audit now carries an audit_digest and exact request replay
guard; downstream evidence programs and research plans therefore inherit a tamper-evident intake
coverage primitive for measured, unmeasured, uninterpretable, and conflicting states.
The neurosurgery_evidence_acquisition tool is the next autonomous worker wave: it turns the same
explicit missing/uninterpretable/conflicting/provenance gaps into a bounded dual-plane worklist,
querying only caller-supplied validated real-glioma and/or PubMed snapshots. Each step carries a
source tag, trigger, deterministic digest, local match/truncation status, fallback-to-specialty-scan
flag, and replayable references; missing sources remain explicit obligations. Rust, MCP, Python
evidence_acquisition(), TypeScript evidenceAcquisition(), and the offline CLI expose this
provider-free surface. The lifecycle variants (evidence_acquisition_start, bounded
evidence_acquisition_advance, and evidence_acquisition_finish, with matching Python and
TypeScript methods) let a caller persist and resume a digest-bound checkpoint; changed request,
query, or snapshot bytes are refused before replay. It never fetches, needs an API key, opens
asset bytes, or promotes a population/citation match to a case finding, and
human_review_required remains true. scripts/run_neurosurgical_acquisition_worker.ps1
drives the caller-owned checkpoint loop locally and writes no credentials or clinical state.
It accepts -CaseAssetManifestPath plus the optional -CaseAssetManifestQueryPath and
-CaseAssetReviewDispositionPath, so the same worker can carry a real de-identified multimodal
review projection and its persisted reviewer state through every wave.
When a real de-identified case_asset_manifest is supplied, the acquisition report also carries
the manifest report digest and bounded asset review items (missing source, digest, timestamp,
uninterpretable, conflicting, or requested-class obligations). Start/advance/finish re-bind that
digest on every replay, so a local worker cannot silently drop multimodal provenance while
replaying population or citation queries. The offline CLI accepts the same projection with
--case-asset-manifest <path> and --case-asset-manifest-query <path> alongside
--research-plan --autonomous-acquisition; Python and TypeScript expose matching optional
arguments on each lifecycle method.
For real glioma research, use the provenance-bound public snapshot in
data/neurosurgery/glioma_public_snapshot.json
and refresh it (without a provider key) with
scripts/refresh_glioma_public_data.ps1.
The checked-in data/neurosurgery/glioma_extended_snapshot.json
adds the real NCI GDC TCGA-LGG project (516 aggregate cases) alongside TCGA-GBM (617); it is
generated by the same script with -GdcProjectIds @("TCGA-GBM","TCGA-LGG"). The baseline remains
unchanged for replay compatibility, while callers can opt into the broader glioma population
bundle and its distinct source digest. The checked-in extended bundle also uses the broader
real PubMed query (glioma OR glioblastoma OR diffuse midline glioma OR oligodendroglioma OR astrocytoma) AND (molecular OR genomic OR IDH OR MGMT OR methylation) under the stable
pubmed_glioma_molecular source ID, so lower-grade and histomolecular terminology is not silently
excluded from the citation plane. Each extended GDC project also carries aggregate file/data-type
facets (for example somatic mutation, aligned-read, slide-image, transcript-fusion, and
methylation availability) without exposing files, samples, or assay values.
For an end-to-end candidate workflow, scripts/run_glioma_refresh_review.ps1
validates the baseline, refreshes a separate candidate from public endpoints, runs the core
refresh audit, and writes a report without replacing the baseline; promotion remains an explicit
reviewer action. It accepts the same -GdcProjectIds, -PubMedTerm, and -PubMedSourceId
scope controls as the low-level refresh script, so the candidate audit can cover the wider
real-glioma population without silently changing the baseline.
The refresh script defaults to a bounded 20-record PubMed window and accepts -PubMedLimit 1..50
for an explicit corpus size. -PubMedTerm and -PubMedSourceId widen the real citation lane
without losing query/source provenance; replacement of an existing snapshot is atomic and cleans
its temporary backup after promotion.
Source IDs are stable across retrieval dates; timestamps and content hashes carry freshness and
change information without turning every refresh into a remove-and-add event.
The neurosurgery_real_data_refresh_audit tool is the restart-safe reconciliation layer for that
workflow: give it two independently validated snapshots and it composes structural diff, coverage,
freshness (when requested), review-queue obligations, and the research brief into one digest-bound
report. It preserves stable source/record identity, emits explicit refresh-review reasons, and never
accepts, merges, fetches, ranks, or writes a candidate snapshot. The Rust CLI
(--real-data-refresh-audit), Python real_data_refresh_audit(), and TypeScript
realDataRefreshAudit() facades expose the same provider-free contract; human review remains
required.
For long-running work, the neurosurgery_session MCP tool provides digest-bound start/advance/
finish checkpoints so a caller can resume one read-only specialty tool at a time without hidden
server state. Checkpoints also bind the canonical specialty route, session identity, event status,
and terminal hold, so identity or route mutations fail closed before a resumed tool runs.
Every terminal AgentResponse now carries a response_digest over its complete route, tool trace,
evidence-gap projection, and nested provenance summaries. Rust callers can invoke
validate_integrity() for persisted-envelope checks and validate_for_request(...) for exact
request replay; session finish rejects a response that fails either structural envelope gate.
Mission envelopes now also carry the same bounded evidence_acquisition plan, so a single
provider-free mission exposes the specialty route, source-linked research plan, real-data/literature
packet, and resumable acquisition worklist together without merging evidence planes.
They also carry an evidence_program: six protocol-defined review tracks per lane (for example
glioma histomolecular identity, imaging phenotype, surgery/function, response endpoints,
microenvironment, and trial design) are projected onto exact IDs in the attached real snapshots.
neurosurgery_evidence_program and the Python evidence_program() / TypeScript
evidenceProgram() facades expose the same agenda directly. Track matches are transparent
lexical retrieval observations with bounded references, required observation classes, and
specialist reviewer roles. Each track also carries metadata-only observation coverage copied from
the typed intake audit (measured, unmeasured, uninterpretable, or conflicting), missing
classes, and provenance gaps; this is a worklist signal, never a sufficiency score. Empty and
truncated tracks remain unknown. The program is read-only,
provider-free, network-free, synthetic-data-free, and human-review gated—it does not rank
evidence, make a glioma classification, or emit treatment or operative guidance.
When a persisted case_asset_review_disposition ledger is supplied with the manifest, its
digest and pending/resolved counts are carried into both the evidence program and acquisition
plan; stale or tampered reviewer state is refused.
When a real de-identified case_asset_manifest is supplied, each track also joins its required
observation classes to digest-only imaging, pathology, molecular, operative, functional,
developmental, longitudinal, or anatomical coverage. observed, present_not_observed, and
missing states make the next export/review obligation actionable without reading asset bytes;
the optional asset_coverage_complete flag is inventory metadata, not clinical sufficiency.
Tracks also emit a deterministic review_worklist for observation/provenance gaps and unresolved
asset classes, giving a local worker explicit next metadata checks without inventing findings.
Evidence-program reports self-validate their canonical tracks, coverage/count invariants,
source references, freshness bindings, and digest; mission audits replay them against the exact
request and supplied snapshots before handoff.
Persisted case-asset projections expose validate_integrity() and
validate_for_request(...) guards; synthesis, evidence-program, and acquisition joins refuse a
tampered or request-mismatched report before it can enter a digest-bound handoff. This protects
restart/review workflows without pretending that an upstream asset digest proves the asset's
clinical truth.
The offline CLI exposes the same pass with --evidence-program, --real-glioma <snapshot>
and/or --public-literature <snapshot>; add --evidence-program-query <query.json> to bound
lane, track, reference, abstract, or freshness controls.
data/neurosurgery/evidence_program_query.json
is an all-six-lane query template for the checked-in PubMed snapshot.
Mission envelopes also include a final mission_audit receipt. It verifies specialty/status
identity, request digests, real/public snapshot digests, required report-plane presence, the
case-asset-to-synthesis and case-asset-to-evidence-program bindings, and the provider-free human-review boundary. integrity_ok is
an assembly/provenance invariant only; it is not a clinical readiness or evidence-quality score.
Persisted mission envelopes now have a single replay gate: Rust
NeurosurgicalMissionResult::validate_integrity() checks the terminal response/session chain and
all nested receipts without inputs, while validate_for_inputs(...) rebuilds the mission audit
against the exact request and caller-owned snapshots. Changed request or snapshot bytes fail
closed before a worker can reuse the packet. The MCP neurosurgery_mission tool accepts
operation: "validate"; Python validate_mission(), TypeScript validateMission(), and the
offline CLI --validate-mission <mission.json> expose the same no-key, read-only replay check.
When a mission carries a DICOM or FHIR receipt, exact replay additionally requires the original
sanitized metadata export (--mission-case-dicom or --mission-case-fhir on the CLI, or the
matching case-import object on the MCP validation call); otherwise validation fails closed rather
than treating receipt-shape integrity as source replay.
The neurosurgery_catalogue MCP tool exposes all specialty profiles and read-only tool specs
before execution, while neurosurgery_real_data_query searches the validated public bundle by
stable record text, cBioPortal molecular-profile modality, trial status, exact registry phase or
study-type facets, inclusive registry update-date bounds, exact GDC genomic_data_type file
facets, case-insensitive PubMed publication_type/mesh_term indexing facets, inclusive PubMed
publication_date_from/publication_date_to bounds, record-kind/source facet, or explicit
relationship facet, including PMID/title/DOI/abstract/MeSH matches from the PubMed lane. These
indexing facets narrow literature metadata but do not act as study-quality scores.
Genomic-project hits additionally expose aggregate GDC file/data-type facets when present, keeping
modality availability source-linked without returning files, samples, or molecular values.
PubMed hits carry bounded source-text excerpts and indexing tags for reviewer inspection. Clinical
trial hits also preserve optional ClinicalTrials.gov study type, aggregate enrollment target,
intervention names, phases, and last-update date; portal-study hits preserve optional public sample
counts; PubMed hits preserve publication dates. Partial PubMed chronology (year-only or month-only
source dates) remains missing rather than being padded with an invented day. Missing upstream
fields remain absent rather than guessed. Hits also carry explicit study↔profile/publication relationships so a caller can traverse
the evidence graph without inferring links from prose. Molecular-profile rows describe available assay modalities only;
they never expose mutation, expression, or patient-level values. Responses also include deterministic
counts of profile modalities and explicit relationships so a reviewer can see assay coverage and
cross-source connectivity before inspecting source-linked metadata.
PubMed hits are metadata-only and require reviewer verification before substantive use; the Rust
summary also exposes a PMID crosswalk to flag unmatched portal citations without inferring cohort
identity. The Python SDK exposes the same provider-free lifecycle through
LocalNeurosurgicalAgent, including bounded session iteration, catalogue discovery, and public
record queries for UI or worker integrations.
Persisted real-data and PubMed query results now expose validate_integrity() plus exact
validate_for_inputs(...) replay; mission audits invoke those gates so a changed query, hit list,
or count projection cannot be smuggled into a persisted mission.
neurosurgery_real_data_trial_landscape adds a digest-bound, provider-free ClinicalTrials.gov
metadata reconnaissance over the same validated snapshot: bounded status, multi-label phase,
study-design, intervention, update-date, source, missingness, and truncation projections. It
never ranks trials or infers eligibility, efficacy, safety, outcomes, or patient-level meaning;
multi-phase rows are counted explicitly rather than collapsed into a misleading trial total.
neurosurgery_real_data_molecular_coverage adds the complementary cBioPortal availability
ledger: exact alteration-type/datatype facets, per-study profile counts, analysis-visible and
patient-level metadata flags, description coverage, explicit missing alteration/datatype counts,
aggregate GDC project file/data-type facets, and explicit row/study/facet
truncation or missing-facet reasons. It inventories only public assay metadata already in the snapshot—no
mutation/expression values or sample identifiers—and is digest-bound, replayable, provider-free,
network-free, and human-review gated. The canonical evidence packet includes this ledger
automatically alongside the trial and comparative cohort landscapes.
neurosurgery_real_data_cohort_landscape adds the comparative genomic-project view used by the
autonomous loop and is included automatically in newly generated evidence packets and missions.
It compares the source-linked TCGA/GDC projects already present in the validated
bundle, reporting aggregate released-case inventory and per-project file/data-type availability
with explicit truncation and missing-metadata reasons. The view is read-only, provider-free, and
metadata-only: rows are citation surfaces, counts are descriptive planning context, and it never
opens files, exposes samples or molecular values, merges cohorts, or makes a clinical claim.
For natural-language entry, neurosurgery_intake_plan (and the Python intake_plan() /
TypeScript intakePlan() facades) performs deterministic lexical routing into the six closed
specialty routes. It returns bounded candidates, abstains on weak or ambiguous wording, and lists
caller-supplied evidence snapshot classes, reviewer roles, and next research actions. The question
is represented in the returned plan only by a SHA-256 digest; scores are routing units, not
probabilities or clinical risk, and an explicit specialty is only a research-routing override.
This makes free-text intake useful without adding a model provider, credential, network,
patient-file, diagnosis, or procedure capability.
The closed vocabulary includes specialist subtopics rather than only disease names: glioma
histomolecular markers and treatment-effect terms; petroclival/cavernous-sinus and cranial-nerve
topics; craniosynostosis suture and syndromic terms; encephalocele variants and CSF rhinorrhea;
spinal dysraphism, tethering, and neurogenic-bladder terms; and Chiari measurements, cine-MRI, and
CSF-flow terms. These are routing labels only and never become inferred findings.
neurosurgery_intake_mission (and intake_mission() / intakeMission()) composes that planner
with a guarded research-only mission: ambiguous questions return a digest-only abstention,
selected glioma routes require the validated real glioma snapshot (with PubMed as optional
supplement), and the other specialties require the validated PubMed snapshot. Executed results
contain no raw question or request payload and remain provider-free, network-free, read-only, and
held for human review.
Callers may optionally include a de-identified case_request with observations, provenance, and
evidence. It is validated before any bundle query and carried into the guarded route, so a real
case can be reviewed without the old empty-case fallback; the case payload is never echoed in the
intake envelope. If omitted, the mission still runs the route but exposes the resulting observation
gaps for human follow-up.
An optional case_asset_manifest plus case_asset_manifest_query carries real, de-identified
multimodal asset metadata into the nested mission. The manifest is digest-bound, requires explicit
asset states, and never opens bytes; use the same pair with the Rust CLI's --intake-mission.
The intake mission also accepts case_dicom_import and case_fhir_import directly (Python
intake_mission(..., case_dicom_import=..., case_fhir_import=...), TypeScript
intakeMission(..., caseDicomImport, caseFhirImport), MCP fields, or CLI
--intake-case-dicom/--intake-case-fhir). These imports take the same independently validated,
digest-only route and may be combined with each other, but not with a second asset manifest.
An already persisted case_asset_review_disposition ledger can be supplied in the same intake
mission call (Python case_asset_review_disposition=..., TypeScript
caseAssetReviewDisposition, or the MCP field). Its report digest and reviewer counts are
validated before evidence handoff and rebound into synthesis, evidence programming, acquisition,
and the final audit; it never changes the manifest or creates a clinical conclusion.
If a real case is exported through FHIR, neurosurgery_case_fhir_import (Rust
NeurosurgicalAgent::case_fhir_import, Python case_fhir_import(), TypeScript
caseFhirImport(), or CLI --case-fhir-import <import.json>) projects a caller-sanitized FHIR
Bundle into that same digest-only asset boundary. The import requires deidentified: true,
synthetic_data: false, bounded resourceType/id metadata, and an explicit asset-kind/status/
provenance hint; it
rejects identifiers, patient references, narratives, codes, measurements, and raw text. The
Bundle is never echoed or interpreted, unclassified resources become reviewer tasks, and the
report can be replayed against the exact request, Bundle, and hints without an API key or network.
If the imaging archive exports standard DICOM JSON, neurosurgery_case_dicom_import (Rust
NeurosurgicalAgent::case_dicom_import, Python case_dicom_import(), TypeScript
caseDicomImport(), or CLI --case-dicom-import <import.json>) projects only bounded
series-level metadata such as modality, body region, study/series/SOP UID digests, dates,
descriptions, and series number. It accepts one dataset or an array (up to 512 datasets and 4 MiB
of metadata), refuses patient-identifying tags and PixelData, ignores unknown/private tags, never
opens DICOM bytes, and never interprets an image. Missing SeriesInstanceUID, acquisition dates,
modality, body region, and object-byte SHA-256 digests become explicit review obligations; the
digest-bound report is replayable, non-synthetic, provider-free, network-free, and human-review
gated.
For a single end-to-end handoff, neurosurgery_case_dicom_evidence_workflow (Rust
NeurosurgicalAgent::case_dicom_evidence_workflow, Python case_dicom_evidence_workflow(),
TypeScript caseDicomEvidenceWorkflow(), or CLI --case-dicom-evidence-workflow) composes
that real metadata projection with validated real glioma/PubMed records, evidence synthesis, the
six-track review program, and a resumable local acquisition checkpoint. Every nested report is
bound to the same request and DICOM manifest digest; the output remains provider-free,
network-free, read-only, non-synthetic, and held for human review.
The repeatable PowerShell wrapper
scripts/run_neurosurgical_dicom_evidence_workflow.ps1
validates inputs, runs the offline CLI, and writes a caller-selected report without promoting
data or retaining credentials.
For a mission-level glioma dossier, pass the same DICOM import as case_dicom_import to
neurosurgery_mission (Python run_research_mission(..., case_dicom_import=...), TypeScript
runResearchMission(..., caseDicomImport), or CLI --mission-case-dicom <import.json> together
with --mission --real-glioma). The mission carries the DICOM receipt and verifies that its
manifest digest is rebound through synthesis, evidence programming, and acquisition; this
convenience lane is real-glioma-only and can be composed with a sanitized FHIR import for a
multimodal digest-only manifest, but not with a second asset manifest or disposition.
For a repeatable local run of that mission-level lane, use
scripts/run_neurosurgical_mission_with_dicom.ps1;
it validates the DICOM/manifest/synthesis bindings and refuses a nonzero mission audit before
writing the report.
The same mission envelope accepts a sanitized FHIR metadata import as case_fhir_import (Python
run_research_mission(..., case_fhir_import=...), TypeScript runResearchMission(..., caseFhirImport), or CLI --mission-case-fhir <import.json>). It works with a real glioma bundle,
a cross-specialty PubMed bundle, or both; the FHIR receipt's digest-only manifest is rebound through
the same synthesis, evidence-program, acquisition, and mission-audit planes. FHIR resources and
clinical values are never returned or interpreted. FHIR and DICOM imports may be supplied together;
their independently validated digest-only projections are unioned into one multimodal manifest
while both child receipts remain visible. A separate asset manifest or disposition ledger cannot
be mixed into an import-backed mission.
Intake missions and portfolios also accept an optional caller-clocked freshness policy inline
or via the CLI --intake-freshness <query.json> flag. Resulting real/PubMed freshness reports are
digest-bound; omission means freshness is unclaimed and the server never consults its own clock.
When it executes, only the planner's matched closed-vocabulary terms become bounded local
real-data/PubMed filters; the original free text is never echoed into those reports. An explicit
specialty-only hint uses that lane's canonical corpus term (for example glioblastoma for
glioma) when no lexical terms were matched.
The same intake orchestration is available without MCP: pipe a flat JSON intake query to
bioprism-neurosurgery --intake-mission or --intake-portfolio and pass the checked-in
--real-glioma and/or --public-literature snapshots. These CLI modes perform the same
validation, provenance checks, and human-review hold with no provider, API key, or network.
For a repeatable worker that refreshes both public bundles into non-promoted candidates, audits
their drift, and then runs the portfolio against the validated candidates, use
scripts/run_neurosurgical_intake_portfolio.ps1.
It emits one machine-readable worker envelope and never promotes a candidate snapshot. Supply
-FreshnessQueryPath to bind a caller-owned source-age clock, or
-CaseAssetManifestPath plus the optional -CaseAssetManifestQueryPath to carry real,
de-identified multimodal provenance into a selected-lane portfolio. A persisted
case_asset_review_disposition ledger can accompany that manifest and is replayed into the
nested mission's synthesis/acquisition audit; all-six-lane portfolios refuse both the manifest
and its ledger. The PowerShell worker accepts the same ledger through
-CaseAssetReviewDispositionPath.
For cross-specialty reconnaissance, neurosurgery_intake_portfolio (and
intake_portfolio() / intakePortfolio()) fans those filters across one selected lane or an
explicit all-six-lane portfolio. Each lane remains independent and source-linked; an all-lane
portfolio requires both the PubMed snapshot and the real glioma snapshot because glioma is part
of the requested scope. A selected-lane portfolio can carry the metadata-only case-asset manifest
pair; an all-lane portfolio refuses a single-specialty asset attachment, including its reviewer
ledger. A selected-lane call may carry case_asset_review_disposition= through the nested
mission. The worker verifies the selected lane's nested evidence-synthesis asset digest and coverage counts before emitting its
envelope.
Use neurosurgery_evidence_graph (or evidence_graph() / evidenceGraph()) when a reviewer
needs the explicit, bounded study/profile/PMID crosswalk: it returns source URIs, root traversal,
component/isolate counts, omissions, and a digest without inferring biology, causality, or clinical
action.
A complementary neurosurgery_real_data_coverage report audits the same real snapshot by source,
record kind, trial-update/publication-date axis, assay modality, abstract availability, and explicit
study/profile/PMID linkage gaps. It preserves missing dates, exposes retrieval metadata, and binds a
coverage digest; it does not score freshness or evidence quality, merge cohorts, or make clinical
claims.
Coverage reports expose validate_integrity() and validate_for_inputs(...); mission audits use
the exact replay check before a local worker can consume the coverage plane.
neurosurgery_real_data_reconciliation is the companion cross-source identifier ledger. It
replays one validated snapshot and reports only exact PMID/normalized-DOI findings: portal PMIDs
missing from the local literature window, PMIDs shared by multiple portal studies, and DOIs shared
by multiple literature rows. Counts remain visible when findings are truncated, identifiers are
never merged or repaired, and any finding sets requires_review; this is metadata review work,
not a biological, clinical, or evidence-quality conclusion. It is available as
RealGliomaBundle::reconcile, LocalNeurosurgicalAgent.real_data_reconciliation(), and
realDataReconciliation() with no provider, network, or API key.
Real-data missions also attach a bounded real_data_trial_landscape inventory over the
ClinicalTrials.gov rows and a real_data_molecular_coverage inventory over cBioPortal assay/profile
metadata. Both are digest-bound to the same validated snapshot, preserve truncation and missing
metadata as review obligations, and never rank trials, infer eligibility, expose patient-level
assay calls, or make efficacy, safety, diagnostic, prognostic, or treatment claims.
neurosurgery_real_data_freshness is the explicit age posture companion: provide a caller-owned
UTC as_of timestamp and max_age_days policy to classify each source as current, stale, or
future_dated. A future-dated source forces requires_review; age is never treated as evidence
quality, applicability, or clinical relevance. The report is digest-bound, read-only, provider-free,
and available for the cross-specialty PubMed snapshot as neurosurgery_public_literature_freshness.
Freshness reports expose validate_integrity() and exact replay methods for real-glioma and
cross-specialty snapshots; mission audits refuse a stale or future-dated posture that has drifted
from its caller-supplied clock or source bundle.
Real-data missions include the ordered, source-linked research_plan, coverage audit, bounded
real_data_trial_landscape and real_data_molecular_coverage inventories, metadata review queue,
bounded evidence packet, explicit evidence graph, digest-bound
real_data_autonomous_workflow, and real_data_reasoning_context automatically alongside any optional bounded record query and the
resumable human-review workflow. The plan and queue turn explicit intake gaps into caller-owned
next-review tasks; the packet/context are source-addressable input for a caller-owned local model or
reviewer. Neither is a model invocation or clinical conclusion. Public-literature missions carry
the corresponding bounded PMID evidence packet and automatically run the lane-scoped
public_literature_integrity_audit before packet/brief/context handoff. Missing DOI, abstract,
publication-type, and MeSH metadata plus duplicate identifiers remain explicit review obligations;
they are never treated as negative evidence.
The same mission envelope carries a bounded public_literature_review_queue with stable
source-linked reviewer tasks so real metadata gaps become actionable review work without a
provider key or clinical interpretation.
That queue exposes validate_integrity() and validate_for_inputs(...), keeping persisted task
rows tied to the exact integrity audit and public snapshot.
The companion neurosurgery_public_literature_workbench joins each selected lane's closed
specialty profile (identity, spatial, temporal, evidence-question, confounder, and reviewer-role
axes) to exact snapshot coverage, abstract availability, metadata gaps, and integrity-review
counts. It is navigation metadata rather than a readiness or quality score: lanes are never
ranked, missing fields are never imputed, and no diagnosis, prognosis, treatment, triage, or
procedural action is emitted. Use --public-literature-workbench <public> with a JSON query on
stdin, Python public_literature_workbench(), or TypeScript publicLiteratureWorkbench();
public-literature missions attach the request-specialty workbench automatically.
The integrity audit, workbench, matrix, and portfolio reports expose digest/exact-replay checks;
persisted multi-lane review state must be replayed against the same public snapshot before use.
The neurosurgery_public_literature_portfolio pass composes that workbench into one bounded
multi-lane handoff: every selected specialty receives an exact lexical query result, its profile
and coverage lane, and a stable reviewer queue (all six lanes by default). It uses only the
validated real PubMed snapshot and preserves explicit hit, review-item, omission, and truncation
counts. The portfolio is provider-free (provider: none, network: false, synthetic_data: false),
does not rank evidence or infer a clinical conclusion, and never fetches URLs, opens credentials,
or writes durable state. Use --public-literature-portfolio <public> with JSON on stdin, Python
public_literature_portfolio(), or TypeScript publicLiteraturePortfolio().
Observations may also carry caller-supplied UTC observed_at values and de-identified timepoint
labels. The neurosurgery_evidence_audit response (and --temporal-audit CLI mode) now includes a
digest-bound temporal_alignment report with ordered timestamps, same-time observations, undated
records, required specialty classes without dates, and caller-order inversions. This is an explicit
longitudinal metadata audit—not a progression, response, prognosis, diagnosis, or treatment model;
dates are never inferred from free text.
For refresh monitoring, neurosurgery_real_data_diff compares two validated snapshots and exposes
added, removed, or changed public records plus source-metadata changes by stable identifier; it
never copies abstracts, scores freshness, merges cohorts, or makes a clinical claim.
Diff reports expose validate_integrity() and validate_for_inputs(...) so refresh decisions can
be replayed against the exact before/after snapshots.
The composed refresh audit applies the same nested integrity and exact-replay checks across the
diff, coverage, freshness, review queue, and research brief planes.
neurosurgery_real_data_review_queue then derives a bounded, digest-addressed human-review queue
from explicit snapshot gaps (missing crosswalks, unlinked citations, absent/clipped abstracts,
unknown registry dates, or unknown sample counts) without imputing values or assigning clinical
urgency.
neurosurgery_real_data_review_disposition applies caller-owned reviewed, unresolved, or
not_applicable state to emitted queue tasks, verifies the queue digest, and preserves omitted or
undecided obligations as pending; it never edits source facts or produces a clinical conclusion.
neurosurgery_real_data_evidence_packet composes the validated summary, coverage, explicit
crosswalk, bounded source-linked query hits, canonical ClinicalTrials.gov trial landscape, and
review queue into one packet digest for a local model or human reviewer; nested omissions and
unknowns remain visible. The packet also carries the canonical cBioPortal molecular-availability
ledger (per-study profile/modalities, explicit description gaps, and boundedness) so a local worker
can see what assay metadata is actually present before reasoning. Both real-glioma and
cross-specialty literature packets accept an optional freshness query with an explicit UTC
as_of and return the digest-bound current/stale/future-dated source posture when requested;
omitting it never invents a clock or claims that the snapshot is fresh.
The real-glioma packet also carries a canonical PMID/normalized-DOI reconciliation ledger;
missing or shared identifiers remain explicit provenance-review obligations before a local model
can rely on the crosswalk.
neurosurgery_real_data_reasoning_context renders that packet into a deterministic, bounded
local-model context with digest-bound headers, source-addressable record blocks, optional
untrusted abstract excerpts, and explicit character/query omissions. It never invokes a model or
turns source text into a clinical conclusion.
The context envelope exposes validate_integrity() and validate_for_inputs(...) as well; a
worker must verify the persisted context against the exact snapshot before handing it to a local
model or reviewer. Mission construction binds its context query to the same record and freshness
scope used by the evidence packet.
The packet itself exposes validate_integrity() and validate_for_inputs(...); nested coverage,
graph, query, trial-landscape, molecular-coverage, reconciliation, queue, and freshness projections must retain
one bundle digest and exact persisted bounds before a local worker can consume the handoff. The
packet schema is bioprism-neurosurgery-real-data-evidence-packet/0.4; older /0.1, /0.2, and
/0.3 artifacts must be regenerated because the canonical trial, molecular, and identifier
reconciliation ledgers are now part of the digest-bound handoff.
The cross-specialty PubMed packet and reasoning context expose the same integrity and exact-replay
methods, so non-glioma lanes receive identical stale/tamper protection before local-model or
reviewer handoff.
The six-lane literature matrix, workbench, and portfolio reports are likewise digest-checked and
replayable against the supplied snapshot; a multi-lane handoff cannot silently drift from its
per-lane query, review queue, or specialty profile.
neurosurgery_real_data_autonomous_workflow composes the same packet into a deterministic,
restart-safe provenance → completeness → context review wave. It emits only source-addressable
metadata tasks (including explicit freshness-policy checks, stale-source refresh actions, and
bounded-projection expansion holds when a caller supplies an age clock or small result limits),
accepts a persisted human disposition report to resume work, keeps truncation and unresolved items
visible, and ends at a human-synthesis gate. If max_actions caps the workflow queue itself, the
same hold remains active so omitted context actions or the human-signoff gate cannot be mistaken
for a complete handoff; autonomous means orchestration, not clinical
prioritization or approval.
Persisted waves expose validate_integrity() and validate_for_inputs(...), verifying packet
binding, action dependency closure, bounded truncation, open-obligation counts, and exact snapshot
replay before another worker resumes them.
neurosurgery_specialty_evidence_map adds a lane-specific identity/spatial/functional/temporal
coverage map for glioma, cranial base, craniosynostosis, encephalocele, spina bifida, and Chiari.
It turns the generic route into an explicit specialist inventory while retaining source IDs,
timestamp coverage, conflicts, and uncollected dimensions; it never interprets observation values.
neurosurgery_real_data_draft_audit is the companion local-model boundary: it requires every
caller-owned draft claim to cite a record emitted by that packet, blocks patient-case and clinical-
action posture, and labels accepted rows grounded_for_human_review without pretending to
fact-check or clinically interpret claim text.
A separate six-specialty PubMed snapshot at
data/neurosurgery/neurosurgical_public_literature_snapshot.json
covers glioma, cranial base, craniosynostosis, encephalocele, spina bifida, and Chiari. Refresh it
with scripts/refresh_neurosurgical_public_literature.ps1,
validate it locally, and pass it to planWithPublicLiterature/plan_with_public_literature or the
neurosurgery_public_literature_query MCP tool. The route attaches only the requested specialty
lane as unverified citation metadata and still ends at human review; it never converts abstracts
into patient findings or clinical actions.
The checked-in snapshot has 145 source-hashed records and 138 abstracts across the six lanes.
Each PubMed lane uses a stable source ID across refreshes, keeping retrieval time and content
change auditable without manufacturing a new source identity on every run.
Python and TypeScript expose ReviewedPubMedRetrievalAdapter for a live, explicitly approved
acquisition of 1--6 fixed lanes. Its pure preflight binds the lane/query set, parser surface, and
transport configuration; execution permits exactly one PubMed ESearch → ESummary → EFetch
sequence per lane and enforces the resulting request ceiling plus per-response, aggregate-byte,
tree, record, and bundle bounds. EFetch accepts and strips only the allow-listed external NLM DTD
declaration before parsing and projection; entity declarations, alternate doctypes, and malformed
XML fail closed. The durable receipt retains source IDs, digests, and counts but excludes query
strings and article content. Deployments can supply their separately registered NCBI tool and
developer email only as a pair; both are placed on every request while durable artifacts retain
only a configured flag and integrity digest. The one-lane
create_reviewed_pubmed_autonomous_evidence_registration() /
createReviewedPubMedAutonomousEvidenceRegistration() helpers connect a reviewed single-lane plan
to the generic evidence runtime's acquire/project callbacks, validate the transient bundle and
receipt, and project only digest metadata without widening the approved source plan. This is the
first reviewed live-retrieval adapter, not general web research or evidence validation; broader
sources, shared coordination, uncertain-call reconciliation, evidence-quality enforcement, and
independent claim-integrity review remain deployment work.
Python and TypeScript also expose ReviewedCBioPortalRetrievalAdapter for two fixed public
catalogue lanes (gbm_tcga, lgg_tcga). After a network-free prepare() and literal dispatch
approval, it issues exactly two bounded GETs per selected study: the study summary and one sorted
SUMMARY molecular-profile page capped at 128 rows. It keeps only allow-listed study descriptors,
aggregate sample counts, and profile metadata; sample, patient, clinical, and molecular-value routes
are outside the plan. Plans bind the endpoint, fields, pagination, transport identity, and fixed
study set. Receipts bind the normalized catalogue and counts; autonomous evidence receives only
bundle/source digests. Full profile pages are refused as potentially truncated, missing counts remain
unknown, and source metadata stays transient. The public API is documented as beta and can change;
the adapter fails closed on identity, response, or profile-schema drift. See the official
API overview and
OpenAPI reference.
It supplies catalogue coverage, not evidence quality or exhaustive glioma discovery.
For a safe before/after refresh, use
scripts/run_neurosurgical_public_literature_refresh_review.ps1:
it validates the baseline, creates a separate candidate, runs the cross-specialty refresh audit,
and leaves promotion to an explicit human reviewer.
neurosurgery_literature_link_audit bridges the real glioma literature index to a selected
public-literature lane using exact PMID and normalized DOI identifiers only. It makes the
12 known glioma overlaps, unmatched bounded windows, metadata field drift, and identifier
conflicts explicit; it does not infer cohort identity, evidence quality, biology, or clinical
meaning. Use --literature-link-audit <real> <public>, Python literature_link_audit(), or
TypeScript literatureLinkAudit() for this provider-free, read-only human-review handoff.
neurosurgery_public_literature_integrity_audit is the pre-synthesis corpus gate: it audits
selected lanes for missing DOI/abstract/publication-type/MeSH metadata and duplicate normalized
DOIs, returning source-addressable issue rows and explicit truncation. Use
--public-literature-integrity-audit <public>, Python public_literature_integrity_audit(), or
TypeScript publicLiteratureIntegrityAudit(); it reports completeness obligations only and never
silently repairs, merges, scores, or clinically interprets records.
neurosurgery_public_literature_workbench provides the lane-complete reviewer navigation view
over the same validated snapshot, preserving per-lane profiles, source IDs, record/abstract
counts, and bounded integrity obligations. It is deterministic and provider-free (provider: none, network: false, synthetic_data: false) and does not turn coverage into a clinical score.
Each lane also reports non-exclusive metadata-derived design strata (human-indexed,
animal/preclinical, in-vitro/cell-line, review/synthesis, imaging/diagnostic, surgical/procedural,
developmental/genetic, outcome/follow-up, and interventional) with exact PMIDs. Overlap and
unclassified rows are review obligations, never evidence-quality grades or clinical conclusions.
For restart-safe cross-specialty refresh review, neurosurgery_public_literature_refresh_audit
compares two independently validated snapshots and composes a bounded source/PMID diff, the
six-lane coverage matrix, and optional caller-owned freshness posture. It reports changed field
names and stable/added/removed identities without copying abstract text, and never fetches, merges,
accepts, or promotes the candidate. Use the Rust CLI flag
--public-literature-refresh-audit <before> <after>, Python
public_literature_refresh_audit(), or TypeScript publicLiteratureRefreshAudit(); the report is
provider-free (provider: none, network: false) and remains a human-review handoff.
The neurosurgery_public_literature_evidence_packet and
neurosurgery_public_literature_draft_audit MCP tools (also available as
public_literature_evidence_packet() / publicLiteratureEvidencePacket() and
public_literature_draft_audit() / publicLiteratureDraftAudit()) make that corpus a bounded
local-model handoff: packet records are emitted with PMID/source links, and every accepted draft
claim must cite one of those emitted PMIDs. The result is only a structural
grounded_for_human_review posture; it is not abstract fact-checking, study-quality assessment,
or a clinical conclusion, and it requires no OpenAI key.
neurosurgery_public_literature_reasoning_context (also
public_literature_reasoning_context() / publicLiteratureReasoningContext()) renders that
packet into bounded, source-addressable context for a caller-owned local model. Abstract excerpts
remain explicitly untrusted, citation/character omissions are reported, and no provider, network,
API key, or clinical interpretation is involved. Public-literature missions include the same
public_literature_reasoning_context envelope automatically.
neurosurgery_public_literature_matrix adds a lane-complete reconnaissance pass: one bounded
query can fan out across selected specialties (or all six), while each lane keeps its own packet,
PMID identities, empty/truncation state, and digest. It reports corpus shape only; it does not merge
cohorts or infer cross-specialty biology.
Both SDKs also expose the typed glioma panel vocabulary, so assay provenance and explicit
missingness can be submitted without inventing a diagnostic label. The dependency-free
TypeScript SDK exports the same LocalNeurosurgicalAgent facade from typescript/.
For marker-level grounding, neurosurgery_glioma_molecular_map (Rust
glioma_molecular_map, Python glioma_molecular_map(), TypeScript gliomaMolecularMap()) maps
requested IDH1/IDH2, MGMT, EGFR, TERT, H3, 1p/19q, methylation, and related marker terms onto
exact records in the validated real-glioma and PubMed snapshots. It preserves caller assay
missingness, reports truncation and zero-hit review obligations, and never treats a literature or
population match as a patient result. The map is read-only, provider-free, network-free, and
human-review gated.
For real case handoff, neurosurgery_case_asset_manifest (Rust
NeurosurgicalAgent::case_asset_manifest, Python case_asset_manifest(), TypeScript
caseAssetManifest()) accepts a caller-owned, de-identified manifest for imaging series,
pathology, molecular assays, operative notes, functional/developmental assessments,
longitudinal outcomes, and anatomical models. Every entry is bound to a SHA-256 content digest,
source kind, explicit observation state, optional modality/body region, and an observation timepoint; the projection never
opens asset bytes, extracts identifiers, calls a provider, or interprets a scan/report. It refuses
synthetic manifests, direct identifiers, malformed digests, duplicate asset IDs, and specialty
drift, then emits deterministic per-kind coverage, missingness, provenance gaps, and a bounded
review queue. This is a real-data intake/provenance seam—not a pixel/content clinical parser—and
it always returns a human-review hold. When an archive can export standard DICOM JSON, use
neurosurgery_case_dicom_import (Rust NeurosurgicalAgent::case_dicom_import, Python
case_dicom_import(), TypeScript caseDicomImport(), or CLI --case-dicom-import) to project
bounded series metadata. It refuses patient-identifying tags and PixelData, ignores unknown/private
tags, never opens DICOM bytes, and turns missing UIDs, dates, modality, body region, or object-byte
digests into explicit reviewer obligations.
Reports now include an ordered, typed research worklist that separates missing caller evidence from
uninterpretable or conflicting evidence and names the observations and reviewer roles needed for
the next review step; it never schedules a test or recommends care.
Its runResearchMission/run_research_mission helper composes catalogue discovery, optional
real-bundle querying, optional case-asset provenance, and the bounded session lifecycle; glioma
missions require a validated public bundle and always return a human-review hold. Pass the
de-identified manifest with caseAssetManifest/case_asset_manifest (or the CLI
--case-asset-manifest flag) to carry metadata-only multimodal provenance in the mission; the
evidence_synthesis.case_asset_report_digest field binds that projection into the same ledger;
evidence_synthesis.case_asset_summary also exposes asset/observation/provenance counts, requested
kinds still missing, review-item counts, and truncation without exposing asset bytes or identifiers.
When present, evidence_synthesis.case_asset_review_items carries the bounded digest-only review
obligations themselves.
Pass a persisted case_asset_review_disposition with the mission to carry reviewer progress
forward; the mission audit verifies its manifest/synthesis bindings and leaves unresolved or
undecided items visible as workflow state.
neurosurgery_case_asset_review_disposition (Rust
NeurosurgicalAgent::case_asset_review_disposition, Python case_asset_review_disposition(),
TypeScript caseAssetReviewDisposition()) applies caller-owned reviewed, unresolved, or
not_applicable state to returned review-item sequence numbers. The resulting ledger is bound to
the manifest report_digest, canonicalizes decision order, rejects duplicate/unknown sequences,
and keeps omitted or undecided obligations pending. It stores no local IDs, asset bytes, secrets,
clinical meaning, or external workflow state.
The direct evidence-synthesis MCP tool and SDK facades accept that persisted ledger alongside the
same manifest projection; digest/count mismatches fail closed, while the resulting synthesis
exposes only the disposition digest and pending/resolved/unresolved counts for resumable human
review.
The offline CLI supports the same