{"data":{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:26933193", "kind": "science-record", "revision": 7, "content_hash": "sha256:176602dc996d61269aa097f77a59379203e97e1a2c8e875470bbaff58acbae63", "created_at": "2026-11-01T15:40:16Z", "updated_at": "2026-11-01T21:58:54Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Adjuvant-induced Human Monocyte Secretome Profiles Reveal Adjuvant- and Age-specific Protein Signatures.", "doi": "10.1074/mcp.M115.055541", "pmid": "26933193", "authors": ["Djin-Ye Oh", "David J Dowling", "Saima Ahmed", "Hyungwon Choi", "Spencer Brightman", "Ilana Bergelson", "Sebastian T Berger", "John F Sauld", "Matthew Pettengill", "Alvin T Kho", "Henry J Pollack", "Hanno Steen", "Ofer Levy"], "journal": "Molecular & cellular proteomics : MCP", "year": 2016, "abstract": "Adjuvants boost vaccine responses, enhancing protective immunity against infections that are most common among the very young. Many adjuvants activate innate immunity, some via Toll-Like Receptors (TLRs), whose activities varies with age. Accordingly, characterization of age-specific adjuvant-induced immune responses may inform rational adjuvant design targeting vulnerable populations. In this study, we employed proteomics to characterize the adjuvant-induced changes of secretomes from human newborn and adult monocytes in response to Alum, the most commonly used adjuvant in licensed vaccines; Monophosphoryl Lipid A (MPLA), a TLR4-activating adjuvant component of a licensed Human Papilloma Virus vaccine; and R848 an imidazoquinoline TLR7/8 agonist that is a candidate adjuvant for early life vaccines. Monocytes were incubated in vitro for 24 h with vehicle, Alum, MPLA, or R848 and supernatants collected for proteomic analysis employing liquid chromatography-mass spectrometry (LC-MS) (data available via ProteomeXchange, ID PXD003534). 1894 non-redundant proteins were identified, of which ∼30 - 40% were common to all treatment conditions and ∼5% were treatment-specific. Adjuvant-stimulated secretome profiles, as identified by cluster analyses of over-represented proteins, varied with age and adjuvant type. Adjuvants, especially Alum, activated multiple innate immune pathways as assessed by functional enrichment analyses. Release of lactoferrin, pentraxin 3, and matrix metalloproteinase-9 was confirmed in newborn and adult whole blood and blood monocytes stimulated with adjuvants alone or adjuvanted licensed vaccines with distinct clinical reactogenicity profiles. MPLA-induced adult monocyte secretome profiles correlated in silico with transcriptome profiles induced in adults immunized with the MPLA-adjuvanted RTS,S malaria vaccine (Mosquirix™). Overall, adjuvants such as Alum, MPLA and R848 give rise to distinct and age-specific monocyte secretome profiles, paralleling responses to adjuvant-containing vaccines in vivo Age-specific in vitro modeling coupled with proteomics may provide fresh insight into the ontogeny of adjuvant action thereby informing targeted adjuvanted vaccine development for distinct age groups.", "claims": [{"id": "claim-method", "statement": "Proteins enriched after adjuvant treatment but not medium treatment were identified employing a customized version of the model-based statistical analysis tool QSpec based on SpC, using the count data model with paired design option and normalization by the total number of SpC in each sample replicate (45).", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:26933193", "locator": "sections[17] \"Label-free Protein Quantification and Analysis of Differential Protein Expression\" paragraph 2", "quote": "Proteins enriched after adjuvant treatment but not medium treatment were identified employing a customized version of the model-based statistical analysis tool QSpec based on SpC, using the count data model with paired design option and normalization by the total number of SpC in each sample replicate (45)."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The mass spectrometry proteomics data have been deposited to the ProteomeXchange Consortium (40) via the PRIDE partner repository with the data set identifier PXD003534 and 10.6019/PXD003534.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:26933193", "locator": "sections[14] \"LC-MS Analysis\" paragraph 2", "quote": "The mass spectrometry proteomics data have been deposited to the ProteomeXchange Consortium (40) via the PRIDE partner repository with the data set identifier PXD003534 and 10.6019/PXD003534."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "partial", "objective": null, "steps": [{"id": "read_published_estimate", "order": 1, "name": "Read the published estimate from the source", "kind": "other", "state": "complete", "blocked_on": null, "description": "The claim, method and evidence span published with the source article.", "duration_hours": null, "parameters": {}, "inputs": ["source:pmid:26933193"], "outputs": ["the published estimate and its evidence"], "instruments": [], "reagents": []}, {"id": "obtain_source_data", "order": 2, "name": "Obtain the source data from the named repository", "kind": "data-preparation", "state": "complete", "blocked_on": null, "description": "The GEO series accession resolves and its sample accessions are listed. This lane did not download the dataset or read its licence.", "duration_hours": null, "parameters": {}, "inputs": ["data:geo:PXD003534"], "outputs": ["the source data with its repository provenance"], "instruments": [], "reagents": []}, {"id": "run_analysis", "order": 3, "name": "Run the published analysis", "kind": "analysis", "state": "blocked", "blocked_on": "method:group_comparison_wilcoxon", "description": "Apply the paper's statistical method to the resolved series and compare the result with the published target.", "duration_hours": null, "parameters": {}, "inputs": ["data:geo:PXD003534"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": ["step:run_analysis blocked on method:group_comparison_wilcoxon"]}, "data": {"state": "partial", "assets": [{"id": "source:pmid:26933193", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.1074/mcp.M115.055541", "sha256": "sha256:9ae10aa2cd0abee208e4ce2fae961a07a902dfdca65d206b4d564eeb48b6c6dc", "bytes": 78153, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.1074/mcp.M115.055541", "version": null, "note": "Full article fetched from PMC; 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Ingenuity Pathway Analysis (IPA) was used to identify canonical pathways represented in the sets of adjuvant-induced proteins (n = 7 newborns and n = 6 adults). Proteins significantly up-regulated in the Alum-, MPLA-, and R848-induced secretomes. Shown are only those pathways represented by more than one protein in at least one of the adult/newborn datasets, with a p value < 0.05 per IPA; disease-specific pathways are excluded from the graph", "structure": {"pmcid": "PMC5083103", "section_index": 28, "section_title": "Pathway Analysis", "row_count": 165, "column_count": 4}, "table": {"label": "Table III", "caption": "Monocyte secretomes demonstrate activation of distinct canonical pathways varying by adjuvant and age. Ingenuity Pathway Analysis (IPA) was used to identify canonical pathways represented in the sets of adjuvant-induced proteins (n = 7 newborns and n = 6 adults). Proteins significantly up-regulated in the Alum-, MPLA-, and R848-induced secretomes. Shown are only those pathways represented by more than one protein in at least one of the adult/newborn datasets, with a p value < 0.05 per IPA; disease-specific pathways are excluded from the graph", "rows": [["Treatment", "Pathways", "-log10 (p value)", "Significantly up in newborn/adult"], ["Adult alum", "Caveolar-mediated endocytosis signaling", "2.56", "Yes"], ["", "Integrin signaling", "1.72", "Yes"], ["", "Actin cytoskeleton signaling", "1.66", "No"], ["", "MSP-RON signaling pathway", "1.31", "Yes"], ["Adult MPLA", "Acute phase response signaling", "1.24", "Yes"], ["", "LXR/RXR Activation", "8.56", "Yes"], ["", "Coagulation system", "6.39", "No"], ["", "Granulocyte adhesion and diapedesis", "6.22", "Yes"], ["", "Caveolar-mediated endocytosis signaling", "6.15", "Yes"], ["", "Leukocyte extravasation signaling", "5.70", "Yes"], ["", "Complement system", "4.96", "Yes"], ["", "FXR/RXR Activation", "4.75", "Yes"], ["", "Communication between innate and adaptive immune cells", "4.53", "Yes"], ["", "Extrinsic prothrombin activation pathway", "4.36", "No"], ["", "Dendritic cell maturation", "4.02", "No"], ["", "Agranulocyte adhesion and diapedesis", "3.93", "Yes"], ["", "IL-8 Signaling", "3.83", "Yes"], ["", "Intrinsic prothrombin activation pathway", "3.61", "No"], ["", "Antigen presentation pathway", "3.25", "No"], ["", "Inhibition of matrix metalloproteases", "3.22", "No"], ["", "Virus entry via endocytic pathways", "3.21", "Yes"], ["", "Glucocorticoid receptor signaling", "3.03", "No"], ["", "Paxillin signaling", "3.03", "Yes"], ["", "Dermatan sulfate degradation (Metazoa)", "2.78", "No"], ["", "Agrin interactions at neuromuscular junction", "2.50", "Yes"], ["", "IL-10 Signaling", "2.48", "Yes"], ["", "TREM1 signaling", "2.45", "Yes"], ["", "TR/RXR activation", "2.21", "No"], ["", "Crosstalk between dendritic cells and natural killer cells", "2.16", "Yes"], ["", "Cytotoxic T lymphocyte-mediated apoptosis of target cells", "2.09", "No"], ["", "Inhibition of angiogenesis by TSP1", "2.07", "Yes"], ["", "IL-6 signaling", "1.84", "Yes"], ["", "Role of PRRs in recognition of bacteria and viruses", "1.82", "Yes"], ["", "Hematopoiesis from pluripotent stem cells", "1.80", "No"], ["", "Relaxin signaling", "1.70", "Yes"], ["", "Role of cytokines in mediating Communication between immune cells", "1.66", "Yes"], ["", "melatonin signaling", "1.45", "No"], ["", "Macropinocytosis signaling", "1.45", "Yes"], ["", "Endothelin-1 signaling", "1.43", "No"], ["", "Ephrin receptor signaling", "1.40", "No"], ["", "NF-κB activation by viruses", "1.39", "Yes"], ["", "Toll-like receptor signaling", "1.39", "Yes"], ["", "Production of nitric oxide and reactive oxygen species in macrophages", "1.36", "No"], ["", "Integrin-linked kinase signaling", "1.35", "Yes"], ["Adult R848", "Acute phase response signaling", "12.8", "Yes"], ["", "LXR/RXR activation", "10.2", "Yes"], ["", "Granulocyte adhesion and diapedesis", "8.84", "Yes"], ["", "Agranulocyte adhesion and diapedesis", "6.21", "Yes"], ["", "FXR/RXR activation", "6.08", "Yes"], ["", "Leukocyte extravasation signaling", "5.89", "Yes"], ["", "Complement system", "5.05", "No"], ["", "IL-8 signaling", "4.98", "Yes"], ["", "Coagulation system", "4.89", "No"], ["", "Inhibition of matrix metalloproteases", "4.75", "Yes"], ["", "Communication between innate and adaptive immune cells", "4.65", "Yes"], ["", "Extrinsic prothrombin activation pathway", "4.44", "No"], ["", "Glucocorticoid receptor signaling", "4.02", "Yes"], ["", "IL-6 signaling", "3.93", "Yes"], ["", "IL-10 signaling", "3.74", "Yes"], ["", "TREM1 signaling", "3.70", "Yes"], ["", "Intrinsic prothrombin activation pathway", "3.68", "No"], ["", "Dendritic cell maturation", "3.17", "No"], ["", "Paxillin signaling", "3.12", "Yes"], ["", "Chondroitin sulfate degradation (Metazoa)", "2.89", "No"], ["", "Role of cytokines in mediating communication between immune cells", "2.89", "Yes"], ["", "Dermatan sulfate degradation (Metazoa)", "2.83", "No"], ["", "Role of PRRs in recognition of bacteria and viruses", "2.82", "Yes"], ["", "Cytokine production in macrophages and Th cells by IL-17A/IL-17F", "2.61", "No"], ["", "Agrin interactions at neuromuscular junction", "2.57", "Yes"], ["", "Toll-like receptor signaling", "2.46", "Yes"], ["", "NF-κB signaling", "2.28", "Yes"], ["", "Crosstalk between dendritic cells and natural killer cells", "2.22", "Yes"], ["", "Clathrin-mediated endocytosis signaling", "2.15", "No"], ["", "Inhibition of angiogenesis by TSP1", "2.11", "Yes"], ["", "HIF1α signaling", "2.07", "Yes"], ["", "Oncostatin M signaling", "2.06", "Yes"], ["", "Integrin signaling", "2.06", "Yes"], ["", "IL-17A signaling in fibroblasts", "2.04", "Yes"], ["", "Hematopoiesis from pluripotent stem cells", "1.84", "No"], ["", "MSP-RON signaling pathway", "1.81", "Yes"], ["", "Macropinocytosis signaling", "1.49", "Yes"], ["", "NF-κB activation by viruses", "1.43", "Yes"], ["", "Integrin-linked kinase signaling", "1.41", "Yes"], 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The physical bench the paper used is not, so a physical validation cannot be run here."}, "data": {"tier": "R1", "reachable": true, "accessions": ["PXD003534", "10.6019/PXD003534"], "resolved_accessions": ["PXD003534"], "statements": ["The mass spectrometry proteomics data have been deposited to the ProteomeXchange Consortium (40) via the PRIDE partner repository with the data set identifier PXD003534 and 10.6019/PXD003534."], "basis": "The paper names PXD003534 in ProteomeXchange Consortium via the PRIDE partner repository and the accession resolves in the repository. No dataset was downloaded and no licence was read."}}, "can_run": {"dsl_operations": [], "assets": ["source:pmid:26933193", "data:geo:PXD003534", "asset:table:pmid:26933193:1", "asset:table:pmid:26933193:2", "asset:table:pmid:26933193:3", "asset:table:pmid:26933193:4"], "steps": []}, "must_build": {"dsl_operations": [{"operation": "group_comparison_wilcoxon", "unlocks_papers": null, "priority": null}], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:PXD003534"]}, "gaps": []}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": null, "independence": "same_provider"}, "evidence_check": {"method": "verbatim", "availability": "verbatim"}, "calls": 0, "usage": {}}, "human_critique": null, "stages": [{"id": "extraction", "state": "complete", "reader": "MiniMax-M3.1-Flash", "provider": "minimax"}], "gaps": ["review.independent_reader", "review.machine_critique", "review.human_critique"]}, "execution": {"state": "absent", "status": "not_run", "mode": null, "runs": [], "gaps": ["execution.not_run"]}, "provenance": {"entities": [{"id": "pmid:26933193", "type": "paper", "label": "pmid:26933193"}, {"id": "source:pmid:26933193", "type": "manuscript", "label": "PMID 26933193 full text"}, {"id": "data:geo:PXD003534", "type": "dataset", "label": "GEO PXD003534"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:26933193", "type": "paper", "label": "pmid:26933193"}, {"id": "source:pmid:26933193", "type": "manuscript", "label": "PMID 26933193 full text"}, {"id": "data:geo:PXD003534", "type": "dataset", "label": "GEO PXD003534"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-26933193", "type": "extraction", "used": ["source:pmid:26933193"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-PXD003534", "type": "accession_resolution", "used": ["data:geo:PXD003534"], "agent": "agent:corpus-assay-engine"}], "agents": [{"id": "agent:corpus-assay-engine", "type": "software", "label": "Corpus assay engine"}, {"id": "agent:minimax-reader", "type": "software", "label": "MiniMax literature reader"}], "source_run_id": "reading-sci-2026-11-01", "dsl_catalogue_fingerprint": "343fb30756ba6ec3", "capability_table_fingerprint": "2cb3e42f047d2ecf", "snapshot_id": "ba34b49490d9bfaf"}, "lineage": {"parent_id": "pmid:26933193", "parent_hash": "sha256:832553eae7f0c43b10b8af9ebb6dc6fbd729b2ddf8f2031e8383c4e27e9988d5", "fork_of": null, "generation": 6}, "gaps": ["asset:data:geo:PXD003534 licence not read", "asset:data:geo:PXD003534 not downloaded", "execution.not_run", "method.group_comparison_wilcoxon", "method.reader_named_unmapped", "review.human_critique", "review.independent_reader", "review.machine_critique", "step:run_analysis blocked on method:group_comparison_wilcoxon"], "assays": [{"role": "data_generation", "definition_id": "mass_spectrometry", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.99, "evidence": ["mic analysis employing liquid chromatography-mass spectrometry (LC-MS) (data available via ProteomeXchange,", "A, B, Distribution of proteins determined by LC-MS/MS in the supernatants of differentially treate", "wborn and adult human monocytes, we analyzed proteomic data sets using unsupervised two-way hierarc", "able populations. In this study, we employed proteomics to characterize the adjuvant-induced changes"], "order_basis": "paper_text_order:476", "id": "assay:1"}, {"role": "data_generation", "definition_id": "rna_seq", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.83, "evidence": ["secretome profiles correlated in silico with transcriptome profiles induced in adults immunized with th", "vant-induced secretome to adjuvanted-induced transcriptome, was from 24 adult study participants. Flow"], "order_basis": "paper_text_order:1821", "id": "assay:2"}, {"role": "data_generation", "definition_id": "animal_model", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.77, "evidence": ["ng responses to adjuvant-containing vaccines in vivo Age-specific in vitro modeling coupled with"], "order_basis": "paper_text_order:2102", "id": "assay:3"}, {"role": "data_generation", "definition_id": "flow_cytometry", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.93, "evidence": ["ptome, was from 24 adult study participants. Flow cytometry analysis employed a MoFlo Legacy cytometer ("], "order_basis": "paper_text_order:4880", "id": "assay:4"}, {"role": "data_generation", "definition_id": "cell_culture", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.77, "evidence": ["ied in the supernatants from CD14+ monocytes cultured in the presence of Alum (5 μg/ml), MPLA (100 -"], "order_basis": "paper_text_order:7504", "id": "assay:5"}, {"role": "analysis", "definition_id": "group_comparison", "definition_version": "f2132e96ae6c7a4e", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"dsl_catalogue": "f2132e96ae6c7a4e"}, "confidence": 0.8, "evidence": ["Wilcoxon"], "order_basis": "consumes_earlier_output", "id": "assay:6"}]},"meta":{"api_version":"v1","automation_ladder_snapshot":"ba34b49490d9bfaf","automation_ladder_caveats":["Method extraction is rule-based and has no hand-judged accuracy sample. Evidence bands order textual support; method agreement intervals are null (n=0), never probabilities. Work-type validation does not validate methods.","Operation coverage describes only explicitly named methods. It does not prove a complete protocol, compatible parameters, successful compilation or re-execution. Unrecognised or ambiguous methods require review.","Data reachability is a textual accession or public-data statement. No dataset was downloaded or checked for access, completeness or licence.","Capabilities are planning states seeded from the dated equipment register. No bench ownership, completed quote or partner booking is inferred. Procurement counts are dependencies, not guaranteed replications or financial returns.","Tier and blocker counts are deterministic assessments of this corpus, not measured agreement. R3 is reserved for procurement; unresolved methods and data require human work (R4). The most restrictive axis wins, with capability, method, data as tie-breaks. Resolving one blocker can leave another at the same tier."],"engine":"corpus_engine","engine_provider":"rule_based_v1+lex99e1195c7d6f","run_id":"run-20261023T122449232913","source":"esearch","source_detail":"PubMed mirror biomed_pubmed (read-only)","run_status":"complete","imported_at":"2026-11-03T20:16:52+00:00","generated_at":"2026-11-04T02:44:43+00:00","total_papers":5529,"total_assays_tracked":29,"automatable_assay_families":6,"validated":true,"caveat_count":9,"blocking_caveats":5,"caveats":[{"code":"low_evidence_dominates","basis":["4,152 of 5,529 classifications (75.1%) matched no cue evidence and sit at the 0.05 floor.","34 of 230 data_only calls (14.8%) are in that group."],"claim":"Work type and confidence bands","gloss":"Most records were classified from their title and framing alone, with assay-cue coverage at zero.","detail":"Most classifications in this run rest on no matched evidence at all. At the evidence floor the work type comes from title framing and a fixed prior, not from anything in the paper, so the published work-type split should be read as a rough triage signal rather than a measured distribution. The impact is bounded but not removed: since 2026-10-23 the engine excludes floor-confidence records from the shortlist entirely and publishes them separately as held out, so the recommendation is unaffected even though the census is.","status":"unverified","severity":"high"},{"code":"runtime_is_modelled","basis":["Runtime is summed from published per-assay hour figures. Timing awaits the first executed replication.","4,407 of 5,529 records (79.7%) model to 0.00 hours because no assay was matched, which the ranking then reads as \"cheapest\".","0 of 10 shortlisted records carry a 0.00-hour estimate."],"claim":"Estimated replication runtime","gloss":"The hour figures are estimates built from assay mentions; timing awaits the first executed replication.","detail":"The hour figures are a cost model derived from the bench steps implied by each matched assay family. The first executed replication will supply measured timing. Records without an assay match currently receive a zero-hour model value.","status":"unverified","severity":"high"},{"code":"signal_score_without_citations","basis":["5,529 of 5,529 records (100.0%) have no citation count from the source metadata."],"claim":"Signal score","gloss":"The signal score uses publication-type weight because the mirror supplied zero citation counts.","detail":"The source supplied no citation counts for any record in this run, so the signal score is publication-type weight only. The citation term of the ranking is inert here, and the shortlist is ordered by publication type alone.","status":"unverified","severity":"high"},{"code":"abstract_absent","basis":["1,667 of 5,529 records (30.2%) carry no abstract at all."],"claim":"Evidence base for classification","gloss":"Some records contain a title and publication type only, defining the available classification evidence.","detail":"Where the mirror contains a title and publication types only, those fields define the classifier evidence. A methods section is required for fuller automated and human review.","status":"unverified","severity":"medium"},{"code":"classifier_agreement_measured","basis":["Published two-way decision agreement 77.7% (310 of 399 decidable records) from a stratified hand-check of 438 real records.","Three-way diagnostic agreement 73.9% (288 of 390 decidable records).","data_only agreement 75.2% (100 of 133 decidable).","48 record(s) could not be decided from title and abstract and were excluded from the denominator.","56 analysis-only records were published under another work type, so the data_only share is not an upper bound."],"claim":"Published automatable decision","gloss":"This figure has been checked against a human reading the same papers, so we know how often it is right.","detail":"The published automatable / not-automatable distribution comes from a rule-based classifier that was hand-checked against a fixed ground-truth definition. The agreement rates below are measured, not estimated. The three-way work type remains a diagnostic and is reported separately.","status":"measured","severity":"high"},{"code":"llm_comparison_not_measured","basis":["rule_based_v1+lex99e1195c7d6f produced 5,529 of 5,529 classifications.","Measured on 438 labelled records; these are RULE-BASED figures, not model results."],"claim":"Rule-based versus LLM agreement","gloss":"Every number here is the rule engine’s own. Model comparison begins when a working API credential is connected and measured.","detail":"The published two-way decision agreed with a human reading on 310 of 399 decidable records (77.7%). The diagnostic three-way label agreed on 288 of 390 decidable records (73.9%). Every percentage in this run belongs to the rule engine. Model comparison begins when a working API credential is connected and measured.","status":"not_measured","severity":"high"},{"code":"confidence_is_a_band","basis":["low band: 135 of 210 hand-judged records were correct, 64.3% [57.6, 70.5] (95% CI).","medium band: 80 of 104 hand-judged records were correct, 76.9% [68.0, 84.0] (95% CI).","high band: 73 of 76 hand-judged records were correct, 96.0% [89.0, 98.7] (95% CI).","A fitted calibrated probability was built, measured and withdrawn: it overstated held-out accuracy and reorders nothing."],"claim":"Confidence band and evidence score","gloss":"The confidence band carries a measured accuracy interval; 0.85 represents relative rank strength.","detail":"Confidence on this run is a BAND plus its measured accuracy interval. The number stored alongside each record is a monotone evidence score that orders records; 0.85 represents relative rank strength. A fitted probability was withdrawn after it overstated held-out accuracy. Threshold on the band.","status":"measured","severity":"medium"},{"code":"three_way_split_is_diagnostic","basis":["The corpus is published at the two-way decision: automatable or not-automatable. The three-way split (data_only / physical / mixed) is published as a diagnostic with its measured reliability attached, not as a claim, because the rule engine's `mixed` call cannot be defended.","The engine called 22 record(s) mixed; 10 matched the human judgement (45.5%, 95% CI 26.9-65.3).","The engine's `mixed` call is right on 10/22 hand-judged records (45.5%, 95% CI 26.9%-65.3%); a constant `physical` guess scores 36.4%.","The engine's `mixed` call does not reliably beat a constant `physical` guess on the hand-judged records it labels mixed.","The sign of that difference flips between two independent samples, so the three-way refinement is not demonstrably informative.","The mixed stratum contributes a disproportionate share of errors relative to its size.","At title-only depth the physical/mixed split collapses: a title says that work was done, not whether it was also analysed."],"claim":"The published decision is two-way","gloss":"The three-way split is shown for diagnosis only. The published split is two ways.","detail":"Count and filter the corpus on automatable versus not-automatable. The data_only / physical / mixed split remains an internal engine diagnostic because the mixed call has lower measured reliability.","status":"measured","severity":"medium"},{"code":"automatable_flag_unproven","basis":["6 of 29 assay families are marked automatable now: meta_analysis, machine_learning, survival_analysis, pca, molecular_docking, differential_expression.","The flag is a rule over assay family and work type; validation begins with the first executed replication.","It inherits the 75.2% data_only agreement rate, because the flag requires the record to be analysis-only."],"claim":"Automatable now","gloss":"This flag marks assay families the rules classify as data-only. The first executed replication will validate it.","detail":"This flag marks families the rules consider replicable from data alone. Its validity depends on the analysis-only classification and will be measured through an executed replication.","status":"unverified","severity":"medium"}],"confidence_policy":"band_with_measured_interval","confidence_contract":{"policy":"band_with_measured_interval","summary":"Confidence is reported as a BAND with a measured accuracy interval. The raw evidence score supplies monotone ordering. A fitted point estimate was withdrawn after it overstated held-out accuracy.","evidence_score":"A monotone evidence score in [0,1] built from cue mass, axis separation and text coverage. Use it to order records. Interpret 0.85 as relative rank strength.","confidence_band":"low | medium | high. Consumers threshold on this value.","band_accuracy":"Wilson 95% interval on the measured agreement of the hand-judged records in this band.","calibrated_confidence":"WITHDRAWN. Reintroduction requires held-out evidence demonstrating reliable estimates across every bin."},"band_accuracy":{"low":{"n":210,"low":0.576,"band":"low","high":0.7046,"agree":135,"accuracy":0.6429},"high":{"n":76,"low":0.8903,"band":"high","high":0.9865,"agree":73,"accuracy":0.9605},"medium":{"n":104,"low":0.6795,"band":"medium","high":0.8397,"agree":80,"accuracy":0.7692}},"provider":"rule_based_v1+lex99e1195c7d6f","lexicon_id":"99e1195c7d6f","contract_published_at":"2026-10-23T12:25:29.022232+00:00","confidence_is_band":true,"confidence_is_probability":false,"decision_taxonomy":"two_way","decidable_fraction_two_way":0.8854,"decidable_fraction_two_way_low":0.8565,"decidable_fraction_two_way_high":0.9143,"decidable_fraction_three_way":0.8586,"decidable_fraction_three_way_low":0.8287,"decidable_fraction_three_way_high":0.8884,"decidable_population":5529,"validation_sample_size":438,"three_way_cost_fraction":0.0268,"three_way_cost_records":148,"decision_counts":{"automatable":230,"not_automatable":5299},"decision_split":{"automatable":{"count":230,"share":0.04159884246699222},"not_automatable":{"count":5299,"share":0.9584011575330078}},"diagnostic_work_type_counts":{"mixed":24,"physical":5275,"data_only":230}}}