{"data":{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:32671099", "kind": "science-record", "revision": 7, "content_hash": "sha256:51e78bc4cf22f323b3f0ddfc948aa72c33f16a598f8d7ada04e7e387760405ad", "created_at": "2026-11-01T15:41:06Z", "updated_at": "2026-11-01T22:01:55Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Comparative Platelet Releasate Proteomic Profiling of Acute Coronary Syndrome versus Stable Coronary Artery Disease.", "doi": "10.3389/fcvm.2020.00101", "pmid": "32671099", "authors": ["Patricia B Maguire", "Martin E Parsons", "Paulina B Szklanna", "Monika Zdanyte", "Patrick Münzer", "Madhumita Chatterjee", "Kieran Wynne", "Dominik Rath", "Shane P Comer", "Melanie Hayden", "Fionnuala Ní Áinle", "Meinrad Gawaz"], "journal": "Frontiers in cardiovascular medicine", "year": 2020, "abstract": "Upon activation, platelets release a host of soluble and vesicular signals, collectively termed the \"platelet releasate\" (PR). The contents of this PR play a significant role in haemostasis, inflammation, and pathologic sequelae. Despite this, proteomic studies investigating the PR in coronary artery disease have not been performed. Here, we undertook a comparative label-free quantitative (LFQ) proteomic profiling of the 1 U/ml thrombin-induced PR from 13 acute coronary syndrome vs. 14 stable angina pectoris patients using a tandem mass spectrometry approach. Data are available via ProteomeXchange with identifier PXD009356. 318 PR proteins were identified across both cohorts with 9 proteins found to be differentially released, including tetranectin (CLEC3B), protein disulfide-isomerase-A3 (PDIA3), coagulation factor V (F5), and fibronectin (FN1). Strikingly, these 9 differential proteins were all associated with the gene ontology cellular component term \"extracellular vesicle\" and reduced levels of EVs were detected in the corresponding plasma of ST-segment elevation myocardial infarction (STEMI) patients. Network analysis revealed 3 proteins either reduced (F5; FN1) or absent (CLEC3B) in the PR of STEMI patients that are strongly connected to both the clotting cascade and major druggable targets on platelets. This moderated proteomic signature may prove useful for non-invasive risk assessment of the progression of coronary artery disease. These data further contribute to the growing evidence-base of using the platelet releasate as a predictor of pathological state and disease severity.", "claims": [{"id": "claim-method", "statement": "The alteration in the secretion levels of the remaining 14 proteins (difference between the mean log2 LFQ values >1/1) were evaluated for statistical significance (p < 0.05) utilizing Student's t-test analysis with an FDR value of 0.05 and an S0 correction factor of 0.1, denoted by the black hyperbolic lines (Figure 2C) (24).", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:32671099", "locator": "sections[7] \"Results\" paragraph 4", "quote": "The alteration in the secretion levels of the remaining 14 proteins (difference between the mean log2 LFQ values >1/1) were evaluated for statistical significance (p < 0.05) utilizing Student's t-test analysis with an FDR value of 0.05 and an S0 correction factor of 0.1, denoted by the black hyperbolic lines (Figure 2C) (24)."}], "state": "complete"}, {"id": "claim-data-access", "statement": "Raw MS data has been deposited to the ProteomeXchange Consortium via the PRIDE partner repository with the dataset identifier PXD009356.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:32671099", "locator": "sections[6] \"Protein ID, Quantification, and Statistical Rationale\" paragraph 2", "quote": "Raw MS data has been deposited to the ProteomeXchange Consortium via the PRIDE partner repository with the dataset identifier PXD009356."}], "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:32671099"], "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:PXD009356"], "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:student_t", "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:PXD009356"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": ["step:run_analysis blocked on method:student_t"]}, "data": {"state": "partial", "assets": [{"id": "source:pmid:32671099", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.3389/fcvm.2020.00101", "sha256": "sha256:90491cbd8b2de90581b294b1caf7825da41e7916b34dd3b38af2ca282ad4afab", "bytes": 36237, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.3389/fcvm.2020.00101", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC7328343", "source": "europe_pmc_fulltext", "coverage": "whole_body", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:PXD009356", "role": "raw", "format": "geo-series", "media_type": "application/vnd.ncbi.geo-series+json", "uri": "https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=PXD009356", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "PXD009356", "version": null, "note": "Raw MS data has been deposited to the ProteomeXchange Consortium via the PRIDE partner repository with the dataset identifier PXD009356.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "Raw MS data has been deposited to the ProteomeXchange Consortium via the PRIDE partner repository with the dataset identifier PXD009356.", "access_statement_kind": "data_availability_statement", "sample_accessions": [], "sample_count": null, "group_sizes": null, "group_sizes_basis": null, "platform": null, "taxon": null, "title": "Comparative platelet releasate proteome profiling of acute coronary syndrome versus stable coronary artery disease", "resolution_checked_at": "2026-10-31T18:35:55Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}, {"id": "asset:table:pmid:32671099:1", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:697c441b64585949acc9cd493f4acaeb51baf52d20e36fcb88beb9817709cb1a", "bytes": 2395, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[3]/table-wrap[1]#T1", "version": null, "note": "Patient demographics, cardiovascular risk factors, medication on admission and lipid profile parameters in those with STEMI and SAP.", "structure": {"pmcid": "PMC7328343", "section_index": 3, "section_title": "Patient Characteristics and Blood Sampling", "row_count": 26, "column_count": 5}, "table": {"label": "Table 1", "caption": "Patient demographics, cardiovascular risk factors, medication on admission and lipid profile parameters in those with STEMI and SAP.", "rows": [["Characteristics", "All (n = 27)", "STEMI (n = 13)", "SAP (n = 14)", "p-value"], ["Male n (%)", "21 (77.8%)", "11 (84.6%)", "10 (71.4%)", "0.678"], ["Age, years (mean ± SD)", "67.81 (±12.9)", "71.46 (± 11.8)", "64.42 (±13.5)", "0.163"], ["Body mass index (mean ± SD)", "27.31 (±4.0)", "25.23 (±2.6)", "28.44 (±4.3)", "0.116"], ["Cardiovascular risk factors"], ["Arterial Hypertension n (%)", "22 (81.5%)", "11 (84.6%)", "11 (78.6%)", "0.686"], ["Hyperlipidemia n (%)", "11 (40.7%)", "5 (38.5%)", "6 (42.9%)", "0.082"], ["Diabetes mellitus n (%)", "8 (29.6%)", "3 (23.1%)", "5 (35.7%)", "0.472"], ["Current smoking n (%)", "6 (22.2%)", "2 (15.4%)", "4 (28.6%)", "0.410"], ["Obesity n (%)", "6 (22.2%)", "1 (7.7%)", "5 (35.7%)", "0.080"], ["Renal function (GFR) (Mean ± SD)", "79.26 (±24.7)", "80.86 (±26.8)", "77.66 (±23.3)", "0.748"], ["Medication on admission"], ["Acetylsalicylic acid n (%)", "11 (40.7%)", "2 (15.4%)", "9 (64.3%)", "0.017"], ["Clopidogrel n (%)", "4 (14.81%)", "0 (0.0%)", "4 (28.6%)", "0.011"], ["Prasugrel n (%)", "1 (3.7%)", "0 (0.0%)", "1 (7.1%)", "0.024"], ["Ticagrelor n (%)", "1 (3.7%)", "0 (0.0%)", "1 (7.1%)", "0.024"], ["Oral anticoagulants n (%)", "3 (11.1%)", "0 (0.0%)", "3 (21.4%)", "0.014"], ["Angiotensin-converting enzyme inhibitors n (%)", "8 (29.6%)", "1 (7.7%)", "7 (50.0%)", "0.011"], ["Angiotensin II receptor antagonists n (%)", "4 (14.8%)", "2 (15.4%)", "2 (14.3%)", "0.372"], ["Beta-blockers n (%)", "13 (48.1%)", "3 (23.1%)", "10 (71.4%)", "0.016"], ["Statins n (%)", "10 (37.0%)", "1 (7.7%)", "9 (64.3%)", "0.004"], ["Lipid profile parameters"], ["Total cholesterol mg/dl (mean ± SD)mmol/l (mean ± SD)", "167.7 (±33.7) 4.4 (±0.9)", "169.0 (±37.0) 4.4 (±1.0)", "166.6 (±32.3) 4.3 (±0.8)", "0.872"], ["LDL-cholesterol mg/dl (mean ± SD)mmol/l (mean ± SD)", "103.3 (±32.1) 2.7 (±0.8)", "106.9 (±39.1) 2.8 (±1.0)", "101.2 (±28.9) 2.6 (±0.7)", "0.721"], ["HDL-cholesterolmg/dl (mean ± SD)mmol/l (mean ± SD)", "44.1 (±15.1) 1.1 (±0.4)", "39.3 (±21.2) 1.1 (±0.5)", "46.0 (±10.3) 1.2 (±0.3)", "0.324"], ["Triglyceridesmg/dl (mean ± SD)mmol/l (mean ± SD)", "138.8 (±67.0) 1.6 (±0.8)", "123.0 (±70.7) 1.4 (±0.8)", "152.0 (±63.7) 1.7 (±0.7)", "0.306"]], "row_count": 26, "column_count": 5, "numeric_cells": 91, "header_rows": 1, "locator": "section[3]/table-wrap[1]#T1"}}, {"id": "asset:table:pmid:32671099:2", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:de4109ced104bb11a93930e4068655a6301e752742d91e4c88f9ce59eee99d4a", "bytes": 2131, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[7]/table-wrap[1]#T2", "version": null, "note": "9 PR proteins differentially released in STEMI vs. SAP.", "structure": {"pmcid": "PMC7328343", "section_index": 7, "section_title": "Results", "row_count": 14, "column_count": 6}, "table": {"label": "Table 2", "caption": "9 PR proteins differentially released in STEMI vs. SAP.", "rows": [["Gene name", "Protein name", "SAP log2 LFQ", "STEMI log2 LFQ", "Difference (mean log2 LFQ values)", "Function"], ["Proteins unique to STEMI"], ["FAH", "Fumarylacetoacetase", "NaN", "22.398", "NaN", "Final enzyme in the tyrosine catabolism pathway. FAH deficiency is associated with Type 1 hereditary tyrosinemia"], ["Proteins unique to SAP"], ["CLEC3B", "Tetranectin", "24.613", "NaN", "NaN", "Binds to Kringle 4 domain of plasminogen. May be involved in the packaging of molecules destined for exocytosis."], ["HSP90AA1", "Heat shock protein HSP 90-alpha", "24.132", "NaN", "NaN", "Molecular chaperone, involved in platelet activation. Extracellularly, mediates immune-regulatory & tissue remodeling."], ["Proteins with increased secretion in STEMI"], ["GPI", "Glucose-6-phosphate isomerase", "24.76", "26.013", "1.171", "Glycolytic enzyme. Can also function extracellularly as a cytokine, an angiogenic, or neurotrophic factor."], ["PDIA3", "Protein disulfide-isomerase A3", "26.026", "26.671", "1.093", "Protein folding, Molecular chaperone, secreted from platelets, Mediates platelet aggregation, haemostasis & thrombosis."], ["SAA1", "Serum amyloid A-1 protein", "22.977", "23.784", "2.692", "Major acute phase protein highly expressed in inflammation/tissue injury. Plays a role in HDL metabolism & cholesterol homeostasis. High levels associated with chronic inflammatory diseases including atherosclerosis."], ["SOD1", "Superoxide dismutase", "25.693", "27.181", "1.147", "One of two isozymes responsible for destroying free superoxide radicals in the body"], ["Proteins with decreased secretion in STEMI"], ["F5", "Coagulation factor V", "28.229", "27.63", "1.679", "Critical cofactor for the prothrombinase activity of Factor Xa that results in the activation of prothrombin to thrombin"], ["FN1", "Fibronectin", "29.416", "28.669", "2.768", "Component of subendothelial matrices and abundant in plasma. Important for stabilization of platelet aggregates after vascular injury."]], "row_count": 14, "column_count": 6, "numeric_cells": 27, "header_rows": 1, "locator": "section[7]/table-wrap[1]#T2"}}], "gaps": ["asset:data:geo:PXD009356 not downloaded", "asset:data:geo:PXD009356 licence not read"]}, "analysis": {"state": "partial", "methods": [{"id": "method-1", "family": "group_comparison", "specific": "student_t_test", "label": "Group comparison", "dsl_operations": [], "missing_operations": ["student_t"], "expressible": false, "parameters": {}, "data_shapes": ["two_or_more_groups_continuous"], "evidence": {"score": 1.0, "band": "verbatim", "quote": "The alteration in the secretion levels of the remaining 14 proteins (difference between the mean log2 LFQ values >1/1) were evaluated for statistical significance (p < 0.05) utilizing Student's t-test analysis with an FDR value of 0.05 and an S0 correction factor of 0.1, denoted by the black hyperbolic lines (Figure 2C) (24)."}}], "targets": [], "gaps": ["method.student_t"]}, "capability": {"state": "complete", "requirements": [{"capability_id": "capability:computational_analysis", "label": "Computational analysis platform", "assay_families": ["meta_analysis", "machine_learning", "survival_analysis", "statistical_regression", "pca", "molecular_docking", "network_analysis", "differential_expression", "gwas"], "availability_state": "owned", "tier_unlocked": "R1", "candidate": "Automated Assays Laravel application and simulated adapters"}], "gaps": []}, "readiness": {"state": "complete", "tier": "R1", "blocking_axis": "none", "blocked_on": "nothing:replicable_now", "axes": {"method": {"tier": "R1", "expressible": false, "required_operations": [], "missing_operations": ["student_t"], "basis": "The paper names the method it used and the corpus's method extractor maps it onto the DSL catalogue: student_t_test."}, "capability": {"tier": "R1", "capability_id": "capability:computational_analysis", "availability_state": "owned", "basis": "The computational analysis is owned. The physical bench the paper used is not, so a physical validation cannot be run here."}, "data": {"tier": "R1", "reachable": true, "accessions": ["PXD009356"], "resolved_accessions": ["PXD009356"], "statements": ["Raw MS data has been deposited to the ProteomeXchange Consortium via the PRIDE partner repository with the dataset identifier PXD009356."], "basis": "The paper names PXD009356 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:32671099", "data:geo:PXD009356", "asset:table:pmid:32671099:1", "asset:table:pmid:32671099:2"], "steps": []}, "must_build": {"dsl_operations": [{"operation": "student_t", "unlocks_papers": null, "priority": null}], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:PXD009356"]}, "gaps": []}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-10-31T18:21:02Z", "independence": "single_reader"}, "evidence_check": {"method": "verbatim", "availability": "verbatim"}, "calls": 3, "usage": {"prompt_tokens": 29541, "completion_tokens": 616, "cached_tokens": 792}}, "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:32671099", "type": "paper", "label": "pmid:32671099"}, {"id": "source:pmid:32671099", "type": "manuscript", "label": "PMID 32671099 full text"}, {"id": "data:geo:PXD009356", "type": "dataset", "label": "GEO PXD009356"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:32671099", "type": "paper", "label": "pmid:32671099"}, {"id": "source:pmid:32671099", "type": "manuscript", "label": "PMID 32671099 full text"}, {"id": "data:geo:PXD009356", "type": "dataset", "label": "GEO PXD009356"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-32671099", "type": "extraction", "used": ["source:pmid:32671099"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-PXD009356", "type": "accession_resolution", "used": ["data:geo:PXD009356"], "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:32671099", "parent_hash": "sha256:5c599ed3df57cf12968950419a3dd92b369a723bbd31120d285906a90d21adb9", "fork_of": null, "generation": 6}, "gaps": ["asset:data:geo:PXD009356 licence not read", "asset:data:geo:PXD009356 not downloaded", "execution.not_run", "method.student_t", "review.human_critique", "review.independent_reader", "review.machine_critique", "step:run_analysis blocked on method:student_t"], "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": ["Comparative Platelet Releasate Proteomic Profiling of Acute Coronary Syndrome versus", "tion, and pathologic sequelae. Despite this, proteomic studies investigating the PR in coronary art", "a comparative label-free quantitative (LFQ) proteomic profiling of the 1 U/ml thrombin-induced PR", "uggable targets on platelets. This moderated proteomic signature may prove useful for non-invasive"], "order_basis": "paper_text_order:0", "id": "assay:1"}, {"role": "analysis", "definition_id": "group_comparison", "definition_version": "f2132e96ae6c7a4e", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"dsl_catalogue": "f2132e96ae6c7a4e"}, "confidence": 1.0, "evidence": ["The alteration in the secretion levels of the remaining 14 proteins (difference between the mean log2 LFQ values >1/1) were evaluated for statistical significance (p < 0.05) utilizing Student's t-test analysis with an FDR value of 0.05 and an S0 correction factor of 0.1, denoted by the black hyperbolic lines (Figure 2C) (24)."], "order_basis": "consumes_earlier_output", "id": "assay:2"}]},"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":"2026-11-04T02:38:36+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}}}