{"data":{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:30370674", "kind": "science-record", "revision": 8, "content_hash": "sha256:92c090637c2364337dcf90faa977b640d8440f30c53591cd136d4f07ffbda74b", "created_at": "2026-11-01T15:40:38Z", "updated_at": "2026-11-01T22:43:36Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Characterisation of infection associated microRNA and protein cargo in extracellular vesicles of Theileria annulata infected leukocytes.", "doi": "10.1111/cmi.12969", "pmid": "30370674", "authors": ["Victoria Gillan", "Deborah M Simpson", "Jane Kinnaird", "Kirsty Maitland", "Brian Shiels", "Eileen Devaney"], "journal": "Cellular microbiology", "year": 2019, "abstract": "The protozoan parasites Theileria annulata and Theileria parva are unique amongst intracellular eukaryotic pathogens as they induce a transformation-like phenotype in their bovine host cell. T. annulata causes tropical theileriosis, which is frequently fatal, with infected leukocytes becoming metastatic and forming foci in multiple organs resulting in destruction of the lymphoid system. Exosomes, a subset of extracellular vesicles (EV), are critical in metastatic progression in many cancers. Here, we characterised the cargo of EV from a control bovine lymphosarcoma cell line (BL20) and BL20 infected with T. annulata (TBL20) by comparative mass spectrometry and microRNA (miRNA) profiling (data available via ProteomeXchange, identifier PXD010713 and NCBI GEO, accession number GSE118456, respectively). Ingenuity pathway analysis that many infection-associated proteins essential to migration and extracellular matrix digestion were upregulated in EV from TBL20 cells compared with BL20 controls. An altered repertoire of host miRNA, many with known roles in tumour and/or infection biology, was also observed. Focusing on the tumour suppressor miRNA, bta-miR-181a and bta-miR-181b, we identified putative messenger RNA targets and confirmed the interaction of bta-miR181a with ICAM-1. We propose that EV and their miRNA cargo play an important role in the manipulation of the host cell phenotype and the pathobiology of Theileria infection.", "claims": [{"id": "claim-method", "statement": "To increase the confidence of downstream analysis, in addition to statistical significance (ANOVA p ≤ 0.05), only those proteins identified by two or more unique peptides and exhibiting a fold change ≥2 were selected, resulting in a total of 479 significantly differentially expressed proteins.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:30370674", "locator": "sections[4] \"BL20‐EV and TBL20‐EV exhibit differences in protein composition/cargo\" paragraph 3", "quote": "To increase the confidence of downstream analysis, in addition to statistical significance (ANOVA p ≤ 0.05), only those proteins identified by two or more unique peptides and exhibiting a fold change ≥2 were selected, resulting in a total of 479 significantly differentially expressed proteins."}], "state": "complete"}, {"id": "claim-data-access", "statement": "data available via ProteomeXchange, identifier PXD010713 and NCBI GEO, accession number GSE118456, respectively", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:30370674", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "data available via ProteomeXchange, identifier PXD010713 and NCBI GEO, accession number GSE118456, respectively"}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "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:30370674"], "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:GSE118456"], "outputs": ["the source data with its repository provenance"], "instruments": [], "reagents": []}, {"id": "run_analysis", "order": 3, "name": "Run the published analysis", "kind": "analysis", "state": "complete", "blocked_on": null, "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:GSE118456"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:30370674", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.1111/cmi.12969", "sha256": "sha256:ddd4dd755fa35f672195216fd53fa589f613ffb3d4e14c2e352a73eb9673c5a8", "bytes": 63750, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.1111/cmi.12969", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC6492283", "source": "europe_pmc_fulltext", "coverage": "whole_body", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE118456", "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=GSE118456", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE118456", "version": null, "note": "data available via ProteomeXchange, identifier PXD010713 and NCBI GEO, accession number GSE118456, respectively", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "data available via ProteomeXchange, identifier PXD010713 and NCBI GEO, accession number GSE118456, respectively", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM3330473", "GSM3330474", "GSM3330475", "GSM3330476", "GSM3330477", "GSM3330478", "GSM3330479", "GSM3330480"], "sample_count": 8, "group_sizes": null, "group_sizes_basis": null, "platform": "19172", "taxon": "Bos taurus", "title": "miRNA profiling of extracellular vesicles from Theileria annulata infected B cells (TBL20) and their uninfected control counterparts (BL20)", "resolution_checked_at": "2026-11-01T15:39:54Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}, {"id": "data:geo:PXD010713", "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=PXD010713", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "PXD010713", "version": null, "note": "data available via ProteomeXchange, identifier PXD010713 and NCBI GEO, accession number GSE118456, respectively", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "data available via ProteomeXchange, identifier PXD010713 and NCBI GEO, accession number GSE118456, respectively", "access_statement_kind": "data_availability_statement", "sample_accessions": [], "sample_count": null, "group_sizes": null, "group_sizes_basis": null, "platform": null, "taxon": null, "title": "Bovine extracellular vesicle LC-MSMS C4PR_LIV", "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:30370674:1", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:0a9eed31f46f16a81544e21736655069c1db077255907c4f564ec3a1a4911b0e", "bytes": 1174, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[5]/table-wrap[1]#cmi12969-tbl-0001", "version": null, "note": "Host miRNA differentially expressed in TBL20‐EV compared with BL20‐EV", "structure": {"pmcid": "PMC6492283", "section_index": 5, "section_title": "BL20‐EV and TBL20‐EV exhibit differences in miRNA cargo", "row_count": 7, "column_count": 3}, "table": {"label": "Table 1", "caption": "Host miRNA differentially expressed in TBL20‐EV compared with BL20‐EV", "rows": [["microRNA", "Log2 (p value)", "Function"], ["bta‐miR‐222", "1.63 (p = 1.5E‐05)", "Oncogene in many human malignancies (Felicetti et al., 2016; Kara et al., 2015; Li et al., 2016; M. Wang et al., 2016)"], ["bta‐miR‐24‐3p", "2.66 (p = 1.5E‐05)", "Promotes cell proliferation and inhibits apoptosis in human breast cancer (Lu et al., 2015)"], ["bta‐miR‐27a‐3p", "3.39 (p = 3.3E‐05)", "Promotes cellular proliferation (Kara et al., 2015; Nakata et al., 2015; Wu et al., 2015)"], ["bta‐miR‐155", "2.94 (p = 9.3E‐04)", "Tumour associated miRNA (Faraoni, Antonetti, Cardone, & Bonmassar, 2009; Jurkovicova et al., 2014; Kara et al., 2015)"], ["bta‐miR‐146a", "2.76 (p = 4.3E‐05)", "Tumour associated miRNA (Petrovic, Davidovic, Bajic, Obradovic, & Isenovic, 2017; Sun et al., 2015)"], ["bta‐miR‐181a/b", "−1.35/−1.05 (p = 8E‐05/2E‐05)", "Tumour suppressors (Shi et al., 2008; H. Wang et al., 2015; Weng et al., 2015)"]], "row_count": 7, "column_count": 3, "numeric_cells": 18, "header_rows": 1, "locator": "section[5]/table-wrap[1]#cmi12969-tbl-0001"}}, {"id": "asset:table:pmid:30370674:2", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:91bdb033ff6cc8c0e1d6c815a0d915e30b43f46fd6c9dc336804b2d4c18e3b0c", "bytes": 1942, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[6]/table-wrap[1]#cmi12969-tbl-0002", "version": null, "note": "The top 15 upregulated proteins in TBL20‐EV compared with BL20‐EV and predicted bta‐miR‐181a and bta‐miR‐181b binding sites", "structure": {"pmcid": "PMC6492283", "section_index": 6, "section_title": "Computational analysis of bta‐miR‐181a and b mRNA targets", "row_count": 17, "column_count": 5}, "table": {"label": "Table 2", "caption": "The top 15 upregulated proteins in TBL20‐EV compared with BL20‐EV and predicted bta‐miR‐181a and bta‐miR‐181b binding sites", "rows": [["Gene", "Fold change (up in TBL20‐EV)", "q value", "No. of miR‐181a binding sites (combined ddG)", "No. of miR‐181b binding sites (combined ddG)"], ["VTA1_BOVIN Vacuolar protein sorting‐associated proteinb", "16.5", "3.13E‐08", "4(−2.99)", "3 (−5.37)"], ["ICAM‐1_BOVIN Intercellular adhesion molecule 1", "9.6", "4.96E‐08", "2 (−9.01)", "0"], ["NEUM_BOVIN Neuromodulin", "56.2", "7.06E‐08", "1 (2.51)", "1 (−4.86)"], ["TSN6_BOVIN Tetraspanin‐6b", "12.6", "8.72E‐08", "1 (−6)", "1 (−9)"], ["VPS4B_BOVIN Vacuolar protein sorting‐associated protein 4Bb", "9.5", "8.72E‐08", "2 (−4.88)", "2 (−6.32)"], ["MFGM_BOVIN Lactadherin", "6.6", "8.72E‐08", "0", "0"], ["SATT_BOVIN Neutral amino acid transporter A", "7.3", "1.85E‐07", "0", "1 (−6)"], ["ITA5_BOVIN Integrin alpha‐5", "6.1", "2.02E‐07", "0", "1 (0.7)"], ["IST1_BOVIN IST1 homologueb", "10.5", "2.58E‐07", "1 (2)", "3 (−9)"], ["TMEDA_BOVIN Transmembrane emp24 domain‐containing protein 10b", "5.4", "2.58E‐07", "3 (−4.51)", "3 (−4.1)"], ["VPS28_BOVIN Vacuolar protein sorting‐associated protein 28 homologueb", "6.8", "2.91E‐07", "3 (−4.13)", "1 (0.51)"], ["CHM1B_BOVIN Charged multivesicular body protein 1bb", "9", "3.00E‐07", "2 (0.2)", "3 (5.58)"], ["MMP‐9_BOVIN Matrix metalloproteinase‐9", "23.3", "9.12E‐07", "1 (−13.05)", "1 (−11.84)"], ["VAPA_BOVIN Vesicle‐associated membrane protein‐associated protein Ab", "10.4", "9.12E‐07", "2 (−4.76)", "2 (−5.83)"], ["MPP7_BOVIN MAGUK p55 Subfamily Member 7", "7.5", "9.12E‐07", "4 (−5.69)", "2 (−8.05)"], ["aHA1A_BOVIN BOLA‐1 Class I histocompatibility antigen, alpha chain", "3.8", "8.47E‐06", "2 (−11.95)", "2 (−14.5)"]], "row_count": 17, "column_count": 5, "numeric_cells": 77, "header_rows": 1, "locator": "section[6]/table-wrap[1]#cmi12969-tbl-0002"}}], "gaps": ["asset:data:geo:GSE118456 not downloaded", "asset:data:geo:GSE118456 licence not read", "asset:data:geo:PXD010713 not downloaded", "asset:data:geo:PXD010713 licence not read"]}, "analysis": {"state": "complete", "methods": [{"id": "method-1", "family": "group_comparison", "specific": "anova", "label": "Group comparison", "dsl_operations": ["group_summary", "welch_t", "bootstrap_mean_difference", "group_comparison_anova"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["two_or_more_groups_continuous"], "evidence": {"score": 1.0, "band": "verbatim", "quote": "To increase the confidence of downstream analysis, in addition to statistical significance (ANOVA p ≤ 0.05), only those proteins identified by two or more unique peptides and exhibiting a fold change ≥2 were selected, resulting in a total of 479 significantly differentially expressed proteins."}}], "targets": [], "gaps": []}, "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": true, "required_operations": ["group_summary", "welch_t", "bootstrap_mean_difference", "group_comparison_anova"], "missing_operations": [], "basis": "The paper names the method it used and the corpus's method extractor maps it onto the DSL catalogue: anova."}, "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": ["PXD010713", "10.6019/PXD010713", "GSE118456"], "resolved_accessions": ["PXD010713", "GSE118456"], "statements": ["data available via ProteomeXchange, identifier PXD010713 and NCBI GEO, accession number GSE118456, respectively"], "basis": "The paper names PXD010713, GSE118456 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": ["group_summary", "welch_t", "bootstrap_mean_difference", "group_comparison_anova"], "assets": ["source:pmid:30370674", "data:geo:GSE118456", "asset:table:pmid:30370674:1", "asset:table:pmid:30370674:2"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:GSE118456"]}, "gaps": []}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-10-31T18:12:39Z", "independence": "single_reader"}, "evidence_check": {"method": "verbatim", "availability": "verbatim"}, "calls": 3, "usage": {"prompt_tokens": 54908, "completion_tokens": 1489, "cached_tokens": 776}}, "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:30370674", "type": "paper", "label": "pmid:30370674"}, {"id": "source:pmid:30370674", "type": "manuscript", "label": "PMID 30370674 full text"}, {"id": "data:geo:GSE118456", "type": "dataset", "label": "GEO GSE118456"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:30370674", "type": "paper", "label": "pmid:30370674"}, {"id": "source:pmid:30370674", "type": "manuscript", "label": "PMID 30370674 full text"}, {"id": "data:geo:GSE118456", "type": "dataset", "label": "GEO GSE118456"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-30370674", "type": "extraction", "used": ["source:pmid:30370674"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-GSE118456", "type": "accession_resolution", "used": ["data:geo:GSE118456"], "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:30370674", "parent_hash": "sha256:a875500dfb552e266bee5883fe2ee1fb2d99b663a71db28b6da4deaa9feee02c", "fork_of": null, "generation": 7}, "gaps": ["asset:data:geo:GSE118456 licence not read", "asset:data:geo:GSE118456 not downloaded", "asset:data:geo:PXD010713 licence not read", "asset:data:geo:PXD010713 not downloaded", "execution.not_run", "review.human_critique", "review.independent_reader", "review.machine_critique"], "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": ["cted with T. annulata (TBL20) by comparative mass spectrometry and microRNA (miRNA) profiling (data availab", "cation was performed using Progenesis QI for Proteomics v.2.0 (Waters Ltd., Newcastle‐upon‐Tyne, Uni", "ween experimental groups. IPA was applied to proteomic data for functional clustering of proteins i", "described previously (Shiels et al., 1992). Proteomic sample preparation and LC–MS analysis Six bi"], "order_basis": "paper_text_order:739", "id": "assay:1"}, {"role": "analysis", "definition_id": "group_comparison", "definition_version": "f2132e96ae6c7a4e", "definition_digest": null, "required_operations": ["group_summary", "welch_t", "bootstrap_mean_difference", "group_comparison_anova"], "support_state": "supported", "source_hashes": {"dsl_catalogue": "f2132e96ae6c7a4e"}, "confidence": 1.0, "evidence": ["To increase the confidence of downstream analysis, in addition to statistical significance (ANOVA p ≤ 0.05), only those proteins identified by two or more unique peptides and exhibiting a fold change ≥2 were selected, resulting in a total of 479 significantly differentially expressed proteins."], "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":"2026-11-04T03:35:41+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}}}