{"data":{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:32336950", "kind": "science-record", "revision": 8, "content_hash": "sha256:0ed1beceff789ed9c070240e19cb1664bc9ea941a6b47e8bc3958c7bfb4dbd8a", "created_at": "2026-11-01T15:41:00Z", "updated_at": "2026-11-01T22:44:47Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Bioinformatics combined with quantitative proteomics analyses and identification of potential biomarkers in cholangiocarcinoma.", "doi": "10.1186/s12935-020-01212-z", "pmid": "32336950", "authors": ["Zijian Da", "Long Gao", "Gang Su", "Jia Yao", "Wenkang Fu", "Jinduo Zhang", "Xu Zhang", "Zhaoji Pei", "Ping Yue", "Bing Bai", "Yanyan Lin", "Wenbo Meng", "Xun Li"], "journal": "Cancer cell international", "year": 2020, "abstract": "BACKGROUND: Cholangiocarcinoma (CCA) is an invasive malignancy arising from biliary epithelial cells; it is the most common primary tumour of the bile tract and has a poor prognosis. The aim of this study was to screen prognostic biomarkers for CCA by integrated multiomics analysis.\nMETHODS: The GSE32225 dataset was derived from the Gene Expression Omnibus (GEO) database and comprehensively analysed by using R software and The Cancer Genome Atlas (TCGA) database to obtain the differentially expressed RNAs (DERNAs) associated with CCA prognosis. Quantitative isobaric tags for relative and absolute quantification (iTRAQ) proteomics was used to screen differentially expressed proteins (DEPs) between CCA and nontumour tissues. Through integrated analysis of DERNA and DEP data, we obtained candidate proteins APOF, ITGAV and CASK, and immunohistochemistry was used to detect the expression of these proteins in CCA. The relationship between CASK expression and CCA prognosis was further analysed.\nRESULTS: Through bioinformatics analysis, 875 DERNAs were identified, of which 10 were associated with the prognosis of the CCA patients. A total of 487 DEPs were obtained by using the iTRAQ technique. Comprehensive analysis of multiomics data showed that CASK, ITGAV and APOF expression at both the mRNA and protein levels were different in CCA compared with nontumour tissues. CASK was found to be expressed in the cytoplasm and nucleus of CCA cells in 38 (45%) of 84 patients with CCA. Our results suggested that patients with positive CASK expression had significantly better overall survival (OS) and recurrence-free survival (RFS) than those with negative CASK expression. Univariate and multivariate analyses demonstrated that negative expression of CASK was a significantly independent risk factor for OS and RFS in CCA patients.\nCONCLUSIONS: CASK may be a tumour suppressor; its low expression is an independent risk factor for a poor prognosis in CCA patients, and so it could be used as a clinically valuable prognostic marker.", "claims": [{"id": "claim-method", "statement": "Matrix files from the GSE32225 dataset were obtained from the GEO (https://www.ncbi.nlm.nih.gov/geo/) database. We used the “limma” package to identify DERNAs between CCA tissues and nontumour tissues [16].", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:32336950", "locator": "sections[3] \"Data obtaining and preprocessing\" paragraph 2", "quote": "Matrix files from the GSE32225 dataset were obtained from the GEO (https://www.ncbi.nlm.nih.gov/geo/) database."}, {"asset": "source:pmid:32336950", "locator": "sections[4] \"Identification of differentially expressed RNAs\" paragraph 2", "quote": "We used the “limma” package to identify DERNAs between CCA tissues and nontumour tissues [16]."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The data used to sustain the results of this work are included in the article and its supplementary information files.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:32336950", "locator": "sections[36] \"notes\" paragraph 1", "quote": "The data used to sustain the results of this work are included in the article and its supplementary information files."}], "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:32336950"], "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": "blocked", "blocked_on": "data:accession_absent", "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": [], "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": [], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": ["step:obtain_source_data blocked on data:accession_absent"]}, "data": {"state": "partial", "assets": [{"id": "source:pmid:32336950", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.1186/s12935-020-01212-z", "sha256": "sha256:19f30492b3d1285ab1fa8cd11287bc1337a2781a660a9cef8edf0112e7ebfa37", "bytes": 43018, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.1186/s12935-020-01212-z", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC7178764", "source": "europe_pmc_fulltext", "coverage": "whole_body_without_references", "text_hash_scope": "rendered_section_body"}}, {"id": "asset:table:pmid:32336950:1", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:f8ffdafecd4d494b54a77e05a825aebe8b703a5566c193d6987c02625ac65cd6", "bytes": 659, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[7]/table-wrap[1]#Tab1", "version": null, "note": "Summary of clinic parameters of CCA patients collected for iTRAQ", "structure": {"pmcid": "PMC7178764", "section_index": 7, "section_title": "Selection of patients and collection of clinical samples", "row_count": 7, "column_count": 6}, "table": {"label": "Table 1", "caption": "Summary of clinic parameters of CCA patients collected for iTRAQ", "rows": [["Code", "Pathology diagnosis", "Age", "Gender", "Grade", "Lymph node metastasis"], ["1", "Cholangiocarcinoma", "51", "Female", "Well", "Positive"], ["2", "Cholangiocarcinoma", "55", "Female", "Poorly", "Negative"], ["3", "Cholangiocarcinoma", "51", "Male", "Poorly", "Positive"], ["4", "Cholangiocarcinoma", "58", "Male", "Moderately", "Positive"], ["5", "Cholangiocarcinoma", "72", "Male", "Moderately", "Negative"], ["6", "Cholangiocarcinoma", "75", "Male", "Moderately", "Negative"]], "row_count": 7, "column_count": 6, "numeric_cells": 12, "header_rows": 1, "locator": "section[7]/table-wrap[1]#Tab1"}}, {"id": "asset:table:pmid:32336950:2", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:533f898afb5cbd3360d0e805982939f688407fd182d0d216aedc1107d2d8e65f", "bytes": 719, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[7]/table-wrap[2]#Tab2", "version": null, "note": "Summary of clinical characteristic of CCA patients collected for TMAs", "structure": {"pmcid": "PMC7178764", "section_index": 7, "section_title": "Selection of patients and collection of clinical samples", "row_count": 25, "column_count": 2}, "table": {"label": "Table 2", "caption": "Summary of clinical characteristic of CCA patients collected for TMAs", "rows": [["Characteristic", "No. patients (%)"], ["Age"], ["< 55", "34 (39.5)"], ["≥ 55", "52 (60.5)"], ["Gender"], ["Female", "43 (50.0)"], ["Male", "43 (50.0)"], ["Histologic grade"], ["Poorly", "17 (19.8)"], ["Moderate", "64 (74.4)"], ["Well", "5 (5.8)"], ["T classification"], ["T1", "6 (7.0)"], ["T2", "59 (68.6)"], ["T3", "18 (20.9)"], ["T4", "3 (3.5)"], ["N classification"], ["N0", "58 (67.4)"], ["N1", "28 (32.6)"], ["Vascular invasion"], ["No", "57 (66.3)"], ["Yes", "29 (33.7)"], ["Recurrence"], ["No", "31 (36.0)"], ["Yes", "55 (64.0)"]], "row_count": 25, "column_count": 2, "numeric_cells": 19, "header_rows": 1, "locator": "section[7]/table-wrap[2]#Tab2"}}, {"id": "asset:table:pmid:32336950:3", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:df1108a2ee693463b0a30e01e3f3bab32d8bcc2d953d4bb63ccc1a2b700f2bbf", "bytes": 417, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[20]/table-wrap[1]#Tab3", "version": null, "note": "The Basic Properties of candidate protein", "structure": {"pmcid": "PMC7178764", "section_index": 20, "section_title": "Differentially expressed proteins (DEPs) and integrated analysis", "row_count": 4, "column_count": 5}, "table": {"label": "Table 3", "caption": "The Basic Properties of candidate protein", "rows": [["Accession no.", "Gene symbol", "Sequence coverage (%)", "Peptides", "Gene ID"], ["sp|O14936|CSKP_HUMAN", "CASK", "9.5", "5", "8573"], ["sp|Q13790|APOF_HUMAN", "APOF", "24.7", "16", "319"], ["sp|P06756|ITAV_HUMAN", "ITGAV", "4.3", "1", "3685"]], "row_count": 4, "column_count": 5, "numeric_cells": 12, "header_rows": 1, "locator": "section[20]/table-wrap[1]#Tab3"}}, {"id": "asset:table:pmid:32336950:4", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:43e66d0ba4298f79cee8f3b33b33ebb1cd490501173a90b6fcecfc6a5878cc90", "bytes": 1133, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[23]/table-wrap[1]#Tab4", "version": null, "note": "The summary of relationship between CASK expression and clinicopathological features of CCA patients", "structure": {"pmcid": "PMC7178764", "section_index": 23, "section_title": "Relationship between CASK expression and clinicopathological features of CCA patients", "row_count": 31, "column_count": 4}, "table": {"label": "Table 4", "caption": "The summary of relationship between CASK expression and clinicopathological features of CCA patients", "rows": [["Category", "No. patients (%)", "CASK", "P value"], ["Negative", "Positive", ""], ["Age", "0.974"], ["< 55", "33 (39.3)", "18", "15"], ["≥ 55", "51 (60.7)", "28", "23"], ["Gender", "0.130"], ["Female", "43 (51.2)", "27", "16"], ["Male", "41 (48.8)", "19", "22"], ["Histologic grade", "0.300"], ["Poorly", "17 (20.2)", "12", "5"], ["Moderate", "62 (73.8)", "32", "30"], ["Well", "5 (6.0)", "2", "3"], ["Stage", "0.491"], ["I", "8 (9.5)", "3", "5"], ["II", "38 (45.2)", "19", "19"], ["III", "25 (29.8)", "16", "9"], ["IV", "13 (15.5)", "8", "5"], ["T classification", "0.017"], ["T1", "6 (7.1)", "2", "4"], ["T2", "58 (69.0)", "30", "28"], ["T3", "17 (20.2)", "14", "3"], ["T4", "3 (3.7)", "0", "3"], ["N classification", "0.757"], ["N0", "56 (66.7)", "30", "26"], ["N1", "28 (33.3)", "16", "12"], ["Vascular invasion", "0.009"], ["No", "56 (66.7)", "25", "31"], ["Yes", "28 (33.3)", "21", "7"], ["Recurrence", "0.117"], ["No", "30 (35.7)", "13", "17"], ["Yes", "54 (64.3)", "33", "21"]], "row_count": 31, "column_count": 4, "numeric_cells": 73, "header_rows": 2, "locator": "section[23]/table-wrap[1]#Tab4"}}, {"id": "asset:table:pmid:32336950:5", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:6964e2b60d34f2ba76dbce3695b630b6a14b76703211d03cc34bd288beeb77d3", "bytes": 903, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[24]/table-wrap[1]#Tab5", "version": null, "note": "Univariate analysis and multivariate analysis of the relationship of CASK expression with OS among CCA patients", "structure": {"pmcid": "PMC7178764", "section_index": 24, "section_title": "Relationship between positive CASK expression and overall survival rate", "row_count": 10, "column_count": 7}, "table": {"label": "Table 5", "caption": "Univariate analysis and multivariate analysis of the relationship of CASK expression with OS among CCA patients", "rows": [["Parameter", "Univariate analysis", "Multivariate analysis"], ["HR", "95% CI", "P", "HR", "95% CI", "P"], ["Age", "1.018", "0.560–1.854", "0.952", "", "", ""], ["Gender", "0.746", "0.422–1.318", "0.313", "", "", ""], ["Histologic grade", "2.050", "1.126–3.732", "0.019", "1.795", "0.939–3.430", "0.077"], ["Stage", "1.681", "1.208–2.340", "0.002", "1.528", "0.944–2.474", "0.085"], ["T classification", "1.262", "0.852–1.869", "0.246", "", "", ""], ["N classification", "1.659", "0.930–2.960", "0.087", "", "", ""], ["Vascular invasion", "2.644", "1.501–4.656", "0.001", "1.236", "0.523–2.918", "0.629"], ["CASK", "2.155", "1.188–3.909", "0.012", "2.031", "1.083–3.809", "0.027"]], "row_count": 10, "column_count": 7, "numeric_cells": 38, "header_rows": 2, "locator": "section[24]/table-wrap[1]#Tab5"}}, {"id": "asset:table:pmid:32336950:6", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:e926fe009cdf15dc5d598334615b0af3f1b1705b67de72471b4d23b27b46cf1c", "bytes": 904, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[25]/table-wrap[1]#Tab6", "version": null, "note": "Univariate analysis and multivariate analysis of the relationship of CASK expression with RFS among CCA patients", "structure": {"pmcid": "PMC7178764", "section_index": 25, "section_title": "Relationship between positive CASK expression and recurrence-free survival rate", "row_count": 10, "column_count": 7}, "table": {"label": "Table 6", "caption": "Univariate analysis and multivariate analysis of the relationship of CASK expression with RFS among CCA patients", "rows": [["Parameter", "Univariate analysis", "Multivariate analysis"], ["HR", "95% CI", "P", "HR", "95% CI", "P"], ["Age", "1.157", "0.655–2.045", "0.616", "", "", ""], ["Gender", "0.835", "0.485–1.437", "0.515", "", "", ""], ["Histologic grade", "1.983", "1.130–3.481", "0.017", "1.918", "1.044–3.526", "0.036"], ["Stage", "1.750", "1.273–2.408", "0.001", "1.612", "1.034–2.514", "0.035"], ["T classification", "1.377", "0.946–2.004", "0.095", "", "", ""], ["N classification", "1.591", "0.910–2.780", "0.103", "", "", ""], ["Vascular invasion", "2.797", "1.625–4.816", "0.000", "1.325", "0.616–2.851", "0.472"], ["CASK", "2.229", "1.259–3.947", "0.006", "2.114", "1.163–3.844", "0.014"]], "row_count": 10, "column_count": 7, "numeric_cells": 38, "header_rows": 2, "locator": "section[25]/table-wrap[1]#Tab6"}}], "gaps": []}, "analysis": {"state": "partial", "methods": [{"id": "method-1", "family": "differential_expression", "specific": "limma_voom", "label": "Differential expression analysis", "dsl_operations": ["normalise_counts", "differential_expression_fit", "fdr_bh"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["count_matrix_with_condition"], "evidence": {"score": 1.0, "band": "reordered", "quote": "Matrix files from the GSE32225 dataset were obtained from the GEO (https://www.ncbi.nlm.nih.gov/geo/) database. We used the “limma” package to identify DERNAs between CCA tissues and nontumour tissues [16]."}}, {"id": "method-2", "family": "survival_analysis", "specific": "cox_proportional_hazards", "label": "Survival analysis", "dsl_operations": ["cox_ph"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["time_to_event_with_censoring"], "evidence": {"score": 0.8, "band": "high", "quote": "Cox regression"}}, {"id": "method-3", "family": "survival_analysis", "specific": "log_rank_test", "label": "Survival analysis", "dsl_operations": ["logrank_test"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["time_to_event_with_censoring"], "evidence": {"score": 0.8, "band": "high", "quote": "log-rank"}}], "targets": [], "gaps": ["method.reader_differs_from_extractor"]}, "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": "blocked", "tier": "R4", "blocking_axis": "data", "blocked_on": "data:accession_absent", "axes": {"method": {"tier": "R1", "expressible": true, "required_operations": ["normalise_counts", "differential_expression_fit", "fdr_bh"], "missing_operations": [], "basis": "The paper names the method it used and the corpus's method extractor maps it onto the DSL catalogue: limma_voom."}, "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": "R4", "reachable": false, "accessions": [], "resolved_accessions": [], "statements": ["The data used to sustain the results of this work are included in the article and its supplementary information files."], "basis": "The paper names no accession to its source data, so the data has to come from the authors."}}, "can_run": {"dsl_operations": ["normalise_counts", "differential_expression_fit", "fdr_bh"], "assets": ["source:pmid:32336950", "asset:table:pmid:32336950:1", "asset:table:pmid:32336950:2", "asset:table:pmid:32336950:3", "asset:table:pmid:32336950:4", "asset:table:pmid:32336950:5", "asset:table:pmid:32336950:6"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:None"]}, "gaps": ["data:accession_absent"]}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-10-31T19:00:55Z", "independence": "single_reader"}, "evidence_check": {"method": "reordered", "availability": "verbatim"}, "calls": 3, "usage": {"prompt_tokens": 32328, "completion_tokens": 1436, "cached_tokens": 793}}, "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:32336950", "type": "paper", "label": "pmid:32336950"}, {"id": "source:pmid:32336950", "type": "manuscript", "label": "PMID 32336950 full text"}, {"id": "data:geo:None", "type": "dataset", "label": "GEO None"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:32336950", "type": "paper", "label": "pmid:32336950"}, {"id": "source:pmid:32336950", "type": "manuscript", "label": "PMID 32336950 full text"}, {"id": "data:geo:None", "type": "dataset", "label": "GEO None"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-32336950", "type": "extraction", "used": ["source:pmid:32336950"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-None", "type": "accession_resolution", "used": ["data:geo:None"], "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:32336950", "parent_hash": "sha256:b82d0e2851a7f89189430b2ff111fcb67bf8066dbd140a1cc5ee3eb0b17e5904", "fork_of": null, "generation": 7}, "gaps": ["execution.not_run", "method.reader_differs_from_extractor", "review.human_critique", "review.independent_reader", "review.machine_critique", "step:obtain_source_data blocked on data:accession_absent"], "assays": [{"role": "data_generation", "definition_id": "ihc", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.99, "evidence": ["candidate proteins APOF, ITGAV and CASK, and immunohistochemistry was used to detect the expression of these p", "versity from 2011 to 2016, and were used for immunohistochemical detection and tissue microarray (TMA) constr"], "order_basis": "paper_text_order:924", "id": "assay:1"}, {"role": "data_generation", "definition_id": "microarray", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.93, "evidence": ["for immunohistochemical detection and tissue microarray (TMA) construction, respectively. This exper"], "order_basis": "paper_text_order:3344", "id": "assay:2"}, {"role": "analysis", "definition_id": "differential_expression", "definition_version": "f2132e96ae6c7a4e", "definition_digest": null, "required_operations": ["normalise_counts", "differential_expression_fit", "fdr_bh"], "support_state": "supported", "source_hashes": {"dsl_catalogue": "f2132e96ae6c7a4e"}, "confidence": 1.0, "evidence": ["Matrix files from the GSE32225 dataset were obtained from the GEO (https://www.ncbi.nlm.nih.gov/geo/) database. We used the “limma” package to identify DERNAs between CCA tissues and nontumour tissues [16]."], "order_basis": "consumes_earlier_output", "id": "assay:3"}]},"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":"2026-11-04T01:35:16+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}}}