{"data":{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:29240723", "kind": "science-record", "revision": 8, "content_hash": "sha256:adbbd2e22ea9e5fac252ab1ec2bbd0b2e3e2592fd2b7f91271aca6659fef5c71", "created_at": "2026-11-01T15:40:30Z", "updated_at": "2026-11-01T21:59:37Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Identification of Key Genes and Pathways in Tongue Squamous Cell Carcinoma Using Bioinformatics Analysis.", "doi": "10.12659/msm.905035", "pmid": "29240723", "authors": ["Huayong Zhang", "Jianmin Liu", "Xiaoyan Fu", "Ankui Yang"], "journal": "Medical science monitor : international medical journal of experimental and clinical research", "year": 2017, "abstract": "BACKGROUND Tongue squamous cell carcinoma (TSCC) is a major type of oral cancers and has remained an intractable cancer over the past decades. The aim of this study was to identify differentially expressed genes (DEGs) during TSCC and reveal their potential mechanisms. MATERIAL AND METHODS The gene expression profiles of GSE13601 were downloaded from the GEO database. The GSE13601 dataset contains 57 samples, including 31 tongue SCC samples and 26 matched normal mucosa samples. Gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes pathway (KEGG) enrichment analyses were performed; Cytoscape software was used for the protein-protein interaction (PPI) network and module analysis of the DEGs. RESULTS We identified a total of 1,050 upregulated DEGs (uDEGs) and 702 downregulated DEGs (dDEGs) of TSCC. The GO analysis results showed that uDEGs were significantly enriched in the following biological processes (BP): signal transduction, positive or negative regulation of cell proliferation, and negative regulation of cell proliferation. The dDEGs were significantly enriched in the following biological processes: signal transduction, cell adhesion, and apoptotic process. The KEGG pathway analysis showed that uDEGs were enriched in metabolic pathways, pathways in cancer, and PI3K-Akt signaling pathway, while the dDEGs were enriched in focal adhesion and ECM-receptor interaction. The top centrality hub genes RAC1, APP, EGFR, KNG1, AGT, and HRAS were identified from the PPI network. Module analysis revealed that TSCC was associated with significant pathways, including neuroactive ligand-receptor interaction, calcium signaling pathway, and chemokine signaling pathway. CONCLUSIONS The present study identified key genes and signal pathways, which deepen our understanding of the molecular mechanisms of carcinogenesis and development of the disease, and might be used as diagnostic and therapeutic molecular biomarkers for TSCC.", "claims": [{"id": "claim-method", "statement": "The adjusted p values (adj. p) were applied to correct the false positive results by default Benjamini-Hochberg false discovery rate method.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:29240723", "locator": "sections[4] \"Data processing\" paragraph 2", "quote": "The adjusted p values (adj. p) were applied to correct the false positive results by default Benjamini-Hochberg false discovery rate method."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The Gene Expression Omnibus (GEO, http://www.ncbi.nlm.nih.gov/geo) is a public functional genomics data repository including array- and sequence-based data, and is freely available for users. The gene expression profiles of GSE13601 were obtained from the GEO database. The GSE13601 dataset has 57 samples, including 31 TSCC samples and 26 matched normal mucosa samples.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:29240723", "locator": "sections[3] \"Datasets\" paragraph 2", "quote": "The Gene Expression Omnibus (GEO, http://www.ncbi.nlm.nih.gov/geo) is a public functional genomics data repository including array- and sequence-based data, and is freely available for users."}, {"asset": "source:pmid:29240723", "locator": "sections[3] \"Datasets\" paragraph 2", "quote": "The gene expression profiles of GSE13601 were obtained from the GEO database."}, {"asset": "source:pmid:29240723", "locator": "sections[3] \"Datasets\" paragraph 2", "quote": "The GSE13601 dataset has 57 samples, including 31 TSCC samples and 26 matched normal mucosa samples."}], "state": "complete"}, {"id": "claim-target-result", "statement": "Using GEO2R on GSE13601 downloaded from the GEO database, with adj. p<0.01 and |log2FC|>1 as the statistical criteria, the study identified 1,752 DEGs in TSCC tissues versus normal tissues: 1,050 upregulated and 702 downregulated.", "kind": "quantitative", "target": {"value": 0.01, "unit": "p-value", "tolerance": null, "source": "Based on the GEO2R analysis, using the adj. p<0.01 and |log2FC|>1 criteria, a total of 1,752 DEGs were identified, consisting of 1,050 upregulated DEGs (uDEGs) and 702 downregulated DEGs (dDEGs) in TSCC tissues compared with normal tissues."}, "evidence": [{"asset": "source:pmid:29240723", "locator": "sections[0] \"Abstract\" paragraph 2", "quote": "The gene expression profiles of GSE13601 were downloaded from the GEO database."}, {"asset": "source:pmid:29240723", "locator": "sections[9] \"Identification of DEGs\" paragraph 2", "quote": "Based on the GEO2R analysis, using the adj. p<0.01 and |log2FC|>1 criteria, a total of 1,752 DEGs were identified, consisting of 1,050 upregulated DEGs (uDEGs) and 702 downregulated DEGs (dDEGs) in TSCC tissues compared with normal tissues."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "Using GEO2R on GSE13601 downloaded from the GEO database, with adj. p<0.01 and |log2FC|>1 as the statistical criteria, the study identified 1,752 DEGs in TSCC tissues versus normal tissues: 1,050 upregulated and 702 downregulated.", "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:29240723"], "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:GSE13601"], "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:GSE13601"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:29240723", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.12659/msm.905035", "sha256": "sha256:1a365ae83a3390538c4a2005dc9366cab407b2e9143031c549ca20e450c485e8", "bytes": 34796, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.12659/msm.905035", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC5738838", "source": "europe_pmc_fulltext", "coverage": "whole_body", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE13601", "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=GSE13601", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE13601", "version": null, "note": "The Gene Expression Omnibus (GEO, http://www.ncbi.nlm.nih.gov/geo) is a public functional genomics data repository including array- and sequence-based data, and is freely available for users. The gene expression profiles of GSE13601 were obtained from the GEO database. The GSE13601 dataset has 57 samples, including 31 TSCC samples and 26 matched normal mucosa samples.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The Gene Expression Omnibus (GEO, http://www.ncbi.nlm.nih.gov/geo) is a public functional genomics data repository including array- and sequence-based data, and is freely available for users. The gene expression profiles of GSE13601 were obtained from the GEO database. 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null, "platform": "8300", "taxon": "Homo sapiens", "title": "Oral tongue cancer gene expression profiling: Identification of novel potential prognosticators", "resolution_checked_at": "2026-11-01T15:39:54Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}, {"id": "asset:table:pmid:29240723:1", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:a8f1e1d95c9ec25d7573f161b26699a80dd93609e337426ddca307e82a853a49", "bytes": 2846, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[10]/table-wrap[1]#t1-medscimonit-23-5924", "version": null, "note": "Gene ontology analysis of differentially expressed genes associated with TSCC.", "structure": {"pmcid": "PMC5738838", "section_index": 10, "section_title": "GO term enrichment analysis", "row_count": 31, "column_count": 6}, "table": {"label": "Table 1", "caption": "Gene ontology analysis of differentially expressed genes associated with TSCC.", "rows": [["Expression", "Category", "Term/gene function", "Gene count", "%", "P value"], ["Up-regulated", "GOTERM_BP_DIRECT", "GO: 0007165~signal transduction", "95", "9.59", "8.67E-05"], ["GOTERM_BP_DIRECT", "GO: 0045944~positive regulation of transcription from RNA polymerase II promoter", "82", "8.27", "1.72E-04"], ["GOTERM_BP_DIRECT", "GO: 0000122~negative regulation of transcription from RNA polymerase II promoter", "60", "6.05", "0.002"], ["GOTERM_BP_DIRECT", "GO: 0008285~negative regulation of cell proliferation", "45", "4.54", "1.50E-05"], ["GOTERM_BP_DIRECT", "GO: 0007155~cell adhesion", "45", "4.54", "2.35E-04"], ["GOTERM_CC_DIRECT", "GO: 0005886~plasma membrane", "263", "26.54", "6.71E-05"], ["GOTERM_CC_DIRECT", "GO: 0005829~cytosol", "223", "22.50", "8.89E-05"], ["GOTERM_CC_DIRECT", "GO: 0070062~extracellular exosome", "215", "21.70", "1.05E-09"], ["GOTERM_CC_DIRECT", "GO: 0005576~extracellular region", "141", "14.23", "5.09E-10"], ["GOTERM_CC_DIRECT", "GO: 0005615~extracellular space", "134", "13.52", "5.39E-13"], ["GOTERM_MF_DIRECT", "GO: 0005515~protein binding", "372", "37.53", "0.004"], ["GOTERM_MF_DIRECT", "GO: 0005524~ATP binding", "106", "10.70", "0.003"], ["GOTERM_MF_DIRECT", "GO: 0005509~calcium ion binding", "77", "7.77", "1.41E-08"], ["GOTERM_MF_DIRECT", "GO: 0042803~protein homodimerization activity", "66", "6.66", "5.29E-05"], ["GOTERM_MF_DIRECT", "GO: 0003700~transcription factor activity, sequence-specific DNA binding", "64", "6.46", "0.003"], ["Down-regulated", "GOTERM_BP_DIRECT", "GO: 0007165~signal transduction", "83", "12.56", "6.42E-08"], ["GOTERM_BP_DIRECT", "GO: 0007155~cell adhesion", "57", "8.62", "1.90E-14"], ["GOTERM_BP_DIRECT", "GO: 0006915~apoptotic process", "47", "7.11", "1.69E-06"], ["GOTERM_BP_DIRECT", "GO: 0008284~positive regulation of cell proliferation", "44", "6.66", "2.66E-07"], ["GOTERM_BP_DIRECT", "GO: 0008285~negative regulation of cell proliferation", "42", "6.35", "2.26E-08"], ["GOTERM_CC_DIRECT", "GO: 0005737~cytoplasm", "273", "41.30", "3.74E-13"], ["GOTERM_CC_DIRECT", "GO: 0005634~nucleus", "242", "36.61", "3.76E-05"], ["GOTERM_CC_DIRECT", "GO: 0005829~cytosol", "235", "35.55", "1.36E-26"], ["GOTERM_CC_DIRECT", "GO: 0070062~extracellular exosome", "227", "34.34", "9.35E-36"], ["GOTERM_CC_DIRECT", "GO: 0005886~plasma membrane", "202", "30.56", "2.95E-07"], ["GOTERM_MF_DIRECT", "GO: 0005515~protein binding", "350", "52.95", "1.77E-20"], ["GOTERM_MF_DIRECT", "GO: 0005524~ATP binding", "89", "13.46", "3.73E-05"], ["GOTERM_MF_DIRECT", "GO: 0044822~poly(A) RNA binding", "65", "9.83", "0.001"], ["GOTERM_MF_DIRECT", "GO: 0005509~calcium ion binding", "52", "7.867", "2.02E-05"], ["GOTERM_MF_DIRECT", "GO: 0042802~identical protein binding", "46", "6.96", "2.95E-05"]], "row_count": 31, "column_count": 6, "numeric_cells": 120, "header_rows": 1, "locator": 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cancer", "47", "4.74", "0.001"], ["hsa04151", "PI3K-Akt signaling pathway", "39", "3.94", "0.011"], ["hsa04020", "Calcium signaling pathway", "37", "3.73", "3.28E-08"], ["hsa04010", "MAPK signaling pathway", "36", "3.63", "3.35E-04"], ["Down-regulated", "hsa05200", "Pathways in cancer", "47", "7.11", "4.92E-07"], ["hsa04151", "PI3K-Akt signaling pathway", "42", "6.35", "1.47E-06"], ["hsa04510", "Focal adhesion", "38", "5.75", "6.87E-11"], ["hsa04512", "ECM-receptor interaction", "29", "4.39", "4.14E-15"], ["hsa05205", "Proteoglycans in cancer", "29", "4.39", "3.33E-06"]], "row_count": 11, "column_count": 6, "numeric_cells": 40, "header_rows": 1, "locator": "section[11]/table-wrap[1]#t2-medscimonit-23-5924"}}, {"id": "asset:table:pmid:29240723:3", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:0b2b38fded73ef16f20b745e09c00e66bb9115be96805bd7a95adfa749c3e18f", "bytes": 829, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[12]/table-wrap[1]#t3-medscimonit-23-5924", "version": null, "note": "The top 10 differentially expressed genes with higher scores, respectively, identified by the three centrality methods.", "structure": {"pmcid": "PMC5738838", "section_index": 12, "section_title": "PPI network construction and modules selection", "row_count": 11, "column_count": 6}, "table": {"label": "Table 3", "caption": "The top 10 differentially expressed genes with higher scores, respectively, identified by the three centrality methods.", "rows": [["Subgraph", "Degree", "Closeness"], ["APP", "7.93E10", "RAC1", "78.0", "RAC1", "0.01866"], ["KNG1", "7.47E10", "APP", "74.0", "EGFR", "0.01864"], ["AGT", "7.20E10", "EGFR", "59.0", "HRAS", "0.01863"], ["RGS19", "4.86E10", "KNG1", "58.0", "BCL2", "0.01861"], ["GNAI1", "3.64E10", "CDK1", "56.0", "CDC42", "0.01860"], ["GCG", "3.51E10", "AGT", "55.0", "HIF1A", "0.01860"], ["ADCY8", "3.27E10", "HRAS", "55.0", "PRKCA", "0.01860"], ["ADCY1", "3.03E10", "CDC42", "55.0", "CDKN1A", "0.01859"], ["CXCL12", "2.97E10", "ADCY8", "54.0", "MMP9", "0.01859"], ["GNA15", "2.74E10", "GCG", "50.0", "MAX", "0.01858"]], "row_count": 11, "column_count": 6, "numeric_cells": 35, "header_rows": 1, "locator": "section[12]/table-wrap[1]#t3-medscimonit-23-5924"}}, {"id": "asset:table:pmid:29240723:4", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:296d11c2e64e033d862cde42723276549cb69d7f935e3310c3ac0b75773e0422", "bytes": 1018, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[12]/table-wrap[2]#t4-medscimonit-23-5924", "version": null, "note": "GO and pathway analysis of genes in selected module.", "structure": {"pmcid": "PMC5738838", "section_index": 12, "section_title": "PPI network construction and modules selection", "row_count": 13, "column_count": 5}, "table": {"label": "Table 4", "caption": "GO and pathway analysis of genes in selected module.", "rows": [["Category", "Pathway ID", "Term/gene and function", "Count", "P-value"], ["KEGG_PATHWAY", "hsa4080", "Neuroactive ligand-receptor interaction", "16", "2.83E-17"], ["hsa4020", "Calcium signaling pathway", "12", "1.50E-13"], ["hsa4062", "Chemokine signaling pathway", "12", "1.50E-13"], ["GOTERM_BP_DIRECT", "GO.0007165", "Signal transduction", "31", "1.74E-10"], ["GO.0044700", "Single organism signaling", "29", "3.40E-08"], ["GO.0007154", "Cell communication", "29", "5.69E-08"], ["GOTERM_CC_DIRECT", "GO.0005886", "Plasma membrane", "28", "1.20E-07"], ["GO.0071944", "Cell periphery", "28", "1.38E-07"], ["GO.0044459", "Plasma membrane part", "21", "1.20E-07"], ["GOTERM_MF_DIRECT", "GO.0005515", "Protein binding", "20", "0.0176"], ["GO.0005102", "Receptor binding", "19", "7.39E-11"], ["GO.0004871", "Signal transducer activity", "16", "5.68E-06"]], "row_count": 13, "column_count": 5, "numeric_cells": 36, "header_rows": 1, "locator": "section[12]/table-wrap[2]#t4-medscimonit-23-5924"}}], "gaps": ["asset:data:geo:GSE13601 not downloaded", "asset:data:geo:GSE13601 licence not read"]}, "analysis": {"state": "partial", "methods": [{"id": "method-1", "family": "network_analysis", "specific": "ppi_network", "label": "Network / pathway analysis", "dsl_operations": ["build_graph", "centrality_scores", "pathway_enrich"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["edge_list"], "evidence": {"score": 0.7, "band": "medium", "quote": "protein-protein interaction"}}, {"id": "method-2", "family": "network_analysis", "specific": "pathway_enrichment", "label": "Network / pathway analysis", "dsl_operations": ["pathway_enrich"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["edge_list"], "evidence": {"score": 0.8, "band": "high", "quote": "pathway enrichment"}}, {"id": "method-3", "family": "network_analysis", 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A run that reproduces the effect is judged against this threshold."}], "gaps": ["method.reader_named_unmapped"]}, "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": ["build_graph", "centrality_scores", "pathway_enrich"], "missing_operations": [], "basis": "The paper names the method it used and the corpus's method extractor maps it onto the DSL catalogue: ppi_network."}, "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": ["GSE13601"], "resolved_accessions": ["GSE13601"], "statements": ["The Gene Expression Omnibus (GEO, http://www.ncbi.nlm.nih.gov/geo) is a public functional genomics data repository including array- and sequence-based data, and is freely available for users. The gene expression profiles of GSE13601 were obtained from the GEO database. The GSE13601 dataset has 57 samples, including 31 TSCC samples and 26 matched normal mucosa samples."], "basis": "The paper names GSE13601 in Gene Expression Omnibus (GEO) and the accession resolves in the repository. No dataset was downloaded and no licence was read."}}, "can_run": {"dsl_operations": ["build_graph", "centrality_scores", "pathway_enrich"], "assets": ["source:pmid:29240723", "data:geo:GSE13601", "asset:table:pmid:29240723:1", "asset:table:pmid:29240723:2", "asset:table:pmid:29240723:3", "asset:table:pmid:29240723:4"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:GSE13601"]}, "gaps": []}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-10-31T18:32:59Z", "independence": "same_provider"}, "evidence_check": {"method": "verbatim", "availability": null}, "calls": 8, "usage": {"prompt_tokens": 75313, "completion_tokens": 2337, "cached_tokens": 1841}}, "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:29240723", "type": "paper", "label": "pmid:29240723"}, {"id": "source:pmid:29240723", "type": "manuscript", "label": "PMID 29240723 full text"}, {"id": "data:geo:GSE13601", "type": "dataset", "label": "GEO GSE13601"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:29240723", "type": "paper", "label": "pmid:29240723"}, {"id": "source:pmid:29240723", "type": "manuscript", "label": "PMID 29240723 full text"}, {"id": "data:geo:GSE13601", "type": "dataset", "label": "GEO GSE13601"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-29240723", "type": "extraction", "used": ["source:pmid:29240723"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-GSE13601", "type": "accession_resolution", "used": ["data:geo:GSE13601"], "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:29240723", "parent_hash": "sha256:a9edf42b1e5014ea4a712bf5327958f565ce73f1f337e5091efb2bfcdc59ea64", "fork_of": null, "generation": 7}, "gaps": ["asset:data:geo:GSE13601 licence not read", "asset:data:geo:GSE13601 not downloaded", "execution.not_run", "method.reader_named_unmapped", "review.human_critique", "review.independent_reader", "review.machine_critique"], "assays": [{"role": "analysis", "definition_id": "network_analysis", "definition_version": "f2132e96ae6c7a4e", "definition_digest": null, "required_operations": ["build_graph", "centrality_scores", "pathway_enrich"], "support_state": "supported", "source_hashes": {"dsl_catalogue": "f2132e96ae6c7a4e"}, "confidence": 0.7, "evidence": ["protein-protein interaction"], "order_basis": "analysis_only", "id": "assay:1"}]},"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":"2026-11-04T02:45:47+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}}}