{"data":{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:32429566", "kind": "science-record", "revision": 7, "content_hash": "sha256:018e2d7bf936931e3006cfc526e8c2ee1cc07a0ee5d21d5dd7d898dbc65d101d", "created_at": "2026-11-01T15:41:02Z", "updated_at": "2026-11-01T21:23:16Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Metabolic Plasticity in Ovarian Cancer Stem Cells.", "doi": "10.3390/cancers12051267", "pmid": "32429566", "authors": ["Alia Ghoneum", "Daniela Gonzalez", "Ammar Yasser Abdulfattah", "Neveen Said"], "journal": "Cancers", "year": 2020, "abstract": "Ovarian Cancer is the fifth most common cancer in females and remains the most lethal gynecological malignancy as most patients are diagnosed at late stages of the disease. Despite initial responses to therapy, recurrence of chemo-resistant disease is common. The presence of residual cancer stem cells (CSCs) with the unique ability to adapt to several metabolic and signaling pathways represents a major challenge in developing novel targeted therapies. The objective of this study is to investigate the transcripts of putative ovarian cancer stem cell (OCSC) markers in correlation with transcripts of receptors, transporters, and enzymes of the energy generating metabolic pathways involved in high grade serous ovarian cancer (HGSOC). We conducted correlative analysis in data downloaded from The Cancer Genome Atlas (TCGA), studies of experimental OCSCs and their parental lines from Gene Expression Omnibus (GEO), and Cancer Cell Line Encyclopedia (CCLE). We found positive correlations between the transcripts of OCSC markers, specifically CD44, and glycolytic markers. TCGA datasets revealed that NOTCH1, CD133, CD44, CD24, and ALDH1A1, positively and significantly correlated with tricarboxylic acid cycle (TCA) enzymes. OVCAR3-OCSCs (cancer stem cells derived from a well-established epithelial ovarian cancer cell line) exhibited enrichment of the electron transport chain (ETC) mainly in complexes I, III, IV, and V, further supporting reliance on the oxidative phosphorylation (OXPHOS) phenotype. OVCAR3-OCSCs also exhibited significant increase in CD36, ACACA, SCD, and CPT1A, with CD44, CD133, and ALDH1A1 exhibiting positive correlations with lipid metabolic enzymes. TCGA data show positive correlations between OCSC markers and glutamine metabolism enzymes, whereas in OCSC experimental models of GSE64999, GSE28799, and CCLE, the number of positive and negative correlations observed was significantly lower and was different between model systems. Appropriate integration and validation of data model systems with those in patients' specimens is needed not only to bridge our knowledge gap of metabolic programing of OCSCs, but also in designing novel strategies to target the metabolic plasticity of dormant, resistant, and CSCs.", "claims": [{"id": "claim-method", "statement": "The differential expression of the OCSCs markers and the enzymes involved in the metabolic pathways in OCSCs and their parental cells was analyzed by the multiple t-test with Holm–Sidak method, and each gene was analyzed individually between the two groups, without assuming a consistent SD with p ≤ 0.05.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:32429566", "locator": "sections[4] \"2.2. Data Analysis\" paragraph 2", "quote": "The differential expression of the OCSCs markers and the enzymes involved in the metabolic pathways in OCSCs and their parental cells was analyzed by the multiple t-test with Holm–Sidak method, and each gene was analyzed individually between the two groups, without assuming a consistent SD with p ≤ 0.05."}], "state": "complete"}, {"id": "claim-data-access", "statement": "Gene expression profiles of two studies of OCSC GSE28799 [41] and GSE64999 [42] with platform information of GPL570 and GPL17077, respectively, were extracted from Gene Expression Omnibus (GEO). Both included ovarian cancer spheroids and their parental cells. GSE28799 included OVCAR3-derived spheroids and their parental OVCAR3 in triplicates.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:32429566", "locator": "sections[3] \"2.1. Microarray Extraction\" paragraph 2", "quote": "Gene expression profiles of two studies of OCSC GSE28799 [41] and GSE64999 [42] with platform information of GPL570 and GPL17077, respectively, were extracted from Gene Expression Omnibus (GEO). Both included ovarian cancer spheroids and their parental cells. GSE28799 included OVCAR3-derived spheroids and their parental OVCAR3 in triplicates."}], "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:32429566"], "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:GSE28799"], "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:GSE28799"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:32429566", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.3390/cancers12051267", "sha256": "sha256:55af975f75c16e5bae97d2ec89b8ae412c30e9ef1ace895aa799a41095719032", "bytes": 75683, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.3390/cancers12051267", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC7281273", "source": "europe_pmc_fulltext", "coverage": "whole_body", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE28799", "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=GSE28799", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE28799", "version": null, "note": "Gene expression profiles of two studies of OCSC GSE28799 [41] and GSE64999 [42] with platform information of GPL570 and GPL17077, respectively, were extracted from Gene Expression Omnibus (GEO). 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GSE28799 included OVCAR3-derived spheroids and their parental OVCAR3 in triplicates.", "access_statement_kind": "repository_route_statement", "sample_accessions": ["GSM713222", "GSM713223", "GSM713224", "GSM713227", "GSM713228", "GSM713229"], "sample_count": 6, "group_sizes": null, "group_sizes_basis": null, "platform": "570", "taxon": "Homo sapiens", "title": "Isolation and characterization of stem-like cells from a human ovarian cancer cell line", "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:GSE64999", "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=GSE64999", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE64999", "version": null, "note": "Gene expression profiles of two studies of OCSC GSE28799 [41] and GSE64999 [42] with platform information of GPL570 and GPL17077, respectively, were extracted from Gene Expression Omnibus (GEO). Both included ovarian cancer spheroids and their parental cells. GSE28799 included OVCAR3-derived spheroids and their parental OVCAR3 in triplicates.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "Gene expression profiles of two studies of OCSC GSE28799 [41] and GSE64999 [42] with platform information of GPL570 and GPL17077, respectively, were extracted from Gene Expression Omnibus (GEO). Both included ovarian cancer spheroids and their parental cells. 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Red indicates significant positive and blue indicates negative correlations.", "structure": {"pmcid": "PMC7281273", "section_index": 7, "section_title": "3.2. Correlation between OCSCs Markers and Glycolysis", "row_count": 19, "column_count": 19}, "table": {"label": "Table 1", "caption": "Pearson Correlation between the expression of CSC transcripts and the transcripts of glucose transporters and the key enzymes involved in glycolysis in ovarian cancer specimens from TCGA and curated from GEPIA. Red indicates significant positive and blue indicates negative correlations.", "rows": [["TCGA", "CD44", "", "CD24", "", "CD117", "", "CD133", "", "ALDH1A1", "", "SOX2", "", "4-Oct", "", "NANOG", "", "NOTCH1", ""], ["", "Pearson R", "p-Value", "Pearson R", "p-Value", "Pearson R", "p-Value", "Pearson R", "p-Value", "Pearson R", "p-Value", "Pearson R", "p-Value", "Pearson R", "p-Value", "Pearson R", "p-Value", "Pearson R", "p-Value"], ["HK1", "0.29", "0.00", "7e−04", "0.99", "0.15", "0.00", "0.14", "0.00", "0.13", "0.01", "0.03", "0.60", "0.03", "0.61", "0.06", "0.25", "0.40", "0.00"], ["HK2", "0.13", "0.01", "0.09", "0.08", "0.20", "2.9e−05", "0.14", "0.00", "0.09", "0.07", "0.01", "0.82", "0.11", "0.03", "0.03", "0.60", "0.30", "4.9e−10"], ["SLC2A1", "0.09", "0.07", "0.00", "0.95", "0.23", "1.7e−06", "0.04", "0.42", "0.10", "0.03", "0.00", "0.87", "0.00", "0.95", "0.03", "0.60", "0.22", "2.9e−06"], ["SLC2A2", "0.07", "0.16", "−0.03", "0.60", "0.12", "0.02", "−0.04", "0.42", "0.08", "0.09", "−0.03", "0.48", "−0.04", "0.43", "0.01", "0.77", "0.19", "0.00"], ["SLC2A3", "0.31", "9.7e−11", "−0.02", "0.68", "0.19", "0.00", "0.00", "0.95", "0.07", "0.15", "0.11", "0.02", "−0.03", "0.54", "0.03", "0.49", "0.24", "3.3e−07"], ["SLC2A4", "0.01", "0.77", "0.04", "0.37", "0.19", "9.4e−05", "0.01", "0.87", "0.00", "0.97", "0.09", "0.06", "0.01", "0.77", "0.09", "0.06", "0.18", "0.00"], ["SLC2A5", "0.45", "0.00", "0.02", "0.74", "0.06", "0.24", "0.00", "0.98", "−0.03", "0.61", "−0.03", "0.57", "0.03", "0.52", "−0.05", "0.29", "0.18", "0.00"], ["SLC2A6", "0.24", "5e−07", "−0.12", "0.01", "0.00", "0.90", "0.00", "0.89", "0.05", "0.31", "0.00", "0.86", "−0.04", "0.40", "−0.05", "0.28", "0.29", "1e−09"], ["PGK1", "0.30", "4.4 × 1010", "−0.01", "0.82", "0.02", "0.63", "0.02", "0.69", "0.19", "8.7e−05", "0.10", "0.04", "0.00", "1.00", "0.04", "0.45", "0.14", "0.00"], ["PFKFB3", "0.35", "0.00", "0.00", "0.93", "0.11", "0.02", "0.11", "0.03", "0.04", "0.39", "0.10", "0.03", "0.09", "0.07", "−0.01", "0.77", "0.28", "6.9e−09"], ["LDHA", "0.20", "3.5e−05", "−0.03", "0.60", "−0.02", "0.74", "−0.03", "0.60", "0.13", "0.01", "0.06", "0.24", "0.04", "0.46", "0.00", "0.97", "−0.02", "0.65"], ["FBP1", "0.40", "0.00", "−0.11", "0.02", "−0.06", "0.24", "0.00", "0.98", "0.11", "0.03", "0.06", "0.19", "0.00", "0.96", "0.00", "0.93", "0.03", "0.48"], ["PDK1", "0.12", "0.01", "0.02", "0.66", "0.04", "0.38", "0.06", "0.23", "0.24", "3.9e−07", "0.04", "0.41", "0.04", "0.42", "0.01", "0.80", "0.13", "0.01"], ["PDHA", "0.12", "0.01", "−0.02", "0.75", "−0.02", "0.70", "0.07", "0.13", "0.14", "0.01", "0.09", "0.06", "0.08", "0.11", "0.03", "0.51", "0.22", "5.4e−06"], ["TPI1", "0.07", "0.15", "0.05", "0.33", "−0.04", "0.47", "−0.06", "0.25", "0.03", "0.56", "0.02", "0.75", "−0.01", "0.77", "0.08", "0.10", "−0.02", "0.74"], ["ENO1", "0.23", "1.3e−06", "0.07", "0.17", "−0.02", "0.71", "0.09", "0.08", "0.10", "0.05", "0.01", "0.86", "0.13", "0.01", "−0.04", "0.47", "0.12", "0.02"], ["PHGDH", "0.02", "0.71", "0.03", "0.50", "0.19", "5.3e−05", "0.10", "0.05", "0.20", "4.8e−05", "0.22", "6.4e−06", "−0.05", "0.30", "0.14", "0.00", "0.14", "0.00"]], "row_count": 19, "column_count": 19, "numeric_cells": 311, "header_rows": 2, "locator": "section[7]/table-wrap[1]#cancers-12-01267-t001"}}, {"id": "asset:table:pmid:32429566:2", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:e9b781092a3c2cc32c247abbbc02a919cef3cddd99bd0d0393cdfb7fef719b92", "bytes": 2459, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[8]/table-wrap[1]#cancers-12-01267-t002", "version": null, "note": "Correlation of OCSC markers with TCA enzymes in TCGA. Pearson Correlation between the expression of CSC transcripts and the transcripts of the key TCA enzymes in ovarian cancer specimens from TCGA and curated from GEPIA. Red indicates significant positive, blue indicates negative correlations, and black indicates insignificant p-values of either positive or negative correlations.", "structure": {"pmcid": "PMC7281273", "section_index": 8, "section_title": "3.3. Correlation between OCSCs Markers and TCA Cycle", "row_count": 13, "column_count": 19}, "table": {"label": "Table 2", "caption": "Correlation of OCSC markers with TCA enzymes in TCGA. Pearson Correlation between the expression of CSC transcripts and the transcripts of the key TCA enzymes in ovarian cancer specimens from TCGA and curated from GEPIA. Red indicates significant positive, blue indicates negative correlations, and black indicates insignificant p-values of either positive or negative correlations.", "rows": [["TCGA", "CD44", "", "CD24", "", "CD117", "", "CD133", "", "ALDH1A1", "", "SOX2", "", "4-Oct", "", "NANOG", "", "NOTCH1", ""], ["", "Pearson R", "p-Value", "Pearson R", "p-Value", "Pearson R", "p-Value", "Pearson R", "p-Value", "Pearson R", "p-Value", "Pearson R", "p-Value", "Pearson R", "p-Value", "Pearson R", "p-Value", "Pearson R", "p-Value"], ["CS", "0.19", "8.2e−05", "0.16", "0.00", "0.23", "9.9e−07", "0.09", "0.06", "0.15", "0.00", "0.00", "0.96", "0.07", "0.18", "0.11", "0.02", "0.39", "0.00"], ["ACO1", "0.30", "1.6e−10", "0.08", "0.09", "0.21", "1.1e−05", "0.24", "7.6e−07", "0.30", "5.1e−10", "0.10", "0.05", "0.11", "0.02", "0.00", "0.99", "0.34", "2.8e−13"], ["ACO2", "0.18", "0.00", "0.11", "0.02", "−0.06", "0.17", "0.04", "0.41", "−0.03", "0.58", "−0.03", "0.58", "0.10", "0.05", "−0.04", "0.45", "0.24", "3.6e−07"], ["IDH1", "0.12", "0.01", "0.08", "0.11", "0.01", "0.77", "0.06", "0.21", "0.16", "0.00", "0.09", "0.08", "0.01", "0.88", "0.02", "0.63", "0.17", "0.00"], ["IDH2", "0.16", "0.00", "0.07", "0.13", "0.11", "0.03", "0.07", "0.14", "0.09", "0.08", "0.05", "0.27", "−0.03", "0.51", "0.04", "0.39", "0.25", "2.6e−07"], ["IDH3A", "0.16", "0.00", "−0.09", "0.06", "−0.04", "0.44", "0.07", "0.15", "0.09", "0.06", "0.04", "0.37", "−0.03", "0.58", "−0.01", "0.77", "0.24", "4.2e−07"], ["IDH3B", "−0.08", "0.12", "0.09", "0.06", "0.09", "0.07", "0.04", "0.48", "0.03", "0.60", "−0.05", "0.35", "0.06", "0.21", "0.04", "0.47", "0.24", "6e−07"], ["SUCLG1", "0.13", "0.01", "0.16", "0.00", "0.01", "0.86", "0.01", "0.81", "0.13", "0.01", "0.00", "0.90", "0.00", "0.99", "0.03", "0.50", "0.04", "0.41"], ["SUCLG2", "0.19", "9.3e−05", "0.01", "0.89", "−0.08", "0.12", "0.05", "0.27", "0.06", "0.22", "0.08", "0.12", "0.11", "0.02", "0.00", "0.90", "0.05", "0.28"], ["MDH2", "0.20", "4.4e−05", "0.00", "0.92", "−0.1", "0.05", "0.00", "0.96", "0.00", "0.97", "0.01", "0.79", "0.07", "0.17", "0.01", "0.87", "0.10", "0.04"], ["ME2", "0.27", "9.6e−09", "0.16", "0.00", "0.05", "0.33", "0.08", "0.09", "0.09", "0.07", "0.04", "0.45", "0.13", "0.01", "−0.03", "0.65", "0.12", "0.01"]], "row_count": 13, "column_count": 19, "numeric_cells": 203, "header_rows": 2, "locator": "section[8]/table-wrap[1]#cancers-12-01267-t002"}}, {"id": "asset:table:pmid:32429566:3", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:02b3e3c8c267d29c4ce12b15d1f9da6fa6f9befa364cede27fc273a85f8aeb53", "bytes": 7676, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[9]/table-wrap[1]#cancers-12-01267-t003", "version": null, "note": "Pearson correlation between the expression of CSC transcripts and the transcripts of the key enzymes involved in the ETC in patients’ data curated from TCGA. Red indicates significant positive, blue indicates negative correlations, and black indicates insignificant p-values of either positive or negative correlations.", "structure": {"pmcid": "PMC7281273", "section_index": 9, "section_title": "3.4. OXPHOS in Ovarian Cancer Stem Cells", "row_count": 51, "column_count": 19}, "table": {"label": "Table 3", "caption": "Pearson correlation between the expression of CSC transcripts and the transcripts of the key enzymes involved in the ETC in patients’ data curated from TCGA. Red indicates significant positive, blue indicates negative correlations, and black indicates insignificant p-values of either positive or negative correlations.", "rows": [["TCGA", ""], ["", "CD44", "", "CD24", "", "CD117", "", "CD133", "", "ALDH1A1", "", "SOX2", "", "4-Oct", "", "NANOG", "", "NOTCH1", ""], ["Complex I", "Pearson R", "p-Value", "Pearson R", "p-Value", "Pearson R", "p-Value", "Pearson R", "p-Value", "Pearson R", "p-Value", "Pearson R", "p-Value", "Pearson R", "p-Value", "Pearson R", "p-Value", "Pearson R", "p-Value"], ["NDUFA10", "0.04", "0.44", "0.02", "0.72", "−0.02", "0.72", "−0.03", "0.52", "0.09", "0.06", "−0.02", "0.62", "−0.03", "0.53", "0.00", "0.93", "0.10", "0.05"], ["NDUFA11", "−0.02", "0.62", "0.08", "0.10", "0.00", "0.93", "−0.05", "0.29", "−0.01", "0.86", "−0.02", "0.67", "−0.07", "0.16", "0.05", "0.30", "−0.15", "0.00"], ["NDUFAF4", "−0.12", "0.01", "0.23", "1.6e−06", "−0.06", "0.22", "−0.09", "0.05", "0.03", "0.54", "−0.02", "0.76", "0.00", "1.00", "0.05", "0.29", "−0.13", "0.01"], ["NDUFA2", "−0.13", "0.01", "−0.03", "0.48", "−0.19", "1e−04", "−0.11", "0.02", "−0.02", "0.66", "−0.02", "0.64", "−0.09", "0.06", "0.01", "0.83", "−0.29", "1.7e−09"], ["NDUFB7", "−0.12", "0.01", "−0.02", "0.67", "−0.15", "0.00", "−0.09", "0.06", "−0.05", "0.32", "−0.04", "0.40", "−0.07", "0.15", "0.03", "0.49", "−0.18", "0.00"], ["NDUFS1", "0.20", "2.8e−05", "0.16", "0.00", "0.14", "0.00", "0.14", "0.00", "0.17", "0.00", "0.02", "0.69", "0.07", "0.14", "0.03", "0.57", "0.39", "0.00"], ["NDUFS2", "0.18", "0.00", "0.13", "0.01", "0.15", "0.00", "0.13", "0.01", "0.06", "0.23", "0.09", "0.06", "0.15", "0.00", "0.16", "0.00", "0.36", "1.3e−14"], ["NDUFS3", "0.12", "0.01", "−0.05", "0.29", "−0.12", "0.01", "−0.02", "0.74", "0.00", "0.93", "0.04", "0.39", "0.04", "0.39", "0.02", "0.62", "−0.10", "0.05"], ["NDUFS7", "0.15", "0.00", "−0.02", "0.73", "−0.18", "0.00", "−0.08", "0.10", "−0.03", "0.49", "−0.01", "0.89", "−0.01", "0.86", "−0.02", "0.69", "−0.11", "0.02"], ["NDUFV1", "0.05", "0.33", "−0.02", "0.71", "−0.13", "0.01", "−0.01", "0.80", "−0.04", "0.43", "0.03", "0.51", "0.18", "0.00", "0.03", "0.61", "0.08", "0.11"], ["NDUFV2", "−0.02", "0.71", "0.05", "0.29", "−0.11", "0.02", "0.15", "0.00", "0.02", "0.65", "0.06", "0.18", "−1e−04", "1.00", "0.05", "0.35", "0.01", "0.88"], ["NDUFV3", "0.06", "0.24", "−0.01", "0.84", "−0.03", "0.56", "0.07", "0.14", "0.09", "0.07", "0.03", "0.52", "0.10", "0.03", "0.08", "0.10", "0.15", "0.00"], ["Complex II", ""], ["SDHA", "0.11", "0.03", "0.03", "0.52", "−0.04", "0.46", "0.05", "0.35", "0.03", "0.52", "0.11", "0.03", "0.06", "0.20", "0.04", "0.39", "0.16", "0.00"], ["SDHB", "0.18", "0.00", "0.09", "0.07", "−0.05", "0.28", "0.05", "0.29", "−0.02", "0.76", "−0.05", "0.29", "0.08", "0.10", "−0.03", "0.56", "0.03", "0.54"], ["SDHC", "0.16", "0.00", "0.11", "0.03", "0.10", "0.04", "0.07", "0.15", "0.21", "1.4e−05", "0.06", "0.23", "−0.0029", "0.95", "0.11", "0.03", "0.11", "0.02"], ["SDHD", "0.03", "0.59", "0.08", "0.09", "−0.12", "0.01", "0.02", "0.72", "0.00", "0.96", "0.02", "0.75", "0.04", "0.46", "−0.04", "0.43", "−0.03", "0.48"], ["Complex III", ""], ["UQCRB", "−0.12", "0.02", "−0.06", "0.19", "−0.20", "2.6e−05", "−0.08", "0.09", "−0.14", "0.00", "−0.06", "0.20", "−0.1", "0.04", "−0.04", "0.47", "−0.20", "2.1e−05"], ["UQCRC1", "0.03", "0.54", "0.08", "0.09", "0.00", "0.94", "0.06", "0.25", "0.08", "0.09", "0.04", "0.39", "0.06", "0.20", "0.13", "0.01", "0.17", "0.00"], ["UQCRC2", "0.21", "1.3e−05", "0.17", "0.00", "0.05", "0.31", "0.07", "0.17", "0.00", "0.92", "−0.06", "0.23", "0.15", "0.00", "0.04", "0.37", "0.07", "0.16"], ["UQCRH", "−0.04", "0.42", "−0.13", "0.01", "−0.13", "0.01", "−0.01", "0.82", "−0.01", "0.84", "0.00", "1.00", "−0.03", "0.58", "−0.08", "0.12", "−0.17", "0.00"], ["UQCRQ", "−0.05", "0.34", "−0.06", "0.20", "−0.17", "0.00", "−0.06", "0.19", "−0.03", "0.60", "−0.02", "0.70", "−0.01", "0.77", "−0.04", "0.41", "−0.31", "3.6e−11"], ["UQCR10", "0.04", "0.43", "0.15", "0.00", "−0.1", "0.04", "0.03", "0.50", "0.00", "0.97", "−0.02", "0.70", "0.06", "0.23", "−0.02", "0.66", "−0.11", "0.02"], ["UQCR11", "−0.03", "0.57", "−0.05", "0.32", "−0.21", "9.6e−06", "−0.10", "0.04", "−0.07", "0.18", "−0.03", "0.50", "−0.1", "0.04", "−0.03", "0.59", "−0.29", "8e−10"], ["CYCS", "0.09", "0.05", "0.07", "0.18", "−0.06", "0.20", "−0.04", "0.43", "0.09", "0.06", "−0.02", "0.73", "0.02", "0.64", "0.03", "0.60", "0.11", "0.03"], ["Complex IV", ""], ["COX4I1", "0.01", "0.81", "0.10", "0.05", "−0.15", "0.00", "0.03", "0.57", "−0.09", "0.07", "−0.06", "0.26", "0.03", "0.50", "−0.06", "0.21", "−0.19", "1e−04"], ["COX4I2", "−0.07", "0.18", "0.06", "0.22", "0.25", "2.2e−07", "0.01", "0.83", "0.17", "0.00", "−0.01", "0.82", "−0.08", "0.10", "0.16", "0.00", "0.15", "0.00"], ["COX5A", "0.00", "0.95", "−0.09", "0.08", "−0.19", "9.3e−05", "−0.04", "0.42", "0.00", "0.95", "−0.04", "0.43", "−0.04", "0.42", "−0.05", "0.31", "−0.13", "0.01"], ["COX5B", "−0.22", "6.6e−06", "0.10", "0.04", "−0.18", "0.00", "−0.07", "0.13", "−0.09", "0.08", "−0.02", "0.64", "−0.02", "0.68", "−0.04", "0.36", "−0.27", "1.7e−08"], ["COX6A1", "−0.1", "0.04", "0.03", "0.53", "−0.11", "0.03", "−0.06", "0.23", "0.07", "0.13", "0.01", "0.87", "−0.10", "0.04", "0.06", "0.19", "−0.12", "0.02"], ["COX6A2", "−0.13", "0.01", "0.09", "0.06", "0.20", "3.1e−05", "0.00", "0.92", "0.14", "0.00", "0.02", "0.69", "−0.07", "0.14", "0.24", "3.6e−07", "0.04", "0.39"], ["COX6B1", "−0.06", "0.21", "−0.03", "0.61", "−0.02", "0.73", "−0.06", "0.23", "0.07", "0.15", "−0.01", "0.87", "0.01", "0.85", "0.07", "0.15", "−0.19", "0.00"], ["COX6B2", "−0.04", "0.38", "−0.01", "0.77", "0.06", "0.20", "−0.03", "0.54", "0.00", "0.94", "−0.03", "0.48", "0.00", "0.96", "0.07", "0.15", "0.23", "2.6e−06"], ["COX6C", "−0.09", "0.05", "−0.12", "0.01", "−0.20", "5e−05", "−0.032", "0.51", "−0.13", "0.01", "−0.04", "0.39", "−0.12", "0.01", "−0.01", "0.91", "−0.12", "0.01"], ["COX7A1", "−0.02", "0.64", "−0.06", "0.24", "0.13", "0.01", "−0.03", "0.56", "0.08", "0.09", "−0.04", "0.38", "−0.06", "0.19", "0.02", "0.67", "0.00", "0.99"], ["COX7A2", "−0.08", "0.09", "0.09", "0.05", "−0.04", "0.40", "−0.09", "0.06", "0.02", "0.74", "0.00", "0.93", "−0.08", "0.09", "0.01", "0.87", "−0.19", "5.8e−05"], ["COX7B", "−0.02", "0.70", "−0.01", "0.78", "−0.19", "1e−04", "−0.07", "0.14", "0.01", "0.78", "0.00", "0.95", "−0.07", "0.15", "0.00", "0.98", "−0.27", "1.1e−08"], ["COX7C", "−0.21", "9.9e−06", "0.03", "0.55", "−0.08", "0.09", "−0.09", "0.08", "−0.10", "0.04", "−0.09", "0.06", "0.00", "0.96", "−0.01", "0.84", "−0.30", "2.8e−10"], ["Complex V", ""], ["ATP5C1", "0.03", "0.51", "0.08", "0.11", "−0.06", "0.24", "−0.06", "0.22", "−0.02", "0.62", "0.01", "0.87", "−0.05", "0.36", "−0.05", "0.28", "−0.07", "0.13"], ["ATP5D", "−0.02", "0.63", "−0.01", "0.91", "−0.22", "7.6e−06", "−0.11", "0.02", "−0.15", "0.00", "−0.06", "0.26", "0.00", "0.93", "−0.04", "0.38", "−0.18", "0.00"], ["ATP5E", "−0.14", "0.00", "0.00", "0.93", "−0.05", "0.33", "−0.03", "0.54", "0.03", "0.52", "0.06", "0.26", "−0.10", "0.04", "0.02", "0.76", "−0.19", "0.00"], ["ATP5G3", "0.07", "0.14", "−0.04", "0.36", "−0.16", "0.00", "−0.08", "0.08", "−0.01", "0.87", "−0.06", "0.23", "−0.05", "0.34", "−0.07", "0.17", "−0.13", "0.01"], ["ATP5J", "−0.03", "0.52", "−0.02", "0.65", "−0.10", "0.05", "−0.04", "0.44", "0.17", "0.00", "−0.01", "0.84", "0.01", "0.89", "0.00", "0.97", "−0.17", "0.00"], ["ATP5O", "−0.10", "0.04", "−0.02", "0.75", "−0.10", "0.03", "−0.06", "0.23", "−0.07", "0.14", "−0.07", "0.14", "0.06", "0.25", "0.04", "0.46", "−0.19", "0.00"], ["ATP5S", "0.02", "0.71", "0.00", "0.99", "0.08", "0.10", "0.10", "0.03", "0.14", "0.00", "−0.01", "0.78", "0.05", "0.32", "0.13", "0.01", "0.10", "0.04"]], "row_count": 51, "column_count": 19, "numeric_cells": 801, "header_rows": 3, "locator": "section[9]/table-wrap[1]#cancers-12-01267-t003"}}, {"id": "asset:table:pmid:32429566:4", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:c09953c5c5be5e51d6f3c69469e1f975b6280fb5b29bbb34255f7d8c338a7ff0", "bytes": 2163, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[10]/table-wrap[1]#cancers-12-01267-t004", "version": null, "note": "Correlation between OCSC markers and lipid transporters and key enzymes in lipid metabolism in TCGA. Red indicates significant positive, and black indicates insignificant p-values of either positive or negative correlations.", "structure": {"pmcid": "PMC7281273", "section_index": 10, "section_title": "3.5. Correlation of OCSC Markers With Lipid Metabolism", "row_count": 12, "column_count": 19}, "table": {"label": "Table 4", "caption": "Correlation between OCSC markers and lipid transporters and key enzymes in lipid metabolism in TCGA. Red indicates significant positive, and black indicates insignificant p-values of either positive or negative correlations.", "rows": [["TCGA", "CD44", "", "CD24", "", "CD117", "", "CD133", "", "ALDH1A1", "", "SOX2", "", "4-Oct", "", "NANOG", "", "NOTCH1", ""], ["", "Pearson R", "p-Value", "Pearson R", "p-Value", "Pearson R", "p-Value", "Pearson R", "p-Value", "Pearson R", "p-Value", "Pearson R", "p-Value", "Pearson R", "p-Value", "Pearson R", "p-Value", "Pearson R", "p-Value"], ["FABP4", "0.04", "0.43", "−0.04", "0.44", "0.05", "0.28", "−0.07", "0.13", "0.05", "0.33", "−0.04", "0.43", "0.00", "0.87", "−0.06", "0.21", "0.07", "0.13"], ["CD36", "0.17", "0.00", "−0.02", "0.63", "0.11", "0.02", "−0.07", "0.14", "0.09", "0.07", "0.03", "0.51", "−0.03", "0.55", "0.00", "0.90", "0.24", "4e−07"], ["ACLY", "0.21", "9e−06", "0.13", "0.01", "0.37", "3.1e−15", "0.21", "1.8e−05", "0.15", "0.00", "0.04", "0.43", "0.01", "0.85", "0.12", "0.02", "0.51", "0.00"], ["ACACA", "0.16", "0.00", "0.20", "3.1e−05", "0.19", "0.00", "0.22", "4.5e−06", "0.10", "0.03", "0.01", "0.79", "0.08", "0.11", "0.02", "0.73", "0.32", "6.3e−12"], ["ACACB", "0.10", "0.04", "0.00", "0.99", "0.27", "1.7e−08", "0.11", "0.02", "0.13", "0.01", "0.03", "0.58", "0.10", "0.04", "0.12", "0.02", "0.40", "0.00"], ["CPT1A", "0.12", "0.01", "0.03", "0.56", "0.11", "0.02", "0.16", "0.00", "0.09", "0.07", "0.06", "0.20", "0.09", "0.07", "0.00", "0.89", "0.35", "7.1e−14"], ["CPT1B", "0.16", "0.00", "−0.07", "0.15", "−0.05", "0.30", "−0.02", "0.64", "0.00", "0.93", "0.12", "0.02", "0.13", "0.01", "0.08", "0.11", "0.17", "3e−04"], ["CPT2", "0.19", "7.7e−05", "0.03", "0.57", "0.08", "0.08", "0.18", "0.00", "0.18", "0.00", "0.09", "0.06", "0.06", "0.20", "0.09", "0.07", "0.29", "7.1e−10"], ["FASN", "0.08", "0.08", "0.06", "0.25", "0.10", "0.03", "0.05", "0.31", "0.05", "0.28", "0.00", "0.85", "−0.02", "0.66", "0.02", "0.67", "0.42", "0.00"], ["SCD1", "0.27", "1.3e−08", "0.06", "0.20", "0.11", "0.02", "0.08", "0.10", "0.08", "0.12", "0.11", "0.03", "−0.05", "0.28", "−0.02", "0.67", "0.27", "1.5e−08"]], "row_count": 12, "column_count": 19, "numeric_cells": 186, "header_rows": 2, "locator": "section[10]/table-wrap[1]#cancers-12-01267-t004"}}, {"id": "asset:table:pmid:32429566:5", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:31b381770795ed5f0ac12b44026fa7062da3fe04a91f903c2486f7145e0aa874", "bytes": 2233, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[11]/table-wrap[1]#cancers-12-01267-t005", "version": null, "note": "Correlation between OCSC markers and glutamate transporters and key enzymes in glutamate/glutamine metabolism in TCGA. Red indicates significant positive and black indicates insignificant p-values of either positive or negative correlations.", "structure": {"pmcid": "PMC7281273", "section_index": 11, "section_title": "3.6. Glutamine/Glutamate Metabolism in OCSCs", "row_count": 12, "column_count": 19}, "table": {"label": "Table 5", "caption": "Correlation between OCSC markers and glutamate transporters and key enzymes in glutamate/glutamine metabolism in TCGA. Red indicates significant positive and black indicates insignificant p-values of either positive or negative correlations.", "rows": [["TCGA", "CD44", "", "CD24", "", "CD117", "", "CD133", "", "ALDH1A1", "", "SOX2", "", "4-Oct", "", "NANOG", "", "NOTCH1", ""], ["", "Pearson R", "p-Value", "Pearson R", "p-Value", "Pearson R", "p-Value", "Pearson R", "p-Value", "Pearson R", "p-Value", "Pearson R", "p-Value", "Pearson R", "p-Value", "Pearson R", "p-Value", "Pearson R", "p-Value"], ["SLC1A1", "0.32", "1.2e−11", "0.10", "0.05", "0.04", "0.39", "0.20", "3.9e−05", "0.12", "0.01", "0.15", "0.00", "0.18", "0.00", "−0.04", "0.40", "0.09", "0.06"], ["SLC1A2", "0.16", "0.00", "0.00", "0.93", "0.25", "1e−07", "0.12", "0.01", "0.22", "4.1e−06", "0.05", "0.31", "0.04", "0.44", "0.07", "0.13", "0.14", "0.00"], ["SLC1A3", "0.20", "4.6e−05", "0.08", "0.12", "0.09", "0.08", "0.18", "0.00", "−0.04", "0.47", "0.08", "0.11", "0.20", "4.8e−05", "−0.01", "0.82", "0.15", "0.00"], ["SLC1A4", "0.27", "1.5e−08", "−0.03", "0.60", "0.27", "1.8e−08", "0.13", "0.01", "0.25", "2.3e−07", "0.11", "0.02", "0.00", "0.99", "0.09", "0.06", "0.36", "1.4e−14"], ["SLC1A5", "0.24", "3.7e−07", "−0.08", "0.10", "0.06", "0.21", "0.03", "0.56", "0.05", "0.35", "0.15", "0.00", "0.03", "0.50", "−0.03", "0.58", "0.22", "7.4e−06"], ["SLC1A6", "−0.02", "0.64", "0.02", "0.76", "0.03", "0.53", "0.02", "0.69", "0.00", "0.96", "0.01", "0.78", "−0.04", "0.38", "0.06", "0.21", "0.04", "0.40"], ["SLC1A7", "0.09", "0.08", "−0.06", "0.21", "0.43", "0.00", "0.25", "2.4e−07", "0.16", "0.00", "−0.05", "0.35", "−0.03", "0.50", "−0.04", "0.47", "0.33", "2e−12"], ["GLS", "0.15", "0.00", "−0.01", "0.86", "0.11", "0.02", "−0.01", "0.86", "0.18", "0.00", "0.03", "0.49", "0.05", "0.30", "0.13", "0.01", "0.36", "2.8e−14"], ["GLUD1", "0.10", "0.03", "0.02", "0.73", "0.11", "0.03", "0.06", "0.20", "0.11", "0.02", "−0.02", "0.68", "0.14", "0.00", "0.05", "0.35", "0.25", "2.2e−07"], ["GLUD2", "0.19", "7.8e−05", "0.04", "0.73", "0.25", "2.6e−07", "0.05", "0.31", "0.26", "4.8e−08", "0.09", "0.08", "0.15", "0.00", "0.31", "9.3e−11", "0.27", "1.3e−08"]], "row_count": 12, "column_count": 19, "numeric_cells": 185, "header_rows": 2, "locator": "section[11]/table-wrap[1]#cancers-12-01267-t005"}}], "gaps": ["asset:data:geo:GSE28799 not downloaded", "asset:data:geo:GSE28799 licence not read", "asset:data:geo:GSE64999 not downloaded", "asset:data:geo:GSE64999 licence not read"]}, "analysis": {"state": "partial", "methods": [{"id": "method-1", "family": "correlation_analysis", "specific": "pearson", "label": "Correlation analysis", "dsl_operations": ["pearson_r"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["paired_numeric_columns"], "evidence": {"score": 0.8, "band": "high", "quote": "Pearson Correlation"}}, {"id": "method-2", "family": null, "specific": null, "label": "multiple t-test with Holm–Sidak method", "dsl_operations": [], "missing_operations": [], "expressible": null, "parameters": {}, "data_shapes": [], "evidence": {"score": 1.0, "band": "verbatim", "quote": "The differential expression of the OCSCs markers and the enzymes involved in the metabolic pathways in OCSCs and their parental cells was analyzed by the multiple t-test with Holm–Sidak method, and each gene was analyzed individually between the two groups, without assuming a consistent SD with p ≤ 0.05."}}], "targets": [], "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": ["pearson_r"], "missing_operations": [], "basis": "The paper names the method it used and the corpus's method extractor maps it onto the DSL catalogue: pearson."}, "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": ["GSE28799", "GSE64999"], "resolved_accessions": ["GSE28799", "GSE64999"], "statements": ["Gene expression profiles of two studies of OCSC GSE28799 [41] and GSE64999 [42] with platform information of GPL570 and GPL17077, respectively, were extracted from Gene Expression Omnibus (GEO). Both included ovarian cancer spheroids and their parental cells. GSE28799 included OVCAR3-derived spheroids and their parental OVCAR3 in triplicates."], "basis": "The paper names GSE28799, GSE64999 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": ["pearson_r"], "assets": ["source:pmid:32429566", "data:geo:GSE28799", "asset:table:pmid:32429566:1", "asset:table:pmid:32429566:2", "asset:table:pmid:32429566:3", "asset:table:pmid:32429566:4", "asset:table:pmid:32429566:5"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:GSE28799"]}, "gaps": []}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-10-31T18:20:06Z", "independence": "single_reader"}, "evidence_check": {"method": "verbatim", "availability": null}, "calls": 3, "usage": {"prompt_tokens": 57818, "completion_tokens": 2344, "cached_tokens": 784}}, "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:32429566", "type": "paper", "label": "pmid:32429566"}, {"id": "source:pmid:32429566", "type": "manuscript", "label": "PMID 32429566 full text"}, {"id": "data:geo:GSE28799", "type": "dataset", "label": "GEO GSE28799"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:32429566", "type": "paper", "label": "pmid:32429566"}, {"id": "source:pmid:32429566", "type": "manuscript", "label": "PMID 32429566 full text"}, {"id": "data:geo:GSE28799", "type": "dataset", "label": "GEO GSE28799"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-32429566", "type": "extraction", "used": ["source:pmid:32429566"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-GSE28799", "type": "accession_resolution", "used": ["data:geo:GSE28799"], "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:32429566", "parent_hash": "sha256:96e2b62e1274cf4fa9f8107eb06bf79dc35de16627281c172b848a74e40af59a", "fork_of": null, "generation": 6}, "gaps": ["asset:data:geo:GSE28799 licence not read", "asset:data:geo:GSE28799 not downloaded", "asset:data:geo:GSE64999 licence not read", "asset:data:geo:GSE64999 not downloaded", "execution.not_run", "method.reader_named_unmapped", "review.human_critique", "review.independent_reader", "review.machine_critique"], "assays": [{"role": "analysis", "definition_id": "correlation_analysis", "definition_version": "f2132e96ae6c7a4e", "definition_digest": null, "required_operations": ["pearson_r"], "support_state": "supported", "source_hashes": {"dsl_catalogue": "f2132e96ae6c7a4e"}, "confidence": 0.8, "evidence": ["Pearson Correlation"], "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":"2026-11-04T01:32:25+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}}}