{"data":{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:30175120", "kind": "science-record", "revision": 7, "content_hash": "sha256:ba7c5b37d25133ad68a895b668e32521326323a1bae204086140f11701f1f94a", "created_at": "2026-11-01T15:40:37Z", "updated_at": "2026-11-01T22:00:01Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Identification of Key Genes and Pathways in Triple-Negative Breast Cancer by Integrated Bioinformatics Analysis.", "doi": "10.1155/2018/2760918", "pmid": "30175120", "authors": ["Pengzhi Dong", "Bing Yu", "Lanlan Pan", "Xiaoxuan Tian", "Fangfang Liu"], "journal": "BioMed research international", "year": 2018, "abstract": "PURPOSE: Triple-negative breast cancer refers to breast cancer that does not express estrogen receptor (ER), progesterone receptor (PR), or human epidermal growth factor receptor 2 (Her2). This study aimed to identify the key pathways and genes and find the potential initiation and progression mechanism of triple-negative breast cancer (TNBC).\nMETHODS: We downloaded the gene expression profiles of GSE76275 from Gene Expression Omnibus (GEO) datasets. This microarray Super-Series sets are composed of gene expression data from 265 samples which included 67 non-TNBC and 198 TNBC. Next, all the differentially expressed genes (DEGs) with p<0.01 and fold change ≥1.5 or ≤-1.5 were identified.\nRESULT: 56 upregulated and 151 downregulated genes were listed and the gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes pathway (KEGG) enrichment analysis was performed. These significantly changed genes were mainly involved in the biological process termed prostate gland morphogenesis, inner ear morphogenesis, cell maturation, digestive tract morphogenesis, autonomic nervous system development, monovalent inorganic anion homeostasis, neural crest cell development, regulation of dendrite extension and glial cell proliferation, immune system process termed T cell differentiation, regulation of immune response, and macrophage activation. Genes are mainly involved in the KEGG pathway termed Oocyte meiosis. All DEGs underwent survival analysis using datasets from The Cancer Genome Atlas (TCGA) integrated by cBioPortal, of which amplification of SRY-related HMG-box 8 (SOX8), androgen receptor (AR), and Chromosome 9 Open Reading Frame 152 (C9orf152) were significantly negative while Nik Related Kinase (NRK) and RAS oncogene family 30 (RAB30) were positively correlated to the life expectancy (p<0.05).\nCONCLUSIONS: In conclusion, these pathways and genes identified could help understanding the mechanism of development of TNBC. Besides, SOX8, AR, C9orf152, NRK and RAB30, and other key genes and pathways might be promising targets for the TNBC treatment.", "claims": [{"id": "claim-method", "statement": "In this study, survival analysis refers to the Overall Survival Kaplan-Meier Estimate. Survival analysis was performed using datasets termed Breast Cancer (METABRIC, Nature 2012 & Nat Commun 2016) from cBioPortal database.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:30175120", "locator": "sections[7] \"2.5. Survival Analysis\" paragraph 2", "quote": "In this study, survival analysis refers to the Overall Survival Kaplan-Meier Estimate. Survival analysis was performed using datasets termed Breast Cancer (METABRIC, Nature 2012 & Nat Commun 2016) from cBioPortal database."}], "state": "complete"}, {"id": "claim-data-access", "statement": "Data Availability For GEO data downloading, readers can visit the website https://www.ncbi.nlm.nih.gov/ and choose “GEO datasets” in the drop-down list.For gene enrichment analysis, a web based tool DAVID (https://david.ncifcrf.gov/) was used.For inferring the protein-protein interaction, we use web based tool named STRING (https://string-db.org/) according to the instruction. For drawing the network, Cytoscape 3.5 was used. For life span expectation analysis, we visit cBioportal.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:30175120", "locator": "sections[15] \"Data Availability\" paragraph 2", "quote": "Data Availability For GEO data downloading, readers can visit the website https://www.ncbi.nlm.nih.gov/ and choose “GEO datasets” in the drop-down list.For gene enrichment analysis, a web based tool DAVID (https://david.ncifcrf.gov/) was used.For inferring the protein-protein interaction, we use web based tool named STRING (https://string-db.org/) according to the instruction. For drawing the network, Cytoscape 3.5 was used. For life span expectation analysis, we visit cBioportal."}], "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:30175120"], "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:GSE76275"], "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:GSE76275"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:30175120", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.1155/2018/2760918", "sha256": "sha256:8b81350dccc0bfda8701bc3f76165e42060a4c2b96fafcdd750919225045aa00", "bytes": 35891, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.1155/2018/2760918", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC6098886", "source": "europe_pmc_fulltext", "coverage": "whole_body", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE76275", "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=GSE76275", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE76275", "version": null, "note": "Data Availability For GEO data downloading, readers can visit the website https://www.ncbi.nlm.nih.gov/ and choose “GEO datasets” in the drop-down list.For gene enrichment analysis, a web based tool DAVID (https://david.ncifcrf.gov/) was used.For inferring the protein-protein interaction, we use web based tool named STRING (https://string-db.org/) according to the instruction. For drawing the network, Cytoscape 3.5 was used. For life span expectation analysis, we visit cBioportal.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "Data Availability For GEO data downloading, readers can visit the website https://www.ncbi.nlm.nih.gov/ and choose “GEO datasets” in the drop-down list.For gene enrichment analysis, a web based tool DAVID (https://david.ncifcrf.gov/) was used.For inferring the protein-protein interaction, we use web based tool named STRING (https://string-db.org/) according to the instruction. For drawing the network, Cytoscape 3.5 was used. For life span expectation analysis, we visit cBioportal.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM1974566", "GSM1974567", "GSM1974568", "GSM1974569", "GSM1974570", "GSM1974571", "GSM1974572", "GSM1974573", "GSM1974574", "GSM1974575", "GSM1974576", "GSM1974577", "GSM1974578", "GSM1974579", "GSM1974580", "GSM1974581", "GSM1974582", "GSM1974583", "GSM1974584", "GSM1974585", "GSM1974586", "GSM1974587", "GSM1974588", "GSM1974589", "GSM1974590", "GSM1974591", "GSM1974592", "GSM1974593", "GSM1974594", "GSM1974595", "GSM1974596", "GSM1974597", "GSM1974598", "GSM1974599", "GSM1974600", "GSM1974601", "GSM1974602", "GSM1974603", "GSM1974604", "GSM1974605", "GSM1974606", "GSM1974607", "GSM1974608", "GSM1974609", "GSM1974610", "GSM1974611", "GSM1974612", "GSM1974613", "GSM1974614", "GSM1974615", "GSM1974616", "GSM1974617", "GSM1974618", "GSM1974619", "GSM1974620", "GSM1974621", "GSM1974622", "GSM1974623", "GSM1974624", "GSM1974625", "GSM1974626", "GSM1974627", "GSM1974628", "GSM1974629", "GSM1974630", "GSM1974631", "GSM1974632", "GSM1974633", "GSM1974634", "GSM1974635", "GSM1974636", "GSM1974637", "GSM1974638", "GSM1974639", "GSM1974640", "GSM1974641", "GSM1974642", "GSM1974643", "GSM1974644", "GSM1974645", "GSM1974646", "GSM1974647", "GSM1974648", "GSM1974649", "GSM1974650", "GSM1974651", "GSM1974652", "GSM1974653", "GSM1974654", "GSM1974655", "GSM1974656", "GSM1974657", "GSM1974658", "GSM1974659", "GSM1974660", "GSM1974661", "GSM1974662", "GSM1974663", "GSM1974664", "GSM1974665", "GSM1974666", "GSM1974667", "GSM1974668", "GSM1974669", "GSM1974670", "GSM1974671", "GSM1974672", "GSM1974673", "GSM1974674", "GSM1974675", "GSM1974676", "GSM1974677", "GSM1974678", "GSM1974679", "GSM1974680", "GSM1974681", "GSM1974682", "GSM1974683", "GSM1974684", "GSM1974685", "GSM1974686", "GSM1974687", "GSM1974688", "GSM1974689", "GSM1974690", "GSM1974691", "GSM1974692", "GSM1974693", "GSM1974694", "GSM1974695", "GSM1974696", "GSM1974697", "GSM1974698", "GSM1974699", "GSM1974700", "GSM1974701", "GSM1974702", "GSM1974703", "GSM1974704", "GSM1974705", "GSM1974706", "GSM1974707", "GSM1974708", "GSM1974709", "GSM1974710", "GSM1974711", "GSM1974712", "GSM1974713", "GSM1974714", "GSM1974715", "GSM1974716", "GSM1974717", "GSM1974718", "GSM1974719", "GSM1974720", "GSM1974721", "GSM1974722", "GSM1974723", "GSM1974724", "GSM1974725", "GSM1974726", "GSM1974727", "GSM1974728", "GSM1974729", "GSM1974730", "GSM1974731", "GSM1974732", "GSM1974733", "GSM1974734", "GSM1974735", "GSM1974736", "GSM1974737", "GSM1974738", "GSM1974739", "GSM1974740", "GSM1974741", "GSM1974742", "GSM1974743", "GSM1974744", "GSM1974745", "GSM1974746", "GSM1974747", "GSM1974748", "GSM1974749", "GSM1974750", "GSM1974751", "GSM1974752", "GSM1974753", "GSM1974754", "GSM1974755", "GSM1974756", "GSM1974757", "GSM1974758", "GSM1974759", "GSM1974760", "GSM1974761", "GSM1974762", "GSM1974763", "GSM1978883", "GSM1978884", "GSM1978885", "GSM1978886", "GSM1978887", "GSM1978888", "GSM1978889", "GSM1978890", "GSM1978891", "GSM1978892", "GSM1978893", "GSM1978894", "GSM1978895", "GSM1978896", "GSM1978897", "GSM1978898", "GSM1978899", "GSM1978900", "GSM1978901", "GSM1978902", "GSM1978903", "GSM1978904", "GSM1978905", "GSM1978906", "GSM1978907", "GSM1978908", "GSM1978909", "GSM1978910", "GSM1978911", "GSM1978912", "GSM1978913", "GSM1978914", "GSM1978915", "GSM1978916", "GSM1978917", "GSM1978918", "GSM1978919", "GSM1978920", "GSM1978921", "GSM1978922", "GSM1978923", "GSM1978924", "GSM1978925", "GSM1978926", "GSM1978927", "GSM1978928", "GSM1978929", "GSM1978930", "GSM1978931", "GSM1978932", "GSM1978933", "GSM1978934", "GSM1978935", "GSM1978936", "GSM1978937", "GSM1978938", "GSM1978939", "GSM1978940", "GSM1978941", "GSM1978942", "GSM1978943", "GSM1978944", "GSM1978945", "GSM1978946", "GSM1978947", "GSM1978948", "GSM1978949"], "sample_count": 265, "group_sizes": null, "group_sizes_basis": null, "platform": "570", "taxon": "Homo sapiens", "title": "Comprehensive genomic analysis identify novel subtypes and targets of triple-negative breast cancer", "resolution_checked_at": "2026-11-01T15:39:55Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}, {"id": "asset:table:pmid:30175120:1", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:880b98b12d0563f614dc4ad7c96746b284c5b2dcfaf8911ff52d988a97f20b77", "bytes": 590, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[10]/table-wrap[1]#tab1", "version": null, "note": "Cellular component (GO) enrichment analysis result of differentially expressed genes (DEGs) with fold change ≥1.5 or ≤-1.5 and p<0.01.", "structure": {"pmcid": "PMC6098886", "section_index": 10, "section_title": "3.2. Gene Ontology (GO) Term Enrichment Analysis and Kyoto Encyclopedia of Genes and Genomes (KEGG) Pathway Analysis of DEGs", "row_count": 8, "column_count": 4}, "table": {"label": "Table 1", "caption": "Cellular component (GO) enrichment analysis result of differentially expressed genes (DEGs) with fold change ≥1.5 or ≤-1.5 and p<0.01.", "rows": [["#pathway ID", "pathway description", "observed gene count", "false discovery rate"], ["GO.0005576", "extracellular region", "59", "0.00607"], [""], ["GO.0044421", "extracellular region part", "50", "0.00967"], [""], ["GO.0070062", "extracellular exosome", "41", "0.00967"], [""], ["GO.0031982", "vesicle", "46", "0.0402"]], "row_count": 8, "column_count": 4, "numeric_cells": 12, "header_rows": 1, "locator": "section[10]/table-wrap[1]#tab1"}}, {"id": "asset:table:pmid:30175120:2", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:433b0b41ef7fe48f0b6cf91188ac796c537eabf846d4784a21122e3964f293e5", "bytes": 1369, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[10]/table-wrap[2]#tab2", "version": null, "note": "Molecular function (GO) enrichment analysis result of differentially expressed genes (DEGs) with fold change ≥1.5 or ≤-1.5 and p<0.01.", "structure": {"pmcid": "PMC6098886", "section_index": 10, "section_title": "3.2. Gene Ontology (GO) Term Enrichment Analysis and Kyoto Encyclopedia of Genes and Genomes (KEGG) Pathway Analysis of DEGs", "row_count": 18, "column_count": 4}, "table": {"label": "Table 2", "caption": "Molecular function (GO) enrichment analysis result of differentially expressed genes (DEGs) with fold change ≥1.5 or ≤-1.5 and p<0.01.", "rows": [["#pathway ID", "pathway description", "observed gene count", "false discovery rate"], ["GO.0000977", "RNA polymerase II regulatory region sequence-specific DNA binding", "16", "0.001"], [""], ["GO.0044212", "transcription regulatory region DNA binding", "19", "0.001"], [""], ["GO.0001228", "transcriptional activator activity, RNA polymerase II transcription regulatory region sequence-specific binding", "12", "0.00502"], [""], ["GO.0000982", "transcription factor activity, RNA polymerase II core promoter proximal region sequence-specific binding", "12", "0.00599"], [""], ["GO.0001077", "transcriptional activator activity, RNA polymerase II core promoter proximal region sequence-specific binding", "10", "0.00714"], [""], ["GO.0000976", "transcription regulatory region sequence-specific DNA binding", "15", "0.00808"], [""], ["GO.0000981", "RNA polymerase II transcription factor activity, sequence-specific DNA binding", "14", "0.0459"], [""], ["GO.0000987", "core promoter proximal region sequence-specific DNA binding", "10", "0.0459"], [""], ["GO.0001158", "enhancer sequence-specific DNA binding", "5", "0.0459"]], "row_count": 18, "column_count": 4, "numeric_cells": 27, "header_rows": 1, "locator": "section[10]/table-wrap[2]#tab2"}}, {"id": "asset:table:pmid:30175120:3", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:0278b31afd7fc370d78c1fe600de800b6184f75bac2f839ef49e1fcaf04af7c5", "bytes": 941, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[10]/table-wrap[3]#tab3", "version": null, "note": "Biological process (GO) enrichment analysis result of differentially expressed genes (DEGs) with fold change ≥1.5 or ≤-1.5 and p<0.01.", "structure": {"pmcid": "PMC6098886", "section_index": 10, "section_title": "3.2. Gene Ontology (GO) Term Enrichment Analysis and Kyoto Encyclopedia of Genes and Genomes (KEGG) Pathway Analysis of DEGs", "row_count": 18, "column_count": 4}, "table": {"label": "Table 3", "caption": "Biological process (GO) enrichment analysis result of differentially expressed genes (DEGs) with fold change ≥1.5 or ≤-1.5 and p<0.01.", "rows": [["#pathway ID", "pathway description", "observed gene count", "false discovery rate"], ["GO.0014032", "neural crest cell development", "6", "0.0203"], [""], ["GO.0014033", "neural crest cell differentiation", "6", "0.0203"], [""], ["GO.0030855", "epithelial cell differentiation", "15", "0.0203"], [""], ["GO.0040007", "growth", "14", "0.0203"], [""], ["GO.0048589", "developmental growth", "12", "0.0203"], [""], ["GO.0051094", "positive regulation of developmental process", "23", "0.0203"], [""], ["GO.0060429", "epithelium development", "22", "0.0203"], [""], ["GO.0042127", "regulation of cell proliferation", "27", "0.0239"], [""], ["GO.0002064", "epithelial cell development", "9", "0.0382"]], "row_count": 18, "column_count": 4, "numeric_cells": 27, "header_rows": 1, "locator": "section[10]/table-wrap[3]#tab3"}}, {"id": "asset:table:pmid:30175120:4", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:dadf33dfe2e215a64cbd1a13d3d53c48aae2001429aaf758b8c017d9fd460a19", "bytes": 495, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[10]/table-wrap[4]#tab4", "version": null, "note": "KEGG pathway analysis", "structure": {"pmcid": "PMC6098886", "section_index": 10, "section_title": "3.2. Gene Ontology (GO) Term Enrichment Analysis and Kyoto Encyclopedia of Genes and Genomes (KEGG) Pathway Analysis of DEGs", "row_count": 20, "column_count": 2}, "table": {"label": "Table 4", "caption": "KEGG pathway analysis", "rows": [["Category", "KEGG_PATHWAY"], ["Term", "hsa04114: Oocyte meiosis"], [""], ["Count", "4"], [""], ["%", "0.016343875"], [""], ["P Value", "0.0711977"], [""], ["Genes", "PGR, AR, BUB1, CDC20"], [""], ["List Total", "62"], [""], ["Pop Hits", "109"], [""], ["Pop Total", "6910"], [""], ["Fold Enrichment", "4.089967446"], [""], ["Bonferroni", "0.999835961"]], "row_count": 20, "column_count": 2, "numeric_cells": 10, "header_rows": 1, "locator": "section[10]/table-wrap[4]#tab4"}}], "gaps": ["asset:data:geo:GSE76275 not downloaded", "asset:data:geo:GSE76275 licence not read"]}, "analysis": {"state": "complete", "methods": [{"id": "method-1", "family": "survival_analysis", "specific": "kaplan_meier", "label": "Survival analysis", "dsl_operations": ["survival_km"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["time_to_event_with_censoring"], "evidence": {"score": 1.0, "band": "verbatim", "quote": "In this study, survival analysis refers to the Overall Survival Kaplan-Meier Estimate. Survival analysis was performed using datasets termed Breast Cancer (METABRIC, Nature 2012 & Nat Commun 2016) from cBioPortal database."}}, {"id": "method-2", "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": 0.8, "band": "high", "quote": "Protein-Protein Interaction"}}, {"id": "method-3", "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"}}], "targets": [], "gaps": []}, "capability": {"state": "complete", "requirements": [{"capability_id": "capability:computational_analysis", "label": "Computational analysis platform", "assay_families": ["meta_analysis", "machine_learning", "survival_analysis", "statistical_regression", "pca", "molecular_docking", "network_analysis", "differential_expression", "gwas"], "availability_state": "owned", "tier_unlocked": "R1", "candidate": "Automated Assays Laravel application and simulated adapters"}], "gaps": []}, "readiness": {"state": "complete", "tier": "R1", "blocking_axis": "none", "blocked_on": "nothing:replicable_now", "axes": {"method": {"tier": "R1", "expressible": true, "required_operations": ["survival_km"], "missing_operations": [], "basis": "The paper names the method it used and the corpus's method extractor maps it onto the DSL catalogue: kaplan_meier."}, "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": ["GSE76275"], "resolved_accessions": ["GSE76275"], "statements": ["Data Availability For GEO data downloading, readers can visit the website https://www.ncbi.nlm.nih.gov/ and choose “GEO datasets” in the drop-down list.For gene enrichment analysis, a web based tool DAVID (https://david.ncifcrf.gov/) was used.For inferring the protein-protein interaction, we use web based tool named STRING (https://string-db.org/) according to the instruction. For drawing the network, Cytoscape 3.5 was used. For life span expectation analysis, we visit cBioportal."], "basis": "The paper names GSE76275 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": ["survival_km"], "assets": ["source:pmid:30175120", "data:geo:GSE76275", "asset:table:pmid:30175120:1", "asset:table:pmid:30175120:2", "asset:table:pmid:30175120:3", "asset:table:pmid:30175120:4"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:GSE76275"]}, "gaps": []}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-10-31T18:12:19Z", "independence": "single_reader"}, "evidence_check": {"method": "verbatim", "availability": "verbatim"}, "calls": 3, "usage": {"prompt_tokens": 29916, "completion_tokens": 1613, "cached_tokens": 10248}}, "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:30175120", "type": "paper", "label": "pmid:30175120"}, {"id": "source:pmid:30175120", "type": "manuscript", "label": "PMID 30175120 full text"}, {"id": "data:geo:GSE76275", "type": "dataset", "label": "GEO GSE76275"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:30175120", "type": "paper", "label": "pmid:30175120"}, {"id": "source:pmid:30175120", "type": "manuscript", "label": "PMID 30175120 full text"}, {"id": "data:geo:GSE76275", "type": "dataset", "label": "GEO GSE76275"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-30175120", "type": "extraction", "used": ["source:pmid:30175120"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-GSE76275", "type": "accession_resolution", "used": ["data:geo:GSE76275"], "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:30175120", "parent_hash": "sha256:c1dc34efb8b2fe2f23e089013d90dc14b5dc3474cbb0b887fa3cecae54ef1b84", "fork_of": null, "generation": 6}, "gaps": ["asset:data:geo:GSE76275 licence not read", "asset:data:geo:GSE76275 not downloaded", "execution.not_run", "review.human_critique", "review.independent_reader", "review.machine_critique"], "assays": [{"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": ["Gene Expression Omnibus (GEO) datasets. This microarray Super-Series sets are composed of gene expre"], "order_basis": "paper_text_order:528", "id": "assay:1"}, {"role": "analysis", "definition_id": "survival_analysis", "definition_version": "f2132e96ae6c7a4e", "definition_digest": null, "required_operations": ["survival_km"], "support_state": "supported", "source_hashes": {"dsl_catalogue": "f2132e96ae6c7a4e"}, "confidence": 1.0, "evidence": ["In this study, survival analysis refers to the Overall Survival Kaplan-Meier Estimate. Survival analysis was performed using datasets termed Breast Cancer (METABRIC, Nature 2012 & Nat Commun 2016) from cBioPortal database."], "order_basis": "consumes_earlier_output", "id": "assay:2"}]},"meta":{"api_version":"v1","automation_ladder_snapshot":"ba34b49490d9bfaf","automation_ladder_caveats":["Method extraction is rule-based and has no hand-judged accuracy sample. Evidence bands order textual support; method agreement intervals are null (n=0), never probabilities. Work-type validation does not validate methods.","Operation coverage describes only explicitly named methods. It does not prove a complete protocol, compatible parameters, successful compilation or re-execution. Unrecognised or ambiguous methods require review.","Data reachability is a textual accession or public-data statement. No dataset was downloaded or checked for access, completeness or licence.","Capabilities are planning states seeded from the dated equipment register. No bench ownership, completed quote or partner booking is inferred. Procurement counts are dependencies, not guaranteed replications or financial returns.","Tier and blocker counts are deterministic assessments of this corpus, not measured agreement. R3 is reserved for procurement; unresolved methods and data require human work (R4). The most restrictive axis wins, with capability, method, data as tie-breaks. Resolving one blocker can leave another at the same tier."],"engine":"corpus_engine","engine_provider":"rule_based_v1+lex99e1195c7d6f","run_id":"run-20261023T122449232913","source":"esearch","source_detail":"PubMed mirror biomed_pubmed (read-only)","run_status":"complete","imported_at":"2026-11-03T20:16:52+00:00","generated_at":"2026-11-04T01:46:58+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}}}