{"data":{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:31316139", "kind": "science-record", "revision": 5, "content_hash": "sha256:3ca8d9283c6112ecbf5169161c2f0ab08d0a77b7cd6fc35df02bfa7881c1d5b9", "created_at": "2026-11-01T15:40:47Z", "updated_at": "2026-11-01T18:51:04Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Proteogenomic Analysis of Protein Sequence Alterations in Breast Cancer Cells.", "doi": "10.1038/s41598-019-46897-z", "pmid": "31316139", "authors": ["Iulia M Lazar", "Arba Karcini", "Shreya Ahuja", "Carly Estrada-Palma"], "journal": "Scientific reports", "year": 2019, "abstract": "Cancer evolves as a result of an accumulation of mutations and chromosomal aberrations. Developments in sequencing technologies have enabled the discovery and cataloguing of millions of such mutations. The identification of protein-level alterations, typically by using reversed-phase protein arrays or mass spectrometry, has lagged, however, behind gene and transcript-level observations. In this study, we report the use of mass spectrometry for detecting the presence of mutations-missense, indels and frame shifts-in MCF7 and SKBR3 breast cancer, and non-tumorigenic MCF10A cells. The mutations were identified by expanding the database search process of raw mass spectrometry files by including an in-house built database of mutated peptides (XMAn-v1) that complemented a minimally redundant, canonical database of Homo sapiens proteins. The work resulted in the identification of nearly 300 mutated peptide sequences, of which ~50 were characterized by quality tandem mass spectra. We describe the criteria that were used to select the mutated peptide sequences, evaluate the parameters that characterized these peptides, and assess the artifacts that could have led to false peptide identifications. Further, we discuss the functional domains and biological processes that may be impacted by the observed peptide alterations, and how protein-level detection can support the efforts of identifying cancer driving mutations and genes. Mass spectrometry data are available via ProteomeXchange with identifier PXD014458.", "claims": [{"id": "claim-data-access", "statement": "Data analyzed in this study are included in the Supplementary Information files that include: full list of peptides with altered amino acid sequences, peptide characteristics and Proteome Discoverer search parameters; spectral count data for the mutated peptides, non-mutated counterparts and parent proteins; matches to cancer driver genes and protein variants; full tandem mass spectra of selected peptides. The mass spectrometry raw files that generated high quality mutated peptide tandem mass spectra have been deposited to the ProteomeXchange Consortium via the PRIDE68 partner repository with the dataset identifier PXD014458.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:31316139", "locator": "sections[20] \"notes\" paragraph 1", "quote": "Data analyzed in this study are included in the Supplementary Information files that include: full list of peptides with altered amino acid sequences, peptide characteristics and Proteome Discoverer search parameters; spectral count data for the mutated peptides, non-mutated counterparts and parent proteins; matches to cancer driver genes and protein variants; full tandem mass spectra of selected peptides. The mass spectrometry raw files that generated high quality mutated peptide tandem mass spectra have been deposited to the ProteomeXchange Consortium via the PRIDE68 partner repository with the dataset identifier PXD014458."}], "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:31316139"], "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:PXD014458"], "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:PXD014458"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:31316139", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.1038/s41598-019-46897-z", "sha256": "sha256:191bbafc5185795ea6d9ef1f9df13c53fc927bc2ac695c04f6fe06fc50a031f0", "bytes": 55962, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.1038/s41598-019-46897-z", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC6637242", "source": "europe_pmc_fulltext", "coverage": "whole_body_without_references", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:PXD014458", "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=PXD014458", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "PXD014458", "version": null, "note": "Data analyzed in this study are included in the Supplementary Information files that include: full list of peptides with altered amino acid sequences, peptide characteristics and Proteome Discoverer search parameters; spectral count data for the mutated peptides, non-mutated counterparts and parent proteins; matches to cancer driver genes and protein variants; full tandem mass spectra of selected peptides. The mass spectrometry raw files that generated high quality mutated peptide tandem mass spectra have been deposited to the ProteomeXchange Consortium via the PRIDE68 partner repository with the dataset identifier PXD014458.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "Data analyzed in this study are included in the Supplementary Information files that include: full list of peptides with altered amino acid sequences, peptide characteristics and Proteome Discoverer search parameters; spectral count data for the mutated peptides, non-mutated counterparts and parent proteins; matches to cancer driver genes and protein variants; full tandem mass spectra of selected peptides. The mass spectrometry raw files that generated high quality mutated peptide tandem mass spectra have been deposited to the ProteomeXchange Consortium via the PRIDE68 partner repository with the dataset identifier PXD014458.", "access_statement_kind": "data_availability_statement", "sample_accessions": [], "sample_count": null, "group_sizes": null, "group_sizes_basis": null, "platform": null, "taxon": null, "title": "Proteomic breast cancer data set for exploring somatic mutations", "resolution_checked_at": "2026-10-31T18:35:55Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}, {"id": "asset:table:pmid:31316139:1", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:5dd9849854076a1cc0b432684c72b63e10bd547de555f245cbcfe1e9f02d81bb", "bytes": 5380, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[5]/table-wrap[1]#Tab1", "version": null, "note": "Selected peptides with mutated sequences.", "structure": {"pmcid": "PMC6637242", "section_index": 5, "section_title": "Artifacts that can lead to false positive identifications", "row_count": 53, "column_count": 6}, "table": {"label": "Table 1", "caption": "Selected peptides with mutated sequences.", "rows": [["Sequence", "UniProt ID", "Protein Name", "Mutation", "Cells line presence", "Pfam Domain"], ["AFQHLSEAVQAAEEEAQPPSWSCGLAAGVIDAYMTLADFCDQQLR", "P78527", "DNA-dependent protein kinase catalytic subunit", "P3405L", "MCF10", "FAT"], ["AGNVSKDEIDSAVKMLVSLK", "P23381", "Tryptophan–tRNA ligase, cytoplasmic", "A31V", "MCF10", "WHEP-TRS"], ["AINQSQSVQESLESLLQSIGEVEQNLEGK", "Q9UPN3-5", "Isoform 4 of Microtubule-actin cross-linking factor 1", "A2547?", "MCF10", ""], ["ALMLQGVDLLDDAVAVTMGPK", "C9JL25", "60 kDa heat shock protein, mitochondrial (Fragment)", "A90D", "MCF7, MCF10, SKBR3", "Cpn60 TCP1"], ["AMQAAGQIPATALLPTMTPDGLSVTPTPVPVVGSQMTR", "P26368", "Splicing factor U2AF 65 kDa subunit", "A131S", "MCF7", ""], ["ASTVKSVLELIPELNEKGEAYNSLMK", "P42704", "Leu-rich PPR motif-containing protein, mitochondrial", "E1318G", "MCF7, MCF10", ""], ["CAPLFSGTEHHASLIDSLLHTVYRLSK", "Q92736", "Ryanodine receptor 2", "A2536S", "MCF7", ""], ["CQEKWDKLLLTSTEK", "Q7L0Y3", "Mitochondrial ribonuclease P protein 1", "Y262C", "MCF7, MCF10", "tRNA m1G MT"], ["DDLQFLADLEELITKFQVFRISQR", "Q9Y6X0", "SET-binding protein", "H971Q", "MCF7, MCF10, SKBR3", ""], ["DIMTYVSSFYHAFSGAQK", "O43707", "Alpha-actinin-4", "A256D", "MCF7, MCF10", "CH"], ["DQEGQDLLLFIDNIFR", "P06576", "ATP synthase subunit beta, mitochondrial", "V301L", "SKBR3", "ATP-synt ab"], ["EAMQQADDWLGIPQVITPEEIVDPNVDEHSVMTYMSQFPK", "P21333", "Filamin-A", "L261M", "MCF7, MCF10", "CH"], ["EAVMSFSITETEKIK", "Q5T4T6", "Synaptonemal complex protein 2-like", "N353S", "MCF10", ""], ["EFADSLGIPFLETSAKNAMNVEQSFMTMAAEIK", "P62820", "Ras-related protein Rab-1A", "T159M", "SKBR3, MCF7", "Ras"], ["EFDTLSGKVEESPDK", "Q9BXX2", "Ankyrin repeat domain-containing protein 30B", "L760V", "SKBR3", ""], ["EIYPYVIQERRPTLNELGISTPEELGLDKV", "P20674", "Cytochrome c oxidase subunit 5 A, mitochondrial", "L130R", "SKBR3, MCF7", "COX5A"], ["EQLQQEQALLEEIER", "Q15149", "Plectin", "R1386Q", "SKBR3, MCF7", ""], ["FGLAHLMALGLGPWMAVEIPDLIQK", "Q9Y3C8", "Ubiquitin-fold modifier-conjugating enzyme 1", "L146M", "MCF10", "UFC1"], ["FQSSAVMALQEGCEAYLVGLFEDTNLCAIHAK", "P68431", "Histone H3.1", "A96G", "SKBR3, MCF10", "Histone"], ["FTLDCTHPVEDGIMDAANYEQFLQER", "P35268", "60 S ribosomal protein L22", "39Y", "SKBR3, MCF10", "Ribosomal L22e"], ["GCIEKLSEDVEQLKK", "P61266", "Syntaxin-1B", "V53L", "MCF7", "Syntaxin"], ["GFDFVTFESPADAK", "P38159-3", "Isoform 3 of RNA-binding motif protein, X chr", "A52D", "MCF10", "RRM 1"], ["GFGFITFTNPEHASDAMR", "P98179", "Putative RNA-binding protein 3", "V62D", "MCF7", "RRM 1"], ["GMLDLLEVHLLDFPNIVIK", "Q6P2Q9", "Pre-mRNA-processing-splicing factor 8", "P1871L", "MCF7", "PRP8 domainIV"], ["GTAAAAAAAAAAAAAK (insertion in frame)", "P50914", "60 S ribosomal protein L14", "A159_K160insAAA", "MCF7, MCF10", ""], ["HQGVMVGMCQKDSYVGDEAQSK", "P68133", "Actin, alpha skeletal muscle", "G50C", "MCF7, MCF10, SKBR3", "Actin"], ["HRILPEKYPPPTELLDLQPLPVSALR", "O75643", "U5 small nuclear ribonucleoprotein 200 kDa helicase", "L1289R", "MCF7", ""], ["IMSLVDPNHCGLVTFQAFIDFMSR", "O43707", "Alpha-actinin-4", "S823C", "SKBR3, MCF7", ""], ["KHTLSFVDVGTGK", "P31040", "Ubiquinone flavoprotein subunit, mitochondrial", "Y629F", "MCF7", "Succ DH flav C"], ["KSQESLTENPSETLKPATSISSTSQTKGINVK", "F5GXV7", "Neurobeachin", "I1735T", "MCF10", ""], ["LCGLLVLGSWCISVMGFLLETLTILR", "O60412", "Olfactory receptor 7C2", "S156F", "MCF10", "7tm 4"], ["LCYVALYFEQEMATAASSSSLEK", "Q6S8J3", "POTE ankyrin domain family member E", "D922Y", "MCF7", "Actin"], ["LDTNSDGQLDYSEFLNLIGGLAMACHDSFLK", "P31949", "Protein S100-A11", "F77Y", "MCF10", "EF-hand 1"], ["LFDHLESPTPNPTEPLFLAQAEVYK", "P49327", "Fatty acid synthase", "P972L", "SKBR3", "PS-DH"], ["LFLASLAAAGSGTDAQVALENEVK", "Q7Z6Z7", "E3 ubiquitin-protein ligase HUWE1", "V2153E", "SKBR3", ""], ["LTENLSALQR", "Q8TD16-2", "Isoform 2 of Protein bicaudal D homolog 2", "R398Q", "MCF7", "BicD"], ["LTQAQIFDYSEIPNFPR", "P00491", "Purine nucleoside phosphorylase", "G51S", "MCF7", "PNP UDP 1"], ["MDATFIGNSTAIQELFK", "P04350", "Tubulin beta-4A chain", "A364D", "MCF7, MCF10, SKBR3", "Tubulin C"], ["MHDMNTDQENLVGTHDAPIR", "O43684", "Mitotic checkpoint protein BUB3", "L84M", "MCF7", ""], ["MLVVLRQGTREEDDVVSEDLVQQDVQDLYEAGELK", "P08133", "Annexin A6", "L162R", "SKBR3", ""], ["QVHPDTGISSKVMGIMNSFVNDIFER", "P23527", "Histone H2B type 1-O", "A59V", "SKBR3, MCF7", "Histone"], ["QVYPDTGISSKAMGIMNSFVNDIFER", "O60814", "Histone H2B type 1-K", "H50Y", "SKBR3, MCF7", "Histone"], ["SDASSGQSGSRSASRTTR", "P20930", "Filaggrin", "R884S", "SKBR3", ""], ["SLGQNPTEAELQDMINEVDADGNGTIDFPEFFTMMAR", "P62158", "Calmodulin", "L70F", "MCF7, MCF10, SKBR3", "EF-hand 7"], ["SMGIMNSFVNDIFER", "Q8N257", "Histone H2B type 3-B", "A59S", "MCF7, MCF10, SKBR3", "Histone"], ["SVIVVLRLNVDLQAVVIFELVY (del/frame shift)", "Q8TC27", "Disintegrin and metalloproteinase domain protein 32", "K388fs*39", "SKBR3, MCF7", ""], ["SYELPDGQVITIGKER", "P68133", "Actin, alpha skeletal muscle", "N254K", "MCF7, MCF10, SKBR3", "Actin"], ["TSPDPLPVSAAPSKAGLPR", "Q13469", "Nuclear factor of activated T-cells, cytoplasmic 2", "S330L", "MCF7", ""], ["TTGIVMDSGDGVTHTVPIYEAYALPHAILR", "P63261", "Actin, cytoplasmic 2", "G168A", "MCF7, MCF10, SKBR3", "Actin"], ["TVSLGAGSKDELHIVEAEAMNYEGSPIK", "P06748-3", "Isoform 3 of Nucleophosmin", "A53S", "SKBR3, MCF10", "Nucleoplasmin"], ["VSELEEFINGPNNAHIQQVGDR", "P53675", "Clathrin heavy chain 2", "D1188E", "MCF10", "Clathrin"], ["VTNGAFTGEISLGMIK", "P60174-1", "Isoform 2 of Triosephosphate isomerase", "P81L", "SKBR3, MCF7", "TIM"]], "row_count": 53, "column_count": 6, "numeric_cells": 162, "header_rows": 1, "locator": "section[5]/table-wrap[1]#Tab1"}}, {"id": "asset:table:pmid:31316139:2", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:821ff33d1370179d0e0d43de353987adc33e9ad0fa5d11cd94468f5f272edeee", "bytes": 719, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[7]/table-wrap[1]#Tab2", "version": null, "note": "Hypothetical spectral count scenarios that reflect the detectability of mutated peptides and proteins in a subpopulation of cancer cells that carry the mutation.", "structure": {"pmcid": "PMC6637242", "section_index": 7, "section_title": "Discussion", "row_count": 4, "column_count": 5}, "table": {"label": "Table 2", "caption": "Hypothetical spectral count scenarios that reflect the detectability of mutated peptides and proteins in a subpopulation of cancer cells that carry the mutation.", "rows": [["", "Small cell number/Low abundance protein", "Large cell number/Low abundance protein", "Small cell number/High abundance protein", "Large cell number/High abundance protein"], ["Spectral counts of the mutated peptides", "Zero-to-low", "Low", "Low", "High"], ["Spectral counts of the non-mutated counter-peptides", "Low", "Zero-to-low", "High", "Low"], ["Spectral counts of the mutated protein", "Low", "Low", "High", "High"]], "row_count": 4, "column_count": 5, "numeric_cells": 0, "header_rows": 1, "locator": "section[7]/table-wrap[1]#Tab2"}}], "gaps": ["asset:data:geo:PXD014458 not downloaded", "asset:data:geo:PXD014458 licence not read"]}, "analysis": {"state": "absent", "methods": [], "targets": [], "gaps": ["method", "operations"]}, "capability": {"state": "complete", "requirements": [{"capability_id": "capability:computational_analysis", "label": "Computational analysis platform", "assay_families": ["meta_analysis", "machine_learning", "survival_analysis", "statistical_regression", "pca", "molecular_docking", "network_analysis", "differential_expression", "gwas"], "availability_state": "owned", "tier_unlocked": "R1", "candidate": "Automated Assays Laravel application and simulated adapters"}], "gaps": []}, "readiness": {"state": "blocked", "tier": "R4", "blocking_axis": "method", "blocked_on": "method:not_determinable", "axes": {"method": {"tier": "R4", "expressible": false, "required_operations": [], "missing_operations": [], "basis": "The reader quoted the method the paper names (not named), but the corpus's method extractor could not map it onto a DSL operation, so the method is published but not expressible."}, "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": ["PXD014458"], "resolved_accessions": ["PXD014458"], "statements": ["Data analyzed in this study are included in the Supplementary Information files that include: full list of peptides with altered amino acid sequences, peptide characteristics and Proteome Discoverer search parameters; spectral count data for the mutated peptides, non-mutated counterparts and parent proteins; matches to cancer driver genes and protein variants; full tandem mass spectra of selected peptides. The mass spectrometry raw files that generated high quality mutated peptide tandem mass spectra have been deposited to the ProteomeXchange Consortium via the PRIDE68 partner repository with the dataset identifier PXD014458."], "basis": "The paper names PXD014458 in ProteomeXchange Consortium via the PRIDE partner repository and the accession resolves in the repository. No dataset was downloaded and no licence was read."}}, "can_run": {"dsl_operations": [], "assets": ["source:pmid:31316139", "data:geo:PXD014458", "asset:table:pmid:31316139:1", "asset:table:pmid:31316139:2"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:PXD014458"]}, "gaps": ["method:not_determinable"]}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-10-31T18:47:38Z", "independence": "single_reader"}, "evidence_check": {"method": null, "availability": "verbatim"}, "calls": 3, "usage": {"prompt_tokens": 39564, "completion_tokens": 1530, "cached_tokens": 792}}, "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:31316139", "type": "paper", "label": "pmid:31316139"}, {"id": "source:pmid:31316139", "type": "manuscript", "label": "PMID 31316139 full text"}, {"id": "data:geo:PXD014458", "type": "dataset", "label": "GEO PXD014458"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:31316139", "type": "paper", "label": "pmid:31316139"}, {"id": "source:pmid:31316139", "type": "manuscript", "label": "PMID 31316139 full text"}, {"id": "data:geo:PXD014458", "type": "dataset", "label": "GEO PXD014458"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-31316139", "type": "extraction", "used": ["source:pmid:31316139"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-PXD014458", "type": "accession_resolution", "used": ["data:geo:PXD014458"], "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:31316139", "parent_hash": "sha256:977d36b3e84e8cc344a57888ae34dd9c6f4d66736253eb1375acbbb9d36e45b1", "fork_of": null, "generation": 4}, "gaps": ["asset:data:geo:PXD014458 licence not read", "asset:data:geo:PXD014458 not downloaded", "execution.not_run", "method", "operations", "review.human_critique", "review.independent_reader", "review.machine_critique"], "assays": [{"role": "data_generation", "definition_id": "mass_spectrometry", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.99, "evidence": ["ly by using reversed-phase protein arrays or mass spectrometry, has lagged, however, behind gene and transc", "vations. In this study, we report the use of mass spectrometry for detecting the presence of mutations-miss", "expanding the database search process of raw mass spectrometry files by including an in-house built databas", "ntifying cancer driving mutations and genes. Mass spectrometry data are available via ProteomeXchange with"], "order_basis": "paper_text_order:337", "id": "assay:1"}, {"role": "data_generation", "definition_id": "cell_culture", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.99, "evidence": ["tations-missense, indels and frame shifts-in MCF7 and SKBR3 breast cancer, and non-tumorigenic", "Methods Materials The breast cancer (MCF7, SKBR3) and nontumorigenic (MCF10) cell line", "rious factors: SKBR3 in McCoy 5 A + FBS 10%; MCF7 in EMEM + bovine insulin 10 μg/mL + FBS 10%;"], "order_basis": "paper_text_order:555", "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":"2026-11-04T00:35:33+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}}}