{"data":{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:28883813", "kind": "science-record", "revision": 6, "content_hash": "sha256:de847a1c7bb5914da8bae61ab49285c4405efbc0b7b80e88699911f1597db197", "created_at": "2026-11-01T15:40:28Z", "updated_at": "2026-11-01T21:21:03Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "A Structural and Functional Elucidation of the Rumen Microbiome Influenced by Various Diets and Microenvironments.", "doi": "10.3389/fmicb.2017.01605", "pmid": "28883813", "authors": ["Simon Deusch", "Amélia Camarinha-Silva", "Jürgen Conrad", "Uwe Beifuss", "Markus Rodehutscord", "Jana Seifert"], "journal": "Frontiers in microbiology", "year": 2017, "abstract": "The structure and function of the microbiome inhabiting the rumen are, amongst other factors, mainly shaped by the animal's feed intake. Describing the influence of different diets on the inherent community arrangement and associated metabolic activities of the most active ruminal fractions (bacteria and archaea) is of great interest for animal nutrition, biotechnology, and climatology. Samples were obtained from three fistulated Jersey cows rotationally fed with corn silage, grass silage or grass hay, each supplemented with a concentrate mixture. Samples were fractionated into ruminal fluid, particle-associated rumen liquid, and solid matter. DNA, proteins and metabolites were analyzed subsequently. DNA extracts were used for Illumina sequencing of the 16S rRNA gene and the metabolomes of rumen fluids were determined by 500 MHz-NMR spectroscopy. Tryptic peptides derived from protein extracts were measured by LC-ESI-MS/MS and spectra were processed by a two-step database search for quantitative metaproteome characterization. Data are available via ProteomeXchange with the identifier PXD006070. Protein- and DNA-based datasets revealed significant differences between sample fractions and diets and affirmed similar trends concerning shifts in phylogenetic composition. Ribosomal genes and proteins belonging to the phylum of Proteobacteria, particularly Succinivibrionaceae, exhibited a higher abundance in corn silage-based samples while fiber-degraders of the Lachnospiraceae family emerged in great quantities throughout the solid phase fractions. The analysis of 8163 quantified bacterial proteins revealed the presence of 166 carbohydrate active enzymes in varying abundance. Cellulosome affiliated proteins were less expressed in the grass silage, glycoside hydrolases appeared in slightest numbers in the corn silage. Most expressed glycoside hydrolases belonged to families 57 and 2. Enzymes analogous to ABC transporters for amino acids and monosaccharides were more abundant in the corn silage whereas oligosaccharide transporters showed a higher abundance in the fiber-rich diets. Proteins involved in carbon metabolism were detected in high numbers and identification of metabolites like short-chain fatty acids, methylamines and phenylpropionate by NMR enabled linkage between producers and products. This study forms a solid basis to retrieve deeper insight into the complex network of microbial adaptation in the rumen.", "claims": [{"id": "claim-method", "statement": "One-way analysis of similarities (ANOSIM) was used to determine statistical differences in protein and OTU abundance between diets, sample fractions and host animals (Clarke and Warwick, 2001).", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:28883813", "locator": "sections[11] \"Statistical analyses\" paragraph 2", "quote": "One-way analysis of similarities (ANOSIM) was used to determine statistical differences in protein and OTU abundance between diets, sample fractions and host animals (Clarke and Warwick, 2001)."}], "state": "complete"}, {"id": "claim-data-access", "statement": "Data are available via ProteomeXchange with the identifier PXD006070.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:28883813", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "Data are available via ProteomeXchange with the identifier PXD006070."}], "state": "complete"}, {"id": "claim-target-result", "statement": "ANOSIM showed that bacterial protein abundance differed significantly between corn silage and grass silage diets (R = 0.600, P = 0.0001) and between corn silage and hay diets (R = 0.442, P = 0.0001); the underlying sequencing and mass-spectrometry data are available through the European Nucleotide Archive under accession PRJEB19491 and ProteomeXchange under identifier PXD006070.", "kind": "quantitative", "target": {"value": 0.0001, "unit": "p-value", "tolerance": null, "source": "ANOSIM verified significant differences in bacterial protein abundances regarding the diets with an R-value of 0.600 (P = 0.0001) for the corn silage- and grass silage-based samples and 0.442 (P = 0.0001) for the corn silage- and hay-derived samples."}, "evidence": [{"asset": "source:pmid:28883813", "locator": "sections[13] \"Metaproteomics and amplicon sequencing of the rumen microbiome\" paragraph 2", "quote": "ANOSIM verified significant differences in bacterial protein abundances regarding the diets with an R-value of 0.600 (P = 0.0001) for the corn silage- and grass silage-based samples and 0.442 (P = 0.0001) for the corn silage- and hay-derived samples."}, {"asset": "source:pmid:28883813", "locator": "sections[11] \"Statistical analyses\" paragraph 2", "quote": "One-way analysis of similarities (ANOSIM) was used to determine statistical differences in protein and OTU abundance between diets, sample fractions and host animals (Clarke and Warwick, 2001)."}, {"asset": "source:pmid:28883813", "locator": "sections[6] \"Illumina amplicon sequencing\" paragraph 2", "quote": "Sequences were submitted to European Nucleotide Archive under the study accession number PRJEB19491."}, {"asset": "source:pmid:28883813", "locator": "sections[9] \"Bioinformatic data analysis\" paragraph 2", "quote": "The mass spectrometry data have been deposited to the ProteomeXchange Consortium via the PRIDE partner repository (Vizcaino et al., 2016) with the dataset identifier PXD006070."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "ANOSIM showed that bacterial protein abundance differed significantly between corn silage and grass silage diets (R = 0.600, P = 0.0001) and between corn silage and hay diets (R = 0.442, P = 0.0001); the underlying sequencing and mass-spectrometry data are available through the European Nucleotide Archive under accession PRJEB19491 and ProteomeXchange under identifier PXD006070.", "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:28883813"], "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:PXD006070"], "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:PXD006070"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:28883813", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.3389/fmicb.2017.01605", "sha256": "sha256:e29ad67d08018284adacd01d6f25e6bb1a83f5bec09698bc339a84b123a8aac6", "bytes": 108976, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.3389/fmicb.2017.01605", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC5573736", "source": "europe_pmc_fulltext", "coverage": "whole_body", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:PXD006070", "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=PXD006070", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "PXD006070", "version": null, "note": "Data are available via ProteomeXchange with the identifier PXD006070.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "Data are available via ProteomeXchange with the identifier PXD006070.", "access_statement_kind": "data_availability_statement", "sample_accessions": [], "sample_count": null, "group_sizes": null, "group_sizes_basis": null, "platform": null, "taxon": null, "title": "Rumen metaproteome -  A Structural and Functional Elucidation of the Rumen Microbiome Influenced by Various Diets and Microenvironments", "resolution_checked_at": "2026-10-31T18:35:55Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}, {"id": "data:geo:PRJEB19491", "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=PRJEB19491", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "PRJEB19491", "version": null, "note": "Data are available via ProteomeXchange with the identifier PXD006070.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "Data are available via ProteomeXchange with the identifier PXD006070.", "access_statement_kind": "data_availability_statement", "sample_accessions": [], "sample_count": null, "group_sizes": null, "group_sizes_basis": null, "platform": null, "taxon": null, "title": null, "resolution_checked_at": "2026-10-31T18:35:43Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}, {"id": "asset:table:pmid:28883813:1", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:43177c4e561dc3287c07eab96e7f0c09efd81878ca629640b0db635a94e36c6c", "bytes": 934, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[4]/table-wrap[1]#T1", "version": null, "note": "The measured chemical characteristics of the three forage sources and the thereof calculated properties of the final total mixed rations fed to the cows.", "structure": {"pmcid": "PMC5573736", "section_index": 4, "section_title": "Animals and diets", "row_count": 10, "column_count": 7}, "table": {"label": "Table 1", "caption": "The measured chemical characteristics of the three forage sources and the thereof calculated properties of the final total mixed rations fed to the cows.", "rows": [["Components (% of dry matter)", "Basic forages", "Total mixed rations"], ["", "CS", "GS", "H", "CS diet", "GS diet", "H diet"], ["Dry matter (%)", "38.3", "61.8", "97.0", "63.4", "60.6", "71.4"], ["Crude ash", "4.1", "11.9", "8.8", "5.3", "8.9", "7.4"], ["Ether extract", "3.2", "3.7", "2.5", "2.8", "3.2", "2.6"], ["Crude protein", "7.8", "12.8", "13.1", "14.2", "15.3", "15.4"], ["Neutral detergent fiber (organic)", "41.3", "52.9", "58.9", "27.2", "33.2", "36.0"], ["Acid detergent fiber (organic)", "21.0", "31.8", "33.6", "13.3", "18.8", "19.6"], ["Acid detergent lignin", "1.7", "2.6", "3.0", "1.0", "1.4", "1.6"], ["Non-fiber carbohydrates", "43.7", "18.7", "16.7", "50.5", "39.5", "38.6"]], "row_count": 10, "column_count": 7, "numeric_cells": 48, "header_rows": 2, "locator": "section[4]/table-wrap[1]#T1"}}, {"id": "asset:table:pmid:28883813:2", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:905bf0af930d5393d2e1a088f28b444c7ad89abd5b7228e3f89983232b0f0b52", "bytes": 932, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[13]/table-wrap[1]#T2", "version": null, "note": "Analysis of similarity of the metaproteomic- and the 16S rRNA gene-based datasets.", "structure": {"pmcid": "PMC5573736", "section_index": 13, "section_title": "Metaproteomics and amplicon sequencing of the rumen microbiome", "row_count": 14, "column_count": 6}, "table": {"label": "Table 2", "caption": "Analysis of similarity of the metaproteomic- and the 16S rRNA gene-based datasets.", "rows": [["", "", "LFQ-values of 8,163 bacterial proteins", "Abundance of 1,484 bacterial OTUs"], ["", "", "R", "P", "R", "P"], ["", "Diets*", "0.418", "0.0001", "0.366", "0.0001"], ["", "Fractions*", "0.244", "0.0004", "0.379", "0.0001"], ["", "Cows", "0.143", "0.0090", "0.176", "0.0070"], ["Diets", "GS:H", "0.248", "0.0100", "0.078", "0.1630"], ["", "CS:GS*", "0.600", "0.0001", "0.500", "0.0003"], ["", "CS:H*", "0.442", "0.0001", "0.558", "0.0001"], ["Fractions", "RF:LP", "0.053", "0.1870", "−0.045", "0.6980"], ["", "RF:SP*", "0.321", "0.0008", "0.561", "0.0002"], ["", "LP:SP*", "0.362", "0.0001", "0.596", "0.0001"], ["Cows", "28:59", "0.088", "0.1090", "0.133", "0.0790"], ["", "23:59", "0.169", "0.0280", "0.207", "0.0280"], ["", "23:28", "0.180", "0.0150", "0.202", "0.0270"]], "row_count": 14, "column_count": 6, "numeric_cells": 53, "header_rows": 2, "locator": "section[13]/table-wrap[1]#T2"}}, {"id": "asset:table:pmid:28883813:3", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:082e9bac3f4748898a031fa1b2b57e4ef43ab0677d24fd94926152c905200b8a", "bytes": 1622, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[19]/table-wrap[1]#T3", "version": null, "note": "Average (∅) concentration (mM) and standard error of mean (SEM) of compounds identified in the RF fractions (n = 3) are shown.", "structure": {"pmcid": "PMC5573736", "section_index": 19, "section_title": "Metabolites in rumen fluid", "row_count": 24, "column_count": 7}, "table": {"label": "Table 3", "caption": "Average (∅) concentration (mM) and standard error of mean (SEM) of compounds identified in the RF fractions (n = 3) are shown.", "rows": [["Metabolite", "Average concentration (mM) and SEM (n = 3)"], ["", "Corn RF", "Grass RF", "Hay RF"], ["", "∅", "SEM", "∅", "SEM", "∅", "SEM"], ["2-Phenylpropionate*", "0.14", "0.02", "0.12", "0.05", "0.15", "0.05"], ["3-Phenylpropionate*", "0.38", "0.05", "0.40", "0.08", "0.39", "0.10"], ["Acetate*", "54.86", "3.79", "59.70", "8.49", "55.95", "3.41"], ["Adipate", "1.78", "0.67", "1.66", "0.34", "1.45", "0.58"], ["Aspartate", "0.23", "0.07", "0.39", "0.15", "0.31", "0.12"], ["Butyrate*", "14.98", "2.20", "16.84", "5.58", "15.81", "1.54"], ["Dimethylamine*", "0.10", "0.07", "0.29", "0.08", "0.28", "0.05"], ["Formate", "0.14", "0.03", "0.10", "0.02", "0.11", "0.02"], ["Fumarate", "0.02", "0.00", "0.01", "0.00", "0.02", "0.00"], ["Isobutyrate*", "1.43", "0.57", "1.29", "0.42", "1.51", "0.49"], ["Isovalerate*", "1.31", "0.26", "1.09", "0.32", "1.02", "0.04"], ["Lactate", "1.18", "1.11", "0.84", "0.45", "5.25", "4.35"], ["Methylamine*", "0.49", "0.15", "0.94", "0.12", "0.70", "0.16"], ["Phenylacetate*", "0.13", "0.05", "0.17", "0.11", "0.19", "0.09"], ["Pimelate", "4.54", "0.53", "3.13", "0.70", "3.73", "0.19"], ["Propionate*", "15.22", "3.17", "15.94", "3.34", "13.86", "1.30"], ["Succinate", "0.38", "0.38", "0.10", "0.05", "0.25", "0.11"], ["Trimethylamine*", "0.17", "0.13", "0.59", "0.35", "0.62", "0.49"], ["Urea", "2.74", "1.21", "2.68", "1.54", "2.98", "0.86"], ["Valerate*", "5.27", "0.95", "2.99", "0.42", "4.15", "0.31"], ["Acetate : Propionate", "3.60", "3.75", "4.04"]], "row_count": 24, "column_count": 7, "numeric_cells": 126, "header_rows": 3, "locator": "section[19]/table-wrap[1]#T3"}}], "gaps": ["asset:data:geo:PXD006070 not downloaded", "asset:data:geo:PXD006070 licence not read", "asset:data:geo:PRJEB19491 not downloaded", "asset:data:geo:PRJEB19491 licence not read"]}, "analysis": {"state": "partial", "methods": [{"id": "method-1", "family": null, "specific": null, "label": "One-way analysis of similarities (ANOSIM)", "dsl_operations": [], "missing_operations": [], "expressible": null, "parameters": {}, "data_shapes": [], "evidence": {"score": 1.0, "band": "verbatim", "quote": "One-way analysis of similarities (ANOSIM) was used to determine statistical differences in protein and OTU abundance between diets, sample fractions and host animals (Clarke and Warwick, 2001)."}}], "targets": [{"id": "target-published-estimate", "claim_id": "claim-target-result", "operation": null, "expected_value": 0.0001, "unit": "p-value", "tolerance": null, "state": "complete", "note": "The threshold the paper applied to its own result, as the paper states it. A run that reproduces the effect is judged against this threshold."}], "gaps": ["method.reader_named_unmapped"]}, "capability": {"state": "complete", "requirements": [{"capability_id": "capability:computational_analysis", "label": "Computational analysis platform", "assay_families": ["meta_analysis", "machine_learning", "survival_analysis", "statistical_regression", "pca", "molecular_docking", "network_analysis", "differential_expression", "gwas"], "availability_state": "owned", "tier_unlocked": "R1", "candidate": "Automated Assays Laravel application and simulated adapters"}], "gaps": []}, "readiness": {"state": "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 (One-way analysis of similarities (ANOSIM)), 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": ["PRJEB19491", "PXD006070"], "resolved_accessions": ["PXD006070"], "statements": ["Data are available via ProteomeXchange with the identifier PXD006070."], "basis": "The paper names PXD006070 in European Nucleotide Archive and the accession resolves in the repository. No dataset was downloaded and no licence was read."}}, "can_run": {"dsl_operations": [], "assets": ["source:pmid:28883813", "data:geo:PXD006070", "asset:table:pmid:28883813:1", "asset:table:pmid:28883813:2", "asset:table:pmid:28883813:3"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:PXD006070"]}, "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": "2026-10-31T18:32:12Z", "independence": "same_provider"}, "evidence_check": {"method": "verbatim", "availability": "verbatim"}, "calls": 8, "usage": {"prompt_tokens": 226937, "completion_tokens": 3661, "cached_tokens": 1824}}, "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:28883813", "type": "paper", "label": "pmid:28883813"}, {"id": "source:pmid:28883813", "type": "manuscript", "label": "PMID 28883813 full text"}, {"id": "data:geo:PXD006070", "type": "dataset", "label": "GEO PXD006070"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:28883813", "type": "paper", "label": "pmid:28883813"}, {"id": "source:pmid:28883813", "type": "manuscript", "label": "PMID 28883813 full text"}, {"id": "data:geo:PXD006070", "type": "dataset", "label": "GEO PXD006070"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-28883813", "type": "extraction", "used": ["source:pmid:28883813"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-PXD006070", "type": "accession_resolution", "used": ["data:geo:PXD006070"], "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:28883813", "parent_hash": "sha256:3e93580c21404689d13754a0aeceb50a5c23924fd440ab8b62a2531f5baf5706", "fork_of": null, "generation": 5}, "gaps": ["asset:data:geo:PRJEB19491 licence not read", "asset:data:geo:PRJEB19491 not downloaded", "asset:data:geo:PXD006070 licence not read", "asset:data:geo:PXD006070 not downloaded", "execution.not_run", "method.reader_named_unmapped", "review.human_critique", "review.independent_reader", "review.machine_critique"], "assays": [{"role": "data_generation", "definition_id": "amplicon_seq", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.93, "evidence": ["cts were used for Illumina sequencing of the 16S rRNA gene and the metabolomes of rumen fluids wer"], "order_basis": "paper_text_order:834", "id": "assay:1"}, {"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": ["ed from protein extracts were measured by LC-ESI-MS/MS and spectra were processed by a two-step", "ions fed to the cows. Sample preparation for mass spectrometry Samples were thawed and vortexed prior to sa"], "order_basis": "paper_text_order:996", "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":"2026-11-04T02:52:15+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}}}