{"data":{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:32586320", "kind": "science-record", "revision": 6, "content_hash": "sha256:8fe37fbe9b9b214067d52dcfc73e5a8794216a72e175c96183e7006e86ea3095", "created_at": "2026-11-01T15:41:04Z", "updated_at": "2026-11-01T21:23:24Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Alterations in the chondrocyte surfaceome in response to pro-inflammatory cytokines.", "doi": "10.1186/s12860-020-00288-9", "pmid": "32586320", "authors": ["Bernadette Jeremiasse", "Csaba Matta", "Christopher R Fellows", "David J Boocock", "Julia R Smith", "Susan Liddell", "Floris Lafeber", "Willem E van Spil", "Ali Mobasheri"], "journal": "BMC molecular and cell biology", "year": 2020, "abstract": "BACKGROUND: Chondrocytes are exposed to an inflammatory micro-environment in the extracellular matrix (ECM) of articular cartilage in joint diseases such as osteoarthritis (OA) and rheumatoid arthritis (RA). In OA, degenerative changes and low-grade inflammation within the joint transform the behaviour and metabolism of chondrocytes, disturb the balance between ECM synthesis and degradation, and alter the osmolality and ionic composition of the micro-environment. We hypothesize that chondrocytes adjust their physiology to the inflammatory microenvironment by modulating the expression of cell surface proteins, collectively referred to as the 'surfaceome'. Therefore, the aim of this study was to characterize the surfaceome of primary equine chondrocytes isolated from healthy joints following exposure to the pro-inflammatory cytokines interleukin-1-beta (IL-1β) and tumour necrosis factor-alpha (TNF-α). We employed combined methodology that we recently developed for investigating the surfaceome in stem cells. Membrane proteins were isolated using an aminooxy-biotinylation technique and analysed by mass spectrometry using high throughput shotgun proteomics. Selected proteins were validated by western blotting.\nRESULTS: Amongst the 431 unique cell surface proteins identified, a high percentage of low-abundance proteins, such as ion channels, receptors and transporter molecules were detected. Data are available via ProteomeXchange with identifier PXD014773. A high number of proteins exhibited different expression patterns following chondrocyte stimulation with pro-inflammatory cytokines. Low density lipoprotein related protein 1 (LPR-1), thrombospondin-1 (TSP-1), voltage dependent anion channel (VDAC) 1-2 and annexin A1 were considered to be of special interest and were analysed further by western blotting.\nCONCLUSIONS: Our results provide, for the first time, a repository for proteomic data on differentially expressed low-abundance membrane proteins on the surface of chondrocytes in response to pro-inflammatory stimuli.", "claims": [{"id": "claim-data-access", "statement": "The mass spectrometry proteomics data have been deposited to the ProteomeXchange Consortium via the PRIDE [88] partner repository with the dataset identifier PXD014773.1", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:32586320", "locator": "sections[25] \"Availability of data and materials\" paragraph 2", "quote": "The mass spectrometry proteomics data have been deposited to the ProteomeXchange Consortium via the PRIDE [88] partner repository with the dataset identifier PXD014773.1"}], "state": "complete"}], "gaps": []}, "experiment": {"state": "partial", "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:32586320"], "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": "blocked", "blocked_on": "data:accession_absent", "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": [], "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": [], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": ["step:obtain_source_data blocked on data:accession_absent"]}, "data": {"state": "partial", "assets": [{"id": "source:pmid:32586320", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.1186/s12860-020-00288-9", "sha256": "sha256:3a4cbba5d6b80624d6c113631ac6f64e780cad7a7288693ec22fe37f88beacf7", "bytes": 83081, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.1186/s12860-020-00288-9", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC7318434", "source": "europe_pmc_fulltext", "coverage": "whole_body", "text_hash_scope": "rendered_section_body"}}, {"id": "asset:table:pmid:32586320:1", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:81c3a469c673f142bb271cfaf54819d31c5da84834e0af75819415c5278cc2cf", "bytes": 3146, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[7]/table-wrap[1]#Tab2", "version": null, "note": "Results of an overrepresentation analysis on the identified proteins in unstimulated equine articular chondrocytes carried out using the Reactome resource. The analysis is based on a statistical (hypergeometric distribution) test that determines whether certain Reactome pathways are over-represented (enriched) in the submitted data. This test produces a probability score, which is corrected for false discovery rate using the Benjamani-Hochberg method. The 25 most relevant pathways sorted by p-value are shown. Table extracted from Reactome Pathway Analysis Report", "structure": {"pmcid": "PMC7318434", "section_index": 7, "section_title": "Cytokine treatment results in the over-representation of different pathways and protein interactions", "row_count": 27, "column_count": 7}, "table": {"label": "Table 2", "caption": "Results of an overrepresentation analysis on the identified proteins in unstimulated equine articular chondrocytes carried out using the Reactome resource. The analysis is based on a statistical (hypergeometric distribution) test that determines whether certain Reactome pathways are over-represented (enriched) in the submitted data. This test produces a probability score, which is corrected for false discovery rate using the Benjamani-Hochberg method. The 25 most relevant pathways sorted by p-value are shown. Table extracted from Reactome Pathway Analysis Report", "rows": [["Pathway name", "Entities", "Reactions"], ["found", "ratio", "p-value", "FDRa", "found", "ratio"], ["Neutrophil degranulation", "66 / 480", "0.033", "1.11e-16", "1.51e-13", "10 / 10", "8.01e-04"], ["Formation of the cornified envelope", "33 / 138", "0.01", "7.77e-16", "5.29e-13", "11 / 27", "0.002"], ["Extracellular matrix organization", "47 / 329", "0.023", "1.37e-13", "6.24e-11", "181 / 318", "0.025"], ["Integrin cell surface interactions", "21 / 86", "0.006", "1.02e-10", "3.47e-08", "46 / 54", "0.004"], ["Axon guidance", "59 / 584", "0.04", "1.33e-10", "3.61e-08", "182 / 297", "0.024"], ["Keratinization", "33 / 226", "0.016", "3.80e-10", "8.64e-08", "18 / 34", "0.003"], ["Developmental Biology", "92 / 1207", "0.084", "2.00e-09", "3.88e-07", "206 / 511", "0.041"], ["Platelet degranulation", "24 / 137", "0.009", "3.30e-09", "5.61e-07", "8 / 11", "8.81e-04"], ["Response to elevated platelet cytosolic Ca2+", "24 / 144", "0.01", "8.45e-09", "1.28e-06", "8 / 14", "0.001"], ["Platelet activation, signaling and aggregation", "35 / 293", "0.02", "1.76e-08", "2.40e-06", "42 / 114", "0.009"], ["Interleukin-12 family signaling", "18 / 96", "0.007", "1.13e-07", "1.39e-05", "33 / 114", "0.009"], ["EPH-Ephrin signaling", "18 / 101", "0.007", "2.35e-07", "2.66e-05", "52 / 56", "0.004"], ["Innate Immune System", "91 / 1328", "0.092", "3.22e-07", "3.35e-05", "174 / 696", "0.056"], ["Cell junction organization", "17 / 94", "0.007", "4.15e-07", "4.02e-05", "26 / 37", "0.003"], ["Signaling by Receptor Tyrosine Kinases", "48 / 554", "0.038", "6.84e-07", "6.03e-05", "261 / 657", "0.053"], ["Cell-Cell communication", "20 / 133", "0.009", "7.12e-07", "6.03e-05", "36 / 60", "0.005"], ["Hemostasis", "63 / 821", "0.057", "7.54e-07", "6.03e-05", "83 / 327", "0.026"], ["Non-integrin membrane-ECM interactions", "13 / 61", "0.004", "1.64e-06", "1.23e-04", "16 / 22", "0.002"], ["Gene and protein expression by JAK-STAT signaling after Interleukin-12 stimulation", "14 / 73", "0.005", "2.21e-06", "1.56e-04", "7 / 36", "0.003"], ["Interleukin-12 signaling", "15 / 84", "0.006", "2.29e-06", "1.56e-04", "9 / 56", "0.004"], ["EPH-ephrin mediated repulsion of cells", "12 / 55", "0.004", "3.23e-06", "2.06e-04", "9 / 9", "7.21e-04"], ["Syndecan interactions", "9 / 29", "0.002", "3.47e-06", "2.06e-04", "9 / 15", "0.001"], ["Degradation of the extracellular matrix", "20 / 148", "0.01", "3.49e-06", "2.06e-04", "53 / 105", "0.008"], ["Immune System", "156 / 2822", "0.196", "7.43e-06", "4.16e-04", "344 / 1597", "0.128"], ["L1CAM interactions", "18 / 130", "0.009", "7.70e-06", "4.16e-04", "21 / 54", "0.004"]], "row_count": 27, "column_count": 7, "numeric_cells": 153, "header_rows": 2, "locator": "section[7]/table-wrap[1]#Tab2"}}, {"id": "asset:table:pmid:32586320:2", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:9a5805cbfd55add91deaa032d8f98c7611033296ab82f5077dd27d42a6a7faab", "bytes": 3333, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[7]/table-wrap[2]#Tab3", "version": null, "note": "Results of an overrepresentation analysis on the identified proteins following cytokine stimulation in equine articular chondrocytes carried out using the Reactome resource. The analysis is based on a statistical (hypergeometric distribution) test that determines whether certain Reactome pathways are over-represented (enriched) in the submitted data. This test produces a probability score, which is corrected for false discovery rate using the Benjamani-Hochberg method. The 25 most relevant pathways sorted by p-value are shown. Table extracted from Reactome Pathway Analysis Report", "structure": {"pmcid": "PMC7318434", "section_index": 7, "section_title": "Cytokine treatment results in the over-representation of different pathways and protein interactions", "row_count": 27, "column_count": 7}, "table": {"label": "Table 3", "caption": "Results of an overrepresentation analysis on the identified proteins following cytokine stimulation in equine articular chondrocytes carried out using the Reactome resource. The analysis is based on a statistical (hypergeometric distribution) test that determines whether certain Reactome pathways are over-represented (enriched) in the submitted data. This test produces a probability score, which is corrected for false discovery rate using the Benjamani-Hochberg method. The 25 most relevant pathways sorted by p-value are shown. Table extracted from Reactome Pathway Analysis Report", "rows": [["Pathway name", "Entities", "Reactions"], ["found", "ratio", "p-value", "FDRa", "found", "ratio"], ["Neutrophil degranulation", "56 / 480", "0.033", "1.11e-16", "1.27e-13", "10 / 10", "8.01e-04"], ["Formation of the cornified envelope", "28 / 138", "0.01", "1.94e-14", "1.11e-11", "13 / 27", "0.002"], ["Extracellular matrix organization", "42 / 329", "0.023", "4.09e-14", "1.56e-11", "183 / 318", "0.025"], ["RAB geranylgeranylation", "18 / 68", "0.005", "1.39e-11", "3.99e-09", "2 / 5", "4.00e-04"], ["Integrin cell surface interactions", "18 / 86", "0.006", "5.71e-10", "1.31e-07", "45 / 54", "0.004"], ["Keratinization", "28 / 226", "0.016", "1.55e-09", "2.97e-07", "20 / 34", "0.003"], ["Non-integrin membrane-ECM interactions", "15 / 61", "0.004", "1.88e-09", "3.06e-07", "19 / 22", "0.002"], ["Platelet degranulation", "21 / 137", "0.009", "5.09e-09", "7.28e-07", "8 / 11", "8.81e-04"], ["Response to elevated platelet cytosolic Ca2+", "21 / 144", "0.01", "1.19e-08", "1.51e-06", "8 / 14", "0.001"], ["Cell-Cell communication", "20 / 133", "0.009", "1.61e-08", "1.84e-06", "46 / 60", "0.005"], ["Syndecan interactions", "10 / 29", "0.002", "4.43e-08", "4.61e-06", "12 / 15", "0.001"], ["Axon guidance", "45 / 584", "0.04", "4.92e-08", "4.67e-06", "147 / 297", "0.024"], ["Developmental Biology", "73 / 1207", "0.084", "6.41e-08", "5.64e-06", "167 / 511", "0.041"], ["Post-translational protein phosphorylation", "17 / 109", "0.008", "1.16e-07", "9.37e-06", "1 / 1", "8.01e-05"], ["Cell junction organization", "15 / 94", "0.007", "4.83e-07", "3.67e-05", "26 / 37", "0.003"], ["Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs)", "17 / 127", "0.009", "9.31e-07", "6.61e-05", "1 / 14", "0.001"], ["Transport of small molecules", "58 / 963", "0.067", "1.97e-06", "1.32e-04", "97 / 438", "0.035"], ["Insulin-like Growth Factor-2 mRNA Binding Proteins (IGF2BPs/IMPs/VICKZs) bind RNA", "6 / 13", "9.01e-04", "4.45e-06", "2.80e-04", "2 / 3", "2.40e-04"], ["ATF6 (ATF6-alpha) activates chaperone genes", "6 / 15", "0.001", "9.96e-06", "5.98e-04", "3 / 5", "4.00e-04"], ["Vesicle-mediated transport", "49 / 824", "0.057", "1.83e-05", "0.001", "115 / 251", "0.02"], ["Adherens junctions interactions", "8 / 35", "0.002", "1.93e-05", "0.001", "16 / 16", "0.001"], ["ATF6 (ATF6-alpha) activates chaperones", "6 / 17", "0.001", "2.00e-05", "0.001", "4 / 10", "8.01e-04"], ["Transport of inorganic cations/anions and amino acids/oligopeptides", "17 / 165", "0.011", "2.71e-05", "0.001", "23 / 75", "0.006"], ["Platelet activation, signaling and aggregation", "24 / 293", "0.02", "2.78e-05", "0.001", "33 / 114", "0.009"], ["Innate Immune System", "69 / 1328", "0.092", "2.80e-05", "0.001", "88 / 696", "0.056"]], "row_count": 27, "column_count": 7, "numeric_cells": 151, "header_rows": 2, "locator": "section[7]/table-wrap[2]#Tab3"}}, {"id": "asset:table:pmid:32586320:3", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:9314699836305f506e63f7f74824eb472bf8d3fb68dda447e773e78892b520c6", "bytes": 1872, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[13]/table-wrap[1]#Tab1", "version": null, "note": "Detailed specification of primary and secondary antibodies employed for western blotting", "structure": {"pmcid": "PMC7318434", "section_index": 13, "section_title": "Validation of catabolic protein markers in chondrocyte monolayer cultures exposed to pro-inflammatory cytokines using western blots and DMMB assays", "row_count": 21, "column_count": 8}, "table": {"label": "Table 1", "caption": "Detailed specification of primary and secondary antibodies employed for western blotting", "rows": [["Primary antibody", "Supplier", "Catalog number", "Dilution", "Secondary antibody", "Supplier", "Catalog number", "Dilution"], ["Annexin A1", "LifeSpan Biosciences", "LS-C382041 (polyclonal)", "1:500", "IRDye 800CW Goat", "LI-COR Biosciences", "926–32,211", "1:10,000"], ["Anti-Rabbit IgG"], ["LRP1", "Abcam", "ab92544 (monoclonal)", "1:400", "IRDye 680RD Goat", "LI-COR Biosciences", "926–68,070", "1:8000"], ["Anti-Mouse IgG"], ["MMP-1 (C-terminal)", "Aviva Systems Biology", "ARP42040 (polyclonal)", "1:1000", "IRDye 800CW Goat", "LI-COR Biosciences", "926–32,211", "1:10,000"], ["Anti-Rabbit IgG"], ["MMP-13 (middle region)", "Aviva Systems Biology", "ARP56350 (polyclonal)", "1:500", "IRDye 800CW Goat", "LI-COR Biosciences", "926–32,211", "1:10,000"], ["Anti-Rabbit IgG"], ["MMP-3 (middle region)", "Aviva Systems Biology", "ARP42042 (polyclonal)", "1:1000", "IRDye 800CW Goat", "LI-COR Biosciences", "926–32,211", "1:10,000"], ["Anti-Rabbit IgG"], ["TSP-1", "Abcam", "ab1823 (monoclonal)", "1:500a;", "IRDye 680RD Goat", "LI-COR Biosciences", "926–68,070a;", "1:5000a"], ["1:1000b", "Anti-Mouse IgGa;", "", "", ""], ["IRDye 800CW Goat", "", "926–32,210b", "1:10,000b"], ["Anti-Mouse IgGb", "", "", ""], ["VDAC1 (C-terminal)", "Aviva Systems Biology", "ARP35122 (polyclonal)", "1:250", "IRDye 680RD Goat", "LI-COR Biosciences", "926–68,071", "1:5000"], ["Anti-Rabbit IgG"], ["VDAC2 (N-terminal)", "Aviva Systems Biology", "ARP35123 (polyclonal)", "1:250", "IRDye 680RD Goat", "LI-COR Biosciences", "926–68,071", "1:5000"], ["Anti-Rabbit IgG"], ["β-actin", "LI-COR Biosciences", "926–42,210 (monoclonal)", "1:500", "IRDye 800CW Goat", "LI-COR Biosciences", "926–32,211", "1:10,000"], ["Anti-Rabbit IgG"]], "row_count": 21, "column_count": 8, "numeric_cells": 53, "header_rows": 1, "locator": "section[13]/table-wrap[1]#Tab1"}}], "gaps": []}, "analysis": {"state": "partial", "methods": [{"id": "method-1", "family": null, "specific": null, "label": "paired Student t-tests", "dsl_operations": [], "missing_operations": [], "expressible": null, "parameters": {}, "data_shapes": [], "evidence": {"score": 1.0, "band": "reordered", "quote": "“GraphPad Prism 7.02 and Microsoft Excel software were used to produce graphic images and perform paired Student t-tests.”"}}], "targets": [], "gaps": ["method.reader_named_unmapped"]}, "capability": {"state": "complete", "requirements": [{"capability_id": "capability:computational_analysis", "label": "Computational analysis platform", "assay_families": ["meta_analysis", "machine_learning", "survival_analysis", "statistical_regression", "pca", "molecular_docking", "network_analysis", "differential_expression", "gwas"], "availability_state": "owned", "tier_unlocked": "R1", "candidate": "Automated Assays Laravel application and simulated adapters"}], "gaps": []}, "readiness": {"state": "blocked", "tier": "R4", "blocking_axis": "data", "blocked_on": "data:accession_absent", "axes": {"method": {"tier": "R4", "expressible": false, "required_operations": [], "missing_operations": [], "basis": "The reader quoted the method the paper names (paired Student t-tests), 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": "R4", "reachable": false, "accessions": ["PXD014773.1"], "resolved_accessions": [], "statements": ["The mass spectrometry proteomics data have been deposited to the ProteomeXchange Consortium via the PRIDE [88] partner repository with the dataset identifier PXD014773.1"], "basis": "The paper names PXD014773.1, but the accession does not resolve in the repository (no reason recorded), so the data cannot be reached from here. No dataset was downloaded and no licence was read."}}, "can_run": {"dsl_operations": [], "assets": ["source:pmid:32586320", "asset:table:pmid:32586320:1", "asset:table:pmid:32586320:2", "asset:table:pmid:32586320:3"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:None"]}, "gaps": ["data:accession_absent"]}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-10-31T18:20:36Z", "independence": "single_reader"}, "evidence_check": {"method": "reordered", "availability": "verbatim"}, "calls": 3, "usage": {"prompt_tokens": 62188, "completion_tokens": 1323, "cached_tokens": 784}}, "human_critique": null, "stages": [{"id": "extraction", "state": "complete", "reader": "MiniMax-M3.1-Flash", "provider": "minimax"}], "gaps": ["review.independent_reader", "review.machine_critique", "review.human_critique"]}, "execution": {"state": "absent", "status": "not_run", "mode": null, "runs": [], "gaps": ["execution.not_run"]}, "provenance": {"entities": [{"id": "pmid:32586320", "type": "paper", "label": "pmid:32586320"}, {"id": "source:pmid:32586320", "type": "manuscript", "label": "PMID 32586320 full text"}, {"id": "data:geo:None", "type": "dataset", "label": "GEO None"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:32586320", "type": "paper", "label": "pmid:32586320"}, {"id": "source:pmid:32586320", "type": "manuscript", "label": "PMID 32586320 full text"}, {"id": "data:geo:None", "type": "dataset", "label": "GEO None"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-32586320", "type": "extraction", "used": ["source:pmid:32586320"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-None", "type": "accession_resolution", "used": ["data:geo:None"], "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:32586320", "parent_hash": "sha256:53487d3f2b588291f294a1a14efef1f4a517a1f02107835fed5a135b99074cc5", "fork_of": null, "generation": 5}, "gaps": ["execution.not_run", "method.reader_named_unmapped", "review.human_critique", "review.independent_reader", "review.machine_critique", "step:obtain_source_data blocked on data:accession_absent"], "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": ["ooxy-biotinylation technique and analysed by mass spectrometry using high throughput shotgun proteomics. Se", "s spectrometry using high throughput shotgun proteomics. Selected proteins were validated by western", "tokine-treated and control samples following mass spectrometry, as well as literature supporting their invo", "cant. Availability of data and materials The mass spectrometry proteomics data have been deposited to the P"], "order_basis": "paper_text_order:1151", "id": "assay:1"}, {"role": "data_generation", "definition_id": "western_blot", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.99, "evidence": ["teomics. Selected proteins were validated by western blotting. RESULTS: Amongst the 431 unique cell surfac", "pecial interest and were analysed further by western blotting. CONCLUSIONS: Our results provide, for the f", "d also quantified some of the proteins using western blotting. The experimental workflow is presented in F", "10 ng/mL) for 1 h at 37 °C. The samples for western blotting were paired: for each pair, controls and cyt"], "order_basis": "paper_text_order:1247", "id": "assay:2"}, {"role": "data_generation", "definition_id": "cell_culture", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.77, "evidence": ["e primary equine articular chondrocytes were cultured in T175 flasks for 72 h with or without IL-1β a"], "order_basis": "paper_text_order:2776", "id": "assay:3"}, {"role": "data_generation", "definition_id": "apoptosis_assay", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.69, "evidence": ["e upon cytokine exposure. Figure S2. Rate of apoptosis of chondrocytes under pro-inflammatory versu"], "order_basis": "paper_text_order:8087", "id": "assay:4"}]},"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":"2026-11-04T00:32:53+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}}}