{"data":{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:40765736", "kind": "science-record", "revision": 4, "content_hash": "sha256:3899fe1e725a942cb23a45014e4c2a93852291dbc752c8da794b33f85033c03e", "created_at": "2026-11-01T20:30:51Z", "updated_at": "2026-11-01T22:56:57Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Integrated Bioinformatics and Experimental Validation Reveal Macrophage Polarization-Related Biomarkers for Osteoarthritis Diagnosis.", "doi": "10.2147/JMDH.S537507", "pmid": "40765736", "authors": ["Qiwang He", "Lingling Liu", "Xinyu Hu", "Lixia Lin", "Zhenyu Song", "Yuyang Xia", "Qianming Lin", "Jihua Wei", "Shanlang Li"], "journal": "Journal of multidisciplinary healthcare", "year": 2025, "abstract": "Purpose: Osteoarthritis (OA) is the most common type of arthritis and early detection is crucial to improving prognosis. In this study, we identified crucial genes associated with macrophage polarization in OA and constructed a diagnostic model to provide novel insights for diagnostic and therapeutic strategies.\nMethods: The GSE55235 and GSE55457 datasets were merged through the GEO database to identify genes related to macrophage polarization by conducting weighted gene co-expression network analysis (WGCNA) and differential expression analysis. Least absolute shrinkage and selection operator (LASSO), random forest (RF), and support vector machine recursive feature elimination (SVM-RFE) algorithms were used to identify hub genes and construct a diagnostic model validated through internal datasets and multiple external bulk RNA-seq and single-cell RNA-seq data. Additionally, various analyses, including immune infiltration, gene set enrichment analysis, competing endogenous RNA (ceRNA) construction, and drug prediction, were conducted. Finally, clinical samples were clinically validated through RT-qPCR (OA: Control = 10: 5) and IHC (6: 5) experiments.\nResults: Three hub genes (MYC, SIK1, and NFIL3) were identified, and the diagnostic model constructed using them demonstrated good diagnostic efficacy in both internal and external datasets (internal AUC = 0.965, external AUC = 0.847). In vitro experiments revealed that the hub genes in the synovial tissue of OA patients were significantly down-regulated (P < 0.01), confirming their potential as diagnostic biomarkers.\nConclusion: We constructed an OA diagnostic model related to macrophage polarization through comprehensive bioinformatics analysis, and the results indicated that these genes have high diagnostic value. However, further clinical studies and experimental assessments are needed to validate these findings.", "claims": [{"id": "claim-method", "statement": "The “limma” package was utilized to analyze DEGs, with the differential screening criteria: | log2FC | > 2.0, adj. P < 0.05.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:40765736", "locator": "sections[3] \"Data Collection and Processing\" paragraph 4", "quote": "The “limma” package was utilized to analyze DEGs, with the differential screening criteria: | log2FC | > 2.0, adj. P < 0.05."}], "state": "complete"}, {"id": "claim-data-access", "statement": "This study analyzed publicly available datasets. These data can be found here: National Center for Biotechnology Information (NCBI), Gene Expression Omnibus (GEO), https://www.ncbi.nlm.nih.gov/geo/.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:40765736", "locator": "sections[39] \"Data Sharing Statement\" paragraph 2", "quote": "This study analyzed publicly available datasets. These data can be found here: National Center for Biotechnology Information (NCBI), Gene Expression Omnibus (GEO), https://www.ncbi.nlm.nih.gov/geo/."}], "state": "complete"}, {"id": "claim-target-result", "statement": "A macrophage-polarization-related OA diagnostic model based on MYC, SIK1, and NFIL3 achieved an internal AUC of 0.965 and an external AUC of 0.847.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:40765736", "locator": "sections[0] \"Abstract\" paragraph 3", "quote": "Three hub genes (MYC, SIK1, and NFIL3) were identified, and the diagnostic model constructed using them demonstrated good diagnostic efficacy in both internal and external datasets (internal AUC = 0.965, external AUC = 0.847)."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "A macrophage-polarization-related OA diagnostic model based on MYC, SIK1, and NFIL3 achieved an internal AUC of 0.965 and an external AUC of 0.847.", "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:40765736"], "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:GSE152805"], "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:GSE152805"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:40765736", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.2147/JMDH.S537507", "sha256": "sha256:5b0f98217bcaf35017073b2e4c123a2cf51a93f25c5fe03264cd3405849c4271", "bytes": 65637, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.2147/JMDH.S537507", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC12323875", "source": "europe_pmc_fulltext", "coverage": "whole_body", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE152805", "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=GSE152805", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE152805", "version": null, "note": "This study analyzed publicly available datasets. These data can be found here: National Center for Biotechnology Information (NCBI), Gene Expression Omnibus (GEO), https://www.ncbi.nlm.nih.gov/geo/.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "This study analyzed publicly available datasets. These data can be found here: National Center for Biotechnology Information (NCBI), Gene Expression Omnibus (GEO), https://www.ncbi.nlm.nih.gov/geo/.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM4626763", "GSM4626764", "GSM4626765", "GSM4626766", "GSM4626767", "GSM4626768", "GSM4626769", "GSM4626770", "GSM4626771"], "sample_count": 9, "group_sizes": null, "group_sizes_basis": null, "platform": "20301", "taxon": "Homo sapiens", "title": "Synovial Cell Cross-talk with Cartilage Plays a Major Role in the Pathogenesis of Osteoarthritis", "resolution_checked_at": "2026-11-01T19:09:46Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}, {"id": "data:geo:GSE176308", "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=GSE176308", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE176308", "version": null, "note": "This study analyzed publicly available datasets. These data can be found here: National Center for Biotechnology Information (NCBI), Gene Expression Omnibus (GEO), https://www.ncbi.nlm.nih.gov/geo/.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "This study analyzed publicly available datasets. These data can be found here: National Center for Biotechnology Information (NCBI), Gene Expression Omnibus (GEO), https://www.ncbi.nlm.nih.gov/geo/.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM5362559", "GSM5362560", "GSM5362561"], "sample_count": 3, "group_sizes": null, "group_sizes_basis": null, "platform": "18573", "taxon": "Homo sapiens", "title": "Identification of distinct synovial fibroblast subsets associated with pain and progression of knee osteoarthritis using single-cell RNA sequencing", "resolution_checked_at": "2026-11-01T20:16:08Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}, {"id": "data:geo:GSE1919", "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=GSE1919", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE1919", "version": null, "note": "This study analyzed publicly available datasets. These data can be found here: National Center for Biotechnology Information (NCBI), Gene Expression Omnibus (GEO), https://www.ncbi.nlm.nih.gov/geo/.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "This study analyzed publicly available datasets. These data can be found here: National Center for Biotechnology Information (NCBI), Gene Expression Omnibus (GEO), https://www.ncbi.nlm.nih.gov/geo/.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM34379", "GSM34383", "GSM34385", "GSM34388", "GSM34391", "GSM34393", "GSM34394", "GSM34395", "GSM34396", "GSM34397", "GSM34398", "GSM34399", "GSM34400", "GSM34401", "GSM34402"], "sample_count": 15, "group_sizes": null, "group_sizes_basis": null, "platform": "91", "taxon": "Homo sapiens", "title": "Rheumatoid arthritis", "resolution_checked_at": "2026-11-01T15:39:54Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}, {"id": "data:geo:GSE206848", "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=GSE206848", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE206848", "version": null, "note": "This study analyzed publicly available datasets. These data can be found here: National Center for Biotechnology Information (NCBI), Gene Expression Omnibus (GEO), https://www.ncbi.nlm.nih.gov/geo/.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "This study analyzed publicly available datasets. These data can be found here: National Center for Biotechnology Information (NCBI), Gene Expression Omnibus (GEO), https://www.ncbi.nlm.nih.gov/geo/.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM6265690", "GSM6265691", "GSM6265692", "GSM6265693", "GSM6265694", "GSM6265695", "GSM6265696", "GSM6265697", "GSM6265698", "GSM6265699", "GSM6265700", "GSM6265701", "GSM6265702", "GSM6265703", "GSM6265704", "GSM6265705"], "sample_count": 16, "group_sizes": null, "group_sizes_basis": null, "platform": "570", "taxon": "Homo sapiens", "title": "Dysregulated gene expression in human osteoarthritic (OA) and rheumatoid arthritis (RA) synovium", "resolution_checked_at": "2026-11-01T20:16:08Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}, {"id": "data:geo:GSE55235", "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=GSE55235", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE55235", "version": null, "note": "This study analyzed publicly available datasets. These data can be found here: National Center for Biotechnology Information (NCBI), Gene Expression Omnibus (GEO), https://www.ncbi.nlm.nih.gov/geo/.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "This study analyzed publicly available datasets. These data can be found here: National Center for Biotechnology Information (NCBI), Gene Expression Omnibus (GEO), https://www.ncbi.nlm.nih.gov/geo/.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM1332201", "GSM1332202", "GSM1332203", "GSM1332204", "GSM1332205", "GSM1332206", "GSM1332207", "GSM1332208", "GSM1332209", "GSM1332210", "GSM1332211", "GSM1332212", "GSM1332213", "GSM1332214", "GSM1332215", "GSM1332216", "GSM1332217", "GSM1332218", "GSM1332219", "GSM1332220", "GSM1332221", "GSM1332222", "GSM1332223", "GSM1332224", "GSM1332225", "GSM1332226", "GSM1332227", "GSM1332228", "GSM1332229", "GSM1332230"], "sample_count": 30, "group_sizes": null, "group_sizes_basis": null, "platform": "96", "taxon": "Homo sapiens", "title": "Identification of rheumatoid arthritis and osteoarthritis patients by transcriptome-based rule set generation", "resolution_checked_at": "2026-11-01T15:39:54Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}, {"id": "data:geo:GSE55457", "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=GSE55457", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE55457", "version": null, "note": "This study analyzed publicly available datasets. These data can be found here: National Center for Biotechnology Information (NCBI), Gene Expression Omnibus (GEO), https://www.ncbi.nlm.nih.gov/geo/.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "This study analyzed publicly available datasets. These data can be found here: National Center for Biotechnology Information (NCBI), Gene Expression Omnibus (GEO), https://www.ncbi.nlm.nih.gov/geo/.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM1337304", "GSM1337305", "GSM1337306", "GSM1337307", "GSM1337308", "GSM1337309", "GSM1337310", "GSM1337311", "GSM1337312", "GSM1337313", "GSM1337314", "GSM1337315", "GSM1337316", "GSM1337317", "GSM1337318", "GSM1337319", "GSM1337320", "GSM1337321", "GSM1337322", "GSM1337323", "GSM1337324", "GSM1337325", "GSM1337326", "GSM1337327", "GSM1337328", "GSM1337329", "GSM1337330", "GSM1337331", "GSM1337332", "GSM1337333", "GSM1337334", "GSM1337335", "GSM1337336"], "sample_count": 33, "group_sizes": null, "group_sizes_basis": null, "platform": "96", "taxon": "Homo sapiens", "title": "Identification of rheumatoid arthritis and osteoarthritis patients by transcriptome-based rule set generation [Jena]", "resolution_checked_at": "2026-11-01T15:39:54Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}], "gaps": ["asset:data:geo:GSE152805 not downloaded", "asset:data:geo:GSE152805 licence not read", "asset:data:geo:GSE176308 not downloaded", "asset:data:geo:GSE176308 licence not read", "asset:data:geo:GSE1919 not downloaded", "asset:data:geo:GSE1919 licence not read", "asset:data:geo:GSE206848 not downloaded", "asset:data:geo:GSE206848 licence not read", "asset:data:geo:GSE55235 not downloaded", "asset:data:geo:GSE55235 licence not read", "asset:data:geo:GSE55457 not downloaded", "asset:data:geo:GSE55457 licence not read"]}, "analysis": {"state": "complete", "methods": [{"id": "method-1", "family": "differential_expression", "specific": "limma_voom", "label": "Differential expression analysis", "dsl_operations": ["normalise_counts", "differential_expression_fit", "fdr_bh"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["count_matrix_with_condition"], "evidence": {"score": 1.0, "band": "verbatim", "quote": "The “limma” package was utilized to analyze DEGs, with the differential screening criteria: | log2FC | > 2.0, adj. P < 0.05."}}, {"id": "method-2", "family": "machine_learning", "specific": "random_forest", "label": "Machine learning", "dsl_operations": [], "missing_operations": ["machine_learning_random_forest"], "expressible": false, "parameters": {}, "data_shapes": ["labelled_feature_matrix"], "evidence": {"score": 0.7, "band": "medium", "quote": "random forest"}}, {"id": "method-3", "family": "machine_learning", "specific": "support_vector_machine", "label": "Machine learning", "dsl_operations": ["train_classifier", "cross_validate", "roc_auc"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["labelled_feature_matrix"], "evidence": {"score": 0.7, "band": "medium", "quote": "support vector machine"}}], "targets": [], "gaps": []}, "capability": {"state": "complete", "requirements": [{"capability_id": "capability:computational_analysis", "label": "Computational analysis platform", "assay_families": ["meta_analysis", "machine_learning", "survival_analysis", "statistical_regression", "pca", "molecular_docking", "network_analysis", "differential_expression", "gwas"], "availability_state": "owned", "tier_unlocked": "R1", "candidate": "Automated Assays Laravel application and simulated adapters"}], "gaps": []}, "readiness": {"state": "complete", "tier": "R1", "blocking_axis": "none", "blocked_on": "nothing:replicable_now", "axes": {"method": {"tier": "R1", "expressible": true, "required_operations": ["normalise_counts", "differential_expression_fit", "fdr_bh"], "missing_operations": [], "basis": "The paper names the method it used and the corpus's method extractor maps it onto the DSL catalogue: limma_voom."}, "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": ["GSE55235", "GSE55457", "GSE206848", "GSE1919", "GSE176308", "GSE152805"], "resolved_accessions": ["GSE55235", "GSE55457", "GSE206848", "GSE1919", "GSE176308", "GSE152805"], "statements": ["This study analyzed publicly available datasets. These data can be found here: National Center for Biotechnology Information (NCBI), Gene Expression Omnibus (GEO), https://www.ncbi.nlm.nih.gov/geo/."], "basis": "The paper names GSE55235, GSE55457, GSE206848, GSE1919, GSE176308, GSE152805 in Gene Expression Omnibus (GEO) and the accession resolves in the repository. No dataset was downloaded and no licence was read."}}, "can_run": {"dsl_operations": ["normalise_counts", "differential_expression_fit", "fdr_bh"], "assets": ["source:pmid:40765736", "data:geo:GSE152805"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:GSE152805"]}, "gaps": []}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-11-01T19:58:31Z", "independence": "single_reader"}, "evidence_check": {"method": "verbatim", "availability": "verbatim"}, "calls": 5, "usage": {"prompt_tokens": 18079, "completion_tokens": 2121, "cached_tokens": 264}}, "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:40765736", "type": "paper", "label": "pmid:40765736"}, {"id": "source:pmid:40765736", "type": "manuscript", "label": "PMID 40765736 full text"}, {"id": "data:geo:GSE152805", "type": "dataset", "label": "GEO GSE152805"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:40765736", "type": "paper", "label": "pmid:40765736"}, {"id": "source:pmid:40765736", "type": "manuscript", "label": "PMID 40765736 full text"}, {"id": "data:geo:GSE152805", "type": "dataset", "label": "GEO GSE152805"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-40765736", "type": "extraction", "used": ["source:pmid:40765736"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-GSE152805", "type": "accession_resolution", "used": ["data:geo:GSE152805"], "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:40765736", "parent_hash": "sha256:c3e698553e19c5245b5de1375028ceb756f0793e944ae7a62a408da7f1850824", "fork_of": null, "generation": 3}, "gaps": ["asset:data:geo:GSE152805 licence not read", "asset:data:geo:GSE152805 not downloaded", "asset:data:geo:GSE176308 licence not read", "asset:data:geo:GSE176308 not downloaded", "asset:data:geo:GSE1919 licence not read", "asset:data:geo:GSE1919 not downloaded", "asset:data:geo:GSE206848 licence not read", "asset:data:geo:GSE206848 not downloaded", "asset:data:geo:GSE55235 licence not read", "asset:data:geo:GSE55235 not downloaded", "asset:data:geo:GSE55457 licence not read", "asset:data:geo:GSE55457 not downloaded", "execution.not_run", "review.human_critique", "review.independent_reader", "review.machine_critique"], "assays": [{"role": "data_generation", "definition_id": "rna_seq", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.99, "evidence": ["internal datasets and multiple external bulk RNA-seq and single-cell RNA-seq data. Additionally,", "ltiple external bulk RNA-seq and single-cell RNA-seq data. Additionally, various analyses, includ"], "order_basis": "paper_text_order:925", "id": "assay:1"}, {"role": "data_generation", "definition_id": "scrna_seq", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "unsupported", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.93, "evidence": ["asets and multiple external bulk RNA-seq and single-cell RNA-seq data. Additionally, various analyses, includ"], "order_basis": "paper_text_order:937", "id": "assay:2"}, {"role": "data_generation", "definition_id": "qpcr", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.99, "evidence": ["al samples were clinically validated through RT-qPCR (OA: Control = 10: 5) and IHC (6: 5) experim", "samples were clinically validated through RT-qPCR (OA: Control = 10: 5) and IHC (6: 5) experim", "nto two groups, with 10 samples allocated to RT-qPCR experiments and six samples allocated to imm", "sisting of five samples, which were used for RT-qPCR and IHC experiments, respectively. The resea"], "order_basis": "paper_text_order:1200", "id": "assay:3"}, {"role": "data_generation", "definition_id": "ihc", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.99, "evidence": ["ed through RT-qPCR (OA: Control = 10: 5) and IHC (6: 5) experiments. Results: Three hub genes", "PCR experiments and six samples allocated to immunohistochemistry (IHC) experiments. Additionally, 10 normal s", "x samples allocated to immunohistochemistry (IHC) experiments. Additionally, 10 normal synovi", "ive samples, which were used for RT-qPCR and IHC experiments, respectively. The research comp"], "order_basis": "paper_text_order:1234", "id": "assay:4"}, {"role": "analysis", "definition_id": "differential_expression", "definition_version": "f2132e96ae6c7a4e", "definition_digest": null, "required_operations": ["normalise_counts", "differential_expression_fit", "fdr_bh"], "support_state": "supported", "source_hashes": {"dsl_catalogue": "f2132e96ae6c7a4e"}, "confidence": 1.0, "evidence": ["The “limma” package was utilized to analyze DEGs, with the differential screening criteria: | log2FC | > 2.0, adj. P < 0.05."], "order_basis": "consumes_earlier_output", "id": "assay:5"}]},"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":"2026-11-04T00:29:28+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}}}