{"data":{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:39398336", "kind": "science-record", "revision": 1, "content_hash": "sha256:955b397d593d1b524798609e8967aed264d0e9f356576d4d25dd7c599c14b8be", "created_at": "2026-11-01T20:29:37Z", "updated_at": "2026-11-01T20:29:37Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Shared diagnostic genes and potential mechanisms between polycystic ovary syndrome and recurrent miscarriage revealed by integrated transcriptomics analysis and machine learning.", "doi": "10.3389/fendo.2024.1335106", "pmid": "39398336", "authors": ["Juanjuan He", "Ahui Liu", "Haofei Shen", "Yanbiao Jiang", "Min Gao", "Liulin Yu", "Wenjing Du", "Xuehong Zhang", "Fen Fu"], "journal": "Frontiers in endocrinology", "year": 2024, "abstract": "Objective: More and more studies have found that polycystic ovary syndrome (PCOS) is significantly associated with recurrent spontaneous abortion (RSA), but the specific mechanism is not yet clear.\nMethods: Based on the GEO database, we downloaded the PCOS (GSE10946, GSE6798 and GSE137684) and RSA (GSE165004, GSE26787 and GSE22490) datasets and performed differential analysis, weighted gene co-expression network (WGCNA), functional enrichment, and machine learning, respectively, on the datasets of the two diseases, Nomogram and integrated bioinformatics analysis such as immune infiltration analysis. Finally, the reliability of the diagnostic gene was verified by external verification and collection of human specimens.\nResults: In this study, PCOS and RSA datasets were obtained from Gene Expression Omnibus (GEO) database, and a total of 23 shared genes were obtained by differential analysis and WGCNA analysis. GO results showed that the shared genes were mainly enriched in the functions of lipid catabolism and cell cycle transition (G1/S). DO enrichment revealed that shared genes are mainly involved in ovarian diseases, lipid metabolism disorders and psychological disorders. KEGG analysis showed significant enrichment of Regulation of lipolysis in adipocytes, Prolactin signaling pathway, FoxO signaling pathway, Hippo signaling pathway and other pathways. A diagnostic gene FAM166 B was obtained by machine learning and Nomogram screening, which mainly played an important role in Cellular component. GSEA analysis revealed that FAM166B may be involved in the development of PCOS and RSA by regulating the cell cycle, amino acid metabolism, lipid metabolism, and carbohydrate metabolism. CIBERSORT analysis showed that the high expression of FAM166 B was closely related to the imbalance of multiple immune cells. Further verification by qPCR suggested that FAM166 B could be used as a common marker of PCOS and RSA.\nConclusions: In summary, this study identified FAM166B as a common biomarker for PCOS and RSA, and conducted in-depth research and analysis of this gene, providing new data for basic experimental research and early prognosis, diagnosis and treatment of clinical diseases.", "claims": [{"id": "claim-data-access", "statement": "Publicly available datasets used in this study can be downloaded from the GEO database (http://www.ncbi.nlm.nih.gov/geo/). The PCOS group includes three datasets with GSE10946 and GSE6798 and GSE137684. GSE165004 and GSE26787 and GSE22490 are involved in the RSA group. If necessary, please contact the corresponding author to obtain the original data.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:39398336", "locator": "sections[30] \"Data availability statement\" paragraph 2", "quote": "Publicly available datasets used in this study can be downloaded from the GEO database (http://www.ncbi.nlm.nih.gov/geo/). The PCOS group includes three datasets with GSE10946 and GSE6798 and GSE137684. GSE165004 and GSE26787 and GSE22490 are involved in the RSA group. If necessary, please contact the corresponding author to obtain the original data."}], "state": "complete"}, {"id": "claim-target-result", "statement": "FAM166B was identified as the best shared diagnostic gene for PCOS and RSA.", "kind": "quantitative", "target": {"value": 0.772, "unit": "auc", "tolerance": null, "source": "In addition, in the external validation cohorts of PCOS and RSA, the expression level of FAM166B was consistent with that of the training group ( Figures 6C, G ), and had higher diagnostic performance in the validation cohorts of PCOS and RSA (AUC = 0.772, 0.859) ( Figures 6D, H )."}, "evidence": [{"asset": "source:pmid:39398336", "locator": "sections[22] \"Identification and verification of shared diagnostic genes\" paragraph 2", "quote": "Finally, FAM166B was identified as the best shared diagnostic gene."}, {"asset": "source:pmid:39398336", "locator": "sections[22] \"Identification and verification of shared diagnostic genes\" paragraph 4", "quote": "In addition, in the external validation cohorts of PCOS and RSA, the expression level of FAM166B was consistent with that of the training group ( Figures 6C, G ), and had higher diagnostic performance in the validation cohorts of PCOS and RSA (AUC = 0.772, 0.859) ( Figures 6D, H )."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "FAM166B was identified as the best shared diagnostic gene for PCOS and RSA.", "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:39398336"], "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:GSE10946"], "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:GSE10946"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:39398336", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.3389/fendo.2024.1335106", "sha256": "sha256:352780fabb0e894de6c8dfe7a9f1a20bf8f0c2521c2b8c75b3592fb416e8e56b", "bytes": 59491, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.3389/fendo.2024.1335106", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC11466764", "source": "europe_pmc_fulltext", "coverage": "whole_body", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE10946", "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=GSE10946", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE10946", "version": null, "note": "Publicly available datasets used in this study can be downloaded from the GEO database (http://www.ncbi.nlm.nih.gov/geo/). The PCOS group includes three datasets with GSE10946 and GSE6798 and GSE137684. GSE165004 and GSE26787 and GSE22490 are involved in the RSA group. If necessary, please contact the corresponding author to obtain the original data.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "Publicly available datasets used in this study can be downloaded from the GEO database (http://www.ncbi.nlm.nih.gov/geo/). The PCOS group includes three datasets with GSE10946 and GSE6798 and GSE137684. GSE165004 and GSE26787 and GSE22490 are involved in the RSA group. If necessary, please contact the corresponding author to obtain the original data.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM277438", "GSM277439", "GSM277440", "GSM277441", "GSM277442", "GSM277443", "GSM277444", "GSM277445", "GSM277446", "GSM277447", "GSM277448", "GSM277449", "GSM277450", "GSM277451", "GSM277452", "GSM277453", "GSM277454", "GSM277455", "GSM277456", "GSM277457", "GSM277458", "GSM277459", "GSM277460"], "sample_count": 23, "group_sizes": null, "group_sizes_basis": null, "platform": "570", "taxon": "Homo sapiens", "title": "Gene expression microarray profiles of cumulus cells in lean and overweight-obese polycystic ovary syndrome patients", "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:GSE137684", "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=GSE137684", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE137684", "version": null, "note": "Publicly available datasets used in this study can be downloaded from the GEO database (http://www.ncbi.nlm.nih.gov/geo/). The PCOS group includes three datasets with GSE10946 and GSE6798 and GSE137684. GSE165004 and GSE26787 and GSE22490 are involved in the RSA group. If necessary, please contact the corresponding author to obtain the original data.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "Publicly available datasets used in this study can be downloaded from the GEO database (http://www.ncbi.nlm.nih.gov/geo/). The PCOS group includes three datasets with GSE10946 and GSE6798 and GSE137684. GSE165004 and GSE26787 and GSE22490 are involved in the RSA group. If necessary, please contact the corresponding author to obtain the original data.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM4084711", "GSM4084712", "GSM4084713", "GSM4084714", "GSM4084715", "GSM4084716", "GSM4084717", "GSM4084718", "GSM4084719", "GSM4084720", "GSM4084721", "GSM4084722"], "sample_count": 12, "group_sizes": null, "group_sizes_basis": null, "platform": "17077", "taxon": "Homo sapiens", "title": "Differential messenger RNA expression in Granulosa Cells from polycystic ovary syndrome with Normoandrogen and Hyperandrogen: Identification of gene sets through bioinformatic Filtering analysis", "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:GSE165004", "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=GSE165004", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE165004", "version": null, "note": "Publicly available datasets used in this study can be downloaded from the GEO database (http://www.ncbi.nlm.nih.gov/geo/). The PCOS group includes three datasets with GSE10946 and GSE6798 and GSE137684. GSE165004 and GSE26787 and GSE22490 are involved in the RSA group. If necessary, please contact the corresponding author to obtain the original data.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "Publicly available datasets used in this study can be downloaded from the GEO database (http://www.ncbi.nlm.nih.gov/geo/). The PCOS group includes three datasets with GSE10946 and GSE6798 and GSE137684. GSE165004 and GSE26787 and GSE22490 are involved in the RSA group. If necessary, please contact the corresponding author to obtain the original data.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM5024320", "GSM5024321", "GSM5024322", "GSM5024323", "GSM5024324", "GSM5024325", "GSM5024326", "GSM5024327", "GSM5024328", "GSM5024329", "GSM5024330", "GSM5024331", "GSM5024332", "GSM5024333", "GSM5024334", "GSM5024335", "GSM5024336", "GSM5024337", "GSM5024338", "GSM5024339", "GSM5024340", "GSM5024341", "GSM5024342", "GSM5024343", "GSM5024344", "GSM5024345", "GSM5024346", "GSM5024347", "GSM5024348", "GSM5024349", "GSM5024350", "GSM5024351", "GSM5024352", "GSM5024353", "GSM5024354", "GSM5024355", "GSM5024356", "GSM5024357", "GSM5024358", "GSM5024359", "GSM5024360", "GSM5024361", "GSM5024362", "GSM5024363", "GSM5024364", "GSM5024365", "GSM5024366", "GSM5024367", "GSM5024368", "GSM5024369", "GSM5024370", "GSM5024371", "GSM5024372", "GSM5024373", "GSM5024374", "GSM5024375", "GSM5024376", "GSM5024377", "GSM5024378", "GSM5024379", "GSM5024380", "GSM5024381", "GSM5024382", "GSM5024383", "GSM5024384", "GSM5024385", "GSM5024386", "GSM5024387", "GSM5024388", "GSM5024389", "GSM5024390", "GSM5024391"], "sample_count": 72, "group_sizes": null, "group_sizes_basis": null, "platform": "16699", "taxon": "Homo sapiens", "title": "Endometrial Tissue RNA expression in recurrent pregnancy losses and unexplained infertility vs. conrol", "resolution_checked_at": "2026-11-01T18:06:43Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}, {"id": "data:geo:GSE22490", "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=GSE22490", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE22490", "version": null, "note": "Publicly available datasets used in this study can be downloaded from the GEO database (http://www.ncbi.nlm.nih.gov/geo/). The PCOS group includes three datasets with GSE10946 and GSE6798 and GSE137684. GSE165004 and GSE26787 and GSE22490 are involved in the RSA group. If necessary, please contact the corresponding author to obtain the original data.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "Publicly available datasets used in this study can be downloaded from the GEO database (http://www.ncbi.nlm.nih.gov/geo/). The PCOS group includes three datasets with GSE10946 and GSE6798 and GSE137684. GSE165004 and GSE26787 and GSE22490 are involved in the RSA group. If necessary, please contact the corresponding author to obtain the original data.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM558664", "GSM558665", "GSM558666", "GSM558667", "GSM558668", "GSM558669", "GSM558670", "GSM558671", "GSM558672", "GSM558673"], "sample_count": 10, "group_sizes": null, "group_sizes_basis": null, "platform": "570", "taxon": "Homo sapiens", "title": "Increased placental expression and maternal serum levels of apoptosis-inducing TRAIL in recurrent miscarriage", "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:GSE26787", "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=GSE26787", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE26787", "version": null, "note": "Publicly available datasets used in this study can be downloaded from the GEO database (http://www.ncbi.nlm.nih.gov/geo/). 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The PCOS group includes three datasets with GSE10946 and GSE6798 and GSE137684. GSE165004 and GSE26787 and GSE22490 are involved in the RSA group. If necessary, please contact the corresponding author to obtain the original data.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "Publicly available datasets used in this study can be downloaded from the GEO database (http://www.ncbi.nlm.nih.gov/geo/). The PCOS group includes three datasets with GSE10946 and GSE6798 and GSE137684. GSE165004 and GSE26787 and GSE22490 are involved in the RSA group. If necessary, please contact the corresponding author to obtain the original data.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM155631", "GSM155643", "GSM155644", "GSM155729", "GSM156170", "GSM156171", "GSM156176", "GSM156177", "GSM156178", "GSM156179", "GSM156180", "GSM156181", "GSM156184", "GSM156186", "GSM156187", "GSM156510", "GSM156511", "GSM156512", "GSM156749", "GSM156750", "GSM156751", "GSM156752", "GSM156753", "GSM156763", "GSM156946", "GSM156948", "GSM156949", "GSM156950", "GSM156951"], "sample_count": 29, "group_sizes": null, "group_sizes_basis": null, "platform": "570", "taxon": "Homo sapiens", "title": "Reduced expression of mitochondrial oxidative metabolism genes in skeletal muscle of women with PCOS", "resolution_checked_at": "2026-11-01T20:16:08Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}], "gaps": ["asset:data:geo:GSE10946 not downloaded", "asset:data:geo:GSE10946 licence not read", "asset:data:geo:GSE137684 not downloaded", "asset:data:geo:GSE137684 licence not read", "asset:data:geo:GSE165004 not downloaded", "asset:data:geo:GSE165004 licence not read", "asset:data:geo:GSE22490 not downloaded", "asset:data:geo:GSE22490 licence not read", "asset:data:geo:GSE26787 not downloaded", "asset:data:geo:GSE26787 licence not read", "asset:data:geo:GSE6798 not downloaded", "asset:data:geo:GSE6798 licence not read"]}, "analysis": {"state": "absent", "methods": [], "targets": [{"id": "target-published-estimate", "claim_id": "claim-target-result", "operation": null, "expected_value": 0.772, "unit": "auc", "tolerance": null, "state": "complete", "note": "The published estimate as the reader quoted it from the paper. No tolerance is published because the paper states none."}], "gaps": ["method", "operations"]}, "capability": {"state": "complete", "requirements": [{"capability_id": "capability:computational_analysis", "label": "Computational analysis platform", "assay_families": ["meta_analysis", "machine_learning", "survival_analysis", "statistical_regression", "pca", "molecular_docking", "network_analysis", "differential_expression", "gwas"], "availability_state": "owned", "tier_unlocked": "R1", "candidate": "Automated Assays Laravel application and simulated adapters"}], "gaps": []}, "readiness": {"state": "blocked", "tier": "R4", "blocking_axis": "method", "blocked_on": "method:not_determinable", "axes": {"method": {"tier": "R4", "expressible": false, "required_operations": [], "missing_operations": [], "basis": "The reader quoted the method the paper names (not named), but the corpus's method extractor could not map it onto a DSL operation, so the method is published but not expressible."}, "capability": {"tier": "R1", "capability_id": "capability:computational_analysis", "availability_state": "owned", "basis": "The computational analysis is owned. The physical bench the paper used is not, so a physical validation cannot be run here."}, "data": {"tier": "R1", "reachable": true, "accessions": ["GSE10946", "GSE6798", "GSE137684", "GSE165004", "GSE26787", "GSE22490"], "resolved_accessions": ["GSE10946", "GSE6798", "GSE137684", "GSE165004", "GSE26787", "GSE22490"], "statements": ["Publicly available datasets used in this study can be downloaded from the GEO database (http://www.ncbi.nlm.nih.gov/geo/). The PCOS group includes three datasets with GSE10946 and GSE6798 and GSE137684. GSE165004 and GSE26787 and GSE22490 are involved in the RSA group. If necessary, please contact the corresponding author to obtain the original data."], "basis": "The paper names GSE10946, GSE6798, GSE137684, GSE165004, GSE26787, GSE22490 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": [], "assets": ["source:pmid:39398336", "data:geo:GSE10946"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:GSE10946"]}, "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": "2026-11-01T19:35:00Z", "independence": "single_reader"}, "evidence_check": {"method": null, "availability": "verbatim"}, "calls": 5, "usage": {"prompt_tokens": 16633, "completion_tokens": 2035, "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:39398336", "type": "paper", "label": "pmid:39398336"}, {"id": "source:pmid:39398336", "type": "manuscript", "label": "PMID 39398336 full text"}, {"id": "data:geo:GSE10946", "type": "dataset", "label": "GEO GSE10946"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:39398336", "type": "paper", "label": "pmid:39398336"}, {"id": "source:pmid:39398336", "type": "manuscript", "label": "PMID 39398336 full text"}, {"id": "data:geo:GSE10946", "type": "dataset", "label": "GEO GSE10946"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-39398336", "type": "extraction", "used": ["source:pmid:39398336"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-GSE10946", "type": "accession_resolution", "used": ["data:geo:GSE10946"], "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": null, "parent_hash": null, "fork_of": null, "generation": 0}, "gaps": ["asset:data:geo:GSE10946 licence not read", "asset:data:geo:GSE10946 not downloaded", "asset:data:geo:GSE137684 licence not read", "asset:data:geo:GSE137684 not downloaded", "asset:data:geo:GSE165004 licence not read", "asset:data:geo:GSE165004 not downloaded", "asset:data:geo:GSE22490 licence not read", "asset:data:geo:GSE22490 not downloaded", "asset:data:geo:GSE26787 licence not read", "asset:data:geo:GSE26787 not downloaded", "asset:data:geo:GSE6798 licence not read", "asset:data:geo:GSE6798 not downloaded", "execution.not_run", "method", "operations", "review.human_critique", "review.independent_reader", "review.machine_critique"], "assays": [{"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": ["ltiple immune cells. Further verification by qPCR suggested that FAM166 B could be used as a c", "ator for freezing and storage for subsequent RT-qPCR. In addition, chorionic villus tissue sample", "igerated tube at -80°C for use in subsequent RT-qPCR. The study was approved by the Ethics Commit", "due to the small sample size. Validation of RT-qPCR in human tissues. (A) The expression level o"], "order_basis": "paper_text_order:1992", "id": "assay:1"}]},"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":"2026-11-04T02:16:52+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}}}