{"data":{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:39521940", "kind": "science-record", "revision": 4, "content_hash": "sha256:2a91fba7d9728f0aa8b9805f5aa3fba00b301fc1ad7f6b71b64d1e1a411733cb", "created_at": "2026-11-01T20:29:47Z", "updated_at": "2026-11-01T22:55:34Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Exploring the ceRNA network involving AGAP2-AS1 as a novel biomarker for preeclampsia.", "doi": "10.1038/s41598-024-79224-2", "pmid": "39521940", "authors": ["Fan Lu", "Ni Zeng", "Xiang Xiao", "Xingxing Wang", "Han Gong", "Houkang Lei"], "journal": "Scientific reports", "year": 2024, "abstract": "Preeclampsia (PE) is an important research subject in obstetrics. Nevertheless, the underlying mechanisms of PE remain elusive. PE-related expression datasets (GSE96983, GSE96984 and GSE24129) were downloaded from the Gene Expression Omnibus (GEO) database. Firstly, the differentially expressed messenger RNAs (DE-mRNAs), DE-microRNA (DE-miRNAs) and DE-long non-coding RNA (DE-lncRNAs) between PE and control cohorts were identified, and the ceRNA network was constructed. Then candidate hub genes were obtained through five algorithms by the protein-protein intersection (PPI) network of the mRNAs. Further, five hub genes were identified by receiver operating characteristic (ROC) curve and gene expression profiles: DAXX, EFNB1, NCOR2, RBBP4 and SOCS1. The function of 5 hub genes was analyzed and the interaction between drugs and hub genes was predicted. A total of 5 small molecule drugs were predicted, namely benzbromarone, 9,10-phenanthrenequinone, chembl312032, insulin and aldesleukin. AGAP2-AS1 was mainly located in exosome and cytoplasm. Agap2-as1-related regulatory subnetworks were extracted from ceRNA networks which included 41 mRNAs, 2 miRNAs and 1 lncRNA, including the regulated relationship pairs AGAP2-AS1-hsa-miR-497-5p-SRPRB, and AGAP2-AS1-hsa-miR-195-5p-RPL36. In summary, we constructed a competitive endogenous RNA (ceRNA) network to identify five potential biomarkers (DAXX, EFNB1, NCOR2, SOCS1 and RBBP4) of PE. The in-depth analysis of the AGAP2-AS1 regulatory network will help to uncover more important molecules closely related to PE and provide a scientific Reference.", "claims": [{"id": "claim-method", "statement": "Firstly, the gene expression matrix of three PE samples and four control samples in the GSE96984 dataset was analyzed by the voom method in the “limma” R package (version 3.48.3) (|log2FC| > 0.5 and P < 0.05)61, and DE-mRNAs and DE-lncRNAs between the PE groups and the control groups were identified.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:39521940", "locator": "sections[13] \"Creation of the competing endogenous RNA (ceRNA) network\" paragraph 2", "quote": "Firstly, the gene expression matrix of three PE samples and four control samples in the GSE96984 dataset was analyzed by the voom method in the “limma” R package (version 3.48.3) (|log2FC| > 0.5 and P < 0.05)61, and DE-mRNAs and DE-lncRNAs between the PE groups and the control groups were identified."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The datasets used and analyzed in the current study are available from the GEO database (https://www.ncbi.nlm.nih.gov/gds) [GSE96983, GSE96984 and GSE24129], StarBase (Http://starbase.sysu.edu.cn), miRTarBase Database (Http://mirtarbase.mbc.nctu.edu.tw), DGIdb database (https://dgidb.org), lncLocator Database (www.csbio.sjtu.edu.cn/bioinf/lncLocator).", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:39521940", "locator": "sections[26] \"notes\" paragraph 1", "quote": "The datasets used and analyzed in the current study are available from the GEO database (https://www.ncbi.nlm.nih.gov/gds) [GSE96983, GSE96984 and GSE24129], StarBase (Http://starbase.sysu.edu.cn), miRTarBase Database (Http://mirtarbase.mbc.nctu.edu.tw), DGIdb database (https://dgidb.org), lncLocator Database (www.csbio.sjtu.edu.cn/bioinf/lncLocator)."}], "state": "complete"}, {"id": "claim-target-result", "statement": "The study identified five potential PE biomarkers: DAXX, EFNB1, NCOR2, SOCS1 and RBBP4.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:39521940", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "In summary, we constructed a competitive endogenous RNA (ceRNA) network to identify five potential biomarkers (DAXX, EFNB1, NCOR2, SOCS1 and RBBP4) of PE."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "The study identified five potential PE biomarkers: DAXX, EFNB1, NCOR2, SOCS1 and RBBP4.", "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:39521940"], "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:GSE24129"], "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:GSE24129"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:39521940", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.1038/s41598-024-79224-2", "sha256": 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(https://www.ncbi.nlm.nih.gov/gds) [GSE96983, GSE96984 and GSE24129], StarBase (Http://starbase.sysu.edu.cn), miRTarBase Database (Http://mirtarbase.mbc.nctu.edu.tw), DGIdb database (https://dgidb.org), lncLocator Database (www.csbio.sjtu.edu.cn/bioinf/lncLocator).", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The datasets used and analyzed in the current study are available from the GEO database (https://www.ncbi.nlm.nih.gov/gds) [GSE96983, GSE96984 and GSE24129], StarBase (Http://starbase.sysu.edu.cn), miRTarBase Database (Http://mirtarbase.mbc.nctu.edu.tw), DGIdb database (https://dgidb.org), lncLocator Database (www.csbio.sjtu.edu.cn/bioinf/lncLocator).", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM2548592", "GSM2548593", "GSM2548594", "GSM2548595", "GSM2548596", "GSM2548597", "GSM2548598"], "sample_count": 7, "group_sizes": null, "group_sizes_basis": null, "platform": "20712", "taxon": 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"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": ["GSE96983", "GSE96984", "GSE24129"], "resolved_accessions": ["GSE96983", "GSE96984", "GSE24129"], "statements": ["The datasets used and analyzed in the current study are available from the GEO database (https://www.ncbi.nlm.nih.gov/gds) [GSE96983, GSE96984 and GSE24129], StarBase (Http://starbase.sysu.edu.cn), miRTarBase Database (Http://mirtarbase.mbc.nctu.edu.tw), DGIdb database (https://dgidb.org), lncLocator Database (www.csbio.sjtu.edu.cn/bioinf/lncLocator)."], "basis": "The paper names GSE96983, GSE96984, GSE24129 in 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:39521940", "data:geo:GSE24129"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:GSE24129"]}, "gaps": []}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-11-01T19:38:03Z", "independence": "single_reader"}, "evidence_check": {"method": "verbatim", "availability": "verbatim"}, "calls": 5, "usage": {"prompt_tokens": 11787, "completion_tokens": 1739, "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:39521940", "type": "paper", "label": "pmid:39521940"}, {"id": "source:pmid:39521940", "type": "manuscript", "label": "PMID 39521940 full text"}, {"id": "data:geo:GSE24129", "type": "dataset", "label": "GEO GSE24129"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:39521940", "type": "paper", "label": "pmid:39521940"}, {"id": "source:pmid:39521940", "type": "manuscript", "label": "PMID 39521940 full text"}, {"id": "data:geo:GSE24129", "type": "dataset", "label": "GEO GSE24129"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-39521940", "type": "extraction", "used": ["source:pmid:39521940"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-GSE24129", "type": "accession_resolution", "used": ["data:geo:GSE24129"], "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:39521940", "parent_hash": "sha256:8f1bfc34afb920c30b28b7814a84a1bd2e5bb001ca320488a1bd4a4c2832ced9", "fork_of": null, "generation": 3}, "gaps": ["asset:data:geo:GSE24129 licence not read", "asset:data:geo:GSE24129 not downloaded", "asset:data:geo:GSE96983 licence not read", "asset:data:geo:GSE96983 not downloaded", "asset:data:geo:GSE96984 licence not read", "asset:data:geo:GSE96984 not downloaded", "execution.not_run", "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": ["time quantitative-Polymerase Chain Reaction (RT-qPCR). DAXX, EFNB1, NCOR2, and SOCS1 were highly", "Materials and methods Sample collection and RT-qPCR A total of 8 PE patients and 8 controls at A", "d placenta samples were collected to perform RT-qPCR. This study was approved by Ethics Committee", "perform reverse transcription analysis. The RT-qPCR analysis was performed using the 2xUniversal"], "order_basis": "paper_text_order:1814", "id": "assay:1"}, {"role": "data_generation", "definition_id": "animal_model", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.77, "evidence": ["ts (ACOG)2. 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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}}}