{"data":{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:39347397", "kind": "science-record", "revision": 3, "content_hash": "sha256:9e2919a7184cba9dcc2090bfafd4f7a670bb10a56ce24e7f4dfb44a53bc24d49", "created_at": "2026-11-01T20:29:33Z", "updated_at": "2026-11-01T22:55:18Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Exploring tumor microenvironment in molecular subtyping and prognostic signatures in ovarian cancer and identification of SH2D1A as a key regulator of ovarian cancer carcinogenesis.", "doi": "10.1016/j.heliyon.2024.e38014", "pmid": "39347397", "authors": ["Hongrui Guo", "Liwen Zhang", "Huancheng Su", "Jiaolin Yang", "Jing Lei", "Xiaoli Li", "Sanyuan Zhang", "Xinglin Zhang"], "journal": "Heliyon", "year": 2024, "abstract": "Introduction: A deadly gynecological cancer, ovarian cancer (OV), has a poor prognosis because of late-stage diagnosis and few targeted therapies. Addressing the tumor microenvironment (TME) in solid tumors has shown promise since it is crucial in promoting cancer progression.\nMethods: We obtained bulk RNA-seq data from TCGA-OV, GSE26712, GSE102073, and ICGC cohorts, as well as scRNA-seq data from EMTAB8107, GSE118828, GSE130000, and GSE154600 cohorts using the TISCH2 database. The ConsensusClusterPlus package was used to cluster the OV tumor tissues hierarchically to determine two molecularly different groups (C1 and C2). A total of ten different types of machine learning techniques with 101 combinations were used for prognostic model construction. Using eight TME algorithms integrated into the IOBR R package, the bulk RNA-seq dataset was analyzed. For in vitro experiments, OVCAR3 and SKOV3, two OV cell lines, were used. The migratory potential of the ovarian cancer cells was assessed using Transwell assay, while proliferation was assessed using CCK8 assay.\nResults: Based on TME-related gene set expression, two distinct molecular subgroups (C1 and C2) were identified through consensus clustering, with C1 showing higher TME activity. Further analysis indicated that C1 had increased cancer-associated fibroblasts (CAFs), M1 macrophages, and CD8+ T cells, suggesting a more activated and pro-inflammatory TME. Drug sensitivity analysis revealed that 5-Fluorouracil might be beneficial to C1 patients. Functional differences between C1 and C2 were identified, including cell adhesion, mononuclear cell differentiation, and leukocyte migration. A machine learning model was developed to create a TME-related prognostic signature, demonstrating strong prognostic capabilities across multiple datasets. High-risk patients showed a more immune-suppressive TME and higher tumor stemness. ScRNA-seq disclosed a highly activated TME-related signature in OV. Cancer cell lines had significantly higher SH2D1A mRNA expression than normal ovarian epithelial cells. We observed that SH2D1A knockdown in 2 ovarian cancer cell lines (OVCAR3 and SKOV3) reduced migration and proliferation through a series of in-vitro experiments.\nConclusion: TME-associated genes were efficient in ovarian cancer molecular subtyping. A TME-based prognosis model was constructed for vigorous prognostic stratification efficacy across multiple datasets. Moreover, we identified a pivotal role of SH2D1A in promoting proliferation and migration in ovarian cancer.", "claims": [{"id": "claim-method", "statement": "The study utilized the survival package to conduct Cox and Kaplan-Meier regression analyses to evaluate the association between predictor variables and survival outcomes.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:39347397", "locator": "sections[13] \"Statistical analysis\" paragraph 2", "quote": "The study utilized the survival package to conduct Cox and Kaplan-Meier regression analyses to evaluate the association between predictor variables and survival outcomes."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The original contributions presented in the study are included in the article/supplementary material. 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method it used and the corpus's method extractor maps it onto the DSL catalogue: kaplan_meier."}, "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": ["GSE26712", "GSE102073", "EMTAB8107", "GSE118828", "GSE130000", "GSE154600"], "resolved_accessions": ["GSE26712", "GSE102073", "EMTAB8107", "GSE118828", "GSE130000", "GSE154600"], "statements": ["The original contributions presented in the study are included in the article/supplementary material. Further inquiries can be directed to the corresponding author."], "basis": "The paper names GSE26712, GSE102073, EMTAB8107, GSE118828, GSE130000, GSE154600 in GEO and the accession resolves in the repository. No dataset was downloaded and no licence was read."}}, "can_run": {"dsl_operations": ["survival_km"], "assets": ["source:pmid:39347397", "data:geo:EMTAB8107"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:EMTAB8107"]}, "gaps": []}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-11-01T19:33:45Z", "independence": "single_reader"}, "evidence_check": {"method": "verbatim", "availability": "verbatim"}, "calls": 5, "usage": {"prompt_tokens": 13524, "completion_tokens": 2783, "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:39347397", "type": "paper", "label": "pmid:39347397"}, {"id": "source:pmid:39347397", "type": "manuscript", "label": "PMID 39347397 full text"}, {"id": "data:geo:EMTAB8107", "type": "dataset", "label": "GEO EMTAB8107"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:39347397", "type": "paper", "label": "pmid:39347397"}, {"id": "source:pmid:39347397", "type": "manuscript", "label": "PMID 39347397 full text"}, {"id": "data:geo:EMTAB8107", "type": "dataset", "label": "GEO EMTAB8107"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-39347397", "type": "extraction", "used": ["source:pmid:39347397"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-EMTAB8107", "type": "accession_resolution", "used": ["data:geo:EMTAB8107"], "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:39347397", "parent_hash": "sha256:440904c838b449ee71663409dfeec0f0be7b0107111ba09ac11b2add80e43ad2", "fork_of": null, "generation": 2}, "gaps": ["asset:data:geo:EMTAB8107 licence not read", "asset:data:geo:EMTAB8107 not downloaded", "asset:data:geo:GSE102073 licence not read", "asset:data:geo:GSE102073 not downloaded", "asset:data:geo:GSE118828 licence not read", "asset:data:geo:GSE118828 not downloaded", "asset:data:geo:GSE130000 licence not read", "asset:data:geo:GSE130000 not downloaded", "asset:data:geo:GSE154600 licence not read", "asset:data:geo:GSE154600 not downloaded", "asset:data:geo:GSE26712 licence not read", "asset:data:geo:GSE26712 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": ["ancer progression. Methods: We obtained bulk RNA-seq data from TCGA-OV, GSE26712, GSE102073, and", "integrated into the IOBR R package, the bulk RNA-seq dataset was analyzed. For in vitro experimen"], "order_basis": "paper_text_order:441", "id": "assay:1"}, {"role": "data_generation", "definition_id": "apoptosis_assay", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.93, "evidence": ["ssay, while proliferation was assessed using CCK8 assay. Results: Based on TME-related gene se"], "order_basis": "paper_text_order:1200", "id": "assay:2"}, {"role": "data_generation", "definition_id": "transfection", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.85, "evidence": ["an epithelial cells. We observed that SH2D1A knockdown in 2 ovarian cancer cell lines (OVCAR3 and S"], "order_basis": "paper_text_order:2234", "id": "assay:3"}, {"role": "analysis", "definition_id": "survival_analysis", "definition_version": "f2132e96ae6c7a4e", "definition_digest": null, "required_operations": ["survival_km"], "support_state": "supported", "source_hashes": {"dsl_catalogue": "f2132e96ae6c7a4e"}, "confidence": 1.0, "evidence": ["The study utilized the survival package to conduct Cox and Kaplan-Meier regression analyses to evaluate the association between predictor variables and survival outcomes."], "order_basis": "consumes_earlier_output", "id": "assay:4"}]},"meta":{"api_version":"v1","automation_ladder_snapshot":"ba34b49490d9bfaf","automation_ladder_caveats":["Method extraction is rule-based and has no hand-judged accuracy sample. Evidence bands order textual support; method agreement intervals are null (n=0), never probabilities. Work-type validation does not validate methods.","Operation coverage describes only explicitly named methods. It does not prove a complete protocol, compatible parameters, successful compilation or re-execution. Unrecognised or ambiguous methods require review.","Data reachability is a textual accession or public-data statement. No dataset was downloaded or checked for access, completeness or licence.","Capabilities are planning states seeded from the dated equipment register. No bench ownership, completed quote or partner booking is inferred. Procurement counts are dependencies, not guaranteed replications or financial returns.","Tier and blocker counts are deterministic assessments of this corpus, not measured agreement. R3 is reserved for procurement; unresolved methods and data require human work (R4). The most restrictive axis wins, with capability, method, data as tie-breaks. Resolving one blocker can leave another at the same tier."],"engine":"corpus_engine","engine_provider":"rule_based_v1+lex99e1195c7d6f","run_id":"run-20261023T122449232913","source":"esearch","source_detail":"PubMed mirror biomed_pubmed (read-only)","run_status":"complete","imported_at":"2026-11-03T20:16:52+00:00","generated_at":"2026-11-04T03:03:31+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}}}