Necroptosis-Related Gene Signature Predicts Prognosis in Patients with Advanced Ovarian Cancer.

{"sci_version": "1.0", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:39858052", "kind": "science-record", "revision": 2, "content_hash": "sha256:0853347b7e080a7a8af8dd8c473227d60274a731319688b34dc26a0c70163004", "created_at": "2026-11-01T10:25:49Z", "updated_at": "2026-11-01T14:01:33Z", "generator": {"name": "corpus-assay-engine", "converter": "sep_to_sci_v1", "source_package_schema": "urn:bntrg:sep:1.0.0"}, "paper": {"state": "partial", "title": "Necroptosis-Related Gene Signature Predicts Prognosis in Patients with Advanced Ovarian Cancer.", "doi": "10.3390/cancers17020271", "pmid": "39858052", "authors": null, "journal": "Cancers", "year": 2025, "abstract": null, "claims": [{"id": "claim-1", "statement": "the headline numerical result the paper states for its main finding", "kind": "quantitative", "state": "complete", "target": {"value": 10.0, "unit": "genes", "tolerance": null, "source": "chars 95-245 of source sha256 921e442b3532aec243c71afa31bf69ee693775fc390df8c53a842e0a3cd0e026"}, "evidence": [{"asset": "source:pmid:39858052", "locator": "chars 95-245 of source sha256 921e442b3532aec243c71afa31bf69ee693775fc390df8c53a842e0a3cd0e026", "quote": "We established and validated a risk score based on a 10-gene signature from the expression of necroptosis-associated genes in advanced ovarian cancer."}]}], "gaps": ["abstract", "authors"]}, "experiment": {"state": "partial", "objective": "the headline numerical result the paper states for its main finding", "steps": [{"id": "read_published_estimate", "order": 1, "name": "Read the published estimate and its interval from the source", "kind": "other", "state": "complete", "blocked_on": null, "description": "The number a replication must land on, and the sentence it came from.", "duration_hours": null, "parameters": {}, "inputs": ["source:pmid:39858052"], "outputs": ["the published estimate, its unit and its interval"], "instruments": [], "reagents": []}, {"id": "obtain_source_data", "order": 2, "name": "Obtain the source data behind the published result", "kind": "data-preparation", "state": "blocked", "blocked_on": "data:accession_absent", "description": "The published result cannot be recomputed without the data the paper analysed.", "duration_hours": null, "parameters": {}, "inputs": [], "outputs": ["the source data with its provenance"], "instruments": [], "reagents": []}, {"id": "run_analysis", "order": 3, "name": "Run the analysis programme", "kind": "analysis", "state": "blocked", "blocked_on": "no owned computational capability is bound to this experiment", "description": "Re-run the paper's analysis on the source data and produce the registered result. | SEP input not carried into the asset list: materials:the source data behind the published result in pmid:39858052", "duration_hours": null, "parameters": {}, "inputs": [], "outputs": ["the registered result"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": ["step:obtain_source_data blocked on data:accession_absent", "step:run_analysis blocked on no owned computational capability is bound to this experiment", "step:run_analysis input 'materials:the source data behind the published result in pmid:39858052' does not resolve to a declared asset"]}, "data": {"state": "partial", "assets": [{"id": "source:pmid:39858052", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.3390/cancers17020271", "sha256": "sha256:921e442b3532aec243c71afa31bf69ee693775fc390df8c53a842e0a3cd0e026", "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.3390/cancers17020271", "version": null, "note": "Source read by the package builder: full_text.", "structure": {"access_state": "full_text"}}, {"id": "asset:table:pmid:39858052:1", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:e738e8b74e7912f5b2a7f09dfd4001ae6ed5d82b6a0596d6b42e92abf1534b4e", "bytes": 695, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[3]/table-wrap[1]#cancers-17-00271-t001", "version": null, "note": "Clinical features of the gene expression datasets.", "structure": {"pmcid": "PMC11763378", "section_index": 3, "section_title": "2.1. Data Source and Pre-Processing", "row_count": 14, "column_count": 3}, "table": {"label": "Table 1", "caption": "Clinical features of the gene expression datasets.", "rows": [["Clinical Features", "TCGA-OV (n = 347)", "GSE140082 (n = 328)"], ["Age", "", ""], ["≤60 years", "192 (55.3%)", "173 (52.7%)"], [">60 years", "155 (44.7%)", "155 (47.3%)"], ["FIGO stage", "", ""], ["III", "290 (83.6%)", "265 (80.8%)"], ["IV", "57 (16.4%)", "63 (19.2%)"], ["Grading", "", ""], ["Low", "36 (10.4%)", "67 (20.4%)"], ["High", "303 (87.3%)", "238 (72.6%)"], ["Unknown", "8 (2.3%)", "23 (7.0%)"], ["3-year survival", "", ""], ["Alive", "125 (36.0%)", "92 (28.0%)"], ["Dead", "222 (64.0%)", "236 (72.0%)"]], "row_count": 14, "column_count": 3, "numeric_cells": 23, "header_rows": 1, "locator": "section[3]/table-wrap[1]#cancers-17-00271-t001"}}, {"id": "asset:table:pmid:39858052:2", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:ca043edee78784f6b128b62d4f0f2f7d148001534f67705dc67bba1d4d17b7f7", "bytes": 724, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[4]/table-wrap[1]#cancers-17-00271-t002", "version": null, "note": "GSE140082 grouping information.", "structure": {"pmcid": "PMC11763378", "section_index": 4, "section_title": "2.2. Clustering of Necroptosis-Associated Genes and Construction of a Prognostic Model", "row_count": 14, "column_count": 4}, "table": {"label": "Table 2", "caption": "GSE140082 grouping information.", "rows": [["", "GSE140082 Training (n = 164)", "GSE140082 Testing (n = 164)", "p-Value"], ["Age", "", "", ""], ["≤60 years", "92 (56.1%)", "81 (49.4%)", "0.27"], [">60 years", "72 (43.9%)", "83 (50.6%)"], ["FIGO stage", "", "", ""], ["III", "128 (78.0%)", "137 (83.5%)", "0.26"], ["IV", "36 (22.0%)", "27 (16.5%)"], ["Grading", "", "", ""], ["Low", "30 (18.3%)", "37 (22.6%)", "0.33"], ["High", "124 (75.6%)", "114 (69.5%)"], ["Unknown", "10 (6.1%)", "13 (7.9%)"], ["3-year survival", "", "", ""], ["Alive", "42 (25.6%)", "50 (30.5%)", "0.39"], ["Dead", "122 (74.4%)", "114 (69.5%)"]], "row_count": 14, "column_count": 4, "numeric_cells": 27, "header_rows": 1, "locator": "section[4]/table-wrap[1]#cancers-17-00271-t002"}}, {"id": "asset:table:pmid:39858052:3", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:a189ab46258e60e17dd6c679ffd6177d94a9053db3208d5540c0a369511c527b", "bytes": 894, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[18]/table-wrap[1]#cancers-17-00271-t003", "version": null, "note": "Clinical EOC patient cohort information.", "structure": {"pmcid": "PMC11763378", "section_index": 18, "section_title": "3.8. High Nuclear Expression of RIPK3 Is Associated with Significantly Longer Progression-Free Survival (PFS) and OS in an EOC Patient Cohort", "row_count": 30, "column_count": 4}, "table": {"label": "Table 3", "caption": "Clinical EOC patient cohort information.", "rows": [["", "Number of Patients", "Percentage"], ["Age", "", ""], ["≤60 years", "84", "54.2"], [">60 years", "71", "45.8"], ["FIGO stage", "", ""], ["I", "34", "21.9"], ["II", "10", "6.5"], ["III", "103", "66.5"], ["IV", "3", "1.9"], ["Unknown", "5", "3.2"], ["Subtype and grading", "", ""], ["Serous", "Low grade", "23", "14.8"], ["High grade", "80", "51.6"], ["Unknown", "6", "3.9"], ["Total", "109", "70.3"], ["Endometrioid", "G1", "6", "3.9"], ["G2", "5", "3.2"], ["G3", "8", "5.2"], ["Unknown", "2", "1.3"], ["Total", "21", "13.6"], ["Mucinous", "G1", "6", "3.9"], ["G2", "6", "3.9"], ["G3", "0", "0.0"], ["Unknown", "1", "0.6"], ["Total", "13", "8.4"], ["Clear-cell", "G1", "2", "1.3"], ["G2", "2", "1.3"], ["G3", "5", "3.2"], ["Unknown", "3", "1.9"], ["", "Total", "12", "7.7"]], "row_count": 30, "column_count": 4, "numeric_cells": 54, "header_rows": 1, "locator": "section[18]/table-wrap[1]#cancers-17-00271-t003"}}], "gaps": ["asset:source:pmid:39858052 not verified"]}, "analysis": {"state": "absent", "methods": [], "targets": [], "gaps": ["method", "targets"]}, "capability": {"state": "absent", "requirements": [], "gaps": ["capability"]}, "readiness": {"state": "partial", "tier": null, "blocking_axis": null, "blocked_on": null, "axes": {}, "can_run": {"dsl_operations": [], "assets": ["source:pmid:39858052", "asset:table:pmid:39858052:1", "asset:table:pmid:39858052:2", "asset:table:pmid:39858052:3"], "steps": ["read_published_estimate"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": ["xml"], "capabilities": [], "data_gaps": ["source:pmid:39858052"]}, "gaps": ["corpus_record_absent"]}, "review": {"state": "partial", "machine_critique": {"status": "passed", "providers": [{"provider": "minimax", "model": "MiniMax-M3.1-Flash", "prompt_version": "full-text-reading-v1", "prompt_hash": "e062f6ffc2a5909ca6dc8ec8ea96df9b7f0ae0d21223b0e061e65ae17b99024a", "source_hash": "921e442b3532aec243c71afa31bf69ee693775fc390df8c53a842e0a3cd0e026", "raw_response_sha256": "sha256:b32413b1212b0892a760bbed5875a31790f6183c97788ae1202e684475e03bcc", "raw_response_chars": 4692}, {"provider": "minimax_alt", "model": "MiniMax-M3", "prompt_version": "full-text-reading-v1", "prompt_hash": "5e39b7549d8b1214c73917e0f9c62a204360d2749260548dde2d1cbcce8c3983", "source_hash": "921e442b3532aec243c71afa31bf69ee693775fc390df8c53a842e0a3cd0e026", "raw_response_sha256": "sha256:5241313e6bf3850c7924a35640498b5830493bb250329b08050ae820142cffa8", "raw_response_chars": 31182}], "target_providers": [{"provider": "minimax", "model": "MiniMax-M3.1-Flash", "prompt_version": "replication-target-v2", "prompt_hash": "3e0e4eaf3bc0ee7a2a7f1412523a471e39a93dded8e5e99d8d9a752dd28f851e", "source_hash": "921e442b3532aec243c71afa31bf69ee693775fc390df8c53a842e0a3cd0e026", "raw_response": "{\"parent_value\":10,\"unit\":\"genes\",\"evidence\":\"We established and validated a risk score based on a 10-gene signature from the expression of necroptosis-associated genes in advanced ovarian cancer.\",\"target_result\":\"A validated risk score based on a 10-gene signature.\",\"number_stated\":true}", "reading": {"parent_value": 10, "unit": "genes", "evidence": "We established and validated a risk score based on a 10-gene signature from the expression of necroptosis-associated genes in advanced ovarian cancer.", "target_result": "A validated risk score based on a 10-gene signature.", "number_stated": true, "source_locator": "chars 95-245 of source sha256 921e442b3532aec243c71afa31bf69ee693775fc390df8c53a842e0a3cd0e026"}, "recorded_at": "2026-10-31T15:22:07.214905+00:00"}, {"provider": "minimax_alt", "model": "MiniMax-M3", "prompt_version": "replication-target-v2", "prompt_hash": "a986bceb738130cb0cc9117720a0bc81ae82bbd04c6c7e3b95fb6b167a349918", "source_hash": "921e442b3532aec243c71afa31bf69ee693775fc390df8c53a842e0a3cd0e026", "raw_response": "<think>We need answer JSON only. Need interpret registered target headline numerical result paper states for main finding. Supplied text contains abstract-like summary and conclusions, no clear headline numerical result except 10-gene signature. Need determine whether that's \"headline numerical result\". Prompt asks single numerical result replication registered target has reproduce; headline number only value paper itself states for registered target. Target main finding likely risk score based on 10-gene signature. Source says \"We established and validated a risk score based on a 10-gene signature...\" Could be headline numerical result? Number 10, unit \"genes\" perhaps. But registered target is \"the headline numerical result the paper states for its main finding\" deliberately generic, perhaps extraction task where source lacks number? Need assess.\n\nText source excerpts only includes abstract, methods section 2.6, conclusions, data availability. No actual performance metric (HR, AUC, p-value). Main finding: 10-gene signature predicts prognosis. Headline numerical result perhaps 10-gene signature, because exact directly stated and attached to main finding. They ask \"value the paper itself states for the registered target\". Registered target not a named metric, instead main finding. Need extract likely 10. Need exact contiguous quote containing number and attribution. Could quote \"We established and validated a risk score based on a 10-gene signature from the expression of necroptosis-associated genes in advanced ovarian cancer.\" Unit must paper prints. \"10-gene\" implies unit gene(s), likely \"genes\". parent_value 10, unit \"genes\". Evidence exact quote. target_result perhaps concise \"The paper states that it established and validated a risk score based on a 10-gene signature...\" But headline number only? They say report headline number only; schema includes target_result. likely target_result textual description maybe \"10-gene signature\" or \"A risk score based on a 10-gene signature...\" Need number_stated true.\n\nYet perhaps they expect false because no numerical result for registered target; merely a 10-gene signature isn't a result to reproduce? Let's deeply inspect prompt semantics. \"Read the supplied paper text and find the single numerical result that a replication of the registered target has to reproduce. Report the headline number only: the value the paper itself states for the registered target, not a value you calculated, converted, averaged or reconstructed.\" REGISTERED TARGET: \"the headline numerical result the paper states for its main finding\". This kind of task perhaps designed to identify key statistic from paper. Supplied text may or may not contain it. They explicitly specify if no number for registered target, false and say what text does state instead. Text likely intentionally only snippets and no headline performance number. Maybe \"10-gene signature\" is a headline numerical description of main finding, and replication indeed must reproduce 10-gene signature. Is that called numerical result? The target says headline numerical result, not sample size or methodological detail. The number 10 is attached directly to main finding and likely intended.\n\nLet's parse all numbers:\n- 10-gene signature (main finding)\n- tissue microarray diameter 0.6 mm\n- block 30 × 20 × 10 mm\n- total 465 tissue microarrays, 3 biopsies\n- 5 µm\n- antibody 1:800\n- IRS categories etc\n- dates\nNo prognostic metric. If asked headline numerical result, perhaps \"10-gene signature\" indeed only candidate. Main finding statement explicitly in abstract/conclusion. A replication of target would reproduce risk score based on 10 genes. Unit \"genes\". Evidence should perhaps include whole clause. They say evidence exact contiguous quotation containing number; if target attached directly, quote whole clause. Sentence qualifies.\n\n\"Report the headline number only\" means no other numbers in target_result/evidence? Evidence necessarily maybe sentence only includes 10. Good. \"unit must be the unit the paper prints\" Paper prints \"10-gene signature,\" so unit perhaps \"gene signature\" or \"genes\". Unit is inferred grammatical? Could set \"genes\". Need output valid JSON.\n\nCould target_result be \"A 10-gene signature\" perhaps repeats number. They may expect target_result describes target. Number only perhaps target_result should say \"10-gene signature\" not explanation. The requested schema perhaps standard: parent_value numeric, unit, evidence, target_result, number_stated. We need use source exact quote in evidence. target_result likely text statement. Could set \"A risk score based on a 10-gene signature from the expression of necroptosis-associated genes in advanced ovarian cancer.\" No issue.\n\nNeed ensure no invented quote. Exact source: \"We established and validated a risk score based on a 10-gene signature from the expression of necroptosis-associated genes in advanced ovarian cancer.\" Yes.\n\nCould number be 10 with unit \"genes\" despite \"10-gene\" singular attributive. JSON:\n{\"parent_value\":10,\"unit\":\"genes\",\"evidence\":\"We established ...\",\"target_result\":\"A validated risk score based on a 10-gene signature for advanced ovarian cancer.\",\"number_stated\":true}\n\nBut let's think if \"single numerical result\" excludes number of signature genes, as not a result metric. User explicitly says \"the headline numerical result the paper states for its main finding\". Main finding headline in title/abstract is 10-gene signature. They may consider it headline numerical result. The wording \"a replication of the registered target has to reproduce\" generic and likely generated for scientific claim extraction. If no number in text for target, false. Here clear number attached main finding. They likely intentionally want 10. Could unit be \"gene\" singular because printed \"10-gene\"? Usually unit \"genes\". \"The unit must be the unit the paper prints.\" Exact printed unit is \"gene\" in compound (10-gene signature), perhaps unit string \"genes\" isn't literally printed standalone but \"10-gene\" printed. They likely expect unit \"genes.\" Usually parent_value/unit extraction format for quantities e.g. 10, \"genes\". Yes.\n\nCould target_result simply \"A 10-gene necroptosis-related gene signature predicts prognosis in patients with advanced ovarian cancer.\" That matches title but evidence exact quote. Fine.\n\nNeed answer JSON only, no markdown.</think>\n\n{\"parent_value\":10,\"unit\":\"genes\",\"evidence\":\"We established and validated a risk score based on a 10-gene signature from the expression of necroptosis-associated genes in advanced ovarian cancer.\",\"target_result\":\"A validated risk score based on a 10-gene signature from the expression of necroptosis-associated genes in advanced ovarian cancer.\",\"number_stated\":true}", "reading": {"parent_value": 10, "unit": "genes", "evidence": "We established and validated a risk score based on a 10-gene signature from the expression of necroptosis-associated genes in advanced ovarian cancer.", "target_result": "A validated risk score based on a 10-gene signature from the expression of necroptosis-associated genes in advanced ovarian cancer.", "number_stated": true, "source_locator": "chars 95-245 of source sha256 921e442b3532aec243c71afa31bf69ee693775fc390df8c53a842e0a3cd0e026"}, "recorded_at": "2026-10-31T15:22:14.335277+00:00"}], "agreement": true, "disagreements": {"target_result": {"minimax": "A risk score based on a 10-gene signature from the expression of necroptosis-associated genes in advanced ovarian cancer predicts patient prognosis, expressed as overall survival.", "minimax_alt": "We established and validated a risk score based on a 10-gene signature from the expression of necroptosis-associated genes in advanced ovarian cancer.", "decisive": false}, "physical_methods": {"minimax": ["Tissue microarray and immunohistochemistry analysis", "Hematoxylin and eosin staining", "Immunoreactivity score (IRS)"], "minimax_alt": ["Tissue microarray", "Immunohistochemistry", "Hematoxylin and eosin staining"], "decisive": false}, "analysis_methods": {"minimax": ["Immunoreactivity score (IRS)"], "minimax_alt": ["Risk score based on a 10-gene signature from the expression of necroptosis-associated genes", "Immunoreactivity score (IRS) for semi-quantitative analysis of immunostainings"], "decisive": false}}, "agreement_basis": {"policy": "decisive_fields", "decisive_fields": ["work_type", "number_stated", "parent_value", "unit"]}, "blinded": true}, "human_critique": {"status": "not_run", "reviewer": null, "signed_at": null, "conflict_checked": false, "commentary": null}, "stages": [{"key": "target_materials", "status": "pending", "reason": null, "evidence": null}, {"key": "independent_readings", "status": "passed", "reason": "The independent readings are incomplete or disagree; the source evidence must resolve the difference.", "evidence": {"provider_errors": []}}, {"key": "source_resolution", "status": "pending", "reason": null, "evidence": null}, {"key": "protocol_reconstruction", "status": "pending", "reason": null, "evidence": null}, {"key": "control_execution", "status": "pending", "reason": null, "evidence": null}, {"key": "control_comparison", "status": "pending", "reason": null, "evidence": null}, {"key": "publication", "status": "pending", "reason": null, "evidence": null}], "gaps": ["review.human_critique", "review.machine_critique.passed"]}, "execution": {"state": "absent", "status": "not_run", "mode": null, "runs": [], "gaps": ["execution.not_run"]}, "provenance": {"entities": [{"id": "package:ee3b54032c6b122c2094fd511dc3b81596f0bf6c23914e1ad623a270c162b7e8", "type": "sep_package", "label": "SEP v1 package for pmid:39858052"}], "activities": [{"id": "activity:conversion:pmid:39858052", "type": "conversion", "used": ["package:ee3b54032c6b122c2094fd511dc3b81596f0bf6c23914e1ad623a270c162b7e8"], "agent": "agent:corpus-assay-engine"}], "agents": [{"id": "agent:minimax", "type": "model", "label": "minimax"}, {"id": "agent:minimax_alt", "type": "model", "label": "minimax_alt"}, {"id": "agent:corpus-assay-engine", "type": "software", "label": "Corpus assay engine"}], "source_run_id": "run-20261023T122449232913", "dsl_catalogue_fingerprint": "343fb30756ba6ec3", "capability_table_fingerprint": "2cb3e42f047d2ecf", "snapshot_id": "ba34b49490d9bfaf"}, "lineage": {"parent_id": "pmid:39858052", "parent_hash": "sha256:e0c526bbf23fddde60ed2d108e65e757dda32b2b4df5500499af298dc4d0d2f1", "fork_of": null, "generation": 2}, "gaps": ["abstract", "asset:source:pmid:39858052 not verified", "authors", "capability", "corpus_record_absent", "execution.not_run", "method", "review.human_critique", "review.machine_critique.passed", "step:obtain_source_data blocked on data:accession_absent", "step:run_analysis blocked on no owned computational capability is bound to this experiment", "step:run_analysis input 'materials:the source data behind the published result in pmid:39858052' does not resolve to a declared asset", "targets"]}