Identification of mitophagy-related genes impacting patient survival in glioma.

{"sci_version": "1.0", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:39923213", "kind": "science-record", "revision": 2, "content_hash": "sha256:5c4e666248ecea3339e810d6788ba4df8697e3165753ae230de2803f9beff477", "created_at": "2026-11-01T10:25:49Z", "updated_at": "2026-11-01T14:01:34Z", "generator": {"name": "corpus-assay-engine", "converter": "sep_to_sci_v1", "source_package_schema": "urn:bntrg:sep:1.0.0"}, "paper": {"state": "partial", "title": "Identification of mitophagy-related genes impacting patient survival in glioma.", "doi": "10.1007/s12672-025-01916-6", "pmid": "39923213", "authors": null, "journal": "Discover oncology", "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": 14.0, "unit": "mrgs", "tolerance": null, "source": "chars 1821-1886 of source sha256 a318e285f701320c8a183fff9146472893da470cd7eaf49a436e1c5f8daa51e0"}, "evidence": [{"asset": "source:pmid:39923213", "locator": "chars 1821-1886 of source sha256 a318e285f701320c8a183fff9146472893da470cd7eaf49a436e1c5f8daa51e0", "quote": "We developed a robust and accurate prognostic model with 14 MRGs."}]}], "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:39923213"], "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:not_downloaded", "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:39923213", "duration_hours": null, "parameters": {}, "inputs": [], "outputs": ["the registered result"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": ["step:obtain_source_data blocked on data:not_downloaded", "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:39923213' does not resolve to a declared asset"]}, "data": {"state": "partial", "assets": [{"id": "source:pmid:39923213", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.1007/s12672-025-01916-6", "sha256": "sha256:a318e285f701320c8a183fff9146472893da470cd7eaf49a436e1c5f8daa51e0", "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.1007/s12672-025-01916-6", "version": null, "note": "Source read by the package builder: full_text.", "structure": {"access_state": "full_text"}}, {"id": "asset:table:pmid:39923213:1", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:64e57a32c38e42cad8650e4fbfde6be3f6a65e056e41c7e88d0fd14968797aa0", "bytes": 1105, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[13]/table-wrap[1]#Tab1", "version": null, "note": "Results of multivariable cox regression analysis", "structure": {"pmcid": "PMC11807950", "section_index": 13, "section_title": "The independent prognostic value of the risk score", "row_count": 14, "column_count": 7}, "table": {"label": "Table 1", "caption": "Results of multivariable cox regression analysis", "rows": [["Characteristics", "Total (N)", "Univariate analysis", "", "Multivariate analysis"], ["Hazard ratio (95% CI)", "P value", "Hazard ratio (95% CI)", "P value"], ["Risk score", "695", "3.074 (2.704–3.494)", "< 0.001", "", "1.555 (1.211–1.996)", "< 0.001"], ["Age", "634", "1.066 (1.056–1.076)", "< 0.001", "", "1.032 (1.021–1.044)", "< 0.001"], ["Grade", "634", "", "", "", "", ""], ["G2", "222", "Reference", "", "", "Reference", ""], ["G3", "244", "2.967 (1.986–4.433)", "< 0.001", "", "1.966 (1.279–3.021)", "0.002"], ["G4", "168", "18.600 (12.448–27.794)", "< 0.001", "", "2.787 (1.562–4.971)", "< 0.001"], ["Gender", "634", "", "", "", "", ""], ["Male", "367", "Reference", "", "", "Reference", ""], ["Female", "267", "0.778 (0.603–1.003)", "0.053", "", "0.872 (0.668–1.139)", "0.315"], ["IDH status", "685", "", "", "", "", ""], ["WT", "246", "Reference", "", "", "Reference", ""], ["Mutant", "439", "0.116 (0.089–0.151)", "< 0.001", "", "0.500 (0.309–0.810)", "0.005"]], "row_count": 14, "column_count": 7, "numeric_cells": 38, "header_rows": 2, "locator": "section[13]/table-wrap[1]#Tab1"}}], "gaps": ["asset:source:pmid:39923213 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:39923213", "asset:table:pmid:39923213:1"], "steps": ["read_published_estimate"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": ["xml"], "capabilities": [], "data_gaps": ["source:pmid:39923213"]}, "gaps": ["corpus_record_absent"]}, "review": {"state": "partial", "machine_critique": {"status": "blocked", "providers": [{"provider": "minimax", "model": "MiniMax-M3.1-Flash", "prompt_version": "full-text-reading-v1", "prompt_hash": "890a1a0bbf345deaf8b775e1ee2eec29876b099b762a2c67b42910f450b0bbfb", "source_hash": "a318e285f701320c8a183fff9146472893da470cd7eaf49a436e1c5f8daa51e0", "raw_response_sha256": "sha256:f832b81bd7bcf48c308bffa359a0e8b667b9d7a680a77987ddc3b9722a2ef420", "raw_response_chars": 4172}, {"provider": "minimax_alt", "model": "MiniMax-M3", "prompt_version": "full-text-reading-v1", "prompt_hash": "d2df4a7c678ce1122994ca1518e385c49f6ba771948a3ca2311ac8079e61b049", "source_hash": "a318e285f701320c8a183fff9146472893da470cd7eaf49a436e1c5f8daa51e0", "raw_response_sha256": "sha256:b59e8d33cdf42123af6c2cc606b095e44376c1390f70213386c9ce895bb0d938", "raw_response_chars": 29499}], "target_providers": [{"provider": "minimax", "model": "MiniMax-M3.1-Flash", "prompt_version": "replication-target-v2", "prompt_hash": "559961b55109f86f8ea598047ada8b1f50cb6117a939b27ba4f375d2ebcae2b8", "source_hash": "a318e285f701320c8a183fff9146472893da470cd7eaf49a436e1c5f8daa51e0", "raw_response": "{\"parent_value\":14,\"unit\":\"MRGs\",\"evidence\":\"We developed a robust and accurate prognostic model with 14 MRGs.\",\"target_result\":\"The paper states that it developed a robust and accurate prognostic model with 14 MRGs.\",\"number_stated\":true}", "reading": {"parent_value": 14, "unit": "MRGs", "evidence": "We developed a robust and accurate prognostic model with 14 MRGs.", "target_result": "The paper states that it developed a robust and accurate prognostic model with 14 MRGs.", "number_stated": true, "source_locator": "chars 1821-1886 of source sha256 a318e285f701320c8a183fff9146472893da470cd7eaf49a436e1c5f8daa51e0"}, "recorded_at": "2026-10-31T15:22:42.166208+00:00"}, {"provider": "minimax_alt", "model": "MiniMax-M3", "prompt_version": "replication-target-v2", "prompt_hash": "803399a4b42963283640fe6fe6739bde1baba72b23d4b68afccf28212179d010", "source_hash": "a318e285f701320c8a183fff9146472893da470cd7eaf49a436e1c5f8daa51e0", "raw_response": "<think>We need answer JSON only. Need interpret target: headline numerical result paper states for main finding. Likely 14 MRGs? Need exact contiguous quote contains number and attribution. Source repeatedly: \"We developed a robust and accurate prognostic model with 14 MRGs.\" Registered target headline numerical result main finding. Could be p < 0.01? Need determine \"single numerical result that replication ... reproduce\", headline number. Paper abstract conclusion says model with 14 MRGs. But perhaps main numerical result is p < 0.01 survival high vs low. Need infer wording.\n\nThey ask value paper itself states for registered target, not calculate. Registered target: \"the headline numerical result the paper states for its main finding\". Main finding: prognostic model using 14 mitophagy-related genes. Headline number likely 14 MRGs. Unit \"MRGs\" perhaps number stated 14, unit MRGs. Evidence exact clause whole. target_result perhaps \"The paper states that it developed a prognostic model with 14 MRGs.\" number_stated true, parent_value 14, unit \"MRGs\". Exact evidence: \"We developed a robust and accurate prognostic model with 14 MRGs.\" This meets exact quote.\n\nCould \"p < 0.01\" be headline numerical result? It's not a value exactly and parent_value schema number. Yet likely extractors identify numerical claims, often headline result e.g. \"14 genes\". Prompt intentionally target generic. Need choose single.\n\nLet's inspect source structure: Abstract says established novel prognostic model via 14 MRGs, identified 26, lasso 14. Main model result with 14 MRGs. The headline numerical result could be 14 MRGs. Need no added explanation perhaps JSON.\n\nEnsure valid JSON.</think>\n\n{\"parent_value\":14,\"unit\":\"MRGs\",\"evidence\":\"We developed a robust and accurate prognostic model with 14 MRGs.\",\"target_result\":\"The paper states that it developed a prognostic model with 14 MRGs.\",\"number_stated\":true}", "reading": {"parent_value": 14, "unit": "MRGs", "evidence": "We developed a robust and accurate prognostic model with 14 MRGs.", "target_result": "The paper states that it developed a prognostic model with 14 MRGs.", "number_stated": true, "source_locator": "chars 1821-1886 of source sha256 a318e285f701320c8a183fff9146472893da470cd7eaf49a436e1c5f8daa51e0"}, "recorded_at": "2026-10-31T15:22:40.709133+00:00"}], "agreement": false, "disagreements": {"target_result": {"minimax": "A prognostic model comprising 14 mitophagy-related genes (MRGs); patients with a high-risk score had considerably poorer overall survival than those with a low-risk score in both the training and validating cohorts (p < 0.01).", "minimax_alt": "The 14-MRG prognostic model showed considerably poorer overall survival in the high-risk group than in the low-risk group in both the training and validating cohorts (p < 0.01).", "decisive": false}, "analysis_methods": {"minimax": ["Univariate Cox regression", "Least absolute shrinkage and selection operator (Lasso) regression analysis", "Survival analysis", "Univariate Cox regression", "Multivariate Cox regression"], "minimax_alt": ["survival analysis", "univariate Cox regression", "multivariate Cox regression", "least absolute shrinkage and selection operator (Lasso) regression"], "decisive": false}, "statistical_method": {"minimax": "Least absolute shrinkage and selection operator (Lasso) regression analysis", "minimax_alt": "survival analysis", "decisive": true}}, "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": "blocked", "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.blocked"]}, "execution": {"state": "absent", "status": "not_run", "mode": null, "runs": [], "gaps": ["execution.not_run"]}, "provenance": {"entities": [{"id": "package:5d05c17cd699330955ba8b93b9de51bf585eb699df9877a84bb8e3d318d55cd0", "type": "sep_package", "label": "SEP v1 package for pmid:39923213"}], "activities": [{"id": "activity:conversion:pmid:39923213", "type": "conversion", "used": ["package:5d05c17cd699330955ba8b93b9de51bf585eb699df9877a84bb8e3d318d55cd0"], "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:39923213", "parent_hash": "sha256:0171c92769cf01ffecaccd6b929f1b214d3f821580b99e1d0566d515bdc03e40", "fork_of": null, "generation": 2}, "gaps": ["abstract", "asset:source:pmid:39923213 not verified", "authors", "capability", "corpus_record_absent", "execution.not_run", "method", "review.human_critique", "review.machine_critique.blocked", "step:obtain_source_data blocked on data:not_downloaded", "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:39923213' does not resolve to a declared asset", "targets"]}