Pan-gastrointestinal adenocarcinoma analysis uncovers the prognostic and immune correlates of ferroptosis-related genes.

{"sci_version": "1.0", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:39944588", "kind": "science-record", "revision": 1, "content_hash": "sha256:49575b70a3ff756739a1230fa2d3cdf41f2c7e5e691dc8a9e0c1b502b81e13e1", "created_at": "2026-11-01T10:25:49Z", "updated_at": "2026-11-01T10:25:49Z", "generator": {"name": "corpus-assay-engine", "converter": "sep_to_sci_v1", "source_package_schema": "urn:bntrg:sep:1.0.0"}, "paper": {"state": "partial", "title": "Pan-gastrointestinal adenocarcinoma analysis uncovers the prognostic and immune correlates of ferroptosis-related genes.", "doi": "10.21037/tgh-24-15", "pmid": "39944588", "authors": null, "journal": "Translational gastroenterology and hepatology", "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": 0.67, "unit": "hazard ratio (hr)", "tolerance": null, "source": "chars 1159-1355 of source sha256 66736f01379a293914326c1a9d7f4d73c2cf6db431519866a1e78d2f34898734"}, "evidence": [{"asset": "source:pmid:39944588", "locator": "chars 1159-1355 of source sha256 66736f01379a293914326c1a9d7f4d73c2cf6db431519866a1e78d2f34898734", "quote": "The ferroptosis-score was significantly associated with favorable overall survival both in the training cohort [TCGA: P=0.003; hazard ratio (HR), 0.67, 95% confidence interval (95% CI): 0.52–0.87]"}]}], "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:39944588"], "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:39944588", "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:39944588' does not resolve to a declared asset"]}, "data": {"state": "partial", "assets": [{"id": "source:pmid:39944588", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.21037/tgh-24-15", "sha256": "sha256:66736f01379a293914326c1a9d7f4d73c2cf6db431519866a1e78d2f34898734", "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.21037/tgh-24-15", "version": null, "note": "Source read by the package builder: full_text.", "structure": {"access_state": "full_text"}}], "gaps": ["asset:source:pmid:39944588 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:39944588"], "steps": ["read_published_estimate"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": ["xml"], "capabilities": [], "data_gaps": ["source:pmid:39944588"]}, "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": "d54686694fe6d7d26773d093b676989e57b11af52c090129cd91c38edafa26de", "source_hash": "66736f01379a293914326c1a9d7f4d73c2cf6db431519866a1e78d2f34898734", "raw_response_sha256": "sha256:550ecc47be9586b5a89585953a997f74497c579fcfecec69b05d9b9b38068a62", "raw_response_chars": 8366}, {"provider": "minimax_alt", "model": "MiniMax-M3", "prompt_version": "full-text-reading-v1", "prompt_hash": "fd067a9cd63957cd06c88755851f7310ec8cdb7900c66f2f8a6c48124085feea", "source_hash": "66736f01379a293914326c1a9d7f4d73c2cf6db431519866a1e78d2f34898734", "raw_response_sha256": "sha256:87519868106415bb8a5d7a863c67e38795f93559296a97a2abcac24d7b7b3c20", "raw_response_chars": 62773}], "target_providers": [{"provider": "minimax", "model": "MiniMax-M3.1-Flash", "prompt_version": "replication-target-v2", "prompt_hash": "7b4fefc9454e9c7602bdc239544279d69dc6a5b83fdbc9a9b9647c694450477e", "source_hash": "66736f01379a293914326c1a9d7f4d73c2cf6db431519866a1e78d2f34898734", "raw_response": "{\"parent_value\":0.67,\"unit\":\"hazard ratio (HR)\",\"evidence\":\"The ferroptosis-score was significantly associated with favorable overall survival both in the training cohort [TCGA: P=0.003; hazard ratio (HR), 0.67, 95% confidence interval (95% CI): 0.52–0.87]\",\"target_result\":\"The headline training-cohort result was a hazard ratio of 0.67 for the ferroptosis-score and overall survival.\",\"number_stated\":true}", "reading": {"parent_value": 0.67, "unit": "hazard ratio (HR)", "evidence": "The ferroptosis-score was significantly associated with favorable overall survival both in the training cohort [TCGA: P=0.003; hazard ratio (HR), 0.67, 95% confidence interval (95% CI): 0.52–0.87]", "target_result": "The headline training-cohort result was a hazard ratio of 0.67 for the ferroptosis-score and overall survival.", "number_stated": true, "source_locator": "chars 1159-1355 of source sha256 66736f01379a293914326c1a9d7f4d73c2cf6db431519866a1e78d2f34898734"}, "recorded_at": "2026-10-31T15:30:53.772146+00:00"}, {"provider": "minimax_alt", "model": "MiniMax-M3", "prompt_version": "replication-target-v2", "prompt_hash": "b6851b14169329a4f31f14bcc80a49db5b120472100e17d8b6e4b884b4300c63", "source_hash": "66736f01379a293914326c1a9d7f4d73c2cf6db431519866a1e78d2f34898734", "raw_response": "<think>We need answer JSON only. Need determine single numerical result replication registered target headline main finding. Source abstract states training cohort TCGA P=.003 HR 0.67 CI .52-.87, validation HRs. \"headline number\" likely HR 0.67? Registered target main finding. Need report value paper states for registered target, not calculated. Unit printed perhaps hazard ratio? Need exact contiguous quotation contains number. Number likely 0.67, unit \"hazard ratio (HR)\"? Evidence exact clause/sentence. They request headline number only, unit paper prints. Could choose HR 0.67 and unit \"hazard ratio (HR)\" or maybe no unit? JSON fields.\n\nNeed carefully interpret. The main finding: ferroptosis-score significantly associated favorable overall survival in training cohort TCGA: P=0.003; hazard ratio (HR), 0.67, 95% CI. Headline numerical result likely HR 0.67. Replication of registered target has to reproduce. Could target be AUC? No such. Need quote whole clause attribution. Exact contiguous evidence perhaps \"The ferroptosis-score was significantly associated with favorable overall survival both in the training cohort [TCGA: P=0.003; hazard ratio (HR), 0.67, 95% confidence interval (95% CI): 0.52–0.87]\" This exact quote contains and attribution. unit \"hazard ratio (HR)\" maybe dimensionless. They say unit must be unit paper prints. Hazard ratio isn't unit exactly but metric. Could put \"hazard ratio (HR)\". target_result concise.\n\nNeed \"headline number only\" means parent_value 0.67, evidence quote can include surrounding clause mandated. Unit perhaps \"hazard ratio (HR)\" but JSON expected. Could use \"hazard ratio\" exactly printed. Exact quote must exact contiguous; use sentence maybe ends before and? Quote can be clause. Ensure no shortening? User says \"do not shorten it\" likely evidence exact quotation, not necessarily entire source. They explicitly say quote whole clause. So quote full clause: \"The ferroptosis-score was significantly associated with favorable overall survival both in the training cohort [TCGA: P=0.003; hazard ratio (HR), 0.67, 95% confidence interval (95% CI): 0.52–0.87] and across the four validation cohorts ...\" To attach target to number, likely whole sentence ideally. Evidence exact full sentence from Results, including all cohorts. They said \"headline number only\" perhaps evidence can full sentence. Need choose target result 0.67 from training cohort. Full sentence includes multiple numbers but parent_value one. Is that okay? \"single numerical result\" and \"headline number only\" likely answer number 0.67; evidence necessarily includes CI and P. Could quote clause with training cohort. Exact contiguous quotation from source text. It can be: \"The ferroptosis-score was significantly associated with favorable overall survival both in the training cohort [TCGA: P=0.003; hazard ratio (HR), 0.67, 95% confidence interval (95% CI): 0.52–0.87]\" But grammatically this is contiguous substring, though not complete sentence. \"do not shorten it\" perhaps asks exact full quote, no ellipsis; likely this clause suffices.\n\nCould unit be \"hazard ratio (HR)\"? Unit field maybe empty because HR unitless. But instruction says unit must be unit paper prints. Paper prints \"hazard ratio (HR)\" and value 0.67. Usually extraction benchmark expects unit maybe \"HR\". Registered target is main finding perhaps target_result should identify \"training-cohort hazard ratio for overall survival\". Parent value 0.67. Unit \"hazard ratio (HR)\" is a measure not unit. We can set unit \"hazard ratio (HR)\" to preserve printed designation. Maybe unit should be \"\" if unitless, but required says unit string and \"unit must be unit paper prints.\" It might expect unit \"HR\". Need infer task origin: \"headline numerical result\" perhaps compare numerical value. They want fields parent_value, unit, evidence, target_result, number_stated. Parent value could be 0.67. Unit \"hazard ratio (HR)\". target_result perhaps \"The ferroptosis-score was significantly associated with favorable overall survival in the TCGA training cohort.\" Fine.\n\nNeed exact evidence. Let's ensure punctuation exactly: \"The ferroptosis-score was significantly associated with favorable overall survival both in the training cohort [TCGA: P=0.003; hazard ratio (HR), 0.67, 95% confidence interval (95% CI): 0.52–0.87] and across the four validation cohorts (GSE17536: P=0.03; HR, 0.57, 95% CI: 0.34–0.96; GSE19417: P=0.047; HR, 0.53, 95% CI: 0.28–1.01; GSE84437: P=0.004; HR, 0.68, 95% CI: 0.51–0.90; GSE103479: P=0.03; HR, 0.55, 95% CI: 0.32–0.96).\" Full exact quote. But then evidence contains five numerical results, conflicting single headline? Yet attribution to 0.67 clear due \"training cohort\". Could quote full clause up to bracket only, no ellipsis. User: \"Attribution may be carried by the text's own wording... When that is how the text links them, quote the whole clause so a reader can check the attribution for themselves.\" The clause is \"The ferroptosis-score was significantly associated with favorable overall survival both in the training cohort [TCGA: ...]\" likely quote. Exact contiguous. \"do not shorten it\" likely means don't use \"...\" to skip. This is okay.\n\nCould headline numerical result instead be cohort sample n=828? Main finding headline HR clearly. Maybe title/abstract first quantitative result is P=.003 and HR=.67. Replication target likely wants effect size HR. \"headline number\" convention chooses primary metric, likely HR. Need not choose p-value. Unit \"hazard ratio\". If asking numerical result replication target, likely they registered target in some broader task perhaps main finding statistic. Source says association; primary result is HR. So yes.\n\nNeed JSON valid, no markdown. Evidence exact. Should unit be \"hazard ratio (HR)\" or \"HR\"? They demand paper prints unit. Exact paper wording is \"hazard ratio (HR), 0.67\". Unit designation perhaps \"hazard ratio (HR)\". Maybe dimensionless so unit should be \"\". Yet schema insists string but can empty. They specifically say unit must be unit paper prints, likely if no physical unit, use metric label. In similar tasks, unit may be \"hazard ratio (HR)\". Let's phrase.\n\ntarget_result could be \"Training-cohort hazard ratio for overall survival in the TCGA cohort.\" Or perhaps must state what text says instead only if false. Here number stated true, target_result should identify target result. Maybe \"TCGA training-cohort overall-survival hazard ratio for the ferroptosis-score.\" Fine.\n\nEvidence full clause perhaps:\n\"The ferroptosis-score was significantly associated with favorable overall survival both in the training cohort [TCGA: P=0.003; hazard ratio (HR), 0.67, 95% confidence interval (95% CI): 0.52–0.87]\"\nIs the phrase \"whole clause\" ending without \"and across...\" weird. Better full sentence exactly, but then multiple numbers. They asked single number but evidence can have context. To identify training HR, full sentence works. Yet registered target \"headline numerical result\" perhaps no explicit cohort registration. Full sentence may expose multiple candidates. The training cohort is labeled. We can quote the exact complete first clause, but source punctuation uses \"and across...\" continuing. A clause technically includes \"both ... and across...\" Full sentence is safest and exact. Evidence can include all because exact contiguous quote. But perhaps instruction \"headline number only\" means don't report other results in target_result, not evidence. We'll do full sentence.\n\nCould quote just abstract sentence same exact. Full sentence includes all. Unit printed \"hazard ratio (HR)\" and then subsequent cohorts \"HR\". Use \"hazard ratio (HR)\".\n\nNeed ensure en dash exact. JSON Unicode okay. Return only object.</think>\n\n{\"parent_value\":0.67,\"unit\":\"hazard ratio (HR)\",\"evidence\":\"The ferroptosis-score was significantly associated with favorable overall survival both in the training cohort [TCGA: P=0.003; hazard ratio (HR), 0.67, 95% confidence interval (95% CI): 0.52–0.87] and across the four validation cohorts (GSE17536: P=0.03; HR, 0.57, 95% CI: 0.34–0.96; GSE19417: P=0.047; HR, 0.53, 95% CI: 0.28–1.01; GSE84437: P=0.004; HR, 0.68, 95% CI: 0.51–0.90; GSE103479: P=0.03; HR, 0.55, 95% CI: 0.32–0.96).\",\"target_result\":\"Overall-survival hazard ratio for the ferroptosis-score in the TCGA training cohort.\",\"number_stated\":true}", "reading": {"parent_value": 0.67, "unit": "hazard ratio (HR)", "evidence": "The ferroptosis-score was significantly associated with favorable overall survival both in the training cohort [TCGA: P=0.003; hazard ratio (HR), 0.67, 95% confidence interval (95% CI): 0.52–0.87] and across the four validation cohorts (GSE17536: P=0.03; HR, 0.57, 95% CI: 0.34–0.96; GSE19417: P=0.047; HR, 0.53, 95% CI: 0.28–1.01; GSE84437: P=0.004; HR, 0.68, 95% CI: 0.51–0.90; GSE103479: P=0.03; HR, 0.55, 95% CI: 0.32–0.96).", "target_result": "Overall-survival hazard ratio for the ferroptosis-score in the TCGA training cohort.", "number_stated": true, "source_locator": "chars 1159-1587 of source sha256 66736f01379a293914326c1a9d7f4d73c2cf6db431519866a1e78d2f34898734"}, "recorded_at": "2026-10-31T15:31:03.536915+00:00"}], "agreement": false, "disagreements": {"target_result": {"minimax": "The ferroptosis-score was significantly associated with favorable overall survival in the TCGA training cohort (P=0.003; HR, 0.67, 95% CI: 0.52–0.87) and in four validation cohorts: GSE17536 (P=0.03; HR, 0.57, 95% CI: 0.34–0.96), GSE19417 (P=0.047; HR, 0.53, 95% CI: 0.28–1.01), GSE84437 (P=0.004; HR, 0.68, 95% CI: 0.51–0.90), and GSE103479 (P=0.03; HR, 0.55, 95% CI: 0.32–0.96).", "minimax_alt": "The ferroptosis-score was significantly associated with favorable overall survival both in the training cohort [TCGA: P=0.003; hazard ratio (HR), 0.67, 95% confidence interval (95% CI): 0.52–0.87] and across the four validation cohorts (GSE17536: P=0.03; HR, 0.57, 95% CI: 0.34–0.96; GSE19417: P=0.047; HR, 0.53, 95% CI: 0.28–1.01; GSE84437: P=0.004; HR, 0.68, 95% CI: 0.51–0.90; GSE103479: P=0.03; HR, 0.55, 95% CI: 0.32–0.96).", "decisive": false}, "analysis_methods": {"minimax": ["gene set variation analysis (GSVA)", "univariable Cox regression analysis", "multivariate Cox regression analysis", "Kaplan-Meier survival analysis", "log-rank test"], "minimax_alt": ["gene set variation analysis (GSVA)", "Kaplan-Meier survival analysis", "log-rank tests", "univariable Cox analysis", "multivariate Cox regression analysis"], "decisive": false}, "statistical_method": {"minimax": "Univariable and multivariable Cox regression analyses, together with Kaplan-Meier survival analysis with log-rank tests", "minimax_alt": "Kaplan-Meier analyses with log-rank tests; univariable and multivariable Cox regression analyses", "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:603a6498c272921e6e66fe5f0a88ffd323ac195775b2302664fc6f0ac276a341", "type": "sep_package", "label": "SEP v1 package for pmid:39944588"}], "activities": [{"id": "activity:conversion:pmid:39944588", "type": "conversion", "used": ["package:603a6498c272921e6e66fe5f0a88ffd323ac195775b2302664fc6f0ac276a341"], "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": "1adc8b70-7bf6-4f3c-a13a-9c7da19b4229", "parent_hash": "603a6498c272921e6e66fe5f0a88ffd323ac195775b2302664fc6f0ac276a341", "fork_of": null, "generation": 1}, "gaps": ["abstract", "asset:source:pmid:39944588 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:39944588' does not resolve to a declared asset", "targets"]}