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pmid:40823088

Oxidative stress-related genes in uveal melanoma: the role of CALM1 in modulating oxidative stress and apoptosis and its prognostic significance.

Frontiers in oncology · 2025 doi:10.3389/fonc.2025.1618601

Paper

partial

Experiment

partial

Data

partial

Analysis

absent

Execution

absent

Execution evidence has not yet been added to this .science file. Explore its methods, data and open questions to plan the next step.
Record details sci_version · id · kind · revision · content_hash · schema · created_at · updated_at · generator
id
pmid:40823088
kind
science-record
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sha256:1b1e0093ca2792dbfaa508acaa6aa23c889c65684d6f9a1a99712233959ebf2a
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https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json
created_at
2026-11-01T10:25:52Z
updated_at
2026-11-01T10:25:52Z
generator object · 3 fields
name
corpus-assay-engine
converter
sep_to_sci_v1
source_package_schema
urn:bntrg:sep:1.0.0
paper object · 10 fields
state
partial
title
Oxidative stress-related genes in uveal melanoma: the role of CALM1 in modulating oxidative stress and apoptosis and its prognostic significance.
doi
10.3389/fonc.2025.1618601
pmid
40823088
authors
null
journal
Frontiers in oncology
year
2025
abstract
null
claims array · 1 item
[0] object · 6 fields
id
claim-1
statement
the headline numerical result the paper states for its main finding
kind
quantitative
state
complete
target object · 4 fields
value
0.844
unit
auc
tolerance
null
source
chars 1856-1965 of source sha256 474987771cf5cc5ba459c32e4e4808a29928490b534d2768d058e75c700b6022
evidence array · 1 item
[0] object · 3 fields
asset
source:pmid:40823088
locator
chars 1856-1965 of source sha256 474987771cf5cc5ba459c32e4e4808a29928490b534d2768d058e75c700b6022
quote
The risk signature model demonstrated strong predictive accuracy for a 5-year overall survival (AUC = 0.844).
gaps array · 2 items
[0]
abstract
[1]
authors
experiment object · 8 fields
state
partial
objective
the headline numerical result the paper states for its main finding
steps array · 3 items
[0] object · 13 fields
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.
parameters object · 0 fields
inputs array · 1 item
[0]
source:pmid:40823088
outputs array · 1 item
[0]
the published estimate, its unit and its interval
instruments array · 0 items
reagents array · 0 items
[1] object · 13 fields
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obtain_source_data
order
2
name
Obtain the source data behind the published result
kind
data-preparation
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blocked
blocked_on
data:not_downloaded
description
The published result cannot be recomputed without the data the paper analysed.
parameters object · 0 fields
inputs array · 0 items
outputs array · 1 item
[0]
the source data with its provenance
instruments array · 0 items
reagents array · 0 items
[2] object · 13 fields
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run_analysis
order
3
name
Run the analysis programme
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analysis
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blocked
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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:40823088
parameters object · 0 fields
inputs array · 0 items
outputs array · 1 item
[0]
the registered result
instruments array · 0 items
reagents array · 0 items
materials array · 0 items
instruments array · 0 items
reagents array · 0 items
conditions object · 0 fields
gaps array · 3 items
[0]
step:obtain_source_data blocked on data:not_downloaded
[1]
step:run_analysis blocked on no owned computational capability is bound to this experiment
[2]
step:run_analysis input 'materials:the source data behind the published result in pmid:40823088' does not resolve to a declared asset
data object · 3 fields
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partial
assets array · 1 item
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source:pmid:40823088
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manuscript
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xml
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application/xml
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https://doi.org/10.3389/fonc.2025.1618601
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10.3389/fonc.2025.1618601
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null
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Source read by the package builder: full_text.
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full_text
gaps array · 1 item
[0]
asset:source:pmid:40823088 not verified
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[1]
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capability
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partial
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null
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null
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[0]
source:pmid:40823088
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[0]
read_published_estimate
must_build object · 5 fields
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[0]
xml
capabilities array · 0 items
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[0]
source:pmid:40823088
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[0]
corpus_record_absent
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partial
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passed
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minimax
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minimax_alt
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474987771cf5cc5ba459c32e4e4808a29928490b534d2768d058e75c700b6022
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minimax
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MiniMax-M3.1-Flash
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474987771cf5cc5ba459c32e4e4808a29928490b534d2768d058e75c700b6022
raw_response
{"parent_value":0.844,"unit":"AUC","evidence":"The risk signature model demonstrated strong predictive accuracy for a 5-year overall survival (AUC = 0.844).","target_result":"5-year overall survival AUC = 0.844","number_stated":true}
reading object · 6 fields
parent_value
0.844
unit
AUC
evidence
The risk signature model demonstrated strong predictive accuracy for a 5-year overall survival (AUC = 0.844).
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5-year overall survival AUC = 0.844
number_stated
true
source_locator
chars 1856-1965 of source sha256 474987771cf5cc5ba459c32e4e4808a29928490b534d2768d058e75c700b6022
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2026-10-31T15:31:42.379880+00:00
[1] object · 8 fields
provider
minimax_alt
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MiniMax-M3
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source_hash
474987771cf5cc5ba459c32e4e4808a29928490b534d2768d058e75c700b6022
raw_response
<think>We need answer JSON only. Need identify headline numerical result paper states for main finding registered target. Likely AUC=0.844, unit maybe AUC? Need exact contiguous quote containing number. "The risk signature model demonstrated strong predictive accuracy for a 5-year overall survival (AUC = 0.844)." Headline number perhaps 0.844. Unit must paper prints. AUC is dimensionless, perhaps unit "AUC". They ask parent_value number. Unit printed perhaps "AUC" or empty? Need infer expected extraction. The main headline numerical result likely AUC 0.844. Unit must be unit paper prints. Since AUC is not really unit, but printed metric. Could set unit "AUC". Evidence exact contiguous quote whole clause. target_result describe. Ensure exact. JSON.</think> {"parent_value":0.844,"unit":"AUC","evidence":"The risk signature model demonstrated strong predictive accuracy for a 5-year overall survival (AUC = 0.844).","target_result":"The risk signature model predicted 5-year overall survival with an AUC of 0.844.","number_stated":true}
reading object · 6 fields
parent_value
0.844
unit
AUC
evidence
The risk signature model demonstrated strong predictive accuracy for a 5-year overall survival (AUC = 0.844).
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The risk signature model predicted 5-year overall survival with an AUC of 0.844.
number_stated
true
source_locator
chars 1856-1965 of source sha256 474987771cf5cc5ba459c32e4e4808a29928490b534d2768d058e75c700b6022
recorded_at
2026-10-31T15:31:41.829275+00:00
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Differential gene expression analysis
[1]
Protein–protein interaction (PPI) network analysis
[2]
Least absolute shrinkage and selection operator (LASSO) regression
[3]
Random forest
[4]
Support vector machine (SVM)
[5]
Gradient boosting machine (GBM)
[6]
Neural network (NNET)
[7]
Extreme gradient boosting (XGBoost)
[8]
Risk signature model
[9]
Area under the receiver operating characteristic (ROC) curve (AUC)
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[0]
Differential gene expression analysis
[1]
Protein–protein interaction (PPI) networks
[2]
least absolute shrinkage and selection operator (LASSO) regression
[3]
random forest
[4]
support vector machine (SVM) regression
[5]
gradient boosting machine (GBM)
[6]
neural network algorithm (NNET)
[7]
eXtreme gradient boosting (XGBoost)
[8]
risk signature model
[9]
10-fold cross-validation
[10]
area under the ROC curve (AUC)
[11]
immune infiltration analysis
[12]
Wilcoxon rank-sum test
[13]
One-way analysis of variance (ANOVA)
decisive
false
agreement_basis object · 2 fields
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decisive_fields
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work_type
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number_stated
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parent_value
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true
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null
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null
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null
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target_materials
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null
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null
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passed
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The independent readings are incomplete or disagree; the source evidence must resolve the difference.
evidence object · 1 field
provider_errors array · 0 items
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source_resolution
status
pending
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null
evidence
null
[3] object · 4 fields
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protocol_reconstruction
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pending
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null
evidence
null
[4] object · 4 fields
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control_execution
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pending
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null
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null
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pending
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null
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null
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null
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null
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[0]
review.human_critique
[1]
review.machine_critique.passed
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null
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sep_package
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activity:conversion:pmid:40823088
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minimax
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agent:minimax_alt
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minimax_alt
[2] object · 3 fields
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agent:corpus-assay-engine
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abstract
[1]
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[5]
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[7]
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step:obtain_source_data blocked on data:not_downloaded
[10]
step:run_analysis blocked on no owned computational capability is bound to this experiment
[11]
step:run_analysis input 'materials:the source data behind the published result in pmid:40823088' does not resolve to a declared asset
[12]
targets
Complete file
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"model": "MiniMax-M3", "prompt_version": "full-text-reading-v1", "prompt_hash": "2642e8604acfcc029ec68cbbd56420a7c3be7b5eccf622d1f1e06414ac4b5a0f", "source_hash": "474987771cf5cc5ba459c32e4e4808a29928490b534d2768d058e75c700b6022", "raw_response_sha256": "sha256:c9b9932231e5fc73d9b6f524217927a4077a7a2502c76c029a78ce681575fd04", "raw_response_chars": 54587}], "target_providers": [{"provider": "minimax", "model": "MiniMax-M3.1-Flash", "prompt_version": "replication-target-v2", "prompt_hash": "68a127905ae5a2573a9dba60239d08e90f4a25eb378b21d93a9d1596447cec07", "source_hash": "474987771cf5cc5ba459c32e4e4808a29928490b534d2768d058e75c700b6022", "raw_response": "{\"parent_value\":0.844,\"unit\":\"AUC\",\"evidence\":\"The risk signature model demonstrated strong predictive accuracy for a 5-year overall survival (AUC = 0.844).\",\"target_result\":\"5-year overall survival AUC = 0.844\",\"number_stated\":true}", "reading": {"parent_value": 0.844, "unit": "AUC", "evidence": "The risk signature model demonstrated strong predictive accuracy for a 5-year overall survival (AUC = 0.844).", "target_result": "5-year overall survival AUC = 0.844", "number_stated": true, "source_locator": "chars 1856-1965 of source sha256 474987771cf5cc5ba459c32e4e4808a29928490b534d2768d058e75c700b6022"}, "recorded_at": "2026-10-31T15:31:42.379880+00:00"}, {"provider": "minimax_alt", "model": "MiniMax-M3", "prompt_version": "replication-target-v2", "prompt_hash": "2c12fdbcf37a9f305ff5e636726f6d79ae0d4f4461dd9c81c2b86d1992cd611d", "source_hash": "474987771cf5cc5ba459c32e4e4808a29928490b534d2768d058e75c700b6022", "raw_response": "<think>We need answer JSON only. Need identify headline numerical result paper states for main finding registered target. Likely AUC=0.844, unit maybe AUC? Need exact contiguous quote containing number. \"The risk signature model demonstrated strong predictive accuracy for a 5-year overall survival (AUC = 0.844).\" Headline number perhaps 0.844. Unit must paper prints. AUC is dimensionless, perhaps unit \"AUC\". They ask parent_value number. Unit printed perhaps \"AUC\" or empty? Need infer expected extraction. The main headline numerical result likely AUC 0.844. Unit must be unit paper prints. Since AUC is not really unit, but printed metric. Could set unit \"AUC\". Evidence exact contiguous quote whole clause. target_result describe. Ensure exact. JSON.</think>\n\n{\"parent_value\":0.844,\"unit\":\"AUC\",\"evidence\":\"The risk signature model demonstrated strong predictive accuracy for a 5-year overall survival (AUC = 0.844).\",\"target_result\":\"The risk signature model predicted 5-year overall survival with an AUC of 0.844.\",\"number_stated\":true}", "reading": {"parent_value": 0.844, "unit": "AUC", "evidence": "The risk signature model demonstrated strong predictive accuracy for a 5-year overall survival (AUC = 0.844).", "target_result": "The risk signature model predicted 5-year overall survival with an AUC of 0.844.", "number_stated": true, "source_locator": "chars 1856-1965 of source sha256 474987771cf5cc5ba459c32e4e4808a29928490b534d2768d058e75c700b6022"}, "recorded_at": "2026-10-31T15:31:41.829275+00:00"}], "agreement": true, "disagreements": {"analysis_methods": {"minimax": ["Differential gene expression analysis", "Protein–protein interaction (PPI) network analysis", "Least absolute shrinkage and selection operator (LASSO) regression", "Random forest", "Support vector machine (SVM)", "Gradient boosting machine (GBM)", "Neural network (NNET)", "Extreme gradient boosting (XGBoost)", "Risk signature model", "Area under the receiver operating characteristic (ROC) curve (AUC)"], "minimax_alt": ["Differential gene expression analysis", "Protein–protein interaction (PPI) networks", "least absolute shrinkage and selection operator (LASSO) regression", "random forest", "support vector machine (SVM) regression", "gradient boosting machine (GBM)", "neural network algorithm (NNET)", "eXtreme gradient boosting (XGBoost)", "risk signature model", "10-fold cross-validation", "area under the ROC curve (AUC)", "immune infiltration analysis", "Wilcoxon rank-sum test", "One-way analysis of variance (ANOVA)"], "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:c4f6dbfe61fbfbf70912f0ed9402bae49056633a4853ab391606bb938017a8da", "type": "sep_package", "label": "SEP v1 package for pmid:40823088"}], "activities": [{"id": "activity:conversion:pmid:40823088", "type": "conversion", "used": ["package:c4f6dbfe61fbfbf70912f0ed9402bae49056633a4853ab391606bb938017a8da"], "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": "2e95f883-84b5-4c73-9e6e-99412f9f5acb", "parent_hash": "c4f6dbfe61fbfbf70912f0ed9402bae49056633a4853ab391606bb938017a8da", "fork_of": null, "generation": 1}, "gaps": ["abstract", "asset:source:pmid:40823088 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: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:40823088' does not resolve to a declared asset", "targets"]}