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pmid:40673074

Identification of prognostic-related tumor microenvironment genes in lung adenocarcinoma and establishment of a prognostic prediction model.

Translational lung cancer research · 2025 doi:10.21037/tlcr-24-297

Paper

partial

Experiment

partial

Data

partial

Analysis

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Execution

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Record details sci_version · id · kind · revision · content_hash · schema · created_at · updated_at · generator
sci_version
1.0
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pmid:40673074
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science-record
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2
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sha256:ffa34918fb82366b85ad0fed9548195ac64679adc0d4d5d0ad44bcb0067caee6
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https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json
created_at
2026-11-01T10:25:51Z
updated_at
2026-11-01T14:01:44Z
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corpus-assay-engine
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sep_to_sci_v1
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paper object · 10 fields
state
partial
title
Identification of prognostic-related tumor microenvironment genes in lung adenocarcinoma and establishment of a prognostic prediction model.
doi
10.21037/tlcr-24-297
pmid
40673074
authors
null
journal
Translational lung cancer research
year
2025
abstract
null
claims array · 1 item
[0] object · 6 fields
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claim-1
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the headline numerical result the paper states for its main finding
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qualitative
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blocked
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null
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null
tolerance
null
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null
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[0]
abstract
[1]
authors
experiment object · 8 fields
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partial
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the headline numerical result the paper states for its main finding
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[0] object · 13 fields
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read_published_estimate
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Read the published estimate and its interval from the source
kind
other
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complete
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null
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The number a replication must land on, and the sentence it came from.
duration_hours
null
parameters object · 0 fields
inputs array · 1 item
[0]
source:pmid:40673074
outputs array · 1 item
[0]
the published estimate, its unit and its interval
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[1] object · 13 fields
id
obtain_source_data
order
2
name
Obtain the source data behind the published result
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data-preparation
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blocked
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The published result cannot be recomputed without the data the paper analysed.
duration_hours
null
parameters object · 0 fields
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the source data with its provenance
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order
3
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Run the analysis programme
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analysis
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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:40673074
duration_hours
null
parameters object · 0 fields
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the registered result
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step:obtain_source_data blocked on data:not_downloaded
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step:run_analysis input 'materials:the source data behind the published result in pmid:40673074' does not resolve to a declared asset
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partial
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xml
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https://doi.org/10.21037/tlcr-24-297
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10.21037/tlcr-24-297
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Source read by the package builder: full_text.
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Statistical comparison of the clinical information of ITME gene groups with different expression levels
structure object · 5 fields
pmcid
PMC12261383
section_index
16
section_title
The correlation between the ITME genes and the clinical characteristics
row_count
33
column_count
20
table object · 8 fields
label
Table 1
caption
Statistical comparison of the clinical information of ITME gene groups with different expression levels
rows array · 33 items
[0] array · 10 items
[0]
Characteristics total cases
[1]
ABCC2 expression
[2]
[3]
ECT2L expression
[4]
[5]
CD200R1 expression
[6]
[7]
ACSM5 expression
[8]
[9]
CLEC17A expression
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[0]
Low (N=250)
[1]
High (N=251)
[2]
P value
[3]
Low (N=250)
[4]
High (N=251)
[5]
P value
[6]
Low (N=250)
[7]
High (N=251)
[8]
P value
[9]
Low (N=250)
[10]
High (N=251)
[11]
P value
[12]
Low (N=250)
[13]
High (N=251)
[14]
P value
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[0]
Age (years)
[1]
[2]
[3]
0.44
[4]
[5]
[6]
[7]
0.85
[8]
[9]
[10]
[11]
0.44
[12]
[13]
[14]
[15]
0.02
[16]
[17]
[18]
[19]
0.50
[3] array · 20 items
[0]
≤60
[1]
82
[2]
75
[3]
[4]
[5]
80
[6]
77
[7]
[8]
[9]
83
[10]
74
[11]
[12]
[13]
91
[14]
66
[15]
[16]
[17]
82
[18]
75
[19]
[4] array · 12 items
[0]
>60
[1]
161
[2]
173
[3]
[4]
166
[5]
168
[6]
164
[7]
170
[8]
153
[9]
181
[10]
162
[11]
172
[5] array · 20 items
[0]
Gender
[1]
[2]
[3]
0.11
[4]
[5]
[6]
[7]
0.046
[8]
[9]
[10]
[11]
0.002
[12]
[13]
[14]
[15]
0.24
[16]
[17]
[18]
[19]
0.003
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[0]
Male
[1]
106
[2]
125
[3]
[4]
[5]
126
[6]
105
[7]
[8]
[9]
133
[10]
98
[11]
[12]
[13]
122
[14]
109
[15]
[16]
[17]
132
[18]
99
[19]
[7] array · 12 items
[0]
Female
[1]
144
[2]
126
[3]
[4]
124
[5]
146
[6]
117
[7]
153
[8]
128
[9]
142
[10]
118
[11]
152
[8] array · 20 items
[0]
Pathologic M
[1]
[2]
[3]
0.14
[4]
[5]
[6]
[7]
>0.99
[8]
[9]
[10]
[11]
0.09
[12]
[13]
[14]
[15]
0.53
[16]
[17]
[18]
[19]
0.21
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[0]
M0
[1]
168
[2]
165
[3]
[4]
[5]
169
[6]
164
[7]
[8]
[9]
171
[10]
162
[11]
[12]
[13]
171
[14]
162
[15]
[16]
[17]
177
[18]
156
[19]
[10] array · 12 items
[0]
M1
[1]
8
[2]
16
[3]
[4]
12
[5]
12
[6]
17
[7]
7
[8]
14
[9]
10
[10]
16
[11]
8
[11] array · 20 items
[0]
Pathologic N
[1]
[2]
[3]
0.44
[4]
[5]
[6]
[7]
0.17
[8]
[9]
[10]
[11]
0.003
[12]
[13]
[14]
[15]
0.02
[16]
[17]
[18]
[19]
0.08
[12] array · 20 items
[0]
N0
[1]
164
[2]
160
[3]
[4]
[5]
155
[6]
169
[7]
[8]
[9]
147
[10]
177
[11]
[12]
[13]
152
[14]
172
[15]
[16]
[17]
150
[18]
174
[19]
[13] array · 12 items
[0]
N1
[1]
45
[2]
49
[3]
[4]
46
[5]
48
[6]
52
[7]
42
[8]
49
[9]
45
[10]
54
[11]
40
[14] array · 12 items
[0]
N2
[1]
39
[2]
31
[3]
[4]
43
[5]
27
[6]
46
[7]
24
[8]
45
[9]
25
[10]
41
[11]
29
[15] array · 12 items
[0]
N3
[1]
0
[2]
2
[3]
[4]
1
[5]
1
[6]
0
[7]
2
[8]
2
[9]
0
[10]
1
[11]
1
[16] array · 20 items
[0]
Pathologic T
[1]
[2]
[3]
0.45
[4]
[5]
[6]
[7]
0.009
[8]
[9]
[10]
[11]
<0.001
[12]
[13]
[14]
[15]
<0.001
[16]
[17]
[18]
[19]
<0.001
[17] array · 20 items
[0]
T1
[1]
77
[2]
90
[3]
[4]
[5]
66
[6]
101
[7]
[8]
[9]
60
[10]
107
[11]
[12]
[13]
64
[14]
103
[15]
[16]
[17]
60
[18]
107
[19]
[18] array · 12 items
[0]
T2
[1]
140
[2]
127
[3]
[4]
144
[5]
123
[6]
146
[7]
121
[8]
142
[9]
125
[10]
142
[11]
125
[19] array · 12 items
[0]
T3
[1]
25
[2]
20
[3]
[4]
26
[5]
19
[6]
30
[7]
15
[8]
28
[9]
17
[10]
33
[11]
12
[20] array · 12 items
[0]
T4
[1]
8
[2]
11
[3]
[4]
12
[5]
7
[6]
12
[7]
7
[8]
15
[9]
4
[10]
12
[11]
7
[21] array · 19 items
[0]
Pathologic stage
[1]
[2]
0.19
[3]
[4]
[5]
[6]
0.13
[7]
[8]
[9]
[10]
<0.001
[11]
[12]
[13]
[14]
<0.001
[15]
[16]
[17]
[18]
0.001
[22] array · 20 items
[0]
1
[1]
141
[2]
127
[3]
[4]
[5]
123
[6]
145
[7]
[8]
[9]
110
[10]
158
[11]
[12]
[13]
114
[14]
154
[15]
[16]
[17]
112
[18]
156
[19]
[23] array · 12 items
[0]
2
[1]
55
[2]
64
[3]
[4]
62
[5]
57
[6]
67
[7]
52
[8]
65
[9]
54
[10]
67
[11]
52
[24] array · 12 items
[0]
3
[1]
42
[2]
39
[3]
[4]
49
[5]
32
[6]
52
[7]
29
[8]
53
[9]
28
[10]
49
[11]
32
[25] array · 12 items
[0]
4
[1]
8
[2]
17
[3]
[4]
13
[5]
12
[6]
17
[7]
8
[8]
14
[9]
11
[10]
17
[11]
8
[26] array · 19 items
[0]
Smoking history
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[2]
0.87
[3]
[4]
[5]
[6]
0.90
[7]
[8]
[9]
[10]
0.66
[11]
[12]
[13]
[14]
0.09
[15]
[16]
[17]
[18]
0.40
[27] array · 20 items
[0]
Never
[1]
18
[2]
10
[3]
[4]
[5]
13
[6]
15
[7]
[8]
[9]
15
[10]
13
[11]
[12]
[13]
12
[14]
16
[15]
[16]
[17]
15
[18]
13
[19]
[28] array · 12 items
[0]
Reform
[1]
74
[2]
53
[3]
[4]
61
[5]
66
[6]
58
[7]
69
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67
[9]
60
[10]
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[11]
69
[29] array · 12 items
[0]
Current
[1]
27
[2]
19
[3]
[4]
24
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22
[6]
24
[7]
22
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31
[9]
15
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26
[11]
20
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Radiation therapy
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0.68
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Yes
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28
[2]
32
[3]
[4]
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30
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30
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32
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[12]
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31
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29
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[16]
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[19]
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No
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195
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193
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190
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198
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199
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section[16]/table-wrap[1]#t1
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[0]
asset:source:pmid:40673074 not verified
analysis object · 4 fields
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targets
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read_published_estimate
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xml
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corpus_record_absent
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minimax
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{"parent_value":0.70,"unit":"AUC","evidence":"Further, a prognostic RS prediction model was constructed based on these 5 genes, and the results showed that patients with low RS had significantly higher overall survival (OS; P<0.001), relapse-free survival (RFS; P=0.009) and disease-free survival (DFS; P=0.005) than the high RS group, and it had a certain predictive accuracy [area under the curve (AUC)] of 5 years OS =0.70).","target_result":"5-year overall survival AUC = 0.70","number_stated":true}
reading object · 6 fields
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evidence
Further, a prognostic RS prediction model was constructed based on these 5 genes, and the results showed that patients with low RS had significantly higher overall survival (OS; P<0.001), relapse-free survival (RFS; P=0.009) and disease-free survival (DFS; P=0.005) than the high RS group, and it had a certain predictive accuracy [area under the curve (AUC)] of 5 years OS =0.70).
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5-year overall survival AUC = 0.70
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true
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chars 1489-1870 of source sha256 a88866479f3678f10f49eed336479aa7d594fc86ea61978853695f7919edd081
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2026-10-31T15:21:21.740318+00:00
[1] object · 8 fields
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raw_response
<think>We need answer JSON only. Need determine single numerical result replication registered target headline numerical result paper states for main finding. Source has various numbers. Registered target broad "headline numerical result the paper states for its main finding". Likely 5 crucial TME genes? They ask headline number only, unit paper prints. Evidence exact contiguous quote containing number, attribution whole clause. Need infer desired parent_value likely 5, unit "genes", evidence "We identified 5 crucial TME genes: ABCC2, ECT2L, CD200R1, ACSM5, and CLEC17A." target_result likely "5 crucial TME genes" perhaps string. The headline numerical result main finding could alternatively AUC 0.70 for 5-year OS. But wording "headline numerical result the paper states for its main finding" and source abstract says identified 5 crucial TME genes, model AUC 0.70. Which is registered target? The target is "the headline numerical result the paper states for its main finding". Could be 5. The singular numerical result replication of registered target has to reproduce. Main finding explicitly "We identified 5 crucial TME genes..." This is headline. Unit genes. Need exact evidence quote. JSON: {"parent_value":5,"unit":"genes","evidence":"We identified 5 crucial TME genes: ABCC2, ECT2L, CD200R1, ACSM5, and CLEC17A.","target_result":"5 crucial TME genes","number_stated":true} Check unit must unit paper prints. It prints "5 crucial TME genes", "5 genes"; unit "genes" reasonable. Could unit be "TME genes"? The instruction unit must be unit paper prints. Usually unit extraction expects e.g. genes. Exact phrase says 5 crucial TME genes. Use "TME genes" perhaps unit is genes. Headline number only maybe "5" and unit "TME genes". Need think deeply. The source title/abstract main finding: "We identified 5 crucial TME genes..." and conclusions. Asked "single numerical result that a replication of registered target has to reproduce." Likely benchmark has registered targets from paper and asks find numeric result. Could target be headline numerical result, perhaps "5 crucial TME genes". Need not include list? Evidence can full sentence. target_result likely textual. They want headline number only in parent_value. I'd answer.</think> {"parent_value":5,"unit":"TME genes","evidence":"We identified 5 crucial TME genes: ABCC2, ECT2L, CD200R1, ACSM5, and CLEC17A.","target_result":"5 crucial TME genes","number_stated":true}
reading object · 6 fields
parent_value
5
unit
TME genes
evidence
We identified 5 crucial TME genes: ABCC2, ECT2L, CD200R1, ACSM5, and CLEC17A.
target_result
5 crucial TME genes
number_stated
true
source_locator
chars 1158-1235 of source sha256 a88866479f3678f10f49eed336479aa7d594fc86ea61978853695f7919edd081
recorded_at
2026-10-31T15:21:24.004050+00:00
agreement
false
disagreements object · 5 fields
target_result object · 3 fields
minimax
Patients with low RS had significantly higher overall survival (OS; P<0.001), relapse-free survival (RFS; P=0.009), and disease-free survival (DFS; P=0.005) than the high-RS group, with a 5-year OS AUC of 0.70; these findings were consistent in the GSE50081 cohort.
minimax_alt
The prognostic risk score model achieved a 5-year overall survival (OS) area under the curve (AUC) of 0.70.
decisive
false
analysis_methods object · 3 fields
minimax array · 8 items
[0]
ESTIMATE algorithm
[1]
limma package for screening TME-DEGs
[2]
Cor package for correlation analysis
[3]
multivariate Cox regression
[4]
LASSO Cox regression
[5]
ROC curve analysis and AUC calculation
[6]
T-test
[7]
Fisher's test
minimax_alt array · 10 items
[0]
ESTIMATE algorithm for stromal and immune-cell estimation
[1]
Tumor Immune Estimation Resource (TIMER) for immune-cell infiltration associations
[2]
limma package for screening TME-DEGs
[3]
Cor package for correlation analysis
[4]
multivariate Cox regression
[5]
least absolute shrinkage and selection operator (LASSO) regression
[6]
LASSO Cox regression analysis using the Survival and lars packages
[7]
receiver operating characteristic (ROC) curve analysis and area under the curve (AUC) calculation
[8]
T-test
[9]
Fisher’s test
decisive
false
statistical_method object · 3 fields
minimax
LASSO Cox regression analysis
minimax_alt
Receiver operating characteristic (ROC) curve analysis with area under the curve (AUC) calculation using the ‘ROC package’.
decisive
true
parent_value object · 3 fields
minimax
0.7
minimax_alt
5
decisive
true
unit object · 3 fields
minimax
AUC
minimax_alt
TME genes
decisive
true
agreement_basis object · 2 fields
policy
decisive_fields
decisive_fields array · 4 items
[0]
work_type
[1]
number_stated
[2]
parent_value
[3]
unit
blinded
true
human_critique object · 5 fields
status
not_run
reviewer
null
signed_at
null
conflict_checked
false
commentary
null
stages array · 7 items
[0] object · 4 fields
key
target_materials
status
pending
reason
null
evidence
null
[1] object · 4 fields
key
independent_readings
status
blocked
reason
The independent readings are incomplete or disagree; the source evidence must resolve the difference.
evidence object · 1 field
provider_errors array · 0 items
[2] object · 4 fields
key
source_resolution
status
pending
reason
null
evidence
null
[3] object · 4 fields
key
protocol_reconstruction
status
pending
reason
null
evidence
null
[4] object · 4 fields
key
control_execution
status
pending
reason
null
evidence
null
[5] object · 4 fields
key
control_comparison
status
pending
reason
null
evidence
null
[6] object · 4 fields
key
publication
status
pending
reason
null
evidence
null
gaps array · 2 items
[0]
review.human_critique
[1]
review.machine_critique.blocked
execution object · 5 fields
state
absent
status
not_run
mode
null
runs array · 0 items
gaps array · 1 item
[0]
execution.not_run
provenance object · 7 fields
entities array · 1 item
[0] object · 3 fields
id
package:cef0b99bc2e31543f607dee8632b2cdc063198600492599aad5f13160164c586
type
sep_package
label
SEP v1 package for pmid:40673074
activities array · 1 item
[0] object · 4 fields
id
activity:conversion:pmid:40673074
type
conversion
used array · 1 item
[0]
package:cef0b99bc2e31543f607dee8632b2cdc063198600492599aad5f13160164c586
agent
agent:corpus-assay-engine
agents array · 3 items
[0] object · 3 fields
id
agent:minimax
type
model
label
minimax
[1] object · 3 fields
id
agent:minimax_alt
type
model
label
minimax_alt
[2] object · 3 fields
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 object · 4 fields
parent_id
pmid:40673074
parent_hash
sha256:44145972ec0ce71841c72feb9bdbea7e4709842d49c406bca645050258402338
fork_of
null
generation
2
gaps array · 13 items
[0]
abstract
[1]
asset:source:pmid:40673074 not verified
[2]
authors
[3]
capability
[4]
corpus_record_absent
[5]
execution.not_run
[6]
method
[7]
review.human_critique
[8]
review.machine_critique.blocked
[9]
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:40673074' does not resolve to a declared asset
[12]
targets
Complete file 
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null}, "evidence": []}], "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:40673074"], "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:40673074", "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:40673074' does not resolve to a declared asset"]}, "data": {"state": "partial", "assets": [{"id": "source:pmid:40673074", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.21037/tlcr-24-297", "sha256": "sha256:a88866479f3678f10f49eed336479aa7d594fc86ea61978853695f7919edd081", "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.21037/tlcr-24-297", "version": null, "note": "Source read by the package builder: full_text.", "structure": {"access_state": "full_text"}}, {"id": "asset:table:pmid:40673074:1", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:0a1a66964e6de279250911d62879edb809ffb36a7c3c57bff29a08f6e41e0b59", "bytes": 3011, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[16]/table-wrap[1]#t1", "version": null, "note": "Statistical comparison of the clinical information of ITME gene groups with different expression levels", "structure": {"pmcid": "PMC12261383", "section_index": 16, "section_title": "The correlation between the ITME genes and the clinical characteristics", "row_count": 33, "column_count": 20}, "table": {"label": "Table 1", "caption": "Statistical comparison of the clinical information of ITME gene groups with different expression levels", "rows": [["Characteristics total cases", "ABCC2 expression", "", "ECT2L expression", "", "CD200R1 expression", "", "ACSM5 expression", "", "CLEC17A expression"], ["Low (N=250)", "High (N=251)", "P value", "Low (N=250)", "High (N=251)", "P value", "Low (N=250)", "High (N=251)", "P value", "Low (N=250)", "High (N=251)", "P value", "Low (N=250)", "High (N=251)", "P value"], ["Age (years)", "", "", "0.44", "", "", "", "0.85", "", "", "", "0.44", "", "", "", "0.02", "", "", "", "0.50"], ["≤60", "82", "75", "", "", "80", "77", "", "", "83", "74", "", "", "91", "66", "", "", "82", "75", ""], [">60", "161", "173", "", "166", "168", "164", "170", "153", "181", "162", "172"], ["Gender", "", "", "0.11", "", "", "", "0.046", "", "", "", "0.002", "", "", "", "0.24", "", "", "", "0.003"], ["Male", "106", "125", "", "", "126", "105", "", "", "133", "98", "", "", "122", "109", "", "", "132", "99", ""], ["Female", "144", "126", "", "124", "146", "117", "153", "128", "142", "118", "152"], ["Pathologic M", "", "", "0.14", "", "", "", ">0.99", "", "", "", "0.09", "", "", "", "0.53", "", "", "", "0.21"], ["M0", "168", "165", "", "", "169", "164", "", "", "171", "162", "", "", "171", "162", "", "", "177", "156", ""], ["M1", "8", "16", "", "12", "12", "17", "7", "14", "10", "16", "8"], ["Pathologic N", "", "", "0.44", "", "", "", "0.17", "", "", "", "0.003", "", "", "", "0.02", "", "", "", "0.08"], ["N0", "164", "160", "", "", "155", "169", "", "", "147", "177", "", "", "152", "172", "", "", "150", "174", ""], ["N1", "45", "49", "", "46", "48", "52", "42", "49", "45", "54", "40"], ["N2", "39", "31", "", "43", "27", "46", "24", "45", "25", "41", "29"], ["N3", "0", "2", "", "1", "1", "0", "2", "2", "0", "1", "1"], ["Pathologic T", "", "", "0.45", "", "", "", "0.009", "", "", "", "<0.001", "", "", "", "<0.001", "", "", "", "<0.001"], ["T1", "77", "90", "", "", "66", "101", "", "", "60", "107", "", "", "64", "103", "", "", "60", "107", ""], ["T2", "140", "127", "", "144", "123", "146", "121", "142", "125", "142", "125"], ["T3", "25", "20", "", "26", "19", "30", "15", "28", "17", "33", "12"], ["T4", "8", "11", "", "12", "7", "12", "7", "15", "4", "12", "7"], ["Pathologic stage", "", "0.19", "", "", "", "0.13", "", "", "", "<0.001", "", "", "", "<0.001", "", "", "", "0.001"], ["1", "141", "127", "", "", "123", "145", "", "", "110", "158", "", "", "114", "154", "", "", "112", "156", ""], ["2", "55", "64", "", "62", "57", "67", "52", "65", "54", "67", "52"], ["3", "42", "39", "", "49", "32", "52", "29", "53", "28", "49", "32"], ["4", "8", "17", "", "13", "12", "17", "8", "14", "11", "17", "8"], ["Smoking history", "", "0.87", "", "", "", "0.90", "", "", "", "0.66", "", "", "", "0.09", "", "", "", "0.40"], ["Never", "18", "10", "", "", "13", "15", "", "", "15", "13", "", "", "12", "16", "", "", "15", "13", ""], ["Reform", "74", "53", "", "61", "66", "58", "69", "67", "60", "58", "69"], ["Current", "27", "19", "", "24", "22", "24", "22", "31", "15", "26", "20"], ["Radiation therapy", "", "0.68", "", "", "", "0.89", "", "", "", "0.58", "", "", "", "0.89", "", "", "", "0.58"], ["Yes", "28", "32", "", "", "30", "30", "", "", "32", "28", "", "", "31", "29", "", "", "32", "28", ""], ["No", "195", "193", "", "190", "198", "189", "199", "196", "192", "190", "198"]], "row_count": 33, "column_count": 20, "numeric_cells": 288, "header_rows": 2, "locator": "section[16]/table-wrap[1]#t1"}}], "gaps": ["asset:source:pmid:40673074 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:40673074", "asset:table:pmid:40673074:1"], "steps": ["read_published_estimate"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": ["xml"], "capabilities": [], "data_gaps": ["source:pmid:40673074"]}, "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": "209bdd375a4e9ca8c4963ef302b7bb2b0b1c48d13b13605b45000f96fae7ab72", "source_hash": "a88866479f3678f10f49eed336479aa7d594fc86ea61978853695f7919edd081", "raw_response_sha256": "sha256:eb0e296143dd472d7016b3a8f4b56cd0ca25c84f3f3a2c0a9a35cb9873a70afc", "raw_response_chars": 4815}, {"provider": "minimax_alt", "model": "MiniMax-M3", "prompt_version": "full-text-reading-v1", "prompt_hash": "da7127b20cff8d5312ca393c25bea09bd2f9a9c1237e0f5afdb25be6f9347232", "source_hash": "a88866479f3678f10f49eed336479aa7d594fc86ea61978853695f7919edd081", "raw_response_sha256": "sha256:206d555c12434d8c6aff87bcd2a194be30e52f75b88e94c3e61349009b5898b0", "raw_response_chars": 60542}], "target_providers": [{"provider": "minimax", "model": "MiniMax-M3.1-Flash", "prompt_version": "replication-target-v2", "prompt_hash": "38064a1533894c43f5580c49d7884eb9ca901569b67478463176f8f947d93fda", "source_hash": "a88866479f3678f10f49eed336479aa7d594fc86ea61978853695f7919edd081", "raw_response": "{\"parent_value\":0.70,\"unit\":\"AUC\",\"evidence\":\"Further, a prognostic RS prediction model was constructed based on these 5 genes, and the results showed that patients with low RS had significantly higher overall survival (OS; P<0.001), relapse-free survival (RFS; P=0.009) and disease-free survival (DFS; P=0.005) than the high RS group, and it had a certain predictive accuracy [area under the curve (AUC)] of 5 years OS =0.70).\",\"target_result\":\"5-year overall survival AUC = 0.70\",\"number_stated\":true}", "reading": {"parent_value": 0.7, "unit": "AUC", "evidence": "Further, a prognostic RS prediction model was constructed based on these 5 genes, and the results showed that patients with low RS had significantly higher overall survival (OS; P<0.001), relapse-free survival (RFS; P=0.009) and disease-free survival (DFS; P=0.005) than the high RS group, and it had a certain predictive accuracy [area under the curve (AUC)] of 5 years OS =0.70).", "target_result": "5-year overall survival AUC = 0.70", "number_stated": true, "source_locator": "chars 1489-1870 of source sha256 a88866479f3678f10f49eed336479aa7d594fc86ea61978853695f7919edd081"}, "recorded_at": "2026-10-31T15:21:21.740318+00:00"}, {"provider": "minimax_alt", "model": "MiniMax-M3", "prompt_version": "replication-target-v2", "prompt_hash": "ebc32c32beb26f4f10969547480f5dcceea38d699792ceb4c8558a93a33e90f7", "source_hash": "a88866479f3678f10f49eed336479aa7d594fc86ea61978853695f7919edd081", "raw_response": "<think>We need answer JSON only. Need determine single numerical result replication registered target headline numerical result paper states for main finding. Source has various numbers. Registered target broad \"headline numerical result the paper states for its main finding\". Likely 5 crucial TME genes? They ask headline number only, unit paper prints. Evidence exact contiguous quote containing number, attribution whole clause. Need infer desired parent_value likely 5, unit \"genes\", evidence \"We identified 5 crucial TME genes: ABCC2, ECT2L, CD200R1, ACSM5, and CLEC17A.\" target_result likely \"5 crucial TME genes\" perhaps string. The headline numerical result main finding could alternatively AUC 0.70 for 5-year OS. But wording \"headline numerical result the paper states for its main finding\" and source abstract says identified 5 crucial TME genes, model AUC 0.70. Which is registered target? The target is \"the headline numerical result the paper states for its main finding\". Could be 5. The singular numerical result replication of registered target has to reproduce. Main finding explicitly \"We identified 5 crucial TME genes...\" This is headline. Unit genes. Need exact evidence quote. JSON:\n{\"parent_value\":5,\"unit\":\"genes\",\"evidence\":\"We identified 5 crucial TME genes: ABCC2, ECT2L, CD200R1, ACSM5, and CLEC17A.\",\"target_result\":\"5 crucial TME genes\",\"number_stated\":true}\nCheck unit must unit paper prints. It prints \"5 crucial TME genes\", \"5 genes\"; unit \"genes\" reasonable. Could unit be \"TME genes\"? The instruction unit must be unit paper prints. Usually unit extraction expects e.g. genes. Exact phrase says 5 crucial TME genes. Use \"TME genes\" perhaps unit is genes. Headline number only maybe \"5\" and unit \"TME genes\". Need think deeply.\n\nThe source title/abstract main finding: \"We identified 5 crucial TME genes...\" and conclusions. Asked \"single numerical result that a replication of registered target has to reproduce.\" Likely benchmark has registered targets from paper and asks find numeric result. Could target be headline numerical result, perhaps \"5 crucial TME genes\". Need not include list? Evidence can full sentence. target_result likely textual. They want headline number only in parent_value. I'd answer.</think>\n\n{\"parent_value\":5,\"unit\":\"TME genes\",\"evidence\":\"We identified 5 crucial TME genes: ABCC2, ECT2L, CD200R1, ACSM5, and CLEC17A.\",\"target_result\":\"5 crucial TME genes\",\"number_stated\":true}", "reading": {"parent_value": 5, "unit": "TME genes", "evidence": "We identified 5 crucial TME genes: ABCC2, ECT2L, CD200R1, ACSM5, and CLEC17A.", "target_result": "5 crucial TME genes", "number_stated": true, "source_locator": "chars 1158-1235 of source sha256 a88866479f3678f10f49eed336479aa7d594fc86ea61978853695f7919edd081"}, "recorded_at": "2026-10-31T15:21:24.004050+00:00"}], "agreement": false, "disagreements": {"target_result": {"minimax": "Patients with low RS had significantly higher overall survival (OS; P<0.001), relapse-free survival (RFS; P=0.009), and disease-free survival (DFS; P=0.005) than the high-RS group, with a 5-year OS AUC of 0.70; these findings were consistent in the GSE50081 cohort.", "minimax_alt": "The prognostic risk score model achieved a 5-year overall survival (OS) area under the curve (AUC) of 0.70.", "decisive": false}, "analysis_methods": {"minimax": ["ESTIMATE algorithm", "limma package for screening TME-DEGs", "Cor package for correlation analysis", "multivariate Cox regression", "LASSO Cox regression", "ROC curve analysis and AUC calculation", "T-test", "Fisher's test"], "minimax_alt": ["ESTIMATE algorithm for stromal and immune-cell estimation", "Tumor Immune Estimation Resource (TIMER) for immune-cell infiltration associations", "limma package for screening TME-DEGs", "Cor package for correlation analysis", "multivariate Cox regression", "least absolute shrinkage and selection operator (LASSO) regression", "LASSO Cox regression analysis using the Survival and lars packages", "receiver operating characteristic (ROC) curve analysis and area under the curve (AUC) calculation", "T-test", "Fisher’s test"], "decisive": false}, "statistical_method": {"minimax": "LASSO Cox regression analysis", "minimax_alt": "Receiver operating characteristic (ROC) curve analysis with area under the curve (AUC) calculation using the ‘ROC package’.", "decisive": true}, "parent_value": {"minimax": 0.7, "minimax_alt": 5, "decisive": true}, "unit": {"minimax": "AUC", "minimax_alt": "TME genes", "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:cef0b99bc2e31543f607dee8632b2cdc063198600492599aad5f13160164c586", "type": "sep_package", "label": "SEP v1 package for pmid:40673074"}], "activities": [{"id": "activity:conversion:pmid:40673074", "type": "conversion", "used": ["package:cef0b99bc2e31543f607dee8632b2cdc063198600492599aad5f13160164c586"], "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:40673074", "parent_hash": "sha256:44145972ec0ce71841c72feb9bdbea7e4709842d49c406bca645050258402338", "fork_of": null, "generation": 2}, "gaps": ["abstract", "asset:source:pmid:40673074 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:40673074' does not resolve to a declared asset", "targets"]}