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pmid:39910129

Integrative analysis of anoikis-related prognostic signature to evaluate the immune landscape and predict therapeutic response in stomach adenocarcinoma.

Scientific reports · 2025 doi:10.1038/s41598-025-88882-9

Paper

partial

Experiment

partial

Data

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Analysis

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Record details sci_version · id · kind · revision · content_hash · schema · created_at · updated_at · generator
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pmid:39910129
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2026-11-01T10:25:49Z
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title
Integrative analysis of anoikis-related prognostic signature to evaluate the immune landscape and predict therapeutic response in stomach adenocarcinoma.
doi
10.1038/s41598-025-88882-9
pmid
39910129
authors
null
journal
Scientific reports
year
2025
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null
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The anoikis risk score (ARS) incorporated 7 genes and stratified patients into highand low-risk subgroups by median value splitting.
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abstract
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the headline numerical result the paper states for its main finding
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the published estimate, its unit and its interval
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Baseline of clinical characteristics between low- and high-risk subgroups.
structure object · 5 fields
pmcid
PMC11799156
section_index
27
section_title
Validation of the prognostic risk signature via GEO datasets
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44
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Table 1
caption
Baseline of clinical characteristics between low- and high-risk subgroups.
rows array · 44 items
[0] array · 6 items
[0]
Characteristic
[1]
Levels
[2]
Low-risk
[3]
High-risk
[4]
p
[5]
Method
[1] array · 6 items
[0]
n
[1]
[2]
188
[3]
188
[4]
[5]
[2] array · 6 items
[0]
Status, n (%)
[1]
Alive
[2]
123 (65.4%)
[3]
97 (51.6%)
[4]
0.007
[5]
Chi-square
[3] array · 6 items
[0]
[1]
Dead
[2]
65 (34.6%)
[3]
91 (48.4%)
[4]
[5]
[4] array · 6 items
[0]
Age, n (%)
[1]
< 60
[2]
45 (23.9%)
[3]
71 (37.8%)
[4]
0.004
[5]
Chi-square
[5] array · 6 items
[0]
[1]
≥ 60
[2]
143 (76.1%)
[3]
117 (62.2%)
[4]
[5]
[6] array · 6 items
[0]
T Stage, n (%)
[1]
T1
[2]
14 (7.5%)
[3]
3 (1.6%)
[4]
0.075
[5]
Fisher’s test
[7] array · 6 items
[0]
[1]
T2
[2]
41 (21.6%)
[3]
38 (20.3%)
[4]
[5]
[8] array · 6 items
[0]
[1]
T3
[2]
87 (46.3%)
[3]
82 (43.6%)
[4]
[5]
[9] array · 6 items
[0]
[1]
T4
[2]
43 (22.9%)
[3]
64 (34.1%)
[4]
[5]
[10] array · 6 items
[0]
[1]
TX
[2]
3 (1.6%)
[3]
1 (0.5%)
[4]
[5]
[11] array · 6 items
[0]
N Stage, n (%)
[1]
N0
[2]
59 (31.4%)
[3]
54 (28.7%)
[4]
0.177
[5]
Fisher’s test
[12] array · 6 items
[0]
[1]
N1
[2]
49 (26.1%)
[3]
51 (27.1%)
[4]
[5]
[13] array · 6 items
[0]
[1]
N2
[2]
39 (20.7%)
[3]
35 (18.6%)
[4]
[5]
[14] array · 6 items
[0]
[1]
N3
[2]
36 (19.2%)
[3]
42 (22.4%)
[4]
[5]
[15] array · 6 items
[0]
[1]
NX
[2]
5 (2.6%)
[3]
6 (3.2%)
[4]
[5]
[16] array · 6 items
[0]
M Stage, n (%)
[1]
M0
[2]
174 (92.6%)
[3]
165 (87.8%)
[4]
0.289
[5]
Fisher’s test
[17] array · 6 items
[0]
[1]
M1
[2]
8 (4.2%)
[3]
14 (7.4%)
[4]
[5]
[18] array · 6 items
[0]
[1]
MX
[2]
6 (3.2%)
[3]
9 (4.8%)
[4]
[5]
[19] array · 6 items
[0]
Stage, n (%)
[1]
Stage I
[2]
32 (17.0%)
[3]
17 (9.0%)
[4]
0.441
[5]
Fisher’s test
[20] array · 6 items
[0]
[1]
Stage II
[2]
54 (28.7%)
[3]
65 (34.6%)
[4]
[5]
[21] array · 6 items
[0]
[1]
Stage III
[2]
80 (42.5%)
[3]
81 (43.1%)
[4]
[5]
[22] array · 6 items
[0]
[1]
Stage IV
[2]
15 (8.0%)
[3]
18 (9.6%)
[4]
[5]
[23] array · 6 items
[0]
[1]
Unknown
[2]
7 (3.7%)
[3]
7 (3.7%)
[4]
[5]
[24] array · 6 items
[0]
Gender, n (%)
[1]
Female
[2]
63 (33.5%)
[3]
67 (35.6%)
[4]
0.664
[5]
Chi-square
[25] array · 6 items
[0]
[1]
Male
[2]
125 (66.5%)
[3]
121 (64.4%)
[4]
[5]
[26] array · 6 items
[0]
Race, n (%)
[1]
White
[2]
110 (58.5%)
[3]
130 (69.2%)
[4]
0.017
[5]
Fisher’s test
[27] array · 6 items
[0]
[1]
Asian
[2]
42 (22.4%)
[3]
41 (21.8%)
[4]
[5]
[28] array · 6 items
[0]
[1]
Black or African American
[2]
10 (5.3%)
[3]
1 (0.5%)
[4]
[5]
[29] array · 6 items
[0]
[1]
Native Hawaiian or other pacific islander
[2]
1 (0.5%)
[3]
0 (0.0%)
[4]
[5]
[30] array · 6 items
[0]
[1]
Not reported
[2]
25 (13.3%)
[3]
16 (8.5%)
[4]
[5]
[31] array · 6 items
[0]
Grade, n (%)
[1]
G1
[2]
5 (2.7%)
[3]
4 (2.1%)
[4]
0.002
[5]
Fisher’s test
[32] array · 6 items
[0]
[1]
G2
[2]
81 (43.1%)
[3]
47 (25.0%)
[4]
[5]
[33] array · 6 items
[0]
[1]
G3
[2]
98 (52.1%)
[3]
132 (70.2%)
[4]
[5]
[34] array · 6 items
[0]
[1]
GX
[2]
4 (2.1%)
[3]
5 (2.7%)
[4]
[5]
[35] array · 6 items
[0]
Classification, n (%)
[1]
Adenocarcinoma, intestinal type
[2]
40 (21.3%)
[3]
34 (18.1%)
[4]
0.001
[5]
Fisher’s test
[36] array · 6 items
[0]
[1]
Adenocarcinoma, NOS
[2]
56 (29.8%)
[3]
76 (40.4%)
[4]
[5]
[37] array · 6 items
[0]
[1]
Adenocarcinoma with mixed subtypes
[2]
0 (0.0%)
[3]
1 (0.5%)
[4]
[5]
[38] array · 6 items
[0]
[1]
Carcinoma, diffuse type
[2]
25 (13.3%)
[3]
39 (20.7%)
[4]
[5]
[39] array · 6 items
[0]
[1]
Mucinous adenocarcinoma
[2]
7 (3.7%)
[3]
10 (5.3%)
[4]
[5]
[40] array · 6 items
[0]
[1]
Papillary adenocarcinoma, NOS
[2]
6 (3.2%)
[3]
0 (0.0%)
[4]
[5]
[41] array · 6 items
[0]
[1]
Signet ring cell carcinoma
[2]
8 (4.3%)
[3]
5 (2.7%)
[4]
[5]
[42] array · 6 items
[0]
[1]
Tubular adenocarcinoma
[2]
46 (24.5%)
[3]
23 (12.2%)
[4]
[5]
[43] array · 6 items
[0]
Time, median (IQR)
[1]
[2]
495 (282.5, 851.5)
[3]
420 (272.25, 688.5)
[4]
< 0.001
[5]
Wilcoxon test
row_count
44
column_count
6
numeric_cells
99
header_rows
1
locator
section[27]/table-wrap[1]#Tab1
[2] object · 16 fields
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read_table
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note
Univariate and multivariate Cox regression analysis of clinical characteristics in STAD patients.
structure object · 5 fields
pmcid
PMC11799156
section_index
27
section_title
Validation of the prognostic risk signature via GEO datasets
row_count
53
column_count
6
table object · 8 fields
label
Table 2
caption
Univariate and multivariate Cox regression analysis of clinical characteristics in STAD patients.
rows array · 53 items
[0] array · 4 items
[0]
Characteristic
[1]
Total(N)
[2]
Univariate analysis
[3]
Multivariate analysis
[1] array · 4 items
[0]
Hazard ratio (95% CI)
[1]
p-value
[2]
Hazard ratio (95% CI)
[3]
p-value
[2] array · 6 items
[0]
Age
[1]
376
[2]
[3]
[4]
[5]
[3] array · 6 items
[0]
< 60
[1]
116
[2]
Reference
[3]
[4]
[5]
[4] array · 6 items
[0]
>=60
[1]
260
[2]
0.662 (0.478–0.918)
[3]
0.013
[4]
2.156 (1.475–3.150)
[5]
< 0.001
[5] array · 6 items
[0]
Gender
[1]
376
[2]
[3]
[4]
[5]
[6] array · 6 items
[0]
Male
[1]
246
[2]
Reference
[3]
[4]
[5]
[7] array · 6 items
[0]
Female
[1]
130
[2]
0.774 (0.549–1.090)
[3]
0.142
[4]
0.750 (0.521–1.079)
[5]
0.750
[8] array · 6 items
[0]
Race
[1]
376
[2]
[3]
[4]
[5]
[9] array · 6 items
[0]
White
[1]
240
[2]
Reference
[3]
[4]
[5]
[10] array · 6 items
[0]
Asian
[1]
83
[2]
0.166 (0.023–1.206)
[3]
0.076
[4]
1.253 (0.755–2.081)
[5]
0.383
[11] array · 6 items
[0]
Black or African American
[1]
11
[2]
0.134 (0.018–1.001)
[3]
0.050
[4]
1.251 (0.518–3.023)
[5]
0.619
[12] array · 6 items
[0]
Native Hawaiian or other pacific islander
[1]
1
[2]
0.185 (0.025–1.398)
[3]
0.102
[4]
3.646 (0.378–35.180)
[5]
0.263
[13] array · 6 items
[0]
Not reported
[1]
41
[2]
0.217 (0.026–1.785)
[3]
0.155
[4]
1.640 (0.860–3.128)
[5]
0.133
[14] array · 6 items
[0]
T Stage
[1]
376
[2]
[3]
[4]
[5]
[15] array · 6 items
[0]
T1
[1]
17
[2]
Reference
[3]
[4]
[5]
[16] array · 6 items
[0]
T2
[1]
79
[2]
3.492 (0.831–14.671)
[3]
0.088
[4]
3.611 (0.755–17.283)
[5]
0.108
[17] array · 6 items
[0]
T3
[1]
169
[2]
4.717 (1.157–19.223)
[3]
0.030
[4]
7.060 (1.246–39.997)
[5]
0.027
[18] array · 6 items
[0]
T4
[1]
107
[2]
4.985 (1.209–20.551)
[3]
0.026
[4]
6.134 (1.050-35.851)
[5]
0.044
[19] array · 6 items
[0]
TX
[1]
4
[2]
18.731 (3.412-102.832)
[3]
0.001
[4]
11.017 (1.327–91.439)
[5]
0.026
[20] array · 6 items
[0]
N Stage
[1]
376
[2]
[3]
[4]
[5]
[21] array · 6 items
[0]
N0
[1]
113
[2]
Reference
[3]
[4]
[5]
[22] array · 6 items
[0]
N1
[1]
100
[2]
1.646 (1.041–2.603)
[3]
0.033
[4]
1.957 (1.004–3.816)
[5]
0.049
[23] array · 6 items
[0]
N2
[1]
74
[2]
1.531 (0.922–2.541)
[3]
0.100
[4]
1.583 (0.693–3.615)
[5]
0.272
[24] array · 6 items
[0]
N3
[1]
78
[2]
2.670 (1.691–4.216)
[3]
< 0.001
[4]
2.511 (1.097–5.752)
[5]
0.029
[25] array · 6 items
[0]
NX
[1]
11
[2]
1.123 (0.411–3.074)
[3]
0.031
[4]
3.375 (0.917–12.430)
[5]
0.067
[26] array · 6 items
[0]
M Stage
[1]
376
[2]
[3]
[4]
[5]
[27] array · 6 items
[0]
M0
[1]
339
[2]
Reference
[3]
[4]
[5]
[28] array · 6 items
[0]
M1
[1]
22
[2]
2.416 (1.362–4.284)
[3]
0.003
[4]
2.216 (0.016–4.426)
[5]
0.120
[29] array · 6 items
[0]
MX
[1]
15
[2]
1.705 (0.751–3.875)
[3]
0.202
[4]
1.184 (0.484–2.894)
[5]
0.712
[30] array · 6 items
[0]
Pathological Stage
[1]
376
[2]
[3]
[4]
[5]
[31] array · 6 items
[0]
Stage I
[1]
49
[2]
Reference
[3]
[4]
[5]
[32] array · 6 items
[0]
Stage II
[1]
119
[2]
1.357 (0.719–2.562)
[3]
0.346
[4]
0.562 (0.209–1.515)
[5]
0.255
[33] array · 6 items
[0]
Stage III
[1]
161
[2]
2.029 (1.124–3.665)
[3]
0.019
[4]
0.559 (0.157-2.000)
[5]
0.372
[34] array · 6 items
[0]
Stage IV
[1]
33
[2]
3.874 (1.949-7.700)
[3]
< 0.001
[4]
0.604 (0.135–2.695)
[5]
0.509
[35] array · 6 items
[0]
Unknown
[1]
14
[2]
4.442 (1.940-10.168)
[3]
< 0.001
[4]
1.345 (0.338–5.357)
[5]
0.674
[36] array · 6 items
[0]
Grade
[1]
[2]
[3]
[4]
[5]
[37] array · 6 items
[0]
G1
[1]
9
[2]
Reference
[3]
[4]
[5]
[38] array · 6 items
[0]
G2
[1]
128
[2]
1.123 (0.350–3.609)
[3]
0.845
[4]
1.863 (0.460–7.542)
[5]
0.383
[39] array · 6 items
[0]
G3
[1]
230
[2]
1.469 (0.465–4.635)
[3]
0.512
[4]
2.357 (0.590–9.414)
[5]
0.225
[40] array · 6 items
[0]
GX
[1]
9
[2]
1.864 (0.417–8.338)
[3]
0.415
[4]
2.785 (0.497–15.613)
[5]
0.244
[41] array · 6 items
[0]
Classification
[1]
[2]
[3]
[4]
[5]
[42] array · 6 items
[0]
Adenocarcinoma, intestinal type
[1]
74
[2]
Reference
[3]
[4]
[5]
[43] array · 6 items
[0]
Adenocarcinoma, NOS
[1]
132
[2]
1.064 (0.693–1.634)
[3]
0.778
[4]
0.969 (0.589–1.594)
[5]
0.902
[44] array · 6 items
[0]
Adenocarcinoma with mixed subtypes
[1]
1
[2]
0.000 (0.000-Inf)
[3]
0.960
[4]
0.000 (0.000-Inf)
[5]
0.943
[45] array · 6 items
[0]
Carcinoma, diffuse type
[1]
64
[2]
0.770 (0.456-1.300)
[3]
0.328
[4]
0.672 (0.368–1.226)
[5]
0.195
[46] array · 6 items
[0]
Mucinous adenocarcinoma
[1]
17
[2]
0.308 (0.095–1.004)
[3]
0.051
[4]
0.211 (0.062–0.721)
[5]
0.013
[47] array · 6 items
[0]
Papillary adenocarcinoma, NOS
[1]
6
[2]
0.934 (0.286–3.048)
[3]
0.910
[4]
2.414 (0.592–9.845)
[5]
0.219
[48] array · 6 items
[0]
Signet ring cell carcinoma
[1]
13
[2]
1.976 (0.945–4.129)
[3]
0.070
[4]
1.729 (0.750–3.986)
[5]
0.199
[49] array · 6 items
[0]
Tubular adenocarcinoma
[1]
69
[2]
0.845 (0.509–1.404)
[3]
0.516
[4]
0.811 (0.468–1.406)
[5]
0.456
[50] array · 6 items
[0]
ARS
[1]
376
[2]
[3]
[4]
[5]
[51] array · 6 items
[0]
Low Risk
[1]
189
[2]
Reference
[3]
[4]
[5]
[52] array · 6 items
[0]
High Risk
[1]
187
[2]
1.685 (1.224–2.320)
[3]
< 0.001
[4]
2.171 (1.495–3.153)
[5]
< 0.001
row_count
53
column_count
6
numeric_cells
177
header_rows
2
locator
section[27]/table-wrap[2]#Tab2
gaps array · 1 item
[0]
asset:source:pmid:39910129 not verified
analysis object · 4 fields
state
absent
methods array · 0 items
targets array · 0 items
gaps array · 2 items
[0]
method
[1]
targets
capability object · 3 fields
state
absent
requirements array · 0 items
gaps array · 1 item
[0]
capability
readiness object · 8 fields
state
partial
tier
null
blocking_axis
null
blocked_on
null
axes object · 0 fields
can_run object · 3 fields
dsl_operations array · 0 items
assets array · 3 items
[0]
source:pmid:39910129
[1]
asset:table:pmid:39910129:1
[2]
asset:table:pmid:39910129:2
steps array · 1 item
[0]
read_published_estimate
must_build object · 5 fields
dsl_operations array · 0 items
converters array · 0 items
readers array · 1 item
[0]
xml
capabilities array · 0 items
data_gaps array · 1 item
[0]
source:pmid:39910129
gaps array · 1 item
[0]
corpus_record_absent
review object · 5 fields
state
partial
machine_critique object · 7 fields
status
passed
providers array · 2 items
[0] object · 7 fields
provider
minimax
model
MiniMax-M3.1-Flash
prompt_version
full-text-reading-v1
prompt_hash
a4ebd015d48fcd36b6f3401214d9d59b9bb85c0a9b612cc63759dc50831e9ab2
source_hash
685966f890478b4f645ee99b8fdc95e68da913cdb8a4e244b4b4a2ff66c98b87
raw_response_sha256
sha256:55262a32e13b596ffbf3ff3d42795f1fadd79e4d326c56f1651cdc9aef12c7c6
raw_response_chars
5554
[1] object · 7 fields
provider
minimax_alt
model
MiniMax-M3
prompt_version
full-text-reading-v1
prompt_hash
03f046fd856957ce3cc57eed31cffbb53d60c2347c5f8c14bf1d84e761106c95
source_hash
685966f890478b4f645ee99b8fdc95e68da913cdb8a4e244b4b4a2ff66c98b87
raw_response_sha256
sha256:62abb5d066ab889886f1aa420f91be9e024dca28a9e66bde08867bda3db209d8
raw_response_chars
53646
target_providers array · 2 items
[0] object · 8 fields
provider
minimax
model
MiniMax-M3.1-Flash
prompt_version
replication-target-v2
prompt_hash
43f81c6076c141c6905d39dd68a047a2e0151ddfbe426913dcb44e9693d99faf
source_hash
685966f890478b4f645ee99b8fdc95e68da913cdb8a4e244b4b4a2ff66c98b87
raw_response
{"parent_value":7,"unit":"genes","evidence":"The anoikis risk score (ARS) incorporated 7 genes and stratified patients into highand low-risk subgroups by median value splitting.","target_result":"The anoikis risk score incorporated 7 genes.","number_stated":true}
reading object · 6 fields
parent_value
7
unit
genes
evidence
The anoikis risk score (ARS) incorporated 7 genes and stratified patients into highand low-risk subgroups by median value splitting.
target_result
The anoikis risk score incorporated 7 genes.
number_stated
true
source_locator
chars 763-895 of source sha256 685966f890478b4f645ee99b8fdc95e68da913cdb8a4e244b4b4a2ff66c98b87
recorded_at
2026-10-31T15:22:47.488941+00:00
[1] object · 8 fields
provider
minimax_alt
model
MiniMax-M3
prompt_version
replication-target-v2
prompt_hash
70dfc8da0a66737dbcb9cbee727ada46cb49e33ec0c6bf64ef99f13675fd8aab
source_hash
685966f890478b4f645ee99b8fdc95e68da913cdb8a4e244b4b4a2ff66c98b87
raw_response
<think>We need answer JSON only. Need determine registered target headline numerical result paper states for main finding. Source supplied appears excerpts, perhaps missing key prognostic signature construction section? Need identify single numerical result replication of registered target. "the headline numerical result the paper itself states for its registered target" Target abstract says ARS incorporated 7 genes and stratified by median. But headline numerical result maybe C-index? Need parse source. They ask parent_value perhaps expected numeric and unit. Need infer from source text. The source text includes various numbers, but main finding likely prognostic signature performance. Maybe "7 genes" is numerical result? Yet "headline numerical result" could be paper's target: number of genes in risk signature. Replication has to reproduce. Need exact contiguous quotation containing number. They explicitly say report headline number only, value paper states for registered target. Unit paper prints. We need decide. Let's inspect supplied text. Abstract: "The anoikis risk score (ARS) incorporated 7 genes and stratified patients into highand low-risk subgroups by median value splitting." This is a headline quantitative characteristic. Main finding perhaps the paper title/signature. In excerpt, no C-index values, HR, AUC numeric values. There is R=0.47 etc. Target phrasing generic: "the headline numerical result the paper states for its main finding". Could mean answer extraction benchmark where registered target perhaps title of paper? They expect a number central to main result. We need extract only source claims. Maybe headline is "7 genes." Unit likely "genes". Evidence exact quote whole clause. target_result could concise. Could also be 2652 protein-coding DEGs (1289 up, 1363 down), perhaps not headline main finding. Or 18 cell types. But main paper's finding: "novel prognostic signature"; key number: 7 genes. Since target says "headline numerical result the paper itself states for its main finding" perhaps they intend "ARS incorporated 7 genes". parent_value 7, unit "genes". Evidence exact contiguous quote. Need ensure JSON valid, no markdown. target_result perhaps "The anoikis risk score (ARS) incorporated 7 genes." Evidence exact quotation perhaps "The anoikis risk score (ARS) incorporated 7 genes and stratified patients into highand low-risk subgroups by median value splitting." Unit "genes". number_stated true. But user asks headline number only; JSON requires fields. target_result should maybe not introduce extra number? Could say "The anoikis risk score incorporated seven genes."</think> {"parent_value":7,"unit":"genes","evidence":"The anoikis risk score (ARS) incorporated 7 genes and stratified patients into highand low-risk subgroups by median value splitting.","target_result":"The anoikis risk score incorporated 7 genes.","number_stated":true}
reading object · 6 fields
parent_value
7
unit
genes
evidence
The anoikis risk score (ARS) incorporated 7 genes and stratified patients into highand low-risk subgroups by median value splitting.
target_result
The anoikis risk score incorporated 7 genes.
number_stated
true
source_locator
chars 763-895 of source sha256 685966f890478b4f645ee99b8fdc95e68da913cdb8a4e244b4b4a2ff66c98b87
recorded_at
2026-10-31T15:22:50.626727+00:00
agreement
true
disagreements object · 3 fields
target_result object · 3 fields
minimax
The anoikis risk score (ARS) incorporated 7 genes and stratified stomach adenocarcinoma patients into high- and low-risk subgroups, with the low-risk subgroup having better outcomes.
minimax_alt
The anoikis risk score (ARS) incorporated 7 genes and stratified patients into highand low-risk subgroups by median value splitting.
decisive
false
physical_methods object · 3 fields
minimax array · 1 item
[0]
In vitro CRABP2 knockdown experiments assessing gastric cancer cell proliferation, migration, invasion, and apoptosis
minimax_alt array · 2 items
[0]
in vitro CRABP2 knockdown experiments in gastric cancer cells
[1]
measurement of gastric cancer cell proliferation, migration, invasion, and apoptosis
decisive
false
analysis_methods object · 3 fields
minimax array · 18 items
[0]
LASSO regression
[1]
Cox regression
[2]
Median-value splitting into high- and low-risk subgroups
[3]
External cohort validation
[4]
Nomogram construction
[5]
Time-dependent AUC
[6]
Calibration curve analysis
[7]
Decision curve analysis
[8]
C-index estimation
[9]
Spearman correlation analysis
[10]
Single-cell RNA sequencing analysis
[11]
Gene Ontology and KEGG enrichment analysis
[12]
Gene set enrichment analysis
[13]
Gene set variation analysis
[14]
ESTIMATE
[15]
ssGSEA
[16]
CIBERSORT
[17]
TIDE
minimax_alt array · 18 items
[0]
LASSO and Cox regression
[1]
median-value risk-group stratification
[2]
external validation in independent cohorts
[3]
nomogram construction
[4]
time-dependent AUC, calibration curves, and decision curve analysis (DCA)
[5]
Gene Ontology (GO) and Kyoto Encyclopedia of Genes Genomes (KEGG) enrichment analysis
[6]
Gene Set Enrichment Analysis (GSEA) and Gene Set Variation Analysis (GSVA)
[7]
ESTIMATE
[8]
single-sample Gene Set Enrichment Analysis (ssGSEA), CIBERSORT, MCPcounter, xCell, IPS, and TIMER
[9]
Tumor Immune Dysfunction and Exclusion (TIDE) analysis
[10]
maftools somatic-mutation analysis
[11]
pRRophetic drug-sensitivity prediction
[12]
single-cell RNA-seq analysis using Seurat, t-SNE, and CellChat
[13]
Wilcoxon test
[14]
t test
[15]
C-index
[16]
Spearman correlation
[17]
chi-square test
decisive
false
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
passed
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.passed
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:98766c9da04cf6127bfc9405013c0b54aeae080fb01915bd88c284ee71a3ebb7
type
sep_package
label
SEP v1 package for pmid:39910129
activities array · 1 item
[0] object · 4 fields
id
activity:conversion:pmid:39910129
type
conversion
used array · 1 item
[0]
package:98766c9da04cf6127bfc9405013c0b54aeae080fb01915bd88c284ee71a3ebb7
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:39910129
parent_hash
sha256:7e417093e123dc64a830916ccb4dab42d35b004dc845d96ec6e9541170e8143c
fork_of
null
generation
2
gaps array · 13 items
[0]
abstract
[1]
asset:source:pmid:39910129 not verified
[2]
authors
[3]
capability
[4]
corpus_record_absent
[5]
execution.not_run
[6]
method
[7]
review.human_critique
[8]
review.machine_critique.passed
[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:39910129' does not resolve to a declared asset
[12]
targets
Complete file 
{"sci_version": "1.0", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:39910129", "kind": "science-record", "revision": 2, "content_hash": "sha256:33337bbb0865e4b3624bc7d6104a339251e93bcf627f86ab5bc35dcbd1fc26cb", "created_at": "2026-11-01T10:25:49Z", "updated_at": "2026-11-01T14:01:33Z", "generator": {"name": "corpus-assay-engine", "converter": "sep_to_sci_v1", "source_package_schema": "urn:bntrg:sep:1.0.0"}, "paper": {"state": "partial", "title": "Integrative analysis of anoikis-related prognostic signature to evaluate the immune landscape and predict therapeutic response in stomach adenocarcinoma.", "doi": "10.1038/s41598-025-88882-9", "pmid": "39910129", "authors": null, "journal": "Scientific reports", "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": 7.0, "unit": "genes", "tolerance": null, "source": "chars 763-895 of source sha256 685966f890478b4f645ee99b8fdc95e68da913cdb8a4e244b4b4a2ff66c98b87"}, "evidence": [{"asset": "source:pmid:39910129", "locator": "chars 763-895 of source sha256 685966f890478b4f645ee99b8fdc95e68da913cdb8a4e244b4b4a2ff66c98b87", "quote": "The anoikis risk score (ARS) incorporated 7 genes and stratified patients into highand low-risk subgroups by median value splitting."}]}], "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:39910129"], "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:39910129", "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:39910129' does not resolve to a declared asset"]}, "data": {"state": "partial", "assets": [{"id": "source:pmid:39910129", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.1038/s41598-025-88882-9", "sha256": "sha256:685966f890478b4f645ee99b8fdc95e68da913cdb8a4e244b4b4a2ff66c98b87", "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.1038/s41598-025-88882-9", "version": null, "note": "Source read by the package builder: full_text.", "structure": {"access_state": "full_text"}}, {"id": "asset:table:pmid:39910129:1", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:9f0c2c22796431cab0776a16c72349354648c9187f79f43ad1c4e5bcf7260dc7", "bytes": 2721, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[27]/table-wrap[1]#Tab1", "version": null, "note": "Baseline of clinical characteristics between low- and high-risk subgroups.", "structure": {"pmcid": "PMC11799156", "section_index": 27, "section_title": "Validation of the prognostic risk signature via GEO datasets", "row_count": 44, "column_count": 6}, "table": {"label": "Table 1", "caption": "Baseline of clinical characteristics between low- and high-risk subgroups.", "rows": [["Characteristic", "Levels", "Low-risk", "High-risk", "p", "Method"], ["n", "", "188", "188", "", ""], ["Status, n (%)", "Alive", "123 (65.4%)", "97 (51.6%)", "0.007", "Chi-square"], ["", "Dead", "65 (34.6%)", "91 (48.4%)", "", ""], ["Age, n (%)", "< 60", "45 (23.9%)", "71 (37.8%)", "0.004", "Chi-square"], ["", "≥ 60", "143 (76.1%)", "117 (62.2%)", "", ""], ["T Stage, n (%)", "T1", "14 (7.5%)", "3 (1.6%)", "0.075", "Fisher’s test"], ["", "T2", "41 (21.6%)", "38 (20.3%)", "", ""], ["", "T3", "87 (46.3%)", "82 (43.6%)", "", ""], ["", "T4", "43 (22.9%)", "64 (34.1%)", "", ""], ["", "TX", "3 (1.6%)", "1 (0.5%)", "", ""], ["N Stage, n (%)", "N0", "59 (31.4%)", "54 (28.7%)", "0.177", "Fisher’s test"], ["", "N1", "49 (26.1%)", "51 (27.1%)", "", ""], ["", "N2", "39 (20.7%)", "35 (18.6%)", "", ""], ["", "N3", "36 (19.2%)", "42 (22.4%)", "", ""], ["", "NX", "5 (2.6%)", "6 (3.2%)", "", ""], ["M Stage, n (%)", "M0", "174 (92.6%)", "165 (87.8%)", "0.289", "Fisher’s test"], ["", "M1", "8 (4.2%)", "14 (7.4%)", "", ""], ["", "MX", "6 (3.2%)", "9 (4.8%)", "", ""], ["Stage, n (%)", "Stage I", "32 (17.0%)", "17 (9.0%)", "0.441", "Fisher’s test"], ["", "Stage II", "54 (28.7%)", "65 (34.6%)", "", ""], ["", "Stage III", "80 (42.5%)", "81 (43.1%)", "", ""], ["", "Stage IV", "15 (8.0%)", "18 (9.6%)", "", ""], ["", "Unknown", "7 (3.7%)", "7 (3.7%)", "", ""], ["Gender, n (%)", "Female", "63 (33.5%)", "67 (35.6%)", "0.664", "Chi-square"], ["", "Male", "125 (66.5%)", "121 (64.4%)", "", ""], ["Race, n (%)", "White", "110 (58.5%)", "130 (69.2%)", "0.017", "Fisher’s test"], ["", "Asian", "42 (22.4%)", "41 (21.8%)", "", ""], ["", "Black or African American", "10 (5.3%)", "1 (0.5%)", "", ""], ["", "Native Hawaiian or other pacific islander", "1 (0.5%)", "0 (0.0%)", "", ""], ["", "Not reported", "25 (13.3%)", "16 (8.5%)", "", ""], ["Grade, n (%)", "G1", "5 (2.7%)", "4 (2.1%)", "0.002", "Fisher’s test"], ["", "G2", "81 (43.1%)", "47 (25.0%)", "", ""], ["", "G3", "98 (52.1%)", "132 (70.2%)", "", ""], ["", "GX", "4 (2.1%)", "5 (2.7%)", "", ""], ["Classification, n (%)", "Adenocarcinoma, intestinal type", "40 (21.3%)", "34 (18.1%)", "0.001", "Fisher’s test"], ["", "Adenocarcinoma, NOS", "56 (29.8%)", "76 (40.4%)", "", ""], ["", "Adenocarcinoma with mixed subtypes", "0 (0.0%)", "1 (0.5%)", "", ""], ["", "Carcinoma, diffuse type", "25 (13.3%)", "39 (20.7%)", "", ""], ["", "Mucinous adenocarcinoma", "7 (3.7%)", "10 (5.3%)", "", ""], ["", "Papillary adenocarcinoma, NOS", "6 (3.2%)", "0 (0.0%)", "", ""], ["", "Signet ring cell carcinoma", "8 (4.3%)", "5 (2.7%)", "", ""], ["", "Tubular adenocarcinoma", "46 (24.5%)", "23 (12.2%)", "", ""], ["Time, median (IQR)", "", "495 (282.5, 851.5)", "420 (272.25, 688.5)", "< 0.001", "Wilcoxon test"]], "row_count": 44, "column_count": 6, "numeric_cells": 99, "header_rows": 1, "locator": "section[27]/table-wrap[1]#Tab1"}}, {"id": "asset:table:pmid:39910129:2", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:449ff4cfb2754a4cc84ddd5bed6586123e76670b386310ddd6ac5e08fdd879a7", "bytes": 3718, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[27]/table-wrap[2]#Tab2", "version": null, "note": "Univariate and multivariate Cox regression analysis of clinical characteristics in STAD patients.", "structure": {"pmcid": "PMC11799156", "section_index": 27, "section_title": "Validation of the prognostic risk signature via GEO datasets", "row_count": 53, "column_count": 6}, "table": {"label": "Table 2", "caption": "Univariate and multivariate Cox regression analysis of clinical characteristics in STAD patients.", "rows": [["Characteristic", "Total(N)", "Univariate analysis", "Multivariate analysis"], ["Hazard ratio (95% CI)", "p-value", "Hazard ratio (95% CI)", "p-value"], ["Age", "376", "", "", "", ""], ["< 60", "116", "Reference", "", "", ""], [">=60", "260", "0.662 (0.478–0.918)", "0.013", "2.156 (1.475–3.150)", "< 0.001"], ["Gender", "376", "", "", "", ""], ["Male", "246", "Reference", "", "", ""], ["Female", "130", "0.774 (0.549–1.090)", "0.142", "0.750 (0.521–1.079)", "0.750"], ["Race", "376", "", "", "", ""], ["White", "240", "Reference", "", "", ""], ["Asian", "83", "0.166 (0.023–1.206)", "0.076", "1.253 (0.755–2.081)", "0.383"], ["Black or African American", "11", "0.134 (0.018–1.001)", "0.050", "1.251 (0.518–3.023)", "0.619"], ["Native Hawaiian or other pacific islander", "1", "0.185 (0.025–1.398)", "0.102", "3.646 (0.378–35.180)", "0.263"], ["Not reported", "41", "0.217 (0.026–1.785)", "0.155", "1.640 (0.860–3.128)", "0.133"], ["T Stage", "376", "", "", "", ""], ["T1", "17", "Reference", "", "", ""], ["T2", "79", "3.492 (0.831–14.671)", "0.088", "3.611 (0.755–17.283)", "0.108"], ["T3", "169", "4.717 (1.157–19.223)", "0.030", "7.060 (1.246–39.997)", "0.027"], ["T4", "107", "4.985 (1.209–20.551)", "0.026", "6.134 (1.050-35.851)", "0.044"], ["TX", "4", "18.731 (3.412-102.832)", "0.001", "11.017 (1.327–91.439)", "0.026"], ["N Stage", "376", "", "", "", ""], ["N0", "113", "Reference", "", "", ""], ["N1", "100", "1.646 (1.041–2.603)", "0.033", "1.957 (1.004–3.816)", "0.049"], ["N2", "74", "1.531 (0.922–2.541)", "0.100", "1.583 (0.693–3.615)", "0.272"], ["N3", "78", "2.670 (1.691–4.216)", "< 0.001", "2.511 (1.097–5.752)", "0.029"], ["NX", "11", "1.123 (0.411–3.074)", "0.031", "3.375 (0.917–12.430)", "0.067"], ["M Stage", "376", "", "", "", ""], ["M0", "339", "Reference", "", "", ""], ["M1", "22", "2.416 (1.362–4.284)", "0.003", "2.216 (0.016–4.426)", "0.120"], ["MX", "15", "1.705 (0.751–3.875)", "0.202", "1.184 (0.484–2.894)", "0.712"], ["Pathological Stage", "376", "", "", "", ""], ["Stage I", "49", "Reference", "", "", ""], ["Stage II", "119", "1.357 (0.719–2.562)", "0.346", "0.562 (0.209–1.515)", "0.255"], ["Stage III", "161", "2.029 (1.124–3.665)", "0.019", "0.559 (0.157-2.000)", "0.372"], ["Stage IV", "33", "3.874 (1.949-7.700)", "< 0.001", "0.604 (0.135–2.695)", "0.509"], ["Unknown", "14", "4.442 (1.940-10.168)", "< 0.001", "1.345 (0.338–5.357)", "0.674"], ["Grade", "", "", "", "", ""], ["G1", "9", "Reference", "", "", ""], ["G2", "128", "1.123 (0.350–3.609)", "0.845", "1.863 (0.460–7.542)", "0.383"], ["G3", "230", "1.469 (0.465–4.635)", "0.512", "2.357 (0.590–9.414)", "0.225"], ["GX", "9", "1.864 (0.417–8.338)", "0.415", "2.785 (0.497–15.613)", "0.244"], ["Classification", "", "", "", "", ""], ["Adenocarcinoma, intestinal type", "74", "Reference", "", "", ""], ["Adenocarcinoma, NOS", "132", "1.064 (0.693–1.634)", "0.778", "0.969 (0.589–1.594)", "0.902"], ["Adenocarcinoma with mixed subtypes", "1", "0.000 (0.000-Inf)", "0.960", "0.000 (0.000-Inf)", "0.943"], ["Carcinoma, diffuse type", "64", "0.770 (0.456-1.300)", "0.328", "0.672 (0.368–1.226)", "0.195"], ["Mucinous adenocarcinoma", "17", "0.308 (0.095–1.004)", "0.051", "0.211 (0.062–0.721)", "0.013"], ["Papillary adenocarcinoma, NOS", "6", "0.934 (0.286–3.048)", "0.910", "2.414 (0.592–9.845)", "0.219"], ["Signet ring cell carcinoma", "13", "1.976 (0.945–4.129)", "0.070", "1.729 (0.750–3.986)", "0.199"], ["Tubular adenocarcinoma", "69", "0.845 (0.509–1.404)", "0.516", "0.811 (0.468–1.406)", "0.456"], ["ARS", "376", "", "", "", ""], ["Low Risk", "189", "Reference", "", "", ""], ["High Risk", "187", "1.685 (1.224–2.320)", "< 0.001", "2.171 (1.495–3.153)", "< 0.001"]], "row_count": 53, "column_count": 6, "numeric_cells": 177, "header_rows": 2, "locator": "section[27]/table-wrap[2]#Tab2"}}], "gaps": ["asset:source:pmid:39910129 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:39910129", "asset:table:pmid:39910129:1", "asset:table:pmid:39910129:2"], "steps": ["read_published_estimate"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": ["xml"], "capabilities": [], "data_gaps": ["source:pmid:39910129"]}, "gaps": ["corpus_record_absent"]}, "review": {"state": "partial", "machine_critique": {"status": "passed", "providers": [{"provider": "minimax", "model": "MiniMax-M3.1-Flash", "prompt_version": "full-text-reading-v1", "prompt_hash": "a4ebd015d48fcd36b6f3401214d9d59b9bb85c0a9b612cc63759dc50831e9ab2", "source_hash": "685966f890478b4f645ee99b8fdc95e68da913cdb8a4e244b4b4a2ff66c98b87", "raw_response_sha256": "sha256:55262a32e13b596ffbf3ff3d42795f1fadd79e4d326c56f1651cdc9aef12c7c6", "raw_response_chars": 5554}, {"provider": "minimax_alt", "model": "MiniMax-M3", "prompt_version": "full-text-reading-v1", "prompt_hash": "03f046fd856957ce3cc57eed31cffbb53d60c2347c5f8c14bf1d84e761106c95", "source_hash": "685966f890478b4f645ee99b8fdc95e68da913cdb8a4e244b4b4a2ff66c98b87", "raw_response_sha256": "sha256:62abb5d066ab889886f1aa420f91be9e024dca28a9e66bde08867bda3db209d8", "raw_response_chars": 53646}], "target_providers": [{"provider": "minimax", "model": "MiniMax-M3.1-Flash", "prompt_version": "replication-target-v2", "prompt_hash": "43f81c6076c141c6905d39dd68a047a2e0151ddfbe426913dcb44e9693d99faf", "source_hash": "685966f890478b4f645ee99b8fdc95e68da913cdb8a4e244b4b4a2ff66c98b87", "raw_response": "{\"parent_value\":7,\"unit\":\"genes\",\"evidence\":\"The anoikis risk score (ARS) incorporated 7 genes and stratified patients into highand low-risk subgroups by median value splitting.\",\"target_result\":\"The anoikis risk score incorporated 7 genes.\",\"number_stated\":true}", "reading": {"parent_value": 7, "unit": "genes", "evidence": "The anoikis risk score (ARS) incorporated 7 genes and stratified patients into highand low-risk subgroups by median value splitting.", "target_result": "The anoikis risk score incorporated 7 genes.", "number_stated": true, "source_locator": "chars 763-895 of source sha256 685966f890478b4f645ee99b8fdc95e68da913cdb8a4e244b4b4a2ff66c98b87"}, "recorded_at": "2026-10-31T15:22:47.488941+00:00"}, {"provider": "minimax_alt", "model": "MiniMax-M3", "prompt_version": "replication-target-v2", "prompt_hash": "70dfc8da0a66737dbcb9cbee727ada46cb49e33ec0c6bf64ef99f13675fd8aab", "source_hash": "685966f890478b4f645ee99b8fdc95e68da913cdb8a4e244b4b4a2ff66c98b87", "raw_response": "<think>We need answer JSON only. Need determine registered target headline numerical result paper states for main finding. Source supplied appears excerpts, perhaps missing key prognostic signature construction section? Need identify single numerical result replication of registered target. \"the headline numerical result the paper itself states for its registered target\" Target abstract says ARS incorporated 7 genes and stratified by median. But headline numerical result maybe C-index? Need parse source. They ask parent_value perhaps expected numeric and unit. Need infer from source text. The source text includes various numbers, but main finding likely prognostic signature performance. Maybe \"7 genes\" is numerical result? Yet \"headline numerical result\" could be paper's target: number of genes in risk signature. Replication has to reproduce. Need exact contiguous quotation containing number. They explicitly say report headline number only, value paper states for registered target. Unit paper prints. We need decide.\n\nLet's inspect supplied text. Abstract: \"The anoikis risk score (ARS) incorporated 7 genes and stratified patients into highand low-risk subgroups by median value splitting.\" This is a headline quantitative characteristic. Main finding perhaps the paper title/signature. In excerpt, no C-index values, HR, AUC numeric values. There is R=0.47 etc. Target phrasing generic: \"the headline numerical result the paper states for its main finding\". Could mean answer extraction benchmark where registered target perhaps title of paper? They expect a number central to main result. We need extract only source claims. Maybe headline is \"7 genes.\" Unit likely \"genes\". Evidence exact quote whole clause. target_result could concise.\n\nCould also be 2652 protein-coding DEGs (1289 up, 1363 down), perhaps not headline main finding. Or 18 cell types. But main paper's finding: \"novel prognostic signature\"; key number: 7 genes. Since target says \"headline numerical result the paper itself states for its main finding\" perhaps they intend \"ARS incorporated 7 genes\". parent_value 7, unit \"genes\". Evidence exact contiguous quote.\n\nNeed ensure JSON valid, no markdown. target_result perhaps \"The anoikis risk score (ARS) incorporated 7 genes.\" Evidence exact quotation perhaps \"The anoikis risk score (ARS) incorporated 7 genes and stratified patients into highand low-risk subgroups by median value splitting.\" Unit \"genes\". number_stated true. But user asks headline number only; JSON requires fields. target_result should maybe not introduce extra number? Could say \"The anoikis risk score incorporated seven genes.\"</think>\n\n{\"parent_value\":7,\"unit\":\"genes\",\"evidence\":\"The anoikis risk score (ARS) incorporated 7 genes and stratified patients into highand low-risk subgroups by median value splitting.\",\"target_result\":\"The anoikis risk score incorporated 7 genes.\",\"number_stated\":true}", "reading": {"parent_value": 7, "unit": "genes", "evidence": "The anoikis risk score (ARS) incorporated 7 genes and stratified patients into highand low-risk subgroups by median value splitting.", "target_result": "The anoikis risk score incorporated 7 genes.", "number_stated": true, "source_locator": "chars 763-895 of source sha256 685966f890478b4f645ee99b8fdc95e68da913cdb8a4e244b4b4a2ff66c98b87"}, "recorded_at": "2026-10-31T15:22:50.626727+00:00"}], "agreement": true, "disagreements": {"target_result": {"minimax": "The anoikis risk score (ARS) incorporated 7 genes and stratified stomach adenocarcinoma patients into high- and low-risk subgroups, with the low-risk subgroup having better outcomes.", "minimax_alt": "The anoikis risk score (ARS) incorporated 7 genes and stratified patients into highand low-risk subgroups by median value splitting.", "decisive": false}, "physical_methods": {"minimax": ["In vitro CRABP2 knockdown experiments assessing gastric cancer cell proliferation, migration, invasion, and apoptosis"], "minimax_alt": ["in vitro CRABP2 knockdown experiments in gastric cancer cells", "measurement of gastric cancer cell proliferation, migration, invasion, and apoptosis"], "decisive": false}, "analysis_methods": {"minimax": ["LASSO regression", "Cox regression", "Median-value splitting into high- and low-risk subgroups", "External cohort validation", "Nomogram construction", "Time-dependent AUC", "Calibration curve analysis", "Decision curve analysis", "C-index estimation", "Spearman correlation analysis", "Single-cell RNA sequencing analysis", "Gene Ontology and KEGG enrichment analysis", "Gene set enrichment analysis", "Gene set variation analysis", "ESTIMATE", "ssGSEA", "CIBERSORT", "TIDE"], "minimax_alt": ["LASSO and Cox regression", "median-value risk-group stratification", "external validation in independent cohorts", "nomogram construction", "time-dependent AUC, calibration curves, and decision curve analysis (DCA)", "Gene Ontology (GO) and Kyoto Encyclopedia of Genes Genomes (KEGG) enrichment analysis", "Gene Set Enrichment Analysis (GSEA) and Gene Set Variation Analysis (GSVA)", "ESTIMATE", "single-sample Gene Set Enrichment Analysis (ssGSEA), CIBERSORT, MCPcounter, xCell, IPS, and TIMER", "Tumor Immune Dysfunction and Exclusion (TIDE) analysis", "maftools somatic-mutation analysis", "pRRophetic drug-sensitivity prediction", "single-cell RNA-seq analysis using Seurat, t-SNE, and CellChat", "Wilcoxon test", "t test", "C-index", "Spearman correlation", "chi-square test"], "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:98766c9da04cf6127bfc9405013c0b54aeae080fb01915bd88c284ee71a3ebb7", "type": "sep_package", "label": "SEP v1 package for pmid:39910129"}], "activities": [{"id": "activity:conversion:pmid:39910129", "type": "conversion", "used": ["package:98766c9da04cf6127bfc9405013c0b54aeae080fb01915bd88c284ee71a3ebb7"], "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:39910129", "parent_hash": "sha256:7e417093e123dc64a830916ccb4dab42d35b004dc845d96ec6e9541170e8143c", "fork_of": null, "generation": 2}, "gaps": ["abstract", "asset:source:pmid:39910129 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:39910129' does not resolve to a declared asset", "targets"]}