Corpus Engine Towards a reproducible .science file.
← All .science files

pmid:40417419

Association of High Tumor-Stroma Ratio with Prostate Cancer Progression: Insights from Clinical and Genomic Data.

International journal of general medicine · 2025 doi:10.2147/ijgm.s515066

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
sci_version
1.0
id
pmid:40417419
kind
science-record
revision
2
content_hash
sha256:8118c5fd451efa86381f0df300901f63eec974decbba2068537a15bd4b145d03
schema
https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json
created_at
2026-11-01T10:25:51Z
updated_at
2026-11-01T14:01:41Z
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
Association of High Tumor-Stroma Ratio with Prostate Cancer Progression: Insights from Clinical and Genomic Data.
doi
10.2147/ijgm.s515066
pmid
40417419
authors
null
journal
International journal of general medicine
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
qualitative
state
blocked
target object · 4 fields
value
null
unit
null
tolerance
null
source
null
evidence array · 0 items
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.
duration_hours
null
parameters object · 0 fields
inputs array · 1 item
[0]
source:pmid:40417419
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
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 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
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:40417419
duration_hours
null
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:40417419' does not resolve to a declared asset
data object · 3 fields
state
partial
assets array · 3 items
[0] object · 15 fields
id
source:pmid:40417419
role
manuscript
format
xml
media_type
application/xml
uri
https://doi.org/10.2147/ijgm.s515066
sha256
sha256:d72fed1bf1f5b64c81cc55b830de6a2a8dfe51ef032bf6f46831eb7faad0270b
bytes
null
access
open
state
resolved
reader
null
reader_status
reader_required
identifier
10.2147/ijgm.s515066
version
null
note
Source read by the package builder: full_text.
structure object · 1 field
access_state
full_text
[1] object · 16 fields
id
asset:table:pmid:40417419:1
role
table
format
jats-table
media_type
application/vnd.jats.table+json
uri
null
sha256
sha256:570d9e0323116ab465b66748052bb327863b10e4edf1c8489a4ae95759af1323
bytes
1984
access
open
state
verified
reader
read_table
reader_status
available
identifier
section[23]/table-wrap[1]#t0001
version
null
note
Comparisons of Characteristics Between Prostate Cancer Patients with High TSR and Those with Low TSR in TCGA Cohort
structure object · 5 fields
pmcid
PMC12103176
section_index
23
section_title
TSR Evaluation in TCGA and LUSH Cohort
row_count
35
column_count
5
table object · 8 fields
label
Table 1
caption
Comparisons of Characteristics Between Prostate Cancer Patients with High TSR and Those with Low TSR in TCGA Cohort
rows array · 35 items
[0] array · 5 items
[0]
Characteristic
[1]
Overall (%)
[2]
Low TSR (%)
[3]
High TSR (%)
[4]
P Valuea
[1] array · 5 items
[0]
Sample
[1]
453 (100)
[2]
218 (48.12)
[3]
235 (51.88)
[4]
[2] array · 5 items
[0]
Age, median (IQR), year
[1]
61 (56, 66)
[2]
61 (55, 66)
[3]
62 (57, 66)
[4]
0.153
[3] array · 5 items
[0]
Age, year
[1]
[2]
[3]
[4]
0.03
[4] array · 5 items
[0]
41–57
[1]
149 (32.89)
[2]
83 (38.07)
[3]
66 (28.09)
[4]
[5] array · 5 items
[0]
58–78
[1]
304 (67.11)
[2]
135 (61.93)
[3]
169 (71.91)
[4]
[6] array · 5 items
[0]
Race
[1]
[2]
[3]
[4]
0.157
[7] array · 5 items
[0]
Asian
[1]
13 (2.87)
[2]
8 (3.67)
[3]
5 (2.13)
[4]
[8] array · 5 items
[0]
Black
[1]
51 (11.26)
[2]
31 (14.22)
[3]
20 (8.51)
[4]
[9] array · 5 items
[0]
White
[1]
376 (82.80)
[2]
174 (79.82)
[3]
202 (85.96)
[4]
[10] array · 5 items
[0]
Unknown
[1]
13 (2.87)
[2]
5 (2.29)
[3]
8 (3.40)
[4]
[11] array · 5 items
[0]
Gleason Score
[1]
[2]
[3]
[4]
< 0.001
[12] array · 5 items
[0]
< 8
[1]
266 (58.72)
[2]
150 (68.81)
[3]
116 (49.36)
[4]
[13] array · 5 items
[0]
≥ 8
[1]
187 (41.28)
[2]
68 (31.19)
[3]
119 (50.64)
[4]
[14] array · 5 items
[0]
Pathologic T stage
[1]
[2]
[3]
[4]
0.004
[15] array · 5 items
[0]
pT2
[1]
178 (39.29)
[2]
102 (46.79)
[3]
76 (32.34)
[4]
[16] array · 5 items
[0]
pT3
[1]
264 (58.28)
[2]
113 (51.83)
[3]
151 (64.26)
[4]
[17] array · 5 items
[0]
pT4
[1]
11 (2.43)
[2]
3 (1.38)
[3]
8 (3.40)
[4]
[18] array · 5 items
[0]
Pathologic N stage
[1]
[2]
[3]
[4]
0.008
[19] array · 5 items
[0]
pN0
[1]
319 (70.64)
[2]
156 (71.56)
[3]
163 (69.36)
[4]
[20] array · 5 items
[0]
pN1
[1]
73 (16.14)
[2]
25 (11.47)
[3]
48 (20.43)
[4]
[21] array · 5 items
[0]
Unknown
[1]
61 (13.46)
[2]
37 (16.97)
[3]
24 (10.21)
[4]
[22] array · 5 items
[0]
Seminal Vesicle Invasion
[1]
[2]
[3]
[4]
< 0.001
[23] array · 5 items
[0]
NO
[1]
321 (70.86)
[2]
173 (79.36)
[3]
148 (62.98)
[4]
[24] array · 5 items
[0]
YES
[1]
132 (29.14)
[2]
45 (20.64)
[3]
87 (37.02)
[4]
[25] array · 5 items
[0]
Residual Tumor
[1]
[2]
[3]
[4]
0.001
[26] array · 5 items
[0]
NO
[1]
286 (63.12)
[2]
155 (71.10)
[3]
131 (55.74)
[4]
[27] array · 5 items
[0]
YES
[1]
141 (31.06)
[2]
50 (22.94)
[3]
91 (38.72)
[4]
[28] array · 5 items
[0]
Unknown
[1]
26 (5.74)
[2]
13 (5.96)
[3]
13 (5.53)
[4]
[29] array · 5 items
[0]
BCR status
[1]
[2]
[3]
[4]
< 0.001
[30] array · 5 items
[0]
NO
[1]
355 (78.37)
[2]
189 (86.70)
[3]
166 (70.64)
[4]
[31] array · 5 items
[0]
YES
[1]
98 (21.63)
[2]
29 (13.30)
[3]
69 (29.36)
[4]
[32] array · 5 items
[0]
PFI status
[1]
[2]
[3]
[4]
0.002
[33] array · 5 items
[0]
NO
[1]
365 (80.57)
[2]
189 (86.70)
[3]
176 (74.89)
[4]
[34] array · 5 items
[0]
YES
[1]
88 (19.43)
[2]
29 (13.30)
[3]
59 (25.11)
[4]
row_count
35
column_count
5
numeric_cells
89
header_rows
1
locator
section[23]/table-wrap[1]#t0001
[2] object · 16 fields
id
asset:table:pmid:40417419:2
role
table
format
jats-table
media_type
application/vnd.jats.table+json
uri
null
sha256
sha256:40b23700405510e4432cc5f48ccc97ff01727c77942157b2f8ff14bdadbd2001
bytes
2941
access
open
state
verified
reader
read_table
reader_status
available
identifier
section[23]/table-wrap[2]#t0002
version
null
note
Comparisons of Characteristics Between Prostate Cancer Patients with High TSR and Those with Low TSR in the LUSH Cohort
structure object · 5 fields
pmcid
PMC12103176
section_index
23
section_title
TSR Evaluation in TCGA and LUSH Cohort
row_count
56
column_count
5
table object · 8 fields
label
Table 2
caption
Comparisons of Characteristics Between Prostate Cancer Patients with High TSR and Those with Low TSR in the LUSH Cohort
rows array · 56 items
[0] array · 5 items
[0]
Characteristic
[1]
Overall (%)
[2]
Low TSR (%)
[3]
High TSR (%)
[4]
P Valuea
[1] array · 5 items
[0]
Sample
[1]
320 (100)
[2]
168 (52.50)
[3]
152 (47.50)
[4]
[2] array · 5 items
[0]
Age, median (IQR), year
[1]
68 (64, 73)
[2]
68 (64, 71)
[3]
69 (64, 74)
[4]
0.12
[3] array · 5 items
[0]
Age, year
[1]
[2]
[3]
[4]
0.045
[4] array · 5 items
[0]
43–69
[1]
188 (58.75)
[2]
108 (64.29)
[3]
80 (52.63)
[4]
[5] array · 5 items
[0]
70–83
[1]
132 (41.25)
[2]
60 (35.71)
[3]
72 (47.37)
[4]
[6] array · 5 items
[0]
BMI
[1]
[2]
[3]
[4]
0.626
[7] array · 5 items
[0]
18–23
[1]
134 (41.88)
[2]
73 (43.45)
[3]
61 (40.13)
[4]
[8] array · 5 items
[0]
24–35
[1]
186 (58.13)
[2]
95 (56.55)
[3]
91 (59.87)
[4]
[9] array · 5 items
[0]
Blood Group
[1]
[2]
[3]
[4]
0.237
[10] array · 5 items
[0]
A
[1]
87 (27.19)
[2]
48 (28.57)
[3]
39 (25.66)
[4]
[11] array · 5 items
[0]
B
[1]
95 (29.69)
[2]
43 (25.60)
[3]
52 (34.21)
[4]
[12] array · 5 items
[0]
AB
[1]
29 (9.06)
[2]
19 (11.31)
[3]
10 (6.58)
[4]
[13] array · 5 items
[0]
O
[1]
109 (34.06)
[2]
58 (34.52)
[3]
51 (33.55)
[4]
[14] array · 5 items
[0]
Gleason Score
[1]
[2]
[3]
[4]
< 0.001
[15] array · 5 items
[0]
< 8
[1]
150 (46.88)
[2]
95 (56.55)
[3]
55 (36.18)
[4]
[16] array · 5 items
[0]
≥ 8
[1]
170 (53.12)
[2]
73 (43.45)
[3]
97 (63.82)
[4]
[17] array · 5 items
[0]
Ki67
[1]
[2]
[3]
[4]
0.344
[18] array · 5 items
[0]
< 0.05
[1]
76 (23.75)
[2]
44 (26.19)
[3]
32 (21.05)
[4]
[19] array · 5 items
[0]
≥ 0.05
[1]
244 (76.25)
[2]
124 (73.81)
[3]
120 (78.95)
[4]
[20] array · 5 items
[0]
Seminal Vesicle Invasion
[1]
[2]
[3]
[4]
0.04
[21] array · 5 items
[0]
NO
[1]
227 (70.94)
[2]
128 (76.19)
[3]
99 (65.13)
[4]
[22] array · 5 items
[0]
YES
[1]
93 (29.06)
[2]
40 (23.81)
[3]
53 (34.87)
[4]
[23] array · 5 items
[0]
FPSA
[1]
[2]
[3]
[4]
0.021
[24] array · 5 items
[0]
< 1.9
[1]
203 (63.44)
[2]
117 (69.64)
[3]
86 (56.58)
[4]
[25] array · 5 items
[0]
≥ 1.9
[1]
117 (36.56)
[2]
51 (30.36)
[3]
66 (43.42)
[4]
[26] array · 5 items
[0]
TPSA
[1]
[2]
[3]
[4]
0.002
[27] array · 5 items
[0]
< 15.5
[1]
182 (56.88)
[2]
110 (65.48)
[3]
72 (34.52)
[4]
[28] array · 5 items
[0]
≥ 15.5
[1]
138 (43.12)
[2]
58 (47.37)
[3]
80 (52.63)
[4]
[29] array · 5 items
[0]
WBC count
[1]
[2]
[3]
[4]
1
[30] array · 5 items
[0]
< 8.9
[1]
257 (80.31)
[2]
135 (80.36)
[3]
122 (80.26)
[4]
[31] array · 5 items
[0]
≥ 8.9
[1]
63 (19.69)
[2]
33 (19.64)
[3]
30 (19.74)
[4]
[32] array · 5 items
[0]
RBC count
[1]
[2]
[3]
[4]
0.687
[33] array · 5 items
[0]
< 3.45
[1]
35 (10.94)
[2]
20 (11.90)
[3]
15 (9.87)
[4]
[34] array · 5 items
[0]
≥ 3.45
[1]
285 (89.06)
[2]
148 (88.10)
[3]
137 (90.13)
[4]
[35] array · 5 items
[0]
Microscopic Pyuria
[1]
[2]
[3]
[4]
0.713
[36] array · 5 items
[0]
Negative
[1]
124 (38.75)
[2]
63 (37.50)
[3]
61 (40.13)
[4]
[37] array · 5 items
[0]
Positive
[1]
196 (61.25)
[2]
105 (62.50)
[3]
91 (59.87)
[4]
[38] array · 5 items
[0]
Microscopic Hematuria
[1]
[2]
[3]
[4]
1
[39] array · 5 items
[0]
Negative
[1]
114 (35.62)
[2]
60 (35.71)
[3]
54 (35.53)
[4]
[40] array · 5 items
[0]
Positive
[1]
206 (64.38)
[2]
108 (64.29)
[3]
98 (64.47)
[4]
[41] array · 5 items
[0]
ELR
[1]
[2]
[3]
[4]
0.366
[42] array · 5 items
[0]
< 0.034
[1]
80 (25.00)
[2]
38 (22.62)
[3]
42 (27.63)
[4]
[43] array · 5 items
[0]
≥ 0.034
[1]
240 (75.00)
[2]
130 (77.38)
[3]
110 (72.37)
[4]
[44] array · 5 items
[0]
BLR
[1]
[2]
[3]
[4]
0.964
[45] array · 5 items
[0]
< 0.017
[1]
148 (46.25)
[2]
77 (45.83)
[3]
71 (46.71)
[4]
[46] array · 5 items
[0]
≥ 0.017
[1]
172 (53.75)
[2]
91 (54.17)
[3]
81 (53.29)
[4]
[47] array · 5 items
[0]
NLR
[1]
[2]
[3]
[4]
0.459
[48] array · 5 items
[0]
< 3.197
[1]
216 (67.50)
[2]
117 (69.64)
[3]
99 (65.13)
[4]
[49] array · 5 items
[0]
≥ 3.197
[1]
104 (32.50)
[2]
51 (30.36)
[3]
53 (34.87)
[4]
[50] array · 5 items
[0]
MLR
[1]
[2]
[3]
[4]
0.36
[51] array · 5 items
[0]
< 0.259
[1]
138 (43.12)
[2]
77 (45.83)
[3]
61 (40.13)
[4]
[52] array · 5 items
[0]
≥ 0.259
[1]
182 (56.88)
[2]
91 (54.17)
[3]
91 (59.87)
[4]
[53] array · 5 items
[0]
BCR status
[1]
[2]
[3]
[4]
< 0.001
[54] array · 5 items
[0]
NO
[1]
171 (53.44)
[2]
113 (67.26)
[3]
58 (38.16)
[4]
[55] array · 5 items
[0]
YES
[1]
149 (46.56)
[2]
55 (32.74)
[3]
94 (61.84)
[4]
row_count
56
column_count
5
numeric_cells
157
header_rows
1
locator
section[23]/table-wrap[2]#t0002
gaps array · 1 item
[0]
asset:source:pmid:40417419 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:40417419
[1]
asset:table:pmid:40417419:1
[2]
asset:table:pmid:40417419:2
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:40417419
gaps array · 1 item
[0]
corpus_record_absent
review object · 5 fields
state
partial
machine_critique object · 7 fields
status
blocked
providers array · 0 items
target_providers array · 0 items
agreement
false
disagreements array · 0 items
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 · 4 items
[0] object · 4 fields
provider
minimax
model
null
reason
HTTP Error 429: Too Many Requests
raw_response
null
[1] object · 4 fields
provider
minimax_alt
model
null
reason
HTTP Error 429: Too Many Requests
raw_response
null
[2] object · 4 fields
provider
minimax
model
null
reason
HTTP Error 429: Too Many Requests
raw_response
null
[3] object · 4 fields
provider
minimax_alt
model
null
reason
HTTP Error 429: Too Many Requests
raw_response
null
[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 · 3 items
[0]
review.human_critique
[1]
review.machine_critique.blocked
[2]
review.machine_critique.providers
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:43f853aee2ca93ebd2f903b4ac2496ba58e8c25f43074e1728244d7c204bfaba
type
sep_package
label
SEP v1 package for pmid:40417419
activities array · 1 item
[0] object · 4 fields
id
activity:conversion:pmid:40417419
type
conversion
used array · 1 item
[0]
package:43f853aee2ca93ebd2f903b4ac2496ba58e8c25f43074e1728244d7c204bfaba
agent
agent:corpus-assay-engine
agents array · 1 item
[0] 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:40417419
parent_hash
sha256:63e047a84bc7569231860ffb81faebc1e97b8b6aedc7fb874f5d6470fbcd82ef
fork_of
null
generation
2
gaps array · 14 items
[0]
abstract
[1]
asset:source:pmid:40417419 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]
review.machine_critique.providers
[10]
step:obtain_source_data blocked on data:not_downloaded
[11]
step:run_analysis blocked on no owned computational capability is bound to this experiment
[12]
step:run_analysis input 'materials:the source data behind the published result in pmid:40417419' does not resolve to a declared asset
[13]
targets
Complete file 
{"sci_version": "1.0", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:40417419", "kind": "science-record", "revision": 2, "content_hash": "sha256:8118c5fd451efa86381f0df300901f63eec974decbba2068537a15bd4b145d03", "created_at": "2026-11-01T10:25:51Z", "updated_at": "2026-11-01T14:01:41Z", "generator": {"name": "corpus-assay-engine", "converter": "sep_to_sci_v1", "source_package_schema": "urn:bntrg:sep:1.0.0"}, "paper": {"state": "partial", "title": "Association of High Tumor-Stroma Ratio with Prostate Cancer Progression: Insights from Clinical and Genomic Data.", "doi": "10.2147/ijgm.s515066", "pmid": "40417419", "authors": null, "journal": "International journal of general medicine", "year": 2025, "abstract": null, "claims": [{"id": "claim-1", "statement": "the headline numerical result the paper states for its main finding", "kind": "qualitative", "state": "blocked", "target": {"value": null, "unit": null, "tolerance": null, "source": 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:40417419"], "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:40417419", "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:40417419' does not resolve to a declared asset"]}, "data": {"state": "partial", "assets": [{"id": "source:pmid:40417419", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.2147/ijgm.s515066", "sha256": "sha256:d72fed1bf1f5b64c81cc55b830de6a2a8dfe51ef032bf6f46831eb7faad0270b", "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.2147/ijgm.s515066", "version": null, "note": "Source read by the package builder: full_text.", "structure": {"access_state": "full_text"}}, {"id": "asset:table:pmid:40417419:1", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:570d9e0323116ab465b66748052bb327863b10e4edf1c8489a4ae95759af1323", "bytes": 1984, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[23]/table-wrap[1]#t0001", "version": null, "note": "Comparisons of Characteristics Between Prostate Cancer Patients with High TSR and Those with Low TSR in TCGA Cohort", "structure": {"pmcid": "PMC12103176", "section_index": 23, "section_title": "TSR Evaluation in TCGA and LUSH Cohort", "row_count": 35, "column_count": 5}, "table": {"label": "Table 1", "caption": "Comparisons of Characteristics Between Prostate Cancer Patients with High TSR and Those with Low TSR in TCGA Cohort", "rows": [["Characteristic", "Overall (%)", "Low TSR (%)", "High TSR (%)", "P Valuea"], ["Sample", "453 (100)", "218 (48.12)", "235 (51.88)", ""], ["Age, median (IQR), year", "61 (56, 66)", "61 (55, 66)", "62 (57, 66)", "0.153"], ["Age, year", "", "", "", "0.03"], ["41–57", "149 (32.89)", "83 (38.07)", "66 (28.09)", ""], ["58–78", "304 (67.11)", "135 (61.93)", "169 (71.91)", ""], ["Race", "", "", "", "0.157"], ["Asian", "13 (2.87)", "8 (3.67)", "5 (2.13)", ""], ["Black", "51 (11.26)", "31 (14.22)", "20 (8.51)", ""], ["White", "376 (82.80)", "174 (79.82)", "202 (85.96)", ""], ["Unknown", "13 (2.87)", "5 (2.29)", "8 (3.40)", ""], ["Gleason Score", "", "", "", "< 0.001"], ["< 8", "266 (58.72)", "150 (68.81)", "116 (49.36)", ""], ["≥ 8", "187 (41.28)", "68 (31.19)", "119 (50.64)", ""], ["Pathologic T stage", "", "", "", "0.004"], ["pT2", "178 (39.29)", "102 (46.79)", "76 (32.34)", ""], ["pT3", "264 (58.28)", "113 (51.83)", "151 (64.26)", ""], ["pT4", "11 (2.43)", "3 (1.38)", "8 (3.40)", ""], ["Pathologic N stage", "", "", "", "0.008"], ["pN0", "319 (70.64)", "156 (71.56)", "163 (69.36)", ""], ["pN1", "73 (16.14)", "25 (11.47)", "48 (20.43)", ""], ["Unknown", "61 (13.46)", "37 (16.97)", "24 (10.21)", ""], ["Seminal Vesicle Invasion", "", "", "", "< 0.001"], ["NO", "321 (70.86)", "173 (79.36)", "148 (62.98)", ""], ["YES", "132 (29.14)", "45 (20.64)", "87 (37.02)", ""], ["Residual Tumor", "", "", "", "0.001"], ["NO", "286 (63.12)", "155 (71.10)", "131 (55.74)", ""], ["YES", "141 (31.06)", "50 (22.94)", "91 (38.72)", ""], ["Unknown", "26 (5.74)", "13 (5.96)", "13 (5.53)", ""], ["BCR status", "", "", "", "< 0.001"], ["NO", "355 (78.37)", "189 (86.70)", "166 (70.64)", ""], ["YES", "98 (21.63)", "29 (13.30)", "69 (29.36)", ""], ["PFI status", "", "", "", "0.002"], ["NO", "365 (80.57)", "189 (86.70)", "176 (74.89)", ""], ["YES", "88 (19.43)", "29 (13.30)", "59 (25.11)", ""]], "row_count": 35, "column_count": 5, "numeric_cells": 89, "header_rows": 1, "locator": "section[23]/table-wrap[1]#t0001"}}, {"id": "asset:table:pmid:40417419:2", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:40b23700405510e4432cc5f48ccc97ff01727c77942157b2f8ff14bdadbd2001", "bytes": 2941, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[23]/table-wrap[2]#t0002", "version": null, "note": "Comparisons of Characteristics Between Prostate Cancer Patients with High TSR and Those with Low TSR in the LUSH Cohort", "structure": {"pmcid": "PMC12103176", "section_index": 23, "section_title": "TSR Evaluation in TCGA and LUSH Cohort", "row_count": 56, "column_count": 5}, "table": {"label": "Table 2", "caption": "Comparisons of Characteristics Between Prostate Cancer Patients with High TSR and Those with Low TSR in the LUSH Cohort", "rows": [["Characteristic", "Overall (%)", "Low TSR (%)", "High TSR (%)", "P Valuea"], ["Sample", "320 (100)", "168 (52.50)", "152 (47.50)", ""], ["Age, median (IQR), year", "68 (64, 73)", "68 (64, 71)", "69 (64, 74)", "0.12"], ["Age, year", "", "", "", "0.045"], ["43–69", "188 (58.75)", "108 (64.29)", "80 (52.63)", ""], ["70–83", "132 (41.25)", "60 (35.71)", "72 (47.37)", ""], ["BMI", "", "", "", "0.626"], ["18–23", "134 (41.88)", "73 (43.45)", "61 (40.13)", ""], ["24–35", "186 (58.13)", "95 (56.55)", "91 (59.87)", ""], ["Blood Group", "", "", "", "0.237"], ["A", "87 (27.19)", "48 (28.57)", "39 (25.66)", ""], ["B", "95 (29.69)", "43 (25.60)", "52 (34.21)", ""], ["AB", "29 (9.06)", "19 (11.31)", "10 (6.58)", ""], ["O", "109 (34.06)", "58 (34.52)", "51 (33.55)", ""], ["Gleason Score", "", "", "", "< 0.001"], ["< 8", "150 (46.88)", "95 (56.55)", "55 (36.18)", ""], ["≥ 8", "170 (53.12)", "73 (43.45)", "97 (63.82)", ""], ["Ki67", "", "", "", "0.344"], ["< 0.05", "76 (23.75)", "44 (26.19)", "32 (21.05)", ""], ["≥ 0.05", "244 (76.25)", "124 (73.81)", "120 (78.95)", ""], ["Seminal Vesicle Invasion", "", "", "", "0.04"], ["NO", "227 (70.94)", "128 (76.19)", "99 (65.13)", ""], ["YES", "93 (29.06)", "40 (23.81)", "53 (34.87)", ""], ["FPSA", "", "", "", "0.021"], ["< 1.9", "203 (63.44)", "117 (69.64)", "86 (56.58)", ""], ["≥ 1.9", "117 (36.56)", "51 (30.36)", "66 (43.42)", ""], ["TPSA", "", "", "", "0.002"], ["< 15.5", "182 (56.88)", "110 (65.48)", "72 (34.52)", ""], ["≥ 15.5", "138 (43.12)", "58 (47.37)", "80 (52.63)", ""], ["WBC count", "", "", "", "1"], ["< 8.9", "257 (80.31)", "135 (80.36)", "122 (80.26)", ""], ["≥ 8.9", "63 (19.69)", "33 (19.64)", "30 (19.74)", ""], ["RBC count", "", "", "", "0.687"], ["< 3.45", "35 (10.94)", "20 (11.90)", "15 (9.87)", ""], ["≥ 3.45", "285 (89.06)", "148 (88.10)", "137 (90.13)", ""], ["Microscopic Pyuria", "", "", "", "0.713"], ["Negative", "124 (38.75)", "63 (37.50)", "61 (40.13)", ""], ["Positive", "196 (61.25)", "105 (62.50)", "91 (59.87)", ""], ["Microscopic Hematuria", "", "", "", "1"], ["Negative", "114 (35.62)", "60 (35.71)", "54 (35.53)", ""], ["Positive", "206 (64.38)", "108 (64.29)", "98 (64.47)", ""], ["ELR", "", "", "", "0.366"], ["< 0.034", "80 (25.00)", "38 (22.62)", "42 (27.63)", ""], ["≥ 0.034", "240 (75.00)", "130 (77.38)", "110 (72.37)", ""], ["BLR", "", "", "", "0.964"], ["< 0.017", "148 (46.25)", "77 (45.83)", "71 (46.71)", ""], ["≥ 0.017", "172 (53.75)", "91 (54.17)", "81 (53.29)", ""], ["NLR", "", "", "", "0.459"], ["< 3.197", "216 (67.50)", "117 (69.64)", "99 (65.13)", ""], ["≥ 3.197", "104 (32.50)", "51 (30.36)", "53 (34.87)", ""], ["MLR", "", "", "", "0.36"], ["< 0.259", "138 (43.12)", "77 (45.83)", "61 (40.13)", ""], ["≥ 0.259", "182 (56.88)", "91 (54.17)", "91 (59.87)", ""], ["BCR status", "", "", "", "< 0.001"], ["NO", "171 (53.44)", "113 (67.26)", "58 (38.16)", ""], ["YES", "149 (46.56)", "55 (32.74)", "94 (61.84)", ""]], "row_count": 56, "column_count": 5, "numeric_cells": 157, "header_rows": 1, "locator": "section[23]/table-wrap[2]#t0002"}}], "gaps": ["asset:source:pmid:40417419 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:40417419", "asset:table:pmid:40417419:1", "asset:table:pmid:40417419:2"], "steps": ["read_published_estimate"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": ["xml"], "capabilities": [], "data_gaps": ["source:pmid:40417419"]}, "gaps": ["corpus_record_absent"]}, "review": {"state": "partial", "machine_critique": {"status": "blocked", "providers": [], "target_providers": [], "agreement": false, "disagreements": [], "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": [{"provider": "minimax", "model": null, "reason": "HTTP Error 429: Too Many Requests", "raw_response": null}, {"provider": "minimax_alt", "model": null, "reason": "HTTP Error 429: Too Many Requests", "raw_response": null}, {"provider": "minimax", "model": null, "reason": "HTTP Error 429: Too Many Requests", "raw_response": null}, {"provider": "minimax_alt", "model": null, "reason": "HTTP Error 429: Too Many Requests", "raw_response": null}]}}, {"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", "review.machine_critique.providers"]}, "execution": {"state": "absent", "status": "not_run", "mode": null, "runs": [], "gaps": ["execution.not_run"]}, "provenance": {"entities": [{"id": "package:43f853aee2ca93ebd2f903b4ac2496ba58e8c25f43074e1728244d7c204bfaba", "type": "sep_package", "label": "SEP v1 package for pmid:40417419"}], "activities": [{"id": "activity:conversion:pmid:40417419", "type": "conversion", "used": ["package:43f853aee2ca93ebd2f903b4ac2496ba58e8c25f43074e1728244d7c204bfaba"], "agent": "agent:corpus-assay-engine"}], "agents": [{"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:40417419", "parent_hash": "sha256:63e047a84bc7569231860ffb81faebc1e97b8b6aedc7fb874f5d6470fbcd82ef", "fork_of": null, "generation": 2}, "gaps": ["abstract", "asset:source:pmid:40417419 not verified", "authors", "capability", "corpus_record_absent", "execution.not_run", "method", "review.human_critique", "review.machine_critique.blocked", "review.machine_critique.providers", "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:40417419' does not resolve to a declared asset", "targets"]}