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

pmid:32158466

Establishment of a Prognostic Model Using Immune-Related Genes in Patients With Hepatocellular Carcinoma.

Wen-Jie Wang · Han Wang · Ting-Yan Hua · Wei Song · Jie Zhu · Jing-Jing Wang · Yue-Qing Huang · Zhi-Liang Ding

Frontiers in genetics · 2020 doi:10.3389/fgene.2020.00055

Paper

complete

Experiment

complete

Data

partial

Analysis

partial

Execution

absent

Execution evidence has not yet been added to this .science file. Explore its methods, data and open questions to plan the next step.
Record details sci_version · id · kind · revision · content_hash · schema · created_at · updated_at · generator
id
pmid:32158466
kind
science-record
content_hash
sha256:d93fa398727d8063f41ac303a46b1c6d839ad8e1994f3e90e7a16b9d93f7d8e4
schema
https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json
created_at
2026-11-01T15:40:57Z
updated_at
2026-11-01T22:44:38Z
generator object · 2 fields
name
corpus-assay-engine
run_id
reading-sci-2026-11-01
paper object · 10 fields
state
complete
title
Establishment of a Prognostic Model Using Immune-Related Genes in Patients With Hepatocellular Carcinoma.
doi
10.3389/fgene.2020.00055
pmid
32158466
authors array · 8 items
[0]
Wen-Jie Wang
[1]
Han Wang
[2]
Ting-Yan Hua
[3]
Wei Song
[4]
Jie Zhu
[5]
Jing-Jing Wang
[6]
Yue-Qing Huang
[7]
Zhi-Liang Ding
journal
Frontiers in genetics
year
2020
abstract
Hepatocellular carcinoma (HCC) is one of the most prevalent neoplasms worldwide, particularly in China. Immune-related genes (IRGs) and immune infiltrating lymphocytes play specific roles in tumor growth. Considering how important immunotherapy has become for HCC treatment in the past decade, our objective was to establish a prognostic model by screening survival-related IRGs in patients with HCC. Using edgeR, we identified differentially expressed IRGs (DEIRGs), DEmiRNAs, and DElncRNAs. Functional enrichment analysis of DEIRGs was performed to investigate the biological functions of IRGs via gene ontology annotation and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analyses. Protein-protein interaction and competing endogenous RNA networks were established using Cytoscape. Survival-associated IRGs were selected via univariate COX regression analysis, a The Cancer Genome Atlas (TCGA) prognostic model and GSE76427 validation model were developed using multivariate COX regression analysis test by AIC (Akaike Information Criterion). We identified 116 DEIRGs in patients with HCC; the "cytokine-cytokine receptor interaction" pathway was found to be the most enriched pathway. Via the prognostic model helped us classify patients into high- and low-risk score groups based on overall survival (OS); high risk score was associated with worse OS, and a positive correlation was observed between the prognostic model and immune cell infiltration. To summarize, we established a prognostic model using survival-related IRGs that provides sufficient information for prognosis prediction and immunotherapy of patients with HCC.
claims array · 2 items
[0] object · 6 fields
id
claim-method
statement
Survival curves were generated using the Kaplan-Meier method, and the log-rank test was used to compare differences between the two groups.
kind
methodological
target
null
evidence array · 1 item
[0] object · 3 fields
asset
source:pmid:32158466
locator
sections[12] "Statistical Analysis" paragraph 2
quote
Survival curves were generated using the Kaplan-Meier method, and the log-rank test was used to compare differences between the two groups.
state
complete
[1] object · 6 fields
id
claim-data-access
statement
The datasets analysed for this study were obtained from TCGA data portal (https://portal.gdc.cancer.gov/) and GEO data portal (https://www.ncbi.nlm.nih.gov/geo/).
kind
methodological
target
null
evidence array · 1 item
[0] object · 3 fields
asset
source:pmid:32158466
locator
sections[24] "Data Availability Statement" paragraph 2
quote
The datasets analysed for this study were obtained from TCGA data portal (https://portal.gdc.cancer.gov/) and GEO data portal (https://www.ncbi.nlm.nih.gov/geo/).
state
complete
gaps array · 0 items
experiment object · 8 fields
state
complete
objective
null
steps array · 3 items
[0] object · 13 fields
id
read_published_estimate
order
1
name
Read the published estimate from the source
kind
other
state
complete
blocked_on
null
description
The claim, method and evidence span published with the source article.
parameters object · 0 fields
inputs array · 1 item
[0]
source:pmid:32158466
outputs array · 1 item
[0]
the published estimate and its evidence
instruments array · 0 items
reagents array · 0 items
[1] object · 13 fields
id
obtain_source_data
order
2
name
Obtain the source data from the named repository
kind
data-preparation
state
complete
blocked_on
null
description
The GEO series accession resolves and its sample accessions are listed. This lane did not download the dataset or read its licence.
parameters object · 0 fields
inputs array · 1 item
[0]
data:geo:GSE76427
outputs array · 1 item
[0]
the source data with its repository provenance
instruments array · 0 items
reagents array · 0 items
[2] object · 13 fields
id
run_analysis
order
3
name
Run the published analysis
kind
analysis
state
complete
blocked_on
null
description
Apply the paper's statistical method to the resolved series and compare the result with the published target.
parameters object · 0 fields
inputs array · 1 item
[0]
data:geo:GSE76427
outputs array · 1 item
[0]
the replicated result and its comparison
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 · 0 items
data object · 3 fields
state
partial
assets array · 5 items
[0] object · 15 fields
id
source:pmid:32158466
role
manuscript
format
xml
media_type
application/xml
uri
https://doi.org/10.3389/fgene.2020.00055
sha256
sha256:5ca7d968fc72f15367368e6ec4582b020d4f8d600c59927b922bc023e8726465
bytes
32848
access
open
state
resolved
reader
null
reader_status
reader_required
identifier
10.3389/fgene.2020.00055
version
null
note
Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.
structure object · 4 fields
pmcid
PMC7052339
source
europe_pmc_fulltext
coverage
whole_body_without_references
text_hash_scope
rendered_section_body
[1] object · 15 fields
id
data:geo:GSE76427
role
raw
format
geo-series
media_type
application/vnd.ncbi.geo-series+json
uri
https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE76427
sha256
null
bytes
null
access
open
state
resolved
reader
null
reader_status
reader_required
identifier
GSE76427
version
null
note
The datasets analysed for this study were obtained from TCGA data portal (https://portal.gdc.cancer.gov/) and GEO data portal (https://www.ncbi.nlm.nih.gov/geo/).
structure object · 15 fields
repository
GEO
access_route
GEO accession URL
access_statement_verbatim
The datasets analysed for this study were obtained from TCGA data portal (https://portal.gdc.cancer.gov/) and GEO data portal (https://www.ncbi.nlm.nih.gov/geo/).
access_statement_kind
data_availability_statement
sample_accessions array · 167 items
[0]
GSM2011285
[1]
GSM2011286
[2]
GSM2011287
[3]
GSM2011288
[4]
GSM2011289
[5]
GSM2011290
[6]
GSM2011291
[7]
GSM2011292
[8]
GSM2011293
[9]
GSM2011294
[10]
GSM2011295
[11]
GSM2011296
[12]
GSM2011297
[13]
GSM2011298
[14]
GSM2011299
[15]
GSM2011300
[16]
GSM2011301
[17]
GSM2011302
[18]
GSM2011303
[19]
GSM2011304
[20]
GSM2011305
[21]
GSM2011306
[22]
GSM2011307
[23]
GSM2011308
[24]
GSM2011309
[25]
GSM2011310
[26]
GSM2011311
[27]
GSM2011312
[28]
GSM2011313
[29]
GSM2011314
[30]
GSM2011315
[31]
GSM2011316
[32]
GSM2011317
[33]
GSM2011318
[34]
GSM2011319
[35]
GSM2011320
[36]
GSM2011321
[37]
GSM2011322
[38]
GSM2011323
[39]
GSM2011324
[40]
GSM2011325
[41]
GSM2011326
[42]
GSM2011327
[43]
GSM2011328
[44]
GSM2011329
[45]
GSM2011330
[46]
GSM2011331
[47]
GSM2011332
[48]
GSM2011333
[49]
GSM2011334
[50]
GSM2011335
[51]
GSM2011336
[52]
GSM2011337
[53]
GSM2011338
[54]
GSM2011339
[55]
GSM2011340
[56]
GSM2011341
[57]
GSM2011342
[58]
GSM2011343
[59]
GSM2011344
[60]
GSM2011345
[61]
GSM2011346
[62]
GSM2011347
[63]
GSM2011348
[64]
GSM2011349
[65]
GSM2011350
[66]
GSM2011351
[67]
GSM2011352
[68]
GSM2011353
[69]
GSM2011354
[70]
GSM2011355
[71]
GSM2011356
[72]
GSM2011357
[73]
GSM2011358
[74]
GSM2011359
[75]
GSM2011360
[76]
GSM2011361
[77]
GSM2011362
[78]
GSM2011363
[79]
GSM2011364
[80]
GSM2011365
[81]
GSM2011366
[82]
GSM2011367
[83]
GSM2011368
[84]
GSM2011369
[85]
GSM2011370
[86]
GSM2011371
[87]
GSM2011372
[88]
GSM2011373
[89]
GSM2011374
[90]
GSM2011375
[91]
GSM2011376
[92]
GSM2011377
[93]
GSM2011378
[94]
GSM2011379
[95]
GSM2011380
[96]
GSM2011381
[97]
GSM2011382
[98]
GSM2011383
[99]
GSM2011384
[100]
GSM2011385
[101]
GSM2011386
[102]
GSM2011387
[103]
GSM2011388
[104]
GSM2011389
[105]
GSM2011390
[106]
GSM2011391
[107]
GSM2011392
[108]
GSM2011393
[109]
GSM2011394
[110]
GSM2011395
[111]
GSM2011396
[112]
GSM2011397
[113]
GSM2011398
[114]
GSM2011399
[115]
GSM2011400
[116]
GSM2011401
[117]
GSM2011402
[118]
GSM2011403
[119]
GSM2011404
[120]
GSM2011405
[121]
GSM2011406
[122]
GSM2011407
[123]
GSM2011408
[124]
GSM2011409
[125]
GSM2011410
[126]
GSM2011411
[127]
GSM2011412
[128]
GSM2011413
[129]
GSM2011414
[130]
GSM2011415
[131]
GSM2011416
[132]
GSM2011417
[133]
GSM2011418
[134]
GSM2011419
[135]
GSM2011420
[136]
GSM2011421
[137]
GSM2011422
[138]
GSM2011423
[139]
GSM2011424
[140]
GSM2011425
[141]
GSM2011426
[142]
GSM2011427
[143]
GSM2011428
[144]
GSM2011429
[145]
GSM2011430
[146]
GSM2011431
[147]
GSM2011432
[148]
GSM2011433
[149]
GSM2011434
[150]
GSM2011435
[151]
GSM2011436
[152]
GSM2011437
[153]
GSM2011438
[154]
GSM2011439
[155]
GSM2011440
[156]
GSM2011441
[157]
GSM2011442
[158]
GSM2011443
[159]
GSM2011444
[160]
GSM2011445
[161]
GSM2011446
[162]
GSM2011447
[163]
GSM2011448
[164]
GSM2011449
[165]
GSM2011450
[166]
GSM2011451
sample_count
167
group_sizes
null
group_sizes_basis
null
platform
10558
taxon
Homo sapiens
title
Microarray expression data for tumor and adjacent non-tumor tissues from hepatocellular carcinoma patients
resolution_checked_at
2026-11-01T15:39:55Z
resolution_check
identifier_resolution_only_no_download_no_licence_read
downloaded
false
licence_read
false
[2] object · 16 fields
id
asset:table:pmid:32158466:1
role
table
format
jats-table
media_type
application/vnd.jats.table+json
uri
null
sha256
sha256:7217c4d36371392a30b79e62ffaec443fde28866cbaa0fa21c626e6eeb290dba
bytes
887
access
open
state
verified
reader
read_table
reader_status
available
identifier
section[4]/table-wrap[1]#T1
version
null
note
The clinical features of TCGA hepatocellular carcinoma patients.
structure object · 5 fields
pmcid
PMC7052339
section_index
4
section_title
Data Acquisition and Processing
row_count
25
column_count
3
table object · 8 fields
label
Table 1
caption
The clinical features of TCGA hepatocellular carcinoma patients.
rows array · 25 items
[0] array · 1 item
[0]
Clinical features
[1] array · 3 items
[0]
Age (years)
[1]
media
[2]
73
[2] array · 3 items
[0]
[1]
Rage
[2]
18-90
[3] array · 3 items
[0]
[1]
Numbers of patients (n=374)
[2]
Numbers of patients (%)
[4] array · 3 items
[0]
Gender
[1]
Female
[2]
120 (32.09)
[5] array · 3 items
[0]
[1]
Male
[2]
254 (67.91)
[6] array · 3 items
[0]
Grade
[1]
G1
[2]
55 (14.71)
[7] array · 3 items
[0]
[1]
G2
[2]
179 (47.86)
[8] array · 3 items
[0]
[1]
G3
[2]
136 (36.36)
[9] array · 3 items
[0]
[1]
unknown
[2]
4 (1.07)
[10] array · 3 items
[0]
T stage
[1]
T1
[2]
185 (49.47)
[11] array · 3 items
[0]
[1]
T2
[2]
94 (24.13)
[12] array · 3 items
[0]
[1]
T3
[2]
81 (21.66)
[13] array · 3 items
[0]
[1]
T4
[2]
13 (4.74)
[14] array · 3 items
[0]
N stage
[1]
0
[2]
257 (68.72)
[15] array · 3 items
[0]
[1]
1
[2]
5 (1.37)
[16] array · 3 items
[0]
[1]
unknown
[2]
113 (29.91)
[17] array · 3 items
[0]
M stage
[1]
0
[2]
364 (97.32)
[18] array · 3 items
[0]
[1]
1
[2]
5 (1.34)
[19] array · 3 items
[0]
[1]
unknown
[2]
5 (1.34)
[20] array · 3 items
[0]
AJCC stage
[1]
I
[2]
175 (46.78)
[21] array · 3 items
[0]
[1]
II
[2]
86 (25.27)
[22] array · 3 items
[0]
[1]
III
[2]
86 (25.27)
[23] array · 3 items
[0]
[1]
IV
[2]
5 (1.34)
[24] array · 3 items
[0]
[1]
unknown
[2]
5 (1.34)
locator
section[4]/table-wrap[1]#T1
[3] object · 16 fields
id
asset:table:pmid:32158466:2
role
table
format
jats-table
media_type
application/vnd.jats.table+json
uri
null
sha256
sha256:cf21b691b474672e671ce9625890207a884a9538652f9fb9282260101445f2d8
bytes
876
access
open
state
verified
reader
read_table
reader_status
available
identifier
section[11]/table-wrap[1]#T2
version
null
note
Primer sequences for qRT-PCR.
structure object · 5 fields
pmcid
PMC7052339
section_index
11
section_title
Quantitative Real-Time PCR (qRT-PCR)
row_count
17
column_count
2
table object · 8 fields
label
Table 2
caption
Primer sequences for qRT-PCR.
rows array · 17 items
[0] array · 2 items
[0]
Primer
[1]
Seqence 5'-3'
[1] array · 2 items
[0]
IL11 forward
[1]
GTGGCCAAGATACAGCTGTCGC
[2] array · 2 items
[0]
IL11 reverse
[1]
GGTAGGACAGTAGGTCCGCTC
[3] array · 2 items
[0]
IL17 forward
[1]
AGA GAT ATC CCT CTG TGATC
[4] array · 2 items
[0]
IL17 reverse
[1]
TAC CCC AAA GTT ATC TCA GG
[5] array · 2 items
[0]
SPP1 forward
[1]
TCACCTGTGCCATACCAGTT
[6] array · 2 items
[0]
SPP1 reverse
[1]
TGTGGTCATGGCTTTCGTTG
[7] array · 2 items
[0]
MAPT forward
[1]
AAGATCGGCTCCACTGAGAA
[8] array · 2 items
[0]
MAPT reverse
[1]
ATGAGCCACACTTGGAGGTC
[9] array · 2 items
[0]
BIRC5 forward
[1]
CGCATCTCTACATTCAAG
[10] array · 2 items
[0]
BIRC5 reverse
[1]
ATGTTCCTCTCTCGTGAT
[11] array · 2 items
[0]
miR-204 forward
[1]
ACACTCCAGCTGGGTTCCCTTTGTCATCC
[12] array · 2 items
[0]
miR-204 reverse
[1]
CTCAACTGGTGTCGTGGA
[13] array · 2 items
[0]
SNHG12 forward
[1]
TCTGGTGATCGAGGACTTCC
[14] array · 2 items
[0]
SNHG12 reverse
[1]
ACCTCCTCAGTATCACACACT
[15] array · 2 items
[0]
GAPDH forward
[1]
CAACGAATTTGGCTACAGCA
[16] array · 2 items
[0]
GAPDH reverse
[1]
AGGGGTCTACATGGCAACTG
locator
section[11]/table-wrap[1]#T2
[4] object · 16 fields
id
asset:table:pmid:32158466:3
role
table
format
jats-table
media_type
application/vnd.jats.table+json
uri
null
sha256
sha256:4a1ffc96dfbfaa3f487d0b3f1801829ac910f9f9549b530ece730583ddef8267
bytes
825
access
open
state
verified
reader
read_table
reader_status
available
identifier
section[20]/table-wrap[1]#T3
version
null
note
Univariate and Multivariate Cox regression analysis of survival associated IRGS.
structure object · 5 fields
pmcid
PMC7052339
section_index
20
section_title
Clinical Outcome of Patients With HCC Using the IRGPM
row_count
9
column_count
5
table object · 8 fields
label
Table 3
caption
Univariate and Multivariate Cox regression analysis of survival associated IRGS.
rows array · 9 items
[0] array · 2 items
[0]
Risk Factors
[1]
Overall Survival (OS)
[1] array · 3 items
[0]
[1]
Univariate analysis
[2]
Multivariate analysis
[2] array · 5 items
[0]
[1]
HR (95% CI)
[2]
P value
[3]
OR (95% CI)
[4]
P value
[3] array · 5 items
[0]
Age
[1]
1.002(0.986−1.017
[2]
0.824
[3]
1.006(0.990−1.022)
[4]
0.484
[4] array · 5 items
[0]
gender
[1]
0.886(0.578−1.358)
[2]
0.580
[3]
1.110(0.713−1.729)
[4]
0.643
[5] array · 5 items
[0]
grade
[1]
1.173(0.886−1.551)
[2]
0.265
[3]
1.125(0.827−1.531)
[4]
0.452
[6] array · 5 items
[0]
AJCC stage
[1]
1.866(1.488−2.341)
[2]
<0.001**
[3]
1.247(0.461−3.378)
[4]
0.664
[7] array · 5 items
[0]
T stage
[1]
1.826(1.472−2.265)
[2]
<0.001**
[3]
1.408(0.541−3.666)
[4]
0.483
[8] array · 5 items
[0]
Risk score
[1]
2.238 (1.293-3.872)
[2]
<0.001**
[3]
2.071 (1.183-3.625)
[4]
<0.001**
locator
section[20]/table-wrap[1]#T3
gaps array · 2 items
[0]
asset:data:geo:GSE76427 not downloaded
[1]
asset:data:geo:GSE76427 licence not read
analysis object · 4 fields
state
partial
methods array · 8 items
[0] object · 10 fields
id
method-1
family
survival_analysis
specific
kaplan_meier
label
Survival analysis
dsl_operations array · 1 item
[0]
survival_km
missing_operations array · 0 items
parameters object · 0 fields
data_shapes array · 1 item
[0]
time_to_event_with_censoring
evidence object · 3 fields
score
1
band
verbatim
quote
Survival curves were generated using the Kaplan-Meier method, and the log-rank test was used to compare differences between the two groups.
[1] object · 10 fields
id
method-2
family
group_comparison
specific
student_t_test
label
Group comparison
dsl_operations array · 0 items
missing_operations array · 1 item
[0]
student_t
expressible
false
parameters object · 0 fields
data_shapes array · 1 item
[0]
two_or_more_groups_continuous
evidence object · 3 fields
score
0.8
band
high
quote
Student's t-test
[2] object · 10 fields
id
method-3
family
group_comparison
specific
anova
label
Group comparison
dsl_operations array · 4 items
[0]
group_summary
[1]
welch_t
[2]
bootstrap_mean_difference
[3]
group_comparison_anova
missing_operations array · 0 items
parameters object · 0 fields
data_shapes array · 1 item
[0]
two_or_more_groups_continuous
evidence object · 3 fields
score
0.8
band
high
quote
analysis of variance
[3] object · 10 fields
id
method-4
family
survival_analysis
specific
cox_proportional_hazards
label
Survival analysis
dsl_operations array · 1 item
[0]
cox_ph
missing_operations array · 0 items
parameters object · 0 fields
data_shapes array · 1 item
[0]
time_to_event_with_censoring
evidence object · 3 fields
score
0.7
band
medium
quote
COX regression
[4] object · 10 fields
id
method-5
family
survival_analysis
specific
log_rank_test
label
Survival analysis
dsl_operations array · 1 item
[0]
logrank_test
missing_operations array · 0 items
parameters object · 0 fields
data_shapes array · 1 item
[0]
time_to_event_with_censoring
evidence object · 3 fields
score
0.8
band
high
quote
log-rank
[5] object · 10 fields
id
method-6
family
differential_expression
specific
edger
label
Differential expression analysis
dsl_operations array · 3 items
[0]
normalise_counts
[1]
differential_expression_fit
[2]
fdr_bh
missing_operations array · 0 items
parameters object · 0 fields
data_shapes array · 1 item
[0]
count_matrix_with_condition
evidence object · 3 fields
score
0.7
band
medium
quote
edgeR
[6] object · 10 fields
id
method-7
family
network_analysis
specific
ppi_network
label
Network / pathway analysis
dsl_operations array · 3 items
[0]
build_graph
[1]
centrality_scores
[2]
pathway_enrich
missing_operations array · 0 items
parameters object · 0 fields
data_shapes array · 1 item
[0]
edge_list
evidence object · 3 fields
score
0.7
band
medium
quote
Protein-protein interaction
[7] object · 10 fields
id
method-8
family
diagnostic_evaluation
specific
roc
label
Diagnostic test evaluation
dsl_operations array · 6 items
[0]
confusion_counts
[1]
roc_curve
[2]
sensitivity_specificity
[3]
solve_confusion_matrix
[4]
classification_metrics
[5]
published_precision_envelope
missing_operations array · 0 items
parameters object · 0 fields
data_shapes array · 1 item
[0]
reference_standard_and_test
evidence object · 3 fields
score
0.8
band
high
quote
ROC curve
targets array · 0 items
gaps array · 1 item
[0]
method.reader_differs_from_extractor
capability object · 3 fields
state
complete
requirements array · 1 item
[0] object · 6 fields
capability_id
capability:computational_analysis
label
Computational analysis platform
assay_families array · 9 items
[0]
meta_analysis
[1]
machine_learning
[2]
survival_analysis
[3]
statistical_regression
[4]
pca
[5]
molecular_docking
[6]
network_analysis
[7]
differential_expression
[8]
gwas
candidate
Automated Assays Laravel application and simulated adapters
gaps array · 0 items
readiness object · 8 fields
state
complete
tier
R1
blocked_on
nothing:replicable_now
axes object · 3 fields
method object · 5 fields
tier
R1
expressible
true
required_operations array · 1 item
[0]
survival_km
missing_operations array · 0 items
basis
The paper names the method it used and the corpus's method extractor maps it onto the DSL catalogue: kaplan_meier.
capability object · 4 fields
tier
R1
capability_id
capability:computational_analysis
availability_state
owned
basis
The computational analysis is owned. The physical bench the paper used is not, so a physical validation cannot be run here.
data object · 6 fields
tier
R1
reachable
true
accessions array · 1 item
[0]
GSE76427
resolved_accessions array · 1 item
[0]
GSE76427
statements array · 1 item
[0]
The datasets analysed for this study were obtained from TCGA data portal (https://portal.gdc.cancer.gov/) and GEO data portal (https://www.ncbi.nlm.nih.gov/geo/).
basis
The paper names GSE76427 in Gene Expression Omnibus (GEO) data portal and the accession resolves in the repository. No dataset was downloaded and no licence was read.
can_run object · 3 fields
dsl_operations array · 1 item
[0]
survival_km
assets array · 5 items
[0]
source:pmid:32158466
[1]
data:geo:GSE76427
[2]
asset:table:pmid:32158466:1
[3]
asset:table:pmid:32158466:2
[4]
asset:table:pmid:32158466:3
steps array · 1 item
[0]
run_analysis
must_build object · 5 fields
dsl_operations array · 0 items
converters array · 0 items
readers array · 0 items
capabilities array · 0 items
data_gaps array · 1 item
[0]
data:geo:GSE76427
gaps array · 0 items
review object · 5 fields
state
partial
machine_critique object · 5 fields
kind
extraction_review
reader object · 5 fields
model
MiniMax-M3.1-Flash
provider
minimax
provider_family
minimax
read_at
2026-10-31T18:18:38Z
independence
single_reader
evidence_check object · 2 fields
method
verbatim
availability
verbatim
calls
3
usage object · 3 fields
prompt_tokens
25713
completion_tokens
1069
cached_tokens
776
stages array · 1 item
[0] object · 4 fields
id
extraction
state
complete
reader
MiniMax-M3.1-Flash
provider
minimax
gaps array · 3 items
[0]
review.independent_reader
[1]
review.machine_critique
[2]
review.human_critique
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 · 3 items
[0] object · 3 fields
id
pmid:32158466
type
paper
label
pmid:32158466
[1] object · 3 fields
id
source:pmid:32158466
type
manuscript
label
PMID 32158466 full text
[2] object · 3 fields
id
data:geo:GSE76427
type
dataset
label
GEO GSE76427
activities array · 3 items
[0] object · 4 fields
id
activity-reading-sci-2026-11-01
type
classification
used array · 3 items
[0] object · 3 fields
id
pmid:32158466
type
paper
label
pmid:32158466
[1] object · 3 fields
id
source:pmid:32158466
type
manuscript
label
PMID 32158466 full text
[2] object · 3 fields
id
data:geo:GSE76427
type
dataset
label
GEO GSE76427
agent
agent:corpus-assay-engine
[1] object · 4 fields
id
activity-read-32158466
type
extraction
used array · 1 item
[0]
source:pmid:32158466
agent
agent:minimax-reader
[2] object · 4 fields
id
activity-resolve-GSE76427
type
accession_resolution
used array · 1 item
[0]
data:geo:GSE76427
agent
agent:corpus-assay-engine
agents array · 2 items
[0] object · 3 fields
id
agent:corpus-assay-engine
type
software
label
Corpus assay engine
[1] object · 3 fields
id
agent:minimax-reader
type
software
label
MiniMax literature reader
source_run_id
reading-sci-2026-11-01
dsl_catalogue_fingerprint
343fb30756ba6ec3
capability_table_fingerprint
2cb3e42f047d2ecf
snapshot_id
ba34b49490d9bfaf
lineage object · 4 fields
parent_id
pmid:32158466
parent_hash
sha256:c72a87ad6d3fe71206a5f78ed9f8a8c7984bb70433dde77d02598be50a9fc4b7
fork_of
null
gaps array · 7 items
[0]
asset:data:geo:GSE76427 licence not read
[1]
asset:data:geo:GSE76427 not downloaded
[2]
execution.not_run
[3]
method.reader_differs_from_extractor
[4]
review.human_critique
[5]
review.independent_reader
[6]
review.machine_critique
assays array · 1 item
[0] object · 11 fields
role
analysis
definition_id
survival_analysis
definition_version
f2132e96ae6c7a4e
required_operations array · 1 item
[0]
survival_km
support_state
supported
source_hashes object · 1 field
dsl_catalogue
f2132e96ae6c7a4e
evidence array · 1 item
[0]
Survival curves were generated using the Kaplan-Meier method, and the log-rank test was used to compare differences between the two groups.
order_basis
analysis_only
id
assay:1
Complete file
{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:32158466", "kind": "science-record", "revision": 8, "content_hash": "sha256:d93fa398727d8063f41ac303a46b1c6d839ad8e1994f3e90e7a16b9d93f7d8e4", "created_at": "2026-11-01T15:40:57Z", "updated_at": "2026-11-01T22:44:38Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Establishment of a Prognostic Model Using Immune-Related Genes in Patients With Hepatocellular Carcinoma.", "doi": "10.3389/fgene.2020.00055", "pmid": "32158466", "authors": ["Wen-Jie Wang", "Han Wang", "Ting-Yan Hua", "Wei Song", "Jie Zhu", "Jing-Jing Wang", "Yue-Qing Huang", "Zhi-Liang Ding"], "journal": "Frontiers in genetics", "year": 2020, "abstract": "Hepatocellular carcinoma (HCC) is one of the most prevalent neoplasms worldwide, particularly in China. Immune-related genes (IRGs) and immune infiltrating lymphocytes play specific roles in tumor growth. Considering how important immunotherapy has become for HCC treatment in the past decade, our objective was to establish a prognostic model by screening survival-related IRGs in patients with HCC. Using edgeR, we identified differentially expressed IRGs (DEIRGs), DEmiRNAs, and DElncRNAs. Functional enrichment analysis of DEIRGs was performed to investigate the biological functions of IRGs via gene ontology annotation and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analyses. Protein-protein interaction and competing endogenous RNA networks were established using Cytoscape. Survival-associated IRGs were selected via univariate COX regression analysis, a The Cancer Genome Atlas (TCGA) prognostic model and GSE76427 validation model were developed using multivariate COX regression analysis test by AIC (Akaike Information Criterion). We identified 116 DEIRGs in patients with HCC; the \"cytokine-cytokine receptor interaction\" pathway was found to be the most enriched pathway. Via the prognostic model helped us classify patients into high- and low-risk score groups based on overall survival (OS); high risk score was associated with worse OS, and a positive correlation was observed between the prognostic model and immune cell infiltration. To summarize, we established a prognostic model using survival-related IRGs that provides sufficient information for prognosis prediction and immunotherapy of patients with HCC.", "claims": [{"id": "claim-method", "statement": "Survival curves were generated using the Kaplan-Meier method, and the log-rank test was used to compare differences between the two groups.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:32158466", "locator": "sections[12] \"Statistical Analysis\" paragraph 2", "quote": "Survival curves were generated using the Kaplan-Meier method, and the log-rank test was used to compare differences between the two groups."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The datasets analysed for this study were obtained from TCGA data portal (https://portal.gdc.cancer.gov/) and GEO data portal (https://www.ncbi.nlm.nih.gov/geo/).", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:32158466", "locator": "sections[24] \"Data Availability Statement\" paragraph 2", "quote": "The datasets analysed for this study were obtained from TCGA data portal (https://portal.gdc.cancer.gov/) and GEO data portal (https://www.ncbi.nlm.nih.gov/geo/)."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": null, "steps": [{"id": "read_published_estimate", "order": 1, "name": "Read the published estimate from the source", "kind": "other", "state": "complete", "blocked_on": null, "description": "The claim, method and evidence span published with the source article.", "duration_hours": null, "parameters": {}, "inputs": ["source:pmid:32158466"], "outputs": ["the published estimate and its evidence"], "instruments": [], "reagents": []}, {"id": "obtain_source_data", "order": 2, "name": "Obtain the source data from the named repository", "kind": "data-preparation", "state": "complete", "blocked_on": null, "description": "The GEO series accession resolves and its sample accessions are listed. This lane did not download the dataset or read its licence.", "duration_hours": null, "parameters": {}, "inputs": ["data:geo:GSE76427"], "outputs": ["the source data with its repository provenance"], "instruments": [], "reagents": []}, {"id": "run_analysis", "order": 3, "name": "Run the published analysis", "kind": "analysis", "state": "complete", "blocked_on": null, "description": "Apply the paper's statistical method to the resolved series and compare the result with the published target.", "duration_hours": null, "parameters": {}, "inputs": ["data:geo:GSE76427"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:32158466", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.3389/fgene.2020.00055", "sha256": "sha256:5ca7d968fc72f15367368e6ec4582b020d4f8d600c59927b922bc023e8726465", "bytes": 32848, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.3389/fgene.2020.00055", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC7052339", "source": "europe_pmc_fulltext", "coverage": "whole_body_without_references", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE76427", "role": "raw", "format": "geo-series", "media_type": "application/vnd.ncbi.geo-series+json", "uri": "https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE76427", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE76427", "version": null, "note": "The datasets analysed for this study were obtained from TCGA data portal (https://portal.gdc.cancer.gov/) and GEO data portal (https://www.ncbi.nlm.nih.gov/geo/).", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The datasets analysed for this study were obtained from TCGA data portal (https://portal.gdc.cancer.gov/) and GEO data portal (https://www.ncbi.nlm.nih.gov/geo/).", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM2011285", "GSM2011286", "GSM2011287", "GSM2011288", "GSM2011289", "GSM2011290", "GSM2011291", "GSM2011292", "GSM2011293", "GSM2011294", "GSM2011295", "GSM2011296", "GSM2011297", "GSM2011298", "GSM2011299", "GSM2011300", "GSM2011301", "GSM2011302", "GSM2011303", "GSM2011304", "GSM2011305", "GSM2011306", "GSM2011307", "GSM2011308", "GSM2011309", "GSM2011310", "GSM2011311", "GSM2011312", "GSM2011313", "GSM2011314", "GSM2011315", "GSM2011316", "GSM2011317", "GSM2011318", "GSM2011319", "GSM2011320", "GSM2011321", "GSM2011322", "GSM2011323", "GSM2011324", "GSM2011325", "GSM2011326", "GSM2011327", "GSM2011328", "GSM2011329", "GSM2011330", "GSM2011331", "GSM2011332", "GSM2011333", "GSM2011334", "GSM2011335", "GSM2011336", "GSM2011337", "GSM2011338", "GSM2011339", "GSM2011340", "GSM2011341", "GSM2011342", "GSM2011343", "GSM2011344", "GSM2011345", "GSM2011346", "GSM2011347", "GSM2011348", "GSM2011349", "GSM2011350", "GSM2011351", "GSM2011352", "GSM2011353", "GSM2011354", "GSM2011355", "GSM2011356", "GSM2011357", "GSM2011358", "GSM2011359", "GSM2011360", "GSM2011361", "GSM2011362", "GSM2011363", "GSM2011364", "GSM2011365", "GSM2011366", "GSM2011367", "GSM2011368", "GSM2011369", "GSM2011370", "GSM2011371", "GSM2011372", "GSM2011373", "GSM2011374", "GSM2011375", "GSM2011376", "GSM2011377", "GSM2011378", "GSM2011379", "GSM2011380", "GSM2011381", "GSM2011382", "GSM2011383", "GSM2011384", "GSM2011385", "GSM2011386", "GSM2011387", "GSM2011388", "GSM2011389", "GSM2011390", "GSM2011391", "GSM2011392", "GSM2011393", "GSM2011394", "GSM2011395", "GSM2011396", "GSM2011397", "GSM2011398", "GSM2011399", "GSM2011400", "GSM2011401", "GSM2011402", "GSM2011403", "GSM2011404", "GSM2011405", "GSM2011406", "GSM2011407", "GSM2011408", "GSM2011409", "GSM2011410", "GSM2011411", "GSM2011412", "GSM2011413", "GSM2011414", "GSM2011415", "GSM2011416", "GSM2011417", "GSM2011418", "GSM2011419", "GSM2011420", "GSM2011421", "GSM2011422", "GSM2011423", "GSM2011424", "GSM2011425", "GSM2011426", "GSM2011427", "GSM2011428", "GSM2011429", "GSM2011430", "GSM2011431", "GSM2011432", "GSM2011433", "GSM2011434", "GSM2011435", "GSM2011436", "GSM2011437", "GSM2011438", "GSM2011439", "GSM2011440", "GSM2011441", "GSM2011442", "GSM2011443", "GSM2011444", "GSM2011445", "GSM2011446", "GSM2011447", "GSM2011448", "GSM2011449", "GSM2011450", "GSM2011451"], "sample_count": 167, "group_sizes": null, "group_sizes_basis": null, "platform": "10558", "taxon": "Homo sapiens", "title": "Microarray expression data for tumor and adjacent non-tumor tissues from hepatocellular carcinoma patients", "resolution_checked_at": "2026-11-01T15:39:55Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}, {"id": "asset:table:pmid:32158466:1", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:7217c4d36371392a30b79e62ffaec443fde28866cbaa0fa21c626e6eeb290dba", "bytes": 887, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[4]/table-wrap[1]#T1", "version": null, "note": "The clinical features of TCGA hepatocellular carcinoma patients.", "structure": {"pmcid": "PMC7052339", "section_index": 4, "section_title": "Data Acquisition and Processing", "row_count": 25, "column_count": 3}, "table": {"label": "Table 1", "caption": "The clinical features of TCGA hepatocellular carcinoma patients.", "rows": [["Clinical features"], ["Age (years)", "media", "73"], ["", "Rage", "18-90"], ["", "Numbers of patients (n=374)", "Numbers of patients (%)"], ["Gender", "Female", "120 (32.09)"], ["", "Male", "254 (67.91)"], ["Grade", "G1", "55 (14.71)"], ["", "G2", "179 (47.86)"], ["", "G3", "136 (36.36)"], ["", "unknown", "4 (1.07)"], ["T stage", "T1", "185 (49.47)"], ["", "T2", "94 (24.13)"], ["", "T3", "81 (21.66)"], ["", "T4", "13 (4.74)"], ["N stage", "0", "257 (68.72)"], ["", "1", "5 (1.37)"], ["", "unknown", "113 (29.91)"], ["M stage", "0", "364 (97.32)"], ["", "1", "5 (1.34)"], ["", "unknown", "5 (1.34)"], ["AJCC stage", "I", "175 (46.78)"], ["", "II", "86 (25.27)"], ["", "III", "86 (25.27)"], ["", "IV", "5 (1.34)"], ["", "unknown", "5 (1.34)"]], "row_count": 25, "column_count": 3, "numeric_cells": 28, "header_rows": 1, "locator": "section[4]/table-wrap[1]#T1"}}, {"id": "asset:table:pmid:32158466:2", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:cf21b691b474672e671ce9625890207a884a9538652f9fb9282260101445f2d8", "bytes": 876, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[11]/table-wrap[1]#T2", "version": null, "note": "Primer sequences for qRT-PCR.", "structure": {"pmcid": "PMC7052339", "section_index": 11, "section_title": "Quantitative Real-Time PCR (qRT-PCR)", "row_count": 17, "column_count": 2}, "table": {"label": "Table 2", "caption": "Primer sequences for qRT-PCR.", "rows": [["Primer", "Seqence 5'-3'"], ["IL11 forward", "GTGGCCAAGATACAGCTGTCGC"], ["IL11 reverse", "GGTAGGACAGTAGGTCCGCTC"], ["IL17 forward", "AGA GAT ATC CCT CTG TGATC"], ["IL17 reverse", "TAC CCC AAA GTT ATC TCA GG"], ["SPP1 forward", "TCACCTGTGCCATACCAGTT"], ["SPP1 reverse", "TGTGGTCATGGCTTTCGTTG"], ["MAPT forward", "AAGATCGGCTCCACTGAGAA"], ["MAPT reverse", "ATGAGCCACACTTGGAGGTC"], ["BIRC5 forward", "CGCATCTCTACATTCAAG"], ["BIRC5 reverse", "ATGTTCCTCTCTCGTGAT"], ["miR-204 forward", "ACACTCCAGCTGGGTTCCCTTTGTCATCC"], ["miR-204 reverse", "CTCAACTGGTGTCGTGGA"], ["SNHG12 forward", "TCTGGTGATCGAGGACTTCC"], ["SNHG12 reverse", "ACCTCCTCAGTATCACACACT"], ["GAPDH forward", "CAACGAATTTGGCTACAGCA"], ["GAPDH reverse", "AGGGGTCTACATGGCAACTG"]], "row_count": 17, "column_count": 2, "numeric_cells": 9, "header_rows": 1, "locator": "section[11]/table-wrap[1]#T2"}}, {"id": "asset:table:pmid:32158466:3", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:4a1ffc96dfbfaa3f487d0b3f1801829ac910f9f9549b530ece730583ddef8267", "bytes": 825, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[20]/table-wrap[1]#T3", "version": null, "note": "Univariate and Multivariate Cox regression analysis of survival associated IRGS.", "structure": {"pmcid": "PMC7052339", "section_index": 20, "section_title": "Clinical Outcome of Patients With HCC Using the IRGPM", "row_count": 9, "column_count": 5}, "table": {"label": "Table 3", "caption": "Univariate and Multivariate Cox regression analysis of survival associated IRGS.", "rows": [["Risk Factors", "Overall Survival (OS)"], ["", "Univariate analysis", "Multivariate analysis"], ["", "HR (95% CI)", "P value", "OR (95% CI)", "P value"], ["Age", "1.002(0.986−1.017", "0.824", "1.006(0.990−1.022)", "0.484"], ["gender", "0.886(0.578−1.358)", "0.580", "1.110(0.713−1.729)", "0.643"], ["grade", "1.173(0.886−1.551)", "0.265", "1.125(0.827−1.531)", "0.452"], ["AJCC stage", "1.866(1.488−2.341)", "<0.001**", "1.247(0.461−3.378)", "0.664"], ["T stage", "1.826(1.472−2.265)", "<0.001**", "1.408(0.541−3.666)", "0.483"], ["Risk score", "2.238 (1.293-3.872)", "<0.001**", "2.071 (1.183-3.625)", "<0.001**"]], "row_count": 9, "column_count": 5, "numeric_cells": 26, "header_rows": 3, "locator": "section[20]/table-wrap[1]#T3"}}], "gaps": ["asset:data:geo:GSE76427 not downloaded", "asset:data:geo:GSE76427 licence not read"]}, "analysis": {"state": "partial", "methods": [{"id": "method-1", "family": "survival_analysis", "specific": "kaplan_meier", "label": "Survival analysis", "dsl_operations": ["survival_km"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["time_to_event_with_censoring"], "evidence": {"score": 1.0, "band": "verbatim", "quote": "Survival curves were generated using the Kaplan-Meier method, and the log-rank test was used to compare differences between the two groups."}}, {"id": "method-2", "family": "group_comparison", "specific": "student_t_test", "label": "Group comparison", "dsl_operations": [], "missing_operations": ["student_t"], "expressible": false, "parameters": {}, "data_shapes": ["two_or_more_groups_continuous"], "evidence": {"score": 0.8, "band": "high", "quote": "Student's t-test"}}, {"id": "method-3", "family": "group_comparison", "specific": "anova", "label": "Group comparison", "dsl_operations": ["group_summary", "welch_t", "bootstrap_mean_difference", "group_comparison_anova"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["two_or_more_groups_continuous"], "evidence": {"score": 0.8, "band": "high", "quote": "analysis of variance"}}, {"id": "method-4", "family": "survival_analysis", "specific": "cox_proportional_hazards", "label": "Survival analysis", "dsl_operations": ["cox_ph"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["time_to_event_with_censoring"], "evidence": {"score": 0.7, "band": "medium", "quote": "COX regression"}}, {"id": "method-5", "family": "survival_analysis", "specific": "log_rank_test", "label": "Survival analysis", "dsl_operations": ["logrank_test"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["time_to_event_with_censoring"], "evidence": {"score": 0.8, "band": "high", "quote": "log-rank"}}, {"id": "method-6", "family": "differential_expression", "specific": "edger", "label": "Differential expression analysis", "dsl_operations": ["normalise_counts", "differential_expression_fit", "fdr_bh"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["count_matrix_with_condition"], "evidence": {"score": 0.7, "band": "medium", "quote": "edgeR"}}, {"id": "method-7", "family": "network_analysis", "specific": "ppi_network", "label": "Network / pathway analysis", "dsl_operations": ["build_graph", "centrality_scores", "pathway_enrich"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["edge_list"], "evidence": {"score": 0.7, "band": "medium", "quote": "Protein-protein interaction"}}, {"id": "method-8", "family": "diagnostic_evaluation", "specific": "roc", "label": "Diagnostic test evaluation", "dsl_operations": ["confusion_counts", "roc_curve", "sensitivity_specificity", "solve_confusion_matrix", "classification_metrics", "published_precision_envelope"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["reference_standard_and_test"], "evidence": {"score": 0.8, "band": "high", "quote": "ROC curve"}}], "targets": [], "gaps": ["method.reader_differs_from_extractor"]}, "capability": {"state": "complete", "requirements": [{"capability_id": "capability:computational_analysis", "label": "Computational analysis platform", "assay_families": ["meta_analysis", "machine_learning", "survival_analysis", "statistical_regression", "pca", "molecular_docking", "network_analysis", "differential_expression", "gwas"], "availability_state": "owned", "tier_unlocked": "R1", "candidate": "Automated Assays Laravel application and simulated adapters"}], "gaps": []}, "readiness": {"state": "complete", "tier": "R1", "blocking_axis": "none", "blocked_on": "nothing:replicable_now", "axes": {"method": {"tier": "R1", "expressible": true, "required_operations": ["survival_km"], "missing_operations": [], "basis": "The paper names the method it used and the corpus's method extractor maps it onto the DSL catalogue: kaplan_meier."}, "capability": {"tier": "R1", "capability_id": "capability:computational_analysis", "availability_state": "owned", "basis": "The computational analysis is owned. The physical bench the paper used is not, so a physical validation cannot be run here."}, "data": {"tier": "R1", "reachable": true, "accessions": ["GSE76427"], "resolved_accessions": ["GSE76427"], "statements": ["The datasets analysed for this study were obtained from TCGA data portal (https://portal.gdc.cancer.gov/) and GEO data portal (https://www.ncbi.nlm.nih.gov/geo/)."], "basis": "The paper names GSE76427 in Gene Expression Omnibus (GEO) data portal and the accession resolves in the repository. No dataset was downloaded and no licence was read."}}, "can_run": {"dsl_operations": ["survival_km"], "assets": ["source:pmid:32158466", "data:geo:GSE76427", "asset:table:pmid:32158466:1", "asset:table:pmid:32158466:2", "asset:table:pmid:32158466:3"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:GSE76427"]}, "gaps": []}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-10-31T18:18:38Z", "independence": "single_reader"}, "evidence_check": {"method": "verbatim", "availability": "verbatim"}, "calls": 3, "usage": {"prompt_tokens": 25713, "completion_tokens": 1069, "cached_tokens": 776}}, "human_critique": null, "stages": [{"id": "extraction", "state": "complete", "reader": "MiniMax-M3.1-Flash", "provider": "minimax"}], "gaps": ["review.independent_reader", "review.machine_critique", "review.human_critique"]}, "execution": {"state": "absent", "status": "not_run", "mode": null, "runs": [], "gaps": ["execution.not_run"]}, "provenance": {"entities": [{"id": "pmid:32158466", "type": "paper", "label": "pmid:32158466"}, {"id": "source:pmid:32158466", "type": "manuscript", "label": "PMID 32158466 full text"}, {"id": "data:geo:GSE76427", "type": "dataset", "label": "GEO GSE76427"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:32158466", "type": "paper", "label": "pmid:32158466"}, {"id": "source:pmid:32158466", "type": "manuscript", "label": "PMID 32158466 full text"}, {"id": "data:geo:GSE76427", "type": "dataset", "label": "GEO GSE76427"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-32158466", "type": "extraction", "used": ["source:pmid:32158466"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-GSE76427", "type": "accession_resolution", "used": ["data:geo:GSE76427"], "agent": "agent:corpus-assay-engine"}], "agents": [{"id": "agent:corpus-assay-engine", "type": "software", "label": "Corpus assay engine"}, {"id": "agent:minimax-reader", "type": "software", "label": "MiniMax literature reader"}], "source_run_id": "reading-sci-2026-11-01", "dsl_catalogue_fingerprint": "343fb30756ba6ec3", "capability_table_fingerprint": "2cb3e42f047d2ecf", "snapshot_id": "ba34b49490d9bfaf"}, "lineage": {"parent_id": "pmid:32158466", "parent_hash": "sha256:c72a87ad6d3fe71206a5f78ed9f8a8c7984bb70433dde77d02598be50a9fc4b7", "fork_of": null, "generation": 7}, "gaps": ["asset:data:geo:GSE76427 licence not read", "asset:data:geo:GSE76427 not downloaded", "execution.not_run", "method.reader_differs_from_extractor", "review.human_critique", "review.independent_reader", "review.machine_critique"], "assays": [{"role": "analysis", "definition_id": "survival_analysis", "definition_version": "f2132e96ae6c7a4e", "definition_digest": null, "required_operations": ["survival_km"], "support_state": "supported", "source_hashes": {"dsl_catalogue": "f2132e96ae6c7a4e"}, "confidence": 1.0, "evidence": ["Survival curves were generated using the Kaplan-Meier method, and the log-rank test was used to compare differences between the two groups."], "order_basis": "analysis_only", "id": "assay:1"}]}