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

pmid:33143224

MYC Targets Scores Are Associated with Cancer Aggressiveness and Poor Survival in ER-Positive Primary and Metastatic Breast Cancer.

Amy Schulze · Masanori Oshi · Itaru Endo · Kazuaki Takabe

International journal of molecular sciences · 2020 doi:10.3390/ijms21218127

Paper

complete

Experiment

complete

Data

partial

Analysis

complete

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:33143224
kind
science-record
content_hash
sha256:600f2909ddcad07758b9eebbcf2b70adba24f79983d1fc00d8b88577b016e226
schema
https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json
created_at
2026-11-01T15:41:14Z
updated_at
2026-11-01T21:24:02Z
generator object · 2 fields
name
corpus-assay-engine
run_id
reading-sci-2026-11-01
paper object · 10 fields
state
complete
title
MYC Targets Scores Are Associated with Cancer Aggressiveness and Poor Survival in ER-Positive Primary and Metastatic Breast Cancer.
doi
10.3390/ijms21218127
pmid
33143224
authors array · 4 items
[0]
Amy Schulze
[1]
Masanori Oshi
[2]
Itaru Endo
[3]
Kazuaki Takabe
journal
International journal of molecular sciences
year
2020
abstract
MYC is one of the most studied oncogenes that is known to promote cell proliferation. We utilized MYC targets v1 and MYC targets v2 scores of gene set variation analysis and hypothesized that these scores correlate with tumor aggressiveness and survival outcomes. We examined a total of 3109 breast cancer patients from TCGA, METABRIC, and GSE124647 cohorts. In each cohort, the patients were divided into high- and low-score groups using the upper third value as the cut off. As expected, higher scores were related to increased cell proliferation and worse clinical and pathologic features. High MYC targets scores were associated with worse survival, specifically in primary ER-positive breast cancer, consistently in both TCGA and METABRIC cohorts. In ER-positive breast cancer, high MYC targets v1, but not v2 score, was associated with high mutation load, and high MYC targets v1 and v2 scores were both associated with increased infiltration of pro- and anti-cancerous immune cells. We found that high MYC scores were associated with worse survival in metastatic breast cancer. Our findings show that the MYC targets v1 and v2 scores are associated with tumor aggressiveness and poor prognosis in ER-positive primary tumors, as well as in metastatic breast cancer.
claims array · 2 items
[0] object · 6 fields
id
claim-method
statement
For survival analysis, the Kaplan–Meier method with log-rank test was used.
kind
methodological
target
null
evidence array · 1 item
[0] object · 3 fields
asset
source:pmid:33143224
locator
sections[14] "4.4. Other" paragraph 2
quote
For survival analysis, the Kaplan–Meier method with log-rank test was used.
state
complete
[1] object · 6 fields
id
claim-data-access
statement
We used the Pan Cancer Clinical Data Resource [15] and the cBio Cancer Genomic Portal [34] to obtain data regarding tumor gene expression and clinical data from the TCGA-BRCA project, which our group has previously reported [35,36]. There were 1065 tumors that were studied in total.
kind
methodological
target
null
evidence array · 1 item
[0] object · 3 fields
asset
source:pmid:33143224
locator
sections[11] "4.1. The Cancer Genome Atlas Breast Cancer Cohort" paragraph 2
quote
We used the Pan Cancer Clinical Data Resource [15] and the cBio Cancer Genomic Portal [34] to obtain data regarding tumor gene expression and clinical data from the TCGA-BRCA project, which our group has previously reported [35,36]. There were 1065 tumors that were studied in total.
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:33143224
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:GSE124647
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:GSE124647
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 · 3 items
[0] object · 15 fields
id
source:pmid:33143224
role
manuscript
format
xml
media_type
application/xml
uri
https://doi.org/10.3390/ijms21218127
sha256
sha256:cdb26077232e40d1201164cbc7909ad0b40d903ee4b1db21cfed90eaabd579b3
bytes
38738
access
open
state
resolved
reader
null
reader_status
reader_required
identifier
10.3390/ijms21218127
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
PMC7663719
source
europe_pmc_fulltext
coverage
whole_body
text_hash_scope
rendered_section_body
[1] object · 15 fields
id
data:geo:GSE124647
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=GSE124647
sha256
null
bytes
null
access
open
state
resolved
reader
null
reader_status
reader_required
identifier
GSE124647
version
null
note
We used the Pan Cancer Clinical Data Resource [15] and the cBio Cancer Genomic Portal [34] to obtain data regarding tumor gene expression and clinical data from the TCGA-BRCA project, which our group has previously reported [35,36]. There were 1065 tumors that were studied in total.
structure object · 15 fields
repository
GEO
access_route
GEO accession URL
access_statement_verbatim
We used the Pan Cancer Clinical Data Resource [15] and the cBio Cancer Genomic Portal [34] to obtain data regarding tumor gene expression and clinical data from the TCGA-BRCA project, which our group has previously reported [35,36]. There were 1065 tumors that were studied in total.
access_statement_kind
repository_route_statement
sample_accessions array · 140 items
[0]
GSM3538497
[1]
GSM3538498
[2]
GSM3538499
[3]
GSM3538500
[4]
GSM3538501
[5]
GSM3538502
[6]
GSM3538503
[7]
GSM3538504
[8]
GSM3538505
[9]
GSM3538506
[10]
GSM3538507
[11]
GSM3538508
[12]
GSM3538509
[13]
GSM3538510
[14]
GSM3538511
[15]
GSM3538512
[16]
GSM3538513
[17]
GSM3538514
[18]
GSM3538515
[19]
GSM3538516
[20]
GSM3538517
[21]
GSM3538518
[22]
GSM3538519
[23]
GSM3538520
[24]
GSM3538521
[25]
GSM3538522
[26]
GSM3538523
[27]
GSM3538524
[28]
GSM3538525
[29]
GSM3538526
[30]
GSM3538527
[31]
GSM3538528
[32]
GSM3538529
[33]
GSM3538530
[34]
GSM3538531
[35]
GSM3538532
[36]
GSM3538533
[37]
GSM3538534
[38]
GSM3538535
[39]
GSM3538536
[40]
GSM3538537
[41]
GSM3538538
[42]
GSM3538539
[43]
GSM3538540
[44]
GSM3538541
[45]
GSM3538542
[46]
GSM3538543
[47]
GSM3538544
[48]
GSM3538545
[49]
GSM3538546
[50]
GSM3538547
[51]
GSM3538548
[52]
GSM3538549
[53]
GSM3538550
[54]
GSM3538551
[55]
GSM3538552
[56]
GSM3538553
[57]
GSM3538554
[58]
GSM3538555
[59]
GSM3538556
[60]
GSM3538557
[61]
GSM3538558
[62]
GSM3538559
[63]
GSM3538560
[64]
GSM3538561
[65]
GSM3538562
[66]
GSM3538563
[67]
GSM3538564
[68]
GSM3538565
[69]
GSM3538566
[70]
GSM3538567
[71]
GSM3538568
[72]
GSM3538569
[73]
GSM3538570
[74]
GSM3538571
[75]
GSM3538572
[76]
GSM3538573
[77]
GSM3538574
[78]
GSM3538575
[79]
GSM3538576
[80]
GSM3538577
[81]
GSM3538578
[82]
GSM3538579
[83]
GSM3538580
[84]
GSM3538581
[85]
GSM3538582
[86]
GSM3538583
[87]
GSM3538584
[88]
GSM3538585
[89]
GSM3538586
[90]
GSM3538587
[91]
GSM3538588
[92]
GSM3538589
[93]
GSM3538590
[94]
GSM3538591
[95]
GSM3538592
[96]
GSM3538593
[97]
GSM3538594
[98]
GSM3538595
[99]
GSM3538596
[100]
GSM3538597
[101]
GSM3538598
[102]
GSM3538599
[103]
GSM3538600
[104]
GSM3538601
[105]
GSM3538602
[106]
GSM3538603
[107]
GSM3538604
[108]
GSM3538605
[109]
GSM3538606
[110]
GSM3538607
[111]
GSM3538608
[112]
GSM3538609
[113]
GSM3538610
[114]
GSM3538611
[115]
GSM3538612
[116]
GSM3538613
[117]
GSM3538614
[118]
GSM3538615
[119]
GSM3538616
[120]
GSM3538617
[121]
GSM3538618
[122]
GSM3538619
[123]
GSM3538620
[124]
GSM3538621
[125]
GSM3538622
[126]
GSM3538623
[127]
GSM3538624
[128]
GSM3538625
[129]
GSM3538626
[130]
GSM3538627
[131]
GSM3538628
[132]
GSM3538629
[133]
GSM3538630
[134]
GSM3538631
[135]
GSM3538632
[136]
GSM3538633
[137]
GSM3538634
[138]
GSM3538635
[139]
GSM3538636
sample_count
140
group_sizes
null
group_sizes_basis
null
platform
96
taxon
Homo sapiens
title
SET ER/PR - A robust 18-gene Predictor for Sensitivity to Endocrine Therapy for Metastatic Breast Cancer
resolution_checked_at
2026-11-01T15:39:54Z
resolution_check
identifier_resolution_only_no_download_no_licence_read
downloaded
false
licence_read
false
[2] object · 16 fields
id
asset:table:pmid:33143224:1
role
table
format
jats-table
media_type
application/vnd.jats.table+json
uri
null
sha256
sha256:c16cdc9c6025b8773752369a3180d7536baa5e7fb33c48f2aa90e22de967c42f
bytes
529
access
open
state
verified
reader
read_table
reader_status
available
identifier
section[15]/table-wrap[1]#array1
version
null
note
null
structure object · 5 fields
pmcid
PMC7663719
section_index
15
section_title
Abbreviations
row_count
9
column_count
2
table object · 8 fields
label
null
caption
null
rows array · 9 items
[0] array · 2 items
[0]
ER
[1]
Estrogen receptor
[1] array · 2 items
[0]
HER2
[1]
Human epidermal growth factor receptor 2
[2] array · 2 items
[0]
TNBC
[1]
Triple-negative breast cancer
[3] array · 2 items
[0]
TCGA
[1]
The Cancer Genome Atlas
[4] array · 2 items
[0]
METABRIC
[1]
Molecular Taxonomy of Breast Cancer International Consortium
[5] array · 2 items
[0]
DFS
[1]
Disease-free survival
[6] array · 2 items
[0]
DSS
[1]
Disease-specific survival
[7] array · 2 items
[0]
PFS
[1]
Progression-free survival
[8] array · 2 items
[0]
AJCC
[1]
American Joint Committee on Cancer
locator
section[15]/table-wrap[1]#array1
gaps array · 2 items
[0]
asset:data:geo:GSE124647 not downloaded
[1]
asset:data:geo:GSE124647 licence not read
analysis object · 4 fields
state
complete
methods array · 1 item
[0] object · 10 fields
id
method-1
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
1
band
verbatim
quote
For survival analysis, the Kaplan–Meier method with log-rank test was used.
targets array · 0 items
gaps array · 0 items
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]
logrank_test
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: log_rank_test.
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]
GSE124647
resolved_accessions array · 1 item
[0]
GSE124647
statements array · 1 item
[0]
We used the Pan Cancer Clinical Data Resource [15] and the cBio Cancer Genomic Portal [34] to obtain data regarding tumor gene expression and clinical data from the TCGA-BRCA project, which our group has previously reported [35,36]. There were 1065 tumors that were studied in total.
basis
The paper names GSE124647 in Gene Expression Omnibus 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]
logrank_test
assets array · 3 items
[0]
source:pmid:33143224
[1]
data:geo:GSE124647
[2]
asset:table:pmid:33143224:1
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:GSE124647
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
2026-10-31T18:23:52Z
independence
single_reader
evidence_check object · 2 fields
method
verbatim
availability
null
calls
3
usage object · 3 fields
prompt_tokens
33084
completion_tokens
1726
cached_tokens
784
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:33143224
type
paper
label
pmid:33143224
[1] object · 3 fields
id
source:pmid:33143224
type
manuscript
label
PMID 33143224 full text
[2] object · 3 fields
id
data:geo:GSE124647
type
dataset
label
GEO GSE124647
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:33143224
type
paper
label
pmid:33143224
[1] object · 3 fields
id
source:pmid:33143224
type
manuscript
label
PMID 33143224 full text
[2] object · 3 fields
id
data:geo:GSE124647
type
dataset
label
GEO GSE124647
agent
agent:corpus-assay-engine
[1] object · 4 fields
id
activity-read-33143224
type
extraction
used array · 1 item
[0]
source:pmid:33143224
agent
agent:minimax-reader
[2] object · 4 fields
id
activity-resolve-GSE124647
type
accession_resolution
used array · 1 item
[0]
data:geo:GSE124647
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:33143224
parent_hash
sha256:b60c38ad690b925e176c8ad0460a1cc28b9a0bf5b70f1dbdf78505b6466ab864
fork_of
null
gaps array · 6 items
[0]
asset:data:geo:GSE124647 licence not read
[1]
asset:data:geo:GSE124647 not downloaded
[2]
execution.not_run
[3]
review.human_critique
[4]
review.independent_reader
[5]
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]
logrank_test
support_state
supported
source_hashes object · 1 field
dsl_catalogue
f2132e96ae6c7a4e
evidence array · 1 item
[0]
For survival analysis, the Kaplan–Meier method with log-rank test was used.
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:33143224", "kind": "science-record", "revision": 7, "content_hash": "sha256:600f2909ddcad07758b9eebbcf2b70adba24f79983d1fc00d8b88577b016e226", "created_at": "2026-11-01T15:41:14Z", "updated_at": "2026-11-01T21:24:02Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "MYC Targets Scores Are Associated with Cancer Aggressiveness and Poor Survival in ER-Positive Primary and Metastatic Breast Cancer.", "doi": "10.3390/ijms21218127", "pmid": "33143224", "authors": ["Amy Schulze", "Masanori Oshi", "Itaru Endo", "Kazuaki Takabe"], "journal": "International journal of molecular sciences", "year": 2020, "abstract": "MYC is one of the most studied oncogenes that is known to promote cell proliferation. We utilized MYC targets v1 and MYC targets v2 scores of gene set variation analysis and hypothesized that these scores correlate with tumor aggressiveness and survival outcomes. We examined a total of 3109 breast cancer patients from TCGA, METABRIC, and GSE124647 cohorts. In each cohort, the patients were divided into high- and low-score groups using the upper third value as the cut off. As expected, higher scores were related to increased cell proliferation and worse clinical and pathologic features. High MYC targets scores were associated with worse survival, specifically in primary ER-positive breast cancer, consistently in both TCGA and METABRIC cohorts. In ER-positive breast cancer, high MYC targets v1, but not v2 score, was associated with high mutation load, and high MYC targets v1 and v2 scores were both associated with increased infiltration of pro- and anti-cancerous immune cells. We found that high MYC scores were associated with worse survival in metastatic breast cancer. Our findings show that the MYC targets v1 and v2 scores are associated with tumor aggressiveness and poor prognosis in ER-positive primary tumors, as well as in metastatic breast cancer.", "claims": [{"id": "claim-method", "statement": "For survival analysis, the Kaplan–Meier method with log-rank test was used.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:33143224", "locator": "sections[14] \"4.4. Other\" paragraph 2", "quote": "For survival analysis, the Kaplan–Meier method with log-rank test was used."}], "state": "complete"}, {"id": "claim-data-access", "statement": "We used the Pan Cancer Clinical Data Resource [15] and the cBio Cancer Genomic Portal [34] to obtain data regarding tumor gene expression and clinical data from the TCGA-BRCA project, which our group has previously reported [35,36]. There were 1065 tumors that were studied in total.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:33143224", "locator": "sections[11] \"4.1. The Cancer Genome Atlas Breast Cancer Cohort\" paragraph 2", "quote": "We used the Pan Cancer Clinical Data Resource [15] and the cBio Cancer Genomic Portal [34] to obtain data regarding tumor gene expression and clinical data from the TCGA-BRCA project, which our group has previously reported [35,36]. There were 1065 tumors that were studied in total."}], "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:33143224"], "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:GSE124647"], "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:GSE124647"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:33143224", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.3390/ijms21218127", "sha256": "sha256:cdb26077232e40d1201164cbc7909ad0b40d903ee4b1db21cfed90eaabd579b3", "bytes": 38738, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.3390/ijms21218127", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC7663719", "source": "europe_pmc_fulltext", "coverage": "whole_body", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE124647", "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=GSE124647", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE124647", "version": null, "note": "We used the Pan Cancer Clinical Data Resource [15] and the cBio Cancer Genomic Portal [34] to obtain data regarding tumor gene expression and clinical data from the TCGA-BRCA project, which our group has previously reported [35,36]. There were 1065 tumors that were studied in total.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "We used the Pan Cancer Clinical Data Resource [15] and the cBio Cancer Genomic Portal [34] to obtain data regarding tumor gene expression and clinical data from the TCGA-BRCA project, which our group has previously reported [35,36]. There were 1065 tumors that were studied in total.", "access_statement_kind": "repository_route_statement", "sample_accessions": ["GSM3538497", "GSM3538498", "GSM3538499", "GSM3538500", "GSM3538501", "GSM3538502", "GSM3538503", "GSM3538504", "GSM3538505", "GSM3538506", "GSM3538507", "GSM3538508", "GSM3538509", "GSM3538510", "GSM3538511", "GSM3538512", "GSM3538513", "GSM3538514", "GSM3538515", "GSM3538516", "GSM3538517", "GSM3538518", "GSM3538519", "GSM3538520", "GSM3538521", "GSM3538522", "GSM3538523", "GSM3538524", "GSM3538525", "GSM3538526", "GSM3538527", "GSM3538528", "GSM3538529", "GSM3538530", "GSM3538531", "GSM3538532", "GSM3538533", "GSM3538534", "GSM3538535", "GSM3538536", "GSM3538537", "GSM3538538", "GSM3538539", "GSM3538540", "GSM3538541", "GSM3538542", "GSM3538543", "GSM3538544", "GSM3538545", "GSM3538546", "GSM3538547", "GSM3538548", "GSM3538549", "GSM3538550", "GSM3538551", "GSM3538552", "GSM3538553", "GSM3538554", "GSM3538555", "GSM3538556", "GSM3538557", "GSM3538558", "GSM3538559", "GSM3538560", "GSM3538561", "GSM3538562", "GSM3538563", "GSM3538564", "GSM3538565", "GSM3538566", "GSM3538567", "GSM3538568", "GSM3538569", "GSM3538570", "GSM3538571", "GSM3538572", "GSM3538573", "GSM3538574", "GSM3538575", "GSM3538576", "GSM3538577", "GSM3538578", "GSM3538579", "GSM3538580", "GSM3538581", "GSM3538582", "GSM3538583", "GSM3538584", "GSM3538585", "GSM3538586", "GSM3538587", "GSM3538588", "GSM3538589", "GSM3538590", "GSM3538591", "GSM3538592", "GSM3538593", "GSM3538594", "GSM3538595", "GSM3538596", "GSM3538597", "GSM3538598", "GSM3538599", "GSM3538600", "GSM3538601", "GSM3538602", "GSM3538603", "GSM3538604", "GSM3538605", "GSM3538606", "GSM3538607", "GSM3538608", "GSM3538609", "GSM3538610", "GSM3538611", "GSM3538612", "GSM3538613", "GSM3538614", "GSM3538615", "GSM3538616", "GSM3538617", "GSM3538618", "GSM3538619", "GSM3538620", "GSM3538621", "GSM3538622", "GSM3538623", "GSM3538624", "GSM3538625", "GSM3538626", "GSM3538627", "GSM3538628", "GSM3538629", "GSM3538630", "GSM3538631", "GSM3538632", "GSM3538633", "GSM3538634", "GSM3538635", "GSM3538636"], "sample_count": 140, "group_sizes": null, "group_sizes_basis": null, "platform": "96", "taxon": "Homo sapiens", "title": "SET ER/PR - A robust 18-gene Predictor for Sensitivity to Endocrine Therapy for Metastatic Breast Cancer", "resolution_checked_at": "2026-11-01T15:39:54Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}, {"id": "asset:table:pmid:33143224:1", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:c16cdc9c6025b8773752369a3180d7536baa5e7fb33c48f2aa90e22de967c42f", "bytes": 529, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[15]/table-wrap[1]#array1", "version": null, "note": null, "structure": {"pmcid": "PMC7663719", "section_index": 15, "section_title": "Abbreviations", "row_count": 9, "column_count": 2}, "table": {"label": null, "caption": null, "rows": [["ER", "Estrogen receptor"], ["HER2", "Human epidermal growth factor receptor 2"], ["TNBC", "Triple-negative breast cancer"], ["TCGA", "The Cancer Genome Atlas"], ["METABRIC", "Molecular Taxonomy of Breast Cancer International Consortium"], ["DFS", "Disease-free survival"], ["DSS", "Disease-specific survival"], ["PFS", "Progression-free survival"], ["AJCC", "American Joint Committee on Cancer"]], "row_count": 9, "column_count": 2, "numeric_cells": 1, "header_rows": 0, "locator": "section[15]/table-wrap[1]#array1"}}], "gaps": ["asset:data:geo:GSE124647 not downloaded", "asset:data:geo:GSE124647 licence not read"]}, "analysis": {"state": "complete", "methods": [{"id": "method-1", "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": 1.0, "band": "verbatim", "quote": "For survival analysis, the Kaplan–Meier method with log-rank test was used."}}], "targets": [], "gaps": []}, "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": ["logrank_test"], "missing_operations": [], "basis": "The paper names the method it used and the corpus's method extractor maps it onto the DSL catalogue: log_rank_test."}, "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": ["GSE124647"], "resolved_accessions": ["GSE124647"], "statements": ["We used the Pan Cancer Clinical Data Resource [15] and the cBio Cancer Genomic Portal [34] to obtain data regarding tumor gene expression and clinical data from the TCGA-BRCA project, which our group has previously reported [35,36]. There were 1065 tumors that were studied in total."], "basis": "The paper names GSE124647 in Gene Expression Omnibus and the accession resolves in the repository. No dataset was downloaded and no licence was read."}}, "can_run": {"dsl_operations": ["logrank_test"], "assets": ["source:pmid:33143224", "data:geo:GSE124647", "asset:table:pmid:33143224:1"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:GSE124647"]}, "gaps": []}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-10-31T18:23:52Z", "independence": "single_reader"}, "evidence_check": {"method": "verbatim", "availability": null}, "calls": 3, "usage": {"prompt_tokens": 33084, "completion_tokens": 1726, "cached_tokens": 784}}, "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:33143224", "type": "paper", "label": "pmid:33143224"}, {"id": "source:pmid:33143224", "type": "manuscript", "label": "PMID 33143224 full text"}, {"id": "data:geo:GSE124647", "type": "dataset", "label": "GEO GSE124647"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:33143224", "type": "paper", "label": "pmid:33143224"}, {"id": "source:pmid:33143224", "type": "manuscript", "label": "PMID 33143224 full text"}, {"id": "data:geo:GSE124647", "type": "dataset", "label": "GEO GSE124647"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-33143224", "type": "extraction", "used": ["source:pmid:33143224"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-GSE124647", "type": "accession_resolution", "used": ["data:geo:GSE124647"], "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:33143224", "parent_hash": "sha256:b60c38ad690b925e176c8ad0460a1cc28b9a0bf5b70f1dbdf78505b6466ab864", "fork_of": null, "generation": 6}, "gaps": ["asset:data:geo:GSE124647 licence not read", "asset:data:geo:GSE124647 not downloaded", "execution.not_run", "review.human_critique", "review.independent_reader", "review.machine_critique"], "assays": [{"role": "analysis", "definition_id": "survival_analysis", "definition_version": "f2132e96ae6c7a4e", "definition_digest": null, "required_operations": ["logrank_test"], "support_state": "supported", "source_hashes": {"dsl_catalogue": "f2132e96ae6c7a4e"}, "confidence": 1.0, "evidence": ["For survival analysis, the Kaplan–Meier method with log-rank test was used."], "order_basis": "analysis_only", "id": "assay:1"}]}