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

pmid:31475200

High TRIAP1 expression in penile carcinoma is associated with high risk of recurrence and poor survival.

Jiayi Zhang · Rong Cong · Kai Zhao · Yi Wang · Ninghong Song · Min Gu

Annals of translational medicine · 2019 doi:10.21037/atm.2019.06.47

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:31475200
kind
science-record
content_hash
sha256:63eb88afb34e9851cedba7edf08de5780203195c214d93f24c526e38500f1805
schema
https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json
created_at
2026-11-01T17:33:02Z
updated_at
2026-11-01T21:22:27Z
generator object · 2 fields
name
corpus-assay-engine
run_id
reading-sci-2026-11-01
paper object · 10 fields
state
complete
title
High TRIAP1 expression in penile carcinoma is associated with high risk of recurrence and poor survival.
doi
10.21037/atm.2019.06.47
pmid
31475200
authors array · 6 items
[0]
Jiayi Zhang
[1]
Rong Cong
[2]
Kai Zhao
[3]
Yi Wang
[4]
Ninghong Song
[5]
Min Gu
journal
Annals of translational medicine
year
2019
abstract
BACKGROUND: TP53-regulated inhibitor of apoptosis 1 (TRIAP1), also known as p53 cell survival factor or p53CSV, is reported to be associated with resistance of apoptosis in different human malignancies, but the potential role of TRIAP1 in penile carcinoma (PeCa) has not been well studied. This study aimed to analyze the association between TRIAP1 expression and clinical outcome in PeCa patients. METHODS: Bioinformatics was used to analyze the differential TRIAP1 expression in PeCa compared with normal tissues in Gene Expression Omnibus (GEO) Dataset (GSE57955). The expression of TRIAP1 in tumor specimens from 57 patients undergoing radical penile surgery was detected by immunohistochemistry (IHC). Differential TRIAP1 expression in various human malignancies was also assessed by GEPIA web-tool based on The Cancer Genome Atlas (TCGA) Datasets. Subsequently, the relationship between TRIAP1 expression and clinical prognosis of PeCa patients was analyzed. RESULTS: Both IHC and GEO Dataset (GSE57955) showed that TRIAP1 was significantly overexpressed in PeCa tissues when compared with normal tissues. Based on patient data and IHC on clinical specimens, we found that strong intensity of TRIAP1 expression was significantly related with higher histological grade (P=0.049) and elevated local recurrence rate (P=0.023), suggesting TRIAP1 as a potential predictor in recurrence. Further, high TRIAP1 expression was identified to be a hazardous prognostic factor for local recurrence-free survival (RFS). CONCLUSIONS: High TRIAP1 expression in PeCa is associated with high risk of recurrence and poor survival, suggesting TRIAP1 may become a potential prognostic factor for PeCa.
claims array · 3 items
[0] object · 6 fields
id
claim-method
statement
Bioinformatics was used to analyze the differential TRIAP1 expression in PeCa compared with normal tissues in Gene Expression Omnibus (GEO) Dataset (GSE57955).
kind
methodological
target
null
evidence array · 1 item
[0] object · 3 fields
asset
source:pmid:31475200
locator
sections[0] "Abstract" paragraph 2
quote
Bioinformatics was used to analyze the differential TRIAP1 expression in PeCa compared with normal tissues in Gene Expression Omnibus (GEO) Dataset (GSE57955).
state
complete
[1] object · 6 fields
id
claim-data-access
statement
Bioinformatics was used to analyze the differential TRIAP1 expression in PeCa compared with normal tissues in Gene Expression Omnibus (GEO) Dataset (GSE57955).
kind
methodological
target
null
evidence array · 1 item
[0] object · 3 fields
asset
source:pmid:31475200
locator
sections[0] "Abstract" paragraph 2
quote
Bioinformatics was used to analyze the differential TRIAP1 expression in PeCa compared with normal tissues in Gene Expression Omnibus (GEO) Dataset (GSE57955).
state
complete
[2] object · 6 fields
id
claim-target-result
statement
Based on patient data and IHC on clinical specimens, we found that strong intensity of TRIAP1 expression was significantly related with higher histological grade (P=0.049) and elevated local recurrence rate (P=0.023), suggesting TRIAP1 as a potential predictor in recurrence.
kind
qualitative
target
null
evidence array · 1 item
[0] object · 3 fields
asset
source:pmid:31475200
locator
sections[0] "Abstract" paragraph 3
quote
Based on patient data and IHC on clinical specimens, we found that strong intensity of TRIAP1 expression was significantly related with higher histological grade (P=0.049) and elevated local recurrence rate (P=0.023), suggesting TRIAP1 as a potential predictor in recurrence.
state
complete
gaps array · 0 items
experiment object · 8 fields
state
complete
objective
Based on patient data and IHC on clinical specimens, we found that strong intensity of TRIAP1 expression was significantly related with higher histological grade (P=0.049) and elevated local recurrence rate (P=0.023), suggesting TRIAP1 as a potential predictor in recurrence.
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:31475200
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:GSE57955
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:GSE57955
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 · 2 items
[0] object · 15 fields
id
source:pmid:31475200
role
manuscript
format
xml
media_type
application/xml
uri
https://doi.org/10.21037/atm.2019.06.47
sha256
sha256:53a052ddd43a490f58afa04059c4e9f37f75a44782e4766ba29d6d1976dcd3a9
bytes
1657
access
open
state
resolved
reader
null
reader_status
reader_required
identifier
10.21037/atm.2019.06.47
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
PMC6694233
source
ncbi_pmc_fulltext
coverage
whole_body
text_hash_scope
rendered_section_body
[1] object · 15 fields
id
data:geo:GSE57955
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=GSE57955
sha256
null
bytes
null
access
open
state
resolved
reader
null
reader_status
reader_required
identifier
GSE57955
version
null
note
Bioinformatics was used to analyze the differential TRIAP1 expression in PeCa compared with normal tissues in Gene Expression Omnibus (GEO) Dataset (GSE57955).
structure object · 15 fields
repository
GEO
access_route
GEO accession URL
access_statement_verbatim
Bioinformatics was used to analyze the differential TRIAP1 expression in PeCa compared with normal tissues in Gene Expression Omnibus (GEO) Dataset (GSE57955).
access_statement_kind
repository_route_statement
sample_accessions array · 39 items
[0]
GSM1398486
[1]
GSM1398487
[2]
GSM1398488
[3]
GSM1398489
[4]
GSM1398490
[5]
GSM1398491
[6]
GSM1398492
[7]
GSM1398493
[8]
GSM1398494
[9]
GSM1398495
[10]
GSM1398496
[11]
GSM1398497
[12]
GSM1398498
[13]
GSM1398499
[14]
GSM1398500
[15]
GSM1398501
[16]
GSM1398502
[17]
GSM1398503
[18]
GSM1398504
[19]
GSM1398505
[20]
GSM1398506
[21]
GSM1398507
[22]
GSM1398508
[23]
GSM1398509
[24]
GSM1398510
[25]
GSM1398511
[26]
GSM1398512
[27]
GSM1398513
[28]
GSM1398514
[29]
GSM1398515
[30]
GSM1398516
[31]
GSM1398517
[32]
GSM1398518
[33]
GSM1398519
[34]
GSM1398520
[35]
GSM1398521
[36]
GSM1398522
[37]
GSM1398523
[38]
GSM1398524
sample_count
39
group_sizes
null
group_sizes_basis
null
platform
6480
taxon
Homo sapiens
title
Large scale gene expression analysis uncover new molecules related to biology and HPV mediated carcinogenesis in penile tumors
resolution_checked_at
2026-11-01T17:30:42Z
resolution_check
identifier_resolution_only_no_download_no_licence_read
downloaded
false
licence_read
false
gaps array · 2 items
[0]
asset:data:geo:GSE57955 not downloaded
[1]
asset:data:geo:GSE57955 licence not read
analysis object · 4 fields
state
partial
methods array · 1 item
[0] object · 10 fields
id
method-1
family
null
specific
null
label
Bioinformatics
dsl_operations array · 0 items
missing_operations array · 0 items
parameters object · 0 fields
data_shapes array · 0 items
evidence object · 3 fields
score
1
band
verbatim
quote
Bioinformatics was used to analyze the differential TRIAP1 expression in PeCa compared with normal tissues in Gene Expression Omnibus (GEO) Dataset (GSE57955).
targets array · 0 items
gaps array · 1 item
[0]
method.reader_named_unmapped
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
blocked
tier
R4
blocking_axis
method
blocked_on
method:not_determinable
axes object · 3 fields
method object · 5 fields
tier
R4
expressible
false
required_operations array · 0 items
missing_operations array · 0 items
basis
The reader quoted the method the paper names (Bioinformatics), but the corpus's method extractor could not map it onto a DSL operation, so the method is published but not expressible.
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]
GSE57955
resolved_accessions array · 1 item
[0]
GSE57955
statements array · 1 item
[0]
Bioinformatics was used to analyze the differential TRIAP1 expression in PeCa compared with normal tissues in Gene Expression Omnibus (GEO) Dataset (GSE57955).
basis
The paper names GSE57955 in Gene Expression Omnibus (GEO) and the accession resolves in the repository. No dataset was downloaded and no licence was read.
can_run object · 3 fields
dsl_operations array · 0 items
assets array · 2 items
[0]
source:pmid:31475200
[1]
data:geo:GSE57955
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:GSE57955
gaps array · 1 item
[0]
method:not_determinable
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
2026-11-01T16:58:39Z
independence
single_reader
evidence_check object · 2 fields
method
verbatim
availability
null
calls
5
usage object · 3 fields
prompt_tokens
1979
completion_tokens
1010
cached_tokens
0
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:31475200
type
paper
label
pmid:31475200
[1] object · 3 fields
id
source:pmid:31475200
type
manuscript
label
PMID 31475200 full text
[2] object · 3 fields
id
data:geo:GSE57955
type
dataset
label
GEO GSE57955
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:31475200
type
paper
label
pmid:31475200
[1] object · 3 fields
id
source:pmid:31475200
type
manuscript
label
PMID 31475200 full text
[2] object · 3 fields
id
data:geo:GSE57955
type
dataset
label
GEO GSE57955
agent
agent:corpus-assay-engine
[1] object · 4 fields
id
activity-read-31475200
type
extraction
used array · 1 item
[0]
source:pmid:31475200
agent
agent:minimax-reader
[2] object · 4 fields
id
activity-resolve-GSE57955
type
accession_resolution
used array · 1 item
[0]
data:geo:GSE57955
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:31475200
parent_hash
sha256:f442a7157540483e82771fb3ad506e06b759198cb7955ca578199b17606c1710
fork_of
null
gaps array · 7 items
[0]
asset:data:geo:GSE57955 licence not read
[1]
asset:data:geo:GSE57955 not downloaded
[2]
execution.not_run
[3]
method.reader_named_unmapped
[4]
review.human_critique
[5]
review.independent_reader
[6]
review.machine_critique
assays array · 2 items
[0] object · 11 fields
role
data_generation
definition_id
apoptosis_assay
definition_version
99e1195c7d6f
required_operations array · 0 items
support_state
partial
source_hashes object · 1 field
assay_lexicon
99e1195c7d6f
confidence
0.93
evidence array · 2 items
[0]
BACKGROUND: TP53-regulated inhibitor of apoptosis 1 (TRIAP1), also known as p53 cell survival
[1]
reported to be associated with resistance of apoptosis in different human malignancies, but the pot
order_basis
paper_text_order:105
id
assay:1
[1] object · 11 fields
role
data_generation
definition_version
99e1195c7d6f
required_operations array · 0 items
support_state
partial
source_hashes object · 1 field
assay_lexicon
99e1195c7d6f
confidence
0.99
evidence array · 4 items
[0]
going radical penile surgery was detected by immunohistochemistry (IHC). Differential TRIAP1 expression in var
[1]
urgery was detected by immunohistochemistry (IHC). Differential TRIAP1 expression in various
[2]
of PeCa patients was analyzed. RESULTS: Both IHC and GEO Dataset (GSE57955) showed that TRIAP
[3]
th normal tissues. Based on patient data and IHC on clinical specimens, we found that strong
order_basis
paper_text_order:739
id
assay:2
Complete file
{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:31475200", "kind": "science-record", "revision": 3, "content_hash": "sha256:63eb88afb34e9851cedba7edf08de5780203195c214d93f24c526e38500f1805", "created_at": "2026-11-01T17:33:02Z", "updated_at": "2026-11-01T21:22:27Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "High TRIAP1 expression in penile carcinoma is associated with high risk of recurrence and poor survival.", "doi": "10.21037/atm.2019.06.47", "pmid": "31475200", "authors": ["Jiayi Zhang", "Rong Cong", "Kai Zhao", "Yi Wang", "Ninghong Song", "Min Gu"], "journal": "Annals of translational medicine", "year": 2019, "abstract": "BACKGROUND: TP53-regulated inhibitor of apoptosis 1 (TRIAP1), also known as p53 cell survival factor or p53CSV, is reported to be associated with resistance of apoptosis in different human malignancies, but the potential role of TRIAP1 in penile carcinoma (PeCa) has not been well studied. This study aimed to analyze the association between TRIAP1 expression and clinical outcome in PeCa patients.\nMETHODS: Bioinformatics was used to analyze the differential TRIAP1 expression in PeCa compared with normal tissues in Gene Expression Omnibus (GEO) Dataset (GSE57955). The expression of TRIAP1 in tumor specimens from 57 patients undergoing radical penile surgery was detected by immunohistochemistry (IHC). Differential TRIAP1 expression in various human malignancies was also assessed by GEPIA web-tool based on The Cancer Genome Atlas (TCGA) Datasets. Subsequently, the relationship between TRIAP1 expression and clinical prognosis of PeCa patients was analyzed.\nRESULTS: Both IHC and GEO Dataset (GSE57955) showed that TRIAP1 was significantly overexpressed in PeCa tissues when compared with normal tissues. Based on patient data and IHC on clinical specimens, we found that strong intensity of TRIAP1 expression was significantly related with higher histological grade (P=0.049) and elevated local recurrence rate (P=0.023), suggesting TRIAP1 as a potential predictor in recurrence. Further, high TRIAP1 expression was identified to be a hazardous prognostic factor for local recurrence-free survival (RFS).\nCONCLUSIONS: High TRIAP1 expression in PeCa is associated with high risk of recurrence and poor survival, suggesting TRIAP1 may become a potential prognostic factor for PeCa.", "claims": [{"id": "claim-method", "statement": "Bioinformatics was used to analyze the differential TRIAP1 expression in PeCa compared with normal tissues in Gene Expression Omnibus (GEO) Dataset (GSE57955).", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:31475200", "locator": "sections[0] \"Abstract\" paragraph 2", "quote": "Bioinformatics was used to analyze the differential TRIAP1 expression in PeCa compared with normal tissues in Gene Expression Omnibus (GEO) Dataset (GSE57955)."}], "state": "complete"}, {"id": "claim-data-access", "statement": "Bioinformatics was used to analyze the differential TRIAP1 expression in PeCa compared with normal tissues in Gene Expression Omnibus (GEO) Dataset (GSE57955).", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:31475200", "locator": "sections[0] \"Abstract\" paragraph 2", "quote": "Bioinformatics was used to analyze the differential TRIAP1 expression in PeCa compared with normal tissues in Gene Expression Omnibus (GEO) Dataset (GSE57955)."}], "state": "complete"}, {"id": "claim-target-result", "statement": "Based on patient data and IHC on clinical specimens, we found that strong intensity of TRIAP1 expression was significantly related with higher histological grade (P=0.049) and elevated local recurrence rate (P=0.023), suggesting TRIAP1 as a potential predictor in recurrence.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:31475200", "locator": "sections[0] \"Abstract\" paragraph 3", "quote": "Based on patient data and IHC on clinical specimens, we found that strong intensity of TRIAP1 expression was significantly related with higher histological grade (P=0.049) and elevated local recurrence rate (P=0.023), suggesting TRIAP1 as a potential predictor in recurrence."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "Based on patient data and IHC on clinical specimens, we found that strong intensity of TRIAP1 expression was significantly related with higher histological grade (P=0.049) and elevated local recurrence rate (P=0.023), suggesting TRIAP1 as a potential predictor in recurrence.", "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:31475200"], "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:GSE57955"], "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:GSE57955"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:31475200", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.21037/atm.2019.06.47", "sha256": "sha256:53a052ddd43a490f58afa04059c4e9f37f75a44782e4766ba29d6d1976dcd3a9", "bytes": 1657, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.21037/atm.2019.06.47", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC6694233", "source": "ncbi_pmc_fulltext", "coverage": "whole_body", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE57955", "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=GSE57955", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE57955", "version": null, "note": "Bioinformatics was used to analyze the differential TRIAP1 expression in PeCa compared with normal tissues in Gene Expression Omnibus (GEO) Dataset (GSE57955).", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "Bioinformatics was used to analyze the differential TRIAP1 expression in PeCa compared with normal tissues in Gene Expression Omnibus (GEO) Dataset (GSE57955).", "access_statement_kind": "repository_route_statement", "sample_accessions": ["GSM1398486", "GSM1398487", "GSM1398488", "GSM1398489", "GSM1398490", "GSM1398491", "GSM1398492", "GSM1398493", "GSM1398494", "GSM1398495", "GSM1398496", "GSM1398497", "GSM1398498", "GSM1398499", "GSM1398500", "GSM1398501", "GSM1398502", "GSM1398503", "GSM1398504", "GSM1398505", "GSM1398506", "GSM1398507", "GSM1398508", "GSM1398509", "GSM1398510", "GSM1398511", "GSM1398512", "GSM1398513", "GSM1398514", "GSM1398515", "GSM1398516", "GSM1398517", "GSM1398518", "GSM1398519", "GSM1398520", "GSM1398521", "GSM1398522", "GSM1398523", "GSM1398524"], "sample_count": 39, "group_sizes": null, "group_sizes_basis": null, "platform": "6480", "taxon": "Homo sapiens", "title": "Large scale gene expression analysis uncover new molecules related to biology and HPV mediated carcinogenesis in penile tumors", "resolution_checked_at": "2026-11-01T17:30:42Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}], "gaps": ["asset:data:geo:GSE57955 not downloaded", "asset:data:geo:GSE57955 licence not read"]}, "analysis": {"state": "partial", "methods": [{"id": "method-1", "family": null, "specific": null, "label": "Bioinformatics", "dsl_operations": [], "missing_operations": [], "expressible": null, "parameters": {}, "data_shapes": [], "evidence": {"score": 1.0, "band": "verbatim", "quote": "Bioinformatics was used to analyze the differential TRIAP1 expression in PeCa compared with normal tissues in Gene Expression Omnibus (GEO) Dataset (GSE57955)."}}], "targets": [], "gaps": ["method.reader_named_unmapped"]}, "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": "blocked", "tier": "R4", "blocking_axis": "method", "blocked_on": "method:not_determinable", "axes": {"method": {"tier": "R4", "expressible": false, "required_operations": [], "missing_operations": [], "basis": "The reader quoted the method the paper names (Bioinformatics), but the corpus's method extractor could not map it onto a DSL operation, so the method is published but not expressible."}, "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": ["GSE57955"], "resolved_accessions": ["GSE57955"], "statements": ["Bioinformatics was used to analyze the differential TRIAP1 expression in PeCa compared with normal tissues in Gene Expression Omnibus (GEO) Dataset (GSE57955)."], "basis": "The paper names GSE57955 in Gene Expression Omnibus (GEO) and the accession resolves in the repository. No dataset was downloaded and no licence was read."}}, "can_run": {"dsl_operations": [], "assets": ["source:pmid:31475200", "data:geo:GSE57955"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:GSE57955"]}, "gaps": ["method:not_determinable"]}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-11-01T16:58:39Z", "independence": "single_reader"}, "evidence_check": {"method": "verbatim", "availability": null}, "calls": 5, "usage": {"prompt_tokens": 1979, "completion_tokens": 1010, "cached_tokens": 0}}, "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:31475200", "type": "paper", "label": "pmid:31475200"}, {"id": "source:pmid:31475200", "type": "manuscript", "label": "PMID 31475200 full text"}, {"id": "data:geo:GSE57955", "type": "dataset", "label": "GEO GSE57955"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:31475200", "type": "paper", "label": "pmid:31475200"}, {"id": "source:pmid:31475200", "type": "manuscript", "label": "PMID 31475200 full text"}, {"id": "data:geo:GSE57955", "type": "dataset", "label": "GEO GSE57955"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-31475200", "type": "extraction", "used": ["source:pmid:31475200"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-GSE57955", "type": "accession_resolution", "used": ["data:geo:GSE57955"], "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:31475200", "parent_hash": "sha256:f442a7157540483e82771fb3ad506e06b759198cb7955ca578199b17606c1710", "fork_of": null, "generation": 2}, "gaps": ["asset:data:geo:GSE57955 licence not read", "asset:data:geo:GSE57955 not downloaded", "execution.not_run", "method.reader_named_unmapped", "review.human_critique", "review.independent_reader", "review.machine_critique"], "assays": [{"role": "data_generation", "definition_id": "apoptosis_assay", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.93, "evidence": ["BACKGROUND: TP53-regulated inhibitor of apoptosis 1 (TRIAP1), also known as p53 cell survival", "reported to be associated with resistance of apoptosis in different human malignancies, but the pot"], "order_basis": "paper_text_order:105", "id": "assay:1"}, {"role": "data_generation", "definition_id": "ihc", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.99, "evidence": ["going radical penile surgery was detected by immunohistochemistry (IHC). Differential TRIAP1 expression in var", "urgery was detected by immunohistochemistry (IHC). Differential TRIAP1 expression in various", "of PeCa patients was analyzed. RESULTS: Both IHC and GEO Dataset (GSE57955) showed that TRIAP", "th normal tissues. Based on patient data and IHC on clinical specimens, we found that strong"], "order_basis": "paper_text_order:739", "id": "assay:2"}]}