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

pmid:40386529

Analysis of significance of CARD11 and MYO1G expressions in pulmonary tuberculosis and their predictive value for prognosis of recurrence.

Fengxia Liu · Shengxun Lin · Li Li · Bei Xu · Tingting Chang

Journal of medical biochemistry · 2025 doi:10.5937/jomb0-54554

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:40386529
kind
science-record
content_hash
sha256:cb98d2f92952ba7693d8697c96ae21639428ad9d56c1bd2ccec45983786c70e4
schema
https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json
created_at
2026-11-01T20:30:32Z
updated_at
2026-11-01T22:14:04Z
generator object · 2 fields
name
corpus-assay-engine
run_id
reading-sci-2026-11-01
paper object · 10 fields
state
complete
title
Analysis of significance of CARD11 and MYO1G expressions in pulmonary tuberculosis and their predictive value for prognosis of recurrence.
doi
10.5937/jomb0-54554
pmid
40386529
authors array · 5 items
[0]
Fengxia Liu
[1]
Shengxun Lin
[2]
Li Li
[3]
Bei Xu
[4]
Tingting Chang
journal
Journal of medical biochemistry
year
2025
abstract
Pulmonary tuberculosis (PTB) is one of the most common infectious diseases worldwide, with extremely high morbidity and mortality. An in-depth understanding of the molecular pathogenesis of PTB is crucial for finding novel diagnostic and therapeutic approaches in the future. In this study, we identified 52 differentially expressed genes (DEGs) from the GSE34608 dataset in the Gene Expression Omnibus (GEO) database, and the protein-protein interaction (PPI) network showed that these DEGs included 42 nodes and 20 edges. We found that CARD11 and MYO1G were closely associated with T cell activation by functional enrichment analysis. Upon further clinical case analysis, we found that the expressions of CARD11 and MYO1G in the peripheral blood of patients with PTB were lower than those of healthy individuals. Meanwhile, through Receiver operating characteristic (ROC) curve analysis, we found that CARD11 and MYO1G showed excellent diagnostic effects on the occurrence and prognosis of PTB recurrence. Thus, CARD11 and MYO1G are promising indicators for assessing PTB in the future.
claims array · 3 items
[0] object · 6 fields
id
claim-method
statement
The receiver operator characteristic (ROC) curve analysed the diagnostic value.
kind
methodological
target
null
evidence array · 1 item
[0] object · 3 fields
asset
source:pmid:40386529
locator
sections[11] "Statistical analysis" paragraph 2
quote
The receiver operator characteristic (ROC) curve analysed the diagnostic value.
state
complete
[1] object · 6 fields
id
claim-data-access
statement
The data used to support the findings of this study are available from the corresponding author upon request.
kind
methodological
target
null
evidence array · 1 item
[0] object · 3 fields
asset
source:pmid:40386529
locator
sections[21] "Availability of data and materials" paragraph 2
quote
The data used to support the findings of this study are available from the corresponding author upon request.
state
complete
[2] object · 6 fields
id
claim-target-result
statement
The study identified 52 differentially expressed genes from GSE34608, with the resulting protein-protein interaction network containing 42 nodes and 20 edges.
kind
qualitative
target
null
evidence array · 1 item
[0] object · 3 fields
asset
source:pmid:40386529
locator
sections[0] "Abstract" paragraph 1
quote
In this study, we identified 52 differentially expressed genes (DEGs) from the GSE34608 dataset in the Gene Expression Omnibus (GEO) database, and the protein-protein interaction (PPI) network showed that these DEGs included 42 nodes and 20 edges.
state
complete
gaps array · 0 items
experiment object · 8 fields
state
complete
objective
The study identified 52 differentially expressed genes from GSE34608, with the resulting protein-protein interaction network containing 42 nodes and 20 edges.
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:40386529
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:GSE34608
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:GSE34608
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:40386529
role
manuscript
format
xml
media_type
application/xml
uri
https://doi.org/10.5937/jomb0-54554
sha256
sha256:274d41f2d9ba00e534c44138534ca6d438ea82ecab7859652fccd50b34714549
bytes
16911
access
open
state
resolved
reader
null
reader_status
reader_required
identifier
10.5937/jomb0-54554
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
PMC12085172
source
europe_pmc_fulltext
coverage
whole_body_without_references
text_hash_scope
rendered_section_body
[1] object · 15 fields
id
data:geo:GSE34608
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=GSE34608
sha256
null
bytes
null
access
open
state
resolved
reader
null
reader_status
reader_required
identifier
GSE34608
version
null
note
The data used to support the findings of this study are available from the corresponding author upon request.
structure object · 15 fields
repository
GEO
access_route
GEO accession URL
access_statement_verbatim
The data used to support the findings of this study are available from the corresponding author upon request.
access_statement_kind
data_availability_statement
sample_accessions array · 68 items
[0]
GSM851793
[1]
GSM851794
[2]
GSM851795
[3]
GSM851796
[4]
GSM851797
[5]
GSM851798
[6]
GSM851799
[7]
GSM851800
[8]
GSM851801
[9]
GSM851802
[10]
GSM851803
[11]
GSM851804
[12]
GSM851805
[13]
GSM851806
[14]
GSM851807
[15]
GSM851808
[16]
GSM851809
[17]
GSM851810
[18]
GSM851811
[19]
GSM851812
[20]
GSM851813
[21]
GSM851814
[22]
GSM851815
[23]
GSM851816
[24]
GSM851850
[25]
GSM851851
[26]
GSM851852
[27]
GSM851853
[28]
GSM851854
[29]
GSM851855
[30]
GSM851856
[31]
GSM851857
[32]
GSM851858
[33]
GSM851859
[34]
GSM851860
[35]
GSM851861
[36]
GSM851862
[37]
GSM851863
[38]
GSM851864
[39]
GSM851865
[40]
GSM851866
[41]
GSM851867
[42]
GSM851868
[43]
GSM851869
[44]
GSM851870
[45]
GSM851871
[46]
GSM851872
[47]
GSM851873
[48]
GSM851874
[49]
GSM851875
[50]
GSM851876
[51]
GSM851877
[52]
GSM851878
[53]
GSM851879
[54]
GSM851880
[55]
GSM851881
[56]
GSM851882
[57]
GSM851883
[58]
GSM851884
[59]
GSM851885
[60]
GSM851886
[61]
GSM851887
[62]
GSM851888
[63]
GSM851889
[64]
GSM851890
[65]
GSM851891
[66]
GSM851892
[67]
GSM851893
sample_count
68
group_sizes
null
group_sizes_basis
null
platform
7731;6480
taxon
Homo sapiens
title
Gene and microRNA expression in pulmonary tuberculosis and sarcoidosis
resolution_checked_at
2026-11-01T18:46:34Z
resolution_check
identifier_resolution_only_no_download_no_licence_read
downloaded
false
licence_read
false
gaps array · 2 items
[0]
asset:data:geo:GSE34608 not downloaded
[1]
asset:data:geo:GSE34608 licence not read
analysis object · 4 fields
state
partial
methods array · 3 items
[0] object · 10 fields
id
method-1
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
[1] object · 10 fields
id
method-2
family
contingency_analysis
specific
chi_square
label
Categorical (contingency table) analysis
dsl_operations array · 1 item
[0]
chi_square_test
missing_operations array · 0 items
parameters object · 0 fields
data_shapes array · 1 item
[0]
categorical_cross_tabulation
evidence object · 3 fields
score
0.8
band
high
quote
chi-square
[2] object · 10 fields
id
method-3
family
null
specific
null
label
receiver operator characteristic (ROC) curve analysis
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
The receiver operator characteristic (ROC) curve analysed the diagnostic value.
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
complete
tier
R1
blocked_on
nothing:replicable_now
axes object · 3 fields
method object · 5 fields
tier
R1
expressible
true
required_operations array · 3 items
[0]
build_graph
[1]
centrality_scores
[2]
pathway_enrich
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: ppi_network.
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]
GSE34608
resolved_accessions array · 1 item
[0]
GSE34608
statements array · 1 item
[0]
The data used to support the findings of this study are available from the corresponding author upon request.
basis
The paper names GSE34608 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 · 3 items
[0]
build_graph
[1]
centrality_scores
[2]
pathway_enrich
assets array · 2 items
[0]
source:pmid:40386529
[1]
data:geo:GSE34608
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:GSE34608
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
2026-11-01T19:52:39Z
independence
single_reader
evidence_check object · 2 fields
method
verbatim
availability
verbatim
calls
5
usage object · 3 fields
prompt_tokens
5788
completion_tokens
1822
cached_tokens
264
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:40386529
type
paper
label
pmid:40386529
[1] object · 3 fields
id
source:pmid:40386529
type
manuscript
label
PMID 40386529 full text
[2] object · 3 fields
id
data:geo:GSE34608
type
dataset
label
GEO GSE34608
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:40386529
type
paper
label
pmid:40386529
[1] object · 3 fields
id
source:pmid:40386529
type
manuscript
label
PMID 40386529 full text
[2] object · 3 fields
id
data:geo:GSE34608
type
dataset
label
GEO GSE34608
agent
agent:corpus-assay-engine
[1] object · 4 fields
id
activity-read-40386529
type
extraction
used array · 1 item
[0]
source:pmid:40386529
agent
agent:minimax-reader
[2] object · 4 fields
id
activity-resolve-GSE34608
type
accession_resolution
used array · 1 item
[0]
data:geo:GSE34608
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:40386529
parent_hash
sha256:1e18686a7276a1feeceaa7560f8650336215e51c2dd8216a9fcc47a94d83dca0
fork_of
null
gaps array · 7 items
[0]
asset:data:geo:GSE34608 licence not read
[1]
asset:data:geo:GSE34608 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 · 1 item
[0] object · 11 fields
role
analysis
definition_id
network_analysis
definition_version
f2132e96ae6c7a4e
required_operations array · 3 items
[0]
build_graph
[1]
centrality_scores
[2]
pathway_enrich
support_state
supported
source_hashes object · 1 field
dsl_catalogue
f2132e96ae6c7a4e
evidence array · 1 item
[0]
protein-protein interaction
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:40386529", "kind": "science-record", "revision": 3, "content_hash": "sha256:cb98d2f92952ba7693d8697c96ae21639428ad9d56c1bd2ccec45983786c70e4", "created_at": "2026-11-01T20:30:32Z", "updated_at": "2026-11-01T22:14:04Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Analysis of significance of CARD11 and MYO1G expressions in pulmonary tuberculosis and their predictive value for prognosis of recurrence.", "doi": "10.5937/jomb0-54554", "pmid": "40386529", "authors": ["Fengxia Liu", "Shengxun Lin", "Li Li", "Bei Xu", "Tingting Chang"], "journal": "Journal of medical biochemistry", "year": 2025, "abstract": "Pulmonary tuberculosis (PTB) is one of the most common infectious diseases worldwide, with extremely high morbidity and mortality. An in-depth understanding of the molecular pathogenesis of PTB is crucial for finding novel diagnostic and therapeutic approaches in the future. In this study, we identified 52 differentially expressed genes (DEGs) from the GSE34608 dataset in the Gene Expression Omnibus (GEO) database, and the protein-protein interaction (PPI) network showed that these DEGs included 42 nodes and 20 edges. We found that CARD11 and MYO1G were closely associated with T cell activation by functional enrichment analysis. Upon further clinical case analysis, we found that the expressions of CARD11 and MYO1G in the peripheral blood of patients with PTB were lower than those of healthy individuals. Meanwhile, through Receiver operating characteristic (ROC) curve analysis, we found that CARD11 and MYO1G showed excellent diagnostic effects on the occurrence and prognosis of PTB recurrence. Thus, CARD11 and MYO1G are promising indicators for assessing PTB in the future.", "claims": [{"id": "claim-method", "statement": "The receiver operator characteristic (ROC) curve analysed the diagnostic value.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:40386529", "locator": "sections[11] \"Statistical analysis\" paragraph 2", "quote": "The receiver operator characteristic (ROC) curve analysed the diagnostic value."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The data used to support the findings of this study are available from the corresponding author upon request.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:40386529", "locator": "sections[21] \"Availability of data and materials\" paragraph 2", "quote": "The data used to support the findings of this study are available from the corresponding author upon request."}], "state": "complete"}, {"id": "claim-target-result", "statement": "The study identified 52 differentially expressed genes from GSE34608, with the resulting protein-protein interaction network containing 42 nodes and 20 edges.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:40386529", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "In this study, we identified 52 differentially expressed genes (DEGs) from the GSE34608 dataset in the Gene Expression Omnibus (GEO) database, and the protein-protein interaction (PPI) network showed that these DEGs included 42 nodes and 20 edges."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "The study identified 52 differentially expressed genes from GSE34608, with the resulting protein-protein interaction network containing 42 nodes and 20 edges.", "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:40386529"], "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:GSE34608"], "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:GSE34608"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:40386529", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.5937/jomb0-54554", "sha256": "sha256:274d41f2d9ba00e534c44138534ca6d438ea82ecab7859652fccd50b34714549", "bytes": 16911, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.5937/jomb0-54554", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC12085172", "source": "europe_pmc_fulltext", "coverage": "whole_body_without_references", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE34608", "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=GSE34608", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE34608", "version": null, "note": "The data used to support the findings of this study are available from the corresponding author upon request.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The data used to support the findings of this study are available from the corresponding author upon request.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM851793", "GSM851794", "GSM851795", "GSM851796", "GSM851797", "GSM851798", "GSM851799", "GSM851800", "GSM851801", "GSM851802", "GSM851803", "GSM851804", "GSM851805", "GSM851806", "GSM851807", "GSM851808", "GSM851809", "GSM851810", "GSM851811", "GSM851812", "GSM851813", "GSM851814", "GSM851815", "GSM851816", "GSM851850", "GSM851851", "GSM851852", "GSM851853", "GSM851854", "GSM851855", "GSM851856", "GSM851857", "GSM851858", "GSM851859", "GSM851860", "GSM851861", "GSM851862", "GSM851863", "GSM851864", "GSM851865", "GSM851866", "GSM851867", "GSM851868", "GSM851869", "GSM851870", "GSM851871", "GSM851872", "GSM851873", "GSM851874", "GSM851875", "GSM851876", "GSM851877", "GSM851878", "GSM851879", "GSM851880", "GSM851881", "GSM851882", "GSM851883", "GSM851884", "GSM851885", "GSM851886", "GSM851887", "GSM851888", "GSM851889", "GSM851890", "GSM851891", "GSM851892", "GSM851893"], "sample_count": 68, "group_sizes": null, "group_sizes_basis": null, "platform": "7731;6480", "taxon": "Homo sapiens", "title": "Gene and microRNA expression in pulmonary tuberculosis and sarcoidosis", "resolution_checked_at": "2026-11-01T18:46:34Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}], "gaps": ["asset:data:geo:GSE34608 not downloaded", "asset:data:geo:GSE34608 licence not read"]}, "analysis": {"state": "partial", "methods": [{"id": "method-1", "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-2", "family": "contingency_analysis", "specific": "chi_square", "label": "Categorical (contingency table) analysis", "dsl_operations": ["chi_square_test"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["categorical_cross_tabulation"], "evidence": {"score": 0.8, "band": "high", "quote": "chi-square"}}, {"id": "method-3", "family": null, "specific": null, "label": "receiver operator characteristic (ROC) curve analysis", "dsl_operations": [], "missing_operations": [], "expressible": null, "parameters": {}, "data_shapes": [], "evidence": {"score": 1.0, "band": "verbatim", "quote": "The receiver operator characteristic (ROC) curve analysed the diagnostic value."}}], "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": "complete", "tier": "R1", "blocking_axis": "none", "blocked_on": "nothing:replicable_now", "axes": {"method": {"tier": "R1", "expressible": true, "required_operations": ["build_graph", "centrality_scores", "pathway_enrich"], "missing_operations": [], "basis": "The paper names the method it used and the corpus's method extractor maps it onto the DSL catalogue: ppi_network."}, "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": ["GSE34608"], "resolved_accessions": ["GSE34608"], "statements": ["The data used to support the findings of this study are available from the corresponding author upon request."], "basis": "The paper names GSE34608 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": ["build_graph", "centrality_scores", "pathway_enrich"], "assets": ["source:pmid:40386529", "data:geo:GSE34608"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:GSE34608"]}, "gaps": []}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-11-01T19:52:39Z", "independence": "single_reader"}, "evidence_check": {"method": "verbatim", "availability": "verbatim"}, "calls": 5, "usage": {"prompt_tokens": 5788, "completion_tokens": 1822, "cached_tokens": 264}}, "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:40386529", "type": "paper", "label": "pmid:40386529"}, {"id": "source:pmid:40386529", "type": "manuscript", "label": "PMID 40386529 full text"}, {"id": "data:geo:GSE34608", "type": "dataset", "label": "GEO GSE34608"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:40386529", "type": "paper", "label": "pmid:40386529"}, {"id": "source:pmid:40386529", "type": "manuscript", "label": "PMID 40386529 full text"}, {"id": "data:geo:GSE34608", "type": "dataset", "label": "GEO GSE34608"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-40386529", "type": "extraction", "used": ["source:pmid:40386529"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-GSE34608", "type": "accession_resolution", "used": ["data:geo:GSE34608"], "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:40386529", "parent_hash": "sha256:1e18686a7276a1feeceaa7560f8650336215e51c2dd8216a9fcc47a94d83dca0", "fork_of": null, "generation": 2}, "gaps": ["asset:data:geo:GSE34608 licence not read", "asset:data:geo:GSE34608 not downloaded", "execution.not_run", "method.reader_named_unmapped", "review.human_critique", "review.independent_reader", "review.machine_critique"], "assays": [{"role": "analysis", "definition_id": "network_analysis", "definition_version": "f2132e96ae6c7a4e", "definition_digest": null, "required_operations": ["build_graph", "centrality_scores", "pathway_enrich"], "support_state": "supported", "source_hashes": {"dsl_catalogue": "f2132e96ae6c7a4e"}, "confidence": 0.7, "evidence": ["protein-protein interaction"], "order_basis": "analysis_only", "id": "assay:1"}]}