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

pmid:37880698

Anti-atherosclerotic effects of naringenin and quercetin from Folium Artemisiae argyi by attenuating Interleukin-1 beta (IL-1β)/ matrix metalloproteinase 9 (MMP9): network pharmacology-based analysis and validation.

Lei Zhang · Zhihui Yang · Xinyi Li · Yunqing Hua · Guanwei Fan · Feng He

BMC complementary medicine and therapies · 2023 doi:10.1186/s12906-023-04223-1

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:37880698
kind
science-record
content_hash
sha256:02347b3aaed71f57645c3edf81996f9ab9f21a52fec78d511c75915580cc5d1d
schema
https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json
created_at
2026-11-01T19:02:44Z
updated_at
2026-11-01T22:10:31Z
generator object · 2 fields
name
corpus-assay-engine
run_id
reading-sci-2026-11-01
paper object · 10 fields
state
complete
title
Anti-atherosclerotic effects of naringenin and quercetin from Folium Artemisiae argyi by attenuating Interleukin-1 beta (IL-1β)/ matrix metalloproteinase 9 (MMP9): network pharmacology-based analysis and validation.
doi
10.1186/s12906-023-04223-1
pmid
37880698
authors array · 6 items
[0]
Lei Zhang
[1]
Zhihui Yang
[2]
Xinyi Li
[3]
Yunqing Hua
[4]
Guanwei Fan
[5]
Feng He
journal
BMC complementary medicine and therapies
year
2023
abstract
Effective components and related target genes of Folium Artemisiae argyi were screened from Traditional Chinese Medicines for Systems Pharmacology Database and Analysis Platform. The therapeutic targets of atherosclerosis were searched in the MalaCards and OMIM databases. Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis were performed in WebGestalt online and verified according to ClueGo and Pedia apps in Cytoscape. Then, the protein-protein interaction network was analyzed using the STRING database and constructed using Cytoscape. Differential expression of target genes was identified in GSE9128 and GSE71226 by GEO2R. And then, molecular docking was performed using the Molecular Operating Environment. Finally, we validated the protein expression of Interleukin-6 (IL-6)/IL-1β /MMP9 by qRT-PCR and Western blot in Raw264.7 which was induced by LPS. A total of 232 potential target genes and 8 ingredients of Folium Artemisiae argyi were identified. Quercetin and naringenin are potential candidate bioactive agents in treating atherosclerosis. Vascular endothelial growth factor (VEGFA), MMP9 and IL-1β could be potential target genes. KEGG analysis demonstrated that the fluid shear stress and atherosclerosis pathway play a crucial role in the anti-atherosclerosis effect of Folium Artemisiae argyi. Gene Expression Omnibus (GEO) validation demonstrated that VEGFA was downregulated, while MMP9 and IL-1β were upregulated in patients with atherosclerosis. Molecular docking suggested that only MMP9 had a good combination with quercetin. The cell experiment results suggested that naringenin and quercetin have strong anti-inflammation effects, and significantly inhibit the expression of MMP9. Practical ApplicationsArtemisiae argyi is a traditional Chinese herbal medicine that has been widely used for its antibacterial and anti-inflammatory effects. This research demonstrated the bioactive ingredients, potential targets, and molecular mechanism of Folium Artemisiae argyi in treating atherosclerosis. It also suggests a reliable approach in investigating the therapeutic effect of traditional Chinese herbal medicine in treating Atherosclerotic cardiovascular disease (ASCVD).
claims array · 3 items
[0] object · 6 fields
id
claim-method
statement
Statistical analysis was performed by GraphPad (PRISM 7.0.a), statistical significance was considered as p < 0.05, the differences among groups were analyzed with one-way ANVOA .
kind
methodological
target
null
evidence array · 1 item
[0] object · 3 fields
asset
source:pmid:37880698
locator
sections[12] "Data analysis" paragraph 2
quote
Statistical analysis was performed by GraphPad (PRISM 7.0.a), statistical significance was considered as p < 0.05, the differences among groups were analyzed with one-way ANVOA .
state
complete
[1] object · 6 fields
id
claim-data-access
statement
The datasets used and/or analysed during the current study are available from the corresponding author on reasonable request. The data that support the findings of this study are openly available in [“figshare “] at 10.6084/m9.figshare.21916380.
kind
methodological
target
null
evidence array · 1 item
[0] object · 3 fields
asset
source:pmid:37880698
locator
sections[29] "notes" paragraph 1
quote
The datasets used and/or analysed during the current study are available from the corresponding author on reasonable request. The data that support the findings of this study are openly available in [“figshare “] at 10.6084/m9.figshare.21916380.
state
complete
[2] object · 6 fields
id
claim-target-result
statement
A total of 232 potential target genes and 8 ingredients of Folium Artemisiae argyi were identified.
kind
qualitative
target
null
evidence array · 1 item
[0] object · 3 fields
asset
source:pmid:37880698
locator
sections[0] "Abstract" paragraph 1
quote
A total of 232 potential target genes and 8 ingredients of Folium Artemisiae argyi were identified.
state
complete
gaps array · 0 items
experiment object · 8 fields
state
complete
objective
A total of 232 potential target genes and 8 ingredients of Folium Artemisiae argyi were identified.
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:37880698
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:GSE71226
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:GSE71226
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:37880698
role
manuscript
format
xml
media_type
application/xml
uri
https://doi.org/10.1186/s12906-023-04223-1
sha256
sha256:ba0073ebc7b6c817eb1b74c6805e309718411e49ad8eb56e0f4454d09c13d85b
bytes
28568
access
open
state
resolved
reader
null
reader_status
reader_required
identifier
10.1186/s12906-023-04223-1
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
PMC10601115
source
europe_pmc_fulltext
coverage
whole_body_without_references
text_hash_scope
rendered_section_body
[1] object · 15 fields
id
data:geo:GSE71226
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=GSE71226
sha256
null
bytes
null
access
open
state
resolved
reader
null
reader_status
reader_required
identifier
GSE71226
version
null
note
The datasets used and/or analysed during the current study are available from the corresponding author on reasonable request. The data that support the findings of this study are openly available in [“figshare “] at 10.6084/m9.figshare.21916380.
structure object · 15 fields
repository
GEO
access_route
GEO accession URL
access_statement_verbatim
The datasets used and/or analysed during the current study are available from the corresponding author on reasonable request. The data that support the findings of this study are openly available in [“figshare “] at 10.6084/m9.figshare.21916380.
access_statement_kind
data_availability_statement
sample_accessions array · 6 items
[0]
GSM1830987
[1]
GSM1830988
[2]
GSM1830989
[3]
GSM1830990
[4]
GSM1830991
[5]
GSM1830992
sample_count
6
group_sizes
null
group_sizes_basis
null
platform
570
taxon
Homo sapiens
title
Expression data from coronary heart disease in Chinese Han people
resolution_checked_at
2026-11-01T18:46:34Z
resolution_check
identifier_resolution_only_no_download_no_licence_read
downloaded
false
licence_read
false
[2] object · 15 fields
id
data:geo:GSE9128
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=GSE9128
sha256
null
bytes
null
access
open
state
resolved
reader
null
reader_status
reader_required
identifier
GSE9128
version
null
note
The datasets used and/or analysed during the current study are available from the corresponding author on reasonable request. The data that support the findings of this study are openly available in [“figshare “] at 10.6084/m9.figshare.21916380.
structure object · 15 fields
repository
GEO
access_route
GEO accession URL
access_statement_verbatim
The datasets used and/or analysed during the current study are available from the corresponding author on reasonable request. The data that support the findings of this study are openly available in [“figshare “] at 10.6084/m9.figshare.21916380.
access_statement_kind
data_availability_statement
sample_accessions array · 11 items
[0]
GSM231003
[1]
GSM231004
[2]
GSM231005
[3]
GSM231006
[4]
GSM231007
[5]
GSM231008
[6]
GSM231009
[7]
GSM231010
[8]
GSM231011
[9]
GSM231012
[10]
GSM231013
sample_count
11
group_sizes
null
group_sizes_basis
null
platform
96
taxon
Homo sapiens
title
Expression data from heart failure vs control peripheral blood mononuclear cells.
resolution_checked_at
2026-11-01T18:06:44Z
resolution_check
identifier_resolution_only_no_download_no_licence_read
downloaded
false
licence_read
false
gaps array · 4 items
[0]
asset:data:geo:GSE71226 not downloaded
[1]
asset:data:geo:GSE71226 licence not read
[2]
asset:data:geo:GSE9128 not downloaded
[3]
asset:data:geo:GSE9128 licence not read
analysis object · 4 fields
state
partial
methods array · 2 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
null
specific
null
label
one-way ANVOA
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
Statistical analysis was performed by GraphPad (PRISM 7.0.a), statistical significance was considered as p < 0.05, the differences among groups were analyzed with one-way ANVOA .
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 · 2 items
[0]
GSE9128
[1]
GSE71226
resolved_accessions array · 2 items
[0]
GSE9128
[1]
GSE71226
statements array · 1 item
[0]
The datasets used and/or analysed during the current study are available from the corresponding author on reasonable request. The data that support the findings of this study are openly available in [“figshare “] at 10.6084/m9.figshare.21916380.
basis
The paper names GSE9128, GSE71226 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:37880698
[1]
data:geo:GSE71226
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:GSE71226
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
2026-11-01T18:57:06Z
independence
single_reader
evidence_check object · 2 fields
method
verbatim
availability
verbatim
calls
5
usage object · 3 fields
prompt_tokens
8973
completion_tokens
1075
cached_tokens
265
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:37880698
type
paper
label
pmid:37880698
[1] object · 3 fields
id
source:pmid:37880698
type
manuscript
label
PMID 37880698 full text
[2] object · 3 fields
id
data:geo:GSE71226
type
dataset
label
GEO GSE71226
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:37880698
type
paper
label
pmid:37880698
[1] object · 3 fields
id
source:pmid:37880698
type
manuscript
label
PMID 37880698 full text
[2] object · 3 fields
id
data:geo:GSE71226
type
dataset
label
GEO GSE71226
agent
agent:corpus-assay-engine
[1] object · 4 fields
id
activity-read-37880698
type
extraction
used array · 1 item
[0]
source:pmid:37880698
agent
agent:minimax-reader
[2] object · 4 fields
id
activity-resolve-GSE71226
type
accession_resolution
used array · 1 item
[0]
data:geo:GSE71226
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:37880698
parent_hash
sha256:7e78fe6e228144c13da95b0529530e29fe840fb645deacdfdfb88787967bd012
fork_of
null
gaps array · 9 items
[0]
asset:data:geo:GSE71226 licence not read
[1]
asset:data:geo:GSE71226 not downloaded
[2]
asset:data:geo:GSE9128 licence not read
[3]
asset:data:geo:GSE9128 not downloaded
[4]
execution.not_run
[5]
method.reader_named_unmapped
[6]
review.human_critique
[7]
review.independent_reader
[8]
review.machine_critique
assays array · 2 items
[0] object · 11 fields
role
data_generation
definition_id
western_blot
definition_version
99e1195c7d6f
required_operations array · 0 items
support_state
partial
source_hashes object · 1 field
assay_lexicon
99e1195c7d6f
confidence
0.93
evidence array · 1 item
[0]
erleukin-6 (IL-6)/IL-1β /MMP9 by qRT-PCR and Western blot in Raw264.7 which was induced by LPS. A tota
order_basis
paper_text_order:994
id
assay:1
[1] 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
consumes_earlier_output
id
assay:2
Complete file
{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:37880698", "kind": "science-record", "revision": 3, "content_hash": "sha256:02347b3aaed71f57645c3edf81996f9ab9f21a52fec78d511c75915580cc5d1d", "created_at": "2026-11-01T19:02:44Z", "updated_at": "2026-11-01T22:10:31Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Anti-atherosclerotic effects of naringenin and quercetin from Folium Artemisiae argyi by attenuating Interleukin-1 beta (IL-1β)/ matrix metalloproteinase 9 (MMP9): network pharmacology-based analysis and validation.", "doi": "10.1186/s12906-023-04223-1", "pmid": "37880698", "authors": ["Lei Zhang", "Zhihui Yang", "Xinyi Li", "Yunqing Hua", "Guanwei Fan", "Feng He"], "journal": "BMC complementary medicine and therapies", "year": 2023, "abstract": "Effective components and related target genes of Folium Artemisiae argyi were screened from Traditional Chinese Medicines for Systems Pharmacology Database and Analysis Platform. The therapeutic targets of atherosclerosis were searched in the MalaCards and OMIM databases. Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis were performed in WebGestalt online and verified according to ClueGo and Pedia apps in Cytoscape. Then, the protein-protein interaction network was analyzed using the STRING database and constructed using Cytoscape. Differential expression of target genes was identified in GSE9128 and GSE71226 by GEO2R. And then, molecular docking was performed using the Molecular Operating Environment. Finally, we validated the protein expression of Interleukin-6 (IL-6)/IL-1β /MMP9 by qRT-PCR and Western blot in Raw264.7 which was induced by LPS. A total of 232 potential target genes and 8 ingredients of Folium Artemisiae argyi were identified. Quercetin and naringenin are potential candidate bioactive agents in treating atherosclerosis. Vascular endothelial growth factor (VEGFA), MMP9 and IL-1β could be potential target genes. KEGG analysis demonstrated that the fluid shear stress and atherosclerosis pathway play a crucial role in the anti-atherosclerosis effect of Folium Artemisiae argyi. Gene Expression Omnibus (GEO) validation demonstrated that VEGFA was downregulated, while MMP9 and IL-1β were upregulated in patients with atherosclerosis. Molecular docking suggested that only MMP9 had a good combination with quercetin. The cell experiment results suggested that naringenin and quercetin have strong anti-inflammation effects, and significantly inhibit the expression of MMP9. Practical ApplicationsArtemisiae argyi is a traditional Chinese herbal medicine that has been widely used for its antibacterial and anti-inflammatory effects. This research demonstrated the bioactive ingredients, potential targets, and molecular mechanism of Folium Artemisiae argyi in treating atherosclerosis. It also suggests a reliable approach in investigating the therapeutic effect of traditional Chinese herbal medicine in treating Atherosclerotic cardiovascular disease (ASCVD).", "claims": [{"id": "claim-method", "statement": "Statistical analysis was performed by GraphPad (PRISM 7.0.a), statistical significance was considered as p < 0.05, the differences among groups were analyzed with one-way ANVOA .", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:37880698", "locator": "sections[12] \"Data analysis\" paragraph 2", "quote": "Statistical analysis was performed by GraphPad (PRISM 7.0.a), statistical significance was considered as p < 0.05, the differences among groups were analyzed with one-way ANVOA ."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The datasets used and/or analysed during the current study are available from the corresponding author on reasonable request. The data that support the findings of this study are openly available in [“figshare “] at 10.6084/m9.figshare.21916380.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:37880698", "locator": "sections[29] \"notes\" paragraph 1", "quote": "The datasets used and/or analysed during the current study are available from the corresponding author on reasonable request. The data that support the findings of this study are openly available in [“figshare “] at 10.6084/m9.figshare.21916380."}], "state": "complete"}, {"id": "claim-target-result", "statement": "A total of 232 potential target genes and 8 ingredients of Folium Artemisiae argyi were identified.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:37880698", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "A total of 232 potential target genes and 8 ingredients of Folium Artemisiae argyi were identified."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "A total of 232 potential target genes and 8 ingredients of Folium Artemisiae argyi were identified.", "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:37880698"], "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:GSE71226"], "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:GSE71226"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:37880698", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.1186/s12906-023-04223-1", "sha256": "sha256:ba0073ebc7b6c817eb1b74c6805e309718411e49ad8eb56e0f4454d09c13d85b", "bytes": 28568, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.1186/s12906-023-04223-1", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC10601115", "source": "europe_pmc_fulltext", "coverage": "whole_body_without_references", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE71226", "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=GSE71226", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE71226", "version": null, "note": "The datasets used and/or analysed during the current study are available from the corresponding author on reasonable request. The data that support the findings of this study are openly available in [“figshare “] at 10.6084/m9.figshare.21916380.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The datasets used and/or analysed during the current study are available from the corresponding author on reasonable request. The data that support the findings of this study are openly available in [“figshare “] at 10.6084/m9.figshare.21916380.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM1830987", "GSM1830988", "GSM1830989", "GSM1830990", "GSM1830991", "GSM1830992"], "sample_count": 6, "group_sizes": null, "group_sizes_basis": null, "platform": "570", "taxon": "Homo sapiens", "title": "Expression data from coronary heart disease in Chinese Han people", "resolution_checked_at": "2026-11-01T18:46:34Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}, {"id": "data:geo:GSE9128", "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=GSE9128", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE9128", "version": null, "note": "The datasets used and/or analysed during the current study are available from the corresponding author on reasonable request. The data that support the findings of this study are openly available in [“figshare “] at 10.6084/m9.figshare.21916380.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The datasets used and/or analysed during the current study are available from the corresponding author on reasonable request. The data that support the findings of this study are openly available in [“figshare “] at 10.6084/m9.figshare.21916380.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM231003", "GSM231004", "GSM231005", "GSM231006", "GSM231007", "GSM231008", "GSM231009", "GSM231010", "GSM231011", "GSM231012", "GSM231013"], "sample_count": 11, "group_sizes": null, "group_sizes_basis": null, "platform": "96", "taxon": "Homo sapiens", "title": "Expression data from heart failure vs control peripheral blood mononuclear cells.", "resolution_checked_at": "2026-11-01T18:06:44Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}], "gaps": ["asset:data:geo:GSE71226 not downloaded", "asset:data:geo:GSE71226 licence not read", "asset:data:geo:GSE9128 not downloaded", "asset:data:geo:GSE9128 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": null, "specific": null, "label": "one-way ANVOA", "dsl_operations": [], "missing_operations": [], "expressible": null, "parameters": {}, "data_shapes": [], "evidence": {"score": 1.0, "band": "verbatim", "quote": "Statistical analysis was performed by GraphPad (PRISM 7.0.a), statistical significance was considered as p < 0.05, the differences among groups were analyzed with one-way ANVOA ."}}], "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": ["GSE9128", "GSE71226"], "resolved_accessions": ["GSE9128", "GSE71226"], "statements": ["The datasets used and/or analysed during the current study are available from the corresponding author on reasonable request. The data that support the findings of this study are openly available in [“figshare “] at 10.6084/m9.figshare.21916380."], "basis": "The paper names GSE9128, GSE71226 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:37880698", "data:geo:GSE71226"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:GSE71226"]}, "gaps": []}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-11-01T18:57:06Z", "independence": "single_reader"}, "evidence_check": {"method": "verbatim", "availability": "verbatim"}, "calls": 5, "usage": {"prompt_tokens": 8973, "completion_tokens": 1075, "cached_tokens": 265}}, "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:37880698", "type": "paper", "label": "pmid:37880698"}, {"id": "source:pmid:37880698", "type": "manuscript", "label": "PMID 37880698 full text"}, {"id": "data:geo:GSE71226", "type": "dataset", "label": "GEO GSE71226"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:37880698", "type": "paper", "label": "pmid:37880698"}, {"id": "source:pmid:37880698", "type": "manuscript", "label": "PMID 37880698 full text"}, {"id": "data:geo:GSE71226", "type": "dataset", "label": "GEO GSE71226"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-37880698", "type": "extraction", "used": ["source:pmid:37880698"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-GSE71226", "type": "accession_resolution", "used": ["data:geo:GSE71226"], "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:37880698", "parent_hash": "sha256:7e78fe6e228144c13da95b0529530e29fe840fb645deacdfdfb88787967bd012", "fork_of": null, "generation": 2}, "gaps": ["asset:data:geo:GSE71226 licence not read", "asset:data:geo:GSE71226 not downloaded", "asset:data:geo:GSE9128 licence not read", "asset:data:geo:GSE9128 not downloaded", "execution.not_run", "method.reader_named_unmapped", "review.human_critique", "review.independent_reader", "review.machine_critique"], "assays": [{"role": "data_generation", "definition_id": "western_blot", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.93, "evidence": ["erleukin-6 (IL-6)/IL-1β /MMP9 by qRT-PCR and Western blot in Raw264.7 which was induced by LPS. A tota"], "order_basis": "paper_text_order:994", "id": "assay:1"}, {"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": "consumes_earlier_output", "id": "assay:2"}]}