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

pmid:36080270

Exosome Proteomics Reveals the Deregulation of Coagulation, Complement and Lipid Metabolism Proteins in Gestational Diabetes Mellitus.

Elena G Bernea · Viorel I Suica · Elena Uyy · Aurel Cerveanu-Hogas · Raluca M Boteanu · Luminita Ivan · Iuliana Ceausu · Doina A Mihai · Constantin Ionescu-Tîrgoviște · Felicia Antohe

Molecules (Basel, Switzerland) · 2022 doi:10.3390/molecules27175502

Paper

complete

Experiment

complete

Data

partial

Analysis

complete

Execution

absent

Execution evidence has not yet been added to this .science file. Explore its methods, data and open questions to plan the next step.
Record details sci_version · id · kind · revision · content_hash · schema · created_at · updated_at · generator
id
pmid:36080270
kind
science-record
content_hash
sha256:0367894c7c4d2cf6e8f06c219b1006fd5d66ac6714070967008763ca82ae4970
schema
https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json
created_at
2026-11-01T18:15:18Z
updated_at
2026-11-01T22:50:01Z
generator object · 2 fields
name
corpus-assay-engine
run_id
reading-sci-2026-11-01
paper object · 10 fields
state
complete
title
Exosome Proteomics Reveals the Deregulation of Coagulation, Complement and Lipid Metabolism Proteins in Gestational Diabetes Mellitus.
doi
10.3390/molecules27175502
pmid
36080270
authors array · 10 items
[0]
Elena G Bernea
[1]
Viorel I Suica
[2]
Elena Uyy
[3]
Aurel Cerveanu-Hogas
[4]
Raluca M Boteanu
[5]
Luminita Ivan
[6]
Iuliana Ceausu
[7]
Doina A Mihai
[8]
Constantin Ionescu-Tîrgoviște
[9]
Felicia Antohe
journal
Molecules (Basel, Switzerland)
year
2022
abstract
Exosomes are small extracellular vesicles with a variable protein cargo in consonance with cell origin and pathophysiological conditions. Gestational diabetes mellitus (GDM) is characterized by different levels of chronic low-grade inflammation and vascular dysfunction; however, there are few data characterizing the serum exosomal protein cargo of GDM patients and associated signaling pathways. Eighteen pregnant women were enrolled in the study: 8 controls (CG) and 10 patients with GDM. Blood samples were collected from patients, for exosomes' concentration. Protein abundance alterations were demonstrated by relative mass spectrometric analysis and their association with clinical parameters in GDM patients was performed using Pearson's correlation analysis. The proteomics analysis revealed 78 significantly altered proteins when comparing GDM to CG, related to complement and coagulation cascades, platelet activation, prothrombotic factors and cholesterol metabolism. Down-regulation of Complement C3 (C3), Complement C5 (C5), C4-B (C4B), C4b-binding protein beta chain (C4BPB) and C4b-binding protein alpha chain (C4BPA), and up-regulation of C7, C9 and F12 were found in GDM. Our data indicated significant correlations between factors involved in the pathogenesis of GDM and clinical parameters that may improve the understanding of GDM pathophysiology. Data are available via ProteomeXchange with identifier PXD035673.
claims array · 2 items
[0] object · 6 fields
id
claim-method
statement
For mass spectrometric bioinformatics analysis, statistical algorithms were employed for correcting the ANOVA-obtained p-values using the Benjamini–Hochberg algorithm based on the false discovery rate (FDR). For the other experiments, the data were expressed as the mean ± standard deviation (SD). Pearson’s correlation analysis was performed on patients’ characteristics associated with GDM and serum level parameters. Statistical analysis was performed by t-test; p < 0.05 was regarded as significant difference.
kind
methodological
target
null
evidence array · 1 item
[0] object · 3 fields
asset
source:pmid:36080270
locator
sections[18] "4.6. Statistical Analysis" paragraph 2
quote
For mass spectrometric bioinformatics analysis, statistical algorithms were employed for correcting the ANOVA-obtained p-values using the Benjamini–Hochberg algorithm based on the false discovery rate (FDR). For the other experiments, the data were expressed as the mean ± standard deviation (SD). Pearson’s correlation analysis was performed on patients’ characteristics associated with GDM and serum level parameters. Statistical analysis was performed by t-test; p < 0.05 was regarded as significant difference.
state
complete
[1] object · 6 fields
id
claim-data-access
statement
The mass spectrometry data were deposited in the PRIDE [60,61] repository via ProteomeXchange [62] with the dataset identifier PXD035673.
kind
methodological
target
null
evidence array · 1 item
[0] object · 3 fields
asset
source:pmid:36080270
locator
sections[25] "notes" paragraph 1
quote
The mass spectrometry data were deposited in the PRIDE [60,61] repository via ProteomeXchange [62] with the dataset identifier PXD035673.
state
complete
gaps array · 0 items
experiment object · 8 fields
state
complete
objective
null
steps array · 3 items
[0] object · 13 fields
id
read_published_estimate
order
1
name
Read the published estimate from the source
kind
other
state
complete
blocked_on
null
description
The claim, method and evidence span published with the source article.
parameters object · 0 fields
inputs array · 1 item
[0]
source:pmid:36080270
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:PXD035673
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:PXD035673
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:36080270
role
manuscript
format
xml
media_type
application/xml
uri
https://doi.org/10.3390/molecules27175502
sha256
sha256:fc4291f17db8281666e30a19545404070e09118602ece6c5372c47ea4519d51b
bytes
49191
access
open
state
resolved
reader
null
reader_status
reader_required
identifier
10.3390/molecules27175502
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
PMC9457917
source
europe_pmc_fulltext
coverage
whole_body_without_references
text_hash_scope
rendered_section_body
[1] object · 15 fields
id
data:geo:PXD035673
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=PXD035673
sha256
null
bytes
null
access
open
state
resolved
reader
null
reader_status
reader_required
identifier
PXD035673
version
null
note
The mass spectrometry data were deposited in the PRIDE [60,61] repository via ProteomeXchange [62] with the dataset identifier PXD035673.
structure object · 15 fields
repository
GEO
access_route
GEO accession URL
access_statement_verbatim
The mass spectrometry data were deposited in the PRIDE [60,61] repository via ProteomeXchange [62] with the dataset identifier PXD035673.
access_statement_kind
data_availability_statement
sample_accessions array · 0 items
sample_count
null
group_sizes
null
group_sizes_basis
null
platform
null
taxon
null
title
Exosome proteomics reveals the deregulation of coagulation, complement and lipid metabolism proteins in gestational diabetes mellitus
resolution_checked_at
2026-11-01T18:06:51Z
resolution_check
identifier_resolution_only_no_download_no_licence_read
downloaded
false
licence_read
false
gaps array · 2 items
[0]
asset:data:geo:PXD035673 not downloaded
[1]
asset:data:geo:PXD035673 licence not read
analysis object · 4 fields
state
complete
methods array · 2 items
[0] object · 10 fields
id
method-1
family
group_comparison
specific
anova
label
Group comparison
dsl_operations array · 4 items
[0]
group_summary
[1]
welch_t
[2]
bootstrap_mean_difference
[3]
group_comparison_anova
missing_operations array · 0 items
parameters object · 0 fields
data_shapes array · 1 item
[0]
two_or_more_groups_continuous
evidence object · 3 fields
score
1
band
verbatim
quote
For mass spectrometric bioinformatics analysis, statistical algorithms were employed for correcting the ANOVA-obtained p-values using the Benjamini–Hochberg algorithm based on the false discovery rate (FDR). For the other experiments, the data were expressed as the mean ± standard deviation (SD). Pearson’s correlation analysis was performed on patients’ characteristics associated with GDM and serum level parameters. Statistical analysis was performed by t-test; p < 0.05 was regarded as significant difference.
[1] object · 10 fields
id
method-2
family
correlation_analysis
specific
pearson
label
Correlation analysis
dsl_operations array · 1 item
[0]
pearson_r
missing_operations array · 0 items
parameters object · 0 fields
data_shapes array · 1 item
[0]
paired_numeric_columns
evidence object · 3 fields
score
0.7
band
medium
quote
Pearson's correlation
targets array · 0 items
gaps array · 0 items
capability object · 3 fields
state
complete
requirements array · 1 item
[0] object · 6 fields
capability_id
capability:computational_analysis
label
Computational analysis platform
assay_families array · 9 items
[0]
meta_analysis
[1]
machine_learning
[2]
survival_analysis
[3]
statistical_regression
[4]
pca
[5]
molecular_docking
[6]
network_analysis
[7]
differential_expression
[8]
gwas
candidate
Automated Assays Laravel application and simulated adapters
gaps array · 0 items
readiness object · 8 fields
state
complete
tier
R1
blocked_on
nothing:replicable_now
axes object · 3 fields
method object · 5 fields
tier
R1
expressible
true
required_operations array · 4 items
[0]
group_summary
[1]
welch_t
[2]
bootstrap_mean_difference
[3]
group_comparison_anova
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: anova.
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]
PXD035673
resolved_accessions array · 1 item
[0]
PXD035673
statements array · 1 item
[0]
The mass spectrometry data were deposited in the PRIDE [60,61] repository via ProteomeXchange [62] with the dataset identifier PXD035673.
basis
The paper names PXD035673 in PRIDE repository via ProteomeXchange and the accession resolves in the repository. No dataset was downloaded and no licence was read.
can_run object · 3 fields
dsl_operations array · 4 items
[0]
group_summary
[1]
welch_t
[2]
bootstrap_mean_difference
[3]
group_comparison_anova
assets array · 2 items
[0]
source:pmid:36080270
[1]
data:geo:PXD035673
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:PXD035673
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
2026-11-01T18:04:10Z
independence
single_reader
evidence_check object · 2 fields
method
verbatim
availability
verbatim
calls
5
usage object · 3 fields
prompt_tokens
13666
completion_tokens
887
cached_tokens
256
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:36080270
type
paper
label
pmid:36080270
[1] object · 3 fields
id
source:pmid:36080270
type
manuscript
label
PMID 36080270 full text
[2] object · 3 fields
id
data:geo:PXD035673
type
dataset
label
GEO PXD035673
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:36080270
type
paper
label
pmid:36080270
[1] object · 3 fields
id
source:pmid:36080270
type
manuscript
label
PMID 36080270 full text
[2] object · 3 fields
id
data:geo:PXD035673
type
dataset
label
GEO PXD035673
agent
agent:corpus-assay-engine
[1] object · 4 fields
id
activity-read-36080270
type
extraction
used array · 1 item
[0]
source:pmid:36080270
agent
agent:minimax-reader
[2] object · 4 fields
id
activity-resolve-PXD035673
type
accession_resolution
used array · 1 item
[0]
data:geo:PXD035673
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:36080270
parent_hash
sha256:17d9e4ef8bbce159c8a85f1342eff80b005d2cfedf8e052d0fcf59018069710a
fork_of
null
gaps array · 6 items
[0]
asset:data:geo:PXD035673 licence not read
[1]
asset:data:geo:PXD035673 not downloaded
[2]
execution.not_run
[3]
review.human_critique
[4]
review.independent_reader
[5]
review.machine_critique
assays array · 2 items
[0] object · 11 fields
role
data_generation
definition_id
mass_spectrometry
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]
Exosome Proteomics Reveals the Deregulation of Coagulation, Com
[1]
ed using Pearson's correlation analysis. The proteomics analysis revealed 78 significantly altered p
[2]
ce alterations were demonstrated by relative mass spectrometric analysis and their association with clinical
[3]
e Preparation and Nano Liquid Chromatography—Mass Spectrometry Analysis The concentrated exosomes were homo
order_basis
paper_text_order:0
id
assay:1
[1] object · 11 fields
role
analysis
definition_id
group_comparison
definition_version
f2132e96ae6c7a4e
required_operations array · 4 items
[0]
group_summary
[1]
welch_t
[2]
bootstrap_mean_difference
[3]
group_comparison_anova
support_state
supported
source_hashes object · 1 field
dsl_catalogue
f2132e96ae6c7a4e
evidence array · 1 item
[0]
For mass spectrometric bioinformatics analysis, statistical algorithms were employed for correcting the ANOVA-obtained p-values using the Benjamini–Hochberg algorithm based on the false discovery rate (FDR). For the other experiments, the data were expressed as the mean ± standard deviation (SD). Pearson’s correlation analysis was performed on patients’ characteristics associated with GDM and serum level parameters. Statistical analysis was performed by t-test; p < 0.05 was regarded as significant difference.
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:36080270", "kind": "science-record", "revision": 5, "content_hash": "sha256:0367894c7c4d2cf6e8f06c219b1006fd5d66ac6714070967008763ca82ae4970", "created_at": "2026-11-01T18:15:18Z", "updated_at": "2026-11-01T22:50:01Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Exosome Proteomics Reveals the Deregulation of Coagulation, Complement and Lipid Metabolism Proteins in Gestational Diabetes Mellitus.", "doi": "10.3390/molecules27175502", "pmid": "36080270", "authors": ["Elena G Bernea", "Viorel I Suica", "Elena Uyy", "Aurel Cerveanu-Hogas", "Raluca M Boteanu", "Luminita Ivan", "Iuliana Ceausu", "Doina A Mihai", "Constantin Ionescu-Tîrgoviște", "Felicia Antohe"], "journal": "Molecules (Basel, Switzerland)", "year": 2022, "abstract": "Exosomes are small extracellular vesicles with a variable protein cargo in consonance with cell origin and pathophysiological conditions. Gestational diabetes mellitus (GDM) is characterized by different levels of chronic low-grade inflammation and vascular dysfunction; however, there are few data characterizing the serum exosomal protein cargo of GDM patients and associated signaling pathways. Eighteen pregnant women were enrolled in the study: 8 controls (CG) and 10 patients with GDM. Blood samples were collected from patients, for exosomes' concentration. Protein abundance alterations were demonstrated by relative mass spectrometric analysis and their association with clinical parameters in GDM patients was performed using Pearson's correlation analysis. The proteomics analysis revealed 78 significantly altered proteins when comparing GDM to CG, related to complement and coagulation cascades, platelet activation, prothrombotic factors and cholesterol metabolism. Down-regulation of Complement C3 (C3), Complement C5 (C5), C4-B (C4B), C4b-binding protein beta chain (C4BPB) and C4b-binding protein alpha chain (C4BPA), and up-regulation of C7, C9 and F12 were found in GDM. Our data indicated significant correlations between factors involved in the pathogenesis of GDM and clinical parameters that may improve the understanding of GDM pathophysiology. Data are available via ProteomeXchange with identifier PXD035673.", "claims": [{"id": "claim-method", "statement": "For mass spectrometric bioinformatics analysis, statistical algorithms were employed for correcting the ANOVA-obtained p-values using the Benjamini–Hochberg algorithm based on the false discovery rate (FDR). For the other experiments, the data were expressed as the mean ± standard deviation (SD). Pearson’s correlation analysis was performed on patients’ characteristics associated with GDM and serum level parameters. Statistical analysis was performed by t-test; p < 0.05 was regarded as significant difference.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:36080270", "locator": "sections[18] \"4.6. Statistical Analysis\" paragraph 2", "quote": "For mass spectrometric bioinformatics analysis, statistical algorithms were employed for correcting the ANOVA-obtained p-values using the Benjamini–Hochberg algorithm based on the false discovery rate (FDR). For the other experiments, the data were expressed as the mean ± standard deviation (SD). Pearson’s correlation analysis was performed on patients’ characteristics associated with GDM and serum level parameters. Statistical analysis was performed by t-test; p < 0.05 was regarded as significant difference."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The mass spectrometry data were deposited in the PRIDE [60,61] repository via ProteomeXchange [62] with the dataset identifier PXD035673.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:36080270", "locator": "sections[25] \"notes\" paragraph 1", "quote": "The mass spectrometry data were deposited in the PRIDE [60,61] repository via ProteomeXchange [62] with the dataset identifier PXD035673."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": null, "steps": [{"id": "read_published_estimate", "order": 1, "name": "Read the published estimate from the source", "kind": "other", "state": "complete", "blocked_on": null, "description": "The claim, method and evidence span published with the source article.", "duration_hours": null, "parameters": {}, "inputs": ["source:pmid:36080270"], "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:PXD035673"], "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:PXD035673"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:36080270", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.3390/molecules27175502", "sha256": "sha256:fc4291f17db8281666e30a19545404070e09118602ece6c5372c47ea4519d51b", "bytes": 49191, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.3390/molecules27175502", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC9457917", "source": "europe_pmc_fulltext", "coverage": "whole_body_without_references", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:PXD035673", "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=PXD035673", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "PXD035673", "version": null, "note": "The mass spectrometry data were deposited in the PRIDE [60,61] repository via ProteomeXchange [62] with the dataset identifier PXD035673.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The mass spectrometry data were deposited in the PRIDE [60,61] repository via ProteomeXchange [62] with the dataset identifier PXD035673.", "access_statement_kind": "data_availability_statement", "sample_accessions": [], "sample_count": null, "group_sizes": null, "group_sizes_basis": null, "platform": null, "taxon": null, "title": "Exosome proteomics reveals the deregulation of coagulation, complement and lipid metabolism proteins in gestational diabetes mellitus", "resolution_checked_at": "2026-11-01T18:06:51Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}], "gaps": ["asset:data:geo:PXD035673 not downloaded", "asset:data:geo:PXD035673 licence not read"]}, "analysis": {"state": "complete", "methods": [{"id": "method-1", "family": "group_comparison", "specific": "anova", "label": "Group comparison", "dsl_operations": ["group_summary", "welch_t", "bootstrap_mean_difference", "group_comparison_anova"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["two_or_more_groups_continuous"], "evidence": {"score": 1.0, "band": "verbatim", "quote": "For mass spectrometric bioinformatics analysis, statistical algorithms were employed for correcting the ANOVA-obtained p-values using the Benjamini–Hochberg algorithm based on the false discovery rate (FDR). For the other experiments, the data were expressed as the mean ± standard deviation (SD). Pearson’s correlation analysis was performed on patients’ characteristics associated with GDM and serum level parameters. Statistical analysis was performed by t-test; p < 0.05 was regarded as significant difference."}}, {"id": "method-2", "family": "correlation_analysis", "specific": "pearson", "label": "Correlation analysis", "dsl_operations": ["pearson_r"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["paired_numeric_columns"], "evidence": {"score": 0.7, "band": "medium", "quote": "Pearson's correlation"}}], "targets": [], "gaps": []}, "capability": {"state": "complete", "requirements": [{"capability_id": "capability:computational_analysis", "label": "Computational analysis platform", "assay_families": ["meta_analysis", "machine_learning", "survival_analysis", "statistical_regression", "pca", "molecular_docking", "network_analysis", "differential_expression", "gwas"], "availability_state": "owned", "tier_unlocked": "R1", "candidate": "Automated Assays Laravel application and simulated adapters"}], "gaps": []}, "readiness": {"state": "complete", "tier": "R1", "blocking_axis": "none", "blocked_on": "nothing:replicable_now", "axes": {"method": {"tier": "R1", "expressible": true, "required_operations": ["group_summary", "welch_t", "bootstrap_mean_difference", "group_comparison_anova"], "missing_operations": [], "basis": "The paper names the method it used and the corpus's method extractor maps it onto the DSL catalogue: anova."}, "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": ["PXD035673"], "resolved_accessions": ["PXD035673"], "statements": ["The mass spectrometry data were deposited in the PRIDE [60,61] repository via ProteomeXchange [62] with the dataset identifier PXD035673."], "basis": "The paper names PXD035673 in PRIDE repository via ProteomeXchange and the accession resolves in the repository. No dataset was downloaded and no licence was read."}}, "can_run": {"dsl_operations": ["group_summary", "welch_t", "bootstrap_mean_difference", "group_comparison_anova"], "assets": ["source:pmid:36080270", "data:geo:PXD035673"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:PXD035673"]}, "gaps": []}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-11-01T18:04:10Z", "independence": "single_reader"}, "evidence_check": {"method": "verbatim", "availability": "verbatim"}, "calls": 5, "usage": {"prompt_tokens": 13666, "completion_tokens": 887, "cached_tokens": 256}}, "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:36080270", "type": "paper", "label": "pmid:36080270"}, {"id": "source:pmid:36080270", "type": "manuscript", "label": "PMID 36080270 full text"}, {"id": "data:geo:PXD035673", "type": "dataset", "label": "GEO PXD035673"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:36080270", "type": "paper", "label": "pmid:36080270"}, {"id": "source:pmid:36080270", "type": "manuscript", "label": "PMID 36080270 full text"}, {"id": "data:geo:PXD035673", "type": "dataset", "label": "GEO PXD035673"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-36080270", "type": "extraction", "used": ["source:pmid:36080270"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-PXD035673", "type": "accession_resolution", "used": ["data:geo:PXD035673"], "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:36080270", "parent_hash": "sha256:17d9e4ef8bbce159c8a85f1342eff80b005d2cfedf8e052d0fcf59018069710a", "fork_of": null, "generation": 4}, "gaps": ["asset:data:geo:PXD035673 licence not read", "asset:data:geo:PXD035673 not downloaded", "execution.not_run", "review.human_critique", "review.independent_reader", "review.machine_critique"], "assays": [{"role": "data_generation", "definition_id": "mass_spectrometry", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.99, "evidence": ["Exosome Proteomics Reveals the Deregulation of Coagulation, Com", "ed using Pearson's correlation analysis. The proteomics analysis revealed 78 significantly altered p", "ce alterations were demonstrated by relative mass spectrometric analysis and their association with clinical", "e Preparation and Nano Liquid Chromatography—Mass Spectrometry Analysis The concentrated exosomes were homo"], "order_basis": "paper_text_order:0", "id": "assay:1"}, {"role": "analysis", "definition_id": "group_comparison", "definition_version": "f2132e96ae6c7a4e", "definition_digest": null, "required_operations": ["group_summary", "welch_t", "bootstrap_mean_difference", "group_comparison_anova"], "support_state": "supported", "source_hashes": {"dsl_catalogue": "f2132e96ae6c7a4e"}, "confidence": 1.0, "evidence": ["For mass spectrometric bioinformatics analysis, statistical algorithms were employed for correcting the ANOVA-obtained p-values using the Benjamini–Hochberg algorithm based on the false discovery rate (FDR). For the other experiments, the data were expressed as the mean ± standard deviation (SD). Pearson’s correlation analysis was performed on patients’ characteristics associated with GDM and serum level parameters. Statistical analysis was performed by t-test; p < 0.05 was regarded as significant difference."], "order_basis": "consumes_earlier_output", "id": "assay:2"}]}