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

pmid:36494437

Acute and chronic blood serum proteome changes in patients with methanol poisoning.

Pavel Cejnar · Tatiana Anatolievna Smirnova · Stepanka Kuckova · Ales Prochazka · Ivan Zak · Karel Harant · Sergey Zakharov

Scientific reports · 2022 doi:10.1038/s41598-022-25492-9

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:36494437
kind
science-record
content_hash
sha256:0d77e4c2afa69a0cfa0a1d5fb57b4dd313ba18dabb65366c6988c32a300d898e
schema
https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json
created_at
2026-11-01T19:00:59Z
updated_at
2026-11-01T21:29:38Z
generator object · 2 fields
name
corpus-assay-engine
run_id
reading-sci-2026-11-01
paper object · 10 fields
state
complete
title
Acute and chronic blood serum proteome changes in patients with methanol poisoning.
doi
10.1038/s41598-022-25492-9
pmid
36494437
authors array · 7 items
[0]
Pavel Cejnar
[1]
Tatiana Anatolievna Smirnova
[2]
Stepanka Kuckova
[3]
Ales Prochazka
[4]
Ivan Zak
[5]
Karel Harant
[6]
Sergey Zakharov
journal
Scientific reports
year
2022
abstract
Twenty-four blood serum samples from patients with acute methanol poisoning (M) from the mass methanol poisoning outbreak in the Czech Republic in 2012 were compared with 46 patient samples taken four years after poisoning (S) (overlap of 10 people with group M) and with a control group (C) of 24 samples of patients with a similar proportion of chronic alcohol abuse. When comparing any two groups, tens to hundreds of proteins with a significant change in concentration were identified. Fifteen proteins showed significant changes when compared between any two groups. The group with acute methanol poisoning showed significant changes in protein concentrations for at least 64 proteins compared to the other groups. Among the most important identified proteins closely related to intoxication are mainly those involved in blood coagulation, metabolism of vitamin A (increased retinol-binding protein), immune response (e.g., increased complement factor I, complement factors C3 and C5), and lipid transport (increased apolipoprotein A I, apolipoprotein A II, adiponectin). For blood coagulation, the most affected proteins with significant changes in the methanol poisoning group were von Willebrand factor, carboxypeptidase N, alpha-2-antiplasmin (all increased), inter-alpha-trypsin inhibitor heavy chain H4, kininogen-1, plasma serine protease inhibitor, plasminogen (all decreased). However, heparin administration used for the methanol poisoning group could have interfered with some of the changes in their concentrations. Data are available via ProteomeXchange with the identifier PXD035726.
claims array · 3 items
[0] object · 6 fields
id
claim-method
statement
The Student’s t-test (α = 0.05) over protein intensity quantification values and the Benjamini-Hochberg42 correction (α = 0.05) for multiple comparisons for an aggregated number of tests over several comparisons were run using the default R package “stats”.
kind
methodological
target
null
evidence array · 1 item
[0] object · 3 fields
asset
source:pmid:36494437
locator
sections[12] "Identification of proteins with significant changes in intensities" paragraph 2
quote
The Student’s t-test (α = 0.05) over protein intensity quantification values and the Benjamini-Hochberg42 correction (α = 0.05) for multiple comparisons for an aggregated number of tests over several comparisons were run using the default R package “stats”.
state
complete
[1] object · 6 fields
id
claim-data-access
statement
The acquired mass spectrometry proteomics data were deposited to the ProteomeXchange Consortium via the PRIDE34 partner repository with the dataset identifier PXD035726 including lists of found peptides and proteins. The list of proteins used for analyses and the complete list of proteins with a significant change in intensity between groups, both in Excel format, are also available in the supplement.
kind
methodological
target
null
evidence array · 1 item
[0] object · 3 fields
asset
source:pmid:36494437
locator
sections[36] "notes" paragraph 1
quote
The acquired mass spectrometry proteomics data were deposited to the ProteomeXchange Consortium via the PRIDE34 partner repository with the dataset identifier PXD035726 including lists of found peptides and proteins. The list of proteins used for analyses and the complete list of proteins with a significant change in intensity between groups, both in Excel format, are also available in the supplement.
state
complete
[2] object · 6 fields
id
claim-target-result
statement
The group with acute methanol poisoning showed significant changes in protein concentrations for at least 64 proteins compared to the other groups.
kind
qualitative
target
null
evidence array · 1 item
[0] object · 3 fields
asset
source:pmid:36494437
locator
sections[0] "Abstract" paragraph 1
quote
The group with acute methanol poisoning showed significant changes in protein concentrations for at least 64 proteins compared to the other groups.
state
complete
gaps array · 0 items
experiment object · 8 fields
state
complete
objective
The group with acute methanol poisoning showed significant changes in protein concentrations for at least 64 proteins compared to the other groups.
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:36494437
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:PXD035726
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:PXD035726
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:36494437
role
manuscript
format
xml
media_type
application/xml
uri
https://doi.org/10.1038/s41598-022-25492-9
sha256
sha256:c199580041c70eeafc8080f8303aeba63e5af62dfaae2e2fd4b4ec2245488597
bytes
69119
access
open
state
resolved
reader
null
reader_status
reader_required
identifier
10.1038/s41598-022-25492-9
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
PMC9734099
source
europe_pmc_fulltext
coverage
whole_body_without_references
text_hash_scope
rendered_section_body
[1] object · 15 fields
id
data:geo:PXD035726
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=PXD035726
sha256
null
bytes
null
access
open
state
resolved
reader
null
reader_status
reader_required
identifier
PXD035726
version
null
note
The acquired mass spectrometry proteomics data were deposited to the ProteomeXchange Consortium via the PRIDE34 partner repository with the dataset identifier PXD035726 including lists of found peptides and proteins. The list of proteins used for analyses and the complete list of proteins with a significant change in intensity between groups, both in Excel format, are also available in the supplement.
structure object · 15 fields
repository
GEO
access_route
GEO accession URL
access_statement_verbatim
The acquired mass spectrometry proteomics data were deposited to the ProteomeXchange Consortium via the PRIDE34 partner repository with the dataset identifier PXD035726 including lists of found peptides and proteins. The list of proteins used for analyses and the complete list of proteins with a significant change in intensity between groups, both in Excel format, are also available in the supplement.
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
Human serum samples - Acute and chronic blood serum proteome changes in patients with methanol poisoning
resolution_checked_at
2026-11-01T18:46:41Z
resolution_check
identifier_resolution_only_no_download_no_licence_read
downloaded
false
licence_read
false
gaps array · 2 items
[0]
asset:data:geo:PXD035726 not downloaded
[1]
asset:data:geo:PXD035726 licence not read
analysis object · 4 fields
state
partial
methods array · 1 item
[0] object · 10 fields
id
method-1
family
null
specific
null
label
Student’s t-test with Benjamini-Hochberg correction for multiple comparisons
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 Student’s t-test (α = 0.05) over protein intensity quantification values and the Benjamini-Hochberg42 correction (α = 0.05) for multiple comparisons for an aggregated number of tests over several comparisons were run using the default R package “stats”.
targets array · 0 items
gaps array · 1 item
[0]
method.reader_named_unmapped
capability object · 3 fields
state
complete
requirements array · 1 item
[0] object · 6 fields
capability_id
capability:computational_analysis
label
Computational analysis platform
assay_families array · 9 items
[0]
meta_analysis
[1]
machine_learning
[2]
survival_analysis
[3]
statistical_regression
[4]
pca
[5]
molecular_docking
[6]
network_analysis
[7]
differential_expression
[8]
gwas
candidate
Automated Assays Laravel application and simulated adapters
gaps array · 0 items
readiness object · 8 fields
state
blocked
tier
R4
blocking_axis
method
blocked_on
method:not_determinable
axes object · 3 fields
method object · 5 fields
tier
R4
expressible
false
required_operations array · 0 items
missing_operations array · 0 items
basis
The reader quoted the method the paper names (Student’s t-test with Benjamini-Hochberg correction for multiple comparisons), but the corpus's method extractor could not map it onto a DSL operation, so the method is published but not expressible.
capability object · 4 fields
tier
R1
capability_id
capability:computational_analysis
availability_state
owned
basis
The computational analysis is owned. The physical bench the paper used is not, so a physical validation cannot be run here.
data object · 6 fields
tier
R1
reachable
true
accessions array · 1 item
[0]
PXD035726
resolved_accessions array · 1 item
[0]
PXD035726
statements array · 1 item
[0]
The acquired mass spectrometry proteomics data were deposited to the ProteomeXchange Consortium via the PRIDE34 partner repository with the dataset identifier PXD035726 including lists of found peptides and proteins. The list of proteins used for analyses and the complete list of proteins with a significant change in intensity between groups, both in Excel format, are also available in the supplement.
basis
The paper names PXD035726 in ProteomeXchange Consortium via the PRIDE partner repository and the accession resolves in the repository. No dataset was downloaded and no licence was read.
can_run object · 3 fields
dsl_operations array · 0 items
assets array · 2 items
[0]
source:pmid:36494437
[1]
data:geo:PXD035726
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:PXD035726
gaps array · 1 item
[0]
method:not_determinable
review object · 5 fields
state
partial
machine_critique object · 5 fields
kind
extraction_review
reader object · 5 fields
model
MiniMax-M3.1-Flash
provider
minimax
provider_family
minimax
read_at
2026-11-01T18:18:55Z
independence
single_reader
evidence_check object · 2 fields
method
verbatim
availability
verbatim
calls
5
usage object · 3 fields
prompt_tokens
19093
completion_tokens
1136
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:36494437
type
paper
label
pmid:36494437
[1] object · 3 fields
id
source:pmid:36494437
type
manuscript
label
PMID 36494437 full text
[2] object · 3 fields
id
data:geo:PXD035726
type
dataset
label
GEO PXD035726
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:36494437
type
paper
label
pmid:36494437
[1] object · 3 fields
id
source:pmid:36494437
type
manuscript
label
PMID 36494437 full text
[2] object · 3 fields
id
data:geo:PXD035726
type
dataset
label
GEO PXD035726
agent
agent:corpus-assay-engine
[1] object · 4 fields
id
activity-read-36494437
type
extraction
used array · 1 item
[0]
source:pmid:36494437
agent
agent:minimax-reader
[2] object · 4 fields
id
activity-resolve-PXD035726
type
accession_resolution
used array · 1 item
[0]
data:geo:PXD035726
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:36494437
parent_hash
sha256:05e78b57f8f7a724f22bc5a3f76da472fc158f4a4f8e749b8a1752430369dc0f
fork_of
null
gaps array · 7 items
[0]
asset:data:geo:PXD035726 licence not read
[1]
asset:data:geo:PXD035726 not downloaded
[2]
execution.not_run
[3]
method.reader_named_unmapped
[4]
review.human_critique
[5]
review.independent_reader
[6]
review.machine_critique
Complete file
{"sci_version": "1.0", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:36494437", "kind": "science-record", "revision": 2, "content_hash": "sha256:0d77e4c2afa69a0cfa0a1d5fb57b4dd313ba18dabb65366c6988c32a300d898e", "created_at": "2026-11-01T19:00:59Z", "updated_at": "2026-11-01T21:29:38Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Acute and chronic blood serum proteome changes in patients with methanol poisoning.", "doi": "10.1038/s41598-022-25492-9", "pmid": "36494437", "authors": ["Pavel Cejnar", "Tatiana Anatolievna Smirnova", "Stepanka Kuckova", "Ales Prochazka", "Ivan Zak", "Karel Harant", "Sergey Zakharov"], "journal": "Scientific reports", "year": 2022, "abstract": "Twenty-four blood serum samples from patients with acute methanol poisoning (M) from the mass methanol poisoning outbreak in the Czech Republic in 2012 were compared with 46 patient samples taken four years after poisoning (S) (overlap of 10 people with group M) and with a control group (C) of 24 samples of patients with a similar proportion of chronic alcohol abuse. When comparing any two groups, tens to hundreds of proteins with a significant change in concentration were identified. Fifteen proteins showed significant changes when compared between any two groups. The group with acute methanol poisoning showed significant changes in protein concentrations for at least 64 proteins compared to the other groups. Among the most important identified proteins closely related to intoxication are mainly those involved in blood coagulation, metabolism of vitamin A (increased retinol-binding protein), immune response (e.g., increased complement factor I, complement factors C3 and C5), and lipid transport (increased apolipoprotein A I, apolipoprotein A II, adiponectin). For blood coagulation, the most affected proteins with significant changes in the methanol poisoning group were von Willebrand factor, carboxypeptidase N, alpha-2-antiplasmin (all increased), inter-alpha-trypsin inhibitor heavy chain H4, kininogen-1, plasma serine protease inhibitor, plasminogen (all decreased). However, heparin administration used for the methanol poisoning group could have interfered with some of the changes in their concentrations. Data are available via ProteomeXchange with the identifier PXD035726.", "claims": [{"id": "claim-method", "statement": "The Student’s t-test (α = 0.05) over protein intensity quantification values and the Benjamini-Hochberg42 correction (α = 0.05) for multiple comparisons for an aggregated number of tests over several comparisons were run using the default R package “stats”.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:36494437", "locator": "sections[12] \"Identification of proteins with significant changes in intensities\" paragraph 2", "quote": "The Student’s t-test (α = 0.05) over protein intensity quantification values and the Benjamini-Hochberg42 correction (α = 0.05) for multiple comparisons for an aggregated number of tests over several comparisons were run using the default R package “stats”."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The acquired mass spectrometry proteomics data were deposited to the ProteomeXchange Consortium via the PRIDE34 partner repository with the dataset identifier PXD035726 including lists of found peptides and proteins. The list of proteins used for analyses and the complete list of proteins with a significant change in intensity between groups, both in Excel format, are also available in the supplement.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:36494437", "locator": "sections[36] \"notes\" paragraph 1", "quote": "The acquired mass spectrometry proteomics data were deposited to the ProteomeXchange Consortium via the PRIDE34 partner repository with the dataset identifier PXD035726 including lists of found peptides and proteins. The list of proteins used for analyses and the complete list of proteins with a significant change in intensity between groups, both in Excel format, are also available in the supplement."}], "state": "complete"}, {"id": "claim-target-result", "statement": "The group with acute methanol poisoning showed significant changes in protein concentrations for at least 64 proteins compared to the other groups.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:36494437", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "The group with acute methanol poisoning showed significant changes in protein concentrations for at least 64 proteins compared to the other groups."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "The group with acute methanol poisoning showed significant changes in protein concentrations for at least 64 proteins compared to the other groups.", "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:36494437"], "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:PXD035726"], "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:PXD035726"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:36494437", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.1038/s41598-022-25492-9", "sha256": "sha256:c199580041c70eeafc8080f8303aeba63e5af62dfaae2e2fd4b4ec2245488597", "bytes": 69119, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.1038/s41598-022-25492-9", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC9734099", "source": "europe_pmc_fulltext", "coverage": "whole_body_without_references", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:PXD035726", "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=PXD035726", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "PXD035726", "version": null, "note": "The acquired mass spectrometry proteomics data were deposited to the ProteomeXchange Consortium via the PRIDE34 partner repository with the dataset identifier PXD035726 including lists of found peptides and proteins. The list of proteins used for analyses and the complete list of proteins with a significant change in intensity between groups, both in Excel format, are also available in the supplement.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The acquired mass spectrometry proteomics data were deposited to the ProteomeXchange Consortium via the PRIDE34 partner repository with the dataset identifier PXD035726 including lists of found peptides and proteins. The list of proteins used for analyses and the complete list of proteins with a significant change in intensity between groups, both in Excel format, are also available in the supplement.", "access_statement_kind": "data_availability_statement", "sample_accessions": [], "sample_count": null, "group_sizes": null, "group_sizes_basis": null, "platform": null, "taxon": null, "title": "Human serum samples - Acute and chronic blood serum proteome changes in patients with methanol poisoning", "resolution_checked_at": "2026-11-01T18:46:41Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}], "gaps": ["asset:data:geo:PXD035726 not downloaded", "asset:data:geo:PXD035726 licence not read"]}, "analysis": {"state": "partial", "methods": [{"id": "method-1", "family": null, "specific": null, "label": "Student’s t-test with Benjamini-Hochberg correction for multiple comparisons", "dsl_operations": [], "missing_operations": [], "expressible": null, "parameters": {}, "data_shapes": [], "evidence": {"score": 1.0, "band": "verbatim", "quote": "The Student’s t-test (α = 0.05) over protein intensity quantification values and the Benjamini-Hochberg42 correction (α = 0.05) for multiple comparisons for an aggregated number of tests over several comparisons were run using the default R package “stats”."}}], "targets": [], "gaps": ["method.reader_named_unmapped"]}, "capability": {"state": "complete", "requirements": [{"capability_id": "capability:computational_analysis", "label": "Computational analysis platform", "assay_families": ["meta_analysis", "machine_learning", "survival_analysis", "statistical_regression", "pca", "molecular_docking", "network_analysis", "differential_expression", "gwas"], "availability_state": "owned", "tier_unlocked": "R1", "candidate": "Automated Assays Laravel application and simulated adapters"}], "gaps": []}, "readiness": {"state": "blocked", "tier": "R4", "blocking_axis": "method", "blocked_on": "method:not_determinable", "axes": {"method": {"tier": "R4", "expressible": false, "required_operations": [], "missing_operations": [], "basis": "The reader quoted the method the paper names (Student’s t-test with Benjamini-Hochberg correction for multiple comparisons), but the corpus's method extractor could not map it onto a DSL operation, so the method is published but not expressible."}, "capability": {"tier": "R1", "capability_id": "capability:computational_analysis", "availability_state": "owned", "basis": "The computational analysis is owned. The physical bench the paper used is not, so a physical validation cannot be run here."}, "data": {"tier": "R1", "reachable": true, "accessions": ["PXD035726"], "resolved_accessions": ["PXD035726"], "statements": ["The acquired mass spectrometry proteomics data were deposited to the ProteomeXchange Consortium via the PRIDE34 partner repository with the dataset identifier PXD035726 including lists of found peptides and proteins. The list of proteins used for analyses and the complete list of proteins with a significant change in intensity between groups, both in Excel format, are also available in the supplement."], "basis": "The paper names PXD035726 in ProteomeXchange Consortium via the PRIDE partner repository and the accession resolves in the repository. No dataset was downloaded and no licence was read."}}, "can_run": {"dsl_operations": [], "assets": ["source:pmid:36494437", "data:geo:PXD035726"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:PXD035726"]}, "gaps": ["method:not_determinable"]}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-11-01T18:18:55Z", "independence": "single_reader"}, "evidence_check": {"method": "verbatim", "availability": "verbatim"}, "calls": 5, "usage": {"prompt_tokens": 19093, "completion_tokens": 1136, "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:36494437", "type": "paper", "label": "pmid:36494437"}, {"id": "source:pmid:36494437", "type": "manuscript", "label": "PMID 36494437 full text"}, {"id": "data:geo:PXD035726", "type": "dataset", "label": "GEO PXD035726"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:36494437", "type": "paper", "label": "pmid:36494437"}, {"id": "source:pmid:36494437", "type": "manuscript", "label": "PMID 36494437 full text"}, {"id": "data:geo:PXD035726", "type": "dataset", "label": "GEO PXD035726"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-36494437", "type": "extraction", "used": ["source:pmid:36494437"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-PXD035726", "type": "accession_resolution", "used": ["data:geo:PXD035726"], "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:36494437", "parent_hash": "sha256:05e78b57f8f7a724f22bc5a3f76da472fc158f4a4f8e749b8a1752430369dc0f", "fork_of": null, "generation": 1}, "gaps": ["asset:data:geo:PXD035726 licence not read", "asset:data:geo:PXD035726 not downloaded", "execution.not_run", "method.reader_named_unmapped", "review.human_critique", "review.independent_reader", "review.machine_critique"]}