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

pmid:33746583

Screening, identification and interaction analysis of key MicroRNAs and genes in Asthenozoospermia.

Liman Li · Song Chen

International journal of medical sciences · 2021 doi:10.7150/ijms.54460

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:33746583
kind
science-record
content_hash
sha256:ce129bbf0fb58923b9959f5307e9b2b846ab6d99b9803e2e5602f6948973747f
schema
https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json
created_at
2026-11-01T15:41:29Z
updated_at
2026-11-01T22:03:22Z
generator object · 2 fields
name
corpus-assay-engine
run_id
reading-sci-2026-11-01
paper object · 10 fields
state
complete
title
Screening, identification and interaction analysis of key MicroRNAs and genes in Asthenozoospermia.
doi
10.7150/ijms.54460
pmid
33746583
authors array · 2 items
[0]
Liman Li
[1]
Song Chen
journal
International journal of medical sciences
year
2021
abstract
Background: Asthenozoospermia, one of the most common causes of male infertility, is a complicate multifactorial pathological condition that genetic factors are involved in. However, the epigenetic signature and mechanism of asthenozoospermia still remain limited. Our study aimed to confirm the key microRNAs (miRNAs) and genes in asthenozoospermia and demonstrate the underlying epigenetic regulatory mechanisms. Methods: We screened out and pooled previous studies to extracted potential differentially expressed miRNAs (DEMs). GSE22331 and a published profile dataset were integrated to identify differentially expressed genes (DEGs). Pathway and gene ontology analysis were performed using DAVID. A protein-protein network (PPI) was constructed using STRING. The target genes of DEMs were predicted using TargetScan and the miRNA-mRNA network was built. Results: We reported 3 DEMs and 423 DEGs by pooling included dataset and published studies. Pathway analysis showed that these DEGs might participate in signaling pathways regulating pluripotency of stem cells, Wnt signaling pathway and Notch signaling pathway. 25 hub genes were identified, and the most significant gene was BDNF. We screened out the overlapped DEGs between the predicted target genes of 3 DEMs and the 423 DEGs. Finally, a potential miRNA-mRNA regulatory network was constructed. Conclusion: This study firstly pooled several published studies and a GEO dataset to determine the significance of potential miRNAs and genes, such as miR-374b, miR-193a, miR-34b, BDNF, NTRK2, HNRNPD and EFTUD2 in regulating asthenozoospermia and underscore their interactions in the pathophysiological mechanism. Our results provided theoretical basis and new clues for potential therapeutic treatment in asthenozoospermia. Validations in vivo and in vitro are required in future studies.
claims array · 2 items
[0] object · 6 fields
id
claim-method
statement
mRNA between the normozoospermic and asthenozoospermic groups with q-value (FDR) ≤ 0.001 and fold-change (FC) ≥ 2 (|log2FC| > 1) was considered significantly changed, and we reanalyzed the changed mRNA in our following study 26.
kind
methodological
target
null
evidence array · 1 item
[0] object · 3 fields
asset
source:pmid:33746583
locator
sections[4] "Data processing of DEGs" paragraph 2
quote
mRNA between the normozoospermic and asthenozoospermic groups with q-value (FDR) ≤ 0.001 and fold-change (FC) ≥ 2 (|log2FC| > 1) was considered significantly changed, and we reanalyzed the changed mRNA in our following study 26.
state
complete
[1] object · 6 fields
id
claim-data-access
statement
Literature research results are available from the authors upon reasonable request.
kind
methodological
target
null
evidence array · 1 item
[0] object · 3 fields
asset
source:pmid:33746583
locator
sections[21] "Availability of data and materials" paragraph 2
quote
Literature research results are available from the authors upon reasonable request.
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:33746583
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:GSE22331
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:GSE22331
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:33746583
role
manuscript
format
xml
media_type
application/xml
uri
https://doi.org/10.7150/ijms.54460
sha256
sha256:a46fce6af16ff3c95e890d7d337b20b025f959616c6842694d5f6e8df99c2a2c
bytes
36360
access
open
state
resolved
reader
null
reader_status
reader_required
identifier
10.7150/ijms.54460
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
PMC7976570
source
europe_pmc_fulltext
coverage
whole_body
text_hash_scope
rendered_section_body
[1] object · 15 fields
id
data:geo:GSE22331
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=GSE22331
sha256
null
bytes
null
access
open
state
resolved
reader
null
reader_status
reader_required
identifier
GSE22331
version
null
note
Literature research results are available from the authors upon reasonable request.
structure object · 15 fields
repository
GEO
access_route
GEO accession URL
access_statement_verbatim
Literature research results are available from the authors upon reasonable request.
access_statement_kind
data_availability_statement
sample_accessions array · 2 items
[0]
GSM555952
[1]
GSM555953
sample_count
2
group_sizes
null
group_sizes_basis
null
platform
570
taxon
Homo sapiens
title
Expression data from ejaculated spermatozoa of normozoospermic and asthenozoospermic men
resolution_checked_at
2026-11-01T15:39:54Z
resolution_check
identifier_resolution_only_no_download_no_licence_read
downloaded
false
licence_read
false
[2] object · 16 fields
id
asset:table:pmid:33746583:1
role
table
format
jats-table
media_type
application/vnd.jats.table+json
uri
null
sha256
sha256:533802b296418e2cdad57a0771ae0be5339d2f6715413e945bc9f3472989a2af
bytes
572
access
open
state
verified
reader
read_table
reader_status
available
identifier
section[10]/table-wrap[1]#T1
version
null
note
Information of 4 studies
structure object · 5 fields
pmcid
PMC7976570
section_index
10
section_title
DEMs in asthenozoospermia
row_count
5
column_count
3
table object · 8 fields
label
Table 1
caption
Information of 4 studies
rows array · 5 items
[0] array · 3 items
[0]
Study
[1]
Samples
[2]
Inclusion criteria of miRNAs
[1] array · 3 items
[0]
Wang 2011
[1]
A = a pool of 58 samples; N = a pool of 100 samples
[2]
Copy numbers > 50 and FC > 2
[2] array · 3 items
[0]
Abu-Halima 2013
[1]
A = 9; N = 9
[2]
FC > 2 and P value < 0.05
[3] array · 3 items
[0]
Salas-Huetos 2015
[1]
A = 10; N = 10
[2]
Significant difference of the mean normCt value between two groups (P value < 0.05)
[4] array · 3 items
[0]
Heidary 2019
[1]
A = 10; N = 10
[2]
FC > 2 and P value < 0.05
locator
section[10]/table-wrap[1]#T1
gaps array · 2 items
[0]
asset:data:geo:GSE22331 not downloaded
[1]
asset:data:geo:GSE22331 licence not read
analysis object · 4 fields
state
partial
methods array · 3 items
[0] object · 10 fields
id
method-1
family
network_analysis
specific
ppi_network
label
Network / pathway analysis
dsl_operations array · 3 items
[0]
build_graph
[1]
centrality_scores
[2]
pathway_enrich
missing_operations array · 0 items
parameters object · 0 fields
data_shapes array · 1 item
[0]
edge_list
evidence object · 3 fields
score
0.7
band
medium
quote
PPI
[1] object · 10 fields
id
method-2
family
network_analysis
specific
pathway_enrichment
label
Network / pathway analysis
dsl_operations array · 1 item
[0]
pathway_enrich
missing_operations array · 0 items
parameters object · 0 fields
data_shapes array · 1 item
[0]
edge_list
evidence object · 3 fields
score
0.8
band
high
quote
GO enrichment
[2] object · 10 fields
id
method-3
family
null
specific
null
label
Differential-expression filtering by fold change (FC), with false discovery rate (FDR) applied where available
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
mRNA between the normozoospermic and asthenozoospermic groups with q-value (FDR) ≤ 0.001 and fold-change (FC) ≥ 2 (|log2FC| > 1) was considered significantly changed, and we reanalyzed the changed mRNA in our following study 26.
targets array · 0 items
gaps array · 1 item
[0]
method.reader_named_unmapped
capability object · 3 fields
state
complete
requirements array · 1 item
[0] object · 6 fields
capability_id
capability:computational_analysis
label
Computational analysis platform
assay_families array · 9 items
[0]
meta_analysis
[1]
machine_learning
[2]
survival_analysis
[3]
statistical_regression
[4]
pca
[5]
molecular_docking
[6]
network_analysis
[7]
differential_expression
[8]
gwas
candidate
Automated Assays Laravel application and simulated adapters
gaps array · 0 items
readiness object · 8 fields
state
complete
tier
R1
blocked_on
nothing:replicable_now
axes object · 3 fields
method object · 5 fields
tier
R1
expressible
true
required_operations array · 3 items
[0]
build_graph
[1]
centrality_scores
[2]
pathway_enrich
missing_operations array · 0 items
basis
The paper names the method it used and the corpus's method extractor maps it onto the DSL catalogue: ppi_network.
capability object · 4 fields
tier
R1
capability_id
capability:computational_analysis
availability_state
owned
basis
The computational analysis is owned. The physical bench the paper used is not, so a physical validation cannot be run here.
data object · 6 fields
tier
R1
reachable
true
accessions array · 1 item
[0]
GSE22331
resolved_accessions array · 1 item
[0]
GSE22331
statements array · 1 item
[0]
Literature research results are available from the authors upon reasonable request.
basis
The paper names GSE22331 in GEO database 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 · 3 items
[0]
source:pmid:33746583
[1]
data:geo:GSE22331
[2]
asset:table:pmid:33746583:1
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:GSE22331
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
2026-10-31T18:28:10Z
independence
single_reader
evidence_check object · 2 fields
method
verbatim
availability
verbatim
calls
3
usage object · 3 fields
prompt_tokens
30749
completion_tokens
1701
cached_tokens
792
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:33746583
type
paper
label
pmid:33746583
[1] object · 3 fields
id
source:pmid:33746583
type
manuscript
label
PMID 33746583 full text
[2] object · 3 fields
id
data:geo:GSE22331
type
dataset
label
GEO GSE22331
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:33746583
type
paper
label
pmid:33746583
[1] object · 3 fields
id
source:pmid:33746583
type
manuscript
label
PMID 33746583 full text
[2] object · 3 fields
id
data:geo:GSE22331
type
dataset
label
GEO GSE22331
agent
agent:corpus-assay-engine
[1] object · 4 fields
id
activity-read-33746583
type
extraction
used array · 1 item
[0]
source:pmid:33746583
agent
agent:minimax-reader
[2] object · 4 fields
id
activity-resolve-GSE22331
type
accession_resolution
used array · 1 item
[0]
data:geo:GSE22331
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:33746583
parent_hash
sha256:ac5d3028c2290f2a4f065dbf392b865edbfbe6e12c137ec07fae5dd360d8596d
fork_of
null
gaps array · 7 items
[0]
asset:data:geo:GSE22331 licence not read
[1]
asset:data:geo:GSE22331 not downloaded
[2]
execution.not_run
[3]
method.reader_named_unmapped
[4]
review.human_critique
[5]
review.independent_reader
[6]
review.machine_critique
assays array · 2 items
[0] object · 11 fields
role
data_generation
definition_id
animal_model
definition_version
99e1195c7d6f
required_operations array · 0 items
support_state
partial
source_hashes object · 1 field
assay_lexicon
99e1195c7d6f
confidence
0.77
evidence array · 1 item
[0]
treatment in asthenozoospermia. Validations in vivo and in vitro are required in future studies.
order_basis
paper_text_order:1851
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]
PPI
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:33746583", "kind": "science-record", "revision": 7, "content_hash": "sha256:ce129bbf0fb58923b9959f5307e9b2b846ab6d99b9803e2e5602f6948973747f", "created_at": "2026-11-01T15:41:29Z", "updated_at": "2026-11-01T22:03:22Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Screening, identification and interaction analysis of key MicroRNAs and genes in Asthenozoospermia.", "doi": "10.7150/ijms.54460", "pmid": "33746583", "authors": ["Liman Li", "Song Chen"], "journal": "International journal of medical sciences", "year": 2021, "abstract": "Background: Asthenozoospermia, one of the most common causes of male infertility, is a complicate multifactorial pathological condition that genetic factors are involved in. However, the epigenetic signature and mechanism of asthenozoospermia still remain limited. Our study aimed to confirm the key microRNAs (miRNAs) and genes in asthenozoospermia and demonstrate the underlying epigenetic regulatory mechanisms. Methods: We screened out and pooled previous studies to extracted potential differentially expressed miRNAs (DEMs). GSE22331 and a published profile dataset were integrated to identify differentially expressed genes (DEGs). Pathway and gene ontology analysis were performed using DAVID. A protein-protein network (PPI) was constructed using STRING. The target genes of DEMs were predicted using TargetScan and the miRNA-mRNA network was built. Results: We reported 3 DEMs and 423 DEGs by pooling included dataset and published studies. Pathway analysis showed that these DEGs might participate in signaling pathways regulating pluripotency of stem cells, Wnt signaling pathway and Notch signaling pathway. 25 hub genes were identified, and the most significant gene was BDNF. We screened out the overlapped DEGs between the predicted target genes of 3 DEMs and the 423 DEGs. Finally, a potential miRNA-mRNA regulatory network was constructed. Conclusion: This study firstly pooled several published studies and a GEO dataset to determine the significance of potential miRNAs and genes, such as miR-374b, miR-193a, miR-34b, BDNF, NTRK2, HNRNPD and EFTUD2 in regulating asthenozoospermia and underscore their interactions in the pathophysiological mechanism. Our results provided theoretical basis and new clues for potential therapeutic treatment in asthenozoospermia. Validations in vivo and in vitro are required in future studies.", "claims": [{"id": "claim-method", "statement": "mRNA between the normozoospermic and asthenozoospermic groups with q-value (FDR) ≤ 0.001 and fold-change (FC) ≥ 2 (|log2FC| > 1) was considered significantly changed, and we reanalyzed the changed mRNA in our following study 26.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:33746583", "locator": "sections[4] \"Data processing of DEGs\" paragraph 2", "quote": "mRNA between the normozoospermic and asthenozoospermic groups with q-value (FDR) ≤ 0.001 and fold-change (FC) ≥ 2 (|log2FC| > 1) was considered significantly changed, and we reanalyzed the changed mRNA in our following study 26."}], "state": "complete"}, {"id": "claim-data-access", "statement": "Literature research results are available from the authors upon reasonable request.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:33746583", "locator": "sections[21] \"Availability of data and materials\" paragraph 2", "quote": "Literature research results are available from the authors upon reasonable request."}], "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:33746583"], "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:GSE22331"], "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:GSE22331"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:33746583", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.7150/ijms.54460", "sha256": "sha256:a46fce6af16ff3c95e890d7d337b20b025f959616c6842694d5f6e8df99c2a2c", "bytes": 36360, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.7150/ijms.54460", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC7976570", "source": "europe_pmc_fulltext", "coverage": "whole_body", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE22331", "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=GSE22331", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE22331", "version": null, "note": "Literature research results are available from the authors upon reasonable request.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "Literature research results are available from the authors upon reasonable request.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM555952", "GSM555953"], "sample_count": 2, "group_sizes": null, "group_sizes_basis": null, "platform": "570", "taxon": "Homo sapiens", "title": "Expression data from ejaculated spermatozoa of normozoospermic and asthenozoospermic men", "resolution_checked_at": "2026-11-01T15:39:54Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}, {"id": "asset:table:pmid:33746583:1", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:533802b296418e2cdad57a0771ae0be5339d2f6715413e945bc9f3472989a2af", "bytes": 572, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[10]/table-wrap[1]#T1", "version": null, "note": "Information of 4 studies", "structure": {"pmcid": "PMC7976570", "section_index": 10, "section_title": "DEMs in asthenozoospermia", "row_count": 5, "column_count": 3}, "table": {"label": "Table 1", "caption": "Information of 4 studies", "rows": [["Study", "Samples", "Inclusion criteria of miRNAs"], ["Wang 2011", "A = a pool of 58 samples; N = a pool of 100 samples", "Copy numbers > 50 and FC > 2"], ["Abu-Halima 2013", "A = 9; N = 9", "FC > 2 and P value < 0.05"], ["Salas-Huetos 2015", "A = 10; N = 10", "Significant difference of the mean normCt value between two groups (P value < 0.05)"], ["Heidary 2019", "A = 10; N = 10", "FC > 2 and P value < 0.05"]], "row_count": 5, "column_count": 3, "numeric_cells": 12, "header_rows": 1, "locator": "section[10]/table-wrap[1]#T1"}}], "gaps": ["asset:data:geo:GSE22331 not downloaded", "asset:data:geo:GSE22331 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": "PPI"}}, {"id": "method-2", "family": "network_analysis", "specific": "pathway_enrichment", "label": "Network / pathway analysis", "dsl_operations": ["pathway_enrich"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["edge_list"], "evidence": {"score": 0.8, "band": "high", "quote": "GO enrichment"}}, {"id": "method-3", "family": null, "specific": null, "label": "Differential-expression filtering by fold change (FC), with false discovery rate (FDR) applied where available", "dsl_operations": [], "missing_operations": [], "expressible": null, "parameters": {}, "data_shapes": [], "evidence": {"score": 1.0, "band": "verbatim", "quote": "mRNA between the normozoospermic and asthenozoospermic groups with q-value (FDR) ≤ 0.001 and fold-change (FC) ≥ 2 (|log2FC| > 1) was considered significantly changed, and we reanalyzed the changed mRNA in our following study 26."}}], "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": ["GSE22331"], "resolved_accessions": ["GSE22331"], "statements": ["Literature research results are available from the authors upon reasonable request."], "basis": "The paper names GSE22331 in GEO database 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:33746583", "data:geo:GSE22331", "asset:table:pmid:33746583:1"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:GSE22331"]}, "gaps": []}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-10-31T18:28:10Z", "independence": "single_reader"}, "evidence_check": {"method": "verbatim", "availability": "verbatim"}, "calls": 3, "usage": {"prompt_tokens": 30749, "completion_tokens": 1701, "cached_tokens": 792}}, "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:33746583", "type": "paper", "label": "pmid:33746583"}, {"id": "source:pmid:33746583", "type": "manuscript", "label": "PMID 33746583 full text"}, {"id": "data:geo:GSE22331", "type": "dataset", "label": "GEO GSE22331"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:33746583", "type": "paper", "label": "pmid:33746583"}, {"id": "source:pmid:33746583", "type": "manuscript", "label": "PMID 33746583 full text"}, {"id": "data:geo:GSE22331", "type": "dataset", "label": "GEO GSE22331"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-33746583", "type": "extraction", "used": ["source:pmid:33746583"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-GSE22331", "type": "accession_resolution", "used": ["data:geo:GSE22331"], "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:33746583", "parent_hash": "sha256:ac5d3028c2290f2a4f065dbf392b865edbfbe6e12c137ec07fae5dd360d8596d", "fork_of": null, "generation": 6}, "gaps": ["asset:data:geo:GSE22331 licence not read", "asset:data:geo:GSE22331 not downloaded", "execution.not_run", "method.reader_named_unmapped", "review.human_critique", "review.independent_reader", "review.machine_critique"], "assays": [{"role": "data_generation", "definition_id": "animal_model", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.77, "evidence": ["treatment in asthenozoospermia. Validations in vivo and in vitro are required in future studies."], "order_basis": "paper_text_order:1851", "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": ["PPI"], "order_basis": "consumes_earlier_output", "id": "assay:2"}]}