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

pmid:29077704

Variability in the protein profiles in spermatozoa of two sturgeon species.

Ping Li · Wei Guo · Huamei Yue · Chuangju Li · Hao Du · Xinmei Qiao · Zhigang Liu · Qiong Zhou · Qiwei Wei

PloS one · 2017 doi:10.1371/journal.pone.0186003

Paper

complete

Experiment

partial

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:29077704
kind
science-record
content_hash
sha256:42e829f772e40e34f4ae7787cb42b3bc8dba56ba3e3e7ec159f65868b812a54a
schema
https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json
created_at
2026-11-01T15:40:29Z
updated_at
2026-11-01T21:59:33Z
generator object · 2 fields
name
corpus-assay-engine
run_id
reading-sci-2026-11-01
paper object · 10 fields
state
complete
title
Variability in the protein profiles in spermatozoa of two sturgeon species.
doi
10.1371/journal.pone.0186003
pmid
29077704
authors array · 9 items
[0]
Ping Li
[1]
Wei Guo
[2]
Huamei Yue
[3]
Chuangju Li
[4]
Hao Du
[5]
Xinmei Qiao
[6]
Zhigang Liu
[7]
Qiong Zhou
[8]
Qiwei Wei
journal
PloS one
year
2017
abstract
Conventional sperm analysis (i.e., motility and fertility) has been used to evaluate sperm quality. Understanding the quality of sperm on the molecular level in the sturgeons, Acipenser baerii and A. schrenckii, is essential for the improvement of the conservation of genetic resources and farming performance. In this study, we used the iTRAQ proteomics approach to perform proteomic profiling of spermatozoa associated with sperm quality in sturgeons (Data are available via ProteomeXchange with identifier PXD006108). The results showed 291 and 359 differentially expressed proteins in A. baerii and A. schrenckii, respectively, of which 72 were common to both species and all were upregulated in high quality compared with low quality samples. The differentially expressed proteins were mainly categorized into the generation of precursor metabolites and energy and oxidation, and they were localized to the mitochondria. Three distinguishing pathways, Arginine and proline metabolism, Pyruvate metabolism and the Citrate cycle (TCA cycle) were found to play an important role in energy metabolism, and some substrates could be used in the sperm medium for storage and cryopreservation. The quantity levels of two proteins, CKMT1 and LDHB, were verified by western blot analysis. Moreover, other potential biomarkers involved in oxidation reduction, ubiquitin-proteasome-dependent proteolysis, chaperones and binding activity were also discussed. Our study is the first to use the iTRAQ-based proteomics approach to analyse the sturgeon spermatozoa proteome, and the results that we obtained are valuable for the prediction of sperm quality and reproduction management in these threatened species.
claims array · 1 item
[0] object · 6 fields
id
claim-method
statement
Protein quantification was carried out based on a unique peptide. A cut-off of a 1.5-fold change was chosen, and proteins with quantification ratios of 1.5 for low (<0.67) or high (>1.5) relative protein levels were considered as differentially regulated.
kind
methodological
target
null
evidence array · 1 item
[0] object · 3 fields
asset
source:pmid:29077704
locator
sections[9] "Data analysis" paragraph 2
quote
Protein quantification was carried out based on a unique peptide. A cut-off of a 1.5-fold change was chosen, and proteins with quantification ratios of 1.5 for low (<0.67) or high (>1.5) relative protein levels were considered as differentially regulated.
state
complete
gaps array · 0 items
experiment object · 8 fields
state
partial
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:29077704
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
blocked
blocked_on
data:accession_absent
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 · 0 items
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 · 1 field
e_value
were selected using an E-value cut-off of 10−5
inputs array · 0 items
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 · 1 item
[0]
step:obtain_source_data blocked on data:accession_absent
data object · 3 fields
state
partial
assets array · 4 items
[0] object · 15 fields
id
source:pmid:29077704
role
manuscript
format
xml
media_type
application/xml
uri
https://doi.org/10.1371/journal.pone.0186003
sha256
sha256:a0999e4bb2b286bffc061aa5335ff585b2db90ee718ce36ec75db85752fba370
bytes
40219
access
open
state
resolved
reader
null
reader_status
reader_required
identifier
10.1371/journal.pone.0186003
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
PMC5659609
source
europe_pmc_fulltext
coverage
whole_body_without_references
text_hash_scope
rendered_section_body
[1] object · 16 fields
id
asset:table:pmid:29077704:1
role
table
format
jats-table
media_type
application/vnd.jats.table+json
uri
null
sha256
sha256:f0d2d7ed5b643633a04781652a5e311f88160f3dede347b962adbb5b88e52293
bytes
238
access
open
state
verified
reader
read_table
reader_status
available
identifier
section[13]/table-wrap[1]#pone.0186003.t001
version
null
note
Sperm quality parameters from A. baerii (n = 11) and A. schrenckii (n = 7).
structure object · 5 fields
pmcid
PMC5659609
section_index
13
section_title
Sperm motility and fertility parameters
row_count
0
column_count
0
table object · 8 fields
label
Table 1
caption
Sperm quality parameters from A. baerii (n = 11) and A. schrenckii (n = 7).
rows array · 0 items
locator
section[13]/table-wrap[1]#pone.0186003.t001
[2] object · 16 fields
id
asset:table:pmid:29077704:2
role
table
format
jats-table
media_type
application/vnd.jats.table+json
uri
null
sha256
sha256:dddf5eeab484ba1dcaed78d6a111abb8ec73f01c49e9f240eb43118443d76119
bytes
251
access
open
state
verified
reader
read_table
reader_status
available
identifier
section[14]/table-wrap[1]#pone.0186003.t002
version
null
note
Potential biomarkers related to sperm quality in A. baerii (AB) and A. schrenckii (ASK).
structure object · 5 fields
pmcid
PMC5659609
section_index
14
section_title
The proteome of sperm in A. baerii and A. schrenckii by iTRAQ analysis
row_count
0
column_count
0
table object · 8 fields
label
Table 2
caption
Potential biomarkers related to sperm quality in A. baerii (AB) and A. schrenckii (ASK).
rows array · 0 items
locator
section[14]/table-wrap[1]#pone.0186003.t002
[3] object · 16 fields
id
asset:table:pmid:29077704:3
role
table
format
jats-table
media_type
application/vnd.jats.table+json
uri
null
sha256
sha256:6f72af571de7dc86cf0dc4ea0ed2ddb0630b9e4a470dc04dce755b9caf1ff5d4
bytes
176
access
open
state
verified
reader
read_table
reader_status
available
identifier
section[15]/table-wrap[1]#pone.0186003.t003
version
null
note
Protein list.
structure object · 5 fields
pmcid
PMC5659609
section_index
15
section_title
Functional classification and interaction of differentially expressed proteins
row_count
0
column_count
0
table object · 8 fields
label
Table 3
caption
Protein list.
rows array · 0 items
locator
section[15]/table-wrap[1]#pone.0186003.t003
gaps array · 0 items
analysis object · 4 fields
state
partial
methods array · 2 items
[0] object · 10 fields
id
method-1
family
sequence_alignment
specific
blast
label
Sequence alignment / homology
dsl_operations array · 2 items
[0]
sequence_align
[1]
alignment_identity
missing_operations array · 0 items
parameters object · 1 field
e_value
were selected using an E-value cut-off of 10−5
data_shapes array · 1 item
[0]
sequence_records
evidence object · 3 fields
score
0.8
band
high
quote
BLAST
[1] object · 10 fields
id
method-2
family
null
specific
null
label
8-plex iTRAQ label-based relative quantification with unique-peptide fold-change classification
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
Protein quantification was carried out based on a unique peptide. A cut-off of a 1.5-fold change was chosen, and proteins with quantification ratios of 1.5 for low (<0.67) or high (>1.5) relative protein levels were considered as differentially regulated.
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
blocked_on
data:accession_absent
axes object · 3 fields
method object · 5 fields
tier
R1
expressible
true
required_operations array · 2 items
[0]
sequence_align
[1]
alignment_identity
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: blast.
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
R4
reachable
false
accessions array · 0 items
resolved_accessions array · 0 items
statements array · 0 items
basis
The paper names no accession to its source data, so the data has to come from the authors.
can_run object · 3 fields
dsl_operations array · 2 items
[0]
sequence_align
[1]
alignment_identity
assets array · 4 items
[0]
source:pmid:29077704
[1]
asset:table:pmid:29077704:1
[2]
asset:table:pmid:29077704:2
[3]
asset:table:pmid:29077704:3
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:None
gaps array · 1 item
[0]
data:accession_absent
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
null
independence
same_provider
evidence_check object · 2 fields
method
verbatim
availability
null
calls
0
usage object · 0 fields
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:29077704
type
paper
label
pmid:29077704
[1] object · 3 fields
id
source:pmid:29077704
type
manuscript
label
PMID 29077704 full text
[2] object · 3 fields
id
data:geo:None
type
dataset
label
GEO None
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:29077704
type
paper
label
pmid:29077704
[1] object · 3 fields
id
source:pmid:29077704
type
manuscript
label
PMID 29077704 full text
[2] object · 3 fields
id
data:geo:None
type
dataset
label
GEO None
agent
agent:corpus-assay-engine
[1] object · 4 fields
id
activity-read-29077704
type
extraction
used array · 1 item
[0]
source:pmid:29077704
agent
agent:minimax-reader
[2] object · 4 fields
id
activity-resolve-None
type
accession_resolution
used array · 1 item
[0]
data:geo:None
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:29077704
parent_hash
sha256:b5739590c0c039f85012a607806fc29a0aa36e7e2751358d239c6ea885a70864
fork_of
null
gaps array · 6 items
[0]
execution.not_run
[1]
method.reader_named_unmapped
[2]
review.human_critique
[3]
review.independent_reader
[4]
review.machine_critique
[5]
step:obtain_source_data blocked on data:accession_absent
assays array · 3 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 · 3 items
[0]
erformance. In this study, we used the iTRAQ proteomics approach to perform proteomic profiling of s
[1]
sed the iTRAQ proteomics approach to perform proteomic profiling of spermatozoa associated with spe
[2]
ur study is the first to use the iTRAQ-based proteomics approach to analyse the sturgeon spermatozoa
order_basis
paper_text_order:375
id
assay:1
[1] 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]
o proteins, CKMT1 and LDHB, were verified by western blot analysis. Moreover, other potential biomarke
order_basis
paper_text_order:1292
id
assay:2
[2] object · 11 fields
role
analysis
definition_id
sequence_alignment
definition_version
f2132e96ae6c7a4e
required_operations array · 2 items
[0]
sequence_align
[1]
alignment_identity
support_state
supported
source_hashes object · 1 field
dsl_catalogue
f2132e96ae6c7a4e
evidence array · 1 item
[0]
BLAST
order_basis
consumes_earlier_output
id
assay:3
Complete file
{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:29077704", "kind": "science-record", "revision": 7, "content_hash": "sha256:42e829f772e40e34f4ae7787cb42b3bc8dba56ba3e3e7ec159f65868b812a54a", "created_at": "2026-11-01T15:40:29Z", "updated_at": "2026-11-01T21:59:33Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Variability in the protein profiles in spermatozoa of two sturgeon species.", "doi": "10.1371/journal.pone.0186003", "pmid": "29077704", "authors": ["Ping Li", "Wei Guo", "Huamei Yue", "Chuangju Li", "Hao Du", "Xinmei Qiao", "Zhigang Liu", "Qiong Zhou", "Qiwei Wei"], "journal": "PloS one", "year": 2017, "abstract": "Conventional sperm analysis (i.e., motility and fertility) has been used to evaluate sperm quality. Understanding the quality of sperm on the molecular level in the sturgeons, Acipenser baerii and A. schrenckii, is essential for the improvement of the conservation of genetic resources and farming performance. In this study, we used the iTRAQ proteomics approach to perform proteomic profiling of spermatozoa associated with sperm quality in sturgeons (Data are available via ProteomeXchange with identifier PXD006108). The results showed 291 and 359 differentially expressed proteins in A. baerii and A. schrenckii, respectively, of which 72 were common to both species and all were upregulated in high quality compared with low quality samples. The differentially expressed proteins were mainly categorized into the generation of precursor metabolites and energy and oxidation, and they were localized to the mitochondria. Three distinguishing pathways, Arginine and proline metabolism, Pyruvate metabolism and the Citrate cycle (TCA cycle) were found to play an important role in energy metabolism, and some substrates could be used in the sperm medium for storage and cryopreservation. The quantity levels of two proteins, CKMT1 and LDHB, were verified by western blot analysis. Moreover, other potential biomarkers involved in oxidation reduction, ubiquitin-proteasome-dependent proteolysis, chaperones and binding activity were also discussed. Our study is the first to use the iTRAQ-based proteomics approach to analyse the sturgeon spermatozoa proteome, and the results that we obtained are valuable for the prediction of sperm quality and reproduction management in these threatened species.", "claims": [{"id": "claim-method", "statement": "Protein quantification was carried out based on a unique peptide. A cut-off of a 1.5-fold change was chosen, and proteins with quantification ratios of 1.5 for low (<0.67) or high (>1.5) relative protein levels were considered as differentially regulated.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:29077704", "locator": "sections[9] \"Data analysis\" paragraph 2", "quote": "Protein quantification was carried out based on a unique peptide. A cut-off of a 1.5-fold change was chosen, and proteins with quantification ratios of 1.5 for low (<0.67) or high (>1.5) relative protein levels were considered as differentially regulated."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "partial", "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:29077704"], "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": "blocked", "blocked_on": "data:accession_absent", "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": [], "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": {"e_value": "were selected using an E-value cut-off of 10−5"}, "inputs": [], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": ["step:obtain_source_data blocked on data:accession_absent"]}, "data": {"state": "partial", "assets": [{"id": "source:pmid:29077704", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.1371/journal.pone.0186003", "sha256": "sha256:a0999e4bb2b286bffc061aa5335ff585b2db90ee718ce36ec75db85752fba370", "bytes": 40219, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.1371/journal.pone.0186003", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC5659609", "source": "europe_pmc_fulltext", "coverage": "whole_body_without_references", "text_hash_scope": "rendered_section_body"}}, {"id": "asset:table:pmid:29077704:1", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:f0d2d7ed5b643633a04781652a5e311f88160f3dede347b962adbb5b88e52293", "bytes": 238, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[13]/table-wrap[1]#pone.0186003.t001", "version": null, "note": "Sperm quality parameters from A. baerii (n = 11) and A. schrenckii (n = 7).", "structure": {"pmcid": "PMC5659609", "section_index": 13, "section_title": "Sperm motility and fertility parameters", "row_count": 0, "column_count": 0}, "table": {"label": "Table 1", "caption": "Sperm quality parameters from A. baerii (n = 11) and A. schrenckii (n = 7).", "rows": [], "row_count": 0, "column_count": 0, "numeric_cells": 0, "header_rows": 0, "locator": "section[13]/table-wrap[1]#pone.0186003.t001"}}, {"id": "asset:table:pmid:29077704:2", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:dddf5eeab484ba1dcaed78d6a111abb8ec73f01c49e9f240eb43118443d76119", "bytes": 251, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[14]/table-wrap[1]#pone.0186003.t002", "version": null, "note": "Potential biomarkers related to sperm quality in A. baerii (AB) and A. schrenckii (ASK).", "structure": {"pmcid": "PMC5659609", "section_index": 14, "section_title": "The proteome of sperm in A. baerii and A. schrenckii by iTRAQ analysis", "row_count": 0, "column_count": 0}, "table": {"label": "Table 2", "caption": "Potential biomarkers related to sperm quality in A. baerii (AB) and A. schrenckii (ASK).", "rows": [], "row_count": 0, "column_count": 0, "numeric_cells": 0, "header_rows": 0, "locator": "section[14]/table-wrap[1]#pone.0186003.t002"}}, {"id": "asset:table:pmid:29077704:3", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:6f72af571de7dc86cf0dc4ea0ed2ddb0630b9e4a470dc04dce755b9caf1ff5d4", "bytes": 176, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[15]/table-wrap[1]#pone.0186003.t003", "version": null, "note": "Protein list.", "structure": {"pmcid": "PMC5659609", "section_index": 15, "section_title": "Functional classification and interaction of differentially expressed proteins", "row_count": 0, "column_count": 0}, "table": {"label": "Table 3", "caption": "Protein list.", "rows": [], "row_count": 0, "column_count": 0, "numeric_cells": 0, "header_rows": 0, "locator": "section[15]/table-wrap[1]#pone.0186003.t003"}}], "gaps": []}, "analysis": {"state": "partial", "methods": [{"id": "method-1", "family": "sequence_alignment", "specific": "blast", "label": "Sequence alignment / homology", "dsl_operations": ["sequence_align", "alignment_identity"], "missing_operations": [], "expressible": true, "parameters": {"e_value": "were selected using an E-value cut-off of 10−5"}, "data_shapes": ["sequence_records"], "evidence": {"score": 0.8, "band": "high", "quote": "BLAST"}}, {"id": "method-2", "family": null, "specific": null, "label": "8-plex iTRAQ label-based relative quantification with unique-peptide fold-change classification", "dsl_operations": [], "missing_operations": [], "expressible": null, "parameters": {}, "data_shapes": [], "evidence": {"score": 1.0, "band": "verbatim", "quote": "Protein quantification was carried out based on a unique peptide. A cut-off of a 1.5-fold change was chosen, and proteins with quantification ratios of 1.5 for low (<0.67) or high (>1.5) relative protein levels were considered as differentially regulated."}}], "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": "data", "blocked_on": "data:accession_absent", "axes": {"method": {"tier": "R1", "expressible": true, "required_operations": ["sequence_align", "alignment_identity"], "missing_operations": [], "basis": "The paper names the method it used and the corpus's method extractor maps it onto the DSL catalogue: blast."}, "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": "R4", "reachable": false, "accessions": [], "resolved_accessions": [], "statements": [], "basis": "The paper names no accession to its source data, so the data has to come from the authors."}}, "can_run": {"dsl_operations": ["sequence_align", "alignment_identity"], "assets": ["source:pmid:29077704", "asset:table:pmid:29077704:1", "asset:table:pmid:29077704:2", "asset:table:pmid:29077704:3"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:None"]}, "gaps": ["data:accession_absent"]}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": null, "independence": "same_provider"}, "evidence_check": {"method": "verbatim", "availability": null}, "calls": 0, "usage": {}}, "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:29077704", "type": "paper", "label": "pmid:29077704"}, {"id": "source:pmid:29077704", "type": "manuscript", "label": "PMID 29077704 full text"}, {"id": "data:geo:None", "type": "dataset", "label": "GEO None"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:29077704", "type": "paper", "label": "pmid:29077704"}, {"id": "source:pmid:29077704", "type": "manuscript", "label": "PMID 29077704 full text"}, {"id": "data:geo:None", "type": "dataset", "label": "GEO None"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-29077704", "type": "extraction", "used": ["source:pmid:29077704"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-None", "type": "accession_resolution", "used": ["data:geo:None"], "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:29077704", "parent_hash": "sha256:b5739590c0c039f85012a607806fc29a0aa36e7e2751358d239c6ea885a70864", "fork_of": null, "generation": 6}, "gaps": ["execution.not_run", "method.reader_named_unmapped", "review.human_critique", "review.independent_reader", "review.machine_critique", "step:obtain_source_data blocked on data:accession_absent"], "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": ["erformance. In this study, we used the iTRAQ proteomics approach to perform proteomic profiling of s", "sed the iTRAQ proteomics approach to perform proteomic profiling of spermatozoa associated with spe", "ur study is the first to use the iTRAQ-based proteomics approach to analyse the sturgeon spermatozoa"], "order_basis": "paper_text_order:375", "id": "assay:1"}, {"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": ["o proteins, CKMT1 and LDHB, were verified by western blot analysis. Moreover, other potential biomarke"], "order_basis": "paper_text_order:1292", "id": "assay:2"}, {"role": "analysis", "definition_id": "sequence_alignment", "definition_version": "f2132e96ae6c7a4e", "definition_digest": null, "required_operations": ["sequence_align", "alignment_identity"], "support_state": "supported", "source_hashes": {"dsl_catalogue": "f2132e96ae6c7a4e"}, "confidence": 0.8, "evidence": ["BLAST"], "order_basis": "consumes_earlier_output", "id": "assay:3"}]}