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

pmid:25124718

Proteomic analysis of the Plasmodium male gamete reveals the key role for glycolysis in flagellar motility.

Arthur M Talman · Judith H Prieto · Sara Marques · Ceereena Ubaida-Mohien · Mara Lawniczak · Mark N Wass · Tao Xu · Roland Frank · Andrea Ecker · Rebecca S Stanway · Sanjeev Krishna · Michael J E Sternberg · Georges K Christophides · David R Graham · Rhoel R Dinglasan · John R Yates · Robert E Sinden

Malaria journal · 2014 doi:10.1186/1475-2875-13-315

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:25124718
kind
science-record
content_hash
sha256:2acf9cc119fcb6b60c6e854b54d92651569db8bb528ba1ce18e372043d98fada
schema
https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json
created_at
2026-11-01T15:40:05Z
updated_at
2026-11-01T21:19:51Z
generator object · 2 fields
name
corpus-assay-engine
run_id
reading-sci-2026-11-01
paper object · 10 fields
state
complete
title
Proteomic analysis of the Plasmodium male gamete reveals the key role for glycolysis in flagellar motility.
doi
10.1186/1475-2875-13-315
pmid
25124718
authors array · 17 items
[0]
Arthur M Talman
[1]
Judith H Prieto
[2]
Sara Marques
[3]
Ceereena Ubaida-Mohien
[4]
Mara Lawniczak
[5]
Mark N Wass
[6]
Tao Xu
[7]
Roland Frank
[8]
Andrea Ecker
[9]
Rebecca S Stanway
[10]
Sanjeev Krishna
[11]
Michael J E Sternberg
[12]
Georges K Christophides
[13]
David R Graham
[14]
Rhoel R Dinglasan
[15]
John R Yates
[16]
Robert E Sinden
journal
Malaria journal
year
2014
abstract
BACKGROUND: Gametogenesis and fertilization play crucial roles in malaria transmission. While male gametes are thought to be amongst the simplest eukaryotic cells and are proven targets of transmission blocking immunity, little is known about their molecular organization. For example, the pathway of energy metabolism that power motility, a feature that facilitates gamete encounter and fertilization, is unknown. METHODS: Plasmodium berghei microgametes were purified and analysed by whole-cell proteomic analysis for the first time. Data are available via ProteomeXchange with identifier PXD001163. RESULTS: 615 proteins were recovered, they included all male gamete proteins described thus far. Amongst them were the 11 enzymes of the glycolytic pathway. The hexose transporter was localized to the gamete plasma membrane and it was shown that microgamete motility can be suppressed effectively by inhibitors of this transporter and of the glycolytic pathway. CONCLUSIONS: This study describes the first whole-cell proteomic analysis of the malaria male gamete. It identifies glycolysis as the likely exclusive source of energy for flagellar beat, and provides new insights in original features of Plasmodium flagellar organization.
claims array · 2 items
[0] object · 6 fields
id
claim-method
statement
Combination was performed using an unsupervised machine-learning strategy which estimates peptide identification FDR from reversed decoy searches [27].
kind
methodological
target
null
evidence array · 1 item
[0] object · 3 fields
asset
source:pmid:25124718
locator
sections[4] "Proteomics" paragraph 4
quote
Combination was performed using an unsupervised machine-learning strategy which estimates peptide identification FDR from reversed decoy searches [27].
state
complete
[1] object · 6 fields
id
claim-data-access
statement
The mass spectrometry proteomics data have been deposited to the ProteomeXchange Consortium [29] via the PRIDE partner repository [30] with the dataset identifier PXD001163.
kind
methodological
target
null
evidence array · 1 item
[0] object · 3 fields
asset
source:pmid:25124718
locator
sections[4] "Proteomics" paragraph 4
quote
The mass spectrometry proteomics data have been deposited to the ProteomeXchange Consortium [29] via the PRIDE partner repository [30] with the dataset identifier PXD001163.
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:25124718
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:PXD001163
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:PXD001163
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 · 4 items
[0] object · 15 fields
id
source:pmid:25124718
role
manuscript
format
xml
media_type
application/xml
uri
https://doi.org/10.1186/1475-2875-13-315
sha256
sha256:5c72402ef475d263fb52f9cdfa15a1c65013dd609642ae1fccca39c88e110a03
bytes
55890
access
open
state
resolved
reader
null
reader_status
reader_required
identifier
10.1186/1475-2875-13-315
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
PMC4150949
source
europe_pmc_fulltext
coverage
whole_body
text_hash_scope
rendered_section_body
[1] object · 15 fields
id
data:geo:PXD001163
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=PXD001163
sha256
null
bytes
null
access
open
state
resolved
reader
null
reader_status
reader_required
identifier
PXD001163
version
null
note
The mass spectrometry proteomics data have been deposited to the ProteomeXchange Consortium [29] via the PRIDE partner repository [30] with the dataset identifier PXD001163.
structure object · 15 fields
repository
GEO
access_route
GEO accession URL
access_statement_verbatim
The mass spectrometry proteomics data have been deposited to the ProteomeXchange Consortium [29] via the PRIDE partner repository [30] with the dataset identifier PXD001163.
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
Proteomic analysis of the Plasmodium male gamete reveals a key role for glycolysis in flagellar motility
resolution_checked_at
2026-10-31T18:35:55Z
resolution_check
identifier_resolution_only_no_download_no_licence_read
downloaded
false
licence_read
false
[2] object · 16 fields
id
asset:table:pmid:25124718:1
role
table
format
jats-table
media_type
application/vnd.jats.table+json
uri
null
sha256
sha256:613e657bc097d9b569cf3838efdea92ab24944a623adc30aaf8a8472e82af8e6
bytes
802
access
open
state
verified
reader
read_table
reader_status
available
identifier
section[10]/table-wrap[1]#Tab1
version
null
note
Proteins identified in the proteome for which experimental evidence suggests they play a role in male gamete biology
structure object · 5 fields
pmcid
PMC4150949
section_index
10
section_title
Proteomic analysis identifies a male gamete proteome
row_count
11
column_count
5
table object · 8 fields
label
Table 1
caption
Proteins identified in the proteome for which experimental evidence suggests they play a role in male gamete biology
rows array · 11 items
[0] array · 5 items
[0]
Accession
[1]
Seq count
[2]
Name
[3]
Function
[4]
Reference
[1] array · 5 items
[0]
PBANKA_061520
[1]
24
[2]
CDPK4
[3]
activation
[4]
[53]
[2] array · 5 items
[0]
PBANKA_121260
[1]
2
[2]
HAP2
[3]
fusion
[4]
[54]
[3] array · 5 items
[0]
PBANKA_093370
[1]
4
[2]
MAP2
[3]
cytokinesis
[4]
[55]
[4] array · 5 items
[0]
PBANKA_030600
[1]
11
[2]
P230p
[3]
?
[4]
[56]
[5] array · 5 items
[0]
PBANKA_135960
[1]
13
[2]
P48/45
[3]
adhesion
[4]
[57]
[6] array · 5 items
[0]
PBANKA_030610
[1]
53
[2]
Pb230
[3]
adhesion
[4]
[58]
[7] array · 5 items
[0]
PBANKA_143220
[1]
12
[2]
MDV1
[3]
egress
[4]
[59]
[8] array · 5 items
[0]
PBANKA_131270
[1]
23
[2]
GEST
[3]
egress
[4]
[60]
[9] array · 5 items
[0]
PBANKA_091740
[1]
3
[2]
PF16
[3]
flagellar
[4]
[61]
[10] array · 5 items
[0]
PBANKA_103010
[1]
8
[2]
actin II
[3]
flagellar
[4]
[62]
locator
section[10]/table-wrap[1]#Tab1
[3] object · 16 fields
id
asset:table:pmid:25124718:2
role
table
format
jats-table
media_type
application/vnd.jats.table+json
uri
null
sha256
sha256:f1ffd52a3bcc96ef51995ae6dd916940ad8b026e97667431a35cdeffb0e467f8
bytes
1384
access
open
state
verified
reader
read_table
reader_status
available
identifier
section[13]/table-wrap[1]#Tab2
version
null
note
Glycolytic enzymes identified in the proteome
structure object · 5 fields
pmcid
PMC4150949
section_index
13
section_title
Energy metabolism in Plasmodiummale gametes
row_count
23
column_count
4
table object · 8 fields
label
Table 2
caption
Glycolytic enzymes identified in the proteome
rows array · 23 items
[0] array · 4 items
[0]
P. bergheiaccession no
[1]
Seq count
[2]
Spectra
[3]
Description
[1] array · 4 items
[0]
Glycolytic enzymes
[1]
[2]
[3]
[2] array · 4 items
[0]
PBANKA_121090
[1]
6
[2]
8
[3]
Phosphoglucomutase
[3] array · 4 items
[0]
PBANKA_121430
[1]
38
[2]
457
[3]
Enolase
[4] array · 4 items
[0]
PBANKA_092810
[1]
23
[2]
85
[3]
Phosphoglycerate mutase
[5] array · 4 items
[0]
PBANKA_111770
[1]
3
[2]
7
[3]
Malate dehydrogenase
[6] array · 4 items
[0]
PBANKA_134010
[1]
24
[2]
239
[3]
LDH L-lactate dehydrogenase
[7] array · 4 items
[0]
PBANKA_134040
[1]
26
[2]
144
[3]
Oxidoreductase
[8] array · 4 items
[0]
PBANKA_100880
[1]
21
[2]
55
[3]
Glucose-6-phosphate isomerase
[9] array · 4 items
[0]
PBANKA_130380
[1]
20
[2]
102
[3]
Triose-phosphate isomerase
[10] array · 4 items
[0]
PBANKA_130860
[1]
47
[2]
597
[3]
ALDO2 fructose-bisphosphate aldolase 2
[11] array · 4 items
[0]
PBANKA_132640
[1]
53
[2]
548
[3]
Glyceraldehyde-3-phosphate dehydrogenase
[12] array · 4 items
[0]
PBANKA_040480
[1]
12
[2]
27
[3]
FAD-dependent glycerol-3-phosphate dehydrogenase
[13] array · 4 items
[0]
PBANKA_071550
[1]
5
[2]
11
[3]
Phosphoglycerate mutase
[14] array · 4 items
[0]
PBANKA_112290
[1]
17
[2]
75
[3]
Hexokinase
[15] array · 4 items
[0]
PBANKA_112560
[1]
22
[2]
161
[3]
Pyruvate kinase
[16] array · 4 items
[0]
PBANKA_081640
[1]
27
[2]
65
[3]
6-phosphofructokinase
[17] array · 4 items
[0]
PBANKA_082340
[1]
26
[2]
122
[3]
Phosphoglycerate kinase
[18] array · 4 items
[0]
Transporter
[1]
[2]
[3]
[19] array · 4 items
[0]
PBANKA_030250
[1]
8
[2]
30
[3]
HT hexose transporter
[20] array · 4 items
[0]
Reference proteins
[1]
[2]
[3]
[21] array · 4 items
[0]
PBANKA_121260
[1]
2
[2]
2
[3]
HAP2 generative cell specific 1
[22] array · 4 items
[0]
PBANKA_120690
[1]
51
[2]
656
[3]
Beta tubulin
locator
section[13]/table-wrap[1]#Tab2
gaps array · 2 items
[0]
asset:data:geo:PXD001163 not downloaded
[1]
asset:data:geo:PXD001163 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
unsupervised machine-learning strategy for combining peptide identifications and estimating false discovery rate from reversed decoy searches
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
Combination was performed using an unsupervised machine-learning strategy which estimates peptide identification FDR from reversed decoy searches [27].
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 (unsupervised machine-learning strategy for combining peptide identifications and estimating false discovery rate from reversed decoy searches), 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]
PXD001163
resolved_accessions array · 1 item
[0]
PXD001163
statements array · 1 item
[0]
The mass spectrometry proteomics data have been deposited to the ProteomeXchange Consortium [29] via the PRIDE partner repository [30] with the dataset identifier PXD001163.
basis
The paper names PXD001163 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 · 4 items
[0]
source:pmid:25124718
[1]
data:geo:PXD001163
[2]
asset:table:pmid:25124718:1
[3]
asset:table:pmid:25124718:2
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:PXD001163
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
null
independence
same_provider
evidence_check object · 2 fields
method
verbatim
availability
verbatim
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:25124718
type
paper
label
pmid:25124718
[1] object · 3 fields
id
source:pmid:25124718
type
manuscript
label
PMID 25124718 full text
[2] object · 3 fields
id
data:geo:PXD001163
type
dataset
label
GEO PXD001163
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:25124718
type
paper
label
pmid:25124718
[1] object · 3 fields
id
source:pmid:25124718
type
manuscript
label
PMID 25124718 full text
[2] object · 3 fields
id
data:geo:PXD001163
type
dataset
label
GEO PXD001163
agent
agent:corpus-assay-engine
[1] object · 4 fields
id
activity-read-25124718
type
extraction
used array · 1 item
[0]
source:pmid:25124718
agent
agent:minimax-reader
[2] object · 4 fields
id
activity-resolve-PXD001163
type
accession_resolution
used array · 1 item
[0]
data:geo:PXD001163
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:25124718
parent_hash
sha256:287e147dd33850c9ff1a0fd075419c6f9c9cdf09a136931fa182250815e07171
fork_of
null
gaps array · 7 items
[0]
asset:data:geo:PXD001163 licence not read
[1]
asset:data:geo:PXD001163 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:25124718", "kind": "science-record", "revision": 4, "content_hash": "sha256:2acf9cc119fcb6b60c6e854b54d92651569db8bb528ba1ce18e372043d98fada", "created_at": "2026-11-01T15:40:05Z", "updated_at": "2026-11-01T21:19:51Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Proteomic analysis of the Plasmodium male gamete reveals the key role for glycolysis in flagellar motility.", "doi": "10.1186/1475-2875-13-315", "pmid": "25124718", "authors": ["Arthur M Talman", "Judith H Prieto", "Sara Marques", "Ceereena Ubaida-Mohien", "Mara Lawniczak", "Mark N Wass", "Tao Xu", "Roland Frank", "Andrea Ecker", "Rebecca S Stanway", "Sanjeev Krishna", "Michael J E Sternberg", "Georges K Christophides", "David R Graham", "Rhoel R Dinglasan", "John R Yates", "Robert E Sinden"], "journal": "Malaria journal", "year": 2014, "abstract": "BACKGROUND: Gametogenesis and fertilization play crucial roles in malaria transmission. While male gametes are thought to be amongst the simplest eukaryotic cells and are proven targets of transmission blocking immunity, little is known about their molecular organization. For example, the pathway of energy metabolism that power motility, a feature that facilitates gamete encounter and fertilization, is unknown.\nMETHODS: Plasmodium berghei microgametes were purified and analysed by whole-cell proteomic analysis for the first time. Data are available via ProteomeXchange with identifier PXD001163.\nRESULTS: 615 proteins were recovered, they included all male gamete proteins described thus far. Amongst them were the 11 enzymes of the glycolytic pathway. The hexose transporter was localized to the gamete plasma membrane and it was shown that microgamete motility can be suppressed effectively by inhibitors of this transporter and of the glycolytic pathway.\nCONCLUSIONS: This study describes the first whole-cell proteomic analysis of the malaria male gamete. It identifies glycolysis as the likely exclusive source of energy for flagellar beat, and provides new insights in original features of Plasmodium flagellar organization.", "claims": [{"id": "claim-method", "statement": "Combination was performed using an unsupervised machine-learning strategy which estimates peptide identification FDR from reversed decoy searches [27].", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:25124718", "locator": "sections[4] \"Proteomics\" paragraph 4", "quote": "Combination was performed using an unsupervised machine-learning strategy which estimates peptide identification FDR from reversed decoy searches [27]."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The mass spectrometry proteomics data have been deposited to the ProteomeXchange Consortium [29] via the PRIDE partner repository [30] with the dataset identifier PXD001163.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:25124718", "locator": "sections[4] \"Proteomics\" paragraph 4", "quote": "The mass spectrometry proteomics data have been deposited to the ProteomeXchange Consortium [29] via the PRIDE partner repository [30] with the dataset identifier PXD001163."}], "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:25124718"], "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:PXD001163"], "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:PXD001163"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:25124718", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.1186/1475-2875-13-315", "sha256": "sha256:5c72402ef475d263fb52f9cdfa15a1c65013dd609642ae1fccca39c88e110a03", "bytes": 55890, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.1186/1475-2875-13-315", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC4150949", "source": "europe_pmc_fulltext", "coverage": "whole_body", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:PXD001163", "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=PXD001163", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "PXD001163", "version": null, "note": "The mass spectrometry proteomics data have been deposited to the ProteomeXchange Consortium [29] via the PRIDE partner repository [30] with the dataset identifier PXD001163.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The mass spectrometry proteomics data have been deposited to the ProteomeXchange Consortium [29] via the PRIDE partner repository [30] with the dataset identifier PXD001163.", "access_statement_kind": "data_availability_statement", "sample_accessions": [], "sample_count": null, "group_sizes": null, "group_sizes_basis": null, "platform": null, "taxon": null, "title": "Proteomic analysis of the Plasmodium male gamete reveals a key role for glycolysis in flagellar motility", "resolution_checked_at": "2026-10-31T18:35:55Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}, {"id": "asset:table:pmid:25124718:1", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:613e657bc097d9b569cf3838efdea92ab24944a623adc30aaf8a8472e82af8e6", "bytes": 802, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[10]/table-wrap[1]#Tab1", "version": null, "note": "Proteins identified in the proteome for which experimental evidence suggests they play a role in male gamete biology", "structure": {"pmcid": "PMC4150949", "section_index": 10, "section_title": "Proteomic analysis identifies a male gamete proteome", "row_count": 11, "column_count": 5}, "table": {"label": "Table 1", "caption": "Proteins identified in the proteome for which experimental evidence suggests they play a role in male gamete biology", "rows": [["Accession", "Seq count", "Name", "Function", "Reference"], ["PBANKA_061520", "24", "CDPK4", "activation", "[53]"], ["PBANKA_121260", "2", "HAP2", "fusion", "[54]"], ["PBANKA_093370", "4", "MAP2", "cytokinesis", "[55]"], ["PBANKA_030600", "11", "P230p", "?", "[56]"], ["PBANKA_135960", "13", "P48/45", "adhesion", "[57]"], ["PBANKA_030610", "53", "Pb230", "adhesion", "[58]"], ["PBANKA_143220", "12", "MDV1", "egress", "[59]"], ["PBANKA_131270", "23", "GEST", "egress", "[60]"], ["PBANKA_091740", "3", "PF16", "flagellar", "[61]"], ["PBANKA_103010", "8", "actin II", "flagellar", "[62]"]], "row_count": 11, "column_count": 5, "numeric_cells": 34, "header_rows": 1, "locator": "section[10]/table-wrap[1]#Tab1"}}, {"id": "asset:table:pmid:25124718:2", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:f1ffd52a3bcc96ef51995ae6dd916940ad8b026e97667431a35cdeffb0e467f8", "bytes": 1384, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[13]/table-wrap[1]#Tab2", "version": null, "note": "Glycolytic enzymes identified in the proteome", "structure": {"pmcid": "PMC4150949", "section_index": 13, "section_title": "Energy metabolism in Plasmodiummale gametes", "row_count": 23, "column_count": 4}, "table": {"label": "Table 2", "caption": "Glycolytic enzymes identified in the proteome", "rows": [["P. bergheiaccession no", "Seq count", "Spectra", "Description"], ["Glycolytic enzymes", "", "", ""], ["PBANKA_121090", "6", "8", "Phosphoglucomutase"], ["PBANKA_121430", "38", "457", "Enolase"], ["PBANKA_092810", "23", "85", "Phosphoglycerate mutase"], ["PBANKA_111770", "3", "7", "Malate dehydrogenase"], ["PBANKA_134010", "24", "239", "LDH L-lactate dehydrogenase"], ["PBANKA_134040", "26", "144", "Oxidoreductase"], ["PBANKA_100880", "21", "55", "Glucose-6-phosphate isomerase"], ["PBANKA_130380", "20", "102", "Triose-phosphate isomerase"], ["PBANKA_130860", "47", "597", "ALDO2 fructose-bisphosphate aldolase 2"], ["PBANKA_132640", "53", "548", "Glyceraldehyde-3-phosphate dehydrogenase"], ["PBANKA_040480", "12", "27", "FAD-dependent glycerol-3-phosphate dehydrogenase"], ["PBANKA_071550", "5", "11", "Phosphoglycerate mutase"], ["PBANKA_112290", "17", "75", "Hexokinase"], ["PBANKA_112560", "22", "161", "Pyruvate kinase"], ["PBANKA_081640", "27", "65", "6-phosphofructokinase"], ["PBANKA_082340", "26", "122", "Phosphoglycerate kinase"], ["Transporter", "", "", ""], ["PBANKA_030250", "8", "30", "HT hexose transporter"], ["Reference proteins", "", "", ""], ["PBANKA_121260", "2", "2", "HAP2 generative cell specific 1"], ["PBANKA_120690", "51", "656", "Beta tubulin"]], "row_count": 23, "column_count": 4, "numeric_cells": 63, "header_rows": 1, "locator": "section[13]/table-wrap[1]#Tab2"}}], "gaps": ["asset:data:geo:PXD001163 not downloaded", "asset:data:geo:PXD001163 licence not read"]}, "analysis": {"state": "partial", "methods": [{"id": "method-1", "family": null, "specific": null, "label": "unsupervised machine-learning strategy for combining peptide identifications and estimating false discovery rate from reversed decoy searches", "dsl_operations": [], "missing_operations": [], "expressible": null, "parameters": {}, "data_shapes": [], "evidence": {"score": 1.0, "band": "verbatim", "quote": "Combination was performed using an unsupervised machine-learning strategy which estimates peptide identification FDR from reversed decoy searches [27]."}}], "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 (unsupervised machine-learning strategy for combining peptide identifications and estimating false discovery rate from reversed decoy searches), 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": ["PXD001163"], "resolved_accessions": ["PXD001163"], "statements": ["The mass spectrometry proteomics data have been deposited to the ProteomeXchange Consortium [29] via the PRIDE partner repository [30] with the dataset identifier PXD001163."], "basis": "The paper names PXD001163 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:25124718", "data:geo:PXD001163", "asset:table:pmid:25124718:1", "asset:table:pmid:25124718:2"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:PXD001163"]}, "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": null, "independence": "same_provider"}, "evidence_check": {"method": "verbatim", "availability": "verbatim"}, "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:25124718", "type": "paper", "label": "pmid:25124718"}, {"id": "source:pmid:25124718", "type": "manuscript", "label": "PMID 25124718 full text"}, {"id": "data:geo:PXD001163", "type": "dataset", "label": "GEO PXD001163"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:25124718", "type": "paper", "label": "pmid:25124718"}, {"id": "source:pmid:25124718", "type": "manuscript", "label": "PMID 25124718 full text"}, {"id": "data:geo:PXD001163", "type": "dataset", "label": "GEO PXD001163"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-25124718", "type": "extraction", "used": ["source:pmid:25124718"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-PXD001163", "type": "accession_resolution", "used": ["data:geo:PXD001163"], "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:25124718", "parent_hash": "sha256:287e147dd33850c9ff1a0fd075419c6f9c9cdf09a136931fa182250815e07171", "fork_of": null, "generation": 3}, "gaps": ["asset:data:geo:PXD001163 licence not read", "asset:data:geo:PXD001163 not downloaded", "execution.not_run", "method.reader_named_unmapped", "review.human_critique", "review.independent_reader", "review.machine_critique"]}