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

pmid:26693507

The dynamic interactome of human Aha1 upon Y223 phosphorylation.

Donald Wolfgeher · Diana M Dunn · Mark R Woodford · Dimitra Bourboulia · Gennady Bratslavsky · Mehdi Mollapour · Stephen J Kron · Andrew W Truman

Data in brief · 2015 doi:10.1016/j.dib.2015.10.028

Paper

complete

Experiment

complete

Data

partial

Analysis

complete

Execution

absent

Execution evidence has not yet been added to this .science file. Explore its methods, data and open questions to plan the next step.
Record details sci_version · id · kind · revision · content_hash · schema · created_at · updated_at · generator
id
pmid:26693507
kind
science-record
content_hash
sha256:a4ddb9b9b36a2a0cbb491ed95fbcec84fdc43dddc89ae9d5288d7848ff6734fb
schema
https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json
created_at
2026-11-01T15:40:14Z
updated_at
2026-11-01T22:42:29Z
generator object · 2 fields
name
corpus-assay-engine
run_id
reading-sci-2026-11-01
paper object · 10 fields
state
complete
title
The dynamic interactome of human Aha1 upon Y223 phosphorylation.
doi
10.1016/j.dib.2015.10.028
pmid
26693507
authors array · 8 items
[0]
Donald Wolfgeher
[1]
Diana M Dunn
[2]
Mark R Woodford
[3]
Dimitra Bourboulia
[4]
Gennady Bratslavsky
[5]
Mehdi Mollapour
[6]
Stephen J Kron
[7]
Andrew W Truman
journal
Data in brief
year
2015
abstract
Heat Shock Protein 90 (Hsp90) is an essential chaperone that supports the function of a wide range of signaling molecules. Hsp90 binds to a suite of co-chaperone proteins that regulate Hsp90 function through alteration of intrinsic ATPase activity. Several studies have determined Aha1 to be an important co-chaperone whose binding to Hsp90 is modulated by phosphorylation, acetylation and SUMOylation of Hsp90 [1], [2]. In this study, we applied quantitative affinity-purification mass spectrometry (AP-MS) proteomics to understand how phosphorylation of hAha1 at Y223 altered global client/co-chaperone interaction [3]. Specifically, we characterized and compared the interactomes of Aha1-Y223F (phospho-mutant form) and Aha1-Y223E (phospho-mimic form). We identified 99 statistically significant interactors of hAha1, a high proportion of which (84%) demonstrated preferential binding to the phospho-mimic form of hAha1. The mass spectrometry proteomics data have been deposited to the ProteomeXchange Consortium (http://proteomecentral.proteomexchange.org) via the PRIDE partner repository [4] with the dataset identifier PXD001737.
claims array · 3 items
[0] object · 6 fields
id
claim-method
statement
An ANOVA test was then performed to identify proteins that indicate significant variability (P-value<0.05) between biological replicates within each group.
kind
methodological
target
null
evidence array · 1 item
[0] object · 3 fields
asset
source:pmid:26693507
locator
sections[8] "LC–MS/MS data analysis, statistical analysis" paragraph 4
quote
An ANOVA test was then performed to identify proteins that indicate significant variability (P-value<0.05) between biological replicates within each group.
state
complete
[1] object · 6 fields
id
claim-data-access
statement
The mass spectrometry proteomics data have been deposited to the ProteomeXchange Consortium (http://proteomecentral.proteomexchange.org) via the PRIDE partner repository [4] with the dataset identifier PXD001737.
kind
methodological
target
null
evidence array · 1 item
[0] object · 3 fields
asset
source:pmid:26693507
locator
sections[0] "Abstract" paragraph 2
quote
The mass spectrometry proteomics data have been deposited to the ProteomeXchange Consortium (http://proteomecentral.proteomexchange.org) via the PRIDE partner repository [4] with the dataset identifier PXD001737.
state
complete
[2] object · 6 fields
id
claim-target-result
statement
Using the R statistical package with ANOVA testing and data deposited through ProteomeXchange via the PRIDE partner repository under PXD001737, the study identified 99 statistically significant hAha1 interactors, 84% of which preferentially bound the phospho-mimic form of hAha1.
kind
quantitative
target object · 4 fields
value
84
unit
per cent
tolerance
null
source
We identified 99 statistically significant interactors of hAha1, a high proportion of which (84%) demonstrated preferential binding to the phospho-mimic form of hAha1.
evidence array · 4 items
[0] object · 3 fields
asset
source:pmid:26693507
locator
sections[8] "LC–MS/MS data analysis, statistical analysis" paragraph 4
quote
Further statistical analysis was performed using the R statistical package (http://www.r-project.org/).
[1] object · 3 fields
asset
source:pmid:26693507
locator
sections[8] "LC–MS/MS data analysis, statistical analysis" paragraph 4
quote
An ANOVA test was then performed to identify proteins that indicate significant variability (P-value<0.05) between biological replicates within each group.
[2] object · 3 fields
asset
source:pmid:26693507
locator
sections[0] "Abstract" paragraph 2
quote
The mass spectrometry proteomics data have been deposited to the ProteomeXchange Consortium (http://proteomecentral.proteomexchange.org) via the PRIDE partner repository [4] with the dataset identifier PXD001737.
[3] object · 3 fields
asset
source:pmid:26693507
locator
sections[0] "Abstract" paragraph 1
quote
We identified 99 statistically significant interactors of hAha1, a high proportion of which (84%) demonstrated preferential binding to the phospho-mimic form of hAha1.
state
complete
gaps array · 0 items
experiment object · 8 fields
state
complete
objective
Using the R statistical package with ANOVA testing and data deposited through ProteomeXchange via the PRIDE partner repository under PXD001737, the study identified 99 statistically significant hAha1 interactors, 84% of which preferentially bound the phospho-mimic form of hAha1.
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:26693507
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:PXD001737
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:PXD001737
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:26693507
role
manuscript
format
xml
media_type
application/xml
uri
https://doi.org/10.1016/j.dib.2015.10.028
sha256
sha256:285bb668764e516276a8306c7e0f25fad1f0ad0cea7f3003e2527f5e84437ee4
bytes
10863
access
open
state
resolved
reader
null
reader_status
reader_required
identifier
10.1016/j.dib.2015.10.028
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
PMC4659802
source
europe_pmc_fulltext
coverage
whole_body_without_references
text_hash_scope
rendered_section_body
[1] object · 15 fields
id
data:geo:PXD001737
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=PXD001737
sha256
null
bytes
null
access
open
state
resolved
reader
null
reader_status
reader_required
identifier
PXD001737
version
null
note
The mass spectrometry proteomics data have been deposited to the ProteomeXchange Consortium (http://proteomecentral.proteomexchange.org) via the PRIDE partner repository [4] with the dataset identifier PXD001737.
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 (http://proteomecentral.proteomexchange.org) via the PRIDE partner repository [4] with the dataset identifier PXD001737.
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
c-Abl Dependent Tyrosine Phosphorylation of theCo-chaperone Aha1 Regulates Interaction with Hsp90
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:26693507:1
role
table
format
jats-table
media_type
application/vnd.jats.table+json
uri
null
sha256
sha256:e022115a3822defd81a98a1dbb9a35a08cd45cc7d810c1b2b761b6a5afad108b
bytes
1005
access
open
state
verified
reader
read_table
reader_status
available
identifier
section[1]/table-wrap[1]#t0005
version
null
note
null
structure object · 5 fields
pmcid
PMC4659802
section_index
1
section_title
Specifications table
row_count
9
column_count
2
table object · 8 fields
label
null
caption
null
rows array · 9 items
[0] array · 2 items
[0]
Subject area
[1]
Biology
[1] array · 2 items
[0]
More specific subject area
[1]
Molecular chaperones, Mass spectrometry, phosphorylation
[2] array · 2 items
[0]
Type of data
[1]
18O Quant LC–MS/MS Mass spectrometry data
[3] array · 2 items
[0]
How data was acquired
[1]
Mass spectrometry. Thermo Q-Exactive Orbitrap
[4] array · 2 items
[0]
Data format
[1]
*.Raw
[5] array · 2 items
[0]
Experimental factors
[1]
HEK293 cells expressing either FLAG–hAha1–Y223E or FLAG–Aha1–Y223F
[6] array · 2 items
[0]
Experimental features
[1]
FLAG–hAha1–Y223E or FLAG–Aha1–Y223F complexes were purified by magnetic bead immunoprecipitation and processed by mass spectrometry
[7] array · 2 items
[0]
Data source location
[1]
The University of Chicago, Chicago, Illinois, USA
[8] array · 2 items
[0]
Data accessibility
[1]
The mass spectrometry proteomics data have been deposited to the ProteomeXchange Consortium (http://proteomecentral.proteomexchange.org) via the PRIDE partner repository with the dataset identifier PXD001737.
locator
section[1]/table-wrap[1]#t0005
gaps array · 2 items
[0]
asset:data:geo:PXD001737 not downloaded
[1]
asset:data:geo:PXD001737 licence not read
analysis object · 4 fields
state
complete
methods array · 1 item
[0] object · 10 fields
id
method-1
family
group_comparison
specific
anova
label
Group comparison
dsl_operations array · 4 items
[0]
group_summary
[1]
welch_t
[2]
bootstrap_mean_difference
[3]
group_comparison_anova
missing_operations array · 0 items
parameters object · 0 fields
data_shapes array · 1 item
[0]
two_or_more_groups_continuous
evidence object · 3 fields
score
1
band
verbatim
quote
An ANOVA test was then performed to identify proteins that indicate significant variability (P-value<0.05) between biological replicates within each group.
targets array · 2 items
[0] object · 8 fields
id
target-published-estimate
claim_id
claim-target-result
operation
bootstrap_mean_difference
unit
per cent
tolerance
null
state
complete
note
The published estimate as the reader quoted it from the paper. No tolerance is published because the paper states none.
[1] object · 8 fields
id
target-published-estimate-p-value
claim_id
claim-target-result
operation
bootstrap_mean_difference
unit
p-value
tolerance
null
state
complete
note
The threshold the paper applied to its own result, as the paper states it. A run that reproduces the effect is judged against this threshold.
gaps array · 0 items
capability object · 3 fields
state
complete
requirements array · 1 item
[0] object · 6 fields
capability_id
capability:computational_analysis
label
Computational analysis platform
assay_families array · 9 items
[0]
meta_analysis
[1]
machine_learning
[2]
survival_analysis
[3]
statistical_regression
[4]
pca
[5]
molecular_docking
[6]
network_analysis
[7]
differential_expression
[8]
gwas
candidate
Automated Assays Laravel application and simulated adapters
gaps array · 0 items
readiness object · 8 fields
state
complete
tier
R1
blocked_on
nothing:replicable_now
axes object · 3 fields
method object · 5 fields
tier
R1
expressible
true
required_operations array · 4 items
[0]
group_summary
[1]
welch_t
[2]
bootstrap_mean_difference
[3]
group_comparison_anova
missing_operations array · 0 items
basis
The paper names the method it used and the corpus's method extractor maps it onto the DSL catalogue: anova.
capability object · 4 fields
tier
R1
capability_id
capability:computational_analysis
availability_state
owned
basis
The computational analysis is owned. The physical bench the paper used is not, so a physical validation cannot be run here.
data object · 6 fields
tier
R1
reachable
true
accessions array · 1 item
[0]
PXD001737
resolved_accessions array · 1 item
[0]
PXD001737
statements array · 1 item
[0]
The mass spectrometry proteomics data have been deposited to the ProteomeXchange Consortium (http://proteomecentral.proteomexchange.org) via the PRIDE partner repository [4] with the dataset identifier PXD001737.
basis
The paper names PXD001737 in ProteomeXchange Consortium and the accession resolves in the repository. No dataset was downloaded and no licence was read.
can_run object · 3 fields
dsl_operations array · 4 items
[0]
group_summary
[1]
welch_t
[2]
bootstrap_mean_difference
[3]
group_comparison_anova
assets array · 3 items
[0]
source:pmid:26693507
[1]
data:geo:PXD001737
[2]
asset:table:pmid:26693507:1
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:PXD001737
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
2026-10-31T18:26:29Z
independence
same_provider
evidence_check object · 2 fields
method
verbatim
availability
verbatim
calls
8
usage object · 3 fields
prompt_tokens
28413
completion_tokens
2484
cached_tokens
1817
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:26693507
type
paper
label
pmid:26693507
[1] object · 3 fields
id
source:pmid:26693507
type
manuscript
label
PMID 26693507 full text
[2] object · 3 fields
id
data:geo:PXD001737
type
dataset
label
GEO PXD001737
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:26693507
type
paper
label
pmid:26693507
[1] object · 3 fields
id
source:pmid:26693507
type
manuscript
label
PMID 26693507 full text
[2] object · 3 fields
id
data:geo:PXD001737
type
dataset
label
GEO PXD001737
agent
agent:corpus-assay-engine
[1] object · 4 fields
id
activity-read-26693507
type
extraction
used array · 1 item
[0]
source:pmid:26693507
agent
agent:minimax-reader
[2] object · 4 fields
id
activity-resolve-PXD001737
type
accession_resolution
used array · 1 item
[0]
data:geo:PXD001737
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:26693507
parent_hash
sha256:f7c9861d73171e39d04d5170d4ccf3c7759f8e531d7b019c9ac330cf62d0e385
fork_of
null
gaps array · 6 items
[0]
asset:data:geo:PXD001737 licence not read
[1]
asset:data:geo:PXD001737 not downloaded
[2]
execution.not_run
[3]
review.human_critique
[4]
review.independent_reader
[5]
review.machine_critique
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 · 4 items
[0]
e applied quantitative affinity-purification mass spectrometry (AP-MS) proteomics to understand how phospho
[1]
ding to the phospho-mimic form of hAha1. The mass spectrometry proteomics data have been deposited to the P
[2]
inity-purification mass spectrometry (AP-MS) proteomics to understand how phosphorylation of hAha1 a
[3]
biological replicates within each group. The mass spectrometry proteomic data have been deposited to the Pr
order_basis
paper_text_order:502
id
assay:1
[1] object · 11 fields
role
data_generation
definition_id
cell_culture
definition_version
99e1195c7d6f
required_operations array · 0 items
support_state
partial
source_hashes object · 1 field
assay_lexicon
99e1195c7d6f
confidence
0.99
evidence array · 2 items
[0]
Experimental design, materials and methods HEK293 cell lines expressing either hAha1–Y223F–FLA
[1]
taining 5% CO2. Protein extraction from both HEK293 cells was carried out using methods previous
order_basis
paper_text_order:1202
id
assay:2
[2] object · 11 fields
role
analysis
definition_id
group_comparison
definition_version
f2132e96ae6c7a4e
required_operations array · 4 items
[0]
group_summary
[1]
welch_t
[2]
bootstrap_mean_difference
[3]
group_comparison_anova
support_state
supported
source_hashes object · 1 field
dsl_catalogue
f2132e96ae6c7a4e
evidence array · 1 item
[0]
An ANOVA test was then performed to identify proteins that indicate significant variability (P-value<0.05) between biological replicates within each group.
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:26693507", "kind": "science-record", "revision": 8, "content_hash": "sha256:a4ddb9b9b36a2a0cbb491ed95fbcec84fdc43dddc89ae9d5288d7848ff6734fb", "created_at": "2026-11-01T15:40:14Z", "updated_at": "2026-11-01T22:42:29Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "The dynamic interactome of human Aha1 upon Y223 phosphorylation.", "doi": "10.1016/j.dib.2015.10.028", "pmid": "26693507", "authors": ["Donald Wolfgeher", "Diana M Dunn", "Mark R Woodford", "Dimitra Bourboulia", "Gennady Bratslavsky", "Mehdi Mollapour", "Stephen J Kron", "Andrew W Truman"], "journal": "Data in brief", "year": 2015, "abstract": "Heat Shock Protein 90 (Hsp90) is an essential chaperone that supports the function of a wide range of signaling molecules. Hsp90 binds to a suite of co-chaperone proteins that regulate Hsp90 function through alteration of intrinsic ATPase activity. Several studies have determined Aha1 to be an important co-chaperone whose binding to Hsp90 is modulated by phosphorylation, acetylation and SUMOylation of Hsp90 [1], [2]. In this study, we applied quantitative affinity-purification mass spectrometry (AP-MS) proteomics to understand how phosphorylation of hAha1 at Y223 altered global client/co-chaperone interaction [3]. Specifically, we characterized and compared the interactomes of Aha1-Y223F (phospho-mutant form) and Aha1-Y223E (phospho-mimic form). We identified 99 statistically significant interactors of hAha1, a high proportion of which (84%) demonstrated preferential binding to the phospho-mimic form of hAha1. The mass spectrometry proteomics data have been deposited to the ProteomeXchange Consortium (http://proteomecentral.proteomexchange.org) via the PRIDE partner repository [4] with the dataset identifier PXD001737.", "claims": [{"id": "claim-method", "statement": "An ANOVA test was then performed to identify proteins that indicate significant variability (P-value<0.05) between biological replicates within each group.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:26693507", "locator": "sections[8] \"LC–MS/MS data analysis, statistical analysis\" paragraph 4", "quote": "An ANOVA test was then performed to identify proteins that indicate significant variability (P-value<0.05) between biological replicates within each group."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The mass spectrometry proteomics data have been deposited to the ProteomeXchange Consortium (http://proteomecentral.proteomexchange.org) via the PRIDE partner repository [4] with the dataset identifier PXD001737.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:26693507", "locator": "sections[0] \"Abstract\" paragraph 2", "quote": "The mass spectrometry proteomics data have been deposited to the ProteomeXchange Consortium (http://proteomecentral.proteomexchange.org) via the PRIDE partner repository [4] with the dataset identifier PXD001737."}], "state": "complete"}, {"id": "claim-target-result", "statement": "Using the R statistical package with ANOVA testing and data deposited through ProteomeXchange via the PRIDE partner repository under PXD001737, the study identified 99 statistically significant hAha1 interactors, 84% of which preferentially bound the phospho-mimic form of hAha1.", "kind": "quantitative", "target": {"value": 84.0, "unit": "per cent", "tolerance": null, "source": "We identified 99 statistically significant interactors of hAha1, a high proportion of which (84%) demonstrated preferential binding to the phospho-mimic form of hAha1."}, "evidence": [{"asset": "source:pmid:26693507", "locator": "sections[8] \"LC–MS/MS data analysis, statistical analysis\" paragraph 4", "quote": "Further statistical analysis was performed using the R statistical package (http://www.r-project.org/)."}, {"asset": "source:pmid:26693507", "locator": "sections[8] \"LC–MS/MS data analysis, statistical analysis\" paragraph 4", "quote": "An ANOVA test was then performed to identify proteins that indicate significant variability (P-value<0.05) between biological replicates within each group."}, {"asset": "source:pmid:26693507", "locator": "sections[0] \"Abstract\" paragraph 2", "quote": "The mass spectrometry proteomics data have been deposited to the ProteomeXchange Consortium (http://proteomecentral.proteomexchange.org) via the PRIDE partner repository [4] with the dataset identifier PXD001737."}, {"asset": "source:pmid:26693507", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "We identified 99 statistically significant interactors of hAha1, a high proportion of which (84%) demonstrated preferential binding to the phospho-mimic form of hAha1."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "Using the R statistical package with ANOVA testing and data deposited through ProteomeXchange via the PRIDE partner repository under PXD001737, the study identified 99 statistically significant hAha1 interactors, 84% of which preferentially bound the phospho-mimic form of hAha1.", "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:26693507"], "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:PXD001737"], "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:PXD001737"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:26693507", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.1016/j.dib.2015.10.028", "sha256": "sha256:285bb668764e516276a8306c7e0f25fad1f0ad0cea7f3003e2527f5e84437ee4", "bytes": 10863, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.1016/j.dib.2015.10.028", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC4659802", "source": "europe_pmc_fulltext", "coverage": "whole_body_without_references", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:PXD001737", "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=PXD001737", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "PXD001737", "version": null, "note": "The mass spectrometry proteomics data have been deposited to the ProteomeXchange Consortium (http://proteomecentral.proteomexchange.org) via the PRIDE partner repository [4] with the dataset identifier PXD001737.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The mass spectrometry proteomics data have been deposited to the ProteomeXchange Consortium (http://proteomecentral.proteomexchange.org) via the PRIDE partner repository [4] with the dataset identifier PXD001737.", "access_statement_kind": "data_availability_statement", "sample_accessions": [], "sample_count": null, "group_sizes": null, "group_sizes_basis": null, "platform": null, "taxon": null, "title": "c-Abl Dependent Tyrosine Phosphorylation  of theCo-chaperone Aha1  Regulates Interaction with Hsp90", "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:26693507:1", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:e022115a3822defd81a98a1dbb9a35a08cd45cc7d810c1b2b761b6a5afad108b", "bytes": 1005, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[1]/table-wrap[1]#t0005", "version": null, "note": null, "structure": {"pmcid": "PMC4659802", "section_index": 1, "section_title": "Specifications table", "row_count": 9, "column_count": 2}, "table": {"label": null, "caption": null, "rows": [["Subject area", "Biology"], ["More specific subject area", "Molecular chaperones, Mass spectrometry, phosphorylation"], ["Type of data", "18O Quant LC–MS/MS Mass spectrometry data"], ["How data was acquired", "Mass spectrometry. Thermo Q-Exactive Orbitrap"], ["Data format", "*.Raw"], ["Experimental factors", "HEK293 cells expressing either FLAG–hAha1–Y223E or FLAG–Aha1–Y223F"], ["Experimental features", "FLAG–hAha1–Y223E or FLAG–Aha1–Y223F complexes were purified by magnetic bead immunoprecipitation and processed by mass spectrometry"], ["Data source location", "The University of Chicago, Chicago, Illinois, USA"], ["Data accessibility", "The mass spectrometry proteomics data have been deposited to the ProteomeXchange Consortium (http://proteomecentral.proteomexchange.org) via the PRIDE partner repository with the dataset identifier PXD001737."]], "row_count": 9, "column_count": 2, "numeric_cells": 4, "header_rows": 0, "locator": "section[1]/table-wrap[1]#t0005"}}], "gaps": ["asset:data:geo:PXD001737 not downloaded", "asset:data:geo:PXD001737 licence not read"]}, "analysis": {"state": "complete", "methods": [{"id": "method-1", "family": "group_comparison", "specific": "anova", "label": "Group comparison", "dsl_operations": ["group_summary", "welch_t", "bootstrap_mean_difference", "group_comparison_anova"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["two_or_more_groups_continuous"], "evidence": {"score": 1.0, "band": "verbatim", "quote": "An ANOVA test was then performed to identify proteins that indicate significant variability (P-value<0.05) between biological replicates within each group."}}], "targets": [{"id": "target-published-estimate", "claim_id": "claim-target-result", "operation": "bootstrap_mean_difference", "expected_value": 84.0, "unit": "per cent", "tolerance": null, "state": "complete", "note": "The published estimate as the reader quoted it from the paper. No tolerance is published because the paper states none."}, {"id": "target-published-estimate-p-value", "claim_id": "claim-target-result", "operation": "bootstrap_mean_difference", "expected_value": 0.05, "unit": "p-value", "tolerance": null, "state": "complete", "note": "The threshold the paper applied to its own result, as the paper states it. A run that reproduces the effect is judged against this threshold."}], "gaps": []}, "capability": {"state": "complete", "requirements": [{"capability_id": "capability:computational_analysis", "label": "Computational analysis platform", "assay_families": ["meta_analysis", "machine_learning", "survival_analysis", "statistical_regression", "pca", "molecular_docking", "network_analysis", "differential_expression", "gwas"], "availability_state": "owned", "tier_unlocked": "R1", "candidate": "Automated Assays Laravel application and simulated adapters"}], "gaps": []}, "readiness": {"state": "complete", "tier": "R1", "blocking_axis": "none", "blocked_on": "nothing:replicable_now", "axes": {"method": {"tier": "R1", "expressible": true, "required_operations": ["group_summary", "welch_t", "bootstrap_mean_difference", "group_comparison_anova"], "missing_operations": [], "basis": "The paper names the method it used and the corpus's method extractor maps it onto the DSL catalogue: anova."}, "capability": {"tier": "R1", "capability_id": "capability:computational_analysis", "availability_state": "owned", "basis": "The computational analysis is owned. The physical bench the paper used is not, so a physical validation cannot be run here."}, "data": {"tier": "R1", "reachable": true, "accessions": ["PXD001737"], "resolved_accessions": ["PXD001737"], "statements": ["The mass spectrometry proteomics data have been deposited to the ProteomeXchange Consortium (http://proteomecentral.proteomexchange.org) via the PRIDE partner repository [4] with the dataset identifier PXD001737."], "basis": "The paper names PXD001737 in ProteomeXchange Consortium and the accession resolves in the repository. No dataset was downloaded and no licence was read."}}, "can_run": {"dsl_operations": ["group_summary", "welch_t", "bootstrap_mean_difference", "group_comparison_anova"], "assets": ["source:pmid:26693507", "data:geo:PXD001737", "asset:table:pmid:26693507:1"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:PXD001737"]}, "gaps": []}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-10-31T18:26:29Z", "independence": "same_provider"}, "evidence_check": {"method": "verbatim", "availability": "verbatim"}, "calls": 8, "usage": {"prompt_tokens": 28413, "completion_tokens": 2484, "cached_tokens": 1817}}, "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:26693507", "type": "paper", "label": "pmid:26693507"}, {"id": "source:pmid:26693507", "type": "manuscript", "label": "PMID 26693507 full text"}, {"id": "data:geo:PXD001737", "type": "dataset", "label": "GEO PXD001737"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:26693507", "type": "paper", "label": "pmid:26693507"}, {"id": "source:pmid:26693507", "type": "manuscript", "label": "PMID 26693507 full text"}, {"id": "data:geo:PXD001737", "type": "dataset", "label": "GEO PXD001737"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-26693507", "type": "extraction", "used": ["source:pmid:26693507"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-PXD001737", "type": "accession_resolution", "used": ["data:geo:PXD001737"], "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:26693507", "parent_hash": "sha256:f7c9861d73171e39d04d5170d4ccf3c7759f8e531d7b019c9ac330cf62d0e385", "fork_of": null, "generation": 7}, "gaps": ["asset:data:geo:PXD001737 licence not read", "asset:data:geo:PXD001737 not downloaded", "execution.not_run", "review.human_critique", "review.independent_reader", "review.machine_critique"], "assays": [{"role": "data_generation", "definition_id": "mass_spectrometry", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.99, "evidence": ["e applied quantitative affinity-purification mass spectrometry (AP-MS) proteomics to understand how phospho", "ding to the phospho-mimic form of hAha1. The mass spectrometry proteomics data have been deposited to the P", "inity-purification mass spectrometry (AP-MS) proteomics to understand how phosphorylation of hAha1 a", "biological replicates within each group. The mass spectrometry proteomic data have been deposited to the Pr"], "order_basis": "paper_text_order:502", "id": "assay:1"}, {"role": "data_generation", "definition_id": "cell_culture", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.99, "evidence": ["Experimental design, materials and methods HEK293 cell lines expressing either hAha1–Y223F–FLA", "taining 5% CO2. Protein extraction from both HEK293 cells was carried out using methods previous"], "order_basis": "paper_text_order:1202", "id": "assay:2"}, {"role": "analysis", "definition_id": "group_comparison", "definition_version": "f2132e96ae6c7a4e", "definition_digest": null, "required_operations": ["group_summary", "welch_t", "bootstrap_mean_difference", "group_comparison_anova"], "support_state": "supported", "source_hashes": {"dsl_catalogue": "f2132e96ae6c7a4e"}, "confidence": 1.0, "evidence": ["An ANOVA test was then performed to identify proteins that indicate significant variability (P-value<0.05) between biological replicates within each group."], "order_basis": "consumes_earlier_output", "id": "assay:3"}]}