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

pmid:41373777

Identification of Colorectal Cancer-Related RNA Markers from Whole Blood Using Integrated Bioinformatics Analysis.

International journal of molecular sciences · 2025 doi:10.3390/ijms262311625

Paper

partial

Experiment

partial

Data

partial

Analysis

absent

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:41373777
kind
science-record
content_hash
sha256:2f3961d750fb0861754d6427194d91e7d6dc3d15e8663f068ae01a62d40ca0b7
schema
https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json
created_at
2026-11-01T10:25:54Z
updated_at
2026-11-01T14:01:52Z
generator object · 3 fields
name
corpus-assay-engine
converter
sep_to_sci_v1
source_package_schema
urn:bntrg:sep:1.0.0
paper object · 10 fields
state
partial
title
Identification of Colorectal Cancer-Related RNA Markers from Whole Blood Using Integrated Bioinformatics Analysis.
doi
10.3390/ijms262311625
pmid
41373777
authors
null
journal
International journal of molecular sciences
year
2025
abstract
null
claims array · 1 item
[0] object · 6 fields
id
claim-1
statement
the headline numerical result the paper states for its main finding
kind
qualitative
state
blocked
target object · 4 fields
value
null
unit
null
tolerance
null
source
null
evidence array · 0 items
gaps array · 2 items
[0]
abstract
[1]
authors
experiment object · 8 fields
state
partial
objective
the headline numerical result the paper states for its main finding
steps array · 3 items
[0] object · 13 fields
id
read_published_estimate
order
1
name
Read the published estimate and its interval from the source
kind
other
state
complete
blocked_on
null
description
The number a replication must land on, and the sentence it came from.
parameters object · 0 fields
inputs array · 1 item
[0]
source:pmid:41373777
outputs array · 1 item
[0]
the published estimate, its unit and its interval
instruments array · 0 items
reagents array · 0 items
[1] object · 13 fields
id
obtain_source_data
order
2
name
Obtain the source data behind the published result
kind
data-preparation
state
blocked
blocked_on
data:not_downloaded
description
The published result cannot be recomputed without the data the paper analysed.
parameters object · 0 fields
inputs array · 0 items
outputs array · 1 item
[0]
the source data with its provenance
instruments array · 0 items
reagents array · 0 items
[2] object · 13 fields
id
run_analysis
order
3
name
Run the analysis programme
kind
analysis
state
blocked
blocked_on
no owned computational capability is bound to this experiment
description
Re-run the paper's analysis on the source data and produce the registered result. | SEP input not carried into the asset list: materials:the source data behind the published result in pmid:41373777
parameters object · 0 fields
inputs array · 0 items
outputs array · 1 item
[0]
the registered result
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 · 3 items
[0]
step:obtain_source_data blocked on data:not_downloaded
[1]
step:run_analysis blocked on no owned computational capability is bound to this experiment
[2]
step:run_analysis input 'materials:the source data behind the published result in pmid:41373777' does not resolve to a declared asset
data object · 3 fields
state
partial
assets array · 5 items
[0] object · 15 fields
id
source:pmid:41373777
role
manuscript
format
xml
media_type
application/xml
uri
https://doi.org/10.3390/ijms262311625
sha256
sha256:00766163598e77204e9d7ff697627f72f74934071c4a511c052ccd0979c47a2e
bytes
null
access
open
state
resolved
reader
null
reader_status
reader_required
identifier
10.3390/ijms262311625
version
null
note
Source read by the package builder: full_text.
structure object · 1 field
access_state
full_text
[1] object · 16 fields
id
asset:table:pmid:41373777:1
role
table
format
jats-table
media_type
application/vnd.jats.table+json
uri
null
sha256
sha256:62606f1fd840a914d341e18e55abe8dfe0ba7e1b2e420116966eb26a2c07ec51
bytes
510
access
open
state
verified
reader
read_table
reader_status
available
identifier
section[4]/table-wrap[1]#ijms-26-11625-t001
version
null
note
Summary of DEGs Derived from Six Public Datasets Used to Construct the WB-PADs dataset.
structure object · 5 fields
pmcid
PMC12692440
section_index
4
section_title
2.2. Construction of the WB-PADs Dataset
row_count
7
column_count
5
table object · 8 fields
label
Table 1
caption
Summary of DEGs Derived from Six Public Datasets Used to Construct the WB-PADs dataset.
rows array · 7 items
[0] array · 5 items
[0]
No.
[1]
Dataset
[2]
Up-RegulatedGenes
[3]
Down-RegulatedGenes
[4]
Total
[1] array · 5 items
[0]
1
[1]
WB-Hub
[2]
45
[3]
87
[4]
132
[2] array · 5 items
[0]
2
[1]
WB-TF
[2]
24
[3]
103
[4]
127
[3] array · 5 items
[0]
3
[1]
WB-GWAS
[2]
11
[3]
42
[4]
53
[4] array · 5 items
[0]
4
[1]
WB-eQTL
[2]
43
[3]
151
[4]
194
[5] array · 5 items
[0]
5
[1]
WB-DigSeE
[2]
21
[3]
27
[4]
48
[6] array · 5 items
[0]
6
[1]
WB-CoReCG
[2]
33
[3]
64
[4]
97
locator
section[4]/table-wrap[1]#ijms-26-11625-t001
[2] object · 16 fields
id
asset:table:pmid:41373777:2
role
table
format
jats-table
media_type
application/vnd.jats.table+json
uri
null
sha256
sha256:505fd1ef115f42a4039d85b871b19317adb5f47e9a5c2dcd38ea5af2bd91abf7
bytes
442
access
open
state
verified
reader
read_table
reader_status
available
identifier
section[5]/table-wrap[1]#ijms-26-11625-t002
version
null
note
Demographic and clinical characteristics of participants in the WB-K RNA-seq cohort.
structure object · 5 fields
pmcid
PMC12692440
section_index
5
section_title
2.3. Construction of the WB-K Dataset
row_count
5
column_count
3
table object · 8 fields
label
Table 2
caption
Demographic and clinical characteristics of participants in the WB-K RNA-seq cohort.
rows array · 5 items
[0] array · 3 items
[0]
Characteristics
[1]
Healthy Control, n (%)
[2]
Colorectal Cancer, n (%)
[1] array · 3 items
[0]
Age (SD)
[1]
54.0 (7.6)
[2]
46.8 (8.1)
[2] array · 3 items
[0]
Gender (%)
[1]
[2]
[3] array · 3 items
[0]
Male
[1]
5 (50.0)
[2]
5 (50.0)
[4] array · 3 items
[0]
Female
[1]
5 (50.0)
[2]
5 (50.0)
locator
section[5]/table-wrap[1]#ijms-26-11625-t002
[3] object · 16 fields
id
asset:table:pmid:41373777:3
role
table
format
jats-table
media_type
application/vnd.jats.table+json
uri
null
sha256
sha256:567e3599ac30d3091cc019eac6e576f348ae491aa197e9513e78c83e3c79841a
bytes
587
access
open
state
verified
reader
read_table
reader_status
available
identifier
section[6]/table-wrap[1]#ijms-26-11625-t003
version
null
note
Five candidate genes showing consistent differential expression patterns in both WB-PADs and WB-K datasets.
structure object · 5 fields
pmcid
PMC12692440
section_index
6
section_title
2.4. Selection of Candidate Genes for Clinical Validation
row_count
7
column_count
5
table object · 8 fields
label
Table 3
caption
Five candidate genes showing consistent differential expression patterns in both WB-PADs and WB-K datasets.
rows array · 7 items
[0] array · 3 items
[0]
Gene Symbol
[1]
log2FC
[2]
p-Value
[1] array · 4 items
[0]
WB Dataset
[1]
WB-K Dataset
[2]
WB Dataset
[3]
WB-K Dataset
[2] array · 5 items
[0]
DLG5
[1]
−0.59
[2]
−0.63
[3]
0.0005
[4]
0.007
[3] array · 5 items
[0]
CD177
[1]
1.09
[2]
1.34
[3]
0.00001
[4]
0.03
[4] array · 5 items
[0]
SH2D1B
[1]
−0.58
[2]
−0.86
[3]
0.000001
[4]
0.01
[5] array · 5 items
[0]
NQO2
[1]
0.57
[2]
0.77
[3]
0.000002
[4]
0.01
[6] array · 5 items
[0]
KRT73
[1]
−0.76
[2]
−1.00
[3]
0.0001
[4]
0.001
locator
section[6]/table-wrap[1]#ijms-26-11625-t003
[4] object · 16 fields
id
asset:table:pmid:41373777:4
role
table
format
jats-table
media_type
application/vnd.jats.table+json
uri
null
sha256
sha256:3686d1cbb2975826ed4b3ade62e2639bcf830165d3f02ab99cc96f29e8f0923c
bytes
426
access
open
state
verified
reader
read_table
reader_status
available
identifier
section[15]/table-wrap[1]#ijms-26-11625-t004
version
null
note
Clinicopathologic characteristics of study participants.
structure object · 5 fields
pmcid
PMC12692440
section_index
15
section_title
4.5. Patient Cohorts
row_count
5
column_count
3
table object · 8 fields
label
Table 4
caption
Clinicopathologic characteristics of study participants.
rows array · 5 items
[0] array · 3 items
[0]
Characteristics
[1]
Healthy Control, n (%)
[2]
Colorectal Cancer, n (%)
[1] array · 3 items
[0]
Age, y (SD)
[1]
63.2 (11.2)
[2]
48.9 (9.8)
[2] array · 3 items
[0]
Gender, n (%)
[1]
[2]
[3] array · 3 items
[0]
Male
[1]
60 (59.4)
[2]
64 (57.7)
[4] array · 3 items
[0]
Female
[1]
41 (40.6)
[2]
47 (42.3)
locator
section[15]/table-wrap[1]#ijms-26-11625-t004
gaps array · 1 item
[0]
asset:source:pmid:41373777 not verified
analysis object · 4 fields
state
absent
methods array · 0 items
targets array · 0 items
gaps array · 2 items
[0]
method
[1]
targets
capability object · 3 fields
state
absent
requirements array · 0 items
gaps array · 1 item
[0]
capability
readiness object · 8 fields
state
partial
tier
null
blocked_on
null
axes object · 0 fields
can_run object · 3 fields
dsl_operations array · 0 items
assets array · 5 items
[0]
source:pmid:41373777
[1]
asset:table:pmid:41373777:1
[2]
asset:table:pmid:41373777:2
[3]
asset:table:pmid:41373777:3
[4]
asset:table:pmid:41373777:4
steps array · 1 item
[0]
read_published_estimate
must_build object · 5 fields
dsl_operations array · 0 items
converters array · 0 items
readers array · 1 item
[0]
xml
capabilities array · 0 items
data_gaps array · 1 item
[0]
source:pmid:41373777
gaps array · 1 item
[0]
corpus_record_absent
review object · 5 fields
state
partial
machine_critique object · 7 fields
status
blocked
providers array · 0 items
target_providers array · 0 items
agreement
false
disagreements array · 0 items
agreement_basis object · 2 fields
policy
decisive_fields
decisive_fields array · 4 items
[0]
work_type
[1]
number_stated
[2]
parent_value
[3]
unit
blinded
true
human_critique object · 5 fields
status
not_run
reviewer
null
signed_at
null
conflict_checked
false
commentary
null
stages array · 7 items
[0] object · 4 fields
key
target_materials
status
pending
reason
null
evidence
null
[1] object · 4 fields
key
independent_readings
status
blocked
reason
The independent readings are incomplete or disagree; the source evidence must resolve the difference.
evidence object · 1 field
provider_errors array · 4 items
[0] object · 4 fields
provider
minimax
model
null
reason
HTTP Error 429: Too Many Requests
raw_response
null
[1] object · 4 fields
provider
minimax_alt
model
null
reason
HTTP Error 429: Too Many Requests
raw_response
null
[2] object · 4 fields
provider
minimax
model
null
reason
HTTP Error 429: Too Many Requests
raw_response
null
[3] object · 4 fields
provider
minimax_alt
model
null
reason
HTTP Error 429: Too Many Requests
raw_response
null
[2] object · 4 fields
key
source_resolution
status
pending
reason
null
evidence
null
[3] object · 4 fields
key
protocol_reconstruction
status
pending
reason
null
evidence
null
[4] object · 4 fields
key
control_execution
status
pending
reason
null
evidence
null
[5] object · 4 fields
key
control_comparison
status
pending
reason
null
evidence
null
[6] object · 4 fields
key
publication
status
pending
reason
null
evidence
null
gaps array · 3 items
[0]
review.human_critique
[1]
review.machine_critique.blocked
[2]
review.machine_critique.providers
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 · 1 item
[0] object · 3 fields
id
package:458bec1febd775aa9029c32b7683d3fa8083ad4b4e27e075955d488df48dc8a9
type
sep_package
label
SEP v1 package for pmid:41373777
activities array · 1 item
[0] object · 4 fields
id
activity:conversion:pmid:41373777
type
conversion
used array · 1 item
[0]
package:458bec1febd775aa9029c32b7683d3fa8083ad4b4e27e075955d488df48dc8a9
agent
agent:corpus-assay-engine
agents array · 1 item
[0] object · 3 fields
id
agent:corpus-assay-engine
type
software
label
Corpus assay engine
source_run_id
run-20261023T122449232913
dsl_catalogue_fingerprint
343fb30756ba6ec3
capability_table_fingerprint
2cb3e42f047d2ecf
snapshot_id
ba34b49490d9bfaf
lineage object · 4 fields
parent_id
pmid:41373777
parent_hash
sha256:bb9838b86083a35765f587c693e4c9a20bd48a08bcd097130d4f29ac74d10a23
fork_of
null
gaps array · 14 items
[0]
abstract
[1]
asset:source:pmid:41373777 not verified
[2]
authors
[3]
capability
[4]
corpus_record_absent
[5]
execution.not_run
[6]
method
[7]
review.human_critique
[8]
review.machine_critique.blocked
[9]
review.machine_critique.providers
[10]
step:obtain_source_data blocked on data:not_downloaded
[11]
step:run_analysis blocked on no owned computational capability is bound to this experiment
[12]
step:run_analysis input 'materials:the source data behind the published result in pmid:41373777' does not resolve to a declared asset
[13]
targets
Complete file
{"sci_version": "1.0", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:41373777", "kind": "science-record", "revision": 2, "content_hash": "sha256:2f3961d750fb0861754d6427194d91e7d6dc3d15e8663f068ae01a62d40ca0b7", "created_at": "2026-11-01T10:25:54Z", "updated_at": "2026-11-01T14:01:52Z", "generator": {"name": "corpus-assay-engine", "converter": "sep_to_sci_v1", "source_package_schema": "urn:bntrg:sep:1.0.0"}, "paper": {"state": "partial", "title": "Identification of Colorectal Cancer-Related RNA Markers from Whole Blood Using Integrated Bioinformatics Analysis.", "doi": "10.3390/ijms262311625", "pmid": "41373777", "authors": null, "journal": "International journal of molecular sciences", "year": 2025, "abstract": null, "claims": [{"id": "claim-1", "statement": "the headline numerical result the paper states for its main finding", "kind": "qualitative", "state": "blocked", "target": {"value": null, "unit": null, "tolerance": null, "source": null}, "evidence": []}], "gaps": ["abstract", "authors"]}, "experiment": {"state": "partial", "objective": "the headline numerical result the paper states for its main finding", "steps": [{"id": "read_published_estimate", "order": 1, "name": "Read the published estimate and its interval from the source", "kind": "other", "state": "complete", "blocked_on": null, "description": "The number a replication must land on, and the sentence it came from.", "duration_hours": null, "parameters": {}, "inputs": ["source:pmid:41373777"], "outputs": ["the published estimate, its unit and its interval"], "instruments": [], "reagents": []}, {"id": "obtain_source_data", "order": 2, "name": "Obtain the source data behind the published result", "kind": "data-preparation", "state": "blocked", "blocked_on": "data:not_downloaded", "description": "The published result cannot be recomputed without the data the paper analysed.", "duration_hours": null, "parameters": {}, "inputs": [], "outputs": ["the source data with its provenance"], "instruments": [], "reagents": []}, {"id": "run_analysis", "order": 3, "name": "Run the analysis programme", "kind": "analysis", "state": "blocked", "blocked_on": "no owned computational capability is bound to this experiment", "description": "Re-run the paper's analysis on the source data and produce the registered result. | SEP input not carried into the asset list: materials:the source data behind the published result in pmid:41373777", "duration_hours": null, "parameters": {}, "inputs": [], "outputs": ["the registered result"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": ["step:obtain_source_data blocked on data:not_downloaded", "step:run_analysis blocked on no owned computational capability is bound to this experiment", "step:run_analysis input 'materials:the source data behind the published result in pmid:41373777' does not resolve to a declared asset"]}, "data": {"state": "partial", "assets": [{"id": "source:pmid:41373777", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.3390/ijms262311625", "sha256": "sha256:00766163598e77204e9d7ff697627f72f74934071c4a511c052ccd0979c47a2e", "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.3390/ijms262311625", "version": null, "note": "Source read by the package builder: full_text.", "structure": {"access_state": "full_text"}}, {"id": "asset:table:pmid:41373777:1", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:62606f1fd840a914d341e18e55abe8dfe0ba7e1b2e420116966eb26a2c07ec51", "bytes": 510, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[4]/table-wrap[1]#ijms-26-11625-t001", "version": null, "note": "Summary of DEGs Derived from Six Public Datasets Used to Construct the WB-PADs dataset.", "structure": {"pmcid": "PMC12692440", "section_index": 4, "section_title": "2.2. Construction of the WB-PADs Dataset", "row_count": 7, "column_count": 5}, "table": {"label": "Table 1", "caption": "Summary of DEGs Derived from Six Public Datasets Used to Construct the WB-PADs dataset.", "rows": [["No.", "Dataset", "Up-RegulatedGenes", "Down-RegulatedGenes", "Total"], ["1", "WB-Hub", "45", "87", "132"], ["2", "WB-TF", "24", "103", "127"], ["3", "WB-GWAS", "11", "42", "53"], ["4", "WB-eQTL", "43", "151", "194"], ["5", "WB-DigSeE", "21", "27", "48"], ["6", "WB-CoReCG", "33", "64", "97"]], "row_count": 7, "column_count": 5, "numeric_cells": 24, "header_rows": 1, "locator": "section[4]/table-wrap[1]#ijms-26-11625-t001"}}, {"id": "asset:table:pmid:41373777:2", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:505fd1ef115f42a4039d85b871b19317adb5f47e9a5c2dcd38ea5af2bd91abf7", "bytes": 442, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[5]/table-wrap[1]#ijms-26-11625-t002", "version": null, "note": "Demographic and clinical characteristics of participants in the WB-K RNA-seq cohort.", "structure": {"pmcid": "PMC12692440", "section_index": 5, "section_title": "2.3. Construction of the WB-K Dataset", "row_count": 5, "column_count": 3}, "table": {"label": "Table 2", "caption": "Demographic and clinical characteristics of participants in the WB-K RNA-seq cohort.", "rows": [["Characteristics", "Healthy Control, n (%)", "Colorectal Cancer, n (%)"], ["Age (SD)", "54.0 (7.6)", "46.8 (8.1)"], ["Gender (%)", "", ""], ["Male", "5 (50.0)", "5 (50.0)"], ["Female", "5 (50.0)", "5 (50.0)"]], "row_count": 5, "column_count": 3, "numeric_cells": 6, "header_rows": 1, "locator": "section[5]/table-wrap[1]#ijms-26-11625-t002"}}, {"id": "asset:table:pmid:41373777:3", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:567e3599ac30d3091cc019eac6e576f348ae491aa197e9513e78c83e3c79841a", "bytes": 587, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[6]/table-wrap[1]#ijms-26-11625-t003", "version": null, "note": "Five candidate genes showing consistent differential expression patterns in both WB-PADs and WB-K datasets.", "structure": {"pmcid": "PMC12692440", "section_index": 6, "section_title": "2.4. Selection of Candidate Genes for Clinical Validation", "row_count": 7, "column_count": 5}, "table": {"label": "Table 3", "caption": "Five candidate genes showing consistent differential expression patterns in both WB-PADs and WB-K datasets.", "rows": [["Gene Symbol", "log2FC", "p-Value"], ["WB Dataset", "WB-K Dataset", "WB Dataset", "WB-K Dataset"], ["DLG5", "−0.59", "−0.63", "0.0005", "0.007"], ["CD177", "1.09", "1.34", "0.00001", "0.03"], ["SH2D1B", "−0.58", "−0.86", "0.000001", "0.01"], ["NQO2", "0.57", "0.77", "0.000002", "0.01"], ["KRT73", "−0.76", "−1.00", "0.0001", "0.001"]], "row_count": 7, "column_count": 5, "numeric_cells": 22, "header_rows": 2, "locator": "section[6]/table-wrap[1]#ijms-26-11625-t003"}}, {"id": "asset:table:pmid:41373777:4", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:3686d1cbb2975826ed4b3ade62e2639bcf830165d3f02ab99cc96f29e8f0923c", "bytes": 426, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[15]/table-wrap[1]#ijms-26-11625-t004", "version": null, "note": "Clinicopathologic characteristics of study participants.", "structure": {"pmcid": "PMC12692440", "section_index": 15, "section_title": "4.5. Patient Cohorts", "row_count": 5, "column_count": 3}, "table": {"label": "Table 4", "caption": "Clinicopathologic characteristics of study participants.", "rows": [["Characteristics", "Healthy Control, n (%)", "Colorectal Cancer, n (%)"], ["Age, y (SD)", "63.2 (11.2)", "48.9 (9.8)"], ["Gender, n (%)", "", ""], ["Male", "60 (59.4)", "64 (57.7)"], ["Female", "41 (40.6)", "47 (42.3)"]], "row_count": 5, "column_count": 3, "numeric_cells": 6, "header_rows": 1, "locator": "section[15]/table-wrap[1]#ijms-26-11625-t004"}}], "gaps": ["asset:source:pmid:41373777 not verified"]}, "analysis": {"state": "absent", "methods": [], "targets": [], "gaps": ["method", "targets"]}, "capability": {"state": "absent", "requirements": [], "gaps": ["capability"]}, "readiness": {"state": "partial", "tier": null, "blocking_axis": null, "blocked_on": null, "axes": {}, "can_run": {"dsl_operations": [], "assets": ["source:pmid:41373777", "asset:table:pmid:41373777:1", "asset:table:pmid:41373777:2", "asset:table:pmid:41373777:3", "asset:table:pmid:41373777:4"], "steps": ["read_published_estimate"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": ["xml"], "capabilities": [], "data_gaps": ["source:pmid:41373777"]}, "gaps": ["corpus_record_absent"]}, "review": {"state": "partial", "machine_critique": {"status": "blocked", "providers": [], "target_providers": [], "agreement": false, "disagreements": [], "agreement_basis": {"policy": "decisive_fields", "decisive_fields": ["work_type", "number_stated", "parent_value", "unit"]}, "blinded": true}, "human_critique": {"status": "not_run", "reviewer": null, "signed_at": null, "conflict_checked": false, "commentary": null}, "stages": [{"key": "target_materials", "status": "pending", "reason": null, "evidence": null}, {"key": "independent_readings", "status": "blocked", "reason": "The independent readings are incomplete or disagree; the source evidence must resolve the difference.", "evidence": {"provider_errors": [{"provider": "minimax", "model": null, "reason": "HTTP Error 429: Too Many Requests", "raw_response": null}, {"provider": "minimax_alt", "model": null, "reason": "HTTP Error 429: Too Many Requests", "raw_response": null}, {"provider": "minimax", "model": null, "reason": "HTTP Error 429: Too Many Requests", "raw_response": null}, {"provider": "minimax_alt", "model": null, "reason": "HTTP Error 429: Too Many Requests", "raw_response": null}]}}, {"key": "source_resolution", "status": "pending", "reason": null, "evidence": null}, {"key": "protocol_reconstruction", "status": "pending", "reason": null, "evidence": null}, {"key": "control_execution", "status": "pending", "reason": null, "evidence": null}, {"key": "control_comparison", "status": "pending", "reason": null, "evidence": null}, {"key": "publication", "status": "pending", "reason": null, "evidence": null}], "gaps": ["review.human_critique", "review.machine_critique.blocked", "review.machine_critique.providers"]}, "execution": {"state": "absent", "status": "not_run", "mode": null, "runs": [], "gaps": ["execution.not_run"]}, "provenance": {"entities": [{"id": "package:458bec1febd775aa9029c32b7683d3fa8083ad4b4e27e075955d488df48dc8a9", "type": "sep_package", "label": "SEP v1 package for pmid:41373777"}], "activities": [{"id": "activity:conversion:pmid:41373777", "type": "conversion", "used": ["package:458bec1febd775aa9029c32b7683d3fa8083ad4b4e27e075955d488df48dc8a9"], "agent": "agent:corpus-assay-engine"}], "agents": [{"id": "agent:corpus-assay-engine", "type": "software", "label": "Corpus assay engine"}], "source_run_id": "run-20261023T122449232913", "dsl_catalogue_fingerprint": "343fb30756ba6ec3", "capability_table_fingerprint": "2cb3e42f047d2ecf", "snapshot_id": "ba34b49490d9bfaf"}, "lineage": {"parent_id": "pmid:41373777", "parent_hash": "sha256:bb9838b86083a35765f587c693e4c9a20bd48a08bcd097130d4f29ac74d10a23", "fork_of": null, "generation": 2}, "gaps": ["abstract", "asset:source:pmid:41373777 not verified", "authors", "capability", "corpus_record_absent", "execution.not_run", "method", "review.human_critique", "review.machine_critique.blocked", "review.machine_critique.providers", "step:obtain_source_data blocked on data:not_downloaded", "step:run_analysis blocked on no owned computational capability is bound to this experiment", "step:run_analysis input 'materials:the source data behind the published result in pmid:41373777' does not resolve to a declared asset", "targets"]}