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pmid:40789725

Clinical outcomes and interventions related to sedentary behaviours in childhood, adolescent, and young adult cancer patients and survivors: a scoping review protocol.

BMJ open · 2025 doi:10.1136/bmjopen-2025-100965

Paper

partial

Experiment

partial

Data

partial

Analysis

absent

Execution

absent

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Record details sci_version · id · kind · revision · content_hash · schema · created_at · updated_at · generator
id
pmid:40789725
kind
science-record
content_hash
sha256:b10fa7b81bb17c93f5a830a8ac62f4935642b453abd399718990611f68b7c887
schema
https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json
created_at
2026-11-01T10:25:52Z
updated_at
2026-11-01T14:01:45Z
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
Clinical outcomes and interventions related to sedentary behaviours in childhood, adolescent, and young adult cancer patients and survivors: a scoping review protocol.
doi
10.1136/bmjopen-2025-100965
pmid
40789725
authors
null
journal
BMJ open
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:40789725
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:40789725
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:40789725' does not resolve to a declared asset
data object · 3 fields
state
partial
assets array · 4 items
[0] object · 15 fields
id
source:pmid:40789725
role
manuscript
format
xml
media_type
application/xml
uri
https://doi.org/10.1136/bmjopen-2025-100965
sha256
sha256:07ab07519681501b6f8f58cf469ea0b2b90cd81c74bac134a86d67bff2df42c3
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null
access
open
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resolved
reader
null
reader_status
reader_required
identifier
10.1136/bmjopen-2025-100965
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:40789725:1
role
table
format
jats-table
media_type
application/vnd.jats.table+json
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null
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sha256:65d73c14193ffc8363e35e657db7036e4a1cd2cd4d564d39a210cfd638395465
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access
open
state
verified
reader
read_table
reader_status
available
identifier
section[5]/table-wrap[1]#T1
version
null
note
Search strategy for PubMed
structure object · 5 fields
pmcid
PMC12352156
section_index
5
section_title
Search strategy
row_count
4
column_count
2
table object · 8 fields
label
Table 1
caption
Search strategy for PubMed
rows array · 4 items
[0] array · 2 items
[0]
Domain/concept
[1]
Search terms
[1] array · 2 items
[0]
Paediatrics
[1]
“Child”[MeSH] OR “Adolescent”[MeSH] OR “Young Adult” [MeSH] OR “Minors” [MeSH] OR “Pediatrics” [MeSH] OR “Hospitals, Pediatric”[MeSH] OR “paediatric*” OR “toddler*” OR “preschool*” OR “pre school*” OR “child*” OR “kid” OR “kids” OR “juvenile*” OR “minor*” OR “youth*” OR “youngster*” OR “girl*” OR “boys” OR “boys” OR “elementary school*” OR “grade school*” OR “preadolescen*“ OR “pre adolescen*” OR “preteen*” OR “pre teen*” OR “middle school*” OR “adolescen*” OR “teen*” OR “high school*” OR “pediatric*” OR “young adult*”
[2] array · 2 items
[0]
Cancer patients and survivors
[1]
“Neoplasms” [MeSH] OR “Cancer Survivors” [MeSH] OR (“Neoplasms” [MeSH] AND “Survivors” [MeSH]) OR “oncolog*” OR “neoplas*”OR “tumor*” OR “tumour*” OR “cancer*” OR “malignan*” OR “metasta*” OR “carcinogenesis” OR “carcinoma*” OR “sarcoma*” OR “leukemia*” OR “leukaemia*” OR “lymphoma*” OR “Hodgkin* disease” OR “glioma*” OR “astrocytoma*” OR “craniopharyngioma*” OR “ependymoma*” OR “medulloblastoma*” OR “retinoblastoma*” OR “neuroblastoma*” OR “Langerhans cell histiocytosis” OR “hepatoblastoma” OR “cholangiocarcinoma” OR “nephroblastoma” OR “rhabdomyosarcoma*” OR “osteosarcoma*” OR “fibrosarcoma*” OR “melanoma*” OR “angiosarcoma*” OR “antineoplastic*” OR “anti-neoplastic*” OR “anti neoplastic*” OR “cancer survivor*”
[3] array · 2 items
[0]
Sedentary behaviour
[1]
“Sedentary Behavior” [MeSH] OR “Sitting Position” [MeSH] OR “sedentary” OR “sedentary behaviour*” OR “sedentary behavior*” OR “sedentary lifestyle*” OR “sedentarism” OR “sedentary time” OR “sitting” OR “inactiv* lifestyle*” OR “inactiv* behavi*” OR “lack of physical activit*” OR “physical inactive*” OR “television” OR “television viewing” OR “television time” OR “television watching” OR “TV viewing” OR “TV time” OR “TV viewing” OR “screen time” OR “computer use” OR “computer time” OR “video gam*”
locator
section[5]/table-wrap[1]#T1
[2] object · 16 fields
id
asset:table:pmid:40789725:2
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table
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jats-table
media_type
application/vnd.jats.table+json
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null
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sha256:617cb35bdaa4f29c8e7cc71362d901e4b6a39aee9435af18692c77fdd775aa74
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open
state
verified
reader
read_table
reader_status
available
identifier
section[8]/table-wrap[1]#T2
version
null
note
Data charting table for observational studies
structure object · 5 fields
pmcid
PMC12352156
section_index
8
section_title
Data extraction and charting
row_count
29
column_count
3
table object · 8 fields
label
Table 2
caption
Data charting table for observational studies
rows array · 29 items
[0] array · 3 items
[0]
Data category
[1]
Data item
[2]
Description
[1] array · 1 item
[0]
Study characteristics
[2] array · 3 items
[0]
[1]
Author(s)
[2]
[3] array · 3 items
[0]
[1]
Year of publication
[2]
[4] array · 3 items
[0]
[1]
Country of study
[2]
[5] array · 3 items
[0]
[1]
Study design
[2]
Specify if study is cross-sectional, case-control, cohortor other study type.
[6] array · 3 items
[0]
[1]
Study duration
[2]
[7] array · 3 items
[0]
Study objective(s)
[1]
[2]
Describe the stated objective/aims of the study.
[8] array · 1 item
[0]
Sample characteristics
[9] array · 3 items
[0]
[1]
Sample size
[2]
List N for total number of participants, and if applicable, N for number of participants in each study group.
[10] array · 3 items
[0]
[1]
Age at study enrolment
[2]
Specify mean age and range for the study sample if age is continuous variable or N, % for each age category if listed as categorical variable.
[11] array · 3 items
[0]
[1]
Sex
[2]
Report N, % for each sex listed.
[12] array · 3 items
[0]
[1]
Race
[2]
Report N, % for each race category listed.
[13] array · 3 items
[0]
[1]
Ethnicity
[2]
Report N, % for each ethnicity category listed.
[14] array · 3 items
[0]
[1]
Other socioeconomic characteristics
[2]
Specify any other reported sociodemographic characteristics, including income, parental education, insurance type, etc. List N, % for each reported category.
[15] array · 3 items
[0]
[1]
Age at cancer diagnosis
[2]
Specify mean age and range for the study sample if age is continuous variable or N, % for each age category if listed as categorical variable.
[16] array · 3 items
[0]
[1]
Cancer diagnoses
[2]
List each cancer type reported and specify N,% for each.
[17] array · 3 items
[0]
[1]
Treatment status
[2]
Specify if participants were on or off treatment at the time of study completion. If mixed population, report N, % for both those on and off treatment.
[18] array · 1 item
[0]
Sedentary behaviour (SB) reporting
[19] array · 3 items
[0]
[1]
Type of SB
[2]
Specify which type of SB is being measured/reported with units, such as total sedentary time, screen time, sedentary breaks, etc.
[20] array · 3 items
[0]
[1]
Measurement method
[2]
Specify if SB is measured via self-report, device measurement or both. If both, report which type of SB is measured by which method.
[21] array · 3 items
[0]
[1]
Summary SB data
[2]
Report main SB data in mean and range if continuous and/or N, % if categorical.
[22] array · 1 item
[0]
Main study outcomes
[23] array · 3 items
[0]
[1]
Cardiometabolic outcomes
[2]
Specify any cardiometabolic outcomes reported with applicable units and measurement type, such as cardiorespiratory fitness, weight, body mass index, resting heart rate, glucose metabolism/insulin sensitivity, cholesterol levels, etc.
[24] array · 3 items
[0]
[1]
Patient-reported outcomes (PROs)
[2]
Specify any PROs reported with measurement type, such as quality of life, fatigue, treatment-related symptoms, mood, etc.
[25] array · 3 items
[0]
[1]
Morbidity and survival-related outcomes
[2]
Specify any morbidity or mortality-related outcomes reported with measurement type, such as number of chronic diseases, incidence of secondary malignancy, incidence of cardiac disease, all-cause mortality, cancer-related mortality, etc.
[26] array · 3 items
[0]
[1]
Other outcomes
[2]
Describe any other study outcomes reported that are not included in the above categories. Specify measurement type and units, if applicable.
[27] array · 3 items
[0]
Covariates
[1]
[2]
Specify covariates included in study analysis.
[28] array · 3 items
[0]
Study limitations
[1]
[2]
List any limitations noted in the study discussion as well as those determined by reviewer including sample size, sample demographics, study type, confounding, potential biases, etc.
locator
section[8]/table-wrap[1]#T2
[3] object · 16 fields
id
asset:table:pmid:40789725:3
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table
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jats-table
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application/vnd.jats.table+json
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null
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sha256:7963c75141e191a6f8978b1aa4c4f0cfdab3ed75885210db7d598d8ddc9ba969
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verified
reader
read_table
reader_status
available
identifier
section[8]/table-wrap[2]#T3
version
null
note
Data charting table for interventional studies
structure object · 5 fields
pmcid
PMC12352156
section_index
8
section_title
Data extraction and charting
row_count
28
column_count
3
table object · 8 fields
label
Table 3
caption
Data charting table for interventional studies
rows array · 28 items
[0] array · 3 items
[0]
Data category
[1]
Data item
[2]
Description
[1] array · 1 item
[0]
Study characteristics
[2] array · 3 items
[0]
[1]
Author(s)
[2]
[3] array · 3 items
[0]
[1]
Year of publication
[2]
[4] array · 3 items
[0]
[1]
Country of study
[2]
[5] array · 3 items
[0]
[1]
Study design
[2]
Specify if study is a randomised controlled trial (RCT), cluster RCT, non-randomised trial, etc.
[6] array · 3 items
[0]
[1]
Study duration
[2]
[7] array · 3 items
[0]
Study objectives
[1]
[2]
Describe the stated objective/aims of the study.
[8] array · 1 item
[0]
Sample characteristics
[9] array · 3 items
[0]
[1]
Sample size
[2]
List N for total number of participants, and if applicable N for number of participants in each study group.
[10] array · 3 items
[0]
[1]
Age at study enrolment
[2]
Specify mean age and range for the study sample if age is continuous variable or N, % for each age category if listed as categorical variable.
[11] array · 3 items
[0]
[1]
Sex
[2]
Report N, % for each sex listed.
[12] array · 3 items
[0]
[1]
Race
[2]
Report N, % for each race category listed.
[13] array · 3 items
[0]
[1]
Ethnicity
[2]
Report N, % for each ethnicity category listed.
[14] array · 3 items
[0]
[1]
Other socioeconomic characteristics
[2]
Specify any other reported sociodemographic characteristics, including income, parental education, insurance type, etc. List N, % for each reported category.
[15] array · 3 items
[0]
[1]
Age at cancer diagnosis
[2]
Specify mean age and range for the study sample if age is continuous variable or N, % for each age category if listed as categorical variable.
[16] array · 3 items
[0]
[1]
Cancer diagnoses
[2]
List each cancer type reported and specify N, % for each.
[17] array · 3 items
[0]
[1]
Treatment status
[2]
Specify if participants were on or off treatment at the time of study completion. If mixed population, report N, % for both those on and off treatment.
[18] array · 1 item
[0]
Intervention characteristics
[19] array · 3 items
[0]
[1]
Intervention type
[2]
Specify how many intervention arms are included and the intervention components for each arm.
[20] array · 3 items
[0]
[1]
Intervention duration
[2]
[21] array · 3 items
[0]
[1]
Intervention goals/aims
[2]
Specific aims of the intervention, such as reducing total sedentary time, increase sedentary breaks, etc.
[22] array · 1 item
[0]
Sedentary behaviour (SB) measurement
[23] array · 3 items
[0]
[1]
Type of SB
[2]
Specify which type of SB is being measured/reported with units, such as total sedentary time, screen time, sedentary breaks, etc.
[24] array · 3 items
[0]
[1]
Measurement method
[2]
Specify if SB is measured via self-report, device measurement or both. If both, report which type of SB is measured by which method.
[25] array · 3 items
[0]
Results
[1]
[2]
Describe any within and/or between group-differences in SB reported as well as any other associated outcomes (physical activity, patient-reported outcomes, biomarkers, etc.).
[26] array · 3 items
[0]
Covariates
[1]
[2]
Describe covariates included in study analysis.
[27] array · 3 items
[0]
Study limitations
[1]
[2]
List any limitations noted in the study discussion as well as those determined by reviewer including sample size, sample demographics, randomisation, confounding, potential biases, etc.
locator
section[8]/table-wrap[2]#T3
gaps array · 1 item
[0]
asset:source:pmid:40789725 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 · 4 items
[0]
source:pmid:40789725
[1]
asset:table:pmid:40789725:1
[2]
asset:table:pmid:40789725:2
[3]
asset:table:pmid:40789725:3
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:40789725
gaps array · 1 item
[0]
corpus_record_absent
review object · 5 fields
state
partial
machine_critique object · 7 fields
status
passed
providers array · 2 items
[0] object · 7 fields
provider
minimax
model
MiniMax-M3.1-Flash
prompt_version
full-text-reading-v1
prompt_hash
feb83a8cae33fa654fb22db5bad3d7d786687da7b22cbf57f1d5a67ce354c904
source_hash
07ab07519681501b6f8f58cf469ea0b2b90cd81c74bac134a86d67bff2df42c3
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sha256:e9036ac98ac1ef128a1bb08429387632eacf31132cc0d9fb06b2464e3bbfe4a8
raw_response_chars
2447
[1] object · 7 fields
provider
minimax_alt
model
MiniMax-M3
prompt_version
full-text-reading-v1
prompt_hash
742470c22470425b5c6f03c51bae9b17a1182aecb1db93e80ac4ea074ecbf434
source_hash
07ab07519681501b6f8f58cf469ea0b2b90cd81c74bac134a86d67bff2df42c3
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sha256:3c16d236513b66720e418593bd5761a79495588124808b9c91044527e5625496
raw_response_chars
32870
target_providers array · 2 items
[0] object · 8 fields
provider
minimax
model
MiniMax-M3.1-Flash
prompt_version
replication-target-v2
prompt_hash
88fd145ea624060d1a2f6674a37ee792d56937d1f259690f87aa55a0e4dc0419
source_hash
07ab07519681501b6f8f58cf469ea0b2b90cd81c74bac134a86d67bff2df42c3
raw_response
{"parent_value":0,"unit":"","evidence":"","target_result":"The source text is a scoping review protocol and states that results are currently being summarised; it reports no numerical result for the registered target.","number_stated":false}
reading object · 6 fields
parent_value
0
unit
evidence
target_result
The source text is a scoping review protocol and states that results are currently being summarised; it reports no numerical result for the registered target.
number_stated
false
source_locator
null
recorded_at
2026-10-31T15:28:20.125400+00:00
[1] object · 8 fields
provider
minimax_alt
model
MiniMax-M3
prompt_version
replication-target-v2
prompt_hash
53c5022dc1f04e6ff4f1a7ce002ef2c8362c01efa4f32f9b9ad4c2d96c86299e
source_hash
07ab07519681501b6f8f58cf469ea0b2b90cd81c74bac134a86d67bff2df42c3
raw_response
<think>We need answer JSON only. Need parse request. Need identify single numerical result replication of registered target has to reproduce; headline numerical result paper states for main finding. Source is protocol, no results, likely no number for registered target. Need set number_stated false, parent_value 0, unit/evidence empty, target_result say text does state instead. Need be careful schema, JSON valid. What does "say in target_result what the text does state instead." We need formulate concise perhaps "The text states that this is a scoping review protocol and that results are currently being summarised; it reports no headline numerical result." Evidence empty, unit empty, parent_value 0. Need perhaps mention registration URL? Since registered target maybe OSF link, but target asks headline numerical result. Source states no number. Could target_result be "The source describes a scoping review protocol and states that database searches, article screening, and data extraction have been completed and results are currently being summarised; it does not state a headline numerical result." Need ensure no evidence quote requirement only if number. They explicitly if no number set ... leave unit and evidence empty, and say in target_result what text does state instead. Good. But let's deeply consider ambiguity: There are numbers in text (five databases, ages, dates, 2025), but no result. Need not extract. "registered target" perhaps OSF registration and replication target? User likely benchmark designed to detect hallucination. Source protocol no numerical result. Return exact schema fields. JSON strings. parent_value number 0. number_stated false. Need ensure target_result perhaps source wording with no number? "The text states that the scoping review's database searches, article screening, and data extraction have been completed and that results are currently being summarised; no headline numerical result is stated." This paraphrases target_result permitted. Evidence empty string. unit empty string. Could quote exact source in target_result? They ask "say in target_result what the text does state instead." Could state protocol status. Maybe exact quote useful, but evidence must empty according instruction. We can say "The paper states: 'As of July 2025, database searches, article screening, and data extraction have been completed, and results are currently being summarised.' It does not state a headline numerical result." Does including July 2025 in target_result create issue? likely okay, but requested headline number only and no result. Better target_result: "The source describes a scoping review protocol and states that results are currently being summarised; it does not state a headline numerical result." This says what text states instead but paraphrase. They said "say ... what the text does state instead," no exact quote requirement in no-number branch except evidence empty. Could include quote, but target_result should perhaps mention protocol/aim. Need not overdo. Let's ensure output only JSON no markdown.</think> {"parent_value":0,"unit":"","evidence":"","target_result":"The source describes a scoping review protocol and states that results are currently being summarised; it does not state a headline numerical result.","number_stated":false}
reading object · 6 fields
parent_value
0
unit
evidence
target_result
The source describes a scoping review protocol and states that results are currently being summarised; it does not state a headline numerical result.
number_stated
false
source_locator
null
recorded_at
2026-10-31T15:28:22.094528+00:00
agreement
true
disagreements object · 2 fields
target_result object · 3 fields
minimax
No headline numerical result is reported; the paper is a scoping review protocol whose results were still being summarised.
minimax_alt
No headline numerical result is reported in the supplied text; this is a scoping review protocol whose results were still being summarised.
decisive
false
analysis_methods object · 3 fields
minimax array · 3 items
[0]
Arksey and O’Malley scoping review methodology framework
[1]
descriptive and quantitative summary of each study’s key characteristics and results
[2]
study-specific quality assessment using established tools
minimax_alt array · 3 items
[0]
Arksey and O’Malley five-stage scoping review methodology framework
[1]
Descriptive and quantitative summary of each study’s key characteristics and results
[2]
Study-specific quality assessment using established tools
decisive
false
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
passed
reason
The independent readings are incomplete or disagree; the source evidence must resolve the difference.
evidence object · 1 field
provider_errors array · 0 items
[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 · 2 items
[0]
review.human_critique
[1]
review.machine_critique.passed
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:69d7910580da9e3beb1ebb020f2d5d28808134662ec3f0ee32d2f9d3d4be4503
type
sep_package
label
SEP v1 package for pmid:40789725
activities array · 1 item
[0] object · 4 fields
id
activity:conversion:pmid:40789725
type
conversion
used array · 1 item
[0]
package:69d7910580da9e3beb1ebb020f2d5d28808134662ec3f0ee32d2f9d3d4be4503
agent
agent:corpus-assay-engine
agents array · 3 items
[0] object · 3 fields
id
agent:minimax
type
model
label
minimax
[1] object · 3 fields
id
agent:minimax_alt
type
model
label
minimax_alt
[2] 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:40789725
parent_hash
sha256:0a7c00ed6837fd54b5d9554c49bec195add35ebf2d468bc0e1f6d52b28f5ab6e
fork_of
null
gaps array · 13 items
[0]
abstract
[1]
asset:source:pmid:40789725 not verified
[2]
authors
[3]
capability
[4]
corpus_record_absent
[5]
execution.not_run
[6]
method
[7]
review.human_critique
[8]
review.machine_critique.passed
[9]
step:obtain_source_data blocked on data:not_downloaded
[10]
step:run_analysis blocked on no owned computational capability is bound to this experiment
[11]
step:run_analysis input 'materials:the source data behind the published result in pmid:40789725' does not resolve to a declared asset
[12]
targets
Complete file
{"sci_version": "1.0", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:40789725", "kind": "science-record", "revision": 2, "content_hash": "sha256:b10fa7b81bb17c93f5a830a8ac62f4935642b453abd399718990611f68b7c887", "created_at": "2026-11-01T10:25:52Z", "updated_at": "2026-11-01T14:01:45Z", "generator": {"name": "corpus-assay-engine", "converter": "sep_to_sci_v1", "source_package_schema": "urn:bntrg:sep:1.0.0"}, "paper": {"state": "partial", "title": "Clinical outcomes and interventions related to sedentary behaviours in childhood, adolescent, and young adult cancer patients and survivors: a scoping review protocol.", "doi": "10.1136/bmjopen-2025-100965", "pmid": "40789725", "authors": null, "journal": "BMJ open", "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:40789725"], "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:40789725", "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:40789725' does not resolve to a declared asset"]}, "data": {"state": "partial", "assets": [{"id": "source:pmid:40789725", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.1136/bmjopen-2025-100965", "sha256": "sha256:07ab07519681501b6f8f58cf469ea0b2b90cd81c74bac134a86d67bff2df42c3", "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.1136/bmjopen-2025-100965", "version": null, "note": "Source read by the package builder: full_text.", "structure": {"access_state": "full_text"}}, {"id": "asset:table:pmid:40789725:1", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:65d73c14193ffc8363e35e657db7036e4a1cd2cd4d564d39a210cfd638395465", "bytes": 2412, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[5]/table-wrap[1]#T1", "version": null, "note": "Search strategy for PubMed", "structure": {"pmcid": "PMC12352156", "section_index": 5, "section_title": "Search strategy", "row_count": 4, "column_count": 2}, "table": {"label": "Table 1", "caption": "Search strategy for PubMed", "rows": [["Domain/concept", "Search terms"], ["Paediatrics", "“Child”[MeSH] OR “Adolescent”[MeSH] OR “Young Adult” [MeSH] OR “Minors” [MeSH] OR “Pediatrics” [MeSH] OR “Hospitals, Pediatric”[MeSH] OR “paediatric*” OR “toddler*” OR “preschool*” OR “pre school*” OR “child*” OR “kid” OR “kids” OR “juvenile*” OR “minor*” OR “youth*” OR “youngster*” OR “girl*” OR “boys” OR “boys” OR “elementary school*” OR “grade school*” OR “preadolescen*“ OR “pre adolescen*” OR “preteen*” OR “pre teen*” OR “middle school*” OR “adolescen*” OR “teen*” OR “high school*” OR “pediatric*” OR “young adult*”"], ["Cancer patients and survivors", "“Neoplasms” [MeSH] OR “Cancer Survivors” [MeSH] OR (“Neoplasms” [MeSH] AND “Survivors” [MeSH]) OR “oncolog*” OR “neoplas*”OR “tumor*” OR “tumour*” OR “cancer*” OR “malignan*” OR “metasta*” OR “carcinogenesis” OR “carcinoma*” OR “sarcoma*” OR “leukemia*” OR “leukaemia*” OR “lymphoma*” OR “Hodgkin* disease” OR “glioma*” OR “astrocytoma*” OR “craniopharyngioma*” OR “ependymoma*” OR “medulloblastoma*” OR “retinoblastoma*” OR “neuroblastoma*” OR “Langerhans cell histiocytosis” OR “hepatoblastoma” OR “cholangiocarcinoma” OR “nephroblastoma” OR “rhabdomyosarcoma*” OR “osteosarcoma*” OR “fibrosarcoma*” OR “melanoma*” OR “angiosarcoma*” OR “antineoplastic*” OR “anti-neoplastic*” OR “anti neoplastic*” OR “cancer survivor*”"], ["Sedentary behaviour", "“Sedentary Behavior” [MeSH] OR “Sitting Position” [MeSH] OR “sedentary” OR “sedentary behaviour*” OR “sedentary behavior*” OR “sedentary lifestyle*” OR “sedentarism” OR “sedentary time” OR “sitting” OR “inactiv* lifestyle*” OR “inactiv* behavi*” OR “lack of physical activit*” OR “physical inactive*” OR “television” OR “television viewing” OR “television time” OR “television watching” OR “TV viewing” OR “TV time” OR “TV viewing” OR “screen time” OR “computer use” OR “computer time” OR “video gam*”"]], "row_count": 4, "column_count": 2, "numeric_cells": 0, "header_rows": 1, "locator": "section[5]/table-wrap[1]#T1"}}, {"id": "asset:table:pmid:40789725:2", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:617cb35bdaa4f29c8e7cc71362d901e4b6a39aee9435af18692c77fdd775aa74", "bytes": 3324, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[8]/table-wrap[1]#T2", "version": null, "note": "Data charting table for observational studies", "structure": {"pmcid": "PMC12352156", "section_index": 8, "section_title": "Data extraction and charting", "row_count": 29, "column_count": 3}, "table": {"label": "Table 2", "caption": "Data charting table for observational studies", "rows": [["Data category", "Data item", "Description"], ["Study characteristics"], ["", "Author(s)", ""], ["", "Year of publication", ""], ["", "Country of study", ""], ["", "Study design", "Specify if study is cross-sectional, case-control, cohortor other study type."], ["", "Study duration", ""], ["Study objective(s)", "", "Describe the stated objective/aims of the study."], ["Sample characteristics"], ["", "Sample size", "List N for total number of participants, and if applicable, N for number of participants in each study group."], ["", "Age at study enrolment", "Specify mean age and range for the study sample if age is continuous variable or N, % for each age category if listed as categorical variable."], ["", "Sex", "Report N, % for each sex listed."], ["", "Race", "Report N, % for each race category listed."], ["", "Ethnicity", "Report N, % for each ethnicity category listed."], ["", "Other socioeconomic characteristics", "Specify any other reported sociodemographic characteristics, including income, parental education, insurance type, etc. List N, % for each reported category."], ["", "Age at cancer diagnosis", "Specify mean age and range for the study sample if age is continuous variable or N, % for each age category if listed as categorical variable."], ["", "Cancer diagnoses", "List each cancer type reported and specify N,% for each."], ["", "Treatment status", "Specify if participants were on or off treatment at the time of study completion. If mixed population, report N, % for both those on and off treatment."], ["Sedentary behaviour (SB) reporting"], ["", "Type of SB", "Specify which type of SB is being measured/reported with units, such as total sedentary time, screen time, sedentary breaks, etc."], ["", "Measurement method", "Specify if SB is measured via self-report, device measurement or both. If both, report which type of SB is measured by which method."], ["", "Summary SB data", "Report main SB data in mean and range if continuous and/or N, % if categorical."], ["Main study outcomes"], ["", "Cardiometabolic outcomes", "Specify any cardiometabolic outcomes reported with applicable units and measurement type, such as cardiorespiratory fitness, weight, body mass index, resting heart rate, glucose metabolism/insulin sensitivity, cholesterol levels, etc."], ["", "Patient-reported outcomes (PROs)", "Specify any PROs reported with measurement type, such as quality of life, fatigue, treatment-related symptoms, mood, etc."], ["", "Morbidity and survival-related outcomes", "Specify any morbidity or mortality-related outcomes reported with measurement type, such as number of chronic diseases, incidence of secondary malignancy, incidence of cardiac disease, all-cause mortality, cancer-related mortality, etc."], ["", "Other outcomes", "Describe any other study outcomes reported that are not included in the above categories. Specify measurement type and units, if applicable."], ["Covariates", "", "Specify covariates included in study analysis."], ["Study limitations", "", "List any limitations noted in the study discussion as well as those determined by reviewer including sample size, sample demographics, study type, confounding, potential biases, etc."]], "row_count": 29, "column_count": 3, "numeric_cells": 0, "header_rows": 1, "locator": "section[8]/table-wrap[1]#T2"}}, {"id": "asset:table:pmid:40789725:3", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:7963c75141e191a6f8978b1aa4c4f0cfdab3ed75885210db7d598d8ddc9ba969", "bytes": 2852, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[8]/table-wrap[2]#T3", "version": null, "note": "Data charting table for interventional studies", "structure": {"pmcid": "PMC12352156", "section_index": 8, "section_title": "Data extraction and charting", "row_count": 28, "column_count": 3}, "table": {"label": "Table 3", "caption": "Data charting table for interventional studies", "rows": [["Data category", "Data item", "Description"], ["Study characteristics"], ["", "Author(s)", ""], ["", "Year of publication", ""], ["", "Country of study", ""], ["", "Study design", "Specify if study is a randomised controlled trial (RCT), cluster RCT, non-randomised trial, etc."], ["", "Study duration", ""], ["Study objectives", "", "Describe the stated objective/aims of the study."], ["Sample characteristics"], ["", "Sample size", "List N for total number of participants, and if applicable N for number of participants in each study group."], ["", "Age at study enrolment", "Specify mean age and range for the study sample if age is continuous variable or N, % for each age category if listed as categorical variable."], ["", "Sex", "Report N, % for each sex listed."], ["", "Race", "Report N, % for each race category listed."], ["", "Ethnicity", "Report N, % for each ethnicity category listed."], ["", "Other socioeconomic characteristics", "Specify any other reported sociodemographic characteristics, including income, parental education, insurance type, etc. List N, % for each reported category."], ["", "Age at cancer diagnosis", "Specify mean age and range for the study sample if age is continuous variable or N, % for each age category if listed as categorical variable."], ["", "Cancer diagnoses", "List each cancer type reported and specify N, % for each."], ["", "Treatment status", "Specify if participants were on or off treatment at the time of study completion. If mixed population, report N, % for both those on and off treatment."], ["Intervention characteristics"], ["", "Intervention type", "Specify how many intervention arms are included and the intervention components for each arm."], ["", "Intervention duration", ""], ["", "Intervention goals/aims", "Specific aims of the intervention, such as reducing total sedentary time, increase sedentary breaks, etc."], ["Sedentary behaviour (SB) measurement"], ["", "Type of SB", "Specify which type of SB is being measured/reported with units, such as total sedentary time, screen time, sedentary breaks, etc."], ["", "Measurement method", "Specify if SB is measured via self-report, device measurement or both. If both, report which type of SB is measured by which method."], ["Results", "", "Describe any within and/or between group-differences in SB reported as well as any other associated outcomes (physical activity, patient-reported outcomes, biomarkers, etc.)."], ["Covariates", "", "Describe covariates included in study analysis."], ["Study limitations", "", "List any limitations noted in the study discussion as well as those determined by reviewer including sample size, sample demographics, randomisation, confounding, potential biases, etc."]], "row_count": 28, "column_count": 3, "numeric_cells": 0, "header_rows": 1, "locator": "section[8]/table-wrap[2]#T3"}}], "gaps": ["asset:source:pmid:40789725 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:40789725", "asset:table:pmid:40789725:1", "asset:table:pmid:40789725:2", "asset:table:pmid:40789725:3"], "steps": ["read_published_estimate"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": ["xml"], "capabilities": [], "data_gaps": ["source:pmid:40789725"]}, "gaps": ["corpus_record_absent"]}, "review": {"state": "partial", "machine_critique": {"status": "passed", "providers": [{"provider": "minimax", "model": "MiniMax-M3.1-Flash", "prompt_version": "full-text-reading-v1", "prompt_hash": "feb83a8cae33fa654fb22db5bad3d7d786687da7b22cbf57f1d5a67ce354c904", "source_hash": "07ab07519681501b6f8f58cf469ea0b2b90cd81c74bac134a86d67bff2df42c3", "raw_response_sha256": "sha256:e9036ac98ac1ef128a1bb08429387632eacf31132cc0d9fb06b2464e3bbfe4a8", "raw_response_chars": 2447}, {"provider": "minimax_alt", "model": "MiniMax-M3", "prompt_version": "full-text-reading-v1", "prompt_hash": "742470c22470425b5c6f03c51bae9b17a1182aecb1db93e80ac4ea074ecbf434", "source_hash": "07ab07519681501b6f8f58cf469ea0b2b90cd81c74bac134a86d67bff2df42c3", "raw_response_sha256": "sha256:3c16d236513b66720e418593bd5761a79495588124808b9c91044527e5625496", "raw_response_chars": 32870}], "target_providers": [{"provider": "minimax", "model": "MiniMax-M3.1-Flash", "prompt_version": "replication-target-v2", "prompt_hash": "88fd145ea624060d1a2f6674a37ee792d56937d1f259690f87aa55a0e4dc0419", "source_hash": "07ab07519681501b6f8f58cf469ea0b2b90cd81c74bac134a86d67bff2df42c3", "raw_response": "{\"parent_value\":0,\"unit\":\"\",\"evidence\":\"\",\"target_result\":\"The source text is a scoping review protocol and states that results are currently being summarised; it reports no numerical result for the registered target.\",\"number_stated\":false}", "reading": {"parent_value": 0, "unit": "", "evidence": "", "target_result": "The source text is a scoping review protocol and states that results are currently being summarised; it reports no numerical result for the registered target.", "number_stated": false, "source_locator": null}, "recorded_at": "2026-10-31T15:28:20.125400+00:00"}, {"provider": "minimax_alt", "model": "MiniMax-M3", "prompt_version": "replication-target-v2", "prompt_hash": "53c5022dc1f04e6ff4f1a7ce002ef2c8362c01efa4f32f9b9ad4c2d96c86299e", "source_hash": "07ab07519681501b6f8f58cf469ea0b2b90cd81c74bac134a86d67bff2df42c3", "raw_response": "<think>We need answer JSON only. Need parse request. Need identify single numerical result replication of registered target has to reproduce; headline numerical result paper states for main finding. Source is protocol, no results, likely no number for registered target. Need set number_stated false, parent_value 0, unit/evidence empty, target_result say text does state instead. Need be careful schema, JSON valid. What does \"say in target_result what the text does state instead.\" We need formulate concise perhaps \"The text states that this is a scoping review protocol and that results are currently being summarised; it reports no headline numerical result.\" Evidence empty, unit empty, parent_value 0. Need perhaps mention registration URL? Since registered target maybe OSF link, but target asks headline numerical result. Source states no number. Could target_result be \"The source describes a scoping review protocol and states that database searches, article screening, and data extraction have been completed and results are currently being summarised; it does not state a headline numerical result.\" Need ensure no evidence quote requirement only if number. They explicitly if no number set ... leave unit and evidence empty, and say in target_result what text does state instead. Good.\n\nBut let's deeply consider ambiguity: There are numbers in text (five databases, ages, dates, 2025), but no result. Need not extract. \"registered target\" perhaps OSF registration and replication target? User likely benchmark designed to detect hallucination. Source protocol no numerical result. Return exact schema fields. JSON strings. parent_value number 0. number_stated false.\n\nNeed ensure target_result perhaps source wording with no number? \"The text states that the scoping review's database searches, article screening, and data extraction have been completed and that results are currently being summarised; no headline numerical result is stated.\" This paraphrases target_result permitted. Evidence empty string. unit empty string.\n\nCould quote exact source in target_result? They ask \"say in target_result what the text does state instead.\" Could state protocol status. Maybe exact quote useful, but evidence must empty according instruction. We can say \"The paper states: 'As of July 2025, database searches, article screening, and data extraction have been completed, and results are currently being summarised.' It does not state a headline numerical result.\" Does including July 2025 in target_result create issue? likely okay, but requested headline number only and no result. Better target_result: \"The source describes a scoping review protocol and states that results are currently being summarised; it does not state a headline numerical result.\" This says what text states instead but paraphrase. They said \"say ... what the text does state instead,\" no exact quote requirement in no-number branch except evidence empty. Could include quote, but target_result should perhaps mention protocol/aim. Need not overdo.\n\nLet's ensure output only JSON no markdown.</think>\n\n{\"parent_value\":0,\"unit\":\"\",\"evidence\":\"\",\"target_result\":\"The source describes a scoping review protocol and states that results are currently being summarised; it does not state a headline numerical result.\",\"number_stated\":false}", "reading": {"parent_value": 0, "unit": "", "evidence": "", "target_result": "The source describes a scoping review protocol and states that results are currently being summarised; it does not state a headline numerical result.", "number_stated": false, "source_locator": null}, "recorded_at": "2026-10-31T15:28:22.094528+00:00"}], "agreement": true, "disagreements": {"target_result": {"minimax": "No headline numerical result is reported; the paper is a scoping review protocol whose results were still being summarised.", "minimax_alt": "No headline numerical result is reported in the supplied text; this is a scoping review protocol whose results were still being summarised.", "decisive": false}, "analysis_methods": {"minimax": ["Arksey and O’Malley scoping review methodology framework", "descriptive and quantitative summary of each study’s key characteristics and results", "study-specific quality assessment using established tools"], "minimax_alt": ["Arksey and O’Malley five-stage scoping review methodology framework", "Descriptive and quantitative summary of each study’s key characteristics and results", "Study-specific quality assessment using established tools"], "decisive": false}}, "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": "passed", "reason": "The independent readings are incomplete or disagree; the source evidence must resolve the difference.", "evidence": {"provider_errors": []}}, {"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.passed"]}, "execution": {"state": "absent", "status": "not_run", "mode": null, "runs": [], "gaps": ["execution.not_run"]}, "provenance": {"entities": [{"id": "package:69d7910580da9e3beb1ebb020f2d5d28808134662ec3f0ee32d2f9d3d4be4503", "type": "sep_package", "label": "SEP v1 package for pmid:40789725"}], "activities": [{"id": "activity:conversion:pmid:40789725", "type": "conversion", "used": ["package:69d7910580da9e3beb1ebb020f2d5d28808134662ec3f0ee32d2f9d3d4be4503"], "agent": "agent:corpus-assay-engine"}], "agents": [{"id": "agent:minimax", "type": "model", "label": "minimax"}, {"id": "agent:minimax_alt", "type": "model", "label": "minimax_alt"}, {"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:40789725", "parent_hash": "sha256:0a7c00ed6837fd54b5d9554c49bec195add35ebf2d468bc0e1f6d52b28f5ab6e", "fork_of": null, "generation": 2}, "gaps": ["abstract", "asset:source:pmid:40789725 not verified", "authors", "capability", "corpus_record_absent", "execution.not_run", "method", "review.human_critique", "review.machine_critique.passed", "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:40789725' does not resolve to a declared asset", "targets"]}