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

pmid:39853414

Identification of a metabolic-immune signature associated with prognosis in colon cancer and exploration of potential predictive efficacy of immunotherapy response.

Clinical and experimental medicine · 2025 doi:10.1007/s10238-025-01566-6

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:39853414
kind
science-record
content_hash
sha256:e575ad4fbf642def48d2c0f0ac9d13b2bd03044afef361da65c7a59fd23f4727
schema
https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json
created_at
2026-11-01T10:25:49Z
updated_at
2026-11-01T10:25:49Z
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 a metabolic-immune signature associated with prognosis in colon cancer and exploration of potential predictive efficacy of immunotherapy response.
doi
10.1007/s10238-025-01566-6
pmid
39853414
authors
null
journal
Clinical and experimental medicine
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
quantitative
state
complete
target object · 4 fields
value
6
unit
genes
tolerance
null
source
chars 1623-1799 of source sha256 0bd8e933f1d09fadb938b328f1dd637d1d86ced9ab9eba6edcccf178795d401a
evidence array · 1 item
[0] object · 3 fields
asset
source:pmid:39853414
locator
chars 1623-1799 of source sha256 0bd8e933f1d09fadb938b328f1dd637d1d86ced9ab9eba6edcccf178795d401a
quote
We established the Metabolism and Immune-Related Prognostic Score (MIRPS) based on six genes (CD36, PCOLCE2, SCG2, CALB2, STC2, CLDN23) to predict the prognosis of CC patients.
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:39853414
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:39853414
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:39853414' does not resolve to a declared asset
data object · 3 fields
state
partial
assets array · 1 item
[0] object · 15 fields
id
source:pmid:39853414
role
manuscript
format
xml
media_type
application/xml
uri
https://doi.org/10.1007/s10238-025-01566-6
sha256
sha256:0bd8e933f1d09fadb938b328f1dd637d1d86ced9ab9eba6edcccf178795d401a
bytes
null
access
open
state
resolved
reader
null
reader_status
reader_required
identifier
10.1007/s10238-025-01566-6
version
null
note
Source read by the package builder: full_text.
structure object · 1 field
access_state
full_text
gaps array · 1 item
[0]
asset:source:pmid:39853414 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 · 1 item
[0]
source:pmid:39853414
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:39853414
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
af2640af71a712ca129c4c831b70a5b222922eaf64afdd0bc440a8a1a9db3e1c
source_hash
0bd8e933f1d09fadb938b328f1dd637d1d86ced9ab9eba6edcccf178795d401a
raw_response_sha256
sha256:d1e608e3149499ff47088dbee6db1daf494a16d260a47881ea472ce8a18f0e14
raw_response_chars
5087
[1] object · 7 fields
provider
minimax_alt
model
MiniMax-M3
prompt_version
full-text-reading-v1
prompt_hash
0cc9f1ef0fc3d98332188833d93137714d13060354b8da30ab40389037f11878
source_hash
0bd8e933f1d09fadb938b328f1dd637d1d86ced9ab9eba6edcccf178795d401a
raw_response_sha256
sha256:8508bbc5b3d0e91279aa870cb0d59382dfb7d7e2ef82460eed680fde934a9580
raw_response_chars
32035
target_providers array · 2 items
[0] object · 8 fields
provider
minimax
model
MiniMax-M3.1-Flash
prompt_version
replication-target-v2
prompt_hash
2c0a297dc83e66385343fe6ea1cb55ed5d70595e42de028791bc1658b3adedb7
source_hash
0bd8e933f1d09fadb938b328f1dd637d1d86ced9ab9eba6edcccf178795d401a
raw_response
{"parent_value":6,"unit":"genes","evidence":"We established the Metabolism and Immune-Related Prognostic Score (MIRPS) based on six genes (CD36, PCOLCE2, SCG2, CALB2, STC2, CLDN23) to predict the prognosis of CC patients.","target_result":"The main prognostic signature, MIRPS, was established based on six genes.","number_stated":true}
reading object · 6 fields
parent_value
6
unit
genes
evidence
We established the Metabolism and Immune-Related Prognostic Score (MIRPS) based on six genes (CD36, PCOLCE2, SCG2, CALB2, STC2, CLDN23) to predict the prognosis of CC patients.
target_result
The main prognostic signature, MIRPS, was established based on six genes.
number_stated
true
source_locator
chars 1623-1799 of source sha256 0bd8e933f1d09fadb938b328f1dd637d1d86ced9ab9eba6edcccf178795d401a
recorded_at
2026-10-31T15:21:44.088132+00:00
[1] object · 8 fields
provider
minimax_alt
model
MiniMax-M3
prompt_version
replication-target-v2
prompt_hash
6c97d9098b9693d1c6617037b4272bf47b8fff2b17521ebc0ed6f31a0818b706
source_hash
0bd8e933f1d09fadb938b328f1dd637d1d86ced9ab9eba6edcccf178795d401a
raw_response
<think>We need answer JSON only. Need infer registered target headline numerical result paper states main finding. Source abstract has training cohort 417, validation 232, six genes, thresholds etc. Asked single numerical result replication registered target has reproduce, headline number only value paper itself states for registered target. Need determine perhaps headline numerical result is number of genes in MIRPS signature: six genes? They explicitly say "based on six genes (CD36...)" Main finding signature based on six genes. Numerical result likely "6 genes". Evidence exact contiguous quote containing number and target linkage, whole clause. Unit printed? "genes". Need report headline number only perhaps value 6, unit "genes". Evidence exact quote. Could also be cohort 417/232 but target is headline numerical result for main finding. Main finding MIRPS based on six genes. They emphasize single numerical result. likely six. Need ensure evidence exact quote. "We established the Metabolism and Immune-Related Prognostic Score (MIRPS) based on six genes (CD36, PCOLCE2, SCG2, CALB2, STC2, CLDN23) to predict the prognosis of CC patients." This exact contiguous sentence. Parent_value must number; 6. Unit paper prints "genes". target_result perhaps "MIRPS was established based on six genes." number_stated true. But perhaps headline result expected "six" converted to numeric 6? They ask value paper states, numerical result. Parent_value number. Paper prints word six, not digit. Unit "genes". Evidence contains number as word. Fine. Could target be cohort sample size? "The training cohort with 417 patients ... validation cohort of 232" not headline numerical result. The main finding is MIRPS and signature based on six genes. Need quote clause perhaps whole sentence as attribution. JSON valid.</think> {"parent_value":6,"unit":"genes","evidence":"We established the Metabolism and Immune-Related Prognostic Score (MIRPS) based on six genes (CD36, PCOLCE2, SCG2, CALB2, STC2, CLDN23) to predict the prognosis of CC patients.","target_result":"The MIRPS signature was established based on six genes.","number_stated":true}
reading object · 6 fields
parent_value
6
unit
genes
evidence
We established the Metabolism and Immune-Related Prognostic Score (MIRPS) based on six genes (CD36, PCOLCE2, SCG2, CALB2, STC2, CLDN23) to predict the prognosis of CC patients.
target_result
The MIRPS signature was established based on six genes.
number_stated
true
source_locator
chars 1623-1799 of source sha256 0bd8e933f1d09fadb938b328f1dd637d1d86ced9ab9eba6edcccf178795d401a
recorded_at
2026-10-31T15:21:41.717010+00:00
agreement
true
disagreements object · 3 fields
target_result object · 3 fields
minimax
MIRPS, a prognostic signature based on six genes (CD36, PCOLCE2, SCG2, CALB2, STC2, CLDN23), was established for predicting prognosis in colon cancer patients.
minimax_alt
We established the Metabolism and Immune-Related Prognostic Score (MIRPS) based on six genes (CD36, PCOLCE2, SCG2, CALB2, STC2, CLDN23) to predict the prognosis of CC patients.
decisive
false
physical_methods object · 3 fields
minimax array · 1 item
[0]
Immunohistochemical staining
minimax_alt array · 1 item
[0]
Immunohistochemical staining of clinical samples to assess gene expression levels
decisive
false
analysis_methods object · 3 fields
minimax array · 9 items
[0]
Differential gene expression analysis
[1]
Least absolute shrinkage and selection operator (LASSO) Cox algorithm
[2]
Gene ontology (GO) analysis
[3]
Gene set enrichment analysis (GSEA)
[4]
Single-sample gene set enrichment analysis (ssGSEA)
[5]
Single nucleotide variation (SNV) analysis
[6]
Immune infiltration analysis
[7]
Immune factors analysis
[8]
Correlation analysis
minimax_alt array · 10 items
[0]
Differential gene expression analysis
[1]
Least absolute shrinkage and selection operator (LASSO) Cox algorithm
[2]
Gene ontology (GO) analysis
[3]
Gene set enrichment analysis (GSEA)
[4]
Single-sample GSEA (ssGSEA) using the R package 'GSVA'
[5]
Single nucleotide variation (SNV) analysis
[6]
Immune infiltration analysis
[7]
Immune factors analysis
[8]
Single-cell sequencing analysis
[9]
Correlation analysis
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:8b74b97e4b9af409597cad1170a241a6288a08e05e7af247f0965c057b83348b
type
sep_package
label
SEP v1 package for pmid:39853414
activities array · 1 item
[0] object · 4 fields
id
activity:conversion:pmid:39853414
type
conversion
used array · 1 item
[0]
package:8b74b97e4b9af409597cad1170a241a6288a08e05e7af247f0965c057b83348b
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
f735889f-1a09-47d5-9f68-bff8630f84d4
parent_hash
8b74b97e4b9af409597cad1170a241a6288a08e05e7af247f0965c057b83348b
fork_of
null
gaps array · 13 items
[0]
abstract
[1]
asset:source:pmid:39853414 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:39853414' 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:39853414", "kind": "science-record", "revision": 1, "content_hash": "sha256:e575ad4fbf642def48d2c0f0ac9d13b2bd03044afef361da65c7a59fd23f4727", "created_at": "2026-11-01T10:25:49Z", "updated_at": "2026-11-01T10:25:49Z", "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 a metabolic-immune signature associated with prognosis in colon cancer and exploration of potential predictive efficacy of immunotherapy response.", "doi": "10.1007/s10238-025-01566-6", "pmid": "39853414", "authors": null, "journal": "Clinical and experimental medicine", "year": 2025, "abstract": null, "claims": [{"id": "claim-1", "statement": "the headline numerical result the paper states for its main finding", "kind": "quantitative", "state": "complete", "target": {"value": 6.0, "unit": "genes", "tolerance": null, "source": "chars 1623-1799 of source sha256 0bd8e933f1d09fadb938b328f1dd637d1d86ced9ab9eba6edcccf178795d401a"}, "evidence": [{"asset": "source:pmid:39853414", "locator": "chars 1623-1799 of source sha256 0bd8e933f1d09fadb938b328f1dd637d1d86ced9ab9eba6edcccf178795d401a", "quote": "We established the Metabolism and Immune-Related Prognostic Score (MIRPS) based on six genes (CD36, PCOLCE2, SCG2, CALB2, STC2, CLDN23) to predict the prognosis of CC patients."}]}], "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:39853414"], "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:39853414", "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:39853414' does not resolve to a declared asset"]}, "data": {"state": "partial", "assets": [{"id": "source:pmid:39853414", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.1007/s10238-025-01566-6", "sha256": "sha256:0bd8e933f1d09fadb938b328f1dd637d1d86ced9ab9eba6edcccf178795d401a", "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.1007/s10238-025-01566-6", "version": null, "note": "Source read by the package builder: full_text.", "structure": {"access_state": "full_text"}}], "gaps": ["asset:source:pmid:39853414 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:39853414"], "steps": ["read_published_estimate"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": ["xml"], "capabilities": [], "data_gaps": ["source:pmid:39853414"]}, "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": "af2640af71a712ca129c4c831b70a5b222922eaf64afdd0bc440a8a1a9db3e1c", "source_hash": "0bd8e933f1d09fadb938b328f1dd637d1d86ced9ab9eba6edcccf178795d401a", "raw_response_sha256": "sha256:d1e608e3149499ff47088dbee6db1daf494a16d260a47881ea472ce8a18f0e14", "raw_response_chars": 5087}, {"provider": "minimax_alt", "model": "MiniMax-M3", "prompt_version": "full-text-reading-v1", "prompt_hash": "0cc9f1ef0fc3d98332188833d93137714d13060354b8da30ab40389037f11878", "source_hash": "0bd8e933f1d09fadb938b328f1dd637d1d86ced9ab9eba6edcccf178795d401a", "raw_response_sha256": "sha256:8508bbc5b3d0e91279aa870cb0d59382dfb7d7e2ef82460eed680fde934a9580", "raw_response_chars": 32035}], "target_providers": [{"provider": "minimax", "model": "MiniMax-M3.1-Flash", "prompt_version": "replication-target-v2", "prompt_hash": "2c0a297dc83e66385343fe6ea1cb55ed5d70595e42de028791bc1658b3adedb7", "source_hash": "0bd8e933f1d09fadb938b328f1dd637d1d86ced9ab9eba6edcccf178795d401a", "raw_response": "{\"parent_value\":6,\"unit\":\"genes\",\"evidence\":\"We established the Metabolism and Immune-Related Prognostic Score (MIRPS) based on six genes (CD36, PCOLCE2, SCG2, CALB2, STC2, CLDN23) to predict the prognosis of CC patients.\",\"target_result\":\"The main prognostic signature, MIRPS, was established based on six genes.\",\"number_stated\":true}", "reading": {"parent_value": 6, "unit": "genes", "evidence": "We established the Metabolism and Immune-Related Prognostic Score (MIRPS) based on six genes (CD36, PCOLCE2, SCG2, CALB2, STC2, CLDN23) to predict the prognosis of CC patients.", "target_result": "The main prognostic signature, MIRPS, was established based on six genes.", "number_stated": true, "source_locator": "chars 1623-1799 of source sha256 0bd8e933f1d09fadb938b328f1dd637d1d86ced9ab9eba6edcccf178795d401a"}, "recorded_at": "2026-10-31T15:21:44.088132+00:00"}, {"provider": "minimax_alt", "model": "MiniMax-M3", "prompt_version": "replication-target-v2", "prompt_hash": "6c97d9098b9693d1c6617037b4272bf47b8fff2b17521ebc0ed6f31a0818b706", "source_hash": "0bd8e933f1d09fadb938b328f1dd637d1d86ced9ab9eba6edcccf178795d401a", "raw_response": "<think>We need answer JSON only. Need infer registered target headline numerical result paper states main finding. Source abstract has training cohort 417, validation 232, six genes, thresholds etc. Asked single numerical result replication registered target has reproduce, headline number only value paper itself states for registered target. Need determine perhaps headline numerical result is number of genes in MIRPS signature: six genes? They explicitly say \"based on six genes (CD36...)\" Main finding signature based on six genes. Numerical result likely \"6 genes\". Evidence exact contiguous quote containing number and target linkage, whole clause. Unit printed? \"genes\". Need report headline number only perhaps value 6, unit \"genes\". Evidence exact quote. Could also be cohort 417/232 but target is headline numerical result for main finding. Main finding MIRPS based on six genes. They emphasize single numerical result. likely six.\n\nNeed ensure evidence exact quote. \"We established the Metabolism and Immune-Related Prognostic Score (MIRPS) based on six genes (CD36, PCOLCE2, SCG2, CALB2, STC2, CLDN23) to predict the prognosis of CC patients.\" This exact contiguous sentence. Parent_value must number; 6. Unit paper prints \"genes\". target_result perhaps \"MIRPS was established based on six genes.\" number_stated true.\n\nBut perhaps headline result expected \"six\" converted to numeric 6? They ask value paper states, numerical result. Parent_value number. Paper prints word six, not digit. Unit \"genes\". Evidence contains number as word. Fine.\n\nCould target be cohort sample size? \"The training cohort with 417 patients ... validation cohort of 232\" not headline numerical result. The main finding is MIRPS and signature based on six genes. Need quote clause perhaps whole sentence as attribution. JSON valid.</think>\n\n{\"parent_value\":6,\"unit\":\"genes\",\"evidence\":\"We established the Metabolism and Immune-Related Prognostic Score (MIRPS) based on six genes (CD36, PCOLCE2, SCG2, CALB2, STC2, CLDN23) to predict the prognosis of CC patients.\",\"target_result\":\"The MIRPS signature was established based on six genes.\",\"number_stated\":true}", "reading": {"parent_value": 6, "unit": "genes", "evidence": "We established the Metabolism and Immune-Related Prognostic Score (MIRPS) based on six genes (CD36, PCOLCE2, SCG2, CALB2, STC2, CLDN23) to predict the prognosis of CC patients.", "target_result": "The MIRPS signature was established based on six genes.", "number_stated": true, "source_locator": "chars 1623-1799 of source sha256 0bd8e933f1d09fadb938b328f1dd637d1d86ced9ab9eba6edcccf178795d401a"}, "recorded_at": "2026-10-31T15:21:41.717010+00:00"}], "agreement": true, "disagreements": {"target_result": {"minimax": "MIRPS, a prognostic signature based on six genes (CD36, PCOLCE2, SCG2, CALB2, STC2, CLDN23), was established for predicting prognosis in colon cancer patients.", "minimax_alt": "We established the Metabolism and Immune-Related Prognostic Score (MIRPS) based on six genes (CD36, PCOLCE2, SCG2, CALB2, STC2, CLDN23) to predict the prognosis of CC patients.", "decisive": false}, "physical_methods": {"minimax": ["Immunohistochemical staining"], "minimax_alt": ["Immunohistochemical staining of clinical samples to assess gene expression levels"], "decisive": false}, "analysis_methods": {"minimax": ["Differential gene expression analysis", "Least absolute shrinkage and selection operator (LASSO) Cox algorithm", "Gene ontology (GO) analysis", "Gene set enrichment analysis (GSEA)", "Single-sample gene set enrichment analysis (ssGSEA)", "Single nucleotide variation (SNV) analysis", "Immune infiltration analysis", "Immune factors analysis", "Correlation analysis"], "minimax_alt": ["Differential gene expression analysis", "Least absolute shrinkage and selection operator (LASSO) Cox algorithm", "Gene ontology (GO) analysis", "Gene set enrichment analysis (GSEA)", "Single-sample GSEA (ssGSEA) using the R package 'GSVA'", "Single nucleotide variation (SNV) analysis", "Immune infiltration analysis", "Immune factors analysis", "Single-cell sequencing analysis", "Correlation analysis"], "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:8b74b97e4b9af409597cad1170a241a6288a08e05e7af247f0965c057b83348b", "type": "sep_package", "label": "SEP v1 package for pmid:39853414"}], "activities": [{"id": "activity:conversion:pmid:39853414", "type": "conversion", "used": ["package:8b74b97e4b9af409597cad1170a241a6288a08e05e7af247f0965c057b83348b"], "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": "f735889f-1a09-47d5-9f68-bff8630f84d4", "parent_hash": "8b74b97e4b9af409597cad1170a241a6288a08e05e7af247f0965c057b83348b", "fork_of": null, "generation": 1}, "gaps": ["abstract", "asset:source:pmid:39853414 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:39853414' does not resolve to a declared asset", "targets"]}