← 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
generator object · 3 fields
paper object · 10 fields
claims array · 1 item
[0] object · 6 fields
target object · 4 fields
evidence array · 1 item
[0] object · 3 fields
gaps array · 2 items
experiment object · 8 fields
steps array · 3 items
[0] object · 13 fields
parameters object · 0 fields
inputs array · 1 item
outputs array · 1 item
instruments array · 0 items
reagents array · 0 items
[1] object · 13 fields
parameters object · 0 fields
inputs array · 0 items
outputs array · 1 item
instruments array · 0 items
reagents array · 0 items
[2] object · 13 fields
parameters object · 0 fields
inputs array · 0 items
outputs array · 1 item
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
data object · 3 fields
assets array · 1 item
[0] object · 15 fields
structure object · 1 field
gaps array · 1 item
capability object · 3 fields
readiness object · 8 fields
axes object · 0 fields
can_run object · 3 fields
dsl_operations array · 0 items
assets array · 1 item
steps array · 1 item
must_build object · 5 fields
dsl_operations array · 0 items
converters array · 0 items
readers array · 1 item
capabilities array · 0 items
data_gaps array · 1 item
gaps array · 1 item
review object · 5 fields
machine_critique object · 7 fields
providers array · 2 items
[0] object · 7 fields
[1] object · 7 fields
target_providers array · 2 items
[0] object · 8 fields
reading object · 6 fields
[1] object · 8 fields
reading object · 6 fields
disagreements object · 3 fields
target_result object · 3 fields
physical_methods object · 3 fields
minimax array · 1 item
minimax_alt array · 1 item
analysis_methods object · 3 fields
minimax array · 9 items
minimax_alt array · 10 items
agreement_basis object · 2 fields
decisive_fields array · 4 items
human_critique object · 5 fields
stages array · 7 items
[0] object · 4 fields
[1] object · 4 fields
evidence object · 1 field
provider_errors array · 0 items
[2] object · 4 fields
[3] object · 4 fields
[4] object · 4 fields
[5] object · 4 fields
[6] object · 4 fields
gaps array · 2 items
provenance object · 7 fields
entities array · 1 item
activities array · 1 item
agents array · 3 items
lineage object · 4 fields
gaps array · 13 items
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"]}