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pmid:39883234

FOXP3 as a prognostic marker and therapeutic target in immunogenic cell death modulation for clear cell renal cell carcinoma.

Discover oncology · 2025 doi:10.1007/s12672-025-01831-w

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:39883234
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science-record
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sha256:6e43131e533f3014b4c2c2dfac8482ba514ff2c17480d26c199383e0b9a71049
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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
FOXP3 as a prognostic marker and therapeutic target in immunogenic cell death modulation for clear cell renal cell carcinoma.
doi
10.1007/s12672-025-01831-w
pmid
39883234
authors
null
journal
Discover oncology
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
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complete
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0.781
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auc
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null
source
chars 5043-5196 of source sha256 ef0ca94bfb80c40560513ace0d81acf61eb4f03179ce7ca95ffbfdca9acce840
evidence array · 1 item
[0] object · 3 fields
asset
source:pmid:39883234
locator
chars 5043-5196 of source sha256 ef0ca94bfb80c40560513ace0d81acf61eb4f03179ce7ca95ffbfdca9acce840
quote
Diagnostic ROC curve indicated that FOXP3 has good accuracy in distinguishing between cancer and adjacent normal tissues, with an AUC of 0.781 (Fig. 6B).
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:39883234
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
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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
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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:39883234
parameters object · 0 fields
inputs array · 0 items
outputs array · 1 item
[0]
the registered result
instruments array · 0 items
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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:39883234' does not resolve to a declared asset
data object · 3 fields
state
partial
assets array · 1 item
[0] object · 15 fields
id
source:pmid:39883234
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xml
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application/xml
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https://doi.org/10.1007/s12672-025-01831-w
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sha256:ef0ca94bfb80c40560513ace0d81acf61eb4f03179ce7ca95ffbfdca9acce840
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null
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10.1007/s12672-025-01831-w
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null
note
Source read by the package builder: full_text.
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full_text
gaps array · 1 item
[0]
asset:source:pmid:39883234 not verified
analysis object · 4 fields
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[0]
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[1]
targets
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capability
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partial
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null
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null
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assets array · 1 item
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source:pmid:39883234
steps array · 1 item
[0]
read_published_estimate
must_build object · 5 fields
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[0]
xml
capabilities array · 0 items
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[0]
source:pmid:39883234
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corpus_record_absent
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partial
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minimax
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MiniMax-M3.1-Flash
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minimax
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MiniMax-M3.1-Flash
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ef0ca94bfb80c40560513ace0d81acf61eb4f03179ce7ca95ffbfdca9acce840
raw_response
{"parent_value":0.781,"unit":"AUC","evidence":"Diagnostic ROC curve indicated that FOXP3 has good accuracy in distinguishing between cancer and adjacent normal tissues, with an AUC of 0.781 (Fig. 6B).","target_result":"FOXP3 diagnostic ROC AUC","number_stated":true}
reading object · 6 fields
parent_value
0.781
unit
AUC
evidence
Diagnostic ROC curve indicated that FOXP3 has good accuracy in distinguishing between cancer and adjacent normal tissues, with an AUC of 0.781 (Fig. 6B).
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FOXP3 diagnostic ROC AUC
number_stated
true
source_locator
chars 5043-5196 of source sha256 ef0ca94bfb80c40560513ace0d81acf61eb4f03179ce7ca95ffbfdca9acce840
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source_hash
ef0ca94bfb80c40560513ace0d81acf61eb4f03179ce7ca95ffbfdca9acce840
raw_response
<think>We need answer JSON only. Need identify single numerical result replication registered target headline numerical result paper states for main finding. Source includes multiple numbers. Main finding perhaps FOXP3 AUC 0.781 as headline numerical result? Need infer. They ask "registered target: the headline numerical result the paper states for its main finding." We need report value paper itself states, not calculated. Unit paper prints. Evidence exact contiguous quote containing number and attribution via direct wording. Candidate "Diagnostic ROC curve indicated that FOXP3 has good accuracy in distinguishing between cancer and adjacent normal tissues, with an AUC of 0.781 (Fig. 6B)." Headline numerical result likely AUC 0.781. Could perhaps 11 genes. But paper main finding FOXP3 as prognostic marker and therapeutic target; headline numerical result perhaps AUC 0.781. Need parent_value 0.781, unit maybe "AUC" or empty? They say unit must be unit paper prints. AUC is dimensionless and paper prints "AUC of 0.781." Unit likely "AUC". Evidence whole clause exact. target_result description perhaps "FOXP3 has an AUC of 0.781 for distinguishing..." Need ensure source exact quotation no shorten. Exact contiguous quote. Could quote sentence. "Diagnostic ROC curve indicated that FOXP3 has good accuracy in distinguishing between cancer and adjacent normal tissues, with an AUC of 0.781 (Fig. 6B)." Yes. Question wording nuanced: "find the single numerical result that a replication of the registered target has to reproduce." Maybe target registered is "headline numerical result the paper states for its main finding." Need select one. Other salient numerical: 11 genes, 18 genes, 3464, p &lt;0.001, AUC .781. Main finding is FOXP3. Its quantitative headline is AUC .781. Unit printed maybe no conventional unit. Unit string could be "AUC". In schema parent_value numeric. Need not include extra. target_result likely "FOXP3's diagnostic ROC AUC was 0.781." But this paraphrases? target_result unrestricted. Evidence exact. number_stated true. Could unit be "" because AUC isn't a unit? User says "The unit must be the unit the paper prints." Paper prints "AUC", not a unit exactly. They likely expect unit "AUC". We should state "AUC". Let's ensure JSON valid, no markdown.</think> {"parent_value":0.781,"unit":"AUC","evidence":"Diagnostic ROC curve indicated that FOXP3 has good accuracy in distinguishing between cancer and adjacent normal tissues, with an AUC of 0.781 (Fig. 6B).","target_result":"FOXP3 had an AUC of 0.781 for distinguishing ccRCC from adjacent normal tissues.","number_stated":true}
reading object · 6 fields
parent_value
0.781
unit
AUC
evidence
Diagnostic ROC curve indicated that FOXP3 has good accuracy in distinguishing between cancer and adjacent normal tissues, with an AUC of 0.781 (Fig. 6B).
target_result
FOXP3 had an AUC of 0.781 for distinguishing ccRCC from adjacent normal tissues.
number_stated
true
source_locator
chars 5043-5196 of source sha256 ef0ca94bfb80c40560513ace0d81acf61eb4f03179ce7ca95ffbfdca9acce840
recorded_at
2026-10-31T15:22:18.342976+00:00
agreement
true
disagreements object · 3 fields
target_result object · 3 fields
minimax
FOXP3 had an AUC of 0.781 for distinguishing ccRCC cancer tissue from adjacent normal tissue.
minimax_alt
FOXP3 achieved an AUC of 0.781 for distinguishing ccRCC cancer tissue from adjacent normal tissue.
decisive
false
physical_methods object · 3 fields
minimax array · 1 item
[0]
FOXP3 knockdown experiments in ccRCC cell lines
minimax_alt array · 3 items
[0]
FOXP3 knockdown in ccRCC cell lines
[1]
Cell proliferation measurement
[2]
Cell migration measurement
decisive
false
analysis_methods object · 3 fields
minimax array · 12 items
[0]
consensus clustering
[1]
principal component analysis (PCA)
[2]
univariate Cox regression analysis
[3]
Kaplan-Meier (KM) curve analysis
[4]
receiver operating characteristic (ROC) curve analysis
[5]
Gene Set Enrichment Analysis (GSEA)
[6]
ESTIMATE
[7]
immune cell infiltration analysis
[8]
functional pathway enrichment analysis
[9]
somatic mutation analysis using the maftools R package
[10]
tumor mutational burden (TMB) analysis
[11]
drug sensitivity analysis using the prophetic package
minimax_alt array · 12 items
[0]
Consensus clustering
[1]
Principal component analysis (PCA) for ICD signature development
[2]
Differential expression analysis using an adjusted p-value threshold of < 0.001
[3]
Univariate Cox regression
[4]
Receiver operating characteristic (ROC) curve analysis
[5]
Kaplan-Meier (KM) survival analysis
[6]
Gene set enrichment analysis (GSEA)
[7]
ESTIMATE
[8]
maftools somatic mutation profiling
[9]
Tumor mutational burden comparison
[10]
prophetic-package IC50 analysis
[11]
TCIA immune-therapy response comparison
decisive
false
agreement_basis object · 2 fields
policy
decisive_fields
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work_type
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number_stated
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parent_value
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null
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null
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independent_readings
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source_resolution
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null
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null
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null
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review.human_critique
[1]
review.machine_critique.passed
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step:obtain_source_data blocked on data:not_downloaded
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step:run_analysis blocked on no owned computational capability is bound to this experiment
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step:run_analysis input 'materials:the source data behind the published result in pmid:39883234' does not resolve to a declared asset
[12]
targets
Complete file
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{"provider": "minimax_alt", "model": "MiniMax-M3", "prompt_version": "full-text-reading-v1", "prompt_hash": "f5747ca32fe6f2a687fe6f5eaa1138b79b976c2ac23f11293dc87222fc20b514", "source_hash": "ef0ca94bfb80c40560513ace0d81acf61eb4f03179ce7ca95ffbfdca9acce840", "raw_response_sha256": "sha256:58b46d4f9edec5307dc07f29f847b1e84f638d3f42cdd2b625a907fc82c8edbc", "raw_response_chars": 48759}], "target_providers": [{"provider": "minimax", "model": "MiniMax-M3.1-Flash", "prompt_version": "replication-target-v2", "prompt_hash": "5f579c41bbe31e7afb3ab55fe8e14ba0f1cf321ee9885faacfa12a4be9d15ebe", "source_hash": "ef0ca94bfb80c40560513ace0d81acf61eb4f03179ce7ca95ffbfdca9acce840", "raw_response": "{\"parent_value\":0.781,\"unit\":\"AUC\",\"evidence\":\"Diagnostic ROC curve indicated that FOXP3 has good accuracy in distinguishing between cancer and adjacent normal tissues, with an AUC of 0.781 (Fig. 6B).\",\"target_result\":\"FOXP3 diagnostic ROC AUC\",\"number_stated\":true}", "reading": {"parent_value": 0.781, "unit": "AUC", "evidence": "Diagnostic ROC curve indicated that FOXP3 has good accuracy in distinguishing between cancer and adjacent normal tissues, with an AUC of 0.781 (Fig. 6B).", "target_result": "FOXP3 diagnostic ROC AUC", "number_stated": true, "source_locator": "chars 5043-5196 of source sha256 ef0ca94bfb80c40560513ace0d81acf61eb4f03179ce7ca95ffbfdca9acce840"}, "recorded_at": "2026-10-31T15:22:17.392092+00:00"}, {"provider": "minimax_alt", "model": "MiniMax-M3", "prompt_version": "replication-target-v2", "prompt_hash": "e3fda92cbd0255e0780e1b749a3c15e3d4d8305a7f52ec2fd1f0cde8fdd81c28", "source_hash": "ef0ca94bfb80c40560513ace0d81acf61eb4f03179ce7ca95ffbfdca9acce840", "raw_response": "<think>We need answer JSON only. Need identify single numerical result replication registered target headline numerical result paper states for main finding. Source includes multiple numbers. Main finding perhaps FOXP3 AUC 0.781 as headline numerical result? Need infer. They ask \"registered target: the headline numerical result the paper states for its main finding.\" We need report value paper itself states, not calculated. Unit paper prints. Evidence exact contiguous quote containing number and attribution via direct wording. Candidate \"Diagnostic ROC curve indicated that FOXP3 has good accuracy in distinguishing between cancer and adjacent normal tissues, with an AUC of 0.781 (Fig. 6B).\" Headline numerical result likely AUC 0.781. Could perhaps 11 genes. But paper main finding FOXP3 as prognostic marker and therapeutic target; headline numerical result perhaps AUC 0.781. Need parent_value 0.781, unit maybe \"AUC\" or empty? They say unit must be unit paper prints. AUC is dimensionless and paper prints \"AUC of 0.781.\" Unit likely \"AUC\". Evidence whole clause exact. target_result description perhaps \"FOXP3 has an AUC of 0.781 for distinguishing...\" Need ensure source exact quotation no shorten. Exact contiguous quote. Could quote sentence. \"Diagnostic ROC curve indicated that FOXP3 has good accuracy in distinguishing between cancer and adjacent normal tissues, with an AUC of 0.781 (Fig. 6B).\" Yes.\n\nQuestion wording nuanced: \"find the single numerical result that a replication of the registered target has to reproduce.\" Maybe target registered is \"headline numerical result the paper states for its main finding.\" Need select one. Other salient numerical: 11 genes, 18 genes, 3464, p &lt;0.001, AUC .781. Main finding is FOXP3. Its quantitative headline is AUC .781. Unit printed maybe no conventional unit. Unit string could be \"AUC\". In schema parent_value numeric.\n\nNeed not include extra. target_result likely \"FOXP3's diagnostic ROC AUC was 0.781.\" But this paraphrases? target_result unrestricted. Evidence exact. number_stated true.\n\nCould unit be \"\" because AUC isn't a unit? User says \"The unit must be the unit the paper prints.\" Paper prints \"AUC\", not a unit exactly. They likely expect unit \"AUC\". We should state \"AUC\". Let's ensure JSON valid, no markdown.</think>\n\n{\"parent_value\":0.781,\"unit\":\"AUC\",\"evidence\":\"Diagnostic ROC curve indicated that FOXP3 has good accuracy in distinguishing between cancer and adjacent normal tissues, with an AUC of 0.781 (Fig. 6B).\",\"target_result\":\"FOXP3 had an AUC of 0.781 for distinguishing ccRCC from adjacent normal tissues.\",\"number_stated\":true}", "reading": {"parent_value": 0.781, "unit": "AUC", "evidence": "Diagnostic ROC curve indicated that FOXP3 has good accuracy in distinguishing between cancer and adjacent normal tissues, with an AUC of 0.781 (Fig. 6B).", "target_result": "FOXP3 had an AUC of 0.781 for distinguishing ccRCC from adjacent normal tissues.", "number_stated": true, "source_locator": "chars 5043-5196 of source sha256 ef0ca94bfb80c40560513ace0d81acf61eb4f03179ce7ca95ffbfdca9acce840"}, "recorded_at": "2026-10-31T15:22:18.342976+00:00"}], "agreement": true, "disagreements": {"target_result": {"minimax": "FOXP3 had an AUC of 0.781 for distinguishing ccRCC cancer tissue from adjacent normal tissue.", "minimax_alt": "FOXP3 achieved an AUC of 0.781 for distinguishing ccRCC cancer tissue from adjacent normal tissue.", "decisive": false}, "physical_methods": {"minimax": ["FOXP3 knockdown experiments in ccRCC cell lines"], "minimax_alt": ["FOXP3 knockdown in ccRCC cell lines", "Cell proliferation measurement", "Cell migration measurement"], "decisive": false}, "analysis_methods": {"minimax": ["consensus clustering", "principal component analysis (PCA)", "univariate Cox regression analysis", "Kaplan-Meier (KM) curve analysis", "receiver operating characteristic (ROC) curve analysis", "Gene Set Enrichment Analysis (GSEA)", "ESTIMATE", "immune cell infiltration analysis", "functional pathway enrichment analysis", "somatic mutation analysis using the maftools R package", "tumor mutational burden (TMB) analysis", "drug sensitivity analysis using the prophetic package"], "minimax_alt": ["Consensus clustering", "Principal component analysis (PCA) for ICD signature development", "Differential expression analysis using an adjusted p-value threshold of < 0.001", "Univariate Cox regression", "Receiver operating characteristic (ROC) curve analysis", "Kaplan-Meier (KM) survival analysis", "Gene set enrichment analysis (GSEA)", "ESTIMATE", "maftools somatic mutation profiling", "Tumor mutational burden comparison", "prophetic-package IC50 analysis", "TCIA immune-therapy response comparison"], "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:0702b507456f621de667a0342b032c46d0b4bc6c5e0e604f32e776437281e7a2", "type": "sep_package", "label": "SEP v1 package for pmid:39883234"}], "activities": [{"id": "activity:conversion:pmid:39883234", "type": "conversion", "used": ["package:0702b507456f621de667a0342b032c46d0b4bc6c5e0e604f32e776437281e7a2"], "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": "1881d9fe-1847-4ed6-9280-97b997453cc8", "parent_hash": "0702b507456f621de667a0342b032c46d0b4bc6c5e0e604f32e776437281e7a2", "fork_of": null, "generation": 1}, "gaps": ["abstract", "asset:source:pmid:39883234 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:39883234' does not resolve to a declared asset", "targets"]}