Evidence claim

Relevance of vep-lit-20261014-protocol-livesey2025-dms-all to use-case-missense-pp3-bp4-calibrated-evidence

Use case: Use calibrated computational evidence for missense variants (PP3/BP4)
Assessed by: Livesey and Marsh 2025 DMS benchmark: pairwise |Spearman| win rate, all 36 DMS sets
Relevance: Proxy evidence
Endpoint: Average pairwise win rate of each missense VEP against 96 others, by |Spearman| with 36 human DMS datasets

Relevance judgement drafted by the extraction agent; independently reviewed, automated review only.

97 reviewed evaluations

Evidence

Source checking verifies the cited claim or transcription. It does not establish independent reproduction.

Evidence table

Inspect claims, sources and review details

Trace each statement to its source and review. A context-only reference supports the record generally; it does not verify an individual field. Source checking does not reproduce an experiment.

One row per statement and cited source. Multiple citations are not independent evaluations. Shared locators are labelled explicitly.

19 evidence rows matching the loaded filters

Claims, original sources and review scope · Release 2026-10-22-1b7cf027e4f6
Property and statement	Original source and location	Review and provenance
Citation locations 1 values source id vep-lit-20261014-source-livesey2025-supplementary-2 locator Supplementary Material 2 Table S3; Methods 'Spearman's correlation and rank score' Context-only references	Livesey and Marsh 2025, Supplementary Material 2 (Tables S1-S8) Original source ↗ vep-lit-20261014-source-livesey2025-supplementary-2: Supplementary Material 2 Table S3; Methods 'Spearman's correlation and rank score' Version: 13059_2025_3575_MOESM2_ESM.xlsx as published with PMC12016141 Retrieved: 2026-10-14T13:36:25Z	not individually reviewed No individual claim review recorded Audit details Field: `attributes.citation_locators` Source artifact SHA-256: `1b0d792d1a5d3daa95545a7973cabb131c45e42c952e7e5a447a72deef1d1e70` Hash scope: Hash scope not separately documented; inspect source record
Comparison group livesey-marsh-2025-vep-ranking Context-only references	Livesey and Marsh 2025, Supplementary Material 2 (Tables S1-S8) Original source ↗ vep-lit-20261014-source-livesey2025-supplementary-2: Supplementary Material 2 Table S3; Methods 'Spearman's correlation and rank score' Version: 13059_2025_3575_MOESM2_ESM.xlsx as published with PMC12016141 Retrieved: 2026-10-14T13:36:25Z	not individually reviewed No individual claim review recorded Audit details Field: `attributes.comparison_group` Source artifact SHA-256: `1b0d792d1a5d3daa95545a7973cabb131c45e42c952e7e5a447a72deef1d1e70` Hash scope: Hash scope not separately documented; inspect source record
Comparison title Livesey and Marsh 2025 VEP rankings Context-only references	Livesey and Marsh 2025, Supplementary Material 2 (Tables S1-S8) Original source ↗ vep-lit-20261014-source-livesey2025-supplementary-2: Supplementary Material 2 Table S3; Methods 'Spearman's correlation and rank score' Version: 13059_2025_3575_MOESM2_ESM.xlsx as published with PMC12016141 Retrieved: 2026-10-14T13:36:25Z	not individually reviewed No individual claim review recorded Audit details Field: `attributes.comparison_title` Source artifact SHA-256: `1b0d792d1a5d3daa95545a7973cabb131c45e42c952e7e5a447a72deef1d1e70` Hash scope: Hash scope not separately documented; inspect source record
Constraints 3 values Inspect every linked evaluation's source locator before citing a result. Do not combine this mapping's evaluations with any other protocol's results. Compare rows only within this protocol. Context-only references	Livesey and Marsh 2025, Supplementary Material 2 (Tables S1-S8) Original source ↗ vep-lit-20261014-source-livesey2025-supplementary-2: Supplementary Material 2 Table S3; Methods 'Spearman's correlation and rank score' Version: 13059_2025_3575_MOESM2_ESM.xlsx as published with PMC12016141 Retrieved: 2026-10-14T13:36:25Z	not individually reviewed No individual claim review recorded Audit details Field: `attributes.constraints` Source artifact SHA-256: `1b0d792d1a5d3daa95545a7973cabb131c45e42c952e7e5a447a72deef1d1e70` Hash scope: Hash scope not separately documented; inspect source record
Endpoint Average pairwise win rate of each missense VEP against 96 others, by \|Spearman\| with 36 human DMS datasets Context-only references	Livesey and Marsh 2025, Supplementary Material 2 (Tables S1-S8) Original source ↗ vep-lit-20261014-source-livesey2025-supplementary-2: Supplementary Material 2 Table S3; Methods 'Spearman's correlation and rank score' Version: 13059_2025_3575_MOESM2_ESM.xlsx as published with PMC12016141 Retrieved: 2026-10-14T13:36:25Z	not individually reviewed No individual claim review recorded Audit details Field: `attributes.endpoint` Source artifact SHA-256: `1b0d792d1a5d3daa95545a7973cabb131c45e42c952e7e5a447a72deef1d1e70` Hash scope: Hash scope not separately documented; inspect source record
Claimed field links:assessed_by:vep-lit-20261014-protocol-livesey2025-dms-all Context-only references	Livesey and Marsh 2025, Supplementary Material 2 (Tables S1-S8) Original source ↗ vep-lit-20261014-source-livesey2025-supplementary-2: Supplementary Material 2 Table S3; Methods 'Spearman's correlation and rank score' Version: 13059_2025_3575_MOESM2_ESM.xlsx as published with PMC12016141 Retrieved: 2026-10-14T13:36:25Z	not individually reviewed No individual claim review recorded Audit details Field: `attributes.field` Source artifact SHA-256: `1b0d792d1a5d3daa95545a7973cabb131c45e42c952e7e5a447a72deef1d1e70` Hash scope: Hash scope not separately documented; inspect source record
Headline metric pairwise-win-rate Context-only references	Livesey and Marsh 2025, Supplementary Material 2 (Tables S1-S8) Original source ↗ vep-lit-20261014-source-livesey2025-supplementary-2: Supplementary Material 2 Table S3; Methods 'Spearman's correlation and rank score' Version: 13059_2025_3575_MOESM2_ESM.xlsx as published with PMC12016141 Retrieved: 2026-10-14T13:36:25Z	not individually reviewed No individual claim review recorded Audit details Field: `attributes.headline_metric` Source artifact SHA-256: `1b0d792d1a5d3daa95545a7973cabb131c45e42c952e7e5a447a72deef1d1e70` Hash scope: Hash scope not separately documented; inspect source record
Limitations 5 values DMS phenotypes are chosen per protein and are not pathogenicity labels. Rank scores are relative to the VEP set compared; they are not a correlation and cannot be compared with other tables. No calibration to ACMG/AMP evidence strength and no thresholds. Correlation is assessed within each protein, so the ranking does not test whether scores are comparable across genes; the authors report that DMS and clinical rankings agree closely for population-free and population-tuned VEPs (Pearson r 0.978 and 0.994) and less for clinical-trained VEPs (Results, Fig. 4). Transcribed from the source; no reproduction by Rewire and no human scientific review. Context-only references	Livesey and Marsh 2025, Supplementary Material 2 (Tables S1-S8) Original source ↗ vep-lit-20261014-source-livesey2025-supplementary-2: Supplementary Material 2 Table S3; Methods 'Spearman's correlation and rank score' Version: 13059_2025_3575_MOESM2_ESM.xlsx as published with PMC12016141 Retrieved: 2026-10-14T13:36:25Z	not individually reviewed No individual claim review recorded Audit details Field: `attributes.limitations` Source artifact SHA-256: `1b0d792d1a5d3daa95545a7973cabb131c45e42c952e7e5a447a72deef1d1e70` Hash scope: Hash scope not separately documented; inspect source record
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93fc887334181cc257a844dbee3d027cb1ec229053eebf132d3d6a563fce63c1 record id vep-lit-20261014-source-livesey2025-supplementary-2 fields status attributes.artifact_sha256 sha256 654913943e661a8ff6fba0bccdcdaaebf17cf0bb54a9e6f39ddffd5b248c330d Context-only references	Livesey and Marsh 2025, Supplementary Material 2 (Tables S1-S8) Original source ↗ vep-lit-20261014-source-livesey2025-supplementary-2: Supplementary Material 2 Table S3; Methods 'Spearman's correlation and rank score' Version: 13059_2025_3575_MOESM2_ESM.xlsx as published with PMC12016141 Retrieved: 2026-10-14T13:36:25Z	not individually reviewed No individual claim review recorded Audit details Field: `attributes.pins` Source artifact SHA-256: `1b0d792d1a5d3daa95545a7973cabb131c45e42c952e7e5a447a72deef1d1e70` Hash scope: Hash scope not separately documented; inspect source record
Rationale Proxy: DMS-based ranking avoids clinical-label circularity, which the calibrations cannot fully remove, and so is an independent check on which predictors to calibrate; it gives no thresholds or evidence strengths. Context-only references	Livesey and Marsh 2025, Supplementary Material 2 (Tables S1-S8) Original source ↗ vep-lit-20261014-source-livesey2025-supplementary-2: Supplementary Material 2 Table S3; Methods 'Spearman's correlation and rank score' Version: 13059_2025_3575_MOESM2_ESM.xlsx as published with PMC12016141 Retrieved: 2026-10-14T13:36:25Z	not individually reviewed No individual claim review recorded Audit details Field: `attributes.rationale` Source artifact SHA-256: `1b0d792d1a5d3daa95545a7973cabb131c45e42c952e7e5a447a72deef1d1e70` Hash scope: Hash scope not separately documented; inspect source record

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Release 2026-10-22-1b7cf027e4f6 · Record review: source checked

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Livesey and Marsh 2025, Supplementary Material 2 (Tables S1-S8) · Original source · 13059_2025_3575_MOESM2_ESM.xlsx as published with PMC12016141

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Technical metadata and extraction receipts

Stable ID: use-case-mapping-vep-uc-20261014-missense-pp3-bp4-calibrated-evidence-livesey2025-dms-all

field: links:assessed_by:vep-lit-20261014-protocol-livesey2025-dms-all
value: vep-lit-20261014-protocol-livesey2025-dms-all
relevance: proxy
endpoint: Average pairwise win rate of each missense VEP against 96 others, by |Spearman| with 36 human DMS datasets
rationale: Proxy: DMS-based ranking avoids clinical-label circularity, which the calibrations cannot fully remove, and so is an independent check on which predictors to calibrate; it gives no thresholds or evidence strengths.
constraints: Inspect every linked evaluation's source locator before citing a result.; Do not combine this mapping's evaluations with any other protocol's results.; Compare rows only within this protocol.
limitations: DMS phenotypes are chosen per protein and are not pathogenicity labels.; Rank scores are relative to the VEP set compared; they are not a correlation and cannot be compared with other tables.; No calibration to ACMG/AMP evidence strength and no thresholds.; Correlation is assessed within each protein, so the ranking does not test whether scores are comparable across genes; the authors report that DMS and clinical rankings agree closely for population-free and population-tuned VEPs (Pearson r 0.978 and 0.994) and less for clinical-trained VEPs (Results, Fig. 4).; Transcribed from the source; no reproduction by Rewire and no human scientific review.
citation locators: source id: vep-lit-20261014-source-livesey2025-supplementary-2; locator: Supplementary Material 2 Table S3; Methods 'Spearman's correlation and rank score'
source locator: vep-lit-20261014-source-livesey2025-supplementary-2: Supplementary Material 2 Table S3; Methods 'Spearman's correlation and rank score'
headline metric: pairwise-win-rate
comparison group: livesey-marsh-2025-vep-ranking
comparison title: Livesey and Marsh 2025 VEP rankings
stratum label: DMS benchmark, all 36 DMS sets
stratum order: 1
reason: VEP use-case pass 2026-10-14: relevance of a protocol to a new use case (rewire-benchmark-data #151/#152).
review: reviewer: claude; reviewer note: Claude review agent; no human review claimed. Independent Claude (Opus 5.5) review agent, separate from the extraction agent that built this batch. Automated review only. Transcription, not reproduction.; reviewed at: 2026-10-14T16:00:00Z; method: ai-assisted-source-review; scope-review; method note: Checked the endpoint against the use case's question, inputs, exclusions and output; checked each limitation and number against the cited sources, re-downloaded and hash-matched; listed every evaluation on the protocol in reviewed_evaluations (values of evaluations already in the store were checked by their own independent reviews).; note: Judgement drafted by the extraction agent and revised in review (docs/reviews/vep-use-cases-2026-10-14-review.md).
reviewed evaluations: vep-lit-20261014-eval-livesey2025-dms-all-3cnet; vep-lit-20261014-eval-livesey2025-dms-all-alphamissense; vep-lit-20261014-eval-livesey2025-dms-all-alphscore; vep-lit-20261014-eval-livesey2025-dms-all-bayesdel; vep-lit-20261014-eval-livesey2025-dms-all-bayesdel-noaf; vep-lit-20261014-eval-livesey2025-dms-all-blosum62; vep-lit-20261014-eval-livesey2025-dms-all-cadd-1-6; vep-lit-20261014-eval-livesey2025-dms-all-cadd-1-7; vep-lit-20261014-eval-livesey2025-dms-all-capice; vep-lit-20261014-eval-livesey2025-dms-all-carp; vep-lit-20261014-eval-livesey2025-dms-all-clinpred; vep-lit-20261014-eval-livesey2025-dms-all-condel; vep-lit-20261014-eval-livesey2025-dms-all-cpt-1; vep-lit-20261014-eval-livesey2025-dms-all-dann; vep-lit-20261014-eval-livesey2025-dms-all-deepsav; vep-lit-20261014-eval-livesey2025-dms-all-deepsequence; vep-lit-20261014-eval-livesey2025-dms-all-demask; vep-lit-20261014-eval-livesey2025-dms-all-deogen2; vep-lit-20261014-eval-livesey2025-dms-all-eigen; vep-lit-20261014-eval-livesey2025-dms-all-envision; vep-lit-20261014-eval-livesey2025-dms-all-escott; vep-lit-20261014-eval-livesey2025-dms-all-esm-1b; vep-lit-20261014-eval-livesey2025-dms-all-esm-1v; vep-lit-20261014-eval-livesey2025-dms-all-esm2; vep-lit-20261014-eval-livesey2025-dms-all-eve; vep-lit-20261014-eval-livesey2025-dms-all-evmutation-epistatic; vep-lit-20261014-eval-livesey2025-dms-all-evmutation-independent; vep-lit-20261014-eval-livesey2025-dms-all-fathmm; vep-lit-20261014-eval-livesey2025-dms-all-fathmm-mkl; vep-lit-20261014-eval-livesey2025-dms-all-fathmm-xf; vep-lit-20261014-eval-livesey2025-dms-all-fitcons; vep-lit-20261014-eval-livesey2025-dms-all-gemme; vep-lit-20261014-eval-livesey2025-dms-all-genocanyon; vep-lit-20261014-eval-livesey2025-dms-all-gerp-plus-plus; vep-lit-20261014-eval-livesey2025-dms-all-gmvp; vep-lit-20261014-eval-livesey2025-dms-all-grantham; vep-lit-20261014-eval-livesey2025-dms-all-igemme; vep-lit-20261014-eval-livesey2025-dms-all-inmerf; vep-lit-20261014-eval-livesey2025-dms-all-lassie; vep-lit-20261014-eval-livesey2025-dms-all-list-s2; vep-lit-20261014-eval-livesey2025-dms-all-lrt; vep-lit-20261014-eval-livesey2025-dms-all-m-cap; vep-lit-20261014-eval-livesey2025-dms-all-maverick-benign; vep-lit-20261014-eval-livesey2025-dms-all-metalr; vep-lit-20261014-eval-livesey2025-dms-all-metarnn; vep-lit-20261014-eval-livesey2025-dms-all-metasvm; vep-lit-20261014-eval-livesey2025-dms-all-mistic; vep-lit-20261014-eval-livesey2025-dms-all-moipred-benign; vep-lit-20261014-eval-livesey2025-dms-all-mpc; vep-lit-20261014-eval-livesey2025-dms-all-msa-transformer; vep-lit-20261014-eval-livesey2025-dms-all-mutationassessor; vep-lit-20261014-eval-livesey2025-dms-all-mutationtcn; vep-lit-20261014-eval-livesey2025-dms-all-mutformer; vep-lit-20261014-eval-livesey2025-dms-all-mutpred; vep-lit-20261014-eval-livesey2025-dms-all-mutscore; vep-lit-20261014-eval-livesey2025-dms-all-mvp; vep-lit-20261014-eval-livesey2025-dms-all-mvppt; vep-lit-20261014-eval-livesey2025-dms-all-panther; vep-lit-20261014-eval-livesey2025-dms-all-phact; vep-lit-20261014-eval-livesey2025-dms-all-phactboost; vep-lit-20261014-eval-livesey2025-dms-all-phastcons; vep-lit-20261014-eval-livesey2025-dms-all-phd-snp; vep-lit-20261014-eval-livesey2025-dms-all-phd-snpg; vep-lit-20261014-eval-livesey2025-dms-all-phylop; vep-lit-20261014-eval-livesey2025-dms-all-polyphen2-humdiv; vep-lit-20261014-eval-livesey2025-dms-all-polyphen2-humvar; vep-lit-20261014-eval-livesey2025-dms-all-ponp2; vep-lit-20261014-eval-livesey2025-dms-all-popeve; vep-lit-20261014-eval-livesey2025-dms-all-primateai; vep-lit-20261014-eval-livesey2025-dms-all-progen2; vep-lit-20261014-eval-livesey2025-dms-all-protgpt2; vep-lit-20261014-eval-livesey2025-dms-all-provean; vep-lit-20261014-eval-livesey2025-dms-all-revel; vep-lit-20261014-eval-livesey2025-dms-all-rhapsody; vep-lit-20261014-eval-livesey2025-dms-all-rita; vep-lit-20261014-eval-livesey2025-dms-all-saprot; vep-lit-20261014-eval-livesey2025-dms-all-sequence-unet; vep-lit-20261014-eval-livesey2025-dms-all-sift; vep-lit-20261014-eval-livesey2025-dms-all-sift4g; vep-lit-20261014-eval-livesey2025-dms-all-sigma; vep-lit-20261014-eval-livesey2025-dms-all-siphy; vep-lit-20261014-eval-livesey2025-dms-all-snap2; vep-lit-20261014-eval-livesey2025-dms-all-snpred; vep-lit-20261014-eval-livesey2025-dms-all-snps-and-go; vep-lit-20261014-eval-livesey2025-dms-all-snps-and-go3d; vep-lit-20261014-eval-livesey2025-dms-all-spri; vep-lit-20261014-eval-livesey2025-dms-all-suspect; vep-lit-20261014-eval-livesey2025-dms-all-trancepteve; vep-lit-20261014-eval-livesey2025-dms-all-tranception; vep-lit-20261014-eval-livesey2025-dms-all-uneecon; vep-lit-20261014-eval-livesey2025-dms-all-unirep-evotune; vep-lit-20261014-eval-livesey2025-dms-all-varity-er; vep-lit-20261014-eval-livesey2025-dms-all-varity-r; vep-lit-20261014-eval-livesey2025-dms-all-vespa; vep-lit-20261014-eval-livesey2025-dms-all-vespal; vep-lit-20261014-eval-livesey2025-dms-all-vest4; vep-lit-20261014-eval-livesey2025-dms-all-wavenet
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