Evidence claim

Relevance of Splice-altering variant classification, SPiP benchmark variant set (99,601 variants) (Fortier et al. Table 3) to "Select a patient-RNA splicing-variant validation workflow"

Use case: Select a patient-RNA splicing-variant validation workflow
Assessed by: Splice-altering variant classification, SPiP benchmark variant set (99,601 variants) (Fortier et al. Table 3)
Relevance: Proxy evidence
Endpoint: Sensitivity, specificity, F1 and balanced accuracy of SpliceAI, CI-SpliceAI, OpenSpliceAI and a legacy N-of-4 vote on the SPiP benchmark variant set (99,601 variants)

Proxy: DNA-based splice predictors scored against experimentally established splicing outcomes, the sequence-classification kind of evidence the use case keeps separate from patient-RNA recovery; inputs are variants, not patient RNA-seq.

4 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 rna-splicing-20261011-fortier2026-source-article locator Methods 'SPiP benchmark dataset'; Results 'SPiP benchmark results'; Table 3 Context-only references	Analyzing the performance of deep learning splice prediction algorithms (Fortier, Rudy and Scherer, PLOS One 2026) Original source ↗ rna-splicing-20261011-fortier2026-source-article: Methods 'SPiP benchmark dataset'; Results 'SPiP benchmark results'; Table 3 Version: PLOS One 21(5):e0348885, published 2026-05-13; PMC13170886 full-text XML Retrieved: 2026-10-11T21:37:04Z	not individually reviewed No individual claim review recorded Audit details Field: `attributes.citation_locators` Source artifact SHA-256: `dffe74cee7782cbdfdbc9423cf00f0a846b3d720b90b10e9732d6f768c485176` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Comparison group fortier2026-spliceai-reimplementations Context-only references	Analyzing the performance of deep learning splice prediction algorithms (Fortier, Rudy and Scherer, PLOS One 2026) Original source ↗ rna-splicing-20261011-fortier2026-source-article: Methods 'SPiP benchmark dataset'; Results 'SPiP benchmark results'; Table 3 Version: PLOS One 21(5):e0348885, published 2026-05-13; PMC13170886 full-text XML Retrieved: 2026-10-11T21:37:04Z	not individually reviewed No individual claim review recorded Audit details Field: `attributes.comparison_group` Source artifact SHA-256: `dffe74cee7782cbdfdbc9423cf00f0a846b3d720b90b10e9732d6f768c485176` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Comparison title SpliceAI and its open-source reimplementations on six splice benchmarks (Fortier et al. 2026) Context-only references	Analyzing the performance of deep learning splice prediction algorithms (Fortier, Rudy and Scherer, PLOS One 2026) Original source ↗ rna-splicing-20261011-fortier2026-source-article: Methods 'SPiP benchmark dataset'; Results 'SPiP benchmark results'; Table 3 Version: PLOS One 21(5):e0348885, published 2026-05-13; PMC13170886 full-text XML Retrieved: 2026-10-11T21:37:04Z	not individually reviewed No individual claim review recorded Audit details Field: `attributes.comparison_title` Source artifact SHA-256: `dffe74cee7782cbdfdbc9423cf00f0a846b3d720b90b10e9732d6f768c485176` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Constraints 2 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; variant sets, labels and thresholds differ. Context-only references	Analyzing the performance of deep learning splice prediction algorithms (Fortier, Rudy and Scherer, PLOS One 2026) Original source ↗ rna-splicing-20261011-fortier2026-source-article: Methods 'SPiP benchmark dataset'; Results 'SPiP benchmark results'; Table 3 Version: PLOS One 21(5):e0348885, published 2026-05-13; PMC13170886 full-text XML Retrieved: 2026-10-11T21:37:04Z	not individually reviewed No individual claim review recorded Audit details Field: `attributes.constraints` Source artifact SHA-256: `dffe74cee7782cbdfdbc9423cf00f0a846b3d720b90b10e9732d6f768c485176` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Endpoint Sensitivity, specificity, F1 and balanced accuracy of SpliceAI, CI-SpliceAI, OpenSpliceAI and a legacy N-of-4 vote on the SPiP benchmark variant set (99,601 variants) Context-only references	Analyzing the performance of deep learning splice prediction algorithms (Fortier, Rudy and Scherer, PLOS One 2026) Original source ↗ rna-splicing-20261011-fortier2026-source-article: Methods 'SPiP benchmark dataset'; Results 'SPiP benchmark results'; Table 3 Version: PLOS One 21(5):e0348885, published 2026-05-13; PMC13170886 full-text XML Retrieved: 2026-10-11T21:37:04Z	not individually reviewed No individual claim review recorded Audit details Field: `attributes.endpoint` Source artifact SHA-256: `dffe74cee7782cbdfdbc9423cf00f0a846b3d720b90b10e9732d6f768c485176` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Claimed field links:assessed_by:rna-splicing-20261011-fortier2026-protocol-spip Context-only references	Analyzing the performance of deep learning splice prediction algorithms (Fortier, Rudy and Scherer, PLOS One 2026) Original source ↗ rna-splicing-20261011-fortier2026-source-article: Methods 'SPiP benchmark dataset'; Results 'SPiP benchmark results'; Table 3 Version: PLOS One 21(5):e0348885, published 2026-05-13; PMC13170886 full-text XML Retrieved: 2026-10-11T21:37:04Z	not individually reviewed No individual claim review recorded Audit details Field: `attributes.field` Source artifact SHA-256: `dffe74cee7782cbdfdbc9423cf00f0a846b3d720b90b10e9732d6f768c485176` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Headline metric balanced-accuracy Context-only references	Analyzing the performance of deep learning splice prediction algorithms (Fortier, Rudy and Scherer, PLOS One 2026) Original source ↗ rna-splicing-20261011-fortier2026-source-article: Methods 'SPiP benchmark dataset'; Results 'SPiP benchmark results'; Table 3 Version: PLOS One 21(5):e0348885, published 2026-05-13; PMC13170886 full-text XML Retrieved: 2026-10-11T21:37:04Z	not individually reviewed No individual claim review recorded Audit details Field: `attributes.headline_metric` Source artifact SHA-256: `dffe74cee7782cbdfdbc9423cf00f0a846b3d720b90b10e9732d6f768c485176` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Limitations 4 values Labels and variant sets are reused from earlier publications. CI-SpliceAI was trained on all human chromosomes, so no benchmark variant is held out from its training; ABCA4 lies on a test chromosome held out by both SpliceAI and OpenSpliceAI (Methods 'Technical overview of deep learning methods'; Discussion). No uncertainty intervals are printed; significance is from two-proportion Z-tests on accuracy in the Results. Independent of the SpliceAI, CI-SpliceAI and OpenSpliceAI developers; the authors' employer supplies the Legacy Ensemble software, so those rows are author_reported. Variant-level splicing effect, not pathogenicity or diagnostic yield; tissue context is not modelled. Context-only references	Analyzing the performance of deep learning splice prediction algorithms (Fortier, Rudy and Scherer, PLOS One 2026) Original source ↗ rna-splicing-20261011-fortier2026-source-article: Methods 'SPiP benchmark dataset'; Results 'SPiP benchmark results'; Table 3 Version: PLOS One 21(5):e0348885, published 2026-05-13; PMC13170886 full-text XML Retrieved: 2026-10-11T21:37:04Z	not individually reviewed No individual claim review recorded Audit details Field: `attributes.limitations` Source artifact SHA-256: `dffe74cee7782cbdfdbc9423cf00f0a846b3d720b90b10e9732d6f768c485176` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Pinned records 23 values record id rna-splicing-20261011-fortier2026-eval-spip-ci-spliceai fields status links attributes.origin attributes.comparison sha256 de341050f809e2b242d4c0f43b75ac82d312ae173f522d877f2b12616ebc9bca record id rna-splicing-20261011-fortier2026-eval-spip-legacy-ensemble fields status links attributes.origin attributes.comparison sha256 e445080cf7fa17ab291bf4fb157fa792456a32d0159ecc5a1a8c98b4b1baa0bb record id rna-splicing-20261011-fortier2026-eval-spip-openspliceai fields status links attributes.origin attributes.comparison sha256 50c16188f689eee0dbcfc7b6b55a9786be600e7e7836369017f0a6e354013568 record id rna-splicing-20261011-fortier2026-eval-spip-spliceai fields status links attributes.origin attributes.comparison sha256 0555f4d323df304bd87fc78e0f02aa3a7af26d801d8d7d050bd9de65fb49793d record id rna-splicing-20261011-fortier2026-protocol-spip fields status name description facets source_ids links attributes sha256 7f9b7f319a705291eadf779c78c490b47a26e5f22d3628fba96a79202f1216ba record id rna-splicing-20261011-fortier2026-result-spip-ci-spliceai-balanced-accuracy fields status attributes.metric attributes.metric_qualifier attributes.printed_value attributes.numeric_value sha256 6fdabc6259abfd92ba4f3688dc9ef320fd7b845309e98e513004f4a06669693c record id rna-splicing-20261011-fortier2026-result-spip-ci-spliceai-f1-score fields status attributes.metric attributes.metric_qualifier attributes.printed_value attributes.numeric_value sha256 0c051a3d4aedf444d55174e390b6b3ea5548c447d5f99e9aa59138b4e3d53116 record id rna-splicing-20261011-fortier2026-result-spip-ci-spliceai-recall fields status attributes.metric attributes.metric_qualifier attributes.printed_value attributes.numeric_value sha256 e9033e17716462dd93ca7fcdb08946240b96575e4e5b88ff48fb2b8230c669d9 record id rna-splicing-20261011-fortier2026-result-spip-ci-spliceai-specificity fields status attributes.metric attributes.metric_qualifier attributes.printed_value attributes.numeric_value sha256 9b44f016ba759ae4473fae46741ba0b751dd9810f8fc52d73dcc5f2cf851aa38 record id rna-splicing-20261011-fortier2026-result-spip-legacy-ensemble-balanced-accuracy fields status attributes.metric attributes.metric_qualifier attributes.printed_value attributes.numeric_value sha256 d60f17d8ac94b1e7af8e89ee1240fe7c53213e543803d2ff580f037cc0fda4a9 record id rna-splicing-20261011-fortier2026-result-spip-legacy-ensemble-f1-score fields status attributes.metric attributes.metric_qualifier attributes.printed_value attributes.numeric_value sha256 3a50ea4e7f1994b3146b5ad88cfc0815f50d9019874117d861e5745228ce0ce3 record id rna-splicing-20261011-fortier2026-result-spip-legacy-ensemble-recall fields status attributes.metric attributes.metric_qualifier attributes.printed_value attributes.numeric_value sha256 fad024226b84287b97ff3ef84e8dd965fec53073fafe2c5f65e91d88ee846746 record id rna-splicing-20261011-fortier2026-result-spip-legacy-ensemble-specificity fields status attributes.metric attributes.metric_qualifier attributes.printed_value attributes.numeric_value sha256 383b08f1fd79e02c6ca0d9a219d08461b5d6924d845ac9b1c2c67db4eaa9bda0 record id rna-splicing-20261011-fortier2026-result-spip-openspliceai-balanced-accuracy fields status attributes.metric attributes.metric_qualifier attributes.printed_value attributes.numeric_value sha256 823e13b2faeb7b0456337e2b92f7c50792c4e27a03e7a44e07c59e33f75a3e66 record id rna-splicing-20261011-fortier2026-result-spip-openspliceai-f1-score fields status attributes.metric attributes.metric_qualifier attributes.printed_value attributes.numeric_value sha256 e1c807046618f241a129eeaa70c38f0f5c8dec4e122dc54d3ea97ebcbaea9406 record id rna-splicing-20261011-fortier2026-result-spip-openspliceai-recall fields status attributes.metric attributes.metric_qualifier attributes.printed_value attributes.numeric_value sha256 737e0719088588abf3bfde5b72dc684d8f83309bac2666b8d39d7800524ff2c2 record id rna-splicing-20261011-fortier2026-result-spip-openspliceai-specificity fields status attributes.metric attributes.metric_qualifier attributes.printed_value attributes.numeric_value sha256 9b44f016ba759ae4473fae46741ba0b751dd9810f8fc52d73dcc5f2cf851aa38 record id rna-splicing-20261011-fortier2026-result-spip-spliceai-balanced-accuracy fields status attributes.metric attributes.metric_qualifier attributes.printed_value attributes.numeric_value sha256 52f252327a6fdad5a3d4aeff29a3fb5f04bcb34854261e12742dad7efb935302 record id rna-splicing-20261011-fortier2026-result-spip-spliceai-f1-score fields status attributes.metric attributes.metric_qualifier attributes.printed_value attributes.numeric_value sha256 acf956306adc1a503e9b241d7256a6f3b621c7ec5069dea3c495311a9f07b572 record id rna-splicing-20261011-fortier2026-result-spip-spliceai-recall fields status attributes.metric attributes.metric_qualifier attributes.printed_value attributes.numeric_value sha256 096224d9845f1806f2b08377c0ea74c6d172899c56beede444dc38c1f7625c07 record id rna-splicing-20261011-fortier2026-result-spip-spliceai-specificity fields status attributes.metric attributes.metric_qualifier attributes.printed_value attributes.numeric_value sha256 9b44f016ba759ae4473fae46741ba0b751dd9810f8fc52d73dcc5f2cf851aa38 record id rna-splicing-20261011-fortier2026-source-article fields status attributes.artifact_sha256 sha256 f632aac0a971c54f908ad18bc9965d498c05b69bd07552d9915807db55a22233 record id use-case-patient-rna-splicing-validation fields status name description facets attributes.question attributes.decision attributes.inputs attributes.output attributes.exclusions attributes.setting attributes.clinical_scope attributes.intended_users sha256 b85cad56e15fbfad66a2e70c3b193ed56c464e5e44b62a19b12f391e409ec897 Context-only references	Analyzing the performance of deep learning splice prediction algorithms (Fortier, Rudy and Scherer, PLOS One 2026) Original source ↗ rna-splicing-20261011-fortier2026-source-article: Methods 'SPiP benchmark dataset'; Results 'SPiP benchmark results'; Table 3 Version: PLOS One 21(5):e0348885, published 2026-05-13; PMC13170886 full-text XML Retrieved: 2026-10-11T21:37:04Z	not individually reviewed No individual claim review recorded Audit details Field: `attributes.pins` Source artifact SHA-256: `dffe74cee7782cbdfdbc9423cf00f0a846b3d720b90b10e9732d6f768c485176` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Rationale Proxy: DNA-based splice predictors scored against experimentally established splicing outcomes, the sequence-classification kind of evidence the use case keeps separate from patient-RNA recovery; inputs are variants, not patient RNA-seq. Context-only references	Analyzing the performance of deep learning splice prediction algorithms (Fortier, Rudy and Scherer, PLOS One 2026) Original source ↗ rna-splicing-20261011-fortier2026-source-article: Methods 'SPiP benchmark dataset'; Results 'SPiP benchmark results'; Table 3 Version: PLOS One 21(5):e0348885, published 2026-05-13; PMC13170886 full-text XML Retrieved: 2026-10-11T21:37:04Z	not individually reviewed No individual claim review recorded Audit details Field: `attributes.rationale` Source artifact SHA-256: `dffe74cee7782cbdfdbc9423cf00f0a846b3d720b90b10e9732d6f768c485176` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact

How to read the evidence

Sources and history

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

1 source record and release history

Analyzing the performance of deep learning splice prediction algorithms (Fortier, Rudy and Scherer, PLOS One 2026) · Original source · PLOS One 21(5):e0348885, published 2026-05-13; PMC13170886 full-text XML

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Technical metadata and extraction receipts

Stable ID: use-case-mapping-rna-splicing-20261011-fortier2026-spip

field: links:assessed_by:rna-splicing-20261011-fortier2026-protocol-spip
value: rna-splicing-20261011-fortier2026-protocol-spip
relevance: proxy
endpoint: Sensitivity, specificity, F1 and balanced accuracy of SpliceAI, CI-SpliceAI, OpenSpliceAI and a legacy N-of-4 vote on the SPiP benchmark variant set (99,601 variants)
rationale: Proxy: DNA-based splice predictors scored against experimentally established splicing outcomes, the sequence-classification kind of evidence the use case keeps separate from patient-RNA recovery; inputs are variants, not patient RNA-seq.
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; variant sets, labels and thresholds differ.
limitations: Labels and variant sets are reused from earlier publications. CI-SpliceAI was trained on all human chromosomes, so no benchmark variant is held out from its training; ABCA4 lies on a test chromosome held out by both SpliceAI and OpenSpliceAI (Methods 'Technical overview of deep learning methods'; Discussion).; No uncertainty intervals are printed; significance is from two-proportion Z-tests on accuracy in the Results.; Independent of the SpliceAI, CI-SpliceAI and OpenSpliceAI developers; the authors' employer supplies the Legacy Ensemble software, so those rows are author_reported.; Variant-level splicing effect, not pathogenicity or diagnostic yield; tissue context is not modelled.
citation locators: source id: rna-splicing-20261011-fortier2026-source-article; locator: Methods 'SPiP benchmark dataset'; Results 'SPiP benchmark results'; Table 3
source locator: rna-splicing-20261011-fortier2026-source-article: Methods 'SPiP benchmark dataset'; Results 'SPiP benchmark results'; Table 3
headline metric: balanced-accuracy
comparison group: fortier2026-spliceai-reimplementations
comparison title: SpliceAI and its open-source reimplementations on six splice benchmarks (Fortier et al. 2026)
stratum label: SPiP benchmark variant set (99,601 variants)
stratum order: 3
reason: Recorded from the 2026-10-11 use-case literature pass (data/omics/use-case-coverage-rna-splicing-20261011-fortier2026). Independently reviewed in docs/reviews/use-cases/splicing-cnv-use-cases-2026-10-12.md.
review: method: source-hash-verification; independent-cell-check; automated-source-review; scope-review; reviewer: claude; reviewer note: Independent Claude review agent reviewer-scnv; did not extract this batch; no human review claimed; date: 2026-10-12; artifact sha256: dffe74cee7782cbdfdbc9423cf00f0a846b3d720b90b10e9732d6f768c485176; retrieval url: https://www.ebi.ac.uk/europepmc/webservices/rest/PMC13170886/fullTextXML; method note: Drafted by the collector agent uc-splicing-cnv from the pinned source.; note: Checked by reviewer-scnv against the pinned source; verdict in docs/reviews/use-cases/splicing-cnv-use-cases-2026-10-12.md and in this batch's review.md.
reviewed evaluations: rna-splicing-20261011-fortier2026-eval-spip-ci-spliceai; rna-splicing-20261011-fortier2026-eval-spip-legacy-ensemble; rna-splicing-20261011-fortier2026-eval-spip-openspliceai; rna-splicing-20261011-fortier2026-eval-spip-spliceai
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