Published January 17, 2025
| Version v3
Dataset
Open
PhEval: A Framework for Evaluating Phenotype-Driven Variant and Gene Prioritisation Algorithms
Authors/Creators
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1.
Queen Mary University of London
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2.
European Bioinformatics Institute
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3.
University of Colorado Anschutz Medical Campus
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4.
University of North Carolina Chapel Hill
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5.
Lawrence Berkeley National Laboratory
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6.
National and Kapodistrian University of Athens
- 7. Semanticly
- 8. Wellcome Trust Sanger Institute
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9.
Charité - Universitätsmedizin Berlin
Description
This repository contains the complete corpora and PhEval processed TSV results referenced in the study "PhEval: A Framework for Evaluating Phenotype-Driven Variant and Gene Prioritisation Algorithms". The provided materials are integral to the benchmarking process and include:
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Phenopacket Corpora:
- Phenotype-Only Dataset: Phenopacket store containing phenotypic data without genomic or structural variant information.
- Phenotype and Genomic Variant Dataset: Phenopacket store with phenotypic data and associated genomic variants.
- Phenotype and Structural Variant Dataset: Structural variant corpus combining phenotypic data with structural variant information.
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PhEval TSV Results:
- TSV files summarizing the outcomes of nine different benchmarking configurations tested in the paper, including:
- Phenotype-Only Tools: Exomiser (phenotype-only mode), Phen2Gene, PhenoGenius, and GADO.
- Phenotype and Genomic Variant Tools: Exomiser (with VCF), LIRICAL, and AI-MARRVEL.
- Structural Variant Tools: Exomiser and SvAnna.
- TSV files summarizing the outcomes of nine different benchmarking configurations tested in the paper, including: