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ZENODO
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Dataset . 2025
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ZENODO
Dataset . 2025
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PhEval: A Framework for Evaluating Phenotype-Driven Variant and Gene Prioritisation Algorithms

Authors: Bridges, Yasemin; de Souza, Vinicius; Cortes, Katherina; Haendel, Melissa; Harris, Nomi L; Korn, Daniel; Marinakis, Nikolaos; +8 Authors

PhEval: A Framework for Evaluating Phenotype-Driven Variant and Gene Prioritisation Algorithms

Abstract

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: 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. 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.

  • BIP!
    Impact byBIP!
    selected citations
    These citations are derived from selected sources.
    This is an alternative to the "Influence" indicator, which also reflects the overall/total impact of an article in the research community at large, based on the underlying citation network (diachronically).
    0
    popularity
    This indicator reflects the "current" impact/attention (the "hype") of an article in the research community at large, based on the underlying citation network.
    Average
    influence
    This indicator reflects the overall/total impact of an article in the research community at large, based on the underlying citation network (diachronically).
    Average
    impulse
    This indicator reflects the initial momentum of an article directly after its publication, based on the underlying citation network.
    Average
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selected citations
These citations are derived from selected sources.
This is an alternative to the "Influence" indicator, which also reflects the overall/total impact of an article in the research community at large, based on the underlying citation network (diachronically).
BIP!Citations provided by BIP!
popularity
This indicator reflects the "current" impact/attention (the "hype") of an article in the research community at large, based on the underlying citation network.
BIP!Popularity provided by BIP!
influence
This indicator reflects the overall/total impact of an article in the research community at large, based on the underlying citation network (diachronically).
BIP!Influence provided by BIP!
impulse
This indicator reflects the initial momentum of an article directly after its publication, based on the underlying citation network.
BIP!Impulse provided by BIP!
0
Average
Average
Average