OMArk: Quality Assessment Data for Gene Repertoire Annotation

Supplementary data for the OMArk paper includes simulated proteomes with errors, UniProt Reference Proteomes from 2021, and Ensembl Metazoa proteomes from versions 52 and 54. The dataset was created by Yannis Nevers at the University of Lausanne and contains archives for OMAmer databases, OMArk results, and BUSCO assessments. It supports the evaluation of the OMArk tool for assessing the completeness and contamination of proteome annotations.

Use Cases

• Benchmarking proteome quality assessment tools based on simulated proteomes with introduced errors.
• Analyzing bias in annotation tools based on source proteomes from Ensembl and NCBI.
• Investigating gene repertoire changes between proteome versions based on Ensembl Metazoa assembly data.
• Validating contamination detection algorithms using the provided reference proteome experiment data.

Strengths

• Includes simulated proteomes with artificially introduced errors and contaminants for controlled performance testing.
• Contains quality assessments for the UniProt Reference Proteomes (2021_04 release).
• Provides comparative results for Ensembl Metazoa proteomes across two different versions (52 and 54).

Limitations

• Row count and total dataset size are unknown, which may limit suitability assessment.
• Column-level documentation is absent; field semantics must be inferred after download.
• Last update date is unknown; freshness unverified.

Provenance

Source

University of Lausanne, associated with the OMArk research paper.

Collection Method

Derived from public databases including OMA (November 2022 Release), UniProt Reference Proteomes, and Ensembl Metazoa, with simulated data generation.

Time Range

Reference data includes UniProt release from 2021 and OMA database from November 2022.