Ensembl Genomes Fungi ID history converter

Ensembl Genomes Fungi ID history converter converts Ensembl identifiers from older Ensembl releases to their current equivalents for fungal genomes to maintain continuity in genomic analyses.

Key Features:

• ID Conversion: Converts sets of Ensembl IDs from previous releases into updated identifiers for fungal genomes.
• Ensembl Database Integration: Accesses Ensembl Genomes databases and annotations covering 87 fungal species to map identifiers.
• REST API Integration: Uses the Ensembl REST API to perform large-scale ID conversion requests.
• BioMart Access: Retrieves regulatory and annotation data via BioMart to support identifier mapping and regulatory queries.
• Public Data Provenance: Performs data transformations using publicly available Ensembl resources to support reproducibility.

Scientific Applications:

• Genomic Research Continuity: Enables integration of historical fungal genomic datasets with current assemblies for downstream analyses.
• Data Consistency: Standardizes identifiers across Ensembl releases to support longitudinal studies and meta-analyses.
• Comparative Genomics: Facilitates accurate cross-species comparisons by standardizing identifiers among fungal species.
• Genome Annotation Updates: Supports updating genome annotations in fungal genomes to align with current Ensembl annotations.
• Phenotypic and Variant Studies: Allows variant and phenotype analyses to be updated to current gene identifiers.
• Regulatory Data Exploration: Supports retrieval and comparison of regulatory data for fungal genomes via BioMart.

Methodology:

The tool accesses Ensembl Genomes databases and annotations, employs the Ensembl REST API for large-scale ID conversion requests, and uses BioMart and other publicly available Ensembl resources for regulatory and annotation data retrieval.