Ensembl Genomes Plants ID history converter

Ensembl Genomes Plants ID history converter converts historical Ensembl Gene IDs for plant genomes into their current Ensembl release equivalents to maintain consistent gene identifiers across releases.

Key Features:

• ID Conversion: Maps historical Ensembl Gene IDs to current release identifiers for plant genomes.
• Integration with Ensembl Resources: Uses Ensembl databases, including main and early access sites and annotations covering 87 species, as data sources.
• Support for Multiple Species: Targets plant genomes while leveraging Ensembl annotations for other model organisms such as human, mouse, zebrafish, and rat.
• Data Updates and Annotations: Aligns ID mappings with the latest genome assemblies and gene annotations from Ensembl.
• REST API Integration: Performs conversions via the Ensembl REST API to support larger-scale ID mapping.
• Regulatory Data Access: Retrieves regulatory annotations through BioMart to associate regulatory data with mapped gene IDs.

Scientific Applications:

• Genomic Research: Enables longitudinal studies by preserving consistent gene identifiers across Ensembl release versions.
• Comparative Genomics: Supports cross-species and within-plant comparative analyses by providing accurate ID mappings.
• Functional Genomics: Facilitates studies of gene function and regulation by maintaining identifier continuity through successive Ensembl releases.

Methodology:

Accesses Ensembl databases containing historical and current gene annotations; employs algorithms to map old IDs to new IDs based on Ensembl genomic data; and uses the Ensembl REST API and BioMart services for data retrieval and conversions.