is a Data Source.
OrthoDB is a comprehensive database of orthologous protein-coding genes across multiple species, providing evolutionary and functional annotations of orthologous groups.
biological systems, organisms
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| ID | Name | URL | Category | Format | Description |
|---|---|---|---|---|---|
| orthodb.site | OrthoDB Web Interface | www.orthodb.org | GraphicalInterface | ❔ | Web interface for exploring OrthoDB data |
| orthodb.api.sparql | OrthoDB SPARQL Endpoint | sparql.orthodb.org | ProgrammingInterface | ❔ | SPARQL endpoint for querying OrthoDB ... |
| orthodb.api.rest | OrthoDB API | api | ProgrammingInterface | ❔ | RESTful API for programmatic access t... |
| orthodb.species | OrthoDB Species Data | odb12v1_species.tab.gz (629.3 KB) | Product | tsv | Tab-separated file with species infor... |
| orthodb.ogs | OrthoDB Orthologous Groups | odb12v1_OGs.tab.gz (138.5 MB) | Product | tsv | Tab-separated file with information a... |
| orthodb.og2genes | OrthoDB OG to Genes Mapping | odb12v1_OG2genes.tab.gz (4.6 GB) | MappingProduct | tsv | Tab-separated file mapping orthologou... |
| orthodb.genes | OrthoDB Genes Data | odb12v1_genes.tab.gz (4.5 GB) | Product | tsv | Tab-separated file with gene informat... |
| orthodb.gene_xrefs | OrthoDB Gene Cross-references | odb12v1_gene_xrefs.tab.gz (4.4 GB) | MappingProduct | tsv | Tab-separated file with gene cross-re... |
| orthodb.og_xrefs | OrthoDB OG Functional Annotations | odb12v1_OG_xrefs.tab.gz (333.1 MB) | Product | tsv | Tab-separated file with orthologous g... |
| orthodb.aa_fasta | OrthoDB Protein Sequences | odb12v1_aa_fasta.gz (36.3 GB) | Product | fasta | FASTA-formatted amino acid sequences ... |
| orthodb.cds_fasta | OrthoDB CDS Sequences | odb12v1_cds_fasta.gz (53.6 GB) | Product | fasta | FASTA-formatted coding sequences for ... |
OrthoDB is a comprehensive database of orthologous protein-coding genes across multiple species with a hierarchical catalog of orthologs. It provides evolutionary and functional annotations of orthologous groups at various taxonomic levels, covering Eukaryotes, Prokaryotes, and Viruses.
The database contains information for more than 31,000 species, including:
OrthoDB offers several key features:
The database is widely used in comparative genomics, molecular evolution studies, functional annotation, and gene family evolution analysis. It serves as a foundation for the popular BUSCO tool (Benchmarking Universal Single-Copy Orthologs) for genome assembly and annotation assessment.
OrthoDB is maintained by the Zdobnov Lab at the University of Geneva and the Swiss Institute of Bioinformatics (SIB), with regular updates incorporating new genome sequences and improving data quality. Access is provided through a user-friendly web interface, a SPARQL endpoint for semantic web queries, a RESTful API for programmatic access, and bulk downloads in various formats.
Created: May 07, 2025 | Last modified: December 07, 2025