OrthoDB in 2020: evolutionary and functional annotations of orthologs.

Evgeny M Zdobnov,Dmitry Kuznetsov,Matthew Berkeley,Mosè Manni,Fredrik Tegenfeldt,Evgenia V Kriventseva

doi:10.1093/nar/gkaa1009

Abstract

OrthoDB provides evolutionary and functional annotations of orthologs, inferred for a vast number of available organisms. OrthoDB is leading in the coverage and genomic diversity sampling of Eukaryotes, Prokaryotes and Viruses, and the sampling of Bacteria is further set to increase three-fold. The user interface has been enhanced in response to the massive growth in data. OrthoDB provides three views on the data: (i) a list of orthologous groups related to a user query, which are now arranged to visualize their hierarchical relations, (ii) a detailed view of an orthologous group, now featuring a Sankey diagram to facilitate navigation between the levels of orthology, from more finely-resolved to more general groups of orthologs, as well as an arrangement of orthologs into an interactive organism taxonomy structure, and (iii) we added a gene-centric view, showing the gene functional annotations and the pair-wise orthologs in example species. The OrthoDB standalone software for delineation of orthologs, Orthologer, is freely available. Online BUSCO assessments and mapping to OrthoDB of user-uploaded data enable interactive exploration of related annotations and generation of comparative charts. OrthoDB strives to predict orthologs from the broadest coverage of species, as well as to extensively collate available functional annotations, and to compute evolutionary annotations such as evolutionary rate and phyletic profile. OrthoDB data can be assessed via SPARQL RDF, REST API, downloaded or browsed online from https://orthodb.org.

Highlights

OrthoDB is a leading resource of evolutionary and functional annotations of orthologs [1]
OrthoDB provides three views on the data: (i) a list of orthologous groups related to a user query, which are arranged to visualize their hierarchical relations, (ii) a detailed view of an orthologous group, featuring a Sankey diagram to facilitate navigation between the levels of orthology, from more finely-resolved to more general groups of orthologs, as well as an arrangement of orthologs into an interactive organism taxonomy structure, and (iii) we added a gene-centric view, showing the gene functional annotations and the pair-wise orthologs in example species
Coined for a pair of species, the term orthologs referred to genes that derive from a single gene in the last common ancestor (LCA) of the species [4]

Summary

Introduction

OrthoDB is a leading resource of evolutionary and functional annotations of orthologs [1]. OrthoDB provides evolutionary and functional annotations of orthologs, inferred for a vast number of available organisms. OrthoDB provides three views on the data: (i) a list of orthologous groups related to a user query, which are arranged to visualize their hierarchical relations, (ii) a detailed view of an orthologous group, featuring a Sankey diagram to facilitate navigation between the levels of orthology, from more finely-resolved to more general groups of orthologs, as well as an arrangement of orthologs into an interactive organism taxonomy structure, and (iii) we added a gene-centric view, showing the gene functional annotations and the pair-wise orthologs in example species.

Results

Conclusion