PhylomeDB is a database of complete phylomes derived for different genomes within a specific taxonomic range. It provides alignments, phylogentic trees and tree-based orthology predictions for all encoded proteins.

Prefix

phylomedb

Keywords

genome life science phylogenetics phylogenomics phylogeny protein taxonomy

Links

Homepage

Contact

Toni Gabaldón   0000-0003-0019-1735   tgabaldon

Pattern for Local Unique Identifiers

Local identifiers in PhylomeDB should match this regular expression:
^\w+$

Example Local Unique Identifier

Phy000CLXM_RAT   Resolve

Pattern for CURIES

Compact URIs (CURIEs) constructed from PhylomeDB should match this regular expression:
^phylomedb:\w+$

Example CURIE

phylomedb:Phy000CLXM_RAT

Publications

• 2022 PhylomeDB V5: an expanding repository for genome-wide catalogues of annotated gene phylogenies
• 2013 PhylomeDB v4: zooming into the plurality of evolutionary histories of a genome
• 2010 PhylomeDB v3.0: an expanding repository of genome-wide collections of trees, alignments and phylogeny-based orthology and paralogy predictions
• 2007 PhylomeDB: a database for genome-wide collections of gene phylogenies

The metaregistry provides mappings between the Bioregistry and other registries. There are 7 mappings to external registries for this resource with 4 unique external prefixes.

A provider turns a local unique identifiers from a resource into a URI. Many providers are also resolvable as URLs (i.e., they can be used in a web browser).

The local unique identifier Phy000CLXM_RAT is used to demonstrate the providers available for PhylomeDB. A guide for curating additional providers can be found here.

Additional providers curated in the Bioregistry are listed here. These are typically inherited from Identifiers.org or Prefix Commons, and need extra curation.