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
Metaregistry PhylomeDB

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.

Registry Name Registry Metaprefix External Prefix Curate
BioContext biocontext PHYLOMEDB
FAIRSharing FAIRSharing logo fairsharing FAIRsharing.7hxxc4
Integbio Integbio logo integbio nbdc01764
Identifiers.org Identifiers.org logo miriam phylomedb
N2T Name-to-Thing logo n2t phylomedb
Prefix Commons Prefix Commons logo prefixcommons phylomedb
UniProt UniProt Cross-ref database logo uniprot DB-0144
Providers

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.

Name Metaprefix URI
PhylomeDB phylomedb http://phylomedb.org/?seqid=Phy000CLXM_RAT
Bioregistry bioregistry https://bioregistry.io/phylomedb:Phy000CLXM_RAT
Identifiers.org miriam https://identifiers.org/phylomedb:Phy000CLXM_RAT
Name-to-Thing n2t https://n2t.net/phylomedb:Phy000CLXM_RAT
Extra Providers

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

Code Name URL
bio2rdf Bio2RDF http://bio2rdf.org/phylomedb:Phy000CLXM_RAT