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.

Missing Contact
Pattern for Local Unique Identifiers

Local identifiers in PhylomeDB should match this regular expression:

Example Local Unique Identifier
Phy000CLXM_RAT   Resolve
Pattern for CURIES

Compact URIs (CURIEs) constructed from PhylomeDB should match this regular expression:

Example CURIE
Metaregistry PhylomeDB

The metaregistry provides mappings between the Bioregistry and other registries. There are 6 mappings to external registries for phylomedb with 3 unique external prefixes.

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

Providers are various services that resolve CURIEs to URLs. The example CURIE phylomedb:Phy000CLXM_RAT is used to demonstrate the provides available for phylomedb. Generation of OLS and BioPortal URLs requires additional programmatic logic beyond string formatting.

Name Metaprefix URI
PhylomeDB phylomedb
Bioregistry bioregistry miriam
Name-to-Thing n2t