Functional annotations
======

This directory hosts functional annotations of the protein sequences in
individual genomes (see proteins/).

 - With the exceptions of UniRef and MetaCyc, all annotation systems uses
   UniRef as a proxy.

Typical filename patterns:

 - x.map: Mapping of protein IDs (UniRef and MetaCyc) or UniRef entries (all
   others) to entries of X in a specific system.
   * Note: Multiple targets per line (tab-delimited) are allowed.
 - x.name or x_name.txt: Mapping of entries to descriptive names.
 - x-to-y.map: Mapping of entries of X to entries of Y within the same system.

Main annotation systems:

 - uniref: Annotation by UniRef release 2019_07 (UniRef90 then UniRef50).
   * https://www.uniprot.org/help/uniref

 - metacyc: Annotation by MetaCyc release 23.0, including proteins and higher
   hierarchies, such as genes, reactions, compounds, and pathways.
   * https://metacyc.org/

 - go: Mapping of UniRef entries to Gene Ontology (GO) entries, divided into
   three categories: molecular function, biological process, and cellular
   component.
   * http://geneontology.org/

Additional annotation systems:

 - kegg: Mapping of UniRef entries to KEGG Ontology (KO) entries.
   * https://www.genome.jp/kegg/

 - eggnog: Mapping of UniRef entries to EggNOG entries.
   * http://eggnog.embl.de/

 - orthodb: Mapping of UniRef entries to OrthoDB entries.
   * https://www.orthodb.org/

 - refseq: Mapping of UniRef entries to NCBI RefSeq protein IDs.
   * https://www.ncbi.nlm.nih.gov/refseq/