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Update Taxonomy and Pathway Information

jcvi edited this page · 3 revisions

The current versions of the SQLite and MySQL databases contain the following lookup data and version

KEGG 2011-09-01
GENE ONTOLOGY 2011-09-05
NCBI TAXONOMY 2011-09-30

To update this information, execute the metarep_update_database.pl under
the scripts/perl directory
https://github.com/jcvi/METAREP/blob/master/scripts/perl/metarep_update_database.pl

use the --update_db argument (default=123) to specify which information should to updated
1 KEGG
2 NCBI_TAXONOMY
3 GO

Multiple databases can be specified, e.g. —update_db=23 to update the NCBI taxonomy and GO.
1=KEGG requires a LEGG license and local KEGG snapshot.The following KEGG directories and files are being used
genes/fasta/genes.pep
genes/organisms
genes/ko/ko
ligand/enzyme/enzyme [enzyme information, lowest level]
genes/genome/genome
brite/ko/ko01000.keg [enzyme hierarchy]
brite/ko/ko00001.keg [ko pathways]
pathway/ec/ec.list [ec pathways]

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