G E N E   O N T O L O G Y
The following example explains how to set-up an archive for the daily release of the daily Gene Ontology Database release in RDF-XML format.
Files
For this example you need the following files:
GO.keys The key specification needed when merging theGene Ontology RDF-XML versions into an archive.
Commands
The first command creates a new archive named GO using the above key specification. Remember to modify the path of the DEFAULT_SCHEMA depending on where you stored GO.keys on your local machine. The data for the GO archive will be stored in a directory named /home/archive/go and the archive data file will be compressed using gzip.
CREATE ARCHIVE GO OF XML HAVING PROPERTIES
DIRECTORY=/home/archive/go,
DEFAULT_SCHEMA=GO.keys,
COMPRESSION=GZIP
Should you later decide to rather store the data in an uncompressed format you can alter the archive properties accordingly using:
ALTER ARCHIVE GO SET
COMPRESSION=NONE
To merge the current releases of the Gene Ontology Database into the archive use the following command:
INSERT INTO GO FROM TYPE XML
XML_FILENAME=http://archive.geneontology.org/latest-termdb/go_daily-termdb.rdf-xml.gz,
COMPRESSED=true
You may want to create a data source for the daily Gene Ontology RDF-XML file. Such a data source is basically a shortcut for the properties in the above INSERT INTO-statement:
CREATE DATA SOURCE GO_RDF_DAILY OF XML HAVING PROPERTIES
XML_FILENAME=http://archive.geneontology.org/latest-termdb/go_daily-termdb.rdf-xml.gz,
COMPRESSED=true
The data source GO_RDF_DAILY can now be used to merge the current file on the Web into archive GO:
INSERT INTO GO FROM SOURCE GO_RDF_DAILY
The following query is an example GO query that retrieves all GO terms that are DNA replication checkpoints (GO accession 0000076):
SELECT /go/RDF/term
FROM GO
WHERE /go/RDF/term/is_a/resource MATCHES 'GO:0000076'