### UPDATE GO DATABASE (DONE 04-11-24)
# Adopted from an earlier process Gill did for his private go database
# Update GO database (2005-07-26, hartera)
# Download the terms and make the database.

# Added symlink for the build dir:  /cluster/data/geneOntology
# so store1 doesn't need to be directly referenced (2007-01-10 kate)

    ssh hgwdev
        
    mkdir /cluster/data/geneOntology/20041124
    cd /cluster/data/geneOntology/20041124

    wget --timestamping http://www.godatabase.org/dev/database/archive/latest/go_200411-assocdb-data.gz

    hgsql mysql <<end
    create database go041124;
    end
    zcat go_*data.gz | hgsql go041124

# Download the associations
    wget --timestamping ftp://ftp.geneontology.org/pub/go/gene-associations/gene_association.goa_uniprot.gz

# Note no specific taxon specified, this will import everything
    zcat gene_association.goa_uniprot.gz | hgGoAssociation go041124 goaPart stdin 
# Passed 4502016 of 5291097 of 5291097, 85.09%

# Ask sys-admin to point go to go041124

# Asked sys-admin to rename database to go041115 and point go to the new name -- kuhn 12-06-04

# REBUILD GO WITH LATEST VERSION (DONE, 2005-07-26, hartera)
# Re-made GO database as above, only the dates in names have changed
# so downloads are in /cluster/store1/geneOntology/20050726 and the database
# is called go050726. 
# Download file of terms is go_200507-assocdb-data.gz (July 18, 2005)
# Download file of associations is gene_association.goa_uniprot.gz 
# (June 16, 2005)
# hgGoAssociation:
# Passed 5515470 of 6413534 of 6413534, 86.00% 
##########################################################################
# UPDATE GO DATABASE (DONE, 2006-12-20, Fan)

# UPDATE GO DATABASE
# Download the terms and make the database.
ssh hgwdev
mkdir /cluster/store1/geneOntology/20061219
cd /cluster/store1/geneOntology/20061219

wget --timestamping
http://www.godatabase.org/dev/database/archive/latest/go_200612-assocdb-data.gz

hgsql mysql <<end
create database go061219;
end
zcat go_*data.gz | sed -e 's/ENGINE=MyISAM DEFAULT
CHARSET=latin1/TYPE=MyISAM/g' >j.tmp
hgsql go061219 <j.tmp
rm j.tmp

wget --timestamping
ftp://ftp.geneontology.org/pub/go/gene-associations/gene_association.goa_uniprot.gz

# The format of gene_association.goa_uniprot.gz changed, there is comment
# lines at the head now.
# Updated hgGoAssociation.c to skip those initial comment lines.

zcat gene_association.goa_uniprot.gz\
|/cluster/home/fanhsu/bin/x86_64/hgGoAssociation go061219 goaPart stdin
# Passed 9049274 of 10512956 of 10512956, 86.08%

# Ask sys-admin to switch the database pointer go to point to go061219.
##########################################################################
### UPDATE GO DATABASE (DONE 07-01-16, Fan)

# UPDATE GO DATABASE
# Download the terms and make the database.
ssh hgwdev
mkdir /cluster/store1/geneOntology/20070111
cd /cluster/store1/geneOntology/20070111

wget --timestamping \
http://www.godatabase.org/dev/database/archive/latest/go_200701-assocdb-data.gz

hgsql mysql -e 'create database go070111'

zcat go_*data.gz | sed -e 's/ENGINE=MyISAM DEFAULT CHARSET=latin1/TYPE=MyISAM/g' >j.tmp
hgsql go070111 <j.tmp
rm j.tmp

# Please note the new place to get gene_association.goa_uniprot.gz
wget --timestamping \
ftp://ftp.ebi.ac.uk/pub/databases/GO/goa/UNIPROT/gene_association.goa_uniprot.gz

zcat gene_association.goa_uniprot.gz\
|hgGoAssociation go070111 goaPart stdin

# Passed 10341476 of 12083865 of 12083865, 85.58%

# angie suggests running this at the end (it only make goaPart.as):
# makeTableDescriptions go hg/lib/goaPart.as (BK 2007-07-05)

# Ask sys-admin to switch the database pointer go to point to go061219.

##########################################################################
### UPDATE GO DATABASE (DONE 1/30/08, Fan)

# UPDATE GO DATABASE
# Download the terms and make the database.
ssh hgwdev
mkdir /cluster/store1/geneOntology/20080130
cd /cluster/store1/geneOntology/20080130

wget --timestamping
http://archive.geneontology.org/latest/go_200801-assocdb-data.gz

hgsql mysql -e 'create database go080130'

zcat go_*data.gz | sed -e 's/ENGINE=MyISAM DEFAULT CHARSET=latin1/TYPE=MyISAM/g' >j.tmp
hgsql go080130 <j.tmp
rm j.tmp

# Please note the new place to get gene_association.goa_uniprot.gz
wget --timestamping \
ftp://ftp.ebi.ac.uk/pub/databases/GO/goa/UNIPROT/gene_association.goa_uniprot.gz

zcat gene_association.goa_uniprot.gz\
|hgGoAssociation go080130 goaPart stdin

Passed 16890026 of 25763098 of 25763098, 65.56%

# Ask sys-admin to switch the database pointer go to point to go080130.
##########################################################################