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bellerbrock/Ontology Update example

Last active March 17, 2021 20:51
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Ontology Update example
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Ontology Update example
# Start by cloning or pulling the latest updates in the ibp-sweetpotato-traits and Chado repos
git clone https://github.com/Planteome/ibp-sweetpotato-traits.git
git clone https://github.com/GMOD/Chado.git
# Load the ontology terms, then update cvterm paths. It may be necessary to add to Chado modules to perl5lib: export PERL5LIB=/home/production/cxgn/Chado/chado/lib:$PERL5LIB
perl Chado/chado/bin/gmod_load_cvterms.pl -H db4.sgn.cornell.edu -D sandbox_batatabase -s CO_331 -d Pg -r postgres -p <PASSWORD> -n SweetpotatoTrait -u -v ibp-sweetpotato-traits/sweetpotato_trait.obo
perl Chado/chado/bin/gmod_make_cvtermpath.pl -H db4.sgn.cornell.edu -D sandbox_batatabase -d Pg -u postgres -p <PASSWORD> -c SweetpotatoTrait
# Example for other ontologies
perl Chado/chado/bin/gmod_load_cvterms.pl -H breedbase_db -D breedbase -s SGNSTAT -d Pg -r postgres -p postgres -n SGNStatistics_ontology -u -v sgn/ontology/cxgn_statistics.obo
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