NAME

       load_cvterms.pl - compares which terms are new in the file compared to the database and
       inserts them

SYNOPSIS

       Usage: perl load_cvterms.pl -H dbhost -D dbname [-vdntuFo] file

       parameters

       -g      GMOD database profile name (can provide host, DB name, password, username, and
               driver) Default: 'default'

       -s      database name for linking (must be in db table, e.g. GO )

       -n      controlled vocabulary name (e.g 'biological_process').  optional. If not given,
               terms of all namespaces related with database name will be handled.

       -F      File format. Can be obo or go_flat and others supported by Bio::OntologyIO.
               Default: obo

       -u      update all the terms. Without -u, the terms in the database won't be updated to
               the contents of the file, in terms of definitions, etc. New terms will still be
               added.

       -v      verbose output

       -o      outfile for writing errors and verbose messages (optional)

       -t      trial mode. Don't perform any store operations at all.  (trial mode cannot test
               inserting associated data for new terms)

       The following options are required if not using GMOD profile

       -H   hostname for database [required if -p isn't used]

       -D   database name [required if -p isn't used]

       -p   password (if you need to provide a password to connect to your db)

       -r   username (if you need to provide a username to connect to your database)

       -d   driver name (e.g. 'Pg' for postgres). Driver name can be provided in gmod_config

       The script parses the ontology in the file and the corresponding ontology in the database,
       if present. It compares which terms are new in the file compared to the database and
       inserts them, and compares all the relationships that are new and inserts them. It removes
       the relationships that were not specified in the file from the database. It never removes
       a term entry from the database.

       This script works with Chado schema (see gmod.org) and accesse the following tables:

       db
       dbxref
       cv
       cvterm
       cvterm_relationship
       cvtermsynonym
       cvterm_dbxref
       cvtermprop

       Terms that are in the database but not in the file are set to is_obsolete=1.  All the
       terms that are present in the database are updated (if using -u option) to reflect the
       term definitions that are in the file.  New terms that are in the file but not in the
       database are stored.  The following data are associated with each term insert/update:

       Term name
       Term definition
       Relationships with other terms
       Synonyms
       Secondary ids
       Definition dbxrefs
       Comments

AUTHOR

       Lukas Mueller <lam87@cornell.edu>

       Naama Menda <nm249@cornell.edu>

VERSION AND DATE

       Version 0.15, September 2010.