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scripts/biosql/load_ontology.pl  view on Meta::CPAN

=item --remove

Flag to remove terms before actually adding them (this necessitates a
prior lookup). Note that this is not relevant for relationships (if
one is found by lookup, removing and re-adding has essentially the
same result as leaving it untouched).

=item --noobsolete

Flag to exclude from upload terms marked as obsolete. Note that with
this flag, any update, removal, or object merge that you specify using
other parameters will not apply to obsolete terms. I.e., if you have
terms existing in your database that are marked as obsolete in the
input file, using this flag will prevent the existing terms from being
updated to reflect the obsolete status. Therefore, this flag is best
used when first loading an ontology. You may want to consider using
--updobsolete instead.

Note that relationships found in the input file(s) that reference an
obsolete term will be omitted from loading with this flag in effect.

=item --updobsolete

Flag to exclude from upload terms marked as obsolete unless they are
already present in the database. If they are, they will be updated,
and the --mergeobjs procedure will apply. If they are not, they will
be treated as if --noobsolete had been specified. Note that
relationships will not be updated for obsolete terms.

In contrast to --noobsolete, using this flag will increase the
database operations mildly (because of the look-ups necessary to
determine whether obsolete terms are present, and the subsequent
update for those that are), but it will capture change of status for
existing terms. At the same time, you won't load obsolete terms from a

scripts/biosql/load_ontology.pl  view on Meta::CPAN

    # this is a truly OntologyIO compliant parser, or so I hope

    # loop over the input stream(s)
    while( my $ont = $ontin->$nextobj ) {
        # don't forget to add namespace if the parser doesn't supply one
        $ont->name($namespace) unless $ont->name();
        
        print STDERR "Loading ontology ",$ont->name(),":\n\t... terms\n";

        # in order to allow callbacks to the user and generally a
        # better ability to interfere with and customize the upload
        # process, we load all terms first here instead of simply
        # going for the relationships

        foreach my $term ($ont->get_all_terms()) {
            # call the persistence handler - there is only one right now
            persist_term('-term' => $term, @persist_args);
        }

        # after all terms have been processed, we run through the relationships
        # more or less non-interactively (i.e., without invoking a callback)