| Subject: | unknown oboContentUrl in obo2owl.pl |
| Date: | Thu, 26 Apr 2018 16:17:42 +0200 |
| To: | bug-onto-perl [...] rt.cpan.org |
| From: | "Wells, Isabelle" <isabelle.wells [...] roche.com> |
Hello,
I've downloaded and installed ONTO-PERL-1.45 as I would like to use the
script to translate the GeneOntology OBO file into OWL format.
However using both go2owl.pl or obo2owl.pl on the 2 .obo files listed at
http://geneontology.org/page/download-ontology (as of 26.04.2018) returns
the same error message.
eg the command: perl obo2owl.pl -f go-basic.obo returns:
Use of uninitialized value $oboContentUrl in pattern match (m//) at
/pstore/home/wellsi/perl5/lib/perl5/OBO/Core/Ontology.pm line 2933.
OWL export: you must provide a valid URL, e.g. export('owl', *STDOUT,
*STDERR, 'http://www.cellcycleontology.org/ontology/owl/') at
/pstore/home/wellsi/perl5/lib/perl5/OBO/Core/Ontology.pm line 2933.
OBO::Core::Ontology::export2owl(OBO::Core::Ontology=HASH(0x1b42118),
GLOB(0x7eeee8), GLOB(0x7eef48), undef, undef) called at
/pstore/home/wellsi/perl5/lib/perl5/OBO/Core/Ontology.pm line 4252
OBO::Core::Ontology::export(OBO::Core::Ontology=HASH(0x1b42118),
"owl", GLOB(0x7eeee8), GLOB(0x7eef48), undef, undef) called at
/pstore/home/wellsi/perl5/bin/obo2owl.pl line 56
Is there something like a defined URL expected in the obo files?
Many thanks,
Isabelle