Skip Menu |
 

This queue is for tickets about the onto-perl CPAN distribution.

Report information
The Basics
Id: 125216
Status: new
Priority: 0/
Queue: onto-perl

People
Owner: Nobody in particular
Requestors: isabelle.wells [...] roche.com
Cc:
AdminCc:

Bug Information
Severity: (no value)
Broken in: (no value)
Fixed in: (no value)



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>
Download (untitled) / with headers
text/plain 1.1k
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


This service is sponsored and maintained by Best Practical Solutions and runs on Perl.org infrastructure.

Please report any issues with rt.cpan.org to rt-cpan-admin@bestpractical.com.