[Bioperl-l] Re: [Gmod-schema] install problems, continued (fwd)

[Jason Stajich]

--
Jason Stajich
Duke University
jason at cgt.mc.duke.edu

---------- Forwarded message ----------
Date: Fri, 27 Feb 2004 14:30:57 -0500 (EST)
From: Don Gilbert <gilbertd at bio.indiana.edu>
To: cain at cshl.org, p.lijnzaad at med.uu.nl
Cc: gmod-schema at lists.sourceforge.net
Subject: Re: [Gmod-schema] install problems, continued


THere is a problem with bioperl-1.4 related to ontology parsing.
I'm assuming people in bioperl/ontology world know about this, but
here is what I found -- Bio/Ontology/RelationshipType.pm
has been reverted to remove some of Allen Day's necessary patches
and now it won't parse SO and some of the other standard bio ontology data.

- Don

------------- EXCEPTION: Bio::Root::Exception -------------
MSG: Found unknown type of relationship: [derived_from]
Known types are: [IS_A], [PART_OF], [CONTAINS], [FOUND_IN]
STACK: Error::throw
STACK: Bio::Root::Root::throw /bio/biodb/common/perl/lib/Bio/Root/Root.pm:328
STACK: Bio::Ontology::RelationshipType::get_instance /bio/biodb/common/perl/lib/Bio/Ontology/RelationshipType.pm:143
STACK: Bio::Ontology::SimpleGOEngine::add_relationship_type /bio/biodb/common/perl/lib/Bio/Ontology/SimpleGOEngine.pm:284
STACK: Bio::OntologyIO::dagflat::_parse_flat_file /bio/biodb/common/perl/lib/Bio/OntologyIO/dagflat.pm:556
STACK: Bio::OntologyIO::dagflat::parse /bio/biodb/common/perl/lib/Bio/OntologyIO/dagflat.pm:250
STACK: Bio::OntologyIO::dagflat::next_ontology /bio/biodb/common/perl/lib/Bio/OntologyIO/dagflat.pm:284
STACK: /bio/biodb/gmod/bin/gmod_load_ontology.pl:119
-----------------------------------------------------------
Problem loading ontology /bio/biodb/gmod/data/ontologies/song/so.ontology: 65280 at bin/

-- reinstated below comment out, leading to lots of errors
-- UC versus lc terms, and derived_from, other relations not in perl module.


cricket.% diff
  [bioperl-eariler]/Bio/Ontology/RelationshipType.pm
  [bioperl-1.4]/Bio/Ontology/RelationshipType.pm
1c1
< # $Id: RelationshipType.pm,v 1.11 2003/06/20 18:31:44 allenday Exp $
---
> # $Id: RelationshipType.pm,v 1.5.2.5 2003/09/08 12:16:19 heikki Exp $
136,145c136,141
<
< #
< #see the cell ontology.  this code is too strict, even for dag-edit files. -allen
< #
< #    if ( ! (($name eq IS_A) || ($name eq PART_OF) ||
< #         ($name eq CONTAINS) || ( $name eq FOUND_IN ))) {
< #        my $msg = "Found unknown type of relationship: [" . $name . "]\n";
< #        $msg .= "Known types are: [" . IS_A . "], [" . PART_OF . "], [" . CONTAINS . "], [" . FOUND_IN . "]";
< #        $class->throw( $msg );
< #    }
---
>     if ( ! (($name eq IS_A) || ($name eq PART_OF) ||
>           ($name eq CONTAINS) || ( $name eq FOUND_IN ))) {
>         my $msg = "Found unknown type of relationship: [" . $name . "]\n";
>         $msg .= "Known types are: [" . IS_A . "], [" . PART_OF . "], [" . CONTAINS . "], [" . FOUND_IN . "]";
>         $class->throw( $msg );
>     }
364a361,363
>


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