[Bioperl-l] New GO Parser and errors loading biosql database

[Law, Annie]

Hi,

I would appreciate help with the following.
I have installed the newest bioperl-db and biosql schema from cvs.
I tried to load the database with information from godatabase.org and got
some errors listed further below (the
Tables did not fill at all).
Next I tried to load the database with Locuslink data from NCBI.

1)I got the LL file from NCBI and tried to load an empty datbase with a
LL_tmpl file (for human) and 
It seemed to load properly and the tables were filling up but then it
stopped after about 900 bioentries.
I'm not sure what went wrong.  There seem to be a complaint about duplicate
entry but I don't think I should
Modify the source file.

[root@ data]# perl /root/bioperl-db/scripts/biosql/load_seqdatabase.pl
--dbuser=root 
 --dbpass=mss22 --dbname bioseqdb --namespace "LocusLink" -format locuslink
/var/lib/mysql/LL_
_tmpl --dbpass=bioinf1 --dbname bioseqdb --namespace "LocusLink" -format
locuslink /var/lib/mysql/LL_tmpl
Loading /var/lib/mysql/LL_tmpl ...

-------------------- WARNING ---------------------
MSG: insert in Bio::DB::BioSQL::TermAdaptor (driver) failed, values were
("GO:0005699","kinetochore","","") FKs (6)
Duplicate entry 'kinetochore-6' for key 2
---------------------------------------------------
Could not store 1063: 
------------- EXCEPTION  -------------
MSG: create: object (Bio::Annotation::OntologyTerm) failed to insert or to
be found by unique key
STACK Bio::DB::BioSQL::BasePersistenceAdaptor::create
/usr/lib/perl5/site_perl/5.8.0/Bio/DB/BioSQL/BasePersistenceAdaptor.pm:207
STACK Bio::DB::BioSQL::BasePersistenceAdaptor::store
/usr/lib/perl5/site_perl/5.8.0/Bio/DB/BioSQL/BasePersistenceAdaptor.pm:253
STACK Bio::DB::Persistent::PersistentObject::store
/usr/lib/perl5/site_perl/5.8.0/Bio/DB/Persistent/PersistentObject.pm:270
STACK Bio::DB::BioSQL::AnnotationCollectionAdaptor::store_children
/usr/lib/perl5/site_perl/5.8.0/Bio/DB/BioSQL/AnnotationCollectionAdaptor.pm:
219
STACK Bio::DB::BioSQL::BasePersistenceAdaptor::create
/usr/lib/perl5/site_perl/5.8.0/Bio/DB/BioSQL/BasePersistenceAdaptor.pm:215
STACK Bio::DB::BioSQL::BasePersistenceAdaptor::store
/usr/lib/perl5/site_perl/5.8.0/Bio/DB/BioSQL/BasePersistenceAdaptor.pm:253
STACK Bio::DB::Persistent::PersistentObject::store
/usr/lib/perl5/site_perl/5.8.0/Bio/DB/Persistent/PersistentObject.pm:270
STACK Bio::DB::BioSQL::SeqAdaptor::store_children
/usr/lib/perl5/site_perl/5.8.0/Bio/DB/BioSQL/SeqAdaptor.pm:226
STACK Bio::DB::BioSQL::BasePersistenceAdaptor::create
/usr/lib/perl5/site_perl/5.8.0/Bio/DB/BioSQL/BasePersistenceAdaptor.pm:215
STACK Bio::DB::BioSQL::BasePersistenceAdaptor::store
/usr/lib/perl5/site_perl/5.8.0/Bio/DB/BioSQL/BasePersistenceAdaptor.pm:253
STACK Bio::DB::Persistent::PersistentObject::store
/usr/lib/perl5/site_perl/5.8.0/Bio/DB/Persistent/PersistentObject.pm:270
STACK (eval) /root/bioperl-db/scripts/biosql/load_seqdatabase.pl:517
STACK toplevel /root/bioperl-db/scripts/biosql/load_seqdatabase.pl:500

--------------------------------------


2) Updating GO parser
I saw that the GO parser was updated recently and I have located the code
version 1.17.2.1 I downloaded the new version.  I am using bioperl 1.4.
Should I just take the new dagflat.pm and replace the old one or are there
more steps involved?  When I download whole Modules I need to use make
commands.

Also I saw that dagflat.pm requires graph.pm.  Is this graph.pm part of the
bioperl 1.4 package I couldn't seem to find it or do I need to download and
install from CPAN.  I searched CPAN for graph.pm and got several hits.  Is
this the one I need? http://search.cpan.org/~mverb/GDGraph-1.43/
Do I also need GD.pm? I think I saw somewhere that it is required?
http://search.cpan.org/~lds/GD-2.11/GD.pm
Although this could be a mistake

Where is the best place to install GD and graph.pm (with dagflat.pm or the
main perl library)?   
I'm not sure whether the main perl library is /usr/lib/perl5/5.8.0 or
/usr/lib/perl5/site_perl/5.8.0/Bio


3) I installed Bioperl-db and downloaded the biosql schema successfully but
when I tried to use the Load_ontology.pl I got some errors which seem to be
saying that I am missing some main modules such as goflat (I recorded a
script of the output). But I have goflat.pm.  
Am I calling the perl script incorrectly?  Or are there still some modules I
need to install? I'm not sure that I am using the correct
Syntax for the format field.

Thanks very much,
Annie.

[root@ data]# perl /root/bioperl-db/scripts/biosql/load_ontology.pl
--dbuser=root --d
dbpass=mss22 --dbname bioseqdb --noobsolete --namespace "Gene Ontology"
--fmtargs "-defs_file,/root/Go.defs" 
--format goflat ./component.ontology ./process.ontology ./function.ontology

Bio::OntologyIO: goflat cannot be found
Exception 
------------- EXCEPTION  -------------
MSG: Failed to load module Bio::OntologyIO::goflat. Can't locate
Graph/Directed.pm in @INC (@INC contains:
/usr/lib/perl5/5.8.0/i386-linux-thread-multi /usr/lib/perl5/5.8.0
/usr/lib/perl5/site_perl/5.8.0/i386-linux-thread-multi
/usr/lib/perl5/site_perl/5.8.0 /usr/lib/perl5/site_perl
/usr/lib/perl5/vendor_perl/5.8.0/i386-linux-thread-multi
/usr/lib/perl5/vendor_perl/5.8.0 /usr/lib/perl5/vendor_perl
/usr/lib/perl5/5.8.0/i386-linux-thread-multi /usr/lib/perl5/5.8.0 .) at
/usr/lib/perl5/site_perl/5.8.0/Bio/Ontology/SimpleGOEngine.pm line 95.
BEGIN failed--compilation aborted at
/usr/lib/perl5/site_perl/5.8.0/Bio/Ontology/SimpleGOEngine.pm line 95.
Compilation failed in require at
/usr/lib/perl5/site_perl/5.8.0/Bio/OntologyIO/dagflat.pm line 105.
BEGIN failed--compilation aborted at
/usr/lib/perl5/site_perl/5.8.0/Bio/OntologyIO/dagflat.pm line 105.
Compilation failed in require at
/usr/lib/perl5/site_perl/5.8.0/Bio/OntologyIO/goflat.pm line 105.
BEGIN failed--compilation aborted at
/usr/lib/perl5/site_perl/5.8.0/Bio/OntologyIO/goflat.pm line 105.
Compilation failed in require at
/usr/lib/perl5/site_perl/5.8.0/Bio/Root/Root.pm line 394.

STACK Bio::Root::Root::_load_module
/usr/lib/perl5/site_perl/5.8.0/Bio/Root/Root.pm:396
STACK (eval) /usr/lib/perl5/site_perl/5.8.0/Bio/OntologyIO.pm:255
STACK Bio::OntologyIO::_load_format_module
/usr/lib/perl5/site_perl/5.8.0/Bio/OntologyIO.pm:254
STACK Bio::OntologyIO::new
/usr/lib/perl5/site_perl/5.8.0/Bio/OntologyIO.pm:165
STACK toplevel /root/bioperl-db/scripts/biosql/load_ontology.pl:449

--------------------------------------

For more information about the OntologyIO system please see the docs.
This includes ways of checking for formats at compile time, not run time
Parsing input ...
Can't call method "next_ontology" on an undefined value at
/root/bioperl-db/scripts/biosql/load_ontology.pl line 455.