[Bioperl-l] [BioSQL-l] Problem loading GO.

Leighton Pritchard lpritc at scri.ac.uk
Tue Apr 17 09:35:44 EDT 2007


Hi Hilmar, 

Thanks for the very quick response.  Apologies for the long reply, but I
thought it might be useful if anyone else happens across the same
problems that I did.

On Tue, 2007-04-17 at 00:00 -0400, Hilmar Lapp wrote:
> Apparently the parser  
> fails to parse out database and accession for this db_xref of term GO: 
> 0018901.
> 
> If you can edit the obo file, you can try deleting the db_xref(s) for  
> that term that look odd (or delete all if you don't need them).

You're spot on - see further down for details...

> Note that the argument for --fmtargs here should read
> "-defs_file,/path/to/Downloads/GO.defs". (Note that within the quotes  
> there is no tilde expansion.)

D'oh!  Thanks for the note - my bad, there.

> This is one the things why you've got to love MySQL (and I am correct  
> in inferring that you're using MySQL?). 

The 'choice' was forced upon me ;)

> It may be necessary to widen the length of dbname.accession here, for  
> example to 80 chars? Let me know if you need help with the DDL  
> command to do this.

I've fixed that now (and added it to my local biosqldb-mysql.sql
schema), but with a clean BioSQL schema and using:

[lpritc at lplinuxdev sql]$ bp_load_ontology.pl --host localhost --dbname
biosql --namespace "Gene Ontology" --dbuser lpritc --dbpass ********
--format goflat --fmtargs
"-defs_file,/home/lpritc/Downloads/GO.defs" /home/lpritc/Downloads/function.ontology 

I was still getting errors with the GO flatfile:

Loading ontology Gene Ontology:
        ... terms

-------------------- WARNING ---------------------
MSG: insert in Bio::DB::BioSQL::DBLinkAdaptor (driver) failed, values
were ("","","0","") FKs ()
Column 'dbname' cannot be null
---------------------------------------------------
Could not store term GO:0047554, name '2-pyrone-4,6-dicarboxylate
lactonase activity':

------------- EXCEPTION: Bio::Root::Exception -------------
MSG: create: object (Bio::Annotation::DBLink) failed to insert or to be
found by unique key
STACK: Error::throw
STACK:
Bio::Root::Root::throw /usr/lib/perl5/site_perl/5.8.8/Bio/Root/Root.pm:359
STACK:
Bio::DB::BioSQL::BasePersistenceAdaptor::create /usr/lib/perl5/site_perl/5.8.8/Bio/DB/BioSQL/BasePersistenceAdaptor.pm:206
STACK:
Bio::DB::BioSQL::TermAdaptor::store_children /usr/lib/perl5/site_perl/5.8.8/Bio/DB/BioSQL/TermAdaptor.pm:293
STACK:
Bio::DB::BioSQL::BasePersistenceAdaptor::create /usr/lib/perl5/site_perl/5.8.8/Bio/DB/BioSQL/BasePersistenceAdaptor.pm:214
STACK:
Bio::DB::BioSQL::BasePersistenceAdaptor::store /usr/lib/perl5/site_perl/5.8.8/Bio/DB/BioSQL/BasePersistenceAdaptor.pm:251
STACK:
Bio::DB::Persistent::PersistentObject::store /usr/lib/perl5/site_perl/5.8.8/Bio/DB/Persistent/PersistentObject.pm:271
STACK: main::persist_term /usr/bin/bp_load_ontology.pl:805
STACK: /usr/bin/bp_load_ontology.pl:610
-----------------------------------------------------------

 at /usr/bin/bp_load_ontology.pl line 817
        main::persist_term('-term',
'Bio::Ontology::GOterm=HASH(0x88497a4)', '-db',
'Bio::DB::BioSQL::DBAdaptor=HASH(0x897f074)', '-termfactory',
'Bio::Ontology::TermFactory=HASH(0x8d64ad8)', '-throw',
'CODE(0x851abc8)', '-mergeobs', ...) called
at /usr/bin/bp_load_ontology.pl line 610

I tracked this down to an apparently poor formatting of the GO.defs file
(note that the first and third definition_lines appear to be two halves
of the same entry):

term: 2-pyrone-4,6-dicarboxylate lactonase activity
goid: GO:0047554
definition: Catalysis of the reaction: 2-pyrone-4,6-dicarboxylate + H2O
= 4-carboxy-2-hydroxyhexa-2,4-dienedioate.
definition_reference: :6-DICARBOXYLATE-LACTONASE-RXN
definition_reference: EC:3.1.1.57
definition_reference: MetaCyc:2-PYRONE-4

I found 43 similar errors for other GOIDs, and it appears to result from
the occurrence of the string "\," in a dbxref - mostly MetaCyc entries,
but also some UM-BBD_pathwayID entries.

These errors appear to have followed through into the generation of the
OBO format files in each case, e.g.:

def: "Catalysis of the reaction: 2-pyrone-4,6-dicarboxylate + H2O =
4-carboxy-2-hydroxyhexa-2,4-dienedioate." [:6-DICARBOXYLATE-LACTONASE-RXN, EC:3.1.1.57, MetaCyc:2-PYRONE-4]

and so is something for the GO guys to fix, I guess.


Another error is thrown after fixing the above, though (with the same
command as before):

Loading ontology Gene Ontology:
        ... terms

-------------------- WARNING ---------------------
MSG: insert in Bio::DB::BioSQL::TermAdaptor (driver) failed, values were
("GO:0006905","vesicle transport","OBSOLETE (was not defined before
being made obsolete).","X","") FKs (1)
Duplicate entry 'vesicle transport-1-X' for key 3
---------------------------------------------------
Could not store term GO:0006905, name 'vesicle transport':

------------- EXCEPTION: Bio::Root::Exception -------------
MSG: create: object (Bio::Ontology::GOterm) failed to insert or to be
found by unique key
STACK: Error::throw
STACK:
Bio::Root::Root::throw /usr/lib/perl5/site_perl/5.8.8/Bio/Root/Root.pm:359
STACK:
Bio::DB::BioSQL::BasePersistenceAdaptor::create /usr/lib/perl5/site_perl/5.8.8/Bio/DB/BioSQL/BasePersistenceAdaptor.pm:206
STACK:
Bio::DB::BioSQL::BasePersistenceAdaptor::store /usr/lib/perl5/site_perl/5.8.8/Bio/DB/BioSQL/BasePersistenceAdaptor.pm:251
STACK:
Bio::DB::Persistent::PersistentObject::store /usr/lib/perl5/site_perl/5.8.8/Bio/DB/Persistent/PersistentObject.pm:271
STACK: main::persist_term /usr/bin/bp_load_ontology.pl:805
STACK: /usr/bin/bp_load_ontology.pl:610
-----------------------------------------------------------

 at /usr/bin/bp_load_ontology.pl line 817
        main::persist_term('-term',
'Bio::Ontology::GOterm=HASH(0xbcac418)', '-db',
'Bio::DB::BioSQL::DBAdaptor=HASH(0x957805c)', '-termfactory',
'Bio::Ontology::TermFactory=HASH(0x995db20)', '-throw',
'CODE(0x9113bd0)', '-mergeobs', ...) called
at /usr/bin/bp_load_ontology.pl line 610

There are duplicate terms, identical in the term table except for GOID:
GO:0006905 and GO:0005480.  They are both "vesicle transport", and
obsoleted:

term: vesicle transport
goid: GO:0005480
definition: OBSOLETE (was not defined before being made obsolete).
definition_reference: GOC:go_curators
comment: This term was made obsolete because it represents a biological
process and not a molecular function. To update annotations, use the
biological process term 'vesicle-mediated transport ; GO:0016192'.

term: vesicle transport
goid: GO:0006905
definition: OBSOLETE (was not defined before being made obsolete).
definition_reference: GOC:go_curators
comment: This term was made obsolete because the meaning of the term is
ambiguous. To update annotations, consider the biological process term
'vesicle-mediated transport ; GO:0016192'.

I used the --noobsolete flag to avoid this error - reasoning that since
I'm populating the database for the first time, ignoring the obsolete
terms won't hurt - but finally this error was thrown:

Loading ontology Gene Ontology:
        ... terms

-------------------- WARNING ---------------------
MSG: insert in Bio::DB::BioSQL::DBLinkAdaptor (driver) failed, values
were ("PMID","","0","") FKs ()
Column 'accession' cannot be null
---------------------------------------------------
Could not store term GO:0032933, name 'SREBP-mediated signaling
pathway':

------------- EXCEPTION: Bio::Root::Exception -------------
MSG: create: object (Bio::Annotation::DBLink) failed to insert or to be
found by unique key
STACK: Error::throw
STACK:
Bio::Root::Root::throw /usr/lib/perl5/site_perl/5.8.8/Bio/Root/Root.pm:359
STACK:
Bio::DB::BioSQL::BasePersistenceAdaptor::create /usr/lib/perl5/site_perl/5.8.8/Bio/DB/BioSQL/BasePersistenceAdaptor.pm:206
STACK:
Bio::DB::BioSQL::TermAdaptor::store_children /usr/lib/perl5/site_perl/5.8.8/Bio/DB/BioSQL/TermAdaptor.pm:293
STACK:
Bio::DB::BioSQL::BasePersistenceAdaptor::create /usr/lib/perl5/site_perl/5.8.8/Bio/DB/BioSQL/BasePersistenceAdaptor.pm:214
STACK:
Bio::DB::BioSQL::BasePersistenceAdaptor::store /usr/lib/perl5/site_perl/5.8.8/Bio/DB/BioSQL/BasePersistenceAdaptor.pm:251
STACK:
Bio::DB::Persistent::PersistentObject::store /usr/lib/perl5/site_perl/5.8.8/Bio/DB/Persistent/PersistentObject.pm:271
STACK: main::persist_term /usr/bin/bp_load_ontology.pl:805
STACK: /usr/bin/bp_load_ontology.pl:610
-----------------------------------------------------------

 at /usr/bin/bp_load_ontology.pl line 817
        main::persist_term('-term',
'Bio::Ontology::GOterm=HASH(0xbe18f14)', '-db',
'Bio::DB::BioSQL::DBAdaptor=HASH(0x99bbf2c)', '-termfactory',
'Bio::Ontology::TermFactory=HASH(0x9da0ad8)', '-throw',
'CODE(0x9556bb4)', '-mergeobs', ...) called
at /usr/bin/bp_load_ontology.pl line 610

with the offending entry being 

term: SREBP-mediated signaling pathway
goid: GO:0032933
definition: A series of molecular signals from the endoplasmic reticulum
to the nucleus generated as a consequence of altered levels of one or
more lipids, and resulting in the activation of transcription by SREBP.
definition_reference: GOC:mah
definition_reference: PMID:0

I commented out the definition_reference for PMID:0, which seemed to fix
matters.

The process.ontology and component.ontology files then went into the
database without a hitch.  Thanks again for your help,

L.

-- 
Dr Leighton Pritchard B.Sc.(Hons) MRSC
D131, Plant Pathology Programme, SCRI
Errol Road, Invergowrie, Perth and Kinross, Scotland DD2 5DA
e:lpritc at scri.ac.uk            w:http://bioinf.scri.ac.uk/lp
gpg/pgp: 0xFEFC205C
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