From florian.mittag at uni-tuebingen.de  Thu Jun  4 09:52:58 2009
From: florian.mittag at uni-tuebingen.de (Florian Mittag)
Date: Thu, 4 Jun 2009 15:52:58 +0200
Subject: [BioSQL-l] Question about VARCHAR BINARY
Message-ID: <200906041552.59221.florian.mittag@uni-tuebingen.de>

Hi everyone!

I'm new to BioSQL and just started using it, when I noticed that some tables 
contain columns with type VARCHAR BINARY, e.g. the column "name" in the 
table "biodatabase". May I ask, what is the reason behind this?

We switched to a DB2 database for some performance issues and set up the 
BioSQL schema, and MySQL's VARCHAR BINARY corresponds with DB2's VARBINARY, 
which is somewhat annoying because the content of those columns is displayed 
hexadecimal on command line interface and the visualizer we are using just 
shows "BINARY, x bytes".

Since I'm new BioSQL I just might miss an important point, but it seems to me 
that there is no reason to have those columns defined as BINARY, because only 
text is stored in them.

Could you please enlighten me? ;-)


Regards,
  Florian

From biopython at maubp.freeserve.co.uk  Mon Jun 22 08:13:42 2009
From: biopython at maubp.freeserve.co.uk (Peter)
Date: Mon, 22 Jun 2009 13:13:42 +0100
Subject: [BioSQL-l] BioSQL at BOSC 2009?
In-Reply-To: <74D4CC78-FC7B-4595-9D24-EB6B3ED43318@gmx.net>
References: <320fb6e00905160512m66848611l432a81f22866b37f@mail.gmail.com>
	<1BD503B3-D805-4882-87DD-820138792DB2@gmx.net>
	<320fb6e00905161423l4df26525hbc9a824419c7a370@mail.gmail.com>
	<74D4CC78-FC7B-4595-9D24-EB6B3ED43318@gmx.net>
Message-ID: <320fb6e00906220513n42fd4c63y1dd7907023ade512@mail.gmail.com>

On Sat, May 16, 2009 at 10:57 PM, Hilmar Lapp<hlapp at gmx.net> wrote:
>
>
> On May 16, 2009, at 5:23 PM, Peter wrote:
>
>> I will be staying for all of ISMB
>
> I am too. Should we doodle something once the program is out?
>
> ? ? ? ?-hilmar

Hi again,

Well the program is out. When would be a good time to
get together at BOSC/ISMB 2009 to talk about BioSQL?

As I mentioned earlier, I am there for all of ISMB but Brad
Chapman (another Biopython developer and BioSQL user)
will only be at BOSC itself, the Friday before, and the Monday
afterwards (day one of ISMB).

We have Biopython BoF sessions planned for both days of
BOSC (one more of a tutorial, one more of a hackathon) but
as we should have several Biopython coders present, Brad
and I could try and split our time with a BioSQL BoF session
at BOSC (on either the Saturday or the Sunday).

I have already started a list of possible topics - some of which
have come up on the Biopython mailing lists.

One idea was to look into using BioSQL on SQLite, which would
require a new schema. One reason this is appealing for Biopython
is SQLite is included with Python 2.5+, so this could make getting
started with BioSQL easier.

Peter


From andreas.draeger at uni-tuebingen.de  Mon Jun 22 09:11:31 2009
From: andreas.draeger at uni-tuebingen.de (Andreas Draeger)
Date: Mon, 22 Jun 2009 15:11:31 +0200
Subject: [BioSQL-l] Question about VARCHAR BINARY
In-Reply-To: <200906041552.59221.florian.mittag@uni-tuebingen.de>
References: <200906041552.59221.florian.mittag@uni-tuebingen.de>
Message-ID: <4A3F8303.4090103@uni-tuebingen.de>

Florian Mittag wrote:
> I'm new to BioSQL and just started using it, when I noticed that some tables 
> contain columns with type VARCHAR BINARY, e.g. the column "name" in the 
> table "biodatabase". May I ask, what is the reason behind this?
> 
> We switched to a DB2 database for some performance issues and set up the 
> BioSQL schema, and MySQL's VARCHAR BINARY corresponds with DB2's VARBINARY, 
> which is somewhat annoying because the content of those columns is displayed 
> hexadecimal on command line interface and the visualizer we are using just 
> shows "BINARY, x bytes".

Dear all,

I encountered the same problem since I am now also using DB2 with 
BioJava bindings using Hibernate.

When retrieving a Namespace object from the biodatabase table, the 
getName() method returns a hexadecimal code instead of the desired name 
String. However, this happened although I queried the database using the 
String "Genebank". This means Hibernate was able to obtain the correct 
object using the name "Genebank", but converts everything to hex codes.

This seems to be related to the column having a binary type. I tried to 
get into this but without any success. It would be great to get any help 
on this.

Cheers,
Andreas

-- 
Dipl.-Bioinform. Andreas Dr?ger
Eberhard Karls University T?bingen
Center for Bioinformatics (ZBIT)
Sand 1
72076 T?bingen
Germany

Phone: +49-7071-29-70436
Fax:   +49-7071-29-5091

From achille.zappa at istge.it  Mon Jun 22 10:12:18 2009
From: achille.zappa at istge.it (Achille Zappa)
Date: Mon, 22 Jun 2009 16:12:18 +0200 (CEST)
Subject: [BioSQL-l] Can I load ontologies into BioSQL?
Message-ID: <59386.10.2.4.168.1245679938.squirrel@webmail.istge.it>

Hi guys

I'm working with biosql and I try to figure out how to load ontologies
into biosql.

I've tried to load the flat files gene ontologies :

load_ontology.pl   --driver mysql --dbuser xxx --dbpass xxx --host
localhost --dbname biosql --namespace "Gene Ontology" --format goflat
--fmtargs "-defs_file,GO.defs"  function.ontology process.ontology
component.ontology

as in the script info but I have an error,

a lot of  ------------ WARNING ---------------------
MSG: DBLink exists in the dblink of _default
---------------------------------------------------
and at the end
------------- EXCEPTION: Bio::Root::Exception -------------
MSG: format error (file /home/user/Download/process.ontology) offending line:
     -negative regulation of angiogenesis ; GO:0016525 ; synonym:down
regulation of angiogenesis ; synonym:down\-regulation of angiogenesis
; synonym:downregulation of angiogenesis ; synonym:inhibition of
angiogenesis % negative regulation of developmental process ;
GO:0051093 % regulation of angiogenesis ; GO:0045765

STACK: Error::throw
STACK: Bio::Root::Root::throw
/usr/lib/perl5/vendor_perl/5.10.0/Bio/Root/Root.pm:357
STACK: Bio::OntologyIO::dagflat::_parse_flat_file
/usr/lib/perl5/vendor_perl/5.10.0/Bio/OntologyIO/dagflat.pm:627
STACK: Bio::OntologyIO::dagflat::parse
/usr/lib/perl5/vendor_perl/5.10.0/Bio/OntologyIO/dagflat.pm:284
STACK: Bio::OntologyIO::dagflat::next_ontology
/usr/lib/perl5/vendor_perl/5.10.0/Bio/OntologyIO/dagflat.pm:317
STACK: load_ontology.pl:604
-----------------------------------------------------------

could you help me?
is it possible to use the OBO format with the loader?
those GO flat files are deprecated by the Gene Ontology site
is there a list of format to use with the biosql perl scripts?

thank you
regards
Achille





-- 
Achille Zappa
-Bioinformatics
 National Cancer Research Institute (IST)
 Largo Benzi 10
 16132 Genova - ITALY
 Tel. 010 5737288
-IEIIT - Sezione di Genova
 National Research Council (CNR)
 via De Marini, 6
 16149 Genova - ITALY


Aiutaci TU ad aiutare TANTI: Il tuo 5 per MILLE a sostegno della nostra RICERCA.
 Come fare:
 Nella prossima dichiarazione dei redditi metti la firma 
 nell'apposito riquadro del 5 per mille,
 scrivendo anche il codice fiscale dell'Istituto Nazionale per la Ricerca sul Cancro di Genova :
  c.f. 80 100 850 108
 Istituto Nazionale per la Ricerca sul Cancro
 L.go R. Benzi, 10 -16132 Genova
 http://www.istge.it

From florian.mittag at uni-tuebingen.de  Thu Jun  4 13:52:58 2009
From: florian.mittag at uni-tuebingen.de (Florian Mittag)
Date: Thu, 4 Jun 2009 15:52:58 +0200
Subject: [BioSQL-l] Question about VARCHAR BINARY
Message-ID: <200906041552.59221.florian.mittag@uni-tuebingen.de>

Hi everyone!

I'm new to BioSQL and just started using it, when I noticed that some tables 
contain columns with type VARCHAR BINARY, e.g. the column "name" in the 
table "biodatabase". May I ask, what is the reason behind this?

We switched to a DB2 database for some performance issues and set up the 
BioSQL schema, and MySQL's VARCHAR BINARY corresponds with DB2's VARBINARY, 
which is somewhat annoying because the content of those columns is displayed 
hexadecimal on command line interface and the visualizer we are using just 
shows "BINARY, x bytes".

Since I'm new BioSQL I just might miss an important point, but it seems to me 
that there is no reason to have those columns defined as BINARY, because only 
text is stored in them.

Could you please enlighten me? ;-)


Regards,
  Florian


From biopython at maubp.freeserve.co.uk  Mon Jun 22 12:13:42 2009
From: biopython at maubp.freeserve.co.uk (Peter)
Date: Mon, 22 Jun 2009 13:13:42 +0100
Subject: [BioSQL-l] BioSQL at BOSC 2009?
In-Reply-To: <74D4CC78-FC7B-4595-9D24-EB6B3ED43318@gmx.net>
References: <320fb6e00905160512m66848611l432a81f22866b37f@mail.gmail.com>
	<1BD503B3-D805-4882-87DD-820138792DB2@gmx.net>
	<320fb6e00905161423l4df26525hbc9a824419c7a370@mail.gmail.com>
	<74D4CC78-FC7B-4595-9D24-EB6B3ED43318@gmx.net>
Message-ID: <320fb6e00906220513n42fd4c63y1dd7907023ade512@mail.gmail.com>

On Sat, May 16, 2009 at 10:57 PM, Hilmar Lapp<hlapp at gmx.net> wrote:
>
>
> On May 16, 2009, at 5:23 PM, Peter wrote:
>
>> I will be staying for all of ISMB
>
> I am too. Should we doodle something once the program is out?
>
> ? ? ? ?-hilmar

Hi again,

Well the program is out. When would be a good time to
get together at BOSC/ISMB 2009 to talk about BioSQL?

As I mentioned earlier, I am there for all of ISMB but Brad
Chapman (another Biopython developer and BioSQL user)
will only be at BOSC itself, the Friday before, and the Monday
afterwards (day one of ISMB).

We have Biopython BoF sessions planned for both days of
BOSC (one more of a tutorial, one more of a hackathon) but
as we should have several Biopython coders present, Brad
and I could try and split our time with a BioSQL BoF session
at BOSC (on either the Saturday or the Sunday).

I have already started a list of possible topics - some of which
have come up on the Biopython mailing lists.

One idea was to look into using BioSQL on SQLite, which would
require a new schema. One reason this is appealing for Biopython
is SQLite is included with Python 2.5+, so this could make getting
started with BioSQL easier.

Peter



From andreas.draeger at uni-tuebingen.de  Mon Jun 22 13:11:31 2009
From: andreas.draeger at uni-tuebingen.de (Andreas Draeger)
Date: Mon, 22 Jun 2009 15:11:31 +0200
Subject: [BioSQL-l] Question about VARCHAR BINARY
In-Reply-To: <200906041552.59221.florian.mittag@uni-tuebingen.de>
References: <200906041552.59221.florian.mittag@uni-tuebingen.de>
Message-ID: <4A3F8303.4090103@uni-tuebingen.de>

Florian Mittag wrote:
> I'm new to BioSQL and just started using it, when I noticed that some tables 
> contain columns with type VARCHAR BINARY, e.g. the column "name" in the 
> table "biodatabase". May I ask, what is the reason behind this?
> 
> We switched to a DB2 database for some performance issues and set up the 
> BioSQL schema, and MySQL's VARCHAR BINARY corresponds with DB2's VARBINARY, 
> which is somewhat annoying because the content of those columns is displayed 
> hexadecimal on command line interface and the visualizer we are using just 
> shows "BINARY, x bytes".

Dear all,

I encountered the same problem since I am now also using DB2 with 
BioJava bindings using Hibernate.

When retrieving a Namespace object from the biodatabase table, the 
getName() method returns a hexadecimal code instead of the desired name 
String. However, this happened although I queried the database using the 
String "Genebank". This means Hibernate was able to obtain the correct 
object using the name "Genebank", but converts everything to hex codes.

This seems to be related to the column having a binary type. I tried to 
get into this but without any success. It would be great to get any help 
on this.

Cheers,
Andreas

-- 
Dipl.-Bioinform. Andreas Dr?ger
Eberhard Karls University T?bingen
Center for Bioinformatics (ZBIT)
Sand 1
72076 T?bingen
Germany

Phone: +49-7071-29-70436
Fax:   +49-7071-29-5091


From achille.zappa at istge.it  Mon Jun 22 14:12:18 2009
From: achille.zappa at istge.it (Achille Zappa)
Date: Mon, 22 Jun 2009 16:12:18 +0200 (CEST)
Subject: [BioSQL-l] Can I load ontologies into BioSQL?
Message-ID: <59386.10.2.4.168.1245679938.squirrel@webmail.istge.it>

Hi guys

I'm working with biosql and I try to figure out how to load ontologies
into biosql.

I've tried to load the flat files gene ontologies :

load_ontology.pl   --driver mysql --dbuser xxx --dbpass xxx --host
localhost --dbname biosql --namespace "Gene Ontology" --format goflat
--fmtargs "-defs_file,GO.defs"  function.ontology process.ontology
component.ontology

as in the script info but I have an error,

a lot of  ------------ WARNING ---------------------
MSG: DBLink exists in the dblink of _default
---------------------------------------------------
and at the end
------------- EXCEPTION: Bio::Root::Exception -------------
MSG: format error (file /home/user/Download/process.ontology) offending line:
     -negative regulation of angiogenesis ; GO:0016525 ; synonym:down
regulation of angiogenesis ; synonym:down\-regulation of angiogenesis
; synonym:downregulation of angiogenesis ; synonym:inhibition of
angiogenesis % negative regulation of developmental process ;
GO:0051093 % regulation of angiogenesis ; GO:0045765

STACK: Error::throw
STACK: Bio::Root::Root::throw
/usr/lib/perl5/vendor_perl/5.10.0/Bio/Root/Root.pm:357
STACK: Bio::OntologyIO::dagflat::_parse_flat_file
/usr/lib/perl5/vendor_perl/5.10.0/Bio/OntologyIO/dagflat.pm:627
STACK: Bio::OntologyIO::dagflat::parse
/usr/lib/perl5/vendor_perl/5.10.0/Bio/OntologyIO/dagflat.pm:284
STACK: Bio::OntologyIO::dagflat::next_ontology
/usr/lib/perl5/vendor_perl/5.10.0/Bio/OntologyIO/dagflat.pm:317
STACK: load_ontology.pl:604
-----------------------------------------------------------

could you help me?
is it possible to use the OBO format with the loader?
those GO flat files are deprecated by the Gene Ontology site
is there a list of format to use with the biosql perl scripts?

thank you
regards
Achille





-- 
Achille Zappa
-Bioinformatics
 National Cancer Research Institute (IST)
 Largo Benzi 10
 16132 Genova - ITALY
 Tel. 010 5737288
-IEIIT - Sezione di Genova
 National Research Council (CNR)
 via De Marini, 6
 16149 Genova - ITALY


Aiutaci TU ad aiutare TANTI: Il tuo 5 per MILLE a sostegno della nostra RICERCA.
 Come fare:
 Nella prossima dichiarazione dei redditi metti la firma 
 nell'apposito riquadro del 5 per mille,
 scrivendo anche il codice fiscale dell'Istituto Nazionale per la Ricerca sul Cancro di Genova :
  c.f. 80 100 850 108
 Istituto Nazionale per la Ricerca sul Cancro
 L.go R. Benzi, 10 -16132 Genova
 http://www.istge.it