From sanjay.harke at gmail.com Thu Apr 2 06:36:48 2009 From: sanjay.harke at gmail.com (Sanjay Harke) Date: Thu, 2 Apr 2009 16:06:48 +0530 Subject: [BioSQL-l] Regarding help for MYSQL-BIOSQL-BIOPERL Message-ID: <31bb4380904020336s1bb25d44xc275510cfa4acb86@mail.gmail.com> Respected sir, Kindly guide me about how use Mysql with Biosql? how install Biosql schema? This mysql database my local database i want use for my work analysis. Kindly guide me. sanjay From biopython at maubp.freeserve.co.uk Thu Apr 2 09:25:40 2009 From: biopython at maubp.freeserve.co.uk (Peter) Date: Thu, 2 Apr 2009 14:25:40 +0100 Subject: [BioSQL-l] Regarding help for MYSQL-BIOSQL-BIOPERL In-Reply-To: <31bb4380904020336s1bb25d44xc275510cfa4acb86@mail.gmail.com> References: <31bb4380904020336s1bb25d44xc275510cfa4acb86@mail.gmail.com> Message-ID: <320fb6e00904020625k41817242h72b5bc9b1b2c35d5@mail.gmail.com> On Thu, Apr 2, 2009 at 11:36 AM, Sanjay Harke wrote: > > Respected sir, > > Kindly guide me about > how use Mysql with Biosql? > how install Biosql schema? > This mysql database my local database i want use for my work analysis. > Kindly guide me. > > sanjay The main page www.biosql.org links to this INSTALL document: http://code.open-bio.org/svnweb/index.cgi/biosql/checkout/biosql-schema/trunk/INSTALL See also this Biopython page which starts by how to install BioSQL on MySQL, http://www.biopython.org/wiki/BioSQL Your title implies you want to use BioPerl - so you'll need to install that too. For more specific help you'd need to tell us which operating system you plan to use (e.g. Linux, Mac OS, Windows XP). Peter From sanjay.harke at gmail.com Thu Apr 2 13:40:58 2009 From: sanjay.harke at gmail.com (Sanjay Harke) Date: Thu, 2 Apr 2009 23:10:58 +0530 Subject: [BioSQL-l] Regarding help for MYSQL-BIOSQL-BIOPERL In-Reply-To: <320fb6e00904020625k41817242h72b5bc9b1b2c35d5@mail.gmail.com> References: <31bb4380904020336s1bb25d44xc275510cfa4acb86@mail.gmail.com> <320fb6e00904020625k41817242h72b5bc9b1b2c35d5@mail.gmail.com> Message-ID: <31bb4380904021040j3bf5df59w2e64d5f1379c5697@mail.gmail.com> Respected Peter, following are mine queries, I am using Window 2003 server. for database i am using MySql server. Already Install Bioperl. Now guide me about how to Install BioSql on my Pc? how install Biosql schema? How to use local database with Bioperl? sanjay From biopython at maubp.freeserve.co.uk Fri Apr 3 05:27:49 2009 From: biopython at maubp.freeserve.co.uk (Peter) Date: Fri, 3 Apr 2009 10:27:49 +0100 Subject: [BioSQL-l] Regarding help for MYSQL-BIOSQL-BIOPERL In-Reply-To: <31bb4380904021040j3bf5df59w2e64d5f1379c5697@mail.gmail.com> References: <31bb4380904020336s1bb25d44xc275510cfa4acb86@mail.gmail.com> <320fb6e00904020625k41817242h72b5bc9b1b2c35d5@mail.gmail.com> <31bb4380904021040j3bf5df59w2e64d5f1379c5697@mail.gmail.com> Message-ID: <320fb6e00904030227n558e6598p666875ff6af2986@mail.gmail.com> On Thu, Apr 2, 2009 at 6:40 PM, Sanjay Harke wrote: > > Respected Peter, > Hello again, Are you signed up to the BioSQL mailing list? General questions like this should be sent to the mailing list rather than just particular people like me or Hilmar. http://lists.open-bio.org/mailman/listinfo/biosql-l > following are mine queries, > > I am using Window 2003 server. > for database i am using MySql server. So you have installed MySQL server, good. See http://www.mysql.com/ for their documentation. > Already Install Bioperl. Good. > Now guide me about how to Install BioSql on my Pc? > how install Biosql schema? As I said before, I also recommend this Biopython page which starts by how to install BioSQL on MySQL (just ignore the Biopython bits): http://www.biopython.org/wiki/BioSQL The main page www.biosql.org links to this INSTALL document: http://code.open-bio.org/svnweb/index.cgi/biosql/checkout/biosql-schema/trunk/INSTALL > How to use local database with Bioperl? I have very little experience of using BioPerl with BioSQL - I use Biopython. I agree that this page isn't very helpful, but perhaps there is more documentation elsewhere which I don't know about: http://bioperl.org/wiki/Bioperl-db Peter From georgkam at gmail.com Fri Apr 3 08:09:38 2009 From: georgkam at gmail.com (georgkam at gmail.com) Date: Fri, 03 Apr 2009 12:09:38 +0000 Subject: [BioSQL-l] Regarding help for MYSQL-BIOSQL-BIOPERL In-Reply-To: <320fb6e00904030227n558e6598p666875ff6af2986@mail.gmail.com> Message-ID: <000e0cd2474637c9f20466a56ca1@google.com> Hey I have a written a tutorial on setting up BioSQL with rails on my blog http://biorelated.wordpress.com/2009/01/07/bio-graphics-biosql-and-rails-part-1 http://biorelated.wordpress.com/2009/01/08/bio-graphics-biosql-and-rails-part-2/ :) GG On Apr 3, 2009 12:27pm, Peter wrote: > On Thu, Apr 2, 2009 at 6:40 PM, Sanjay Harke sanjay.harke at gmail.com> > wrote: > > > > Respected Peter, > > > Hello again, > Are you signed up to the BioSQL mailing list? General questions like > this should be sent to the mailing list rather than just particular > people like me or Hilmar. > http://lists.open-bio.org/mailman/listinfo/biosql-l > > following are mine queries, > > > > I am using Window 2003 server. > > for database i am using MySql server. > So you have installed MySQL server, good. See http://www.mysql.com/ > for their documentation. > > Already Install Bioperl. > Good. > > Now guide me about how to Install BioSql on my Pc? > > how install Biosql schema? > As I said before, I also recommend this Biopython page which starts by > how to install BioSQL on MySQL (just ignore the Biopython bits): > http://www.biopython.org/wiki/BioSQL > The main page www.biosql.org links to this INSTALL document: > http://code.open-bio.org/svnweb/index.cgi/biosql/checkout/biosql-schema/trunk/INSTALL > > How to use local database with Bioperl? > I have very little experience of using BioPerl with BioSQL - I use > Biopython. I agree that this page isn't very helpful, but perhaps > there is more documentation elsewhere which I don't know about: > http://bioperl.org/wiki/Bioperl-db > Peter > _______________________________________________ > BioSQL-l mailing list > BioSQL-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/biosql-l From cjfields at illinois.edu Thu Apr 16 16:19:16 2009 From: cjfields at illinois.edu (Chris Fields) Date: Thu, 16 Apr 2009 15:19:16 -0500 Subject: [BioSQL-l] bioperl-db, CORBA, and Oracle Message-ID: <7EA5FDDE-F402-4B0A-9195-E815B7C4AA1D@illinois.edu> Allen Day indicated (in an RT bug report) that bioperl-db has references to several modules not in CPAN, all CORBA-related (via bioperl-corba-server). Should we remove those, or is anyone still using them? The modules aren't available via CPAN. scripts/corba/bioenv_server.pl (references Bio::CorbaServer::BioEnv) scripts/corba/caching_corba_server.pl (references Bio::CorbaServer::BioEnv and Bio::CorbaClient::SeqDB) Related to this is an additional module in CPAN but apparently required separately: CORBA::ORBit (referenced in scripts/corba/bioenv_server.pl, scripts/ corba/test_bioenv.pl, and scripts/corba/caching_corba_server.pl) Also, there appears to be a requirement for DBD::Oracle in Bio::DB::BioSQL::Oracle::BasePersistenceAdaptorDriver that's popping up. I can add that to the 'recommends' but it doesn't really fit in with this category (i.e. if I use MySQL I shouldn't need to worry about it). * DBD::Oracle (referenced in Bio::DB::BioSQL::Oracle::BiosequenceAdaptorDriver and Bio::DB::BioSQL::Oracle::BasePersistenceAdaptorDriver Here's the RT ticket: https://rt.cpan.org/Ticket/Display.html?id=44466 chris From ccanchaya at gmail.com Mon Apr 20 11:44:24 2009 From: ccanchaya at gmail.com (Carlos A. Canchaya) Date: Mon, 20 Apr 2009 17:44:24 +0200 Subject: [BioSQL-l] Can I load ontologies into BioSQL? Message-ID: Hi guys I'm working with biosql and I try to figure out how to load ontologies into biosql. I've tried load_ontology.pl --driver mysql --dbuser carlos --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, ------------------- WARNING --------------------- MSG: DBLink exists in the dblink of _default --------------------------------------------------- ------------- EXCEPTION ------------- MSG: format error (file 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 Bio::OntologyIO::dagflat::_parse_flat_file /usr/local/share/perl/ 5.10.0/Bio/OntologyIO/dagflat.pm:627 STACK Bio::OntologyIO::dagflat::parse /usr/local/share/perl/5.10.0/Bio/ OntologyIO/dagflat.pm:284 STACK Bio::OntologyIO::dagflat::next_ontology /usr/local/share/perl/ 5.10.0/Bio/OntologyIO/dagflat.pm:317 STACK toplevel /usr/local/share/biosql/bioperl-db/scripts/biosql/ load_ontology.pl:604 ------------------------------------- Any suggestion? Cheers, Carlos From sanjay.harke at gmail.com Thu Apr 2 10:36:48 2009 From: sanjay.harke at gmail.com (Sanjay Harke) Date: Thu, 2 Apr 2009 16:06:48 +0530 Subject: [BioSQL-l] Regarding help for MYSQL-BIOSQL-BIOPERL Message-ID: <31bb4380904020336s1bb25d44xc275510cfa4acb86@mail.gmail.com> Respected sir, Kindly guide me about how use Mysql with Biosql? how install Biosql schema? This mysql database my local database i want use for my work analysis. Kindly guide me. sanjay From biopython at maubp.freeserve.co.uk Thu Apr 2 13:25:40 2009 From: biopython at maubp.freeserve.co.uk (Peter) Date: Thu, 2 Apr 2009 14:25:40 +0100 Subject: [BioSQL-l] Regarding help for MYSQL-BIOSQL-BIOPERL In-Reply-To: <31bb4380904020336s1bb25d44xc275510cfa4acb86@mail.gmail.com> References: <31bb4380904020336s1bb25d44xc275510cfa4acb86@mail.gmail.com> Message-ID: <320fb6e00904020625k41817242h72b5bc9b1b2c35d5@mail.gmail.com> On Thu, Apr 2, 2009 at 11:36 AM, Sanjay Harke wrote: > > Respected sir, > > Kindly guide me about > how use Mysql with Biosql? > how install Biosql schema? > This mysql database my local database i want use for my work analysis. > Kindly guide me. > > sanjay The main page www.biosql.org links to this INSTALL document: http://code.open-bio.org/svnweb/index.cgi/biosql/checkout/biosql-schema/trunk/INSTALL See also this Biopython page which starts by how to install BioSQL on MySQL, http://www.biopython.org/wiki/BioSQL Your title implies you want to use BioPerl - so you'll need to install that too. For more specific help you'd need to tell us which operating system you plan to use (e.g. Linux, Mac OS, Windows XP). Peter From sanjay.harke at gmail.com Thu Apr 2 17:40:58 2009 From: sanjay.harke at gmail.com (Sanjay Harke) Date: Thu, 2 Apr 2009 23:10:58 +0530 Subject: [BioSQL-l] Regarding help for MYSQL-BIOSQL-BIOPERL In-Reply-To: <320fb6e00904020625k41817242h72b5bc9b1b2c35d5@mail.gmail.com> References: <31bb4380904020336s1bb25d44xc275510cfa4acb86@mail.gmail.com> <320fb6e00904020625k41817242h72b5bc9b1b2c35d5@mail.gmail.com> Message-ID: <31bb4380904021040j3bf5df59w2e64d5f1379c5697@mail.gmail.com> Respected Peter, following are mine queries, I am using Window 2003 server. for database i am using MySql server. Already Install Bioperl. Now guide me about how to Install BioSql on my Pc? how install Biosql schema? How to use local database with Bioperl? sanjay From biopython at maubp.freeserve.co.uk Fri Apr 3 09:27:49 2009 From: biopython at maubp.freeserve.co.uk (Peter) Date: Fri, 3 Apr 2009 10:27:49 +0100 Subject: [BioSQL-l] Regarding help for MYSQL-BIOSQL-BIOPERL In-Reply-To: <31bb4380904021040j3bf5df59w2e64d5f1379c5697@mail.gmail.com> References: <31bb4380904020336s1bb25d44xc275510cfa4acb86@mail.gmail.com> <320fb6e00904020625k41817242h72b5bc9b1b2c35d5@mail.gmail.com> <31bb4380904021040j3bf5df59w2e64d5f1379c5697@mail.gmail.com> Message-ID: <320fb6e00904030227n558e6598p666875ff6af2986@mail.gmail.com> On Thu, Apr 2, 2009 at 6:40 PM, Sanjay Harke wrote: > > Respected Peter, > Hello again, Are you signed up to the BioSQL mailing list? General questions like this should be sent to the mailing list rather than just particular people like me or Hilmar. http://lists.open-bio.org/mailman/listinfo/biosql-l > following are mine queries, > > I am using Window 2003 server. > for database i am using MySql server. So you have installed MySQL server, good. See http://www.mysql.com/ for their documentation. > Already Install Bioperl. Good. > Now guide me about how to Install BioSql on my Pc? > how install Biosql schema? As I said before, I also recommend this Biopython page which starts by how to install BioSQL on MySQL (just ignore the Biopython bits): http://www.biopython.org/wiki/BioSQL The main page www.biosql.org links to this INSTALL document: http://code.open-bio.org/svnweb/index.cgi/biosql/checkout/biosql-schema/trunk/INSTALL > How to use local database with Bioperl? I have very little experience of using BioPerl with BioSQL - I use Biopython. I agree that this page isn't very helpful, but perhaps there is more documentation elsewhere which I don't know about: http://bioperl.org/wiki/Bioperl-db Peter From georgkam at gmail.com Fri Apr 3 12:09:38 2009 From: georgkam at gmail.com (georgkam at gmail.com) Date: Fri, 03 Apr 2009 12:09:38 +0000 Subject: [BioSQL-l] Regarding help for MYSQL-BIOSQL-BIOPERL In-Reply-To: <320fb6e00904030227n558e6598p666875ff6af2986@mail.gmail.com> Message-ID: <000e0cd2474637c9f20466a56ca1@google.com> Hey I have a written a tutorial on setting up BioSQL with rails on my blog http://biorelated.wordpress.com/2009/01/07/bio-graphics-biosql-and-rails-part-1 http://biorelated.wordpress.com/2009/01/08/bio-graphics-biosql-and-rails-part-2/ :) GG On Apr 3, 2009 12:27pm, Peter wrote: > On Thu, Apr 2, 2009 at 6:40 PM, Sanjay Harke sanjay.harke at gmail.com> > wrote: > > > > Respected Peter, > > > Hello again, > Are you signed up to the BioSQL mailing list? General questions like > this should be sent to the mailing list rather than just particular > people like me or Hilmar. > http://lists.open-bio.org/mailman/listinfo/biosql-l > > following are mine queries, > > > > I am using Window 2003 server. > > for database i am using MySql server. > So you have installed MySQL server, good. See http://www.mysql.com/ > for their documentation. > > Already Install Bioperl. > Good. > > Now guide me about how to Install BioSql on my Pc? > > how install Biosql schema? > As I said before, I also recommend this Biopython page which starts by > how to install BioSQL on MySQL (just ignore the Biopython bits): > http://www.biopython.org/wiki/BioSQL > The main page www.biosql.org links to this INSTALL document: > http://code.open-bio.org/svnweb/index.cgi/biosql/checkout/biosql-schema/trunk/INSTALL > > How to use local database with Bioperl? > I have very little experience of using BioPerl with BioSQL - I use > Biopython. I agree that this page isn't very helpful, but perhaps > there is more documentation elsewhere which I don't know about: > http://bioperl.org/wiki/Bioperl-db > Peter > _______________________________________________ > BioSQL-l mailing list > BioSQL-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/biosql-l From cjfields at illinois.edu Thu Apr 16 20:19:16 2009 From: cjfields at illinois.edu (Chris Fields) Date: Thu, 16 Apr 2009 15:19:16 -0500 Subject: [BioSQL-l] bioperl-db, CORBA, and Oracle Message-ID: <7EA5FDDE-F402-4B0A-9195-E815B7C4AA1D@illinois.edu> Allen Day indicated (in an RT bug report) that bioperl-db has references to several modules not in CPAN, all CORBA-related (via bioperl-corba-server). Should we remove those, or is anyone still using them? The modules aren't available via CPAN. scripts/corba/bioenv_server.pl (references Bio::CorbaServer::BioEnv) scripts/corba/caching_corba_server.pl (references Bio::CorbaServer::BioEnv and Bio::CorbaClient::SeqDB) Related to this is an additional module in CPAN but apparently required separately: CORBA::ORBit (referenced in scripts/corba/bioenv_server.pl, scripts/ corba/test_bioenv.pl, and scripts/corba/caching_corba_server.pl) Also, there appears to be a requirement for DBD::Oracle in Bio::DB::BioSQL::Oracle::BasePersistenceAdaptorDriver that's popping up. I can add that to the 'recommends' but it doesn't really fit in with this category (i.e. if I use MySQL I shouldn't need to worry about it). * DBD::Oracle (referenced in Bio::DB::BioSQL::Oracle::BiosequenceAdaptorDriver and Bio::DB::BioSQL::Oracle::BasePersistenceAdaptorDriver Here's the RT ticket: https://rt.cpan.org/Ticket/Display.html?id=44466 chris From ccanchaya at gmail.com Mon Apr 20 15:44:24 2009 From: ccanchaya at gmail.com (Carlos A. Canchaya) Date: Mon, 20 Apr 2009 17:44:24 +0200 Subject: [BioSQL-l] Can I load ontologies into BioSQL? Message-ID: Hi guys I'm working with biosql and I try to figure out how to load ontologies into biosql. I've tried load_ontology.pl --driver mysql --dbuser carlos --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, ------------------- WARNING --------------------- MSG: DBLink exists in the dblink of _default --------------------------------------------------- ------------- EXCEPTION ------------- MSG: format error (file 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 Bio::OntologyIO::dagflat::_parse_flat_file /usr/local/share/perl/ 5.10.0/Bio/OntologyIO/dagflat.pm:627 STACK Bio::OntologyIO::dagflat::parse /usr/local/share/perl/5.10.0/Bio/ OntologyIO/dagflat.pm:284 STACK Bio::OntologyIO::dagflat::next_ontology /usr/local/share/perl/ 5.10.0/Bio/OntologyIO/dagflat.pm:317 STACK toplevel /usr/local/share/biosql/bioperl-db/scripts/biosql/ load_ontology.pl:604 ------------------------------------- Any suggestion? Cheers, Carlos