From daniel.lang at biologie.uni-freiburg.de Tue Dec 7 09:18:45 2004 From: daniel.lang at biologie.uni-freiburg.de (Daniel Lang) Date: Tue Dec 7 09:16:21 2004 Subject: [BioSQL-l] citation Message-ID: <41B5BBC5.1090606@biologie.uni-freiburg.de> Hi, How do I cite BioSQL? -- Daniel Lang University of Freiburg, Plant Biotechnology Sonnenstr. 5, D-79104 Freiburg phone: +49 761 203 6988 homepage: http://www.plant-biotech.net/ e-mail: daniel.lang@biologie.uni-freiburg.de ################################################# My software never has bugs. It just develops random features. ################################################# From m_conte at hotmail.com Fri Dec 10 05:49:43 2004 From: m_conte at hotmail.com (matthieu CONTE) Date: Fri Dec 10 10:11:14 2004 Subject: [BioSQL-l] tigr.pm In-Reply-To: <200412101145.03569.manuel.ruiz@cirad.fr> Message-ID: I am trying to load tigr rice data in my biosql db with the load_seqdatabase.pl using the lastest tigr parser on the CVS. I still have the same problem with null field Thanks perl load_seqdatabase.pl --dbuser biosql --dbpass biosql --namespace tigr_arath --format tigr /home/conte/pipeline_orthologues/data/arath_tigr/CHR1.R5v01212004.xml Loading /home/conte/pipeline_orthologues/data/arath_tigr/CHR1.R5v01212004.xml ... -------------------- WARNING --------------------- MSG: insert in Bio::DB::BioSQL::LocationAdaptor (driver) failed, values were ("130","2000","","1") FKs (16962,) Column 'strand' cannot be null --------------------------------------------------- ************************************** m_conte@hotmail.com CIRAD ************************************** _________________________________________________________________ MSN Messenger : dialoguez en temps r?el avec vos amis ! http://g.msn.fr/FR1001/866 From hlapp at gnf.org Fri Dec 10 12:34:54 2004 From: hlapp at gnf.org (Hilmar Lapp) Date: Fri Dec 10 12:32:21 2004 Subject: [BioSQL-l] tigr.pm In-Reply-To: References: Message-ID: Strand is NOT NULLable in all three (MySQL, Pg, Oracle) versions of the schema. This constraint could be relaxed, as Strand is not part of any unique key constraint. OTOH the designated value for an unknown strand is 0 in bioperl, not NULL or undef. Furthermore, the schema defines 0 as the default value for the Strand column. Unfortunately, this doesn't help if the column is explicitly inserted as NULL. I could add a fix to the LocationAdapter to default a null strand to 0. Any opinions? I'm leaning towards adding a fix to LocationAdapter to fix this problem immediately and forever. -hilmar On Dec 10, 2004, at 2:49 AM, matthieu CONTE wrote: > I am trying to load tigr rice data in my biosql db with the > load_seqdatabase.pl using the lastest tigr parser on the CVS. > I still have the same problem with null field > > Thanks > > perl load_seqdatabase.pl --dbuser biosql --dbpass biosql --namespace > tigr_arath --format tigr > /home/conte/pipeline_orthologues/data/arath_tigr/CHR1.R5v01212004.xml > Loading > /home/conte/pipeline_orthologues/data/arath_tigr/CHR1.R5v01212004.xml > ... > > -------------------- WARNING --------------------- > MSG: insert in Bio::DB::BioSQL::LocationAdaptor (driver) failed, > values were ("130","2000","","1") FKs (16962,) > Column 'strand' cannot be null > --------------------------------------------------- > > ************************************** > m_conte@hotmail.com > CIRAD > ************************************** > > _________________________________________________________________ > MSN Messenger : dialoguez en temps r?el avec vos amis ! > http://g.msn.fr/FR1001/866 > > _______________________________________________ > BioSQL-l mailing list > BioSQL-l@open-bio.org > http://open-bio.org/mailman/listinfo/biosql-l > -- ------------------------------------------------------------- Hilmar Lapp email: lapp at gnf.org GNF, San Diego, Ca. 92121 phone: +1-858-812-1757 ------------------------------------------------------------- From laurichj at bioinfo.ucr.edu Fri Dec 10 16:09:19 2004 From: laurichj at bioinfo.ucr.edu (Josh Lauricha Hi) Date: Fri Dec 10 16:07:07 2004 Subject: [Bioperl-l] Re: [BioSQL-l] tigr.pm In-Reply-To: References:

Message-ID: <20041210210919.GB17108@bioinfo.ucr.edu> The problem with setting strand in tigr.pm is that, for simplicity, I've already reversed the strands to the positive oriantation. So while their not "unknown" they are neither positive nor negative. Marking a positive strand as positive is fine, but marking a negative strand as negative is not, since it has been reversed already. It might be misinterpreted (by code or people) that a negative strand must be reversed again. On Fri 12/10/04 09:34, Hilmar Lapp wrote: > Strand is NOT NULLable in all three (MySQL, Pg, Oracle) versions of the > schema. > > This constraint could be relaxed, as Strand is not part of any unique > key constraint. > > OTOH the designated value for an unknown strand is 0 in bioperl, not > NULL or undef. > > Furthermore, the schema defines 0 as the default value for the Strand > column. Unfortunately, this doesn't help if the column is explicitly > inserted as NULL. > > I could add a fix to the LocationAdapter to default a null strand to 0. > > Any opinions? I'm leaning towards adding a fix to LocationAdapter to > fix this problem immediately and forever. > > -hilmar > > On Dec 10, 2004, at 2:49 AM, matthieu CONTE wrote: > > >I am trying to load tigr rice data in my biosql db with the > >load_seqdatabase.pl using the lastest tigr parser on the CVS. > >I still have the same problem with null field > > > >Thanks > > > >perl load_seqdatabase.pl --dbuser biosql --dbpass biosql --namespace > >tigr_arath --format tigr > >/home/conte/pipeline_orthologues/data/arath_tigr/CHR1.R5v01212004.xml > >Loading > >/home/conte/pipeline_orthologues/data/arath_tigr/CHR1.R5v01212004.xml > >... > > > >-------------------- WARNING --------------------- > >MSG: insert in Bio::DB::BioSQL::LocationAdaptor (driver) failed, > >values were ("130","2000","","1") FKs (16962,) > >Column 'strand' cannot be null > >--------------------------------------------------- > > > >************************************** > >m_conte@hotmail.com > >CIRAD > >************************************** > > > >_________________________________________________________________ > >MSN Messenger : dialoguez en temps r?el avec vos amis ! > >http://g.msn.fr/FR1001/866 > > > >_______________________________________________ > >BioSQL-l mailing list > >BioSQL-l@open-bio.org > >http://open-bio.org/mailman/listinfo/biosql-l > > > -- > ------------------------------------------------------------- > Hilmar Lapp email: lapp at gnf.org > GNF, San Diego, Ca. 92121 phone: +1-858-812-1757 > ------------------------------------------------------------- > > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l@portal.open-bio.org > http://portal.open-bio.org/mailman/listinfo/bioperl-l > -- ------------------------------------------------------ | Josh Lauricha | Ford, you're turning | | laurichj@bioinfo.ucr.edu | into a penguin. Stop | | Bioinformatics, UCR | it | |----------------------------------------------------| | OpenPG: | | 4E7D 0FC0 DB6C E91D 4D7B C7F3 9BE9 8740 E4DC 6184 | |----------------------------------------------------| From bhurwitz3 at mac.com Wed Dec 15 16:48:41 2004 From: bhurwitz3 at mac.com (Bonnie Hurwitz) Date: Wed Dec 15 16:50:00 2004 Subject: [BioSQL-l] socket / port Message-ID: <15AD38C0-4EE3-11D9-9D3A-000D9344D428@mac.com> Hi, Is there a way to specify which socket and port you would like mysql to use when using the load_seqdatabase.pl script from bioperl? -Bonnie From hlapp at gnf.org Wed Dec 15 17:59:47 2004 From: hlapp at gnf.org (Hilmar Lapp) Date: Wed Dec 15 17:57:20 2004 Subject: [BioSQL-l] socket / port In-Reply-To: <15AD38C0-4EE3-11D9-9D3A-000D9344D428@mac.com> Message-ID: <048A57D2-4EED-11D9-9A39-000A959EB4C4@gnf.org> My knee-jerk response was going to be --port. I've realized, however, that although Bio::DB::BioDB accepts the port as a named argument, the script doesn't let you specify it. I'll fix that, and the name of the argument will be --port. -hilmar On Wednesday, December 15, 2004, at 01:48 PM, Bonnie Hurwitz wrote: > Hi, > > Is there a way to specify which socket and port you would like mysql > to use when using the load_seqdatabase.pl script from bioperl? > > -Bonnie > > _______________________________________________ > BioSQL-l mailing list > BioSQL-l@open-bio.org > http://open-bio.org/mailman/listinfo/biosql-l > -- ------------------------------------------------------------- Hilmar Lapp email: lapp at gnf.org GNF, San Diego, Ca. 92121 phone: +1-858-812-1757 ------------------------------------------------------------- From hlapp at gnf.org Thu Dec 16 01:38:28 2004 From: hlapp at gnf.org (Hilmar Lapp) Date: Thu Dec 16 01:35:39 2004 Subject: [BioSQL-l] socket / port In-Reply-To: <048A57D2-4EED-11D9-9A39-000A959EB4C4@gnf.org> Message-ID: <181643C1-4F2D-11D9-AE59-000A959EB4C4@gnf.org> Fixed and committed. Let me know if it doesn't work for you. You will need to allow for a bit of a delay in order for the anonymous cvs server to reflect the change. -hilmar On Wednesday, December 15, 2004, at 02:59 PM, Hilmar Lapp wrote: > My knee-jerk response was going to be --port. I've realized, however, > that although Bio::DB::BioDB accepts the port as a named argument, the > script doesn't let you specify it. I'll fix that, and the name of the > argument will be --port. > > -hilmar > > On Wednesday, December 15, 2004, at 01:48 PM, Bonnie Hurwitz wrote: > >> Hi, >> >> Is there a way to specify which socket and port you would like mysql >> to use when using the load_seqdatabase.pl script from bioperl? >> >> -Bonnie >> >> _______________________________________________ >> BioSQL-l mailing list >> BioSQL-l@open-bio.org >> http://open-bio.org/mailman/listinfo/biosql-l >> > -- > ------------------------------------------------------------- > Hilmar Lapp email: lapp at gnf.org > GNF, San Diego, Ca. 92121 phone: +1-858-812-1757 > ------------------------------------------------------------- > > > _______________________________________________ > BioSQL-l mailing list > BioSQL-l@open-bio.org > http://open-bio.org/mailman/listinfo/biosql-l > -- ------------------------------------------------------------- Hilmar Lapp email: lapp at gnf.org GNF, San Diego, Ca. 92121 phone: +1-858-812-1757 ------------------------------------------------------------- From hlapp at gnf.org Thu Dec 16 05:18:43 2004 From: hlapp at gnf.org (Hilmar Lapp) Date: Thu Dec 16 05:21:04 2004 Subject: [BioSQL-l] tigr.pm In-Reply-To: Message-ID: On Friday, December 10, 2004, at 09:34 AM, Hilmar Lapp wrote: > I could add a fix to the LocationAdapter to default a null strand to 0. > > Any opinions? I'm leaning towards adding a fix to LocationAdapter to > fix this problem immediately and forever. I'm taking this back. This is exactly what LocationAdapter does already. There shouldn't be an undefined strand that ever makes it to an INSERT attempt. Which version are you using? -hilmar -- ------------------------------------------------------------- Hilmar Lapp email: lapp at gnf.org GNF, San Diego, Ca. 92121 phone: +1-858-812-1757 ------------------------------------------------------------- From gd at firewall.biotec.tu-dresden.de Fri Dec 17 10:21:52 2004 From: gd at firewall.biotec.tu-dresden.de (Gihan) Date: Tue Dec 28 13:52:11 2004 Subject: [BioSQL-l] bioseq swissprot Medline links Message-ID: <41C2F990.2010205@biotec.tu-dresden.de> Hi all, We installed swissprot as the first database in the bioseqdb scheme (using load_seqdatabase.pl) and apparently it looked succesful (using --safe). However, when we tried to join the bioentry table to the dbxref through bioentry_dbxref to get the MEDLINE refrences it seems like these link doesnt exist for MEDLINE but for PDB for example . Any idea how to get those links working?? Cheers, Gihan Dawelbait PhD student, BioTec Dresden From hlapp at gnf.org Thu Dec 30 23:51:24 2004 From: hlapp at gnf.org (Hilmar Lapp) Date: Thu Dec 30 23:48:24 2004 Subject: [BioSQL-l] bioseq swissprot Medline links In-Reply-To: <41C2F990.2010205@biotec.tu-dresden.de> Message-ID: <9FBBDE66-5AE7-11D9-8063-000A959EB4C4@gnf.org> What was the query that you issued? Note that the references (RN lines and friends) in swissprot end up as rows in the table reference, with bioentry_reference being the association table with bioentry. The reference table does have a foreign key to dbxref for the actual pubmed or medline id. So, in order to just get bioentries and pubmed/medline ids in the query you still need to join through bioentry_reference and reference. BTW there were certain problems with swissprot reference parsing in certain versions of bioperl. You may want to read the respective email to the bioperl-l list if you haven't yet: http://bioperl.org/pipermail/bioperl-l/2004-December/017649.html -hilmar On Friday, December 17, 2004, at 07:21 AM, Gihan wrote: > Hi all, > > We installed swissprot as the first database in the bioseqdb scheme > (using load_seqdatabase.pl) and apparently it looked succesful (using > --safe). However, when we tried to join the bioentry table to the > dbxref > through bioentry_dbxref to get the MEDLINE refrences it seems like > these link doesnt exist for MEDLINE but for PDB for example . > > Any idea how to get those links working?? > > Cheers, > Gihan Dawelbait > PhD student, > BioTec Dresden > > > > > > _______________________________________________ > BioSQL-l mailing list > BioSQL-l@open-bio.org > http://open-bio.org/mailman/listinfo/biosql-l > -- ------------------------------------------------------------- Hilmar Lapp email: lapp at gnf.org GNF, San Diego, Ca. 92121 phone: +1-858-812-1757 -------------------------------------------------------------