From lacava at gmail.com Fri Jul 3 19:17:43 2009 From: lacava at gmail.com (John LaCava) Date: Fri, 3 Jul 2009 19:17:43 -0400 Subject: [BioSQL-l] Question regarding BioPerl / BioSQL - InterPro Optional IDs References: <48FCB39E-5CA8-4BE9-825D-49CFB14FDBB7@gmail.com> Message-ID: Hi all, Tried this on the BioPerl-l but seemed to make sense to try here as well. I am trying to use the BioPerl-db script: "load_seqdatabase.pl" to parse a SwissProt ".dat" file (Yeast.dat, this is the yeast proteome with annotations etc.). The particular entry I am interested is the InterPro optional ID, which is the domain name. I have put a short stub up which displays the 4 pieces of info I want to parse into my data base. That can be found here: http://github.com/johnraekwon/BioPerl---BioSQL---InterPro-Optional-IDs/tree/master You can see that near the bottom, we get the optional ID: $protein_ids->{interpro_domain} = $dblink->{optional_id}; I do not think the bioperl script load_seqdatabase.pl retrieves this information. At least, I cannot find it in the db built from parsing a test .dat file. I would like some help figuring out: 1) WHY doesn't it retrieve this information, since it seems to be parsing "all" annotations... 2) HOW might I edit the script to include this particular annotation of interest in the info it passes to my db (biosql) I am a bit out of my depth on this, and so, any help is appreciated. Cheers, John From stevey_mac2k2 at hotmail.com Sat Jul 4 06:17:13 2009 From: stevey_mac2k2 at hotmail.com (Steven McGowan) Date: Sat, 4 Jul 2009 10:17:13 +0000 Subject: [BioSQL-l] Having problems installing BioSQL on Mac 10.5 Message-ID: Hi,I'm trying to load a schema for biosql.I have created a database called "biosql" in MySQL, but i'm trying to load the biosql-schema/sql in MySQL with the command:>mysql -u root biosql < biosqldb-mysql.sqlThe "biosqldb-mysql.sql file is currently located on my mac in:/Users/stevey_mac2k2/Desktop/ExerciseTwo/biosql-1.0.1/sql My MySQL is currently saved in:usr/local/mysql-5.1.35-osx10.5-x86/binI have created a .profile for my mysql commands with the script:export PATH=/usr/local/mysql-5.1.35-osx10.5-x86/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/bin:/usr/X11/bin:$PATHi try the command:bash-3.2# mysql -u root biosql < biosqldb-mysql.sqlbash: mysql: command not foundAny help would be greatly appreciated.Thanks! _________________________________________________________________ Get the best of MSN on your mobile http://clk.atdmt.com/UKM/go/147991039/direct/01/ From holland at eaglegenomics.com Sat Jul 4 07:02:27 2009 From: holland at eaglegenomics.com (Richard Holland) Date: Sat, 04 Jul 2009 12:02:27 +0100 Subject: [BioSQL-l] Having problems installing BioSQL on Mac 10.5 In-Reply-To: References: Message-ID: <1246705347.5437.34.camel@buzzybee> First thing to check is that MySQL is correctly installed. Is there a 'mysql' program in the following location: /usr/local/mysql-5.1.35-osx10.5-x86/bin Secondly, type the following command in your shell: echo $PATH and see if it includes the path to your MySQL installation. In either case what you've got here is not a problem with BioSQL, but with the MySQL installation process. Your best place to ask for help in this respect would be the MySQL support pages or mailing lists. cheers, Richard -- Richard Holland, BSc MBCS Operations and Delivery Director, Eagle Genomics Ltd T: +44 (0)1223 654481 ext 3 | E: holland at eaglegenomics.com http://www.eaglegenomics.com/ From hlapp at gmx.net Sat Jul 4 07:57:18 2009 From: hlapp at gmx.net (Hilmar Lapp) Date: Sat, 4 Jul 2009 07:57:18 -0400 Subject: [BioSQL-l] Can I load ontologies into BioSQL? In-Reply-To: <59386.10.2.4.168.1245679938.squirrel@webmail.istge.it> References: <59386.10.2.4.168.1245679938.squirrel@webmail.istge.it> Message-ID: (FYI, changed to BioPerl list as this is a BioPerl issue with the old GO format. -hilmar) On Jun 22, 2009, at 10:12 AM, Achille Zappa wrote: > 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 > _______________________________________________ > BioSQL-l mailing list > BioSQL-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/biosql-l -- =========================================================== : Hilmar Lapp -:- Durham, NC -:- hlapp at gmx dot net : =========================================================== From hlapp at gmx.net Sat Jul 4 09:18:32 2009 From: hlapp at gmx.net (Hilmar Lapp) Date: Sat, 4 Jul 2009 09:18:32 -0400 Subject: [BioSQL-l] Question regarding BioPerl / BioSQL - InterPro Optional IDs In-Reply-To: References: <48FCB39E-5CA8-4BE9-825D-49CFB14FDBB7@gmail.com> Message-ID: <41958574-1C50-4A21-889F-8A02043190C8@gmx.net> The problem here is that Bioperl-db (the persistence mapper between BioSQL and BioPerl) loses the optional_id property of Bio::Annotation::DBLink objects. Moreover, the dbxref table in BioSQL doesn't actually provide for the opportunity to store two identifiers (or accessions) for one db_xref, so storing this bit of information is actually not as straightforward as one might wish b/c it would need to go into the dbxref_qualifier_value table, and I would not be surprised if the other Bio* projects with a mapping to BioSQL don't store or retrieve this either (though it'd be good to hear if anyone does). Here are a couple of ideas for how this issue might be addressed. - Write a Bio::Seq::BaseSeqProcessor-derived object that for every incoming sequence massages all Interpro links to either substitute the primary_id with the optional_id, or to add a second DBLink annotation with the optional_id of the original one as its primary_id. (pros: relatively easy, entirely under your control; cons: you either lose the primary_id now, or have two dbxref annotations for each of the original ones.) - Add a column to the dbxref table, and code to Bioperl-db, that store, de/serialize the extra ID. (pros: not losing or duplicating any data; cons: change is significant in terms of schema stability, requires new release, depends on implementation in Bioperl-db, necessitates update of all other Bio* language bindings) - De/serialize the optional_id as an entry in the dbxref_qualifier_value table. (pros: technically it's the Right Way as that's what the table was intended for; cons: implementing in Bioperl- db is more involved as we now need to transform an object property to a child object and back) So I'd say this is a bug in Bioperl-db in that the dbxref_qualifier_value table isn't utilized here. Would you mind filing it? In the meantime, if you just need something that works, you could try the first of the above ideas. -hilmar On Jul 3, 2009, at 7:17 PM, John LaCava wrote: > Hi all, > > Tried this on the BioPerl-l but seemed to make sense to try here as > well. > > I am trying to use the BioPerl-db script: > > "load_seqdatabase.pl" to parse a SwissProt ".dat" file (Yeast.dat, > this is the yeast proteome with annotations etc.). > > The particular entry I am interested is the InterPro optional ID, > which is the domain name. > > I have put a short stub up which displays the 4 pieces of info I > want to parse into my data base. > That can be found here: > > http://github.com/johnraekwon/BioPerl---BioSQL---InterPro-Optional-IDs/tree/master > > You can see that near the bottom, we get the optional ID: > $protein_ids->{interpro_domain} = $dblink->{optional_id}; > > I do not think the bioperl script load_seqdatabase.pl retrieves this > information. At least, I cannot find it in the db built from > parsing a test .dat file. > I would like some help figuring out: > 1) WHY doesn't it retrieve this information, since it seems to be > parsing "all" annotations... > 2) HOW might I edit the script to include this particular annotation > of interest in the info it passes to my db (biosql) > > I am a bit out of my depth on this, and so, any help is appreciated. > > Cheers, > John > > > _______________________________________________ > BioSQL-l mailing list > BioSQL-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/biosql-l -- =========================================================== : Hilmar Lapp -:- Durham, NC -:- hlapp at gmx dot net : =========================================================== From hlapp at gmx.net Sat Jul 4 09:22:19 2009 From: hlapp at gmx.net (Hilmar Lapp) Date: Sat, 4 Jul 2009 09:22:19 -0400 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: Hi Florian, sorry this fell through the cracks, too much traveling. VARCHAR BINARY in MySQL means that the column is a VARCHAR type but values (and searches against them) are treated case-sensitive. Since treating VARCHAR values case sensitive is standard in SQL everywhere else and presumably also in DB2, you should map it to a simple VARCHAR type. Where did you find that MySQL's VARCHAR BINARY needs to be VARBINARY in DB2? -hilmar On Jun 4, 2009, at 9:52 AM, Florian Mittag wrote: > 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 > _______________________________________________ > BioSQL-l mailing list > BioSQL-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/biosql-l -- =========================================================== : Hilmar Lapp -:- Durham, NC -:- hlapp at gmx dot net : =========================================================== From biopython at maubp.freeserve.co.uk Sun Jul 5 06:24:14 2009 From: biopython at maubp.freeserve.co.uk (Peter) Date: Sun, 5 Jul 2009 11:24:14 +0100 Subject: [BioSQL-l] SQLite support In-Reply-To: <320fb6e00812150243w4b0dc223g40abcf684af1ccf5@mail.gmail.com> References: <1f864af10812150224y540f1ba6y6b30168102885fcd@mail.gmail.com> <320fb6e00812150243w4b0dc223g40abcf684af1ccf5@mail.gmail.com> Message-ID: <320fb6e00907050324i6d64d3abreb4d0c256bf1bdc4@mail.gmail.com> On Mon, Dec 15, 2008 at 11:43 AM, Peter wrote: > On Mon, Dec 15, 2008, vanaquisl vanaquisl wrote: >> >> Hi folks, >> >> I am a brand new BioSQL user and I'd like to know if there will be a SQLite >> support in the near future? > > As far as I know, BioSQL does not currently include a schema for SQLite. This was one of the things Brad Chapman and I discussed with Hilmar Lapp last week at BOSC/ISMB 2009. I've just filed BioSQL enhancement Bug 2870 on this: http://bugzilla.open-bio.org/show_bug.cgi?id=2870 >> I am about to use SQLite for a standalone lightweight Biopython application >> and it would be very helpful if I could use BioSQL directly. > > Biopython can talk to a BioSQL database run on MySQL (using MySQLdb), > PostgreSQL (using either Psycopg or Psycopg2). In theory it could be > extended to use any supported BioSQL database (provided there are > python bindings for the database software, in the case of SQLite using > pysqlite would probably fine). We have a proof of principle implementation of the Biopython BioSQL bindings working with BioSQL on SQLite, see enhancement Bug 2866: http://bugzilla.open-bio.org/show_bug.cgi?id=2866 Peter From lacava at gmail.com Sun Jul 5 16:30:52 2009 From: lacava at gmail.com (John LaCava) Date: Sun, 5 Jul 2009 16:30:52 -0400 Subject: [BioSQL-l] Syntax for load_interpro.pl? Message-ID: Greetings, I am attempting to use this script, but I don't seem to be able to determine the appropriate syntax. Documentation on this script seems minimal. Moreover, I am not yet terribly experienced with these endeavors. Could someone possibly provide me with an example syntax? e.g. > load_interpro.pl ... then what? I must specify -db -file -version ? I tried a couple of ways, but I get the similar errors each time: e.g. /usr/local/bin/bp_load_interpro.pl: line 29: syntax error near unexpected token `$file,' /usr/local/bin/bp_load_interpro.pl: line 29: `my ($file, $version);' Also, from reading the comments, it appears this is supposed to be made obsolete or superseded by the script load_ontologies.pl. Why is this? Sorry to bother, and thanks in advance. John From hlapp at gmx.net Sun Jul 5 17:58:27 2009 From: hlapp at gmx.net (Hilmar Lapp) Date: Sun, 5 Jul 2009 17:58:27 -0400 Subject: [BioSQL-l] Syntax for load_interpro.pl? In-Reply-To: References: Message-ID: <1F926EFE-0B0B-4FAC-B12F-4E0DE11C485A@gmx.net> (Changed to and responded on Bioperl list as it is part of bioperl-db) On Jul 5, 2009, at 4:30 PM, John LaCava wrote: > Greetings, > > I am attempting to use this script, but I don't seem to be able to > determine the appropriate syntax. > Documentation on this script seems minimal. Moreover, I am not yet > terribly experienced with > these endeavors. > > Could someone possibly provide me with an example syntax? > > e.g. > load_interpro.pl ... > > then what? > > I must specify -db -file -version ? > > I tried a couple of ways, but I get the similar errors each time: > > e.g. > /usr/local/bin/bp_load_interpro.pl: line 29: syntax error near > unexpected token `$file,' > /usr/local/bin/bp_load_interpro.pl: line 29: `my ($file, $version);' > > Also, from reading the comments, it appears this is supposed to be > made obsolete or superseded by > the script load_ontologies.pl. Why is this? > > Sorry to bother, and thanks in advance. > > John > _______________________________________________ > BioSQL-l mailing list > BioSQL-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/biosql-l -- =========================================================== : Hilmar Lapp -:- Durham, NC -:- hlapp at gmx dot net : =========================================================== From sanjay.harke at gmail.com Mon Jul 6 01:01:34 2009 From: sanjay.harke at gmail.com (Sanjay Harke) Date: Mon, 6 Jul 2009 10:31:34 +0530 Subject: [BioSQL-l] BioSQL- connectivity Message-ID: <31bb4380907052201v6e16ac8dn449064bb4606292f@mail.gmail.com> Dear sir, Kindly guide me about BioSQL database connectivity. Here i installed BioSql on my PC. For database connectivity i am facing about it. sanjay From roy.chaudhuri at gmail.com Mon Jul 6 06:05:36 2009 From: roy.chaudhuri at gmail.com (Roy Chaudhuri) Date: Mon, 06 Jul 2009 11:05:36 +0100 Subject: [BioSQL-l] BioSQL- connectivity In-Reply-To: <31bb4380907052201v6e16ac8dn449064bb4606292f@mail.gmail.com> References: <31bb4380907052201v6e16ac8dn449064bb4606292f@mail.gmail.com> Message-ID: <4A51CC70.2040003@gmail.com> Hi Sanjay, You have sent several messages like this to the BioSQL and BioPerl mailing lists, and not received many replies. The reason for this is not that we do not want to help, just that you do not include enough detail about what your problem is. What have you tried? What error messages do you get? Which operating system and database software are you using? Have you read all the relevant documentation? Have you tried searching the internet and specifically the mailing list archives for problems similar to the one you are facing? You are more likely to get a response on the mailing list if you clearly define exactly what your problem is and the steps you have tried to overcome it. Roy. Sanjay Harke wrote: > Dear sir, > > Kindly guide me about BioSQL database connectivity. > Here i installed BioSql on my PC. > For database connectivity i am facing about it. > > sanjay > _______________________________________________ > BioSQL-l mailing list > BioSQL-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/biosql-l From roy.chaudhuri at gmail.com Mon Jul 6 07:39:33 2009 From: roy.chaudhuri at gmail.com (Roy Chaudhuri) Date: Mon, 06 Jul 2009 12:39:33 +0100 Subject: [BioSQL-l] BioSQL- connectivity In-Reply-To: <31bb4380907060351u4fb0041dla533cdf1e4f35ad8@mail.gmail.com> References: <31bb4380907052201v6e16ac8dn449064bb4606292f@mail.gmail.com> <4A51CC70.2040003@gmail.com> <31bb4380907060351u4fb0041dla533cdf1e4f35ad8@mail.gmail.com> Message-ID: <4A51E275.3060809@gmail.com> Hi Sanjay, Please keep replies on the mailing list (reply to all), that way others can also respond. I don't think there is a tutorial for BioSQL using BioPerl. There are some links to useful documentation on the BioSQL wiki: http://biosql.org/wiki/Main_Page The BioSQL INSTALL file provides instructions for getting your database set up and loading sequences into it: http://code.open-bio.org/svnweb/index.cgi/biosql/view/biosql-schema/trunk/INSTALL There are some examples of retrieving a sequence from a BioSQL database using BioPerl in Hilmar's Persistent BioPerl presentation: http://precedings.nature.com/documents/1233/version/1 Try loading your BioSQL database with some sequences, then retrieving them using code based on the examples in the presentation. If you run into problems e-mail the mailing list with a full description of what you were trying to do (including the code you were using, and any error messages that were reported), and I'm sure someone will be able to help. Roy. Sanjay Harke wrote: > Dear sir, > > Do you have any basic tutorial on Biosql-Bioperl ? > If available kindly send me it. > > sanjay From florian.mittag at uni-tuebingen.de Mon Jul 6 08:34:49 2009 From: florian.mittag at uni-tuebingen.de (Florian Mittag) Date: Mon, 6 Jul 2009 14:34:49 +0200 Subject: [BioSQL-l] Question about VARCHAR BINARY In-Reply-To: References: <200906041552.59221.florian.mittag@uni-tuebingen.de> Message-ID: <200907061434.49402.florian.mittag@uni-tuebingen.de> Hi Hilmar, thanks for the answer, we sortof solved the problem differently, because other databases (like PostgreSQL) do not specifiy those columns as VARBINARY, so we simply took those scheme as the foundation for our DB2 scheme. On Saturday 04 July 2009 15:22, Hilmar Lapp wrote: > Hi Florian, > > sorry this fell through the cracks, too much traveling. VARCHAR BINARY > in MySQL means that the column is a VARCHAR type but values (and > searches against them) are treated case-sensitive. Oh, I didn't know that. I thought it was about handling non-displayable characters. > Since treating VARCHAR values case sensitive is standard in SQL > everywhere else and presumably also in DB2, you should map it to a > simple VARCHAR type. > > Where did you find that MySQL's VARCHAR BINARY needs to be VARBINARY > in DB2? Chapter 11: MySQL converter ftp://ftp.software.ibm.com/software/data/db2/migration/mtk/mtk_2050.pdf Florian > On Jun 4, 2009, at 9:52 AM, Florian Mittag wrote: > > 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 > > _______________________________________________ > > BioSQL-l mailing list > > BioSQL-l at lists.open-bio.org > > http://lists.open-bio.org/mailman/listinfo/biosql-l From biopython at maubp.freeserve.co.uk Mon Jul 6 12:19:54 2009 From: biopython at maubp.freeserve.co.uk (Peter) Date: Mon, 6 Jul 2009 17:19:54 +0100 Subject: [BioSQL-l] [Bioperl-l] DB2 driver for BioPerl In-Reply-To: <200907061808.18651.florian.mittag@uni-tuebingen.de> References: <200907021128.21239.florian.mittag@uni-tuebingen.de> <5EC3CB83-22AD-4C79-9F6C-047ED58B7962@gmx.net> <200907061808.18651.florian.mittag@uni-tuebingen.de> Message-ID: <320fb6e00907060919w1ce69284r30fede63ec05adbb@mail.gmail.com> On BioPerl-l, July 2009, Florian Mittag wrote: > ... > Okay, I'll do that, but that will take some time and I'll probably turn to > this mailings for further assistance with more specific questions. > ... > I will keep you updated on the Perl issues and hope to have some useful > results by the end of the week. And I hope you excuse me for posting things > here that are hardly related to BioPerl, but the some problems are a complex > entanglement of issues with BioSQL, BioPerl and BioJava, so it's hard to > decide where to post it ;-) You may want to cross post some things (e.g. the hibernate issue to BioSQL and BioJava lists). I've CC'd this reply to BioSQL-l for example. I think some guidance from Hilmar on this etiquette would help ;) I would not expect BioJava people to follow BioPerl-l for example. (Although here I am as a Biopython person keeping an eye on BioPerl-l sometimes). I assume (hope?) that people from all the Bio* projects with BioSQL bindings will be following the BioSQL-l mailing list - so for anything clearly cross project like the schemas themselves, at very least please CC the BioSQL-l mailing list. Peter (Biopython) From biopython at maubp.freeserve.co.uk Thu Jul 9 08:29:14 2009 From: biopython at maubp.freeserve.co.uk (Peter) Date: Thu, 9 Jul 2009 13:29:14 +0100 Subject: [BioSQL-l] SQLite support In-Reply-To: <320fb6e00907050324i6d64d3abreb4d0c256bf1bdc4@mail.gmail.com> References: <1f864af10812150224y540f1ba6y6b30168102885fcd@mail.gmail.com> <320fb6e00812150243w4b0dc223g40abcf684af1ccf5@mail.gmail.com> <320fb6e00907050324i6d64d3abreb4d0c256bf1bdc4@mail.gmail.com> Message-ID: <320fb6e00907090529t61239952y1c86963f13c1db78@mail.gmail.com> On Sun, Jul 5, 2009 at 11:24 AM, Peter wrote: > On Mon, Dec 15, 2008 at 11:43 AM, Peter wrote: >> On Mon, Dec 15, 2008, vanaquisl vanaquisl wrote: >>> >>> Hi folks, >>> >>> I am a brand new BioSQL user and I'd like to know if there will be a SQLite >>> support in the near future? >> >> As far as I know, BioSQL does not currently include a schema for SQLite. > > This was one of the things Brad Chapman and I discussed with Hilmar Lapp > last week at BOSC/ISMB 2009. I've just filed BioSQL enhancement Bug 2870 > on this: http://bugzilla.open-bio.org/show_bug.cgi?id=2870 > >>> I am about to use SQLite for a standalone lightweight Biopython application >>> and it would be very helpful if I could use BioSQL directly. >> >> Biopython can talk to a BioSQL database run on MySQL (using MySQLdb), >> PostgreSQL (using either Psycopg or Psycopg2). ?In theory it could be >> extended to use any supported BioSQL database (provided there are >> python bindings for the database software, in the case of SQLite using >> pysqlite would probably fine). > > We have a proof of principle implementation of the Biopython BioSQL > bindings working with BioSQL on SQLite, see enhancement Bug 2866: > http://bugzilla.open-bio.org/show_bug.cgi?id=2866 Hi Hilmar, I've filed a BioSQL enhancement bug 2870 for adding an SQLite schema to BioSQL, and Brad has attached his proposed schema (converted from that for MySQL) to the bug: http://bugzilla.open-bio.org/show_bug.cgi?id=2870 Could you take a look at this please? If you are happy with it, we'd like to have it included in BioSQL v1.0.2 (even if Biopython is initially the only Bio* project to support it). Thanks, Peter From florian.mittag at uni-tuebingen.de Thu Jul 9 11:16:12 2009 From: florian.mittag at uni-tuebingen.de (Florian Mittag) Date: Thu, 9 Jul 2009 17:16:12 +0200 Subject: [BioSQL-l] Problems in DB2 with VARCHAR, TEXT and CLOB using BioJava Message-ID: <200907091716.13639.florian.mittag@uni-tuebingen.de> Hi all! I'm posting this to both the BioSQL and the BioJava-dev mailinglist because the problem resides in both domains, I hope this is okay. We're working on getting BioJava to run with a DB2 Express-C backend for various reasons. We've encountered several problems during this task, but this one seems to have no real solution. When adapting the BioSQL schema to DB2, the official IBM conversion guide tells us to use the data type CLOB where MySQL uses TEXT. (Chapter 11 in ftp://ftp.software.ibm.com/software/data/db2/migration/mtk/mtk_2050.pdf) So far, no problem. But when we tried reading some genebank files with BioJava, the DB2 driver threw an exception: SQL0401N The data types of the operands for the operation "=" are not compatible. SQLSTATE=42818 SQLCODE=-401 Explanation: The class org.biojavax.bio.db.biosql.BioSQLRichObjectBuilder defines some Hibernate queries, of which one has the conditions: "from DocRef as cr where cr.authors = ? and cr.location = ? and cr.title = ?" All three columns "authors", "location", and "title" are of type TEXT in MySQL and of type CLOB in DB2, so comparing them with "=" leads to the above error message. The way I see it, there are only two possible solutions to this problem: 1) Change the query to "from DocRef as cr where cr.authors LIKE '?' and cr.location LIKE '?' and cr.title LIKE '?'" 2) Change the data type to something comparable with "=", like VARCHAR. Solution 1 is no real solution to me, because comparing values with "LIKE" usually is slow and it seems a bit odd to change a query that works with other databases just for DB2. But taking a closer look, solution 2 has some problems, too: Although VARCHARs in DB2 can have a length of theoretically 32767, in reality they are limited by the page size of the database, which can be 32K at maximum. Since this particular table "reference" has three columns of this type, the sum of their lengths must not exceed 32767, so they could only be something like VARCHAR(10000). I have never encountered cases in which values come even close to the length of 10000, but you can never be sure. And that is why I post here. For me, the way to go is pretty clear, but we intend to be as compatible as possible with the original BioSQL. Maybe you could give me some input on how to solve this problem with as few casualties as possible ;-) Thanks, Florian From hlapp at gmx.net Sat Jul 11 07:47:34 2009 From: hlapp at gmx.net (Hilmar Lapp) Date: Sat, 11 Jul 2009 07:47:34 -0400 Subject: [BioSQL-l] Problems in DB2 with VARCHAR, TEXT and CLOB using BioJava In-Reply-To: <200907091716.13639.florian.mittag@uni-tuebingen.de> References: <200907091716.13639.florian.mittag@uni-tuebingen.de> Message-ID: <5614AEDA-3406-4844-8690-7653A2C4297C@gmx.net> Hi Florian: On Jul 9, 2009, at 11:16 AM, Florian Mittag wrote: > [...] > 2) Change the data type to something comparable with "=", like > VARCHAR. That's the way to go. The reason they are not VARCHAR in MySQL is because it is limited to 256 characters there. > [...] > Although VARCHARs in DB2 can have a length of theoretically 32767, > in reality > they are limited by the page size of the database, which can be 32K at > maximum. Since this particular table "reference" has three columns > of this > type, the sum of their lengths must not exceed 32767, so they could > only be > something like VARCHAR(10000). That sounds great though. You may have noticed that the columns are all of type VARCHAR in the Oracle version of the schema with the following widths: Title VARCHAR2(1000) Authors VARCHAR2(4000) Location VARCHAR2(512) That has always served me well. Feel free to use larger widths though if you think you need them. -hilmar -- =========================================================== : Hilmar Lapp -:- Durham, NC -:- hlapp at gmx dot net : =========================================================== From hlapp at gmx.net Thu Jul 16 06:44:29 2009 From: hlapp at gmx.net (Hilmar Lapp) Date: Thu, 16 Jul 2009 11:44:29 +0100 Subject: [BioSQL-l] adding PostGreSQL support to PhyloDB code In-Reply-To: References: Message-ID: <2F6256EB-E12E-414A-9B62-67FB678D42AA@gmx.net> Hi Dave, funny you should ask. I'm at the Computational Phyloinformatics course which is being held this year at the Gulbenkian in Portugal. We're in the SQL section right now and my plan for the final course project, starting Sat night, is to have the students collaboratively write that. Since I haven't tried this before, we'll see whether that ends in disaster or a usable product :-) -hilmar On Jul 16, 2009, at 10:32 AM, Kidd, David M wrote: > > Dear Hilmar and James, > > We are looking into linking networks stored in PhyloDB to spatial > information in the PostGIS extension. > > I have installed the PhyoDB schema on a PostGreSQL database and > would like to amend phyloimport.pl and other code at http://code.open-bio.org/svnweb/index.cgi/biosql/view/biosql-schema/trunk/ > to work with PostgreSQL. I see in the header of phyimport.pl that > PGSQL support is listed as one of a number of things to do along > with a couple of other important features. > > I thought I would inform you of our interest and enquire if you, or > anyone else you know of has made any progress with these additions > before I start hacking into the code. > > Best wishes > > - Dave > > David M. Kidd > > Research Associate > Center for Population Biology > Silwood Park Campus > Imperial College London > 0207 594 2211 > > -- =========================================================== : Hilmar Lapp -:- Durham, NC -:- hlapp at gmx dot net : =========================================================== From hlapp at gmx.net Thu Jul 16 07:04:24 2009 From: hlapp at gmx.net (Hilmar Lapp) Date: Thu, 16 Jul 2009 12:04:24 +0100 Subject: [BioSQL-l] adding PostGreSQL support to PhyloDB code In-Reply-To: References: <2F6256EB-E12E-414A-9B62-67FB678D42AA@gmx.net> Message-ID: <455710F3-4B0B-485D-8F7C-812199178585@gmx.net> On Jul 16, 2009, at 11:52 AM, Kidd, David M wrote: > it looks like we need an alternative connection string format along > the lines of "DSN=PostgreSQL30;UID=postgres;SERVER=192.168.1.102; > Port=5432;"; as well. Did you experience a problem with that? Is some part of the code balking at this? If yes, that's presumably a bug. Could you submit it to bugzilla? (http://bugzilla.open-bio.org/ ) > [...] Is there going to any attempt to fix the names issue as well? Which names issue? -hilmar -- =========================================================== : Hilmar Lapp -:- Durham, NC -:- hlapp at gmx dot net : =========================================================== From florian.mittag at uni-tuebingen.de Fri Jul 10 08:32:42 2009 From: florian.mittag at uni-tuebingen.de (Florian Mittag) Date: Fri, 10 Jul 2009 14:32:42 +0200 Subject: [BioSQL-l] load_ncbi_taxonomy.pl for DB2 Message-ID: <200907101432.42657.florian.mittag@uni-tuebingen.de> Hi everyone! I just completed and tested the changes we've made on the load_ncbi_taxonomy.pl script from BioSQL 1.0.1. Basically, only 3 changes were necessary, but some things have to be considered when running the script: 1) Although DB2 v9.7 supports TRUNCATE TABLE, when I specify the --allow_truncate option the script gave me the error SQL0428N "The SQL statement is only allowed as the first statement in a unit of work." (https://publib.boulder.ibm.com/infocenter/db2luw/v9r7/index.jsp?topic=/com.ibm.db2.luw.messages.sql.doc/doc/msql00428n.html) My solution is to just not set allow_truncate, so the script will use a DELETE command. 2) Specifying hostname and port will lead to an error saying that the database wasn't found. Searching the web I found information suggesting that you have to add a remote database to the catalog (or something) on the server and the client and then you are able to point to the database through its name. My solution is to run the script on the machine where the DB2 instance is running and everything is fine. I've run into some other problems before, but those were mostly caused by me forgetting to set the right environment variables, so that shouldn't be a problem for someone who actually knows something about DB2 ;-) I hope this helps. As for the database schema for DB2, we have scripts to create the database with all its tables and constraints, but as you might see from my other posts here, we're not completely done and have to do more tests. Now, I'm awaiting your feedback ;-) Regards, Florian -------------- next part -------------- A non-text attachment was scrubbed... Name: load_ncbi_taxonomy.diff Type: text/x-diff Size: 1193 bytes Desc: not available URL: From jamesestill at gmail.com Thu Jul 16 13:02:40 2009 From: jamesestill at gmail.com (James Estill) Date: Thu, 16 Jul 2009 13:02:40 -0400 Subject: [BioSQL-l] adding PostGreSQL support to PhyloDB code In-Reply-To: <2F6256EB-E12E-414A-9B62-67FB678D42AA@gmx.net> References: <2F6256EB-E12E-414A-9B62-67FB678D42AA@gmx.net> Message-ID: I have not been working on getting these to work with PostgreSQL. That would be awesome to get that working. I initially just did the MySQL version so that there would be a somewhat usable product by the end of the GSOC and I am still using MySQL for my research. I think that there will also need to be some updates to bring the code up to date with the new PhyloDB schema but I have not looked at this in the last year. On Thu, Jul 16, 2009 at 6:44 AM, Hilmar Lapp wrote: > Hi Dave, > funny you should ask. I'm at the Computational Phyloinformatics course > which is being held this year at the Gulbenkian in Portugal. We're in the > SQL section right now and my plan for the final course project, starting Sat > night, is to have the students collaboratively write that. Since I haven't > tried this before, we'll see whether that ends in disaster or a usable > product :-) > > -hilmar > > On Jul 16, 2009, at 10:32 AM, Kidd, David M wrote: > > > Dear Hilmar and James, > > We are looking into linking networks stored in PhyloDB to spatial > information in the PostGIS extension. > > I have installed the PhyoDB schema on a PostGreSQL database and would like > to amend phyloimport.pl and other code at > http://code.open-bio.org/svnweb/index.cgi/biosql/view/biosql-schema/trunk/ to > work with PostgreSQL. I see in the header of phyimport.pl that PGSQL > support is listed as one of a number of things to do along with a couple of > other important features. > > I thought I would inform you of our interest and enquire if you, or anyone > else you know of has made any progress with these additions before I start > hacking into the code. > > Best wishes > > - Dave > > > David M. Kidd > > Research Associate > Center for Population Biology > Silwood Park Campus > Imperial College London > 0207 594 2211 > > > > -- > =========================================================== > : Hilmar Lapp -:- Durham, NC -:- hlapp at gmx dot net : > =========================================================== > > > > -- ----------------------------------------- James C. Estill JamesEstill at gmail.com http://jestill.myweb.uga.edu ----------------------------------------- From haili at mpiz-koeln.mpg.de Tue Jul 21 06:11:30 2009 From: haili at mpiz-koeln.mpg.de (Song Haili) Date: Tue, 21 Jul 2009 12:11:30 +0200 Subject: [BioSQL-l] Error when loading Gene Ontology to biosql Message-ID: Dear all, I am using perl-5.10.0, BioPerl-1.6.0, and bioperl-db obtaind by using CPAN a few days before. Until now, I can load taxonomy and sequence data into database successfully. However, I got the following error message when trying to load Gene Ontology data into biosql database. Any help will be appreciated. Jane command used: perl load_ontology.pl --driver Pg --host pg-server --dbname sifter -dbuser sifter --dbpass password ??namespace "Gene Ontology" --format goflat component.ontology process.ontology function.ontology --fmtargs "-defs_file, GO.defs" --noobsolete error: ------------- EXCEPTION ------------- MSG: Could not open ??namespace: No such file or directory STACK Bio::Root::IO::_initialize_io /opt/share/local/users/haili/bioperl-live/Bio/Root/IO.pm:323 STACK Bio::OntologyIO::dagflat::parse /opt/share/local/users/haili/bioperl-live/Bio/OntologyIO/dagflat.pm:277 STACK Bio::OntologyIO::dagflat::next_ontology /opt/share/local/users/haili/bioperl-live/Bio/OntologyIO/dagflat.pm:330 STACK toplevel load_ontology.pl:604 ------------------------------------- From florian.mittag at uni-tuebingen.de Tue Jul 21 07:54:24 2009 From: florian.mittag at uni-tuebingen.de (Florian Mittag) Date: Tue, 21 Jul 2009 13:54:24 +0200 Subject: [BioSQL-l] Error when loading Gene Ontology to biosql In-Reply-To: References: Message-ID: <200907211354.25034.florian.mittag@uni-tuebingen.de> Hi! AFAIK the goflat format is deprecated. Use the .obo files and format instead, that should work. perl load_ontology.pl --driver Pg --host pg-server --dbname sifter --dbuser sifter --dbpass password --namespace "Gene Ontology" --format obo gene_ontology.1_2.obo --noobsolete On Tuesday 21 July 2009 12:11, Song Haili wrote: > Dear all, > I am using perl-5.10.0, BioPerl-1.6.0, and bioperl-db obtaind by using CPAN > a few days before. Until now, I can load taxonomy and sequence data into > database successfully. However, I got the following error message when > trying to load Gene Ontology data into biosql database. Any help will be > appreciated. Jane > > command used: > perl load_ontology.pl --driver Pg --host pg-server --dbname sifter -dbuser > sifter --dbpass password ??namespace "Gene Ontology" --format goflat > component.ontology process.ontology function.ontology --fmtargs > "-defs_file, GO.defs" --noobsolete > > error: > ------------- EXCEPTION ------------- > MSG: Could not open ??namespace: No such file or directory > STACK Bio::Root::IO::_initialize_io > /opt/share/local/users/haili/bioperl-live/Bio/Root/IO.pm:323 STACK > Bio::OntologyIO::dagflat::parse > /opt/share/local/users/haili/bioperl-live/Bio/OntologyIO/dagflat.pm:277 > STACK Bio::OntologyIO::dagflat::next_ontology > /opt/share/local/users/haili/bioperl-live/Bio/OntologyIO/dagflat.pm:330 > STACK toplevel load_ontology.pl:604 > ------------------------------------- From haili at mpiz-koeln.mpg.de Tue Jul 21 11:32:19 2009 From: haili at mpiz-koeln.mpg.de (Song Haili) Date: Tue, 21 Jul 2009 17:32:19 +0200 Subject: [BioSQL-l] Error when loading Gene Ontology to biosql In-Reply-To: <200907211354.25034.florian.mittag@uni-tuebingen.de> References: <200907211354.25034.florian.mittag@uni-tuebingen.de> Message-ID: Hello All, The previous error was solved by the help of Florian. Florian, Thank you very much. But I got another error using the way Florian suggested. I thought it was because parameter --fmtargs was not specified. So I tried to include it with the value "-defs_file, GO.defs", but it didn't work. I think maybe GO.defs is not the right file. Is it?? But how or where to get the right file if it is. Or any other ideas about how to solve this error? Thank you very much in advance. command: perl load_ontology.pl --driver Pg --host pg-server --dbname sifter? --dbuser sifter --dbpass password --namespace "Gene Ontology" --format obo gene_ontology.obo --fmtargs "-defs_file, GO.defs" --noobsolete error: ------------- EXCEPTION ------------- MSG: OBO File Format Error - Cannot find tag format-version and/ default-namespace . These are required header. STACK Bio::OntologyIO::obo::_header /opt/share/local/users/haili/bioperl-live/Bio/OntologyIO/obo.pm:518 STACK Bio::OntologyIO::obo::parse /opt/share/local/users/haili/bioperl-live/Bio/OntologyIO/obo.pm:209 STACK Bio::OntologyIO::obo::next_ontology /opt/share/local/users/haili/bioperl-live/Bio/OntologyIO/obo.pm:342 STACK toplevel load_ontology.pl:604 ------------------------------------- ----- Original Message ----- From: Florian Mittag Date: Tuesday, July 21, 2009 14:41 Subject: Re: [BioSQL-l] Error when loading Gene Ontology to biosql To: biosql-l at lists.open-bio.org > Hi! > > AFAIK the goflat format is deprecated. Use the .obo files and > format instead, > that should work. > > perl load_ontology.pl --driver Pg --host pg-server --dbname sifter > --dbuser sifter --dbpass password --namespace "Gene Ontology" -- > format obo > ??????? gene_ontology.1_2.obo > --noobsolete > > > On Tuesday 21 July 2009 12:11, Song Haili wrote: > > Dear all, > > I am using perl-5.10.0, BioPerl-1.6.0, and bioperl-db obtaind > by using CPAN > > a few days before. Until now, I can load taxonomy and sequence > data into > > database successfully. However, I got the following error > message when > > trying to load Gene Ontology data into biosql database. Any > help will be > > appreciated. Jane > > > > command used: > > perl load_ontology.pl --driver Pg --host pg-server --dbname > sifter -dbuser > > sifter --dbpass password ??namespace "Gene Ontology" --format goflat > > component.ontology process.ontology function.ontology --fmtargs > > "-defs_file, GO.defs" --noobsolete > > > > error: > > ------------- EXCEPTION ------------- > > MSG: Could not open ??namespace: No such file or directory > > STACK Bio::Root::IO::_initialize_io > > /opt/share/local/users/haili/bioperl-live/Bio/Root/IO.pm:323 STACK > > Bio::OntologyIO::dagflat::parse > > /opt/share/local/users/haili/bioperl- > live/Bio/OntologyIO/dagflat.pm:277> STACK > Bio::OntologyIO::dagflat::next_ontology> > /opt/share/local/users/haili/bioperl-live/Bio/OntologyIO/dagflat.pm:330 > > STACK toplevel load_ontology.pl:604 > > ------------------------------------- > > _______________________________________________ > BioSQL-l mailing list > BioSQL-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/biosql-l From hlapp at gmx.net Tue Jul 21 13:19:19 2009 From: hlapp at gmx.net (Hilmar Lapp) Date: Tue, 21 Jul 2009 13:19:19 -0400 Subject: [BioSQL-l] Error when loading Gene Ontology to biosql In-Reply-To: References: <200907211354.25034.florian.mittag@uni-tuebingen.de> Message-ID: Song: GO.defs is not in OBO format. Where did you find that you need it when you load .obo formatted files? You don't need the --fmtargs argument for .obo files other than if you want to specify the ontology name. -hilmar On Jul 21, 2009, at 11:32 AM, Song Haili wrote: > > Hello All, > The previous error was solved by the help of Florian. Florian, Thank > you very much. > But I got another error using the way Florian suggested. I thought > it was because parameter --fmtargs was not specified. So I tried to > include it with the value "-defs_file, GO.defs", but it didn't work. > I think maybe GO.defs is not the right file. Is it? But how or > where to get the right file if it is. Or any other ideas about how > to solve this error? Thank you very much in advance. > command: > perl load_ontology.pl --driver Pg --host pg-server --dbname sifter > --dbuser sifter --dbpass password --namespace "Gene Ontology" -- > format obo gene_ontology.obo --fmtargs "-defs_file, GO.defs" -- > noobsolete > error: > ------------- EXCEPTION ------------- > MSG: OBO File Format Error - > Cannot find tag format-version and/ default-namespace . These are > required header. > > STACK Bio::OntologyIO::obo::_header /opt/share/local/users/haili/ > bioperl-live/Bio/OntologyIO/obo.pm:518 > STACK Bio::OntologyIO::obo::parse /opt/share/local/users/haili/ > bioperl-live/Bio/OntologyIO/obo.pm:209 > STACK Bio::OntologyIO::obo::next_ontology /opt/share/local/users/ > haili/bioperl-live/Bio/OntologyIO/obo.pm:342 > STACK toplevel load_ontology.pl:604 > ------------------------------------- > > ----- Original Message ----- > From: Florian Mittag > Date: Tuesday, July 21, 2009 14:41 > Subject: Re: [BioSQL-l] Error when loading Gene Ontology to biosql > To: biosql-l at lists.open-bio.org > >> Hi! >> >> AFAIK the goflat format is deprecated. Use the .obo files and >> format instead, >> that should work. >> >> perl load_ontology.pl --driver Pg --host pg-server --dbname sifter >> --dbuser sifter --dbpass password --namespace "Gene Ontology" -- >> format obo >> gene_ontology.1_2.obo >> --noobsolete >> >> >> On Tuesday 21 July 2009 12:11, Song Haili wrote: >>> Dear all, >>> I am using perl-5.10.0, BioPerl-1.6.0, and bioperl-db obtaind >> by using CPAN >>> a few days before. Until now, I can load taxonomy and sequence >> data into >>> database successfully. However, I got the following error >> message when >>> trying to load Gene Ontology data into biosql database. Any >> help will be >>> appreciated. Jane >>> >>> command used: >>> perl load_ontology.pl --driver Pg --host pg-server --dbname >> sifter -dbuser >>> sifter --dbpass password ??namespace "Gene Ontology" --format >>> goflat >>> component.ontology process.ontology function.ontology --fmtargs >>> "-defs_file, GO.defs" --noobsolete >>> >>> error: >>> ------------- EXCEPTION ------------- >>> MSG: Could not open ??namespace: No such file or directory >>> STACK Bio::Root::IO::_initialize_io >>> /opt/share/local/users/haili/bioperl-live/Bio/Root/IO.pm:323 STACK >>> Bio::OntologyIO::dagflat::parse >>> /opt/share/local/users/haili/bioperl- >> live/Bio/OntologyIO/dagflat.pm:277> STACK >> Bio::OntologyIO::dagflat::next_ontology> >> /opt/share/local/users/haili/bioperl-live/Bio/OntologyIO/dagflat.pm: >> 330 >>> STACK toplevel load_ontology.pl:604 >>> ------------------------------------- >> >> _______________________________________________ >> BioSQL-l mailing list >> BioSQL-l at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/biosql-l > > _______________________________________________ > BioSQL-l mailing list > BioSQL-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/biosql-l -- =========================================================== : Hilmar Lapp -:- Durham, NC -:- hlapp at gmx dot net : =========================================================== From haili at mpiz-koeln.mpg.de Wed Jul 22 03:50:34 2009 From: haili at mpiz-koeln.mpg.de (Song Haili) Date: Wed, 22 Jul 2009 09:50:34 +0200 Subject: [BioSQL-l] Error when loading Gene Ontology to biosql In-Reply-To: References: <200907211354.25034.florian.mittag@uni-tuebingen.de> Message-ID: Hello Hilmar, Thank you very much for your help. I got the same error even I don't use the argument --fmtargs. Actually that was the first try before I use --fmtargs. Any idea on how to solve this problem? Thanks in advance. command: perl load_ontology.pl --driver Pg --host pg-server --dbname sifter? --dbuser sifter --dbpass password --namespace "Gene Ontology" --format obo gene_ontology.obo --noobsolete error: ------------- EXCEPTION ------------- MSG: OBO File Format Error - Cannot find tag format-version and/ default-namespace . These are required header. STACK Bio::OntologyIO::obo::_header /opt/share/local/users/haili/bioperl-live/Bio/OntologyIO/obo.pm:518 STACK Bio::OntologyIO::obo::parse /opt/share/local/users/haili/bioperl-live/Bio/OntologyIO/obo.pm:209 STACK Bio::OntologyIO::obo::next_ontology /opt/share/local/users/haili/bioperl-live/Bio/OntologyIO/obo.pm:342 STACK toplevel load_ontology.pl:604 ------------------------------------- ----- Original Message ----- From: Hilmar Lapp Date: Tuesday, July 21, 2009 19:19 Subject: Re: [BioSQL-l] Error when loading Gene Ontology to biosql To: Song Haili Cc: florian.mittag at uni-tuebingen.de, biosql-l at lists.open-bio.org > Song: GO.defs is not in OBO format. Where did you find that you > need? > it when you load .obo formatted files? You don't need the -- > fmtargs? > argument for .obo files other than if you want to specify the > ontology? > name. > > -hilmar > > On Jul 21, 2009, at 11:32 AM, Song Haili wrote: > > > > > Hello All, > > The previous error was solved by the help of Florian. Florian, > Thank? > > you very much. > > But I got another error using the way Florian suggested. I > thought? > > it was because parameter --fmtargs was not specified. So I > tried to? > > include it with the value "-defs_file, GO.defs", but it didn't > work.? > > I think maybe GO.defs is not the right file. Is it?? But > how or? > > where to get the right file if it is. Or any other ideas about > how? > > to solve this error? Thank you very much in advance. > > command: > > perl load_ontology.pl --driver Pg --host pg-server --dbname > sifter?? > > --dbuser sifter --dbpass password --namespace "Gene Ontology" - > - > > format obo gene_ontology.obo --fmtargs "-defs_file, GO.defs" -- > > > noobsolete > > error: > > ------------- EXCEPTION ------------- > > MSG: OBO File Format Error - > > Cannot find tag format-version and/ default-namespace . These > are? > > required header. > > > > STACK Bio::OntologyIO::obo::_header > /opt/share/local/users/haili/ > > bioperl-live/Bio/OntologyIO/obo.pm:518 > > STACK Bio::OntologyIO::obo::parse > /opt/share/local/users/haili/ > > bioperl-live/Bio/OntologyIO/obo.pm:209 > > STACK Bio::OntologyIO::obo::next_ontology > /opt/share/local/users/ > > haili/bioperl-live/Bio/OntologyIO/obo.pm:342 > > STACK toplevel load_ontology.pl:604 > > ------------------------------------- > > > > ----- Original Message ----- > > From: Florian Mittag > > Date: Tuesday, July 21, 2009 14:41 > > Subject: Re: [BioSQL-l] Error when loading Gene Ontology to biosql > > To: biosql-l at lists.open-bio.org > > > >> Hi! > >> > >> AFAIK the goflat format is deprecated. Use the .obo files and > >> format instead, > >> that should work. > >> > >> perl load_ontology.pl --driver Pg --host pg-server --dbname sifter > >>? --dbuser sifter --dbpass password --namespace "Gene > Ontology" -- > >> format obo > >>???????? > gene_ontology.1_2.obo>> --noobsolete > >> > >> > >> On Tuesday 21 July 2009 12:11, Song Haili wrote: > >>> Dear all, > >>> I am using perl-5.10.0, BioPerl-1.6.0, and bioperl-db obtaind > >> by using CPAN > >>> a few days before. Until now, I can load taxonomy and sequence > >> data into > >>> database successfully. However, I got the following error > >> message when > >>> trying to load Gene Ontology data into biosql database. Any > >> help will be > >>> appreciated. Jane > >>> > >>> command used: > >>> perl load_ontology.pl --driver Pg --host pg-server --dbname > >> sifter -dbuser > >>> sifter --dbpass password ??namespace "Gene Ontology" -- > format? > >>> goflat > >>> component.ontology process.ontology function.ontology --fmtargs > >>> "-defs_file, GO.defs" --noobsolete > >>> > >>> error: > >>> ------------- EXCEPTION ------------- > >>> MSG: Could not open ??namespace: No such file or directory > >>> STACK Bio::Root::IO::_initialize_io > >>> /opt/share/local/users/haili/bioperl-live/Bio/Root/IO.pm:323 STACK > >>> Bio::OntologyIO::dagflat::parse > >>> /opt/share/local/users/haili/bioperl- > >> live/Bio/OntologyIO/dagflat.pm:277> STACK > >> Bio::OntologyIO::dagflat::next_ontology> > >> /opt/share/local/users/haili/bioperl- > live/Bio/OntologyIO/dagflat.pm: > >> 330 > >>> STACK toplevel load_ontology.pl:604 > >>> ------------------------------------- > >> > >> _______________________________________________ > >> BioSQL-l mailing list > >> BioSQL-l at lists.open-bio.org > >> http://lists.open-bio.org/mailman/listinfo/biosql-l > > > > _______________________________________________ > > BioSQL-l mailing list > > BioSQL-l at lists.open-bio.org > > http://lists.open-bio.org/mailman/listinfo/biosql-l > > -- > =========================================================== > : Hilmar Lapp? -:-? Durham, NC? -:-? hlapp > at gmx dot net : > =========================================================== > > > From florian.mittag at uni-tuebingen.de Wed Jul 22 04:44:18 2009 From: florian.mittag at uni-tuebingen.de (Florian Mittag) Date: Wed, 22 Jul 2009 10:44:18 +0200 Subject: [BioSQL-l] Error when loading Gene Ontology to biosql In-Reply-To: References: Message-ID: <200907221044.18292.florian.mittag@uni-tuebingen.de> Hi Song, just to be clear: Did you download the file gene_ontology.1_2.obo from http://www.geneontology.org/GO.downloads.ontology.shtml ? (http://www.geneontology.org/ontology/obo_format_1_2/gene_ontology.1_2.obo) You need to specify the correct file then, because the command you described expects a file called "gene_ontology.obo", which is not the orginial name of the file to download. On Wednesday 22 July 2009 09:50, Song Haili wrote: > Hello Hilmar, > Thank you very much for your help. > I got the same error even I don't use the argument --fmtargs. Actually that > was the first try before I use --fmtargs. Any idea on how to solve this > problem? Thanks in advance. > > command: > perl load_ontology.pl --driver Pg --host pg-server --dbname sifter? > --dbuser sifter --dbpass password --namespace "Gene Ontology" --format obo > gene_ontology.obo --noobsolete error: > ------------- EXCEPTION ------------- > MSG: OBO File Format Error - > Cannot find tag format-version and/ default-namespace . These are required > header. > > STACK Bio::OntologyIO::obo::_header > /opt/share/local/users/haili/bioperl-live/Bio/OntologyIO/obo.pm:518 STACK > Bio::OntologyIO::obo::parse > /opt/share/local/users/haili/bioperl-live/Bio/OntologyIO/obo.pm:209 STACK > Bio::OntologyIO::obo::next_ontology > /opt/share/local/users/haili/bioperl-live/Bio/OntologyIO/obo.pm:342 STACK > toplevel load_ontology.pl:604 > ------------------------------------- > > ----- Original Message ----- > From: Hilmar Lapp > Date: Tuesday, July 21, 2009 19:19 > Subject: Re: [BioSQL-l] Error when loading Gene Ontology to biosql > To: Song Haili > Cc: florian.mittag at uni-tuebingen.de, biosql-l at lists.open-bio.org > > > Song: GO.defs is not in OBO format. Where did you find that you > > need? > > it when you load .obo formatted files? You don't need the -- > > fmtargs? > > argument for .obo files other than if you want to specify the > > ontology? > > name. > > > > -hilmar > > > > On Jul 21, 2009, at 11:32 AM, Song Haili wrote: > > > Hello All, > > > The previous error was solved by the help of Florian. Florian, > > > > Thank? > > > > > you very much. > > > But I got another error using the way Florian suggested. I > > > > thought? > > > > > it was because parameter --fmtargs was not specified. So I > > > > tried to? > > > > > include it with the value "-defs_file, GO.defs", but it didn't > > > > work.? > > > > > I think maybe GO.defs is not the right file. Is it?? But > > > > how or? > > > > > where to get the right file if it is. Or any other ideas about > > > > how? > > > > > to solve this error? Thank you very much in advance. > > > command: > > > perl load_ontology.pl --driver Pg --host pg-server --dbname > > > > sifter?? > > > > > --dbuser sifter --dbpass password --namespace "Gene Ontology" - > > > > - > > > > > format obo gene_ontology.obo --fmtargs "-defs_file, GO.defs" -- > > > > > > noobsolete > > > error: > > > ------------- EXCEPTION ------------- > > > MSG: OBO File Format Error - > > > Cannot find tag format-version and/ default-namespace . These > > > > are? > > > > > required header. > > > > > > STACK Bio::OntologyIO::obo::_header > > > > /opt/share/local/users/haili/ > > > > > bioperl-live/Bio/OntologyIO/obo.pm:518 > > > STACK Bio::OntologyIO::obo::parse > > > > /opt/share/local/users/haili/ > > > > > bioperl-live/Bio/OntologyIO/obo.pm:209 > > > STACK Bio::OntologyIO::obo::next_ontology > > > > /opt/share/local/users/ > > > > > haili/bioperl-live/Bio/OntologyIO/obo.pm:342 > > > STACK toplevel load_ontology.pl:604 > > > ------------------------------------- > > > > > > ----- Original Message ----- > > > From: Florian Mittag > > > Date: Tuesday, July 21, 2009 14:41 > > > Subject: Re: [BioSQL-l] Error when loading Gene Ontology to biosql > > > To: biosql-l at lists.open-bio.org > > > > > >> Hi! > > >> > > >> AFAIK the goflat format is deprecated. Use the .obo files and > > >> format instead, > > >> that should work. > > >> > > >> perl load_ontology.pl --driver Pg --host pg-server --dbname sifter > > >>? --dbuser sifter --dbpass password --namespace "Gene > > > > Ontology" -- > > > > >> format obo > > >>???????? > > > > gene_ontology.1_2.obo>> --noobsolete > > > > >> On Tuesday 21 July 2009 12:11, Song Haili wrote: > > >>> Dear all, > > >>> I am using perl-5.10.0, BioPerl-1.6.0, and bioperl-db obtaind > > >> > > >> by using CPAN > > >> > > >>> a few days before. Until now, I can load taxonomy and sequence > > >> > > >> data into > > >> > > >>> database successfully. However, I got the following error > > >> > > >> message when > > >> > > >>> trying to load Gene Ontology data into biosql database. Any > > >> > > >> help will be > > >> > > >>> appreciated. Jane > > >>> > > >>> command used: > > >>> perl load_ontology.pl --driver Pg --host pg-server --dbname > > >> > > >> sifter -dbuser > > >> > > >>> sifter --dbpass password ??namespace "Gene Ontology" -- > > > > format? > > > > >>> goflat > > >>> component.ontology process.ontology function.ontology --fmtargs > > >>> "-defs_file, GO.defs" --noobsolete > > >>> > > >>> error: > > >>> ------------- EXCEPTION ------------- > > >>> MSG: Could not open ??namespace: No such file or directory > > >>> STACK Bio::Root::IO::_initialize_io > > >>> /opt/share/local/users/haili/bioperl-live/Bio/Root/IO.pm:323 STACK > > >>> Bio::OntologyIO::dagflat::parse > > >>> /opt/share/local/users/haili/bioperl- > > >> > > >> live/Bio/OntologyIO/dagflat.pm:277> STACK > > >> Bio::OntologyIO::dagflat::next_ontology> > > >> /opt/share/local/users/haili/bioperl- > > > > live/Bio/OntologyIO/dagflat.pm: > > >> 330 > > >> > > >>> STACK toplevel load_ontology.pl:604 > > >>> ------------------------------------- > > >> > > >> _______________________________________________ > > >> BioSQL-l mailing list > > >> BioSQL-l at lists.open-bio.org > > >> http://lists.open-bio.org/mailman/listinfo/biosql-l > > > > > > _______________________________________________ > > > BioSQL-l mailing list > > > BioSQL-l at lists.open-bio.org > > > http://lists.open-bio.org/mailman/listinfo/biosql-l > > > > -- > > =========================================================== > > > > : Hilmar Lapp? -:-? Durham, NC? -:-? hlapp > > > > at gmx dot net : > > =========================================================== From haili at mpiz-koeln.mpg.de Wed Jul 22 07:08:20 2009 From: haili at mpiz-koeln.mpg.de (Song Haili) Date: Wed, 22 Jul 2009 13:08:20 +0200 Subject: [BioSQL-l] Error when loading Gene Ontology to biosql In-Reply-To: <200907221044.18292.florian.mittag@uni-tuebingen.de> References: <200907221044.18292.florian.mittag@uni-tuebingen.de> Message-ID: Hi Florian, Aha, that's the problem. Gene_ontology.1_2.obo works fine. I didn't use gene_ontology.1_2.obo, but as you can see instead I used gene_ontology.obo (ftp://ftp.geneontology.org/pub/go/ontology/gene_ontology.obo). However, I don't understand why I can't use gene_ontology.obo which I think, does not differ a lot with gene_ontology.1_2.obo at the beginning of the two files. Thanks a lot again, Florian and Hilmar. song ----- Original Message ----- From: Florian Mittag Date: Wednesday, July 22, 2009 10:44 Subject: Re: [BioSQL-l] Error when loading Gene Ontology to biosql To: Song Haili Cc: biosql-l at lists.open-bio.org > Hi Song, > > just to be clear: Did you download the file > gene_ontology.1_2.obo from > http://www.geneontology.org/GO.downloads.ontology.shtml ? > > (http://www.geneontology.org/ontology/obo_format_1_2/gene_ontology.1_2.obo) > > You need to specify the correct file then, because the command > you described > expects a file called "gene_ontology.obo", which is not the > orginial name of > the file to download. > > On Wednesday 22 July 2009 09:50, Song Haili wrote: > > Hello Hilmar, > > Thank you very much for your help. > > I got the same error even I don't use the argument --fmtargs. > Actually that > > was the first try before I use --fmtargs. Any idea on how to > solve this > > problem? Thanks in advance. > > > > command: > > perl load_ontology.pl --driver Pg --host pg-server --dbname sifter? > > --dbuser sifter --dbpass password --namespace "Gene Ontology" - > -format obo > > gene_ontology.obo --noobsolete error: > > ------------- EXCEPTION ------------- > > MSG: OBO File Format Error - > > Cannot find tag format-version and/ default-namespace . These > are required > > header. > > > > STACK Bio::OntologyIO::obo::_header > > /opt/share/local/users/haili/bioperl- > live/Bio/OntologyIO/obo.pm:518 STACK > > Bio::OntologyIO::obo::parse > > /opt/share/local/users/haili/bioperl- > live/Bio/OntologyIO/obo.pm:209 STACK > > Bio::OntologyIO::obo::next_ontology > > /opt/share/local/users/haili/bioperl- > live/Bio/OntologyIO/obo.pm:342 STACK > > toplevel load_ontology.pl:604 > > ------------------------------------- > > > > ----- Original Message ----- > > From: Hilmar Lapp > > Date: Tuesday, July 21, 2009 19:19 > > Subject: Re: [BioSQL-l] Error when loading Gene Ontology to biosql > > To: Song Haili > > Cc: florian.mittag at uni-tuebingen.de, biosql-l at lists.open-bio.org > > > > > Song: GO.defs is not in OBO format. Where did you find that you > > > need? > > > it when you load .obo formatted files? You don't need the -- > > > fmtargs? > > > argument for .obo files other than if you want to specify the > > > ontology? > > > name. > > > > > >? -hilmar > > > > > > On Jul 21, 2009, at 11:32 AM, Song Haili wrote: > > > > Hello All, > > > > The previous error was solved by the help of Florian. Florian, > > > > > > Thank? > > > > > > > you very much. > > > > But I got another error using the way Florian suggested. I > > > > > > thought? > > > > > > > it was because parameter --fmtargs was not specified. So I > > > > > > tried to? > > > > > > > include it with the value "-defs_file, GO.defs", but it didn't > > > > > > work.? > > > > > > > I think maybe GO.defs is not the right file. Is it?? But > > > > > > how or? > > > > > > > where to get the right file if it is. Or any other ideas about > > > > > > how? > > > > > > > to solve this error? Thank you very much in advance. > > > > command: > > > > perl load_ontology.pl --driver Pg --host pg-server --dbname > > > > > > sifter?? > > > > > > > --dbuser sifter --dbpass password --namespace "Gene > Ontology" - > > > > > > - > > > > > > > format obo gene_ontology.obo --fmtargs "-defs_file, > GO.defs" -- > > > > > > > > noobsolete > > > > error: > > > > ------------- EXCEPTION ------------- > > > > MSG: OBO File Format Error - > > > > Cannot find tag format-version and/ default-namespace . These > > > > > > are? > > > > > > > required header. > > > > > > > > STACK Bio::OntologyIO::obo::_header > > > > > > /opt/share/local/users/haili/ > > > > > > > bioperl-live/Bio/OntologyIO/obo.pm:518 > > > > STACK Bio::OntologyIO::obo::parse > > > > > > /opt/share/local/users/haili/ > > > > > > > bioperl-live/Bio/OntologyIO/obo.pm:209 > > > > STACK Bio::OntologyIO::obo::next_ontology > > > > > > /opt/share/local/users/ > > > > > > > haili/bioperl-live/Bio/OntologyIO/obo.pm:342 > > > > STACK toplevel load_ontology.pl:604 > > > > ------------------------------------- > > > > > > > > ----- Original Message ----- > > > > From: Florian Mittag > > > > Date: Tuesday, July 21, 2009 14:41 > > > > Subject: Re: [BioSQL-l] Error when loading Gene Ontology > to biosql > > > > To: biosql-l at lists.open-bio.org > > > > > > > >> Hi! > > > >> > > > >> AFAIK the goflat format is deprecated. Use the .obo files and > > > >> format instead, > > > >> that should work. > > > >> > > > >> perl load_ontology.pl --driver Pg --host pg-server -- > dbname sifter > > > >>? --dbuser sifter --dbpass password --namespace "Gene > > > > > > Ontology" -- > > > > > > >> format obo > > > >>???????? > > > > > > gene_ontology.1_2.obo>> --noobsolete > > > > > > >> On Tuesday 21 July 2009 12:11, Song Haili wrote: > > > >>> Dear all, > > > >>> I am using perl-5.10.0, BioPerl-1.6.0, and bioperl-db obtaind > > > >> > > > >> by using CPAN > > > >> > > > >>> a few days before. Until now, I can load taxonomy and sequence > > > >> > > > >> data into > > > >> > > > >>> database successfully. However, I got the following error > > > >> > > > >> message when > > > >> > > > >>> trying to load Gene Ontology data into biosql database. Any > > > >> > > > >> help will be > > > >> > > > >>> appreciated. Jane > > > >>> > > > >>> command used: > > > >>> perl load_ontology.pl --driver Pg --host pg-server --dbname > > > >> > > > >> sifter -dbuser > > > >> > > > >>> sifter --dbpass password ??namespace "Gene Ontology" -- > > > > > > format? > > > > > > >>> goflat > > > >>> component.ontology process.ontology function.ontology -- > fmtargs> > >>> "-defs_file, GO.defs" --noobsolete > > > >>> > > > >>> error: > > > >>> ------------- EXCEPTION ------------- > > > >>> MSG: Could not open ??namespace: No such file or directory > > > >>> STACK Bio::Root::IO::_initialize_io > > > >>> /opt/share/local/users/haili/bioperl- > live/Bio/Root/IO.pm:323 STACK > > > >>> Bio::OntologyIO::dagflat::parse > > > >>> /opt/share/local/users/haili/bioperl- > > > >> > > > >> live/Bio/OntologyIO/dagflat.pm:277> STACK > > > >> Bio::OntologyIO::dagflat::next_ontology> > > > >> /opt/share/local/users/haili/bioperl- > > > > > > live/Bio/OntologyIO/dagflat.pm: > > > >> 330 > > > >> > > > >>> STACK toplevel load_ontology.pl:604 > > > >>> ------------------------------------- > > > >> > > > >> _______________________________________________ > > > >> BioSQL-l mailing list > > > >> BioSQL-l at lists.open-bio.org > > > >> http://lists.open-bio.org/mailman/listinfo/biosql-l > > > > > > > > _______________________________________________ > > > > BioSQL-l mailing list > > > > BioSQL-l at lists.open-bio.org > > > > http://lists.open-bio.org/mailman/listinfo/biosql-l > > > > > > -- > > > =========================================================== > > > > > > : Hilmar Lapp? -:-? Durham, NC? -:-? hlapp > > > > > > at gmx dot net : > > > =========================================================== From ccanchaya at gmail.com Wed Jul 22 11:05:49 2009 From: ccanchaya at gmail.com (Carlos A. Canchaya) Date: Wed, 22 Jul 2009 17:05:49 +0200 Subject: [BioSQL-l] Error when loading Gene Ontology to biosql In-Reply-To: References: <200907221044.18292.florian.mittag@uni-tuebingen.de> Message-ID: Hi guys, I've tried to execute load_ontologies following your suggestions as load_ontology.pl --driver Pg --dbname biosql --dbuser yyy --dbpass xxx --namespace "Gene Ontology" --fmtargs GO.defs --format obo gene_ontology.1_2.obo However I have many warnings first --------------------- WARNING --------------------- MSG: DBLink exists in the dblink of _default --------------------------------------------------- and then --------------------- WARNING --------------------- MSG: DBLink exists in the dblink of _default --------------------------------------------------- Could not store term GO:0001404, name 'invasive growth': ------------- EXCEPTION: Bio::Root::Exception ------------- MSG: create: object (Bio::Ontology::OBOterm) failed to insert or to be found by unique key STACK: Error::throw STACK: Bio::Root::Root::throw /home/carlos/nascent/download/bioperl- live//Bio/Root/Root.pm:357 STACK: Bio::DB::BioSQL::BasePersistenceAdaptor::create /usr/local/ share/perl/5.10.0/Bio/DB/BioSQL/BasePersistenceAdaptor.pm:219 STACK: Bio::DB::BioSQL::BasePersistenceAdaptor::store /usr/local/share/ perl/5.10.0/Bio/DB/BioSQL/BasePersistenceAdaptor.pm:264 STACK: Bio::DB::Persistent::PersistentObject::store /usr/local/share/ perl/5.10.0/Bio/DB/Persistent/PersistentObject.pm:284 STACK: main::persist_term /tmp/BioPerl-db-1.6.0/scripts/biosql/ load_ontology.pl:812 STACK: /tmp/BioPerl-db-1.6.0/scripts/biosql/load_ontology.pl:617 ----------------------------------------------------------- at /tmp/BioPerl-db-1.6.0/scripts/biosql/load_ontology.pl line 824 main::persist_term('-term', 'Bio::Ontology::OBOterm=HASH(0x9c86078)', '-db', 'Bio::DB::BioSQL::DBAdaptor=HASH(0x936ed50)', '-termfactory', undef, '- throw', 'CODE(0x8f49a50)', '-mergeobs', ...) called at /tmp/BioPerl- db-1.6.0/scripts/biosql/load_ontology.pl line 617 Any ideas why? Thanks in advance, Carlos Carlos Canchaya ccanchaya at gmail.com On Jul 22, 2009, at 1:08 PM, Song Haili wrote: > Hi Florian, > Aha, that's the problem. Gene_ontology.1_2.obo works fine. I didn't > use gene_ontology.1_2.obo, but as you can see instead I used > gene_ontology.obo (ftp://ftp.geneontology.org/pub/go/ontology/gene_ontology.obo > ). However, I don't understand why I can't use gene_ontology.obo > which I think, does not differ a lot with gene_ontology.1_2.obo at > the beginning of the two files. Thanks a lot again, Florian and > Hilmar. > song > > ----- Original Message ----- > From: Florian Mittag > Date: Wednesday, July 22, 2009 10:44 > Subject: Re: [BioSQL-l] Error when loading Gene Ontology to biosql > To: Song Haili > Cc: biosql-l at lists.open-bio.org > >> Hi Song, >> >> just to be clear: Did you download the file >> gene_ontology.1_2.obo from >> http://www.geneontology.org/GO.downloads.ontology.shtml ? >> >> (http://www.geneontology.org/ontology/obo_format_1_2/gene_ontology.1_2.obo >> ) >> >> You need to specify the correct file then, because the command >> you described >> expects a file called "gene_ontology.obo", which is not the >> orginial name of >> the file to download. >> >> On Wednesday 22 July 2009 09:50, Song Haili wrote: >>> Hello Hilmar, >>> Thank you very much for your help. >>> I got the same error even I don't use the argument --fmtargs. >> Actually that >>> was the first try before I use --fmtargs. Any idea on how to >> solve this >>> problem? Thanks in advance. >>> >>> command: >>> perl load_ontology.pl --driver Pg --host pg-server --dbname sifter >>> --dbuser sifter --dbpass password --namespace "Gene Ontology" - >> -format obo >>> gene_ontology.obo --noobsolete error: >>> ------------- EXCEPTION ------------- >>> MSG: OBO File Format Error - >>> Cannot find tag format-version and/ default-namespace . These >> are required >>> header. >>> >>> STACK Bio::OntologyIO::obo::_header >>> /opt/share/local/users/haili/bioperl- >> live/Bio/OntologyIO/obo.pm:518 STACK >>> Bio::OntologyIO::obo::parse >>> /opt/share/local/users/haili/bioperl- >> live/Bio/OntologyIO/obo.pm:209 STACK >>> Bio::OntologyIO::obo::next_ontology >>> /opt/share/local/users/haili/bioperl- >> live/Bio/OntologyIO/obo.pm:342 STACK >>> toplevel load_ontology.pl:604 >>> ------------------------------------- >>> >>> ----- Original Message ----- >>> From: Hilmar Lapp >>> Date: Tuesday, July 21, 2009 19:19 >>> Subject: Re: [BioSQL-l] Error when loading Gene Ontology to biosql >>> To: Song Haili >>> Cc: florian.mittag at uni-tuebingen.de, biosql-l at lists.open-bio.org >>> >>>> Song: GO.defs is not in OBO format. Where did you find that you >>>> need >>>> it when you load .obo formatted files? You don't need the -- >>>> fmtargs >>>> argument for .obo files other than if you want to specify the >>>> ontology >>>> name. >>>> >>>> -hilmar >>>> >>>> On Jul 21, 2009, at 11:32 AM, Song Haili wrote: >>>>> Hello All, >>>>> The previous error was solved by the help of Florian. Florian, >>>> >>>> Thank >>>> >>>>> you very much. >>>>> But I got another error using the way Florian suggested. I >>>> >>>> thought >>>> >>>>> it was because parameter --fmtargs was not specified. So I >>>> >>>> tried to >>>> >>>>> include it with the value "-defs_file, GO.defs", but it didn't >>>> >>>> work. >>>> >>>>> I think maybe GO.defs is not the right file. Is it? But >>>> >>>> how or >>>> >>>>> where to get the right file if it is. Or any other ideas about >>>> >>>> how >>>> >>>>> to solve this error? Thank you very much in advance. >>>>> command: >>>>> perl load_ontology.pl --driver Pg --host pg-server --dbname >>>> >>>> sifter >>>> >>>>> --dbuser sifter --dbpass password --namespace "Gene >> Ontology" - >>>> >>>> - >>>> >>>>> format obo gene_ontology.obo --fmtargs "-defs_file, >> GO.defs" -- >>>>> >>>>> noobsolete >>>>> error: >>>>> ------------- EXCEPTION ------------- >>>>> MSG: OBO File Format Error - >>>>> Cannot find tag format-version and/ default-namespace . These >>>> >>>> are >>>> >>>>> required header. >>>>> >>>>> STACK Bio::OntologyIO::obo::_header >>>> >>>> /opt/share/local/users/haili/ >>>> >>>>> bioperl-live/Bio/OntologyIO/obo.pm:518 >>>>> STACK Bio::OntologyIO::obo::parse >>>> >>>> /opt/share/local/users/haili/ >>>> >>>>> bioperl-live/Bio/OntologyIO/obo.pm:209 >>>>> STACK Bio::OntologyIO::obo::next_ontology >>>> >>>> /opt/share/local/users/ >>>> >>>>> haili/bioperl-live/Bio/OntologyIO/obo.pm:342 >>>>> STACK toplevel load_ontology.pl:604 >>>>> ------------------------------------- >>>>> >>>>> ----- Original Message ----- >>>>> From: Florian Mittag >>>>> Date: Tuesday, July 21, 2009 14:41 >>>>> Subject: Re: [BioSQL-l] Error when loading Gene Ontology >> to biosql >>>>> To: biosql-l at lists.open-bio.org >>>>> >>>>>> Hi! >>>>>> >>>>>> AFAIK the goflat format is deprecated. Use the .obo files and >>>>>> format instead, >>>>>> that should work. >>>>>> >>>>>> perl load_ontology.pl --driver Pg --host pg-server -- >> dbname sifter >>>>>> --dbuser sifter --dbpass password --namespace "Gene >>>> >>>> Ontology" -- >>>> >>>>>> format obo >>>>>> >>>> >>>> gene_ontology.1_2.obo>> --noobsolete >>>> >>>>>> On Tuesday 21 July 2009 12:11, Song Haili wrote: >>>>>>> Dear all, >>>>>>> I am using perl-5.10.0, BioPerl-1.6.0, and bioperl-db obtaind >>>>>> >>>>>> by using CPAN >>>>>> >>>>>>> a few days before. Until now, I can load taxonomy and sequence >>>>>> >>>>>> data into >>>>>> >>>>>>> database successfully. However, I got the following error >>>>>> >>>>>> message when >>>>>> >>>>>>> trying to load Gene Ontology data into biosql database. Any >>>>>> >>>>>> help will be >>>>>> >>>>>>> appreciated. Jane >>>>>>> >>>>>>> command used: >>>>>>> perl load_ontology.pl --driver Pg --host pg-server --dbname >>>>>> >>>>>> sifter -dbuser >>>>>> >>>>>>> sifter --dbpass password ??namespace "Gene Ontology" -- >>>> >>>> format >>>> >>>>>>> goflat >>>>>>> component.ontology process.ontology function.ontology -- >> fmtargs> > >>> "-defs_file, GO.defs" --noobsolete >>>>>>> >>>>>>> error: >>>>>>> ------------- EXCEPTION ------------- >>>>>>> MSG: Could not open ??namespace: No such file or directory >>>>>>> STACK Bio::Root::IO::_initialize_io >>>>>>> /opt/share/local/users/haili/bioperl- >> live/Bio/Root/IO.pm:323 STACK >>>>>>> Bio::OntologyIO::dagflat::parse >>>>>>> /opt/share/local/users/haili/bioperl- >>>>>> >>>>>> live/Bio/OntologyIO/dagflat.pm:277> STACK >>>>>> Bio::OntologyIO::dagflat::next_ontology> >>>>>> /opt/share/local/users/haili/bioperl- >>>> >>>> live/Bio/OntologyIO/dagflat.pm: >>>>>> 330 >>>>>> >>>>>>> STACK toplevel load_ontology.pl:604 >>>>>>> ------------------------------------- >>>>>> >>>>>> _______________________________________________ >>>>>> BioSQL-l mailing list >>>>>> BioSQL-l at lists.open-bio.org >>>>>> http://lists.open-bio.org/mailman/listinfo/biosql-l >>>>> >>>>> _______________________________________________ >>>>> BioSQL-l mailing list >>>>> BioSQL-l at lists.open-bio.org >>>>> http://lists.open-bio.org/mailman/listinfo/biosql-l >>>> >>>> -- >>>> =========================================================== >>>> >>>> : Hilmar Lapp -:- Durham, NC -:- hlapp >>>> >>>> at gmx dot net : >>>> =========================================================== > > _______________________________________________ > BioSQL-l mailing list > BioSQL-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/biosql-l From hlapp at gmx.net Wed Jul 22 14:15:29 2009 From: hlapp at gmx.net (Hilmar Lapp) Date: Wed, 22 Jul 2009 14:15:29 -0400 Subject: [BioSQL-l] Error when loading Gene Ontology to biosql In-Reply-To: References: <200907221044.18292.florian.mittag@uni-tuebingen.de> Message-ID: Please leave off the --fmtargs GO.defs argument - this is not a file in the .obo format. -hilmar On Jul 22, 2009, at 11:05 AM, Carlos A. Canchaya wrote: > Hi guys, > > I've tried to execute load_ontologies following your suggestions as > > load_ontology.pl --driver Pg --dbname biosql --dbuser yyy --dbpass > xxx --namespace "Gene Ontology" --fmtargs GO.defs --format obo > gene_ontology.1_2.obo > > However I have many warnings first > > --------------------- WARNING --------------------- > MSG: DBLink exists in the dblink of _default > --------------------------------------------------- > > and then > > --------------------- WARNING --------------------- > MSG: DBLink exists in the dblink of _default > --------------------------------------------------- > Could not store term GO:0001404, name 'invasive growth': > > ------------- EXCEPTION: Bio::Root::Exception ------------- > MSG: create: object (Bio::Ontology::OBOterm) failed to insert or to > be found by unique key > STACK: Error::throw > STACK: Bio::Root::Root::throw /home/carlos/nascent/download/bioperl- > live//Bio/Root/Root.pm:357 > STACK: Bio::DB::BioSQL::BasePersistenceAdaptor::create /usr/local/ > share/perl/5.10.0/Bio/DB/BioSQL/BasePersistenceAdaptor.pm:219 > STACK: Bio::DB::BioSQL::BasePersistenceAdaptor::store /usr/local/ > share/perl/5.10.0/Bio/DB/BioSQL/BasePersistenceAdaptor.pm:264 > STACK: Bio::DB::Persistent::PersistentObject::store /usr/local/share/ > perl/5.10.0/Bio/DB/Persistent/PersistentObject.pm:284 > STACK: main::persist_term /tmp/BioPerl-db-1.6.0/scripts/biosql/ > load_ontology.pl:812 > STACK: /tmp/BioPerl-db-1.6.0/scripts/biosql/load_ontology.pl:617 > ----------------------------------------------------------- > > at /tmp/BioPerl-db-1.6.0/scripts/biosql/load_ontology.pl line 824 > main::persist_term('-term', > 'Bio::Ontology::OBOterm=HASH(0x9c86078)', '-db', > 'Bio::DB::BioSQL::DBAdaptor=HASH(0x936ed50)', '-termfactory', undef, > '-throw', 'CODE(0x8f49a50)', '-mergeobs', ...) called at /tmp/ > BioPerl-db-1.6.0/scripts/biosql/load_ontology.pl line 617 > > > Any ideas why? > > Thanks in advance, > > Carlos > > > Carlos Canchaya > ccanchaya at gmail.com > > > > On Jul 22, 2009, at 1:08 PM, Song Haili wrote: > >> Hi Florian, >> Aha, that's the problem. Gene_ontology.1_2.obo works fine. I didn't >> use gene_ontology.1_2.obo, but as you can see instead I used >> gene_ontology.obo (ftp://ftp.geneontology.org/pub/go/ontology/gene_ontology.obo >> ). However, I don't understand why I can't use gene_ontology.obo >> which I think, does not differ a lot with gene_ontology.1_2.obo at >> the beginning of the two files. Thanks a lot again, Florian and >> Hilmar. >> song >> >> ----- Original Message ----- >> From: Florian Mittag >> Date: Wednesday, July 22, 2009 10:44 >> Subject: Re: [BioSQL-l] Error when loading Gene Ontology to biosql >> To: Song Haili >> Cc: biosql-l at lists.open-bio.org >> >>> Hi Song, >>> >>> just to be clear: Did you download the file >>> gene_ontology.1_2.obo from >>> http://www.geneontology.org/GO.downloads.ontology.shtml ? >>> >>> (http://www.geneontology.org/ontology/obo_format_1_2/gene_ontology.1_2.obo >>> ) >>> >>> You need to specify the correct file then, because the command >>> you described >>> expects a file called "gene_ontology.obo", which is not the >>> orginial name of >>> the file to download. >>> >>> On Wednesday 22 July 2009 09:50, Song Haili wrote: >>>> Hello Hilmar, >>>> Thank you very much for your help. >>>> I got the same error even I don't use the argument --fmtargs. >>> Actually that >>>> was the first try before I use --fmtargs. Any idea on how to >>> solve this >>>> problem? Thanks in advance. >>>> >>>> command: >>>> perl load_ontology.pl --driver Pg --host pg-server --dbname sifter >>>> --dbuser sifter --dbpass password --namespace "Gene Ontology" - >>> -format obo >>>> gene_ontology.obo --noobsolete error: >>>> ------------- EXCEPTION ------------- >>>> MSG: OBO File Format Error - >>>> Cannot find tag format-version and/ default-namespace . These >>> are required >>>> header. >>>> >>>> STACK Bio::OntologyIO::obo::_header >>>> /opt/share/local/users/haili/bioperl- >>> live/Bio/OntologyIO/obo.pm:518 STACK >>>> Bio::OntologyIO::obo::parse >>>> /opt/share/local/users/haili/bioperl- >>> live/Bio/OntologyIO/obo.pm:209 STACK >>>> Bio::OntologyIO::obo::next_ontology >>>> /opt/share/local/users/haili/bioperl- >>> live/Bio/OntologyIO/obo.pm:342 STACK >>>> toplevel load_ontology.pl:604 >>>> ------------------------------------- >>>> >>>> ----- Original Message ----- >>>> From: Hilmar Lapp >>>> Date: Tuesday, July 21, 2009 19:19 >>>> Subject: Re: [BioSQL-l] Error when loading Gene Ontology to biosql >>>> To: Song Haili >>>> Cc: florian.mittag at uni-tuebingen.de, biosql-l at lists.open-bio.org >>>> >>>>> Song: GO.defs is not in OBO format. Where did you find that you >>>>> need >>>>> it when you load .obo formatted files? You don't need the -- >>>>> fmtargs >>>>> argument for .obo files other than if you want to specify the >>>>> ontology >>>>> name. >>>>> >>>>> -hilmar >>>>> >>>>> On Jul 21, 2009, at 11:32 AM, Song Haili wrote: >>>>>> Hello All, >>>>>> The previous error was solved by the help of Florian. Florian, >>>>> >>>>> Thank >>>>> >>>>>> you very much. >>>>>> But I got another error using the way Florian suggested. I >>>>> >>>>> thought >>>>> >>>>>> it was because parameter --fmtargs was not specified. So I >>>>> >>>>> tried to >>>>> >>>>>> include it with the value "-defs_file, GO.defs", but it didn't >>>>> >>>>> work. >>>>> >>>>>> I think maybe GO.defs is not the right file. Is it? But >>>>> >>>>> how or >>>>> >>>>>> where to get the right file if it is. Or any other ideas about >>>>> >>>>> how >>>>> >>>>>> to solve this error? Thank you very much in advance. >>>>>> command: >>>>>> perl load_ontology.pl --driver Pg --host pg-server --dbname >>>>> >>>>> sifter >>>>> >>>>>> --dbuser sifter --dbpass password --namespace "Gene >>> Ontology" - >>>>> >>>>> - >>>>> >>>>>> format obo gene_ontology.obo --fmtargs "-defs_file, >>> GO.defs" -- >>>>>> >>>>>> noobsolete >>>>>> error: >>>>>> ------------- EXCEPTION ------------- >>>>>> MSG: OBO File Format Error - >>>>>> Cannot find tag format-version and/ default-namespace . These >>>>> >>>>> are >>>>> >>>>>> required header. >>>>>> >>>>>> STACK Bio::OntologyIO::obo::_header >>>>> >>>>> /opt/share/local/users/haili/ >>>>> >>>>>> bioperl-live/Bio/OntologyIO/obo.pm:518 >>>>>> STACK Bio::OntologyIO::obo::parse >>>>> >>>>> /opt/share/local/users/haili/ >>>>> >>>>>> bioperl-live/Bio/OntologyIO/obo.pm:209 >>>>>> STACK Bio::OntologyIO::obo::next_ontology >>>>> >>>>> /opt/share/local/users/ >>>>> >>>>>> haili/bioperl-live/Bio/OntologyIO/obo.pm:342 >>>>>> STACK toplevel load_ontology.pl:604 >>>>>> ------------------------------------- >>>>>> >>>>>> ----- Original Message ----- >>>>>> From: Florian Mittag >>>>>> Date: Tuesday, July 21, 2009 14:41 >>>>>> Subject: Re: [BioSQL-l] Error when loading Gene Ontology >>> to biosql >>>>>> To: biosql-l at lists.open-bio.org >>>>>> >>>>>>> Hi! >>>>>>> >>>>>>> AFAIK the goflat format is deprecated. Use the .obo files and >>>>>>> format instead, >>>>>>> that should work. >>>>>>> >>>>>>> perl load_ontology.pl --driver Pg --host pg-server -- >>> dbname sifter >>>>>>> --dbuser sifter --dbpass password --namespace "Gene >>>>> >>>>> Ontology" -- >>>>> >>>>>>> format obo >>>>>>> >>>>> >>>>> gene_ontology.1_2.obo>> --noobsolete >>>>> >>>>>>> On Tuesday 21 July 2009 12:11, Song Haili wrote: >>>>>>>> Dear all, >>>>>>>> I am using perl-5.10.0, BioPerl-1.6.0, and bioperl-db obtaind >>>>>>> >>>>>>> by using CPAN >>>>>>> >>>>>>>> a few days before. Until now, I can load taxonomy and sequence >>>>>>> >>>>>>> data into >>>>>>> >>>>>>>> database successfully. However, I got the following error >>>>>>> >>>>>>> message when >>>>>>> >>>>>>>> trying to load Gene Ontology data into biosql database. Any >>>>>>> >>>>>>> help will be >>>>>>> >>>>>>>> appreciated. Jane >>>>>>>> >>>>>>>> command used: >>>>>>>> perl load_ontology.pl --driver Pg --host pg-server --dbname >>>>>>> >>>>>>> sifter -dbuser >>>>>>> >>>>>>>> sifter --dbpass password ??namespace "Gene Ontology" -- >>>>> >>>>> format >>>>> >>>>>>>> goflat >>>>>>>> component.ontology process.ontology function.ontology -- >>> fmtargs> > >>> "-defs_file, GO.defs" --noobsolete >>>>>>>> >>>>>>>> error: >>>>>>>> ------------- EXCEPTION ------------- >>>>>>>> MSG: Could not open ??namespace: No such file or directory >>>>>>>> STACK Bio::Root::IO::_initialize_io >>>>>>>> /opt/share/local/users/haili/bioperl- >>> live/Bio/Root/IO.pm:323 STACK >>>>>>>> Bio::OntologyIO::dagflat::parse >>>>>>>> /opt/share/local/users/haili/bioperl- >>>>>>> >>>>>>> live/Bio/OntologyIO/dagflat.pm:277> STACK >>>>>>> Bio::OntologyIO::dagflat::next_ontology> >>>>>>> /opt/share/local/users/haili/bioperl- >>>>> >>>>> live/Bio/OntologyIO/dagflat.pm: >>>>>>> 330 >>>>>>> >>>>>>>> STACK toplevel load_ontology.pl:604 >>>>>>>> ------------------------------------- >>>>>>> >>>>>>> _______________________________________________ >>>>>>> BioSQL-l mailing list >>>>>>> BioSQL-l at lists.open-bio.org >>>>>>> http://lists.open-bio.org/mailman/listinfo/biosql-l >>>>>> >>>>>> _______________________________________________ >>>>>> BioSQL-l mailing list >>>>>> BioSQL-l at lists.open-bio.org >>>>>> http://lists.open-bio.org/mailman/listinfo/biosql-l >>>>> >>>>> -- >>>>> =========================================================== >>>>> >>>>> : Hilmar Lapp -:- Durham, NC -:- hlapp >>>>> >>>>> at gmx dot net : >>>>> =========================================================== >> >> _______________________________________________ >> BioSQL-l mailing list >> BioSQL-l at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/biosql-l > > > _______________________________________________ > BioSQL-l mailing list > BioSQL-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/biosql-l -- =========================================================== : Hilmar Lapp -:- Durham, NC -:- hlapp at gmx dot net : =========================================================== From ccanchaya at gmail.com Thu Jul 23 03:27:25 2009 From: ccanchaya at gmail.com (Carlos A. Canchaya) Date: Thu, 23 Jul 2009 09:27:25 +0200 Subject: [BioSQL-l] Error when loading Gene Ontology to biosql In-Reply-To: References: <200907221044.18292.florian.mittag@uni-tuebingen.de> Message-ID: <5A932B73-5D17-4F82-A366-B6BE217FD213@gmail.com> Hi Hilmar, thanks for the help. I've tried now this load_ontology.pl --driver Pg --dbname biosql --dbuser yyyy--dbpass xxxx --namespace "Gene Ontology" --format obo gene_ontology.1_2.obo downloaded from here http://www.geneontology.org/ontology/obo_format_1_2/gene_ontology.1_2.obo and I have this error message. --------------------- WARNING --------------------- MSG: DBLink exists in the dblink of _default --------------------------------------------------- Could not store term GO:0001404, name 'invasive growth': ------------- EXCEPTION: Bio::Root::Exception ------------- MSG: create: object (Bio::Ontology::OBOterm) failed to insert or to be found by unique key STACK: Error::throw STACK: Bio::Root::Root::throw /usr/local/share/perl/5.10.0/Bio/Root/ Root.pm:357 STACK: Bio::DB::BioSQL::BasePersistenceAdaptor::create /usr/local/ share/perl/5.10.0/Bio/DB/BioSQL/BasePersistenceAdaptor.pm:219 STACK: Bio::DB::BioSQL::BasePersistenceAdaptor::store /usr/local/share/ perl/5.10.0/Bio/DB/BioSQL/BasePersistenceAdaptor.pm:264 STACK: Bio::DB::Persistent::PersistentObject::store /usr/local/share/ perl/5.10.0/Bio/DB/Persistent/PersistentObject.pm:284 STACK: main::persist_term /tmp/BioPerl-db-1.6.0/scripts/biosql/ load_ontology.pl:812 STACK: /tmp/BioPerl-db-1.6.0/scripts/biosql/load_ontology.pl:617 ----------------------------------------------------------- at /tmp/BioPerl-db-1.6.0/scripts/biosql/load_ontology.pl line 824 main::persist_term('-term', 'Bio::Ontology::OBOterm=HASH(0x9330318)', '-db', 'Bio::DB::BioSQL::DBAdaptor=HASH(0x8a17ac0)', '-termfactory', undef, '- throw', 'CODE(0x85f4708)', '-mergeobs', ...) called at /tmp/BioPerl- db-1.6.0/scripts/biosql/load_ontology.pl line 617 Any hints to know where the problem would be? Thanks in advance, Carlos Carlos Canchaya ccanchaya at gmail.com On Jul 22, 2009, at 8:15 PM, Hilmar Lapp wrote: > Please leave off the --fmtargs GO.defs argument - this is not a file > in the .obo format. > > -hilmar > > On Jul 22, 2009, at 11:05 AM, Carlos A. Canchaya wrote: > >> Hi guys, >> >> I've tried to execute load_ontologies following your suggestions as >> >> load_ontology.pl --driver Pg --dbname biosql --dbuser yyy --dbpass >> xxx --namespace "Gene Ontology" --fmtargs GO.defs --format obo >> gene_ontology.1_2.obo >> >> However I have many warnings first >> >> --------------------- WARNING --------------------- >> MSG: DBLink exists in the dblink of _default >> --------------------------------------------------- >> >> and then >> >> --------------------- WARNING --------------------- >> MSG: DBLink exists in the dblink of _default >> --------------------------------------------------- >> Could not store term GO:0001404, name 'invasive growth': >> >> ------------- EXCEPTION: Bio::Root::Exception ------------- >> MSG: create: object (Bio::Ontology::OBOterm) failed to insert or to >> be found by unique key >> STACK: Error::throw >> STACK: Bio::Root::Root::throw /home/carlos/nascent/download/bioperl- >> live//Bio/Root/Root.pm:357 >> STACK: Bio::DB::BioSQL::BasePersistenceAdaptor::create /usr/local/ >> share/perl/5.10.0/Bio/DB/BioSQL/BasePersistenceAdaptor.pm:219 >> STACK: Bio::DB::BioSQL::BasePersistenceAdaptor::store /usr/local/ >> share/perl/5.10.0/Bio/DB/BioSQL/BasePersistenceAdaptor.pm:264 >> STACK: Bio::DB::Persistent::PersistentObject::store /usr/local/ >> share/perl/5.10.0/Bio/DB/Persistent/PersistentObject.pm:284 >> STACK: main::persist_term /tmp/BioPerl-db-1.6.0/scripts/biosql/ >> load_ontology.pl:812 >> STACK: /tmp/BioPerl-db-1.6.0/scripts/biosql/load_ontology.pl:617 >> ----------------------------------------------------------- >> >> at /tmp/BioPerl-db-1.6.0/scripts/biosql/load_ontology.pl line 824 >> main::persist_term('-term', >> 'Bio::Ontology::OBOterm=HASH(0x9c86078)', '-db', >> 'Bio::DB::BioSQL::DBAdaptor=HASH(0x936ed50)', '-termfactory', >> undef, '-throw', 'CODE(0x8f49a50)', '-mergeobs', ...) called at / >> tmp/BioPerl-db-1.6.0/scripts/biosql/load_ontology.pl line 617 >> >> >> Any ideas why? >> >> Thanks in advance, >> >> Carlos >> >> >> Carlos Canchaya >> ccanchaya at gmail.com >> >> >> >> On Jul 22, 2009, at 1:08 PM, Song Haili wrote: >> >>> Hi Florian, >>> Aha, that's the problem. Gene_ontology.1_2.obo works fine. I >>> didn't use gene_ontology.1_2.obo, but as you can see instead I >>> used gene_ontology.obo (ftp://ftp.geneontology.org/pub/go/ontology/gene_ontology.obo >>> ). However, I don't understand why I can't use gene_ontology.obo >>> which I think, does not differ a lot with gene_ontology.1_2.obo at >>> the beginning of the two files. Thanks a lot again, Florian and >>> Hilmar. >>> song >>> >>> ----- Original Message ----- >>> From: Florian Mittag >>> Date: Wednesday, July 22, 2009 10:44 >>> Subject: Re: [BioSQL-l] Error when loading Gene Ontology to biosql >>> To: Song Haili >>> Cc: biosql-l at lists.open-bio.org >>> >>>> Hi Song, >>>> >>>> just to be clear: Did you download the file >>>> gene_ontology.1_2.obo from >>>> http://www.geneontology.org/GO.downloads.ontology.shtml ? >>>> >>>> (http://www.geneontology.org/ontology/obo_format_1_2/gene_ontology.1_2.obo >>>> ) >>>> >>>> You need to specify the correct file then, because the command >>>> you described >>>> expects a file called "gene_ontology.obo", which is not the >>>> orginial name of >>>> the file to download. >>>> >>>> On Wednesday 22 July 2009 09:50, Song Haili wrote: >>>>> Hello Hilmar, >>>>> Thank you very much for your help. >>>>> I got the same error even I don't use the argument --fmtargs. >>>> Actually that >>>>> was the first try before I use --fmtargs. Any idea on how to >>>> solve this >>>>> problem? Thanks in advance. >>>>> >>>>> command: >>>>> perl load_ontology.pl --driver Pg --host pg-server --dbname sifter >>>>> --dbuser sifter --dbpass password --namespace "Gene Ontology" - >>>> -format obo >>>>> gene_ontology.obo --noobsolete error: >>>>> ------------- EXCEPTION ------------- >>>>> MSG: OBO File Format Error - >>>>> Cannot find tag format-version and/ default-namespace . These >>>> are required >>>>> header. >>>>> >>>>> STACK Bio::OntologyIO::obo::_header >>>>> /opt/share/local/users/haili/bioperl- >>>> live/Bio/OntologyIO/obo.pm:518 STACK >>>>> Bio::OntologyIO::obo::parse >>>>> /opt/share/local/users/haili/bioperl- >>>> live/Bio/OntologyIO/obo.pm:209 STACK >>>>> Bio::OntologyIO::obo::next_ontology >>>>> /opt/share/local/users/haili/bioperl- >>>> live/Bio/OntologyIO/obo.pm:342 STACK >>>>> toplevel load_ontology.pl:604 >>>>> ------------------------------------- >>>>> >>>>> ----- Original Message ----- >>>>> From: Hilmar Lapp >>>>> Date: Tuesday, July 21, 2009 19:19 >>>>> Subject: Re: [BioSQL-l] Error when loading Gene Ontology to biosql >>>>> To: Song Haili >>>>> Cc: florian.mittag at uni-tuebingen.de, biosql-l at lists.open-bio.org >>>>> >>>>>> Song: GO.defs is not in OBO format. Where did you find that you >>>>>> need >>>>>> it when you load .obo formatted files? You don't need the -- >>>>>> fmtargs >>>>>> argument for .obo files other than if you want to specify the >>>>>> ontology >>>>>> name. >>>>>> >>>>>> -hilmar >>>>>> >>>>>> On Jul 21, 2009, at 11:32 AM, Song Haili wrote: >>>>>>> Hello All, >>>>>>> The previous error was solved by the help of Florian. Florian, >>>>>> >>>>>> Thank >>>>>> >>>>>>> you very much. >>>>>>> But I got another error using the way Florian suggested. I >>>>>> >>>>>> thought >>>>>> >>>>>>> it was because parameter --fmtargs was not specified. So I >>>>>> >>>>>> tried to >>>>>> >>>>>>> include it with the value "-defs_file, GO.defs", but it didn't >>>>>> >>>>>> work. >>>>>> >>>>>>> I think maybe GO.defs is not the right file. Is it? But >>>>>> >>>>>> how or >>>>>> >>>>>>> where to get the right file if it is. Or any other ideas about >>>>>> >>>>>> how >>>>>> >>>>>>> to solve this error? Thank you very much in advance. >>>>>>> command: >>>>>>> perl load_ontology.pl --driver Pg --host pg-server --dbname >>>>>> >>>>>> sifter >>>>>> >>>>>>> --dbuser sifter --dbpass password --namespace "Gene >>>> Ontology" - >>>>>> >>>>>> - >>>>>> >>>>>>> format obo gene_ontology.obo --fmtargs "-defs_file, >>>> GO.defs" -- >>>>>>> >>>>>>> noobsolete >>>>>>> error: >>>>>>> ------------- EXCEPTION ------------- >>>>>>> MSG: OBO File Format Error - >>>>>>> Cannot find tag format-version and/ default-namespace . These >>>>>> >>>>>> are >>>>>> >>>>>>> required header. >>>>>>> >>>>>>> STACK Bio::OntologyIO::obo::_header >>>>>> >>>>>> /opt/share/local/users/haili/ >>>>>> >>>>>>> bioperl-live/Bio/OntologyIO/obo.pm:518 >>>>>>> STACK Bio::OntologyIO::obo::parse >>>>>> >>>>>> /opt/share/local/users/haili/ >>>>>> >>>>>>> bioperl-live/Bio/OntologyIO/obo.pm:209 >>>>>>> STACK Bio::OntologyIO::obo::next_ontology >>>>>> >>>>>> /opt/share/local/users/ >>>>>> >>>>>>> haili/bioperl-live/Bio/OntologyIO/obo.pm:342 >>>>>>> STACK toplevel load_ontology.pl:604 >>>>>>> ------------------------------------- >>>>>>> >>>>>>> ----- Original Message ----- >>>>>>> From: Florian Mittag >>>>>>> Date: Tuesday, July 21, 2009 14:41 >>>>>>> Subject: Re: [BioSQL-l] Error when loading Gene Ontology >>>> to biosql >>>>>>> To: biosql-l at lists.open-bio.org >>>>>>> >>>>>>>> Hi! >>>>>>>> >>>>>>>> AFAIK the goflat format is deprecated. Use the .obo files and >>>>>>>> format instead, >>>>>>>> that should work. >>>>>>>> >>>>>>>> perl load_ontology.pl --driver Pg --host pg-server -- >>>> dbname sifter >>>>>>>> --dbuser sifter --dbpass password --namespace "Gene >>>>>> >>>>>> Ontology" -- >>>>>> >>>>>>>> format obo >>>>>>>> >>>>>> >>>>>> gene_ontology.1_2.obo>> --noobsolete >>>>>> >>>>>>>> On Tuesday 21 July 2009 12:11, Song Haili wrote: >>>>>>>>> Dear all, >>>>>>>>> I am using perl-5.10.0, BioPerl-1.6.0, and bioperl-db obtaind >>>>>>>> >>>>>>>> by using CPAN >>>>>>>> >>>>>>>>> a few days before. Until now, I can load taxonomy and sequence >>>>>>>> >>>>>>>> data into >>>>>>>> >>>>>>>>> database successfully. However, I got the following error >>>>>>>> >>>>>>>> message when >>>>>>>> >>>>>>>>> trying to load Gene Ontology data into biosql database. Any >>>>>>>> >>>>>>>> help will be >>>>>>>> >>>>>>>>> appreciated. Jane >>>>>>>>> >>>>>>>>> command used: >>>>>>>>> perl load_ontology.pl --driver Pg --host pg-server --dbname >>>>>>>> >>>>>>>> sifter -dbuser >>>>>>>> >>>>>>>>> sifter --dbpass password ??namespace "Gene Ontology" -- >>>>>> >>>>>> format >>>>>> >>>>>>>>> goflat >>>>>>>>> component.ontology process.ontology function.ontology -- >>>> fmtargs> > >>> "-defs_file, GO.defs" --noobsolete >>>>>>>>> >>>>>>>>> error: >>>>>>>>> ------------- EXCEPTION ------------- >>>>>>>>> MSG: Could not open ??namespace: No such file or directory >>>>>>>>> STACK Bio::Root::IO::_initialize_io >>>>>>>>> /opt/share/local/users/haili/bioperl- >>>> live/Bio/Root/IO.pm:323 STACK >>>>>>>>> Bio::OntologyIO::dagflat::parse >>>>>>>>> /opt/share/local/users/haili/bioperl- >>>>>>>> >>>>>>>> live/Bio/OntologyIO/dagflat.pm:277> STACK >>>>>>>> Bio::OntologyIO::dagflat::next_ontology> >>>>>>>> /opt/share/local/users/haili/bioperl- >>>>>> >>>>>> live/Bio/OntologyIO/dagflat.pm: >>>>>>>> 330 >>>>>>>> >>>>>>>>> STACK toplevel load_ontology.pl:604 >>>>>>>>> ------------------------------------- >>>>>>>> >>>>>>>> _______________________________________________ >>>>>>>> BioSQL-l mailing list >>>>>>>> BioSQL-l at lists.open-bio.org >>>>>>>> http://lists.open-bio.org/mailman/listinfo/biosql-l >>>>>>> >>>>>>> _______________________________________________ >>>>>>> BioSQL-l mailing list >>>>>>> BioSQL-l at lists.open-bio.org >>>>>>> http://lists.open-bio.org/mailman/listinfo/biosql-l >>>>>> >>>>>> -- >>>>>> =========================================================== >>>>>> >>>>>> : Hilmar Lapp -:- Durham, NC -:- hlapp >>>>>> >>>>>> at gmx dot net : >>>>>> =========================================================== >>> >>> _______________________________________________ >>> BioSQL-l mailing list >>> BioSQL-l at lists.open-bio.org >>> http://lists.open-bio.org/mailman/listinfo/biosql-l >> >> >> _______________________________________________ >> BioSQL-l mailing list >> BioSQL-l at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/biosql-l > > -- > =========================================================== > : Hilmar Lapp -:- Durham, NC -:- hlapp at gmx dot net : > =========================================================== > > > From hlapp at gmx.net Thu Jul 23 08:49:48 2009 From: hlapp at gmx.net (Hilmar Lapp) Date: Thu, 23 Jul 2009 08:49:48 -0400 Subject: [BioSQL-l] Error when loading Gene Ontology to biosql In-Reply-To: <5A932B73-5D17-4F82-A366-B6BE217FD213@gmail.com> References: <200907221044.18292.florian.mittag@uni-tuebingen.de> <5A932B73-5D17-4F82-A366-B6BE217FD213@gmail.com> Message-ID: <1E596269-ED8F-4ADF-9B54-A9A0CF908620@gmx.net> Hi Carlos - that's an odd error that we haven't seen yet. My first impulse would be to suspect that your database wasn't empty when you ran this, and that the error you got is due to a term in the input file clashing with one you already have in the database. You can check this by looking into your database: SQL> SELECT * FROM term WHERE identifier = 'GO:0001404' or name = 'invasive growth'; Does this return anything? Note that load_ontology.pl is perfectly equipped to update an existing ontology - check the POD and look for the --lookup command line option (and the several options following it in the POD with which you can modify the exact update behavior). By default though the script will assume that it is loading a new ontology. -hilmar On Jul 23, 2009, at 3:27 AM, Carlos A. Canchaya wrote: > Hi Hilmar, > > thanks for the help. I've tried now this > > load_ontology.pl --driver Pg --dbname biosql --dbuser yyyy--dbpass > xxxx --namespace "Gene Ontology" --format obo gene_ontology.1_2.obo > > downloaded from here > > http://www.geneontology.org/ontology/obo_format_1_2/gene_ontology.1_2.obo > > and I have this error message. > > --------------------- WARNING --------------------- > MSG: DBLink exists in the dblink of _default > --------------------------------------------------- > Could not store term GO:0001404, name 'invasive growth': > > ------------- EXCEPTION: Bio::Root::Exception ------------- > MSG: create: object (Bio::Ontology::OBOterm) failed to insert or to > be found by unique key > STACK: Error::throw > STACK: Bio::Root::Root::throw /usr/local/share/perl/5.10.0/Bio/Root/ > Root.pm:357 > STACK: Bio::DB::BioSQL::BasePersistenceAdaptor::create /usr/local/ > share/perl/5.10.0/Bio/DB/BioSQL/BasePersistenceAdaptor.pm:219 > STACK: Bio::DB::BioSQL::BasePersistenceAdaptor::store /usr/local/ > share/perl/5.10.0/Bio/DB/BioSQL/BasePersistenceAdaptor.pm:264 > STACK: Bio::DB::Persistent::PersistentObject::store /usr/local/share/ > perl/5.10.0/Bio/DB/Persistent/PersistentObject.pm:284 > STACK: main::persist_term /tmp/BioPerl-db-1.6.0/scripts/biosql/ > load_ontology.pl:812 > STACK: /tmp/BioPerl-db-1.6.0/scripts/biosql/load_ontology.pl:617 > ----------------------------------------------------------- > > at /tmp/BioPerl-db-1.6.0/scripts/biosql/load_ontology.pl line 824 > main::persist_term('-term', > 'Bio::Ontology::OBOterm=HASH(0x9330318)', '-db', > 'Bio::DB::BioSQL::DBAdaptor=HASH(0x8a17ac0)', '-termfactory', undef, > '-throw', 'CODE(0x85f4708)', '-mergeobs', ...) called at /tmp/ > BioPerl-db-1.6.0/scripts/biosql/load_ontology.pl line 617 > > Any hints to know where the problem would be? > > Thanks in advance, > > Carlos > > Carlos Canchaya > ccanchaya at gmail.com > > > > On Jul 22, 2009, at 8:15 PM, Hilmar Lapp wrote: > >> Please leave off the --fmtargs GO.defs argument - this is not a >> file in the .obo format. >> >> -hilmar >> >> On Jul 22, 2009, at 11:05 AM, Carlos A. Canchaya wrote: >> >>> Hi guys, >>> >>> I've tried to execute load_ontologies following your suggestions as >>> >>> load_ontology.pl --driver Pg --dbname biosql --dbuser yyy --dbpass >>> xxx --namespace "Gene Ontology" --fmtargs GO.defs --format obo >>> gene_ontology.1_2.obo >>> >>> However I have many warnings first >>> >>> --------------------- WARNING --------------------- >>> MSG: DBLink exists in the dblink of _default >>> --------------------------------------------------- >>> >>> and then >>> >>> --------------------- WARNING --------------------- >>> MSG: DBLink exists in the dblink of _default >>> --------------------------------------------------- >>> Could not store term GO:0001404, name 'invasive growth': >>> >>> ------------- EXCEPTION: Bio::Root::Exception ------------- >>> MSG: create: object (Bio::Ontology::OBOterm) failed to insert or >>> to be found by unique key >>> STACK: Error::throw >>> STACK: Bio::Root::Root::throw /home/carlos/nascent/download/ >>> bioperl-live//Bio/Root/Root.pm:357 >>> STACK: Bio::DB::BioSQL::BasePersistenceAdaptor::create /usr/local/ >>> share/perl/5.10.0/Bio/DB/BioSQL/BasePersistenceAdaptor.pm:219 >>> STACK: Bio::DB::BioSQL::BasePersistenceAdaptor::store /usr/local/ >>> share/perl/5.10.0/Bio/DB/BioSQL/BasePersistenceAdaptor.pm:264 >>> STACK: Bio::DB::Persistent::PersistentObject::store /usr/local/ >>> share/perl/5.10.0/Bio/DB/Persistent/PersistentObject.pm:284 >>> STACK: main::persist_term /tmp/BioPerl-db-1.6.0/scripts/biosql/ >>> load_ontology.pl:812 >>> STACK: /tmp/BioPerl-db-1.6.0/scripts/biosql/load_ontology.pl:617 >>> ----------------------------------------------------------- >>> >>> at /tmp/BioPerl-db-1.6.0/scripts/biosql/load_ontology.pl line 824 >>> main::persist_term('-term', >>> 'Bio::Ontology::OBOterm=HASH(0x9c86078)', '-db', >>> 'Bio::DB::BioSQL::DBAdaptor=HASH(0x936ed50)', '-termfactory', >>> undef, '-throw', 'CODE(0x8f49a50)', '-mergeobs', ...) called at / >>> tmp/BioPerl-db-1.6.0/scripts/biosql/load_ontology.pl line 617 >>> >>> >>> Any ideas why? >>> >>> Thanks in advance, >>> >>> Carlos >>> >>> >>> Carlos Canchaya >>> ccanchaya at gmail.com >>> >>> >>> >>> On Jul 22, 2009, at 1:08 PM, Song Haili wrote: >>> >>>> Hi Florian, >>>> Aha, that's the problem. Gene_ontology.1_2.obo works fine. I >>>> didn't use gene_ontology.1_2.obo, but as you can see instead I >>>> used gene_ontology.obo (ftp://ftp.geneontology.org/pub/go/ontology/gene_ontology.obo >>>> ). However, I don't understand why I can't use gene_ontology.obo >>>> which I think, does not differ a lot with gene_ontology.1_2.obo >>>> at the beginning of the two files. Thanks a lot again, Florian >>>> and Hilmar. >>>> song >>>> >>>> ----- Original Message ----- >>>> From: Florian Mittag >>>> Date: Wednesday, July 22, 2009 10:44 >>>> Subject: Re: [BioSQL-l] Error when loading Gene Ontology to biosql >>>> To: Song Haili >>>> Cc: biosql-l at lists.open-bio.org >>>> >>>>> Hi Song, >>>>> >>>>> just to be clear: Did you download the file >>>>> gene_ontology.1_2.obo from >>>>> http://www.geneontology.org/GO.downloads.ontology.shtml ? >>>>> >>>>> (http://www.geneontology.org/ontology/obo_format_1_2/gene_ontology.1_2.obo >>>>> ) >>>>> >>>>> You need to specify the correct file then, because the command >>>>> you described >>>>> expects a file called "gene_ontology.obo", which is not the >>>>> orginial name of >>>>> the file to download. >>>>> >>>>> On Wednesday 22 July 2009 09:50, Song Haili wrote: >>>>>> Hello Hilmar, >>>>>> Thank you very much for your help. >>>>>> I got the same error even I don't use the argument --fmtargs. >>>>> Actually that >>>>>> was the first try before I use --fmtargs. Any idea on how to >>>>> solve this >>>>>> problem? Thanks in advance. >>>>>> >>>>>> command: >>>>>> perl load_ontology.pl --driver Pg --host pg-server --dbname >>>>>> sifter >>>>>> --dbuser sifter --dbpass password --namespace "Gene Ontology" - >>>>> -format obo >>>>>> gene_ontology.obo --noobsolete error: >>>>>> ------------- EXCEPTION ------------- >>>>>> MSG: OBO File Format Error - >>>>>> Cannot find tag format-version and/ default-namespace . These >>>>> are required >>>>>> header. >>>>>> >>>>>> STACK Bio::OntologyIO::obo::_header >>>>>> /opt/share/local/users/haili/bioperl- >>>>> live/Bio/OntologyIO/obo.pm:518 STACK >>>>>> Bio::OntologyIO::obo::parse >>>>>> /opt/share/local/users/haili/bioperl- >>>>> live/Bio/OntologyIO/obo.pm:209 STACK >>>>>> Bio::OntologyIO::obo::next_ontology >>>>>> /opt/share/local/users/haili/bioperl- >>>>> live/Bio/OntologyIO/obo.pm:342 STACK >>>>>> toplevel load_ontology.pl:604 >>>>>> ------------------------------------- >>>>>> >>>>>> ----- Original Message ----- >>>>>> From: Hilmar Lapp >>>>>> Date: Tuesday, July 21, 2009 19:19 >>>>>> Subject: Re: [BioSQL-l] Error when loading Gene Ontology to >>>>>> biosql >>>>>> To: Song Haili >>>>>> Cc: florian.mittag at uni-tuebingen.de, biosql-l at lists.open-bio.org >>>>>> >>>>>>> Song: GO.defs is not in OBO format. Where did you find that you >>>>>>> need >>>>>>> it when you load .obo formatted files? You don't need the -- >>>>>>> fmtargs >>>>>>> argument for .obo files other than if you want to specify the >>>>>>> ontology >>>>>>> name. >>>>>>> >>>>>>> -hilmar >>>>>>> >>>>>>> On Jul 21, 2009, at 11:32 AM, Song Haili wrote: >>>>>>>> Hello All, >>>>>>>> The previous error was solved by the help of Florian. Florian, >>>>>>> >>>>>>> Thank >>>>>>> >>>>>>>> you very much. >>>>>>>> But I got another error using the way Florian suggested. I >>>>>>> >>>>>>> thought >>>>>>> >>>>>>>> it was because parameter --fmtargs was not specified. So I >>>>>>> >>>>>>> tried to >>>>>>> >>>>>>>> include it with the value "-defs_file, GO.defs", but it didn't >>>>>>> >>>>>>> work. >>>>>>> >>>>>>>> I think maybe GO.defs is not the right file. Is it? But >>>>>>> >>>>>>> how or >>>>>>> >>>>>>>> where to get the right file if it is. Or any other ideas about >>>>>>> >>>>>>> how >>>>>>> >>>>>>>> to solve this error? Thank you very much in advance. >>>>>>>> command: >>>>>>>> perl load_ontology.pl --driver Pg --host pg-server --dbname >>>>>>> >>>>>>> sifter >>>>>>> >>>>>>>> --dbuser sifter --dbpass password --namespace "Gene >>>>> Ontology" - >>>>>>> >>>>>>> - >>>>>>> >>>>>>>> format obo gene_ontology.obo --fmtargs "-defs_file, >>>>> GO.defs" -- >>>>>>>> >>>>>>>> noobsolete >>>>>>>> error: >>>>>>>> ------------- EXCEPTION ------------- >>>>>>>> MSG: OBO File Format Error - >>>>>>>> Cannot find tag format-version and/ default-namespace . These >>>>>>> >>>>>>> are >>>>>>> >>>>>>>> required header. >>>>>>>> >>>>>>>> STACK Bio::OntologyIO::obo::_header >>>>>>> >>>>>>> /opt/share/local/users/haili/ >>>>>>> >>>>>>>> bioperl-live/Bio/OntologyIO/obo.pm:518 >>>>>>>> STACK Bio::OntologyIO::obo::parse >>>>>>> >>>>>>> /opt/share/local/users/haili/ >>>>>>> >>>>>>>> bioperl-live/Bio/OntologyIO/obo.pm:209 >>>>>>>> STACK Bio::OntologyIO::obo::next_ontology >>>>>>> >>>>>>> /opt/share/local/users/ >>>>>>> >>>>>>>> haili/bioperl-live/Bio/OntologyIO/obo.pm:342 >>>>>>>> STACK toplevel load_ontology.pl:604 >>>>>>>> ------------------------------------- >>>>>>>> >>>>>>>> ----- Original Message ----- >>>>>>>> From: Florian Mittag >>>>>>>> Date: Tuesday, July 21, 2009 14:41 >>>>>>>> Subject: Re: [BioSQL-l] Error when loading Gene Ontology >>>>> to biosql >>>>>>>> To: biosql-l at lists.open-bio.org >>>>>>>> >>>>>>>>> Hi! >>>>>>>>> >>>>>>>>> AFAIK the goflat format is deprecated. Use the .obo files and >>>>>>>>> format instead, >>>>>>>>> that should work. >>>>>>>>> >>>>>>>>> perl load_ontology.pl --driver Pg --host pg-server -- >>>>> dbname sifter >>>>>>>>> --dbuser sifter --dbpass password --namespace "Gene >>>>>>> >>>>>>> Ontology" -- >>>>>>> >>>>>>>>> format obo >>>>>>>>> >>>>>>> >>>>>>> gene_ontology.1_2.obo>> --noobsolete >>>>>>> >>>>>>>>> On Tuesday 21 July 2009 12:11, Song Haili wrote: >>>>>>>>>> Dear all, >>>>>>>>>> I am using perl-5.10.0, BioPerl-1.6.0, and bioperl-db obtaind >>>>>>>>> >>>>>>>>> by using CPAN >>>>>>>>> >>>>>>>>>> a few days before. Until now, I can load taxonomy and >>>>>>>>>> sequence >>>>>>>>> >>>>>>>>> data into >>>>>>>>> >>>>>>>>>> database successfully. However, I got the following error >>>>>>>>> >>>>>>>>> message when >>>>>>>>> >>>>>>>>>> trying to load Gene Ontology data into biosql database. Any >>>>>>>>> >>>>>>>>> help will be >>>>>>>>> >>>>>>>>>> appreciated. Jane >>>>>>>>>> >>>>>>>>>> command used: >>>>>>>>>> perl load_ontology.pl --driver Pg --host pg-server --dbname >>>>>>>>> >>>>>>>>> sifter -dbuser >>>>>>>>> >>>>>>>>>> sifter --dbpass password ??namespace "Gene Ontology" -- >>>>>>> >>>>>>> format >>>>>>> >>>>>>>>>> goflat >>>>>>>>>> component.ontology process.ontology function.ontology -- >>>>> fmtargs> > >>> "-defs_file, GO.defs" --noobsolete >>>>>>>>>> >>>>>>>>>> error: >>>>>>>>>> ------------- EXCEPTION ------------- >>>>>>>>>> MSG: Could not open ??namespace: No such file or >>>>>>>>>> directory >>>>>>>>>> STACK Bio::Root::IO::_initialize_io >>>>>>>>>> /opt/share/local/users/haili/bioperl- >>>>> live/Bio/Root/IO.pm:323 STACK >>>>>>>>>> Bio::OntologyIO::dagflat::parse >>>>>>>>>> /opt/share/local/users/haili/bioperl- >>>>>>>>> >>>>>>>>> live/Bio/OntologyIO/dagflat.pm:277> STACK >>>>>>>>> Bio::OntologyIO::dagflat::next_ontology> >>>>>>>>> /opt/share/local/users/haili/bioperl- >>>>>>> >>>>>>> live/Bio/OntologyIO/dagflat.pm: >>>>>>>>> 330 >>>>>>>>> >>>>>>>>>> STACK toplevel load_ontology.pl:604 >>>>>>>>>> ------------------------------------- >>>>>>>>> >>>>>>>>> _______________________________________________ >>>>>>>>> BioSQL-l mailing list >>>>>>>>> BioSQL-l at lists.open-bio.org >>>>>>>>> http://lists.open-bio.org/mailman/listinfo/biosql-l >>>>>>>> >>>>>>>> _______________________________________________ >>>>>>>> BioSQL-l mailing list >>>>>>>> BioSQL-l at lists.open-bio.org >>>>>>>> http://lists.open-bio.org/mailman/listinfo/biosql-l >>>>>>> >>>>>>> -- >>>>>>> =========================================================== >>>>>>> >>>>>>> : Hilmar Lapp -:- Durham, NC -:- hlapp >>>>>>> >>>>>>> at gmx dot net : >>>>>>> =========================================================== >>>> >>>> _______________________________________________ >>>> BioSQL-l mailing list >>>> BioSQL-l at lists.open-bio.org >>>> http://lists.open-bio.org/mailman/listinfo/biosql-l >>> >>> >>> _______________________________________________ >>> BioSQL-l mailing list >>> BioSQL-l at lists.open-bio.org >>> http://lists.open-bio.org/mailman/listinfo/biosql-l >> >> -- >> =========================================================== >> : Hilmar Lapp -:- Durham, NC -:- hlapp at gmx dot net : >> =========================================================== >> >> >> > > > _______________________________________________ > BioSQL-l mailing list > BioSQL-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/biosql-l -- =========================================================== : Hilmar Lapp -:- Durham, NC -:- hlapp at gmx dot net : =========================================================== From biopython at maubp.freeserve.co.uk Thu Jul 23 09:32:39 2009 From: biopython at maubp.freeserve.co.uk (Peter) Date: Thu, 23 Jul 2009 14:32:39 +0100 Subject: [BioSQL-l] [Biopython] Storing SeqRecord objects with annotation In-Reply-To: <8E8262E4-FEA0-4839-957B-A5B4A56F8E49@gmx.net> References: <320fb6e00907230320r49809329p620f3d1d4a39fb36@mail.gmail.com> <8E8262E4-FEA0-4839-957B-A5B4A56F8E49@gmx.net> Message-ID: <320fb6e00907230632q730aa496g4a07c50d5860bd54@mail.gmail.com> Hi Hilmar! I've CC'd this to the BioSQL list. The start of the thread was here: http://lists.open-bio.org/pipermail/biopython/2009-July/005385.html On Thu, Jul 23, 2009 at 2:01 PM, Hilmar Lapp wrote: > > On Jul 23, 2009, at 6:20 AM, Peter wrote: > >> Currently the BioSQL schema doesn't have any explicit support >> for "per letter annotation" > > I haven't been following the thread closely and so may be missing what is > really meant by this. If, however, you mean associating annotation to a > specific letter (position) in the sequence, BioSQL does support this - you'd > create a seqfeature with appropriate location, and attach the annotation to > the seqfeature. > > Bioentry annotations are location-less, by comparison. By "per letter annotation" we mean essentially a list of annotation data, with one entry for each letter in the sequence. For example, a sequencing quality score (from a FASTQ file) where this is one integer per letter (i.e. per base pair). Or, a secondary structure prediction, encoded as one character per letter (which could apply to proteins and nucleotides). This sort of thing could be done by using on feature per letter, but it would be dreadfully inefficient for storing in the database. >> [...] >> You can record any object in the SeqRecord's annotation dictionary. >> However, saving the result to a file will be tricky - and it wouldn't >> work in BioSQL either. > > Note that that's not entirely true. If you have a textual serialization > (such as XML) of your object, you *can* store it in > bioentry_qualifier_value. This is what we do in BioPerl with a TagTree > annotation object that supports a nested hierarchical annotation > structure needed for lossless representation of some UniProt lines. This was what I mentioned earlier in the thread - using XML or JSON to turn the object into a long string. However, we really need the Bio* projects to agree on some standards here, rather than each project adding its own additions ad hoc (which will make interoperation much trickier). For example, I was unaware you (BioPerl) had already pressed ahead with this for the UniProt data - which rather proves my point. > Obviously, that won't allow you to query very well by individual > elements of your custom annotation object. But you can build a > custom index (e.g., using Lucene) that does that. Yes, doing searches on an XML/JSON encoded string is an issue. But right now we are probably more interested in just solving the persistence of more complex objects. Peter From cjfields at illinois.edu Thu Jul 23 20:39:25 2009 From: cjfields at illinois.edu (Chris Fields) Date: Thu, 23 Jul 2009 19:39:25 -0500 Subject: [BioSQL-l] Error when loading Gene Ontology to biosql In-Reply-To: <1E596269-ED8F-4ADF-9B54-A9A0CF908620@gmx.net> References: <200907221044.18292.florian.mittag@uni-tuebingen.de> <5A932B73-5D17-4F82-A366-B6BE217FD213@gmail.com> <1E596269-ED8F-4ADF-9B54-A9A0CF908620@gmx.net> Message-ID: <52ED5492-14F1-443C-AB1E-67685A464656@illinois.edu> The warning is interesting, as it derives from our rollback of feature/ annotation stuff in bioperl. It indicates the specified DBLink is duplicated in the Bio::Ontology::Term. The exception makes sense in light of that (and seems to confirm the link was already present). chris On Jul 23, 2009, at 7:49 AM, Hilmar Lapp wrote: > Hi Carlos - that's an odd error that we haven't seen yet. My first > impulse would be to suspect that your database wasn't empty when you > ran this, and that the error you got is due to a term in the input > file clashing with one you already have in the database. > > You can check this by looking into your database: > > SQL> SELECT * FROM term WHERE identifier = 'GO:0001404' or name = > 'invasive growth'; > > Does this return anything? > > Note that load_ontology.pl is perfectly equipped to update an > existing ontology - check the POD and look for the --lookup command > line option (and the several options following it in the POD with > which you can modify the exact update behavior). By default though > the script will assume that it is loading a new ontology. > > -hilmar > > On Jul 23, 2009, at 3:27 AM, Carlos A. Canchaya wrote: > >> Hi Hilmar, >> >> thanks for the help. I've tried now this >> >> load_ontology.pl --driver Pg --dbname biosql --dbuser yyyy--dbpass >> xxxx --namespace "Gene Ontology" --format obo gene_ontology.1_2.obo >> >> downloaded from here >> >> http://www.geneontology.org/ontology/obo_format_1_2/gene_ontology.1_2.obo >> >> and I have this error message. >> >> --------------------- WARNING --------------------- >> MSG: DBLink _default >> --------------------------------------------------- >> Could not store term GO:0001404, name 'invasive growth': >> >> ------------- EXCEPTION: Bio::Root::Exception ------------- >> MSG: create: object (Bio::Ontology::OBOterm) failed to insert or to >> be found by unique key >> STACK: Error::throw >> STACK: Bio::Root::Root::throw /usr/local/share/perl/5.10.0/Bio/Root/ >> Root.pm:357 >> STACK: Bio::DB::BioSQL::BasePersistenceAdaptor::create /usr/local/ >> share/perl/5.10.0/Bio/DB/BioSQL/BasePersistenceAdaptor.pm:219 >> STACK: Bio::DB::BioSQL::BasePersistenceAdaptor::store /usr/local/ >> share/perl/5.10.0/Bio/DB/BioSQL/BasePersistenceAdaptor.pm:264 >> STACK: Bio::DB::Persistent::PersistentObject::store /usr/local/ >> share/perl/5.10.0/Bio/DB/Persistent/PersistentObject.pm:284 >> STACK: main::persist_term /tmp/BioPerl-db-1.6.0/scripts/biosql/ >> load_ontology.pl:812 >> STACK: /tmp/BioPerl-db-1.6.0/scripts/biosql/load_ontology.pl:617 >> ----------------------------------------------------------- >> >> at /tmp/BioPerl-db-1.6.0/scripts/biosql/load_ontology.pl line 824 >> main::persist_term('-term', >> 'Bio::Ontology::OBOterm=HASH(0x9330318)', '-db', >> 'Bio::DB::BioSQL::DBAdaptor=HASH(0x8a17ac0)', '-termfactory', >> undef, '-throw', 'CODE(0x85f4708)', '-mergeobs', ...) called at / >> tmp/BioPerl-db-1.6.0/scripts/biosql/load_ontology.pl line 617 >> >> Any hints to know where the problem would be? >> >> Thanks in advance, >> >> Carlos >> >> Carlos Canchaya >> ccanchaya at gmail.com >> >> >> >> On Jul 22, 2009, at 8:15 PM, Hilmar Lapp wrote: >> >>> Please leave off the --fmtargs GO.defs argument - this is not a >>> file in the .obo format. >>> >>> -hilmar >>> >>> On Jul 22, 2009, at 11:05 AM, Carlos A. Canchaya wrote: >>> >>>> Hi guys, >>>> >>>> I've tried to execute load_ontologies following your suggestions as >>>> >>>> load_ontology.pl --driver Pg --dbname biosql --dbuser yyy -- >>>> dbpass xxx --namespace "Gene Ontology" --fmtargs GO.defs --format >>>> obo gene_ontology.1_2.obo >>>> >>>> However I have many warnings first >>>> >>>> --------------------- WARNING --------------------- >>>> MSG: DBLink exists in the dblink of _default >>>> --------------------------------------------------- >>>> >>>> and then >>>> >>>> --------------------- WARNING --------------------- >>>> MSG: DBLink exists in the dblink of _default >>>> --------------------------------------------------- >>>> Could not store term GO:0001404, name 'invasive growth': >>>> >>>> ------------- EXCEPTION: Bio::Root::Exception ------------- >>>> MSG: create: object (Bio::Ontology::OBOterm) failed to insert or >>>> to be found by unique key >>>> STACK: Error::throw >>>> STACK: Bio::Root::Root::throw /home/carlos/nascent/download/ >>>> bioperl-live//Bio/Root/Root.pm:357 >>>> STACK: Bio::DB::BioSQL::BasePersistenceAdaptor::create /usr/local/ >>>> share/perl/5.10.0/Bio/DB/BioSQL/BasePersistenceAdaptor.pm:219 >>>> STACK: Bio::DB::BioSQL::BasePersistenceAdaptor::store /usr/local/ >>>> share/perl/5.10.0/Bio/DB/BioSQL/BasePersistenceAdaptor.pm:264 >>>> STACK: Bio::DB::Persistent::PersistentObject::store /usr/local/ >>>> share/perl/5.10.0/Bio/DB/Persistent/PersistentObject.pm:284 >>>> STACK: main::persist_term /tmp/BioPerl-db-1.6.0/scripts/biosql/ >>>> load_ontology.pl:812 >>>> STACK: /tmp/BioPerl-db-1.6.0/scripts/biosql/load_ontology.pl:617 >>>> ----------------------------------------------------------- >>>> >>>> at /tmp/BioPerl-db-1.6.0/scripts/biosql/load_ontology.pl line 824 >>>> main::persist_term('-term', >>>> 'Bio::Ontology::OBOterm=HASH(0x9c86078)', '-db', >>>> 'Bio::DB::BioSQL::DBAdaptor=HASH(0x936ed50)', '-termfactory', >>>> undef, '-throw', 'CODE(0x8f49a50)', '-mergeobs', ...) called at / >>>> tmp/BioPerl-db-1.6.0/scripts/biosql/load_ontology.pl line 617 >>>> >>>> >>>> Any ideas why? >>>> >>>> Thanks in advance, >>>> >>>> Carlos >>>> >>>> >>>> Carlos Canchaya >>>> ccanchaya at gmail.com >>>> >>>> >>>> >>>> On Jul 22, 2009, at 1:08 PM, Song Haili wrote: >>>> >>>>> Hi Florian, >>>>> Aha, that's the problem. Gene_ontology.1_2.obo works fine. I >>>>> didn't use gene_ontology.1_2.obo, but as you can see instead I >>>>> used gene_ontology.obo (ftp://ftp.geneontology.org/pub/go/ontology/gene_ontology.obo >>>>> ). However, I don't understand why I can't use gene_ontology.obo >>>>> which I think, does not differ a lot with gene_ontology.1_2.obo >>>>> at the beginning of the two files. Thanks a lot again, Florian >>>>> and Hilmar. >>>>> song >>>>> >>>>> ----- Original Message ----- >>>>> From: Florian Mittag >>>>> Date: Wednesday, July 22, 2009 10:44 >>>>> Subject: Re: [BioSQL-l] Error when loading Gene Ontology to biosql >>>>> To: Song Haili >>>>> Cc: biosql-l at lists.open-bio.org >>>>> >>>>>> Hi Song, >>>>>> >>>>>> just to be clear: Did you download the file >>>>>> gene_ontology.1_2.obo from >>>>>> http://www.geneontology.org/GO.downloads.ontology.shtml ? >>>>>> >>>>>> (http://www.geneontology.org/ontology/obo_format_1_2/gene_ontology.1_2.obo >>>>>> ) >>>>>> >>>>>> You need to specify the correct file then, because the command >>>>>> you described >>>>>> expects a file called "gene_ontology.obo", which is not the >>>>>> orginial name of >>>>>> the file to download. >>>>>> >>>>>> On Wednesday 22 July 2009 09:50, Song Haili wrote: >>>>>>> Hello Hilmar, >>>>>>> Thank you very much for your help. >>>>>>> I got the same error even I don't use the argument --fmtargs. >>>>>> Actually that >>>>>>> was the first try before I use --fmtargs. Any idea on how to >>>>>> solve this >>>>>>> problem? Thanks in advance. >>>>>>> >>>>>>> command: >>>>>>> perl load_ontology.pl --driver Pg --host pg-server --dbname >>>>>>> sifter >>>>>>> --dbuser sifter --dbpass password --namespace "Gene Ontology" - >>>>>> -format obo >>>>>>> gene_ontology.obo --noobsolete error: >>>>>>> ------------- EXCEPTION ------------- >>>>>>> MSG: OBO File Format Error - >>>>>>> Cannot find tag format-version and/ default-namespace . These >>>>>> are required >>>>>>> header. >>>>>>> >>>>>>> STACK Bio::OntologyIO::obo::_header >>>>>>> /opt/share/local/users/haili/bioperl- >>>>>> live/Bio/OntologyIO/obo.pm:518 STACK >>>>>>> Bio::OntologyIO::obo::parse >>>>>>> /opt/share/local/users/haili/bioperl- >>>>>> live/Bio/OntologyIO/obo.pm:209 STACK >>>>>>> Bio::OntologyIO::obo::next_ontology >>>>>>> /opt/share/local/users/haili/bioperl- >>>>>> live/Bio/OntologyIO/obo.pm:342 STACK >>>>>>> toplevel load_ontology.pl:604 >>>>>>> ------------------------------------- >>>>>>> >>>>>>> ----- Original Message ----- >>>>>>> From: Hilmar Lapp >>>>>>> Date: Tuesday, July 21, 2009 19:19 >>>>>>> Subject: Re: [BioSQL-l] Error when loading Gene Ontology to >>>>>>> biosql >>>>>>> To: Song Haili >>>>>>> Cc: florian.mittag at uni-tuebingen.de, biosql-l at lists.open-bio.org >>>>>>> >>>>>>>> Song: GO.defs is not in OBO format. Where did you find that you >>>>>>>> need >>>>>>>> it when you load .obo formatted files? You don't need the -- >>>>>>>> fmtargs >>>>>>>> argument for .obo files other than if you want to specify the >>>>>>>> ontology >>>>>>>> name. >>>>>>>> >>>>>>>> -hilmar >>>>>>>> >>>>>>>> On Jul 21, 2009, at 11:32 AM, Song Haili wrote: >>>>>>>>> Hello All, >>>>>>>>> The previous error was solved by the help of Florian. Florian, >>>>>>>> >>>>>>>> Thank >>>>>>>> >>>>>>>>> you very much. >>>>>>>>> But I got another error using the way Florian suggested. I >>>>>>>> >>>>>>>> thought >>>>>>>> >>>>>>>>> it was because parameter --fmtargs was not specified. So I >>>>>>>> >>>>>>>> tried to >>>>>>>> >>>>>>>>> include it with the value "-defs_file, GO.defs", but it didn't >>>>>>>> >>>>>>>> work. >>>>>>>> >>>>>>>>> I think maybe GO.defs is not the right file. Is it? But >>>>>>>> >>>>>>>> how or >>>>>>>> >>>>>>>>> where to get the right file if it is. Or any other ideas about >>>>>>>> >>>>>>>> how >>>>>>>> >>>>>>>>> to solve this error? Thank you very much in advance. >>>>>>>>> command: >>>>>>>>> perl load_ontology.pl --driver Pg --host pg-server --dbname >>>>>>>> >>>>>>>> sifter >>>>>>>> >>>>>>>>> --dbuser sifter --dbpass password --namespace "Gene >>>>>> Ontology" - >>>>>>>> >>>>>>>> - >>>>>>>> >>>>>>>>> format obo gene_ontology.obo --fmtargs "-defs_file, >>>>>> GO.defs" -- >>>>>>>>> >>>>>>>>> noobsolete >>>>>>>>> error: >>>>>>>>> ------------- EXCEPTION ------------- >>>>>>>>> MSG: OBO File Format Error - >>>>>>>>> Cannot find tag format-version and/ default-namespace . These >>>>>>>> >>>>>>>> are >>>>>>>> >>>>>>>>> required header. >>>>>>>>> >>>>>>>>> STACK Bio::OntologyIO::obo::_header >>>>>>>> >>>>>>>> /opt/share/local/users/haili/ >>>>>>>> >>>>>>>>> bioperl-live/Bio/OntologyIO/obo.pm:518 >>>>>>>>> STACK Bio::OntologyIO::obo::parse >>>>>>>> >>>>>>>> /opt/share/local/users/haili/ >>>>>>>> >>>>>>>>> bioperl-live/Bio/OntologyIO/obo.pm:209 >>>>>>>>> STACK Bio::OntologyIO::obo::next_ontology >>>>>>>> >>>>>>>> /opt/share/local/users/ >>>>>>>> >>>>>>>>> haili/bioperl-live/Bio/OntologyIO/obo.pm:342 >>>>>>>>> STACK toplevel load_ontology.pl:604 >>>>>>>>> ------------------------------------- >>>>>>>>> >>>>>>>>> ----- Original Message ----- >>>>>>>>> From: Florian Mittag >>>>>>>>> Date: Tuesday, July 21, 2009 14:41 >>>>>>>>> Subject: Re: [BioSQL-l] Error when loading Gene Ontology >>>>>> to biosql >>>>>>>>> To: biosql-l at lists.open-bio.org >>>>>>>>> >>>>>>>>>> Hi! >>>>>>>>>> >>>>>>>>>> AFAIK the goflat format is deprecated. Use the .obo files and >>>>>>>>>> format instead, >>>>>>>>>> that should work. >>>>>>>>>> >>>>>>>>>> perl load_ontology.pl --driver Pg --host pg-server -- >>>>>> dbname sifter >>>>>>>>>> --dbuser sifter --dbpass password --namespace "Gene >>>>>>>> >>>>>>>> Ontology" -- >>>>>>>> >>>>>>>>>> format obo >>>>>>>>>> >>>>>>>> >>>>>>>> gene_ontology.1_2.obo>> --noobsolete >>>>>>>> >>>>>>>>>> On Tuesday 21 July 2009 12:11, Song Haili wrote: >>>>>>>>>>> Dear all, >>>>>>>>>>> I am using perl-5.10.0, BioPerl-1.6.0, and bioperl-db >>>>>>>>>>> obtaind >>>>>>>>>> >>>>>>>>>> by using CPAN >>>>>>>>>> >>>>>>>>>>> a few days before. Until now, I can load taxonomy and >>>>>>>>>>> sequence >>>>>>>>>> >>>>>>>>>> data into >>>>>>>>>> >>>>>>>>>>> database successfully. However, I got the following error >>>>>>>>>> >>>>>>>>>> message when >>>>>>>>>> >>>>>>>>>>> trying to load Gene Ontology data into biosql database. Any >>>>>>>>>> >>>>>>>>>> help will be >>>>>>>>>> >>>>>>>>>>> appreciated. Jane >>>>>>>>>>> >>>>>>>>>>> command used: >>>>>>>>>>> perl load_ontology.pl --driver Pg --host pg-server --dbname >>>>>>>>>> >>>>>>>>>> sifter -dbuser >>>>>>>>>> >>>>>>>>>>> sifter --dbpass password ??namespace "Gene Ontology" -- >>>>>>>> >>>>>>>> format >>>>>>>> >>>>>>>>>>> goflat >>>>>>>>>>> component.ontology process.ontology function.ontology -- >>>>>> fmtargs> > >>> "-defs_file, GO.defs" --noobsolete >>>>>>>>>>> >>>>>>>>>>> error: >>>>>>>>>>> ------------- EXCEPTION ------------- >>>>>>>>>>> MSG: Could not open ??namespace: No such file or >>>>>>>>>>> directory >>>>>>>>>>> STACK Bio::Root::IO::_initialize_io >>>>>>>>>>> /opt/share/local/users/haili/bioperl- >>>>>> live/Bio/Root/IO.pm:323 STACK >>>>>>>>>>> Bio::OntologyIO::dagflat::parse >>>>>>>>>>> /opt/share/local/users/haili/bioperl- >>>>>>>>>> >>>>>>>>>> live/Bio/OntologyIO/dagflat.pm:277> STACK >>>>>>>>>> Bio::OntologyIO::dagflat::next_ontology> >>>>>>>>>> /opt/share/local/users/haili/bioperl- >>>>>>>> >>>>>>>> live/Bio/OntologyIO/dagflat.pm: >>>>>>>>>> 330 >>>>>>>>>> >>>>>>>>>>> STACK toplevel load_ontology.pl:604 >>>>>>>>>>> ------------------------------------- >>>>>>>>>> >>>>>>>>>> _______________________________________________ >>>>>>>>>> BioSQL-l mailing list >>>>>>>>>> BioSQL-l at lists.open-bio.org >>>>>>>>>> http://lists.open-bio.org/mailman/listinfo/biosql-l >>>>>>>>> >>>>>>>>> _______________________________________________ >>>>>>>>> BioSQL-l mailing list >>>>>>>>> BioSQL-l at lists.open-bio.org >>>>>>>>> http://lists.open-bio.org/mailman/listinfo/biosql-l >>>>>>>> >>>>>>>> -- >>>>>>>> =========================================================== >>>>>>>> >>>>>>>> : Hilmar Lapp -:- Durham, NC -:- hlapp >>>>>>>> >>>>>>>> at gmx dot net : >>>>>>>> =========================================================== >>>>> >>>>> _______________________________________________ >>>>> BioSQL-l mailing list >>>>> BioSQL-l at lists.open-bio.org >>>>> http://lists.open-bio.org/mailman/listinfo/biosql-l >>>> >>>> >>>> _______________________________________________ >>>> BioSQL-l mailing list >>>> BioSQL-l at lists.open-bio.org >>>> http://lists.open-bio.org/mailman/listinfo/biosql-l >>> >>> -- >>> =========================================================== >>> : Hilmar Lapp -:- Durham, NC -:- hlapp at gmx dot net : >>> =========================================================== >>> >>> >>> >> >> >> _______________________________________________ >> BioSQL-l mailing list >> BioSQL-l at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/biosql-l > > -- > =========================================================== > : Hilmar Lapp -:- Durham, NC -:- hlapp at gmx dot net : > =========================================================== > > > > > _______________________________________________ > BioSQL-l mailing list > BioSQL-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/biosql-l From pmr at ebi.ac.uk Mon Jul 27 04:55:43 2009 From: pmr at ebi.ac.uk (Peter Rice) Date: Mon, 27 Jul 2009 09:55:43 +0100 Subject: [BioSQL-l] Open-bio cross-project issues In-Reply-To: <320fb6e00907240632h53600e73s63590a8deb4e8ffe@mail.gmail.com> References: <320fb6e00907240632h53600e73s63590a8deb4e8ffe@mail.gmail.com> Message-ID: <4A6D6B8F.9060108@ebi.ac.uk> Peter C. wrote (to bioperl-l, biopython-l, emboss-dev): > Hi all, > > Peter Rice kindly said he will look into an OBF cross project mailing > list, but in the meantime this has been cross posted to the Biopython, > BioPerl, and EMBOSS development lists. There is a list already for this purpose - open-bio-l I think we will also need a cross-project wiki space on the OBF site. Is there something already used by other projects or should we set something up? I am cross-posting this to other OBF project lists to encourage developers interested in combining efforts to address common problems. This started with FASTQ short read formats, and open-bio-l (a low volume list) has also seen discussion of common test data sets. Please sign up to open-bio-l (if you are not there already) and post suggestions for cross-project issues there. The list subscription page is: http://lists.open-bio.org/mailman/listinfo/open-bio-l Please feel free to forward this to any other projects I may have missed (I picked the obvious addresses from the list.open-bio-org server) regards, Peter Rice From biopython at maubp.freeserve.co.uk Tue Jul 28 07:58:07 2009 From: biopython at maubp.freeserve.co.uk (Peter) Date: Tue, 28 Jul 2009 12:58:07 +0100 Subject: [BioSQL-l] SQLite support In-Reply-To: <320fb6e00907090529t61239952y1c86963f13c1db78@mail.gmail.com> References: <1f864af10812150224y540f1ba6y6b30168102885fcd@mail.gmail.com> <320fb6e00812150243w4b0dc223g40abcf684af1ccf5@mail.gmail.com> <320fb6e00907050324i6d64d3abreb4d0c256bf1bdc4@mail.gmail.com> <320fb6e00907090529t61239952y1c86963f13c1db78@mail.gmail.com> Message-ID: <320fb6e00907280458q56f74ec6iefa420ac1caab8da@mail.gmail.com> On Thu, Jul 9, 2009 at 1:29 PM, Peter wrote: > Hi Hilmar, > > I've filed a BioSQL enhancement bug 2870 for adding an SQLite > schema to BioSQL, and Brad has attached his proposed schema > (converted from that for MySQL) to the bug: > > http://bugzilla.open-bio.org/show_bug.cgi?id=2870 > > Could you take a look at this please? If you are happy with it, we'd like > to have it included in BioSQL v1.0.2 (even if Biopython is initially the > only Bio* project to support it). Have you had a chance to look at this yet Hilmar? Brad is keen to include BioSQL support for SQLite in the next release of Biopython (hopefully within the next week or two), but to do this I'd like your blessing, and for the proposed SQLite BioSQL schema to be added to the BioSQL SVN repository. Thanks, Peter From lacava at gmail.com Fri Jul 3 23:17:43 2009 From: lacava at gmail.com (John LaCava) Date: Fri, 3 Jul 2009 19:17:43 -0400 Subject: [BioSQL-l] Question regarding BioPerl / BioSQL - InterPro Optional IDs References: <48FCB39E-5CA8-4BE9-825D-49CFB14FDBB7@gmail.com> Message-ID: Hi all, Tried this on the BioPerl-l but seemed to make sense to try here as well. I am trying to use the BioPerl-db script: "load_seqdatabase.pl" to parse a SwissProt ".dat" file (Yeast.dat, this is the yeast proteome with annotations etc.). The particular entry I am interested is the InterPro optional ID, which is the domain name. I have put a short stub up which displays the 4 pieces of info I want to parse into my data base. That can be found here: http://github.com/johnraekwon/BioPerl---BioSQL---InterPro-Optional-IDs/tree/master You can see that near the bottom, we get the optional ID: $protein_ids->{interpro_domain} = $dblink->{optional_id}; I do not think the bioperl script load_seqdatabase.pl retrieves this information. At least, I cannot find it in the db built from parsing a test .dat file. I would like some help figuring out: 1) WHY doesn't it retrieve this information, since it seems to be parsing "all" annotations... 2) HOW might I edit the script to include this particular annotation of interest in the info it passes to my db (biosql) I am a bit out of my depth on this, and so, any help is appreciated. Cheers, John From stevey_mac2k2 at hotmail.com Sat Jul 4 10:17:13 2009 From: stevey_mac2k2 at hotmail.com (Steven McGowan) Date: Sat, 4 Jul 2009 10:17:13 +0000 Subject: [BioSQL-l] Having problems installing BioSQL on Mac 10.5 Message-ID: Hi,I'm trying to load a schema for biosql.I have created a database called "biosql" in MySQL, but i'm trying to load the biosql-schema/sql in MySQL with the command:>mysql -u root biosql < biosqldb-mysql.sqlThe "biosqldb-mysql.sql file is currently located on my mac in:/Users/stevey_mac2k2/Desktop/ExerciseTwo/biosql-1.0.1/sql My MySQL is currently saved in:usr/local/mysql-5.1.35-osx10.5-x86/binI have created a .profile for my mysql commands with the script:export PATH=/usr/local/mysql-5.1.35-osx10.5-x86/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/bin:/usr/X11/bin:$PATHi try the command:bash-3.2# mysql -u root biosql < biosqldb-mysql.sqlbash: mysql: command not foundAny help would be greatly appreciated.Thanks! _________________________________________________________________ Get the best of MSN on your mobile http://clk.atdmt.com/UKM/go/147991039/direct/01/ From holland at eaglegenomics.com Sat Jul 4 11:02:27 2009 From: holland at eaglegenomics.com (Richard Holland) Date: Sat, 04 Jul 2009 12:02:27 +0100 Subject: [BioSQL-l] Having problems installing BioSQL on Mac 10.5 In-Reply-To: References: Message-ID: <1246705347.5437.34.camel@buzzybee> First thing to check is that MySQL is correctly installed. Is there a 'mysql' program in the following location: /usr/local/mysql-5.1.35-osx10.5-x86/bin Secondly, type the following command in your shell: echo $PATH and see if it includes the path to your MySQL installation. In either case what you've got here is not a problem with BioSQL, but with the MySQL installation process. Your best place to ask for help in this respect would be the MySQL support pages or mailing lists. cheers, Richard -- Richard Holland, BSc MBCS Operations and Delivery Director, Eagle Genomics Ltd T: +44 (0)1223 654481 ext 3 | E: holland at eaglegenomics.com http://www.eaglegenomics.com/ From hlapp at gmx.net Sat Jul 4 11:57:18 2009 From: hlapp at gmx.net (Hilmar Lapp) Date: Sat, 4 Jul 2009 07:57:18 -0400 Subject: [BioSQL-l] Can I load ontologies into BioSQL? In-Reply-To: <59386.10.2.4.168.1245679938.squirrel@webmail.istge.it> References: <59386.10.2.4.168.1245679938.squirrel@webmail.istge.it> Message-ID: (FYI, changed to BioPerl list as this is a BioPerl issue with the old GO format. -hilmar) On Jun 22, 2009, at 10:12 AM, Achille Zappa wrote: > 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 > _______________________________________________ > BioSQL-l mailing list > BioSQL-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/biosql-l -- =========================================================== : Hilmar Lapp -:- Durham, NC -:- hlapp at gmx dot net : =========================================================== From hlapp at gmx.net Sat Jul 4 13:18:32 2009 From: hlapp at gmx.net (Hilmar Lapp) Date: Sat, 4 Jul 2009 09:18:32 -0400 Subject: [BioSQL-l] Question regarding BioPerl / BioSQL - InterPro Optional IDs In-Reply-To: References: <48FCB39E-5CA8-4BE9-825D-49CFB14FDBB7@gmail.com> Message-ID: <41958574-1C50-4A21-889F-8A02043190C8@gmx.net> The problem here is that Bioperl-db (the persistence mapper between BioSQL and BioPerl) loses the optional_id property of Bio::Annotation::DBLink objects. Moreover, the dbxref table in BioSQL doesn't actually provide for the opportunity to store two identifiers (or accessions) for one db_xref, so storing this bit of information is actually not as straightforward as one might wish b/c it would need to go into the dbxref_qualifier_value table, and I would not be surprised if the other Bio* projects with a mapping to BioSQL don't store or retrieve this either (though it'd be good to hear if anyone does). Here are a couple of ideas for how this issue might be addressed. - Write a Bio::Seq::BaseSeqProcessor-derived object that for every incoming sequence massages all Interpro links to either substitute the primary_id with the optional_id, or to add a second DBLink annotation with the optional_id of the original one as its primary_id. (pros: relatively easy, entirely under your control; cons: you either lose the primary_id now, or have two dbxref annotations for each of the original ones.) - Add a column to the dbxref table, and code to Bioperl-db, that store, de/serialize the extra ID. (pros: not losing or duplicating any data; cons: change is significant in terms of schema stability, requires new release, depends on implementation in Bioperl-db, necessitates update of all other Bio* language bindings) - De/serialize the optional_id as an entry in the dbxref_qualifier_value table. (pros: technically it's the Right Way as that's what the table was intended for; cons: implementing in Bioperl- db is more involved as we now need to transform an object property to a child object and back) So I'd say this is a bug in Bioperl-db in that the dbxref_qualifier_value table isn't utilized here. Would you mind filing it? In the meantime, if you just need something that works, you could try the first of the above ideas. -hilmar On Jul 3, 2009, at 7:17 PM, John LaCava wrote: > Hi all, > > Tried this on the BioPerl-l but seemed to make sense to try here as > well. > > I am trying to use the BioPerl-db script: > > "load_seqdatabase.pl" to parse a SwissProt ".dat" file (Yeast.dat, > this is the yeast proteome with annotations etc.). > > The particular entry I am interested is the InterPro optional ID, > which is the domain name. > > I have put a short stub up which displays the 4 pieces of info I > want to parse into my data base. > That can be found here: > > http://github.com/johnraekwon/BioPerl---BioSQL---InterPro-Optional-IDs/tree/master > > You can see that near the bottom, we get the optional ID: > $protein_ids->{interpro_domain} = $dblink->{optional_id}; > > I do not think the bioperl script load_seqdatabase.pl retrieves this > information. At least, I cannot find it in the db built from > parsing a test .dat file. > I would like some help figuring out: > 1) WHY doesn't it retrieve this information, since it seems to be > parsing "all" annotations... > 2) HOW might I edit the script to include this particular annotation > of interest in the info it passes to my db (biosql) > > I am a bit out of my depth on this, and so, any help is appreciated. > > Cheers, > John > > > _______________________________________________ > BioSQL-l mailing list > BioSQL-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/biosql-l -- =========================================================== : Hilmar Lapp -:- Durham, NC -:- hlapp at gmx dot net : =========================================================== From hlapp at gmx.net Sat Jul 4 13:22:19 2009 From: hlapp at gmx.net (Hilmar Lapp) Date: Sat, 4 Jul 2009 09:22:19 -0400 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: Hi Florian, sorry this fell through the cracks, too much traveling. VARCHAR BINARY in MySQL means that the column is a VARCHAR type but values (and searches against them) are treated case-sensitive. Since treating VARCHAR values case sensitive is standard in SQL everywhere else and presumably also in DB2, you should map it to a simple VARCHAR type. Where did you find that MySQL's VARCHAR BINARY needs to be VARBINARY in DB2? -hilmar On Jun 4, 2009, at 9:52 AM, Florian Mittag wrote: > 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 > _______________________________________________ > BioSQL-l mailing list > BioSQL-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/biosql-l -- =========================================================== : Hilmar Lapp -:- Durham, NC -:- hlapp at gmx dot net : =========================================================== From biopython at maubp.freeserve.co.uk Sun Jul 5 10:24:14 2009 From: biopython at maubp.freeserve.co.uk (Peter) Date: Sun, 5 Jul 2009 11:24:14 +0100 Subject: [BioSQL-l] SQLite support In-Reply-To: <320fb6e00812150243w4b0dc223g40abcf684af1ccf5@mail.gmail.com> References: <1f864af10812150224y540f1ba6y6b30168102885fcd@mail.gmail.com> <320fb6e00812150243w4b0dc223g40abcf684af1ccf5@mail.gmail.com> Message-ID: <320fb6e00907050324i6d64d3abreb4d0c256bf1bdc4@mail.gmail.com> On Mon, Dec 15, 2008 at 11:43 AM, Peter wrote: > On Mon, Dec 15, 2008, vanaquisl vanaquisl wrote: >> >> Hi folks, >> >> I am a brand new BioSQL user and I'd like to know if there will be a SQLite >> support in the near future? > > As far as I know, BioSQL does not currently include a schema for SQLite. This was one of the things Brad Chapman and I discussed with Hilmar Lapp last week at BOSC/ISMB 2009. I've just filed BioSQL enhancement Bug 2870 on this: http://bugzilla.open-bio.org/show_bug.cgi?id=2870 >> I am about to use SQLite for a standalone lightweight Biopython application >> and it would be very helpful if I could use BioSQL directly. > > Biopython can talk to a BioSQL database run on MySQL (using MySQLdb), > PostgreSQL (using either Psycopg or Psycopg2). In theory it could be > extended to use any supported BioSQL database (provided there are > python bindings for the database software, in the case of SQLite using > pysqlite would probably fine). We have a proof of principle implementation of the Biopython BioSQL bindings working with BioSQL on SQLite, see enhancement Bug 2866: http://bugzilla.open-bio.org/show_bug.cgi?id=2866 Peter From lacava at gmail.com Sun Jul 5 20:30:52 2009 From: lacava at gmail.com (John LaCava) Date: Sun, 5 Jul 2009 16:30:52 -0400 Subject: [BioSQL-l] Syntax for load_interpro.pl? Message-ID: Greetings, I am attempting to use this script, but I don't seem to be able to determine the appropriate syntax. Documentation on this script seems minimal. Moreover, I am not yet terribly experienced with these endeavors. Could someone possibly provide me with an example syntax? e.g. > load_interpro.pl ... then what? I must specify -db -file -version ? I tried a couple of ways, but I get the similar errors each time: e.g. /usr/local/bin/bp_load_interpro.pl: line 29: syntax error near unexpected token `$file,' /usr/local/bin/bp_load_interpro.pl: line 29: `my ($file, $version);' Also, from reading the comments, it appears this is supposed to be made obsolete or superseded by the script load_ontologies.pl. Why is this? Sorry to bother, and thanks in advance. John From hlapp at gmx.net Sun Jul 5 21:58:27 2009 From: hlapp at gmx.net (Hilmar Lapp) Date: Sun, 5 Jul 2009 17:58:27 -0400 Subject: [BioSQL-l] Syntax for load_interpro.pl? In-Reply-To: References: Message-ID: <1F926EFE-0B0B-4FAC-B12F-4E0DE11C485A@gmx.net> (Changed to and responded on Bioperl list as it is part of bioperl-db) On Jul 5, 2009, at 4:30 PM, John LaCava wrote: > Greetings, > > I am attempting to use this script, but I don't seem to be able to > determine the appropriate syntax. > Documentation on this script seems minimal. Moreover, I am not yet > terribly experienced with > these endeavors. > > Could someone possibly provide me with an example syntax? > > e.g. > load_interpro.pl ... > > then what? > > I must specify -db -file -version ? > > I tried a couple of ways, but I get the similar errors each time: > > e.g. > /usr/local/bin/bp_load_interpro.pl: line 29: syntax error near > unexpected token `$file,' > /usr/local/bin/bp_load_interpro.pl: line 29: `my ($file, $version);' > > Also, from reading the comments, it appears this is supposed to be > made obsolete or superseded by > the script load_ontologies.pl. Why is this? > > Sorry to bother, and thanks in advance. > > John > _______________________________________________ > BioSQL-l mailing list > BioSQL-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/biosql-l -- =========================================================== : Hilmar Lapp -:- Durham, NC -:- hlapp at gmx dot net : =========================================================== From sanjay.harke at gmail.com Mon Jul 6 05:01:34 2009 From: sanjay.harke at gmail.com (Sanjay Harke) Date: Mon, 6 Jul 2009 10:31:34 +0530 Subject: [BioSQL-l] BioSQL- connectivity Message-ID: <31bb4380907052201v6e16ac8dn449064bb4606292f@mail.gmail.com> Dear sir, Kindly guide me about BioSQL database connectivity. Here i installed BioSql on my PC. For database connectivity i am facing about it. sanjay From roy.chaudhuri at gmail.com Mon Jul 6 10:05:36 2009 From: roy.chaudhuri at gmail.com (Roy Chaudhuri) Date: Mon, 06 Jul 2009 11:05:36 +0100 Subject: [BioSQL-l] BioSQL- connectivity In-Reply-To: <31bb4380907052201v6e16ac8dn449064bb4606292f@mail.gmail.com> References: <31bb4380907052201v6e16ac8dn449064bb4606292f@mail.gmail.com> Message-ID: <4A51CC70.2040003@gmail.com> Hi Sanjay, You have sent several messages like this to the BioSQL and BioPerl mailing lists, and not received many replies. The reason for this is not that we do not want to help, just that you do not include enough detail about what your problem is. What have you tried? What error messages do you get? Which operating system and database software are you using? Have you read all the relevant documentation? Have you tried searching the internet and specifically the mailing list archives for problems similar to the one you are facing? You are more likely to get a response on the mailing list if you clearly define exactly what your problem is and the steps you have tried to overcome it. Roy. Sanjay Harke wrote: > Dear sir, > > Kindly guide me about BioSQL database connectivity. > Here i installed BioSql on my PC. > For database connectivity i am facing about it. > > sanjay > _______________________________________________ > BioSQL-l mailing list > BioSQL-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/biosql-l From roy.chaudhuri at gmail.com Mon Jul 6 11:39:33 2009 From: roy.chaudhuri at gmail.com (Roy Chaudhuri) Date: Mon, 06 Jul 2009 12:39:33 +0100 Subject: [BioSQL-l] BioSQL- connectivity In-Reply-To: <31bb4380907060351u4fb0041dla533cdf1e4f35ad8@mail.gmail.com> References: <31bb4380907052201v6e16ac8dn449064bb4606292f@mail.gmail.com> <4A51CC70.2040003@gmail.com> <31bb4380907060351u4fb0041dla533cdf1e4f35ad8@mail.gmail.com> Message-ID: <4A51E275.3060809@gmail.com> Hi Sanjay, Please keep replies on the mailing list (reply to all), that way others can also respond. I don't think there is a tutorial for BioSQL using BioPerl. There are some links to useful documentation on the BioSQL wiki: http://biosql.org/wiki/Main_Page The BioSQL INSTALL file provides instructions for getting your database set up and loading sequences into it: http://code.open-bio.org/svnweb/index.cgi/biosql/view/biosql-schema/trunk/INSTALL There are some examples of retrieving a sequence from a BioSQL database using BioPerl in Hilmar's Persistent BioPerl presentation: http://precedings.nature.com/documents/1233/version/1 Try loading your BioSQL database with some sequences, then retrieving them using code based on the examples in the presentation. If you run into problems e-mail the mailing list with a full description of what you were trying to do (including the code you were using, and any error messages that were reported), and I'm sure someone will be able to help. Roy. Sanjay Harke wrote: > Dear sir, > > Do you have any basic tutorial on Biosql-Bioperl ? > If available kindly send me it. > > sanjay From florian.mittag at uni-tuebingen.de Mon Jul 6 12:34:49 2009 From: florian.mittag at uni-tuebingen.de (Florian Mittag) Date: Mon, 6 Jul 2009 14:34:49 +0200 Subject: [BioSQL-l] Question about VARCHAR BINARY In-Reply-To: References: <200906041552.59221.florian.mittag@uni-tuebingen.de> Message-ID: <200907061434.49402.florian.mittag@uni-tuebingen.de> Hi Hilmar, thanks for the answer, we sortof solved the problem differently, because other databases (like PostgreSQL) do not specifiy those columns as VARBINARY, so we simply took those scheme as the foundation for our DB2 scheme. On Saturday 04 July 2009 15:22, Hilmar Lapp wrote: > Hi Florian, > > sorry this fell through the cracks, too much traveling. VARCHAR BINARY > in MySQL means that the column is a VARCHAR type but values (and > searches against them) are treated case-sensitive. Oh, I didn't know that. I thought it was about handling non-displayable characters. > Since treating VARCHAR values case sensitive is standard in SQL > everywhere else and presumably also in DB2, you should map it to a > simple VARCHAR type. > > Where did you find that MySQL's VARCHAR BINARY needs to be VARBINARY > in DB2? Chapter 11: MySQL converter ftp://ftp.software.ibm.com/software/data/db2/migration/mtk/mtk_2050.pdf Florian > On Jun 4, 2009, at 9:52 AM, Florian Mittag wrote: > > 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 > > _______________________________________________ > > BioSQL-l mailing list > > BioSQL-l at lists.open-bio.org > > http://lists.open-bio.org/mailman/listinfo/biosql-l From biopython at maubp.freeserve.co.uk Mon Jul 6 16:19:54 2009 From: biopython at maubp.freeserve.co.uk (Peter) Date: Mon, 6 Jul 2009 17:19:54 +0100 Subject: [BioSQL-l] [Bioperl-l] DB2 driver for BioPerl In-Reply-To: <200907061808.18651.florian.mittag@uni-tuebingen.de> References: <200907021128.21239.florian.mittag@uni-tuebingen.de> <5EC3CB83-22AD-4C79-9F6C-047ED58B7962@gmx.net> <200907061808.18651.florian.mittag@uni-tuebingen.de> Message-ID: <320fb6e00907060919w1ce69284r30fede63ec05adbb@mail.gmail.com> On BioPerl-l, July 2009, Florian Mittag wrote: > ... > Okay, I'll do that, but that will take some time and I'll probably turn to > this mailings for further assistance with more specific questions. > ... > I will keep you updated on the Perl issues and hope to have some useful > results by the end of the week. And I hope you excuse me for posting things > here that are hardly related to BioPerl, but the some problems are a complex > entanglement of issues with BioSQL, BioPerl and BioJava, so it's hard to > decide where to post it ;-) You may want to cross post some things (e.g. the hibernate issue to BioSQL and BioJava lists). I've CC'd this reply to BioSQL-l for example. I think some guidance from Hilmar on this etiquette would help ;) I would not expect BioJava people to follow BioPerl-l for example. (Although here I am as a Biopython person keeping an eye on BioPerl-l sometimes). I assume (hope?) that people from all the Bio* projects with BioSQL bindings will be following the BioSQL-l mailing list - so for anything clearly cross project like the schemas themselves, at very least please CC the BioSQL-l mailing list. Peter (Biopython) From biopython at maubp.freeserve.co.uk Thu Jul 9 12:29:14 2009 From: biopython at maubp.freeserve.co.uk (Peter) Date: Thu, 9 Jul 2009 13:29:14 +0100 Subject: [BioSQL-l] SQLite support In-Reply-To: <320fb6e00907050324i6d64d3abreb4d0c256bf1bdc4@mail.gmail.com> References: <1f864af10812150224y540f1ba6y6b30168102885fcd@mail.gmail.com> <320fb6e00812150243w4b0dc223g40abcf684af1ccf5@mail.gmail.com> <320fb6e00907050324i6d64d3abreb4d0c256bf1bdc4@mail.gmail.com> Message-ID: <320fb6e00907090529t61239952y1c86963f13c1db78@mail.gmail.com> On Sun, Jul 5, 2009 at 11:24 AM, Peter wrote: > On Mon, Dec 15, 2008 at 11:43 AM, Peter wrote: >> On Mon, Dec 15, 2008, vanaquisl vanaquisl wrote: >>> >>> Hi folks, >>> >>> I am a brand new BioSQL user and I'd like to know if there will be a SQLite >>> support in the near future? >> >> As far as I know, BioSQL does not currently include a schema for SQLite. > > This was one of the things Brad Chapman and I discussed with Hilmar Lapp > last week at BOSC/ISMB 2009. I've just filed BioSQL enhancement Bug 2870 > on this: http://bugzilla.open-bio.org/show_bug.cgi?id=2870 > >>> I am about to use SQLite for a standalone lightweight Biopython application >>> and it would be very helpful if I could use BioSQL directly. >> >> Biopython can talk to a BioSQL database run on MySQL (using MySQLdb), >> PostgreSQL (using either Psycopg or Psycopg2). ?In theory it could be >> extended to use any supported BioSQL database (provided there are >> python bindings for the database software, in the case of SQLite using >> pysqlite would probably fine). > > We have a proof of principle implementation of the Biopython BioSQL > bindings working with BioSQL on SQLite, see enhancement Bug 2866: > http://bugzilla.open-bio.org/show_bug.cgi?id=2866 Hi Hilmar, I've filed a BioSQL enhancement bug 2870 for adding an SQLite schema to BioSQL, and Brad has attached his proposed schema (converted from that for MySQL) to the bug: http://bugzilla.open-bio.org/show_bug.cgi?id=2870 Could you take a look at this please? If you are happy with it, we'd like to have it included in BioSQL v1.0.2 (even if Biopython is initially the only Bio* project to support it). Thanks, Peter From florian.mittag at uni-tuebingen.de Thu Jul 9 15:16:12 2009 From: florian.mittag at uni-tuebingen.de (Florian Mittag) Date: Thu, 9 Jul 2009 17:16:12 +0200 Subject: [BioSQL-l] Problems in DB2 with VARCHAR, TEXT and CLOB using BioJava Message-ID: <200907091716.13639.florian.mittag@uni-tuebingen.de> Hi all! I'm posting this to both the BioSQL and the BioJava-dev mailinglist because the problem resides in both domains, I hope this is okay. We're working on getting BioJava to run with a DB2 Express-C backend for various reasons. We've encountered several problems during this task, but this one seems to have no real solution. When adapting the BioSQL schema to DB2, the official IBM conversion guide tells us to use the data type CLOB where MySQL uses TEXT. (Chapter 11 in ftp://ftp.software.ibm.com/software/data/db2/migration/mtk/mtk_2050.pdf) So far, no problem. But when we tried reading some genebank files with BioJava, the DB2 driver threw an exception: SQL0401N The data types of the operands for the operation "=" are not compatible. SQLSTATE=42818 SQLCODE=-401 Explanation: The class org.biojavax.bio.db.biosql.BioSQLRichObjectBuilder defines some Hibernate queries, of which one has the conditions: "from DocRef as cr where cr.authors = ? and cr.location = ? and cr.title = ?" All three columns "authors", "location", and "title" are of type TEXT in MySQL and of type CLOB in DB2, so comparing them with "=" leads to the above error message. The way I see it, there are only two possible solutions to this problem: 1) Change the query to "from DocRef as cr where cr.authors LIKE '?' and cr.location LIKE '?' and cr.title LIKE '?'" 2) Change the data type to something comparable with "=", like VARCHAR. Solution 1 is no real solution to me, because comparing values with "LIKE" usually is slow and it seems a bit odd to change a query that works with other databases just for DB2. But taking a closer look, solution 2 has some problems, too: Although VARCHARs in DB2 can have a length of theoretically 32767, in reality they are limited by the page size of the database, which can be 32K at maximum. Since this particular table "reference" has three columns of this type, the sum of their lengths must not exceed 32767, so they could only be something like VARCHAR(10000). I have never encountered cases in which values come even close to the length of 10000, but you can never be sure. And that is why I post here. For me, the way to go is pretty clear, but we intend to be as compatible as possible with the original BioSQL. Maybe you could give me some input on how to solve this problem with as few casualties as possible ;-) Thanks, Florian From hlapp at gmx.net Sat Jul 11 11:47:34 2009 From: hlapp at gmx.net (Hilmar Lapp) Date: Sat, 11 Jul 2009 07:47:34 -0400 Subject: [BioSQL-l] Problems in DB2 with VARCHAR, TEXT and CLOB using BioJava In-Reply-To: <200907091716.13639.florian.mittag@uni-tuebingen.de> References: <200907091716.13639.florian.mittag@uni-tuebingen.de> Message-ID: <5614AEDA-3406-4844-8690-7653A2C4297C@gmx.net> Hi Florian: On Jul 9, 2009, at 11:16 AM, Florian Mittag wrote: > [...] > 2) Change the data type to something comparable with "=", like > VARCHAR. That's the way to go. The reason they are not VARCHAR in MySQL is because it is limited to 256 characters there. > [...] > Although VARCHARs in DB2 can have a length of theoretically 32767, > in reality > they are limited by the page size of the database, which can be 32K at > maximum. Since this particular table "reference" has three columns > of this > type, the sum of their lengths must not exceed 32767, so they could > only be > something like VARCHAR(10000). That sounds great though. You may have noticed that the columns are all of type VARCHAR in the Oracle version of the schema with the following widths: Title VARCHAR2(1000) Authors VARCHAR2(4000) Location VARCHAR2(512) That has always served me well. Feel free to use larger widths though if you think you need them. -hilmar -- =========================================================== : Hilmar Lapp -:- Durham, NC -:- hlapp at gmx dot net : =========================================================== From hlapp at gmx.net Thu Jul 16 10:44:29 2009 From: hlapp at gmx.net (Hilmar Lapp) Date: Thu, 16 Jul 2009 11:44:29 +0100 Subject: [BioSQL-l] adding PostGreSQL support to PhyloDB code In-Reply-To: References: Message-ID: <2F6256EB-E12E-414A-9B62-67FB678D42AA@gmx.net> Hi Dave, funny you should ask. I'm at the Computational Phyloinformatics course which is being held this year at the Gulbenkian in Portugal. We're in the SQL section right now and my plan for the final course project, starting Sat night, is to have the students collaboratively write that. Since I haven't tried this before, we'll see whether that ends in disaster or a usable product :-) -hilmar On Jul 16, 2009, at 10:32 AM, Kidd, David M wrote: > > Dear Hilmar and James, > > We are looking into linking networks stored in PhyloDB to spatial > information in the PostGIS extension. > > I have installed the PhyoDB schema on a PostGreSQL database and > would like to amend phyloimport.pl and other code at http://code.open-bio.org/svnweb/index.cgi/biosql/view/biosql-schema/trunk/ > to work with PostgreSQL. I see in the header of phyimport.pl that > PGSQL support is listed as one of a number of things to do along > with a couple of other important features. > > I thought I would inform you of our interest and enquire if you, or > anyone else you know of has made any progress with these additions > before I start hacking into the code. > > Best wishes > > - Dave > > David M. Kidd > > Research Associate > Center for Population Biology > Silwood Park Campus > Imperial College London > 0207 594 2211 > > -- =========================================================== : Hilmar Lapp -:- Durham, NC -:- hlapp at gmx dot net : =========================================================== From hlapp at gmx.net Thu Jul 16 11:04:24 2009 From: hlapp at gmx.net (Hilmar Lapp) Date: Thu, 16 Jul 2009 12:04:24 +0100 Subject: [BioSQL-l] adding PostGreSQL support to PhyloDB code In-Reply-To: References: <2F6256EB-E12E-414A-9B62-67FB678D42AA@gmx.net> Message-ID: <455710F3-4B0B-485D-8F7C-812199178585@gmx.net> On Jul 16, 2009, at 11:52 AM, Kidd, David M wrote: > it looks like we need an alternative connection string format along > the lines of "DSN=PostgreSQL30;UID=postgres;SERVER=192.168.1.102; > Port=5432;"; as well. Did you experience a problem with that? Is some part of the code balking at this? If yes, that's presumably a bug. Could you submit it to bugzilla? (http://bugzilla.open-bio.org/ ) > [...] Is there going to any attempt to fix the names issue as well? Which names issue? -hilmar -- =========================================================== : Hilmar Lapp -:- Durham, NC -:- hlapp at gmx dot net : =========================================================== From florian.mittag at uni-tuebingen.de Fri Jul 10 12:32:42 2009 From: florian.mittag at uni-tuebingen.de (Florian Mittag) Date: Fri, 10 Jul 2009 14:32:42 +0200 Subject: [BioSQL-l] load_ncbi_taxonomy.pl for DB2 Message-ID: <200907101432.42657.florian.mittag@uni-tuebingen.de> Hi everyone! I just completed and tested the changes we've made on the load_ncbi_taxonomy.pl script from BioSQL 1.0.1. Basically, only 3 changes were necessary, but some things have to be considered when running the script: 1) Although DB2 v9.7 supports TRUNCATE TABLE, when I specify the --allow_truncate option the script gave me the error SQL0428N "The SQL statement is only allowed as the first statement in a unit of work." (https://publib.boulder.ibm.com/infocenter/db2luw/v9r7/index.jsp?topic=/com.ibm.db2.luw.messages.sql.doc/doc/msql00428n.html) My solution is to just not set allow_truncate, so the script will use a DELETE command. 2) Specifying hostname and port will lead to an error saying that the database wasn't found. Searching the web I found information suggesting that you have to add a remote database to the catalog (or something) on the server and the client and then you are able to point to the database through its name. My solution is to run the script on the machine where the DB2 instance is running and everything is fine. I've run into some other problems before, but those were mostly caused by me forgetting to set the right environment variables, so that shouldn't be a problem for someone who actually knows something about DB2 ;-) I hope this helps. As for the database schema for DB2, we have scripts to create the database with all its tables and constraints, but as you might see from my other posts here, we're not completely done and have to do more tests. Now, I'm awaiting your feedback ;-) Regards, Florian -------------- next part -------------- A non-text attachment was scrubbed... Name: load_ncbi_taxonomy.diff Type: text/x-diff Size: 1193 bytes Desc: not available URL: From jamesestill at gmail.com Thu Jul 16 17:02:40 2009 From: jamesestill at gmail.com (James Estill) Date: Thu, 16 Jul 2009 13:02:40 -0400 Subject: [BioSQL-l] adding PostGreSQL support to PhyloDB code In-Reply-To: <2F6256EB-E12E-414A-9B62-67FB678D42AA@gmx.net> References: <2F6256EB-E12E-414A-9B62-67FB678D42AA@gmx.net> Message-ID: I have not been working on getting these to work with PostgreSQL. That would be awesome to get that working. I initially just did the MySQL version so that there would be a somewhat usable product by the end of the GSOC and I am still using MySQL for my research. I think that there will also need to be some updates to bring the code up to date with the new PhyloDB schema but I have not looked at this in the last year. On Thu, Jul 16, 2009 at 6:44 AM, Hilmar Lapp wrote: > Hi Dave, > funny you should ask. I'm at the Computational Phyloinformatics course > which is being held this year at the Gulbenkian in Portugal. We're in the > SQL section right now and my plan for the final course project, starting Sat > night, is to have the students collaboratively write that. Since I haven't > tried this before, we'll see whether that ends in disaster or a usable > product :-) > > -hilmar > > On Jul 16, 2009, at 10:32 AM, Kidd, David M wrote: > > > Dear Hilmar and James, > > We are looking into linking networks stored in PhyloDB to spatial > information in the PostGIS extension. > > I have installed the PhyoDB schema on a PostGreSQL database and would like > to amend phyloimport.pl and other code at > http://code.open-bio.org/svnweb/index.cgi/biosql/view/biosql-schema/trunk/ to > work with PostgreSQL. I see in the header of phyimport.pl that PGSQL > support is listed as one of a number of things to do along with a couple of > other important features. > > I thought I would inform you of our interest and enquire if you, or anyone > else you know of has made any progress with these additions before I start > hacking into the code. > > Best wishes > > - Dave > > > David M. Kidd > > Research Associate > Center for Population Biology > Silwood Park Campus > Imperial College London > 0207 594 2211 > > > > -- > =========================================================== > : Hilmar Lapp -:- Durham, NC -:- hlapp at gmx dot net : > =========================================================== > > > > -- ----------------------------------------- James C. Estill JamesEstill at gmail.com http://jestill.myweb.uga.edu ----------------------------------------- From haili at mpiz-koeln.mpg.de Tue Jul 21 10:11:30 2009 From: haili at mpiz-koeln.mpg.de (Song Haili) Date: Tue, 21 Jul 2009 12:11:30 +0200 Subject: [BioSQL-l] Error when loading Gene Ontology to biosql Message-ID: Dear all, I am using perl-5.10.0, BioPerl-1.6.0, and bioperl-db obtaind by using CPAN a few days before. Until now, I can load taxonomy and sequence data into database successfully. However, I got the following error message when trying to load Gene Ontology data into biosql database. Any help will be appreciated. Jane command used: perl load_ontology.pl --driver Pg --host pg-server --dbname sifter -dbuser sifter --dbpass password ??namespace "Gene Ontology" --format goflat component.ontology process.ontology function.ontology --fmtargs "-defs_file, GO.defs" --noobsolete error: ------------- EXCEPTION ------------- MSG: Could not open ??namespace: No such file or directory STACK Bio::Root::IO::_initialize_io /opt/share/local/users/haili/bioperl-live/Bio/Root/IO.pm:323 STACK Bio::OntologyIO::dagflat::parse /opt/share/local/users/haili/bioperl-live/Bio/OntologyIO/dagflat.pm:277 STACK Bio::OntologyIO::dagflat::next_ontology /opt/share/local/users/haili/bioperl-live/Bio/OntologyIO/dagflat.pm:330 STACK toplevel load_ontology.pl:604 ------------------------------------- From florian.mittag at uni-tuebingen.de Tue Jul 21 11:54:24 2009 From: florian.mittag at uni-tuebingen.de (Florian Mittag) Date: Tue, 21 Jul 2009 13:54:24 +0200 Subject: [BioSQL-l] Error when loading Gene Ontology to biosql In-Reply-To: References: Message-ID: <200907211354.25034.florian.mittag@uni-tuebingen.de> Hi! AFAIK the goflat format is deprecated. Use the .obo files and format instead, that should work. perl load_ontology.pl --driver Pg --host pg-server --dbname sifter --dbuser sifter --dbpass password --namespace "Gene Ontology" --format obo gene_ontology.1_2.obo --noobsolete On Tuesday 21 July 2009 12:11, Song Haili wrote: > Dear all, > I am using perl-5.10.0, BioPerl-1.6.0, and bioperl-db obtaind by using CPAN > a few days before. Until now, I can load taxonomy and sequence data into > database successfully. However, I got the following error message when > trying to load Gene Ontology data into biosql database. Any help will be > appreciated. Jane > > command used: > perl load_ontology.pl --driver Pg --host pg-server --dbname sifter -dbuser > sifter --dbpass password ??namespace "Gene Ontology" --format goflat > component.ontology process.ontology function.ontology --fmtargs > "-defs_file, GO.defs" --noobsolete > > error: > ------------- EXCEPTION ------------- > MSG: Could not open ??namespace: No such file or directory > STACK Bio::Root::IO::_initialize_io > /opt/share/local/users/haili/bioperl-live/Bio/Root/IO.pm:323 STACK > Bio::OntologyIO::dagflat::parse > /opt/share/local/users/haili/bioperl-live/Bio/OntologyIO/dagflat.pm:277 > STACK Bio::OntologyIO::dagflat::next_ontology > /opt/share/local/users/haili/bioperl-live/Bio/OntologyIO/dagflat.pm:330 > STACK toplevel load_ontology.pl:604 > ------------------------------------- From haili at mpiz-koeln.mpg.de Tue Jul 21 15:32:19 2009 From: haili at mpiz-koeln.mpg.de (Song Haili) Date: Tue, 21 Jul 2009 17:32:19 +0200 Subject: [BioSQL-l] Error when loading Gene Ontology to biosql In-Reply-To: <200907211354.25034.florian.mittag@uni-tuebingen.de> References: <200907211354.25034.florian.mittag@uni-tuebingen.de> Message-ID: Hello All, The previous error was solved by the help of Florian. Florian, Thank you very much. But I got another error using the way Florian suggested. I thought it was because parameter --fmtargs was not specified. So I tried to include it with the value "-defs_file, GO.defs", but it didn't work. I think maybe GO.defs is not the right file. Is it?? But how or where to get the right file if it is. Or any other ideas about how to solve this error? Thank you very much in advance. command: perl load_ontology.pl --driver Pg --host pg-server --dbname sifter? --dbuser sifter --dbpass password --namespace "Gene Ontology" --format obo gene_ontology.obo --fmtargs "-defs_file, GO.defs" --noobsolete error: ------------- EXCEPTION ------------- MSG: OBO File Format Error - Cannot find tag format-version and/ default-namespace . These are required header. STACK Bio::OntologyIO::obo::_header /opt/share/local/users/haili/bioperl-live/Bio/OntologyIO/obo.pm:518 STACK Bio::OntologyIO::obo::parse /opt/share/local/users/haili/bioperl-live/Bio/OntologyIO/obo.pm:209 STACK Bio::OntologyIO::obo::next_ontology /opt/share/local/users/haili/bioperl-live/Bio/OntologyIO/obo.pm:342 STACK toplevel load_ontology.pl:604 ------------------------------------- ----- Original Message ----- From: Florian Mittag Date: Tuesday, July 21, 2009 14:41 Subject: Re: [BioSQL-l] Error when loading Gene Ontology to biosql To: biosql-l at lists.open-bio.org > Hi! > > AFAIK the goflat format is deprecated. Use the .obo files and > format instead, > that should work. > > perl load_ontology.pl --driver Pg --host pg-server --dbname sifter > --dbuser sifter --dbpass password --namespace "Gene Ontology" -- > format obo > ??????? gene_ontology.1_2.obo > --noobsolete > > > On Tuesday 21 July 2009 12:11, Song Haili wrote: > > Dear all, > > I am using perl-5.10.0, BioPerl-1.6.0, and bioperl-db obtaind > by using CPAN > > a few days before. Until now, I can load taxonomy and sequence > data into > > database successfully. However, I got the following error > message when > > trying to load Gene Ontology data into biosql database. Any > help will be > > appreciated. Jane > > > > command used: > > perl load_ontology.pl --driver Pg --host pg-server --dbname > sifter -dbuser > > sifter --dbpass password ??namespace "Gene Ontology" --format goflat > > component.ontology process.ontology function.ontology --fmtargs > > "-defs_file, GO.defs" --noobsolete > > > > error: > > ------------- EXCEPTION ------------- > > MSG: Could not open ??namespace: No such file or directory > > STACK Bio::Root::IO::_initialize_io > > /opt/share/local/users/haili/bioperl-live/Bio/Root/IO.pm:323 STACK > > Bio::OntologyIO::dagflat::parse > > /opt/share/local/users/haili/bioperl- > live/Bio/OntologyIO/dagflat.pm:277> STACK > Bio::OntologyIO::dagflat::next_ontology> > /opt/share/local/users/haili/bioperl-live/Bio/OntologyIO/dagflat.pm:330 > > STACK toplevel load_ontology.pl:604 > > ------------------------------------- > > _______________________________________________ > BioSQL-l mailing list > BioSQL-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/biosql-l From hlapp at gmx.net Tue Jul 21 17:19:19 2009 From: hlapp at gmx.net (Hilmar Lapp) Date: Tue, 21 Jul 2009 13:19:19 -0400 Subject: [BioSQL-l] Error when loading Gene Ontology to biosql In-Reply-To: References: <200907211354.25034.florian.mittag@uni-tuebingen.de> Message-ID: Song: GO.defs is not in OBO format. Where did you find that you need it when you load .obo formatted files? You don't need the --fmtargs argument for .obo files other than if you want to specify the ontology name. -hilmar On Jul 21, 2009, at 11:32 AM, Song Haili wrote: > > Hello All, > The previous error was solved by the help of Florian. Florian, Thank > you very much. > But I got another error using the way Florian suggested. I thought > it was because parameter --fmtargs was not specified. So I tried to > include it with the value "-defs_file, GO.defs", but it didn't work. > I think maybe GO.defs is not the right file. Is it? But how or > where to get the right file if it is. Or any other ideas about how > to solve this error? Thank you very much in advance. > command: > perl load_ontology.pl --driver Pg --host pg-server --dbname sifter > --dbuser sifter --dbpass password --namespace "Gene Ontology" -- > format obo gene_ontology.obo --fmtargs "-defs_file, GO.defs" -- > noobsolete > error: > ------------- EXCEPTION ------------- > MSG: OBO File Format Error - > Cannot find tag format-version and/ default-namespace . These are > required header. > > STACK Bio::OntologyIO::obo::_header /opt/share/local/users/haili/ > bioperl-live/Bio/OntologyIO/obo.pm:518 > STACK Bio::OntologyIO::obo::parse /opt/share/local/users/haili/ > bioperl-live/Bio/OntologyIO/obo.pm:209 > STACK Bio::OntologyIO::obo::next_ontology /opt/share/local/users/ > haili/bioperl-live/Bio/OntologyIO/obo.pm:342 > STACK toplevel load_ontology.pl:604 > ------------------------------------- > > ----- Original Message ----- > From: Florian Mittag > Date: Tuesday, July 21, 2009 14:41 > Subject: Re: [BioSQL-l] Error when loading Gene Ontology to biosql > To: biosql-l at lists.open-bio.org > >> Hi! >> >> AFAIK the goflat format is deprecated. Use the .obo files and >> format instead, >> that should work. >> >> perl load_ontology.pl --driver Pg --host pg-server --dbname sifter >> --dbuser sifter --dbpass password --namespace "Gene Ontology" -- >> format obo >> gene_ontology.1_2.obo >> --noobsolete >> >> >> On Tuesday 21 July 2009 12:11, Song Haili wrote: >>> Dear all, >>> I am using perl-5.10.0, BioPerl-1.6.0, and bioperl-db obtaind >> by using CPAN >>> a few days before. Until now, I can load taxonomy and sequence >> data into >>> database successfully. However, I got the following error >> message when >>> trying to load Gene Ontology data into biosql database. Any >> help will be >>> appreciated. Jane >>> >>> command used: >>> perl load_ontology.pl --driver Pg --host pg-server --dbname >> sifter -dbuser >>> sifter --dbpass password ??namespace "Gene Ontology" --format >>> goflat >>> component.ontology process.ontology function.ontology --fmtargs >>> "-defs_file, GO.defs" --noobsolete >>> >>> error: >>> ------------- EXCEPTION ------------- >>> MSG: Could not open ??namespace: No such file or directory >>> STACK Bio::Root::IO::_initialize_io >>> /opt/share/local/users/haili/bioperl-live/Bio/Root/IO.pm:323 STACK >>> Bio::OntologyIO::dagflat::parse >>> /opt/share/local/users/haili/bioperl- >> live/Bio/OntologyIO/dagflat.pm:277> STACK >> Bio::OntologyIO::dagflat::next_ontology> >> /opt/share/local/users/haili/bioperl-live/Bio/OntologyIO/dagflat.pm: >> 330 >>> STACK toplevel load_ontology.pl:604 >>> ------------------------------------- >> >> _______________________________________________ >> BioSQL-l mailing list >> BioSQL-l at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/biosql-l > > _______________________________________________ > BioSQL-l mailing list > BioSQL-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/biosql-l -- =========================================================== : Hilmar Lapp -:- Durham, NC -:- hlapp at gmx dot net : =========================================================== From haili at mpiz-koeln.mpg.de Wed Jul 22 07:50:34 2009 From: haili at mpiz-koeln.mpg.de (Song Haili) Date: Wed, 22 Jul 2009 09:50:34 +0200 Subject: [BioSQL-l] Error when loading Gene Ontology to biosql In-Reply-To: References: <200907211354.25034.florian.mittag@uni-tuebingen.de> Message-ID: Hello Hilmar, Thank you very much for your help. I got the same error even I don't use the argument --fmtargs. Actually that was the first try before I use --fmtargs. Any idea on how to solve this problem? Thanks in advance. command: perl load_ontology.pl --driver Pg --host pg-server --dbname sifter? --dbuser sifter --dbpass password --namespace "Gene Ontology" --format obo gene_ontology.obo --noobsolete error: ------------- EXCEPTION ------------- MSG: OBO File Format Error - Cannot find tag format-version and/ default-namespace . These are required header. STACK Bio::OntologyIO::obo::_header /opt/share/local/users/haili/bioperl-live/Bio/OntologyIO/obo.pm:518 STACK Bio::OntologyIO::obo::parse /opt/share/local/users/haili/bioperl-live/Bio/OntologyIO/obo.pm:209 STACK Bio::OntologyIO::obo::next_ontology /opt/share/local/users/haili/bioperl-live/Bio/OntologyIO/obo.pm:342 STACK toplevel load_ontology.pl:604 ------------------------------------- ----- Original Message ----- From: Hilmar Lapp Date: Tuesday, July 21, 2009 19:19 Subject: Re: [BioSQL-l] Error when loading Gene Ontology to biosql To: Song Haili Cc: florian.mittag at uni-tuebingen.de, biosql-l at lists.open-bio.org > Song: GO.defs is not in OBO format. Where did you find that you > need? > it when you load .obo formatted files? You don't need the -- > fmtargs? > argument for .obo files other than if you want to specify the > ontology? > name. > > -hilmar > > On Jul 21, 2009, at 11:32 AM, Song Haili wrote: > > > > > Hello All, > > The previous error was solved by the help of Florian. Florian, > Thank? > > you very much. > > But I got another error using the way Florian suggested. I > thought? > > it was because parameter --fmtargs was not specified. So I > tried to? > > include it with the value "-defs_file, GO.defs", but it didn't > work.? > > I think maybe GO.defs is not the right file. Is it?? But > how or? > > where to get the right file if it is. Or any other ideas about > how? > > to solve this error? Thank you very much in advance. > > command: > > perl load_ontology.pl --driver Pg --host pg-server --dbname > sifter?? > > --dbuser sifter --dbpass password --namespace "Gene Ontology" - > - > > format obo gene_ontology.obo --fmtargs "-defs_file, GO.defs" -- > > > noobsolete > > error: > > ------------- EXCEPTION ------------- > > MSG: OBO File Format Error - > > Cannot find tag format-version and/ default-namespace . These > are? > > required header. > > > > STACK Bio::OntologyIO::obo::_header > /opt/share/local/users/haili/ > > bioperl-live/Bio/OntologyIO/obo.pm:518 > > STACK Bio::OntologyIO::obo::parse > /opt/share/local/users/haili/ > > bioperl-live/Bio/OntologyIO/obo.pm:209 > > STACK Bio::OntologyIO::obo::next_ontology > /opt/share/local/users/ > > haili/bioperl-live/Bio/OntologyIO/obo.pm:342 > > STACK toplevel load_ontology.pl:604 > > ------------------------------------- > > > > ----- Original Message ----- > > From: Florian Mittag > > Date: Tuesday, July 21, 2009 14:41 > > Subject: Re: [BioSQL-l] Error when loading Gene Ontology to biosql > > To: biosql-l at lists.open-bio.org > > > >> Hi! > >> > >> AFAIK the goflat format is deprecated. Use the .obo files and > >> format instead, > >> that should work. > >> > >> perl load_ontology.pl --driver Pg --host pg-server --dbname sifter > >>? --dbuser sifter --dbpass password --namespace "Gene > Ontology" -- > >> format obo > >>???????? > gene_ontology.1_2.obo>> --noobsolete > >> > >> > >> On Tuesday 21 July 2009 12:11, Song Haili wrote: > >>> Dear all, > >>> I am using perl-5.10.0, BioPerl-1.6.0, and bioperl-db obtaind > >> by using CPAN > >>> a few days before. Until now, I can load taxonomy and sequence > >> data into > >>> database successfully. However, I got the following error > >> message when > >>> trying to load Gene Ontology data into biosql database. Any > >> help will be > >>> appreciated. Jane > >>> > >>> command used: > >>> perl load_ontology.pl --driver Pg --host pg-server --dbname > >> sifter -dbuser > >>> sifter --dbpass password ??namespace "Gene Ontology" -- > format? > >>> goflat > >>> component.ontology process.ontology function.ontology --fmtargs > >>> "-defs_file, GO.defs" --noobsolete > >>> > >>> error: > >>> ------------- EXCEPTION ------------- > >>> MSG: Could not open ??namespace: No such file or directory > >>> STACK Bio::Root::IO::_initialize_io > >>> /opt/share/local/users/haili/bioperl-live/Bio/Root/IO.pm:323 STACK > >>> Bio::OntologyIO::dagflat::parse > >>> /opt/share/local/users/haili/bioperl- > >> live/Bio/OntologyIO/dagflat.pm:277> STACK > >> Bio::OntologyIO::dagflat::next_ontology> > >> /opt/share/local/users/haili/bioperl- > live/Bio/OntologyIO/dagflat.pm: > >> 330 > >>> STACK toplevel load_ontology.pl:604 > >>> ------------------------------------- > >> > >> _______________________________________________ > >> BioSQL-l mailing list > >> BioSQL-l at lists.open-bio.org > >> http://lists.open-bio.org/mailman/listinfo/biosql-l > > > > _______________________________________________ > > BioSQL-l mailing list > > BioSQL-l at lists.open-bio.org > > http://lists.open-bio.org/mailman/listinfo/biosql-l > > -- > =========================================================== > : Hilmar Lapp? -:-? Durham, NC? -:-? hlapp > at gmx dot net : > =========================================================== > > > From florian.mittag at uni-tuebingen.de Wed Jul 22 08:44:18 2009 From: florian.mittag at uni-tuebingen.de (Florian Mittag) Date: Wed, 22 Jul 2009 10:44:18 +0200 Subject: [BioSQL-l] Error when loading Gene Ontology to biosql In-Reply-To: References: Message-ID: <200907221044.18292.florian.mittag@uni-tuebingen.de> Hi Song, just to be clear: Did you download the file gene_ontology.1_2.obo from http://www.geneontology.org/GO.downloads.ontology.shtml ? (http://www.geneontology.org/ontology/obo_format_1_2/gene_ontology.1_2.obo) You need to specify the correct file then, because the command you described expects a file called "gene_ontology.obo", which is not the orginial name of the file to download. On Wednesday 22 July 2009 09:50, Song Haili wrote: > Hello Hilmar, > Thank you very much for your help. > I got the same error even I don't use the argument --fmtargs. Actually that > was the first try before I use --fmtargs. Any idea on how to solve this > problem? Thanks in advance. > > command: > perl load_ontology.pl --driver Pg --host pg-server --dbname sifter? > --dbuser sifter --dbpass password --namespace "Gene Ontology" --format obo > gene_ontology.obo --noobsolete error: > ------------- EXCEPTION ------------- > MSG: OBO File Format Error - > Cannot find tag format-version and/ default-namespace . These are required > header. > > STACK Bio::OntologyIO::obo::_header > /opt/share/local/users/haili/bioperl-live/Bio/OntologyIO/obo.pm:518 STACK > Bio::OntologyIO::obo::parse > /opt/share/local/users/haili/bioperl-live/Bio/OntologyIO/obo.pm:209 STACK > Bio::OntologyIO::obo::next_ontology > /opt/share/local/users/haili/bioperl-live/Bio/OntologyIO/obo.pm:342 STACK > toplevel load_ontology.pl:604 > ------------------------------------- > > ----- Original Message ----- > From: Hilmar Lapp > Date: Tuesday, July 21, 2009 19:19 > Subject: Re: [BioSQL-l] Error when loading Gene Ontology to biosql > To: Song Haili > Cc: florian.mittag at uni-tuebingen.de, biosql-l at lists.open-bio.org > > > Song: GO.defs is not in OBO format. Where did you find that you > > need? > > it when you load .obo formatted files? You don't need the -- > > fmtargs? > > argument for .obo files other than if you want to specify the > > ontology? > > name. > > > > -hilmar > > > > On Jul 21, 2009, at 11:32 AM, Song Haili wrote: > > > Hello All, > > > The previous error was solved by the help of Florian. Florian, > > > > Thank? > > > > > you very much. > > > But I got another error using the way Florian suggested. I > > > > thought? > > > > > it was because parameter --fmtargs was not specified. So I > > > > tried to? > > > > > include it with the value "-defs_file, GO.defs", but it didn't > > > > work.? > > > > > I think maybe GO.defs is not the right file. Is it?? But > > > > how or? > > > > > where to get the right file if it is. Or any other ideas about > > > > how? > > > > > to solve this error? Thank you very much in advance. > > > command: > > > perl load_ontology.pl --driver Pg --host pg-server --dbname > > > > sifter?? > > > > > --dbuser sifter --dbpass password --namespace "Gene Ontology" - > > > > - > > > > > format obo gene_ontology.obo --fmtargs "-defs_file, GO.defs" -- > > > > > > noobsolete > > > error: > > > ------------- EXCEPTION ------------- > > > MSG: OBO File Format Error - > > > Cannot find tag format-version and/ default-namespace . These > > > > are? > > > > > required header. > > > > > > STACK Bio::OntologyIO::obo::_header > > > > /opt/share/local/users/haili/ > > > > > bioperl-live/Bio/OntologyIO/obo.pm:518 > > > STACK Bio::OntologyIO::obo::parse > > > > /opt/share/local/users/haili/ > > > > > bioperl-live/Bio/OntologyIO/obo.pm:209 > > > STACK Bio::OntologyIO::obo::next_ontology > > > > /opt/share/local/users/ > > > > > haili/bioperl-live/Bio/OntologyIO/obo.pm:342 > > > STACK toplevel load_ontology.pl:604 > > > ------------------------------------- > > > > > > ----- Original Message ----- > > > From: Florian Mittag > > > Date: Tuesday, July 21, 2009 14:41 > > > Subject: Re: [BioSQL-l] Error when loading Gene Ontology to biosql > > > To: biosql-l at lists.open-bio.org > > > > > >> Hi! > > >> > > >> AFAIK the goflat format is deprecated. Use the .obo files and > > >> format instead, > > >> that should work. > > >> > > >> perl load_ontology.pl --driver Pg --host pg-server --dbname sifter > > >>? --dbuser sifter --dbpass password --namespace "Gene > > > > Ontology" -- > > > > >> format obo > > >>???????? > > > > gene_ontology.1_2.obo>> --noobsolete > > > > >> On Tuesday 21 July 2009 12:11, Song Haili wrote: > > >>> Dear all, > > >>> I am using perl-5.10.0, BioPerl-1.6.0, and bioperl-db obtaind > > >> > > >> by using CPAN > > >> > > >>> a few days before. Until now, I can load taxonomy and sequence > > >> > > >> data into > > >> > > >>> database successfully. However, I got the following error > > >> > > >> message when > > >> > > >>> trying to load Gene Ontology data into biosql database. Any > > >> > > >> help will be > > >> > > >>> appreciated. Jane > > >>> > > >>> command used: > > >>> perl load_ontology.pl --driver Pg --host pg-server --dbname > > >> > > >> sifter -dbuser > > >> > > >>> sifter --dbpass password ??namespace "Gene Ontology" -- > > > > format? > > > > >>> goflat > > >>> component.ontology process.ontology function.ontology --fmtargs > > >>> "-defs_file, GO.defs" --noobsolete > > >>> > > >>> error: > > >>> ------------- EXCEPTION ------------- > > >>> MSG: Could not open ??namespace: No such file or directory > > >>> STACK Bio::Root::IO::_initialize_io > > >>> /opt/share/local/users/haili/bioperl-live/Bio/Root/IO.pm:323 STACK > > >>> Bio::OntologyIO::dagflat::parse > > >>> /opt/share/local/users/haili/bioperl- > > >> > > >> live/Bio/OntologyIO/dagflat.pm:277> STACK > > >> Bio::OntologyIO::dagflat::next_ontology> > > >> /opt/share/local/users/haili/bioperl- > > > > live/Bio/OntologyIO/dagflat.pm: > > >> 330 > > >> > > >>> STACK toplevel load_ontology.pl:604 > > >>> ------------------------------------- > > >> > > >> _______________________________________________ > > >> BioSQL-l mailing list > > >> BioSQL-l at lists.open-bio.org > > >> http://lists.open-bio.org/mailman/listinfo/biosql-l > > > > > > _______________________________________________ > > > BioSQL-l mailing list > > > BioSQL-l at lists.open-bio.org > > > http://lists.open-bio.org/mailman/listinfo/biosql-l > > > > -- > > =========================================================== > > > > : Hilmar Lapp? -:-? Durham, NC? -:-? hlapp > > > > at gmx dot net : > > =========================================================== From haili at mpiz-koeln.mpg.de Wed Jul 22 11:08:20 2009 From: haili at mpiz-koeln.mpg.de (Song Haili) Date: Wed, 22 Jul 2009 13:08:20 +0200 Subject: [BioSQL-l] Error when loading Gene Ontology to biosql In-Reply-To: <200907221044.18292.florian.mittag@uni-tuebingen.de> References: <200907221044.18292.florian.mittag@uni-tuebingen.de> Message-ID: Hi Florian, Aha, that's the problem. Gene_ontology.1_2.obo works fine. I didn't use gene_ontology.1_2.obo, but as you can see instead I used gene_ontology.obo (ftp://ftp.geneontology.org/pub/go/ontology/gene_ontology.obo). However, I don't understand why I can't use gene_ontology.obo which I think, does not differ a lot with gene_ontology.1_2.obo at the beginning of the two files. Thanks a lot again, Florian and Hilmar. song ----- Original Message ----- From: Florian Mittag Date: Wednesday, July 22, 2009 10:44 Subject: Re: [BioSQL-l] Error when loading Gene Ontology to biosql To: Song Haili Cc: biosql-l at lists.open-bio.org > Hi Song, > > just to be clear: Did you download the file > gene_ontology.1_2.obo from > http://www.geneontology.org/GO.downloads.ontology.shtml ? > > (http://www.geneontology.org/ontology/obo_format_1_2/gene_ontology.1_2.obo) > > You need to specify the correct file then, because the command > you described > expects a file called "gene_ontology.obo", which is not the > orginial name of > the file to download. > > On Wednesday 22 July 2009 09:50, Song Haili wrote: > > Hello Hilmar, > > Thank you very much for your help. > > I got the same error even I don't use the argument --fmtargs. > Actually that > > was the first try before I use --fmtargs. Any idea on how to > solve this > > problem? Thanks in advance. > > > > command: > > perl load_ontology.pl --driver Pg --host pg-server --dbname sifter? > > --dbuser sifter --dbpass password --namespace "Gene Ontology" - > -format obo > > gene_ontology.obo --noobsolete error: > > ------------- EXCEPTION ------------- > > MSG: OBO File Format Error - > > Cannot find tag format-version and/ default-namespace . These > are required > > header. > > > > STACK Bio::OntologyIO::obo::_header > > /opt/share/local/users/haili/bioperl- > live/Bio/OntologyIO/obo.pm:518 STACK > > Bio::OntologyIO::obo::parse > > /opt/share/local/users/haili/bioperl- > live/Bio/OntologyIO/obo.pm:209 STACK > > Bio::OntologyIO::obo::next_ontology > > /opt/share/local/users/haili/bioperl- > live/Bio/OntologyIO/obo.pm:342 STACK > > toplevel load_ontology.pl:604 > > ------------------------------------- > > > > ----- Original Message ----- > > From: Hilmar Lapp > > Date: Tuesday, July 21, 2009 19:19 > > Subject: Re: [BioSQL-l] Error when loading Gene Ontology to biosql > > To: Song Haili > > Cc: florian.mittag at uni-tuebingen.de, biosql-l at lists.open-bio.org > > > > > Song: GO.defs is not in OBO format. Where did you find that you > > > need? > > > it when you load .obo formatted files? You don't need the -- > > > fmtargs? > > > argument for .obo files other than if you want to specify the > > > ontology? > > > name. > > > > > >? -hilmar > > > > > > On Jul 21, 2009, at 11:32 AM, Song Haili wrote: > > > > Hello All, > > > > The previous error was solved by the help of Florian. Florian, > > > > > > Thank? > > > > > > > you very much. > > > > But I got another error using the way Florian suggested. I > > > > > > thought? > > > > > > > it was because parameter --fmtargs was not specified. So I > > > > > > tried to? > > > > > > > include it with the value "-defs_file, GO.defs", but it didn't > > > > > > work.? > > > > > > > I think maybe GO.defs is not the right file. Is it?? But > > > > > > how or? > > > > > > > where to get the right file if it is. Or any other ideas about > > > > > > how? > > > > > > > to solve this error? Thank you very much in advance. > > > > command: > > > > perl load_ontology.pl --driver Pg --host pg-server --dbname > > > > > > sifter?? > > > > > > > --dbuser sifter --dbpass password --namespace "Gene > Ontology" - > > > > > > - > > > > > > > format obo gene_ontology.obo --fmtargs "-defs_file, > GO.defs" -- > > > > > > > > noobsolete > > > > error: > > > > ------------- EXCEPTION ------------- > > > > MSG: OBO File Format Error - > > > > Cannot find tag format-version and/ default-namespace . These > > > > > > are? > > > > > > > required header. > > > > > > > > STACK Bio::OntologyIO::obo::_header > > > > > > /opt/share/local/users/haili/ > > > > > > > bioperl-live/Bio/OntologyIO/obo.pm:518 > > > > STACK Bio::OntologyIO::obo::parse > > > > > > /opt/share/local/users/haili/ > > > > > > > bioperl-live/Bio/OntologyIO/obo.pm:209 > > > > STACK Bio::OntologyIO::obo::next_ontology > > > > > > /opt/share/local/users/ > > > > > > > haili/bioperl-live/Bio/OntologyIO/obo.pm:342 > > > > STACK toplevel load_ontology.pl:604 > > > > ------------------------------------- > > > > > > > > ----- Original Message ----- > > > > From: Florian Mittag > > > > Date: Tuesday, July 21, 2009 14:41 > > > > Subject: Re: [BioSQL-l] Error when loading Gene Ontology > to biosql > > > > To: biosql-l at lists.open-bio.org > > > > > > > >> Hi! > > > >> > > > >> AFAIK the goflat format is deprecated. Use the .obo files and > > > >> format instead, > > > >> that should work. > > > >> > > > >> perl load_ontology.pl --driver Pg --host pg-server -- > dbname sifter > > > >>? --dbuser sifter --dbpass password --namespace "Gene > > > > > > Ontology" -- > > > > > > >> format obo > > > >>???????? > > > > > > gene_ontology.1_2.obo>> --noobsolete > > > > > > >> On Tuesday 21 July 2009 12:11, Song Haili wrote: > > > >>> Dear all, > > > >>> I am using perl-5.10.0, BioPerl-1.6.0, and bioperl-db obtaind > > > >> > > > >> by using CPAN > > > >> > > > >>> a few days before. Until now, I can load taxonomy and sequence > > > >> > > > >> data into > > > >> > > > >>> database successfully. However, I got the following error > > > >> > > > >> message when > > > >> > > > >>> trying to load Gene Ontology data into biosql database. Any > > > >> > > > >> help will be > > > >> > > > >>> appreciated. Jane > > > >>> > > > >>> command used: > > > >>> perl load_ontology.pl --driver Pg --host pg-server --dbname > > > >> > > > >> sifter -dbuser > > > >> > > > >>> sifter --dbpass password ??namespace "Gene Ontology" -- > > > > > > format? > > > > > > >>> goflat > > > >>> component.ontology process.ontology function.ontology -- > fmtargs> > >>> "-defs_file, GO.defs" --noobsolete > > > >>> > > > >>> error: > > > >>> ------------- EXCEPTION ------------- > > > >>> MSG: Could not open ??namespace: No such file or directory > > > >>> STACK Bio::Root::IO::_initialize_io > > > >>> /opt/share/local/users/haili/bioperl- > live/Bio/Root/IO.pm:323 STACK > > > >>> Bio::OntologyIO::dagflat::parse > > > >>> /opt/share/local/users/haili/bioperl- > > > >> > > > >> live/Bio/OntologyIO/dagflat.pm:277> STACK > > > >> Bio::OntologyIO::dagflat::next_ontology> > > > >> /opt/share/local/users/haili/bioperl- > > > > > > live/Bio/OntologyIO/dagflat.pm: > > > >> 330 > > > >> > > > >>> STACK toplevel load_ontology.pl:604 > > > >>> ------------------------------------- > > > >> > > > >> _______________________________________________ > > > >> BioSQL-l mailing list > > > >> BioSQL-l at lists.open-bio.org > > > >> http://lists.open-bio.org/mailman/listinfo/biosql-l > > > > > > > > _______________________________________________ > > > > BioSQL-l mailing list > > > > BioSQL-l at lists.open-bio.org > > > > http://lists.open-bio.org/mailman/listinfo/biosql-l > > > > > > -- > > > =========================================================== > > > > > > : Hilmar Lapp? -:-? Durham, NC? -:-? hlapp > > > > > > at gmx dot net : > > > =========================================================== From ccanchaya at gmail.com Wed Jul 22 15:05:49 2009 From: ccanchaya at gmail.com (Carlos A. Canchaya) Date: Wed, 22 Jul 2009 17:05:49 +0200 Subject: [BioSQL-l] Error when loading Gene Ontology to biosql In-Reply-To: References: <200907221044.18292.florian.mittag@uni-tuebingen.de> Message-ID: Hi guys, I've tried to execute load_ontologies following your suggestions as load_ontology.pl --driver Pg --dbname biosql --dbuser yyy --dbpass xxx --namespace "Gene Ontology" --fmtargs GO.defs --format obo gene_ontology.1_2.obo However I have many warnings first --------------------- WARNING --------------------- MSG: DBLink exists in the dblink of _default --------------------------------------------------- and then --------------------- WARNING --------------------- MSG: DBLink exists in the dblink of _default --------------------------------------------------- Could not store term GO:0001404, name 'invasive growth': ------------- EXCEPTION: Bio::Root::Exception ------------- MSG: create: object (Bio::Ontology::OBOterm) failed to insert or to be found by unique key STACK: Error::throw STACK: Bio::Root::Root::throw /home/carlos/nascent/download/bioperl- live//Bio/Root/Root.pm:357 STACK: Bio::DB::BioSQL::BasePersistenceAdaptor::create /usr/local/ share/perl/5.10.0/Bio/DB/BioSQL/BasePersistenceAdaptor.pm:219 STACK: Bio::DB::BioSQL::BasePersistenceAdaptor::store /usr/local/share/ perl/5.10.0/Bio/DB/BioSQL/BasePersistenceAdaptor.pm:264 STACK: Bio::DB::Persistent::PersistentObject::store /usr/local/share/ perl/5.10.0/Bio/DB/Persistent/PersistentObject.pm:284 STACK: main::persist_term /tmp/BioPerl-db-1.6.0/scripts/biosql/ load_ontology.pl:812 STACK: /tmp/BioPerl-db-1.6.0/scripts/biosql/load_ontology.pl:617 ----------------------------------------------------------- at /tmp/BioPerl-db-1.6.0/scripts/biosql/load_ontology.pl line 824 main::persist_term('-term', 'Bio::Ontology::OBOterm=HASH(0x9c86078)', '-db', 'Bio::DB::BioSQL::DBAdaptor=HASH(0x936ed50)', '-termfactory', undef, '- throw', 'CODE(0x8f49a50)', '-mergeobs', ...) called at /tmp/BioPerl- db-1.6.0/scripts/biosql/load_ontology.pl line 617 Any ideas why? Thanks in advance, Carlos Carlos Canchaya ccanchaya at gmail.com On Jul 22, 2009, at 1:08 PM, Song Haili wrote: > Hi Florian, > Aha, that's the problem. Gene_ontology.1_2.obo works fine. I didn't > use gene_ontology.1_2.obo, but as you can see instead I used > gene_ontology.obo (ftp://ftp.geneontology.org/pub/go/ontology/gene_ontology.obo > ). However, I don't understand why I can't use gene_ontology.obo > which I think, does not differ a lot with gene_ontology.1_2.obo at > the beginning of the two files. Thanks a lot again, Florian and > Hilmar. > song > > ----- Original Message ----- > From: Florian Mittag > Date: Wednesday, July 22, 2009 10:44 > Subject: Re: [BioSQL-l] Error when loading Gene Ontology to biosql > To: Song Haili > Cc: biosql-l at lists.open-bio.org > >> Hi Song, >> >> just to be clear: Did you download the file >> gene_ontology.1_2.obo from >> http://www.geneontology.org/GO.downloads.ontology.shtml ? >> >> (http://www.geneontology.org/ontology/obo_format_1_2/gene_ontology.1_2.obo >> ) >> >> You need to specify the correct file then, because the command >> you described >> expects a file called "gene_ontology.obo", which is not the >> orginial name of >> the file to download. >> >> On Wednesday 22 July 2009 09:50, Song Haili wrote: >>> Hello Hilmar, >>> Thank you very much for your help. >>> I got the same error even I don't use the argument --fmtargs. >> Actually that >>> was the first try before I use --fmtargs. Any idea on how to >> solve this >>> problem? Thanks in advance. >>> >>> command: >>> perl load_ontology.pl --driver Pg --host pg-server --dbname sifter >>> --dbuser sifter --dbpass password --namespace "Gene Ontology" - >> -format obo >>> gene_ontology.obo --noobsolete error: >>> ------------- EXCEPTION ------------- >>> MSG: OBO File Format Error - >>> Cannot find tag format-version and/ default-namespace . These >> are required >>> header. >>> >>> STACK Bio::OntologyIO::obo::_header >>> /opt/share/local/users/haili/bioperl- >> live/Bio/OntologyIO/obo.pm:518 STACK >>> Bio::OntologyIO::obo::parse >>> /opt/share/local/users/haili/bioperl- >> live/Bio/OntologyIO/obo.pm:209 STACK >>> Bio::OntologyIO::obo::next_ontology >>> /opt/share/local/users/haili/bioperl- >> live/Bio/OntologyIO/obo.pm:342 STACK >>> toplevel load_ontology.pl:604 >>> ------------------------------------- >>> >>> ----- Original Message ----- >>> From: Hilmar Lapp >>> Date: Tuesday, July 21, 2009 19:19 >>> Subject: Re: [BioSQL-l] Error when loading Gene Ontology to biosql >>> To: Song Haili >>> Cc: florian.mittag at uni-tuebingen.de, biosql-l at lists.open-bio.org >>> >>>> Song: GO.defs is not in OBO format. Where did you find that you >>>> need >>>> it when you load .obo formatted files? You don't need the -- >>>> fmtargs >>>> argument for .obo files other than if you want to specify the >>>> ontology >>>> name. >>>> >>>> -hilmar >>>> >>>> On Jul 21, 2009, at 11:32 AM, Song Haili wrote: >>>>> Hello All, >>>>> The previous error was solved by the help of Florian. Florian, >>>> >>>> Thank >>>> >>>>> you very much. >>>>> But I got another error using the way Florian suggested. I >>>> >>>> thought >>>> >>>>> it was because parameter --fmtargs was not specified. So I >>>> >>>> tried to >>>> >>>>> include it with the value "-defs_file, GO.defs", but it didn't >>>> >>>> work. >>>> >>>>> I think maybe GO.defs is not the right file. Is it? But >>>> >>>> how or >>>> >>>>> where to get the right file if it is. Or any other ideas about >>>> >>>> how >>>> >>>>> to solve this error? Thank you very much in advance. >>>>> command: >>>>> perl load_ontology.pl --driver Pg --host pg-server --dbname >>>> >>>> sifter >>>> >>>>> --dbuser sifter --dbpass password --namespace "Gene >> Ontology" - >>>> >>>> - >>>> >>>>> format obo gene_ontology.obo --fmtargs "-defs_file, >> GO.defs" -- >>>>> >>>>> noobsolete >>>>> error: >>>>> ------------- EXCEPTION ------------- >>>>> MSG: OBO File Format Error - >>>>> Cannot find tag format-version and/ default-namespace . These >>>> >>>> are >>>> >>>>> required header. >>>>> >>>>> STACK Bio::OntologyIO::obo::_header >>>> >>>> /opt/share/local/users/haili/ >>>> >>>>> bioperl-live/Bio/OntologyIO/obo.pm:518 >>>>> STACK Bio::OntologyIO::obo::parse >>>> >>>> /opt/share/local/users/haili/ >>>> >>>>> bioperl-live/Bio/OntologyIO/obo.pm:209 >>>>> STACK Bio::OntologyIO::obo::next_ontology >>>> >>>> /opt/share/local/users/ >>>> >>>>> haili/bioperl-live/Bio/OntologyIO/obo.pm:342 >>>>> STACK toplevel load_ontology.pl:604 >>>>> ------------------------------------- >>>>> >>>>> ----- Original Message ----- >>>>> From: Florian Mittag >>>>> Date: Tuesday, July 21, 2009 14:41 >>>>> Subject: Re: [BioSQL-l] Error when loading Gene Ontology >> to biosql >>>>> To: biosql-l at lists.open-bio.org >>>>> >>>>>> Hi! >>>>>> >>>>>> AFAIK the goflat format is deprecated. Use the .obo files and >>>>>> format instead, >>>>>> that should work. >>>>>> >>>>>> perl load_ontology.pl --driver Pg --host pg-server -- >> dbname sifter >>>>>> --dbuser sifter --dbpass password --namespace "Gene >>>> >>>> Ontology" -- >>>> >>>>>> format obo >>>>>> >>>> >>>> gene_ontology.1_2.obo>> --noobsolete >>>> >>>>>> On Tuesday 21 July 2009 12:11, Song Haili wrote: >>>>>>> Dear all, >>>>>>> I am using perl-5.10.0, BioPerl-1.6.0, and bioperl-db obtaind >>>>>> >>>>>> by using CPAN >>>>>> >>>>>>> a few days before. Until now, I can load taxonomy and sequence >>>>>> >>>>>> data into >>>>>> >>>>>>> database successfully. However, I got the following error >>>>>> >>>>>> message when >>>>>> >>>>>>> trying to load Gene Ontology data into biosql database. Any >>>>>> >>>>>> help will be >>>>>> >>>>>>> appreciated. Jane >>>>>>> >>>>>>> command used: >>>>>>> perl load_ontology.pl --driver Pg --host pg-server --dbname >>>>>> >>>>>> sifter -dbuser >>>>>> >>>>>>> sifter --dbpass password ??namespace "Gene Ontology" -- >>>> >>>> format >>>> >>>>>>> goflat >>>>>>> component.ontology process.ontology function.ontology -- >> fmtargs> > >>> "-defs_file, GO.defs" --noobsolete >>>>>>> >>>>>>> error: >>>>>>> ------------- EXCEPTION ------------- >>>>>>> MSG: Could not open ??namespace: No such file or directory >>>>>>> STACK Bio::Root::IO::_initialize_io >>>>>>> /opt/share/local/users/haili/bioperl- >> live/Bio/Root/IO.pm:323 STACK >>>>>>> Bio::OntologyIO::dagflat::parse >>>>>>> /opt/share/local/users/haili/bioperl- >>>>>> >>>>>> live/Bio/OntologyIO/dagflat.pm:277> STACK >>>>>> Bio::OntologyIO::dagflat::next_ontology> >>>>>> /opt/share/local/users/haili/bioperl- >>>> >>>> live/Bio/OntologyIO/dagflat.pm: >>>>>> 330 >>>>>> >>>>>>> STACK toplevel load_ontology.pl:604 >>>>>>> ------------------------------------- >>>>>> >>>>>> _______________________________________________ >>>>>> BioSQL-l mailing list >>>>>> BioSQL-l at lists.open-bio.org >>>>>> http://lists.open-bio.org/mailman/listinfo/biosql-l >>>>> >>>>> _______________________________________________ >>>>> BioSQL-l mailing list >>>>> BioSQL-l at lists.open-bio.org >>>>> http://lists.open-bio.org/mailman/listinfo/biosql-l >>>> >>>> -- >>>> =========================================================== >>>> >>>> : Hilmar Lapp -:- Durham, NC -:- hlapp >>>> >>>> at gmx dot net : >>>> =========================================================== > > _______________________________________________ > BioSQL-l mailing list > BioSQL-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/biosql-l From hlapp at gmx.net Wed Jul 22 18:15:29 2009 From: hlapp at gmx.net (Hilmar Lapp) Date: Wed, 22 Jul 2009 14:15:29 -0400 Subject: [BioSQL-l] Error when loading Gene Ontology to biosql In-Reply-To: References: <200907221044.18292.florian.mittag@uni-tuebingen.de> Message-ID: Please leave off the --fmtargs GO.defs argument - this is not a file in the .obo format. -hilmar On Jul 22, 2009, at 11:05 AM, Carlos A. Canchaya wrote: > Hi guys, > > I've tried to execute load_ontologies following your suggestions as > > load_ontology.pl --driver Pg --dbname biosql --dbuser yyy --dbpass > xxx --namespace "Gene Ontology" --fmtargs GO.defs --format obo > gene_ontology.1_2.obo > > However I have many warnings first > > --------------------- WARNING --------------------- > MSG: DBLink exists in the dblink of _default > --------------------------------------------------- > > and then > > --------------------- WARNING --------------------- > MSG: DBLink exists in the dblink of _default > --------------------------------------------------- > Could not store term GO:0001404, name 'invasive growth': > > ------------- EXCEPTION: Bio::Root::Exception ------------- > MSG: create: object (Bio::Ontology::OBOterm) failed to insert or to > be found by unique key > STACK: Error::throw > STACK: Bio::Root::Root::throw /home/carlos/nascent/download/bioperl- > live//Bio/Root/Root.pm:357 > STACK: Bio::DB::BioSQL::BasePersistenceAdaptor::create /usr/local/ > share/perl/5.10.0/Bio/DB/BioSQL/BasePersistenceAdaptor.pm:219 > STACK: Bio::DB::BioSQL::BasePersistenceAdaptor::store /usr/local/ > share/perl/5.10.0/Bio/DB/BioSQL/BasePersistenceAdaptor.pm:264 > STACK: Bio::DB::Persistent::PersistentObject::store /usr/local/share/ > perl/5.10.0/Bio/DB/Persistent/PersistentObject.pm:284 > STACK: main::persist_term /tmp/BioPerl-db-1.6.0/scripts/biosql/ > load_ontology.pl:812 > STACK: /tmp/BioPerl-db-1.6.0/scripts/biosql/load_ontology.pl:617 > ----------------------------------------------------------- > > at /tmp/BioPerl-db-1.6.0/scripts/biosql/load_ontology.pl line 824 > main::persist_term('-term', > 'Bio::Ontology::OBOterm=HASH(0x9c86078)', '-db', > 'Bio::DB::BioSQL::DBAdaptor=HASH(0x936ed50)', '-termfactory', undef, > '-throw', 'CODE(0x8f49a50)', '-mergeobs', ...) called at /tmp/ > BioPerl-db-1.6.0/scripts/biosql/load_ontology.pl line 617 > > > Any ideas why? > > Thanks in advance, > > Carlos > > > Carlos Canchaya > ccanchaya at gmail.com > > > > On Jul 22, 2009, at 1:08 PM, Song Haili wrote: > >> Hi Florian, >> Aha, that's the problem. Gene_ontology.1_2.obo works fine. I didn't >> use gene_ontology.1_2.obo, but as you can see instead I used >> gene_ontology.obo (ftp://ftp.geneontology.org/pub/go/ontology/gene_ontology.obo >> ). However, I don't understand why I can't use gene_ontology.obo >> which I think, does not differ a lot with gene_ontology.1_2.obo at >> the beginning of the two files. Thanks a lot again, Florian and >> Hilmar. >> song >> >> ----- Original Message ----- >> From: Florian Mittag >> Date: Wednesday, July 22, 2009 10:44 >> Subject: Re: [BioSQL-l] Error when loading Gene Ontology to biosql >> To: Song Haili >> Cc: biosql-l at lists.open-bio.org >> >>> Hi Song, >>> >>> just to be clear: Did you download the file >>> gene_ontology.1_2.obo from >>> http://www.geneontology.org/GO.downloads.ontology.shtml ? >>> >>> (http://www.geneontology.org/ontology/obo_format_1_2/gene_ontology.1_2.obo >>> ) >>> >>> You need to specify the correct file then, because the command >>> you described >>> expects a file called "gene_ontology.obo", which is not the >>> orginial name of >>> the file to download. >>> >>> On Wednesday 22 July 2009 09:50, Song Haili wrote: >>>> Hello Hilmar, >>>> Thank you very much for your help. >>>> I got the same error even I don't use the argument --fmtargs. >>> Actually that >>>> was the first try before I use --fmtargs. Any idea on how to >>> solve this >>>> problem? Thanks in advance. >>>> >>>> command: >>>> perl load_ontology.pl --driver Pg --host pg-server --dbname sifter >>>> --dbuser sifter --dbpass password --namespace "Gene Ontology" - >>> -format obo >>>> gene_ontology.obo --noobsolete error: >>>> ------------- EXCEPTION ------------- >>>> MSG: OBO File Format Error - >>>> Cannot find tag format-version and/ default-namespace . These >>> are required >>>> header. >>>> >>>> STACK Bio::OntologyIO::obo::_header >>>> /opt/share/local/users/haili/bioperl- >>> live/Bio/OntologyIO/obo.pm:518 STACK >>>> Bio::OntologyIO::obo::parse >>>> /opt/share/local/users/haili/bioperl- >>> live/Bio/OntologyIO/obo.pm:209 STACK >>>> Bio::OntologyIO::obo::next_ontology >>>> /opt/share/local/users/haili/bioperl- >>> live/Bio/OntologyIO/obo.pm:342 STACK >>>> toplevel load_ontology.pl:604 >>>> ------------------------------------- >>>> >>>> ----- Original Message ----- >>>> From: Hilmar Lapp >>>> Date: Tuesday, July 21, 2009 19:19 >>>> Subject: Re: [BioSQL-l] Error when loading Gene Ontology to biosql >>>> To: Song Haili >>>> Cc: florian.mittag at uni-tuebingen.de, biosql-l at lists.open-bio.org >>>> >>>>> Song: GO.defs is not in OBO format. Where did you find that you >>>>> need >>>>> it when you load .obo formatted files? You don't need the -- >>>>> fmtargs >>>>> argument for .obo files other than if you want to specify the >>>>> ontology >>>>> name. >>>>> >>>>> -hilmar >>>>> >>>>> On Jul 21, 2009, at 11:32 AM, Song Haili wrote: >>>>>> Hello All, >>>>>> The previous error was solved by the help of Florian. Florian, >>>>> >>>>> Thank >>>>> >>>>>> you very much. >>>>>> But I got another error using the way Florian suggested. I >>>>> >>>>> thought >>>>> >>>>>> it was because parameter --fmtargs was not specified. So I >>>>> >>>>> tried to >>>>> >>>>>> include it with the value "-defs_file, GO.defs", but it didn't >>>>> >>>>> work. >>>>> >>>>>> I think maybe GO.defs is not the right file. Is it? But >>>>> >>>>> how or >>>>> >>>>>> where to get the right file if it is. Or any other ideas about >>>>> >>>>> how >>>>> >>>>>> to solve this error? Thank you very much in advance. >>>>>> command: >>>>>> perl load_ontology.pl --driver Pg --host pg-server --dbname >>>>> >>>>> sifter >>>>> >>>>>> --dbuser sifter --dbpass password --namespace "Gene >>> Ontology" - >>>>> >>>>> - >>>>> >>>>>> format obo gene_ontology.obo --fmtargs "-defs_file, >>> GO.defs" -- >>>>>> >>>>>> noobsolete >>>>>> error: >>>>>> ------------- EXCEPTION ------------- >>>>>> MSG: OBO File Format Error - >>>>>> Cannot find tag format-version and/ default-namespace . These >>>>> >>>>> are >>>>> >>>>>> required header. >>>>>> >>>>>> STACK Bio::OntologyIO::obo::_header >>>>> >>>>> /opt/share/local/users/haili/ >>>>> >>>>>> bioperl-live/Bio/OntologyIO/obo.pm:518 >>>>>> STACK Bio::OntologyIO::obo::parse >>>>> >>>>> /opt/share/local/users/haili/ >>>>> >>>>>> bioperl-live/Bio/OntologyIO/obo.pm:209 >>>>>> STACK Bio::OntologyIO::obo::next_ontology >>>>> >>>>> /opt/share/local/users/ >>>>> >>>>>> haili/bioperl-live/Bio/OntologyIO/obo.pm:342 >>>>>> STACK toplevel load_ontology.pl:604 >>>>>> ------------------------------------- >>>>>> >>>>>> ----- Original Message ----- >>>>>> From: Florian Mittag >>>>>> Date: Tuesday, July 21, 2009 14:41 >>>>>> Subject: Re: [BioSQL-l] Error when loading Gene Ontology >>> to biosql >>>>>> To: biosql-l at lists.open-bio.org >>>>>> >>>>>>> Hi! >>>>>>> >>>>>>> AFAIK the goflat format is deprecated. Use the .obo files and >>>>>>> format instead, >>>>>>> that should work. >>>>>>> >>>>>>> perl load_ontology.pl --driver Pg --host pg-server -- >>> dbname sifter >>>>>>> --dbuser sifter --dbpass password --namespace "Gene >>>>> >>>>> Ontology" -- >>>>> >>>>>>> format obo >>>>>>> >>>>> >>>>> gene_ontology.1_2.obo>> --noobsolete >>>>> >>>>>>> On Tuesday 21 July 2009 12:11, Song Haili wrote: >>>>>>>> Dear all, >>>>>>>> I am using perl-5.10.0, BioPerl-1.6.0, and bioperl-db obtaind >>>>>>> >>>>>>> by using CPAN >>>>>>> >>>>>>>> a few days before. Until now, I can load taxonomy and sequence >>>>>>> >>>>>>> data into >>>>>>> >>>>>>>> database successfully. However, I got the following error >>>>>>> >>>>>>> message when >>>>>>> >>>>>>>> trying to load Gene Ontology data into biosql database. Any >>>>>>> >>>>>>> help will be >>>>>>> >>>>>>>> appreciated. Jane >>>>>>>> >>>>>>>> command used: >>>>>>>> perl load_ontology.pl --driver Pg --host pg-server --dbname >>>>>>> >>>>>>> sifter -dbuser >>>>>>> >>>>>>>> sifter --dbpass password ??namespace "Gene Ontology" -- >>>>> >>>>> format >>>>> >>>>>>>> goflat >>>>>>>> component.ontology process.ontology function.ontology -- >>> fmtargs> > >>> "-defs_file, GO.defs" --noobsolete >>>>>>>> >>>>>>>> error: >>>>>>>> ------------- EXCEPTION ------------- >>>>>>>> MSG: Could not open ??namespace: No such file or directory >>>>>>>> STACK Bio::Root::IO::_initialize_io >>>>>>>> /opt/share/local/users/haili/bioperl- >>> live/Bio/Root/IO.pm:323 STACK >>>>>>>> Bio::OntologyIO::dagflat::parse >>>>>>>> /opt/share/local/users/haili/bioperl- >>>>>>> >>>>>>> live/Bio/OntologyIO/dagflat.pm:277> STACK >>>>>>> Bio::OntologyIO::dagflat::next_ontology> >>>>>>> /opt/share/local/users/haili/bioperl- >>>>> >>>>> live/Bio/OntologyIO/dagflat.pm: >>>>>>> 330 >>>>>>> >>>>>>>> STACK toplevel load_ontology.pl:604 >>>>>>>> ------------------------------------- >>>>>>> >>>>>>> _______________________________________________ >>>>>>> BioSQL-l mailing list >>>>>>> BioSQL-l at lists.open-bio.org >>>>>>> http://lists.open-bio.org/mailman/listinfo/biosql-l >>>>>> >>>>>> _______________________________________________ >>>>>> BioSQL-l mailing list >>>>>> BioSQL-l at lists.open-bio.org >>>>>> http://lists.open-bio.org/mailman/listinfo/biosql-l >>>>> >>>>> -- >>>>> =========================================================== >>>>> >>>>> : Hilmar Lapp -:- Durham, NC -:- hlapp >>>>> >>>>> at gmx dot net : >>>>> =========================================================== >> >> _______________________________________________ >> BioSQL-l mailing list >> BioSQL-l at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/biosql-l > > > _______________________________________________ > BioSQL-l mailing list > BioSQL-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/biosql-l -- =========================================================== : Hilmar Lapp -:- Durham, NC -:- hlapp at gmx dot net : =========================================================== From ccanchaya at gmail.com Thu Jul 23 07:27:25 2009 From: ccanchaya at gmail.com (Carlos A. Canchaya) Date: Thu, 23 Jul 2009 09:27:25 +0200 Subject: [BioSQL-l] Error when loading Gene Ontology to biosql In-Reply-To: References: <200907221044.18292.florian.mittag@uni-tuebingen.de> Message-ID: <5A932B73-5D17-4F82-A366-B6BE217FD213@gmail.com> Hi Hilmar, thanks for the help. I've tried now this load_ontology.pl --driver Pg --dbname biosql --dbuser yyyy--dbpass xxxx --namespace "Gene Ontology" --format obo gene_ontology.1_2.obo downloaded from here http://www.geneontology.org/ontology/obo_format_1_2/gene_ontology.1_2.obo and I have this error message. --------------------- WARNING --------------------- MSG: DBLink exists in the dblink of _default --------------------------------------------------- Could not store term GO:0001404, name 'invasive growth': ------------- EXCEPTION: Bio::Root::Exception ------------- MSG: create: object (Bio::Ontology::OBOterm) failed to insert or to be found by unique key STACK: Error::throw STACK: Bio::Root::Root::throw /usr/local/share/perl/5.10.0/Bio/Root/ Root.pm:357 STACK: Bio::DB::BioSQL::BasePersistenceAdaptor::create /usr/local/ share/perl/5.10.0/Bio/DB/BioSQL/BasePersistenceAdaptor.pm:219 STACK: Bio::DB::BioSQL::BasePersistenceAdaptor::store /usr/local/share/ perl/5.10.0/Bio/DB/BioSQL/BasePersistenceAdaptor.pm:264 STACK: Bio::DB::Persistent::PersistentObject::store /usr/local/share/ perl/5.10.0/Bio/DB/Persistent/PersistentObject.pm:284 STACK: main::persist_term /tmp/BioPerl-db-1.6.0/scripts/biosql/ load_ontology.pl:812 STACK: /tmp/BioPerl-db-1.6.0/scripts/biosql/load_ontology.pl:617 ----------------------------------------------------------- at /tmp/BioPerl-db-1.6.0/scripts/biosql/load_ontology.pl line 824 main::persist_term('-term', 'Bio::Ontology::OBOterm=HASH(0x9330318)', '-db', 'Bio::DB::BioSQL::DBAdaptor=HASH(0x8a17ac0)', '-termfactory', undef, '- throw', 'CODE(0x85f4708)', '-mergeobs', ...) called at /tmp/BioPerl- db-1.6.0/scripts/biosql/load_ontology.pl line 617 Any hints to know where the problem would be? Thanks in advance, Carlos Carlos Canchaya ccanchaya at gmail.com On Jul 22, 2009, at 8:15 PM, Hilmar Lapp wrote: > Please leave off the --fmtargs GO.defs argument - this is not a file > in the .obo format. > > -hilmar > > On Jul 22, 2009, at 11:05 AM, Carlos A. Canchaya wrote: > >> Hi guys, >> >> I've tried to execute load_ontologies following your suggestions as >> >> load_ontology.pl --driver Pg --dbname biosql --dbuser yyy --dbpass >> xxx --namespace "Gene Ontology" --fmtargs GO.defs --format obo >> gene_ontology.1_2.obo >> >> However I have many warnings first >> >> --------------------- WARNING --------------------- >> MSG: DBLink exists in the dblink of _default >> --------------------------------------------------- >> >> and then >> >> --------------------- WARNING --------------------- >> MSG: DBLink exists in the dblink of _default >> --------------------------------------------------- >> Could not store term GO:0001404, name 'invasive growth': >> >> ------------- EXCEPTION: Bio::Root::Exception ------------- >> MSG: create: object (Bio::Ontology::OBOterm) failed to insert or to >> be found by unique key >> STACK: Error::throw >> STACK: Bio::Root::Root::throw /home/carlos/nascent/download/bioperl- >> live//Bio/Root/Root.pm:357 >> STACK: Bio::DB::BioSQL::BasePersistenceAdaptor::create /usr/local/ >> share/perl/5.10.0/Bio/DB/BioSQL/BasePersistenceAdaptor.pm:219 >> STACK: Bio::DB::BioSQL::BasePersistenceAdaptor::store /usr/local/ >> share/perl/5.10.0/Bio/DB/BioSQL/BasePersistenceAdaptor.pm:264 >> STACK: Bio::DB::Persistent::PersistentObject::store /usr/local/ >> share/perl/5.10.0/Bio/DB/Persistent/PersistentObject.pm:284 >> STACK: main::persist_term /tmp/BioPerl-db-1.6.0/scripts/biosql/ >> load_ontology.pl:812 >> STACK: /tmp/BioPerl-db-1.6.0/scripts/biosql/load_ontology.pl:617 >> ----------------------------------------------------------- >> >> at /tmp/BioPerl-db-1.6.0/scripts/biosql/load_ontology.pl line 824 >> main::persist_term('-term', >> 'Bio::Ontology::OBOterm=HASH(0x9c86078)', '-db', >> 'Bio::DB::BioSQL::DBAdaptor=HASH(0x936ed50)', '-termfactory', >> undef, '-throw', 'CODE(0x8f49a50)', '-mergeobs', ...) called at / >> tmp/BioPerl-db-1.6.0/scripts/biosql/load_ontology.pl line 617 >> >> >> Any ideas why? >> >> Thanks in advance, >> >> Carlos >> >> >> Carlos Canchaya >> ccanchaya at gmail.com >> >> >> >> On Jul 22, 2009, at 1:08 PM, Song Haili wrote: >> >>> Hi Florian, >>> Aha, that's the problem. Gene_ontology.1_2.obo works fine. I >>> didn't use gene_ontology.1_2.obo, but as you can see instead I >>> used gene_ontology.obo (ftp://ftp.geneontology.org/pub/go/ontology/gene_ontology.obo >>> ). However, I don't understand why I can't use gene_ontology.obo >>> which I think, does not differ a lot with gene_ontology.1_2.obo at >>> the beginning of the two files. Thanks a lot again, Florian and >>> Hilmar. >>> song >>> >>> ----- Original Message ----- >>> From: Florian Mittag >>> Date: Wednesday, July 22, 2009 10:44 >>> Subject: Re: [BioSQL-l] Error when loading Gene Ontology to biosql >>> To: Song Haili >>> Cc: biosql-l at lists.open-bio.org >>> >>>> Hi Song, >>>> >>>> just to be clear: Did you download the file >>>> gene_ontology.1_2.obo from >>>> http://www.geneontology.org/GO.downloads.ontology.shtml ? >>>> >>>> (http://www.geneontology.org/ontology/obo_format_1_2/gene_ontology.1_2.obo >>>> ) >>>> >>>> You need to specify the correct file then, because the command >>>> you described >>>> expects a file called "gene_ontology.obo", which is not the >>>> orginial name of >>>> the file to download. >>>> >>>> On Wednesday 22 July 2009 09:50, Song Haili wrote: >>>>> Hello Hilmar, >>>>> Thank you very much for your help. >>>>> I got the same error even I don't use the argument --fmtargs. >>>> Actually that >>>>> was the first try before I use --fmtargs. Any idea on how to >>>> solve this >>>>> problem? Thanks in advance. >>>>> >>>>> command: >>>>> perl load_ontology.pl --driver Pg --host pg-server --dbname sifter >>>>> --dbuser sifter --dbpass password --namespace "Gene Ontology" - >>>> -format obo >>>>> gene_ontology.obo --noobsolete error: >>>>> ------------- EXCEPTION ------------- >>>>> MSG: OBO File Format Error - >>>>> Cannot find tag format-version and/ default-namespace . These >>>> are required >>>>> header. >>>>> >>>>> STACK Bio::OntologyIO::obo::_header >>>>> /opt/share/local/users/haili/bioperl- >>>> live/Bio/OntologyIO/obo.pm:518 STACK >>>>> Bio::OntologyIO::obo::parse >>>>> /opt/share/local/users/haili/bioperl- >>>> live/Bio/OntologyIO/obo.pm:209 STACK >>>>> Bio::OntologyIO::obo::next_ontology >>>>> /opt/share/local/users/haili/bioperl- >>>> live/Bio/OntologyIO/obo.pm:342 STACK >>>>> toplevel load_ontology.pl:604 >>>>> ------------------------------------- >>>>> >>>>> ----- Original Message ----- >>>>> From: Hilmar Lapp >>>>> Date: Tuesday, July 21, 2009 19:19 >>>>> Subject: Re: [BioSQL-l] Error when loading Gene Ontology to biosql >>>>> To: Song Haili >>>>> Cc: florian.mittag at uni-tuebingen.de, biosql-l at lists.open-bio.org >>>>> >>>>>> Song: GO.defs is not in OBO format. Where did you find that you >>>>>> need >>>>>> it when you load .obo formatted files? You don't need the -- >>>>>> fmtargs >>>>>> argument for .obo files other than if you want to specify the >>>>>> ontology >>>>>> name. >>>>>> >>>>>> -hilmar >>>>>> >>>>>> On Jul 21, 2009, at 11:32 AM, Song Haili wrote: >>>>>>> Hello All, >>>>>>> The previous error was solved by the help of Florian. Florian, >>>>>> >>>>>> Thank >>>>>> >>>>>>> you very much. >>>>>>> But I got another error using the way Florian suggested. I >>>>>> >>>>>> thought >>>>>> >>>>>>> it was because parameter --fmtargs was not specified. So I >>>>>> >>>>>> tried to >>>>>> >>>>>>> include it with the value "-defs_file, GO.defs", but it didn't >>>>>> >>>>>> work. >>>>>> >>>>>>> I think maybe GO.defs is not the right file. Is it? But >>>>>> >>>>>> how or >>>>>> >>>>>>> where to get the right file if it is. Or any other ideas about >>>>>> >>>>>> how >>>>>> >>>>>>> to solve this error? Thank you very much in advance. >>>>>>> command: >>>>>>> perl load_ontology.pl --driver Pg --host pg-server --dbname >>>>>> >>>>>> sifter >>>>>> >>>>>>> --dbuser sifter --dbpass password --namespace "Gene >>>> Ontology" - >>>>>> >>>>>> - >>>>>> >>>>>>> format obo gene_ontology.obo --fmtargs "-defs_file, >>>> GO.defs" -- >>>>>>> >>>>>>> noobsolete >>>>>>> error: >>>>>>> ------------- EXCEPTION ------------- >>>>>>> MSG: OBO File Format Error - >>>>>>> Cannot find tag format-version and/ default-namespace . These >>>>>> >>>>>> are >>>>>> >>>>>>> required header. >>>>>>> >>>>>>> STACK Bio::OntologyIO::obo::_header >>>>>> >>>>>> /opt/share/local/users/haili/ >>>>>> >>>>>>> bioperl-live/Bio/OntologyIO/obo.pm:518 >>>>>>> STACK Bio::OntologyIO::obo::parse >>>>>> >>>>>> /opt/share/local/users/haili/ >>>>>> >>>>>>> bioperl-live/Bio/OntologyIO/obo.pm:209 >>>>>>> STACK Bio::OntologyIO::obo::next_ontology >>>>>> >>>>>> /opt/share/local/users/ >>>>>> >>>>>>> haili/bioperl-live/Bio/OntologyIO/obo.pm:342 >>>>>>> STACK toplevel load_ontology.pl:604 >>>>>>> ------------------------------------- >>>>>>> >>>>>>> ----- Original Message ----- >>>>>>> From: Florian Mittag >>>>>>> Date: Tuesday, July 21, 2009 14:41 >>>>>>> Subject: Re: [BioSQL-l] Error when loading Gene Ontology >>>> to biosql >>>>>>> To: biosql-l at lists.open-bio.org >>>>>>> >>>>>>>> Hi! >>>>>>>> >>>>>>>> AFAIK the goflat format is deprecated. Use the .obo files and >>>>>>>> format instead, >>>>>>>> that should work. >>>>>>>> >>>>>>>> perl load_ontology.pl --driver Pg --host pg-server -- >>>> dbname sifter >>>>>>>> --dbuser sifter --dbpass password --namespace "Gene >>>>>> >>>>>> Ontology" -- >>>>>> >>>>>>>> format obo >>>>>>>> >>>>>> >>>>>> gene_ontology.1_2.obo>> --noobsolete >>>>>> >>>>>>>> On Tuesday 21 July 2009 12:11, Song Haili wrote: >>>>>>>>> Dear all, >>>>>>>>> I am using perl-5.10.0, BioPerl-1.6.0, and bioperl-db obtaind >>>>>>>> >>>>>>>> by using CPAN >>>>>>>> >>>>>>>>> a few days before. Until now, I can load taxonomy and sequence >>>>>>>> >>>>>>>> data into >>>>>>>> >>>>>>>>> database successfully. However, I got the following error >>>>>>>> >>>>>>>> message when >>>>>>>> >>>>>>>>> trying to load Gene Ontology data into biosql database. Any >>>>>>>> >>>>>>>> help will be >>>>>>>> >>>>>>>>> appreciated. Jane >>>>>>>>> >>>>>>>>> command used: >>>>>>>>> perl load_ontology.pl --driver Pg --host pg-server --dbname >>>>>>>> >>>>>>>> sifter -dbuser >>>>>>>> >>>>>>>>> sifter --dbpass password ??namespace "Gene Ontology" -- >>>>>> >>>>>> format >>>>>> >>>>>>>>> goflat >>>>>>>>> component.ontology process.ontology function.ontology -- >>>> fmtargs> > >>> "-defs_file, GO.defs" --noobsolete >>>>>>>>> >>>>>>>>> error: >>>>>>>>> ------------- EXCEPTION ------------- >>>>>>>>> MSG: Could not open ??namespace: No such file or directory >>>>>>>>> STACK Bio::Root::IO::_initialize_io >>>>>>>>> /opt/share/local/users/haili/bioperl- >>>> live/Bio/Root/IO.pm:323 STACK >>>>>>>>> Bio::OntologyIO::dagflat::parse >>>>>>>>> /opt/share/local/users/haili/bioperl- >>>>>>>> >>>>>>>> live/Bio/OntologyIO/dagflat.pm:277> STACK >>>>>>>> Bio::OntologyIO::dagflat::next_ontology> >>>>>>>> /opt/share/local/users/haili/bioperl- >>>>>> >>>>>> live/Bio/OntologyIO/dagflat.pm: >>>>>>>> 330 >>>>>>>> >>>>>>>>> STACK toplevel load_ontology.pl:604 >>>>>>>>> ------------------------------------- >>>>>>>> >>>>>>>> _______________________________________________ >>>>>>>> BioSQL-l mailing list >>>>>>>> BioSQL-l at lists.open-bio.org >>>>>>>> http://lists.open-bio.org/mailman/listinfo/biosql-l >>>>>>> >>>>>>> _______________________________________________ >>>>>>> BioSQL-l mailing list >>>>>>> BioSQL-l at lists.open-bio.org >>>>>>> http://lists.open-bio.org/mailman/listinfo/biosql-l >>>>>> >>>>>> -- >>>>>> =========================================================== >>>>>> >>>>>> : Hilmar Lapp -:- Durham, NC -:- hlapp >>>>>> >>>>>> at gmx dot net : >>>>>> =========================================================== >>> >>> _______________________________________________ >>> BioSQL-l mailing list >>> BioSQL-l at lists.open-bio.org >>> http://lists.open-bio.org/mailman/listinfo/biosql-l >> >> >> _______________________________________________ >> BioSQL-l mailing list >> BioSQL-l at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/biosql-l > > -- > =========================================================== > : Hilmar Lapp -:- Durham, NC -:- hlapp at gmx dot net : > =========================================================== > > > From hlapp at gmx.net Thu Jul 23 12:49:48 2009 From: hlapp at gmx.net (Hilmar Lapp) Date: Thu, 23 Jul 2009 08:49:48 -0400 Subject: [BioSQL-l] Error when loading Gene Ontology to biosql In-Reply-To: <5A932B73-5D17-4F82-A366-B6BE217FD213@gmail.com> References: <200907221044.18292.florian.mittag@uni-tuebingen.de> <5A932B73-5D17-4F82-A366-B6BE217FD213@gmail.com> Message-ID: <1E596269-ED8F-4ADF-9B54-A9A0CF908620@gmx.net> Hi Carlos - that's an odd error that we haven't seen yet. My first impulse would be to suspect that your database wasn't empty when you ran this, and that the error you got is due to a term in the input file clashing with one you already have in the database. You can check this by looking into your database: SQL> SELECT * FROM term WHERE identifier = 'GO:0001404' or name = 'invasive growth'; Does this return anything? Note that load_ontology.pl is perfectly equipped to update an existing ontology - check the POD and look for the --lookup command line option (and the several options following it in the POD with which you can modify the exact update behavior). By default though the script will assume that it is loading a new ontology. -hilmar On Jul 23, 2009, at 3:27 AM, Carlos A. Canchaya wrote: > Hi Hilmar, > > thanks for the help. I've tried now this > > load_ontology.pl --driver Pg --dbname biosql --dbuser yyyy--dbpass > xxxx --namespace "Gene Ontology" --format obo gene_ontology.1_2.obo > > downloaded from here > > http://www.geneontology.org/ontology/obo_format_1_2/gene_ontology.1_2.obo > > and I have this error message. > > --------------------- WARNING --------------------- > MSG: DBLink exists in the dblink of _default > --------------------------------------------------- > Could not store term GO:0001404, name 'invasive growth': > > ------------- EXCEPTION: Bio::Root::Exception ------------- > MSG: create: object (Bio::Ontology::OBOterm) failed to insert or to > be found by unique key > STACK: Error::throw > STACK: Bio::Root::Root::throw /usr/local/share/perl/5.10.0/Bio/Root/ > Root.pm:357 > STACK: Bio::DB::BioSQL::BasePersistenceAdaptor::create /usr/local/ > share/perl/5.10.0/Bio/DB/BioSQL/BasePersistenceAdaptor.pm:219 > STACK: Bio::DB::BioSQL::BasePersistenceAdaptor::store /usr/local/ > share/perl/5.10.0/Bio/DB/BioSQL/BasePersistenceAdaptor.pm:264 > STACK: Bio::DB::Persistent::PersistentObject::store /usr/local/share/ > perl/5.10.0/Bio/DB/Persistent/PersistentObject.pm:284 > STACK: main::persist_term /tmp/BioPerl-db-1.6.0/scripts/biosql/ > load_ontology.pl:812 > STACK: /tmp/BioPerl-db-1.6.0/scripts/biosql/load_ontology.pl:617 > ----------------------------------------------------------- > > at /tmp/BioPerl-db-1.6.0/scripts/biosql/load_ontology.pl line 824 > main::persist_term('-term', > 'Bio::Ontology::OBOterm=HASH(0x9330318)', '-db', > 'Bio::DB::BioSQL::DBAdaptor=HASH(0x8a17ac0)', '-termfactory', undef, > '-throw', 'CODE(0x85f4708)', '-mergeobs', ...) called at /tmp/ > BioPerl-db-1.6.0/scripts/biosql/load_ontology.pl line 617 > > Any hints to know where the problem would be? > > Thanks in advance, > > Carlos > > Carlos Canchaya > ccanchaya at gmail.com > > > > On Jul 22, 2009, at 8:15 PM, Hilmar Lapp wrote: > >> Please leave off the --fmtargs GO.defs argument - this is not a >> file in the .obo format. >> >> -hilmar >> >> On Jul 22, 2009, at 11:05 AM, Carlos A. Canchaya wrote: >> >>> Hi guys, >>> >>> I've tried to execute load_ontologies following your suggestions as >>> >>> load_ontology.pl --driver Pg --dbname biosql --dbuser yyy --dbpass >>> xxx --namespace "Gene Ontology" --fmtargs GO.defs --format obo >>> gene_ontology.1_2.obo >>> >>> However I have many warnings first >>> >>> --------------------- WARNING --------------------- >>> MSG: DBLink exists in the dblink of _default >>> --------------------------------------------------- >>> >>> and then >>> >>> --------------------- WARNING --------------------- >>> MSG: DBLink exists in the dblink of _default >>> --------------------------------------------------- >>> Could not store term GO:0001404, name 'invasive growth': >>> >>> ------------- EXCEPTION: Bio::Root::Exception ------------- >>> MSG: create: object (Bio::Ontology::OBOterm) failed to insert or >>> to be found by unique key >>> STACK: Error::throw >>> STACK: Bio::Root::Root::throw /home/carlos/nascent/download/ >>> bioperl-live//Bio/Root/Root.pm:357 >>> STACK: Bio::DB::BioSQL::BasePersistenceAdaptor::create /usr/local/ >>> share/perl/5.10.0/Bio/DB/BioSQL/BasePersistenceAdaptor.pm:219 >>> STACK: Bio::DB::BioSQL::BasePersistenceAdaptor::store /usr/local/ >>> share/perl/5.10.0/Bio/DB/BioSQL/BasePersistenceAdaptor.pm:264 >>> STACK: Bio::DB::Persistent::PersistentObject::store /usr/local/ >>> share/perl/5.10.0/Bio/DB/Persistent/PersistentObject.pm:284 >>> STACK: main::persist_term /tmp/BioPerl-db-1.6.0/scripts/biosql/ >>> load_ontology.pl:812 >>> STACK: /tmp/BioPerl-db-1.6.0/scripts/biosql/load_ontology.pl:617 >>> ----------------------------------------------------------- >>> >>> at /tmp/BioPerl-db-1.6.0/scripts/biosql/load_ontology.pl line 824 >>> main::persist_term('-term', >>> 'Bio::Ontology::OBOterm=HASH(0x9c86078)', '-db', >>> 'Bio::DB::BioSQL::DBAdaptor=HASH(0x936ed50)', '-termfactory', >>> undef, '-throw', 'CODE(0x8f49a50)', '-mergeobs', ...) called at / >>> tmp/BioPerl-db-1.6.0/scripts/biosql/load_ontology.pl line 617 >>> >>> >>> Any ideas why? >>> >>> Thanks in advance, >>> >>> Carlos >>> >>> >>> Carlos Canchaya >>> ccanchaya at gmail.com >>> >>> >>> >>> On Jul 22, 2009, at 1:08 PM, Song Haili wrote: >>> >>>> Hi Florian, >>>> Aha, that's the problem. Gene_ontology.1_2.obo works fine. I >>>> didn't use gene_ontology.1_2.obo, but as you can see instead I >>>> used gene_ontology.obo (ftp://ftp.geneontology.org/pub/go/ontology/gene_ontology.obo >>>> ). However, I don't understand why I can't use gene_ontology.obo >>>> which I think, does not differ a lot with gene_ontology.1_2.obo >>>> at the beginning of the two files. Thanks a lot again, Florian >>>> and Hilmar. >>>> song >>>> >>>> ----- Original Message ----- >>>> From: Florian Mittag >>>> Date: Wednesday, July 22, 2009 10:44 >>>> Subject: Re: [BioSQL-l] Error when loading Gene Ontology to biosql >>>> To: Song Haili >>>> Cc: biosql-l at lists.open-bio.org >>>> >>>>> Hi Song, >>>>> >>>>> just to be clear: Did you download the file >>>>> gene_ontology.1_2.obo from >>>>> http://www.geneontology.org/GO.downloads.ontology.shtml ? >>>>> >>>>> (http://www.geneontology.org/ontology/obo_format_1_2/gene_ontology.1_2.obo >>>>> ) >>>>> >>>>> You need to specify the correct file then, because the command >>>>> you described >>>>> expects a file called "gene_ontology.obo", which is not the >>>>> orginial name of >>>>> the file to download. >>>>> >>>>> On Wednesday 22 July 2009 09:50, Song Haili wrote: >>>>>> Hello Hilmar, >>>>>> Thank you very much for your help. >>>>>> I got the same error even I don't use the argument --fmtargs. >>>>> Actually that >>>>>> was the first try before I use --fmtargs. Any idea on how to >>>>> solve this >>>>>> problem? Thanks in advance. >>>>>> >>>>>> command: >>>>>> perl load_ontology.pl --driver Pg --host pg-server --dbname >>>>>> sifter >>>>>> --dbuser sifter --dbpass password --namespace "Gene Ontology" - >>>>> -format obo >>>>>> gene_ontology.obo --noobsolete error: >>>>>> ------------- EXCEPTION ------------- >>>>>> MSG: OBO File Format Error - >>>>>> Cannot find tag format-version and/ default-namespace . These >>>>> are required >>>>>> header. >>>>>> >>>>>> STACK Bio::OntologyIO::obo::_header >>>>>> /opt/share/local/users/haili/bioperl- >>>>> live/Bio/OntologyIO/obo.pm:518 STACK >>>>>> Bio::OntologyIO::obo::parse >>>>>> /opt/share/local/users/haili/bioperl- >>>>> live/Bio/OntologyIO/obo.pm:209 STACK >>>>>> Bio::OntologyIO::obo::next_ontology >>>>>> /opt/share/local/users/haili/bioperl- >>>>> live/Bio/OntologyIO/obo.pm:342 STACK >>>>>> toplevel load_ontology.pl:604 >>>>>> ------------------------------------- >>>>>> >>>>>> ----- Original Message ----- >>>>>> From: Hilmar Lapp >>>>>> Date: Tuesday, July 21, 2009 19:19 >>>>>> Subject: Re: [BioSQL-l] Error when loading Gene Ontology to >>>>>> biosql >>>>>> To: Song Haili >>>>>> Cc: florian.mittag at uni-tuebingen.de, biosql-l at lists.open-bio.org >>>>>> >>>>>>> Song: GO.defs is not in OBO format. Where did you find that you >>>>>>> need >>>>>>> it when you load .obo formatted files? You don't need the -- >>>>>>> fmtargs >>>>>>> argument for .obo files other than if you want to specify the >>>>>>> ontology >>>>>>> name. >>>>>>> >>>>>>> -hilmar >>>>>>> >>>>>>> On Jul 21, 2009, at 11:32 AM, Song Haili wrote: >>>>>>>> Hello All, >>>>>>>> The previous error was solved by the help of Florian. Florian, >>>>>>> >>>>>>> Thank >>>>>>> >>>>>>>> you very much. >>>>>>>> But I got another error using the way Florian suggested. I >>>>>>> >>>>>>> thought >>>>>>> >>>>>>>> it was because parameter --fmtargs was not specified. So I >>>>>>> >>>>>>> tried to >>>>>>> >>>>>>>> include it with the value "-defs_file, GO.defs", but it didn't >>>>>>> >>>>>>> work. >>>>>>> >>>>>>>> I think maybe GO.defs is not the right file. Is it? But >>>>>>> >>>>>>> how or >>>>>>> >>>>>>>> where to get the right file if it is. Or any other ideas about >>>>>>> >>>>>>> how >>>>>>> >>>>>>>> to solve this error? Thank you very much in advance. >>>>>>>> command: >>>>>>>> perl load_ontology.pl --driver Pg --host pg-server --dbname >>>>>>> >>>>>>> sifter >>>>>>> >>>>>>>> --dbuser sifter --dbpass password --namespace "Gene >>>>> Ontology" - >>>>>>> >>>>>>> - >>>>>>> >>>>>>>> format obo gene_ontology.obo --fmtargs "-defs_file, >>>>> GO.defs" -- >>>>>>>> >>>>>>>> noobsolete >>>>>>>> error: >>>>>>>> ------------- EXCEPTION ------------- >>>>>>>> MSG: OBO File Format Error - >>>>>>>> Cannot find tag format-version and/ default-namespace . These >>>>>>> >>>>>>> are >>>>>>> >>>>>>>> required header. >>>>>>>> >>>>>>>> STACK Bio::OntologyIO::obo::_header >>>>>>> >>>>>>> /opt/share/local/users/haili/ >>>>>>> >>>>>>>> bioperl-live/Bio/OntologyIO/obo.pm:518 >>>>>>>> STACK Bio::OntologyIO::obo::parse >>>>>>> >>>>>>> /opt/share/local/users/haili/ >>>>>>> >>>>>>>> bioperl-live/Bio/OntologyIO/obo.pm:209 >>>>>>>> STACK Bio::OntologyIO::obo::next_ontology >>>>>>> >>>>>>> /opt/share/local/users/ >>>>>>> >>>>>>>> haili/bioperl-live/Bio/OntologyIO/obo.pm:342 >>>>>>>> STACK toplevel load_ontology.pl:604 >>>>>>>> ------------------------------------- >>>>>>>> >>>>>>>> ----- Original Message ----- >>>>>>>> From: Florian Mittag >>>>>>>> Date: Tuesday, July 21, 2009 14:41 >>>>>>>> Subject: Re: [BioSQL-l] Error when loading Gene Ontology >>>>> to biosql >>>>>>>> To: biosql-l at lists.open-bio.org >>>>>>>> >>>>>>>>> Hi! >>>>>>>>> >>>>>>>>> AFAIK the goflat format is deprecated. Use the .obo files and >>>>>>>>> format instead, >>>>>>>>> that should work. >>>>>>>>> >>>>>>>>> perl load_ontology.pl --driver Pg --host pg-server -- >>>>> dbname sifter >>>>>>>>> --dbuser sifter --dbpass password --namespace "Gene >>>>>>> >>>>>>> Ontology" -- >>>>>>> >>>>>>>>> format obo >>>>>>>>> >>>>>>> >>>>>>> gene_ontology.1_2.obo>> --noobsolete >>>>>>> >>>>>>>>> On Tuesday 21 July 2009 12:11, Song Haili wrote: >>>>>>>>>> Dear all, >>>>>>>>>> I am using perl-5.10.0, BioPerl-1.6.0, and bioperl-db obtaind >>>>>>>>> >>>>>>>>> by using CPAN >>>>>>>>> >>>>>>>>>> a few days before. Until now, I can load taxonomy and >>>>>>>>>> sequence >>>>>>>>> >>>>>>>>> data into >>>>>>>>> >>>>>>>>>> database successfully. However, I got the following error >>>>>>>>> >>>>>>>>> message when >>>>>>>>> >>>>>>>>>> trying to load Gene Ontology data into biosql database. Any >>>>>>>>> >>>>>>>>> help will be >>>>>>>>> >>>>>>>>>> appreciated. Jane >>>>>>>>>> >>>>>>>>>> command used: >>>>>>>>>> perl load_ontology.pl --driver Pg --host pg-server --dbname >>>>>>>>> >>>>>>>>> sifter -dbuser >>>>>>>>> >>>>>>>>>> sifter --dbpass password ??namespace "Gene Ontology" -- >>>>>>> >>>>>>> format >>>>>>> >>>>>>>>>> goflat >>>>>>>>>> component.ontology process.ontology function.ontology -- >>>>> fmtargs> > >>> "-defs_file, GO.defs" --noobsolete >>>>>>>>>> >>>>>>>>>> error: >>>>>>>>>> ------------- EXCEPTION ------------- >>>>>>>>>> MSG: Could not open ??namespace: No such file or >>>>>>>>>> directory >>>>>>>>>> STACK Bio::Root::IO::_initialize_io >>>>>>>>>> /opt/share/local/users/haili/bioperl- >>>>> live/Bio/Root/IO.pm:323 STACK >>>>>>>>>> Bio::OntologyIO::dagflat::parse >>>>>>>>>> /opt/share/local/users/haili/bioperl- >>>>>>>>> >>>>>>>>> live/Bio/OntologyIO/dagflat.pm:277> STACK >>>>>>>>> Bio::OntologyIO::dagflat::next_ontology> >>>>>>>>> /opt/share/local/users/haili/bioperl- >>>>>>> >>>>>>> live/Bio/OntologyIO/dagflat.pm: >>>>>>>>> 330 >>>>>>>>> >>>>>>>>>> STACK toplevel load_ontology.pl:604 >>>>>>>>>> ------------------------------------- >>>>>>>>> >>>>>>>>> _______________________________________________ >>>>>>>>> BioSQL-l mailing list >>>>>>>>> BioSQL-l at lists.open-bio.org >>>>>>>>> http://lists.open-bio.org/mailman/listinfo/biosql-l >>>>>>>> >>>>>>>> _______________________________________________ >>>>>>>> BioSQL-l mailing list >>>>>>>> BioSQL-l at lists.open-bio.org >>>>>>>> http://lists.open-bio.org/mailman/listinfo/biosql-l >>>>>>> >>>>>>> -- >>>>>>> =========================================================== >>>>>>> >>>>>>> : Hilmar Lapp -:- Durham, NC -:- hlapp >>>>>>> >>>>>>> at gmx dot net : >>>>>>> =========================================================== >>>> >>>> _______________________________________________ >>>> BioSQL-l mailing list >>>> BioSQL-l at lists.open-bio.org >>>> http://lists.open-bio.org/mailman/listinfo/biosql-l >>> >>> >>> _______________________________________________ >>> BioSQL-l mailing list >>> BioSQL-l at lists.open-bio.org >>> http://lists.open-bio.org/mailman/listinfo/biosql-l >> >> -- >> =========================================================== >> : Hilmar Lapp -:- Durham, NC -:- hlapp at gmx dot net : >> =========================================================== >> >> >> > > > _______________________________________________ > BioSQL-l mailing list > BioSQL-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/biosql-l -- =========================================================== : Hilmar Lapp -:- Durham, NC -:- hlapp at gmx dot net : =========================================================== From biopython at maubp.freeserve.co.uk Thu Jul 23 13:32:39 2009 From: biopython at maubp.freeserve.co.uk (Peter) Date: Thu, 23 Jul 2009 14:32:39 +0100 Subject: [BioSQL-l] [Biopython] Storing SeqRecord objects with annotation In-Reply-To: <8E8262E4-FEA0-4839-957B-A5B4A56F8E49@gmx.net> References: <320fb6e00907230320r49809329p620f3d1d4a39fb36@mail.gmail.com> <8E8262E4-FEA0-4839-957B-A5B4A56F8E49@gmx.net> Message-ID: <320fb6e00907230632q730aa496g4a07c50d5860bd54@mail.gmail.com> Hi Hilmar! I've CC'd this to the BioSQL list. The start of the thread was here: http://lists.open-bio.org/pipermail/biopython/2009-July/005385.html On Thu, Jul 23, 2009 at 2:01 PM, Hilmar Lapp wrote: > > On Jul 23, 2009, at 6:20 AM, Peter wrote: > >> Currently the BioSQL schema doesn't have any explicit support >> for "per letter annotation" > > I haven't been following the thread closely and so may be missing what is > really meant by this. If, however, you mean associating annotation to a > specific letter (position) in the sequence, BioSQL does support this - you'd > create a seqfeature with appropriate location, and attach the annotation to > the seqfeature. > > Bioentry annotations are location-less, by comparison. By "per letter annotation" we mean essentially a list of annotation data, with one entry for each letter in the sequence. For example, a sequencing quality score (from a FASTQ file) where this is one integer per letter (i.e. per base pair). Or, a secondary structure prediction, encoded as one character per letter (which could apply to proteins and nucleotides). This sort of thing could be done by using on feature per letter, but it would be dreadfully inefficient for storing in the database. >> [...] >> You can record any object in the SeqRecord's annotation dictionary. >> However, saving the result to a file will be tricky - and it wouldn't >> work in BioSQL either. > > Note that that's not entirely true. If you have a textual serialization > (such as XML) of your object, you *can* store it in > bioentry_qualifier_value. This is what we do in BioPerl with a TagTree > annotation object that supports a nested hierarchical annotation > structure needed for lossless representation of some UniProt lines. This was what I mentioned earlier in the thread - using XML or JSON to turn the object into a long string. However, we really need the Bio* projects to agree on some standards here, rather than each project adding its own additions ad hoc (which will make interoperation much trickier). For example, I was unaware you (BioPerl) had already pressed ahead with this for the UniProt data - which rather proves my point. > Obviously, that won't allow you to query very well by individual > elements of your custom annotation object. But you can build a > custom index (e.g., using Lucene) that does that. Yes, doing searches on an XML/JSON encoded string is an issue. But right now we are probably more interested in just solving the persistence of more complex objects. Peter From cjfields at illinois.edu Fri Jul 24 00:39:25 2009 From: cjfields at illinois.edu (Chris Fields) Date: Thu, 23 Jul 2009 19:39:25 -0500 Subject: [BioSQL-l] Error when loading Gene Ontology to biosql In-Reply-To: <1E596269-ED8F-4ADF-9B54-A9A0CF908620@gmx.net> References: <200907221044.18292.florian.mittag@uni-tuebingen.de> <5A932B73-5D17-4F82-A366-B6BE217FD213@gmail.com> <1E596269-ED8F-4ADF-9B54-A9A0CF908620@gmx.net> Message-ID: <52ED5492-14F1-443C-AB1E-67685A464656@illinois.edu> The warning is interesting, as it derives from our rollback of feature/ annotation stuff in bioperl. It indicates the specified DBLink is duplicated in the Bio::Ontology::Term. The exception makes sense in light of that (and seems to confirm the link was already present). chris On Jul 23, 2009, at 7:49 AM, Hilmar Lapp wrote: > Hi Carlos - that's an odd error that we haven't seen yet. My first > impulse would be to suspect that your database wasn't empty when you > ran this, and that the error you got is due to a term in the input > file clashing with one you already have in the database. > > You can check this by looking into your database: > > SQL> SELECT * FROM term WHERE identifier = 'GO:0001404' or name = > 'invasive growth'; > > Does this return anything? > > Note that load_ontology.pl is perfectly equipped to update an > existing ontology - check the POD and look for the --lookup command > line option (and the several options following it in the POD with > which you can modify the exact update behavior). By default though > the script will assume that it is loading a new ontology. > > -hilmar > > On Jul 23, 2009, at 3:27 AM, Carlos A. Canchaya wrote: > >> Hi Hilmar, >> >> thanks for the help. I've tried now this >> >> load_ontology.pl --driver Pg --dbname biosql --dbuser yyyy--dbpass >> xxxx --namespace "Gene Ontology" --format obo gene_ontology.1_2.obo >> >> downloaded from here >> >> http://www.geneontology.org/ontology/obo_format_1_2/gene_ontology.1_2.obo >> >> and I have this error message. >> >> --------------------- WARNING --------------------- >> MSG: DBLink _default >> --------------------------------------------------- >> Could not store term GO:0001404, name 'invasive growth': >> >> ------------- EXCEPTION: Bio::Root::Exception ------------- >> MSG: create: object (Bio::Ontology::OBOterm) failed to insert or to >> be found by unique key >> STACK: Error::throw >> STACK: Bio::Root::Root::throw /usr/local/share/perl/5.10.0/Bio/Root/ >> Root.pm:357 >> STACK: Bio::DB::BioSQL::BasePersistenceAdaptor::create /usr/local/ >> share/perl/5.10.0/Bio/DB/BioSQL/BasePersistenceAdaptor.pm:219 >> STACK: Bio::DB::BioSQL::BasePersistenceAdaptor::store /usr/local/ >> share/perl/5.10.0/Bio/DB/BioSQL/BasePersistenceAdaptor.pm:264 >> STACK: Bio::DB::Persistent::PersistentObject::store /usr/local/ >> share/perl/5.10.0/Bio/DB/Persistent/PersistentObject.pm:284 >> STACK: main::persist_term /tmp/BioPerl-db-1.6.0/scripts/biosql/ >> load_ontology.pl:812 >> STACK: /tmp/BioPerl-db-1.6.0/scripts/biosql/load_ontology.pl:617 >> ----------------------------------------------------------- >> >> at /tmp/BioPerl-db-1.6.0/scripts/biosql/load_ontology.pl line 824 >> main::persist_term('-term', >> 'Bio::Ontology::OBOterm=HASH(0x9330318)', '-db', >> 'Bio::DB::BioSQL::DBAdaptor=HASH(0x8a17ac0)', '-termfactory', >> undef, '-throw', 'CODE(0x85f4708)', '-mergeobs', ...) called at / >> tmp/BioPerl-db-1.6.0/scripts/biosql/load_ontology.pl line 617 >> >> Any hints to know where the problem would be? >> >> Thanks in advance, >> >> Carlos >> >> Carlos Canchaya >> ccanchaya at gmail.com >> >> >> >> On Jul 22, 2009, at 8:15 PM, Hilmar Lapp wrote: >> >>> Please leave off the --fmtargs GO.defs argument - this is not a >>> file in the .obo format. >>> >>> -hilmar >>> >>> On Jul 22, 2009, at 11:05 AM, Carlos A. Canchaya wrote: >>> >>>> Hi guys, >>>> >>>> I've tried to execute load_ontologies following your suggestions as >>>> >>>> load_ontology.pl --driver Pg --dbname biosql --dbuser yyy -- >>>> dbpass xxx --namespace "Gene Ontology" --fmtargs GO.defs --format >>>> obo gene_ontology.1_2.obo >>>> >>>> However I have many warnings first >>>> >>>> --------------------- WARNING --------------------- >>>> MSG: DBLink exists in the dblink of _default >>>> --------------------------------------------------- >>>> >>>> and then >>>> >>>> --------------------- WARNING --------------------- >>>> MSG: DBLink exists in the dblink of _default >>>> --------------------------------------------------- >>>> Could not store term GO:0001404, name 'invasive growth': >>>> >>>> ------------- EXCEPTION: Bio::Root::Exception ------------- >>>> MSG: create: object (Bio::Ontology::OBOterm) failed to insert or >>>> to be found by unique key >>>> STACK: Error::throw >>>> STACK: Bio::Root::Root::throw /home/carlos/nascent/download/ >>>> bioperl-live//Bio/Root/Root.pm:357 >>>> STACK: Bio::DB::BioSQL::BasePersistenceAdaptor::create /usr/local/ >>>> share/perl/5.10.0/Bio/DB/BioSQL/BasePersistenceAdaptor.pm:219 >>>> STACK: Bio::DB::BioSQL::BasePersistenceAdaptor::store /usr/local/ >>>> share/perl/5.10.0/Bio/DB/BioSQL/BasePersistenceAdaptor.pm:264 >>>> STACK: Bio::DB::Persistent::PersistentObject::store /usr/local/ >>>> share/perl/5.10.0/Bio/DB/Persistent/PersistentObject.pm:284 >>>> STACK: main::persist_term /tmp/BioPerl-db-1.6.0/scripts/biosql/ >>>> load_ontology.pl:812 >>>> STACK: /tmp/BioPerl-db-1.6.0/scripts/biosql/load_ontology.pl:617 >>>> ----------------------------------------------------------- >>>> >>>> at /tmp/BioPerl-db-1.6.0/scripts/biosql/load_ontology.pl line 824 >>>> main::persist_term('-term', >>>> 'Bio::Ontology::OBOterm=HASH(0x9c86078)', '-db', >>>> 'Bio::DB::BioSQL::DBAdaptor=HASH(0x936ed50)', '-termfactory', >>>> undef, '-throw', 'CODE(0x8f49a50)', '-mergeobs', ...) called at / >>>> tmp/BioPerl-db-1.6.0/scripts/biosql/load_ontology.pl line 617 >>>> >>>> >>>> Any ideas why? >>>> >>>> Thanks in advance, >>>> >>>> Carlos >>>> >>>> >>>> Carlos Canchaya >>>> ccanchaya at gmail.com >>>> >>>> >>>> >>>> On Jul 22, 2009, at 1:08 PM, Song Haili wrote: >>>> >>>>> Hi Florian, >>>>> Aha, that's the problem. Gene_ontology.1_2.obo works fine. I >>>>> didn't use gene_ontology.1_2.obo, but as you can see instead I >>>>> used gene_ontology.obo (ftp://ftp.geneontology.org/pub/go/ontology/gene_ontology.obo >>>>> ). However, I don't understand why I can't use gene_ontology.obo >>>>> which I think, does not differ a lot with gene_ontology.1_2.obo >>>>> at the beginning of the two files. Thanks a lot again, Florian >>>>> and Hilmar. >>>>> song >>>>> >>>>> ----- Original Message ----- >>>>> From: Florian Mittag >>>>> Date: Wednesday, July 22, 2009 10:44 >>>>> Subject: Re: [BioSQL-l] Error when loading Gene Ontology to biosql >>>>> To: Song Haili >>>>> Cc: biosql-l at lists.open-bio.org >>>>> >>>>>> Hi Song, >>>>>> >>>>>> just to be clear: Did you download the file >>>>>> gene_ontology.1_2.obo from >>>>>> http://www.geneontology.org/GO.downloads.ontology.shtml ? >>>>>> >>>>>> (http://www.geneontology.org/ontology/obo_format_1_2/gene_ontology.1_2.obo >>>>>> ) >>>>>> >>>>>> You need to specify the correct file then, because the command >>>>>> you described >>>>>> expects a file called "gene_ontology.obo", which is not the >>>>>> orginial name of >>>>>> the file to download. >>>>>> >>>>>> On Wednesday 22 July 2009 09:50, Song Haili wrote: >>>>>>> Hello Hilmar, >>>>>>> Thank you very much for your help. >>>>>>> I got the same error even I don't use the argument --fmtargs. >>>>>> Actually that >>>>>>> was the first try before I use --fmtargs. Any idea on how to >>>>>> solve this >>>>>>> problem? Thanks in advance. >>>>>>> >>>>>>> command: >>>>>>> perl load_ontology.pl --driver Pg --host pg-server --dbname >>>>>>> sifter >>>>>>> --dbuser sifter --dbpass password --namespace "Gene Ontology" - >>>>>> -format obo >>>>>>> gene_ontology.obo --noobsolete error: >>>>>>> ------------- EXCEPTION ------------- >>>>>>> MSG: OBO File Format Error - >>>>>>> Cannot find tag format-version and/ default-namespace . These >>>>>> are required >>>>>>> header. >>>>>>> >>>>>>> STACK Bio::OntologyIO::obo::_header >>>>>>> /opt/share/local/users/haili/bioperl- >>>>>> live/Bio/OntologyIO/obo.pm:518 STACK >>>>>>> Bio::OntologyIO::obo::parse >>>>>>> /opt/share/local/users/haili/bioperl- >>>>>> live/Bio/OntologyIO/obo.pm:209 STACK >>>>>>> Bio::OntologyIO::obo::next_ontology >>>>>>> /opt/share/local/users/haili/bioperl- >>>>>> live/Bio/OntologyIO/obo.pm:342 STACK >>>>>>> toplevel load_ontology.pl:604 >>>>>>> ------------------------------------- >>>>>>> >>>>>>> ----- Original Message ----- >>>>>>> From: Hilmar Lapp >>>>>>> Date: Tuesday, July 21, 2009 19:19 >>>>>>> Subject: Re: [BioSQL-l] Error when loading Gene Ontology to >>>>>>> biosql >>>>>>> To: Song Haili >>>>>>> Cc: florian.mittag at uni-tuebingen.de, biosql-l at lists.open-bio.org >>>>>>> >>>>>>>> Song: GO.defs is not in OBO format. Where did you find that you >>>>>>>> need >>>>>>>> it when you load .obo formatted files? You don't need the -- >>>>>>>> fmtargs >>>>>>>> argument for .obo files other than if you want to specify the >>>>>>>> ontology >>>>>>>> name. >>>>>>>> >>>>>>>> -hilmar >>>>>>>> >>>>>>>> On Jul 21, 2009, at 11:32 AM, Song Haili wrote: >>>>>>>>> Hello All, >>>>>>>>> The previous error was solved by the help of Florian. Florian, >>>>>>>> >>>>>>>> Thank >>>>>>>> >>>>>>>>> you very much. >>>>>>>>> But I got another error using the way Florian suggested. I >>>>>>>> >>>>>>>> thought >>>>>>>> >>>>>>>>> it was because parameter --fmtargs was not specified. So I >>>>>>>> >>>>>>>> tried to >>>>>>>> >>>>>>>>> include it with the value "-defs_file, GO.defs", but it didn't >>>>>>>> >>>>>>>> work. >>>>>>>> >>>>>>>>> I think maybe GO.defs is not the right file. Is it? But >>>>>>>> >>>>>>>> how or >>>>>>>> >>>>>>>>> where to get the right file if it is. Or any other ideas about >>>>>>>> >>>>>>>> how >>>>>>>> >>>>>>>>> to solve this error? Thank you very much in advance. >>>>>>>>> command: >>>>>>>>> perl load_ontology.pl --driver Pg --host pg-server --dbname >>>>>>>> >>>>>>>> sifter >>>>>>>> >>>>>>>>> --dbuser sifter --dbpass password --namespace "Gene >>>>>> Ontology" - >>>>>>>> >>>>>>>> - >>>>>>>> >>>>>>>>> format obo gene_ontology.obo --fmtargs "-defs_file, >>>>>> GO.defs" -- >>>>>>>>> >>>>>>>>> noobsolete >>>>>>>>> error: >>>>>>>>> ------------- EXCEPTION ------------- >>>>>>>>> MSG: OBO File Format Error - >>>>>>>>> Cannot find tag format-version and/ default-namespace . These >>>>>>>> >>>>>>>> are >>>>>>>> >>>>>>>>> required header. >>>>>>>>> >>>>>>>>> STACK Bio::OntologyIO::obo::_header >>>>>>>> >>>>>>>> /opt/share/local/users/haili/ >>>>>>>> >>>>>>>>> bioperl-live/Bio/OntologyIO/obo.pm:518 >>>>>>>>> STACK Bio::OntologyIO::obo::parse >>>>>>>> >>>>>>>> /opt/share/local/users/haili/ >>>>>>>> >>>>>>>>> bioperl-live/Bio/OntologyIO/obo.pm:209 >>>>>>>>> STACK Bio::OntologyIO::obo::next_ontology >>>>>>>> >>>>>>>> /opt/share/local/users/ >>>>>>>> >>>>>>>>> haili/bioperl-live/Bio/OntologyIO/obo.pm:342 >>>>>>>>> STACK toplevel load_ontology.pl:604 >>>>>>>>> ------------------------------------- >>>>>>>>> >>>>>>>>> ----- Original Message ----- >>>>>>>>> From: Florian Mittag >>>>>>>>> Date: Tuesday, July 21, 2009 14:41 >>>>>>>>> Subject: Re: [BioSQL-l] Error when loading Gene Ontology >>>>>> to biosql >>>>>>>>> To: biosql-l at lists.open-bio.org >>>>>>>>> >>>>>>>>>> Hi! >>>>>>>>>> >>>>>>>>>> AFAIK the goflat format is deprecated. Use the .obo files and >>>>>>>>>> format instead, >>>>>>>>>> that should work. >>>>>>>>>> >>>>>>>>>> perl load_ontology.pl --driver Pg --host pg-server -- >>>>>> dbname sifter >>>>>>>>>> --dbuser sifter --dbpass password --namespace "Gene >>>>>>>> >>>>>>>> Ontology" -- >>>>>>>> >>>>>>>>>> format obo >>>>>>>>>> >>>>>>>> >>>>>>>> gene_ontology.1_2.obo>> --noobsolete >>>>>>>> >>>>>>>>>> On Tuesday 21 July 2009 12:11, Song Haili wrote: >>>>>>>>>>> Dear all, >>>>>>>>>>> I am using perl-5.10.0, BioPerl-1.6.0, and bioperl-db >>>>>>>>>>> obtaind >>>>>>>>>> >>>>>>>>>> by using CPAN >>>>>>>>>> >>>>>>>>>>> a few days before. Until now, I can load taxonomy and >>>>>>>>>>> sequence >>>>>>>>>> >>>>>>>>>> data into >>>>>>>>>> >>>>>>>>>>> database successfully. However, I got the following error >>>>>>>>>> >>>>>>>>>> message when >>>>>>>>>> >>>>>>>>>>> trying to load Gene Ontology data into biosql database. Any >>>>>>>>>> >>>>>>>>>> help will be >>>>>>>>>> >>>>>>>>>>> appreciated. Jane >>>>>>>>>>> >>>>>>>>>>> command used: >>>>>>>>>>> perl load_ontology.pl --driver Pg --host pg-server --dbname >>>>>>>>>> >>>>>>>>>> sifter -dbuser >>>>>>>>>> >>>>>>>>>>> sifter --dbpass password ??namespace "Gene Ontology" -- >>>>>>>> >>>>>>>> format >>>>>>>> >>>>>>>>>>> goflat >>>>>>>>>>> component.ontology process.ontology function.ontology -- >>>>>> fmtargs> > >>> "-defs_file, GO.defs" --noobsolete >>>>>>>>>>> >>>>>>>>>>> error: >>>>>>>>>>> ------------- EXCEPTION ------------- >>>>>>>>>>> MSG: Could not open ??namespace: No such file or >>>>>>>>>>> directory >>>>>>>>>>> STACK Bio::Root::IO::_initialize_io >>>>>>>>>>> /opt/share/local/users/haili/bioperl- >>>>>> live/Bio/Root/IO.pm:323 STACK >>>>>>>>>>> Bio::OntologyIO::dagflat::parse >>>>>>>>>>> /opt/share/local/users/haili/bioperl- >>>>>>>>>> >>>>>>>>>> live/Bio/OntologyIO/dagflat.pm:277> STACK >>>>>>>>>> Bio::OntologyIO::dagflat::next_ontology> >>>>>>>>>> /opt/share/local/users/haili/bioperl- >>>>>>>> >>>>>>>> live/Bio/OntologyIO/dagflat.pm: >>>>>>>>>> 330 >>>>>>>>>> >>>>>>>>>>> STACK toplevel load_ontology.pl:604 >>>>>>>>>>> ------------------------------------- >>>>>>>>>> >>>>>>>>>> _______________________________________________ >>>>>>>>>> BioSQL-l mailing list >>>>>>>>>> BioSQL-l at lists.open-bio.org >>>>>>>>>> http://lists.open-bio.org/mailman/listinfo/biosql-l >>>>>>>>> >>>>>>>>> _______________________________________________ >>>>>>>>> BioSQL-l mailing list >>>>>>>>> BioSQL-l at lists.open-bio.org >>>>>>>>> http://lists.open-bio.org/mailman/listinfo/biosql-l >>>>>>>> >>>>>>>> -- >>>>>>>> =========================================================== >>>>>>>> >>>>>>>> : Hilmar Lapp -:- Durham, NC -:- hlapp >>>>>>>> >>>>>>>> at gmx dot net : >>>>>>>> =========================================================== >>>>> >>>>> _______________________________________________ >>>>> BioSQL-l mailing list >>>>> BioSQL-l at lists.open-bio.org >>>>> http://lists.open-bio.org/mailman/listinfo/biosql-l >>>> >>>> >>>> _______________________________________________ >>>> BioSQL-l mailing list >>>> BioSQL-l at lists.open-bio.org >>>> http://lists.open-bio.org/mailman/listinfo/biosql-l >>> >>> -- >>> =========================================================== >>> : Hilmar Lapp -:- Durham, NC -:- hlapp at gmx dot net : >>> =========================================================== >>> >>> >>> >> >> >> _______________________________________________ >> BioSQL-l mailing list >> BioSQL-l at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/biosql-l > > -- > =========================================================== > : Hilmar Lapp -:- Durham, NC -:- hlapp at gmx dot net : > =========================================================== > > > > > _______________________________________________ > BioSQL-l mailing list > BioSQL-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/biosql-l From pmr at ebi.ac.uk Mon Jul 27 08:55:43 2009 From: pmr at ebi.ac.uk (Peter Rice) Date: Mon, 27 Jul 2009 09:55:43 +0100 Subject: [BioSQL-l] Open-bio cross-project issues In-Reply-To: <320fb6e00907240632h53600e73s63590a8deb4e8ffe@mail.gmail.com> References: <320fb6e00907240632h53600e73s63590a8deb4e8ffe@mail.gmail.com> Message-ID: <4A6D6B8F.9060108@ebi.ac.uk> Peter C. wrote (to bioperl-l, biopython-l, emboss-dev): > Hi all, > > Peter Rice kindly said he will look into an OBF cross project mailing > list, but in the meantime this has been cross posted to the Biopython, > BioPerl, and EMBOSS development lists. There is a list already for this purpose - open-bio-l I think we will also need a cross-project wiki space on the OBF site. Is there something already used by other projects or should we set something up? I am cross-posting this to other OBF project lists to encourage developers interested in combining efforts to address common problems. This started with FASTQ short read formats, and open-bio-l (a low volume list) has also seen discussion of common test data sets. Please sign up to open-bio-l (if you are not there already) and post suggestions for cross-project issues there. The list subscription page is: http://lists.open-bio.org/mailman/listinfo/open-bio-l Please feel free to forward this to any other projects I may have missed (I picked the obvious addresses from the list.open-bio-org server) regards, Peter Rice From biopython at maubp.freeserve.co.uk Tue Jul 28 11:58:07 2009 From: biopython at maubp.freeserve.co.uk (Peter) Date: Tue, 28 Jul 2009 12:58:07 +0100 Subject: [BioSQL-l] SQLite support In-Reply-To: <320fb6e00907090529t61239952y1c86963f13c1db78@mail.gmail.com> References: <1f864af10812150224y540f1ba6y6b30168102885fcd@mail.gmail.com> <320fb6e00812150243w4b0dc223g40abcf684af1ccf5@mail.gmail.com> <320fb6e00907050324i6d64d3abreb4d0c256bf1bdc4@mail.gmail.com> <320fb6e00907090529t61239952y1c86963f13c1db78@mail.gmail.com> Message-ID: <320fb6e00907280458q56f74ec6iefa420ac1caab8da@mail.gmail.com> On Thu, Jul 9, 2009 at 1:29 PM, Peter wrote: > Hi Hilmar, > > I've filed a BioSQL enhancement bug 2870 for adding an SQLite > schema to BioSQL, and Brad has attached his proposed schema > (converted from that for MySQL) to the bug: > > http://bugzilla.open-bio.org/show_bug.cgi?id=2870 > > Could you take a look at this please? If you are happy with it, we'd like > to have it included in BioSQL v1.0.2 (even if Biopython is initially the > only Bio* project to support it). Have you had a chance to look at this yet Hilmar? Brad is keen to include BioSQL support for SQLite in the next release of Biopython (hopefully within the next week or two), but to do this I'd like your blessing, and for the proposed SQLite BioSQL schema to be added to the BioSQL SVN repository. Thanks, Peter