From daniel.lang at biologie.uni-freiburg.de Mon Apr 5 13:05:33 2004 From: daniel.lang at biologie.uni-freiburg.de (Daniel Lang) Date: Mon Apr 5 13:11:33 2004 Subject: [BioSQL-l] redundant qualifier values & Bio::SeqFeature::SimilarityPair Message-ID: <407191DD.4090504@biologie.uni-freiburg.de> Hi, I am trying to populate a biosql database (postgres) with "home-made" RichSeqs objects. On first sight, I looks like everything is OK, but when I retrieve the sequences and write them e.g. in genbank format, there are some sequences, where the qualifiers are doubled or even tripled: ... FEATURES Location/Qualifiers source 1..551 /tissue_type="mixture of chloronemata, caulonemata and malformed buds" /tissue_type="mixture of chloronemata, caulonemata and malformed buds" /tissue_type="mixture of chloronemata, caulonemata and malformed buds" /clone_lib="normalized full length cDNA library, chloronemata, caulonemata and malformed buds" /clone_lib="normalized full length cDNA library, chloronemata, caulonemata and malformed buds" /clone_lib="normalized full length cDNA library, chloronemata, caulonemata and malformed buds" /sub_species="patens" /sub_species="patens" /sub_species="patens" /clone="pphb37e20" /clone="pphb37e20" /clone="pphb37e20" /organism="Physcomitrella patens subsp. patens" /organism="Physcomitrella patens subsp. patens" /organism="Physcomitrella patens subsp. patens" /mol_type="mRNA" /mol_type="mRNA" /mol_type="mRNA" /db_xref="taxon:145481" /db_xref="taxon:145481" /db_xref="taxon:145481" ATAIL 1..28 /ACTION="annot" /ACTION="annot" /ACTION="annot" /ORIENT="REVERSE" /ORIENT="REVERSE" /ORIENT="REVERSE" ... Of course, the underlying data is non-redundant... Correspondingly, these qualifier_values are stored redundantly in the seqfeature_qualifier_value table with a different rank: seqfeature_id | term_id | rank | value ---------------+---------+------+-------------------------------------------------------------------------------------------------------------------- 1 | 5 | 1 | pphb37e20 1 | 5 | 2 | pphb37e20 1 | 5 | 3 | pphb37e20 1 | 6 | 1 | normalized full length cDNA library, chloronemata, caulonemata and malformed buds 1 | 6 | 2 | normalized full length cDNA library, chloronemata, caulonemata and malformed buds 1 | 6 | 3 | normalized full length cDNA library, chloronemata, caulonemata and malformed buds But when I write the constructed object in genbank or embl format in the first place, the qualifiers are correct?! Bio::Annotation::Reference s are also affected... Additionally not all data I intend to insert is integrated... Here a code snipplet: if($seq->isa("Bio::AnnotatableI")) { flatten_annotations($seq->annotation); } $adp= $db->get_object_adaptor($seq); my $pseq = $db->create_persistent($seq) unless $seq->isa("Bio::DB::PersistentObjectI"); $pseq->namespace($namespace); $pseq->store(); $adp->commit(); Any ideas what is happening? Additionally I?d like to know if there is an adapter or a way to store Bio::SeqFeature::SimilarityPair s in the schema yet? Thanks in advance, Daniel -- Daniel Lang University of Freiburg, Plant Biotechnology Sonnenstr. 5, D-79104 Freiburg phone: +49 761 203 6988 homepage: http://www.plant-biotech.net/ e-mail: daniel.lang@biologie.uni-freiburg.de ################################################# >REALITY.SYS corrupted: Reboot universe? (Y/N/A) ################################################# Join MOSS 2004 in Freiburg, Germany from September 12th - 15th: registration and information @ http://www.plant-biotech.net/moss2004 From hlapp at gnf.org Mon Apr 5 14:01:14 2004 From: hlapp at gnf.org (Hilmar Lapp) Date: Mon Apr 5 14:06:14 2004 Subject: [BioSQL-l] redundant qualifier values & Bio::SeqFeature::SimilarityPair In-Reply-To: <407191DD.4090504@biologie.uni-freiburg.de> Message-ID: <3A955D4A-872B-11D8-B89F-000A959EB4C4@gnf.org> Without any investigation into when this is actually happening, what I can tell you is that this sort of duplication is not supposed on happen when you create (insert) a fresh sequence into the database. Try to check whether this is what is happening in your situation (I doubt it). The situation when this would happen naturally is when you update a previously looked up sequence after you merged it with new annotation and didn't carefully reconcile the new annotation with the existing one to avoid any duplication. This reconciliation step is non-trivial, as it requires you to make some decisions (is an annotation that is on the existing but not on the new sequence record stale [to be removed] or non-public [to be kept]), and to find a good measure of when two annotations are identical. I believe the merge function examples that come with bioperl-db will attempt to reconcile annotations for bioentries, but probably not for their features (BTW updating features themselves suffers from the same problem). I'd have to check, but that's my guess. -hilmar On Monday, April 5, 2004, at 10:05 AM, Daniel Lang wrote: > Hi, > I am trying to populate a biosql database (postgres) with "home-made" > RichSeqs objects. On first sight, I looks like everything is OK, but > when I retrieve the sequences and write them e.g. in genbank format, > there are some sequences, where the qualifiers are doubled or even > tripled: > ... > FEATURES Location/Qualifiers > source 1..551 > /tissue_type="mixture of chloronemata, > caulonemata and > malformed buds" > /tissue_type="mixture of chloronemata, > caulonemata and > malformed buds" > /tissue_type="mixture of chloronemata, > caulonemata and > malformed buds" > /clone_lib="normalized full length cDNA library, > chloronemata, caulonemata and malformed buds" > /clone_lib="normalized full length cDNA library, > chloronemata, caulonemata and malformed buds" > /clone_lib="normalized full length cDNA library, > chloronemata, caulonemata and malformed buds" > /sub_species="patens" > /sub_species="patens" > /sub_species="patens" > /clone="pphb37e20" > /clone="pphb37e20" > /clone="pphb37e20" > /organism="Physcomitrella patens subsp. patens" > /organism="Physcomitrella patens subsp. patens" > /organism="Physcomitrella patens subsp. patens" > /mol_type="mRNA" > /mol_type="mRNA" > /mol_type="mRNA" > /db_xref="taxon:145481" > /db_xref="taxon:145481" > /db_xref="taxon:145481" > ATAIL 1..28 > /ACTION="annot" > /ACTION="annot" > /ACTION="annot" > /ORIENT="REVERSE" > /ORIENT="REVERSE" > /ORIENT="REVERSE" > ... > > Of course, the underlying data is non-redundant... > Correspondingly, these qualifier_values are stored redundantly in the > seqfeature_qualifier_value table with a different rank: > > seqfeature_id | term_id | rank | value > ---------------+---------+------ > +---------------------------------------------------------------------- > ---------------------------------------------- > 1 | 5 | 1 | pphb37e20 > 1 | 5 | 2 | pphb37e20 > 1 | 5 | 3 | pphb37e20 > 1 | 6 | 1 | normalized full length cDNA library, > chloronemata, caulonemata and malformed buds > 1 | 6 | 2 | normalized full length cDNA library, > chloronemata, caulonemata and malformed buds > 1 | 6 | 3 | normalized full length cDNA library, > chloronemata, caulonemata and malformed buds > > > But when I write the constructed object in genbank or embl format in > the first place, the qualifiers are correct?! > Bio::Annotation::Reference s are also affected... > > Additionally not all data I intend to insert is integrated... > > Here a code snipplet: > if($seq->isa("Bio::AnnotatableI")) { > flatten_annotations($seq->annotation); > } > $adp= $db->get_object_adaptor($seq); > > my $pseq = $db->create_persistent($seq) unless > $seq->isa("Bio::DB::PersistentObjectI"); > $pseq->namespace($namespace); > $pseq->store(); > $adp->commit(); > > Any ideas what is happening? > > Additionally I?d like to know if there is an adapter or a way to store > Bio::SeqFeature::SimilarityPair s in the schema yet? > > Thanks in advance, > Daniel > > -- > > Daniel Lang > University of Freiburg, Plant Biotechnology > Sonnenstr. 5, D-79104 Freiburg > phone: +49 761 203 6988 > homepage: http://www.plant-biotech.net/ > e-mail: daniel.lang@biologie.uni-freiburg.de > > ################################################# > >REALITY.SYS corrupted: Reboot universe? (Y/N/A) > ################################################# > > Join MOSS 2004 in Freiburg, Germany from September 12th - 15th: > registration and information @ http://www.plant-biotech.net/moss2004 > > > > > _______________________________________________ > BioSQL-l mailing list > BioSQL-l@open-bio.org > http://open-bio.org/mailman/listinfo/biosql-l > -- ------------------------------------------------------------- Hilmar Lapp email: lapp at gnf.org GNF, San Diego, Ca. 92121 phone: +1-858-812-1757 ------------------------------------------------------------- From daniel.lang at biologie.uni-freiburg.de Tue Apr 6 06:05:11 2004 From: daniel.lang at biologie.uni-freiburg.de (Daniel Lang) Date: Tue Apr 6 06:11:17 2004 Subject: [BioSQL-l] redundant qualifier values & Bio::SeqFeature::SimilarityPair In-Reply-To: <3A955D4A-872B-11D8-B89F-000A959EB4C4@gnf.org> References: <3A955D4A-872B-11D8-B89F-000A959EB4C4@gnf.org> Message-ID: <407280D7.8000404@biologie.uni-freiburg.de> Thanks, Hilmar for the fast answer... My error! You were perfectly right! But my second questions still remains: >> Additionally I?d like to know if there is an adapter or a way to >> store Bio::SeqFeature::SimilarityPair s in the schema yet? Daniel:) Hilmar Lapp wrote: > Without any investigation into when this is actually happening, what I > can tell you is that this sort of duplication is not supposed on happen > when you create (insert) a fresh sequence into the database. Try to > check whether this is what is happening in your situation (I doubt it). > > The situation when this would happen naturally is when you update a > previously looked up sequence after you merged it with new annotation > and didn't carefully reconcile the new annotation with the existing one > to avoid any duplication. This reconciliation step is non-trivial, as > it requires you to make some decisions (is an annotation that is on the > existing but not on the new sequence record stale [to be removed] or > non-public [to be kept]), and to find a good measure of when two > annotations are identical. > > I believe the merge function examples that come with bioperl-db will > attempt to reconcile annotations for bioentries, but probably not for > their features (BTW updating features themselves suffers from the same > problem). I'd have to check, but that's my guess. > > -hilmar -- Daniel Lang University of Freiburg, Plant Biotechnology Sonnenstr. 5, D-79104 Freiburg phone: +49 761 203 6988 homepage: http://www.plant-biotech.net/ e-mail: daniel.lang@biologie.uni-freiburg.de ################################################# >REALITY.SYS corrupted: Reboot universe? (Y/N/A) ################################################# Join MOSS 2004 in Freiburg, Germany from September 12th - 15th: registration and information @ http://www.plant-biotech.net/moss2004 From hlapp at gnf.org Tue Apr 6 13:05:53 2004 From: hlapp at gnf.org (Hilmar Lapp) Date: Tue Apr 6 13:10:50 2004 Subject: [BioSQL-l] redundant qualifier values & Bio::SeqFeature::SimilarityPair In-Reply-To: <407280D7.8000404@biologie.uni-freiburg.de> Message-ID: On Tuesday, April 6, 2004, at 03:05 AM, Daniel Lang wrote: > But my second questions still remains: > >> Additionally I?d like to know if there is an adapter or a way to > >> store Bio::SeqFeature::SimilarityPair s in the schema yet? > Sorry for missing that. No, there isn't. They'll be stored as features (SeqFeatureI), as that is what they also are, but all the similarity pair information will be lost. You're more than welcome to write the adaptor :-) -hilmar -- ------------------------------------------------------------- Hilmar Lapp email: lapp at gnf.org GNF, San Diego, Ca. 92121 phone: +1-858-812-1757 ------------------------------------------------------------- From daniel.lang at biologie.uni-freiburg.de Thu Apr 8 08:37:39 2004 From: daniel.lang at biologie.uni-freiburg.de (Daniel Lang) Date: Thu Apr 8 08:43:55 2004 Subject: [BioSQL-l] Bio::SeqFeature::Generic score & source tags in Biosql Message-ID: <40754793.7000102@biologie.uni-freiburg.de> Hi, I?m wondering why the score & source tags of the GenericFeature objects I insert attached to RichSeqs into a biosql db are missing in seqfeature_qualifier_value? Are they somewhere else? I?ve set them using Bio::SeqFeature::Generic::score() & source()... Other tags I added using add_tag_value method are present... Do those to have special meaning? - Because source is also missing and score becomes /note="score..." when writing the Objects directly to genbank format... Thanks in advance, Daniel -- Daniel Lang University of Freiburg, Plant Biotechnology Sonnenstr. 5, D-79104 Freiburg phone: +49 761 203 6988 homepage: http://www.plant-biotech.net/ e-mail: daniel.lang@biologie.uni-freiburg.de ################################################# >REALITY.SYS corrupted: Reboot universe? (Y/N/A) ################################################# Join MOSS 2004 in Freiburg, Germany from September 12th - 15th: registration and information @ http://www.plant-biotech.net/moss2004 From mbatesalann at netscape.net Sun Apr 11 19:11:23 2004 From: mbatesalann at netscape.net (mbatesalann@netscape.net) Date: Sun Apr 11 19:16:03 2004 Subject: [BioSQL-l] REPLY BACK Message-ID: Dear Friend, As you read this, I don't want you to feel sorry for me, because, I believe everyone will die someday. 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If you set a value then it should be present as a foreign key to the term table. score I thought gets translated into a tag/value pair, and would hence end up as value in the seqfeature_qualifier_value table. I just realized that this is apparently not the case. The problem is that score() is actually not defined in Bio::SeqFeatureI. I'm not sure what the best approach here is; maybe adding the translation to to Bio::SeqFeature::AnnotationAdaptor would be the best way to implement this. -hilmar On Thursday, April 8, 2004, at 05:37 AM, Daniel Lang wrote: > Hi, > I?m wondering why the score & source tags of the GenericFeature > objects I insert attached to RichSeqs into a biosql db are missing in > seqfeature_qualifier_value? > Are they somewhere else? > I?ve set them using Bio::SeqFeature::Generic::score() & source()... > Other tags I added using add_tag_value method are present... > > Do those to have special meaning? - Because source is also missing and > score becomes /note="score..." when writing the Objects directly to > genbank format... > > Thanks in advance, > Daniel > > -- > > Daniel Lang > University of Freiburg, Plant Biotechnology > Sonnenstr. 5, D-79104 Freiburg > phone: +49 761 203 6988 > homepage: http://www.plant-biotech.net/ > e-mail: daniel.lang@biologie.uni-freiburg.de > > ################################################# > >REALITY.SYS corrupted: Reboot universe? 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April 2004) and got stuck with the follwing message: Loading ontology Gene Ontology: ... terms Could not store GO:0001529 (elastin): ------------- EXCEPTION ------------- MSG: create: object (Bio::Ontology::GOterm) failed to insert or to be found by unique key STACK Bio::DB::BioSQL::BasePersistenceAdaptor::create /usr/lib/perl5/site_perl/5.8.0/Bio/DB/BioSQL/BasePersistenceAdaptor.pm:207 STACK Bio::DB::BioSQL::BasePersistenceAdaptor::store /usr/lib/perl5/site_perl/5.8.0/Bio/DB/BioSQL/BasePersistenceAdaptor.pm:253 STACK Bio::DB::Persistent::PersistentObject::store /usr/lib/perl5/site_perl/5.8.0/Bio/DB/Persistent/PersistentObject.pm:270 STACK (eval) load_ontology.pl:489 STACK toplevel load_ontology.pl:471 -------------------------------------- If i try to override the problems with --safe I get about 150 Errors.(btw. Item GO:0001529 is not in my Biosql DB). We also tried to use the latest bioperl Version (1.4.1) and get the same errors. Now I wonder what is wrong with my Bioperl Installtion. Many thanks in advance, Raphael From hlapp at gnf.org Wed Apr 28 13:28:30 2004 From: hlapp at gnf.org (Hilmar Lapp) Date: Wed Apr 28 13:32:53 2004 Subject: [BioSQL-l] load_ontology.pl Problem In-Reply-To: <408E5567.2010102@informatik.hu-berlin.de> Message-ID: <775CBC4B-9939-11D8-BBE5-000A959EB4C4@gnf.org> Elastin has probably been obsoleted. My guess is that you don't have a term with ID GO:0001529, but you do have a term with name 'elastin' in the Gene Ontology, which is probably not obsoleted. Obsolete terms need to be dealt with in some way in biosql, and you need to choose which way. Check out the load_ontology.pl POD where it talks about the options for obsolete terms. Also, depending on whether you want obsolete terms in the database (there are reasons for possibly wanting this, if that sounds strange) you may need to expand the unique key constraint on the term table to include the is_obsolete column. Check out the schema DDL, there is a commented out inclusion of that column documented. BTW for GO upload to work properly you need to use the latest cvs snapshot from the 1.4 branch. I'm not aware that 1.4.1 has already been released, but maybe I'm confusing this. At least I can't find the release tag. As for bioperl-db, given the stack trace you are not using 0.1, but rather the post-Singapore version. Hth, -hilmar On Tuesday, April 27, 2004, at 05:43 AM, Raphael A. Bauer wrote: > Hi List, > > I encountered a problem parsing the Gene Ontology using Bioperl 1.2.1 > and bioperl-db 0.1 (?). > > The parsing of the Gene Ontology Files into a BioSQL Schema worked > fine many times about 2 Months ago. Today I tried to parse the new GO > Files (26. April 2004) and got stuck with the follwing message: > > > Loading ontology Gene Ontology: > ... terms > Could not store GO:0001529 (elastin): > > ------------- EXCEPTION ------------- > MSG: create: object (Bio::Ontology::GOterm) failed to insert or to be > found by unique key > STACK Bio::DB::BioSQL::BasePersistenceAdaptor::create > /usr/lib/perl5/site_perl/5.8.0/Bio/DB/BioSQL/ > BasePersistenceAdaptor.pm:207 > STACK Bio::DB::BioSQL::BasePersistenceAdaptor::store > /usr/lib/perl5/site_perl/5.8.0/Bio/DB/BioSQL/ > BasePersistenceAdaptor.pm:253 > STACK Bio::DB::Persistent::PersistentObject::store > /usr/lib/perl5/site_perl/5.8.0/Bio/DB/Persistent/ > PersistentObject.pm:270 > STACK (eval) load_ontology.pl:489 > STACK toplevel load_ontology.pl:471 > > -------------------------------------- > > > If i try to override the problems with --safe I get about 150 > Errors.(btw. Item GO:0001529 is not in my Biosql DB). > > We also tried to use the latest bioperl Version (1.4.1) and get the > same errors. > > Now I wonder what is wrong with my Bioperl Installtion. > > > > Many thanks in advance, > > Raphael > > > _______________________________________________ > BioSQL-l mailing list > BioSQL-l@open-bio.org > http://open-bio.org/mailman/listinfo/biosql-l > -- ------------------------------------------------------------- Hilmar Lapp email: lapp at gnf.org GNF, San Diego, Ca. 92121 phone: +1-858-812-1757 ------------------------------------------------------------- From sapphire21fiona at hotmail.com Fri Apr 30 19:58:26 2004 From: sapphire21fiona at hotmail.com (perry) Date: Fri Apr 30 20:02:40 2004 Subject: [BioSQL-l] Forget V1AGRA, there's a new game in town! Message-ID: <1083369506-5709@excite.com> The Biggest New Drug since V1agra! Many times as powerful. C1AL1S has been seen all over TV as of late. So why is it so much better than V1agra? 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