From: Chetna D. W. <ch...@ug...> - 2003-05-12 16:34:01
|
Hi all, It would be great if I can get insight into following: 1) GenBank I am trying to load data from GenBank with the command ga GUS::Common::Plugin::GBParser --gbRel=133 --file=/home/gusdev/GenBank/TcNCBIgenomic.gb I am getting SQL Error: foreign key violation for tables SRes.DbRef and DoTS.ExternalNASequence. I wanted to know more about how to solve the dependencies in these tables. In order to solve this dependency I might need the InsertDbRefAndDbRefNASequence.pm and thats not functional as of yet. I was wondering if its up and running. 2) GeneOntology We have successfully installed Taxonomy in the gus 3.0 database at this end. I need to know what version and files do I need to put all the 3 ontologies in the database. Also what are the dependencies in loading Gene Ontology in terms of data. 3) Following is the list of tables we have filled in to work with gus: Core.Algorithm Core.AlgorithmInvocation Core.Userinfo Core.Projectinfo Core.Groupinfo Core.Machine SRes.Taxon SRes.Taxonname SRes.GeneticCode I would be very happy to call you guys over phone (if possible) at a good time if you think that the answers are really long and complex to talk over email. Hope to hear from you all, Thanks, Chetna |
From: Deborah F. P. <pi...@pc...> - 2003-05-12 17:39:21
|
Hi Chetna, Is your GBParser.pm updated from CVS? There were several changes made to the plugin for GUS3.0. I used the plugin in it's current form and it performed well. Here is a sample command line I used when testing the plugin: ga GUS::Common::Plugin::GBParser --gbRel 132 --file /ptolemy/share/data/thirdparty/genbank/133/gbrod4.seq.gz --debug --log gbrod5.seq.log --db_rel_id 6547 > & gbrod5.err & Your command is missing the --db_rel_id option which is the external_database_release_id of GenBank release 133 from the ExternalDatabaseRelease table. I just made this a required option so you can update from CVS to get that change. Can you e-mail the actual errors you get? It should not be necessary for the dbref table to be filled to run GBParser. Debbie On Mon, 12 May 2003, Chetna D. Warade wrote: > Hi all, > > It would be great if I can get insight into following: > > 1) GenBank > > I am trying to load data from GenBank with the command > > ga GUS::Common::Plugin::GBParser --gbRel=133 > --file=/home/gusdev/GenBank/TcNCBIgenomic.gb > > I am getting SQL Error: foreign key violation for tables SRes.DbRef and > DoTS.ExternalNASequence. > > I wanted to know more about how to solve the dependencies in these > tables. > > In order to solve this dependency I might need the > InsertDbRefAndDbRefNASequence.pm and thats not functional as of yet. I > was wondering if its up and running. > > 2) GeneOntology > > We have successfully installed Taxonomy in the gus 3.0 database at this > end. I need to know what version and files do I need to put all the 3 > ontologies in the database. Also what are the dependencies in loading > Gene Ontology in terms of data. > > 3) Following is the list of tables we have filled in to work with gus: > Core.Algorithm > Core.AlgorithmInvocation > Core.Userinfo > Core.Projectinfo > Core.Groupinfo > Core.Machine > SRes.Taxon > SRes.Taxonname > SRes.GeneticCode > > I would be very happy to call you guys over phone (if possible) at a > good time if you think that the answers are really long and complex to > talk over email. > > Hope to hear from you all, > Thanks, > Chetna > > > > > ------------------------------------------------------- > Enterprise Linux Forum Conference & Expo, June 4-6, 2003, Santa Clara > The only event dedicated to issues related to Linux enterprise solutions > www.enterpriselinuxforum.com > > _______________________________________________ > Gusdev-gusdev mailing list > Gus...@li... > https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev > |
From: Deborah F. P. <pi...@pc...> - 2003-05-13 03:48:03
|
Sorry, there's no log option. On Mon, 12 May 2003, Deborah F. Pinney wrote: > Hi Chetna, > > Is your GBParser.pm updated from CVS? There were several changes made to > the plugin for GUS3.0. I used the plugin in it's current form and it > performed well. > > Here is a sample command line I used when testing the plugin: > > ga GUS::Common::Plugin::GBParser --gbRel 132 --file > /ptolemy/share/data/thirdparty/genbank/133/gbrod4.seq.gz --debug --log > gbrod5.seq.log --db_rel_id 6547 > & gbrod5.err & > > > Your command is missing the --db_rel_id option which is the > external_database_release_id of GenBank release 133 from the > ExternalDatabaseRelease table. I just made this a required option so you > can update from CVS to get that change. > > Can you e-mail the actual errors you get? It should not be necessary for > the dbref table to be filled to run GBParser. > > Debbie > > > > > > > > On Mon, 12 May 2003, Chetna D. Warade wrote: > > > Hi all, > > > > It would be great if I can get insight into following: > > > > 1) GenBank > > > > I am trying to load data from GenBank with the command > > > > ga GUS::Common::Plugin::GBParser --gbRel=133 > > --file=/home/gusdev/GenBank/TcNCBIgenomic.gb > > > > I am getting SQL Error: foreign key violation for tables SRes.DbRef and > > DoTS.ExternalNASequence. > > > > I wanted to know more about how to solve the dependencies in these > > tables. > > > > In order to solve this dependency I might need the > > InsertDbRefAndDbRefNASequence.pm and thats not functional as of yet. I > > was wondering if its up and running. > > > > 2) GeneOntology > > > > We have successfully installed Taxonomy in the gus 3.0 database at this > > end. I need to know what version and files do I need to put all the 3 > > ontologies in the database. Also what are the dependencies in loading > > Gene Ontology in terms of data. > > > > 3) Following is the list of tables we have filled in to work with gus: > > Core.Algorithm > > Core.AlgorithmInvocation > > Core.Userinfo > > Core.Projectinfo > > Core.Groupinfo > > Core.Machine > > SRes.Taxon > > SRes.Taxonname > > SRes.GeneticCode > > > > I would be very happy to call you guys over phone (if possible) at a > > good time if you think that the answers are really long and complex to > > talk over email. > > > > Hope to hear from you all, > > Thanks, > > Chetna > > > > > > > > > > ------------------------------------------------------- > > Enterprise Linux Forum Conference & Expo, June 4-6, 2003, Santa Clara > > The only event dedicated to issues related to Linux enterprise solutions > > www.enterpriselinuxforum.com > > > > _______________________________________________ > > Gusdev-gusdev mailing list > > Gus...@li... > > https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev > > > > > > ------------------------------------------------------- > Enterprise Linux Forum Conference & Expo, June 4-6, 2003, Santa Clara > The only event dedicated to issues related to Linux enterprise solutions > www.enterpriselinuxforum.com > > _______________________________________________ > Gusdev-gusdev mailing list > Gus...@li... > https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev > |
From: MICHAEL L. <lu...@cs...> - 2003-05-13 14:40:26
|
Hello-- My name is Michael, and I will be working here in the Kissinger lab over the summer on the GUS project. In regards to the following command: ga GUS::Common::Plugin::GBParser --gbRel 132 --file /ptolemy/share/data/thirdparty/genbank/133/gbrod4.seq.gz --debug --log gbrod5.seq.log --db_rel_id 6547 > & gbrod5.err & What does the number 6547 refer to? I downloaded an gbrod4 file from genbank and looked for this number, but could not find it. From the following post: > Your command is missing the --db_rel_id option which is the > external_database_release_id of GenBank release 133 from the > ExternalDatabaseRelease table. I just made this a required option so you > can update from CVS to get that change. I would assume it to be the same as gbRel. Any help would be much appreciated... Michael Luchtan http://www.cs.uga.edu/~luchtan On Mon, 12 May 2003, Deborah F. Pinney wrote: > Hi Chetna, > > Is your GBParser.pm updated from CVS? There were several changes made to > the plugin for GUS3.0. I used the plugin in it's current form and it > performed well. > > Here is a sample command line I used when testing the plugin: > > ga GUS::Common::Plugin::GBParser --gbRel 132 --file > /ptolemy/share/data/thirdparty/genbank/133/gbrod4.seq.gz --debug --log > gbrod5.seq.log --db_rel_id 6547 > & gbrod5.err & > > > Your command is missing the --db_rel_id option which is the > external_database_release_id of GenBank release 133 from the > ExternalDatabaseRelease table. I just made this a required option so you > can update from CVS to get that change. > > Can you e-mail the actual errors you get? It should not be necessary for > the dbref table to be filled to run GBParser. > > Debbie > > > > > > > > On Mon, 12 May 2003, Chetna D. Warade wrote: > > > Hi all, > > > > It would be great if I can get insight into following: > > > > 1) GenBank > > > > I am trying to load data from GenBank with the command > > > > ga GUS::Common::Plugin::GBParser --gbRel=133 > > --file=/home/gusdev/GenBank/TcNCBIgenomic.gb > > > > I am getting SQL Error: foreign key violation for tables SRes.DbRef and > > DoTS.ExternalNASequence. > > > > I wanted to know more about how to solve the dependencies in these > > tables. > > > > In order to solve this dependency I might need the > > InsertDbRefAndDbRefNASequence.pm and thats not functional as of yet. I > > was wondering if its up and running. > > > > 2) GeneOntology > > > > We have successfully installed Taxonomy in the gus 3.0 database at this > > end. I need to know what version and files do I need to put all the 3 > > ontologies in the database. Also what are the dependencies in loading > > Gene Ontology in terms of data. > > > > 3) Following is the list of tables we have filled in to work with gus: > > Core.Algorithm > > Core.AlgorithmInvocation > > Core.Userinfo > > Core.Projectinfo > > Core.Groupinfo > > Core.Machine > > SRes.Taxon > > SRes.Taxonname > > SRes.GeneticCode > > > > I would be very happy to call you guys over phone (if possible) at a > > good time if you think that the answers are really long and complex to > > talk over email. > > > > Hope to hear from you all, > > Thanks, > > Chetna > > > > > > > > > > ------------------------------------------------------- > > Enterprise Linux Forum Conference & Expo, June 4-6, 2003, Santa Clara > > The only event dedicated to issues related to Linux enterprise solutions > > www.enterpriselinuxforum.com > > > > _______________________________________________ > > Gusdev-gusdev mailing list > > Gus...@li... > > https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev > > > > > > ------------------------------------------------------- > Enterprise Linux Forum Conference & Expo, June 4-6, 2003, Santa Clara > The only event dedicated to issues related to Linux enterprise solutions > www.enterpriselinuxforum.com > > _______________________________________________ > Gusdev-gusdev mailing list > Gus...@li... > https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev > |
From: Steve F. <st...@pc...> - 2003-05-13 01:37:54
|
chetna- I think Dave Barkan can probably answer your question about loading GO ontologies. Dave... can you answer Chetna's question 2) below? steve Chetna D. Warade wrote: >Hi all, > >It would be great if I can get insight into following: > >1) GenBank > >I am trying to load data from GenBank with the command > >ga GUS::Common::Plugin::GBParser --gbRel=133 >--file=/home/gusdev/GenBank/TcNCBIgenomic.gb > >I am getting SQL Error: foreign key violation for tables SRes.DbRef and >DoTS.ExternalNASequence. > >I wanted to know more about how to solve the dependencies in these >tables. > >In order to solve this dependency I might need the >InsertDbRefAndDbRefNASequence.pm and thats not functional as of yet. I >was wondering if its up and running. > >2) GeneOntology > >We have successfully installed Taxonomy in the gus 3.0 database at this >end. I need to know what version and files do I need to put all the 3 >ontologies in the database. Also what are the dependencies in loading >Gene Ontology in terms of data. > >3) Following is the list of tables we have filled in to work with gus: >Core.Algorithm >Core.AlgorithmInvocation >Core.Userinfo >Core.Projectinfo >Core.Groupinfo >Core.Machine >SRes.Taxon >SRes.Taxonname >SRes.GeneticCode > >I would be very happy to call you guys over phone (if possible) at a >good time if you think that the answers are really long and complex to >talk over email. > >Hope to hear from you all, >Thanks, >Chetna > > > > >------------------------------------------------------- >Enterprise Linux Forum Conference & Expo, June 4-6, 2003, Santa Clara >The only event dedicated to issues related to Linux enterprise solutions >www.enterpriselinuxforum.com > >_______________________________________________ >Gusdev-gusdev mailing list >Gus...@li... >https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev > > |
From: Dave B. <db...@pc...> - 2003-05-13 15:10:34
|
Hi Chetna and folks-- > >2) GeneOntology > > > >We have successfully installed Taxonomy in the gus 3.0 database at this > >end. I need to know what version and files do I need to put all the 3 > >ontologies in the database. Also what are the dependencies in loading > >Gene Ontology in terms of data. The three ontology files are located at ftp://ftp.geneontology.org/pub/go/ontology/ They are named process.ontology, component.ontology, and function.ontology. Whatever is at that ftp site should be the latest version. Use --createRelease option when running the plugin to automatically generate an External Database Release Id (in SRes.ExternalDatabaseRelease) for these releases of the ontology branches. Note that there must be entries in SRes.ExternalDatabase with names "GO Function", "GO Component", and "GO Process." (This could definitely be done better, avoiding hardcoding names like this which are set in our version of GUS. Let me know if you have trouble with this and I will change it). Specify the directory of the files with the --file_path option. To load a specific branch, specify the corresponding file with the --flat_file option; to load all three just leave this blank. You need to have two entries in SRes.GORelationshipType populated; they correspond to the two different types of relationships a GO Term can have with its child in the GO hierarchy, "isa" and "partof." (These should be set in the 'name' attribute of the GoRelationshipType table and have corresponding ids). More information on this representation is available at http://www.geneontology.org/doc/GO.doc.html#datarep The other command lines should be self-explanatory but again let me know if you have any trouble. Dave |
From: Dave B. <db...@pc...> - 2003-05-13 15:14:41
|
Just in case it's not clear, the name of the plugin to load all of this is LoadGoOntology; it is located in the GUS/GOPredict component. dave On Tue, 13 May 2003, Dave Barkan wrote: > Hi Chetna and folks-- > > > >2) GeneOntology > > > > > >We have successfully installed Taxonomy in the gus 3.0 database at this > > >end. I need to know what version and files do I need to put all the 3 > > >ontologies in the database. Also what are the dependencies in loading > > >Gene Ontology in terms of data. > > The three ontology files are located at > > ftp://ftp.geneontology.org/pub/go/ontology/ > > They are named process.ontology, component.ontology, and > function.ontology. > > Whatever is at that ftp site should be the latest version. Use > --createRelease > option when running the plugin to automatically generate an External > Database Release Id (in SRes.ExternalDatabaseRelease) for these releases > of the ontology branches. Note that there must be entries in > SRes.ExternalDatabase with names "GO Function", "GO Component", and > "GO Process." (This could definitely be done better, avoiding hardcoding > names like this which are set in our version of GUS. Let me know if you > have trouble with this and I will change it). > > Specify the directory of the files with the --file_path option. To load a > specific branch, specify the corresponding file with the --flat_file > option; to load all three just leave this blank. > > You need to have two entries in SRes.GORelationshipType populated; they > correspond to the two different types of relationships a GO Term can have > with its child in the GO hierarchy, "isa" and "partof." (These should be > set in the 'name' attribute of the GoRelationshipType table and have > corresponding ids). More information on this representation is available > at > > http://www.geneontology.org/doc/GO.doc.html#datarep > > The other command lines should be self-explanatory but again let me know > if you have any trouble. > > Dave > > > > > > > ------------------------------------------------------- > Enterprise Linux Forum Conference & Expo, June 4-6, 2003, Santa Clara > The only event dedicated to issues related to Linux enterprise solutions > www.enterpriselinuxforum.com > > _______________________________________________ > Gusdev-gusdev mailing list > Gus...@li... > https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev > |