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Taxonomy
by Ben Woodcroft-3
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Hi,
I'm trying to load the NCBI taxonomy into my Chado instance, and I'm unsure as to how to go about it. The only code I can find is in gmod-1.0/load/bin/load_taxonomy.pl, apparently written by Allan Day. It seems to fail, though, with this error message: Loading data into dbxref table ... Loading data into organism table ... Loading data into organism_dbxref table ... Loading data into organism_relationship table ... DBD::Pg::st execute failed: ERROR: relation "organism_relationship" does not exist at load_taxonomy.pl line 132. pg_endcopy cannot be called until a COPY is issued at load_taxonomy.pl line 138. Issuing rollback() for database handle being DESTROY'd without explicit disconnect(). I agree with the compiler, organism_relationship is not a table in the current version of Chado. I could modify the script, but is there an easier way? Thanks, ben -- FYI: My email addresses at unimelb, uq and gmail all redirect to the same place. ------------------------------------------------------------------------- Sponsored by: SourceForge.net Community Choice Awards: VOTE NOW! Studies have shown that voting for your favorite open source project, along with a healthy diet, reduces your potential for chronic lameness and boredom. Vote Now at http://www.sourceforge.net/community/cca08 _______________________________________________ Gmod-schema mailing list Gmod-schema@... https://lists.sourceforge.net/lists/listinfo/gmod-schema |
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Re: Taxonomy
by Hilmar Lapp
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Hi Ben,
organism_relationship has been retired a year ago in an effort to consolidate the organism and the phylogeny models. I suspect that the script you mention has never been updated to reflect that. Would you mind sharing what you are trying to accomplish? -hilmar On Jul 6, 2008, at 11:29 PM, Ben Woodcroft wrote: Hi, -- =========================================================== : Hilmar Lapp -:- Durham, NC -:- hlapp at gmx dot net : =========================================================== ------------------------------------------------------------------------- Sponsored by: SourceForge.net Community Choice Awards: VOTE NOW! Studies have shown that voting for your favorite open source project, along with a healthy diet, reduces your potential for chronic lameness and boredom. Vote Now at http://www.sourceforge.net/community/cca08 _______________________________________________ Gmod-schema mailing list Gmod-schema@... https://lists.sourceforge.net/lists/listinfo/gmod-schema |
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Re: Taxonomy
by Ben Woodcroft-3
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I'm trying to upload the taxonomy so I can classify species on a large scale. Asking questions like 'What are all the scientific names of vertebrates?'
Sorry I can't be too specific - my particular goals are quite hazy in my own mind at the moment even. I just figure this should be something that is canonical, so I thought there might be a solution out there that I was unaware of. Thanks for the quick reply, ben 2008/7/7 Hilmar Lapp <hlapp@...>:
-- FYI: My email addresses at unimelb, uq and gmail all redirect to the same place. ------------------------------------------------------------------------- Sponsored by: SourceForge.net Community Choice Awards: VOTE NOW! Studies have shown that voting for your favorite open source project, along with a healthy diet, reduces your potential for chronic lameness and boredom. Vote Now at http://www.sourceforge.net/community/cca08 _______________________________________________ Gmod-schema mailing list Gmod-schema@... https://lists.sourceforge.net/lists/listinfo/gmod-schema |
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Re: Taxonomy
by Hilmar Lapp
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I was asking because if you don't need a GMOD tool (such as GBrowse, CMap, Apollo, etc) for accomplishing your goal, you might want to look into using BioSQL instead. It should be relatively well supported by Bioruby meanwhile (if I recall correctly that that's your Bio* toolkit of choice), and it comes with a script load_ncbi_taxonomy.pl that does what the name suggests, and as the last step computes the nested set values that you can use for making queries like the one you quote below pretty simple.
-hilmar On Jul 6, 2008, at 11:58 PM, Ben Woodcroft wrote: I'm trying to upload the taxonomy so I can classify species on a large scale. Asking questions like 'What are all the scientific names of vertebrates?' -- =========================================================== : Hilmar Lapp -:- Durham, NC -:- hlapp at gmx dot net : =========================================================== ------------------------------------------------------------------------- Sponsored by: SourceForge.net Community Choice Awards: VOTE NOW! Studies have shown that voting for your favorite open source project, along with a healthy diet, reduces your potential for chronic lameness and boredom. Vote Now at http://www.sourceforge.net/community/cca08 _______________________________________________ Gmod-schema mailing list Gmod-schema@... https://lists.sourceforge.net/lists/listinfo/gmod-schema |
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Re: Taxonomy
by Ben Woodcroft-3
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hmm, yeh bioruby is my thing. Thanks for your thoughts - I'll figure something out.
Thanks, ben 2008/7/7 Hilmar Lapp <hlapp@...>:
-- FYI: My email addresses at unimelb, uq and gmail all redirect to the same place. ------------------------------------------------------------------------- Sponsored by: SourceForge.net Community Choice Awards: VOTE NOW! Studies have shown that voting for your favorite open source project, along with a healthy diet, reduces your potential for chronic lameness and boredom. Vote Now at http://www.sourceforge.net/community/cca08 _______________________________________________ Gmod-schema mailing list Gmod-schema@... https://lists.sourceforge.net/lists/listinfo/gmod-schema |
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Re: Taxonomy
by Chris Mungall
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You could load the .obo or .chadoxml into the cv module. On Jul 7, 2008, at 5:16 AM, Hilmar Lapp wrote: > I was asking because if you don't need a GMOD tool (such as > GBrowse, CMap, Apollo, etc) for accomplishing your goal, you might > want to look into using BioSQL instead. It should be relatively > well supported by Bioruby meanwhile (if I recall correctly that > that's your Bio* toolkit of choice), and it comes with a script > load_ncbi_taxonomy.pl that does what the name suggests, and as the > last step computes the nested set values that you can use for > making queries like the one you quote below pretty simple. > > -hilmar > > On Jul 6, 2008, at 11:58 PM, Ben Woodcroft wrote: > >> I'm trying to upload the taxonomy so I can classify species on a >> large scale. Asking questions like 'What are all the scientific >> names of vertebrates?' >> >> Sorry I can't be too specific - my particular goals are quite hazy >> in my own mind at the moment even. >> >> I just figure this should be something that is canonical, so I >> thought there might be a solution out there that I was unaware of. >> >> Thanks for the quick reply, >> ben >> >> 2008/7/7 Hilmar Lapp <hlapp@...>: >> Hi Ben, >> >> organism_relationship has been retired a year ago in an effort to >> consolidate the organism and the phylogeny models. I suspect that >> the script you mention has never been updated to reflect that. >> >> Would you mind sharing what you are trying to accomplish? >> >> -hilmar >> >> On Jul 6, 2008, at 11:29 PM, Ben Woodcroft wrote: >> >>> Hi, >>> >>> I'm trying to load the NCBI taxonomy into my Chado instance, and >>> I'm unsure as to how to go about it. >>> >>> The only code I can find is in gmod-1.0/load/bin/ >>> load_taxonomy.pl, apparently written by Allan Day. >>> >>> It seems to fail, though, with this error message: >>> Loading data into dbxref table ... >>> Loading data into organism table ... >>> Loading data into organism_dbxref table ... >>> Loading data into organism_relationship table ... >>> DBD::Pg::st execute failed: ERROR: relation >>> "organism_relationship" does not exist at load_taxonomy.pl line 132. >>> pg_endcopy cannot be called until a COPY is issued at >>> load_taxonomy.pl line 138. >>> Issuing rollback() for database handle being DESTROY'd without >>> explicit disconnect(). >>> >>> I agree with the compiler, organism_relationship is not a table >>> in the current version of Chado. I could modify the script, but >>> is there an easier way? >>> >>> Thanks, >>> ben >>> >>> -- >>> FYI: My email addresses at unimelb, uq and gmail all redirect to >>> the same place. >>> -------------------------------------------------------------------- >>> ----- >>> Sponsored by: SourceForge.net Community Choice Awards: VOTE NOW! >>> Studies have shown that voting for your favorite open source >>> project, >>> along with a healthy diet, reduces your potential for chronic >>> lameness >>> and boredom. Vote Now at http://www.sourceforge.net/community/ >>> cca08_______________________________________________ >>> Gmod-schema mailing list >>> Gmod-schema@... >>> https://lists.sourceforge.net/lists/listinfo/gmod-schema >> >> -- >> =========================================================== >> : Hilmar Lapp -:- Durham, NC -:- hlapp at gmx dot net : >> =========================================================== >> >> >> >> >> >> >> -- >> FYI: My email addresses at unimelb, uq and gmail all redirect to >> the same place. >> --------------------------------------------------------------------- >> ---- >> Sponsored by: SourceForge.net Community Choice Awards: VOTE NOW! >> Studies have shown that voting for your favorite open source project, >> along with a healthy diet, reduces your potential for chronic >> lameness >> and boredom. Vote Now at http://www.sourceforge.net/community/ >> cca08_______________________________________________ >> Gmod-schema mailing list >> Gmod-schema@... >> https://lists.sourceforge.net/lists/listinfo/gmod-schema > > -- > =========================================================== > : Hilmar Lapp -:- Durham, NC -:- hlapp at gmx dot net : > =========================================================== > > > > ---------------------------------------------------------------------- > --- > Sponsored by: SourceForge.net Community Choice Awards: VOTE NOW! > Studies have shown that voting for your favorite open source project, > along with a healthy diet, reduces your potential for chronic lameness > and boredom. Vote Now at http://www.sourceforge.net/community/ > cca08_______________________________________________ > Gmod-schema mailing list > Gmod-schema@... > https://lists.sourceforge.net/lists/listinfo/gmod-schema ------------------------------------------------------------------------- Sponsored by: SourceForge.net Community Choice Awards: VOTE NOW! Studies have shown that voting for your favorite open source project, along with a healthy diet, reduces your potential for chronic lameness and boredom. Vote Now at http://www.sourceforge.net/community/cca08 _______________________________________________ Gmod-schema mailing list Gmod-schema@... https://lists.sourceforge.net/lists/listinfo/gmod-schema |
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