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From: Isabelle P. <isa...@sb...> - 2008-12-15 18:28:57
|
> This command will no longer work with the new updates to the plugin
> applied 2 days ago and reflected in the plugin John Brestelli sent to
> Isabelle (also available in the gus svn trunk). The new
> version takes in just one .obo file.
Thanks Elisabetta.
The new plugin works great. There is an minor issue with a very long GO
synonym that required a change in the SRes.GOSynonym table. The problem
might be specific for Postgres, where the SRes.GOSynonym.TEXT column
type is set by default to varchar(255).
This needs to be increased to accommodate the GO synonym to avoid this
error:
DBD::Pg::st execute failed: ERROR: value too long for type character
varying(255)
ERROR:
SQL ERROR!! involving
INSERT INTO SRes.GOSynonym ( external_database_release_id,
source_id, go_term_id, group_write, other_read, group_read,
go_synonym_id, user_read, row_user_id, modification_date, other_write,
row_alg_invocation_id, row_project_id, text, row_group_id, user_write )
VALUES ( ?, null, ?, ?, ?, ?, ?, ?, ?, now(), ?, ?, ?, ?, ?, ? )
Values: 170, 3222, 1, 1, 1, 4048, 1, 1, 0, 16, 1,
UDP-D-xylose:glycoprotein (D-xylose to the 3,6-disubstituted mannose of
N4-{N-acetyl-beta-D-glucosaminyl-(1->2)-alpha-D-mannosyl-(1->3)-[N-acety
l-beta-D-glucosaminyl-(1->2)-alpha-D-mannosyl-(1->6)]-beta-D-mannosyl-(1
->4)-N-acetyl-beta-D-glucosaminyl-(1->4)-N-acetyl-beta-D-glucosaminyl}as
paragine) 2-beta-D-xylosyltransferase activity, 1, 1 at
/core/trypdb/gus-test/GUS/gus_home/lib/perl/GUS/ObjRelP/DbiDbHandle.pm
line 166
Increasing the column size solves this issue, e.g. for Postgres:
alter table GOSynonym alter column text type varchar(1000);
Thanks,
Isabelle
--
Isabelle Phan, DPhil
Seattle Biomedical Research Institute
+1(206)256 7113
|
|
From: Elisabetta M. <man...@pc...> - 2008-12-13 11:21:36
|
This command will no longer work with the new updates to the plugin applied 2 days ago and reflected in the plugin John Brestelli sent to Isabelle (also available in the gus svn trunk). The new version takes in just one .obo file. The updates were necessary because the former version of the plugin was no longer working with the most recent GO files released for function, process and component. Elisabetta On Fri, 12 Dec 2008, Jian Lu wrote: > Try this command (use your own filePath) > > ga GUS::Supported::Plugin::InsertGeneOntology --filePath=/home/data/go > --functionExtDbName='GO Function' --processExtDbName='GO Process' > --componentExtDbName='GO Component' --commit > > We have been using it for a long time without any problem. But recently > it failed and gave a message 'out of memory'. I am not sure it is > hardware issue, GO file format issue or something else. > > Isabelle Phan wrote: >> Hello >> >> how do I load GO terms into GUS? The wiki information is outdated. I read the InsertGeneOntology plugin documentation but I am not sure I understand it. This in particular makes no sense to me: >> >> "you must provide either the (component, function, process)ExtDbName argument or set --create and provide the (component, function, process)ExtDbName argument for every branch you are loading." >> >> Please can you give an example? >> >> After several trial and error, I guessed that this command should load the GO component: >> >> ga GUS::Supported::Plugin::InsertGeneOntology --filePath=/core/trypdb/gus-test/data/go/ --createRelease --flatFile=component.ontology --componentExtDbName="GO Component" --commit >> >> Is this correct? When I ran that command, the loading did not complete after 2 hours. I suspect locking of foreign key constraints in postgres. Is there a way around this? >> >> thanks, >> >> Isabelle >> -- >> Isabelle Phan, DPhil >> Seattle Biomedical Research Institute >> +1(206)256 7113 >> >> >> ------------------------------------------------------------------------------ >> SF.Net email is Sponsored by MIX09, March 18-20, 2009 in Las Vegas, Nevada. >> The future of the web can't happen without you. Join us at MIX09 to help >> pave the way to the Next Web now. Learn more and register at >> http://ad.doubleclick.net/clk;208669438;13503038;i?http://2009.visitmix.com/ >> _______________________________________________ >> Gusdev-gusdev mailing list >> Gus...@li... >> https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev >> > > > ------------------------------------------------------------------------------ > SF.Net email is Sponsored by MIX09, March 18-20, 2009 in Las Vegas, Nevada. > The future of the web can't happen without you. Join us at MIX09 to help > pave the way to the Next Web now. Learn more and register at > http://ad.doubleclick.net/clk;208669438;13503038;i?http://2009.visitmix.com/ > _______________________________________________ > Gusdev-gusdev mailing list > Gus...@li... > https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev > -- Elisabetta Manduchi, Ph.D. Computational Biology and Informatics Laboratory Center for Bioinformatics University of Pennsylvania 1428 Blockley Hall 423 Guardian Drive Philadelphia, PA 19104-6021 phone: 215-573-4408 fax: 215 573-3111 email: man...@pc... web: http://www.cbil.upenn.edu/~manduchi --- |
|
From: Jian Lu <jl...@vb...> - 2008-12-13 09:43:58
|
Try this command (use your own filePath) ga GUS::Supported::Plugin::InsertGeneOntology --filePath=/home/data/go --functionExtDbName='GO Function' --processExtDbName='GO Process' --componentExtDbName='GO Component' --commit We have been using it for a long time without any problem. But recently it failed and gave a message 'out of memory'. I am not sure it is hardware issue, GO file format issue or something else. Isabelle Phan wrote: > Hello > > how do I load GO terms into GUS? The wiki information is outdated. I read the InsertGeneOntology plugin documentation but I am not sure I understand it. This in particular makes no sense to me: > > "you must provide either the (component, function, process)ExtDbName argument or set --create and provide the (component, function, process)ExtDbName argument for every branch you are loading." > > Please can you give an example? > > After several trial and error, I guessed that this command should load the GO component: > > ga GUS::Supported::Plugin::InsertGeneOntology --filePath=/core/trypdb/gus-test/data/go/ --createRelease --flatFile=component.ontology --componentExtDbName="GO Component" --commit > > Is this correct? When I ran that command, the loading did not complete after 2 hours. I suspect locking of foreign key constraints in postgres. Is there a way around this? > > thanks, > > Isabelle > -- > Isabelle Phan, DPhil > Seattle Biomedical Research Institute > +1(206)256 7113 > > > ------------------------------------------------------------------------------ > SF.Net email is Sponsored by MIX09, March 18-20, 2009 in Las Vegas, Nevada. > The future of the web can't happen without you. Join us at MIX09 to help > pave the way to the Next Web now. Learn more and register at > http://ad.doubleclick.net/clk;208669438;13503038;i?http://2009.visitmix.com/ > _______________________________________________ > Gusdev-gusdev mailing list > Gus...@li... > https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev > |
|
From: Isabelle P. <isa...@sb...> - 2008-12-13 01:17:13
|
FYI I solved my problem by executing this raw SQL statement:
INSERT INTO core.databaseversion (database_version_id, version, modification_date, user_read, user_write,group_read, group_write, other_read, other_write, row_user_id, row_group_id, row_project_id, row_alg_invocation_id) VALUES (
nextval('core.databaseversion_sq'), 3.5 , current_timestamp,1,1,1,1,1,0,1,1,1,1);
:-)
Isabelle
-----Original Message-----
From: Isabelle Phan
Sent: Fri 12/12/2008 4:46 PM
To: John E. Brestelli
Cc: gus...@li...
Subject: RE: [GUSDEV] svn GUS broken?
> You need to install Error.pm from cpan to use the trunk version of GUS.
I did, and the installation completes, which is great, but I still can't use plugins. Now I get this error:
$ ga +meta --commit
FATAL: Database version does not match required version for Plugin.
Database Version: Plugin Version: 3.5
How do I set the Database Version?
thanks,
Isabelle
|
|
From: Isabelle P. <isa...@sb...> - 2008-12-13 00:46:49
|
> You need to install Error.pm from cpan to use the trunk version of GUS. I did, and the installation completes, which is great, but I still can't use plugins. Now I get this error: $ ga +meta --commit FATAL: Database version does not match required version for Plugin. Database Version: Plugin Version: 3.5 How do I set the Database Version? thanks, Isabelle |
|
From: John E. B. <jbr...@pc...> - 2008-12-12 23:54:21
|
Hmmm... I guess this component is internal. The bit I was referring to says "Required Perl Modules: DBI, DBD-Oracle and/or DB-Pg, Error, Parse-Yapp, XML-Simple, and XML-Parser or XML-SAX" john On Fri, 12 Dec 2008, Isabelle Phan wrote: > Thanks for the prompt reply! > > I am sorry I can't see > $PROJECT_HOME/GUS/Website/documentation/3.5/install/installguide.html > > > There is no Website directory in my project checked out from subversion. > > How do I get it? > > > Isabelle > > -----Original Message----- > From: John E. Brestelli [mailto:jbr...@pc...] > Sent: Fri 12/12/2008 3:25 PM > To: Isabelle Phan > Cc: gus...@li... > Subject: Re: [GUSDEV] svn GUS broken? > > Hi Isabelle - Since the 3.5 release one other perl module is now required. > These are listed in: > $PROJECT_HOME/GUS/Website/documentation/3.5/install/installguide.html > > You need to install Error.pm from cran to use the trunk version of GUS. > > john > > > On Fri, 12 Dec 2008, Isabelle Phan wrote: > >> Hello >> >> I'm having problems running plugins since installing GUS from subversion: >> >> Base class package "Error" is empty. >> (Perhaps you need to 'use' the module which defines that package first.) >> at /core/trypdb/gus-test/GUS/gus_home/lib/perl/GUS/PluginMgr/PluginError.pm line 2 >> >> Has anybody seen this? >> >> thanks >> >> Isabelle >> >> -----Original Message----- >> From: Isabelle Phan [mailto:isa...@sb...] >> Sent: Fri 12/12/2008 3:03 PM >> To: gus...@li... >> Subject: Re: [GUSDEV] how do I load GO terms >> >> Hello >> >> I'm installing GUS from svn and getting this error on build: >> >> [InstallSchema] ERROR [main] (InstallSchemaTask.java:113) - Null version, skipping. Note: You will need to manually add a version number to the DB >> [InstallSchema] ERROR [main] (InstallSchemaTask.java:113) - Null version, skipping. Note: You will need to manually add a version number to the DB >> >> what is this? Has anybody seen this? >> >> thanks >> >> Isabelle >> >> -- >> Isabelle Phan, DPhil >> Seattle Biomedical Research Institute >> +1(206)256 7113 >> >> >> ------------------------------------------------------------------------------ >> SF.Net email is Sponsored by MIX09, March 18-20, 2009 in Las Vegas, Nevada. >> The future of the web can't happen without you. Join us at MIX09 to help >> pave the way to the Next Web now. Learn more and register at >> http://ad.doubleclick.net/clk;208669438;13503038;i?http://2009.visitmix.com/ >> _______________________________________________ >> Gusdev-gusdev mailing list >> Gus...@li... >> https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev >> >> >> >> ------------------------------------------------------------------------------ >> SF.Net email is Sponsored by MIX09, March 18-20, 2009 in Las Vegas, Nevada. >> The future of the web can't happen without you. Join us at MIX09 to help >> pave the way to the Next Web now. Learn more and register at >> http://ad.doubleclick.net/clk;208669438;13503038;i?http://2009.visitmix.com/ >> _______________________________________________ >> Gusdev-gusdev mailing list >> Gus...@li... >> https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev >> > > > > > ------------------------------------------------------------------------------ > SF.Net email is Sponsored by MIX09, March 18-20, 2009 in Las Vegas, Nevada. > The future of the web can't happen without you. Join us at MIX09 to help > pave the way to the Next Web now. Learn more and register at > http://ad.doubleclick.net/clk;208669438;13503038;i?http://2009.visitmix.com/ > _______________________________________________ > Gusdev-gusdev mailing list > Gus...@li... > https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev > |
|
From: John E. B. <jbr...@pc...> - 2008-12-12 23:51:33
|
Argh... It must be the end of the week. Sorry, I didn't see the bottom of your message. (You already tried to insert into sres.externaldatabase) constraint "pk_externaldatabase" is a primary key constraint. We use sequences to select a unique number for the primary key of each table. -> The sequence for "Sres.ExternalDatabase" is "sres.externaldatabase_sq" It seems there is a conflict between existing rows in Sres.ExternalDatabase and the values the plugin is trying to insert. (Less likely but possible, your max allowed value from this sequence has exceeded the size of your primary key column). Please run these 2 commands in sql: select sres.externaldatabase_sq.nextval from dual; desc sres.externaldatabase; 1.Check that none of your existing rows in sres.externaldatabase have an "external_database_id" matching the sequence value. 2.Check the sequence value against the size of the "external_database_id" field in Sres.ExternalDatabase. thanks john On Fri, 12 Dec 2008, Isabelle Phan wrote: > Hello John > > Thanks for the new plugin. I unfortunately can't make it to work: > > $> ga GUS::Supported::Plugin::InsertGeneOntology > --oboFile=gene_ontology.obo --extDbRlsName="GO ontology" > --extDbRlsVer="4.513" --commit > Couldn't find an external database release id for db 'GO ontology' > version '4.513'. Use the plugins InsertExternalDatabase and > InsertExternalDatabaseRls to insert this information into the database > at /core/trypdb/gus-test/GUS/gus_home/lib/perl/GUS/PluginMgr/Plugin.pm > line 818, <OBO> line 14. > > > $> ga GUS::Supported::Plugin::InsertExternalDatabase --name 'GO > ontology' --commit > DBD::Pg::st execute failed: ERROR: duplicate key violates unique > constraint "pk_externaldatabase" > > I don't understand: When I look into the table, I don't see that row: > > gus=> select * from externaldatabase where name like '%GO%'; > external_database_id | name | modification_date | > user_read | user_write | group_read | group_write | other_read | > other_write | row_user_id | row_group_id | row_project_id | > row_alg_invocation_id > ----------------------+--------------+----------------------------+----- > ------+------------+------------+-------------+------------+------------ > -+-------------+--------------+----------------+----------------------- > 3002 | GO Component | 2008-12-10 16:57:17.446902 | > 1 | 1 | 1 | 1 | 1 | 0 | > 1 | 1 | 1 | 10 > 3005 | GOC | 2008-12-10 16:57:17.446902 | > 1 | 1 | 1 | 1 | 1 | 0 | > 1 | 1 | 1 | 10 > 3024 | GOA | 2008-12-10 16:57:17.446902 | > 1 | 1 | 1 | 1 | 1 | 0 | > 1 | 1 | 1 | 10 > 3001 | GO Function | 2008-12-10 16:57:17.446902 | > 1 | 1 | 1 | 1 | 1 | 0 | > 1 | 1 | 1 | 10 > 3003 | GO Process | 2008-12-10 16:57:17.446902 | > 1 | 1 | 1 | 1 | 1 | 0 | > 1 | 1 | 1 | 10 > (5 rows) > > -- > Isabelle Phan, DPhil > Seattle Biomedical Research Institute > +1(206)256 7113 > > >> -----Original Message----- >> From: John E. Brestelli [mailto:jbr...@pc...] >> Sent: Thursday, December 11, 2008 3:11 PM >> To: Isabelle Phan >> Subject: RE: [GUSDEV] how do I load GO terms >> >> The files that plugin consumes have changed to the point it has >> become outdated. >> >> I just replaced that plugin in the svn repository with one >> which uses a >> different input file >> (http://www.geneontology.org/ontology/gene_ontology.obo) >> >> I've attached the new plugin. Please replace the >> InsertGeneOntology.pm in >> your $PROJECT_HOME and rebuild. (I think you could also >> checkout the svn >> to stay current) >> >> I need to be leaving now but can help more tomorrow if this >> still isn't >> working. >> >> john >> >> >> On Thu, 11 Dec 2008, Isabelle Phan wrote: >> >>> 3.5 >>> >>> Thanks >>> >>> Isabelle >>> >>>> -----Original Message----- >>>> From: John E. Brestelli [mailto:jbr...@pc...] >>>> Sent: Thursday, December 11, 2008 2:40 PM >>>> To: Isabelle Phan >>>> Subject: Re: [GUSDEV] how do I load GO terms >>>> >>>> Hi Isabelle - Which Version of GUS are you using? >>>> >>>> john >>>> >>> >> > |
|
From: Isabelle P. <isa...@sb...> - 2008-12-12 23:50:08
|
Thanks for the prompt reply! I am sorry I can't see $PROJECT_HOME/GUS/Website/documentation/3.5/install/installguide.html There is no Website directory in my project checked out from subversion. How do I get it? Isabelle -----Original Message----- From: John E. Brestelli [mailto:jbr...@pc...] Sent: Fri 12/12/2008 3:25 PM To: Isabelle Phan Cc: gus...@li... Subject: Re: [GUSDEV] svn GUS broken? Hi Isabelle - Since the 3.5 release one other perl module is now required. These are listed in: $PROJECT_HOME/GUS/Website/documentation/3.5/install/installguide.html You need to install Error.pm from cran to use the trunk version of GUS. john On Fri, 12 Dec 2008, Isabelle Phan wrote: > Hello > > I'm having problems running plugins since installing GUS from subversion: > > Base class package "Error" is empty. > (Perhaps you need to 'use' the module which defines that package first.) > at /core/trypdb/gus-test/GUS/gus_home/lib/perl/GUS/PluginMgr/PluginError.pm line 2 > > Has anybody seen this? > > thanks > > Isabelle > > -----Original Message----- > From: Isabelle Phan [mailto:isa...@sb...] > Sent: Fri 12/12/2008 3:03 PM > To: gus...@li... > Subject: Re: [GUSDEV] how do I load GO terms > > Hello > > I'm installing GUS from svn and getting this error on build: > > [InstallSchema] ERROR [main] (InstallSchemaTask.java:113) - Null version, skipping. Note: You will need to manually add a version number to the DB > [InstallSchema] ERROR [main] (InstallSchemaTask.java:113) - Null version, skipping. Note: You will need to manually add a version number to the DB > > what is this? Has anybody seen this? > > thanks > > Isabelle > > -- > Isabelle Phan, DPhil > Seattle Biomedical Research Institute > +1(206)256 7113 > > > ------------------------------------------------------------------------------ > SF.Net email is Sponsored by MIX09, March 18-20, 2009 in Las Vegas, Nevada. > The future of the web can't happen without you. Join us at MIX09 to help > pave the way to the Next Web now. Learn more and register at > http://ad.doubleclick.net/clk;208669438;13503038;i?http://2009.visitmix.com/ > _______________________________________________ > Gusdev-gusdev mailing list > Gus...@li... > https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev > > > > ------------------------------------------------------------------------------ > SF.Net email is Sponsored by MIX09, March 18-20, 2009 in Las Vegas, Nevada. > The future of the web can't happen without you. Join us at MIX09 to help > pave the way to the Next Web now. Learn more and register at > http://ad.doubleclick.net/clk;208669438;13503038;i?http://2009.visitmix.com/ > _______________________________________________ > Gusdev-gusdev mailing list > Gus...@li... > https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev > |
|
From: John E. B. <jbr...@pc...> - 2008-12-12 23:25:19
|
Hi Isabelle - Since the 3.5 release one other perl module is now required. These are listed in: $PROJECT_HOME/GUS/Website/documentation/3.5/install/installguide.html You need to install Error.pm from cran to use the trunk version of GUS. john On Fri, 12 Dec 2008, Isabelle Phan wrote: > Hello > > I'm having problems running plugins since installing GUS from subversion: > > Base class package "Error" is empty. > (Perhaps you need to 'use' the module which defines that package first.) > at /core/trypdb/gus-test/GUS/gus_home/lib/perl/GUS/PluginMgr/PluginError.pm line 2 > > Has anybody seen this? > > thanks > > Isabelle > > -----Original Message----- > From: Isabelle Phan [mailto:isa...@sb...] > Sent: Fri 12/12/2008 3:03 PM > To: gus...@li... > Subject: Re: [GUSDEV] how do I load GO terms > > Hello > > I'm installing GUS from svn and getting this error on build: > > [InstallSchema] ERROR [main] (InstallSchemaTask.java:113) - Null version, skipping. Note: You will need to manually add a version number to the DB > [InstallSchema] ERROR [main] (InstallSchemaTask.java:113) - Null version, skipping. Note: You will need to manually add a version number to the DB > > what is this? Has anybody seen this? > > thanks > > Isabelle > > -- > Isabelle Phan, DPhil > Seattle Biomedical Research Institute > +1(206)256 7113 > > > ------------------------------------------------------------------------------ > SF.Net email is Sponsored by MIX09, March 18-20, 2009 in Las Vegas, Nevada. > The future of the web can't happen without you. Join us at MIX09 to help > pave the way to the Next Web now. Learn more and register at > http://ad.doubleclick.net/clk;208669438;13503038;i?http://2009.visitmix.com/ > _______________________________________________ > Gusdev-gusdev mailing list > Gus...@li... > https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev > > > > ------------------------------------------------------------------------------ > SF.Net email is Sponsored by MIX09, March 18-20, 2009 in Las Vegas, Nevada. > The future of the web can't happen without you. Join us at MIX09 to help > pave the way to the Next Web now. Learn more and register at > http://ad.doubleclick.net/clk;208669438;13503038;i?http://2009.visitmix.com/ > _______________________________________________ > Gusdev-gusdev mailing list > Gus...@li... > https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev > |
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From: John E. B. <jbr...@pc...> - 2008-12-12 23:20:36
|
Hi Isabelle - This plugin requires that a few rows already exist in in the Sres.ExternalDatabase and SRes.ExternalDatabaseRelease tables. -> These are used to track your dataset Run these 2 plugins first. ga GUS::Supported::Plugin::InsertExternalDatabase --name 'GO ontology' --commit ga ga GUS::Supported::Plugin::InsertExternalDatabaseRls --databaseName 'GO ontology' --databaseVersion '4.513' --commit john On Fri, 12 Dec 2008, Isabelle Phan wrote: > Hello John > > Thanks for the new plugin. I unfortunately can't make it to work: > > $> ga GUS::Supported::Plugin::InsertGeneOntology > --oboFile=gene_ontology.obo --extDbRlsName="GO ontology" > --extDbRlsVer="4.513" --commit > Couldn't find an external database release id for db 'GO ontology' > version '4.513'. Use the plugins InsertExternalDatabase and > InsertExternalDatabaseRls to insert this information into the database > at /core/trypdb/gus-test/GUS/gus_home/lib/perl/GUS/PluginMgr/Plugin.pm > line 818, <OBO> line 14. > > > $> ga GUS::Supported::Plugin::InsertExternalDatabase --name 'GO > ontology' --commit > DBD::Pg::st execute failed: ERROR: duplicate key violates unique > constraint "pk_externaldatabase" > > I don't understand: When I look into the table, I don't see that row: > > gus=> select * from externaldatabase where name like '%GO%'; > external_database_id | name | modification_date | > user_read | user_write | group_read | group_write | other_read | > other_write | row_user_id | row_group_id | row_project_id | > row_alg_invocation_id > ----------------------+--------------+----------------------------+----- > ------+------------+------------+-------------+------------+------------ > -+-------------+--------------+----------------+----------------------- > 3002 | GO Component | 2008-12-10 16:57:17.446902 | > 1 | 1 | 1 | 1 | 1 | 0 | > 1 | 1 | 1 | 10 > 3005 | GOC | 2008-12-10 16:57:17.446902 | > 1 | 1 | 1 | 1 | 1 | 0 | > 1 | 1 | 1 | 10 > 3024 | GOA | 2008-12-10 16:57:17.446902 | > 1 | 1 | 1 | 1 | 1 | 0 | > 1 | 1 | 1 | 10 > 3001 | GO Function | 2008-12-10 16:57:17.446902 | > 1 | 1 | 1 | 1 | 1 | 0 | > 1 | 1 | 1 | 10 > 3003 | GO Process | 2008-12-10 16:57:17.446902 | > 1 | 1 | 1 | 1 | 1 | 0 | > 1 | 1 | 1 | 10 > (5 rows) > > -- > Isabelle Phan, DPhil > Seattle Biomedical Research Institute > +1(206)256 7113 > > >> -----Original Message----- >> From: John E. Brestelli [mailto:jbr...@pc...] >> Sent: Thursday, December 11, 2008 3:11 PM >> To: Isabelle Phan >> Subject: RE: [GUSDEV] how do I load GO terms >> >> The files that plugin consumes have changed to the point it has >> become outdated. >> >> I just replaced that plugin in the svn repository with one >> which uses a >> different input file >> (http://www.geneontology.org/ontology/gene_ontology.obo) >> >> I've attached the new plugin. Please replace the >> InsertGeneOntology.pm in >> your $PROJECT_HOME and rebuild. (I think you could also >> checkout the svn >> to stay current) >> >> I need to be leaving now but can help more tomorrow if this >> still isn't >> working. >> >> john >> >> >> On Thu, 11 Dec 2008, Isabelle Phan wrote: >> >>> 3.5 >>> >>> Thanks >>> >>> Isabelle >>> >>>> -----Original Message----- >>>> From: John E. Brestelli [mailto:jbr...@pc...] >>>> Sent: Thursday, December 11, 2008 2:40 PM >>>> To: Isabelle Phan >>>> Subject: Re: [GUSDEV] how do I load GO terms >>>> >>>> Hi Isabelle - Which Version of GUS are you using? >>>> >>>> john >>>> >>> >> > |
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From: Isabelle P. <isa...@sb...> - 2008-12-12 23:14:56
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Hello
I'm having problems running plugins since installing GUS from subversion:
Base class package "Error" is empty.
(Perhaps you need to 'use' the module which defines that package first.)
at /core/trypdb/gus-test/GUS/gus_home/lib/perl/GUS/PluginMgr/PluginError.pm line 2
Has anybody seen this?
thanks
Isabelle
-----Original Message-----
From: Isabelle Phan [mailto:isa...@sb...]
Sent: Fri 12/12/2008 3:03 PM
To: gus...@li...
Subject: Re: [GUSDEV] how do I load GO terms
Hello
I'm installing GUS from svn and getting this error on build:
[InstallSchema] ERROR [main] (InstallSchemaTask.java:113) - Null version, skipping. Note: You will need to manually add a version number to the DB
[InstallSchema] ERROR [main] (InstallSchemaTask.java:113) - Null version, skipping. Note: You will need to manually add a version number to the DB
what is this? Has anybody seen this?
thanks
Isabelle
--
Isabelle Phan, DPhil
Seattle Biomedical Research Institute
+1(206)256 7113
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From: Isabelle P. <isa...@sb...> - 2008-12-12 23:04:23
|
Hello I'm installing GUS from svn and getting this error on build: [InstallSchema] ERROR [main] (InstallSchemaTask.java:113) - Null version, skipping. Note: You will need to manually add a version number to the DB [InstallSchema] ERROR [main] (InstallSchemaTask.java:113) - Null version, skipping. Note: You will need to manually add a version number to the DB what is this? Has anybody seen this? thanks Isabelle -- Isabelle Phan, DPhil Seattle Biomedical Research Institute +1(206)256 7113 |
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From: Chris S. <sto...@pc...> - 2008-12-12 02:39:43
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Hi Isabelle. A timely request- sorry that we did not get to it before you ran into the error. It was on our to do list to address this. John B., can you move the plugin and respond to Isabelle. Thanks, Chris On Dec 11, 2008, at 4:41 PM, Isabelle Phan wrote: > Hello > > how do I load GO terms into GUS? The wiki information is outdated. I > read the InsertGeneOntology plugin documentation but I am not sure I > understand it. This in particular makes no sense to me: > > "you must provide either the (component, function, process)ExtDbName > argument or set --create and provide the (component, function, > process)ExtDbName argument for every branch you are loading." > > Please can you give an example? > > After several trial and error, I guessed that this command should > load the GO component: > > ga GUS::Supported::Plugin::InsertGeneOntology --filePath=/core/ > trypdb/gus-test/data/go/ --createRelease -- > flatFile=component.ontology --componentExtDbName="GO Component" -- > commit > > Is this correct? When I ran that command, the loading did not > complete after 2 hours. I suspect locking of foreign key constraints > in postgres. Is there a way around this? > > thanks, > > Isabelle > -- > Isabelle Phan, DPhil > Seattle Biomedical Research Institute > +1(206)256 7113 > > > ------------------------------------------------------------------------------ > SF.Net email is Sponsored by MIX09, March 18-20, 2009 in Las Vegas, > Nevada. > The future of the web can't happen without you. Join us at MIX09 to > help > pave the way to the Next Web now. Learn more and register at > http://ad.doubleclick.net/clk;208669438;13503038;i?http://2009.visitmix.com/ > _______________________________________________ > Gusdev-gusdev mailing list > Gus...@li... > https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev |
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From: Isabelle P. <isa...@sb...> - 2008-12-11 22:18:02
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Hello how do I load GO terms into GUS? The wiki information is outdated. I read the InsertGeneOntology plugin documentation but I am not sure I understand it. This in particular makes no sense to me: "you must provide either the (component, function, process)ExtDbName argument or set --create and provide the (component, function, process)ExtDbName argument for every branch you are loading." Please can you give an example? After several trial and error, I guessed that this command should load the GO component: ga GUS::Supported::Plugin::InsertGeneOntology --filePath=/core/trypdb/gus-test/data/go/ --createRelease --flatFile=component.ontology --componentExtDbName="GO Component" --commit Is this correct? When I ran that command, the loading did not complete after 2 hours. I suspect locking of foreign key constraints in postgres. Is there a way around this? thanks, Isabelle -- Isabelle Phan, DPhil Seattle Biomedical Research Institute +1(206)256 7113 |
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From: John I. <io...@gm...> - 2008-12-10 22:20:23
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Isabelle, The version of GUS I'm using (like yours, apparently) has no "lowercase_name" column; just "external_database_id" and "name", plus the eleven GUS housekeeping columns. I suggest you remove the lowercase_name element from the input XML. We should probably do the same with the copy on the download site. John Iodice On Tue, Dec 9, 2008 at 10:04 PM, Isabelle Phan <isa...@sb...>wrote: > Hello > > I just installed GUS 3.5 from www.gusdb.org/download . I am using > Postgres and trying to load ExternalDatabase.xml as described in > http://wiki.biowebdb.org/index.php/Gus#GUS::Supported::Plugin::LoadGusXm > l > > It does not work (see stack trace below), apparently because of a > mismatch with the schema created during the installation. > > Where do I find a copy of ExternalDatabase.xml that is compatible with > the GUS 3.5 schema? > > Thanks, > > > Isabelle > > $> ga GUS::Supported::Plugin::LoadGusXml --filename > ../data/ExternalDatabase.xml > Tue Dec 9 18:30:22 2008 ARGS algoinvo 1 > Tue Dec 9 18:30:22 2008 ARGS comment > Tue Dec 9 18:30:22 2008 ARGS commit 0 > Tue Dec 9 18:30:22 2008 ARGS debug 0 > Tue Dec 9 18:30:22 2008 ARGS filename > ../data/ExternalDatabase.xml > Tue Dec 9 18:30:22 2008 ARGS group > Tue Dec 9 18:30:22 2008 ARGS gusconfigfile > /core/trypdb/gus-test/GUS/gus.properties > Tue Dec 9 18:30:22 2008 ARGS help > Tue Dec 9 18:30:22 2008 ARGS helpHTML > Tue Dec 9 18:30:22 2008 ARGS project > Tue Dec 9 18:30:22 2008 ARGS refresh > Tue Dec 9 18:30:22 2008 ARGS sqlVerbose 0 > Tue Dec 9 18:30:22 2008 ARGS user > Tue Dec 9 18:30:22 2008 ARGS verbose 0 > Tue Dec 9 18:30:22 2008 ARGS veryVerbose 0 > Tue Dec 9 18:30:22 2008 COMMIT commit off > Tue Dec 9 18:30:22 2008 ALGINVID 5 > > ERROR: > ERROR: attempting to access attribute 'lowercase_name' of table > ExternalDatabase, but that table does not have such an attribute > > at /core/trypdb/gus-test/GUS/gus_home/lib/perl/GUS/ObjRelP/DbiRow.pm > line 729 > > GUS::ObjRelP::DbiRow::checkAttribute('GUS::Model::SRes::ExternalDatabase > =HASH(0xf3b4530)', 'lowercase_name') called at > /core/trypdb/gus-test/GUS/gus_home/lib/perl/GUS/ObjRelP/DbiRow.pm line > 88 > > GUS::ObjRelP::DbiRow::set('GUS::Model::SRes::ExternalDatabase=HASH(0xf3b > 4530)', 'lowercase_name', 'assembly') called at > /core/trypdb/gus-test/GUS/gus_home/lib/perl/GUS/Model/GusRow.pm line > 1902 > > GUS::Model::GusRow::parseXML('GUS::Model::SRes::ExternalDatabase=HASH(0x > f3b4530)', 'ARRAY(0xee1ce10)', 1) called at > /core/trypdb/gus-test/GUS/gus_home/lib/perl/GUS/Model/GusRow.pm line > 1952 > > GUS::Model::GusRow::parseXML('GUS::Model::Core::AlgorithmInvocation=HASH > (0xf0572b0)', 'ARRAY(0xee1ce10)') called at > /core/trypdb/gus-test/GUS/gus_home/lib/perl/GUS/Supported/Plugin/LoadGus > Xml.pm line 140 > > GUS::Supported::Plugin::LoadGusXml::process('GUS::Supported::Plugin::Loa > dGusXml=HASH(0xe677420)', 'ARRAY(0xee1ce10)') called at > /core/trypdb/gus-test/GUS/gus_home/lib/perl/GUS/Supported/Plugin/LoadGus > Xml.pm line 117 > > GUS::Supported::Plugin::LoadGusXml::run('GUS::Supported::Plugin::LoadGus > Xml=HASH(0xe677420)', 'HASH(0xf2e57b0)') called at > /core/trypdb/gus-test/GUS/gus_home/lib/perl/GUS/PluginMgr/GusApplication > .pm line 469 > eval {...} called at > /core/trypdb/gus-test/GUS/gus_home/lib/perl/GUS/PluginMgr/GusApplication > .pm line 461 > > GUS::PluginMgr::GusApplication::doMajorMode_RunOrReport('GUS::PluginMgr: > :GusApplication=HASH(0xe6512a0)', 'GUS::Supported::Plugin::LoadGusXml', > 1) called at > /core/trypdb/gus-test/GUS/gus_home/lib/perl/GUS/PluginMgr/GusApplication > .pm line 380 > > GUS::PluginMgr::GusApplication::doMajorMode_Run('GUS::PluginMgr::GusAppl > ication=HASH(0xe6512a0)', 'GUS::Supported::Plugin::LoadGusXml') called > at > /core/trypdb/gus-test/GUS/gus_home/lib/perl/GUS/PluginMgr/GusApplication > .pm line 288 > > GUS::PluginMgr::GusApplication::doMajorMode('GUS::PluginMgr::GusApplicat > ion=HASH(0xe6512a0)', 'GUS::Supported::Plugin::LoadGusXml') called at > /core/trypdb/gus-test/GUS/gus_home/lib/perl/GUS/PluginMgr/GusApplication > .pm line 197 > > GUS::PluginMgr::GusApplication::parseAndRun('GUS::PluginMgr::GusApplicat > ion=HASH(0xe6512a0)', 'ARRAY(0xe651d70)') called at > /core/trypdb/gus-test/GUS/gus_home/bin/ga line 11 > > STACK TRACE: > at /core/trypdb/gus-test/GUS/gus_home/lib/perl/GUS/ObjRelP/DbiRow.pm > line 729 > > GUS::ObjRelP::DbiRow::checkAttribute('GUS::Model::SRes::ExternalDatabase > =HASH(0xf3b4530)', 'lowercase_name') called at > /core/trypdb/gus-test/GUS/gus_home/lib/perl/GUS/ObjRelP/DbiRow.pm line > 88 > > GUS::ObjRelP::DbiRow::set('GUS::Model::SRes::ExternalDatabase=HASH(0xf3b > 4530)', 'lowercase_name', 'assembly') called at > /core/trypdb/gus-test/GUS/gus_home/lib/perl/GUS/Model/GusRow.pm line > 1902 > > GUS::Model::GusRow::parseXML('GUS::Model::SRes::ExternalDatabase=HASH(0x > f3b4530)', 'ARRAY(0xee1ce10)', 1) called at > /core/trypdb/gus-test/GUS/gus_home/lib/perl/GUS/Model/GusRow.pm line > 1952 > > GUS::Model::GusRow::parseXML('GUS::Model::Core::AlgorithmInvocation=HASH > (0xf0572b0)', 'ARRAY(0xee1ce10)') called at > /core/trypdb/gus-test/GUS/gus_home/lib/perl/GUS/Supported/Plugin/LoadGus > Xml.pm line 140 > > GUS::Supported::Plugin::LoadGusXml::process('GUS::Supported::Plugin::Loa > dGusXml=HASH(0xe677420)', 'ARRAY(0xee1ce10)') called at > /core/trypdb/gus-test/GUS/gus_home/lib/perl/GUS/Supported/Plugin/LoadGus > Xml.pm line 117 > > GUS::Supported::Plugin::LoadGusXml::run('GUS::Supported::Plugin::LoadGus > Xml=HASH(0xe677420)', 'HASH(0xf2e57b0)') called at > /core/trypdb/gus-test/GUS/gus_home/lib/perl/GUS/PluginMgr/GusApplication > .pm line 469 > eval {...} called at > /core/trypdb/gus-test/GUS/gus_home/lib/perl/GUS/PluginMgr/GusApplication > .pm line 461 > > GUS::PluginMgr::GusApplication::doMajorMode_RunOrReport('GUS::PluginMgr: > :GusApplication=HASH(0xe6512a0)', 'GUS::Supported::Plugin::LoadGusXml', > 1) called at > /core/trypdb/gus-test/GUS/gus_home/lib/perl/GUS/PluginMgr/GusApplication > .pm line 380 > > GUS::PluginMgr::GusApplication::doMajorMode_Run('GUS::PluginMgr::GusAppl > ication=HASH(0xe6512a0)', 'GUS::Supported::Plugin::LoadGusXml') called > at > /core/trypdb/gus-test/GUS/gus_home/lib/perl/GUS/PluginMgr/GusApplication > .pm line 288 > > GUS::PluginMgr::GusApplication::doMajorMode('GUS::PluginMgr::GusApplicat > ion=HASH(0xe6512a0)', 'GUS::Supported::Plugin::LoadGusXml') called at > /core/trypdb/gus-test/GUS/gus_home/lib/perl/GUS/PluginMgr/GusApplication > .pm line 197 > > GUS::PluginMgr::GusApplication::parseAndRun('GUS::PluginMgr::GusApplicat > ion=HASH(0xe6512a0)', 'ARRAY(0xe651d70)') called at > /core/trypdb/gus-test/GUS/gus_home/bin/ga line 11 > -- > Isabelle Phan, DPhil > Seattle Biomedical Research Institute > +1(206)256 7113 > > > ------------------------------------------------------------------------------ > SF.Net email is Sponsored by MIX09, March 18-20, 2009 in Las Vegas, Nevada. > The future of the web can't happen without you. Join us at MIX09 to help > pave the way to the Next Web now. Learn more and register at > > http://ad.doubleclick.net/clk;208669438;13503038;i?http://2009.visitmix.com/ > _______________________________________________ > Gusdev-gusdev mailing list > Gus...@li... > https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev > |
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From: Chris S. <sto...@pc...> - 2008-12-10 04:17:15
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Hi Isabelle, You might try some pointers here: http://gusdb.org/wiki/index.php/How%20we%20built%20TheileriaDB.org which is for a post-gres version. John, can you help? Thanks, Chris On Dec 9, 2008, at 10:04 PM, Isabelle Phan wrote: > Hello > > I just installed GUS 3.5 from www.gusdb.org/download . I am using > Postgres and trying to load ExternalDatabase.xml as described in > http://wiki.biowebdb.org/index.php/ > Gus#GUS::Supported::Plugin::LoadGusXm > l > > It does not work (see stack trace below), apparently because of a > mismatch with the schema created during the installation. > > Where do I find a copy of ExternalDatabase.xml that is compatible with > the GUS 3.5 schema? > > Thanks, > > > Isabelle > > $> ga GUS::Supported::Plugin::LoadGusXml --filename > ../data/ExternalDatabase.xml > Tue Dec 9 18:30:22 2008 ARGS algoinvo 1 > Tue Dec 9 18:30:22 2008 ARGS comment > Tue Dec 9 18:30:22 2008 ARGS commit 0 > Tue Dec 9 18:30:22 2008 ARGS debug 0 > Tue Dec 9 18:30:22 2008 ARGS filename > ../data/ExternalDatabase.xml > Tue Dec 9 18:30:22 2008 ARGS group > Tue Dec 9 18:30:22 2008 ARGS gusconfigfile > /core/trypdb/gus-test/GUS/gus.properties > Tue Dec 9 18:30:22 2008 ARGS help > Tue Dec 9 18:30:22 2008 ARGS helpHTML > Tue Dec 9 18:30:22 2008 ARGS project > Tue Dec 9 18:30:22 2008 ARGS refresh > Tue Dec 9 18:30:22 2008 ARGS sqlVerbose 0 > Tue Dec 9 18:30:22 2008 ARGS user > Tue Dec 9 18:30:22 2008 ARGS verbose 0 > Tue Dec 9 18:30:22 2008 ARGS veryVerbose 0 > Tue Dec 9 18:30:22 2008 COMMIT commit off > Tue Dec 9 18:30:22 2008 ALGINVID 5 > > ERROR: > ERROR: attempting to access attribute 'lowercase_name' of table > ExternalDatabase, but that table does not have such an attribute > > at /core/trypdb/gus-test/GUS/gus_home/lib/perl/GUS/ObjRelP/DbiRow.pm > line 729 > > GUS > ::ObjRelP::DbiRow::checkAttribute('GUS::Model::SRes::ExternalDatabase > =HASH(0xf3b4530)', 'lowercase_name') called at > /core/trypdb/gus-test/GUS/gus_home/lib/perl/GUS/ObjRelP/DbiRow.pm line > 88 > > GUS > ::ObjRelP::DbiRow::set('GUS::Model::SRes::ExternalDatabase=HASH(0xf3b > 4530)', 'lowercase_name', 'assembly') called at > /core/trypdb/gus-test/GUS/gus_home/lib/perl/GUS/Model/GusRow.pm line > 1902 > > GUS > ::Model::GusRow::parseXML('GUS::Model::SRes::ExternalDatabase=HASH(0x > f3b4530)', 'ARRAY(0xee1ce10)', 1) called at > /core/trypdb/gus-test/GUS/gus_home/lib/perl/GUS/Model/GusRow.pm line > 1952 > > GUS > ::Model::GusRow::parseXML('GUS::Model::Core::AlgorithmInvocation=HASH > (0xf0572b0)', 'ARRAY(0xee1ce10)') called at > /core/trypdb/gus-test/GUS/gus_home/lib/perl/GUS/Supported/Plugin/ > LoadGus > Xml.pm line 140 > > GUS > ::Supported::Plugin::LoadGusXml::process('GUS::Supported::Plugin::Loa > dGusXml=HASH(0xe677420)', 'ARRAY(0xee1ce10)') called at > /core/trypdb/gus-test/GUS/gus_home/lib/perl/GUS/Supported/Plugin/ > LoadGus > Xml.pm line 117 > > GUS > ::Supported::Plugin::LoadGusXml::run('GUS::Supported::Plugin::LoadGus > Xml=HASH(0xe677420)', 'HASH(0xf2e57b0)') called at > /core/trypdb/gus-test/GUS/gus_home/lib/perl/GUS/PluginMgr/ > GusApplication > .pm line 469 > eval {...} called at > /core/trypdb/gus-test/GUS/gus_home/lib/perl/GUS/PluginMgr/ > GusApplication > .pm line 461 > > GUS > ::PluginMgr::GusApplication::doMajorMode_RunOrReport('GUS::PluginMgr: > :GusApplication=HASH(0xe6512a0)', > 'GUS::Supported::Plugin::LoadGusXml', > 1) called at > /core/trypdb/gus-test/GUS/gus_home/lib/perl/GUS/PluginMgr/ > GusApplication > .pm line 380 > > GUS > ::PluginMgr::GusApplication::doMajorMode_Run('GUS::PluginMgr::GusAppl > ication=HASH(0xe6512a0)', 'GUS::Supported::Plugin::LoadGusXml') called > at > /core/trypdb/gus-test/GUS/gus_home/lib/perl/GUS/PluginMgr/ > GusApplication > .pm line 288 > > GUS > ::PluginMgr::GusApplication::doMajorMode('GUS::PluginMgr::GusApplicat > ion=HASH(0xe6512a0)', 'GUS::Supported::Plugin::LoadGusXml') called at > /core/trypdb/gus-test/GUS/gus_home/lib/perl/GUS/PluginMgr/ > GusApplication > .pm line 197 > > GUS > ::PluginMgr::GusApplication::parseAndRun('GUS::PluginMgr::GusApplicat > ion=HASH(0xe6512a0)', 'ARRAY(0xe651d70)') called at > /core/trypdb/gus-test/GUS/gus_home/bin/ga line 11 > > STACK TRACE: > at /core/trypdb/gus-test/GUS/gus_home/lib/perl/GUS/ObjRelP/DbiRow.pm > line 729 > > GUS > ::ObjRelP::DbiRow::checkAttribute('GUS::Model::SRes::ExternalDatabase > =HASH(0xf3b4530)', 'lowercase_name') called at > /core/trypdb/gus-test/GUS/gus_home/lib/perl/GUS/ObjRelP/DbiRow.pm line > 88 > > GUS > ::ObjRelP::DbiRow::set('GUS::Model::SRes::ExternalDatabase=HASH(0xf3b > 4530)', 'lowercase_name', 'assembly') called at > /core/trypdb/gus-test/GUS/gus_home/lib/perl/GUS/Model/GusRow.pm line > 1902 > > GUS > ::Model::GusRow::parseXML('GUS::Model::SRes::ExternalDatabase=HASH(0x > f3b4530)', 'ARRAY(0xee1ce10)', 1) called at > /core/trypdb/gus-test/GUS/gus_home/lib/perl/GUS/Model/GusRow.pm line > 1952 > > GUS > ::Model::GusRow::parseXML('GUS::Model::Core::AlgorithmInvocation=HASH > (0xf0572b0)', 'ARRAY(0xee1ce10)') called at > /core/trypdb/gus-test/GUS/gus_home/lib/perl/GUS/Supported/Plugin/ > LoadGus > Xml.pm line 140 > > GUS > ::Supported::Plugin::LoadGusXml::process('GUS::Supported::Plugin::Loa > dGusXml=HASH(0xe677420)', 'ARRAY(0xee1ce10)') called at > /core/trypdb/gus-test/GUS/gus_home/lib/perl/GUS/Supported/Plugin/ > LoadGus > Xml.pm line 117 > > GUS > ::Supported::Plugin::LoadGusXml::run('GUS::Supported::Plugin::LoadGus > Xml=HASH(0xe677420)', 'HASH(0xf2e57b0)') called at > /core/trypdb/gus-test/GUS/gus_home/lib/perl/GUS/PluginMgr/ > GusApplication > .pm line 469 > eval {...} called at > /core/trypdb/gus-test/GUS/gus_home/lib/perl/GUS/PluginMgr/ > GusApplication > .pm line 461 > > GUS > ::PluginMgr::GusApplication::doMajorMode_RunOrReport('GUS::PluginMgr: > :GusApplication=HASH(0xe6512a0)', > 'GUS::Supported::Plugin::LoadGusXml', > 1) called at > /core/trypdb/gus-test/GUS/gus_home/lib/perl/GUS/PluginMgr/ > GusApplication > .pm line 380 > > GUS > ::PluginMgr::GusApplication::doMajorMode_Run('GUS::PluginMgr::GusAppl > ication=HASH(0xe6512a0)', 'GUS::Supported::Plugin::LoadGusXml') called > at > /core/trypdb/gus-test/GUS/gus_home/lib/perl/GUS/PluginMgr/ > GusApplication > .pm line 288 > > GUS > ::PluginMgr::GusApplication::doMajorMode('GUS::PluginMgr::GusApplicat > ion=HASH(0xe6512a0)', 'GUS::Supported::Plugin::LoadGusXml') called at > /core/trypdb/gus-test/GUS/gus_home/lib/perl/GUS/PluginMgr/ > GusApplication > .pm line 197 > > GUS > ::PluginMgr::GusApplication::parseAndRun('GUS::PluginMgr::GusApplicat > ion=HASH(0xe6512a0)', 'ARRAY(0xe651d70)') called at > /core/trypdb/gus-test/GUS/gus_home/bin/ga line 11 > -- > Isabelle Phan, DPhil > Seattle Biomedical Research Institute > +1(206)256 7113 > > ------------------------------------------------------------------------------ > SF.Net email is Sponsored by MIX09, March 18-20, 2009 in Las Vegas, > Nevada. > The future of the web can't happen without you. Join us at MIX09 to > help > pave the way to the Next Web now. Learn more and register at > http://ad.doubleclick.net/clk;208669438;13503038;i?http://2009.visitmix.com/ > _______________________________________________ > Gusdev-gusdev mailing list > Gus...@li... > https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev |
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From: Isabelle P. <isa...@sb...> - 2008-12-10 03:25:56
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Hello I just installed GUS 3.5 from www.gusdb.org/download . I am using Postgres and trying to load ExternalDatabase.xml as described in http://wiki.biowebdb.org/index.php/Gus#GUS::Supported::Plugin::LoadGusXm l It does not work (see stack trace below), apparently because of a mismatch with the schema created during the installation. Where do I find a copy of ExternalDatabase.xml that is compatible with the GUS 3.5 schema? Thanks, Isabelle $> ga GUS::Supported::Plugin::LoadGusXml --filename ../data/ExternalDatabase.xml Tue Dec 9 18:30:22 2008 ARGS algoinvo 1 Tue Dec 9 18:30:22 2008 ARGS comment Tue Dec 9 18:30:22 2008 ARGS commit 0 Tue Dec 9 18:30:22 2008 ARGS debug 0 Tue Dec 9 18:30:22 2008 ARGS filename ../data/ExternalDatabase.xml Tue Dec 9 18:30:22 2008 ARGS group Tue Dec 9 18:30:22 2008 ARGS gusconfigfile /core/trypdb/gus-test/GUS/gus.properties Tue Dec 9 18:30:22 2008 ARGS help Tue Dec 9 18:30:22 2008 ARGS helpHTML Tue Dec 9 18:30:22 2008 ARGS project Tue Dec 9 18:30:22 2008 ARGS refresh Tue Dec 9 18:30:22 2008 ARGS sqlVerbose 0 Tue Dec 9 18:30:22 2008 ARGS user Tue Dec 9 18:30:22 2008 ARGS verbose 0 Tue Dec 9 18:30:22 2008 ARGS veryVerbose 0 Tue Dec 9 18:30:22 2008 COMMIT commit off Tue Dec 9 18:30:22 2008 ALGINVID 5 ERROR: ERROR: attempting to access attribute 'lowercase_name' of table ExternalDatabase, but that table does not have such an attribute at /core/trypdb/gus-test/GUS/gus_home/lib/perl/GUS/ObjRelP/DbiRow.pm line 729 GUS::ObjRelP::DbiRow::checkAttribute('GUS::Model::SRes::ExternalDatabase =HASH(0xf3b4530)', 'lowercase_name') called at /core/trypdb/gus-test/GUS/gus_home/lib/perl/GUS/ObjRelP/DbiRow.pm line 88 GUS::ObjRelP::DbiRow::set('GUS::Model::SRes::ExternalDatabase=HASH(0xf3b 4530)', 'lowercase_name', 'assembly') called at /core/trypdb/gus-test/GUS/gus_home/lib/perl/GUS/Model/GusRow.pm line 1902 GUS::Model::GusRow::parseXML('GUS::Model::SRes::ExternalDatabase=HASH(0x f3b4530)', 'ARRAY(0xee1ce10)', 1) called at /core/trypdb/gus-test/GUS/gus_home/lib/perl/GUS/Model/GusRow.pm line 1952 GUS::Model::GusRow::parseXML('GUS::Model::Core::AlgorithmInvocation=HASH (0xf0572b0)', 'ARRAY(0xee1ce10)') called at /core/trypdb/gus-test/GUS/gus_home/lib/perl/GUS/Supported/Plugin/LoadGus Xml.pm line 140 GUS::Supported::Plugin::LoadGusXml::process('GUS::Supported::Plugin::Loa dGusXml=HASH(0xe677420)', 'ARRAY(0xee1ce10)') called at /core/trypdb/gus-test/GUS/gus_home/lib/perl/GUS/Supported/Plugin/LoadGus Xml.pm line 117 GUS::Supported::Plugin::LoadGusXml::run('GUS::Supported::Plugin::LoadGus Xml=HASH(0xe677420)', 'HASH(0xf2e57b0)') called at /core/trypdb/gus-test/GUS/gus_home/lib/perl/GUS/PluginMgr/GusApplication .pm line 469 eval {...} called at /core/trypdb/gus-test/GUS/gus_home/lib/perl/GUS/PluginMgr/GusApplication .pm line 461 GUS::PluginMgr::GusApplication::doMajorMode_RunOrReport('GUS::PluginMgr: :GusApplication=HASH(0xe6512a0)', 'GUS::Supported::Plugin::LoadGusXml', 1) called at /core/trypdb/gus-test/GUS/gus_home/lib/perl/GUS/PluginMgr/GusApplication .pm line 380 GUS::PluginMgr::GusApplication::doMajorMode_Run('GUS::PluginMgr::GusAppl ication=HASH(0xe6512a0)', 'GUS::Supported::Plugin::LoadGusXml') called at /core/trypdb/gus-test/GUS/gus_home/lib/perl/GUS/PluginMgr/GusApplication .pm line 288 GUS::PluginMgr::GusApplication::doMajorMode('GUS::PluginMgr::GusApplicat ion=HASH(0xe6512a0)', 'GUS::Supported::Plugin::LoadGusXml') called at /core/trypdb/gus-test/GUS/gus_home/lib/perl/GUS/PluginMgr/GusApplication .pm line 197 GUS::PluginMgr::GusApplication::parseAndRun('GUS::PluginMgr::GusApplicat ion=HASH(0xe6512a0)', 'ARRAY(0xe651d70)') called at /core/trypdb/gus-test/GUS/gus_home/bin/ga line 11 STACK TRACE: at /core/trypdb/gus-test/GUS/gus_home/lib/perl/GUS/ObjRelP/DbiRow.pm line 729 GUS::ObjRelP::DbiRow::checkAttribute('GUS::Model::SRes::ExternalDatabase =HASH(0xf3b4530)', 'lowercase_name') called at /core/trypdb/gus-test/GUS/gus_home/lib/perl/GUS/ObjRelP/DbiRow.pm line 88 GUS::ObjRelP::DbiRow::set('GUS::Model::SRes::ExternalDatabase=HASH(0xf3b 4530)', 'lowercase_name', 'assembly') called at /core/trypdb/gus-test/GUS/gus_home/lib/perl/GUS/Model/GusRow.pm line 1902 GUS::Model::GusRow::parseXML('GUS::Model::SRes::ExternalDatabase=HASH(0x f3b4530)', 'ARRAY(0xee1ce10)', 1) called at /core/trypdb/gus-test/GUS/gus_home/lib/perl/GUS/Model/GusRow.pm line 1952 GUS::Model::GusRow::parseXML('GUS::Model::Core::AlgorithmInvocation=HASH (0xf0572b0)', 'ARRAY(0xee1ce10)') called at /core/trypdb/gus-test/GUS/gus_home/lib/perl/GUS/Supported/Plugin/LoadGus Xml.pm line 140 GUS::Supported::Plugin::LoadGusXml::process('GUS::Supported::Plugin::Loa dGusXml=HASH(0xe677420)', 'ARRAY(0xee1ce10)') called at /core/trypdb/gus-test/GUS/gus_home/lib/perl/GUS/Supported/Plugin/LoadGus Xml.pm line 117 GUS::Supported::Plugin::LoadGusXml::run('GUS::Supported::Plugin::LoadGus Xml=HASH(0xe677420)', 'HASH(0xf2e57b0)') called at /core/trypdb/gus-test/GUS/gus_home/lib/perl/GUS/PluginMgr/GusApplication .pm line 469 eval {...} called at /core/trypdb/gus-test/GUS/gus_home/lib/perl/GUS/PluginMgr/GusApplication .pm line 461 GUS::PluginMgr::GusApplication::doMajorMode_RunOrReport('GUS::PluginMgr: :GusApplication=HASH(0xe6512a0)', 'GUS::Supported::Plugin::LoadGusXml', 1) called at /core/trypdb/gus-test/GUS/gus_home/lib/perl/GUS/PluginMgr/GusApplication .pm line 380 GUS::PluginMgr::GusApplication::doMajorMode_Run('GUS::PluginMgr::GusAppl ication=HASH(0xe6512a0)', 'GUS::Supported::Plugin::LoadGusXml') called at /core/trypdb/gus-test/GUS/gus_home/lib/perl/GUS/PluginMgr/GusApplication .pm line 288 GUS::PluginMgr::GusApplication::doMajorMode('GUS::PluginMgr::GusApplicat ion=HASH(0xe6512a0)', 'GUS::Supported::Plugin::LoadGusXml') called at /core/trypdb/gus-test/GUS/gus_home/lib/perl/GUS/PluginMgr/GusApplication .pm line 197 GUS::PluginMgr::GusApplication::parseAndRun('GUS::PluginMgr::GusApplicat ion=HASH(0xe6512a0)', 'ARRAY(0xe651d70)') called at /core/trypdb/gus-test/GUS/gus_home/bin/ga line 11 -- Isabelle Phan, DPhil Seattle Biomedical Research Institute +1(206)256 7113 |
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From: Diogo T. <di...@gm...> - 2008-10-10 17:43:23
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Helo All, I´m tryng to use the script parseBlastFilesForSimilarity.pl to condense the results of the RPS-blast, but i have a problem, the script generate a "wrong" condensed file. I think is because the structure of this file is different from the result's file from the Blastp. The CBIL modul don't understand the result's file of Rps-blast (the scructure of file), i think this is the problem! I try to use the option --rpsblast of the script parseBlastFilesForSimilarity.pl, but don't work too. Anyone have the same problem? Anyone can help? Many thanks! Diogo Tschoeke Fiocruz- Brazil |
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From: Fabiana F. <bia...@gm...> - 2008-06-18 21:47:29
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hello every body, I am trying to install GUS 3.5. So, when installation is in progress exist a error "java.lang.outofmamery". I tried to increase heap size, but it was not work. i did: $java -Xms128m -Xmn512m build GUS install -append". I readed in some codes in the GUS's folders that there is a option to skil the compilation. So i used. can i do it?. I am not sure about that. Thanks |
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From: Brian B. <br...@pc...> - 2008-05-20 16:33:48
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In the upcoming release of GUS (3.6), we are proposing changing the views on the imp tables in GUS to clarify the superclass / subclass relationships. Note that this will have NO impact on the underlying imp tables, all columns there remain the same. Currently the superclass view (and thus all views) of GUS objects contain all the named attributes from the imp table. This is the intent for the shared attributes such as sequence, length, etc for sequence tables. However, we also have a requirement that all columns that will be referenced as foreign keys be named attributes in the imp tables because we need to make certain that they are used appropriately and naming them helps clarify this usage. We are proposing to clean up the superclass views of the imp tables so that these views contain only attributes that are truly common among all the classes. This would mean removing those named attributes that are foreign keys but only relevant to one (or a few) subclasses. Examples from the AAFeature object would be removal of motif_aa_sequence_id, pfam_entry_id and repeat_type_id as these attributes are only relevant for specific subclasses such as RepeatRegionAAFeature (for repeat_type_id). As examples: AAFeature column nulls? type AA_Feature_ID no NUMBER(10,0) AA_SEQUENCE_ID no DoTS::AASequence (NUMBER(10,0) ) Feature_NAME_ID DoTS::FeatureName (NUMBER(10,0) ) PARENT_ID DoTS::AAFeature (NUMBER(10,0) ) NA_Feature_ID DoTS::NAFeature (NUMBER(10,0) ) SUBCLASS_VIEW STRING(30) SEQUENCE_ONTOLOGY_ID SRes::SequenceOntology (NUMBER(10,0) ) DESCRIPTION STRING(4000) EXTERNAL_DATABASE_RELEASE_ID SRes::ExternalDatabaseRelease (NUMBER (10,0) ) SOURCE_ID STRING(50) PREDICTION_ALGORITHM_ID Core::Algorithm (NUMBER(5,0) ) IS_PREDICTED no NUMBER(1,0) REVIEW_STATUS_ID SRes::ReviewStatus (NUMBER(12,0) ) RepeatRegionAAFeature would have all the above columns plus: column nulls? type REPEAT_TYPE_ID DoTS::RepeatType (NUMBER(10,0) ) PERIOD NUMBER(12,0) COPYNUM FLOAT CONSENSUS_SIZE NUMBER(12,0) PERCENT_MATCH NUMBER(3,0) PERCENT_INDEL NUMBER(3,0) SCORE FLOAT CONSENSUS STRING(4000) ALGORITHM_NAME STRING(255) This change has the added benefit that the PERL object layer will be better able to deal with instances where there are two foreign key attributes in a single object as is the case for features that have both aa_sequence_id and motif_aa_sequence_id. Questions / concerns? -Brian Brian P. Brunk, Ph.D. ApiDB Manager 1403 Blockley Hall Penn Center For Bioinformatics University of Pennsylvania Philadelphia PA 19104-6021 Tel: 215-573-3118 Fax: 215-573-3111 |
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From: F I. <fr...@pc...> - 2008-01-31 22:42:48
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Hi Diogo, The first issue does not seem like a bug, but the second possibly is. For the second one, the problem may be more obvious to someone else in the group. I'd like to encourage other people to give a answer, but here is what I see so far: The first, InsertBlastSimilarities, is a supported plugin. I doesn't look like an error, though; if no "subjects" exist in the sequence tables, the error can be resolved by inserting the missing subjects with the InsertNewExternalSequences plugin. The second issue is with community plugin, OrthologGroupsMCL, and it seems like a soft error. I'm not sure I understand the issue - I'm guessing there are sequence IDs in the OrthoMCL file that were not loaded into aasequence? If so, it would make sense for it to fail, but it should do so more graciously. -Frank P.S Full notes from the InsertBlastSimilarities plugin: "The definition lines of the sequences involved in the BLAST (both query and subject) must begin with the na_sequence_ids of those sequences. The standard way to acheive that is to first load the sequences into GUS, using the InsertNewExternalSequences plugin, and then to extract them into a file with the dumpSequences FromTable.pl command. That command places the na_sequence_id of the sequence as the first thing in the definition line. The plugin assumes that all subject sequences are stored in the same table, and that all query sequences are stored in the same table (but possibly different from the subject sequences). The subjectTable and queryTable arguments indicate which tables the sequences are in, respectively. (This is because the Similarity table forms similarities between table/rows in GUS; therefore, the plugin must specify which tables the sequences are in.)" >> *From: *"Diogo Tschoeke" <di...@gm... <mailto:di...@gm...>> >> *Date: *January 30, 2008 9:02:22 AM EST >> *To: *GUSDEV <Gus...@li... >> <mailto:Gus...@li...>> >> *Subject: **[GUSDEV] Problems in GUS* >> >> Hello all, >> >> I work with GUS on Brazil at Instituto Oswaldo Cruz, and have some >> questions: >> In plugin InsertBlastSimilarities when I have a query with zero >> subject, something like that: >ABQ58803.1 (0 subjects) >> this result is not inserted on GUS, it's correct? >> Another question is when I use de pluggin: OrthologGroupsMCL >> i have this error >> DBD::Pg::st execute failed: ERROR: null value in column >> "aa_sequence_id" violates not-null constraint >> ERROR: >> >> SQL ERROR!! involving >> >> INSERT INTO DoTS.AASequenceSequenceGroup >> >> I know wich aa_sequence_id is a PK of the table dots.aasequenceimp, >> and the pluggin it's not working because the OrthoMCL plugin not found >> some sequences in GUS, but OrthoMCL file's have this sequences, it's >> correct? >> >> Somebody help me? >> >> Thank's >> >> Diogo Tschoeke >> Oswaldo Cruz Institute >> Rio de Janeiro, Brazil >> |
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From: Diogo T. <di...@gm...> - 2008-01-30 14:09:07
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Hello all,
I work with GUS on Brazil at Instituto Oswaldo Cruz, and have some
questions:
In plugin InsertBlastSimilarities when I have a query with zero subject,
something like that: >ABQ58803.1 (0 subjects)
this result is not inserted on GUS, it's correct?
Another question is when I use de pluggin: OrthologGroupsMCL
i have this error
DBD::Pg::st execute failed: ERROR: null value in column "aa_sequence_id"
violates not-null constraint
ERROR:
SQL ERROR!! involving
INSERT INTO DoTS.AASequenceSequenceGroup
I know wich aa_sequence_id is a PK of the table dots.aasequenceimp, and the
pluggin it's not working because the OrthoMCL plugin not found some
sequences in GUS, but OrthoMCL file's have this sequences, it's correct?
Somebody help me?
Thank's
Diogo Tschoeke
Oswaldo Cruz Institute
Rio de Janeiro, Brazil
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From: Jian Lu <jl...@vb...> - 2008-01-29 19:24:41
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Hi Frank, I am working on PATRIC project at VBI. We have the following tables/views that have been modified to meet the data needs. DoTS/DoTSVer TABLES: alter table Dots.SECONDARYACCS modify (SECONDARY_ACCS VARCHAR2(20)); alter table DotsVer.SECONDARYACCSVer modify (SECONDARY_ACCS VARCHAR2(20)); VIEWS: Source/SourceVer: add a new column: STRING43 AS MOL_TYPE ProteinFeature/ProteinFeatureVer: add new columns: STRING15 AS PROTEIN_ID, CLOB1 AS TRANSLATION Repeats/RepeatsVer: add new columns: STRING13 AS TRANSPOSON, STRING14 AS INSERTION_SEQ RNAType/RNATypeVer: add new columns: CLOB1 AS TRANSLATION, NUMBER3 AS ANTICODON_CENTER, FLOAT1 AS SCORE SRes/SResVer alter table SRes.GOSYNONYM modify (TEXT VARCHAR2(1000)); alter table SResVer.GOSYNONYMVer modify (TEXT VARCHAR2(1000)); alter table SRes.ExternalDatabaseEntry modify(DESCRIPTION VARCHAR2(4000)); alter table SResVer.ExternalDatabaseEntryVer modify(DESCRIPTION VARCHAR2(4000)); alter table SRes.SequenceOntology modify(DEFINITION VARCHAR2(2000)); alter table SResVer.SequenceOntologyVer modify(DEFINITION VARCHAR2(2000)); Frank Innamorato wrote: > *Proposed Schema changes for GUS 3.6 Release* > > CBIL will be releasing GUS v3.6 in the first quarter of this year. > Before the schema is finalized, we are asking for review from the GUS > community. > > We have compiled a series of changes based upon the GUS bug tracker, > as well as from informal modifications that have occurred in other GUS > installations. > > Please review the current proposed changes for GUS 3.6 within the next > two weeks. > The changes can be found on the wiki page Proposed Schema Changes > <http://www.gusdb.org/wiki/index.php/Proposed%20Schema%20Changes> > > *IMPORTANT - Do not modify these pages!* > Please submit suggestions on the GUS-3.6 Schema Change Request > <http://www.gusdb.org/wiki/index.php/GUS-3.6%20Schema%20Change%20Request> > wiki page, or send an email to fr...@pc... > > The GUS 3.6 schema wiki pages are incomplete and are still being > updated. Changes will be occurring regularly as contributer > submissions are being addressed. Please note: the GUS 3.6 release > will NOT include a schema upgrade script, and will not focus on index > changes. Index changes are tracked and will occur in a future > release. Indexes will be added for new tables, and some minor index > changes may be included in the release. > > Thanks, > -Frank > > Frank Innamorato > Database Administrator > Computational Biology and Informatics Laboratory > Penn Center for Bioinformatics > 1410 Blockley Hall > 423 Guardian Drive > University of Pennsylvania > Philadelphia, PA 19104 > ------------------------------------------------------------------------ > > ------------------------------------------------------------------------- > This SF.net email is sponsored by: Microsoft > Defy all challenges. Microsoft(R) Visual Studio 2008. > http://clk.atdmt.com/MRT/go/vse0120000070mrt/direct/01/ > ------------------------------------------------------------------------ > > _______________________________________________ > Gusdev-gusdev mailing list > Gus...@li... > https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev > |
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From: Frank I. <inn...@pc...> - 2008-01-24 05:52:46
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<!DOCTYPE html PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN"> <html> <head> </head> <body bgcolor="#ffffff" text="#000000"> <b>Proposed Schema changes for GUS 3.6 Release</b><br> <br> CBIL will be releasing GUS v3.6 in the first quarter of this year. Before the schema is finalized, we are asking for review from the GUS community. <br> <br> We have compiled a series of changes based upon the GUS bug tracker, as well as from informal modifications that have occurred in other GUS installations.<br> <br> Please review the current proposed changes for GUS 3.6 within the next two weeks.<br> The changes can be found on the wiki page <a href="http://www.gusdb.org/wiki/index.php/Proposed%20Schema%20Changes" class="wiki">Proposed Schema Changes</a> <br> <br> <b>IMPORTANT - Do not modify these pages!</b><br> Please submit suggestions on the <a href="http://www.gusdb.org/wiki/index.php/GUS-3.6%20Schema%20Change%20Request" class="wiki">GUS-3.6 Schema Change Request</a> wiki page, or send an email to <a class="moz-txt-link-abbreviated" href="mailto:fr...@pc...">fr...@pc...</a><br> <br> The GUS 3.6 schema wiki pages are incomplete and are still being updated. Changes will be occurring regularly as contributer submissions are being addressed. Please note: the GUS 3.6 release will NOT include a schema upgrade script, and will not focus on index changes. Index changes are tracked and will occur in a future release. Indexes will be added for new tables, and some minor index changes may be included in the release.<br> <br> Thanks,<br> -Frank<br> <br> <div style="margin: 0px;">Frank Innamorato</div> <div style="margin: 0px;">Database Administrator</div> <div style="margin: 0px;">Computational Biology and Informatics Laboratory</div> <div style="margin: 0px;">Penn Center for Bioinformatics</div> <div style="margin: 0px;">1410 Blockley Hall</div> <div style="margin: 0px;">423 Guardian Drive</div> <div style="margin: 0px;">University of Pennsylvania</div> <div style="margin: 0px;">Philadelphia, PA 19104</div> </body> </html> |
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From: Haiming W. <hw...@ug...> - 2007-10-05 03:38:17
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Hi Chris, Most pieces of information are descriptive and may not appear in every Genbank record. We'd like to show them on an isolate record page as attributes if they are available. One or two qualifiers are required to ask questions, such as the 'country' qualifier will be used to find isolate's geographical distribution. DoTS.source table can handle most of those qualifiers. DoTS.Miscellaneous seems to be a good candidate for the expansion. I'll check with Frank for the upcoming schema updates. Thanks very much for your help! -Haiming Chris Stoeckert wrote: > Hi Haiming, > Another view of NAFeature used to handle GenBank qualifiers (that we > were not using at the time the DoTS schema was created) is > DoTS.Miscellaneous > http://www.gusdb.org/SchemaBrowser/table.htm?schema=DoTS&table=Miscellaneous > <http://www.gusdb.org/SchemaBrowser/table.htm?schema=DoTS&table=Miscellaneous> > Note that most of the columns are of type string so some of this > information could be packed into EVIDENCE or PCR_CONDITIONS. Between > that view and DoTS.Source you might find a field to put things. Not a > clean solution but may be sufficient for now. > > What is the anticipated use of those pieces of information? Is this > primarily archival? descriptive? Or will there be queries of the > nature: provide all isolates from the USA collected after the year > 2000? For the first two cases, proper structuring is less urgent but > for the latter we would certainly want to add the appropriate > attributes. Frank is working on a 3.6 version of GUS and this could be > a candidate for inclusion. > > Cheers, > Chris > > Chris Stoeckert, Ph.D. > Research Professor, Dept. of Genetics > 1415 Blockley Hall, Center for Bioinformatics > 423 Guardian Dr., University of Pennsylvania > Philadelphia, PA 19104 > Ph: 215-573-4409 FAX: 215-573-3111 > http://www.cbil.upenn.edu > > > On Oct 4, 2007, at 11:08 AM, Haiming Wang wrote: > >> Hi, >> >> I'm loading isolate genbank records into GUS using >> GUS::Supported::Plugin::InsertSequenceFeatures. It works well except >> some qualifiers (under source) do not have corresponding columns in >> DOTS.SOURCE table. Those qualifiers include "country, >> collection_date, collected_by, environmental_sample, PCR_primers, >> virion...", such as >> >> /organism="Cryptosporidium environmental sequence" >> /mol_type="genomic DNA" >> /isolation_source="environmental water sample" >> /db_xref="taxon:310753" >> /clone="JF#1" >> /environmental_sample >> /country="USA: Massachusetts" >> /collection_date="Jun-2001" >> /collected_by="Kristen Jellison" >> PCR_primers=fwd_name: CPB-DIAGF, rev_name:CPB-DIAGR" >> ... >> >> Please refer to the attached genbank file - 117671303.gb, for details >> >> I'd like to know if we intend to add those qualifier-match columns in >> DOTS.SOURCE table. Otherwise, we need several special handlers to >> deal with them. Thanks for your inputs! >> >> -Haiming >> >> >> p.s. all the qualifiers in Genbank source >> >> Feature Key source >> >> Mandatory qualifiers /organism="text" >> /mol_type="genomic DNA", "genomic RNA", "mRNA"... >> Optional qualifiers /cell_line="text" >> /cell_type="text" >> /chromosome="text" >> /citation=[number] >> /clone="text" >> /clone_lib="text" >> /collected_by="text" >> /collection_date="text" >> /country="<country_value>[:<region>][, <locality>]" >> /cultivar="text" >> /db_xref="<database>:<identifier>" >> /dev_stage="text" >> /ecotype="text" >> /environmental_sample >> /focus >> /frequency="text" >> /germline >> /haplotype="text" >> /identified_by="text" >> /isolate="text" >> /isolation_source="text" >> /label=feature_label >> /lab_host="text" >> /lat_lon="text" >> /macronuclear >> /map="text" >> /note="text" >> /organelle=<organelle_value> >> /PCR_primers="[fwd_name: XXX, ]fwd_seq: xxxxx, >> [rev_name: YYY, ]rev_seq: yyyyy" >> /plasmid="text" >> /pop_variant="text" >> /proviral >> /rearranged >> /segment="text" >> /serotype="text" >> /serovar="text" >> /sex="text" >> /specimen_voucher="text" >> /specific_host="text" >> /strain="text" >> /sub_clone="text" >> /sub_species="text" >> /sub_strain="text" >> /tissue_lib="text" >> /tissue_type="text" >> /transgenic >> /variety="text" >> /virion >> LOCUS EF060289 425 bp DNA linear ENV >> 14-NOV-2006 >> DEFINITION Cryptosporidium environmental sequence clone JF#1 18S >> small subunit >> ribosomal RNA gene, partial sequence. >> ACCESSION EF060289 >> VERSION EF060289.1 GI:117671303 >> KEYWORDS ENV. >> SOURCE Cryptosporidium environmental sequence >> ORGANISM Cryptosporidium environmental sequence >> Eukaryota; Alveolata; Apicomplexa; Coccidia; Eucoccidiorida; >> Eimeriorina; Cryptosporidiidae; Cryptosporidium; >> environmental >> samples. >> REFERENCE 1 (bases 1 to 425) >> AUTHORS Jellison,K.L., Distel,D.L., Hemond,H.F. and Schauer,D.B. >> TITLE Phylogenetic analysis implicates birds as an important >> source of >> Cryptosporidium spp. oocysts in agricultural watersheds >> JOURNAL Unpublished >> REFERENCE 2 (bases 1 to 425) >> AUTHORS Jellison,K.L. >> TITLE Direct Submission >> JOURNAL Submitted (12-OCT-2006) Civil and Environmental >> Engineering, Lehigh >> University, Fritz Engineering Laboratory, 13 E. Packer >> Avenue, >> Bethlehem, PA 18015, USA >> FEATURES Location/Qualifiers >> source 1..425 >> /organism="Cryptosporidium environmental sequence" >> /mol_type="genomic DNA" >> /isolation_source="environmental water sample" >> /db_xref="taxon:310753" >> /clone="JF#1" >> /environmental_sample >> /country="USA: Massachusetts" >> /collection_date="Jun-2001" >> /collected_by="Kristen Jellison" >> /PCR_primers="fwd_name: CPB-DIAGF, rev_name: >> CPB-DIAGR" >> rRNA <1..>425 >> /product="18S small subunit ribosomal RNA" >> ORIGIN >> 1 aagctcgtag ttggatttct gctaatattc tatgtaaatg cttttgcctt >> tacatgttgt >> 61 tagccttccc cgtattactg cttcagtatg cggattttac tttgagaaaa >> ttagagtgct >> 121 taaagcaggc ttttgccttg aatactccag catggaataa tattaaagat >> ttttatcttt >> 181 cttattggtt ctaagataaa aataatgatt aatagggaca gttgggggca >> tttgtattta >> 241 acagtcagag gtgaaattct tagatttgtt aaagacaaac tagtgcgaaa >> gcatttgcca >> 301 aggatgtttt cattaatcaa gaacgaaagt taggggatcg aagacgatca >> gataccgtcg >> 361 tagtcttaac cataaactat gccaactaga gattggaggt tgttccttac >> tccttcagca >> 421 cctta >> // >> LOCUS EF060290 425 bp DNA linear ENV >> 14-NOV-2006 >> DEFINITION Cryptosporidium environmental sequence clone JF#2 18S >> small subunit >> ribosomal RNA gene, partial sequence. >> ACCESSION EF060290 >> VERSION EF060290.1 GI:117671304 >> KEYWORDS ENV. >> SOURCE Cryptosporidium environmental sequence >> ORGANISM Cryptosporidium environmental sequence >> Eukaryota; Alveolata; Apicomplexa; Coccidia; Eucoccidiorida; >> Eimeriorina; Cryptosporidiidae; Cryptosporidium; >> environmental >> samples. >> REFERENCE 1 (bases 1 to 425) >> AUTHORS Jellison,K.L., Distel,D.L., Hemond,H.F. and Schauer,D.B. >> TITLE Phylogenetic analysis implicates birds as an important >> source of >> Cryptosporidium spp. oocysts in agricultural watersheds >> JOURNAL Unpublished >> REFERENCE 2 (bases 1 to 425) >> AUTHORS Jellison,K.L. >> TITLE Direct Submission >> JOURNAL Submitted (12-OCT-2006) Civil and Environmental >> Engineering, Lehigh >> University, Fritz Engineering Laboratory, 13 E. Packer >> Avenue, >> Bethlehem, PA 18015, USA >> FEATURES Location/Qualifiers >> source 1..425 >> /organism="Cryptosporidium environmental sequence" >> /mol_type="genomic DNA" >> /isolation_source="environmental water sample" >> /db_xref="taxon:310753" >> /clone="JF#2" >> /environmental_sample >> /country="USA: Massachusetts" >> /collection_date="Jun-2001" >> /collected_by="Kristen Jellison" >> /note="PCR_primers=fwd_name: CPB-DIAGF, rev_name: >> CPB-DIAGR" >> rRNA <1..>425 >> /product="18S small subunit ribosomal RNA" >> ORIGIN >> 1 aagctcgtag ttggatttct gctaatattc tatgtaaatg cttttgcctt >> tacatgttgt >> 61 tagccttccc cgtattactg cttcagtatg cggattttac tttgagaaaa >> ttagagtgct >> 121 taaagcaggc tcttgccttg aatactccag catggaataa taccaaggat >> ttttgtcctt >> 181 cttattggtt ctaggataga aataatgatt aatagggaca gttgggggca >> tttgtattta >> 241 acagccagag gtgaaattct tagacttgtt aaagacaaac tagtgcgaaa >> gcatttgcca >> 301 aggatgtttt cattaatcaa gaacgaaagt taggggatcg aagacgatca >> gataccgtcg >> 361 tagtcttaac cataaactat gccaactaga gattggaggt tgttccttac >> tccttcagca >> 421 cctta >> // >> LOCUS EF060291 429 bp DNA linear ENV >> 14-NOV-2006 >> DEFINITION Cryptosporidium environmental sequence clone JF#3 18S >> small subunit >> ribosomal RNA gene, partial sequence. >> ACCESSION EF060291 >> VERSION EF060291.1 GI:117671305 >> KEYWORDS ENV. >> SOURCE Cryptosporidium environmental sequence >> ORGANISM Cryptosporidium environmental sequence >> Eukaryota; Alveolata; Apicomplexa; Coccidia; Eucoccidiorida; >> Eimeriorina; Cryptosporidiidae; Cryptosporidium; >> environmental >> samples. >> REFERENCE 1 (bases 1 to 429) >> AUTHORS Jellison,K.L., Distel,D.L., Hemond,H.F. and Schauer,D.B. >> TITLE Phylogenetic analysis implicates birds as an important >> source of >> Cryptosporidium spp. oocysts in agricultural watersheds >> JOURNAL Unpublished >> REFERENCE 2 (bases 1 to 429) >> AUTHORS Jellison,K.L. >> TITLE Direct Submission >> JOURNAL Submitted (12-OCT-2006) Civil and Environmental >> Engineering, Lehigh >> University, Fritz Engineering Laboratory, 13 E. Packer >> Avenue, >> Bethlehem, PA 18015, USA >> FEATURES Location/Qualifiers >> source 1..429 >> /organism="Cryptosporidium environmental sequence" >> /mol_type="genomic DNA" >> /isolation_source="environmental water sample" >> /db_xref="taxon:310753" >> /clone="JF#3" >> /environmental_sample >> /country="USA: Massachusetts" >> /collection_date="Aug-2001" >> /collected_by="Kristen Jellison" >> /note="PCR_primers=fwd_name: CPB-DIAGF, rev_name: >> CPB-DIAGR" >> rRNA <1..>429 >> /product="18S small subunit ribosomal RNA" >> ORIGIN >> 1 aagctcgtag ttggatttct gttagtgtct tatatcttgt actttattgt >> acttgtatag >> 61 tactaacata attcatatta ctttttagta ttatgaaatt ttactttgag >> aaaattagag >> 121 tgcttaaagc aggcttttgc cttgaatact ccagcatgga ataatacgaa >> ggatttttat >> 181 ctttcttatt ggttctaaga taaaaataat ggttaatagg aacagttggg >> ggcatttgta >> 241 tttaacagtc agaggtgaaa ttcttagatt tgttaaagac aaactaatgc >> gaaagcattt >> 301 gccaaggatg ttttcattaa tcaagaacga aagttagggg atcgaagacg >> atcagatacc >> 361 gtcgtagtct taaccataaa ctatgccaac tagagattgg aggttgttcc >> ttactccttc >> 421 agcacctta >> // >> LOCUS EF060292 430 bp DNA linear ENV >> 14-NOV-2006 >> DEFINITION Cryptosporidium environmental sequence clone JF#4 18S >> small subunit >> ribosomal RNA gene, partial sequence. >> ACCESSION EF060292 >> VERSION EF060292.1 GI:117671306 >> KEYWORDS ENV. >> SOURCE Cryptosporidium environmental sequence >> ORGANISM Cryptosporidium environmental sequence >> Eukaryota; Alveolata; Apicomplexa; Coccidia; Eucoccidiorida; >> Eimeriorina; Cryptosporidiidae; Cryptosporidium; >> environmental >> samples. >> REFERENCE 1 (bases 1 to 430) >> AUTHORS Jellison,K.L., Distel,D.L., Hemond,H.F. and Schauer,D.B. >> TITLE Phylogenetic analysis implicates birds as an important >> source of >> Cryptosporidium spp. oocysts in agricultural watersheds >> JOURNAL Unpublished >> REFERENCE 2 (bases 1 to 430) >> AUTHORS Jellison,K.L. >> TITLE Direct Submission >> JOURNAL Submitted (12-OCT-2006) Civil and Environmental >> Engineering, Lehigh >> University, Fritz Engineering Laboratory, 13 E. Packer >> Avenue, >> Bethlehem, PA 18015, USA >> FEATURES Location/Qualifiers >> source 1..430 >> /organism="Cryptosporidium environmental sequence" >> /mol_type="genomic DNA" >> /isolation_source="environmental water sample" >> /db_xref="taxon:310753" >> /clone="JF#4" >> /environmental_sample >> /country="USA: Massachusetts" >> /collection_date="Nov-2001" >> /collected_by="Kristen Jellison" >> /note="PCR_primers=fwd_name: CPB-DIAGF, rev_name: >> CPB-DIAGR" >> rRNA <1..>430 >> /product="18S small subunit ribosomal RNA" >> ORIGIN >> 1 aagctcgtag ttggatttct gttaattgtt tatatgattt atcttataat >> atttatatag >> 61 cattaacata attcatatta ctatttttag tatatgaaat tttactttga >> gaaaattaga >> 121 gtgcttaaag caggcttttg ccttgaatac tccagcatgg aataatatta >> aagattttta >> 181 tctttcttat tggttctaag atagaaataa tgattaatag ggacagttgg >> gggcatttgt >> 241 atttaacagt cagaggtgaa attcttagat ttgttaaaga caaactagtg >> cgaaagcatt >> 301 tgccaaggat gttttcatta atcaagaacg aaagttaggg gatcgaagac >> gatcagatac >> 361 cgtcgtagac ttaaccataa actatgccaa ctagagattg gaggttgttc >> cttactcctt >> 421 cagcacctta >> // >> LOCUS EF060293 432 bp DNA linear ENV >> 14-NOV-2006 >> DEFINITION Cryptosporidium environmental sequence clone JF#5 18S >> small subunit >> ribosomal RNA gene, partial sequence. >> ACCESSION EF060293 >> VERSION EF060293.1 GI:117671307 >> KEYWORDS ENV. >> SOURCE Cryptosporidium environmental sequence >> ORGANISM Cryptosporidium environmental sequence >> Eukaryota; Alveolata; Apicomplexa; Coccidia; Eucoccidiorida; >> Eimeriorina; Cryptosporidiidae; Cryptosporidium; >> environmental >> samples. >> REFERENCE 1 (bases 1 to 432) >> AUTHORS Jellison,K.L., Distel,D.L., Hemond,H.F. and Schauer,D.B. >> TITLE Phylogenetic analysis implicates birds as an important >> source of >> Cryptosporidium spp. oocysts in agricultural watersheds >> JOURNAL Unpublished >> REFERENCE 2 (bases 1 to 432) >> AUTHORS Jellison,K.L. >> TITLE Direct Submission >> JOURNAL Submitted (12-OCT-2006) Civil and Environmental >> Engineering, Lehigh >> University, Fritz Engineering Laboratory, 13 E. Packer >> Avenue, >> Bethlehem, PA 18015, USA >> FEATURES Location/Qualifiers >> source 1..432 >> /organism="Cryptosporidium environmental sequence" >> /mol_type="genomic DNA" >> /isolation_source="environmental water sample" >> /db_xref="taxon:310753" >> /clone="JF#5" >> /environmental_sample >> /country="USA: Massachusetts" >> /collection_date="Nov-2001" >> /collected_by="Kristen Jellison" >> /note="PCR_primers=fwd_name: CPB-DIAGF, rev_name: >> CPB-DIAGR" >> rRNA <1..>432 >> /product="18S small subunit ribosomal RNA" >> ORIGIN >> 1 aagctcgtag ttggatttct gttaattgtt tatatttgtt atctattgat >> acttgtataa >> 61 cactaacata attcatatta ctatttatct agtatatgaa agtttacttt >> gagaaaatta >> 121 gagtgcttaa agcaggcttt tgccttgaat actccaacat ggaataatat >> aaaagatttt >> 181 tatctttctt attggttcta agatagaaat aatgattaat agggacagtt >> gggggcattt >> 241 gtatttaaca gtcagaggtg aaattcttag atttgttaaa gacaaactag >> tgcgaaagca >> 301 tttgccaagg atgttttcat taatcaagaa cgaaagttag gggatcgaag >> acgatcagat >> 361 accgccgtag tcttaaccat aaactatgcc aactagagat tggaggttgt >> tccttactcc >> 421 ttcagcacct ta >> // >> LOCUS EF060294 432 bp DNA linear ENV >> 14-NOV-2006 >> DEFINITION Cryptosporidium environmental sequence clone JF#6 18S >> small subunit >> ribosomal RNA gene, partial sequence. >> ACCESSION EF060294 >> VERSION EF060294.1 GI:117671308 >> KEYWORDS ENV. >> SOURCE Cryptosporidium environmental sequence >> ORGANISM Cryptosporidium environmental sequence >> Eukaryota; Alveolata; Apicomplexa; Coccidia; Eucoccidiorida; >> Eimeriorina; Cryptosporidiidae; Cryptosporidium; >> environmental >> samples. >> REFERENCE 1 (bases 1 to 432) >> AUTHORS Jellison,K.L., Distel,D.L., Hemond,H.F. and Schauer,D.B. >> TITLE Phylogenetic analysis implicates birds as an important >> source of >> Cryptosporidium spp. oocysts in agricultural watersheds >> JOURNAL Unpublished >> REFERENCE 2 (bases 1 to 432) >> AUTHORS Jellison,K.L. >> TITLE Direct Submission >> JOURNAL Submitted (12-OCT-2006) Civil and Environmental >> Engineering, Lehigh >> University, Fritz Engineering Laboratory, 13 E. Packer >> Avenue, >> Bethlehem, PA 18015, USA >> FEATURES Location/Qualifiers >> source 1..432 >> /organism="Cryptosporidium environmental sequence" >> /mol_type="genomic DNA" >> /isolation_source="environmental water sample" >> /db_xref="taxon:310753" >> /clone="JF#6" >> /environmental_sample >> /country="USA: Massachusetts" >> /collection_date="Nov-2001" >> /collected_by="Kristen Jellison" >> /note="PCR_primers=fwd_name: CPB-DIAGF, rev_name: >> CPB-DIAGR" >> rRNA <1..>432 >> /product="18S small subunit ribosomal RNA" >> ORIGIN >> 1 aagctcgtag ttggatttct gttaattgtt tatatttgtt atctattgat >> acttgtataa >> 61 cattaacata attcatatta ctatttatct agtatatgaa attttacttt >> gagaaaatta >> 121 gagtgcttaa agcaggcttt tgccttgaat actccagcat ggaataatat >> taaagatttt >> 181 tatcattctt attggttcta agatagaaat aatgattaat agggacagtt >> gggggcattt >> 241 gtatttaaca gtcagaggtg aaattcttag atttgttaaa gacaaactag >> tgcgaaagca >> 301 tttgccaagg atgttttcat taatcaagaa cgaaagttag gggatcgaag >> acgatcagat >> 361 accgtcgtag tcataaccat aaactatgcc aactagagat tggaggttgt >> tccttactcc >> 421 ttcagcacct ta >> // >> LOCUS EF060295 425 bp DNA linear ENV >> 14-NOV-2006 >> DEFINITION Cryptosporidium environmental sequence clone Cow 18S >> small subunit >> ribosomal RNA gene, partial sequence. >> ACCESSION EF060295 >> VERSION EF060295.1 GI:117671309 >> KEYWORDS ENV. >> SOURCE Cryptosporidium environmental sequence >> ORGANISM Cryptosporidium environmental sequence >> Eukaryota; Alveolata; Apicomplexa; Coccidia; Eucoccidiorida; >> Eimeriorina; Cryptosporidiidae; Cryptosporidium; >> environmental >> samples. >> REFERENCE 1 (bases 1 to 425) >> AUTHORS Jellison,K.L., Hemond,H.F. and Schauer,D.B. >> TITLE Sources and species of Cryptosporidium oocysts in the >> Wachusett >> Reservoir watershed >> JOURNAL Appl. Environ. Microbiol. 68 (2), 569-575 (2002) >> PUBMED 11823192 >> REFERENCE 2 (bases 1 to 425) >> AUTHORS Jellison,K.L., Distel,D.L., Hemond,H.F. and Schauer,D.B. >> TITLE Phylogenetic analysis implicates birds as an important >> source of >> Cryptosporidium spp. oocysts in agricultural watersheds >> JOURNAL Unpublished >> REFERENCE 3 (bases 1 to 425) >> AUTHORS Jellison,K.L., Distel,D.L. and Hemond,H.F. >> TITLE Direct Submission >> JOURNAL Submitted (12-OCT-2006) Civil and Environmental >> Engineering, Lehigh >> University, Fritz Engineering Laboratory, 13 E. Packer >> Avenue, >> Bethlehem, PA 18015, United States >> FEATURES Location/Qualifiers >> source 1..425 >> /organism="Cryptosporidium environmental sequence" >> /mol_type="genomic DNA" >> /isolation_source="adult Bos taurus" >> /db_xref="taxon:310753" >> /clone="Cow" >> /environmental_sample >> /country="USA: Massachusetts" >> /collection_date="Jun-2000" >> /collected_by="Kristen Jellison" >> /note="PCR_primers=fwd_name: CPB-DIAGF, rev_name: >> CPB-DIAGR" >> rRNA <1..>425 >> /product="18S small subunit ribosomal RNA" >> ORIGIN >> 1 aagctcgtag ttggatttct gttaattttt atatataata tcacgatatt >> tatataatat >> 61 taacataatt catattactt tttagtatat gaaactttac tttgagaaaa >> ttagagtgct >> 121 taaagcaggc tattgccttg aatactccag catggaataa tattaaggat >> ttttattctt >> 181 cttattggtt ctagaataaa aatgatgatt aatagggaca gttgggggca >> tttgtattta >> 241 acagtcagag gtgaaattct tagatttgtt aaagacaaac tactgcgaaa >> gcatttgcca >> 301 aggatgtttt cattaatcaa gaacgaaagt taggggatcg aagacgatca >> gataccgtcg >> 361 tagtcttaac cattaactat gccaactaga gattggaggt tgttccttac >> tccttcagca >> 421 cctta >> // >> LOCUS EF060296 431 bp DNA linear ENV >> 14-NOV-2006 >> DEFINITION Cryptosporidium environmental sequence clone Manure 18S small >> subunit ribosomal RNA gene, partial sequence. >> ACCESSION EF060296 >> VERSION EF060296.1 GI:117671310 >> KEYWORDS ENV. >> SOURCE Cryptosporidium environmental sequence >> ORGANISM Cryptosporidium environmental sequence >> Eukaryota; Alveolata; Apicomplexa; Coccidia; Eucoccidiorida; >> Eimeriorina; Cryptosporidiidae; Cryptosporidium; >> environmental >> samples. >> REFERENCE 1 (bases 1 to 431) >> AUTHORS Jellison,K.L., Hemond,H.F. and Schauer,D.B. >> TITLE Sources and species of Cryptosporidium oocysts in the >> Wachusett >> Reservoir watershed >> JOURNAL Appl. Environ. Microbiol. 68 (2), 569-575 (2002) >> PUBMED 11823192 >> REFERENCE 2 (bases 1 to 431) >> AUTHORS Jellison,K.L., Distel,D.L., Hemond,H.F. and Schauer,D.B. >> TITLE Phylogenetic analysis implicates birds as an important >> source of >> Cryptosporidium spp. oocysts in agricultural watersheds >> JOURNAL Unpublished >> REFERENCE 3 (bases 1 to 431) >> AUTHORS Jellison,K.L. >> TITLE Direct Submission >> JOURNAL Submitted (12-OCT-2006) Civil and Environmental >> Engineering, Lehigh >> University, Fritz Engineering Laboratory, 13 E. Packer >> Avenue, >> Bethlehem, PA 18015, USA >> FEATURES Location/Qualifiers >> source 1..431 >> /organism="Cryptosporidium environmental sequence" >> /mol_type="genomic DNA" >> /isolation_source="farm manure pit" >> /db_xref="taxon:310753" >> /clone="Manure" >> /environmental_sample >> /country="USA: Massachusetts" >> /collection_date="Jun-2000" >> /collected_by="Kristen Jellison" >> /note="PCR_primers=fwd_name: CPB-DIAGF, rev_name: >> CPB-DIAGR" >> rRNA <1..>431 >> /product="18S small subunit ribosomal RNA" >> ORIGIN >> 1 aagctcgtag ttggatttct gttgtataat ttataatatt accaaggtaa >> ttattatatt >> 61 atcaacatcc ttcctattat attctaaata tataggaaat tttactttga >> gaaaattaga >> 121 gtgcttaaag caggcaactg ccttgaatac tccagcatgg aataataagt >> aaggactttt >> 181 gtctttctta ttggttctag gacaaaagta atggttaata gggacagttg >> ggggcattcg >> 241 tatttaacag ccagaggtga aattcttaga tttgttaaag acgaactact >> gcgaaagcat >> 301 ttgccaagga tgttttcatt aatcaagaac gaaagttagg ggatcgaaga >> cgatcagata >> 361 ccgtcgtagt cttaaccata aactatgccg actagagatt ggaggttgtt >> ccttactcct >> 421 tcagcacctt a >> // >> LOCUS EF060297 431 bp DNA linear ENV >> 14-NOV-2006 >> DEFINITION Cryptosporidium environmental sequence clone SF 18S small >> subunit >> ribosomal RNA gene, partial sequence. >> ACCESSION EF060297 >> VERSION EF060297.1 GI:117671311 >> KEYWORDS ENV. >> SOURCE Cryptosporidium environmental sequence >> ORGANISM Cryptosporidium environmental sequence >> Eukaryota; Alveolata; Apicomplexa; Coccidia; Eucoccidiorida; >> Eimeriorina; Cryptosporidiidae; Cryptosporidium; >> environmental >> samples. >> REFERENCE 1 (bases 1 to 431) >> AUTHORS Jellison,K.L., Hemond,H.F. and Schauer,D.B. >> TITLE Sources and species of Cryptosporidium oocysts in the >> Wachusett >> Reservoir watershed >> JOURNAL Appl. Environ. Microbiol. 68 (2), 569-575 (2002) >> PUBMED 11823192 >> REFERENCE 2 (bases 1 to 431) >> AUTHORS Jellison,K.L., Distel,D.L., Hemond,H.F. and Schauer,D.B. >> TITLE Phylogenetic analysis implicates birds as an important >> source of >> Cryptosporidium spp. oocysts in agricultural watersheds >> JOURNAL Unpublished >> REFERENCE 3 (bases 1 to 431) >> AUTHORS Jellison,K.L. >> TITLE Direct Submission >> JOURNAL Submitted (12-OCT-2006) Civil and Environmental >> Engineering, Lehigh >> University, Fritz Engineering Laboratory, 13 E. Packer >> Avenue, >> Bethlehem, PA 18015, USA >> FEATURES Location/Qualifiers >> source 1..431 >> /organism="Cryptosporidium environmental sequence" >> /mol_type="genomic DNA" >> /isolation_source="environmental water sample" >> /db_xref="taxon:310753" >> /clone="SF" >> /environmental_sample >> /country="USA: Massachusetts" >> /collection_date="Mar-1999" >> /collected_by="Kristen Jellison" >> /note="PCR_primers=fwd_name: CPB-DIAGF, rev_name: >> CPB-DIAGR" >> rRNA <1..>431 >> /product="18S small subunit ribosomal RNA" >> ORIGIN >> 1 aagctcgtag ttggatttct gctgtataat ttataatatt accaaggtaa >> ttattatatt >> 61 atcaacatcc ttcctattat attctaaata tataggaaat tttactttga >> gaaaattaga >> 121 gtgcttaaag caggcaactg ccttgaatac tccagcatgg aataataagt >> aaggactttt >> 181 gtctttctta ttggttctag gacaaaagta atggttaata gggacagttg >> ggggcattcg >> 241 tatttaacag ccagaggtga agttcttaga tttgttaaag acgaactact >> gcgaaagcat >> 301 ttgccaagga tgttttcatt aatcaagaac gaaagttagg ggatcgaaga >> cgatcagata >> 361 ccgtcgtagt cttaaccata aactatgccg actagagatt ggaggttgtt >> ccttactcct >> 421 tcagcacctt a >> // >> >> _______________________________________________ >> ApiDB mailing list >> Ap...@pc... <mailto:Ap...@pc...> >> https://mail.pcbi.upenn.edu/mailman/listinfo/apidb > |
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