gusdev-gusdev — Topics concerning GUS development

[GUSDEV] Fwd: SequenceGroup table

[Chris S. <sto...@pc...>]

Hi All,
Have not gotten any response to the email so am taking this as an  
indication that it's OK to move ahead with this proposal.
Will set this up in our local instances but also put this on the GUS  
bug tracker for inclusion in the next release.

BTW, we really are planning to have another release. This month we  
hope to have someone start going through all the patch, bug fixes,  
and schema changes on the tracker to plan the release.

Cheers,
Chris

Begin forwarded message:

> From: Chris Stoeckert <sto...@pc...>
> Date: February 21, 2007 6:09:07 PM EST
> To: GUS-Dev gusdev-gusdev <gus...@li...>
> Subject: SequenceGroup table
>
> Hi,
> We are loading a new set of OrthoMCL generated ortholog groups into  
> an instance of GUS and found that the current  SequenceGroup parent  
> table has several specifically-named attributes (i.e., no generic  
> attributes) that we can use for our purposes without renaming. The  
> attributes we want to capture are quality metrics for an ortholog  
> group. For example we'd like to capture the ave e-value rather that  
> min and max as currently provided in SequenceGroup and all of its  
> views including OrthologGroup.
>
> I'd like to make the following proposal, get feedback, and put in  
> the GUS schema bug tracker.
> 1) Create a OrthoMCL view. This would be specific to our GUS  
> instances but could be used as a template for renaming attributes  
> in OrthologGroup. On the right I've indicated with <- the parent  
> attribute that might be used where the name differs.
>
> Column	nulls?	type
> SEQUENCE_GROUP_ID	NO	NUMBER
> SUBCLASS_VIEW	NO	STRING(100)
> NAME		STRING(500)
> DESCRIPTION		STRING(2000)
> NUMBER_OF_MEMBERS	NO	NUMBER
> NUMBER_OF_TAXA		NUMBER
> AVE_PERCENT_IDENTITY		FLOAT <-MIN_MATCH_IDENTITY
> AVE_PERCENT_COVERAGE		FLOAT  <- MIN_PERCENT_MATCH
> AVE_E_VALUE		FLOAT <- MIN_PVALUE_MANT
> AVE_DOMAIN_SHARING		FLOAT <- MAX_SCORE
> BLAST_MATCH_RATIO		FLOAT <- MIN_SCORE
> SEQ_GROUP_EXPERIMENT_ID		FOREIGN KEY
> plus the usual housekeeping columns
>
> In this proposal, the OrthoMCLGroup attributes would have the same  
> type but different semantics as implied by the names of attributes  
> in the parent class and queries can easily avoid this by use of  
> subclass view.
>
> 2) Rename the SequenceGroup attributes to be more generic.  
> Suggested changes are:
> MAX_MATCH_IDENTITY -> GROUP_IDENTITY_METRIC1
> MIN_MATCH_IDENTITY -> GROUP_IDENTITY_METRIC2
> MAX_PERCENT_MATCH -> GROUP_MATCH_METRIC1
> MIN_PERCENT_MATCH -> GROUP_MATCH_METRIC2
> MAX_PVALUE_MANT -> GROUP_PVALUE_MANT
> MAX_PVALUE_EXP -> GROUP_PVALUE_EXP
> MAX_PVALUE_MANT -> GROUP_EVALUE_MANT
> MAX_PVALUE_EXP -> GROUP_EVALUE_EXP
> MAX_SCORE -> GROUP_QUALITY_METRIC1
> MIN_SCORE -> GROUP_QUALITY_METRIC2
>
> Thoughts?
> 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
>
>

[GUSDEV] SequenceGroup table

[Chris S. <sto...@pc...>]

Hi,
We are loading a new set of OrthoMCL generated ortholog groups into  
an instance of GUS and found that the current  SequenceGroup parent  
table has several specifically-named attributes (i.e., no generic  
attributes) that we can use for our purposes without renaming. The  
attributes we want to capture are quality metrics for an ortholog  
group. For example we'd like to capture the ave e-value rather that  
min and max as currently provided in SequenceGroup and all of its  
views including OrthologGroup.

I'd like to make the following proposal, get feedback, and put in the  
GUS schema bug tracker.
1) Create a OrthoMCL view. This would be specific to our GUS  
instances but could be used as a template for renaming attributes in  
OrthologGroup. On the right I've indicated with <- the parent  
attribute that might be used where the name differs.

Column	nulls?	type
SEQUENCE_GROUP_ID	NO	NUMBER
SUBCLASS_VIEW	NO	STRING(100)
NAME		STRING(500)
DESCRIPTION		STRING(2000)
NUMBER_OF_MEMBERS	NO	NUMBER
NUMBER_OF_TAXA		NUMBER
AVE_PERCENT_IDENTITY		FLOAT <-MIN_MATCH_IDENTITY
AVE_PERCENT_COVERAGE		FLOAT  <- MIN_PERCENT_MATCH
AVE_E_VALUE		FLOAT <- MIN_PVALUE_MANT
AVE_DOMAIN_SHARING		FLOAT <- MAX_SCORE
BLAST_MATCH_RATIO		FLOAT <- MIN_SCORE
SEQ_GROUP_EXPERIMENT_ID		FOREIGN KEY
plus the usual housekeeping columns

In this proposal, the OrthoMCLGroup attributes would have the same  
type but different semantics as implied by the names of attributes in  
the parent class and queries can easily avoid this by use of subclass  
view.

2) Rename the SequenceGroup attributes to be more generic. Suggested  
changes are:
MAX_MATCH_IDENTITY -> GROUP_IDENTITY_METRIC1
MIN_MATCH_IDENTITY -> GROUP_IDENTITY_METRIC2
MAX_PERCENT_MATCH -> GROUP_MATCH_METRIC1
MIN_PERCENT_MATCH -> GROUP_MATCH_METRIC2
MAX_PVALUE_MANT -> GROUP_PVALUE_MANT
MAX_PVALUE_EXP -> GROUP_PVALUE_EXP
MAX_PVALUE_MANT -> GROUP_EVALUE_MANT
MAX_PVALUE_EXP -> GROUP_EVALUE_EXP
MAX_SCORE -> GROUP_QUALITY_METRIC1
MIN_SCORE -> GROUP_QUALITY_METRIC2

Thoughts?
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

Re: [GUSDEV] Using LoadFastaSequences plugin

[John I. <io...@pc...>]

Dhivya,

It's not clear what exactly is going wrong.  The uniqueness of  
algorithm_param_key_id values should be maintained using a database  
sequence.   One could picture a bug that results in a failure to get  
the sequence nextval, but it's hard to picture the sequence returning  
65 twice.

One could imagine that the primary-key incrementing is failing across  
the board, but that core.AlgorithmParamKey is the first table into  
which a second record gets written (after one record each are put  
into AlgorithmImplementation and AlgorithmInvocation).

Some questions:

Have other plugins run successfully?

Are there any rows in core.AlgorithmParamKey before you run the  
plugin?  (and, if so, what are their primary-key values?)

What happens when you give the following SQL statement to psql?
select nextval('core.algorithmparamkey_sq');

What happens when you run that statement a second time?

What version of PostgreSQL are you using?  (we're using 7.4.16)

John


On Feb 12, 2007, at 10:50 AM, Mark S. Heiges wrote:

> Does anyone have any advice on this?
>
> On Jan 18, 2007, at 8:50 AM, Dhivya Aras wrote:
>
>> Hi,
>>
>> I'm trying to use the LoadFastaSequences plugin to load GUS tables
>> with the fasta sequences or certain nrdb proteins.
>>
>> But, when I run the plugin I get an error about a primary key
>> constraint violation. When I tested by removing the primary key
>> constraint, the plugin loaded duplicates (for primary key column,
>> algorithm_param_key_id) into algorithmparamkey table.
>>
>> I'm using GUS3.5 with postgres.
>>
>>
>> On running the registration for the plugin
>>
>> ga +create GUS::Supported::Plugin::LoadFastaSequences --commit
>>
>>
>> The stack trace contains the following:
>>
>> DBD::Pg::st execute failed: ERROR:  duplicate key violates unique
>> constraint "al
>> gorithmparamkey_pkey" at /home/gus/GUS/gus_home/lib/perl/GUS/
>> ObjRelP/DbiDbHandle
>> .pm line 147.
>>
>>  SQL ERROR!! involving
>>
>>     INSERT INTO Core.AlgorithmParamKey (  group_read,
>> algorithm_param_key_id, us
>> er_read, algorithm_implementation_id, other_write,
>> modification_date, algorithm_
>> param_key_type_id, row_group_id, algorithm_param_key, user_write,
>> group_write, o
>> ther_read, description, row_user_id, row_alg_invocation_id,
>> row_project_id, is_l
>> ist_valued )
>>     VALUES   (  ?, ?, ?, ?, ?, now
>> (), ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ? )
>>  Values: 1, 65, 1, 21, 0, 1, 1, regexSourceId, 1, 1, 1, The regular
>> expression t
>> o pick the source_id of the sequence from the defline, 1, 1, 1, 0
>> at /home/gus/G
>> US/gus_home/lib/perl/GUS/ObjRelP/DbiDbHandle.pm line 166
>>         GUS::ObjRelP::DbiDbHandle::death
>> ('GUS::ObjRelP::DbiDbHandle=HASH(0x89bb1
>> 8c)', '\x{a} SQL ERROR!! involving\x{a} \x{a}    INSERT INTO
>> Core.AlgorithmParam
>> ...') called at /home/gus/GUS/gus_home/lib/perl/GUS/ObjRelP/
>> DbiDbHandle.pm line
>> 150
>>         GUS::ObjRelP::DbiDbHandle::sqlExec
>> ('GUS::ObjRelP::DbiDbHandle=HASH(0x89b
>> b18c)', 'GUS::ObjRelP::DbiDbHandle::st=HASH(0x8fbce10)', 'ARRAY
>> (0x8fbceac)', '\x
>> {a}    INSERT INTO Core.AlgorithmParamKey (  group_read,
>> algori...') called at /
>> home/gus/GUS/gus_home/lib/perl/GUS/ObjRelP/DbiRow.pm line 666
>>         GUS::ObjRelP::DbiRow::quote_and_insert
>> ('GUS::Model::Core::AlgorithmParam
>> Key=HASH(0x8fad2f8)', 'HASH(0x8fb8874)') called at /home/gus/GUS/
>> gus_home/lib/pe
>> rl/GUS/ObjRelP/DbiRow.pm line 613
>>         GUS::ObjRelP::DbiRow::insert
>> ('GUS::Model::Core::AlgorithmParamKey=HASH(0
>> x8fad2f8)') called at /home/gus/GUS/gus_home/lib/perl/GUS/Model/
>> GusRow.pm line 1
>> 692
>>         GUS::Model::GusRow::submit
>> ('GUS::Model::Core::AlgorithmParamKey=HASH(0x8
>> fad2f8)', 'undef', 1) called at /home/gus/GUS/gus_home/lib/perl/GUS/
>> Model/GusRow
>> .pm line 1779
>>         GUS::Model::GusRow::submitChildrenInClass
>> ('GUS::Model::Core::AlgorithmIm
>> plementation=HASH(0x8f5f7f8)',
>> 'GUS::Model::Core::AlgorithmParamKey') called at
>> /home/gus/GUS/gus_home/lib/perl/GUS/Model/GusRow.pm line 1760
>>         GUS::Model::GusRow::submitAllChildren
>> ('GUS::Model::Core::AlgorithmImplem
>> entation=HASH(0x8f5f7f8)') called at /home/gus/GUS/gus_home/lib/
>> perl/GUS/Model/G
>> usRow.pm line 1699
>>         GUS::Model::GusRow::submit
>> ('GUS::Model::Core::AlgorithmImplementation=HA
>> SH(0x8f5f7f8)', 'undef', 1) called at /home/gus/GUS/gus_home/lib/
>> perl/GUS/Model/
>> GusRow.pm line 1779
>>         GUS::Model::GusRow::submitChildrenInClass
>> ('GUS::Model::Core::Algorithm=H
>> ASH(0x8f5d500)', 'GUS::Model::Core::AlgorithmImplementation')
>> called at /home/gu                                     s/GUS/
>> gus_home/lib/perl/GUS/Model/GusRow.pm line 1760
>>         GUS::Model::GusRow::submitAllChildren
>> ('GUS::Model::Core::Algorithm=HASH
>> (                                     0x8f5d500)') called at /home/
>> gus/GUS/gus_home/lib/perl/GUS/Model/GusRow.pm
>> line                                      1699
>>         GUS::Model::GusRow::submit('GUS::Model::Core::Algorithm=HASH
>> (0x8f5d500)'                                     ) called at /home/
>> gus/GUS/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm
>> line                                      900
>>
>> GUS::PluginMgr::GusApplication::create_or_update_implementation
>> ('GUS::Pl
>> uginMgr::GusApplication=HASH(0x877dc20)', 0,
>> 'GUS::Supported::Plugin::LoadFastaS
>>   equences') called at /home/gus/GUS/gus_home/lib/perl/GUS/
>> PluginMgr/GusApplicatio                                     n.pm
>> line 546
>>         GUS::PluginMgr::GusApplication::doMajorMode_Create
>> ('GUS::PluginMgr::GusA
>> pplication=HASH(0x877dc20)',
>> 'GUS::Supported::Plugin::LoadFastaSequences')
>> calle                                     d at /home/gus/GUS/
>> gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm line 337
>>         GUS::PluginMgr::GusApplication::doMajorMode
>> ('GUS::PluginMgr::GusApplicat
>> ion=HASH(0x877dc20)', 'GUS::Supported::Plugin::LoadFastaSequences')
>> called at /h                                     ome/gus/GUS/
>> gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm line 246
>>         GUS::PluginMgr::GusApplication::parseAndRun
>> ('GUS::PluginMgr::GusApplicat
>> ion HASH(0x877dc20)', 'ARRAY(0x87916d0)') called at /home/gus/GUS/
>> gus_home/bin/ga line 11
>>
>>
>>
>> Any ideas about why this could be happening and how to fix it?
>>
>> Thanks
>> dhivya arasappan
>>
>>
>>
>>
>>
>>
>>
>> Bored stiff? Loosen up...
>> Download and play hundreds of games for free on Yahoo! Games.
>
>
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Re: [GUSDEV] Using LoadFastaSequences plugin

[Mark S. H. <mh...@ug...>]

Does anyone have any advice on this?

On Jan 18, 2007, at 8:50 AM, Dhivya Aras wrote:

> Hi,
>
> I'm trying to use the LoadFastaSequences plugin to load GUS tables  
> with the fasta sequences or certain nrdb proteins.
>
> But, when I run the plugin I get an error about a primary key  
> constraint violation. When I tested by removing the primary key  
> constraint, the plugin loaded duplicates (for primary key column,  
> algorithm_param_key_id) into algorithmparamkey table.
>
> I'm using GUS3.5 with postgres.
>
>
> On running the registration for the plugin
>
> ga +create GUS::Supported::Plugin::LoadFastaSequences --commit
>
>
> The stack trace contains the following:
>
> DBD::Pg::st execute failed: ERROR:  duplicate key violates unique  
> constraint "al
> gorithmparamkey_pkey" at /home/gus/GUS/gus_home/lib/perl/GUS/ 
> ObjRelP/DbiDbHandle
> .pm line 147.
>
>  SQL ERROR!! involving
>
>     INSERT INTO Core.AlgorithmParamKey (  group_read,  
> algorithm_param_key_id, us
> er_read, algorithm_implementation_id, other_write,  
> modification_date, algorithm_
> param_key_type_id, row_group_id, algorithm_param_key, user_write,  
> group_write, o
> ther_read, description, row_user_id, row_alg_invocation_id,  
> row_project_id, is_l
> ist_valued )
>     VALUES   (  ?, ?, ?, ?, ?, now 
> (), ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ? )
>  Values: 1, 65, 1, 21, 0, 1, 1, regexSourceId, 1, 1, 1, The regular  
> expression t
> o pick the source_id of the sequence from the defline, 1, 1, 1, 0  
> at /home/gus/G
> US/gus_home/lib/perl/GUS/ObjRelP/DbiDbHandle.pm line 166
>         GUS::ObjRelP::DbiDbHandle::death 
> ('GUS::ObjRelP::DbiDbHandle=HASH(0x89bb1
> 8c)', '\x{a} SQL ERROR!! involving\x{a} \x{a}    INSERT INTO  
> Core.AlgorithmParam
> ...') called at /home/gus/GUS/gus_home/lib/perl/GUS/ObjRelP/ 
> DbiDbHandle.pm line
> 150
>         GUS::ObjRelP::DbiDbHandle::sqlExec 
> ('GUS::ObjRelP::DbiDbHandle=HASH(0x89b
> b18c)', 'GUS::ObjRelP::DbiDbHandle::st=HASH(0x8fbce10)', 'ARRAY 
> (0x8fbceac)', '\x
> {a}    INSERT INTO Core.AlgorithmParamKey (  group_read,  
> algori...') called at /
> home/gus/GUS/gus_home/lib/perl/GUS/ObjRelP/DbiRow.pm line 666
>         GUS::ObjRelP::DbiRow::quote_and_insert 
> ('GUS::Model::Core::AlgorithmParam
> Key=HASH(0x8fad2f8)', 'HASH(0x8fb8874)') called at /home/gus/GUS/ 
> gus_home/lib/pe
> rl/GUS/ObjRelP/DbiRow.pm line 613
>         GUS::ObjRelP::DbiRow::insert 
> ('GUS::Model::Core::AlgorithmParamKey=HASH(0
> x8fad2f8)') called at /home/gus/GUS/gus_home/lib/perl/GUS/Model/ 
> GusRow.pm line 1
> 692
>         GUS::Model::GusRow::submit 
> ('GUS::Model::Core::AlgorithmParamKey=HASH(0x8
> fad2f8)', 'undef', 1) called at /home/gus/GUS/gus_home/lib/perl/GUS/ 
> Model/GusRow
> .pm line 1779
>         GUS::Model::GusRow::submitChildrenInClass 
> ('GUS::Model::Core::AlgorithmIm
> plementation=HASH(0x8f5f7f8)',  
> 'GUS::Model::Core::AlgorithmParamKey') called at
> /home/gus/GUS/gus_home/lib/perl/GUS/Model/GusRow.pm line 1760
>         GUS::Model::GusRow::submitAllChildren 
> ('GUS::Model::Core::AlgorithmImplem
> entation=HASH(0x8f5f7f8)') called at /home/gus/GUS/gus_home/lib/ 
> perl/GUS/Model/G
> usRow.pm line 1699
>         GUS::Model::GusRow::submit 
> ('GUS::Model::Core::AlgorithmImplementation=HA
> SH(0x8f5f7f8)', 'undef', 1) called at /home/gus/GUS/gus_home/lib/ 
> perl/GUS/Model/
> GusRow.pm line 1779
>         GUS::Model::GusRow::submitChildrenInClass 
> ('GUS::Model::Core::Algorithm=H                                      
> ASH(0x8f5d500)', 'GUS::Model::Core::AlgorithmImplementation')  
> called at /home/gu                                     s/GUS/ 
> gus_home/lib/perl/GUS/Model/GusRow.pm line 1760
>         GUS::Model::GusRow::submitAllChildren 
> ('GUS::Model::Core::Algorithm=HASH 
> (                                     0x8f5d500)') called at /home/ 
> gus/GUS/gus_home/lib/perl/GUS/Model/GusRow.pm  
> line                                      1699
>         GUS::Model::GusRow::submit('GUS::Model::Core::Algorithm=HASH 
> (0x8f5d500)'                                     ) called at /home/ 
> gus/GUS/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm  
> line                                      900
>          
> GUS::PluginMgr::GusApplication::create_or_update_implementation 
> ('GUS::Pl                                      
> uginMgr::GusApplication=HASH(0x877dc20)', 0,  
> 'GUS::Supported::Plugin::LoadFastaS                                    
>   equences') called at /home/gus/GUS/gus_home/lib/perl/GUS/ 
> PluginMgr/GusApplicatio                                     n.pm  
> line 546
>         GUS::PluginMgr::GusApplication::doMajorMode_Create 
> ('GUS::PluginMgr::GusA                                      
> pplication=HASH(0x877dc20)',  
> 'GUS::Supported::Plugin::LoadFastaSequences')  
> calle                                     d at /home/gus/GUS/ 
> gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm line 337
>         GUS::PluginMgr::GusApplication::doMajorMode 
> ('GUS::PluginMgr::GusApplicat                                      
> ion=HASH(0x877dc20)', 'GUS::Supported::Plugin::LoadFastaSequences')  
> called at /h                                     ome/gus/GUS/ 
> gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm line 246
>         GUS::PluginMgr::GusApplication::parseAndRun 
> ('GUS::PluginMgr::GusApplicat                                      
> ion HASH(0x877dc20)', 'ARRAY(0x87916d0)') called at /home/gus/GUS/ 
> gus_home/bin/ga line 11
>
>
>
> Any ideas about why this could be happening and how to fix it?
>
> Thanks
> dhivya arasappan
>
>
>
>
>
>
>
> Bored stiff? Loosen up...
> Download and play hundreds of games for free on Yahoo! Games.

[GUSDEV] Superclass view of imp tables ... dots::aafeature

[Brian B. <br...@pc...>]

I would like to raise for discussion an issue that we have been faced  
with here at Penn in the last couple of weeks.  It turns out that in  
GUS3.5 all named attributes of imp tables are now included in the  
superclass view.  Following is the aafeature view:


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)
PFAM_ENTRY_ID		DoTS::PfamEntry (NUMBER(10,0) )
MOTIF_AA_SEQUENCE_ID		DoTS::AASequence (NUMBER(10,0) )
REPEAT_TYPE_ID		DoTS::RepeatType (NUMBER(10,0) )
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) )
MODIFICATION_DATE	no	DATE

My understanding of the intent of superclass views is that they have  
attributes that are common to all subclasses in a typical class  
hierarchy.  From a biological perspective, this would be attributes  
that are common to all (or at least nearly all) features.  Because  
all named attributes are now in this view, there are a number of  
attributes that are not relevant for all aafeatures (or even the  
majority of aafeatures).  This is because GUS also has a requirement  
that all fields used in foreign key references must be named  
attributes.  This is for clarity and makes obvious sense.  This  
means, however, that now these foreign key attributes are included in  
the superclass view (and inherited by all the subclasses).  The above  
table has three such attributes that I think would be much better  
served only  in the specific views that need them such as  
DoTS::RepeatRegionAAFeature for repeat_type_id.  I don't see any  
views where it is obvious to me one would want to use pfam_entry_id  
or motif_aa_sequence_id.

PFAM_ENTRY_ID		DoTS::PfamEntry (NUMBER(10,0) )
MOTIF_AA_SEQUENCE_ID		DoTS::AASequence (NUMBER(10,0) )
REPEAT_TYPE_ID		DoTS::RepeatType (NUMBER(10,0) )

The motif_aa_sequence_id is particularly problematic as this causes  
there to be two foreign key references into the aasequence table.   
The PERL object layer only supports having two foreign key references  
to a table via manual entries into the special cases file.  This  
works fine for a limited number of tables (views) but is overwhelming  
when dealing with a large number such as for all the aafeature views.

I would propose that we drop these extra named attributes from the  
superclass views in the next release of GUS.  This will clean up all  
the views and make them easier to understand.  It will also alleviate  
problems with the PERL object layer related to multiple foreign key  
references.  For those views that contain multiple references such as  
RepeatRegionAAFeature, we should enter the necessary lines in the  
special_cases file so that the objects work without coding around the  
limitation (which is what I suspect persons are doing now).

Comments?

-Brian

Brian P. Brunk, Ph.D.
ApiDB Senior Manager
1424 Blockley Hall
Penn Center For Bioinformatics
University of Pennsylvania
Philadelphia PA 19104-6021
Tel: 215-573-3118
Fax: 215-573-3111

Re: [GUSDEV] Storing a provider name for an external database

[Elisabetta M. <man...@pc...>]

I'm not familiar with the specs of these datasets. The following could 
possibly be used to store the info in a way semantically consistent with 
other datasets we store in GUS (e.g. in RAD) at CBIL, but the issue is 
then how to best link this to the particular data for the dataset you 
have (e.g. for microarray studies we have a linking table linking studies 
to assays).

dataset name = Study.Study.name

data provider's name = Study.contact_id->SRes.Contact.name (if individual 
use SRes.Contact.first and last too)

short version of the provider's name = concatenate to SRes.Contact.name in 
parentheses

uri = Study.Study.bibliographic_reference_id->SRes.BibliographicReference.uri
with bib_type "online-resource".

Elisabetta

---

On Thu, 25 Jan 2007, Chris Stoeckert wrote:

> Hi John,
> I'm putting this on the gusdev list as non-ApiDB users may have
> similar questions or some insights to offer.
>
> As we just discussed offline, your task here is not to capture where
> the dataset was downloaded but rather who submitted the dataset to
> the resource (e.g., GenBank)  we got it from. ExternalDatabase and
> ExternalDatabaseRelease are meant for the former. Provider
> information (who should be given attribution) should be captured in
> the SRes.Contact table. I don't see an explicit attribute for a home
> page (the URL) but perhaps one of the RAD people can suggest a
> solution since they use Contact extensively for attribution of
> microrarray studies and and samples.
>
> Chris
>
> On Jan 24, 2007, at 5:04 PM, John Iodice wrote:
>
>> Chris,
>>
>> The attribution info at the bottom of PlasmoDB sequence pages is
>> currently generated by the JSP code, as a function of the species
>> and sequence source_id.  The attribution data in the GFF files we
>> upload to to the Interoperability Working Group are calculated in
>> the SQL in the model files.  We'd like to store this attribution
>> info in the database instead.
>>
>> There are four character strings to be stored for each dataset:
>>
>> the dataset name (e.g. "Plasmodium falciparum mitochondrial genome")
>> the data provider's name ("London School of Hygiene & Tropical
>> Medicine")
>> a short version of the provider's name ("LSHTM")
>> the URL ("http://www.lshtm.ac.uk/pmbu/staff/dconway/dconway.html")
>>
>> Steve and I talked about this today.  We're proposing to store the
>> dataset name, short name and URL in ExternalDatabase.name,
>> ExternalDatabaseRelease.id_type, and
>> ExternalDatabaseRelease.id_url, respectively.  We're proposing the
>> addition of a new varchar column named "provider" to the
>> ExternalDatabaseRelease table.
>>
>> What do you think of this?  Is there a better way?  Does GUS
>> already support this?
>>
>> Thanks for any feedback you can give us.
>>
>> John
>
>
> -------------------------------------------------------------------------
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Re: [GUSDEV] Storing a provider name for an external database

[Chris S. <sto...@pc...>]

Hi John,
I'm putting this on the gusdev list as non-ApiDB users may have  
similar questions or some insights to offer.

As we just discussed offline, your task here is not to capture where  
the dataset was downloaded but rather who submitted the dataset to  
the resource (e.g., GenBank)  we got it from. ExternalDatabase and  
ExternalDatabaseRelease are meant for the former. Provider  
information (who should be given attribution) should be captured in  
the SRes.Contact table. I don't see an explicit attribute for a home  
page (the URL) but perhaps one of the RAD people can suggest a  
solution since they use Contact extensively for attribution of  
microrarray studies and and samples.

Chris

On Jan 24, 2007, at 5:04 PM, John Iodice wrote:

> Chris,
>
> The attribution info at the bottom of PlasmoDB sequence pages is  
> currently generated by the JSP code, as a function of the species  
> and sequence source_id.  The attribution data in the GFF files we  
> upload to to the Interoperability Working Group are calculated in  
> the SQL in the model files.  We'd like to store this attribution  
> info in the database instead.
>
> There are four character strings to be stored for each dataset:
>
> the dataset name (e.g. "Plasmodium falciparum mitochondrial genome")
> the data provider's name ("London School of Hygiene & Tropical  
> Medicine")
> a short version of the provider's name ("LSHTM")
> the URL ("http://www.lshtm.ac.uk/pmbu/staff/dconway/dconway.html")
>
> Steve and I talked about this today.  We're proposing to store the  
> dataset name, short name and URL in ExternalDatabase.name,  
> ExternalDatabaseRelease.id_type, and  
> ExternalDatabaseRelease.id_url, respectively.  We're proposing the  
> addition of a new varchar column named "provider" to the  
> ExternalDatabaseRelease table.
>
> What do you think of this?  Is there a better way?  Does GUS  
> already support this?
>
> Thanks for any feedback you can give us.
>
> John

[GUSDEV] Using LoadFastaSequences plugin

[Dhivya A. <dhi...@ya...>]

Hi,

I'm trying to use the LoadFastaSequences plugin to load GUS tables with the fasta sequences or certain nrdb proteins. 

But, when I run the plugin I get an error about a primary key constraint violation. When I tested by removing the primary key constraint, the plugin loaded duplicates (for primary key column, algorithm_param_key_id) into algorithmparamkey table.

I'm using GUS3.5 with postgres.


On running the registration for the plugin

ga +create GUS::Supported::Plugin::LoadFastaSequences --commit


The stack trace contains the following:

DBD::Pg::st execute failed: ERROR:  duplicate key violates unique constraint "al
gorithmparamkey_pkey" at /home/gus/GUS/gus_home/lib/perl/GUS/ObjRelP/DbiDbHandle
.pm line 147.

 SQL ERROR!! involving

    INSERT INTO Core.AlgorithmParamKey (  group_read, algorithm_param_key_id, us
er_read, algorithm_implementation_id, other_write, modification_date, algorithm_
param_key_type_id, row_group_id, algorithm_param_key, user_write, group_write, o
ther_read, description, row_user_id, row_alg_invocation_id, row_project_id, is_l
ist_valued )
    VALUES   (  ?, ?, ?, ?, ?, now(), ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ? )
 Values: 1, 65, 1, 21, 0, 1, 1, regexSourceId, 1, 1, 1, The regular expression t
o pick the source_id of the sequence from the defline, 1, 1, 1, 0 at /home/gus/G
US/gus_home/lib/perl/GUS/ObjRelP/DbiDbHandle.pm line 166
        GUS::ObjRelP::DbiDbHandle::death('GUS::ObjRelP::DbiDbHandle=HASH(0x89bb1
8c)', '\x{a} SQL ERROR!! involving\x{a} \x{a}    INSERT INTO Core.AlgorithmParam
...') called at /home/gus/GUS/gus_home/lib/perl/GUS/ObjRelP/DbiDbHandle.pm line
150
        GUS::ObjRelP::DbiDbHandle::sqlExec('GUS::ObjRelP::DbiDbHandle=HASH(0x89b
b18c)', 'GUS::ObjRelP::DbiDbHandle::st=HASH(0x8fbce10)', 'ARRAY(0x8fbceac)', '\x
{a}    INSERT INTO Core.AlgorithmParamKey (  group_read, algori...') called at /
home/gus/GUS/gus_home/lib/perl/GUS/ObjRelP/DbiRow.pm line 666
        GUS::ObjRelP::DbiRow::quote_and_insert('GUS::Model::Core::AlgorithmParam
Key=HASH(0x8fad2f8)', 'HASH(0x8fb8874)') called at /home/gus/GUS/gus_home/lib/pe
rl/GUS/ObjRelP/DbiRow.pm line 613
        GUS::ObjRelP::DbiRow::insert('GUS::Model::Core::AlgorithmParamKey=HASH(0
x8fad2f8)') called at /home/gus/GUS/gus_home/lib/perl/GUS/Model/GusRow.pm line 1
692
        GUS::Model::GusRow::submit('GUS::Model::Core::AlgorithmParamKey=HASH(0x8
fad2f8)', 'undef', 1) called at /home/gus/GUS/gus_home/lib/perl/GUS/Model/GusRow
.pm line 1779
        GUS::Model::GusRow::submitChildrenInClass('GUS::Model::Core::AlgorithmIm
plementation=HASH(0x8f5f7f8)', 'GUS::Model::Core::AlgorithmParamKey') called at
/home/gus/GUS/gus_home/lib/perl/GUS/Model/GusRow.pm line 1760
        GUS::Model::GusRow::submitAllChildren('GUS::Model::Core::AlgorithmImplem
entation=HASH(0x8f5f7f8)') called at /home/gus/GUS/gus_home/lib/perl/GUS/Model/G
usRow.pm line 1699
        GUS::Model::GusRow::submit('GUS::Model::Core::AlgorithmImplementation=HA
SH(0x8f5f7f8)', 'undef', 1) called at /home/gus/GUS/gus_home/lib/perl/GUS/Model/
GusRow.pm line 1779
        GUS::Model::GusRow::submitChildrenInClass('GUS::Model::Core::Algorithm=H                                     ASH(0x8f5d500)', 'GUS::Model::Core::AlgorithmImplementation') called at /home/gu                                     s/GUS/gus_home/lib/perl/GUS/Model/GusRow.pm line 1760
        GUS::Model::GusRow::submitAllChildren('GUS::Model::Core::Algorithm=HASH(                                     0x8f5d500)') called at /home/gus/GUS/gus_home/lib/perl/GUS/Model/GusRow.pm line                                      1699
        GUS::Model::GusRow::submit('GUS::Model::Core::Algorithm=HASH(0x8f5d500)'                                     ) called at /home/gus/GUS/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm line                                      900
        GUS::PluginMgr::GusApplication::create_or_update_implementation('GUS::Pl                                     uginMgr::GusApplication=HASH(0x877dc20)', 0, 'GUS::Supported::Plugin::LoadFastaS                                     equences') called at /home/gus/GUS/gus_home/lib/perl/GUS/PluginMgr/GusApplicatio                                     n.pm line 546
        GUS::PluginMgr::GusApplication::doMajorMode_Create('GUS::PluginMgr::GusA                                     pplication=HASH(0x877dc20)', 'GUS::Supported::Plugin::LoadFastaSequences') calle                                     d at /home/gus/GUS/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm line 337
        GUS::PluginMgr::GusApplication::doMajorMode('GUS::PluginMgr::GusApplicat                                     ion=HASH(0x877dc20)', 'GUS::Supported::Plugin::LoadFastaSequences') called at /h                                     ome/gus/GUS/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm line 246
        GUS::PluginMgr::GusApplication::parseAndRun('GUS::PluginMgr::GusApplicat                                     ion HASH(0x877dc20)', 'ARRAY(0x87916d0)') called at /home/gus/GUS/gus_home/bin/ga line 11



 Any ideas about why this could be happening and how to fix it? 
 
 Thanks
 dhivya arasappan







 
---------------------------------
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Re: [GUSDEV] [CBIL] Fwd: loadNRDB script

[Brian B. <br...@pc...>]

Dhivya, your gus.config file ($GUS_HOME/config/gus.config) specifies  
the database login information.  This is used by the gus application  
to determine which database to connect to so if you want to change  
between databases you will need to edit this file.

-Brian

On Jan 15, 2007, at 2:52 PM, Dhivya Aras wrote:

> Hi Chris,
>
> THanks for that information. I was able to get all the input  
> parameters and you were right about the gi_taxid_prot.dmp- It is a  
> download from ncbi, though not part of the nrdb bundle.
> I didnt know who would be the right person for this question: So,  
> Chris, Brian or anyone in the group, if you have any ideas, let me  
> know.
> I have two gus dbs on my machine. I actually wanted to run the  
> loadNRDB script on the backup version but I couldnt find any input  
> parameter where I can specify which database the NRDB will be  
> loaded in. How would I specify this? Does it have to do the  
> location/path where I'm running the script from?
>
> thanks
> dhivya
>
>
>
> Chris Stoeckert <sto...@pc...> wrote:
> Hi Dhivya,
> I'm putting this back onto the gusdev so that answers may help  
> others (or others can correct my answers). I should also warn you  
> that as PI of the project, I don't actually run any of the code so  
> this is a test of how well I understand what's going on. ;)
>>         sres.externaldatabaserelease.version for this instance of  
>> NRDB
>>         sres.externaldatabase.name for NRDB
> To load nrdb or any other external "database" (really data source),  
> that source needs to be entered into externaldatabase and the  
> version (can simply be date when you downloaded it) entered into  
> databaserelease. These can be entered manually into those tables.
> If this is a new version, then NRDB should already be in  
> externaldatabase. You simply need to enter a new row in  
> externaldatabaserelease for NRDB and give whatever you put in the  
> version field.
>
>>         pathname for the gi_taxid_prot.dmp file
> I'm guessing that this is a pointer to the dump file that comes  
> with NRDB providing the taxon_id for each protein sequence but  
> that's just a guess.
>
> Chris
>
> On Jan 12, 2007, at 5:01 PM, Dhivya Aras wrote:
>
>> Hi Chris,
>>
>> I'm trying to load a new NRDB version into gus using loadNRDB  
>> plugin. It requires several compulsory input parameters. I dont  
>> understand what three of them are. The ga help describes it as:
>>
>> externalDatabaseVersion *string* (Required)
>>
>>         sres.externaldatabaserelease.version for this instance of  
>> NRDB
>>
>>
>> gitax *file* (Required)
>>
>>         pathname for the gi_taxid_prot.dmp file
>>
>> and
>>
>> externalDatabaseName *string* (Required)
>>
>>         sres.externaldatabase.name for NRDB
>>
>> Could you point me some docs or information about these arguments?
>> thanks
>> dhivya
>>
>>
>>
>> Chris Stoeckert <sto...@pc...> wrote:
>> Hi Brian,
>> Dhivya found the Djob plugin but did not find any documentation on  
>> how to run. Can you point him at the appropriate place or person? 
>> Can this be added to the GUS svn somewhere?
>> Thanks,
>> 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 Jan 11, 2007, at 8:15 AM, Brian Brunk wrote:
>>
>>> blastSimilarity does not appear to be in the GUS distribution,  
>>> nor is it in CBIL/Bio.  In my project_home it is in DJob.  Seems  
>>> to me like  blastSimilarity should be in the GUS distribution  
>>> that one can download from the gusdb.org site (or check out of  
>>> the repository).  I also have a script called  
>>> parseBlastFilesForSimilarity.pl that takes in BLAST file names on  
>>> stdin that is very useful for parsing blast files into the format  
>>> to be loaded into the db that could be included.
>>>
>>> -Brian
>>>
>>> On Jan 10, 2007, at 4:52 PM, Chris Stoeckert wrote:
>>>
>>>> Hi,
>>>> Can anyone help with this question about the input file to  
>>>> InsertBlastSimilarities?
>>>> Thanks,
>>>> Chris
>>>>
>>>> Begin forwarded message:
>>>>
>>>>> From: Dhivya Aras <dhi...@ya...>
>>>>> Date: January 10, 2007 4:25:25 PM EST
>>>>> To: Chris Stoeckert <sto...@pc...>
>>>>> Subject: Re: [GUSDEV] loading COG and blast annotation results  
>>>>> into GUS
>>>>>
>>>>> Hi Chris,
>>>>>
>>>>> I understand that to load the blast data into the two tables,  
>>>>> similarity and similarityspan, I need to use the gus supported  
>>>>> plugin, InsertBlastSimilarities. But, this plugin asks for an  
>>>>> input file 'generated by the blastSimilarity command  
>>>>> (distributed with GUS in the CBIL/Bio component)'. Any idea  
>>>>> where I can find this blastSimilarity utility?
>>>>>
>>>>> Thanks
>>>>> dhivya
>>>>>
>>>>>
>>>>> Chris Stoeckert <sto...@pc...> wrote:
>>>>> Again, answers in-line.
>>>>> Chris
>>>>>
>>>>> On Jan 9, 2007, at 2:27 PM, Dhivya Aras wrote:
>>>>>
>>>>>> Hi Chris,
>>>>>>
>>>>>> I did look at the GUS schema browser- unfortunately most  
>>>>>> tables dont have any documentation- I could just see the  
>>>>>> attributes in each table and maybe a small description of the  
>>>>>> attribute.
>>>>>>
>>>>>> But thanks to your reply, I do understand the necessity for  
>>>>>> the two tables , similarity and similarityspan now. The way I  
>>>>>> understand it- the query_table_id points to a table in which  
>>>>>> the query sequence data is and the query_id indicates the row  
>>>>>> in that table. So, for example, if the query_table_id points  
>>>>>> to externalNASequence, I'm assuming the query_id points to the  
>>>>>> primary key of that table, Na_Sequence_ID. Am I right in this  
>>>>>> assumption?
>>>>>
>>>>> yes that's right.
>>>>>
>>>>>> Basically, I have an exisiting gus db with data and I have  
>>>>>> some new blastp results of AA sequences against NRDB. Here's  
>>>>>> what I think needs to be done to put these new blast results  
>>>>>> into the GUS db. Please fill in  gaps as I'm vague on some areas.
>>>>>>
>>>>>> 1. Store each hsp in the similarityspan table. I've mapped all  
>>>>>> the blast fields to the table's fields- thats not a problem.
>>>>> yes
>>>>>
>>>>>> 2. SInce the query is an AA sequence, which table should the  
>>>>>> query_table_id point to? TranslatedAASequence with the  
>>>>>> query_id pointing to AA_Sequence_id?
>>>>> yes (assuming you are doing a blastp with a sequence from  
>>>>> TranslatedAASequence - note that AASequence could also come  
>>>>> from other views of AASequence).
>>>>>
>>>>>> 3. Since the subject is from the NRDB, I'm guessing that the  
>>>>>> query_table_id should point to externalAASequence with the  
>>>>>> query_id pointing to AA_Sequence_ID.
>>>>>
>>>>> yes (assuming you loaded nrdb into ExternalAASequence).
>>>>>
>>>>>> 4. I think these are the only tables I would be affecting for  
>>>>>> adding these new blastP results. Am I right?
>>>>>
>>>>> yes (mostly). Using ga you'll also get audit tables populated  
>>>>> like algorithm invocation.
>>>>>
>>>>>> I know I've asked quite a few questions, but I'm really not  
>>>>>> able to find too much information on what the tables and  
>>>>>> fields mean and what they contain. So I'm hoping you can help  
>>>>>> me out.
>>>>> No problem - we need to improve the docs.
>>>>>
>>>>>> thanks
>>>>>> dhivya
>>>>>>
>>>>>> Chris Stoeckert <sto...@pc...> wrote:
>>>>>>
>>>>>> See answers in-line. Also, did you look at the documentation  
>>>>>> in the GUS schema browser? The tables (I know many don't)  
>>>>>> actually have table and attribute descriptions. Were they too  
>>>>>> vague (i.e. do we need to improve them?
>>>>>>
>>>>>> Chris
>>>>>>
>>>>>>> Thanks for replying. I have currently been working on putting  
>>>>>>> my blast results in similarity and similarityspan tables.  
>>>>>>> But, I have two questions about these tables. Maybe you could  
>>>>>>> help me out here.
>>>>>>>
>>>>>>> 1. SImilarity and SImilarityspan have pretty much the same  
>>>>>>> fields except than similarityspan is a child table of  
>>>>>>> Similarity. So, why do I even need the SImilaritySpan table?
>>>>>> These tables have different purposes (and semantics). Think of  
>>>>>> Similarity as global (what's the overall similarity between  
>>>>>> two proteins) and SimilaritySpan as local (what are the  
>>>>>> individual HSPs).
>>>>>>
>>>>>>> 2. I couldnt find any fields in the Similarity table for  
>>>>>>> storing the actual query and subject annotation. Most  
>>>>>>> probably this can be done by referring to some other table  
>>>>>>> with the annotation. But I find that the only two fields  
>>>>>>> refferring to other tables are query_table_id and  
>>>>>>> subject_table_id which just refer to the core.TableInfo. I'm  
>>>>>>> confused about these two fields and exactly how they can be  
>>>>>>> used to refer to the query and subject annotation?
>>>>>>
>>>>>> The query and subject sequences are identified (as you may  
>>>>>> have guessed) with the soft links query_table_id and  
>>>>>> subject_table_id although these attributes can point to  
>>>>>> anything relevant. Our semantics are that they point the  
>>>>>> entities (e.g., nucleic acid sequence, amino acid sequence,  
>>>>>> possibly dbref) and annotation is associated with those entities.
>>>>>>
>>>>>>> Any help or suggestions would be helpful.
>>>>>>>
>>>>>>> Thanks
>>>>>>> dhivya
>>>>>>>
>>>>>>> Chris Stoeckert <sto...@pc...> wrote:
>>>>>>> Dear Dhivya,
>>>>>>> Sorry for the long delay in replying.
>>>>>>> You guessed correctly about Similarity and SImilaritySpan.  
>>>>>>> These were
>>>>>>> designed to hold BLAST results (as well as results from other  
>>>>>>> analyses).
>>>>>>>
>>>>>>> For ortholog tables you might check the GUS schema browser  
>>>>>>> (http://
>>>>>>> www.gusdb.org/SchemaBrowser/) and scroll down to the categories:
>>>>>>> Paralogs and Family; Sequence Ortholog, Paralog, Family AA  
>>>>>>> Ortholog.
>>>>>>>
>>>>>>> Looking over old notes for OrthoMCL, it looks like
>>>>>>> DoTS.BestSimilarityPair is the table that we store summarized
>>>>>>> ortholog info data for queries.
>>>>>>>
>>>>>>> Hope this helps,
>>>>>>> Chris
>>>>>>>
>>>>>>> On Dec 16, 2006, at 3:38 PM, Dhivya Aras wrote:
>>>>>>>
>>>>>>> > Hi everyone,
>>>>>>> >
>>>>>>> > I would like to store COG annotation and blast results in  
>>>>>>> GUS. I
>>>>>>> > did find two tables named similarity and similarityspan in  
>>>>>>> the dots
>>>>>>> > schema - It looks like this can hold blast results but I  
>>>>>>> need to
>>>>>>> > investigate more.
>>>>>>> >
>>>>>>> > As far as COG is concerned, I couldnt find any table  
>>>>>>> supporting
>>>>>>> > this data. I was told that orthoMcl data is stored in
>>>>>>> > dots.SequenceGroup and dots.SequenceSequenceGroup, but I'm not
>>>>>>> > sure it that would best suit my needs. So, if anyone who  
>>>>>>> has used
>>>>>>> > GUS for these purposes before or just has an idea, pleas  
>>>>>>> let me
>>>>>>> > know. I would really appreciate it.
>>>>>>> >
>>>>>>> > thanks
>>>>>>> > dhivya arasappan
>>>>>>> > __________________________________________________
>>>>>>> > Do You Yahoo!?
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>>>>>>> >  
>>>>>>> ---------------------------------------------------------------- 
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>>>>>>> page=join.php&p=sourceforge&CID=DEVDEV__________________________ 
>>>>>>> ______
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>>>>>>> _____________________
>>>>>>> Gusdev-gusdev mailing list
>>>>>>> Gus...@li...
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>>>>>>
>>>>>> ----------------------------------------------------------------- 
>>>>>> --------
>>>>>> Take Surveys. Earn Cash. Influence the Future of IT
>>>>>> Join SourceForge.net's Techsay panel and you'll get the chance  
>>>>>> to share your
>>>>>> opinions on IT & business topics through brief surveys - and  
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>>>>>> page=join.php&p=sourceforge&CID=DEVDEV___________________________ 
>>>>>> ____________________
>>>>>> Gusdev-gusdev mailing list
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>>>>>>
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>>>>>
>>>>>
>>>>>
>>>>> Need a quick answer? Get one in minutes from people who know.  
>>>>> Ask your question on Yahoo! Answers.
>>>>
>>>> _______________________________________________
>>>> CBIL mailing list
>>>> CB...@pc...
>>>> https://mail.pcbi.upenn.edu/mailman/listinfo/cbil
>>>
>>> Brian P. Brunk, Ph.D.
>>> ApiDB Senior Manager
>>> 1424 Blockley Hall
>>> Penn Center For Bioinformatics
>>> University of Pennsylvania
>>> Philadelphia PA 19104-6021
>>> Tel: 215-573-3118
>>> Fax: 215-573-3111
>>>
>>>
>>
>>
>>
>> Need a quick answer? Get one in minutes from people who know. Ask  
>> your question on Yahoo! Answers.
>
>
>
> Don't pick lemons.
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Brian P. Brunk, Ph.D.
ApiDB Senior Manager
1424 Blockley Hall
Penn Center For Bioinformatics
University of Pennsylvania
Philadelphia PA 19104-6021
Tel: 215-573-3118
Fax: 215-573-3111

Re: [GUSDEV] [CBIL] Fwd: loadNRDB script

[Dhivya A. <dhi...@ya...>]

                      Hi Chris,

THanks for that information. I was able to get all the input parameters and you were right about the gi_taxid_prot.dmp- It is a download from ncbi, though not part of the nrdb bundle.

I didnt know who would be the right person for this question: So, Chris, Brian or anyone in the group, if you have any ideas, let me know.
I have two gus dbs on my machine. I actually wanted to run the loadNRDB script on the backup version but I couldnt find any input parameter where I can specify which database the NRDB will be loaded in. How would I specify this? Does it have to do the location/path where I'm running the script from?

thanks
dhivya

 
 

Chris Stoeckert <sto...@pc...> wrote: Hi Dhivya,I'm putting this back onto the gusdev so that answers may help others (or others can correct my answers). I should also warn you that as PI of the project, I don't actually run any of the code so this is a test of how well I understand what's going on. ;)
        sres.externaldatabaserelease.version for this instance of NRDB
        sres.externaldatabase.name for NRDB
To load nrdb or any other external "database" (really data source), that source needs to be entered into externaldatabase and the version (can simply be date when you downloaded it) entered into databaserelease. These can be entered manually into those tables.If this is a new version, then NRDB should already be in externaldatabase. You simply need to enter a new row in externaldatabaserelease for NRDB and give whatever you put in the version field.

        pathname for the gi_taxid_prot.dmp file
I'm guessing that this is a pointer to the dump file that comes with NRDB providing the taxon_id for each protein sequence but that's just a guess.


Chris

On Jan 12, 2007, at 5:01 PM, Dhivya Aras wrote:

Hi Chris,

I'm trying to load a new NRDB version into gus using loadNRDB plugin. It requires several compulsory input parameters. I dont understand what three of them are. The ga help describes it as:

externalDatabaseVersion *string* (Required)

        sres.externaldatabaserelease.version for this instance of NRDB


gitax *file* (Required)

        pathname for the gi_taxid_prot.dmp file

and

externalDatabaseName *string* (Required)

        sres.externaldatabase.name for NRDB

Could you point me some docs or information about these arguments?
thanks
dhivya



Chris Stoeckert <sto...@pc...> wrote: Hi Brian,Dhivya found the Djob plugin but did not find any documentation on how to run. Can you point him at the appropriate place or person?Can this be added to the GUS svn somewhere?
Thanks,
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 Jan 11, 2007, at 8:15 AM, Brian Brunk wrote:

blastSimilarity does not appear to be in the GUS distribution, nor is it in CBIL/Bio.  In my project_home it is in DJob.  Seems to me like  blastSimilarity should be in the GUS distribution that one can download from the gusdb.org site (or check out of the repository).  I also have a script called parseBlastFilesForSimilarity.pl that takes in BLAST file names on stdin that is very useful for parsing blast files into the format to be loaded into the db that could be included.


-Brian

On Jan 10, 2007, at 4:52 PM, Chris Stoeckert wrote:

Hi,Can anyone help with this question about the input file to InsertBlastSimilarities?
Thanks,
Chris

Begin forwarded message:

From: Dhivya Aras <dhi...@ya...>
Date: January 10, 2007 4:25:25 PM EST
To: Chris Stoeckert <sto...@pc...>
Subject: Re: [GUSDEV] loading COG and blast annotation results into GUS


 Hi Chris,
   
  I understand that to load the blast data into the two tables, similarity and similarityspan, I need to use the gus supported plugin, InsertBlastSimilarities. But, this plugin asks for an input file 'generated by the blastSimilarity command (distributed with GUS in the CBIL/Bio component)'. Any idea where I can find this blastSimilarity utility?
   
  Thanks
  dhivya
   
  
Chris Stoeckert <sto...@pc...> wrote:
  Again, answers in-line.  Chris
  
    On Jan 9, 2007, at 2:27 PM, Dhivya Aras wrote:

  Hi Chris,

I did look at the GUS schema browser- unfortunately most tables dont have any documentation- I could just see the attributes in each table and maybe a small description of the attribute.

But thanks to your reply, I do understand the necessity for the two tables , similarity and similarityspan now. The way I understand it- the query_table_id points to a table in which the query sequence data is and the query_id indicates the row in that table. So, for example, if the query_table_id points to externalNASequence, I'm assuming the query_id points to the primary key of that table, Na_Sequence_ID. Am I right in this assumption?
  

yes that's right.
  
  Basically, I have an exisiting gus db with data and I have some new blastp results of AA sequences against NRDB. Here's what I think needs to be done to put these new blast results into the GUS db. Please fill in  gaps as I'm vague on some areas.

1. Store each hsp in the similarityspan table. I've mapped all the blast fields to the table's fields- thats not a problem.
yes
  
  2. SInce the query is an AA sequence, which table should the query_table_id point to? TranslatedAASequence with the query_id pointing to AA_Sequence_id?
  yes (assuming you are doing a blastp with a sequence from TranslatedAASequence - note that AASequence could also come from other views of AASequence). 

  3. Since the subject is from the NRDB, I'm guessing that the query_table_id should point to externalAASequence with the query_id pointing to AA_Sequence_ID.
  

yes (assuming you loaded nrdb into ExternalAASequence).
  
  4. I think these are the only tables I would be affecting for adding these new blastP results. Am I right?  

  yes (mostly). Using ga you'll also get audit tables populated like algorithm invocation. 

  I know I've asked quite a few questions, but I'm really not able to find too much information on what the tables and fields mean and what they contain. So I'm hoping you can help me out.
No problem - we need to improve the docs.
  
  thanks
dhivya

Chris Stoeckert <sto...@pc...> wrote:    

See answers in-line. Also, did you look at the documentation in the GUS schema browser? The tables (I know many don't) actually have table and attribute descriptions. Were they too vague (i.e. do we need to improve them?  

  Chris
  

      Thanks for replying. I have currently been working on putting my blast results in similarity and similarityspan tables. But, I have two questions about these tables. Maybe you could help me out here.

1. SImilarity and SImilarityspan have pretty much the same fields except than similarityspan is a child table of Similarity. So, why do I even need the SImilaritySpan table?
  These tables have different purposes (and semantics). Think of Similarity as global (what's the overall similarity between two proteins) and SimilaritySpan as local (what are the individual HSPs).

  2. I couldnt find any fields in the Similarity table for storing the actual query and subject annotation. Most probably this can be done by referring to some other table with the annotation. But I find that the only two fields refferring to other tables are query_table_id and subject_table_id which just refer to the core.TableInfo. I'm confused about these two fields and exactly how they can be used to refer to the query and subject annotation?
  

  The query and subject sequences are identified (as you may have guessed) with the soft links query_table_id and subject_table_id although these attributes can point to anything relevant. Our semantics are that they point the entities (e.g., nucleic acid sequence, amino acid sequence, possibly dbref) and annotation is associated with those entities.    

  Any help or suggestions would be helpful. 

Thanks
dhivya

Chris Stoeckert <sto...@pc...> wrote:  Dear Dhivya,
Sorry for the long delay in replying.
You guessed correctly about Similarity and SImilaritySpan. These were 
designed to hold BLAST results (as well as results from other analyses).

For ortholog tables you might check the GUS schema browser (http:// 
www.gusdb.org/SchemaBrowser/) and scroll down to the categories: 
Paralogs and Family; Sequence Ortholog, Paralog, Family AA Ortholog.

Looking over old notes for OrthoMCL, it looks like 
DoTS.BestSimilarityPair is the table that we store summarized 
ortholog info data for queries.

Hope this helps,
Chris

On Dec 16, 2006, at 3:38 PM, Dhivya Aras wrote:

> Hi everyone,
>
> I would like to store COG annotation and blast results in GUS. I 
> did find two tables named similarity and similarityspan in the dots 
> schema - It looks like this can hold blast results but I need to 
> investigate more.
>
> As far as COG is concerned, I couldnt find any table supporting 
> this data. I was told that orthoMcl data is stored in 
> dots.SequenceGroup and dots.SequenceSequenceGroup, but I'm not 
> sure it that would best suit my needs. So, if anyone who has used 
> GUS for these purposes before or just has an idea, pleas let me 
> know. I would really appreciate it.
>
> thanks
> dhivya arasappan
> __________________________________________________
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_______________________________________________
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https://mail.pcbi.upenn.edu/mailman/listinfo/cbil
 

 Brian P. Brunk, Ph.D.
ApiDB Senior Manager
1424 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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Re: [GUSDEV] [CBIL] Fwd: loading COG and blast annotation results into GUS

[Chris S. <sto...@pc...>]

Hi Dhivya,
I'm putting this back onto the gusdev so that answers may help others  
(or others can correct my answers). I should also warn you that as PI  
of the project, I don't actually run any of the code so this is a  
test of how well I understand what's going on. ;)
>         sres.externaldatabaserelease.version for this instance of NRDB
>         sres.externaldatabase.name for NRDB
To load nrdb or any other external "database" (really data source),  
that source needs to be entered into externaldatabase and the version  
(can simply be date when you downloaded it) entered into  
databaserelease. These can be entered manually into those tables.
If this is a new version, then NRDB should already be in  
externaldatabase. You simply need to enter a new row in  
externaldatabaserelease for NRDB and give whatever you put in the  
version field.

>         pathname for the gi_taxid_prot.dmp file
I'm guessing that this is a pointer to the dump file that comes with  
NRDB providing the taxon_id for each protein sequence but that's just  
a guess.

Chris

On Jan 12, 2007, at 5:01 PM, Dhivya Aras wrote:

> Hi Chris,
>
> I'm trying to load a new NRDB version into gus using loadNRDB  
> plugin. It requires several compulsory input parameters. I dont  
> understand what three of them are. The ga help describes it as:
>
> externalDatabaseVersion *string* (Required)
>
>         sres.externaldatabaserelease.version for this instance of NRDB
>
>
> gitax *file* (Required)
>
>         pathname for the gi_taxid_prot.dmp file
>
> and
>
> externalDatabaseName *string* (Required)
>
>         sres.externaldatabase.name for NRDB
>
> Could you point me some docs or information about these arguments?
> thanks
> dhivya
>
>
>
> Chris Stoeckert <sto...@pc...> wrote:
> Hi Brian,
> Dhivya found the Djob plugin but did not find any documentation on  
> how to run. Can you point him at the appropriate place or person? 
> Can this be added to the GUS svn somewhere?
> Thanks,
> 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 Jan 11, 2007, at 8:15 AM, Brian Brunk wrote:
>
>> blastSimilarity does not appear to be in the GUS distribution, nor  
>> is it in CBIL/Bio.  In my project_home it is in DJob.  Seems to me  
>> like  blastSimilarity should be in the GUS distribution that one  
>> can download from the gusdb.org site (or check out of the  
>> repository).  I also have a script called  
>> parseBlastFilesForSimilarity.pl that takes in BLAST file names on  
>> stdin that is very useful for parsing blast files into the format  
>> to be loaded into the db that could be included.
>>
>> -Brian
>>
>> On Jan 10, 2007, at 4:52 PM, Chris Stoeckert wrote:
>>
>>> Hi,
>>> Can anyone help with this question about the input file to  
>>> InsertBlastSimilarities?
>>> Thanks,
>>> Chris
>>>
>>> Begin forwarded message:
>>>
>>>> From: Dhivya Aras <dhi...@ya...>
>>>> Date: January 10, 2007 4:25:25 PM EST
>>>> To: Chris Stoeckert <sto...@pc...>
>>>> Subject: Re: [GUSDEV] loading COG and blast annotation results  
>>>> into GUS
>>>>
>>>> Hi Chris,
>>>>
>>>> I understand that to load the blast data into the two tables,  
>>>> similarity and similarityspan, I need to use the gus supported  
>>>> plugin, InsertBlastSimilarities. But, this plugin asks for an  
>>>> input file 'generated by the blastSimilarity command  
>>>> (distributed with GUS in the CBIL/Bio component)'. Any idea  
>>>> where I can find this blastSimilarity utility?
>>>>
>>>> Thanks
>>>> dhivya
>>>>
>>>>
>>>> Chris Stoeckert <sto...@pc...> wrote:
>>>> Again, answers in-line.
>>>> Chris
>>>>
>>>> On Jan 9, 2007, at 2:27 PM, Dhivya Aras wrote:
>>>>
>>>>> Hi Chris,
>>>>>
>>>>> I did look at the GUS schema browser- unfortunately most tables  
>>>>> dont have any documentation- I could just see the attributes in  
>>>>> each table and maybe a small description of the attribute.
>>>>>
>>>>> But thanks to your reply, I do understand the necessity for the  
>>>>> two tables , similarity and similarityspan now. The way I  
>>>>> understand it- the query_table_id points to a table in which  
>>>>> the query sequence data is and the query_id indicates the row  
>>>>> in that table. So, for example, if the query_table_id points to  
>>>>> externalNASequence, I'm assuming the query_id points to the  
>>>>> primary key of that table, Na_Sequence_ID. Am I right in this  
>>>>> assumption?
>>>>
>>>> yes that's right.
>>>>
>>>>> Basically, I have an exisiting gus db with data and I have some  
>>>>> new blastp results of AA sequences against NRDB. Here's what I  
>>>>> think needs to be done to put these new blast results into the  
>>>>> GUS db. Please fill in  gaps as I'm vague on some areas.
>>>>>
>>>>> 1. Store each hsp in the similarityspan table. I've mapped all  
>>>>> the blast fields to the table's fields- thats not a problem.
>>>> yes
>>>>
>>>>> 2. SInce the query is an AA sequence, which table should the  
>>>>> query_table_id point to? TranslatedAASequence with the query_id  
>>>>> pointing to AA_Sequence_id?
>>>> yes (assuming you are doing a blastp with a sequence from  
>>>> TranslatedAASequence - note that AASequence could also come from  
>>>> other views of AASequence).
>>>>
>>>>> 3. Since the subject is from the NRDB, I'm guessing that the  
>>>>> query_table_id should point to externalAASequence with the  
>>>>> query_id pointing to AA_Sequence_ID.
>>>>
>>>> yes (assuming you loaded nrdb into ExternalAASequence).
>>>>
>>>>> 4. I think these are the only tables I would be affecting for  
>>>>> adding these new blastP results. Am I right?
>>>>
>>>> yes (mostly). Using ga you'll also get audit tables populated  
>>>> like algorithm invocation.
>>>>
>>>>> I know I've asked quite a few questions, but I'm really not  
>>>>> able to find too much information on what the tables and fields  
>>>>> mean and what they contain. So I'm hoping you can help me out.
>>>> No problem - we need to improve the docs.
>>>>
>>>>> thanks
>>>>> dhivya
>>>>>
>>>>> Chris Stoeckert <sto...@pc...> wrote:
>>>>>
>>>>> See answers in-line. Also, did you look at the documentation in  
>>>>> the GUS schema browser? The tables (I know many don't) actually  
>>>>> have table and attribute descriptions. Were they too vague  
>>>>> (i.e. do we need to improve them?
>>>>>
>>>>> Chris
>>>>>
>>>>>> Thanks for replying. I have currently been working on putting  
>>>>>> my blast results in similarity and similarityspan tables. But,  
>>>>>> I have two questions about these tables. Maybe you could help  
>>>>>> me out here.
>>>>>>
>>>>>> 1. SImilarity and SImilarityspan have pretty much the same  
>>>>>> fields except than similarityspan is a child table of  
>>>>>> Similarity. So, why do I even need the SImilaritySpan table?
>>>>> These tables have different purposes (and semantics). Think of  
>>>>> Similarity as global (what's the overall similarity between two  
>>>>> proteins) and SimilaritySpan as local (what are the individual  
>>>>> HSPs).
>>>>>
>>>>>> 2. I couldnt find any fields in the Similarity table for  
>>>>>> storing the actual query and subject annotation. Most probably  
>>>>>> this can be done by referring to some other table with the  
>>>>>> annotation. But I find that the only two fields refferring to  
>>>>>> other tables are query_table_id and subject_table_id which  
>>>>>> just refer to the core.TableInfo. I'm confused about these two  
>>>>>> fields and exactly how they can be used to refer to the query  
>>>>>> and subject annotation?
>>>>>
>>>>> The query and subject sequences are identified (as you may have  
>>>>> guessed) with the soft links query_table_id and  
>>>>> subject_table_id although these attributes can point to  
>>>>> anything relevant. Our semantics are that they point the  
>>>>> entities (e.g., nucleic acid sequence, amino acid sequence,  
>>>>> possibly dbref) and annotation is associated with those entities.
>>>>>
>>>>>> Any help or suggestions would be helpful.
>>>>>>
>>>>>> Thanks
>>>>>> dhivya
>>>>>>
>>>>>> Chris Stoeckert <sto...@pc...> wrote:
>>>>>> Dear Dhivya,
>>>>>> Sorry for the long delay in replying.
>>>>>> You guessed correctly about Similarity and SImilaritySpan.  
>>>>>> These were
>>>>>> designed to hold BLAST results (as well as results from other  
>>>>>> analyses).
>>>>>>
>>>>>> For ortholog tables you might check the GUS schema browser  
>>>>>> (http://
>>>>>> www.gusdb.org/SchemaBrowser/) and scroll down to the categories:
>>>>>> Paralogs and Family; Sequence Ortholog, Paralog, Family AA  
>>>>>> Ortholog.
>>>>>>
>>>>>> Looking over old notes for OrthoMCL, it looks like
>>>>>> DoTS.BestSimilarityPair is the table that we store summarized
>>>>>> ortholog info data for queries.
>>>>>>
>>>>>> Hope this helps,
>>>>>> Chris
>>>>>>
>>>>>> On Dec 16, 2006, at 3:38 PM, Dhivya Aras wrote:
>>>>>>
>>>>>> > Hi everyone,
>>>>>> >
>>>>>> > I would like to store COG annotation and blast results in  
>>>>>> GUS. I
>>>>>> > did find two tables named similarity and similarityspan in  
>>>>>> the dots
>>>>>> > schema - It looks like this can hold blast results but I  
>>>>>> need to
>>>>>> > investigate more.
>>>>>> >
>>>>>> > As far as COG is concerned, I couldnt find any table supporting
>>>>>> > this data. I was told that orthoMcl data is stored in
>>>>>> > dots.SequenceGroup and dots.SequenceSequenceGroup, but I'm not
>>>>>> > sure it that would best suit my needs. So, if anyone who has  
>>>>>> used
>>>>>> > GUS for these purposes before or just has an idea, pleas let me
>>>>>> > know. I would really appreciate it.
>>>>>> >
>>>>>> > thanks
>>>>>> > dhivya arasappan
>>>>>> > __________________________________________________
>>>>>> > Do You Yahoo!?
>>>>>> > Tired of spam? Yahoo! Mail has the best spam protection around
>>>>>> > http://mail.yahoo.com
>>>>>> >
>>>>>> >  
>>>>>> ----------------------------------------------------------------- 
>>>>>> -----
>>>>>> > ---
>>>>>> > Take Surveys. Earn Cash. Influence the Future of IT
>>>>>> > Join SourceForge.net's Techsay panel and you'll get the  
>>>>>> chance to
>>>>>> > share your
>>>>>> > opinions on IT & business topics through brief surveys - and  
>>>>>> earn cash
>>>>>> > http://www.techsay.com/default.php?
>>>>>> >  
>>>>>> page=join.php&p=sourceforge&CID=DEVDEV___________________________ 
>>>>>> _____
>>>>>> > _______________
>>>>>> > Gusdev-gusdev mailing list
>>>>>> > Gus...@li...
>>>>>> > https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev
>>>>>>
>>>>>>
>>>>>> ----------------------------------------------------------------- 
>>>>>> --------
>>>>>> Take Surveys. Earn Cash. Influence the Future of IT
>>>>>> Join SourceForge.net's Techsay panel and you'll get the chance  
>>>>>> to share your
>>>>>> opinions on IT & business topics through brief surveys - and  
>>>>>> earn cash
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>>>>>> page=join.php&p=sourceforge&CID=DEVDEV
>>>>>> _______________________________________________
>>>>>> Gusdev-gusdev mailing list
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>>>>>>
>>>>>> __________________________________________________
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>>>>>> Tired of spam? Yahoo! Mail has the best spam protection around
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>>>>>> --------
>>>>>> Take Surveys. Earn Cash. Influence the Future of IT
>>>>>> Join SourceForge.net's Techsay panel and you'll get the chance  
>>>>>> to share your
>>>>>> opinions on IT & business topics through brief surveys - and  
>>>>>> earn cash
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>>>>>> page=join.php&p=sourceforge&CID=DEVDEV___________________________ 
>>>>>> ____________________
>>>>>> Gusdev-gusdev mailing list
>>>>>> Gus...@li...
>>>>>> https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev
>>>>>
>>>>> ------------------------------------------------------------------ 
>>>>> -------
>>>>> Take Surveys. Earn Cash. Influence the Future of IT
>>>>> Join SourceForge.net's Techsay panel and you'll get the chance  
>>>>> to share your
>>>>> opinions on IT & business topics through brief surveys - and  
>>>>> earn cash
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>>>>> ___________________
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>>>>
>>>>
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>>>> Ask your question on Yahoo! Answers.
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>>> _______________________________________________
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>>
>> Brian P. Brunk, Ph.D.
>> ApiDB Senior Manager
>> 1424 Blockley Hall
>> Penn Center For Bioinformatics
>> University of Pennsylvania
>> Philadelphia PA 19104-6021
>> Tel: 215-573-3118
>> Fax: 215-573-3111
>>
>>
>
>
>
> Need a quick answer? Get one in minutes from people who know. Ask  
> your question on Yahoo! Answers.

Re: [GUSDEV] ISF tables description

[Elisabetta M. <man...@pc...>]

Hi Michael,
you should be able to obtain the relations (and for some tables, their 
purpose) by clicking on the table links from the schema browser available 
at www.gusdb.org. As far as I know, that is the only document available 
with this sort of info.
BTW none of the table involved in this plugin are RAD tables (too bad, 
because the RAD tables are probably the ones with most documentation in 
the schema browser).
Elisabetta

---

On Fri, 12 Jan 2007 mro...@cs... wrote:

> Dear gusdev members:
>
> I have sucessfully run the ISF InsertSequenceFeaures plugin.
>
> I was able to identify and access all 24 affected tables and the
> corresponding 8 "dependend on" tables.
>
> I am in search of information concerning the purpose of each table, and if
> there is a RAD document already made so that I can determine the relations
> of each table.
>
> Thanks and Happy New Year
>
> Michael Robinson
> Bioinformatics Research Group (Biorg)
> Florida International University
> Miami, Florida, USA 33199
>
>
>
> -------------------------------------------------------------------------
> Take Surveys. Earn Cash. Influence the Future of IT
> Join SourceForge.net's Techsay panel and you'll get the chance to share your
> opinions on IT & business topics through brief surveys - and earn cash
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>

[GUSDEV] ISF tables description

[<mro...@cs...>]

Dear gusdev members:

I have sucessfully run the ISF InsertSequenceFeaures plugin.

I was able to identify and access all 24 affected tables and the
corresponding 8 "dependend on" tables.

I am in search of information concerning the purpose of each table, and i=
f
there is a RAD document already made so that I can determine the relation=
s
of each table.

Thanks and Happy New Year

Michael Robinson
Bioinformatics Research Group (Biorg)
Florida International University
Miami, Florida, USA 33199

Re: [GUSDEV] loading COG and blast annotation results into GUS

[Brian B. <br...@pc...>]

Dhivya-

Just to be a bit more specific on the issue of the query_table_id and  
subject_table_id.  As you note, those have foreign key constraints to  
the core.tableinfo table.  These attributes tell you which table  
contains the query and subject sequences.  Usually this will be one  
of the NASequence or AASequence tables.  There are two associated  
attributes, query_id and subject_id, that identify the row in those  
tables that correspond to the actual query and subject sequences.

-Brian

On Jan 8, 2007, at 3:28 PM, Chris Stoeckert wrote:

>
> See answers in-line. Also, did you look at the documentation in the  
> GUS schema browser? The tables (I know many don't) actually have  
> table and attribute descriptions. Were they too vague (i.e. do we  
> need to improve them?
>
> Chris
>
>> Thanks for replying. I have currently been working on putting my  
>> blast results in similarity and similarityspan tables. But, I have  
>> two questions about these tables. Maybe you could help me out here.
>>
>> 1. SImilarity and SImilarityspan have pretty much the same fields  
>> except than similarityspan is a child table of Similarity. So, why  
>> do I even need the SImilaritySpan table?
> These tables have different purposes (and semantics). Think of  
> Similarity as global (what's the overall similarity between two  
> proteins) and SimilaritySpan as local (what are the individual HSPs).
>
>> 2. I couldnt find any fields in the Similarity table for storing  
>> the actual query and subject annotation. Most probably this can be  
>> done by referring to some other table with the annotation. But I  
>> find that the only two fields refferring to other tables are  
>> query_table_id and subject_table_id which just refer to the  
>> core.TableInfo. I'm confused about these two fields and exactly  
>> how they can be used to refer to the query and subject annotation?
>
> The query and subject sequences are identified (as you may have  
> guessed) with the soft links query_table_id and subject_table_id  
> although these attributes can point to anything relevant. Our  
> semantics are that they point the entities (e.g., nucleic acid  
> sequence, amino acid sequence, possibly dbref) and annotation is  
> associated with those entities.
>
>> Any help or suggestions would be helpful.
>>
>> Thanks
>> dhivya
>>
>> Chris Stoeckert <sto...@pc...> wrote:
>> Dear Dhivya,
>> Sorry for the long delay in replying.
>> You guessed correctly about Similarity and SImilaritySpan. These were
>> designed to hold BLAST results (as well as results from other  
>> analyses).
>>
>> For ortholog tables you might check the GUS schema browser (http://
>> www.gusdb.org/SchemaBrowser/) and scroll down to the categories:
>> Paralogs and Family; Sequence Ortholog, Paralog, Family AA Ortholog.
>>
>> Looking over old notes for OrthoMCL, it looks like
>> DoTS.BestSimilarityPair is the table that we store summarized
>> ortholog info data for queries.
>>
>> Hope this helps,
>> Chris
>>
>> On Dec 16, 2006, at 3:38 PM, Dhivya Aras wrote:
>>
>> > Hi everyone,
>> >
>> > I would like to store COG annotation and blast results in GUS. I
>> > did find two tables named similarity and similarityspan in the dots
>> > schema - It looks like this can hold blast results but I need to
>> > investigate more.
>> >
>> > As far as COG is concerned, I couldnt find any table supporting
>> > this data. I was told that orthoMcl data is stored in
>> > dots.SequenceGroup and dots.SequenceSequenceGroup, but I'm not
>> > sure it that would best suit my needs. So, if anyone who has used
>> > GUS for these purposes before or just has an idea, pleas let me
>> > know. I would really appreciate it.
>> >
>> > thanks
>> > dhivya arasappan
>> > __________________________________________________
>> > Do You Yahoo!?
>> > Tired of spam? Yahoo! Mail has the best spam protection around
>> > http://mail.yahoo.com
>> >
>> >  
>> --------------------------------------------------------------------- 
>> -
>> > ---
>> > Take Surveys. Earn Cash. Influence the Future of IT
>> > Join SourceForge.net's Techsay panel and you'll get the chance to
>> > share your
>> > opinions on IT & business topics through brief surveys - and  
>> earn cash
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>> >  
>> page=join.php&p=sourceforge&CID=DEVDEV_______________________________ 
>> _
>> > _______________
>> > Gusdev-gusdev mailing list
>> > Gus...@li...
>> > https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev
>>
>>
>> --------------------------------------------------------------------- 
>> ----
>> Take Surveys. Earn Cash. Influence the Future of IT
>> Join SourceForge.net's Techsay panel and you'll get the chance to  
>> share your
>> opinions on IT & business topics through brief surveys - and earn  
>> cash
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>> page=join.php&p=sourceforge&CID=DEVDEV
>> _______________________________________________
>> Gusdev-gusdev mailing list
>> Gus...@li...
>> https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev
>>
>> __________________________________________________
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>> Tired of spam? Yahoo! Mail has the best spam protection around
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>> ----
>> Take Surveys. Earn Cash. Influence the Future of IT
>> Join SourceForge.net's Techsay panel and you'll get the chance to  
>> share your
>> opinions on IT & business topics through brief surveys - and earn  
>> cash
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>> page=join.php&p=sourceforge&CID=DEVDEV_______________________________ 
>> ________________
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>
> ---------------------------------------------------------------------- 
> ---
> Take Surveys. Earn Cash. Influence the Future of IT
> Join SourceForge.net's Techsay panel and you'll get the chance to  
> share your
> opinions on IT & business topics through brief surveys - and earn cash
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Brian P. Brunk, Ph.D.
ApiDB Senior Manager
1424 Blockley Hall
Penn Center For Bioinformatics
University of Pennsylvania
Philadelphia PA 19104-6021
Tel: 215-573-3118
Fax: 215-573-3111

Re: [GUSDEV] loading COG and blast annotation results into GUS

[Chris S. <sto...@pc...>]

See answers in-line. Also, did you look at the documentation in the  
GUS schema browser? The tables (I know many don't) actually have  
table and attribute descriptions. Were they too vague (i.e. do we  
need to improve them?

Chris

> Thanks for replying. I have currently been working on putting my  
> blast results in similarity and similarityspan tables. But, I have  
> two questions about these tables. Maybe you could help me out here.
>
> 1. SImilarity and SImilarityspan have pretty much the same fields  
> except than similarityspan is a child table of Similarity. So, why  
> do I even need the SImilaritySpan table?
These tables have different purposes (and semantics). Think of  
Similarity as global (what's the overall similarity between two  
proteins) and SimilaritySpan as local (what are the individual HSPs).

> 2. I couldnt find any fields in the Similarity table for storing  
> the actual query and subject annotation. Most probably this can be  
> done by referring to some other table with the annotation. But I  
> find that the only two fields refferring to other tables are  
> query_table_id and subject_table_id which just refer to the  
> core.TableInfo. I'm confused about these two fields and exactly how  
> they can be used to refer to the query and subject annotation?

The query and subject sequences are identified (as you may have  
guessed) with the soft links query_table_id and subject_table_id  
although these attributes can point to anything relevant. Our  
semantics are that they point the entities (e.g., nucleic acid  
sequence, amino acid sequence, possibly dbref) and annotation is  
associated with those entities.

> Any help or suggestions would be helpful.
>
> Thanks
> dhivya
>
> Chris Stoeckert <sto...@pc...> wrote:
> Dear Dhivya,
> Sorry for the long delay in replying.
> You guessed correctly about Similarity and SImilaritySpan. These were
> designed to hold BLAST results (as well as results from other  
> analyses).
>
> For ortholog tables you might check the GUS schema browser (http://
> www.gusdb.org/SchemaBrowser/) and scroll down to the categories:
> Paralogs and Family; Sequence Ortholog, Paralog, Family AA Ortholog.
>
> Looking over old notes for OrthoMCL, it looks like
> DoTS.BestSimilarityPair is the table that we store summarized
> ortholog info data for queries.
>
> Hope this helps,
> Chris
>
> On Dec 16, 2006, at 3:38 PM, Dhivya Aras wrote:
>
> > Hi everyone,
> >
> > I would like to store COG annotation and blast results in GUS. I
> > did find two tables named similarity and similarityspan in the dots
> > schema - It looks like this can hold blast results but I need to
> > investigate more.
> >
> > As far as COG is concerned, I couldnt find any table supporting
> > this data. I was told that orthoMcl data is stored in
> > dots.SequenceGroup and dots.SequenceSequenceGroup, but I'm not
> > sure it that would best suit my needs. So, if anyone who has used
> > GUS for these purposes before or just has an idea, pleas let me
> > know. I would really appreciate it.
> >
> > thanks
> > dhivya arasappan
> > __________________________________________________
> > Do You Yahoo!?
> > Tired of spam? Yahoo! Mail has the best spam protection around
> > http://mail.yahoo.com
> >
> >  
> ----------------------------------------------------------------------
> > ---
> > Take Surveys. Earn Cash. Influence the Future of IT
> > Join SourceForge.net's Techsay panel and you'll get the chance to
> > share your
> > opinions on IT & business topics through brief surveys - and earn  
> cash
> > http://www.techsay.com/default.php?
> >  
> page=join.php&p=sourceforge&CID=DEVDEV________________________________
> > _______________
> > Gusdev-gusdev mailing list
> > Gus...@li...
> > https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev
>
>
> ---------------------------------------------------------------------- 
> ---
> Take Surveys. Earn Cash. Influence the Future of IT
> Join SourceForge.net's Techsay panel and you'll get the chance to  
> share your
> opinions on IT & business topics through brief surveys - and earn cash
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>
> __________________________________________________
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>
> ---------------------------------------------------------------------- 
> ---
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> Join SourceForge.net's Techsay panel and you'll get the chance to  
> share your
> opinions on IT & business topics through brief surveys - and earn cash
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> https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev

Re: [GUSDEV] loading COG and blast annotation results into GUS

[Dhivya A. <dhi...@ya...>]

Hi,
 
 Thanks for replying. I have currently been working on putting my blast results in similarity and similarityspan tables. But, I have two questions about these tables. Maybe you could help me out here.
 
 1. SImilarity and SImilarityspan have pretty much the same fields except than similarityspan is a child table of Similarity. So, why do I even need the SImilaritySpan table?
 
 2. I couldnt find any fields in the Similarity table for storing the actual query and subject annotation. Most probably this can be done by referring to some other table with the annotation. But I find that the only two fields refferring to other tables are query_table_id and subject_table_id which just refer to the core.TableInfo. I'm confused about these two fields and exactly how they can be used to refer to the query and subject annotation?
 
 Any help or suggestions would be helpful. 
 
 Thanks
 dhivya

Chris Stoeckert <sto...@pc...> wrote: Dear Dhivya,
Sorry for the long delay in replying.
You guessed correctly about Similarity and SImilaritySpan. These were  
designed to hold BLAST results (as well as results from other analyses).

For ortholog tables you might check the GUS schema browser (http:// 
www.gusdb.org/SchemaBrowser/) and scroll down to the categories:  
Paralogs and Family; Sequence Ortholog, Paralog, Family AA Ortholog.

Looking over old notes for OrthoMCL, it looks like  
DoTS.BestSimilarityPair is the table that we store summarized  
ortholog info data for queries.

Hope this helps,
Chris

On Dec 16, 2006, at 3:38 PM, Dhivya Aras wrote:

> Hi everyone,
>
> I would like to store COG annotation and blast results in GUS. I  
> did find two tables named similarity and similarityspan in the dots  
> schema - It looks like this can hold blast results but I need to  
> investigate more.
>
> As far as COG is concerned, I couldnt find any table supporting  
> this data. I was told that orthoMcl data is stored in  
> dots.SequenceGroup and  dots.SequenceSequenceGroup, but I'm not  
> sure it that would best suit my needs. So, if anyone who has used  
> GUS for these purposes before or just has an idea, pleas let me  
> know. I would really appreciate it.
>
> thanks
> dhivya arasappan
> __________________________________________________
> Do You Yahoo!?
> Tired of spam? Yahoo! Mail has the best spam protection around
> http://mail.yahoo.com
>
> ---------------------------------------------------------------------- 
> ---
> Take Surveys. Earn Cash. Influence the Future of IT
> Join SourceForge.net's Techsay panel and you'll get the chance to  
> share your
> opinions on IT & business topics through brief surveys - and earn cash
> http://www.techsay.com/default.php? 
> page=join.php&p=sourceforge&CID=DEVDEV________________________________ 
> _______________
> Gusdev-gusdev mailing list
> Gus...@li...
> https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev


-------------------------------------------------------------------------
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Re: [GUSDEV] loading COG and blast annotation results into GUS

[Chris S. <sto...@pc...>]

Dear Dhivya,
Sorry for the long delay in replying.
You guessed correctly about Similarity and SImilaritySpan. These were  
designed to hold BLAST results (as well as results from other analyses).

For ortholog tables you might check the GUS schema browser (http:// 
www.gusdb.org/SchemaBrowser/) and scroll down to the categories:  
Paralogs and Family; Sequence Ortholog, Paralog, Family AA Ortholog.

Looking over old notes for OrthoMCL, it looks like  
DoTS.BestSimilarityPair is the table that we store summarized  
ortholog info data for queries.

Hope this helps,
Chris

On Dec 16, 2006, at 3:38 PM, Dhivya Aras wrote:

> Hi everyone,
>
> I would like to store COG annotation and blast results in GUS. I  
> did find two tables named similarity and similarityspan in the dots  
> schema - It looks like this can hold blast results but I need to  
> investigate more.
>
> As far as COG is concerned, I couldnt find any table supporting  
> this data. I was told that orthoMcl data is stored in  
> dots.SequenceGroup and  dots.SequenceSequenceGroup, but I'm not  
> sure it that would best suit my needs. So, if anyone who has used  
> GUS for these purposes before or just has an idea, pleas let me  
> know. I would really appreciate it.
>
> thanks
> dhivya arasappan
> __________________________________________________
> Do You Yahoo!?
> Tired of spam? Yahoo! Mail has the best spam protection around
> http://mail.yahoo.com
>
> ---------------------------------------------------------------------- 
> ---
> Take Surveys. Earn Cash. Influence the Future of IT
> Join SourceForge.net's Techsay panel and you'll get the chance to  
> share your
> opinions on IT & business topics through brief surveys - and earn cash
> http://www.techsay.com/default.php? 
> page=join.php&p=sourceforge&CID=DEVDEV________________________________ 
> _______________
> Gusdev-gusdev mailing list
> Gus...@li...
> https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev

[GUSDEV] loading COG and blast annotation results into GUS

[Dhivya A. <dhi...@ya...>]

Hi everyone,
   
  I would like to store COG annotation and blast results in GUS. I did find two tables named similarity and similarityspan in the dots schema - It looks like this can hold blast results but I need to investigate more. 
   
  As far as COG is concerned, I couldnt find any table supporting this data. I was told that orthoMcl data is stored in dots.SequenceGroup and  dots.SequenceSequenceGroup, but I'm not sure it that would best suit my needs. So, if anyone who has used GUS for these purposes before or just has an idea, pleas let me know. I would really appreciate it.
   
  thanks
  dhivya arasappan

 __________________________________________________
Do You Yahoo!?
Tired of spam?  Yahoo! Mail has the best spam protection around 
http://mail.yahoo.com 

[GUSDEV] MR_Ti: batch loading microarray annotation data into GUS

[Junmin L. <ju...@pc...>]

Hi, there,

We just start to work on a project called MR_Ti, a meta data loader, which 
can load annotation data for microarray experiment. Basically it will 
replace many, if not all, of manual steps involved in RAD-SA forms with 
this single data loading scripts.

Currently it can accept MAGE docs, like spreadsheet tab2mage or MAGE-TAB
(http://tab2mage.sourceforge.net/), or MAGE-ML
http://www.mged.org/Workgroups/MAGE/mage-ml.html. Later on we can load
SOFT format from GEO.

The tab2mage or MAGE-TAB format is very useful for in-house data loading,
you only need to give PI three piece of spreadsheets, they fill it out
with experiment infor. sample preparation, scanning protocol, and etc.

The code are in iterative release cycles, accept one or two channel data. 
We are seeking the users to try it, and give us feedback so we can better 
develop this.

Let me know if you like this idea, and if you like, I can give you further 
details.

Thanks,
---junmin

Programmer Analyst
CBIL
UPenn, Center for Bioinformatics

[GUSDEV] LoadTaxon

[<mro...@cs...>]

Steve and gusdev members,

I need you help again.

I run the following (three consecutive times):

ga GUS::Supported::Plugin::LoadTaxon
--gencode ~/taxon/11-27-2006/gencode.dmp
--names ~/taxon/11-27-2006/names.dmp
--nodes ~/taxon/11-27-2006/nodes.dmp
--merged ~/taxon/11-27-2006/merged.dmp --commit

the first time when I got to

Mon Nov 27 14:56:10 2006        Processed ncbi_tax_id : 83469
Mon Nov 27 14:56:10 2006        Processed ncbi_tax_id : 195787

when I lost the network connection.

I logged back in and re-started the process, when it gets to:

Mon Nov 27 16:11:19 2006        Processed ncbi_tax_id : 188885
Mon Nov 27 16:11:19 2006        Inserting and updating TaxonName

it sat there for over one hour, I stopped it and re-run it with the same
results.

Which do you think is the best route to fix this problem.



Thank you very much for your help

Michael R

[GUSDEV] open cursor problem/DBA scripts

[marc j. <de...@ho...>]

I raised the cursors from 300 to 1300 to 3000 and I still get the same error 
message about
cursors.

I'm curious.  I've been trying to resolve this issue for some time now.
I haven't had a lot of responses from this mailing list. Has anyone actually
verified that these DBA scripts work?

Regards,

Marc

ps. BTW, I acknowledge that the problem might be my installation.  Just 
trying to figure it out.

_________________________________________________________________
Find a local pizza place, music store, museum and more…then map the best 
route!  http://local.live.com?FORM=MGA001

Re: [GUSDEV] ISF defaults

[<mro...@cs...>]

Steve,

The Core.TableInfo is also empty.

Since the installer did not load the default values,

at    http://www.gusdb.org/documentation/older/vbidoc.pdf

i looked in page 17 "Loading Data Into Gus" (i realize this is for versio=
n
3.0 but since we do not have a similar documentation for version 3.5) i
was wondering if i can follow those instructions to do "Initial
Population" of the tables they refer to, or is there any other place that
i can find the same information for the current version.


Thank you

Michael R


> i thought that the installer loaded default values into that table.
>
> how about Core.TableInfo, is it filled?
>
> yes, you do have to add the data you describe below
>
> steve
>
> mro...@cs... wrote:
>
>>Steve,
>>
>>The Core.ProjectInfo table is empty, so I will create a record in
>>
>> project_id            | numeric(4,0)                | not null
>> name                  | character varying(40)       | not null
>> description           | character varying(255)      |
>> release               | character varying(20)       |
>> modification_date     | timestamp without time zone | not null
>> user_read             | numeric(1,0)                | not null
>> user_write            | numeric(1,0)                | not null
>> group_read            | numeric(1,0)                | not null
>> group_write           | numeric(1,0)                | not null
>> other_read            | numeric(1,0)                | not null
>> other_write           | numeric(1,0)                | not null
>> row_user_id           | numeric(12,0)               | not null
>> row_group_id          | numeric(4,0)                | not null
>> row_project_id        | numeric(4,0)                | not null
>> row_alg_invocation_id | numeric(12,0)               | not null
>>Indexes:
>>    "pk_projectinfo" primary key, btree (project_id)
>>
>>
>>
>>with the value "Database Administration" to match my gus.config file, n=
ow
>>I assume that this value correspond to the field "name". Do I need to p=
ut
>>any data in the other fields or is this up to me?
>>
>>Also before running ISF do I need to put any data in:
>>
>>        - SequenceOntology   (InsertSequenceOntology plugin)
>>        - NCBI Taxon   (LoadTaxon plugin)
>>        - External database and release (InsertExternalDatabase and
>>                                  InsertExternalDatabaseRls plugins)
>>        - at least one row in SequenceType so you can say what type of
>>          sequence you are loading (you can use LoadRow plugin for this
>>
>>
>>Thanks very much
>>
>>Michael R
>>
>>
>>
>>
>>
>>>Michael-
>>>
>>>There is a table in gus called Core.ProjectInfo.  In contains info abo=
ut
>>>your "project."   When you run a plugin, the plugin needs to know what
>>>the name of your project is so that all the rows you insert will be
>>>assigned to your project.   The plugin discovers the name of your
>>>project by looking in the gus.config file.
>>>
>>>The error message is telling you that the gus.config file is declaring
>>>your project's name to be "Database Administration" while there is no
>>>row in Core.ProjectInfo with name set to "Database Administration".
>>>
>>>Have you looked at the rows in that table?  Is there one with name
>>>"Database Administration"?   On my GUS instance, I have a row with nam=
e
>>>"Database administration"  (note the small 'a').   I suspect that this
>>>row was put in by the gus installer.   So perhaps you just need to
>>>change your config file to that.
>>>
>>>steve
>>>
>>>mro...@cs... wrote:
>>>
>>>
>>>
>>>>Steve,
>>>>
>>>>I understand that you are in charge of ISF.
>>>>
>>>>I am trying to run the ISF plugin in a brand new install and I get th=
e
>>>>following error:
>>>>
>>>>No row in Core.ProjectInfo has name =3D Database Administration'.  Th=
is
>>>>value was found in the project=3D property of your gus.config file.
>>>>Please
>>>>be sure it is correct and has been registered in the database
>>>>**** GUS::PluginMgr::PluginError Failed running 'ga +meta --commit'
>>>> with
>>>>stderr:
>>>>Operation now in progress**** GUS::PluginMgr::PluginError Failed
>>>>running 'ga +update GUS::Supported::Plugin::InsertSequenceFeatures --
>>>>commit' with stderr:
>>>>
>>>>I already checked my gus.config file and it has the entry
>>>>
>>>>project=3DDatabase Administration
>>>>
>>>>
>>>>I would like to know if this and maybe other default values must be
>>>>inserted into the database before trying to insert data.
>>>>
>>>>
>>>>I found in the gusdev site the following:
>>>>
>>>>   From: Steve Fischer <sfischer@pc...> - 2005-08-31 10:32
>>>>   for those of you who are using the beta version of the ISF plugin:
>>>>   1. i will improve its documentation to indicate what it expects to
>>>>      already be in the database:
>>>>          - SequenceOntology   (InsertSequenceOntology plugin)
>>>>          - NCBI Taxon   (LoadTaxon plugin)
>>>>          - External database and release (InsertExternalDatabase and
>>>>                                   InsertExternalDatabaseRls plugins)
>>>>          - at least one row in SequenceType so you can say what type
>>>> of
>>>>            sequence you are loading (you can use LoadRow plugin for
>>>>this)
>>>>
>>>>   2.  i will improve the error messages so that it better detects th=
e
>>>>       absence of these, and makes it more clear what to do.
>>>>
>>>>
>>>>
>>>>I am sorry if I ask the same question so many times but I am stuck an=
d
>>>>can
>>>>not continue until I find an answer.
>>>>
>>>>
>>>>Thank you
>>>>
>>>>
>>>>Michael Robinson
>>>>Bioinformatics Research Group (Biorg)
>>>>Florida International University
>>>>Miami, Florida, USA 33199
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>
>>
>>
>>
>

Re: [GUSDEV] ISF defaults

[Steve F. <sfi...@pc...>]

i thought that the installer loaded default values into that table.

how about Core.TableInfo, is it filled?

yes, you do have to add the data you describe below

steve

mro...@cs... wrote:

>Steve,
>
>The Core.ProjectInfo table is empty, so I will create a record in
>
> project_id            | numeric(4,0)                | not null
> name                  | character varying(40)       | not null
> description           | character varying(255)      |
> release               | character varying(20)       |
> modification_date     | timestamp without time zone | not null
> user_read             | numeric(1,0)                | not null
> user_write            | numeric(1,0)                | not null
> group_read            | numeric(1,0)                | not null
> group_write           | numeric(1,0)                | not null
> other_read            | numeric(1,0)                | not null
> other_write           | numeric(1,0)                | not null
> row_user_id           | numeric(12,0)               | not null
> row_group_id          | numeric(4,0)                | not null
> row_project_id        | numeric(4,0)                | not null
> row_alg_invocation_id | numeric(12,0)               | not null
>Indexes:
>    "pk_projectinfo" primary key, btree (project_id)
>
>
>
>with the value "Database Administration" to match my gus.config file, now
>I assume that this value correspond to the field "name". Do I need to put
>any data in the other fields or is this up to me?
>
>Also before running ISF do I need to put any data in:
>
>        - SequenceOntology   (InsertSequenceOntology plugin)
>        - NCBI Taxon   (LoadTaxon plugin)
>        - External database and release (InsertExternalDatabase and
>                                  InsertExternalDatabaseRls plugins)
>        - at least one row in SequenceType so you can say what type of
>          sequence you are loading (you can use LoadRow plugin for this
>
>
>Thanks very much
>
>Michael R
>
>
>
>  
>
>>Michael-
>>
>>There is a table in gus called Core.ProjectInfo.  In contains info about
>>your "project."   When you run a plugin, the plugin needs to know what
>>the name of your project is so that all the rows you insert will be
>>assigned to your project.   The plugin discovers the name of your
>>project by looking in the gus.config file.
>>
>>The error message is telling you that the gus.config file is declaring
>>your project's name to be "Database Administration" while there is no
>>row in Core.ProjectInfo with name set to "Database Administration".
>>
>>Have you looked at the rows in that table?  Is there one with name
>>"Database Administration"?   On my GUS instance, I have a row with name
>>"Database administration"  (note the small 'a').   I suspect that this
>>row was put in by the gus installer.   So perhaps you just need to
>>change your config file to that.
>>
>>steve
>>
>>mro...@cs... wrote:
>>
>>    
>>
>>>Steve,
>>>
>>>I understand that you are in charge of ISF.
>>>
>>>I am trying to run the ISF plugin in a brand new install and I get the
>>>following error:
>>>
>>>No row in Core.ProjectInfo has name = Database Administration'.  This
>>>value was found in the project= property of your gus.config file.
>>>Please
>>>be sure it is correct and has been registered in the database
>>>**** GUS::PluginMgr::PluginError Failed running 'ga +meta --commit' with
>>>stderr:
>>>Operation now in progress**** GUS::PluginMgr::PluginError Failed
>>>running 'ga +update GUS::Supported::Plugin::InsertSequenceFeatures --
>>>commit' with stderr:
>>>
>>>I already checked my gus.config file and it has the entry
>>>
>>>project=Database Administration
>>>
>>>
>>>I would like to know if this and maybe other default values must be
>>>inserted into the database before trying to insert data.
>>>
>>>
>>>I found in the gusdev site the following:
>>>
>>>   From: Steve Fischer <sfischer@pc...> - 2005-08-31 10:32
>>>   for those of you who are using the beta version of the ISF plugin:
>>>   1. i will improve its documentation to indicate what it expects to
>>>      already be in the database:
>>>          - SequenceOntology   (InsertSequenceOntology plugin)
>>>          - NCBI Taxon   (LoadTaxon plugin)
>>>          - External database and release (InsertExternalDatabase and
>>>                                   InsertExternalDatabaseRls plugins)
>>>          - at least one row in SequenceType so you can say what type of
>>>            sequence you are loading (you can use LoadRow plugin for
>>>this)
>>>
>>>   2.  i will improve the error messages so that it better detects the
>>>       absence of these, and makes it more clear what to do.
>>>
>>>
>>>
>>>I am sorry if I ask the same question so many times but I am stuck and
>>>can
>>>not continue until I find an answer.
>>>
>>>
>>>Thank you
>>>
>>>
>>>Michael Robinson
>>>Bioinformatics Research Group (Biorg)
>>>Florida International University
>>>Miami, Florida, USA 33199
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>      
>>>
>
>  
>

Re: [GUSDEV] ISF defaults

[Steve F. <sfi...@pc...>]

Michael-

There is a table in gus called Core.ProjectInfo.  In contains info about 
your "project."   When you run a plugin, the plugin needs to know what 
the name of your project is so that all the rows you insert will be 
assigned to your project.   The plugin discovers the name of your 
project by looking in the gus.config file.

The error message is telling you that the gus.config file is declaring 
your project's name to be "Database Administration" while there is no 
row in Core.ProjectInfo with name set to "Database Administration". 

Have you looked at the rows in that table?  Is there one with name 
"Database Administration"?   On my GUS instance, I have a row with name 
"Database administration"  (note the small 'a').   I suspect that this 
row was put in by the gus installer.   So perhaps you just need to 
change your config file to that.

steve
mro...@cs... wrote:

>Steve,
>
>I understand that you are in charge of ISF.
>
>I am trying to run the ISF plugin in a brand new install and I get the
>following error:
>
> No row in Core.ProjectInfo has name = Database Administration'.  This
> value was found in the project= property of your gus.config file.  Please
> be sure it is correct and has been registered in the database
> **** GUS::PluginMgr::PluginError Failed running 'ga +meta --commit' with
> stderr:
> Operation now in progress**** GUS::PluginMgr::PluginError Failed
> running 'ga +update GUS::Supported::Plugin::InsertSequenceFeatures --
> commit' with stderr:
>
>I already checked my gus.config file and it has the entry
>
> project=Database Administration
>
>
>I would like to know if this and maybe other default values must be
>inserted into the database before trying to insert data.
>
>
>I found in the gusdev site the following:
>
>    From: Steve Fischer <sfischer@pc...> - 2005-08-31 10:32
>    for those of you who are using the beta version of the ISF plugin:
>    1. i will improve its documentation to indicate what it expects to
>       already be in the database:
>           - SequenceOntology   (InsertSequenceOntology plugin)
>           - NCBI Taxon   (LoadTaxon plugin)
>           - External database and release (InsertExternalDatabase and
>                                    InsertExternalDatabaseRls plugins)
>           - at least one row in SequenceType so you can say what type of
>             sequence you are loading (you can use LoadRow plugin for this)
>
>    2.  i will improve the error messages so that it better detects the
>        absence of these, and makes it more clear what to do.
>
>
>
>I am sorry if I ask the same question so many times but I am stuck and can
>not continue until I find an answer.
>
>
>Thank you
>
>
>Michael Robinson
>Bioinformatics Research Group (Biorg)
>Florida International University
>Miami, Florida, USA 33199
>
>
>
>
>
>
>  
>

Re: [GUSDEV] ISF defaults

[<mro...@cs...>]

Steve,

The Core.ProjectInfo table is empty, so I will create a record in

 project_id            | numeric(4,0)                | not null
 name                  | character varying(40)       | not null
 description           | character varying(255)      |
 release               | character varying(20)       |
 modification_date     | timestamp without time zone | not null
 user_read             | numeric(1,0)                | not null
 user_write            | numeric(1,0)                | not null
 group_read            | numeric(1,0)                | not null
 group_write           | numeric(1,0)                | not null
 other_read            | numeric(1,0)                | not null
 other_write           | numeric(1,0)                | not null
 row_user_id           | numeric(12,0)               | not null
 row_group_id          | numeric(4,0)                | not null
 row_project_id        | numeric(4,0)                | not null
 row_alg_invocation_id | numeric(12,0)               | not null
Indexes:
    "pk_projectinfo" primary key, btree (project_id)



with the value "Database Administration" to match my gus.config file, now
I assume that this value correspond to the field "name". Do I need to put
any data in the other fields or is this up to me?

Also before running ISF do I need to put any data in:

        - SequenceOntology   (InsertSequenceOntology plugin)
        - NCBI Taxon   (LoadTaxon plugin)
        - External database and release (InsertExternalDatabase and
                                  InsertExternalDatabaseRls plugins)
        - at least one row in SequenceType so you can say what type of
          sequence you are loading (you can use LoadRow plugin for this


Thanks very much

Michael R



> Michael-
>
> There is a table in gus called Core.ProjectInfo.  In contains info abou=
t
> your "project."   When you run a plugin, the plugin needs to know what
> the name of your project is so that all the rows you insert will be
> assigned to your project.   The plugin discovers the name of your
> project by looking in the gus.config file.
>
> The error message is telling you that the gus.config file is declaring
> your project's name to be "Database Administration" while there is no
> row in Core.ProjectInfo with name set to "Database Administration".
>
> Have you looked at the rows in that table?  Is there one with name
> "Database Administration"?   On my GUS instance, I have a row with name
> "Database administration"  (note the small 'a').   I suspect that this
> row was put in by the gus installer.   So perhaps you just need to
> change your config file to that.
>
> steve
>
> mro...@cs... wrote:
>
>>Steve,
>>
>>I understand that you are in charge of ISF.
>>
>>I am trying to run the ISF plugin in a brand new install and I get the
>>following error:
>>
>> No row in Core.ProjectInfo has name =3D Database Administration'.  Thi=
s
>> value was found in the project=3D property of your gus.config file.
>> Please
>> be sure it is correct and has been registered in the database
>> **** GUS::PluginMgr::PluginError Failed running 'ga +meta --commit' wi=
th
>> stderr:
>> Operation now in progress**** GUS::PluginMgr::PluginError Failed
>> running 'ga +update GUS::Supported::Plugin::InsertSequenceFeatures --
>> commit' with stderr:
>>
>>I already checked my gus.config file and it has the entry
>>
>> project=3DDatabase Administration
>>
>>
>>I would like to know if this and maybe other default values must be
>>inserted into the database before trying to insert data.
>>
>>
>>I found in the gusdev site the following:
>>
>>    From: Steve Fischer <sfischer@pc...> - 2005-08-31 10:32
>>    for those of you who are using the beta version of the ISF plugin:
>>    1. i will improve its documentation to indicate what it expects to
>>       already be in the database:
>>           - SequenceOntology   (InsertSequenceOntology plugin)
>>           - NCBI Taxon   (LoadTaxon plugin)
>>           - External database and release (InsertExternalDatabase and
>>                                    InsertExternalDatabaseRls plugins)
>>           - at least one row in SequenceType so you can say what type =
of
>>             sequence you are loading (you can use LoadRow plugin for
>> this)
>>
>>    2.  i will improve the error messages so that it better detects the
>>        absence of these, and makes it more clear what to do.
>>
>>
>>
>>I am sorry if I ask the same question so many times but I am stuck and
>> can
>>not continue until I find an answer.
>>
>>
>>Thank you
>>
>>
>>Michael Robinson
>>Bioinformatics Research Group (Biorg)
>>Florida International University
>>Miami, Florida, USA 33199
>>
>>
>>
>>
>>
>>
>>
>>
>