gusdev-gusdev — Topics concerning GUS development

[Gusdev-gusdev] CVS

[Angel P. <an...@ma...>]

Hello all,
It seems that the cvsweb.sanger.ac.uk defaults to the ensembl project 
root. It is not at all clear where GUS files are. After looking around 
for a minute or two, I found some pull-down box to specify the "Project 
Root". But that was only because I knew what I was looking for and also 
knew that Sanger has more than one CVSROOT on that site.

I suggest to change the GUSDB.org website to update the link to

http://cvsweb.sanger.ac.uk/cgi-bin/viewcvs.cgi/?root=GUS
from
http://cvsweb.sanger.ac.uk/cgi-bin/viewcvs.cgi/

-angel

-- 

Angel Pizarro
Director, Bioinformatics Facility
Institute for Translational Medicine and Therapeutics
University of Pennsylvania
806 BRB II/III
421 Curie Blvd.
Philadelphia, PA 19104-6160

P: 215-573-3736
F: 215-573-9004

[Gusdev-gusdev] LoadBLATAlignment

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

I loaded some est BLAT alignments dots.blatalignment with 
LoadBLATAlignment (ver 1.32) (how many times can I write blat alignment 
in one sentence?).

My dots.GeneFeatureSeqOverlap table  is empty and I'm thinking there 
should be data there because it's a child of blatalignment, PlasmoDB 
uses it and GFSO looks more usable than BA for finding est/gene 
overlaps. Although, since I aligned ests against whole contigs instead 
of individual sequences maybe GFSO won't help me.

Is there a plugin to populate GFSO?

Thanks,
Mark

Re: [Gusdev-gusdev] GUS 3.0 build.xml issue

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

the next thing for you to test is try to compile your simple file with=20
Ant.   Do you know how to use Ant?   Its very easy.

We'll look on our side.

besides the problem mike informed you of, we haven't seen this problem=20
before.

steve

Doma, Narsimha R. (Contr) wrote:

>Thanks for the detail mail Mike,
>1. We created a sample java file using java.util.logging package that wo=
rked fine
>2. We renamed the conf file as you said but no luck
>3. We rechecked all our ENV variables every thing looks good
>
>Looks like something is missing in our environment or in build file itse=
lf=20
>(if possible can you test the build file in any of your environments) ?
>
>we are working from our end to fix this issue,=20
>Any help is much appreciated in this regard
>
>Thanks
>Narsimha
>
>-----Original Message-----
>From: Michael Saffitz [mailto:msa...@pc...]
>Sent: Monday, March 28, 2005 3:28 PM
>To: Doma, Narsimha R. (Contr)
>Cc: gus...@li...; Lancaon, Johanan
>Subject: Re: [Gusdev-gusdev] GUS 3.0 build.xml issue
>
>
>
>Hi Narsimha,
>
>Steve and I just discussed your issue.  One thing to be careful of,=20
>especially on RedHat Enterprise Linux, is the ant.conf file in /etc.=20
>I've found that removing it (or moving it to /etc/ant.conf.save) solved=20
>several issues for us here at CBIL.  With it present, the system tends=20
>to use the built in ant, and not any local copies you may have installed.
>
>--Mike
>
>
>Doma, Narsimha R. (Contr) wrote:
> =20
>
>>Hi ,
>>
>>I am trying to install the GUS platform (first time)
>>we could download all the software and followed the CBIL install guide
>>
>>when are trying to run the build first time  the build process was trou=
ghs the error message saying
>>"CALSSPATH" issue with the java.util.logging class not found error and =
related errors follows=20
>>
>>is there any build script know errors? any pointers for new build scrip=
t ?
>>Please help us in this process
>>Thanks
>>Narsimha
>>
>>
>>-------------------------------------------------------
>>SF email is sponsored by - The IT Product Guide
>>Read honest & candid reviews on hundreds of IT Products from real users.
>>Discover which products truly live up to the hype. Start reading now.
>>http://ads.osdn.com/?ad_ide95&alloc_id=14396&op=CCk
>>_______________________________________________
>>Gusdev-gusdev mailing list
>>Gus...@li...
>>https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev
>>   =20
>>
>
>
>-------------------------------------------------------
>SF email is sponsored by - The IT Product Guide
>Read honest & candid reviews on hundreds of IT Products from real users.
>Discover which products truly live up to the hype. Start reading now.
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>_______________________________________________
>Gusdev-gusdev mailing list
>Gus...@li...
>https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev
> =20
>

RE: [Gusdev-gusdev] GUS 3.0 build.xml issue

[Doma, N. R. \(Contr\) <Nar...@ng...>]

Thanks for the detail mail Mike,
1. We created a sample java file using java.util.logging package that =
worked fine
2. We renamed the conf file as you said but no luck
3. We rechecked all our ENV variables every thing looks good

Looks like something is missing in our environment or in build file =
itself=20
(if possible can you test the build file in any of your environments) ?

we are working from our end to fix this issue,=20
Any help is much appreciated in this regard

Thanks
Narsimha

-----Original Message-----
From: Michael Saffitz [mailto:msa...@pc...]
Sent: Monday, March 28, 2005 3:28 PM
To: Doma, Narsimha R. (Contr)
Cc: gus...@li...; Lancaon, Johanan
Subject: Re: [Gusdev-gusdev] GUS 3.0 build.xml issue



Hi Narsimha,

Steve and I just discussed your issue.  One thing to be careful of,=20
especially on RedHat Enterprise Linux, is the ant.conf file in /etc.=20
I've found that removing it (or moving it to /etc/ant.conf.save) solved=20
several issues for us here at CBIL.  With it present, the system tends=20
to use the built in ant, and not any local copies you may have =
installed.

--Mike


Doma, Narsimha R. (Contr) wrote:
> Hi ,
>=20
> I am trying to install the GUS platform (first time)
> we could download all the software and followed the CBIL install guide
>=20
> when are trying to run the build first time  the build process was =
troughs the error message saying
> "CALSSPATH" issue with the java.util.logging class not found error and =
related errors follows=20
>=20
> is there any build script know errors? any pointers for new build =
script ?
> Please help us in this process
> Thanks
> Narsimha
>=20
>=20
> -------------------------------------------------------
> SF email is sponsored by - The IT Product Guide
> Read honest & candid reviews on hundreds of IT Products from real =
users.
> Discover which products truly live up to the hype. Start reading now.
> http://ads.osdn.com/?ad_ide95&alloc_id=14396&op=CCk
> _______________________________________________
> Gusdev-gusdev mailing list
> Gus...@li...
> https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev

Re: [Gusdev-gusdev] GUS 3.0 build.xml issue

[Michael S. <msa...@pc...>]

Hi Narsimha,

Steve and I just discussed your issue.  One thing to be careful of,=20
especially on RedHat Enterprise Linux, is the ant.conf file in /etc.=20
I've found that removing it (or moving it to /etc/ant.conf.save) solved=20
several issues for us here at CBIL.  With it present, the system tends=20
to use the built in ant, and not any local copies you may have installed.

--Mike


Doma, Narsimha R. (Contr) wrote:
> Hi ,
>=20
> I am trying to install the GUS platform (first time)
> we could download all the software and followed the CBIL install guide
>=20
> when are trying to run the build first time  the build process was trou=
ghs the error message saying
> "CALSSPATH" issue with the java.util.logging class not found error and =
related errors follows=20
>=20
> is there any build script know errors? any pointers for new build scrip=
t ?
> Please help us in this process
> Thanks
> Narsimha
>=20
>=20
> -------------------------------------------------------
> SF email is sponsored by - The IT Product Guide
> Read honest & candid reviews on hundreds of IT Products from real users=
.
> Discover which products truly live up to the hype. Start reading now.
> http://ads.osdn.com/?ad_ide95&alloc_id=14396&op=CCk
> _______________________________________________
> Gusdev-gusdev mailing list
> Gus...@li...
> https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev

Re: [Gusdev-gusdev] Assemblies

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

take a look at VirtualSequence

steve

Josef Jurek wrote:

>I need to store some assembled contigs in GUS along
>with the the sequences that these contigs were assembled from.
>There are a few tables that appear that they are for
>just such a purpose:
>
>  DoTS::Assembly                 The Assembly view of NASequenceImp
>                                 stores information and consensus sequences
>                                 generated by assembling EST and mRNA sequences
>                                 using the cap4 algorithm (Paracel)
>
>  DoTS::AssemblyAnatomyPercent   Materialized view that maps Assemblies to
>                                 the Anatomy ontology based on source library of
>                                 the contained sequences
>
>  DoTS::AssemblySNP              Table to record information about SNPs found
>                                 in Assemblies
>
>  DoTS::AssemblySequence         Table to hold the specific information about
>                                 sequences contained in Assemblies
>
>  DoTS::AssemblySequenceSNP      table that records the specifics of the
>                                 putative SNP in this AssemblySequence
>
>However, these tables seem to be intended for specific types of
>assemblies using the Paracel cap4 software and/or assemblies
>of EST/mRNA sequences.  I am using another assembler and assembling
>genomic sequences.
>
>As it looks as though these assembly tables were added for a specific
>technique, I wonder if they could be expanded/generalized so that
>one could store information for any type of assembly.
>
>I suppose I could just use DoTS.Evidence to link my contigs
>to the sequences that they were assembled from.
>
>Has anyone any comments?
>
>Thanks, Josef
>
>
>
>Josef Jurek, Ph.D.
>
>Daphne Preuss Laboratory
>Molecular Genetics and Cell Biology
>The University of Chicago
>ju...@cs...
>
>voice: (773) 834-3985
>fax:   (773) 702-6648
>
>
>
>-------------------------------------------------------
>SF email is sponsored by - The IT Product Guide
>Read honest & candid reviews on hundreds of IT Products from real users.
>Discover which products truly live up to the hype. Start reading now.
>http://ads.osdn.com/?ad_id=6595&alloc_id=14396&op=click
>_______________________________________________
>Gusdev-gusdev mailing list
>Gus...@li...
>https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev
>  
>

[Gusdev-gusdev] Assemblies

[<ju...@cs...>]

I need to store some assembled contigs in GUS along
with the the sequences that these contigs were assembled from.
There are a few tables that appear that they are for
just such a purpose:

  DoTS::Assembly                 The Assembly view of NASequenceImp
                                 stores information and consensus sequences
                                 generated by assembling EST and mRNA sequences
                                 using the cap4 algorithm (Paracel)

  DoTS::AssemblyAnatomyPercent   Materialized view that maps Assemblies to
                                 the Anatomy ontology based on source library of
                                 the contained sequences

  DoTS::AssemblySNP              Table to record information about SNPs found
                                 in Assemblies

  DoTS::AssemblySequence         Table to hold the specific information about
                                 sequences contained in Assemblies

  DoTS::AssemblySequenceSNP      table that records the specifics of the
                                 putative SNP in this AssemblySequence

However, these tables seem to be intended for specific types of
assemblies using the Paracel cap4 software and/or assemblies
of EST/mRNA sequences.  I am using another assembler and assembling
genomic sequences.

As it looks as though these assembly tables were added for a specific
technique, I wonder if they could be expanded/generalized so that
one could store information for any type of assembly.

I suppose I could just use DoTS.Evidence to link my contigs
to the sequences that they were assembled from.

Has anyone any comments?

Thanks, Josef



Josef Jurek, Ph.D.

Daphne Preuss Laboratory
Molecular Genetics and Cell Biology
The University of Chicago
ju...@cs...

voice: (773) 834-3985
fax:   (773) 702-6648

Re: [Gusdev-gusdev] GUS 3.0 build.xml issue

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

narsimha-

please send the error messages.

java.util.logging is part of jdk 1.4.   what version of jdk are you runni=
ng?

steve

Doma, Narsimha R. (Contr) wrote:

>Hi ,
>
>I am trying to install the GUS platform (first time)
>we could download all the software and followed the CBIL install guide
>
>when are trying to run the build first time  the build process was troug=
hs the error message saying
>"CALSSPATH" issue with the java.util.logging class not found error and r=
elated errors follows=20
>
>is there any build script know errors? any pointers for new build script=
 ?
>Please help us in this process
>Thanks
>Narsimha
>
>
>-------------------------------------------------------
>SF email is sponsored by - The IT Product Guide
>Read honest & candid reviews on hundreds of IT Products from real users.
>Discover which products truly live up to the hype. Start reading now.
>http://ads.osdn.com/?ad_ide95&alloc_id=14396&op=CCk
>_______________________________________________
>Gusdev-gusdev mailing list
>Gus...@li...
>https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev
> =20
>

[Gusdev-gusdev] GUS 3.0 build.xml issue

[Doma, N. R. \(Contr\) <Nar...@ng...>]

Hi ,

I am trying to install the GUS platform (first time)
we could download all the software and followed the CBIL install guide

when are trying to run the build first time  the build process was =
troughs the error message saying
"CALSSPATH" issue with the java.util.logging class not found error and =
related errors follows=20

is there any build script know errors? any pointers for new build script =
?
Please help us in this process
Thanks
Narsimha

Re: [Gusdev-gusdev] sres.externaldatabase lowecase_name?

[Hongxian He <hon...@pc...>]

Even at CBIL, lower() does not seem to do the trick for all (although i 
wonder if there are typos in some entries... and now all lowercase_names 
are in lower case...)


SQL> select count(*) from sres.externaldatabase where lower(name) != 
lowercase_name;

  COUNT(*)
----------
         8

SQL> select name, lowercase_name from sres.externaldatabase where 
lower(name) != lowercase_name;

NAME
--------------------------------------------------------------------------------
LOWERCASE_NAME
--------------------------------------------------------------------------------
Mouse Ensembl Peptides
mouse ensemble peptides

Mosquito Ensembl Peptides
mosquito ensemble peptides

Methanococcus jannaschii DSM2661 orfs
Methanococcus jannaschii DSM2661 orfs

HqPromoterAnalysis
hq_analysis

EPD Matrices
epd_matrices

Mouse Ensembl Peptides
mouse ensemble peptides

Scripps/GNF malaria array (scrmalaria)
affymetrix_gnf_malariachip

T1DBase
T1DBase


8 rows selected.


Hongxian

Ed Robinson wrote:

>We use the lowercase name as a place to store the database
>names we find in NRDB. e.g. (pir).  I don't know if this is
>appropriate or not, but it is an important field for how we
>deal with NRDB.
>
>-ed
>
>
>---- Original message ----
>  
>
>>Date: Thu, 24 Mar 2005 13:32:06 -0500
>>From: Michael Saffitz <msa...@pc...>  
>>Subject: [Gusdev-gusdev] sres.externaldatabase lowecase_name?  
>>To: "cbil >> 'cbil'" <cb...@pc...>, gusdev-gusdev
>>    
>>
><gus...@li...>
>  
>
>>Does anyone know why we have lowercase_name as a field in 
>>sres.externaldatabase?  Anyone using this?
>>
>>I'd like to remove it in GUS 3.5.  If you need to get the
>>    
>>
>lowercase 
>  
>
>>name, do:
>>
>>select lower(name) from sres.externaldatabase...
>>
>>Any objections?
>>
>>--Mike
>>
>>
>>-------------------------------------------------------
>>SF email is sponsored by - The IT Product Guide
>>Read honest & candid reviews on hundreds of IT Products from
>>    
>>
>real users.
>  
>
>>Discover which products truly live up to the hype. Start
>>    
>>
>reading now.
>  
>
>>http://ads.osdn.com/?ad_id=6595&alloc_id=14396&op=click
>>_______________________________________________
>>Gusdev-gusdev mailing list
>>Gus...@li...
>>https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev
>>    
>>
>-----------------
>Ed Robinson
>Center for Tropical and Emerging Global Diseases
>University of Georgia, Athens, GA 30602
>ero...@ug.../(706)542.1447/254.8883
>  
>


-- 
---------------------------------------------
HONGXIAN HE, Post-doctoral Researcher
1423 Blockley Hall, Center for Bioinformatics
423 Guardian Dr., University of Pennsylvania
Philadelphia, PA 19104
Phone: 215-746-7016 | FAX: 215-573-3111
---------------------------------------------

Re: [Gusdev-gusdev] sres.externaldatabase lowecase_name?

[Ed R. <ero...@ug...>]

We use the lowercase name as a place to store the database
names we find in NRDB. e.g. (pir).  I don't know if this is
appropriate or not, but it is an important field for how we
deal with NRDB.

-ed


---- Original message ----
>Date: Thu, 24 Mar 2005 13:32:06 -0500
>From: Michael Saffitz <msa...@pc...>  
>Subject: [Gusdev-gusdev] sres.externaldatabase lowecase_name?  
>To: "cbil >> 'cbil'" <cb...@pc...>, gusdev-gusdev
<gus...@li...>
>
>
>Does anyone know why we have lowercase_name as a field in 
>sres.externaldatabase?  Anyone using this?
>
>I'd like to remove it in GUS 3.5.  If you need to get the
lowercase 
>name, do:
>
>select lower(name) from sres.externaldatabase...
>
>Any objections?
>
>--Mike
>
>
>-------------------------------------------------------
>SF email is sponsored by - The IT Product Guide
>Read honest & candid reviews on hundreds of IT Products from
real users.
>Discover which products truly live up to the hype. Start
reading now.
>http://ads.osdn.com/?ad_id=6595&alloc_id=14396&op=click
>_______________________________________________
>Gusdev-gusdev mailing list
>Gus...@li...
>https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev
-----------------
Ed Robinson
Center for Tropical and Emerging Global Diseases
University of Georgia, Athens, GA 30602
ero...@ug.../(706)542.1447/254.8883

[Gusdev-gusdev] sres.externaldatabase lowecase_name?

[Michael S. <msa...@pc...>]

Does anyone know why we have lowercase_name as a field in 
sres.externaldatabase?  Anyone using this?

I'd like to remove it in GUS 3.5.  If you need to get the lowercase 
name, do:

select lower(name) from sres.externaldatabase...

Any objections?

--Mike

Re: [Gusdev-gusdev] SRes.Reference Schema Change for 3.5

[Michael S. <msa...@pc...>]

I don't remember if I replied to this or not, but these changes have 
been accepted for 3.5:

http://gusdb.org/wiki/index.php/Gus3.5RoadMap

--Mike


Ed Robinson wrote:
> I need to up the SRes.Reference.journal_or_book_name from 255
> characters to 1000 characters.  I would also like to recommend
> that we up the authors column to 1000 characters and the title
> column to 1000 characters.
> 
> Plesae let me know if these changes will be in 3.5.
> 
> -Ed
> -----------------
> Ed Robinson
> Center for Tropical and Emerging Global Diseases
> University of Georgia, Athens, GA 30602
> ero...@ug.../(706)542.1447/254.8883
> 
> 
> -------------------------------------------------------
> SF email is sponsored by - The IT Product Guide
> Read honest & candid reviews on hundreds of IT Products from real users.
> Discover which products truly live up to the hype. Start reading now.
> http://ads.osdn.com/?ad_id=6595&alloc_id=14396&op=click
> _______________________________________________
> Gusdev-gusdev mailing list
> Gus...@li...
> https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev

[Gusdev-gusdev] Official: new bug/feature tracker

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

folks-

we have put in place a bugzilla based bug/feature tracker (thanks Mike 
Saffitz).  You can get it from gusdb.org.

this is the new, official and ONLY way to submit bug and feature 
requests (including schema modifications).

Its fine to discuss proposed modifications on the mailing list.  but, to 
make an actual request you must use the tracker.

thanks very much,
steve

Re: [Gusdev-gusdev] SRes.Reference Schema Change for 3.5

[Angel P. <an...@ma...>]

What about SRes.BibliographicReference? Looks like there are dup tables.
Angel

Ed Robinson wrote:

>I need to up the SRes.Reference.journal_or_book_name from 255
>characters to 1000 characters.  I would also like to recommend
>that we up the authors column to 1000 characters and the title
>column to 1000 characters.
>
>Plesae let me know if these changes will be in 3.5.
>
>-Ed
>-----------------
>Ed Robinson
>Center for Tropical and Emerging Global Diseases
>University of Georgia, Athens, GA 30602
>ero...@ug.../(706)542.1447/254.8883
>
>
>-------------------------------------------------------
>SF email is sponsored by - The IT Product Guide
>Read honest & candid reviews on hundreds of IT Products from real users.
>Discover which products truly live up to the hype. Start reading now.
>http://ads.osdn.com/?ad_id=6595&alloc_id=14396&op=click
>_______________________________________________
>Gusdev-gusdev mailing list
>Gus...@li...
>https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev
>
>  
>

-- 

Angel Pizarro
Director, Bioinformatics Facility
Institute for Translational Medicine and Therapeutics
University of Pennsylvania
806 BRB II/III
421 Curie Blvd.
Philadelphia, PA 19104-6160

P: 215-573-3736
F: 215-573-9004

[Gusdev-gusdev] SRes.Reference Schema Change for 3.5

[Ed R. <ero...@ug...>]

I need to up the SRes.Reference.journal_or_book_name from 255
characters to 1000 characters.  I would also like to recommend
that we up the authors column to 1000 characters and the title
column to 1000 characters.

Plesae let me know if these changes will be in 3.5.

-Ed
-----------------
Ed Robinson
Center for Tropical and Emerging Global Diseases
University of Georgia, Athens, GA 30602
ero...@ug.../(706)542.1447/254.8883

Re: [Gusdev-gusdev] add stable_id columns to Gene, RNA, Protein

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

how about public_id?

Chris Stoeckert wrote:

> The distinction between internal project generated identifier and 
> imported identifier is an important one. I must say that "stable_id" 
> sounds terrible. How about "project_gene_id" for project generated 
> gene IDs and something analogous for RNAs and proteins?
> Chris
>
> On Mar 11, 2005, at 3:11 PM, Steve Fischer wrote:
>
>> The stable_id is the id provided by the project for the Gene.   In 
>> combination with a row_project_id it should be an alternate key.
>>
>> There is no source_id in Gene.  A source_id is for an external 
>> source.   these are not that.  these are generated by the project 
>> itself.
>> An example from AllGenes is DG1234555.
>>
>> steve
>>
>> Angel Pizarro wrote:
>>
>>> What is "stable_id"? Is an id stable across instances? If so, your 
>>> are getting mighty close to the notion of an accession, and hence 
>>> the source_id column.
>>>
>>> angel
>>>
>>> Steve Fischer wrote:
>>>
>>>> I'd like to see if we can include this in 3.5.
>>>>
>>>> Steve
>>>>
>>>>
>>>> -------------------------------------------------------
>>>> SF email is sponsored by - The IT Product Guide
>>>> Read honest & candid reviews on hundreds of IT Products from real 
>>>> users.
>>>> Discover which products truly live up to the hype. Start reading now.
>>>> http://ads.osdn.com/?ad_id=6595&alloc_id=14396&op=click
>>>> _______________________________________________
>>>> Gusdev-gusdev mailing list
>>>> Gus...@li...
>>>> https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev
>>>>
>>>
>>
>>
>> -------------------------------------------------------
>> SF email is sponsored by - The IT Product Guide
>> Read honest & candid reviews on hundreds of IT Products from real users.
>> Discover which products truly live up to the hype. Start reading now.
>> http://ads.osdn.com/?ad_id=6595&alloc_id=14396&op=click
>> _______________________________________________
>> Gusdev-gusdev mailing list
>> Gus...@li...
>> https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev
>
>
>
>
> -------------------------------------------------------
> SF email is sponsored by - The IT Product Guide
> Read honest & candid reviews on hundreds of IT Products from real users.
> Discover which products truly live up to the hype. Start reading now.
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> _______________________________________________
> Gusdev-gusdev mailing list
> Gus...@li...
> https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev

Re: [Gusdev-gusdev] add stable_id columns to Gene, RNA, Protein

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

The distinction between internal project generated identifier and 
imported identifier is an important one. I must say that "stable_id" 
sounds terrible. How about "project_gene_id" for project generated gene 
IDs and something analogous for RNAs and proteins?
Chris

On Mar 11, 2005, at 3:11 PM, Steve Fischer wrote:

> The stable_id is the id provided by the project for the Gene.   In 
> combination with a row_project_id it should be an alternate key.
>
> There is no source_id in Gene.  A source_id is for an external source. 
>   these are not that.  these are generated by the project itself.
> An example from AllGenes is DG1234555.
>
> steve
>
> Angel Pizarro wrote:
>
>> What is "stable_id"? Is an id stable across instances? If so, your 
>> are getting mighty close to the notion of an accession, and hence the 
>> source_id column.
>>
>> angel
>>
>> Steve Fischer wrote:
>>
>>> I'd like to see if we can include this in 3.5.
>>>
>>> Steve
>>>
>>>
>>> -------------------------------------------------------
>>> SF email is sponsored by - The IT Product Guide
>>> Read honest & candid reviews on hundreds of IT Products from real 
>>> users.
>>> Discover which products truly live up to the hype. Start reading now.
>>> http://ads.osdn.com/?ad_id=6595&alloc_id=14396&op=click
>>> _______________________________________________
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>>>
>>
>
>
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Re: [Gusdev-gusdev] add stable_id columns to Gene, RNA, Protein

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

The stable_id is the id provided by the project for the Gene.   In 
combination with a row_project_id it should be an alternate key.

There is no source_id in Gene.  A source_id is for an external source.   
these are not that.  these are generated by the project itself. 

An example from AllGenes is DG1234555.

steve

Angel Pizarro wrote:

> What is "stable_id"? Is an id stable across instances? If so, your are 
> getting mighty close to the notion of an accession, and hence the 
> source_id column.
>
> angel
>
> Steve Fischer wrote:
>
>> I'd like to see if we can include this in 3.5.
>>
>> Steve
>>
>>
>> -------------------------------------------------------
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Re: [Gusdev-gusdev] add stable_id columns to Gene, RNA, Protein

[Angel P. <an...@ma...>]

What is "stable_id"? Is an id stable across instances? If so, your are 
getting mighty close to the notion of an accession, and hence the 
source_id column.

angel

Steve Fischer wrote:

> I'd like to see if we can include this in 3.5.
>
> Steve
>
>
> -------------------------------------------------------
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-- 

Angel Pizarro
Director, Bioinformatics Facility
Institute for Translational Medicine and Therapeutics
University of Pennsylvania
806 BRB II/III
421 Curie Blvd.
Philadelphia, PA 19104-6160

P: 215-573-3736
F: 215-573-9004

[Gusdev-gusdev] add stable_id columns to Gene, RNA, Protein

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

I'd like to see if we can include this in 3.5.

Steve

Re: [Gusdev-gusdev] Something about GUS Schemas

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

Hi Fabricio,
Steve and I are working on a paper on GUS that should address this and=20=

I hope to circulate a draft shortly.
In the meantime I'm happy to try and answer questions. How much detail=20=

were you looking for? The really short version is that DoTS is for=20
sequence and sequence annotation. Sequence and feature tables are for=20
importing this information from external resources (e.g. GenBank),=20
whereas central dogma tables are for relating concepts of gene, RNAs,=20
and proteins based on sequence and features. RAD is for gene expression=20=

data mostly array-based. We had a paper on RAD detailing it (Manduchi=20
et al. Bioinformatics 2004). TESS is for relationships between=20
transcription factors and regulatory sequences captured in=20
grammar-based rules. SRes is for controlled vocabularies and ontologies=20=

referred to by other tables in GUS. Core is for tracking table info,=20
users, plugins, and algorithms. In GUS 3.5 we'll be introducing Study=20
for experimental design and descriptions (moved from RAD) and Prot for=20=

capturing 2D gel electrophoresis and mass spec based on mzXML and RAPAD=20=

(Jones et al/ Bioinformatics 2004). Hope this helps.
Chris

On Mar 7, 2005, at 1:36 PM, fab...@de... wrote:

> Hi all,
>
> I'm needing some document that could has an overview about GUS=20
> schemas. Does
> anyone know where I can find something explaining these schemas?=20
> Explaining
> what kind of data could be stored? What's the importance of any=20
> schemas?
>
> Any help?
>
> Thanks a lot,
>
> Fabricio
>
>
>
> ----------------------------------------------------------------
> This message was sent using IMP, the Internet Messaging Program.
>
>
> -------------------------------------------------------
> SF email is sponsored by - The IT Product Guide
> Read honest & candid reviews on hundreds of IT Products from real=20
> users.
> Discover which products truly live up to the hype. Start reading now.
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> _______________________________________________
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[Gusdev-gusdev] unknown error

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

<html><div style='background-color:'><DIV class=RTE>Hello,</DIV>
<DIV class=RTE>&nbsp;</DIV>
<DIV class=RTE>Does anyone know why this command: ga GUS::Common:Plugin::SubmitRow --help</DIV>
<DIV class=RTE>&nbsp;</DIV>
<DIV class=RTE>Gives this error:</DIV>
<DIV class=RTE>&nbsp;</DIV>
<DIV class=RTE>ERROR: syntax error at (eval 1) line 1, near "require GUS::Common:"</DIV>
<DIV class=RTE><BR>--------------------------- STACK TRACE -------------------------<BR>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; GUS::PluginMgr::Plugin::error('GUS::PluginMgr::GusApplication=HASH(0x804c8c4)','syntax error at (eval 1) line 1, near "require GUS::Common:"\x{a}') called at /opt/gus/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm line 254<BR>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; GUS::PluginMgr::GusApplication::newFromPluginName('GUS::PluginMgr::GusApplication=HASH(0x804c8c4)','GUS::Common:Plugin::SubmitRow') called at /opt/gus/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm line 398<BR>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; GUS::PluginMgr::GusApplication::doMajorMode_RunOrReport('GUS::PluginMgr::GusApplication=HASH(0x804c8c4)','GUS::Common:Plugin::SubmitRow',1) called at /opt/gus/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm line 
383<BR>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; GUS::PluginMgr::GusApplication::doMajorMode_Run('GUS::PluginMgr::GusApplication=HASH(0x804c8c4)','GUS::Common:Plugin::SubmitRow') called at /opt/gus/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm line 289<BR>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; GUS::PluginMgr::GusApplication::doMajorMode('GUS::PluginMgr::GusApplication=HASH(0x804c8c4)','GUS::Common:Plugin::SubmitRow') called at /opt/gus/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm line 198<BR>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; GUS::PluginMgr::GusApplication::parseAndRun('GUS::PluginMgr::GusApplication=HASH(0x804c8c4)','ARRAY(0x805ff68)') called at /opt/gus/gus_home/bin/ga line 11</DIV></div></html>

[Gusdev-gusdev] Something about GUS Schemas

[<fab...@de...>]

Hi all,

I'm needing some document that could has an overview about GUS schemas. D=
oes
anyone know where I can find something explaining these schemas? Explaini=
ng
what kind of data could be stored? What's the importance of any schemas?

Any help?

Thanks a lot,

Fabricio



----------------------------------------------------------------
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Re: [Gusdev-gusdev] Trash Tables

[Bindu G. <bi...@pc...>]

Ed -
Plasmodb has also been using RNAFeature; i dont know about the RNAType 
table. As Debbie writes, schema consolidation should consolidate these 
views, if it is possible.

Bindu

On Mar 4, 2005, at 10:07 AM, pi...@pc... wrote:

> There may be other uses of RNAFeature but the plugins I run use RNA 
> feature for
> mRNA features either predicted from an assembly of transcript 
> sequences or an
> mRNA sequence obtained from GenBank. Currently, RNAType and RNAFeature 
> have
> quite different attributes and seem to be intended for different uses 
> although
> it may be that they can be consolidated as they are both views of 
> RNAFeature.
>
>
>
>  Quoting Ed Robinson <ero...@ug...>:
>
>> What do you use RNA feature for as opposed to RNA type?
>>
>> ---- Original message ----
>>> Date: Fri,  4 Mar 2005 09:33:19 -0500
>>> From: pi...@pc...
>>> Subject: Re: [Gusdev-gusdev] Trash Tables
>>> To: Ed Robinson <ero...@ug...>
>>> Cc: gus...@li...
>>>
>>> We definitely use RNAFeature but I am not so sure about
>> ExonLocation. These are
>>> issues that should be raised in the schema discussions
>> because we may want to
>>> consolidate the views.
>>>
>>>                                                       Debbie
>>>
>>>
>>> Quoting Ed Robinson <ero...@ug...>:
>>>
>>>> We've stumbled upon a couple tables/views which seem
>>>> redundant.  Is anyone using these?
>>>>
>>>> Dots.ExonLocation - is completely subsumed by the fields in
>>>> dots.nalocation.
>>>>
>>>> Dots.RNAType, vs Dots.RNAFeature, these tables seem to belong
>>>> to one concept of a RNAFeature, is anyone using RNAFeature?
>>>> We want to use RNAType.
>>>>
>>>> All and any feedback would be appreciated.
>>>>
>>>> -Ed
>>>>
>>>>
>>>>
>>>> -----------------
>>>> Ed Robinson
>>>> Center for Tropical and Emerging Global Diseases
>>>> University of Georgia, Athens, GA 30602
>>>> ero...@ug.../(706)542.1447/254.8883
>>>>
>>>>
>>>> -------------------------------------------------------
>>>> SF email is sponsored by - The IT Product Guide
>>>> Read honest & candid reviews on hundreds of IT Products
>> from real users.
>>>> Discover which products truly live up to the hype. Start
>> reading now.
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>>>> _______________________________________________
>>>> Gusdev-gusdev mailing list
>>>> Gus...@li...
>>>> https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev
>>>>
>>>
>>>
>> -----------------
>> Ed Robinson
>> Center for Tropical and Emerging Global Diseases
>> University of Georgia, Athens, GA 30602
>> ero...@ug.../(706)542.1447/254.8883
>>
>
>
>
>
> -------------------------------------------------------
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> Read honest & candid reviews on hundreds of IT Products from real 
> users.
> Discover which products truly live up to the hype. Start reading now.
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