gusdev-gusdev — Topics concerning GUS development

Re: [Gusdev-gusdev] problem w/ docs on SourceForge CVS

[Steve F. <st...@SN...>]

hmm... Internet Explorer did the correct thing with the .ppt file: 
 brought up the dialogue asking me to save or open the file.

in Netscape, when i tried this on the .rtf file it also acted correctly.

I don't have powerpoint on my home computer, so when i return from 
vacation next week, i'll try the .ppt files from work

steve

Steve Fischer wrote:

> folks-
>
> i uploaded the .ppt files from the PSU-CBIL meeting, as we discuseed 
> in our last phone conference.
>
> two problems:
>  1. small: i imported it under the root rather than under scratch/.  
> (I can write the sourceforge admins to have them correct this.)
>  2. big: from what i can see, there isn't a way to access the .ppt 
> files correctly.  The "download" "HEAD" and "view" links brink up a 
> Netscape window which attempts to display the binary files as text. 
> Those are the only links offered. (I used cvs admin -kb to alert the 
> CVS server that these files are binary, but that didn't help)
>
> Here is a sample page with the big problem:
> http://cvs.sourceforge.net/cgi-bin/viewcvs.cgi/gusdev/GUS-PSU-meeting-06-2002/Biojava.ppt 
>
>
> steve
>
>
>
> -------------------------------------------------------
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[Gusdev-gusdev] problem w/ docs on SourceForge CVS

[Steve F. <st...@SN...>]

folks-

i uploaded the .ppt files from the PSU-CBIL meeting, as we discuseed in 
our last phone conference.

two problems:
  1. small: i imported it under the root rather than under scratch/.  (I 
can write the sourceforge admins to have them correct this.)
  2. big: from what i can see, there isn't a way to access the .ppt 
files correctly.  The "download" "HEAD" and "view" links brink up a 
Netscape window which attempts to display the binary files as text. 
 Those are the only links offered. (I used cvs admin -kb to alert the 
CVS server that these files are binary, but that didn't help)

Here is a sample page with the big problem:
http://cvs.sourceforge.net/cgi-bin/viewcvs.cgi/gusdev/GUS-PSU-meeting-06-2002/Biojava.ppt

steve

Re: [Gusdev-gusdev] GUS

[steve f. <st...@SN...>]

Paul-

good idea.  and, indeed, there really isn't one.  we do have 
www.gusdev.org, the sourceforge site, which is, i think, what you should 
use for now.

unfortunately, it isn't a very presentable site.

we'll need to think about how to address this.

steve

Pjm wrote:

>
> I would like to have a link to the GUS home page, if one exists.
>
> I can find lots of links to allgenes, plasmodb, various papers and 
> people but no actual GUS home page. I was hoping to link to it so it 
> would explain what GUS is  and what it can do.
>
>
>
>
> -------------------------------------------------------
> This sf.net email is sponsored by: OSDN - Tired of that same old
> cell phone?  Get a new here for FREE!
> https://www.inphonic.com/r.asp?r=sourceforge1&refcode1=vs3390
> _______________________________________________
> Gusdev-gusdev mailing list
> Gus...@li...
> https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev
>
>

[Gusdev-gusdev] GUS

[Pjm <pj...@sa...>]

I would like to have a link to the GUS home page, if one exists.

I can find lots of links to allgenes, plasmodb, various papers and people but no 
actual GUS home page. I was hoping to link to it so it would explain what GUS is 
  and what it can do.

Re: [Gusdev-gusdev] ISMB2002 Posters

[Steve F. <st...@SN...>]

yes, we can get Li Li's poster there.  we'll also put the two gus 
posters there as well.

jonathan schug-  can you open the ISMB2002 write privileges to group?

steve

Keith James wrote:

>Hi,
>
>I read with interest the TESS-II poster available in the downloads
>directory. Would it be possible to see Li Li's poster too? (I've seem
>to have lost her e-mail address so I can't mail her direct.)
>
>thanks,
>
>Keith
>

[Gusdev-gusdev] ISMB2002 Posters

[Keith J. <kd...@sa...>]

Hi,

I read with interest the TESS-II poster available in the downloads
directory. Would it be possible to see Li Li's poster too? (I've seem
to have lost her e-mail address so I can't mail her direct.)

thanks,

Keith

-- 

- Keith James <kd...@sa...> bioinformatics programming support -
- Pathogen Sequencing Unit, The Wellcome Trust Sanger Institute, UK -

Re: [Gusdev-gusdev] Oracle Segment Rollback in GUS

[<cra...@SN...>]

Arnaud Kerhornou wrote:
> 
> Hi Jonathan
> 
> The installation of GUSdev went fine. I've got a question about the
> rollback segment. It is called in the GUS code, "BIGRBS0", any
> particular reason for ? What is the size of it ?
> 

Arnaud-

I created it just because I felt that the default rollback segments were
rather small; certain large operations would result in a "snapshot too old/
rollback segment too small" error and I wanted a larger rollback segment to
use in such cases.  For simplicity we decided to modify the Perl object layer 
to use it by default.  The size is arbitrary and in GUSdev it happens to be 
around 20 GB:


CREATE TABLESPACE BIGRBS DATAFILE
'/usr/local/oracle/u02/oradata/gusdev/rbs_big01.dbf' SIZE 2000M AUTOEXTEND OFF,
'/usr/local/oracle/u02/oradata/gusdev/rbs_big02.dbf' SIZE 2000M AUTOEXTEND OFF,
'/usr/local/oracle/u02/oradata/gusdev/rbs_big03.dbf' SIZE 2000M AUTOEXTEND OFF,
'/usr/local/oracle/u02/oradata/gusdev/rbs_big04.dbf' SIZE 2000M AUTOEXTEND OFF,
'/usr/local/oracle/u02/oradata/gusdev/rbs_big05.dbf' SIZE 2000M AUTOEXTEND OFF,
'/usr/local/oracle/u02/oradata/gusdev/rbs_big06.dbf' SIZE 2000M AUTOEXTEND OFF,
'/usr/local/oracle/u02/oradata/gusdev/rbs_big07.dbf' SIZE 2000M AUTOEXTEND OFF,
'/usr/local/oracle/u02/oradata/gusdev/rbs_big08.dbf' SIZE 2000M AUTOEXTEND OFF,
'/usr/local/oracle/u02/oradata/gusdev/rbs_big09.dbf' SIZE 2000M AUTOEXTEND OFF,
'/usr/local/oracle/u02/oradata/gusdev/rbs_big10.dbf' SIZE 2000M AUTOEXTEND OFF
DEFAULT STORAGE ( INITIAL 1024K NEXT 1024K MINEXTENTS 16 MAXEXTENTS UNLIMITED);

CREATE PUBLIC ROLLBACK SEGMENT BIGRBS0 TABLESPACE BIGRBS;
ALTER ROLLBACK SEGMENT "BIGRBS0" ONLINE;


Jonathan

-- 
Jonathan Crabtree
Center for Bioinformatics, University of Pennsylvania
1406 Blockley Hall, 423 Guardian Drive Philadelphia, PA 19104-6021
215-573-3115

[Gusdev-gusdev] Oracle Segment Rollback in GUS

[Arnaud K. <ax...@sa...>]

Hi Jonathan

The installation of GUSdev went fine. I've got a question about the 
rollback segment. It is called in the GUS code, "BIGRBS0", any 
particular reason for ? What is the size of it ?

Thanks
Arnaud

-- 
Arnaud Kerhornou

The Wellcome Trust Sanger Institute
The Pathogen Sequencing Unit
Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
Work: +44 (0) 1223 494955
Fax: +44 (0) 1223 494919

[Gusdev-gusdev] New files for GUSdev schema.

[Jonathan C. <cra...@sn...>]

Paul-

I've just placed a new .tar.gz file with the GUSdev/GUSwww create database
scripts on our download site:

<http://www.cbil.upenn.edu/downloads/GUS/schema/gusdev-sql-aug-12-2002.tar.gz>

There are a number of improvements over the last set of files, not least
of which is the fact that I tested everything before tar'ing it up this
time around!  As you requested I've also included the contents of the
following tables:

Taxon
Taxon3
TaxonName
GeneticCode

The latter three will replace the first one in GUS 3.0 (with Taxon3
getting renamed to Taxon.)  And, as I mentioned in my previous e-mail,
"Taxon" came from GSDB, whereas "Taxon3" (and the two tables associated
with it) was loaded from flat files downloaded from NCBI.  I think
everything should be explained in the accompanying README file, but let me
know if you have any questions.  The next step will be to package up (and
test) the Perl object layer and Java servlet code, although I'm
contemplating making some changes to the part of the database schema with
which the servlet code interacts (the "guswww-" files in this release.)

Note that there are a couple of problems with loading the Taxon tables
this way (using INSERT statments through SQL*Plus); the first is that it's
probably slightly slower than using the Perl object layer and the second
is that (at least how I currently have it set up) you lose the tracking
information (i.e., an informative entry in AlgorithmInvocation.)

Jonathan

Re: [Fwd: [Fwd: Re: [Gusdev-gusdev] GUSdev schema]]

[<cra...@SN...>]

Pjm wrote:
> 
> Jonathan,
> 
> thanks for putting the file gusdev-sql-jul-25-2002.tar.gz on the download site.
> Since we have to put bootstrap/dictinary data into the rows of our schema I was
> wondering how we could share some of these things. For example, the taxon table
> could easily be shared (does this relate to NCBI Ids at all?).
> 
> Another reason for doing this is so when we (and others..) install GUS we can
> run our parsers straight away and populate the schema with our favourite data.
> Could the bootstrap data be added to the install script please?
> 
> Paul.
> 

Hi Paul-

Angel discovered some problems with the CREATE VIEW statements in that file.  I'm
just ironing out the last of the problems with it and will have an updated version
on the site in a couple of hours.  The new version has two files with actual data: 
1) the 4 or 5 "bootstrap" rows needed for those common tables, and 2) the contents of 
the TableInfo table.  I had the Taxon table on my list of things to add, and I think
it would be straightforward to just dump that as well.  I *believe* that the current
gusdev Taxon table is essentially a copy of a similar table from GSDB.  However,
we have a new set of taxon tables for GUS 3.0 ("Taxon3" in GUSdev) that Debbie 
populated using NCBI's flat files.

Jonathan

Re: [Fwd: [Fwd: Re: [Gusdev-gusdev] GUSdev schema]]

[Pjm <pj...@sa...>]

Jonathan,

thanks for putting the file gusdev-sql-jul-25-2002.tar.gz on the download site. 
Since we have to put bootstrap/dictinary data into the rows of our schema I was 
wondering how we could share some of these things. For example, the taxon table 
could easily be shared (does this relate to NCBI Ids at all?).

Another reason for doing this is so when we (and others..) install GUS we can 
run our parsers straight away and populate the schema with our favourite data. 
Could the bootstrap data be added to the install script please?

Paul.

Jonathan Crabtree wrote:
> On Sun, 4 Aug 2002, Paul Mooney wrote:
> 
>>hi all,
>>
>>I have finally got back on to a computer - no more cold turkey...
>>
>>Arnaud has told me the java layer makes some calls to perl which try to query
>>tables that do not exist in our schema because it is a couple of months older.
>>Rather than try to patch the schema and to avoid any other problems like this
>>it seems a good idea to get a point-in-time snapshot of GUSdev.
> 
> #
> 
>>1st we need the schema - we are develping the EMBL parser with what we have
>>running now. The java layer will be needed once we are happy we have loaded a
>>good range of data so we can run the query servlet stuff. We will want to
>>modify this (hack :) so we can point to GeneDB gene pages in the prototype.
>>
>>Arnaud might be able to give time scales on when the data loading is in a good
>>enough state for a web interface but I imagine we will need the web stuff
>>within 2 weeks. Is this do-able?
>>
>>Does this help at all?
>>
> 
> 
> Paul-
> 
> Yes, thanks.  I think 2 weeks is doable.  So basically the plan is to
> start with an empty snapshot of the latest GUSdev schema and use the EMBL
> parser to populate it?  It might also help if I could have a quick look at
> the EMBL parser, or at least just find out which tables it's loading.
> Anyway, I should have an updated set of schema creation scripts ready in
> the next day or two.
> 
> Jonathan
> 
> 

Re: [Fwd: [Fwd: Re: [Gusdev-gusdev] GUSdev schema]]

[Arnaud K. <ax...@sa...>]

Jonathan

First, I agree on a 2-week timescale.
We're going to use a generic parser by using bioperl and populate an 
empty GUSdev instance.
The first stage will be to generate bioperl objects from any format 
(embl, genbank that bioperl recognises), then gus objects.

We have already done in the past, for pombe data, a GUS script to 
populate data from XML files, so it will just be made generic by 
changing the parsing stage.

The objects we're planning to generate are:

    * Sequence:
        => ExternalNASequence objects

    * Features:
        => GeneFeature objects,
        => ExonFeature,
        => RNAFeature,
        => TranslatedAAFeature,
        => TranslatedAASequence,
        => SignalPeptideFeature,

        => Re. Transmembrane and Pfam domains, should we generate 
PredictedAAFeature objects ?

    * Central Dogma:
        => Gene objects,
        => RNA,
        => Protein,
       
    * GO associations:
        => ProteinGOProcess, ProteinGOFunction, ProteinGOComponent objects.

Do you have any comments on these objects ?
What does the website expect to be populated re. Pfam and transmembrane 
domains ?

cheers
Arnaud

Jonathan Crabtree wrote:

>On Sun, 4 Aug 2002, Paul Mooney wrote:
>
>>hi all,
>>
>>I have finally got back on to a computer - no more cold turkey...
>>
>>Arnaud has told me the java layer makes some calls to perl which try to query
>>tables that do not exist in our schema because it is a couple of months older.
>>Rather than try to patch the schema and to avoid any other problems like this
>>it seems a good idea to get a point-in-time snapshot of GUSdev.
>>
>#
>
>>1st we need the schema - we are develping the EMBL parser with what we have
>>running now. The java layer will be needed once we are happy we have loaded a
>>good range of data so we can run the query servlet stuff. We will want to
>>modify this (hack :) so we can point to GeneDB gene pages in the prototype.
>>
>>Arnaud might be able to give time scales on when the data loading is in a good
>>enough state for a web interface but I imagine we will need the web stuff
>>within 2 weeks. Is this do-able?
>>
>>Does this help at all?
>>
>
>Paul-
>
>Yes, thanks.  I think 2 weeks is doable.  So basically the plan is to
>start with an empty snapshot of the latest GUSdev schema and use the EMBL
>parser to populate it?  It might also help if I could have a quick look at
>the EMBL parser, or at least just find out which tables it's loading.
>Anyway, I should have an updated set of schema creation scripts ready in
>the next day or two.
>
>Jonathan
>
>

Re: [Gusdev-gusdev] BibliographicReference

[Valerie W. <va...@sa...>]

sounds fine.

Angel Pizarro wrote:
> 
> If this is from an internal project to PSU, I will create an external
> table for BibRef annotations, such as 'manually reviewed', 'mined', etc. I
> don't want to add information not intrinsic to the entry in the same
> table.
> 
> Angel
> 
>  On Wed, 31 Jul 2002, Valerie Wood wrote:
> > > Lastly, what is your intent with the 'is_curated' bit column?
> > > Angel
> >
> >
> > We need to be able to add a flag to distinguish between papers which
> > have been read and manually curated,
> > and those which have been mined but not curator reviewed to extract data
> >
> > Val
> >
> >
> >

-- 
----------------------------------------------------------------------------------
Valerie Wood		       Tel: 01223 494954
S. Pombe Genome Project	       Fax: 01223 494919 		       
The Sanger Centre              email: va...@sa...
Wellcome Trust Genome Campus   http://www.sanger.ac.uk/Projects/S_pombe 
Cambridge                      
CB10 1SA

Re: [Gusdev-gusdev] BibliographicReference

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

If this is from an internal project to PSU, I will create an external
table for BibRef annotations, such as 'manually reviewed', 'mined', etc. I
don't want to add information not intrinsic to the entry in the same
table.

Angel

 On Wed, 31 Jul 2002, Valerie Wood wrote:
> > Lastly, what is your intent with the 'is_curated' bit column?
> > Angel
>
>
> We need to be able to add a flag to distinguish between papers which
> have been read and manually curated,
> and those which have been mined but not curator reviewed to extract data
>
> Val
>
>
>

Re: [Gusdev-gusdev] BibliographicReference

[Valerie W. <va...@sa...>]

Angel Pizarro wrote:
> 
> Arnaud,
> this is a bit over powered for what we use, but I think it not all
> that much more, except the bit about the authors. Can I make the
> compromise to keep the author field in the table in addition to a
> normalized set of tables for those that choose to use them?
> 
> ALso I had forgotten to add an (external_db_release_id, source_id) tuple
> to the table before I sent it out. This would only take care of one
> external reference, though. A possible solution would be to use a many to
> many relation to DbRef for all of the external ids such as pubmed and
> medline.
> 
> Lastly, what is your intent with the 'is_curated' bit column?
> Angel


We need to be able to add a flag to distinguish between papers which
have been read and manually curated,
and those which have been mined but not curator reviewed to extract data

Val


-- 
----------------------------------------------------------------------------------
Valerie Wood		       Tel: 01223 494954
S. Pombe Genome Project	       Fax: 01223 494919 		       
The Sanger Centre              email: va...@sa...
Wellcome Trust Genome Campus   http://www.sanger.ac.uk/Projects/S_pombe 
Cambridge                      
CB10 1SA

Re: [Gusdev-gusdev] BibliographicReference

[Arnaud K. <ax...@sa...>]

Hi Angel

Angel Pizarro wrote:

>Arnaud,
>this is a bit over powered for what we use, but I think it not all
>that much more, except the bit about the authors. Can I make the
>compromise to keep the author field in the table in addition to a
>normalized set of tables for those that choose to use them?
>
Do you mean you want to keep the authors column in addition of a table 
authors ? If so it's fine.

>
>ALso I had forgotten to add an (external_db_release_id, source_id) tuple
>to the table before I sent it out. This would only take care of one
>external reference, though. A possible solution would be to use a many to
>many relation to DbRef for all of the external ids such as pubmed and
>medline.
>
or the ExternalDatabaseLink table.

>
>Lastly, what is your intent with the 'is_curated' bit column?
>Angel
>
Val is going to answer to your question.

cheers
Arnaud

>
>On Mon, 29 Jul 2002, Arnaud Kerhornou wrote:
>
>>Hi Angel
>>
>>some comments:
>>
>>Could it be possible to add the following fields:
>>    * abstract,
>>    * pubmed_id,
>>    * medline_id,
>>    * is_curated,
>>    * the list of keywords, in a separate table, ReferenceKeyword.
>>
>>Also, we would like to store each author in a separate entry instead of
>>a unique column.
>>
>>Besides, to facilitate the queries, it would be better to have a many to
>>many relationships between BibliographicReference and the two tables,
>>ReferenceKeyword and Author.
>>
>>cheers
>>Arnaud
>>
>>Angel Pizarro wrote:
>>
>>>I want to add a table BibliographicReference to GUS30 SRes, in addition to
>>>the Reference table, or at least revamp the Reference table by adding the
>>>missing columns that are in BibRef (attached below).
>>>
>>>The reasoning is that the Reference table is a hold-over from parsing
>>>genbank records for this type of info. Thus the position column refers to
>>>the positional information from genbank features. Also we have the old
>>>'remark' column from Jian Wang's days of schema design. Here is the schema
>>>def for BibRef:
>>>
>>>CREATE TABLE SRes.BibliographicReference (
>>>	BIBLIOGRAPHIC_REFERENCE_ID NUMBER(10) NOT NULL,
>>>	TITLE VARCHAR2 ( 100 ) NOT NULL,
>>>	AUTHORS VARCHAR2 ( 100 ) NOT NULL,
>>>	PUBLICATION VARCHAR2 ( 100 ),
>>>	EDITOR VARCHAR2 ( 100 ),
>>>	YEAR NUMBER(5),
>>>	VOLUME VARCHAR2 ( 100 ),
>>>	ISSUE VARCHAR2 ( 100 ),
>>>	PAGES VARCHAR2 ( 100 ),
>>>	URI VARCHAR2 ( 100 ),
>>>	MODIFICATION_DATE DATE NOT NULL,
>>>	USER_READ NUMBER ( 1 ) NOT NULL,
>>>	USER_WRITE NUMBER ( 1 ) NOT NULL,
>>>	GROUP_READ NUMBER ( 1 ) NOT NULL,
>>>	GROUP_WRITE NUMBER ( 1 ) NOT NULL,
>>>	OTHER_READ NUMBER ( 1 ) NOT NULL,
>>>	OTHER_WRITE NUMBER ( 1 ) NOT NULL,
>>>	ROW_USER_ID NUMBER ( 12 ) NOT NULL,
>>>	ROW_GROUP_ID NUMBER ( 12 ) NOT NULL,
>>>	ROW_PROJECT_ID NUMBER ( 12 ) NOT NULL,
>>>	ROW_ALG_INVOCATION_ID NUMBER ( 12 ) NOT NULL,
>>>	CONSTRAINT PK_BIBLIOGRAPHICREFERNECE PRIMARY KEY
>>>(BIBLIOGRAPHIC_REFERENCE_ID)
>>>);
>>>
>>>
>>>
>>>
>>
>

[Gusdev-gusdev] conference call summary

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

Conference call summary July 23, 2002
CBIL: Jonathan Crabtree, Sharon Diskin, Yongchang Gan, Li Li, Joan 
Mazzarelli, Debbie Pinney, Angel Pizarro, Jonathan Schug, Chris Stoeckert

PSU: Matt Berriman, Christiane Herz-Fowler, Keith James, Paul Mooney, 
Christopher Peacock,
Marie-Adele Rajandream, Adrian Tivey

Agenda:
	*	time scale and priorities for completing GUS 3.0
Jonathan C. reported that we will be migrating GUSdev to GUS3.0 over the 
next 3-4 weeks. Once data is migrated, then testing of plugins can be 
done. The web interfaces need to be adjusted to use GUS3.0 too. AllGenes 
has been made GUS3.0 compliant but obviously has not been tested. At 
issue is the ability to query GUS through GeneDB and to be able to 
demonstrate this at the upcoming Woods Hole meeting in September. 
Because of the uncertainties involved in bringing the new system online, 
it may be best to implement the current GUSdev for which all the plugins 
and interfaces are available. We need to make the current schema and 
code available for GUSdev. Note that RAD3 (in GUS3.0) is currently being 
populated along with supporting tables in CORE and SRES. Also note that 
the next public releases of AllGenes and PlamoDB will be with GUSdev and 
that public views of GUS3.0 probably won't occur until November/December.
ACTION ITEMS: JC- generate CREATE TABLE statements of current GUSdev. 
CBIL: Update files as necessary at 
http://www.cbil.upenn.edu/downloads/GUS/

	*	our suggested new tables protein properties and protein 
features, did you
guys have any comments on this for us ?
The ProteinProperty table and protein features views of AAFeatureImp 
proposed by Arnaud by email are OK with CBIL. The views can be used with 
the Interaction table to specify interactions of sequences. Note that 
interactions between proteins (at the central dogma level) can also be 
made.

	*	availability of up-to-date Plugins for loading of the controlled
vocabulary tables eg for GO, Taxon into GUS 3.0
Jonathan S. reported that it should only take a day or two to adjust the 
current plugins to work on loading GUS3.0. No immediate plans to do this 
but if needed can schedule it.

	*	availability of Plugin for populating EMBL and Swall into External
NASequence
Angel reported that current plugins for populating sequence and feature 
tables from GenBank flat files can be adapted to use EMBL and SWall 
files. The current plugin just needs to call parsers for these (which 
need to be written).

	*	Additional keys and qualifiers for Artemis to simplify 
transfer of data
into GUS / GeneDB
It was noted and agreed that all keys and qualifiers should make use of 
controlled vocabulary/ontology tables in SRES (e.g. SequenceOntology).

	*	Annotation interface
Joan reported that the CBIL group had gone over Artemis and Apollo but 
will probably create their own stand-alone annotation tool using 
whatever parts of code they can borrow from these. At issue for CBIL was 
the need for various accessory programs (from BLAST to Perl tk) for 
Artemis to be installed locally. CBIL's annotators are distributed 
around the world and need to use accessory programs (like BLAST) over 
the web. PSU and CBIL have overlapping requirements and will continue to 
share ideas and hopefully code.
ACTION ITEM: SD send latest requirements document out. (this was done 
but stuck due limit in sourceforge mail size).

	*	Biojava and GUS Central Dogma objects
Paul reported that work is proceeding on the central dogma objects but 
they are not ready to release yet.
ACTION ITEM: PM send BioJava for GUS objects to JC as is to give him a 
preview.

	*	Phenotype tables
SeqVariation view of NAFeatureImp can be linked to Phenotype table 
through a linking table SeqVariationPhenotype. This allows changes at 
the genomic level to be linked to phenotype.
ACTION ITEM: CS create Phenotype and associated tables in SRES.

	*	Population ortholog tables
Li described population of ortholog tables. There are two parts: a 
general part for loading sequences, BLAST comparisons, and loading the 
Similarity table; and a specific part for using the similarities to 
create ortholog and paralog groups. Li is using reciprocal best hits 
combined with a graph clustering approach. Plugins for the general part 
are available. Ortholog tables for proteins are present in GUSdev; these 
have been expanded in GUS3.0. Keith raised the issue of curating 
orthologs. PSU will look into populating ortholog tables by curators 
directly.
ACTION ITEM: LL will make her code for populating ortholog tables 
available by September.

	*	CVS
Sanger CVS relies on Sanger administrators but are very likely to be 
more responsive than Sourceforge administrators. Sanger does not have 
trackers but this is not something of interest. Sourceforge does have a 
nice web site for browsing CVS and mail archives. Sanger also has a web 
view for read-only. Will continue with Sourceforge for now but will 
continue to look into Sanger site.
Step releases were thought to be useful by both teams.  Paul suggested a 
naming convention for tagging the CVS tree or the release. A step 
release would cover schema/perl/java/html etc. so one could for example 
check out PlasmoDB as of Release-123-01-Apr-2002.  It is not an 
immediate requirement but something to consider for the future.
ACTION ITEM: PM send URL for Sanger web view of CVS. Find out if 
available for read write.

[Gusdev-gusdev] Re: [Fwd: Re: proposed modifications to GO Schema for GUS3.0]

[Arnaud K. <ax...@sa...>]

Sharon Diskin wrote:

> Hi Arnaud,
>
> Welcome back.
>
> I believe Jonathan S. is re-writing the plugin that loads GO, and that 
> he is using some sort of generic underlying parser to do this.  If I 
> understand correctly,  the parsing code may be generic enough and 
> would likely just require writing some small amount of code to do the 
> correct mapping.  

Re. the Sequence Ontology I can only see a SequenceOntology table. Would 
it be possible to have the same design for SO (or for any others) than 
for GO, I mean not only store SO terms but also their relationships ?

>
> Jonathan - is this correct?  
>
> Thanks,
> Sharon
>
> Arnaud Kerhornou wrote:
>
>> Hi Sharon
>>
>> I was away last week but Matt has replied to you regarding the 
>> comment field.
>> Also re. the population of the GO terms into GUS, will the plugin be 
>> generic enough to be used for others ontologies such as Sequence 
>> Ontology or the Parasite Life Cycle Ontology which we are planning to 
>> use ?
>>
>> cheers
>> Arnaud
>>
>> Sharon Diskin wrote:
>>
>>> Okay, thanks.   Does this mean that a single comment field added to 
>>> the GOTerm table is sufficient in your view?  
>>>
>>> Alternatively, we could use the DoTS.Comments table to store 
>>> comments, these can then be associated through the Evidence table to 
>>> any row in GUS.  So, another option would be to use the Comments 
>>> table to store the text, and link it to the GOTerm entry through the 
>>> Evidence table.  If this is not an appropriate use of the Evidence 
>>> table, then we could just create a GOTermComments linking table.  
>>>
>>> cheers,
>>> sharon
>>>
>>> Arnaud Kerhornou wrote:
>>>
>>>> Hi Sharon
>>>>
>>>> I forward you an example of a GO comment given by Matt.
>>>>
>>>> cheers
>>>> Arnaud
>>>>
>>>> -------- Original Message --------
>>>> Subject: Re: proposed modifications to GO Schema for GUS3.0
>>>> Date: Tue, 16 Jul 2002 13:19:51 +0100
>>>> From: Matt Berriman <mb...@sa...>
>>>> To: Arnaud Kerhornou <ax...@sa...>
>>>> References: 
>>>> <Pin...@sn...> 
>>>> <3D2...@sa...> <3D2...@pc...> 
>>>> <3D2...@sa...> <3D2...@pc...> 
>>>> <3D3...@sa...>
>>>>
>>>>
>>>>
>>>>Here's a complete entry from the GO database:
>>>>
>>>>term: C-terminal protein farnesylation
>>>>
>>>>goid: GO:0006503
>>>>
>>>>definition: The covalent or non-covalent attachment of a farnesyl moiety 
>>>>to the carboxy terminus of a protein. OBSOLETE.
>>>>
>>>>definition_reference: GO:jl
>>>>
>>>>comment: This term was made obsolete because the process is not exclusive to the carboxy terminus 
>>>>of a protein. Consider instead the biological process term 'protein amino acid farnesylation ; 
>>>>GO:0018347'.
>>>>
>>>>cheers
>>>>Matt
>>>>
>>>>
>>>>Arnaud Kerhornou wrote:
>>>>
>>>>> Sharon Diskin wrote:
>>>>>
>>>>>>
>>>>>>> Also re. the GOTerm table, would it be possible to add a comment 
>>>>>>> field ?
>>>>>>
>>>>>>
>>>>>>
>>>>>> I do not have a problem with this.  Does anyone else have an opinion 
>>>>>> on this?  What type of information would you put in the comment field?
>>>>>
>>>>>
>>>>> Matt,
>>>>>
>>>>> Do you have
>>>> an
>>>> 
>>>>exa
>>>>mple of comment you want to store ?
>>>>>
>>>>> I should mention than the GO database design allows to store several 
>>>>> comments (one to many relationship), one comment field might be enough 
>>>>> though and would keep the design simple.
>>>>>
>>>>> cheers
>>>>> Arnaud
>>>>>
>>>>>>
>>>>>> Cheers,
>>>>>> Sharon
>>>>>>
>>>>>> p.s.  I will be out of town until Monday July 22nd.
>>>>>>
>>>>>>>
>>>>>>> cheers
>>>>>>> Arnaud
>>>>>>>
>>>>>>> Sharon Diskin wrote:
>>>>>>>
>>>>>>>> Hi Arnaud,
>>>>>>>>
>>>>>>>> I've attached the new GO schema and documentation that Jonathan 
>>>>>>>> Schug and I have come up. We believe that this new schema addresses 
>>>>>>>> your concern about the association date and also provides a better 
>>>>>>>> way of tracking multiple instances/sources of the same association 
>>>>
>>>>>>
>>>>;>
>>>>> (s
>>>>ee description of GOAssociationInstance table).
>>>>>>>>
>>>>>>>>
>>>>>>>> Regarding your other question concerning the 'DB:Ref' and 'from or 
>>>>>>>> with', we see these being tracked using the generic Evidence 
>>>>>>>> table.   The 'from or with' would be Evidence for the 
>>>>>>>> GOAssocInstEvidCode entry as it is connected to a specific evidence 
>>>>>>>> code that is assigned to the association.  The 'DB:Ref' (such as in 
>>>>>>>> the PubMed example you mentioned) would be Evidence for the 
>>>>>>>> GOAssociationInstance entry as it is _not_ connected to a specific 
>>>>>>>> evidence code, but rather the association as a whole.  More details 
>>>>>>>> can be found in the attached documentation.
>>>>>>>>
>>>>>>>>
>>>>>>>> Any feedback is welcome.  Also, if any of this is unclear, just l
>>>>et 
>>>>>&
>>>>gt;>&g
>>>>t; us know.
>>>>
>>>>>>>>
>>>>>>>> Cheers,
>>>>>>>> Sharon
>>>>>>>>
>>>>>>>>
>>>>>>>
>>>>>>
>>>>>
>>>>>
>>>>>
>>>>
>>>>-- 
>>>>
>>>>  Dr Matthew Berriman 
>>>>  Senior Computer Biologist - Pathogen Sequencing Unit - 
>>>>  The Wellcome Trust Sanger Institute
>>>>  Tel +44 (0)1223 494817 -  Fax +44 (0)1223 494919 
>>>>  http://www.sanger.ac.uk
>>>>
>>>>        
>>>>
>>
>

Re: [Gusdev-gusdev] BibliographicReference

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

Arnaud,
this is a bit over powered for what we use, but I think it not all
that much more, except the bit about the authors. Can I make the
compromise to keep the author field in the table in addition to a
normalized set of tables for those that choose to use them?

ALso I had forgotten to add an (external_db_release_id, source_id) tuple
to the table before I sent it out. This would only take care of one
external reference, though. A possible solution would be to use a many to
many relation to DbRef for all of the external ids such as pubmed and
medline.

Lastly, what is your intent with the 'is_curated' bit column?
Angel

On Mon, 29 Jul 2002, Arnaud Kerhornou wrote:

> Hi Angel
>
> some comments:
>
> Could it be possible to add the following fields:
>     * abstract,
>     * pubmed_id,
>     * medline_id,
>     * is_curated,
>     * the list of keywords, in a separate table, ReferenceKeyword.
>
> Also, we would like to store each author in a separate entry instead of
> a unique column.
>
> Besides, to facilitate the queries, it would be better to have a many to
> many relationships between BibliographicReference and the two tables,
> ReferenceKeyword and Author.
>
> cheers
> Arnaud
>
> Angel Pizarro wrote:
>
> >I want to add a table BibliographicReference to GUS30 SRes, in addition to
> >the Reference table, or at least revamp the Reference table by adding the
> >missing columns that are in BibRef (attached below).
> >
> >The reasoning is that the Reference table is a hold-over from parsing
> >genbank records for this type of info. Thus the position column refers to
> >the positional information from genbank features. Also we have the old
> >'remark' column from Jian Wang's days of schema design. Here is the schema
> >def for BibRef:
> >
> >CREATE TABLE SRes.BibliographicReference (
> >	BIBLIOGRAPHIC_REFERENCE_ID NUMBER(10) NOT NULL,
> >	TITLE VARCHAR2 ( 100 ) NOT NULL,
> >	AUTHORS VARCHAR2 ( 100 ) NOT NULL,
> >	PUBLICATION VARCHAR2 ( 100 ),
> >	EDITOR VARCHAR2 ( 100 ),
> >	YEAR NUMBER(5),
> >	VOLUME VARCHAR2 ( 100 ),
> >	ISSUE VARCHAR2 ( 100 ),
> >	PAGES VARCHAR2 ( 100 ),
> >	URI VARCHAR2 ( 100 ),
> >	MODIFICATION_DATE DATE NOT NULL,
> >	USER_READ NUMBER ( 1 ) NOT NULL,
> >	USER_WRITE NUMBER ( 1 ) NOT NULL,
> >	GROUP_READ NUMBER ( 1 ) NOT NULL,
> >	GROUP_WRITE NUMBER ( 1 ) NOT NULL,
> >	OTHER_READ NUMBER ( 1 ) NOT NULL,
> >	OTHER_WRITE NUMBER ( 1 ) NOT NULL,
> >	ROW_USER_ID NUMBER ( 12 ) NOT NULL,
> >	ROW_GROUP_ID NUMBER ( 12 ) NOT NULL,
> >	ROW_PROJECT_ID NUMBER ( 12 ) NOT NULL,
> >	ROW_ALG_INVOCATION_ID NUMBER ( 12 ) NOT NULL,
> >	CONSTRAINT PK_BIBLIOGRAPHICREFERNECE PRIMARY KEY
> >(BIBLIOGRAPHIC_REFERENCE_ID)
> >);
> >
> >
> >
> >
>
>

[Gusdev-gusdev] Re: [Fwd: Re: proposed modifications to GO Schema for GUS3.0]

[Sharon D. <di...@SN...>]

Hi Arnaud,

Welcome back.

I believe Jonathan S. is re-writing the plugin that loads GO, and that 
he is using some sort of generic underlying parser to do this.  If I 
understand correctly,  the parsing code may be generic enough and would 
likely just require writing some small amount of code to do the correct 
mapping.  

Jonathan - is this correct?  

Thanks,
Sharon

Arnaud Kerhornou wrote:

> Hi Sharon
>
> I was away last week but Matt has replied to you regarding the comment 
> field.
> Also re. the population of the GO terms into GUS, will the plugin be 
> generic enough to be used for others ontologies such as Sequence 
> Ontology or the Parasite Life Cycle Ontology which we are planning to 
> use ?
>
> cheers
> Arnaud
>
> Sharon Diskin wrote:
>
>> Okay, thanks.   Does this mean that a single comment field added to 
>> the GOTerm table is sufficient in your view?  
>>
>> Alternatively, we could use the DoTS.Comments table to store 
>> comments, these can then be associated through the Evidence table to 
>> any row in GUS.  So, another option would be to use the Comments 
>> table to store the text, and link it to the GOTerm entry through the 
>> Evidence table.  If this is not an appropriate use of the Evidence 
>> table, then we could just create a GOTermComments linking table.  
>>
>> cheers,
>> sharon
>>
>> Arnaud Kerhornou wrote:
>>
>>> Hi Sharon
>>>
>>> I forward you an example of a GO comment given by Matt.
>>>
>>> cheers
>>> Arnaud
>>>
>>> -------- Original Message --------
>>> Subject: Re: proposed modifications to GO Schema for GUS3.0
>>> Date: Tue, 16 Jul 2002 13:19:51 +0100
>>> From: Matt Berriman <mb...@sa...>
>>> To: Arnaud Kerhornou <ax...@sa...>
>>> References: 
>>> <Pin...@sn...> 
>>> <3D2...@sa...> <3D2...@pc...> 
>>> <3D2...@sa...> <3D2...@pc...> 
>>> <3D3...@sa...>
>>>
>>>
>>>
>>>Here's a complete entry from the GO database:
>>>
>>>term: C-terminal protein farnesylation
>>>
>>>goid: GO:0006503
>>>
>>>definition: The covalent or non-covalent attachment of a farnesyl moiety 
>>>to the carboxy terminus of a protein. OBSOLETE.
>>>
>>>definition_reference: GO:jl
>>>
>>>comment: This term was made obsolete because the process is not exclusive to the carboxy terminus 
>>>of a protein. Consider instead the biological process term 'protein amino acid farnesylation ; 
>>>GO:0018347'.
>>>
>>>cheers
>>>Matt
>>>
>>>
>>>Arnaud Kerhornou wrote:
>>>
>>>> Sharon Diskin wrote:
>>>>
>>>>>
>>>>>> Also re. the GOTerm table, would it be possible to add a comment 
>>>>>> field ?
>>>>>
>>>>>
>>>>>
>>>>> I do not have a problem with this.  Does anyone else have an opinion 
>>>>> on this?  What type of information would you put in the comment field?
>>>>
>>>>
>>>> Matt,
>>>>
>>>> Do you have an
>>> 
>>>exa
>>>mple of comment you want to store ?
>>>>
>>>> I should mention than the GO database design allows to store several 
>>>> comments (one to many relationship), one comment field might be enough 
>>>> though and would keep the design simple.
>>>>
>>>> cheers
>>>> Arnaud
>>>>
>>>>>
>>>>> Cheers,
>>>>> Sharon
>>>>>
>>>>> p.s.  I will be out of town until Monday July 22nd.
>>>>>
>>>>>>
>>>>>> cheers
>>>>>> Arnaud
>>>>>>
>>>>>> Sharon Diskin wrote:
>>>>>>
>>>>>>> Hi Arnaud,
>>>>>>>
>>>>>>> I've attached the new GO schema and documentation that Jonathan 
>>>>>>> Schug and I have come up. We believe that this new schema addresses 
>>>>>>> your concern about the association date and also provides a better 
>>>>>>> way of tracking multiple instances/sources of the same association 
>>>>>
>>>;>
>>>> (s
>>>ee description of GOAssociationInstance table).
>>>>>>>
>>>>>>>
>>>>>>> Regarding your other question concerning the 'DB:Ref' and 'from or 
>>>>>>> with', we see these being tracked using the generic Evidence 
>>>>>>> table.   The 'from or with' would be Evidence for the 
>>>>>>> GOAssocInstEvidCode entry as it is connected to a specific evidence 
>>>>>>> code that is assigned to the association.  The 'DB:Ref' (such as in 
>>>>>>> the PubMed example you mentioned) would be Evidence for the 
>>>>>>> GOAssociationInstance entry as it is _not_ connected to a specific 
>>>>>>> evidence code, but rather the association as a whole.  More details 
>>>>>>> can be found in the attached documentation.
>>>>>>>
>>>>>>>
>>>>>>> Any feedback is welcome.  Also, if any of this is unclear, just let 
>>>>&
>>>gt;>&g
>>>t; us know.
>>>
>>>>>>>
>>>>>>> Cheers,
>>>>>>> Sharon
>>>>>>>
>>>>>>>
>>>>>>
>>>>>
>>>>
>>>>
>>>>
>>>
>>>-- 
>>>
>>>  Dr Matthew Berriman 
>>>  Senior Computer Biologist - Pathogen Sequencing Unit - 
>>>  The Wellcome Trust Sanger Institute
>>>  Tel +44 (0)1223 494817 -  Fax +44 (0)1223 494919 
>>>  http://www.sanger.ac.uk
>>>
>

[Gusdev-gusdev] Re: [Fwd: Re: proposed modifications to GO Schema for GUS3.0]

[Arnaud K. <ax...@sa...>]

Hi Sharon

I was away last week but Matt has replied to you regarding the comment 
field.
Also re. the population of the GO terms into GUS, will the plugin be 
generic enough to be used for others ontologies such as Sequence 
Ontology or the Parasite Life Cycle Ontology which we are planning to use ?

cheers
Arnaud

Sharon Diskin wrote:

> Okay, thanks.   Does this mean that a single comment field added to 
> the GOTerm table is sufficient in your view?  
>
> Alternatively, we could use the DoTS.Comments table to store comments, 
> these can then be associated through the Evidence table to any row in 
> GUS.  So, another option would be to use the Comments table to store 
> the text, and link it to the GOTerm entry through the Evidence table. 
>  If this is not an appropriate use of the Evidence table, then we 
> could just create a GOTermComments linking table.  
>
> cheers,
> sharon
>
> Arnaud Kerhornou wrote:
>
>> Hi Sharon
>>
>> I forward you an example of a GO comment given by Matt.
>>
>> cheers
>> Arnaud
>>
>> -------- Original Message --------
>> Subject: Re: proposed modifications to GO Schema for GUS3.0
>> Date: Tue, 16 Jul 2002 13:19:51 +0100
>> From: Matt Berriman <mb...@sa...>
>> To: Arnaud Kerhornou <ax...@sa...>
>> References: 
>> <Pin...@sn...> 
>> <3D2...@sa...> <3D2...@pc...> 
>> <3D2...@sa...> <3D2...@pc...> 
>> <3D3...@sa...>
>>
>>
>>
>>Here's a complete entry from the GO database:
>>
>>term: C-terminal protein farnesylation
>>
>>goid: GO:0006503
>>
>>definition: The covalent or non-covalent attachment of a farnesyl moiety 
>>to the carboxy terminus of a protein. OBSOLETE.
>>
>>definition_reference: GO:jl
>>
>>comment: This term was made obsolete because the process is not exclusive to the carboxy terminus 
>>of a protein. Consider instead the biological process term 'protein amino acid farnesylation ; 
>>GO:0018347'.
>>
>>cheers
>>Matt
>>
>>
>>Arnaud Kerhornou wrote:
>>
>>> Sharon Diskin wrote:
>>>
>>>>
>>>>> Also re. the GOTerm table, would it be possible to add a comment 
>>>>> field ?
>>>>
>>>>
>>>>
>>>> I do not have a problem with this.  Does anyone else have an opinion 
>>>> on this?  What type of information would you put in the comment field?
>>>
>>>
>>> Matt,
>>>
>>> Do you have an 
>>exa
>>mple of comment you want to store ?
>>>
>>> I should mention than the GO database design allows to store several 
>>> comments (one to many relationship), one comment field might be enough 
>>> though and would keep the design simple.
>>>
>>> cheers
>>> Arnaud
>>>
>>>>
>>>> Cheers,
>>>> Sharon
>>>>
>>>> p.s.  I will be out of town until Monday July 22nd.
>>>>
>>>>>
>>>>> cheers
>>>>> Arnaud
>>>>>
>>>>> Sharon Diskin wrote:
>>>>>
>>>>>> Hi Arnaud,
>>>>>>
>>>>>> I've attached the new GO schema and documentation that Jonathan 
>>>>>> Schug and I have come up. We believe that this new schema addresses 
>>>>>> your concern about the association date and also provides a better 
>>>>>> way of tracking multiple instances/sources of the same association 
>>>>>
>>> (s
>>ee description of GOAssociationInstance table).
>>>>>>
>>>>>>
>>>>>> Regarding your other question concerning the 'DB:Ref' and 'from or 
>>>>>> with', we see these being tracked using the generic Evidence 
>>>>>> table.   The 'from or with' would be Evidence for the 
>>>>>> GOAssocInstEvidCode entry as it is connected to a specific evidence 
>>>>>> code that is assigned to the association.  The 'DB:Ref' (such as in 
>>>>>> the PubMed example you mentioned) would be Evidence for the 
>>>>>> GOAssociationInstance entry as it is _not_ connected to a specific 
>>>>>> evidence code, but rather the association as a whole.  More details 
>>>>>> can be found in the attached documentation.
>>>>>>
>>>>>>
>>>>>> Any feedback is welcome.  Also, if any of this is unclear, just let 
>>>>>&g
>>t; us know.
>>
>>>>>>
>>>>>> Cheers,
>>>>>> Sharon
>>>>>>
>>>>>>
>>>>>
>>>>
>>>
>>>
>>>
>>
>>-- 
>>
>>  Dr Matthew Berriman 
>>  Senior Computer Biologist - Pathogen Sequencing Unit - 
>>  The Wellcome Trust Sanger Institute
>>  Tel +44 (0)1223 494817 -  Fax +44 (0)1223 494919 
>>  http://www.sanger.ac.uk
>>

Re: [Gusdev-gusdev] BibliographicReference

[Arnaud K. <ax...@sa...>]

Hi Angel

some comments:

Could it be possible to add the following fields:
    * abstract,
    * pubmed_id,
    * medline_id,
    * is_curated,
    * the list of keywords, in a separate table, ReferenceKeyword.

Also, we would like to store each author in a separate entry instead of 
a unique column.

Besides, to facilitate the queries, it would be better to have a many to 
many relationships between BibliographicReference and the two tables, 
ReferenceKeyword and Author.

cheers
Arnaud

Angel Pizarro wrote:

>I want to add a table BibliographicReference to GUS30 SRes, in addition to
>the Reference table, or at least revamp the Reference table by adding the
>missing columns that are in BibRef (attached below).
>
>The reasoning is that the Reference table is a hold-over from parsing
>genbank records for this type of info. Thus the position column refers to
>the positional information from genbank features. Also we have the old
>'remark' column from Jian Wang's days of schema design. Here is the schema
>def for BibRef:
>
>CREATE TABLE SRes.BibliographicReference (
>	BIBLIOGRAPHIC_REFERENCE_ID NUMBER(10) NOT NULL,
>	TITLE VARCHAR2 ( 100 ) NOT NULL,
>	AUTHORS VARCHAR2 ( 100 ) NOT NULL,
>	PUBLICATION VARCHAR2 ( 100 ),
>	EDITOR VARCHAR2 ( 100 ),
>	YEAR NUMBER(5),
>	VOLUME VARCHAR2 ( 100 ),
>	ISSUE VARCHAR2 ( 100 ),
>	PAGES VARCHAR2 ( 100 ),
>	URI VARCHAR2 ( 100 ),
>	MODIFICATION_DATE DATE NOT NULL,
>	USER_READ NUMBER ( 1 ) NOT NULL,
>	USER_WRITE NUMBER ( 1 ) NOT NULL,
>	GROUP_READ NUMBER ( 1 ) NOT NULL,
>	GROUP_WRITE NUMBER ( 1 ) NOT NULL,
>	OTHER_READ NUMBER ( 1 ) NOT NULL,
>	OTHER_WRITE NUMBER ( 1 ) NOT NULL,
>	ROW_USER_ID NUMBER ( 12 ) NOT NULL,
>	ROW_GROUP_ID NUMBER ( 12 ) NOT NULL,
>	ROW_PROJECT_ID NUMBER ( 12 ) NOT NULL,
>	ROW_ALG_INVOCATION_ID NUMBER ( 12 ) NOT NULL,
>	CONSTRAINT PK_BIBLIOGRAPHICREFERNECE PRIMARY KEY
>(BIBLIOGRAPHIC_REFERENCE_ID)
>);
>
>
>
>

[Gusdev-gusdev] BibliographicReference

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

I want to add a table BibliographicReference to GUS30 SRes, in addition to
the Reference table, or at least revamp the Reference table by adding the
missing columns that are in BibRef (attached below).

The reasoning is that the Reference table is a hold-over from parsing
genbank records for this type of info. Thus the position column refers to
the positional information from genbank features. Also we have the old
'remark' column from Jian Wang's days of schema design. Here is the schema
def for BibRef:

CREATE TABLE SRes.BibliographicReference (
	BIBLIOGRAPHIC_REFERENCE_ID NUMBER(10) NOT NULL,
	TITLE VARCHAR2 ( 100 ) NOT NULL,
	AUTHORS VARCHAR2 ( 100 ) NOT NULL,
	PUBLICATION VARCHAR2 ( 100 ),
	EDITOR VARCHAR2 ( 100 ),
	YEAR NUMBER(5),
	VOLUME VARCHAR2 ( 100 ),
	ISSUE VARCHAR2 ( 100 ),
	PAGES VARCHAR2 ( 100 ),
	URI VARCHAR2 ( 100 ),
	MODIFICATION_DATE DATE NOT NULL,
	USER_READ NUMBER ( 1 ) NOT NULL,
	USER_WRITE NUMBER ( 1 ) NOT NULL,
	GROUP_READ NUMBER ( 1 ) NOT NULL,
	GROUP_WRITE NUMBER ( 1 ) NOT NULL,
	OTHER_READ NUMBER ( 1 ) NOT NULL,
	OTHER_WRITE NUMBER ( 1 ) NOT NULL,
	ROW_USER_ID NUMBER ( 12 ) NOT NULL,
	ROW_GROUP_ID NUMBER ( 12 ) NOT NULL,
	ROW_PROJECT_ID NUMBER ( 12 ) NOT NULL,
	ROW_ALG_INVOCATION_ID NUMBER ( 12 ) NOT NULL,
	CONSTRAINT PK_BIBLIOGRAPHICREFERNECE PRIMARY KEY
(BIBLIOGRAPHIC_REFERENCE_ID)
);

[Gusdev-gusdev] GUSdev schema

[Jonathan C. <cra...@sn...>]

I've started to work on improving the scripts for dumping and loading the
GUSdev and GUS 3.0 schemas.  Since I'll be out of the office until around
mid-day Monday I've placed a snapshot of what I've done so far on the CBIL
download site:

http://www.cbil.upenn.edu/downloads/GUS/schema/

The relevant file is 'gusdev-sql-jul-25-2002.tar.gz' and it contains
up-to-date load scripts for the sequences, tables, views, constraints, and
indexes in GUSdev.  The major improvement is that the scripts now all
prompt for the 'schema', i.e. the name of the user under whom the objects
are to be created, and also the names of the tablespaces where the tables
and indexes should be placed.  As noted in the README file, I have tested
the scripts to create the sequences, tables, and views, but not those for
the constraints and indexes.  When I get back on Monday I'll work on
adding the following:

 -script to create the owning schema (not as important for gusdev since
  there is only one)
 -scripts/utility to automate the process of populating the essential
  system tables (i.e. TableInfo, UserInfo, Algorithm, etc.)
 -scripts to automate granting permissions on the various objects to users
  other than the owning schema

I'm also trying to make sure that all the changes I make will carry over
to GUS 3.0, and in general I want to make sure that people implementing
the database can choose whatever names they want for the schemas involved.

Jonathan

[Gusdev-gusdev] cvsweb

[pjm <pj...@sa...>]

here is what James (the sys admin) says about webcvs.