From darin.london at duke.edu  Tue Mar  6 11:03:59 2007
From: darin.london at duke.edu (Darin London)
Date: Tue, 06 Mar 2007 11:03:59 -0500
Subject: [BioSQL-l] Announcing BOSC 2007
Message-ID: <45ED90EF.7030000@duke.edu>

The BOSC Organizing Committee are proud to announce BOSC 2007, occurring
in Vienna, Austria on July 19th, 20th.  The conference this year
promises to be exciting, as the BOSC developers attempt to define and
solve currently intractable problems in Bioinformatics. Please refer to
the following website for complete information, and requests for
submissions.   Thank you, and we hope to see you in Vienna.

http://open-bio.org/wiki/BOSC_2007


The BOSC organizing Committee


Please pass this email on to anyone that would be interested.

From samborsky_d at yahoo.com  Thu Mar  8 17:19:20 2007
From: samborsky_d at yahoo.com (Dmitry Samborskiy)
Date: Fri, 9 Mar 2007 01:19:20 +0300 (MSK)
Subject: [BioSQL-l] BioSQL seqfeature_qualifier_value optimization
Message-ID: <992313.41554.qm@web30609.mail.mud.yahoo.com>

Hello Everybody,

I use BioPerl-DB and BioSQL project.
I suggest to make one extra index to optimize the search by FT tag values.

On MySQL it could be done with

CREATE INDEX value_ind ON seqfeature_qualifier_value (term_id, value(64));

Best regards,
  Dmitry Samborskiy



	

	
		
________________________________________________________
?? ??? ? Yahoo!? 
????????? ??????????? ? ??????????. Yahoo! ?????! http://ru.mail.yahoo.com

From hlapp at gmx.net  Sat Mar 10 12:54:17 2007
From: hlapp at gmx.net (Hilmar Lapp)
Date: Sat, 10 Mar 2007 12:54:17 -0500
Subject: [BioSQL-l] BioSQL seqfeature_qualifier_value optimization
In-Reply-To: <992313.41554.qm@web30609.mail.mud.yahoo.com>
References: <992313.41554.qm@web30609.mail.mud.yahoo.com>
Message-ID: <CDB26186-5927-4368-B116-3F6F2E30A4F3@gmx.net>

Is this a new MySQL 5.0 feature? Does it mean take the first 64 chars  
and discard the rest for indexing?

Sorry, I'm no longer up-to-date w/ MySQL's feature list since 4.1.x.

	-hilmar

On Mar 8, 2007, at 5:19 PM, Dmitry Samborskiy wrote:

> Hello Everybody,
>
> I use BioPerl-DB and BioSQL project.
> I suggest to make one extra index to optimize the search by FT tag  
> values.
>
> On MySQL it could be done with
>
> CREATE INDEX value_ind ON seqfeature_qualifier_value (term_id, value 
> (64));
>
> Best regards,
>   Dmitry Samborskiy
>
>
>
> 	
>
> 	
> 		
> ________________________________________________________
> ?? ??? ? Yahoo!?
> ????????? ??????????? ? ??????????.  
> Yahoo! ?????! http://ru.mail.yahoo.com
> _______________________________________________
> BioSQL-l mailing list
> BioSQL-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biosql-l

-- 
===========================================================
: Hilmar Lapp  -:-  Durham, NC  -:-  hlapp at gmx dot net :
===========================================================







From hlapp at gmx.net  Sat Mar 10 13:28:47 2007
From: hlapp at gmx.net (Hilmar Lapp)
Date: Sat, 10 Mar 2007 13:28:47 -0500
Subject: [BioSQL-l] BioSQL seqfeature_qualifier_value optimization
In-Reply-To: <248017.48917.qm@web30613.mail.mud.yahoo.com>
References: <248017.48917.qm@web30613.mail.mud.yahoo.com>
Message-ID: <5F3DC5C7-B6A5-409F-B098-39CAB63B2DA4@gmx.net>


On Mar 10, 2007, at 1:15 PM, Dmitry Samborskiy wrote:

> Hilmar Lapp <hlapp at gmx.net> wrote:
>
>> Is this a new MySQL 5.0 feature?
>
> No, it seems that it was even before v.4.1, see:
>
> http://dev.mysql.com/doc/refman/4.1/en/create-index.html
>
> And it works with all base DB types: MyISAM, InnoDB, or BDB.

Interesting. I missed that. That's what happens if you don't use  
MySQL :-)

>
>> Does it mean take the first 64 chars
>> and discard the rest for indexing?
>
> Exactly. Below is the citation from the page mentioned above:
>
>> For CHAR, VARCHAR, BINARY, and VARBINARY  columns, indexes can be  
>> created
> that > use only the leading part of column values, using col_name 
> (length)
> syntax to > specify an index prefix length. BLOB and TEXT columns  
> also can be
> indexed, but > a prefix length *must* be given.
>
> I used 64 because it's quite enough in almost all cases (since  
> index is just a
> optimization tool for making search faster).
>
>> Sorry, I'm no longer up-to-date w/ MySQL's feature list since 4.1.x.
>
> Me too. I use mysql-4.1.16-1.FC4.1 (Fedora Core 4).
>
> I don't know how to figure the same index in Oracle/PosgreSQL.
> But I hope it's possible...

You cannot index LOB columns in Oracle. You can index an initial  
substring of a text field in both Oracle and PostgreSQL because you  
can have function indexes. They will only be used though if the query  
uses the exact same function.

	-hilmar

>
> Thanks for your attention.
>
> Best wishes,
>   Dmitry Samborskiy
>
>
>
> --- Hilmar Lapp <hlapp at gmx.net> wrote:
>
>> Is this a new MySQL 5.0 feature? Does it mean take the first 64 chars
>> and discard the rest for indexing?
>>
>> Sorry, I'm no longer up-to-date w/ MySQL's feature list since 4.1.x.
>>
>> 	-hilmar
>>
>> On Mar 8, 2007, at 5:19 PM, Dmitry Samborskiy wrote:
>>
>>> Hello Everybody,
>>>
>>> I use BioPerl-DB and BioSQL project.
>>> I suggest to make one extra index to optimize the search by FT tag
>>> values.
>>>
>>> On MySQL it could be done with
>>>
>>> CREATE INDEX value_ind ON seqfeature_qualifier_value (term_id, value
>>> (64));
>>>
>>> Best regards,
>>>   Dmitry Samborskiy
>>>
>>>
>>>
>>> 	
>>>
>>> 	
>>> 		
>>> ________________________________________________________
>>> ?? ??? ? Yahoo!?
>>> ????????? ??????????? ? ??????????.
>>> Yahoo! ?????! http://ru.mail.yahoo.com
>>> _______________________________________________
>>> BioSQL-l mailing list
>>> BioSQL-l at lists.open-bio.org
>>> http://lists.open-bio.org/mailman/listinfo/biosql-l
>>
>> -- 
>> ===========================================================
>> : Hilmar Lapp  -:-  Durham, NC  -:-  hlapp at gmx dot net :
>> ===========================================================
>>
>>
>>
>>
>>
>>
>
>
>
> 	
>
> 	
> 		
> ________________________________________________________
> ?? ??? ? Yahoo!?
> ????????? ??????????? ? ??????????.  
> Yahoo! ?????! http://ru.mail.yahoo.com

-- 
===========================================================
: Hilmar Lapp  -:-  Durham, NC  -:-  hlapp at gmx dot net :
===========================================================







From cjfields at uiuc.edu  Fri Mar 16 15:44:54 2007
From: cjfields at uiuc.edu (Chris Fields)
Date: Fri, 16 Mar 2007 14:44:54 -0500
Subject: [BioSQL-l] Bio::Annotation::StructuredValue
Message-ID: <8C776F12-19CF-4511-91F2-ED9640FB995C@uiuc.edu>

Does bioperl-db store Bio::Annotation::StructuredValue (i.e. in  
SwissProt)?  I am thinking of using StructuredValue, Data::Stag, or  
Class::Meta for some of my RNA structural data work but didn't know  
if StructuredValues would persist via bioperl-db.

I also noticed there is an outstanding BioPerl bug (http:// 
bugzilla.open-bio.org/show_bug.cgi?id=1825) where Hilmar suggested  
reimplementing StructuredValueto use Data::Stag, so I thought I might  
give it a try.

chris

From hlapp at gmx.net  Sat Mar 17 10:26:04 2007
From: hlapp at gmx.net (Hilmar Lapp)
Date: Sat, 17 Mar 2007 10:26:04 -0400
Subject: [BioSQL-l] Bio::Annotation::StructuredValue
In-Reply-To: <8C776F12-19CF-4511-91F2-ED9640FB995C@uiuc.edu>
References: <8C776F12-19CF-4511-91F2-ED9640FB995C@uiuc.edu>
Message-ID: <1F43323F-22D8-4A1D-A62E-46E60A59D97C@gmx.net>


On Mar 16, 2007, at 3:44 PM, Chris Fields wrote:

> Does bioperl-db store Bio::Annotation::StructuredValue (i.e. in
> SwissProt)?

It does b/c B::A::StructuredValue ISA B::A::SimpleValue and it  
handles the latter.

This isn't ideal because if you're like me you'd want all the  
individual values to each translate to its own row. I was using a  
SeqProcessor to convert the StructuredValue objects into arrays of  
SimpleValue objects.

Obviously, this will lose the structure between them (i.e., in  
reality it's not just a flat array), but for enabling indexed  
searches it works well.

With Uniprot no longer collapsing per sequence, the thing that gets  
lost is the semantic context of each token, but as you found out  
correctly it gets lost at the bioperl level already.

>   I am thinking of using StructuredValue, Data::Stag, or
> Class::Meta for some of my RNA structural data work but didn't know
> if StructuredValues would persist via bioperl-db.

At this point they are either flattened out (through the overridden  
value() method), or you convert them upfront into an array, using a  
SeqProcessor.

BioSQL has no provision for storing the fact that a number of tag/ 
value associations (which is what B::A::SimpleValues are) comprise of  
a "bag" of annotation that belongs together.

You could, however, persist that through embedding the tags in an  
ontology (tags are ontology terms) that captures that (through  
rel.ships).


>
> I also noticed there is an outstanding BioPerl bug (http://
> bugzilla.open-bio.org/show_bug.cgi?id=1825) where Hilmar suggested
> reimplementing StructuredValueto use Data::Stag, so I thought I might
> give it a try.

Sounds good :-)

I hope the above makes some sense. Let me know if not.

	-hilmar

>
> chris
> _______________________________________________
> BioSQL-l mailing list
> BioSQL-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biosql-l

-- 
===========================================================
: Hilmar Lapp  -:-  Durham, NC  -:-  hlapp at gmx dot net :
===========================================================






From cjfields at uiuc.edu  Thu Mar 22 18:29:15 2007
From: cjfields at uiuc.edu (Chris Fields)
Date: Thu, 22 Mar 2007 17:29:15 -0500
Subject: [BioSQL-l] [Bioperl-l]  Bio::Annotation::StructuredValue
In-Reply-To: <1F43323F-22D8-4A1D-A62E-46E60A59D97C@gmx.net>
References: <8C776F12-19CF-4511-91F2-ED9640FB995C@uiuc.edu>
	<1F43323F-22D8-4A1D-A62E-46E60A59D97C@gmx.net>
Message-ID: <70781A22-76D3-4B71-8364-1FAED30179CE@uiuc.edu>

On Mar 17, 2007, at 9:26 AM, Hilmar Lapp wrote:

> On Mar 16, 2007, at 3:44 PM, Chris Fields wrote:
>
>> Does bioperl-db store Bio::Annotation::StructuredValue (i.e. in
>> SwissProt)?
>
> It does b/c B::A::StructuredValue ISA B::A::SimpleValue and it
> handles the latter.
>
> This isn't ideal because if you're like me you'd want all the
> individual values to each translate to its own row. I was using a
> SeqProcessor to convert the StructuredValue objects into arrays of
> SimpleValue objects.
>
> Obviously, this will lose the structure between them (i.e., in
> reality it's not just a flat array), but for enabling indexed
> searches it works well.
>
> With Uniprot no longer collapsing per sequence, the thing that gets
> lost is the semantic context of each token, but as you found out
> correctly it gets lost at the bioperl level already.

Yes, unfortunately, though the use of an ontology would help as you  
suggest below.

>>   I am thinking of using StructuredValue, Data::Stag, or
>> Class::Meta for some of my RNA structural data work but didn't know
>> if StructuredValues would persist via bioperl-db.
>
> At this point they are either flattened out (through the overridden
> value() method), or you convert them upfront into an array, using a
> SeqProcessor.
>
> BioSQL has no provision for storing the fact that a number of tag/
> value associations (which is what B::A::SimpleValues are) comprise of
> a "bag" of annotation that belongs together.
>
> You could, however, persist that through embedding the tags in an
> ontology (tags are ontology terms) that captures that (through
> rel.ships).

I will likely use this approach, though there are no applicable SO/GO  
terms that I can use so I'll have to roll my own for now.  I may use  
something similar to the RNAML tags for sec. structure.

>> I also noticed there is an outstanding BioPerl bug (http://
>> bugzilla.open-bio.org/show_bug.cgi?id=1825) where Hilmar suggested
>> reimplementing StructuredValueto use Data::Stag, so I thought I might
>> give it a try.
>
> Sounds good :-)
>
> I hope the above makes some sense. Let me know if not.
>
> 	-hilmar

Makes perfect sense!  Just needed to run it by someone on the BioSQL  
end since I'll want to make my data a bit more persistent.  I think I  
will go with Bio::StructuredValue implementing Data::Stag since it  
has pretty much everything I need.

chris


From cjfields at uiuc.edu  Tue Mar 27 17:17:51 2007
From: cjfields at uiuc.edu (Chris Fields)
Date: Tue, 27 Mar 2007 16:17:51 -0500
Subject: [BioSQL-l] Question about BioPerl Bugzilla Bug 2213
In-Reply-To: <7600DB635DB2234CBBED9CDD990C4DB0023A28@exchmail.CMH.Internal>
References: <7600DB635DB2234CBBED9CDD990C4DB0023A28@exchmail.CMH.Internal>
Message-ID: <4E406CFC-A7B8-4F15-AE90-192791AA507F@uiuc.edu>

First, you should direct this to the mail list in case anyone else  
can add to this.  I may not be able to get to this anytime real soon.

 From the bug report:

"The postprocessing in SpeciesAdaptor does mess things up in some  
cases.  The
issue is directly related to recent changes in Bio::Species and and  
could be
taken care of by simply not running any postprocessing and foregoing the
lineage checking altogether in Bio::Species::classification(), where the
exception occurs.

However, I believe doing so may break functionality with older
bioperl-db/BioSQL installations since data is stored based on the older
Bio::Species system (single-name genus and species).  Maybe Hilmar  
can comment?"

As noted in the bug report this is still considered a developer  
series; even though most of the core modules work well together there  
are still some interoperability issues present (as this bug  
demonstrates).

Maybe having a BioSQL TaxonAdaptor module would be a workaround;  
Bio::Species is-now-a Bio::Taxon (whereas pre-1.5.2 versions aren't),  
so if we had a module that stored data in the newer context it might  
work around this.  Hilmar?

chris

On Mar 27, 2007, at 3:42 PM, Carrel, Michael, G wrote:

> Chris,
>
>
>
> I am trying to apply this patch to my BioPerl-DB 1.5.2 code and  
> don't understand what the changes are in the Bio/DB/BioSQL/ 
> SpeciesAdaptor.pm code. What does the "+=pod" text mean? Same for  
> "+=cut"? Are we commenting out lines 256 through 280?
>
>
>
> The text says that "massaging" code was commented out, but I don't  
> understand exactly what lines are commented out. Please explain in  
> more detail what the changes are in the SpeciesAdaptor.pm file.
>
>
>
> I believe I understand the changes in the Bio/DB/BioSQL/mysql/ 
> SpeciesAdaptorDriver.pm code file...commenting out the one line
>
> (  #$clf[0]->[0] = $obj->binomial();  ).
>
>
>
> Thank you,
>
>
>
> Mike Carrel
>
> Network Analyst
>
> 816-234-1571
>
> mgcarrel at cmh.edu
>
> <image001.png>
>
>
>
> <image001.png>
> <Carrel, Michael, G.vcf>

Christopher Fields
Postdoctoral Researcher
Lab of Dr. Robert Switzer
Dept of Biochemistry
University of Illinois Urbana-Champaign




From darin.london at duke.edu  Tue Mar  6 16:03:59 2007
From: darin.london at duke.edu (Darin London)
Date: Tue, 06 Mar 2007 11:03:59 -0500
Subject: [BioSQL-l] Announcing BOSC 2007
Message-ID: <45ED90EF.7030000@duke.edu>

The BOSC Organizing Committee are proud to announce BOSC 2007, occurring
in Vienna, Austria on July 19th, 20th.  The conference this year
promises to be exciting, as the BOSC developers attempt to define and
solve currently intractable problems in Bioinformatics. Please refer to
the following website for complete information, and requests for
submissions.   Thank you, and we hope to see you in Vienna.

http://open-bio.org/wiki/BOSC_2007


The BOSC organizing Committee


Please pass this email on to anyone that would be interested.


From samborsky_d at yahoo.com  Thu Mar  8 22:19:20 2007
From: samborsky_d at yahoo.com (Dmitry Samborskiy)
Date: Fri, 9 Mar 2007 01:19:20 +0300 (MSK)
Subject: [BioSQL-l] BioSQL seqfeature_qualifier_value optimization
Message-ID: <992313.41554.qm@web30609.mail.mud.yahoo.com>

Hello Everybody,

I use BioPerl-DB and BioSQL project.
I suggest to make one extra index to optimize the search by FT tag values.

On MySQL it could be done with

CREATE INDEX value_ind ON seqfeature_qualifier_value (term_id, value(64));

Best regards,
  Dmitry Samborskiy



	

	
		
________________________________________________________
?? ??? ? Yahoo!? 
????????? ??????????? ? ??????????. Yahoo! ?????! http://ru.mail.yahoo.com


From hlapp at gmx.net  Sat Mar 10 17:54:17 2007
From: hlapp at gmx.net (Hilmar Lapp)
Date: Sat, 10 Mar 2007 12:54:17 -0500
Subject: [BioSQL-l] BioSQL seqfeature_qualifier_value optimization
In-Reply-To: <992313.41554.qm@web30609.mail.mud.yahoo.com>
References: <992313.41554.qm@web30609.mail.mud.yahoo.com>
Message-ID: <CDB26186-5927-4368-B116-3F6F2E30A4F3@gmx.net>

Is this a new MySQL 5.0 feature? Does it mean take the first 64 chars  
and discard the rest for indexing?

Sorry, I'm no longer up-to-date w/ MySQL's feature list since 4.1.x.

	-hilmar

On Mar 8, 2007, at 5:19 PM, Dmitry Samborskiy wrote:

> Hello Everybody,
>
> I use BioPerl-DB and BioSQL project.
> I suggest to make one extra index to optimize the search by FT tag  
> values.
>
> On MySQL it could be done with
>
> CREATE INDEX value_ind ON seqfeature_qualifier_value (term_id, value 
> (64));
>
> Best regards,
>   Dmitry Samborskiy
>
>
>
> 	
>
> 	
> 		
> ________________________________________________________
> ?? ??? ? Yahoo!?
> ????????? ??????????? ? ??????????.  
> Yahoo! ?????! http://ru.mail.yahoo.com
> _______________________________________________
> BioSQL-l mailing list
> BioSQL-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biosql-l

-- 
===========================================================
: Hilmar Lapp  -:-  Durham, NC  -:-  hlapp at gmx dot net :
===========================================================








From hlapp at gmx.net  Sat Mar 10 18:28:47 2007
From: hlapp at gmx.net (Hilmar Lapp)
Date: Sat, 10 Mar 2007 13:28:47 -0500
Subject: [BioSQL-l] BioSQL seqfeature_qualifier_value optimization
In-Reply-To: <248017.48917.qm@web30613.mail.mud.yahoo.com>
References: <248017.48917.qm@web30613.mail.mud.yahoo.com>
Message-ID: <5F3DC5C7-B6A5-409F-B098-39CAB63B2DA4@gmx.net>


On Mar 10, 2007, at 1:15 PM, Dmitry Samborskiy wrote:

> Hilmar Lapp <hlapp at gmx.net> wrote:
>
>> Is this a new MySQL 5.0 feature?
>
> No, it seems that it was even before v.4.1, see:
>
> http://dev.mysql.com/doc/refman/4.1/en/create-index.html
>
> And it works with all base DB types: MyISAM, InnoDB, or BDB.

Interesting. I missed that. That's what happens if you don't use  
MySQL :-)

>
>> Does it mean take the first 64 chars
>> and discard the rest for indexing?
>
> Exactly. Below is the citation from the page mentioned above:
>
>> For CHAR, VARCHAR, BINARY, and VARBINARY  columns, indexes can be  
>> created
> that > use only the leading part of column values, using col_name 
> (length)
> syntax to > specify an index prefix length. BLOB and TEXT columns  
> also can be
> indexed, but > a prefix length *must* be given.
>
> I used 64 because it's quite enough in almost all cases (since  
> index is just a
> optimization tool for making search faster).
>
>> Sorry, I'm no longer up-to-date w/ MySQL's feature list since 4.1.x.
>
> Me too. I use mysql-4.1.16-1.FC4.1 (Fedora Core 4).
>
> I don't know how to figure the same index in Oracle/PosgreSQL.
> But I hope it's possible...

You cannot index LOB columns in Oracle. You can index an initial  
substring of a text field in both Oracle and PostgreSQL because you  
can have function indexes. They will only be used though if the query  
uses the exact same function.

	-hilmar

>
> Thanks for your attention.
>
> Best wishes,
>   Dmitry Samborskiy
>
>
>
> --- Hilmar Lapp <hlapp at gmx.net> wrote:
>
>> Is this a new MySQL 5.0 feature? Does it mean take the first 64 chars
>> and discard the rest for indexing?
>>
>> Sorry, I'm no longer up-to-date w/ MySQL's feature list since 4.1.x.
>>
>> 	-hilmar
>>
>> On Mar 8, 2007, at 5:19 PM, Dmitry Samborskiy wrote:
>>
>>> Hello Everybody,
>>>
>>> I use BioPerl-DB and BioSQL project.
>>> I suggest to make one extra index to optimize the search by FT tag
>>> values.
>>>
>>> On MySQL it could be done with
>>>
>>> CREATE INDEX value_ind ON seqfeature_qualifier_value (term_id, value
>>> (64));
>>>
>>> Best regards,
>>>   Dmitry Samborskiy
>>>
>>>
>>>
>>> 	
>>>
>>> 	
>>> 		
>>> ________________________________________________________
>>> ?? ??? ? Yahoo!?
>>> ????????? ??????????? ? ??????????.
>>> Yahoo! ?????! http://ru.mail.yahoo.com
>>> _______________________________________________
>>> BioSQL-l mailing list
>>> BioSQL-l at lists.open-bio.org
>>> http://lists.open-bio.org/mailman/listinfo/biosql-l
>>
>> -- 
>> ===========================================================
>> : Hilmar Lapp  -:-  Durham, NC  -:-  hlapp at gmx dot net :
>> ===========================================================
>>
>>
>>
>>
>>
>>
>
>
>
> 	
>
> 	
> 		
> ________________________________________________________
> ?? ??? ? Yahoo!?
> ????????? ??????????? ? ??????????.  
> Yahoo! ?????! http://ru.mail.yahoo.com

-- 
===========================================================
: Hilmar Lapp  -:-  Durham, NC  -:-  hlapp at gmx dot net :
===========================================================








From cjfields at uiuc.edu  Fri Mar 16 19:44:54 2007
From: cjfields at uiuc.edu (Chris Fields)
Date: Fri, 16 Mar 2007 14:44:54 -0500
Subject: [BioSQL-l] Bio::Annotation::StructuredValue
Message-ID: <8C776F12-19CF-4511-91F2-ED9640FB995C@uiuc.edu>

Does bioperl-db store Bio::Annotation::StructuredValue (i.e. in  
SwissProt)?  I am thinking of using StructuredValue, Data::Stag, or  
Class::Meta for some of my RNA structural data work but didn't know  
if StructuredValues would persist via bioperl-db.

I also noticed there is an outstanding BioPerl bug (http:// 
bugzilla.open-bio.org/show_bug.cgi?id=1825) where Hilmar suggested  
reimplementing StructuredValueto use Data::Stag, so I thought I might  
give it a try.

chris


From hlapp at gmx.net  Sat Mar 17 14:26:04 2007
From: hlapp at gmx.net (Hilmar Lapp)
Date: Sat, 17 Mar 2007 10:26:04 -0400
Subject: [BioSQL-l] Bio::Annotation::StructuredValue
In-Reply-To: <8C776F12-19CF-4511-91F2-ED9640FB995C@uiuc.edu>
References: <8C776F12-19CF-4511-91F2-ED9640FB995C@uiuc.edu>
Message-ID: <1F43323F-22D8-4A1D-A62E-46E60A59D97C@gmx.net>


On Mar 16, 2007, at 3:44 PM, Chris Fields wrote:

> Does bioperl-db store Bio::Annotation::StructuredValue (i.e. in
> SwissProt)?

It does b/c B::A::StructuredValue ISA B::A::SimpleValue and it  
handles the latter.

This isn't ideal because if you're like me you'd want all the  
individual values to each translate to its own row. I was using a  
SeqProcessor to convert the StructuredValue objects into arrays of  
SimpleValue objects.

Obviously, this will lose the structure between them (i.e., in  
reality it's not just a flat array), but for enabling indexed  
searches it works well.

With Uniprot no longer collapsing per sequence, the thing that gets  
lost is the semantic context of each token, but as you found out  
correctly it gets lost at the bioperl level already.

>   I am thinking of using StructuredValue, Data::Stag, or
> Class::Meta for some of my RNA structural data work but didn't know
> if StructuredValues would persist via bioperl-db.

At this point they are either flattened out (through the overridden  
value() method), or you convert them upfront into an array, using a  
SeqProcessor.

BioSQL has no provision for storing the fact that a number of tag/ 
value associations (which is what B::A::SimpleValues are) comprise of  
a "bag" of annotation that belongs together.

You could, however, persist that through embedding the tags in an  
ontology (tags are ontology terms) that captures that (through  
rel.ships).


>
> I also noticed there is an outstanding BioPerl bug (http://
> bugzilla.open-bio.org/show_bug.cgi?id=1825) where Hilmar suggested
> reimplementing StructuredValueto use Data::Stag, so I thought I might
> give it a try.

Sounds good :-)

I hope the above makes some sense. Let me know if not.

	-hilmar

>
> chris
> _______________________________________________
> BioSQL-l mailing list
> BioSQL-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biosql-l

-- 
===========================================================
: Hilmar Lapp  -:-  Durham, NC  -:-  hlapp at gmx dot net :
===========================================================







From cjfields at uiuc.edu  Thu Mar 22 22:29:15 2007
From: cjfields at uiuc.edu (Chris Fields)
Date: Thu, 22 Mar 2007 17:29:15 -0500
Subject: [BioSQL-l] [Bioperl-l]  Bio::Annotation::StructuredValue
In-Reply-To: <1F43323F-22D8-4A1D-A62E-46E60A59D97C@gmx.net>
References: <8C776F12-19CF-4511-91F2-ED9640FB995C@uiuc.edu>
	<1F43323F-22D8-4A1D-A62E-46E60A59D97C@gmx.net>
Message-ID: <70781A22-76D3-4B71-8364-1FAED30179CE@uiuc.edu>

On Mar 17, 2007, at 9:26 AM, Hilmar Lapp wrote:

> On Mar 16, 2007, at 3:44 PM, Chris Fields wrote:
>
>> Does bioperl-db store Bio::Annotation::StructuredValue (i.e. in
>> SwissProt)?
>
> It does b/c B::A::StructuredValue ISA B::A::SimpleValue and it
> handles the latter.
>
> This isn't ideal because if you're like me you'd want all the
> individual values to each translate to its own row. I was using a
> SeqProcessor to convert the StructuredValue objects into arrays of
> SimpleValue objects.
>
> Obviously, this will lose the structure between them (i.e., in
> reality it's not just a flat array), but for enabling indexed
> searches it works well.
>
> With Uniprot no longer collapsing per sequence, the thing that gets
> lost is the semantic context of each token, but as you found out
> correctly it gets lost at the bioperl level already.

Yes, unfortunately, though the use of an ontology would help as you  
suggest below.

>>   I am thinking of using StructuredValue, Data::Stag, or
>> Class::Meta for some of my RNA structural data work but didn't know
>> if StructuredValues would persist via bioperl-db.
>
> At this point they are either flattened out (through the overridden
> value() method), or you convert them upfront into an array, using a
> SeqProcessor.
>
> BioSQL has no provision for storing the fact that a number of tag/
> value associations (which is what B::A::SimpleValues are) comprise of
> a "bag" of annotation that belongs together.
>
> You could, however, persist that through embedding the tags in an
> ontology (tags are ontology terms) that captures that (through
> rel.ships).

I will likely use this approach, though there are no applicable SO/GO  
terms that I can use so I'll have to roll my own for now.  I may use  
something similar to the RNAML tags for sec. structure.

>> I also noticed there is an outstanding BioPerl bug (http://
>> bugzilla.open-bio.org/show_bug.cgi?id=1825) where Hilmar suggested
>> reimplementing StructuredValueto use Data::Stag, so I thought I might
>> give it a try.
>
> Sounds good :-)
>
> I hope the above makes some sense. Let me know if not.
>
> 	-hilmar

Makes perfect sense!  Just needed to run it by someone on the BioSQL  
end since I'll want to make my data a bit more persistent.  I think I  
will go with Bio::StructuredValue implementing Data::Stag since it  
has pretty much everything I need.

chris



From cjfields at uiuc.edu  Tue Mar 27 21:17:51 2007
From: cjfields at uiuc.edu (Chris Fields)
Date: Tue, 27 Mar 2007 16:17:51 -0500
Subject: [BioSQL-l] Question about BioPerl Bugzilla Bug 2213
In-Reply-To: <7600DB635DB2234CBBED9CDD990C4DB0023A28@exchmail.CMH.Internal>
References: <7600DB635DB2234CBBED9CDD990C4DB0023A28@exchmail.CMH.Internal>
Message-ID: <4E406CFC-A7B8-4F15-AE90-192791AA507F@uiuc.edu>

First, you should direct this to the mail list in case anyone else  
can add to this.  I may not be able to get to this anytime real soon.

 From the bug report:

"The postprocessing in SpeciesAdaptor does mess things up in some  
cases.  The
issue is directly related to recent changes in Bio::Species and and  
could be
taken care of by simply not running any postprocessing and foregoing the
lineage checking altogether in Bio::Species::classification(), where the
exception occurs.

However, I believe doing so may break functionality with older
bioperl-db/BioSQL installations since data is stored based on the older
Bio::Species system (single-name genus and species).  Maybe Hilmar  
can comment?"

As noted in the bug report this is still considered a developer  
series; even though most of the core modules work well together there  
are still some interoperability issues present (as this bug  
demonstrates).

Maybe having a BioSQL TaxonAdaptor module would be a workaround;  
Bio::Species is-now-a Bio::Taxon (whereas pre-1.5.2 versions aren't),  
so if we had a module that stored data in the newer context it might  
work around this.  Hilmar?

chris

On Mar 27, 2007, at 3:42 PM, Carrel, Michael, G wrote:

> Chris,
>
>
>
> I am trying to apply this patch to my BioPerl-DB 1.5.2 code and  
> don't understand what the changes are in the Bio/DB/BioSQL/ 
> SpeciesAdaptor.pm code. What does the "+=pod" text mean? Same for  
> "+=cut"? Are we commenting out lines 256 through 280?
>
>
>
> The text says that "massaging" code was commented out, but I don't  
> understand exactly what lines are commented out. Please explain in  
> more detail what the changes are in the SpeciesAdaptor.pm file.
>
>
>
> I believe I understand the changes in the Bio/DB/BioSQL/mysql/ 
> SpeciesAdaptorDriver.pm code file...commenting out the one line
>
> (  #$clf[0]->[0] = $obj->binomial();  ).
>
>
>
> Thank you,
>
>
>
> Mike Carrel
>
> Network Analyst
>
> 816-234-1571
>
> mgcarrel at cmh.edu
>
> <image001.png>
>
>
>
> <image001.png>
> <Carrel, Michael, G.vcf>

Christopher Fields
Postdoctoral Researcher
Lab of Dr. Robert Switzer
Dept of Biochemistry
University of Illinois Urbana-Champaign