[InterMine Dev] dev Digest, Vol 46, Issue 8

Kalpana Karra kkarra at stanford.edu
Tue Mar 12 15:43:10 GMT 2013


JD,

In YeastMine, there is a 'SEQUENCE' tab where you can get the sequence both DNA and protein. 

http://yeastmine.yeastgenome.org/yeastmine/template.do?name=Gene_GenomicDNA&scope=global
http://yeastmine.yeastgenome.org/yeastmine/template.do?name=Gene_ProteinSequence&scope=global

-K



On Mar 12, 2013, at 5:00 AM, dev-request at intermine.org wrote:

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> Today's Topics:
> 
>   1. Storage of long sequences (JD Wong)
>   2. Re: Storage of long sequences (Alex Kalderimis)
>   3. Re: Storage of long sequences (JD Wong)
>   4. Re: Storage of long sequences (Julie Sullivan)
>   5. Re: Storage of long sequences (JD Wong)
>   6. About the ObjectStoreQueryDurationException (Chen Yian)
> 
> 
> ----------------------------------------------------------------------
> 
> Message: 1
> Date: Mon, 11 Mar 2013 14:41:57 -0400
> From: JD Wong <jdmswong at gmail.com>
> To: Intermine Developer List <dev at intermine.org>
> Subject: [InterMine Dev] Storage of long sequences
> Message-ID:
> 	<CAGuHHn98iG0U9oqJAKoCzEiq6x++mzHc5pQmBjzu6m0+PhTzgg at mail.gmail.com>
> Content-Type: text/plain; charset="iso-8859-1"
> 
> Hello developer list,
> 
> In my mine's production database, I'm looking for a query to display the
> sequence for a specific protein.  Does anybody know where in the database
> sequences are stored?
> 
> Thank you!
> -JD
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> ------------------------------
> 
> Message: 2
> Date: Mon, 11 Mar 2013 18:55:39 +0000
> From: Alex Kalderimis <alex at intermine.org>
> To: dev at intermine.org
> Subject: Re: [InterMine Dev] Storage of long sequences
> Message-ID: <2657107.JgL5QtnOdB at kokako>
> Content-Type: text/plain; charset="us-ascii"
> 
> On Monday 11 March 2013 14:41:57 JD Wong wrote:
>> Hello developer list,
>> 
>> In my mine's production database, I'm looking for a query to display the
>> sequence for a specific protein.  Does anybody know where in the database
>> sequences are stored?
>> 
>> Thank you!
>> -JD
> 
> For efficiency's sake, sequence is stored as a CLOB, and the sequence for a 
> specific item is read out by index (or at least it is for nucleic sequence - I 
> believe it is much the same for protein sequence).
> 
> As for writing db queries, while that is possible intermine is meant to be a 
> black-box of sorts and one isn't meant to rely on data being in certain 
> tables, and you certainly aren't expected to write your own sql. May I suggest 
> using the webservices for this? Of if you are in java-land, you can connect to 
> the db using the object store itself, and perform ObjectStore queries 
> natively.
> 
> Alex
> 
> 
> 
> ------------------------------
> 
> Message: 3
> Date: Mon, 11 Mar 2013 15:13:13 -0400
> From: JD Wong <jdmswong at gmail.com>
> To: Alex Kalderimis <alex at intermine.org>
> Cc: dev at intermine.org
> Subject: Re: [InterMine Dev] Storage of long sequences
> Message-ID:
> 	<CAGuHHn8Ka+WGxCjsfEeUgGHzkB7r3dprnuBeaWxJjkAgA00c=w at mail.gmail.com>
> Content-Type: text/plain; charset="iso-8859-1"
> 
> Hi Alex,
> 
> Sounds good, thanks for the fast reply!
> 
> -JD
> 
> On Mon, Mar 11, 2013 at 2:55 PM, Alex Kalderimis <alex at intermine.org> wrote:
> 
>> On Monday 11 March 2013 14:41:57 JD Wong wrote:
>>> Hello developer list,
>>> 
>>> In my mine's production database, I'm looking for a query to display the
>>> sequence for a specific protein.  Does anybody know where in the database
>>> sequences are stored?
>>> 
>>> Thank you!
>>> -JD
>> 
>> For efficiency's sake, sequence is stored as a CLOB, and the sequence for a
>> specific item is read out by index (or at least it is for nucleic sequence
>> - I
>> believe it is much the same for protein sequence).
>> 
>> As for writing db queries, while that is possible intermine is meant to be
>> a
>> black-box of sorts and one isn't meant to rely on data being in certain
>> tables, and you certainly aren't expected to write your own sql. May I
>> suggest
>> using the webservices for this? Of if you are in java-land, you can
>> connect to
>> the db using the object store itself, and perform ObjectStore queries
>> natively.
>> 
>> Alex
>> 
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> ------------------------------
> 
> Message: 4
> Date: Mon, 11 Mar 2013 19:18:23 +0000
> From: Julie Sullivan <julie at flymine.org>
> To: JD Wong <jdmswong at gmail.com>
> Cc: Intermine Developer List <dev at intermine.org>
> Subject: Re: [InterMine Dev] Storage of long sequences
> Message-ID: <513E2DFF.70700 at flymine.org>
> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
> 
> "sequence" is marked as a reserved word (mistakenly imo), so the table is called 
> "intermine_sequence".
> 
> On 11/03/13 18:41, JD Wong wrote:
>> Hello developer list,
>> 
>> In my mine's production database, I'm looking for a query to display the
>> sequence for a specific protein.  Does anybody know where in the database
>> sequences are stored?
>> 
>> Thank you!
>> -JD
>> 
>> 
>> 
>> 
>> _______________________________________________
>> dev mailing list
>> dev at intermine.org
>> http://mail.intermine.org/cgi-bin/mailman/listinfo/dev
> 
> 
> 
> ------------------------------
> 
> Message: 5
> Date: Mon, 11 Mar 2013 16:56:25 -0400
> From: JD Wong <jdmswong at gmail.com>
> To: Julie Sullivan <julie at flymine.org>
> Cc: Intermine Developer List <dev at intermine.org>
> Subject: Re: [InterMine Dev] Storage of long sequences
> Message-ID:
> 	<CAGuHHn8H269e_wrHs95qY1ow+=vkQxLQJ3TQHdaAu5UaEFHR7A at mail.gmail.com>
> Content-Type: text/plain; charset="iso-8859-1"
> 
> Hi Julie,
> 
> intermine_sequence seems to map to residues, Alex mentioned sequences are
> stored in CLOBs.  For debugging purposes, do you know where I can find
> these?
> 
> Thanks,
> -JD
> 
> On Mon, Mar 11, 2013 at 3:18 PM, Julie Sullivan <julie at flymine.org> wrote:
> 
>> "sequence" is marked as a reserved word (mistakenly imo), so the table is
>> called "intermine_sequence".
>> 
>> 
>> On 11/03/13 18:41, JD Wong wrote:
>> 
>>> Hello developer list,
>>> 
>>> In my mine's production database, I'm looking for a query to display the
>>> sequence for a specific protein.  Does anybody know where in the database
>>> sequences are stored?
>>> 
>>> Thank you!
>>> -JD
>>> 
>>> 
>>> 
>>> 
>>> ______________________________**_________________
>>> dev mailing list
>>> dev at intermine.org
>>> http://mail.intermine.org/cgi-**bin/mailman/listinfo/dev<http://mail.intermine.org/cgi-bin/mailman/listinfo/dev>
>>> 
>> 
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> ------------------------------
> 
> Message: 6
> Date: Tue, 12 Mar 2013 18:22:20 +0900
> From: Chen Yian <chenyian at nibio.go.jp>
> To: Intermine ML <dev at intermine.org>
> Subject: [InterMine Dev] About the ObjectStoreQueryDurationException
> Message-ID: <513EF3CC.2010701 at nibio.go.jp>
> Content-Type: text/plain; charset=UTF-8; format=flowed
> 
> Hi all,
> 
> Someone constructed an improper query which associated with many classes 
> and without any constraint.
> Since the query could be expected to return several million results,
> when it was executed I got the ObjectStoreQueryDurationException finally.
> Though the system threw the Exception and stopped working for the query, 
> PostgreSQL was still running.
> These threads occupied all resources for a while and some of them even 
> hang.
> Probably the problem itself is related to PostgreSQL,
> but is there any suggestion for preventing this kind of 'accident'?
> 
> Best,
> 
> Chen
> 
> 
> 
> 
> 
> 
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> End of dev Digest, Vol 46, Issue 8
> **********************************




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