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

JD Wong jdmswong at gmail.com
Tue Mar 12 16:02:26 GMT 2013


Hi Kalpana,

Thanks for your input.  I'm actually asking about accessing the sequences
in the database directly, for simple debugging purposes.  It's not very
important though, but may help to know.

-JD

On Tue, Mar 12, 2013 at 11:43 AM, Kalpana Karra <kkarra at stanford.edu> wrote:

> 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:
>
> > Send dev mailing list submissions to
> >       dev at intermine.org
> >
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> > When replying, please edit your Subject line so it is more specific
> > than "Re: Contents of dev digest..."
> >
> >
> > 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
> > -------------- next part --------------
> > An HTML attachment was scrubbed...
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> http://mail.intermine.org/pipermail/dev/attachments/20130311/14ea58ca/attachment-0001.html
> >
> >
> > ------------------------------
> >
> > 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
> >>
> > -------------- next part --------------
> > An HTML attachment was scrubbed...
> > URL: <
> http://mail.intermine.org/pipermail/dev/attachments/20130311/65699390/attachment-0001.html
> >
> >
> > ------------------------------
> >
> > 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>
> >>>
> >>
> > -------------- next part --------------
> > An HTML attachment was scrubbed...
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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
> >
> >
> >
> >
> >
> >
> > ------------------------------
> >
> > _______________________________________________
> > dev mailing list
> > dev at intermine.org
> > http://mail.intermine.org/cgi-bin/mailman/listinfo/dev
> >
> >
> > End of dev Digest, Vol 46, Issue 8
> > **********************************
>
>
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