Subject: Sequence Classes and CORBA Servers

From: Gerald Loeffler <[email-masked]>
Date: Mon, 10 Nov 1997 13:09:58 +0100

Hi!

If you are interested in Bioinformatics at the protein/DNA sequence level and OO
technology I would highly appreciate if you could have a look at the questions
below!

I'll summarise - of course (-:

=============================================================================

1) Are there any "standard" C++, Java or IDL specifications for classes that
represent
    a) DNA sequences,
    b) RNA sequences,
    c) Protein sequences,
    d) Pairwise and multiple sequence alignments?

2) What's the relation of the above sequence class specifications to existing
flat-file sequence formats (EMBL, GenBank, PIR, SwissProt, ...)?

3) Are there any CORBA servers available now (or in the near future) that give a
piece of CORBA complient client code approximately the level of access to
sequence databases that a human user has using popular WWW interfaces.
Specifically, the CORBA server should deliver:
    a) A single sequence entry (as an object of one of the above sequence
classes) upon specification of a sequence ID (accession number).
    b) A set of sequence entries (as a collection of objects of one of the above
sequence classes) upon specification of a query expression.
    c) An ordered list of sequences (as a collection of objects of one of the
above sequence classes) and maybe alignments as the result of a homology search
against the remote database using BLAST, FASTA, ....

4) Instead of relying on remote CORBA servers one can also install sequence
databases locally. Are there implementations (C++ libraries or Java packages)
that perform the tasks given in question 3 above, but access locally installed
(flat-file) sequence databases instead of remote CORBA servers?

=============================================================================

Why all this? Well, it's obvious that I would like to write programs that
automate procedures that I can now easily perform (in low volume) using the WWW:
do homology searches, request specific sequence entries and so on. And I would
like to write _real_ programs, not just scripts that tediously wrap these tasks
into email messages that are then sent off to an email-based server.

The first prerequisite to doing this is to have an OO representation of
sequences. Although it doesn't seem difficult to come up with a reasonable
specification of DNA, RNA or protein sequences, this would presumably be yet
another specification - hence question 1.

This representation of sequences should really be independent of any flat-file
sequence format. That is, I don't want to have to deal with EMBL DNA sequence
objects and GenBank DNA sequence objects at this level. Hence question 2.

And then of course it would be great to actually have CORBA compliant servers
that I can use from my programs to query remotely installed sequence databases
and to execute some common algorithms like BLAST, FASTA, (multiple) sequence
alignments, etc.. The results of these algorithms should be returned as objects
of the same "standard" sequence classes that I locally use to represent
sequences. Hence question 3.

CORBA-based access to remote sequence databases might be to ambitious. Instead,
I could install the common sequence databases locally (as flat files) and access
them using a class library that represents sequences as objects of these
"standard" sequence classes - question 4.

By the way: I expect being called naive for asking these questions (-:

    Thank you very much indeed for taking the time to answer this!!
    gerald
--
Gerald Loeffler
PostDoc in Theoretical Biophysics

EMail: [email-masked]
WWW:   http://www.imp.univie.ac.at/Loeffler/
Phone: +43 1 79730 554
Fax:   +43 1 7987153
SMail: I.M.P. - Research Institute of Molecular Pathology
       Dr. Bohr-Gasse 7
       A-1030 Vienna
       AUSTRIA

---

From: Philip Lijnzaad <[email-masked]>
Date: Mon, 10 Nov 1997 16:04:23 GMT

[ I narrowed the response a bit, but then again I probably shouldn't
have. So this time the chemistry lists are included. Sorry. ] 

Hi,

as you maybe know, the EBI has been advocating the use of CORBA in Molecular
Biology for a while now.

There is currently an effort underway to standardize classes for use in the
field of Life Sciences Research (i.e. Molecular Biology and more). The Life
Sciences Research SIG (special interest group) has been set up recently (
homepage: http://lsr.ebi.ac.uk/ ). They have issued a Request For Information
(RFI), to get an impression of what the current status is, and of what 'the
field' would like to see incorporated in the standards. (Your mail actually
shows a great deal of overlap with the RFI!)  This RFI has been circulated in
the field, and responses are actually due today; see
http://lsr.ebi.ac.uk/docs/corbamed/97-09-16.html. Everybody (not just OMG
members) is invited to respond to this RFI; the

The ultimate goal of this process is to produce a set of IDL specifcations
that are useful for work in the Life Sciences.

> sequence databases that a human user has using popular WWW interfaces.

Have a look at the following URLs: 

http://industry.ebi.ac.uk/~corba/

http://sunny.ebi.ac.uk/RandD/
http://sunny.ebi.ac.uk/RandD/EBIBasicSequence.html

http://industry.ebi.ac.uk/~slidel/embl-corba/

http://industry.ebi.ac.uk/contrib/corba/SeqDB/

(some of these servers are very much in a prototype stage; do not expect too
much in terms of functionality or stability).  We are working on a next
generation server for the EMBL Nucleotide Sequence Database, which will have
a simpler interface and will be more stable.

> alignments, etc.. 

Where would the method for searching go, into something like BioSequence,
BioSequenceFactory, SeqSearchEngine ? These are the kind of questions that
must be addressed. Many of them are not trivial.

> CORBA-based access to remote sequence databases might be too ambitious. 

Well, we're working on it :-) but there are a number of issues that aren't so
simple. Especially general querying is difficult, but other, less technical
points are things like style and nomenclature also need to be
resolved. Anyway, thanks for blowing some life into this mailing list.  Kind
regards,

                                                                      Philip

-- 
Philip Lijnzaad, [email-masked] | European Bioinformatics Institute
+44 (0)1223 49 4639                 | Wellcome Trust Genome Campus, Hinxton
+44 (0)1223 49 4468 (fax)           | Cambridge CB10 1SD,  GREAT BRITAIN
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