[Biocorba-l] biocorba and the OMG spec

[Scott Markel]

Juha,

Juha Muilu wrote:
> 
> Hi All,
> 
> Thanks Jason and Brad for the emails. It would be really nice to make
> the BSA and Biocorba specs more compatible at least so that mapping
> becomes easy and unique.
> 
> Unfortunately it may not be possible to do any major changes into the
> BSA spec anymore. Extensions are of course possible.  (Can somebody
> who knows the OMG procedures comment on this?).

Small fixes will be made this fall to the BSA specification.  This is the
work of the BSA FTF (Finalization Task Force).  Members of the FTF are
the submitters and the evaluation team.  Major changes require the
issuance of a new RFP.  The current plan is to draft one or more of these
at the OMG meeting in two weeks.  I know that the BSA submitters would
like to add in more bio-objects, so one of the RFPs will probably focus
on that.  Examples include pattern matching, phylogenetic tree, and
assembly.  Another RFP may cover gene analysis.

Please note that any issues that anyone has with OMG specs can be sent
to issues@omg.org.  You do not have to be an OMG member to raise issues.
You can also send BSA issues to the BSA FTF mailing list
biomolecular-ftf@omg.org.  If you send issues to one of the submitters,
e.g., me or Martin Senger, we'll forward them to the right place.

> Ideally it would be nice if the interfaces used in the
> Biocorba and BSA could inherit from common general base classes where
> more specialized functionality is needed, like extensions for the
> GNOME bonoboo and life cycle support.  However, the handling of the
> value type objects in a uniform manner may be tricky.
> Any idea do we get OBV for perl ever?
> 
> By quickly looking I found following possible mapping problems in the specs:
> 
> - First is the use of accession numbers and identifiers:
> 
>   ID string in the BSA uses syntax convention specified in the CORBA naming
>   services (CosNaming::StringName). Basically the ID contains
>   "/"-separated components (starting from the data source etc. to the
>   accession number) so that it becomes unique. Version is indicated by
>   the "kind"-part which is marked as "." at the end of the ID.
>   The spec is rather loose and may not be possible to map to
>   Biocorba ids.
> 
>   Also the ID can contain only chars: 'a-z', '0-9', '$', '-', '_' and '.'
>   '.' is discouraged and must be escaped. Hope the Biocorba uses these also
> 
> - BioSequence and Annotation objects contains also information about
>   the basis of an object. I.e is it "computational" (like consensus sequence) or
>   "experimental" (also both or "not known"). This is missing in biocorba
> 
> - SeqFeatures may not be possible to map at all. First BSA uses name
>   value pairs as specified in CORBA property services, where the
>   value is type of CORBA Any. Biocorba uses string lists.
> 
>   Interpretation of long name value lists is also difficult and in the BSA spec
>   qualifiers are in a separate field. I think the purpose is
>   to provide proper hiding place for the EMBL/GenBank feature table info (
>   I may be wrong)

No, you're right.  That was exactly the intent.

>   In the BSA there is only one way relationship between SeqFeature and
>   BioSequence. (From seq to feature). Wrong or right ?

Right.  This is something I'd personally like to change.

>   Strand types also includes, in addition to PLUS and MINUS, BOTH (!),
>   NOT KNOWN and NOT APPLICABLE
> 
>   Sequence region can be also recursive composite region
> 
> - In BSA SeqFeature (actually SeqAnnotation) is subclass of Annotation.
>   Annotation applies to whole sequence and SeqAnnotation to certain
>   region. The Annotation is perhaps not clearly specified in Biocorba
> 
> OK this list may not complete... but hope it initiates more discussion
> 
> Thanks very much for setting up the mailing list and the biocorba-web site.
> Good work !!
> 
> Please have a look at our work at http://industry.ebi.ac.uk/openBSA
> We have the analysis server already working and some other things are more
> or less alpha stage. Especially documentation, ...but we are working on it

Scott

-- 
Scott Markel, Ph.D.       NetGenics, Inc.
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