[Open-bio-l] OBDA redux?

[Hamish McWilliam]

> Just a quick update on this: the old OBDA specs were still in CVS in the obda-specs module (the old obda site had the module wrong).  I ran git cvsimport on that after I copied the CVS repo to my laptop, so it's now on github:
>
> https://github.com/OBF/OBDA
>
> We could probably work on updates from there.

At the risk of derailing the current thread... a few comments on the
"modules" in the old ODBA:

- BioCorba: while CORBA may live on in some embedded applications it
has mostly been replaced by SOAP and REST web services. I suspect
there are few copies of the BioCorba IDLs surviving today. Possibly of
historic interest, but since it doesn't actually include the IDLs it
is not really of any use.

- biofetch: originally implemented in EBI's dbfetch, also implemented
by BioRuby as biofetch which had a few extensions. EBI's dbfetch has
since been reimplemented and attempts to be compatible but only
provides partial support along with various extensions, including
those from BioRuby. See http://www.ebi.ac.uk/Tools/dbfetch/syntax.jsp.
I'm aware of client support in BioPerl, BioRuby and EMBOSS, not sure
of the current status for BioJava and BioPython.

- BioSQL: as you all know over at http://www.biosql.org/. The document
should probably be updated to point there.

- bioindex: the flat-file and BDB indexing formats. To which the
SQLite option will be added?

- naming: obsolete URN scheme. Various ontologies (e.g. EDAM) provide
possible replacements when required.

- bioregistry: database discovery and meta-data. From having tried to
implement this, the bioregisty is too limited in the available
meta-data to be very useful, especially when it comes to data format
handling. Compare with the database definitions in EMBOSS
(http://emboss.sourceforge.net/docs/themes/Databases.html) and the
dbfetch meta-data
(http://www.ebi.ac.uk/Tools/dbfetch/syntax.jsp#Meta-information).

- XEmbl: REST and SOAP access to EMBL-Bank entries in XML. The EBI's
XEmbl service was replaced by the dbfetch
(http://www.ebi.ac.uk/Tools/dbfetch/) and WSDbfetch
(http://www.ebi.ac.uk/Tools/webservices/services/dbfetch) services,
since these provide roughly the same functionality with wider data
format support.

Since I've been attempting to get dbfetch to support the biofetch and
bioregistry specifications, my interest is much more at the web
service end of things. I can certainly see options for using the
current alternatives in dbfetch and EMBOSS to revise the
specifications for biofetch and bioregistry.

Hamish



>
> chris
>
> On Nov 18, 2011, at 7:45 AM, Fields, Christopher J wrote:
>
>> On Nov 18, 2011, at 5:21 AM, Peter Cock wrote:
>>
>>> On Fri, Nov 18, 2011 at 10:55 AM, Raoul Bonnal <bonnal at ingm.org> wrote:
>>>> ...
>>>> And which are the information you want to extract once you
>>>> have your index ?
>>>>
>>>
>>> Biopython and BioPerl have their SeqIO parsers hooked up
>>> to indexing code. This means you can access a record via its
>>> ID, and it is parsed for you on demand - just like if you'd
>>> iterated over the file in order parsing the records one by one.
>>>
>>> Biopython (not sure about BioPerl) can also just fetch the raw
>>> text of that record.
>>
>> Re: BioPerl, I'm not sure about the OBDA implementations, but I know the older Bio::Index modules allow this.  I would be surprised if the OBDA-specific code didn't, but adding this should be easy.
>>
>> chris