[Open-bio-l] OBDA redux?

[Peter Cock]

On Thu, Dec 15, 2011 at 10:01 PM, Hamish McWilliam
<hamish.mcwilliam at bioinfo-user.org.uk> wrote:
>> 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:

Well, given the broad title of OBDA redux, why not?

> - 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 has mostly been replaced by SOAP and REST web services.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.

As far as I know, BioCorba is defunct.

> - 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.

Current Biopython doesn't have anything for this, but I would probably
want to implement this as a client not a server.

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

Agreed, done:
https://github.com/OBF/OBDA/commit/5798f0b4a0e3b7fd0595e0ab3017d3afdda53549

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

Basically yes.

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

This also has implications for the bioindex code as we need to
specify the file format being indexed (e.g. FASTA or GenBank).

> - 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).

There was some partial code for this in Biopython, but it was
deprecated and removed some time ago.

> - 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.

Presumably the XML format for EMBL is now one of the ISNDC
formats also used at the NCBI? In any case, that whole folder
is purely describing an (obsolete) EBI service, so can we just
delete it it?

> 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

How does biofetch/bioregistry compare to DAS?

Separately, I suggest we rename the OBDA/preamble.txt
file to README (or README.*) so it gets shown in GitHub,
and then update it following this discussion with some
context (like dates current status of the different parts).

We should probably make the old OBDA CVS read only now.

Peter