[BBF Standards] data exchange -- say no to web services

[Raik Gruenberg]

 > Interesting. There are two websites out there that I would like to
 > mention (as well as Freebase, though I do not know about its
 > relevance). In particular, check out these groups:

Freebase is interesting because it shows the power of triple-based knowledge. 
They basically re-invent RDF and put an excellent user interface on top of it. 
The kind of questions you can ask there and the freedom to link everything with 
everything is far surpassing relational database technology. The problem I see 
is that:
* they don't follow the existing standards
* it's closed source
* most important, all information rests on their server -- defying the semantic 
web idea.

 >
 > http://dataportability.org/ (more for social networks)
 > http://theinfo.org/ -- for processing large datasets.
 >
 > A good first step might be to make the bioinformatics databases expose
 > MySQL/PostgreSQL interfaces to the public for automated querying. Would
 > this be useful?

I am not an expert here, but I believe some do. This still leaves the data 
isolated though and doesn't tell you anything about their meaning. Web services 
are then often used to offer APIs to access the data but this requires an 
explicit programing effort for every link and has the described problems.
That's why efforts like Moby -- to centralize and unify web services. Some 
databases start providing direct RDF, though (e.g. uniprot).

Greetings,
Raik

Bryan Bishop wrote:
> On Monday 11 February 2008, Raik Gruenberg wrote:
>>> The number of web service providers in the field of bioinformatics
>>> is
>>  > increasing every year. In theory, these services are interoperable
>> and > independent of specific computer languages. However, each
>> service uses its own > definition of data types and method naming
>> conventions. Moreover, > theseservices are often not usable by
>> specific languages (partly, due to the > lack of compliance of the
>> SOAP/WSDL specification in the language's library).
>>
>> ... and then they need to fix up the mess with an extra layer of
>> ontologies of web services while the actual data seem to remain
>> undescribed and disconnected.
> 
> Interesting. There are two websites out there that I would like to 
> mention (as well as Freebase, though I do not know about its 
> relevance). In particular, check out these groups:
> 
> http://dataportability.org/ (more for social networks)
> http://theinfo.org/ -- for processing large datasets.
> 
> A good first step might be to make the bioinformatics databases expose 
> MySQL/PostgreSQL interfaces to the public for automated querying. Would 
> this be useful?
> 
> - Bryan
> ________________________________________
> Bryan Bishop
> http://heybryan.org/
> 
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> Standards mailing list
> Standards at biobricks.org
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> 
> 

-- 
________________________________

Dr. Raik Gruenberg
http://www.raiks.de/contact.html
________________________________