[MOBY-l] Services inputs and outputs

[Pieter Neerincx]

Hi Victor,

On 18 Jul 2008, at 23:43, Victor Manuel wrote:

> thanks Peter. I would like to use the moby in a different context,  
> but as far as I understand the moby does not offer any service  
> discovery capability unless u follow moby standards;

Yes, in order to make automated service discovery by computers  
possible you'd have to stick to some standard. If there wouldn't be a  
standard of some kind you could use text mining on human readable  
descriptions of services, but with the current state of the art in  
text mining your succes rate in discovering compatible services would  
be ... eh rather unimpressive.

> so it works as a kind of yellow pages where u can only be found if  
> you publish according to pre-defined standards, am I right?

Yes.

> is there any experience of using biomoby in a non bio setting?

AFAIK You would the first to boldly go were only bioinformaticians  
have gone before... But I remember a recent discussion on languages  
used in the ontologies. For bioinformatics supporting English only  
would be sufficient as it is the de facto standard in Science, but  
mentioned he wanted to keep the option open to use Moby for other  
things than Bio...

> Also, from where could I download the bio moby ontology of data types?

There is not really a web page where you can download the ontologies.  
BioMoby Centrals are a combination of MySQL databases + Apache web  
servers and normally you use the BioMoby code base (Perl or Java) to  
interact with BioMoby Central.

Just as a quick hack you could try several URLs like these:

http://moby.ucalgary.ca/RESOURCES/MOBY-S/Objects
http://moby.ucalgary.ca/RESOURCES/MOBY-S/ServiceInstances
http://moby.ucalgary.ca/RESOURCES/MOBY-S/Namespaces

These URLs are mostly used by clients who want to download the entire  
respective ontologies for caching purposes. There should also be a
../ServiceTypes
../Full
but nobody is caching that yet and therefore it's not implemented yet.  
So for that info you'd really have to use the codebase to interact  
with BioMoby.


> how are the ontologies being aligned, Mark mentioned that my grid  
> ontologies were being aligned with biomoby ontologies, where can I  
> get the mapped ontology? or for that matter the file in which this  
> alignment is specified.

Maybe Mark can chime in on this one...

> Where can I get the doc describing all the moby standards? Cheers.

As mentioned before the best primer to get you started would be the  
the BioMoby 1.0 paper:

http://bib.oxfordjournals.org/cgi/content/abstract/9/3/220

Cheers,

Pi

> sorry bout my newbe questions but I am trying to figure out which  
> service discovery mechanism could I use in a non bio setting. Cheers.
>
>
>
> ----- Original Message ----
> From: Pieter Neerincx <pieter.neerincx at gmail.com>
> To: Victor Manuel <vmgcastellanos at yahoo.com>
> Cc: moby-l at lists.open-bio.org
> Sent: Friday, July 18, 2008 9:30:10 AM
> Subject: Re: [MOBY-l] Services inputs and outputs
>
> Hi Victor,
>
> On 18•Jul•2008, at 3:52 PM, Victor Manuel wrote:
>
>> Is there an ontology describing biomoby inputs and outputs?
>
> Yes, that is what BioMoby was designed for in the first place :)
>
>> does biomoby provide any web service discovery mechanism?
>
> Yes, that is what the BioMoby ontologies mentioned above were designed
> for in the first place :)
>
>> does biomoby standardizes the description of web services in bionfo?
>
> Partially, that is what BioMoby was designed for in the first place :)
> The inputs and outputs are standardised as well as service types, but
> there is also a "free text form" description field to describe a
> service. The latter is just meant to be a human readable string and is
> not standardised (not even on language, so you might find some non-
> english stuff in there...)
>
> Both the inputs & outputs as well as service types and the services
> themselves are stored in ontologies. These are available from
> repositories called BioMoby Central. There is one official public one
> and several institutes host their own BioMoby Centrals either for
> development or for services which are not publicly available.
>
> Looks like you could use a BioMoby primer; the BioMoby 1.0 paper would
> be good start:
>
> http://bib.oxfordjournals.org/cgi/content/abstract/9/3/220
>
> Cheers,
>
> Pi
>
>
>>
>>
>>
>> -
>>>
>>
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-------------------------------------------------------------
Wageningen University and Research centre (WUR)
Laboratory of Bioinformatics
Transitorium (building 312) room 1034

Dreijenlaan 3
6703 HA Wageningen
The Netherlands

phone:  +31 (0)317-483 060
mobile: +31 (0)6-143 66 783
e-mail: pieter.neerincx at gmail.com
skype:  pieter.online
-------------------------------------------------------------