[MOBY-dev] Primitives as primary input

[Mark Wilkinson]

I agree with Paul (or did Paul agree with me??) that email and url are  
namespaces.  Paul's argument that it doesn't make sense to sub-class an  
email or a url is a compelling one, which also gives me some assurance  
that this decision is correct.

...on the other hand, there have been several requests from people in the  
community to create subclasses of namespaces (e.g. NCBI-->NCBI_gi), and in  
the case of IRRI their need was sufficiently strong that they ended up  
created objects that represented their identifiers such that they could  
sub-class them at the object level!  So there is a clear desire and  
apparent need to be able to categorize namespaces as well...

M



On Thu, 10 Jan 2008 10:07:56 -0800, Pieter Neerincx  
<Pieter.Neerincx at wur.nl> wrote:

> Hi,
>
> On 10-jan-2008, at 17:35, Mark Wilkinson wrote:
>
>> Hi Andreas!
>>
>> That's a very interesting case!  Is "email" a data-type (Object) or a  
>> semantic-type (Namespace)??  It is a semantic type in the sense that  
>> all email addresses are unique, and therefore behave as identifiers...  
>> but it is often used as a data-type in that it would be associated with  
>> other information like an address and telephone number.
>>
>> Personally I would be tempted to make a new namespace 'emailAddress' or  
>> something like that, since semantic "precision" is the goal of these  
>> two ontologies.
>>
>> What did we do for URLs?  ...LOL!  Okay, I just went to have a look in  
>> the ontologies and we have an Object "URL" and a Namespace "URL"!!!  I  
>> guess others have had the same question and made different decisions  
>> :-)  I see that it is Pieter's services that consume the Object "URL" -  
>> maybe he can explain to us why he chose to make URL an object rather  
>> than a namespace.
>>
>> Pieter?
>
> I've been struggling with this question as well. If you check the object  
> ontology you'll see I also registered an Email object. Email addresses  
> and URLs can be both a data-type (Object) and a semantic-type  
> (Namespace), so maybe it would be best to use both. Actually I was  
> waiting for a response of the founding father a.k.a. chief architect to  
> clarify this one :)...
>
> We give several courses which involve BioMOBY and usually the part where  
> the students have to:
>   * choose whether to recycle existing objects & namespaces or design  
> new objects & namespaces
>   * and if they choose to design new ones, come up with the exact  
> structure for those objects & namespaces
> is the most difficult part of the entire course.
>
> Cheers,
>
> Pi
>
>
>> M
>>
>>
>>
>> On Thu, 10 Jan 2008 03:20:11 -0800, Andreas Groscurth  
>> <groscurt at mpiz-koeln.mpg.de> wrote:
>>
>>> And hi again,
>>>
>>> we just had the discussion here... is it recommended to use primitives  
>>> as
>>> primary input ? Or are there actually only for use in secondary  
>>> parameters or
>>> as part of a complex datatype ?
>>>
>>> E.g. if a service requires an email as input - give it an object with
>>> namespace 'email' or similar - or could I use String with namespace  
>>> 'email'
>>>
>>> Thanks and byebye
>>> andreas
>>>
>>
>>
>>
>> ----
>> Mark Wilkinson
>> Assistant Professor, Dept. Medical Genetics
>> University of British Columbia
>> PI Bioinformatics
>> iCAPTURE Centre, St. Paul's Hospital
>> Tel:  604 682 2344 x62129
>> Fax:  604 806 9274
>>
>> ***CONFIDENTIALITY NOTICE***
>> This electronic message is intended only for the use of the addressee  
>> and may contain information that is privileged and confidential.  Any  
>> dissemination, distribution or copying of this communication by  
>> unauthorized individuals is strictly prohibited. If you have received  
>> this communication in error, please notify the sender immediately by  
>> reply e-mail and delete the original and all copies from your system.
>> _______________________________________________
>> MOBY-dev mailing list
>> MOBY-dev at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/moby-dev
>>
>
> -------------------------------------------------------------
> Wageningen University and Research centre (WUR)
> Laboratory of Bioinformatics
> Transitorium (building 312) room 1034
>
> Dreijenlaan 3
> 6703 HA Wageningen
> The Netherlands
>
> phone:  0317-483 039
> fax: 0317-483 584
> mobile: 06-143 66 783
> mail: pieter.neerincx at wur.nl
> skype: pieter.online
> ------------------------------------------------------------
>
>
> _______________________________________________
> MOBY-dev mailing list
> MOBY-dev at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/moby-dev



-- 
--
Mark Wilkinson
Assistant Professor, Dept. Medical Genetics
University of British Columbia
PI Bioinformatics
iCAPTURE Centre, St. Paul's Hospital
Tel:  604 682 2344 x62129
Fax:  604 806 9274

***CONFIDENTIALITY NOTICE***
This electronic message is intended only for the use of the addressee and  
may contain information that is privileged and confidential.  Any  
dissemination, distribution or copying of this communication by  
unauthorized individuals is strictly prohibited. If you have received this  
communication in error, please notify the sender immediately by reply  
e-mail and delete the original and all copies from your system.