[MOBY-dev] Primitives as primary input

Thu Jan 10 19:05:18 UTC 2008

On 10-jan-2008, at 19:31, Mark Wilkinson wrote:

> 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...

Yes, that would really help! :)

Pi

> 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
>>>
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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:  0317-483 039
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>
>
>
> -- 
> --
> 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
------------------------------------------------------------