[MOBY-dev] Cleaning up the Object ontology - Inheriting from base Object

[Rebecca Ernst]

Hi all!

I go with Mark in this discussion.

If, like Pieter explained here, one ID is pointing to a user and another 
to a program this should be specified in the namespace.
Like namespace_user and namespace_program.

I usually compare the namespace/id principle with phonenumbers. If 
someone tells you his phonenumber '77345' this is not sufficient but 
together with a namespace 'area-code' this is a valid pair of information.

If I get it right Pieter and Martin want is a namespace 'City' which can 
then be used for objects 'phonenumber', 'citycode', 'adress', etc. I 
believe that this is not what namespaces (and objects) are meant to be.

Cheers,
Rebecca




Pieter Neerincx wrote:

>Hi all,
>
>I'm with Martin here. I have quite a few Objects that inherit from  
>the base Object without having any HAS or HASA relationships. Most of  
>them are very generic things like for example "Program", "DataBase"  
>and "User". They can have different IDs and have different namespaces  
>depending on the service they are used for. And the namespace alone  
>is not enough. Within the same namespace I can have multiple things  
>which are only an ID, but one pointing to a user and another pointing  
>to a program and I think it's to be able to see the difference  
>directly from the name of the element instead of adding all kind of  
>child elements that only cause more overhead in XML parsing.
>
>Just my € 2c,
>
>Pi
>
>On 17-Feb-2006, at 1:19 AM, Martin Senger wrote:
>
>  
>
>>>Here is my position statement - please feel free to attack it or  
>>>support
>>>it:
>>>
>>>      
>>>
>>   I am not going to attack it, and I am far away from supporting it.
>>
>>    
>>
>>>Statement:  Any Object that is registered as deriving from base  
>>>Object,
>>>without any HAS or HASA relationships, should be considered invalid.
>>>
>>>      
>>>
>>   My position is clear here, and without any heat in my heart (my  
>>heart
>>has already burned in the pre-xmas discussion you mentioned) I just  
>>state
>>that this is unacceptable for me.
>>
>>    
>>
>>>My proposal:  The Registry should trap attempts to register  
>>>Objects that
>>>derive from base Object without any additional syntactic  
>>>complexity, and
>>>refuse to register them.
>>>
>>>      
>>>
>>   Which would mean (IMO), at least, to loose quite a chunk of Biomoby
>>users and developers.
>>
>>   Martin
>>
>>-- 
>>Martin Senger
>>   email: martin.senger at gmail.com
>>   skype: martinsenger
>>consulting for:
>>   International Rice Research Institute
>>   Biometrics and Bioinformatics Unit
>>   DAPO BOX 7777, Metro Manila
>>   Philippines, phone: +63-2-580-5600 (ext.2324)
>>
>>
>>_______________________________________________
>>MOBY-dev mailing list
>>MOBY-dev at biomoby.org
>>http://biomoby.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: 0317-483 060
>fax: 0317-483 584
>mobile: 06-143 66 783
>pieter.neerincx at wur.nl
>
>
>
>
>_______________________________________________
>MOBY-dev mailing list
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>
>  
>

-- 
Rebecca Ernst
MIPS, Inst. for Bioinformatics
GSF Research Center for Environment and Health
Ingolstaedter Landstr. 1
85764 Neuherberg
fon: +49 89 3187 3583
email: Rebecca.Ernst at gsf.de