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

[Pieter Neerincx]

On  17Feb2006, at 17:28, Paul Gordon wrote:

> I support Martin's position, but would add a caveat:  since we are all
> sharing the same ontology, it would be nice if no one hogged the  
> generic
> words like "Person" and "DataBase" if they are specific to their
> services instead of generic objects representing any Person or
> DataBase.  Perhaps DutchPerson or DutchDatabase in your app Pieter?
> Well maybe not, but you get the idea... :-)

Don't worry, I realize that the power of the ontology is the level of  
recycle-ability of objects. If everybody designs yet another object  
specific to their services, building workflows will be just as  
difficult with as without ontology.
Therefore a "DataBase"  or "User" object should be generic. If I need  
some kind of specialized "DutchBase" object specific for a certain  
service I'll create a new one that inherits from the "base" DataBase  
object and/or I'll restrict the namespaces.

>
> Right now in the registry if I send a generic object I get over a
> hundred services back, almost none of which will actually consume the
> object without dying a horrible death.  I think proper namespace
> restriction in service registration is a bigger issue than people
> creating new name-only ontology objects...

You are absolutely right! Add to that dead services and improper  
registered services and it can be pretty difficult for BioMOBY  
newbies to find some working workflow examples.

>
> My CAN $0.02.

Looks like we could use a BioMOBY currency converter service :)

Pi

>
>> 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
>>
>>
>>
>>
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>>
>>
>
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Wageningen University and Research centre (WUR)
Laboratory of Bioinformatics
Transitorium (building 312) room 1038
Dreijenlaan 3
6703 HA Wageningen
phone: 0317-484 706
fax: 0317-483 584
mobile: 06-143 66 783
pieter.neerincx at wur.nl