[MOBY-dev] Migration of database to new API

[Benjamin Good]

Jumping in since I was mentioned ...

In the current version of moby, as I understand it at least, I have  
to side with Martin on this (sorry Mark, don't fire me!).

Ahab, as well as other generic clients, benefits substantially from  
meaningful object and service names.  Taking your (Mark's) argument  
further, we might as well eliminate human-readable names altogether  
and simply assign a unique number to each one - which is fine for the  
use as a machine name, but totally useless to an anonymous human user  
of the data-type.

To be precise, in the current formulation of BioMoby, the ONLY  
semantics associated with the data-types are encoded in the names of  
the objects.  Thus, until we have a consistent framework for encoding  
semantics in another more robust fashion, like a separate ontology  
that has nothing to do with syntax, we should at least attempt to  
encourage meaningful and consistent naming strategies.

-Ben



On Aug 26, 2005, at 6:12 PM, mark wilkinson wrote:

> I strongly disagree in return :-)
>
> If I have an object called "sequence" there is no indication in the  
> name that it is a fasta sequence or an embl sequence or a genbank  
> sequence or whatever.  The fact that it is called sequence-v2 is no  
> more nor less confusing!
>
> (Ben is sitting here beside me in the pub chuckling about the  
> dangers of mixing semantics meaning into names :-) )
>
> M
>
>
> -----Original Message-----
> From: Martin Senger <senger at ebi.ac.uk>
> Date: Sat, 27 Aug 2005 02:06:55
> To:markw at illuminae.com,       Core developer announcements <moby- 
> dev at portal.open-bio.org>
> Cc:mobydev <moby-dev at biomoby.org>
> Subject: Re: [MOBY-dev] Migration of database to new API
>
>
>> There is no need for a name change again.  The object will forever  
>> be called -v2
>>
>> It's just an identifier...
>>
>>
>    Strongly disagree. The names are visible to people in many  
> clients that
> list them. They should be named sensibly. Adding an artificial  
> suffix v2
> just without any compelling reasons is a bad design (and there is no
> compelling reason for that).
>    I will better stop now (you got me agian!¬)...
>
>    Martin
>
> -- 
> Martin Senger
>    email: martin.senger at gmail.com
>    skype: martinsenger
> International Rice Research Institute
> Biometrics and Bioinformatics Unit
> DAPO BOX 7777, Metro Manila
> Philippines, phone: +63-2-580-5600 (ext.2324)
>
>
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> --
> Mark Wilkinson
> ...on the road!
>
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