[BBF Standards] Amorphous languages for bio fabs

[Ralph Santos]

Hi,

Thanks for pointing this out.  I've been studying this area, but I'm new 
enough to it that I'm still learning as I go.  By way of agreement, I 
have been finding that as I study the available web ontologies and 
ontology design it offers some highly valuable perspectives that I would 
like to see brought into the standardization effort.

In particular, one thing I've been thinking about quite a bit regarding 
the current standards discussion is that we might want to separate the 
data types and domains we wish to cite in the biobrick standards versus 
the uses to which we put them.  I think that such a perspective not only 
lends itself to helping us figure out how a biobrick standard can fit in 
with existing web ontologies, but also I believe it can help us evolve 
the standard by breaking the domain down into clean, well-defined 
concepts which can lend itself to clearly defined data exchanged 
standards based on a coherent logical model.

As for reusing existing ontologies, I would very much like to see that 
done.  By raising a discussion about vocabularies for chemical species 
and cellular anatomy from the perspective of biobricks I'd much rather 
see us define it in terms of restrictions upon and expansions of a 
pre-existing ontology rather than having us create a new one out of 
whole cloth.  I wanted to avoid citing web ontology terms for the 
benefit of those who might not know about it, but perhaps that wasn't a 
good decision on my part.

Having said all of that, I think it might be worth citing some web 
ontology development resources focused on defining or designing 
ontologies so that interested people can learn more.  I'm new enough to 
this that I don't have many, but my favorite intro is this one:

  
http://protege.stanford.edu/publications/ontology_development/ontology101-noy-mcguinness.html

In any case, I appreciate your comments and hope you can help me in my 
ham-fisted efforts.

Thanks,
---ralf

Herbert M Sauro wrote:
> Note that there are already developed (or under development) ontologies 
> that describe many of the concepts you mention. I would recommend 
> investigating these and it they are not appropriate for synthetic 
> biology then either expand existing ones or develop a new subset to 
> accommodate particular aspects that aren't covered.
>
> Herbert Sauro
>
> Ralph Santos wrote:
>   
>> Hi,
>>
>> Allow me to thank you as well for the articles you cited in your 
>> original message.  It explores some really fascinating ideas.
>>
>>