[BBF Standards] data exchange issue 1: Abstraction

[Ralph Santos]

Randy Rettberg wrote:
>> (1) Right now, parts include so many different kinds of entities
>> (snippets of DNA including biobrick ends, full plasmids, small RNA's,
>> etc.) that one cannot sensically abstract a part in any uniform  
>> fashion.
>>     
>
> Raif,
>
> There are separate issues here. A catalog will have different kinds  
> of things you can
> buy. For example, the apple catalog has macintosh products, but i  
> also has extended warranties,
> and software. All are products, but the are sub categories are  
> distinct. Primers and plasmid backbones
> are examples of unusual parts.
>
> There are also errors in the Registry. Parts are defined to NOT have  
> biobrick ends on their sequence.
> If they do it is an error. Also, full plasmids consisting of a  
> plasmid backbone and a part are also errors.
> Composite parts that are entered as basic parts are also errors, but  
> necessary until we support a wider
> variety of scars.
>
> Randy Rettberg
>
>
>
>
> _______________________________________________
> Standards mailing list
> Standards at biobricks.org
> http://biobricks.org/mailman/listinfo/standards_biobricks.org
>   
Randy,

First, thanks and allow me to apologize for not clearly differentiating 
my name from Raik's.

Second, the heterogeneity of parts does not speak to the inability to 
meaningfully abstract or generalize parts.  Consider that even if one 
were to filter out, say, all the promoter parts in the registry there's 
currently no well-defined procedure for looking up any particular bit of 
information about those parts.  For instance, if one were to gather all 
the information about all the promoters, can one mechanistically 
tabulate the signal to which they respond?  I'm trying to state a 
desirable behavior that I'd like to see the standard realize in due 
course once it's developed.

Third, speaking to the second paragraph of your message regarding errors 
and the definition of parts, if there already are pre-existing rules 
that are already in effect they should be posted on the wiki for this 
group to keep them in mind and work with them.  Part of establishing a 
standard is simply posting it clearly so that everybody can know about 
it and communicating it to everyone who needs to know in a clear and 
consistent fashion.  If this rule of a part not including the end 
sequences is stated somewhere I'd like to see a reference: a URL, 
anything.  I'm not asking this to be facetious, I'm asking this because 
if there are already pre-existing publication rules it's mandatory and 
essential that they be posted or cited as part of the material for use 
by the standards discussion so that everyone participating is fully 
cognizant of them.


---ralf