Re: [Obo-phenotype] base pair and nucleotide

[Chris M. <cj...@be...>]

On Dec 17, 2009, at 12:15 PM, D. MacAlpine wrote:

> Thanks nicole!
>
> this is more complicated than I first thought...  A bp is common  
> unit of
> measurement for double stranded DNA as in 500 bp of DNA which would be
> 500 paired nucleotides.
>
> However, for single stranded RNA or DNA we simply count the number of
> nucleotides (nt).  Which are a chemical entity.  So in this case,  
> maybe
> there is no unit.  For example, what would the unit be if we were just
> counting horses in a field?

"horses"?

there's a near-infinite cross-product of such "units", e.g. "monkeys  
per hectare".

If we had designed UO rationally we would have placed standard SI  
units in a separate ID space, and had a separate application ontology  
from domain-specific "counts of X" type terms. But "base pair" is  
gradfathered into UO now...

> Best,
>
> Dave
>
>
> On Thu, Dec 17, 2009 at 11:05:58AM -0800, Nicole Washington wrote:
>> Hello,
>>
>> I am writing concerning the definition of the term 'base pair':
>> [Term]
>> id: UO:0000244
>> name: base pair
>> def: "A length unit which contains one nucleotide." [UO:GVG]
>> synonym: "bp" EXACT []
>> is_a: UO:0000189 ! count
>> This term is under a bit of scrutiny because its definition doesn't  
>> fit
>> exactly with what its name implies.  The name implies that there is a
>> length of one nucleotide, but in a "pair" on opposite strands. The
>> definition really applies to a "nucleotide" rather than a "base  
>> pair".
>> Can the name of the term be changed, or a nucleotide term be added  
>> and
>> the definition of this term be updated?
>> Nicole
>>
>
> -- 
> David MacAlpine, PhD              Email: Dav...@du...
> Assistant Professor               Phone: 919.681.6077
> Pharmacology and Cancer Biology
> Duke University Medical Center
> C318 LSRC Box 3813
> Durham, NC 27710
>