Re: [SO-devel] allele, haplotype for human geneticists

[David S. D. <del...@mh...>]

Hi Karen,

I see that sequence_variant ended up on the obsolete list.

Are the concepts Allele and Haplotype gone forever?

David



David S. DeLuca
Institute for Transfusion Medicine
Hannover Medical School
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del...@mh...
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Chris Mungall wrote:
> Hi Marcela
>
> These terms are in SO already. I don't know whether or not they  
> should go in SOFA as I've never understood what SOFA is intended for.
>
> On Aug 30, 2007, at 2:49 PM, Marcela K. Tello-Ruiz wrote:
>
>   
>> Hi,
>>
>> Is there any plan to include allele or haplotype in the SOFA ontology?
>> They both could be considered a "sequence_variant" but it would be
>> useful to be able to distinguish sequence variants involving a single
>> base pair vs multiple (contiguous) base pairs.
>>
>> In human genetics is common practice to refer to genetic variants
>> involving a single SNP as "alleles", and  to multi-SNP variants as
>> "haplotypes", but I know these same terms are used differently across
>> organisms, and so it gets complicated to generalize...  Any  
>> suggestions
>> on how to deal with this?
>>
>> Thanks,
>>
>> Marcela
>>
>>
>> -- 
>> Marcela Karey Tello-Ruiz, PhD
>> Cold Spring Harbor Laboratory
>> Williams #5
>> Cold Spring Harbor, NY 11724
>> Ph. 516-367-6985
>> Fax 516-367-6851
>>
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