Re: [Treebase-devel] [CDAO-discuss] RES: lat/lon in nexml

[Arlin S. <sto...@um...>]

If you folks could give the CDAO group a specific use-case or user  
scenario involving a segmented alignment, with data, we can try to  
represent it using current CDAO concepts, and if thats not possible,  
we'll explore possible revisions.

I'm imagining that the use case is going to be something like this.   
There is a character-data-and-trees thing based on sequence data, in  
which the "alignment" is a hybrid in which, for a given OTU, the row  
that belongs to the OTU combines multiple data sources.   A specific  
example would be that for a species called OTU1, the first part of the  
sequence comes from specimen (isolate, strain) A of that species, and  
the second part comes from specimen B which was sequenced in a  
different lab.  For OTU2, it might be the case that the whole sequence  
comes from one specimen.

To complete this use case, we would like to know what kinds of queries  
or operations need to be supported.

Arlin
-------
Arlin Stoltzfus (sto...@um...)
Fellow, CARB; Adj. Assoc. Prof., UMBI; Research Biologist, NIST
CARB, 9600 Gudelsky Drive, Rockville, MD
tel: 240 314 6208; web: www.molevol.org

On Feb 12, 2010, at 4:25 PM, Francisco Prosdocimi wrote:

> Hi Hilmar,
>
> -----Mensagem original-----
> De: Hilmar Lapp [mailto:hl...@ne...]
>> If the alignment isn't concatenated with sequences from multiple
>> specimens, couldn't (in fact, shouldn't) you attach the lat/long to
>> the OTU, though? I.e., where do you attach the specimen currently,  
>> and
>> it do you attach lat/long in a different fashion than the specimen?
>
> If I understood well the problem...
> CDAO presents an OTU annotation concept, and users can instantiate  
> it with any desirable information about the specimen, such as lat/ 
> long.
> One can also develop and inherit other ontologies into CDAO to  
> provide more sophisticated concepts for specific applications and  
> annotations.
>
>
>> CDAOers: what are status and plans for describing the parts of an
>> alignment right now, and is there support, current or planned, for
>> partitions / segments of an alignment?
>
> Current CDAO version has already incorporated Julie's Multiple  
> Alignment Ontology (MAO; Thompson et al., 2005).
> MAO presents concepts such as "domain" and "subalignment", I suppose  
> they can be used in this context.
>
> Ciao,
> Francisco
>
>
>
> -- 
> Prof. Francisco Prosdocimi, PhD
> -----------------------------
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