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

[Matt <dia...@gm...>]

Will there be other nodes/places to add lat/long at?

Lat/long on cells seems to be problematic in some ways, though it's
preferable to attaching it to row segments.  For one, it fails for
practically all morphological matrices in which OTUs have many
specimens.  For sequences there are also scenarios where a cell may be
derived from many specimens (consensus sequences).  I suppose though
that you could add many lat/longs to one cell (through specimens?)?

Matt

On Sat, Feb 13, 2010 at 11:01 AM, Rutger Vos <rut...@gm...> wrote:
> OK, maybe it is better to attach it to the OTU, I hadn't really
> considered that because in the db the coordinates are attached to row
> segments, but I suppose this makes more sense.
>
> On Fri, Feb 12, 2010 at 11:38 PM, Hilmar Lapp <hl...@ne...> wrote:
>> (cross-posting to cdao re: alignment partitions)
>>
>> On Feb 11, 2010, at 11:49 PM, Rutger Vos wrote:
>>
>>> I have added lat/lon as semantic annotations on individual cells using
>>> DwC:DecimalLatitude and DwC:DecimalLongitude. [...]
>>>
>>> Conceivably, verbosity could be reduced by attaching the annotations
>>> on <seq> elements instead, but i) although multiple <seq> elements are
>>> allowed "in principle", I don't think any of our tools actually
>>> support this; ii) cdao has no concept of row segments, so the
>>> annotations would be lost if we transformed to nexml to rdf.
>>
>> 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?
>>
>> 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?
>>
>>        -hilmar
>>
>> --
>> ===========================================================
>> : Hilmar Lapp  -:- Durham, NC -:- informatics.nescent.org :
>> ===========================================================
>>
>>
>>
>>
>
>
>
> --
> Dr. Rutger A. Vos
> School of Biological Sciences
> Philip Lyle Building, Level 4
> University of Reading
> Reading
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> Tel: +44 (0) 118 378 7535
> http://www.nexml.org
> http://rutgervos.blogspot.com
>
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