Re: [Treebase-devel] search by DOI

[Carl B. <cbo...@gm...>]

Hi Hilmar, list,

Good point, I see the importance of not departing from the standards.

I wouldn't phrase this as an "absence of data", but rather as fundemental
metadata describing the kind of data provided -- i.e. is the data just a
topology, is it a phylogram where branch lengths describe mutational steps,
or is it a chronogram/ultrametric tree where branch lengths are calibrated
into units of time?  (notably, knowing whether a tree was ultrametric/time
calibrated or if branch lengths were in units of mutational steps would be
very useful thing to know through the API).  I'm not quite sure why this is
any less metadata while things like tb:kind.tree (i.e. Species Tree  / gene
tree), or tb.quality, etc.



-Carl

On Mon, Feb 20, 2012 at 8:33 PM, Hilmar Lapp <hl...@ne...> wrote:

> I agree this would be quite useful. At present all PhyloWS query
> attributes map directly to attributes of the data. Querying presence of
> absence of would be a departure from that.
>
> I think ideally I'd like to see this supported through CDAO terms. Whether
> a tree has branch lengths or not is a piece of semantic metadata about the
> tree. A tree with branch lengths could be declared as an Instance of the
> subclass of trees that also have branch lengths.
>
> -hilmar
>
> On Feb 20, 2012, at 8:41 PM, Carl Boettiger wrote:
>
> Hi Treebase developers,
>
> How difficult would it be to include the ability to restrict phylows API
> queries to only trees having branch length data?  Can this be done already?
> If not, is it a straight forward modification?  I would find this very
> useful (and would reduce my load on the server, since otherwise I have to
> do pull down each tree and check if it has this data...)
>
> Many thanks,
>
> Carl
>
> On Fri, Feb 17, 2012 at 10:32 AM, Rutger Vos <rut...@gm...> wrote:
>
>> Hi all,
>>
>> I've made some recent enhancements to the search facilities:
>>
>> - there was a bug in searching by tree quality, this has now been
>> corrected
>>
>> - we can now search by doi, it is an option in the pull down menu on the
>> study search page, and has also been added to the PhyloWS API:
>>
>> http://purl.org/phylo/treebase/dev/phylows/study/find?query=prism.doi=
>> "10.1016/j.ympev.2009.03.021"
>>
>> - I also added buttons to the twitter account and the mendeley group.
>>
>> Maybe we can push these things to production?
>>
>> Rutger
>>
>> --
>> Dr. Rutger A. Vos
>> Bioinformaticist
>> NCB Naturalis
>> Visiting address: Office A109, Einsteinweg 2, 2333 CC, Leiden, the
>> Netherlands
>> Mailing address: Postbus 9517, 2300 RA, Leiden, the Netherlands
>> http://rutgervos.blogspot.com
>>
>>
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>
>
> --
> Carl Boettiger
> UC Davis
> http://www.carlboettiger.info/
>
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-- 
Carl Boettiger
UC Davis
http://www.carlboettiger.info/