[Phylobase-devl] NeXML and R

Tue Aug 14 17:38:47 CEST 2012

Hi all,

  I agree with what Rutger and Hilmar suggest. As far as phylobase is
concerned, the tree format has currently a slot to store annotations
that was created with NeXML in mind. However, at this stage, it's not
used by anything other than the validation of the object, so it could
be used for the NeXML annotations.

  It would be great to complete NeXML support within NCL, as this
would provide a nice way to import NeXML objects into R given that
phylobase provides methods for converting objects to most commonly
used tree format in R. Unfortunately I can't really help with this
part given that I don't know C++ but I would be happy to write the
modifications that would be needed in phylobase.

  Cheers,
   -- François

On Tue, Aug 14, 2012 at 5:21 PM, Hilmar Lapp <hlapp at nescent.org> wrote:
> Hi Carl,
>
> I think from an interoperability and reusability standpoint, the best strategy would be to build out the support that has been started earlier in the Phylobase package. I believe the NeXML support in there started out using the XML support in R. One problem that ran into and sort of get stalled by is that the phylo4 data structure isn't yet prepared for storing arbitrary annotations, I think.
>
> NeXML support was started in NCL (NEXUS Class Library) in a Google Summer of Code project a few years back, but isn't complete and isn't in the main trunk. Completing that would hold lots of potential, too, though.
>
> I'm copying the nexml and phylobase developers lists.
>
>         -hilmar
>
> On Aug 14, 2012, at 7:41 AM, Rutger Vos wrote:
>
>> Hi Carl,
>>
>> thanks for writing in! Yes, it would be great if there was NeXML
>> support in R. I'm not actually an R programmer - though I'd like to
>> somehow absorb that ability over time, and would be willing to
>> advice/help out - but it is evident that there is a need.
>>
>> Ideally it would expose NeXML data in a way that is reasonably
>> compatible with the different phylogenetics packages for R (ape? ouch?
>> phylobase? treebase? I don't know the landscape that well). To me it
>> seems that there are the following possibilities:
>>
>> 1. a new, simple API just for reading and writing NeXML, which other
>> package authors can import
>>
>> 2. NeXML I/O in NCL (C++) is completed, package authors build on that,
>> perhaps by way of phylobase?
>>
>> 3. anarchy, different authors build their own NeXML parsers, each with
>> their own bugs (instead of all bugs in one place).
>>
>> The ideal scenario, I think, would be 2, but it would be harder than
>> 1. I vote against 3. By the way, Brian O'Meara does a lot in R, it
>> would be a good idea to solicit his opinion as well, especially in
>> relation to the DateLife R webservice he's nurturing.
>>
>> Best wishes,
>>
>> Rutger
>>
>> On Tue, Aug 14, 2012 at 2:10 AM, Carl Boettiger <cboettig at gmail.com> wrote:
>>> Dear TreeBASE developers,
>>>
>>> It appears that the NeXML format isn't currently supported in the R
>>> environment, but offers much richer information than the old nexus format,
>>> as exemplified by the treebase files under each.  As I've mentioned before
>>> on this list, I've written a little R package for accessing TreeBASE, which
>>> relies on nexus formats for compatibility with existing R packages.  I think
>>> this would be a great opportunity to introduce a NeXML format reader into R,
>>> and am trying to figure out where the best place is to start.  I think
>>> there's considerable NeXML expertise on this list, and was wondering if I
>>> might find anyone else interested in helping with this effort, or give some
>>> input to get me jump-started?
>>>
>>> I see that NeXML has C++, Java, PERL, Python, javascript and ruby
>>> implementations already, and I'm wondering if the best thing to do would be
>>> to wrap something like the C++ library, or start from scratch since R has a
>>> pretty solid XML library already.  Phylogenies in R are represented using a
>>> few different and mostly very crude data structures, and we could benefit a
>>> lot as R developers from a richer object -- but there's also a large
>>> community of legacy formats and software relying on those formats to
>>> support.  I could hack something together that worked, but I think I need a
>>> bit more community input to do this right.  Anyone interested?
>>>
>>> Carl
>>>
>>>
>>>
>>> --
>>> Carl Boettiger
>>> UC Davis
>>> http://www.carlboettiger.info/
>>>
>>>
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>>
>>
>>
>> --
>> 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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>> Exclusive live event will cover all the ways today's security and
>> threat landscape has changed and how IT managers can respond. Discussions
>> will include endpoint security, mobile security and the latest in malware
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>
> --
> ===========================================================
> : Hilmar Lapp  -:- Durham, NC -:- informatics.nescent.org :
> ===========================================================
>
>
>
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