[Tdwg-phylo] Publishing a tree in RDF

Arlin Stoltzfus arlin at umd.edu
Tue Oct 19 18:58:57 CEST 2010


It sounds like you have the skills and interest to do this.  Our first  
goal is very modest: just assess what's possible given currently  
available tools.   I only know about one so far, which will translate  
a file into CDAO with the option to add it to a triple store.  A web  
server interface is here:


If you know about other tools, that would be great.

The next step (weeks from now) would be to look ahead to the future  
and identify gaps.  If you are interested, all you need to do is to  
sign up for TDWG twiki access (if you don't have it already) and start  


On Oct 19, 2010, at 12:33 PM, Chris Baron wrote:

> Hi,
> My name is Chris Baron - a software developer, computer science  
> graduate student interested in linked data, working in BioSync at  
> the Field Museum on tree visualization.  I have a few ideas on how  
> to publish trees in RDF (have even created a tool to do so) and  
> would like to speak to Biologists about how their data exists at  
> publication so I can form a proper solution.
> On Tue, Oct 19, 2010 at 5:00 AM, <tdwg-phylo-request at lists.tdwg.org>  
> wrote:
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> Today's Topics:
>   1. publishing trees in CDAO as linked open data? (Arlin Stoltzfus)
> ----------------------------------------------------------------------
> Message: 1
> Date: Mon, 18 Oct 2010 12:32:39 -0400
> From: Arlin Stoltzfus <arlin at umd.edu>
> Subject: [Tdwg-phylo] publishing trees in CDAO as linked open data?
> To: CDAO list <cdao-discuss at lists.sourceforge.net>, Phylogenetics
>        Standards       Interest Group <tdwg-phylo at lists.tdwg.org>
> Message-ID: <BAAFA68C-2622-409A-B530-1CABADC36016 at umd.edu>
> Content-Type: text/plain; charset="US-ASCII"; format=flowed; delsp=yes
> Dear all--
> At the Biodiversity Information Standards (TDWG) meeting last month, a
> sub-group of the phylogenetic standards working group started a
> project to assess "current best practices for publishing trees
> electronically".   At present, probably the best way to publish a tree
> is to use the TreeBASE submission process, which makes it possible to
> upload a NEXUS file and create associations of OTUs with taxon IDs,
> and of data rows with accessions, and so on.  But there are also some
> other possibilities.  The preliminary report is being assembled here:
>   http://wiki.tdwg.org/twiki/bin/view/Phylogenetics/LinkingTrees2010
> Our plan is (over the next 6 weeks) to get feedback on this
> preliminary report, then analyze the results and prepare a more
> extensive report for publication.
> One possibility that we haven't examined yet is to publish a tree
> electronically by rendering it in RDF in the language of CDAO
> (Comparative Data Analysis Ontology) and then contributing it to the
> Linked-Open-Data cloud in some way.
> Does anyone out there want to explore this idea and contribute the
> results to the TDWG project?   If so, please let me know.
> Arlin
> -------
> Arlin Stoltzfus (arlin at umd.edu)
> Fellow, IBBR; Adj. Assoc. Prof., UMCP; Research Biologist, NIST
> IBBR, 9600 Gudelsky Drive, Rockville, MD
> tel: 240 314 6208; web: www.molevol.org
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> End of tdwg-phylo Digest, Vol 2, Issue 3
> ****************************************
> -- 
> Chris Baron
> <ATT00001.txt>

Arlin Stoltzfus (arlin at umd.edu)
Fellow, IBBR; Adj. Assoc. Prof., UMCP; Research Biologist, NIST
IBBR, 9600 Gudelsky Drive, Rockville, MD
tel: 240 314 6208; web: www.molevol.org

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