[Tdwg-phylo] Publishing a tree in RDF

Chris Baron topher.baron at gmail.com
Tue Oct 19 18:33:08 CEST 2010


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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Chris Baron
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