[Tdwg-phylo] Publishing a tree in RDF

[Chris Baron]

I've written a plugin to transform relational database data into RDF :
http://www.web2py.com/semantic

If anyone keeps their data in a relational database, this would be useful.

On Tue, Oct 19, 2010 at 11:58 AM, Arlin Stoltzfus <arlin at umd.edu> wrote:

> Chris--
>
> 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:
>
>   http://www.cs.nmsu.edu/~cdaostore/phylows.php<http://www.cs.nmsu.edu/%7Ecdaostore/phylows.php>
>
> 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 working.
>
> Arlin
>
> 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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>>   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
> <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
>
>


-- 
Chris Baron
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