[Tdwg-phylo] Publishing a tree in RDF

[Hilmar Lapp]

Hi Chris - you probably know the Triplify project? http://triplify.org/

	-hilmar

On Oct 19, 2010, at 1:03 PM, Chris Baron wrote:

> 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
>
> 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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>> 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
>
>
>
>
> -- 
> Chris Baron
> _______________________________________________
> tdwg-phylo mailing list
> tdwg-phylo at lists.tdwg.org
> http://lists.tdwg.org/mailman/listinfo/tdwg-phylo

-- 
===========================================================
: Hilmar Lapp  -:- Durham, NC -:- informatics.nescent.org :
===========================================================



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