On Wed, Oct 20, 2010 at 5:00 AM,
<tdwg-phylo-request@lists.tdwg.org> wrote:
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Today's Topics:
1. Re: Publishing a tree in RDF (Hilmar Lapp)
----------------------------------------------------------------------
Message: 1
Date: Tue, 19 Oct 2010 17:27:21 -0400
From: Hilmar Lapp <hlapp@nescent.org>
Subject: Re: [Tdwg-phylo] Publishing a tree in RDF
To: Chris Baron <topher.baron@gmail.com>
Cc: "tdwg-phylo@lists.tdwg.org" <tdwg-phylo@lists.tdwg.org>
Message-ID: <FE252B2A-D7C2-4873-B5B0-4695D382CABE@nescent.org>
Content-Type: text/plain; charset="us-ascii"
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@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@lists.tdwg.org> wrote:
>> Send tdwg-phylo mailing list submissions to
>> tdwg-phylo@lists.tdwg.org
>>
>> To subscribe or unsubscribe via the World Wide Web, visit
>> http://lists.tdwg.org/mailman/listinfo/tdwg-phylo
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>> tdwg-phylo-request@lists.tdwg.org
>>
>> You can reach the person managing the list at
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>>
>> When replying, please edit your Subject line so it is more specific
>> than "Re: Contents of tdwg-phylo digest..."
>>
>>
>> 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@umd.edu>
>> Subject: [Tdwg-phylo] publishing trees in CDAO as linked open data?
>> To: CDAO list <cdao-discuss@lists.sourceforge.net>, Phylogenetics
>> Standards Interest Group <tdwg-phylo@lists.tdwg.org>
>> Message-ID: <BAAFA68C-2622-409A-B530-1CABADC36016@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@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@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@lists.tdwg.org
> http://lists.tdwg.org/mailman/listinfo/tdwg-phylo
--
===========================================================
: Hilmar Lapp -:- Durham, NC -:- informatics.nescent.org :
===========================================================
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