[Tdwg-phylo] Publishing a tree in RDF

Wed Oct 20 20:43:38 CEST 2010

Yes, Triplify was the inspiration to the web2py plugin.

Also, I've been working on a phylogentic tree editor called tred.
http://code.google.com/p/tred/

Its still a little rough, but usable/stable.  Realizing that many Biologists
do not have their data in a relational database one could upload their
newick, nexus, etc to tred, edit the tree then export to CDAO.  I'd be happy
to add functionality to tred for this purpose if people will use it.

On Wed, Oct 20, 2010 at 5:00 AM, <tdwg-phylo-request at lists.tdwg.org> wrote:

> Send tdwg-phylo mailing list submissions to
>        tdwg-phylo at lists.tdwg.org
>
> To subscribe or unsubscribe via the World Wide Web, visit
>        http://lists.tdwg.org/mailman/listinfo/tdwg-phylo
> or, via email, send a message with subject or body 'help' to
>        tdwg-phylo-request at lists.tdwg.org
>
> You can reach the person managing the list at
>        tdwg-phylo-owner at lists.tdwg.org
>
> When replying, please edit your Subject line so it is more specific
> than "Re: Contents of tdwg-phylo digest..."
>
>
> 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 at nescent.org>
> Subject: Re: [Tdwg-phylo] Publishing a tree in RDF
> To: Chris Baron <topher.baron at gmail.com>
> Cc: "tdwg-phylo at lists.tdwg.org" <tdwg-phylo at lists.tdwg.org>
> Message-ID: <FE252B2A-D7C2-4873-B5B0-4695D382CABE at 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 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:
> >> Send tdwg-phylo mailing list submissions to
> >>        tdwg-phylo at lists.tdwg.org
> >>
> >> To subscribe or unsubscribe via the World Wide Web, visit
> >>        http://lists.tdwg.org/mailman/listinfo/tdwg-phylo
> >> or, via email, send a message with subject or body 'help' to
> >>        tdwg-phylo-request at lists.tdwg.org
> >>
> >> You can reach the person managing the list at
> >>        tdwg-phylo-owner at lists.tdwg.org
> >>
> >> 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 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
> >>
> >>
> >>
> >> ------------------------------
> >>
> >> _______________________________________________
> >> tdwg-phylo mailing list
> >> tdwg-phylo at lists.tdwg.org
> >> http://lists.tdwg.org/mailman/listinfo/tdwg-phylo
> >>
> >>
> >> 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 :
> ===========================================================
>
>
>
> -------------- next part --------------
> An HTML attachment was scrubbed...
> URL:
> http://lists.tdwg.org/pipermail/tdwg-phylo/attachments/20101019/e5594996/attachment-0001.html
>
> ------------------------------
>
> _______________________________________________
> tdwg-phylo mailing list
> tdwg-phylo at lists.tdwg.org
> http://lists.tdwg.org/mailman/listinfo/tdwg-phylo
>
>
> End of tdwg-phylo Digest, Vol 2, Issue 5
> ****************************************
>

-- 
Chris Baron
-------------- next part --------------
An HTML attachment was scrubbed...
URL: http://lists.tdwg.org/pipermail/tdwg-phylo/attachments/20101020/5e4f0d6d/attachment.html 