[open-science] HACKATHON-Semantic Web Identifiers for bioscience

Matt Jones jones at nceas.ucsb.edu
Fri Dec 2 20:08:59 UTC 2011

Hi Puneet,
So are you at Macquarie University with Alroy's PaleoDB group?  If so, you
might look up Josh Madin (http://acropora.bio.mq.edu.au/people/joshua-madin/)
who's on the faculty there at Macquarie, as he did a lot of work on
semantically annotating ecological data with our projects -- he used to be
at NCEAS -- and this involved building ontologies that reference biological
taxa.  Its still an interest of ours on the Semtools (
http://semtools.ecoinformatics.org) and SONet (
http://sonet.ecoinformatics.org) projects.  Josh wrote some good overview
papers on our work that might be relevant to you:

Madin, J., S. Bowers, M. Schildhauer, S. Krivov, D. Pennington, and F.
Villa. 2007. An ontology for describing and synthesizing ecological
observation data. Ecological Informatics 2:279-296. doi:

Madin, J. S., S. Bowers, M. P. Schildhauer, and M. B. Jones. 2008.
Advancing ecological research with ontologies. Trends in ecology &
evolution 23:159-68. doi: 10.1016/j.tree.2007.11.007.
We're also looking for a semantics postdoc or maybe a semantics engineer
right now for SONet if you know anyone that might be right for this kind of


Matt Jones
NCEAS, UC Santa Barbara

On Fri, Dec 2, 2011 at 10:53 AM, Puneet Kishor <punkish at eidesis.org> wrote:

> On Dec 2, 2011, at 1:46 PM, Matt Jones wrote:
> > Puneet --
> >
> > Just some relevant pointers... ..
> >
> > PS I was involved in discussions about paleodb.org when Alroy first
> > launched it at NCEAS; I'm happy to see its had such longevity and is
> > supporting such an effective open data community.
> > ..
> Thanks for the links Matt. I am learning a lot of new stuff (I am really a
> computers/semweb/REST kinda person) so I have miles to go in the taxonomy
> department, but I am looking forward to it.
> Alroy and others have done a fantastic job building and shepherding
> Paleodb, and its value is evident from the tremendous amount of research it
> has generated. I am glad to be supporting that work, while also think about
> how to add more value, offer more ways to access its information.
> --
> Puneet Kishor http://punkish.org
> science http://earth-base.org
> advocacy http://creativecommons.org
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