Re: new use case for SPE ontology: PlosOne's Topaz publishing platform

This is fantastic news, AJ!

Having one of the major STM publishers make a commitment to provide  
new, SWTech and ontology aware publishing applications with a UI that  
makes this advanced publishing technology accessible to all authors  
is an absolute pre-requisite to making 21st century techniques for  
knowledge discovery available to all investigators.  One would also  
hope the extra value provided by such advanced scientific publication  
environments can help to answer the question posed by STM publishers  
as to how they can re-orient their business models, if they are no  
longer allowed to fall-back on the revenue provided by "locked down"  
IP-based content.

I would strongly suggest if there is any component of Amit's proposed  
system that includes ontology-based annotation/description of  
research data, serious consideration be given to reviewing the  
systems being assembled to utilize the PaTO and OBI OBO Foundry  
ontologies designed to formalize phenotype traits and investigation  
details (protocols, assays, devices, reagents, environmental factors,  
etc.), respectively.  A very large assembly of experts across many  
fields of biomedical research - including many associated with The  
Gene Ontology effort over the years - have invested much time into  
creating these formal semantic frameworks.  As we've discussed, OBI/ 
FuGO is seeking to include other such efforts such as EXPO.  I've  
also been lobbying for review of SWAN and SPE.  Alan Ruttenberg and  
Trish Whetzel would be able to provide more detail on how OBI/FuGO  
could be made to work in such a scenario.  Chris Mungall and  
colleagues could provide more details on the use of PaTO, though a  
new Wiki they've started includes much of the required detail (http:// 
bioontology.org/wiki/index.php/PATO:About), including a BNF  
description of how the PaTO formalism is to be applied.

Remember, OBI/FuGO and PaTO are both being provided in OWL, so they  
are by their nature SWTech ready.  Whether or not the dialect of OWL  
being used fits the needs of efforts underway here in the W3C SW  
HCLSIG is a question well worth discussing, documenting, and passing  
on to the respective ontology curators.  They will certainly want to  
do what they can to be applicable to our objectives here, as sharing  
and interoperability are at the CORE of their objectives.

If this PLoS effort - and others that are also underway, as well as  
those that follow - is implemented correctly, we'll no longer have to  
see valuable data which publishers even make the effort to put online  
- the oxymoronically named "supplemental data/info" - lost the nether- 
world of the net as yet another unstructured, semantically  
unspecified data dustbin.

Cheers,
Bill


On Sep 4, 2006, at 2:25 PM, AJ Chen wrote:

> Exciting update for scientific publishing task: I met with Amit  
> Kapoor who heads the Topaz project under Plos. They are building a  
> new publishing platform for PlosOne, http://www.plosone.org/, a new  
> open access journal from Plos. Amit is interested in using ontology  
> and semantic web technology to add new features to Topaz software,  
> which is also open source.  We discussed the possibility of using  
> SPE ontology and collaboration.  It looks very promising! Topas  
> publishing platform has an architecture that can implement  
> community-supported ontology like SPE for scientific publishing.  I  
> think this is a very concrete use case.  I welcome any suggestion  
> as how to pursue this use case so that we can really develop SPE  
> ontology to something with practical use right away.
>
> www.web2express.org/demo/ demonstrates another use case. You may  
> take a look at it if you haven't done so.  I'll appreciate any  
> comment.
>
>
> AJ
> -- 
> AJ Chen, PhD
> http://web2express.org

Bill Bug
Senior Research Analyst/Ontological Engineer

Laboratory for Bioimaging  & Anatomical Informatics
www.neuroterrain.org
Department of Neurobiology & Anatomy
Drexel University College of Medicine
2900 Queen Lane
Philadelphia, PA    19129
215 991 8430 (ph)
610 457 0443 (mobile)
215 843 9367 (fax)


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