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Re: Questions about SPE ontology

From: William Bug <William.Bug@DrexelMed.edu>
Date: Tue, 29 Aug 2006 05:20:33 -0500
Message-Id: <533D1836-8375-43A0-87DD-398F9DE3836B@DrexelMed.edu>
Cc: public-semweb-lifesci@w3.org
To: Marco Brandizi <brandizi@ebi.ac.uk>
Hi Marco,

Many thanks for your substantive remarks regarding the details of  
applying RDF +/- OWL to this particular issue.  These are very  
important points to flesh out, and your experience obviously provides  
valuable insight on the problem.

Regarding the other knowledge representation projects related to the  
encapsulation of investigation-related information, in addition to  
the two you mention - SWAN and EXPO - there are also - in no  
particular order:
	1) the community-based Ontology of Biomedical Investigation (OBI/ 
FuGO) effort;
	2) the ExperiBase project;
	3) the proteomics-related ontologies in the Charelston Core project  
from Xiaoshu Wang and his colleagues;
	4) the work Matthias Samwald and colleagues have been doing on The  
Semantic Synapse project;
	5) several efforts related to this topic from the bioimaging  
community which are under consideration for inclusion in the OBI effort:
		a) DICOM [http://www.rsna.org/Technology/DICOM/dicom.cfm];
  		b) the Neuroimaging Informatics Technology Initiative [NIfTI -  
http://nifti.nimh.nih.gov/];
		c) work from the fMRI Data Center (http://www.fmridc.org/f/fmridc/ 
dmt/index.html);
  		d) the Biomedical Research Information Network (BIRN) [XCEDE  
schema - http://www.nbirn.net/Resources/Downloads/XCEDE/index.htm];
		e) the RSNA-sponsored RadLex project [http://www.rsna.org/RadLex/]);
		f) see also http://bioontology.org/wiki/index.php/ 
Workshop_on_Ontology_of_Images;
	6) the software classification effort sponsored by the NIH NCBCs  
(http://www.na-mic.org/Wiki/index.php/ 
SDIWG:NCBC_Software_Classification);
	7) BrainML (http://brainml.org).

These employ a range of formal syntactical implementations from XML  
Schemas on through OWL-based ontologies.

I've taken the liberty of adding these to the SPE Wiki page cited below.

OBI, by the way, is the proposed new name for what was formerly known  
as FuGO, which in the course of broadening it's community-outreach  
and inclusion has found the need to broaden the scope of the  
ontology.  Larisa N. Soldatova who is the lead author on the EXPO  
ontology has been interacting with the OBI/FuGO group with an eye  
toward interfacing/integrating EXPO with OBI.

I expect I'm preaching to the converted here on this issue, but  
obviously, as Marco points out, ensuring these efforts have  
commensurate, formal semantic implementations will be an absolute pre- 
requisite for these individual efforts to fully realize their  
intended goals.  This does not necessarily imply they all must use  
the same normative syntax or link to a single, foundational ontology  
but provisions *MUST* be made to ensure they are algorithmically  
commensurate, if they are to contribute to the overall semantically- 
specified, biomedical investigation-related knowledge ecosystem.

Cheers,
Bill


On Aug 29, 2006, at 3:03 AM, Marco Brandizi wrote:

>
> Sorry, I meant to send the message below to the mailing list... not  
> only to the sender...
>
> Thanks to AJ for the prompt reply.
>
>
> AJ Chen wrote:
>> I uploaded one mock example for each of the class (object) of the  
>> SPE ontology to the wiki at http://esw.w3.org/topic/HCLS/ 
>> ScientificPublishingTaskForce.  Hope these
> ...
>> The examples are created from the demo application at http:// 
>> web2express.org/demo/. You can take a look at the demo to see how  
>> easy it is to publish experiment data and research tool information.
>
> Hi all,
>
> I've been following the developments of SPE ontology and applications
> for a while, since my PhD Project is related to the idea of formal
> representation of experiments and the knowledge belonging to  
> experiment
> cycle (hyphotesis, conclusions, people and their interests, etc.).
>
> I'd like to ask some questions about the SPE project.
>
> - So far there are similar ongoing projects:
>   - http://swan.mindinformatics.org/
>   - http://expo.sourceforge.net/
>
> I'd like some words of comparison of the above projects (expecially  
> from
> the respective authors) and about possible plans for joining the
> efforts. What are the differences in main entities, relations,  
> contexts
> and communities in which the projects have started?
>
> - Is SPE defined in RDF or is OWL used as well, so that some inference
> capabilities of OWL could be exploited?
>
>
>
> - Concerning SPE, I guess that Hypothesis and Conclusion are still  
> under
> development (they're mentioned in Requirements document but not in 0.2
> specification), what shape would these entities have? I read from
> requirements:
>
>> Note: Hypothesis, Dada and Conclusion may be simply represented by
>> string or literal, which is sufficient for search engine application.
>> But, it may offer advantages for some applications if they are
>> represented as object. If anyone has an application that requires
>> object representation for Hypothesis, Dada and Conclusion of an
>> experiment, please contribute a use case and define the objects
>
> I'd like to exchange opinions about this point. Having a simple text,
> plus some meta-data, as an hypothesis or a conclusion ("claims" in the
> follow), is simple and may be somehow useful. However, having further
> formalization could be even more useful, particularly modeling a  
> claim,
> as a triple/statement would allow to re-use such pieces of  
> knowledge in
> a semantic-web fashion (machine-readable knowledge, inference etc.).
>
> But I'm feeling that handling statements in RDF world is not so easy,
> expecially if ones wants to do something at the level of OWL and
> inference. I am attempting to at least trace who is claiming what and
> why, by means of named graphs and the good NG4J library for Jena  
> [1]. It
> is somehow useful and allows selection of sub-sets of statements [2],
> however, it is not so much clear how the idea of quadlets could be
> integrated with the upstream layers of OWL and layers, and of course
> with the DL theory (C-OWL? Modal DL? Simple filters that, at the level
> of named graphs and RDF define what is "true" and can be used upstream
> with OWL? Is there some standardization effort?).
>
> Opinions and suggestions welcome.
>
> Cheers.
>
>
> [1] http://www.wiwiss.fu-berlin.de/suhl/bizer/ng4j/
> [2]http://www.wiwiss.fu-berlin.de/suhl/bizer/pub/Bizer-TriQLP- 
> Browser-SWPW.pdf
>
> -- 
>
> ====================================================================== 
> =========
> Marco Brandizi <brandizi@ebi.ac.uk>
> http://gca.btbs.unimib.it/brandizi
>
>
>

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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Received on Tuesday, 29 August 2006 10:20:53 GMT

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