Re: HCLSig July 6 Teleconference Agenda

Hi AJ,

Another project of relevance to this topic obviously is the  
Experibase project (http://experibase.mit.edu/).

So it appears, at a minimum, SPE should in some way be informed by  
the work being done on the following projects:

	1) FuGO ([http://fugo.sourceforge.net/]) & FuGE ([http:// 
fuge.sourceforge.net/])

	2) Reporting Structures for Biological Investigations (RSBI [http:// 
www.mged.org/Workgroups/rsbi/rsbi.html])
	
	3) EXPO ([http://sourceforge.net/projects/expo])

	4) Experibase ([http://experibase.mit.edu/])

	5) Biological Imaging (a subset)
		a) Open Microscopy Environment ([http://www.openmicroscopy.org/])
		b) Neuroimaging Informatics Technology Initiative ([http:// 
nifti.nimh.nih.gov/])
		c) DICOM
		d) BIRN XCEDE Schema (http://www.nbirn.net/Resources/Downloads/ 
XCEDE/index.htm)
		e) fMRICD Data Management tools (http://www.fmridc.org/f/fmridc/dmt/ 
index.html?id=SUCbLuWt)

	6) NCBC Biomedical Software Classification ([http://na-mic.org/Wiki/ 
index.php/SDIWG:NCBC_Software_Classification])
		* something critical to the reporting of most biological imaging data

Cheers,
Bill
		


On Jul 7, 2006, at 4:10 PM, AJ Chen wrote:

> >1. You may use owl:sameAs to indicate the same experiment published
> >in two different ontologies.
>
> I think you are missing my point. We have other ontologies, like  
> the biological pathways exchange language (BioPAX), that describe  
> biological information -- in the case of BioPAX it is molecular  
> interactions and pathways. This ontology does NOT describe an  
> experiment. Datafiles that use this ontology contain instances of  
> such classes like "protein", "molecularInteraction", "pathway".  
> These are not experiments.
> You should find a way to connect (with an edge between two nodes)  
> such RDF/OWL graphs to the RDF/OWL of your experiment ontology.  
> Your ontology should, in my opinion, define a RDF property that can  
> act as such a connection.
>
> Thanks for correcting me. Your suggestion to have a property to   
> uniquely identify (and correlate) the resource of main concepts of  
> an experiment. This is similar to correlate the materials and tools  
> used in the protocols or procedures.  The "Protocol" class has an  
> property called "productUsed", which should have value as URI of  
> the product (reagent or any tool).  If product providers can define  
> and publish their product resources, then anyone will know exactly  
> what tools were used by the experiment assuming the tools are  
> listed for the published experiment.
>
> >2. SPE uses many properties defined in FOAF, but I find it
> >difficult to re-use its classes like Person, Group, Organization
> >because they miss some of the properties required by SPE's
> >corresponding classes.How do you re-use a FOAF class if the class
> >you need has additional properties?
>
> You could simply add the properties you need without a problem. Or  
> (if you want to leave the original FOAF class untouched for some  
> reason), you could define a subclass for each of the classes of  
> FOAF, and make your additions to these subclasses. (e.g. a subclass  
> "scientific-project" of "foaf:project", a subclass "researcher" of  
> "foaf:person" and so on).
>
> This is what I thought. In any case, a new class is needed to make  
> clear what extra properties it has.  Since the scope of this task  
> is to provide general terms for all research areas, scientifc or  
> social or political or whatever, better choice of class names are  
> "Project", "Researcher", "Experiment", etc.
>
> AJ

Bill Bug
Senior 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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