Re: HCLSig July 6 Teleconference Agenda

Fri, 07 Jul 2006 23:49:31 -0700

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:


2) Reporting Structures for Biological Investigations (RSBI [http://www.mged.org/Workgroups/rsbi/rsbi.html])

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

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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