Hi
Eric,
Just
wanted to point out how this overlaps with the current FuGE (http://fuge.sourceforge.net/) and FUGO
(http://fugo.sourceforge.net/)
efforts. These are focused on systems biology and are intended to provide
the underpinnings of reporting gene _expression_, gel, mass spec, and -omics
experiments/investigations.
The
goal of FuGE (Functional Genomic Experiments) is for the most part to
provide:
"a. Publishing
Protocols
b. Publishing Regants and
Products
c. Stating the Hypothesis
(and model using RDF) that is being tested by the experiment; this includes
which citations are supportive or alternative to ones
hypothesis
d. Publishing Experimental
Data (possibly as RDF-OWL aggregates and tables)
e. Articulating the Results and
Conclusions; specifically, whether the experiment refutes or supports the
central Hypothesis (most of us agree we cannot 'prove' a hypothesis, only
disprove it)"
But it is a UML based model that will then have an equivalent XML Schema
generated. The advantage, I think, this approach has over a pure ontology
representation is that it better captures the actual work-flow of these
experiments for the interchange of data and annotation. That being said,
the UML model incorporates a way to annotate the class objects with ontology
Individuals with a reference to the Individual's RDF class and its
ontology. The UML model adds the additional semantics of identifiers
(typically expressed as LSIDs) that allows tying reference
elements generated in the XML Schema to the full definition of an
object. So a biological sample can be fully described in one document then
referenced by a treatment that incorporates it into a prep.
So,
for instance, typically a hypothesis is specific to the particular
experiment/investigation. In FuGE, it is simply a Description class with a
text attribute associated by a Hypothesis association to the Investigation
class. But in the XML document, this specific Description can be annotated
by references to ontologies that allow hypothesis to be translated to RDF
upon import. We used the OMG Ontology Definition Metamodel specification
mapping of Individuals from OWL/RDF to UML so that these could then be mapped
back to an OWL/RDF representation for reasoning (http://www.omg.org/ontology/ontology_info.htm#RFIs,RFPs).
FUGO
is intended to become part of the OBO ontologies and FUGO's goal is to provide
general annotation terms for these type of experiments.
cheers,
Michael
Michael Miller
-----Original Message----- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Eric Neumann Sent: Monday, July 03, 2006 6:57 AM To: AJ Chen Cc: w3c semweb hcls Subject: Re: ontology specs for self-publishing experiment
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Title: Message
- ontology specs for self-publishing experiment AJ Chen
- Re: ontology specs for self-publishing ex... Eric Neumann
- RE: ontology specs for self-publishin... Miller, Michael D (Rosetta)
- Re: ontology specs for self-publi... William Bug
- Re: ontology specs for self-p... Alan Rector
- Re: Nonsemantic Identifi... Adrian Walker
- Re: ontology specs for s... Phillip Lord
- Re: ontology specs f... Alan Rector
- Re: ontology spe... Trish Whetzel
- Re: ontology spe... Alan Ruttenberg
- Ontology entity ... William Bug
- RE: Ontology ent... Nigam Shah
- Distributed onto... Mark Musen