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RE: ontology specs for self-publishing experiment

From: Miller, Michael D (Rosetta) <Michael_Miller@Rosettabio.com>
Date: Thu, 6 Jul 2006 09:38:16 -0700
To: "Tim Clark" <twclark@nmr.mgh.harvard.edu>
cc: "w3c semweb hcls" <public-semweb-lifesci@w3.org>, "SWAN Team" <swan-team@mind-informatics.org>
Message-ID: <E1FyWs9-00059b-9Z@lisa.w3.org>
Hi Tim,
Essentially the idea of FuGE-OM is that it will be complete in itself as
a Platform Independent Model (in OMG/MDA terms) and will have a FuGE-ML
XML schema (a Platform Specific Model--PSM) generated by AndroMDA.  MGED
will (most likely) provide support in the form of a FuGEstk with most
likely Java and Perl PSM support.
It is possible that some group may want an RDF PSM version of FuGE!
It will soon be vetted through a process by PSI, MGED and any interested
parties and be available for extending into whatever life sciences
domains.  PSI has extended it for GEL-OM
(http://psidev.sourceforge.net/gps/index.html), as a great example, and
work has started to extend it as MAGEv2.
FuGE provides the underpinnings for describing the flow of material and
data as protocols are applied, including annotation.  One thing to
remember is that the ontology support in FuGE is entirely neutral as to
what ontologies these ontology individuals are referencing--no more
information about particular ontologies or how ontology classes are
related belong in a FuGE derived document except the URI to get to the
referenced class if it is in an existing ontology.  It is expected that
applications importing FuGE documents will either have or look up the
information on these referenced ontologies after import if the
application wishes to support knowledge based tools.  Use of FuGE does
not mandate that an application be ontology aware, FuGE is a data and
annotation exchange specification.
It is hoped that in the different domains of life sciences that have a
need to describe experiments/studies/investigations, that FuGE provides
a good core model to extend into the domain-specific
data/material/protocols.  It is actually a mistake to mention FuGE
development and ontology development as needing to go together.  The
only real need the FuGE model needs as feedback is how well the Ontology
Individual support is modeled in UML.  
Then, I do believe, for best use of the FuGE model and its extensions,
great ontologies are needed and tools to take these references in a FuGE
document to go out to the semantic web and make connections and to allow
researchers to have ontologies to annotate their experiments to be
exported.  But FuGE development itself doesn't need awareness of this
ontology development effort.
I am always reminded of two observations, if one has a hammer,
everything looks like a nail and anything can be programmed in COBOL.
Not everything, I believe is best modeled as an ontology, in particular,
as I have said, the real life flow of a life science
experiment/investigation.  Yes, it can be done but it is an awkward
Michael Miller 
Lead Software Developer 
Rosetta Biosoftware Business Unit 

	-----Original Message-----
	From: William Bug [mailto:William.Bug@DrexelMed.edu] 
	Sent: Thursday, July 06, 2006 8:20 AM
	To: Tim Clark
	Cc: Miller, Michael D (Rosetta); Eric Neumann; AJ Chen; w3c
semweb hcls; SWAN Team
	Subject: Re: ontology specs for self-publishing experiment
	Dear Tim,

	I think this is an excellent idea - and comes at a very
propitious time.

	I would suggest including participants on the FuGO, PaTO, and
EXPO projects as well. 


	On Jul 6, 2006, at 9:23 AM, Tim Clark wrote:

		The FuGE project may have some interesting overlaps with
SWAN.  Current phase of SWAN is focused on construction of annotation
and publishing tools for semantically characterized hypotheses, claims,
findings, counterclaims, etc on digital resources in neuromedicine, at
the community level.  This is planned to be followed by a complementary
phase involving management and characterization of laboratory results
using an extension of the same ontology.  

		I propose we arrange mutual presentations and
discussions to see if any synergies exist such that we might take
advantage or each others' work. 



		Tim Clark 617-947-7098 (mobile)

		Director of Research Programs
		Harvard University Initiative in Innovative Computing
		60 Oxford Street, Cambridge, MA 02138

		Director of Informatics
		MassGeneral Institute for Neurodegenerative Disease
		114 16th Street, Charlestown, MA 02129

		On Jul 5, 2006, at 7:38 PM, Miller, Michael D (Rosetta)

			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
			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.
			Michael Miller 
			Lead Software Developer 
			Rosetta Biosoftware Business Unit 

			-----Original Message-----
			From: public-semweb-lifesci-request@w3.org
[mailto:public-semweb-lifesci-request@w3.org] 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

				This is a great start, and thanks for
taking this on! I would like to see this task force propose a conceptual
framework within the two months. It does not have to be final, but I
think we need to have others on the list review the ontologies
hFile&do=get&target=SPE_Specs.html) and requirements
(http://esw.w3.org/topic/HCLS/SciPubSPERequirements) you have proposed,
ask questions about them, and adjust/expand as needed.
				I think there has been good discussions
on this topic in the past, and I would also refer folks to the SWAN
paper by Gao et al.  http://www.websemanticsjournal.org/ps/pub/2006-17 .
This work is inline with with what Tim Clark has been proposing to the
group, and I think it is a useful model to consider. Perhaps we can
combine these efforts and propose a workable (demo anyone?) by the end
of summer...
				In terms of gathering more Scientific
Publishing of Experiments (SPE) requirements, I wanted to list some
items that appear to be inter-related and relevant:
				1. By Publishing experiments, one must
also consider (i.e., include in the ontology):
				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)
				2. Hypotheses should be defined in terms
of authorship (ala DC), what the proposed new concepts is, and what
(experimental) fact (or claim) is required to support it. It should also
refer to earlier hypotheses either by:
				a. extension of an earlier tested and
supported hypothesis: refinement
				b. similarity or congruence with another
untested hypothesis: supportive
				c. being an alternative to another
hypothesis, that will qualify itself through the refutation of the
earlier one: refutation
				This would allow one to define rules and
queries that can traverse the lineage of hypotheses (forwards and
backwards, similar to citations), and how one papers work can be related
to ongoing work on different fronts that have branched.
				3. "Publication" should be a specific
concept in SPE, that would serve to be the hub of DC metadata as well as
the above experimental data and hypotheses. Different non-disjoint
Publication "Roles" could be defined, such as  Peer-Reviewed,
Electronically-Published, Topic Review, and Follow-up Data. I would also
invite the folks interested in Clinical Publications to specify what
requirements they feel should be included, (e.g. regulatory
applications, Common Technical Document).
				I also think it would be useful if we
could add a Concept Map graphic for the proposed SPE ontology (class
relations mainly). Sometime ideas can get expressed faster to the larger
community using images.

				From: AJ Chen <canovaj@gmail.com
69b7d63t405579e7a61e7ef8%40mail.gmail.com%253E> > 
				Date: Sun, 25 Jun 2006 16:00:23 -0700
				To: public-semweb-lifesci@w3.org
				I added the first draft of specs for the
ontology being developed for
				self-publishing experiment. see the link
on the task wiki page -

				This specs document and the requiremnets
document are meant to be only the
				starting point for discussion.  I truly
hope more people in this group will
				participate in this open development
process, making comments or providing
				changes to the documents.

				While the ontology is being developed by
this community, I am going to
				develop a self-publishing tool that
implements the ontology, which allows
				you to try this new way of sharing
research information. With easy-to-use
				tools to demonstrate the benefits of
sharing and searching experiment
				information in semantic data format, it
will help attract more people to
				contribute to the development of the
ontology as well as the tools.


				Eric Neumann, PhD
				co-chair, W3C Healthcare and Life
				and Senior Director Product Strategy
				Teranode Corporation
				83 South King Street, Suite 800
				Seattle, WA 98104
				+1 (781)856-9132

	Bill Bug
	Senior Analyst/Ontological Engineer

	Laboratory for Bioimaging  & Anatomical Informatics
	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)

	Please Note: I now have a new email - William.Bug@DrexelMed.edu

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Received on Thursday, 6 July 2006 16:38:52 GMT

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