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RE: ontology specs for self-publishing experiment

From: Miller, Michael D (Rosetta) <Michael_Miller@Rosettabio.com>
Date: Wed, 5 Jul 2006 10:38:50 -0700
To: "Eric Neumann" <eneumann@teranode.com>, "AJ Chen" <canovaj@gmail.com>
cc: "w3c semweb hcls" <public-semweb-lifesci@w3.org>
Message-ID: <E1FyBOD-0000W4-Nk@maggie.w3.org>
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 
Lead Software Developer 
Rosetta Biosoftware Business Unit 
www.rosettabio.com 

-----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 experiment



	
	
	AJ,
	
	
	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
(http://esw.w3.org/topic/HCLS/ScientificPublishingTaskForce?action=Attac
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.
	
	
	cheers,
	Eric





		From: AJ Chen <canovaj@gmail.com
<mailto:canovaj@gmail.com?Subject=Re%3A%20ontology%20specs%20for%20self-
publishing%20experiment&In-Reply-To=%253C70055a110606251600m469b7d63t405
579e7a61e7ef8%40mail.gmail.com%253E&References=%253C70055a110606251600m4
69b7d63t405579e7a61e7ef8%40mail.gmail.com%253E> > 
		Date: Sun, 25 Jun 2006 16:00:23 -0700
		Message-ID:
<70055a110606251600m469b7d63t405579e7a61e7ef8@mail.gmail.com> 
		To: public-semweb-lifesci@w3.org
<mailto:public-semweb-lifesci@w3.org?Subject=Re%3A%20ontology%20specs%20
for%20self-publishing%20experiment&In-Reply-To=%253C70055a110606251600m4
69b7d63t405579e7a61e7ef8%40mail.gmail.com%253E&References=%253C70055a110
606251600m469b7d63t405579e7a61e7ef8%40mail.gmail.com%253E>  
		I added the first draft of specs for the ontology being
developed for
		self-publishing experiment. see the link on the task
wiki page -
	
http://esw.w3.org/topic/HCLS/ScientificPublishingTaskForce
<http://esw.w3.org/topic/HCLS/ScientificPublishingTaskForce> 

		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.

		Best,
		AJ



	
	

	Eric Neumann, PhD

	co-chair, W3C Healthcare and Life Sciences,

	and Senior Director Product Strategy

	Teranode Corporation

	83 South King Street, Suite 800

	Seattle, WA 98104

	+1 (781)856-9132

	www.teranode.com 
Received on Wednesday, 5 July 2006 17:42:31 GMT

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