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RE: ontology specs for self-publishing experiment

From: Trish Whetzel <whetzel@pcbi.upenn.edu>
Date: Thu, 6 Jul 2006 12:45:54 -0400 (EDT)
To: "Miller, Michael D (Rosetta)" <Michael_Miller@Rosettabio.com>
cc: Tim Clark <twclark@nmr.mgh.harvard.edu>, w3c semweb hcls <public-semweb-lifesci@w3.org>, SWAN Team <swan-team@mind-informatics.org>
Message-ID: <Pine.LNX.4.61.0607061242470.22595@hera.pcbi.upenn.edu>

Hi all,

As a terribly simple question, is it possible to take the actual FuGE-ML 
that is generated on a per instance reporting of an 
experiment/study/investigation and then convert than to RDF for use 
with semantic web technologies?


> 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
> stretch.
> cheers,
> Michael
> Michael Miller
> Lead Software Developer
> Rosetta Biosoftware Business Unit
> www.rosettabio.com
> 	-----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.
> 	Cheers,
> 	Bill
> 	On Jul 6, 2006, at 9:23 AM, Tim Clark wrote:
> 		Michael
> 		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.
> 		Best
> 		Tim
> ------------------------------------------------------------------------
> ------
> 		Tim Clark 617-947-7098 (mobile)
> 		Director of Research Programs
> 		Harvard University Initiative in Innovative Computing
> 		60 Oxford Street, Cambridge, MA 02138
> 		http://iic.harvard.edu
> 		Director of Informatics
> 		MassGeneral Institute for Neurodegenerative Disease
> 		114 16th Street, Charlestown, MA 02129
> 		http://www.mindinformatics.org
> ------------------------------------------------------------------------
> ------
> 		On Jul 5, 2006, at 7:38 PM, Miller, Michael D (Rosetta)
> wrote:
> 			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
> 	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)
> 	Please Note: I now have a new email - William.Bug@DrexelMed.edu
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Received on Thursday, 6 July 2006 17:50:52 UTC

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