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RE: [Obo-relations] FuGE and Ontologies

From: Miller, Michael D (Rosetta) <Michael_Miller@Rosettabio.com>
Date: Fri, 1 Jun 2007 09:56:55 -0700
To: "William Bug" <William.Bug@DrexelMed.edu>, "Kei Cheung" <kei.cheung@yale.edu>
cc: "Smith, Barry" <phismith@buffalo.edu>, "Kashyap, Vipul" <VKASHYAP1@PARTNERS.ORG>, samwald@gmx.at, public-semweb-lifesci@w3.org, obo-relations@lists.sourceforge.net, "Paul Spellman" <spellman@bdgp.lbl.gov>
Message-ID: <E1HuARB-0007v4-59@aji.w3.org>
hi bill and kei,
 
i've changed the subject, since this is moving away from the original
topic.
 
"Yes - you are right, of course - right now the TGEN infrastructure for
the consortium is committed to providing MAGE-ML instances [1]."
 
that's great.
 
"the FuGE-stk [2] will provide a means to "convert" MAGE-ML to FuGE-ML"
 
not exactly, the folks (myself included) that worked on FuGE but with a
focus on microarrays are working on MAGEv2 and there is a commitment to
provide a way to translate to/from MAGEv1 <-> MAGEv2.  at the minimum
this would be a mapping but if there is time and resources available,
this would also have an implementation in the MAGEstk v2.  
 
MAGEv2 is being built on top of FuGE as an extension to add in
microarray specific classes (extending Data as ArrayDesign,
DesignElementData, etc, Material as Array, QPCRPlate, etc, and
DimensionElement as DesignElement extended by Feature, Reporter, and
CompositeElement).
 
we have not been quite as organized as the MAGEv1 effort so the work
doesn't have a high visibility yet, plus we have been working on
MAGE-TAB, a simplified, spreadsheet version of the MAGE-OM model.
 
i'm hoping we can get back on track soon, we are not that far from
completion, perhaps the NIH or BIRN microarray folks would be willing to
host a MAGEv2 meeting? (note, this would have little to do with ontology
development!)
 
"many of the experts working on FuGE .. are looking for assistance in
how to make use of ontologies when representing microarray data in a
FuGE instance"
 
yes, but note that this has nothing to do with ontology modeling per se
but simply the best way to model ontology annotation for the objects of
a FuGE document.  in essence, a FuGE object, such as a Material that
represents a rat or the Investigation itself, becomes either implicitly
or explicitly an Individual of the desired classes from whatever
ontologies that are appropriate.  it then inherits the properties of
those classes (if there are any) and can specify slot instances.  it is
anticipated that OBI will be usable for most of the basic annotation
then, perhaps, specialized ontologies in the domain of the particular
investigation can annotation more exactly.
 
most specifically, information and relationships of these referenced
classes would not be in the FuGE document, just the information
necessary to look them up in the ontology itself.
 
we modeled the FuGE ontology package from the Individual diagram of an
early draft of OMG's Ontology Definition MetaModel (ODM).  that section
was actually explicitly dropped from the final version of the ODM
because it had problems with OWL Full (and perhaps DL), but we
anticipate that the vast majority of desired ontology annotation can be
captured via this model.
 
temporal and containment/association relationships are actually intended
to be captured by the FuGE objects (the flow of Material and Data
through ProtocolApplications, the various associations between FuGE
classes)
 
"there is both an eye toward - and a need for - automatic conversion"
 
interestingly enough, if one can generate MAGEv1 to capture the details
of the microarray experiment, one could also use FuGE to export the
Material/BioSource individuals as stand alone with the ontology
annotation and tie them together via the identifier attribute.
 
"may require a MAGE-ML import into a FuGE DDL database - then export
from the database - I'm not clear on this yet"
 
since MAGE-ML has an in-memory model and FuGE does also, then it should
be just as easy to auto-generate bridging code based on a mapping
between the two in-memory models as to have to write to a database first
(which requires the same mapping!).
 
also note that the application/database doesn't have to be based on a
FuGE DDL database, it simply needs to be able to import MAGE-ML and
export FuGE.  i would be out of work if it did.
 
cheers,
michael
 
Michael Miller 
Lead Software Developer 
Rosetta Biosoftware Business Unit 
www.rosettabio.com 


________________________________

	From: public-semweb-lifesci-request@w3.org
[mailto:public-semweb-lifesci-request@w3.org] On Behalf Of William Bug
	Sent: Thursday, May 31, 2007 7:36 PM
	To: Kei Cheung
	Cc: Smith, Barry; Kashyap, Vipul; samwald@gmx.at;
public-semweb-lifesci@w3.org; obo-relations@lists.sourceforge.net
	Subject: Re: [Obo-relations] Advancing translational research
with the Semantic Web (Not clear about definition of
<is_location_of_process>)
	
	
	Hi Kei, 

	Yes - you are right, of course - right now the TGEN
infrastructure for the consortium is committed to providing MAGE-ML
instances [1]. 

	My understanding from speaking with FuGE folks is that the the
FuGE-stk [2] will provide a means to "convert" MAGE-ML to FuGE-ML (may
require a MAGE-ML import into a FuGE DDL database - then export from the
database - I'm not clear on this yet).  Since many of the FuGE model
developers were a part of the MGED MAGE model development project, there
is both an eye toward - and a need for - automatic conversion. As FuGE
is intended to cover ALL of functional genomics beyond microarray alone,
there's a bit more abstraction in the data model and some more specific
parts of the model will likely not be needed for microarray data.

	I'm not completely clear on how automatic it will be, but folks
such as Michael Miller who have contributed to the HCLS IG list before
would certainly be able to give us the most comprehensive answer to that
question that is available at this time.

	One example I found recently is out of the bioinformatics unit
at Newcastle U. - the Centre for Integrated System Biology of Aging and
Nutrition [3] [4].  In addition to being one of the first public systems
based on the Milestone 3 release of FuGE & the FuGE-stk, it has a means
of transferring data from the ArrayExpress backend - maxdLoad2 [5].
Since the latter system is capable of importing MAGE-ML instances, this
provides a route via which one can get from MAGE-ML to FuGE-ML.

	Of course, we could skip the FuGE step and just look at how to
use OBI and other OBO Foundry ontologies to create a SemWebTech
repository for NIH Neuroscience Microarray Consortium data as is - in
MAGE-ML or in the backend model - akin to the ones Alan et al. have set
up for the HCLS demo at the NeuroCommons.  We are working with
annotating MAGE-based microarray data within MouseBIRN as well, so it
would be wonderful, if there were some way for this to be included.  One
of the goals of what we are doing for microarray data in BIRN is to stay
in sync with the consortium in such a way so as to make it possible for
us to query consortium data - and visa versa.  There are some folks on
BIRN whose are also associated with the consortium (I believe the Autism
groups recently added to BIRN are participants of the consortium).
	
	
	Do you know whether others on the consortium - or TGEN itself -
are working on this task?  We might want to have a call that includes
some of the core informatics folks in the consortium, in addition to
yourself.

	Cheers,
	Bill


	[1]
http://arrayconsortium.tgen.org/np2/public/dataAndAnalysisPolicies.jsp
	[2] http://fuge.sourceforge.net/dev/index.php
	[3] http://www.cisban.ac.uk/cisbanDPI.html
	[4]
http://www.cs.ncl.ac.uk/research/pubs/trs/abstract.php?number=1016
	[5] http://www.cisban.ac.uk/resources.html

	On May 31, 2007, at 10:05 PM, Kei Cheung wrote:


		Hi Bill,

		Thanks for describing the evolution of MGED into FuGO.
As I understand it, the consortium's microarray data can be exported in
MAGE-ML (XML) format. Would it be possible to convert it to the FuGE
format?

		Cheers,

		-Kei

		William Bug wrote:


			Barry beat me to the punch here - 
			BUT - 
			I would not want to miss out on the specific
value of the proposal Kei has made.

			I believe looking closely at how the OBI
representation of microarray-associated instruments, protocols,
reagents, data artifacts, algorithms, etc. - could be put to use in
describing some of the data being produced for the NIH Neuroscience
Microarray Consortium that you are contributing to, Kei.  As you may
already know, many of the experts working on FuGE (grown out of MAGE
which used the MGED Ontology as its shared semantic framework) are
looking for assistance in how to make use of ontologies when
representing microarray data in a FuGE instance.  As you also probably
know, the original FuGE-associated ontology, FuGO, has expanded its
domain to cover all forms of biomedical investigation (Ontology of
Biomedical Investigation - aka the OBI that Barry cited).  This was a
part of the evolution of FuGO as it began to participate in the OBO
Foundry AND make a commitment to use BOTH the OBO Relations ontology and
BFO.

			With that in mind - and considering the NIH
Neuroscience Microarray Consortium is committed to providing array data
in FuGE format - it could be very helpful both to understand how OBI can
be used to provide a formal semantic representation of important
experimental provenance information AND how SemWebTech in general could
be used to provide a more flexible - and query-able - framework in which
to access this semantic information.

			Cheers,
			Bill

			On May 31, 2007, at 9:21 PM, Kei Cheung wrote:



				Smith, Barry wrote:


				At 08:52 PM 5/31/2007, Kei Cheung wrote:


				Hi Barry,

				Welcome to the SWHCLS list. Such a
discussion reminds me of the Nature paper: "Are the current ontologies
in biology good ontologies?"
(http://www.nature.com/nbt/journal/v23/n9/full/nbt0905-1095.html). The
paper uses the MGED (microarray) ontology to illustrate some of the
ontological issues. I'm just curious how the BFO principles and practice
can help make such a microarray ontology more ontologically sound and
therefore more machine readable.




				We are already working on it:

				http://obi.sf.net

				BS


				That's great! I hope we can develop some
real use case of it.

				-Kei






			Bill Bug
			Senior Research 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 <mailto:William.Bug@DrexelMed.edu>








	
	Bill Bug
	Senior Research 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
Received on Friday, 1 June 2007 16:57:26 GMT

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