P.S.: Allyson Lister who participates on the Newcastle U. project I
cited below is also a very active participant on the OBI project.
http://www.cisban.ac.uk/staff.html
P.P.S.: Sorry for the cross-posting, but I believe there are others
on the OBI developer list who might be interested in this specific
discussion.
On May 31, 2007, at 10:36 PM, William Bug wrote:
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 - [EMAIL PROTECTED]
<mailto:[EMAIL PROTECTED]>
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 - [EMAIL PROTECTED]
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 - [EMAIL PROTECTED]
