1. What is the
MGED Ontology (MO)?
The MO mission
statement:
The primary
purpose of the MGED Ontology is to provide standard terms for the annotation of
microarray experiments. These terms will enable structured queries on elements
of the experiments. Furthermore, the terms will also enable unambiguous
descriptions of how the experiment was performed. The terms will be provided in
the form of ontology; which means that the terms will be organized into classes
with properties and will be defined. The standard ontology format OWL will be
used. For descriptions of biological material (biomaterial) and certain
treatments used in the experiment, terms may come from external resources that
are specified in the Ontology. Software programs utilizing the Ontology are
expected to generate forms for annotation, populate databases directly, or
generate files in the established MAGE-ML format. Thus, the Ontology will be
used directly by investigators annotating their microarray experiments as well
as by software and database developers and therefore will be developed with
these very practical applications in mind.
2. What is the
status of the MO?
The MO is
available as a production release in OWL format; the most recent version can be
found here http://mged.sourceforge.net/ontologies/MGEDontology.php.
Earlier versions were produced in DAML+OIL format; these are still available
but are no longer being updated as the MO changes. These can be downloaded
here: http://mged.sourceforge.net/ontologies/MGEDontology.php
3. How do I
contribute to the development of the MO?
New terms can be
submitted via the MO term tracker on sourceforge http://sourceforge.net/tracker/?atid=603031&group_id=16076&func=browse
There is also a
mailing list to raise queries, sign up here:
https://lists.sourceforge.net/lists/listinfo/mged-ontologies
MO phone calls
are also held occasionally to develop the MO. Email the list above if you would
like to join in.
4. What is the
future of MO?
We intend to
continue to maintain MO as a resource for the annotation of microarray
experiments indefinitely; meaning we will continue to add new terms and refine
the MO to improve its applicability.
At some point in
the future FuGO will be a viable alternative for the annotation of microarray
experiments. At that time we will establish mapping procedures from MO to FuGO
to allow transition to using FuGO as a primary annotation source. We expect
that by end 2008 the MO will be redundant with FuGO.
5. What is the
MO relationship to FuGO?
The MO developers
are contributing to the development of the FuGO so that the FuGO is useful for
the annotation of microarray experiments
FuGO: http://fugo.sourceforge.net/
FuGO Mission Statement:
The Functional
Genomics Ontology (FuGO) project seeks to develop an integrated ontology that
provides both a set of 'universal' terms, i.e. terms applicable across various
biological and technological domains, and domain-specific extensions for terms
relevant only to a given domain. The purpose of this ontology is to support the
consistent annotation of functional genomics experiments, regardless of the
particular field of study. The ontology will model the design of an
investigation, the protocols and instrumentation used, the data generated and
the types of analysis performed on it.
6. Who funds
the MO?
The MO is funded
by NIH Grant P41HG003619 awarded by the National Human Genome Research
Institute (NHGRI) and the National Institute for Biomedical Imaging and
Biotechnology (NIBIB).
Sponsors of the
MGED society also provide support for the MO. A list of MGED Sponsors is here http://www.mged.org/Main_Page_Links/Sponsors/sponsors.html
7. How do I
cite the MO?
To reference the
MO please cite this paper:
Whetzel PL, Parkinson H, Causton HC, Fan L, Fostel J, Fragoso G, Game L, Heiskanen M, Morrison N, Rocca-Serra P, Sansone SA, Taylor C, White J, Stoeckert CJ Jr. (2006)
The MGED
Ontology; a resource for semantics-based description of microarray experiments.
Bioinformatics.
2006 Jan 21; [Epub ahead of print]
Pubmed PMID:
16428806
8. Who is
using the MO?
The following
groups are known to be using the MO. Please email mged-ontologies@lists.sourceforge.net
to be added to this list
|
Name
|
URL |
|
BuG@Sbase |
http://bugs.sgul.ac.uk/bugsbase/ |
|
CaArray |
|
|
Chemical
Effects in
Biological Systems |
|
|
maxd |
|
|
MIAMExpress |
|
|
MiMiR |
http://microarray.csc.mrc.ac.uk/_private/activities/data_warehouse_text.htm |
|
NASCArrays |
http://affymetrix.arabidopsis.info/narrays/experimentbrowse.pl |
|
RAD
StudyAnnotator |
|
|
SMD
Experiment Set Creator |
|
|
Tox-MIAMExpress |
9. What tools
are available to use the MO?
There are tools
provided as part of the MAGEstk toolkit for handling the MO
MAGEstk
sourceforge page
http://sourceforge.net/project/showfiles.php?group_id=16076
Java Tools:
MGEDOntologyEntry-2004-11-29-src.jar <http://prdownloads.sourceforge.net/mged/MGEDOntologyEntry-2004-11-29-src.jar?download>
MGEDOntologyEntry-2004-11-29.jar <http://prdownloads.sourceforge.net/mged/MGEDOntologyEntry-2004-11-29-src.jar?download>
10. The MO
sounds great, where can I get it?
You can download
the current version in OWL format from
http://mged.sourceforge.net/ontologies/MGEDOntology.owl
You can also view
the MO via the NCICB Ontology Browser:
An html version
is also provided for browsing:
http://mged.sourceforge.net/ontologies/MGEDontology.php
FAQ Authors:
Helen Parkinson, Chris Stoeckert, Joe White, Feb 2006.