The MGED Ontology FAQ:

 

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 Earlier versions were produced in DAML+OIL format; these are still available but are no longer being updated as the MO changes.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

http://caarraydb.nci.nih.gov/caarray/index.jsp

Chemical Effects

in Biological

Systems

http://cebs.niehs.nih.gov/

maxd

http://bioinf.man.ac.uk/microarray/maxd/

MIAMExpress

http://www.ebi.ac.uk/miamexpress/  

MiMiR

http://microarray.csc.mrc.ac.uk/_private/activities/data_warehouse_text.htm  

NASCArrays

http://affymetrix.arabidopsis.info/narrays/experimentbrowse.pl

RAD StudyAnnotator

https://www.cbil.upenn.edu/RAD/StudyAnnotator/

SMD Experiment Set Creator

http://genome-www.stanford.edu/microarray

Tox-MIAMExpress

http://www.ebi.ac.uk/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.