Title: MGED Ontology MO
1MGED Ontology (MO)
- A resource for creation of MAGE-ML documents that
are MIAME Compliant
2The MGED Ontology Home Page
http//mged.sourceforge.net/ontologies/
3The Computational View of Microarray Information
Need an ontology to unambiguously represent this
information.
4An Experimental Ontology
- An ontology for microarray experiments
- Not an ontology of life but of experiments
- Parts are applicable to describing experiments in
general - Our approach to interfacing with other ontologies
is experimental - Not mapping terms from related ontologies
- Provide a framework to hang other ontologies off
of - Know where to find different types of annotation
- How to interpret that annotation
5The MGED Ontology is Structured in DAMLOIL using
OILed 3.4
6MGED Ontology BiosourceOntologyEntry
DiseaseState
7How do you use it?
- Currently it is only a term dictionary
- Reference the terms via MAGE OntologyEntry class
through a stable URI - To direct development and population of web-entry
forms - MIAME Express (EBI)
- RAD Forms (CBIL)
8The MGED Ontology in Action MIAMExpress
9RAD schema uses MAGE/MIAME
MAGE Experiment Array BioMaterial BioAssay BioAssa
yData Protocol, Descr. HigherLevelAnalysis
MIAME Experimental Design Array
design Samples Hybridization, Measure Normalizatio
n .
10The MGED Ontology in Action RAD
- Add screen shot of study factor
11RAD Generic Form for BioMaterial Characteristics
12Summary of the history
- The MGED Ontology Working Group exists
- Have released Version 1.6
- Using OILed ontology editor
- http//mged.sf.net/ontologies
- Journals are starting to recommend MIAME
information as part of a submission - See Nature article
- Hard to find what you need and how this relates
to a MAGE document
13A new mission
- Produce a Core Ontology
- Organize ontology according to MAGE packages
- Class names have been changed to facilitate
mapping and properties adjusted to avoid
conflicts. - Core ontology does not cover all of MAGE or
contain all MAGE associations. Scope of ontology
is supporting MAGE ontology entry associations,
adding constraints within MAGE structure, and
adding further structure and depth to MAGE
classes without changing base classes. - Definitions are derived from MAGE OMG
specification where appropriate and available. - Enumerated lists are represented as instances of
a class where these lists are open ended.
14The new hierarchy
Screen shot of package hierarchy
15Why the redundancy with MAGE?
- Easier to find what you need
- The structure gives a concrete context to terms
- Translation between MAGE and MGED Ontology (MO)
instances will be easier - Possibly through use of ObjectMap
- We can use the MO to test for MIAME compliance of
MAGE docs
16Future directions
- Stabilize the Core ontology and coordinate this
closely to MAGE-ML 1.0 - Move to using OWL for transfer of the ontology
and do integrity checks - Tools for translation between MAGE MO
- EBI ArrayExpress has plans for this, as does CBIL
- Provide a better input method for the community
- Web submissions for new terms and extensions
- Voting scheme for alternate definitions?
17Acknowledgements
- MGED Ontology
- The MGED Ontology Working Group
- Chris Stoeckert
- Helen Parkinson (EBI)
- Trish Whetzel
- Nelson Axelrod
- MAGE working group
www.mged.org
18Acknowledgements
- Chris Stoeckert (UPENN)
- Trish whetzel (UPENN)
- Helen Parkinson (EBI)
19MGED Ontology BiomaterialDescription
BiosourceProperty Age