System for Aligning and Merging Biomedical Ontologies
toolKit for Aligning and Merging Ontologies
for comparative evaluation of the non-interactive alignment components,
including alignment algorithms, combination algorithms and filters.
http://www.ida.liu.se/~iislab/projects/KitAMO/
KitAMO
http://www.ida.liu.se/~iislab/projects/SAMBO/
SAMBO
Department of Computer and Information Science, Linköpings universitet, Sweden
Aligning Biomedical Ontologies
He Tan, Patrick Lambrix
Due to the recent explosion of the amount of on-line accessible biomedical data and tools, finding and retrieving
the relevant information is not an easy task. The vision of a Semantic Web for life sciences alleviates these
difficulties. A key technology for the Semantic Web are ontologies. In recent years many biomedical ontologies
have been developed and many of these ontologies contain overlapping information. Often we would therefore
want to be able to use multiple ontologies. For example, applications may need to use ontologies from different
areas and from different views on one area. Ontology builders may want to create a new ontology using existing
ontologies or combining knowledge from small ontologies. To obtain good results, we need to find the
relationships between terms in the different ontologies, i.e. we need to align them.
SIGNAL-ONTOLOGY (SigO)
Aligning ontologies is to define the relations between the terms in different ontologies
Aligning Ontologies
•
GENE ONTOLOGY (GO)
Immune Response
i- Allergic Response
i- Antigen Processing and Presentation
i- B Cell Activation
i- B Cell Development
i- Complement Signaling
synonym complement activation
i- Cytokine Response
i- Immune Suppression
i- Inflammation
i- Intestinal Immunity
i- Leukotriene Response
i- Leukotriene Metabolism
i- Natural Killer Cell Response
i- T Cell Activation
i- T Cell Development
i- T Cell Selection in Thymus
equivalent concepts
equivalent relations
is-a relation
immune response
i- acute-phase response
i- anaphylaxis
i- antigen presentation
i- antigen processing
i- cellular defense response
i- cytokine metabolism
i- cytokine biosynthesis
synonym cytokine production
…
p- regulation of cytokine biosynthesis
…
…
i- B-cell activation
i- B-cell differentiation
i- B-cell proliferation
i- cellular defense response
…
i- T-cell activation
i- activation of natural killer cell activity
…
An Ontology Alignment Framework
ƒ Use as a basis for building ontology
alignment systems
ƒ Provide support for experimenting with
different alignment strategies and their
combinations
Book Chapters:
Lambrix P, Tan H, `Ontology alignment and merging', chapter in Burger, Davidson, Baldock, (eds), Anatomy
Ontologies for Bioinformatics: Principles and Practice, Springer, 2007. To appear.
Lambrix P, Tan H, Jakoniene V, Strömbäck L, `Biological Ontologies', chapter in Baker, Cheung (eds), Semantic
Web: Revolutionizing Knowledge Discovery in the Life Sciences, Springer, 2006. To appear.
Journal Publications:
Lambrix P, Tan H, 'SAMBO - A System for Aligning and Merging Biomedical Ontologies', Journal of Web
Semantics, Special issue on Semantic Web for the Life Sciences, 4(3):196-206, 2006.
Lambrix P, Tan H, `A Tool for Evaluating Ontology Alignment Strategies', Journal on Data Semantics, VIII,
2006.