BioTop

A Top-Domain Ontology for the Life Sciences

BioTop is a top-domain ontology that provides definitions for the foundational entities of biomedicine as a basic vocabulary to unambiguously describe facts in this domain. BioTop can be used as top-level model for creating new ontologies for more specific domains or as aid for aligning or improving existing ones.

BioTop follows formal design principles (as propagated by the OBO Foundry initiative) and is implemented in OWL2. BioTop makes use of several Description Logics (DL) constructors. The use of OWL2 enables maintaining consistency by continuous classification during development, and to automatically infer its hierarchical structure.

The initial version of BioTop had rested upon the idea to create a formally-based redesign and expansion of GENIA, an ontology applied for corpus annotation in molecular biology. After that, BioTop has been continuously expanded.

In 2011, a simplified version, BioTop was released (BioTopLite). Since 2013, BioTopLite was reviewed and updated, with clearer stataments and nominalizations. This led to the creation of BioTopLite2 (BTL2).

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Contributors

Publications

Previous contributions

2013

- Schulz S, Boeker M. BioTopLite: An Upper Level Ontology for the Life Sciences. Evolution, Design and Application. In: Furbach U, Staab S, eds. Informatik 2013. Koblenz: IOS Press; 2013.


2011

- Schulz S, Spackman K, James A, Cocos C, Boeker M. Scalable representations of diseases in biomedical ontologies. J Biomed Semantics. 2011;2 Suppl 2(1):S6. doi:10.1186/2041-1480-2-S2-S6.


2009

- Schulz S, Beisswanger E, van den Hoek L, Bodenreider O, van Mulligen EM. Alignment of the UMLS semantic network with BioTop: Methodology and assessment. Bioinformatics. 2009;25(12):69-76.


2008

- Beisswanger E, Schulz S, Stenzhorn H, Hahn U. BIOTOP: An Upper Domain Ontology for the Life Sciences. Appl Ontol. 2008;3(4):205-212.
- Stenzhorn H, Schulz S, Beißwanger E, Hahn U, Hoek L van den, Mulligen E van. BioTop and ChemTop – Top-Domain Ontologies for Biology and Chemistry. In: Bizer C, Joshi A, eds. Proc. of the 7th International Semantic Web Conference - ISWC’08. Karlsruhe, Germany: CEUR Workshop Proceedings; 2008. doi:10.1.1.176.7471.
- Schulz S, Stenzhorn H, Boeker M. The ontology of biological taxa. Bioinformatics. 2008;24(13):313-321.
- Schulz S, Boeker M, Stenzhorn H. How granularity issues concern biomedical ontology integration. Stud Health Technol Inform. 2008;136:863-868.

2007

- Stenzhorn H, Beißwanger E, Schulz S Towards a Top-domain Ontology for Linking Biomedical Ontologies. In: Kuhn KA, Warren JR, Leong T-Y, eds. Medinfo 2007: Proceedings of the 12th World Congress on Health (Medical) Informatics; Building Sustainable Health Systems. Amsterdam: IOS Press; 2007:1225-1229.


2006

- Schulz S, Beisswanger E, Hahn U, Wermter J, Kumar A, Stenzhorn H. From GENIA to BioTop: Towards a Top-Level Ontology for Biology. In: Bennett B, Fellbaum C, eds. Frontiers in Artificial Intelligence and Applications - FOIS’06. Maryland, USA: IOS Press; 2006:103-114.
- Schulz S, Beisswanger E, Wermter J, Hahn U. Towards an upper level ontology for molecular biology. AMIA Annu Symp Proc. 2006:694-698.

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