Overview

The flood of data and factual knowledge in biology and medicine requires principled approaches to their proper analysis and management. A cornerstone in this effort constitutes the precise and complete description of the fundamental entities within this domain in terms of formal ontologies.

However, biomedical ontology development often still do not adhere to basic design principles: For example, even very low-level domain terms often lack precise and unambiguous (logical) definitions. This impedes the move towards semantic standardization that is needed for their intended knowledge management task. Rather, it leads to inconsistencies, fragmentation and overlap both within and inbetween different ontologies.

In light of this we introduce BioTop, 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 furthermore serve as top-level model for creating new ontologies for more specific domains or as aid for aligning or improving existing ones.

BioTop is founded upon formal design principles (as propagated by the OBO Foundry initiative) and implemented in OWL-DL, the standard ontology language on the Semantic Web. BioTop makes use of the whole range of constructors of OWL-DL. The use of OWL-DL makes it possible to apply description logics reasoners for maintaining consistency by continuous classficiation during development and to automatically infer its hierarchical structure. To this end, we try to fully define as much classes as possible (in terms of necessary and sufficient conditions).

The initial version of BioTop 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, now also providing upper-level categories for clinical medicine and health care. In 2011, a simplified version, BioTop was released.

In 2008 BioTop had been re-engineered towards systematic modularization in order to clearly highlight its biomedical focus. To this end, a significant amount of axioms originally found in BioTop have been migrated into a newly created ontology, called ChemTop. In the modularization process, the following principles have been obeyed: The boundary of all modules should coincide with a given particular subdomain, e.g. biology vs. chemistry proper. All modules have to follow the same principles as the top-level arrangement. The size of each modules should be such that it can be handled easily by (human) editors and tools, e.g. reasoners. Modules covering neighbor subdomains may exhibit a limited (and documented) degree of overlap. Bridging files link modules between themselves as well as with the top-level ontology.

In connection with this modularization efforts we have further carried out some other alignment efforts:

• top-level ontology Basic Formal Ontology (BFO): Some difficulties were encountered in regard to granularity-dependent classes such as "FiatObjectPart" as well as the mapping of immaterial entities such as "Mind" (cf. MIE paper). BioTop developers actively contribute to the ongoing BFO 2.0 redesign process. The goal is to make BioTop and BioTopLite fully compatible with BFO 2.0.
• Descriptive Ontology for Linguistic and Cognitive Engineering (DOLCE)
• OBO Relation Ontology (RO)
• UMLS Semantic Network (SN): This mapping required a substantial extension of the original BioTop role hierarchy and the representation of many SN relations as kinds of BioTop processual entities (cf. UMLS-Mapping).

Implementation

To access the latest release version (29 January 2012) you can download the following files:

biotoplite	self-standing BioTopLite ontology (with less classes and relations compared to BioTop)
BioTopLite2	NEW: EXPERIMENTAL RELEASE OF BioTopLite 2
biotop	self-standing BioTop ontology (without special chemistry classes or reference to external top-level ontologies)
biotop-bfo-ro	bridge BioTop-BFO/RO - connects BFO, RO and BioTop
biotop-chemtop-bfo-ro	bridge file including biotop-bfo-ro and biotop-chemtop - connects BioTop with the top-level ontologies BFO and RO on the one hand and ChemTop on the other.
biotop-dolce-ro	bridge BioTop-DOLCE/RO - connects DOLCE, RO and BioTop
umlssn	UMLS Semantic Network in OWL
biotop-umlssn	connects BioTop mit umlssn

Older release versions:

11 November 2009 29 March 2010 1 July 2010

Attention:

BioTop is distributed under the Creative Commons - Attribution License. BioTop is work in progress! So its implementation is constantly changing and most likely contains bugs and rough edges! If you work offline or behind a firewall you should additionally download BFO 1.1 and RO 1.0 light The downloaded OWL files need to be classified by a reasoner to infer all class relations inferrable from the source class definitions.

Users and Examples

• The Biomedical Denotation Ontology (BioDenO). An extension of BioTop that formally describes categories used in text mining.
• UMLS-Mapping. A stable version of BioTop, together with an OWL-DL version of the UMLS Semantic Network and a brigding ontology [zipped].
• BOOTStrep: Bootstrapping Of Ontologies and Terminologies STrategic REsearch Project
• taxdemo: A small and demonstrative ontology of how biological taxa can be based on BioTop and described in the ISMB paper (You can download the implementation or get a graphical view of it.)

Publications

Elena Beißwanger, Stefan Schulz, Holger Stenzhorn and Udo Hahn
BioTop: An Upper Domain Ontology for the Life Sciences - A Description of its Current Structure, Contents, and Interfaces to OBO Ontologies
in Applied Ontology, Volume 3, Issue 4, Pages 205-212, IOS Press, Amsterdam, The Netherlands, December 2008

Holger Stenzhorn, Stefan Schulz, Elena Beißwanger, Udo Hahn, László van den Hoek and Erik van Mulligen
BioTop and ChemTop - Top-Domain Ontologies for Biology and Chemistry (Poster)
in Proc. of the 7th International Semantic Web Conference (ISWC 2008), Karlsruhe, Germany, October 2008

Stefan Schulz, Martin Boeker and Holger Stenzhorn
The Ontology of Biological Taxa
in Proc. of the 16th International Conference on Intelligent Systems for Molecular Biology (ISMB 2008), Toronto, Canada, July 2008
See also the Users and Examples section for an implementation of the BioTax demonstrative ontology from the paper.

Stefan Schulz, Martin Boeker and Holger Stenzhorn
How Granularity Issues Concern Biomedical Ontology Integration
in Proc. of the International Congress of the European Federation for Medical Informatics (MIE 2008), Göteborg, Sweden, Mai 2008

Stefan Schulz, Elena Beißwanger, Udo Hahn, Joachim Wermter, Holger Stenzhorn and Anand Kumar
From GENIA to BioTop - Towards a top-level Ontology for Biology
in Proc. of the Internat. Conference on Formal Ontology in Information Systems (FOIS 2006), Baltimore, USA, November 2006

Stefan Schulz, Elena Beißwanger, Joachim Wermter and Udo Hahn
Towards an Upper Level Ontology for Molecular Biology
in Proc. of the American Medical Informatics Association Annual Conference (AMIA 2006), Washington, November 2006

Holger Stenzhorn, Stefan Schulz and Elena Beißwanger
Towards a Top-Domain Ontology for Linking Biomedical Ontologies
in Proc. of the 12th World Congress on Health (Medical) Informatics (Medinfo 2007), Brisbane, Australia, August 2007

Feedback

You can discuss all topics on the theroretical background or implementation issues of BioTop in its own discussion group.

You may also directly contact Stefan Schulz, the main contributor to BioTop.

This page was last updated on May 13th, 2014.