Zoomorphology

, Volume 128, Issue 3, pp 201–217 | Cite as

The future role of bio-ontologies for developing a general data standard in biology: chance and challenge for zoo-morphology

Review

Abstract

Due to lack of common data standards, the communicability and comparability of biological data across various levels of organization and taxonomic groups is continuously decreasing. However, the interdependence between molecular and higher levels of organization is of growing interest and calls for co-operations between biologists from different methodological and theoretical backgrounds. A general data standard in biology would greatly facilitate such co-operations. This article examines the role that defined and formalized vocabularies (i.e., ontologies) could have in developing such a data standard. I suggest basic criteria for developing data standards on grounds of distinguishing content, concept, nomenclatural, and format standards and discuss the role of data bases and their use of bio-ontologies in current activities for data standardization in biology. General principles of ontology development are introduced, including foundational ontology properties (e.g. class–subclass, parthood), and how concepts are defined. After addressing problems that are specific to morphological data, the notion of a general structure concept for morphology is introduced and why it is required for developing a morphological ontology. The necessity for a general morphological ontology to be taxon-independent and free of homology assumptions is discussed and how it can solve the problems of morphology. The article concludes with an outlook on how the use of ontologies will likely establish some sort of general data standard in biology and why the development of a set of commonly used foundational ontology properties and the use of globally unique identifiers for all classes defined in ontologies is crucial for its success.

Keywords

Bio-ontology Data standard Linguistic problem of morphology Morphology RDF 

Notes

Acknowledgments

I thank Thomas Bartolomaeus and Markus Koch for discussion and valuable suggestions for an earlier draft of this paper. I also want to thank Ronald Jenner, as well as two other anonymous referees, for reading, criticizing, and commenting on an early manuscript. It goes without saying, however, that I am solely responsible for all the arguments and statements in this paper. This study was supported by the SPP 1174 of the German Research Foundation (DFG) (VO 1244/3-2). I am also grateful to the taxpayers of Germany.

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Copyright information

© Springer-Verlag 2008

Authors and Affiliations

  1. 1.FU Berlin, Fachbereich Biologie Chemie PharmazieSystematik und Evolution der TiereBerlinGermany

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