The future role of bio-ontologies for developing a general data standard in biology: chance and challenge for zoo-morphology |
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Authors: | Lars Vogt |
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Institution: | 1.FU Berlin, Fachbereich Biologie Chemie Pharmazie,Systematik und Evolution der Tiere,Berlin,Germany |
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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. |
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Keywords: | Bio-ontology Data standard Linguistic problem of morphology Morphology RDF |
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