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Outline
The role of Bio-Ontologies [BOs] in biological databases Four interpretive steps in standardization The epistemic status of BO terms: situating concepts A new type of theory in biology? Back to Mary Hesses network view Implications: data travel and use across research contexts Conclusion: on technology and theory-making
Goal: enhance availability and usability of data across research contexts Means: formal representations of areas of knowledge in which the
essential terms are combined with structuring rules that describe the relationship between the terms. Knowledge that is structured in a bioontology can then be linked to the molecular databases (Bard and Rhee 2004) Precisely defined terms related through DAGs structures Association of terms with datasets
Search by GO
Returns set of genes annotated to this term Search returns annotations to terms and subterms (children)
BO Terms as Standards
Standard = Coordination device facilitating interdisciplinary research (Berg 2004) BO terms as neutral tools for scientific communication and exchange:
Data are attached to specific BO terms purely for the purposes of retrieval by biologists interested in investigating the phenomenon to which the term refer No theoretical interpretation involved: BO terms are broad classificatory concepts conceived to pass on information without distorting or interpreting it
Select data about gene product TSK from publication: Suzuki et al., 2005 Plant Cell Physiol. 46:736-742. TONSOKU Is Expressed in S Phase of the Cell Cycle and Its Defect Delays Cell Cycle Progression in Arabidopsis Associate with term G2/M transition of mitotic cell cycle, which is defined as progression from G2 phase to M phase of the mitotic cell cycle Looking for data on the mitotic cell cycle, researchers find gene product TSK as relevant to the G2/M transition Gene product TSK could be relevant to researching other parts of the mitotic cell cycle but there is no evidence for this, so the database does not report this possibility = the biological relevance of dataset Y is restricted to the phenomenon captured by the term G2/M transition, thus excluding other, possibly relevant phenomena
Abstract
Bio-ontologies are often presented as a neutral tool for the diffusion of facts about organisms to biologists: that is, as a way to standardise the terminology and relations among terms used to describe biological processes, so that the immense amount of (especially microbiological) data recently accumulated on various aspects of the main model organisms can be brought together and made accessible to the whole biological community. In this paper, I argue that bio-ontologies are not a neutral vehicle for the diffusion of evidence. Rather, they constitute a new type of biological theory, incorporating a specific perspective on biological phenomena, through which data are re-interpreted in order to fit specific research goals. Notably, one of these goals consists of integrating the available knowledge about various aspects of any organisms into an overall understanding of their biology. The main issues that I shall address in this paper are thus the following: how well do biological facts circulate through bio-ontologies? How effective is the use of bio-ontologies towards obtaining integration in biology? And what kind of integration is that is it actually possible to distinguish it from a kind of theoretical unification? In addressing these questions, I focus on the use of one of the bio-ontologies, the so-called Gene Ontology, to structure and display data about Arabidopsis thaliana within The Arabidopsis Information Resource.
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