Basic Formal Ontology for bioinformatics

IFOMIS Reports (2005)
Download Edit this record How to cite View on PhilPapers
Abstract
Two senses of ‘ontology’ can be distinguished in the current literature. First is the sense favored by information scientists, who view ontologies as software implementations designed to capture in some formal way the consensus conceptualization shared by those working on information systems or databases in a given domain. [Gruber 1993] Second is the sense favored by philosophers, who regard ontologies as theories of different types of entities (objects, processes, relations, functions) [Smith 2003]. Where information systems ontologists seek to maximize reasoning efficiency even at the price of simplifications on the side of representation, philosophical ontologists argue that representational adequacy can bring benefits for the stability and resistance to error of an ontological framework and also for its extendibility in the future. In bioinformatics, however, a third sense of ‘ontology’ has established itself, above all as a result of the successes of the Gene Ontology (hereafter: GO), which is a tool for the representation and processing of information about gene products and their biological functions [Gene Ontology Consortium 2000]. We show how Basic Formal Ontology (BFO) has established itself as an overarching ontology drawing on all three of the strands distinguished above, and describe applications of BFO especially in the treatment of biological granularity.
PhilPapers/Archive ID
KUMIR
Upload history
Archival date: 2018-06-03
View other versions
Chapters BETA
Added to PP index
2013-11-17

Total views
192 ( #27,470 of 58,210 )

Recent downloads (6 months)
31 ( #24,839 of 58,210 )

How can I increase my downloads?

Downloads since first upload
This graph includes both downloads from PhilArchive and clicks on external links on PhilPapers.