History of IFOMIS

The Institute for Formal Ontology and Medical Information Science (IFOMIS) was founded in April 2002 as a result of the award to Barry Smith of the Wolfgang Paul Prize from the Alexander von Humboldt Foundation and the German Federal Ministry for Education and Research. Initially, IFOMIS was founded in the Faculty of Medicine in the University of Leipzig, but the Institute was translocated in 2004 to the Saarland University in Saarbrücken in order to take advantage of the greater opportunities in Saarbrücken for cross-disciplinary collaboration at the forefront of information-based research.

The goal of IFOMIS is to advance research in ontology in the domain of medical information science and, more generally, to show how the expertise of philosophers and logicians can be beneficially applied in the field of biomedicine. Doctoral and postdoctoral researchers drawn from philosophy and logic, and also from medicine, biology, chemistry, linguistics and computer science have benefited from its research and training programs.

IFOMIS researchers can claim to have brought about a transformation in logical sophistication of research in biomedical ontology and to have created techniques for evidence-based ontology development which have been adopted for use by prestigious biomedical informatics projects throughout the world. The methodology has led to the creation of a Top Level Ontology “Basic Formal Ontology” (BFO), which is now serving as integrating framework for a range of biomedical ontology projects.

In 2005, Barry Smith joined the Gene Ontology (GO) Consortium to found the OBO (Open Biomedical Ontologies) library, which in 2005 became institutionalized as the ‘OBO Foundry’ (http://obofoundry.org). Barry Smith is still one of the OBO Foundry coordinators. The goal of the OBO Foundry is to establish a suite of interoperable, high-quality ontologies to be used in the annotation of biomedical data, and to provide effective guidance to biologists and others engaged in ontology creation, in ways designed to promote algorithmic reasoning, biological accuracy, and intelligibility to the humans who maintain and use them.

IFOMIS researchers have been involved in creating, revising or evaluating a.o. the following ontologies: Basic Formal Ontology, Cell Ontology (CL), Environment Ontology (EnvO), Foundational Model of Anatomy (FMA), Functional Genomics Investigation Ontology (FUGO), GALEN, Gene Ontology (GO), HL7 Reference Information Model (RIM), International Classification of Functions and Disabilities (ICF), LinkBase, National Cancer Institute Thesaurus (NCIT), Ontology for Biomedical Investigations (OBI), Phenotypic Quality Ontology (PaTO), Plant Ontology (PO), Protein Ontology (PRO), Relation Ontology (RO), RNA Ontology (RnaO), Sequence Ontology (SO), SNOMED CT, Upper Biomedical Ontology (OBO-UBO), ACGT Master Ontology (ACGT MO), WordNet.

Publications

  • Jansen L. and Smith B. eds. (2008). Biomedizinische Ontologie. Zürich: vdf Hochschulverlag.
  • Munn K. and Smith B. (2009). Applied Ontology: An Introduction. Frankfurt: Ontos Verlag.
  • Johansson I. and Lynoe N. (2009). Medicine & Philosophy: a Twenty-First Century Introduction. Frankfurt: Ontos Verlag.