title: HuPSON: the human physiology simulation ontology.
abstract: BACKGROUND
  Large biomedical simulation initiatives, such as the Virtual Physiological Human (VPH), are substantially dependent on controlled vocabularies to facilitate the exchange of information, of data and of models. Hindering these initiatives is a lack of a comprehensive ontology that covers the essential concepts of the simulation domain.
  
  
  RESULTS
  We propose a first version of a newly constructed ontology, HuPSON, as a basis for shared semantics and interoperability of simulations, of models, of algorithms and of other resources in this domain. The ontology is based on the Basic Formal Ontology, and adheres to the MIREOT principles; the constructed ontology has been evaluated via structural features, competency questions and use case scenarios.The ontology is freely available at: http://www.scai.fraunhofer.de/en/business-research-areas/bioinformatics/downloads.html (owl files) and http://bishop.scai.fraunhofer.de/scaiview/ (browser).
  
  
  CONCLUSIONS
  HuPSON provides a framework for a) annotating simulation experiments, b) retrieving relevant information that are required for modelling, c) enabling interoperability of algorithmic approaches used in biomedical simulation, d) comparing simulation results and e) linking knowledge-based approaches to simulation-based approaches. It is meant to foster a more rapid uptake of semantic technologies in the modelling and simulation domain, with particular focus on the VPH domain.
authors.affiliation: Fraunhofer Institute for Algorithms and Scientific Computing (SCAI), Schloss Birlinghoven, Sankt Augustin, Germany. michaela.guendel@scai-extern.fraunhofer.de.
authors.forename: Michaela
authors.initials: M
authors.lastname: Gündel
authors.forename: Erfan
authors.initials: E
authors.lastname: Younesi
authors.forename: Ashutosh
authors.initials: A
authors.lastname: Malhotra
authors.forename: Jiali
authors.initials: J
authors.lastname: Wang
authors.forename: Hui
authors.initials: H
authors.lastname: Li
authors.forename: Bijun
authors.initials: B
authors.lastname: Zhang
authors.forename: Bernard
authors.initials: B
authors.lastname: de Bono
authors.forename: Heinz-Theodor
authors.initials: HT
authors.lastname: Mevissen
authors.forename: Martin
authors.initials: M
authors.lastname: Hofmann-Apitius