HuPSON: the human physiology simulation ontology.

Michaela Gündel,Bernard De Bono,Hui Li,Heinz-Theodor Mevissen,Martin Hofmann-Apitius,Jiali Wang,Erfan Younesi,Bijun Zhang,Ashutosh Malhotra

doi:10.1186/2041-1480-4-35

Abstract

BackgroundLarge 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.ResultsWe 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).ConclusionsHuPSON 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.

Highlights

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
Scope and purpose Human Physiology Simulation Ontology (HuPSON) provides a framework for a) annotation of simulation experiments with standard ontology terms, b) textmining based information retrieval that is required for modelling, c) interoperability of algorithmic approaches used in biomedical simulation, d) comparability of simulation results and interoperability on different structural scales and e) linking knowledge-based approaches to simulation-based approaches
A computer simulation consists of simulation steps that use algorithms and scientific techniques and is performed on a model

Summary

Introduction

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. The aim of SemSim is to create semantic interoperability of biosimulation models by creating machine-readable definitions While this is a valid approach to creating interoperability and the integration of resources, the problem remains that semantic information is spread among different external sources and an additional tool (e.g. SemGen [14], the RICORDO toolkit [13]) is needed

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