A linked data platform for finite element biosimulations

Abstract

Biosimulation models have been recently introduced to understand the exact causative factors that give rise to impairment in human organs. Finite Element Method (FEM) provides a mathematical framework to simulate dynamic biological systems, with applications ranging from human ear, cardiovascular, to neurovascular research. Due to lack of a well-integrated data infrastructure, the steps involved in the execution and comparative evaluation of large Finite Element (FE) simulations are time consuming and are performed in isolated environments. In this paper, we present a Linked Data platform to improve the automation in integration, analysis and visualisation of biosimulation models for the inner-ear (cochlea) mechanics. The proposed platform aims to help domain scientists and clinicians for exploring and analysing Finite Element (FE) numerical data and simulation results obtained from multiple domains such as biological, geometrical, mathematical, physical models. We validate the platform by conducting a qualitative survey and perform quantitative experiments to record overall performance.

An Artifact-based Workflow for Finite-Element Simulation Studies

“…Another approach to support FEA simulation studies is to use ontologies, which provide a formal specification of the different work products in terms of their attributes and relations. Thus, we can use ontologies to share knowledge about the geometrical and physical model across different software suites [72,73,74,75], to derive processing parameters [76,77] and to document these studies [78,79].…”

Demonstrating a Linked Data Visualiser for Finite Element Biosimulations

“…For instance, all the eight (8) parameters and their values shown in the Figure 1 are taken from separate experimental data files stored in different formats (e.g, .dat, unv, .pak, etc. [1] which aims at improving the automation in interpretation and visualisation of finite element (FE) models for inner ear (cochlea) mechanics in an integrated fashion. Figure 2 represents the systematic work flow of the SIFEM Visualiser.…”

Extending inner-ear anatomical concepts in the Foundational Model of Anatomy (FMA) ontology

“…The SIFEM project results in the delivery of an infrastructure, which will semantically integrate finite element simulation data with experimental and clinical data, aiming towards the delivery of a robust multiscale model of the inner-ear. SIFEM aims at developing a linked data platform [2] for finite element biosimulation of the sensorineural hearing loss.…”