Semantics for Biosimulation models (SemSim)

 

The SemSim project is an approach to annotating, sharing and reusing biosimulation models. This project is a core use case for the Semantics for Biological Processes research group. As described below, it depends on the idea of reference ontologies, and uses the Ontology of Physics for Biology as its reference ontology for process knowledge.

Research problem statement:

Current biosimulation resources exist as unconnected silos. Thus, researchers cannot easily query, merge or connect models across these repositories.

 

Solution approach:

Inspired by ideas from the semantic web and from software reuse, we aim to:

  1. Annotate models with their semantics, connecting them to knowlege resources such as the Foundational Model of Anatomy, the Ontology of Physics for Biology, and others
  2. Develop methods and tools that help researchers modularize these models, and then merge models, creating robust, multi-scale, and multi-domain biosimulation models