We found a match
Your institution may have access to this item. Find your institution then sign in to continue.
- Title
Representing physiological processes and their participants with PhysioMaps.
- Authors
Cook, Daniel L.; Neal, Maxwell L.; Hoehndorf, Robert; Gkoutos, Georgios V.; Gennari, John H.
- Abstract
Background: As the number and size of biological knowledge resources for physiology grows, researchers need improved tools for searching and integrating knowledge and physiological models. Unfortunately, current resources--databases, simulation models, and knowledge bases, for example--are only occasionally and idiosyncratically explicit about the semantics of the biological entities and processes that they describe. Results: We present a formal approach, based on the semantics of biophysics as represented in the Ontology of Physics for Biology, that divides physiological knowledge into three partitions: structural knowledge, process knowledge and biophysical knowledge. We then computationally integrate these partitions across multiple structural and biophysical domains as computable ontologies by which such knowledge can be archived, reused, and displayed. Our key result is the semiautomatic parsing of biosimulation model code into PhysioMaps that can be displayed and interrogated for qualitative responses to hypothetical perturbations. Conclusions: Strong, explicit semantics of biophysics can provide a formal, computational basis for integrating physiological knowledge in a manner that supports visualization of the physiological content of biosimulation models across spatial scales and biophysical domains.
- Subjects
DATABASES; SIMULATION methods &; models; ONTOLOGY; BIOPHYSICS; SEMANTICS; PHYSIOLOGY; VISUALIZATION
- Publication
Journal of Biomedical Semantics, 2013, Vol 4, Issue Suppl 1, p1
- ISSN
2041-1480
- Publication type
Article
- DOI
10.1186/2041-1480-4-S1-S2