PDON: Parkinson’s disease ontology for representation and modeling of the Parkinson’s disease knowledge domain

• DOI: 10.1186/s12976-015-0017-y
• Publication Date: 2015-09-22T12:13:36Z
• Authors: Erfan Younesi; Ashutosh Malhotra; Michaela Gündel; Phil Scordis; Alpha Tom Kodamullil; Matt Page; Bernd Müller; Stephan Springstubbe; Ullrich Wüllner; Dieter Scheller; Martin Hofmann-Ap...
• Keywords: Open Biomedical Ontologies

Despite the unprecedented and increasing amount of data, relatively little progress has been made in molecular characterization mechanisms underlying Parkinson's disease. In area research, there is a pressing need to integrate various pieces information into meaningful context presumed disease mechanism(s). Disease ontologies provide novel means for organizing, integrating, standardizing knowledge domains specific compact, formalized computer-readable form serve as reference exchange or systems modeling mechanism. The ontology was built according life cycle building. Structural, functional, expert evaluation performed ensure quality usability ontology. A novelty metric introduced measure gain new using Finally, cause-and-effect model around PINK1 two gene expression studies from Gene Expression Omnibus database were re-annotated demonstrate with subclass-based taxonomic hierarchy covers broad spectrum major biomedical concepts clinical features disease, also reflects different views on held by biologists, clinicians drug developers. current version contains 632 concepts, which are organized under nine views. structural showed balanced dispersion concept classes throughout functional demonstrated that ontology-driven literature search could not present map. able answer questions related when evaluated experts. added value re-annotation datasets relevant delivers domain form, can be further edited enriched scientific community used construct, represent automatically extend Parkinson's-related computable models. practical browsing editing publicly accessed at http://bioportal.bioontology.org/ontologies/PDON .