GORouter: an RDF model for providing semantic query and inference services for Gene Ontology and its associations

Background: The most renowned biological ontology, Gene Ontology (GO) is widely used for annotations of genes and gene products of different organisms. However, there are shortcomings in the Resource Description Framework (RDF) data file provided by the GO consortium: 1) Lack of sufficient semantic relationships between pairs of terms coming from the three independent GO sub-ontologies, that limit the power to provide complex semantic queries and inference services based on it. 2) The term-centric view of GO annotation data and the fact that all information is stored in a single file. This makes attempts to retrieve GO annotations based on big volume datasets unmanageable. 3) No support of GOSlim. Results: We propose a RDF model, GORouter, which encodes heterogeneous original data in a uniform RDF format, creates additional ontology mappings between GO terms, and introduces a set of inference rulebases. Furthermore, we use the Oracle Network Data Model (NDM) as the native RDF data rep...

• Type: Journal
• Year: 2008
• Where: BMCBI
• Authors: Qingwei Xu, Yixiang Shi, Qiang Lu, Guo-qing Zhang, Qing-ming Luo, Yixue Li
• Keywords: BMCBI 2008, Independent Go Sub-ontologies, Semantic, Sufficient Semantic Relationships