Profiling of semantically annotated proteins

We have exploited semantic annotations of biological entities to develop a novel approach to infer new knowledge. We demonstrate this in four use cases based on the Gene Expression Ontology, an applied ontology that we developed to serve the needs of researchers involved in the analysis of genes and proteins implicated in transcriptional control of pathways/diseases. We have found that semantic annotations associated with biological entities in various commonly used data sources support the identification of related entities, thereby emulating associations that can be inferred from sequence or other structural similarities between these entities. We demonstrate how those semantic annotations can be used to make inferences about the respective biological entities.