We present an analysis of some considerations involved in expressing the Gene Ontology (GO) as a machine-processible ontology, reflecting principles of formal ontology. GO is a controlled vocabulary that is intended to facilitate communication between biologists by standardizing usage of terms in database annotations. Making such controlled vocabularies maximally useful in support of bioinforma...

Despite the dramatic growth of online genomic data, their understanding is still in early stage. To have meaningful interpretation, it requires the integration of various types of data that are relevant, such as gene sequence, protein interaction and metabolic pathway. Gene Ontology, an ontology proposed by molecular biologist community, is a possible tool to help address some of the difficulti...