In this report, we present the development of the Ontology of Genes and Genomes (OGG), a biological ontology in the domain of genes and genomes. To integrate with other ontologies, OGG is aligned with the Basic Formal Ontology (BFO). OGGspecific term IDs and annotations are designed by mapping to NCBI Taxonomy IDs and NCBI Entrez Gene IDs. Each gene in OGG has over 10 annotation items, includes...

Gene Ontology terms have been actively used to annotate various protein sets. SWISS-PROT, TrEMBL, and InterPro are protein databases that are annotated according to the Gene Ontology terms. However, direct implementation of the Gene Ontology terms for annotation of anonymous protein sequences is not easy, especially for species not commonly represented in biological databases. UTMGO is develope...

Protein complexes are of great importance in understanding the principles of cellular organization and function. The increase in available protein-protein interaction data, gene ontology and other resources make it possible to develop computational methods for protein complex prediction. Most existing methods focus mainly on the topological structure of protein-protein interaction networks, and...

This chapter is a tutorial on using Gene Ontology resources in the Python programming language. This entails querying the Gene Ontology graph, retrieving Gene Ontology annotations, performing gene enrichment analyses, and computing basic semantic similarity between GO terms. An interactive version of the tutorial, including solutions, is available at http://gohandbook.org .