The prominent role protein kinases play in cell regulation and disease has given rise to an abundance of information about the structure, function, interactions and evolution of these proteins. This information, however, is currently spread across several heterogeneous resources, an obstacle to the kind of integrative approaches needed in utilizing existing knowledge for research related to diseases. We have designed and developed an ontology for protein kinases, ProKinO, that serves as a useful and efficient representation of the integrated knowledge about these complex proteins which are intimately involved in the genesis and behavior of cancer cells. ProKinO captures concepts and relationships important to protein kinases and the instances are populated from disparate resources including KinBase, COSMIC, Protein Data Bank, UniProt and Pfam. ProKinO has potential applications in text mining in the protein kinase literature; cancer genome annotation in cancer genome sequencing studies and research related to protein kinases and associated domains.