Ontologies in biology: design, applications and future challenges

By J. Bard, Seung Yon Rhee. Nature reviews genetics, 2004

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Use and misuse of the gene ontology annotations (2008, background): “jpg" NDATA ITEM> ]> The accumulation of data produced by genome-scale research requires explicitly defined vocabularies to describe the biological attributes of genes in order to allow integration, retrieval and computation of the dat”
From brain maps to cognitive ontologies: informatics and the search for mental structure (2015, background): “We review below several important benefits (for others, see Bard & Rhee 2004, Bodenreider & Stevens 2006, Rubin et al. 2008).”
NCI Thesaurus: A semantic model integrating cancer-related clinical and molecular information (2007, background): “At the same time, there has been a blossoming of biomedical ontologies attempting to more richly represent knowledge in particular fields in ways that often overlap with logic-based terminology efforts [9].”
The Cognitive Atlas: Toward a Knowledge Foundation for Cognitive Neuroscience (2011, background): “Ontologies have also provided the basis for effective knowledge accumulation in molecular biology and genomics (Bard and Rhee, 2004).”
The Mammalian Phenotype Ontology: enabling robust annotation and comparative analysis (2009, methodology): “12 We have built an ontology describing mammalian phenotype (MP) to classify and organize these descriptions for mouse and other mammalian species and for facilitating comparisons across species.”