TY - JOUR T1 - On the Use of Gene Ontology Annotations to Assess Functional Similarity among Orthologs and Paralogs: A Short Report A1 - Thomas, Paul D. A1 - Wood, Valerie A1 - Mungall, Christopher J. A1 - Lewis, Suzanna E. A1 - Blake, Judith A. A1 - on behalf of the Gene Ontology Consortium Y1 - 2012/02/16 N2 - Author Summary Understanding gene function—how individual genes contribute to the biology of an organism at the molecular, cellular and organism levels—is one of the primary aims of biomedical research. It has been a longstanding tenet of model organism research that experimental knowledge obtained in one organism is often applicable to other organisms, particularly if the organisms share the relevant genes because they inherited them from their common ancestor. Nevertheless this tenet is, like any hypothesis, not beyond question. A recent paper has termed this hypothesis a “conjecture,” and performed a statistical analysis, the results of which were interpreted as evidence against the hypothesis. This statistical analysis relied on a computational representation of gene function, the Gene Ontology (GO). As representatives of the international consortium that produces the GO, we show how the apparent evidence against the “ortholog conjecture” can be better explained as an artifact of how molecular biology knowledge is accumulated. In short, a complementarity between knowledge obtained in mouse and human experimental systems was incorrectly interpreted as a disagreement. We discuss the proper interpretation of GO annotations and potential sources of bias, with an eye toward enhancing the informed use of the GO by the scientific community. JF - PLOS Computational Biology JA - PLOS Computational Biology VL - 8 IS - 2 UR - https://doi.org/10.1371/journal.pcbi.1002386 SP - e1002386 EP - PB - Public Library of Science M3 - doi:10.1371/journal.pcbi.1002386 ER -