Ontologies are widely used to create biomedical annotations. Considerable effort goes into curation of publications to create annotations of genes and gene products as well as in the annotation of data sets. However, ‘annotation’ has different meanings in these two contexts, leading to enormous confusion within the bioinformatics community. In this work, we delineate the two meanings of annotation. We demonstrate that the semantics of these two interpretations are different and have significant bearing on how annotations of each type are created, stored, and used.
