Where have the 'unknown' terms gone?

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Good principles of ontological design state that terms should represent biological entities that actually exist, e.g., functional activities that are catalyzed by enzymes, biological processes that are carried out in cells, specific locations or complexes in cells, etc. To adhere to these principles the Gene Ontology Consortium has removed the terms, "biological process unknown" (GO:0000004), "molecular function unknown" (GO:0005554) and "cellular component unknown" (GO:0008372) from the ontology. The "unknown" terms violated this principle of sound ontological design because they did not represent actual biological entities but instead represented annotation status. Annotations to "unknown" terms distinguished between genes that were curated when no information was available and genes that were not yet curated (i.e., not annotated). Annotation status is now indicated by annotating to the root nodes, i.e. "biological_process" (GO:0008150), "molecular_function" (GO:0003674), or "cellular_component" (GO:0005575). These annotations continue to signify that a given gene product is expected to have a molecular function, biological process, or cellular component, but that no information was available as of the date of annotation. Adhering to principles of correct ontology design should allow GO users to take advantage of existing tools and reasoning methods developed by the ontological community.