idk (I Don’t Know) – Ontology, Semantic Web – Cablegate

While researching the idk (I Don’t Know) post I ran across the suggestion unknown was not appropriate for an ontology:

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. (, 5 December 2010)

I wonder about the restriction, “…entities that actually exist.” means?

If a leak of documents occurs, a leaker exists, but in a topic map, I would say that was a role, not an individual.

If the unknown person is represented as an annotation to a role, how do I annotate such an annotation with information about the unknown/unidentified leaker?

Being unknown, I don’t think we can get that with an ontology, at least not directly.


PS: A topic map can represent unknown functions, etc., as first class subjects (using topics) for an appropriate use case.

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