Provide a standard Namespace prefix for terms not currently available for any namespace allows users to use a placeholder namespace value that BEL tools can automatically provide replacements as they become available in the supported terminologies.
Authors: William Hayes ([email protected])
Encourage the use of a placeholder namespace prefix when the term does not exist in any of the supported namespaces. This is to mitigate the number of private namespaces needed and often created when a term does not exist in a public and parallel namespace. For example, Selventa created several namespaces to accommodate new terms and concepts that were parallel to available namespaces - e.g. SDIS (Selventa Disease) vs DO (Disease Ontology).
With a standard namespace prefix for a term, we can find cases where a term is not based on a current namespace and evaluate the available namespaces for a match when that term/concept is added to the namespace and then propose the replacement to the user.
User tries to add a term into a BEL Assertion (e.g. p(newterm)). When not found in the available namespaces, the term is entered as p(TBD:newterm). The BEL assertion is evaluated periodically to see if a match is found in any of the Protein namespaces since the TBD:newterm (newterm is just a generic name for any term that is added) is used in a protein context. A match to the newterm in a non-protein context would not be considered a match.
In a BEL Nanopub editing environment, the TBD:newterm could be presented if no other matches are available. The editing environment could periodically evaluate all of the TBD:newterm1, TDB:newterm2, … namespace values against the appropriate context namespace values to see if any matches are available. If a match is available, the match could be presented via a notification to the creator or curator of the nanopubs using the TDB:newterm namespace value to permit replacement.
Best practice would be for the user adding a TBD:newterm to propose adding that concept to the parent ontology or terminology associated with the relevant namespace.
Questions from Natalie Catlett:
What happens when a curator enters a TBD term that has a strange BEL function/type?
Will it get fixed in TBD after someone reviews/edits the original nanopub?
What if TBD terms are entered with misspellings?
Questions from Charlie Hoyt:
This does not require any changes to the BEL Specification. BEL documentation would need to be updated to officially recognize TBD as a namespace prefix used for this purpose.
There are no backwards compatibility issues associated with this BEP.
Not required for this BEP.