bep

[WITHDRAWN] Namespace Placeholder: TBD

History

Abstract

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.

Preamble

BEP-Id: BEP-0002

Status: Draft

Version: 1

BEL-Version: 2.0.0

Authors: William Hayes ([email protected])

Created-Date: 2018-06-08

Type: Process

Rationale and Goals

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.

Use Cases

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.

Discussion

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:

If we were to agree to set using TBD as the namespace keyword for “placeholder” namespaces, how would this look in BEL Script? Even if BEL.bio won’t support BEL Script as a first class citizen, we haven’t officially deprecated or decommissioned it and other tools will have to cope with entities that won’t be backed by a namespace. Logically, I don’t think this is a big problem, but it might be from the technical implementation side.

Specification

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.

Backwards Compatibility

There are no backwards compatibility issues associated with this BEP.

Reference Implementation

Not required for this BEP.

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