As a demonstration of adding new terms into BCO-SM, we will use the following NTR (new term request) from @jaclynsaunders 's recent work which includes the example term: CHEBI:16493, aka 1-deoxy-D-xylulose 5-phosphate.
Examining the term on OLS, we see that the term is subclass to a variety of hierarchies, two of which are shown here:
As explained in the New Term Requests section of the BCODMONT technical docs, we'd check to make sure requested terms isn't yet in the model, then one would create an issue such as this one. Following further along the instructions, note that if an appropriate superclass for a term doesn't exist it may need to be added.
In this example we find the most relevant branch of the ChemistryCompound module, the carbon compound hierarchy.
This is an example of where BCO-SM is a simplification of the imported OBO ontology CHEBI, in which case it is the job of the ontologist to find or create an appropriate superclass term for the newly requested term to be a child of in the BCO-SM model.
In this example, a reasonable course of action would be to also import the term carbohydrate derivative: CHEBI:63299 (in addition to CHEBI:16493 the requested term) to serve as the parent term. If in such a case the intermediate term would only have one child term then it might not make sense to import. Ontology hierarchies with single node intermediates a -> b -> c,d... can be a sign that the intermediate might not merit be it's own term.
In this case however, we also know that other carbohydrate derivative terms such as CHEBI:28681N,N'-diacetylchitobiose will also be requested. Thus adding the superclass concept carbohydrate derivative to BCO-SM might be a reasonable course of action.
A logical place to insert carbohydrate derivative into BCO-SM would likely be as subclass to carbohydrate. Thus as a result of this issue we'll add the following new terms to the BCO-SM carbohydrate hierarchy:
As a demonstration of adding new terms into BCO-SM, we will use the following NTR (new term request) from @jaclynsaunders 's recent work which includes the example term:
CHEBI:16493, aka1-deoxy-D-xylulose 5-phosphate.Examining the term on OLS, we see that the term is subclass to a variety of hierarchies, two of which are shown here:
As explained in the New Term Requests section of the BCODMONT technical docs, we'd check to make sure requested terms isn't yet in the model, then one would create an issue such as this one. Following further along the instructions, note that if an appropriate superclass for a term doesn't exist it may need to be added.
In this example we find the most relevant branch of the
ChemistryCompoundmodule, thecarbon compoundhierarchy.This is an example of where BCO-SM is a simplification of the imported OBO ontology CHEBI, in which case it is the job of the ontologist to find or create an appropriate superclass term for the newly requested term to be a child of in the BCO-SM model.
In this example, a reasonable course of action would be to also import the term
carbohydrate derivative:CHEBI:63299(in addition toCHEBI:16493the requested term) to serve as the parent term. If in such a case the intermediate term would only have one child term then it might not make sense to import. Ontology hierarchies with single node intermediatesa -> b -> c,d...can be a sign that the intermediate might not merit be it's own term.In this case however, we also know that other
carbohydrate derivativeterms such asCHEBI:28681N,N'-diacetylchitobiosewill also be requested. Thus adding the superclass conceptcarbohydrate derivativeto BCO-SM might be a reasonable course of action.A logical place to insert
carbohydrate derivativeinto BCO-SM would likely be as subclass tocarbohydrate. Thus as a result of this issue we'll add the following new terms to the BCO-SM carbohydrate hierarchy: