This really comes down to whether the extension will only be used privately (i.e., by yourself or the organization you work for) or whether the extension has value for the community in general.
In the private case you can create your own ontology that imports chebi and then you can add the extensions you want to your ontology. Importing chebi will allow you to get access to newer releases of chebi whereas maintaining your own copy of chebi will cause you to be stuck with that version of chebi.
In the general case it is best to open an issue in the issue tracker of chebi. Further, chebi allows you to become a user which seems to allow you to submit changes. This way your changes (once accepted) will benefit the community in general.
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