Importing External Prefixes

While the Bioregistry automatically imports all prefixes from external registries with similar scope and sufficient minimum metadata and quality standards (e.g., Identifiers.org), it only partially aligns most external registries (e.g., BioPortal). This is a tutorial on how to import a prefix from one of the partially aligned registries on an as-needed basis. More specifically, it describes importing the Food classification (FOODEX2) ontology from AgroPortal. Pull request #573 contains the relevant diff for the changes described in this tutorial.

Identify a prefix of interest from AgroPortal (or another) curation sheet (e.g., here)
Pick a prefix for the Bioregistry. This doesn’t have to be the same as the external one, but usually it is. If the external prefix is too short or too vague, it might be a good chance to improve on this. Further, keep in mind that Bioregistry requires lowercase, so the best choice here is foodex2
Go into the bioregistry.json file and use the prefix as a key for a new dictionary object.
The only thing you need inside the object is "mappings" which itself is a dictionary object where the key is the metaprefix for the external registry (in this case agroportal) and the value is the external registry’s prefix (in this case FOODEX2).
```
 "foodex2": {
     "mappings": {
         "agroportal": "FOODEX2"
     }
 }
```
Make sure the Bioregistry is installed in editable mode
Run the alignment script for the registry. In this case, it’s python -m bioregistry.align.bioportal
Run unit tests with tox -e py. This reveals that the alignment doesn’t pull in enough metadata to meet the minimum requirements. In this case, OntoPortal instances (e.g., AgroPortal, BioPortal, etc.) don’t provide a well-defined example local unique identifier (though note they provide an unstandardized example_iri field that might be helpful)
Curate an example identifier. In this case, the AgroPortal’s example_iri gives enough information to pull out an example identifier.
Add any additional curations