FAQ: Troubleshooting

Why do I get a “Error: No such option: -i” message

The --input or -i option must come before the subcommand name. This is because the input option is one of the few options that are shared across all subcommands. For example, you should write runoak -i my-ont.owl lexmatch -o results.sssom.tsv

How do I get a BioPortal API key?

See the instructions on Bioportal Adapter.

My OBO Format file won’t parse

The default parser used for obo files is Pronto. Pronto strictly enforces obo format syntax rules, and not all ontologies conform. To get around this, current best practice is to convert the obo to owl, and then work with either owl or sqlite files. Guidance may change on this in the near future as we make this easier.

My OWL file takes too long to load

By default, rdflib is used to parse OWL files (via sparql_adapter), and this is known to be slow. If fast loading is important, we recommend you use sqlite that is converted from the OWL, via sql_adapter.

My cached SQLite ontology is out of date

We use pystow to cache pre-made sqlite3 databases. Currently pystow does not have any cache management capabilities - this means it is up to you to purge old copies.

For example, to purge a stale copy of the cl database:

rm ~/.data/oaklib/cl.db*

Note it is necessary to delete both the .db file and the .db.gz file

I don’t understand the interface/method I want to use

We are always striving to improve the documentation.

Please file an issue and we fill try and improve the documentation based on your feedback.