Frequently Asked Questions

This is a list of Frequently Asked Questions about OAK. Feel free to suggest new entries!

Warning

This FAQ is still quite incomplete!

How do I…

… Install OAK

See Part 1: Getting Started of the tutorial.

… get all ancestors of a term?

On the command line you can use the commands ancestors, tree, viz, all of which are variants of fetching and displaying ancestors. In programs you can use OboGraph Interface

… Contribute code

Please consult the CONTRIBUTING.md guide

What is…

OAK for

OAK is for both technical and non-technical users of ontologies. Non-technical users can use the cli to query ontologies in a variety of ways. Technical users can write Python code that uses the OAK library to perform ontology-related tasks, ranging from basic lookup, search, graph traversals, validation, data annotation, mapping, and OWL processing.

An iterator

See Iterator in the glossary

Using OAK with…

The Command Line

OAK provides a fully-featured command line interface. See Part 8: Applying Changes to Ontologies of the tutorial.

Bioportal

OAK can be used to query any ontology in Bioportal - or many of the Portals in the OntoPortal alliance. See Bioportal Endpoint.

OLS

OAK can be used to query any ontology in OLS. See ols_implementation.

SQLite

OAK can query any SQL database that conforms to the :term`Semantic SQL` standard. SQLite is a database system that works directly with files rather than through a database management system. It is frequently the most performant way to work with ontologies in OAK, as there is no parsing involved. See Part 8: Applying Changes to Ontologies.

Command Line

What do the codes “i” and “p” mean?

Many commands take a --predicates option, the value is a comma separated list of CURIEs. You can use “i” as a shortcut for is_a (rdfs:subClassOf) and “p” as a shortcut for part_of (BFO:0000050)

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 Endpoint.

… 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.

… It takes a long time to load my OWL file

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