Part 2: Basic Python


This part of the tutorial will walk through how to use basic OAK functionality within a Python program. We will be making use of lightweight obo format files - future parts of this tutorial will instruct on how to use other formats and remote endpoints.


For this tutorial some basic Python knowledge is assumed. Familiarity with object-oriented concepts is also useful.

Install Poetry

For this section we are going to use Poetry to set up a project. If you are an experienced developer feel free to adapt these instructions to your favored package manager, otherwise we advise sticking closely to the instructions.

Create a new project

poetry new --src -n my-oak-demo
cd my-oak-demo
poetry add oaklib

Basic Concepts

The two basic concepts you will learn here are:

  • Adaptors (Implementations): How to create a connector object that can talk to a backend or work with a particular file format

  • Interfaces: How to perform operations on a basic ontology interface, regardless of the backend

Code the first example

We are going to use an example from the Basic Ontology Interface, using the Cell Ontology (CL).

Then create a python program: my_oak_demo/ and add the following:

>>> from oaklib import get_adapter
>>> adapter = get_adapter("sqlite:obo:cl")

Next, let’s perform some basic lookup operations on the ontology:

>>> print(adapter.label('CL:4023017'))
sst GABAergic cortical interneuron
>>> print(adapter.definition('CL:4023017'))
A GABAergic neuron located in the cerebral cortex that expresses somatostatin (sst)

You can look up the methods above in the documentation for the Basic Ontology Interface

Now we will query for outgoing relationships from the sst GABAergic cortical interneuron:

>>> for s, p, o in adapter.relationships(['CL:4023017']):
...     print(s, p, o)
CL:4023017 RO:0002292 PR:000015665
CL:4023017 rdfs:subClassOf CL:0010011

Extending the example

Next we will write a function that takes as input

  • an ontology adapter

  • a term ID (term:CURIE)

And write out information about that term

>>> from oaklib import BasicOntologyInterface
>>> def show_info(adapter: BasicOntologyInterface, term_id: str):
...     print(f"ID: {term_id}")
...     print(f"Name: {adapter.label(term_id)}")
...     print(f"Definition: {adapter.definition(term_id)}")
...     for rel, parent in adapter.outgoing_relationships(term_id):
...         print(f'  {rel} ({adapter.label(rel)}) {parent} ({adapter.label(parent)})')

We can now try this:

>>> show_info(adapter, 'CL:4023017')
ID: CL:4023017
Name: sst GABAergic cortical interneuron
Definition: A GABAergic neuron located in the cerebral cortex that expresses somatostatin (sst)
  RO:0002292 (expresses) PR:000015665 (somatostatin)
  rdfs:subClassOf (None) CL:0010011 (cerebral cortex GABAergic interneuron)