Ontology Access Toolkit (OAK) is a Python library for common Ontology operations over a variety of Adapters.

This library provides a collection of different Interfaces for different kinds of ontology operations, including:

  • basic features of an Ontology Element, such as its Label, Definition, Relationships, or Synonyms.

  • Search an ontology for a term.

  • Apply modifications to terms, including adding, deleting, or updating

  • numerous specialized operations, such as Graph Traversal, or Axiom processing, Ontology Alignment, or :term`Text Annotation`.

These interfaces are separated from any particular backend. This means the same API can be used regardless of whether the ontology:

  • is served by a remote API such as OLS or BioPortal.

  • is present locally on the filesystem in OWL, OBO Format, OBO Graphs, or SQLite formats.

  • is to be downloaded from a remote Ontology Repository such as the OBO Library.

  • is queried from a remote database, including SPARQL endpoints, A SQL database, a Solr/ES endpoint.

Basic Python Example

The following code will load an ontology from a SQLite database, lookup basic information on terms matching a search

>>> from oaklib import get_adapter
>>> adapter = get_adapter("sqlite:obo:cl")
>>> for curie in adapter.basic_search("T cell"):
...     print(f'{curie} ! {adapter.label(curie)}')
...     print(f'Definition: {adapter.definition(curie)}')
...     for rel, fillers in adapter.outgoing_relationship_map(curie).items():
...         print(f'  RELATION: {rel} ! {adapter.label(rel)}')
...         for filler in fillers:
...             print(f'     * {filler} ! {adapter.label(filler)}')
CL:0000084 ! T cell
Definition: A type of lymphocyte whose defining characteristic is the expression of a T cell receptor complex.
   RELATION: RO:0002202 ! develops from
      * CL:0000827 ! pro-T cell
   RELATION: RO:0002215 ! capable of
      * GO:0002456 ! T cell mediated immunity
   RELATION: rdfs:subClassOf ! None
      * CL:0000542 ! lymphocyte

Basic Command Line Example

$ runoak -i sqlite:obo:obi info "assay"

This does a basic lookup of the term “assay” in OBI