FAQ: Architecture and Design

What is an interface?

OAK is designed so that application developers can focus on coding to an interface without worrying about the details of the implementation.

For example, the following code will talk to the SQLite backend for CL to find all IS_A descendants of “neuron”, and show them alongside their labels:

>>> from oaklib import get_adapter
>>> from oaklib.datamodels.vocabulary import IS_A
>>> adapter = get_adapter("sqlite:obo:cl")
>>> for d in adapter.descendants("CL:0000540", predicates=[IS_A]):
...     print(d, adapter.label(d))

...
CL:0011103 sympathetic neuron
...

In this case, the developer does not need to know anything about the underlying implementation. It could be SQL or a flat file.

In this case, the ancestors and label methods are both part of the basic_ontology_imerface

The actual implementation when sqlite:obo:cl is used as an input selector is the SQL Database Adapter, but the application developer doesn’t need to know this.

What is a Data Model?

A Datamodel is a way of structuring data for a particular domain. OAK takes a pluralistic approach, and supports many different data models for different tasks. These are often coupled with interfaces:

Basic Ontology Interface avoids data models and yields simple structures like lists of tuples
Text Annotator Interface uses the https://w3id.org/oak/text-annotator data model
Mapping Provider Interface uses the SSSOM data model
Class Enrichment Calculation Interface uses the https://w3id.org/oak/class-enrichment data model
Patcher Interface uses the KGCL data model
Association Provider Interface uses the https://w3id.org/oak/association data model
Validator Interface uses the https://w3id.org/oak/validation
…

When used within Python, an object oriented structure is followed, where the different attributes of the data model are accessed via . notation.

For example, Mapping Provider Interface provides a method sssom_mappings which yields Mapping objects conforming to the SSSOM data model. A mapping object has fields like subject_id:

>>> from oaklib import get_adapter
>>> adapter = get_adapter("tests/input/go-nucleus.obo")
>>> for mapping in adapter.sssom_mappings(["GO:0005886"], source="Wikipedia"):
...     print(mapping.subject_id, mapping.object_id)
GO:0005886 Wikipedia:Cell_membrane

OAK uses a mixture of native an external data models.

Native data models have the OAK w3id namespace - for example, https://w3id.org/oak/class-enrichment.

What is an iterator and why does OAK use them so much?

OAK uses iterators in place of lists in a lot of places, in order to make the code more scalable and more amenable to streaming.

See Iterator.