Interfaces

oaklib provides a variety of interfaces that abstract away from implementation details and provide a coherent set of operations to perform on an ontology. Developers can code to the interface largely without worrying about whether the implementation is a relational database, a local file, etc.

For example, the UbergraphImplementation implements SearchInterface which has the method SearchInterface.basic_search(), so you can write code like this:

>>> from oaklib.implementations.ubergraph import UbergraphImplementation
>>> oi = UbergraphImplementation()
>>> for r in oi.basic_search('CA4 hippocampus'):
...     print(r)

The most common operations are found in the BasicOntologyInterface

Contents:

• Basic Ontology Interface
  • Code
• Search Interface
  • Command Line
  • Datamodels
  • Code
• Subsetting
• Validator Interface
• Relation Graph
• Mapping Provider
  • Synopsis
  • About
  • Data Model
  • Implementations
  • Command Line Use
  • Code
    • Example
    • Autodoc
• OboGraph Interface
• Text Annotator Interface
• Summary Statistics
• Patcher Interface
• Semantic Similarity Interface
• Class Enrichment Calculation Interface

Note

Some interfaces may not be “pure” interfaces is that they may provide a default implementation, which may or may not be overridden by an implementation