Take Your Terms from Ontologies (TYTO) is a lightweight Python tool that makes the semantic web more user-friendly and accessible.
TYTO provides a handy interface for ontologies for use in your Python application. It automatically generates symbols for URIs based on the ontology terms themselves. Currently the following ontologies are supported:
- Sequence Ontology (SO)
- Systems Biology Ontology (SBO)
- National Cancer Institute Thesaurus (NCIT)
- Ontology of Units and Measures (OM)
For example:
>>> from tyto import SO, SBO
RDFLib Version: 5.0.0
>>> print(SO.promoter)
http://purl.obolibrary.org/obo/SO_0000167
>>> print(SBO.systems_biology_representation)
http://biomodels.net/SBO/SBO_0000000
These symbols are not hard-coded, rather they are dynamically generated by querying the appropriate ontology endpoints. Alternatively an ontology can be imported from a local OWL file.
Additionally ontologies have methods that allow for other types of inference.
>>> SO.get_term_by_uri('http://purl.obolibrary.org/obo/SO_0000167')
'promoter'
An interface for a new ontology can be configured as follows, thus allowing for dynamic lookup of terms and URIs.
my_ontology = Ontology(endpoint='http://myendpoint.org/sparql#', path='./ontologies/my_ontology.owl')
Tyto deroepstorffi, otherwise known as the Andaman masked owl, is the mascot for this repo. An owl was considered an appropriate choice because TYTO leverages the Web Ontology Language (OWL).
Development of this library has been supported by the DARPA Synergistic Discovery and Design (SD2) program and Raytheon BBN Technologies.