Tyto
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 out-of-the-box:
- Sequence Ontology (SO)
- Systems Biology Ontology (SBO)
- National Cancer Institute Thesaurus (NCIT)
- Ontology of Units and Measures (OM)
- NCBI Taxonomy (NCBITaxon)
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 ontology lookup services on the web. Currently, the Ontobee and EBI Ontology Lookup Services are supported. Additionally, an ontology can be imported from a local OWL file.
Since these ontology lookup services host hundreds of ontologies, Tyto does not currently ship with pre-defined interfaces to every ontology. However, a new Ontology interface can be configured with minimal effort. All of the heavy-lifting has already been implemented on the back-end.
>>> from tyto import EBIOntologyLookupService, Ontology
>>> KISAO = Ontology(uri='http://www.biomodels.net/kisao/KISAO_FULL#', endpoints=[EBIOntologyLookupService])
>>> KISAO.Gillespie_direct_algorithm
'http://www.biomodels.net/kisao/KISAO#KISAO_0000029'
Documentation
Inference and reasoning
Additionally Tyto supports reasoning and inference over ontology terms. For example, the following evaluates to True because the Sequence Ontology categorizes an inducible_promoter as a specialized type of promoter.
>>> tyto.SO.inducible_promoter.is_a(tyto.SO.promoter)
True
Other inference methods include:
term1.is_a(term2)
term1.is_descendant_of(term2)
term1.is_ancestor_of(term2)
term1.get_parents()
term1.get_children()
About our mascot
Tyto is the genus of birds to which owls belong, alluding to the Web Ontology Language (OWL) in which most ontologies are encoded. Tyto's logo is derived from the "Owl of Minerva" which is licensed under CC BY-SA 4.0.
Acknowledgments
If you make use of Tyto, please cite:
Bryan A. Bartley, "Tyto: A Python Tool Enabling Better Annotation Practices for Synthetic Biology Data-Sharing", ACS Synthetic Biology, online February, 2022. DOI: 10.1021/acssynbio.1c00450
Development of this library has been supported by the DARPA Synergistic Discovery and Design (SD2) program and Raytheon BBN Technologies.