FAQ: Ontologies
What is an ontology?
See the section Basics in the The OAK Guide.
Do we need ontologies now we have ChatGPT?
Large Language Models (LLMs) fine-tuned on instruction tasks display impressive abilities to work with knowledge using a purely natural language interface. However, at this time, LLMs lack any grounding for the answers they provide, something ontologies are very good at.
The OAK developers are very interested in the fusion of LLM research and knowledge-based ontology research. See our OntoGPT project for examples.
What is OWL?
OWL (Web Ontology Language) is a data model for expressing ontologies, oriented around set-theoretic logical Axioms.
See OWL.
What is OBO Format?
OBO Format is a simple format for expressing a subset of OWL in a way that is easily read and produced.
See OBO Format.
What is OBO
OBO (Open Bio Ontologies) is a repository of ontologies intending to conform to common standards.
Note
OBO does not require OBO Format.
What’s a synonym and how do I access them?
See the section Aliases and Synonyms in the OAK guide.
You can query for synonyms on the command line:
runoak -i sqlite:obo:cl aliases "T cell"
curie |
pred |
alias |
|---|---|---|
CL:0000084 |
rdfs:label |
T cell |
CL:0000084 |
oio:hasExactSynonym |
T lymphocyte |
CL:0000084 |
oio:hasExactSynonym |
T-cell |
CL:0000084 |
oio:hasExactSynonym |
T-lymphocyte |
CL:0000084 |
oio:hasRelatedSynonym |
immature T cell |
CL:0000084 |
oio:hasRelatedSynonym |
mature T cell |