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Ontology Curator Pathway

There is no one single accepted methodology for building ontologies in the OBO-World. We can distinguish at least two major schools of ontology curation

  • GO-style ontology curation
  • OBI-style ontology curation

Note that there are many more variants, probably as many as there are ontologies. Both schools differ only in how they curate their ontologies - the final product is always an ontology in accordance with OBO Principles. These are some of the main differences of the two schools:

GO-style OBI-style
Edit format Historically developed in OBO format Developed in an OWL format
Annotation properties Many annotation properties from the oboInOwl namespace, for example for synonyms and provenance. Many annotation properties from the IAO namespace.
Upper Ontology Hesitant alignment with BFO, often uncommitted. Strong alignment with BFO.
Logic Tend do be simple existential restrictions (some), ontologies in OWL 2 EL. No class expression nesting. Simple logical definition patterns geared towards automating classification Tend to use a lot more expressive logic, including only and not. Class expression nesting can be more complex.
Examples GO, Uberon, Mondo, HPO, PATO OBI, IAO, OGMS

There are a lot of processes happening that are bringing these schools together, sharing best practices (GitHub, documentation) and reconciling metadata conventions and annotation properties in the OBO Metadata Ontology (OMO). The Upper Level alignment is now done by members of both schools through the Core Ontology for Biology and Biomedicine (COB). While these processes are ongoing, we decided to curate separate pathways for both schools: