Add to documentation: other ontology tools in py-land about ontology-access-kit HOT 3 CLOSED

Just a brief answer now.

Other libraries mentioned during the workshop we should add to the docs (either by adding the interfaces here, or by explaining why we don't)

I think you mean implementations?

the goal isn't to wrap every possible library - instead to provide an implementation every possible source.

So for .obo files, I think obonet, pyobo, and pronto are all really good contenders with roughly similar functionality. We went with pronto as a first pass as the underlying fastobo library is correct and fast, but there are downsides with super-strictness, so we can revisit any of these.

I don't think rdftab is a candidate for an implementation per se - it's a way of populating a sql database, and we have https://incatools.github.io/ontology-access-kit/implementations/sqldb.html which will work with any rdftab populated database that also has the semsql views layered on.

the question of how to wrap owl in python is a very good one, so candidates are owlready2, funowl, and horned-owl+pyo3. Although people may not be aware of how much of owl is already exposed through the sql_database route, and it would be easy to expose more.

from ontology-access-kit.

There's also https://github.com/jannahastings/py-horned-owl which is a set of Python bindings for the https://github.com/phillord/horned-owl Rust library. py-horned-owl is a proof-of-concept -- maybe usable for some things, but not recommended for production. I funded Janna's work on it, but Janna has a new position, and I don't plan to pursue this path.

The path I'm pursuing is LDTab as a successor to RDFTab: representing RDF and OWL using SQL and JSON, supported by Wiring. I am using that stuff in production, but it's very much work in progress and not documented.

from ontology-access-kit.

Closing as done

from ontology-access-kit.