Switch CL build to use the Whelk reasoner

obophenotype / cell-ontology

An ontology of cell types

https://obophenotype.github.io/cell-ontology/

Creative Commons Attribution 4.0 International

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Switch CL build to use the Whelk reasoner #2717

Closed dosumis closed 3 weeks ago

dosumis commented 3 weeks ago

This is required for reasoning to take advantage of property chains added for https://github.com/oborel/obo-relations/issues/787

ROBOT supports Whelk

CC @balhoff - I assume no down-sides. Please yell if I'm wrong. Thanks!

gouttegd commented 3 weeks ago

Note that while Whelk has just been updated to version 1.2.1 in ROBOT (two days ago), the version available in the ODK as of now is still 1.0.4.

balhoff commented 3 weeks ago

@dosumis @gouttegd Whelk is slower and uses more memory, but supports these additional axiom types. It's possible you won't notice for CL. Whelk 1.0.4 does not use property ranges, but 1.2.1 does.

gouttegd commented 3 weeks ago

From a quick test:

With ELK: make test runs in ~2min and consumes ~6.5 GB of RAM
With WHELK: make test runs in ~3.30min and consumes ~7.6GB of RAN

Strictly speaking it’s almost a doubling of the running time, but that seems sustainable to me.