Many large OBO ontologies use EL++ reasoning (e.g. Elk), performing DL reasoning on smaller chunks (e.g. relations). Having said that newer reasoners like Konkl

Many large OBO ontologies use EL++ reasoning (e.g. Elk), performing DL reasoning on smaller chunks (e.g. relations). Having said that newer reasoners like Konklude apparently do well with DL reasoning over combinations of large ontologies. For "data" / ABoxes we have had a lot of success with the RL subset. We use this a lot https://github.com/balhoff/arachne https://github.com/balhoff/arachne But ultimately it depends on what you want to do. In the life sciences subsets of FOL only buy you so much, and some kind of statistical or probabilistic inference is required. Mostly this is combined with logical inference in crude ad-hoc ways...