Serena Lotreck

Ok so it definitely looks like it's the grounding, here are the times from running it on a single doc with the `time` command in bash: ``` real 6m6.517s user...

> A quick check for this may be to temporarily disable annotation for a specific class, or change the domain of the corresponding slot to `string` so it doesn't ground...

> Also depends on how your grounding: semsql, bioportal, Gilda… @cmungall what grounding approach am I using if my annotators are all prefixed with `sqlite:obo:`, and where I should go...

Ok so I did a closer read of the paper as well as looking at the implementation of grounding [here](https://github.com/monarch-initiative/ontogpt/blob/466e86b77dc44ac5b04ec89da735255cddc713f7/src/ontogpt/engines/spires_engine.py#L575), and took a cursory skim through the semantic-sql docs. >...

This is great, thank you! I'll hold off on adding specific identifiers to the schema until I've exhausted other options since it may not be a huge boost anyway. I'll...

I tried just running the verbatim version of `taxslim.obo` that you provided, and damn what a speedup!! ``` real 1m7.614s user 0m57.557s sys 0m27.794s real 1m6.706s user 0m57.438s sys 0m27.624s...

It definitely got faster after turning the slim Taxonomy into an sqlite database! Cut off about 10 seconds. ChEBI has a Lite version of the ontology, which I made into...

Hi all, Just wanted to update on this and ask some questions. Before spending time optimizing, I decided to make sure that switching to the slim ontology didn't affect performance...

@caufieldjh wondering if this has been fixed? I'm running OntoGPT on a large quantity of documents and the ballooining size of the YAML is severely slowing down my ability to...

Looks like that fixed it, thanks!