ontogpt

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> Strengthening The Organization and Reporting of Microbiome Studies (STORMS) is a checklist for reporting on human microbiome studies, organized into six sections covering all sections of a scientific publication,...

caufieldjh

Is there an option to use GPU for the LLM, the inference speed is a little too slow. My GPU utilization is almost zero.

4

on local model

doubleplusplus

Using value set expansion with non-OBO annotator leads to 404 error

2

Originally seen in #346. Using a Bioportal ontology (like bioportal:SNOMEDCT) as an annotator works fine on its own. If used in a value set expansion, e.g., with a `reachable_from`, it...

caufieldjh

industrial-production-specific SPIRES

2

...I am trying to build an industrial-production-specific SPIRES. I found the upper level production ontology built by Industrial Foundry Ontology. Do you have any suggestions how to inverse-engineeringly design a...

caufieldjh

Requesting model `orca-2-7b` raises `llm.UnknownModelError`

5

Issue c/o Bart Kleijngeld: Using the `llm` package to call `orca-2-7b` directly works as expected: ``` $ llm -m orca-2-7b "Hi!" 100%|█████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████| 3.83G/3.83G [05:58

caufieldjh

Provide equivalencies for phenotype terms

6

From @matentzn at today's Monarch Huddle: > Wishlist to OntoGPT team: we need a scalable solution to suggestion EQs for phenotype ontologies.

caufieldjh

Evaluate extractor

3

Hi, I'm not so clear what the evaluation function does (the document is not super clear). Does it evaluate the extraction I got (how)? Can it evaluate my own schema...

kluo9

Extraction of MAXO annotations is helpful but would be much more helpful if we get the output in a format compatible with the other MAXO annotations, as seen here: https://github.com/monarch-initiative/maxo-annotations/blob/master/annotations/maxo-annotations.tsv...

caufieldjh

Relax truncation with `pubmed-annotate`

1

The `pubmed-annotate` command currently truncates inputs to ~3K characters. That's not necessary with the larger context models, so it can be relaxed and/or added as a CLI parameter.

caufieldjh

Hey Harry! I noticed that GPT will provide the full name of foods, for example take this input: "Sample from Samso Cheese" (Apparently[ a cheese from Denmark](https://en.wikipedia.org/wiki/Sams%C3%B8_cheese)). It will extract...

rickbeeloo