CLI

The command line interface for Lettuce can run any of the Lettuce components, as specified in command-line arguments.

poetry run lettuce-cli -informal_names "betnovate scalp application"

The arguments used by the CLI are defined by BaseOptions

Provide a string for Lettuce to infer a concept for. You can supply multiple names by using the flag more than once

Choose whether to perform vector search on supplied informal names

Enabling vector search will require a vector database to be built

Choose whether to have an LLM infer an OMOP concept for supplied informal names

Enabling LLM usage will download the model weights for an LLM, which requires ~5 Gb disk space

Controls LLM generation randomness

The OMOP vocabularies to query in the OMOP-CDM database. Supply a comma separated list, e.g.

"RxNorm, RxNorm extension"

Controls whether to query the concept_ancestor table

The maximum levels of separation to return ancestors from the concept_ancestor query

The maximum levels of separation to return descendants from the concept_ancestor query

Controls whether to return concept synonyms from the OMOP-CDM query

The fuzzy match threshold to use when filtering OMOP concept names

The LLM used to infer concepts from an informal name. One of:

Defaults to LLAMA_3_1_8B

The model used to generate embeddings

⚠️

The model used to generate query embeddings and used to build the vector database must be the same or the vector search will be nonsense

One of:

Defaults to BGESMALL