commands.txt

Ontology URL-
http://purl.obolibrary.org/obo/go/go-basic.obo

Artical URL-


Building-
python3 examples/simple-app/app/ontologyGrounding/build_ontology_index.py --url http://purl.obolibrary.org/obo/go/go-basic.obo --output-dir data --cache-dir tmp/cache --embedding-type gemini --embedding-model gemini-embedding-001 --batch-size 200 --collection-name ontology-gemini-embedding-001

Indexing-
python3 examples/simple-app/app/main.py indexer index --input-file examples/input-data/book.txt --output-dir data --cache-dir tmp/cache --llm-type gemini --llm-model gemini-2.5-flash --embedding-type gemini --embedding-model gemini-embedding-001 --ontology-enable --ontology-top-k 10 --ontology-threshold 0.60

graphCreation-
python3 examples/simple-app/app/main.py indexer visualize --llm-model gemini-2.5-flash --output tmp/graph.html --output-dir data --graph summarized

BASELINE RAG-
Indexing- 
uv run python examples/simple-app/app/main.py baseline index --input-file examples/input-data/book.txt --output-dir tmp/out --cache-dir tmp/cache --embedding-type gemini --embedding-model embedding-001
Query-
uv run python examples/simple-app/app/main.py baseline query --output-dir tmp/out --cache-dir tmp/cache --llm-type gemini --llm-model gemini-2.5-flash --embedding-type gemini --embedding-model embedding-001 --query "What are the main themes in this story?" --top-k 4

Batch-
python3 examples/simple-app/app/batch_qa.py run --output-dir data --cache-dir tmp/cache --llm-type gemini --llm-model gemini-2.5-flash --embedding-type gemini --embedding-model gemini-embedding-001 --level 1

Report-
python3 examples/simple-app/app/batch_qa.py --output-dir tmp --cache-dir tmp/cache --llm-type gemini --llm-model gemini-2.5-flash --embedding-type gemini --embedding-model gemini-embedding-001