├── .github └── workflows │ ├── LangSmith_evaluation.yml │ ├── docs.yml │ ├── pr_agent.yml │ ├── qodo-cover-pr.yml │ ├── qodo-cover-pro.yml │ ├── qodo-cover.yml │ └── test_main.yml ├── .gitignore ├── .pr_agent.toml ├── .python-version ├── Dockerfile ├── LICENSE.txt ├── Procfile ├── README.md ├── app ├── __init__.py ├── config │ ├── langgraph.json │ ├── logging.ini │ ├── params.ini │ ├── params_alternative.ini │ └── sparql.ini ├── core │ ├── __init__.py │ ├── agents │ │ ├── __init__.py │ │ ├── agents_factory.py │ │ ├── enpkg │ │ │ ├── __init__.py │ │ │ ├── agent.py │ │ │ ├── prompt.py │ │ │ ├── tool_chemicals.py │ │ │ ├── tool_smiles.py │ │ │ ├── tool_target.py │ │ │ └── tool_taxon.py │ │ ├── entry │ │ │ ├── __init__.py │ │ │ ├── agent.py │ │ │ ├── prompt.py │ │ │ └── tool_filesparser.py │ │ ├── interpreter │ │ │ ├── __init__.py │ │ │ ├── agent.py │ │ │ ├── prompt.py │ │ │ ├── tool_interpreter.py │ │ │ └── tool_spectrum.py │ │ ├── sparql │ │ │ ├── __init__.py │ │ │ ├── agent.py │ │ │ ├── prompt.py │ │ │ ├── tool_merge_result.py │ │ │ ├── tool_sparql.py │ │ │ └── tool_wikidata_query.py │ │ ├── supervisor │ │ │ ├── __init__.py │ │ │ ├── agent.py │ │ │ └── prompt.py │ │ └── validator │ │ │ ├── __init__.py │ │ │ ├── agent.py │ │ │ ├── prompt.py │ │ │ └── tool_validator.py │ ├── example_queries │ │ ├── all_distances_between_species.sparql │ │ ├── collect_chromatogram_info.sparql │ │ ├── count_species_per_family.sparql │ │ ├── retrieve_complete_taxonomy.sparql │ │ └── species_with_tetraketide_meroterpenoids.sparql │ ├── graph_management │ │ ├── RdfGraphCustom.py │ │ └── __init__.py │ ├── llm_handler.py │ ├── main.py │ ├── memory │ │ ├── __init__.py │ │ ├── custom_sqlite_file.py │ │ ├── database_manager.py │ │ ├── test_db_connection.py │ │ └── tools_database.py │ ├── questions.py │ ├── session.py │ ├── tests │ │ ├── __init__.py │ │ ├── evaluation.py │ │ └── test_utils.py │ ├── utils.py │ └── workflow │ │ └── langraph_workflow.py ├── data │ ├── ChEMBLTarget.csv │ ├── README.md │ ├── chemical_taxonomy.csv │ ├── evaluation_dataset.csv │ ├── example_queries │ │ ├── all_distances_between_species.sparql │ │ ├── collect_chromatogram_info.sparql │ │ ├── count_species_per_family.sparql │ │ ├── retrieve_complete_taxonomy.sparql │ │ └── species_with_tetraketide_meroterpenoids.sparql │ ├── faiss_db │ │ ├── index.faiss │ │ └── index.pkl │ ├── npc_all.csv │ ├── npcclass.csv │ ├── queries.json │ ├── standard_questions.txt │ ├── submitted_plants.csv │ └── taxon_wikidata.csv ├── graphs │ ├── graph.pkl │ ├── graph_info.txt │ ├── schema.jsonld │ └── schema.ttl ├── notebooks │ └── LLM_chain_agent.ipynb └── tests │ ├── installation_test.py │ ├── questions.json │ ├── retrieving_log_file.ipynb │ ├── tests_entity_fishing.ipynb │ └── tests_ontology.ipynb ├── assets └── logo.png ├── docker-compose.yml ├── docs ├── api-reference │ ├── agents.md │ ├── core.md │ └── graph-management.md ├── assets │ ├── images │ │ └── hero-bg.png │ ├── javascripts │ │ ├── navigation.js │ │ └── 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