LICENSE
README.md
pyproject.toml
src/ontogpt/__init__.py
src/ontogpt/cli.py
src/ontogpt.egg-info/PKG-INFO
src/ontogpt.egg-info/SOURCES.txt
src/ontogpt.egg-info/dependency_links.txt
src/ontogpt.egg-info/entry_points.txt
src/ontogpt.egg-info/requires.txt
src/ontogpt.egg-info/top_level.txt
src/ontogpt/clients/__init__.py
src/ontogpt/clients/llm_client.py
src/ontogpt/clients/pubmed_client.py
src/ontogpt/clients/soup_client.py
src/ontogpt/clients/wikipedia_client.py
src/ontogpt/converters/__init__.py
src/ontogpt/converters/ontology_converter.py
src/ontogpt/engines/__init__.py
src/ontogpt/engines/embedding_similarity_engine.py
src/ontogpt/engines/generic_engine.py
src/ontogpt/engines/halo_engine.py
src/ontogpt/engines/knowledge_engine.py
src/ontogpt/engines/mapping_engine.py
src/ontogpt/engines/pheno_engine.py
src/ontogpt/engines/reasoner_engine.py
src/ontogpt/engines/resolver.py
src/ontogpt/engines/spires_engine.py
src/ontogpt/engines/synonym_engine.py
src/ontogpt/engines/topic_classifier_engine.py
src/ontogpt/evaluation/__init__.py
src/ontogpt/evaluation/evaluation_engine.py
src/ontogpt/evaluation/resolver.py
src/ontogpt/evaluation/ctd/__init__.py
src/ontogpt/evaluation/ctd/eval_ctd.py
src/ontogpt/evaluation/ctd/eval_ctd_ner.py
src/ontogpt/evaluation/drugmechdb/__init__.py
src/ontogpt/evaluation/drugmechdb/eval_drugmechdb.py
src/ontogpt/evaluation/drugmechdb/datamodel/drugmechdb.py
src/ontogpt/evaluation/go/eval_go.py
src/ontogpt/evaluation/hpoa/__init__.py
src/ontogpt/evaluation/hpoa/eval_hpoa.py
src/ontogpt/evaluation/maxo/__init__.py
src/ontogpt/evaluation/maxo/eval_maxo.py
src/ontogpt/io/__init__.py
src/ontogpt/io/csv_exporter.py
src/ontogpt/io/csv_wrapper.py
src/ontogpt/io/exporter.py
src/ontogpt/io/html_exporter.py
src/ontogpt/io/json_wrapper.py
src/ontogpt/io/markdown_exporter.py
src/ontogpt/io/owl_exporter.py
src/ontogpt/io/rdf_exporter.py
src/ontogpt/io/template_loader.py
src/ontogpt/io/utils.py
src/ontogpt/io/yaml_wrapper.py
src/ontogpt/ontex/__init__.py
src/ontogpt/ontex/extractor.py
src/ontogpt/prompts/__init__.py
src/ontogpt/prompts/enrichment/__init__.py
src/ontogpt/prompts/mapping/__init__.py
src/ontogpt/prompts/phenopacket/__init__.py
src/ontogpt/prompts/qa/__init__.py
src/ontogpt/prompts/reasoning/__init__.py
src/ontogpt/templates/__init__.py
src/ontogpt/templates/adverse_outcome_pathway.py
src/ontogpt/templates/all_disease_grounding.py
src/ontogpt/templates/alzrd.py
src/ontogpt/templates/alzrd_section.py
src/ontogpt/templates/biological_process.py
src/ontogpt/templates/biotic_interaction.py
src/ontogpt/templates/cell_type.py
src/ontogpt/templates/class_enrichment.py
src/ontogpt/templates/composite_disease.py
src/ontogpt/templates/condition.py
src/ontogpt/templates/core.py
src/ontogpt/templates/ctd.py
src/ontogpt/templates/ctd_ner.py
src/ontogpt/templates/data_sheets_schema.py
src/ontogpt/templates/datasheet.py
src/ontogpt/templates/desiccation.py
src/ontogpt/templates/diagnostic_procedure.py
src/ontogpt/templates/dietitian_notes.py
src/ontogpt/templates/drug.py
src/ontogpt/templates/drug_to_disease.py
src/ontogpt/templates/ecosim_methods.py
src/ontogpt/templates/ecosim_simple.py
src/ontogpt/templates/emapa_simple.py
src/ontogpt/templates/environmental_metadata.py
src/ontogpt/templates/environmental_sample.py
src/ontogpt/templates/environmental_sample_ungrounded.py
src/ontogpt/templates/error_analysis.py
src/ontogpt/templates/figure.py
src/ontogpt/templates/food.py
src/ontogpt/templates/foodon_simple.py
src/ontogpt/templates/gene_description_term.py
src/ontogpt/templates/gene_extraction.py
src/ontogpt/templates/genesummary.py
src/ontogpt/templates/go_simple.py
src/ontogpt/templates/go_terms.py
src/ontogpt/templates/go_terms_relational.py
src/ontogpt/templates/gocam.py
src/ontogpt/templates/halo.py
src/ontogpt/templates/human_phenotype.py
src/ontogpt/templates/ibd.py
src/ontogpt/templates/ibd_literature.py
src/ontogpt/templates/kidney.py
src/ontogpt/templates/maxo.py
src/ontogpt/templates/mendelian_disease.py
src/ontogpt/templates/metabolic_process.py
src/ontogpt/templates/metagenome_study.py
src/ontogpt/templates/mic.py
src/ontogpt/templates/miro.py
src/ontogpt/templates/mondo_simple.py
src/ontogpt/templates/nmdc_schema_data.py
src/ontogpt/templates/onto_usage.py
src/ontogpt/templates/ontology_class.py
src/ontogpt/templates/ontology_issue.py
src/ontogpt/templates/pathology.py
src/ontogpt/templates/personinfo.py
src/ontogpt/templates/phenopackets.py
src/ontogpt/templates/phenotype.py
src/ontogpt/templates/predator_prey.py
src/ontogpt/templates/reaction.py
src/ontogpt/templates/recipe.py
src/ontogpt/templates/storms.py
src/ontogpt/templates/table_arrays.py
src/ontogpt/templates/table_values.py
src/ontogpt/templates/traits.py
src/ontogpt/templates/treatment.py
src/ontogpt/templates/vbo_char.py
src/ontogpt/templates/vbo_names.py
src/ontogpt/utils/__init__.py
src/ontogpt/utils/clinical_cases.py
src/ontogpt/utils/model_utils.py
src/ontogpt/utils/multilingual.py
src/ontogpt/utils/output_parser.py
src/ontogpt/utils/output_parser_bulleted.py
src/ontogpt/utils/parse_utils.py
src/ontogpt/utils/pymupdf_helpers.py
src/ontogpt/webapp/__init__.py
src/ontogpt/webapp/main.py