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| TxAgent: An AI Agent for Therapeutic Reasoning Across a Universe of Tools | |
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| <!-- Model overview --> | |
| <section class="hero is-small"> | |
| <div class="hero-body content-container"> | |
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| <h2 class="title is-2 has-text-centered">TxAgent model</h2> | |
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| src="static/images/txagent.jpg" | |
| alt="TxAgent model" | |
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| <!-- End model overview --> | |
| <!-- Paper abstract --> | |
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| <h2 class="title is-3">Abstract</h2> | |
| <div class="content has-text-justified"> | |
| <p> | |
| Precision therapeutics require multimodal adaptive models that | |
| generate personalized treatment recommendations. We introduce | |
| TxAgent, an AI agent that leverages multi-step reasoning and | |
| real-time biomedical knowledge retrieval across a toolbox of 211 | |
| tools to analyze drug interactions, contraindications, and | |
| patient-specific treatment strategies. TxAgent evaluates how | |
| drugs interact at molecular, pharmacokinetic, and clinical | |
| levels, identifies contraindications based on patient | |
| comorbidities and concurrent medications, and tailors treatment | |
| strategies to individual patient characteristics, including age, | |
| genetic factors, and disease progression. TxAgent retrieves and | |
| synthesizes evidence from multiple biomedical sources, assesses | |
| interactions between drugs and patient conditions, and refines | |
| treatment recommendations through iterative reasoning. It | |
| selects tools based on task objectives and executes structured | |
| function calls to solve therapeutic tasks that require clinical | |
| reasoning and cross-source validation. The ToolUniverse | |
| consolidates 211 tools from trusted sources, including all US | |
| FDA-approved drugs since 1939 and validated clinical insights | |
| from Open Targets. TxAgent outperforms leading LLMs, tool-use | |
| models, and reasoning agents across five new benchmarks: DrugPC, | |
| BrandPC, GenericPC, TreatmentPC, and DescriptionPC, covering | |
| 3,168 drug reasoning tasks and 456 personalized treatment | |
| scenarios. It achieves 92.1% accuracy in open-ended drug | |
| reasoning tasks, surpassing GPT-4o by up to 25.8% and | |
| outperforming DeepSeek-R1 (671B) in structured multi-step | |
| reasoning. TxAgent generalizes across drug name variants and | |
| descriptions, maintaining a variance of <0.01 between brand, | |
| generic, and description-based drug references, exceeding | |
| existing tool-use LLMs by over 55%. By integrating multi-step | |
| inference, real-time knowledge grounding, and tool- assisted | |
| decision-making, TxAgent ensures that treatment recommendations | |
| align with established clinical guidelines and real-world | |
| evidence, reducing the risk of adverse events and improving | |
| therapeutic decision-making. | |
| </p> | |
| </div> | |
| </div> | |
| </div> | |
| </div> | |
| </section> | |
| <!-- End paper abstract --> | |
| <!-- Model capabilities --> | |
| <section class="hero is-small"> | |
| <div class="hero-body content-container"> | |
| <div class="container"> | |
| <h2 class="title is-2 has-text-centered">TxAgent capabilities</h2> | |
| <div class="container is-centered has-text-centered"> | |
| <img | |
| src="static/images/txagent_capabilities.jpg" | |
| alt="TxAgent Capabilities" | |
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| <section class="section hero is-light py-2 content"> | |
| <div class="has-text-left py-2"> | |
| <ul> | |
| <li> | |
| <b>Knowledge grounding using tool calls</b>: TxAgent | |
| utilizes tools to obtain verified knowledge and provides | |
| outputs based on it. | |
| </li> | |
| <li> | |
| <b>Goal-oriented tool selection</b>: TxAgent proactively | |
| requests tools from ToolUniverse using the ToolRAG model and | |
| selects and applies the most suitable tool from the | |
| available candidates. | |
| </li> | |
| <li> | |
| <b>Problem solving with multi-step reasoning</b>: TxAgent | |
| manages complex tasks or unexpected responses from tools | |
| through multiple iterations of thought and function calls. | |
| </li> | |
| <li> | |
| <b>Leveraging constantly updated knowledge bases</b>: | |
| TxAgent accesses continuously updated databases via tools to | |
| handle problems that go beyond the TxAgent’s intrinsic | |
| knowledge. | |
| </li> | |
| </ul> | |
| </div> | |
| </section> | |
| </div> | |
| </div> | |
| </div> | |
| </section> | |
| <!-- End model capabilities --> | |
| <!--BibTex citation --> | |
| <section class="section" id="BibTeX"> | |
| <div class="container is-max-desktop content"> | |
| <h2 class="title">BibTeX</h2> | |
| <pre><code>@misc{gao2025txagent, | |
| title={TxAgent: An AI Agent for Therapeutic Reasoning Across a Universe of Tools}, | |
| author={Shanghua Gao and Richard Zhu and Zhenglun Kong and Ayush Noori and Xiaorui Su and Curtis Ginder and Theodoros Tsiligkaridis and Marinka Zitnik}, | |
| year={2025}, | |
| eprint={2503.10970}, | |
| archivePrefix={arXiv}, | |
| primaryClass={cs.AI}, | |
| url={https://arxiv.org/abs/2503.10970}, | |
| }</code></pre> | |
| </div> | |
| </section> | |
| <!--End BibTex citation --> | |
| <!--BibTex citation --> | |
| <section class="section" id="BibTeX"> | |
| <div class="container is-max-desktop content"> | |
| <h2 class="title">Contact</h2> | |
| <p>If you have any questions or suggestions, please email | |
| <a href="mailto:[email protected]">Shanghua Gao</a> and | |
| <a href="mailto:[email protected]">Marinka Zitnik</a>. | |
| </p> | |
| </div> | |
| </section> | |
| <!--End BibTex citation --> | |
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| <p> | |
| We gratefully acknowledge the support of NIH R01-HD108794, NSF CAREER 2339524, US DoD FA8702-15-D-0001, Harvard Data Science Initiative, Amazon Faculty Research, Google Research Scholar Program, AstraZeneca Research, Roche Alliance with Distinguished Scientists, Sanofi iDEA-iTECH, Pfizer Research, Gates Foundation (INV-079038), Chan Zuckerberg Initiative, John and Virginia Kaneb Fellowship at Harvard Medical School, Biswas Computational Biology Initiative in partnership with the Milken Institute, Harvard Medical School Dean's Innovation Fund for the Use of Artificial Intelligence, and Kempner Institute for the Study of Natural and Artificial Intelligence at Harvard University. Any opinions, findings, conclusions or recommendations expressed in this material are those of the authors and do not necessarily reflect the views of the funders. | |
| We thank Owen Queen and Thomas Hartvigsen for their valuable discussions on this project and NVIDIA AI for providing access to DeepSeek R1 models. | |
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| <script> | |
| const dataDict = { | |
| "Adverse Events, Risks, Safety": { | |
| "Adverse Events and Alarms": [ | |
| "get_drug_adverse_events_by_chemblId", | |
| "get_drug_name_by_adverse_reaction", | |
| "get_adverse_reactions_by_drug_name", | |
| "get_drug_names_by_alarm", | |
| "get_alarms_by_drug_name", | |
| ], | |
| "Warnings and Risks": [ | |
| "get_drug_warnings_by_chemblId", | |
| "get_drug_names_by_boxed_warning", | |
| "get_boxed_warning_info_by_drug_name", | |
| "get_drug_name_by_warnings", | |
| "get_warnings_by_drug_name", | |
| "get_warnings_and_cautions_by_drug_name", | |
| "get_drug_names_by_warnings_and_cautions", | |
| "get_drug_names_by_risk", | |
| "get_risk_info_by_drug_name", | |
| "get_user_safety_warning_by_drug_names", | |
| "get_drug_names_by_user_safety_warning", | |
| "get_drug_names_by_food_safety_warnings", | |
| "get_drug_withdrawn_blackbox_status_by_chemblId", | |
| ], | |
| "Nonclinical Toxicology": [ | |
| "get_drug_names_by_nonclinical_toxicology_info", | |
| "get_nonclinical_toxicology_info_by_drug_name", | |
| ], | |
| "Carcinogenic, Mutagenic, Fertility, Impairment Info": [ | |
| "get_drug_names_by_carcinogenic, mutagenic, fertility, impairment_info", | |
| "get_carcinogenic, mutagenic, fertility, impairment_info_by_drug_name", | |
| ], | |
| "Other Safety Info": [ | |
| "get_drug_name_by_other_safety_info", | |
| "get_other_safety_info_by_drug_name", | |
| ], | |
| "Safety Summary": [ | |
| "get_drug_names_by_safety_summary", | |
| "get_safety_summary_by_drug_name", | |
| ], | |
| Contraindications: [ | |
| "get_drug_names_by_contraindications", | |
| "get_contraindications_by_drug_name", | |
| "get_do_not_use_info_by_drug_name", | |
| ], | |
| Precautions: [ | |
| "get_drug_names_by_general_precautions", | |
| "get_general_precautions_by_drug_name", | |
| "get_drug_name_by_precautions", | |
| "get_precautions_by_drug_name", | |
| ], | |
| "Nonteratogenic Effects": [ | |
| "get_drug_names_by_nonteratogenic_effects", | |
| "get_nonteratogenic_effects_by_drug_name", | |
| ], | |
| "Teratogenic Effects": [ | |
| "get_drug_names_by_teratogenic_effects", | |
| "get_teratogenic_effects_by_drug_name", | |
| ], | |
| "Overdosage Info": [ | |
| "get_drug_names_by_overdosage_info", | |
| "get_overdosage_info_by_drug_name", | |
| ], | |
| "Stop Use Info": [ | |
| "get_drug_name_by_stop_use_info", | |
| "get_stop_use_info_by_drug_name", | |
| ], | |
| "Lab Test Interference": [ | |
| "get_drug_names_by_lab_test_interference", | |
| "get_lab_test_interference_info_by_drug_name", | |
| ], | |
| "Residue Warning": [ | |
| "get_drug_names_by_residue_warning", | |
| "get_residue_warning_by_drug_name", | |
| ], | |
| "Environmental Warning": [ | |
| "get_drug_name_by_environmental_warning", | |
| "get_environmental_warning_by_drug_name", | |
| ], | |
| "Target Safety Profile": ["get_target_safety_profile_by_ensemblID"], | |
| }, | |
| "Addiction and Abuse": { | |
| "Drug Abuse": [ | |
| "get_drug_names_by_abuse_info", | |
| "get_abuse_info_by_drug_name", | |
| "get_drug_name_by_abuse_types_and_related_adverse_reactions_and_controlled_substance_status", | |
| "get_abuse_types_and_related_adverse_reactions_and_controlled_substance_status_by_drug_name", | |
| ], | |
| "Drug Dependence": [ | |
| "get_drug_name_by_dependence_info", | |
| "get_dependence_info_by_drug_name", | |
| ], | |
| "Controlled Substance": [ | |
| "get_drug_names_by_controlled_substance_DEA_schedule", | |
| "get_controlled_substance_DEA_schedule_info_by_drug_name", | |
| "get_drug_name_by_abuse_types_and_related_adverse_reactions_and_controlled_substance_status", | |
| "get_abuse_types_and_related_adverse_reactions_and_controlled_substance_status_by_drug_name", | |
| ], | |
| }, | |
| "Drug Patient Populations": { | |
| Pregnancy: [ | |
| "get_drug_names_by_pregnancy_effects_info", | |
| "get_pregnancy_effects_info_by_drug_name", | |
| "get_drug_name_by_pregnancy_or_breastfeeding_info", | |
| "get_pregnancy_or_breastfeeding_info_by_drug_name", | |
| "get_drug_name_by_labor_and_delivery_info", | |
| "get_labor_and_delivery_info_by_drug_name", | |
| "get_drug_names_by_teratogenic_effects", | |
| "get_teratogenic_effects_by_drug_name", | |
| ], | |
| "Nursing Mother": [ | |
| "get_drug_names_by_info_for_nursing_mothers", | |
| "get_info_for_nursing_mothers_by_drug_name", | |
| "get_drug_name_by_pregnancy_or_breastfeeding_info", | |
| "get_pregnancy_or_breastfeeding_info_by_drug_name", | |
| ], | |
| "Pediatric Use": [ | |
| "get_drug_names_by_pediatric_use", | |
| "get_pediatric_use_info_by_drug_name", | |
| "get_drug_names_by_child_safety_info", | |
| "get_child_safety_info_by_drug_name", | |
| ], | |
| "General Patient Pop. Info": [ | |
| "get_drug_names_by_population_use", | |
| "get_population_use_info_by_drug_name", | |
| ], | |
| "Geriatric Use": [ | |
| "get_drug_names_by_geriatric_use", | |
| "get_geriatric_use_info_by_drug_name", | |
| ], | |
| }, | |
| "Drug Administration and Handling": { | |
| Storage: [ | |
| "get_drug_name_by_storage_and_handling_info", | |
| "get_storage_and_handling_info_by_drug_name", | |
| "get_dosage_and_storage_information_by_drug_name", | |
| ], | |
| "Safe Handling": [ | |
| "get_drug_names_by_safe_handling_warning", | |
| "get_safe_handling_warnings_by_drug_name", | |
| ], | |
| Disposal: [ | |
| "get_drug_names_by_disposal_info", | |
| "get_disposal_info_by_drug_name", | |
| ], | |
| Dosing: [ | |
| "get_drug_name_by_dosage_info", | |
| "get_drug_names_by_dosage_forms_and_strengths_info", | |
| "get_dosage_forms_and_strengths_by_drug_name", | |
| "get_dosage_and_storage_information_by_drug_name", | |
| ], | |
| "Route of Administration": [ | |
| "get_drug_names_by_route", | |
| "get_route_info_by_drug_name", | |
| ], | |
| "Setup Instructions": [ | |
| "get_drug_names_by_assembly_installation_info", | |
| "get_assembly_installation_info_by_drug_name", | |
| "get_drug_name_by_calibration_instructions", | |
| "get_calibration_instructions_by_drug_name", | |
| ], | |
| "General Instructions": [ | |
| "get_drug_names_by_instructions_for_use", | |
| "get_instructions_for_use_by_drug_name", | |
| ], | |
| Accessories: [ | |
| "get_drug_names_by_accessories", | |
| "get_accessories_info_by_drug_name", | |
| ], | |
| "Assoc. Devices": [ | |
| "get_drug_name_by_device_use", | |
| "get_device_use_by_drug_name", | |
| ], | |
| }, | |
| Pharmacology: { | |
| Pharmacokinetics: [ | |
| "get_drug_names_by_pharmacokinetics", | |
| "get_pharmacokinetics_by_drug_name", | |
| ], | |
| Pharmacodynamics: [ | |
| "get_drug_name_by_pharmacodynamics", | |
| "get_pharmacodynamics_by_drug_name", | |
| ], | |
| "Clinical Pharmacology": [ | |
| "get_drug_names_by_clinical_pharmacology", | |
| "get_clinical_pharmacology_by_drug_name", | |
| ], | |
| "Animal Pharmacology": [ | |
| "get_drug_names_by_animal_pharmacology_info", | |
| "get_animal_pharmacology_info_by_drug_name", | |
| ], | |
| }, | |
| "Drug Use, Mechanism, Composition": { | |
| "Mechanism of Action": [ | |
| "get_mechanism_of_action_by_drug_name", | |
| "get_drug_names_by_mechanism_of_action", | |
| "get_drug_mechanisms_of_action_by_chemblId", | |
| ], | |
| Ingredients: [ | |
| "get_active_ingredient_info_by_drug_name", | |
| "get_drug_names_by_active_ingredient", | |
| "get_drug_name_by_inactive_ingredient", | |
| "get_inactive_ingredient_info_by_drug_name", | |
| "get_drug_names_by_ingredient", | |
| "get_ingredients_by_drug_name", | |
| "get_active_ingredient_application_number_manufacturer_name_NDC_number_administration_route_by_drug_name", | |
| ], | |
| Indication: [ | |
| "get_drug_names_by_indication", | |
| "get_indications_by_drug_name", | |
| "get_drug_indications_by_chemblId", | |
| "get_approved_indications_by_drug_chemblId", | |
| "get_purpose_info_by_drug_name", | |
| ], | |
| }, | |
| "ID and Labeling Tools": { | |
| "Drug Name/Description and ID Map": [ | |
| "get_brand_name_generic_name", | |
| "get_drug_synonyms_by_chemblId", | |
| "get_drug_trade_names_by_chemblId", | |
| "get_drug_description_by_chemblId", | |
| "get_drug_id_description_by_name", | |
| "get_known_drugs_by_drug_chemblId", | |
| ], | |
| "Drug Label Document and Set IDs": [ | |
| "get_drug_name_by_document_id", | |
| "get_document_id_by_drug_name", | |
| "get_drug_name_by_set_id", | |
| "get_drug_name_by_application_number_NUI_identifier_SPL_document_ID_SPL_set_ID", | |
| ], | |
| "Disease Name/Description and ID Map": [ | |
| "get_disease_synonyms_by_efoId", | |
| "get_disease_id_description_by_name", | |
| "get_disease_description_by_efoId", | |
| "get_drug_name_by_set_id", | |
| ], | |
| "Target Name/Description and ID Map": [ | |
| "get_target_id_description_by_name", | |
| "get_target_synonyms_by_ensemblID", | |
| ], | |
| "App Num., Manufacturer Name, Other IDs": [ | |
| "get_active_ingredient_application_number_manufacturer_name_NDC_number_administration_route_by_drug_name", | |
| "get_drug_names_by_application_number_manufacturer_name_NDC_number", | |
| "get_drug_name_by_application_number_NUI_identifier_SPL_document_ID_SPL_set_ID", | |
| ], | |
| "Phenotype Name and ID Map": [ | |
| "get_phenotype_by_HPO_ID", | |
| "get_HPO_ID_by_phenotype", | |
| ], | |
| }, | |
| "General Clinical Annotations": { | |
| "SPL Indexing Data Elements and Unclassified Section": [ | |
| "get_drug_names_by_spl_indexing_data_elements", | |
| "get_spl_indexing_data_elements_by_drug_name", | |
| "get_spl_unclassified_section_by_drug_name", | |
| ], | |
| "Label Effective Time": [ | |
| "get_drug_names_by_effective_time", | |
| "get_effective_time_by_drug_name", | |
| ], | |
| "Approval Status": ["get_drug_approval_status_by_chemblId"], | |
| "Dear Health Care Provider Letter and Recent Changes": [ | |
| "get_dear_health_care_provider_letter_info_by_drug_name", | |
| "get_drug_names_by_dear_health_care_provider_letter_info", | |
| "get_recent_changes_by_drug_name", | |
| ], | |
| "Health Claims": [ | |
| "get_drug_names_by_health_claim", | |
| "get_health_claims_by_drug_name", | |
| ], | |
| "Questions Contact": ["get_contact_for_questions_info_by_drug_name"], | |
| }, | |
| "Clinical Laboratory Info": { | |
| "Lab Tests": [ | |
| "get_drug_names_by_lab_tests", | |
| "get_lab_tests_by_drug_name", | |
| ], | |
| Microbiology: [ | |
| "get_drug_name_by_microbiology", | |
| "get_microbiology_info_by_drug_name", | |
| ], | |
| }, | |
| "General Info for Patients and Relatives": { | |
| "Consult Doctor/Pharmacist": [ | |
| "get_drug_name_by_info_on_doctor_consultation", | |
| "get_info_on_doctor_consultation_by_drug_name", | |
| "get_drug_names_by_info_on_consulting_doctor, pharmacist_for_drug_interactions", | |
| "get_info_on_consulting_doctor, pharmacist_for_drug_interactions_by_drug_name", | |
| ], | |
| "Info for Owners/Caregivers": [ | |
| "get_drug_names_by_information_for_owners_or_caregivers", | |
| "get_information_for_owners_or_caregivers_by_drug_name", | |
| ], | |
| "Drug Info for Patients": [ | |
| "get_info_for_patients_by_drug_name", | |
| "get_drug_name_by_principal_display_panel", | |
| "get_principal_display_panel_by_drug_name", | |
| "get_drug_names_by_medication_guide", | |
| "get_medication_guide_info_by_drug_name", | |
| "get_drug_name_from_patient_package_insert", | |
| "get_patient_package_insert_from_drug_name", | |
| "get_drug_names_by_patient_medication_info", | |
| "get_patient_medication_info_by_drug_name", | |
| "get_when_using_info", | |
| ], | |
| "Avoid While Using Drug": ["get_when_using_info"], | |
| }, | |
| "Disease, Phenotype, Target, Drug Links": { | |
| "Drug-Disease Associations": [ | |
| "get_similar_entities_by_drug_chemblId", | |
| "get_similar_entities_by_disease_efoId", | |
| "get_assoc._drugs_by_disease_efoId", | |
| "get_assoc._diseases_by_drug_chemblId", | |
| ], | |
| "Drug-Target Associations": [ | |
| "get_similar_entities_by_drug_chemblId", | |
| "get_similar_entities_by_target_ensemblID", | |
| "get_assoc._drugs_by_target_ensemblID", | |
| "get_assoc._targets_by_drug_chemblId", | |
| ], | |
| "Target-Disease/Phenotype Associations": [ | |
| "get_similar_entities_by_target_ensemblID", | |
| "get_similar_entities_by_disease_efoId", | |
| "get_assoc._diseases_by_target_ensemblID", | |
| "get_assoc._targets_by_disease_efoId", | |
| "get_assoc._diseases_phenotypes_by_target_ensemblID", | |
| ], | |
| "Disease-Disease/Phenotype Associations": [ | |
| "get_similar_entities_by_disease_efoId", | |
| "get_joint_assoc._diseases_by_HPO_ID_list", | |
| "get_assoc._phenotypes_by_disease_efoId", | |
| ], | |
| "Target-Target Associations": [ | |
| "get_target_homologues_by_ensemblID", | |
| "get_similar_entities_by_target_ensemblID", | |
| "get_target_interactions_by_ensemblID", | |
| ], | |
| "Drug-Drug Associations": [ | |
| "get_drug_names_by_drug_interactions", | |
| "get_drug_interactions_by_drug_name", | |
| "get_similar_entities_by_drug_chemblId", | |
| ], | |
| Pharmacogenomics: [ | |
| "drug_pharmacogenomics_data", | |
| "get_drug_name_by_pharmacogenomics", | |
| "get_pharmacogenomics_info_by_drug_name", | |
| ], | |
| }, | |
| "Biological Annotation Tools": { | |
| "Target Biological Annotation": [ | |
| "get_target_gene_ontology_by_ensemblID", | |
| "get_target_genomic_location_by_ensemblID", | |
| "get_target_subcellular_locations_by_ensemblID", | |
| "get_target_classes_by_ensemblID", | |
| "get_biological_mouse_models_by_ensemblID", | |
| ], | |
| "Disease Biological Annotation": [ | |
| "get_disease_therapeutic_areas_by_efoId", | |
| "get_disease_ancestors_parents_by_efoId", | |
| "get_disease_descendants_children_by_efoId", | |
| "get_disease_locations_by_efoId", | |
| ], | |
| "Gene Ontology": [ | |
| "get_gene_ontology_terms_by_goID", | |
| "get_target_gene_ontology_by_ensemblID", | |
| ], | |
| "Drug Parent Child Molecules": [ | |
| "get_parent_child_molecules_by_drug_chembl_ID", | |
| ], | |
| }, | |
| Publications: { | |
| Publications: [ | |
| "get_publications_by_disease_efoId", | |
| "get_publications_by_target_ensemblID", | |
| "get_publications_by_drug_chemblId", | |
| ], | |
| "Clinical Studies": [ | |
| "get_drug_names_by_clinical_studies", | |
| "get_clinical_studies_info_by_drug_name", | |
| ], | |
| "Reference Documents": [ | |
| "get_drug_name_by_reference", | |
| "get_reference_info_by_drug_name", | |
| ], | |
| }, | |
| Search: { | |
| "Search Tools": [ | |
| "multi_entity_search_by_query_string", | |
| "search_category_counts_by_query_string", | |
| ], | |
| }, | |
| "Target Characterization": { | |
| "Target Therapeutic Potential": [ | |
| "get_target_tractability_by_ensemblID", | |
| "get_target_enabling_packages_by_ensemblID", | |
| "get_chemical_probes_by_target_ensemblID", | |
| "get_target_constraint_info_by_ensemblID", | |
| ], | |
| }, | |
| }; | |
| function toSentenceCase(str) { | |
| // Replace underscores with spaces and convert the entire string to lowercase. | |
| let formatted = str.replace(/_/g, " ").toLowerCase(); | |
| // Capitalize only the first letter. | |
| formatted = formatted.charAt(0).toUpperCase() + formatted.slice(1); | |
| // Ensure "ID" stays properly capitalized. | |
| formatted = formatted.replace(/chemblid/gi, "ChEMBL ID"); | |
| formatted = formatted.replace(/ensemblid/gi, "Ensembl ID"); | |
| formatted = formatted.replace(/efoid/gi, "EFO ID"); | |
| formatted = formatted.replace(/hpo/gi, "HPO"); | |
| formatted = formatted.replace(/ids/gi, "IDs"); | |
| formatted = formatted.replace( | |
| /application number nui identifier spl document id spl set id/gi, | |
| "app. number, NUI identifier, SPL doc. ID, SPL set ID" | |
| ); | |
| formatted = formatted.replace( | |
| /Get active ingredient application number manufacturer name ndc number administration route/gi, | |
| "get active ingredient, app. num., manufacturer, NDC num., administration" | |
| ); | |
| formatted = formatted.replace( | |
| /Get drug name by application number manufacturer name ndc number/gi, | |
| "get drug name by app. number, manufacturer, NDC number" | |
| ); | |
| formatted = formatted.replace(/goID/gi, "GO ID"); | |
| formatted = formatted.replace( | |
| /controlled substance dea schedule/gi, | |
| "DEA schedule" | |
| ); | |
| formatted = formatted.replace(/spl/gi, "SPL"); | |
| return formatted.replace(/\bId\b/gi, "ID"); | |
| } | |
| // Global variables to manage drill-down state. | |
| let currentLevel = 1; // 1 for Tier 1, 2 for Tier 2, 3 for Tier 3. | |
| let currentTier1 = null; // Holds the key for the current top-level slice. | |
| let chart; // To store the Highcharts chart instance. | |
| let currentTier1Color = null; | |
| let currentTier2Color = null; | |
| // Sorted data structure | |
| let sortedDataDict = {}; | |
| // Function to sort dataDict by the total number of Tier 3 values | |
| function sortDataDict() { | |
| // Calculate totals for each Tier 1 key | |
| const tier1Totals = {}; | |
| for (const topKey in dataDict) { | |
| let total = 0; | |
| const tier2Totals = {}; | |
| // Calculate totals for each Tier 2 key within this Tier 1 | |
| for (const subKey in dataDict[topKey]) { | |
| const count = dataDict[topKey][subKey].length; | |
| tier2Totals[subKey] = count; | |
| total += count; | |
| } | |
| tier1Totals[topKey] = { | |
| total: total, | |
| tier2Totals: tier2Totals, | |
| }; | |
| } | |
| // Sort Tier 1 keys by total count (descending) | |
| const sortedTier1Keys = Object.keys(tier1Totals).sort( | |
| (a, b) => tier1Totals[b].total - tier1Totals[a].total | |
| ); | |
| // Build the sorted data structure | |
| sortedDataDict = {}; | |
| for (const topKey of sortedTier1Keys) { | |
| sortedDataDict[topKey] = {}; | |
| // Sort Tier 2 keys by their individual counts (descending) | |
| const tier2Totals = tier1Totals[topKey].tier2Totals; | |
| const sortedTier2Keys = Object.keys(tier2Totals).sort( | |
| (a, b) => tier2Totals[b] - tier2Totals[a] | |
| ); | |
| // Add sorted Tier 2 keys with their values | |
| for (const subKey of sortedTier2Keys) { | |
| sortedDataDict[topKey][subKey] = dataDict[topKey][subKey]; | |
| } | |
| } | |
| return sortedDataDict; | |
| } | |
| // Function to load Tier 1 data (top-level slices) with an outer ring showing Tier 2 subcategories. | |
| function loadTier1() { | |
| currentLevel = 1; | |
| currentTier1 = null; | |
| const newData = []; | |
| // Create the central node. | |
| newData.push({ | |
| id: "root", | |
| name: "ToolUniverse", | |
| value: 1, // inner slice made very small. | |
| color: "skyblue", | |
| }); | |
| let index = 1; | |
| // For each top-level key, create a Tier 1 slice and add an outer ring (level 3) for its Tier 2 subcategories. | |
| for (const topKey in sortedDataDict) { | |
| // Calculate total value as the sum of all Tier 2 subcategory counts. | |
| let total = 0; | |
| const tier2Obj = sortedDataDict[topKey]; | |
| for (const subKey in tier2Obj) { | |
| total += tier2Obj[subKey].length; | |
| } | |
| // Set a specific color for Tier 1 (cycling through chart colors) | |
| const color = | |
| chart.options.colors[(index - 1) % chart.options.colors.length]; | |
| // Tier 1 slice (level 2). | |
| const tier1Id = "tier1_" + index; | |
| newData.push({ | |
| id: tier1Id, | |
| parent: "root", | |
| name: toSentenceCase(topKey), | |
| value: total, | |
| originalKey: topKey, | |
| color: color, | |
| }); | |
| // Level 3: For each Tier 2 category, add a slice whose width is proportional to its item count. | |
| let tier2Index = 1; | |
| for (const subKey in tier2Obj) { | |
| newData.push({ | |
| id: tier1Id + "_tier2_" + tier2Index, | |
| parent: tier1Id, | |
| name: "", // no label for the outer ring | |
| // Set value proportional to the number of items in the subcategory. | |
| value: tier2Obj[subKey].length, | |
| originalKey: subKey, | |
| color: Highcharts.color(color).brighten(0.1).get(), | |
| dataLabels: { enabled: false }, | |
| }); | |
| tier2Index++; | |
| } | |
| index++; | |
| } | |
| chart.series[0].setData(newData, true); | |
| chart.setTitle({ text: "ToolUniverse" }); | |
| } | |
| // Function to load Tier 2 data (second-level slices) with an outer ring showing the number of Tier 3 items. | |
| function loadTier2(topKey) { | |
| currentLevel = 2; | |
| currentTier1 = topKey; | |
| const newData = []; | |
| // Central node is now the Tier 1 label. | |
| newData.push({ | |
| id: "root", | |
| name: toSentenceCase(topKey), | |
| value: 1, | |
| color: Highcharts.color(currentTier1Color).brighten(-0.05).get(), | |
| }); | |
| let index = 1; | |
| const secondLevelObj = sortedDataDict[topKey]; | |
| // Define a maximum brighten value (adjust as needed) | |
| const maxBrighten = 0.2; | |
| const brightenStep = | |
| Object.keys(secondLevelObj).length > 1 | |
| ? maxBrighten / (Object.keys(secondLevelObj).length - 1) | |
| : 0; | |
| // For each Tier 2 category, add a slice (level 2) and then an outer ring (level 3) for its Tier 3 items. | |
| for (const subKey in secondLevelObj) { | |
| const parentColor = Highcharts.color(currentTier1Color) | |
| .brighten(brightenStep * index) | |
| .get(); | |
| const tier2Id = "tier2_" + index; | |
| newData.push({ | |
| id: tier2Id, | |
| parent: "root", | |
| name: toSentenceCase(subKey), | |
| value: secondLevelObj[subKey].length, | |
| originalKey: subKey, | |
| color: parentColor, | |
| }); | |
| // Level 3: for each Tier 3 item under this Tier 2 category. | |
| let tier3Index = 1; | |
| const children = secondLevelObj[subKey]; | |
| for (const item of children) { | |
| newData.push({ | |
| id: tier2Id + "_tier3_" + tier3Index, | |
| parent: tier2Id, | |
| name: "", // no label for the outer ring | |
| value: 1, // each Tier 3 item is given a unit value (adjust if needed) | |
| originalKey: item, | |
| color: Highcharts.color(parentColor).brighten(0.1).get(), | |
| dataLabels: { enabled: false }, | |
| }); | |
| tier3Index++; | |
| } | |
| index++; | |
| } | |
| chart.series[0].setData(newData, true); | |
| chart.setTitle({ text: "ToolUniverse: " + toSentenceCase(topKey) }); | |
| } | |
| // Function to load Tier 3 data (third-level slices). | |
| // (Since Tier 3 is the lowest level, we keep its configuration unchanged.) | |
| function loadTier3(topKey, subKey) { | |
| currentLevel = 3; | |
| const newData = []; | |
| // Central node is now the Tier 2 label. | |
| newData.push({ | |
| id: "root", | |
| name: toSentenceCase(subKey), | |
| value: 1, | |
| color: Highcharts.color(currentTier2Color).brighten(-0.05).get(), | |
| }); | |
| let index = 1; | |
| const children = sortedDataDict[topKey][subKey]; | |
| const maxBrighten = 0.2; | |
| const brightenStep = | |
| children.length > 1 ? maxBrighten / (children.length - 1) : 0; | |
| for (const item of children) { | |
| newData.push({ | |
| id: "tier3_" + index, | |
| parent: "root", | |
| name: toSentenceCase(item), | |
| value: 1, | |
| originalKey: item, | |
| color: Highcharts.color(currentTier2Color) | |
| .brighten(brightenStep * index) | |
| .get(), | |
| }); | |
| index++; | |
| } | |
| chart.series[0].setData(newData, true); | |
| chart.setTitle({ text: "ToolUniverse: " + toSentenceCase(subKey) }); | |
| } | |
| // Render the initial 3-level sunburst chart. | |
| chart = Highcharts.chart("tooluniverse-container", { | |
| chart: { | |
| height: "100%", | |
| }, | |
| title: { | |
| text: "ToolUniverse", | |
| }, | |
| series: [ | |
| { | |
| type: "sunburst", | |
| data: [], // Data will be loaded via loadTier1(). | |
| // We assign colors manually. | |
| colorByPoint: false, | |
| allowDrillToNode: false, | |
| dataLabels: { | |
| format: "{point.name}", | |
| distance: 20, | |
| style: { | |
| fontSize: "10px", | |
| textAlign: "center", | |
| width: "80px", | |
| whiteSpace: "normal", | |
| textOutline: "none", | |
| color: "#000000", | |
| }, | |
| rotation: "auto", | |
| }, | |
| // Configure levels: | |
| levels: [ | |
| { | |
| level: 1, | |
| levelSize: { unit: "pixels", value: 40 }, | |
| }, | |
| { | |
| level: 2, | |
| levelSize: { unit: "percentage", value: 70 }, | |
| }, | |
| { | |
| level: 3, | |
| levelSize: { unit: "pixels", value: 15 }, | |
| dataLabels: { enabled: false }, | |
| }, | |
| ], | |
| // Define click events on individual slices. | |
| point: { | |
| events: { | |
| click: function () { | |
| // If the central node is clicked, drill up. | |
| if (this.id === "root") { | |
| if (currentLevel === 2) { | |
| loadTier1(); | |
| } else if (currentLevel === 3) { | |
| loadTier2(currentTier1); | |
| } | |
| } else { | |
| // Drill down based on the current level. | |
| if ( | |
| currentLevel === 1 && | |
| sortedDataDict[this.options.originalKey] | |
| ) { | |
| currentTier1Color = this.color; | |
| loadTier2(this.options.originalKey); | |
| } else if ( | |
| currentLevel === 2 && | |
| currentTier1 && | |
| sortedDataDict[currentTier1][this.options.originalKey] | |
| ) { | |
| currentTier2Color = this.color; | |
| loadTier3(currentTier1, this.options.originalKey); | |
| } | |
| } | |
| }, | |
| }, | |
| }, | |
| }, | |
| ], | |
| tooltip: { | |
| headerFormat: "", | |
| pointFormat: "<b>{point.name}</b>", | |
| }, | |
| colors: [ | |
| "#FFA15A", | |
| "#636efa", | |
| "#ab63fa", | |
| "#FF6692", | |
| "#EF553B", | |
| "#00cc96", | |
| "#B6E880", | |
| "#19d3f3", | |
| "#f2ce3f", | |
| ], | |
| }); | |
| // First, sort the data dictionary. | |
| sortDataDict(); | |
| // Load the initial top-level (Tier 1) view. | |
| loadTier1(); | |
| </script> | |