tooluniverse 1.0.6__py3-none-any.whl → 1.0.7__py3-none-any.whl

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  1. tooluniverse/__init__.py +31 -0
  2. tooluniverse/agentic_tool.py +40 -4
  3. tooluniverse/arxiv_tool.py +2 -6
  4. tooluniverse/base_tool.py +174 -25
  5. tooluniverse/biorxiv_tool.py +35 -16
  6. tooluniverse/cellosaurus_tool.py +1332 -0
  7. tooluniverse/compose_scripts/enhanced_multi_agent_literature_search.py +310 -0
  8. tooluniverse/compose_scripts/multi_agent_literature_search.py +794 -0
  9. tooluniverse/compose_scripts/tool_graph_generation.py +68 -35
  10. tooluniverse/compose_scripts/tool_metadata_generator.py +205 -105
  11. tooluniverse/compose_tool.py +93 -8
  12. tooluniverse/core_tool.py +46 -44
  13. tooluniverse/crossref_tool.py +89 -4
  14. tooluniverse/data/agentic_tools.json +1271 -1179
  15. tooluniverse/data/alphafold_tools.json +356 -105
  16. tooluniverse/data/arxiv_tools.json +88 -81
  17. tooluniverse/data/biorxiv_tools.json +69 -64
  18. tooluniverse/data/cellosaurus_tools.json +260 -0
  19. tooluniverse/data/chembl_tools.json +27 -12
  20. tooluniverse/data/clinicaltrials_gov_tools.json +377 -302
  21. tooluniverse/data/compose_tools.json +123 -16
  22. tooluniverse/data/core_tools.json +107 -99
  23. tooluniverse/data/crossref_tools.json +131 -63
  24. tooluniverse/data/dailymed_tools.json +17 -3
  25. tooluniverse/data/dataset_tools.json +1031 -588
  26. tooluniverse/data/dblp_tools.json +135 -64
  27. tooluniverse/data/disease_target_score_tools.json +20 -10
  28. tooluniverse/data/doaj_tools.json +133 -87
  29. tooluniverse/data/embedding_tools.json +362 -299
  30. tooluniverse/data/enrichr_tools.json +34 -27
  31. tooluniverse/data/europe_pmc_tools.json +108 -16
  32. tooluniverse/data/fatcat_tools.json +71 -66
  33. tooluniverse/data/fda_drug_adverse_event_tools.json +1061 -445
  34. tooluniverse/data/fda_drug_labeling_tools.json +6858 -6901
  35. tooluniverse/data/finder_tools.json +32 -37
  36. tooluniverse/data/gene_ontology_tools.json +19 -7
  37. tooluniverse/data/gwas_tools.json +1720 -959
  38. tooluniverse/data/hal_tools.json +69 -64
  39. tooluniverse/data/hpa_tools.json +53 -14
  40. tooluniverse/data/humanbase_tools.json +51 -43
  41. tooluniverse/data/idmap_tools.json +76 -70
  42. tooluniverse/data/literature_search_tools.json +306 -0
  43. tooluniverse/data/mcp_client_tools_example.json +122 -107
  44. tooluniverse/data/medlineplus_tools.json +50 -10
  45. tooluniverse/data/medrxiv_tools.json +69 -64
  46. tooluniverse/data/molecule_2d_tools.json +134 -0
  47. tooluniverse/data/molecule_3d_tools.json +164 -0
  48. tooluniverse/data/monarch_tools.json +112 -110
  49. tooluniverse/data/odphp_tools.json +389 -119
  50. tooluniverse/data/openaire_tools.json +89 -79
  51. tooluniverse/data/openalex_tools.json +100 -31
  52. tooluniverse/data/opentarget_tools.json +1457 -1372
  53. tooluniverse/data/osf_preprints_tools.json +77 -73
  54. tooluniverse/data/packages/bioinformatics_core_tools.json +40 -10
  55. tooluniverse/data/packages/cheminformatics_tools.json +20 -5
  56. tooluniverse/data/packages/genomics_tools.json +36 -9
  57. tooluniverse/data/packages/machine_learning_tools.json +36 -9
  58. tooluniverse/data/packages/scientific_computing_tools.json +20 -5
  59. tooluniverse/data/packages/single_cell_tools.json +20 -5
  60. tooluniverse/data/packages/structural_biology_tools.json +16 -4
  61. tooluniverse/data/packages/visualization_tools.json +20 -5
  62. tooluniverse/data/pmc_tools.json +111 -103
  63. tooluniverse/data/protein_structure_3d_tools.json +138 -0
  64. tooluniverse/data/pubchem_tools.json +37 -12
  65. tooluniverse/data/pubmed_tools.json +126 -58
  66. tooluniverse/data/pubtator_tools.json +68 -60
  67. tooluniverse/data/rcsb_pdb_tools.json +1532 -1221
  68. tooluniverse/data/semantic_scholar_tools.json +55 -22
  69. tooluniverse/data/special_tools.json +8 -6
  70. tooluniverse/data/tool_composition_tools.json +112 -82
  71. tooluniverse/data/unified_guideline_tools.json +707 -0
  72. tooluniverse/data/url_fetch_tools.json +102 -82
  73. tooluniverse/data/uspto_tools.json +49 -30
  74. tooluniverse/data/wikidata_sparql_tools.json +42 -39
  75. tooluniverse/data/xml_tools.json +3274 -3113
  76. tooluniverse/data/zenodo_tools.json +84 -76
  77. tooluniverse/dblp_tool.py +76 -6
  78. tooluniverse/default_config.py +13 -0
  79. tooluniverse/doaj_tool.py +76 -17
  80. tooluniverse/doctor.py +48 -0
  81. tooluniverse/europe_pmc_tool.py +132 -17
  82. tooluniverse/exceptions.py +170 -0
  83. tooluniverse/execute_function.py +784 -362
  84. tooluniverse/fatcat_tool.py +0 -1
  85. tooluniverse/generate_tools.py +198 -0
  86. tooluniverse/hal_tool.py +1 -1
  87. tooluniverse/llm_clients.py +101 -124
  88. tooluniverse/mcp_tool_registry.py +4 -1
  89. tooluniverse/medrxiv_tool.py +32 -13
  90. tooluniverse/memory_manager.py +166 -0
  91. tooluniverse/molecule_2d_tool.py +274 -0
  92. tooluniverse/molecule_3d_tool.py +441 -0
  93. tooluniverse/odphp_tool.py +49 -14
  94. tooluniverse/openaire_tool.py +5 -20
  95. tooluniverse/openalex_tool.py +34 -0
  96. tooluniverse/osf_preprints_tool.py +1 -1
  97. tooluniverse/pmc_tool.py +54 -56
  98. tooluniverse/protein_structure_3d_tool.py +295 -0
  99. tooluniverse/pubmed_tool.py +69 -6
  100. tooluniverse/remote/boltz/boltz_mcp_server.py +3 -1
  101. tooluniverse/remote/uspto_downloader/uspto_downloader_mcp_server.py +3 -1
  102. tooluniverse/semantic_scholar_tool.py +40 -10
  103. tooluniverse/smcp.py +140 -205
  104. tooluniverse/smcp_server.py +97 -55
  105. tooluniverse/tool_registry.py +35 -3
  106. tooluniverse/tools/ADMETAI_predict_BBB_penetrance.py +46 -0
  107. tooluniverse/tools/ADMETAI_predict_CYP_interactions.py +46 -0
  108. tooluniverse/tools/ADMETAI_predict_bioavailability.py +46 -0
  109. tooluniverse/tools/ADMETAI_predict_clearance_distribution.py +49 -0
  110. tooluniverse/tools/ADMETAI_predict_nuclear_receptor_activity.py +49 -0
  111. tooluniverse/tools/ADMETAI_predict_physicochemical_properties.py +49 -0
  112. tooluniverse/tools/ADMETAI_predict_solubility_lipophilicity_hydration.py +49 -0
  113. tooluniverse/tools/ADMETAI_predict_stress_response.py +46 -0
  114. tooluniverse/tools/ADMETAI_predict_toxicity.py +46 -0
  115. tooluniverse/tools/AdvancedCodeQualityAnalyzer.py +63 -0
  116. tooluniverse/tools/AdverseEventICDMapper.py +46 -0
  117. tooluniverse/tools/AdverseEventPredictionQuestionGenerator.py +52 -0
  118. tooluniverse/tools/AdverseEventPredictionQuestionGeneratorWithContext.py +59 -0
  119. tooluniverse/tools/ArXiv_search_papers.py +63 -0
  120. tooluniverse/tools/ArgumentDescriptionOptimizer.py +55 -0
  121. tooluniverse/tools/BioRxiv_search_preprints.py +52 -0
  122. tooluniverse/tools/BiomarkerDiscoveryWorkflow.py +55 -0
  123. tooluniverse/tools/CORE_search_papers.py +67 -0
  124. tooluniverse/tools/CallAgent.py +46 -0
  125. tooluniverse/tools/ChEMBL_search_similar_molecules.py +59 -0
  126. tooluniverse/tools/CodeOptimizer.py +55 -0
  127. tooluniverse/tools/CodeQualityAnalyzer.py +71 -0
  128. tooluniverse/tools/ComprehensiveDrugDiscoveryPipeline.py +49 -0
  129. tooluniverse/tools/Crossref_search_works.py +55 -0
  130. tooluniverse/tools/DBLP_search_publications.py +52 -0
  131. tooluniverse/tools/DOAJ_search_articles.py +55 -0
  132. tooluniverse/tools/DailyMed_get_spl_by_setid.py +52 -0
  133. tooluniverse/tools/DailyMed_search_spls.py +79 -0
  134. tooluniverse/tools/DataAnalysisValidityReviewer.py +49 -0
  135. tooluniverse/tools/DescriptionAnalyzer.py +55 -0
  136. tooluniverse/tools/DescriptionQualityEvaluator.py +59 -0
  137. tooluniverse/tools/DomainExpertValidator.py +63 -0
  138. tooluniverse/tools/DrugSafetyAnalyzer.py +59 -0
  139. tooluniverse/tools/EthicalComplianceReviewer.py +49 -0
  140. tooluniverse/tools/EuropePMC_Guidelines_Search.py +52 -0
  141. tooluniverse/tools/EuropePMC_search_articles.py +52 -0
  142. tooluniverse/tools/ExperimentalDesignScorer.py +55 -0
  143. tooluniverse/tools/FAERS_count_additive_administration_routes.py +52 -0
  144. tooluniverse/tools/FAERS_count_additive_adverse_reactions.py +71 -0
  145. tooluniverse/tools/FAERS_count_additive_event_reports_by_country.py +63 -0
  146. tooluniverse/tools/FAERS_count_additive_reaction_outcomes.py +63 -0
  147. tooluniverse/tools/FAERS_count_additive_reports_by_reporter_country.py +63 -0
  148. tooluniverse/tools/FAERS_count_additive_seriousness_classification.py +63 -0
  149. tooluniverse/tools/FAERS_count_country_by_drug_event.py +63 -0
  150. tooluniverse/tools/FAERS_count_death_related_by_drug.py +49 -0
  151. tooluniverse/tools/FAERS_count_drug_routes_by_event.py +52 -0
  152. tooluniverse/tools/FAERS_count_drugs_by_drug_event.py +63 -0
  153. tooluniverse/tools/FAERS_count_outcomes_by_drug_event.py +63 -0
  154. tooluniverse/tools/FAERS_count_patient_age_distribution.py +49 -0
  155. tooluniverse/tools/FAERS_count_reactions_by_drug_event.py +71 -0
  156. tooluniverse/tools/FAERS_count_reportercountry_by_drug_event.py +63 -0
  157. tooluniverse/tools/FAERS_count_seriousness_by_drug_event.py +63 -0
  158. tooluniverse/tools/FDA_get_abuse_dependence_info_by_drug_name.py +55 -0
  159. tooluniverse/tools/FDA_get_abuse_info_by_drug_name.py +55 -0
  160. tooluniverse/tools/FDA_get_accessories_info_by_drug_name.py +55 -0
  161. tooluniverse/tools/FDA_get_active_ingredient_info_by_drug_name.py +55 -0
  162. tooluniverse/tools/FDA_get_adverse_reactions_by_drug_name.py +55 -0
  163. tooluniverse/tools/FDA_get_alarms_by_drug_name.py +55 -0
  164. tooluniverse/tools/FDA_get_animal_pharmacology_info_by_drug_name.py +55 -0
  165. tooluniverse/tools/FDA_get_assembly_installation_info_by_drug_name.py +55 -0
  166. tooluniverse/tools/FDA_get_boxed_warning_info_by_drug_name.py +55 -0
  167. tooluniverse/tools/FDA_get_brand_name_generic_name.py +52 -0
  168. tooluniverse/tools/FDA_get_calibration_instructions_by_drug_name.py +55 -0
  169. tooluniverse/tools/FDA_get_carcinogenic_mutagenic_fertility_by_drug_name.py +55 -0
  170. tooluniverse/tools/FDA_get_child_safety_info_by_drug_name.py +55 -0
  171. tooluniverse/tools/FDA_get_clinical_pharmacology_by_drug_name.py +55 -0
  172. tooluniverse/tools/FDA_get_clinical_studies_info_by_drug_name.py +55 -0
  173. tooluniverse/tools/FDA_get_contact_for_questions_info_by_drug_name.py +55 -0
  174. tooluniverse/tools/FDA_get_contraindications_by_drug_name.py +55 -0
  175. tooluniverse/tools/FDA_get_controlled_substance_DEA_schedule_info_by_drug_name.py +55 -0
  176. tooluniverse/tools/FDA_get_dear_health_care_provider_letter_info_by_drug_name.py +55 -0
  177. tooluniverse/tools/FDA_get_dependence_info_by_drug_name.py +55 -0
  178. tooluniverse/tools/FDA_get_disposal_info_by_drug_name.py +55 -0
  179. tooluniverse/tools/FDA_get_do_not_use_info_by_drug_name.py +55 -0
  180. tooluniverse/tools/FDA_get_document_id_by_drug_name.py +55 -0
  181. tooluniverse/tools/FDA_get_dosage_and_storage_information_by_drug_name.py +55 -0
  182. tooluniverse/tools/FDA_get_dosage_forms_and_strengths_by_drug_name.py +55 -0
  183. tooluniverse/tools/FDA_get_drug_generic_name.py +46 -0
  184. tooluniverse/tools/FDA_get_drug_interactions_by_drug_name.py +55 -0
  185. tooluniverse/tools/FDA_get_drug_name_by_SPL_ID.py +55 -0
  186. tooluniverse/tools/FDA_get_drug_name_by_adverse_reaction.py +59 -0
  187. tooluniverse/tools/FDA_get_drug_name_by_calibration_instructions.py +59 -0
  188. tooluniverse/tools/FDA_get_drug_name_by_dependence_info.py +59 -0
  189. tooluniverse/tools/FDA_get_drug_name_by_document_id.py +55 -0
  190. tooluniverse/tools/FDA_get_drug_name_by_dosage_info.py +55 -0
  191. tooluniverse/tools/FDA_get_drug_name_by_environmental_warning.py +59 -0
  192. tooluniverse/tools/FDA_get_drug_name_by_inactive_ingredient.py +59 -0
  193. tooluniverse/tools/FDA_get_drug_name_by_info_on_conditions_for_doctor_consultation.py +55 -0
  194. tooluniverse/tools/FDA_get_drug_name_by_labor_and_delivery_info.py +59 -0
  195. tooluniverse/tools/FDA_get_drug_name_by_microbiology.py +59 -0
  196. tooluniverse/tools/FDA_get_drug_name_by_other_safety_info.py +55 -0
  197. tooluniverse/tools/FDA_get_drug_name_by_pharmacodynamics.py +59 -0
  198. tooluniverse/tools/FDA_get_drug_name_by_pharmacogenomics.py +59 -0
  199. tooluniverse/tools/FDA_get_drug_name_by_precautions.py +55 -0
  200. tooluniverse/tools/FDA_get_drug_name_by_pregnancy_or_breastfeeding_info.py +59 -0
  201. tooluniverse/tools/FDA_get_drug_name_by_principal_display_panel.py +59 -0
  202. tooluniverse/tools/FDA_get_drug_name_by_reference.py +55 -0
  203. tooluniverse/tools/FDA_get_drug_name_by_set_id.py +55 -0
  204. tooluniverse/tools/FDA_get_drug_name_by_stop_use_info.py +55 -0
  205. tooluniverse/tools/FDA_get_drug_name_by_storage_and_handling_info.py +55 -0
  206. tooluniverse/tools/FDA_get_drug_name_by_warnings.py +55 -0
  207. tooluniverse/tools/FDA_get_drug_name_from_patient_package_insert.py +59 -0
  208. tooluniverse/tools/FDA_get_drug_names_by_abuse_dependence_info.py +55 -0
  209. tooluniverse/tools/FDA_get_drug_names_by_abuse_info.py +63 -0
  210. tooluniverse/tools/FDA_get_drug_names_by_accessories.py +63 -0
  211. tooluniverse/tools/FDA_get_drug_names_by_active_ingredient.py +63 -0
  212. tooluniverse/tools/FDA_get_drug_names_by_alarm.py +63 -0
  213. tooluniverse/tools/FDA_get_drug_names_by_animal_pharmacology_info.py +63 -0
  214. tooluniverse/tools/FDA_get_drug_names_by_application_number_NDC_number.py +59 -0
  215. tooluniverse/tools/FDA_get_drug_names_by_assembly_installation_info.py +63 -0
  216. tooluniverse/tools/FDA_get_drug_names_by_boxed_warning.py +63 -0
  217. tooluniverse/tools/FDA_get_drug_names_by_child_safety_info.py +63 -0
  218. tooluniverse/tools/FDA_get_drug_names_by_clinical_pharmacology.py +63 -0
  219. tooluniverse/tools/FDA_get_drug_names_by_clinical_studies.py +63 -0
  220. tooluniverse/tools/FDA_get_drug_names_by_consulting_doctor_pharmacist_info.py +63 -0
  221. tooluniverse/tools/FDA_get_drug_names_by_contraindications.py +63 -0
  222. tooluniverse/tools/FDA_get_drug_names_by_controlled_substance_DEA_schedule.py +63 -0
  223. tooluniverse/tools/FDA_get_drug_names_by_dear_health_care_provider_letter_info.py +63 -0
  224. tooluniverse/tools/FDA_get_drug_names_by_disposal_info.py +63 -0
  225. tooluniverse/tools/FDA_get_drug_names_by_dosage_forms_and_strengths_info.py +63 -0
  226. tooluniverse/tools/FDA_get_drug_names_by_drug_interactions.py +63 -0
  227. tooluniverse/tools/FDA_get_drug_names_by_effective_time.py +63 -0
  228. tooluniverse/tools/FDA_get_drug_names_by_food_safety_warnings.py +63 -0
  229. tooluniverse/tools/FDA_get_drug_names_by_general_precautions.py +63 -0
  230. tooluniverse/tools/FDA_get_drug_names_by_geriatric_use.py +63 -0
  231. tooluniverse/tools/FDA_get_drug_names_by_health_claim.py +63 -0
  232. tooluniverse/tools/FDA_get_drug_names_by_indication.py +55 -0
  233. tooluniverse/tools/FDA_get_drug_names_by_info_for_nursing_mothers.py +63 -0
  234. tooluniverse/tools/FDA_get_drug_names_by_information_for_owners_or_caregivers.py +63 -0
  235. tooluniverse/tools/FDA_get_drug_names_by_ingredient.py +63 -0
  236. tooluniverse/tools/FDA_get_drug_names_by_instructions_for_use.py +63 -0
  237. tooluniverse/tools/FDA_get_drug_names_by_lab_test_interference.py +63 -0
  238. tooluniverse/tools/FDA_get_drug_names_by_lab_tests.py +63 -0
  239. tooluniverse/tools/FDA_get_drug_names_by_mechanism_of_action.py +63 -0
  240. tooluniverse/tools/FDA_get_drug_names_by_medication_guide.py +63 -0
  241. tooluniverse/tools/FDA_get_drug_names_by_nonclinical_toxicology_info.py +63 -0
  242. tooluniverse/tools/FDA_get_drug_names_by_nonteratogenic_effects.py +63 -0
  243. tooluniverse/tools/FDA_get_drug_names_by_overdosage_info.py +63 -0
  244. tooluniverse/tools/FDA_get_drug_names_by_pediatric_use.py +63 -0
  245. tooluniverse/tools/FDA_get_drug_names_by_pharmacokinetics.py +63 -0
  246. tooluniverse/tools/FDA_get_drug_names_by_population_use.py +63 -0
  247. tooluniverse/tools/FDA_get_drug_names_by_pregnancy_effects_info.py +63 -0
  248. tooluniverse/tools/FDA_get_drug_names_by_residue_warning.py +63 -0
  249. tooluniverse/tools/FDA_get_drug_names_by_risk.py +63 -0
  250. tooluniverse/tools/FDA_get_drug_names_by_route.py +63 -0
  251. tooluniverse/tools/FDA_get_drug_names_by_safe_handling_warning.py +63 -0
  252. tooluniverse/tools/FDA_get_drug_names_by_safety_summary.py +63 -0
  253. tooluniverse/tools/FDA_get_drug_names_by_spl_indexing_data_elements.py +63 -0
  254. tooluniverse/tools/FDA_get_drug_names_by_teratogenic_effects.py +63 -0
  255. tooluniverse/tools/FDA_get_drug_names_by_user_safety_warning.py +63 -0
  256. tooluniverse/tools/FDA_get_drug_names_by_warnings_and_cautions.py +63 -0
  257. tooluniverse/tools/FDA_get_drugs_by_carcinogenic_mutagenic_fertility.py +63 -0
  258. tooluniverse/tools/FDA_get_effective_time_by_drug_name.py +55 -0
  259. tooluniverse/tools/FDA_get_environmental_warning_by_drug_name.py +55 -0
  260. tooluniverse/tools/FDA_get_general_precautions_by_drug_name.py +55 -0
  261. tooluniverse/tools/FDA_get_geriatric_use_info_by_drug_name.py +55 -0
  262. tooluniverse/tools/FDA_get_health_claims_by_drug_name.py +55 -0
  263. tooluniverse/tools/FDA_get_inactive_ingredient_info_by_drug_name.py +55 -0
  264. tooluniverse/tools/FDA_get_indications_by_drug_name.py +55 -0
  265. tooluniverse/tools/FDA_get_info_for_nursing_mothers_by_drug_name.py +55 -0
  266. tooluniverse/tools/FDA_get_info_for_patients_by_drug_name.py +55 -0
  267. tooluniverse/tools/FDA_get_info_on_conditions_for_doctor_consultation_by_drug_name.py +55 -0
  268. tooluniverse/tools/FDA_get_info_on_consulting_doctor_pharmacist_by_drug_name.py +55 -0
  269. tooluniverse/tools/FDA_get_information_for_owners_or_caregivers_by_drug_name.py +55 -0
  270. tooluniverse/tools/FDA_get_ingredients_by_drug_name.py +55 -0
  271. tooluniverse/tools/FDA_get_instructions_for_use_by_drug_name.py +55 -0
  272. tooluniverse/tools/FDA_get_lab_test_interference_info_by_drug_name.py +55 -0
  273. tooluniverse/tools/FDA_get_lab_tests_by_drug_name.py +55 -0
  274. tooluniverse/tools/FDA_get_labor_and_delivery_info_by_drug_name.py +55 -0
  275. tooluniverse/tools/FDA_get_manufacturer_name_NDC_number_by_drug_name.py +55 -0
  276. tooluniverse/tools/FDA_get_mechanism_of_action_by_drug_name.py +55 -0
  277. tooluniverse/tools/FDA_get_medication_guide_info_by_drug_name.py +55 -0
  278. tooluniverse/tools/FDA_get_microbiology_info_by_drug_name.py +55 -0
  279. tooluniverse/tools/FDA_get_nonclinical_toxicology_info_by_drug_name.py +55 -0
  280. tooluniverse/tools/FDA_get_nonteratogenic_effects_by_drug_name.py +55 -0
  281. tooluniverse/tools/FDA_get_other_safety_info_by_drug_name.py +55 -0
  282. tooluniverse/tools/FDA_get_overdosage_info_by_drug_name.py +55 -0
  283. tooluniverse/tools/FDA_get_patient_package_insert_from_drug_name.py +55 -0
  284. tooluniverse/tools/FDA_get_pediatric_use_info_by_drug_name.py +55 -0
  285. tooluniverse/tools/FDA_get_pharmacodynamics_by_drug_name.py +55 -0
  286. tooluniverse/tools/FDA_get_pharmacogenomics_info_by_drug_name.py +55 -0
  287. tooluniverse/tools/FDA_get_pharmacokinetics_by_drug_name.py +55 -0
  288. tooluniverse/tools/FDA_get_population_use_info_by_drug_name.py +55 -0
  289. tooluniverse/tools/FDA_get_precautions_by_drug_name.py +55 -0
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  574. tooluniverse/tools/get_diffdock_info.py +46 -0
  575. tooluniverse/tools/get_dscribe_info.py +49 -0
  576. tooluniverse/tools/get_ec_number_by_entity_id.py +46 -0
  577. tooluniverse/tools/get_elephant_info.py +44 -0
  578. tooluniverse/tools/get_em_3d_fitting_and_reconstruction_details.py +49 -0
  579. tooluniverse/tools/get_emdb_ids_by_pdb_id.py +46 -0
  580. tooluniverse/tools/get_episcanpy_info.py +44 -0
  581. tooluniverse/tools/get_ete3_info.py +44 -0
  582. tooluniverse/tools/get_faiss_info.py +46 -0
  583. tooluniverse/tools/get_fanc_info.py +46 -0
  584. tooluniverse/tools/get_flask_info.py +46 -0
  585. tooluniverse/tools/get_flowio_info.py +46 -0
  586. tooluniverse/tools/get_flowkit_info.py +46 -0
  587. tooluniverse/tools/get_flowutils_info.py +46 -0
  588. tooluniverse/tools/get_freesasa_info.py +44 -0
  589. tooluniverse/tools/get_galpy_info.py +44 -0
  590. tooluniverse/tools/get_gene_name_by_entity_id.py +46 -0
  591. tooluniverse/tools/get_geopandas_info.py +44 -0
  592. tooluniverse/tools/get_gget_info.py +46 -0
  593. tooluniverse/tools/get_googlesearch_python_info.py +46 -0
  594. tooluniverse/tools/get_gseapy_info.py +49 -0
  595. tooluniverse/tools/get_h5py_info.py +46 -0
  596. tooluniverse/tools/get_harmony_pytorch_info.py +46 -0
  597. tooluniverse/tools/get_hmmlearn_info.py +46 -0
  598. tooluniverse/tools/get_holoviews_info.py +44 -0
  599. tooluniverse/tools/get_host_organism_by_pdb_id.py +46 -0
  600. tooluniverse/tools/get_htmd_info.py +44 -0
  601. tooluniverse/tools/get_hyperopt_info.py +49 -0
  602. tooluniverse/tools/get_igraph_info.py +49 -0
  603. tooluniverse/tools/get_imageio_info.py +44 -0
  604. tooluniverse/tools/get_imbalanced_learn_info.py +44 -0
  605. tooluniverse/tools/get_jcvi_info.py +46 -0
  606. tooluniverse/tools/get_joblib_info.py +44 -0
  607. tooluniverse/tools/get_joint_associated_diseases_by_HPO_ID_list.py +55 -0
  608. tooluniverse/tools/get_khmer_info.py +46 -0
  609. tooluniverse/tools/get_kipoiseq_info.py +44 -0
  610. tooluniverse/tools/get_lifelines_info.py +49 -0
  611. tooluniverse/tools/get_ligand_bond_count_by_pdb_id.py +46 -0
  612. tooluniverse/tools/get_ligand_smiles_by_chem_comp_id.py +49 -0
  613. tooluniverse/tools/get_lightgbm_info.py +44 -0
  614. tooluniverse/tools/get_loompy_info.py +46 -0
  615. tooluniverse/tools/get_mageck_info.py +46 -0
  616. tooluniverse/tools/get_matplotlib_info.py +49 -0
  617. tooluniverse/tools/get_mdanalysis_info.py +46 -0
  618. tooluniverse/tools/get_mdtraj_info.py +44 -0
  619. tooluniverse/tools/get_mne_info.py +44 -0
  620. tooluniverse/tools/get_molfeat_info.py +44 -0
  621. tooluniverse/tools/get_molvs_info.py +44 -0
  622. tooluniverse/tools/get_mordred_info.py +44 -0
  623. tooluniverse/tools/get_msprime_info.py +49 -0
  624. tooluniverse/tools/get_mudata_info.py +49 -0
  625. tooluniverse/tools/get_mutation_annotations_by_pdb_id.py +46 -0
  626. tooluniverse/tools/get_neo_info.py +44 -0
  627. tooluniverse/tools/get_netcdf4_info.py +44 -0
  628. tooluniverse/tools/get_networkx_info.py +46 -0
  629. tooluniverse/tools/get_nglview_info.py +44 -0
  630. tooluniverse/tools/get_nilearn_info.py +44 -0
  631. tooluniverse/tools/get_numba_info.py +46 -0
  632. tooluniverse/tools/get_numpy_info.py +46 -0
  633. tooluniverse/tools/get_oligosaccharide_descriptors_by_entity_id.py +49 -0
  634. tooluniverse/tools/get_openbabel_info.py +49 -0
  635. tooluniverse/tools/get_openchem_info.py +46 -0
  636. tooluniverse/tools/get_opencv_info.py +49 -0
  637. tooluniverse/tools/get_openmm_info.py +49 -0
  638. tooluniverse/tools/get_optlang_info.py +46 -0
  639. tooluniverse/tools/get_optuna_info.py +44 -0
  640. tooluniverse/tools/get_palantir_info.py +44 -0
  641. tooluniverse/tools/get_pandas_info.py +49 -0
  642. tooluniverse/tools/get_patsy_info.py +44 -0
  643. tooluniverse/tools/get_pdbfixer_info.py +46 -0
  644. tooluniverse/tools/get_phenotype_by_HPO_ID.py +46 -0
  645. tooluniverse/tools/get_pillow_info.py +44 -0
  646. tooluniverse/tools/get_plantcv_info.py +46 -0
  647. tooluniverse/tools/get_plip_info.py +46 -0
  648. tooluniverse/tools/get_plotly_info.py +44 -0
  649. tooluniverse/tools/get_poliastro_info.py +46 -0
  650. tooluniverse/tools/get_polymer_entity_annotations.py +49 -0
  651. tooluniverse/tools/get_polymer_entity_count_by_pdb_id.py +46 -0
  652. tooluniverse/tools/get_polymer_entity_ids_by_pdb_id.py +46 -0
  653. tooluniverse/tools/get_polymer_entity_type_by_entity_id.py +49 -0
  654. tooluniverse/tools/get_polymer_molecular_weight_by_entity_id.py +49 -0
  655. tooluniverse/tools/get_poretools_info.py +44 -0
  656. tooluniverse/tools/get_prody_info.py +46 -0
  657. tooluniverse/tools/get_protein_classification_by_pdb_id.py +49 -0
  658. tooluniverse/tools/get_protein_metadata_by_pdb_id.py +46 -0
  659. tooluniverse/tools/get_pubchempy_info.py +44 -0
  660. tooluniverse/tools/get_pybedtools_info.py +49 -0
  661. tooluniverse/tools/get_pybigwig_info.py +46 -0
  662. tooluniverse/tools/get_pydeseq2_info.py +46 -0
  663. tooluniverse/tools/get_pyensembl_info.py +44 -0
  664. tooluniverse/tools/get_pyephem_info.py +44 -0
  665. tooluniverse/tools/get_pyfaidx_info.py +49 -0
  666. tooluniverse/tools/get_pyfasta_info.py +44 -0
  667. tooluniverse/tools/get_pykalman_info.py +46 -0
  668. tooluniverse/tools/get_pyliftover_info.py +49 -0
  669. tooluniverse/tools/get_pymassspec_info.py +46 -0
  670. tooluniverse/tools/get_pymed_info.py +46 -0
  671. tooluniverse/tools/get_pymzml_info.py +46 -0
  672. tooluniverse/tools/get_pypdf2_info.py +46 -0
  673. tooluniverse/tools/get_pyranges_info.py +49 -0
  674. tooluniverse/tools/get_pyrosetta_info.py +44 -0
  675. tooluniverse/tools/get_pysam_info.py +46 -0
  676. tooluniverse/tools/get_pyscenic_info.py +46 -0
  677. tooluniverse/tools/get_pyscf_info.py +46 -0
  678. tooluniverse/tools/get_pyscreener_info.py +46 -0
  679. tooluniverse/tools/get_pytdc_info.py +46 -0
  680. tooluniverse/tools/get_python_libsbml_info.py +46 -0
  681. tooluniverse/tools/get_pytorch_info.py +49 -0
  682. tooluniverse/tools/get_pyvcf_info.py +44 -0
  683. tooluniverse/tools/get_pyvis_info.py +44 -0
  684. tooluniverse/tools/get_qutip_info.py +44 -0
  685. tooluniverse/tools/get_rasterio_info.py +44 -0
  686. tooluniverse/tools/get_rdkit_info.py +46 -0
  687. tooluniverse/tools/get_refinement_resolution_by_pdb_id.py +49 -0
  688. tooluniverse/tools/get_release_deposit_dates_by_pdb_id.py +49 -0
  689. tooluniverse/tools/get_reportlab_info.py +49 -0
  690. tooluniverse/tools/get_requests_info.py +49 -0
  691. tooluniverse/tools/get_ruptures_info.py +46 -0
  692. tooluniverse/tools/get_scanorama_info.py +44 -0
  693. tooluniverse/tools/get_scanpy_info.py +49 -0
  694. tooluniverse/tools/get_schnetpack_info.py +49 -0
  695. tooluniverse/tools/get_scholarly_info.py +46 -0
  696. tooluniverse/tools/get_scikit_bio_info.py +49 -0
  697. tooluniverse/tools/get_scikit_image_info.py +46 -0
  698. tooluniverse/tools/get_scikit_learn_info.py +49 -0
  699. tooluniverse/tools/get_scipy_info.py +46 -0
  700. tooluniverse/tools/get_scrublet_info.py +49 -0
  701. tooluniverse/tools/get_scvelo_info.py +49 -0
  702. tooluniverse/tools/get_scvi_tools_info.py +44 -0
  703. tooluniverse/tools/get_seaborn_info.py +49 -0
  704. tooluniverse/tools/get_sequence_by_pdb_id.py +46 -0
  705. tooluniverse/tools/get_sequence_lengths_by_pdb_id.py +46 -0
  706. tooluniverse/tools/get_sequence_positional_features_by_instance_id.py +49 -0
  707. tooluniverse/tools/get_skopt_info.py +44 -0
  708. tooluniverse/tools/get_souporcell_info.py +46 -0
  709. tooluniverse/tools/get_source_organism_by_pdb_id.py +46 -0
  710. tooluniverse/tools/get_space_group_by_pdb_id.py +46 -0
  711. tooluniverse/tools/get_statsmodels_info.py +49 -0
  712. tooluniverse/tools/get_structure_determination_software_by_pdb_id.py +49 -0
  713. tooluniverse/tools/get_structure_title_by_pdb_id.py +46 -0
  714. tooluniverse/tools/get_structure_validation_metrics_by_pdb_id.py +49 -0
  715. tooluniverse/tools/get_sunpy_info.py +44 -0
  716. tooluniverse/tools/get_sympy_info.py +46 -0
  717. tooluniverse/tools/get_target_cofactor_info.py +46 -0
  718. tooluniverse/tools/get_taxonomy_by_pdb_id.py +46 -0
  719. tooluniverse/tools/get_tiledb_info.py +46 -0
  720. tooluniverse/tools/get_tiledbsoma_info.py +46 -0
  721. tooluniverse/tools/get_torch_geometric_info.py +49 -0
  722. tooluniverse/tools/get_tqdm_info.py +46 -0
  723. tooluniverse/tools/get_trackpy_info.py +46 -0
  724. tooluniverse/tools/get_tskit_info.py +46 -0
  725. tooluniverse/tools/get_umap_learn_info.py +49 -0
  726. tooluniverse/tools/get_uniprot_accession_by_entity_id.py +49 -0
  727. tooluniverse/tools/get_velocyto_info.py +44 -0
  728. tooluniverse/tools/get_viennarna_info.py +49 -0
  729. tooluniverse/tools/get_webpage_text_from_url.py +52 -0
  730. tooluniverse/tools/get_webpage_title.py +49 -0
  731. tooluniverse/tools/get_xarray_info.py +44 -0
  732. tooluniverse/tools/get_xesmf_info.py +44 -0
  733. tooluniverse/tools/get_xgboost_info.py +44 -0
  734. tooluniverse/tools/get_zarr_info.py +44 -0
  735. tooluniverse/tools/gwas_get_association_by_id.py +49 -0
  736. tooluniverse/tools/gwas_get_associations_for_snp.py +67 -0
  737. tooluniverse/tools/gwas_get_associations_for_study.py +55 -0
  738. tooluniverse/tools/gwas_get_associations_for_trait.py +55 -0
  739. tooluniverse/tools/gwas_get_snp_by_id.py +46 -0
  740. tooluniverse/tools/gwas_get_snps_for_gene.py +55 -0
  741. tooluniverse/tools/gwas_get_studies_for_trait.py +75 -0
  742. tooluniverse/tools/gwas_get_study_by_id.py +46 -0
  743. tooluniverse/tools/gwas_get_variants_for_trait.py +55 -0
  744. tooluniverse/tools/gwas_search_associations.py +75 -0
  745. tooluniverse/tools/gwas_search_snps.py +63 -0
  746. tooluniverse/tools/gwas_search_studies.py +75 -0
  747. tooluniverse/tools/humanbase_ppi_analysis.py +67 -0
  748. tooluniverse/tools/mesh_get_subjects_by_pharmacological_action.py +63 -0
  749. tooluniverse/tools/mesh_get_subjects_by_subject_id.py +63 -0
  750. tooluniverse/tools/mesh_get_subjects_by_subject_name.py +63 -0
  751. tooluniverse/tools/mesh_get_subjects_by_subject_scope_or_definition.py +63 -0
  752. tooluniverse/tools/odphp_itemlist.py +49 -0
  753. tooluniverse/tools/odphp_myhealthfinder.py +67 -0
  754. tooluniverse/tools/odphp_outlink_fetch.py +59 -0
  755. tooluniverse/tools/odphp_topicsearch.py +67 -0
  756. tooluniverse/tools/openalex_literature_search.py +67 -0
  757. tooluniverse/tools/reactome_disease_target_score.py +52 -0
  758. tooluniverse/tools/search_clinical_trials.py +67 -0
  759. tooluniverse/tools/visualize_molecule_2d.py +83 -0
  760. tooluniverse/tools/visualize_molecule_3d.py +91 -0
  761. tooluniverse/tools/visualize_protein_structure_3d.py +79 -0
  762. tooluniverse/unified_guideline_tools.py +1210 -0
  763. tooluniverse/unpaywall_tool.py +0 -1
  764. tooluniverse/utils.py +71 -2
  765. tooluniverse/visualization_tool.py +897 -0
  766. tooluniverse/wikidata_sparql_tool.py +1 -2
  767. tooluniverse/zenodo_tool.py +1 -3
  768. {tooluniverse-1.0.6.dist-info → tooluniverse-1.0.7.dist-info}/METADATA +11 -2
  769. tooluniverse-1.0.7.dist-info/RECORD +855 -0
  770. {tooluniverse-1.0.6.dist-info → tooluniverse-1.0.7.dist-info}/entry_points.txt +3 -0
  771. tooluniverse/test/list_azure_openai_models.py +0 -210
  772. tooluniverse/test/mcp_server_test.py +0 -0
  773. tooluniverse/test/test_admetai_tool.py +0 -370
  774. tooluniverse/test/test_agentic_tool.py +0 -129
  775. tooluniverse/test/test_agentic_tool_azure_models.py +0 -91
  776. tooluniverse/test/test_alphafold_tool.py +0 -108
  777. tooluniverse/test/test_api_key_validation_min.py +0 -64
  778. tooluniverse/test/test_chem_tool.py +0 -37
  779. tooluniverse/test/test_claude_sdk.py +0 -93
  780. tooluniverse/test/test_compose_lieraturereview.py +0 -63
  781. tooluniverse/test/test_compose_tool.py +0 -448
  782. tooluniverse/test/test_dailymed.py +0 -69
  783. tooluniverse/test/test_dataset_tool.py +0 -200
  784. tooluniverse/test/test_disease_target_score.py +0 -56
  785. tooluniverse/test/test_drugbank_filter_examples.py +0 -179
  786. tooluniverse/test/test_efo.py +0 -31
  787. tooluniverse/test/test_enrichr_tool.py +0 -21
  788. tooluniverse/test/test_europe_pmc_tool.py +0 -20
  789. tooluniverse/test/test_fda_adv.py +0 -95
  790. tooluniverse/test/test_fda_drug_labeling.py +0 -91
  791. tooluniverse/test/test_gene_ontology_tools.py +0 -66
  792. tooluniverse/test/test_global_fallback.py +0 -288
  793. tooluniverse/test/test_gwas_tool.py +0 -139
  794. tooluniverse/test/test_hooks_direct.py +0 -219
  795. tooluniverse/test/test_hpa.py +0 -625
  796. tooluniverse/test/test_humanbase_tool.py +0 -20
  797. tooluniverse/test/test_idmap_tools.py +0 -61
  798. tooluniverse/test/test_list_built_in_tools.py +0 -33
  799. tooluniverse/test/test_mcp_server.py +0 -211
  800. tooluniverse/test/test_mcp_tool.py +0 -247
  801. tooluniverse/test/test_medlineplus.py +0 -220
  802. tooluniverse/test/test_odphp_tool.py +0 -166
  803. tooluniverse/test/test_openalex_tool.py +0 -32
  804. tooluniverse/test/test_openrouter_client.py +0 -288
  805. tooluniverse/test/test_opentargets.py +0 -28
  806. tooluniverse/test/test_pubchem_tool.py +0 -116
  807. tooluniverse/test/test_pubtator_tool.py +0 -37
  808. tooluniverse/test/test_rcsb_pdb_tool.py +0 -86
  809. tooluniverse/test/test_reactome.py +0 -54
  810. tooluniverse/test/test_semantic_scholar_tool.py +0 -24
  811. tooluniverse/test/test_software_tools.py +0 -147
  812. tooluniverse/test/test_stdio_hooks.py +0 -285
  813. tooluniverse/test/test_tool_description_optimizer.py +0 -49
  814. tooluniverse/test/test_tool_finder.py +0 -26
  815. tooluniverse/test/test_tool_finder_llm.py +0 -252
  816. tooluniverse/test/test_tools_find.py +0 -195
  817. tooluniverse/test/test_uniprot_tools.py +0 -74
  818. tooluniverse/test/test_uspto_tool.py +0 -72
  819. tooluniverse/test/test_xml_tool.py +0 -113
  820. tooluniverse-1.0.6.dist-info/RECORD +0 -230
  821. {tooluniverse-1.0.6.dist-info → tooluniverse-1.0.7.dist-info}/WHEEL +0 -0
  822. {tooluniverse-1.0.6.dist-info → tooluniverse-1.0.7.dist-info}/licenses/LICENSE +0 -0
  823. {tooluniverse-1.0.6.dist-info → tooluniverse-1.0.7.dist-info}/top_level.txt +0 -0
tooluniverse/data/dataset_tools.json CHANGED
@@ -1,646 +1,1089 @@
1
1
  [
2
- {
3
- "type": "DatasetTool",
4
- "name": "drugbank_vocab_search",
5
- "description": "Search the DrugBank vocabulary dataset for drugs by name, ID, synonyms, or other fields using text-based queries. Returns detailed drug information including DrugBank ID, common name, CAS number, UNII, and synonyms.",
6
- "hf_dataset_path": {
7
- "repo_id": "agenticx/DrugbankVocabulary",
8
- "path_in_repo": "drugbank_vocabulary.csv",
9
- "token": null,
10
- "save_to_local_dir": "src/tooluniverse/test"
11
- },
12
- "parameter": {
13
- "type": "object",
14
- "properties": {
15
- "query": {
16
- "type": "string",
17
- "description": "Search query string. Can be drug name, synonym, DrugBank ID, or any text to search for.",
18
- "minLength": 1,
19
- "required": true
20
- },
21
- "search_fields": {
22
- "type": "array",
23
- "items": {"type": "string"},
24
- "description": "Fields to search in. Available fields: 'DrugBank ID', 'Accession Numbers', 'Common name', 'CAS', 'UNII', 'Synonyms', 'Standard InChI Key'."
25
- },
26
- "case_sensitive": {
27
- "type": "boolean",
28
- "description": "Whether the search should be case sensitive."
29
- },
30
- "exact_match": {
31
- "type": "boolean",
32
- "description": "Whether to perform exact matching instead of substring matching."
33
- },
34
- "limit": {
35
- "type": "integer",
36
- "description": "Maximum number of results to return.",
37
- "minimum": 1,
38
- "maximum": 1000
39
- }
40
- }
2
+ {
3
+ "type": "DatasetTool",
4
+ "name": "drugbank_vocab_search",
5
+ "description": "Search the DrugBank vocabulary dataset for drugs by name, ID, synonyms, or other fields using text-based queries. Returns detailed drug information including DrugBank ID, common name, CAS number, UNII, and synonyms.",
6
+ "hf_dataset_path": {
7
+ "repo_id": "agenticx/DrugbankVocabulary",
8
+ "path_in_repo": "drugbank_vocabulary.csv",
9
+ "token": null,
10
+ "save_to_local_dir": "src/tooluniverse/test"
11
+ },
12
+ "parameter": {
13
+ "type": "object",
14
+ "properties": {
15
+ "query": {
16
+ "type": "string",
17
+ "description": "Search query string. Can be drug name, synonym, DrugBank ID, or any text to search for.",
18
+ "minLength": 1
41
19
  },
42
- "query_schema": {
43
- "search_fields": ["Common name", "Synonyms", "DrugBank ID"],
44
- "case_sensitive": false,
45
- "exact_match": false,
46
- "limit": 10
20
+ "search_fields": {
21
+ "type": "array",
22
+ "items": {
23
+ "type": "string"
24
+ },
25
+ "description": "Fields to search in. Available fields: 'DrugBank ID', 'Accession Numbers', 'Common name', 'CAS', 'UNII', 'Synonyms', 'Standard InChI Key'."
47
26
  },
48
- "return_schema": {
49
- "type": "object",
50
- "description": "Search results with matched drug records and search metadata",
51
- "properties": {
52
- "query": {
53
- "type": "string",
54
- "description": "The original search query string"
55
- },
56
- "total_results": {
57
- "type": "integer",
58
- "description": "Total number of matching results found"
59
- },
60
- "results": {
61
- "type": "array",
62
- "description": "Array of matching drug records",
63
- "items": {
64
- "type": "object",
65
- "properties": {
66
- "DrugBank ID": {"type": "string", "description": "Drug identifier (e.g., 'DB00945')"},
67
- "Accession Numbers": {"type": "string", "description": "Alternative drug identifiers"},
68
- "Common name": {"type": "string", "description": "Drug common name (e.g., 'Acetylsalicylic acid')"},
69
- "CAS": {"type": "string", "description": "Chemical Abstracts Service number"},
70
- "UNII": {"type": "string", "description": "Unique Ingredient Identifier"},
71
- "Synonyms": {"type": "string", "description": "Alternative drug names and synonyms"},
72
- "Standard InChI Key": {"type": "string", "description": "International Chemical Identifier key"},
73
- "matched_fields": {
74
- "type": "array",
75
- "items": {"type": "string"},
76
- "description": "Fields that matched the search query (e.g., ['Synonyms', 'Common name'])"
77
- }
78
- }
79
- }
80
- },
81
- "search_parameters": {
82
- "type": "object",
83
- "description": "Parameters used for the search",
84
- "properties": {
85
- "search_fields": {"type": "array", "items": {"type": "string"}},
86
- "case_sensitive": {"type": "boolean"},
87
- "exact_match": {"type": "boolean"},
88
- "limit": {"type": "integer"}
89
- }
90
- }
91
- }
27
+ "case_sensitive": {
28
+ "type": "boolean",
29
+ "description": "Whether the search should be case sensitive."
30
+ },
31
+ "exact_match": {
32
+ "type": "boolean",
33
+ "description": "Whether to perform exact matching instead of substring matching."
34
+ },
35
+ "limit": {
36
+ "type": "integer",
37
+ "description": "Maximum number of results to return.",
38
+ "minimum": 1,
39
+ "maximum": 1000
92
40
  }
41
+ },
42
+ "required": [
43
+ "query",
44
+ "search_fields",
45
+ "case_sensitive",
46
+ "exact_match",
47
+ "limit"
48
+ ]
93
49
  },
94
- {
95
- "type": "DatasetTool",
96
- "name": "drugbank_vocab_filter",
97
- "description": "Filter the DrugBank vocabulary dataset based on specific field criteria. Use simple field-value pairs to filter drugs by properties like names, IDs, and chemical identifiers.",
98
- "hf_dataset_path": {
99
- "repo_id": "agenticx/DrugbankVocabulary",
100
- "path_in_repo": "drugbank_vocabulary.csv",
101
- "token": null,
102
- "save_to_local_dir": "src/tooluniverse/test"
103
- },
104
- "parameter": {
105
- "type": "object",
106
- "properties": {
107
- "field": {
108
- "type": "string",
109
- "description": "The field to filter on",
110
- "enum": [
111
- "DrugBank ID",
112
- "Accession Numbers",
113
- "Common name",
114
- "CAS",
115
- "UNII",
116
- "Synonyms",
117
- "Standard InChI Key"
118
- ]
119
- },
120
- "condition": {
121
- "type": "string",
122
- "description": "The type of filtering condition to apply. Filter is case-insensitive.",
123
- "enum": [
124
- "contains",
125
- "starts_with",
126
- "ends_with",
127
- "exact",
128
- "not_empty"
129
- ]
130
- },
131
- "value": {
132
- "type": "string",
133
- "description": "The value to filter by. Not required when condition is 'not_empty'. Examples: 'insulin' (for contains), 'DB00' (for starts_with), 'acid' (for ends_with), 'Aspirin' (for exact)",
134
- "required": false
135
- },
136
- "limit": {
137
- "type": "integer",
138
- "description": "Maximum number of results to return.",
139
- "minimum": 1,
140
- "maximum": 1000
141
- }
142
- }
50
+ "query_schema": {
51
+ "search_fields": [
52
+ "Common name",
53
+ "Synonyms",
54
+ "DrugBank ID"
55
+ ],
56
+ "case_sensitive": false,
57
+ "exact_match": false,
58
+ "limit": 10
59
+ },
60
+ "return_schema": {
61
+ "type": "object",
62
+ "description": "Search results with matched drug records and search metadata",
63
+ "properties": {
64
+ "query": {
65
+ "type": "string",
66
+ "description": "The original search query string"
143
67
  },
144
- "query_schema": {
145
- "field": "Common name",
146
- "condition": "contains",
147
- "limit": 10
68
+ "total_results": {
69
+ "type": "integer",
70
+ "description": "Total number of matching results found"
148
71
  },
149
- "return_schema": {
72
+ "results": {
73
+ "type": "array",
74
+ "description": "Array of matching drug records",
75
+ "items": {
150
76
  "type": "object",
151
- "description": "Filter results with matched drug records and filter metadata",
152
77
  "properties": {
153
- "total_matches": {
154
- "type": "integer",
155
- "description": "Total number of records matching the filter criteria"
156
- },
157
- "returned_results": {
158
- "type": "integer",
159
- "description": "Number of results actually returned (limited by 'limit' parameter)"
78
+ "DrugBank ID": {
79
+ "type": "string",
80
+ "description": "Drug identifier (e.g., 'DB00945')"
81
+ },
82
+ "Accession Numbers": {
83
+ "type": "string",
84
+ "description": "Alternative drug identifiers"
85
+ },
86
+ "Common name": {
87
+ "type": "string",
88
+ "description": "Drug common name (e.g., 'Acetylsalicylic acid')"
89
+ },
90
+ "CAS": {
91
+ "type": "string",
92
+ "description": "Chemical Abstracts Service number"
93
+ },
94
+ "UNII": {
95
+ "type": "string",
96
+ "description": "Unique Ingredient Identifier"
97
+ },
98
+ "Synonyms": {
99
+ "type": "string",
100
+ "description": "Alternative drug names and synonyms"
101
+ },
102
+ "Standard InChI Key": {
103
+ "type": "string",
104
+ "description": "International Chemical Identifier key"
105
+ },
106
+ "matched_fields": {
107
+ "type": "array",
108
+ "items": {
109
+ "type": "string"
160
110
  },
161
- "results": {
162
- "type": "array",
163
- "description": "Array of filtered drug records",
164
- "items": {
165
- "type": "object",
166
- "properties": {
167
- "DrugBank ID": {"type": "string", "description": "Drug identifier (e.g., 'DB00001')"},
168
- "Accession Numbers": {"type": "string", "description": "Alternative drug identifiers"},
169
- "Common name": {"type": "string", "description": "Drug common name (e.g., 'Lepirudin')"},
170
- "CAS": {"type": "string", "description": "Chemical Abstracts Service number"},
171
- "UNII": {"type": "string", "description": "Unique Ingredient Identifier"},
172
- "Synonyms": {"type": "string", "description": "Alternative drug names and synonyms"},
173
- "Standard InChI Key": {"type": "string", "description": "International Chemical Identifier key"}
174
- }
175
- }
176
- },
177
- "applied_filter": {
178
- "type": "string",
179
- "description": "Human-readable description of the applied filter (e.g., 'Common name contains insulin')"
180
- },
181
- "filter_parameters": {
182
- "type": "object",
183
- "description": "Parameters used for filtering",
184
- "properties": {
185
- "field": {"type": "string"},
186
- "condition": {"type": "string"},
187
- "value": {"type": ["string", "null"]},
188
- "limit": {"type": "integer"}
189
- }
190
- }
111
+ "description": "Fields that matched the search query (e.g., ['Synonyms', 'Common name'])"
112
+ }
113
+ }
114
+ }
115
+ },
116
+ "search_parameters": {
117
+ "type": "object",
118
+ "description": "Parameters used for the search",
119
+ "properties": {
120
+ "search_fields": {
121
+ "type": "array",
122
+ "items": {
123
+ "type": "string"
124
+ }
125
+ },
126
+ "case_sensitive": {
127
+ "type": "boolean"
128
+ },
129
+ "exact_match": {
130
+ "type": "boolean"
131
+ },
132
+ "limit": {
133
+ "type": "integer"
191
134
  }
135
+ }
192
136
  }
137
+ }
138
+ }
139
+ },
140
+ {
141
+ "type": "DatasetTool",
142
+ "name": "drugbank_vocab_filter",
143
+ "description": "Filter the DrugBank vocabulary dataset based on specific field criteria. Use simple field-value pairs to filter drugs by properties like names, IDs, and chemical identifiers.",
144
+ "hf_dataset_path": {
145
+ "repo_id": "agenticx/DrugbankVocabulary",
146
+ "path_in_repo": "drugbank_vocabulary.csv",
147
+ "token": null,
148
+ "save_to_local_dir": "src/tooluniverse/test"
193
149
  },
194
- {
195
- "type": "DatasetTool",
196
- "name": "drugbank_full_search",
197
- "description": "Search the cleaned DrugBank dataframe (one row per drug) by ID, common name, or synonym. Returns identifiers, ATC, main pharmacology text fields, and protein partners. For best results, it is recommended that one uses `drugbank_vocab_search` to obtain DrugBank ID from other keywords first, and use this tool with DrugBank ID.",
198
- "hf_dataset_path": {
199
- "repo_id": "agenticx/DrugbankRawParquet",
200
- "path_in_repo": "drugbank_raw.parquet",
201
- "token": null,
202
- "save_to_local_dir": "src/tooluniverse/test"
203
- },
204
- "parameter": {
205
- "type": "object",
206
- "properties": {
207
- "query": {
208
- "type": "string",
209
- "description": "Free-text query (e.g. 'DB00945', 'acetylsalicylic', 'Acarbosa').",
210
- "required": true
211
- },
212
- "search_fields": {
213
- "type": "array",
214
- "items": { "type": "string" },
215
- "description": "Columns to search in. Choose from: 'drugbank_id', 'name', 'synonyms'."
216
- },
217
- "case_sensitive": {
218
- "type": "boolean",
219
- "description": "Match text with exact case if true."
220
- },
221
- "exact_match": {
222
- "type": "boolean",
223
- "description": "Field value must equal query exactly if true; otherwise substring match."
224
- },
225
- "limit": {
226
- "type": "integer",
227
- "description": "Max number of rows to return.",
228
- "minimum": 1,
229
- "maximum": 1000
230
- }
231
- }
150
+ "parameter": {
151
+ "type": "object",
152
+ "properties": {
153
+ "field": {
154
+ "type": "string",
155
+ "description": "The field to filter on",
156
+ "enum": [
157
+ "DrugBank ID",
158
+ "Accession Numbers",
159
+ "Common name",
160
+ "CAS",
161
+ "UNII",
162
+ "Synonyms",
163
+ "Standard InChI Key"
164
+ ]
232
165
  },
233
- "query_schema": {
234
- "search_fields": ["name", "synonyms", "drugbank_id"],
235
- "case_sensitive": false,
236
- "exact_match": false,
237
- "limit": 10
166
+ "condition": {
167
+ "type": "string",
168
+ "description": "The type of filtering condition to apply. Filter is case-insensitive.",
169
+ "enum": [
170
+ "contains",
171
+ "starts_with",
172
+ "ends_with",
173
+ "exact",
174
+ "not_empty"
175
+ ]
238
176
  },
239
- "return_schema": {
240
- "type": "object",
241
- "description": "Search results plus metadata.",
242
- "properties": {
243
- "query": { "type": "string" },
244
- "total_results": { "type": "integer" },
245
-
246
- "results": {
247
- "type": "array",
248
- "description": "Each element is one DrugBank hit with core info only.",
249
- "items": {
250
- "type": "object",
251
- "properties": {
252
- "drugbank_id": { "type": "string" },
253
- "name": { "type": "string" },
254
-
255
- "groups": { "type": "array", "items": { "type": "string" } },
256
- "atc_codes": { "type": "array", "items": { "type": "string" } },
257
-
258
- "indication": { "type": ["string","null"] },
259
- "pharmacodynamics": { "type": ["string","null"] },
260
- "moa": { "type": ["string","null"] },
261
- "absorption": { "type": ["string","null"] },
262
- "metabolism": { "type": ["string","null"] },
263
- "toxicity": { "type": ["string","null"] },
264
- "half_life": { "type": ["string","null"] },
265
-
266
- "targets": { "type": "array", "items": { "type": "string" } },
267
- "enzymes": { "type": "array", "items": { "type": "string" } },
268
- "carriers": { "type": "array", "items": { "type": "string" } },
269
- "transporters": { "type": "array", "items": { "type": "string" } },
270
-
271
- "matched_fields": {
272
- "type": "array",
273
- "items": { "type": "string" },
274
- "description": "Subset of search_fields that contained the match."
275
- }
276
- }
277
- }
278
- },
279
- "search_parameters": {
280
- "type": "object",
281
- "properties": {
282
- "search_fields": { "type": "array", "items": { "type": "string" } },
283
- "case_sensitive":{ "type": "boolean" },
284
- "exact_match": { "type": "boolean" },
285
- "limit": { "type": "integer" }
286
- }
287
- }
288
- }
177
+ "value": {
178
+ "type": "string",
179
+ "description": "The value to filter by. Not required when condition is 'not_empty'. Examples: 'insulin' (for contains), 'DB00' (for starts_with), 'acid' (for ends_with), 'Aspirin' (for exact)"
180
+ },
181
+ "limit": {
182
+ "type": "integer",
183
+ "description": "Maximum number of results to return.",
184
+ "minimum": 1,
185
+ "maximum": 1000
289
186
  }
187
+ },
188
+ "required": [
189
+ "field",
190
+ "condition",
191
+ "limit"
192
+ ]
193
+ },
194
+ "query_schema": {
195
+ "field": "Common name",
196
+ "condition": "contains",
197
+ "limit": 10
290
198
  },
291
- {
292
- "type": "DatasetTool",
293
- "name": "drugbank_links_search",
294
- "description": "Search the cross-reference table linking DrugBank IDs to external identifiers (CAS, KEGG, PubChem, ChEBI, PharmGKB, UniProt, etc.) and web resources.",
295
- "hf_dataset_path": {
296
- "repo_id": "agenticx/DrugLinks",
297
- "path_in_repo": "drug_links.csv",
298
- "token": null,
299
- "save_to_local_dir": "src/tooluniverse/test"
300
- },
301
- "parameter": {
199
+ "return_schema": {
200
+ "type": "object",
201
+ "description": "Filter results with matched drug records and filter metadata",
202
+ "properties": {
203
+ "total_matches": {
204
+ "type": "integer",
205
+ "description": "Total number of records matching the filter criteria"
206
+ },
207
+ "returned_results": {
208
+ "type": "integer",
209
+ "description": "Number of results actually returned (limited by 'limit' parameter)"
210
+ },
211
+ "results": {
212
+ "type": "array",
213
+ "description": "Array of filtered drug records",
214
+ "items": {
302
215
  "type": "object",
303
216
  "properties": {
304
- "query": {
305
- "type": "string",
306
- "description": "Free-text query (e.g. 'DB00002', 'Cetuximab').",
307
- "required": true
308
- },
309
- "search_fields": {
310
- "type": "array",
311
- "items": { "type": "string" },
312
- "description": "Columns to search. Choose from: 'DrugBank ID', 'Name', 'CAS Number', 'Drug Type', 'KEGG Compound ID', 'KEGG Drug ID', 'PubChem Compound ID', 'PubChem Substance ID', 'ChEBI ID', 'PharmGKB ID', 'HET ID', 'UniProt ID', 'Wikipedia ID', 'Drugs.com Link', 'NDC ID', 'ChemSpider ID', 'BindingDB ID', 'TTD ID'."
313
- },
314
- "case_sensitive": {
315
- "type": "boolean",
316
- "description": "Match text with exact case if true."
317
- },
318
- "exact_match": {
319
- "type": "boolean",
320
- "description": "Field value must equal query exactly if true; otherwise substring match."
321
- },
322
- "limit": {
323
- "type": "integer",
324
- "description": "Maximum number of rows to return.",
325
- "minimum": 1,
326
- "maximum": 1000
327
- }
217
+ "DrugBank ID": {
218
+ "type": "string",
219
+ "description": "Drug identifier (e.g., 'DB00001')"
220
+ },
221
+ "Accession Numbers": {
222
+ "type": "string",
223
+ "description": "Alternative drug identifiers"
224
+ },
225
+ "Common name": {
226
+ "type": "string",
227
+ "description": "Drug common name (e.g., 'Lepirudin')"
228
+ },
229
+ "CAS": {
230
+ "type": "string",
231
+ "description": "Chemical Abstracts Service number"
232
+ },
233
+ "UNII": {
234
+ "type": "string",
235
+ "description": "Unique Ingredient Identifier"
236
+ },
237
+ "Synonyms": {
238
+ "type": "string",
239
+ "description": "Alternative drug names and synonyms"
240
+ },
241
+ "Standard InChI Key": {
242
+ "type": "string",
243
+ "description": "International Chemical Identifier key"
244
+ }
328
245
  }
246
+ }
329
247
  },
330
- "query_schema": {
331
- "search_fields": ["DrugBank ID", "Name"],
332
- "case_sensitive": false,
333
- "exact_match": false,
334
- "limit": 10
248
+ "applied_filter": {
249
+ "type": "string",
250
+ "description": "Human-readable description of the applied filter (e.g., 'Common name contains insulin')"
335
251
  },
336
- "return_schema": {
337
- "type": "object",
338
- "description": "Search results plus metadata.",
339
- "properties": {
340
- "query": { "type": "string" },
341
- "total_results": { "type": "integer" },
342
-
343
- "results": {
344
- "type": "array",
345
- "items": {
346
- "type": "object",
347
- "properties": {
348
- "DrugBank ID": { "type": "string" },
349
- "Name": { "type": "string" },
350
- "CAS Number": { "type": ["string","null"] },
351
- "Drug Type": { "type": ["string","null"] },
352
- "KEGG Compound ID": { "type": ["string","null"] },
353
- "KEGG Drug ID": { "type": ["string","null"] },
354
- "PubChem Compound ID": { "type": ["string","null"] },
355
- "PubChem Substance ID": { "type": ["string","null"] },
356
- "ChEBI ID": { "type": ["string","null"] },
357
- "PharmGKB ID": { "type": ["string","null"] },
358
- "HET ID": { "type": ["string","null"] },
359
- "UniProt ID": { "type": ["string","null"] },
360
- "UniProt Title": { "type": ["string","null"] },
361
- "GenBank ID": { "type": ["string","null"] },
362
- "DPD ID": { "type": ["string","null"] },
363
- "RxList Link": { "type": ["string","null"] },
364
- "Pdrhealth Link": { "type": ["string","null"] },
365
- "Wikipedia ID": { "type": ["string","null"] },
366
- "Drugs.com Link": { "type": ["string","null"] },
367
- "NDC ID": { "type": ["string","null"] },
368
- "ChemSpider ID": { "type": ["string","null"] },
369
- "BindingDB ID": { "type": ["string","null"] },
370
- "TTD ID": { "type": ["string","null"] },
371
-
372
- "matched_fields": {
373
- "type": "array",
374
- "description": "Subset of search_fields that contained the match.",
375
- "items": { "type": "string" }
376
- }
377
- }
378
- }
379
- },
380
-
381
- "search_parameters": {
382
- "type": "object",
383
- "properties": {
384
- "search_fields": { "type": "array", "items": { "type": "string" } },
385
- "case_sensitive": { "type": "boolean" },
386
- "exact_match": { "type": "boolean" },
387
- "limit": { "type": "integer" }
388
- }
389
- }
252
+ "filter_parameters": {
253
+ "type": "object",
254
+ "description": "Parameters used for filtering",
255
+ "properties": {
256
+ "field": {
257
+ "type": "string"
258
+ },
259
+ "condition": {
260
+ "type": "string"
261
+ },
262
+ "value": {
263
+ "type": [
264
+ "string",
265
+ "null"
266
+ ]
267
+ },
268
+ "limit": {
269
+ "type": "integer"
390
270
  }
271
+ }
391
272
  }
273
+ }
274
+ }
275
+ },
276
+ {
277
+ "type": "DatasetTool",
278
+ "name": "drugbank_full_search",
279
+ "description": "Search the cleaned DrugBank dataframe (one row per drug) by ID, common name, or synonym. Returns identifiers, ATC, main pharmacology text fields, and protein partners. For best results, it is recommended that one uses `drugbank_vocab_search` to obtain DrugBank ID from other keywords first, and use this tool with DrugBank ID.",
280
+ "hf_dataset_path": {
281
+ "repo_id": "agenticx/DrugbankRawParquet",
282
+ "path_in_repo": "drugbank_raw.parquet",
283
+ "token": null,
284
+ "save_to_local_dir": "src/tooluniverse/test"
392
285
  },
393
- {
394
- "type": "DatasetTool",
395
- "name": "dict_search",
396
- "description": "Search the DICTrank dataset for drug-induced cardiotoxicity (DICT) risk information by trade name, generic name, or active ingredient. Searching with exact match is not recommeded.",
397
- "hf_dataset_path": {
398
- "repo_id": "agenticx/DICTrank",
399
- "path_in_repo": "DICTrank.csv",
400
- "token": null,
401
- "save_to_local_dir": "src/tooluniverse/test"
402
- },
403
- "parameter": {
404
- "type": "object",
405
- "properties": {
406
- "query": {
407
- "type": "string",
408
- "description": "Free-text query (e.g. 'ZYPREXA', 'Olanzapine').",
409
- "required": true
410
- },
411
- "search_fields": {
412
- "type": "array",
413
- "items": { "type": "string" },
414
- "description": "Columns to search. Choose from: 'Trade Name', 'Generic/Proper Name(s)', 'Active Ingredient(s)'."
415
- },
416
- "case_sensitive": {
417
- "type": "boolean",
418
- "description": "Match text with exact case if true."
419
- },
420
- "exact_match": {
421
- "type": "boolean",
422
- "description": "Field value must equal query exactly if true; otherwise substring match."
423
- },
424
- "limit": {
425
- "type": "integer",
426
- "description": "Maximum number of rows to return.",
427
- "minimum": 1,
428
- "maximum": 1000
429
- }
430
- }
286
+ "parameter": {
287
+ "type": "object",
288
+ "properties": {
289
+ "query": {
290
+ "type": "string",
291
+ "description": "Free-text query (e.g. 'DB00945', 'acetylsalicylic', 'Acarbosa')."
292
+ },
293
+ "search_fields": {
294
+ "type": "array",
295
+ "items": {
296
+ "type": "string"
297
+ },
298
+ "description": "Columns to search in. Choose from: 'drugbank_id', 'name', 'synonyms'."
299
+ },
300
+ "case_sensitive": {
301
+ "type": "boolean",
302
+ "description": "Match text with exact case if true."
303
+ },
304
+ "exact_match": {
305
+ "type": "boolean",
306
+ "description": "Field value must equal query exactly if true; otherwise substring match."
431
307
  },
432
- "query_schema": {
433
- "search_fields": ["Trade Name", "Generic/Proper Name(s)", "Active Ingredient(s)"],
434
- "case_sensitive": false,
435
- "exact_match": false,
436
- "limit": 10
308
+ "limit": {
309
+ "type": "integer",
310
+ "description": "Max number of rows to return.",
311
+ "minimum": 1,
312
+ "maximum": 1000
313
+ }
314
+ },
315
+ "required": [
316
+ "query",
317
+ "search_fields",
318
+ "case_sensitive",
319
+ "exact_match",
320
+ "limit"
321
+ ]
322
+ },
323
+ "query_schema": {
324
+ "search_fields": [
325
+ "name",
326
+ "synonyms",
327
+ "drugbank_id"
328
+ ],
329
+ "case_sensitive": false,
330
+ "exact_match": false,
331
+ "limit": 10
332
+ },
333
+ "return_schema": {
334
+ "type": "object",
335
+ "description": "Search results plus metadata.",
336
+ "properties": {
337
+ "query": {
338
+ "type": "string"
437
339
  },
438
- "return_schema": {
340
+ "total_results": {
341
+ "type": "integer"
342
+ },
343
+ "results": {
344
+ "type": "array",
345
+ "description": "Each element is one DrugBank hit with core info only.",
346
+ "items": {
439
347
  "type": "object",
440
- "description": "Search results plus metadata.",
441
348
  "properties": {
442
- "query": { "type": "string" },
443
- "total_results": { "type": "integer" },
444
-
445
- "results": {
446
- "type": "array",
447
- "items": {
448
- "type": "object",
449
- "properties": {
450
- "Trade Name": { "type": "string" },
451
- "Generic/Proper Name(s)": { "type": "string" },
452
- "Active Ingredient(s)": { "type": "string" },
453
- "Cardiotoxicity": { "type": ["string","null"] },
454
- "DICT Concern": { "type": ["string","null"] },
455
- "Keywords": { "type": ["string","null"] },
456
- "DIC Severity Level": { "type": ["string","null"] },
457
-
458
- "matched_fields": {
459
- "type": "array",
460
- "description": "Subset of search_fields that contained the match.",
461
- "items": { "type": "string" }
462
- }
463
- }
464
- }
465
- },
466
-
467
- "search_parameters": {
468
- "type": "object",
469
- "properties": {
470
- "search_fields": { "type": "array", "items": { "type": "string" } },
471
- "case_sensitive": { "type": "boolean" },
472
- "exact_match": { "type": "boolean" },
473
- "limit": { "type": "integer" }
474
- }
349
+ "drugbank_id": {
350
+ "type": "string"
351
+ },
352
+ "name": {
353
+ "type": "string"
354
+ },
355
+ "groups": {
356
+ "type": "array",
357
+ "items": {
358
+ "type": "string"
359
+ }
360
+ },
361
+ "atc_codes": {
362
+ "type": "array",
363
+ "items": {
364
+ "type": "string"
365
+ }
366
+ },
367
+ "indication": {
368
+ "type": [
369
+ "string",
370
+ "null"
371
+ ]
372
+ },
373
+ "pharmacodynamics": {
374
+ "type": [
375
+ "string",
376
+ "null"
377
+ ]
378
+ },
379
+ "moa": {
380
+ "type": [
381
+ "string",
382
+ "null"
383
+ ]
384
+ },
385
+ "absorption": {
386
+ "type": [
387
+ "string",
388
+ "null"
389
+ ]
390
+ },
391
+ "metabolism": {
392
+ "type": [
393
+ "string",
394
+ "null"
395
+ ]
396
+ },
397
+ "toxicity": {
398
+ "type": [
399
+ "string",
400
+ "null"
401
+ ]
402
+ },
403
+ "half_life": {
404
+ "type": [
405
+ "string",
406
+ "null"
407
+ ]
408
+ },
409
+ "targets": {
410
+ "type": "array",
411
+ "items": {
412
+ "type": "string"
413
+ }
414
+ },
415
+ "enzymes": {
416
+ "type": "array",
417
+ "items": {
418
+ "type": "string"
419
+ }
420
+ },
421
+ "carriers": {
422
+ "type": "array",
423
+ "items": {
424
+ "type": "string"
475
425
  }
426
+ },
427
+ "transporters": {
428
+ "type": "array",
429
+ "items": {
430
+ "type": "string"
431
+ }
432
+ },
433
+ "matched_fields": {
434
+ "type": "array",
435
+ "items": {
436
+ "type": "string"
437
+ },
438
+ "description": "Subset of search_fields that contained the match."
439
+ }
476
440
  }
441
+ }
442
+ },
443
+ "search_parameters": {
444
+ "type": "object",
445
+ "properties": {
446
+ "search_fields": {
447
+ "type": "array",
448
+ "items": {
449
+ "type": "string"
450
+ }
451
+ },
452
+ "case_sensitive": {
453
+ "type": "boolean"
454
+ },
455
+ "exact_match": {
456
+ "type": "boolean"
457
+ },
458
+ "limit": {
459
+ "type": "integer"
460
+ }
461
+ }
462
+ }
463
+ }
464
+ }
465
+ },
466
+ {
467
+ "type": "DatasetTool",
468
+ "name": "drugbank_links_search",
469
+ "description": "Search the cross-reference table linking DrugBank IDs to external identifiers (CAS, KEGG, PubChem, ChEBI, PharmGKB, UniProt, etc.) and web resources.",
470
+ "hf_dataset_path": {
471
+ "repo_id": "agenticx/DrugLinks",
472
+ "path_in_repo": "drug_links.csv",
473
+ "token": null,
474
+ "save_to_local_dir": "src/tooluniverse/test"
475
+ },
476
+ "parameter": {
477
+ "type": "object",
478
+ "properties": {
479
+ "query": {
480
+ "type": "string",
481
+ "description": "Free-text query (e.g. 'DB00002', 'Cetuximab')."
482
+ },
483
+ "search_fields": {
484
+ "type": "array",
485
+ "items": {
486
+ "type": "string"
487
+ },
488
+ "description": "Columns to search. Choose from: 'DrugBank ID', 'Name', 'CAS Number', 'Drug Type', 'KEGG Compound ID', 'KEGG Drug ID', 'PubChem Compound ID', 'PubChem Substance ID', 'ChEBI ID', 'PharmGKB ID', 'HET ID', 'UniProt ID', 'Wikipedia ID', 'Drugs.com Link', 'NDC ID', 'ChemSpider ID', 'BindingDB ID', 'TTD ID'."
489
+ },
490
+ "case_sensitive": {
491
+ "type": "boolean",
492
+ "description": "Match text with exact case if true."
493
+ },
494
+ "exact_match": {
495
+ "type": "boolean",
496
+ "description": "Field value must equal query exactly if true; otherwise substring match."
497
+ },
498
+ "limit": {
499
+ "type": "integer",
500
+ "description": "Maximum number of rows to return.",
501
+ "minimum": 1,
502
+ "maximum": 1000
477
503
  }
504
+ },
505
+ "required": [
506
+ "query",
507
+ "search_fields",
508
+ "case_sensitive",
509
+ "exact_match",
510
+ "limit"
511
+ ]
512
+ },
513
+ "query_schema": {
514
+ "search_fields": [
515
+ "DrugBank ID",
516
+ "Name"
517
+ ],
518
+ "case_sensitive": false,
519
+ "exact_match": false,
520
+ "limit": 10
478
521
  },
479
- {
480
- "type": "DatasetTool",
481
- "name": "dili_search",
482
- "description": "Search the DILIrank dataset for drug-induced liver-injury (DILI) risk information by compound name. Searching with exact match is not recommeded.",
483
- "hf_dataset_path": {
484
- "repo_id": "agenticx/DILIrank",
485
- "path_in_repo": "DILIrank.csv",
486
- "token": null,
487
- "save_to_local_dir": "src/tooluniverse/test"
488
- },
489
- "parameter": {
522
+ "return_schema": {
523
+ "type": "object",
524
+ "description": "Search results plus metadata.",
525
+ "properties": {
526
+ "query": {
527
+ "type": "string"
528
+ },
529
+ "total_results": {
530
+ "type": "integer"
531
+ },
532
+ "results": {
533
+ "type": "array",
534
+ "items": {
490
535
  "type": "object",
491
536
  "properties": {
492
- "query": {
493
- "type": "string",
494
- "description": "Free-text query (e.g. 'acetaminophen').",
495
- "required": true
496
- },
497
- "search_fields": {
498
- "type": "array",
499
- "items": { "type": "string" },
500
- "description": "Columns to search. Choose from: 'Compound Name'."
501
- },
502
- "case_sensitive": {
503
- "type": "boolean",
504
- "description": "Match text with exact case if true."
505
- },
506
- "exact_match": {
507
- "type": "boolean",
508
- "description": "Field value must equal query exactly if true; otherwise substring match."
509
- },
510
- "limit": {
511
- "type": "integer",
512
- "description": "Maximum number of rows to return.",
513
- "minimum": 1,
514
- "maximum": 1000
537
+ "DrugBank ID": {
538
+ "type": "string"
539
+ },
540
+ "Name": {
541
+ "type": "string"
542
+ },
543
+ "CAS Number": {
544
+ "type": [
545
+ "string",
546
+ "null"
547
+ ]
548
+ },
549
+ "Drug Type": {
550
+ "type": [
551
+ "string",
552
+ "null"
553
+ ]
554
+ },
555
+ "KEGG Compound ID": {
556
+ "type": [
557
+ "string",
558
+ "null"
559
+ ]
560
+ },
561
+ "KEGG Drug ID": {
562
+ "type": [
563
+ "string",
564
+ "null"
565
+ ]
566
+ },
567
+ "PubChem Compound ID": {
568
+ "type": [
569
+ "string",
570
+ "null"
571
+ ]
572
+ },
573
+ "PubChem Substance ID": {
574
+ "type": [
575
+ "string",
576
+ "null"
577
+ ]
578
+ },
579
+ "ChEBI ID": {
580
+ "type": [
581
+ "string",
582
+ "null"
583
+ ]
584
+ },
585
+ "PharmGKB ID": {
586
+ "type": [
587
+ "string",
588
+ "null"
589
+ ]
590
+ },
591
+ "HET ID": {
592
+ "type": [
593
+ "string",
594
+ "null"
595
+ ]
596
+ },
597
+ "UniProt ID": {
598
+ "type": [
599
+ "string",
600
+ "null"
601
+ ]
602
+ },
603
+ "UniProt Title": {
604
+ "type": [
605
+ "string",
606
+ "null"
607
+ ]
608
+ },
609
+ "GenBank ID": {
610
+ "type": [
611
+ "string",
612
+ "null"
613
+ ]
614
+ },
615
+ "DPD ID": {
616
+ "type": [
617
+ "string",
618
+ "null"
619
+ ]
620
+ },
621
+ "RxList Link": {
622
+ "type": [
623
+ "string",
624
+ "null"
625
+ ]
626
+ },
627
+ "Pdrhealth Link": {
628
+ "type": [
629
+ "string",
630
+ "null"
631
+ ]
632
+ },
633
+ "Wikipedia ID": {
634
+ "type": [
635
+ "string",
636
+ "null"
637
+ ]
638
+ },
639
+ "Drugs.com Link": {
640
+ "type": [
641
+ "string",
642
+ "null"
643
+ ]
644
+ },
645
+ "NDC ID": {
646
+ "type": [
647
+ "string",
648
+ "null"
649
+ ]
650
+ },
651
+ "ChemSpider ID": {
652
+ "type": [
653
+ "string",
654
+ "null"
655
+ ]
656
+ },
657
+ "BindingDB ID": {
658
+ "type": [
659
+ "string",
660
+ "null"
661
+ ]
662
+ },
663
+ "TTD ID": {
664
+ "type": [
665
+ "string",
666
+ "null"
667
+ ]
668
+ },
669
+ "matched_fields": {
670
+ "type": "array",
671
+ "description": "Subset of search_fields that contained the match.",
672
+ "items": {
673
+ "type": "string"
515
674
  }
675
+ }
516
676
  }
677
+ }
517
678
  },
518
- "query_schema": {
519
- "search_fields": ["Compound Name"],
520
- "case_sensitive": false,
521
- "exact_match": false,
522
- "limit": 10
679
+ "search_parameters": {
680
+ "type": "object",
681
+ "properties": {
682
+ "search_fields": {
683
+ "type": "array",
684
+ "items": {
685
+ "type": "string"
686
+ }
687
+ },
688
+ "case_sensitive": {
689
+ "type": "boolean"
690
+ },
691
+ "exact_match": {
692
+ "type": "boolean"
693
+ },
694
+ "limit": {
695
+ "type": "integer"
696
+ }
697
+ }
698
+ }
699
+ }
700
+ }
701
+ },
702
+ {
703
+ "type": "DatasetTool",
704
+ "name": "dict_search",
705
+ "description": "Search the DICTrank dataset for drug-induced cardiotoxicity (DICT) risk information by trade name, generic name, or active ingredient. Searching with exact match is not recommeded.",
706
+ "hf_dataset_path": {
707
+ "repo_id": "agenticx/DICTrank",
708
+ "path_in_repo": "DICTrank.csv",
709
+ "token": null,
710
+ "save_to_local_dir": "src/tooluniverse/test"
711
+ },
712
+ "parameter": {
713
+ "type": "object",
714
+ "properties": {
715
+ "query": {
716
+ "type": "string",
717
+ "description": "Free-text query (e.g. 'ZYPREXA', 'Olanzapine')."
718
+ },
719
+ "search_fields": {
720
+ "type": "array",
721
+ "items": {
722
+ "type": "string"
723
+ },
724
+ "description": "Columns to search. Choose from: 'Trade Name', 'Generic/Proper Name(s)', 'Active Ingredient(s)'."
523
725
  },
524
- "return_schema": {
726
+ "case_sensitive": {
727
+ "type": "boolean",
728
+ "description": "Match text with exact case if true."
729
+ },
730
+ "exact_match": {
731
+ "type": "boolean",
732
+ "description": "Field value must equal query exactly if true; otherwise substring match."
733
+ },
734
+ "limit": {
735
+ "type": "integer",
736
+ "description": "Maximum number of rows to return.",
737
+ "minimum": 1,
738
+ "maximum": 1000
739
+ }
740
+ },
741
+ "required": [
742
+ "query",
743
+ "search_fields",
744
+ "case_sensitive",
745
+ "exact_match",
746
+ "limit"
747
+ ]
748
+ },
749
+ "query_schema": {
750
+ "search_fields": [
751
+ "Trade Name",
752
+ "Generic/Proper Name(s)",
753
+ "Active Ingredient(s)"
754
+ ],
755
+ "case_sensitive": false,
756
+ "exact_match": false,
757
+ "limit": 10
758
+ },
759
+ "return_schema": {
760
+ "type": "object",
761
+ "description": "Search results plus metadata.",
762
+ "properties": {
763
+ "query": {
764
+ "type": "string"
765
+ },
766
+ "total_results": {
767
+ "type": "integer"
768
+ },
769
+ "results": {
770
+ "type": "array",
771
+ "items": {
525
772
  "type": "object",
526
- "description": "Search results plus metadata.",
527
773
  "properties": {
528
- "query": { "type": "string" },
529
- "total_results": { "type": "integer" },
530
-
531
- "results": {
532
- "type": "array",
533
- "items": {
534
- "type": "object",
535
- "properties": {
536
- "Compound Name": { "type": "string" },
537
- "Severity Class": { "type": ["integer","null"] },
538
- "DILI Concern": { "type": ["string","null"] },
539
-
540
- "matched_fields": {
541
- "type": "array",
542
- "description": "Subset of search_fields that contained the match.",
543
- "items": { "type": "string" }
544
- }
545
- }
546
- }
547
- },
548
-
549
- "search_parameters": {
550
- "type": "object",
551
- "properties": {
552
- "search_fields": { "type": "array", "items": { "type": "string" } },
553
- "case_sensitive": { "type": "boolean" },
554
- "exact_match": { "type": "boolean" },
555
- "limit": { "type": "integer" }
556
- }
774
+ "Trade Name": {
775
+ "type": "string"
776
+ },
777
+ "Generic/Proper Name(s)": {
778
+ "type": "string"
779
+ },
780
+ "Active Ingredient(s)": {
781
+ "type": "string"
782
+ },
783
+ "Cardiotoxicity": {
784
+ "type": [
785
+ "string",
786
+ "null"
787
+ ]
788
+ },
789
+ "DICT Concern": {
790
+ "type": [
791
+ "string",
792
+ "null"
793
+ ]
794
+ },
795
+ "Keywords": {
796
+ "type": [
797
+ "string",
798
+ "null"
799
+ ]
800
+ },
801
+ "DIC Severity Level": {
802
+ "type": [
803
+ "string",
804
+ "null"
805
+ ]
806
+ },
807
+ "matched_fields": {
808
+ "type": "array",
809
+ "description": "Subset of search_fields that contained the match.",
810
+ "items": {
811
+ "type": "string"
557
812
  }
813
+ }
558
814
  }
815
+ }
816
+ },
817
+ "search_parameters": {
818
+ "type": "object",
819
+ "properties": {
820
+ "search_fields": {
821
+ "type": "array",
822
+ "items": {
823
+ "type": "string"
824
+ }
825
+ },
826
+ "case_sensitive": {
827
+ "type": "boolean"
828
+ },
829
+ "exact_match": {
830
+ "type": "boolean"
831
+ },
832
+ "limit": {
833
+ "type": "integer"
834
+ }
835
+ }
836
+ }
837
+ }
838
+ }
839
+ },
840
+ {
841
+ "type": "DatasetTool",
842
+ "name": "dili_search",
843
+ "description": "Search the DILIrank dataset for drug-induced liver-injury (DILI) risk information by compound name. Searching with exact match is not recommeded.",
844
+ "hf_dataset_path": {
845
+ "repo_id": "agenticx/DILIrank",
846
+ "path_in_repo": "DILIrank.csv",
847
+ "token": null,
848
+ "save_to_local_dir": "src/tooluniverse/test"
849
+ },
850
+ "parameter": {
851
+ "type": "object",
852
+ "properties": {
853
+ "query": {
854
+ "type": "string",
855
+ "description": "Free-text query (e.g. 'acetaminophen')."
856
+ },
857
+ "search_fields": {
858
+ "type": "array",
859
+ "items": {
860
+ "type": "string"
861
+ },
862
+ "description": "Columns to search. Choose from: 'Compound Name'."
863
+ },
864
+ "case_sensitive": {
865
+ "type": "boolean",
866
+ "description": "Match text with exact case if true."
867
+ },
868
+ "exact_match": {
869
+ "type": "boolean",
870
+ "description": "Field value must equal query exactly if true; otherwise substring match."
871
+ },
872
+ "limit": {
873
+ "type": "integer",
874
+ "description": "Maximum number of rows to return.",
875
+ "minimum": 1,
876
+ "maximum": 1000
559
877
  }
878
+ },
879
+ "required": [
880
+ "query",
881
+ "search_fields",
882
+ "case_sensitive",
883
+ "exact_match",
884
+ "limit"
885
+ ]
886
+ },
887
+ "query_schema": {
888
+ "search_fields": [
889
+ "Compound Name"
890
+ ],
891
+ "case_sensitive": false,
892
+ "exact_match": false,
893
+ "limit": 10
560
894
  },
561
- {
562
- "type": "DatasetTool",
563
- "name": "diqt_search",
564
- "description": "Search the DIQTA dataset for drug-induced QT-interval prolongation risk information by generic name or DrugBank ID. Searching with exact match is not recommeded for generic name.",
565
- "hf_dataset_path": {
566
- "repo_id": "agenticx/DIQTA",
567
- "path_in_repo": "DIQTA.csv",
568
- "token": null,
569
- "save_to_local_dir": "src/tooluniverse/test"
570
- },
571
- "parameter": {
895
+ "return_schema": {
896
+ "type": "object",
897
+ "description": "Search results plus metadata.",
898
+ "properties": {
899
+ "query": {
900
+ "type": "string"
901
+ },
902
+ "total_results": {
903
+ "type": "integer"
904
+ },
905
+ "results": {
906
+ "type": "array",
907
+ "items": {
572
908
  "type": "object",
573
909
  "properties": {
574
- "query": {
575
- "type": "string",
576
- "description": "Free-text query (e.g. 'Astemizole', 'DB00637').",
577
- "required": true
578
- },
579
- "search_fields": {
580
- "type": "array",
581
- "items": { "type": "string" },
582
- "description": "Columns to search. Choose from: 'Generic/Proper Name(s)', 'DrugBank ID'."
583
- },
584
- "case_sensitive": {
585
- "type": "boolean",
586
- "description": "Match text with exact case if true."
587
- },
588
- "exact_match": {
589
- "type": "boolean",
590
- "description": "Field value must equal query exactly if true; otherwise substring match."
591
- },
592
- "limit": {
593
- "type": "integer",
594
- "description": "Maximum number of rows to return.",
595
- "minimum": 1,
596
- "maximum": 1000
910
+ "Compound Name": {
911
+ "type": "string"
912
+ },
913
+ "Severity Class": {
914
+ "type": [
915
+ "integer",
916
+ "null"
917
+ ]
918
+ },
919
+ "DILI Concern": {
920
+ "type": [
921
+ "string",
922
+ "null"
923
+ ]
924
+ },
925
+ "matched_fields": {
926
+ "type": "array",
927
+ "description": "Subset of search_fields that contained the match.",
928
+ "items": {
929
+ "type": "string"
597
930
  }
931
+ }
598
932
  }
933
+ }
934
+ },
935
+ "search_parameters": {
936
+ "type": "object",
937
+ "properties": {
938
+ "search_fields": {
939
+ "type": "array",
940
+ "items": {
941
+ "type": "string"
942
+ }
943
+ },
944
+ "case_sensitive": {
945
+ "type": "boolean"
946
+ },
947
+ "exact_match": {
948
+ "type": "boolean"
949
+ },
950
+ "limit": {
951
+ "type": "integer"
952
+ }
953
+ }
954
+ }
955
+ }
956
+ }
957
+ },
958
+ {
959
+ "type": "DatasetTool",
960
+ "name": "diqt_search",
961
+ "description": "Search the DIQTA dataset for drug-induced QT-interval prolongation risk information by generic name or DrugBank ID. Searching with exact match is not recommeded for generic name.",
962
+ "hf_dataset_path": {
963
+ "repo_id": "agenticx/DIQTA",
964
+ "path_in_repo": "DIQTA.csv",
965
+ "token": null,
966
+ "save_to_local_dir": "src/tooluniverse/test"
967
+ },
968
+ "parameter": {
969
+ "type": "object",
970
+ "properties": {
971
+ "query": {
972
+ "type": "string",
973
+ "description": "Free-text query (e.g. 'Astemizole', 'DB00637')."
974
+ },
975
+ "search_fields": {
976
+ "type": "array",
977
+ "items": {
978
+ "type": "string"
979
+ },
980
+ "description": "Columns to search. Choose from: 'Generic/Proper Name(s)', 'DrugBank ID'."
981
+ },
982
+ "case_sensitive": {
983
+ "type": "boolean",
984
+ "description": "Match text with exact case if true."
599
985
  },
600
- "query_schema": {
601
- "search_fields": ["Generic/Proper Name(s)", "DrugBank ID"],
602
- "case_sensitive": false,
603
- "exact_match": false,
604
- "limit": 100
986
+ "exact_match": {
987
+ "type": "boolean",
988
+ "description": "Field value must equal query exactly if true; otherwise substring match."
605
989
  },
606
- "return_schema": {
990
+ "limit": {
991
+ "type": "integer",
992
+ "description": "Maximum number of rows to return.",
993
+ "minimum": 1,
994
+ "maximum": 1000
995
+ }
996
+ },
997
+ "required": [
998
+ "query",
999
+ "search_fields",
1000
+ "case_sensitive",
1001
+ "exact_match",
1002
+ "limit"
1003
+ ]
1004
+ },
1005
+ "query_schema": {
1006
+ "search_fields": [
1007
+ "Generic/Proper Name(s)",
1008
+ "DrugBank ID"
1009
+ ],
1010
+ "case_sensitive": false,
1011
+ "exact_match": false,
1012
+ "limit": 100
1013
+ },
1014
+ "return_schema": {
1015
+ "type": "object",
1016
+ "description": "Search results plus metadata.",
1017
+ "properties": {
1018
+ "query": {
1019
+ "type": "string"
1020
+ },
1021
+ "total_results": {
1022
+ "type": "integer"
1023
+ },
1024
+ "results": {
1025
+ "type": "array",
1026
+ "items": {
607
1027
  "type": "object",
608
- "description": "Search results plus metadata.",
609
1028
  "properties": {
610
- "query": { "type": "string" },
611
- "total_results": { "type": "integer" },
612
-
613
- "results": {
614
- "type": "array",
615
- "items": {
616
- "type": "object",
617
- "properties": {
618
- "Generic/Proper Name(s)": { "type": "string" },
619
- "Type": { "type": ["string","null"] },
620
- "DrugBank ID": { "type": ["string","null"] },
621
- "DIQT Concern": { "type": ["string","null"] },
622
- "Severity Score": { "type": ["number","null"] },
623
-
624
- "matched_fields": {
625
- "type": "array",
626
- "description": "Subset of search_fields that contained the match.",
627
- "items": { "type": "string" }
628
- }
629
- }
630
- }
631
- },
632
-
633
- "search_parameters": {
634
- "type": "object",
635
- "properties": {
636
- "search_fields": { "type": "array", "items": { "type": "string" } },
637
- "case_sensitive": { "type": "boolean" },
638
- "exact_match": { "type": "boolean" },
639
- "limit": { "type": "integer" }
640
- }
1029
+ "Generic/Proper Name(s)": {
1030
+ "type": "string"
1031
+ },
1032
+ "Type": {
1033
+ "type": [
1034
+ "string",
1035
+ "null"
1036
+ ]
1037
+ },
1038
+ "DrugBank ID": {
1039
+ "type": [
1040
+ "string",
1041
+ "null"
1042
+ ]
1043
+ },
1044
+ "DIQT Concern": {
1045
+ "type": [
1046
+ "string",
1047
+ "null"
1048
+ ]
1049
+ },
1050
+ "Severity Score": {
1051
+ "type": [
1052
+ "number",
1053
+ "null"
1054
+ ]
1055
+ },
1056
+ "matched_fields": {
1057
+ "type": "array",
1058
+ "description": "Subset of search_fields that contained the match.",
1059
+ "items": {
1060
+ "type": "string"
641
1061
  }
1062
+ }
1063
+ }
1064
+ }
1065
+ },
1066
+ "search_parameters": {
1067
+ "type": "object",
1068
+ "properties": {
1069
+ "search_fields": {
1070
+ "type": "array",
1071
+ "items": {
1072
+ "type": "string"
1073
+ }
1074
+ },
1075
+ "case_sensitive": {
1076
+ "type": "boolean"
1077
+ },
1078
+ "exact_match": {
1079
+ "type": "boolean"
1080
+ },
1081
+ "limit": {
1082
+ "type": "integer"
642
1083
  }
1084
+ }
643
1085
  }
1086
+ }
644
1087
  }
645
-
1088
+ }
646
1089
  ]