tooluniverse 1.0.6__py3-none-any.whl → 1.0.8__py3-none-any.whl

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  1. tooluniverse/__init__.py +56 -10
  2. tooluniverse/admetai_tool.py +8 -4
  3. tooluniverse/agentic_tool.py +40 -4
  4. tooluniverse/arxiv_tool.py +2 -6
  5. tooluniverse/base_tool.py +210 -25
  6. tooluniverse/biogrid_tool.py +118 -0
  7. tooluniverse/biorxiv_tool.py +35 -16
  8. tooluniverse/build_optimizer.py +87 -0
  9. tooluniverse/cache/__init__.py +3 -0
  10. tooluniverse/cache/memory_cache.py +99 -0
  11. tooluniverse/cache/result_cache_manager.py +235 -0
  12. tooluniverse/cache/sqlite_backend.py +257 -0
  13. tooluniverse/cellosaurus_tool.py +1332 -0
  14. tooluniverse/clinvar_tool.py +90 -0
  15. tooluniverse/compose_scripts/enhanced_multi_agent_literature_search.py +310 -0
  16. tooluniverse/compose_scripts/multi_agent_literature_search.py +794 -0
  17. tooluniverse/compose_scripts/tool_graph_generation.py +68 -35
  18. tooluniverse/compose_scripts/tool_metadata_generator.py +205 -105
  19. tooluniverse/compose_tool.py +93 -8
  20. tooluniverse/core_tool.py +46 -44
  21. tooluniverse/crossref_tool.py +89 -4
  22. tooluniverse/custom_tool.py +28 -0
  23. tooluniverse/data/agentic_tools.json +1271 -1179
  24. tooluniverse/data/alphafold_tools.json +356 -105
  25. tooluniverse/data/arxiv_tools.json +85 -81
  26. tooluniverse/data/biorxiv_tools.json +69 -64
  27. tooluniverse/data/cellosaurus_tools.json +260 -0
  28. tooluniverse/data/chembl_tools.json +27 -12
  29. tooluniverse/data/clinicaltrials_gov_tools.json +377 -302
  30. tooluniverse/data/compose_tools.json +123 -16
  31. tooluniverse/data/core_tools.json +104 -99
  32. tooluniverse/data/crossref_tools.json +131 -63
  33. tooluniverse/data/dailymed_tools.json +17 -3
  34. tooluniverse/data/dataset_tools.json +1031 -588
  35. tooluniverse/data/dblp_tools.json +135 -64
  36. tooluniverse/data/disease_target_score_tools.json +20 -10
  37. tooluniverse/data/doaj_tools.json +131 -87
  38. tooluniverse/data/drug_discovery_agents.json +292 -0
  39. tooluniverse/data/embedding_tools.json +362 -299
  40. tooluniverse/data/enrichr_tools.json +34 -27
  41. tooluniverse/data/europe_pmc_tools.json +107 -16
  42. tooluniverse/data/fatcat_tools.json +71 -66
  43. tooluniverse/data/fda_drug_adverse_event_tools.json +1061 -445
  44. tooluniverse/data/fda_drug_labeling_tools.json +6858 -6901
  45. tooluniverse/data/finder_tools.json +32 -37
  46. tooluniverse/data/gene_ontology_tools.json +19 -7
  47. tooluniverse/data/genomics_tools.json +174 -0
  48. tooluniverse/data/geo_tools.json +86 -0
  49. tooluniverse/data/gwas_tools.json +1720 -959
  50. tooluniverse/data/hal_tools.json +69 -64
  51. tooluniverse/data/hpa_tools.json +53 -14
  52. tooluniverse/data/humanbase_tools.json +51 -43
  53. tooluniverse/data/idmap_tools.json +76 -70
  54. tooluniverse/data/literature_search_tools.json +306 -0
  55. tooluniverse/data/markitdown_tools.json +51 -0
  56. tooluniverse/data/mcp_client_tools_example.json +122 -107
  57. tooluniverse/data/medlineplus_tools.json +50 -10
  58. tooluniverse/data/medrxiv_tools.json +69 -64
  59. tooluniverse/data/molecule_2d_tools.json +134 -0
  60. tooluniverse/data/molecule_3d_tools.json +164 -0
  61. tooluniverse/data/monarch_tools.json +112 -110
  62. tooluniverse/data/odphp_tools.json +389 -119
  63. tooluniverse/data/openaire_tools.json +89 -79
  64. tooluniverse/data/openalex_tools.json +96 -31
  65. tooluniverse/data/opentarget_tools.json +1457 -1372
  66. tooluniverse/data/osf_preprints_tools.json +77 -73
  67. tooluniverse/data/packages/bioinformatics_core_tools.json +40 -10
  68. tooluniverse/data/packages/cheminformatics_tools.json +20 -5
  69. tooluniverse/data/packages/genomics_tools.json +36 -9
  70. tooluniverse/data/packages/machine_learning_tools.json +36 -9
  71. tooluniverse/data/packages/scientific_computing_tools.json +20 -5
  72. tooluniverse/data/packages/single_cell_tools.json +20 -5
  73. tooluniverse/data/packages/structural_biology_tools.json +16 -4
  74. tooluniverse/data/packages/visualization_tools.json +20 -5
  75. tooluniverse/data/pmc_tools.json +108 -103
  76. tooluniverse/data/ppi_tools.json +139 -0
  77. tooluniverse/data/protein_structure_3d_tools.json +138 -0
  78. tooluniverse/data/pubchem_tools.json +37 -12
  79. tooluniverse/data/pubmed_tools.json +124 -58
  80. tooluniverse/data/pubtator_tools.json +68 -60
  81. tooluniverse/data/rcsb_pdb_tools.json +1532 -1221
  82. tooluniverse/data/semantic_scholar_tools.json +54 -22
  83. tooluniverse/data/special_tools.json +8 -6
  84. tooluniverse/data/tool_composition_tools.json +112 -82
  85. tooluniverse/data/unified_guideline_tools.json +909 -0
  86. tooluniverse/data/url_fetch_tools.json +102 -82
  87. tooluniverse/data/uspto_tools.json +49 -30
  88. tooluniverse/data/wikidata_sparql_tools.json +42 -39
  89. tooluniverse/data/xml_tools.json +3274 -3113
  90. tooluniverse/data/zenodo_tools.json +83 -76
  91. tooluniverse/dblp_tool.py +76 -6
  92. tooluniverse/dbsnp_tool.py +71 -0
  93. tooluniverse/default_config.py +19 -0
  94. tooluniverse/doaj_tool.py +76 -17
  95. tooluniverse/doctor.py +48 -0
  96. tooluniverse/ensembl_tool.py +61 -0
  97. tooluniverse/europe_pmc_tool.py +132 -17
  98. tooluniverse/exceptions.py +170 -0
  99. tooluniverse/execute_function.py +930 -387
  100. tooluniverse/fatcat_tool.py +0 -1
  101. tooluniverse/generate_tools.py +481 -0
  102. tooluniverse/genomics_gene_search_tool.py +56 -0
  103. tooluniverse/geo_tool.py +116 -0
  104. tooluniverse/gnomad_tool.py +63 -0
  105. tooluniverse/hal_tool.py +1 -1
  106. tooluniverse/llm_clients.py +101 -124
  107. tooluniverse/markitdown_tool.py +159 -0
  108. tooluniverse/mcp_client_tool.py +10 -5
  109. tooluniverse/mcp_tool_registry.py +4 -1
  110. tooluniverse/medrxiv_tool.py +32 -13
  111. tooluniverse/memory_manager.py +166 -0
  112. tooluniverse/molecule_2d_tool.py +274 -0
  113. tooluniverse/molecule_3d_tool.py +441 -0
  114. tooluniverse/odphp_tool.py +49 -14
  115. tooluniverse/openaire_tool.py +5 -20
  116. tooluniverse/openalex_tool.py +34 -0
  117. tooluniverse/osf_preprints_tool.py +1 -1
  118. tooluniverse/pmc_tool.py +54 -56
  119. tooluniverse/protein_structure_3d_tool.py +295 -0
  120. tooluniverse/pubmed_tool.py +69 -6
  121. tooluniverse/remote/boltz/boltz_mcp_server.py +3 -1
  122. tooluniverse/remote/uspto_downloader/uspto_downloader_mcp_server.py +3 -1
  123. tooluniverse/semantic_scholar_tool.py +40 -10
  124. tooluniverse/smcp.py +149 -213
  125. tooluniverse/smcp_server.py +97 -55
  126. tooluniverse/string_tool.py +112 -0
  127. tooluniverse/tool_registry.py +35 -3
  128. tooluniverse/tools/ADMETAI_predict_BBB_penetrance.py +46 -0
  129. tooluniverse/tools/ADMETAI_predict_CYP_interactions.py +46 -0
  130. tooluniverse/tools/ADMETAI_predict_bioavailability.py +46 -0
  131. tooluniverse/tools/ADMETAI_predict_clearance_distribution.py +49 -0
  132. tooluniverse/tools/ADMETAI_predict_nuclear_receptor_activity.py +49 -0
  133. tooluniverse/tools/ADMETAI_predict_physicochemical_properties.py +49 -0
  134. tooluniverse/tools/ADMETAI_predict_solubility_lipophilicity_hydration.py +49 -0
  135. tooluniverse/tools/ADMETAI_predict_stress_response.py +46 -0
  136. tooluniverse/tools/ADMETAI_predict_toxicity.py +46 -0
  137. tooluniverse/tools/ADMETAnalyzerAgent.py +59 -0
  138. tooluniverse/tools/AdvancedCodeQualityAnalyzer.py +63 -0
  139. tooluniverse/tools/AdverseEventICDMapper.py +46 -0
  140. tooluniverse/tools/AdverseEventPredictionQuestionGenerator.py +52 -0
  141. tooluniverse/tools/AdverseEventPredictionQuestionGeneratorWithContext.py +59 -0
  142. tooluniverse/tools/ArXiv_search_papers.py +63 -0
  143. tooluniverse/tools/ArgumentDescriptionOptimizer.py +55 -0
  144. tooluniverse/tools/BioRxiv_search_preprints.py +52 -0
  145. tooluniverse/tools/BiomarkerDiscoveryWorkflow.py +55 -0
  146. tooluniverse/tools/CMA_Guidelines_Search.py +52 -0
  147. tooluniverse/tools/CORE_search_papers.py +67 -0
  148. tooluniverse/tools/CallAgent.py +46 -0
  149. tooluniverse/tools/ChEMBL_search_similar_molecules.py +59 -0
  150. tooluniverse/tools/ClinVar_search_variants.py +52 -0
  151. tooluniverse/tools/ClinicalTrialDesignAgent.py +63 -0
  152. tooluniverse/tools/CodeOptimizer.py +55 -0
  153. tooluniverse/tools/CodeQualityAnalyzer.py +71 -0
  154. tooluniverse/tools/CompoundDiscoveryAgent.py +59 -0
  155. tooluniverse/tools/ComprehensiveDrugDiscoveryPipeline.py +49 -0
  156. tooluniverse/tools/Crossref_search_works.py +55 -0
  157. tooluniverse/tools/DBLP_search_publications.py +52 -0
  158. tooluniverse/tools/DOAJ_search_articles.py +55 -0
  159. tooluniverse/tools/DailyMed_get_spl_by_setid.py +52 -0
  160. tooluniverse/tools/DailyMed_search_spls.py +79 -0
  161. tooluniverse/tools/DataAnalysisValidityReviewer.py +49 -0
  162. tooluniverse/tools/DescriptionAnalyzer.py +55 -0
  163. tooluniverse/tools/DescriptionQualityEvaluator.py +59 -0
  164. tooluniverse/tools/DiseaseAnalyzerAgent.py +52 -0
  165. tooluniverse/tools/DomainExpertValidator.py +63 -0
  166. tooluniverse/tools/DrugInteractionAnalyzerAgent.py +52 -0
  167. tooluniverse/tools/DrugOptimizationAgent.py +63 -0
  168. tooluniverse/tools/DrugSafetyAnalyzer.py +59 -0
  169. tooluniverse/tools/Ensembl_lookup_gene_by_symbol.py +52 -0
  170. tooluniverse/tools/EthicalComplianceReviewer.py +49 -0
  171. tooluniverse/tools/EuropePMC_Guidelines_Search.py +52 -0
  172. tooluniverse/tools/EuropePMC_search_articles.py +52 -0
  173. tooluniverse/tools/ExperimentalDesignScorer.py +55 -0
  174. tooluniverse/tools/FAERS_count_additive_administration_routes.py +52 -0
  175. tooluniverse/tools/FAERS_count_additive_adverse_reactions.py +71 -0
  176. tooluniverse/tools/FAERS_count_additive_event_reports_by_country.py +63 -0
  177. tooluniverse/tools/FAERS_count_additive_reaction_outcomes.py +63 -0
  178. tooluniverse/tools/FAERS_count_additive_reports_by_reporter_country.py +63 -0
  179. tooluniverse/tools/FAERS_count_additive_seriousness_classification.py +63 -0
  180. tooluniverse/tools/FAERS_count_country_by_drug_event.py +63 -0
  181. tooluniverse/tools/FAERS_count_death_related_by_drug.py +49 -0
  182. tooluniverse/tools/FAERS_count_drug_routes_by_event.py +52 -0
  183. tooluniverse/tools/FAERS_count_drugs_by_drug_event.py +63 -0
  184. tooluniverse/tools/FAERS_count_outcomes_by_drug_event.py +63 -0
  185. tooluniverse/tools/FAERS_count_patient_age_distribution.py +49 -0
  186. tooluniverse/tools/FAERS_count_reactions_by_drug_event.py +71 -0
  187. tooluniverse/tools/FAERS_count_reportercountry_by_drug_event.py +63 -0
  188. tooluniverse/tools/FAERS_count_seriousness_by_drug_event.py +63 -0
  189. tooluniverse/tools/FDA_get_abuse_dependence_info_by_drug_name.py +55 -0
  190. tooluniverse/tools/FDA_get_abuse_info_by_drug_name.py +55 -0
  191. tooluniverse/tools/FDA_get_accessories_info_by_drug_name.py +55 -0
  192. tooluniverse/tools/FDA_get_active_ingredient_info_by_drug_name.py +55 -0
  193. tooluniverse/tools/FDA_get_adverse_reactions_by_drug_name.py +55 -0
  194. tooluniverse/tools/FDA_get_alarms_by_drug_name.py +55 -0
  195. tooluniverse/tools/FDA_get_animal_pharmacology_info_by_drug_name.py +55 -0
  196. tooluniverse/tools/FDA_get_assembly_installation_info_by_drug_name.py +55 -0
  197. tooluniverse/tools/FDA_get_boxed_warning_info_by_drug_name.py +55 -0
  198. tooluniverse/tools/FDA_get_brand_name_generic_name.py +52 -0
  199. tooluniverse/tools/FDA_get_calibration_instructions_by_drug_name.py +55 -0
  200. tooluniverse/tools/FDA_get_carcinogenic_mutagenic_fertility_by_drug_name.py +55 -0
  201. tooluniverse/tools/FDA_get_child_safety_info_by_drug_name.py +55 -0
  202. tooluniverse/tools/FDA_get_clinical_pharmacology_by_drug_name.py +55 -0
  203. tooluniverse/tools/FDA_get_clinical_studies_info_by_drug_name.py +55 -0
  204. tooluniverse/tools/FDA_get_contact_for_questions_info_by_drug_name.py +55 -0
  205. tooluniverse/tools/FDA_get_contraindications_by_drug_name.py +55 -0
  206. tooluniverse/tools/FDA_get_controlled_substance_DEA_schedule_info_by_drug_name.py +55 -0
  207. tooluniverse/tools/FDA_get_dear_health_care_provider_letter_info_by_drug_name.py +55 -0
  208. tooluniverse/tools/FDA_get_dependence_info_by_drug_name.py +55 -0
  209. tooluniverse/tools/FDA_get_disposal_info_by_drug_name.py +55 -0
  210. tooluniverse/tools/FDA_get_do_not_use_info_by_drug_name.py +55 -0
  211. tooluniverse/tools/FDA_get_document_id_by_drug_name.py +55 -0
  212. tooluniverse/tools/FDA_get_dosage_and_storage_information_by_drug_name.py +55 -0
  213. tooluniverse/tools/FDA_get_dosage_forms_and_strengths_by_drug_name.py +55 -0
  214. tooluniverse/tools/FDA_get_drug_generic_name.py +46 -0
  215. tooluniverse/tools/FDA_get_drug_interactions_by_drug_name.py +55 -0
  216. tooluniverse/tools/FDA_get_drug_name_by_SPL_ID.py +55 -0
  217. tooluniverse/tools/FDA_get_drug_name_by_adverse_reaction.py +59 -0
  218. tooluniverse/tools/FDA_get_drug_name_by_calibration_instructions.py +59 -0
  219. tooluniverse/tools/FDA_get_drug_name_by_dependence_info.py +59 -0
  220. tooluniverse/tools/FDA_get_drug_name_by_document_id.py +55 -0
  221. tooluniverse/tools/FDA_get_drug_name_by_dosage_info.py +55 -0
  222. tooluniverse/tools/FDA_get_drug_name_by_environmental_warning.py +59 -0
  223. tooluniverse/tools/FDA_get_drug_name_by_inactive_ingredient.py +59 -0
  224. tooluniverse/tools/FDA_get_drug_name_by_info_on_conditions_for_doctor_consultation.py +55 -0
  225. tooluniverse/tools/FDA_get_drug_name_by_labor_and_delivery_info.py +59 -0
  226. tooluniverse/tools/FDA_get_drug_name_by_microbiology.py +59 -0
  227. tooluniverse/tools/FDA_get_drug_name_by_other_safety_info.py +55 -0
  228. tooluniverse/tools/FDA_get_drug_name_by_pharmacodynamics.py +59 -0
  229. tooluniverse/tools/FDA_get_drug_name_by_pharmacogenomics.py +59 -0
  230. tooluniverse/tools/FDA_get_drug_name_by_precautions.py +55 -0
  231. tooluniverse/tools/FDA_get_drug_name_by_pregnancy_or_breastfeeding_info.py +59 -0
  232. tooluniverse/tools/FDA_get_drug_name_by_principal_display_panel.py +59 -0
  233. tooluniverse/tools/FDA_get_drug_name_by_reference.py +55 -0
  234. tooluniverse/tools/FDA_get_drug_name_by_set_id.py +55 -0
  235. tooluniverse/tools/FDA_get_drug_name_by_stop_use_info.py +55 -0
  236. tooluniverse/tools/FDA_get_drug_name_by_storage_and_handling_info.py +55 -0
  237. tooluniverse/tools/FDA_get_drug_name_by_warnings.py +55 -0
  238. tooluniverse/tools/FDA_get_drug_name_from_patient_package_insert.py +59 -0
  239. tooluniverse/tools/FDA_get_drug_names_by_abuse_dependence_info.py +55 -0
  240. tooluniverse/tools/FDA_get_drug_names_by_abuse_info.py +63 -0
  241. tooluniverse/tools/FDA_get_drug_names_by_accessories.py +63 -0
  242. tooluniverse/tools/FDA_get_drug_names_by_active_ingredient.py +63 -0
  243. tooluniverse/tools/FDA_get_drug_names_by_alarm.py +63 -0
  244. tooluniverse/tools/FDA_get_drug_names_by_animal_pharmacology_info.py +63 -0
  245. tooluniverse/tools/FDA_get_drug_names_by_application_number_NDC_number.py +59 -0
  246. tooluniverse/tools/FDA_get_drug_names_by_assembly_installation_info.py +63 -0
  247. tooluniverse/tools/FDA_get_drug_names_by_boxed_warning.py +63 -0
  248. tooluniverse/tools/FDA_get_drug_names_by_child_safety_info.py +63 -0
  249. tooluniverse/tools/FDA_get_drug_names_by_clinical_pharmacology.py +63 -0
  250. tooluniverse/tools/FDA_get_drug_names_by_clinical_studies.py +63 -0
  251. tooluniverse/tools/FDA_get_drug_names_by_consulting_doctor_pharmacist_info.py +63 -0
  252. tooluniverse/tools/FDA_get_drug_names_by_contraindications.py +63 -0
  253. tooluniverse/tools/FDA_get_drug_names_by_controlled_substance_DEA_schedule.py +63 -0
  254. tooluniverse/tools/FDA_get_drug_names_by_dear_health_care_provider_letter_info.py +63 -0
  255. tooluniverse/tools/FDA_get_drug_names_by_disposal_info.py +63 -0
  256. tooluniverse/tools/FDA_get_drug_names_by_dosage_forms_and_strengths_info.py +63 -0
  257. tooluniverse/tools/FDA_get_drug_names_by_drug_interactions.py +63 -0
  258. tooluniverse/tools/FDA_get_drug_names_by_effective_time.py +63 -0
  259. tooluniverse/tools/FDA_get_drug_names_by_food_safety_warnings.py +63 -0
  260. tooluniverse/tools/FDA_get_drug_names_by_general_precautions.py +63 -0
  261. tooluniverse/tools/FDA_get_drug_names_by_geriatric_use.py +63 -0
  262. tooluniverse/tools/FDA_get_drug_names_by_health_claim.py +63 -0
  263. tooluniverse/tools/FDA_get_drug_names_by_indication.py +55 -0
  264. tooluniverse/tools/FDA_get_drug_names_by_info_for_nursing_mothers.py +63 -0
  265. tooluniverse/tools/FDA_get_drug_names_by_information_for_owners_or_caregivers.py +63 -0
  266. tooluniverse/tools/FDA_get_drug_names_by_ingredient.py +63 -0
  267. tooluniverse/tools/FDA_get_drug_names_by_instructions_for_use.py +63 -0
  268. tooluniverse/tools/FDA_get_drug_names_by_lab_test_interference.py +63 -0
  269. tooluniverse/tools/FDA_get_drug_names_by_lab_tests.py +63 -0
  270. tooluniverse/tools/FDA_get_drug_names_by_mechanism_of_action.py +63 -0
  271. tooluniverse/tools/FDA_get_drug_names_by_medication_guide.py +63 -0
  272. tooluniverse/tools/FDA_get_drug_names_by_nonclinical_toxicology_info.py +63 -0
  273. tooluniverse/tools/FDA_get_drug_names_by_nonteratogenic_effects.py +63 -0
  274. tooluniverse/tools/FDA_get_drug_names_by_overdosage_info.py +63 -0
  275. tooluniverse/tools/FDA_get_drug_names_by_pediatric_use.py +63 -0
  276. tooluniverse/tools/FDA_get_drug_names_by_pharmacokinetics.py +63 -0
  277. tooluniverse/tools/FDA_get_drug_names_by_population_use.py +63 -0
  278. tooluniverse/tools/FDA_get_drug_names_by_pregnancy_effects_info.py +63 -0
  279. tooluniverse/tools/FDA_get_drug_names_by_residue_warning.py +63 -0
  280. tooluniverse/tools/FDA_get_drug_names_by_risk.py +63 -0
  281. tooluniverse/tools/FDA_get_drug_names_by_route.py +63 -0
  282. tooluniverse/tools/FDA_get_drug_names_by_safe_handling_warning.py +63 -0
  283. tooluniverse/tools/FDA_get_drug_names_by_safety_summary.py +63 -0
  284. tooluniverse/tools/FDA_get_drug_names_by_spl_indexing_data_elements.py +63 -0
  285. tooluniverse/tools/FDA_get_drug_names_by_teratogenic_effects.py +63 -0
  286. tooluniverse/tools/FDA_get_drug_names_by_user_safety_warning.py +63 -0
  287. tooluniverse/tools/FDA_get_drug_names_by_warnings_and_cautions.py +63 -0
  288. tooluniverse/tools/FDA_get_drugs_by_carcinogenic_mutagenic_fertility.py +63 -0
  289. tooluniverse/tools/FDA_get_effective_time_by_drug_name.py +55 -0
  290. tooluniverse/tools/FDA_get_environmental_warning_by_drug_name.py +55 -0
  291. tooluniverse/tools/FDA_get_general_precautions_by_drug_name.py +55 -0
  292. tooluniverse/tools/FDA_get_geriatric_use_info_by_drug_name.py +55 -0
  293. tooluniverse/tools/FDA_get_health_claims_by_drug_name.py +55 -0
  294. tooluniverse/tools/FDA_get_inactive_ingredient_info_by_drug_name.py +55 -0
  295. tooluniverse/tools/FDA_get_indications_by_drug_name.py +55 -0
  296. tooluniverse/tools/FDA_get_info_for_nursing_mothers_by_drug_name.py +55 -0
  297. tooluniverse/tools/FDA_get_info_for_patients_by_drug_name.py +55 -0
  298. tooluniverse/tools/FDA_get_info_on_conditions_for_doctor_consultation_by_drug_name.py +55 -0
  299. tooluniverse/tools/FDA_get_info_on_consulting_doctor_pharmacist_by_drug_name.py +55 -0
  300. tooluniverse/tools/FDA_get_information_for_owners_or_caregivers_by_drug_name.py +55 -0
  301. tooluniverse/tools/FDA_get_ingredients_by_drug_name.py +55 -0
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  776. tooluniverse/tools/gwas_get_associations_for_trait.py +55 -0
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  781. tooluniverse/tools/gwas_get_variants_for_trait.py +55 -0
  782. tooluniverse/tools/gwas_search_associations.py +75 -0
  783. tooluniverse/tools/gwas_search_snps.py +63 -0
  784. tooluniverse/tools/gwas_search_studies.py +75 -0
  785. tooluniverse/tools/humanbase_ppi_analysis.py +67 -0
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  789. tooluniverse/tools/mesh_get_subjects_by_subject_scope_or_definition.py +63 -0
  790. tooluniverse/tools/odphp_itemlist.py +49 -0
  791. tooluniverse/tools/odphp_myhealthfinder.py +67 -0
  792. tooluniverse/tools/odphp_outlink_fetch.py +59 -0
  793. tooluniverse/tools/odphp_topicsearch.py +67 -0
  794. tooluniverse/tools/openalex_literature_search.py +67 -0
  795. tooluniverse/tools/reactome_disease_target_score.py +52 -0
  796. tooluniverse/tools/search_clinical_trials.py +67 -0
  797. tooluniverse/tools/visualize_molecule_2d.py +83 -0
  798. tooluniverse/tools/visualize_molecule_3d.py +91 -0
  799. tooluniverse/tools/visualize_protein_structure_3d.py +79 -0
  800. tooluniverse/ucsc_tool.py +60 -0
  801. tooluniverse/unified_guideline_tools.py +2328 -0
  802. tooluniverse/unpaywall_tool.py +0 -1
  803. tooluniverse/utils.py +122 -6
  804. tooluniverse/visualization_tool.py +897 -0
  805. tooluniverse/wikidata_sparql_tool.py +1 -2
  806. tooluniverse/zenodo_tool.py +3 -4
  807. {tooluniverse-1.0.6.dist-info → tooluniverse-1.0.8.dist-info}/METADATA +19 -4
  808. tooluniverse-1.0.8.dist-info/RECORD +891 -0
  809. {tooluniverse-1.0.6.dist-info → tooluniverse-1.0.8.dist-info}/entry_points.txt +3 -0
  810. tooluniverse/test/list_azure_openai_models.py +0 -210
  811. tooluniverse/test/mcp_server_test.py +0 -0
  812. tooluniverse/test/test_admetai_tool.py +0 -370
  813. tooluniverse/test/test_agentic_tool.py +0 -129
  814. tooluniverse/test/test_agentic_tool_azure_models.py +0 -91
  815. tooluniverse/test/test_alphafold_tool.py +0 -108
  816. tooluniverse/test/test_api_key_validation_min.py +0 -64
  817. tooluniverse/test/test_chem_tool.py +0 -37
  818. tooluniverse/test/test_claude_sdk.py +0 -93
  819. tooluniverse/test/test_compose_lieraturereview.py +0 -63
  820. tooluniverse/test/test_compose_tool.py +0 -448
  821. tooluniverse/test/test_dailymed.py +0 -69
  822. tooluniverse/test/test_dataset_tool.py +0 -200
  823. tooluniverse/test/test_disease_target_score.py +0 -56
  824. tooluniverse/test/test_drugbank_filter_examples.py +0 -179
  825. tooluniverse/test/test_efo.py +0 -31
  826. tooluniverse/test/test_enrichr_tool.py +0 -21
  827. tooluniverse/test/test_europe_pmc_tool.py +0 -20
  828. tooluniverse/test/test_fda_adv.py +0 -95
  829. tooluniverse/test/test_fda_drug_labeling.py +0 -91
  830. tooluniverse/test/test_gene_ontology_tools.py +0 -66
  831. tooluniverse/test/test_global_fallback.py +0 -288
  832. tooluniverse/test/test_gwas_tool.py +0 -139
  833. tooluniverse/test/test_hooks_direct.py +0 -219
  834. tooluniverse/test/test_hpa.py +0 -625
  835. tooluniverse/test/test_humanbase_tool.py +0 -20
  836. tooluniverse/test/test_idmap_tools.py +0 -61
  837. tooluniverse/test/test_list_built_in_tools.py +0 -33
  838. tooluniverse/test/test_mcp_server.py +0 -211
  839. tooluniverse/test/test_mcp_tool.py +0 -247
  840. tooluniverse/test/test_medlineplus.py +0 -220
  841. tooluniverse/test/test_odphp_tool.py +0 -166
  842. tooluniverse/test/test_openalex_tool.py +0 -32
  843. tooluniverse/test/test_openrouter_client.py +0 -288
  844. tooluniverse/test/test_opentargets.py +0 -28
  845. tooluniverse/test/test_pubchem_tool.py +0 -116
  846. tooluniverse/test/test_pubtator_tool.py +0 -37
  847. tooluniverse/test/test_rcsb_pdb_tool.py +0 -86
  848. tooluniverse/test/test_reactome.py +0 -54
  849. tooluniverse/test/test_semantic_scholar_tool.py +0 -24
  850. tooluniverse/test/test_software_tools.py +0 -147
  851. tooluniverse/test/test_stdio_hooks.py +0 -285
  852. tooluniverse/test/test_tool_description_optimizer.py +0 -49
  853. tooluniverse/test/test_tool_finder.py +0 -26
  854. tooluniverse/test/test_tool_finder_llm.py +0 -252
  855. tooluniverse/test/test_tools_find.py +0 -195
  856. tooluniverse/test/test_uniprot_tools.py +0 -74
  857. tooluniverse/test/test_uspto_tool.py +0 -72
  858. tooluniverse/test/test_xml_tool.py +0 -113
  859. tooluniverse-1.0.6.dist-info/RECORD +0 -230
  860. {tooluniverse-1.0.6.dist-info → tooluniverse-1.0.8.dist-info}/WHEEL +0 -0
  861. {tooluniverse-1.0.6.dist-info → tooluniverse-1.0.8.dist-info}/licenses/LICENSE +0 -0
  862. {tooluniverse-1.0.6.dist-info → tooluniverse-1.0.8.dist-info}/top_level.txt +0 -0
@@ -1,326 +1,401 @@
1
1
  [
2
- {
3
- "name": "search_clinical_trials",
4
- "description": "Search for clinical trials registered on clinicaltrials.gov based on title, conditions, interventions, outcome measures, and status. Returns a paginated list of studies, containing the NCT ID and description of each trial. You can then take the NCT IDs and use 'get_clinical_trials_*' tools to get detailed information about specific protocol fields for specific studies, or 'extract_clinical_trials_efficacy/safety' tools to get efficacy or adverse events results from specific studies. If you wish to see the next page of results, you can use the 'nextPageToken' value from the previous output of this tool and input it as the 'pageToken' parameter in the next query. Note that currently the search is limited to trials beyond phase 1.",
5
- "parameter": {
6
- "type": "object",
7
- "properties": {
8
- "condition": {
9
- "type": "string",
10
- "description": "Query for condition or disease using Essie expression syntax (e.g., 'lung cancer', '(head OR neck) AND pain AND NOT \"back pain\"'). ",
11
- "required": false
12
- },
13
- "intervention": {
14
- "type": "string",
15
- "description": "Query for intervention/treatment using Essie expression syntax (e.g., 'chemotherapy', 'immunotherapy', 'olaparib', 'combination therapy').",
16
- "required": false
17
- },
18
- "query_term": {
19
- "type": "string",
20
- "description": "Query for 'other terms' with Essie expression syntax (e.g., 'combination', 'AREA[LastUpdatePostDate]RANGE[2023-01-15,MAX]', 'Phase II'). Can be used to search for all other protocol fields, including but not limited to title, outcome measures, status, phase, location, etc."
21
- },
22
- "pageSize": {
23
- "type": "integer",
24
- "description": "Maximum number of studies to return per page (default 10, max 1000).",
25
- "required": false
26
- },
27
- "pageToken": {
28
- "type": "string",
29
- "description": "Token to retrieve the next page of results, obtained from the 'nextPageToken' field of the previous response. Do not specify it for first page. When you make an initial request to the API which supports pagination, the response will include a nextPageToken. This token can then be used as a parameter in the subsequent API request to retrieve the next set of data.",
30
- "required": false
31
- }
32
- }
2
+ {
3
+ "name": "search_clinical_trials",
4
+ "description": "Search for clinical trials registered on clinicaltrials.gov based on title, conditions, interventions, outcome measures, and status. Returns a paginated list of studies, containing the NCT ID and description of each trial. You can then take the NCT IDs and use 'get_clinical_trials_*' tools to get detailed information about specific protocol fields for specific studies, or 'extract_clinical_trials_efficacy/safety' tools to get efficacy or adverse events results from specific studies. If you wish to see the next page of results, you can use the 'nextPageToken' value from the previous output of this tool and input it as the 'pageToken' parameter in the next query. Note that currently the search is limited to trials beyond phase 1.",
5
+ "parameter": {
6
+ "type": "object",
7
+ "properties": {
8
+ "condition": {
9
+ "type": "string",
10
+ "description": "Query for condition or disease using Essie expression syntax (e.g., 'lung cancer', '(head OR neck) AND pain AND NOT \"back pain\"'). "
33
11
  },
34
- "query_schema": {
35
- "pageSize": 10
12
+ "intervention": {
13
+ "type": "string",
14
+ "description": "Query for intervention/treatment using Essie expression syntax (e.g., 'chemotherapy', 'immunotherapy', 'olaparib', 'combination therapy')."
36
15
  },
37
- "label": ["ClinicalTrials.gov", "Clinical Trial", "Intervention", "Adverse Effect", "Efficacy", "Search"],
38
- "type": "ClinicalTrialsSearchTool",
39
- "tool_url": "/studies"
40
- },
41
-
42
- {
43
- "name": "get_clinical_trial_descriptions",
44
- "description": "Retrieves detailed identification information for trials, including titles, phases, and descriptions, using their NCT IDs.",
45
- "parameter": {
46
- "type": "object",
47
- "properties": {
48
- "nct_ids": {
49
- "type": "array",
50
- "description": "List of NCT IDs of the clinical trials (e.g., ['NCT04852770', 'NCT01728545']).",
51
- "items": {
52
- "type": "string"
53
- },
54
- "required": true
55
- },
56
- "description_type": {
57
- "type": "string",
58
- "description": "Type of information to retrieve. Options are 'brief' for brief descriptions or 'full' for full descriptions.",
59
- "enum": ["brief", "full"]
60
- }
61
- }
16
+ "query_term": {
17
+ "type": "string",
18
+ "description": "Query for 'other terms' with Essie expression syntax (e.g., 'combination', 'AREA[LastUpdatePostDate]RANGE[2023-01-15,MAX]', 'Phase II'). Can be used to search for all other protocol fields, including but not limited to title, outcome measures, status, phase, location, etc."
62
19
  },
63
- "query_schema": {
64
- "description_type": "brief"
20
+ "pageSize": {
21
+ "type": "integer",
22
+ "description": "Maximum number of studies to return per page (default 10, max 1000)."
65
23
  },
66
- "label": ["ClinicalTrials.gov", "Clinical Trial", "Study", "Description"],
67
- "type": "ClinicalTrialsDetailsTool",
68
- "tool_url": "/studies/{nctId}"
24
+ "pageToken": {
25
+ "type": "string",
26
+ "description": "Token to retrieve the next page of results, obtained from the 'nextPageToken' field of the previous response. Do not specify it for first page. When you make an initial request to the API which supports pagination, the response will include a nextPageToken. This token can then be used as a parameter in the subsequent API request to retrieve the next set of data."
27
+ }
28
+ },
29
+ "required": [
30
+ "query_term"
31
+ ]
69
32
  },
70
-
71
- {
72
- "name": "get_clinical_trial_status_and_dates",
73
- "description": "Retrieves trial status and start and completion dates, using their NCT IDs.",
74
- "parameter": {
75
- "type": "object",
76
- "properties": {
77
- "nct_ids": {
78
- "type": "array",
79
- "description": "List of NCT IDs of the clinical trials (e.g., ['NCT04852770', 'NCT01728545']).",
80
- "items": {
81
- "type": "string"
82
- },
83
- "required": true
84
- },
85
- "status_and_date": {
86
- "type": "string",
87
- "description": "Placeholder."
88
- }
89
- }
90
- },
91
- "query_schema": {},
92
- "label": ["ClinicalTrials.gov", "Clinical Trial", "Study", "Status", "Dates"],
93
- "type": "ClinicalTrialsDetailsTool",
94
- "tool_url": "/studies/{nctId}"
33
+ "query_schema": {
34
+ "pageSize": 10
95
35
  },
96
-
97
- {
98
- "name": "get_clinical_trial_conditions_and_interventions",
99
- "description": "Retrieves the list of conditions or diseases and the interventions and arm groups that the clinical trials are focused on, using their NCT IDs.",
100
- "parameter": {
101
- "type": "object",
102
- "properties": {
103
- "nct_ids": {
104
- "type": "array",
105
- "description": "List of NCT IDs of the clinical trials (e.g., ['NCT04852770', 'NCT01728545']).",
106
- "items": {
107
- "type": "string"
108
- },
109
- "required": true
110
- },
111
- "condition_and_intervention": {
112
- "type": "string",
113
- "description": "Placeholder."
114
- }
115
- }
36
+ "label": [
37
+ "ClinicalTrials.gov",
38
+ "Clinical Trial",
39
+ "Intervention",
40
+ "Adverse Effect",
41
+ "Efficacy",
42
+ "Search"
43
+ ],
44
+ "type": "ClinicalTrialsSearchTool",
45
+ "tool_url": "/studies"
46
+ },
47
+ {
48
+ "name": "get_clinical_trial_descriptions",
49
+ "description": "Retrieves detailed identification information for trials, including titles, phases, and descriptions, using their NCT IDs.",
50
+ "parameter": {
51
+ "type": "object",
52
+ "properties": {
53
+ "nct_ids": {
54
+ "type": "array",
55
+ "description": "List of NCT IDs of the clinical trials (e.g., ['NCT04852770', 'NCT01728545']).",
56
+ "items": {
57
+ "type": "string"
58
+ }
116
59
  },
117
- "query_schema": {},
118
- "label": ["ClinicalTrials.gov", "Clinical Trial", "Study", "Condition", "Intervention", "Arm Group"],
119
- "type": "ClinicalTrialsDetailsTool",
120
- "tool_url": "/studies/{nctId}"
60
+ "description_type": {
61
+ "type": "string",
62
+ "description": "Type of information to retrieve. Options are 'brief' for brief descriptions or 'full' for full descriptions.",
63
+ "enum": [
64
+ "brief",
65
+ "full"
66
+ ]
67
+ }
68
+ },
69
+ "required": [
70
+ "nct_ids",
71
+ "description_type"
72
+ ]
73
+ },
74
+ "query_schema": {
75
+ "description_type": "brief"
121
76
  },
122
-
123
- {
124
- "name": "get_clinical_trial_eligibility_criteria",
125
- "description": "Retrieves the eligibility criteria for the clinical trials, using their NCT IDs.",
126
- "parameter": {
127
- "type": "object",
128
- "properties": {
129
- "nct_ids": {
130
- "type": "array",
131
- "description": "List of NCT IDs of the clinical trials (e.g., ['NCT04852770', 'NCT01728545']).",
132
- "items": {
133
- "type": "string"
134
- },
135
- "required": true
136
- },
137
- "eligibility_criteria": {
138
- "type": "string",
139
- "description": "Placeholder."
140
- }
141
- }
77
+ "label": [
78
+ "ClinicalTrials.gov",
79
+ "Clinical Trial",
80
+ "Study",
81
+ "Description"
82
+ ],
83
+ "type": "ClinicalTrialsDetailsTool",
84
+ "tool_url": "/studies/{nctId}"
85
+ },
86
+ {
87
+ "name": "get_clinical_trial_status_and_dates",
88
+ "description": "Retrieves trial status and start and completion dates, using their NCT IDs.",
89
+ "parameter": {
90
+ "type": "object",
91
+ "properties": {
92
+ "nct_ids": {
93
+ "type": "array",
94
+ "description": "List of NCT IDs of the clinical trials (e.g., ['NCT04852770', 'NCT01728545']).",
95
+ "items": {
96
+ "type": "string"
97
+ }
142
98
  },
143
- "query_schema": {},
144
- "label": ["ClinicalTrials.gov", "Clinical Trial", "Study", "Eligibility Criteria"],
145
- "type": "ClinicalTrialsDetailsTool",
146
- "tool_url": "/studies/{nctId}"
99
+ "status_and_date": {
100
+ "type": "string",
101
+ "description": "Placeholder."
102
+ }
103
+ },
104
+ "required": [
105
+ "nct_ids",
106
+ "status_and_date"
107
+ ]
147
108
  },
148
-
149
- {
150
- "name": "get_clinical_trial_locations",
151
- "description": "Retrieves the locations where the clinical trials are being conducted, using their NCT IDs.",
152
- "parameter": {
153
- "type": "object",
154
- "properties": {
155
- "nct_ids": {
156
- "type": "array",
157
- "description": "List of NCT IDs of the clinical trials (e.g., ['NCT04852770', 'NCT01728545']).",
158
- "items": {
159
- "type": "string"
160
- },
161
- "required": true
162
- },
163
- "location": {
164
- "type": "string",
165
- "description": "Placeholder."
166
- }
167
- }
109
+ "query_schema": {},
110
+ "label": [
111
+ "ClinicalTrials.gov",
112
+ "Clinical Trial",
113
+ "Study",
114
+ "Status",
115
+ "Dates"
116
+ ],
117
+ "type": "ClinicalTrialsDetailsTool",
118
+ "tool_url": "/studies/{nctId}"
119
+ },
120
+ {
121
+ "name": "get_clinical_trial_conditions_and_interventions",
122
+ "description": "Retrieves the list of conditions or diseases and the interventions and arm groups that the clinical trials are focused on, using their NCT IDs.",
123
+ "parameter": {
124
+ "type": "object",
125
+ "properties": {
126
+ "nct_ids": {
127
+ "type": "array",
128
+ "description": "List of NCT IDs of the clinical trials (e.g., ['NCT04852770', 'NCT01728545']).",
129
+ "items": {
130
+ "type": "string"
131
+ }
168
132
  },
169
- "query_schema": {},
170
- "label": ["ClinicalTrials.gov", "Clinical Trial", "Study", "Location"],
171
- "type": "ClinicalTrialsDetailsTool",
172
- "tool_url": "/studies/{nctId}"
133
+ "condition_and_intervention": {
134
+ "type": "string",
135
+ "description": "Placeholder."
136
+ }
137
+ },
138
+ "required": [
139
+ "nct_ids",
140
+ "condition_and_intervention"
141
+ ]
173
142
  },
174
-
175
- {
176
- "name": "get_clinical_trial_outcome_measures",
177
- "description": "Retrieves the outcome measures for the clinical trials, using their NCT IDs.",
178
- "parameter": {
179
- "type": "object",
180
- "properties": {
181
- "nct_ids": {
182
- "type": "array",
183
- "description": "List of NCT IDs of the clinical trials (e.g., ['NCT04852770', 'NCT01728545']).",
184
- "items": {
185
- "type": "string"
186
- },
187
- "required": true
188
- },
189
- "outcome_measures": {
190
- "type": "string",
191
- "description": "Decides whether to retrieve primary, secondary, or all outcome measures. Options are 'primary', 'secondary', or 'all'. Default is 'primary'.",
192
- "enum": ["primary", "secondary", "all"],
193
- "required": false
194
- }
195
- }
143
+ "query_schema": {},
144
+ "label": [
145
+ "ClinicalTrials.gov",
146
+ "Clinical Trial",
147
+ "Study",
148
+ "Condition",
149
+ "Intervention",
150
+ "Arm Group"
151
+ ],
152
+ "type": "ClinicalTrialsDetailsTool",
153
+ "tool_url": "/studies/{nctId}"
154
+ },
155
+ {
156
+ "name": "get_clinical_trial_eligibility_criteria",
157
+ "description": "Retrieves the eligibility criteria for the clinical trials, using their NCT IDs.",
158
+ "parameter": {
159
+ "type": "object",
160
+ "properties": {
161
+ "nct_ids": {
162
+ "type": "array",
163
+ "description": "List of NCT IDs of the clinical trials (e.g., ['NCT04852770', 'NCT01728545']).",
164
+ "items": {
165
+ "type": "string"
166
+ }
196
167
  },
197
- "query_schema": {
198
- "outcome_measures": "primary"
168
+ "eligibility_criteria": {
169
+ "type": "string",
170
+ "description": "Placeholder."
171
+ }
172
+ },
173
+ "required": [
174
+ "nct_ids",
175
+ "eligibility_criteria"
176
+ ]
177
+ },
178
+ "query_schema": {},
179
+ "label": [
180
+ "ClinicalTrials.gov",
181
+ "Clinical Trial",
182
+ "Study",
183
+ "Eligibility Criteria"
184
+ ],
185
+ "type": "ClinicalTrialsDetailsTool",
186
+ "tool_url": "/studies/{nctId}"
187
+ },
188
+ {
189
+ "name": "get_clinical_trial_locations",
190
+ "description": "Retrieves the locations where the clinical trials are being conducted, using their NCT IDs.",
191
+ "parameter": {
192
+ "type": "object",
193
+ "properties": {
194
+ "nct_ids": {
195
+ "type": "array",
196
+ "description": "List of NCT IDs of the clinical trials (e.g., ['NCT04852770', 'NCT01728545']).",
197
+ "items": {
198
+ "type": "string"
199
+ }
199
200
  },
200
- "label": ["ClinicalTrials.gov", "Clinical Trial", "Study", "Outcome Measures"],
201
- "type": "ClinicalTrialsDetailsTool",
202
- "tool_url": "/studies/{nctId}"
201
+ "location": {
202
+ "type": "string",
203
+ "description": "Placeholder."
204
+ }
205
+ },
206
+ "required": [
207
+ "nct_ids",
208
+ "location"
209
+ ]
203
210
  },
204
-
205
- {
206
- "name": "get_clinical_trial_references",
207
- "description": "Retrieves the references (if any) for the clinical trials, using their NCT IDs.",
208
- "parameter": {
209
- "type": "object",
210
- "properties": {
211
- "nct_ids": {
212
- "type": "array",
213
- "description": "List of NCT IDs of the clinical trials (e.g., ['NCT04852770', 'NCT01728545']).",
214
- "items": {
215
- "type": "string"
216
- },
217
- "required": true
218
- },
219
- "references": {
220
- "type": "string",
221
- "description": "Placeholder."
222
- }
223
- }
211
+ "query_schema": {},
212
+ "label": [
213
+ "ClinicalTrials.gov",
214
+ "Clinical Trial",
215
+ "Study",
216
+ "Location"
217
+ ],
218
+ "type": "ClinicalTrialsDetailsTool",
219
+ "tool_url": "/studies/{nctId}"
220
+ },
221
+ {
222
+ "name": "get_clinical_trial_outcome_measures",
223
+ "description": "Retrieves the outcome measures for the clinical trials, using their NCT IDs.",
224
+ "parameter": {
225
+ "type": "object",
226
+ "properties": {
227
+ "nct_ids": {
228
+ "type": "array",
229
+ "description": "List of NCT IDs of the clinical trials (e.g., ['NCT04852770', 'NCT01728545']).",
230
+ "items": {
231
+ "type": "string"
232
+ }
224
233
  },
225
- "query_schema": {},
226
- "label": ["ClinicalTrials.gov", "Clinical Trial", "Study", "References"],
227
- "type": "ClinicalTrialsDetailsTool",
228
- "tool_url": "/studies/{nctId}"
234
+ "outcome_measures": {
235
+ "type": "string",
236
+ "description": "Decides whether to retrieve primary, secondary, or all outcome measures. Options are 'primary', 'secondary', or 'all'. Default is 'primary'.",
237
+ "enum": [
238
+ "primary",
239
+ "secondary",
240
+ "all"
241
+ ]
242
+ }
243
+ },
244
+ "required": [
245
+ "nct_ids"
246
+ ]
247
+ },
248
+ "query_schema": {
249
+ "outcome_measures": "primary"
229
250
  },
230
-
231
- {
232
- "name": "extract_clinical_trial_outcomes",
233
- "description": "Extracts detailed trial outcome results (e.g., overall survival months, p-values, etc.) from clinicaltrials.gov, using their NCT IDs.",
234
- "parameter": {
235
- "type": "object",
236
- "properties": {
237
- "nct_ids": {
238
- "type": "array",
239
- "description": "List of NCT IDs of the clinical trials (e.g., ['NCT04852770', 'NCT01728545']).",
240
- "items": {
241
- "type": "string"
242
- },
243
- "required": true
244
- },
245
- "outcome_measure": {
246
- "type": "string",
247
- "description": "Outcome measure to extract. Example values include 'primary' (primary outcomes only), 'secondary' (secondary outcomes only), 'all' (all outcomes), or specific measure names such as 'survival', 'overall survival'. For specific measure names, outcome measures will be matched as long as the input partially matches their titles or descriptions (case agnostic). Querying for specific measure names is recommended after getting an overview of outcome measures ('primary'). If querying for specific measure names does not return any results, this parameter should be set to 'primary' for sanity check. By default, the value is set to 'primary', i.e. the tool will extract all primary outcome results.",
248
- "required": false
249
- }
250
- }
251
+ "label": [
252
+ "ClinicalTrials.gov",
253
+ "Clinical Trial",
254
+ "Study",
255
+ "Outcome Measures"
256
+ ],
257
+ "type": "ClinicalTrialsDetailsTool",
258
+ "tool_url": "/studies/{nctId}"
259
+ },
260
+ {
261
+ "name": "get_clinical_trial_references",
262
+ "description": "Retrieves the references (if any) for the clinical trials, using their NCT IDs.",
263
+ "parameter": {
264
+ "type": "object",
265
+ "properties": {
266
+ "nct_ids": {
267
+ "type": "array",
268
+ "description": "List of NCT IDs of the clinical trials (e.g., ['NCT04852770', 'NCT01728545']).",
269
+ "items": {
270
+ "type": "string"
271
+ }
251
272
  },
252
- "query_schema": {
253
- "outcome_measure": "primary"
273
+ "references": {
274
+ "type": "string",
275
+ "description": "Placeholder."
276
+ }
277
+ },
278
+ "required": [
279
+ "nct_ids",
280
+ "references"
281
+ ]
282
+ },
283
+ "query_schema": {},
284
+ "label": [
285
+ "ClinicalTrials.gov",
286
+ "Clinical Trial",
287
+ "Study",
288
+ "References"
289
+ ],
290
+ "type": "ClinicalTrialsDetailsTool",
291
+ "tool_url": "/studies/{nctId}"
292
+ },
293
+ {
294
+ "name": "extract_clinical_trial_outcomes",
295
+ "description": "Extracts detailed trial outcome results (e.g., overall survival months, p-values, etc.) from clinicaltrials.gov, using their NCT IDs.",
296
+ "parameter": {
297
+ "type": "object",
298
+ "properties": {
299
+ "nct_ids": {
300
+ "type": "array",
301
+ "description": "List of NCT IDs of the clinical trials (e.g., ['NCT04852770', 'NCT01728545']).",
302
+ "items": {
303
+ "type": "string"
304
+ }
254
305
  },
255
- "label": ["ClinicalTrials.gov", "Clinical Trial", "Study", "Outcome", "Efficacy", "Primary Outcome", "Secondary Outcome"],
256
- "type": "ClinicalTrialsDetailsTool",
257
- "tool_url": "/studies/{nctId}"
306
+ "outcome_measure": {
307
+ "type": "string",
308
+ "description": "Outcome measure to extract. Example values include 'primary' (primary outcomes only), 'secondary' (secondary outcomes only), 'all' (all outcomes), or specific measure names such as 'survival', 'overall survival'. For specific measure names, outcome measures will be matched as long as the input partially matches their titles or descriptions (case agnostic). Querying for specific measure names is recommended after getting an overview of outcome measures ('primary'). If querying for specific measure names does not return any results, this parameter should be set to 'primary' for sanity check. By default, the value is set to 'primary', i.e. the tool will extract all primary outcome results."
309
+ }
310
+ },
311
+ "required": [
312
+ "nct_ids"
313
+ ]
314
+ },
315
+ "query_schema": {
316
+ "outcome_measure": "primary"
258
317
  },
259
-
260
- {
261
- "name": "extract_clinical_trial_adverse_events",
262
- "description": "Extracts detailed adverse event results from clinicaltrials.gov, using their NCT IDs.",
263
- "parameter": {
264
- "type": "object",
265
- "properties": {
266
- "nct_ids": {
267
- "type": "array",
268
- "description": "List of NCT IDs of the clinical trials (e.g., ['NCT04852770', 'NCT01728545']).",
269
- "items": {
270
- "type": "string"
271
- },
272
- "required": true
273
- },
274
- "organ_systems": {
275
- "type": "array",
276
- "description": "List of organs or organ systems to filter adverse events (see enum for exact text). Adverse events will be matched only if the input exactly matches their terms (case agnostic). If not specified, all adverse events will be returned. By default, all adverse events will be returned.",
277
- "items": {
278
- "type": "string",
279
- "enum": [
280
- "Blood and Lymphatic System Disorders",
281
- "Cardiac Disorders",
282
- "Congenital, Familial and Genetic Disorders",
283
- "Ear and Labyrinth Disorders",
284
- "Endocrine Disorders",
285
- "Eye Disorders",
286
- "Gastrointestinal Disorders",
287
- "General Disorders",
288
- "Hepatobiliary Disorders",
289
- "Immune System Disorders",
290
- "Infections and Infestations",
291
- "Injury, Poisoning and Procedural Complications",
292
- "Investigations",
293
- "Metabolism and Nutrition Disorders",
294
- "Musculoskeletal and Connective Tissue Disorders",
295
- "Neoplasms Benign, Malignant and Unspecified (Including Cysts and Polyps)",
296
- "Nervous System Disorders",
297
- "Pregnancy, Puerperium and Perinatal Conditions",
298
- "Product Issues",
299
- "Psychiatric Disorders",
300
- "Renal and Urinary Disorders",
301
- "Reproductive System and Breast Disorders",
302
- "Respiratory, Thoracic and Mediastinal Disorders",
303
- "Skin and Subcutaneous Tissue Disorders",
304
- "Social Circumstances",
305
- "Surgical and Medical Procedures",
306
- "Vascular Disorders"
307
- ]
308
- },
309
- "required": false
310
- },
311
- "adverse_event_type": {
312
- "type": "string",
313
- "description": "Type of adverse events to extract. Options are 'serious' (serious adverse events only), 'other' (non-serious adverse events only), 'all' (all adverse events), or specific event names such as 'nausea', 'neutropenia', 'epilepsy' (from MedDRA). For specific event names, adverse events will be matched as long as the input partially matches their terms (case agnostic). Querying for specific adverse event names is recommended as there are typically many adverse events logged. If querying for specific event names does not return any results, this parameter should be set to 'serious' for sanity check. By default, the value is set to 'serious', i.e. the tool will extract all serious adverse events.",
314
- "required": false
315
- }
316
- }
318
+ "label": [
319
+ "ClinicalTrials.gov",
320
+ "Clinical Trial",
321
+ "Study",
322
+ "Outcome",
323
+ "Efficacy",
324
+ "Primary Outcome",
325
+ "Secondary Outcome"
326
+ ],
327
+ "type": "ClinicalTrialsDetailsTool",
328
+ "tool_url": "/studies/{nctId}"
329
+ },
330
+ {
331
+ "name": "extract_clinical_trial_adverse_events",
332
+ "description": "Extracts detailed adverse event results from clinicaltrials.gov, using their NCT IDs.",
333
+ "parameter": {
334
+ "type": "object",
335
+ "properties": {
336
+ "nct_ids": {
337
+ "type": "array",
338
+ "description": "List of NCT IDs of the clinical trials (e.g., ['NCT04852770', 'NCT01728545']).",
339
+ "items": {
340
+ "type": "string"
341
+ }
317
342
  },
318
- "query_schema": {
319
- "adverse_event_type": "serious"
343
+ "organ_systems": {
344
+ "type": "array",
345
+ "description": "List of organs or organ systems to filter adverse events (see enum for exact text). Adverse events will be matched only if the input exactly matches their terms (case agnostic). If not specified, all adverse events will be returned. By default, all adverse events will be returned.",
346
+ "items": {
347
+ "type": "string",
348
+ "enum": [
349
+ "Blood and Lymphatic System Disorders",
350
+ "Cardiac Disorders",
351
+ "Congenital, Familial and Genetic Disorders",
352
+ "Ear and Labyrinth Disorders",
353
+ "Endocrine Disorders",
354
+ "Eye Disorders",
355
+ "Gastrointestinal Disorders",
356
+ "General Disorders",
357
+ "Hepatobiliary Disorders",
358
+ "Immune System Disorders",
359
+ "Infections and Infestations",
360
+ "Injury, Poisoning and Procedural Complications",
361
+ "Investigations",
362
+ "Metabolism and Nutrition Disorders",
363
+ "Musculoskeletal and Connective Tissue Disorders",
364
+ "Neoplasms Benign, Malignant and Unspecified (Including Cysts and Polyps)",
365
+ "Nervous System Disorders",
366
+ "Pregnancy, Puerperium and Perinatal Conditions",
367
+ "Product Issues",
368
+ "Psychiatric Disorders",
369
+ "Renal and Urinary Disorders",
370
+ "Reproductive System and Breast Disorders",
371
+ "Respiratory, Thoracic and Mediastinal Disorders",
372
+ "Skin and Subcutaneous Tissue Disorders",
373
+ "Social Circumstances",
374
+ "Surgical and Medical Procedures",
375
+ "Vascular Disorders"
376
+ ]
377
+ }
320
378
  },
321
- "label": ["ClinicalTrials.gov", "Clinical Trial", "Study", "Adverse Event", "Safety"],
322
- "type": "ClinicalTrialsDetailsTool",
323
- "tool_url": "/studies/{nctId}"
324
- }
325
-
379
+ "adverse_event_type": {
380
+ "type": "string",
381
+ "description": "Type of adverse events to extract. Options are 'serious' (serious adverse events only), 'other' (non-serious adverse events only), 'all' (all adverse events), or specific event names such as 'nausea', 'neutropenia', 'epilepsy' (from MedDRA). For specific event names, adverse events will be matched as long as the input partially matches their terms (case agnostic). Querying for specific adverse event names is recommended as there are typically many adverse events logged. If querying for specific event names does not return any results, this parameter should be set to 'serious' for sanity check. By default, the value is set to 'serious', i.e. the tool will extract all serious adverse events."
382
+ }
383
+ },
384
+ "required": [
385
+ "nct_ids"
386
+ ]
387
+ },
388
+ "query_schema": {
389
+ "adverse_event_type": "serious"
390
+ },
391
+ "label": [
392
+ "ClinicalTrials.gov",
393
+ "Clinical Trial",
394
+ "Study",
395
+ "Adverse Event",
396
+ "Safety"
397
+ ],
398
+ "type": "ClinicalTrialsDetailsTool",
399
+ "tool_url": "/studies/{nctId}"
400
+ }
326
401
  ]