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/gwas_tools.json CHANGED
@@ -1,1082 +1,1843 @@
1
1
  [
2
- {
3
- "type": "GWASAssociationSearch",
4
- "name": "gwas_search_associations",
5
- "description": "Search for GWAS associations by various criteria including EFO trait, rs ID, accession ID, with sorting and pagination support.",
6
- "parameter": {
7
- "type": "object",
8
- "properties": {
9
- "efo_trait": {
10
- "type": "string",
11
- "description": "EFO trait identifier or name",
12
- "required": false
13
- },
14
- "rs_id": {
15
- "type": "string",
16
- "description": "dbSNP rs identifier",
17
- "required": false
18
- },
19
- "accession_id": {
20
- "type": "string",
21
- "description": "Study accession identifier",
22
- "required": false
23
- },
24
- "sort": {
25
- "type": "string",
26
- "description": "Sort field (e.g., 'p_value', 'or_value')",
27
- "required": false
28
- },
29
- "direction": {
30
- "type": "string",
31
- "description": "Sort direction ('asc' or 'desc')",
32
- "required": false
33
- },
34
- "size": {
35
- "type": "integer",
36
- "description": "Number of results to return",
37
- "required": false
38
- },
39
- "page": {
40
- "type": "integer",
41
- "description": "Page number for pagination",
42
- "required": false
43
- }
44
- }
2
+ {
3
+ "type": "GWASAssociationSearch",
4
+ "name": "gwas_search_associations",
5
+ "description": "Search for GWAS associations by various criteria including EFO trait, rs ID, accession ID, with sorting and pagination support.",
6
+ "parameter": {
7
+ "type": "object",
8
+ "properties": {
9
+ "efo_trait": {
10
+ "type": "string",
11
+ "description": "EFO trait identifier or name"
12
+ },
13
+ "rs_id": {
14
+ "type": "string",
15
+ "description": "dbSNP rs identifier"
16
+ },
17
+ "accession_id": {
18
+ "type": "string",
19
+ "description": "Study accession identifier"
45
20
  },
46
- "label": [
47
- "GWAS",
48
- "Association",
49
- "Genetics",
50
- "Search"
51
- ],
52
- "return_schema": {
21
+ "sort": {
22
+ "type": "string",
23
+ "description": "Sort field (e.g., 'p_value', 'or_value')"
24
+ },
25
+ "direction": {
26
+ "type": "string",
27
+ "description": "Sort direction ('asc' or 'desc')"
28
+ },
29
+ "size": {
30
+ "type": "integer",
31
+ "description": "Number of results to return"
32
+ },
33
+ "page": {
34
+ "type": "integer",
35
+ "description": "Page number for pagination"
36
+ }
37
+ },
38
+ "required": []
39
+ },
40
+ "label": [
41
+ "GWAS",
42
+ "Association",
43
+ "Genetics",
44
+ "Search"
45
+ ],
46
+ "return_schema": {
47
+ "type": "object",
48
+ "description": "GWAS associations search results with pagination metadata",
49
+ "properties": {
50
+ "data": {
51
+ "type": "array",
52
+ "description": "Array of GWAS association objects",
53
+ "items": {
53
54
  "type": "object",
54
- "description": "GWAS associations search results with pagination metadata",
55
55
  "properties": {
56
- "data": {
57
- "type": "array",
58
- "description": "Array of GWAS association objects",
59
- "items": {
60
- "type": "object",
61
- "properties": {
62
- "association_id": {"type": "integer", "description": "Unique association identifier"},
63
- "p_value": {"type": "number", "description": "Statistical p-value"},
64
- "beta": {"type": "string", "description": "Effect size (beta coefficient)"},
65
- "efo_traits": {
66
- "type": "array",
67
- "items": {
68
- "type": "object",
69
- "properties": {
70
- "efo_id": {"type": "string"},
71
- "efo_trait": {"type": "string"}
72
- }
73
- }
74
- },
75
- "reported_trait": {"type": "array", "items": {"type": "string"}},
76
- "accession_id": {"type": "string", "description": "Study accession ID"},
77
- "pubmed_id": {"type": "string", "description": "PubMed reference"},
78
- "first_author": {"type": "string", "description": "First author name"},
79
- "snp_effect_allele": {"type": "array", "items": {"type": "string"}},
80
- "snp_allele": {
81
- "type": "array",
82
- "items": {
83
- "type": "object",
84
- "properties": {
85
- "rs_id": {"type": "string"},
86
- "effect_allele": {"type": "string"}
87
- }
88
- }
89
- },
90
- "locations": {"type": "array", "items": {"type": "string"}},
91
- "mapped_genes": {"type": "array", "items": {"type": "string"}},
92
- "ci_lower": {"type": "number", "description": "Lower confidence interval"},
93
- "ci_upper": {"type": "number", "description": "Upper confidence interval"},
94
- "risk_frequency": {"type": "string", "description": "Risk allele frequency"},
95
- "range": {"type": "string", "description": "Effect size range"},
96
- "_links": {"type": "object", "description": "API links"}
97
- }
56
+ "association_id": {
57
+ "type": "integer",
58
+ "description": "Unique association identifier"
59
+ },
60
+ "p_value": {
61
+ "type": "number",
62
+ "description": "Statistical p-value"
63
+ },
64
+ "beta": {
65
+ "type": "string",
66
+ "description": "Effect size (beta coefficient)"
67
+ },
68
+ "efo_traits": {
69
+ "type": "array",
70
+ "items": {
71
+ "type": "object",
72
+ "properties": {
73
+ "efo_id": {
74
+ "type": "string"
75
+ },
76
+ "efo_trait": {
77
+ "type": "string"
98
78
  }
99
- },
100
- "metadata": {
101
- "type": "object",
102
- "description": "Pagination and navigation metadata",
103
- "properties": {
104
- "pagination": {
105
- "type": "object",
106
- "properties": {
107
- "size": {"type": "integer"},
108
- "totalElements": {"type": "integer"},
109
- "totalPages": {"type": "integer"},
110
- "number": {"type": "integer"}
111
- }
112
- },
113
- "links": {"type": "object", "description": "Navigation links"}
79
+ }
80
+ }
81
+ },
82
+ "reported_trait": {
83
+ "type": "array",
84
+ "items": {
85
+ "type": "string"
86
+ }
87
+ },
88
+ "accession_id": {
89
+ "type": "string",
90
+ "description": "Study accession ID"
91
+ },
92
+ "pubmed_id": {
93
+ "type": "string",
94
+ "description": "PubMed reference"
95
+ },
96
+ "first_author": {
97
+ "type": "string",
98
+ "description": "First author name"
99
+ },
100
+ "snp_effect_allele": {
101
+ "type": "array",
102
+ "items": {
103
+ "type": "string"
104
+ }
105
+ },
106
+ "snp_allele": {
107
+ "type": "array",
108
+ "items": {
109
+ "type": "object",
110
+ "properties": {
111
+ "rs_id": {
112
+ "type": "string"
113
+ },
114
+ "effect_allele": {
115
+ "type": "string"
114
116
  }
117
+ }
118
+ }
119
+ },
120
+ "locations": {
121
+ "type": "array",
122
+ "items": {
123
+ "type": "string"
115
124
  }
125
+ },
126
+ "mapped_genes": {
127
+ "type": "array",
128
+ "items": {
129
+ "type": "string"
130
+ }
131
+ },
132
+ "ci_lower": {
133
+ "type": "number",
134
+ "description": "Lower confidence interval"
135
+ },
136
+ "ci_upper": {
137
+ "type": "number",
138
+ "description": "Upper confidence interval"
139
+ },
140
+ "risk_frequency": {
141
+ "type": "string",
142
+ "description": "Risk allele frequency"
143
+ },
144
+ "range": {
145
+ "type": "string",
146
+ "description": "Effect size range"
147
+ },
148
+ "_links": {
149
+ "type": "object",
150
+ "description": "API links"
151
+ }
116
152
  }
117
- }
118
- },
119
- {
120
- "type": "GWASStudySearch",
121
- "name": "gwas_search_studies",
122
- "description": "Search for GWAS studies by various criteria including EFO trait, disease trait, cohort, GxE interactions, and summary statistics availability.",
123
- "parameter": {
124
- "type": "object",
125
- "properties": {
126
- "efo_trait": {
127
- "type": "string",
128
- "description": "EFO trait identifier or name",
129
- "required": false
130
- },
131
- "disease_trait": {
132
- "type": "string",
133
- "description": "Disease trait name",
134
- "required": false
135
- },
136
- "cohort": {
137
- "type": "string",
138
- "description": "Cohort name (e.g., 'UKB' for UK Biobank)",
139
- "required": false
153
+ }
154
+ },
155
+ "metadata": {
156
+ "type": "object",
157
+ "description": "Pagination and navigation metadata",
158
+ "properties": {
159
+ "pagination": {
160
+ "type": "object",
161
+ "properties": {
162
+ "size": {
163
+ "type": "integer"
140
164
  },
141
- "gxe": {
142
- "type": "boolean",
143
- "description": "Filter for Gene-by-Environment interaction studies",
144
- "required": false
165
+ "totalElements": {
166
+ "type": "integer"
145
167
  },
146
- "full_pvalue_set": {
147
- "type": "boolean",
148
- "description": "Filter for studies with full summary statistics",
149
- "required": false
168
+ "totalPages": {
169
+ "type": "integer"
150
170
  },
151
- "size": {
152
- "type": "integer",
153
- "description": "Number of results to return",
154
- "required": false
155
- },
156
- "page": {
157
- "type": "integer",
158
- "description": "Page number for pagination",
159
- "required": false
171
+ "number": {
172
+ "type": "integer"
160
173
  }
174
+ }
175
+ },
176
+ "links": {
177
+ "type": "object",
178
+ "description": "Navigation links"
161
179
  }
180
+ }
181
+ }
182
+ }
183
+ }
184
+ },
185
+ {
186
+ "type": "GWASStudySearch",
187
+ "name": "gwas_search_studies",
188
+ "description": "Search for GWAS studies by various criteria including EFO trait, disease trait, cohort, GxE interactions, and summary statistics availability.",
189
+ "parameter": {
190
+ "type": "object",
191
+ "properties": {
192
+ "efo_trait": {
193
+ "type": "string",
194
+ "description": "EFO trait identifier or name"
195
+ },
196
+ "disease_trait": {
197
+ "type": "string",
198
+ "description": "Disease trait name"
199
+ },
200
+ "cohort": {
201
+ "type": "string",
202
+ "description": "Cohort name (e.g., 'UKB' for UK Biobank)"
162
203
  },
163
- "label": [
164
- "GWAS",
165
- "Study",
166
- "Research",
167
- "Search"
168
- ],
169
- "return_schema": {
204
+ "gxe": {
205
+ "type": "boolean",
206
+ "description": "Filter for Gene-by-Environment interaction studies"
207
+ },
208
+ "full_pvalue_set": {
209
+ "type": "boolean",
210
+ "description": "Filter for studies with full summary statistics"
211
+ },
212
+ "size": {
213
+ "type": "integer",
214
+ "description": "Number of results to return"
215
+ },
216
+ "page": {
217
+ "type": "integer",
218
+ "description": "Page number for pagination"
219
+ }
220
+ },
221
+ "required": []
222
+ },
223
+ "label": [
224
+ "GWAS",
225
+ "Study",
226
+ "Research",
227
+ "Search"
228
+ ],
229
+ "return_schema": {
230
+ "type": "object",
231
+ "description": "GWAS studies search results with pagination metadata",
232
+ "properties": {
233
+ "data": {
234
+ "type": "array",
235
+ "description": "Array of GWAS study objects",
236
+ "items": {
170
237
  "type": "object",
171
- "description": "GWAS studies search results with pagination metadata",
172
238
  "properties": {
173
- "data": {
174
- "type": "array",
175
- "description": "Array of GWAS study objects",
176
- "items": {
177
- "type": "object",
178
- "properties": {
179
- "accession_id": {"type": "string", "description": "Study accession identifier"},
180
- "disease_trait": {"type": "string", "description": "Disease or trait name"},
181
- "efo_traits": {
182
- "type": "array",
183
- "items": {
184
- "type": "object",
185
- "properties": {
186
- "efo_id": {"type": "string"},
187
- "efo_trait": {"type": "string"}
188
- }
189
- }
190
- },
191
- "initial_sample_size": {"type": "string", "description": "Initial sample size description"},
192
- "replication_sample_size": {"type": "string", "description": "Replication sample size"},
193
- "discovery_ancestry": {"type": "array", "items": {"type": "string"}},
194
- "replication_ancestry": {"type": "array", "items": {"type": "string"}},
195
- "cohort": {"type": "array", "items": {"type": "string"}},
196
- "genotyping_technologies": {"type": "array", "items": {"type": "string"}},
197
- "platforms": {"type": "string", "description": "Genotyping platforms used"},
198
- "snp_count": {"type": "integer", "description": "Number of SNPs analyzed"},
199
- "imputed": {"type": "boolean", "description": "Whether data was imputed"},
200
- "pooled": {"type": "boolean", "description": "Whether data was pooled"},
201
- "gxe": {"type": "boolean", "description": "Gene-environment interaction study"},
202
- "gxg": {"type": "boolean", "description": "Gene-gene interaction study"},
203
- "full_summary_stats_available": {"type": "boolean", "description": "Full summary statistics available"},
204
- "full_summary_stats": {"type": "string", "description": "URL to full summary statistics"},
205
- "pubmed_id": {"type": "string", "description": "PubMed reference"},
206
- "terms_of_license": {"type": "string", "description": "Data usage license"},
207
- "array_manufacturer": {"type": "array", "items": {"type": "string"}},
208
- "_links": {"type": "object", "description": "API links"}
209
- }
210
- }
211
- },
212
- "metadata": {
213
- "type": "object",
214
- "description": "Pagination and navigation metadata",
215
- "properties": {
216
- "pagination": {
217
- "type": "object",
218
- "properties": {
219
- "size": {"type": "integer"},
220
- "totalElements": {"type": "integer"},
221
- "totalPages": {"type": "integer"},
222
- "number": {"type": "integer"}
223
- }
224
- },
225
- "links": {"type": "object", "description": "Navigation links"}
239
+ "accession_id": {
240
+ "type": "string",
241
+ "description": "Study accession identifier"
242
+ },
243
+ "disease_trait": {
244
+ "type": "string",
245
+ "description": "Disease or trait name"
246
+ },
247
+ "efo_traits": {
248
+ "type": "array",
249
+ "items": {
250
+ "type": "object",
251
+ "properties": {
252
+ "efo_id": {
253
+ "type": "string"
254
+ },
255
+ "efo_trait": {
256
+ "type": "string"
226
257
  }
258
+ }
259
+ }
260
+ },
261
+ "initial_sample_size": {
262
+ "type": "string",
263
+ "description": "Initial sample size description"
264
+ },
265
+ "replication_sample_size": {
266
+ "type": "string",
267
+ "description": "Replication sample size"
268
+ },
269
+ "discovery_ancestry": {
270
+ "type": "array",
271
+ "items": {
272
+ "type": "string"
273
+ }
274
+ },
275
+ "replication_ancestry": {
276
+ "type": "array",
277
+ "items": {
278
+ "type": "string"
279
+ }
280
+ },
281
+ "cohort": {
282
+ "type": "array",
283
+ "items": {
284
+ "type": "string"
285
+ }
286
+ },
287
+ "genotyping_technologies": {
288
+ "type": "array",
289
+ "items": {
290
+ "type": "string"
227
291
  }
292
+ },
293
+ "platforms": {
294
+ "type": "string",
295
+ "description": "Genotyping platforms used"
296
+ },
297
+ "snp_count": {
298
+ "type": "integer",
299
+ "description": "Number of SNPs analyzed"
300
+ },
301
+ "imputed": {
302
+ "type": "boolean",
303
+ "description": "Whether data was imputed"
304
+ },
305
+ "pooled": {
306
+ "type": "boolean",
307
+ "description": "Whether data was pooled"
308
+ },
309
+ "gxe": {
310
+ "type": "boolean",
311
+ "description": "Gene-environment interaction study"
312
+ },
313
+ "gxg": {
314
+ "type": "boolean",
315
+ "description": "Gene-gene interaction study"
316
+ },
317
+ "full_summary_stats_available": {
318
+ "type": "boolean",
319
+ "description": "Full summary statistics available"
320
+ },
321
+ "full_summary_stats": {
322
+ "type": "string",
323
+ "description": "URL to full summary statistics"
324
+ },
325
+ "pubmed_id": {
326
+ "type": "string",
327
+ "description": "PubMed reference"
328
+ },
329
+ "terms_of_license": {
330
+ "type": "string",
331
+ "description": "Data usage license"
332
+ },
333
+ "array_manufacturer": {
334
+ "type": "array",
335
+ "items": {
336
+ "type": "string"
337
+ }
338
+ },
339
+ "_links": {
340
+ "type": "object",
341
+ "description": "API links"
342
+ }
228
343
  }
229
- }
230
- },
231
- {
232
- "type": "GWASSNPSearch",
233
- "name": "gwas_search_snps",
234
- "description": "Search for GWAS single nucleotide polymorphisms (SNPs) by rs ID or mapped gene.",
235
- "parameter": {
236
- "type": "object",
237
- "properties": {
238
- "rs_id": {
239
- "type": "string",
240
- "description": "dbSNP rs identifier",
241
- "required": false
344
+ }
345
+ },
346
+ "metadata": {
347
+ "type": "object",
348
+ "description": "Pagination and navigation metadata",
349
+ "properties": {
350
+ "pagination": {
351
+ "type": "object",
352
+ "properties": {
353
+ "size": {
354
+ "type": "integer"
242
355
  },
243
- "mapped_gene": {
244
- "type": "string",
245
- "description": "Gene name or symbol",
246
- "required": false
356
+ "totalElements": {
357
+ "type": "integer"
247
358
  },
248
- "size": {
249
- "type": "integer",
250
- "description": "Number of results to return",
251
- "required": false
359
+ "totalPages": {
360
+ "type": "integer"
252
361
  },
253
- "page": {
254
- "type": "integer",
255
- "description": "Page number for pagination",
256
- "required": false
362
+ "number": {
363
+ "type": "integer"
257
364
  }
365
+ }
366
+ },
367
+ "links": {
368
+ "type": "object",
369
+ "description": "Navigation links"
258
370
  }
371
+ }
372
+ }
373
+ }
374
+ }
375
+ },
376
+ {
377
+ "type": "GWASSNPSearch",
378
+ "name": "gwas_search_snps",
379
+ "description": "Search for GWAS single nucleotide polymorphisms (SNPs) by rs ID or mapped gene.",
380
+ "parameter": {
381
+ "type": "object",
382
+ "properties": {
383
+ "rs_id": {
384
+ "type": "string",
385
+ "description": "dbSNP rs identifier"
386
+ },
387
+ "mapped_gene": {
388
+ "type": "string",
389
+ "description": "Gene name or symbol"
390
+ },
391
+ "size": {
392
+ "type": "integer",
393
+ "description": "Number of results to return"
259
394
  },
260
- "label": [
261
- "GWAS",
262
- "SNP",
263
- "Variant",
264
- "Search"
265
- ],
266
- "return_schema": {
395
+ "page": {
396
+ "type": "integer",
397
+ "description": "Page number for pagination"
398
+ }
399
+ },
400
+ "required": []
401
+ },
402
+ "label": [
403
+ "GWAS",
404
+ "SNP",
405
+ "Variant",
406
+ "Search"
407
+ ],
408
+ "return_schema": {
409
+ "type": "object",
410
+ "description": "GWAS SNPs search results with pagination metadata",
411
+ "properties": {
412
+ "data": {
413
+ "type": "array",
414
+ "description": "Array of SNP objects",
415
+ "items": {
267
416
  "type": "object",
268
- "description": "GWAS SNPs search results with pagination metadata",
269
417
  "properties": {
270
- "data": {
271
- "type": "array",
272
- "description": "Array of SNP objects",
273
- "items": {
274
- "type": "object",
275
- "properties": {
276
- "rs_id": {"type": "string", "description": "dbSNP rs identifier"},
277
- "merged": {"type": "integer", "description": "Merged status"},
278
- "functional_class": {"type": "string", "description": "Functional classification"},
279
- "last_update_date": {"type": "string", "description": "Last update timestamp"},
280
- "locations": {
281
- "type": "array",
282
- "items": {
283
- "type": "object",
284
- "properties": {
285
- "chromosome_name": {"type": "string"},
286
- "chromosome_position": {"type": "integer"},
287
- "region": {
288
- "type": "object",
289
- "properties": {
290
- "name": {"type": "string"}
291
- }
292
- }
293
- }
294
- }
295
- },
296
- "alleles": {"type": "string", "description": "Allele information"},
297
- "most_severe_consequence": {"type": "string", "description": "Most severe functional consequence"},
298
- "mapped_genes": {"type": "array", "items": {"type": "string"}},
299
- "maf": {"type": "number", "description": "Minor allele frequency"},
300
- "minor_allele": {"type": "string", "description": "Minor allele"},
301
- "_links": {"type": "object", "description": "API links"}
418
+ "rs_id": {
419
+ "type": "string",
420
+ "description": "dbSNP rs identifier"
421
+ },
422
+ "merged": {
423
+ "type": "integer",
424
+ "description": "Merged status"
425
+ },
426
+ "functional_class": {
427
+ "type": "string",
428
+ "description": "Functional classification"
429
+ },
430
+ "last_update_date": {
431
+ "type": "string",
432
+ "description": "Last update timestamp"
433
+ },
434
+ "locations": {
435
+ "type": "array",
436
+ "items": {
437
+ "type": "object",
438
+ "properties": {
439
+ "chromosome_name": {
440
+ "type": "string"
441
+ },
442
+ "chromosome_position": {
443
+ "type": "integer"
444
+ },
445
+ "region": {
446
+ "type": "object",
447
+ "properties": {
448
+ "name": {
449
+ "type": "string"
302
450
  }
451
+ }
303
452
  }
304
- },
305
- "metadata": {
306
- "type": "object",
307
- "description": "Pagination and navigation metadata",
308
- "properties": {
309
- "pagination": {
310
- "type": "object",
311
- "properties": {
312
- "size": {"type": "integer"},
313
- "totalElements": {"type": "integer"},
314
- "totalPages": {"type": "integer"},
315
- "number": {"type": "integer"}
316
- }
317
- },
318
- "links": {"type": "object", "description": "Navigation links"}
319
- }
453
+ }
320
454
  }
321
- }
322
- }
323
- },
324
- {
325
- "type": "GWASAssociationByID",
326
- "name": "gwas_get_association_by_id",
327
- "description": "Get a specific GWAS association by its unique identifier.",
328
- "parameter": {
329
- "type": "object",
330
- "properties": {
331
- "association_id": {
332
- "type": "string",
333
- "description": "GWAS association identifier",
334
- "required": true
455
+ },
456
+ "alleles": {
457
+ "type": "string",
458
+ "description": "Allele information"
459
+ },
460
+ "most_severe_consequence": {
461
+ "type": "string",
462
+ "description": "Most severe functional consequence"
463
+ },
464
+ "mapped_genes": {
465
+ "type": "array",
466
+ "items": {
467
+ "type": "string"
335
468
  }
469
+ },
470
+ "maf": {
471
+ "type": "number",
472
+ "description": "Minor allele frequency"
473
+ },
474
+ "minor_allele": {
475
+ "type": "string",
476
+ "description": "Minor allele"
477
+ },
478
+ "_links": {
479
+ "type": "object",
480
+ "description": "API links"
481
+ }
336
482
  }
483
+ }
337
484
  },
338
- "label": [
339
- "GWAS",
340
- "Association",
341
- "Lookup"
342
- ],
343
- "return_schema": {
344
- "type": "object",
345
- "description": "Single GWAS association object",
346
- "properties": {
347
- "association_id": {"type": "integer", "description": "Unique association identifier"},
348
- "p_value": {"type": "number", "description": "Statistical p-value"},
349
- "beta": {"type": "string", "description": "Effect size (beta coefficient)"},
350
- "efo_traits": {
351
- "type": "array",
352
- "items": {
353
- "type": "object",
354
- "properties": {
355
- "efo_id": {"type": "string"},
356
- "efo_trait": {"type": "string"}
357
- }
358
- }
485
+ "metadata": {
486
+ "type": "object",
487
+ "description": "Pagination and navigation metadata",
488
+ "properties": {
489
+ "pagination": {
490
+ "type": "object",
491
+ "properties": {
492
+ "size": {
493
+ "type": "integer"
359
494
  },
360
- "reported_trait": {"type": "array", "items": {"type": "string"}},
361
- "accession_id": {"type": "string", "description": "Study accession ID"},
362
- "pubmed_id": {"type": "string", "description": "PubMed reference"},
363
- "first_author": {"type": "string", "description": "First author name"},
364
- "snp_effect_allele": {"type": "array", "items": {"type": "string"}},
365
- "snp_allele": {
366
- "type": "array",
367
- "items": {
368
- "type": "object",
369
- "properties": {
370
- "rs_id": {"type": "string"},
371
- "effect_allele": {"type": "string"}
372
- }
373
- }
495
+ "totalElements": {
496
+ "type": "integer"
497
+ },
498
+ "totalPages": {
499
+ "type": "integer"
374
500
  },
375
- "locations": {"type": "array", "items": {"type": "string"}},
376
- "mapped_genes": {"type": "array", "items": {"type": "string"}},
377
- "ci_lower": {"type": "number", "description": "Lower confidence interval"},
378
- "ci_upper": {"type": "number", "description": "Upper confidence interval"},
379
- "risk_frequency": {"type": "string", "description": "Risk allele frequency"},
380
- "range": {"type": "string", "description": "Effect size range"},
381
- "_links": {"type": "object", "description": "API links"}
501
+ "number": {
502
+ "type": "integer"
503
+ }
504
+ }
505
+ },
506
+ "links": {
507
+ "type": "object",
508
+ "description": "Navigation links"
382
509
  }
510
+ }
511
+ }
512
+ }
513
+ }
514
+ },
515
+ {
516
+ "type": "GWASAssociationByID",
517
+ "name": "gwas_get_association_by_id",
518
+ "description": "Get a specific GWAS association by its unique identifier.",
519
+ "parameter": {
520
+ "type": "object",
521
+ "properties": {
522
+ "association_id": {
523
+ "type": "string",
524
+ "description": "GWAS association identifier"
383
525
  }
526
+ },
527
+ "required": [
528
+ "association_id"
529
+ ]
384
530
  },
385
- {
386
- "type": "GWASStudyByID",
387
- "name": "gwas_get_study_by_id",
388
- "description": "Get a specific GWAS study by its unique identifier.",
389
- "parameter": {
531
+ "label": [
532
+ "GWAS",
533
+ "Association",
534
+ "Lookup"
535
+ ],
536
+ "return_schema": {
537
+ "type": "object",
538
+ "description": "Single GWAS association object",
539
+ "properties": {
540
+ "association_id": {
541
+ "type": "integer",
542
+ "description": "Unique association identifier"
543
+ },
544
+ "p_value": {
545
+ "type": "number",
546
+ "description": "Statistical p-value"
547
+ },
548
+ "beta": {
549
+ "type": "string",
550
+ "description": "Effect size (beta coefficient)"
551
+ },
552
+ "efo_traits": {
553
+ "type": "array",
554
+ "items": {
390
555
  "type": "object",
391
556
  "properties": {
392
- "study_id": {
393
- "type": "string",
394
- "description": "GWAS study identifier",
395
- "required": true
396
- }
557
+ "efo_id": {
558
+ "type": "string"
559
+ },
560
+ "efo_trait": {
561
+ "type": "string"
562
+ }
397
563
  }
564
+ }
565
+ },
566
+ "reported_trait": {
567
+ "type": "array",
568
+ "items": {
569
+ "type": "string"
570
+ }
571
+ },
572
+ "accession_id": {
573
+ "type": "string",
574
+ "description": "Study accession ID"
575
+ },
576
+ "pubmed_id": {
577
+ "type": "string",
578
+ "description": "PubMed reference"
579
+ },
580
+ "first_author": {
581
+ "type": "string",
582
+ "description": "First author name"
583
+ },
584
+ "snp_effect_allele": {
585
+ "type": "array",
586
+ "items": {
587
+ "type": "string"
588
+ }
398
589
  },
399
- "label": [
400
- "GWAS",
401
- "Study",
402
- "Lookup"
403
- ],
404
- "return_schema": {
590
+ "snp_allele": {
591
+ "type": "array",
592
+ "items": {
405
593
  "type": "object",
406
- "description": "Single GWAS study object",
407
594
  "properties": {
408
- "accession_id": {"type": "string", "description": "Study accession identifier"},
409
- "disease_trait": {"type": "string", "description": "Disease or trait name"},
410
- "efo_traits": {
411
- "type": "array",
412
- "items": {
413
- "type": "object",
414
- "properties": {
415
- "efo_id": {"type": "string"},
416
- "efo_trait": {"type": "string"}
417
- }
418
- }
419
- },
420
- "initial_sample_size": {"type": "string", "description": "Initial sample size description"},
421
- "replication_sample_size": {"type": "string", "description": "Replication sample size"},
422
- "discovery_ancestry": {"type": "array", "items": {"type": "string"}},
423
- "replication_ancestry": {"type": "array", "items": {"type": "string"}},
424
- "cohort": {"type": "array", "items": {"type": "string"}},
425
- "genotyping_technologies": {"type": "array", "items": {"type": "string"}},
426
- "platforms": {"type": "string", "description": "Genotyping platforms used"},
427
- "snp_count": {"type": "integer", "description": "Number of SNPs analyzed"},
428
- "imputed": {"type": "boolean", "description": "Whether data was imputed"},
429
- "pooled": {"type": "boolean", "description": "Whether data was pooled"},
430
- "gxe": {"type": "boolean", "description": "Gene-environment interaction study"},
431
- "gxg": {"type": "boolean", "description": "Gene-gene interaction study"},
432
- "full_summary_stats_available": {"type": "boolean", "description": "Full summary statistics available"},
433
- "full_summary_stats": {"type": "string", "description": "URL to full summary statistics"},
434
- "pubmed_id": {"type": "string", "description": "PubMed reference"},
435
- "terms_of_license": {"type": "string", "description": "Data usage license"},
436
- "array_manufacturer": {"type": "array", "items": {"type": "string"}},
437
- "_links": {"type": "object", "description": "API links"}
595
+ "rs_id": {
596
+ "type": "string"
597
+ },
598
+ "effect_allele": {
599
+ "type": "string"
600
+ }
438
601
  }
602
+ }
603
+ },
604
+ "locations": {
605
+ "type": "array",
606
+ "items": {
607
+ "type": "string"
608
+ }
609
+ },
610
+ "mapped_genes": {
611
+ "type": "array",
612
+ "items": {
613
+ "type": "string"
614
+ }
615
+ },
616
+ "ci_lower": {
617
+ "type": "number",
618
+ "description": "Lower confidence interval"
619
+ },
620
+ "ci_upper": {
621
+ "type": "number",
622
+ "description": "Upper confidence interval"
623
+ },
624
+ "risk_frequency": {
625
+ "type": "string",
626
+ "description": "Risk allele frequency"
627
+ },
628
+ "range": {
629
+ "type": "string",
630
+ "description": "Effect size range"
631
+ },
632
+ "_links": {
633
+ "type": "object",
634
+ "description": "API links"
439
635
  }
636
+ }
637
+ }
638
+ },
639
+ {
640
+ "type": "GWASStudyByID",
641
+ "name": "gwas_get_study_by_id",
642
+ "description": "Get a specific GWAS study by its unique identifier.",
643
+ "parameter": {
644
+ "type": "object",
645
+ "properties": {
646
+ "study_id": {
647
+ "type": "string",
648
+ "description": "GWAS study identifier"
649
+ }
650
+ },
651
+ "required": [
652
+ "study_id"
653
+ ]
440
654
  },
441
- {
442
- "type": "GWASSNPByID",
443
- "name": "gwas_get_snp_by_id",
444
- "description": "Get a specific GWAS SNP by its rs ID.",
445
- "parameter": {
446
- "type": "object",
447
- "properties": {
448
- "rs_id": {
449
- "type": "string",
450
- "description": "dbSNP rs identifier",
451
- "required": true
452
- }
453
- }
655
+ "label": [
656
+ "GWAS",
657
+ "Study",
658
+ "Lookup"
659
+ ],
660
+ "return_schema": {
661
+ "type": "object",
662
+ "description": "Single GWAS study object",
663
+ "properties": {
664
+ "accession_id": {
665
+ "type": "string",
666
+ "description": "Study accession identifier"
667
+ },
668
+ "disease_trait": {
669
+ "type": "string",
670
+ "description": "Disease or trait name"
454
671
  },
455
- "label": [
456
- "GWAS",
457
- "SNP",
458
- "Lookup"
459
- ],
460
- "return_schema": {
672
+ "efo_traits": {
673
+ "type": "array",
674
+ "items": {
461
675
  "type": "object",
462
- "description": "Single SNP object",
463
676
  "properties": {
464
- "rs_id": {"type": "string", "description": "dbSNP rs identifier"},
465
- "merged": {"type": "integer", "description": "Merged status"},
466
- "functional_class": {"type": "string", "description": "Functional classification"},
467
- "last_update_date": {"type": "string", "description": "Last update timestamp"},
468
- "locations": {
469
- "type": "array",
470
- "items": {
471
- "type": "object",
472
- "properties": {
473
- "chromosome_name": {"type": "string"},
474
- "chromosome_position": {"type": "integer"},
475
- "region": {
476
- "type": "object",
477
- "properties": {
478
- "name": {"type": "string"}
479
- }
480
- }
481
- }
482
- }
483
- },
484
- "alleles": {"type": "string", "description": "Allele information"},
485
- "most_severe_consequence": {"type": "string", "description": "Most severe functional consequence"},
486
- "mapped_genes": {"type": "array", "items": {"type": "string"}},
487
- "maf": {"type": "number", "description": "Minor allele frequency"},
488
- "minor_allele": {"type": "string", "description": "Minor allele"},
489
- "_links": {"type": "object", "description": "API links"}
677
+ "efo_id": {
678
+ "type": "string"
679
+ },
680
+ "efo_trait": {
681
+ "type": "string"
682
+ }
490
683
  }
684
+ }
685
+ },
686
+ "initial_sample_size": {
687
+ "type": "string",
688
+ "description": "Initial sample size description"
689
+ },
690
+ "replication_sample_size": {
691
+ "type": "string",
692
+ "description": "Replication sample size"
693
+ },
694
+ "discovery_ancestry": {
695
+ "type": "array",
696
+ "items": {
697
+ "type": "string"
698
+ }
699
+ },
700
+ "replication_ancestry": {
701
+ "type": "array",
702
+ "items": {
703
+ "type": "string"
704
+ }
705
+ },
706
+ "cohort": {
707
+ "type": "array",
708
+ "items": {
709
+ "type": "string"
710
+ }
711
+ },
712
+ "genotyping_technologies": {
713
+ "type": "array",
714
+ "items": {
715
+ "type": "string"
716
+ }
717
+ },
718
+ "platforms": {
719
+ "type": "string",
720
+ "description": "Genotyping platforms used"
721
+ },
722
+ "snp_count": {
723
+ "type": "integer",
724
+ "description": "Number of SNPs analyzed"
725
+ },
726
+ "imputed": {
727
+ "type": "boolean",
728
+ "description": "Whether data was imputed"
729
+ },
730
+ "pooled": {
731
+ "type": "boolean",
732
+ "description": "Whether data was pooled"
733
+ },
734
+ "gxe": {
735
+ "type": "boolean",
736
+ "description": "Gene-environment interaction study"
737
+ },
738
+ "gxg": {
739
+ "type": "boolean",
740
+ "description": "Gene-gene interaction study"
741
+ },
742
+ "full_summary_stats_available": {
743
+ "type": "boolean",
744
+ "description": "Full summary statistics available"
745
+ },
746
+ "full_summary_stats": {
747
+ "type": "string",
748
+ "description": "URL to full summary statistics"
749
+ },
750
+ "pubmed_id": {
751
+ "type": "string",
752
+ "description": "PubMed reference"
753
+ },
754
+ "terms_of_license": {
755
+ "type": "string",
756
+ "description": "Data usage license"
757
+ },
758
+ "array_manufacturer": {
759
+ "type": "array",
760
+ "items": {
761
+ "type": "string"
762
+ }
763
+ },
764
+ "_links": {
765
+ "type": "object",
766
+ "description": "API links"
767
+ }
768
+ }
769
+ }
770
+ },
771
+ {
772
+ "type": "GWASSNPByID",
773
+ "name": "gwas_get_snp_by_id",
774
+ "description": "Get a specific GWAS SNP by its rs ID.",
775
+ "parameter": {
776
+ "type": "object",
777
+ "properties": {
778
+ "rs_id": {
779
+ "type": "string",
780
+ "description": "dbSNP rs identifier"
491
781
  }
782
+ },
783
+ "required": [
784
+ "rs_id"
785
+ ]
492
786
  },
493
- {
494
- "type": "GWASVariantsForTrait",
495
- "name": "gwas_get_variants_for_trait",
496
- "description": "Get all variants associated with a specific trait with pagination support.",
497
- "parameter": {
787
+ "label": [
788
+ "GWAS",
789
+ "SNP",
790
+ "Lookup"
791
+ ],
792
+ "return_schema": {
793
+ "type": "object",
794
+ "description": "Single SNP object",
795
+ "properties": {
796
+ "rs_id": {
797
+ "type": "string",
798
+ "description": "dbSNP rs identifier"
799
+ },
800
+ "merged": {
801
+ "type": "integer",
802
+ "description": "Merged status"
803
+ },
804
+ "functional_class": {
805
+ "type": "string",
806
+ "description": "Functional classification"
807
+ },
808
+ "last_update_date": {
809
+ "type": "string",
810
+ "description": "Last update timestamp"
811
+ },
812
+ "locations": {
813
+ "type": "array",
814
+ "items": {
498
815
  "type": "object",
499
816
  "properties": {
500
- "efo_trait": {
501
- "type": "string",
502
- "description": "EFO trait identifier or name",
503
- "required": true
504
- },
505
- "size": {
506
- "type": "integer",
507
- "description": "Number of results to return per page",
508
- "required": false
509
- },
510
- "page": {
511
- "type": "integer",
512
- "description": "Page number for pagination",
513
- "required": false
817
+ "chromosome_name": {
818
+ "type": "string"
819
+ },
820
+ "chromosome_position": {
821
+ "type": "integer"
822
+ },
823
+ "region": {
824
+ "type": "object",
825
+ "properties": {
826
+ "name": {
827
+ "type": "string"
828
+ }
514
829
  }
830
+ }
515
831
  }
832
+ }
833
+ },
834
+ "alleles": {
835
+ "type": "string",
836
+ "description": "Allele information"
837
+ },
838
+ "most_severe_consequence": {
839
+ "type": "string",
840
+ "description": "Most severe functional consequence"
841
+ },
842
+ "mapped_genes": {
843
+ "type": "array",
844
+ "items": {
845
+ "type": "string"
846
+ }
516
847
  },
517
- "label": [
518
- "GWAS",
519
- "Variants",
520
- "Trait",
521
- "Genetics"
522
- ],
523
- "return_schema": {
848
+ "maf": {
849
+ "type": "number",
850
+ "description": "Minor allele frequency"
851
+ },
852
+ "minor_allele": {
853
+ "type": "string",
854
+ "description": "Minor allele"
855
+ },
856
+ "_links": {
857
+ "type": "object",
858
+ "description": "API links"
859
+ }
860
+ }
861
+ }
862
+ },
863
+ {
864
+ "type": "GWASVariantsForTrait",
865
+ "name": "gwas_get_variants_for_trait",
866
+ "description": "Get all variants associated with a specific trait with pagination support.",
867
+ "parameter": {
868
+ "type": "object",
869
+ "properties": {
870
+ "efo_trait": {
871
+ "type": "string",
872
+ "description": "EFO trait identifier or name"
873
+ },
874
+ "size": {
875
+ "type": "integer",
876
+ "description": "Number of results to return per page"
877
+ },
878
+ "page": {
879
+ "type": "integer",
880
+ "description": "Page number for pagination"
881
+ }
882
+ },
883
+ "required": [
884
+ "efo_trait"
885
+ ]
886
+ },
887
+ "label": [
888
+ "GWAS",
889
+ "Variants",
890
+ "Trait",
891
+ "Genetics"
892
+ ],
893
+ "return_schema": {
894
+ "type": "object",
895
+ "description": "GWAS variants for trait results with pagination metadata",
896
+ "properties": {
897
+ "data": {
898
+ "type": "array",
899
+ "description": "Array of variant objects",
900
+ "items": {
524
901
  "type": "object",
525
- "description": "GWAS variants for trait results with pagination metadata",
526
902
  "properties": {
527
- "data": {
528
- "type": "array",
529
- "description": "Array of variant objects",
530
- "items": {
531
- "type": "object",
532
- "properties": {
533
- "rs_id": {"type": "string", "description": "dbSNP rs identifier"},
534
- "merged": {"type": "integer", "description": "Merged status"},
535
- "functional_class": {"type": "string", "description": "Functional classification"},
536
- "last_update_date": {"type": "string", "description": "Last update timestamp"},
537
- "locations": {
538
- "type": "array",
539
- "items": {
540
- "type": "object",
541
- "properties": {
542
- "chromosome_name": {"type": "string"},
543
- "chromosome_position": {"type": "integer"},
544
- "region": {
545
- "type": "object",
546
- "properties": {
547
- "name": {"type": "string"}
548
- }
549
- }
550
- }
551
- }
552
- },
553
- "alleles": {"type": "string", "description": "Allele information"},
554
- "most_severe_consequence": {"type": "string", "description": "Most severe functional consequence"},
555
- "mapped_genes": {"type": "array", "items": {"type": "string"}},
556
- "maf": {"type": "number", "description": "Minor allele frequency"},
557
- "minor_allele": {"type": "string", "description": "Minor allele"},
558
- "_links": {"type": "object", "description": "API links"}
903
+ "rs_id": {
904
+ "type": "string",
905
+ "description": "dbSNP rs identifier"
906
+ },
907
+ "merged": {
908
+ "type": "integer",
909
+ "description": "Merged status"
910
+ },
911
+ "functional_class": {
912
+ "type": "string",
913
+ "description": "Functional classification"
914
+ },
915
+ "last_update_date": {
916
+ "type": "string",
917
+ "description": "Last update timestamp"
918
+ },
919
+ "locations": {
920
+ "type": "array",
921
+ "items": {
922
+ "type": "object",
923
+ "properties": {
924
+ "chromosome_name": {
925
+ "type": "string"
926
+ },
927
+ "chromosome_position": {
928
+ "type": "integer"
929
+ },
930
+ "region": {
931
+ "type": "object",
932
+ "properties": {
933
+ "name": {
934
+ "type": "string"
559
935
  }
936
+ }
560
937
  }
561
- },
562
- "metadata": {
563
- "type": "object",
564
- "description": "Pagination and navigation metadata",
565
- "properties": {
566
- "pagination": {
567
- "type": "object",
568
- "properties": {
569
- "size": {"type": "integer"},
570
- "totalElements": {"type": "integer"},
571
- "totalPages": {"type": "integer"},
572
- "number": {"type": "integer"}
573
- }
574
- },
575
- "links": {"type": "object", "description": "Navigation links"}
576
- }
938
+ }
577
939
  }
940
+ },
941
+ "alleles": {
942
+ "type": "string",
943
+ "description": "Allele information"
944
+ },
945
+ "most_severe_consequence": {
946
+ "type": "string",
947
+ "description": "Most severe functional consequence"
948
+ },
949
+ "mapped_genes": {
950
+ "type": "array",
951
+ "items": {
952
+ "type": "string"
953
+ }
954
+ },
955
+ "maf": {
956
+ "type": "number",
957
+ "description": "Minor allele frequency"
958
+ },
959
+ "minor_allele": {
960
+ "type": "string",
961
+ "description": "Minor allele"
962
+ },
963
+ "_links": {
964
+ "type": "object",
965
+ "description": "API links"
966
+ }
578
967
  }
579
- }
580
- },
581
- {
582
- "type": "GWASAssociationsForTrait",
583
- "name": "gwas_get_associations_for_trait",
584
- "description": "Get all associations for a specific trait, sorted by p-value (most significant first).",
585
- "parameter": {
586
- "type": "object",
587
- "properties": {
588
- "efo_trait": {
589
- "type": "string",
590
- "description": "EFO trait identifier or name",
591
- "required": true
592
- },
968
+ }
969
+ },
970
+ "metadata": {
971
+ "type": "object",
972
+ "description": "Pagination and navigation metadata",
973
+ "properties": {
974
+ "pagination": {
975
+ "type": "object",
976
+ "properties": {
593
977
  "size": {
594
- "type": "integer",
595
- "description": "Number of results to return per page",
596
- "required": false
978
+ "type": "integer"
979
+ },
980
+ "totalElements": {
981
+ "type": "integer"
597
982
  },
598
- "page": {
599
- "type": "integer",
600
- "description": "Page number for pagination",
601
- "required": false
983
+ "totalPages": {
984
+ "type": "integer"
985
+ },
986
+ "number": {
987
+ "type": "integer"
602
988
  }
989
+ }
990
+ },
991
+ "links": {
992
+ "type": "object",
993
+ "description": "Navigation links"
603
994
  }
995
+ }
996
+ }
997
+ }
998
+ }
999
+ },
1000
+ {
1001
+ "type": "GWASAssociationsForTrait",
1002
+ "name": "gwas_get_associations_for_trait",
1003
+ "description": "Get all associations for a specific trait, sorted by p-value (most significant first).",
1004
+ "parameter": {
1005
+ "type": "object",
1006
+ "properties": {
1007
+ "efo_trait": {
1008
+ "type": "string",
1009
+ "description": "EFO trait identifier or name"
1010
+ },
1011
+ "size": {
1012
+ "type": "integer",
1013
+ "description": "Number of results to return per page"
604
1014
  },
605
- "label": [
606
- "GWAS",
607
- "Associations",
608
- "Trait",
609
- "Significance"
610
- ],
611
- "return_schema": {
1015
+ "page": {
1016
+ "type": "integer",
1017
+ "description": "Page number for pagination"
1018
+ }
1019
+ },
1020
+ "required": [
1021
+ "efo_trait"
1022
+ ]
1023
+ },
1024
+ "label": [
1025
+ "GWAS",
1026
+ "Associations",
1027
+ "Trait",
1028
+ "Significance"
1029
+ ],
1030
+ "return_schema": {
1031
+ "type": "object",
1032
+ "description": "GWAS associations for trait results with pagination metadata",
1033
+ "properties": {
1034
+ "data": {
1035
+ "type": "array",
1036
+ "description": "Array of GWAS association objects",
1037
+ "items": {
612
1038
  "type": "object",
613
- "description": "GWAS associations for trait results with pagination metadata",
614
1039
  "properties": {
615
- "data": {
616
- "type": "array",
617
- "description": "Array of GWAS association objects",
618
- "items": {
619
- "type": "object",
620
- "properties": {
621
- "association_id": {"type": "integer", "description": "Unique association identifier"},
622
- "p_value": {"type": "number", "description": "Statistical p-value"},
623
- "beta": {"type": "string", "description": "Effect size (beta coefficient)"},
624
- "efo_traits": {
625
- "type": "array",
626
- "items": {
627
- "type": "object",
628
- "properties": {
629
- "efo_id": {"type": "string"},
630
- "efo_trait": {"type": "string"}
631
- }
632
- }
633
- },
634
- "reported_trait": {"type": "array", "items": {"type": "string"}},
635
- "accession_id": {"type": "string", "description": "Study accession ID"},
636
- "pubmed_id": {"type": "string", "description": "PubMed reference"},
637
- "first_author": {"type": "string", "description": "First author name"},
638
- "snp_effect_allele": {"type": "array", "items": {"type": "string"}},
639
- "snp_allele": {
640
- "type": "array",
641
- "items": {
642
- "type": "object",
643
- "properties": {
644
- "rs_id": {"type": "string"},
645
- "effect_allele": {"type": "string"}
646
- }
647
- }
648
- },
649
- "locations": {"type": "array", "items": {"type": "string"}},
650
- "mapped_genes": {"type": "array", "items": {"type": "string"}},
651
- "ci_lower": {"type": "number", "description": "Lower confidence interval"},
652
- "ci_upper": {"type": "number", "description": "Upper confidence interval"},
653
- "risk_frequency": {"type": "string", "description": "Risk allele frequency"},
654
- "range": {"type": "string", "description": "Effect size range"},
655
- "_links": {"type": "object", "description": "API links"}
656
- }
1040
+ "association_id": {
1041
+ "type": "integer",
1042
+ "description": "Unique association identifier"
1043
+ },
1044
+ "p_value": {
1045
+ "type": "number",
1046
+ "description": "Statistical p-value"
1047
+ },
1048
+ "beta": {
1049
+ "type": "string",
1050
+ "description": "Effect size (beta coefficient)"
1051
+ },
1052
+ "efo_traits": {
1053
+ "type": "array",
1054
+ "items": {
1055
+ "type": "object",
1056
+ "properties": {
1057
+ "efo_id": {
1058
+ "type": "string"
1059
+ },
1060
+ "efo_trait": {
1061
+ "type": "string"
657
1062
  }
658
- },
659
- "metadata": {
660
- "type": "object",
661
- "description": "Pagination and navigation metadata",
662
- "properties": {
663
- "pagination": {
664
- "type": "object",
665
- "properties": {
666
- "size": {"type": "integer"},
667
- "totalElements": {"type": "integer"},
668
- "totalPages": {"type": "integer"},
669
- "number": {"type": "integer"}
670
- }
671
- },
672
- "links": {"type": "object", "description": "Navigation links"}
1063
+ }
1064
+ }
1065
+ },
1066
+ "reported_trait": {
1067
+ "type": "array",
1068
+ "items": {
1069
+ "type": "string"
1070
+ }
1071
+ },
1072
+ "accession_id": {
1073
+ "type": "string",
1074
+ "description": "Study accession ID"
1075
+ },
1076
+ "pubmed_id": {
1077
+ "type": "string",
1078
+ "description": "PubMed reference"
1079
+ },
1080
+ "first_author": {
1081
+ "type": "string",
1082
+ "description": "First author name"
1083
+ },
1084
+ "snp_effect_allele": {
1085
+ "type": "array",
1086
+ "items": {
1087
+ "type": "string"
1088
+ }
1089
+ },
1090
+ "snp_allele": {
1091
+ "type": "array",
1092
+ "items": {
1093
+ "type": "object",
1094
+ "properties": {
1095
+ "rs_id": {
1096
+ "type": "string"
1097
+ },
1098
+ "effect_allele": {
1099
+ "type": "string"
673
1100
  }
1101
+ }
674
1102
  }
1103
+ },
1104
+ "locations": {
1105
+ "type": "array",
1106
+ "items": {
1107
+ "type": "string"
1108
+ }
1109
+ },
1110
+ "mapped_genes": {
1111
+ "type": "array",
1112
+ "items": {
1113
+ "type": "string"
1114
+ }
1115
+ },
1116
+ "ci_lower": {
1117
+ "type": "number",
1118
+ "description": "Lower confidence interval"
1119
+ },
1120
+ "ci_upper": {
1121
+ "type": "number",
1122
+ "description": "Upper confidence interval"
1123
+ },
1124
+ "risk_frequency": {
1125
+ "type": "string",
1126
+ "description": "Risk allele frequency"
1127
+ },
1128
+ "range": {
1129
+ "type": "string",
1130
+ "description": "Effect size range"
1131
+ },
1132
+ "_links": {
1133
+ "type": "object",
1134
+ "description": "API links"
1135
+ }
675
1136
  }
676
- }
677
- },
678
- {
679
- "type": "GWASAssociationsForSNP",
680
- "name": "gwas_get_associations_for_snp",
681
- "description": "Get all associations for a specific SNP with optional sorting.",
682
- "parameter": {
683
- "type": "object",
684
- "properties": {
685
- "rs_id": {
686
- "type": "string",
687
- "description": "dbSNP rs identifier",
688
- "required": true
689
- },
690
- "sort": {
691
- "type": "string",
692
- "description": "Sort field (e.g., 'p_value', 'or_value')",
693
- "required": false
1137
+ }
1138
+ },
1139
+ "metadata": {
1140
+ "type": "object",
1141
+ "description": "Pagination and navigation metadata",
1142
+ "properties": {
1143
+ "pagination": {
1144
+ "type": "object",
1145
+ "properties": {
1146
+ "size": {
1147
+ "type": "integer"
694
1148
  },
695
- "direction": {
696
- "type": "string",
697
- "description": "Sort direction ('asc' or 'desc')",
698
- "required": false
1149
+ "totalElements": {
1150
+ "type": "integer"
699
1151
  },
700
- "size": {
701
- "type": "integer",
702
- "description": "Number of results to return per page",
703
- "required": false
1152
+ "totalPages": {
1153
+ "type": "integer"
704
1154
  },
705
- "page": {
706
- "type": "integer",
707
- "description": "Page number for pagination",
708
- "required": false
1155
+ "number": {
1156
+ "type": "integer"
709
1157
  }
1158
+ }
1159
+ },
1160
+ "links": {
1161
+ "type": "object",
1162
+ "description": "Navigation links"
710
1163
  }
1164
+ }
1165
+ }
1166
+ }
1167
+ }
1168
+ },
1169
+ {
1170
+ "type": "GWASAssociationsForSNP",
1171
+ "name": "gwas_get_associations_for_snp",
1172
+ "description": "Get all associations for a specific SNP with optional sorting.",
1173
+ "parameter": {
1174
+ "type": "object",
1175
+ "properties": {
1176
+ "rs_id": {
1177
+ "type": "string",
1178
+ "description": "dbSNP rs identifier"
711
1179
  },
712
- "label": [
713
- "GWAS",
714
- "Associations",
715
- "SNP",
716
- "Traits"
717
- ],
718
- "return_schema": {
1180
+ "sort": {
1181
+ "type": "string",
1182
+ "description": "Sort field (e.g., 'p_value', 'or_value')"
1183
+ },
1184
+ "direction": {
1185
+ "type": "string",
1186
+ "description": "Sort direction ('asc' or 'desc')"
1187
+ },
1188
+ "size": {
1189
+ "type": "integer",
1190
+ "description": "Number of results to return per page"
1191
+ },
1192
+ "page": {
1193
+ "type": "integer",
1194
+ "description": "Page number for pagination"
1195
+ }
1196
+ },
1197
+ "required": [
1198
+ "rs_id"
1199
+ ]
1200
+ },
1201
+ "label": [
1202
+ "GWAS",
1203
+ "Associations",
1204
+ "SNP",
1205
+ "Traits"
1206
+ ],
1207
+ "return_schema": {
1208
+ "type": "object",
1209
+ "description": "GWAS associations for SNP results with pagination metadata",
1210
+ "properties": {
1211
+ "data": {
1212
+ "type": "array",
1213
+ "description": "Array of GWAS association objects",
1214
+ "items": {
719
1215
  "type": "object",
720
- "description": "GWAS associations for SNP results with pagination metadata",
721
1216
  "properties": {
722
- "data": {
723
- "type": "array",
724
- "description": "Array of GWAS association objects",
725
- "items": {
726
- "type": "object",
727
- "properties": {
728
- "association_id": {"type": "integer", "description": "Unique association identifier"},
729
- "p_value": {"type": "number", "description": "Statistical p-value"},
730
- "beta": {"type": "string", "description": "Effect size (beta coefficient)"},
731
- "efo_traits": {
732
- "type": "array",
733
- "items": {
734
- "type": "object",
735
- "properties": {
736
- "efo_id": {"type": "string"},
737
- "efo_trait": {"type": "string"}
738
- }
739
- }
740
- },
741
- "reported_trait": {"type": "array", "items": {"type": "string"}},
742
- "accession_id": {"type": "string", "description": "Study accession ID"},
743
- "pubmed_id": {"type": "string", "description": "PubMed reference"},
744
- "first_author": {"type": "string", "description": "First author name"},
745
- "snp_effect_allele": {"type": "array", "items": {"type": "string"}},
746
- "snp_allele": {
747
- "type": "array",
748
- "items": {
749
- "type": "object",
750
- "properties": {
751
- "rs_id": {"type": "string"},
752
- "effect_allele": {"type": "string"}
753
- }
754
- }
755
- },
756
- "locations": {"type": "array", "items": {"type": "string"}},
757
- "mapped_genes": {"type": "array", "items": {"type": "string"}},
758
- "ci_lower": {"type": "number", "description": "Lower confidence interval"},
759
- "ci_upper": {"type": "number", "description": "Upper confidence interval"},
760
- "risk_frequency": {"type": "string", "description": "Risk allele frequency"},
761
- "range": {"type": "string", "description": "Effect size range"},
762
- "_links": {"type": "object", "description": "API links"}
763
- }
1217
+ "association_id": {
1218
+ "type": "integer",
1219
+ "description": "Unique association identifier"
1220
+ },
1221
+ "p_value": {
1222
+ "type": "number",
1223
+ "description": "Statistical p-value"
1224
+ },
1225
+ "beta": {
1226
+ "type": "string",
1227
+ "description": "Effect size (beta coefficient)"
1228
+ },
1229
+ "efo_traits": {
1230
+ "type": "array",
1231
+ "items": {
1232
+ "type": "object",
1233
+ "properties": {
1234
+ "efo_id": {
1235
+ "type": "string"
1236
+ },
1237
+ "efo_trait": {
1238
+ "type": "string"
764
1239
  }
765
- },
766
- "metadata": {
767
- "type": "object",
768
- "description": "Pagination and navigation metadata",
769
- "properties": {
770
- "pagination": {
771
- "type": "object",
772
- "properties": {
773
- "size": {"type": "integer"},
774
- "totalElements": {"type": "integer"},
775
- "totalPages": {"type": "integer"},
776
- "number": {"type": "integer"}
777
- }
778
- },
779
- "links": {"type": "object", "description": "Navigation links"}
1240
+ }
1241
+ }
1242
+ },
1243
+ "reported_trait": {
1244
+ "type": "array",
1245
+ "items": {
1246
+ "type": "string"
1247
+ }
1248
+ },
1249
+ "accession_id": {
1250
+ "type": "string",
1251
+ "description": "Study accession ID"
1252
+ },
1253
+ "pubmed_id": {
1254
+ "type": "string",
1255
+ "description": "PubMed reference"
1256
+ },
1257
+ "first_author": {
1258
+ "type": "string",
1259
+ "description": "First author name"
1260
+ },
1261
+ "snp_effect_allele": {
1262
+ "type": "array",
1263
+ "items": {
1264
+ "type": "string"
1265
+ }
1266
+ },
1267
+ "snp_allele": {
1268
+ "type": "array",
1269
+ "items": {
1270
+ "type": "object",
1271
+ "properties": {
1272
+ "rs_id": {
1273
+ "type": "string"
1274
+ },
1275
+ "effect_allele": {
1276
+ "type": "string"
780
1277
  }
1278
+ }
1279
+ }
1280
+ },
1281
+ "locations": {
1282
+ "type": "array",
1283
+ "items": {
1284
+ "type": "string"
1285
+ }
1286
+ },
1287
+ "mapped_genes": {
1288
+ "type": "array",
1289
+ "items": {
1290
+ "type": "string"
781
1291
  }
1292
+ },
1293
+ "ci_lower": {
1294
+ "type": "number",
1295
+ "description": "Lower confidence interval"
1296
+ },
1297
+ "ci_upper": {
1298
+ "type": "number",
1299
+ "description": "Upper confidence interval"
1300
+ },
1301
+ "risk_frequency": {
1302
+ "type": "string",
1303
+ "description": "Risk allele frequency"
1304
+ },
1305
+ "range": {
1306
+ "type": "string",
1307
+ "description": "Effect size range"
1308
+ },
1309
+ "_links": {
1310
+ "type": "object",
1311
+ "description": "API links"
1312
+ }
782
1313
  }
783
- }
784
- },
785
- {
786
- "type": "GWASStudiesForTrait",
787
- "name": "gwas_get_studies_for_trait",
788
- "description": "Get studies for a specific trait with optional filters for cohort, GxE interactions, and summary statistics.",
789
- "parameter": {
790
- "type": "object",
791
- "properties": {
792
- "efo_trait": {
793
- "type": "string",
794
- "description": "EFO trait identifier or name",
795
- "required": false
796
- },
797
- "disease_trait": {
798
- "type": "string",
799
- "description": "Disease trait name",
800
- "required": false
801
- },
802
- "cohort": {
803
- "type": "string",
804
- "description": "Cohort name (e.g., 'UKB' for UK Biobank)",
805
- "required": false
1314
+ }
1315
+ },
1316
+ "metadata": {
1317
+ "type": "object",
1318
+ "description": "Pagination and navigation metadata",
1319
+ "properties": {
1320
+ "pagination": {
1321
+ "type": "object",
1322
+ "properties": {
1323
+ "size": {
1324
+ "type": "integer"
806
1325
  },
807
- "gxe": {
808
- "type": "boolean",
809
- "description": "Filter for Gene-by-Environment interaction studies",
810
- "required": false
1326
+ "totalElements": {
1327
+ "type": "integer"
811
1328
  },
812
- "full_pvalue_set": {
813
- "type": "boolean",
814
- "description": "Filter for studies with full summary statistics",
815
- "required": false
1329
+ "totalPages": {
1330
+ "type": "integer"
816
1331
  },
817
- "size": {
818
- "type": "integer",
819
- "description": "Number of results to return per page",
820
- "required": false
821
- },
822
- "page": {
823
- "type": "integer",
824
- "description": "Page number for pagination",
825
- "required": false
1332
+ "number": {
1333
+ "type": "integer"
826
1334
  }
1335
+ }
1336
+ },
1337
+ "links": {
1338
+ "type": "object",
1339
+ "description": "Navigation links"
827
1340
  }
1341
+ }
1342
+ }
1343
+ }
1344
+ }
1345
+ },
1346
+ {
1347
+ "type": "GWASStudiesForTrait",
1348
+ "name": "gwas_get_studies_for_trait",
1349
+ "description": "Get studies for a specific trait with optional filters for cohort, GxE interactions, and summary statistics.",
1350
+ "parameter": {
1351
+ "type": "object",
1352
+ "properties": {
1353
+ "efo_trait": {
1354
+ "type": "string",
1355
+ "description": "EFO trait identifier or name"
1356
+ },
1357
+ "disease_trait": {
1358
+ "type": "string",
1359
+ "description": "Disease trait name"
828
1360
  },
829
- "label": [
830
- "GWAS",
831
- "Studies",
832
- "Trait",
833
- "Research"
834
- ],
835
- "return_schema": {
1361
+ "cohort": {
1362
+ "type": "string",
1363
+ "description": "Cohort name (e.g., 'UKB' for UK Biobank)"
1364
+ },
1365
+ "gxe": {
1366
+ "type": "boolean",
1367
+ "description": "Filter for Gene-by-Environment interaction studies"
1368
+ },
1369
+ "full_pvalue_set": {
1370
+ "type": "boolean",
1371
+ "description": "Filter for studies with full summary statistics"
1372
+ },
1373
+ "size": {
1374
+ "type": "integer",
1375
+ "description": "Number of results to return per page"
1376
+ },
1377
+ "page": {
1378
+ "type": "integer",
1379
+ "description": "Page number for pagination"
1380
+ }
1381
+ },
1382
+ "required": []
1383
+ },
1384
+ "label": [
1385
+ "GWAS",
1386
+ "Studies",
1387
+ "Trait",
1388
+ "Research"
1389
+ ],
1390
+ "return_schema": {
1391
+ "type": "object",
1392
+ "description": "GWAS studies for trait results with pagination metadata",
1393
+ "properties": {
1394
+ "data": {
1395
+ "type": "array",
1396
+ "description": "Array of GWAS study objects",
1397
+ "items": {
836
1398
  "type": "object",
837
- "description": "GWAS studies for trait results with pagination metadata",
838
1399
  "properties": {
839
- "data": {
840
- "type": "array",
841
- "description": "Array of GWAS study objects",
842
- "items": {
843
- "type": "object",
844
- "properties": {
845
- "accession_id": {"type": "string", "description": "Study accession identifier"},
846
- "disease_trait": {"type": "string", "description": "Disease or trait name"},
847
- "efo_traits": {
848
- "type": "array",
849
- "items": {
850
- "type": "object",
851
- "properties": {
852
- "efo_id": {"type": "string"},
853
- "efo_trait": {"type": "string"}
854
- }
855
- }
856
- },
857
- "initial_sample_size": {"type": "string", "description": "Initial sample size description"},
858
- "replication_sample_size": {"type": "string", "description": "Replication sample size"},
859
- "discovery_ancestry": {"type": "array", "items": {"type": "string"}},
860
- "replication_ancestry": {"type": "array", "items": {"type": "string"}},
861
- "cohort": {"type": "array", "items": {"type": "string"}},
862
- "genotyping_technologies": {"type": "array", "items": {"type": "string"}},
863
- "platforms": {"type": "string", "description": "Genotyping platforms used"},
864
- "snp_count": {"type": "integer", "description": "Number of SNPs analyzed"},
865
- "imputed": {"type": "boolean", "description": "Whether data was imputed"},
866
- "pooled": {"type": "boolean", "description": "Whether data was pooled"},
867
- "gxe": {"type": "boolean", "description": "Gene-environment interaction study"},
868
- "gxg": {"type": "boolean", "description": "Gene-gene interaction study"},
869
- "full_summary_stats_available": {"type": "boolean", "description": "Full summary statistics available"},
870
- "full_summary_stats": {"type": "string", "description": "URL to full summary statistics"},
871
- "pubmed_id": {"type": "string", "description": "PubMed reference"},
872
- "terms_of_license": {"type": "string", "description": "Data usage license"},
873
- "array_manufacturer": {"type": "array", "items": {"type": "string"}},
874
- "_links": {"type": "object", "description": "API links"}
875
- }
876
- }
877
- },
878
- "metadata": {
879
- "type": "object",
880
- "description": "Pagination and navigation metadata",
881
- "properties": {
882
- "pagination": {
883
- "type": "object",
884
- "properties": {
885
- "size": {"type": "integer"},
886
- "totalElements": {"type": "integer"},
887
- "totalPages": {"type": "integer"},
888
- "number": {"type": "integer"}
889
- }
890
- },
891
- "links": {"type": "object", "description": "Navigation links"}
1400
+ "accession_id": {
1401
+ "type": "string",
1402
+ "description": "Study accession identifier"
1403
+ },
1404
+ "disease_trait": {
1405
+ "type": "string",
1406
+ "description": "Disease or trait name"
1407
+ },
1408
+ "efo_traits": {
1409
+ "type": "array",
1410
+ "items": {
1411
+ "type": "object",
1412
+ "properties": {
1413
+ "efo_id": {
1414
+ "type": "string"
1415
+ },
1416
+ "efo_trait": {
1417
+ "type": "string"
892
1418
  }
1419
+ }
1420
+ }
1421
+ },
1422
+ "initial_sample_size": {
1423
+ "type": "string",
1424
+ "description": "Initial sample size description"
1425
+ },
1426
+ "replication_sample_size": {
1427
+ "type": "string",
1428
+ "description": "Replication sample size"
1429
+ },
1430
+ "discovery_ancestry": {
1431
+ "type": "array",
1432
+ "items": {
1433
+ "type": "string"
1434
+ }
1435
+ },
1436
+ "replication_ancestry": {
1437
+ "type": "array",
1438
+ "items": {
1439
+ "type": "string"
1440
+ }
1441
+ },
1442
+ "cohort": {
1443
+ "type": "array",
1444
+ "items": {
1445
+ "type": "string"
893
1446
  }
1447
+ },
1448
+ "genotyping_technologies": {
1449
+ "type": "array",
1450
+ "items": {
1451
+ "type": "string"
1452
+ }
1453
+ },
1454
+ "platforms": {
1455
+ "type": "string",
1456
+ "description": "Genotyping platforms used"
1457
+ },
1458
+ "snp_count": {
1459
+ "type": "integer",
1460
+ "description": "Number of SNPs analyzed"
1461
+ },
1462
+ "imputed": {
1463
+ "type": "boolean",
1464
+ "description": "Whether data was imputed"
1465
+ },
1466
+ "pooled": {
1467
+ "type": "boolean",
1468
+ "description": "Whether data was pooled"
1469
+ },
1470
+ "gxe": {
1471
+ "type": "boolean",
1472
+ "description": "Gene-environment interaction study"
1473
+ },
1474
+ "gxg": {
1475
+ "type": "boolean",
1476
+ "description": "Gene-gene interaction study"
1477
+ },
1478
+ "full_summary_stats_available": {
1479
+ "type": "boolean",
1480
+ "description": "Full summary statistics available"
1481
+ },
1482
+ "full_summary_stats": {
1483
+ "type": "string",
1484
+ "description": "URL to full summary statistics"
1485
+ },
1486
+ "pubmed_id": {
1487
+ "type": "string",
1488
+ "description": "PubMed reference"
1489
+ },
1490
+ "terms_of_license": {
1491
+ "type": "string",
1492
+ "description": "Data usage license"
1493
+ },
1494
+ "array_manufacturer": {
1495
+ "type": "array",
1496
+ "items": {
1497
+ "type": "string"
1498
+ }
1499
+ },
1500
+ "_links": {
1501
+ "type": "object",
1502
+ "description": "API links"
1503
+ }
894
1504
  }
895
- }
896
- },
897
- {
898
- "type": "GWASSNPsForGene",
899
- "name": "gwas_get_snps_for_gene",
900
- "description": "Get all SNPs mapped to a specific gene.",
901
- "parameter": {
902
- "type": "object",
903
- "properties": {
904
- "mapped_gene": {
905
- "type": "string",
906
- "description": "Gene name or symbol",
907
- "required": true
908
- },
1505
+ }
1506
+ },
1507
+ "metadata": {
1508
+ "type": "object",
1509
+ "description": "Pagination and navigation metadata",
1510
+ "properties": {
1511
+ "pagination": {
1512
+ "type": "object",
1513
+ "properties": {
909
1514
  "size": {
910
- "type": "integer",
911
- "description": "Number of results to return per page",
912
- "required": false
1515
+ "type": "integer"
913
1516
  },
914
- "page": {
915
- "type": "integer",
916
- "description": "Page number for pagination",
917
- "required": false
1517
+ "totalElements": {
1518
+ "type": "integer"
1519
+ },
1520
+ "totalPages": {
1521
+ "type": "integer"
1522
+ },
1523
+ "number": {
1524
+ "type": "integer"
918
1525
  }
1526
+ }
1527
+ },
1528
+ "links": {
1529
+ "type": "object",
1530
+ "description": "Navigation links"
919
1531
  }
1532
+ }
1533
+ }
1534
+ }
1535
+ }
1536
+ },
1537
+ {
1538
+ "type": "GWASSNPsForGene",
1539
+ "name": "gwas_get_snps_for_gene",
1540
+ "description": "Get all SNPs mapped to a specific gene.",
1541
+ "parameter": {
1542
+ "type": "object",
1543
+ "properties": {
1544
+ "mapped_gene": {
1545
+ "type": "string",
1546
+ "description": "Gene name or symbol"
920
1547
  },
921
- "label": [
922
- "GWAS",
923
- "SNPs",
924
- "Gene",
925
- "Mapping"
926
- ],
927
- "return_schema": {
1548
+ "size": {
1549
+ "type": "integer",
1550
+ "description": "Number of results to return per page"
1551
+ },
1552
+ "page": {
1553
+ "type": "integer",
1554
+ "description": "Page number for pagination"
1555
+ }
1556
+ },
1557
+ "required": [
1558
+ "mapped_gene"
1559
+ ]
1560
+ },
1561
+ "label": [
1562
+ "GWAS",
1563
+ "SNPs",
1564
+ "Gene",
1565
+ "Mapping"
1566
+ ],
1567
+ "return_schema": {
1568
+ "type": "object",
1569
+ "description": "GWAS SNPs for gene results with pagination metadata",
1570
+ "properties": {
1571
+ "data": {
1572
+ "type": "array",
1573
+ "description": "Array of SNP objects",
1574
+ "items": {
928
1575
  "type": "object",
929
- "description": "GWAS SNPs for gene results with pagination metadata",
930
1576
  "properties": {
931
- "data": {
932
- "type": "array",
933
- "description": "Array of SNP objects",
934
- "items": {
935
- "type": "object",
936
- "properties": {
937
- "rs_id": {"type": "string", "description": "dbSNP rs identifier"},
938
- "merged": {"type": "integer", "description": "Merged status"},
939
- "functional_class": {"type": "string", "description": "Functional classification"},
940
- "last_update_date": {"type": "string", "description": "Last update timestamp"},
941
- "locations": {
942
- "type": "array",
943
- "items": {
944
- "type": "object",
945
- "properties": {
946
- "chromosome_name": {"type": "string"},
947
- "chromosome_position": {"type": "integer"},
948
- "region": {
949
- "type": "object",
950
- "properties": {
951
- "name": {"type": "string"}
952
- }
953
- }
954
- }
955
- }
956
- },
957
- "alleles": {"type": "string", "description": "Allele information"},
958
- "most_severe_consequence": {"type": "string", "description": "Most severe functional consequence"},
959
- "mapped_genes": {"type": "array", "items": {"type": "string"}},
960
- "maf": {"type": "number", "description": "Minor allele frequency"},
961
- "minor_allele": {"type": "string", "description": "Minor allele"},
962
- "_links": {"type": "object", "description": "API links"}
1577
+ "rs_id": {
1578
+ "type": "string",
1579
+ "description": "dbSNP rs identifier"
1580
+ },
1581
+ "merged": {
1582
+ "type": "integer",
1583
+ "description": "Merged status"
1584
+ },
1585
+ "functional_class": {
1586
+ "type": "string",
1587
+ "description": "Functional classification"
1588
+ },
1589
+ "last_update_date": {
1590
+ "type": "string",
1591
+ "description": "Last update timestamp"
1592
+ },
1593
+ "locations": {
1594
+ "type": "array",
1595
+ "items": {
1596
+ "type": "object",
1597
+ "properties": {
1598
+ "chromosome_name": {
1599
+ "type": "string"
1600
+ },
1601
+ "chromosome_position": {
1602
+ "type": "integer"
1603
+ },
1604
+ "region": {
1605
+ "type": "object",
1606
+ "properties": {
1607
+ "name": {
1608
+ "type": "string"
963
1609
  }
1610
+ }
964
1611
  }
965
- },
966
- "metadata": {
967
- "type": "object",
968
- "description": "Pagination and navigation metadata",
969
- "properties": {
970
- "pagination": {
971
- "type": "object",
972
- "properties": {
973
- "size": {"type": "integer"},
974
- "totalElements": {"type": "integer"},
975
- "totalPages": {"type": "integer"},
976
- "number": {"type": "integer"}
977
- }
978
- },
979
- "links": {"type": "object", "description": "Navigation links"}
980
- }
1612
+ }
981
1613
  }
1614
+ },
1615
+ "alleles": {
1616
+ "type": "string",
1617
+ "description": "Allele information"
1618
+ },
1619
+ "most_severe_consequence": {
1620
+ "type": "string",
1621
+ "description": "Most severe functional consequence"
1622
+ },
1623
+ "mapped_genes": {
1624
+ "type": "array",
1625
+ "items": {
1626
+ "type": "string"
1627
+ }
1628
+ },
1629
+ "maf": {
1630
+ "type": "number",
1631
+ "description": "Minor allele frequency"
1632
+ },
1633
+ "minor_allele": {
1634
+ "type": "string",
1635
+ "description": "Minor allele"
1636
+ },
1637
+ "_links": {
1638
+ "type": "object",
1639
+ "description": "API links"
1640
+ }
982
1641
  }
983
- }
984
- },
985
- {
986
- "type": "GWASAssociationsForStudy",
987
- "name": "gwas_get_associations_for_study",
988
- "description": "Get all associations for a specific study, sorted by p-value.",
989
- "parameter": {
990
- "type": "object",
991
- "properties": {
992
- "accession_id": {
993
- "type": "string",
994
- "description": "Study accession identifier",
995
- "required": true
996
- },
1642
+ }
1643
+ },
1644
+ "metadata": {
1645
+ "type": "object",
1646
+ "description": "Pagination and navigation metadata",
1647
+ "properties": {
1648
+ "pagination": {
1649
+ "type": "object",
1650
+ "properties": {
997
1651
  "size": {
998
- "type": "integer",
999
- "description": "Number of results to return per page",
1000
- "required": false
1652
+ "type": "integer"
1653
+ },
1654
+ "totalElements": {
1655
+ "type": "integer"
1001
1656
  },
1002
- "page": {
1003
- "type": "integer",
1004
- "description": "Page number for pagination",
1005
- "required": false
1657
+ "totalPages": {
1658
+ "type": "integer"
1659
+ },
1660
+ "number": {
1661
+ "type": "integer"
1006
1662
  }
1663
+ }
1664
+ },
1665
+ "links": {
1666
+ "type": "object",
1667
+ "description": "Navigation links"
1007
1668
  }
1669
+ }
1670
+ }
1671
+ }
1672
+ }
1673
+ },
1674
+ {
1675
+ "type": "GWASAssociationsForStudy",
1676
+ "name": "gwas_get_associations_for_study",
1677
+ "description": "Get all associations for a specific study, sorted by p-value.",
1678
+ "parameter": {
1679
+ "type": "object",
1680
+ "properties": {
1681
+ "accession_id": {
1682
+ "type": "string",
1683
+ "description": "Study accession identifier"
1684
+ },
1685
+ "size": {
1686
+ "type": "integer",
1687
+ "description": "Number of results to return per page"
1008
1688
  },
1009
- "label": [
1010
- "GWAS",
1011
- "Associations",
1012
- "Study",
1013
- "Results"
1014
- ],
1015
- "return_schema": {
1689
+ "page": {
1690
+ "type": "integer",
1691
+ "description": "Page number for pagination"
1692
+ }
1693
+ },
1694
+ "required": [
1695
+ "accession_id"
1696
+ ]
1697
+ },
1698
+ "label": [
1699
+ "GWAS",
1700
+ "Associations",
1701
+ "Study",
1702
+ "Results"
1703
+ ],
1704
+ "return_schema": {
1705
+ "type": "object",
1706
+ "description": "GWAS associations for study results with pagination metadata",
1707
+ "properties": {
1708
+ "data": {
1709
+ "type": "array",
1710
+ "description": "Array of GWAS association objects",
1711
+ "items": {
1016
1712
  "type": "object",
1017
- "description": "GWAS associations for study results with pagination metadata",
1018
1713
  "properties": {
1019
- "data": {
1020
- "type": "array",
1021
- "description": "Array of GWAS association objects",
1022
- "items": {
1023
- "type": "object",
1024
- "properties": {
1025
- "association_id": {"type": "integer", "description": "Unique association identifier"},
1026
- "p_value": {"type": "number", "description": "Statistical p-value"},
1027
- "beta": {"type": "string", "description": "Effect size (beta coefficient)"},
1028
- "efo_traits": {
1029
- "type": "array",
1030
- "items": {
1031
- "type": "object",
1032
- "properties": {
1033
- "efo_id": {"type": "string"},
1034
- "efo_trait": {"type": "string"}
1035
- }
1036
- }
1037
- },
1038
- "reported_trait": {"type": "array", "items": {"type": "string"}},
1039
- "accession_id": {"type": "string", "description": "Study accession ID"},
1040
- "pubmed_id": {"type": "string", "description": "PubMed reference"},
1041
- "first_author": {"type": "string", "description": "First author name"},
1042
- "snp_effect_allele": {"type": "array", "items": {"type": "string"}},
1043
- "snp_allele": {
1044
- "type": "array",
1045
- "items": {
1046
- "type": "object",
1047
- "properties": {
1048
- "rs_id": {"type": "string"},
1049
- "effect_allele": {"type": "string"}
1050
- }
1051
- }
1052
- },
1053
- "locations": {"type": "array", "items": {"type": "string"}},
1054
- "mapped_genes": {"type": "array", "items": {"type": "string"}},
1055
- "ci_lower": {"type": "number", "description": "Lower confidence interval"},
1056
- "ci_upper": {"type": "number", "description": "Upper confidence interval"},
1057
- "risk_frequency": {"type": "string", "description": "Risk allele frequency"},
1058
- "range": {"type": "string", "description": "Effect size range"},
1059
- "_links": {"type": "object", "description": "API links"}
1060
- }
1714
+ "association_id": {
1715
+ "type": "integer",
1716
+ "description": "Unique association identifier"
1717
+ },
1718
+ "p_value": {
1719
+ "type": "number",
1720
+ "description": "Statistical p-value"
1721
+ },
1722
+ "beta": {
1723
+ "type": "string",
1724
+ "description": "Effect size (beta coefficient)"
1725
+ },
1726
+ "efo_traits": {
1727
+ "type": "array",
1728
+ "items": {
1729
+ "type": "object",
1730
+ "properties": {
1731
+ "efo_id": {
1732
+ "type": "string"
1733
+ },
1734
+ "efo_trait": {
1735
+ "type": "string"
1061
1736
  }
1062
- },
1063
- "metadata": {
1064
- "type": "object",
1065
- "description": "Pagination and navigation metadata",
1066
- "properties": {
1067
- "pagination": {
1068
- "type": "object",
1069
- "properties": {
1070
- "size": {"type": "integer"},
1071
- "totalElements": {"type": "integer"},
1072
- "totalPages": {"type": "integer"},
1073
- "number": {"type": "integer"}
1074
- }
1075
- },
1076
- "links": {"type": "object", "description": "Navigation links"}
1737
+ }
1738
+ }
1739
+ },
1740
+ "reported_trait": {
1741
+ "type": "array",
1742
+ "items": {
1743
+ "type": "string"
1744
+ }
1745
+ },
1746
+ "accession_id": {
1747
+ "type": "string",
1748
+ "description": "Study accession ID"
1749
+ },
1750
+ "pubmed_id": {
1751
+ "type": "string",
1752
+ "description": "PubMed reference"
1753
+ },
1754
+ "first_author": {
1755
+ "type": "string",
1756
+ "description": "First author name"
1757
+ },
1758
+ "snp_effect_allele": {
1759
+ "type": "array",
1760
+ "items": {
1761
+ "type": "string"
1762
+ }
1763
+ },
1764
+ "snp_allele": {
1765
+ "type": "array",
1766
+ "items": {
1767
+ "type": "object",
1768
+ "properties": {
1769
+ "rs_id": {
1770
+ "type": "string"
1771
+ },
1772
+ "effect_allele": {
1773
+ "type": "string"
1077
1774
  }
1775
+ }
1776
+ }
1777
+ },
1778
+ "locations": {
1779
+ "type": "array",
1780
+ "items": {
1781
+ "type": "string"
1782
+ }
1783
+ },
1784
+ "mapped_genes": {
1785
+ "type": "array",
1786
+ "items": {
1787
+ "type": "string"
1788
+ }
1789
+ },
1790
+ "ci_lower": {
1791
+ "type": "number",
1792
+ "description": "Lower confidence interval"
1793
+ },
1794
+ "ci_upper": {
1795
+ "type": "number",
1796
+ "description": "Upper confidence interval"
1797
+ },
1798
+ "risk_frequency": {
1799
+ "type": "string",
1800
+ "description": "Risk allele frequency"
1801
+ },
1802
+ "range": {
1803
+ "type": "string",
1804
+ "description": "Effect size range"
1805
+ },
1806
+ "_links": {
1807
+ "type": "object",
1808
+ "description": "API links"
1809
+ }
1810
+ }
1811
+ }
1812
+ },
1813
+ "metadata": {
1814
+ "type": "object",
1815
+ "description": "Pagination and navigation metadata",
1816
+ "properties": {
1817
+ "pagination": {
1818
+ "type": "object",
1819
+ "properties": {
1820
+ "size": {
1821
+ "type": "integer"
1822
+ },
1823
+ "totalElements": {
1824
+ "type": "integer"
1825
+ },
1826
+ "totalPages": {
1827
+ "type": "integer"
1828
+ },
1829
+ "number": {
1830
+ "type": "integer"
1078
1831
  }
1832
+ }
1833
+ },
1834
+ "links": {
1835
+ "type": "object",
1836
+ "description": "Navigation links"
1079
1837
  }
1838
+ }
1080
1839
  }
1840
+ }
1081
1841
  }
1842
+ }
1082
1843
  ]