tooluniverse 0.1.4__py3-none-any.whl → 1.0.0__py3-none-any.whl

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Files changed (187) hide show
  1. tooluniverse/__init__.py +340 -4
  2. tooluniverse/admetai_tool.py +84 -0
  3. tooluniverse/agentic_tool.py +563 -0
  4. tooluniverse/alphafold_tool.py +96 -0
  5. tooluniverse/base_tool.py +129 -6
  6. tooluniverse/boltz_tool.py +207 -0
  7. tooluniverse/chem_tool.py +192 -0
  8. tooluniverse/compose_scripts/__init__.py +1 -0
  9. tooluniverse/compose_scripts/biomarker_discovery.py +293 -0
  10. tooluniverse/compose_scripts/comprehensive_drug_discovery.py +186 -0
  11. tooluniverse/compose_scripts/drug_safety_analyzer.py +89 -0
  12. tooluniverse/compose_scripts/literature_tool.py +34 -0
  13. tooluniverse/compose_scripts/output_summarizer.py +279 -0
  14. tooluniverse/compose_scripts/tool_description_optimizer.py +681 -0
  15. tooluniverse/compose_scripts/tool_discover.py +705 -0
  16. tooluniverse/compose_scripts/tool_graph_composer.py +448 -0
  17. tooluniverse/compose_tool.py +371 -0
  18. tooluniverse/ctg_tool.py +1002 -0
  19. tooluniverse/custom_tool.py +81 -0
  20. tooluniverse/dailymed_tool.py +108 -0
  21. tooluniverse/data/admetai_tools.json +155 -0
  22. tooluniverse/data/agentic_tools.json +1156 -0
  23. tooluniverse/data/alphafold_tools.json +87 -0
  24. tooluniverse/data/boltz_tools.json +9 -0
  25. tooluniverse/data/chembl_tools.json +16 -0
  26. tooluniverse/data/clait_tools.json +108 -0
  27. tooluniverse/data/clinicaltrials_gov_tools.json +326 -0
  28. tooluniverse/data/compose_tools.json +202 -0
  29. tooluniverse/data/dailymed_tools.json +70 -0
  30. tooluniverse/data/dataset_tools.json +646 -0
  31. tooluniverse/data/disease_target_score_tools.json +712 -0
  32. tooluniverse/data/efo_tools.json +17 -0
  33. tooluniverse/data/embedding_tools.json +319 -0
  34. tooluniverse/data/enrichr_tools.json +31 -0
  35. tooluniverse/data/europe_pmc_tools.json +22 -0
  36. tooluniverse/data/expert_feedback_tools.json +10 -0
  37. tooluniverse/data/fda_drug_adverse_event_tools.json +491 -0
  38. tooluniverse/data/fda_drug_labeling_tools.json +544 -168
  39. tooluniverse/data/fda_drugs_with_brand_generic_names_for_tool.py +76929 -148860
  40. tooluniverse/data/finder_tools.json +209 -0
  41. tooluniverse/data/gene_ontology_tools.json +113 -0
  42. tooluniverse/data/gwas_tools.json +1082 -0
  43. tooluniverse/data/hpa_tools.json +333 -0
  44. tooluniverse/data/humanbase_tools.json +47 -0
  45. tooluniverse/data/idmap_tools.json +74 -0
  46. tooluniverse/data/mcp_client_tools_example.json +113 -0
  47. tooluniverse/data/mcpautoloadertool_defaults.json +28 -0
  48. tooluniverse/data/medlineplus_tools.json +141 -0
  49. tooluniverse/data/monarch_tools.json +1 -1
  50. tooluniverse/data/openalex_tools.json +36 -0
  51. tooluniverse/data/opentarget_tools.json +82 -58
  52. tooluniverse/data/output_summarization_tools.json +101 -0
  53. tooluniverse/data/packages/bioinformatics_core_tools.json +1756 -0
  54. tooluniverse/data/packages/categorized_tools.txt +206 -0
  55. tooluniverse/data/packages/cheminformatics_tools.json +347 -0
  56. tooluniverse/data/packages/earth_sciences_tools.json +74 -0
  57. tooluniverse/data/packages/genomics_tools.json +776 -0
  58. tooluniverse/data/packages/image_processing_tools.json +38 -0
  59. tooluniverse/data/packages/machine_learning_tools.json +789 -0
  60. tooluniverse/data/packages/neuroscience_tools.json +62 -0
  61. tooluniverse/data/packages/original_tools.txt +0 -0
  62. tooluniverse/data/packages/physics_astronomy_tools.json +62 -0
  63. tooluniverse/data/packages/scientific_computing_tools.json +560 -0
  64. tooluniverse/data/packages/single_cell_tools.json +453 -0
  65. tooluniverse/data/packages/software_tools.json +4954 -0
  66. tooluniverse/data/packages/structural_biology_tools.json +396 -0
  67. tooluniverse/data/packages/visualization_tools.json +399 -0
  68. tooluniverse/data/pubchem_tools.json +215 -0
  69. tooluniverse/data/pubtator_tools.json +68 -0
  70. tooluniverse/data/rcsb_pdb_tools.json +1332 -0
  71. tooluniverse/data/reactome_tools.json +19 -0
  72. tooluniverse/data/semantic_scholar_tools.json +26 -0
  73. tooluniverse/data/special_tools.json +2 -25
  74. tooluniverse/data/tool_composition_tools.json +88 -0
  75. tooluniverse/data/toolfinderkeyword_defaults.json +34 -0
  76. tooluniverse/data/txagent_client_tools.json +9 -0
  77. tooluniverse/data/uniprot_tools.json +211 -0
  78. tooluniverse/data/url_fetch_tools.json +94 -0
  79. tooluniverse/data/uspto_downloader_tools.json +9 -0
  80. tooluniverse/data/uspto_tools.json +811 -0
  81. tooluniverse/data/xml_tools.json +3275 -0
  82. tooluniverse/dataset_tool.py +296 -0
  83. tooluniverse/default_config.py +165 -0
  84. tooluniverse/efo_tool.py +42 -0
  85. tooluniverse/embedding_database.py +630 -0
  86. tooluniverse/embedding_sync.py +396 -0
  87. tooluniverse/enrichr_tool.py +266 -0
  88. tooluniverse/europe_pmc_tool.py +52 -0
  89. tooluniverse/execute_function.py +1775 -95
  90. tooluniverse/extended_hooks.py +444 -0
  91. tooluniverse/gene_ontology_tool.py +194 -0
  92. tooluniverse/graphql_tool.py +158 -36
  93. tooluniverse/gwas_tool.py +358 -0
  94. tooluniverse/hpa_tool.py +1645 -0
  95. tooluniverse/humanbase_tool.py +389 -0
  96. tooluniverse/logging_config.py +254 -0
  97. tooluniverse/mcp_client_tool.py +764 -0
  98. tooluniverse/mcp_integration.py +413 -0
  99. tooluniverse/mcp_tool_registry.py +925 -0
  100. tooluniverse/medlineplus_tool.py +337 -0
  101. tooluniverse/openalex_tool.py +228 -0
  102. tooluniverse/openfda_adv_tool.py +283 -0
  103. tooluniverse/openfda_tool.py +393 -160
  104. tooluniverse/output_hook.py +1122 -0
  105. tooluniverse/package_tool.py +195 -0
  106. tooluniverse/pubchem_tool.py +158 -0
  107. tooluniverse/pubtator_tool.py +168 -0
  108. tooluniverse/rcsb_pdb_tool.py +38 -0
  109. tooluniverse/reactome_tool.py +108 -0
  110. tooluniverse/remote/boltz/boltz_mcp_server.py +50 -0
  111. tooluniverse/remote/depmap_24q2/depmap_24q2_mcp_tool.py +442 -0
  112. tooluniverse/remote/expert_feedback/human_expert_mcp_tools.py +2013 -0
  113. tooluniverse/remote/expert_feedback/simple_test.py +23 -0
  114. tooluniverse/remote/expert_feedback/start_web_interface.py +188 -0
  115. tooluniverse/remote/expert_feedback/web_only_interface.py +0 -0
  116. tooluniverse/remote/expert_feedback_mcp/human_expert_mcp_server.py +1611 -0
  117. tooluniverse/remote/expert_feedback_mcp/simple_test.py +34 -0
  118. tooluniverse/remote/expert_feedback_mcp/start_web_interface.py +91 -0
  119. tooluniverse/remote/immune_compass/compass_tool.py +327 -0
  120. tooluniverse/remote/pinnacle/pinnacle_tool.py +328 -0
  121. tooluniverse/remote/transcriptformer/transcriptformer_tool.py +586 -0
  122. tooluniverse/remote/uspto_downloader/uspto_downloader_mcp_server.py +61 -0
  123. tooluniverse/remote/uspto_downloader/uspto_downloader_tool.py +120 -0
  124. tooluniverse/remote_tool.py +99 -0
  125. tooluniverse/restful_tool.py +53 -30
  126. tooluniverse/scripts/generate_tool_graph.py +408 -0
  127. tooluniverse/scripts/visualize_tool_graph.py +829 -0
  128. tooluniverse/semantic_scholar_tool.py +62 -0
  129. tooluniverse/smcp.py +2452 -0
  130. tooluniverse/smcp_server.py +975 -0
  131. tooluniverse/test/mcp_server_test.py +0 -0
  132. tooluniverse/test/test_admetai_tool.py +370 -0
  133. tooluniverse/test/test_agentic_tool.py +129 -0
  134. tooluniverse/test/test_alphafold_tool.py +71 -0
  135. tooluniverse/test/test_chem_tool.py +37 -0
  136. tooluniverse/test/test_compose_lieraturereview.py +63 -0
  137. tooluniverse/test/test_compose_tool.py +448 -0
  138. tooluniverse/test/test_dailymed.py +69 -0
  139. tooluniverse/test/test_dataset_tool.py +200 -0
  140. tooluniverse/test/test_disease_target_score.py +56 -0
  141. tooluniverse/test/test_drugbank_filter_examples.py +179 -0
  142. tooluniverse/test/test_efo.py +31 -0
  143. tooluniverse/test/test_enrichr_tool.py +21 -0
  144. tooluniverse/test/test_europe_pmc_tool.py +20 -0
  145. tooluniverse/test/test_fda_adv.py +95 -0
  146. tooluniverse/test/test_fda_drug_labeling.py +91 -0
  147. tooluniverse/test/test_gene_ontology_tools.py +66 -0
  148. tooluniverse/test/test_gwas_tool.py +139 -0
  149. tooluniverse/test/test_hpa.py +625 -0
  150. tooluniverse/test/test_humanbase_tool.py +20 -0
  151. tooluniverse/test/test_idmap_tools.py +61 -0
  152. tooluniverse/test/test_mcp_server.py +211 -0
  153. tooluniverse/test/test_mcp_tool.py +247 -0
  154. tooluniverse/test/test_medlineplus.py +220 -0
  155. tooluniverse/test/test_openalex_tool.py +32 -0
  156. tooluniverse/test/test_opentargets.py +28 -0
  157. tooluniverse/test/test_pubchem_tool.py +116 -0
  158. tooluniverse/test/test_pubtator_tool.py +37 -0
  159. tooluniverse/test/test_rcsb_pdb_tool.py +86 -0
  160. tooluniverse/test/test_reactome.py +54 -0
  161. tooluniverse/test/test_semantic_scholar_tool.py +24 -0
  162. tooluniverse/test/test_software_tools.py +147 -0
  163. tooluniverse/test/test_tool_description_optimizer.py +49 -0
  164. tooluniverse/test/test_tool_finder.py +26 -0
  165. tooluniverse/test/test_tool_finder_llm.py +252 -0
  166. tooluniverse/test/test_tools_find.py +195 -0
  167. tooluniverse/test/test_uniprot_tools.py +74 -0
  168. tooluniverse/test/test_uspto_tool.py +72 -0
  169. tooluniverse/test/test_xml_tool.py +113 -0
  170. tooluniverse/tool_finder_embedding.py +267 -0
  171. tooluniverse/tool_finder_keyword.py +693 -0
  172. tooluniverse/tool_finder_llm.py +699 -0
  173. tooluniverse/tool_graph_web_ui.py +955 -0
  174. tooluniverse/tool_registry.py +416 -0
  175. tooluniverse/uniprot_tool.py +155 -0
  176. tooluniverse/url_tool.py +253 -0
  177. tooluniverse/uspto_tool.py +240 -0
  178. tooluniverse/utils.py +369 -41
  179. tooluniverse/xml_tool.py +369 -0
  180. tooluniverse-1.0.0.dist-info/METADATA +377 -0
  181. tooluniverse-1.0.0.dist-info/RECORD +186 -0
  182. {tooluniverse-0.1.4.dist-info → tooluniverse-1.0.0.dist-info}/WHEEL +1 -1
  183. tooluniverse-1.0.0.dist-info/entry_points.txt +9 -0
  184. tooluniverse-0.1.4.dist-info/METADATA +0 -141
  185. tooluniverse-0.1.4.dist-info/RECORD +0 -18
  186. {tooluniverse-0.1.4.dist-info → tooluniverse-1.0.0.dist-info}/licenses/LICENSE +0 -0
  187. {tooluniverse-0.1.4.dist-info → tooluniverse-1.0.0.dist-info}/top_level.txt +0 -0
tooluniverse-0.1.4.dist-info/METADATA DELETED
@@ -1,141 +0,0 @@
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- Metadata-Version: 2.4
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- Name: tooluniverse
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- Version: 0.1.4
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- Summary: A collection of biomedical tools designed for use by Agentic AI.
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- Home-page: https://github.com/mims-harvard/TxAgent
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- Author: Shanghua Gao
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- Author-email: shanghuagao@gmail.com
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- Requires-Python: >=3.6
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- Description-Content-Type: text/markdown
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- License-File: LICENSE
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- Requires-Dist: requests
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- Requires-Dist: numpy
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- Requires-Dist: graphql-core
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- Dynamic: license-file
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-
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- # ToolUniverse
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-
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- [![ProjectPage](https://img.shields.io/badge/Page-TxAgent-red)](https://zitniklab.hms.harvard.edu/TxAgent)
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- [![PaperLink](https://img.shields.io/badge/Arxiv-TxAgent-red)](https://arxiv.org/pdf/2503.10970)
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- [![TxAgent-PIP](https://img.shields.io/badge/Pip-TxAgent-blue)](https://pypi.org/project/txagent/)
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- [![ToolUniverse-PIP](https://img.shields.io/badge/Pip-ToolUniverse-blue)](https://pypi.org/project/tooluniverse/)
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- [![TxAgent](https://img.shields.io/badge/Code-TxAgent-purple)](https://github.com/mims-harvard/TxAgent)
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- [![ToolUniverse](https://img.shields.io/badge/Code-ToolUniverse-purple)](https://github.com/mims-harvard/ToolUniverse)
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- [![HuggingFace](https://img.shields.io/badge/HuggingFace-TxAgentT1-yellow)](https://huggingface.co/collections/mims-harvard/txagent-67c8e54a9d03a429bb0c622c)
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-
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- <body>
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- <section class="hero">
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- <div class="hero-body">
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- <div class="container is-max-desktop">
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- <div class="columns is-centered">
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- <div class="column has-text-centered">
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- <h1 class="title is-1 publication-title">
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- </h1>
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- <div class="is-size-5 publication-authors">
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- <!-- Paper authors -->
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- <span class="author-block">
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- <a href="https://shgao.site" target="_blank">Shanghua Gao</a
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- >,</span
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- >
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- <span class="author-block">
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- <a
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- href="https://www.linkedin.com/in/richard-zhu-4236901a7/"
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- target="_blank"
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- >Richard Zhu</a
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- >,</span
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- >
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- <span class="author-block">
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- <a href="https://zlkong.github.io/homepage/" target="_blank"
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- >Zhenglun Kong</a
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- >,</span
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- >
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- <span class="author-block">
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- <a href="https://www.ayushnoori.com/" target="_blank"
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- >Ayush Noori</a
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- >,</span
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- >
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- <span class="author-block">
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- <a
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- href="https://scholar.google.com/citations?hl=zh-CN&user=Awdn73MAAAAJ"
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- target="_blank"
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- >Xiaorui Su</a
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- >,</span
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- >
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- <span class="author-block">
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- <a
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- href="https://www.linkedin.com/in/curtisginder/"
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- target="_blank"
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- >Curtis Ginder</a
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- >,</span
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- >
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- <span class="author-block">
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- <a href="https://sites.google.com/view/theo-t" target="_blank"
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- >Theodoros Tsiligkaridis</a
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- >,</span
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- >
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- <span class="author-block">
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- <a href="https://zitniklab.hms.harvard.edu/" target="_blank"
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- >Marinka Zitnik</a
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- >
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- </div>
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-
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-
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- ToolUniverse is a collection of biomedical tools designed for use by Agentic AI. It is a critical component of TxAgent, providing the agent with the ability to access and leverage a vast array of biomedical knowledge to solve complex therapeutic reasoning tasks. ToolUniverse includes 211 biomedical tools that address various aspects of drugs and diseases. These tools are linked to trusted sources, including all US FDA-approved drugs since 1939 and validated clinical insights from Open Targets and Monarch Initiative.
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-
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- ![TxAgent](img/TxAgent_ToolUniverse.jpg)
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-
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-
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- # Install
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-
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- ### Install from source
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-
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- ```
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- python -m pip install . --no-cache-dir
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- ```
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-
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- ### Install from Pypi
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- Pip page (https://pypi.org/project/tooluniverse)
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-
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- ```
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- pip install tooluniverse
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- ```
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-
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- # Usage
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-
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- **Get all tools**
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-
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- ```
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- from tooluniverse import ToolUniverse
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- tooluni = ToolUniverse()
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- tooluni.load_tools()
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- tool_name_list, tool_desc_list = tooluni.refresh_tool_name_desc()
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- print(tool_name_list)
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- print(tool_desc_list)
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- ```
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-
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- **Function call to a tool**
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-
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- ```
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- from tooluniverse import ToolUniverse
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- tooluni = ToolUniverse()
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- tooluni.load_tools()
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- query = {"name": "get_indications_by_drug_name", "arguments": {"drug_name": "KISUNLA"}}
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- tooluni.run(query)
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- ```
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- ## Citation
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-
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- ```
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- @misc{gao2025txagent,
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- title={TxAgent: An AI Agent for Therapeutic Reasoning Across a Universe of Tools},
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- author={Shanghua Gao and Richard Zhu and Zhenglun Kong and Ayush Noori and Xiaorui Su and Curtis Ginder and Theodoros Tsiligkaridis and Marinka Zitnik},
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- year={2025},
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- eprint={2503.10970},
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- archivePrefix={arXiv},
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- primaryClass={cs.AI},
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- url={https://arxiv.org/abs/2503.10970},
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- }
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- ```
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-
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- ## Contact
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- If you have any questions or suggestions, please email [Shanghua Gao](mailto:shanghuagao@gmail.com) and [Marinka Zitnik](mailto:marinka@hms.harvard.edu).
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-
tooluniverse-0.1.4.dist-info/RECORD DELETED
@@ -1,18 +0,0 @@
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- tooluniverse/__init__.py,sha256=j44hf13WM50HQJRi7aloeTG6y6872wJtfX8ydsaiJFI,652
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- tooluniverse/base_tool.py,sha256=WMGgr02lhEsVzHgt7NIeynXQ2wZtu97yZI-lQWOSoSs,1145
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- tooluniverse/execute_function.py,sha256=CmA8AIfyolkcooASD2_3pXgF1BqESU5_VUqdHSYiM_M,10139
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- tooluniverse/graphql_tool.py,sha256=WU-9YAYbmfbfGwGDn7Y22DVju9t68CKuv_JNz_11NkM,5120
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- tooluniverse/openfda_tool.py,sha256=s4ctA7ckID7VA1wRceRGknFV5zu9sR7fqTJ8oa9U0q4,21056
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- tooluniverse/restful_tool.py,sha256=5HoTyCSd507D4Qjcqjd16o8Y4BFZ02Zm4cGuczIXWdw,4078
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- tooluniverse/utils.py,sha256=zh1IopojPBIJzK_8eGytTmWlPckluQQZTpiCQONw-pY,6416
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- tooluniverse/data/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
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- tooluniverse/data/fda_drug_labeling_tools.json,sha256=iRYkuNk6ohCbNELMbfPghtlCGthjzZch_9Ukr-yjaJI,209383
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- tooluniverse/data/fda_drugs_with_brand_generic_names_for_tool.py,sha256=Clb7kQpPaXPTT_rdDLoinfwF8JbrdRaBis-0TYcT0BU,6510589
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- tooluniverse/data/monarch_tools.json,sha256=I5KvamNZRvkKBaKbM6Ypo333m-RejQhqScX8h-uket4,3567
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- tooluniverse/data/opentarget_tools.json,sha256=nNvl-vYqS8nLfyIvHO40Fsnx6HJxwInUuS0mrrh6xmY,66201
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- tooluniverse/data/special_tools.json,sha256=tOI0TFpdjZBEE5Af1Vc4CeXQ0gAkz39xho9hDVBYR70,1518
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- tooluniverse-0.1.4.dist-info/licenses/LICENSE,sha256=Unq9Y3buGL9J0vFop03FYZiVweytt1xdgLIh2n9ck2c,1115
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- tooluniverse-0.1.4.dist-info/METADATA,sha256=-qi9jrg4MLNop0QFi9ezycLwM-81Poo0J9CkAD4k7Lg,5220
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- tooluniverse-0.1.4.dist-info/WHEEL,sha256=1tXe9gY0PYatrMPMDd6jXqjfpz_B-Wqm32CPfRC58XU,91
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- tooluniverse-0.1.4.dist-info/top_level.txt,sha256=zZ8YeCJ5FAkEwdd_mxsFtSCQMBDgBdxrrmHo3RNBiWs,13
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- tooluniverse-0.1.4.dist-info/RECORD,,