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

tooluniverse/data/compose_tools.json

@@ -0,0 +1,202 @@
+[
+  {
+    "type": "ComposeTool",
+    "name": "DrugSafetyAnalyzer",
+    "description": "Comprehensive drug safety analysis combining adverse event data, literature review, and molecular information",
+    "parameter": {
+      "type": "object",
+      "properties": {
+        "drug_name": {
+          "type": "string",
+          "description": "Name of the drug to analyze"
+        },
+        "patient_sex": {
+          "type": "string",
+          "enum": ["Male", "Female"],
+          "description": "Filter by patient sex (optional)"
+        },
+        "serious_events_only": {
+          "type": "boolean",
+          "description": "Focus only on serious adverse events",
+          "default": false
+        }
+      },
+      "required": ["drug_name"]
+    },
+    "auto_load_dependencies": true,
+    "fail_on_missing_tools": false,
+    "required_tools": [
+      "PubChem_get_CID_by_compound_name",
+      "PubChem_get_compound_properties_by_CID",
+      "EuropePMC_search_articles"
+    ],
+    "composition_file": "drug_safety_analyzer.py",
+    "composition_function": "compose"
+  },
+  {
+    "type": "ComposeTool",
+    "name": "ToolDescriptionOptimizer",
+    "description": "Optimizes a tool's description and parameter descriptions by generating test cases, executing them, analyzing the results, and suggesting improved descriptions for both the tool and its arguments. Optionally saves a comprehensive optimization report to a file without overwriting the original.",
+    "parameter": {
+      "type": "object",
+      "properties": {
+        "tool_config": {
+          "type": "object",
+          "description": "The full configuration of the tool to optimize."
+        },
+        "save_to_file": {
+          "type": "boolean",
+          "description": "If true, save the optimized description to a file (do not overwrite the original).",
+          "default": false
+        },
+        "output_file": {
+          "type": "string",
+          "description": "Optional file path to save the optimized description. If not provided, use '<tool_name>_optimized_description.txt'."
+        },
+        "max_iterations": {
+          "type": "integer",
+          "description": "Maximum number of optimization rounds to perform.",
+          "default": 3
+        },
+        "satisfaction_threshold": {
+          "type": "number",
+          "description": "Quality score threshold (1-10) to consider optimization satisfactory.",
+          "default": 8
+        }
+      },
+      "required": ["tool_config"]
+    },
+    "auto_load_dependencies": true,
+    "fail_on_missing_tools": false,
+    "required_tools": [
+      "TestCaseGenerator",
+      "DescriptionAnalyzer",
+      "ArgumentDescriptionOptimizer",
+      "DescriptionQualityEvaluator"
+    ],
+    "composition_file": "tool_description_optimizer.py",
+    "composition_function": "compose"
+  },
+  {
+    "type": "ComposeTool",
+    "name": "ToolDiscover",
+    "description": "Generates new ToolUniverse-compliant tools based on short descriptions through an intelligent discovery and refinement process. Automatically determines the optimal tool type and category, discovers similar existing tools, generates initial specifications, and iteratively refines the tool configuration using agentic optimization tools until it meets quality standards.",
+    "parameter": {
+      "type": "object",
+      "properties": {
+        "tool_description": {
+          "type": "string",
+          "description": "Short description of the desired tool functionality and purpose. Tool Discover will automatically analyze this to determine the optimal tool type (PackageTool, RESTTool, XMLTool, or AgenticTool) and appropriate category."
+        },
+        "max_iterations": {
+          "type": "integer",
+          "description": "Maximum number of refinement iterations to perform.",
+          "default": 20
+        },
+        "save_to_file": {
+          "type": "boolean",
+          "description": "Whether to save the generated tool configuration and report to a file.",
+          "default": true
+        },
+        "output_file": {
+          "type": "string",
+          "description": "Optional file path to save the generated tool. If not provided, uses auto-generated filename."
+        }
+      },
+      "required": ["tool_description"]
+    },
+    "auto_load_dependencies": true,
+    "fail_on_missing_tools": false,
+    "required_tools": [],
+    "composition_file": "tool_discover.py",
+    "composition_function": "compose"
+  },
+  {
+    "type": "ComposeTool",
+    "name": "LiteratureSearchTool",
+    "description": "Comprehensive literature search and summary tool that searches multiple databases (EuropePMC, OpenAlex, PubTator) and generates AI-powered summaries of research findings",
+    "parameter": {
+      "type": "object",
+      "properties": {
+        "research_topic": {
+          "type": "string",
+          "description": "The research topic or query to search for in the literature"
+        }
+      },
+      "required": ["research_topic"]
+    },
+    "auto_load_dependencies": true,
+    "fail_on_missing_tools": false,
+    "required_tools": [
+      "EuropePMC_search_articles",
+      "openalex_literature_search",
+      "PubTator3_LiteratureSearch",
+      "MedicalLiteratureReviewer"
+    ],
+    "composition_file": "literature_tool.py",
+    "composition_function": "compose"
+  },
+  {
+    "type": "ComposeTool",
+    "name": "ComprehensiveDrugDiscoveryPipeline",
+    "description": "Complete end-to-end drug discovery workflow from disease to optimized candidates. Identifies targets, discovers lead compounds, screens for ADMET properties, assesses safety, and validates with literature.",
+    "parameter": {
+      "type": "object",
+      "properties": {
+        "disease_efo_id": {
+          "type": "string",
+          "description": "The EFO ID of the disease for drug discovery (e.g., 'EFO_0001074' for Alzheimer's disease)"
+        }
+      },
+      "required": ["disease_efo_id"]
+    },
+    "auto_load_dependencies": true,
+    "fail_on_missing_tools": false,
+    "required_tools": [
+      "OpenTargets_get_associated_targets_by_disease_efoId",
+      "OpenTargets_get_associated_drugs_by_disease_efoId",
+      "ADMETAI_predict_BBB_penetrance",
+      "ADMETAI_predict_bioavailability",
+      "ADMETAI_predict_toxicity",
+      "PubChem_get_CID_by_compound_name",
+      "PubChem_get_compound_properties_by_CID",
+      "LiteratureSearchTool"
+    ],
+    "composition_file": "comprehensive_drug_discovery.py",
+    "composition_function": "compose"
+  },
+  {
+    "type": "ComposeTool",
+    "name": "BiomarkerDiscoveryWorkflow",
+    "description": "Discover and validate biomarkers for a specific disease condition using literature analysis, expression data, pathway enrichment, and clinical validation.",
+    "parameter": {
+      "type": "object",
+      "properties": {
+        "disease_condition": {
+          "type": "string",
+          "description": "The disease condition to discover biomarkers for (e.g., 'breast cancer', 'Alzheimer's disease')"
+        },
+        "sample_type": {
+          "type": "string",
+          "description": "The type of sample to analyze (e.g., 'blood', 'tissue', 'plasma')",
+          "default": "blood"
+        }
+      },
+      "required": ["disease_condition"]
+    },
+    "auto_load_dependencies": true,
+    "fail_on_missing_tools": false,
+    "required_tools": [
+      "LiteratureSearchTool",
+      "HPA_search_genes_by_query",
+      "HPA_get_comprehensive_gene_details_by_ensembl_id",
+      "HPA_get_biological_processes_by_gene",
+      "HPA_get_contextual_biological_process_analysis",
+      "HPA_get_protein_interactions_by_gene",
+      "HPA_get_cancer_prognostics_by_gene",
+      "FDA_get_drug_names_by_clinical_pharmacology"
+    ],
+    "composition_file": "biomarker_discovery.py",
+    "composition_function": "compose"
+  }
+]

tooluniverse/data/dailymed_tools.json

@@ -0,0 +1,70 @@
+[
+  {
+    "type": "SearchSPLTool",
+    "name": "DailyMed_search_spls",
+    "description": "Search SPL list using multiple filter conditions (drug_name/ndc/rxcui/setid) and return metadata + data array.",
+    "parameter": {
+      "type": "object",
+      "properties": {
+        "drug_name": {
+          "type": "string",
+          "description": "Generic or brand name of the drug, e.g., 'TAMSULOSIN HYDROCHLORIDE'."
+        },
+        "ndc": {
+          "type": "string",
+          "description": "National Drug Code (NDC)."
+        },
+        "rxcui": {
+          "type": "string",
+          "description": "RxNorm Code (RXCUI)."
+        },
+        "setid": {
+          "type": "string",
+          "format": "uuid",
+          "description": "Set ID corresponding to the SPL."
+        },
+        "published_date_gte": {
+          "type": "string",
+          "description": "Published date >= specified date, format 'YYYY-MM-DD'."
+        },
+        "published_date_eq": {
+          "type": "string",
+          "description": "Published date == specified date, format 'YYYY-MM-DD'."
+        },
+        "pagesize": {
+          "type": "integer",
+          "description": "Number of items per page, maximum 100, default 100.",
+          "default": 100
+        },
+        "page": {
+          "type": "integer",
+          "description": "Page number, starts from 1, default 1.",
+          "default": 1
+        }
+      },
+      "required": []
+    }
+  },
+  {
+    "type": "GetSPLBySetIDTool",
+    "name": "DailyMed_get_spl_by_setid",
+    "description": "Get complete label corresponding to SPL Set ID, returns content in XML or JSON format.",
+    "parameter": {
+      "type": "object",
+      "properties": {
+        "setid": {
+          "type": "string",
+          "format": "uuid",
+          "description": "SPL Set ID to query."
+        },
+        "format": {
+          "type": "string",
+          "enum": ["xml"],
+          "default": "xml",
+          "description": "Return format, only supports 'xml'."
+        }
+      },
+      "required": ["setid"]
+    }
+  }
+]