tooluniverse 0.2.0__py3-none-any.whl → 1.0.1__py3-none-any.whl

tooluniverse/data/alphafold_tools.json

@@ -0,0 +1,87 @@
+[
+  {
+    "name": "alphafold_get_prediction_by_uniprot_id",
+    "description": "Retrieve AlphaFold-predicted 3D protein structure metadata and download links for a given UniProt accession ID.",
+    "type": "AlphaFoldRESTTool",
+    "parameter": {
+      "type": "object",
+      "properties": {
+        "uniprot_id": {
+          "type": "string",
+          "description": "UniProt accession ID (e.g., 'P69905' for hemoglobin alpha)."
+        }
+      },
+      "required": ["uniprot_id"]
+    },
+    "fields": {
+      "endpoint": "/prediction/{uniprot_id}",
+      "return_format": "JSON"
+    },
+    "return_schema": {
+      "type": "object",
+      "description": "AlphaFold predicted protein structure metadata.",
+      "properties": {
+        "uniprotAccession": {
+          "type": "string",
+          "description": "UniProt accession ID"
+        },
+        "uniprotDescription": {
+          "type": "string",
+          "description": "Protein description"
+        },
+        "organismScientificName": {
+          "type": "string",
+          "description": "Scientific name of the source organism"
+        },
+        "gene": {
+          "type": "string",
+          "description": "Gene name if available"
+        },
+        "modelCreatedDate": {
+          "type": "string",
+          "description": "Date this AlphaFold model was created"
+        },
+        "globalMetricValue": {
+          "type": "number",
+          "description": "Global pLDDT confidence score"
+        },
+        "fractionPlddtVeryLow": {
+          "type": "number",
+          "description": "Fraction of residues with very low pLDDT (<50)"
+        },
+        "fractionPlddtLow": {
+          "type": "number",
+          "description": "Fraction of residues with low pLDDT (50–70)"
+        },
+        "fractionPlddtConfident": {
+          "type": "number",
+          "description": "Fraction of residues with confident pLDDT (70–90)"
+        },
+        "fractionPlddtVeryHigh": {
+          "type": "number",
+          "description": "Fraction of residues with very high pLDDT (>90)"
+        },
+        "pdbUrl": {
+          "type": "string",
+          "description": "Download link for PDB file"
+        },
+        "cifUrl": {
+          "type": "string",
+          "description": "Download link for CIF file"
+        },
+        "bcifUrl": {
+          "type": "string",
+          "description": "Download link for BCIF file"
+        },
+        "paeImageUrl": {
+          "type": "string",
+          "description": "Predicted aligned error plot image URL"
+        },
+        "paeDocUrl": {
+          "type": "string",
+          "description": "Predicted aligned error JSON URL"
+        }
+      }
+    }
+  }
+]

tooluniverse/data/boltz_tools.json

@@ -0,0 +1,9 @@
+[
+    {
+        "name": "mcp_auto_loader_boltz",
+        "description": "Run Boltz2 docking and affinity prediction using MCP protocol",
+        "type": "MCPAutoLoaderTool",
+        "server_url": "http://${BOLTZ_MCP_SERVER_HOST}:8080/mcp",
+        "required_api_keys": ["BOLTZ_MCP_SERVER_HOST"]
+    }
+]

tooluniverse/data/chembl_tools.json

@@ -0,0 +1,16 @@
+[
+    {
+        "type": "ChEMBLTool",
+        "name": "ChEMBL_search_similar_molecules",
+        "description": "Search for molecules similar to a given SMILES, chembl_id, or compound or drug name, using the ChEMBL Web Services.",
+        "parameter": {
+            "type": "object",
+            "properties": {
+                "query": { "type": "string", "description": "SMILES string, chembl_id, or compound or drug name." },
+                "similarity_threshold": { "type": "integer", "description": "Similarity threshold (0–100).", "default": 80 },
+                "max_results": { "type": "integer", "description": "Maximum number of results to return.", "default": 20 }
+            },
+            "required": ["query"]
+        }
+    }
+]

tooluniverse/data/clinicaltrials_gov_tools.json

@@ -0,0 +1,326 @@
+[
+    {
+        "name": "search_clinical_trials",
+        "description": "Search for clinical trials registered on clinicaltrials.gov based on title, conditions, interventions, outcome measures, and status. Returns a paginated list of studies, containing the NCT ID and description of each trial. You can then take the NCT IDs and use 'get_clinical_trials_*' tools to get detailed information about specific protocol fields for specific studies, or 'extract_clinical_trials_efficacy/safety' tools to get efficacy or adverse events results from specific studies. If you wish to see the next page of results, you can use the 'nextPageToken' value from the previous output of this tool and input it as the 'pageToken' parameter in the next query. Note that currently the search is limited to trials beyond phase 1.",
+        "parameter": {
+            "type": "object",
+            "properties": {
+                "condition": {
+                    "type": "string",
+                    "description": "Query for condition or disease using Essie expression syntax (e.g., 'lung cancer', '(head OR neck) AND pain AND NOT \"back pain\"'). ",
+                    "required": false
+                },
+                "intervention": {
+                    "type": "string",
+                    "description": "Query for intervention/treatment using Essie expression syntax (e.g., 'chemotherapy', 'immunotherapy', 'olaparib', 'combination therapy').",
+                    "required": false
+                },
+                "query_term": {
+                    "type": "string",
+                    "description": "Query for 'other terms' with Essie expression syntax (e.g., 'combination', 'AREA[LastUpdatePostDate]RANGE[2023-01-15,MAX]', 'Phase II'). Can be used to search for all other protocol fields, including but not limited to title, outcome measures, status, phase, location, etc."
+                },
+                "pageSize": {
+                    "type": "integer",
+                    "description": "Maximum number of studies to return per page (default 10, max 1000).",
+                    "required": false
+                },
+                "pageToken": {
+                    "type": "string",
+                    "description": "Token to retrieve the next page of results, obtained from the 'nextPageToken' field of the previous response. Do not specify it for first page. When you make an initial request to the API which supports pagination, the response will include a nextPageToken. This token can then be used as a parameter in the subsequent API request to retrieve the next set of data.",
+                    "required": false
+                }
+            }
+        },
+        "query_schema": {
+            "pageSize": 10
+        },
+        "label": ["ClinicalTrials.gov", "Clinical Trial", "Intervention", "Adverse Effect", "Efficacy", "Search"],
+        "type": "ClinicalTrialsSearchTool",
+        "tool_url": "/studies"
+    },
+
+    {
+        "name": "get_clinical_trial_descriptions",
+        "description": "Retrieves detailed identification information for trials, including titles, phases, and descriptions, using their NCT IDs.",
+        "parameter": {
+            "type": "object",
+            "properties": {
+                "nct_ids": {
+                    "type": "array",
+                    "description": "List of NCT IDs of the clinical trials (e.g., ['NCT04852770', 'NCT01728545']).",
+                    "items": {
+                        "type": "string"
+                    },
+                    "required": true
+                },
+                "description_type": {
+                    "type": "string",
+                    "description": "Type of information to retrieve. Options are 'brief' for brief descriptions or 'full' for full descriptions.",
+                    "enum": ["brief", "full"]
+                }
+            }
+        },
+        "query_schema": {
+            "description_type": "brief"
+        },
+        "label": ["ClinicalTrials.gov", "Clinical Trial", "Study", "Description"],
+        "type": "ClinicalTrialsDetailsTool",
+        "tool_url": "/studies/{nctId}"
+    },
+
+    {
+        "name": "get_clinical_trial_status_and_dates",
+        "description": "Retrieves trial status and start and completion dates, using their NCT IDs.",
+        "parameter": {
+            "type": "object",
+            "properties": {
+                "nct_ids": {
+                    "type": "array",
+                    "description": "List of NCT IDs of the clinical trials (e.g., ['NCT04852770', 'NCT01728545']).",
+                    "items": {
+                        "type": "string"
+                    },
+                    "required": true
+                },
+                "status_and_date": {
+                    "type": "string",
+                    "description": "Placeholder."
+                }
+            }
+        },
+        "query_schema": {},
+        "label": ["ClinicalTrials.gov", "Clinical Trial", "Study", "Status", "Dates"],
+        "type": "ClinicalTrialsDetailsTool",
+        "tool_url": "/studies/{nctId}"
+    },
+
+    {
+        "name": "get_clinical_trial_conditions_and_interventions",
+        "description": "Retrieves the list of conditions or diseases and the interventions and arm groups that the clinical trials are focused on, using their NCT IDs.",
+        "parameter": {
+            "type": "object",
+            "properties": {
+                "nct_ids": {
+                    "type": "array",
+                    "description": "List of NCT IDs of the clinical trials (e.g., ['NCT04852770', 'NCT01728545']).",
+                    "items": {
+                        "type": "string"
+                    },
+                    "required": true
+                },
+                "condition_and_intervention": {
+                    "type": "string",
+                    "description": "Placeholder."
+                }
+            }
+        },
+        "query_schema": {},
+        "label": ["ClinicalTrials.gov", "Clinical Trial", "Study", "Condition", "Intervention", "Arm Group"],
+        "type": "ClinicalTrialsDetailsTool",
+        "tool_url": "/studies/{nctId}"
+    },
+
+    {
+        "name": "get_clinical_trial_eligibility_criteria",
+        "description": "Retrieves the eligibility criteria for the clinical trials, using their NCT IDs.",
+        "parameter": {
+            "type": "object",
+            "properties": {
+                "nct_ids": {
+                    "type": "array",
+                    "description": "List of NCT IDs of the clinical trials (e.g., ['NCT04852770', 'NCT01728545']).",
+                    "items": {
+                        "type": "string"
+                    },
+                    "required": true
+                },
+                "eligibility_criteria": {
+                    "type": "string",
+                    "description": "Placeholder."
+                }
+            }
+        },
+        "query_schema": {},
+        "label": ["ClinicalTrials.gov", "Clinical Trial", "Study", "Eligibility Criteria"],
+        "type": "ClinicalTrialsDetailsTool",
+        "tool_url": "/studies/{nctId}"
+    },
+
+    {
+        "name": "get_clinical_trial_locations",
+        "description": "Retrieves the locations where the clinical trials are being conducted, using their NCT IDs.",
+        "parameter": {
+            "type": "object",
+            "properties": {
+                "nct_ids": {
+                    "type": "array",
+                    "description": "List of NCT IDs of the clinical trials (e.g., ['NCT04852770', 'NCT01728545']).",
+                    "items": {
+                        "type": "string"
+                    },
+                    "required": true
+                },
+                "location": {
+                    "type": "string",
+                    "description": "Placeholder."
+                }
+            }
+        },
+        "query_schema": {},
+        "label": ["ClinicalTrials.gov", "Clinical Trial", "Study", "Location"],
+        "type": "ClinicalTrialsDetailsTool",
+        "tool_url": "/studies/{nctId}"
+    },
+
+    {
+        "name": "get_clinical_trial_outcome_measures",
+        "description": "Retrieves the outcome measures for the clinical trials, using their NCT IDs.",
+        "parameter": {
+            "type": "object",
+            "properties": {
+                "nct_ids": {
+                    "type": "array",
+                    "description": "List of NCT IDs of the clinical trials (e.g., ['NCT04852770', 'NCT01728545']).",
+                    "items": {
+                        "type": "string"
+                    },
+                    "required": true
+                },
+                "outcome_measures": {
+                   "type": "string",
+                    "description": "Decides whether to retrieve primary, secondary, or all outcome measures. Options are 'primary', 'secondary', or 'all'. Default is 'primary'.",
+                    "enum": ["primary", "secondary", "all"],
+                    "required": false
+                }
+            }
+        },
+        "query_schema": {
+            "outcome_measures": "primary"
+        },
+        "label": ["ClinicalTrials.gov", "Clinical Trial", "Study", "Outcome Measures"],
+        "type": "ClinicalTrialsDetailsTool",
+        "tool_url": "/studies/{nctId}"
+    },
+
+    {
+        "name": "get_clinical_trial_references",
+        "description": "Retrieves the references (if any) for the clinical trials, using their NCT IDs.",
+        "parameter": {
+            "type": "object",
+            "properties": {
+                "nct_ids": {
+                    "type": "array",
+                    "description": "List of NCT IDs of the clinical trials (e.g., ['NCT04852770', 'NCT01728545']).",
+                    "items": {
+                        "type": "string"
+                    },
+                    "required": true
+                },
+                "references": {
+                    "type": "string",
+                    "description": "Placeholder."
+                }
+            }
+        },
+        "query_schema": {},
+        "label": ["ClinicalTrials.gov", "Clinical Trial", "Study", "References"],
+        "type": "ClinicalTrialsDetailsTool",
+        "tool_url": "/studies/{nctId}"
+    },
+
+    {
+        "name": "extract_clinical_trial_outcomes",
+        "description": "Extracts detailed trial outcome results (e.g., overall survival months, p-values, etc.) from clinicaltrials.gov, using their NCT IDs.",
+        "parameter": {
+            "type": "object",
+            "properties": {
+                "nct_ids": {
+                    "type": "array",
+                    "description": "List of NCT IDs of the clinical trials (e.g., ['NCT04852770', 'NCT01728545']).",
+                    "items": {
+                        "type": "string"
+                    },
+                    "required": true
+                },
+                "outcome_measure": {
+                    "type": "string",
+                    "description": "Outcome measure to extract. Example values include 'primary' (primary outcomes only), 'secondary' (secondary outcomes only), 'all' (all outcomes), or specific measure names such as 'survival', 'overall survival'. For specific measure names, outcome measures will be matched as long as the input partially matches their titles or descriptions (case agnostic). Querying for specific measure names is recommended after getting an overview of outcome measures ('primary'). If querying for specific measure names does not return any results, this parameter should be set to 'primary' for sanity check. By default, the value is set to 'primary', i.e. the tool will extract all primary outcome results.",
+                    "required": false
+                }
+            }
+        },
+        "query_schema": {
+            "outcome_measure": "primary"
+        },
+        "label": ["ClinicalTrials.gov", "Clinical Trial", "Study", "Outcome", "Efficacy", "Primary Outcome", "Secondary Outcome"],
+        "type": "ClinicalTrialsDetailsTool",
+        "tool_url": "/studies/{nctId}"
+    },
+
+    {
+        "name": "extract_clinical_trial_adverse_events",
+        "description": "Extracts detailed adverse event results from clinicaltrials.gov, using their NCT IDs.",
+        "parameter": {
+            "type": "object",
+            "properties": {
+                "nct_ids": {
+                    "type": "array",
+                    "description": "List of NCT IDs of the clinical trials (e.g., ['NCT04852770', 'NCT01728545']).",
+                    "items": {
+                        "type": "string"
+                    },
+                    "required": true
+                },
+                "organ_systems": {
+                    "type": "array",
+                    "description": "List of organs or organ systems to filter adverse events (see enum for exact text). Adverse events will be matched only if the input exactly matches their terms (case agnostic). If not specified, all adverse events will be returned. By default, all adverse events will be returned.",
+                    "items": {
+                        "type": "string",
+                        "enum": [
+                            "Blood and Lymphatic System Disorders",
+                            "Cardiac Disorders",
+                            "Congenital, Familial and Genetic Disorders",
+                            "Ear and Labyrinth Disorders",
+                            "Endocrine Disorders",
+                            "Eye Disorders",
+                            "Gastrointestinal Disorders",
+                            "General Disorders",
+                            "Hepatobiliary Disorders",
+                            "Immune System Disorders",
+                            "Infections and Infestations",
+                            "Injury, Poisoning and Procedural Complications",
+                            "Investigations",
+                            "Metabolism and Nutrition Disorders",
+                            "Musculoskeletal and Connective Tissue Disorders",
+                            "Neoplasms Benign, Malignant and Unspecified (Including Cysts and Polyps)",
+                            "Nervous System Disorders",
+                            "Pregnancy, Puerperium and Perinatal Conditions",
+                            "Product Issues",
+                            "Psychiatric Disorders",
+                            "Renal and Urinary Disorders",
+                            "Reproductive System and Breast Disorders",
+                            "Respiratory, Thoracic and Mediastinal Disorders",
+                            "Skin and Subcutaneous Tissue Disorders",
+                            "Social Circumstances",
+                            "Surgical and Medical Procedures",
+                            "Vascular Disorders"
+                        ]
+                    },
+                    "required": false
+                },
+                "adverse_event_type": {
+                    "type": "string",
+                    "description": "Type of adverse events to extract. Options are 'serious' (serious adverse events only), 'other' (non-serious adverse events only), 'all' (all adverse events), or specific event names such as 'nausea', 'neutropenia', 'epilepsy' (from MedDRA). For specific event names, adverse events will be matched as long as the input partially matches their terms (case agnostic). Querying for specific adverse event names is recommended as there are typically many adverse events logged. If querying for specific event names does not return any results, this parameter should be set to 'serious' for sanity check. By default, the value is set to 'serious', i.e. the tool will extract all serious adverse events.",
+                    "required": false
+                }
+            }
+        },
+        "query_schema": {
+            "adverse_event_type": "serious"
+        },
+        "label": ["ClinicalTrials.gov", "Clinical Trial", "Study", "Adverse Event", "Safety"],
+        "type": "ClinicalTrialsDetailsTool",
+        "tool_url": "/studies/{nctId}"
+    }
+
+]

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"
+  }
+]