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

tooluniverse/data/finder_tools.json

@@ -0,0 +1,209 @@
+[
+  {
+    "type": "ToolFinderEmbedding",
+    "name": "Tool_RAG",
+    "description": "Retrieve related tools from the toolbox based on the provided description",
+    "parameter": {
+      "type": "object",
+      "properties": {
+        "description": {
+          "type": "string",
+          "description": "The description of the tool capability required.",
+          "required": true
+        },
+        "limit": {
+          "type": "integer",
+          "description": "The number of tools to retrieve",
+          "required": true
+        }
+      }
+    },
+    "required": [
+      "description",
+      "limit"
+    ],
+    "configs": {
+      "tool_finder_model": "mims-harvard/ToolRAG-T1-GTE-Qwen2-1.5B",
+      "exclude_tools": [
+        "Tool_RAG",
+        "Tool_Finder",
+        "Finish",
+        "CallAgent",
+        "Tool_Finder_LLM",
+        "Tool_Finder_Keyword"
+      ]
+    }
+  },
+  {
+    "type": "ToolFinderEmbedding",
+    "name": "Tool_Finder",
+    "description": "Retrieve related tools from the toolbox based on the provided description, advanced version with more functionality.",
+    "parameter": {
+      "type": "object",
+      "properties": {
+        "description": {
+          "type": "string",
+          "description": "The description of the tool capability required.",
+          "required": true
+        },
+        "limit": {
+          "type": "integer",
+          "description": "The number of tools to retrieve",
+          "required": true
+        },
+        "picked_tool_names": {
+          "type": "array",
+          "items": {
+            "type": "string"
+          },
+          "description": "Pre-selected tool names to process. If provided, tool selection will skip these tools.",
+          "required": false
+        },
+        "return_call_result": {
+          "type": "boolean",
+          "description": "Whether to return both prompts and tool names. If false, returns only tool prompts.",
+          "required": false
+        },
+        "categories": {
+          "type": "array",
+          "items": {
+            "type": "string"
+          },
+          "description": "Optional list of tool categories to filter by",
+          "required": false
+        }
+      }
+    },
+    "required": [
+      "description",
+      "limit"
+    ],
+    "configs": {
+      "tool_finder_model": "mims-harvard/ToolRAG-T1-GTE-Qwen2-1.5B",
+      "exclude_tools": [
+        "Tool_RAG",
+        "Tool_Finder",
+        "Finish",
+        "CallAgent",
+        "Tool_Finder_LLM",
+        "Tool_Finder_Keyword"
+      ]
+    }
+  },
+  {
+    "type": "ToolFinderLLM",
+    "name": "Tool_Finder_LLM",
+    "description": "LLM-based tool finder that uses natural language processing to intelligently select relevant tools based on user queries. This tool analyzes all available tool descriptions and uses an LLM to determine which tools would be most helpful for a given task or question.",
+    "parameter": {
+      "type": "object",
+      "properties": {
+        "description": {
+          "type": "string",
+          "description": "The description of the tool capability required.",
+          "required": true
+        },
+        "limit": {
+          "type": "integer",
+          "description": "The number of tools to retrieve",
+          "required": true
+        },
+        "picked_tool_names": {
+          "type": "array",
+          "items": {
+            "type": "string"
+          },
+          "description": "Pre-selected tool names to process. If provided, tool selection will skip these tools.",
+          "required": false
+        },
+        "return_call_result": {
+          "type": "boolean",
+          "description": "Whether to return both prompts and tool names. If false, returns only tool prompts.",
+          "required": false
+        },
+        "categories": {
+          "type": "array",
+          "items": {
+            "type": "string"
+          },
+          "description": "Optional list of tool categories to filter by",
+          "required": false
+        }
+      },
+      "required": [
+        "description",
+        "limit"
+      ]
+    },
+    "configs": {
+      "api_type": "CHATGPT",
+      "model_id": "gpt-4o-1120",
+      "temperature": 0.1,
+      "max_new_tokens": 4096,
+      "return_json": true,
+      "return_list_only": true,
+      "exclude_tools": [
+        "Tool_RAG",
+        "Tool_Finder",
+        "Finish",
+        "CallAgent",
+        "Tool_Finder_LLM",
+        "Tool_Finder_Keyword"
+      ]
+    }
+  },
+  {
+    "type": "ToolFinderKeyword",
+    "name": "Tool_Finder_Keyword",
+    "description": "Simple keyword-based tool finder for discovering relevant tools using text matching",
+    "parameter": {
+      "type": "object",
+      "properties": {
+        "description": {
+          "type": "string",
+          "description": "The description of the tool capability required.",
+          "required": true
+        },
+        "limit": {
+          "type": "integer",
+          "description": "The number of tools to retrieve",
+          "required": true
+        },
+        "picked_tool_names": {
+          "type": "array",
+          "items": {
+            "type": "string"
+          },
+          "description": "Pre-selected tool names to process. If provided, tool selection will skip these tools.",
+          "required": false
+        },
+        "return_call_result": {
+          "type": "boolean",
+          "description": "Whether to return both prompts and tool names. If false, returns only tool prompts.",
+          "required": false
+        },
+        "categories": {
+          "type": "array",
+          "items": {
+            "type": "string"
+          },
+          "description": "Optional list of tool categories to filter by",
+          "required": false
+        }
+      }
+    },
+    "required": [
+      "description",
+      "limit"
+    ],
+    "configs": {
+      "exclude_tools": [
+        "Tool_RAG",
+        "Tool_Finder",
+        "Finish",
+        "CallAgent",
+        "Tool_Finder_LLM",
+        "Tool_Finder_Keyword"
+      ]
+    }
+  }
+]

tooluniverse/data/gene_ontology_tools.json

@@ -0,0 +1,113 @@
+[
+  {
+    "name": "GO_search_terms",
+    "description": "Searches for Gene Ontology (GO) terms by a keyword using the GOlr search engine. Returns GO terms and related biological entities.",
+    "type": "GeneOntologyTool",
+    "parameter": {
+      "type": "object",
+      "properties": {
+        "query": {
+          "type": "string",
+          "description": "The keyword to search for, e.g., 'apoptosis' or 'kinase activity'."
+        }
+      },
+      "required": ["query"]
+    },
+    "fields": {
+      "endpoint": "http://golr-aux.geneontology.io/solr/select?fq=document_category:\"ontology_class\"&q=*:*&fq=annotation_class_label:\"{query}\"&wt=json&rows=10",
+      "input_description": "Input search keyword, e.g., 'cell cycle'.",
+      "output_description": "Returns GO terms matching the search keyword with their details."
+    }
+  },
+  {
+    "name": "GO_get_term_details",
+    "description": "Retrieves detailed information for a specific GO ID using the Biolink API, including definition, synonyms, and annotations.",
+    "type": "GeneOntologyTool",
+    "parameter": {
+      "type": "object",
+      "properties": {
+        "id": {
+          "type": "string",
+          "description": "The standard GO term ID, e.g., 'GO:0006915' for apoptotic process."
+        }
+      },
+      "required": ["id"]
+    },
+    "fields": {
+      "endpoint": "http://api.geneontology.org/api/bioentity/function/{id}",
+      "input_description": "Input GO term ID, e.g., 'GO:0006915'.",
+      "output_description": "Returns complete term details including definition, synonyms, and annotations."
+    }
+  },
+  {
+    "name": "GO_get_term_by_id",
+    "description": "Retrieves basic GO term information by ID using GOlr search.",
+    "type": "GeneOntologyTool",
+    "parameter": {
+      "type": "object",
+      "properties": {
+        "id": {
+          "type": "string",
+          "description": "The standard GO term ID, e.g., 'GO:0006915' for apoptotic process."
+        }
+      },
+      "required": ["id"]
+    },
+    "fields": {
+      "endpoint": "http://golr-aux.geneontology.io/solr/select?fq=document_category:\"ontology_class\"&q=*:*&fq=id:\"{id}\"&wt=json",
+      "extract_path": "response.docs[0]",
+      "input_description": "Input GO term ID, e.g., 'GO:0006915'.",
+      "output_description": "Returns the GO term details including label, definition, and namespace."
+    }
+  },
+  {
+    "name": "GO_get_genes_for_term",
+    "description": "Finds all genes/proteins associated with a specific Gene Ontology term using the Biolink API.",
+    "type": "GeneOntologyTool",
+    "parameter": {
+      "type": "object",
+      "properties": {
+        "id": {
+          "type": "string",
+          "description": "The standard GO term ID, e.g., 'GO:0006915'."
+        },
+        "taxon": {
+          "type": "string",
+          "description": "Optional species filter using a NCBI taxon ID. For example, Human is 'NCBITaxon:9606', and Mouse is 'NCBITaxon:10090'."
+        },
+        "rows": {
+            "type": "integer",
+            "description": "The number of genes to return. Default is 100."
+        }
+      },
+      "required": ["id"]
+    },
+    "fields": {
+      "endpoint": "http://api.geneontology.org/api/bioentity/function/{id}",
+      "extract_path": "associations[*].subject",
+      "input_description": "Input GO term ID, e.g., 'GO:0006915'.",
+      "output_description": "Returns a list of genes/proteins associated with the GO term."
+    }
+  },
+  {
+    "name": "GO_get_annotations_for_gene",
+    "description": "Finds all GO annotations for a specific gene/protein using GOlr search.",
+    "type": "GeneOntologyTool",
+    "parameter": {
+      "type": "object",
+      "properties": {
+        "gene_id": {
+          "type": "string",
+          "description": "A gene identifier such as gene symbol (e.g., 'TP53') or database ID."
+        }
+      },
+      "required": ["gene_id"]
+    },
+    "fields": {
+      "endpoint": "http://golr-aux.geneontology.io/solr/select?fq=document_category:\"annotation\"&q=*:*&fq=bioentity_label:\"{gene_id}\"&wt=json&rows=50",
+      "extract_path": "response.docs",
+      "input_description": "Input gene identifier, e.g., 'TP53'.",
+      "output_description": "Returns a list of GO annotations for the gene."
+    }
+  }
+]