tooluniverse 1.0.10__py3-none-any.whl → 1.0.11.1__py3-none-any.whl

tooluniverse/data/interpro_tools.json

@@ -0,0 +1,199 @@
+[
+  {
+    "type": "InterProRESTTool",
+    "name": "InterPro_get_protein_domains",
+    "description": "Get protein domain annotations from InterPro database using UniProt protein ID. Returns domain families, signatures, and functional annotations.",
+    "parameter": {
+      "type": "object",
+      "properties": {
+        "protein_id": {
+          "type": "string",
+          "description": "UniProt protein ID (e.g., P05067, Q9Y6K9)"
+        }
+      },
+      "required": ["protein_id"]
+    },
+    "fields": {
+      "endpoint": "https://www.ebi.ac.uk/interpro/api/entry/interpro/protein/UniProt/{protein_id}",
+      "extract_path": "results",
+      "return_format": "JSON"
+    },
+    "return_schema": {
+      "type": "array",
+      "description": "List of InterPro entries for the protein",
+      "items": {
+        "type": "object",
+        "properties": {
+          "metadata": {
+            "type": "object",
+            "properties": {
+              "accession": {"type": "string"},
+              "name": {"type": "string"},
+              "type": {"type": "string"},
+              "source_database": {"type": "string"},
+              "integrated": {"type": "string"},
+              "member_databases": {"type": "object"},
+              "go_terms": {
+                "type": "array",
+                "items": {
+                  "type": "object",
+                  "properties": {
+                    "identifier": {"type": "string"},
+                    "name": {"type": "string"},
+                    "category": {
+                      "type": "object",
+                      "properties": {
+                        "code": {"type": "string"},
+                        "name": {"type": "string"}
+                      }
+                    }
+                  }
+                }
+              }
+            }
+          },
+          "proteins": {
+            "type": "array",
+            "items": {
+              "type": "object",
+              "properties": {
+                "accession": {"type": "string"},
+                "protein_length": {"type": "integer"},
+                "source_database": {"type": "string"},
+                "organism": {"type": "string"},
+                "in_alphafold": {"type": "boolean"},
+                "in_bfvd": {"type": "boolean"},
+                "entry_protein_locations": {
+                  "type": "array",
+                  "items": {
+                    "type": "object",
+                    "properties": {
+                      "fragments": {"type": "array"},
+                      "representative": {"type": "boolean"},
+                      "model": {"type": "string"},
+                      "score": {"type": "number"}
+                    }
+                  }
+                }
+              }
+            }
+          }
+        }
+      }
+    },
+    "test_examples": [
+      {
+        "protein_id": "P05067"
+      },
+      {
+        "protein_id": "Q9Y6K9"
+      }
+    ]
+  },
+  {
+    "type": "InterProRESTTool",
+    "name": "InterPro_search_domains",
+    "description": "Search InterPro database for protein domains and families by name or accession. Returns matching domain entries with metadata.",
+    "parameter": {
+      "type": "object",
+      "properties": {
+        "query": {
+          "type": "string",
+          "description": "Domain name, accession, or search term (e.g., 'kinase', 'IPR000719')"
+        },
+        "size": {
+          "type": "integer",
+          "description": "Number of results to return (default: 20, max: 100)",
+          "default": 20,
+          "minimum": 1,
+          "maximum": 100
+        }
+      },
+      "required": ["query"]
+    },
+    "fields": {
+      "endpoint": "https://www.ebi.ac.uk/interpro/api/entry/interpro/search?query={query}&size={size}",
+      "extract_path": "results",
+      "return_format": "JSON"
+    },
+    "return_schema": {
+      "type": "array",
+      "description": "List of matching InterPro entries",
+      "items": {
+        "type": "object",
+        "properties": {
+          "metadata": {
+            "type": "object",
+            "properties": {
+              "accession": {"type": "string"},
+              "name": {"type": "string"},
+              "type": {"type": "string"},
+              "source_database": {"type": "string"}
+            }
+          }
+        }
+      }
+    },
+    "test_examples": [
+      {
+        "query": "kinase",
+        "size": 5
+      },
+      {
+        "query": "IPR000719",
+        "size": 1
+      }
+    ]
+  },
+  {
+    "type": "InterProRESTTool",
+    "name": "InterPro_get_domain_details",
+    "description": "Get detailed information about a specific InterPro domain entry including description, hierarchy, and member databases.",
+    "parameter": {
+      "type": "object",
+      "properties": {
+        "accession": {
+          "type": "string",
+          "description": "InterPro accession ID (e.g., IPR000719, IPR000719)"
+        }
+      },
+      "required": ["accession"]
+    },
+    "fields": {
+      "endpoint": "https://www.ebi.ac.uk/interpro/api/entry/interpro/{accession}",
+      "return_format": "JSON"
+    },
+    "return_schema": {
+      "type": "object",
+      "description": "Detailed InterPro entry information",
+      "properties": {
+        "metadata": {
+          "type": "object",
+          "properties": {
+            "accession": {"type": "string"},
+            "name": {"type": "string"},
+            "type": {"type": "string"},
+            "source_database": {"type": "string"},
+            "description": {"type": "string"}
+          }
+        },
+        "hierarchy": {
+          "type": "object",
+          "description": "Domain hierarchy information"
+        },
+        "member_databases": {
+          "type": "object",
+          "description": "Member database signatures"
+        }
+      }
+    },
+    "test_examples": [
+      {
+        "accession": "IPR000719"
+      },
+      {
+        "accession": "IPR000719"
+      }
+    ]
+  }
+]

tooluniverse/data/jaspar_tools.json

@@ -0,0 +1,70 @@
+[
+  {
+    "type": "JASPARRESTTool",
+    "name": "JASPAR_get_transcription_factors",
+    "description": "Get transcription factor binding site matrices from JASPAR",
+    "parameter": {
+      "type": "object",
+      "properties": {
+        "collection": {"type": "string", "default": "CORE", "description": "JASPAR collection"},
+        "limit": {"type": "integer", "default": 20, "description": "Number of results"}
+      }
+    },
+    "fields": {
+      "endpoint": "https://jaspar.elixir.no/api/v1/matrix/?collection={collection}&limit={limit}",
+      "return_format": "JSON"
+    },
+    "return_schema": {
+      "type": "object",
+      "properties": {
+        "results": {
+          "type": "array",
+          "items": {
+            "type": "object",
+            "properties": {
+              "matrix_id": {"type": "string"},
+              "name": {"type": "string"},
+              "collection": {"type": "string"},
+              "species": {"type": "array"},
+              "class": {"type": "string"},
+              "family": {"type": "string"},
+              "tax_group": {"type": "string"},
+              "type": {"type": "string"},
+              "version": {"type": "integer"},
+              "base_id": {"type": "string"},
+              "uniprot_ids": {"type": "array"},
+              "data_type": {"type": "string"},
+              "pubmed_id": {"type": "array"},
+              "jaspar_id": {"type": "string"},
+              "pfm": {
+                "type": "object",
+                "properties": {
+                  "A": {"type": "array"},
+                  "C": {"type": "array"},
+                  "G": {"type": "array"},
+                  "T": {"type": "array"}
+                }
+              },
+              "pwm": {
+                "type": "object",
+                "properties": {
+                  "A": {"type": "array"},
+                  "C": {"type": "array"},
+                  "G": {"type": "array"},
+                  "T": {"type": "array"}
+                }
+              }
+            }
+          }
+        },
+        "count": {"type": "integer"},
+        "next": {"type": "string"},
+        "previous": {"type": "string"}
+      }
+    },
+    "test_examples": [
+      {"collection": "CORE", "limit": 5},
+      {"collection": "CNE", "limit": 10}
+    ]
+  }
+]

tooluniverse/data/kegg_tools.json

@@ -0,0 +1,356 @@
+[
+  {
+    "type": "KEGGSearchPathway",
+    "name": "kegg_search_pathway",
+    "description": "Search KEGG pathways by keyword. Returns pathway IDs and descriptions matching the search term.",
+    "parameter": {
+      "type": "object",
+      "properties": {
+        "keyword": {
+          "type": "string",
+          "description": "Search keyword for pathway names or descriptions (e.g., 'diabetes', 'metabolism')"
+        }
+      },
+      "required": ["keyword"]
+    },
+    "fields": {
+      "endpoint": "/find/pathway",
+      "return_format": "TEXT"
+    },
+    "return_schema": {
+      "type": "object",
+      "description": "KEGG pathway search results",
+      "properties": {
+        "status": {
+          "type": "string",
+          "description": "Status of the request"
+        },
+        "data": {
+          "type": "array",
+          "description": "Array of pathway results",
+          "items": {
+            "type": "object",
+            "properties": {
+              "pathway_id": {
+                "type": "string",
+                "description": "KEGG pathway identifier"
+              },
+              "description": {
+                "type": "string",
+                "description": "Pathway description"
+              }
+            }
+          }
+        },
+        "count": {
+          "type": "integer",
+          "description": "Number of pathways found"
+        },
+        "url": {
+          "type": "string",
+          "description": "API URL used"
+        }
+      }
+    },
+    "test_examples": [
+      {
+        "keyword": "diabetes"
+      },
+      {
+        "keyword": "metabolism"
+      }
+    ],
+    "label": [
+      "KEGG",
+      "Pathway",
+      "Search"
+    ],
+    "metadata": {
+      "tags": ["pathway", "metabolism", "search"],
+      "difficulty_level": "easy",
+      "estimated_execution_time": "< 2 seconds"
+    }
+  },
+  {
+    "type": "KEGGGetPathwayInfo",
+    "name": "kegg_get_pathway_info",
+    "description": "Get detailed pathway information from KEGG by pathway ID. Returns pathway data including genes, compounds, and reactions.",
+    "parameter": {
+      "type": "object",
+      "properties": {
+        "pathway_id": {
+          "type": "string",
+          "description": "KEGG pathway identifier (e.g., 'hsa00010', 'path:hsa00010')"
+        }
+      },
+      "required": ["pathway_id"]
+    },
+    "fields": {
+      "endpoint": "/get",
+      "return_format": "TEXT"
+    },
+    "return_schema": {
+      "type": "object",
+      "description": "KEGG pathway information",
+      "properties": {
+        "status": {
+          "type": "string",
+          "description": "Status of the request"
+        },
+        "data": {
+          "type": "object",
+          "description": "Pathway information",
+          "properties": {
+            "pathway_id": {
+              "type": "string",
+              "description": "KEGG pathway identifier"
+            },
+            "raw_data": {
+              "type": "string",
+              "description": "Raw pathway data from KEGG"
+            },
+            "lines": {
+              "type": "integer",
+              "description": "Number of data lines"
+            }
+          }
+        },
+        "url": {
+          "type": "string",
+          "description": "API URL used"
+        }
+      }
+    },
+    "test_examples": [
+      {
+        "pathway_id": "hsa00010"
+      },
+      {
+        "pathway_id": "hsa04910"
+      }
+    ],
+    "label": [
+      "KEGG",
+      "Pathway",
+      "Information"
+    ],
+    "metadata": {
+      "tags": ["pathway", "details", "genes"],
+      "difficulty_level": "easy",
+      "estimated_execution_time": "< 2 seconds"
+    }
+  },
+  {
+    "type": "KEGGFindGenes",
+    "name": "kegg_find_genes",
+    "description": "Find genes in KEGG database by keyword. Can search across all organisms or within a specific organism.",
+    "parameter": {
+      "type": "object",
+      "properties": {
+        "keyword": {
+          "type": "string",
+          "description": "Search keyword for gene names or descriptions"
+        },
+        "organism": {
+          "type": "string",
+          "description": "Organism code (e.g., 'hsa' for human, 'mmu' for mouse). Optional - searches all organisms if not specified",
+          "default": ""
+        }
+      },
+      "required": ["keyword"]
+    },
+    "fields": {
+      "endpoint": "/find/genes",
+      "return_format": "TEXT"
+    },
+    "return_schema": {
+      "type": "object",
+      "description": "KEGG gene search results",
+      "properties": {
+        "status": {
+          "type": "string",
+          "description": "Status of the request"
+        },
+        "data": {
+          "type": "array",
+          "description": "Array of gene results",
+          "items": {
+            "type": "object",
+            "properties": {
+              "gene_id": {
+                "type": "string",
+                "description": "KEGG gene identifier"
+              },
+              "description": {
+                "type": "string",
+                "description": "Gene description"
+              }
+            }
+          }
+        },
+        "count": {
+          "type": "integer",
+          "description": "Number of genes found"
+        },
+        "url": {
+          "type": "string",
+          "description": "API URL used"
+        }
+      }
+    },
+    "test_examples": [
+      {
+        "keyword": "insulin"
+      },
+      {
+        "keyword": "glucose",
+        "organism": "hsa"
+      }
+    ],
+    "label": [
+      "KEGG",
+      "Gene",
+      "Search"
+    ],
+    "metadata": {
+      "tags": ["gene", "search", "organism"],
+      "difficulty_level": "easy",
+      "estimated_execution_time": "< 2 seconds"
+    }
+  },
+  {
+    "type": "KEGGGetGeneInfo",
+    "name": "kegg_get_gene_info",
+    "description": "Get detailed gene information from KEGG by gene ID. Returns gene data including sequence, function, and pathway associations.",
+    "parameter": {
+      "type": "object",
+      "properties": {
+        "gene_id": {
+          "type": "string",
+          "description": "KEGG gene identifier (e.g., 'hsa:348', 'hsa:3480')"
+        }
+      },
+      "required": ["gene_id"]
+    },
+    "fields": {
+      "endpoint": "/get",
+      "return_format": "TEXT"
+    },
+    "return_schema": {
+      "type": "object",
+      "description": "KEGG gene information",
+      "properties": {
+        "status": {
+          "type": "string",
+          "description": "Status of the request"
+        },
+        "data": {
+          "type": "object",
+          "description": "Gene information",
+          "properties": {
+            "gene_id": {
+              "type": "string",
+              "description": "KEGG gene identifier"
+            },
+            "raw_data": {
+              "type": "string",
+              "description": "Raw gene data from KEGG"
+            },
+            "lines": {
+              "type": "integer",
+              "description": "Number of data lines"
+            }
+          }
+        },
+        "url": {
+          "type": "string",
+          "description": "API URL used"
+        }
+      }
+    },
+    "test_examples": [
+      {
+        "gene_id": "hsa:348"
+      },
+      {
+        "gene_id": "hsa:3480"
+      }
+    ],
+    "label": [
+      "KEGG",
+      "Gene",
+      "Information"
+    ],
+    "metadata": {
+      "tags": ["gene", "details", "sequence"],
+      "difficulty_level": "easy",
+      "estimated_execution_time": "< 2 seconds"
+    }
+  },
+  {
+    "type": "KEGGListOrganisms",
+    "name": "kegg_list_organisms",
+    "description": "List all available organisms in the KEGG database. Returns organism codes, names, and descriptions.",
+    "parameter": {
+      "type": "object",
+      "properties": {},
+      "required": []
+    },
+    "fields": {
+      "endpoint": "/list/organism",
+      "return_format": "TEXT"
+    },
+    "return_schema": {
+      "type": "object",
+      "description": "KEGG organism list",
+      "properties": {
+        "status": {
+          "type": "string",
+          "description": "Status of the request"
+        },
+        "data": {
+          "type": "array",
+          "description": "Array of organism information",
+          "items": {
+            "type": "object",
+            "properties": {
+              "organism_code": {
+                "type": "string",
+                "description": "KEGG organism code (e.g., 'hsa', 'mmu')"
+              },
+              "organism_name": {
+                "type": "string",
+                "description": "Organism scientific name"
+              },
+              "description": {
+                "type": "string",
+                "description": "Organism description"
+              }
+            }
+          }
+        },
+        "count": {
+          "type": "integer",
+          "description": "Number of organisms"
+        },
+        "url": {
+          "type": "string",
+          "description": "API URL used"
+        }
+      }
+    },
+    "test_examples": [
+      {}
+    ],
+    "label": [
+      "KEGG",
+      "Organism",
+      "List"
+    ],
+    "metadata": {
+      "tags": ["organism", "list", "taxonomy"],
+      "difficulty_level": "easy",
+      "estimated_execution_time": "< 2 seconds"
+    }
+  }
+]