tooluniverse 1.0.9.1__py3-none-any.whl → 1.0.11__py3-none-any.whl

tooluniverse/data/dbsnp_tools.json

@@ -0,0 +1,275 @@
+[
+  {
+    "type": "dbSNPGetVariantByRsID",
+    "name": "dbsnp_get_variant_by_rsid",
+    "description": "Get variant information from dbSNP by rsID. Returns genomic coordinates, alleles, and basic variant information.",
+    "parameter": {
+      "type": "object",
+      "properties": {
+        "rsid": {
+          "type": "string",
+          "description": "dbSNP rsID (e.g., 'rs12345', '12345')"
+        }
+      },
+      "required": ["rsid"]
+    },
+    "fields": {
+      "endpoint": "/beta/refsnp",
+      "return_format": "JSON"
+    },
+    "return_schema": {
+      "type": "object",
+      "description": "dbSNP variant information",
+      "properties": {
+        "status": {
+          "type": "string",
+          "description": "Status of the request"
+        },
+        "data": {
+          "type": "object",
+          "description": "Variant information from dbSNP",
+          "properties": {
+            "refsnp_id": {
+              "type": "string",
+              "description": "dbSNP reference ID"
+            },
+            "primary_snapshot_data": {
+              "type": "object",
+              "description": "Primary variant data",
+              "properties": {
+                "placements_with_allele": {
+                  "type": "array",
+                  "description": "Genomic placements",
+                  "items": {
+                    "type": "object",
+                    "properties": {
+                      "seq_id": {
+                        "type": "string",
+                        "description": "Chromosome"
+                      },
+                      "position": {
+                        "type": "integer",
+                        "description": "Genomic position"
+                      },
+                      "alleles": {
+                        "type": "array",
+                        "description": "Allele information"
+                      }
+                    }
+                  }
+                }
+              }
+            }
+          }
+        },
+        "rsid": {
+          "type": "string",
+          "description": "Input rsID"
+        },
+        "url": {
+          "type": "string",
+          "description": "API URL used"
+        }
+      }
+    },
+    "test_examples": [
+      {
+        "rsid": "rs12345"
+      },
+      {
+        "rsid": "rs429358"
+      }
+    ],
+    "label": [
+      "dbSNP",
+      "Variant",
+      "RsID"
+    ],
+    "metadata": {
+      "tags": ["snp", "variant", "genomics"],
+      "difficulty_level": "easy",
+      "estimated_execution_time": "< 2 seconds"
+    }
+  },
+  {
+    "type": "dbSNPSearchByGene",
+    "name": "dbsnp_search_by_gene",
+    "description": "Search for variants in a specific gene. Returns variants associated with the gene symbol.",
+    "parameter": {
+      "type": "object",
+      "properties": {
+        "gene_symbol": {
+          "type": "string",
+          "description": "Gene symbol (e.g., 'BRCA1', 'TP53', 'APOE')"
+        },
+        "limit": {
+          "type": "integer",
+          "description": "Maximum number of results to return",
+          "default": 20,
+          "minimum": 1,
+          "maximum": 100
+        }
+      },
+      "required": ["gene_symbol"]
+    },
+    "fields": {
+      "endpoint": "/beta/refsnp",
+      "return_format": "JSON"
+    },
+    "return_schema": {
+      "type": "object",
+      "description": "dbSNP gene search results",
+      "properties": {
+        "status": {
+          "type": "string",
+          "description": "Status of the request"
+        },
+        "data": {
+          "type": "object",
+          "description": "Search results from dbSNP",
+          "properties": {
+            "variants": {
+              "type": "array",
+              "description": "Array of variant information",
+              "items": {
+                "type": "object",
+                "properties": {
+                  "refsnp_id": {
+                    "type": "string",
+                    "description": "dbSNP reference ID"
+                  },
+                  "gene": {
+                    "type": "string",
+                    "description": "Gene symbol"
+                  },
+                  "position": {
+                    "type": "integer",
+                    "description": "Genomic position"
+                  }
+                }
+              }
+            }
+          }
+        },
+        "gene_symbol": {
+          "type": "string",
+          "description": "Input gene symbol"
+        },
+        "url": {
+          "type": "string",
+          "description": "API URL used"
+        }
+      }
+    },
+    "test_examples": [
+      {
+        "gene_symbol": "BRCA1",
+        "limit": 10
+      },
+      {
+        "gene_symbol": "TP53",
+        "limit": 5
+      }
+    ],
+    "label": [
+      "dbSNP",
+      "Gene",
+      "Search"
+    ],
+    "metadata": {
+      "tags": ["gene", "search", "variants"],
+      "difficulty_level": "easy",
+      "estimated_execution_time": "< 3 seconds"
+    }
+  },
+  {
+    "type": "dbSNPGetFrequencies",
+    "name": "dbsnp_get_frequencies",
+    "description": "Get allele frequencies for a variant from dbSNP. Returns population-specific allele frequency data.",
+    "parameter": {
+      "type": "object",
+      "properties": {
+        "rsid": {
+          "type": "string",
+          "description": "dbSNP rsID (e.g., 'rs12345', '12345')"
+        }
+      },
+      "required": ["rsid"]
+    },
+    "fields": {
+      "endpoint": "/beta/refsnp",
+      "return_format": "JSON"
+    },
+    "return_schema": {
+      "type": "object",
+      "description": "dbSNP allele frequency data",
+      "properties": {
+        "status": {
+          "type": "string",
+          "description": "Status of the request"
+        },
+        "data": {
+          "type": "object",
+          "description": "Variant information from dbSNP",
+          "properties": {
+            "refsnp_id": {
+              "type": "string",
+              "description": "dbSNP reference ID"
+            },
+            "primary_snapshot_data": {
+              "type": "object",
+              "description": "Primary variant data"
+            }
+          }
+        },
+        "frequencies": {
+          "type": "array",
+          "description": "Array of allele frequency data",
+          "items": {
+            "type": "object",
+            "properties": {
+              "population": {
+                "type": "string",
+                "description": "Population name"
+              },
+              "allele": {
+                "type": "string",
+                "description": "Allele"
+              },
+              "frequency": {
+                "type": "number",
+                "description": "Allele frequency"
+              }
+            }
+          }
+        },
+        "rsid": {
+          "type": "string",
+          "description": "Input rsID"
+        },
+        "url": {
+          "type": "string",
+          "description": "API URL used"
+        }
+      }
+    },
+    "test_examples": [
+      {
+        "rsid": "rs429358"
+      },
+      {
+        "rsid": "rs7412"
+      }
+    ],
+    "label": [
+      "dbSNP",
+      "Frequency",
+      "Population"
+    ],
+    "metadata": {
+      "tags": ["frequency", "population", "allele"],
+      "difficulty_level": "easy",
+      "estimated_execution_time": "< 2 seconds"
+    }
+  }
+]

tooluniverse/data/emdb_tools.json

@@ -0,0 +1,61 @@
+[
+  {
+    "type": "EMDBRESTTool",
+    "name": "EMDB_get_structure",
+    "description": "Get electron microscopy structure data from EMDB",
+    "parameter": {
+      "type": "object",
+      "properties": {
+        "emdb_id": {"type": "string", "description": "EMDB structure ID (e.g., EMD-1234)"}
+      },
+      "required": ["emdb_id"]
+    },
+    "fields": {
+      "endpoint": "https://www.ebi.ac.uk/emdb/api/entry/{emdb_id}",
+      "return_format": "JSON"
+    },
+    "return_schema": {
+      "type": "object",
+      "properties": {
+        "emdb_id": {"type": "string"},
+        "title": {"type": "string"},
+        "description": {"type": "string"},
+        "resolution": {"type": "number"},
+        "method": {"type": "string"},
+        "organism": {"type": "string"},
+        "molecule": {"type": "string"},
+        "deposition_date": {"type": "string"},
+        "release_date": {"type": "string"},
+        "authors": {"type": "array"},
+        "journal": {"type": "string"},
+        "volume": {"type": "string"},
+        "page": {"type": "string"},
+        "year": {"type": "integer"},
+        "doi": {"type": "string"},
+        "pdb_id": {"type": "string"},
+        "map_url": {"type": "string"},
+        "contour_level": {"type": "number"},
+        "voxel_size": {
+          "type": "object",
+          "properties": {
+            "x": {"type": "number"},
+            "y": {"type": "number"},
+            "z": {"type": "number"}
+          }
+        },
+        "map_dimensions": {
+          "type": "object",
+          "properties": {
+            "x": {"type": "integer"},
+            "y": {"type": "integer"},
+            "z": {"type": "integer"}
+          }
+        }
+      }
+    },
+    "test_examples": [
+      {"emdb_id": "EMD-1234"},
+      {"emdb_id": "EMD-0001"}
+    ]
+  }
+]

tooluniverse/data/ensembl_tools.json

@@ -0,0 +1,259 @@
+[
+  {
+    "type": "EnsemblLookupGene",
+    "name": "ensembl_lookup_gene",
+    "description": "Lookup gene information by Ensembl gene ID or symbol. Returns gene details including location, description, and external references.",
+    "parameter": {
+      "type": "object",
+      "properties": {
+        "gene_id": {
+          "type": "string",
+          "description": "Ensembl gene ID or symbol (e.g., 'ENSG00000139618' or 'BRCA1')"
+        }
+      },
+      "required": ["gene_id"]
+    },
+    "fields": {
+      "endpoint": "/lookup/id",
+      "return_format": "JSON"
+    },
+    "return_schema": {
+      "type": "object",
+      "description": "Ensembl gene lookup data",
+      "properties": {
+        "status": {
+          "type": "string",
+          "description": "Status of the request"
+        },
+        "data": {
+          "type": "object",
+          "description": "Gene information object",
+          "properties": {
+            "id": {
+              "type": "string",
+              "description": "Ensembl gene ID"
+            },
+            "display_name": {
+              "type": "string",
+              "description": "Gene symbol"
+            },
+            "description": {
+              "type": "string",
+              "description": "Gene description"
+            },
+            "biotype": {
+              "type": "string",
+              "description": "Gene biotype"
+            },
+            "start": {
+              "type": "integer",
+              "description": "Gene start position"
+            },
+            "end": {
+              "type": "integer",
+              "description": "Gene end position"
+            },
+            "strand": {
+              "type": "integer",
+              "description": "Gene strand"
+            },
+            "seq_region_name": {
+              "type": "string",
+              "description": "Chromosome name"
+            }
+          }
+        },
+        "gene_id": {
+          "type": "string",
+          "description": "Input gene ID"
+        }
+      }
+    },
+    "test_examples": [
+      {
+        "description": "Lookup BRCA1 gene information",
+        "input": {
+          "gene_id": "ENSG00000012048"
+        },
+        "expected_output": {
+          "status": "success",
+          "data": "Gene information object with BRCA1 details"
+        }
+      }
+    ],
+    "metadata": {
+      "tags": ["gene", "lookup", "annotation"],
+      "difficulty_level": "easy",
+      "estimated_execution_time": "< 2 seconds"
+    }
+  },
+  {
+    "type": "EnsemblGetSequence",
+    "name": "ensembl_get_sequence",
+    "description": "Get DNA sequence for a gene, transcript, or genomic region. Returns sequence in FASTA format.",
+    "parameter": {
+      "type": "object",
+      "properties": {
+        "sequence_id": {
+          "type": "string",
+          "description": "Ensembl gene/transcript ID or genomic region (e.g., 'ENSG00000139618' or '1:1000000-2000000')"
+        },
+        "type": {
+          "type": "string",
+          "description": "Sequence type: 'genomic', 'cds', 'cdna', 'peptide'",
+          "default": "genomic"
+        }
+      },
+      "required": ["sequence_id"]
+    },
+    "fields": {
+      "endpoint": "/sequence/id",
+      "return_format": "JSON"
+    },
+    "return_schema": {
+      "type": "object",
+      "description": "Ensembl sequence data",
+      "properties": {
+        "status": {
+          "type": "string",
+          "description": "Status of the request"
+        },
+        "data": {
+          "type": "array",
+          "description": "Array of sequence objects",
+          "items": {
+            "type": "object",
+            "properties": {
+              "id": {
+                "type": "string",
+                "description": "Sequence ID"
+              },
+              "seq": {
+                "type": "string",
+                "description": "DNA/protein sequence"
+              },
+              "desc": {
+                "type": "string",
+                "description": "Sequence description"
+              },
+              "molecule": {
+                "type": "string",
+                "description": "Molecule type (dna, rna, protein)"
+              }
+            }
+          }
+        },
+        "sequence_id": {
+          "type": "string",
+          "description": "Input sequence ID"
+        }
+      }
+    },
+    "test_examples": [
+      {
+        "description": "Get genomic sequence for BRCA1 gene",
+        "input": {
+          "sequence_id": "ENSG00000012048",
+          "type": "genomic"
+        },
+        "expected_output": {
+          "status": "success",
+          "data": "Array with sequence object containing BRCA1 genomic sequence"
+        }
+      }
+    ],
+    "metadata": {
+      "tags": ["sequence", "dna", "genomic"],
+      "difficulty_level": "easy",
+      "estimated_execution_time": "< 3 seconds"
+    }
+  },
+  {
+    "type": "EnsemblGetVariants",
+    "name": "ensembl_get_variants",
+    "description": "Get genetic variants in a genomic region. Returns SNP and indel information.",
+    "parameter": {
+      "type": "object",
+      "properties": {
+        "region": {
+          "type": "string",
+          "description": "Genomic region in format 'chromosome:start-end' (e.g., '13:32315086-32400268')"
+        },
+        "species": {
+          "type": "string",
+          "description": "Species name",
+          "default": "homo_sapiens"
+        }
+      },
+      "required": ["region"]
+    },
+    "fields": {
+      "endpoint": "/overlap/region",
+      "return_format": "JSON"
+    },
+    "return_schema": {
+      "type": "object",
+      "description": "Ensembl variant data",
+      "properties": {
+        "status": {
+          "type": "string",
+          "description": "Status of the request"
+        },
+        "data": {
+          "type": "array",
+          "description": "Array of variant objects",
+          "items": {
+            "type": "object",
+            "properties": {
+              "id": {
+                "type": "string",
+                "description": "Variant ID"
+              },
+              "start": {
+                "type": "integer",
+                "description": "Variant start position"
+              },
+              "end": {
+                "type": "integer",
+                "description": "Variant end position"
+              },
+              "strand": {
+                "type": "integer",
+                "description": "Variant strand"
+              },
+              "allele_string": {
+                "type": "string",
+                "description": "Allele string (e.g., 'A/T')"
+              },
+              "consequence_type": {
+                "type": "string",
+                "description": "Variant consequence"
+              }
+            }
+          }
+        },
+        "region": {
+          "type": "string",
+          "description": "Input genomic region"
+        }
+      }
+    },
+    "test_examples": [
+      {
+        "description": "Get variants in BRCA1 region",
+        "input": {
+          "region": "13:32315086-32400268"
+        },
+        "expected_output": {
+          "status": "success",
+          "data": "Array of variant objects in BRCA1 region"
+        }
+      }
+    ],
+    "metadata": {
+      "tags": ["variants", "snp", "indel"],
+      "difficulty_level": "easy",
+      "estimated_execution_time": "< 2 seconds"
+    }
+  }
+]