tooluniverse 1.0.6__py3-none-any.whl → 1.0.8__py3-none-any.whl

tooluniverse/data/finder_tools.json

@@ -8,15 +8,17 @@
       "properties": {
         "description": {
           "type": "string",
-          "description": "The description of the tool capability required.",
-          "required": true
+          "description": "The description of the tool capability required."
         },
         "limit": {
           "type": "integer",
-          "description": "The number of tools to retrieve",
-          "required": true
+          "description": "The number of tools to retrieve"
         }
-      }
+      },
+      "required": [
+        "description",
+        "limit"
+      ]
     },
     "required": [
       "description",
@@ -43,36 +45,35 @@
       "properties": {
         "description": {
           "type": "string",
-          "description": "The description of the tool capability required.",
-          "required": true
+          "description": "The description of the tool capability required."
         },
         "limit": {
           "type": "integer",
-          "description": "The number of tools to retrieve",
-          "required": true
+          "description": "The number of tools to retrieve"
         },
         "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
+          "description": "Pre-selected tool names to process. If provided, tool selection will skip these tools."
         },
         "return_call_result": {
           "type": "boolean",
-          "description": "Whether to return both prompts and tool names. If false, returns only tool prompts.",
-          "required": false
+          "description": "Whether to return both prompts and tool names. If false, returns only tool prompts."
         },
         "categories": {
           "type": "array",
           "items": {
             "type": "string"
           },
-          "description": "Optional list of tool categories to filter by",
-          "required": false
+          "description": "Optional list of tool categories to filter by"
         }
-      }
+      },
+      "required": [
+        "description",
+        "limit"
+      ]
     },
     "required": [
       "description",
@@ -99,34 +100,29 @@
       "properties": {
         "description": {
           "type": "string",
-          "description": "The description of the tool capability required.",
-          "required": true
+          "description": "The description of the tool capability required."
         },
         "limit": {
           "type": "integer",
-          "description": "The number of tools to retrieve",
-          "required": true
+          "description": "The number of tools to retrieve"
         },
         "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
+          "description": "Pre-selected tool names to process. If provided, tool selection will skip these tools."
         },
         "return_call_result": {
           "type": "boolean",
-          "description": "Whether to return both prompts and tool names. If false, returns only tool prompts.",
-          "required": false
+          "description": "Whether to return both prompts and tool names. If false, returns only tool prompts."
         },
         "categories": {
           "type": "array",
           "items": {
             "type": "string"
           },
-          "description": "Optional list of tool categories to filter by",
-          "required": false
+          "description": "Optional list of tool categories to filter by"
         }
       },
       "required": [
@@ -160,36 +156,35 @@
       "properties": {
         "description": {
           "type": "string",
-          "description": "The description of the tool capability required.",
-          "required": true
+          "description": "The description of the tool capability required."
         },
         "limit": {
           "type": "integer",
-          "description": "The number of tools to retrieve",
-          "required": true
+          "description": "The number of tools to retrieve"
         },
         "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
+          "description": "Pre-selected tool names to process. If provided, tool selection will skip these tools."
         },
         "return_call_result": {
           "type": "boolean",
-          "description": "Whether to return both prompts and tool names. If false, returns only tool prompts.",
-          "required": false
+          "description": "Whether to return both prompts and tool names. If false, returns only tool prompts."
         },
         "categories": {
           "type": "array",
           "items": {
             "type": "string"
           },
-          "description": "Optional list of tool categories to filter by",
-          "required": false
+          "description": "Optional list of tool categories to filter by"
         }
-      }
+      },
+      "required": [
+        "description",
+        "limit"
+      ]
     },
     "required": [
       "description",

tooluniverse/data/gene_ontology_tools.json

@@ -11,7 +11,9 @@
           "description": "The keyword to search for, e.g., 'apoptosis' or 'kinase activity'."
         }
       },
-      "required": ["query"]
+      "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",
@@ -31,7 +33,9 @@
           "description": "The standard GO term ID, e.g., 'GO:0006915' for apoptotic process."
         }
       },
-      "required": ["id"]
+      "required": [
+        "id"
+      ]
     },
     "fields": {
       "endpoint": "http://api.geneontology.org/api/bioentity/function/{id}",
@@ -51,7 +55,9 @@
           "description": "The standard GO term ID, e.g., 'GO:0006915' for apoptotic process."
         }
       },
-      "required": ["id"]
+      "required": [
+        "id"
+      ]
     },
     "fields": {
       "endpoint": "http://golr-aux.geneontology.io/solr/select?fq=document_category:\"ontology_class\"&q=*:*&fq=id:\"{id}\"&wt=json",
@@ -76,11 +82,15 @@
           "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."
+          "type": "integer",
+          "description": "The number of genes to return. Default is 100."
         }
       },
-      "required": ["id"]
+      "required": [
+        "id",
+        "taxon",
+        "rows"
+      ]
     },
     "fields": {
       "endpoint": "http://api.geneontology.org/api/bioentity/function/{id}",
@@ -101,7 +111,9 @@
           "description": "A gene identifier such as gene symbol (e.g., 'TP53') or database ID."
         }
       },
-      "required": ["gene_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",

tooluniverse/data/genomics_tools.json

@@ -0,0 +1,174 @@
+[
+  {
+    "type": "EnsemblTool",
+    "name": "Ensembl_lookup_gene_by_symbol",
+    "description": "Lookup Ensembl gene by species and gene symbol, returning core metadata and coordinates (uses /xrefs/symbol then /lookup/id?expand=1).",
+    "parameter": {
+      "type": "object",
+      "properties": {
+        "species": {"type": "string", "description": "Species name (e.g., 'homo_sapiens').", "default": "homo_sapiens"},
+        "symbol": {"type": "string", "description": "Gene symbol (e.g., BRCA1)."}
+      },
+      "required": ["symbol"]
+    },
+    "return_schema": {
+      "type": "object",
+      "description": "Gene metadata including Ensembl ID, name, location, and transcripts count.",
+      "properties": {
+        "id": {"type": "string"},
+        "symbol": {"type": "string"},
+        "display_name": {"type": "string"},
+        "species": {"type": "string"},
+        "seq_region_name": {"type": "string"},
+        "start": {"type": "integer"},
+        "end": {"type": "integer"},
+        "strand": {"type": "integer"},
+        "biotype": {"type": "string"},
+        "transcript_count": {"type": "integer"}
+      }
+    }
+  },
+  {
+    "type": "ClinVarTool",
+    "name": "ClinVar_search_variants",
+    "description": "Search ClinVar via NCBI E-utilities (esearch→esummary) and return concise variant records for a query term.",
+    "parameter": {
+      "type": "object",
+      "properties": {
+        "query": {"type": "string", "description": "ClinVar search term (e.g., BRCA1)."},
+        "retmax": {"type": "integer", "description": "Max records.", "default": 5}
+      },
+      "required": ["query"]
+    },
+    "return_schema": {
+      "type": "array",
+      "items": {
+        "type": "object",
+        "properties": {
+          "uid": {"type": "string"},
+          "accession": {"type": "string"},
+          "title": {"type": "string"},
+          "gene": {"type": "string"},
+          "chr": {"type": "string"},
+          "start": {"type": "integer"},
+          "stop": {"type": "integer"},
+          "spdi": {"type": "string"},
+          "clinical_significance": {"type": "string"}
+        }
+      }
+    }
+  },
+  {
+    "type": "DbSnpTool",
+    "name": "dbSNP_get_variant_by_rsid",
+    "description": "Fetch dbSNP variant by rsID using NCBI Variation Services (refsnp endpoint).",
+    "parameter": {
+      "type": "object",
+      "properties": {
+        "rsid": {"type": "string", "description": "rsID without 'rs' prefix or with (e.g., rs699 or 699)."}
+      },
+      "required": ["rsid"]
+    },
+    "return_schema": {
+      "type": "object",
+      "properties": {
+        "refsnp_id": {"type": "string"},
+        "chrom": {"type": "string"},
+        "pos": {"type": "integer"},
+        "alleles": {"type": "array", "items": {"type": "string"}},
+        "hgvs": {"type": "array", "items": {"type": "string"}}
+      }
+    }
+  },
+  {
+    "type": "UCSCTool",
+    "name": "UCSC_get_genes_by_region",
+    "description": "Query UCSC Genome Browser track API for knownGene features in a genomic window.",
+    "parameter": {
+      "type": "object",
+      "properties": {
+        "genome": {"type": "string", "description": "Genome assembly (e.g., hg38).", "default": "hg38"},
+        "chrom": {"type": "string", "description": "Chromosome (e.g., chr17)."},
+        "start": {"type": "integer", "description": "Start position (0-based)."},
+        "end": {"type": "integer", "description": "End position."},
+        "track": {"type": "string", "description": "Track name.", "default": "knownGene"}
+      },
+      "required": ["chrom", "start", "end"]
+    },
+    "return_schema": {
+      "type": "object",
+      "properties": {
+        "itemsReturned": {"type": "integer"},
+        "features": {
+          "type": "array",
+          "items": {
+            "type": "object",
+            "properties": {
+              "name": {"type": "string"},
+              "geneName": {"type": "string"},
+              "chrom": {"type": "string"},
+              "chromStart": {"type": "integer"},
+              "chromEnd": {"type": "integer"},
+              "strand": {"type": "string"}
+            }
+          }
+        }
+      }
+    }
+  },
+  {
+    "type": "GnomadTool",
+    "name": "gnomAD_query_variant",
+    "description": "Query gnomAD GraphQL for a variant in a dataset (returns ID and genome allele counts/frequency).",
+    "parameter": {
+      "type": "object",
+      "properties": {
+        "variant_id": {"type": "string", "description": "Variant ID like '1-230710048-A-G'."},
+        "dataset": {"type": "string", "description": "Dataset ID (e.g., gnomad_r4).", "default": "gnomad_r4"}
+      },
+      "required": ["variant_id"]
+    },
+    "return_schema": {
+      "type": "object",
+      "properties": {
+        "variantId": {"type": "string"},
+        "genome": {
+          "type": "object",
+          "properties": {"ac": {"type": "integer"}, "an": {"type": "integer"}, "af": {"type": "number"}}
+        }
+      }
+    }
+  },
+  {
+    "type": "GWASGeneSearch",
+    "name": "GWAS_search_associations_by_gene",
+    "description": "Search GWAS Catalog associations by gene name (returns strongest risk allele and p-value fields).",
+    "parameter": {
+      "type": "object",
+      "properties": {
+        "gene_name": {"type": "string", "description": "Gene symbol (e.g., BRCA1)."},
+        "size": {"type": "integer", "description": "Max associations to return.", "default": 5}
+      },
+      "required": ["gene_name"]
+    },
+    "return_schema": {
+      "type": "object",
+      "properties": {
+        "gene_name": {"type": "string"},
+        "association_count": {"type": "integer"},
+        "associations": {
+          "type": "array",
+          "items": {
+            "type": "object",
+            "properties": {
+              "study": {"type": "string"},
+              "strongestRiskAllele": {"type": "string"},
+              "pvalue": {"type": "number"}
+            }
+          }
+        },
+        "total_found": {"type": "integer"}
+      }
+    }
+  }
+]

tooluniverse/data/geo_tools.json

@@ -0,0 +1,86 @@
+[
+  {
+    "type": "GEORESTTool",
+    "name": "GEO_search_expression_data",
+    "description": "Search gene expression data from the GEO database. GEO is a public repository that archives and freely distributes microarray, next-generation sequencing, and other forms of high-throughput functional genomics data.",
+    "parameter": {
+      "type": "object",
+      "properties": {
+        "query": {
+          "type": "string",
+          "description": "Search query (e.g., 'cancer', 'diabetes', 'microarray')",
+          "minLength": 1
+        },
+        "organism": {
+          "type": "string",
+          "description": "Organism name (e.g., 'Homo sapiens', 'Mus musculus')",
+          "default": "Homo sapiens"
+        },
+        "study_type": {
+          "type": "string",
+          "description": "Type of study (e.g., 'expression', 'methylation', 'genome')",
+          "enum": ["expression", "methylation", "genome", "sequence", "other"]
+        },
+        "platform": {
+          "type": "string",
+          "description": "Platform used (e.g., 'GPL96', 'GPL570')"
+        },
+        "date_range": {
+          "type": "string",
+          "description": "Date range in format 'YYYY:YYYY' (e.g., '2020:2023')"
+        },
+        "limit": {
+          "type": "integer",
+          "description": "Maximum number of results to return (default: 50)",
+          "minimum": 1,
+          "maximum": 500,
+          "default": 50
+        },
+        "sort": {
+          "type": "string",
+          "description": "Sort order ('relevance', 'date', 'title')",
+          "enum": ["relevance", "date", "title"],
+          "default": "relevance"
+        }
+      },
+      "required": ["query"]
+    },
+    "fields": {
+      "endpoint": "/esearch.fcgi",
+      "return_format": "JSON"
+    },
+    "return_schema": {
+      "type": "object",
+      "properties": {
+        "success": {"type": "boolean"},
+        "count": {"type": "integer"},
+        "studies": {
+          "type": "array",
+          "items": {
+            "type": "object",
+            "properties": {
+              "id": {"type": "string"},
+              "title": {"type": "string"},
+              "summary": {"type": "string"},
+              "organism": {"type": "string"},
+              "platform": {"type": "string"},
+              "samples": {"type": "integer"},
+              "series_type": {"type": "string"},
+              "publication_date": {"type": "string"},
+              "submission_date": {"type": "string"},
+              "contact": {"type": "string"},
+              "citation": {"type": "string"}
+            }
+          }
+        },
+        "query_translation": {"type": "string"},
+        "error": {"type": "string"}
+      }
+    },
+    "implementation": {
+      "language": "python",
+      "dependencies": ["requests"],
+      "source_file": "geo_tool.py"
+    }
+  }
+]