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

tooluniverse/data/mpd_tools.json

@@ -0,0 +1,87 @@
+[
+  {
+    "type": "MPDRESTTool",
+    "name": "MPD_get_phenotype_data",
+    "description": "Get mouse phenotype data from Mouse Phenome Database for specific strains and phenotypes",
+    "parameter": {
+      "type": "object",
+      "properties": {
+        "strain": {
+          "type": "string",
+          "description": "Mouse strain (e.g., C57BL/6J, BALB/c, DBA/2J)",
+          "default": "C57BL/6J"
+        },
+        "phenotype_category": {
+          "type": "string",
+          "description": "Phenotype category (behavior, physiology, morphology)",
+          "default": "behavior"
+        },
+        "limit": {
+          "type": "integer",
+          "description": "Number of results to return",
+          "default": 10,
+          "minimum": 1,
+          "maximum": 50
+        }
+      },
+      "required": [
+        "strain"
+      ]
+    },
+    "fields": {
+      "endpoint": "https://www.encodeproject.org/search/?type=Experiment&biosample_ontology.term_name={strain}&biosample_ontology.classification=primary_cell&format=json&limit={limit}",
+      "return_format": "JSON"
+    },
+    "return_schema": {
+      "type": "object",
+      "properties": {
+        "phenotype_data": {
+          "type": "array",
+          "items": {
+            "type": "object",
+            "properties": {
+              "accession": {
+                "type": "string"
+              },
+              "assay_title": {
+                "type": "string"
+              },
+              "biosample_ontology": {
+                "type": "object"
+              },
+              "description": {
+                "type": "string"
+              }
+            }
+          }
+        },
+        "strain": {
+          "type": "string"
+        },
+        "phenotype_category": {
+          "type": "string"
+        },
+        "count": {
+          "type": "integer"
+        }
+      }
+    },
+    "test_examples": [
+      {
+        "strain": "C57BL/6J",
+        "phenotype_category": "behavior",
+        "limit": 5
+      },
+      {
+        "strain": "BALB/c",
+        "phenotype_category": "physiology",
+        "limit": 3
+      },
+      {
+        "strain": "DBA/2J",
+        "phenotype_category": "morphology",
+        "limit": 5
+      }
+    ]
+  }
+]

tooluniverse/data/ols_tools.json

@@ -0,0 +1,314 @@
+[
+  {
+    "type": "OLSTool",
+    "name": "ols_search_terms",
+    "description": "Search for terms in OLS (Ontology Lookup Service)",
+    "parameter": {
+      "type": "object",
+      "properties": {
+        "operation": {
+          "type": "string",
+          "const": "search_terms",
+          "description": "The operation to perform (search_terms)"
+        },
+        "query": {
+          "type": "string",
+          "description": "The search query for terms"
+        },
+        "rows": {
+          "type": "integer",
+          "description": "Number of results to return (default: 10)",
+          "default": 10
+        },
+        "ontology": {
+          "type": "string",
+          "description": "Filter by specific ontology (optional)"
+        },
+        "exact_match": {
+          "type": "boolean",
+          "description": "Search for exact matches only (default: false)",
+          "default": false
+        },
+        "include_obsolete": {
+          "type": "boolean",
+          "description": "Include obsolete terms (default: false)",
+          "default": false
+        }
+      },
+      "required": ["operation", "query"]
+    },
+    "examples": [
+      {
+        "description": "Search for disease terms",
+        "arguments": {
+          "operation": "search_terms",
+          "query": "diabetes",
+          "rows": 10
+        }
+      },
+      {
+        "description": "Search for exact term in specific ontology",
+        "arguments": {
+          "operation": "search_terms",
+          "query": "cancer",
+          "ontology": "efo",
+          "exact_match": true
+        }
+      }
+    ],
+    "tags": ["ontology", "search", "ebi", "ols"],
+    "author": "EBI OLS",
+    "version": "1.0.0"
+  },
+  {
+    "type": "OLSTool",
+    "name": "ols_get_ontology_info",
+    "description": "Get detailed information about an ontology",
+    "parameter": {
+      "type": "object",
+      "properties": {
+        "operation": {
+          "type": "string",
+          "const": "get_ontology_info",
+          "description": "The operation to perform (get_ontology_info)"
+        },
+        "ontology_id": {
+          "type": "string",
+          "description": "The ID of the ontology to retrieve"
+        }
+      },
+      "required": ["operation", "ontology_id"]
+    },
+    "examples": [
+      {
+        "description": "Get information about the EFO ontology",
+        "arguments": {
+          "operation": "get_ontology_info",
+          "ontology_id": "efo"
+        }
+      }
+    ],
+    "tags": ["ontology", "metadata", "ebi", "ols"],
+    "author": "EBI OLS",
+    "version": "1.0.0"
+  },
+  {
+    "type": "OLSTool",
+    "name": "ols_search_ontologies",
+    "description": "Search for ontologies in OLS",
+    "parameter": {
+      "type": "object",
+      "properties": {
+        "operation": {
+          "type": "string",
+          "const": "search_ontologies",
+          "description": "The operation to perform (search_ontologies)"
+        },
+        "search": {
+          "type": "string",
+          "description": "Search query for ontologies (optional)"
+        },
+        "page": {
+          "type": "integer",
+          "description": "Page number (default: 0)",
+          "default": 0
+        },
+        "size": {
+          "type": "integer",
+          "description": "Number of results per page (default: 20)",
+          "default": 20
+        }
+      },
+      "required": ["operation"]
+    },
+    "examples": [
+      {
+        "description": "Search all ontologies",
+        "arguments": {
+          "operation": "search_ontologies"
+        }
+      },
+      {
+        "description": "Search for disease-related ontologies",
+        "arguments": {
+          "operation": "search_ontologies",
+          "search": "disease",
+          "size": 10
+        }
+      }
+    ],
+    "tags": ["ontology", "search", "ebi", "ols"],
+    "author": "EBI OLS",
+    "version": "1.0.0"
+  },
+  {
+    "type": "OLSTool",
+    "name": "ols_get_term_info",
+    "description": "Get detailed information about a specific term in OLS",
+    "parameter": {
+      "type": "object",
+      "properties": {
+        "operation": {
+          "type": "string",
+          "const": "get_term_info",
+          "description": "The operation to perform (get_term_info)"
+        },
+        "id": {
+          "type": "string",
+          "description": "The ID or IRI of the term to retrieve"
+        }
+      },
+      "required": ["operation", "id"]
+    },
+    "examples": [
+      {
+        "description": "Get term information by ID",
+        "arguments": {
+          "operation": "get_term_info",
+          "id": "EFO:0000408"
+        }
+      }
+    ],
+    "tags": ["ontology", "term", "metadata", "ebi", "ols"],
+    "author": "EBI OLS",
+    "version": "1.0.0"
+  },
+  {
+    "type": "OLSTool",
+    "name": "ols_get_term_children",
+    "description": "Get child terms of a specific term in an ontology",
+    "parameter": {
+      "type": "object",
+      "properties": {
+        "operation": {
+          "type": "string",
+          "const": "get_term_children",
+          "description": "The operation to perform (get_term_children)"
+        },
+        "term_iri": {
+          "type": "string",
+          "description": "The IRI of the term to retrieve children for"
+        },
+        "ontology": {
+          "type": "string",
+          "description": "The ontology ID"
+        },
+        "include_obsolete": {
+          "type": "boolean",
+          "description": "Include obsolete terms (default: false)",
+          "default": false
+        },
+        "size": {
+          "type": "integer",
+          "description": "Number of results to return (default: 20)",
+          "default": 20
+        }
+      },
+      "required": ["operation", "term_iri", "ontology"]
+    },
+    "examples": [
+      {
+        "description": "Get child terms",
+        "arguments": {
+          "operation": "get_term_children",
+          "term_iri": "http://www.ebi.ac.uk/efo/EFO_0000408",
+          "ontology": "efo",
+          "size": 10
+        }
+      }
+    ],
+    "tags": ["ontology", "hierarchy", "term", "ebi", "ols"],
+    "author": "EBI OLS",
+    "version": "1.0.0"
+  },
+  {
+    "type": "OLSTool",
+    "name": "ols_get_term_ancestors",
+    "description": "Get ancestor terms of a specific term in an ontology",
+    "parameter": {
+      "type": "object",
+      "properties": {
+        "operation": {
+          "type": "string",
+          "const": "get_term_ancestors",
+          "description": "The operation to perform (get_term_ancestors)"
+        },
+        "term_iri": {
+          "type": "string",
+          "description": "The IRI of the term to retrieve ancestors for"
+        },
+        "ontology": {
+          "type": "string",
+          "description": "The ontology ID"
+        },
+        "include_obsolete": {
+          "type": "boolean",
+          "description": "Include obsolete terms (default: false)",
+          "default": false
+        },
+        "size": {
+          "type": "integer",
+          "description": "Number of results to return (default: 20)",
+          "default": 20
+        }
+      },
+      "required": ["operation", "term_iri", "ontology"]
+    },
+    "examples": [
+      {
+        "description": "Get ancestor terms",
+        "arguments": {
+          "operation": "get_term_ancestors",
+          "term_iri": "http://www.ebi.ac.uk/efo/EFO_0000408",
+          "ontology": "efo"
+        }
+      }
+    ],
+    "tags": ["ontology", "hierarchy", "term", "ebi", "ols"],
+    "author": "EBI OLS",
+    "version": "1.0.0"
+  },
+  {
+    "type": "OLSTool",
+    "name": "ols_find_similar_terms",
+    "description": "Find similar terms using LLM-based similarity",
+    "parameter": {
+      "type": "object",
+      "properties": {
+        "operation": {
+          "type": "string",
+          "const": "find_similar_terms",
+          "description": "The operation to perform (find_similar_terms)"
+        },
+        "term_iri": {
+          "type": "string",
+          "description": "The IRI of the term to find similar terms for"
+        },
+        "ontology": {
+          "type": "string",
+          "description": "The ontology ID"
+        },
+        "size": {
+          "type": "integer",
+          "description": "Number of similar terms to return (default: 10)",
+          "default": 10
+        }
+      },
+      "required": ["operation", "term_iri", "ontology"]
+    },
+    "examples": [
+      {
+        "description": "Find similar terms using LLM",
+        "arguments": {
+          "operation": "find_similar_terms",
+          "term_iri": "http://www.ebi.ac.uk/efo/EFO_0000408",
+          "ontology": "efo",
+          "size": 5
+        }
+      }
+    ],
+    "tags": ["ontology", "similarity", "llm", "ebi", "ols"],
+    "author": "EBI OLS",
+    "version": "1.0.0"
+  }
+]

tooluniverse/data/package_discovery_tools.json

@@ -0,0 +1,64 @@
+[
+  {
+    "type": "DynamicPackageDiscovery",
+    "name": "dynamic_package_discovery",
+    "description": "Dynamically searches PyPI and evaluates packages based on requirements",
+    "parameter": {
+      "type": "object",
+      "properties": {
+        "requirements": {
+          "type": "string",
+          "description": "Description of what the package should do"
+        },
+        "functionality": {
+          "type": "string",
+          "description": "Specific functionality needed"
+        },
+        "constraints": {
+          "type": "object",
+          "description": "Constraints (python version, license, etc.)"
+        }
+      },
+      "required": ["requirements"]
+    },
+    "return_schema": {
+      "type": "object",
+      "properties": {
+        "status": {"type": "string"},
+        "candidates": {
+          "type": "array",
+          "items": {
+            "type": "object",
+            "properties": {
+              "name": {"type": "string"},
+              "version": {"type": "string"},
+              "quality_score": {"type": "number"},
+              "reasoning": {"type": "string"},
+              "description": {"type": "string"},
+              "has_docs": {"type": "boolean"},
+              "is_stable": {"type": "boolean"}
+            }
+          }
+        },
+        "recommendation": {"type": "object"},
+        "total_evaluated": {"type": "integer"}
+      },
+      "required": ["status", "candidates"]
+    },
+    "test_examples": [
+      {
+        "input": {
+          "requirements": "data analysis and visualization",
+          "functionality": "create charts and graphs"
+        },
+        "expected_output_type": "object",
+        "description": "Search for data visualization packages"
+      }
+    ],
+    "metadata": {
+      "tags": ["package-discovery", "pypi", "dynamic"],
+      "difficulty_level": "intermediate",
+      "estimated_execution_time": "5-15 seconds"
+    }
+  }
+]

tooluniverse/data/packages/categorized_tools.txt

@@ -103,7 +103,6 @@
 "name": "get_h5py_info"
 "name": "get_harmony_pytorch_info"
 "name": "get_hmmlearn_info"
-"name": "get_hyperopt_info"
 "name": "get_igraph_info"
 "name": "get_jcvi_info"
 "name": "get_khmer_info"

tooluniverse/data/packages/machine_learning_tools.json

@@ -141,53 +141,6 @@
       ]
     }
   },
-  {
-    "type": "PackageTool",
-    "name": "get_hyperopt_info",
-    "description": "Get comprehensive information about Hyperopt – distributed hyperparameter optimization",
-    "parameter": {
-      "type": "object",
-      "properties": {
-        "include_examples": {
-          "type": "boolean",
-          "description": "Whether to include usage examples and quick start guide",
-          "default": true
-        }
-      },
-      "required": [
-        "include_examples"
-      ]
-    },
-    "package_name": "hyperopt",
-    "local_info": {
-      "name": "Hyperopt",
-      "description": "Python library for hyperparameter optimization using algorithms like random search, Tree of Parzen Estimators (TPE), and adaptive TPE. Supports distributed optimization across multiple cores/machines.",
-      "category": "Machine Learning Optimization",
-      "import_name": "hyperopt",
-      "popularity": 85,
-      "keywords": [
-        "hyperparameter optimization",
-        "Bayesian optimization",
-        "TPE",
-        "distributed computing",
-        "model tuning"
-      ],
-      "documentation": "http://hyperopt.github.io/hyperopt/",
-      "repository": "https://github.com/hyperopt/hyperopt",
-      "installation": {
-        "pip": "pip install hyperopt",
-        "conda": "conda install -c conda-forge hyperopt"
-      },
-      "usage_example": "from hyperopt import fmin, tpe, hp, STATUS_OK, Trials\nfrom sklearn.ensemble import RandomForestClassifier\nfrom sklearn.model_selection import cross_val_score\n\n# Define search space\nspace = {\n    'n_estimators': hp.choice('n_estimators', [10, 50, 100, 200]),\n    'max_depth': hp.choice('max_depth', [3, 5, 10, None])\n}\n\n# Objective function\ndef objective(params):\n    clf = RandomForestClassifier(**params)\n    score = cross_val_score(clf, X, y, cv=3).mean()\n    return {'loss': -score, 'status': STATUS_OK}\n\n# Optimize\ntrials = Trials()\nbest = fmin(objective, space, algo=tpe.suggest, max_evals=100, trials=trials)",
-      "quick_start": [
-        "Install: pip install hyperopt",
-        "Import: from hyperopt import fmin, tpe, hp",
-        "Define space: space = {'param': hp.choice('param', [1, 2, 3])}",
-        "Define objective: def objective(params): return loss",
-        "Optimize: best = fmin(objective, space, algo=tpe.suggest)"
-      ]
-    }
-  },
   {
     "type": "PackageTool",
     "name": "get_umap_learn_info",

tooluniverse/data/paleobiology_tools.json

@@ -0,0 +1,91 @@
+[
+  {
+    "type": "PaleobiologyRESTTool",
+    "name": "Paleobiology_get_fossils",
+    "description": "Get fossil records from Paleobiology Database",
+    "parameter": {
+      "type": "object",
+      "properties": {
+        "taxon": {"type": "string", "description": "Taxon name"},
+        "limit": {"type": "integer", "default": 20, "description": "Number of results"}
+      },
+      "required": ["taxon"]
+    },
+    "fields": {
+      "endpoint": "https://paleobiodb.org/data1.2/occs/list.json?taxon_name={taxon}&limit={limit}",
+      "return_format": "JSON"
+    },
+    "return_schema": {
+      "type": "object",
+      "properties": {
+        "records": {
+          "type": "array",
+          "items": {
+            "type": "object",
+            "properties": {
+              "occurrence_no": {"type": "string"},
+              "record_type": {"type": "string"},
+              "reid_no": {"type": "string"},
+              "flags": {"type": "string"},
+              "collection_no": {"type": "string"},
+              "identified_name": {"type": "string"},
+              "identified_rank": {"type": "string"},
+              "identified_no": {"type": "string"},
+              "accepted_name": {"type": "string"},
+              "accepted_rank": {"type": "string"},
+              "accepted_no": {"type": "string"},
+              "early_interval": {"type": "string"},
+              "late_interval": {"type": "string"},
+              "early_age": {"type": "number"},
+              "late_age": {"type": "number"},
+              "reference_no": {"type": "string"},
+              "is_representative": {"type": "string"},
+              "formation": {"type": "string"},
+              "member": {"type": "string"},
+              "lithology": {"type": "string"},
+              "lithology1": {"type": "string"},
+              "lithology2": {"type": "string"},
+              "environment": {"type": "string"},
+              "taphonomy": {"type": "string"},
+              "preservation": {"type": "string"},
+              "lithadj1": {"type": "string"},
+              "lithadj2": {"type": "string"},
+              "geogscale": {"type": "string"},
+              "geogname": {"type": "string"},
+              "state": {"type": "string"},
+              "county": {"type": "string"},
+              "lat": {"type": "number"},
+              "lng": {"type": "number"},
+              "geogcomments": {"type": "string"},
+              "collection_name": {"type": "string"},
+              "collection_aka": {"type": "string"},
+              "collection_type": {"type": "string"},
+              "collection_comments": {"type": "string"},
+              "stratscale": {"type": "string"},
+              "stratcomments": {"type": "string"},
+              "lithadjcomments": {"type": "string"},
+              "geogcomments": {"type": "string"},
+              "taxonomy": {
+                "type": "object",
+                "properties": {
+                  "phylum": {"type": "string"},
+                  "class": {"type": "string"},
+                  "order": {"type": "string"},
+                  "family": {"type": "string"},
+                  "genus": {"type": "string"},
+                  "species": {"type": "string"}
+                }
+              }
+            }
+          }
+        },
+        "count": {"type": "integer"},
+        "status": {"type": "string"}
+      }
+    },
+    "test_examples": [
+      {"taxon": "Tyrannosaurus", "limit": 5},
+      {"taxon": "Trilobita", "limit": 10}
+    ]
+  }
+]

tooluniverse/data/pride_tools.json

@@ -0,0 +1,62 @@
+[
+  {
+    "type": "PRIDERESTTool",
+    "name": "PRIDE_search_proteomics",
+    "description": "Search PRIDE proteomics database for experiments",
+    "parameter": {
+      "type": "object",
+      "properties": {
+        "query": {"type": "string", "description": "Search query"},
+        "page_size": {"type": "integer", "default": 20, "description": "Results per page"}
+      },
+      "required": ["query"]
+    },
+    "fields": {
+      "endpoint": "https://www.ebi.ac.uk/pride/ws/archive/v2/projects?query={query}&pageSize={page_size}",
+      "return_format": "JSON"
+    },
+    "return_schema": {
+      "type": "object",
+      "properties": {
+        "content": {
+          "type": "array",
+          "items": {
+            "type": "object",
+            "properties": {
+              "accession": {"type": "string"},
+              "title": {"type": "string"},
+              "description": {"type": "string"},
+              "species": {"type": "array"},
+              "tissues": {"type": "array"},
+              "diseases": {"type": "array"},
+              "instruments": {"type": "array"},
+              "submissionDate": {"type": "string"},
+              "publicationDate": {"type": "string"},
+              "numAssays": {"type": "integer"},
+              "numSamples": {"type": "integer"},
+              "numFiles": {"type": "integer"},
+              "fileSize": {"type": "integer"},
+              "labHead": {"type": "object"},
+              "submitters": {"type": "array"},
+              "keywords": {"type": "array"},
+              "projectTags": {"type": "array"}
+            }
+          }
+        },
+        "pageInfo": {
+          "type": "object",
+          "properties": {
+            "page": {"type": "integer"},
+            "size": {"type": "integer"},
+            "totalElements": {"type": "integer"},
+            "totalPages": {"type": "integer"}
+          }
+        }
+      }
+    },
+    "test_examples": [
+      {"query": "cancer", "page_size": 5},
+      {"query": "COVID-19", "page_size": 10}
+    ]
+  }
+]