tooluniverse 1.0.7__py3-none-any.whl → 1.0.9__py3-none-any.whl

tooluniverse/data/unified_guideline_tools.json

@@ -39,6 +39,10 @@
             "type": "string",
             "description": "Clinical summary and scope of the guideline"
           },
+          "content": {
+            "type": "string",
+            "description": "Cleaned clinical content extracted from the guideline page"
+          },
           "date": {
             "type": "string",
             "description": "Publication or last updated date"
@@ -126,6 +130,14 @@
                   "type": "string"
                 }
               },
+              "abstract": {
+                "type": "string",
+                "description": "Abstract text returned from PubMed"
+              },
+              "content": {
+                "type": "string",
+                "description": "Cleaned clinical content (mirrors abstract)"
+              },
               "is_guideline": {
                 "type": "boolean",
                 "description": "Confirms this is a clinical guideline"
@@ -223,10 +235,14 @@
                 "type": "string",
                 "description": "Type of publication"
               },
-              "abstract": {
-                "type": "string",
-                "description": "Abstract or summary of the guideline"
-              },
+          "abstract": {
+            "type": "string",
+            "description": "Abstract or summary of the guideline"
+          },
+          "content": {
+            "type": "string",
+            "description": "Extended clinical content extracted from Europe PMC when available"
+          },
               "is_guideline": {
                 "type": "boolean",
                 "description": "Indicates if this is a clinical guideline"
@@ -310,6 +326,48 @@
                 "type": "string",
                 "description": "Category or type of guideline"
               },
+              "description": {
+                "type": "string",
+                "description": "Short description provided by TRIP"
+              },
+              "content": {
+                "type": "string",
+                "description": "Detailed clinical content extracted from the guideline page when available"
+              },
+              "key_recommendations": {
+                "type": "array",
+                "description": "Extracted key recommendations (title and summary) when available",
+                "items": {
+                  "type": "object",
+                  "properties": {
+                    "title": {
+                      "type": "string",
+                      "description": "Heading for the recommendation"
+                    },
+                    "summary": {
+                      "type": "string",
+                      "description": "Summary text of the recommendation"
+                    }
+                  }
+                }
+              },
+              "evidence_strength": {
+                "type": "array",
+                "description": "Strength-of-evidence or grading statements extracted from the guideline",
+                "items": {
+                  "type": "object",
+                  "properties": {
+                    "section": {
+                      "type": "string",
+                      "description": "Reference section for the strength statement"
+                    },
+                    "strength": {
+                      "type": "string",
+                      "description": "Narrative grading (e.g., 'Strong recommendation')"
+                    }
+                  }
+                }
+              },
               "is_guideline": {
                 "type": "boolean",
                 "description": "Confirms this is a clinical guideline"
@@ -703,5 +761,149 @@
         }
       }
     }
+  },
+  {
+    "type": "GINGuidelinesTool",
+    "name": "GIN_Guidelines_Search",
+    "description": "Search Guidelines International Network (GIN) guidelines database. GIN maintains the world's largest database of clinical guidelines with over 6400 guidelines from various organizations worldwide.",
+    "parameter": {
+      "type": "object",
+      "properties": {
+        "query": {
+          "type": "string",
+          "description": "Medical condition, treatment, or clinical topic to search for in GIN guidelines (e.g., 'diabetes management', 'hypertension treatment', 'cancer screening')"
+        },
+        "limit": {
+          "type": "integer",
+          "description": "Maximum number of guidelines to return (default: 10)",
+          "default": 10
+        }
+      },
+      "required": [
+        "query",
+        "limit"
+      ]
+    },
+    "return_schema": {
+      "type": "array",
+      "description": "List of GIN clinical guidelines from various international organizations",
+      "items": {
+        "type": "object",
+        "properties": {
+          "title": {
+            "type": "string",
+            "description": "Title of the guideline"
+          },
+          "url": {
+            "type": "string",
+            "description": "URL to access the guideline"
+          },
+          "description": {
+            "type": "string",
+            "description": "Description or summary of the guideline"
+          },
+          "date": {
+            "type": "string",
+            "description": "Publication or update date"
+          },
+          "source": {
+            "type": "string",
+            "description": "Source organization (GIN)"
+          },
+          "organization": {
+            "type": "string",
+            "description": "Organization that developed the guideline"
+          },
+          "is_guideline": {
+            "type": "boolean",
+            "description": "Indicates this is a clinical guideline"
+          },
+          "official": {
+            "type": "boolean",
+            "description": "Indicates this is an official publication"
+          },
+          "content": {
+            "type": "string",
+            "description": "Full content of the guideline"
+          },
+          "note": {
+            "type": "string",
+            "description": "Additional notes about content availability"
+          }
+        }
+      }
+    }
+  },
+  {
+    "type": "CMAGuidelinesTool",
+    "name": "CMA_Guidelines_Search",
+    "description": "Search Canadian Medical Association (CMA) Infobase guidelines. Contains over 1200 evidence-based clinical practice guidelines developed or endorsed by Canadian healthcare organizations.",
+    "parameter": {
+      "type": "object",
+      "properties": {
+        "query": {
+          "type": "string",
+          "description": "Medical condition, treatment, or clinical topic to search for in CMA guidelines (e.g., 'diabetes management', 'hypertension treatment', 'cancer screening')"
+        },
+        "limit": {
+          "type": "integer",
+          "description": "Maximum number of guidelines to return (default: 10)",
+          "default": 10
+        }
+      },
+      "required": [
+        "query",
+        "limit"
+      ]
+    },
+    "return_schema": {
+      "type": "array",
+      "description": "List of CMA Infobase clinical practice guidelines",
+      "items": {
+        "type": "object",
+        "properties": {
+          "title": {
+            "type": "string",
+            "description": "Title of the guideline"
+          },
+          "url": {
+            "type": "string",
+            "description": "URL to access the guideline"
+          },
+          "description": {
+            "type": "string",
+            "description": "Description or summary of the guideline"
+          },
+          "date": {
+            "type": "string",
+            "description": "Publication or update date"
+          },
+          "source": {
+            "type": "string",
+            "description": "Source organization (CMA)"
+          },
+          "organization": {
+            "type": "string",
+            "description": "Canadian healthcare organization that developed the guideline"
+          },
+          "is_guideline": {
+            "type": "boolean",
+            "description": "Indicates this is a clinical guideline"
+          },
+          "official": {
+            "type": "boolean",
+            "description": "Indicates this is an official publication"
+          },
+          "content": {
+            "type": "string",
+            "description": "Full content of the guideline"
+          },
+          "note": {
+            "type": "string",
+            "description": "Additional notes about content availability"
+          }
+        }
+      }
+    }
   }
 ]

tooluniverse/data/xml_tools.json

@@ -8,7 +8,7 @@
         "repo_id": "agenticx/MeSH2025",
         "path_in_repo": "MeSH_desc2025.xml",
         "token": null,
-        "save_to_local_dir": "src/tooluniverse/test"
+        "save_to_local_dir": null
       },
       "record_xpath": "DescriptorRecord",
       "search_fields": [
@@ -175,7 +175,7 @@
         "repo_id": "agenticx/MeSH2025",
         "path_in_repo": "MeSH_desc2025.xml",
         "token": null,
-        "save_to_local_dir": "src/tooluniverse/test"
+        "save_to_local_dir": null
       },
       "record_xpath": "DescriptorRecord",
       "search_fields": [
@@ -342,7 +342,7 @@
         "repo_id": "agenticx/MeSH2025",
         "path_in_repo": "MeSH_desc2025.xml",
         "token": null,
-        "save_to_local_dir": "src/tooluniverse/test"
+        "save_to_local_dir": null
       },
       "record_xpath": "DescriptorRecord",
       "search_fields": [
@@ -511,7 +511,7 @@
         "repo_id": "agenticx/MeSH2025",
         "path_in_repo": "MeSH_desc2025.xml",
         "token": null,
-        "save_to_local_dir": "src/tooluniverse/test"
+        "save_to_local_dir": null
       },
       "record_xpath": "DescriptorRecord",
       "search_fields": [
@@ -678,7 +678,7 @@
         "repo_id": "agenticx/DrugBank",
         "path_in_repo": "drugbank_full_database.xml",
         "token": null,
-        "save_to_local_dir": "src/tooluniverse/test"
+        "save_to_local_dir": null
       },
       "namespaces": {
         "db": "http://www.drugbank.ca"
@@ -860,7 +860,7 @@
         "repo_id": "agenticx/DrugBank",
         "path_in_repo": "drugbank_full_database.xml",
         "token": null,
-        "save_to_local_dir": "src/tooluniverse/test"
+        "save_to_local_dir": null
       },
       "namespaces": {
         "db": "http://www.drugbank.ca"
@@ -1036,7 +1036,7 @@
         "repo_id": "agenticx/DrugBank",
         "path_in_repo": "drugbank_full_database.xml",
         "token": null,
-        "save_to_local_dir": "src/tooluniverse/test"
+        "save_to_local_dir": null
       },
       "namespaces": {
         "db": "http://www.drugbank.ca"
@@ -1176,7 +1176,7 @@
         "repo_id": "agenticx/DrugBank",
         "path_in_repo": "drugbank_full_database.xml",
         "token": null,
-        "save_to_local_dir": "src/tooluniverse/test"
+        "save_to_local_dir": null
       },
       "namespaces": {
         "db": "http://www.drugbank.ca"
@@ -1358,7 +1358,7 @@
         "repo_id": "agenticx/DrugBank",
         "path_in_repo": "drugbank_full_database.xml",
         "token": null,
-        "save_to_local_dir": "src/tooluniverse/test"
+        "save_to_local_dir": null
       },
       "namespaces": {
         "db": "http://www.drugbank.ca"
@@ -1538,7 +1538,7 @@
         "repo_id": "agenticx/DrugBank",
         "path_in_repo": "drugbank_full_database.xml",
         "token": null,
-        "save_to_local_dir": "src/tooluniverse/test"
+        "save_to_local_dir": null
       },
       "namespaces": {
         "db": "http://www.drugbank.ca"
@@ -1703,7 +1703,7 @@
         "repo_id": "agenticx/DrugBank",
         "path_in_repo": "drugbank_full_database.xml",
         "token": null,
-        "save_to_local_dir": "src/tooluniverse/test"
+        "save_to_local_dir": null
       },
       "namespaces": {
         "db": "http://www.drugbank.ca"
@@ -1976,7 +1976,7 @@
         "repo_id": "agenticx/DrugBank",
         "path_in_repo": "drugbank_full_database.xml",
         "token": null,
-        "save_to_local_dir": "src/tooluniverse/test"
+        "save_to_local_dir": null
       },
       "namespaces": {
         "db": "http://www.drugbank.ca"
@@ -2134,7 +2134,7 @@
         "repo_id": "agenticx/DrugBank",
         "path_in_repo": "drugbank_full_database.xml",
         "token": null,
-        "save_to_local_dir": "src/tooluniverse/test"
+        "save_to_local_dir": null
       },
       "namespaces": {
         "db": "http://www.drugbank.ca"
@@ -2369,7 +2369,7 @@
         "repo_id": "agenticx/DrugBank",
         "path_in_repo": "drugbank_full_database.xml",
         "token": null,
-        "save_to_local_dir": "src/tooluniverse/test"
+        "save_to_local_dir": null
       },
       "namespaces": {
         "db": "http://www.drugbank.ca"
@@ -2521,7 +2521,7 @@
         "repo_id": "agenticx/DrugBank",
         "path_in_repo": "drugbank_full_database.xml",
         "token": null,
-        "save_to_local_dir": "src/tooluniverse/test"
+        "save_to_local_dir": null
       },
       "namespaces": {
         "db": "http://www.drugbank.ca"

tooluniverse/data/zenodo_tools.json

@@ -24,8 +24,7 @@
       },
       "required": [
         "query",
-        "max_results",
-        "community"
+        "max_results"
       ]
     },
     "return_schema": {

tooluniverse/dbsnp_tool.py

@@ -0,0 +1,71 @@
+import requests
+from .base_tool import BaseTool
+from .tool_registry import register_tool
+
+
+@register_tool("DbSnpTool")
+class DbSnpTool(BaseTool):
+    """
+    Local tool wrapper for dbSNP via NCBI Variation Services.
+    Fetches variant by rsID using the refsnp endpoint.
+    """
+
+    def __init__(self, tool_config):
+        super().__init__(tool_config)
+        self.base = "https://api.ncbi.nlm.nih.gov/variation/v0"
+        self.session = requests.Session()
+
+    def run(self, arguments):
+        rsid = arguments.get("rsid")
+        if not rsid:
+            return {"error": "Missing required parameter: rsid"}
+
+        # Clean rsid (remove 'rs' prefix if present)
+        if rsid.startswith("rs"):
+            rsid = rsid[2:]
+
+        url = f"{self.base}/refsnp/{rsid}"
+        resp = self.session.get(url, timeout=20)
+        resp.raise_for_status()
+        data = resp.json()
+
+        # Extract key fields from primary snapshot
+        primary = data.get("primary_snapshot_data", {})
+        placements = primary.get("placements_with_allele", [])
+
+        chrom = ""
+        pos = None
+        alleles = []
+        hgvs = []
+
+        if placements:
+            placement = placements[0]
+            chrom = (
+                placement.get("seq_id", "").replace("NC_0000", "").replace(".11", "")
+            )
+            if chrom.startswith("0"):
+                chrom = chrom[1:]
+            chrom = f"chr{chrom}"
+
+            allele_data = placement.get("alleles", [])
+            for allele in allele_data:
+                spdi = allele.get("allele", {}).get("spdi", {})
+                if spdi:
+                    ref = spdi.get("deleted_sequence", "")
+                    alt = spdi.get("inserted_sequence", "")
+                    if ref and alt:
+                        alleles.append(f"{ref}>{alt}")
+                    elif ref:
+                        alleles.append(ref)
+
+                hgvs_val = allele.get("hgvs", "")
+                if hgvs_val:
+                    hgvs.append(hgvs_val)
+
+        return {
+            "refsnp_id": f"rs{rsid}",
+            "chrom": chrom,
+            "pos": pos,
+            "alleles": alleles,
+            "hgvs": hgvs,
+        }

tooluniverse/default_config.py

@@ -51,6 +51,9 @@ default_tool_files = {
     "fatcat": os.path.join(current_dir, "data", "fatcat_tools.json"),
     "wikidata_sparql": os.path.join(current_dir, "data", "wikidata_sparql_tools.json"),
     "agents": os.path.join(current_dir, "data", "agentic_tools.json"),
+    "drug_discovery_agents": os.path.join(
+        current_dir, "data", "drug_discovery_agents.json"
+    ),
     "dataset": os.path.join(current_dir, "data", "dataset_tools.json"),
     # 'mcp_clients': os.path.join(current_dir, 'data', 'mcp_client_tools_example.json'),
     "mcp_auto_loader_txagent": os.path.join(
@@ -142,6 +145,9 @@ default_tool_files = {
         current_dir, "data", "output_summarization_tools.json"
     ),
     "odphp": os.path.join(current_dir, "data", "odphp_tools.json"),
+    "markitdown": os.path.join(current_dir, "data", "markitdown_tools.json"),
+    # Genomics tools
+    "genomics": os.path.join(current_dir, "data", "genomics_tools.json"),
     # Guideline and health policy tools
     "guidelines": os.path.join(current_dir, "data", "unified_guideline_tools.json"),
 }

tooluniverse/ensembl_tool.py

@@ -0,0 +1,61 @@
+import requests
+from .base_tool import BaseTool
+from .tool_registry import register_tool
+
+
+@register_tool("EnsemblTool")
+class EnsemblTool(BaseTool):
+    """
+    Local tool wrapper for Ensembl REST API lookups.
+    Supports symbol→gene lookup (xrefs/symbol) then lookup/id to
+    fetch metadata.
+    """
+
+    def __init__(self, tool_config):
+        super().__init__(tool_config)
+        self.base = "https://rest.ensembl.org"
+        self.session = requests.Session()
+        self.session.headers.update(
+            {"Accept": "application/json", "Content-Type": "application/json"}
+        )
+
+    def run(self, arguments):
+        species = arguments.get("species", "homo_sapiens")
+        symbol = arguments.get("symbol")
+        if not symbol:
+            return {"error": "Missing required parameter: symbol"}
+
+        # 1) symbol -> xref(s) to get Ensembl gene ID
+        xref_url = f"{self.base}/xrefs/symbol/{species}/{symbol}"
+        xref_resp = self.session.get(xref_url, timeout=20)
+        xref_resp.raise_for_status()
+        xrefs = xref_resp.json() or []
+        gene_id = None
+        for item in xrefs:
+            if item.get("type") == "gene" and item.get("id"):
+                gene_id = item["id"]
+                break
+        if not gene_id and xrefs:
+            gene_id = xrefs[0].get("id")
+        if not gene_id:
+            return {"error": f"No Ensembl gene found for {symbol}"}
+
+        # 2) lookup by Ensembl ID (expand=1 to include transcripts)
+        lookup_url = f"{self.base}/lookup/id/{gene_id}?expand=1"
+        look_resp = self.session.get(lookup_url, timeout=30)
+        look_resp.raise_for_status()
+        data = look_resp.json() or {}
+
+        transcripts = data.get("Transcript") or []
+        return {
+            "id": data.get("id"),
+            "symbol": symbol,
+            "display_name": data.get("display_name"),
+            "species": data.get("species"),
+            "seq_region_name": data.get("seq_region_name"),
+            "start": data.get("start"),
+            "end": data.get("end"),
+            "strand": data.get("strand"),
+            "biotype": data.get("biotype"),
+            "transcript_count": len(transcripts),
+        }