mims-harvard
diff --git a/‎.env.template‎
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diff --git a/‎pyproject.toml‎
Lines changed: 1 addition & 1 deletion b/‎pyproject.toml‎
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diff --git a/‎src/tooluniverse/_lazy_registry_static.py‎
Lines changed: 16 additions & 0 deletions b/‎src/tooluniverse/_lazy_registry_static.py‎
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diff --git a/‎src/tooluniverse/addgene_tool.py‎
Lines changed: 271 additions & 0 deletions b/‎src/tooluniverse/addgene_tool.py‎
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@@ -1,6 +1,8 @@
 # API Keys for ToolUniverse
 # Copy this file to .env and fill in your actual API keys
 
+ADDGENE_API_KEY=your_api_key_here
+
 BOLTZ_MCP_SERVER_HOST=your_api_key_here
 
 BRENDA_EMAIL=your_api_key_here
@@ -9,6 +11,8 @@ BRENDA_PASSWORD=your_api_key_here
 
 DISGENET_API_KEY=your_api_key_here
 
+ESM_MCP_SERVER_HOST=your_api_key_here
+
 EXPERT_FEEDBACK_MCP_SERVER_URL=your_api_key_here
 
 NVIDIA_API_KEY=your_api_key_here
 
@@ -4,7 +4,7 @@ build-backend = "setuptools.build_meta"
 
 [project]
 name = "tooluniverse"
-version = "1.0.21"
+version = "1.0.22"
 description = "A comprehensive collection of scientific tools for Agentic AI, offering integration with the ToolUniverse SDK and MCP Server to support advanced scientific workflows."
 authors = [
     { name = "Shanghua Gao", email = "shanghuagao@gmail.com" }
 
@@ -8,6 +8,7 @@
 STATIC_LAZY_REGISTRY = {
     "ADAStandardsTool": "clinical_society_tools",
     "ADMETAITool": "admetai_tool",
+    "AddgeneTool": "addgene_tool",
     "AHAACCGuidelineTool": "clinical_society_tools",
     "AgenticTool": "agentic_tool",
     "AllenBrainTool": "allen_brain_tool",
@@ -37,9 +38,11 @@
     "Boltz2DockingTool": "boltz_tool",
     "CADDTool": "cadd_tool",
     "CATHTool": "cath_tool",
+    "CancerPrognosisTool": "cancer_prognosis_tool",
     "CBioPortalRESTTool": "cbioportal_tool",
     "CDCRESTTool": "cdc_tool",
     "CELLxGENECensusTool": "cellxgene_census_tool",
+    "CellMarkerTool": "cellmarker_tool",
     "CellPaintingTool": "cellpainting_tool",
     "CIViCTool": "civic_tool",
     "CMAGuidelinesTool": "unified_guideline_tools",
@@ -243,6 +246,7 @@
     "HealthDisparitiesTool": "health_disparities_tool",
     "HumanBaseTool": "humanbase_tool",
     "IBMRXNTool": "ibmrxn_tool",
+    "IDTTool": "idt_tool",
     "ICD10Tool": "icd_tool",
     "ICDTool": "icd_tool",
     "IEDBTool": "iedb_tool",
@@ -252,6 +256,7 @@
     "ITISTool": "itis_tool",
     "IdentifiersOrgTool": "identifiers_org_tool",
     "IntActRESTTool": "intact_tool",
+    "IntOGenTool": "intogen_tool",
     "InterProDomainArchTool": "interpro_domain_arch_tool",
     "InterProEntryTool": "interpro_entry_tool",
     "InterProExtTool": "interpro_ext_tool",
@@ -272,8 +277,10 @@
     "ListTools": "tool_discovery_tools",
     "ListToolsTool": "tool_discovery_tools",
     "MCPAutoLoaderTool": "mcp_client_tool",
+    "MculeTool": "mcule_tool",
     "MCPClientTool": "mcp_client_tool",
     "MCPProxyTool": "mcp_client_tool",
+    "MEMETool": "meme_tool",
     "MCPServerDiscovery": "mcp_client_tool",
     "MGnifyAnalysesTool": "mgnify_tool",
     "MGnifyExpandedTool": "mgnify_expanded_tool",
@@ -282,6 +289,7 @@
     "MarkItDownTool": "markitdown_tool",
     "MeSHTool": "mesh_tool",
     "MedlinePlusRESTTool": "medlineplus_tool",
+    "MetaboAnalystTool": "metaboanalyst_tool",
     "MetaCycTool": "metacyc_tool",
     "MetaboLightsRESTTool": "metabolights_tool",
     "MetabolomicsWorkbenchTool": "metabolomics_workbench_tool",
@@ -305,6 +313,7 @@
     "NCCNGuidelineTool": "clinical_society_tools",
     "NCIThesaurusTool": "nci_thesaurus_tool",
     "NDExTool": "ndex_tool",
+    "NEBTmTool": "neb_tm_tool",
     "NHANESTool": "nhanes_tool",
     "NICEGuidelineFullTextTool": "unified_guideline_tools",
     "NICEWebScrapingTool": "unified_guideline_tools",
@@ -357,13 +366,16 @@
     "PaleobiologyRESTTool": "paleobiology_tool",
     "PathwayCommonsTool": "pathway_commons_tool",
     "PfamTool": "pfam_tool",
+    "PharmacoDBTool": "pharmacodb_tool",
+    "PDCTool": "pdc_tool",
     "PharmGKBTool": "pharmgkb_tool",
     "PharosTool": "pharos_tool",
     "PlantReactomeTool": "plant_reactome_tool",
     "PomBaseTool": "pombase_tool",
     "ProtacDBTool": "protacdb_tool",
     "ProteinStructure3DTool": "protein_structure_3d_tool",
     "ProteinsAPIRESTTool": "proteins_api_tool",
+    "ProteomicsDBTool": "proteomicsdb_tool",
     "ProteinsPlusRESTTool": "proteinsplus_tool",
     "ProteomeXchangeTool": "proteomexchange_tool",
     "PubChemBioAssayTool": "pubchem_bioassay_tool",
@@ -414,6 +426,9 @@
     "SurvivalTool": "survival_tool",
     "SwissDockTool": "swissdock_tool",
     "SwissModelTool": "swissmodel_tool",
+    "SwissADMETool": "swissadme_tool",
+    "SwissTargetTool": "swiss_target_tool",
+    "SYNERGxDBTool": "synergxdb_tool",
     "SynBioHubTool": "synbiohub_tool",
     "TIMERTool": "timer_tool",
     "TRIPDatabaseTool": "unified_guideline_tools",
@@ -463,6 +478,7 @@
     "XMLDatasetTool": "xml_tool",
     "XMLTool": "xml_tool",
     "ZenodoRESTTool": "zenodo_tool",
+    "ZincTool": "zinc_tool",
     "dbSNPGetFrequencies": "dbsnp_tool",
     "dbSNPGetVariantByRsID": "dbsnp_tool",
     "dbSNPRESTTool": "dbsnp_tool",
 
@@ -0,0 +1,271 @@
+"""
+Addgene Developers API Tool
+
+Provides programmatic access to Addgene's plasmid catalog via the official
+Addgene Developers API (https://developers.addgene.org/).
+
+Supports:
+- Searching plasmids by name, gene, species, vector type, purpose, etc.
+- Retrieving detailed plasmid information (cloning, inserts, resistance, growth)
+- Browsing depositors (PIs) via plasmid catalog queries
+
+API Base: https://api.developers.addgene.org
+Authentication: Token-based via ADDGENE_API_KEY environment variable.
+Register at https://developers.addgene.org/ to obtain a free token.
+"""
+
+import os
+import requests
+from typing import Dict, Any, Optional, List
+from .base_tool import BaseTool
+from .tool_registry import register_tool
+
+ADDGENE_API_URL = "https://api.developers.addgene.org"
+
+
+@register_tool("AddgeneTool")
+class AddgeneTool(BaseTool):
+    """
+    Tool for querying the Addgene plasmid repository.
+
+    Addgene is a nonprofit global plasmid repository that archives and
+    distributes plasmids for the scientific community. This tool provides
+    access to:
+    - Plasmid search (by name, gene, species, vector type, purpose)
+    - Plasmid detail retrieval (cloning info, inserts, resistance markers)
+    - Depositor/PI search
+
+    Requires API token via ADDGENE_API_KEY environment variable.
+    Register at https://developers.addgene.org/ for access.
+    """
+
+    def __init__(self, tool_config: Dict[str, Any]):
+        super().__init__(tool_config)
+        self.timeout = tool_config.get("timeout", 30)
+        self.parameter = tool_config.get("parameter", {})
+        self.required = self.parameter.get("required", [])
+        self.api_key = os.environ.get("ADDGENE_API_KEY", "")
+
+    def _get_headers(self):
+        """Get request headers with auth token."""
+        headers = {"Accept": "application/json"}
+        if self.api_key:
+            headers["Authorization"] = "Token " + self.api_key
+        return headers
+
+    def run(self, arguments: Dict[str, Any]) -> Dict[str, Any]:
+        operation = arguments.get("operation")
+        if not operation:
+            return {"status": "error", "error": "Missing required parameter: operation"}
+
+        if not self.api_key:
+            return {
+                "status": "error",
+                "error": (
+                    "Addgene API key required. Set ADDGENE_API_KEY environment variable. "
+                    "Register at https://developers.addgene.org/ for access."
+                ),
+            }
+
+        handlers = {
+            "search_plasmids": self._search_plasmids,
+            "get_plasmid": self._get_plasmid,
+            "search_depositors": self._search_depositors,
+        }
+
+        handler = handlers.get(operation)
+        if not handler:
+            return {
+                "status": "error",
+                "error": "Unknown operation: {}. Available: {}".format(
+                    operation, ", ".join(handlers.keys())
+                ),
+            }
+
+        try:
+            return handler(arguments)
+        except requests.exceptions.Timeout:
+            return {"status": "error", "error": "Addgene API request timed out"}
+        except requests.exceptions.ConnectionError:
+            return {"status": "error", "error": "Failed to connect to Addgene API"}
+        except Exception as e:
+            return {"status": "error", "error": "Operation failed: {}".format(str(e))}
+
+    def _search_plasmids(self, arguments: Dict[str, Any]) -> Dict[str, Any]:
+        """
+        Search Addgene plasmid catalog.
+
+        Supports filtering by name, genes, species, vector_types, purpose,
+        experimental_use, expression, and more.
+        """
+        query = arguments.get("query")
+        organism = arguments.get("organism")
+        vector_type = arguments.get("vector_type")
+        limit = min(int(arguments.get("limit", 10)), 100)
+
+        params = {"page_size": limit}
+
+        if query:
+            params["name"] = query
+        if organism:
+            params["species"] = organism
+        if vector_type:
+            params["vector_types"] = vector_type
+
+        response = requests.get(
+            ADDGENE_API_URL + "/catalog/plasmid/",
+            params=params,
+            headers=self._get_headers(),
+            timeout=self.timeout,
+        )
+
+        if response.status_code == 401:
+            return {
+                "status": "error",
+                "error": "Authentication failed. Check your ADDGENE_API_KEY.",
+            }
+
+        response.raise_for_status()
+        data = response.json()
+
+        results = data.get("results", [])
+        return {
+            "status": "success",
+            "data": {
+                "plasmids": results,
+                "total_count": data.get("count", len(results)),
+                "next_page": data.get("next"),
+            },
+            "metadata": {
+                "source": "Addgene",
+                "query": query,
+                "organism": organism,
+                "vector_type": vector_type,
+            },
+        }
+
+    def _get_plasmid(self, arguments: Dict[str, Any]) -> Dict[str, Any]:
+        """
+        Get detailed information about a specific plasmid.
+
+        Returns full plasmid record including cloning info, inserts,
+        resistance markers, growth conditions, article, depositor comments.
+        """
+        plasmid_id = arguments.get("plasmid_id")
+        if not plasmid_id:
+            return {
+                "status": "error",
+                "error": "Missing required parameter: plasmid_id",
+            }
+
+        plasmid_id = str(plasmid_id).strip()
+
+        response = requests.get(
+            "{}/catalog/plasmid/{}/".format(ADDGENE_API_URL, plasmid_id),
+            headers=self._get_headers(),
+            timeout=self.timeout,
+        )
+
+        if response.status_code == 401:
+            return {
+                "status": "error",
+                "error": "Authentication failed. Check your ADDGENE_API_KEY.",
+            }
+        if response.status_code == 404:
+            return {
+                "status": "error",
+                "error": "Plasmid ID {} not found in Addgene".format(plasmid_id),
+            }
+
+        response.raise_for_status()
+        plasmid = response.json()
+
+        return {
+            "status": "success",
+            "data": plasmid,
+            "metadata": {
+                "source": "Addgene",
+                "plasmid_id": plasmid_id,
+                "url": "https://www.addgene.org/{}/".format(plasmid_id),
+            },
+        }
+
+    def _search_depositors(self, arguments: Dict[str, Any]) -> Dict[str, Any]:
+        """
+        Search for depositors (PIs) by querying plasmids and extracting
+        unique depositor information.
+
+        The Addgene API does not have a dedicated depositor search endpoint,
+        so this searches plasmids filtered by PI name or institution, then
+        extracts and deduplicates depositor info from results.
+        """
+        name = arguments.get("name")
+        institution = arguments.get("institution")
+
+        if not name and not institution:
+            return {
+                "status": "error",
+                "error": "At least one of 'name' or 'institution' is required.",
+            }
+
+        params = {"page_size": 50}
+        if name:
+            params["pis"] = name
+        if institution:
+            # Institution is not a direct filter in the API;
+            # we search by article_authors which may contain institution info
+            params["article_authors"] = institution
+
+        response = requests.get(
+            ADDGENE_API_URL + "/catalog/plasmid/",
+            params=params,
+            headers=self._get_headers(),
+            timeout=self.timeout,
+        )
+
+        if response.status_code == 401:
+            return {
+                "status": "error",
+                "error": "Authentication failed. Check your ADDGENE_API_KEY.",
+            }
+
+        response.raise_for_status()
+        data = response.json()
+
+        results = data.get("results", [])
+
+        # Extract unique depositors from plasmid results
+        depositors = {}
+        for plasmid in results:
+            depositor_list = plasmid.get("depositor", [])
+            for dep in depositor_list:
+                dep_str = str(dep)
+                if dep_str not in depositors:
+                    depositors[dep_str] = {
+                        "name": dep_str,
+                        "plasmid_count": 0,
+                        "example_plasmids": [],
+                    }
+                depositors[dep_str]["plasmid_count"] += 1
+                if len(depositors[dep_str]["example_plasmids"]) < 3:
+                    depositors[dep_str]["example_plasmids"].append(
+                        {"id": plasmid.get("id"), "name": plasmid.get("name")}
+                    )
+
+        depositor_list = sorted(
+            depositors.values(), key=lambda x: x["plasmid_count"], reverse=True
+        )
+
+        return {
+            "status": "success",
+            "data": {
+                "depositors": depositor_list,
+                "total_depositors": len(depositor_list),
+                "total_plasmids_searched": data.get("count", len(results)),
+            },
+            "metadata": {
+                "source": "Addgene",
+                "name_query": name,
+                "institution_query": institution,
+            },
+        }