tooluniverse 1.0.7__py3-none-any.whl → 1.0.8__py3-none-any.whl

tooluniverse/tools/DiseaseAnalyzerAgent.py

@@ -0,0 +1,52 @@
+"""
+DiseaseAnalyzerAgent
+
+AI agent that analyzes disease characteristics and identifies potential therapeutic targets using...
+"""
+
+from typing import Any, Optional, Callable
+from ._shared_client import get_shared_client
+
+
+def DiseaseAnalyzerAgent(
+    disease_name: str,
+    context: Optional[str] = "",
+    *,
+    stream_callback: Optional[Callable[[str], None]] = None,
+    use_cache: bool = False,
+    validate: bool = True,
+) -> Any:
+    """
+    AI agent that analyzes disease characteristics and identifies potential therapeutic targets using...
+
+    Parameters
+    ----------
+    disease_name : str
+        Name of the disease to analyze
+    context : str
+        Additional context or specific focus areas
+    stream_callback : Callable, optional
+        Callback for streaming output
+    use_cache : bool, default False
+        Enable caching
+    validate : bool, default True
+        Validate parameters
+
+    Returns
+    -------
+    Any
+    """
+    # Handle mutable defaults to avoid B006 linting error
+
+    return get_shared_client().run_one_function(
+        {
+            "name": "DiseaseAnalyzerAgent",
+            "arguments": {"disease_name": disease_name, "context": context},
+        },
+        stream_callback=stream_callback,
+        use_cache=use_cache,
+        validate=validate,
+    )
+
+
+__all__ = ["DiseaseAnalyzerAgent"]

tooluniverse/tools/DrugInteractionAnalyzerAgent.py

@@ -0,0 +1,52 @@
+"""
+DrugInteractionAnalyzerAgent
+
+AI agent that analyzes drug-drug interactions and provides clinical recommendations
+"""
+
+from typing import Any, Optional, Callable
+from ._shared_client import get_shared_client
+
+
+def DrugInteractionAnalyzerAgent(
+    compounds: str,
+    patient_context: Optional[str] = "General adult population",
+    *,
+    stream_callback: Optional[Callable[[str], None]] = None,
+    use_cache: bool = False,
+    validate: bool = True,
+) -> Any:
+    """
+    AI agent that analyzes drug-drug interactions and provides clinical recommendations
+
+    Parameters
+    ----------
+    compounds : str
+        List of compounds to analyze for interactions (comma-separated)
+    patient_context : str
+        Patient context (age, comorbidities, medications, etc.)
+    stream_callback : Callable, optional
+        Callback for streaming output
+    use_cache : bool, default False
+        Enable caching
+    validate : bool, default True
+        Validate parameters
+
+    Returns
+    -------
+    Any
+    """
+    # Handle mutable defaults to avoid B006 linting error
+
+    return get_shared_client().run_one_function(
+        {
+            "name": "DrugInteractionAnalyzerAgent",
+            "arguments": {"compounds": compounds, "patient_context": patient_context},
+        },
+        stream_callback=stream_callback,
+        use_cache=use_cache,
+        validate=validate,
+    )
+
+
+__all__ = ["DrugInteractionAnalyzerAgent"]

tooluniverse/tools/DrugOptimizationAgent.py

@@ -0,0 +1,63 @@
+"""
+DrugOptimizationAgent
+
+AI agent that analyzes drug optimization strategies based on ADMET and efficacy data
+"""
+
+from typing import Any, Optional, Callable
+from ._shared_client import get_shared_client
+
+
+def DrugOptimizationAgent(
+    compounds: str,
+    admet_data: Optional[str] = "",
+    efficacy_data: Optional[str] = "",
+    target_profile: Optional[str] = "",
+    *,
+    stream_callback: Optional[Callable[[str], None]] = None,
+    use_cache: bool = False,
+    validate: bool = True,
+) -> Any:
+    """
+    AI agent that analyzes drug optimization strategies based on ADMET and efficacy data
+
+    Parameters
+    ----------
+    compounds : str
+        List of compounds to optimize (comma-separated)
+    admet_data : str
+        ADMET properties and issues
+    efficacy_data : str
+        Efficacy and potency data
+    target_profile : str
+        Target profile and requirements
+    stream_callback : Callable, optional
+        Callback for streaming output
+    use_cache : bool, default False
+        Enable caching
+    validate : bool, default True
+        Validate parameters
+
+    Returns
+    -------
+    Any
+    """
+    # Handle mutable defaults to avoid B006 linting error
+
+    return get_shared_client().run_one_function(
+        {
+            "name": "DrugOptimizationAgent",
+            "arguments": {
+                "compounds": compounds,
+                "admet_data": admet_data,
+                "efficacy_data": efficacy_data,
+                "target_profile": target_profile,
+            },
+        },
+        stream_callback=stream_callback,
+        use_cache=use_cache,
+        validate=validate,
+    )
+
+
+__all__ = ["DrugOptimizationAgent"]

tooluniverse/tools/Ensembl_lookup_gene_by_symbol.py

@@ -0,0 +1,52 @@
+"""
+Ensembl_lookup_gene_by_symbol
+
+Lookup Ensembl gene by species and gene symbol, returning core metadata and coordinates (uses /xr...
+"""
+
+from typing import Any, Optional, Callable
+from ._shared_client import get_shared_client
+
+
+def Ensembl_lookup_gene_by_symbol(
+    symbol: str,
+    species: Optional[str] = "homo_sapiens",
+    *,
+    stream_callback: Optional[Callable[[str], None]] = None,
+    use_cache: bool = False,
+    validate: bool = True,
+) -> dict[str, Any]:
+    """
+    Lookup Ensembl gene by species and gene symbol, returning core metadata and coordinates (uses /xr...
+
+    Parameters
+    ----------
+    species : str
+        Species name (e.g., 'homo_sapiens').
+    symbol : str
+        Gene symbol (e.g., BRCA1).
+    stream_callback : Callable, optional
+        Callback for streaming output
+    use_cache : bool, default False
+        Enable caching
+    validate : bool, default True
+        Validate parameters
+
+    Returns
+    -------
+    dict[str, Any]
+    """
+    # Handle mutable defaults to avoid B006 linting error
+
+    return get_shared_client().run_one_function(
+        {
+            "name": "Ensembl_lookup_gene_by_symbol",
+            "arguments": {"species": species, "symbol": symbol},
+        },
+        stream_callback=stream_callback,
+        use_cache=use_cache,
+        validate=validate,
+    )
+
+
+__all__ = ["Ensembl_lookup_gene_by_symbol"]

tooluniverse/tools/EuropePMC_search_articles.py

@@ -10,7 +10,7 @@ from ._shared_client import get_shared_client
 
 def EuropePMC_search_articles(
     query: str,
-    limit: int,
+    limit: Optional[int] = 5,
     *,
     stream_callback: Optional[Callable[[str], None]] = None,
     use_cache: bool = False,

tooluniverse/tools/GIN_Guidelines_Search.py

@@ -0,0 +1,52 @@
+"""
+GIN_Guidelines_Search
+
+Search Guidelines International Network (GIN) guidelines database. GIN maintains the world's larg...
+"""
+
+from typing import Any, Optional, Callable
+from ._shared_client import get_shared_client
+
+
+def GIN_Guidelines_Search(
+    query: str,
+    limit: int,
+    *,
+    stream_callback: Optional[Callable[[str], None]] = None,
+    use_cache: bool = False,
+    validate: bool = True,
+) -> list[Any]:
+    """
+    Search Guidelines International Network (GIN) guidelines database. GIN maintains the world's larg...
+
+    Parameters
+    ----------
+    query : str
+        Medical condition, treatment, or clinical topic to search for in GIN guidelin...
+    limit : int
+        Maximum number of guidelines to return (default: 10)
+    stream_callback : Callable, optional
+        Callback for streaming output
+    use_cache : bool, default False
+        Enable caching
+    validate : bool, default True
+        Validate parameters
+
+    Returns
+    -------
+    list[Any]
+    """
+    # Handle mutable defaults to avoid B006 linting error
+
+    return get_shared_client().run_one_function(
+        {
+            "name": "GIN_Guidelines_Search",
+            "arguments": {"query": query, "limit": limit},
+        },
+        stream_callback=stream_callback,
+        use_cache=use_cache,
+        validate=validate,
+    )
+
+
+__all__ = ["GIN_Guidelines_Search"]

tooluniverse/tools/GWAS_search_associations_by_gene.py

@@ -0,0 +1,52 @@
+"""
+GWAS_search_associations_by_gene
+
+Search GWAS Catalog associations by gene name (returns strongest risk allele and p-value fields).
+"""
+
+from typing import Any, Optional, Callable
+from ._shared_client import get_shared_client
+
+
+def GWAS_search_associations_by_gene(
+    gene_name: str,
+    size: Optional[int] = 5,
+    *,
+    stream_callback: Optional[Callable[[str], None]] = None,
+    use_cache: bool = False,
+    validate: bool = True,
+) -> dict[str, Any]:
+    """
+    Search GWAS Catalog associations by gene name (returns strongest risk allele and p-value fields).
+
+    Parameters
+    ----------
+    gene_name : str
+        Gene symbol (e.g., BRCA1).
+    size : int
+        Max associations to return.
+    stream_callback : Callable, optional
+        Callback for streaming output
+    use_cache : bool, default False
+        Enable caching
+    validate : bool, default True
+        Validate parameters
+
+    Returns
+    -------
+    dict[str, Any]
+    """
+    # Handle mutable defaults to avoid B006 linting error
+
+    return get_shared_client().run_one_function(
+        {
+            "name": "GWAS_search_associations_by_gene",
+            "arguments": {"gene_name": gene_name, "size": size},
+        },
+        stream_callback=stream_callback,
+        use_cache=use_cache,
+        validate=validate,
+    )
+
+
+__all__ = ["GWAS_search_associations_by_gene"]

tooluniverse/tools/LiteratureSynthesisAgent.py

@@ -0,0 +1,59 @@
+"""
+LiteratureSynthesisAgent
+
+AI agent that synthesizes literature findings and provides evidence-based insights
+"""
+
+from typing import Any, Optional, Callable
+from ._shared_client import get_shared_client
+
+
+def LiteratureSynthesisAgent(
+    topic: str,
+    literature_data: str,
+    focus_area: Optional[str] = "General",
+    *,
+    stream_callback: Optional[Callable[[str], None]] = None,
+    use_cache: bool = False,
+    validate: bool = True,
+) -> Any:
+    """
+    AI agent that synthesizes literature findings and provides evidence-based insights
+
+    Parameters
+    ----------
+    topic : str
+        Research topic or question
+    literature_data : str
+        Literature findings or abstracts to synthesize
+    focus_area : str
+        Specific focus area for synthesis
+    stream_callback : Callable, optional
+        Callback for streaming output
+    use_cache : bool, default False
+        Enable caching
+    validate : bool, default True
+        Validate parameters
+
+    Returns
+    -------
+    Any
+    """
+    # Handle mutable defaults to avoid B006 linting error
+
+    return get_shared_client().run_one_function(
+        {
+            "name": "LiteratureSynthesisAgent",
+            "arguments": {
+                "topic": topic,
+                "literature_data": literature_data,
+                "focus_area": focus_area,
+            },
+        },
+        stream_callback=stream_callback,
+        use_cache=use_cache,
+        validate=validate,
+    )
+
+
+__all__ = ["LiteratureSynthesisAgent"]

tooluniverse/tools/PMC_search_papers.py

@@ -11,9 +11,9 @@ from ._shared_client import get_shared_client
 def PMC_search_papers(
     query: str,
     limit: int,
-    date_from: str,
-    date_to: str,
-    article_type: str,
+    date_from: Optional[str] = None,
+    date_to: Optional[str] = None,
+    article_type: Optional[str] = None,
     *,
     stream_callback: Optional[Callable[[str], None]] = None,
     use_cache: bool = False,

tooluniverse/tools/PubMed_search_articles.py

@@ -10,8 +10,8 @@ from ._shared_client import get_shared_client
 
 def PubMed_search_articles(
     query: str,
-    limit: int,
-    api_key: str,
+    limit: Optional[int] = 10,
+    api_key: Optional[str] = None,
     *,
     stream_callback: Optional[Callable[[str], None]] = None,
     use_cache: bool = False,

tooluniverse/tools/SemanticScholar_search_papers.py

@@ -11,7 +11,7 @@ from ._shared_client import get_shared_client
 def SemanticScholar_search_papers(
     query: str,
     limit: int,
-    api_key: str,
+    api_key: Optional[str] = None,
     *,
     stream_callback: Optional[Callable[[str], None]] = None,
     use_cache: bool = False,

tooluniverse/tools/UCSC_get_genes_by_region.py

@@ -0,0 +1,67 @@
+"""
+UCSC_get_genes_by_region
+
+Query UCSC Genome Browser track API for knownGene features in a genomic window.
+"""
+
+from typing import Any, Optional, Callable
+from ._shared_client import get_shared_client
+
+
+def UCSC_get_genes_by_region(
+    chrom: str,
+    start: int,
+    end: int,
+    genome: Optional[str] = "hg38",
+    track: Optional[str] = "knownGene",
+    *,
+    stream_callback: Optional[Callable[[str], None]] = None,
+    use_cache: bool = False,
+    validate: bool = True,
+) -> dict[str, Any]:
+    """
+    Query UCSC Genome Browser track API for knownGene features in a genomic window.
+
+    Parameters
+    ----------
+    genome : str
+        Genome assembly (e.g., hg38).
+    chrom : str
+        Chromosome (e.g., chr17).
+    start : int
+        Start position (0-based).
+    end : int
+        End position.
+    track : str
+        Track name.
+    stream_callback : Callable, optional
+        Callback for streaming output
+    use_cache : bool, default False
+        Enable caching
+    validate : bool, default True
+        Validate parameters
+
+    Returns
+    -------
+    dict[str, Any]
+    """
+    # Handle mutable defaults to avoid B006 linting error
+
+    return get_shared_client().run_one_function(
+        {
+            "name": "UCSC_get_genes_by_region",
+            "arguments": {
+                "genome": genome,
+                "chrom": chrom,
+                "start": start,
+                "end": end,
+                "track": track,
+            },
+        },
+        stream_callback=stream_callback,
+        use_cache=use_cache,
+        validate=validate,
+    )
+
+
+__all__ = ["UCSC_get_genes_by_region"]

tooluniverse/tools/Zenodo_search_records.py

@@ -11,7 +11,7 @@ from ._shared_client import get_shared_client
 def Zenodo_search_records(
     query: str,
     max_results: int,
-    community: str,
+    community: Optional[str] = None,
     *,
     stream_callback: Optional[Callable[[str], None]] = None,
     use_cache: bool = False,

tooluniverse/tools/__init__.py

@@ -1,7 +1,7 @@
 """
 ToolUniverse Tools
 
-Type-safe Python interface to 654 scientific tools.
+Type-safe Python interface to 670 scientific tools.
 Each tool is in its own module for minimal import overhead.
 
 Usage:
@@ -32,6 +32,7 @@ from .ADMETAI_predict_solubility_lipophilicity_hydration import (
 )
 from .ADMETAI_predict_stress_response import ADMETAI_predict_stress_response
 from .ADMETAI_predict_toxicity import ADMETAI_predict_toxicity
+from .ADMETAnalyzerAgent import ADMETAnalyzerAgent
 from .AdvancedCodeQualityAnalyzer import AdvancedCodeQualityAnalyzer
 from .AdverseEventICDMapper import AdverseEventICDMapper
 from .AdverseEventPredictionQuestionGenerator import (
@@ -44,11 +45,15 @@ from .ArXiv_search_papers import ArXiv_search_papers
 from .ArgumentDescriptionOptimizer import ArgumentDescriptionOptimizer
 from .BioRxiv_search_preprints import BioRxiv_search_preprints
 from .BiomarkerDiscoveryWorkflow import BiomarkerDiscoveryWorkflow
+from .CMA_Guidelines_Search import CMA_Guidelines_Search
 from .CORE_search_papers import CORE_search_papers
 from .CallAgent import CallAgent
 from .ChEMBL_search_similar_molecules import ChEMBL_search_similar_molecules
+from .ClinVar_search_variants import ClinVar_search_variants
+from .ClinicalTrialDesignAgent import ClinicalTrialDesignAgent
 from .CodeOptimizer import CodeOptimizer
 from .CodeQualityAnalyzer import CodeQualityAnalyzer
+from .CompoundDiscoveryAgent import CompoundDiscoveryAgent
 from .ComprehensiveDrugDiscoveryPipeline import ComprehensiveDrugDiscoveryPipeline
 from .Crossref_search_works import Crossref_search_works
 from .DBLP_search_publications import DBLP_search_publications
@@ -58,8 +63,12 @@ from .DailyMed_search_spls import DailyMed_search_spls
 from .DataAnalysisValidityReviewer import DataAnalysisValidityReviewer
 from .DescriptionAnalyzer import DescriptionAnalyzer
 from .DescriptionQualityEvaluator import DescriptionQualityEvaluator
+from .DiseaseAnalyzerAgent import DiseaseAnalyzerAgent
 from .DomainExpertValidator import DomainExpertValidator
+from .DrugInteractionAnalyzerAgent import DrugInteractionAnalyzerAgent
+from .DrugOptimizationAgent import DrugOptimizationAgent
 from .DrugSafetyAnalyzer import DrugSafetyAnalyzer
+from .Ensembl_lookup_gene_by_symbol import Ensembl_lookup_gene_by_symbol
 from .EthicalComplianceReviewer import EthicalComplianceReviewer
 from .EuropePMC_Guidelines_Search import EuropePMC_Guidelines_Search
 from .EuropePMC_search_articles import EuropePMC_search_articles
@@ -441,11 +450,13 @@ from .FDA_retrieve_patient_medication_info_by_drug_name import (
 )
 from .Fatcat_search_scholar import Fatcat_search_scholar
 from .Finish import Finish
+from .GIN_Guidelines_Search import GIN_Guidelines_Search
 from .GO_get_annotations_for_gene import GO_get_annotations_for_gene
 from .GO_get_genes_for_term import GO_get_genes_for_term
 from .GO_get_term_by_id import GO_get_term_by_id
 from .GO_get_term_details import GO_get_term_details
 from .GO_search_terms import GO_search_terms
+from .GWAS_search_associations_by_gene import GWAS_search_associations_by_gene
 from .HAL_search_archive import HAL_search_archive
 from .HPA_get_biological_processes_by_gene import HPA_get_biological_processes_by_gene
 from .HPA_get_cancer_prognostics_by_gene import HPA_get_cancer_prognostics_by_gene
@@ -474,6 +485,7 @@ from .HypothesisGenerator import HypothesisGenerator
 from .LabelGenerator import LabelGenerator
 from .LiteratureContextReviewer import LiteratureContextReviewer
 from .LiteratureSearchTool import LiteratureSearchTool
+from .LiteratureSynthesisAgent import LiteratureSynthesisAgent
 from .MedRxiv_search_preprints import MedRxiv_search_preprints
 from .MedicalLiteratureReviewer import MedicalLiteratureReviewer
 from .MedicalTermNormalizer import MedicalTermNormalizer
@@ -704,6 +716,7 @@ from .Tool_Finder import Tool_Finder
 from .Tool_Finder_Keyword import Tool_Finder_Keyword
 from .Tool_Finder_LLM import Tool_Finder_LLM
 from .Tool_RAG import Tool_RAG
+from .UCSC_get_genes_by_region import UCSC_get_genes_by_region
 from .UniProt_get_alternative_names_by_accession import (
     UniProt_get_alternative_names_by_accession,
 )
@@ -744,6 +757,8 @@ from .cellosaurus_get_cell_line_info import cellosaurus_get_cell_line_info
 from .cellosaurus_query_converter import cellosaurus_query_converter
 from .cellosaurus_search_cell_lines import cellosaurus_search_cell_lines
 from .chembl_disease_target_score import chembl_disease_target_score
+from .convert_to_markdown import convert_to_markdown
+from .dbSNP_get_variant_by_rsid import dbSNP_get_variant_by_rsid
 from .dict_search import dict_search
 from .dili_search import dili_search
 from .diqt_search import diqt_search
@@ -1046,6 +1061,7 @@ from .get_xarray_info import get_xarray_info
 from .get_xesmf_info import get_xesmf_info
 from .get_xgboost_info import get_xgboost_info
 from .get_zarr_info import get_zarr_info
+from .gnomAD_query_variant import gnomAD_query_variant
 from .gwas_get_association_by_id import gwas_get_association_by_id
 from .gwas_get_associations_for_snp import gwas_get_associations_for_snp
 from .gwas_get_associations_for_study import gwas_get_associations_for_study
@@ -1090,6 +1106,7 @@ __all__ = [
     "ADMETAI_predict_solubility_lipophilicity_hydration",
     "ADMETAI_predict_stress_response",
     "ADMETAI_predict_toxicity",
+    "ADMETAnalyzerAgent",
     "AdvancedCodeQualityAnalyzer",
     "AdverseEventICDMapper",
     "AdverseEventPredictionQuestionGenerator",
@@ -1098,11 +1115,15 @@ __all__ = [
     "ArgumentDescriptionOptimizer",
     "BioRxiv_search_preprints",
     "BiomarkerDiscoveryWorkflow",
+    "CMA_Guidelines_Search",
     "CORE_search_papers",
     "CallAgent",
     "ChEMBL_search_similar_molecules",
+    "ClinVar_search_variants",
+    "ClinicalTrialDesignAgent",
     "CodeOptimizer",
     "CodeQualityAnalyzer",
+    "CompoundDiscoveryAgent",
     "ComprehensiveDrugDiscoveryPipeline",
     "Crossref_search_works",
     "DBLP_search_publications",
@@ -1112,8 +1133,12 @@ __all__ = [
     "DataAnalysisValidityReviewer",
     "DescriptionAnalyzer",
     "DescriptionQualityEvaluator",
+    "DiseaseAnalyzerAgent",
     "DomainExpertValidator",
+    "DrugInteractionAnalyzerAgent",
+    "DrugOptimizationAgent",
     "DrugSafetyAnalyzer",
+    "Ensembl_lookup_gene_by_symbol",
     "EthicalComplianceReviewer",
     "EuropePMC_Guidelines_Search",
     "EuropePMC_search_articles",
@@ -1291,11 +1316,13 @@ __all__ = [
     "FDA_retrieve_patient_medication_info_by_drug_name",
     "Fatcat_search_scholar",
     "Finish",
+    "GIN_Guidelines_Search",
     "GO_get_annotations_for_gene",
     "GO_get_genes_for_term",
     "GO_get_term_by_id",
     "GO_get_term_details",
     "GO_search_terms",
+    "GWAS_search_associations_by_gene",
     "HAL_search_archive",
     "HPA_get_biological_processes_by_gene",
     "HPA_get_cancer_prognostics_by_gene",
@@ -1314,6 +1341,7 @@ __all__ = [
     "LabelGenerator",
     "LiteratureContextReviewer",
     "LiteratureSearchTool",
+    "LiteratureSynthesisAgent",
     "MedRxiv_search_preprints",
     "MedicalLiteratureReviewer",
     "MedicalTermNormalizer",
@@ -1430,6 +1458,7 @@ __all__ = [
     "Tool_Finder_Keyword",
     "Tool_Finder_LLM",
     "Tool_RAG",
+    "UCSC_get_genes_by_region",
     "UniProt_get_alternative_names_by_accession",
     "UniProt_get_disease_variants_by_accession",
     "UniProt_get_entry_by_accession",
@@ -1456,6 +1485,8 @@ __all__ = [
     "cellosaurus_query_converter",
     "cellosaurus_search_cell_lines",
     "chembl_disease_target_score",
+    "convert_to_markdown",
+    "dbSNP_get_variant_by_rsid",
     "dict_search",
     "dili_search",
     "diqt_search",
@@ -1708,6 +1739,7 @@ __all__ = [
     "get_xesmf_info",
     "get_xgboost_info",
     "get_zarr_info",
+    "gnomAD_query_variant",
     "gwas_get_association_by_id",
     "gwas_get_associations_for_snp",
     "gwas_get_associations_for_study",