tooluniverse.tools package¶
ToolUniverse Tools
Type-safe Python interface to 669 scientific tools. Each tool is in its own module for minimal import overhead.
- Usage:
from tooluniverse.tools import ArXiv_search_papers result = ArXiv_search_papers(query=”machine learning”)
Get the shared ToolUniverse client instance.
This function implements a thread-safe singleton pattern with support for custom configurations and external instances.
- Parameters:
custom_instance (ToolUniverse | None) – Optional ToolUniverse instance to use instead of the shared singleton. If provided, this instance will be returned directly without any singleton logic.
**config_kwargs – Optional configuration parameters to pass to ToolUniverse constructor. These are only used during the initial creation of the shared instance. If the shared instance already exists, these parameters are ignored.
- Returns:
The client instance to use for tool execution
- Return type:
- Thread Safety:
This function is thread-safe. Multiple threads can call this function concurrently without risk of creating multiple ToolUniverse instances.
- Configuration:
Configuration parameters are only applied during the initial creation of the shared instance. Subsequent calls with different parameters will not affect the already-created instance.
Examples
# Basic usage client = get_shared_client()
# With custom configuration (only effective on first call) client = get_shared_client(hooks_enabled=True, log_level=”DEBUG”)
# Using your own instance my_tu = ToolUniverse(hooks_enabled=True) client = get_shared_client(custom_instance=my_tu)
Reset the shared client (useful for testing or when you need to reload).
This function clears the shared client instance, allowing a new instance to be created on the next call to get_shared_client(). This is primarily useful for testing scenarios where you need to ensure a clean state.
- Thread Safety:
This function is thread-safe and uses the same lock as get_shared_client() to ensure proper synchronization.
Warning
Calling this function while other threads are using the shared client may cause unexpected behavior. It’s recommended to only call this function when you’re certain no other threads are accessing the client.
Examples
# Reset for testing reset_shared_client()
# Now get_shared_client() will create a new instance client = get_shared_client(hooks_enabled=True)
- tooluniverse.tools.ADMETAI_predict_BBB_penetrance(smiles, *, stream_callback=None, use_cache=False, validate=True)[source]¶
Predicts blood-brain barrier (BBB) penetrance for a given list of molecules in SMILES format.
- tooluniverse.tools.ADMETAI_predict_CYP_interactions(smiles, *, stream_callback=None, use_cache=False, validate=True)[source]¶
Predicts CYP enzyme interactions for a given list of molecules in SMILES format.
- tooluniverse.tools.ADMETAI_predict_bioavailability(smiles, *, stream_callback=None, use_cache=False, validate=True)[source]¶
Predicts bioavailability endpoints (Bioavailability_Ma, HIA_Hou, PAMPA_NCATS, Caco2_Wang, Pgp_Bro…
- tooluniverse.tools.ADMETAI_predict_clearance_distribution(smiles, *, stream_callback=None, use_cache=False, validate=True)[source]¶
Predicts clearance and distribution endpoints (Clearance_Hepatocyte_AZ, Clearance_Microsome_AZ, H…
- tooluniverse.tools.ADMETAI_predict_nuclear_receptor_activity(smiles, *, stream_callback=None, use_cache=False, validate=True)[source]¶
Predicts nuclear receptor activity endpoints (NR-AR-LBD, NR-AR, NR-AhR, NR-Aromatase, NR-ER-LBD, …
- tooluniverse.tools.ADMETAI_predict_physicochemical_properties(smiles, *, stream_callback=None, use_cache=False, validate=True)[source]¶
Predicts physicochemical properties (molecular weight, logP, hydrogen bond acceptors/donors, Lipi…
- tooluniverse.tools.ADMETAI_predict_solubility_lipophilicity_hydration(smiles, *, stream_callback=None, use_cache=False, validate=True)[source]¶
Predicts solubility, lipophilicity, and hydration endpoints (Solubility_AqSolDB, Lipophilicity_As…
- tooluniverse.tools.ADMETAI_predict_stress_response(smiles, *, stream_callback=None, use_cache=False, validate=True)[source]¶
Predicts stress response endpoints (SR-ARE, SR-ATAD5, SR-HSE, SR-MMP, SR-p53) for a given list of…
- tooluniverse.tools.ADMETAI_predict_toxicity(smiles, *, stream_callback=None, use_cache=False, validate=True)[source]¶
Predicts toxicity endpoints (AMES, Carcinogens_Lagunin, ClinTox, DILI, LD50_Zhu, Skin_Reaction, h…
- tooluniverse.tools.ADMETAnalyzerAgent(compounds, admet_data, disease_context='', *, stream_callback=None, use_cache=False, validate=True)[source]¶
AI agent that analyzes ADMET data and provides insights on drug-likeness and safety profiles
- tooluniverse.tools.AdvancedCodeQualityAnalyzer(source_code, language='python', analysis_depth='comprehensive', domain_context=None, *, stream_callback=None, use_cache=False, validate=True)[source]¶
Performs deep analysis of code quality including complexity, security, performance, and maintaina…
- Parameters:
source_code (
str) – The source code to analyze for quality assessmentlanguage (
str) – Programming language (python, javascript, etc.)analysis_depth (
str) – Level of analysis depth to performdomain_context (
str) – Domain context for specialized analysis (e.g., bioinformatics, web development)stream_callback (
Callable, optional) – Callback for streaming output
- Return type:
Any
- tooluniverse.tools.AdverseEventICDMapper(source_text, *, stream_callback=None, use_cache=False, validate=True)[source]¶
Extracts adverse events from narrative clinical or pharmacovigilance text and maps each event to …
- tooluniverse.tools.AdverseEventPredictionQuestionGenerator(disease_name, drug_name, *, stream_callback=None, use_cache=False, validate=True)[source]¶
Generates a set of personalized adverse‐event prediction questions for a given disease and drug, …
- tooluniverse.tools.AdverseEventPredictionQuestionGeneratorWithContext(disease_name, drug_name, context_information, *, stream_callback=None, use_cache=False, validate=True)[source]¶
Generates a set of personalized adverse‐event prediction questions for a given disease and drug, …
- Parameters:
- Return type:
Any
- tooluniverse.tools.ArXiv_search_papers(query, limit=10, sort_by='relevance', sort_order='descending', *, stream_callback=None, use_cache=False, validate=True)[source]¶
Search arXiv for papers by keyword using the public arXiv API. Returns papers with title, abstrac…
- Parameters:
query (
str) – Search query for arXiv papers. Use keywords separated by spaces to refine you…limit (
int) – Number of papers to return. This sets the maximum number of papers retrieved …sort_by (
str) – Sort order for results. Options: ‘relevance’, ‘lastUpdatedDate’, ‘submittedDate’sort_order (
str) – Sort direction. Options: ‘ascending’, ‘descending’stream_callback (
Callable, optional) – Callback for streaming output
- Return type:
list[Any]
- tooluniverse.tools.ArgumentDescriptionOptimizer(parameter_schema, test_results, *, stream_callback=None, use_cache=False, validate=True)[source]¶
Optimizes the descriptions of tool arguments/parameters based on test case results and actual usa…
- Parameters:
- Return type:
Any
- tooluniverse.tools.BioRxiv_search_preprints(query, max_results, *, stream_callback=None, use_cache=False, validate=True)[source]¶
Search bioRxiv preprints using the public bioRxiv API. Returns preprints with title, authors, yea…
- tooluniverse.tools.BiomarkerDiscoveryWorkflow(disease_condition, sample_type, *, stream_callback=None, use_cache=False, validate=True)[source]¶
Discover and validate biomarkers for a specific disease condition using literature analysis, expr…
- tooluniverse.tools.CMA_Guidelines_Search(query, limit, *, stream_callback=None, use_cache=False, validate=True)[source]¶
Search Canadian Medical Association (CMA) Infobase guidelines. Contains over 1200 evidence-based …
- tooluniverse.tools.CORE_search_papers(query, limit, year_from=None, year_to=None, language=None, *, stream_callback=None, use_cache=False, validate=True)[source]¶
Search for open access academic papers using CORE API. CORE is the world’s largest collection of …
- Parameters:
query (
str) – Search query for CORE papers. Use keywords separated by spaces to refine your…limit (
int) – Maximum number of papers to return. This sets the maximum number of papers re…year_from (
int) – Start year for publication date filter (e.g., 2020). Optional parameter to li…year_to (
int) – End year for publication date filter (e.g., 2024). Optional parameter to limi…language (
str) – Language filter for papers (e.g., ‘en’, ‘es’, ‘fr’). Optional parameter to li…stream_callback (
Callable, optional) – Callback for streaming output
- Return type:
list[Any]
- tooluniverse.tools.CallAgent(solution, *, stream_callback=None, use_cache=False, validate=True)[source]¶
Give a solution plan to the agent and let it solve the problem. Solution plan should reflect a di…
- tooluniverse.tools.ChEMBL_search_similar_molecules(query, similarity_threshold, max_results, *, stream_callback=None, use_cache=False, validate=True)[source]¶
Search for molecules similar to a given SMILES, chembl_id, or compound or drug name, using the Ch…
- tooluniverse.tools.ClinVar_search_variants(query, retmax=5, *, stream_callback=None, use_cache=False, validate=True)[source]¶
Search ClinVar via NCBI E-utilities (esearch→esummary) and return concise variant records for a q…
- tooluniverse.tools.ClinicalTrialDesignAgent(drug_name, indication, preclinical_data='', target_population='General adult population', *, stream_callback=None, use_cache=False, validate=True)[source]¶
AI agent that designs clinical trial protocols based on preclinical data and regulatory requirements
- tooluniverse.tools.CodeOptimizer(tool_config, quality_evaluation, *, stream_callback=None, use_cache=False, validate=True)[source]¶
Optimizes code implementation for tools based on quality evaluation. Takes tool configuration and…
- tooluniverse.tools.CodeQualityAnalyzer(tool_name, tool_description, tool_parameters, implementation_code, test_cases, test_execution_results=None, *, stream_callback=None, use_cache=False, validate=True)[source]¶
Analyzes code quality from multiple dimensions including algorithmic correctness, functional impl…
- Parameters:
tool_name (
str) – Name of the tool being analyzedtool_description (
str) – Description of what the tool is supposed to dotool_parameters (
str) – JSON string of tool parameters and their typesimplementation_code (
str) – The actual implementation code to analyzetest_cases (
str) – JSON string of test cases for the tooltest_execution_results (
str) – JSON string of test execution results including pass/fail status and actual o…stream_callback (
Callable, optional) – Callback for streaming output
- Return type:
Any
- tooluniverse.tools.CompoundDiscoveryAgent(disease_name, targets, context='', *, stream_callback=None, use_cache=False, validate=True)[source]¶
AI agent that analyzes potential drug compounds using multiple strategies and LLM reasoning
- tooluniverse.tools.ComprehensiveDrugDiscoveryPipeline(disease_efo_id, *, stream_callback=None, use_cache=False, validate=True)[source]¶
Complete end-to-end drug discovery workflow from disease to optimized candidates. Identifies targ…
- Parameters:
- Return type:
Any
- tooluniverse.tools.Crossref_search_works(query, limit, filter, *, stream_callback=None, use_cache=False, validate=True)[source]¶
Search Crossref Works API for articles by keyword. Returns articles with title, abstract, journal…
- Parameters:
query (
str) – Search query for Crossref works. Use keywords separated by spaces to refine y…limit (
int) – Number of articles to return. This sets the maximum number of articles retrie…filter (
str) – Optional filter string for Crossref API. Examples: ‘type:journal-article,from…stream_callback (
Callable, optional) – Callback for streaming output
- Return type:
list[Any]
- tooluniverse.tools.DBLP_search_publications(query, limit, *, stream_callback=None, use_cache=False, validate=True)[source]¶
Search DBLP Computer Science Bibliography for publications. Returns publications with title, auth…
- tooluniverse.tools.DOAJ_search_articles(query, max_results=10, type='articles', *, stream_callback=None, use_cache=False, validate=True)[source]¶
Search DOAJ (Directory of Open Access Journals) for open-access articles. Returns articles with t…
- Parameters:
query (
str) – Search query for DOAJ articles. Supports Lucene syntax for advanced queries.max_results (
int) – Maximum number of articles to return. Default is 10, maximum is 100.type (
str) – Type of search: ‘articles’ or ‘journals’. Default is ‘articles’.stream_callback (
Callable, optional) – Callback for streaming output
- Return type:
list[Any]
- tooluniverse.tools.DailyMed_get_spl_by_setid(setid, format, *, stream_callback=None, use_cache=False, validate=True)[source]¶
Get complete label corresponding to SPL Set ID, returns content in XML or JSON format.
- tooluniverse.tools.DailyMed_search_spls(drug_name, ndc, rxcui, setid, published_date_gte, published_date_eq, pagesize, page, *, stream_callback=None, use_cache=False, validate=True)[source]¶
Search SPL list using multiple filter conditions (drug_name/ndc/rxcui/setid) and return metadata …
- Parameters:
drug_name (
str) – Generic or brand name of the drug, e.g., ‘TAMSULOSIN HYDROCHLORIDE’.ndc (
str) – National Drug Code (NDC).rxcui (
str) – RxNorm Code (RXCUI).setid (
str) – Set ID corresponding to the SPL.published_date_gte (
str) – Published date >= specified date, format ‘YYYY-MM-DD’.published_date_eq (
str) – Published date == specified date, format ‘YYYY-MM-DD’.pagesize (
int) – Number of items per page, maximum 100, default 100.page (
int) – Page number, starts from 1, default 1.stream_callback (
Callable, optional) – Callback for streaming output
- Return type:
Any
- tooluniverse.tools.DataAnalysisValidityReviewer(analysis_section, *, stream_callback=None, use_cache=False, validate=True)[source]¶
Checks statistical choices, assumption testing, and reporting transparency.
- tooluniverse.tools.DescriptionAnalyzer(original_description, test_results, *, stream_callback=None, use_cache=False, validate=True)[source]¶
Analyzes a tool’s original description and the results of multiple test cases, then suggests an i…
- tooluniverse.tools.DescriptionQualityEvaluator(tool_description, parameter_descriptions, test_results, *, stream_callback=None, use_cache=False, validate=True)[source]¶
Evaluates the quality of tool descriptions and parameter descriptions, providing a score and spec…
- Parameters:
- Return type:
Any
- tooluniverse.tools.DiseaseAnalyzerAgent(disease_name, context='', *, stream_callback=None, use_cache=False, validate=True)[source]¶
AI agent that analyzes disease characteristics and identifies potential therapeutic targets using…
- Parameters:
- Return type:
Any
- tooluniverse.tools.DomainExpertValidator(tool_config, domain, validation_aspects='["accuracy", "methodology", "best-practices"]', implementation_code=None, *, stream_callback=None, use_cache=False, validate=True)[source]¶
Provides domain-specific validation and expert recommendations for tools with deep expertise acro…
- Parameters:
tool_config (
str) – JSON string of tool configuration to validatedomain (
str) – Domain expertise area for validationvalidation_aspects (
str) – JSON array string of specific aspects to validateimplementation_code (
str) – Implementation code to validate (optional)stream_callback (
Callable, optional) – Callback for streaming output
- Return type:
Any
- tooluniverse.tools.DrugInteractionAnalyzerAgent(compounds, patient_context='General adult population', *, stream_callback=None, use_cache=False, validate=True)[source]¶
AI agent that analyzes drug-drug interactions and provides clinical recommendations
- tooluniverse.tools.DrugOptimizationAgent(compounds, admet_data='', efficacy_data='', target_profile='', *, stream_callback=None, use_cache=False, validate=True)[source]¶
AI agent that analyzes drug optimization strategies based on ADMET and efficacy data
- Parameters:
- Return type:
Any
- tooluniverse.tools.DrugSafetyAnalyzer(drug_name, patient_sex, serious_events_only, *, stream_callback=None, use_cache=False, validate=True)[source]¶
Comprehensive drug safety analysis combining adverse event data, literature review, and molecular…
- tooluniverse.tools.Ensembl_lookup_gene_by_symbol(symbol, species='homo_sapiens', *, stream_callback=None, use_cache=False, validate=True)[source]¶
Lookup Ensembl gene by species and gene symbol, returning core metadata and coordinates (uses /xr…
- Parameters:
- Return type:
dict[str,Any]
- tooluniverse.tools.EthicalComplianceReviewer(ethics_section, *, stream_callback=None, use_cache=False, validate=True)[source]¶
Checks adherence to ethical standards and disclosure practices.
- tooluniverse.tools.EuropePMC_Guidelines_Search(query, limit, *, stream_callback=None, use_cache=False, validate=True)[source]¶
Search Europe PMC for clinical guidelines and evidence-based recommendations. Europe PMC provides…
- tooluniverse.tools.EuropePMC_search_articles(query, limit=5, *, stream_callback=None, use_cache=False, validate=True)[source]¶
Search for articles on Europe PMC including abstracts. The tool queries the Europe PMC web servic…
- tooluniverse.tools.ExperimentalDesignScorer(hypothesis, design_description, *, stream_callback=None, use_cache=False, validate=True)[source]¶
Assesses a proposed experimental design by assigning scores and structured feedback on hypothesis…
- tooluniverse.tools.FAERS_count_additive_administration_routes(medicinalproducts, serious, *, stream_callback=None, use_cache=False, validate=True)[source]¶
Additive multi-drug data: Enumerate and count administration routes for adverse events across spe…
- Parameters:
- Return type:
Any
- tooluniverse.tools.FAERS_count_additive_adverse_reactions(medicinalproducts, patientsex, patientagegroup, occurcountry, serious, seriousnessdeath, *, stream_callback=None, use_cache=False, validate=True)[source]¶
Additive multi-drug data: Aggregate adverse reaction counts across specified medicinal products, …
- Parameters:
medicinalproducts (
list[Any]) – Array of medicinal product names.patientsex (
str) – Filter by patient sex.patientagegroup (
str) – Filter by patient age group.occurcountry (
str) – Filter by ISO2 country code of occurrence.serious (
str) – Filter by seriousness classification.seriousnessdeath (
str) – Filter for fatal outcomes.stream_callback (
Callable, optional) – Callback for streaming output
- Return type:
Any
- tooluniverse.tools.FAERS_count_additive_event_reports_by_country(medicinalproducts, patientsex, patientagegroup, serious, *, stream_callback=None, use_cache=False, validate=True)[source]¶
Additive multi-drug data: Aggregate report counts by country of occurrence across specified medic…
- tooluniverse.tools.FAERS_count_additive_reaction_outcomes(medicinalproducts, patientsex, patientagegroup, occurcountry, *, stream_callback=None, use_cache=False, validate=True)[source]¶
Additive multi-drug data: Determine reaction outcome counts (e.g., recovered, resolving, fatal) a…
- Parameters:
- Return type:
Any
- tooluniverse.tools.FAERS_count_additive_reports_by_reporter_country(medicinalproducts, patientsex, patientagegroup, serious, *, stream_callback=None, use_cache=False, validate=True)[source]¶
Additive multi-drug data: Aggregate adverse event reports by primary reporter country across medi…
- tooluniverse.tools.FAERS_count_additive_seriousness_classification(medicinalproducts, patientsex, patientagegroup, occurcountry, *, stream_callback=None, use_cache=False, validate=True)[source]¶
Additive multi-drug data: Quantify serious vs non-serious classifications across medicinal produc…
- tooluniverse.tools.FAERS_count_country_by_drug_event(medicinalproduct, patientsex, patientagegroup, serious, *, stream_callback=None, use_cache=False, validate=True)[source]¶
Count the number of adverse event reports per country of occurrence, filtered by drug, patient de…
- Parameters:
- Return type:
Any
Count adverse events associated with patient death for a given drug. Data source: FDA Adverse Eve…
- tooluniverse.tools.FAERS_count_drug_routes_by_event(medicinalproduct, serious, *, stream_callback=None, use_cache=False, validate=True)[source]¶
Count the most common routes of administration for drugs involved in adverse event reports. Data …
- tooluniverse.tools.FAERS_count_drugs_by_drug_event(patientsex, patientagegroup, occurcountry, serious, *, stream_callback=None, use_cache=False, validate=True)[source]¶
Count the number of different drugs involved in FDA adverse event reports, filtered by patient de…
- Parameters:
- Return type:
Any
- tooluniverse.tools.FAERS_count_outcomes_by_drug_event(medicinalproduct, patientsex, patientagegroup, occurcountry, *, stream_callback=None, use_cache=False, validate=True)[source]¶
Count the outcome of adverse reactions (recovered, recovering, fatal, unresolved) filtered by dru…
- tooluniverse.tools.FAERS_count_patient_age_distribution(medicinalproduct, *, stream_callback=None, use_cache=False, validate=True)[source]¶
Analyze the age distribution of patients experiencing adverse events for a specific drug. The age…
- tooluniverse.tools.FAERS_count_reactions_by_drug_event(medicinalproduct, patientsex, patientagegroup, occurcountry, serious, seriousnessdeath, *, stream_callback=None, use_cache=False, validate=True)[source]¶
Count the number of adverse reactions reported for a given drug, filtered by patient details, eve…
- Parameters:
medicinalproduct (
str) – Drug name.patientsex (
str) – Patient sex, leave it blank if you don’t want to apply a filter.patientagegroup (
str) – Patient age group.occurcountry (
str) – Country where event occurred.serious (
str) – Whether the event was serious.seriousnessdeath (
str) – Was death reported?stream_callback (
Callable, optional) – Callback for streaming output
- Return type:
Any
- tooluniverse.tools.FAERS_count_reportercountry_by_drug_event(medicinalproduct, patientsex, patientagegroup, serious, *, stream_callback=None, use_cache=False, validate=True)[source]¶
Count the number of FDA adverse event reports grouped by the country of the primary reporter. Dat…
- Parameters:
- Return type:
Any
- tooluniverse.tools.FAERS_count_seriousness_by_drug_event(medicinalproduct, patientsex, patientagegroup, occurcountry, *, stream_callback=None, use_cache=False, validate=True)[source]¶
Count the number of adverse event reports classified as serious or non-serious, filtered by drug …
- Parameters:
- Return type:
Any
- tooluniverse.tools.FDA_get_abuse_dependence_info_by_drug_name(drug_name, limit=None, skip=None, *, stream_callback=None, use_cache=False, validate=True)[source]¶
Get information about drug abuse and dependence based on the drug name, specifically information …
- tooluniverse.tools.FDA_get_abuse_info_by_drug_name(drug_name, limit=None, skip=None, *, stream_callback=None, use_cache=False, validate=True)[source]¶
Retrieve information about types of abuse based on the drug name.
- tooluniverse.tools.FDA_get_accessories_info_by_drug_name(drug_name, limit=None, skip=None, *, stream_callback=None, use_cache=False, validate=True)[source]¶
Retrieve information about accessories based on the drug name.
- tooluniverse.tools.FDA_get_active_ingredient_info_by_drug_name(drug_name, limit=None, skip=None, *, stream_callback=None, use_cache=False, validate=True)[source]¶
Fetch a list of active ingredients in a specific drug product.
- tooluniverse.tools.FDA_get_adverse_reactions_by_drug_name(drug_name, limit=None, skip=None, *, stream_callback=None, use_cache=False, validate=True)[source]¶
Retrieve adverse reactions information based on the drug name.
- tooluniverse.tools.FDA_get_alarms_by_drug_name(drug_name, limit=None, skip=None, *, stream_callback=None, use_cache=False, validate=True)[source]¶
Retrieve alarms based on the specified drug name.
- tooluniverse.tools.FDA_get_animal_pharmacology_info_by_drug_name(drug_name, limit=None, skip=None, *, stream_callback=None, use_cache=False, validate=True)[source]¶
Retrieve animal pharmacology and toxicology information based on drug names.
- tooluniverse.tools.FDA_get_assembly_installation_info_by_drug_name(drug_name, limit=None, skip=None, *, stream_callback=None, use_cache=False, validate=True)[source]¶
Retrieve assembly or installation instructions based on drug names.
- tooluniverse.tools.FDA_get_boxed_warning_info_by_drug_name(drug_name, limit=None, skip=None, *, stream_callback=None, use_cache=False, validate=True)[source]¶
Retrieve boxed warning and adverse effects information for a specific drug.
- tooluniverse.tools.FDA_get_brand_name_generic_name(drug_name, limit=None, *, stream_callback=None, use_cache=False, validate=True)[source]¶
Retrieve the brand name and generic name from generic name or brand name of a drug.
- Parameters:
- Return type:
Any
- tooluniverse.tools.FDA_get_calibration_instructions_by_drug_name(drug_name, limit=None, skip=None, *, stream_callback=None, use_cache=False, validate=True)[source]¶
Retrieve calibration instructions based on the specified drug name.
- tooluniverse.tools.FDA_get_carcinogenic_mutagenic_fertility_by_drug_name(drug_name, limit=None, skip=None, *, stream_callback=None, use_cache=False, validate=True)[source]¶
Retrieve carcinogenic, mutagenic, or fertility impairment information based on the drug name.
- tooluniverse.tools.FDA_get_child_safety_info_by_drug_name(drug_name, limit=None, skip=None, *, stream_callback=None, use_cache=False, validate=True)[source]¶
Retrieve child safety information for a specific drug based on its name.
- tooluniverse.tools.FDA_get_clinical_pharmacology_by_drug_name(drug_name, limit=None, skip=None, *, stream_callback=None, use_cache=False, validate=True)[source]¶
Retrieve clinical pharmacology information based on drug names.
- tooluniverse.tools.FDA_get_clinical_studies_info_by_drug_name(drug_name, limit=None, skip=None, *, stream_callback=None, use_cache=False, validate=True)[source]¶
Retrieve clinical studies information based on the drug name.
- tooluniverse.tools.FDA_get_contact_for_questions_info_by_drug_name(drug_name, limit=None, skip=None, *, stream_callback=None, use_cache=False, validate=True)[source]¶
Retrieve information on who to contact with questions about the drug based on the provided drug n…
- tooluniverse.tools.FDA_get_contraindications_by_drug_name(drug_name, limit=None, skip=None, *, stream_callback=None, use_cache=False, validate=True)[source]¶
Retrieve contraindications information based on the drug name.
- tooluniverse.tools.FDA_get_controlled_substance_DEA_schedule_info_by_drug_name(drug_name, limit=None, skip=None, *, stream_callback=None, use_cache=False, validate=True)[source]¶
Retrieve information about the controlled substance Drug Enforcement Administratino (DEA) schedul…
- tooluniverse.tools.FDA_get_dear_health_care_provider_letter_info_by_drug_name(drug_name, limit=None, skip=None, *, stream_callback=None, use_cache=False, validate=True)[source]¶
Fetch information about dear health care provider letters for a specific drug. The letters are se…
- tooluniverse.tools.FDA_get_dependence_info_by_drug_name(drug_name, limit=None, skip=None, *, stream_callback=None, use_cache=False, validate=True)[source]¶
Retrieve information about dependence characteristics based on the drug name.
- tooluniverse.tools.FDA_get_disposal_info_by_drug_name(drug_name, limit=None, skip=None, *, stream_callback=None, use_cache=False, validate=True)[source]¶
Retrieve disposal and waste handling information based on the drug name.
- tooluniverse.tools.FDA_get_do_not_use_info_by_drug_name(drug_name, limit=None, skip=None, *, stream_callback=None, use_cache=False, validate=True)[source]¶
Retrieve information about all contraindications for use based on the drug name.
- tooluniverse.tools.FDA_get_document_id_by_drug_name(drug_name, limit=None, skip=None, *, stream_callback=None, use_cache=False, validate=True)[source]¶
Retrieve the document ID based on the drug name.
- tooluniverse.tools.FDA_get_dosage_and_storage_information_by_drug_name(drug_name, limit=None, skip=None, *, stream_callback=None, use_cache=False, validate=True)[source]¶
Retrieve dosage and storage information for a specific drug.
- tooluniverse.tools.FDA_get_dosage_forms_and_strengths_by_drug_name(drug_name, limit=None, skip=None, *, stream_callback=None, use_cache=False, validate=True)[source]¶
Retrieve dosage forms and strengths information based on the drug name.
- tooluniverse.tools.FDA_get_drug_generic_name(drug_name, *, stream_callback=None, use_cache=False, validate=True)[source]¶
Get the drug’s generic name based on the drug’s generic or brand name.
- tooluniverse.tools.FDA_get_drug_interactions_by_drug_name(drug_name, limit=None, skip=None, *, stream_callback=None, use_cache=False, validate=True)[source]¶
Retrieve drug interactions based on the specified drug name.
- tooluniverse.tools.FDA_get_drug_name_by_SPL_ID(field_info, limit=None, skip=None, *, stream_callback=None, use_cache=False, validate=True)[source]¶
Retrieve the drug name based on the FDA application number, NUI unique identifier, document ID of…
- tooluniverse.tools.FDA_get_drug_name_by_adverse_reaction(adverse_reaction, limit=None, skip=None, *, stream_callback=None, use_cache=False, validate=True)[source]¶
Retrieve the drug name based on specific adverse reactions reported. Warning: This tool only outp…
- tooluniverse.tools.FDA_get_drug_name_by_calibration_instructions(calibration_instructions, limit=None, skip=None, *, stream_callback=None, use_cache=False, validate=True)[source]¶
Retrieve the drug name based on the calibration instructions provided.
- tooluniverse.tools.FDA_get_drug_name_by_dependence_info(dependence_info, limit=None, skip=None, *, stream_callback=None, use_cache=False, validate=True)[source]¶
Retrieve the drug name based on information about dependence characteristics.
- tooluniverse.tools.FDA_get_drug_name_by_document_id(document_id, limit=None, skip=None, *, stream_callback=None, use_cache=False, validate=True)[source]¶
Retrieve the drug name based on the document ID.
- tooluniverse.tools.FDA_get_drug_name_by_dosage_info(dosage_info, limit=None, skip=None, *, stream_callback=None, use_cache=False, validate=True)[source]¶
Retrieve the drug name based on dosage and administration information.
- tooluniverse.tools.FDA_get_drug_name_by_environmental_warning(environmental_warning, limit=None, skip=None, *, stream_callback=None, use_cache=False, validate=True)[source]¶
Retrieve the drug name based on the specified environmental warnings.
- tooluniverse.tools.FDA_get_drug_name_by_inactive_ingredient(inactive_ingredient, limit=None, skip=None, *, stream_callback=None, use_cache=False, validate=True)[source]¶
Retrieve the drug name based on the inactive ingredient information.
- tooluniverse.tools.FDA_get_drug_name_by_info_on_conditions_for_doctor_consultation(condition, limit=None, skip=None, *, stream_callback=None, use_cache=False, validate=True)[source]¶
Retrieve the drug names that require asking a doctor before use due to a patient’s specific condi…
- tooluniverse.tools.FDA_get_drug_name_by_labor_and_delivery_info(labor_and_delivery_info, limit=None, skip=None, *, stream_callback=None, use_cache=False, validate=True)[source]¶
Retrieve the drug name based on information about the drug’s use during labor or delivery.
- tooluniverse.tools.FDA_get_drug_name_by_microbiology(microbiology_info, limit=None, skip=None, *, stream_callback=None, use_cache=False, validate=True)[source]¶
Retrieve the drug name based on microbiology field information.
- tooluniverse.tools.FDA_get_drug_name_by_other_safety_info(safety_info, limit=None, skip=None, *, stream_callback=None, use_cache=False, validate=True)[source]¶
Retrieve the drug name based on the provided safety information. This tool looks through safety i…
- tooluniverse.tools.FDA_get_drug_name_by_pharmacodynamics(pharmacodynamics, limit=None, skip=None, *, stream_callback=None, use_cache=False, validate=True)[source]¶
Retrieve the drug name based on pharmacodynamics information.
- tooluniverse.tools.FDA_get_drug_name_by_pharmacogenomics(pharmacogenomics, limit=None, skip=None, *, stream_callback=None, use_cache=False, validate=True)[source]¶
Retrieve the drug name based on pharmacogenomics field information.
- tooluniverse.tools.FDA_get_drug_name_by_precautions(precautions, limit=None, skip=None, *, stream_callback=None, use_cache=False, validate=True)[source]¶
Retrieve the drug name based on the precautions field information.
- tooluniverse.tools.FDA_get_drug_name_by_pregnancy_or_breastfeeding_info(pregnancy_info, limit=None, skip=None, *, stream_callback=None, use_cache=False, validate=True)[source]¶
Retrieve the drug names based on pregnancy or breastfeeding information.
- tooluniverse.tools.FDA_get_drug_name_by_principal_display_panel(display_panel_content, limit=None, skip=None, *, stream_callback=None, use_cache=False, validate=True)[source]¶
Retrieve the drug name based on the content of the principal display panel of the product package.
- tooluniverse.tools.FDA_get_drug_name_by_reference(reference, limit=None, skip=None, *, stream_callback=None, use_cache=False, validate=True)[source]¶
Retrieve the drug name based on the reference information provided in the drug labeling.
- tooluniverse.tools.FDA_get_drug_name_by_set_id(set_id, limit=None, skip=None, *, stream_callback=None, use_cache=False, validate=True)[source]¶
Retrieve the drug name based on the Set ID of the labeling.
- tooluniverse.tools.FDA_get_drug_name_by_stop_use_info(stop_use_info, limit=None, skip=None, *, stream_callback=None, use_cache=False, validate=True)[source]¶
Retrieve the drug name based on the stop use information provided.
- tooluniverse.tools.FDA_get_drug_name_by_storage_and_handling_info(storage_info, limit=None, skip=None, *, stream_callback=None, use_cache=False, validate=True)[source]¶
Retrieve the drug name based on storage and handling information.
- tooluniverse.tools.FDA_get_drug_name_by_warnings(warning_text, limit=None, skip=None, *, stream_callback=None, use_cache=False, validate=True)[source]¶
Retrieve the drug names based on specific warning information.
- tooluniverse.tools.FDA_get_drug_name_from_patient_package_insert(patient_package_insert, limit=None, skip=None, *, stream_callback=None, use_cache=False, validate=True)[source]¶
Retrieve the drug name based on the information provided in the patient package insert.
- tooluniverse.tools.FDA_get_drug_names_by_abuse_dependence_info(abuse_info, limit=None, skip=None, *, stream_callback=None, use_cache=False, validate=True)[source]¶
Retrieve the drug name based on information about drug abuse and dependence, including whether th…
- tooluniverse.tools.FDA_get_drug_names_by_abuse_info(abuse_info, indication=None, limit=None, skip=None, *, stream_callback=None, use_cache=False, validate=True)[source]¶
Retrieve drug names based on information about types of abuse and adverse reactions pertinent to …
- Parameters:
abuse_info (
str) – Information about the types of abuse that can occur with the drug.indication (
str) – The indication or usage of the drug.limit (
int) – The number of records to return.skip (
int) – The number of records to skip.stream_callback (
Callable, optional) – Callback for streaming output
- Return type:
Any
- tooluniverse.tools.FDA_get_drug_names_by_accessories(accessory_name, indication=None, limit=None, skip=None, *, stream_callback=None, use_cache=False, validate=True)[source]¶
Retrieve drug names based on the accessories field information.
- Parameters:
- Return type:
Any
- tooluniverse.tools.FDA_get_drug_names_by_active_ingredient(active_ingredient, indication=None, limit=None, skip=None, *, stream_callback=None, use_cache=False, validate=True)[source]¶
Retrieve drug names based on the active ingredient information.
- Parameters:
- Return type:
Any
- tooluniverse.tools.FDA_get_drug_names_by_alarm(alarm_type, indication=None, limit=None, skip=None, *, stream_callback=None, use_cache=False, validate=True)[source]¶
Retrieve drug names based on the presence of specific alarms, which are related to adverse reacti…
- tooluniverse.tools.FDA_get_drug_names_by_animal_pharmacology_info(pharmacology_info, indication=None, limit=None, skip=None, *, stream_callback=None, use_cache=False, validate=True)[source]¶
Retrieve drug names based on animal pharmacology and toxicology information. Warning: This tool …
- Parameters:
- Return type:
Any
- tooluniverse.tools.FDA_get_drug_names_by_application_number_NDC_number(application_manufacturer_or_NDC_info, limit=None, skip=None, *, stream_callback=None, use_cache=False, validate=True)[source]¶
Retrieve drug names based on the specified FDA application number or National Drug Code (NDC) num…
- tooluniverse.tools.FDA_get_drug_names_by_assembly_installation_info(field_info, indication=None, limit=None, skip=None, *, stream_callback=None, use_cache=False, validate=True)[source]¶
Retrieve drug names based on assembly or installation instructions. Warning: This tool only outpu…
- Parameters:
- Return type:
Any
- tooluniverse.tools.FDA_get_drug_names_by_boxed_warning(warning_text, indication=None, limit=None, skip=None, *, stream_callback=None, use_cache=False, validate=True)[source]¶
Retrieve drug names that have specific boxed warnings and adverse effects.
- Parameters:
- Return type:
Any
- tooluniverse.tools.FDA_get_drug_names_by_child_safety_info(child_safety_info, indication=None, limit=None, skip=None, *, stream_callback=None, use_cache=False, validate=True)[source]¶
Retrieve drug names based on whether the product should be kept out of the reach of children and …
- Parameters:
child_safety_info (
str) – Information pertaining to whether the product should be kept out of the reach…indication (
str) – The indication or usage of the drug.limit (
int) – The number of records to return.skip (
int) – The number of records to skip.stream_callback (
Callable, optional) – Callback for streaming output
- Return type:
Any
- tooluniverse.tools.FDA_get_drug_names_by_clinical_pharmacology(clinical_pharmacology, indication=None, limit=None, skip=None, *, stream_callback=None, use_cache=False, validate=True)[source]¶
Retrieve drug names based on clinical pharmacology information. Warning: This tool only outputs a…
- Parameters:
clinical_pharmacology (
str) – Information about the clinical pharmacology and actions of the drug in humans…indication (
str) – The indication or usage of the drug.limit (
int) – The number of records to return.skip (
int) – The number of records to skip.stream_callback (
Callable, optional) – Callback for streaming output
- Return type:
Any
- tooluniverse.tools.FDA_get_drug_names_by_clinical_studies(clinical_studies, indication, limit=None, skip=None, *, stream_callback=None, use_cache=False, validate=True)[source]¶
Retrieve drug names based on the presence of clinical studies information.
- Parameters:
clinical_studies (
str) – Information related to clinical studies. Use keywords split by blank space.indication (
str) – The indication or usage of the drug.limit (
int) – The number of records to return.skip (
int) – The number of records to skip.stream_callback (
Callable, optional) – Callback for streaming output
- Return type:
Any
- tooluniverse.tools.FDA_get_drug_names_by_consulting_doctor_pharmacist_info(interaction_info, indication=None, limit=None, skip=None, *, stream_callback=None, use_cache=False, validate=True)[source]¶
Retrieve drug names based on information about when a doctor or pharmacist should be consulted re…
- Parameters:
interaction_info (
str) – Information about when a doctor or pharmacist should be consulted regarding d…indication (
str) – The indication or usage of the drug.limit (
int) – The number of records to return.skip (
int) – The number of records to skip.stream_callback (
Callable, optional) – Callback for streaming output
- Return type:
Any
- tooluniverse.tools.FDA_get_drug_names_by_contraindications(contraindication_info, indication=None, limit=None, skip=None, *, stream_callback=None, use_cache=False, validate=True)[source]¶
Retrieve drug names based on specific contraindications information.
- Parameters:
contraindication_info (
str) – Information about situations in which the drug product is contraindicated.indication (
str) – The indication or usage of the drug.limit (
int) – The number of records to return.skip (
int) – The number of records to skip.stream_callback (
Callable, optional) – Callback for streaming output
- Return type:
Any
- tooluniverse.tools.FDA_get_drug_names_by_controlled_substance_DEA_schedule(controlled_substance_schedule, indication=None, limit=None, skip=None, *, stream_callback=None, use_cache=False, validate=True)[source]¶
Retrieve drug names based on the Drug Enforcement Administration (DEA) schedule information.
- Parameters:
controlled_substance_schedule (
str) – The schedule in which the drug is controlled by the Drug Enforcement Administ…indication (
str) – The indication or usage of the drug.limit (
int) – The number of records to return.skip (
int) – The number of records to skip.stream_callback (
Callable, optional) – Callback for streaming output
- Return type:
Any
- tooluniverse.tools.FDA_get_drug_names_by_dear_health_care_provider_letter_info(letter_info, indication=None, limit=None, skip=None, *, stream_callback=None, use_cache=False, validate=True)[source]¶
Fetch drug names based on information about dear health care provider letters. The letters are se…
- Parameters:
letter_info (
str) – Information about the specific dear health care provider letters.indication (
str) – The indication or usage of the drug.limit (
int) – The number of records to return.skip (
int) – The number of records to skip.stream_callback (
Callable, optional) – Callback for streaming output
- Return type:
Any
- tooluniverse.tools.FDA_get_drug_names_by_disposal_info(disposal_info, indication=None, limit=None, skip=None, *, stream_callback=None, use_cache=False, validate=True)[source]¶
Retrieve drug names based on disposal and waste handling information.
- Parameters:
disposal_info (
str) – Information related to the disposal and waste handling of the drug.indication (
str) – The indication or usage of the drug.limit (
int) – The number of records to return.skip (
int) – The number of records to skip.stream_callback (
Callable, optional) – Callback for streaming output
- Return type:
Any
- tooluniverse.tools.FDA_get_drug_names_by_dosage_forms_and_strengths_info(dosage_forms_and_strengths, indication=None, limit=None, skip=None, *, stream_callback=None, use_cache=False, validate=True)[source]¶
Retrieve drug names based on specific dosage forms and strengths information.
- Parameters:
dosage_forms_and_strengths (
str) – Information about the dosage forms and strengths of the drug.indication (
str) – The indication or usage of the drug.limit (
int) – The number of records to return.skip (
int) – The number of records to skip.stream_callback (
Callable, optional) – Callback for streaming output
- Return type:
Any
- tooluniverse.tools.FDA_get_drug_names_by_drug_interactions(interaction_term, indication=None, limit=None, skip=None, *, stream_callback=None, use_cache=False, validate=True)[source]¶
Retrieve a list of drug names that have the specified drug interactions.
- Parameters:
- Return type:
Any
- tooluniverse.tools.FDA_get_drug_names_by_effective_time(effective_time, indication=None, limit=None, skip=None, *, stream_callback=None, use_cache=False, validate=True)[source]¶
Retrieve drug names based on the effective time of the labeling document.
- Parameters:
effective_time (
str) – Date reference to the particular version of the labeling document in YYYYmmdd…indication (
str) – The indication or usage of the drug.limit (
int) – The number of records to return.skip (
int) – The number of records to skip.stream_callback (
Callable, optional) – Callback for streaming output
- Return type:
Any
- tooluniverse.tools.FDA_get_drug_names_by_food_safety_warnings(field_info, indication=None, limit=None, skip=None, *, stream_callback=None, use_cache=False, validate=True)[source]¶
Retrieve drug names based on specific food safety warnings.
- Parameters:
- Return type:
Any
- tooluniverse.tools.FDA_get_drug_names_by_general_precautions(precaution_info, indication=None, limit=None, skip=None, *, stream_callback=None, use_cache=False, validate=True)[source]¶
Retrieve drug names based on specific general precautions information.
- Parameters:
precaution_info (
str) – Information about any special care to be exercised for safe and effective use…indication (
str) – The indication or usage of the drug.limit (
int) – The number of records to return.skip (
int) – The number of records to skip.stream_callback (
Callable, optional) – Callback for streaming output
- Return type:
Any
- tooluniverse.tools.FDA_get_drug_names_by_geriatric_use(geriatric_use, indication=None, limit=None, skip=None, *, stream_callback=None, use_cache=False, validate=True)[source]¶
Retrieve drug names that have specific information about geriatric use.
- Parameters:
geriatric_use (
str) – Information about any limitations on any geriatric indications, needs for spe…indication (
str) – The indication or usage of the drug.limit (
int) – The number of records to return.skip (
int) – The number of records to skip.stream_callback (
Callable, optional) – Callback for streaming output
- Return type:
Any
- tooluniverse.tools.FDA_get_drug_names_by_health_claim(health_claim, indication=None, limit=None, skip=None, *, stream_callback=None, use_cache=False, validate=True)[source]¶
Retrieve drug names based on specific health claims.
- Parameters:
- Return type:
Any
- tooluniverse.tools.FDA_get_drug_names_by_indication(indication, limit=None, skip=None, *, stream_callback=None, use_cache=False, validate=True)[source]¶
Retrieve a list of drug names based on a specific indication or usage.
- tooluniverse.tools.FDA_get_drug_names_by_info_for_nursing_mothers(nursing_mothers_info, indication=None, limit=None, skip=None, *, stream_callback=None, use_cache=False, validate=True)[source]¶
Retrieve drug names based on information related to nursing mothers.
- Parameters:
nursing_mothers_info (
str) – Information about excretion of the drug in human milk and effects on the nurs…indication (
str) – The indication or usage of the drug.limit (
int) – The number of records to return.skip (
int) – The number of records to skip.stream_callback (
Callable, optional) – Callback for streaming output
- Return type:
Any
- tooluniverse.tools.FDA_get_drug_names_by_information_for_owners_or_caregivers(field_info, indication=None, limit=None, skip=None, *, stream_callback=None, use_cache=False, validate=True)[source]¶
Retrieve drug names based on information for owners or caregivers.
- Parameters:
field_info (
str) – The specific information related to owners or caregivers to search for.indication (
str) – The indication or usage of the drug.limit (
int) – The number of records to return.skip (
int) – The number of records to skip.stream_callback (
Callable, optional) – Callback for streaming output
- Return type:
Any
- tooluniverse.tools.FDA_get_drug_names_by_ingredient(ingredient_name, indication=None, limit=None, skip=None, *, stream_callback=None, use_cache=False, validate=True)[source]¶
Retrieve drug names based on a specific ingredient present in the drug product.
- Parameters:
- Return type:
Any
- tooluniverse.tools.FDA_get_drug_names_by_instructions_for_use(instructions_for_use, indication=None, limit=None, skip=None, *, stream_callback=None, use_cache=False, validate=True)[source]¶
Retrieve drug names based on specific instructions for use.
- Parameters:
instructions_for_use (
str) – Information about safe handling and use of the drug product.indication (
str) – The indication or usage of the drug.limit (
int) – The number of records to return.skip (
int) – The number of records to skip.stream_callback (
Callable, optional) – Callback for streaming output
- Return type:
Any
- tooluniverse.tools.FDA_get_drug_names_by_lab_test_interference(lab_test_interference, indication=None, limit=None, skip=None, *, stream_callback=None, use_cache=False, validate=True)[source]¶
Retrieve drug names that have known interference with laboratory tests.
- Parameters:
lab_test_interference (
str) – Information about any known interference by the drug with laboratory tests.indication (
str) – The indication or usage of the drug.limit (
int) – The number of records to return.skip (
int) – The number of records to skip.stream_callback (
Callable, optional) – Callback for streaming output
- Return type:
Any
- tooluniverse.tools.FDA_get_drug_names_by_lab_tests(lab_test_info, indication=None, limit=None, skip=None, *, stream_callback=None, use_cache=False, validate=True)[source]¶
Retrieve drug names based on laboratory tests information.
- Parameters:
- Return type:
Any
- tooluniverse.tools.FDA_get_drug_names_by_mechanism_of_action(mechanism_info, indication=None, limit=None, skip=None, *, stream_callback=None, use_cache=False, validate=True)[source]¶
Retrieve drug names based on the specified mechanism of action information.
- Parameters:
- Return type:
Any
- tooluniverse.tools.FDA_get_drug_names_by_medication_guide(medguide_info, indication=None, limit=None, skip=None, *, stream_callback=None, use_cache=False, validate=True)[source]¶
Retrieve drug names based on the presence of specific information in the medication guide.
- Parameters:
- Return type:
Any
- tooluniverse.tools.FDA_get_drug_names_by_nonclinical_toxicology_info(toxicology_info, indication=None, limit=None, skip=None, *, stream_callback=None, use_cache=False, validate=True)[source]¶
Retrieve drug names based on nonclinical toxicology information.
- Parameters:
- Return type:
Any
- tooluniverse.tools.FDA_get_drug_names_by_nonteratogenic_effects(nonteratogenic_effects, indication=None, limit=None, skip=None, *, stream_callback=None, use_cache=False, validate=True)[source]¶
Retrieve drug names based on the presence of nonteratogenic effects information.
- Parameters:
- Return type:
Any
- tooluniverse.tools.FDA_get_drug_names_by_overdosage_info(overdosage_info, indication=None, limit=None, skip=None, *, stream_callback=None, use_cache=False, validate=True)[source]¶
Retrieve drug names based on information about signs, symptoms, and laboratory findings of acute …
- Parameters:
overdosage_info (
str) – Information about signs, symptoms, and laboratory findings of acute overdosage.indication (
str) – The indication or usage of the drug.limit (
int) – The number of records to return.skip (
int) – The number of records to skip.stream_callback (
Callable, optional) – Callback for streaming output
- Return type:
Any
- tooluniverse.tools.FDA_get_drug_names_by_pediatric_use(pediatric_use_info, indication=None, limit=None, skip=None, *, stream_callback=None, use_cache=False, validate=True)[source]¶
Retrieve drug names based on pediatric use information.
- Parameters:
pediatric_use_info (
str) – Information related to the safe and effective pediatric use of the drug.indication (
str) – The indication or usage of the drug.limit (
int) – The number of records to return.skip (
int) – The number of records to skip.stream_callback (
Callable, optional) – Callback for streaming output
- Return type:
Any
- tooluniverse.tools.FDA_get_drug_names_by_pharmacokinetics(pharmacokinetics_info, indication=None, limit=None, skip=None, *, stream_callback=None, use_cache=False, validate=True)[source]¶
Retrieve drug names based on specific pharmacokinetics information, such as absorption, distribut…
- Parameters:
pharmacokinetics_info (
str) – Information about the clinically significant pharmacokinetics of a drug or ac…indication (
str) – The indication or usage of the drug.limit (
int) – The number of records to return.skip (
int) – The number of records to skip.stream_callback (
Callable, optional) – Callback for streaming output
- Return type:
Any
- tooluniverse.tools.FDA_get_drug_names_by_population_use(population_use, indication=None, limit=None, skip=None, *, stream_callback=None, use_cache=False, validate=True)[source]¶
Retrieve drug names based on their use in specific populations, such as pregnant women, nursing m…
- Parameters:
population_use (
str) – The specific population use to search for (e.g., pregnant women, nursing moth…indication (
str) – The indication or usage of the drug.limit (
int) – The number of records to return.skip (
int) – The number of records to skip.stream_callback (
Callable, optional) – Callback for streaming output
- Return type:
Any
- tooluniverse.tools.FDA_get_drug_names_by_pregnancy_effects_info(pregnancy_info, indication=None, limit=None, skip=None, *, stream_callback=None, use_cache=False, validate=True)[source]¶
Retrieve drug names based on information about effects the drug may have on pregnant women or on …
- Parameters:
- Return type:
Any
- tooluniverse.tools.FDA_get_drug_names_by_residue_warning(residue_warning, indication=None, limit=None, skip=None, *, stream_callback=None, use_cache=False, validate=True)[source]¶
Retrieve drug names based on the presence of residue warnings.
- Parameters:
- Return type:
Any
- tooluniverse.tools.FDA_get_drug_names_by_risk(risk_info, indication=None, limit=None, skip=None, *, stream_callback=None, use_cache=False, validate=True)[source]¶
Retrieve drug names based on specific risk information, especially regarding pregnancy or breastf…
- Parameters:
- Return type:
Any
- tooluniverse.tools.FDA_get_drug_names_by_route(route, indication=None, limit=None, skip=None, *, stream_callback=None, use_cache=False, validate=True)[source]¶
Retrieve the drug names based on the route of administration.
- tooluniverse.tools.FDA_get_drug_names_by_safe_handling_warning(safe_handling_warning, indication=None, limit=None, skip=None, *, stream_callback=None, use_cache=False, validate=True)[source]¶
Retrieve drug names that have specific safe handling warnings.
- Parameters:
- Return type:
Any
- tooluniverse.tools.FDA_get_drug_names_by_safety_summary(summary_text, indication=None, limit=None, skip=None, *, stream_callback=None, use_cache=False, validate=True)[source]¶
Retrieve drug names based on the summary of safety and effectiveness information.
- Parameters:
summary_text (
str) – Text to search within the summary of safety and effectiveness field.indication (
str) – The indication or usage of the drug.limit (
int) – The number of records to return.skip (
int) – The number of records to skip.stream_callback (
Callable, optional) – Callback for streaming output
- Return type:
Any
- tooluniverse.tools.FDA_get_drug_names_by_spl_indexing_data_elements(spl_indexing_data_elements, indication=None, limit=None, skip=None, *, stream_callback=None, use_cache=False, validate=True)[source]¶
Retrieve drug names based on Structured Product Labeling (SPL) indexing data elements.
- Parameters:
- Return type:
Any
- tooluniverse.tools.FDA_get_drug_names_by_teratogenic_effects(teratogenic_effects, indication=None, limit=None, skip=None, *, stream_callback=None, use_cache=False, validate=True)[source]¶
Retrieve drug names based on specific teratogenic effects categories.
- Parameters:
teratogenic_effects (
str) – The teratogenic effects category to search for (e.g., Pregnancy category A, B…indication (
str) – The indication or usage of the drug.limit (
int) – The number of records to return.skip (
int) – The number of records to skip.stream_callback (
Callable, optional) – Callback for streaming output
- Return type:
Any
- tooluniverse.tools.FDA_get_drug_names_by_user_safety_warning(safety_warning, indication=None, limit=None, skip=None, *, stream_callback=None, use_cache=False, validate=True)[source]¶
Retrieve drug names that have specific user safety warnings.
- Parameters:
- Return type:
Any
- tooluniverse.tools.FDA_get_drug_names_by_warnings_and_cautions(warnings_and_cautions_info, indication=None, limit=None, skip=None, *, stream_callback=None, use_cache=False, validate=True)[source]¶
Retrieve drug names based on specific warnings and cautions information.
- Parameters:
- Return type:
Any
- tooluniverse.tools.FDA_get_drugs_by_carcinogenic_mutagenic_fertility(carcinogenic_info, indication=None, limit=None, skip=None, *, stream_callback=None, use_cache=False, validate=True)[source]¶
Retrieve drug names based on the presence of carcinogenic, mutagenic, or fertility impairment inf…
- Parameters:
carcinogenic_info (
str) – Information about carcinogenic, mutagenic, or fertility impairment potential.indication (
str) – The indication or usage of the drug.limit (
int) – The number of records to return.skip (
int) – The number of records to skip.stream_callback (
Callable, optional) – Callback for streaming output
- Return type:
Any
- tooluniverse.tools.FDA_get_effective_time_by_drug_name(drug_name, limit=None, skip=None, *, stream_callback=None, use_cache=False, validate=True)[source]¶
Retrieve effective time of the labeling document based on the drug name.
- tooluniverse.tools.FDA_get_environmental_warning_by_drug_name(drug_name, limit=None, skip=None, *, stream_callback=None, use_cache=False, validate=True)[source]¶
Fetch environmental warnings for a specific drug based on its name.
- tooluniverse.tools.FDA_get_general_precautions_by_drug_name(drug_name, limit=None, skip=None, *, stream_callback=None, use_cache=False, validate=True)[source]¶
Retrieve general precautions information based on the drug name.
- tooluniverse.tools.FDA_get_geriatric_use_info_by_drug_name(drug_name, limit=None, skip=None, *, stream_callback=None, use_cache=False, validate=True)[source]¶
Retrieve information about geriatric use based on the drug name.
- tooluniverse.tools.FDA_get_health_claims_by_drug_name(drug_name, limit=None, skip=None, *, stream_callback=None, use_cache=False, validate=True)[source]¶
Retrieve health claims associated with a specific drug name.
- tooluniverse.tools.FDA_get_inactive_ingredient_info_by_drug_name(drug_name, limit=None, skip=None, *, stream_callback=None, use_cache=False, validate=True)[source]¶
Fetch a list of inactive ingredients in a specific drug product based on the drug name.
- tooluniverse.tools.FDA_get_indications_by_drug_name(drug_name, limit=None, skip=None, *, stream_callback=None, use_cache=False, validate=True)[source]¶
Retrieve indications and usage information based on a specific drug name.
- tooluniverse.tools.FDA_get_info_for_nursing_mothers_by_drug_name(drug_name, limit=None, skip=None, *, stream_callback=None, use_cache=False, validate=True)[source]¶
Retrieve information about nursing mothers for a specific drug.
- tooluniverse.tools.FDA_get_info_for_patients_by_drug_name(drug_name, limit=None, skip=None, *, stream_callback=None, use_cache=False, validate=True)[source]¶
Fetch information for patients based on the drug name.
- tooluniverse.tools.FDA_get_info_on_conditions_for_doctor_consultation_by_drug_name(drug_name, limit=None, skip=None, *, stream_callback=None, use_cache=False, validate=True)[source]¶
Get information about when a doctor should be consulted before using a specific drug.
- tooluniverse.tools.FDA_get_info_on_consulting_doctor_pharmacist_by_drug_name(drug_name, limit=None, skip=None, *, stream_callback=None, use_cache=False, validate=True)[source]¶
Get information about when a doctor or pharmacist should be consulted regarding drug interactions…
- tooluniverse.tools.FDA_get_information_for_owners_or_caregivers_by_drug_name(drug_name, limit=None, skip=None, *, stream_callback=None, use_cache=False, validate=True)[source]¶
Retrieve specific information for owners or caregivers based on the drug name.
- tooluniverse.tools.FDA_get_ingredients_by_drug_name(drug_name, limit=None, skip=None, *, stream_callback=None, use_cache=False, validate=True)[source]¶
Retrieve a list of drug ingredients based on the drug name.
- tooluniverse.tools.FDA_get_instructions_for_use_by_drug_name(drug_name, limit=None, skip=None, *, stream_callback=None, use_cache=False, validate=True)[source]¶
Retrieve instructions for use information based on the drug name.
- tooluniverse.tools.FDA_get_lab_test_interference_info_by_drug_name(drug_name, limit=None, skip=None, *, stream_callback=None, use_cache=False, validate=True)[source]¶
Retrieve information about laboratory test interferences for a specific drug.
- tooluniverse.tools.FDA_get_lab_tests_by_drug_name(drug_name, limit=None, skip=None, *, stream_callback=None, use_cache=False, validate=True)[source]¶
Retrieve laboratory tests information based on drug names.
- tooluniverse.tools.FDA_get_labor_and_delivery_info_by_drug_name(drug_name, limit=None, skip=None, *, stream_callback=None, use_cache=False, validate=True)[source]¶
Retrieve information about the drug’s use during labor or delivery based on the drug name.
- tooluniverse.tools.FDA_get_manufacturer_name_NDC_number_by_drug_name(drug_name, limit=None, skip=None, *, stream_callback=None, use_cache=False, validate=True)[source]¶
Retrieve detailed information about a drug’s active ingredient, FDA application number, manufactu…
- tooluniverse.tools.FDA_get_mechanism_of_action_by_drug_name(drug_name, limit=None, skip=None, *, stream_callback=None, use_cache=False, validate=True)[source]¶
Retrieve the mechanism of action information for a specific drug.
- tooluniverse.tools.FDA_get_medication_guide_info_by_drug_name(drug_name, limit=None, skip=None, *, stream_callback=None, use_cache=False, validate=True)[source]¶
Retrieve medication guide information based on the drug name.
- tooluniverse.tools.FDA_get_microbiology_info_by_drug_name(drug_name, limit=None, skip=None, *, stream_callback=None, use_cache=False, validate=True)[source]¶
Retrieve microbiology information based on the drug name.
- tooluniverse.tools.FDA_get_nonclinical_toxicology_info_by_drug_name(drug_name, limit=None, skip=None, *, stream_callback=None, use_cache=False, validate=True)[source]¶
Retrieve nonclinical toxicology information based on drug names.
- tooluniverse.tools.FDA_get_nonteratogenic_effects_by_drug_name(drug_name, limit=None, skip=None, *, stream_callback=None, use_cache=False, validate=True)[source]¶
Retrieve information about nonteratogenic effects based on the drug name.
- tooluniverse.tools.FDA_get_other_safety_info_by_drug_name(drug_name, limit=None, skip=None, *, stream_callback=None, use_cache=False, validate=True)[source]¶
Retrieve safety information that may not be specified in other fields based on the provided drug …
- tooluniverse.tools.FDA_get_overdosage_info_by_drug_name(drug_name, limit=None, skip=None, *, stream_callback=None, use_cache=False, validate=True)[source]¶
Retrieve information about signs, symptoms, and laboratory findings of acute overdosage based on …
- tooluniverse.tools.FDA_get_patient_package_insert_from_drug_name(drug_name, limit=None, skip=None, *, stream_callback=None, use_cache=False, validate=True)[source]¶
Retrieve the patient package insert information based on the drug name.
- tooluniverse.tools.FDA_get_pediatric_use_info_by_drug_name(drug_name, limit=None, skip=None, *, stream_callback=None, use_cache=False, validate=True)[source]¶
Retrieve pediatric use information based on drug names.
- tooluniverse.tools.FDA_get_pharmacodynamics_by_drug_name(drug_name, limit=None, skip=None, *, stream_callback=None, use_cache=False, validate=True)[source]¶
Retrieve pharmacodynamics information based on the drug name.
- tooluniverse.tools.FDA_get_pharmacogenomics_info_by_drug_name(drug_name, limit=None, skip=None, *, stream_callback=None, use_cache=False, validate=True)[source]¶
Retrieve pharmacogenomics information based on the drug name.
- tooluniverse.tools.FDA_get_pharmacokinetics_by_drug_name(drug_name, limit=None, skip=None, *, stream_callback=None, use_cache=False, validate=True)[source]¶
Retrieve pharmacokinetics information (e.g. absorption, distribution, elimination, metabolism, dr…
- tooluniverse.tools.FDA_get_population_use_info_by_drug_name(drug_name, limit=None, skip=None, *, stream_callback=None, use_cache=False, validate=True)[source]¶
Retrieve information about the use of a drug in specific populations based on the drug name.
- tooluniverse.tools.FDA_get_precautions_by_drug_name(drug_name, limit=None, skip=None, *, stream_callback=None, use_cache=False, validate=True)[source]¶
Retrieve precautions information based on the drug name.
- tooluniverse.tools.FDA_get_pregnancy_effects_info_by_drug_name(drug_name, limit=None, skip=None, *, stream_callback=None, use_cache=False, validate=True)[source]¶
Retrieve information about the effects on pregnancy for a specific drug.
- tooluniverse.tools.FDA_get_pregnancy_or_breastfeeding_info_by_drug_name(drug_name, limit=None, skip=None, *, stream_callback=None, use_cache=False, validate=True)[source]¶
Retrieve the pregnancy or breastfeeding information based on the specified drug name.
- tooluniverse.tools.FDA_get_principal_display_panel_by_drug_name(drug_name, limit=None, skip=None, *, stream_callback=None, use_cache=False, validate=True)[source]¶
Retrieve the content of the principal display panel of the product package based on the drug name.
- tooluniverse.tools.FDA_get_purpose_info_by_drug_name(drug_name, limit=None, skip=None, *, stream_callback=None, use_cache=False, validate=True)[source]¶
Retrieve about the drug product’s indications for use based on the drug name.
- tooluniverse.tools.FDA_get_recent_changes_by_drug_name(drug_name, limit=None, skip=None, *, stream_callback=None, use_cache=False, validate=True)[source]¶
Retrieve recent major changes in labeling for a specific drug.
- tooluniverse.tools.FDA_get_reference_info_by_drug_name(drug_name, limit=None, skip=None, *, stream_callback=None, use_cache=False, validate=True)[source]¶
Retrieve reference information based on the drug name provided.
- tooluniverse.tools.FDA_get_residue_warning_by_drug_name(drug_name, limit=None, skip=None, *, stream_callback=None, use_cache=False, validate=True)[source]¶
Retrieve the residue warning based on drug name.
- tooluniverse.tools.FDA_get_risk_info_by_drug_name(drug_name, limit=None, skip=None, *, stream_callback=None, use_cache=False, validate=True)[source]¶
Retrieve risk information (especially regarding pregnancy or breastfeeding) based on the drug name.
- tooluniverse.tools.FDA_get_route_info_by_drug_name(drug_name, limit=None, skip=None, *, stream_callback=None, use_cache=False, validate=True)[source]¶
Retrieve the route of administration information based on the drug name.
- tooluniverse.tools.FDA_get_safe_handling_warnings_by_drug_name(drug_name, limit=None, skip=None, *, stream_callback=None, use_cache=False, validate=True)[source]¶
Retrieve safe handling warnings for a specific drug based on its name.
- tooluniverse.tools.FDA_get_safety_summary_by_drug_name(drug_name, limit=None, skip=None, *, stream_callback=None, use_cache=False, validate=True)[source]¶
Retrieve a summary of safety and effectiveness information based on the drug name.
- tooluniverse.tools.FDA_get_spl_indexing_data_elements_by_drug_name(drug_name, limit=None, skip=None, *, stream_callback=None, use_cache=False, validate=True)[source]¶
Retrieve Structured Product Labeling (SPL) indexing data elements based on drug names.
- tooluniverse.tools.FDA_get_spl_unclassified_section_by_drug_name(drug_name, limit=None, skip=None, *, stream_callback=None, use_cache=False, validate=True)[source]¶
Retrieve the SPL unclassified section information based on the drug name.
- tooluniverse.tools.FDA_get_stop_use_info_by_drug_name(drug_name, limit=None, skip=None, *, stream_callback=None, use_cache=False, validate=True)[source]¶
Retrieve stop use information based on the drug name provided.
- tooluniverse.tools.FDA_get_storage_and_handling_info_by_drug_name(drug_name, limit=None, skip=None, *, stream_callback=None, use_cache=False, validate=True)[source]¶
Retrieve storage and handling information based on the drug name.
- tooluniverse.tools.FDA_get_teratogenic_effects_by_drug_name(drug_name, limit=None, skip=None, *, stream_callback=None, use_cache=False, validate=True)[source]¶
Retrieve teratogenic effects information based on the drug name.
- tooluniverse.tools.FDA_get_user_safety_warning_by_drug_names(drug_name, limit=None, skip=None, *, stream_callback=None, use_cache=False, validate=True)[source]¶
Retrieve specific user safety warnings based on drug names.
- tooluniverse.tools.FDA_get_warnings_and_cautions_by_drug_name(drug_name, limit=None, skip=None, *, stream_callback=None, use_cache=False, validate=True)[source]¶
Retrieve warnings and cautions information for a specific drug based on its name.
- tooluniverse.tools.FDA_get_warnings_by_drug_name(drug_name, limit=None, skip=None, *, stream_callback=None, use_cache=False, validate=True)[source]¶
Retrieve warning information based on the drug name.
- tooluniverse.tools.FDA_get_when_using_info(drug_name, limit=None, skip=None, *, stream_callback=None, use_cache=False, validate=True)[source]¶
Retrieve information about side effects and substances or activities to avoid while using a speci…
- tooluniverse.tools.FDA_retrieve_device_use_by_drug_name(drug_name, limit=None, skip=None, *, stream_callback=None, use_cache=False, validate=True)[source]¶
Retrieve the intended use of the device based on the drug name.
- tooluniverse.tools.FDA_retrieve_drug_name_by_device_use(intended_use_of_the_device, limit=None, skip=None, *, stream_callback=None, use_cache=False, validate=True)[source]¶
Retrieve the drug name based on the intended use of the device.
- tooluniverse.tools.FDA_retrieve_drug_names_by_patient_medication_info(patient_info, limit=None, skip=None, *, stream_callback=None, use_cache=False, validate=True)[source]¶
Retrieve drug names based on patient medication information, which is about safe use of the drug.
- tooluniverse.tools.FDA_retrieve_patient_medication_info_by_drug_name(drug_name, limit=None, skip=None, *, stream_callback=None, use_cache=False, validate=True)[source]¶
Retrieve patient medication information (which is about safe use of the drug) based on drug names.
- tooluniverse.tools.Fatcat_search_scholar(query, max_results, *, stream_callback=None, use_cache=False, validate=True)[source]¶
Search Internet Archive Scholar via Fatcat releases search. Fatcat is the underlying database pow…
- tooluniverse.tools.Finish(*, stream_callback=None, use_cache=False, validate=True)[source]¶
Indicate the end of multi-step reasoning.
- tooluniverse.tools.GIN_Guidelines_Search(query, limit, *, stream_callback=None, use_cache=False, validate=True)[source]¶
Search Guidelines International Network (GIN) guidelines database. GIN maintains the world’s larg…
- tooluniverse.tools.GO_get_annotations_for_gene(gene_id, *, stream_callback=None, use_cache=False, validate=True)[source]¶
Finds all GO annotations for a specific gene/protein using GOlr search.
- tooluniverse.tools.GO_get_genes_for_term(id, taxon, rows, *, stream_callback=None, use_cache=False, validate=True)[source]¶
Finds all genes/proteins associated with a specific Gene Ontology term using the Biolink API.
- Parameters:
id (
str) – The standard GO term ID, e.g., ‘GO:0006915’.taxon (
str) – Optional species filter using a NCBI taxon ID. For example, Human is ‘NCBITax…rows (
int) – The number of genes to return. Default is 100.stream_callback (
Callable, optional) – Callback for streaming output
- Return type:
Any
- tooluniverse.tools.GO_get_term_by_id(id, *, stream_callback=None, use_cache=False, validate=True)[source]¶
Retrieves basic GO term information by ID using GOlr search.
- tooluniverse.tools.GO_get_term_details(id, *, stream_callback=None, use_cache=False, validate=True)[source]¶
Retrieves detailed information for a specific GO ID using the Biolink API, including definition, …
- tooluniverse.tools.GO_search_terms(query, *, stream_callback=None, use_cache=False, validate=True)[source]¶
Searches for Gene Ontology (GO) terms by a keyword using the GOlr search engine. Returns GO terms…
- tooluniverse.tools.GWAS_search_associations_by_gene(gene_name, size=5, *, stream_callback=None, use_cache=False, validate=True)[source]¶
Search GWAS Catalog associations by gene name (returns strongest risk allele and p-value fields).
- tooluniverse.tools.HAL_search_archive(query, max_results, *, stream_callback=None, use_cache=False, validate=True)[source]¶
Search the French HAL open archive via its public API. Returns documents with title, authors, yea…
- tooluniverse.tools.HPA_get_biological_processes_by_gene(gene_name, filter_processes, *, stream_callback=None, use_cache=False, validate=True)[source]¶
Get biological process information for a gene, with special focus on key processes like apoptosis…
- tooluniverse.tools.HPA_get_cancer_prognostics_by_gene(ensembl_id, *, stream_callback=None, use_cache=False, validate=True)[source]¶
Retrieve prognostic value of a gene across various cancer types, indicating if its expression lev…
- tooluniverse.tools.HPA_get_comparative_expression_by_gene_and_cellline(gene_name, cell_line, *, stream_callback=None, use_cache=False, validate=True)[source]¶
Compare the expression level differences of a gene between a specific cell line and healthy tissu…
- tooluniverse.tools.HPA_get_comprehensive_gene_details_by_ensembl_id(ensembl_id, include_images, include_antibodies, include_expression, *, stream_callback=None, use_cache=False, validate=True)[source]¶
Get detailed in-depth information from gene page using Ensembl Gene ID, including image URLs, ant…
- Parameters:
ensembl_id (
str) – Ensembl Gene ID, e.g., ‘ENSG00000064787’ (BCAS1), ‘ENSG00000141510’ (TP53), e…include_images (
bool) – Whether to include image URL information (immunofluorescence, cell line image…include_antibodies (
bool) – Whether to include detailed antibody information (validation status, Western …include_expression (
bool) – Whether to include detailed expression data (tissue specificity, subcellular …stream_callback (
Callable, optional) – Callback for streaming output
- Return type:
Any
- tooluniverse.tools.HPA_get_contextual_biological_process_analysis(gene_name, context_name, *, stream_callback=None, use_cache=False, validate=True)[source]¶
Analyze a gene’s biological processes in the context of a specific tissue or cell line by integra…
- tooluniverse.tools.HPA_get_disease_expression_by_gene_tissue_disease(gene_name, tissue_type, disease_name, *, stream_callback=None, use_cache=False, validate=True)[source]¶
Compare the expression level of a gene in specific disease state versus healthy state using gene …
- Parameters:
gene_name (
str) – Gene name or gene symbol, e.g., ‘TP53’, ‘BRCA1’, ‘KRAS’, etc.tissue_type (
str) – Tissue type, e.g., ‘brain’, ‘breast’, ‘colon’, ‘lung’, etc., optional parameter.disease_name (
str) – Disease name, supported diseases include: brain_cancer, breast_cancer, colon_…stream_callback (
Callable, optional) – Callback for streaming output
- Return type:
Any
- tooluniverse.tools.HPA_get_gene_basic_info_by_ensembl_id(ensembl_id, *, stream_callback=None, use_cache=False, validate=True)[source]¶
Get gene basic information and expression data from Human Protein Atlas using Ensembl Gene ID. En…
- tooluniverse.tools.HPA_get_gene_tsv_data_by_ensembl_id(ensembl_id, *, stream_callback=None, use_cache=False, validate=True)[source]¶
Get detailed gene data in TSV format from Human Protein Atlas using Ensembl Gene ID (backward com…
- tooluniverse.tools.HPA_get_protein_interactions_by_gene(gene_name, *, stream_callback=None, use_cache=False, validate=True)[source]¶
Fetch known protein-protein interaction partners for a given gene from Human Protein Atlas database.
- tooluniverse.tools.HPA_get_rna_expression_by_source(gene_name, source_type, source_name, *, stream_callback=None, use_cache=False, validate=True)[source]¶
Get RNA expression level (nTPM) for a gene in a specific biological source using optimized column…
- Parameters:
gene_name (
str) – Gene name or gene symbol, e.g., ‘GFAP’, ‘TP53’, ‘BRCA1’, etc.source_type (
str) – The type of biological source. Choose from: ‘tissue’, ‘blood’, ‘brain’, ‘sing…source_name (
str) – The specific name of the biological source, e.g., ‘liver’, ‘heart_muscle’, ‘t…stream_callback (
Callable, optional) – Callback for streaming output
- Return type:
Any
- tooluniverse.tools.HPA_get_rna_expression_in_specific_tissues(ensembl_id, tissue_names, *, stream_callback=None, use_cache=False, validate=True)[source]¶
Query RNA expression levels (nTPM) for a specific gene in one or more user-specified tissues with…
- Parameters:
ensembl_id (
str) – Ensembl Gene ID for the gene, e.g., ‘ENSG00000141510’ for TP53.tissue_names (
list[Any]) – List of tissue names to query, e.g., [‘brain’, ‘liver’, ‘heart muscle’, ‘kidn…stream_callback (
Callable, optional) – Callback for streaming output
- Return type:
Any
- tooluniverse.tools.HPA_get_subcellular_location(gene_name, *, stream_callback=None, use_cache=False, validate=True)[source]¶
Get annotated subcellular locations for a protein using optimized columns parameter. Retrieves bo…
- tooluniverse.tools.HPA_search_genes_by_query(search_query, *, stream_callback=None, use_cache=False, validate=True)[source]¶
Search for matching genes by gene name, keywords, or cell line names and return Ensembl ID list. …
- tooluniverse.tools.HypothesisGenerator(context, domain, number_of_hypotheses, hypothesis_format='concise declarative sentences', *, stream_callback=None, use_cache=False, validate=True)[source]¶
Generates research hypotheses based on provided background context, domain, and desired format. U…
- Parameters:
context (
str) – Background information, observations, or data description from which to deriv…domain (
str) – Field of study or research area (e.g., ‘neuroscience’, ‘ecology’, ‘materials …number_of_hypotheses (
str) – Number of hypotheses to generate (e.g., ‘3’, ‘5’).hypothesis_format (
str) – Optional directive on how to structure each hypothesis. Choose from one of th…stream_callback (
Callable, optional) – Callback for streaming output
- Return type:
Any
- tooluniverse.tools.LabelGenerator(tool_name, tool_description, tool_parameters, category, existing_labels=None, *, stream_callback=None, use_cache=False, validate=True)[source]¶
Generates relevant keyword labels for tools based on their name, description, parameters, and cat…
- Parameters:
tool_name (
str) – The name of the tooltool_description (
str) – Detailed description of what the tool doestool_parameters (
str) – JSON string describing the tool’s input parameters and their typescategory (
str) – The general category or domain the tool belongs toexisting_labels (
str) – JSON array string of existing labels to consider reusing (optional)stream_callback (
Callable, optional) – Callback for streaming output
- Return type:
Any
- tooluniverse.tools.LiteratureContextReviewer(paper_title, literature_review, *, stream_callback=None, use_cache=False, validate=True)[source]¶
Reviews coverage, relevance, and critical synthesis of prior scholarship.
- tooluniverse.tools.LiteratureSearchTool(research_topic, *, stream_callback=None, use_cache=False, validate=True)[source]¶
Comprehensive literature search and summary tool that searches multiple databases (EuropePMC, Ope…
- tooluniverse.tools.LiteratureSynthesisAgent(topic, literature_data, focus_area='General', *, stream_callback=None, use_cache=False, validate=True)[source]¶
AI agent that synthesizes literature findings and provides evidence-based insights
- tooluniverse.tools.MedRxiv_search_preprints(query, max_results, *, stream_callback=None, use_cache=False, validate=True)[source]¶
Search medRxiv preprints using the public medRxiv API. Returns preprints with title, authors, yea…
- tooluniverse.tools.MedicalLiteratureReviewer(research_topic, literature_content, focus_area, study_types, quality_level, review_scope, *, stream_callback=None, use_cache=False, validate=True)[source]¶
Conducts systematic reviews of medical literature on specific topics. Synthesizes findings from m…
- Parameters:
research_topic (
str) – The specific medical/research topic for literature review (e.g., ‘efficacy of…literature_content (
str) – The literature content, abstracts, full studies, or research papers to review…focus_area (
str) – Primary focus area for the review (e.g., ‘therapeutic efficacy’, ‘safety prof…study_types (
str) – Types of studies to prioritize in the analysis (e.g., ‘randomized controlled …quality_level (
str) – Minimum evidence quality level to include (e.g., ‘high quality only’, ‘modera…review_scope (
str) – Scope of the review (e.g., ‘comprehensive systematic review’, ‘rapid review’,…stream_callback (
Callable, optional) – Callback for streaming output
- Return type:
Any
- tooluniverse.tools.MedicalTermNormalizer(raw_terms, *, stream_callback=None, use_cache=False, validate=True)[source]¶
Identifies and corrects misspelled drug or disease names, returning a list of plausible standardi…
- tooluniverse.tools.MedlinePlus_connect_lookup_by_code(cs, c, dn, language, format, *, stream_callback=None, use_cache=False, validate=True)[source]¶
Look up corresponding MedlinePlus page information through MedlinePlus Connect Web Service using …
- Parameters:
cs (
str) – Code system OID, e.g., ICD-10 CM=2.16.840.1.113883.6.90, RXCUI=2.16.840.1.113…c (
str) – Specific code value to query, e.g., “E11.9” (ICD-10 CM) or “637188” (RXCUI).dn (
str) – Optional, descriptive name (English) corresponding to the code, for drugs can…language (
str) – Return information language, “en” for English, “es” for Spanish, default “en”.format (
str) – Return format, options “json” or “xml”, default “json”.stream_callback (
Callable, optional) – Callback for streaming output
- Return type:
Any
- tooluniverse.tools.MedlinePlus_get_genetics_condition_by_name(condition, format, *, stream_callback=None, use_cache=False, validate=True)[source]¶
Get detailed information from MedlinePlus Genetics corresponding to genetic condition name, suppo…
- tooluniverse.tools.MedlinePlus_get_genetics_gene_by_name(gene, format, *, stream_callback=None, use_cache=False, validate=True)[source]¶
Get detailed information from MedlinePlus Genetics corresponding to gene name, supports JSON or X…
- tooluniverse.tools.MedlinePlus_get_genetics_index(*, stream_callback=None, use_cache=False, validate=True)[source]¶
Download index file (XML) of all genetics entries in MedlinePlus, get complete list in one call.
- tooluniverse.tools.MedlinePlus_search_topics_by_keyword(term, db, rettype, *, stream_callback=None, use_cache=False, validate=True)[source]¶
Search for relevant information in MedlinePlus Web Service by keyword across health topics or oth…
- Parameters:
term (
str) – Search keyword, e.g., “diabetes”, needs to be URL encoded before passing.db (
str) – Specify the database to search, e.g., healthTopics (English health topics), h…rettype (
str) – Result return format, options: brief (concise information, default), topic (d…stream_callback (
Callable, optional) – Callback for streaming output
- Return type:
Any
- tooluniverse.tools.MethodologyRigorReviewer(methods_section, *, stream_callback=None, use_cache=False, validate=True)[source]¶
Evaluates design appropriateness, sampling, and procedural transparency.
- tooluniverse.tools.NICE_Clinical_Guidelines_Search(query, limit, *, stream_callback=None, use_cache=False, validate=True)[source]¶
Search NICE (National Institute for Health and Care Excellence) clinical guidelines and evidence-…
- tooluniverse.tools.NICE_Guideline_Full_Text(url, *, stream_callback=None, use_cache=False, validate=True)[source]¶
Fetch complete full text content from a NICE clinical guideline page. Takes a NICE guideline URL …
- Parameters:
- Return type:
dict[str,Any]
- tooluniverse.tools.NoveltySignificanceReviewer(paper_title, abstract, manuscript_text, *, stream_callback=None, use_cache=False, validate=True)[source]¶
Provides a structured peer-review of the work’s originality and potential impact.
- Parameters:
- Return type:
Any
- tooluniverse.tools.OSF_search_preprints(query, max_results, provider, *, stream_callback=None, use_cache=False, validate=True)[source]¶
Search OSF (Open Science Framework) Preprints for research preprints and working papers. OSF Prep…
- Parameters:
query (
str) – Search query for OSF preprints. Use keywords to search across titles and abst…max_results (
int) – Maximum number of results to return. Default is 10, maximum is 100.provider (
str) – Optional preprint provider filter (e.g., ‘osf’, ‘psyarxiv’, ‘socarxiv’). If n…stream_callback (
Callable, optional) – Callback for streaming output
- Return type:
list[Any]
- tooluniverse.tools.OSL_get_efo_id_by_disease_name(disease, *, stream_callback=None, use_cache=False, validate=True)[source]¶
Tool to lookup Experimental Factor Ontology (EFO) IDs for diseases via the EMBL-EBI OLS API.
- tooluniverse.tools.OpenAIRE_search_publications(query, max_results, type, *, stream_callback=None, use_cache=False, validate=True)[source]¶
Search OpenAIRE Explore for research products including publications, datasets, and software. Ope…
- Parameters:
query (
str) – Search query for OpenAIRE research products. Use keywords to search across ti…max_results (
int) – Maximum number of results to return. Default is 10, maximum is 100.type (
str) – Type of research product to search: ‘publications’, ‘datasets’, or ‘software’…stream_callback (
Callable, optional) – Callback for streaming output
- Return type:
list[Any]
- tooluniverse.tools.OpenAlex_Guidelines_Search(query, limit, year_from, year_to, *, stream_callback=None, use_cache=False, validate=True)[source]¶
Search for clinical practice guidelines using OpenAlex scholarly database. Provides access to a c…
- Parameters:
query (
str) – Medical condition or clinical topic to search for guidelines (e.g., ‘diabetes…limit (
int) – Maximum number of guidelines to return (default: 10)year_from (
int) – Filter for guidelines published from this year onwards (optional)year_to (
int) – Filter for guidelines published up to this year (optional)stream_callback (
Callable, optional) – Callback for streaming output
- Return type:
dict[str,Any]
- tooluniverse.tools.OpenTargets_drug_pharmacogenomics_data(chemblId, page=None, *, stream_callback=None, use_cache=False, validate=True)[source]¶
Retrieve pharmacogenomics data for a specific drug, including evidence levels and genotype annota…
- tooluniverse.tools.OpenTargets_get_approved_indications_by_drug_chemblId(chemblId, *, stream_callback=None, use_cache=False, validate=True)[source]¶
Retrieve detailed information about multiple drugs using a list of ChEMBL IDs.
- tooluniverse.tools.OpenTargets_get_associated_diseases_by_drug_chemblId(chemblId, *, stream_callback=None, use_cache=False, validate=True)[source]¶
Retrieve the list of diseases associated with a specific drug chemblId based on clinical trial da…
- tooluniverse.tools.OpenTargets_get_associated_drugs_by_disease_efoId(efoId, size, *, stream_callback=None, use_cache=False, validate=True)[source]¶
Retrieve known drugs associated with a specific disease by disease efoId.
- tooluniverse.tools.OpenTargets_get_associated_drugs_by_target_ensemblID(ensemblId, size, cursor=None, *, stream_callback=None, use_cache=False, validate=True)[source]¶
Get known drugs and information (e.g. id, name, MoA) associated with a specific target ensemblID,…
- Parameters:
- Return type:
Any
- tooluniverse.tools.OpenTargets_get_associated_phenotypes_by_disease_efoId(efoId, *, stream_callback=None, use_cache=False, validate=True)[source]¶
Find HPO phenotypes asosciated with the specified disease efoId.
- tooluniverse.tools.OpenTargets_get_associated_targets_by_disease_efoId(efoId, *, stream_callback=None, use_cache=False, validate=True)[source]¶
Find targets associated with a specific disease or phenotype based on efoId.
- tooluniverse.tools.OpenTargets_get_associated_targets_by_drug_chemblId(chemblId, *, stream_callback=None, use_cache=False, validate=True)[source]¶
Retrieve the list of targets linked to a specific drug chemblId based on its mechanism of action.
- tooluniverse.tools.OpenTargets_get_biological_mouse_models_by_ensemblID(ensemblId, *, stream_callback=None, use_cache=False, validate=True)[source]¶
Retrieve biological mouse models, including allelic compositions and genetic backgrounds, for a s…
- tooluniverse.tools.OpenTargets_get_chemical_probes_by_target_ensemblID(ensemblId, *, stream_callback=None, use_cache=False, validate=True)[source]¶
Retrieve chemical probes associated with a specific target using its ensemblID.
- tooluniverse.tools.OpenTargets_get_disease_ancestors_parents_by_efoId(efoId, *, stream_callback=None, use_cache=False, validate=True)[source]¶
Retrieve the disease ancestors and parents in the ontology using the disease EFO ID.
- tooluniverse.tools.OpenTargets_get_disease_descendants_children_by_efoId(efoId, *, stream_callback=None, use_cache=False, validate=True)[source]¶
Retrieve the disease descendants and children in the ontology using the disease EFO ID.
- tooluniverse.tools.OpenTargets_get_disease_description_by_efoId(efoId, *, stream_callback=None, use_cache=False, validate=True)[source]¶
Retrieve disease description, name, database cros references, obsolete terms, and whether it’s a …
- tooluniverse.tools.OpenTargets_get_disease_id_description_by_name(diseaseName, *, stream_callback=None, use_cache=False, validate=True)[source]¶
Retrieve the efoId and additional details of a disease based on its name.
- tooluniverse.tools.OpenTargets_get_disease_ids_by_efoId(efoId, *, stream_callback=None, use_cache=False, validate=True)[source]¶
Given an EFO ID, retrieve all cross-referenced external disease IDs including MONDO, OMIM, MeSH, …
- tooluniverse.tools.OpenTargets_get_disease_ids_by_name(name, *, stream_callback=None, use_cache=False, validate=True)[source]¶
Given a disease or phenotype name, find all cross-referenced external IDs (e.g., OMIM, MONDO, MeS…
- tooluniverse.tools.OpenTargets_get_disease_locations_by_efoId(efoId, *, stream_callback=None, use_cache=False, validate=True)[source]¶
Retrieve the disease’s direct location and indirect location disease terms and IDs using the dise…
- tooluniverse.tools.OpenTargets_get_disease_synonyms_by_efoId(efoId, *, stream_callback=None, use_cache=False, validate=True)[source]¶
Retrieve disease synonyms by its EFO ID.
- tooluniverse.tools.OpenTargets_get_disease_therapeutic_areas_by_efoId(efoId, *, stream_callback=None, use_cache=False, validate=True)[source]¶
Retrieve the therapeutic areas associated with a specific disease efoId.
- tooluniverse.tools.OpenTargets_get_diseases_phenotypes_by_target_ensembl(ensemblId, *, stream_callback=None, use_cache=False, validate=True)[source]¶
Find diseases or phenotypes associated with a specific target using ensemblId.
- tooluniverse.tools.OpenTargets_get_drug_adverse_events_by_chemblId(chemblId, page=None, *, stream_callback=None, use_cache=False, validate=True)[source]¶
Retrieve significant adverse events reported for a specific drug chemblId.
- tooluniverse.tools.OpenTargets_get_drug_approval_status_by_chemblId(chemblId, *, stream_callback=None, use_cache=False, validate=True)[source]¶
Retrieve the approval status of a specific drug chemblId.
- tooluniverse.tools.OpenTargets_get_drug_chembId_by_generic_name(drugName, *, stream_callback=None, use_cache=False, validate=True)[source]¶
Fetch the drug chemblId and description based on the drug generic name.
- tooluniverse.tools.OpenTargets_get_drug_description_by_chemblId(chemblId, *, stream_callback=None, use_cache=False, validate=True)[source]¶
Get drug name, year of first approval, type, cross references, and max clinical trial phase based…
- tooluniverse.tools.OpenTargets_get_drug_id_description_by_name(drugName, *, stream_callback=None, use_cache=False, validate=True)[source]¶
Fetch the drug chemblId and description based on the drug generic name.
- tooluniverse.tools.OpenTargets_get_drug_indications_by_chemblId(chemblId, *, stream_callback=None, use_cache=False, validate=True)[source]¶
Fetch indications (treatable phenotypes/diseases) for a given drug chemblId.
- tooluniverse.tools.OpenTargets_get_drug_mechanisms_of_action_by_chemblId(chemblId, *, stream_callback=None, use_cache=False, validate=True)[source]¶
Retrieve the mechanisms of action associated with a specific drug using chemblId.
- tooluniverse.tools.OpenTargets_get_drug_synonyms_by_chemblId(chemblId, *, stream_callback=None, use_cache=False, validate=True)[source]¶
Retrieve the synonyms associated with a specific drug chemblId.
- tooluniverse.tools.OpenTargets_get_drug_trade_names_by_chemblId(chemblId, *, stream_callback=None, use_cache=False, validate=True)[source]¶
Retrieve the trade names associated with a specific drug chemblId.
- tooluniverse.tools.OpenTargets_get_drug_warnings_by_chemblId(chemblId, *, stream_callback=None, use_cache=False, validate=True)[source]¶
Retrieve warnings for a specific drug using ChEMBL ID.
- tooluniverse.tools.OpenTargets_get_drug_withdrawn_blackbox_status_by_chemblId(chemblId, *, stream_callback=None, use_cache=False, validate=True)[source]¶
Find withdrawn and black-box warning statuses for a specific drug by chemblId.
- tooluniverse.tools.OpenTargets_get_gene_ontology_terms_by_goID(goIds, *, stream_callback=None, use_cache=False, validate=True)[source]¶
Retrieve Gene Ontology terms based on a list of GO IDs.
- tooluniverse.tools.OpenTargets_get_known_drugs_by_drug_chemblId(chemblId, *, stream_callback=None, use_cache=False, validate=True)[source]¶
Get a list of known drugs and associated information using the specified chemblId.
- tooluniverse.tools.OpenTargets_get_parent_child_molecules_by_drug_chembl_ID(chemblId, *, stream_callback=None, use_cache=False, validate=True)[source]¶
Get parent and child molecules of specified drug chemblId.
- tooluniverse.tools.OpenTargets_get_publications_by_disease_efoId(entityId, additionalIds=None, startYear=None, startMonth=None, endYear=None, endMonth=None, *, stream_callback=None, use_cache=False, validate=True)[source]¶
Retrieve publications related to a disease efoId, including PubMed IDs and publication dates.
- Parameters:
entityId (
str) – The ID of the entity (efoId).additionalIds (
list[Any]) – List of additional IDs to include in the search.startYear (
int) – Year at the lower end of the filter.startMonth (
int) – Month at the lower end of the filter.endYear (
int) – Year at the higher end of the filter.endMonth (
int) – Month at the higher end of the filter.stream_callback (
Callable, optional) – Callback for streaming output
- Return type:
Any
- tooluniverse.tools.OpenTargets_get_publications_by_drug_chemblId(entityId, additionalIds=None, startYear=None, startMonth=None, endYear=None, endMonth=None, *, stream_callback=None, use_cache=False, validate=True)[source]¶
Retrieve publications related to a drug chemblId, including PubMed IDs and publication dates.
- Parameters:
entityId (
str) – The ID of the entity (chemblId).additionalIds (
list[Any]) – List of additional IDs to include in the search.startYear (
int) – Year at the lower end of the filter.startMonth (
int) – Month at the lower end of the filter.endYear (
int) – Year at the higher end of the filter.endMonth (
int) – Month at the higher end of the filter.stream_callback (
Callable, optional) – Callback for streaming output
- Return type:
Any
- tooluniverse.tools.OpenTargets_get_publications_by_target_ensemblID(entityId, additionalIds=None, startYear=None, startMonth=None, endYear=None, endMonth=None, *, stream_callback=None, use_cache=False, validate=True)[source]¶
Retrieve publications related to a target ensemblID, including PubMed IDs and publication dates.
- Parameters:
entityId (
str) – The ID of the entity (ensemblID).additionalIds (
list[Any]) – List of additional IDs to include in the search.startYear (
int) – Year at the lower end of the filter.startMonth (
int) – Month at the lower end of the filter.endYear (
int) – Year at the higher end of the filter.endMonth (
int) – Month at the higher end of the filter.stream_callback (
Callable, optional) – Callback for streaming output
- Return type:
Any
- tooluniverse.tools.OpenTargets_get_similar_entities_by_disease_efoId(efoId, threshold, size, *, stream_callback=None, use_cache=False, validate=True)[source]¶
Retrieve similar entities for a given disease efoId using a model trained with PubMed.
- tooluniverse.tools.OpenTargets_get_similar_entities_by_drug_chemblId(chemblId, threshold, size, *, stream_callback=None, use_cache=False, validate=True)[source]¶
Retrieve similar entities for a given drug chemblId using a model trained with PubMed.
- tooluniverse.tools.OpenTargets_get_similar_entities_by_target_ensemblID(ensemblId, threshold, size, *, stream_callback=None, use_cache=False, validate=True)[source]¶
Retrieve similar entities for a given target ensemblID using a model trained with PubMed.
- tooluniverse.tools.OpenTargets_get_target_classes_by_ensemblID(ensemblId, *, stream_callback=None, use_cache=False, validate=True)[source]¶
Retrieve the target classes associated with a specific target ensemblID.
- tooluniverse.tools.OpenTargets_get_target_constraint_info_by_ensemblID(ensemblId, *, stream_callback=None, use_cache=False, validate=True)[source]¶
Retrieve genetic constraint information for a specific target ensemblID, including expected and o…
- tooluniverse.tools.OpenTargets_get_target_enabling_packages_by_ensemblID(ensemblId, *, stream_callback=None, use_cache=False, validate=True)[source]¶
Retrieve the Target Enabling Packages (TEP) associated with a specific target ensemblID.
- tooluniverse.tools.OpenTargets_get_target_gene_ontology_by_ensemblID(ensemblId, *, stream_callback=None, use_cache=False, validate=True)[source]¶
Retrieve Gene Ontology annotations for a specific target by Ensembl ID.
- tooluniverse.tools.OpenTargets_get_target_genomic_location_by_ensemblID(ensemblId, *, stream_callback=None, use_cache=False, validate=True)[source]¶
Retrieve genomic location data for a specific target, including chromosome, start, end, and strand.
- tooluniverse.tools.OpenTargets_get_target_homologues_by_ensemblID(ensemblId, *, stream_callback=None, use_cache=False, validate=True)[source]¶
Fetch homologues for a specific target by Ensembl ID.
- tooluniverse.tools.OpenTargets_get_target_id_description_by_name(targetName, *, stream_callback=None, use_cache=False, validate=True)[source]¶
Get the ensemblId and description based on the target name.
- tooluniverse.tools.OpenTargets_get_target_interactions_by_ensemblID(ensemblId, page=None, *, stream_callback=None, use_cache=False, validate=True)[source]¶
Retrieve interaction data for a specific target ensemblID, including interaction partners and evi…
- tooluniverse.tools.OpenTargets_get_target_safety_profile_by_ensemblID(ensemblId, *, stream_callback=None, use_cache=False, validate=True)[source]¶
Retrieve known target safety liabilities for a specific target Ensembl ID.
- tooluniverse.tools.OpenTargets_get_target_subcellular_locations_by_ensemblID(ensemblId, *, stream_callback=None, use_cache=False, validate=True)[source]¶
Retrieve information about subcellular locations for a specific target ensemblID.
- tooluniverse.tools.OpenTargets_get_target_synonyms_by_ensemblID(ensemblId, *, stream_callback=None, use_cache=False, validate=True)[source]¶
Retrieve synonyms for specified target, including alternative names and symbols, using given ense…
- tooluniverse.tools.OpenTargets_get_target_tractability_by_ensemblID(ensemblId, *, stream_callback=None, use_cache=False, validate=True)[source]¶
Retrieve tractability assessments, including modality and values, for a specific target ensembl ID.
- tooluniverse.tools.OpenTargets_map_any_disease_id_to_all_other_ids(inputId, *, stream_callback=None, use_cache=False, validate=True)[source]¶
Given any known disease or phenotype ID (EFO, OMIM, MONDO, UMLS, ICD10, MedDRA, etc.), return all…
- tooluniverse.tools.OpenTargets_multi_entity_search_by_query_string(queryString, entityNames=None, page=None, *, stream_callback=None, use_cache=False, validate=True)[source]¶
Perform a multi-entity search based on a query string, filtering by entity names and pagination s…
- Parameters:
queryString (
str) – The search string for querying information.entityNames (
list[Any]) – List of entity names to search for (e.g., target, disease, drug).page (
dict[str,Any]) – Pagination settings with index and size.stream_callback (
Callable, optional) – Callback for streaming output
- Return type:
Any
- tooluniverse.tools.OpenTargets_search_category_counts_by_query_string(queryString, *, stream_callback=None, use_cache=False, validate=True)[source]¶
Get the count of entries in each entity category (disease, target, drug) based on a query string.
- tooluniverse.tools.OpenTargets_target_disease_evidence(efoId, ensemblId, *, stream_callback=None, use_cache=False, validate=True)[source]¶
Explore evidence that supports a specific target-disease association. Input is disease efoId and …
- tooluniverse.tools.OutputSummarizationComposer(tool_output, query_context, tool_name, chunk_size=30000, focus_areas='key_findings_and_results', max_summary_length=10000, *, stream_callback=None, use_cache=False, validate=True)[source]¶
Composes output summarization workflow by chunking long outputs, processing each chunk with AI su…
- Parameters:
tool_output (
str) – The original tool output to be summarizedquery_context (
str) – Context about the original querytool_name (
str) – Name of the tool that generated the outputchunk_size (
int) – Size of each chunk for processingfocus_areas (
str) – Areas to focus on in summarizationmax_summary_length (
int) – Maximum length of final summarystream_callback (
Callable, optional) – Callback for streaming output
- Return type:
Any
- tooluniverse.tools.PMC_search_papers(query, limit, date_from=None, date_to=None, article_type=None, *, stream_callback=None, use_cache=False, validate=True)[source]¶
Search for full-text biomedical literature using PMC (PubMed Central) API. PMC is the free full-t…
- Parameters:
query (
str) – Search query for PMC papers. Use keywords separated by spaces to refine your …limit (
int) – Maximum number of papers to return. This sets the maximum number of papers re…date_from (
str) – Start date for publication date filter (YYYY/MM/DD format). Optional paramete…date_to (
str) – End date for publication date filter (YYYY/MM/DD format). Optional parameter …article_type (
str) – Article type filter (e.g., ‘research-article’, ‘review’, ‘case-report’). Opti…stream_callback (
Callable, optional) – Callback for streaming output
- Return type:
list[Any]
- tooluniverse.tools.ProtocolOptimizer(initial_protocol, *, stream_callback=None, use_cache=False, validate=True)[source]¶
Reviews an initial protocol and delivers targeted revisions that improve clarity, feasibility, ri…
- tooluniverse.tools.PubChem_get_CID_by_SMILES(smiles, *, stream_callback=None, use_cache=False, validate=True)[source]¶
Retrieve corresponding CID list by SMILES string.
- tooluniverse.tools.PubChem_get_CID_by_compound_name(name, *, stream_callback=None, use_cache=False, validate=True)[source]¶
Retrieve corresponding CID list (IdentifierList) by chemical name.
- tooluniverse.tools.PubChem_get_associated_patents_by_CID(cid, *, stream_callback=None, use_cache=False, validate=True)[source]¶
Get a list of patents associated with a specific compound CID.
- tooluniverse.tools.PubChem_get_compound_2D_image_by_CID(cid, image_size, *, stream_callback=None, use_cache=False, validate=True)[source]¶
Get 2D structure image (PNG format) of compound by CID.
- tooluniverse.tools.PubChem_get_compound_properties_by_CID(cid, *, stream_callback=None, use_cache=False, validate=True)[source]¶
Get a set of specified molecular properties through CID (Compound ID), such as molecular weight, …
- tooluniverse.tools.PubChem_get_compound_synonyms_by_CID(cid, *, stream_callback=None, use_cache=False, validate=True)[source]¶
Get complete list of synonyms for compound by CID.
- tooluniverse.tools.PubChem_get_compound_xrefs_by_CID(cid, xref_types, *, stream_callback=None, use_cache=False, validate=True)[source]¶
Get external references (XRefs) for compound by CID, including links to ChEBI, DrugBank, KEGG, etc.
- Parameters:
cid (
int) – Compound ID to query external references for, e.g., 2244.xref_types (
list[Any]) – List of external database types to query, e.g., [“RegistryID”, “RN”, “PubMedI…stream_callback (
Callable, optional) – Callback for streaming output
- Return type:
Any
- tooluniverse.tools.PubChem_search_compounds_by_similarity(smiles, threshold, *, stream_callback=None, use_cache=False, validate=True)[source]¶
Search by similarity (Tanimoto coefficient), returns CID list of compounds with similarity above …
- tooluniverse.tools.PubChem_search_compounds_by_substructure(smiles, *, stream_callback=None, use_cache=False, validate=True)[source]¶
Search for all CIDs in PubChem that contain the given substructure (SMILES).
- tooluniverse.tools.PubMed_Guidelines_Search(query, limit, api_key, *, stream_callback=None, use_cache=False, validate=True)[source]¶
Search PubMed for peer-reviewed clinical practice guidelines using NCBI E-utilities. Filters resu…
- Parameters:
query (
str) – Medical condition, treatment, or clinical topic to search for (e.g., ‘diabete…limit (
int) – Maximum number of guidelines to return (default: 10)api_key (
str) – Optional NCBI API key for higher rate limits. Get your free key at https://ww…stream_callback (
Callable, optional) – Callback for streaming output
- Return type:
dict[str,Any]
- tooluniverse.tools.PubMed_search_articles(query, limit=10, api_key=None, *, stream_callback=None, use_cache=False, validate=True)[source]¶
Search PubMed using NCBI E-utilities (esearch + esummary) and return articles. Returns articles w…
- Parameters:
query (
str) – Search query for PubMed articles. Use keywords separated by spaces to refine …limit (
int) – Number of articles to return. This sets the maximum number of articles retrie…api_key (
str) – Optional NCBI API key for higher rate limits. Get your free key at https://ww…stream_callback (
Callable, optional) – Callback for streaming output
- Return type:
list[Any]
- tooluniverse.tools.PubTator3_EntityAutocomplete(text, entity_type, max_results, *, stream_callback=None, use_cache=False, validate=True)[source]¶
Provides suggestions for the best‐matching standardized PubTator IDs for a partial biomedical ter…
- Parameters:
text (
str) – A few characters or the full name of the biomedical concept you are trying to…entity_type (
str) – Optional filter to restrict suggestions to a single category such as GENE, DI…max_results (
int) – Maximum number of suggestions to return (1 - 50, default = 10).stream_callback (
Callable, optional) – Callback for streaming output
- Return type:
Any
- tooluniverse.tools.PubTator3_LiteratureSearch(query, page, page_size, *, stream_callback=None, use_cache=False, validate=True)[source]¶
Find PubMed articles that match a keyword, a PubTator entity ID (e.g. “@GENE_BRAF”), or an entity…
- Parameters:
query (
str) – What you want to search for. This can be plain keywords, a single PubTator ID…page (
int) – Zero-based results page (optional; default = 0).page_size (
int) – How many PMIDs to return per page (optional; default = 20, maximum = 200).stream_callback (
Callable, optional) – Callback for streaming output
- Return type:
Any
- tooluniverse.tools.QuestionRephraser(question, options=None, *, stream_callback=None, use_cache=False, validate=True)[source]¶
Generates three distinct paraphrases of a given question while ensuring answer options remain val…
- tooluniverse.tools.Reactome_get_pathway_reactions(stId, *, stream_callback=None, use_cache=False, validate=True)[source]¶
Query all Reactions contained under a Pathway using Pathway Stable ID. This is currently the only…
- tooluniverse.tools.ReproducibilityTransparencyReviewer(availability_statement, *, stream_callback=None, use_cache=False, validate=True)[source]¶
Evaluates data, code, and protocol availability for replication.
- tooluniverse.tools.ResultsInterpretationReviewer(results_section, discussion_section, *, stream_callback=None, use_cache=False, validate=True)[source]¶
Judges whether conclusions are data-justified and limitations addressed.
- tooluniverse.tools.ScientificTextSummarizer(text, summary_length, focus_area, *, stream_callback=None, use_cache=False, validate=True)[source]¶
Summarizes biomedical research texts, abstracts, or papers with specified length and focus areas….
- Parameters:
text (
str) – The biomedical text, abstract, or paper content to be summarized.summary_length (
str) – Desired length of summary (e.g., ‘50’, ‘100’, ‘200 words’).focus_area (
str) – What to focus on in the summary (e.g., ‘methodology’, ‘results’, ‘clinical im…stream_callback (
Callable, optional) – Callback for streaming output
- Return type:
Any
- tooluniverse.tools.SemanticScholar_search_papers(query, limit, api_key=None, *, stream_callback=None, use_cache=False, validate=True)[source]¶
Search for papers on Semantic Scholar including abstracts. This tool queries the Semantic Scholar…
- Parameters:
query (
str) – Search query for Semantic Scholar. Use keywords separated by spaces to refine…limit (
int) – Maximum number of papers to return from Semantic Scholar.api_key (
str) – Optional API key for Semantic Scholar to obtain a higher quota.stream_callback (
Callable, optional) – Callback for streaming output
- Return type:
list[Any]
- tooluniverse.tools.TRIP_Database_Guidelines_Search(query, limit, search_type, *, stream_callback=None, use_cache=False, validate=True)[source]¶
Search TRIP Database (Turning Research into Practice) for evidence-based clinical guidelines. TRI…
- Parameters:
query (
str) – Medical condition, treatment, or clinical question (e.g., ‘diabetes managemen…limit (
int) – Maximum number of guidelines to return (default: 10)search_type (
str) – Type of content to search for (default: ‘guideline’). Options include ‘guidel…stream_callback (
Callable, optional) – Callback for streaming output
- Return type:
dict[str,Any]
- tooluniverse.tools.TestCaseGenerator(tool_config, *, stream_callback=None, use_cache=False, validate=True)[source]¶
Generates diverse and representative ToolUniverse tool call dictionaries for a given tool based o…
- Parameters:
- Return type:
Any
- tooluniverse.tools.ToolCompatibilityAnalyzer(source_tool, target_tool, analysis_depth, *, stream_callback=None, use_cache=False, validate=True)[source]¶
Analyzes two tool specifications to determine if one tool’s output can be used as input for anoth…
- Parameters:
source_tool (
str) – The source tool specification (JSON string with name, description, parameter …target_tool (
str) – The target tool specification (JSON string with name, description, parameter …analysis_depth (
str) – Level of analysis depth - quick for basic compatibility, detailed for paramet…stream_callback (
Callable, optional) – Callback for streaming output
- Return type:
Any
- tooluniverse.tools.ToolDescriptionOptimizer(tool_config, save_to_file, output_file, max_iterations, satisfaction_threshold, *, stream_callback=None, use_cache=False, validate=True)[source]¶
Optimizes a tool’s description and parameter descriptions by generating test cases, executing the…
- Parameters:
tool_config (
dict[str,Any]) – The full configuration of the tool to optimize.save_to_file (
bool) – If true, save the optimized description to a file (do not overwrite the origi…output_file (
str) – Optional file path to save the optimized description. If not provided, use ‘<…max_iterations (
int) – Maximum number of optimization rounds to perform.satisfaction_threshold (
float) – Quality score threshold (1-10) to consider optimization satisfactory.stream_callback (
Callable, optional) – Callback for streaming output
- Return type:
Any
- tooluniverse.tools.ToolDiscover(tool_description, max_iterations, save_to_file, output_file, *, stream_callback=None, use_cache=False, validate=True)[source]¶
Generates new ToolUniverse-compliant tools based on short descriptions through an intelligent dis…
- Parameters:
tool_description (
str) – Short description of the desired tool functionality and purpose. Tool Discove…max_iterations (
int) – Maximum number of refinement iterations to perform.save_to_file (
bool) – Whether to save the generated tool configuration and report to a file.output_file (
str) – Optional file path to save the generated tool. If not provided, uses auto-gen…stream_callback (
Callable, optional) – Callback for streaming output
- Return type:
Any
- tooluniverse.tools.ToolGraphComposer(output_path, analysis_depth, min_compatibility_score, exclude_categories, max_tools_per_category, force_rebuild, *, stream_callback=None, use_cache=False, validate=True)[source]¶
Builds a comprehensive graph of tool compatibility relationships in ToolUniverse. Analyzes all av…
- Parameters:
output_path (
str) – Path to save the generated graph files (JSON and pickle formats)analysis_depth (
str) – Level of compatibility analysis to performmin_compatibility_score (
int) – Minimum compatibility score to create an edge in the graphexclude_categories (
list[Any]) – Tool categories to exclude from analysis (e.g., [‘tool_finder’, ‘special_tool…max_tools_per_category (
int) – Maximum number of tools to analyze per category (for performance)force_rebuild (
bool) – Whether to force rebuild even if cached graph existsstream_callback (
Callable, optional) – Callback for streaming output
- Return type:
Any
- tooluniverse.tools.ToolGraphGenerationPipeline(tool_configs, max_tools, output_path, save_intermediate_every, *, stream_callback=None, use_cache=False, validate=True)[source]¶
Generates a directed tool relationship graph among provided tool configs using ToolRelationshipDe…
- Parameters:
tool_configs (
list[Any]) – List of tool configuration objectsmax_tools (
int) – Optional max number of tools to process (debug)output_path (
str) – Path for output graph JSONsave_intermediate_every (
int) – Checkpoint every N processed pairsstream_callback (
Callable, optional) – Callback for streaming output
- Return type:
Any
- tooluniverse.tools.ToolImplementationGenerator(tool_description, tool_parameters, domain='general', complexity_level='intermediate', performance_requirements=None, *, stream_callback=None, use_cache=False, validate=True)[source]¶
Generates domain-specific, functional code implementations based on tool descriptions and require…
- Parameters:
tool_description (
str) – Detailed description of what the tool should accomplishtool_parameters (
str) – JSON string of parameter schema for the tooldomain (
str) – Domain area for specialized implementationcomplexity_level (
str) – Desired complexity level of implementationperformance_requirements (
str) – Performance requirements or constraintsstream_callback (
Callable, optional) – Callback for streaming output
- Return type:
Any
- tooluniverse.tools.ToolMetadataGenerationPipeline(tool_configs, tool_type_mappings, add_existing_tooluniverse_labels, max_new_tooluniverse_labels, *, stream_callback=None, use_cache=False, validate=True)[source]¶
Generates standardized metadata for a batch of ToolUniverse tool configurations by calling ToolMe…
- Parameters:
tool_configs (
list[Any]) – List of raw tool configuration JSON objects to extract and standardize metada…tool_type_mappings (
dict[str,Any]) – Mapping of simplified toolType (keys) to lists of tool ‘type’ values belongin…add_existing_tooluniverse_labels (
bool) – Whether to include labels from existing ToolUniverse tools when labeling the …max_new_tooluniverse_labels (
int) – The maximum number of new ToolUniverse labels to use in the metadata configs …stream_callback (
Callable, optional) – Callback for streaming output
- Return type:
Any
- tooluniverse.tools.ToolMetadataGenerator(tool_config, tool_type_mappings=None, *, stream_callback=None, use_cache=False, validate=True)[source]¶
Generates a JSON structure with the metadata of a tool in ToolUniverse, given the JSON configurat…
- Parameters:
tool_config (
str) – JSON string of the tool configuration to extract metadata fromtool_type_mappings (
dict[str,Any]) – A mapping from a simplified toolType to a list of tool_config.type that fall …stream_callback (
Callable, optional) – Callback for streaming output
- Return type:
Any
- tooluniverse.tools.ToolMetadataStandardizer(metadata_list, limit=None, *, stream_callback=None, use_cache=False, validate=True)[source]¶
Standardizes and groups semantically equivalent metadata strings (e.g., sources, tags) into canon…
- Parameters:
metadata_list (
list[Any]) – List of raw metadata strings (e.g., sources, tags) to standardize and group.limit (
int) – If provided, the maximum number of canonical strings to return. The LLM will …stream_callback (
Callable, optional) – Callback for streaming output
- Return type:
Any
- tooluniverse.tools.ToolOptimizer(tool_config, quality_feedback, optimization_target, *, stream_callback=None, use_cache=False, validate=True)[source]¶
Optimizes tool configurations based on quality feedback. Improves tool specifications and impleme…
- Parameters:
- Return type:
Any
- tooluniverse.tools.ToolOutputSummarizer(tool_output, query_context, tool_name, focus_areas='key_findings_and_results', max_length=32000, *, stream_callback=None, use_cache=False, validate=True)[source]¶
AI-powered tool for summarizing long tool outputs, focusing on key information relevant to the or…
- Parameters:
tool_output (
str) – The original tool output to be summarizedquery_context (
str) – Context about the original query that triggered the tooltool_name (
str) – Name of the tool that generated the outputfocus_areas (
str) – Specific areas to focus on in the summarymax_length (
int) – Maximum length of the summary in charactersstream_callback (
Callable, optional) – Callback for streaming output
- Return type:
Any
- tooluniverse.tools.ToolQualityEvaluator(tool_config, test_cases, evaluation_aspects, *, stream_callback=None, use_cache=False, validate=True)[source]¶
Evaluates the quality of tool configurations and implementations. Provides detailed scoring and f…
- Parameters:
- Return type:
Any
- tooluniverse.tools.ToolRelationshipDetector(tool_a, other_tools, *, stream_callback=None, use_cache=False, validate=True)[source]¶
Analyzes a primary tool against a list of other tools to identify meaningful, directional data fl…
- tooluniverse.tools.ToolSpecificationGenerator(tool_description, tool_category, tool_type, similar_tools, existing_tools_summary, *, stream_callback=None, use_cache=False, validate=True)[source]¶
Generates complete ToolUniverse-compliant tool specifications based on a description and analysis…
- Parameters:
tool_description (
str) – Brief description of the desired tool functionality and purpose.tool_category (
str) – Target category for the tool (e.g., ‘biomedical’, ‘data_analysis’, ‘text_proc…tool_type (
str) – Specific ToolUniverse tool type (e.g., ‘AgenticTool’, ‘RESTTool’, ‘PythonTool’).similar_tools (
str) – JSON string containing configurations of similar existing tools for analysis …existing_tools_summary (
str) – Summary of existing tools in the ecosystem to avoid duplication and identify …stream_callback (
Callable, optional) – Callback for streaming output
- Return type:
Any
- tooluniverse.tools.ToolSpecificationOptimizer(tool_config, optimization_focus='all', target_audience='mixed', similar_tools=None, *, stream_callback=None, use_cache=False, validate=True)[source]¶
Optimizes tool specifications for clarity, completeness, and usability with comprehensive benchma…
- Parameters:
tool_config (
str) – JSON string of current tool configuration to optimizeoptimization_focus (
str) – Primary optimization focustarget_audience (
str) – Target user expertise levelsimilar_tools (
str) – JSON string array of similar tools for comparison and benchmarkingstream_callback (
Callable, optional) – Callback for streaming output
- Return type:
Any
- tooluniverse.tools.Tool_Finder(description, limit, picked_tool_names=None, return_call_result=None, categories=None, *, stream_callback=None, use_cache=False, validate=True)[source]¶
Retrieve related tools from the toolbox based on the provided description, advanced version with …
- Parameters:
description (
str) – The description of the tool capability required.limit (
int) – The number of tools to retrievepicked_tool_names (
list[Any]) – Pre-selected tool names to process. If provided, tool selection will skip the…return_call_result (
bool) – Whether to return both prompts and tool names. If false, returns only tool pr…categories (
list[Any]) – Optional list of tool categories to filter bystream_callback (
Callable, optional) – Callback for streaming output
- Return type:
Any
- tooluniverse.tools.Tool_Finder_Keyword(description, limit, picked_tool_names=None, return_call_result=None, categories=None, *, stream_callback=None, use_cache=False, validate=True)[source]¶
Simple keyword-based tool finder for discovering relevant tools using text matching
- Parameters:
description (
str) – The description of the tool capability required.limit (
int) – The number of tools to retrievepicked_tool_names (
list[Any]) – Pre-selected tool names to process. If provided, tool selection will skip the…return_call_result (
bool) – Whether to return both prompts and tool names. If false, returns only tool pr…categories (
list[Any]) – Optional list of tool categories to filter bystream_callback (
Callable, optional) – Callback for streaming output
- Return type:
Any
- tooluniverse.tools.Tool_Finder_LLM(description, limit, picked_tool_names=None, return_call_result=None, categories=None, *, stream_callback=None, use_cache=False, validate=True)[source]¶
LLM-based tool finder that uses natural language processing to intelligently select relevant tool…
- Parameters:
description (
str) – The description of the tool capability required.limit (
int) – The number of tools to retrievepicked_tool_names (
list[Any]) – Pre-selected tool names to process. If provided, tool selection will skip the…return_call_result (
bool) – Whether to return both prompts and tool names. If false, returns only tool pr…categories (
list[Any]) – Optional list of tool categories to filter bystream_callback (
Callable, optional) – Callback for streaming output
- Return type:
Any
- tooluniverse.tools.Tool_RAG(description, limit, *, stream_callback=None, use_cache=False, validate=True)[source]¶
Retrieve related tools from the toolbox based on the provided description
- Parameters:
- Return type:
Any
- tooluniverse.tools.UCSC_get_genes_by_region(chrom, start, end, genome='hg38', track='knownGene', *, stream_callback=None, use_cache=False, validate=True)[source]¶
Query UCSC Genome Browser track API for knownGene features in a genomic window.
- tooluniverse.tools.UniProt_get_alternative_names_by_accession(accession, *, stream_callback=None, use_cache=False, validate=True)[source]¶
Extract all alternative names (alternativeNames) from UniProtKB entry.
- tooluniverse.tools.UniProt_get_disease_variants_by_accession(accession, *, stream_callback=None, use_cache=False, validate=True)[source]¶
Extract all variants (feature type = VARIANT) and their related annotations from UniProtKB entry.
- tooluniverse.tools.UniProt_get_entry_by_accession(accession, *, stream_callback=None, use_cache=False, validate=True)[source]¶
Get the complete JSON entry for a specified UniProtKB accession.
- tooluniverse.tools.UniProt_get_function_by_accession(accession, *, stream_callback=None, use_cache=False, validate=True)[source]¶
Extract functional annotations from UniProtKB entry (Comment type = FUNCTION).
- tooluniverse.tools.UniProt_get_isoform_ids_by_accession(accession, *, stream_callback=None, use_cache=False, validate=True)[source]¶
Extract all splice isoform IDs from UniProtKB entry (isoformNames).
- tooluniverse.tools.UniProt_get_organism_by_accession(accession, *, stream_callback=None, use_cache=False, validate=True)[source]¶
Extract the organism scientific name from UniProtKB entry.
- tooluniverse.tools.UniProt_get_ptm_processing_by_accession(accession, *, stream_callback=None, use_cache=False, validate=True)[source]¶
Extract all PTM and processing sites from UniProtKB entry (feature type = MODIFIED RESIDUE or SIG…
- tooluniverse.tools.UniProt_get_recommended_name_by_accession(accession, *, stream_callback=None, use_cache=False, validate=True)[source]¶
Extract the recommended protein name (recommendedName) from UniProtKB entry.
- tooluniverse.tools.UniProt_get_sequence_by_accession(accession, *, stream_callback=None, use_cache=False, validate=True)[source]¶
Extract the canonical sequence from UniProtKB entry.
- tooluniverse.tools.UniProt_get_subcellular_location_by_accession(accession, *, stream_callback=None, use_cache=False, validate=True)[source]¶
Extract subcellular localization annotations from UniProtKB entry (Comment type = SUBCELLULAR LOC…
- tooluniverse.tools.Unpaywall_check_oa_status(doi, email, *, stream_callback=None, use_cache=False, validate=True)[source]¶
Query Unpaywall by DOI to check open-access status and OA locations. Requires a contact email for…
- tooluniverse.tools.WHO_Guideline_Full_Text(url, *, stream_callback=None, use_cache=False, validate=True)[source]¶
Fetch full text content from a WHO (World Health Organization) guideline publication page. Extrac…
- Parameters:
- Return type:
dict[str,Any]
- tooluniverse.tools.WHO_Guidelines_Search(query, limit, *, stream_callback=None, use_cache=False, validate=True)[source]¶
Search WHO (World Health Organization) official clinical guidelines and health recommendations. P…
- tooluniverse.tools.Wikidata_SPARQL_query(sparql, max_results, *, stream_callback=None, use_cache=False, validate=True)[source]¶
Execute SPARQL queries against Wikidata to retrieve structured data. This tool powers Scholia-sty…
- tooluniverse.tools.WritingPresentationReviewer(manuscript_text, *, stream_callback=None, use_cache=False, validate=True)[source]¶
Assesses clarity, organization, grammar, and visual presentation quality.
- tooluniverse.tools.Zenodo_search_records(query, max_results, community=None, *, stream_callback=None, use_cache=False, validate=True)[source]¶
Search Zenodo for research data, publications, and datasets. Zenodo is an open-access repository …
- Parameters:
query (
str) – Free text search query for Zenodo records. Use keywords to search across titl…max_results (
int) – Maximum number of results to return. Must be between 1 and 200.community (
str) – Optional community slug to filter results by specific research community (e.g…stream_callback (
Callable, optional) – Callback for streaming output
- Return type:
list[Any]
- tooluniverse.tools.alphafold_get_annotations(qualifier, type, *, stream_callback=None, use_cache=False, validate=True)[source]¶
Retrieve AlphaFold variant annotations (e.g., missense mutations) for a given UniProt accession (…
- tooluniverse.tools.alphafold_get_prediction(qualifier, sequence_checksum, *, stream_callback=None, use_cache=False, validate=True)[source]¶
Retrieve full AlphaFold 3D structure predictions for a given protein. Input must be a UniProt acc…
- tooluniverse.tools.alphafold_get_summary(qualifier, *, stream_callback=None, use_cache=False, validate=True)[source]¶
Retrieve summary details of AlphaFold 3D models for a given protein. Input must be a UniProt acce…
- tooluniverse.tools.call_agentic_human(question, *, stream_callback=None, use_cache=False, validate=True)[source]¶
Produces a concise, practical answer that emulates how a well-informed human would respond to the…
- tooluniverse.tools.cancer_biomarkers_disease_target_score(efoId, pageSize, *, stream_callback=None, use_cache=False, validate=True)[source]¶
Extract disease-target association scores from cancer biomarkers data. This includes known cancer…
- tooluniverse.tools.cancer_gene_census_disease_target_score(efoId, pageSize, *, stream_callback=None, use_cache=False, validate=True)[source]¶
Extract disease-target association scores from Cancer Gene Census. This provides curated cancer g…
- tooluniverse.tools.cellosaurus_get_cell_line_info(accession, format, fields, *, stream_callback=None, use_cache=False, validate=True)[source]¶
Get detailed information about a specific cell line using its Cellosaurus accession number (CVCL_…
- Parameters:
- Return type:
dict[str,Any]
- tooluniverse.tools.cellosaurus_query_converter(query, include_explanation, *, stream_callback=None, use_cache=False, validate=True)[source]¶
Convert natural language queries to Solr syntax for Cellosaurus API searches. Uses semantic simil…
- tooluniverse.tools.cellosaurus_search_cell_lines(q, offset, size, *, stream_callback=None, use_cache=False, validate=True)[source]¶
Search Cellosaurus cell lines using the /search/cell-line endpoint. Supports Solr query syntax fo…
- Parameters:
- Return type:
dict[str,Any]
- tooluniverse.tools.chembl_disease_target_score(efoId, pageSize, *, stream_callback=None, use_cache=False, validate=True)[source]¶
Extract disease-target association scores specifically from ChEMBL database. ChEMBL provides bioa…
- tooluniverse.tools.convert_to_markdown(uri, output_path=None, enable_plugins=False, *, stream_callback=None, use_cache=False, validate=True)[source]¶
Convert a resource described by an http:, https:, file: or data: URI to markdown.
- tooluniverse.tools.dbSNP_get_variant_by_rsid(rsid, *, stream_callback=None, use_cache=False, validate=True)[source]¶
Fetch dbSNP variant by rsID using NCBI Variation Services (refsnp endpoint).
- tooluniverse.tools.dict_search(query, search_fields, case_sensitive, exact_match, limit, *, stream_callback=None, use_cache=False, validate=True)[source]¶
Search the DICTrank dataset for drug-induced cardiotoxicity (DICT) risk information by trade name…
- Parameters:
query (
str) – Free-text query (e.g. ‘ZYPREXA’, ‘Olanzapine’).search_fields (
list[Any]) – Columns to search. Choose from: ‘Trade Name’, ‘Generic/Proper Name(s)’, ‘Acti…case_sensitive (
bool) – Match text with exact case if true.exact_match (
bool) – Field value must equal query exactly if true; otherwise substring match.limit (
int) – Maximum number of rows to return.stream_callback (
Callable, optional) – Callback for streaming output
- Return type:
dict[str,Any]
- tooluniverse.tools.dili_search(query, search_fields, case_sensitive, exact_match, limit, *, stream_callback=None, use_cache=False, validate=True)[source]¶
Search the DILIrank dataset for drug-induced liver-injury (DILI) risk information by compound nam…
- Parameters:
query (
str) – Free-text query (e.g. ‘acetaminophen’).search_fields (
list[Any]) – Columns to search. Choose from: ‘Compound Name’.case_sensitive (
bool) – Match text with exact case if true.exact_match (
bool) – Field value must equal query exactly if true; otherwise substring match.limit (
int) – Maximum number of rows to return.stream_callback (
Callable, optional) – Callback for streaming output
- Return type:
dict[str,Any]
- tooluniverse.tools.diqt_search(query, search_fields, case_sensitive, exact_match, limit, *, stream_callback=None, use_cache=False, validate=True)[source]¶
Search the DIQTA dataset for drug-induced QT-interval prolongation risk information by generic na…
- Parameters:
query (
str) – Free-text query (e.g. ‘Astemizole’, ‘DB00637’).search_fields (
list[Any]) – Columns to search. Choose from: ‘Generic/Proper Name(s)’, ‘DrugBank ID’.case_sensitive (
bool) – Match text with exact case if true.exact_match (
bool) – Field value must equal query exactly if true; otherwise substring match.limit (
int) – Maximum number of rows to return.stream_callback (
Callable, optional) – Callback for streaming output
- Return type:
dict[str,Any]
- tooluniverse.tools.disease_target_score(efoId, datasourceId, pageSize, *, stream_callback=None, use_cache=False, validate=True)[source]¶
Extract disease-target association scores from a specific data source using GraphQL API. This too…
- Parameters:
efoId (
str) – The EFO (Experimental Factor Ontology) ID of the disease, e.g., ‘EFO_0000339’…datasourceId (
str) – The datasource ID to extract scores from. Available options: ‘chembl’, ‘eva’,…pageSize (
int) – Number of results per page (default: 100, max: 100)stream_callback (
Callable, optional) – Callback for streaming output
- Return type:
dict[str,Any]
- tooluniverse.tools.drugbank_filter_drugs_by_name(condition, value, limit, *, stream_callback=None, use_cache=False, validate=True)[source]¶
Filter DrugBank records based on conditions applied to drug names. For example, find drugs whose …
- Parameters:
- Return type:
dict[str,Any]
- tooluniverse.tools.drugbank_full_search(query, search_fields, case_sensitive, exact_match, limit, *, stream_callback=None, use_cache=False, validate=True)[source]¶
Search the cleaned DrugBank dataframe (one row per drug) by ID, common name, or synonym. Returns …
- Parameters:
query (
str) – Free-text query (e.g. ‘DB00945’, ‘acetylsalicylic’, ‘Acarbosa’).search_fields (
list[Any]) – Columns to search in. Choose from: ‘drugbank_id’, ‘name’, ‘synonyms’.case_sensitive (
bool) – Match text with exact case if true.exact_match (
bool) – Field value must equal query exactly if true; otherwise substring match.limit (
int) – Max number of rows to return.stream_callback (
Callable, optional) – Callback for streaming output
- Return type:
dict[str,Any]
- tooluniverse.tools.drugbank_get_drug_basic_info_by_drug_name_or_drugbank_id(query, case_sensitive, exact_match, limit, *, stream_callback=None, use_cache=False, validate=True)[source]¶
Get basic drug information including name, description, CAS number, and approval status by drug n…
- Parameters:
query (
str) – Drug name or DrugBank ID to search forcase_sensitive (
bool) – Select True to perform a case-sensitive searchexact_match (
bool) – Select True to require an exact match with the queried name or IDlimit (
int) – Maximum number of results to returnstream_callback (
Callable, optional) – Callback for streaming output
- Return type:
dict[str,Any]
- tooluniverse.tools.drugbank_get_drug_chemistry_by_drug_name_or_drugbank_id(query, case_sensitive, exact_match, limit, *, stream_callback=None, use_cache=False, validate=True)[source]¶
Get drug chemical properties including molecular formula, weight, and structure by drug name or D…
- Parameters:
query (
str) – Drug name or Drugbank ID to search forcase_sensitive (
bool) – Select True to perform a case-sensitive searchexact_match (
bool) – Select True to require an exact matchlimit (
int) – Maximum number of results to returnstream_callback (
Callable, optional) – Callback for streaming output
- Return type:
dict[str,Any]
- tooluniverse.tools.drugbank_get_drug_interactions_by_drug_name_or_drugbank_id(query, case_sensitive, exact_match, limit, *, stream_callback=None, use_cache=False, validate=True)[source]¶
Get drug interactions and contraindications by drug name or DrugBank ID.
- Parameters:
- Return type:
dict[str,Any]
- tooluniverse.tools.drugbank_get_drug_name_and_description_by_indication(query, case_sensitive, exact_match, limit, *, stream_callback=None, use_cache=False, validate=True)[source]¶
Get drug name, Drugbank ID, and description by its indication.
- Parameters:
- Return type:
dict[str,Any]
- tooluniverse.tools.drugbank_get_drug_name_and_description_by_pathway_name(query, case_sensitive, exact_match, limit, *, stream_callback=None, use_cache=False, validate=True)[source]¶
Get drug names and descriptions by pathway name.
- Parameters:
- Return type:
dict[str,Any]
- tooluniverse.tools.drugbank_get_drug_name_and_description_by_target_name(query, case_sensitive, exact_match, limit, *, stream_callback=None, use_cache=False, validate=True)[source]¶
Get associated drug names and descriptions for a particular target, enzyme, carrier, or transport…
- Parameters:
query (
str) – Target, enzyme, carrier, or transporter name to search forcase_sensitive (
bool) – Select True to perform a case-sensitive searchexact_match (
bool) – Select True to require an exact matchlimit (
int) – Maximum number of results to returnstream_callback (
Callable, optional) – Callback for streaming output
- Return type:
dict[str,Any]
- tooluniverse.tools.drugbank_get_drug_name_description_pharmacology_by_mechanism_of_action(query, case_sensitive, exact_match, limit, *, stream_callback=None, use_cache=False, validate=True)[source]¶
Get drug name, ID, description, pharmacodynamics, mechanism of action, and pharmacokinetics by dr…
- Parameters:
query (
str) – Query string to search for in mechanism of action descriptionscase_sensitive (
bool) – Select True to perform a case-sensitive searchexact_match (
bool) – Select True to require an exact matchlimit (
int) – Maximum number of results to returnstream_callback (
Callable, optional) – Callback for streaming output
- Return type:
dict[str,Any]
- tooluniverse.tools.drugbank_get_drug_pathways_and_reactions_by_drug_name_or_drugbank_id(query, case_sensitive, exact_match, limit, *, stream_callback=None, use_cache=False, validate=True)[source]¶
Get drug pathways and metabolic reactions by drug name or DrugBank ID.
- Parameters:
query (
str) – Drug name or Drugbank ID to search forcase_sensitive (
bool) – Select True to perform a case-sensitive searchexact_match (
bool) – Select True to require an exact matchlimit (
int) – Maximum number of results to returnstream_callback (
Callable, optional) – Callback for streaming output
- Return type:
dict[str,Any]
- tooluniverse.tools.drugbank_get_drug_products_by_name_or_drugbank_id(query, case_sensitive, exact_match, limit, *, stream_callback=None, use_cache=False, validate=True)[source]¶
Get commercial drug products, dosage forms, and pricing informatiomon by drug name or DrugBank ID.
- Parameters:
query (
str) – Drug name or Drugbank ID to search forcase_sensitive (
bool) – Select True to perform a case-sensitive searchexact_match (
bool) – Select True to require an exact matchlimit (
int) – Maximum number of results to returnstream_callback (
Callable, optional) – Callback for streaming output
- Return type:
dict[str,Any]
- tooluniverse.tools.drugbank_get_drug_references_by_drug_name_or_drugbank_id(query, case_sensitive, exact_match, limit, *, stream_callback=None, use_cache=False, validate=True)[source]¶
Get drug literature references, patents, and external links by drug name or DrugBank ID.
- Parameters:
query (
str) – Drug name or Drugbank ID to search for referencescase_sensitive (
bool) – Select True to perform a case-sensitive searchexact_match (
bool) – Select True to require an exact matchlimit (
int) – Maximum number of results to returnstream_callback (
Callable, optional) – Callback for streaming output
- Return type:
dict[str,Any]
- tooluniverse.tools.drugbank_get_indications_by_drug_name_or_drugbank_id(query, case_sensitive, exact_match, limit, *, stream_callback=None, use_cache=False, validate=True)[source]¶
Get drug indications and therapeutic uses by drug name or DrugBank ID.
- Parameters:
- Return type:
dict[str,Any]
- tooluniverse.tools.drugbank_get_pharmacology_by_drug_name_or_drugbank_id(query, case_sensitive, exact_match, limit, *, stream_callback=None, use_cache=False, validate=True)[source]¶
Get drug pharmacodynamics, mechanism of action, and pharmacokinetics by drug name or Drugbank ID.
- Parameters:
query (
str) – Drug name or Drugbank ID to search forcase_sensitive (
bool) – Select True to perform a case-sensitive searchexact_match (
bool) – Select True to require an exact matchlimit (
int) – Maximum number of results to returnstream_callback (
Callable, optional) – Callback for streaming output
- Return type:
dict[str,Any]
- tooluniverse.tools.drugbank_get_safety_by_drug_name_or_drugbank_id(query, case_sensitive, exact_match, limit, *, stream_callback=None, use_cache=False, validate=True)[source]¶
Get drug toxicity, contraindications, and safety information by drug name or DrugBank ID.
- Parameters:
query (
str) – Drug name or Drugbank ID to search forcase_sensitive (
bool) – Select True to perform a case-sensitive searchexact_match (
bool) – Select True to require an exact matchlimit (
int) – Maximum number of results to returnstream_callback (
Callable, optional) – Callback for streaming output
- Return type:
dict[str,Any]
- tooluniverse.tools.drugbank_get_targets_by_drug_name_or_drugbank_id(query, case_sensitive, exact_match, limit, *, stream_callback=None, use_cache=False, validate=True)[source]¶
Get drug targets, enzymes, carriers, and transporters by drug name or DrugBank ID.
- Parameters:
query (
str) – Drug name or Drugbank ID to search forcase_sensitive (
bool) – Select True to perform a case-sensitive searchexact_match (
bool) – Select True to require an exact matchlimit (
int) – Maximum number of results to returnstream_callback (
Callable, optional) – Callback for streaming output
- Return type:
dict[str,Any]
- tooluniverse.tools.drugbank_links_search(query, search_fields, case_sensitive, exact_match, limit, *, stream_callback=None, use_cache=False, validate=True)[source]¶
Search the cross-reference table linking DrugBank IDs to external identifiers (CAS, KEGG, PubChem…
- Parameters:
query (
str) – Free-text query (e.g. ‘DB00002’, ‘Cetuximab’).search_fields (
list[Any]) – Columns to search. Choose from: ‘DrugBank ID’, ‘Name’, ‘CAS Number’, ‘Drug Ty…case_sensitive (
bool) – Match text with exact case if true.exact_match (
bool) – Field value must equal query exactly if true; otherwise substring match.limit (
int) – Maximum number of rows to return.stream_callback (
Callable, optional) – Callback for streaming output
- Return type:
dict[str,Any]
- tooluniverse.tools.drugbank_vocab_filter(field, condition, limit, value=None, *, stream_callback=None, use_cache=False, validate=True)[source]¶
Filter the DrugBank vocabulary dataset based on specific field criteria. Use simple field-value p…
- Parameters:
field (
str) – The field to filter oncondition (
str) – The type of filtering condition to apply. Filter is case-insensitive.value (
str) – The value to filter by. Not required when condition is ‘not_empty’. Examples:…limit (
int) – Maximum number of results to return.stream_callback (
Callable, optional) – Callback for streaming output
- Return type:
dict[str,Any]
- tooluniverse.tools.drugbank_vocab_search(query, search_fields, case_sensitive, exact_match, limit, *, stream_callback=None, use_cache=False, validate=True)[source]¶
Search the DrugBank vocabulary dataset for drugs by name, ID, synonyms, or other fields using tex…
- Parameters:
query (
str) – Search query string. Can be drug name, synonym, DrugBank ID, or any text to s…search_fields (
list[Any]) – Fields to search in. Available fields: ‘DrugBank ID’, ‘Accession Numbers’, ‘C…case_sensitive (
bool) – Whether the search should be case sensitive.exact_match (
bool) – Whether to perform exact matching instead of substring matching.limit (
int) – Maximum number of results to return.stream_callback (
Callable, optional) – Callback for streaming output
- Return type:
dict[str,Any]
- tooluniverse.tools.embedding_database_add(action, database_name, documents, metadata, *, stream_callback=None, use_cache=False, validate=True)[source]¶
Add new documents to an existing embedding database. Generates embeddings for new documents using…
- Parameters:
action (
str) – Action to add documents to existing databasedatabase_name (
str) – Name of the existing database to add documents todocuments (
list[Any]) – List of new document texts to embed and addmetadata (
list[Any]) – Optional metadata for each new document (same length as documents)stream_callback (
Callable, optional) – Callback for streaming output
- Return type:
Any
- tooluniverse.tools.embedding_database_create(action, database_name, documents, metadata, model, description, *, stream_callback=None, use_cache=False, validate=True)[source]¶
Create a new embedding database from a collection of documents. Generates embeddings using OpenAI…
- Parameters:
action (
str) – Action to create database from documentsdatabase_name (
str) – Name for the new database (must be unique)documents (
list[Any]) – List of document texts to embed and storemetadata (
list[Any]) – Optional metadata for each document (same length as documents)model (
str) – OpenAI/Azure OpenAI embedding model to usedescription (
str) – Optional description for the databasestream_callback (
Callable, optional) – Callback for streaming output
- Return type:
Any
- tooluniverse.tools.embedding_database_load(action, database_path, database_name, overwrite, *, stream_callback=None, use_cache=False, validate=True)[source]¶
Load an existing embedding database from a local path or external source. Allows importing databa…
- Parameters:
action (
str) – Action to load database from external sourcedatabase_path (
str) – Path to the existing database directory or filedatabase_name (
str) – Local name to assign to the loaded databaseoverwrite (
bool) – Whether to overwrite existing database with same namestream_callback (
Callable, optional) – Callback for streaming output
- Return type:
Any
- tooluniverse.tools.embedding_database_search(action, database_name, query, top_k, filters, *, stream_callback=None, use_cache=False, validate=True)[source]¶
Search for semantically similar documents in an embedding database. Uses OpenAI embeddings to con…
- Parameters:
action (
str) – Action to search the databasedatabase_name (
str) – Name of the database to search inquery (
str) – Query text to find similar documents fortop_k (
int) – Number of most similar documents to returnfilters (
dict[str,Any]) – Optional metadata filters to apply to search resultsstream_callback (
Callable, optional) – Callback for streaming output
- Return type:
Any
- tooluniverse.tools.embedding_sync_download(action, repository, local_name, overwrite, *, stream_callback=None, use_cache=False, validate=True)[source]¶
Download an embedding database from HuggingFace Hub to local storage. Allows accessing databases …
- Parameters:
action (
str) – Action to download database from HuggingFacerepository (
str) – HuggingFace repository to download from (format: username/repo-name)local_name (
str) – Local name for the downloaded database (optional, defaults to repo name)overwrite (
bool) – Whether to overwrite existing local database with same namestream_callback (
Callable, optional) – Callback for streaming output
- Return type:
Any
- tooluniverse.tools.embedding_sync_upload(action, database_name, repository, description, private, commit_message, *, stream_callback=None, use_cache=False, validate=True)[source]¶
Upload a local embedding database to HuggingFace Hub for sharing and collaboration. Creates a dat…
- Parameters:
action (
str) – Action to upload database to HuggingFacedatabase_name (
str) – Name of the local database to uploadrepository (
str) – HuggingFace repository name (format: username/repo-name)description (
str) – Description for the HuggingFace datasetprivate (
bool) – Whether to create a private repositorycommit_message (
str) – Commit message for the uploadstream_callback (
Callable, optional) – Callback for streaming output
- Return type:
Any
- tooluniverse.tools.enrichr_gene_enrichment_analysis(gene_list, libs, *, stream_callback=None, use_cache=False, validate=True)[source]¶
Perform gene enrichment analysis using Enrichr to find biological pathways, processes, and molecu…
- Parameters:
gene_list (
list[Any]) – List of gene names or symbols to analyze. At least 2 genes are required for p…libs (
list[Any]) – List of enrichment libraries to use for analysis.stream_callback (
Callable, optional) – Callback for streaming output
- Return type:
Any
- tooluniverse.tools.europepmc_disease_target_score(efoId, pageSize, *, stream_callback=None, use_cache=False, validate=True)[source]¶
Extract disease-target association scores from Europe PMC literature. This includes literature-ba…
- tooluniverse.tools.eva_disease_target_score(efoId, pageSize, *, stream_callback=None, use_cache=False, validate=True)[source]¶
Extract disease-target association scores from EVA (European Variation Archive). EVA provides gen…
- tooluniverse.tools.eva_somatic_disease_target_score(efoId, pageSize, *, stream_callback=None, use_cache=False, validate=True)[source]¶
Extract disease-target association scores from EVA somatic mutations. This includes somatic varia…
- tooluniverse.tools.expression_atlas_disease_target_score(efoId, pageSize, *, stream_callback=None, use_cache=False, validate=True)[source]¶
Extract disease-target association scores from Expression Atlas. This provides gene expression data.
- tooluniverse.tools.extract_clinical_trial_adverse_events(nct_ids, organ_systems=None, adverse_event_type=None, *, stream_callback=None, use_cache=False, validate=True)[source]¶
Extracts detailed adverse event results from clinicaltrials.gov, using their NCT IDs.
- Parameters:
nct_ids (
list[Any]) – List of NCT IDs of the clinical trials (e.g., [‘NCT04852770’, ‘NCT01728545’]).organ_systems (
list[Any]) – List of organs or organ systems to filter adverse events (see enum for exact …adverse_event_type (
str) – Type of adverse events to extract. Options are ‘serious’ (serious adverse eve…stream_callback (
Callable, optional) – Callback for streaming output
- Return type:
Any
- tooluniverse.tools.extract_clinical_trial_outcomes(nct_ids, outcome_measure=None, *, stream_callback=None, use_cache=False, validate=True)[source]¶
Extracts detailed trial outcome results (e.g., overall survival months, p-values, etc.) from clin…
- Parameters:
nct_ids (
list[Any]) – List of NCT IDs of the clinical trials (e.g., [‘NCT04852770’, ‘NCT01728545’]).outcome_measure (
str) – Outcome measure to extract. Example values include ‘primary’ (primary outcome…stream_callback (
Callable, optional) – Callback for streaming output
- Return type:
Any
- tooluniverse.tools.genomics_england_disease_target_score(efoId, pageSize, *, stream_callback=None, use_cache=False, validate=True)[source]¶
Extract disease-target association scores from Genomics England data. This includes clinical geno…
- tooluniverse.tools.get_HPO_ID_by_phenotype(query, limit=None, offset=None, *, stream_callback=None, use_cache=False, validate=True)[source]¶
Retrieve the HPO ID of a phenotype or symptom.
- tooluniverse.tools.get_albumentations_info(*, stream_callback=None, use_cache=False, validate=True)[source]¶
Get information about the albumentations package. Fast image augmentation library
- tooluniverse.tools.get_altair_info(*, stream_callback=None, use_cache=False, validate=True)[source]¶
Get information about the altair package. Declarative statistical visualization library
- tooluniverse.tools.get_anndata_info(include_examples, *, stream_callback=None, use_cache=False, validate=True)[source]¶
Get comprehensive information about AnnData – annotated data for computational biology
- tooluniverse.tools.get_arboreto_info(info_type, *, stream_callback=None, use_cache=False, validate=True)[source]¶
Get comprehensive information about Arboreto – gene regulatory network inference
- tooluniverse.tools.get_arxiv_info(include_examples, *, stream_callback=None, use_cache=False, validate=True)[source]¶
Get comprehensive information about arxiv – access to arXiv preprint repository
- tooluniverse.tools.get_ase_info(include_examples, *, stream_callback=None, use_cache=False, validate=True)[source]¶
Get comprehensive information about ASE (Atomic Simulation Environment) – a toolkit for building,…
- tooluniverse.tools.get_assembly_info_by_pdb_id(pdb_id, *, stream_callback=None, use_cache=False, validate=True)[source]¶
Retrieve all associated biological assembly details for a given PDB structure.
- tooluniverse.tools.get_assembly_summary(assembly_id, *, stream_callback=None, use_cache=False, validate=True)[source]¶
Get key assembly composition and symmetry summary for an assembly associated with a PDB entry.
- tooluniverse.tools.get_astropy_info(*, stream_callback=None, use_cache=False, validate=True)[source]¶
Get information about the astropy package. Astronomy and astrophysics library
- tooluniverse.tools.get_binding_affinity_by_pdb_id(pdb_id, *, stream_callback=None, use_cache=False, validate=True)[source]¶
Retrieve binding affinity constants (Kd, Ki, IC50) associated with ligands in a PDB entry.
- tooluniverse.tools.get_biopandas_info(include_examples, *, stream_callback=None, use_cache=False, validate=True)[source]¶
Get comprehensive information about BioPandas – pandas-based molecular structure analysis
- tooluniverse.tools.get_biopython_info(include_examples, *, stream_callback=None, use_cache=False, validate=True)[source]¶
Get comprehensive information about Biopython – powerful tools for computational molecular biolog…
- tooluniverse.tools.get_bioservices_info(*, stream_callback=None, use_cache=False, validate=True)[source]¶
Get information about the bioservices package. Python package: bioservices
- tooluniverse.tools.get_biotite_info(include_examples, *, stream_callback=None, use_cache=False, validate=True)[source]¶
Get comprehensive information about Biotite – comprehensive computational molecular biology library
- tooluniverse.tools.get_bokeh_info(*, stream_callback=None, use_cache=False, validate=True)[source]¶
Get information about the bokeh package. Interactive visualization library for modern web browsers
- tooluniverse.tools.get_brian2_info(*, stream_callback=None, use_cache=False, validate=True)[source]¶
Get information about the brian2 package. Spiking neural network simulator
- tooluniverse.tools.get_cartopy_info(*, stream_callback=None, use_cache=False, validate=True)[source]¶
Get information about the cartopy package. Cartographic projections and geospatial data processing
- tooluniverse.tools.get_catboost_info(*, stream_callback=None, use_cache=False, validate=True)[source]¶
Get information about the catboost package. High-performance gradient boosting library
- tooluniverse.tools.get_cellpose_info(include_examples, *, stream_callback=None, use_cache=False, validate=True)[source]¶
Get comprehensive information about Cellpose – cell segmentation algorithm
- tooluniverse.tools.get_cellrank_info(*, stream_callback=None, use_cache=False, validate=True)[source]¶
Get information about the cellrank package. Trajectory inference and cell fate mapping in single-…
- tooluniverse.tools.get_cellxgene_census_info(info_type, *, stream_callback=None, use_cache=False, validate=True)[source]¶
Get comprehensive information about cellxgene-census – access to the CELLxGENE Census single-cell…
- tooluniverse.tools.get_cftime_info(*, stream_callback=None, use_cache=False, validate=True)[source]¶
Get information about the cftime package. Time-handling functionality from netcdf4-python
- tooluniverse.tools.get_chem_comp_audit_info(pdb_id, *, stream_callback=None, use_cache=False, validate=True)[source]¶
Fetch audit history for a chemical component: action type, date, details, ordinal, and processing…
- tooluniverse.tools.get_chem_comp_charge_and_ambiguity(pdb_id, *, stream_callback=None, use_cache=False, validate=True)[source]¶
Retrieve the formal charge and ambiguity flag of a chemical component.
- tooluniverse.tools.get_chembl_webresource_client_info(*, stream_callback=None, use_cache=False, validate=True)[source]¶
Get information about the chembl-webresource-client package. Python client for ChEMBL web services
- tooluniverse.tools.get_citation_info_by_pdb_id(pdb_id, *, stream_callback=None, use_cache=False, validate=True)[source]¶
Retrieve citation information (authors, journal, year) for a given PDB structure.
- tooluniverse.tools.get_clair3_info(info_type, *, stream_callback=None, use_cache=False, validate=True)[source]¶
Get comprehensive information about Clair3 – variant calling for long-read sequencing
- tooluniverse.tools.get_clinical_trial_conditions_and_interventions(nct_ids, condition_and_intervention, *, stream_callback=None, use_cache=False, validate=True)[source]¶
Retrieves the list of conditions or diseases and the interventions and arm groups that the clinic…
- Parameters:
nct_ids (
list[Any]) – List of NCT IDs of the clinical trials (e.g., [‘NCT04852770’, ‘NCT01728545’]).condition_and_intervention (
str) – Placeholder.stream_callback (
Callable, optional) – Callback for streaming output
- Return type:
Any
- tooluniverse.tools.get_clinical_trial_descriptions(nct_ids, description_type, *, stream_callback=None, use_cache=False, validate=True)[source]¶
Retrieves detailed identification information for trials, including titles, phases, and descripti…
- Parameters:
nct_ids (
list[Any]) – List of NCT IDs of the clinical trials (e.g., [‘NCT04852770’, ‘NCT01728545’]).description_type (
str) – Type of information to retrieve. Options are ‘brief’ for brief descriptions o…stream_callback (
Callable, optional) – Callback for streaming output
- Return type:
Any
- tooluniverse.tools.get_clinical_trial_eligibility_criteria(nct_ids, eligibility_criteria, *, stream_callback=None, use_cache=False, validate=True)[source]¶
Retrieves the eligibility criteria for the clinical trials, using their NCT IDs.
- Parameters:
nct_ids (
list[Any]) – List of NCT IDs of the clinical trials (e.g., [‘NCT04852770’, ‘NCT01728545’]).eligibility_criteria (
str) – Placeholder.stream_callback (
Callable, optional) – Callback for streaming output
- Return type:
Any
- tooluniverse.tools.get_clinical_trial_locations(nct_ids, location, *, stream_callback=None, use_cache=False, validate=True)[source]¶
Retrieves the locations where the clinical trials are being conducted, using their NCT IDs.
- Parameters:
nct_ids (
list[Any]) – List of NCT IDs of the clinical trials (e.g., [‘NCT04852770’, ‘NCT01728545’]).location (
str) – Placeholder.stream_callback (
Callable, optional) – Callback for streaming output
- Return type:
Any
- tooluniverse.tools.get_clinical_trial_outcome_measures(nct_ids, outcome_measures=None, *, stream_callback=None, use_cache=False, validate=True)[source]¶
Retrieves the outcome measures for the clinical trials, using their NCT IDs.
- Parameters:
nct_ids (
list[Any]) – List of NCT IDs of the clinical trials (e.g., [‘NCT04852770’, ‘NCT01728545’]).outcome_measures (
str) – Decides whether to retrieve primary, secondary, or all outcome measures. Opti…stream_callback (
Callable, optional) – Callback for streaming output
- Return type:
Any
- tooluniverse.tools.get_clinical_trial_references(nct_ids, references, *, stream_callback=None, use_cache=False, validate=True)[source]¶
Retrieves the references (if any) for the clinical trials, using their NCT IDs.
- Parameters:
nct_ids (
list[Any]) – List of NCT IDs of the clinical trials (e.g., [‘NCT04852770’, ‘NCT01728545’]).references (
str) – Placeholder.stream_callback (
Callable, optional) – Callback for streaming output
- Return type:
Any
- tooluniverse.tools.get_clinical_trial_status_and_dates(nct_ids, status_and_date, *, stream_callback=None, use_cache=False, validate=True)[source]¶
Retrieves trial status and start and completion dates, using their NCT IDs.
- Parameters:
nct_ids (
list[Any]) – List of NCT IDs of the clinical trials (e.g., [‘NCT04852770’, ‘NCT01728545’]).status_and_date (
str) – Placeholder.stream_callback (
Callable, optional) – Callback for streaming output
- Return type:
Any
- tooluniverse.tools.get_cobra_info(include_examples, *, stream_callback=None, use_cache=False, validate=True)[source]¶
Get comprehensive information about COBRApy – constraint-based metabolic modeling
- tooluniverse.tools.get_cobrapy_info(info_type, *, stream_callback=None, use_cache=False, validate=True)[source]¶
Get comprehensive information about COBRApy – constraint-based metabolic modeling
- tooluniverse.tools.get_cooler_info(include_examples, *, stream_callback=None, use_cache=False, validate=True)[source]¶
Get comprehensive information about Cooler – sparse Hi-C contact matrix storage
- tooluniverse.tools.get_core_refinement_statistics(pdb_id, *, stream_callback=None, use_cache=False, validate=True)[source]¶
Retrieve essential refinement statistics for a given PDB structure including R-factors, occupancy…
- tooluniverse.tools.get_cryosparc_tools_info(info_type, *, stream_callback=None, use_cache=False, validate=True)[source]¶
Get comprehensive information about cryosparc-tools – interface to CryoSPARC cryo-EM processing
- tooluniverse.tools.get_crystal_growth_conditions_by_pdb_id(pdb_id, *, stream_callback=None, use_cache=False, validate=True)[source]¶
Get information about the crystallization method and conditions for a structure.
- tooluniverse.tools.get_crystallization_ph_by_pdb_id(pdb_id, *, stream_callback=None, use_cache=False, validate=True)[source]¶
Fetch the pH used during crystallization of the sample.
- tooluniverse.tools.get_crystallographic_properties_by_pdb_id(pdb_id, *, stream_callback=None, use_cache=False, validate=True)[source]¶
Retrieve crystallographic properties such as unit cell dimensions and space group for a PDB entry.
- tooluniverse.tools.get_cupy_info(*, stream_callback=None, use_cache=False, validate=True)[source]¶
Get information about the cupy package. NumPy-compatible array library accelerated with CUDA
- tooluniverse.tools.get_cyvcf2_info(include_examples, *, stream_callback=None, use_cache=False, validate=True)[source]¶
Get comprehensive information about cyvcf2 – fast VCF/BCF file processing
- tooluniverse.tools.get_dask_info(*, stream_callback=None, use_cache=False, validate=True)[source]¶
Get information about the dask package. Parallel computing with task scheduling
- tooluniverse.tools.get_datamol_info(*, stream_callback=None, use_cache=False, validate=True)[source]¶
Get information about the datamol package. Molecular manipulation made easy
- tooluniverse.tools.get_datashader_info(*, stream_callback=None, use_cache=False, validate=True)[source]¶
Get information about the datashader package. Graphics pipeline system for creating meaningful vi…
- tooluniverse.tools.get_deepchem_info(include_examples, *, stream_callback=None, use_cache=False, validate=True)[source]¶
Get comprehensive information about DeepChem – an open-source toolkit that brings advanced AI/ML …
- tooluniverse.tools.get_deeppurpose_info(info_type, *, stream_callback=None, use_cache=False, validate=True)[source]¶
Get comprehensive information about DeepPurpose – deep learning toolkit for drug discovery
- tooluniverse.tools.get_deeptools_info(info_type, *, stream_callback=None, use_cache=False, validate=True)[source]¶
Get comprehensive information about deepTools – deep sequencing data processing
- tooluniverse.tools.get_deepxde_info(include_examples, *, stream_callback=None, use_cache=False, validate=True)[source]¶
Get comprehensive information about DeepXDE – a library for physics-informed neural networks (PIN…
- tooluniverse.tools.get_dendropy_info(*, stream_callback=None, use_cache=False, validate=True)[source]¶
Get information about the dendropy package. Python package: dendropy
- tooluniverse.tools.get_descriptastorus_info(info_type, *, stream_callback=None, use_cache=False, validate=True)[source]¶
Get comprehensive information about Descriptastorus – molecular descriptor calculation
- tooluniverse.tools.get_diffdock_info(info_type, *, stream_callback=None, use_cache=False, validate=True)[source]¶
Get comprehensive information about DiffDock – diffusion model for molecular docking
- tooluniverse.tools.get_dscribe_info(include_examples, *, stream_callback=None, use_cache=False, validate=True)[source]¶
Get comprehensive information about DScribe – a library for generating machine-learning descripto…
- tooluniverse.tools.get_ec_number_by_entity_id(entity_id, *, stream_callback=None, use_cache=False, validate=True)[source]¶
Retrieve the Enzyme Commission (EC) number(s) for an entity.
- tooluniverse.tools.get_elephant_info(*, stream_callback=None, use_cache=False, validate=True)[source]¶
Get information about the elephant package. Electrophysiology analysis toolkit
- tooluniverse.tools.get_em_3d_fitting_and_reconstruction_details(pdb_id, *, stream_callback=None, use_cache=False, validate=True)[source]¶
Retrieve EM 3D fitting model details and associated 3D reconstruction info for a given PDB entry.
- tooluniverse.tools.get_emdb_ids_by_pdb_id(pdb_id, *, stream_callback=None, use_cache=False, validate=True)[source]¶
Retrieve Electron Microscopy Data Bank (EMDB) identifiers linked to a PDB entry.
- tooluniverse.tools.get_episcanpy_info(*, stream_callback=None, use_cache=False, validate=True)[source]¶
Get information about the episcanpy package. Epigenomics single cell analysis in Python
- tooluniverse.tools.get_ete3_info(*, stream_callback=None, use_cache=False, validate=True)[source]¶
Get information about the ete3 package. Python package: ete3
- tooluniverse.tools.get_faiss_info(include_examples, *, stream_callback=None, use_cache=False, validate=True)[source]¶
Get comprehensive information about Faiss – efficient similarity search and clustering
- tooluniverse.tools.get_fanc_info(info_type, *, stream_callback=None, use_cache=False, validate=True)[source]¶
Get comprehensive information about FAN-C – framework for analyzing nuclear contacts
- tooluniverse.tools.get_flask_info(include_examples, *, stream_callback=None, use_cache=False, validate=True)[source]¶
Get comprehensive information about Flask - a lightweight WSGI web application framework
- tooluniverse.tools.get_flowio_info(info_type, *, stream_callback=None, use_cache=False, validate=True)[source]¶
Get comprehensive information about FlowIO – FCS file I/O for flow cytometry
- tooluniverse.tools.get_flowkit_info(info_type, *, stream_callback=None, use_cache=False, validate=True)[source]¶
Get comprehensive information about FlowKit – flow cytometry analysis toolkit
- tooluniverse.tools.get_flowutils_info(info_type, *, stream_callback=None, use_cache=False, validate=True)[source]¶
Get comprehensive information about FlowUtils – flow cytometry utilities and algorithms
- tooluniverse.tools.get_freesasa_info(*, stream_callback=None, use_cache=False, validate=True)[source]¶
Get information about the freesasa package. Calculate solvent accessible surface areas of proteins
- tooluniverse.tools.get_galpy_info(*, stream_callback=None, use_cache=False, validate=True)[source]¶
Get information about the galpy package. Galactic dynamics library
- tooluniverse.tools.get_gene_name_by_entity_id(entity_id, *, stream_callback=None, use_cache=False, validate=True)[source]¶
Retrieve gene name(s) associated with a polymer entity.
- tooluniverse.tools.get_geopandas_info(*, stream_callback=None, use_cache=False, validate=True)[source]¶
Get information about the geopandas package. Geospatial data manipulation and analysis
- tooluniverse.tools.get_gget_info(include_examples, *, stream_callback=None, use_cache=False, validate=True)[source]¶
Get comprehensive information about gget – genomics command-line tool and Python package
- tooluniverse.tools.get_googlesearch_python_info(info_type, *, stream_callback=None, use_cache=False, validate=True)[source]¶
Get comprehensive information about googlesearch-python – Google search automation
- tooluniverse.tools.get_gseapy_info(include_examples, *, stream_callback=None, use_cache=False, validate=True)[source]¶
Get comprehensive information about GSEApy – Gene Set Enrichment Analysis in Python
- tooluniverse.tools.get_h5py_info(include_examples, *, stream_callback=None, use_cache=False, validate=True)[source]¶
Get comprehensive information about h5py – HDF5 for Python
- tooluniverse.tools.get_harmony_pytorch_info(info_type, *, stream_callback=None, use_cache=False, validate=True)[source]¶
Get comprehensive information about harmony-pytorch – single-cell data integration
- tooluniverse.tools.get_hmmlearn_info(info_type, *, stream_callback=None, use_cache=False, validate=True)[source]¶
Get comprehensive information about hmmlearn – Hidden Markov Models in Python
- tooluniverse.tools.get_holoviews_info(*, stream_callback=None, use_cache=False, validate=True)[source]¶
Get information about the holoviews package. Declarative data visualization in Python
- tooluniverse.tools.get_host_organism_by_pdb_id(pdb_id, *, stream_callback=None, use_cache=False, validate=True)[source]¶
Get the host organism used for protein expression in a PDB entry.
- tooluniverse.tools.get_htmd_info(*, stream_callback=None, use_cache=False, validate=True)[source]¶
Get information about the htmd package. High throughput molecular dynamics platform
- tooluniverse.tools.get_hyperopt_info(include_examples, *, stream_callback=None, use_cache=False, validate=True)[source]¶
Get comprehensive information about Hyperopt – distributed hyperparameter optimization
- tooluniverse.tools.get_igraph_info(include_examples, *, stream_callback=None, use_cache=False, validate=True)[source]¶
Get comprehensive information about igraph – network analysis and visualization
- tooluniverse.tools.get_imageio_info(*, stream_callback=None, use_cache=False, validate=True)[source]¶
Get information about the imageio package. Python library for reading and writing image data
- tooluniverse.tools.get_imbalanced_learn_info(*, stream_callback=None, use_cache=False, validate=True)[source]¶
Get information about the imbalanced-learn package. Python toolbox for imbalanced dataset learning
- tooluniverse.tools.get_jcvi_info(info_type, *, stream_callback=None, use_cache=False, validate=True)[source]¶
Get comprehensive information about JCVI – genome assembly and comparative genomics
- tooluniverse.tools.get_joblib_info(*, stream_callback=None, use_cache=False, validate=True)[source]¶
Get information about the joblib package. Lightweight pipelining with Python functions
- tooluniverse.tools.get_joint_associated_diseases_by_HPO_ID_list(HPO_ID_list, limit=None, offset=None, *, stream_callback=None, use_cache=False, validate=True)[source]¶
Retrieve diseases associated with a list of phenotypes or symptoms by a list of HPO IDs.
- tooluniverse.tools.get_khmer_info(info_type, *, stream_callback=None, use_cache=False, validate=True)[source]¶
Get comprehensive information about khmer – nucleotide sequence k-mer analysis
- tooluniverse.tools.get_kipoiseq_info(*, stream_callback=None, use_cache=False, validate=True)[source]¶
Get information about the kipoiseq package. Kipoi sequence utilities for genomics deep learning
- tooluniverse.tools.get_lifelines_info(include_examples, *, stream_callback=None, use_cache=False, validate=True)[source]¶
Get comprehensive information about lifelines – survival analysis in Python
- tooluniverse.tools.get_ligand_bond_count_by_pdb_id(pdb_id, *, stream_callback=None, use_cache=False, validate=True)[source]¶
Get the number of bonds for each ligand in a given PDB structure.
- tooluniverse.tools.get_ligand_smiles_by_chem_comp_id(chem_comp_id, *, stream_callback=None, use_cache=False, validate=True)[source]¶
Retrieve the SMILES chemical structure string for a given chemical component (ligand) ID.
- tooluniverse.tools.get_lightgbm_info(*, stream_callback=None, use_cache=False, validate=True)[source]¶
Get information about the lightgbm package. Fast gradient boosting framework
- tooluniverse.tools.get_loompy_info(info_type, *, stream_callback=None, use_cache=False, validate=True)[source]¶
Get comprehensive information about loompy – efficient storage for large omics datasets
- tooluniverse.tools.get_mageck_info(info_type, *, stream_callback=None, use_cache=False, validate=True)[source]¶
Get comprehensive information about MAGeCK – CRISPR screen analysis toolkit
- tooluniverse.tools.get_matplotlib_info(include_examples, *, stream_callback=None, use_cache=False, validate=True)[source]¶
Get comprehensive information about Matplotlib – comprehensive library for creating visualization…
- tooluniverse.tools.get_mdanalysis_info(info_type, *, stream_callback=None, use_cache=False, validate=True)[source]¶
Get comprehensive information about MDAnalysis – molecular dynamics trajectory analysis
- tooluniverse.tools.get_mdtraj_info(*, stream_callback=None, use_cache=False, validate=True)[source]¶
Get information about the mdtraj package. Modern library for molecular dynamics trajectory analysis
- tooluniverse.tools.get_mne_info(*, stream_callback=None, use_cache=False, validate=True)[source]¶
Get information about the mne package. MEG and EEG data analysis
- tooluniverse.tools.get_molfeat_info(*, stream_callback=None, use_cache=False, validate=True)[source]¶
Get information about the molfeat package. Simple and robust molecular featurization
- tooluniverse.tools.get_molvs_info(*, stream_callback=None, use_cache=False, validate=True)[source]¶
Get information about the molvs package. Molecule validation and standardization
- tooluniverse.tools.get_mordred_info(*, stream_callback=None, use_cache=False, validate=True)[source]¶
Get information about the mordred package. Molecular descriptor calculator
- tooluniverse.tools.get_msprime_info(include_examples, *, stream_callback=None, use_cache=False, validate=True)[source]¶
Get comprehensive information about msprime – coalescent simulation framework
- tooluniverse.tools.get_mudata_info(include_examples, *, stream_callback=None, use_cache=False, validate=True)[source]¶
Get comprehensive information about MuData – multimodal annotated data for computational biology
- tooluniverse.tools.get_mutation_annotations_by_pdb_id(pdb_id, *, stream_callback=None, use_cache=False, validate=True)[source]¶
Retrieve mutation annotations for a given PDB structure.
- tooluniverse.tools.get_neo_info(*, stream_callback=None, use_cache=False, validate=True)[source]¶
Get information about the neo package. Representation of electrophysiology data
- tooluniverse.tools.get_netcdf4_info(*, stream_callback=None, use_cache=False, validate=True)[source]¶
Get information about the netcdf4 package. Python interface to netCDF C library
- tooluniverse.tools.get_networkx_info(info_type, *, stream_callback=None, use_cache=False, validate=True)[source]¶
Get comprehensive information about NetworkX – network analysis library
- tooluniverse.tools.get_nglview_info(*, stream_callback=None, use_cache=False, validate=True)[source]¶
Get information about the nglview package. Jupyter widget for molecular visualization
- tooluniverse.tools.get_nilearn_info(*, stream_callback=None, use_cache=False, validate=True)[source]¶
Get information about the nilearn package. Machine learning for neuroimaging
- tooluniverse.tools.get_numba_info(info_type, *, stream_callback=None, use_cache=False, validate=True)[source]¶
Get comprehensive information about Numba – JIT compiler for Python
- tooluniverse.tools.get_numpy_info(include_examples, *, stream_callback=None, use_cache=False, validate=True)[source]¶
Get comprehensive information about NumPy - the fundamental package for scientific computing with…
- tooluniverse.tools.get_oligosaccharide_descriptors_by_entity_id(entity_id, *, stream_callback=None, use_cache=False, validate=True)[source]¶
Retrieve structural descriptors for branched entities (e.g., oligosaccharides) in a PDB entry.
- tooluniverse.tools.get_openbabel_info(include_examples, *, stream_callback=None, use_cache=False, validate=True)[source]¶
Get comprehensive information about OpenBabel – chemical format conversion and analysis
- tooluniverse.tools.get_openchem_info(info_type, *, stream_callback=None, use_cache=False, validate=True)[source]¶
Get comprehensive information about OpenChem – deep learning toolkit for drug discovery
- tooluniverse.tools.get_opencv_info(include_examples, *, stream_callback=None, use_cache=False, validate=True)[source]¶
Get comprehensive information about OpenCV-Python – computer vision library
- tooluniverse.tools.get_openmm_info(include_examples, *, stream_callback=None, use_cache=False, validate=True)[source]¶
Get comprehensive information about OpenMM – molecular dynamics simulation toolkit
- tooluniverse.tools.get_optlang_info(info_type, *, stream_callback=None, use_cache=False, validate=True)[source]¶
Get comprehensive information about optlang – optimization language for mathematical programming
- tooluniverse.tools.get_optuna_info(*, stream_callback=None, use_cache=False, validate=True)[source]¶
Get information about the optuna package. Hyperparameter optimization framework
- tooluniverse.tools.get_palantir_info(*, stream_callback=None, use_cache=False, validate=True)[source]¶
Get information about the palantir package. Algorithm for modeling continuous cell state transitions
- tooluniverse.tools.get_pandas_info(include_examples, *, stream_callback=None, use_cache=False, validate=True)[source]¶
Get comprehensive information about pandas - powerful data structures and data analysis tools for…
- tooluniverse.tools.get_patsy_info(*, stream_callback=None, use_cache=False, validate=True)[source]¶
Get information about the patsy package. Python library for describing statistical models
- tooluniverse.tools.get_pdbfixer_info(info_type, *, stream_callback=None, use_cache=False, validate=True)[source]¶
Get comprehensive information about PDBFixer – protein structure preparation tool
- tooluniverse.tools.get_phenotype_by_HPO_ID(id, *, stream_callback=None, use_cache=False, validate=True)[source]¶
Retrieve a phenotype or symptom by its HPO ID.
- tooluniverse.tools.get_pillow_info(*, stream_callback=None, use_cache=False, validate=True)[source]¶
Get information about the pillow package. Python Imaging Library fork
- tooluniverse.tools.get_plantcv_info(info_type, *, stream_callback=None, use_cache=False, validate=True)[source]¶
Get comprehensive information about PlantCV – plant phenotyping with image analysis
- tooluniverse.tools.get_plip_info(info_type, *, stream_callback=None, use_cache=False, validate=True)[source]¶
Get comprehensive information about PLIP – protein-ligand interaction profiler
- tooluniverse.tools.get_plotly_info(*, stream_callback=None, use_cache=False, validate=True)[source]¶
Get information about the plotly package. Interactive plotting library for Python
- tooluniverse.tools.get_poliastro_info(info_type, *, stream_callback=None, use_cache=False, validate=True)[source]¶
Get comprehensive information about poliastro – astrodynamics library
- tooluniverse.tools.get_polymer_entity_annotations(entity_id, *, stream_callback=None, use_cache=False, validate=True)[source]¶
Retrieve functional annotations (Pfam domains, GO terms) and associated UniProt accession IDs for…
- tooluniverse.tools.get_polymer_entity_count_by_pdb_id(pdb_id, *, stream_callback=None, use_cache=False, validate=True)[source]¶
Get the number of distinct polymer entities (chains) in a structure.
- tooluniverse.tools.get_polymer_entity_ids_by_pdb_id(pdb_id, *, stream_callback=None, use_cache=False, validate=True)[source]¶
List polymer entity IDs for a given PDB ID. Useful for building further queries on individual pol…
- tooluniverse.tools.get_polymer_entity_type_by_entity_id(entity_id, *, stream_callback=None, use_cache=False, validate=True)[source]¶
Get the polymer entity type (e.g., Protein, DNA) using the polymer entity ID.
- tooluniverse.tools.get_polymer_molecular_weight_by_entity_id(entity_id, *, stream_callback=None, use_cache=False, validate=True)[source]¶
Retrieve the molecular weight of a polymer entity.
- tooluniverse.tools.get_poretools_info(*, stream_callback=None, use_cache=False, validate=True)[source]¶
Get information about the poretools package. Python package: poretools
- tooluniverse.tools.get_prody_info(info_type, *, stream_callback=None, use_cache=False, validate=True)[source]¶
Get comprehensive information about ProDy – protein dynamics analysis
- tooluniverse.tools.get_protein_classification_by_pdb_id(pdb_id, *, stream_callback=None, use_cache=False, validate=True)[source]¶
Get the classification of the protein structure (e.g., transferase, oxidoreductase).
- tooluniverse.tools.get_protein_metadata_by_pdb_id(pdb_id, *, stream_callback=None, use_cache=False, validate=True)[source]¶
Retrieve basic protein structure metadata, including structure title, experimental method, resolu…
- tooluniverse.tools.get_pubchempy_info(*, stream_callback=None, use_cache=False, validate=True)[source]¶
Get information about the pubchempy package. Python interface for PubChem REST API
- tooluniverse.tools.get_pybedtools_info(include_examples, *, stream_callback=None, use_cache=False, validate=True)[source]¶
Get comprehensive information about pybedtools – Python wrapper for BEDTools
- tooluniverse.tools.get_pybigwig_info(info_type, *, stream_callback=None, use_cache=False, validate=True)[source]¶
Get comprehensive information about pyBigWig – BigWig file access in Python
- tooluniverse.tools.get_pydeseq2_info(info_type, *, stream_callback=None, use_cache=False, validate=True)[source]¶
Get comprehensive information about PyDESeq2 – RNA-seq differential expression analysis
- tooluniverse.tools.get_pyensembl_info(*, stream_callback=None, use_cache=False, validate=True)[source]¶
Get information about the pyensembl package. Python interface to Ensembl reference genome metadata
- tooluniverse.tools.get_pyephem_info(*, stream_callback=None, use_cache=False, validate=True)[source]¶
Get information about the pyephem package. Astronomical computations for Python
- tooluniverse.tools.get_pyfaidx_info(include_examples, *, stream_callback=None, use_cache=False, validate=True)[source]¶
Get comprehensive information about pyfaidx – efficient FASTA file indexing and random access
- tooluniverse.tools.get_pyfasta_info(*, stream_callback=None, use_cache=False, validate=True)[source]¶
Get information about the pyfasta package. Python library for efficient random access to fasta su…
- tooluniverse.tools.get_pykalman_info(info_type, *, stream_callback=None, use_cache=False, validate=True)[source]¶
Get comprehensive information about PyKalman – Kalman filtering and smoothing
- tooluniverse.tools.get_pyliftover_info(include_examples, *, stream_callback=None, use_cache=False, validate=True)[source]¶
Get comprehensive information about PyLiftover – genomic coordinate conversion between assemblies
- tooluniverse.tools.get_pymassspec_info(info_type, *, stream_callback=None, use_cache=False, validate=True)[source]¶
Get comprehensive information about PyMassSpec – mass spectrometry data analysis
- tooluniverse.tools.get_pymed_info(include_examples, *, stream_callback=None, use_cache=False, validate=True)[source]¶
Get comprehensive information about PyMed – PubMed access in Python
- tooluniverse.tools.get_pymzml_info(info_type, *, stream_callback=None, use_cache=False, validate=True)[source]¶
Get comprehensive information about pymzML – mzML file parser for mass spectrometry
- tooluniverse.tools.get_pypdf2_info(info_type, *, stream_callback=None, use_cache=False, validate=True)[source]¶
Get comprehensive information about PyPDF2 – PDF manipulation library
- tooluniverse.tools.get_pyranges_info(include_examples, *, stream_callback=None, use_cache=False, validate=True)[source]¶
Get comprehensive information about PyRanges – efficient genomic interval operations
- tooluniverse.tools.get_pyrosetta_info(*, stream_callback=None, use_cache=False, validate=True)[source]¶
Get information about the pyrosetta package. Python interface to Rosetta macromolecular modeling …
- tooluniverse.tools.get_pysam_info(include_examples, *, stream_callback=None, use_cache=False, validate=True)[source]¶
Get comprehensive information about pysam – interface to SAM/BAM/CRAM files
- tooluniverse.tools.get_pyscenic_info(info_type, *, stream_callback=None, use_cache=False, validate=True)[source]¶
Get comprehensive information about pySCENIC – single-cell regulatory network inference
- tooluniverse.tools.get_pyscf_info(include_examples, *, stream_callback=None, use_cache=False, validate=True)[source]¶
Get comprehensive information about PySCF – a versatile quantum-chemistry framework in Python.
- tooluniverse.tools.get_pyscreener_info(info_type, *, stream_callback=None, use_cache=False, validate=True)[source]¶
Get comprehensive information about PyScreener – high-throughput virtual screening in Python
- tooluniverse.tools.get_pytdc_info(info_type, *, stream_callback=None, use_cache=False, validate=True)[source]¶
Get comprehensive information about PyTDC – Therapeutics Data Commons in Python
- tooluniverse.tools.get_python_libsbml_info(info_type, *, stream_callback=None, use_cache=False, validate=True)[source]¶
Get comprehensive information about python-libsbml – SBML (Systems Biology Markup Language) support
- tooluniverse.tools.get_pytorch_info(include_examples, *, stream_callback=None, use_cache=False, validate=True)[source]¶
Get comprehensive information about PyTorch – an open source machine learning framework
- tooluniverse.tools.get_pyvcf_info(*, stream_callback=None, use_cache=False, validate=True)[source]¶
Get information about the pyvcf package. Python library for parsing and manipulating VCF files
- tooluniverse.tools.get_pyvis_info(*, stream_callback=None, use_cache=False, validate=True)[source]¶
Get information about the pyvis package. Python library for visualizing networks
- tooluniverse.tools.get_qutip_info(*, stream_callback=None, use_cache=False, validate=True)[source]¶
Get information about the qutip package. Quantum toolbox in Python
- tooluniverse.tools.get_rasterio_info(*, stream_callback=None, use_cache=False, validate=True)[source]¶
Get information about the rasterio package. Access to geospatial raster data
- tooluniverse.tools.get_rdkit_info(include_examples, *, stream_callback=None, use_cache=False, validate=True)[source]¶
Get comprehensive information about RDKit – cheminformatics and machine learning toolkit
- tooluniverse.tools.get_refinement_resolution_by_pdb_id(pdb_id, *, stream_callback=None, use_cache=False, validate=True)[source]¶
Retrieve the reported resolution from refinement data for X-ray structures.
- tooluniverse.tools.get_release_deposit_dates_by_pdb_id(pdb_id, *, stream_callback=None, use_cache=False, validate=True)[source]¶
Get the release and deposition dates for a PDB entry.
- tooluniverse.tools.get_reportlab_info(include_examples, *, stream_callback=None, use_cache=False, validate=True)[source]¶
Get comprehensive information about ReportLab – PDF generation library
- tooluniverse.tools.get_requests_info(include_examples, *, stream_callback=None, use_cache=False, validate=True)[source]¶
Get comprehensive information about Requests - Python HTTP library for humans
- tooluniverse.tools.get_ruptures_info(info_type, *, stream_callback=None, use_cache=False, validate=True)[source]¶
Get comprehensive information about ruptures – change point detection library
- tooluniverse.tools.get_scanorama_info(*, stream_callback=None, use_cache=False, validate=True)[source]¶
Get information about the scanorama package. Batch correction and integration of single-cell data
- tooluniverse.tools.get_scanpy_info(include_examples, *, stream_callback=None, use_cache=False, validate=True)[source]¶
Get comprehensive information about Scanpy – scalable single-cell analysis in Python
- tooluniverse.tools.get_schnetpack_info(include_examples, *, stream_callback=None, use_cache=False, validate=True)[source]¶
Get comprehensive information about SchNetPack – a deep-learning toolbox for molecules and materi…
- tooluniverse.tools.get_scholarly_info(info_type, *, stream_callback=None, use_cache=False, validate=True)[source]¶
Get comprehensive information about scholarly – Google Scholar data retrieval
- tooluniverse.tools.get_scikit_bio_info(include_examples, *, stream_callback=None, use_cache=False, validate=True)[source]¶
Get comprehensive information about scikit-bio – bioinformatics library built on scientific Pytho…
- tooluniverse.tools.get_scikit_image_info(info_type, *, stream_callback=None, use_cache=False, validate=True)[source]¶
Get comprehensive information about scikit-image – image processing in Python
- tooluniverse.tools.get_scikit_learn_info(include_examples, *, stream_callback=None, use_cache=False, validate=True)[source]¶
Get comprehensive information about scikit-learn – simple and efficient tools for predictive data…
- tooluniverse.tools.get_scipy_info(info_type, *, stream_callback=None, use_cache=False, validate=True)[source]¶
Get comprehensive information about SciPy – fundamental algorithms for scientific computing
- tooluniverse.tools.get_scrublet_info(include_examples, *, stream_callback=None, use_cache=False, validate=True)[source]¶
Get comprehensive information about Scrublet – single-cell doublet detection
- tooluniverse.tools.get_scvelo_info(include_examples, *, stream_callback=None, use_cache=False, validate=True)[source]¶
Get comprehensive information about scVelo – RNA velocity analysis in single cells
- tooluniverse.tools.get_scvi_tools_info(*, stream_callback=None, use_cache=False, validate=True)[source]¶
Get information about the scvi-tools package. Deep probabilistic analysis of single-cell omics data
- tooluniverse.tools.get_seaborn_info(include_examples, *, stream_callback=None, use_cache=False, validate=True)[source]¶
Get comprehensive information about Seaborn – statistical data visualization
- tooluniverse.tools.get_sequence_by_pdb_id(pdb_id, *, stream_callback=None, use_cache=False, validate=True)[source]¶
Retrieve amino acid or nucleotide sequence of polymer entities for a given PDB structure.
- tooluniverse.tools.get_sequence_lengths_by_pdb_id(pdb_id, *, stream_callback=None, use_cache=False, validate=True)[source]¶
Retrieve the sequence lengths of polymer entities for a given PDB structure.
- tooluniverse.tools.get_sequence_positional_features_by_instance_id(instance_id, *, stream_callback=None, use_cache=False, validate=True)[source]¶
Retrieve sequence positional features (e.g., binding sites, motifs) for a polymer entity instance.
- tooluniverse.tools.get_skopt_info(*, stream_callback=None, use_cache=False, validate=True)[source]¶
Get information about the skopt package. Scikit-Optimize: sequential model-based optimization
- tooluniverse.tools.get_souporcell_info(info_type, *, stream_callback=None, use_cache=False, validate=True)[source]¶
Get comprehensive information about souporcell – scRNA-seq genotype clustering
- tooluniverse.tools.get_source_organism_by_pdb_id(pdb_id, *, stream_callback=None, use_cache=False, validate=True)[source]¶
Retrieve the scientific name of the source organism for a given PDB structure.
- tooluniverse.tools.get_space_group_by_pdb_id(pdb_id, *, stream_callback=None, use_cache=False, validate=True)[source]¶
Get the crystallographic space group of the structure.
- tooluniverse.tools.get_statsmodels_info(include_examples, *, stream_callback=None, use_cache=False, validate=True)[source]¶
Get comprehensive information about statsmodels – statistical modeling and econometrics
- tooluniverse.tools.get_structure_determination_software_by_pdb_id(pdb_id, *, stream_callback=None, use_cache=False, validate=True)[source]¶
Retrieve names of software used during structure determination.
- tooluniverse.tools.get_structure_title_by_pdb_id(pdb_id, *, stream_callback=None, use_cache=False, validate=True)[source]¶
Retrieve the structure title for a given PDB entry.
- tooluniverse.tools.get_structure_validation_metrics_by_pdb_id(pdb_id, *, stream_callback=None, use_cache=False, validate=True)[source]¶
Retrieve structure validation metrics such as R-free, R-work, and clashscore for a PDB entry.
- tooluniverse.tools.get_sunpy_info(*, stream_callback=None, use_cache=False, validate=True)[source]¶
Get information about the sunpy package. Solar data analysis library
- tooluniverse.tools.get_sympy_info(info_type, *, stream_callback=None, use_cache=False, validate=True)[source]¶
Get comprehensive information about SymPy – symbolic mathematics library
- tooluniverse.tools.get_target_cofactor_info(pdb_id, *, stream_callback=None, use_cache=False, validate=True)[source]¶
Retrieve essential cofactor information for a given target including cofactor IDs, mechanism of a…
- tooluniverse.tools.get_taxonomy_by_pdb_id(pdb_id, *, stream_callback=None, use_cache=False, validate=True)[source]¶
Get the scientific name and taxonomy of the organism(s) associated with a PDB entry.
- tooluniverse.tools.get_tiledb_info(info_type, *, stream_callback=None, use_cache=False, validate=True)[source]¶
Get comprehensive information about TileDB – modern database for array data
- tooluniverse.tools.get_tiledbsoma_info(info_type, *, stream_callback=None, use_cache=False, validate=True)[source]¶
Get comprehensive information about TileDB-SOMA – single-cell data storage with TileDB
- tooluniverse.tools.get_torch_geometric_info(include_examples, *, stream_callback=None, use_cache=False, validate=True)[source]¶
Get comprehensive information about PyTorch Geometric – a high-performance library for graph neur…
- tooluniverse.tools.get_tqdm_info(include_examples, *, stream_callback=None, use_cache=False, validate=True)[source]¶
Get comprehensive information about tqdm – fast progress bars for Python
- tooluniverse.tools.get_trackpy_info(info_type, *, stream_callback=None, use_cache=False, validate=True)[source]¶
Get comprehensive information about trackpy – particle tracking toolkit for Python
- tooluniverse.tools.get_tskit_info(info_type, *, stream_callback=None, use_cache=False, validate=True)[source]¶
Get comprehensive information about tskit – tree sequence toolkit for population genetics
- tooluniverse.tools.get_umap_learn_info(include_examples, *, stream_callback=None, use_cache=False, validate=True)[source]¶
Get comprehensive information about UMAP-learn – dimensionality reduction technique
- tooluniverse.tools.get_uniprot_accession_by_entity_id(entity_id, *, stream_callback=None, use_cache=False, validate=True)[source]¶
Fetch UniProt accession numbers associated with a specific polymer entity.
- tooluniverse.tools.get_velocyto_info(*, stream_callback=None, use_cache=False, validate=True)[source]¶
Get information about the velocyto package. RNA velocity analysis for single cell RNA-seq data
- tooluniverse.tools.get_viennarna_info(include_examples, *, stream_callback=None, use_cache=False, validate=True)[source]¶
Get comprehensive information about ViennaRNA – RNA structure prediction and analysis
- tooluniverse.tools.get_webpage_text_from_url(url, timeout, *, stream_callback=None, use_cache=False, validate=True)[source]¶
Render a URL as PDF and extract its text (JavaScript supported).
- tooluniverse.tools.get_webpage_title(url, timeout, *, stream_callback=None, use_cache=False, validate=True)[source]¶
Fetch a webpage and return the content of its <title> tag.
- Parameters:
- Return type:
Any
- tooluniverse.tools.get_xarray_info(*, stream_callback=None, use_cache=False, validate=True)[source]¶
Get information about the xarray package. N-D labeled arrays and datasets in Python
- tooluniverse.tools.get_xesmf_info(*, stream_callback=None, use_cache=False, validate=True)[source]¶
Get information about the xesmf package. Universal regridder for geospatial data
- tooluniverse.tools.get_xgboost_info(*, stream_callback=None, use_cache=False, validate=True)[source]¶
Get information about the xgboost package. Optimized gradient boosting framework
- tooluniverse.tools.get_zarr_info(*, stream_callback=None, use_cache=False, validate=True)[source]¶
Get information about the zarr package. Chunked, compressed, N-dimensional arrays
- tooluniverse.tools.gnomAD_query_variant(variant_id, dataset='gnomad_r4', *, stream_callback=None, use_cache=False, validate=True)[source]¶
Query gnomAD GraphQL for a variant in a dataset (returns ID and genome allele counts/frequency).
- Parameters:
- Return type:
dict[str,Any]
- tooluniverse.tools.gwas_get_association_by_id(association_id, *, stream_callback=None, use_cache=False, validate=True)[source]¶
Get a specific GWAS association by its unique identifier.
- tooluniverse.tools.gwas_get_associations_for_snp(rs_id, sort=None, direction=None, size=None, page=None, *, stream_callback=None, use_cache=False, validate=True)[source]¶
Get all associations for a specific SNP with optional sorting.
- Parameters:
- Return type:
dict[str,Any]
- tooluniverse.tools.gwas_get_associations_for_study(accession_id, size=None, page=None, *, stream_callback=None, use_cache=False, validate=True)[source]¶
Get all associations for a specific study, sorted by p-value.
- tooluniverse.tools.gwas_get_associations_for_trait(efo_trait, size=None, page=None, *, stream_callback=None, use_cache=False, validate=True)[source]¶
Get all associations for a specific trait, sorted by p-value (most significant first).
- tooluniverse.tools.gwas_get_snp_by_id(rs_id, *, stream_callback=None, use_cache=False, validate=True)[source]¶
Get a specific GWAS SNP by its rs ID.
- tooluniverse.tools.gwas_get_snps_for_gene(mapped_gene, size=None, page=None, *, stream_callback=None, use_cache=False, validate=True)[source]¶
Get all SNPs mapped to a specific gene.
- Parameters:
- Return type:
dict[str,Any]
- tooluniverse.tools.gwas_get_studies_for_trait(efo_trait=None, disease_trait=None, cohort=None, gxe=None, full_pvalue_set=None, size=None, page=None, *, stream_callback=None, use_cache=False, validate=True)[source]¶
Get studies for a specific trait with optional filters for cohort, GxE interactions, and summary …
- Parameters:
efo_trait (
str) – EFO trait identifier or namedisease_trait (
str) – Disease trait namecohort (
str) – Cohort name (e.g., ‘UKB’ for UK Biobank)gxe (
bool) – Filter for Gene-by-Environment interaction studiesfull_pvalue_set (
bool) – Filter for studies with full summary statisticssize (
int) – Number of results to return per pagepage (
int) – Page number for paginationstream_callback (
Callable, optional) – Callback for streaming output
- Return type:
dict[str,Any]
- tooluniverse.tools.gwas_get_study_by_id(study_id, *, stream_callback=None, use_cache=False, validate=True)[source]¶
Get a specific GWAS study by its unique identifier.
- tooluniverse.tools.gwas_get_variants_for_trait(efo_trait, size=None, page=None, *, stream_callback=None, use_cache=False, validate=True)[source]¶
Get all variants associated with a specific trait with pagination support.
- tooluniverse.tools.gwas_search_associations(efo_trait=None, rs_id=None, accession_id=None, sort=None, direction=None, size=None, page=None, *, stream_callback=None, use_cache=False, validate=True)[source]¶
Search for GWAS associations by various criteria including EFO trait, rs ID, accession ID, with s…
- Parameters:
efo_trait (
str) – EFO trait identifier or namers_id (
str) – dbSNP rs identifieraccession_id (
str) – Study accession identifiersort (
str) – Sort field (e.g., ‘p_value’, ‘or_value’)direction (
str) – Sort direction (‘asc’ or ‘desc’)size (
int) – Number of results to returnpage (
int) – Page number for paginationstream_callback (
Callable, optional) – Callback for streaming output
- Return type:
dict[str,Any]
- tooluniverse.tools.gwas_search_snps(rs_id=None, mapped_gene=None, size=None, page=None, *, stream_callback=None, use_cache=False, validate=True)[source]¶
Search for GWAS single nucleotide polymorphisms (SNPs) by rs ID or mapped gene.
- tooluniverse.tools.gwas_search_studies(efo_trait=None, disease_trait=None, cohort=None, gxe=None, full_pvalue_set=None, size=None, page=None, *, stream_callback=None, use_cache=False, validate=True)[source]¶
Search for GWAS studies by various criteria including EFO trait, disease trait, cohort, GxE inter…
- Parameters:
efo_trait (
str) – EFO trait identifier or namedisease_trait (
str) – Disease trait namecohort (
str) – Cohort name (e.g., ‘UKB’ for UK Biobank)gxe (
bool) – Filter for Gene-by-Environment interaction studiesfull_pvalue_set (
bool) – Filter for studies with full summary statisticssize (
int) – Number of results to returnpage (
int) – Page number for paginationstream_callback (
Callable, optional) – Callback for streaming output
- Return type:
dict[str,Any]
- tooluniverse.tools.humanbase_ppi_analysis(gene_list, tissue, max_node, interaction, string_mode, *, stream_callback=None, use_cache=False, validate=True)[source]¶
Retrieve tissue-specific protein-protein interactions and biological processes from HumanBase. Re…
- Parameters:
gene_list (
list[Any]) – List of gene names or symbols to analyze for protein-protein interactions. Th…tissue (
str) – Tissue type for tissue-specific interactions. Examples: ‘brain’, ‘heart’, ‘li…max_node (
int) – Maximum number of nodes to retrieve in the interaction network. Warning: the …interaction (
str) – Specific interaction type to filter by. Available types: ‘co-expression’, ‘in…string_mode (
bool) – Whether to return the result in string mode. If True, the result will be a st…stream_callback (
Callable, optional) – Callback for streaming output
- Return type:
Any
- tooluniverse.tools.mesh_get_subjects_by_pharmacological_action(query, case_sensitive, exact_match, limit, *, stream_callback=None, use_cache=False, validate=True)[source]¶
Find MeSH (Medical Subject Heading) subjects with matching pharmacological actions.
- Parameters:
query (
str) – Pharmacological action to search for in MeSH subjectscase_sensitive (
bool) – Select True to perform a case-sensitive search for the pharmacological action…exact_match (
bool) – Select True to require an exact match for the pharmacological action querylimit (
int) – Maximum number of results to returnstream_callback (
Callable, optional) – Callback for streaming output
- Return type:
dict[str,Any]
- tooluniverse.tools.mesh_get_subjects_by_subject_id(query, case_sensitive, exact_match, limit, *, stream_callback=None, use_cache=False, validate=True)[source]¶
Find MeSH (Medical Subject Heading) subjects with a matching subject ID (also called Descriptor UI).
- Parameters:
query (
str) – Query ID to search for among the MeSH subject IDscase_sensitive (
bool) – Select True to perform a case-sensitive search for the queryexact_match (
bool) – Select True to require an exact match for the querylimit (
int) – Maximum number of results to returnstream_callback (
Callable, optional) – Callback for streaming output
- Return type:
dict[str,Any]
- tooluniverse.tools.mesh_get_subjects_by_subject_name(query, case_sensitive, exact_match, limit, *, stream_callback=None, use_cache=False, validate=True)[source]¶
Find MeSH (Medical Subject Heading) subjects with matching names.
- Parameters:
query (
str) – Query string to search for in the name of each MeSH subject and the names of …case_sensitive (
bool) – Select True to perform a case-sensitive search for the queryexact_match (
bool) – Select True to require an exact match for the querylimit (
int) – Maximum number of results to returnstream_callback (
Callable, optional) – Callback for streaming output
- Return type:
dict[str,Any]
- tooluniverse.tools.mesh_get_subjects_by_subject_scope_or_definition(query, case_sensitive, exact_match, limit, *, stream_callback=None, use_cache=False, validate=True)[source]¶
Find MeSH (Medical Subject Heading) subjects with matching scopes (definitions).
- Parameters:
query (
str) – Query string to search for in the scope notes of MeSH subjectscase_sensitive (
bool) – Select True to perform a case-sensitive search for the queryexact_match (
bool) – Select True to require an exact match for the querylimit (
int) – Maximum number of results to returnstream_callback (
Callable, optional) – Callback for streaming output
- Return type:
dict[str,Any]
- tooluniverse.tools.odphp_itemlist(lang, type, *, stream_callback=None, use_cache=False, validate=True)[source]¶
This tools browses and returns available topics and categories and it is helpful to help narrow a…
- tooluniverse.tools.odphp_myhealthfinder(lang, age, sex, pregnant, strip_html, *, stream_callback=None, use_cache=False, validate=True)[source]¶
This tool provides personalized preventive-care recommendations and it is helpful for different a…
- Parameters:
- Return type:
dict[str,Any]
- tooluniverse.tools.odphp_outlink_fetch(urls, max_chars, return_html, *, stream_callback=None, use_cache=False, validate=True)[source]¶
This tool retrieves readable text from ODPHP article links and information sources. This is helpf…
- Parameters:
- Return type:
dict[str,Any]
- tooluniverse.tools.odphp_topicsearch(lang, topicId, categoryId, keyword, strip_html, *, stream_callback=None, use_cache=False, validate=True)[source]¶
Find specific health topics and get their full content. Use when the user mentions a keyword (e.g…
- Parameters:
lang (
str) – Language code (en or es)topicId (
str) – Comma-separated topic IDscategoryId (
str) – Comma-separated category IDskeyword (
str) – Keyword search for topicsstrip_html (
bool) – If true, also return PlainSections[] with HTML removed for each topicstream_callback (
Callable, optional) – Callback for streaming output
- Return type:
dict[str,Any]
- tooluniverse.tools.openalex_literature_search(search_keywords, max_results=10, year_from=None, year_to=None, open_access=None, *, stream_callback=None, use_cache=False, validate=True)[source]¶
Search for academic literature using OpenAlex API. Retrieves papers with title, abstract, authors…
- Parameters:
search_keywords (
str) – Keywords to search for in paper titles, abstracts, and content. Use relevant …max_results (
int) – Maximum number of papers to retrieve (default: 10, maximum: 200).year_from (
int) – Start year for publication date filter (e.g., 2020). Optional parameter to li…year_to (
int) – End year for publication date filter (e.g., 2023). Optional parameter to limi…open_access (
bool) – Filter for open access papers only. Set to true for open access papers, false…stream_callback (
Callable, optional) – Callback for streaming output
- Return type:
list[Any]
- tooluniverse.tools.reactome_disease_target_score(efoId, pageSize, *, stream_callback=None, use_cache=False, validate=True)[source]¶
Extract disease-target association scores from Reactome pathway data. This includes pathway-based…
- tooluniverse.tools.search_clinical_trials(query_term, condition=None, intervention=None, pageSize=None, pageToken=None, *, stream_callback=None, use_cache=False, validate=True)[source]¶
Search for clinical trials registered on clinicaltrials.gov based on title, conditions, intervent…
- Parameters:
condition (
str) – Query for condition or disease using Essie expression syntax (e.g., ‘lung can…intervention (
str) – Query for intervention/treatment using Essie expression syntax (e.g., ‘chemot…query_term (
str) – Query for ‘other terms’ with Essie expression syntax (e.g., ‘combination’, ‘A…pageSize (
int) – Maximum number of studies to return per page (default 10, max 1000).pageToken (
str) – Token to retrieve the next page of results, obtained from the ‘nextPageToken’…stream_callback (
Callable, optional) – Callback for streaming output
- Return type:
Any
- tooluniverse.tools.visualize_molecule_2d(smiles, inchi, molecule_name, width=400, height=400, output_format='png', show_atom_numbers=False, show_bond_numbers=False, include_stereo=True, *, stream_callback=None, use_cache=False, validate=True)[source]¶
Visualize 2D molecular structures using RDKit. Supports SMILES, InChI, molecule names, and variou…
- Parameters:
smiles (
str) – SMILES string representation of the moleculeinchi (
str) – InChI string representation of the moleculemolecule_name (
str) – Common name of the molecule (will be resolved to SMILES via PubChem)width (
int) – Width of the visualization in pixelsheight (
int) – Height of the visualization in pixelsoutput_format (
str) – Output formatshow_atom_numbers (
bool) – Whether to show atom numbersshow_bond_numbers (
bool) – Whether to show bond numbersinclude_stereo (
bool) – Whether to include stereochemistry informationstream_callback (
Callable, optional) – Callback for streaming output
- Return type:
dict[str,Any]
- tooluniverse.tools.visualize_molecule_3d(smiles, mol_content, sdf_content, style='stick', color_scheme='default', width=800, height=600, show_hydrogens=True, show_surface=False, generate_conformers=True, conformer_count=1, *, stream_callback=None, use_cache=False, validate=True)[source]¶
Visualize 3D molecular structures using RDKit and py3Dmol. Supports SMILES, MOL files, SDF conten…
- Parameters:
smiles (
str) – SMILES string representation of the moleculemol_content (
str) – MOL file content as stringsdf_content (
str) – SDF file content as stringstyle (
str) – Visualization stylecolor_scheme (
str) – Color scheme for the moleculewidth (
int) – Width of the visualization in pixelsheight (
int) – Height of the visualization in pixelsshow_hydrogens (
bool) – Whether to show hydrogen atomsshow_surface (
bool) – Whether to show molecular surfacegenerate_conformers (
bool) – Whether to generate multiple conformersconformer_count (
int) – Number of conformers to generatestream_callback (
Callable, optional) – Callback for streaming output
- Return type:
dict[str,Any]
- tooluniverse.tools.visualize_protein_structure_3d(pdb_id, pdb_content, style='cartoon', color_scheme='spectrum', width=800, height=600, show_sidechains=False, show_surface=False, *, stream_callback=None, use_cache=False, validate=True)[source]¶
Visualize 3D protein structures using py3Dmol. Supports PDB IDs, PDB file content, and various vi…
- Parameters:
pdb_id (
str) – PDB identifier (e.g., ‘1CRN’, ‘7CGO’). Either pdb_id or pdb_content must be p…pdb_content (
str) – Raw PDB file content as string. Either pdb_id or pdb_content must be provided.style (
str) – Visualization stylecolor_scheme (
str) – Color scheme for the structurewidth (
int) – Width of the visualization in pixelsheight (
int) – Height of the visualization in pixelsshow_sidechains (
bool) – Whether to show sidechain atomsshow_surface (
bool) – Whether to show molecular surfacestream_callback (
Callable, optional) – Callback for streaming output
- Return type:
dict[str,Any]
Submodules¶
- tooluniverse.tools.ADMETAI_predict_BBB_penetrance module
- tooluniverse.tools.ADMETAI_predict_CYP_interactions module
- tooluniverse.tools.ADMETAI_predict_bioavailability module
- tooluniverse.tools.ADMETAI_predict_clearance_distribution module
- tooluniverse.tools.ADMETAI_predict_nuclear_receptor_activity module
- tooluniverse.tools.ADMETAI_predict_physicochemical_properties module
- tooluniverse.tools.ADMETAI_predict_solubility_lipophilicity_hydration module
- tooluniverse.tools.ADMETAI_predict_stress_response module
- tooluniverse.tools.ADMETAI_predict_toxicity module
- tooluniverse.tools.AdvancedCodeQualityAnalyzer module
- tooluniverse.tools.AdverseEventICDMapper module
- tooluniverse.tools.AdverseEventPredictionQuestionGenerator module
- tooluniverse.tools.AdverseEventPredictionQuestionGeneratorWithContext module
- tooluniverse.tools.ArXiv_search_papers module
- tooluniverse.tools.ArgumentDescriptionOptimizer module
- tooluniverse.tools.BioRxiv_search_preprints module
- tooluniverse.tools.BiomarkerDiscoveryWorkflow module
- tooluniverse.tools.CORE_search_papers module
- tooluniverse.tools.CallAgent module
- tooluniverse.tools.ChEMBL_search_similar_molecules module
- tooluniverse.tools.CodeOptimizer module
- tooluniverse.tools.CodeQualityAnalyzer module
- tooluniverse.tools.ComprehensiveDrugDiscoveryPipeline module
- tooluniverse.tools.Crossref_search_works module
- tooluniverse.tools.DBLP_search_publications module
- tooluniverse.tools.DOAJ_search_articles module
- tooluniverse.tools.DailyMed_get_spl_by_setid module
- tooluniverse.tools.DailyMed_search_spls module
- tooluniverse.tools.DataAnalysisValidityReviewer module
- tooluniverse.tools.DescriptionAnalyzer module
- tooluniverse.tools.DescriptionQualityEvaluator module
- tooluniverse.tools.DomainExpertValidator module
- tooluniverse.tools.DrugSafetyAnalyzer module
- tooluniverse.tools.EthicalComplianceReviewer module
- tooluniverse.tools.EuropePMC_Guidelines_Search module
- tooluniverse.tools.EuropePMC_search_articles module
- tooluniverse.tools.ExperimentalDesignScorer module
- tooluniverse.tools.FAERS_count_additive_administration_routes module
- tooluniverse.tools.FAERS_count_additive_adverse_reactions module
- tooluniverse.tools.FAERS_count_additive_event_reports_by_country module
- tooluniverse.tools.FAERS_count_additive_reaction_outcomes module
- tooluniverse.tools.FAERS_count_additive_reports_by_reporter_country module
- tooluniverse.tools.FAERS_count_additive_seriousness_classification module
- tooluniverse.tools.FAERS_count_country_by_drug_event module
- tooluniverse.tools.FAERS_count_death_related_by_drug module
- tooluniverse.tools.FAERS_count_drug_routes_by_event module
- tooluniverse.tools.FAERS_count_drugs_by_drug_event module
- tooluniverse.tools.FAERS_count_outcomes_by_drug_event module
- tooluniverse.tools.FAERS_count_patient_age_distribution module
- tooluniverse.tools.FAERS_count_reactions_by_drug_event module
- tooluniverse.tools.FAERS_count_reportercountry_by_drug_event module
- tooluniverse.tools.FAERS_count_seriousness_by_drug_event module
- tooluniverse.tools.FDA_get_abuse_dependence_info_by_drug_name module
- tooluniverse.tools.FDA_get_abuse_info_by_drug_name module
- tooluniverse.tools.FDA_get_accessories_info_by_drug_name module
- tooluniverse.tools.FDA_get_active_ingredient_info_by_drug_name module
- tooluniverse.tools.FDA_get_adverse_reactions_by_drug_name module
- tooluniverse.tools.FDA_get_alarms_by_drug_name module
- tooluniverse.tools.FDA_get_animal_pharmacology_info_by_drug_name module
- tooluniverse.tools.FDA_get_assembly_installation_info_by_drug_name module
- tooluniverse.tools.FDA_get_boxed_warning_info_by_drug_name module
- tooluniverse.tools.FDA_get_brand_name_generic_name module
- tooluniverse.tools.FDA_get_calibration_instructions_by_drug_name module
- tooluniverse.tools.FDA_get_carcinogenic_mutagenic_fertility_by_drug_name module
- tooluniverse.tools.FDA_get_child_safety_info_by_drug_name module
- tooluniverse.tools.FDA_get_clinical_pharmacology_by_drug_name module
- tooluniverse.tools.FDA_get_clinical_studies_info_by_drug_name module
- tooluniverse.tools.FDA_get_contact_for_questions_info_by_drug_name module
- tooluniverse.tools.FDA_get_contraindications_by_drug_name module
- tooluniverse.tools.FDA_get_controlled_substance_DEA_schedule_info_by_drug_name module
- tooluniverse.tools.FDA_get_dear_health_care_provider_letter_info_by_drug_name module
- tooluniverse.tools.FDA_get_dependence_info_by_drug_name module
- tooluniverse.tools.FDA_get_disposal_info_by_drug_name module
- tooluniverse.tools.FDA_get_do_not_use_info_by_drug_name module
- tooluniverse.tools.FDA_get_document_id_by_drug_name module
- tooluniverse.tools.FDA_get_dosage_and_storage_information_by_drug_name module
- tooluniverse.tools.FDA_get_dosage_forms_and_strengths_by_drug_name module
- tooluniverse.tools.FDA_get_drug_generic_name module
- tooluniverse.tools.FDA_get_drug_interactions_by_drug_name module
- tooluniverse.tools.FDA_get_drug_name_by_SPL_ID module
- tooluniverse.tools.FDA_get_drug_name_by_adverse_reaction module
- tooluniverse.tools.FDA_get_drug_name_by_calibration_instructions module
- tooluniverse.tools.FDA_get_drug_name_by_dependence_info module
- tooluniverse.tools.FDA_get_drug_name_by_document_id module
- tooluniverse.tools.FDA_get_drug_name_by_dosage_info module
- tooluniverse.tools.FDA_get_drug_name_by_environmental_warning module
- tooluniverse.tools.FDA_get_drug_name_by_inactive_ingredient module
- tooluniverse.tools.FDA_get_drug_name_by_info_on_conditions_for_doctor_consultation module
- tooluniverse.tools.FDA_get_drug_name_by_labor_and_delivery_info module
- tooluniverse.tools.FDA_get_drug_name_by_microbiology module
- tooluniverse.tools.FDA_get_drug_name_by_other_safety_info module
- tooluniverse.tools.FDA_get_drug_name_by_pharmacodynamics module
- tooluniverse.tools.FDA_get_drug_name_by_pharmacogenomics module
- tooluniverse.tools.FDA_get_drug_name_by_precautions module
- tooluniverse.tools.FDA_get_drug_name_by_pregnancy_or_breastfeeding_info module
- tooluniverse.tools.FDA_get_drug_name_by_principal_display_panel module
- tooluniverse.tools.FDA_get_drug_name_by_reference module
- tooluniverse.tools.FDA_get_drug_name_by_set_id module
- tooluniverse.tools.FDA_get_drug_name_by_stop_use_info module
- tooluniverse.tools.FDA_get_drug_name_by_storage_and_handling_info module
- tooluniverse.tools.FDA_get_drug_name_by_warnings module
- tooluniverse.tools.FDA_get_drug_name_from_patient_package_insert module
- tooluniverse.tools.FDA_get_drug_names_by_abuse_dependence_info module
- tooluniverse.tools.FDA_get_drug_names_by_abuse_info module
- tooluniverse.tools.FDA_get_drug_names_by_accessories module
- tooluniverse.tools.FDA_get_drug_names_by_active_ingredient module
- tooluniverse.tools.FDA_get_drug_names_by_alarm module
- tooluniverse.tools.FDA_get_drug_names_by_animal_pharmacology_info module
- tooluniverse.tools.FDA_get_drug_names_by_application_number_NDC_number module
- tooluniverse.tools.FDA_get_drug_names_by_assembly_installation_info module
- tooluniverse.tools.FDA_get_drug_names_by_boxed_warning module
- tooluniverse.tools.FDA_get_drug_names_by_child_safety_info module
- tooluniverse.tools.FDA_get_drug_names_by_clinical_pharmacology module
- tooluniverse.tools.FDA_get_drug_names_by_clinical_studies module
- tooluniverse.tools.FDA_get_drug_names_by_consulting_doctor_pharmacist_info module
- tooluniverse.tools.FDA_get_drug_names_by_contraindications module
- tooluniverse.tools.FDA_get_drug_names_by_controlled_substance_DEA_schedule module
- tooluniverse.tools.FDA_get_drug_names_by_dear_health_care_provider_letter_info module
- tooluniverse.tools.FDA_get_drug_names_by_disposal_info module
- tooluniverse.tools.FDA_get_drug_names_by_dosage_forms_and_strengths_info module
- tooluniverse.tools.FDA_get_drug_names_by_drug_interactions module
- tooluniverse.tools.FDA_get_drug_names_by_effective_time module
- tooluniverse.tools.FDA_get_drug_names_by_food_safety_warnings module
- tooluniverse.tools.FDA_get_drug_names_by_general_precautions module
- tooluniverse.tools.FDA_get_drug_names_by_geriatric_use module
- tooluniverse.tools.FDA_get_drug_names_by_health_claim module
- tooluniverse.tools.FDA_get_drug_names_by_indication module
- tooluniverse.tools.FDA_get_drug_names_by_info_for_nursing_mothers module
- tooluniverse.tools.FDA_get_drug_names_by_information_for_owners_or_caregivers module
- tooluniverse.tools.FDA_get_drug_names_by_ingredient module
- tooluniverse.tools.FDA_get_drug_names_by_instructions_for_use module
- tooluniverse.tools.FDA_get_drug_names_by_lab_test_interference module
- tooluniverse.tools.FDA_get_drug_names_by_lab_tests module
- tooluniverse.tools.FDA_get_drug_names_by_mechanism_of_action module
- tooluniverse.tools.FDA_get_drug_names_by_medication_guide module
- tooluniverse.tools.FDA_get_drug_names_by_nonclinical_toxicology_info module
- tooluniverse.tools.FDA_get_drug_names_by_nonteratogenic_effects module
- tooluniverse.tools.FDA_get_drug_names_by_overdosage_info module
- tooluniverse.tools.FDA_get_drug_names_by_pediatric_use module
- tooluniverse.tools.FDA_get_drug_names_by_pharmacokinetics module
- tooluniverse.tools.FDA_get_drug_names_by_population_use module
- tooluniverse.tools.FDA_get_drug_names_by_pregnancy_effects_info module
- tooluniverse.tools.FDA_get_drug_names_by_residue_warning module
- tooluniverse.tools.FDA_get_drug_names_by_risk module
- tooluniverse.tools.FDA_get_drug_names_by_route module
- tooluniverse.tools.FDA_get_drug_names_by_safe_handling_warning module
- tooluniverse.tools.FDA_get_drug_names_by_safety_summary module
- tooluniverse.tools.FDA_get_drug_names_by_spl_indexing_data_elements module
- tooluniverse.tools.FDA_get_drug_names_by_teratogenic_effects module
- tooluniverse.tools.FDA_get_drug_names_by_user_safety_warning module
- tooluniverse.tools.FDA_get_drug_names_by_warnings_and_cautions module
- tooluniverse.tools.FDA_get_drugs_by_carcinogenic_mutagenic_fertility module
- tooluniverse.tools.FDA_get_effective_time_by_drug_name module
- tooluniverse.tools.FDA_get_environmental_warning_by_drug_name module
- tooluniverse.tools.FDA_get_general_precautions_by_drug_name module
- tooluniverse.tools.FDA_get_geriatric_use_info_by_drug_name module
- tooluniverse.tools.FDA_get_health_claims_by_drug_name module
- tooluniverse.tools.FDA_get_inactive_ingredient_info_by_drug_name module
- tooluniverse.tools.FDA_get_indications_by_drug_name module
- tooluniverse.tools.FDA_get_info_for_nursing_mothers_by_drug_name module
- tooluniverse.tools.FDA_get_info_for_patients_by_drug_name module
- tooluniverse.tools.FDA_get_info_on_conditions_for_doctor_consultation_by_drug_name module
- tooluniverse.tools.FDA_get_info_on_consulting_doctor_pharmacist_by_drug_name module
- tooluniverse.tools.FDA_get_information_for_owners_or_caregivers_by_drug_name module
- tooluniverse.tools.FDA_get_ingredients_by_drug_name module
- tooluniverse.tools.FDA_get_instructions_for_use_by_drug_name module
- tooluniverse.tools.FDA_get_lab_test_interference_info_by_drug_name module
- tooluniverse.tools.FDA_get_lab_tests_by_drug_name module
- tooluniverse.tools.FDA_get_labor_and_delivery_info_by_drug_name module
- tooluniverse.tools.FDA_get_manufacturer_name_NDC_number_by_drug_name module
- tooluniverse.tools.FDA_get_mechanism_of_action_by_drug_name module
- tooluniverse.tools.FDA_get_medication_guide_info_by_drug_name module
- tooluniverse.tools.FDA_get_microbiology_info_by_drug_name module
- tooluniverse.tools.FDA_get_nonclinical_toxicology_info_by_drug_name module
- tooluniverse.tools.FDA_get_nonteratogenic_effects_by_drug_name module
- tooluniverse.tools.FDA_get_other_safety_info_by_drug_name module
- tooluniverse.tools.FDA_get_overdosage_info_by_drug_name module
- tooluniverse.tools.FDA_get_patient_package_insert_from_drug_name module
- tooluniverse.tools.FDA_get_pediatric_use_info_by_drug_name module
- tooluniverse.tools.FDA_get_pharmacodynamics_by_drug_name module
- tooluniverse.tools.FDA_get_pharmacogenomics_info_by_drug_name module
- tooluniverse.tools.FDA_get_pharmacokinetics_by_drug_name module
- tooluniverse.tools.FDA_get_population_use_info_by_drug_name module
- tooluniverse.tools.FDA_get_precautions_by_drug_name module
- tooluniverse.tools.FDA_get_pregnancy_effects_info_by_drug_name module
- tooluniverse.tools.FDA_get_pregnancy_or_breastfeeding_info_by_drug_name module
- tooluniverse.tools.FDA_get_principal_display_panel_by_drug_name module
- tooluniverse.tools.FDA_get_purpose_info_by_drug_name module
- tooluniverse.tools.FDA_get_recent_changes_by_drug_name module
- tooluniverse.tools.FDA_get_reference_info_by_drug_name module
- tooluniverse.tools.FDA_get_residue_warning_by_drug_name module
- tooluniverse.tools.FDA_get_risk_info_by_drug_name module
- tooluniverse.tools.FDA_get_route_info_by_drug_name module
- tooluniverse.tools.FDA_get_safe_handling_warnings_by_drug_name module
- tooluniverse.tools.FDA_get_safety_summary_by_drug_name module
- tooluniverse.tools.FDA_get_spl_indexing_data_elements_by_drug_name module
- tooluniverse.tools.FDA_get_spl_unclassified_section_by_drug_name module
- tooluniverse.tools.FDA_get_stop_use_info_by_drug_name module
- tooluniverse.tools.FDA_get_storage_and_handling_info_by_drug_name module
- tooluniverse.tools.FDA_get_teratogenic_effects_by_drug_name module
- tooluniverse.tools.FDA_get_user_safety_warning_by_drug_names module
- tooluniverse.tools.FDA_get_warnings_and_cautions_by_drug_name module
- tooluniverse.tools.FDA_get_warnings_by_drug_name module
- tooluniverse.tools.FDA_get_when_using_info module
- tooluniverse.tools.FDA_retrieve_device_use_by_drug_name module
- tooluniverse.tools.FDA_retrieve_drug_name_by_device_use module
- tooluniverse.tools.FDA_retrieve_drug_names_by_patient_medication_info module
- tooluniverse.tools.FDA_retrieve_patient_medication_info_by_drug_name module
- tooluniverse.tools.Fatcat_search_scholar module
- tooluniverse.tools.Finish module
- tooluniverse.tools.GO_get_annotations_for_gene module
- tooluniverse.tools.GO_get_genes_for_term module
- tooluniverse.tools.GO_get_term_by_id module
- tooluniverse.tools.GO_get_term_details module
- tooluniverse.tools.GO_search_terms module
- tooluniverse.tools.HAL_search_archive module
- tooluniverse.tools.HPA_get_biological_processes_by_gene module
- tooluniverse.tools.HPA_get_cancer_prognostics_by_gene module
- tooluniverse.tools.HPA_get_comparative_expression_by_gene_and_cellline module
- tooluniverse.tools.HPA_get_comprehensive_gene_details_by_ensembl_id module
- tooluniverse.tools.HPA_get_contextual_biological_process_analysis module
- tooluniverse.tools.HPA_get_disease_expression_by_gene_tissue_disease module
- tooluniverse.tools.HPA_get_gene_basic_info_by_ensembl_id module
- tooluniverse.tools.HPA_get_gene_tsv_data_by_ensembl_id module
- tooluniverse.tools.HPA_get_protein_interactions_by_gene module
- tooluniverse.tools.HPA_get_rna_expression_by_source module
- tooluniverse.tools.HPA_get_rna_expression_in_specific_tissues module
- tooluniverse.tools.HPA_get_subcellular_location module
- tooluniverse.tools.HPA_search_genes_by_query module
- tooluniverse.tools.HypothesisGenerator module
- tooluniverse.tools.LabelGenerator module
- tooluniverse.tools.LiteratureContextReviewer module
- tooluniverse.tools.LiteratureSearchTool module
- tooluniverse.tools.MarkItDown_convert_file module
- tooluniverse.tools.MarkItDown_convert_stream module
- tooluniverse.tools.MarkItDown_list_plugins module
- tooluniverse.tools.MedRxiv_search_preprints module
- tooluniverse.tools.MedicalLiteratureReviewer module
- tooluniverse.tools.MedicalTermNormalizer module
- tooluniverse.tools.MedlinePlus_connect_lookup_by_code module
- tooluniverse.tools.MedlinePlus_get_genetics_condition_by_name module
- tooluniverse.tools.MedlinePlus_get_genetics_gene_by_name module
- tooluniverse.tools.MedlinePlus_get_genetics_index module
- tooluniverse.tools.MedlinePlus_search_topics_by_keyword module
- tooluniverse.tools.MethodologyRigorReviewer module
- tooluniverse.tools.MultiAgentLiteratureSearch module
- tooluniverse.tools.NICE_Clinical_Guidelines_Search module
- tooluniverse.tools.NICE_Guideline_Full_Text module
- tooluniverse.tools.NoveltySignificanceReviewer module
- tooluniverse.tools.OSF_search_preprints module
- tooluniverse.tools.OSL_get_efo_id_by_disease_name module
- tooluniverse.tools.OpenAIRE_search_publications module
- tooluniverse.tools.OpenAlex_Guidelines_Search module
- tooluniverse.tools.OpenTargets_drug_pharmacogenomics_data module
- tooluniverse.tools.OpenTargets_get_approved_indications_by_drug_chemblId module
- tooluniverse.tools.OpenTargets_get_associated_diseases_by_drug_chemblId module
- tooluniverse.tools.OpenTargets_get_associated_drugs_by_disease_efoId module
- tooluniverse.tools.OpenTargets_get_associated_drugs_by_target_ensemblID module
- tooluniverse.tools.OpenTargets_get_associated_phenotypes_by_disease_efoId module
- tooluniverse.tools.OpenTargets_get_associated_targets_by_disease_efoId module
- tooluniverse.tools.OpenTargets_get_associated_targets_by_drug_chemblId module
- tooluniverse.tools.OpenTargets_get_biological_mouse_models_by_ensemblID module
- tooluniverse.tools.OpenTargets_get_chemical_probes_by_target_ensemblID module
- tooluniverse.tools.OpenTargets_get_disease_ancestors_parents_by_efoId module
- tooluniverse.tools.OpenTargets_get_disease_descendants_children_by_efoId module
- tooluniverse.tools.OpenTargets_get_disease_description_by_efoId module
- tooluniverse.tools.OpenTargets_get_disease_id_description_by_name module
- tooluniverse.tools.OpenTargets_get_disease_ids_by_efoId module
- tooluniverse.tools.OpenTargets_get_disease_ids_by_name module
- tooluniverse.tools.OpenTargets_get_disease_locations_by_efoId module
- tooluniverse.tools.OpenTargets_get_disease_synonyms_by_efoId module
- tooluniverse.tools.OpenTargets_get_disease_therapeutic_areas_by_efoId module
- tooluniverse.tools.OpenTargets_get_diseases_phenotypes_by_target_ensembl module
- tooluniverse.tools.OpenTargets_get_drug_adverse_events_by_chemblId module
- tooluniverse.tools.OpenTargets_get_drug_approval_status_by_chemblId module
- tooluniverse.tools.OpenTargets_get_drug_chembId_by_generic_name module
- tooluniverse.tools.OpenTargets_get_drug_description_by_chemblId module
- tooluniverse.tools.OpenTargets_get_drug_id_description_by_name module
- tooluniverse.tools.OpenTargets_get_drug_indications_by_chemblId module
- tooluniverse.tools.OpenTargets_get_drug_mechanisms_of_action_by_chemblId module
- tooluniverse.tools.OpenTargets_get_drug_synonyms_by_chemblId module
- tooluniverse.tools.OpenTargets_get_drug_trade_names_by_chemblId module
- tooluniverse.tools.OpenTargets_get_drug_warnings_by_chemblId module
- tooluniverse.tools.OpenTargets_get_drug_withdrawn_blackbox_status_by_chemblId module
- tooluniverse.tools.OpenTargets_get_gene_ontology_terms_by_goID module
- tooluniverse.tools.OpenTargets_get_known_drugs_by_drug_chemblId module
- tooluniverse.tools.OpenTargets_get_parent_child_molecules_by_drug_chembl_ID module
- tooluniverse.tools.OpenTargets_get_publications_by_disease_efoId module
- tooluniverse.tools.OpenTargets_get_publications_by_drug_chemblId module
- tooluniverse.tools.OpenTargets_get_publications_by_target_ensemblID module
- tooluniverse.tools.OpenTargets_get_similar_entities_by_disease_efoId module
- tooluniverse.tools.OpenTargets_get_similar_entities_by_drug_chemblId module
- tooluniverse.tools.OpenTargets_get_similar_entities_by_target_ensemblID module
- tooluniverse.tools.OpenTargets_get_target_classes_by_ensemblID module
- tooluniverse.tools.OpenTargets_get_target_constraint_info_by_ensemblID module
- tooluniverse.tools.OpenTargets_get_target_enabling_packages_by_ensemblID module
- tooluniverse.tools.OpenTargets_get_target_gene_ontology_by_ensemblID module
- tooluniverse.tools.OpenTargets_get_target_genomic_location_by_ensemblID module
- tooluniverse.tools.OpenTargets_get_target_homologues_by_ensemblID module
- tooluniverse.tools.OpenTargets_get_target_id_description_by_name module
- tooluniverse.tools.OpenTargets_get_target_interactions_by_ensemblID module
- tooluniverse.tools.OpenTargets_get_target_safety_profile_by_ensemblID module
- tooluniverse.tools.OpenTargets_get_target_subcellular_locations_by_ensemblID module
- tooluniverse.tools.OpenTargets_get_target_synonyms_by_ensemblID module
- tooluniverse.tools.OpenTargets_get_target_tractability_by_ensemblID module
- tooluniverse.tools.OpenTargets_map_any_disease_id_to_all_other_ids module
- tooluniverse.tools.OpenTargets_multi_entity_search_by_query_string module
- tooluniverse.tools.OpenTargets_search_category_counts_by_query_string module
- tooluniverse.tools.OpenTargets_target_disease_evidence module
- tooluniverse.tools.OutputSummarizationComposer module
- tooluniverse.tools.PMC_search_papers module
- tooluniverse.tools.ProtocolOptimizer module
- tooluniverse.tools.PubChem_get_CID_by_SMILES module
- tooluniverse.tools.PubChem_get_CID_by_compound_name module
- tooluniverse.tools.PubChem_get_associated_patents_by_CID module
- tooluniverse.tools.PubChem_get_compound_2D_image_by_CID module
- tooluniverse.tools.PubChem_get_compound_properties_by_CID module
- tooluniverse.tools.PubChem_get_compound_synonyms_by_CID module
- tooluniverse.tools.PubChem_get_compound_xrefs_by_CID module
- tooluniverse.tools.PubChem_search_compounds_by_similarity module
- tooluniverse.tools.PubChem_search_compounds_by_substructure module
- tooluniverse.tools.PubMed_Guidelines_Search module
- tooluniverse.tools.PubMed_search_articles module
- tooluniverse.tools.PubTator3_EntityAutocomplete module
- tooluniverse.tools.PubTator3_LiteratureSearch module
- tooluniverse.tools.QuestionRephraser module
- tooluniverse.tools.Reactome_get_pathway_reactions module
- tooluniverse.tools.ReproducibilityTransparencyReviewer module
- tooluniverse.tools.ResultsInterpretationReviewer module
- tooluniverse.tools.ScientificTextSummarizer module
- tooluniverse.tools.SemanticScholar_search_papers module
- tooluniverse.tools.TRIP_Database_Guidelines_Search module
- tooluniverse.tools.TestCaseGenerator module
- tooluniverse.tools.ToolCompatibilityAnalyzer module
- tooluniverse.tools.ToolDescriptionOptimizer module
- tooluniverse.tools.ToolDiscover module
- tooluniverse.tools.ToolGraphComposer module
- tooluniverse.tools.ToolGraphGenerationPipeline module
- tooluniverse.tools.ToolImplementationGenerator module
- tooluniverse.tools.ToolMetadataGenerationPipeline module
- tooluniverse.tools.ToolMetadataGenerator module
- tooluniverse.tools.ToolMetadataStandardizer module
- tooluniverse.tools.ToolOptimizer module
- tooluniverse.tools.ToolOutputSummarizer module
- tooluniverse.tools.ToolQualityEvaluator module
- tooluniverse.tools.ToolRelationshipDetector module
- tooluniverse.tools.ToolSpecificationGenerator module
- tooluniverse.tools.ToolSpecificationOptimizer module
- tooluniverse.tools.Tool_Finder module
- tooluniverse.tools.Tool_Finder_Keyword module
- tooluniverse.tools.Tool_Finder_LLM module
- tooluniverse.tools.Tool_RAG module
- tooluniverse.tools.UniProt_get_alternative_names_by_accession module
- tooluniverse.tools.UniProt_get_disease_variants_by_accession module
- tooluniverse.tools.UniProt_get_entry_by_accession module
- tooluniverse.tools.UniProt_get_function_by_accession module
- tooluniverse.tools.UniProt_get_isoform_ids_by_accession module
- tooluniverse.tools.UniProt_get_organism_by_accession module
- tooluniverse.tools.UniProt_get_ptm_processing_by_accession module
- tooluniverse.tools.UniProt_get_recommended_name_by_accession module
- tooluniverse.tools.UniProt_get_sequence_by_accession module
- tooluniverse.tools.UniProt_get_subcellular_location_by_accession module
- tooluniverse.tools.Unpaywall_check_oa_status module
- tooluniverse.tools.WHO_Guideline_Full_Text module
- tooluniverse.tools.WHO_Guidelines_Search module
- tooluniverse.tools.Wikidata_SPARQL_query module
- tooluniverse.tools.WritingPresentationReviewer module
- tooluniverse.tools.Zenodo_search_records module
- tooluniverse.tools.alphafold_get_annotations module
- tooluniverse.tools.alphafold_get_prediction module
- tooluniverse.tools.alphafold_get_summary module
- tooluniverse.tools.call_agentic_human module
- tooluniverse.tools.cancer_biomarkers_disease_target_score module
- tooluniverse.tools.cancer_gene_census_disease_target_score module
- tooluniverse.tools.cellosaurus_get_cell_line_info module
- tooluniverse.tools.cellosaurus_query_converter module
- tooluniverse.tools.cellosaurus_search_cell_lines module
- tooluniverse.tools.chembl_disease_target_score module
- tooluniverse.tools.convert_to_markdown module
- tooluniverse.tools.dict_search module
- tooluniverse.tools.dili_search module
- tooluniverse.tools.diqt_search module
- tooluniverse.tools.disease_target_score module
- tooluniverse.tools.drugbank_filter_drugs_by_name module
- tooluniverse.tools.drugbank_full_search module
- tooluniverse.tools.drugbank_get_drug_basic_info_by_drug_name_or_drugbank_id module
- tooluniverse.tools.drugbank_get_drug_chemistry_by_drug_name_or_drugbank_id module
- tooluniverse.tools.drugbank_get_drug_interactions_by_drug_name_or_drugbank_id module
- tooluniverse.tools.drugbank_get_drug_name_and_description_by_indication module
- tooluniverse.tools.drugbank_get_drug_name_and_description_by_pathway_name module
- tooluniverse.tools.drugbank_get_drug_name_and_description_by_target_name module
- tooluniverse.tools.drugbank_get_drug_name_description_pharmacology_by_mechanism_of_action module
- tooluniverse.tools.drugbank_get_drug_pathways_and_reactions_by_drug_name_or_drugbank_id module
- tooluniverse.tools.drugbank_get_drug_products_by_name_or_drugbank_id module
- tooluniverse.tools.drugbank_get_drug_references_by_drug_name_or_drugbank_id module
- tooluniverse.tools.drugbank_get_indications_by_drug_name_or_drugbank_id module
- tooluniverse.tools.drugbank_get_pharmacology_by_drug_name_or_drugbank_id module
- tooluniverse.tools.drugbank_get_safety_by_drug_name_or_drugbank_id module
- tooluniverse.tools.drugbank_get_targets_by_drug_name_or_drugbank_id module
- tooluniverse.tools.drugbank_links_search module
- tooluniverse.tools.drugbank_vocab_filter module
- tooluniverse.tools.drugbank_vocab_search module
- tooluniverse.tools.embedding_database_add module
- tooluniverse.tools.embedding_database_create module
- tooluniverse.tools.embedding_database_load module
- tooluniverse.tools.embedding_database_search module
- tooluniverse.tools.embedding_sync_download module
- tooluniverse.tools.embedding_sync_upload module
- tooluniverse.tools.enrichr_gene_enrichment_analysis module
- tooluniverse.tools.europepmc_disease_target_score module
- tooluniverse.tools.eva_disease_target_score module
- tooluniverse.tools.eva_somatic_disease_target_score module
- tooluniverse.tools.expression_atlas_disease_target_score module
- tooluniverse.tools.extract_clinical_trial_adverse_events module
- tooluniverse.tools.extract_clinical_trial_outcomes module
- tooluniverse.tools.genomics_england_disease_target_score module
- tooluniverse.tools.get_HPO_ID_by_phenotype module
- tooluniverse.tools.get_albumentations_info module
- tooluniverse.tools.get_altair_info module
- tooluniverse.tools.get_anndata_info module
- tooluniverse.tools.get_arboreto_info module
- tooluniverse.tools.get_arxiv_info module
- tooluniverse.tools.get_ase_info module
- tooluniverse.tools.get_assembly_info_by_pdb_id module
- tooluniverse.tools.get_assembly_summary module
- tooluniverse.tools.get_astropy_info module
- tooluniverse.tools.get_binding_affinity_by_pdb_id module
- tooluniverse.tools.get_biopandas_info module
- tooluniverse.tools.get_biopython_info module
- tooluniverse.tools.get_bioservices_info module
- tooluniverse.tools.get_biotite_info module
- tooluniverse.tools.get_bokeh_info module
- tooluniverse.tools.get_brian2_info module
- tooluniverse.tools.get_cartopy_info module
- tooluniverse.tools.get_catboost_info module
- tooluniverse.tools.get_cellpose_info module
- tooluniverse.tools.get_cellrank_info module
- tooluniverse.tools.get_cellxgene_census_info module
- tooluniverse.tools.get_cftime_info module
- tooluniverse.tools.get_chem_comp_audit_info module
- tooluniverse.tools.get_chem_comp_charge_and_ambiguity module
- tooluniverse.tools.get_chembl_webresource_client_info module
- tooluniverse.tools.get_citation_info_by_pdb_id module
- tooluniverse.tools.get_clair3_info module
- tooluniverse.tools.get_clinical_trial_conditions_and_interventions module
- tooluniverse.tools.get_clinical_trial_descriptions module
- tooluniverse.tools.get_clinical_trial_eligibility_criteria module
- tooluniverse.tools.get_clinical_trial_locations module
- tooluniverse.tools.get_clinical_trial_outcome_measures module
- tooluniverse.tools.get_clinical_trial_references module
- tooluniverse.tools.get_clinical_trial_status_and_dates module
- tooluniverse.tools.get_cobra_info module
- tooluniverse.tools.get_cobrapy_info module
- tooluniverse.tools.get_cooler_info module
- tooluniverse.tools.get_core_refinement_statistics module
- tooluniverse.tools.get_cryosparc_tools_info module
- tooluniverse.tools.get_crystal_growth_conditions_by_pdb_id module
- tooluniverse.tools.get_crystallization_ph_by_pdb_id module
- tooluniverse.tools.get_crystallographic_properties_by_pdb_id module
- tooluniverse.tools.get_cupy_info module
- tooluniverse.tools.get_cyvcf2_info module
- tooluniverse.tools.get_dask_info module
- tooluniverse.tools.get_datamol_info module
- tooluniverse.tools.get_datashader_info module
- tooluniverse.tools.get_deepchem_info module
- tooluniverse.tools.get_deeppurpose_info module
- tooluniverse.tools.get_deeptools_info module
- tooluniverse.tools.get_deepxde_info module
- tooluniverse.tools.get_dendropy_info module
- tooluniverse.tools.get_descriptastorus_info module
- tooluniverse.tools.get_diffdock_info module
- tooluniverse.tools.get_dscribe_info module
- tooluniverse.tools.get_ec_number_by_entity_id module
- tooluniverse.tools.get_elephant_info module
- tooluniverse.tools.get_em_3d_fitting_and_reconstruction_details module
- tooluniverse.tools.get_emdb_ids_by_pdb_id module
- tooluniverse.tools.get_episcanpy_info module
- tooluniverse.tools.get_ete3_info module
- tooluniverse.tools.get_faiss_info module
- tooluniverse.tools.get_fanc_info module
- tooluniverse.tools.get_flask_info module
- tooluniverse.tools.get_flowio_info module
- tooluniverse.tools.get_flowkit_info module
- tooluniverse.tools.get_flowutils_info module
- tooluniverse.tools.get_freesasa_info module
- tooluniverse.tools.get_galpy_info module
- tooluniverse.tools.get_gene_name_by_entity_id module
- tooluniverse.tools.get_geopandas_info module
- tooluniverse.tools.get_gget_info module
- tooluniverse.tools.get_googlesearch_python_info module
- tooluniverse.tools.get_gseapy_info module
- tooluniverse.tools.get_h5py_info module
- tooluniverse.tools.get_harmony_pytorch_info module
- tooluniverse.tools.get_hmmlearn_info module
- tooluniverse.tools.get_holoviews_info module
- tooluniverse.tools.get_host_organism_by_pdb_id module
- tooluniverse.tools.get_htmd_info module
- tooluniverse.tools.get_hyperopt_info module
- tooluniverse.tools.get_igraph_info module
- tooluniverse.tools.get_imageio_info module
- tooluniverse.tools.get_imbalanced_learn_info module
- tooluniverse.tools.get_jcvi_info module
- tooluniverse.tools.get_joblib_info module
- tooluniverse.tools.get_joint_associated_diseases_by_HPO_ID_list module
- tooluniverse.tools.get_khmer_info module
- tooluniverse.tools.get_kipoiseq_info module
- tooluniverse.tools.get_lifelines_info module
- tooluniverse.tools.get_ligand_bond_count_by_pdb_id module
- tooluniverse.tools.get_ligand_smiles_by_chem_comp_id module
- tooluniverse.tools.get_lightgbm_info module
- tooluniverse.tools.get_loompy_info module
- tooluniverse.tools.get_mageck_info module
- tooluniverse.tools.get_matplotlib_info module
- tooluniverse.tools.get_mdanalysis_info module
- tooluniverse.tools.get_mdtraj_info module
- tooluniverse.tools.get_mne_info module
- tooluniverse.tools.get_molfeat_info module
- tooluniverse.tools.get_molvs_info module
- tooluniverse.tools.get_mordred_info module
- tooluniverse.tools.get_msprime_info module
- tooluniverse.tools.get_mudata_info module
- tooluniverse.tools.get_mutation_annotations_by_pdb_id module
- tooluniverse.tools.get_neo_info module
- tooluniverse.tools.get_netcdf4_info module
- tooluniverse.tools.get_networkx_info module
- tooluniverse.tools.get_nglview_info module
- tooluniverse.tools.get_nilearn_info module
- tooluniverse.tools.get_numba_info module
- tooluniverse.tools.get_numpy_info module
- tooluniverse.tools.get_oligosaccharide_descriptors_by_entity_id module
- tooluniverse.tools.get_openbabel_info module
- tooluniverse.tools.get_openchem_info module
- tooluniverse.tools.get_opencv_info module
- tooluniverse.tools.get_openmm_info module
- tooluniverse.tools.get_optlang_info module
- tooluniverse.tools.get_optuna_info module
- tooluniverse.tools.get_palantir_info module
- tooluniverse.tools.get_pandas_info module
- tooluniverse.tools.get_patsy_info module
- tooluniverse.tools.get_pdbfixer_info module
- tooluniverse.tools.get_phenotype_by_HPO_ID module
- tooluniverse.tools.get_pillow_info module
- tooluniverse.tools.get_plantcv_info module
- tooluniverse.tools.get_plip_info module
- tooluniverse.tools.get_plotly_info module
- tooluniverse.tools.get_poliastro_info module
- tooluniverse.tools.get_polymer_entity_annotations module
- tooluniverse.tools.get_polymer_entity_count_by_pdb_id module
- tooluniverse.tools.get_polymer_entity_ids_by_pdb_id module
- tooluniverse.tools.get_polymer_entity_type_by_entity_id module
- tooluniverse.tools.get_polymer_molecular_weight_by_entity_id module
- tooluniverse.tools.get_poretools_info module
- tooluniverse.tools.get_prody_info module
- tooluniverse.tools.get_protein_classification_by_pdb_id module
- tooluniverse.tools.get_protein_metadata_by_pdb_id module
- tooluniverse.tools.get_pubchempy_info module
- tooluniverse.tools.get_pybedtools_info module
- tooluniverse.tools.get_pybigwig_info module
- tooluniverse.tools.get_pydeseq2_info module
- tooluniverse.tools.get_pyensembl_info module
- tooluniverse.tools.get_pyephem_info module
- tooluniverse.tools.get_pyfaidx_info module
- tooluniverse.tools.get_pyfasta_info module
- tooluniverse.tools.get_pykalman_info module
- tooluniverse.tools.get_pyliftover_info module
- tooluniverse.tools.get_pymassspec_info module
- tooluniverse.tools.get_pymed_info module
- tooluniverse.tools.get_pymzml_info module
- tooluniverse.tools.get_pypdf2_info module
- tooluniverse.tools.get_pyranges_info module
- tooluniverse.tools.get_pyrosetta_info module
- tooluniverse.tools.get_pysam_info module
- tooluniverse.tools.get_pyscenic_info module
- tooluniverse.tools.get_pyscf_info module
- tooluniverse.tools.get_pyscreener_info module
- tooluniverse.tools.get_pytdc_info module
- tooluniverse.tools.get_python_libsbml_info module
- tooluniverse.tools.get_pytorch_info module
- tooluniverse.tools.get_pyvcf_info module
- tooluniverse.tools.get_pyvis_info module
- tooluniverse.tools.get_qutip_info module
- tooluniverse.tools.get_rasterio_info module
- tooluniverse.tools.get_rdkit_info module
- tooluniverse.tools.get_refinement_resolution_by_pdb_id module
- tooluniverse.tools.get_release_deposit_dates_by_pdb_id module
- tooluniverse.tools.get_reportlab_info module
- tooluniverse.tools.get_requests_info module
- tooluniverse.tools.get_ruptures_info module
- tooluniverse.tools.get_scanorama_info module
- tooluniverse.tools.get_scanpy_info module
- tooluniverse.tools.get_schnetpack_info module
- tooluniverse.tools.get_scholarly_info module
- tooluniverse.tools.get_scikit_bio_info module
- tooluniverse.tools.get_scikit_image_info module
- tooluniverse.tools.get_scikit_learn_info module
- tooluniverse.tools.get_scipy_info module
- tooluniverse.tools.get_scrublet_info module
- tooluniverse.tools.get_scvelo_info module
- tooluniverse.tools.get_scvi_tools_info module
- tooluniverse.tools.get_seaborn_info module
- tooluniverse.tools.get_sequence_by_pdb_id module
- tooluniverse.tools.get_sequence_lengths_by_pdb_id module
- tooluniverse.tools.get_sequence_positional_features_by_instance_id module
- tooluniverse.tools.get_skopt_info module
- tooluniverse.tools.get_souporcell_info module
- tooluniverse.tools.get_source_organism_by_pdb_id module
- tooluniverse.tools.get_space_group_by_pdb_id module
- tooluniverse.tools.get_statsmodels_info module
- tooluniverse.tools.get_structure_determination_software_by_pdb_id module
- tooluniverse.tools.get_structure_title_by_pdb_id module
- tooluniverse.tools.get_structure_validation_metrics_by_pdb_id module
- tooluniverse.tools.get_sunpy_info module
- tooluniverse.tools.get_sympy_info module
- tooluniverse.tools.get_target_cofactor_info module
- tooluniverse.tools.get_taxonomy_by_pdb_id module
- tooluniverse.tools.get_tiledb_info module
- tooluniverse.tools.get_tiledbsoma_info module
- tooluniverse.tools.get_torch_geometric_info module
- tooluniverse.tools.get_tqdm_info module
- tooluniverse.tools.get_trackpy_info module
- tooluniverse.tools.get_tskit_info module
- tooluniverse.tools.get_umap_learn_info module
- tooluniverse.tools.get_uniprot_accession_by_entity_id module
- tooluniverse.tools.get_velocyto_info module
- tooluniverse.tools.get_viennarna_info module
- tooluniverse.tools.get_webpage_text_from_url module
- tooluniverse.tools.get_webpage_title module
- tooluniverse.tools.get_xarray_info module
- tooluniverse.tools.get_xesmf_info module
- tooluniverse.tools.get_xgboost_info module
- tooluniverse.tools.get_zarr_info module
- tooluniverse.tools.gwas_get_association_by_id module
- tooluniverse.tools.gwas_get_associations_for_snp module
- tooluniverse.tools.gwas_get_associations_for_study module
- tooluniverse.tools.gwas_get_associations_for_trait module
- tooluniverse.tools.gwas_get_snp_by_id module
- tooluniverse.tools.gwas_get_snps_for_gene module
- tooluniverse.tools.gwas_get_studies_for_trait module
- tooluniverse.tools.gwas_get_study_by_id module
- tooluniverse.tools.gwas_get_variants_for_trait module
- tooluniverse.tools.gwas_search_associations module
- tooluniverse.tools.gwas_search_snps module
- tooluniverse.tools.gwas_search_studies module
- tooluniverse.tools.humanbase_ppi_analysis module
- tooluniverse.tools.mesh_get_subjects_by_pharmacological_action module
- tooluniverse.tools.mesh_get_subjects_by_subject_id module
- tooluniverse.tools.mesh_get_subjects_by_subject_name module
- tooluniverse.tools.mesh_get_subjects_by_subject_scope_or_definition module
- tooluniverse.tools.odphp_itemlist module
- tooluniverse.tools.odphp_myhealthfinder module
- tooluniverse.tools.odphp_outlink_fetch module
- tooluniverse.tools.odphp_topicsearch module
- tooluniverse.tools.openalex_literature_search module
- tooluniverse.tools.reactome_disease_target_score module
- tooluniverse.tools.search_clinical_trials module
- tooluniverse.tools.visualize_molecule_2d module
- tooluniverse.tools.visualize_molecule_3d module
- tooluniverse.tools.visualize_protein_structure_3d module